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Bhunia SS, Saxena AK. Efficiency of Homology Modeling Assisted Molecular Docking in G-protein Coupled Receptors. Curr Top Med Chem 2021; 21:269-294. [PMID: 32901584 DOI: 10.2174/1568026620666200908165250] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/20/2020] [Accepted: 09/01/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Molecular docking is in regular practice to assess ligand affinity on a target protein crystal structure. In the absence of protein crystal structure, the homology modeling or comparative modeling is the best alternative to elucidate the relationship details between a ligand and protein at the molecular level. The development of accurate homology modeling (HM) and its integration with molecular docking (MD) is essential for successful, rational drug discovery. OBJECTIVE The G-protein coupled receptors (GPCRs) are attractive therapeutic targets due to their immense role in human pharmacology. The GPCRs are membrane-bound proteins with the complex constitution, and the understanding of their activation and inactivation mechanisms is quite challenging. Over the past decade, there has been a rapid expansion in the number of solved G-protein-coupled receptor (GPCR) crystal structures; however, the majority of the GPCR structures remain unsolved. In this context, HM guided MD has been widely used for structure-based drug design (SBDD) of GPCRs. METHODS The focus of this review is on the recent (i) developments on HM supported GPCR drug discovery in the absence of GPCR crystal structures and (ii) application of HM in understanding the ligand interactions at the binding site, virtual screening, determining receptor subtype selectivity and receptor behaviour in comparison with GPCR crystal structures. RESULTS The HM in GPCRs has been extremely challenging due to the scarcity in template structures. In such a scenario, it is difficult to get accurate HM that can facilitate understanding of the ligand-receptor interactions. This problem has been alleviated to some extent by developing refined HM based on incorporating active /inactive ligand information and inducing protein flexibility. In some cases, HM proteins were found to outscore crystal structures. CONCLUSION The developments in HM have been highly operative to gain insights about the ligand interaction at the binding site and receptor functioning at the molecular level. Thus, HM guided molecular docking may be useful for rational drug discovery for the GPCRs mediated diseases.
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Affiliation(s)
- Shome S Bhunia
- Global Institute of Pharmaceutical Education and Research, Kashipur, Uttarakhand, India
| | - Anil K Saxena
- Division of Medicinal and Process Chemistry, CSIR-CDRI, Lucknow 226031, India
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Abstract
Despite tremendous efforts, approximately 120 GPCRs remain orphan. Their physiological functions and their potential roles in diseases are poorly understood. Orphan GPCRs are extremely important because they may provide novel therapeutic targets for unmet medical needs. As a complement to experimental approaches, molecular modeling and virtual screening are efficient techniques to discover synthetic surrogate ligands which can help to elucidate the role of oGPCRs. Constitutively activated mutants and recently published active structures of GPCRs provide stimulating opportunities for building active molecular models for oGPCRs and identifying activators using virtual screening of compound libraries. We describe the molecular modeling and virtual screening process we have applied in the discovery of surrogate ligands, and provide examples for CCKA, a simulated oGPCR, and for two oGPCRs, GPR52 and GPR34.
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Affiliation(s)
- Constantino Diaz
- Research Informatics, Evotec (France) SAS, 195 Route d'Espagne, 31036, Toulouse, France.
| | | | - Emilie Pihan
- Research Informatics, Evotec (France) SAS, 195 Route d'Espagne, 31036, Toulouse, France
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Diaz C, Labit-Le Bouteiller C, Yvon S, Cambon-Kernëis A, Roasio A, Jamme MF, Aries A, Feuillerat C, Perret E, Guette F, Dieu P, Miloux B, Albène D, Hasel N, Kaghad M, Ferran E, Lupker J, Ferrara P. A Strategy Combining Differential Low-Throughput Screening and Virtual Screening (DLS-VS) Accelerating the Discovery of new Modulators for the Orphan GPR34 Receptor. Mol Inform 2013; 32:213-29. [PMID: 27481282 DOI: 10.1002/minf.201200047] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 01/05/2012] [Indexed: 12/21/2022]
Abstract
The DLS-VS strategy was developed as an integrated method for identifying chemical modulators for orphan GPCRs. It combines differential low-throughput screening (DLS) and virtual screening (VS). The two cascaded techniques offer complementary advantages and allow the experimental testing of a minimal number of compounds. First, DLS identifies modulators specific for the considered receptor among a set of receptors, through the screening of a small library with diverse chemical compounds. Then, an active molecular model of the receptor is built by homology to a validated template, and it is progressively refined by rotamers modification for key side-chains, by VS of the already screened library, and by iterative selection of the model generating the best enrichment. The refined active model is finally used for the VS of a large chemical library and the selection of a small set of compounds for experimental testing. Applied to the orphan receptor GPR34, the DLS-VS strategy combined the experimental screening of 20 000 compounds and the virtual screening of 1 250 000 compounds. It identified one agonist and eight inverse agonists, showing a high chemical diversity. We describe the method. The strategy can be applied to other GPCRs.
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Affiliation(s)
- Constantino Diaz
- Sanofi-Aventis Recherche & Développement, Centre de Toulouse, 195 Route d'Espagne, 31036 Toulouse, France fax: +33534632156.
| | - Christine Labit-Le Bouteiller
- Sanofi-Aventis Recherche & Développement, Centre de Toulouse, 195 Route d'Espagne, 31036 Toulouse, France fax: +33534632156
| | - Stéphane Yvon
- Sanofi-Aventis Recherche & Développement, Centre de Toulouse, 195 Route d'Espagne, 31036 Toulouse, France fax: +33534632156
| | - Aimée Cambon-Kernëis
- Sanofi-Aventis Recherche & Développement, Centre de Toulouse, 195 Route d'Espagne, 31036 Toulouse, France fax: +33534632156
| | - Annette Roasio
- Sanofi-Aventis Recherche & Développement, Centre de Toulouse, 195 Route d'Espagne, 31036 Toulouse, France fax: +33534632156
| | - Marie-Françoise Jamme
- Sanofi-Aventis Recherche & Développement, Centre de Toulouse, 195 Route d'Espagne, 31036 Toulouse, France fax: +33534632156
| | - Amélie Aries
- Sanofi-Aventis Recherche & Développement, Centre de Toulouse, 195 Route d'Espagne, 31036 Toulouse, France fax: +33534632156
| | - Claude Feuillerat
- Sanofi-Aventis Recherche & Développement, Centre de Toulouse, 195 Route d'Espagne, 31036 Toulouse, France fax: +33534632156
| | - Eric Perret
- Sanofi-Aventis Recherche & Développement, Centre de Toulouse, 195 Route d'Espagne, 31036 Toulouse, France fax: +33534632156
| | - Fréderique Guette
- Sanofi-Aventis Recherche & Développement, Centre de Toulouse, 195 Route d'Espagne, 31036 Toulouse, France fax: +33534632156
| | - Pierre Dieu
- Sanofi-Aventis Recherche & Développement, Centre de Toulouse, 195 Route d'Espagne, 31036 Toulouse, France fax: +33534632156
| | - Brigitte Miloux
- Sanofi-Aventis Recherche & Développement, Centre de Toulouse, 195 Route d'Espagne, 31036 Toulouse, France fax: +33534632156
| | - Danielle Albène
- Sanofi-Aventis Recherche & Développement, Centre de Toulouse, 195 Route d'Espagne, 31036 Toulouse, France fax: +33534632156
| | - Nathalie Hasel
- Sanofi-Aventis Recherche & Développement, Centre de Toulouse, 195 Route d'Espagne, 31036 Toulouse, France fax: +33534632156
| | - Mourad Kaghad
- Sanofi-Aventis Recherche & Développement, Centre de Toulouse, 195 Route d'Espagne, 31036 Toulouse, France fax: +33534632156
| | - Edgardo Ferran
- Sanofi-Aventis Recherche & Développement, Centre de Toulouse, 195 Route d'Espagne, 31036 Toulouse, France fax: +33534632156
| | - Jan Lupker
- Sanofi-Aventis Recherche & Développement, Centre de Toulouse, 195 Route d'Espagne, 31036 Toulouse, France fax: +33534632156
| | - Pascual Ferrara
- Sanofi-Aventis Recherche & Développement, Centre de Toulouse, 195 Route d'Espagne, 31036 Toulouse, France fax: +33534632156
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