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Szwabowski GL, Baker DL, Parrill AL. Application of computational methods for class A GPCR Ligand discovery. J Mol Graph Model 2023; 121:108434. [PMID: 36841204 DOI: 10.1016/j.jmgm.2023.108434] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 02/11/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023]
Abstract
G protein-coupled receptors (GPCR) are integral membrane proteins of considerable interest as targets for drug development due to their role in transmitting cellular signals in a multitude of biological processes. Of the six classes categorizing GPCR (A, B, C, D, E, and F), class A contains the largest number of therapeutically relevant GPCR. Despite their importance as drug targets, many challenges exist for the discovery of novel class A GPCR ligands serving as drug precursors. Though knowledge of the structural and functional characteristics of GPCR has grown significantly over the past 20 years, a large portion of GPCR lack reported, experimentally determined structures. Furthermore, many GPCR have no known endogenous and/or synthetic ligands, limiting further exploration of their biochemical, cellular, and physiological roles. While many successes in GPCR ligand discovery have resulted from experimental high-throughput screening, computational methods have played an increasingly important role in GPCR ligand identification in the past decade. Here we discuss computational techniques applied to GPCR ligand discovery. This review summarizes class A GPCR structure/function and provides an overview of many obstacles currently faced in GPCR ligand discovery. Furthermore, we discuss applications and recent successes of computational techniques used to predict GPCR structure as well as present a summary of ligand- and structure-based methods used to identify potential GPCR ligands. Finally, we discuss computational hit list generation and refinement and provide comprehensive workflows for GPCR ligand identification.
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Affiliation(s)
| | - Daniel L Baker
- Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA
| | - Abby L Parrill
- Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA.
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Drug-Targeted Genomes: Mutability of Ion Channels and GPCRs. Biomedicines 2022; 10:biomedicines10030594. [PMID: 35327396 PMCID: PMC8945769 DOI: 10.3390/biomedicines10030594] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/24/2022] [Accepted: 03/01/2022] [Indexed: 02/04/2023] Open
Abstract
Mutations of ion channels and G-protein-coupled receptors (GPCRs) are not uncommon and can lead to cardiovascular diseases. Given previously reported multiple factors associated with high mutation rates, we sorted the relative mutability of multiple human genes by (i) proximity to telomeres and/or (ii) high adenine and thymine (A+T) content. We extracted genomic information using the genome data viewer and examined the mutability of 118 ion channel and 143 GPCR genes based on their association with factors (i) and (ii). We then assessed these two factors with 31 genes encoding ion channels or GPCRs that are targeted by the United States Food and Drug Administration (FDA)-approved drugs. Out of the 118 ion channel genes studied, 80 met either factor (i) or (ii), resulting in a 68% match. In contrast, a 78% match was found for the 143 GPCR genes. We also found that the GPCR genes (n = 20) targeted by FDA-approved drugs have a relatively lower mutability than those genes encoding ion channels (n = 11), where targeted genes encoding GPCRs were shorter in length. The result of this study suggests that the use of matching rate analysis on factor-druggable genome is feasible to systematically compare the relative mutability of GPCRs and ion channels. The analysis on chromosomes by two factors identified a unique characteristic of GPCRs, which have a significant relationship between their nucleotide sizes and proximity to telomeres, unlike most genetic loci susceptible to human diseases.
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Gong J, Chen Y, Pu F, Sun P, He F, Zhang L, Li Y, Ma Z, Wang H. Understanding Membrane Protein Drug Targets in Computational Perspective. Curr Drug Targets 2020; 20:551-564. [PMID: 30516106 DOI: 10.2174/1389450120666181204164721] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/03/2018] [Accepted: 09/04/2018] [Indexed: 01/16/2023]
Abstract
Membrane proteins play crucial physiological roles in vivo and are the major category of drug targets for pharmaceuticals. The research on membrane protein is a significant part in the drug discovery. The biological process is a cycled network, and the membrane protein is a vital hub in the network since most drugs achieve the therapeutic effect via interacting with the membrane protein. In this review, typical membrane protein targets are described, including GPCRs, transporters and ion channels. Also, we conclude network servers and databases that are referring to the drug, drug-target information and their relevant data. Furthermore, we chiefly introduce the development and practice of modern medicines, particularly demonstrating a series of state-of-the-art computational models for the prediction of drug-target interaction containing network-based approach and machine-learningbased approach as well as showing current achievements. Finally, we discuss the prospective orientation of drug repurposing and drug discovery as well as propose some improved framework in bioactivity data, created or improved predicted approaches, alternative understanding approaches of drugs bioactivity and their biological processes.
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Affiliation(s)
- Jianting Gong
- School of Information Science and Technology, Northeast Normal University, Changchun, China.,Institution of Computational Biology, Northeast Normal University, Changchun, China
| | - Yongbing Chen
- School of Information Science and Technology, Northeast Normal University, Changchun, China.,Institution of Computational Biology, Northeast Normal University, Changchun, China
| | - Feng Pu
- School of Information Science and Technology, Northeast Normal University, Changchun, China.,Institution of Computational Biology, Northeast Normal University, Changchun, China
| | - Pingping Sun
- School of Information Science and Technology, Northeast Normal University, Changchun, China.,Institution of Computational Biology, Northeast Normal University, Changchun, China
| | - Fei He
- School of Information Science and Technology, Northeast Normal University, Changchun, China.,Institution of Computational Biology, Northeast Normal University, Changchun, China
| | - Li Zhang
- School of Computer Science and Engineering, Changchun University of Technology, Changchun, China
| | - Yanwen Li
- School of Information Science and Technology, Northeast Normal University, Changchun, China.,Institution of Computational Biology, Northeast Normal University, Changchun, China
| | - Zhiqiang Ma
- School of Information Science and Technology, Northeast Normal University, Changchun, China.,Institution of Computational Biology, Northeast Normal University, Changchun, China
| | - Han Wang
- School of Information Science and Technology, Northeast Normal University, Changchun, China.,Institution of Computational Biology, Northeast Normal University, Changchun, China
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4
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Willems H, De Cesco S, Svensson F. Computational Chemistry on a Budget: Supporting Drug Discovery with Limited Resources. J Med Chem 2020; 63:10158-10169. [DOI: 10.1021/acs.jmedchem.9b02126] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Henriëtte Willems
- The ALBORADA Drug Discovery Institute, University of Cambridge, Island Research Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0AH, U.K
| | - Stephane De Cesco
- Alzheimer’s Research UK Oxford Drug Discovery Institute, University of Oxford, NDM Research Building, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Fredrik Svensson
- Alzheimer’s Research UK UCL Drug Discovery Institute, University College London, The Cruciform Building, Gower Street, London WC1E 6BT, U.K
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Grebner C, Malmerberg E, Shewmaker A, Batista J, Nicholls A, Sadowski J. Virtual Screening in the Cloud: How Big Is Big Enough? J Chem Inf Model 2019; 60:4274-4282. [PMID: 31682421 DOI: 10.1021/acs.jcim.9b00779] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Virtual screening is a standard tool in Computer-Assisted Drug Design (CADD). Early in a project, it is typical to use ligand-based similarity search methods to find suitable hit molecules. However, the number of compounds which can be screened and the time required are usually limited by computational resources. We describe here a high-throughput virtual screening project using 3D similarity (FastROCS) and automated evaluation workflows on Orion, a cloud computing platform. Cloud resources make this approach fully scalable and flexible, allowing the generation and search of billions of virtual molecules, and give access to an explicit 3D virtual chemistry space not available before. We discuss the impact of the size of the search space with respect to finding novel chemical hits and the size of the required hit list, as well as computational and economical aspects of resource scaling.
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Affiliation(s)
- Christoph Grebner
- Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, SE-43183 Gothenburg, Sweden
| | - Erik Malmerberg
- Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, SE-43183 Gothenburg, Sweden
| | - Andrew Shewmaker
- OpenEye Scientific Software, Inc., 9 Bisbee Court Suite D, Santa Fe, New Mexico 87508, United States
| | - Jose Batista
- OpenEye Scientific Software, Inc., 9 Bisbee Court Suite D, Santa Fe, New Mexico 87508, United States
| | - Anthony Nicholls
- OpenEye Scientific Software, Inc., 9 Bisbee Court Suite D, Santa Fe, New Mexico 87508, United States
| | - Jens Sadowski
- Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, SE-43183 Gothenburg, Sweden
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Sydow D, Burggraaff L, Szengel A, van Vlijmen HWT, IJzerman AP, van Westen GJP, Volkamer A. Advances and Challenges in Computational Target Prediction. J Chem Inf Model 2019; 59:1728-1742. [DOI: 10.1021/acs.jcim.8b00832] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Dominique Sydow
- In silico Toxicology, Institute of Physiology, Charité − Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Lindsey Burggraaff
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Angelika Szengel
- In silico Toxicology, Institute of Physiology, Charité − Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Herman W. T. van Vlijmen
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
- Computational Chemistry, Janssen Research & Development, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Adriaan P. IJzerman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Gerard J. P. van Westen
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Andrea Volkamer
- In silico Toxicology, Institute of Physiology, Charité − Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
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