US20130137856A1 - Protein binding domains stabilizing functional conformational states of gpcrs and uses thereof - Google Patents

Protein binding domains stabilizing functional conformational states of gpcrs and uses thereof Download PDF

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US20130137856A1
US20130137856A1 US13/810,657 US201113810657A US2013137856A1 US 20130137856 A1 US20130137856 A1 US 20130137856A1 US 201113810657 A US201113810657 A US 201113810657A US 2013137856 A1 US2013137856 A1 US 2013137856A1
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gpcr
protein
protein binding
receptor
conformational state
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Jan Steyaert
Els Pardon
Toon Laeremans
Søren Rasmussen
Brian Kobilka
Juan Fung
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Leland Stanford Junior University
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Assigned to BOARD OF TRUSTEES OF THE LELAND STANFORD JUNIOR UNIVERSITY,THE reassignment BOARD OF TRUSTEES OF THE LELAND STANFORD JUNIOR UNIVERSITY,THE ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: FUNG, JUAN JOSE, KOBILKA, BRIAN, RASMUSSEN, SOREN G. F.
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Definitions

  • the disclosure relates to the field of GPCR structure biology and signaling.
  • the disclosure relates to protein binding domains directed against or capable of specifically binding to a functional conformational state of a G protein-coupled receptor (GPCR).
  • GPCR G protein-coupled receptor
  • the disclosure provides protein binding domains that are capable of increasing the stability of a functional conformational state of a GPCR, in particular, increasing the stability of a GPCR in its active conformational state.
  • the protein binding domains hereof can be used as a tool for the structural and functional characterization of G-protein-coupled receptors bound to various natural and synthetic ligands, as well as for screening and drug discovery efforts targeting GPCRs.
  • the invention also encompasses the diagnostic, prognostic and therapeutic usefulness of these protein binding domains for GPCR-related diseases.
  • G protein-coupled receptors are the largest family of membrane proteins in the human genome. They play essential roles in physiologic responses to a diverse set of ligands, such as biogenic amines, amino acids, peptides, proteins, prostanoids, phospholipids, fatty acids, nucleosides, nucleotides, Ca 2+ ions, odorants, bitter and sweet tastants, pheromones and protons (Heilker et al. 2009). GPCRs are therapeutic targets for a broad range of diseases.
  • GPCRs are characterized by seven transmembrane domains with an extracellular amino terminus and an intracellular carboxyl terminus, and are also called seven transmembrane or heptahelical receptors (Rosenbaum et al. 2009). Rhodopsin, a GPCR that is highly specialized for the efficient detection of light, has been the paradigm for GPCR signaling and structural biology due to its biochemical stability and natural abundance in bovine retina (Hofmann et al. 2009). In contrast, many GPCRs exhibit complex functional behavior by modulating the activity of multiple G protein isoforms, as well as G protein independent signaling pathways (e.g., ⁇ -arrestin).
  • a GPCR may exhibit basal activity toward a specific signaling pathway, even in the absence of a ligand.
  • Orthosteric ligands that act on a GPCR can have a spectrum of effects on downstream signaling pathways. Full agonists maximally activate the receptor. Partial agonists elicit a submaximal stimulation, even at saturating concentrations. Inverse agonists inhibit basal activity, while neutral antagonists have no effect on basal activity, but competitively block binding of other ligands.
  • rhodopsin can be crystallized from unmodified protein isolated from native tissue, these other GPCRs required expression in recombinant systems, stabilization of an inactive state by an inverse agonist and biochemical modifications to stabilize the receptor protein.
  • the first crystal structure of the ⁇ 2 AR was stabilized by a selective Fab (Rasmussen et al. 2007).
  • Subsequent structures of the ⁇ 2 AR and the A2 adenosine receptor were obtained with the aid of protein engineering: the insertion of T4Lysozyme into the third intracellular loop as originally described for the ⁇ 2 AR (Rosenbaum et al. 2007).
  • crystals of the avian PAR were grown from protein engineered with amino and carboxyl terminal truncations and deletion of the third intracellular loop, as well as six amino acid substitutions that enhanced thermostability of the purified protein (Warne et al. 2008).
  • a first aspect hereof relates to a protein binding domain capable of specifically binding to a functional conformational state of a GPCR.
  • the protein binding domain is capable of stabilizing a functional conformational state of a GPCR upon binding.
  • the protein binding domain is capable of inducing a functional conformational state in a GPCR upon binding.
  • the functional conformational state of a GPCR is selected from the group consisting of a basal conformational state, or an active conformational state or an inactive conformational state.
  • the functional conformational state of a GPCR is an active conformational state.
  • the protein binding domain is capable of specifically binding to an agonist-bound GPCR and/or enhances the affinity of a GPCR for an agonist.
  • the protein binding domain is capable of increasing the thermostability of a functional conformational state of a GPCR upon binding.
  • the protein binding domain is capable of specifically binding to a conformational epitope of the functional conformational state of a GPCR.
  • the conformational epitope is an intracellular epitope. More preferably, the conformational epitope is comprised in a binding site for a downstream signaling protein. Most preferably, the conformational epitope is comprised in the G protein binding site.
  • the protein binding domain hereof comprises an amino acid sequence that comprises four framework regions and three complementarity-determining regions, or any suitable fragment thereof. More preferably, the protein binding domain is derived from a camelid antibody. Most preferably, the protein binding domain comprises a nanobody sequence, or any suitable fragment thereof.
  • the nanobody comprises a sequence selected from the group consisting of SEQ ID NOS:1-29, or any suitable fragment thereof.
  • the GPCR is a mammalian protein, or a plant protein, or a microbial protein, or a viral protein, or an insect protein.
  • the mammalian protein can be a human protein.
  • the GPCR is chosen from the group comprising a GPCR of the Glutamate family of GPCRs, a GPCR of the Rhodopsin family of GPCRs, a GPCR of the Adhesion family of GPCRs, a GPCR of the Frizzled/Taste2 family of GPCRs, and a GPCR of the Secretin family of GPCRs.
  • the GPCR is an adrenergic receptor, such as an ⁇ -adrenergic receptor or a ⁇ -adrenergic receptor, or wherein the GPCR is a muscarinic receptor, such as an M 1 -muscarinic receptor or an M 2 -muscarinic receptor, or an M 3 -muscarinic receptor, or an M 4 -muscarinic receptor, or an M 5 -muscarinic receptor, or wherein the GPCR is an angiotensin receptor, such as an angiotensin II type 1 receptor or an angiotensin II type 2 receptor.
  • adrenergic receptor such as an ⁇ -adrenergic receptor or a ⁇ -adrenergic receptor
  • a muscarinic receptor such as an M 1 -muscarinic receptor or an M 2 -muscarinic receptor, or an M 3 -muscarinic receptor, or an M 4 -muscarinic receptor, or an M 5 -muscarinic
  • a second aspect hereof relates to a complex comprising: (i) a protein binding domain hereof, (ii) a GPCR in a functional conformational state, and (iii) optionally, a receptor ligand.
  • the receptor ligand can be chosen from the group comprising a small molecule, a protein, a peptide, a protein scaffold, a nucleic acid, an ion, a carbohydrate or an antibody, or any suitable fragment thereof.
  • the complex can be in a solubilized form or immobilized to a solid support. In particular, the complex is crystalline.
  • the invention further encompasses a crystalline form of a complex comprising (i) a protein binding domain, (ii) a GPCR in a functional conformational state, and (iii) optionally, a receptor ligand, wherein the crystalline form is obtained by the use of a protein binding domain hereof.
  • a third aspect hereof relates to a cellular composition
  • a cellular composition comprising a protein binding domain hereof and/or a complex hereof.
  • the protein binding domain comprised in the cellular composition is capable of stabilizing and/or inducing a functional conformational state of a GPCR upon binding of the protein binding domain.
  • a fourth aspect hereof relates to the use of a protein binding domain hereof or a complex hereof or a cellular composition hereof to stabilize and/or induce a functional conformational state of a GPCR.
  • the protein binding domain or the complex or the cellular composition can be used to crystallize and/or to solve the structure of a GPCR in a functional conformational state.
  • crystal structure is determined of a GPCR in a functional conformational state.
  • the above method of determining a crystal structure of a GPCR may further comprise the step of obtaining the atomic coordinates from the crystal.
  • the protein binding domain or the complex or the cellular composition can be used to capture a GPCR in a functional conformational state, optionally with a receptor ligand or with one or more downstream signaling proteins.
  • a method of capturing a GPCR in a functional conformational state comprising the steps of:
  • the above methods of capturing a GPCR in a functional conformational state may comprise the step of purifying the complex.
  • protein binding domain or the complex, or the cellular composition, hereof, in screening and/or identification programs for conformation-specific (drug) compounds or ligands of a GPCR.
  • the above-described method for identifying compounds further comprises the step of forming a complex comprising the protein binding domain and the GPCR in a functional conformational state, hereof.
  • the complex may further comprise a receptor ligand, which can be chosen from the group comprising a small molecule, a protein, a peptide, a protein scaffold, a nucleic acid, an ion, a carbohydrate or an antibody, or any suitable fragment thereof.
  • the receptor ligand is a full agonist, or a partial agonist, or an inverse agonist, or an antagonist.
  • the protein binding domain and/or the complex are provided in essentially purified form.
  • the protein binding domain and/or the complex are provided in a solubilized form.
  • the protein binding domain and/or the complex is immobilized to a solid support.
  • the protein binding domain and/or the complex is provided in a cellular composition.
  • the test compound used in the above-described method for identifying compounds is selected from the group comprising a polypeptide, a peptide, a small molecule, a natural product, a peptidomimetic, a nucleic acid, a lipid, a lipopeptide, a carbohydrate, an antibody or any fragment derived thereof, such as Fab, Fab′ and F(ab′)2, Fd, single-chain Fvs (scFv), single-chain antibodies, disulfide-linked Fvs (dsFv) and fragments comprising either a VL or VH domain, a heavy chain antibody (hcAb), a single domain antibody (sdAb), a minibody, the variable domain derived from camelid heavy chain antibodies (VHH or nanobody), the variable domain of the new antigen receptors derived from shark antibodies (VNAR), a protein scaffold including an alphabody, protein A, protein G, designed ankyrin-repeat domains (DARPins),
  • test compounds are labeled.
  • a library of test compounds may be used.
  • the above-described method for identifying compounds may be a high-throughput screening method.
  • the protein binding domain or the complex or the cellular composition can be used to diagnose or prognose a GPCR-related disease, such as cancer, autoimmune disease, infectious disease, neurological disease, or cardiovascular disease.
  • a GPCR-related disease such as cancer, autoimmune disease, infectious disease, neurological disease, or cardiovascular disease.
  • a fifth aspect hereof relates to a pharmaceutical composition
  • a pharmaceutical composition comprising a therapeutically effective amount of a protein binding domain hereof and at least one of a pharmaceutically acceptable carrier, adjuvant or diluent.
  • a sixth aspect hereof relates to the use of a protein binding domain hereof or a pharmaceutical composition hereof to modulate GPCR signaling activity, more specifically, to block G-protein-mediated signaling.
  • the protein binding domain or the pharmaceutical composition hereof may also be used in the treatment of a GPCR-related disease, such as cancer, autoimmune disease, infectious disease, neurological disease, or cardiovascular disease.
  • a GPCR-related disease such as cancer, autoimmune disease, infectious disease, neurological disease, or cardiovascular disease.
  • a seventh aspect hereof relates to a kit comprising a protein binding domain hereof or a complex hereof or a cellular composition hereof.
  • FIG. 1 ⁇ 2 AR-specific nanobodies bind and stabilize an active state of the receptor:
  • Panel a Representative trace of size-exclusion chromatography (SEC) for Nb80.
  • Purified ⁇ 2 AR (20 ⁇ M) bound to an agonist ( ⁇ 2 AR-agonist) was incubated with and without 40 ⁇ M Nb80 (black and blue, respectively) for two hours at room temperature prior to analyzing by FPLC.
  • the ⁇ 2 AR-agonist elution peak increases in UV absorbance (280 nm) and elutes at an earlier volume than ⁇ 2 AR-agonist alone, with a simultaneous decrease in the Nb80 elution peak (green), suggesting ⁇ 2 AR-agonist-Nb80 complex formation.
  • Incubation of ⁇ 2 AR (20 ⁇ M) bound to an inverse agonist with Nb80 resulted in a smaller shift and smaller increase in UV absorbance when compared to the ⁇ 2 AR-agonist-Nb80 complex.
  • Panel b Dose-response competition binding experiments on Sf9 insect cell membranes expressing ⁇ 2 AR. Seven nanobodies that bound ⁇ 2 AR by SEC were individually incubated for 90 minutes at room temperature with ⁇ 2 AR-expressing membranes. All seven nanobodies increased the affinity of ⁇ 2 AR for ( ⁇ )-isoproterenol (Table 3). Nb80 (blue) was selected as the lead nanobody. Data represent the mean ⁇ s.e. of two independent experiments performed in triplicate.
  • Panel c A fluorescence-based functional assay using monobromobimane- (mBBR-) labeled purified receptor shows that 1 ⁇ M Nb80 (blue) stabilizes a more active state of the ⁇ 2 AR (bound to the full agonist ( ⁇ )-isoproterenol) when compared with receptor in the absence of Nb80 (black).
  • the active state is characterized by a quenching of mBBr fluorescence and a redshift in mBBr fluorescence (Yao et al. 2009).
  • FIG. 2 Representative dot blots showing specificity of nanobodies to the tertiary structure of the ⁇ 2 AR:
  • Panel a Equal amounts of native or SDS-denatured purified ⁇ 2 AR bound to an agonist (top and middle, respectively), or native ⁇ 2 AR bound to an inverse agonist (bottom) were spotted in triplicate on nitrocellulose strips. The strips were blocked with 5% nonfat dry milk in PBS (pH 7.4) with 0.05% TWEEN®-20 and then incubated with 1 mg/ml of indicated nanobodies diluted in blocking buffer. Binding of nanobodies was detected by an anti-histidine (a-6His) primary mouse antibody, followed by incubation with goat-anti-mouse IR-800-labeled secondary antibody.
  • a-6His anti-histidine
  • M1 antibody which recognizes the linear FLAG epitope, was labeled with Alexa-688 and directly detected ⁇ 2 AR. Dot blots were scanned and imaged using the Odyssey Infrared Imaging System (L1-cor Biosciences). Blots detecting nanobodies were processed separately from blots detecting ⁇ 2 AR by M1 since two different channels (800 nm versus 700 nm, respectively) were used for imaging; therefore, blots cannot be directly compared and quantified (i.e., comparison of binding of nanobodies versus M1 binding are only qualitative in nature).
  • Panel b Representative dot blots showing nanobodies with reduced binding to natively folded ⁇ 2 AR.
  • FIG. 3 Selective binding of nanobodies to the active state of the receptor: Purified ⁇ 2 AR (20 ⁇ M) bound to an agonist was incubated with and without 40 ⁇ M nanobodies (black and blue, respectively) for two hours at room temperature prior to analyzing by size exclusion chromatography. Samples of ⁇ 2 AR (20 ⁇ M) bound to an inverse agonist in the presence of nanobodies (red) were also analyzed.
  • the ⁇ 2 AR-agonist elution peak increases in UV absorbance (280 nm) and elutes at an earlier volume (black line) than ⁇ 2 AR-agonist alone (blue), with a simultaneous decrease in the Nb80 elution peak (green), suggesting ⁇ 2 AR-agonist-Nb80 complex formation.
  • the formation of a ⁇ 2 AR-inverse agonist-Nb80 complex is not observed (red line).
  • FIG. 4 Selective binding of nanobodies to the active state of the receptor: Purified ⁇ 2 AR (20 ⁇ M) bound to an agonist was incubated with and without 40 ⁇ M nanobodies (black and blue, respectively) for two hours at room temperature prior to analyzing by size exclusion chromatography.
  • FIG. 5 Fluorescence emission spectra showing nanobody-induced conformational changes of monobromobimane-labeled ⁇ 2 AR: Nanobodies that increase agonist binding affinity for the ⁇ 2 AR stabilize an active state of the receptor.
  • a fluorescence-based functional assay using mono-bromobimane- (mBBr-) labeled purified receptor shows that 1 ⁇ M of nanobodies 65, 67, 69, 71, 72 and 84 (red) stabilize a more active state of the ⁇ 2 AR (bound to the full agonist isoproterenol) when compared with receptor in the absence of nanobodies (black).
  • This active state is characterized by a quenching of mBBr fluorescence and a redshift in mBBr fluorescence (Yao et al. 2009).
  • FIG. 6 Effect of Nb80 on ⁇ 2 AR structure and function:
  • Panel A The cartoon illustrates the movement of the environmentally sensitive bimane probe attached to Cys265 6.27 in the cytoplasmic end of TM6 from a more buried, hydrophobic environment to a more polar, solvent-exposed position during receptor activation that results in a decrease in the observed fluorescence in FIG. 6 , Panels B and C.
  • Panels B and C Fluorescence emission spectra showing ligand-induced conformational changes of monobromobimane-labeled ⁇ 2 AR reconstituted into high density lipoprotein particles (mBB- ⁇ 2 AR/HDL) in the absence (black solid line) or presence of full agonist isoproterenol (ISO, green wide dashed line), inverse agonist ICI-118,551 (ICI, black dashed line), G s heterotrimer (red solid line), nanobody-80 (Nb80, blue solid lines), and combinations of G s with ISO (red wide dashed line), Nb80 with ISO (blue wide dashed line), and Nb80 with ICI (blue dashed line).
  • ISO green wide dashed line
  • ICI inverse agonist ICI-118,551
  • G s heterotrimer red solid line
  • nanobody-80 nanobody-80
  • combinations of G s with ISO red wide dashed line
  • Nb80 with ISO blue wide dashed line
  • Panels D through F Ligand binding curves for ISO competing against [ 3 H]-dihydroalprenolol ([ 3 H]-DHA) for Panel D, ⁇ 2 AR/HDL reconstituted with G s heterotrimer in the absence or presence GTP ⁇ S, Panel E, ⁇ 2 AR/HDL in the absence and presence of Nb80, and Panel F, ⁇ 2 AR-T4L/HDL in the absence and presence of Nb80. Error bars represent standard errors.
  • FIG. 7 Packing of the agonist- ⁇ 2 AR-T4L-Nb80 complex in crystals farmed in lipidic cubic phase: Three different views of the structure of ⁇ 2 AR indicated in orange, Nb80 in blue, and agonist in green. T4 lysozyme (T4L) could not be modeled due to poor electron density; its likely position is indicated by the light blue circle with black dashed lines connected to the intracellular ends of TM5 and TM6 where it is fused in the ⁇ 2 AR-T4L construct. PyMOL (http://www.pymol.org) was used for the preparation of all figures.
  • FIG. 8 Comparison of the inverse agonist and agonist-Nb80 stabilized crystal structures of the ⁇ 2 AR: The structure of inverse agonist carazolol-bound ⁇ 2 AR-T4L ( ⁇ 2 AR-Cz) is shown in blue with the carazolol in yellow. The structure of agonist bound and Nb80 stabilized ⁇ 2 AR-T4L ( ⁇ 2 AR-Nb80) is shown in orange with agonist in green. These two structures were aligned using Pymol align function.
  • Panel A Side view of the superimposed structures showing significant structural changes in the intracellular and G protein facing part of the receptors.
  • Panel B Side view following 90 degrees rotation on the vertical axis.
  • Panel C Comparison of the extracellular ligand binding domains showing modest structural changes.
  • FIG. 9 Nb80 stabilized intracellular domain compared to inactive ⁇ 2 AR and opsin structures:
  • Panel A Side view of ⁇ 2 AR (orange) with CDRs of Nb80 in light blue (CDR1) and blue (CDR3) interacting with the receptor.
  • Panel B Closer view focusing on CDRs 1 and 3 entering the ⁇ 2 AR. Side chains in TM3, 5, 6, and 7 within 4 ⁇ of the CDRs are shown. The larger CDR3 penetrates 13 ⁇ into the receptor.
  • Panel C Interaction of CDR1 and CDR3 viewed from the intracellular side.
  • Panel D The agonist bound and Nb80 stabilized ⁇ 2 AR-T4L ( ⁇ 2 AR-Nb80) is superimposed with the carazolol-bound inactive structure of ⁇ 2 AR-T4L ( ⁇ 2 AR-Cz).
  • the ionic lock interaction between Asp3.49 and Arg3.50 of the DRY motif in TM3 is broken in the ⁇ 2 AR-Nb80 structure.
  • the intracellular end of TM6 is moved outward and away from the core of the receptor.
  • the arrow indicates a 11.4 ⁇ change in distance between the ⁇ -carbon of Glu6.30 in the structures of ⁇ 2 AR-Cz and ⁇ 2 AR-Nb80.
  • the intracellular ends of TM3 and TM7 move toward the core by 4 ⁇ and 2.5 ⁇ , respectively, while TM5 moves outward by 6 ⁇ .
  • Panel E The ⁇ 2 AR-Nb80 structure superimposed with the structure of opsin crystallized with the C-terminal peptide of G t (transducin).
  • FIG. 10 Nb80 stabilized intracellular domain of ⁇ 2 AR compared to opsin structures:
  • Panel A Interactions between the ⁇ 2 AR and Nb80.
  • Panel B Interactions between opsin and the carboxyl terminal peptide of transducin.
  • FIG. 11 Rearrangement of transmembrane segment packing interactions upon agonist binding:
  • Panel A Packing interactions that stabilize the inactive state are observed between Pro211 in TM5, Ile121 in TM3, Phe282 in TM6 and Asn316 in TM5.
  • Panel B The inward movement of TM5 upon agonist binding disrupts the packing of Ile121 and Pro211 resulting in a rearrangement of interactions between Ile121 and Phe282. These changes contribute to a rotation and outward movement of TM6 and an inward movement of TM7.
  • FIG. 12 Amino acid sequences of the different nanobodies raised against ⁇ 2 AR: Sequences have been aligned using standard software tools. CDRs have been defined according to IMGT numbering (Lefranc et al. 2003).
  • FIG. 13 Effect of Nb80 on the thermal stability of the ⁇ 2 AR receptor: Comparison of the melting curves of detergent-solubilized (DDM) agonist-bound (isoproterenol) ⁇ 2 AR in the presence and absence of Nb80.
  • the apparent melting temperature for ⁇ 2 AR without Nb80 is 12.0° C.
  • the apparent melting temperature for ⁇ 2 AR with Nb80 is 24° C.
  • FIG. 14 Effect of Nb80 on the temperature-induced aggregation of the ⁇ 2 AR receptor:
  • FIG. 14A Detergent-solubilized (DDM) ⁇ 2 AR was heated for ten minutes at 50° C. in the presence of Nb80 or isoproterenol and the aggregation of the receptor was analyzed by SEC.
  • DDM Detergent-solubilized
  • FIG. 14B Temperature dependence of the isoproterenol-bound receptor in the absence of Nb80.
  • FIG. 15 Nb80 has little effect on ⁇ 2 AR binding to the inverse agonist ICI-118,551: ⁇ 2 AR (Panel A) or ⁇ 2 AR-T4L (Panel B) was reconstituted into HDL particles and agonist competition binding experiments were performed in the absence or presence of Nb80.
  • FIG. 16 Nb80 increases ⁇ 2 AR affinity for agonists but not for antagonists: Competitive ligand binding experiments were performed on commercial insect cell-derived membranes containing full-length ⁇ 2 AR in the absence or presence of Nb80. Dose-dependent radio-ligand displacement curves in presence of Nb80 and an irrelevant Nanobody (Irr Nb) for two representative agonists (isoproterenol, procaterol) and two representative antagonists (ICI-118,551 and carvedilol).
  • Irr Nb irrelevant Nanobody
  • FIG. 17 Sequence alignment of human ⁇ 1 AR and human ⁇ 2 AR: Amino acids of the ⁇ 2 -adrenoreceptor that interact with Nb80 in the ⁇ 2 AR-Nb80 interface are underlined.
  • FIG. 18 Nb80 selectively binds the active conformation of the human ⁇ 1 AR receptor: Ligand binding curves for agonists and inverse agonists competing against [ 3 H]-dihydroalprenolol ([ 3 H]-DHA).
  • FIG. 18A Agonist Isoproterenol (ISO) binding to ⁇ 2 AR in the presence and absence of Nb80.
  • FIG. 18B Inverse agonist ICI-118,551 (ICI) binding to ⁇ 2 AR in the presence and absence of Nb80.
  • FIG. 18C Agonist Isoproterenol (ISO) binding to ⁇ 1 AR in the presence and absence of Nb80.
  • FIG. 18D Inverse agonist CGP20712A (CPG) binding to ⁇ 1 AR in the presence and absence of Nb80.
  • protein binding domain refers generally to any non-naturally occurring molecule or part thereof that is able to bind to a protein or peptide using specific intermolecular interactions.
  • a variety of molecules can function as protein binding domains, including, but not limited to, proteinaceous molecules (protein, peptide, protein-like or protein containing), nucleic acid molecules (nucleic acid, nucleic acid-like, nucleic acid containing), and carbohydrate molecules (carbohydrate, carbohydrate-like, carbohydrate containing). A more detailed description can be found further in the specification.
  • polypeptide As used herein, the terms “polypeptide,” “protein,” and “peptide” are used interchangeably herein, and refer to a polymeric form of amino acids of any length, which can include coded and non-coded amino acids, chemically or biochemically modified or derivatized amino acids, and polypeptides having modified peptide backbones.
  • multiprotein complex or “protein complex” or simply “complex” refer to a group of two or more associated polypeptide chains. Proteins in a protein complex are linked by non-covalent protein-protein interactions. The “quaternary structure” is the structural arrangement of the associated folded proteins in the protein complex.
  • a “multimeric complex” refers to a protein complex as defined herein, which may further comprise a non-proteinaceous molecule.
  • nucleic acid molecule As used herein, the terms “nucleic acid molecule,” “polynucleotide,” “polynucleic acid,” and “nucleic acid” are used interchangeably and refer to a polymeric form of nucleotides of any length, either deoxyribonucleotides or ribonucleotides, or analogs thereof. Polynucleotides may have any three-dimensional structure, and may perform any function, known or unknown.
  • Non-limiting examples of polynucleotides include a gene, a gene fragment, exons, introns, messenger RNA (mRNA), transfer RNA, ribosomal RNA, ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence, control regions, isolated RNA of any sequence, nucleic acid probes, and primers.
  • the nucleic acid molecule may be linear or circular.
  • ligand or “receptor ligand” means a molecule that specifically binds to a GPCR, either intracellularly or extracellularly.
  • a ligand may be, without the purpose of being limitative, a protein, a (poly)peptide, a lipid, a small molecule, a protein scaffold, a nucleic acid, an ion, a carbohydrate, an antibody or an antibody fragment, such as a nanobody (all as defined herein).
  • a ligand may be a synthetic or naturally occurring.
  • a ligand also includes a “native ligand,” which is a ligand that is an endogenous, natural ligand for a native GPCR.
  • a “modulator” is a ligand that increases or decreases the signaling activity of a GPCR (i.e., via an intracellular response) when it is in contact with, e.g., binds to, a GPCR that is expressed in a cell.
  • This term includes agonists, full agonists, partial agonists, inverse agonists, and antagonists, of which a more detailed description can be found further in the specification.
  • conformation or conformational state of a protein refers generally to the range of structures that a protein may adopt at any instant in time.
  • determinants of conformation or conformational state include a protein's primary structure as reflected in a protein's amino acid sequence (including modified amino acids) and the environment surrounding the protein.
  • the conformation or conformational state of a protein also relates to structural features such as protein secondary structures (e.g., ⁇ -helix, ⁇ -sheet, among others), tertiary structure (e.g., the three-dimensional folding of a polypeptide chain), and quaternary structure (e.g., interactions of a polypeptide chain with other protein subunits).
  • Post-translational and other modifications to a polypeptide chain such as ligand binding, phosphorylation, sulfation, glycosylation, or attachments of hydrophobic groups, among others, can influence the conformation of a protein.
  • environmental factors such as pH, salt concentration, ionic strength, and osmolality of the surrounding solution, and interaction with other proteins and co-factors, among others, can affect protein conformation.
  • the conformational state of a protein may be determined by either functional assay for activity or binding to another molecule or by means of physical methods such as X-ray crystallography, NMR, or spin labeling, among other methods.
  • a “specific conformational state” is any subset of the range of conformations or conformational states that a protein may adopt.
  • a “functional conformation” or a “functional conformational state,” as used herein, refers to the fact that proteins possess different conformational states having a dynamic range of activity, in particular, ranging from no activity to maximal activity. It should be clear that “a functional conformational state” is meant to cover any conformational state of a GPCR, having any activity, including no activity; and is not meant to cover the denatured states of proteins.
  • CDR complementarity-determining region
  • H and VL heavy chains
  • VH and VL light chains
  • CDR regions account for the basic specificity of the antibody for a particular antigenic determinant structure. Such regions are also referred to as “hypervariable regions.”
  • the CDRs represent non-contiguous stretches of amino acids within the variable regions but, regardless of species, the positional locations of these critical amino acid sequences within the variable heavy and light chain regions have been found to have similar locations within the amino acid sequences of the variable chains.
  • variable heavy and light chains of all canonical antibodies each have three CDR regions, each non-contiguous with the others (termed L1, L2, L3, H1, H2, H3) for the respective light (L) and heavy (H) chains.
  • Nanobodies in particular, generally comprise a single amino acid chain that can be considered to comprise four “framework sequences or regions” or FRs and three “complementarity-determining regions” or CDRs.
  • the nanobodies have three CDR regions, each non-contiguous with the others (termed CDR1, CDR2, CDR3).
  • the delineation of the FR and CDR sequences is based on the IMGT unique numbering system for V-domains and V-like domains (Lefranc et al. 2003).
  • an “epitope,” as used herein, refers to an antigenic determinant of a polypeptide.
  • An epitope could comprise three amino acids in a spatial conformation, which is unique to the epitope. Generally an epitope consists of at least 4, 5, 6, or 7 such amino acids, and more usually, consists of at least 8, 9, or 10 such amino acids. Methods of determining the spatial conformation of amino acids are known in the art and include, for example, x-ray crystallography and two-dimensional nuclear magnetic resonance.
  • a “conformational epitope,” as used herein, refers to an epitope comprising amino acids in a spatial conformation that is unique to a folded three-dimensional conformation of the polypeptide.
  • a conformational epitope consists of amino acids that are discontinuous in the linear sequence that come together in the folded structure of the protein.
  • a conformational epitope may also consist of a linear sequence of amino acids that adopts a conformation that is unique to a folded three-dimensional conformation of the polypeptide (and not present in a denatured state).
  • conformational epitopes consist of amino acids that are discontinuous in the linear sequences of one or more polypeptides that come together upon folding of the different folded polypeptides and their association in a unique quaternary structure.
  • conformational epitopes may here also consist of a linear sequence of amino acids of one or more polypeptides that come together and adopt a conformation that is unique to the quaternary structure.
  • specificity refers to the ability of a protein binding domain, in particular, an immunoglobulin or an immunoglobulin fragment, such as a nanobody, to bind preferentially to one antigen versus a different antigen, and does not necessarily imply high affinity.
  • affinity refers to the degree to which a protein binding domain, in particular, an immunoglobulin such as an antibody, or an immunoglobulin fragment such as a nanobody, binds to an antigen so as to shift the equilibrium of antigen and protein binding domain toward the presence of a complex formed by their binding.
  • an antibody (fragment) of high affinity will bind to the available antigen so as to shift the equilibrium toward high concentration of the resulting complex.
  • the dissociation constant is commonly used to describe the affinity between the protein binding domain and the antigenic target.
  • the dissociation constant is lower than 10 ⁇ 5 M.
  • the dissociation constant is lower than 10 ⁇ 6 M; more preferably, lower than 10 ⁇ 7 M.
  • the dissociation constant is lower than 10 ⁇ 8 M.
  • telomere binding domain in particular, an immunoglobulin such as an antibody, or an immunoglobulin fragment such as a nanobody, to preferentially bind to a particular antigen that is present in a homogeneous mixture of different antigens.
  • a specific binding interaction will discriminate between desirable and undesirable antigens in a sample, in some embodiments more than about ten- to 100-fold or more (e.g., more than about 1000- or 10,000-fold).
  • the terms particularly refer to the ability of a protein binding domain (as defined herein) to preferentially recognize and/or bind to a particular conformational state of a GPCR as compared to another conformational state.
  • an active state-selective protein binding domain will preferentially bind to a GPCR in an active conformational state and will not, or to a lesser degree, bind to a GPCR in an inactive conformational state, and will thus have a higher affinity for the active conformational state.
  • the terms “specifically bind,” “selectively bind,” “preferentially bind,” and grammatical equivalents thereof, are used interchangeably herein.
  • the terms “conformational specific” or “conformational selective” are also used interchangeably herein.
  • an “antigen,” as used herein, means a molecule capable of eliciting an immune response in an animal.
  • the molecule comprises a conformational epitope of a GPCR in a particular conformational state that is not formed or less accessible in another conformational state of the GPCR.
  • a “deletion” is defined here as a change in either amino acid or nucleotide sequence in which one or more amino acid or nucleotide residues, respectively, are absent as compared to an amino acid sequence or nucleotide sequence of a parental polypeptide or nucleic acid.
  • a deletion can involve deletion of about two, about five, about ten, up to about twenty, up to about thirty, or up to about fifty or more amino acids.
  • a protein or a fragment thereof may contain more than one deletion.
  • a deletion may also be a loop deletion, or an N- and/or C-terminal deletion.
  • an “insertion” or “addition” is that change in an amino acid or nucleotide sequence that has resulted in the addition of one or more amino acid or nucleotide residues, respectively, as compared to an amino acid sequence or nucleotide sequence of a parental protein.
  • “Insertion” generally refers to addition of one or more amino acid residues within an amino acid sequence of a polypeptide, while “addition” can be an insertion or refer to amino acid residues added at an N- or C-terminus, or both termini.
  • an insertion or addition is usually of about one, about three, about five, about ten, up to about twenty, up to about thirty, or up to about fifty or more amino acids.
  • a protein or fragment thereof may contain more than one insertion.
  • substitution results from the replacement of one or more amino acids or nucleotides by different amino acids or nucleotides, respectively, as compared to an amino acid sequence or nucleotide sequence of a parental protein or a fragment thereof. It is understood that a protein or a fragment thereof may have conservative amino acid substitutions that have substantially no effect on the protein's activity. By “conservative substitutions” is intended combinations such as gly, ala; val, ile, leu, met; asp, glu; asn, gln; ser, thr; lys, arg; cys, met; and phe, tyr, trp.
  • Crystal or “crystalline structure,” as used herein, refers to a solid material, whose constituent atoms, molecules, or ions are arranged in an orderly repeating pattern extending in all three spatial dimensions.
  • the process of forming a crystalline structure from a fluid or from materials dissolved in the fluid is often referred to as “crystallization” or “crystallogenesis.” Protein crystals are almost always grown in solution. The most common approach is to lower the solubility of its component molecules gradually. Crystal growth in solution is characterized by two steps: nucleation of a microscopic crystallite (possibly having only 100 molecules), followed by growth of that crystallite, ideally to a diffraction-quality crystal.
  • X-ray crystallography is a method of determining the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and diffracts into many specific directions. From the angles and intensities of these diffracted beams, a crystallographer can produce a three-dimensional picture of the density of electrons within the crystal. From this electron density, the mean positions of the atoms in the crystal can be determined, as well as their chemical bonds, their disorder and various other information.
  • atomic coordinates refers to a set of three-dimensional coordinates for atoms within a molecular structure.
  • atomic coordinates are obtained using X-ray crystallography according to methods well known to those of ordinary skill in the art of biophysics. Briefly described, X-ray diffraction patterns can be obtained by diffracting X-rays off a crystal. The diffraction data are used to calculate an electron density map of the unit cell comprising the crystal; the maps are used to establish the positions of the atoms (i.e., the atomic coordinates) within the unit cell.
  • X-ray crystallography contains standard errors.
  • atomic coordinates can be obtained using other experimental biophysical structure determination methods that can include electron diffraction (also known as electron crystallography) and nuclear magnetic resonance (NMR) methods.
  • atomic coordinates can be obtained using molecular modeling tools, which can be based on one or more of ab initio protein folding algorithms, energy minimization, and homology-based modeling. These techniques are well known to persons of ordinary skill in the biophysical and bioinformatic arts.
  • Solving the structure refers to determining the arrangement of atoms or the atomic coordinates of a protein, and is often done by a biophysical method, such as X-ray crystallography.
  • test compound or “test compound” or “candidate compound” or “drug candidate compound,” as used herein, describes any molecule, either naturally occurring or synthetic that is tested in an assay, such as a screening assay or drug discovery assay.
  • these compounds comprise organic or inorganic compounds.
  • the compounds include polynucleotides, lipids or hormone analogs that are characterized by low molecular weights.
  • Other biopolymeric organic test compounds include small peptides or peptide-like molecules (peptidomimetics) comprising from about two to about forty amino acids and larger polypeptides comprising from about forty to about five hundred amino acids, such as antibodies, antibody fragments or antibody conjugates.
  • Test compounds can also be protein scaffolds.
  • test compound libraries may be used, such as combinatorial or randomized libraries that provide a sufficient range of diversity. Examples include, but are not limited to, natural compound libraries, allosteric compound libraries, peptide libraries, antibody fragment libraries, synthetic compound libraries, fragment-based libraries, phage-display libraries, and the like. A more detailed description can be found further in the specification.
  • determining As used herein, the terms “determining,” “measuring,” “assessing,” “monitoring” and “assaying” are used interchangeably and include both quantitative and qualitative determinations.
  • biologically active refers to a GPCR having a biochemical function (e.g., a binding function, a signal transduction function, or an ability to change conformation as a result of ligand binding) of a naturally occurring GPCR.
  • a biochemical function e.g., a binding function, a signal transduction function, or an ability to change conformation as a result of ligand binding
  • terapéuticaally effective amount mean the amount needed to achieve the desired result or results.
  • pharmaceutically acceptable means a material that is not biologically or otherwise undesirable, i.e., the material may be administered to an individual along with the compound without causing any undesirable biological effects or interacting in a deleterious manner with any of the other components of the pharmaceutical composition in which it is contained.
  • GPCRs Structural information on GPCRs will provide insight into the structural, functional and biochemical changes involved in signal transfer from the receptor to intracellular interacting proteins (G proteins, ⁇ -arrestins, etc.) and will delineate ways to interfere with these pharmacologically relevant interactions. Efforts to obtain and crystallize GPCRs are, therefore, of great importance. However, this is a particularly difficult endeavor due to the biochemical challenges in working with GPCRs and the inherent instability of these complexes in detergent solutions. Also, the intrinsic conformational flexibility of GPCRs complicates high-resolution structure analysis of GPCRs alone because growing diffraction-quality crystals require stable, conformationally homogenous proteins (Kobilka et al. 2007). Provided are new experimental and analytical tools to capture or “freeze” functional conformational states of a GPCR of interest, in particular, its active conformational state, allowing the structural and functional analysis of the GPCR, including high resolution structural analysis and many applications derived thereof.
  • Described herein is a protein binding domain that is capable of specifically binding to a functional conformational state of a GPCR.
  • the protein binding domain hereof can be any non-naturally occurring molecule or part thereof (as defined hereinbefore) that is capable of specifically binding to a functional conformational state of a target GPCR.
  • the protein binding domains as described herein are protein scaffolds.
  • the term “protein scaffold” refers generally to folding units that form structures, particularly protein or peptide structures, that comprise frameworks for the binding of another molecule, for instance, a protein (see, e.g., J. Skerra, 2000, for review).
  • a protein binding domain can be derived from a naturally occurring molecule, e.g., from components of the innate or adaptive immune system, or it can be entirely artificially designed.
  • a protein binding domain can be immunoglobulin-based or it can be based on domains present in proteins including, but limited to, microbial proteins, protease inhibitors, toxins, fibronectin, lipocalins, single chain antiparallel coiled coil proteins or repeat motif proteins.
  • protein binding domains examples include, but are not limited to: antibodies, heavy chain antibodies (hcAb), single domain antibodies (sdAb), minibodies, the variable domain derived from camelid heavy chain antibodies (VHH or nanobodies), the variable domain of the new antigen receptors derived from shark antibodies (VNAR), alphabodies, protein A, protein G, designed ankyrin-repeat domains (DARPins), fibronectin type III repeats, anticalins, knottins, engineered CH2 domains (nanoantibodies), peptides and proteins, lipopeptides (e.g., pepducins), DNA, and RNA (see, e.g., Gebauer & Skerra, 2009; Skerra, 2000; Starovasnik et al.
  • G-protein-coupled receptors are polypeptides that share a common structural motif having seven regions of between 22 to 24 hydrophobic amino acids that form seven alpha helices, each of which spans the membrane. Each span is identified by number, i.e., transmembrane-1 (TM1), transmembrane-2 (TM2), etc.
  • transmembrane helices are joined by regions of amino acids between transmembrane-2 and transmembrane-3, transmembrane-4 and transmembrane-5, and transmembrane-6 and transmembrane-7 on the exterior, or “extracellular” side, of the cell membrane, referred to as “extracellular” regions 1, 2 and 3 (EC1, EC2 and EC3), respectively.
  • transmembrane helices are also joined by regions of amino acids between transmembrane-1 and transmembrane-2, transmembrane-3 and transmembrane-4, and transmembrane-5 and transmembrane-6 on the interior, or “intracellular” side, of the cell membrane, referred to as “intracellular” regions 1, 2 and 3 (IC1, IC2 and IC3), respectively.
  • the “carboxy” (“C”) terminus of the receptor lies in the intracellular space within the cell, and the “amino” (“N”) terminus of the receptor lies in the extracellular space outside of the cell. Any of these regions are readily identifiable by analysis of the primary amino acid sequence of a GPCR.
  • GPCR structure and classification is generally well known in the art and further discussion of GPCRs may be found in Probst et al. 1992, Marchese et al. 1994, Lagerström & Schioth 2008, Rosenbaum et al. 2009, and the following books: Jurgen Wess (Ed), Structure Function Analysis of G Protein - Coupled Receptors published by Wiley-Liss (first edition; Oct. 15, 1999); Kevin R. Lynch (Ed), Identification and Expression of G Protein - Coupled Receptors published by John Wiley & Sons (March 1998); and Tatsuya Haga (Ed), G Protein - Coupled Receptors , published by CRC Press (Sep. 24, 1999); and Steve Watson (Ed) G-Protein Linked Receptor Factsbook, published by Academic Press (1st edition; 1994).
  • GPCRs can be grouped on the basis of sequence homology into several distinct families. Although all GPCRs have a similar architecture of seven membrane-spanning ⁇ -helices, the different families within this receptor class show no sequence homology to one another, thus suggesting that the similarity of their transmembrane domain structure might define common functional requirements.
  • a comprehensive view of the GPCR repertoire was possible when the first draft of the human genome became available. Fredriksson and colleagues divided 802 human GPCRs into families on the basis of phylogenetic criteria. This showed that most of the human GPCRs can be found in five main families, termed Glutamate, Rhodopsin, Adhesion, Frizzled/Taste2 and Secretin (Fredriksson et al. 2003).
  • the protein binding domain is directed against or is capable of specifically binding to a functional conformational state of a GPCR, wherein the GPCR is chosen from the group comprising a GPCR of the Glutamate family of GPCRs, a GPCR of the Rhodopsin family of GPCRs, a GPCR of the Adhesion family of GPCRs, a GPCR of the Frizzled/Taste2 family of GPCRs, and a GPCR of the Secretin family of GPCRs.
  • the GPCR is a mammalian protein, or a plant protein, or a microbial protein, or a viral protein, or an insect protein. Even more preferably, the GPCR is a human protein.
  • Rhodopsin a representative of this family, is the first GPCR for which the structure has been solved (Palczewski et al. 2000).
  • ⁇ 2 AR the first receptor interacting with a diffusible ligand for which the structure has been solved (Rosenbaum et al. 2007) also belongs to this family.
  • class B GPCRs or Class 2 (Foord et al. 2005) receptors have recently been subdivided into two families: adhesion and secretin (Fredriksson et al. 2003).
  • Adhesion and secretin receptors are characterized by a relatively long amino terminal extracellular domain involved in ligand-binding. Little is known about the orientation of the transmembrane domains, but it is probably quite different from that of rhodopsin.
  • Ligands for these GPCRs are hormones, such as glucagon, secretin, gonadotropin-releasing hormone and parathyroid hormone.
  • the Glutamate family receptors (Class C or Class 3 receptors) also have a large extracellular domain, which functions like a “Venus fly trap” since it can open and close with the agonist bound inside.
  • Family members are the metabotropic glutamate, the Ca 2+ -sensing and the ⁇ -aminobutyric acid (GABA)-B receptors.
  • GPCRs include, without limitation, serotonin olfactory receptors, glycoprotein hormone receptors, chemokine receptors, adenosine receptors, biogenic amine receptors, melanocortin receptors, neuropeptide receptors, chemotactic receptors, somatostatin receptors, opioid receptors, melatonin receptors, calcitonin receptors, PTH/PTHrP receptors, glucagon receptors, secretin receptors, latrotoxin receptors, metabotropic glutamate receptors, calcium receptors, GABA-B receptors, pheromone receptors, the protease-activated receptors, the rhodopsins and other G-protein-coupled seven transmembrane segment receptors.
  • GPCRs also include these GPCR receptors associated with each other as homomeric or heteromeric dimers or as higher-order oligomers.
  • the amino acid sequences (and the nucleotide sequences of the cDNAs that encode them) of GPCRs are readily available, for example by reference to GenBank (on the World Wide Web at ncbi.nlm.nih.gov/entrez).
  • the GPCR is chosen from the group comprising the adrenergic receptors, preferably the ⁇ -adrenergic receptors, such as the ⁇ 1 -adrenergic receptors and the ⁇ 2 -adrenergic receptors, and the ⁇ -adrenergic receptors, such as the ⁇ 1 -adrenergic receptors, the ⁇ 2 -adrenergic receptors and the ⁇ 3 -adrenergic receptors; or from the group comprising the muscarinic receptors, preferably the M 1 -muscarinic receptors, the M 2 -muscarinic receptors, the M 3 -muscarinic receptors, the M 4 -muscarinic receptors and the M 5 -muscarinic receptors; or from the group of the angiotensin receptors, preferably the angiotensin II type 1 receptor, the angiotensin II type 2 receptor and other atypical angiotensin II receptors
  • a GPCR may be any naturally occurring or non-naturally occurring (i.e., altered by man) polypeptide.
  • naturally occurring in reference to a GPCR means a GPCR that is naturally produced (for example and without limitation, by a mammal, more specifically by a human, or by a virus, or by a plant, or by an insect, amongst others). Such GPCRs are found in nature.
  • non-naturally occurring in reference to a GPCR means a GPCR that is not naturally occurring. Wild-type GPCRs that have been made constitutively active through mutation, and variants of naturally occurring GPCRs are examples of non-naturally occurring GPCRs.
  • Non-naturally occurring GPCR may have an amino acid sequence that is at least 80% identical to, at least 90% identical to, at least 95% identical to or at least 99% identical to, a naturally occurring GPCR.
  • the ⁇ 2 -adrenergic receptor as a particular non-limiting example of a GPCR within the scope hereof, it should be clear from the above that in addition to the human ⁇ 2 -adrenergic receptor (e.g., the sequence described by Genbank accession number NP — 000015), the mouse ⁇ 2 -adrenergic receptor (e.g., as described by Genbank accession no. NM — 007420) or other mammalian ⁇ 2 -adrenergic receptor may also be employed.
  • the human ⁇ 2 -adrenergic receptor e.g., the sequence described by Genbank accession number NP — 000015
  • the mouse ⁇ 2 -adrenergic receptor e.g., as described by Genbank accession no
  • a “human ⁇ 2 -adrenergic receptor” has an amino acid sequence that is at least 95% identical to (e.g., at least 95% or at least 98% identical to) the naturally occurring “human ⁇ 2 -adrenoreceptor” of Genbank accession number NP — 000015.
  • the disclosure also envisages GPCRs with a loop deletion, or an N- and/or C-terminal deletion, or a substitution, or an insertion or addition in relation to its amino acid or nucleotide sequence, or any combination thereof (as defined hereinbefore, and see also Example section). It is further expected that the protein binding domains hereof will generally be capable of binding to all naturally occurring or synthetic analogs, variants, mutants, or alleles of the GPCR.
  • ELISA enzyme linked immunosorbent assays
  • surface Plasmon resonance assays phage display, and the like, which are common practice in the art, for example, and discussed in Sambrook et al. (2001), Molecular Cloning, A Laboratory Manual , Third Ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
  • a unique label or tag will often be used, such as a peptide label, a nucleic acid label, a chemical label, a fluorescent label, or a radio frequency tag, as described further herein.
  • GPCRs are conformationally complex membrane proteins that exhibit a spectrum-functional behavior in response to natural and synthetic ligands. Defining the pathway from agonist binding to protein activation will require a combination of crystal structures of different conformational states of the receptor under investigation in complex with various natural or synthetic ligands (including structures of active agonist-bound states and GPCR-G protein complexes), which will provide snapshots along the activation pathway.
  • the protein binding domain is capable of stabilizing or otherwise increasing the stability of a particular functional conformational state of a GPCR.
  • the protein binding domain is capable of inducing the formation of a functional conformational state in a GPCR upon binding the GPCR.
  • the functional conformation state of the GPCR can be a basal conformational state, or an active conformational state or an inactive conformational state.
  • the protein binding domain is capable of stabilizing a GPCR in its active conformational state and/or is capable of forcing the GPCR to adopt its active conformational state upon binding.
  • a functional conformational state of a GPCR refers to the retaining or holding of a GPCR in a subset of the possible conformations that it could otherwise assume, due to the effects of the interaction of the GPCR with the protein binding domain hereof.
  • a protein that is “conformationally trapped” or “conformationally fixed” or “conformationally locked” or “conformationally frozen,” as used herein is one that is held in a subset of the possible conformations that it could otherwise assume, due to the effects of the interaction of the GPCR with the protein binding domain hereof.
  • a protein binding domain that specifically or selectively binds to a specific conformation or conformational state of a protein refers to a protein binding domain that binds with a higher affinity to a protein in a subset of conformations or conformational states than to other conformations or conformational states that the protein may assume.
  • protein binding domains that specifically or selectively bind to a specific conformation or conformational state of a protein will stabilize this specific conformation or conformational state.
  • a functional conformational state refers to the fact that proteins, in particular, membrane proteins such as GPCRs, possess many different conformational states having a dynamic range of activity, in particular, ranging from no activity to maximal activity (reviewed in Kobilka and Deupi, 2007). It should be clear that “a functional conformational state” is not meant to cover the denatured states of proteins.
  • the functional versatility of GPCRs is inherently coupled to the flexibility of these proteins resulting in such a spectrum of conformations.
  • the conformational energy landscape is intrinsically coupled to such factors as the presence of bound ligands (effector molecules, agonists, antagonists, inverse agonists, etc.), the lipid environment or the binding of interacting proteins.
  • a “basal conformational state” can be defined as a low energy state of the receptor in the absence of a ligand (as defined hereinbefore, e.g., effector molecules, agonists, antagonists, inverse agonists).
  • the probability that a protein will undergo a transition to another conformational state is a function of the energy difference between the two states and the height of the energy barrier between the two states.
  • the energy of ligand binding can be used either to alter the energy barrier between the two states, or to change the relative energy levels between the two states, or both. Changing of the energy barrier would have an effect on the rate of transition between the two states, whereas changing the energy levels would have an effect on the equilibrium distribution of receptors in two states. Binding of an agonist or partial agonist would lower the energy barrier and/or reduce the energy of the more active conformational state relative to the inactive conformational state.
  • An inverse agonist would increase the energy barrier and/or reduce the energy of the “inactive state conformation” relative to the “active conformation.” Coupling of the receptor to its G protein could further alter the energy landscape.
  • the activities of integral membrane proteins, including GPCRs, are also affected by the structures of the lipid molecules that surround them in the membrane. Membrane proteins are not rigid entities, and deform to ensure good hydrophobic matching to the surrounding lipid bilayer. One important parameter is the hydrophobic thickness of the lipid bilayer, defined by the lengths of the lipid fatty acyl chains. Also, the structure of the lipid headgroup region is likely to be important in defining the structures of those parts of a membrane protein that are located in the lipid headgroup region. Among other lipids, palmitoylation and binding of cholesterol to GPCRs may also play a structural role inside monomeric receptors and contribute to the formation/stabilization of receptor oligomers (Lee 2004; Chini and Parenti 2009).
  • Receptor ligands may be “orthosteric” ligands (both natural and synthetic), meaning that they bind to the receptor's active site and are further classified according to their efficacy or, in other words, to the effect they have on receptor signaling through a specific pathway.
  • an “agonist” refers to a ligand that, by binding a receptor, increases the receptor's signaling activity. Full agonists are capable of maximal receptor stimulation; partial agonists are unable to elicit full activity even at saturating concentrations. Partial agonists can also function as “blockers” by preventing the binding of more robust agonists.
  • an “antagonist” refers to a ligand that binds a receptor without stimulating any activity.
  • An “antagonist” is also known as a “blocker” because of its ability to prevent binding of other ligands and, therefore, block agonist-induced activity.
  • an “inverse agonist” refers to an antagonist that, in addition to blocking agonist effects, reduces receptors' basal or constitutive activity below that of the unliganded receptor.
  • GPCRs regulate cellular physiology
  • ligands such as hormones, neurotransmitters or sensory stimuli
  • agonist-bound GPCRs associate with GPCR kinases (GRKs), leading to receptor phosphorylation.
  • GPCR kinases A common outcome of GPCR phosphorylation by GRKs is a decrease in GPCR interactions with G proteins and an increase in GPCR interactions with arrestins, which sterically interdict further G-protein signaling, resulting in receptor desensitization.
  • GPCRs also associate with various proteins outside the families of general GPCR-interacting proteins (G proteins, GRKs, arrestins and other receptors). These GPCR-selective partners can mediate GPCR signaling, organize GPCR signaling through G proteins, direct GPCR trafficking, anchor GPCRs, in particular, subcellular areas and/or influence GPCR pharmacology (Ritter and Hall 2009).
  • ligands may also be “biased ligands” with the ability to selectively stimulate a subset of a receptor's signaling activities, for example, the selective activation of G-protein or ⁇ -arrestin function.
  • Such ligands are known as “biased ligands,” “biased agonists” or “functionally selective agonists.”
  • ligand bias can be an imperfect bias characterized by a ligand stimulation of multiple receptor activities with different relative efficacies for different signals (non-absolute selectivity) or can be a perfect bias characterized by a ligand stimulation of one receptor activity without any stimulation of another known receptor activity.
  • allosteric regulators or otherwise “allosteric modulators,” “allosteric ligands” or “effector molecules” bind at an allosteric site of a GPCR (that is, a regulatory site physically distinct from the protein's active site).
  • allosteric modulators are non-competitive because they bind receptors at a different site and modify receptor function even if the endogenous ligand also is binding. Because of this, allosteric modulators are not limited to simply turning a receptor on or off, the way most drugs are.
  • Allosteric regulators that enhance the protein's activity are referred to herein as “allosteric activators” or “positive allosteric modulators,” whereas, those that decrease the protein's activity are referred to herein as “allosteric inhibitors” or otherwise “negative allosteric modulators.”
  • the protein binding domain hereof is capable of specifically binding to an agonist-bound GPCR and/or enhances the affinity of a GPCR for an agonist. It is preferred that the protein binding domain is capable of increasing the affinity for the agonist at least two-fold, at least five-fold and, more preferably, at least ten-fold upon binding to the receptor as measured by a decrease in EC 50 , IC 50 , K d , or any other measure of affinity or potency known to one of skill in the art.
  • the protein binding domain hereof is capable of increasing the stability of a functional conformational state of a GPCR under non-physiological conditions induced by dilution, concentration, buffer composition, heating, cooling, freezing, detergent, chaotropic agent, or pH.
  • thermodynamic studies of membrane protein folding and stability have proven to be extremely challenging, and complicated by the difficulty of finding conditions for reversible folding.
  • thermostabilize refers to the functional rather than to the thermodynamic properties of a GPCR and to the protein's resistance to irreversible denaturation induced by thermal and/or chemical approaches including, but not limited to, heating, cooling, freezing, chemical denaturants, pH, detergents, salts, additives, proteases or temperature. Irreversible denaturation leads to the irreversible unfolding of the functional conformations of the protein, loss of biological activity and aggregation of the denaturated protein.
  • thermo)stabilize As used herein, apply to GPCRs embedded in lipid particles or lipid layers (for example, lipid monolayers, lipid bilayers, and the like) and to GPCRs that have been solubilized in detergent.
  • the protein binding domain hereof is capable of increasing the thermostability of a functional conformational state of a GPCR, preferably, an active conformational state of a GPCR. In relation to an increased stability to heat, this can be readily determined by measuring ligand binding or by using spectroscopic methods such as fluorescence, CD or light scattering that are sensitive to unfolding at increasing temperatures (see also Example section). It is preferred that the protein binding domain is capable of increasing the stability as measured by an increase in the thermal stability of a GPCR in a functional conformational state with at least 2° C., at least 5° C., at least 8° C., and more preferably at least 10° C. or 15° C. or 20° C.
  • the protein binding domain is capable of increasing the thermal stability of a functional conformation of a GPCR in complex with a ligand such as, but not restricted to, an agonist, an inverse agonist, an antagonist and/or a modulator or an inhibitor of the GPCR or the GPCR-dependent signaling pathway.
  • a ligand such as, but not restricted to, an agonist, an inverse agonist, an antagonist and/or a modulator or an inhibitor of the GPCR or the GPCR-dependent signaling pathway.
  • the protein binding domain hereof is capable of increasing the stability in the presence of a detergent or a chaotrope of a functional conformational state of a GPCR.
  • the protein binding domain is capable of increasing the stability to denaturation induced by thermal or chemical approaches of the active conformational state of a GPCR.
  • the GPCR is typically incubated for a defined time in the presence of a test detergent or a test chaotropic agent and the stability is determined using, for example, ligand binding or a spectroscoptic method, optionally at increasing temperatures as discussed above.
  • the protein binding domain hereof is capable of increasing the stability to extreme pH of a functional conformational state of a GPCR.
  • the protein binding domain is capable of increasing the stability to extreme pH of the active conformational state of a GPCR.
  • a typical test pH would be chosen, for example, in the range 6 to 8, the range 5.5 to 8.5, the range 5 to 9, the range 4.5 to 9.5, more specifically in the range 4.5 to 5.5 (low pH) or in the range 8.5 to 9.5 (high pH).
  • the protein binding domains hereof may generally be directed against any desired GPCR and may, in particular, be directed against any conformational epitope of any GPCR, preferably a functional conformational state of any GPCR, more preferably an active conformational state of a GPCR (all as defined hereinbefore). More particularly, the conformational epitope can be part of an intracellular or extracellular region, or an intramembranous region, or a domain or loop structure of any desired GPCR.
  • the protein binding domains may be directed against any suitable extracellular region, domain, loop or other extracellular conformational epitope of a GPCR, but is preferably directed against one of the extracellular parts of the transmembrane domains or more preferably against one of the extracellular loops that link the transmembrane domains.
  • the protein binding domains may be directed against any suitable intracellular region, domain, loop or other intracellular conformational epitope of a GPCR, but is preferably directed against one of the intracellular parts of the transmembrane domains or, more preferably, against one of the intracellular loops that link the transmembrane domains.
  • a protein binding domain that specifically binds to a “three-dimensional” epitope or “conformational” epitope specifically binds to a tertiary (i.e., three-dimensional) structure of a folded protein, and binds at much reduced (i.e., by a factor of at least 2, 5, 10, 50 or 100) affinity to the linear (i.e., unfolded, denatured) foam of the protein. It is further expected that the protein binding domains hereof will generally bind to all naturally occurring or synthetic analogs, variants, mutants, or alleles of the GPCR.
  • the protein binding domain hereof is capable of specifically binding to an intracellular conformational epitope of a GPCR.
  • the protein binding domain is capable of specifically binding a conformational epitope that is comprised in, located at, or overlaps with, the G protein binding site of a GPCR.
  • the protein binding domains may occupy the G protein binding site of a functional conformational state of a GPCR, more preferably, of an active conformational state of a GPCR.
  • the protein binding domains show G protein-like behavior.
  • G protein-like behavior refers to the property of protein binding domains to preferentially bind agonist-bound receptor versus, for example, inverse agonist-bound receptor. Protein binding domains showing G protein-like behavior also enhance the affinity of the receptor for agonists, which is attributed to the cooperative interaction between agonist-occupied receptor and G protein (see also Example section).
  • the protein binding domain is derived from an innate or adaptive immune system.
  • the protein binding domain is derived from an immunoglobulin.
  • the protein binding domain hereof is an antibody or a derivative thereof.
  • antibody refers generally to a polypeptide encoded by an immunoglobulin gene, or functional fragments thereof, that specifically binds and recognizes an antigen, and is known to the person skilled in the art.
  • a conventional immunoglobulin (antibody) structural unit comprises a tetramer. Each tetramer is composed of two identical pairs of polypeptide chains, each pair having one “light” (about 25 kDa) and one “heavy” chain (about 50-70 kDa).
  • variable light chain VL
  • variable heavy chain VH
  • antibody is meant to include whole antibodies, including single-chain whole antibodies, and antigen-binding fragments.
  • antigen-binding fragments may be antigen-binding antibody fragments that include, but are not limited to, Fab, Fab′ and F(ab′)2, Fd, single-chain Fvs (scFv), single-chain antibodies, disulfide-linked Fvs (dsFv) and fragments comprising or consisting of either a VL or VII domain, and any combination of those or any other functional portion of an immunoglobulin peptide capable of binding to the target antigen.
  • the term “antibodies” is also meant to include heavy chain antibodies, or functional fragments thereof, such as single domain antibodies, more specifically, nanobodies, as defined further herein.
  • the protein binding domain comprises an amino acid sequence comprising four framework regions and three complementarity-determining regions, preferably in a sequence FR1-CDR1-FR2-CDR2-FR3-CDR3-FR4, or any suitable fragment thereof (which will then usually contain at least some of the amino acid residues that form at least one of the complementarity-determining regions).
  • Protein binding domains comprising four FRs and three CDRs are known to the person skilled in the art and have been described, as a non-limiting example, in Wesolowski et al. (2009).
  • the protein binding domain hereof is derived from a camelid antibody. More preferably, the protein binding domain hereof comprises an amino acid sequence of a nanobody, or any suitable fragment thereof. More specifically, the protein binding domain is a nanobody or any suitable fragment thereof.
  • “Camelids” comprise old world camelids ( Camelus bactrianus and Camelus dromedarius ) and new world camelids (for example, Lama paccos, Lama glama, Lama guanicoe and Lama vicugna ).
  • the single variable domain heavy chain antibody is herein designated as a nanobody or a VHH antibody.
  • NanobodyTM, NanobodiesTM and NanocloneTM are trademarks of Ablynx NV (Belgium).
  • the small size and unique biophysical properties of Nbs excel conventional antibody fragments for the recognition of uncommon or hidden epitopes and for binding into cavities or active sites of protein targets.
  • Nbs can be designed as bispecific and bivalent antibodies or attached to reporter molecules (Conrath et al. 2001). Nbs are stable and rigid single domain proteins that can easily be manufactured and survive the gastro-intestinal system. Therefore, Nbs can be used in many applications including drug discovery and therapy (Saerens et al. 2008), but also as a versatile and valuable tool for purification, functional study and crystallization of proteins (Conrath et al. 2009).
  • the nanobodies hereof generally comprise a single amino acid chain that can be considered to comprise four “framework sequences” or FRs and three “complementarity-determining regions” or CDRs (as defined hereinbefore).
  • framework sequences or FRs
  • CDRs complementary metal-oxide-semiconductor
  • Non-limiting examples of nanobodies hereof are described in more detail further herein. It should be clear that framework regions of nanobodies may also contribute to the binding of their antigens (Desmyter et al. 2002; Korotkov et al. 2009).
  • Non-limiting examples of the nanobodies hereof include, but are not limited to, nanobodies as defined by SEQ ID NOS:1-29 (see FIG. 12 , Table 1). The delineation of the CDR sequences is based on the IMGT unique numbering system for V-domains and V-like domains (Lefranc et al. 2003).
  • the above nanobodies can comprise at least one of the complementarity-determining regions (CDRs) with an amino acid sequence selected from SEQ ID NOS:30-70 (see FIG. 12 ; Table 2). More specifically, the above nanobodies can be selected from the group comprising SEQ ID NOS:1-29, or a functional fragment thereof.
  • a “functional fragment” or a “suitable fragment,” as used herein, may, for example, comprise one of the CDR loops.
  • the functional fragment comprises CDR3.
  • the nanobodies consist of any of SEQ ID NOS:1-29 and the functional fragment of the nanobodies consist of any of SEQ ID NOS:30-70.
  • a nucleic acid sequence encoding any of the above nanobodies or functional fragments is also part hereof.
  • expression vectors comprising nucleic acid sequences encoding any of the above nanobodies or functional fragments thereof, as well as host cells expressing such expression vectors.
  • Suitable expression systems include constitutive and inducible expression systems in bacteria or yeasts, virus expression systems, such as baculovirus, semliki forest virus and lentiviruses, or transient transfection in insect or mammalian cells.
  • Suitable host cells include E. coli, Lactococcus lactis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Pichia pastoris , and the like.
  • Suitable animal host cells include HEK 293, COS, S2, CHO, NSO, DT40 and the like. The cloning, expression and/or purification of the nanobodies can be done according to techniques known by the skilled person in the art.
  • the term “nanobody,” as used herein in its broadest sense, is not limited to a specific biological source or to a specific method of preparation.
  • the nanobodies hereof can generally be obtained: (1) by isolating the VHH domain of a naturally occurring heavy chain antibody; (2) by expression of a nucleotide sequence encoding a naturally occurring VHH domain; (3) by “humanization” of a naturally occurring VHH domain or by expression of a nucleic acid encoding such a humanized VHH domain; (4) by “camelization” of a naturally occurring VH domain from any animal species, and, in particular, from a mammalian species, such as from a human being, or by expression of a nucleic acid encoding such a camelized VH domain; (5) by “camelization” of a “domain antibody” or “Dab” as described in the art, or by expression of a nucleic acid encoding such a camelized VH domain; (6) by using synthetic or
  • nanobodies corresponds to the VHH domains of naturally occurring heavy chain antibodies directed against a functional conformational state of a GPCR.
  • naive or synthetic libraries of nanobodies may contain conformational binders against a GPCR in a functional conformational state
  • a preferred embodiment of this invention includes the immunization of a Camelidae with a GPCR in a functional conformational state, optionally bound to a receptor ligand, to expose the immune system of the animal with the conformational epitopes that are unique to the GPCR (for example, agonist-bound GPCR so as to raise antibodies directed against a GPCR in its active conformational state).
  • VHH sequences can preferably be generated or obtained by suitably immunizing a species of Camelid with a GPCR, preferably a GPCR in a functional conformational state, more preferably an active conformational state (i.e., so as to raise an immune response and/or heavy chain antibodies directed against the GPCR), by obtaining a suitable biological sample from the Camelid (such as a blood sample, or any sample of B-cells), and by generating V H H sequences directed against the GPCR, starting from the sample.
  • a suitable biological sample from the Camelid such as a blood sample, or any sample of B-cells
  • Yet another technique for obtaining the desired VHH sequences involves suitably immunizing a transgenic mammal that is capable of expressing heavy chain antibodies (i.e., so as to raise an immune response and/or heavy chain antibodies directed against a GPCR in a functional conformational state), obtaining a suitable biological sample from the transgenic mammal (such as a blood sample, or any sample of B-cells), and then generating VHH sequences directed against the GPCR starting from the sample, using any suitable technique known per se.
  • a suitable biological sample such as a blood sample, or any sample of B-cells
  • VHH sequences directed against the GPCR starting from the sample using any suitable technique known per se.
  • the heavy chain antibody-expressing mice and the further methods and techniques described in WO02085945 and in WO04049794 can be used.
  • the invention encompasses methods of generating protein binding domains hereof.
  • a method is provided of generating nanobodies specifically binding to a conformational epitope of a functional conformational state of a GPCR, comprising:
  • immunization of an animal will be done with a GPCR in the presence of a receptor ligand, wherein the ligand induces a particular functional conformational state of the GPCR.
  • a receptor ligand for example, nanobodies may be generated that are specifically binding to a conformational epitope of an active conformational state of a GPCR by immunizing an animal with a GPCR in the presence of an agonist that induces the formation of an active conformational state of the GPCR (see also Example section).
  • the GPCR may be produced and purified using conventional methods that may employ expressing a recombinant form of the GPCR in a host cell, and purifying the GPCR using affinity chromatography and/or antibody-based methods.
  • the baculovirus/Sf-9 system may be employed for expression, although other expression systems (e.g., bacterial, yeast or mammalian cell systems) may also be used.
  • Exemplary methods for expressing and purifying GCPRs are described in, for example, Kobilka (1995), Eroglu et al. (2002), Chelikani et al. (2006) and the book Identification and Expression of G Protein - Coupled Receptors (Kevin R.
  • a GPCR may also be reconstituted in phospholipid vesicles.
  • methods for reconstituting an active GPCR in phospholipid vesicles are known, and are described in: Luca et al. (2003), Mansoor et al. (2006), Niu et al. (2005), Shimada et al. (2002), and Eroglu et al. (2003), among others.
  • the GPCR and phospholipids may be reconstituted at high density (e.g., 1 mg receptor per mg of phospholipid).
  • the phospholipids vesicles may be tested to confirm that the GPCR is active.
  • a GPCR may be present in the phospholipid vesicle in both orientations (in the normal orientation, and in the “upside down” orientation in which the intracellular loops are on the outside of the vesicle).
  • Other immunization methods with a GPCR include, without limitation, the use of complete cells expressing a GPCR, vaccination with a nucleic acid sequence encoding a GPCR (e.g., DNA vaccination), immunization with viruses or virus-like particles expressing a GPCR, amongst others.
  • Any suitable animal e.g., a warm-blooded animal, in particular, a mammal such as a rabbit, mouse, rat, camel, sheep, cow, shark, or pig or a bird such as a chicken or turkey, may be immunized using any of the techniques well known in the art suitable for generating an immune response.
  • a mammal such as a rabbit, mouse, rat, camel, sheep, cow, shark, or pig or a bird such as a chicken or turkey
  • the screening for nanobodies may, for example, be performed by screening a set, collection or library of cells that express heavy chain antibodies on their surface (e.g., B-cells obtained from a suitably immunized Camelid), or bacteriophages that display a fusion of genIII and nanobody at their surface, by screening of a (na ⁇ ve or immune) library of VHH sequences or nanobody sequences, or by screening of a (na ⁇ ve or immune) library of nucleic acid sequences that encode VHH sequences or nanobody sequences, which may all be performed in a manner known per se, and which method may optionally further comprise one or more other suitable steps, such as, for example and without limitation, a step of affinity maturation, a step of expressing the desired amino acid sequence, a step of screening for binding and/or for activity against the desired antigen (in this case, the GPCR), a
  • a particularly preferred class of protein binding domains hereof comprises nanobodies with an amino acid sequence that corresponds to the amino acid sequence of a naturally occurring VHH domain, but that has been “humanized,” i.e., by replacing one or more amino acid residues in the amino acid sequence of the naturally occurring VHH sequence (and, in particular, in the framework sequences) by one or more of the amino acid residues that occur at the corresponding position(s) in a VH domain from a conventional four-chain antibody from a human being.
  • This can be performed in a manner known per se, which will be clear to the skilled person, on the basis of the further description herein and the prior art on humanization.
  • Such humanized Nanobodies hereof can be obtained in any suitable manner known per se (i.e., as indicated under points (1)-(8) above) and, thus, are not strictly limited to polypeptides that have been obtained using a polypeptide that comprises a naturally occurring VHH domain as a starting material.
  • Humanized nanobodies may have several advantages, such as a reduced immunogenicity, compared to the corresponding naturally occurring VHH domains.
  • Such humanization generally involves replacing one or more amino acid residues in the sequence of a naturally occurring VHH with the amino acid residues that occur at the same position in a human VH domain, such as a human VH3 domain.
  • the humanizing substitutions should be chosen such that the resulting humanized nanobodies still retain the favorable properties of nanobodies as defined herein.
  • the skilled person will be able to select humanizing substitutions or suitable combinations of humanizing substitutions that optimize or achieve a desired or suitable balance between the favorable properties provided by the humanizing substitutions on the one hand and the favorable properties of naturally occurring VHH domains on the other hand.
  • Another particularly preferred class of protein binding domains hereof comprises nanobodies with an amino acid sequence that corresponds to the amino acid sequence of a naturally occurring VH domain, but that has been “camelized,” i.e., by replacing one or more amino acid residues in the amino acid sequence of a naturally occurring VH domain from a conventional four-chain antibody by one or more of the amino acid residues that occur at the corresponding position(s) in a VHH domain of a heavy chain antibody.
  • Such “camelizing” substitutions are preferably inserted at amino acid positions that form and/or are present at the VH-VL interface, and/or at the so-called Camelidae hallmark residues, as defined herein (see, for example, WO9404678).
  • the VH sequence that is used as a starting material or starting point for generating or designing the camelized nanobody is preferably a VH sequence from a mammal, more preferably the VH sequence of a human being, such as a VH3 sequence.
  • camelized nanobodies hereof can be obtained in any suitable manner known per se (i.e., as indicated under points (1)-(8) above) and thus are not strictly limited to polypeptides that have been obtained using a polypeptide that comprises a naturally occurring VH domain as a starting material.
  • both “humanization” and “camelization” can be performed by providing a nucleotide sequence that encodes a naturally occurring VHH domain or VH domain, respectively, and then changing, in a manner known per se, one or more codons in the nucleotide sequence in such a way that the new nucleotide sequence encodes a “humanized” or “camelized” nanobody hereof, respectively.
  • This nucleic acid can then be expressed in a manner known per se, so as to provide the desired nanobody hereof.
  • the amino acid sequence of the desired humanized or camelized nanobody hereof, respectively can be designed and then synthesized de novo using techniques for peptide synthesis known per se.
  • a nucleotide sequence encoding the desired humanized or camelized nanobody hereof, respectively can be designed and then synthesized de novo using techniques for nucleic acid synthesis known per se, after which the nucleic acid thus obtained can be expressed in a manner known per se, so as to provide the desired nanobody hereof.
  • suitable methods and techniques for obtaining the nanobodies hereof and/or nucleic acids encoding the same, starting from naturally occurring VH sequences or preferably VHH sequences will be clear from the skilled person, and may, for example, comprise combining one or more parts of one or more naturally occurring VH sequences (such as one or more FR sequences and/or CDR sequences), one or more parts of one or more naturally occurring VHH sequences (such as one or more FR sequences or CDR sequences), and/or one or more synthetic or semi-synthetic sequences, in a suitable manner, so as to provide a nanobody hereof or a nucleotide sequence or nucleic acid encoding the same.
  • VH sequences such as one or more FR sequences and/or CDR sequences
  • synthetic or semi-synthetic sequences such as one or more synthetic or semi-synthetic sequences
  • analogs of the protein binding domains hereof, preferably to the nanobodies, and in particular analogs of the nanobodies of SEQ ID NOS:1-29 (see Table 1, FIG. 12 ).
  • the term “nanobody hereof” in its broadest sense also covers such analogs.
  • one or more amino acid residues may have been replaced, deleted and/or added, compared to the nanobodies hereof as defined herein.
  • substitutions, insertions, deletions or additions may be made in one or more of the framework regions and/or in one or more of the CDRs and, in particular, analogs of the CDRs of the nanobodies of SEQ ID NOS:1-29, the CDRs corresponding with SEQ ID NOS:30-70 (see Table 2, FIG. 12 ).
  • Analogs are sequences wherein each or any framework region and each or any complementarity-determining region shows at least 80% identity, preferably at least 85% identity, more preferably 90% identity, even more preferably, 95% identity with the corresponding region in the reference sequence (i.e., FR1_analog versus FR1_reference, CDR1_analog versus CDR1_reference, FR2_analog versus FR2_reference, CDR2_analog versus CDR2_reference, FR3_analog versus FR3_reference, CDR3_analog versus CDR3_reference, FR4_analog versus FR4_reference), as measured in a BLASTp alignment (Altschul et al. 1987; FR and CDR definitions according to IMGT unique numbering system for V-domains and V-like domains (Lefranc et al. 2003)).
  • a substitution may, for example, be a conservative substitution (as described herein) and/or an amino acid residue may be replaced by another amino acid residue that naturally occurs at the same position in another VHH domain.
  • any one or more substitutions, deletions or insertions, or any combination thereof, that either improve the properties of the nanobody hereof or that at least do not detract too much from the desired properties or from the balance or combination of desired properties of the nanobody hereof (i.e., to the extent that the nanobody is no longer suited for its intended use), are included within the scope hereof.
  • a skilled person will generally be able to determine and select suitable substitutions, deletions, insertions, additions, or suitable combinations thereof, based on the disclosure herein and optionally after a limited degree of routine experimentation, which may, for example, involve introducing a limited number of possible substitutions and determining their influence on the properties of the nanobodies thus obtained.
  • deletions and/or substitutions may be designed in such a way that one or more sites for post-translational modification (such as one or more glycosylation sites) are removed, as will be within the ability of the person skilled in the art.
  • substitutions or insertions may be designed so as to introduce one or more sites for attachment of functional groups (as described herein), for example, to allow site-specific pegylation.
  • modifications as well as examples of amino acid residues within the protein binding domain sequence, preferably the nanobody sequence, that can be modified (i.e., either on the protein backbone but preferably on a side chain), methods and techniques that can be used to introduce such modifications and the potential uses and advantages of such modifications will be clear to the skilled person.
  • a modification may involve the introduction (e.g., by covalent linking or in another suitable manner) of one or more functional groups, residues or moieties into or onto the nanobody hereof invention and, in particular, of one or more functional groups, residues or moieties that confer one or more desired properties or functionalities to the nanobody hereof.
  • Such functional groups can generally comprise all functional groups and techniques mentioned in the general background art cited hereinabove as well as the functional groups and techniques known per se for the modification of pharmaceutical proteins and, in particular, for the modification of antibodies or antibody fragments (including ScFvs and single domain antibodies), for which reference is, for example, made to Remington's Pharmaceutical Sciences, 16th ed., Mack Publishing Co., Easton, Pa. (1980).
  • Such functional groups may, for example, be linked directly (for example, covalently) to a nanobody hereof, or optionally via a suitable linker or spacer, as will again be clear to the skilled person.
  • One of the most widely used techniques for increasing the half-life and/or reducing immunogenicity of pharmaceutical proteins comprises attachment of a suitable pharmacologically acceptable polymer, such as polyethyleneglycol) (PEG) or derivatives thereof (such as methoxypoly(ethyleneglycol) or mPEG).
  • PEG polyethyleneglycol
  • any suitable form of pegylation can be used, such as the pegylation used in the art for antibodies and antibody fragments (including, but not limited to, single domain antibodies and ScFvs); reference is made to, for example, Chapman, Nat. Biotechnol. 54, 531-545 (2002); by Veronese and Harris, Adv. Drug Deliv. Rev. 54, 453-456 (2003); by Harris and Chess, Nat. Rev.
  • reagents for pegylation of proteins are also commercially available, for example, from Nektar Therapeutics, USA.
  • site-directed pegylation is used, in particular, via a cysteine-residue (see, for example, Yang et al., Protein Engineering 16 (10):761-770 (2003).
  • PEG may be attached to a cysteine residue that naturally occurs in a nanobody hereof.
  • a nanobody hereof may be modified so as to suitably introduce one or more cysteine residues for attachment of PEG, or an amino acid sequence comprising one or more cysteine residues for attachment of PEG may be fused to the N- and/or C-terminus of a nanobody hereof, all using techniques of protein engineering known per se to the skilled person.
  • a PEG is used with a molecular weight of more than 5000, such as more than 10,000 and less than 200,000, such as less than 100,000; for example, in the range of 20,000-80,000.
  • Another, usually less preferred modification comprises N-linked or O-linked glycosylation, usually as part of co-translational and/or post-translational modification, depending on the host cell used for expressing the nanobody or polypeptide hereof.
  • Another technique for increasing the half-life of a nanobody may comprise the engineering into bifunctional nanobodies (for example, one nanobody against the target GPCR and one against a serum protein such as albumin) or into fusions of nanobodies with peptides (for example, a peptide against a serum protein such as albumin).
  • Yet another modification may comprise the introduction of one or more detectable labels or other signal-generating groups or moieties, depending on the intended use of the labeled protein binding domain, in particular, the nanobody.
  • Suitable labels and techniques for attaching, using and detecting them will be clear to the skilled person, and, for example, include, but are not limited to, fluorescent labels (such as fluorescein, isothiocyanate, rhodamine, phycoerythrin, phycocyanin, allophycocyanin, o-phthaldehyde, and fluorescamine and fluorescent metals such as Eu or others metals from the lanthanide series), phosphorescent labels, chemiluminescent labels or bioluminescent labels (such as luminal, isoluminol, theromatic acridinium ester, imidazole, acridinium salts, oxalate ester, dioxetane or GFP and its analogs), radio-isotopes, metals, metals
  • labeled nanobodies and polypeptides hereof may, for example, be used for in vitro, in vivo or in situ assays (including immunoassays known per se such as ELISA, RIA, EIA and other “sandwich assays,” etc.) as well as in vivo diagnostic and imaging purposes, depending on the choice of the specific label.
  • another modification may involve the introduction of a chelating group, for example to chelate one of the metals or metallic cations referred to above.
  • Suitable chelating groups include, without limitation, diethylenetriaminepentaacetic acid (DTPA) or ethylenediaminetetraacetic acid (EDTA).
  • DTPA diethylenetriaminepentaacetic acid
  • EDTA ethylenediaminetetraacetic acid
  • Yet another modification may comprise the introduction of a functional group that is one part of a specific binding pair, such as the biotin-(strept)avidin binding pair.
  • a functional group may be used to link the nanobody hereof to another protein, polypeptide or chemical compound that is bound to the other half of the binding pair, i.e., through formation of the binding pair.
  • a nanobody hereof may be conjugated to biotin, and linked to another protein, polypeptide, compound or carrier conjugated to avidin or streptavidin.
  • such a conjugated nanobody may be used as a reporter, for example, in a diagnostic system where a detectable signal-producing agent is conjugated to avidin or streptavidin.
  • binding pairs may, for example, also be used to bind the nanobody hereof to a carrier, including carriers suitable for pharmaceutical purposes.
  • a carrier including carriers suitable for pharmaceutical purposes.
  • One non-limiting example is the liposomal formulations described by Cao and Suresh, Journal of Drug Targeting 8 (4):257 (2000).
  • Such binding pairs may also be used to link a therapeutically active agent to the nanobody hereof.
  • the nanobody hereof is bivalent and formed by bonding together, either chemically or by recombinant DNA techniques, two monovalent single domains of heavy chains.
  • the nanobody hereof is bi-specific and formed by bonding together two variable domains of heavy chains, each with a different specificity.
  • polypeptides comprising multivalent or multi-specific nanobodies are included here as non-limiting examples.
  • a monovalent nanobody hereof is such that it will bind to an extracellular part, region, domain, loop or other extracellular epitope of a functional conformational state of a GPCR, more preferably, an active conformational state of a GPCR, with an affinity less than 500 nM, preferably less than 200 nM, more preferably less than 10 nM, such as less than 500 pM.
  • a monovalent nanobody hereof is such that it will bind to an intracellular part, region, domain, loop or other intracellular epitope of a functional conformational state of a GPCR, more preferably, an active conformational state of a GPCR with an affinity less than 500 nM, preferably less than 200 nM, more preferably less than 10 nM, such as less than 500 pM.
  • any multivalent or multispecific (as defined herein) nanobody hereof may also be suitably directed against two or more different extracellular or intracellular parts, regions, domains, loops or other extracellular or intracellular epitopes on the same antigen, for example, against two different extracellular or intracellular loops or against two different extracellular or intracellular parts of the transmembrane domains.
  • Such multivalent or multispecific nanobodies hereof may also have (or be engineered and/or selected for) increased avidity and/or improved selectivity for the desired GPCR, and/or for any other desired property or combination of desired properties that may be obtained by the use of such multivalent or multispecific nanobodies.
  • such multivalent or multispecific nanobodies hereof may also have (or be engineered and/or selected for) improved efficacy in modulating signaling activity of a GPCR (see also further herein). It will be appreciated that the multivalent or multispecific nanobodies hereof may additionally be suitably directed to a different antigen, such as, but not limiting to, a ligand interacting with a GPCR or one or more downstream signaling proteins.
  • a second aspect hereof relates to a complex comprising (i) a protein binding domain hereof, (ii) a GPCR in a functional conformational state, and optionally, (iii) a receptor ligand.
  • a “receptor ligand” or a “ligand,” as defined herein, may be a small compound, a protein, a peptide, a protein scaffold, a nucleic acid, an ion, a carbohydrate or an antibody, or any suitable fragment derived thereof, and the like.
  • the ligand is from the agonist class and the receptor is in an active conformational state.
  • the ligand may also be an inverse agonist, an antagonist, or a biased ligand.
  • the ligands may be orthosteric or allosteric.
  • Ligands also include allosteric modulators, potentiators, enhancers, negative allosteric modulators and inhibitors. They may have biological activity by themselves or they may modulate activity only in the presence of another ligand. Neubig et al. (2003) describe many of the classes of ligands.
  • a complex wherein the protein binding domain is bound to the GPCR; preferably, the protein binding domain is bound to the GPCR, wherein the GPCR is bound to a receptor ligand.
  • a stable ternary complex containing a nanobody, a GPCR and an agonist can be purified by affinity chromatography or gel filtration from a mixture, containing (1) a nanobody that is specific for the active conformation of that GPCR, (2) the detergent-solubilized receptor and (3) an agonist.
  • the complex is crystalline.
  • a crystal of the complex is also provided, as well as methods of making the crystal, which are described in greater detail below.
  • a crystalline form of a complex may comprise (i) a protein binding domain hereof, (ii) a GPCR in a functional conformational state, preferably an active conformational state, and optionally, (iii) a receptor ligand, is envisaged, wherein the crystalline form is obtained by the use of a protein binding domain hereof.
  • the complex hereof is in a solubilized form, for example, after aqueous solubilization with a detergent.
  • the complex hereof is immobilized to a solid support.
  • solid supports as well as methods and techniques for immobilization, are described further in the detailed description.
  • the complex hereof is in a “cellular composition,” including an organism, a tissue, a cell, a cell line, and a membrane composition derived from the organism, tissue, cell or cell line.
  • the membrane composition is also meant to include any liposomal composition that may comprise natural or synthetic lipids or a combination thereof.
  • membrane or liposomal compositions include, but are not limited to, organelles, membrane preparations, virus-like lipoparticles, lipid layers (bilayers and monolayers), lipid vesicles, high-density lipoparticles (e.g., nanodisks), and the like. It will be appreciated that a cellular composition, or a membrane-like or liposomal composition, may comprise natural or synthetic lipids.
  • a third aspect relates to a cellular composition, including a membrane or liposomal composition derived thereof (all as defined hereinabove), comprising a protein binding domain and/or a complex hereof.
  • the cellular composition providing and/or expressing the protein binding domain is capable of stabilizing and/or inducing a functional conformational state of a GPCR upon binding of the protein binding domain. It will be understood that it is essential to retain sufficient functionality of the respective proteins, for which methods and techniques are available and known to the person skilled in the art. It will also be appreciated that the cellular composition may provide and/or express a target GPCR endogenously or exogenously.
  • GPCRs formed from membrane fragments or membrane-detergent extracts are reviewed in detail in Cooper (2004), incorporated herein by reference.
  • solubilized receptor preparations are further provided in the Example section.
  • Transfection of target cells can be carried out following principles outlined by Sambrook and Russel ( Molecular Cloning, A Laboratory Manual, 3 rd Edition, Volume 3, Chapter 16, Sections 16.1-16.54).
  • viral transduction can also be performed using reagents such as adenoviral vectors. Selection of the appropriate viral vector system, regulatory regions and host cell is common knowledge within the level of ordinary skill in the art.
  • the resulting transfected cells are maintained in culture or frozen for later use according to standard practices.
  • cells are eukaryotic cells, for example, yeast cells, or cultured cell lines, for example, mammalian cell lines, preferably human cell lines, that express a GPCR of interest.
  • Preferred cell lines functionally expressing the protein binding domain and/or the GPCR include insect cells (e.g., SF-9), human cell lines (e.g., HEK293), rodent cell lines (e.g., CHO-K1), and camelid cell lines (Dubca).
  • insect cells e.g., SF-9
  • human cell lines e.g., HEK293
  • rodent cell lines e.g., CHO-K1
  • camelid cell lines camelid cell lines
  • protein binding domains or the complexes or the cellular composition as described hereinbefore can be used in a variety of context and applications, which will be described in further detail below.
  • GPCRs other than rhodopsin typically have poor stability in detergents and are prone to aggregation and proteolysis. Efforts to crystallize GPCRs have been frustrated by other intrinsic characteristics of integral membrane proteins. The seven hydrophobic transmembrane helices of GPCRs make poor surfaces for crystal contacts, and the extracellular and intracellular domains are often relatively short and/or poorly structured. Besides for rhodopsin (an atypical GPCR in terms of natural abundance and stability), the first crystals of GPCRs were obtained from ⁇ 2 AR bound to a Fab fragment that recognized an epitope composed of the amino and carboxyl terminal ends of the third intracellular loop connecting TMs 5 and 6 (Rasmussen, 2007).
  • a fourth aspect relates to the use of a protein binding domain hereof, or in specific embodiments, a complex comprising the protein binding domain or a cellular composition providing the protein binding domain, to stabilize a GPCR in a functional conformational state, in particular, in an active conformational state; and/or to induce the formation of a particular functional (preferably, active) conformational state within a GPCR.
  • a protein binding domain is a very useful tool to purify, to crystallize and/or to solve the structure of a GPCR in a functional conformational state, in particular, in its active conformational state.
  • the protein binding domains hereof invention which are to be used for purifying, stabilizing, crystallizing and/or solving the structure of a GPCR, may be directed against any desired GPCR and may specifically bind to or recognize a conformational epitope of a functional conformational state, preferably an active conformational state, of any desired GPCR.
  • the conformational epitope can be part of an intracellular or extracellular region, or an intramembranous region, or a domain or loop structure of any desired GPCR.
  • protein binding domains hereof may increase the thermostability of detergent-solubilized receptors, stabilized in a particular conformational state, protecting them from proteolytic degradation and/or aggregation and facilitating the purification and concentration of homogeneous samples of correctly folded receptor. Persons of ordinary skill in the art will recognize that such samples are the preferred starting point for the generation of diffracting crystals.
  • the crystallization of the purified receptor is another major bottleneck in the process of macromolecular structure determination by X-ray crystallography.
  • Successful crystallization requires the formation of nuclei and their subsequent growth to crystals of suitable size. Crystal growth generally occurs spontaneously in a supersaturated solution as a result of homogenous nucleation. Proteins may be crystallized in a typical sparse matrix screening experiment, in which precipitants, additives and protein concentration are sampled extensively, and supersaturation conditions suitable for nucleation and crystal growth can be identified for a particular protein.
  • the protein binding domains hereof in particular, the nanobodies, can be used as tools to increase the probability of obtaining well-ordered crystals by minimizing the conformational heterogeneity in the target GPCR by binding to a particular conformation of the receptor.
  • GPCR-detergent complexes form three-dimensional crystals in which contacts between adjacent protein molecules are made by the polar surfaces of the protein protruding from the detergent micelle (Day et al. 2007). Obviously, the detergent micelle requires space in the crystal lattice. Although attractive interactions between the micelles might stabilize the crystal packing (Rasmussen et al. 2007; Dunn et al. 1997), these interactions do not lead to rigid crystal contacts. Because many membrane proteins, including GPCRs, contain relatively small or highly flexible hydrophilic domains, a strategy to increase the probability of getting well-ordered crystals is to enlarge the polar surface of the protein and/or to reduce their flexibility.
  • Nanobodies hereof can be used to enlarge the polar surfaces of the protein, supplementing the amount of protein surface can facilitate primary contacts between molecules in the crystal lattice. Nanobodies hereof can also reduce the flexibility of its extracellular regions to grow well-ordered crystals. Nanobodies are especially suited for this purpose because they are composed of one single rigid globular domain and are devoid of flexible linker regions unlike conventional antibodies or fragments derived such as Fabs.
  • the complex comprising the protein binding domain hereof and the target GPCR in a functional conformational state may be crystallized using any of a variety of specialized crystallization methods for membrane proteins, many of which are reviewed in Caffrey (2003).
  • the methods are lipid-based methods that include adding lipid to the GPCR-nanobody complex prior to crystallization. Such methods have previously been used to crystallize other membrane proteins.
  • lipidic cubic phase crystallization method exploits spontaneous self-assembling properties of lipids and detergent as vesicles (vesicle-fusion method), discoidal micelles (bicelle method), and liquid crystals or mesophases (in meso or cubic-phase method).
  • Lipidic cubic phase crystallization methods are described in, for example, Landau et al. 1996; Gouaux 1998; Rummel et al. 1998; Nollert et al. 2004, which publications are incorporated by reference for disclosure of those methods.
  • Bicelle crystallization methods are described in, for example, Faham et al. 2005; Faham et al. 2002, which publications are incorporated by reference for disclosure of those methods.
  • a protein binding domain as described hereinbefore to solve a structure of a GPCR.
  • the structure of a protein, in particular a GPCR includes the primary, secondary, tertiary and, if applicable, quaternary structure of the protein. “Solving the structure” as used herein refers to determining the arrangement of atoms or the atomic coordinates of a protein, and is often done by a biophysical method, such as X-ray crystallography.
  • the diffraction data when properly assembled gives the amplitude of the 3D Fourier transform of the molecule's electron density in the unit cell. If the phases are known, the electron density can be simply obtained by Fourier synthesis.
  • MR molecular replacement
  • the success to derive phase information from molecular replacement (MR) alone is questionable when the fraction of proteins with a known structure (the search models) is low (less than 50% of the amino acid content) and/or when the crystals exhibit limited diffraction quality. While the combination of multiple isomorphous replacement (MIR) and MR phasing has proven successful for protein complexes (e.g., Ostermeier et al. 1995; Li et al. 1997; Hunte et al.
  • One embodiment relates to the use of nanobodies for the phasing of GPCR-nanobody complexes by MR or MAD. Nanobodies generally express robustly and are suitable for SeMet incorporation. Phasing a GPCR-nanobody complex by introducing all the SeMet sites in the nanobody alone circumvents the need to incorporate SeMet sites in the GPCR.
  • the protein binding domains as described hereinbefore, in particular, the nanobodies can be used to improve the diffraction quality of the crystals so that the GPCR protein crystal structure can be solved.
  • agonist-bound receptor crystals may provide three-dimensional representations of the active states of GPCRs. These structures will help clarify the conformational changes connecting the ligand-binding and G-protein-interaction sites, and lead to more precise mechanistic hypotheses and eventually new therapeutics. Given the conformational flexibility inherent to ligand-activated GPCRs and the greater heterogeneity exhibited by agonist-bound receptors, stabilizing such a state is not easy.
  • Such efforts can benefit from the stabilization of the agonist-bound receptor conformation by the addition of protein binding domains that are specific for an active conformational state of the receptor.
  • nanobodies that show G-protein-like behavior and exhibit cooperative properties with respect to agonist binding, as are provided herein (see Example section).
  • a method of determining a crystal structure of a GPCR in a functional conformational state comprising the steps of:
  • Determining the crystal structure may be done by a biophysical method such as X-ray crystallography.
  • the method may further comprises a step of obtaining the atomic coordinates of the crystal (as defined hereinbefore).
  • a method for capturing and/or purifying a GPCR in a functional conformational state, preferably an active conformational state by making use of any of the above-described protein binding domains, or complexes or cellular compositions comprising such protein binding domains.
  • Capturing and/or purifying a GPCR in a functional conformational state, preferably an active conformational state, hereof will allow subsequent crystallization, ligand characterization and compound screening, and immunizations, amongst others.
  • methods and techniques include, without limitation, affinity-based methods such as affinity chromatography, affinity purification, immunoprecipitation, protein detection, immunochemistry, and surface-display, amongst others, and are all well known by the skilled in the art.
  • a protein binding domain hereof or a complex or a cellular composition comprising the same as described hereinbefore, to capture a GPCR in a functional conformational state, preferably to capture a GPCR in its active conformational state.
  • capturing of a GPCR in its functional conformational state as described above may include capturing a GPCR in a functional conformational state in complex with a receptor ligand or one or more downstream interacting proteins.
  • a method of capturing a GPCR in a functional conformational state comprising the steps of:
  • a method of capturing a GPCR in a functional conformational state comprising the steps of:
  • any of the methods as described above may further comprise the step of purifying the complex of the protein binding domain and the GPCR in its functional conformational state.
  • a fifth aspect hereof relates to a pharmaceutical composition
  • a pharmaceutical composition comprising a therapeutically effective amount of a protein binding domain hereof and at least one of a pharmaceutically acceptable carrier, adjuvant or diluent.
  • a “carrier” or “adjuvant,” in particular, a “pharmaceutically acceptable carrier” or “pharmaceutically acceptable adjuvant” is any suitable excipient, diluent, carrier and/or adjuvant that, by themselves, do not induce the production of antibodies harmful to the individual receiving the composition nor do they elicit protection. So, pharmaceutically acceptable carriers are inherently non-toxic and nontherapeutic, and they are known to the person skilled in the art. Suitable carriers or adjuvantia typically comprise one or more of the compounds included in the following non-exhaustive list: large slowly metabolized macromolecules such as proteins, polysaccharides, polylactic acids, polyglycolic acids, polymeric amino acids, amino acid copolymers and inactive virus particles.
  • Carriers or adjuvants may be, as a non-limiting example, Ringer's solution, dextrose solution or Hank's solution. Non-aqueous solutions such as fixed oils and ethyl oleate may also be used.
  • a preferred excipient is 5% dextrose in saline. The excipient may contain minor amounts of additives such as substances that enhance isotonicity and chemical stability, including buffers and preservatives.
  • a protein binding domain hereof or a pharmaceutical composition thereof may be by way of oral, inhaled or parenteral administration.
  • the protein binding domain is delivered through intrathecal or intracerebroventricular administration.
  • the active compound may be administered alone or preferably formulated as a pharmaceutical composition.
  • An amount effective to treat a certain disease or disorder that express the antigen recognized by the protein binding domain depends on the usual factors such as the nature and severity of the disorder being treated and the weight of the mammal. However, a unit dose will normally be in the range of 0.1 mg to 1 g, for example, to 0.1 to 500 mg, for example, 0.1 to 50 mg, or 0.1 to 2 mg of protein binding domain or a pharmaceutical composition thereof.
  • Unit doses will normally be administered once a month, once a week, bi-weekly, once or more than once a day, for example, two, three, or four times a day, more usually one to three times a day. It is greatly preferred that the protein binding domain or a pharmaceutical composition thereof is administered in the form of a unit-dose composition, such as a unit dose oral, parenteral, or inhaled composition.
  • compositions are prepared by admixture and are suitably adapted for oral, inhaled or parenteral administration, and as such, may be in the form of tablets, capsules, oral liquid preparations, powders, granules, lozenges, reconstitutable powders, injectable and infusable solutions or suspensions or suppositories or aerosols.
  • Tablets and capsules for oral administration are usually presented in a unit dose, and contain conventional excipients such as binding agents, fillers, diluents, tableting agents, lubricants, disintegrants, colorants, flavorings, and wetting agents.
  • the tablets may be coated according to well-known methods in the art.
  • Suitable fillers for use include cellulose, mannitol, lactose and other similar agents.
  • Suitable disintegrants include starch, polyvinylpyrrolidone and starch derivatives such as sodium starch glycolate.
  • Suitable lubricants include, for example, magnesium stearate.
  • Suitable pharmaceutically acceptable wetting agents include sodium lauryl sulphate.
  • Oral liquid preparations may be in the form of, for example, aqueous or oily suspensions, solutions, emulsions, syrups, or elixirs, or may be presented as a dry product for reconstitution with water or other suitable vehicle before use.
  • Such liquid preparations may contain conventional additives such as suspending agents (for example, sorbitol, syrup, methyl cellulose, gelatin, hydroxyethylcellulose, carboxymethyl cellulose, aluminium stearate gel or hydrogenated edible fats), emulsifying agents (for example, lecithin, sorbitan monooleate, or acacia), non-aqueous vehicles (which may include edible oils, for example, almond oil, fractionated coconut oil, oily esters such as esters of glycerine, propylene glycol, or ethyl alcohol), preservatives (for example, methyl or propyl p-hydroxybenzoate or sorbic acid), and, if desired, conventional flavoring or coloring agents.
  • suspending agents for example, sorbitol, syrup, methyl cellulose, gelatin, hydroxyethylcellulose, carboxymethyl cellulose, aluminium stearate gel or hydrogenated edible fats
  • emulsifying agents for example, lecithin, sorb
  • Oral formulations also include conventional sustained release formulations, such as tablets or granules having an enteric coating.
  • compositions for inhalation are presented for administration to the respiratory tract as a snuff or an aerosol or solution for a nebulizer, or as a microfine powder for insufflation, alone or in combination with an inert carrier such as lactose.
  • the particles of active compound suitably have diameters of less than 50 microns, preferably less than 10 microns, for example between 1 and 5 microns, such as between 2 and 5 microns.
  • a favored inhaled dose will be in the range of 0.05 to 2 mg, for example, 0.05 to 0.5 mg, 0.1 to 1 mg or 0.5 to 2 mg.
  • fluid unit dose forms are prepared containing a compound hereof and a sterile vehicle.
  • the active compound depending on the vehicle and the concentration, can be either suspended or dissolved.
  • Parenteral solutions are normally prepared by dissolving the compound in a vehicle and filter sterilizing before filling into a suitable vial or ampoule and sealing.
  • adjuvants such as a local anesthetic, preservatives and buffering agents are also dissolved in the vehicle.
  • the composition can be frozen after filling into the vial and the water removed under vacuum.
  • Parenteral suspensions are prepared in substantially the same manner except that the compound is suspended in the vehicle instead of being dissolved and sterilized by exposure to ethylene oxide before suspending in the sterile vehicle.
  • a surfactant or wetting agent is included in the composition to facilitate uniform distribution of the active compound.
  • small amounts of bronchodilators for example, sympathomimetic amines (such as isoprenaline, isoetharine, salbutamol, phenylephrine and ephedrine), xanthine derivatives (such as theophylline and aminophylline), corticosteroids (such as prednisolone), and adrenal stimulants (such as ACTH) may be included.
  • sympathomimetic amines such as isoprenaline, isoetharine, salbutamol, phenylephrine and ephedrine
  • xanthine derivatives such as theophylline and aminophylline
  • corticosteroids such as prednisolone
  • adrenal stimulants such as ACTH
  • the compositions will usually be accompanied by written or printed directions for use in the medical treatment concerned.
  • Protein binding domains in particular nanobodies, into cells may be performed as described for peptides, polypeptides and proteins. If the antigen is extracellular or an extracellular domain, the protein binding domain may exert its function by binding to this domain, without need for intracellular delivery.
  • the protein binding domains hereof as described herein may target intracellular conformational epitopes of GPCRs of interest. To use these protein binding domains as effective and safe therapeutics inside a cell, intracellular delivery may be enhanced by protein transduction or delivery systems known in the art. Protein transduction domains (PTDs) have attracted considerable interest in the drug delivery field for their ability to translocate across biological membranes.
  • the PTDs are relatively short (one- to 35-amino acid) sequences that confer this apparent translocation activity to proteins and other macromolecular cargo to which they are conjugated, complexed or fused (Sawant and Torchilin 2010).
  • the HIV-derived TAT peptide (YGRKKRRQRRR (SEQ ID NO: 71), for example, has been used widely for intracellular delivery of various agents ranging from small molecules to proteins, peptides, range of pharmaceutical nanocarriers and imaging agents.
  • receptor-mediated endocytic mechanisms can also be used for intracellular drug delivery.
  • the transferrin receptor-mediated internalization pathway is an efficient cellular uptake pathway that has been exploited for site-specific delivery of drugs and proteins (Qian et al.
  • transferrin This is achieved either chemically by conjugation of transferrin with therapeutic drugs or proteins or genetically by infusion of therapeutic peptides or proteins into the structure of transferrin.
  • Naturally existing proteins such as the iron-binding protein transferrin
  • these proteins are biodegradable, nontoxic, and non-immunogenic.
  • they can achieve site-specific targeting due to the high amounts of their receptors present on the cell surface.
  • Still other delivery systems include, without the purpose of being limitative, polymer- and liposome-based delivery systems.
  • the efficacy of the protein binding domains hereof, and of compositions comprising the same, can be tested using any suitable in vitro assay, cell-based assay, in vivo assay and/or animal model known per se, or any combination thereof, depending on the specific disease or disorder involved.
  • a sixth aspect hereof relates to the use of the protein binding domain or the pharmaceutical composition as described hereinbefore to modulate GPCR signaling activity.
  • the protein binding domains hereof as described herein may bind to the GPCR so as to activate or increase receptor signaling, or, alternatively, so as to decrease or inhibit receptor signaling.
  • the protein binding domains hereof may also bind to the GPCR in such a way that they block off the constitutive activity of the GPCR.
  • the protein binding domains hereof may also bind to the GPCR in such a way that they mediate allosteric modulation (e.g., bind to the GPCR at an allosteric site). In this way, the protein binding domains hereof may modulate the receptor function by binding to different regions in the receptor (e.g., at allosteric sites).
  • the protein binding domains hereof may also bind to the GPCR in such a way that they prolong the duration of the GPCR-mediated signaling or that they enhance receptor signaling by increasing receptor-ligand affinity. Further, the protein binding domains hereof may also bind to the GPCR in such a way that they inhibit or enhance the assembly of GPCR functional homomers or heteromers.
  • the protein binding domain or the pharmaceutical composition as described hereinbefore blocks G-protein-mediated signaling.
  • protein binding domain or the pharmaceutical composition as described hereinbefore for use in the treatment of a GPCR-related disease, such as cancer, autoimmune disease, infectious disease, neurological disease, and cardiovascular disease.
  • Certain of the above-described protein binding domains may have therapeutic utility and may be administered to a subject having a condition in order to treat the subject for the condition.
  • the therapeutic utility for a protein binding domain may be determined by the GPCR to which the protein binding domain binds in that signaling via that GPCR is linked to the condition.
  • the GPCR may be activated in the condition by binding to a ligand.
  • the GPCR may be mutated to make it constitutively active, for example.
  • a subject protein binding domain may be employed for the treatment of a GPCR-mediated condition such as schizophrenia, migraine headache, reflux, asthma, bronchospasm, prostatic hypertrophy, ulcers, epilepsy, angina, allergy, rhinitis, cancer, e.g., prostate cancer, glaucoma and stroke.
  • a GPCR-mediated condition such as schizophrenia, migraine headache, reflux, asthma, bronchospasm, prostatic hypertrophy, ulcers, epilepsy, angina, allergy, rhinitis, cancer, e.g., prostate cancer, glaucoma and stroke.
  • GPCR-related conditions at the On-line Mendelian Inheritance in Man database can be found at the world wide website of the NCBI.
  • a particular embodiment hereof also envisions the use of a protein binding domain or of a pharmaceutical composition for the treatment of a GPCR-related disease or disorder.
  • the protein binding domain may bind to the ⁇ 2 -adrenergic receptor, in which case, it may be employed in the treatment of a condition requiring relaxation of smooth muscle of the uterus or vascular system.
  • a protein binding domain may be thus used for the prevention or alleviation of premature labor pains in pregnancy, or in the treatment of chronic or acute asthma, urticaria, psoriasis, rhinitis, allergic conjunctivitis, acinitis, hay fever, or mastocytosis, which conditions have been linked to the ⁇ 2 -adrenoreceptor.
  • the protein binding domain may be employed as co-therapeutic agents for use in combination with other drug substances such as anti-inflammatory, bronchodilatory or antihistamine drug substances, particularly in the treatment of obstructive or inflammatory airway diseases such as those mentioned hereinbefore, for example, as potentiators of therapeutic activity of such drugs or as a means of reducing required dosaging or potential side effects of such drugs.
  • a subject protein binding domain may be mixed with the other drug substance in a fixed pharmaceutical composition or it may be administered separately, before, simultaneously with or after the other drug substance.
  • these protocols involve administering to an individual suffering from a GPCR-related disease or disorder an effective amount of a protein binding domain that modulates a GPCR to modulate the GPCR in the host and treat the individual for the disorder.
  • one or more compounds that decrease the activity of the GPCR may be administered, whereas when an increase in activity of a certain GPCR is desired, one or more compounds that increase the activity of the GPCR activity may be administered.
  • a variety of individuals are treatable according to the subject methods.
  • such individuals are mammals or mammalian, where these terms are used broadly to describe organisms that are within the class mammalia, including the orders carnivore (e.g., dogs and cats), rodentia (e.g., mice, guinea pigs, and rats), and primates (e.g., humans, chimpanzees, and monkeys).
  • the individuals will be humans.
  • Subject treatment methods are typically performed on individuals with such disorders or on individuals with a desire to avoid such disorders.
  • the protein binding domain or the complex hereof may also be useful for the diagnosis or prognosis of a GPCR-related disease, such as cancer, autoimmune disease, infectious disease, neurological disease, or cardiovascular disease.
  • a GPCR-related disease such as cancer, autoimmune disease, infectious disease, neurological disease, or cardiovascular disease.
  • a major advantage of the protein binding domains hereof is that a GPCR can be kept in a stabilized functional conformation, preferably in an active state conformation.
  • library compounds that selectively bind this active conformation of the receptor have a higher propensity to behave as agonists because orthosteric or allosteric stabilization of the active conformation of the GPCR elicits biological responses.
  • the protein binding domain increases the thermostability of the active conformation of the GPCR, thus protecting the GPCR against irreversible or thermal denaturation induced by the non-native conditions used in compound screening and drug discovery, without the need to rely on mutant GPCRs with increased stability.
  • conformation-selective protein binding domains hereof are highly flexible and reliable. They quickly and reliably screen for and differentiate between receptor agonists, inverse agonists, antagonists and/or modulators as well as inhibitors of GPCRs and GPCR-dependent pathways, thereby increasing the likelihood of identifying a ligand with the desired pharmacological properties.
  • the protein binding domains hereof are capable of stabilizing an active conformational state of a GPCR (and thus show G-protein-like behavior) and destabilizing inactive conformational states, thus increasing the affinity of the GPCR for agonists and decreasing the affinity for inverse agonists or antagonists.
  • protein binding domains such as nanobodies, hereof invention, that recognize the active functional conformation of the GPCR can be efficiently used in high-throughput screening assays to screen for agonists because they increase the affinity of the receptor for agonists, relative to inverse agonists or antagonists.
  • protein binding domains, in particular, nanobodies, that stabilize the inactive state conformation of a GPCR will increase the affinity for an inverse agonist or an antagonist and decrease the affinity for an agonist.
  • Such protein binding domains may be used, for example, to screen for inverse agonists.
  • protein binding domains, particularly nanobodies, that recognize particular functional conformational states, thus modulating the affinities for agonists and inverse agonists in a reciprocal way also form part hereof.
  • encompassed is the use of the protein binding domains, or the complexes, or the cellular compositions, all as described hereinbefore, in screening and/or identification programs for conformation-specific binding partners of a GPCR, which ultimately might lead to potential new drug candidates.
  • envisaged is a method of identifying compounds capable of selectively binding to a functional conformational state of a GPCR, the method comprising the steps of:
  • the above method further comprises a step of forming a complex comprising the protein binding domain and the GPCR in a functional conformational state, more preferably, in an active conformational state.
  • the invention also envisages a method of identifying compounds capable of selectively binding to a functional conformational state of a GPCR, the method comprising the steps of:
  • the protein binding domain as used in any of the above methods is capable of stabilizing and/or inducing a functional conformational state of a GPCR upon binding.
  • the functional conformational state of a GPCR is selected from the group consisting of a basal conformational state, or an active conformational state or an inactive conformational state (as defined hereinbefore).
  • the functional conformational state of a GPCR is an active conformational state.
  • the protein binding domain as used in any of the above screening methods comprises an amino acid sequence that comprises four framework regions and three complementarity-determining regions, or any suitable fragment thereof.
  • the protein binding domain is derived from a camelid antibody.
  • the protein binding domain comprises a nanobody sequence, or any suitable fragment thereof.
  • the nanobody comprises a sequence selected from the group consisting of SEQ ID NOS:1-29, or any suitable fragment thereof.
  • the protein binding domain, the GPCR or the complex comprising the protein binding domain and the GPCR, as used in any of the above screening methods are provided as whole cells, or cell (organelle) extracts such as membrane extracts or fractions thereof, or may be incorporated in lipid layers or vesicles (comprising natural and/or synthetic lipids), high-density lipoparticles, or any nanoparticle, such as nanodisks, or are provided as VLPs, so that sufficient functionality of the respective proteins is retained.
  • Preparations of GPCRs formed from membrane fragments or membrane-detergent extracts are reviewed in detail in Cooper (2004), incorporated herein by reference.
  • GPCRs and/or the complex may also be solubilized in detergents. Non-limiting examples of solubilized receptor preparations are further provided in the Example section.
  • a protein binding domain hereof, a GPCR in a functional conformational state or a complex comprising them onto a suitable solid surface or support that can be arrayed or otherwise multiplexed.
  • suitable solid supports include beads, columns, slides, chips or plates.
  • the solid supports may be particulate (e.g., beads or granules, generally used in extraction columns) or in sheet form (e.g., membranes or filters, glass or plastic slides, microtiter assay plates, dipstick, capillary fill devices or the like), which can be flat, pleated, or hollow fibers or tubes.
  • particulate e.g., beads or granules, generally used in extraction columns
  • sheet form e.g., membranes or filters, glass or plastic slides, microtiter assay plates, dipstick, capillary fill devices or the like
  • Such examples could include silica (porous amorphous silica), i.e., the FLASH series of cartridges containing 60A irregular silica (32-63 ⁇ m or 35-70 ⁇ m) supplied by Biotage (a division of Dyax Corp.), agarose or polyacrylamide supports, for example, the Sepharose range of products supplied by Amersham Pharmacia Biotech, or the Affi-Gel supports supplied by Bio-Rad.
  • macroporous polymers such as the pressure-stable Affi-Prep supports as supplied by Bio-Rad.
  • supports that could be utilized include dextran, collagen, polystyrene, methacrylate, calcium alginate, controlled pore glass, aluminium, titanium and porous ceramics.
  • the solid surface may comprise part of a mass-dependent sensor, for example, a surface plasmon resonance detector. Further examples of commercially available supports are discussed in, for example, Protein Immobilization , R. F. Taylor ed., Marcel Dekker, Inc., New York, (1991).
  • Immobilization may be either non-covalent or covalent.
  • non-covalent immobilization or adsorption on a solid surface of the protein binding domain, the GPCR or the complex comprising the protein binding domain and the GPCR, hereof invention may occur via a surface coating with any of an antibody, or streptavidin or avidin, or a metal ion, recognizing a molecular tag attached to the protein binding domain or the GPCR, according to standard techniques known by the skilled person (e.g., biotin tag, Histidine tag, etc.).
  • the protein binding domain, the GPCR or the complex comprising the protein binding domain and the GPCR, hereof may be attached to a solid surface by covalent cross-linking using conventional coupling chemistries.
  • a solid surface may naturally comprise cross-linkable residues suitable for covalent attachment or it may be coated or derivatized to introduce suitable cross-linkable groups according to methods well known in the art.
  • sufficient functionality of the immobilized protein is retained following direct covalent coupling to the desired matrix via a reactive moiety that does not contain a chemical spacer arm.
  • the mutation of a particular amino acid (in a protein with known or inferred structure) to a lysine or cysteine (or other desired amino acid) can provide a specific site for covalent coupling, for example. It is also possible to reengineer a specific protein to alter the distribution of surface available amino acids involved in the chemical coupling (Kallwass et al. 1993), in effect controlling the orientation of the coupled protein.
  • a similar approach can be applied to the protein binding domains hereof, as well as to the conformationally stabilized GPCRs, whether or not comprised in a complex, so as to provide a means of oriented immobilization without the addition of other peptide tails or domains containing either natural or unnatural amino acids.
  • introduction of mutations in the framework region is preferred, minimizing disruption to the antigen-binding activity of the antibody (fragment).
  • the immobilized proteins may be used in immunoadsorption processes such as immunoassays, for example, ELISA, or immunoaffinity purification processes by contacting the immobilized proteins hereof with a test sample according to standard methods conventional in the art.
  • the immobilized proteins can be arrayed or otherwise multiplexed.
  • the immobilized proteins hereof are used for the screening and selection of compounds that specifically bind to a GPCR in a functional conformational state, in particular, a GPCR in an active conformational state.
  • the protein binding domain or the GPCR in a functional conformational state, or the complex comprising the protein binding domain and the GPCR may be immobilized, depending on the type of application or the type of screening that needs to be done.
  • the choice of the GPCR-stabilizing protein binding domain targeting a particular conformational epitope of the GPCR, will determine the orientation of the GPCR and, accordingly, the desired outcome of the compound identification, e.g., compounds specifically binding to extracellular parts, intramembranal parts or intracellular parts of the conformationally stabilized GPCR.
  • test compound (or a library of test compounds) may be immobilized on a solid surface, such as a chip surface, whereas the protein binding domain, the GPCR or the complex are provided, for example, in a detergent solution or in a membrane-like preparation.
  • neither the protein binding domain, nor the GPCR, nor the test compound is immobilized, for example, in phage-display selection protocols in solution, or radioligand binding assays.
  • Various methods may be used to determine binding between the stabilized GPCR and a test compound, including, for example, enzyme-linked immunosorbent assays (ELISA), surface Plasmon resonance assays, chip-based assays, immunocytofluorescence, yeast two-hybrid technology and phage display, which are common practice in the art, for example, in Sambrook et al. (2001), Molecular Cloning, A Laboratory Manual , Third Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
  • Other methods of detecting binding between a test compound and a GPCR include ultrafiltration with ion spray mass spectroscopy/HPLC methods or other (bio)physical and analytical methods.
  • FRET Fluorescence Energy Resonance Transfer
  • the protein binding domains or the complexes or the cellular compositions as described herein can be used to screen for compounds that modulate (increase or decrease) the biological activity of the GPCR.
  • the desired modulation in biological activity will depend on the GPCR of choice.
  • the compounds to be tested can be any small chemical compound, or a macromolecule, such as a protein, a sugar, nucleic acid or lipid.
  • test compounds will be small chemical compounds, peptides, antibodies or fragments thereof.
  • test compound may be a library of test compounds.
  • high-throughput screening assays for therapeutic compounds such as agonists, antagonists or inverse agonists and/or modulators form part hereof.
  • compound libraries may be used such as allosteric compound libraries, peptide libraries, antibody libraries, fragment-based libraries, synthetic compound libraries, natural compound libraries, phage-display libraries and the like. Methodologies for preparing and screening such libraries are known in the art.
  • high-throughput screening methods involve providing a combinatorial chemical or peptide library containing a large number of potential therapeutic ligands. Such “combinatorial libraries” or “compound libraries” are then screened in one or more assays, as described herein, to identify those library members (particular chemical species or subclasses) that display a desired characteristic activity.
  • a “compound library” is a collection of stored chemicals usually used ultimately in high-throughput screening.
  • a “combinatorial library” is a collection of diverse chemical compounds generated by either chemical synthesis or biological synthesis, by combining a number of chemical “building blocks” such as reagents. Preparation and screening of combinatorial libraries are well known to those of skill in the art.
  • the screening methods as described hereinabove further comprise modifying a test compound that has been shown to bind to a GPCR in a functional conformational state, preferably an active conformational state, and determining whether the modified test compound binds to the GPCR when residing in the particular conformation.
  • the test compound is provided as a biological sample.
  • the sample can be any suitable sample taken from an individual.
  • the sample may be a body fluid sample such as blood, serum, plasma, spinal fluid.
  • the sample is tissue or cell extract.
  • the compounds may bind to the target GPCR resulting in the modulation (activation or inhibition) of the biological function of the GPCR, in particular, the downstream receptor signaling. This modulation of GPCR signaling can occur ortho- or allosterically.
  • the compounds may bind to the target GPCR so as to activate or increase receptor signaling or, alternatively, so as to decrease or inhibit receptor signaling.
  • the compounds may also bind to the target GPCR in such a way that they block off the constitutive activity of the GPCR.
  • the compounds may also bind to the target complex in such a way that they mediate allosteric modulation (e.g., bind to the GPCR at an allosteric site).
  • the compounds may modulate the receptor function by binding to different regions in the GPCR (e.g., at allosteric sites).
  • the compounds hereof may also bind to the target GPCR in such a way that they prolong the duration of the GPCR-mediated signaling or that they enhance receptor signaling by increasing receptor-ligand affinity. Further, the compounds may also bind to the target complex in such a way that they inhibit or enhance the assembly of GPCR functional homomers or heteromers.
  • a ligand may be radiolabeled or fluorescently labeled.
  • the assay may be carried out on whole cells or on membranes obtained from the cells or aqueous-solubilized receptor with a detergent.
  • the compound will be characterized by its ability to alter the binding of the labeled ligand (see also Example section).
  • the compound may decrease the binding between the GPCR and its ligand, or may increase the binding between the GPCR and its ligand, for example, by a factor of at least two-fold, three-fold, four-fold, five-fold, ten-fold, twenty-fold, thirty-fold, fifty-fold, or one hundred-fold.
  • the complex as used in any of the above screening methods further comprises a receptor ligand.
  • the receptor ligand is chosen from the group comprising a small molecule, a polypeptide, an antibody or any fragment derived thereof, a natural product, and the like. More preferably, the receptor ligand is a full agonist, or a partial agonist, or an inverse agonist, or an antagonist, as described hereinbefore.
  • the protein binding domains hereof can also be useful for lead identification and the design of peptidomimetics.
  • a biologically relevant peptide or protein structure as a starting point for lead identification represents one of the most powerful approaches in modern drug discovery.
  • Peptidomimetics are compounds whose essential elements (pharmacophore) mimic a natural peptide or protein in three-dimensional space and that retain the ability to interact with the biological target and produce the same biological effect.
  • Peptidomimetics are designed to circumvent some of the problems associated with a natural peptide, for example, stability against proteolysis (duration of activity) and poor bioavailability. Certain other properties, such as receptor selectivity or potency, often can be substantially improved.
  • the nanobodies hereof may bind with long CDR loops deep into the core of the receptor to exert a biological effect.
  • These peptides and their concomitant structures in the nanobody-GPCR complex can serve as starting points for lead identification and the design of peptidomimetics.
  • the protein binding domains in particular, the nanobodies hereof, can be useful in screening assays.
  • Screening assays for drug discovery can be solid phase or solution phase assays, e.g., a binding assay, such as radioligand binding assays.
  • a binding assay such as radioligand binding assays.
  • high-throughput assays it is possible to screen up to several thousand different modulators or ligands in a single day in 96-, 384- or 1536-well formats.
  • each well of a microtiter plate can be used to run a separate assay against a selected potential modulator, or, if concentration or incubation time effects are to be observed, every five to ten wells can test a single modulator.
  • a single standard microtiter plate can assay about 96 modulators. It is possible to assay many plates per day; assay screens for up to about 6,000, 20,000, 50,000, or more, different compounds are possible today.
  • the protein binding domains can also be useful in cell-based assays.
  • Cell-based assays are also critical for assessing the mechanism of action of new biological targets and biological activity of chemical compounds.
  • Current cell-based assays for GPCRs include measures of pathway activation (Ca 2+ release, cAMP generation or transcriptional activity); measurements of protein trafficking by tagging GPCRs and downstream elements with GFP; and direct measures of interactions between proteins using Forster resonance energy transfer (FRET), bioluminescence resonance energy transfer (BRET) or yeast two-hybrid approaches.
  • FRET Forster resonance energy transfer
  • BRET bioluminescence resonance energy transfer
  • yeast two-hybrid approaches yeast two-hybrid approaches.
  • the efficacy of the compounds and/or compositions comprising the same can be tested using any suitable in vitro assay, cell-based assay, in vivo assay and/or animal model known per se, or any combination thereof, depending on the specific disease or disorder involved.
  • a solid support to which is immobilized a protein binding domain hereof and/or a complex comprising a protein binding domain and a GPCR in a functional conformational state, is provided for use in any of the above screening methods.
  • the test compound as used in any of the above screening methods is selected from the group comprising a polypeptide, a peptide, a small molecule, a natural product, a peptidomimetic, a nucleic acid, a lipid, lipopeptide, a carbohydrate, an antibody or any fragment derived thereof, such as Fab, Fab′ and F(ab′)2, Fd, single-chain Fvs (scFv), single-chain antibodies, disulfide-linked Fvs (dsFv) and fragments comprising either a VL or VH domain, a heavy chain antibody (hcAb), a single domain antibody (sdAb), a minibody, the variable domain derived from camelid heavy chain antibodies (VHH or nanobody), the variable domain of the new antigen receptors derived from shark antibodies (VNAR), a protein scaffold including an alphabody, protein A, protein G, designed ankyrin-repeat domains (DARPins), fibronectin type III
  • test compound may optionally be covalently or non-covalently linked to a detectable label.
  • detectable labels and techniques for attaching, using and detecting them will be clear to the skilled person, and include, but are not limited to, any composition detectable by spectroscopic, photochemical, biochemical, immunochemical, electrical, optical or chemical means.
  • Useful labels include magnetic beads (e.g., dynabeads), fluorescent dyes (e.g., all Alexa Fluor dyes, fluorescein isothiocyanate, Texas red, rhodamine, green fluorescent protein and the like), radiolabels (e.g., 3 H, 125 I, 35 S, 14 C, or 32 P), enzymes (e.g., horse radish peroxidase, alkaline phosphatase), and colorimetric labels such as colloidal gold or colored glass or plastic (e.g., polystyrene, polypropylene, latex, etc.) beads. Means of detecting such labels are well known to those of skill in the art.
  • fluorescent dyes e.g., all Alexa Fluor dyes, fluorescein isothiocyanate, Texas red, rhodamine, green fluorescent protein and the like
  • radiolabels e.g., 3 H, 125 I, 35 S, 14 C, or 32 P
  • radiolabels may be detected using photographic film or scintillation counters
  • fluorescent markers may be detected using a photodetector to detect emitted illumination
  • Enzymatic labels are typically detected by providing the enzyme with a substrate and detecting the reaction product produced by the action of the enzyme on the substrate, and colorimetric labels are detected by simply visualizing the colored label.
  • Other suitable detectable labels were described earlier within the context of the first aspect hereof relating to a protein binding domain.
  • the test compound is an antibody or any fragment derived thereof, as described above, including a nanobody.
  • the test compound may be an antibody (as defined herein in its broadest sense) that has been raised against a complex comprising a protein binding domain hereof and a GPCR (including variants, as described hereinbefore) in a functional conformational state, preferably in an active conformational state.
  • Methods for raising antibodies in vivo are known in the art.
  • immunization of an animal will be done in a similar way as described hereinbefore (immunization with GPCR in presence of receptor ligand; see also Example section) with a GPCR in the presence of a functional conformational state stabilizing protein binding domain, more preferably, an active state stabilizing protein binding domain.
  • the invention also relates to methods for selecting antibodies specific to a GPCR in a functional conformational state, preferably an active conformational state, involving the screening of expression libraries encoding immunoglobulin genes, or portions thereof, expressed in bacteria, yeast, filamentous phages, ribosomes or ribosomal subunits or other display systems on a complex containing a GPCR and a protein binding domain that stabilizes a functional conformational state of the GPCR.
  • a seventh aspect hereof relates to a kit comprising a protein binding domain hereof or a complex hereof or a cellular composition hereof.
  • the kit may further comprise a combination of reagents such as buffers, molecular tags, vector constructs, reference sample material, as well as suitable solid supports, and the like.
  • reagents such as buffers, molecular tags, vector constructs, reference sample material, as well as suitable solid supports, and the like.
  • Such a kit may be useful for any of the applications hereof as described herein.
  • the kit may comprise (a library of) test compounds useful for compound screening applications.
  • a last aspect hereof is the use of any protein binding domain hereof to isolate amino acid sequences that are responsible for specific binding to a conformational epitope of a functional conformational state of a GPCR, in particular, an active conformational state of a GPCR and to construct artificial protein binding domains based on the amino acid sequences.
  • the framework regions and the complementarity-determining regions are known, and the study of derivatives of the protein binding domain, binding to the same conformational epitope of a functional conformational state of a GPCR, in particular, an active conformational state of a GPCR, will allow deducing the essential amino acids involved in binding the conformational epitope.
  • This knowledge can be used to construct a minimal protein binding domain and to create derivatives thereof, which can routinely be done by techniques known by the skilled in the art.
  • a llama Llama glama
  • ⁇ 2 AR-365 recombinant ⁇ 2 AR truncated at Gly365
  • ⁇ 2 AR-365 was expressed in insect cells and antigen was reconstituted as previously described (Day et al. 2007).
  • lymphocytes were isolated from the blood of the immunized llama and a phage library prepared and screened as described in Materials and Methods to the Examples (see further).
  • Two screens identified conformational nanobodies that recognize the native ⁇ 2 AR, but not the denaturated receptor.
  • a first screen we compared the binding of the nanobodies on the native and heat denatured ⁇ 2 AR antigen in an ELISA.
  • one well was coated with phospholipid vesicles containing agonist-bound ⁇ 2 AR-365 (0.1 ⁇ g protein/well). Next, this plate was incubated at 80° C. for two hours. Next, another well of the same plate was coated with phospholipid vesicles containing agonist-bound ⁇ 2 AR-365 (0.1 ⁇ g protein/well) without heating. All of the nanobodies were able to selectively bind the native receptor but not the heat inactivated receptor, indicating that 16 binders recognize conformational epitopes.
  • a next screen we compared the specificity of the nanobodies for a native agonist-bound ⁇ 2 AR receptor, versus a native inverse agonist-bound receptor, versus an SDS denaturated receptor by dot blot analysis.
  • the screen identified 16 different conformational nanobodies that recognize native agonist-bound ⁇ 2 AR-365, but not the inverse agonist, or the heat denatured receptor ( FIG. 2 (dot blots)).
  • the initial screen identified 16 clones that recognized native agonist-bound ⁇ 2 AR, but not heat denatured receptor.
  • Our next goal was to identify nanobodies that had G protein-like behavior.
  • the ⁇ 2 AR preferentially couples to Gs and agonist binding enhances G protein interactions.
  • the ⁇ 2 AR binds agonist with higher affinity. Therefore, we looked at (1) the effect of agonist on nanobody binding to the ⁇ 2 AR using size exclusion chromatography, (2) the effect of nanobodies on ⁇ 2 AR agonist binding affinity in membranes and (3) the effect of nanobodies on ⁇ 2 AR conformational changes as monitored by the environmentally sensitive mono-bromobimane (mBBr) fluorophore.
  • mBBr mono-bromobimane
  • Nanobodies with G Protein-Like Behavior Specifically Bind to Purified Agonist-Bound Receptor
  • Purified nanobodies were incubated with purified, detergent-solubilized ⁇ 2 AR receptor in the presence of an agonist or an inverse agonist that stabilizes an inactive conformation. The mixture was then analyzed by Size Exclusion Chromatography (SEC), which separates protein on the basis of size. Seven of the nanobodies bound to purified ⁇ 2 AR and migrated as a complex on SEC only in the presence of agonist and not an inverse agonist (an example is shown in FIG. 1 , Panel a, FIG. 3 and FIG. 4 ). The remaining nanobodies did not bind with sufficient high affinity to shift the mobility of the ⁇ 2 AR on SEC.
  • SEC Size Exclusion Chromatography
  • Nanobodies with G Protein-Like Behavior Enhance the Affinity of ⁇ 2 AR for Agonists
  • ⁇ 2 AR was labeled at the cytoplasmic end of TM6 at C265 with monobromobimane and reconstituted into HDL particles.
  • TM6 moves relative to TM3 and TM5 upon agonist activation ( FIG. 6 , Panel A), and we have previously shown that the environment around bimane covalently linked to C265 changes with both agonist binding and G protein coupling, resulting in a decrease in bimane intensity and a red shift in ⁇ max (Yao et al. 2009).
  • Nb80 does not recognize the inactive conformation of the ⁇ 2 AR, but binds efficiently to agonist occupied ⁇ 2 AR and produces a change in bimane fluorescence that is indistinguishable from that observed in the presence of Gs and isoproterenol.
  • FIG. 6 Panels D and E, show the effect of Gs and Nb80 on agonist affinity for ⁇ 2 AR.
  • ⁇ 2 AR was reconstituted into HDL particles and agonist competition binding experiments were performed in the absence or presence of Nb80 and Gs.
  • isoproterenol has an inhibition constant (Ki) of 107 nM.
  • Ki inhibition constant
  • In the presence of Gs two affinity states are observed, because not all of the ⁇ 2 AR is coupled to Gs. In the Gs-coupled state, the affinity of isoproterenol increases by 100-fold (Ki 1.07 nM) ( FIG. 6 , Panel D, and Table 4).
  • Nb80 stabilizes a conformation in WT ⁇ 2 AR that is very similar to that stabilized by Gs, such that the energetic coupling of agonist and Gs binding is faithfully mimicked by Nb80.
  • Nanobodies Facilitate Crystallization of Agonist-Bound ⁇ 2 AR
  • the ⁇ 2 AR was originally crystallized bound to the inverse agonist carazolol using two different approaches.
  • the first crystals were obtained from ⁇ 2 AR bound to a Fab fragment that recognized an epitope composed of the amino and carboxyl terminal ends of the third intracellular loop connecting TMs 5 and 6 (Rasmussen et al. 2007).
  • the third intracellular loop was replaced by T4 lysozyme ( ⁇ 2 AR-T4L) (Rosenbaum et al. 2007).
  • Efforts to crystallize ⁇ 2 AR-Fab complex and ⁇ 2 AR-T4L bound to different agonists failed to produce crystals of sufficient quality for structure determination.
  • Nb80 Contributes to the Packing of ⁇ 2 AR in a Crystal Lattice
  • High-resolution diffraction was obtained from crystals of ⁇ 2 AR-T4L-Nb80 grown in LCP. These crystals grew at pH 8.0 in 39% to 44% PEG400, 100 mM Tris, 4% DMSO, and 1% 1,2,3-heptanetriol.
  • FIG. 7 shows the packing of the ⁇ 2 AR-T4L-Nb80 complex in the crystal lattice.
  • Nb80 binds to the cytoplasmic end of the ⁇ 2 AR, with the third complementarity-determining region (CDR) loop projecting into the core of the receptor.
  • CDR complementarity-determining region
  • the ⁇ 2 AR-nanobody complexes are arranged with the lipid bilayers approximately parallel to the be plane of the crystal. Two-fold symmetry-related nanobody molecules interact along the a axis to generate a tightly packed lattice in this direction.
  • receptor molecules interact in an antiparallel arrangement with TM1,2,3 and 4 of one ⁇ 2 AR molecule packing against TM4 and 5 of the adjacent molecule.
  • Contacts are also made between helix 8 and TM5 of parallel lattice neighbor along the b axis, and between the extracellular portion of TM1 and the cytoplasmic end of TM6 of a third, antiparallel neighbor.
  • the packing is weakest along the c axis, which may be due in part to non-specific interactions of the T4L with neighboring receptor and/or nanobody molecules. There is no interpretable electron density for the T4L, but given the visible ends of TM5 and TM6 the position of T4L is highly constrained.
  • T4L adopts a number of orientations relative to the receptor, and perhaps a range of internal conformations due to its hinge motion (Zhang et al. 1995), that average out its density. Nonetheless, T4L likely contributes to the structure of the crystal since we were unable to produce crystals of the native ⁇ 2 AR-nanobody complex under these conditions, although it is possible that the flexible loop that connects TM5 and TM6 in the native receptor prevents lattice formation.
  • FIG. 8 compares the inactive ⁇ 2 AR structure (from the carazolol-bound ⁇ 2 AR-T4L structure) with the active state of ⁇ 2 AR.
  • the largest differences are found at the cytoplasmic face of the receptor, with outward displacement of TM5 and TM6 and an inward movement of TM7 and TM3 in the ⁇ 2 AR-T4L-Nb80 complex relative to the inactive structure ( FIG. 8 , Panels A and B).
  • There are relatively small changes in the extracellular surface FIG. 8 , Panel C).
  • the second intracellular loop (ICL2) between TM3 and TM4 adopts a two-turn alpha helix, similar to that observed in the turkey ⁇ 1 AR structure (Warne et al. 2008).
  • the absence of this helix in the inactive ⁇ 2 AR structure may reflect crystal lattice contacts involving ICL2.
  • FIG. 9 Panels A-C, show in greater detail the interaction of Nb80 with the cytoplasmic side of the ⁇ 2 AR.
  • An eight amino acid sequence of CDR 3 penetrates into a hydrophobic pocket formed by amino acids from TM segments 3, 5, 6 and 7.
  • a four amino acid sequence of CDR1 provides additional stabilizing interactions with cytoplasmic ends of TM segments 5 and 6.
  • FIG. 9 Panel D, compares the cytoplasmic surface of active and inactive conformations of the ⁇ 2 AR.
  • CDR3 occupies a position similar to the carboxyl terminal peptide of transducin in opsin (Scheerer et al. 2008) ( FIG. 10 ).
  • the majority of interactions between Nb80 and the ⁇ 2 AR are mediated by hydrophobic contacts.
  • Nb80 precludes an interaction between Arg131 3.50 and Tyr219 5.58 , even though the tyrosine occupies a similar position in opsin and the active conformation of ⁇ 2 AR-T4L-Nb80.
  • Tyr326 7.53 of the highly conserved NPxxY sequence moves into the space occupied by TM6 in the inactive state.
  • inactive carazolol-bound ⁇ 2 AR-T4L we observed a network of hydrogen bonding interactions involving highly conserved amino acids in TMs 1, 2, 6 and 7 and several water molecules (Rosenbaum et al. 2007). While the resolution of the ⁇ 2 AR-T4L-Nb80 is inadequate to detect waters, it is clear that the structural changes we observe would substantially alter this network.
  • Trp 6.48 is highly conserved in Family A GPCRs, and it has been proposed that its rotameric state plays a role in GPCR activation (rotamer toggle switch) (Shi et al. 2002).
  • Trp286 6.48 lies near the base of the ligand-binding pocket, although its position shifts slightly due to rearrangements of nearby residues Ile121 3.40 and Phe282 6.44 .
  • Trp 6.48 While there is spectroscopic evidence for changes in the environment of Trp 6.48 upon activation of rhodopsin (Ahuja et al. 2009), a rotamer change is not observed in the crystal structures of rhodopsin and low-pH opsin. Moreover, recent mutagenesis experiments on the histamine receptor demonstrate that Trp 6.48 is not required for activation of the 5HT4 receptor by serotonin (Pellissier et al. 2009).
  • a potential conformational link is shown in FIG. 11 .
  • Agonist interactions may stabilize an active receptor conformation that includes a 2.1 ⁇ inward movement of TM5 at position 207 5.46 and 1.4 ⁇ inward movement of the conserved Pro211 5.50 relative to the inactive structure.
  • the relative positions of TM5, TM3, TM6 and TM7 are stabilized by interactions between Pro211 5.50 , Ile121 3.40 , Phe282 6.44 and Asn318 7.45 .
  • Nb80 Stabilizes the Active State Conformation of Members of the Adrenergic Receptor Family
  • Nanobodies that are cross-reactive to related receptors can be used as a tool to stabilize a conformational state of those related receptors.
  • Nb80 selectively binds the active conformation of the human ⁇ 1 AR receptor.
  • ⁇ 1 AR and ⁇ 2 AR are closely related adrenergic receptors.
  • PISA server Karl & Henrick, 2007
  • 30 ⁇ 2 AR AA residues were identified to interact with Nb80 in the ⁇ 2 AR-Nb80 interface.
  • Nb80 does not change the affinity for the antagonist CGP20712A ( FIG. 18D ), demonstrating the selective stabilization of the active state conformation of ⁇ 1 AR by Nb80. No such effect of Nb80 was observed on unrelated receptors like the dopamine D1 receptor (data not shown).
  • Nanobodies with G protein-like behavior likely enhance the affinity of ⁇ 2 AR for agonists (see Example 6). This behavior may have important implications in the discovery of new agonists. For example, Nbs with G protein-like behavior may increase the apparent affinity of GPCRs for agonists, compared to antagonists. This may cause a bias towards agonists among the hits when a compound library is screened against such GPCR-Nb complex.
  • Ligand competition binding experiments were performed in the presence and absence of 500 nM of Nb80 on commercial membranes containing full-length human ⁇ 2 AR. 3 H-dihydroalprenolol (DHA) was used as the competing radioligand. Representative examples of ligand competition binding experiments are shown in FIG. 16 .
  • IC50 values were obtained in the presence of excess Nb80 and compared to the IC50s obtained in the presence of an irrelevant nanobody (negative control). (Table 6). Consistent with Examples 6, 8 and 12, we observe an increase in potency for all agonists when ⁇ 2 AR is in complex with Nb80. Such effect is not observed for antagonists or inverse agonists.
  • Locking the GPCR in a particular conformation has an advantage over using a non-conformationally stabilized target (representing a repertoire of conformations) in screening assay with the aim to identify compounds against that particular conformation, the so-called “druggable” target conformation.
  • the conformational selective Nb80 allows the use of wild-type receptors consequently minimizing the potential risk of artificial conformational changes as a result of site-directed mutagenesis.
  • Nb80 facilitates the identification of ligands that selectively bind ⁇ 2 AR in its active conformation
  • a fragment library consisting of approximately 1500 distinct low molecular weight compounds ( ⁇ 300 Da) is screened for agonists using a competition radioligand binding assay.
  • membranes containing full length ⁇ 2 AR are preincubated with Nb80 or an irrelevant Nb (negative control) and added to 96-well plates containing library compounds and 2 nM of 3 H-dihydroalprenolol (DHA) radioligand (see materials and methods).
  • DHA 3 H-dihydroalprenolol
  • Library compounds that significantly displace the radioligand in the sample containing ⁇ 2 AR in complex with Nb80 as compared to the sample containing the irrelevant nanobody are compounds that preferentially bind the active conformation of the receptor.
  • Library compounds that selectively bind the active conformation of the receptor have a high propensity to behave as agonists because orthosteric or allosteric stabilization of the active conformation of the GPCR elicits biological responses.
  • Selected library compounds have to be further screened for agonism by measuring for example by G protein coupling, downstream signaling events ore physiological output.
  • Thermostabilization of membrane proteins can be achieved through site directed mutagenesis (Zhou & Bowie, 2000; Magnini et al. 2008).
  • binding of conformational selective nanobodies represents an innovative alternative for the thermostabilization of detergent-solubilized GPCRs.
  • the fluorescent thermal stability assay makes use of the thiol-specific fluorochrome N-[4-(7-diethylamino-4-methyl-3-coumarinyl)phenyl]maleimide (CPM) to measure the chemical reactivity of the native cysteines embedded in the protein interior as a sensor for the overall integrity of the folder state of membrane proteins (Alexandrov et al. 2008).
  • CPM thiol-specific fluorochrome N-[4-(7-diethylamino-4-methyl-3-coumarinyl)phenyl]maleimide
  • AT1aR was expressed in insect cells (Shluka et al. 2006) and antigen was reconstituted in lipid vesicles as previously described (Day et al. 2007).
  • lymphocytes were isolated from the blood of the immunized llama and a phage library prepared and screened as described in Materials and Methods to the Examples. Solid-phase ELISAs identified nanobodies that recognize the AT1a receptor.
  • a first screen we compare the binding of the purified nanobodies on the native and heat denatured rat AT1aR antigen in an ELISA. For each nanobody, one well is coated with receptor. Next, this plate is incubated at 80° C. for two hours. Next, another empty well of the same plate is coated with receptor without heating. Nanobodies that are able to selectively bind the native receptor but not the heat inactivated receptor recognize conformational epitopes.
  • Nanobodies are evaluated in a radioligand competition experiment similar to the radioligand assays described in Examples 6, 12, and 13. Nanobodies that increase the affinity of AT1aR to an agonist are considered to stabilize an active conformation of the receptor.
  • a llama Llama glama
  • M3R-T4lysozyme M3R-T4L
  • M3R-T4L M3R-T4lysozyme
  • a first screen we compare the binding of the purified nanobodies on the native and heat denatured rat M3R antigen in an ELISA. For each nanobody, one well is coated with receptor. Next, this plate is incubated at 80° C. for two hours. Next, another empty well of the same plate is coated with receptor without heating. Nanobodies that are able to selectively bind the native receptor but not the heat inactivated receptor recognize conformational epitopes.
  • Nanobodies are evaluated in a radioligand competition experiment similar to the radioligand assays described in Examples 6, 12, and 13. Nanobodies that increase the affinity of M3R to an agonist are considered to stabilize an active conformation of the receptor.
  • ⁇ 2 AR truncated after amino acid 365 ( ⁇ 2 AR-365) having an amino terminal Flag epitope tag was expressed in Sf9 insects cells and purified by sequential M1 antibody and alprenolol affinity chromatography as previously described (Kobilka 1995).
  • ⁇ 2 AR-365 was immobilized on a Flag column (Sigma) and equilibrated with 10 column volumes of a mixture of 5 mg/ml DOPC (Avanti Polar Lipids) and 0.5 mg/ml Lipid A (Sigma) in 1% (w/v) octylglucoside (Anatrace), 100 mM NaCl, 20 mM Hepes pH 7.5, 2 mM CaCl2 and 1 ⁇ M agonist (e.g., isoproterenol). The ⁇ 2 AR was then eluted in the same buffer containing EDTA. The concentration of the eluted ⁇ 2 AR was adjusted to 5 mg/ml.
  • AT1aR with T4lysozyme fusion in the third loop was truncated after amino acid 318 (AT1aR-318).
  • This construct has an amino terminal Flag epitope tag and a C-terminal tag of ten histidines.
  • AT1aR-318 was expressed in Tni insect cells and solubilized in 20 mM Hepes, pH7.4, 1 M NaCl and 0.5% MNG for two hours at room temperature.
  • the receptor was purified by sequential Ni-NTA and FLAG-M1 antibody affinity chromatography.
  • Purified AT1aR was reconstituted in a mixture of 5 mg/ml DOPC (Avanti Polar Lipids) and 0.5 mg/ml Lipid A (Sigma) in 1% (w/v) octylglucoside (Anatrace), 100 mM NaCl, 20 mM Hepes pH 7.5, and 100 ⁇ M agonist (e.g., angiotensin II). The concentration of the eluted At1aR was adjusted to 1-2 mg/ml. The protein was then dialyzed against phosphate buffered saline containing 100 ⁇ M agonist at 4° C. to remove detergent. The reconstituted protein was stored at ⁇ 80° C. prior to use for immunization.
  • M 3 -muscarinic receptor with an amino terminal FLAG epitope tag and carboxy-terminal hexahistidine tag was expressed in Sf9 insect cells in the presence of 1 ⁇ M atropine (Vasudevan et al. 1995).
  • Receptor either had intracellular loop 3 deleted (M3R ⁇ i3) or substituted with T4 lysozyme (M3R-T4L).
  • Cells were centrifuged and then lysed by osmotic shock, and protein was solubilized in 1% dodecylmaltoside, 0.1% cholesterol hemisuccinate, 750 mM sodium chloride, 20 mM HEPES pH 7.5. Solubilized receptor was then purified by nickel affinity chromatography followed by FLAG affinity chromatography. Purified protein was then separated by size exclusion chromatography to select monomeric receptor, which was reconstituted as described (Day et al. 2007).
  • a single llama received six weekly administrations of the reconstituted truncated ⁇ 2 AR.
  • Lymphocytes were isolated from the blood of the immunized llama and total RNA was prepared from these cells.
  • the coding sequences of the nanobody repertoire were amplified by an RT-PCR and cloned into the phage display vector pMES4 (genbank GQ907248) (Conrath et al. 2001).
  • ⁇ 2 AR-specific phages were enriched by in vitro selection on Maxisorp (Nunc) 96-well plates coated with the reconstituted ⁇ 2 AR-365 receptor.
  • Antigen-bound phages were recovered from antigen-coated wells either with thriethylamine pH11 and neutralized with Tris-HCl pH7 or by the addition of freshly grown TG1 E. coli cells. After two rounds of bio-panning, 96 individual colonies were randomly picked and the nanobodies produced as a soluble HIS-tagged protein in the periplasm of the TG1 cells. Solid-phase ELISAs identified 16 different conformational nanobodies that recognize native agonist-bound ⁇ 2 AR-365, but not the heat denatured receptor.
  • One single llama received six weekly administrations of the reconstituted AT1aR-318 bound to its agonist angiotensin. Another single llama received six weekly administrations of AT1aR-318 bound to a biased agonist TRV023.
  • lymphocytes from each llama were isolated separately from the blood. Total RNA was prepared from these cells. From each sample the coding sequences of the nanobody repertoire were amplified by RT-PCR and cloned separately (Conrath et al. 2001) into the phage display vector pMESy4-vector to generate two independent libraries.
  • pMESy4 is a derivative of pMES4 (genbank GQ907248) carrying a C-terminal His6tag followed by the amino acids EPEA (De Genst et al. 2010, J. Mol. Biol. 402:326-343).
  • AT1aR-specific phage was enriched by in vitro selection on Maxisorp (Nunc) 96-well plates coated with the reconstituted truncated AT1aR receptor (a variant of the recombinant receptor without the T4L insertion) bound to angiotensin or to TRV023, respectively.
  • Antigen-bound phage was recovered from antigen-coated wells by trypsin digestion. After two rounds of bio-panning, 92 individual colonies (46 on AT1aR-angiotensin and 46 on AT1aR-TRV023) were randomly picked and the nanobodies were produced as a soluble HisIS-EPEA-tagged protein in the periplasm of the TG1 cells.
  • One single llama received six weekly administrations of reconstituted truncated M3R-T4L bound to the antagonist tiotropium. After immunization, lymphocytes from this llama were isolated from the blood and total RNA was prepared from these cells. The coding sequences of the nanobody repertoire were amplified by RT-PCR and cloned (Conrath et al. 2001) into the phage display vector pMESy4-vector.
  • Antigen formats include virus-like particles (VLPs) carrying the rat M3R ⁇ i3 receptor (i.e., the M3 receptor with a deletion in the third intracellular loop), membranes of human CHO cells containing M3R (Perkin Elmer), recombinant reconstituted M3R-T4L, or recombinant reconstituted M3R ⁇ i3.
  • VLPs virus-like particles carrying the rat M3R ⁇ i3 receptor
  • membranes of human CHO cells containing M3R Perkin Elmer
  • recombinant reconstituted M3R-T4L recombinant reconstituted M3R ⁇ i3.
  • VLPs carrying the rat M3R ⁇ i3 receptor or the human M3R membranes were captured by wheat germ agglutinin coated on Maxisorp (Nunc) 96-well plates.
  • Antigen-bound phage was recovered from antigen-coated wells by a trypsin digestion.
  • phage selected on agonist-bound antigen is eluted using an excess of antagonist or vice versa.
  • HIS-tagged or HIS-EPEA-tagged nanobodies were expressed in WK6 E. coli cells.
  • Periplasmic extracts were subjected to immobilized metal affinity chromatography on nickel (II) sulfate fast-flow sepharose (GE Healthcare).
  • IMAC protein fractions were dialyzed overnight in 100 mM MES pH 6.5, 100 mM NaCl buffer. Dialyzed nanobodies were further purified by cation exchange chromatography (AKTA FPLC with Mono S10/100 GL column).
  • Agonist selective nanobodies were identified by size exclusion chromatography following incubation of 20 ⁇ M agonist or inverse agonist- (carazolol-) bound ⁇ 2 AR-365N for one hour at RT in the absence or presence of 40 ⁇ M nanobody. Chromatography was performed in 0.1% DDM, 20 mM HEPES pH7.5, 100 mM NaCl in the presence of 1 ⁇ M of the respective ligands using an ⁇ KTA FPLC with Superdex 200 10/300 GL column.
  • binding experiments were performed on ⁇ 2 AR-365 expressed in Sf9 insect cell membranes in the absence or presence of 1 ⁇ M nanobody for 90 minutes at RT in binding buffer (75 mM Tris pH7.5, 12.5 mM MgCl 2 , 1 mM EDTA, 0.05% BSA, and 10 ⁇ M GTP ⁇ S) containing 0.5 nM [ 3 H]-dihydroalprenolol and ( ⁇ )-isoproterenol at concentrations ranging from 10 ⁇ 11 M to 10 ⁇ 4 M.
  • Bound radioligand was separated from unbound over Whatman GF/B filters using a Brandel harvester. The data are the mean ⁇ S.E. of two independent experiments performed in triplicate.
  • excitation was set at 370 nm and emission was measured from 430-530 nm with an integration time of 1 s/nm.
  • three individual labeled protein samples were incubated with 1 ⁇ M nanobody or 10 ⁇ M Isoproterenol or both. Emission spectra of the samples were taken after 1 hour incubation. Fluorescence intensity was corrected for background fluorescence from buffer and ligands in all experiments. The data are the mean ⁇ S.E. of two independent experiments performed in triplicate.
  • ⁇ 2 AR-T4L was expressed in Sf-9 insect cell cultures infected with ⁇ 2 AR-T4L baculovirus, and solubilized according to previously described methods (Kobilka 1995). Functional protein was obtained by M1 FLAG affinity chromatography (Sigma) prior to and following alprenolol-Sepharose chromatography (Kobilka 1995). In the second M1 chromatography step, receptor-bound alprenolol was exchanged for a high affinity agonist and dodecylmaltoside was exchanged for the MNG-3 amphiphile for increased receptor stability (Chae and Gellman, unpublished).
  • the agonist-bound and detergent-exchanged ⁇ 2 AR-T4L was eluted in 10 mM HEPES pH 7.5, 100 mM NaCl, 0.02% MNG-3, and 10 ⁇ M agonist followed by removal of N-linked glycosylation by treatment with PNGaseF (NEB).
  • the protein was concentrated to ⁇ 50 mg/ml with a 100 kDa molecular weight cut off Vivaspin concentrator (Vivascience).
  • Agonist-bound ⁇ 2 AR-T4L and nanobody were mixed in 1:1.2 molar ratio, incubated two hours at RT before mixing with liquefied monoolein (M7765, Sigma) containing 10% cholesterol (C8667, Sigma) in 1:1.5 protein to lipid ratio (w/w) using the twin-syringe mixing method developed by Martin Caffrey (Caffrey and Cherezov 2009).
  • Initial crystallization leads were identified using in-house screens and optimized in 24-well glass sandwich plates using 50 nL protein:lipid drops manually delivered and overlaid with 0.8 ⁇ l precipitant solution in each well and sealed with a glass cover slip. Crystals for data collection were grown at 20° C.
  • Diffraction data were measured at beamline 23-ID of the Advanced Photon Source, using a 10 ⁇ m diameter beam.
  • Low dose 1.0° rotation images were used to locate and center crystals for data collection.
  • Data were measured in 1.0° frames with exposure times typically five to ten seconds with a 5 ⁇ attenuated beam. Only 5-10° of data could be measured before significant radiation damage occurred.
  • Data were integrated and scaled with the HKL2000 package (Otwinowski 1997).
  • the search models were 1) the high-resolution carazolol-bound ⁇ 2 AR structure, PDB id 2RH1, but with T4L and all water, ligand and lipid molecules removed) and a nanobody (PDB id 3DWT, water molecules removed) as search models.
  • the rotation and translation function Z scores were 8.7 and 9.0 after placing the ⁇ 2 AR model, and the nanobody model placed subsequently had rotation and translation function Z scores of 3.5 and 11.5.
  • the model was refined in Phenix (Afonine 2005) and Buster (Blanc 2004), using a group B factor model with one B for main chain and one B for side chain atoms. Refinement statistics are given in Table 5. Despite the strong anisotropy (Table 5), the electron density was clear for the placement of side chains.
  • the effect of Nb80 and Gs on the receptors affinity for agonists was compared in competition binding experiments.
  • the ⁇ 2 AR and ⁇ 2 AR-T4L (both truncated at position 365) purified as previously described (Rosenbaum et al. 2007; Rasmussen et al. 2007) were reconstituted in high-density lipoprotein (HDL) particles followed by reconstitution of Gs into HDL particles containing ⁇ 2 AR according to previously published methods (Whorton et al. 2007).
  • 3 H-DHA [ 3 H]-dihydroalprenolol ( 3 H-DHA) was used as radioligand and ( ⁇ )-isoproterenol (ISO) at concentrations ranging from 10 ⁇ 12 to 10 ⁇ 4 M as competitor. Nb80 was used at 1 ⁇ M. GTP ⁇ S was used at 10 ⁇ M. TBS (50 mM Tris pH 7.4, 150 mM NaCl) containing 0.1% BSA was used as binding buffer. Bound 3 H-DHA was separated from unbound on a Brandel harvester by passing over a Whatman GF/B filter (presoaked in TBS with 0.3% polyethylenimine) and washed in cold TBS.
  • Whatman GF/B filter presoaked in TBS with 0.3% polyethylenimine
  • Nanobodies were applied at a final concentration of 500 nM, corresponding to a 3000-fold excess of nanobody versus the adrenergic receptor. Subsequently, an appropriate dilution series of the ligand under investigation was added to the nanobody-bound membrane extracts together with 2 nM of 3 H-DHA radioligand (Perkin Elmer cat nr NET720001MC; specific activity of 104.4 Ci/mmol). The total volume per well was adjusted with incubation buffer to 500 ⁇ l and the reaction mixture was further incubated for another hour at 37° C. in a water bath.
  • 3 H-DHA radioligand Perkin Elmer cat nr NET720001MC; specific activity of 104.4 Ci/mmol
  • a compound library was screened for agonists using a competition radioligand binding assay.
  • 10 ⁇ g of in house prepared membrane extracts from HEK293T cells expressing human ⁇ 2 AR expression level of ⁇ 10 ⁇ mol/mg membrane protein
  • Nb80 or a non-related Nanobody negative control
  • Nanobodies are applied at a final concentration of 500 nM, roughly corresponding to a 3000-fold excess of Nanobody versus the ⁇ 2 AR.
  • Nanobody-loaded membranes are added to 96-well plates containing library compounds and 2 nM of 3 H-dihydroalprenolol (DHA) radioligand.
  • DHA 3 H-dihydroalprenolol
  • the total volume per well is adjusted with incubation buffer to 100 ⁇ l and the reaction mixture is further incubated for another hour at 30° C.
  • membrane-bound radioligand is harvested using a GF/B glass fiber 96-well filterplate (Perkin Elmer) presoaked in 0.3% polyethylenimine. Filter plates are washed with ice-cold wash buffer (50 mM Tris-HCl pH7.4), and dried for 30 minutes at 50° C. After adding 25 ⁇ l of scintillation fluid (MicroScintTM-O, Perkin Elmer), radioactivity (cpm) is measured in a Wallace MicroBeta TriLux scintillation counter.
  • scintillation fluid MicroScintTM-
  • Nanobody 80 induced potency shift of (ant-)agonists show an increased affinity for the ⁇ 2 AR-Nb80 complex.
  • Type competitor for Competitor ID ⁇ 2 AR Potency shift* isoproterenol agonist 8.8 alprenolol antagonist 1.1 carvedilol antagonist 1.2 CGP12177A antagonist 1.0 salmeterol full agonist 3.3 terbutaline partial agonist 4.3 dobutamine partial agonist 2.3 salbutamol partial agonist 4.2 ICI118,551 Inverse agonist 0.9 metaproterenol agonist 2.9 procaterol agonist 2.3 ritodrine agonist 2.7 fenoterol Full agonist 3.7 formoterol agonist 4.0 timolol antagonist 0.6 *Potency shifts were determined as the ratio of the IC50 measured in the presence of an irrelevant Nb (negative control) and the IC50 measured in the presence of Nb80.

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CN112851811A (zh) * 2021-01-28 2021-05-28 姜国胜 一种cd44v6纳米抗体及其作为白血病研究试剂的应用
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