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Mishra S, Corro-Flores M, Krum D, Forouzesh N. Molecular Docking Improved with Human Spatial Perception Using Virtual Reality. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2024; 30:2269-2275. [PMID: 38451773 DOI: 10.1109/tvcg.2024.3372128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
Adaptive steered molecular dynamics (ASMD) is a computational biophysics method in which an external force is applied to a selected set of atoms or a specific reaction coordinate to induce a particular molecular motion. Virtual reality (VR) based methods for protein-ligand docking are beneficial for visualizing on-the-fly interactive molecular dynamics and performing promising docking trajectories. In this paper, we propose a novel method to guide ASMD with optimal trajectories collected from human experiences using interactive molecular dynamics in virtual reality (iMD-VR). We also explain the benefits of using VR as a tool for expediting the process of ligand binding, outlining an experimental protocol that enables iMD-VR users to guide Amprenavir into and out of the binding pockets of HIV-1 protease and recreate their respective crystallographic binding poses within 5 minutes. Later, we discuss our analysis of the results from iMD-VR-assisted ASMD simulation and assess its performance compared to a standard ASMD simulation. From the accuracy point of view, our proposed method calculates higher Potential Mean Force (PMF) values consistently relative to a standard ASMD simulation with an almost twofold increase in all the experiments. Finally, we describe the novelty of the research and discuss results showcasing a faster and more effective convergence of the ligand to the protein's binding site as compared to a standard molecular dynamics simulation, proving the effectiveness of VR in the field of drug discovery. Future work includes the development of an artificial intelligence algorithm capable of predicting optimal binding trajectories for many protein-ligand pairs, as well as the required force needed to steer the ligand to follow the said trajectory.
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Crossley-Lewis J, Dunn J, Buda C, Sunley GJ, Elena AM, Todorov IT, Yong CW, Glowacki DR, Mulholland AJ, Allan NL. Interactive molecular dynamics in virtual reality for modelling materials and catalysts. J Mol Graph Model 2023; 125:108606. [PMID: 37660615 DOI: 10.1016/j.jmgm.2023.108606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 08/17/2023] [Accepted: 08/17/2023] [Indexed: 09/05/2023]
Abstract
Interactive molecular dynamics simulation in virtual reality (iMD-VR) is emerging as a promising technique in molecular science. Here, we demonstrate its use in a range of fifteen applications in materials science and heterogeneous catalysis. In this work, the iMD-VR package Narupa is used with the MD package, DL_POLY [1]. We show how iMD-VR can be used to: (i) investigate the mechanism of lithium fast ion conduction by directing the formation of defects showing that vacancy transport is favoured over interstitialcy mechanisms, and (ii) guide a molecule through a zeolite pore to explore diffusion within zeolites, examining in detail the motion of methyl n-hexanoate in H-ZSM-5 zeolite and identifying bottlenecks restricting diffusion. iMD-VR allows users to manipulate these systems intuitively, to drive changes in them and observe the resulting changes in structure and dynamics. We make these simulations available, as a resource for both teaching and research. All simulation files, with videos, can be found online (https://doi.org/10.5281/zenodo.8252314) and are provided as open-source material.
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Affiliation(s)
- Joe Crossley-Lewis
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Josh Dunn
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Corneliu Buda
- Applied Sciences, bp Innovation and Engineering, BP plc, 150 West Warrenville Road, Naperville, IL, 60563, USA
| | - Glenn J Sunley
- Applied Sciences, bp Innovation and Engineering, BP plc, Saltend, Hull, HU12 8DS, UK
| | - Alin M Elena
- Scientific Computing Department, STFC Daresbury Laboratory, Daresbury, UK
| | - Ilian T Todorov
- Scientific Computing Department, STFC Daresbury Laboratory, Daresbury, UK
| | - Chin W Yong
- Scientific Computing Department, STFC Daresbury Laboratory, Daresbury, UK
| | - David R Glowacki
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Neil L Allan
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
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Deeks HM, Zinovjev K, Barnoud J, Mulholland AJ, van der Kamp MW, Glowacki DR. Free energy along drug-protein binding pathways interactively sampled in virtual reality. Sci Rep 2023; 13:16665. [PMID: 37794083 PMCID: PMC10551034 DOI: 10.1038/s41598-023-43523-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/25/2023] [Indexed: 10/06/2023] Open
Abstract
We describe a two-step approach for combining interactive molecular dynamics in virtual reality (iMD-VR) with free energy (FE) calculation to explore the dynamics of biological processes at the molecular level. We refer to this combined approach as iMD-VR-FE. Stage one involves using a state-of-the-art 'human-in-the-loop' iMD-VR framework to generate a diverse range of protein-ligand unbinding pathways, benefitting from the sophistication of human spatial and chemical intuition. Stage two involves using the iMD-VR-sampled pathways as initial guesses for defining a path-based reaction coordinate from which we can obtain a corresponding free energy profile using FE methods. To investigate the performance of the method, we apply iMD-VR-FE to investigate the unbinding of a benzamidine ligand from a trypsin protein. The binding free energy calculated using iMD-VR-FE is similar for each pathway, indicating internal consistency. Moreover, the resulting free energy profiles can distinguish energetic differences between pathways corresponding to various protein-ligand conformations (e.g., helping to identify pathways that are more favourable) and enable identification of metastable states along the pathways. The two-step iMD-VR-FE approach offers an intuitive way for researchers to test hypotheses for candidate pathways in biomolecular systems, quickly obtaining both qualitative and quantitative insight.
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Affiliation(s)
- Helen M Deeks
- Center for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Kirill Zinovjev
- Departamento de Química Física, Universidad de Valencia, 46100, Burjassot, Spain
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | - Jonathan Barnoud
- Center for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
- CiTIUS | Centro Singular de Investigación en Tecnoloxías Intelixentes da USC, Rúa de Jenaro de la Fuente, s/n, 15705, Santiago de Compostela, A Coruña, Spain
| | - Adrian J Mulholland
- Center for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Marc W van der Kamp
- Center for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK.
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK.
| | - David R Glowacki
- CiTIUS | Centro Singular de Investigación en Tecnoloxías Intelixentes da USC, Rúa de Jenaro de la Fuente, s/n, 15705, Santiago de Compostela, A Coruña, Spain.
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Ridgway H, Orbell JD, Matsoukas MT, Kelaidonis K, Moore GJ, Tsiodras S, Gorgoulis VG, Chasapis CT, Apostolopoulos V, Matsoukas JM. W254 in furin functions as a molecular gate promoting anti-viral drug binding: Elucidation of putative drug tunneling and docking by non-equilibrium molecular dynamics. Comput Struct Biotechnol J 2023; 21:4589-4612. [PMID: 37817778 PMCID: PMC10561063 DOI: 10.1016/j.csbj.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2023] Open
Abstract
Furins are serine endoproteases that process precursor proteins into their biologically active forms, and they play essential roles in normal metabolism and disease presentation, including promoting expression of bacterial virulence factors and viral pathogenesis. Thus, furins represent vital targets for development of antimicrobial and antiviral therapeutics. Recent experimental evidence indicated that dichlorophenyl (DCP)-pyridine "BOS" drugs (e.g., BOS-318) competitively inhibit human furin by an induced-fit mechanism in which tryptophan W254 in the furin catalytic cleft (FCC) functions as a molecular gate, rotating nearly 180o through a steep energy barrier about its chi-1 dihedral to an "open" orientation, exposing a buried (i.e., cryptic) hydrophobic pocket 1. Once exposed, the non-polar DCP group of BOS-318, and similar halo-phenyl groups of analogs, enter the cryptic pocket, stabilizing drug binding. Here, we demonstrate flexible-receptor docking of BOS-318 (and various analogs) was unable to emulate the induced-fit motif, even when tryptophan was replaced with less bulky phenylalanine or glycine. While either substitution allowed access to the hydrophobic pocket for most ligands tested, optimal binding was observed only for W254, inferring a stabilizing effect of the indole sidechain. Furthermore, non-equilibrium steered molecular dynamics (sMD) in which the bound drugs (or their fragments) were extracted from the FCC did not cause closure of the open W254 gate, consistent with the thermodynamic stability of the open or closed W254 orientations. Finally, interactive molecular dynamics (iMD) revealed two putative conduits of drug entry and binding into the FCC, each coupled with W254 dihedral rotation and opening of the cryptic pocket. The iMD simulations further revealed ligand entry and binding in the FCC is likely driven in part by energy fluxes stemming from disruption and re-formation of ligand and protein solvation shells during drug migration from the solution phase into the FCC.
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Affiliation(s)
- Harry Ridgway
- Institute for Sustainable Industries and Liveable Cities, Victoria University, Melbourne, VIC 8001, Australia
- AquaMem Consultants, Rodeo, NM 88056, USA
| | - John D. Orbell
- Institute for Sustainable Industries and Liveable Cities, Victoria University, Melbourne, VIC 8001, Australia
- College of Sport, Health & Engineering, Victoria University, Melbourne, VIC 8001, Australia
| | | | | | - Graham J. Moore
- Pepmetics Inc., 772 Murphy Place, Victoria, BC V8Y 3H4, Canada
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Sotiris Tsiodras
- Department of Internal Medicine, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Vasilis G. Gorgoulis
- Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
- Department of Histology and Embryology, Faculty of Medicine, National Kapodistrian University of Athens, GR-11527 Athens, Greece
- Faculty Institute for Cancer Sciences, Manchester Academic Health Sciences Centre, University of Manchester, M20 4GJ Manchester, UK
- Biomedical Research Foundation, Academy of Athens, GR-11527 Athens, Greece
- Faculty of Health and Medical Sciences, University of Surrey, GU2 7XH Surrey, UK
| | - Christos T. Chasapis
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Vasso Apostolopoulos
- Institute for Health and Sport, Immunology and Translational Research, Victoria University, Melbourne 3030, VIC, Australia
- Immunology Program, Australian Institute for Musculoskeletal Science (AIMSS), Melbourne 3021, VIC, Australia
| | - John M. Matsoukas
- NewDrug/NeoFar PC, Patras Science Park, Patras 26504, Greece
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Institute for Health and Sport, Immunology and Translational Research, Victoria University, Melbourne 3030, VIC, Australia
- Department of Chemistry, University of Patras, 26504 Patras, Greece
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Konagaya A, Gutmann G, Zhang Y. Co-creation environment with cloud virtual reality and real-time artificial intelligence toward the design of molecular robots. J Integr Bioinform 2023; 20:jib-2022-0017. [PMID: 36194394 PMCID: PMC10063180 DOI: 10.1515/jib-2022-0017] [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: 03/15/2022] [Revised: 08/31/2022] [Accepted: 09/07/2022] [Indexed: 11/15/2022] Open
Abstract
This paper describes the design philosophy for our cloud-based virtual reality (VR) co-creation environment (CCE) for molecular modeling. Using interactive VR simulation can provide enhanced perspectives in molecular modeling for intuitive live demonstration and experimentation in the CCE. Then the use of the CCE can enhance knowledge creation by bringing people together to share and create ideas or knowledge that may not emerge otherwise. Our prototype CCE discussed here, which was developed to demonstrate our design philosophy, has already enabled multiple members to log in and touch virtual molecules running on a cloud server with no noticeable network latency via real-time artificial intelligence techniques. The CCE plays an essential role in the rational design of molecular robot parts, which consist of bio-molecules such as DNA and protein molecules.
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Affiliation(s)
- Akihiko Konagaya
- Molecular Robotics Research Institute, Co., Ltd., 4259-3, Nagatsuta, Midori, Yokohama, Japan
- Keisen University, 2-10-1, Minamino, Tama, Tokyo, Japan
| | - Gregory Gutmann
- Molecular Robotics Research Institute, Co., Ltd., 4259-3, Nagatsuta, Midori, Yokohama, Japan
| | - Yuhui Zhang
- Molecular Robotics Research Institute, Co., Ltd., 4259-3, Nagatsuta, Midori, Yokohama, Japan
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Wang A, Durrant JD. Open-Source Browser-Based Tools for Structure-Based Computer-Aided Drug Discovery. Molecules 2022; 27:molecules27144623. [PMID: 35889494 PMCID: PMC9319651 DOI: 10.3390/molecules27144623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/17/2022] [Accepted: 07/18/2022] [Indexed: 01/27/2023] Open
Abstract
We here outline the importance of open-source, accessible tools for computer-aided drug discovery (CADD). We begin with a discussion of drug discovery in general to provide context for a subsequent discussion of structure-based CADD applied to small-molecule ligand discovery. Next, we identify usability challenges common to many open-source CADD tools. To address these challenges, we propose a browser-based approach to CADD tool deployment in which CADD calculations run in modern web browsers on users’ local computers. The browser app approach eliminates the need for user-initiated download and installation, ensures broad operating system compatibility, enables easy updates, and provides a user-friendly graphical user interface. Unlike server apps—which run calculations “in the cloud” rather than on users’ local computers—browser apps do not require users to upload proprietary information to a third-party (remote) server. They also eliminate the need for the difficult-to-maintain computer infrastructure required to run user-initiated calculations remotely. We conclude by describing some CADD browser apps developed in our lab, which illustrate the utility of this approach. Aside from introducing readers to these specific tools, we are hopeful that this review highlights the need for additional browser-compatible, user-friendly CADD software.
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Walters RK, Gale EM, Barnoud J, Glowacki DR, Mulholland AJ. The emerging potential of interactive virtual reality in drug discovery. Expert Opin Drug Discov 2022; 17:685-698. [PMID: 35638298 DOI: 10.1080/17460441.2022.2079632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
INTRODUCTION The potential of virtual reality (VR) to contribute to drug design and development has been recognized for many years. A recent advance is to use VR not only to visualize and interact with molecules, but also to interact with molecular dynamics simulations 'on the fly' (interactive molecular dynamics in VR, IMD-VR), which is useful for flexible docking and examining binding processes and conformational changes. AREAS COVERED The authors use the term 'interactive VR' to refer to software where interactivity is an inherent part of the user VR experience e.g. in making structural modifications or interacting with a physically rigorous molecular dynamics (MD) simulation, as opposed to using VR controllers to rotate and translate the molecule for enhanced visualization. Here, they describe these methods and their application to problems relevant to drug discovery, highlighting the possibilities that they offer in this arena. EXPERT OPINION The ease of viewing and manipulating molecular structures and dynamics, using accessible VR hardware, and the ability to modify structures on the fly (e.g. adding or deleting atoms) - and for groups of researchers to work together in the same virtual environment - makes modern interactive VR a valuable tool to add to the armory of drug design and development methods.
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Affiliation(s)
- Rebecca K Walters
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | - Ella M Gale
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | - Jonathan Barnoud
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
- CiTIUS Intelligent Technologies Research Centre, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - David R Glowacki
- CiTIUS Intelligent Technologies Research Centre, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
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8
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Group VR experiences can produce ego attenuation and connectedness comparable to psychedelics. Sci Rep 2022; 12:8995. [PMID: 35637199 PMCID: PMC9149675 DOI: 10.1038/s41598-022-12637-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 05/12/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractWith a growing body of research highlighting the therapeutic potential of experiential phenomenology which diminishes egoic identity and increases one’s sense of connectedness, there is significant interest in how to elicit such ‘self-transcendent experiences’ (STEs) in laboratory contexts. Psychedelic drugs (YDs) have proven particularly effective in this respect, producing subjective phenomenology which reliably elicits intense STEs. With virtual reality (VR) emerging as a powerful tool for constructing new perceptual environments, we describe a VR framework called ‘Isness-distributed’ (Isness-D) which harnesses the unique affordances of distributed multi-person VR to blur conventional self-other boundaries. Within Isness-D, groups of participants co-habit a shared virtual space, collectively experiencing their bodies as luminous energetic essences with diffuse spatial boundaries. It enables moments of ‘energetic coalescence’, a new class of embodied intersubjective experience where bodies can fluidly merge, enabling participants to include multiple others within their self-representation. To evaluate Isness-D, we adopted a citizen science approach, coordinating an international network of Isness-D 'nodes'. We analyzed the results (N = 58) using 4 different self-report scales previously applied to analyze subjective YD phenomenology (the inclusion of community in self scale, ego-dissolution inventory, communitas scale, and the MEQ30 mystical experience questionnaire). Despite the complexities associated with a distributed experiment like this, the Isness-D scores on all 4 scales were statistically indistinguishable from recently published YD studies, demonstrating that distributed VR can be used to design intersubjective STEs where people dissolve their sense of self in the connection to others.
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Online tools to easily build virtual molecular models for display in augmented and virtual reality on the web. J Mol Graph Model 2022; 114:108164. [PMID: 35325844 DOI: 10.1016/j.jmgm.2022.108164] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/05/2022] [Accepted: 03/07/2022] [Indexed: 11/20/2022]
Abstract
Several groups developed in the last years augmented and virtual reality (AR/VR) software to visualize 3D molecules, most rather static, limited in content, and requiring software installs, some even requiring expensive hardware. We launched in 2020 moleculARweb (https://molecularweb.epfl.ch), a website that offers interactive content for chemistry and structural biology education through commodity web-based AR that works on consumer devices like smartphones, tablets and laptops. Among thousands of users, teachers increasingly request more biological macromolecules to be available, a demand that we cannot address individually. Therefore, to allow users to build their own material, we built a web interface where they can create online AR experiences in few steps starting from Protein Data Bank, AlphaFold or custom uploaded structures, or from virtual objects/scenes exported from the Visual Molecular Dynamics program, without any programming knowledge. The web tool also returns WebXR sessions for viewing and manipulating the models in WebXR-compatible devices including smartphones, tablets, and also immersive VR headsets with WebXR-capable browsers, where models can be manipulated even with bare hands when supported by the device. The tool is accessible for free at https://molecularweb.epfl.ch/pages/pdb2ar.html.
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Plateau-Holleville C, Guionnière S, Boyer B, Jiménez-Garcia B, Levieux G, Mérillou S, Maria M, Montes M. UDock2: interactive real-time multi-body protein-protein docking software. Bioinformatics 2022; 39:btad609. [PMID: 37792496 PMCID: PMC10938049 DOI: 10.1093/bioinformatics/btad609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 08/10/2023] [Accepted: 10/02/2023] [Indexed: 10/06/2023] Open
Abstract
MOTIVATION Protein-protein docking aims at predicting the geometry of protein interactions to gain insights into the mechanisms underlying these processes and develop new strategies for drug discovery. Interactive and user-oriented manipulation tools can support this task complementary to automated software. RESULTS This article presents an interactive multi-body protein-protein docking software, UDock2, designed for research but also usable for teaching and popularization of science purposes due to its high usability. In UDock2, the users tackle the conformational space of protein interfaces using an intuitive real-time docking procedure with on-the-fly scoring. UDock2 integrates traditional computer graphics methods to facilitate the visualization and to provide better insight into protein surfaces, interfaces, and properties. AVAILABILITY AND IMPLEMENTATION UDock2 is open-source, cross-platform (Windows and Linux), and available at http://udock.fr. The code can be accessed at https://gitlab.com/Udock/Udock2.
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Affiliation(s)
| | - Simon Guionnière
- Laboratoire GBCM, EA 7528, Conservatoire National des Arts et Métiers, Hésam Université, 75003 Paris, France
| | - Benjamin Boyer
- Laboratoire GBCM, EA 7528, Conservatoire National des Arts et Métiers, Hésam Université, 75003 Paris, France
| | | | - Guillaume Levieux
- CEDRIC, EA 4626, Conservatoire National des Arts et Métiers, Hésam Université, 75003 Paris, France
| | | | - Maxime Maria
- XLIM, UMR CNRS 7252, University of Limoges, 87000 Limoges, France
| | - Matthieu Montes
- Laboratoire GBCM, EA 7528, Conservatoire National des Arts et Métiers, Hésam Université, 75003 Paris, France
- Institut Universitaire de France (IUF), Paris 75005, France
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11
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Lanrezac A, Férey N, Baaden M. Wielding the power of interactive molecular simulations. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- André Lanrezac
- CNRS, Laboratoire de Biochimie Théorique Université de Paris Paris France
| | - Nicolas Férey
- CNRS, Laboratoire interdisciplinaire des sciences du numérique Université Paris‐Saclay Orsay France
| | - Marc Baaden
- CNRS, Laboratoire de Biochimie Théorique Université de Paris Paris France
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12
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Cook J, Brown M, Sellwood M, Campbell C, Kouppas P, Poronnik P. XR game development as a tool for authentic, experiential, and collaborative learning. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021; 49:846-847. [PMID: 34410022 DOI: 10.1002/bmb.21572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 07/20/2021] [Accepted: 07/29/2021] [Indexed: 06/13/2023]
Abstract
This brief review provides insights into the recent advances made by the Unity game engine into education and the ways that learning resources can be used to teach novice bioscience students to use the VR/AR affordances of the platform. We present our own practises for implementation of a novel gamification task for final-year bioscience students and reflect on the changes we have had to make in order to overcome challenges presented by the COVID-19 pandemic.
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Affiliation(s)
- Jim Cook
- ICT TechLab, The University of Sydney, Darlington, New South Wales, Australia
| | - Martin Brown
- Westmead Living Lab, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Matthew Sellwood
- Media Lab, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, New South Wales, Australia
| | - Craig Campbell
- Media Lab, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, New South Wales, Australia
| | | | - Philip Poronnik
- Media Lab, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, New South Wales, Australia
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Chan HTH, Moesser MA, Walters RK, Malla TR, Twidale RM, John T, Deeks HM, Johnston-Wood T, Mikhailov V, Sessions RB, Dawson W, Salah E, Lukacik P, Strain-Damerell C, Owen CD, Nakajima T, Świderek K, Lodola A, Moliner V, Glowacki DR, Spencer J, Walsh MA, Schofield CJ, Genovese L, Shoemark DK, Mulholland AJ, Duarte F, Morris GM. Discovery of SARS-CoV-2 M pro peptide inhibitors from modelling substrate and ligand binding. Chem Sci 2021; 12:13686-13703. [PMID: 34760153 PMCID: PMC8549791 DOI: 10.1039/d1sc03628a] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 09/05/2021] [Indexed: 12/22/2022] Open
Abstract
The main protease (Mpro) of SARS-CoV-2 is central to viral maturation and is a promising drug target, but little is known about structural aspects of how it binds to its 11 natural cleavage sites. We used biophysical and crystallographic data and an array of biomolecular simulation techniques, including automated docking, molecular dynamics (MD) and interactive MD in virtual reality, QM/MM, and linear-scaling DFT, to investigate the molecular features underlying recognition of the natural Mpro substrates. We extensively analysed the subsite interactions of modelled 11-residue cleavage site peptides, crystallographic ligands, and docked COVID Moonshot-designed covalent inhibitors. Our modelling studies reveal remarkable consistency in the hydrogen bonding patterns of the natural Mpro substrates, particularly on the N-terminal side of the scissile bond. They highlight the critical role of interactions beyond the immediate active site in recognition and catalysis, in particular plasticity at the S2 site. Building on our initial Mpro-substrate models, we used predictive saturation variation scanning (PreSaVS) to design peptides with improved affinity. Non-denaturing mass spectrometry and other biophysical analyses confirm these new and effective 'peptibitors' inhibit Mpro competitively. Our combined results provide new insights and highlight opportunities for the development of Mpro inhibitors as anti-COVID-19 drugs.
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Affiliation(s)
- H T Henry Chan
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Marc A Moesser
- Department of Statistics, University of Oxford 24-29 St Giles' Oxford OX1 3LB UK
| | - Rebecca K Walters
- Centre for Computational Chemistry, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- Intangible Realities Laboratory, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Tika R Malla
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Rebecca M Twidale
- Centre for Computational Chemistry, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Tobias John
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Helen M Deeks
- Centre for Computational Chemistry, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- Intangible Realities Laboratory, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Tristan Johnston-Wood
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Victor Mikhailov
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Richard B Sessions
- School of Biochemistry, University of Bristol, Medical Sciences Building University Walk Bristol BS8 1TD UK
| | - William Dawson
- RIKEN Center for Computational Science 7-1-26 Minatojima-minami-machi, Chuo-ku Kobe Hyogo 650-0047 Japan
| | - Eidarus Salah
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Petra Lukacik
- Diamond Light Source Ltd, Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Claire Strain-Damerell
- Diamond Light Source Ltd, Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - C David Owen
- Diamond Light Source Ltd, Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Takahito Nakajima
- RIKEN Center for Computational Science 7-1-26 Minatojima-minami-machi, Chuo-ku Kobe Hyogo 650-0047 Japan
| | - Katarzyna Świderek
- Biocomp Group, Institute of Advanced Materials (INAM), Universitat Jaume I 12071 Castello Spain
| | - Alessio Lodola
- Food and Drug Department, University of Parma Parco Area delle Scienze, 27/A 43124 Parma Italy
| | - Vicent Moliner
- Biocomp Group, Institute of Advanced Materials (INAM), Universitat Jaume I 12071 Castello Spain
| | - David R Glowacki
- Intangible Realities Laboratory, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - James Spencer
- Intangible Realities Laboratory, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Martin A Walsh
- Diamond Light Source Ltd, Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Luigi Genovese
- Univ. Grenoble Alpes, CEA, IRIG-MEM-L_Sim 38000 Grenoble France
| | - Deborah K Shoemark
- School of Biochemistry, University of Bristol, Medical Sciences Building University Walk Bristol BS8 1TD UK
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Fernanda Duarte
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research 12 Mansfield Road Oxford OX1 3TA UK
| | - Garrett M Morris
- Department of Statistics, University of Oxford 24-29 St Giles' Oxford OX1 3LB UK
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14
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Shannon RJ, Deeks HM, Burfoot E, Clark E, Jones AJ, Mulholland AJ, Glowacki DR. Exploring human-guided strategies for reaction network exploration: Interactive molecular dynamics in virtual reality as a tool for citizen scientists. J Chem Phys 2021; 155:154106. [PMID: 34686059 DOI: 10.1063/5.0062517] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The emerging fields of citizen science and gamification reformulate scientific problems as games or puzzles to be solved. Through engaging the wider non-scientific community, significant breakthroughs may be made by analyzing citizen-gathered data. In parallel, recent advances in virtual reality (VR) technology are increasingly being used within a scientific context and the burgeoning field of interactive molecular dynamics in VR (iMD-VR) allows users to interact with dynamical chemistry simulations in real time. Here, we demonstrate the utility of iMD-VR as a medium for gamification of chemistry research tasks. An iMD-VR "game" was designed to encourage users to explore the reactivity of a particular chemical system, and a cohort of 18 participants was recruited to playtest this game as part of a user study. The reaction game encouraged users to experiment with making chemical reactions between a propyne molecule and an OH radical, and "molecular snapshots" from each game session were then compiled and used to map out reaction pathways. The reaction network generated by users was compared to existing literature networks demonstrating that users in VR capture almost all the important reaction pathways. Further comparisons between humans and an algorithmic method for guiding molecular dynamics show that through using citizen science to explore these kinds of chemical problems, new approaches and strategies start to emerge.
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Affiliation(s)
- Robin J Shannon
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Helen M Deeks
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Eleanor Burfoot
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Edward Clark
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Alex J Jones
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | | | - David R Glowacki
- ArtSci Foundation International, 5th floor Mariner House, Bristol, BS1 4QD, United Kingdom
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15
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Agamennone M, Nicoli A, Bayer S, Weber V, Borro L, Gupta S, Fantacuzzi M, Di Pizio A. Protein-protein interactions at a glance: Protocols for the visualization of biomolecular interactions. Methods Cell Biol 2021; 166:271-307. [PMID: 34752337 DOI: 10.1016/bs.mcb.2021.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Protein-protein interactions (PPIs) play a key role in many biological processes and are intriguing targets for drug discovery campaigns. Advancements in experimental and computational techniques are leading to a growth of data accessibility, and, with it, an increased need for the analysis of PPIs. In this respect, visualization tools are essential instruments to represent and analyze biomolecular interactions. In this chapter, we reviewed some of the available tools, highlighting their features, and describing their functions with practical information on their usage.
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Affiliation(s)
| | - Alessandro Nicoli
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
| | - Sebastian Bayer
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
| | - Verena Weber
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
| | - Luca Borro
- Department of Imaging, Advanced Cardiovascular Imaging Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Shailendra Gupta
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
| | | | - Antonella Di Pizio
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany.
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16
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Sabe VT, Ntombela T, Jhamba LA, Maguire GEM, Govender T, Naicker T, Kruger HG. Current trends in computer aided drug design and a highlight of drugs discovered via computational techniques: A review. Eur J Med Chem 2021; 224:113705. [PMID: 34303871 DOI: 10.1016/j.ejmech.2021.113705] [Citation(s) in RCA: 160] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/12/2021] [Accepted: 07/12/2021] [Indexed: 12/30/2022]
Abstract
Computer-aided drug design (CADD) is one of the pivotal approaches to contemporary pre-clinical drug discovery, and various computational techniques and software programs are typically used in combination, in a bid to achieve the desired outcome. Several approved drugs have been developed with the aid of CADD. On SciFinder®, we evaluated more than 600 publications through systematic searching and refining, using the terms, virtual screening; software methods; computational studies and publication year, in order to obtain data concerning particular aspects of CADD. The primary focus of this review was on the databases screened, virtual screening and/or molecular docking software program used. Furthermore, we evaluated the studies that subsequently performed molecular dynamics (MD) simulations and we reviewed the software programs applied, the application of density functional theory (DFT) calculations and experimental assays. To represent the latest trends, the most recent data obtained was between 2015 and 2020, consequently the most frequently employed techniques and software programs were recorded. Among these, the ZINC database was the most widely preferred with an average use of 31.2%. Structure-based virtual screening (SBVS) was the most prominently used type of virtual screening and it accounted for an average of 57.6%, with AutoDock being the preferred virtual screening/molecular docking program with 41.8% usage. Following the screening process, 38.5% of the studies performed MD simulations to complement the virtual screening and GROMACS with 39.3% usage, was the popular MD software program. Among the computational techniques, DFT was the least applied whereby it only accounts for 0.02% average use. An average of 36.5% of the studies included reports on experimental evaluations following virtual screening. Ultimately, since the inception and application of CADD in pre-clinical drug discovery, more than 70 approved drugs have been discovered, and this number is steadily increasing over time.
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Affiliation(s)
- Victor T Sabe
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa.
| | - Thandokuhle Ntombela
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa.
| | - Lindiwe A Jhamba
- HIV Pathogenesis Program, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Glenn E M Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa; School of Chemistry and Physics, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Thavendran Govender
- Faculty of Science and Agriculture, Department of Chemistry, University of Zululand, KwaDlangezwa, 3886, South Africa
| | - Tricia Naicker
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Hendrik G Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa.
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17
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Xu K, Liu N, Xu J, Guo C, Zhao L, Wang HW, Zhang QC. VRmol: an integrative web-based virtual reality system to explore macromolecular structure. Bioinformatics 2021; 37:1029-1031. [PMID: 32745209 DOI: 10.1093/bioinformatics/btaa696] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 07/21/2020] [Accepted: 07/27/2020] [Indexed: 12/22/2022] Open
Abstract
SUMMARY Structural visualization and analysis are fundamental to explore macromolecular functions. Here, we present a novel integrative web-based virtual reality (VR) system-VRmol, to visualize and study molecular structures in an immersive virtual environment. Importantly, it is integrated with multiple online databases and is able to couple structure studies with associated genomic variations and drug information in a visual interface by cloud-based drug docking. VRmol thus can serve as an integrative platform to aid structure-based translational research and drug design. AVAILABILITY AND IMPLEMENTATION VRmol is freely available (https://VRmol.net), with detailed manual and tutorial (https://VRmol.net/docs). The code of VRmol is available as open source under the MIT license at http://github.com/kuixu/VRmol. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Kui Xu
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Beijing 100084, China.,Beijing Advanced Innovation Center for Structural Biology, Beijing Frotier Research Center for Biological Structures, Beijing 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, Beijing 100084, China
| | - Nan Liu
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frotier Research Center for Biological Structures, Beijing 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, Beijing 100084, China.,Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jingle Xu
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Beijing 100084, China.,Beijing Advanced Innovation Center for Structural Biology, Beijing Frotier Research Center for Biological Structures, Beijing 100084, China
| | - Chunlong Guo
- Tsinghua-Peking Joint Center for Life Sciences, Beijing 100084, China
| | - Lingyun Zhao
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frotier Research Center for Biological Structures, Beijing 100084, China.,Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Hong-Wei Wang
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frotier Research Center for Biological Structures, Beijing 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, Beijing 100084, China.,Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Beijing 100084, China.,Beijing Advanced Innovation Center for Structural Biology, Beijing Frotier Research Center for Biological Structures, Beijing 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, Beijing 100084, China
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18
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Sulimov VB, Kutov DC, Taschilova AS, Ilin IS, Tyrtyshnikov EE, Sulimov AV. Docking Paradigm in Drug Design. Curr Top Med Chem 2021; 21:507-546. [PMID: 33292135 DOI: 10.2174/1568026620666201207095626] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/28/2020] [Accepted: 10/16/2020] [Indexed: 11/22/2022]
Abstract
Docking is in demand for the rational computer aided structure based drug design. A review of docking methods and programs is presented. Different types of docking programs are described. They include docking of non-covalent small ligands, protein-protein docking, supercomputer docking, quantum docking, the new generation of docking programs and the application of docking for covalent inhibitors discovery. Taking into account the threat of COVID-19, we present here a short review of docking applications to the discovery of inhibitors of SARS-CoV and SARS-CoV-2 target proteins, including our own result of the search for inhibitors of SARS-CoV-2 main protease using docking and quantum chemical post-processing. The conclusion is made that docking is extremely important in the fight against COVID-19 during the process of development of antivirus drugs having a direct action on SARS-CoV-2 target proteins.
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Affiliation(s)
- Vladimir B Sulimov
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russian Federation
| | - Danil C Kutov
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russian Federation
| | - Anna S Taschilova
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russian Federation
| | - Ivan S Ilin
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russian Federation
| | - Eugene E Tyrtyshnikov
- Institute of Numerical Mathematics of Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexey V Sulimov
- Research Computer Center of Lomonosov Moscow State University, Moscow, Russian Federation
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19
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Poyade M, Eaglesham C, Trench J, Reid M. A Transferable Psychological Evaluation of Virtual Reality Applied to Safety Training in Chemical Manufacturing. ACS CHEMICAL HEALTH & SAFETY 2021. [DOI: 10.1021/acs.chas.0c00105] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Matthieu Poyade
- School of Simulation and Visualisation (SimVis), Glasgow School of Art, Pacific Quay, Glasgow G51 1EA, United Kingdom
| | - Claire Eaglesham
- School of Simulation and Visualisation (SimVis), Glasgow School of Art, Pacific Quay, Glasgow G51 1EA, United Kingdom
| | - Jordan Trench
- School of Simulation and Visualisation (SimVis), Glasgow School of Art, Pacific Quay, Glasgow G51 1EA, United Kingdom
| | - Marc Reid
- WestCHEM Department of Pure & Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
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20
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Deeks HM, Walters RK, Barnoud J, Glowacki DR, Mulholland AJ. Interactive Molecular Dynamics in Virtual Reality Is an Effective Tool for Flexible Substrate and Inhibitor Docking to the SARS-CoV-2 Main Protease. J Chem Inf Model 2020; 60:5803-5814. [PMID: 33174415 PMCID: PMC7671099 DOI: 10.1021/acs.jcim.0c01030] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Indexed: 01/19/2023]
Abstract
The main protease (Mpro) of the SARS-CoV-2 virus is one focus of drug development efforts for COVID-19. Here, we show that interactive molecular dynamics in virtual reality (iMD-VR) is a useful and effective tool for creating Mpro complexes. We make these tools and models freely available. iMD-VR provides an immersive environment in which users can interact with MD simulations and so build protein complexes in a physically rigorous and flexible way. Recently, we have demonstrated that iMD-VR is an effective method for interactive, flexible docking of small molecule drugs into their protein targets (Deeks et al. PLoS One 2020, 15, e0228461). Here, we apply this approach to both an Mpro inhibitor and an oligopeptide substrate, using experimentally determined crystal structures. For the oligopeptide, we test against a crystallographic structure of the original SARS Mpro. Docking with iMD-VR gives models in agreement with experimentally observed (crystal) structures. The docked structures are also tested in MD simulations and found to be stable. Different protocols for iMD-VR docking are explored, e.g., with and without restraints on protein backbone, and we provide recommendations for its use. We find that it is important for the user to focus on forming binding interactions, such as hydrogen bonds, and not to rely on using simple metrics (such as RMSD), in order to create realistic, stable complexes. We also test the use of apo (uncomplexed) crystal structures for docking and find that they can give good results. This is because of the flexibility and dynamic response allowed by the physically rigorous, atomically detailed simulation approach of iMD-VR. We make our models (and interactive simulations) freely available. The software framework that we use, Narupa, is open source, and uses commodity VR hardware, so these tools are readily accessible to the wider research community working on Mpro (and other COVID-19 targets). These should be widely useful in drug development, in education applications, e.g., on viral enzyme structure and function, and in scientific communication more generally.
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Affiliation(s)
- Helen M. Deeks
- Intangible Realities Laboratory,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
Kingdom
- Centre for Computational Chemistry,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
Kingdom
- Department of Computer Science, Merchant
Venturers Building, University of Bristol,
Woodland Road, Bristol BS8 1UB, United
Kingdom
| | - Rebecca K. Walters
- Intangible Realities Laboratory,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
Kingdom
- Centre for Computational Chemistry,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
Kingdom
- Department of Computer Science, Merchant
Venturers Building, University of Bristol,
Woodland Road, Bristol BS8 1UB, United
Kingdom
| | - Jonathan Barnoud
- Intangible Realities Laboratory,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
Kingdom
- Centre for Computational Chemistry,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
Kingdom
| | - David R. Glowacki
- Intangible Realities Laboratory,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
Kingdom
- Centre for Computational Chemistry,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
Kingdom
- Department of Computer Science, Merchant
Venturers Building, University of Bristol,
Woodland Road, Bristol BS8 1UB, United
Kingdom
| | - Adrian J. Mulholland
- Centre for Computational Chemistry,
School of Chemistry, University of Bristol,
Cantock’s Close, Bristol BS8 1TS, United
Kingdom
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21
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Juárez-Jiménez J, Tew P, O Connor M, Llabrés S, Sage R, Glowacki D, Michel J. Combining Virtual Reality Visualization with Ensemble Molecular Dynamics to Study Complex Protein Conformational Changes. J Chem Inf Model 2020; 60:6344-6354. [PMID: 33180485 DOI: 10.1021/acs.jcim.0c00221] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Molecular dynamics (MD) simulations are increasingly used to elucidate relationships between protein structure, dynamics, and their biological function. Currently, it is extremely challenging to perform MD simulations of large-scale structural rearrangements in proteins that occur on millisecond timescales or beyond, as this requires very significant computational resources, or the use of cumbersome "collective variable" enhanced sampling protocols. Here, we describe a framework that combines ensemble MD simulations and virtual reality visualization (eMD-VR) to enable users to interactively generate realistic descriptions of large amplitude, millisecond timescale protein conformational changes in proteins. Detailed tests demonstrate that eMD-VR substantially decreases the computational cost of folding simulations of a WW domain, without the need to define collective variables a priori. We further show that eMD-VR generated pathways can be combined with Markov state models to describe the thermodynamics and kinetics of large-scale loop motions in the enzyme cyclophilin A. Our results suggest eMD-VR is a powerful tool for exploring protein energy landscapes in bioengineering efforts.
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Affiliation(s)
- Jordi Juárez-Jiménez
- EaStCHEM School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, United Kingdom
| | - Philip Tew
- Interactive Scientific, Engine Shed, Station Approach, Bristol BS1 6QH, United Kingdom
| | - Michael O Connor
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom.,Department of Computer Science, University of Bristol, Merchant Venture's Building, Bristol BS8 1UB, United Kingdom.,Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Salomé Llabrés
- EaStCHEM School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, United Kingdom
| | - Rebecca Sage
- Interactive Scientific, Engine Shed, Station Approach, Bristol BS1 6QH, United Kingdom
| | - David Glowacki
- Intangible Realities Laboratory, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom.,Department of Computer Science, University of Bristol, Merchant Venture's Building, Bristol BS8 1UB, United Kingdom.,Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Julien Michel
- EaStCHEM School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, United Kingdom
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