Patent Application
20100105567
The current invention relates to novel capture agents for binding ligands, and to methods of making these capture agents, as well as methods of identifying capture agents which bind to a specific ligand of interest.
Traditional methods for producing libraries of capture agents, such as the production of antibody libraries are both laborious and expensive. Therefore, a number of attempts have been made to synthetically produce libraries of peptides which can act as capture agents to bind various types of ligand.
Spatially addressable libraries and one-bead one-structure libraries have previously been described for use in screening methods. These can be either a ligand library against a specific receptor, or a receptor library against a specific ligand (Combinatorial Chemistry and high throughput screening, 1, 113, 1998).
Pro. SPIE, 4205, 75 (2001), describes the use of cyclohexapeptides bound to quartz surfaces derivatised with epoxides, or directly to gold surfaces. This document describes peptides in which every other amino acid is varied. The peptides are attached to the surfaces by either lysyl or cysteiyl residues. Binding of amino acids to the surface bound peptides is then assayed.
Cyclic pentapeptide libraries for use in the identification of enzyme inhibitors have also been previously disclosed. Libraries of cyclic and linear peptides were made and iterative synthesis and screening was used to generate enzyme inhibitors (Molecular Diversity, 1, 223, 1995).
WO2005/047502 also discloses a protein library consisting of proteins having random amino acid sequences in which 4 to 12 types of amino acid are present, wherein the amino acids comprise Gly, Ala, Val and Glu or Asp. It also discloses a method of screening for a protein having particular structure or function from the library.
These prior art libraries are able to be produced more rapidly than traditional antibody libraries, but still suffer from the problem that they are expensive to produce and also require a large number of individual peptides to be synthesised in order to provide sufficient sequence diversity to make the libraries effective.
It is therefore an object of the current invention to provide synthetic capture agents having increased sequence diversity.
According to a first aspect of the present invention there is provided a multimeric capture agent for binding a ligand, said multimeric capture agent comprising at least first and second peptide chains, wherein said first and second peptide chains each comprise a chain of between 2 and 100 amino acids, each of said amino acids being substantially enantiomerically pure, and wherein said at least first and second peptide chains are covalently linked.
Preferably, each peptide comprises a chain of between 2 and 100 amino acids, more preferably between 2 and 50 amino acids, and most preferably between 5 and 25 amino acids.
Preferably, each amino acid is selected from a set consisting essentially of less than 20 amino acids, more preferably less than 12 amino acids, even more preferably less than 6 amino acids and most preferably 4 amino acids.
It will be understood that each substantially enantiomerically pure amino acid monomer can be an L-amino acid, a D-amino acid, an amino acid mimetic, a spacer amino acid, a beta amino acid, or any other chiral amino acid monomer. Preferably, the substantially enantiomerically pure amino acids are L-amino acids and/or D-amino acids.
Preferably, the first and second peptides are synthesised on a solid phase, more preferably, the peptides are cleaved from the solid phase prior to use in the first aspect.
Syntheses of peptides and their salts and derivatives, including both solid phase and solution phase peptide syntheses, are well established in the art. See, e.g., Stewart, et al. (1984) Solid Phase Peptide Synthesis (2nd Ed.); and Chan (2000) “FMOC Solid Phase Peptide Synthesis, A Practical Approach,” Oxford University Press. Peptides may be synthesized using an automated peptide synthesizer (e.g., a Pioneer™ Peptide Synthesizer, Applied Biosystems, Foster City, Calif.). For example, a peptide may be prepared on Rink amide resin using FMOC solid phase peptide synthesis followed by trifluoroacetic acid (95%) deprotection and cleavage from the resin.
It will be readily apparent that the first and second peptides can have the same or different primary amino acid sequences.
It will be further apparent that the first and second peptides can be synthesised from first and second amino acid sets and that each amino acid set may be the same or different.
Preferably, each peptide further comprises a reactive group. In a preferred embodiment, the reactive groups present on the peptides react so as to result in the formation of the multimeric capture agent.
In a preferred embodiment, said reactive groups may be protected during peptide synthesis and deprotected prior to use in production of capture agents according to the first aspect. Such techniques are well known to those skilled in the art, for example, standard FMOC-based solid-phase peptide assembly can be used. In this technique, resin bound peptides with protected side chains and free amino termini are generated. The amino groups at the N-terminus may then, be reacted with any compatible carboxylic acid/reactive group conjugate under standard peptide synthesis conditions. For example, cysteine with a trityl or methoxytrityl protected thiol group could be incorporated. Deprotection with trifluoroacetic acid would yield the unprotected peptide in solution.
Preferably, said reactive groups are selected from, but not limited to, thiol groups, maleimide, cyclopentadiene, azide, phosphinothioesters, thioesters, (nitro)thiopyridyl activated thiols and other such compounds known in the art. More preferably, the reactive groups are thiol groups.
It will be understood that any suitable reaction may be used to form the peptide multimers, for example, Diels Alder reaction between e.g. cyclopentadienyl functionalised peptides and maleimide functionalised peptides, Michael reaction between a thiol functionalised peptide and a maleimide functionalised peptide, reaction between a thiol functionalised peptide and a peptide containing an activated thiol group (activated with, for example, a (nitro)thiopyridine moiety) to form a disulfide, Staudinger ligation between an azide functionalised peptide and a phosphinothioester functionalised peptide, and native chemical ligation between a thioester and a N-terminal cysteine.
In preferred embodiments, dimers may be constructed wherein the first and second peptides each have a thiol group (which may or may not be activated) located at a site in the peptide sequence that is on the N-terminal side of the ligand-binding site or on the C-terminal side of the ligand-binding site or located internally within a bipartite ligand-binding site. In any of these embodiments, it will be clear that the thiol group moieties may have the same or opposite orientation as the ligand binding residues and that the location of each thiol group in the first and second peptide is independent.
It will be apparent that, depending upon the amino acid residues present in the peptides, the capture agents will have different characteristics. For example the side chains may provide a positive charge for ligand binding. Preferably, the positive charge is provided by a lysyl residue (four CH2 groups between the peptide chain and the positive charge), an ornithyl residue (three CH2 groups between the peptide chain and the positive charge) or most preferably, a diaminobutyryl residue (with two CH2 groups between the peptide chain and the positive charge).
The amino acid may alternatively provide a hydroxyl group capable of acting as a hydrogen bond donor and/or acceptor for ligand binding. Preferably, the hydroxyl group is provided by a seryl residue (one CH2 group between the peptide chain and the OH group), or more preferably a homoseryl residue (with two CH2 groups between the peptide chain and the OH group).
The amino acid may provide a hydrophobic moiety for ligand binding. Preferably, an alanyl residue (no CH2 group between the peptide chain and the methyl group) or more preferably, an aminobutyryl residue (with one CH2 group between the peptide chain and the methyl group) provides the hydrophobic moiety.
Alternatively, the amino acid may provide a negative charge for ligand binding. Preferably, the negative charge is provided by a glutamyl residue (two CH2 groups between the peptide chain and the carboxylate group), or more preferably, an aspartyl residue (one CH2 group between the peptide chain and the carboxylate group).
It will be apparent to the skilled person that, depending upon the number and sequence of amino acids present in the peptide chain, each chain will have different characteristics. Preferably, the peptides are produced from the set of amino acids in a combinatorial manner, as is well known in the art, such that all possible combinations of amino acids present in the set may be produced, for example, if there are N amino acids in the set and the peptide is of length L, the complete set will comprise NL peptides.
In a preferred embodiment, the peptides are produced such that the side chains are located in space in a manner which is favourable for ligand binding. This may be achieved by, for example, synthesising peptides having alternating L- and D-amino acids as shown in
Alternatively, the peptides may be synthesised using a set comprising beta amino acids as shown in
In a preferred embodiment, the peptides are synthesised such that only every second amino acid is varied, as shown in
This embodiment has the advantage that the side chains are spaced in the most natural and advantageous manner for ligand binding.
It will be obvious to the skilled person that each peptide can comprise one or more of the above types of amino acid and that the specific combinations employed will affect the characteristics of the capture agent containing the varying peptide chains.
It will be apparent that the increased diversity arises from the fact that the capture agents are multimeric. For example, if the multimeric capture agent is a dimer, the possible diversity for any given length of peptide is squared due to the presence of two peptide chains.
In a preferred embodiment, a subset of the possible combinatorial peptides which can be produced from any given set of amino acids will be employed. The subset can be determined through the inclusion of specific rules in the synthesis of the peptide, for example, maximum and minimum levels of each amino acid in the set can be provided.
In a preferred embodiment, the combinatorially produced multimeric capture agents are bound to a substrate.
Preferably, the capture agents are bound to a substrate by an attachment moiety.
It will be understood that the attachment moiety may be any suitable moiety. It will be understood that attachment may be, for example, by covalent, ionic, hydrophobic, polar, streptavidin-biotin, avidin-biotin, or other high affinity non-covalent interactions. In a preferred embodiment, the attachment moiety is a hydrophobic moiety. In another preferred embodiment, the attachment moiety is capable of forming a covalent bond, either directly or indirectly, where indirectly is understood to mean via an intermediate or following chemical modification of the attachment moiety.
Preferably, multiple capture agents are bound to the substrate so as to produce an array. It will be understood that the array may take any convenient form. Thus, the method of the invention is applicable to all types of “high density” arrays, including single-molecule arrays.
In a particularly preferred embodiment, the multimeric capture agents are assembled on the substrate.
Preferably, the array comprises a number of discrete addressable spatially encoded locations. Preferably, each location on the array comprises a different capture agent, and more preferably each location comprises multiple copies of the capture agent.
When referring to immobilisation of molecules (e.g. peptides) to a substrate, the terms “immobilised” and “attached” are used interchangeably herein and both terms are intended to encompass direct or indirect, covalent or non-covalent attachment, unless indicated otherwise, either explicitly or by context. In certain embodiments of the invention, covalent attachment may be preferred, but generally all that is required is that the molecules (e.g. peptides) remain immobilised or attached to the support under the conditions in which it is intended to use the support, for example in applications requiring ligand binding.
Certain embodiments of the invention may make use of solid supports comprised of an inert substrate or matrix (e.g. glass slides, polymer beads etc) which has been “functionalised”, for example by application of a layer or coating of an intermediate material comprising reactive groups which permit covalent attachment to biomolecules such as peptides. Examples of such supports include, but are not limited to, polyacrylamide hydrogels supported on an inert substrate such as glass. In such embodiments, the biomolecules (e.g. peptides) may be directly covalently attached to the intermediate material (e.g. the hydrogel) but the intermediate material may itself be non-covalently attached to the substrate or matrix (e.g. the glass substrate). The term “covalent attachment to a substrate” is to be interpreted accordingly as encompassing this type of arrangement.
In multi-peptide arrays, distinct regions on the array comprise multiple peptide molecules. Preferably, each site on the array comprises multiple copies of one individual peptide multimer.
Multi-peptide arrays of peptide molecules may be produced using techniques generally known in the art.
According to a second aspect of the present invention there is provided a method of producing a multimeric capture agent for binding a ligand, said capture agent comprising at least first and second peptides,
said first peptide further comprising a first reactive group,
said second peptide further comprising a second reactive group,
wherein the reactive groups may be the same or different for each peptide,
said method comprising the steps of;
reacting the first peptide with the second peptide such that the reactive groups present on the peptides react to form a covalently linked dimer.
It will be understood that further peptides having further reactive groups may be reacted with the first and/or second peptides to form higher order multimeric capture agents. It will also be understood that each peptide may include more than one reactive group such that it may react with a plurality of other peptides, to form multimeric capture agents.
Preferably, the first and second peptides are synthesised on a solid phase, more preferably, the peptides are cleaved from the solid phase prior to use in the method of the second aspect.
Syntheses of peptides and their salts and derivatives, including both solid phase and solution phase peptide syntheses, are well established in the art. See, e.g., Stewart, et al. (1984) Solid Phase Peptide Synthesis (2nd Ed.); and Chan (2000) “FMOC Solid Phase Peptide Synthesis, A Practical Approach,” Oxford University Press. Peptides may be synthesized using an automated peptide synthesizer (e.g., a Pioneer™ Peptide Synthesizer, Applied Biosystems, Foster City, Calif.). For example, a peptide may be prepared on Rink amide resin using FMOC solid phase peptide synthesis followed by trifluoroacetic acid (95%) deprotection and cleavage from the resin.
It will be readily apparent that the first and second peptides can have the same or different primary amino acid sequences.
It will be apparent that the first and second peptides can be synthesised from first and second amino acid sets and that each amino acid set may be the same or different.
Preferably, said peptides are between 2 and 100 amino acids in length, more preferably, 2 to 50 amino acids in length, and most preferably, 5 to 25 amino, acids in length.
Preferably, each amino acid is selected from a set consisting essentially of less than 20 amino acids, more preferably less than 12 amino acids, even more preferably less than 6 amino acids and most preferably 4 amino acids.
It will be understood that each amino acid in the set may comprise any of the following monomers, with the proviso that each monomer is substantially enantiomerically pure, an L-amino acid, a D-amino acid, an amino acid mimetic, a spacer amino acid, a beta amino acid, or any other chiral amino acid monomer. Preferably, the substantially enantiomerically pure amino acids are L-amino acids and/or D-amino acids.
In a preferred embodiment, said reactive groups may be protected during peptide synthesis and deprotected prior to use in the method of the second aspect. Such techniques are well known to those skilled in the art, for example, standard FMOC-based solid-phase peptide assembly. In this technique, resin bound peptides with protected side chains and free amino termini are generated. The amino groups at the N-terminus may then be reacted with any compatible carboxylic acid/reactive group conjugate under standard peptide synthesis conditions. For example, cysteine with a trityl or methoxytrityl protected thiol group, could be incorporated. Deprotection with trifluoroacetic acid would yield the unprotected peptide in solution.
Preferably, said reactive groups are selected from, but not limited to thiol groups, maleimide, cyclopentadiene, azide, phosphinothioesters, thioesters, (nitro)thiopyridyl activated thiols and other such compounds known in the art. More preferably, the reactive groups are thiol groups.
It will be understood that any suitable reaction may be used to form the peptide multimers, for example, Diels Alder reaction between e.g. cyclopentadienyl functionalised peptides and maleimide functionalised peptides, Michael reaction between a thiol functionalised peptide and a maleimide functionalised peptide, reaction between a thiol functionalised peptide and a peptide containing an activated thiol group (activated with, for example, a (nitro)thiopyridine moiety) to form a disulfide, Staudinger ligation between an azide functionalised peptide and a phosphinothioester functionalised peptide, and native chemical ligation between a thioester and a N-terminal cysteine.
The reaction scheme outlined in
In preferred embodiments, the dimer may be constructed wherein the first and second peptides each have a thiol group (which may or may not be activated) located at a site in the peptide sequence that is on the N-terminal side of the ligand-binding site or on the C-terminal side of the ligand-binding site or located internally within a bipartite ligand-binding site. In any of these embodiments, it will be clear that the thiol group moieties may have the same or opposite orientation as the ligand binding residues and that the location of each thiol group in the first and second peptides is independent.
It will be apparent that, depending upon the amino acid residues present in the peptides, the capture agents will have different characteristics as discussed in relation to the first aspect.
Preferably, the capture agents produced by the method of the second aspect are attached to a substrate. More preferably, the capture agents produced by the method of the second aspect are attached to the substrate so as to form an array. It will be understood that the array may take any convenient form. Thus, the method of the invention is applicable to all types of “high density” arrays, including single-molecule arrays.
In a particularly preferred embodiment, the multimeric capture agents are assembled on the substrate.
Preferably, the array comprises a number of discrete addressable spatially encoded loci. Preferably, all of said capture agents at a given locus on the array are comprised of the same pairs of peptides. More preferably, each given locus on the array comprises a different capture agent.
When referring to immobilisation of molecules (e.g. peptides) to a substrate, the terms “immobilised” and “attached” are used interchangeably herein and both terms are intended to encompass direct or indirect, covalent or non-covalent attachment, unless indicated otherwise, either explicitly or by context. In certain embodiments of the invention, covalent attachment may be preferred, but generally all that is required is that the molecules (e.g. peptides) remain immobilised or attached to the support under the conditions in which it is intended to use the support, for example in applications requiring ligand binding.
Certain embodiments of the invention may make use of solid supports comprised of an inert substrate or matrix (e.g. glass slides; polymer beads etc) which has been “functionalised”, for example by application of a layer or coating of an intermediate material comprising reactive groups which permit covalent attachment to biomolecules, such as peptides. Examples of such supports include, but are not limited to, polyacrylamide hydrogels supported on an inert substrate such as glass. In such embodiments, the biomolecules (e.g. peptides) may be directly covalently attached to the intermediate material (e.g. the hydrogel) but the intermediate material may itself be non-covalently attached to the substrate or matrix (e.g. the glass substrate). The term “covalent attachment to a substrate” is to be interpreted accordingly as encompassing this type of arrangement.
In multi-peptide arrays, distinct regions on the array comprise multiple peptide molecules. Preferably, each site on the array comprises multiple copies of one individual peptide dimer.
Multi-peptide arrays of peptide molecules may be produced using techniques generally known in the art.
According to a third aspect of the present invention there is provided a method of producing a multimeric capture agent for binding a ligand, said capture agent comprising at least first and second peptides,
said first peptide further comprising a first reactive group and an attachment moiety,
said second peptide further comprising a second reactive group,
wherein the reactive groups may be the same or different for each peptide,
said method comprising the steps of;
a) reacting the first peptide with the second peptide such that reactive groups present on the peptides react to form a multimeric structure; and
b) attaching the first peptide to a substrate via the attachment moiety,
wherein, step a) can be performed before, simultaneously with or subsequently to step b).
Preferably, the first and second peptides are synthesised on a solid phase and can be the same or different, more preferably, the peptides are cleaved from the solid phase prior to use in the method of the third aspect.
Syntheses of peptides and their salts and derivatives, including both solid phase and solution phase peptide syntheses, are well established in the art. See, e.g., Stewart, et al. (1984) Solid Phase Peptide Synthesis (2nd Ed.); and Chan (2000) “FMOC Solid Phase Peptide Synthesis, A Practical Approach,” Oxford University Press. Peptides may be synthesized using an automated peptide synthesizer (e.g., a Pioneer™ Peptide Synthesizer, Applied Biosystems, Foster City, Calif.). For example, a peptide may be prepared on Rink amide resin using FMOC solid phase peptide synthesis followed by trifluoroacetic acid (95%) deprotection and cleavage from the resin.
A first set of monomer units (A) is prepared on a solid phase. The monomer units comprise a ligand-binding moiety (R1-R4) and a reactive group X. If wished X may be protected during synthesis and then deprotected before use.
A second set of monomer units (B) is prepared on a solid phase. These monomer units comprise a ligand-binding moiety (R′1-R′4), a reactive group Y, which may be protected during synthesis and then, deprotected before use, and an attachment moiety Z. If wished Z may also be protected during synthesis and then deprotected before use.
Each of the monomer units in set (A) is cleaved off the solid support to give monomer units (C) in solution.
Each of the monomer units in set (B) is cleaved off the solid support to give monomer units (D) in solution.
Each of the monomer units in set D is then contacted with the surface of a solid support (E) at a spatially encoded location in an array such that Z is used to bring about attachment to the said surface.
Reactions are then performed wherein surface-bound monomer units (F) froth set D are reacted with an excess or equimolar amount of a given solution phase monomer unit (C) such that residue X reacts with residue Y to form a dimeric structure (G) bound to the solid phase.
The arrayed and spatially encoded dimeric structures (G) can then be used for binding to ligands of interest that will bind with suitable affinity, and selectivity.
In this embodiment, a first set of monomer units (A) is prepared on a solid phase. The monomer units comprise a ligand-binding moiety (R1-R4) and a reactive group X, which may be protected during synthesis and then deprotected before use.
A second set of monomer units (B) is also prepared on a solid phase. These monomer units comprise a ligand-binding moiety (R′1-R′4) and a reactive group Y, which may be protected during synthesis and then deprotected before use, and an attachment moiety Z. If wished Z may also be protected during synthesis and then deprotected before use.
Each of the monomer units (B) is cleaved off the solid support to give monomer units (C) in solution. Reactions are then performed wherein a given solid phase-bound monomer unit from set (A) is reacted with an excess or equimolar amount of a given solution phase monomer unit (C) such that residue X reacts with residue Y to form a dimeric structure (D) bound to the solid phase.
Each dimeric structure (D) bound to the solid phase is then cleaved off the solid support to give a solution phase dimeric structure (E).
Each solution phase dimeric structure (E) is finally contacted with a solid surface (F) at a spatially encoded location in an array such that group Z is used to attach the dimeric structure to the said surface.
The arrayed and spatially encoded dimeric structures (G) can then be used for binding to ligands of interest that will bind with suitable affinity, and selectivity.
The positions of X, Y, and Z in the figures are merely illustrative and should not be seen as limiting to the invention.
A first set of monomer units (A) is prepared on a solid phase. The monomer units comprise a ligand-binding moiety (R1-R4) and a reactive group X. If wished X may be protected during synthesis and then deprotected before use.
A second set of monomer units (B) is prepared on a solid phase. These monomer units comprise a ligand-binding moiety (R′1-R′4), a reactive group Y, which may be protected during synthesis and then deprotected before use, and an attachment moiety Z. If wished Z may also be protected during synthesis and then deprotected before use.
Each of the monomer units in set (A) is cleaved off the solid support to give monomer units (C) in solution.
Each of the monomer units in set (B) is cleaved off the solid support to give monomer units (D) in solution.
Each of the monomer units in set D is then contacted with an excess or equimolar amount of a given solution phase monomer unit (C) and the surface of a solid support (E) at a spatially encoded location in an array such that Z is used to bring about attachment to the said surface and such that residue X reacts with residue Y to form a dimeric structure (G) bound to the solid phase.
The arrayed and spatially encoded dimeric structures (G) can then be used for binding to ligands of interest that will bind with suitable affinity, and selectivity.
The most significant advantage of the current invention is the ‘squaring’ (or raising to a higher power) of sequence diversity by the combinatorial joining of pairs (or greater numbers) of monomer units at the array surface.
It will be readily apparent that the first and second peptides can have the same or different primary amino acid sequences.
It will be further apparent that the first and second peptides can be synthesised from first and second amino acid sets and that each amino acid set may be the same or different.
Preferably, each amino acid is selected from a set consisting essentially of less than 20 amino acids, more preferably less than 12 amino acids, even more preferably less than 6 amino acids and most preferably 4 amino acids.
It will be understood that each amino, acid in the set can be an L-amino acid, a D-amino acid, an amino acid mimetic, a spacer amino acid, a beta amino acid, or any other chiral amino acid monomer. Preferably, the amino acids are L-amino acids and/or D-amino acids.
It will be understood that each amino acid in the set is substantially enantiomerically pure.
In a preferred embodiment, said reactive groups may be protected during synthesis and deprotected as previously described prior to use in the method of the third aspect.
Preferably, said reactive groups are selected from the group consisting of thiol, maleimide, cyclopentadiene, azide, phosphinothioesters, thioesters, (nitro)thiopyridyl activated thiols and other such compounds known in the art. More preferably, the reactive groups are thiol groups.
It will be understood that any suitable reaction may be Used to form the peptide multimers, for example, Diels Alder reaction between e.g. cyclopentadienyl functionalised peptides and maleimide functionalised peptides, Michael reaction between a thiol functionalised peptide and a maleimide functionalised, peptide, reaction between a thiol functionalised peptide and a peptide containing an activated thiol group (activated with, for example, a (nitro)thiopyridine moiety) to form a disulfide, Staudinger ligation between an azide functionalised peptide and a phosphinothioester functionalised peptide, and native chemical ligation between a thioester and a N-terminal cysteine.
It will be apparent that, depending upon the amino acid residues present in the peptides, the capture agents will have different characteristics as discussed in relation to the first aspect.
In preferred embodiments, the dimer may be constructed wherein the first and second peptides each have a thiol group (which may or may not be activated) located at a site in the peptide sequence that is on the N-terminal side of the ligand-binding site or on the C-terminal side of the ligand-binding site or located internally within a bipartite ligand-binding site. In any of these embodiments, it will be clear that the thiol group moieties have the same or opposite orientation as the ligand binding site and that the location of each thiol group in the first and second peptide is independent.
It will be understood that the attachment moiety may be any suitable moiety. It will be understood that attachment may be, for example, by covalent, ionic, hydrophobic, polar, streptavidin-biotin, avidin-biotin, or other high affinity non-covalent interactions. In a preferred embodiment, the attachment moiety is a hydrophobic moiety. In another preferred embodiment, the attachment moiety is capable of forming a covalent bond, either directly or indirectly, where indirectly is taken to mean via an intermediate or following chemical modification of the attachment moiety.
In a particularly preferred embodiment, the multimeric capture agents are assembled on the substrate.
If the capture agents are “arrayed” on a substrate, then the array may take any convenient form. Thus, the method of the invention is applicable to all types of “high density” arrays, including single-molecule arrays.
Preferably, the capture agents of the third aspect are located at discrete spatially encoded loci on an array. Preferably, all of said capture agents at a given locus on the array are comprised of the same pairs of peptides. More preferably, each locus on the array, comprises a different capture agent.
When referring to immobilisation of molecules (e.g. peptides) to a substrate, the terms “immobilised” and “attached” are used interchangeably herein and both terms are intended to encompass direct or indirect, covalent or non-covalent attachment, unless indicated otherwise, either explicitly or by context. In certain embodiments of the invention, covalent attachment may be preferred, but generally all that is required is that the molecules (e.g. peptides) remain immobilised or attached to the support under the conditions in which it is intended to use the support, for example in applications requiring ligand binding.
Certain embodiments of the invention may make use of solid supports comprised of an inert substrate or, matrix (e.g. glass slides, polymer beads etc) which has been “functionalised”, for example by application of a layer or coating of an intermediate material comprising reactive groups which permit covalent attachment to biomolecules, such as peptides. Examples of such supports include, but are not limited to, polyacrylamide hydrogels supported on an inert substrate such as glass. In such embodiments, the biomolecules (e.g. peptides) may be directly covalently attached to the intermediate material (e.g. the hydrogel) but the intermediate material may itself be non-covalently attached to the substrate or matrix (e.g. the glass substrate). The term “covalent attachment to a substrate” is to be interpreted accordingly as encompassing this type of arrangement.
In multi-peptide arrays, distinct regions on the array comprise multiple peptide molecules. Preferably, each site on the array comprises multiple copies of one individual peptide dimer.
Multi-peptide arrays of peptide molecules may produced using techniques generally known in the art.
The capture agents according to any of aspects one, two or three can be attached to any suitable substrate by any suitable method. In a preferred embodiment, the capture agents are attached covalently to the substrate.
Preferred reaction schemes for the covalent attachment of capture agents to substrates include, but are not limited to; reaction between sulfhydryls and maleimide derivatised surfaces, Diels-Alder reaction between maleimide derivatised surfaces and diene functionalised capture agents, azide and acetylene 3+2 cycloaddition, thiazolidine ring formation, and the modified Staudinger ligation. Alternatively, covalent attachment of the capture agents to the substrates may be effected in the reverse fashion, for example by reaction between a thiol derivatised surface and maleimide substituted peptide.
In a particularly preferred embodiment, native chemical ligation between thioester-derivatised capture agents and cysteine-derivatised surfaces that present both the amino group and the sulfhydryl group of the cysteine is used to covalently link the capture agents to the substrate.
The most preferable reaction scheme uses native chemical ligation between capture agents with N-terminal cysteines and thioester-derivatised surfaces as shown in
Native chemical ligation generates a peptide bond between an N-terminal cysteine on a peptide and a surface-attached thioester. A particular advantage of this embodiment of the current invention is that protection of peptide side chains is not required. A further particular advantage of this embodiment of the current invention is that the resulting surface-attached peptide has an internal cysteine that may be exploited for the formation of dimeric receptors by disulfide bond formation, or reaction between a thiol and a maleimide functionalised peptide.
The preferred reaction scheme for the preparation of thioester functionalised glass surfaces is shown in
It will be apparent that the multimeric capture agent as described in any of the previous aspects can be produced prior to covalent attachment to a substrate, or may be assembled on the substrate itself. If the capture agent is assembled on the substrate surface, a preferred reaction scheme is shown in
A more preferable route for the preparation of thioester surfaces involves the reaction between an aminated surface and thiolane 2,4-diones of the type shown below:
Thioester surfaces may also be made by derivatising hydroxylated surfaces with thioester silylchloride Conjugates of the type shown below.
According to a fourth aspect of the current invention, there is provided a capture agent for binding a ligand, comprising at least first and second peptides, the first peptide comprising a plurality of hydrophobic amino acid residues and a plurality of non hydrophobic amino acid residues, wherein the amino acids are positioned in the peptide primary structure such that the peptide side chains are located to produce a hydrophobic face and a substantially non hydrophobic ligand-binding face and the second peptide comprising at least one hydrophobic amino acid residue and a plurality of non hydrophobic amino acid residues, wherein said amino acids are positioned in the peptide primary structure such that the amino acid side chains are located to produce a hydrophobic face and a substantially non hydrophobic ligand-binding face.
Preferably, the first peptide comprises a primary structure comprising alternating hydrophobic and non hydrophobic amino acid residues, as shown in
It will be understood by the skilled person that other peptide sequences which result in distribution of the side chains so as to result in a hydrophobic and substantially non hydrophobic face can be easily designed, for example, there may be three non hydrophobic amino acid residues between hydrophobic residues, or any combination of odd numbers of amino acid. Alternatively, the peptide may comprise a combination of, for example, L- D- and beta-amino acids so as to result in a hydrophobic and a substantially non hydrophobic face.
Preferably, the first peptide comprises 4 to 40 hydrophobic amino acid residues, more preferably 6 to 25 and most preferably 6 to 12.
Preferably, each amino acid positioned so as to be located on the ligand-binding face is selected from a set consisting essentially of less than 20 amino acids, more preferably less than 12 amino acids, even more preferably less than 6 amino acids and most preferably 4 amino acids.
It will be understood that each amino acid monomer can be an L-amino acid, a D-amino acid, an amino acid mimetic, a spacer amino acid, a beta amino acid, or any other chiral amino acid monomer. Preferably, amino acids are L-amino acids and/or D-amino acids.
Preferably, each amino acid monomer is substantially enantiomerically pure.
It will be understood that amino acids positioned on the ligand-binding face may also include hydrophobic residues, for example, aminobutyrate residues.
Preferably, the first peptide comprises 10% to 90% hydrophobic amino acid residues, more preferably, 20% to 80%, even more preferably, 30% to 70%, and most preferably 40% to 60% hydrophobic amino acid residues.
In a particularly preferred embodiment, the first peptide comprises 50% hydrophobic amino acid residues.
Preferably, the hydrophobic amino acids which form the hydrophobic face are selected from the group consisting of leucine, isoleucine, norleucine, valine, norvaline, methionine, tyrosine, tryptophan and phenylalanine. More preferably, the hydrophobic amino acids are phenylalanine.
In a preferred embodiment, the capture agent is located on a hydrophobic substrate such that the substantially non hydrophobic ligand-binding face is accessible for ligand binding.
Preferably, the capture agent is bound to the hydrophobic substrate by a hydrophobic interaction between the substrate and the hydrophobic face of the peptide.
It will be understood that the substrate may be any suitable hydrophobic substrate, for example, gold modified by hydrophobic organic thiol treatment, glass modified by surface treatment, or plastic. Preferably, the substrate is plastic.
Alternatively, the substrate may be coated in hydrophobic compound which allows the capture agents to be immobilised thereon in the presence of a substantially aqueous solvent.
It will be apparent that the peptide dimer can be assembled froth the first and second peptides before, simultaneously with or after the first peptide has been contacted with the hydrophobic substrate. In a particularly preferred embodiment, the peptide dimer is assembled on the hydrophobic substrate.
In a preferred embodiment, the second peptide comprises fewer amino acids than the first peptide, and contains fewer hydrophobic residues such that the interaction between the peptide and the hydrophobic surface is relatively weak. In this embodiment, the second peptide is only retained on the hydrophobic substrate when dimerised to the first peptide.
It will be apparent to the skilled person that the length of the first and second peptides and the numbers of hydrophobic amino acid residues required to retain them on the substrate will depend upon the hydrophobicity of the surface and on the hydrophobic amino acids present in the first and second peptides, and also on the nature of the ligand to be bound.
It will also be readily apparent to the skilled person that the amount of peptide retained at the substrate will depend upon the stringency of washing to which the substrate is subjected. Preferably, after immobilisation of the peptides, the substrate is washed with, for example, 1.0 M NaCl in 10 mM tris-HCl (pH 8.0).
Preferably, the second peptide comprises 1-6 hydrophobic amino acid residues, more preferably, 2-5, and most preferably 2-4 hydrophobic amino acid residues on the hydrophobic face.
Preferably, the first and second peptides each contain 10 or fewer ligand-binding residues located on the substantially non hydrophobic ligand-binding face; more preferably, 8 or fewer; more preferably, 6 or fewer; even more preferably, 4 or fewer; and most preferably 3 or fewer.
Preferably, the capture agents according to the fourth aspect are produced from the sets of amino acids in a combinatorial manner as is well known in the art. Preferably, the peptides are produced to a set of rules, resulting in peptides having varied ligand-binding characteristics.
Preferably, the first and second peptides are synthesised on a solid phase, more preferably, the peptides are cleaved from the solid phase prior to use in the fourth aspect.
Syntheses of peptides and their salts and derivatives, including both solid phase and solution phase peptide syntheses, are well established in the art. See, e.g.; Stewart, et al. (1984) Solid Phase Peptide Synthesis (2nd Ed.); and Chan (2000) “FMOC Solid Phase Peptide Synthesis, A Practical. Approach,” Oxford University Press. Peptides may be synthesized using an automated peptide synthesizer (e.g., a Pioneer™ Peptide Synthesizer, Applied Biosystems, Foster City, Calif.). For example a peptide may be prepared on Rink amide resin using FMOC solid phase peptide synthesis followed by trifluoroacetic acid (95%) deprotection and cleavage from the resin.
It will be readily apparent that the at least first and second peptides can have the same or different primary amino acid sequences.
It will be further apparent that the first and second peptides can be synthesised from first and second amino acid sets and that each amino acid set may be the same or different.
Preferably, said first and second peptides each contain at least one reactive group. In a preferred embodiment, the reactive groups present on the peptides react so as to result in the formation of a multimeric capture agent.
In a preferred embodiment, said reactive groups may be protected during peptide synthesis and deprotected prior to use in production of capture agents according to the fourth aspect. Such techniques are well known to those skilled in the art, for example, standard FMOC-based solid-phase peptide assembly. In this technique, resin bound peptides with protected side chains and free amino termini are generated. The amino groups at the N-terminus may then be reacted with any compatible carboxylic acid reactive group conjugate under standard peptide synthesis conditions. For example, cysteine with a trityl or methoxytrityl protected thiol group could be incorporated. Deprotection with trifluoroacetic acid would yield the unprotected peptide in solution.
It will be understood that any suitable reaction may be used to form the peptide multimers, for example, Diels Alder reaction between e.g. cyclopentadienyl functionalised peptides and maleimide functionalised peptides, Michael reaction between a thiol functionalised peptide and a maleimide functionalised peptide, reaction between a thiol functionalised peptide and a peptide containing an activated thiol group (activated with, for example, a (nitro) thiopyridine moiety) to form a disulfide, Staudinger ligation between an azide functionalised peptide, and a phosphinothioester functionalised peptide, and native chemical ligation between a thioester and a N-terminal cysteine. In a preferred embodiment, the peptide multimers are formed by disulphide bond formation.
It will be understood that the reactive groups may be located in the primary peptide structure of the first and second peptides at any suitable position, for example, the reactive groups may be positioned in the primary peptide sequence such that they are positioned on the substantially non hydrophobic ligand-binding face of the peptides and located on the N-terminal side of the ligand-binding site.
Alternatively, the reactive groups may be located in the primary peptide structure of the first and second peptides such that they are positioned on the substantially non hydrophobic ligand-binding face of the peptides, and in the first peptide, on the N-terminal side of the ligand-binding site, and in the second peptide to the C-terminal side of the ligand-binding site.
In a further embodiment, the reactive group may be located in the primary peptide structure of the first and second peptides such that in the first peptide, it is positioned on the substantially non hydrophobic ligand-binding face of the peptides and to the N-terminal side of the ligand-binding site, and in the second peptide it is located on the opposite (hydrophobic) face to the ligand-binding site and to the C-terminal side of the ligand-binding site.
In a preferred embodiment, the reactive group on the first peptide is located in the primary amino acid structure on the substantially non hydrophobic ligand-binding face and to the N-terminal side of the ligand-binding site and in the second peptide, in the hydrophobic face and to the N-terminal side of the ligand-binding site as shown in
Preferably, said reactive groups are selected from, but not limited to, thiol groups, maleimide, cyclopentadiene, azide, phosphinothioesters, thioesters and (nitro)thiopyridyl activated thiols and other such compounds known in the art. More preferably, the reactive groups are thiol groups. Preferably, when the reactive groups are thiol groups, at least one thiol group is an activated thiol. Preferably, the thiol group is activated with either a nitrothiopyridyl or thiopyridyl group.
It will be apparent that, depending upon the amino acid residues present in the peptides, the capture agents will have different characteristics as discussed in relation to the first aspect.
Preferably, the capture agents of the fourth aspect are bound to the substrate so as to produce an array. It will be understood that the array may take any convenient form. Thus, the method of the invention is applicable to all types of “high density” arrays, including single-molecule arrays.
Preferably, the array comprises a number of discrete addressable spatially encoded loci. Preferably, each locus on the array comprises a different capture agent, and more preferably each locus comprises multiple copies of the capture agent.
In a particularly preferred embodiment, the first peptide has the structure set out in SEQ ID No 1;
where X, Y, and Z are the ligand-binding residues and Cys provides a nucleophilic thiol used for dimer formation.
The second peptide has the preferred structure set out in SEQ ID No 2;
where X′, Y′, and Z′ are the ligand-binding residues and CysS(N)P is an activated thiol used for dimer formation (most preferably activated with either a thionitropyridyl group or a thiopyridyl group).
It is to be understood that the preceding preferred embodiment is by way of example only and is not to be taken to be limiting. It will be apparent to the skilled person that many other reactive groups and activating groups can be employed in the current invention.
In the most preferred embodiment, the capture agents according to any of the aspects of the current invention are dispensed onto a suitable substrate to form an addressable spatially encoded array of combinatorially varying dimers. Preferably, the peptides are individually dispensed on to the substrate using a non-contact dispenser (e.g. Piezorray System, Perkin Elmer LAS) and assembled in situ.
According to a further aspect of the present invention there is provided a substrate on which is immobilised at least one capture agent according to the first or fourth aspect of the current invention.
According to a still further aspect of the present invention there is provided a substrate on which is immobilised at least one capture agent produced according to the second or third aspect of the current invention.
According to the present invention, there is also provided a method of identifying a multimeric capture agent which binds to a ligand of interest, said method comprising producing an array of combinatorial capture agents according to any previous aspect, contacting the ligand of interest with the array, and identifying to which capture agent(s) the ligand binds.
It will be apparent to the skilled person that the binding of the ligand to a capture agent can be identified in various ways known in the art, for example, the ligand or the capture agent may be labelled so that the location on the array to which the ligand binds can be identified. This label may be, for example, a radioactive or fluorescent label using, for example, fluorophores. Alternatively, binding of the ligand of interest to a capture agent may be detected by a variety of other techniques known in the art, for example, calorimetry, absorption spectroscopy, NMR methods, atomic force microscopy and scanning tunnelling microscopy, electrophoresis or chromatography, mass spectroscopy, capillary electrophoresis, surface plasmon resonance detection, surface acoustic wave sensing and numerous microcantilever-based approaches.
It will be understood that the multimeric capture agents and arrays of multimeric capture agents of the current invention can be used to identify any analyte of choice, since the specific ligand which will be bound by the capture agent will be dependent upon the length and sequence of the peptides from which the capture agent is formed. In preferred embodiments the ligand comprises a eukaryotic cell, a prokaryotic cell, a virus, a bacteriophage, a prion, a spore, a pollen grain, an allergen, a nucleic acid, a protein, a peptide, a carbohydrate, a lipid, an organic compound, or an inorganic compound. The ligands are preferably physiological or pharmacological metabolites and most preferably physiological or pharmacological metabolites in human or animal bodily fluids that may be used as diagnostic or prognostic healthcare markers.
Additional objects, features, and strengths of the present invention will be made clear by the description below. Further, the advantages of the present invention will be evident from the following explanation in reference to the drawings.
The invention will be further understood with reference to the following experimental examples and accompanying figures in which:—
As used herein, the term spacer amino acid refers to an amino acid, a synthetic amino acid, an amino acid analogue or amino acid mimetic in which the side chains play no part in ligand binding.
As used herein, the term capture agent refers to a peptide molecule having a structure such that when a ligand is brought into contact with the capture agent it is bound thereto.
As used herein, the term multimeric capture agent refers to a capture agent comprising at least two linked subunits.
As used herein, the term peptide refers to a chain comprising 2 or more amino acid residues, synthetic amino acids, amino acid analogues or amino acid mimetics, or any combination thereof. The term peptide and polypeptide are used interchangeably in this specification.
As used herein, the term substantially enantiomerically pure indicates that the residue comprises substantially one type of isomer, with any other isomeric forms being there only as an impurity.
As used herein, the term located in space in a manner favourable to ligand binding indicates that the side chains of the peptides which make up the multimeric capture agent are positioned such that they are able to contact and interact with a ligand.
As used herein, the term substantially non hydrophobic means comprising substantially more hydrophilic residues than hydrophobic residues.
The following series of peptides were synthesised in order to demonstrate peptide self-assembly into an organic solvent layer or onto a hydrophobic surface driven by entropic effects in an aqueous solvent in contact with the said organic solvent layer or hydrophobic surface.
All peptides are labelled with the rhodamine dye TAMRA at the N-terminus. A mixture of the 5-TAMRA and 6-TAMRA isomers was used for the labelling.
In the following, the residue side chains projecting in front of the plane of the paper represent the combinatorially varied ‘ligand-binding face’. The residue side chains projecting, behind the plane of the paper represent the ‘hydrophobic face’ (or negative control residues).
In the set of peptides 2DOS-1 to 2DOS-8, a mixture of four side chains (aspartyl, alanyl, seryl, and lysyl) has been used. In the set of peptides 2DOS-9 to 2DOS-16, four hydrophilic (aspartyl) chains have been used.
In the set of peptides 2DOS-1 to 2DOS-4 and the set of peptides 2DOS-9 to 2DOS-12, five residue side chains have been used for the ‘hydrophobic face’ (or negative control residues). In the set of peptides 2DOS-5 to 2DOS-8 and the set of peptides 2DOS-13 to 2DOS-16, three residue side chains have been used for the ‘hydrophobic face’ (or negative control residues).
For peptides 2DOS-1, 2DOS-5, 2DOS-9, and 2DOS-13, norleucyl residues have been used for the ‘hydrophobic face’. For peptides 2DOS-2, 2DOS-6, 2DOS-10, and 2DOS-14, phenylalanyl residues have been used for the ‘hydrophobic face’. For peptides 2DOS-3, 2DOS-7, 2DOS-11, and 2DOS-15, seryl residues have been used as a weak negative control for the ‘hydrophobic face’. For peptides 2DOS-4, 2DOS-8, 2DOS-12, and 2DOS-16, aspartyl residues have been used as a strong negative control for the ‘hydrophobic face’.
Peptides were synthesised on a 2 μmol scale using standard FMOC chemistry (Alta Bioscience) and were dissolved to 10 μM in 50% (v/v) aqueous acetonitrile.
The retention of peptides 2DOS-1 to 2DOS-16 on a hydrophobic surface (the wells of a polypropylene microtitre plate) was then investigated.
10 mM tris-HCl (pH 8.0) in 50% (v/v) aqueous acetonitrile was used as the solvent for the peptides and for TAMRA.
100 μl aliquots of 10 μM peptides 2DOS-1 to 2DOS-16 and 10 μM TAMRA were placed in the wells of a Costar microtitre plate as shown in
The microtitre plate was imaged at 200 μm resolution on a Typhoon Trio Plus variable mode imager (Amersham Biosciences) with the green (532 nm) laser and the 580 BP 30 filter at the PMT voltages, indicated below and at normal sensitivity. The scan height was set at +3 mm and the sample was pressed during scanning.
The peptides were allowed to evaporate to dryness overnight in the dark and the microtitre plate was again scanned as described above.
The wells were then washed ten times with 250 μl of water.
The residual surface-bound peptides were finally resuspended in 100 μl of 10 mM tris-HCl (pH 8.0) in 50% (v/v) aqueous acetonitrile and the microtitre plate was again scanned as described above.
The fluorescence images were analysed using ImageQuant TL v2003.03 (Amersham Biosciences).
The fluorescence images of the microtitre plate scanned at PMT voltages of 600V, 500V, 400V, and 300V at the three stages of the experiment are shown in
Quantification data (using the data from the 400V scan) is given in Table 2 and shown graphically in
The results show that phenylalanyl residues lead to greater retention than norleucyl residues. They also show that peptides with five hydrophobic ‘anchor residues’ are retained better than equivalent peptides with three hydrophobic ‘anchor residues’. Changing the ‘ligand-binding’ residues from aspartyl, alanyl, seryl, and lysyl to a run of four aspartyl residues leads to a drop in retention on the polypropylene surface.
Further experiments were undertaken to investigate the retention of peptides P1-1 to P1-5 and P2-1 to P2-2, shown in Table 3, on a polypropylene surface.
The polypropylene sheet was wiped with 50% (v/v) aqueous acetonitrile prior to use.
8×replicate 20 nl volumes of 1 μM peptides P1-1 to P1-5 and P2-1 to P2-2 and TAMRA in dimethyl sulphoxide (DMSO) were dispensed at 1 mm spacing to a 3″×1″×1 mm polypropylene sheet using the Piezorray system (PerkinElmer LAS). 500 drops were pre-dispensed using the ‘side shoot’ option and the tuning was set to 72V for 30 μs.
The slide was imaged at 10 μm resolution on a Typhoon Trio Plus variable mode imager (Amersham Biosciences) with the green (532 nm) laser and the 580 BP 30 filter at a PMT voltage of 600 V and at normal sensitivity. The scan height was set at the platen and the samples were pressed during scanning. The fluorescence image was analysed using ImageQuant TL v2003.03 (Amersham Biosciences).
The lower half of the slide (containing the test array) was then washed in 100 ml of 1 M NaCl containing 10 mM tris-HCl (pH 8.0) for one minute and were re-scanned as described above.
The same half of the slide was then washed for a second time in 100 ml of 1 M NaCl containing 10 mM tris-HCl (pH 8.0) for 30 minutes and re-scanned as described above.
The same half of the slide was then washed for a third time in 100 ml of water for 30 minutes and re-scanned as described above.
The fluorescence images for the various arrays are shown in FIGS. 13A,B.
The fluorescence values for the various arrayed peptides shown in FIGS. 13A,B are shown in Tables 4-6 below:
After first wash:
After second wash:
After third wash:
These results are shown graphically in
The figures clearly show that there is a gradient of increasing retention for the peptides correlated to increasing peptide chain length. As can be clearly seen, Peptide P1-5 which has a chain length of 19 amino acids has the highest retention.
The pH resistance of peptide 2DOS-2 (see above) deposited onto a polypropylene hydrophobic surface was investigated:
Twelve 50 μl aliquots of peptide 2DOS-2 in 10 mM tris-HCl (pH 8.0) in 50% (v/v) aqueous acetonitrile were dried down in the wells of a Costar microtitre plate.
The peptide samples were allowed to evaporate to dryness in the dark.
The dried peptide samples in the first eleven wells were incubated with 200 μl of 100 mM phosphate buffer for 30 minutes at room temperature according to the scheme shown in Table 7:
All supernatants were pipetted off and the residual surface-bound peptides in all twelve wells were finally resuspended in 50 μl of 10,mM tris-HCl (pH 8.0) in 50% (v/v) aqueous acetonitrile and the microtitre plate was imaged at 200 μm resolution on a Typhoon Trio Plus variable mode imager (Amersham Biosciences) with the green (532 nm) laser and the 580 BP 30 filter at the PMT voltages indicated below and at normal sensitivity. The scan height was set at +3 mm and the sample was pressed during scanning.
The fluorescence images were analysed using ImageQuant TL v2003.03 (Amersham Biosciences).
Fluorescence images showing the pH resistance of 2DOS-2 deposited on polypropylene are shown in
Quantification data for peptide 2DOS-2 retention (using data from the 300V scan) are given in Table 8 and graphically in
The results show that, the retention of peptide 2DOS-2 on a polypropylene surface is therefore stable over a broad range of pH values, with maximal retention at low and high pH and minimal retention around pH 6.5.
The time-dependent persistence of peptide 2DOS-2 (see above) deposited onto a polypropylene hydrophobic surface in the presence of aqueous buffer was investigated as shown below:
Twelve 100 μl aliquots of 5 μM peptide 2DOS-2 in 5 mM tris-HCl (pH 8.0) in 75% (v/v) aqueous acetonitrile were dispensed to the wells of the top row of a Costar microtitre plate.
The peptide samples were allowed to evaporate to dryness in the dark.
The dried peptide samples in wells 1-10 were incubated with 250 μl of 1 M NaCl in 10 mM tris-HCl (pH 8.0) for the time indicated below at room temperature. All supernatants were pipetted up and down 8 times after incubation and the supernatants were then removed and placed in the wells of the bottom row of the microtitre plate.
The residual surface-bound peptides in all twelve wells were finally resuspended in 50 μl of 10 mM tris-HCl (pH 8.0) in 50% (v/v) aqueous acetonitrile and the microtitre plates were imaged at 200 μm resolution on a Typhoon Trio Plus variable mode imager (Amersham Biosciences) with the green (532 nm) laser and the 580 BP 30 filter at the PMT voltages indicated below and at normal sensitivity. The scan height was set at +3 mm and the sample was pressed during scanning.
The fluorescence images were analysed using ImageQuant TL v2003.03 (Amersham Biosciences).
Fluorescence data for the time-dependent persistence of peptide 2DOS-2 deposited onto a polypropylene hydrophobic surface in the presence of aqueous buffer are shown in FIG. 17:
Quantification data for peptide 2DOS-2 retention (using data from the 300V scan) are shown in Table 9 and
The results show that retention of peptide 2DOS-2 on a hydrophobic polypropylene surface is stable for extended periods of time in 1 M NaCl/10 mM tris-HCl (pH 8.0).
The retention of peptides 2DOS-1 to 2DOS-16 (see above) on polypropylene wells of different geometries was investigated:
10 mM tris-HCl (pH 8.0) in 50% (v/v) aqueous acetonitrile was used as the solvent for the peptides and for TAMRA.
1 μl aliquots of 10 μM peptides 2DOS-1 to 2DOS-16 and 10 μM TAMRA were pipetted into the wells of a Costar V-bottomed polypropylene microtitre plate and a Greiner flat-bottomed polypropylene microtitre plate according to the following scheme as shown in
The peptide samples were allowed to evaporate to dryness in the dark.
The peptide samples in the top two rows of the microtitre plates were then incubated for 15 minutes at room temperature in 250 μl of 1 M NaCl in 10 mM tris-HCl (pH 8.0). After incubation, the wash buffer was pipetted up and down eight times in the well before removing the supernatant.
The washed and untreated peptide samples were then resuspended in 50 μl of 10 mM tris-HCl (pH 8.0) in 50% (v/v) aqueous acetonitrile.
The microtitre plates were imaged at 200 μm resolution on a Typhoon Trio Plus variable mode imager (Amersham Biosciences) with the green (532 nm) laser and the 580 BP 30 filter at the PMT voltages indicated below and at normal sensitivity. The scan height was set at the platen and the sample was pressed during scanning.
The fluorescence images were analysed using ImageQuant TL v2003.03 (Amersham Biosciences).
The fluorescence images of the plates scanned at PMT voltages of 600V and 500V are shown in
Quantification data for the V-bottom wells (using data from the 500V scan) are shown in Table 10 and
Quantification data for the flat-bottom wells (using data from the 500V scan) are shown in Table 11 and
The results show that retention of peptides 2DOS-1 to 2DOS-16 on polypropylene wells of different geometries is comparable, indicating that retention is not dependent upon drying down in wells with a V-bottomed geometry.
The retention of peptides 2DOS-1 to 2DOS-16 (see above) on polypropylene and polystyrene surfaces was compared:
5 mM tris-HCl (pH 8.0) in 75% (v/v) aqueous acetonitrile was used as the solvent for the peptides and for TAMRA.
20 μl aliquots of 5 μM peptides 2DOS-1 to 2DOS-16 and 5 μM TAMRA were pipetted into the wells of a Costar V-bottomed polypropylene microtitre plate, a Greiner V-bottomed polypropylene microtitre plate, and a Greiner V-bottomed polystyrene microtitre plate according to the scheme shown in
The peptide samples were allowed to evaporate to dryness in the dark.
The peptide samples in the top two rows of the microtitre plates were then incubated for 15 minutes at room temperature in 250 μl of 1 M NaCl in 10 mM tris-HCl (pH 8.0). After incubation, the wash buffer was pipetted up and down eight times in the well before removing the supernatant.
The washed and untreated peptide samples were then resuspended in 50 μl of 10 mM tris-HCl (pH 8.0) in 50% (v/v) aqueous acetonitrile.
The microtitre plates were imaged at 200 μm resolution on a Typhoon Trio Plus variable mode imager (Amersham Biosciences) with the green (532 nm) laser and the 580 BP 30 filter at the PMT voltages indicated below and at normal sensitivity. The scan height was set at +3 mm and the sample was pressed during scanning.
The fluorescence images were analysed using ImageQuant TL v2003.03 (Amersham Biosciences).
The fluorescence images of the slides scanned at PMT voltages of 600V, 500V, and 400V are shown in
Peptide samples in the upper half of the plates have been washed and peptide samples in the lower half of the plates are untreated.
Quantification data for the Costar polypropylene V-bottom wells (using data from the 400V scan) are given in Table 12:
Quantification data for the Greiner polypropylene V-bottom wells (using data from the 400V scan) are given in Table 13:
Quantification data for the Greiner polystyrene V-bottom wells (using data from the 400V scan) are given in Table 14:
These data are shown graphically in
The result show that comparable peptide behaviour is seen on all three surfaces, demonstrating that retention is a sequence-specific property of the peptides rather than a property that is peculiar to one particular plastic surface.
Four peptides were synthesised that contain a ‘surface-binding face’ consisting of seven phenylalanyl residues. These peptides also contain a central region consisting of charged and uncharged residues and a variable penultimate residue. The variable penultimate residue was alanyl, seryl, cysteiyl, or nitropyridylthio activated cysteiyl.
An additional four TAMRA-labelled fluorescent peptides were also synthesised that contain an N-terminal TAMRA fluorophore attached to a glycyl residue that is attached to a variable C-terminal residue. The variable C-terminal residue was alanyl, seryl, cysteiyl, or nitropyridylthio activated cysteiyl.
A mixture of the 5-TAMRA and 6-TAMRA isomers as shown in Example 1 was used for the labelling.
The full set of eight peptides is shown in Tables 15 and 16:
The peptides SB-1 to SB-4 and TLSP-1 to TLSP-4 were used in order to investigate dimer formation.
Two different protocols were used. In the ‘liquid phase’ protocol, The SB peptides were dried down onto a polypropylene surface. The TLSP peptides were then added in aqueous solution prior to washing the wells and assaying for retained fluorescent material.
In the ‘co-drying’ protocol, The SB peptides were mixed with the TLSP peptides and both were then dried down together onto a polypropylene surface prior to washing the wells and assaying for retained fluorescent material.
A further protocol in which the SB peptides are mixed with the TLSP peptides in aqueous solution and allowed to react to produce peptide dimers which are then dried down onto a polypropylene surface could easily be achieved by one skilled in the art.
In the ‘liquid phase’ protocol, 50 μl of 10 μM peptides SB-1 to SB-4 in 1 mM NaH2PO4 in 50% (v/v) aqueous acetonitrile were added the wells of a Costar V-bottomed microtitre plate according to the scheme shown in Table 17:
The samples were dried down overnight in the dark.
50 μl′ of 100 μM peptides TLSP-1 to TLSP-4 in 10 mM NaH2PO4 were then added to the wells according to the scheme shown in Table 18:
The samples were incubated at room temperature for one hour in the dark. The supernatants were removed and the wells were washed twice with 200 μl of 1 M NaCl in 10 mM tris-HCl (pH 8.0). 50 μl of 10 mM tris-HCl (pH 8.0) in 50% (v/v) aqueous acetonitrile was finally added to the wells.
The microtitre plate was imaged at 200 μm resolution on a Typhoon Trio Plus variable mode imager (Amersham Biosciences) with the green (532 nm) laser and the 580 BP 30 filter at a PMT voltage of 500 μl and at normal sensitivity. The scan height was set at +3 mm and the sample was pressed during scanning. The fluorescence image was analysed using ImageQuant TL v2003.03 (Amersham Biosciences).
In the ‘co-drying’ protocol, 50 μl of 10 μM peptides SB-1 to SB-4 in 1 mM NaH2PO4 in 50% (v/v) aqueous acetonitrile were added to the wells of a Costar V-bottomed microtitre plate according to the scheme shown in Table 19:
50 μl of 100 μM peptides TLSP-1 to TLSP-4 in 1 mM NaH2PO4 in 50% (v/v) aqueous acetonitrile were then added to the wells according to the scheme shown in Table 20:
The samples were dried down overnight in the dark.
The wells were then washed twice with 200 μl of 1 M NaCl in 10 mM tris-HCl (pH 8.0). 50 μl of 10 mM tris-HCl (pH 8.0) in 50% (v/v) aqueous acetonitrile was finally added to the wells.
The microtitre plate was imaged at 200 μm resolution on a Typhoon Trio Plus variable mode imager (Amersham Biosciences) with the green (532 nm) laser and the 580 BP 30 filter at a PMT voltage of 500 V and at normal sensitivity. The scan height was set at +3 mm and the sample was pressed during scanning. The fluorescence image was analysed using ImageQuant TL v2003.03 (Amersham Biosciences).
The fluorescence image for the microtitre plate from the experiment using the ‘liquid phase’ protocol is shown in
The fluorescence data for the ‘liquid phase’ protocol are given in Table 21:
The results are shown graphically in
The fluorescence image for the microtitre plate from the experiment using the ‘co-drying’ protocol is shown in
The fluorescence data for the ‘co-drying’ protocol are given in the following Table 22:
The results are shown graphically in
The yield of dimer is assayed by the retention of fluorescently labelled peptide which is conditional upon the presence of an unlabelled peptide that can bind to both the polypropylene surface and to the fluorescently labelled peptide.
For the ‘liquid phase protocol’ dimer yields are lower than for the ‘co-drying’ protocol but the chemical specificity for dimer formation is better. Maximal dimer formation is seen when the surface peptide possesses a free thiol group and the solution peptide possesses an S-nitropyridyl activated thiol group. Dimer formation is also observed when the surface peptide possesses an S-nitropyridyl activated thiol group and the solution peptide also possesses an S-nitropyridyl activated thiol group; when the surface peptide possesses a free thiol group and the solution peptide also possesses a free thiol group; and when the surface peptide possesses an S-nitropyridyl activated thiol group and the solution peptide possesses a free thiol group.
Free thiol coupling to free thiols may be due to simple aerobic oxidation, forming disulfide bonds. S-nitropyridyl activated thiol coupling to S-nitropyridyl activated thiols may be a result of incomplete thiol activation, leaving some free thiols able to react with the remaining S-nitropyridyl activated thiols, or some other mechanism.
Results, for the ‘co-drying’ protocol mirror those described above. Dimer yields are generally higher with this method but non-specific binding is also higher. In particular, some reactivity is observed between a hydroxylated peptide attached to the surface and solution peptides containing both free thiol groups and S-nitropyridyl activated thiol groups.
In this example, peptide dimers are fabricated on a planar plastic surface using a Piezorray (PerkinElmer LAS) non-contact dispenser. The Piezorray (PerkinElmer LAS) is specifically designed for pipetting nanolitre volumes to dense arrays. Liquid volumes are controlled by a piezoelectric tip. The Piezorray system contains a source plate holder, an ultrasonic washbowl, a computer and monitor, and a bottle for system liquid.
Polypropylene sheet was obtained from SBA plastics (http://www.sba.co.uk/, Propylex Natural Polypropylene Sheet 2440×1220×1 mm) and was wiped with 50% (v/v) aqueous acetonitrile prior to use.
Six 10×10 arrays of 5nl of 100 μM peptides SB-1 and SB-3 in 1 mM NaH2PO4 in 50% (v/v) aqueous acetonitrile or solvent control were dispensed to 1 mm polypropylene sheet cut to 3″×1″ using the Piezorray system according to the scheme shown in Table 23.
Six 10×10 arrays of 5 nl of 100 μM peptide TLSP-4 in either 1 mM NaH2PO4 in 50% (v/v) aqueous acetonitrile or in 1 mM NaH2PO4 in 50% (v/v) aqueous acetonitrile and 10% (v/v) glycerol were then dispensed over the previous spots using the Piezorray system according to the scheme shown in Table 24:
The samples were incubated at room temperature for 30 minutes in the dark. The slide was then washed in 100 ml of 50 mM NaCl in 10 mM tris-HCl (pH 8.0) followed by running tap water over the slide for one minute.
The microtitre plate was imaged at 10 μm resolution on a Typhoon Trio Plus variable mode imager (Amersham Biosciences) with the green (532 nm) laser and the 580 BP 30 filter at a PMT voltage of 400 V and at normal sensitivity. The scan height was set at the platen and the sample was pressed, during scanning. The fluorescence image was analysed using ImageQuant TL v2003.03 (Amersham Biosciences).
The fluorescence image for the polypropylene slide is shown in
The yield of dimer is assayed by the retention of fluorescently labelled peptide that is conditional upon the presence of an unlabelled peptide that can bind to both the polypropylene surface and to the fluorescently labelled peptide.
Dimer formation is therefore seen when the surface peptide possesses a free thiol group and the solution peptide possesses an S-nitropyridyl activated thiol group. The simple protocol (without glycerol to prevent evaporation) gives a higher yield of dimer.
In this example, twenty 256-element microarrays of dimers comprising peptides L1-P1-1 to 16 and L1-P2-1 to 16 were fabricated in parallel.
1 mm polypropylene sheet was cut to 136 mm×80 mm, lightly abraded with glass paper, and wiped with 50% (v/v) aqueous acetonitrile prior to use.
18×6 nl aliquots of P1 peptides were arrayed down the columns of the polypropylene slide at a spacing 0.72 mm as indicated in Table 25, using the Piezorray system (PerkinElmer LAS).
Sequence of P1 Peptides:
After sample evaporation, 18×12 nl aliquots of L1-P2 peptides in 90% (v/v) DMSO, 1 mM tris-HCl (pH 8.0) were arrayed along the rows of the polypropylene slide at a spacing of 0.72 mm as indicated in Table 26, using the Piezorray system (PerkinElmer LAS).
Sequence of P2 Peptides:
After sample evaporation, the slide was washed for 10 minutes in 50 ml of 10 mM tris-HCl (pH 8.0) containing 0.1% (v/v) Tween-20.
The slide was imaged at 10 μm resolution on a Typhoon Trio Plus variable mode imager (Amersham Biosciences) with the green (532 nm) laser and the 580 BP 30 filter at a PMT voltage of 500V and at normal sensitivity. The scan height was set at the platen. The fluorescence image was analysed using ImageQuant TL v2003.03 (Amersham Biosciences).
The fluorescence image for one 18×18 array of dimer and control spots is shown in
Fluorescent signal is observable for each L1-P1 peptide column dispensed to the array. This indicates that each of the L1-P1 peptides has been successfully dispensed, and is capable of dimer formation. The fluorescent signal is also observable for each L1-P2 peptide row dispensed to the array. This indicates that each of the L1-P2 peptides has been successfully dispensed, and is capable of dimer formation.
The dimer fluorescence is greater for the samples with only TAMRA-labelled P2 peptides compared to the dimer fluorescence for the 16×16 array fabricated with both unlabelled P2 peptides and TAMRA-labelled P2 peptides competing for the L1-P1 peptide thiol groups. This indicates that all of the L1-P2 peptides have successfully competed with their TAMRA-labelled counterparts and have therefore successfully formed peptide, dimers between all sixteen. L1-P1 peptides and all sixteen L1-P2 peptides.
The invention being thus described, it will be obvious that the same way may be varied in many ways. Such variations are not to be regarded as a departure from the spirit and scope of the invention, and all such modifications as would be obvious to one skilled in the art are intended to be included within the scope of the following claims.
The current invention provides synthetic capture agents having increased sequence diversity. The capture agents can functionalize various surfaces, for example, glass or silicon, so as to allow the binding of ligands to the surface, or to form arrays of various types.
| Number | Date | Country | Kind |
|---|---|---|---|
| 0525915.5 | Dec 2005 | GB | national |
| Filing Document | Filing Date | Country | Kind | 371c Date |
|---|---|---|---|---|
| PCT/JP2006/325695 | 12/19/2006 | WO | 00 | 6/18/2008 |
