Patent Application
20190094247
The present invention relates to the screening of binding partners of G-protein coupled receptors (GPCRs) and particularly to conformation specific binding partners of GPCRs.
The listing or discussion of an apparently prior-published document in this specification should not necessarily be taken as an acknowledgement that the document is part of the state of the art or is common general knowledge.
Many GPCRs represent important therapeutic targets which could be exploited by biotherapeutics such as antibodies. The generation of therapeutic antibodies for GPCRs has been extremely difficult due in part to the lack of a suitable immunogen. The usual route is to take small peptide fragments of the receptor for immunization however these do not retain their native conformation and often result in binding partners that can bind to and label the receptor but have no functional agonist or antagonist activity. Due to the unique physical conformation of GPCRs it is also known that biotherapeutics such as antibodies recognise combinations of polypeptide ‘loops’, features that are lost when peptide fragments are used in isolation. It is well known that the local membrane environment of GPCRs maintains the tertiary conformation of the protein, and governs which epitopes are present on the extracellular surface. These epitopes can in theory be recognised by biotherapeutics, however it is non-trivial to raise biotherapeutics, such as antibodies, to membranes or membrane fragments containing a target GPCR as these preparations inevitably contain other non-target GPCRs and membrane-associated proteins, and other membrane components such as lipoproteins, apolipoproteins, lipids, phosophoinsositol lipids and liposacharides which can act as non-desired antigens in the biotherapeutic selection and production process.
Aspects of the invention relate to methods of producing a binding partner of a GPCR, the method comprising: (a) providing a mutant GPCR of a parent GPCR, wherein the mutant GPCR has increased stability in a particular conformation relative to the parent GPCR; (b) providing one or more test compounds; (c) determining whether the or each test compound binds to the mutant GPCR when residing in a particular conformation; and (d) isolating one or more test compounds that bind to the mutant GPCR when residing in the particular conformation.
In some embodiments, methods further comprise determining whether the or each test compound binds to the parent GPCR when residing in the particular conformation and isolating the or each test compound that also binds the parent GPCR when residing in the particular conformation.
In some embodiments, the mutant GPCR is immobilised onto a solid support. In some embodiments, the support is any of a bead, a column, a slide, a chip or a plate. In some embodiments, the mutant GPCR is immobilised onto the support via a covalent interaction. In some embodiments, the support is coated with a polymeric support, such as carboxylated dextran. In some embodiments, the mutant GPCR is immobilised on the support via a non-covalent interaction.
In some embodiments, the support is coated with any of avidin, streptavidin, a metal ion, an antibody to the parent GPCR or an antibody to a molecular tag attached to the mutant GPCR. In some embodiments, the mutant GPCR is immobilised via the C-terminus or an intracellular domain such that the extracellular domains are outward facing. In some embodiments, the mutant GPCR is immobilised via the N-terminus or an extracellular domain such that the intracellular domains are outward facing.
In some embodiments, the mutant GPCR comprises a molecular tag at the C-terminus or N-terminus. In some embodiments, the tag is any of a FLAG tag, a His tag, a c-Myc tag, a DDDDK (SEQ ID NO: 13) tag, an HSV tag, a Halo tag or a biotin tag. In some embodiments, the mutant GPCR is in a whole cell preparation, in a cell membrane fragment, solubilised in detergent, in a lipid monolayer, in a lipid bilayer, in a bead-linked lipid particle, in a solid-supported lipid layer or in a proteoliposome.
In some embodiments, the test compound is immobilised on a solid support. In some embodiments, the solid support is any of a bead, a column, a slide, a chip or a plate. In some embodiments, the mutant GPCR and the test compound are not immobilised on a solid support.
In some embodiments, the test compound is any of a polypeptide; an anticalin; a peptide; an antibody; a chimeric antibody; a single chain antibody; an aptamer; a darpin; a Fab, F(ab′)2, Fv, ScFv or dAb antibody fragment; a small molecule; a natural product; an affibody; a peptidomimetic; a nucleic acid; a peptide nucleic acid molecule; a lipid; a carbohydrate; a protein based on a modular framework including ankyrin repeat proteins, armadillo repeat proteins, leucine rich proteins, tetrariopeptide repeat proteins or Designed Ankyrin Repeat Proteins (DARPins); or proteins based on lipocalin or fibronectin domains or Affilin scaffolds based on either human gamma crystalline or human ubiquitin.
In some embodiments, the test compound is provided as a biological sample. In some embodiments, the sample is any of blood, serum, plasma, spinal fluid, a tissue extract or a cell extract.
In some embodiments, the test compound is a library of test compounds. In some embodiments, the library is any of a peptide library, a protein library, an antibody library, a recombinant combinatorial antibody library or a scFV or Fab phage display library. In some embodiments, the test compound is labelled with any of a peptide tag, a nucleic acid tag, a chemical tag, a fluorescent tag or a radio frequency tag.
In some embodiments, the antibody is an antibody to a mutant GPCR of a parent GPCR, wherein the mutant GPCR has increased stability in a particular conformation relative to the parent GPCR. In some embodiments, the antibody is produced by immunising a lymphocyte with an immunogen of the mutant GPCR. In some embodiments, the lymphocyte is immunised in vivo. In some embodiments, the lymphocyte is immunised in vitro. In some embodiments, the immunogen of the mutant GPCR is all of the mutant GPCR, a fragment thereof or a fusion protein thereof.
In some embodiments, the immunogen of a mutant GPCR is provided in a whole cell preparation, in a cell membrane fragment, solubilised in detergent, in a lipid monolayer, in a lipid bilayer, in a bead-linked lipid particle, in a solid-supported lipid layer or in a proteoliposome. In some embodiments, the immunogen is provided with an adjuvant. In some embodiments, the adjuvant is Titermax or Ribi's adjuvant emulsion.
In some embodiments, methods further comprise modifying the isolated test compound that binds to a mutant GPCR when residing in a particular conformation and determining whether the modified test compound binds to the mutant GPCR when residing in a particular conformation. In some embodiments, methods further comprise determining whether the modified test compound binds to the parent GPCR when residing in the particular conformation.
In some embodiments, more than one mutant GPCR is provided and it is determined whether the test compound binds to each mutant GPCR when residing in a particular conformation; and the test compound which binds to each mutant GPCR when residing in the particular conformation is isolated.
In some embodiments, a mutant GPCR of a first parent GPCR and a mutant GPCR of a second parent GPCR are provided and it is determined whether the test compound binds to each mutant GPCR when residing in a particular conformation; and the test compound which binds to each mutant GPCR when residing in the particular conformation is isolated.
In some embodiments, more than one mutant GPCR is provided and a test compound is selected that binds to a first mutant GPCR but which does not bind, or binds less strongly than to the first mutant GPCR, to at least one other mutant GPCR.
In some embodiments, methods further comprise (i) determining if the isolated test compound affects the function of the GPCR to which it binds and (ii) isolating a test compound that affects the function of the GPCR to which it binds. In some embodiments, in step (i) it is determined if the isolated test compound affects the binding of the GPCR to its natural ligand or analog thereof. In some embodiments, in step (ii) a test compound that decreases binding between the GPCR and its natural ligand or analog thereof is isolated. In some embodiments, in step (ii) a test compound that increases binding between the GPCR and its natural ligand or analog thereof is isolated. In some embodiments, in step (i) it is determined if the isolated test compound modulates activation of the GPCR to which it binds.
In some embodiments, in step (ii) a test compound which modulates any of calcium mobilisation, cAMP levels, kinase pathway activity, gene transcription from a reporter gene under control of the GPCR to which the test compound binds, β-arrestin recruitment, activation of G proteins, GTPase activity or [35S]GTPγS binding is selected.
In some embodiments, in step (ii) an agonist test compound that increases activation of the GPCR to which it binds, is isolated. In some embodiments, in step (ii) an antagonist test compound that decreases activation of the GPCR to which it binds, is isolated.
In some embodiments, the mutant GPCR is provided by: (a) providing one or more mutants of a parent GPCR; (b) selecting a ligand, the ligand being one which binds to the parent GPCR when the GPCR is residing in a particular conformation; (c) determining whether the or each mutant GPCR has increased stability with respect to binding the selected ligand compared to the stability of the parent GPCR with respect to binding that ligand; and (d) selecting those mutants that have an increased stability compared to the parent GPCR with respect to binding the selected ligand. In some embodiments, the one or more mutants are brought into contact with the selected ligand prior to step (c). In some embodiments, the one or more mutants are provided in a solubilised form. In some embodiments, the particular conformation in which the GPCR resides in step (c) corresponds to the class of ligand selected in step (b).
In some embodiments, the selected ligand is from the agonist class of ligands and the particular conformation is an agonist conformation, or the selected ligand is from the antagonist class of ligands and the particular conformation is an antagonist conformation. In some embodiments, the selected ligand is from the agonist class of ligands and the particular conformation in which the GPCR resides in step (c) is the agonist conformation.
In some embodiments, the binding affinity of the mutant for the selected ligand is substantially the same or greater than the binding affinity of the parent for the selected ligand. In some embodiments, the method is repeated for one or more rounds, with the selected mutants having increased stability in step (a) representing the parent GPCR in a subsequent round of the method.
In some embodiments, a mutant GPCR is selected which has increased stability to any one or more of heat, a detergent, a chaotropic agent and an extreme of pH. In some embodiments, a mutant GPCR with increased thermostability is selected. In some embodiments, the ligand is any one of a full agonist, a partial agonist, an inverse agonist, an antagonist. In some embodiments, the ligand is a polypeptide which binds to the GPCR. In certain embodiments, the polypeptide is any of an antibody, an ankyrin, a G protein, an RGS protein, an arrestin, a GPCR kinase, a receptor tyrosine kinase, a RAMP, a NSF, a GPCR, an NMDA receptor subunit NR1 or NR2a, or calcyon, a fibronectin domain framework, or a fragment or derivative thereof that binds to the GPCR.
In some embodiments, in step (b) two or more ligands are selected, the presence of each causes the GPCR to reside in the same particular conformation. In some embodiments, a mutant GPCR is selected which has reduced ability to bind a ligand of a different class to the ligand selected in step (b) compared to its parent. In some embodiments, the GPCR is any one of a β-adrenergic receptor, an adenosine receptor and a neurotensin receptor.
In some embodiments, the mutant GPCR is provided by: (a) carrying out the method of any one of claims 45-60; (b) identifying the position or positions of the mutated amino acid residue or residues in the mutant GPCR or GPCRs which has been selected for increased stability, and (c) synthesising a mutant GPCR which contains a replacement amino acid at one or more of the positions identified. In some embodiments, the mutant GPCR contains a plurality of mutations compared to the parent GPCR.
In some embodiments, the mutant GPCR is provided by: (i) identifying in the amino acid sequence of one or more mutants of a first parent GPCR with increased stability relative to the first parent GPCR, the position or positions at which the one or more mutants have at least one different amino acid residue compared to the first parent GPCR, and (ii) making one or more mutations in the amino acid sequence that defines a second GPCR at the corresponding position or positions, to provide one or more mutants of a second parent GPCR with increased stability relative to the second parent GPCR.
In some embodiments, the one or more mutants of a first parent GPCR are provided according to methods described herein. In some embodiments, the second GPCR is of the same GPCR class or family as the first parent GPCR. In some embodiments, the second GPCR is a GPCR which has at least 20% sequence identity with the first parent GPCR.
In some embodiments, producing a mutant GPCR with increased stability relative to its parent GPCR, the method comprising: (i) providing one or more mutants of a first parent GPCR with increased stability relative to the first parent GPCR; (ii) identifying in a structural membrane protein model the structural motif or motifs in which the one or more mutants have at least one different amino acid residue compared to the first parent GPCR, and (iii) making one or more mutations in the amino acid sequence that defines a corresponding structural motif or motifs in a second parent GPCR, to provide one or more mutants of a second parent GPCR with increased stability relative to the second parent GPCR.
In some embodiments, the structural membrane protein model is a model of an integral membrane protein. In some embodiments, the integral membrane protein has at least 20% sequence identity with the mutant of the first parent GPCR in step (i) across the protein domain in which the mutant has at least one different amino acid relative to the first parent GPCR. In some embodiments, the integral membrane protein is a GPCR. In some embodiments, the GPCR is of the same GPCR class or family as the first parent GPCR.
In some embodiments, the structural membrane protein model is a model of human β2 adrenergic receptor or bovine rhodopsin. In some embodiments, the structural motif is any of a helical interface, a helix kink, a helix opposite a helix kink, a helix surface pointing into the lipid bilayer, a helix surface pointing into the lipid bilayer at the hydrophobic-hydrophilic boundary layer, a loop region or a protein binding pocket.
In some embodiments, the second parent GPCR is the first parent GPCR. In some embodiments, the second parent GPCR is not the first parent GPCR. In some embodiments, the second parent GPCR is a GPCR which has at least 20% sequence identity with the first parent GPCR. In some embodiments, the second GPCR is of the same GPCR class or family as the first parent GPCR.
In some embodiments, methods further comprise: (I) selecting a ligand, the ligand being one which binds to the second parent GPCR when the GPCR is residing in a particular conformation; (II) determining whether the or each mutant of the second parent GPCR when residing in a particular conformation has increased stability with respect to binding the selected ligand compared to the stability of the second parent GPCR when residing in the same particular conformation with respect to binding that ligand, and (III) selecting those mutants that have an increased stability compared to the second parent GPCR with respect to binding the selected ligand. In some embodiments, the particular conformation in which the GPCR resides in step (II) corresponds to the class of ligand selected in step (I).
In some embodiments, the selected ligand is from the agonist class of ligands and the particular conformation is an agonist conformation, or the selected ligand is from the antagonist class of ligands and the particular conformation is an antagonist conformation. In some embodiments, the ligand is any one of a full agonist, a partial agonist, an inverse agonist, an antagonist. In some embodiments, the ligand is a polypeptide which binds to the GPCR. In certain embodiments, the polypeptide is any of an antibody, an ankyrin, a G protein, an RGS protein, an arrestin, a GPCR kinase, a receptor tyrosine kinase, a RAMP, a NSF, a GPCR, an NMDA receptor subunit NR1 or NR2a, or calcyon, a fibronectin domain framework, or a fragment or derivative thereof that binds to the GPCR.
In some embodiments, the binding affinity of the one or more mutants of the second GPCR is substantially the same or greater than the binding affinity of the second parent GPCR for the selected ligand. In some embodiments, the mutant GPCR provided in step (a) is any one of a β-adrenergic receptor, an adenosine receptor, a neurotensin receptor or a muscarinic receptor.
In some embodiments, the mutant GPCR provided in step (a) has, compared to its parent receptor, at least one different amino acid at a position which corresponds to any one or more of the following positions: (i) according to the numbering of the turkey β-adrenergic receptor as set out in
In some embodiments, the mutant GPCR provided in step (a) is a mutant β-adrenergic receptor which, when compared to its corresponding parent receptor, has a different amino acid at a position which corresponds to any one or more of the following positions according to the numbering of the turkey β-adrenergic receptor as set out in
In some embodiments, the mutant β-adrenergic receptor has an amino acid sequence which is at least 20% identical to that of the turkey β-adrenergic receptor whose sequence is set out in
In some embodiments, the mutant GPCR provided in step (a) is a mutant β-adrenergic receptor which has at least one different amino acid residue in a structural motif in which the mutant receptor compared to its parent receptor has a different amino acid at a position which corresponds to any of the following positions according to the numbering of the turkey β-adrenergic receptor as set out in
In some embodiments, the mutant GPCR provided in step (a) is a mutant adenosine receptor which, when compared to its corresponding parent receptor, has a different amino acid at a position which corresponds to any one or more of the following positions according to the numbering of the human adenosine A2a receptor as set out in
In some embodiments, the mutant GPCR provided in step (a) is a mutant adenosine receptor which has at least one different amino acid residue in a structural motif in which the mutant receptor compared to its parent receptor has a different amino acid at a position which corresponds to any of the following positions according to the numbering of the human adenosine A2a receptor as set out in
In some embodiments, the mutant GPCR provided in step (a), is a mutant neurotensin receptor which, when compared to its corresponding parent receptor, has a different amino acid at a position which corresponds to any one or more of the following positions according to the numbering of the rat neurotensin receptor as set out in
In some embodiments, the mutant GPCR provided in step (a) is a mutant neurotensin receptor which has at least one different amino acid residue in a structural motif in which the mutant receptor compared to its parent receptor has a different amino acid at a position which corresponds to any of the following positions according to the numbering of the rat neurotensin receptor as set out in
In some embodiments, the mutant GPCR provided in step (a) is a mutant muscarinic receptor which, when compared to the corresponding wild-type muscarinic receptor, has a different amino acid at a position which corresponds to any one or more of the following positions according to the numbering of the human muscarinic receptor as set out in
In some embodiments, the mutant GPCR provided in step (a) is a mutant muscarinic receptor which has at least one different amino acid residue in a structural motif in which the mutant receptor compared to its parent receptor has a different amino acid at a position which corresponds to any of the following positions according to the numbering of the human muscarinic receptor as set out in
Further aspects of the invention involve methods of producing a binding partner of a GPCR, the method comprising synthesising a binding partner identifiable by carrying out the methods described herein. In some embodiments, a binding partner is obtained by any of the methods described herein. In some embodiments, the binding partner is conformation-specific. In some embodiments, the binding partner is any of a polypeptide; an anticalin; a peptide; an antibody; a chimeric antibody; a single chain antibody; an aptamer; a darpin; a Fab, F(ab′)2, Fv, ScFv or dAb antibody fragment; a small molecule; a natural product; an affibody; a peptidomimetic; a nucleic acid; a peptide nucleic acid molecule; a lipid; a carbohydrate; a protein based on a modular framework including ankyrin repeat proteins, armadillo repeat proteins, leucine rich proteins, tetrariopeptide repeat proteins or Designed Ankyrin Repeat Proteins (DARPins); or proteins based on lipocalin or fibronectin domains or Affilin scaffolds based on either human gamma crystalline or human ubiquitin.
In some embodiments, the binding partner is an antibody. In some embodiments, the binding affinity of the mutant GPCR for the binding partner is substantially the same or greater than the binding affinity of the parent GPCR for the binding partner. In some embodiments, the mutant GPCR has increased stability in a particular conformation relative to the parent GPCR and wherein when a target substance binds to said mutant GPCR, a detectable signal is produced.
Further aspects of the invention relate to biosensors, wherein the mutant GPCR is provided as defined in any of the methods described herein. In some embodiments, the detectable signal is any of a change in colour; fluorescence; evanescence; surface plasmon resonance; electrical conductance or charge separation; ultraviolet, visible or infrared absorption; luminescence; chemiluminescence; electrochemiluminescence; fluorescence anisotropy; fluorescence intensity; fluorescence lifetime; fluorescence polarisation; fluorescence energy transfer; molecular mass; electron spin resonance; nuclear magnetic resonance; hydrodynamic volume or radius; specific gravity; scintillation; field effect resistance; electrical impedance; acoustic impedance; quantum evanescence; resonant scattering; fluorescent quenching; fluorescence correlation spectroscopy; acoustic load; acoustic shear wave velocity; binding force; or interfacial stress.
In some embodiments, the biosensor is a flow-based biosensor, such as a quartz crystal microbalance biosensor, an evanescent wave biosensor, a planar wave guide biosensor, a surface Raman sensor, or a surface plasmon resonance biosensor. In some embodiments, the target substance is any of a molecule, a biomolecule, a peptide, a protein, a carbohydrate, a lipid, a GPCR ligand, a synthetic molecule, a drug, a drug metabolite or a disease biomarker.
The invention will now be described in more detail with respect to the following Figures and Examples wherein:
GPCRs constitute a very large family of proteins that control many physiological processes and are the targets of many effective drugs. Thus, they are of considerable pharmacological importance. A list of GPCRs is given in Foord et al (2005) Pharmacol Rev. 57, 279-288, which is incorporated herein by reference. GPCRs are generally unstable when isolated, and despite considerable efforts, it has only been possible to crystallise bovine rhodopsin, which naturally is exceptionally stable and the beta 2 adrenergic receptor which was crystallised as a fusion protein or in complex with an antibody fragment.
GPCRs are druggable targets, and reference is made particularly to Overington et al (2006) Nature Rev. Drug Discovery 5, 993-996 which indicates that over a quarter of present drugs have a GPCR as a target.
GPCRs are thought to exist in multiple distinct conformations which are associated with different pharmacological classes of ligand such as agonists and antagonists, and to cycle between these conformations in order to function (Kenakin T. (1997) Ann N Y Acad Sci 812, 116-125). Switching between conformations contributes to the difficulty in obtaining crystal structures of receptors.
The generation of conformation specific binding partners to GPCRs is hindered by several factors. For example, GPCRs generally have poor stability when removed from their native membrane environment that severely restricts the range of conditions that can be explored without their immediate denaturation or precipitation. The inability to produce purified GPCRs in their native conformation prevents their use in a wide range of screening paradigms which depend on the use of purified receptors. Thus, GPCR screening has traditionally depended on assays in which the receptor is present in cell membranes or whole cells.
We have developed a methodology for the stabilisation of a GPCR in a particular biologically relevant conformation. Such receptors have a number of advantages as immunogens and/or selection and screening reagents for the generation of binding partners. In particular, they are useful for the generation of conformation-specific binding partners, which will frequently have functional properties, and have previously proven very difficult to generate.
For example, the stability of native, correctly folded receptor throughout the expression, solubilisation and purification steps facilitates a high yield of purified GPCR (milligram quantities from lab-scale cell culture). Furthermore, the stability of folded protein in a range of detergents and solubilisation buffers and additives, without distortion of function, enables optimisation of conditions for immunization, for immobilization on solid surfaces without denaturation (e.g. plastic plates, resins, beads or slides, directly or via affinity tags such as poly-Histidine tags), for the purpose of antibody production and screening or for library screening (such as affibody, antibody, phage or small molecule libraries). For library screening, reduction in non-specific binding by removal of membranous matter and cell-surface “sticky antigens” will give a major improvement in signal/noise. Use of short-chain detergents with highly polar or charged head groups (such as lauryldimethylamine-oxide, octyl D-glucoside or octyl D-maltoside) is also made possible, which will reveal a greater proportion of the antigenic surfaces of the GPCR which are masked by longer-chain detergents such as n-dodecyl beta-D-maltoside (Bamber et al PNAS 103 (2006) 16224-16229). The trapping of particular functional conformations of the receptor will also increase the likelihood of generating conformation-specific, functional binding partners.
Accordingly, a first aspect of the invention provides a method of producing a binding partner of a GPCR, the method comprising:
By “binding partner” we mean a molecule that binds to a particular GPCR. Preferably, the molecule binds selectively to the GPCR. For example, it is preferred if the binding partner has a Kd value (dissociation constant) which is at least five or ten times lower (i.e. higher affinity) than for at least one other GPCR, and preferably more than 100 or 500 times lower. More preferably, the binding partner of a GPCR has a Kd value more than 1000 or 5000 times lower than for at least one other GPCR. However, it will be appreciated that the limits will vary dependent upon the nature of the binding partner. Thus, typically, for small molecule binding partners, the binding partner typically has a Kd value which is at least 50 times or 100 times lower than for at least one other GPCR. Typically, for antibody binding partners, the binding partner typically has a Kd value which is at least 500 or 1000 times lower than for at least one other GPCR.
The use of stabilised GPCRs trapped in particular conformations will increase the likelihood of producing conformation-specific binding partners. Accordingly, it is appreciated that the method may be used to produce a conformation-specific binding partner of a GPCR. Thus, the method may also be used to identify binding partners that have functional activity such as agonists or antagonists (or other pharmacological categories) which will be determined by the conformation in which the GPCR was stabilised.
By “conformation specific”, we mean that the binding partner of the GPCR binds selectively to a particular conformation of the GPCR and thus has a Kd value for that conformation which is lower than for other conformations of the same GPCR. Thus, a conformation specific binding partner will bind to one conformation of a GPCR (and may cause the GPCR to adopt this conformation), but does not bind as strongly to another conformation that the GPCR may be able to adopt. It will be appreciated therefore that, while the difference in affinity between two conformations and the conformation specific binding partner may be small, typically it will be sufficient to alter the equilibrium between conformational states and encourage the GPCR to adopt a particular conformation. Thus, a conformational specific binding partner may be considered to be one which traps a GPCR in a conformation of biological relevance (e.g. ligand bound state). Typically, a conformation specific binding partner has a Kd value (dissociation constant) which is at least five or ten times lower (i.e. higher affinity) than for at least one other conformation of the GPCR conformation, and preferably between 100-10000 times lower.
Typically, the conformational specific binding partner binds to the GPCR with a Kd of from mM to pM or from mM to fM, such as in the range from pM to nM or in the range from nM to pM.
Kd values can be determined readily using methods well known in the art and as described, for example, below.
At equilibrium Kd=[R][L]/[RL]
where the terms in brackets represent the concentration of
In order to determine the Kd the value of these terms must be known. Since the concentration of receptor is not usually known then the Hill-Langmuir equation is used where
Fractional occupancy=[L]/[L]+Kd.
In order to experimentally determine a Kd then, the concentration of free ligand and bound ligand at equilibrium must be known. Typically, this can be done by using a radio-labelled or fluorescently labelled ligand which is incubated with the receptor (present in whole cells or homogenised membranes) until equilibrium is reached. The amount of free ligand vs bound ligand must then be determined by separating the signal from bound vs free ligand. In the case of a radioligand this can be done by centrifugation or filtration to separate bound ligand present on whole cells or membranes from free ligand in solution. Alternatively a scintillation proximity assay is used. In this assay the receptor (in membranes) is bound to a bead containing scintillant and a signal is only detected by the proximity of the radioligand bound to the receptor immobilised on the bead.
The affinity constant may also be determined in a functional assay (KB). Here the receptor in a whole cell or membrane is activated by an agonist ligand and a response measured (e.g. mobilisation of intracellular calcium, G protein activation, increase or decrease in adenylate cyclise or cAMP, activation of a signal transduction pathway such as a MAP-kinase pathway or activation of gene transcription). The ability of an antagonist to inhibit agonist activity can be measured and for a competitive antagonist is equal to the affinity constant.
The stability of the mutant GPCRs in a range of detergents, surfactants and solubilisation buffers enables their purification outside of their normal membrane environment. Therefore, the GPCR can be provided in an isolated form removed from non-desired antigens such as non-target GPCRs, membrane associated proteins and other membrane components such as lipoproteins, apolipoproteins, lipis, phosphoinositol lipids and liposaccharides. Thus the method of the invention allows for the selection of a binding partner of a GPCR in the absence of such non-desired antigens. Thus the invention produces binding partners that have enhanced selectivity for a GPCR over other membrane components.
Mutations of the parent GPCR that confer stability in a particular conformation are not expected to affect the binding of the parent GPCR residing in a particular conformation to a particular binding partner. However, it is appreciated that once a binding partner has been isolated by assessing binding to a mutant GPCR residing in a particular conformation, binding of that binding partner to the parent GPCR residing in the same particular conformation may also be assessed.
Thus, in one embodiment the method further comprises:
Typically, the selected binding partner binds to the mutant GPCR when residing in a particular conformation with a similar potency to its binding to the parent GPCR when residing in the same particular conformation. Typically, the Kd values for the particular binding partner binding the mutant GPCR and the parent GPCR are within 5-10 fold of each other, such as within 2-3 fold. Typically, the binding of the binding partner to the mutant GPCR compared to the parent GPCR would not be more than 5 times weaker and not more than 10 times stronger.
Typically, the selected binding partner binds to the mutant GPCR with approximately equal affinity (that is to say typically within 2-3 fold) or greater affinity than does the parent receptor, when residing in the same conformation. For agonist-conformation mutants, the mutants typically bind the agonist-conformation specific binding partners with the same or higher affinity than the parent GPCR and typically bind antagonist-conformation specific binding partners with the same or lower affinity than the parent GPCR. Similarly for antagonist-conformation mutants, the mutants typically bind the antagonist-conformation specific binding partners with the same or higher affinity than the parent GPCR and typically bind agonist-conformation specific binding partners with the same or lower affinity than the parent GPCR.
Selectivity of binding partners for particular conformations of GPCR or for particular GPCRs and calculation of Kds can be determined using binding assays well known in the art and as described, for example, below. Typically, Kd values are calculated using conventional GPCR assays in membranes wherein the binding affinity at different compound concentrations is measured. Examples of suitable assays include surface plasmon resonance assays and competition assays which are well known in the art and are described below.
Typically, the mutant GPCR used in the present aspect is selected and prepared using any of the methods as described below.
Providing a Mutant GPCR of a Parent GPCR
A mutant GPCR with increased stability relative to its parent GPCR can be provided by the methods described below, and by any of the methods disclosed in PCT applications WO 2008/114020 and PCT/GB2008/004032.
Method 1
A method for selecting a mutant G-protein coupled receptor (GPCR) with increased stability, comprises
The inventors have appreciated that, in order to improve the likelihood of crystallisation of a GPCR in a biologically relevant form (which is therefore pharmacologically useful), it is desirable not only to increase the stability of the protein, but also for the protein to have this increased stability when in a particular conformation. The conformation is determined by a selected ligand, and is a biologically relevant conformation in particular a pharmacologically relevant conformation. Thus, the method of selection may be considered to be a method for selecting mutants of a GPCR which have increased stability of a particular conformation, for example they may have increased conformational thermostability. The method may be used to create stable, conformationally locked GPCRs by mutagenesis. The selected mutant GPCRs are effectively purer forms of the parent molecules in that a much higher proportion of them occupies a particular conformational state. The deliberate selection of a chosen receptor conformation resolved from other conformations by use of a ligand (or ligands) that bind preferentially to this conformation is therefore an important feature of the selection method. The method may also be considered to be a method for selecting mutant GPCRs which are more tractable to crystallisation. This is because it is well known that decreased homogeneity or increased pleiotropy within a population of molecules does not favour crystallisation, and further, that an increased number of conformations of a particular molecule does not favour crystallisation.
Thus a further method for selecting a mutant G-protein coupled receptor (GPCR) with increased stability, comprises
In a review of the druggable genome by Hopkins & Groom (2002) Nature Rev. Drug Discovery 1, 727-730, Table 1 contains a list of protein families many of which are GPCRs. Overington et al (2006) Nature Rev. Drug Discovery 5, 993-996 provides more details of drug targets, and
Suitable GPCRs for use in the practice of the invention include, but are not limited to β-adrenergic receptor, adenosine receptor, in particular adenosine A2a receptor, and neurotensin receptor (NTR). Other suitable GPCRs are well known in the art and include those listed in Hopkins & Groom supra. In addition, the International Union of Pharmacology produce a list of GPCRs (Foord et al (2005) Pharmacol. Rev. 57, 279-288, incorporated herein by reference and this list is periodically updated at iuphar-db.org/GPCR/ReceptorFamiliesForward). It will be noted that GPCRs are divided into different classes, principally based on their amino acid sequence similarities. They are also divided into families by reference to the natural ligands to which they bind. All GPCRs are included in the scope of the invention.
The amino acid sequences (and the nucleotide sequences of the cDNAs which encode them) of many GPCRs are readily available, for example by reference to GenBank. In particular, Foord et al supra gives the human gene symbols and human, mouse and rat gene IDs from Entrez Gene (ncbi.nlm.nih.gov/entrez). It should be noted, also, that because the sequence of the human genome is substantially complete, the amino acid sequences of human GPCRs can be deduced therefrom.
Although the GPCR may be derived from any source, it is particularly preferred if it is from a eukaryotic source. It is particularly preferred if it is derived from a vertebrate source such as a mammal or a bird. It is particularly preferred if the GPCR is derived from rat, mouse, rabbit or dog or non-human primate or man, or from chicken or turkey. For the avoidance of doubt, we include within the meaning of “derived from” that a cDNA or gene was originally obtained using genetic material from the source, but that the protein may be expressed in any host cell subsequently. Thus, it will be plain that a eukaryotic GPCR (such as an avian or mammalian GPCR) may be expressed in a prokaryotic host cell, such as E. coli, but be considered to be avian- or mammalian-derived, as the case may be.
In some instances, the GPCR may be composed of more than one different subunit. For example, the calcitonin gene-related peptide receptor requires the binding of a single transmembrane helix protein (RAMP1) to acquire its physiological ligand binding characteristics. Effector, accessory, auxiliary or GPCR-interacting proteins which combine with the GPCR to form or modulate a functional complex are well known in the art and include, for example, receptor kinases, G-proteins and arrestins (Bockaert et al (2004) Curr Opinion Drug Discov and Dev 7, 649-657).
The mutants of the parent GPCR may be produced in any suitable way and provided in any suitable form. Thus, for example, a series of specific mutants of the parent protein may be made in which each amino acid residue in all or a part of the parent protein is independently changed to another amino acid residue. For example, it may be convenient to make mutations in those parts of the protein which are predicted to be membrane spanning. The three-dimensional structure of rhodopsin is known (Li et al (2004) J Mol Biol 343, 1409-1438; Palczewski et al (2000) Science 289, 739-745), and it is possible to model certain GPCRs using this structure. Thus, conveniently, parts of the GPCR to mutate may be based on modelling. Similarly, computer programs are available which model transmembrane regions of GPCRs based on hydrophobicity (Kyle & Dolittle (1982) J. Mol. Biol. 157, 105-132), and use can be made of such models when selecting parts of the protein to mutate. Conventional site-directed mutagenesis may be employed, or polymerase chain reaction-based procedures well known in the art may be used. It is possible, but less desirable, to use ribosome display methods in the selection of the mutant protein.
Typically, each selected amino acid is replaced by Ala (ie Ala-scanning mutagenesis), although it may be replaced by any other amino acid. If the selected amino acid is Ala, it may conveniently be replaced by Leu. Alternatively, the amino acid may be replaced by Gly (ie Gly-scanning mutagenesis), which may allow a closer packing of neighbouring helices that may lock the protein in a particular conformation. If the selected amino acid is Gly, it may conveniently be replaced by Ala.
Although the amino acid used to replace the given amino acid at a particular position is typically a naturally occurring amino acid, typically an “encodeable” amino acid, it may be a non-natural amino acid (in which case the protein is typically made by chemical synthesis or by use of non-natural amino-acyl tRNAs). An “encodeable” amino acid is one which is incorporated into a polypeptide by translation of mRNA. It is also possible to create non-natural amino acids or introduce non-peptide linkages at a given position by covalent chemical modification, for example by post-translational treatment of the protein or semisynthesis. These post-translational modifications may be natural, such as phosphorylation, glycosylation or palmitoylation, or synthetic or biosynthetic.
Alternatively, the mutants may be produced by a random mutagenesis procedure, which may be of the whole protein or of a selected portion thereof. Random mutagenesis procedures are well known in the art.
Conveniently, the mutant GPCR has one replaced amino acid compared to the parent protein (ie it is mutated at one amino acid position). In this way, the contribution to stability of a single amino acid replacement may be assessed. However, the mutant GPCR assayed for stability may have more than one replaced amino acid compared to the parent protein, such as 2 or 3 or 4 or 5 or 6 replacements.
As is discussed in more detail below, combinations of mutations may be made based on the results of the selection method. It has been found that in some specific cases combining mutations in a single mutant protein leads to a further increase in stability.
Thus, it will be appreciated that the method of selection can be used in an iterative way by, for example, carrying it out to identify single mutations which increase stability, combining those mutations in a single mutant GPCRs which is the GPCR then provided in part (a) of the method. Thus, multiply-mutated mutant proteins can be selected using the method.
The parent GPCR need not be the naturally occurring protein. Conveniently, it may be an engineered version which is capable of expression in a suitable host organism, such as Escherichia coli. For example, as described in Example 1, a convenient engineered version of the turkey β-adrenergic receptor is one which is truncated and lacks residues 1-33 of the amino acid sequence (ie βAR34-424). The parent GPCR may be a truncated form of the naturally occurring protein (truncated at either or both ends), or it may be a fusion, either to the naturally occurring protein or to a fragment thereof. Alternatively or additionally, the parent GPCR, compared to a naturally-occurring GPCR, may be modified in order to improve, for example, solubility, proteolytic stability (eg by truncation, deletion of loops, mutation of glycosylation sites or mutation of reactive amino acid side chains such as cysteine). In any event, the parent GPCR is a protein that is able to bind to the selected ligand which ligand is one which is known to bind the naturally occurring GPCR. Conveniently, the parent GPCR is one which, on addition of an appropriate ligand, can affect any one or more of the downstream activities which are commonly known to be affected by G-protein activation.
However, it will be appreciated that the stability of the mutant is to be compared to a parent in order to be able to assess an increase in stability.
A ligand is selected, the ligand being one which binds to the parent GPCR when residing in a particular conformation. Typically, the ligand will bind to one conformation of the parent GPCR (and may cause the GPCR to adopt this conformation), but does not bind as strongly to another conformation that the GPCR may be able to adopt. Thus, the presence of the ligand may be considered to encourage the GPCR to adopt the particular conformation. Thus, the method may be considered to be a way of selecting mutant GPCRs which are trapped in a conformation of biological relevance (eg ligand bound state), and which are more stable with respect to that conformation.
Preferably the particular conformation in which the GPCR resides in step (c) corresponds to the class of ligand selected in step (b).
Preferably the selected ligand is from the agonist class of ligands and the particular conformation is an agonist conformation, or the selected ligand is from the antagonist class of ligands and the particular conformation is an antagonist conformation.
Preferably the selected ligand is from the agonist class of ligands and the particular conformation in which the GPCR resides in step (c) is the agonist conformation.
Preferably, the selected ligand binding affinity for the mutant receptor should be equal to or greater than that for the wild type receptor; mutants that exhibit significantly reduced binding to the selected ligand are typically rejected.
By “ligand” we include any molecule which binds to the GPCR and which causes the GPCR to reside in a particular conformation. The ligand preferably is one which causes more than half of the GPCR molecules overall to be in a particular conformation.
Many suitable ligands are known.
Typically, the ligand is a full agonist and is able to bind to the GPCR and is capable of eliciting a full (100%) biological response, measured for example by G-protein coupling, downstream signalling events or a physiological output such as vasodilation. Thus, typically, the biological response is GDP/GTP exchange in a G-protein, followed by stimulation of the linked effector pathway. The measurement, typically, is GDP/GTP exchange or a change in the level of the end product of the pathway (eg cAMP, cGMP or inositol phosphates). The ligand may also be a partial agonist and is able to bind to the GPCR and is capable of eliciting a partial (<100%) biological response.
The ligand may also be an inverse agonist, which is a molecule which binds to a receptor and reduces its basal (ie unstimulated by agonist) activity sometimes even to zero.
The ligand may also be an antagonist, which is a molecule which binds to a receptor and blocks binding of an agonist, so preventing a biological response. Inverse agonists and partial agonists may under certain assay conditions be antagonists.
The above ligands may be orthosteric, by which we include the meaning that they combine with the same site as the endogenous agonist; or they may be allosteric or allotopic, by which we include the meaning that they combine with a site distinct from the orthosteric site. The above ligands may be syntopic, by which we include the meaning that they interact with other ligand(s) at the same or an overlapping site. They may be reversible or irreversible.
In relation to antagonists, they may be surmountable, by which we include the meaning that the maximum effect of agonist is not reduced by either pre-treatment or simultaneous treatment with antagonist; or they may be insurmountable, by which we include the meaning that the maximum effect of agonist is reduced by either pre-treatment or simultaneous treatment with antagonist; or they may be neutral, by which we include the meaning the antagonist is one without inverse agonist or partial agonist activity. Antagonists typically are also inverse agonists.
Ligands for use in the selection method may also be allosteric modulators such as positive allosteric modulators, potentiators, negative allosteric modulators and inhibitors. They may have activity as agonists or inverse agonists in their own right or they may only have activity in the presence of an agonist or inverse agonist in which case they are used in combination with such molecules in order to bind to the GPCR.
Neubig et al (2003) Pharmacol. Rev. 55, 597-606, incorporated herein by reference, describes various classes of ligands.
Preferably, the above-mentioned ligands are small organic or inorganic moieties, but they may be peptides or polypeptides. Typically, when the ligand is a small organic or organic moiety, it has a Mr of from 50 to 2000, such as from 100 to 1000, for example from 100 to 500.
Typically, the ligand binds to the GPCR with a Kd of from mM to pM, such as in the range of from pM (micromolar) to nM. Generally, the ligands with the lowest Kd are preferred.
Small organic molecule ligands are well known in the art, for example see the Examples below. Other small molecule ligands include 5HT which is a full agonist at the 5HT1A receptor; eltoprazine which is a partial agonist at the 5HT1A receptor (see Newman-Tancredi et al (1997) Neurophamacology 36, 451-459); (+)-butaclamol and spiperone are dopamine D2 receptor inverse agonists (see Roberts & Strange (2005) Br. J. Pharmacol. 145, 34-42); and WIN55212-3 is a neutral antagonist of CB2 (Savinainen et al (2005) Br. J. Pharmacol. 145, 636-645).
The ligand may be a peptidomimetic, a nucleic acid, a peptide nucleic acid (PNA) or an aptamer. It may be an ion such as Na+ or Zn2+, a lipid such as oleamide, or a carbohydrate such as heparin.
The ligand may be a polypeptide which binds to the GPCR. Such polypeptides (by which we include oligopeptides) are typically from Mr 500 to Mr 50,000, but may be larger. The polypeptide may be a naturally occurring GPCR-interacting protein or other protein which interacts with the GPCR, or a derivative or fragment thereof, provided that it binds selectively to the GPCR in a particular conformation. GPCR-interacting proteins include those associated with signalling and those associated with trafficking, which often act via PDZ domains in the C terminal portion of the GPCR.
Polypeptides which are known to bind certain GPCRs include any of a G protein, an arrestin, a RGS protein, G protein receptor kinase, a RAMP, a 14-3-3 protein, a NSF, a periplakin, a spinophilin, a GPCR kinase, a receptor tyrosine kinase, an ion channel or subunit thereof, an ankyrin and a Shanks or Homer protein. Other polypeptides include NMDA receptor subunits NR1 or NR2a, calcyon, or a fibronectin domain framework. The polypeptide may be one which binds to an extracellular domain of a GPCR, such as fibulin-1. The polypeptide may be another GPCR, which binds to the selected GPCR in a hetero-oligomer. A review of protein-protein interactions at GPCRs is found in Milligan & White (2001) Trends Pharmacol. Sci. 22, 513-518, or in Bockaert et al (2004) Curr. Opinion Drug Discov. Dev. 7, 649-657 incorporated herein by reference.
The polypeptide ligand may conveniently be an antibody which binds to the GPCR. By the term “antibody” we include an immunoglobulin whether natural or partly or wholley synthetically produced. Examples include immunoglobulin isotypes and their isotypic subclasses, and monoclonal antibodies and fragments thereof comprising an antigen binding domains such as Fab, F(ab′)2, single chain Fv (scFv), Fv, domain antibodies (dAbs) and diabodies. Mention is also made of camelid antibodies and engineered camelid antibodies. Such molecules which bind GPCRs are known in the art and in any event can be made using well known technology. Suitable antibodies include ones presently used in radioimmunoassay (RIAs) for GPCRs since they tend to recognise conformational epitopes.
The polypeptide may also be a binding protein based on a modular framework, such as ankyrin repeat proteins, armadillo repeat proteins, leucine rich proteins, tetratriopeptide repeat proteins or Designed Ankyrin Repeat Proteins (DARPins) or proteins based on lipocalin or fibronectin domains or Affilin scaffolds based on either human gamma crystalline or human ubiquitin.
In one embodiment of the selection method, the ligand is covalently joined to the GPCR, such as a G-protein or arrestin fusion protein. Some GPCRs (for example thrombin receptor) are cleaved N-terminally by a protease and the new N-terminus binds to the agonist site. Thus, such GPCRs are natural GPCR-ligand fusions.
It will be appreciated that the use of antibodies, or other “universal” binding polypeptides (such as G-proteins which are known to couple with many different GPCRs) may be particularly advantageous in the use of the method on “orphan” GPCRs for which the natural ligand, and small molecule ligands, are not known.
Once the ligand has been selected, it is then determined whether the or each mutant GPCR has increased stability with respect to binding the selected ligand compared to the parent GPCR with respect to binding that ligand. It will be appreciated that this step (c) is one in which it is determined whether the or each mutant GPCR has an increased stability (compared to its parent) for the particular conformation which is determined by the selected ligand. Thus, the mutant GPCR has increased stability with respect to binding the selected ligand as measured by ligand binding or whilst binding the selected ligand. As is discussed below, it is particularly preferred if the increased stability is assessed whilst binding the selected ligand.
The increased stability is conveniently measured by an extended lifetime of the mutant under the imposed conditions which may lead to instability (such as heat, harsh detergent conditions, chaotropic agents and so on). Destabilisation under the imposed condition is typically determined by measuring denaturation or loss of structure. As is discussed below, this may manifest itself by loss of ligand binding ability or loss of secondary or tertiary structure indicators.
As is described with respect to
In one embodiment the mutant GPCR may be brought into contact with a ligand before being subjected to a procedure in which the stability of the mutant is determined (the mutant GPCR and ligand remaining in contact during the test period). Thus, for example, when the method is being used to select for mutant GPCRs which in one conformation bind to a ligand and which have improved thermostablity, the receptor is contacted with the ligand before being heated, and then the amount of ligand bound to the receptor following heating may be used to express thermostability compared to the parent receptor. This provides a measure of the amount of the GPCR which retains ligand binding capacity following exposure to the denaturing conditions (eg heat), which in turn is an indicator of stability.
In an alternative (but less preferred) embodiment, the mutant GPCR is subjected to a procedure in which the stability of the mutant is determined before being contacted with the ligand. Thus, for example, when the method is being used to select for mutant membrane receptors which in one conformation bind to a ligand and which have improved thermostability, the receptor is heated first, before being contacted with the ligand, and then the amount of ligand bound to the receptor may be used to express thermostability. Again, this provides a measure of the amount of the GPCR which retains ligand binding capacity following exposure to the denaturing conditions.
In both embodiments, it will be appreciated that the comparison of stability of the mutant is made by reference to the parent molecule under the same conditions.
It will be appreciated that in both of these embodiments, the mutants that are selected are ones which have increased stability when residing in the particular conformation compared to the parent protein.
The preferred route may be dependent upon the specific GPCR, and will be dependent upon the number of conformations accessible to the protein in the absence of ligand. In the embodiment described in
From the above, it will be appreciated that the selection method includes a method for selecting a mutant GPCR with increased thermostability, the method comprising (a) providing one or more mutants of a parent GPCR, (b) selecting an antagonist or an agonist which binds the parent GPCR, (c) determining whether the or each mutant has increased thermostability when in the presence of the said antagonist or agonist by measuring the ability of the mutant GPCR to bind the selected said antagonist or agonist at a particular temperature and after a particular time compared to the parent GPCR and (d) selecting those mutant GPCRs that bind more of the selected said antagonist or agonist at the particular temperature and after the particular time than the parent GPCR under the same conditions. In step (c), a fixed period of time at the particular temperature is typically used in measuring the ability of the mutant GPCR to bind the selected said antagonist or agonist. In step (c), typically a temperature and a time is chosen at which binding of the selected said antagonist or agonist by the parent GPCR is reduced by 50% during the fixed period of time at that temperature (which is indicative that 50% of the receptor is inactivated; “quasi” Tm).
Conveniently, when the ligand is used to assay the GPCR (ie used to determine if it is in a non-denatured state), the ligand is detectably labelled, eg radiolabelled or fluorescently labelled. In another embodiment, ligand binding can be assessed by measuring the amount of unbound ligand using a secondary detection system, for example an antibody or other high affinity binding partner covalently linked to a detectable moiety, for example an enzyme which may be used in a colorimetric assay (such as alkaline phosphatase or horseradish peroxidase). FRET methodology may also be used. It will be appreciated that the ligand used to assay the mutant GPCR in determining its stability need not be the same ligand as selected in step (b) of the method.
Although it is convenient to measure the stability of the parent and mutant GPCR by using the ability to bind a ligand as an indicator of the presence of a non-denatured protein, other methods are known in the art. For example, changes in fluorescence spectra can be a sensitive indicator of unfolding, either by use of intrinsic tryptophan fluorescence or the use of extrinsic fluorescent probes such as 1-anilino-8-napthaleneulfonate (ANS), for example as implemented in the Thermofluor™ method (Mezzasalma et al, J Biomol Screening, 2007, April; 12(3):418-428). Proteolytic stability, deuterium/hydrogen exchange measured by mass spectrometry, blue native gels, capillary zone electrophoresis, circular dichroism (CD) spectra and light scattering may also be used to measure unfolding by loss of signals associated with secondary or tertiary structure. However, all these methods require the protein to be purified in reasonable quantities before they can be used (eg high pmol/nmol quantities), whereas the method described in the Examples makes use of pmol amounts of essentially unpurified GPCR.
In a preferred embodiment, in step (b) two or more ligands of the same class are selected, the presence of each causing the GPCR to reside in the same particular conformation. Thus, in this embodiment, one or more ligands (whether natural or non-natural) of the same class (eg full agonist or partial agonist or antagonist or inverse agonist) may be used. Including multiple ligands of the same class in this process, whether in series or in parallel, minimises the theoretical risk of inadvertently engineering and selecting multiply mutated receptor conformations substantially different to the parent, for example in their binding site, but still able, due to compensatory changes, to bind ligand. The following steps may be used to mitigate this risk:
1. Select a chemically distinct set (eg n=2-5) of ligands, in a common pharmacological class as evidenced by for example a binding or functional or spectroscopic assay. These ligands should be thought to bind to a common spatial region of the receptor, as evidenced for example by competitive binding studies using wild type and/or mutated receptors, and/or by molecular modelling, although they will not necessarily express a common pharmacophore.
2. Make single or multiple receptor mutants intended to increase stability, and assay for tight binding using the full set of ligands. The assays can be parallelised, multiplexed or run in series.
3. Confirm authenticity of stabilised receptor mutant by measurement for example of the binding isotherm for each ligand, and by measurement of the stability shift with ligand (the window should typically be narrowed compared to wild type).
In order to guard against changes in apparent affinity caused by perturbations to the binding site upon mutation, preferably ligands of the same pharmacological class, but different chemical class, should be used to profile the receptor. These should typically show similar shifts in affinity (mutant versus parent, e.g. wild type) in spite of having different molecular recognition properties. Binding experiments should preferably be done using labelled ligand within the same pharmacological class.
Nonetheless it should be recognised that conformational substrates may exist that are specific to chemical classes of ligand within the same pharmacological class, and these may be specifically stabilised in the procedure depending on the chemical class of the selected ligand.
Typically the selected ligand binds to the mutant GPCR with a similar potency to its binding to the parent GPCR. Typically, the Kd values for the particular ligand binding the mutant GPCR and the parent GPCR are within 5-10 fold of each other, such as within 2-3 fold. Typically, the binding of the ligand to the mutant GPCR compared to the parent GPCR would be not more than 5 times weaker and not more than 10 times stronger.
Typically, mutant receptors which have been stabilised in the selected conformation should bind the selected ligand with approximately equal affinity (that is to say typically within 2-3 fold) or greater affinity than does the parent receptor. For agonist-conformation mutants, the mutants typically bind the agonists with the same or higher affinity than the parent GPCR and typically bind antagonists with the same or lower affinity than the parent GPCR. Similarly for antagonist-conformation mutants, the mutants typically bind the antagonists with the same or higher affinity than the parent GPCR and typically bind agonists with the same or lower affinity than the parent GPCR.
Mutants that exhibit a significant reduction (typically greater than 2-3 fold) in affinity for the selecting ligand are typically rejected.
Typically, the rank order of binding of a set of ligands of the same class are comparable, although there may be one or two reversals in the order, or there may be an out-tier from the set.
In a further embodiment, two or more ligands that bind simultaneously to the receptor in the same conformation may be used, for example an allosteric modulator and orthosteric agonist.
For the avoidance of doubt, and as is evident from the Examples, it is not necessary to use multiple ligands for the method to be effective.
In a further embodiment, it may be advantageous to select those mutant GPCRs which, while still being able to bind the selected ligand, are not able to bind, or bind less strongly than the parent GPCR, a second selected ligand which is in a different class to the first ligand. Thus, for example, the mutant GPCR may be one that is selected on the basis that it has increased stability with respect to binding a selected antagonist, but the mutant GPCR so selected is further tested to determine whether it binds to a full agonist (or binds less strongly to a full agonist than its parent GPCR). Mutants are selected which do not bind (or have reduced binding of) the full agonist. In this way, further selection is made of a GPCR which is locked into one particular conformation.
It will be appreciated that the selected ligand (with respect to part (b) of the method) and the further (second) ligand as discussed above, may be any pair of ligand classes, for example: antagonist and full agonist; full agonist and antagonist; antagonist and inverse agonist; inverse agonist and antagonist; inverse agonist and full agonist; full agonist and inverse agonist; and so on.
It is preferred that the mutant receptor binds the further (second) ligand with an affinity which is less than 50% of the affinity the parent receptor has for the same further (second) ligand, more preferably less than 10% and still more preferably less than 1% or 0.1% or 0.01% of affinity for the parent receptor. Thus, the Kd for the interaction of the second ligand with mutant receptor is higher than for the parent receptor. As is shown in Example 1, the mutant β-adrenergic receptor βAR-m23 (which was selected by the selection method using an antagonist) binds an agonist 3 orders of magnitude more weakly than its parent (ie Kd is 1000× higher). Similarly, in Example 2, the mutant adenosine A2a receptor Rant21 binds agonist 2-4 orders of magnitude more weakly than its parent.
This type of counter selection is useful because it can be used to direct the mutagenesis procedure more specifically (and therefore more rapidly and more efficiently) along a pathway towards a pure conformation as defined by the ligand.
Preferably, the mutant GPCR is provided in a suitable solubilised form in which it maintains structural integrity and is in a functional form (eg is able to bind ligand). An appropriate solubilising system, such as a suitable detergent (or other amphipathic agent) and buffer system is used, which may be chosen by the person skilled in the art to be effective for the particular protein. Typical detergents which may be used include, for example, dodecylmaltoside (DDM) or CHAPS or octylglucoside (OG) or many others. It may be convenient to include other compounds such as cholesterol hemisuccinate or cholesterol itself or heptane-1,2,3-triol. The presence of glycerol or proline or betaine may be useful. It is important that the GPCR, once solubilised from the membrane in which it resides, must be sufficiently stable to be assayed. For some GPCRs, DDM will be sufficient, but glycerol or other polyols may be added to increase stability for assay purposes, if desired. Further stability for assay purposes may be achieved, for example, by solubilising in a mixture of DDM, CHAPS and cholesterol hemisuccinate, optionally in the presence of glycerol. For particularly unstable GPCRs, it may be desirable to solubilise them using digitonin or amphipols or other polymers which can solubilise GPCRs directly from the membrane, in the absence of traditional detergents and maintain stability typically by allowing a significant number of lipids to remain associated with the GPCR. Nanodiscs may also be used for solubilising extremely unstable membrane proteins in a functional form.
Typically, the mutant GPCR is provided in a crude extract (eg of the membrane fraction from the host cell in which it has been expressed, such as E. coli). It may be provided in a form in which the mutant protein typically comprises at least 75%, more typically at least 80% or 85% or 90% or 95% or 98% or 99% of the protein present in the sample. Of course, it is typically solubilised as discussed above, and so the mutant GPCR is usually associated with detergent molecules and/or lipid molecules.
A mutant GPCR may be selected which has increased stability to any denaturant or denaturing condition such as to any one or more of heat, a detergent, a chaotropic agent or an extreme of pH.
In relation to an increased stability to heat (ie thermostability), this can readily be determined by measuring ligand binding or by using spectroscopic methods such as fluorescence, CD or light scattering at a particular temperature. Typically, when the GPCR binds to a ligand, the ability of the GPCR to bind that ligand at a particular temperature may be used to determine thermostability of the mutant. It may be convenient to determine a “quasi Tm” ie the temperature at which 50% of the receptor is inactivated under stated conditions after incubation for a given period of time (eg 30 minutes). Mutant GPCRs of higher thermostability have an increased quasi Tm compared to their parents.
In relation to an increased stability to a detergent or to a chaotrope, typically the GPCR is incubated for a defined time in the presence of a test detergent or a test chaotropic agent and the stability is determined using, for example, ligand binding or a spectroscopic method as discussed above.
In relation to an extreme of pH, a typical test pH would be chosen (eg in the range 4.5 to 5.5 (low pH) or in the range 8.5 to 9.5 (high pH).
Because relatively harsh detergents are used during crystallisation procedures, it is preferred that the mutant GPCR is stable in the presence of such detergents. The order of “harshness” of certain detergents is DDM, C11→C10→C9→C8 maltoside or glucoside, lauryldimethylamine oxide (LDAO) and SDS. It is particularly preferred if the mutant GPCR is more stable to any of C9 maltoside or glucoside, C8 maltoside or glucoside, LDAO and SDS, and so it is preferred that these detergents are used for stability testing.
Because of its ease of determination, it is preferred that thermostability is determined, and those mutants which have an increased thermostability compared to the parent protein with respect to the selected condition are chosen. It will be appreciated that heat is acting as the denaturant, and this can readily be removed by cooling the sample, for example by placing on ice. It is believed that thermostability may also be a guide to the stability to other denaturants or denaturing conditions. Thus, increased thermostability is likely to translate into stability in denaturing detergents, especially those that are more denaturing than DDM, eg those detergents with a smaller head group and a shorter alkyl chain and/or with a charged head group. We have found that a thermostable GPCR is also more stable towards harsh detergents.
When an extreme of pH is used as the denaturing condition, it will be appreciated that this can be removed quickly by adding a neutralising agent. Similarly, when a chaotrope is used as a denaturant, the denaturing effect can be removed by diluting the sample below the concentration in which the chaotrope exerts its chaotropic effect.
In a particular embodiment of the selection method, the GPCR is β-adrenergic receptor (for example from turkey) and the ligand is dihydroalprenolol (DHA), an antagonist.
In a further preferred embodiment of the selection method, the GPCR is the adenosine A2a receptor (A2aR) (for example, from man) and the ligand is ZM 241385 (4-[2-[[7-amino-2-(2-furyl) [1,2,4]-triazolo[2,3-a][1,3,5]triazin-5-yl]amino]ethyl]phenol), an antagonist or NECA (5′-N-ethylcarboxamido adenosine), an agonist.
In a still further preferred embodiment of the selection method, the GPCR is the neurotensin receptor (NTR) (for example, from rat) and the ligand is neurotensin, an agonist.
Method 2
A method for preparing a mutant GPCR selected as above comprises:
As can be seen in the Examples, surprisingly, changes to a single amino acid within the GPCR may increase the stability of the protein compared to the parent protein with respect to a particular condition in which the protein resides in a particular conformation. Thus, in one embodiment of the method of the second aspect of the invention, a single amino acid residue of the parent protein is changed in the mutant protein. Typically, the amino acid residue is changed to the amino acid residue found in the mutant tested in the method of the first aspect of the invention. However, it may be replaced by any other amino acid residue, such as any naturally-occurring amino acid residue (in particular, a “codeable” amino acid residue) or a non-natural amino acid. Generally, for convenience, the amino acid residue is replaced with one of the 19 other codeable amino acids. Preferably, it is the replaced amino acid residue which is present in the mutant selected in the selection method described above.
Also as can be seen in the Examples, a further increase in stability may be obtained by replacing more than one of the amino acids of the parent protein. Typically, each of the amino acids replaced is one which has been identified using the selection method described above. Typically, each amino acid identified is replaced by the amino acid present in the mutant protein although, as noted above, it may be replaced with any other amino acid.
Typically, the mutant GPCR contains, compared to the parent protein, from 1 to 10 replaced amino acids, preferably from 1 to 8, typically from 2 to 6 such as 2, 3, 4, 5 or 6 replaced amino acids.
It will be appreciated that the multiple mutants may be subject to the selection method. In other words, multiple mutants may be provided in step (a) of the selection. It will be appreciated that multiply mutagenised GPCRs may be made, whose conformation has been selected to create a very stable multiple point mutant protein.
The mutant GPCRs may be prepared by any suitable method. Conveniently, the mutant protein is encoded by a suitable nucleic acid molecule and expressed in a suitable host cell. Suitable nucleic acid molecules encoding the mutant GPCR may be made using standard cloning techniques, site-directed mutagenesis and PCR as is well known in the art. Suitable expression systems include constitutive or inducible expression systems in bacteria or yeasts, virus expression systems such as baculovirus, semliki forest virus and lentiviruses, or transient transfection in insect or mammalian cells. Suitable host cells include E. coli, Lactococcus lactis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Pichia pastoris, Spodoptera frugiperda and Trichoplusiani cells. Suitable animal host cells include HEK 293, COS, S2, CHO, NSO, DT40 and so on. It is known that some GPCRs require specific lipids (eg cholesterol) to function. In that case, it is desirable to select a host cell which contains the lipid. Additionally or alternatively the lipid may be added during isolation and purification of the mutant protein. It will be appreciated that these expression systems and host cells may also be used in the provision of the mutant GPCR in part (a) of the selection method.
Molecular biological methods for cloning and engineering genes and cDNAs, for mutating DNA, and for expressing polypeptides from polynucleotides in host cells are well known in the art, as exemplified in “Molecular cloning, a laboratory manual”, third edition, Sambrook, J. & Russell, D. W. (eds), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., incorporated herein by reference.
It is appreciated that it may be determined whether the selected or prepared mutant GPCR is able to couple to a G protein. It is also preferred if it is determined whether the selected or prepared mutant GPCR is able to bind a plurality of ligands of the same class as the selecting ligand with a comparable spread and/or rank order of affinity as the parent GPCR.
Method 3
As shown in Examples 1-3 and described above, thermostabilising mutations are scattered widely throughout the sequences of the turkey beta1 adrenergic receptor, human adenosine receptor, rat neurotensin receptor and human muscarinic receptor.
Accordingly, a further method for producing a mutant GPCR with increased stability relative to its parent GPCR comprises
The one or more mutants of a first parent GPCR may be selected or prepared according to the selection or preparation methods described above. Hence, this method may also be used to create stable, conformationally locked GPCRs by mutagenesis. For example, following the selection of mutant GPCRs which have increased stability in a particular conformation, the stabilising mutation can be identified and the amino acid at a corresponding position in a second GPCR replaced to produce a mutant GPCR with increased stability in a particular conformation relative to a second parent GPCR.
For the avoidance of doubt the first parent GPCR may be a GPCR which has a naturally-occurring sequence, or it may be a truncated form or it may be a fusion, either to the naturally-occurring protein or to a fragment thereof, or it may contain mutations compared to the naturally-occurring sequence, providing that it retains ligand-binding ability.
Typically, identifying the position or positions at which the one or more mutants have at least one different amino acid residue compared to the first parent GPCR involves aligning their amino acid sequences with that of the parent GPCR, for example using the Clustal W program (Thompson et al., 1994).
By “corresponding position or positions”, we include the meaning of the position in the amino acid sequence of a second GPCR which aligns to the position in the amino acid sequence of the first GPCR, when the first and second GPCRs are compared by alignment, for example by using MacVector and Clustal W. For example, as shown in the alignment in
Having identified the corresponding position or positions in the amino acid sequence of a second GPCR, the amino acids at those positions are replaced with another amino acid. Typically, the amino acids are replaced with the same amino acids which replaced the amino acids at the corresponding positions in the mutant of the first parent GPCR (unless they are already that residue). For example, at position 68 in turkey β1-m23 (R68S), an arginine residue was replaced with a serine residue. Therefore, at the corresponding position in the human β2 receptor, position 60 (K60), the lysine residue is preferably replaced with a serine residue.
Mutations can be made in an amino acid sequence, for example, as described above and using techniques well-established in the art.
It will be appreciated that the second GPCR may be any other GPCR. For example, stabilising mutations in a GPCR from one species may be transferred to a second GPCR from another species. Similarly, stabilising mutations in one particular GPCR isoform may be transferred to a second GPCR which is a different isoform. Preferably, the second parent GPCR is of the same GPCR class or family as the first parent GPCR. Phylogenetic analyses have divided GPCRs into three main classes based on protein sequence similarity, i.e., classes 1, 2, and 3 whose prototypes are rhodopsin, the secretin receptor, and the metabotropic glutamate receptors, respectively (Foord et al (2005) Pharmacol. Rev. 57, 279-288). Thus, the second GPCR may be a GPCR which is of the same GPCR class as the first parent GPCR. Similarly, GPCRs have been divided into families by reference to natural ligands such as glutamate and GABA. Thus, the second GPCR may be of the same GPCR family as the first parent GPCR. A list of GPCR classes and families has been produced by the International Union of Pharmacology (Foord et al (2005) Pharmacol. Rev. 57, 279-288) and this list is periodically updated at iuphar-db.org/GPCR/ReceptorFamiliesForward.
It will be appreciated that the second parent GPCR must be able to be aligned with the first parent GPCR such that the corresponding positions of the mutations in the first GPCR can be determined in the second GPCR. Thus typically, the second parent GPCR has at least 20% sequence identity to the first parent GPCR and more preferably at least 30%, 40%, 50%, 60%, 70%, 80% or 90% sequence identity to the first parent GPCR. However, some GPCRs have low sequence identity (e.g. family B and C GPCRs) and at the same time are very similar in structure. Thus the 20% sequence identity threshold is not absolute.
Method 4
The inventors have reasoned that the identification of structural motifs in which the one or more mutations in a mutant GPCR with increased stability reside, will be useful in producing further mutant GPCRs with increased stability.
Accordingly, a further method for producing a mutant G-protein coupled receptor (GPCR) with increased stability relative to its parent GPCR comprises:
Mapping stabilising mutations onto one or more known structural models can be used to identify particular structural motifs in which such stabilising mutations reside. We have mapped stabilising mutations of the β1-adrenergic receptor onto structural models of the β2-adrenergic receptor (Rasmussen et al (2007) Nature 450, 383-387; Cherezov et al (2007) Science 318:1258-65; Rosenbaum et al (2007) Science 318:1266-1273) in order to identify such motifs. For example, Table (v) lists the turkey β1-adrenergic receptor mutations which we have mapped onto the human β2-adrenergic receptor and describes the corresponding structural motifs in which they reside. As discussed in Example 4, mapping of the Y227A mutation (equivalent to Y219 in the human β2 receptor) onto the human β2-adrenergic receptor reveals its position at the interface between helices such that the mutation may improve packing at the helical interface (see
Such structural motifs, by virtue of them containing stabilising mutations, are important in determining protein stability. Therefore, targeting mutations to these motifs will facilitate the generation of stabilised mutant GPCRs. Indeed, there were several instances where more than one mutation mapped to the same structural motif. For example, the Y227A, V230A and A234L mutations in the turkey β1 adrenergic receptor mapped to the same helical interface, the V89L and M90V mutations mapped to the same helical kink and the F327A and A334L mutations mapped to the same helical surface pointing towards the lipid bilayer (Table (v)). Thus, when one stabilising mutation has been identified, the determination of the structural motif in which that mutation is located will enable the identification of further stabilising mutations.
The one or more mutants of a first parent GPCR may be selected or prepared according to any of the methods described above. Hence, this method may also be used to create stable, conformationally locked GPCRs by mutagenesis. For example, following the selection of mutant GPCRs which have increased stability in a particular conformation, the structural motifs in which such stabilising mutations reside can be identified. Making one or more mutations in the amino acid sequence that defines the corresponding structural motif in another GPCR can then be used to produce a mutant GPCR with increased stability in a particular conformation relative to its parent GPCR.
We have performed a multiple sequence alignment of the human beta-2AR, rat NTR1, turkey beta-1 AR, human Adenosine A2aR and human muscarinic M1 receptor amino acid sequences (
In order to identify the structural motif or motifs, the stabilising mutations are mapped onto a known structure of a membrane protein.
By “membrane protein” we mean a protein that is attached to or associated with a membrane of a cell or organelle. Preferably, the membrane protein is an integral membrane protein that is permanently integrated into the membrane and can only be removed using detergents, non-polar solvents or denaturing agents that physically disrupt the lipid bilayer.
The structural model of a membrane protein may be any suitable structural model. For example, the model may be a known crystal structure. Examples of GPCR crystal structures include bovine rhodopsin (Palczewski, K. et al., Science 289, 739-745. (2000)) and human β2 adrenergic receptor (Rasmussen et al, Nature 450, 383-7 (2007); Cherezov et al (2007) Science 318:1258-65; Rosenbaum et al (2007) Science 318:1266-1273). The coordinates for the human β2 adrenergic receptor structure can be found in the RCSB Protein Data Bank under accession codes: 2rh1, 2r4r and 2r4s. Alternatively, the structural model may be a computer generated model based upon homology or using de novo structure prediction methods (Qian et al Nature (2007) 450: 259-64).
It will be appreciated that stabilising mutations of a given mutant GPCR can be mapped onto a structural model of any membrane protein which has sufficient structural similarity to the GPCR. In particular, the domain of the membrane protein must have sufficient structural similarity to the GPCR domain in which the stabilising mutation resides, for a given mutation to be transferable.
A protein domain is typically defined as a discretely folded assembly of secondary structure elements which may stand alone as a single protein or be part of a larger protein in combination with other domains. It is commonly a functional evolutionary unit.
GPCRs are essentially single domain proteins excluding those with large N-terminal domains. Therefore, typically, the structural model is of a membrane protein which comprises at least one domain that has sufficient structural similarity to the GPCR.
Structural similarity can be determined indirectly by the analysis of sequence identity, or directly by comparison of structures.
With regard to sequence identity, the amino acid sequence encoding the GPCR domain in which the mutant has at least one different amino acid residue compared to the first parent GPCR, is aligned with an amino acid sequence encoding a domain of a membrane protein for which a structural model is available. It will be appreciated that one or more of these sequences may contain an inserted sequence or N-terminal or C-terminal extensions which are additional to the core conserved domain. For optimal alignment, such sequences are removed so as not to skew the analysis. Membrane proteins with sufficient sequence identity across the domain in question may then be used as the structural model for mapping mutations. It has been shown for soluble protein domains that their 3D structure is broadly conserved above 20% sequence identity and well conserved above 30% identity, with the level of structural conservation increasing as sequence identity increases up to 100% (Ginalski, K. Curr Op Struc Biol (2006) 16, 172-177). Thus, it is preferred if the structural membrane protein model is a model of a membrane protein which contains a domain that shares at least 20% sequence identity with the mutant GPCR domain containing the at least one different amino acid residue compared to the first parent GPCR, and more preferably at least 30%, 40%, 50%, 60%, 70%, 80% or 90% sequence identity, and yet more preferably at least 95% or 99% sequence identity.
Sequence identity may be measured by the use of algorithms such as BLAST or PSI-BLAST (Altschul et al, NAR (1997), 25, 3389-3402) or methods based on Hidden Markov Models (Eddy S et al, J Comput Biol (1995) Spring 2 (1) 9-23). Typically, the percent sequence identity between two polypeptides may be determined using any suitable computer program, for example the GAP program of the University of Wisconsin Genetic Computing Group and it will be appreciated that percent identity is calculated in relation to polypeptides whose sequence has been aligned optimally. The alignment may alternatively be carried out using the Clustal W program (Thompson et al., 1994). The parameters used may be as follows: Fast pairwise alignment parameters: K-tuple (word) size; 1, window size; 5, gap penalty; 3, number of top diagonals; 5. Scoring method: x percent. Multiple alignment parameters: gap open penalty; 10, gap extension penalty; 0.05. Scoring matrix: BLOSUM.
In addition to sequence identity, structural similarity can be determined directly by comparison of structural models. Structural models may be used to detect regions of structural similarity not evident from sequence analysis alone, and which may or may not be contiguous in the sequence. For example, family B and C GPCRs are thought to share similar structures; however, their sequence identity is very low. Similarly, the water transporting aquaporins spinach SoPip2, E. coli AqpZ, Methanococcus AqpM, rat Aqp4, human Aqp1 and sheep Aqp0 share low sequence identity but all have similar structures.
Structural models of high fidelity may be constructed for proteins of unknown structure using standard software packages such as MODELLER (Sali A and Blundell T, J Mol Biol (1993) 234(3) 779-815), wherein the structure is modelled on a known structure of a homologous protein. Such modelling improves with increasing sequence identity. Typically, the sequence identity between the sequence of unknown structure and a sequence of known 3D structure is more than 30% (Ginalski, K. Curr Op Struc Biol (2006) 16, 172-177). In addition, de novo structure prediction methods based on sequence alone may be used to model proteins of unknown structure (Qian et al, (2007) Nature 450:259-64). Once structures have been experimentally determined or derived by modelling, regions of structural similarity may be detected by direct comparison of two or more 3D structures. They may, for example, comprise secondary structure elements of a particular architecture and topology which can be detected by the use of software such as DALI (Holm, L and Sander, C (1996) Science 273, 595-603). They may comprise local arrangements of amino acid side chains and the polypeptide backbone, or specific sets of atoms or groups of atoms in a particular spatial arrangement, which may for example also be detected by the use of graph theoretical representations (Artymiuk, P et al, (2005) J Amer Soc Info Sci Tech 56 (5) 518-528). In this approach, the atoms or groups of atoms within the proteins or regions of proteins to be compared are typically represented as the nodes of a graph, with the edges of the graph describing the angles and distances between the nodes. Common patterns in these graphs indicate common structural motifs. This approach may be extended to include any descriptor of atoms or groups of atoms, such as hydrogen bond donor or acceptor, hydrophobicity, shape, charge or aromaticity; for example proteins may be spatially mapped according to such descriptors using GRID and this representation used as a basis for similarity searching (Baroni et al (2007) J Chem Inf Mod 47, 279-294). Descriptions of the methods, availability of software, and guidelines for user-defined selection of parameters, thresholds and tolerances are described in the references given above.
In a preferred embodiment, the structural membrane protein model is a structural GPCR model. It will be appreciated that the structural model of a GPCR may be a model of the first parent GPCR. For example, stabilising mutations within a mutant GPCR having increased stability can be directly mapped onto the first parent GPCR structure and the structural motifs in which such mutations are located, identified. Where the structure of the first parent GPCR is unknown, structural models of other GPCRs may be used. For example, stabilising mutations in a GPCR from one species may be mapped onto a known structural model of the same GPCR from another species. Similarly, stabilising mutations in one particular GPCR isoform may be mapped onto a known structural model of another GPCR isoform. Moreover, stabilising mutations from one GPCR may be mapped onto a GPCR of the same class or family. A list of GPCR classes and families has been produced by the International Union of Pharmacology (Foord et al (2005) Pharmacol. Rev. 57, 279-288) and this list is periodically updated at iuphar-db.org/GPCR/ReceptorFamiliesForward.
As described above, it will be appreciated that the structural model may be of any GPCR provided it has sufficient structural similarity across the domain in which the mutant GPCR has at least one different amino acid compared to the first parent GPCR. Thus, it is preferred if the GPCR shares at least 20% sequence identity with the mutant of the first parent GPCR across the protein domain containing the at least one different amino acid residue compared to the first parent GPCR, and more preferably at least 30%, 40%, 50%, 60%, 70%, 80% or 90% sequence identity, and yet more preferably at least 95% or 99% sequence identity. However, the inventors recognise that the 20% sequence identity threshold is not absolute. GPCRs with less than 20% sequence identity to the first parent GPCR may also serve as a structural model to which stabilising mutations are transferred, wherein the low sequence identity is counterbalanced by other similarities, including, for example, the presence of the same sequence motifs, binding to the same G-protein or having the same function, or having substantially the same hydropathy plots compared to the first parent GPCR.
Mapping of stabilising mutations onto the structural model can be done using any suitable method known in the art. For example, typically, the amino acid sequence of the GPCR for which the structural model is available is aligned with the amino acid sequence of the mutant of the first parent GPCR. The position or positions of the at least one different amino acid residue in the mutant GPCR relative to the first parent GPCR can then be located in the amino acid sequence of the GPCR for which a structural model is available.
By ‘structural motif’ we include the meaning of a three dimensional description of the location in a GPCR structural model of a thermostabilising mutation. For example, the structural motif may be any secondary or tertiary structural motif within the GPCR. By ‘tertiary structural motif’ we include any descriptor of atoms or groups of atoms, such as hydrogen bond donor or acceptor, hydrophobicity, shape, charge or aromaticity. For example, proteins may be spatially mapped according to such descriptors using GRID and this representation used as a basis for defining a structural motif (Baroni et al (2007) J Chem Inf Mod 47, 279-294).
Table (v) lists the structural motifs in which the turkey β1 adrenergic receptor stabilising mutations were found to reside. As seen from the table, the mutations are positioned in a number of distinct localities. Three mutations are in loop regions that are predicted to be accessible to aqueous solvent. Eight mutations are in the transmembrane α-helices and point into the lipid bilayer; three of these mutations are near the end of the helices and may be considered to be at the hydrophobic-hydrophilic boundary layer. Eight mutations are found at the interfaces between transmembrane α-helices, three of which are either within a kinked or distorted region of the helix and another two mutations occur in one helix but are adjacent to one or more other helices which contain a kink adjacent in space to the mutated residue. These latter mutations could affect the packing of the amino acids within the kinked region, which could result in thermostabilisation. Another mutation is in a substrate binding pocket.
Accordingly, in one embodiment, the structural motif is any of a helical interface, a helix kink, a helix opposite a helix kink, a helix surface pointing into the lipid bilayer, a helix surface pointing into the lipid bilayer at the hydrophobic-hydrophilic boundary layer, a loop region or a protein binding pocket.
Identifying a structural motif in which a stabilising mutation resides suggests the importance of that motif in protein stability. Therefore, making one or more mutations in the amino acid sequence that defines a corresponding structural motif or motifs in a second parent GPCR, should provide one or more mutants of a second parent GPCR with increased stability relative to the second parent GPCR.
The amino acid sequence which defines a structural motif is the primary amino acid sequence of the amino acid residues which combine in the secondary or tertiary structure of the protein to form the structural motif. It will be appreciated that such a primary amino acid sequence may comprise contiguous or non-contiguous amino acid residues. Thus, identifying the amino acid sequence which defines the structural motif will involve determining the residues involved and subsequently defining the sequence. Mutations can be made in an amino acid sequence, for example as described above and using techniques well-established in the art.
By “corresponding structural motif or motifs”, we mean the analogous structural motif or motifs identified in the structural model which are present in the second parent GPCR. For example, if a helical interface was identified, the corresponding helical interface in the second parent GPCR would be the interface between the helices which are analogous to the helices present in the structural model. If a helical kink was identified, the corresponding helical kink would be the kink in the helix which is analogous to the kinked helix present in the structural model. An analogous structural motif or motifs in the second parent GPCR can be identified by searching for similar amino acid sequences in the sequence of the second parent GPCR which define the motif or motifs in the structural model, for example, by sequence alignment. Moreover, computer based algorithms are widely available in the art that can be used to predict the presence of protein motifs based on an amino acid sequence. Thus, based upon the relative position of a particular motif within the amino acid sequence and its position relative to other motifs, an analogous structural motif can readily be identified. It will be appreciated that if a structural model of the second parent GPCR is available, the analogous structural motif or motifs can be directly mapped onto the structure of the protein. Typically, the amino acid sequence defining the analogous structural motif has at least 20% sequence identity with the sequence defining the motif in the structural model, more preferably at least 30%, 40%, 50%, 60%, 70%, 80% and 90% sequence identity and yet more preferably 95% and 99% sequence identity.
In one embodiment, the second parent GPCR is the first parent GPCR. For the avoidance of doubt, the second parent GPCR may have the naturally-occurring sequence of the first parent GPCR, or it may be a truncated form or it may be a fusion, either to the naturally occurring protein or to a fragment thereof, or it may contain mutations compared to the naturally-occurring sequence, providing that it retains ligand-binding.
In an alternative embodiment, the second parent GPCR is not the first parent GPCR. For example, a mutant of a first parent GPCR may have been identified that has increased stability but it is desired to generate a mutant of a different GPCR with increased stability. Preferably, the second parent GPCR is of the same GPCR class or family as the first parent GPCR as described above. However, it will be appreciated that the second parent GPCR may be any known GPCR provided that it shares sufficient structural similarity with the first parent GPCR, such that it contains a corresponding structural motif in which the stabilising mutation of the mutant of the first parent GPCR resides. Thus typically, the second parent GPCR has at least 20% sequence identity to the first parent GPCR and more preferably at least 30%, 40%, 50%, 60%, 70%, 80% or 90% sequence identity. However, as mentioned above, some GPCRs have low sequence identity (e.g. family B and C GPCRs) but are similar in structure. Thus the 20% sequence identity threshold is not absolute.
Since there are potentially thousands of mutations that can be screened in a GPCR for increased stability, it is advantageous to target particular mutations which are known to be important in conferring stability. Therefore, it will be appreciated that the methods 3 and 4 may be used in a method of selecting mutant GPCRs with increased stability. In particular, carrying out methods 3 and 4 can be used to target mutations to particular amino acid residues or to amino acid sequences which define structural motifs important in determining stability.
Accordingly, in one embodiment, methods 3 and 4 further comprise:
It will be noted that steps (I), (II) and (III) correspond to steps (b), (c) and (d) of method 1 described above. Accordingly, preferences for the ligand and methods of assessing stability are as defined above with respect to method 1.
Any mutant GPCR with increased stability relative to its parent GPCR, for example those provided by any of methods 1-4 described above, may be used in the present invention. For example, mutant GPCRs with increased stability compared to their parent GPCRs, particularly those with increased thermostability may be used. Particular examples of mutant GPCRs suitable for use in the present invention are provided below.
In one embodiment, the mutant GPCR is a mutant GPCR which has, compared to its parent receptor, at least one different amino acid at a position which corresponds to any one or more of the following positions: (i) according to the numbering of the turkey 3-adrenergic receptor as set out in
Alignment of the turkey β1 AR, human adenosine receptor, rat neurotensin receptor and human muscarinic receptor amino acid sequences in
Mutant β-Adrenergic Receptor
β-adrenergic receptors are well known in the art. They share sequence homology to each other and bind to adrenalin.
In one embodiment, the mutant GPCR is a mutant β-adrenergic receptor which, when compared to the corresponding wild-type β-adrenergic receptor, has a different amino acid at a position which corresponds to any one or more of the following positions according to the numbering of the turkey β-adrenergic receptor as set out in
The mutant β-adrenergic receptor may be a mutant of any β-adrenergic receptor provided that it is mutated at one or more of the amino acid positions as stated by reference to the given turkey β-adrenergic receptor amino acid sequence.
It is particularly preferred if the mutant GPCR is one which has at least 20% amino acid sequence identity when compared to the given turkey β-adrenergic receptor sequence, as determined using MacVector and CLUSTALW (Thompson et al (1994) Nucl. Acids Res. 22, 4673-4680). More preferably, the mutant receptor has at least 30% or at least 40% or at least 50% amino acid sequence identity. There is generally a higher degree of amino acid sequence identity which is conserved around the orthosteric (“active”) site to which the natural ligand binds.
As is described in Example 1 and
Thus, a mutant turkey β-adrenergic receptor in which, compared to its parent, one or more of these amino acid residues have been replaced by another amino acid residue may be used. Mutant β-adrenergic receptors from other sources in which one or more corresponding amino acids in the parent receptor are replaced by another amino acid residue may also be used.
In one embodiment the mutant GPCR is a mutant β-adrenergic receptor which has has at least one different amino acid residue in a structural motif in which the mutant receptor compared to its parent receptor has a different amino acid at a position which corresponds to any of the following positions according to the numbering of the turkey β-adrenergic receptor as set out in
For the avoidance of doubt, the parent may be a β-adrenergic receptor which has a naturally-occurring sequence, or it may be a truncated form or it may be a fusion, either to the naturally occurring protein or to a fragment thereof, or it may contain mutations compared to the naturally-occurring sequenced provided that it retains ligand-binding ability.
By “corresponding amino acid residue” we include the meaning of the amino acid residue in another β-adrenergic receptor which aligns to the given amino acid residue in turkey β-adrenergic receptor when the turkey β-adrenergic receptor and the other β-adrenergic receptor are compared using MacVector and CLUSTALW.
It can be seen that Ile 72 of human β1 corresponds to Ile 55 of turkey β-adrenergic receptor; Ile 47 of human β2 corresponds to Ile 55 of turkey β-adrenergic receptor; and Thr51 of human β3 corresponds to Ile 55 of turkey β-adrenergic receptor. Other corresponding amino acid residues in human β1, β2 and β3 can readily be identified by reference to
It is preferred that the particular amino acid is replaced with an Ala. However, when the particular amino acid residue is an Ala, it is preferred that it is replaced with a Leu (for example, see turkey β-adrenergic Ala 234, Ala 282 and Ala 334 in
It is preferred if the mutant β-adrenergic receptor has a different amino acid compared to its parent at more than one amino acid position since this is likely to give greater stability. Particularly preferred human β1 receptor mutants are those in which one or more of the following amino acid residues are replaced with another amino acid residue: K85, M107, Y244, A316, F361 and F372. Typically, the given amino acid residue is replaced with Ala or Val or Met or Leu or Ile (unless they are already that residue).
Mutant human β1 receptors which have combinations of 3 or 4 or 5 or 6 mutations as described above are preferred.
Particularly preferred human β2 receptor mutants are those in which one or more of the following amino acids are replaced with another amino acid residue: K60, M82, Y219, C265, L310 and F321. Typically, the given amino acid residue is replaced with Ala or Val or Met or Leu or Ile (unless they are already that residue).
Mutant human β2 receptors which have combinations of 3 or 4 or 5 or 6 mutations as described above are preferred.
Particularly preferred human β3 receptor mutants are those in which one or more of the following amino acids are replaced with another amino acid residue: W64, M86, Y224, P284, A330 and F341. Typically, the given amino acid residue is replaced with Ala or Val or Met or Leu or Ile (unless they are already that residue).
Mutant human β3 receptors which have combinations of 3 or 4 or 5 or 6 mutations as described above are preferred.
Particularly preferred combinations of mutations are described in detail in Tables 1 and 2 in Example 1, and suitable mutants include the mutant turkey β-adrenergic receptors, and also include mutant β-adrenergic receptors where amino acids in corresponding position have been replaced by another amino acid, typically the same amino acid as indicated in Tables 1 and 2 in Example 1.
Particularly preferred mutants are those which contain mutations in the amino acids which correspond to the given amino acid residue by reference to turkey β-adrenergic receptor: (R68S, Y227A, A282L, A334L) (see m6-10 in Table 2 below); (M90V, Y227A, F338M) (see m7-7 in Table 2 below); (R68S, M90V, V230A, F327A, A334L) (see m10-8 in Table 2 below); and (R68S, M90V, Y227A, A282L, F327A, F338M) (see m23 in Table 2 below).
Mutant Adenosine Receptor
Adenosine receptors are well known in the art. They share sequence homology to each other and bind to adenosine.
In one embodiment, the mutant GPCR is a mutant adenosine receptor which, when compared to the corresponding wild-type adenosine, has a different amino acid at a position which corresponds to any one or more of the following positions according to the numbering of the human adenosine A2a receptor as set out in
The mutant adenosine receptor may be a mutant of any adenosine receptor provided that it is mutated at one or more of the amino acid positions as stated by reference to the given human adenosine A2a receptor amino acid sequence.
It is particularly preferred if the mutant GPCR is one which has at least 20% amino acid sequence identity when compared to the given human adenosine A2a receptor sequence, as determined using MacVector and CLUSTALW. Preferably, the mutant GPCR has at least 30% or at least 40% or at least 50% or at least 60% sequence identity. Typically, there is a higher degree of sequence conservation at the adenosine binding site.
As is described in Example 2 below, individual replacement of the following amino acid residues in the human adenosine A2a receptor sequence (as shown in
Gly 114, Gly 118, Leu 167, Ala 184, Arg 199, Ala 203, Leu 208, Gln 210, Ser 213, Glu 219, Arg 220, Ser 223, Thr 224, Gln 226, Lys 227, His 230, Leu 241, Pro 260, Ser 263, Leu 267, Leu 272, Thr 279, Asn 284, Gln 311, Pro 313, Lys 315.
Replacement of the following amino acid residues in the human A2a receptor sequence (as shown in
Ala 54, Val 57, His 75, Thr 88, Gly 114, Gly 118, Thr 119, Lys 122, Gly 123, Pro 149, Glu 151, Gly 152, Ala 203, Ala 204, Ala 231, Leu 235, Val 239.
Thus, a mutant human adenosine A2a receptor in which, compared to its parent, one or more of these amino acid residues have been replaced by another amino acid residue may be used. Mutant adenosine receptors from other sources in which one or more corresponding amino acids in the parent receptor are replaced by another amino acid residue may also be used.
In one embodiment, the mutant GPCR is a mutant adenosine receptor which has at least one different amino acid residue in a structural motif in which the mutant receptor compared to its parent receptor has a different amino acid at a position which corresponds to any of the following positions according to the numbering of the human adenosine A2a receptor as set out in
For the avoidance of doubt, the parent may be an adenosine receptor which has a naturally-occurring sequence, or it may be a truncated form or it may be a fusion, either to the naturally-occurring protein or to a fragment thereof, or it may contain mutations compared to the naturally-occurring sequence, provided that it retains ligand-binding ability.
By “corresponding amino acid residue” we include the meaning of the amino acid residue in another adenosine receptor which aligns to the given amino acid residue in human adenosine A2a receptor when the human adenosine A2a receptor and the other adenosine receptor are compared using MacVector and CLUSTALW.
It can be seen that, for example, Ser 115 in the A2b receptor (indicated as AA2BR) corresponds to Gly 114 in the A2a receptor. Similarly, it can be seen that Ala 60 in the A3 receptor (indicated as AA3R) corresponds to Ala 54 in the A2a receptor, and so on. Other corresponding amino acid residues in human adenosine receptors A2b, A3 and A1 can readily be identified by reference to
It is preferred that the particular amino acid in the parent is replaced with an Ala. However, when the particular amino acid residue in the parent is an Ala, it is preferred that it is replaced with a Leu.
It is preferred that the mutant adenosine receptor has a different amino acid compared to its parent at more than one amino acid position. Particularly preferred human adenosine A2b receptors are those in which one or more of the following amino acid residues are replaced with another amino acid residue: A55, T89, R123, L236 and V240. Typically, the given amino acid residue is replaced with Ala or Val or Met or Leu or Ile (unless they are already that residue).
Mutant human adenosine A2b receptors which have combinations of 3 or 4 or 5 mutations as described above are preferred.
Particularly preferred human adenosine A3 receptors are those in which one or more of the following amino acid residues are replaced with another amino acid residue: A60, T94, W128, L232 and L236. Typically, the given amino acid residue is replaced with Ala or Val or Met or Leu or Ile (unless they are already that residue).
Mutant human adenosine A3 receptors which have combinations of 3 or 4 or 5 mutations as described above are preferred.
Particular preferred human adenosine A1 receptors are those in which one or more of the following residues are replaced: A57, T91, A125, L236, and L240. Typically, the given amino acid residue is replaced with Ala or Val or Met or Leu or Ile (unless they are already that residue).
Particularly preferred combinations of mutations are described in detail in Example 2. Suitable mutants include these mutant human adenosine A2a receptors, and also include other mutant adenosine receptors where amino acids in corresponding positions have been replaced by another amino acid, typically the same amino acid as indicated in Example 2.
Particularly preferred adenosine receptor mutants are those which contain mutations in the amino acids which correspond to the given amino residue by reference to human adenosine A2a receptor: (A54L, K122A, L235A) (Rant 17); (A54L, T88A, V239A, A204L) (Rant 19); and (A54L, T88A, V239A, K122A) (Rant 21).
Mutant Neurotensin Receptor
Neurotensin receptors are known in the art. They share sequence homology and bind neurotensin.
In one embodiment, the mutant GPCR is a mutant neurotensin receptor which, when compared to the corresponding wild-type neurotensin receptor, has a different amino acid at a position which corresponds to any one or more of the following positions according to the numbering of the rat neurotensin receptor as set out in
It is particularly preferred if the mutant GPCR is one which has at least 20% amino acid sequence identity when compared to the given rat neurotensin receptor sequence, as determined using MacVector and CLUSTALW. Preferably, the mutant GPCR has at least 30% or at least 40% or at least 50% amino acid sequence identity.
The mutant neurotensin receptor may be a mutant of any neurotensin receptor provided that it is mutated at one or more of the amino acid positions as stated by reference to the given rat neurotensin receptor amino acid sequence.
As is described in Example 3 below, individual replacement of the following amino acid residues in the rat neurotensin receptor sequence (as shown in
As is described in Example 3 below, individual replacement of the following amino acid residues in the rat neurotensin receptor sequence (as shown in
Thus, a mutant rat neurotensin receptor in which, compared to its parent, one or more of these amino acid residues have been replaced by another amino acid residue may be used. Mutant neurotensin receptors from other sources in which one or more corresponding amino acids in the parent receptor are replaced by another amino acid residue may also be used.
In one embodiment the mutant GPCR is a mutant neurotensin receptor which has at least one different amino acid residue in a structural motif in which the mutant receptor compared to its parent receptor has a different amino acid at a position which corresponds to any of the following positions according to the numbering of the rat neurotensin receptor as set out in
For the avoidance of doubt the parent may be a neurotensin receptor which has a naturally-occurring sequence, or it may be a truncated form or it may be a fusion, either to the naturally-occurring protein or to a fragment thereof, or it may contain mutations compared to the naturally-occurring sequence, providing that it retains ligand-binding ability.
By “corresponding amino acid residue” we include the meaning of the amino acid residue in another neurotensin receptor which aligns to the given amino acid residue in rat neurotensin receptor when the rat neurotensin receptor and the other neurotensin receptor are compared using MacVector and CLUSTALW.
It is preferred that the particular amino acid in the parent is replaced with an Ala. However, when the particular amino acid residue in the parent is an Ala, it is preferred that it is replaced with a Leu.
It is preferred that the mutant neurotensin receptor has a different amino acid compared to its parent at more than one amino acid position. Particularly preferred human neurotensin receptors (NTR1) are those in which one or more of the following amino acid residues are replaced with another amino acid residue: Ala 85, His 102, Ile 259, Phe 337 and Phe 353. Typically, the given amino acid residues is replaced with Ala or Val or Met or Leu or Ile (unless they are already that residue).
Mutant human neurotensin receptors (NTR1) which have combinations of 3 or 4 or 5 mutations as described above are preferred.
Particularly preferred human neurotensin receptors (NTR2) are those in which one or more of the following amino acid residues are replaced with another amino acid residue: V54, R69, T229, P331 and F347. Typically, the given amino acid residue is replaced with Ala or Val or Met or Leu or Ile (unless they are already that residue).
Mutant human neurotensin receptors (NTR2) which have combinations of 3 or 4 or 5 mutations as described above are preferred.
Particularly preferred combinations of mutations are described in detail in Example 3. Suitable mutants include these mutant rat neurotensin receptors, and also include other mutant neurotensin receptors where amino acids in corresponding positions have been replaced by another amino acid, typically the same amino acid as indicated in Example 3.
Particularly preferred neurotensin receptor mutants are those which contain mutations in the amino acid residues which correspond to the given amino acid residue by reference to the rat neurotensin receptor: (F358A, A86L, I260A, F342A) (Nag7m); (F358A, H103A, I260A, F342A) (Nag7n).
Mutant Muscarinic Receptor
Muscarinic receptors are known in the art. They share sequence homology and bind muscarine.
In one embodiment, the mutant GPCR is a mutant muscarinic receptor which, when compared to the corresponding wild-type muscarinic receptor, has a different amino acid at a position which corresponds to any one or more of the following positions according to the numbering of the human muscarinic receptor M1 as set out in
It is particularly preferred if the mutant GPCR is one which has at least 20% amino acid sequence identity when compared to the given human muscarinic receptor sequence, as determined using MacVector and CLUSTALW. Preferably, the mutant GPCR has at least 30% or at least 40% or at least 50% amino acid sequence identity.
The mutant muscarinic receptor may be a mutant of any muscarinic receptor provided that it is mutated at one or more of the amino acid positions as stated by reference to the given muscarinic receptor amino acid sequence.
Thus, a mutant human muscarinic receptor in which, compared to its parent, one or more of these amino acid residues have been replaced by another amino acid residue may be used. Mutant muscarinic receptors from other sources in which one or more corresponding amino acids in the parent receptor are replaced by another amino acid residue may also be used.
For the avoidance of doubt the parent may be a muscarinic receptor which has a naturally-occurring sequence, or it may be a truncated form or it may be a fusion, either to the naturally-occurring protein or to a fragment thereof, or it may contain mutations compared to the naturally-occurring sequence, providing that it retains ligand-binding ability.
In one embodiment, the mutant GPCR is a mutant muscarinic receptor. For example, the mutant muscarinic receptor may have at least one different amino acid residue in a structural motif in which the mutant receptor compared to its parent receptor has a different amino acid at a position which corresponds to any of the following positions according to the numbering of the human muscarinic receptor as set out in
By “corresponding amino acid residue” we include the meaning of the amino acid residue in another muscarinic receptor which aligns to the given amino acid residue in human muscarinic receptor when the human muscarinic receptor and the other muscarinic receptor are compared using MacVector and CLUSTALW.
It is preferred that the particular amino acid is replaced with an Ala. However, when the particular amino acid residue is an Ala, it is preferred that it is replaced with a Leu.
It is preferred that the mutant GPCRs used in the invention have increased stability to any one of heat, a detergent, a chaotropic agent and an extreme of pH.
It is preferred if the mutant GPCRs used in the invention have increased thermostability.
It is preferred that the mutant GPCRs used in the invention, including the mutant β-adrenergic, adenosine and neurotensin receptors, have an increased thermostability compared to its parent when in the presence or absence of a ligand thereto. Typically, the ligand is an antagonist, a full agonist, a partial agonist or an inverse agonist, whether orthosteric or allosteric. As discussed above, the ligand may be a polypeptide, such as an antibody.
It is preferred that the mutant GPCRs used in the invention, for example a mutant β-adrenergic receptor or a mutant adenosine receptor or a mutant neurotensin receptor or a mutant muscarinic receptor is at least 2° C. more stable than its parent preferably at least 5° C. more stable, more preferably at least 8° C. more stable and even more preferably at least 10° C. or 15° C. or 20° C. more stable than its parent. Typically, thermostability of the parent and mutant receptors are measured under the same conditions. Typically, thermostability is assayed under a condition in which the GPCR resides in a particular conformation. Typically, this selected condition is the presence of a ligand which binds the GPCR.
It is preferred that the mutant GPCRs used in the invention, when solubilised and purified in a suitable detergent has a similar thermostability to bovine rhodopsin purified in dodecyl maltoside. It is particularly preferred that the mutant GPCR retains at least 50% of its ligand binding activity after heating at 40° C. for 30 minutes. It is further preferred that the mutant GPCR retains at least 50% of its ligand binding activity after heating at 55° C. for 30 minutes.
For the avoidance of doubt, the mutant GPCR provided in step (a) of the method of the first aspect of the invention may be extended or truncated, contain internal deletions or insertions or otherwise altered beyond introduction of stabilising mutations; for example by introduction or deletion of sites for posttranslational modification e.g. glycosylation or phosphorylation or fatty acylation. It may also be chemically modified synthetically, for example by peptide semisynthesis or crosslinking or alkylation. In any event, the mutant GPCR provided has increased stability in a particular conformation relative to its parent GPCR.
Selection of Binding Partners
Selection for binding partners against membrane proteins has previously proven to be a difficult task. The preparation of the required pure antigen is problematic. Membrane proteins are often detergent-solubilised and they are purified as protein-detergent complexes. The type and concentration of detergent is crucial to keep the protein in its native conformation. Some detergents may prevent proteins from binding to plastic and polystyrene surfaces used as common ELISA supports. In addition, adsorption to the solid phase can cause partial denaturation of the protein.
In contrast, the increased stability of mutant GPCRs confers several advantages when the GPCRs are used as immunogens or selection reagents for screening, enabling them to be used as such in a variety of contexts.
Accordingly, in one embodiment, the mutant GPCR may be in a whole cell preparation, a cell membrane fragment, solubilised in detergent or it may be incorporated into a lipid monolayer, a lipid bilayer, a bead-linked lipid particle, another solid-supported lipid layer or a proteoliposome. It is appreciated that when the GPCR is immobilised, the lipid layers may be supported directly as a layer on the surface of the solid support or may be tethered as a layer or vesicle as described in Cooper M. A. J Mol Recognit. 2004 July-August; 17(4):286-315.
The inventors recognise that high throughput membrane-receptor screening is facilitated by immobilising membranes on beads or on surfaces that can be arrayed or otherwise multiplexed. Typically, membrane proteins are deposited on a surface together with lipid in the form of proteoliposomes. The most commonly employed methods for the formation of proteoliposomes start with either prokaryote or eukaryote cells. Membrane proteins can be isolated either in a mixed micelle with detergent, dissolved in an organic solvent or aggregated as membrane fragments by sonication in buffer. Once isolated and purified, the membrane proteins can be reconstituted into vesicles by: a) organic solvent-mediated reconstitutions (for example reverse-phase evaporation, rehydration of lipid-protein films), b) mechanical means (for example sonication, French press, freeze-thaw), or c) detergent-mediated means (for example dialysis, dilution, or direct incorporation into pre-formed vesicles or into bicelles)
The detergent solubilised form of the mutant GPCR may be a partly pure or highly pure preparation. Purification, enabled by the improved stability and optimisation of solubilisation conditions, confers the advantage of removal of extraneous “sticky” antigens and lipids and other cell surface material such as carbohydrate to which, for example, phage may stick to. This is particularly beneficial when the ‘extraneous’ material is charged or hydrophobic since phage particles, for example, are known to stick to hydrophobic or charged surfaces non-specifically. Moreover, certain phage antibodies may themselves bind promiscuously to antigens. A normal level of purity, as assessed by SDS-PAGE, is 80-95%. Therefore, preferably the detergent solubilised form of the mutant GPCR is at least 80% pure, or at least 85% pure, and still more preferably at least 90%, or at least 93%, or at least 95%, pure of other proteins. As is known in the art, higher levels of purity, e.g. at least 99%, can be achieved using additional purification techniques.
Solubilised receptor preparations are typically made in a buffer of 20 mM Tris (pH 7.0), 0.1M (NH4)2SO4, 10% glycerol, 0.07% CHS, 0.33% DOM, 0.33% Chaps, 0.33 mM DOPC/DOPS (7:3), and 1 protease inhibitor tablet per 50 ml buffer. For solubilization trials, 0.5 ml of this solubilization buffer is added to approximately 2×106 cells, and these cell suspensions are sonicated using a probe sonicator (6×1-s pulses) and placed on a rocker at 4° C. After 2 h, the solutions are centrifuged at 4° C. for 20 min at 14,000 rpm using a tabletop centrifuge. The supernatants containing solubilised receptor are then transferred to new tubes and kept frozen at −80° C. until analysis.
Preparations of mutant GPCRs formed from membrane fragments or membrane-detergent extracts are reviewed in detail in Cooper M. A. J Mol Recognit. 2004 July-August; 17(4):286-315, incorporated herein by reference. Of particular interest are methods adapted from Graham, J. M.; Higgins, J. A. Membrane Analysis; Springer-Verlag: New York, 1997 and Dignam, J. D. Methods in Enzymology 1990, 182, 194-203. For example, one method is as follows; i) Spin 500 ml of a suitable cell culture (e.g. CHO, Sf9) at 1000 g for 10 min, re-suspend pellet in ca. twice the pellet volume of a suitable ice-cold 20 mM tris-HCl pH 8, 1 mM EDTA, 1 mM EGTA, 0.1 mM PMSF, 2 μg/ml aprotinin, and 10 μg/ml leupeptin, ii) Homogenize with a Dounce homogenizer (type A) for 10 strokes, then centrifuge at 30,000 g for 20 min, iii) Re-suspend pellet with 50 ml of 20 mM tris HCl pH 8, 3 mM MgCl, 10 ug/ml DNAase I plus PMSF, 2 μg/ml aprotinin and μg/ml leupeptin (solution B) and re-homogenize, iv) Centrifuge at 30,000 g for 20 min. and resuspend pellet in 20 ml of solution B and homogenize again, v) Store at 4° C. for immediate use after snap freezing.
The mutant GPCR may be engineered to include a molecular tag at the C terminus or N-terminus as is well known in the art. The tag may be any of a FLAG tag, a His tag, a c-Myc tag, a DDDDK (SEQ ID NO: 13) tag, an HSV tag, a Halo tag or a biotin tag. Such tags can be used to facilitate phage-based selection protocols in solution and may also be used to confer binding to a solid support. Moreover, such tags will facilitate selection and enrichment of mutant GPCRs from impure preparations using affinity columns, affinity filters, magnetic beads and other examples of selective solid supported reagents, filtration, centrifugation, size-exclusion chromatography and dialysis amongst other methods.
The increased stability of mutant GPCRs in a range of detergents and solubilisation buffers and additives lends them particularly well to being immobilised onto solid surfaces. Thus, in one embodiment the mutant GPCR is immobilised onto a solid support. Various supports are known in the art and include, for example, beads, columns, slides, chips or plates. Immobilisation may be via covalent or non-covalent interaction.
Where immobilisation is via a non-covalent interaction, the support may be coated with any of avidin, streptavidin, a metal ion, an antibody to the parent GPCR or an antibody to a molecular tag attached to the mutant GPCR. For example, the tag may be one recognised by an antibody such as a FLAG tag, or may be a poly-histidine tag enabling binding to a metal ion such as nickel or cobalt, as described for example in Venturi et al, Biochemica et Biophysica Acta 1610 (2003) 46-50. Alternatively, the mutant GPCR may be chemically modified for example with a biotin tag which can be bound to a surface coated with avidin or streptavidin. Moreover, a mutant GPCR may be immobilised via an antibody raised to the native receptor sequence.
Where immobilisation is via a covalent interaction, the support may be coated with a polymeric support such as carboxylated dextran. For example, the mutant GPCR may be covalently immobilised onto a surface coated with a carboxylated polymer via amine coupling. For example, water-soluble carbodiimide mediated activation of a carboxymethylated support such as dextran or hyaluronic acid allows for direct covalent capture of a mutant GPCR via available amino moieties of the protein to form a stable amide linkage. Alternatively, GPCRs can be engineered or further derivatised with sulfydryl-reactive reagents (e.g. pyridinyldithioethanamine (PDEA) or 3-(2-pyridinyldithio)propioic acid N-hydroxysuccinimide ester) (SPDP)) which allows reaction with free surface thiols (e.g. native free Cys, Met residues or with an engineered C-terminal Cys residue) to form a reversible disulfide linkage. In a similar manner, stable thioether bonds may be formed using maleimide coupling reagents such as sulfosuccinimidyl-4-(N-maleimidomethyl)cyclohexanecarboxylate (Sulfo-SMCC) and N-(γ-maleimidobutyrloxy)sulfosuccinimide ester (GMBS). A solid support may also be derivatised with cystamine to effect coupling with disulfide-activated GPCRs. Furthermore, treatment with hydrazine followed by a reductive amination enables coupling with aldheydes. The aldehyde groups may be native to the receptor or formed by mild oxidation of any cis-diols present in the solid support (present in sugar residues of carbohydrates such as dextran, agarose, sepharose, hyaluronic acid and polyaginate). In addition to the above, amino-presenting surfaces can be treated with commercially available bifunctional linking reagents to effect coupling with free amino or sulfhydryl groups on the receptor as described by (Ernst, 0. P. et al. Meth. Enzymol. 2000, 315, 471-489 and Nunomura, W. e et al. J. Biol. Chem. 2000, 275, 24540-24546).
The orientation of the mutant GPCR will depend on the desired outcome of the binding partner identification. For example, for the identification of therapeutic small molecules or antibodies, the mutant GPCR will typically be immobilised via the C-terminus or other intracellular domain to enable the extracellular domains to be outward facing in the assay. To identify native intracellular GPCR binding partners or agents which interfere with GPCR binding, the mutant GPCR is typically immobilised by the N-terminus or extracellular domain. Immobilisation by the N-terminus or extracellular domain may also identify therapeutic molecules that bind to the intracellular domain. However, it will be appreciated that for such molecules to be active in vivo, they must be able to pass through the cell membrane.
In an alternative embodiment, the mutant GPCR is not immobilised and is, for example, solubilised in detergent or present in a whole cell preparation. In this case, the test compound (for example, a library of test compounds) may be immobilised on a solid support, such as a chip surface. A variety of techniques are known in the art for immobilising compounds onto a chip surface, and any may be utilised. For example, suitable techniques include photolithography (Affymetrix, Santa Clara, Calif.), mechanical microspotting (Schena et al., Science (1995) vol. 270, p. 467-470; Synteni, Fremont, Calif.) and ink jetting (Incyte Pharmaceuticals, Palo Alto, Calif.; and Protogene, Palo Alto, Calif.). The address of the test compound/GPCR mutant pair on the chip is used to reveal the identity of the test compound. Other suitable methods are described, for example, in Fang, Y. et al. Drug Discovery Today 2003, 8, 755-761, and references Alves, I. D. et al. Curr. Prot. & Peptide Sci. 2005, 6, 293-312; Barry, R. et al. Proteomics 2004, 4, 3717-3726; Besenicar, M. et al. Chem. Phys. Lipids 2006, 141, 169-178; Cocklin, S. et al. Prot. Sci. 2004, 13, 194-194; Cooper, M. A. J. of Mol. Recognit. 2004, 17, 286-315; Fang, Y. et al. Drug Discov. Today 2003, 8, 755-761; Ferracci, G. et al. Anal. Biochem. 2004, 334, 367-375; Graneli, A. et al. Anal. Biochem. 2007, 367, 87-94; Graneli, A. et al. Biosens. Bioelectron. 2004, 20, 498-504; Groves, J. T. Curr. Op. Drug Discov. Develop. 2002, 5, 606-612; Groves, J. T. et al. J. Immunol. Meth. 2003, 278, 19-32; Harding, P. J. et al. Eur. Biophys. J. Biophys. Let. 2006, 35, 709-712; Komolov, K. E. et al. Anal. Chem. 2006, 78, 1228-1234; Kuroda, K. et al. App. Psychophys. Biofeedback 2006, 31, 127-136; Lang, M. J. et al. Curr. Prot. Peptide Sci. 2006, 7, 335-353; Leifert, W. R. et al. J. Biomol. Screening 2005, 10, 765-779; Martin-Garcia, J. et al. J. Virology 2005, 79, 6703-6713; Minic, J. et al. Biochim. Biophys. Acta-General Subjects 2005, 1724, 324-332; Mozsolits, H. et al. J. Peptide Sci. 2003, 9, 77-89; Navratilova, I. et al. Anal. Biochem. 2006, 355, 132-139; Ott, D. et al. Prot. Eng. Design & Selection 2005, 18, 153-160; Park, P. S. H. et al. Febs Lett. 2004, 567, 344-348; Sobek, J. et al. Combinat. Chem. & High Throughput Screening 2006, 9, 365-380; Stenlund, P. et al. Analytical Biochemistry 2003, 316, 243-250; Winter, E. M. et al. Anal. Chem. 2006, 78, 174-180; Yokogawa, M. et al. J. Am. Chem. So. 2005, 127, 12021-12027; Zurawski, J. A. et al. Biopolymers 2003, 71, 388-389, all of which are incorporated herein by reference.
In one embodiment, neither the GPCR nor the test compound are immobilised, for example in phage-display selection protocols in solution.
The ability to produce milligram quantities of purified GPCRs, stabilised in a particular conformation, enables screening approaches which would not be available to native GPCRs present in biological membranes. Thus, the method of the invention maybe used to identify ligands of ‘orphan’ GPCRs where the natural ligand is unknown. Ligands of orphan GPCRs may be identified from biological samples such as blood or tissue extracts or from libraries of ligands. Similarly, ligands of mutant GPCRs may be identified where the ligands were interacting proteins such as accessory proteins. It is also appreciated that peptide or protein therapeutics may be identified by the methods of the invention as could conformation-specific antibodies. For example, antibodies prepared as described below could be assessed for conformational-specific GPCR binding. In particular, antibodies may be identified from supernatants obtained from B-cells taken from immunised animals, from hybridomas obtained following immortalisation of B-cells from the immunised animal or from recombinant antibody libraries which may be expressed on phage particles or through an in vitro expression system such as ribosome display. The methods of the invention may also be used to determine the mechanism of action of compounds where the mechanism of action has not previously been known. For example, a mixture of GPCRs representing the ‘GPCRome’ or a subset thereof could be screened against compounds to identify if their mechanism of action was via binding to a GPCR. In addition, the invention may be used as a biochemical affinity purification system wherein particular compounds are purified from a mixture of compounds.
The test compound may be provided as a biological sample. In particular, the sample could be any suitable sample taken from an individual. For example, the sample may be a fluid sample such as blood, serum, plasma or spinal fluid. Alternatively, the sample could be a tissue or cell extract.
In one embodiment, the one or more test compounds is a polypeptide. For example, the test compound may be a particular type of polypeptide which is known to bind to certain GPCRs but where the identification of a conformation-specific polypeptide is desired. Alternatively, the polypeptide may be a candidate therapeutic molecule, for example an anticalin (Skerra J Biotechnol (2001) 74(4):257-75).
In one embodiment, the one or more test compounds is a peptide.
In one embodiment, the one or more test compounds is an affibody, a peptidomimetic, a nucleic acid, a peptide nucleic acid (PNA) or an aptamer, or a lipid or a carbohydrate.
In one embodiment, the one or more test compounds is a binding protein based on a modular framework, such as ankyrin repeat proteins, armadillo repeat proteins, leucine rich proteins, tetrariopeptide repeat proteins or Designed Ankyrin Repeat Proteins (DARPins) or proteins based on lipocalin or fibronectin domains or Affilin scaffolds based on either human gamma crystalline or human ubiquitin.
In one embodiment, the one or more test compounds is a small molecule, for example a molecule less than 5000 daltons, or the one or more test compounds is a natural product.
In one embodiment, the one or more test compounds is an antibody. For example, the test compound may be an antibody that has been raised against a mutant GPCR of a parent GPCR, wherein the mutant GPCR has increased stability in a particular conformation relative to the parent GPCR. Preferably, the mutant GPCR is the same mutant GPCR as was provided in step (a).
As used herein, the term “antibody” includes but is not limited to polyclonal, monoclonal, chimaeric, single chain, Fab fragments and fragments produced by a Fab expression library. Such fragments include fragments of whole antibodies which retain their binding activity for a target substance, Fv, F(ab′) and F(ab′)2 fragments, as well as genetically engineering derivatives of antibodies such as single chain antibodies (scFv), fusion proteins, domain antibodies (dAbs) and diabodies. For example, it will be appreciated that recombinant DNA technology may be used to produce further antibodies or chimeric molecules which retain the binding specificity of an original antibody. Such technology may involve fusing the DNA encoding the immunoglobulin variable region, or the complementarity determining regions (CDRs), of an antibody to the constant regions, or constant regions plus framework regions of a different immunoglobulin, as described, for example, in EP-A-184187, GB 2188638A or EP-A-239400. Moreover, a hybridoma or other cell producing an antibody may be subject to genetic mutation or other changes which may or may not alter the binding specificity of antibodies produced. Thus, since antibodies can be modified in a number of ways, the term “antibody” is to be construed as covering any specific binding member or substance having a binding domain with the required specificity. The term therefore includes antibody fragments, derivatives, functional equivalents and homologues of antibodies, including any polypeptide comprising an immunoglobulin binding domain, whether natural or wholly or partially synthetic. Chimeric molecules comprising an immunoglobulin binding domain, or equivalent fused to another polypeptide are therefore included. Furthermore, antibodies and fragments thereof may be human or humanised antibodies, as is well known in the art.
Various procedures known within the art may be used to raise antibodies against a mutant GPCR, or against fragments or fusions thereof.
For example, an antibody to a mutant GPCR having increased stability relative to a parent GPCR may be produced by immunising a lymphocyte with an immunogen of the mutant GPCR, screening the antibodies so produced for an antibody which binds to the GPCR, and isolating the antibody. By ‘immunising a lymphocyte’ we include both in vivo immunisation, where a whole animal is immunised and in vitro immunisation, where lymphocytes are immunised in vitro, for example as described in U.S. Pat. No. 5,290,681.
Preferably, the immunogen of a mutant GPCR is generally all of the mutant GPCR but may also be a part of the mutant GPCR, for example a fragment of the mutant GPCR. For example, the production of a stabilised GPCR may facilitate identification of a part of the GPCR not previously obvious from the native conformation that would benefit from a targeted immunisation approach. The fragment of the mutant GPCR may be any part of the GPCR which is able to elicit an immune response such as an antibody response. It is known that peptides having as few as 5 amino acids may elicit an antibody response, although typically larger peptides are used. Thus, the fragment of the immunogen may have at least 5 amino acids, typically from 5 to 1000 amino acids, such as 5 to 500, 5 to 200, 5 to 100, 5 to 50, 5 to 40, 5 to 30, 5 to 20, for example 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 amino acids.
Furthermore, the immunogen may be a fusion of the mutant GPCR, wherein the GPCR is fused to a second protein known to be immunogenic to lymphocytes. Examples of such immunogenic proteins include but are not limited to keyhole limpet hemocyanin, serum albumin, bovine thyroglobulin, and soybean trypsin inhibitor. The immunogen may also further include an adjuvant to enhance the immunological response to a mutant GPCR in a mammal in vivo. Various adjuvants used to increase the immunological response include, but are not limited to, Freund's (complete and incomplete), mineral gels (e.g., aluminum hydroxide), surface-active substances (e.g., lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, dinitrophenol, etc.), adjuvants usable in humans such as Bacille Calmette-Guerin and Corynebacterium parvum, or similar immunostimulatory agents. An additional example of an adjuvant that can be employed includes MPL-TDM adjuvant (monophosphoryl Lipid A, synthetic trehalose dicorynomycolate). The choice of adjuvant can be important in maintaining the structure of the GPCR and, for this reason, Titermax and oil in water emulsions such as Ribi's adjuvant emulsion are particularly preferred. Stabilised mutant GPCRs may also be linked together on a backbone to produce polyvalent molecules to further increase antigenicity.
It is appreciated that the immunogen of the mutant GPCR may be a variant of the mutant GPCR, provided that it is able to elicit an immune response to the mutant GPCR and does not significantly reduce the stability of the mutant GPCR. Such variants include polypeptides which have one or more amino acid substitutions compared to the mutant GPCR, and as many as 5% substitutions. Typically, the substitutions are conservative substitutions where, for example, a “variant” refers to a protein wherein at one or more positions there have been amino acid insertions, deletions, or substitutions, either conservative or non-conservative, provided that such changes result in a protein that is still able to elicit an immune response against the mutant GPCR and does not significantly reduce the stability of the mutant GPCR. By “conservative substitutions” is intended combinations such as Gly, Ala; Val, Ile, Leu; Asp, Glu; Asn, Gln; Ser, Thr; Lys, Arg; and Phe, Tyr. Such variants of a mutant GPCR can be made using standard methods of protein engineering and site-directed mutagenesis.
It is appreciated that the immunogen may also be a polynucleotide encoding the stabilised GPCR or fragment thereof. For example, the polynucleotide may be taken up into cells in vivo and expressed on the cell surface where it will stimulate an immune response.
The immunogen of a mutant GPCR may be provided as a whole cell preparation, in a cell membrane fragment, solubilised in detergent, in a lipid monolayer, in a lipid bilayer, in a bead-linked lipid particle, in a solid-supported lipid layer or in a proteoliposome, as described above.
For the production of polyclonal antibodies, various suitable host animals (e.g., rabbit, goat, chicken, mouse or other mammal) may be immunized by one or more injections with the immunogen. The polyclonal antibody molecules directed against the immunogenic protein can be isolated from the mammal (e.g., from the serum or egg yolk) and further purified by well known techniques, such as affinity chromatography using protein A or protein G, which provide primarily the IgG fraction of immune serum
Monoclonal antibodies can be prepared using hybridoma methods, such as those described by Kohler and Milstein, Nature, 256:495 (1975). In a hybridoma method, a mouse, hamster, or other appropriate host animal, is typically immunized with an immunizing agent to elicit lymphocytes that produce or are capable of producing antibodies that will specifically bind to the immunizing agent.
Generally, either peripheral blood lymphocytes are used if cells of human origin are desired, or spleen cells or lymph node cells are used if non-human mammalian sources are desired. The lymphocytes are then fused with an immortalized cell line using a suitable fusing agent, such as polyethylene glycol, to form a hybridoma cell (Goding, Monoclonal Antibodies: Principles and Practice, Academic Press, (1986) pp. 59-103). Immortalized cell lines are usually transformed mammalian cells, particularly myeloma cells of rodent, bovine and human origin. Usually, rat or mouse myeloma cell lines are employed. The hybridoma cells can be cultured in a suitable culture medium that preferably contains one or more substances that inhibit the growth or survival of the unfused, immortalized cells. For example, if the parental cells lack the enzyme hypoxanthine guanine phosphoribosyl transferase (HGPRT or HPRT), the culture medium for the hybridomas typically will include hypoxanthine, aminopterin, and thymidine (“HAT medium”), which substances prevent the growth of HGPRT-deficient cells.
Preferred immortalized cell lines are those that fuse efficiently, support stable high level expression of antibody by the selected antibody-producing cells, and are sensitive to a medium such as HAT medium. More preferred immortalized cell lines are murine myeloma lines, which can be obtained, for instance, from the Salk Institute Cell Distribution Center, San Diego, Calif. and the American Type Culture Collection, Manassas, Va. Human myeloma and mouse-human heteromyeloma cell lines also have been described for the production of human monoclonal antibodies (Kozbor, J. Immunol., 133:3001 (1984); Brodeur et al., Monoclonal Antibody Production Techniques and Applications, Marcel Dekker, Inc., New York, (1987) pp. 51-63).
Alternatively, monoclonal antibodies can be generated using the ‘Selected Lymphocyte Antibody Method’ (SLAM) as is well known in the art and described, for example, in Babcook et al. (1996) Proc. Natl. Acad. Sci. 93:7843-7848. Briefly, a single lymphocyte that is producing an antibody with a desired specificity or function within a large population of lymphoid cells is identified. Usually, lymphoid cells derived from an in vivo immunization are screened for those that produce antibodies which bind to selected antigens using an adapted haemolytic plaque assay (Jerne & Nordin, 1963, Science, 140:405) and the genetic information that encodes the specificity of the antibody subsequently retrieved from that lymphocyte.
Monoclonal antibodies can also be made by recombinant DNA methods, such as those described in U.S. Pat. No. 4,816,567. DNA encoding monoclonal antibodies raised against mutant GPCRs with increased stability can be readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of murine antibodies). The hybridoma cells described above serve as a preferred source of such DNA. Once isolated, the DNA can be placed into expression vectors, which are then transfected into host cells such as simian COS cells, Chinese hamster ovary (CHO) cells, or myeloma cells that do not otherwise produce immunoglobulin protein, to obtain the synthesis of monoclonal antibodies in the recombinant host cells. The DNA also can be modified, for example, by substituting the coding sequence for human heavy and light chain constant domains in place of the homologous murine sequences (U.S. Pat. No. 4,816,567; Morrison, Nature 368, 812-13 (1994)) or by covalently joining to the immunoglobulin coding sequence all or part of the coding sequence for a non-immunoglobulin polypeptide. Such a non-immunoglobulin polypeptide can be substituted for the constant domains of an antibody of the invention, or can be substituted for the variable domains of one antigen-combining site of an antibody of the invention to create a chimeric bivalent antibody.
It will be appreciated that single-chain antibodies specific to GPCRs can also be produced (see e.g., U.S. Pat. No. 4,946,778). Antibody fragments that contain the idiotypes to the mutant GPCR may also be produced by techniques known in the art including, but not limited to: (i) an F(ab′)2 fragment produced by pepsin digestion of an antibody molecule; (ii) an Fab fragment generated by reducing the disulfide bridges of an F(ab′)2 fragment; (iii) an Fab fragment generated by the treatment of the antibody molecule with papain and a reducing agent and (iv) Fv fragments. A general review of the techniques involved in the synthesis of antibody fragments which retain their specific binding sites is found in Winter & Milstein (1991) Nature 349, 293-299.
Bispecific antibodies may also be produced. Bispecific antibodies are monoclonal, preferably human or humanized, antibodies that have binding specificities for at least two different antigens. In the present case, one of the binding specificities is for a mutant GPCR. The second binding target is any other antigen, and advantageously is a cell-surface protein or receptor, including another GPCR or receptor subunit. For example, bispecific antibodies would be useful for pairs of GPCRs which can form heterodimers (Milligan. Biochim Biophys Acta. 2007 April; 1768(4):825-35.). In this case, the bispecific antibody may selectively target specific heterodimeric receptors. Bispecific antibodies may also be useful for viral entry co-receptors where one of the co-receptors is a GPCR, e.g CD4 and the GPCRs CCR5 or CXCR4 (Alkhatib G, Berger E A. Eur J Med Res. 2007 Oct. 15; 12(9):375-84). Methods for making bispecific antibodies are known in the art. Traditionally, the recombinant production of bispecific antibodies is based on the co-expression of two immunoglobulin heavy-chain/light-chain pairs, where the two heavy chains have different specificities (Milstein and Cuello, Nature, 305:537-539 (1983)). Because of the random assortment of immunoglobulin heavy and light chains, these hybridomas (quadromas) produce a potential mixture of ten different antibody molecules, of which only one has the correct bispecific structure. The purification of the correct molecule is usually accomplished by affinity chromatography steps. Similar procedures are disclosed in WO 93/08829, published May 13, 1993, and in Traunecker et al., 1991 EMBO J., 10:3655-3659.
It is appreciated that in some instances high throughput screening of test compounds is preferred and that the method may be used as a “library screening” method, a term well known to those skilled in the art. Thus, the test compound may be a library of test compounds. For example, the library may be a peptide or protein library produced, for example, by ribosome display or an antibody library prepared either in vivo, ex vivo or in vitro. Methodologies for preparing and screening such libraries are known in the art.
Thus, rather than the test compound being an antibody raised against a mutant GPCR with increased stability in a particular conformation relative to its parent GPCR and then testing its binding to that GPCR, the test compound may be an antibody library. Thus another method for generating antibodies specific to a GPCR involves screening expression libraries encoding immunoglobulin genes, or portions thereof, expressed in bacteria, yeast, filamentous phages, ribosomes or ribosomal subunits or other display systems. In this method, large libraries of antibody sequences or antibody fragment sequences are obtained from diverse sources such healthy donors, patients or animals (healthy or not). These sequences are cloned and expressed in an appropriate system and antibodies typically selected by binding to a GPCR with increased stability immobilised on a solid surface.
A particular example of an antibody library is a recombinant combinatorial antibody library, for example a scFv or Fab phage display library, prepared using human VL and VH cDNAs prepared from mRNA derived from human lymphocytes (McCafferty et al., Nature 348:552-553 (1990)). According to this technique, antibody V domain genes are cloned in-frame into either a major or minor coat protein gene of a filamentous bacteriophage, such as M 13 or fd, and displayed as functional antibody fragments on the surface of the phage particle. Because the filamentous particle contains a single-stranded DNA copy of the phage genome, selections based on the ability of the antibody to bind to the GPCR with increased stability also result in selection of the gene encoding the antibody exhibiting those properties. Phage display can be performed in a variety of formats; for their review see, e.g., Johnson, Kevin S. and Chiswell, David J., Current Opinion in Structural Biology 3:564-57 1 (1993). Moreover, examples of methods and reagents particularly amenable for use in generating and screening antibody display libraries can be found in, for example, Ladner et al. U.S. Pat. No. 5,223,409; Kang et al. PCT Publication No. WO 92/18619; Dower et al. PCT Publication No. WO 91/17271; Winter et al. PCT Publication No. WO 92/20791; Markland et al PCT Publication No. WO 92/15679; Breitling et al. PCT Publication No. WO 93/01288; McCafferty et al. PCT Publication No. WO 92/01047; Garrard et al. PCT Publication No. WO 92/09690; Fuchs et al. (1991) Bio/Technology 9:1370-1372; Hay et al. (1992) Hum Antibod Hybridomas 3:81-85; Huse et al. (1989) Science 246:1275-1281; McCafferty et al., Nature (1990) 348:552-554; Griffiths et al. (1993) EMBO J. 12:725-734; Hawkins et al. (1992) J. Mol Biol 226:889-896; Clackson et al. (1991) Nature 352:624-628; Gram et al. (1992) PNAS 89:3576-3580; Garrad et al. (1991) Bio/Technology 9:1373-1377; Hoogenboom et al. (1991) Nuc Acid Res 19:4133-4137; and Barbas et al. (1991) PNAS 88:7978-7982.
The methods may also be used to identify a polynucleotide capable of expressing a polypeptide binding partner of a GPCR, for example as described above in relation to phage display methods. Aliquots of an expression library in a suitable vector may be tested for the ability to give the required result. It will be appreciated that several cycles of identifying pools of polynucleotides comprising a polynucleotide having the required property and then rescreening those polynucleotides may be required in order to identify a single species of polynucleotide with the required property.
The invention includes screening methods to identify drugs or lead compounds of use in treating a disease or condition. It is appreciated that screening assays which are capable of high throughput operation are particularly preferred.
It is appreciated that in the methods described herein, which may be drug screening methods, a term well known to those skilled in the art, the test compound may be a drug-like compound or lead compound for the development of a drug-like compound.
The term “drug-like compound” is well known to those skilled in the art, and may include the meaning of a compound that has characteristics that may make it suitable for use in medicine, for example as the active ingredient in a medicament. Thus, for example, a drug-like compound may be a molecule that may be synthesised by the techniques of organic chemistry, less preferably by techniques of molecular biology or biochemistry, and is preferably a small molecule, which may be of less than 5000 daltons and which may be water-soluble. A drug-like compound may additionally exhibit features of selective interaction with a particular protein or proteins and be bioavailable and/or able to penetrate target cellular membranes or the blood:brain barrier, but it will be appreciated that these features are not essential.
The term “lead compound” is similarly well known to those skilled in the art, and may include the meaning that the compound, whilst not itself suitable for use as a drug (for example because it is only weakly potent against its intended target, non-selective in its action, unstable, poorly soluble, difficult to synthesise or has poor bioavailability) may provide a starting-point for the design of other compounds that may have more desirable characteristics.
Thus in one embodiment, the method further comprises modifying a test compound which has been shown to bind to the mutant GPCR when residing in a particular conformation, and determining whether the modified test compound binds to the mutant GPCR when residing in the particular conformation. It will be appreciated that it may be further determined whether the modified test compound also binds to the parent GPCR when residing in the particular conformation.
Various methods may be used to determine binding between a GPCR and a test compound including, for example, enzyme linked immunosorbent assays (ELISA), surface plasmon resonance assays, chip-based assays, immunocytofluorescence, yeast two-hybrid technology and phage display which are common practice in the art and are described, for example, in Plant et al (1995) Analyt Biochem, 226(2), 342-348. and Sambrook et al (2001) Molecular Cloning A Laboratory Manual. Third Edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. Other methods of detecting binding between a test compound and the GPCR include ultrafiltration with ion spray mass spectroscopy/HPLC methods or other physical and analytical methods. Fluorescence Energy Resonance Transfer (FRET) methods, for example, well known to those skilled in the art, may be used, in which binding of two fluorescent labelled entities may be measured by measuring the interaction of the fluorescent labels when in close proximity to each other.
Where the mutant GPCR is provided as a whole cell preparation, a membrane protoplast or a proteoliposome, it will be appreciated that biophysical techniques such as patch clamping, magic angle spinning NMR, fluorescence correlation spectroscopy, fluorescence resonance energy transfer and analytical ultracentrifugation may be used to analyse binding of the mutant GPCR to the test compound (as described in New, R. C., Liposomes: a practical approach. 1st ed.; Oxford University Press: Oxford, 1990, and Graham, J. M.; Higgins, J. A., Membrane Analysis. Springer-Verlag: New York, 1997.) Methods which allow quantitative, non-invasive determination of both the affinity and kinetics of such interactions include direct assays that allow continuous monitoring of membrane-protein binding, or in some cases by ultra-rapid separation of bound and free interactants followed by quantification of the membrane-bound and membrane-free analyte.
It will be appreciated that a bound test compound can be detected using a unique label or tag associated with the compound such as a peptide label, a nucleic acid label (Kerr et al., JACS (1993) vol. 115, p. 2529-2531; and Brenner & Lerner, Proc. Natl. Acad. Sci. USA (1992) vol. 89, p. 5381-5383), a chemical label (Ohlmeyer et al., Proc. Natl. Acad. Sci. USA (1993) vol. 90, p. 109222-10926; and Maclean et al., Proc. Natl. Acad. Sci. USA (1997) vol. 94, p. 2805-2810); a fluorescent label (Yamashita & Weinstock (SmithKline Beecham Corporation), WO95/32425 (1995); and Sebestyen et al., Pept. Proc. Eur. Pept. Symp. 22nd 1992 (1993), p. 63-64), or a radio frequency tag (Nicolaou et al., Angew. Chem. Int. Ed. Engl. (1995) vol. 34, p. 2289-2291; and Moran et al., JACS (1995) vol. 117, p. 10787-10788).
Where the test compound is an antibody against a mutant GPCR with increased stability, produced using any of the methods described above, binding is preferably assayed using immunoprecipitation or by an in vitro binding assay, such as radioimmunoassay (RIA) or enzyme-linked immunoabsorbent assay (ELISA). Such techniques and assays are known in the art. For example, in an ELISA, typically, the stabilised GPCR is immobilised on a microtitre plate or other solid surface. The plates are first incubated with BSA or other similar protein to block non-specific binding sites. Samples containing the antibody (such as serum or egg yolk or hybridoma cell culture supernatant) are then added to the plate and the antibodies allowed to bind to the immobilised GPCR. Bound antibodies are detected by the addition of a second detection antibody which binds to the first antibody and allows detection via its conjugation to an enzyme which catalyzes a reaction which can be subsequently detected. In addition, the binding affinity of antibodies can also be determined by the Scatchard analysis of Munson and Pollard, Anal. Biochem, 107:220 (1980). Preferably, antibodies having a high degree of specificity and a high binding affinity for the target GPCR are isolated.
It will be appreciated that where the antibody is a monoclonal antibody derived from a hybridoma, the hybridoma clones identified as expressing specific antibody can subsequently be subcloned by limiting dilution procedures and grown using standard methods. Suitable culture media for this purpose include, for example, Dulbecco's Modified Eagle's Medium and RPMI-1640 medium. Alternatively, the hybridoma cells can be grown in vivo as ascites in a mammal. The monoclonal antibodies secreted by the subclones can then be isolated or further purified from the culture medium or ascites fluid by conventional immunoglobulin purification procedures such as, for example, protein A-Sepharose, hydroxylapatite chromatography, gel electrophoresis, dialysis, or affinity chromatography.
Where the test compound is a phage display antibody library, binding to a stabilised GPCR may be assessed as follows. Typically, the mutant GPCR with increased stability is coated onto wells of a microtiter plate overnight at 4° C. The wells are washed in PBS and blocked for 1 hour at 37° C. in MPBS (3% milk powder in PBS). Purified phage from a phagemid library e.g. expressing a repertoire of human scFv (10 transducing units (tu)) are then blocked for 1 hour in a final volume of 100 μl of 3% MPBS. The blocked phage are added to the blocked GPCR wells and incubated for 1 hour. Wells are washed 5 times with PBST (PBS containing 0.1% v/v Tween 20) before being wash 5 times with PBS. The bound phage particles are then eluted and used to infect 10 ml exponentially growing E. coli TG1. The infected cells are grown in 2TY broth for 1 hour at 37° C., then spread onto 2TYAG plates and incubated overnight at 30° C. Cultures from this first round of panning selection are superinfected with helper phage and rescued to give, for example, scFv antibody-expressing phage particles for the second round of panning.
An alternative binding assay for phage display antibodies includes the use of soluble selections using biotinylated mutant GPCR protein at a final concentration typically of 100 nM. In this case, purified scFv phage (1012 tu) from a scFv phagemid library (as described above) is suspended in 1 ml 3% MPBS and blocked for 30 minutes. The biotinylated GPCR is then added and incubated at room temperature for 1 hour. The phage/antigen complexes are subsequently added to 250 μl of Dynal M280 Streptavidin magnetic beads that have been blocked for 1 hour at 37° C. in 1 ml of 3% MPBS, and incubated with the beads for a further 15 minutes at room temperature. The beads are captured using a magnetic rack and washed 4 times in 1 ml of 3% MPBS/0.1% (v/v) Tween 20 followed by 3 washes in PBS. After the last PBS wash, beads are resuspended in 100 μl PBS and used to infect 5 ml exponentially growing E. coli. Again, cultures from this first round of soluble selection would be superinfected with helper phage and rescued to give scFv antibody-expressing phage particles for a second round of soluble selection.
It is appreciated that screening assays which are capable of high throughput operation are particularly preferred to determine binding to a mutant GPCR, for example chip-based assays. Stabilised mutant GPCRs are particularly suited to such assays unlike their parent GPCRs which are not stable enough when purified to be used in these formats. In particular, technology called VLSIPS™ has enabled the production of extremely small chips that contain hundreds of thousands or more of different molecular probes, i.e. the test compounds. These biological chips have probes arranged in arrays, each probe assigned a specific location. Biological chips have been produced in which each location has a scale of, for example, ten microns. The chips can be used to determine whether target molecules interact with any of the probes on the chip. After exposing the array to target molecules under selected test conditions, scanning devices can examine each location in the array and determine whether a target molecule has interacted with the probe at that location.
A test compound to a mutant GPCR on a chip surface may be detected by scanning the chip surface for radioactivity or fluorescence. The address of the interacting pair on the chip reveals the identity of the test compound or where there is an array of mutant GPCRs on the chip, the identity of the receptor (see, for example, Kuimelis et al., Addressable Protein Arrays, U.S. Ser. No. 60/080,686, Apr. 3, 1998, now abandoned, and U.S. Ser. No. 09/282,734, Mar. 31, 1999). In the latter case the array of mutant GPCRs may be used as a method for obtaining selectivity data on compounds either for various conformations of the same GPCR or for various GPCRs.
Alternative methods of detecting binding of a mutant GPCR to a test compound, for example DNA, RNA, proteins and phospholipids, small molecules and natural products include surface plasmon resonance assays (SPA), for example as described in Plant et al (2005) Analyt Biochem 226(2), 342-348. The mutant GPCR, immobilised on a SPA bead, may be incubated with a single ligand which is labelled for example with a fluorescent group or the ligand may be a radioligand. The ability of a test compound to bind to the mutant GPCR may then be determined via its ability to displace the fluorescent ligand or the radioligand. In another example, the mutant GPCR is immobilised on a chip surface and binding of test compounds is detected by surface plasmon resonance and related techniques employing evanescent waves. Changes in refractive index can be used to determine the amount of bound compound, the affinity of interaction and the association and dissociation kinetics. An example of this approach has been described for rhodopsin which was immobilised on carboxylated dextran surfaces modified with long alkyl groups. Following amine coupling of the detergent-solubilised receptor, lipid/detergent-mixed micelles were adhered over the immobilized surface. The detergent was eluted in the subsequent buffer flow and the remaining lipid formed a bilayer on the chip surface. (Karlsson O P, Lofas S. Anal Biochem. 2002 Jan. 15; 300(2):132-8.
Where the test compound is a peptide or protein, for example, a ligand for an orphan receptor or an interacting protein, the bound ligand may be eluted and then identified by mass spectrometry such as matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF) or electrospray ionization mass spectrometry (ESI-MS) (Williams C. Addona T A. Trends Biotechnol. 2000 February; 18(2):45, Williams C Curr Opin Biotechnol. 2000 February; 11(1):42-6). The mutant GPCR may be immobilised on a column or bead, or expressed in tagged form in a cell and co-purified with the ligand from such complex mixtures using reagents directed to the tag or directly to the GPCR (Rigaut G, Shevchenko A, Rutz B, Wilm M, Mann M, Séraphin B. Nat Biotechnol. 1999 October; 17(10):1030-2).
The ability to generate high affinity conformation specific binding partners to GPCRs will facilitate the production of therapeutic GPCR binding partners. Thus, it will be appreciated that in addition to establishing binding to a GPCR, it will also be desirable to determine the functional effect of a binding partner on the GPCR.
Accordingly, in an embodiment of the invention, the method further comprises determining if the binding partner affects the function of the GPCR to which it binds and isolating a test compound that affects the function of the GPCR.
For example, in one embodiment, it is determined whether the binding partner alters the binding of the GPCR to its ligand. By ligand, we include any molecule which binds to the GPCR and which causes the GPCR to reside in a particular conformation as described above. Preferably, the ligand is the natural ligand of that GPCR or an analogue thereof. Binding of a GPCR to its ligand can be assayed using standard ligand binding methods known in the art and, for example, as described above. For example, the ligand may be radiolabelled or fluorescently labelled. The binding assay can be performed using the stabilised mutant GPCR or the parent GPCR. Typically, the stabilised GPCR is purified or expressed in a cell such a mammalian, bacterial or insect cell. Typically, the parent receptor is expressed in a cell such as a mammalian, bacterial or insect cell. The assay may be carried out on whole cells or on membranes obtained from the cells. The binding partner will be characterised by its ability to alter the binding of the labelled ligand.
In one embodiment, the binding partner decreases binding between the GPCR and its ligand. For example, the binding partner may decrease binding by a factor of at least 2 fold, 3 fold, 4 fold, 5 fold, 10 fold, 15 fold, 20, fold, 50 fold, 100 fold, 250 fold, 500 fold or 1000 fold. Preferably, the binding partner decreases binding by a factor of between 100-1000 fold, such as between 10-100 fold.
In one embodiment, the binding partner increases binding between the GPCR and its ligand. For example, the binding partner may increase binding by a factor of at least 2 fold, 3 fold, 4 fold, 5 fold, 10 fold, 15 fold, 20, fold, 50 fold, 100 fold, 250 fold, 500 fold or 1000 fold. Preferably, the binding partner increases binding by a factor of between 100-1000 fold, such as between 10-100 fold.
In a further embodiment, it is determined whether the binding partner modulates activation of a GPCR. For example, if a mutant GPCR stabilised in an agonist conformation was provided in step (a) of the method of the invention, the binding partner selected may be an agonist binding partner and thus increase activation of the GPCR. If a mutant GPCR stabilised in an antagonist conformation was provided in step (a) of the method of the invention, the binding partner selected may be an antagonist binding partner and thus decrease activation of the GPCR.
In this assay the parent GPCR or stabilised mutant GPCR is expressed in vivo, for example, in mammalian or insect cells where the GPCR is allowed to couple to well know GPCR signal transduction pathways (Eglen R. M. Functional G protein-coupled receptor assays for primary and secondary screening. Comb Chem High Throughput Screen. 2005 June; 8(4):311-8). Such assays include: calcium mobilisation (Gonzalez J E, Maher M P. Cellular fluorescent indicators and voltage/ion probe reader (VI PR) tools for ion channel and receptor drug discovery. Receptors Channels. 2002; 8(5-6):283-95, Dupriez V J, Maes K, Le Poul E, Burgeon E, Detheux M. Aequorin-based functional assays for G-protein-coupled receptors, ion channels, and tyrosine kinase receptors. Receptors Channels. 2002; 8(5-6):319-30), changes in cAMP levels (Weber M, Ferrer M, Zheng W, Inglese J, Strulovici B, Kunapuli P. A 1536-well cAMP assay for Gs- and Gi-coupled receptors using enzyme fragmentation complementation. Assay Drug Dev Technol. 2004 February; 2(1):39-49.), activation of kinase pathways (Leroy D, Missotten M, Waltzinger C, Martin T, Scheer A. G protein-coupled receptor-mediated ERK1/2 phosphorylation: towards a generic sensor of GPCR activation. J Recept Signal Transduct Res. 2007; 27(1):83-97)., regulation of gene transcription for example via the use of a reporter gene (Liu B, Wu D. Analysis of the coupling of G12/13 to G protein-coupled receptors using a luciferase reporter assay. Methods Mol Biol. 2004; 237:145-9, Kent T C, Thompson K S, Naylor L H. Development of a generic dual-reporter gene assay for screening G-protein-coupled receptors J Biomol Screen. 2005 August; 10(5):437-46), recruitment of β-arrest in (Hudson C C, Oakley R H, Sjaastad M D, Loomis C R. High-content screening of known G protein-coupled receptors by arrestin translocation Methods Enzymol. 2006; 414:63-78), activation of G proteins such as measuring GTPase activity (Jameson E E, Roof R A, Whorton M R, Mosberg H I, Sunahara R K, Neubig R R, Kennedy R T. Real-time detection of basal and stimulated G protein GTPase activity using fluorescent GTP analogues. J Biol Chem. 2005 Mar. 4; 280(9):7712-9) or measuring [35S]GTPgamma(γ)S binding (Rodgers G, Hubert C, McKinzie J, Suter T, Statnick M, Emmerson P, Stancato L. Development of displacement binding and GTPgammaS scintillation proximity assays for the identification of antagonists of the micro-opioid receptor. Assay Drug Dev Technol. 2003 October; 1(5):627-36).
Binding partners are typically selected which modulate the activation of the receptor.
For agonist binding partners the binding partner will typically mimic the activity of the natural ligand of the receptor and produce an increase in receptor activation, G protein activation or signal transduction. This will occur in the absence of an additional agonist. An agonist binding partner may increase receptor activation by a factor of at least 2 fold, 3 fold, 4 fold, 5 fold, 10 fold, 15 fold, 20, fold, 50 fold, 100 fold, 250 fold, 500 fold, 1000 fold, or 10000 fold.
It will be appreciated that there are two ways in which a binding partner may increase receptor activation. For example, the binding partner may act as a direct agonist, in which case receptor activation is typically increased by between 2-1000 fold. In another method, the binding partner may act to amplify the activity of an agonist. For example, the binding partner may increase the potency of the agonist, in which case receptor activation is typically increased by between 2-1000 fold, such as between 10-100 fold, or the binding partner may increase the maximal response produced by the agonist, in which case receptor activation is typically increased by between 2-10 fold. It will be appreciated that activating/amplifying the activity of receptors that are already switched on by endogenous ligand may be preferable to turning on all available receptors, since it is more physiologically specific and may mitigate issues such as desensitisation and undesirable side-effects (Christopoulos A (2002) Nat Rev Drug Discov 1:198-210).
In the case of antagonist binding partners the binding partner will typically act to block the activity of the receptor or its activation by an agonist. The antagonist binding partner may do this by blocking the binding of the agonist or by locking the receptor in an inactive form such that it is unable to couple to G proteins. An antagonist binding partner may decrease receptor activation by a factor of at least 2 fold, 3 fold, 4 fold, 5 fold, 10 fold, 15 fold, 20, fold, 50 fold, 100 fold, 250 fold, 500 fold, 1000 fold or 10000 fold. Typically, an antagonist binding partner would reduce receptor activation to a non-detectable level.
It will be appreciated that it may be desirable to produce a test compound or combination of test compounds that bind to more than one GPCR. For example, the test compound may bind to more than one GPCR of the same class of family. A list of GPCR classes and families has been produced by the International Union of Pharmacology (Foord et al (2005) Pharmacol. Rev. 57, 279-288) and this list is periodically updated at iuphar-db.org/GPCR/ReceptorFamiliesForward. The test compound may bind to one target GPCR and at least one further GPCR. The at least one further GPCR may be a GPCR that has been implicated in a disease pathway, or a GPCR that is involved in the same signalling pathway as the target GPCR, for example a signalling pathway that regulates or modulates a disease pathway. In addition, the at least one further GPCR may be one which enhances or suppresses the action of a test compound on the target GPCR. Such enhancement or suppression of action can be determined using methods well known in the art including binding assays and functional assays as described, for example, above.
Accordingly, in one embodiment more than one mutant GPCR is provided in step (a). For example, at least 2, 3, 4 or 5 mutant GPCRs of a different parent GPCR may be provided in step (a). Thus, in this embodiment, test compounds are selected for which bind to more than one GPCR. The compound may be a cross-reactive compound including, for example, a small molecule, affibody, antibody or diaboody. It will be appreciated that such an approach may lead to improvements in a binding partner's efficacy or potency.
Thus, a test compound may be selected which binds to a first and second GPCR, where the first and second GPCRs may be any pair of GPCRs. For example, the method can be used to select for a bivalent partner that binds to GPCRs which form a heterodimer, in which case the bivalent partner could bind to both receptors at the same time. Examples of appropriate GPCR heterodimers in this context include dopamine D1 and adenosine A1, opioid receptor heterodimers, cannabinoid CB1 and orexin receptors (Marshall F H. Heterodimerization of G-protein-coupled receptors in the CNS. Curr Opin Pharmacol. 2001 February; 1(1):40-4; Kent T, McAlpine C, Sabetnia S, Presland J. G-protein-coupled receptor heterodimerization: assay technologies to clinical significance. Curr Opin Drug Discov Devel. 2007 September; 10(5):580-9). Moreover, a binding partner could be selected for which binds to and modulates the activity of two independent receptors for the purpose of enhanced therapeutic activity. For example, CCK1/opioid receptor peptides bind to both CCK1 and the opoid receptor (Garcia-Lopez M T, González-Muñiz R, Martin-Martinez M, Herranz R. Strategies for design of non peptide CCK1R agonist/antagonist ligands. Curr Top Med Chem. 2007; 7(12):1180-94). Other appropriate examples include a combined beta 2 agonist and muscarinic antagonist; a dopamine D2 antagonist and 5HT2 antagonist; a D2 antagonist and 5HT6 antagonist; and a M1 agonist and 5HT6 antagonist.
It will be appreciated that the more than one GPCR provided in step (a) may or may not reside in the same conformation. For example, a diabody or similar bivalent binding partner may agonise at one end of the molecule and antagonise at another end, in which case the GPCRs would not have to reside in the same conformation.
Typically, where a test compound is selected that binds to more than one GPCR, the test compound binds to each GPCR with a similar potency. Typically, the Kd values for the particular binding partner binding to each of the respective GPCRs are within 5-10 fold of each other, such as within 2-3 fold.
It will be appreciated that the methods of the invention allow for combinations of test compounds that bind to one or more GPCRs to be isolated, either by repeating the method with single test compounds, providing multiple test compounds in one cycle of the method or by using a library of test compounds in the method.
In a further embodiment, it may be advantageous to select those test compounds which, while still able to bind to a first GPCR, are not able to bind, or bind less strongly than to the first GPCR, to at least one other GPCR, for example a second GPCR. It will be appreciated that the first and second GPCRs may be any pair of GPCRs. Thus, for example, the test compound may be one that is selected on the basis that it binds to a first GPCR, but the test compound so selected is further tested to determine whether it binds a second GPCR (or binds less strongly to a second GPCR than the first GPCR). Test compounds are selected which do not bind (or have reduced binding to) the second GPCR. Where the binding partner is therapeutic molecule, such an approach may help to reduce the binding partner's toxicity.
It is preferred that the test compound binds the further (second) GPCR with an affinity which is less than 50% of the affinity the compound has for first GPCR, more preferably less than 10% and still more preferably less than 1% or 0.1% or 0.01% of the affinity the compound has for the first GPCR. Thus, the Kd for the interaction of the test compound with the first GPCR is higher than for the second GPCR.
A second aspect of the invention provides a method for producing a binding partner of a GPCR, the method comprising synthesising a binding partner identifiable by carrying out the method according to the first aspect of the invention.
The binding partners can be synthesised by any suitable method known in the art including the techniques of organic chemistry, molecular biology or biochemistry. For example, if the binding partner is a polypeptide, the binding partner may be made by expressing the nucleic acid molecule encoding the binding partner in a suitable host cell as is known in the art. Antibodies may be synthesised using any of the methods described above including, for example, recombinant DNA technology.
A third aspect of the invention provides a binding partner obtained by any of the methods of the first aspect of the invention.
In an embodiment, the binding partner is a conformation-specific binding partner, as described above.
A fourth aspect of the invention provides a binding partner, for example a conformation-specific binding partner, obtainable by any of the methods of the first aspect of the invention.
The binding partner may be any of a polypeptide; an anticalin; a peptide; an antibody; a chimeric antibody; a single chain antibody; an aptamer; a darpin; a Fab, F(ab′)2, Fv, ScFv or dAb antibody fragment; a small molecule; a natural product; an affibody; a peptidomimetic; a nucleic acid; a peptide nucleic acid molecule; a lipid; a carbohydrate; a protein based on a modular framework including ankyrin repeat proteins, armadillo repeat proteins, leucine rich proteins, tetrariopeptide repeat proteins or Designed Ankyrin Repeat Proteins (DARPins); or proteins based on lipocalin or fibronectin domains or Affilin scaffolds based on either human gamma crystalline or human ubiquitin.
In a preferred embodiment, the binding partner is an antibody. For example, the antibody may be specific to a non-contiguous epitope in the GPCR or may be specific to a contiguous epitope in the GPCR. Preferably, the relevant epitopes in the parent and mutant GPCR recognised by the antibody are similar, whether they be contiguous or non-contiguous. Specifically, extracellular epitopes such as C- or N-terminii or polypeptide loops of the parent and mutant GPCR are preferably similar.
Typically the binding partner to the mutant GPCR with a similar potency to its binding to the parent GPCR. Typically, the Kd values for the particular binding partner binding the mutant GPCR and the parent GPCR are within 5-10 fold of each other, such as within 2-3 fold. Typically, the binding of the binding partner to the mutant GPCR compared to the parent GPCR would be not more than 5 times weaker and not more than 10 times stronger.
Typically, mutant receptors which have been stabilised in the selected conformation should bind the binding partner with approximately equal affinity (that is to say typically within 2-3 fold) or greater affinity than does the parent receptor. For agonist-conformation binding partners, the mutants typically bind the agonists with the same or higher affinity than the parent GPCR and typically bind antagonists with the same or lower affinity than the parent GPCR. Similarly for antagonist-conformation binding partners, the mutants typically bind the antagonists with the same or higher affinity than the parent GPCR and typically bind agonists with the same or lower affinity than the parent GPCR.
It is appreciated that the methods of the invention may be used as a biosensor to detect target substances such as molecules, especially biomolecules. For example, the biosensor may be used to detect biomarkers of disease or drug treatment which may be used as a diagnostic or prognostic. The mutant GPCR may be immobilised on a sensor surface and binding of compounds detected, for example, by surface plasmon resonance as described above. In a further example of a biosensor, compound binding to the receptor can be detected by changes in intrinsic tryptophan fluorescence or using fluorescence resonance energy transfer between an intrinsic tryptophan resident donor and a fluorescent acceptor (Lakowicz J R 1999. Principles of fluorescence spectroscopy, Plenum New York, Martin D D, Budamagunta M S, Ryan R O, Voss J C, Oda M N. J Biol Chem. 2006 Jul. 21; 281(29):20418-26). Alternatively, mutant GPCRs may be used in acoustic biosensors, wherein the mutant GPCRs are immobilised on quartz crystal resonator sensors (QCRS) and the acoustic sensor response used to detect compound—mutant GPCR binding interactions (Cooper M A, Drug Discov Today. 2006 December; 11(23-24):1068-74. Epub 2006 Oct. 20).
Accordingly, a fifth aspect of the invention provides a biosensor comprising a mutant GPCR of a parent GPCR wherein the mutant GPCR has increased stability in a particular conformation relative to the parent GPCR, and wherein when a target substance binds to said mutant GPCR, a detectable signal is produced.
Preferences for the mutant GPCRs and their methods of production are as defined above with respect to the first aspect of the invention.
Preferably, the biosensor is in a chip form or a bead supported form, where the mutant GPCRs are immobilised on a chip or bead and used to detect target substances. However, it will be appreciated that the mutant GPCRs may be provided in soluble form, in which case the biosensor would comprise a solution.
Immobilisation of mutant GPCRs onto a solid support for incorporation into a biosensor can be performed using methods well known in the art and as described above with respect to the first aspect of the invention. Typically, mutant GPCRs are reconstituted onto chip surfaces suitable for direct biosensor analysis via flow-mediated surface reconstitution (Karlsson et al., Analytical Biochemistry 300, 132-138 (2002)). For example, rapid immobilization and reconstitution of GPCRs on carboxylated dextran surfaces modified with long alkyl groups can be achieved following amine coupling of a detergent-solubilized receptor; lipid/detergent-mixed micelles are adhered as they are injected over the immobilized surface, taking advantage of integrated flow cells present in many biosensor systems. The detergent can then be eluted in the subsequent buffer flow leaving functional, intact mutant GPCRs for subsequent screening and analysis. Such mutant GPCR preparations containing detergent are ideally suited for use in a flow-based biosensor, such as quartz crystal microbalance biosensor, an evanescent wave biosensor, a planar wave guide biosensor, a surface Raman sensor, or a surface plasmon resonance biosensor. In the latter case, solubilized receptors can be captured on a GE Healthcare (Biacore) CM4 or CM5 dextran sensor chip. The dextran matrix of the sensor chip is activated by 35 uL of 50 mM N-hydroxysuccinimide and 200 mM N-ethyl-N-[(dimethylamino)propyl]carbodiimide at a flow rate of 5 uL/min, followed by a 7-min injection of 0.1 mg/mL detergent-solubilised GPCR receptor (for example with 25 mM CHAPS in 10 mM MOPS, pH 7.5). Any remaining reactive carboxy groups are deactivated using a 7-min pulse of 1 M ethanolamine hydrochloride, pH 8.5. After the injection, the biosensor chip is washed at high flow rate with the surface plasmon resonance running solution until a stable baseline is restored (ca. 30 min). This washing step works like a flow dialysis procedure and ensures the removal of the detergent from the sensor chip surface; however, it will be appreciated that hydrophobic parts of the GPCR may still be attached to some lipid or detergent molecules in order to maintain functional integrity.
The target substance may be any of a molecule, a biomolecule, a peptide, a protein, a carbohydrate, a lipid, a GPCR ligand, a synthetic molecule, a drug, a drug metabolite or a disease biomarker.
In an embodiment, the detectable signal is any of a change in colour; fluorescence; evanescence; surface plasmon resonance; electrical conductance or charge separation; ultraviolet, visible or infrared absorption; luminescence; chemiluminescence; electrochemiluminescence; fluorescence anisotropy; fluorescence intensity; fluorescence lifetime; fluorescence polarisation; fluorescence energy transfer; molecular mass; electron spin resonance; nuclear magnetic resonance; hydrodynamic volume or radius; specific gravity; scintillation; field effect resistance; electrical impedance; acoustic impedance; quantum evanescence; resonant scattering; fluorescent quenching; fluorescence correlation spectroscopy; acoustic load; acoustic shear wave velocity; binding force; or interfacial stress.
Summary
There are over 500 non-odorant G protein-coupled receptors (GPCRs) encoded by the human genome, many of which are predicted to be potential therapeutic targets, but there is only one structure available, that of bovine rhodopsin, to represent the whole of the family. There are many reasons for the lack of progress in GPCR structure determination, but we hypothesise that improving the detergent-stability of these receptors and simultaneously locking them into one preferred conformation will greatly improve the chances of crystallisation. A generic strategy for the isolation of detergent-solubilised thermostable mutants of a GPCR, the β-adrenergic receptor, was developed based upon alanine scanning mutagenesis followed by an assay for receptor stability. Out of 318 mutants tested, 15 showed a measurable increase in stability. After optimisation of the amino acid residue at the site of each initial mutation, an optimally stable receptor was constructed by combining specific mutations. The most stable mutant receptor, βAR-m23, contained 6 point mutations that led to a Tm 21° C. higher than the native protein and, in the presence of bound antagonist, βARm23 was as stable as bovine rhodopsin. In addition, βAR-m23 was significantly more stable in a wide range of detergents ideal for crystallisation and was preferentially in an antagonist conformation in the absence of ligand.
Results
Selection of Single Mutations that Increase the Thermostability of the β1 Adrenergic Receptor
βAR from turkey erythrocytes is an ideal target for structural studies because it is well characterised and is expressed at high-levels in insect cells using the baculovirus expression system[10,11]. The best overexpression of βAR is obtained using a truncated version of the receptor containing residues 34-424 (βAR34-424) [9] and this was used as the starting point for this work. Alanine scanning mutagenesis was used to define amino residues in βAR34-424 that, when mutated, altered the thermostability of the receptor; if an alanine was present in the sequence it was mutated to a leucine residue. A total of 318 mutations were made to amino acid residues 37-369, a region that encompasses all seven transmembrane domains and 23 amino acid residues at the C terminus; mutations at 15 amino residues were not obtained due to strong secondary structure in the DNA template. After sequencing each mutant to ensure the presence of only the desired mutation, the receptors were functionally expressed in E. coli and assayed for stability.
The assay for thermostability was performed on unpurified detergent-solubilised receptors by heating the receptors at 32° C. for 30 minutes, quenching the reaction on ice and then performing a radioligand binding assay, using the antagonist [3H]-dihydroalprenolol, to determine the number of remaining functional βAR34-424 molecules compared to the unheated control. Heating the unmutated βAR34-424 at 32° C. for 30 min before the assay reduced binding to approximately 50% of the unheated control (
The position and environment predicted for each of the 16 amino residues that gave the best increases in thermostability when mutated were determined by aligning the βAR sequence with that of rhodopsin whose structure is known (
The increase in stability that each individual mutation gave to βAR34-424 was determined by measuring the Tm for each mutant (results not shown); Tm in this context is the temperature that gave a 50% decrease in functional binding after heating the receptor for 30 minutes. Each mutation increased the Tm of βAR34-424 by 1-3° C., with the exception of M90A and Y227A that increased the Tm by 8° C.
Combining Mutations to Make an Optimally Stable Receptor
Initially, mutations that improved thermostability that were adjacent to one another in the primary amino sequence of βAR were combined. Constructions containing the mutations G67A and R68S, or different combinations of the mutations at the end of helix (Y227A, R229Q, V230A and A234L) were expressed and assayed; the Tm values (results not shown) were only 1-3° C. higher than the Tm for βAR34-424 and one mutant was actually slightly less stable, suggesting that combining mutations that are adjacent to one another in the primary amino acid sequence does not greatly improve thermostability. Subsequently, mutations predicted to be distant from one another in the structure were combined. PCR reactions were performed using various mixes of primers to combine up to 5 different mutations in a random manner and then tested for thermostability (Table 1). The best of these combinations increased the Tm more than 10° C. compared to the Tm of βAR34-424. In some cases, there was a clear additive effect upon the Tm with the sequential incorporation of individual mutations. This is seen in a series of 3 mutants, m4-1, m4-7 and m4-2, with the addition of V230A to m4-1 increasing the Tm by 2° C. and the additional mutation D332A in m4-7 increasing the Tm a further 3° C. Mutants that contained Y227A and M90A all showed an increase in Tm of 10° C. or more. Just these two mutations together increased the Tm of βAR34-424 by 13° C. (m7-5), however, the total antagonist binding was less than 50% of βAR34-424 suggesting impaired expression of this mutant. The addition of F338M to m7-5 did not increase the thermostability, but it increased levels of functional expression in E. coli.
The most thermostable mutants obtained, which were still expressed at high levels in E. coli, were m6-10, m7-7 and m10-8. These mutants contained collectively a total of 10 different mutations, with 8 mutations occurring in at least two of the mutants. A second round of mutagenesis was performed using m10-8 as the template and adding or replacing mutations present in m6-10 and m7-7 (
The thermostability assays used to develop βAR34-424 mutants were performed by heating the receptor in the absence of the antagonist, but it is well known that bound ligand stabilises receptors. Therefore, stability assays for βAR34-424 and βAR-m23 were repeated with antagonist bound to the receptors during the heating step (
Characterization of βAR-m23
The three characteristic activities measured for βAR-m23 and βAR34-424 to identify the effect of the six mutations were the affinity of antagonist binding, the relative efficacies of agonist binding and the ability of βAR-m23 to couple to G proteins. Saturation binding experiments to membranes using the antagonist [3H]-dihydroalprenolol (
However, the large decrease in agonist efficacy in βAR-m23 compared to βAR34-424 indicates that the 6 mutations in βAR-m23 have locked the receptor preferentially in an antagonist-bound conformation. From a crystallisation perspective, this is an added bonus to thermostabilisation, because it is essential to have a conformationally homogeneous protein population for the production of diffraction-quality crystals.
All of the thermostability assays used to derive βAR-m23 were performed on receptors solubilised in DDM. The aim of the thermostabilisation process was to produce a receptor that is ideal for crystallography, which means being stable in a variety of different detergents and not just DDM. We therefore tested the stability of βAR-m23 and βAR in a variety of different detergents, concentrating on small detergents that are preferentially used in crystallising integral membrane proteins.
Membranes prepared from E. coli expressing βAR-m23 or βAR34-424 were solubilised in DDM, bound to Ni-NTA agarose then washed with either DDM, decylmaltoside (DM), octylglucoside (OG), lauryldimethylamine oxide (LDAO) or nonylglucoside (NG). Stability assays were performed on the receptors in each of the different detergents (
Crystallisation of Mutant GPCR
Earlier attempts to crystallise several different constructs of turkey beta-adrenegic receptor failed. Despite experimenting with a variety of conditions, using both the native sequence and several truncated and loop-deleted constructs, over many years, no crystals were obtained.
However, once the stabilising mutations from βAR-m23 were transferred into the constructs, several different crystals were obtained in different detergents and different conditions.
The crystals that have been most studied so far were obtained using the purified beta-36 construct (amino acid residues 34-367 of the turkey beta receptor containing the following changes: point mutations C116L and C358A; the 6 thermostabilising point mutations in m23; replacement of amino acid residues 244-278 with the sequence ASKRK; a C terminal His6 tag) expressed in insect cells using the baculovirus expression system, after transferring the receptor into the detergent octyl-thioglucoside. The precipitant used was PEG600 or PEG1000 and the crystals obtained are elongated plates.
Experiments have also been carried out to see whether, once the crystallisation conditions had been defined using the stabilised receptor, it was possible to get crystals using the original non-stablised construct. It was possible that similar or perhaps very small crystals could have been obtained, but, in fact, the “wild type” (i.e. the starting structure from which the mutagenesis began) never gave any crystals.
The crystals are plate-shaped with space group C2 and diffract well, though the cell dimensions do vary depending on the freezing conditions used.
In general, once a GPCR has been stabilised it may be subjected to a variety of well-known techniques for structure determination. The most common technique for crystallising membrane proteins is by vapour diffusion (20, 21), usually using initially a few thousand crystallisation conditions set up using commercial robotic devices (22). However, sometimes the crystals formed by vapour diffusion are small and disordered, so additional techniques may then be employed. One technique involves the co-crystallisation (by vapour diffusion) of the membrane protein with antibodies that bind specifically to conformational epitopes on the proteins' surface (23, 24); this increases the hydrophilic surface of the protein and can form strong crystal contacts. A second alternative is to use a different crystallisation matrix that is commonly called either lipidic cubic phase or lipidic mesophase (25, 26), which has also been developed into a robotic platform (27). This has proven very successful for producing high quality crystals of proteins with only small hydrophilic surfaces e.g. bacteriorhodopsin (28). Membrane protein structures can also be determined to high-resolution by electron crystallography (29).
The evolution of βAR-m23 from βAR34-424 by a combination of alanine scanning mutagenesis and the selection of thermostable mutants has resulted in a GPCR that is ideal for crystallography. The Tm for βAR-m23 is 21° C. higher than for βAR34-424 and, in the presence of antagonist, βAR-m23 has a similar stability to rhodopsin. The increased Tm of βAR-m23 has resulted in an increased stability in a variety of small detergents that inactivate βAR34-424. In addition, the selection strategy employed resulted in a receptor that is preferentially in the antagonist-bound conformation, which will also improve the chances of obtaining crystals, because the population of receptor conformations will be more homogeneous than for wild type βAR34-424. Thus we have achieved a process of conformational stabilisation in a single selection procedure.
It is not at all clear why the particular mutations we have introduced lead to the thermostabilisation of the receptor. Equivalent positions in rhodopsin suggest that the amino acid residues mutated could be pointing into the lipid bilayer, into the centre of the receptor or at the interfaces between these two environments. Given the difficulties in trying to understand the complexities of the thermostabilisation of soluble proteins[15], it seems unlikely that membrane proteins will be any easier to comprehend; we found that there was no particular pattern in the amino acid residues in βAR that, when mutated, led to thermostability. However, since nearly 5% of the mutants produced were more stable than the native receptor, alanine scanning mutagenesis represents an efficient strategy to rapidly identify thermostable mutants.
The procedure we have used to generate βAR-m23 is equally applicable to any membrane protein that has a convenient assay for detecting activity in the detergent solubilized form. While we have selected for stability as a function of temperature as the most convenient primary parameter, the procedure can easily be extended to test primarily for stability, for example, in a harsh detergent, an extreme of pH or in the presence of chaotropic salts. Conformational stabilisation of a variety of human receptors, channels and transporters will make them far more amenable to crystallography and will also allow the improvement in resolution of membrane proteins that have already been crystallised. It is to be hoped that conformational stabilisation will allow membrane protein crystallisation to become a far more tractable problem with a greater probability of rapid success than is currently the case. This should allow routine crystallisation of human membrane proteins in the pharmaceutical industry, resulting in valuable structural insights into drug development.
Methods
Materials.
The truncated β1 adrenergic receptor from turkey (βAR34-424)[9] was kindly provided by Dr Tony Warne (MRC Laboratory of Molecular Biology, Cambridge, UK). This βAR construct encoding residues 34-424 contains the mutation C116L to improve expression[11], and a C-terminal tag of 10 histidines for purification. 1-[4,6-propyl-3H]-dihydroalprenolol ([3H]-DHA) was supplied by Amersham Bioscience, (+) L-norepinephrine bitartrate salt, (−) isoprenaline hydrochloride, (−) alprenolol tartrate salt and s-propranolol hydrochloride were from Sigma.
Mutagenesis of βAR.
The βAR cDNA was ligated into pRGIII to allow the functional expression of βAR in E. coli as a MalE fusion protein[16]. Mutants were generated by PCR using the expression plasmid as template using the QuikChange II methodology (Stratagene). PCR reactions were transformed into XL10-Gold ultracompetent cells (Stratagene) and individual clones were fully sequenced to check that only the desired mutation was present. Different mutations were combined randomly by PCR by including all the pairs of primers that introduced the following mutations: Mut4, G67A, G068A, V230A, D322A and F327A; Mut6, R068S, Y227A, A234L, A282L and A334L; Mut7, M90V, I129V, Y227A, A282L and F338M; Mut10, R68S, M90V, V230A, F327A and A334L. The PCR mixes were transformed and the clones sequenced to determine exactly which mutations were introduced.
Protein Expression and Membrane Preparations.
Expression of βAR and the mutants was performed in XL10 cells (Stratagene). Cultures of 50 ml of 2×TY medium containing ampicillin (100 μg/ml) were grown at 37° C. with shaking until OD600=3 and then induced with 0.4 mM IPTG. Induced cultures were incubated at 25° C. for 4 h and then cells were harvested by centrifugation at 13,000×g for 1 min (aliquots of 2 ml) and stored at −20° C. For the assays, cells were broken by freeze-thaw (five cycles), resuspended in 500 μl of buffer [20 mM Tris pH 8, 0.4 M NaCl, 1 mM EDTA and protease inhibitors (Complete™, Roche)]. After an incubation for 1 h at 4° C. with 100 μg/ml lysozyme and DNase I (Sigma), samples were solubilized with 2% DDM on ice for 30 minutes. Insoluble material was removed by centrifugation (15,000×g, 2 min, 4° C.) and the supernatant was used directly in radioligand binding assays.
For large-scale membrane preparations, 2L and 6L of E. coli culture of βAR and Mut23, respectively, were grown as described above. Cells were harvested by centrifugation at 5,000×g for 20 min, frozen in liquid nitrogen and stored at −80° C. Pellets were resuspended in 10 ml of 20 mM Tris pH 7.5 containing 1× protease inhibitor cocktail (Complete™ EDTA-free, Roche); 1 mg DNase I (Sigma) was added and the final volume was made to 100 ml. Cells were broken by a French press (2 passages, 20,000 psi), and centrifuged at 12,000×g for 45 min at 4° C. to remove cell debris. The supernatant (membranes) was centrifuged at 200,000×g for 30 min at 4° C.; the membrane pellet was resuspended in 15 ml of 20 mM Tris pH 7.5 and stored in 1 ml aliquots at −80° C. after flash-freezing in liquid nitrogen. The protein concentration was determined by the amido black method[17]. These samples were used in radioligand binding assays after thawing and being solubilized in 2% DDM as above.
For competition assays, as well as testing different detergents, DDM-solubilized βAR was partially purified with Ni-NTA agarose (Qiagen). 200 μl of Ni-NTA agarose was added to 2 ml of solubilized samples (10 mg/ml of membrane protein) in 20 mM Tris pH 8, 0.4 M NaCl, 20 mM imidazole pH 8 and incubated for 1 h at 4° C. After incubation, samples were centrifuged at 13,000×g for 30 sec and washed twice with 250 μl of buffer (20 mM Tris pH 8, 0.4 M NaCl, 20 mM imidazole) containing detergent (either 0.1% DDM, 0.1% DM, 0.1% LDAO, 0.3% NG or 0.7% OG).
Receptors were eluted in 2×100 μl of buffer (0.4 M NaCl, 1 mM EDTA, 250 mM imidazole pH 8, plus the relevant detergent). The KD for [3H]-DHA binding to semipurified βAR34-424 and βAR-m23 was, respectively 3.7 nM and 12.5 nM and the final concentration of [3H]-DHA used in the competition assays was 3 times the KD ie 12 nM for βAR34-424 and 40 nM for βAR-m23.
Radioligand Binding and Thermostability Assays.
Single point binding assays contained 20 mM Tris pH 8, 0.4 M NaCl, 1 mM EDTA, 0.1% DDM (or corresponding detergent) with 50 nM [3H]-DHA and 20-100 μg membrane protein in a final volume of 120 μl; equilibration was for 1 h at 4° C. Thermostability was assessed by incubating the binding assay mix, with or without [3H]-DHA at the specified temperature for 30 minutes; reactions were placed on ice and [3H]-DHA added as necessary and equilibrated for a further hour. Receptor-bound and free radioligand were separated by gel filtration as described previously[18]. Non-specific binding was determined in the presence of 1 μM of s-propranolol. Saturation curves were obtained using a range of [3H]-DHA concentration from 0.4 nM to 100 nM. Competition assays were performed using a concentration of [3H]-DHA of 12 nM for βAR34-424 and 40 nM for βAR-m23 (ie three times the KD) and various concentrations of unlabeled ligands (0-100 mM). Radioactivity was counted on a Beckman L56000 liquid scintillation counter and data were analyzed by nonlinear regression using Prism software (GraphPad).
Location of 13AR-m23 Thermostable Mutations in Rhodopsin Structure.
The pdb file for the rhodopsin structure, accession code 1GZM[14], was downloaded from the Protein Data Bank website (pdb.org) and displayed in the program PyMOLX11Hybrid (DeLano Scientific). The equivalent amino acid residues in rhodopsin for the thermostable mutations in βAR were located in the rhodopsin structure based upon an alignment among the four GPCRs with which we are most familiar, namely rhodopsin, β1 adrenergic receptor, neurotensin receptor and adenosine A2a receptor[19].
26 ± 0.4
26 ± 0.5
The structure of the β2 adrenergic receptor has been determined (20, 21), which is 59% identical to the turkey β1 receptor, but with a distinctly different pharmacological profile (22, 23). In order to determine the structural motifs in which the stabilising mutations of the turkey β1 receptor reside, we mapped the mutations onto the human β2 structure (21).
The beta adrenergic receptors were first aligned using ClustalW in the MacVector package; thermostabilising mutations in turkey β1 were highlighted along with the corresponding residue in the human β2 sequence. The human β2 model (pdb accession code 2RH1) was visualised in Pymol and the desired amino acids were shown as space filling models by standard procedures known in the art. The structural motifs in which the stabilising mutations were located, were determined by visual inspection.
Table (v) lists the equivalent positions in the β2 receptor corresponding to the thermostabilising mutations in βAR-m23 and the structural motifs in which they reside.
As seen from Table (v), the mutations are positioned in a number of distinct localities. Three mutations are in loop regions that are predicted to be accessible to aqueous solvent (loop). Eight mutations are in the transmembrane α-helices and point into the lipid bilayer (lipid); three of these mutations are near the end of the helices and may be considered to be at the hydrophilic boundary layer (lipid boundary). Eight mutations are found at the interfaces between transmembrane α-helices (helix-helix interface), three of which are either within a kinked or distorted region of the helix (kink) and another two mutations occur in one helix but are adjacent to one or more other helices which contain a kink adjacent in space to the mutated residue (opposite kink). These latter mutations could affect the packing of the amino acids within the kinked region, which could result in thermostabilisation. Another mutation is in a substrate binding pocket (pocket).
Such structural motifs, by virtue of them containing stabilising mutations, are important in determining protein stability. Therefore, targeting mutations to these motifs will facilitate the generation of stabilised mutant GPCRs. Indeed, there were several instances where more than one mutation mapped to the same structural motif. For example, the Y227A, V230A and A234L mutations in the turkey β1 adrenergic receptor all mapped to the same helical interface, the V89L and M90V mutations mapped to the same helical kink and the F327A and A334L mutations mapped to the same helical surface pointing towards the lipid bilayer (Table (v)). Thus, when one stabilising mutation has been identified, the determination of the structural motif in which that mutation is located will enable the identification of further stabilising mutations.
The generation of mutant GPCRs having increased stability in a particular conformation relative to a parent GPCR provides a number of advantages for screening of binding partners. For example, the present methods reduce the amount of material required for a screen. In standard screens, GPCRs are present in whole cells or in membranes from whole cells which are usually screened by incubation with individual compounds in isolated chambers rather than libraries of compounds. Therefore the present invention provides advantages in terms of time required to carry out a compound screen. The ability to lock a GPCR in a particular conformation provides advantages in that it increases the likelihood of identifying a ligand with the required pharmacological properties. In standard binding screens GPCRs are able to assume a number of different conformations and binding compounds will be identified across different pharmacological types. Reagent costs can be reduced due to the ability to miniaturize the assay formats and this is facilitated by the present method.
Methods
Compound Screening
A mutant GPCR having increased stability in a particular conformation is immobilised on a solid surface and incubated with buffer containing an encoded library of compounds. After a suitable period of time, to allow binding between the mutant GPCR and compounds from the library which selectively bind to the mutant GPCR, the buffer is removed. Next there follows a number of wash steps to remove compounds which have not bound specifically to the mutant GPCR. The reading code, tag or address (such as DNA or RNA) is then used to identify the small molecule bound either whilst still bound to the mutant GPCR or following elution from the GPCR. The conformation specific binding partner is subsequently isolated.
Selection of Antibodies Using Immobilised GPCRS
Immobilised stabilised GPCRs can be used to select antibodies to the receptor from mixtures of antibodies such as would be present in plasma from an animal immunised with the stabilised GPCR, the native receptor or a peptide from the receptor. Antibodies could be identified from supernatants obtained from B-cells taken from immunised animals or from hybridomas obtained following immortalization of B-cells from the immunised animal or from recombinant antibody libraries which may be expressed on phage particles or through an in vitro expression system such as ribosome display. The method has the advantage of selecting antibodies to particular conformations of a receptor. A stabilised GPCR locked in the antagonist or ground state of the receptor would increase the probability of selecting an antagonistic antibody whereas a stabilised GPCR locked in the activated or R* state would increase the probability of selecting an activating antibody. In standard screens antibodies are often selected to GPCRs that bind to peptide epitopes of the receptor but do not have antagonist or agonist properties and therefore are not useful as therapeutic agents.
Summary
We have used stabilised β-adrenergic receptor (β-AR) to generate antibodies using phage display. Positive phage clones showed specificity for β-AR and sub-cloning of selected antibody genes led to successful production of anti-β-AR specific scFv antibodies.
Introduction
The therapeutic application of antibodies in the area of receptor-ligand systems has great potential. However, the primary issue in generating antibodies (either by in vitro or in vivo methods) to G protein coupled receptors (GPCRs) concerns the immunogenic recognition of a specific conformation in a homogeneous antigen preparation, i.e. either an agonistic conformation or antagonistic conformation, rather than creating a pool of antibody binders that recognises purified antigen in multiple conformations in a heterogeneous preparation. In addition, recombinant receptor antigen is usually available only in the extracellular domain form, which precludes any tertiary structure involving other parts of the receptor. The proposed solution to this issue is the application of stabilized GPCRs as the target antigen.
We have demonstrated the utility of stabilised GPCRs (StaRs™) in the generation of recombinant antibodies by the in vitro method of phage display such that antibodies which bind the β adrenergic receptor stabilised in the antagonist conformation may be isolated. Such antibodies can then be subject to functional assays e.g. in ligand binding assays.
Overview of Process
A typical phage display strategy comprises several stages in the process to identify inhibitory scFv clones (
A pool of clones representing a selection output (polyclonal phage ELISA) is assessed for recognition of antigen by phage ELISA. Individual clones can also be assessed by monoclonal phage ELISA and for diversity by sequence analysis, however the preferred method is to subclone the selected population into a recombinant antibody expression vector (pSANG 10-3F) and then perform the assessment by monoclonal scFv ELISA and DNA sequencing. This circumvents the problem of identifying phage antibody binders that subsequently exhibit poor expression as scFv fragments. Selection outputs yielding diverse ELISA positives can then be prioritised for functional screening of larger panels of phage antibodies.
Selection outputs are subjected to a screening campaign, employing a functional high-throughput assay, of periplasmic extracts in order to identify a population of scFv inhibitors. Lastly, the hits from the screening campaign are profiled as scFv by further functional assays, as well as IC50 analysis which assess the efficiency of their inhibitory action.
Methods and Results
2-3 rounds of antibody selections were carried out using stabilised β-AR as antigen and using the “McCafferty” antibody phage display library described in Schofield et al, 2007 (24). Selections were carried out in PBS in the presence (A) or absence (B) of 20 nM ligand (−)-alprenolol during binding and washing steps. Further, for β-AR protein handling, all coating, washing and blocking buffers were supplemented with 0.1% detergent decylmaltoside (Anatrace, Anagrade). The relative success of the selectives was determined using polyclonal phage ELISA and monoclonal phage ELISA.
Optimisation to Immobilise Antigen
Immobilisation strategies were based on taking advantage of the His tagged antigen. In the first instance, immobilisation was done using control proteins rather than βAR-m23. A variety of surfaces, including Ni-NTA plates, were employed in the initial assessment. All were compared against standard passive absorption onto Nunc plates. In all cases, the outcome was evaluated using polyclonal phage ELISA after 2 rounds of selection.
Antibody Selection
Selection, elution and rescue of the library was as described in Schofield et al (2007). 150 μl of β-AR at concentration of 20 μg/ml was coated over night at +4° C. in two (24) wells of a Nickel chelate-plate (Nunc). The receptor was diluted in coating buffer which is 20 mM Tris pH8, 100 mM NaCl, 0.1% decylmaltoside (dec-M) and also 20 nM ligand for selection A. Next day, the wells were rinsed with PBS and blocked for 1 h at room temperature with 3% Marvel milk protein in PBS supplemented with 0.1% dec-M (PBS-M). After coating, the well was rinsed in PBS and 100 μl of phage library pre-blocked in 2% Marvel/PBS was added and incubated for 1 h at room temperature. Following binding, samples were washed 6 times in PBS/0.1% Tween supplemented with 0.1% dec-M and six times in PBS supplemented with 0.1% dec-M. Bound phage was then eluted with Trypsin (24). Eluted phage were added to exponentially growing TG1 cells (at OD600=0.5) and grown at 37° C. for 1 h. Infected cells were plated onto TY plates supplemented with 100 μg/ml ampicillin, 2% glucose and grown overnight at 30° C. Next day, plates were scraped in TY medium supplemented with 100 μg/ml ampicillin, 15% glycerol for storage. The population from this first round of selection was rescued with helper phage and PEG precipitated and 100 μl of these were used in a second round of selections using the same conditions and procedures as described for round 1.
Polyclonal Phage ELISA
For ELISA, βAR was covalently immobilised on Amino plates (Nunc Catalog No: 436008). Coating and washing buffers were supplemented with 20 nM ligand and 0.1% dec-M. The ELISA plate was coated overnight with β-AR at 24 μg/ml and 2 control proteins (CD86 and Notch1) at 5 μg/ml. Next day the wells were washed and blocked with PBS-M. 50 μl/well of polyclonal phage from 2 rounds of selection were added (in PBS-M, at a concentration of 0.1× relative to the initial culture volume) and incubated for 1 hour at room temperature. Wells were washed and incubated with an α-M13 antibody (GE healthcare product No: 27-9421-01), for 1 hour at room temperature. Plates were washed and incubated with Europium labelled anti-mouse antibody (Perkin Elmer, product No: AD 0207), for 1 hour at room temperature. Wells were washed and 50 μl/well of enhancement solution (Perkin Elmer, product No: 4001-0010) added and incubated for 10 min. The results are shown in
Monoclonal Phage ELISA
For this assay, individual clones of round 2 phage from selection A were picked, rescued and PEG precipitated. Again, coating, washing, blocking and antibody detection buffers were supplemented with 20 nM ligand and 0.1% detergent. Wells of a Nunc Amino plate were coated with β-AR for 1 h 30 minutes at room temperature. Coated wells were washed 3 times with PBST and 3 times with PBS and blocked with PBS-M and 50 ul/well of 0.1× phage was added and incubated for 1 h at room temperature. Wells were washed 6 times with PBS and incubated with α-M13 antibody for 1 h at room temperature. After washing 6 times with PBS the wells were incubated with anti-mouse-Eu antibody, 1 h at room temperature. Next, wells were washed and incubated with enhancement solution for 10 min. Out of 69 screened clones, 20 clones were detected as positive (
Specificity Phage ELISA
17 of the positive phage clones from the monoclonal ELISA were tested for binding specificity to β-AR and 3 unrelated proteins. This includes N1-EGF, (EGF domains 1-12 of murine Notch1 fused to a human Fc domain from R&D Systems, catalogue number 1057-TK). The other control proteins include the extracellular domain of murine CD86 and the negative regulatory region of murine Notch1 expressed as a CD4 fusion (CD86 and N1(NRR) respectively) in a transient expression system as described in Chapple et al 2006 (25). In this ELISA both nickel chelate and amino-plate were used for comparison. Again, for wells containing β-AR protein, coating, washing, blocking and antibody binding buffers were supplemented with 20 nM ligand and 0.1% detergent. Wells were washed and incubated with antibodies as described for the monoclonal ELISA in previous section. The assay showed that both His and Amino-plates can be used and that the majority of the anti-β-AR clones do not cross react with the unrelated proteins (
Expression and Screening of Monoclonal scFv
Sub-cloning, antibody single chain Fv (scFv) expression and purification were as described in Schofield et al (2007). Selected antibody genes within the round 2 phage population (selection A) were sub-cloned into the pSANG10-3F vector (26) and transformed into BL21(DE3) cells. 96 colonies were picked and periplasmic expression of the scFv antibody was induced in a 96 well format using standard methods in the art. scFv were recovered from the periplasm and used for ELISA on an Amino plate (Nunc). Washed and blocked wells were incubated for 1 h with 50 μl/well of scFv. Plates were washed and incubated with Europium labelled anti-FLAG antibody for 1 h at room temperature. 12 clones gave a signal above 1000 units with background levels of less than 50 for negative clones (
Positive clones are selected with binding and specifically confirmed in a secondary ELISA, and clones of interest sequenced. Antibody sequences are analysed to identify the number of unique binding clones that have been isolated.
To test for blocking of ligand binding by isolated antibodies, unique positive antibody clones are selected for larger scale preparation (50-500 ml) using periplasmic extraction and immobilised metal affinity chromatography. This material is assessed for the ability to interfere in ligand binding to receptor using robust reporter assays (e.g. inhibition of cAMP generation or inhibition of ligand binding to transfected cells).
Methods and Results:
Binding studies were performed at 10° C. using a Biacore S51 optical biosensor equipped with a streptavidin-coated CM5 chip and equilibrated with running buffer (20 mM trisHCl, 150 mM NaCl, 1 mM EDTA, 1% DMSO, 0.1% decyl maltoside, pH 7.8).
β1AR immobilization.
β1AR36-M23 was minimally biotinylated using EZ-link sulfo-NHS-LC-LC biotin (Pierce #21338): The biotin was added to the receptor preparation, (spiked with 100 uM alprenolol) and allowed to react for three hours at 4° C., after which free biotin was removed via column chromatography.
The biacore sensor chips coated in the stabilised beta receptor could be used to characterise the binding of drugs with activity at the beta receptor. Flow through of the compound allowed the on rate to be determined. Subsequent washing enabled determination of the off rate. These parameters could then be used to determine a kinetic affinity measurement (Kd).
The alprenolol data demonstrates that the biotinylated b1AR is active and this biosensor approach can be used to characterize the compound/receptor interactions.
When the β1AR surface was almost three days old, we retested alprenolol binding to determine how much activity the receptor had lost over time.
β1 AR Capture on Another Spot.
The S51 biosensor has the ability to monitor two reaction spots at one time so we captured the receptor to a density of 8000 RU on another streptavidin-coated spot (
The data from a test run of alprenolol binding to the 8000-RU b1AR spot are provided in
The beta receptor agonist salmeterol was tested using a highest concentration of 1.67 μM, with each concentration tested two or three times (
Salmeterol dissociated much faster and bound the receptor much more weakly than alprenolol or propranolol did. This is to be expected since salmeterol has a low affinity for the β1-AR and in particular has a low affinity for the antagonist stabilised form of the receptor which is used here. In addition, we detected some complexity in the interaction, as indicated by the poor fit of the model to the responses during the dissociation phase (t>60 sec).
Isoproterenol, a non-selective β-adrenergic agonist, was tested using a highest concentration of 2 μM (
Conclusion
1 averaged from two b1AR surfaces
2 preliminary results
Methods
A thermostabilised adenosine A2a receptor (A2a StaR) conformationally selected in the antagonist form (referred to as Rant22) was used to screen compounds from a library in order to identify compounds with activity at the A2a receptor. The StaR was generated as previously described (Magnani et al, Co-evolving stability and conformational homogeneity of the human adenosine A2a receptor. Proc Natl Acad Sci USA. 2008 Aug. 5; 105 (31):10744-9). HEK293T cells transfected with Rant22 A2a receptors were grown in a monolayer in T-175 flasks at 37° C. and 5% CO2 in Dulbeccos Modified Eagle Medium supplemented with 10% fetal bovine serum. Cells were harvested by scraping the cells from the T-175 surface and collected by centrifugation.
Membrane Preparation.
Cell pellets were resuspended in 10 ml 20 mM HEPES, pH 7.4 plus protease inhibitor cocktail tablets (Roche) and were homogenised for 30 s at 20,500 rpm using a tissuemizer. Homogenates were centrifuged at 200×g for 15 min at 4° C. The supernatant was removed and reserved on ice. This procedure was repeated a further two times and the pooled supernatants were then centrifuged at 40,000×g for 45 min at 4° C. Membranes were resuspended in 1 ml aliquots of 20 mM HEPES, pH 7.4 plus protease inhibitor tablets. Protein concentration was determined by a BCA protein assay (Pierce).
Screening Assay.
10 μg aliquots of prepared membrane were incubated with [3H]ZM241385 3.7 nM and an appropriate amount of unlabelled ligand for 60 min at room temperature. A serial dilution ranging from 10 mM-1 μM was screened in a 96 well format. The filter GFC plates were pre soaked in 0.1% PEI for 60 min. Radioactivity was determined by liquid scintillation counting using a Microbeta counter at 3 min/well.
Results
Data was analysed using GraphPad prism to fit concentration response curves. The IC50 of compounds was calculated as the concentration resulting in 50% inhibition of the specific binding of [3H]ZM241385. The data presented in
| Number | Date | Country | Kind |
|---|---|---|---|
| 0724860.2 | Dec 2007 | GB | national |
This application is a continuation of U.S. application Ser. No. 14/255,939, filed Apr. 17, 2014, entitled “METHODS FOR SCREENING FOR BINDING PARTNERS OF G-PROTEIN COUPLED RECEPTORS,” which is a continuation of U.S. application Ser. No. 12/809,181, filed Oct. 20, 2010, entitled “METHODS FOR SCREENING FOR BINDING PARTNERS OF G-PROTEIN COUPLED RECEPTORS,” now U.S. Pat. No. 8,790,933, which is a national stage filing under 35 U.S.C. § 371 of international application PCT/GB2008/004223, filed Dec. 19, 2008, which was published under PCT Article 21(2) in English, and which claims the benefit under § 119(a)-(d) of United Kingdom Application No. 0724860.2, filed Dec. 20, 2007, the entire disclosures of each of which are herein incorporated by reference in their entireties.
| Number | Date | Country | |
|---|---|---|---|
| Parent | 14989744 | Jan 2016 | US |
| Child | 16151991 | US | |
| Parent | 14255939 | Apr 2014 | US |
| Child | 14989744 | US | |
| Parent | 12809181 | Oct 2010 | US |
| Child | 14255939 | US |
