Patent Application
20230227534
The present invention relates to a method for generating variants of a protein. The invention also concern a computer implemented program to carry out said method. The invention further concerns a variant of a protein obtained by the method according to the present invention and polynucleotide encoding said variant.
It is known that membrane receptors sense extracellular stimuli and transduce these signals into intracellular signaling responses. Subtle differences in protein sequence often give rise to profound changes in signaling response with no obvious connection to their structure.
Allostery is a fundamental property that enables long-range communication between distant sites on a molecule. Allostery is known either for protein membrane receptor or soluble protein. It is at the origin of a large diversity of regulatory mechanisms of biological molecular functions but its biophysical underpinnings remain poorly understood. Allosteric communications are thought to be primarily mediated by intraprotein networks of coupled residues (i.e. allosteric residues) physically connecting extracellular and intracellular regions of the protein. Long-range structural coupling can promote the effective communication between distant protein sites through the propagation of even small changes in local structure and dynamics.
These observations suggest that the residue couplings that regulate the intracellular responses to extracellular stimuli largely depend on amino-acid sequence details and fine protein structure and dynamic properties. Hence, predicting how protein sequences and structures encode specific allosteric responses remains particularly challenging.
Better understanding and engineering allostery in protein would greatly benefit not only the study of protein structure, function, and pharmacology but also the design of novel biosensing protein for synthetic and cell biology applications, for instance membrane receptors.
Existing methodologies structural biologists have developed are based on empirical approaches for screening stabilized mutants to facilitate structure determination. However, studying stabilized mutants, for instance thermostabilized mutants, present serious drawback notably because they frequently fail to exhibit the ligand induced signal transduction response associated with the wild type protein.
The document WO02/18590 describes a method for identifying constitutively activating mutations where libraries of mutations are generated and screened using cell-based assays for modified receptor activities. Briefly, this is a scanning mutagenesis approach where small residues are mutated to larger ones with the hope that it will destabilize the resting state of the receptor and eventually stabilize the active state. However, the disclosed method is not a computational approach that can predict with the effect of the mutations on the receptor stability, constitutive activity and ligand-induced activity. The disclosed screening approach lacks a strong rationale for selecting the mutations, has no predictive power and rely on screening enough mutations to identify ones with desired activities. Additionally, such approach often generates mutants that behave rather poorly because mutations often destabilize the resting state instead of stabilizing the active state. An additional weakness is that a screening approach for activating mutations that is not based on a mechanistic understanding of receptor complex signaling functions may lead to receptor variants with constitutive signaling properties distinct from that of the ligand-induced WT because the mutation may inadvertently stabilize a specific subset of the active conformations accessible to the receptor in the case of GPCRs for example that are not 2-state systems.
The document WO2010/149964 describes a method for identifying stabilizing mutations of GPCRs. Based on previous findings, they identify that a local region around position 2.46 is prone to stabilization by mutagenesis. However, this approach lacks a strong rationale for selecting the mutations, has no predictive power and relies on screening enough mutations and neighboring sites to identify ones with enhanced stabilities. For instance, the resulting effects are not consistent across receptors since they vary from substantial stabilization of agonist bound form to non significant stabilization of antagonist-bound forms. Additionally, the engineered receptors tested for signaling were shown to be considerably inactivated by the mutations. Therefore, since such engineered receptors are mostly inactive, they may bias and mislead the search for new drugs.
Therefore, there is a need for a methodology to facilitate protein variant engineering and studying.
The present invention concerns a method for generating variants of a protein based on a native protein regulated by allosteric pathway, the method comprising:
The present invention also concerns a computer implemented method for generating variants of a protein based on a native protein regulated by allosteric pathway, the method comprising:
Also provided is a computer implemented program comprising instructions which, when the program is executed by a computer, cause the computer to carry out the method of the invention.
Further provided is a protein, or an active fragment or analog thereof, obtained by the method of the invention, wherein the sequence of said variant of a protein, or active fragment thereof, comprises at least one mutation in the microswitch region.
Also provided is a polynucleotide encoding a protein, or an active fragment or analog thereof, of the invention.
The above problems are solved at least partially by the present invention.
The invention concerns a computer implemented method for generating variants of a protein based on a native protein regulated by allosteric pathway, the method comprising:
A protein regulated by allosteric pathways, for instance a membrane receptor or a soluble protein, can adopt either an active conformation or an inactive conformation for both ligand free and ligand bound states. The switch between active and inactive conformation involves smaller scale movements of individual amino acid named herein as microswitch. A microswitch corresponds to one amino-acid at one specific position. Since, there are 20 possible amino-acids, the present invention can select 20 different possible microswitches at a given site.
Additionally, multiple microswitches at several sites can be designed simultaneously. Alternatively, the present invention also concerns combinations of microswitches comprising several single amino acids.
Advantageously, one microswitch is coupled to another microswitch pairwise. Alternatively, one microswitch can be paired with more than one microswitch.
The present invention allows generating variants of a protein by selective mutation of microswitches, preferably of at least one pair of coupled microswitch.
One aim of the invention is to select variant with microswitch that shifts the stability or the structural coupling of specific protein conformations.
For example, variants with increased constitutive activity, i.e. activity in ligand free state, namely stability microswitch, can be engineered by introducing the appropriate mutation of the identified microswitch providing an increased stability to the engineered variant. The point is to make more stabilizing contacts in the active versus the inactive ligand-free conformations. Advantageously, point amino acid mutation on stability microswitch allows to modulate the fraction of time the protein spends in each state.
Alternatively, variants with enhanced signaling response to ligand, namely allosteric microswitch, preferably agonist ligand, can be engineered by introducing the appropriate mutation of the identified microswitch to increase ligand/protein binding and/or signal transduction, for instance ligand/receptor. Advantageously, point amino acid mutation allows to modulate selectively the responses to ligands by enhancing or decreasing the protein allosteric sensing properties.
For allosteric microswitch, a score named ΔG-coupling is computed. In one embodiment, ΔG-coupling is calculated from the dynamics correlation between identified microswitch using an elastic model of the protein, for instance
With each GC = Sum (i=1; j>i; i, j<= total nb of microswitches) (Correl_dyn (i, j)). Correl_dyn is the dynamic correlation between microswitches i and j calculated using an elastic network model of the protein.
A change in ligand-induced activity of the variant compared to the native protein is determined by comparison between the ΔL coupling of the variant compared to the one of the native protein. The ΔL activity of the variant is calculated by
wherein variant protein active and inactive conformations are denoted respectively AL, IL for ligand bound states.
For allosteric microswitch, if ΔL activity of the variant is superior to ΔL activity of the native protein, it means the variant exhibits an increased sensitivity to ligand binding compared to the native protein. If ΔL activity of the variant is inferior to ΔL activity of the native protein, it means the variant exhibits a decreased sensitivity to ligand binding compared to the native protein.
For stability microswitch, a score named ΔG-stability is computed. ΔG-stability is computed by the sum of all interactions between the residues of the protein in a specific conformation and in absence of ligand (i.e. the total free energy of the system). In other words, the ΔG-stability is computed from the free energy difference between each conformation in the absence of ligand.
A change in ligand-free activity of the variant compared to the native protein is determined by comparison between the ΔL stability of the variant compared to the one of the native protein. The ΔL activity of the variant is calculated by
For stability microswitch, if ΔL activity of the variant is superior to ΔL activity of the native protein, it means the variant exhibits an increased stability compared to the native protein when bound to the ligand. If ΔL activity of the variant is inferior to ΔL activity of the native protein, it means the variant exhibits a decreased stability compared to the native protein when bound to the ligand.
In one embodiment, the prediction of the activity of the variant is based on a fitness function defined by:
The stability and coupling components can be calculated and studied independently because they correspond to two distinct allosteric properties. However, it is advantageous to use both stability and coupling component to fully describe any allosteric molecular system.
In an embodiment, the variation of allosteric coupling of said variant is chosen among :
Advantages of situation a (above):
Advantages of situation b (above):
In one embodiment, said microswitch is identified by molecular dynamic simulations, for instance long time scale molecular dynamics. Molecular dynamic simulations are for instance described in Battacharya et al, Biophysical Journal, July 2014, 107(2), 422-434. As described in Battacharya et al, pairs of residues with high dynamic correlations or Mutual Information located on either binding sites (i.e. extracellular and intracellular) of the receptor are identified from the simulation trajectories. Pathways linking these sites through non-covalent interactions with other residues are identified that maximize the mutual information between all the connected residues in the pathway. For instance, allosteric microswitches are defined as the residues involved in multiple pathways.
Alternatively, said microswitch can be identified from the structures of a receptor or protein in distinct signaling states. Usually, a microswitch will change conformation when the receptor or protein switches between functional states (Zhou et al., elife 2019; 8:e50279). Additionally, a microswitch can be identified through sequence covariation analysis since it is usually functionally coupled to at least another microswitch in the receptor or protein structure (Sun et al., PNAS 2016 113(13):3539-44).
In an embodiment, the 3D structures of the native protein is generated by homology modeling based on at least one homolog protein. Thus, the present invention can be applied to any protein with available homolog protein. The present invention is not limited to protein for which 3D data structure are available. For instance, so far, less than 5% of all GPCRs have been structurally characterized. Using homology modeling enables to expand the structural coverage and provide reliable structural models for close to 40% of all GPCRs.
In one embodiment, said in silico mutations process is based on random mutagenesis using genetic algorithm. The Genetic algorithm (GA) evolves an initial population of protein sequences to optimize its fitness over multiple generations using two genetic operators: point mutagenesis and cross over recombination between 2 sequences. For a given population of sequences, the GA will calculate the fitness for each sequence. Then, it will create a new population of sequences defining the subsequent generation by preferentially selecting and modifying a subset of the current sequences that have the highest fitness. The probabilities for point mutagenesis and cross over recombination by the GA are defined by the user beforehand.
In one embodiment, the protein is chosen among protein membrane receptor or soluble protein. A protein membrane receptor, i.e. membrane receptor, is defined as protein receptor embedded in a cellular membrane. A soluble protein can also bind a ligand, but the soluble protein is not embedded in the cellular membrane.
In an embodiment, said receptor regulated by allosteric pathway is chosen among GPCR. The method could be applied to other families of multi-pass and single-pass receptors including Cytokine, Tyrosine kinases but also transporters, channels.
In one embodiment, the method further comprises a validation step for testing, preferably in vitro and/or in cellulo testing, preferably in vitro, preferably in cellulo, the predicted activity of the selected variant. It allows to improve the success rate of computational techniques. For instance, the present invention achieves about 80% success rate. A validation step helps to identify and rank the designed protein based on their measured activities. The validation step could also help increasing the success rate by incorporating the result of the validation step to proofread or improve the method according to the present invention, for instance the generation of in silico mutation.
The feedback from the experiments (i.e. failures, successes) is advantageous as it enables to optimize the computational approach and parameters guiding the calculations.
In an embodiment, the method is arranged for generating a variant of protein with an improved parameter for the ligand compared to the one of said ligand with the native protein, said parameter being chosen among sensitivity (defined as the capacity of the ligand to activate the protein), selectivity, affinity, in particular sensitivity.
In one embodiment, the method is arranged for generating a variant of protein designed for interacting with a ligand distinct from or identical to the ligand interacting with the native protein. The present invention enables the design of protein (for instance receptor or biosensor) with fine-tuned properties to a large diversity of ligands without having to design protein (for instance receptor or biosensor) from scratch which is very challenging. By rationally reprogramming the function of existing protein (for instance receptor or biosensor) through a minimal number of mutations, the present invention achieves high success rate and efficiency and can be applied to design protein (for instance receptor or biosensor) for a large variety of ligands and signals.
The invention also concerns a computer implemented program comprising instructions which, when the program is executed by a computer, cause the computer to carry out the method according to the present invention.
The invention further relates to a data processing apparatus comprising means for carrying out the method according to the present invention.
The particular advantages of the data processing apparatus and of the computer implemented program are similar to the ones of the method of the invention and will thus not be repeated here.
The invention further relates to a variant of a protein based on a native protein (hereafter “a protein”), or an active fragment or analog thereof, which protein sequence has been determined, designed, obtained, or is obtainable, by the method according to the present invention, wherein the sequence of said protein, or active fragment or analog thereof, comprises at least one mutation in the microswitch region.
Alternatively, the invention also relates to a protein, or an active fragment or analog thereof, obtained by any method, wherein the sequence of said protein, or active fragment or analog thereof, comprises at least one mutation in the microswitch region.
Preferably, the sequence of the protein of the invention, active fragment or analog thereof, comprises at least one mutation in the microswitch region. Preferably, the sequence of the protein of the invention, active fragment or analog thereof, comprises at least one, for example, 1, 2, 3, 4, 5, etc. mutation(s) in the microswitch region.
As used herein, the terms “protein” or “polypeptide” are used interchangeably and are intended to encompass a singular “polypeptide” as well as plural “polypeptides,” and refers to a molecule composed of monomers (amino acids) linearly linked by amide bonds (also known as peptide bonds). The term “polypeptide” refers to any chain or chains of two or more amino acids, and does not refer to a specific length of the product. Thus, peptides, dipeptides, tripeptides, oligopeptides, “protein,” “amino acid chain,” or any other term used to refer to a chain or chains of two or more amino acids, are included within the definition of “polypeptide,” and the term “polypeptide” may be used instead of, or interchangeably with any of these terms. The terms “polypeptide” or “protein” are also intended to refer to the products of post-expression modifications of the polypeptide, including without limitation glycosylation, acetylation, phosphorylation, amidation, derivatization by known protecting/blocking groups, proteolytic cleavage, or modification by non- naturally occurring amino acids as disclosed herein.
The “protein” or “polypeptide” refers to any protein or polypeptide with available homolog protein. The present invention is thus not limited to protein for which 3D data structure are available.
In one aspect, the protein is selected from the group comprising multi-pass and single-pass receptors including Cytokine, Tyrosine kinases but also transporters, channels, G protein coupled receptors (GPCR), i.e. rhodopsin (family A), secretin (family B), glutamate (family C), adhesion and Frizzled/Taste2.
In case the protein of the invention is a dopamine receptor, more preferably a dopamine D2 receptor, then the sequence of said D2 dopamine receptor will comprise at least one mutation in one or more of the following amino acid position(s) (when referring to the wild-type sequence): 76, 90, 122, 205, 209, 374, 378, 379, 381, 382, 385, 421, 426, and 429. Preferably, the at least one mutation is comprised in one or more of the following amino acid position(s): 205, 374, 378, 381, and 421. More preferably, all five amino acid positions: 205, 374, 378, 381, and 421 are mutated.
In an embodiment, the ligand sensing and/or signaling response is modified when compared to the native sequence of said protein.
In one embodiment, the ligand sensing and/or signaling response is enhanced or decreased when compared to the native sequence of said protein.
The invention also relates to a polynucleotide encoding a protein, or an active fragment or analog thereof, according to the present invention.
A “fragment” of a protein, peptide or polypeptide of the invention refers to a sequence containing less amino acids in length than the protein, peptide or polypeptide of the invention. This sequence can be used as long as it exhibits the same properties, i.e. is biologically active, as the native sequence from which it derives.
The term “analog” refers to a protein, peptide or polypeptide of the invention having an amino acid sequence that differ to some extent from a native sequence peptide, that is an amino acid sequence that varies from the native sequence by amino acid substitutions, whereby one or more amino acids are substituted by another with same characteristics and conformational roles. The amino acid sequence analogs possess substitutions, deletions, and/or insertions at certain positions within the amino acid sequence of the native amino acid sequence. Substitutions can be conservative or non-conservative. Conservative amino acid substitutions are known in the art, and include amino acid substitutions in which one amino acid having certain physical and/or chemical properties is exchanged for another amino acid that has the same chemical or physical properties. For instance, the conservative amino acid substitution may be an acidic amino acid substituted for another acidic amino acid (e.g., Asp or Glu), an amino acid with a nonpolar side chain substituted for another amino acid with a nonpolar side chain (e.g., Ala, Gly, Val, Ile, Leu, Met, Phe, Pro, Trp, Val, etc.), a basic amino acid substituted for another basic amino acid (Lys, Arg, etc.), an amino acid with a polar side chain substituted for another amino acid with a polar side chain (Asn, Cys, Gln, Ser, Thr, Tyr, etc.), etc. Preferably, the substitutions, deletions, and/or insertions at certain positions within the amino acid sequence of the amino acid sequence occur in a region that is different from the microswitch region.
In general, the sequences of such analogs will have a high degree of sequence homology to the reference (native) sequence, e.g., sequence homology of more than 50%, generally more than 60%-70%, even more particularly 80%-85% or more, such as at least 90%-95% or more, when the two sequences are aligned.
Both the analog and fragment of the protein of the invention can include synthetic, non-standard and/or naturally-occurring amino acid sequences (including D-forms and/or retro-inverso isomers) derivable from the naturally occurring amino acid sequence of the protein of the invention. By way of example, the replacement amino acid may be a basic non-standard amino acid, (e.g. L-Ornithine, L-2-amino-3-guanidinopropionic acid, or D-isomers of Lysine, Arginine and Ornithine). Methods for introducing non-standard amino acids into proteins are known in the art, and include recombinant protein synthesis using E. coli auxotrophic expression hosts.
Non-naturally occurring amino acids include, without limitation, trans-3-methylproline, 2,4-methano-proline, cis-4-hydroxyproline, trans-4-hydroxy-proline, N-methylglycine, allo-threonine, methyl-threonine, hydroxy-ethylcysteine, hydroxyethylhomo-cysteine, nitro-glutamine, homoglutamine, pipecolic acid, tert-leucine, norvaline, 2-azaphenylalanine, 3-azaphenyl-alanine, 4-azaphenyl-alanine, and 4-fluorophenylalanine. Several methods are known in the art for incorporating non-naturally occurring amino acid residues into proteins.
The present invention also contemplates one or more polynucleotide(s) encoding a protein, or an active fragment or analog thereof, of the invention.
The present invention also contemplates a gene delivery vector or expression vector or gene therapy vector, preferably in the form of a plasmid or a vector, which comprises one or more polynucleotide(s) encoding a protein, or an active fragment or analog thereof of the invention.
As used herein, a “vector” is capable of transferring nucleic acid sequences to target cells (e.g., viral vectors, non-viral vectors, particulate carriers, and liposomes). The terms “expression vector”, “gene delivery vector” and “gene therapy vector” refer to any vector that is effective to incorporate and express one or more nucleic acid(s), in a cell, preferably under the regulation of a promoter. A cloning or expression vector may comprise additional elements, for example, regulatory and/or post-transcriptional regulatory elements in addition to a promoter, as well as tags at the C- or N- terminus of the nucleic acid to be expressed (e.g. HA signal sequence(s), His tag(s) or flag(s)). The promoter can be inducible and/or cell type-specific for specific expression in a tissue (e.g. neurons such as dopaminergic or serotoninergic neurons, glial cells, ...).
Suitable vectors include derivatives of SV40 and known bacterial plasmids, e. g., E. coli plasmids col El, pCRI, pBR322, pLive, pMB9 and their derivatives, plasmids such as RP4; phage DNAs, e. g., the numerous derivatives of phage X, e. g., NM989, and other phage DNA, e. g., MI 3 and filamentous single stranded phage DNA; yeast plasmids such as the 2 µ plasmid or derivatives thereof; vectors useful in eukaryotic cells, such as vectors useful in insect or mammalian cells; vectors derived from combinations of plasmids and phage DNAs, such as plasmids that have been modified to employ phage DNA or other expression control sequences; and the like. Various viral vectors are used for expressing or delivering nucleic acid to cells in vitro or in vivo. Non-limiting examples are vectors based on Herpes Viruses, Baculovirus (e.g. pFastBac expression vector) Pox- viruses, Adeno-associated virus, Lentivirus, and others. In principle, all of them are suited to deliver the expression cassette comprising one or more polynucleotide(s) encoding the peptides of the invention, variants or fragments thereof and a promoter, optionally an inducible and/or cell type-specific promoter.
Also contemplated in the present invention is a host cell comprising a plasmid or vector of the invention or one or more nucleic acid(s) encoding the peptides of the invention, analogs or fragments thereof. The host cell can be any prokaryotic or eukaryotic cell, preferably the host cell is a eukaryotic cell, most preferably the host cell is a mammalian cell. Even more preferably, the host cell is a human neuronal or glial cell.
In one embodiment, the invention further provides pharmaceutical compositions comprising a therapeutically effective amount of i) a plasmid or a vector of the invention, ii) a host cell of the invention, iii) a polynucleotide encoding a protein, or an active fragment or analog thereof, of the invention, or a iii) a protein of the invention, an active fragment or analog thereof, and a pharmaceutically acceptable excipient, diluent, carrier, salt and/or additive.
“Pharmaceutically acceptable diluent or carrier” means a carrier or diluent that is useful in preparing a pharmaceutical composition that is generally safe, non-toxic, and desirable, and includes carriers or diluents that are acceptable for human pharmaceutical use.
Such pharmaceutically acceptable carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like. Water is a preferred carrier when the pharmaceutical composition is administered intravenously. Saline solutions and aqueous dextrose and glycerol solutions can also be employed as liquid carriers, particularly for injectable solutions.
Pharmaceutically acceptable diluent or carrier include starch, glucose, lactose, sucrose, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene glycol, water, ethanol and the like.
The pharmaceutical compositions may further contain one or more pharmaceutically acceptable salts such as, for example, a mineral acid salt such as a hydrochloride, a hydrobromide, a phosphate, a sulfate, etc.; and the salts of organic acids such as acetates, propionates, malonates, benzoates, etc. Additionally, auxiliary substances, such as wetting or emulsifying agents, pH buffering substances, gels or gelling materials, flavorings, colorants, microspheres, polymers, suspension agents, etc. may also be present herein. In addition, one or more other conventional pharmaceutical ingredients, such as preservatives, humectants, suspending agents, surfactants, antioxidants, anticaking agents, fillers, chelating agents, coating agents, chemical stabilizers, etc. may also be present, especially if the dosage form is a reconstitutable form. Suitable exemplary ingredients include macrocrystalline cellulose, carboxymethyf cellulose sodium, polysorbate 80, phenyletbyl alcohol, chiorobutanol, potassium sorbate, sorbic acid, sulfur dioxide, propyl gallate, the parabens, ethyl vanillin, glycerin, phenol, parachlorophenol, gelatin, albumin and a combination thereof. A thorough discussion of pharmaceutically acceptable excipients is available in REMINGTON’S PHARMACEUTICAL SCIENCES (Mack Pub. Co., N.J. 1991) which is incorporated by reference herein.
Alternatively, the pharmaceutical composition of the invention further comprises one or more additional therapeutic agent.
Alternatively, the vector is a gene delivery vector for site-directed mutagenesis, preferably a viral vector issued for delivering a gene editing system (CRISP, TALEN, etc...) comprising i) at least one sgRNA, or crRNA and tracrRNA, targeting the genomic sequence (target DNA) encoding the protein of interest, and ii) a structure-guided endonuclease such as an RNA-guided endonuclease. Any suitable naturally occurring, or engineered, RNA-guided endonuclease can be employed as long as it is effective for specifically binding a target DNA of the invention and it may be selected from the non-limiting group comprising Cas9, Cpf1, and FEN-1. Preferably, the RNA-guided endonuclease is Cas9.
In a further embodiment, the invention provides a method of treating and/or preventing a disease such as e.g. a neurodegenerative disease or condition, or an associated symptom, in a subject in need thereof, the method comprising administering to said subject a pharmaceutical composition of the invention. Examples of neurodegenerative diseases or conditions comprise Parkinson, Schizophrenia, Huntington, Attention Deficit and Hyperactivity Disorder, and Addiction.
In one embodiment, the protein of the invention is selected from the group comprising from SEQ ID No. 1, SEQ ID No 2, SEQ ID No. 3, SEQ ID No. 4, SEQ ID No. 5, SEQ ID No. 6, SEQ ID No. 7, SEQ ID No. 8, SEQ ID No. 9, SEQ ID No. 10, SEQ ID No. 11, SEQ ID No. 12, SEQ ID No. 13, SEQ ID No. 14, SEQ ID No. 15, SEQ ID No. 16, SEQ ID No. 17, SEQ ID No. 18, SEQ ID No. 19, SEQ ID No. 20, SEQ ID No. 21, SEQ ID No. 22, SEQ ID No. 23, SEQ ID No. 24, SEQ ID No. 25, SEQ ID No. 26, SEQ ID No. 27, SEQ ID No. 28, SEQ ID No. 29, SEQ ID No. 30, SEQ ID No. 33, or an active fragment or analog thereof, or any combination thereof.
The protein, fragment or analog thereof, of the invention, can be prepared by a variety of methods and techniques known in the art such as for example chemical synthesis or recombinant techniques as described in Maniatis et al. 1982, Molecular Cloning, A laboratory Manual, Cold Spring Harbor Laboratory.
The protein, fragment or analog thereof, of the invention, is/are preferably produced, recombinantly, in a cell expression system. A wide variety of unicellular host cells are useful in expressing the polynucleotide sequence (e.g. DNA) encoding the protein, fragment or analog thereof of this invention. These hosts may include well known eukaryotic and prokaryotic hosts, such as strains of E. coli, Pseudomonas, Bacillus, Streptomyces, fungi such as yeasts, and animal cells, such as CHO, YB/20, NSO, SP2/0, RI. 1, B-W and L-M cells, African Green Monkey kidney cells (e. g., COS 1, COS 7, BSCI, BSC40, and BMTIO), insect cells (e. g., Sf9), and human cells and plant cells in tissue culture.
Preferably, the protein of the invention, or active fragment or analog thereof, is characterized in that the ligand sensing and/or signaling response is modified when compared to the native sequence of said protein, or active fragment or analog thereof.
More preferably, the ligand sensing and/or signaling response is enhanced or decreased when compared to the native sequence of said protein, or active fragment or analog thereof. Even more preferably, the ligand sensing and/or signaling response is enhanced when compared to the native sequence of said protein, or active fragment or analog thereof, as shown in the examples and figures.
The invention also contemplates an in-vivo or in-vitro method of identifying an agent that modulates the signaling response of a variant of a protein, or an active fragment or analog thereof, wherein the sequence of said protein variant, or active fragment thereof, comprises at least one mutation in the microswitch region, the method comprising:
The embodiments described for the method also apply to the data processing and computer implemented program according to the present invention mutatis mutandis.
Further particular advantages and features of the invention will become more apparent from the following non-limitative description of at least one embodiment of the invention.
The present examples are intended to illustrate the invention in a non-limitative manner since any feature of an embodiment may be combined with any other feature of a different embodiment in an advantageous manner.
In the following examples, the present invention is applied on GPCR to generate variants of GPCR but the invention is not limited to this class of receptor. The present invention can also be applied to other class of protein receptor.
GPCRs are prime examples of signal transduction across biological membranes. These receptors have evolved to activate several key intracellular pathways and physiological processes in response to a large diversity of extracellular stimuli. GPCR dysfunctions including misfolding, stability loss, and altered signaling activity are often associated with serious diseases. Furthermore, drugs triggering severe side-effects have been found to activate undesired signaling pathways. Hence, the mapping of receptor stability and signal transduction pathways determinants would greatly enhance the development of effective therapies and personalized medicine approaches but has remained very challenging.
In the present example, the point was to generate (in other words engineer) dopamine D2 receptor variants, i.e. proteins of the invention.
In the present example, the 3D structures of ligand free and ligand bound states were engineered by homology modeling.
For the ligand free 3D structures, the closest structurally characterized homologs available were used as templates to model the inactive and active state. The inactive state conformations were modeled starting from the X-ray structure of the antagonist bound dopamine D3 receptor (DRD3, PDBID: 3PBL) sharing 48% sequence identity with D2. The active state conformations were modeled from the active state GPCR structures of two distant homologs: opsin (23% sequence identity with D2) bound to Gt (PDBID: 3CAP, 3DQB) and beta-2 adrenergic receptor (26% sequence identity with D2) in complex with ligand agonist and heterotrimeric Gs (PDBID: 3SN6). Models of D2 inactive and active states were generated without bound ligand or G protein using the homology mode of RosettaMembrane.
From the above-mentioned simulations, ensembles of low energy models were clustered and centers of the most populated clusters were selected as templates for each ligand-free state in the design calculations of stability microswitches. An inactive and an active state models of D2 WT were selected therefrom.
Ligand-bound D2 models were generated by performing ligand docking simulations onto the inactive and active state ligand free D2 models obtained as described above. The ligand conformer libraries were generated using Omega (OpenEye Inc.) with default parameters from Rosetta ARLS. Ligand docking was performed using a combination of Monte Carlo moves, sidechain repacking, and gradient-based minimization with the Rosetta all-atom potential developed for protein-ligand docking. Receptor backbone and sidechain torsions along with ligand torsions, position, and orientation were optimized simultaneously.
All ligand-bound receptor models for a given state (i.e. inactive or active) were gathered together and the 5% lowest-energy models were selected and ranked based on the binding energy with the ligand. The selected ligand bound models were then clustered based on structural similarity of the bound ligand conformation. The representative model of the largest cluster was selected corresponding to the ligand bound model of the D2 receptor in a given state; i.e. ligand-bound D2 inactive and ligand-bound D2 active state conformations.
Allosteric site(s), i.e. microswitches, were defined by mapping the allosteric residues identified using Molecular Dynamics simulations performed on the homologous B2AR receptor onto the above-mentioned D2 structures.
GPCR structures are composed of 3 main regions: the extracellular ligand binding pocket, the intracellular G-protein binding domain and the “transmission” transmembrane (TM) region which connects the two binding regions and allows them to communicate. GPCRs typically switch from inactive to active state conformations upon activating agonist ligand and G-protein binding at the extracellular and intracellular domains, respectively. The structural rearrangements upon receptor activation involve large intracellular reorientations of transmembrane helices (TMH), notably TMH6 and TMH7 and smaller scale movements of individual amino-acids named microswitch across the entire TM domain.
In the present example 1, the TM domain of the selected ligand free and ligand bound models were scanned to identify microswitches with novel allosteric properties at the position 205. Usually, larger number of positions are designed simultaneously.
In the present example, the following amino acids were identified as microswitch:
Random mutagenesis using all 20 possible amino acids at position 205 and search+selection using a Genetic algorithm were performed to optimize the following fitness function :
When the microswitch is selected for stability in the active state (A) only:
Wstability = 1; Wallostery = 0; the microswitch with the highest fitness was Isoleucine 205.
When the microswitch is selected for higher sensitivity to ligand binding only,
Wstability = 0; Wallostery = 1; the microswitch with the highest fitness was Methionine 205.
T205I: ΔG-stability or ΔΔEs = 5.4; ΔG-coupling or ΔΔEc = 0.1
T205M: ΔG-stability or ΔΔEs = 0.1; ΔG-coupling or ΔΔEc = 0.8
Regarding the T205I mutation, since ΔG-stability/ΔΔEs >0, the protein obtained by the method of the invention should have an increased constitutive activity compared to the native receptor. This prediction was confirmed by in vitro testing where this increased of constitutive activity was observed experimentally (top panel of
Regarding the T205M mutation, since ΔG-coupling/ΔΔEc >0, the protein obtained by the method of the invention should have a higher sensitivity for the ligand binding (ligand = dopamine and serotonin). This prediction was confirmed by in vitro testing where this increased of sensitivity was observed experimentally (bottom panel of
Computational modeling of DRD2 active and inactive states. The inactive and active state structures of DRD2 WT were modeled from the close homolog inactive state structure of DRD3 (3PBL) and the more distant homolog active state structure of β2AR, respectively, using the software iPHoLD (Draper-Joyce, C. J. et al. Structure of the adenosine-bound human adenosine A1 receptor-Gi complex. Nature 558, 559-563 (2018)). Low energy representative models of the DRD2 WT were selected for design calculations, as previously described.
Computational design of residue microswitches. The TM region of DRD2 was subjected to complete multi-state design using a fitness function selecting residue microswitches stabilizing the active state structure while decreasing the allosteric coupling between the extracellular ligand binding site and the inactive state conformation of the intracellular G protein binding site. Conformational stability was assessed using an all-atom energy function developed for membrane protein modeling and design. Allosteric couplings were approximated by the correlated dynamic fluctuations between allosteric residues using normal mode calculations (Danev, R. & Baumeister, W. Cryo-EM single particle analysis with the Volta phase plate. Elife 5, 439 (2016)).
Computational de novo design of minimal intracellular loop 3. The kinematic loop design protocol of Rosetta was performed to de novo design short loop structures and sequences connecting the cytoplasmic ends of TM5 and TM6. Loop structures and sequences were selected to maximize stability and optimize conformation for Gαi binding. Loop lengths of three to nine amino acids were tested and the predicted models were clustered, selected by energy and structurally analyzed for distortions of the TM⅚ helical tips. Several designed loops of five to seven residues adopted stable helical structures enabling proper Gαi binding. Selected sequences from these loops with further refined with RosettaMembrane on active state DRD2 models onto which a peptide corresponding to the Gαi C-terminal α5 helix was docked. The final selected 7 residue long designed ICL3 was predicted to retain native receptor-G protein TM contacts while stabilizing the DRD2 active conformation.
Mutagenesis and expression of receptors in HEK293 cells for stability assays. The designed SEQ ID No. 33 contains 5 mutations: T2055.54I, M3746.36L, V3786.40Y, V3816.43L and V4217.48I and a designed minimal ICL3 where residues 222-360 at ICL3 of the WT DRD2 (sequence #22) were replaced with residues LVNTN, as designed in the optimized 7-residue ICL3 described above (with one wild-type amino acid flanking each side of the insertion). The resulting construct was obtained by Quickchange PCR mutagenesis (Stratagene) performed on the HA-tagged human long isoform DRD2 gene (coding for the sequence #22) in the pcDNA3.1 (+) vector. Sequenced mutant plasmids were transiently transfected using lipofectamine (Invitrogen) into HEK293T cells for DRD2 as described (Chen, K.-Y. M., Keri, D. & Barth, P. Computational design of G Protein-Coupled Receptor allosteric signal transductions. Nat. Chem. Biol. 16, 77-86 (2020).). Briefly, 5 × 106 cells were plated on 10 cm tissue culture plates and grown overnight. This was followed by transfection with Lipofectamine 2000 (Invitrogen) and 2 µg of DNA per plate. After 24 hours, the cells were washed with PBS and grown in standard growth medium (DMEM supplemented with L-glutamine (2 mM), penicillin (100 mg/mL), streptomycin (100 mg/mL), and fetal bovine serum (10%)) for an additional 24 hours prior to harvesting.
Membrane preparation and receptor purification. Membranes were prepared from transfected cells using sucrose gradient centrifugation as previously described (Chen et al., Nat Chem Biol 2019; doi: 10.1038/s41589-019-0407-2). Briefly, cells from 10 cm plates were collected by cell scraper with PBS solution. Cells were pelleted and resuspended in cold hypotonic buffer (1 mM Tris-HCL, pH 6.8, 10 mM EDTA, protease inhibitor cocktail). Cells were forced through a 26-gauge needle three times. The cell lysate was layered onto a 38% sucrose solution in buffer A (150 mM NaCl, 1 mM MgCl, 10 mM EDTA, 20 mM Tris-HCI, pH 6.8, protease inhibitor cocktail) in SW-28 ultracentrifuge tubes. Cells were centrifuged at 15,000 rpm at 4° C. for 20 minutes, followed by collection of the interface band with an 18-gauge needle. The collected solution was transferred to Ti-45 ultracentrifuge tubes and the volume brought up to 50 mL with buffer A. The sample was spun at 40,000 rpm at 4° C. for 30 minutes. The membrane pellets from each 10 cm plate was resuspended in 0.5 mL buffer A and stored at -80° C. in 100 uL aliquots.
Receptor variants were partially purified from thawed membrane preparations immediately prior to assaying via anti-HA agarose beads. Membrane preparations were solubilized with 1% n-dodecylmaltoside (DDM) for one hour at 4° C., and loaded onto anti-HA agarose beads (Pierce/Thermo Scientific) for one hour at 4° C. The beads were washed with TBS with 0.1% DDM wash buffer three times and HA-tagged receptor variants were eluted with HA peptide (1 mg/mL in TBS with 0.1% DDM).
Expression and purification of G proteins. Gi2 subunits were cloned into pFastbacl (Invitrogen) followed by transformation into DH10α cells. Recombinant bacmid DNA was isolated and transfected in Sf9 insect cells with Cellfectin II (invitrogen). The transfected cells were grown at 28° C. for 72 hours followed by centrifugation in 15 mL Falcon tubes to pellet cell debris. The supernatant was saved as P1 viral stock. Virus was amplified by infecting Sf9 cells with P1 viral stock solution at a 2-fold multiplicity-of-infection and cultured for 72 hours prior to harvesting. This amplification process was repeated to generate a high-titer P3, which was used for infection and protein expression. P3 stock was used to infect Sf9 cells at an MOI of 4 and harvested 48 hours post infection. Cells were washed three times in ice-cold PBS and resuspended in homogenization buffer (10 mM Tris-HCI, 25 mM NaCl, 10 mM MgCl2, 1 mM EGTA, 1 mM DTT, protease inhibitor cocktail, 10 uM GDP, pH 8.0). Gi2 was purified and reconstituted as described previously (Chen et al., Nat Chem Biol 2019; doi: 10.1038/s41589-019-0407-2).
G protein activation assays. D2DR variants were assayed for their ability to induce guanine nucleotide exchange by the G protein Gi2. To measure constitutive activity the reaction mixture consisted of 4 uM Gi2, 20 uM of [35S]-GTPγS mix, 50 mM Tris-HCI, pH 7.2, 100 mM NaCl, 4 mM MgCl2, 1 mM dithiothreitol. Receptor concentrations were ~10 nM per sample. Reactions were started by adding 150 uL partially purified receptor samples to 300 uL of reaction mixture and incubating on ice over a period of time from 0-30 minutes for timecourse measurements. To measure ligand induced D2DR activities, increasing amounts of dopamine or spiperone were added to the reaction mixtures. Maximal ligand efficacies were obtained with final ligand concentrations of 20 uM and 1 uM for dopamine and spiperone, respectively. Reactions were stopped by filter binding onto Millipore nitrocellulose filters or Whatman fiberglass filters pretreated with polyethylenimine. Filters were washed three times with ice-cold TBS prior to incubation with scintillation fluid. Radioactivity counts were measured on a Beckman LS6000 scintillation counter. Statistical significance of differences in constitutive or ligand-induced activities was assessed by student t-tests.
Ligand binding affinity. To determine the binding affinities of dopamine and spiperone to D2DR variants, anti-HA agarose affinity purified receptor samples prepared as described above were titrated with [3H]-dopamine or [3H]-spiperone in a total volume of 150 uL per sample, incubated for 1 hour on ice followed by loading onto Millipore nitrocellulose filters or Whatman fiberglass filters pretreated with polyethylenimine and washed for scintillation counting as mentioned above. For competition binding, receptor samples were pre-incubated with competing cold ligand for 30 min on ice prior to adding saturating amount of radiolabeled hot ligand (1.2 uM [3H]-dopamine or 10 nM [3H]spiperone). Competition binding and apparent thermostability curves were fitted using GraphPad Prism software and student t-tests were performed to assess statistical significance.
Apparent agonist-bound D2DR stability. Apparent stability of agonist-bound D2DR variants was determined by measuring either receptor binding to agonist (apparent meting temperature) or receptor activities (apparent receptor half-life) as a function of temperature. To measure apparent melting temperature, HA agarose affinity purified receptor samples prepared as described above were first pre-incubated at increasing temperatures for 30 min. The fraction of receptor binding dopamine was then assessed by radioligand binding assay described above. To measure apparent receptor half-life, purified receptor samples were pre-incubated at 37° C. over a time period from 0-60 minutes prior to addition to the reaction mixture containing Gi, [35S]-GTPγS and 20 uM dopamine as described above. Apparent melting temperatures and active state half-life curves were fitted using GraphPad Prism software and analyzed for statistical significance by student t-tests.
The Inventors computationally designed and stabilized the intracellular loop 3 of rhodopsin in a conformation that activates the downstream effector transducing in accordance with the method of the invention. Two sets of mutations located between transmembrane helical (TMH) 6 and 7 (i.e. M257Y on TMH6 and 1305A on TMH7) and in intracellular loop 3 (ICL3) (K231 E.E2321.T251R) predicted to shift the receptor equilibrium toward the active state were generated.
As predicted, while both TMHs 6/7 mutants displayed much larger constitutive activities than WT opsin, the rate of transducin activation of M257Y.I305A was higher than that of M257Y alone (data not shown, manuscript in preparation).
The ICL3 triple mutant (K231E.E232I.T251R) displayed a dramatically increased constitutive activity compared to WT reaching higher than 40% of the light-induced maximal activity and an increased apparent stability (data not shown, manuscript in preparation).
The Inventors showed that receptor enhanced signaling is achieved through designed polar residues which act as functional switches by forming optimal interaction networks only in the active state loop conformation. Remarkably, designed opsins display increased conformational stability and up to 7.5 fold enhancement in transducin activation compared to wild-type opsin while retinal binding and light-induced activities remain unperturbed.
This example further demonstrates that activating microswitches and soluble loop conformations strongly modulate membrane receptor activity and suggests a novel computational protein engineering strategy to manipulate receptor mediated cellular signaling.
While the embodiments have been described in conjunction with a number of embodiments, it is evident that many alternatives, modifications and variations would be or are apparent to those of ordinary skill in the applicable arts. Accordingly, this disclosure is intended to embrace all such alternatives, modifications, equivalents and variations that are within the scope of this disclosure. This is for example particularly the case regarding the different apparatuses and methods which can be used.
| Number | Date | Country | Kind |
|---|---|---|---|
| 19189259.5 | Jul 2019 | EP | regional |
| 20177770.3 | Jun 2020 | EP | regional |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/EP2020/070907 | 7/24/2020 | WO |
