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Qu L, Li T, Cun S, Zheng X, Xiang M, Dong Y, Ji X, Bian L, Li Q, Zhao X. A chromatographic method for determining the interaction between a drug and two target proteins by fabricating a dual-heterogeneous surface. J Chromatogr A 2024; 1715:464606. [PMID: 38154257 DOI: 10.1016/j.chroma.2023.464606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 12/30/2023]
Abstract
Characterization of the drug-target interactions is pivotal throughout the whole procedure of drug development. Most of the current assays, particularly, chromatographic methods lack the capacity to reveal drug adsorption on the muti-target surface. To this end, we derived a reliable and workable mathematical equation for revealing drug bindings to dual targets on the heterogeneous surface starting from the mass balance equation. The derivatization relied on the correlation of drug injection amounts with their retention factors. Experimental validation was performed by determining the binding parameters of three canonical drugs on a heterogeneous surface, which was fabricated by fusing angiotensin receptor type I and type II receptors (AT1R and AT2R) at the terminuses of circularly permuted HaloTag (cpHaloTag) and immobilizing the whole fusion protein onto 6-bromohexanoic acid modified silica gel. We proved that immobilized AT1R-cpHalo-AT2R maintained the original ligand- and antibody-binding activities of the two receptors in three weeks. The association constants of valsartan, candesartan, and telmisartan to AT1R were (6.26±0.14) × 105, (9.66±0.71) × 105, and (3.17±0.03) × 105 L/mol. In the same column, their association constants to AT2R were (1.25±0.04) × 104, (2.30±0.08) × 104, and (8.51±0.06) × 103 L/mol. The patterns of the association constants to AT1R/AT2R (candesartan>valsartan>telmisartan) were in good line with the data by performing nonlinear chromatography on control columns containing immobilized AT1R or AT2R alone. This provided proof of the fact that the derivatization allowed the determination of drug bindings on the heterogeneous surface with the utilization of a single series of injections and linear regression. We reasoned that is simple enough to model the bindings of drug adsorption on commercially available adsorbents in fundamental or industrial fields, thus having the potential to become a universal method for analyzing the bindings of a drug to the heterogeneous surface containing multiple targets.
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Affiliation(s)
- Lejing Qu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Ting Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Sidi Cun
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Xinxin Zheng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Mingjuan Xiang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Yuxuan Dong
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Xu Ji
- Engineering Research Center of Tibetan Medicine Detection Technology, Ministry of Education, Xizang Minzu University, Xianyang 712082, China
| | - Liujiao Bian
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Qian Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Xinfeng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
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2
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Ray M, Sayeed A, Ganshert M, Saha A. Direct Binding Methods to Measure Receptor-Ligand Interactions. J Phys Chem B 2024; 128:3-19. [PMID: 38134048 DOI: 10.1021/acs.jpcb.3c05041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
G-protein-coupled receptors (GPCRs) contribute to numerous physiological processes via complex network mechanisms. While indirect signaling assays (Ca2+ mobilization, cAMP production, and GTPγS binding) have been useful in identifying and characterizing downstream signaling mechanisms of GPCRs, these methods lack measurements of direct binding affinities, kinetics, binding specificity, and selectivity that are important parameters in GPCR drug discovery. In comparison to existing direct methods that use radio- or fluorescent labels, label-free techniques can closely emulate the native interactions around binding partners. Surface plasmon resonance (SPR) is a label-free technique that utilizes the refractive index (RI) property and is applied widely in quantitative GPCR-ligand binding kinetics measurement including small molecules screening. However, purified GPCRs are further embedded in a synthetic lipid environment which is immobilized through different tags to the SPR sensor surface, resulting in a non-native environment. Here, we introduced a methodology that also uses the RI property to measure binding interactions in a label-free, immobilization-free arrangement. The free-solution technique is successfully applied in quantifying the interaction of bioactive lipids to cognate lipid GPCRs, which is not purified but rather present in near-native conditions, i.e., in milieu of other cytoplasmic lipids and proteins. To further consider the wide applicability of these free-solution approaches in biomolecular interaction research, additional applications on a variety of receptor-ligand pairs are imperative.
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Affiliation(s)
- Manisha Ray
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Road, Chicago, Illinois 60660, United States
| | - Aryana Sayeed
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Road, Chicago, Illinois 60660, United States
| | - Madeline Ganshert
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Road, Chicago, Illinois 60660, United States
| | - Arjun Saha
- Department of Chemistry and Biochemistry, University of Wisconsin, Milwaukee Chemistry Bldg, 144, 3210 N Cramer Street, Milwaukee, Wisconsin 53211, United States
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3
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Nakagawa F, Kikkawa M, Chen S, Miyashita Y, Hamaguchi-Suzuki N, Shibuya M, Yamashita S, Nagase L, Yasuda S, Shiroishi M, Senda T, Ito K, Murata T, Ogasawara S. Anti-nanodisc antibodies specifically capture nanodiscs and facilitate molecular interaction kinetics studies for membrane protein. Sci Rep 2023; 13:11627. [PMID: 37468499 DOI: 10.1038/s41598-023-38547-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 07/10/2023] [Indexed: 07/21/2023] Open
Abstract
Nanodisc technology has dramatically advanced the analysis of molecular interactions for membrane proteins. A nanodisc is designed as a vehicle for membrane proteins that provide a native-like phospholipid environment and better thermostability in a detergent-free buffer. This enables the determination of the thermodynamic and kinetic parameters of small molecule binding by surface plasmon resonance. In this study, we generated a nanodisc specific anti-MSP (membrane scaffold protein) monoclonal antibody biND5 for molecular interaction analysis of nanodiscs. The antibody, biND5 bound to various types of nanodiscs with sub-nanomolar to nanomolar affinity. Epitope mapping analysis revealed specific recognition of 8 amino acid residues in the exposed helix-4 structure of MSP. Further, we performed kinetics binding analysis between adenosine A2a receptor reconstituted nanodiscs and small molecule antagonist ZM241385 using biND5 immobilized sensor chips. These results show that biND5 facilitates the molecular interaction kinetics analysis of membrane proteins substituted in nanodiscs.
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Affiliation(s)
- Fuhito Nakagawa
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-Cho, Inage, Chiba, 263-8522, Japan
| | - Marin Kikkawa
- Department of Food and Nutritional Sciences, Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-Ku, Shizuoka, 422-8526, Japan
| | - Sisi Chen
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-Cho, Inage, Chiba, 263-8522, Japan
- Membrane Protein Research Center, Chiba University, 1-33 Yayoi-Cho, Inage, Chiba, 263-8522, Japan
| | - Yasuomi Miyashita
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-Cho, Inage, Chiba, 263-8522, Japan
| | - Norie Hamaguchi-Suzuki
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-Cho, Inage, Chiba, 263-8522, Japan
| | - Minami Shibuya
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-Cho, Inage, Chiba, 263-8522, Japan
| | - Soichi Yamashita
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-Cho, Inage, Chiba, 263-8522, Japan
| | - Lisa Nagase
- Structure Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Satoshi Yasuda
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-Cho, Inage, Chiba, 263-8522, Japan
- Membrane Protein Research Center, Chiba University, 1-33 Yayoi-Cho, Inage, Chiba, 263-8522, Japan
- Department of Quantum Life Science, Graduate School of Science, Chiba University, 1-33 Yayoi-Cho, Inage, Chiba, 263-8522, Japan
| | - Mitsunori Shiroishi
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-Ku, Tokyo, 125-8585, Japan
| | - Toshiya Senda
- Structure Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan
- Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University of Advanced Studies (Soken-Dai), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Keisuke Ito
- Department of Food and Nutritional Sciences, Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-Ku, Shizuoka, 422-8526, Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-Cho, Inage, Chiba, 263-8522, Japan.
- Membrane Protein Research Center, Chiba University, 1-33 Yayoi-Cho, Inage, Chiba, 263-8522, Japan.
- Structure Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan.
- Department of Quantum Life Science, Graduate School of Science, Chiba University, 1-33 Yayoi-Cho, Inage, Chiba, 263-8522, Japan.
| | - Satoshi Ogasawara
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-Cho, Inage, Chiba, 263-8522, Japan.
- Membrane Protein Research Center, Chiba University, 1-33 Yayoi-Cho, Inage, Chiba, 263-8522, Japan.
- Department of Quantum Life Science, Graduate School of Science, Chiba University, 1-33 Yayoi-Cho, Inage, Chiba, 263-8522, Japan.
- Institute for Advanced Academic Research, Chiba University, 1-33 Yayoi-Cho, Inage, Chiba, 263-8522, Japan.
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Mettai M, Daoud I, Mesli F, Kenouche S, Melkemi N, Kherachi R, Belkadi A. Molecular docking/dynamics simulations, MEP analysis, bioisosteric replacement and ADME/T prediction for identification of dual targets inhibitors of Parkinson's disease with novel scaffold. In Silico Pharmacol 2023; 11:3. [PMID: 36687301 PMCID: PMC9852416 DOI: 10.1007/s40203-023-00139-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 01/04/2023] [Indexed: 01/20/2023] Open
Abstract
Monoamine oxidase B and Adenosine A2A receptors are used as key targets for Parkinson's disease. Recently, hMAO-B and hA2AR Dual-targets inhibitory potential of a novel series of Phenylxanthine derivatives has been established in experimental findings. Hence, the current study examines the interactions between 38 compounds of this series with hMAO-B and hA2AR targets using different molecular modeling techniques to investigate the binding mode and stability of the formed complexes. A molecular docking study revealed that the compounds L24 ((E)-3-(3-Chlorophenyl)-N-(4-(1,3-dimethyl-2,6-dioxo-2,3,6,7-tetrahydro-1H-purin-8-yl) phenyl) acrylamide and L32 ((E)-3-(3-Chlorophenyl)-N-(3-(1,3-dimethyl-2,6-dioxo-2,3,6,7-tetrahydro-1H-purin-8-yl)phenyl)acrylamide) had a high affinity (S-score: -10.160 and -7.344 kcal/mol) with the pocket of hMAO-B and hA2AR targets respectively, and the stability of the studied complexes was confirmed during MD simulations. Also, the MEP maps of compounds 24 and 32 were used to identify the nucleophilic and electrophilic attack regions. Moreover, the bioisosteric replacement approach was successfully applied to design two new analogs of each compound with similar biological activities and low energy scores. Furthermore, ADME-T and Drug-likeness results revealed the promising pharmacokinetic properties and oral bioavailability of these compounds. Thus, compounds L24, L32, and their analogs can undergo further analysis and optimization in order to design new lead compounds with higher efficacy toward Parkinson's disease. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-023-00139-3.
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Affiliation(s)
- Merzaka Mettai
- Group of Computational and Pharmaceutical Chemistry LMCE Laboratory, University of Biskra, 07000 Biskra, Algeria
| | - Ismail Daoud
- Department of Matter Sciences, University Mohamed Khider, BP 145 RP, 07000 Biskra, Algeria
- Laboratory of Natural and Bio-actives Substances, Faculty of Science, Tlemcen University, P.O. Box 119, Tlemcen, Algeria
| | - Fouzia Mesli
- Laboratory of Natural and Bio-actives Substances, Faculty of Science, Tlemcen University, P.O. Box 119, Tlemcen, Algeria
| | - Samir Kenouche
- Group of Modeling of Chemical Systems using Quantum Calculations, Applied Chemistry Laboratory, University of Mohamed Khider, 07000 Biskra, Algeria
| | - Nadjib Melkemi
- Group of Computational and Pharmaceutical Chemistry LMCE Laboratory, University of Biskra, 07000 Biskra, Algeria
| | - Rania Kherachi
- Group of Computational and Pharmaceutical Chemistry LMCE Laboratory, University of Biskra, 07000 Biskra, Algeria
| | - Ahlem Belkadi
- Group of Computational and Pharmaceutical Chemistry LMCE Laboratory, University of Biskra, 07000 Biskra, Algeria
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GPCR Agonist-to-Antagonist Conversion: Enabling the Design of Nucleoside Functional Switches for the A 2A Adenosine Receptor. J Med Chem 2022; 65:11648-11657. [PMID: 35977382 PMCID: PMC9469204 DOI: 10.1021/acs.jmedchem.2c00462] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
Modulators of the G protein-coupled A2A adenosine
receptor
(A2AAR) have been considered promising agents to treat
Parkinson’s disease, inflammation, cancer, and central nervous
system disorders. Herein, we demonstrate that a thiophene modification
at the C8 position in the common adenine scaffold converted an A2AAR agonist into an antagonist. We synthesized and characterized
a novel A2AAR antagonist, 2 (LJ-4517), with Ki = 18.3 nM. X-ray crystallographic structures
of 2 in complex with two thermostabilized A2AAR constructs were solved at 2.05 and 2.80 Å resolutions. In
contrast to A2AAR agonists, which simultaneously interact
with both Ser2777.42 and His2787.43, 2 only transiently contacts His2787.43, which can be direct
or water-mediated. The n-hexynyl group of 2 extends into an A2AAR exosite. Structural analysis revealed
that the introduced thiophene modification restricted receptor conformational
rearrangements required for subsequent activation. This approach can
expand the repertoire of adenosine receptor antagonists that can be
designed based on available agonist scaffolds.
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Cancer-Associated Mutations of the Adenosine A2A Receptor Have Diverse Influences on Ligand Binding and Receptor Functions. Molecules 2022; 27:molecules27154676. [PMID: 35897852 PMCID: PMC9331671 DOI: 10.3390/molecules27154676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/14/2022] [Accepted: 07/20/2022] [Indexed: 11/17/2022] Open
Abstract
The adenosine A2A receptor (A2AAR) is a class A G-protein-coupled receptor (GPCR). It is an immune checkpoint in the tumor micro-environment and has become an emerging target for cancer treatment. In this study, we aimed to explore the effects of cancer-patient-derived A2AAR mutations on ligand binding and receptor functions. The wild-type A2AAR and 15 mutants identified by Genomic Data Commons (GDC) in human cancers were expressed in HEK293T cells. Firstly, we found that the binding affinity for agonist NECA was decreased in six mutants but increased for the V275A mutant. Mutations A165V and A265V decreased the binding affinity for antagonist ZM241385. Secondly, we found that the potency of NECA (EC50) in an impedance-based cell-morphology assay was mostly correlated with the binding affinity for the different mutants. Moreover, S132L and H278N were found to shift the A2AAR towards the inactive state. Importantly, we found that ZM241385 could not inhibit the activation of V275A and P285L stimulated by NECA. Taken together, the cancer-associated mutations of A2AAR modulated ligand binding and receptor functions. This study provides fundamental insights into the structure–activity relationship of the A2AAR and provides insights for A2AAR-related personalized treatment in cancer.
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Wang J, Bhattarai A, Do HN, Akhter S, Miao Y. Molecular Simulations and Drug Discovery of Adenosine Receptors. Molecules 2022; 27:2054. [PMID: 35408454 PMCID: PMC9000248 DOI: 10.3390/molecules27072054] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/18/2022] [Accepted: 03/20/2022] [Indexed: 02/02/2023] Open
Abstract
G protein-coupled receptors (GPCRs) represent the largest family of human membrane proteins. Four subtypes of adenosine receptors (ARs), the A1AR, A2AAR, A2BAR and A3AR, each with a unique pharmacological profile and distribution within the tissues in the human body, mediate many physiological functions and serve as critical drug targets for treating numerous human diseases including cancer, neuropathic pain, cardiac ischemia, stroke and diabetes. The A1AR and A3AR preferentially couple to the Gi/o proteins, while the A2AAR and A2BAR prefer coupling to the Gs proteins. Adenosine receptors were the first subclass of GPCRs that had experimental structures determined in complex with distinct G proteins. Here, we will review recent studies in molecular simulations and computer-aided drug discovery of the adenosine receptors and also highlight their future research opportunities.
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Affiliation(s)
| | | | | | | | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047, USA; (J.W.); (A.B.); (H.N.D.); (S.A.)
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Ballante F, Kooistra AJ, Kampen S, de Graaf C, Carlsson J. Structure-Based Virtual Screening for Ligands of G Protein-Coupled Receptors: What Can Molecular Docking Do for You? Pharmacol Rev 2021; 73:527-565. [PMID: 34907092 DOI: 10.1124/pharmrev.120.000246] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
G protein-coupled receptors (GPCRs) constitute the largest family of membrane proteins in the human genome and are important therapeutic targets. During the last decade, the number of atomic-resolution structures of GPCRs has increased rapidly, providing insights into drug binding at the molecular level. These breakthroughs have created excitement regarding the potential of using structural information in ligand design and initiated a new era of rational drug discovery for GPCRs. The molecular docking method is now widely applied to model the three-dimensional structures of GPCR-ligand complexes and screen for chemical probes in large compound libraries. In this review article, we first summarize the current structural coverage of the GPCR superfamily and the understanding of receptor-ligand interactions at atomic resolution. We then present the general workflow of structure-based virtual screening and strategies to discover GPCR ligands in chemical libraries. We assess the state of the art of this research field by summarizing prospective applications of virtual screening based on experimental structures. Strategies to identify compounds with specific efficacy and selectivity profiles are discussed, illustrating the opportunities and limitations of the molecular docking method. Our overview shows that structure-based virtual screening can discover novel leads and will be essential in pursuing the next generation of GPCR drugs. SIGNIFICANCE STATEMENT: Extraordinary advances in the structural biology of G protein-coupled receptors have revealed the molecular details of ligand recognition by this large family of therapeutic targets, providing novel avenues for rational drug design. Structure-based docking is an efficient computational approach to identify novel chemical probes from large compound libraries, which has the potential to accelerate the development of drug candidates.
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Affiliation(s)
- Flavio Ballante
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Albert J Kooistra
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Stefanie Kampen
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Chris de Graaf
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Jens Carlsson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
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9
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Kricker JA, Page CP, Gardarsson FR, Baldursson O, Gudjonsson T, Parnham MJ. Nonantimicrobial Actions of Macrolides: Overview and Perspectives for Future Development. Pharmacol Rev 2021; 73:233-262. [PMID: 34716226 DOI: 10.1124/pharmrev.121.000300] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Macrolides are among the most widely prescribed broad spectrum antibacterials, particularly for respiratory infections. It is now recognized that these drugs, in particular azithromycin, also exert time-dependent immunomodulatory actions that contribute to their therapeutic benefit in both infectious and other chronic inflammatory diseases. Their increased chronic use in airway inflammation and, more recently, of azithromycin in COVID-19, however, has led to a rise in bacterial resistance. An additional crucial aspect of chronic airway inflammation, such as chronic obstructive pulmonary disease, as well as other inflammatory disorders, is the loss of epithelial barrier protection against pathogens and pollutants. In recent years, azithromycin has been shown with time to enhance the barrier properties of airway epithelial cells, an action that makes an important contribution to its therapeutic efficacy. In this article, we review the background and evidence for various immunomodulatory and time-dependent actions of macrolides on inflammatory processes and on the epithelium and highlight novel nonantibacterial macrolides that are being studied for immunomodulatory and barrier-strengthening properties to circumvent the risk of bacterial resistance that occurs with macrolide antibacterials. We also briefly review the clinical effects of macrolides in respiratory and other inflammatory diseases associated with epithelial injury and propose that the beneficial epithelial effects of nonantibacterial azithromycin derivatives in chronic inflammation, even given prophylactically, are likely to gain increasing attention in the future. SIGNIFICANCE STATEMENT: Based on its immunomodulatory properties and ability to enhance the protective role of the lung epithelium against pathogens, azithromycin has proven superior to other macrolides in treating chronic respiratory inflammation. A nonantibiotic azithromycin derivative is likely to offer prophylactic benefits against inflammation and epithelial damage of differing causes while preserving the use of macrolides as antibiotics.
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Affiliation(s)
- Jennifer A Kricker
- EpiEndo Pharmaceuticals, Reykjavik, Iceland (J.A.K., C.P.P., F.R.G., O.B., T.G., M.J.P.); Stem Cell Research Unit, Biomedical Center, University of Iceland, Reykjavik, Iceland (J.A.K., T.G.); Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (C.P.P.); Department of Respiratory Medicine (O.B.), Department of Laboratory Hematology (T.G.), Landspitali-University Hospital, Reykjavik, Iceland; Faculty of Biochemistry, Chemistry and Pharmacy, JW Goethe University Frankfurt am Main, Germany (M.J.P.)
| | - Clive P Page
- EpiEndo Pharmaceuticals, Reykjavik, Iceland (J.A.K., C.P.P., F.R.G., O.B., T.G., M.J.P.); Stem Cell Research Unit, Biomedical Center, University of Iceland, Reykjavik, Iceland (J.A.K., T.G.); Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (C.P.P.); Department of Respiratory Medicine (O.B.), Department of Laboratory Hematology (T.G.), Landspitali-University Hospital, Reykjavik, Iceland; Faculty of Biochemistry, Chemistry and Pharmacy, JW Goethe University Frankfurt am Main, Germany (M.J.P.)
| | - Fridrik Runar Gardarsson
- EpiEndo Pharmaceuticals, Reykjavik, Iceland (J.A.K., C.P.P., F.R.G., O.B., T.G., M.J.P.); Stem Cell Research Unit, Biomedical Center, University of Iceland, Reykjavik, Iceland (J.A.K., T.G.); Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (C.P.P.); Department of Respiratory Medicine (O.B.), Department of Laboratory Hematology (T.G.), Landspitali-University Hospital, Reykjavik, Iceland; Faculty of Biochemistry, Chemistry and Pharmacy, JW Goethe University Frankfurt am Main, Germany (M.J.P.)
| | - Olafur Baldursson
- EpiEndo Pharmaceuticals, Reykjavik, Iceland (J.A.K., C.P.P., F.R.G., O.B., T.G., M.J.P.); Stem Cell Research Unit, Biomedical Center, University of Iceland, Reykjavik, Iceland (J.A.K., T.G.); Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (C.P.P.); Department of Respiratory Medicine (O.B.), Department of Laboratory Hematology (T.G.), Landspitali-University Hospital, Reykjavik, Iceland; Faculty of Biochemistry, Chemistry and Pharmacy, JW Goethe University Frankfurt am Main, Germany (M.J.P.)
| | - Thorarinn Gudjonsson
- EpiEndo Pharmaceuticals, Reykjavik, Iceland (J.A.K., C.P.P., F.R.G., O.B., T.G., M.J.P.); Stem Cell Research Unit, Biomedical Center, University of Iceland, Reykjavik, Iceland (J.A.K., T.G.); Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (C.P.P.); Department of Respiratory Medicine (O.B.), Department of Laboratory Hematology (T.G.), Landspitali-University Hospital, Reykjavik, Iceland; Faculty of Biochemistry, Chemistry and Pharmacy, JW Goethe University Frankfurt am Main, Germany (M.J.P.)
| | - Michael J Parnham
- EpiEndo Pharmaceuticals, Reykjavik, Iceland (J.A.K., C.P.P., F.R.G., O.B., T.G., M.J.P.); Stem Cell Research Unit, Biomedical Center, University of Iceland, Reykjavik, Iceland (J.A.K., T.G.); Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (C.P.P.); Department of Respiratory Medicine (O.B.), Department of Laboratory Hematology (T.G.), Landspitali-University Hospital, Reykjavik, Iceland; Faculty of Biochemistry, Chemistry and Pharmacy, JW Goethe University Frankfurt am Main, Germany (M.J.P.)
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10
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Cheng J, Chen M, Wang S, Liang T, Chen H, Chen CJ, Feng Z, Xie XQ. Binding Characterization of Agonists and Antagonists by MCCS: A Case Study from Adenosine A 2A Receptor. ACS Chem Neurosci 2021; 12:1606-1620. [PMID: 33856784 DOI: 10.1021/acschemneuro.1c00082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Characterizing the structural basis of ligand recognition of adenosine A2A receptor (AA2AR) will facilitate its rational design and development of small molecules with high affinity and selectivity, as well as optimal therapeutic effects for pain, cancers, drug abuse disorders, etc. In the present work, we applied our reported algorithm, molecular complex characterizing system (MCCS), to characterize the binding features of AA2AR based on its reported 3D structures of protein-ligand complexes. First, we compared the binding score to the reported experimental binding affinities of each compound. Then, we calculated an output example of residue energy contribution using MCCS and compared the results with data obtained from MM/GBSA. The consistency in results indicated that MCCS is a powerful, fast, and accurate method. Sequentially, using a receptor-ligand data set of 57 crystallized structures of AA2ARs, we characterized the binding features of the binding pockets in AA2AR, summarized the key residues that distinguish antagonist from agonist, produced heatmaps of residue energy contribution for clustering various statuses of AA2ARs, explored the selectivity between AA2AR and AA1AR, etc. All the information provided new insights into the protein features of AA2AR and will facilitate its rational drug design.
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Affiliation(s)
- Jin Cheng
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, and National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States.,Department of Pharmacy, Jiangsu Vocational College of Medicine, Yancheng, Jiangsu 224005, China
| | - Maozi Chen
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, and National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Siyi Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, and National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Tianjian Liang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, and National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Hui Chen
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, and National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Chih-Jung Chen
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, and National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Zhiwei Feng
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, and National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, and National Center of Excellence for Computational Drug Abuse Research, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
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11
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Zhang K, Huang Y, Shen YJ, Zhang LF, Ma S, Chen TT, Zheng Z, Zhang S, Li B. Imine bond transformation of a dynamic Sm(III) macrocycle-based chemosensor: The indirect approach for detecting cyanuric chloride. Anal Chim Acta 2021; 1144:34-42. [PMID: 33453795 DOI: 10.1016/j.aca.2020.11.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 11/19/2020] [Accepted: 11/21/2020] [Indexed: 01/24/2023]
Abstract
Herein, we report our strategy to develop the efficient chemosensor and real-time monitoring technique for cyanuric chloride (TCT) detection. A luminescent macrocyclic mononuclear Sm(III) complex Sm-2k bearing with two dynamic imine bonds has been constructed via the template synthesis between dialdehyde H2Qk and matched diamine 1,2-bis(2-aminoethoxy)ethane. Sensing experiments reveal that complex Sm-2k exhibits the turn-off fluorescent and colorimetric response for TCT in CH3OH. It is especially encouraging that this optical sensing process is not only rapid within 60 s but also high-efficient in the presence of TCT analogues as well as sensitive with the low limit of detection (LOD, 1.74 μM) and wide linear sensing range. Mechanism studies demonstrate that TCT sensing is mainly based on the imine bond transformation of probe Sm-2k, which is due to the increased acidity induced by TCT. Meanwhile, a smartphone-based analytical method was developed to make complex Sm-2k accessible for the real-time TCT detection by RGB value outputs. It is believed that this work can shed some constructive lights on design of chemosensors and convenient detection technique for highly reactive analytes.
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Affiliation(s)
- Kun Zhang
- Department of Chemistry, Zhejiang Sci-Tech University, Xiasha Higher Education District, Hangzhou, 310018, PR China.
| | - Yan Huang
- Department of Chemistry, Zhejiang Sci-Tech University, Xiasha Higher Education District, Hangzhou, 310018, PR China
| | - Yin-Jing Shen
- Department of Chemistry, Zhejiang Sci-Tech University, Xiasha Higher Education District, Hangzhou, 310018, PR China
| | - Lin-Feng Zhang
- Department of Chemistry, Zhejiang Sci-Tech University, Xiasha Higher Education District, Hangzhou, 310018, PR China
| | - Shuang Ma
- Department of Chemistry, Zhejiang Sci-Tech University, Xiasha Higher Education District, Hangzhou, 310018, PR China
| | - Ting-Ting Chen
- Department of Chemistry, Zhejiang Sci-Tech University, Xiasha Higher Education District, Hangzhou, 310018, PR China
| | - Ziqiang Zheng
- Department of Chemistry, Zhejiang Sci-Tech University, Xiasha Higher Education District, Hangzhou, 310018, PR China
| | - Shishen Zhang
- Department of Chemistry, Zhejiang Sci-Tech University, Xiasha Higher Education District, Hangzhou, 310018, PR China
| | - Benxia Li
- Department of Chemistry, Zhejiang Sci-Tech University, Xiasha Higher Education District, Hangzhou, 310018, PR China
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12
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Jespers W, Åqvist J, Gutiérrez-de-Terán H. Free Energy Calculations for Protein-Ligand Binding Prediction. Methods Mol Biol 2021; 2266:203-226. [PMID: 33759129 DOI: 10.1007/978-1-0716-1209-5_12] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Computational prediction of protein-ligand binding involves initial determination of the binding mode and subsequent evaluation of the strength of the protein-ligand interactions, which directly correlates with ligand binding affinities. As a consequence of increasing computer power, rigorous approaches to calculate protein-ligand binding affinities, such as free energy perturbation (FEP) methods, are becoming an essential part of the toolbox of computer-aided drug design. In this chapter, we provide a general overview of these methods and introduce the QFEP modules, which are open-source API workflows based on our molecular dynamics (MD) package Q. The module QligFEP allows estimation of relative binding affinities along ligand series, while QresFEP is a module to estimate binding affinity shifts caused by single-point mutations of the protein. We herein provide guidelines for the use of each of these modules based on data extracted from ligand-design projects. While these modules are stand-alone, the combined use of the two workflows in a drug-design project yields complementary perspectives of the ligand binding problem, providing two sides of the same coin. The selected case studies illustrate how to use QFEP to approach the two key questions associated with ligand binding prediction: identifying the most favorable binding mode from different alternatives and establishing structure-affinity relationships that allow the rational optimization of hit compounds.
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Affiliation(s)
- Willem Jespers
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Johan Åqvist
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Hugo Gutiérrez-de-Terán
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden.
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13
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Jespers W, Verdon G, Azuaje J, Majellaro M, Keränen H, García‐Mera X, Congreve M, Deflorian F, de Graaf C, Zhukov A, Doré AS, Mason JS, Åqvist J, Cooke RM, Sotelo E, Gutiérrez‐de‐Terán H. X-Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A 2A Adenosine Receptor Antagonists. Angew Chem Int Ed Engl 2020; 59:16536-16543. [PMID: 32542862 PMCID: PMC7540567 DOI: 10.1002/anie.202003788] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 05/18/2020] [Indexed: 01/04/2023]
Abstract
We present a robust protocol based on iterations of free energy perturbation (FEP) calculations, chemical synthesis, biophysical mapping and X-ray crystallography to reveal the binding mode of an antagonist series to the A2A adenosine receptor (AR). Eight A2A AR binding site mutations from biophysical mapping experiments were initially analyzed with sidechain FEP simulations, performed on alternate binding modes. The results distinctively supported one binding mode, which was subsequently used to design new chromone derivatives. Their affinities for the A2A AR were experimentally determined and investigated through a cycle of ligand-FEP calculations, validating the binding orientation of the different chemical substituents proposed. Subsequent X-ray crystallography of the A2A AR with a low and a high affinity chromone derivative confirmed the predicted binding orientation. The new molecules and structures here reported were driven by free energy calculations, and provide new insights on antagonist binding to the A2A AR, an emerging target in immuno-oncology.
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Affiliation(s)
- Willem Jespers
- Department of Cell and Molecular BiologyUppsala University, BMC, Biomedical CenterBox 596UppsalaSweden
| | - Grégory Verdon
- Sosei HeptaresSteinmetz Granta Park, Great AbingtonCambridgeCB21 6DGUK
| | - Jhonny Azuaje
- Departament of Organic ChemistryFaculty of FarmacyUniversidade de Santiago de CompostelaSpain
- Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS)Universidade de Santiago de CompostelaSpain
| | - Maria Majellaro
- Departament of Organic ChemistryFaculty of FarmacyUniversidade de Santiago de CompostelaSpain
- Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS)Universidade de Santiago de CompostelaSpain
| | - Henrik Keränen
- Department of Cell and Molecular BiologyUppsala University, BMC, Biomedical CenterBox 596UppsalaSweden
- Present address: H. Lundbeck A/SOttiliavej 92500ValbyDenmark
| | - Xerardo García‐Mera
- Departament of Organic ChemistryFaculty of FarmacyUniversidade de Santiago de CompostelaSpain
| | - Miles Congreve
- Sosei HeptaresSteinmetz Granta Park, Great AbingtonCambridgeCB21 6DGUK
| | | | - Chris de Graaf
- Sosei HeptaresSteinmetz Granta Park, Great AbingtonCambridgeCB21 6DGUK
| | - Andrei Zhukov
- Sosei HeptaresSteinmetz Granta Park, Great AbingtonCambridgeCB21 6DGUK
| | - Andrew S. Doré
- Sosei HeptaresSteinmetz Granta Park, Great AbingtonCambridgeCB21 6DGUK
| | - Jonathan S. Mason
- Sosei HeptaresSteinmetz Granta Park, Great AbingtonCambridgeCB21 6DGUK
| | - Johan Åqvist
- Department of Cell and Molecular BiologyUppsala University, BMC, Biomedical CenterBox 596UppsalaSweden
| | - Robert M. Cooke
- Sosei HeptaresSteinmetz Granta Park, Great AbingtonCambridgeCB21 6DGUK
| | - Eddy Sotelo
- Departament of Organic ChemistryFaculty of FarmacyUniversidade de Santiago de CompostelaSpain
- Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS)Universidade de Santiago de CompostelaSpain
| | - Hugo Gutiérrez‐de‐Terán
- Department of Cell and Molecular BiologyUppsala University, BMC, Biomedical CenterBox 596UppsalaSweden
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14
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Schneider J, Korshunova K, Si Chaib Z, Giorgetti A, Alfonso-Prieto M, Carloni P. Ligand Pose Predictions for Human G Protein-Coupled Receptors: Insights from the Amber-Based Hybrid Molecular Mechanics/Coarse-Grained Approach. J Chem Inf Model 2020; 60:5103-5116. [PMID: 32786708 DOI: 10.1021/acs.jcim.0c00661] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Human G protein-coupled receptors (hGPCRs) are the most frequent targets of Food and Drug Administration (FDA)-approved drugs. Structural bioinformatics, along with molecular simulation, can support structure-based drug design targeting hGPCRs. In this context, several years ago, we developed a hybrid molecular mechanics (MM)/coarse-grained (CG) approach to predict ligand poses in low-resolution hGPCR models. The approach was based on the GROMOS96 43A1 and PRODRG united-atom force fields for the MM part. Here, we present a new MM/CG implementation using, instead, the Amber 14SB and GAFF all-atom potentials for proteins and ligands, respectively. The new implementation outperforms the previous one, as shown by a variety of applications on models of hGPCR/ligand complexes at different resolutions, and it is also more user-friendly. Thus, it emerges as a useful tool to predict poses in low-resolution models and provides insights into ligand binding similarly to all-atom molecular dynamics, albeit at a lower computational cost.
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Affiliation(s)
- Jakob Schneider
- Computational Biomedicine, Institute for Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Department of Physics, RWTH Aachen University, 52074 Aachen, Germany.,JARA-Institute: Molecular Neuroscience and Neuroimaging, Institute for Neuroscience and Medicine INM-11/JARA-BRAIN Institute JBI-2, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Ksenia Korshunova
- Computational Biomedicine, Institute for Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Department of Physics, RWTH Aachen University, 52074 Aachen, Germany
| | - Zeineb Si Chaib
- Computational Biomedicine, Institute for Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,RWTH Aachen University, 52062 Aachen, Germany
| | - Alejandro Giorgetti
- Computational Biomedicine, Institute for Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Department of Biotechnology, University of Verona, 37314 Verona, Italy.,JARA-HPC, IAS-5/INM-9 Computational Biomedicine, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Mercedes Alfonso-Prieto
- Computational Biomedicine, Institute for Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,JARA-HPC, IAS-5/INM-9 Computational Biomedicine, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Cecile and Oskar Vogt Institute for Brain Research, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Paolo Carloni
- Computational Biomedicine, Institute for Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Department of Physics, RWTH Aachen University, 52074 Aachen, Germany.,JARA-Institute: Molecular Neuroscience and Neuroimaging, Institute for Neuroscience and Medicine INM-11/JARA-BRAIN Institute JBI-2, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,JARA-HPC, IAS-5/INM-9 Computational Biomedicine, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
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15
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Jespers W, Verdon G, Azuaje J, Majellaro M, Keränen H, García‐Mera X, Congreve M, Deflorian F, Graaf C, Zhukov A, Doré AS, Mason JS, Åqvist J, Cooke RM, Sotelo E, Gutiérrez‐de‐Terán H. X‐Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A
2A
Adenosine Receptor Antagonists. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Willem Jespers
- Department of Cell and Molecular BiologyUppsala University, BMC, Biomedical Center Box 596 Uppsala Sweden
| | - Grégory Verdon
- Sosei Heptares Steinmetz Granta Park, Great Abington Cambridge CB21 6DG UK
| | - Jhonny Azuaje
- Departament of Organic ChemistryFaculty of FarmacyUniversidade de Santiago de Compostela Spain
- Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS)Universidade de Santiago de Compostela Spain
| | - Maria Majellaro
- Departament of Organic ChemistryFaculty of FarmacyUniversidade de Santiago de Compostela Spain
- Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS)Universidade de Santiago de Compostela Spain
| | - Henrik Keränen
- Department of Cell and Molecular BiologyUppsala University, BMC, Biomedical Center Box 596 Uppsala Sweden
- Present address: H. Lundbeck A/S Ottiliavej 9 2500 Valby Denmark
| | - Xerardo García‐Mera
- Departament of Organic ChemistryFaculty of FarmacyUniversidade de Santiago de Compostela Spain
| | - Miles Congreve
- Sosei Heptares Steinmetz Granta Park, Great Abington Cambridge CB21 6DG UK
| | | | - Chris Graaf
- Sosei Heptares Steinmetz Granta Park, Great Abington Cambridge CB21 6DG UK
| | - Andrei Zhukov
- Sosei Heptares Steinmetz Granta Park, Great Abington Cambridge CB21 6DG UK
| | - Andrew S. Doré
- Sosei Heptares Steinmetz Granta Park, Great Abington Cambridge CB21 6DG UK
| | - Jonathan S. Mason
- Sosei Heptares Steinmetz Granta Park, Great Abington Cambridge CB21 6DG UK
| | - Johan Åqvist
- Department of Cell and Molecular BiologyUppsala University, BMC, Biomedical Center Box 596 Uppsala Sweden
| | - Robert M. Cooke
- Sosei Heptares Steinmetz Granta Park, Great Abington Cambridge CB21 6DG UK
| | - Eddy Sotelo
- Departament of Organic ChemistryFaculty of FarmacyUniversidade de Santiago de Compostela Spain
- Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS)Universidade de Santiago de Compostela Spain
| | - Hugo Gutiérrez‐de‐Terán
- Department of Cell and Molecular BiologyUppsala University, BMC, Biomedical Center Box 596 Uppsala Sweden
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16
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Jacobson KA, Gao Z, Matricon P, Eddy MT, Carlsson J. Adenosine A2Areceptor antagonists: from caffeine to selective non‐xanthines. Br J Pharmacol 2020; 179:3496-3511. [DOI: 10.1111/bph.15103] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/30/2020] [Accepted: 05/03/2020] [Indexed: 12/12/2022] Open
Affiliation(s)
- Kenneth A. Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic ChemistryNational Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health Bethesda MD USA
| | - Zhan‐Guo Gao
- Molecular Recognition Section, Laboratory of Bioorganic ChemistryNational Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health Bethesda MD USA
| | - Pierre Matricon
- Department of Cell and Molecular Biology, Science for Life LaboratoryUppsala University Uppsala Sweden
| | - Matthew T. Eddy
- Department of ChemistryUniversity of Florida Gainesville FL USA
| | - Jens Carlsson
- Department of Cell and Molecular Biology, Science for Life LaboratoryUppsala University Uppsala Sweden
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17
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Congreve M, de Graaf C, Swain NA, Tate CG. Impact of GPCR Structures on Drug Discovery. Cell 2020; 181:81-91. [DOI: 10.1016/j.cell.2020.03.003] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/03/2020] [Accepted: 03/03/2020] [Indexed: 12/21/2022]
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18
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van der Velden WJC, Heitman LH, Rosenkilde MM. Perspective: Implications of Ligand-Receptor Binding Kinetics for Therapeutic Targeting of G Protein-Coupled Receptors. ACS Pharmacol Transl Sci 2020; 3:179-189. [PMID: 32296761 DOI: 10.1021/acsptsci.0c00012] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Indexed: 12/16/2022]
Abstract
The concept of ligand-receptor binding kinetics has been broadly applied in drug development pipelines focusing on G protein-coupled receptors (GPCRs). The ligand residence time (RT) for a receptor describes how long a ligand-receptor complex exists, and is defined as the reciprocal of the dissociation rate constant (k off). RT has turned out to be a valuable parameter for GPCR researchers focusing on drug development as a good predictor of in vivo efficacy. The positive correlation between RT and in vivo efficacy has been established for several drugs targeting class A GPCRs (e.g., the neurokinin-1 receptor (NK1R), the β2 adrenergic receptor (β2AR), and the muscarinic 3 receptor (M3R)) and for drugs targeting class B1 (e.g., the glucagon-like peptide 1 receptor (GLP-1R)). Recently, the association rate constant (k on) has gained similar attention as another parameter affecting in vivo efficacy. In the current perspective, we address the importance of studying ligand-receptor binding kinetics for therapeutic targeting of GPCRs, with an emphasis on how binding kinetics can be altered by subtle molecular changes in the ligands and/or the receptors and how such changes affect treatment outcome. Moreover, we speculate on the impact of binding kinetic parameters for functional selectivity and sustained receptor signaling from endosomal compartments; phenomena that have gained increasing interest in attempts to improve therapeutic targeting of GPCRs.
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Affiliation(s)
- Wijnand J C van der Velden
- Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK 2200, Denmark
| | - Laura H Heitman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, The Netherlands
| | - Mette M Rosenkilde
- Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen DK 2200, Denmark
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19
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Deganutti G, Moro S, Reynolds CA. A Supervised Molecular Dynamics Approach to Unbiased Ligand–Protein Unbinding. J Chem Inf Model 2020; 60:1804-1817. [DOI: 10.1021/acs.jcim.9b01094] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Giuseppe Deganutti
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, United Kingdom
| | - Stefano Moro
- Molecular Modeling Section, Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131, Padova, Italy
| | - Christopher A. Reynolds
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, United Kingdom
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20
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IJzerman AP, Guo D. Drug-Target Association Kinetics in Drug Discovery. Trends Biochem Sci 2019; 44:861-871. [PMID: 31101454 DOI: 10.1016/j.tibs.2019.04.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/28/2019] [Accepted: 04/08/2019] [Indexed: 02/07/2023]
Abstract
The important role of ligand-receptor binding kinetics in drug design and discovery is increasingly recognized by the drug research community. Over the past decade, accumulating evidence has shown that optimizing the ligand's dissociation rate constant can lead to desirable duration of in vivo target occupancy and, hence, improved pharmacodynamic properties. However, the association rate constant as a pharmacological principle remains less investigated, whereas it can play an equally important role in the selection of drug candidates. This review provides a compilation and discussion of otherwise scarce and dispersed information on this topic, bringing to light the importance of drug-target association in kinetics-directed drug design and discovery.
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Affiliation(s)
- Adriaan P IJzerman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300, RA, Leiden, The Netherlands
| | - Dong Guo
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China.
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21
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Acúrcio RC, Scomparin A, Satchi‐Fainaro R, Florindo HF, Guedes RC. Computer‐aided drug design in new druggable targets for the next generation of immune‐oncology therapies. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1397] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Rita C. Acúrcio
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy Universidade de Lisboa Lisbon Portugal
| | - Anna Scomparin
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine Tel Aviv University Tel Aviv Israel
| | - Ronit Satchi‐Fainaro
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine Tel Aviv University Tel Aviv Israel
| | - Helena F. Florindo
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy Universidade de Lisboa Lisbon Portugal
| | - Rita C. Guedes
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy Universidade de Lisboa Lisbon Portugal
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22
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Jiang X, Yu J, Zhou Z, Kongsted J, Song Y, Pannecouque C, De Clercq E, Kang D, Poongavanam V, Liu X, Zhan P. Molecular design opportunities presented by solvent‐exposed regions of target proteins. Med Res Rev 2019; 39:2194-2238. [DOI: 10.1002/med.21581] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 03/09/2019] [Accepted: 03/16/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Xiangyi Jiang
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
| | - Ji Yu
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
| | - Zhongxia Zhou
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
| | - Jacob Kongsted
- Department of Physics, Chemistry and PharmacyUniversity of Southern Denmark Odense Denmark
| | - Yuning Song
- Department of Clinical PharmacyQilu Hospital of Shandong University Jinan China
| | - Christophe Pannecouque
- Rega Institute for Medical ResearchLaboratory of Virology and Chemotherapy Leuven Belgium
| | - Erik De Clercq
- Rega Institute for Medical ResearchLaboratory of Virology and Chemotherapy Leuven Belgium
| | - Dongwei Kang
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
| | | | - Xinyong Liu
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
| | - Peng Zhan
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
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23
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Congreve M, Brown GA, Borodovsky A, Lamb ML. Targeting adenosine A2A receptor antagonism for treatment of cancer. Expert Opin Drug Discov 2018; 13:997-1003. [DOI: 10.1080/17460441.2018.1534825] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Miles Congreve
- Heptares Therapeutics Limited, Steinmetz Building, Cambridge, Granta Park, UK
| | - Giles A. Brown
- Heptares Therapeutics Limited, Steinmetz Building, Cambridge, Granta Park, UK
| | | | - Michelle L. Lamb
- Medicinal Chemistry, Oncology, IMED Biotech Unit, AstraZeneca, Boston, MA, USA
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24
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Ghattas W, Dubosclard V, Wick A, Bendelac A, Guillot R, Ricoux R, Mahy JP. Receptor-Based Artificial Metalloenzymes on Living Human Cells. J Am Chem Soc 2018; 140:8756-8762. [DOI: 10.1021/jacs.8b04326] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Wadih Ghattas
- Laboratoire de Chimie Bioorganique et Bioinorganique (LCBB) Institut de Chimie Moléculaire et des Matériaux d’Orsay (ICMMO) UMR 8182 CNRS Univ Paris Sud, Université Paris-Saclay, Orsay 91405 Cedex, France
| | - Virginie Dubosclard
- Laboratoire de Chimie Bioorganique et Bioinorganique (LCBB) Institut de Chimie Moléculaire et des Matériaux d’Orsay (ICMMO) UMR 8182 CNRS Univ Paris Sud, Université Paris-Saclay, Orsay 91405 Cedex, France
| | - Arne Wick
- Laboratoire de Chimie Bioorganique et Bioinorganique (LCBB) Institut de Chimie Moléculaire et des Matériaux d’Orsay (ICMMO) UMR 8182 CNRS Univ Paris Sud, Université Paris-Saclay, Orsay 91405 Cedex, France
| | - Audrey Bendelac
- Laboratoire de Chimie Bioorganique et Bioinorganique (LCBB) Institut de Chimie Moléculaire et des Matériaux d’Orsay (ICMMO) UMR 8182 CNRS Univ Paris Sud, Université Paris-Saclay, Orsay 91405 Cedex, France
| | - Régis Guillot
- Laboratoire de Chimie Bioorganique et Bioinorganique (LCBB) Institut de Chimie Moléculaire et des Matériaux d’Orsay (ICMMO) UMR 8182 CNRS Univ Paris Sud, Université Paris-Saclay, Orsay 91405 Cedex, France
| | - Rémy Ricoux
- Laboratoire de Chimie Bioorganique et Bioinorganique (LCBB) Institut de Chimie Moléculaire et des Matériaux d’Orsay (ICMMO) UMR 8182 CNRS Univ Paris Sud, Université Paris-Saclay, Orsay 91405 Cedex, France
| | - Jean-Pierre Mahy
- Laboratoire de Chimie Bioorganique et Bioinorganique (LCBB) Institut de Chimie Moléculaire et des Matériaux d’Orsay (ICMMO) UMR 8182 CNRS Univ Paris Sud, Université Paris-Saclay, Orsay 91405 Cedex, France
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25
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Lee TH, Hirst DJ, Kulkarni K, Del Borgo MP, Aguilar MI. Exploring Molecular-Biomembrane Interactions with Surface Plasmon Resonance and Dual Polarization Interferometry Technology: Expanding the Spotlight onto Biomembrane Structure. Chem Rev 2018; 118:5392-5487. [PMID: 29793341 DOI: 10.1021/acs.chemrev.7b00729] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The molecular analysis of biomolecular-membrane interactions is central to understanding most cellular systems but has emerged as a complex technical challenge given the complexities of membrane structure and composition across all living cells. We present a review of the application of surface plasmon resonance and dual polarization interferometry-based biosensors to the study of biomembrane-based systems using both planar mono- or bilayers or liposomes. We first describe the optical principals and instrumentation of surface plasmon resonance, including both linear and extraordinary transmission modes and dual polarization interferometry. We then describe the wide range of model membrane systems that have been developed for deposition on the chips surfaces that include planar, polymer cushioned, tethered bilayers, and liposomes. This is followed by a description of the different chemical immobilization or physisorption techniques. The application of this broad range of engineered membrane surfaces to biomolecular-membrane interactions is then overviewed and how the information obtained using these techniques enhance our molecular understanding of membrane-mediated peptide and protein function. We first discuss experiments where SPR alone has been used to characterize membrane binding and describe how these studies yielded novel insight into the molecular events associated with membrane interactions and how they provided a significant impetus to more recent studies that focus on coincident membrane structure changes during binding of peptides and proteins. We then discuss the emerging limitations of not monitoring the effects on membrane structure and how SPR data can be combined with DPI to provide significant new information on how a membrane responds to the binding of peptides and proteins.
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Affiliation(s)
- Tzong-Hsien Lee
- Department of Biochemistry and Molecular Biology and Biomedicine Discovery Institute , Monash University , Clayton , VIC 3800 , Australia
| | - Daniel J Hirst
- Department of Biochemistry and Molecular Biology and Biomedicine Discovery Institute , Monash University , Clayton , VIC 3800 , Australia
| | - Ketav Kulkarni
- Department of Biochemistry and Molecular Biology and Biomedicine Discovery Institute , Monash University , Clayton , VIC 3800 , Australia
| | - Mark P Del Borgo
- Department of Biochemistry and Molecular Biology and Biomedicine Discovery Institute , Monash University , Clayton , VIC 3800 , Australia
| | - Marie-Isabel Aguilar
- Department of Biochemistry and Molecular Biology and Biomedicine Discovery Institute , Monash University , Clayton , VIC 3800 , Australia
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26
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Bumbak F, Keen AC, Gunn NJ, Gooley PR, Bathgate RAD, Scott DJ. Optimization and 13CH 3 methionine labeling of a signaling competent neurotensin receptor 1 variant for NMR studies. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1372-1383. [PMID: 29596791 DOI: 10.1016/j.bbamem.2018.03.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 02/19/2018] [Accepted: 03/21/2018] [Indexed: 01/16/2023]
Abstract
Neurotensin is a 13-residue peptide that acts as a neuromodulator of classical neurotransmitters such as dopamine and glutamate in the mammalian central nervous system, mainly by activating the G protein-coupled receptor (GPCR), neurotensin receptor 1 (NTS1). Agonist binding to GPCRs shifts the conformational equilibrium of the transmembrane helices towards distinct, thermodynamically favorable conformations that favor effector protein interactions and promotes cell signaling. The introduction of site specific labels for NMR spectroscopy has proven useful for investigating this dynamic process, but the low expression levels and poor stability of GPCRs is a hindrance to solution NMR experiments. Several thermostabilized mutants of NTS1 have been engineered to circumvent this, with the crystal structures of four of these published. The conformational dynamics of NTS1 however, has not been thoroughly investigated with NMR. It is generally accepted that stabilized GPCRs exhibit attenuated signaling, thus we thoroughly characterized the signaling characteristics of several thermostabilized NTS1 variants to identify an optimal variant for protein NMR studies. A variant termed enNTS1 exhibited the best combination of signaling capability and stability upon solubilization with detergents. enNTS1 was subsequently labeled with 13CH3-methionine in E. coli and purified to homogeneity in the absence of bound ligands. Using solution NMR spectroscopy we observed several well dispersed 13CH3-methionine resonances, many of which exhibited chemical shift changes upon the addition of the high affinity agonist peptide, NT8-13. Thus, enNTS1 represents a novel tool for investigating ligand induced conformational changes in NTS1 to gain insights into the molecular mechanisms underlying neurotensin signaling.
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Affiliation(s)
- Fabian Bumbak
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia; Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Alastair C Keen
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Natalie J Gunn
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia; IBM Research Australia, Southbank, Victoria 3053, Australia
| | - Paul R Gooley
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria 3010, Australia; Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Ross A D Bathgate
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia; Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Daniel J Scott
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia; Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria 3010, Australia.
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Xu B, Vasile S, Østergaard S, Paulsson JF, Pruner J, Åqvist J, Wulff BS, Gutiérrez-de-Terán H, Larhammar D. Elucidation of the Binding Mode of the Carboxyterminal Region of Peptide YY to the Human Y 2 Receptor. Mol Pharmacol 2018; 93:323-334. [PMID: 29367257 DOI: 10.1124/mol.117.110627] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 01/19/2018] [Indexed: 11/22/2022] Open
Abstract
Understanding the agonist-receptor interactions in the neuropeptide Y (NPY)/peptide YY (PYY) signaling system is fundamental for the design of novel modulators of appetite regulation. We report here the results of a multidisciplinary approach to elucidate the binding mode of the native peptide agonist PYY to the human Y2 receptor, based on computational modeling, peptide chemistry and in vitro pharmacological analyses. The preserved binding orientation proposed for full-length PYY and five analogs, truncated at the amino terminus, explains our pharmacological results where truncations of the N-terminal proline helix showed little effect on peptide affinity. This was followed by receptor mutagenesis to investigate the roles of several receptor positions suggested by the modeling. As a complement, PYY-(3-36) analogs were synthesized with modifications at different positions in the common PYY/NPY C-terminal fragment (32TRQRY36-amide). The results were assessed and interpreted by molecular dynamics and Free Energy Perturbation (FEP) simulations of selected mutants, providing a detailed map of the interactions of the PYY/NPY C-terminal fragment with the transmembrane cavity of the Y2 receptor. The amidated C-terminus would be stabilized by polar interactions with Gln2886.55 and Tyr2195.39, while Gln1303.32 contributes to interactions with Q34 in the peptide and T32 is close to the tip of TM7 in the receptor. This leaves the core, α-helix of the peptide exposed to make potential interactions with the extracellular loops. This model agrees with most experimental data available for the Y2 system and can be used as a basis for optimization of Y2 receptor agonists.
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Affiliation(s)
- Bo Xu
- Departments of Neuroscience (B.X., J.P., D.L.) and Cell and Molecular Biology (S.V., J.Å., H.G.-T.), Biomedical Centre, Uppsala University, Uppsala, Sweden; and Protein and Peptide Chemistry 2 (S.Ø.) and Obesity Research (J.F.P., B.S.W.), Novo Nordisk A/S, Måløv, Denmark
| | - Silvana Vasile
- Departments of Neuroscience (B.X., J.P., D.L.) and Cell and Molecular Biology (S.V., J.Å., H.G.-T.), Biomedical Centre, Uppsala University, Uppsala, Sweden; and Protein and Peptide Chemistry 2 (S.Ø.) and Obesity Research (J.F.P., B.S.W.), Novo Nordisk A/S, Måløv, Denmark
| | - Søren Østergaard
- Departments of Neuroscience (B.X., J.P., D.L.) and Cell and Molecular Biology (S.V., J.Å., H.G.-T.), Biomedical Centre, Uppsala University, Uppsala, Sweden; and Protein and Peptide Chemistry 2 (S.Ø.) and Obesity Research (J.F.P., B.S.W.), Novo Nordisk A/S, Måløv, Denmark
| | - Johan F Paulsson
- Departments of Neuroscience (B.X., J.P., D.L.) and Cell and Molecular Biology (S.V., J.Å., H.G.-T.), Biomedical Centre, Uppsala University, Uppsala, Sweden; and Protein and Peptide Chemistry 2 (S.Ø.) and Obesity Research (J.F.P., B.S.W.), Novo Nordisk A/S, Måløv, Denmark
| | - Jasna Pruner
- Departments of Neuroscience (B.X., J.P., D.L.) and Cell and Molecular Biology (S.V., J.Å., H.G.-T.), Biomedical Centre, Uppsala University, Uppsala, Sweden; and Protein and Peptide Chemistry 2 (S.Ø.) and Obesity Research (J.F.P., B.S.W.), Novo Nordisk A/S, Måløv, Denmark
| | - Johan Åqvist
- Departments of Neuroscience (B.X., J.P., D.L.) and Cell and Molecular Biology (S.V., J.Å., H.G.-T.), Biomedical Centre, Uppsala University, Uppsala, Sweden; and Protein and Peptide Chemistry 2 (S.Ø.) and Obesity Research (J.F.P., B.S.W.), Novo Nordisk A/S, Måløv, Denmark
| | - Birgitte S Wulff
- Departments of Neuroscience (B.X., J.P., D.L.) and Cell and Molecular Biology (S.V., J.Å., H.G.-T.), Biomedical Centre, Uppsala University, Uppsala, Sweden; and Protein and Peptide Chemistry 2 (S.Ø.) and Obesity Research (J.F.P., B.S.W.), Novo Nordisk A/S, Måløv, Denmark
| | - Hugo Gutiérrez-de-Terán
- Departments of Neuroscience (B.X., J.P., D.L.) and Cell and Molecular Biology (S.V., J.Å., H.G.-T.), Biomedical Centre, Uppsala University, Uppsala, Sweden; and Protein and Peptide Chemistry 2 (S.Ø.) and Obesity Research (J.F.P., B.S.W.), Novo Nordisk A/S, Måløv, Denmark
| | - Dan Larhammar
- Departments of Neuroscience (B.X., J.P., D.L.) and Cell and Molecular Biology (S.V., J.Å., H.G.-T.), Biomedical Centre, Uppsala University, Uppsala, Sweden; and Protein and Peptide Chemistry 2 (S.Ø.) and Obesity Research (J.F.P., B.S.W.), Novo Nordisk A/S, Måløv, Denmark
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Vasile S, Esguerra M, Jespers W, Oliveira A, Sallander J, Åqvist J, Gutiérrez-de-Terán H. Characterization of Ligand Binding to GPCRs Through Computational Methods. Methods Mol Biol 2018; 1705:23-44. [PMID: 29188557 DOI: 10.1007/978-1-4939-7465-8_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The recent increase in available G protein-coupled receptor structures now contributes decisively to the structure-based ligand design. In this context, computational approaches in combination with medicinal chemistry and pharmacology are extremely helpful. Here, we provide an update on our structure-based computational protocols, used to answer key questions related to GPCR-ligand binding. All combined, these techniques can shed light on ligand binding modes, determine the molecular basis of conformational selection, for agonists and antagonists, as well as of subtype selectivity. To illustrate each of these questions, we will consider examples from existing projects on three families of class A (rhodopsin-like) GPCRs: one small-molecule (nucleotide-like) family, i.e., the adenosine receptors, and two peptide-binding receptors: neuropeptide-Y and angiotensin II receptors. The successful application of the same computational protocols to investigate this diverse group of receptor families gives an idea of the general applicability of our methodology in the characterization of GPCR-ligand binding.
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Affiliation(s)
- Silvana Vasile
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, Uppsala, SE-751 24, Sweden
| | - Mauricio Esguerra
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, Uppsala, SE-751 24, Sweden
| | - Willem Jespers
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, Uppsala, SE-751 24, Sweden
| | - Ana Oliveira
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, Uppsala, SE-751 24, Sweden
| | - Jessica Sallander
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, Uppsala, SE-751 24, Sweden
| | - Johan Åqvist
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, Uppsala, SE-751 24, Sweden
| | - Hugo Gutiérrez-de-Terán
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, Uppsala, SE-751 24, Sweden.
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Structural Mapping of Adenosine Receptor Mutations: Ligand Binding and Signaling Mechanisms. Trends Pharmacol Sci 2018; 39:75-89. [DOI: 10.1016/j.tips.2017.11.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 11/06/2017] [Accepted: 11/06/2017] [Indexed: 12/16/2022]
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30
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Drescher DG, Selvakumar D, Drescher MJ. Analysis of Protein Interactions by Surface Plasmon Resonance. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017; 110:1-30. [PMID: 29412994 DOI: 10.1016/bs.apcsb.2017.07.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Surface plasmon resonance is an optical technique that is utilized for detecting molecular interactions, such as interactions that occur between proteins or other classes of molecules. Binding of a mobile molecule (analyte) to a molecule immobilized on a thin metal film (ligand) changes the refractive index of the film. The angle of extinction of light that is completely reflected after polarized light impinges upon the film, is altered and monitored as a change in detector position for a dip in reflected intensity (the surface plasmon resonance phenomenon). Because the method strictly detects mass, there is no need to label the interacting components, thus eliminating possible changes of their molecular properties. In this chapter, we review essential SPR methodology and present applications to basic science and human disease.
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Affiliation(s)
- Dennis G Drescher
- Wayne State University School of Medicine, Detroit, MI, United States.
| | | | - Marian J Drescher
- Wayne State University School of Medicine, Detroit, MI, United States
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31
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Tian S, Wang X, Li L, Zhang X, Li Y, Zhu F, Hou T, Zhen X. Discovery of Novel and Selective Adenosine A 2A Receptor Antagonists for Treating Parkinson's Disease through Comparative Structure-Based Virtual Screening. J Chem Inf Model 2017; 57:1474-1487. [PMID: 28463561 DOI: 10.1021/acs.jcim.7b00188] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Among non-dopaminergic strategies for combating Parkinson's disease (PD), antagonism of the A2A adenosine receptor (AR) has emerged to show great potential. In this study, on the basis of two crystal structures of the A2A AR with the best capability to distinguish known antagonists from decoys, docking-based virtual screening (VS) was conducted to identify novel A2A AR antagonists. A total of 63 structurally diverse compounds identified by VS were submitted to experimental testing, and 11 of them exhibited substantial activity against the A2A AR (Ki < 10 μM), including two compounds with Ki below 1 μM (compound 43, 0.42 μM; compound 51, 0.27 μM) and good A2A/A1 selectivity (fold < 0.1). Compounds 43 and 51 demonstrated antagonistic activity according to the results of cAMP measurements (cAMP IC50 = 1.67 and 1.80 μM, respectively) and showed good efficacy in the haloperidol-induced catalepsy (HIC) rat model for PD at doses of up to 30 mg/kg. Further lead optimization based on a substructure searching strategy led to the discovery of compound 84 as an excellent A2A AR antagonist (A2A Ki = 54 nM, A2A/A1 fold < 0.1, cAMP IC50 = 0.3 μM) that exhibited significant improvement in anti-PD efficacy in the HIC rat model.
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Affiliation(s)
- Sheng Tian
- Jiangsu Key Laboratory of Translational Research and Therapy for Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University , Suzhou, Jiangsu 215123, China
| | - Xu Wang
- Jiangsu Key Laboratory of Translational Research and Therapy for Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University , Suzhou, Jiangsu 215123, China
| | - Linlang Li
- Jiangsu Key Laboratory of Translational Research and Therapy for Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University , Suzhou, Jiangsu 215123, China
| | - Xiaohu Zhang
- Jiangsu Key Laboratory of Translational Research and Therapy for Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University , Suzhou, Jiangsu 215123, China
| | - Youyong Li
- Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University , Suzhou, Jiangsu 215123, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University , Hangzhou, Zhejiang 310058, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University , Hangzhou, Zhejiang 310058, China
| | - Xuechu Zhen
- Jiangsu Key Laboratory of Translational Research and Therapy for Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University , Suzhou, Jiangsu 215123, China
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32
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Spyrakis F, Ahmed MH, Bayden AS, Cozzini P, Mozzarelli A, Kellogg GE. The Roles of Water in the Protein Matrix: A Largely Untapped Resource for Drug Discovery. J Med Chem 2017; 60:6781-6827. [PMID: 28475332 DOI: 10.1021/acs.jmedchem.7b00057] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The value of thoroughly understanding the thermodynamics specific to a drug discovery/design study is well known. Over the past decade, the crucial roles of water molecules in protein structure, function, and dynamics have also become increasingly appreciated. This Perspective explores water in the biological environment by adopting its point of view in such phenomena. The prevailing thermodynamic models of the past, where water was seen largely in terms of an entropic gain after its displacement by a ligand, are now known to be much too simplistic. We adopt a set of terminology that describes water molecules as being "hot" and "cold", which we have defined as being easy and difficult to displace, respectively. The basis of these designations, which involve both enthalpic and entropic water contributions, are explored in several classes of biomolecules and structural motifs. The hallmarks for characterizing water molecules are examined, and computational tools for evaluating water-centric thermodynamics are reviewed. This Perspective's summary features guidelines for exploiting water molecules in drug discovery.
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Affiliation(s)
- Francesca Spyrakis
- Dipartimento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino , Via Pietro Giuria 9, 10125 Torino, Italy
| | - Mostafa H Ahmed
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University , Richmond, Virginia 23298-0540, United States
| | - Alexander S Bayden
- CMD Bioscience , 5 Science Park, New Haven, Connecticut 06511, United States
| | - Pietro Cozzini
- Dipartimento di Scienze degli Alimenti e del Farmaco, Laboratorio di Modellistica Molecolare, Università degli Studi di Parma , Parco Area delle Scienze 59/A, 43121 Parma, Italy
| | - Andrea Mozzarelli
- Dipartimento di Scienze degli Alimenti e del Farmaco, Laboratorio di Biochimica, Università degli Studi di Parma , Parco Area delle Scienze 23/A, 43121 Parma, Italy.,Istituto di Biofisica, Consiglio Nazionale delle Ricerche , Via Moruzzi 1, 56124 Pisa, Italy
| | - Glen E Kellogg
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University , Richmond, Virginia 23298-0540, United States
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Bradley SJ, Tobin AB. Design of Next-Generation G Protein-Coupled Receptor Drugs: Linking Novel Pharmacology and In Vivo Animal Models. Annu Rev Pharmacol Toxicol 2016; 56:535-59. [PMID: 26738479 DOI: 10.1146/annurev-pharmtox-011613-140012] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Despite the fact that G protein-coupled receptors (GPCRs) are the most successful drug targets in history, this supergene family of cell surface receptors has yet to be fully exploited as targets in the treatment of human disease. Here, we present optimism that this may change in the future by reviewing the substantial progress made in the understanding of GPCR molecular pharmacology that has generated an extensive toolbox of ligand types that include orthosteric, allosteric, and bitopic ligands, many of which show signaling bias. We discuss how combining these advances with recently described transgenic, chemical genetic, and optogenetic animal models will provide the framework to allow for the rational design of next-generation GPCR drugs that possess increased therapeutic efficacy and decreased adverse/toxic responses.
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Affiliation(s)
- Sophie J Bradley
- MRC Toxicology Unit, University of Leicester, Leicester LE1 9HN United Kingdom; ,
| | - Andrew B Tobin
- MRC Toxicology Unit, University of Leicester, Leicester LE1 9HN United Kingdom; ,
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34
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McNeely PM, Naranjo AN, Forsten-Williams K, Robinson AS. A 2AR Binding Kinetics in the Ligand Depletion Regime. SLAS DISCOVERY 2016; 22:166-175. [PMID: 27577981 DOI: 10.1177/1087057116667256] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Ligand binding plays a fundamental role in stimulating the downstream signaling of membrane receptors. Here, ligand-binding kinetics of the full-length human adenosine A2A receptor (A2AR) reconstituted in detergent micelles were measured using a fluorescently labeled ligand via fluorescence anisotropy. Importantly, to optimize the signal-to-noise ratio, these experiments were conducted in the ligand depletion regime. In the ligand depletion regime, the assumptions used to determine analytical solutions for one-site binding models for either one or two ligands in competition are no longer valid. We therefore implemented a numerical solution approach to analyze kinetic binding data as experimental conditions approach the ligand depletion regime. By comparing the results from the numerical and the analytical solutions, we highlight the ligand-receptor ratios at which the analytical solution begins to lose predictive accuracy. Using the numerical solution approach, we determined the kinetic rate constants of the fluorescent ligand, FITC-APEC, and those for three unlabeled ligands using competitive association experiments. The association and dissociation rate constants of the unlabeled ligands determined from the competitive association experiments were then independently validated using competitive dissociation data. Based on this study, a numerical solution is recommended to determine kinetic ligand-binding parameters for experiments conducted in the ligand-depletion regime.
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Affiliation(s)
- Patrick M McNeely
- 1 Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA
| | - Andrea N Naranjo
- 1 Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA
| | | | - Anne Skaja Robinson
- 1 Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA.,2 Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, LA, USA
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In search of novel ligands using a structure-based approach: a case study on the adenosine A 2A receptor. J Comput Aided Mol Des 2016; 30:863-874. [PMID: 27629350 PMCID: PMC5083784 DOI: 10.1007/s10822-016-9963-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 09/02/2016] [Indexed: 12/03/2022]
Abstract
In this work, we present a case study to explore the challenges associated with finding novel molecules for a receptor that has been studied in depth and has a wealth of chemical information available. Specifically, we apply a previously described protocol that incorporates explicit water molecules in the ligand binding site to prospectively screen over 2.5 million drug-like and lead-like compounds from the commercially available eMolecules database in search of novel binders to the adenosine A2A receptor (A2AAR). A total of seventy-one compounds were selected for purchase and biochemical assaying based on high ligand efficiency and high novelty (Tanimoto coefficient ≤0.25 to any A2AAR tested compound). These molecules were then tested for their affinity to the adenosine A2A receptor in a radioligand binding assay. We identified two hits that fulfilled the criterion of ~50 % radioligand displacement at a concentration of 10 μM. Next we selected an additional eight novel molecules that were predicted to make a bidentate interaction with Asn2536.55, a key interacting residue in the binding pocket of the A2AAR. None of these eight molecules were found to be active. Based on these results we discuss the advantages of structure-based methods and the challenges associated with finding chemically novel molecules for well-explored targets.
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Affiliation(s)
- Naomi R. Latorraca
- Department of Computer Science, ‡Biophysics Program, §Department of Molecular
and Cellular
Physiology, and ∥Institute for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
| | - A. J. Venkatakrishnan
- Department of Computer Science, ‡Biophysics Program, §Department of Molecular
and Cellular
Physiology, and ∥Institute for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
| | - Ron O. Dror
- Department of Computer Science, ‡Biophysics Program, §Department of Molecular
and Cellular
Physiology, and ∥Institute for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
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37
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Magnani F, Serrano-Vega MJ, Shibata Y, Abdul-Hussein S, Lebon G, Miller-Gallacher J, Singhal A, Strege A, Thomas JA, Tate CG. A mutagenesis and screening strategy to generate optimally thermostabilized membrane proteins for structural studies. Nat Protoc 2016; 11:1554-71. [PMID: 27466713 PMCID: PMC5268090 DOI: 10.1038/nprot.2016.088] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The thermostability of an integral membrane protein (MP) in detergent solution is a key parameter that dictates the likelihood of obtaining well-diffracting crystals that are suitable for structure determination. However, many mammalian MPs are too unstable for crystallization. We developed a thermostabilization strategy based on systematic mutagenesis coupled to a radioligand-binding thermostability assay that can be applied to receptors, ion channels and transporters. It takes ∼6-12 months to thermostabilize a G-protein-coupled receptor (GPCR) containing 300 amino acid (aa) residues. The resulting thermostabilized MPs are more easily crystallized and result in high-quality structures. This methodology has facilitated structure-based drug design applied to GPCRs because it is possible to determine multiple structures of the thermostabilized receptors bound to low-affinity ligands. Protocols and advice are given on how to develop thermostability assays for MPs and how to combine mutations to make an optimally stable mutant suitable for structural studies. The steps in the procedure include the generation of ∼300 site-directed mutants by Ala/Leu scanning mutagenesis, the expression of each mutant in mammalian cells by transient transfection and the identification of thermostable mutants using a thermostability assay that is based on binding of an (125)I-labeled radioligand to the unpurified, detergent-solubilized MP. Individual thermostabilizing point mutations are then combined to make an optimally stable MP that is suitable for structural biology and other biophysical studies.
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Affiliation(s)
| | | | | | | | | | | | - Ankita Singhal
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Annette Strege
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Jennifer A. Thomas
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Christopher G. Tate
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
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38
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Impact, determination and prediction of drug-receptor residence times for GPCRs. Curr Opin Pharmacol 2016; 30:22-26. [PMID: 27428776 DOI: 10.1016/j.coph.2016.07.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 07/03/2016] [Accepted: 07/04/2016] [Indexed: 01/02/2023]
Abstract
The residence time of a ligand on a GPCR of interest has become an optimization parameter in many examples in drug design. Long residence times can counterbalance unfavorable pharmacokinetic parameters, contributing to compound safety, and short residence times can be a tool to avoid target related side effects. Unlike the prediction and interpretation of the structure-activity relationship (SAR) of a ligand class on a receptor, the understanding and prediction of the structure-kinetics relationship (SKR) is much more demanding. Experimental and computational approaches are described, which serve to either rationalize SKR or to predict the kinetic parameters such as on-rates and off-rates.
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Tehan BG, Christopher JA. The use of conformationally thermostabilised GPCRs in drug discovery: application to fragment, structure and biophysical techniques. Curr Opin Pharmacol 2016; 30:8-13. [PMID: 27400445 DOI: 10.1016/j.coph.2016.06.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 06/16/2016] [Accepted: 06/28/2016] [Indexed: 11/19/2022]
Abstract
Recent developments in receptor stabilisation have facilitated major advances in G protein-coupled receptor (GPCR) research, notably structural biology, over the past eight years. Here we review the application of fragment, structure and biophysical techniques using stabilised GPCRs (StaR proteins), and their impact in the drug discovery process. These techniques have, most recently, been utilised in the discovery of the non-alkyne mGlu5 negative allosteric modulator HTL14242, in addition to the dual orexin receptor antagonist HTL6641, with differentiated residence time kinetics.
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Affiliation(s)
- Benjamin G Tehan
- Heptares Therapeutics, Biopark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, United Kingdom.
| | - John A Christopher
- Heptares Therapeutics, Biopark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, United Kingdom
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40
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Jazayeri A, Andrews SP, Marshall FH. Structurally Enabled Discovery of Adenosine A 2A Receptor Antagonists. Chem Rev 2016; 117:21-37. [PMID: 27333206 DOI: 10.1021/acs.chemrev.6b00119] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Over the past decade there has been a revolution in the field of G protein-coupled receptor (GPCR) structural biology. Many years of innovative research from different areas have come together to fuel this significant change in the fortunes of this field, which for many years was characterized by the paucity of high-resolution structures. The determination to succeed has been in part due to the recognized importance of these proteins as drug targets, and although the pharmaceutical industry has been focusing on these receptors, it can be justifiably argued and demonstrated that many of the approved and commercially successful GPCR drugs can be significantly improved to increase efficacy and/or reduce undesired side effects. In addition, many validated targets in this class remain to be drugged. It is widely recognized that application of structure-based drug design approaches can help medicinal chemists a long way toward discovering better drugs. The achievement of structural biologists in providing high-resolution insight is beginning to transform drug discovery efforts, and there are a number of GPCR drugs that have been discovered by use of structural information that are in clinical development. This review aims to highlight the key developments that have brought success to GPCR structure resolution efforts and exemplify the practical application of structural information for the discovery of adenosine A2A receptor antagonists that have potential to treat multiple conditions.
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Affiliation(s)
- Ali Jazayeri
- Heptares Therapeutics Limited , BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, United Kingdom
| | - Stephen P Andrews
- Heptares Therapeutics Limited , BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, United Kingdom
| | - Fiona H Marshall
- Heptares Therapeutics Limited , BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, United Kingdom
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Zhou G, Aslanian R, Gallo G, Khan T, Kuang R, Purakkattle B, Ruiz MD, Stamford A, Ting P, Wu H, Wang H, Xiao D, Yu T, Zhang Y, Mullins D, Hodgson R. Discovery of aminoquinazoline derivatives as human A2A adenosine receptor antagonists. Bioorg Med Chem Lett 2016; 26:1348-54. [DOI: 10.1016/j.bmcl.2015.11.048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 11/12/2015] [Accepted: 11/16/2015] [Indexed: 10/22/2022]
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42
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Abstract
G protein-coupled receptors (GPCRs) remain a major domain of pharmaceutical discovery. The identification of GPCR lead compounds and their optimization are now structure-based, thanks to advances in X-ray crystallography, molecular modeling, protein engineering and biophysical techniques. In silico screening provides useful hit molecules. New pharmacological approaches to tuning the pleotropic action of GPCRs include: allosteric modulators, biased ligands, GPCR heterodimer-targeted compounds, manipulation of polypharmacology, receptor antibodies and tailoring of drug molecules to fit GPCR pharmacogenomics. Measurements of kinetics and drug efficacy are factors influencing clinical success. With the exception of inhibitors of GPCR kinases, targeting of intracellular GPCR signaling or receptor cycling for therapeutic purposes remains a futuristic concept. New assay approaches are more efficient and multidimensional: cell-based, label-free, fluorescence-based assays, and biosensors. Tailoring GPCR drugs to a patient's genetic background is now being considered. Chemoinformatic tools can predict ADME-tox properties. New imaging technology visualizes drug action in vivo. Thus, there is reason to be optimistic that new technology for GPCR ligand discovery will help reverse the current narrowing of the pharmaceutical pipeline.
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Affiliation(s)
- Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bldg. 8A, Rm. B1A-19, Bethesda, Maryland 20892, USA.
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43
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Zheng X, Bi C, Li Z, Podariu M, Hage DS. Analytical methods for kinetic studies of biological interactions: A review. J Pharm Biomed Anal 2015; 113:163-80. [PMID: 25700721 PMCID: PMC4516701 DOI: 10.1016/j.jpba.2015.01.042] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 01/16/2015] [Accepted: 01/19/2015] [Indexed: 01/13/2023]
Abstract
The rates at which biological interactions occur can provide important information concerning the mechanism and behavior of these processes in living systems. This review discusses several analytical methods that can be used to examine the kinetics of biological interactions. These techniques include common or traditional methods such as stopped-flow analysis and surface plasmon resonance spectroscopy, as well as alternative methods based on affinity chromatography and capillary electrophoresis. The general principles and theory behind these approaches are examined, and it is shown how each technique can be utilized to provide information on the kinetics of biological interactions. Examples of applications are also given for each method. In addition, a discussion is provided on the relative advantages or potential limitations of each technique regarding its use in kinetic studies.
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Affiliation(s)
- Xiwei Zheng
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Cong Bi
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Zhao Li
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Maria Podariu
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - David S Hage
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, USA.
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44
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Vauquelin G, Huber W, Swinney DC. Experimental Methods to Determine Binding Kinetics. THERMODYNAMICS AND KINETICS OF DRUG BINDING 2015. [DOI: 10.1002/9783527673025.ch9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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45
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Heym RG, Hornberger WB, Lakics V, Terstappen GC. Label-free detection of small-molecule binding to a GPCR in the membrane environment. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:979-86. [DOI: 10.1016/j.bbapap.2015.04.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 03/30/2015] [Accepted: 04/07/2015] [Indexed: 10/23/2022]
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46
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Hoffmann C, Castro M, Rinken A, Leurs R, Hill SJ, Vischer HF. Ligand Residence Time at G-protein–Coupled Receptors—Why We Should Take Our Time To Study It. Mol Pharmacol 2015; 88:552-60. [DOI: 10.1124/mol.115.099671] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 07/07/2015] [Indexed: 12/15/2022] Open
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47
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Design strategies to address kinetics of drug binding and residence time. Bioorg Med Chem Lett 2015; 25:2019-27. [DOI: 10.1016/j.bmcl.2015.02.027] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 02/06/2015] [Accepted: 02/11/2015] [Indexed: 02/06/2023]
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48
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Biosensor-based affinities and binding kinetics of small molecule antagonists to the adenosine A(2A) receptor reconstituted in HDL like particles. FEBS Lett 2015; 589:1399-405. [PMID: 25935416 DOI: 10.1016/j.febslet.2015.04.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 04/14/2015] [Accepted: 04/17/2015] [Indexed: 11/23/2022]
Abstract
The options for investigating solubilised G protein-coupled receptors (GPCRs) by biophysical techniques have long been hampered by their instability. A thermostabilised adenosine A2A receptor expressed in insect cells, purified in detergent and reconstituted into high-density lipoprotein (HDL) particles was immobilised onto a Surface Plasmon Resonance sensor chip. This allowed measurement of affinities and kinetics for A2A antagonists with affinities ranging from 50 pM to almost 2 μM. Compared with other formats, reproduction of affinities, and dissociation and association rate constants are good, reasonable and poor respectively, indicating stabilised receptors in HDL particles are useful for investigating specific aspects of GPCR-ligand interactions.
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49
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Heydenreich FM, Vuckovic Z, Matkovic M, Veprintsev DB. Stabilization of G protein-coupled receptors by point mutations. Front Pharmacol 2015; 6:82. [PMID: 25941489 PMCID: PMC4403299 DOI: 10.3389/fphar.2015.00082] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 03/31/2015] [Indexed: 11/13/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are flexible integral membrane proteins involved in transmembrane signaling. Their involvement in many physiological processes makes them interesting targets for drug development. Determination of the structure of these receptors will help to design more specific drugs, however, their structural characterization has so far been hampered by the low expression and their inherent instability in detergents which made protein engineering indispensable for structural and biophysical characterization. Several approaches to stabilize the receptors in a particular conformation have led to breakthroughs in GPCR structure determination. These include truncations of the flexible regions, stabilization by antibodies and nanobodies, fusion partners, high affinity and covalently bound ligands as well as conformational stabilization by mutagenesis. In this review we focus on stabilization of GPCRs by insertion of point mutations, which lead to increased conformational and thermal stability as well as improved expression levels. We summarize existing mutagenesis strategies with different coverage of GPCR sequence space and depth of information, design and transferability of mutations and the molecular basis for stabilization. We also discuss whether mutations alter the structure and pharmacological properties of GPCRs.
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Affiliation(s)
- Franziska M Heydenreich
- Laboratory of Biomolecular Research, Paul Scherrer Institut Villigen, Switzerland ; Department of Biology, ETH Zürich Zürich, Switzerland
| | - Ziva Vuckovic
- Laboratory of Biomolecular Research, Paul Scherrer Institut Villigen, Switzerland ; Department of Biology, ETH Zürich Zürich, Switzerland
| | - Milos Matkovic
- Laboratory of Biomolecular Research, Paul Scherrer Institut Villigen, Switzerland ; Department of Biology, ETH Zürich Zürich, Switzerland
| | - Dmitry B Veprintsev
- Laboratory of Biomolecular Research, Paul Scherrer Institut Villigen, Switzerland ; Department of Biology, ETH Zürich Zürich, Switzerland
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50
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Real-time monitoring of binding events on a thermostabilized human A2A receptor embedded in a lipid bilayer by surface plasmon resonance. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1224-33. [PMID: 25725488 DOI: 10.1016/j.bbamem.2015.02.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 01/19/2015] [Accepted: 02/13/2015] [Indexed: 12/12/2022]
Abstract
Membrane proteins (MPs) are prevalent drug discovery targets involved in many cell processes. Despite their high potential as drug targets, the study of MPs has been hindered by limitations in expression, purification and stabilization in order to acquire thermodynamic and kinetic parameters of small molecules binding. These bottlenecks are grounded on the mandatory use of detergents to isolate and extract MPs from the cell plasma membrane and the coexistence of multiple conformations, which reflects biochemical versatility and intrinsic instability of MPs. In this work ,we set out to define a new strategy to enable surface plasmon resonance (SPR) measurements on a thermostabilized and truncated version of the human adenosine (A2A) G-protein-coupled receptor (GPCR) inserted in a lipid bilayer nanodisc in a label- and detergent-free manner by using a combination of affinity tags and GFP-based fluorescence techniques. We were able to detect and characterize small molecules binding kinetics on a GPCR fully embedded in a lipid environment. By providing a comparison between different binding assays in membranes, nanodiscs and detergent micelles, we show that nanodiscs can be used for small molecule binding studies by SPR to enhance the MP stability and to trigger a more native-like behaviour when compared to kinetics on A2A receptors isolated in detergent. This work provides thus a new methodology in drug discovery to characterize the binding kinetics of small molecule ligands for MPs targets in a lipid environment.
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