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Qian Y, Li L, Liu Y, Zhao P, Xie Z. Breaking the Gender Imbalance: Female Presence in the Computational Chemistry Group at Viva Biotech. J Chem Inf Model 2024. [PMID: 39102346 DOI: 10.1021/acs.jcim.4c00456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
Abstract
The growing field of computational chemistry and artificial intelligence is drawing unprecedented attention in drug discovery. However, the underrepresentation of female scientists persists in the field. While the gender disparity is acknowledged in academic settings, the issue is less addressed and intensifies in the pharmaceutical and biotech industry both at the entry-level and leadership positions. At Viva Biotech, we challenge this norm: over 60% of the full-time employees in our computational chemistry group are women, a testament of our commitment to the pursuit of gender equality. We share our vision of the evolving role of computational chemistry in drug discovery and where women stand and rise in the field. In this article, we discuss how we engage female empowerment with tactical approaches and from personal experiences. The intention is to offer actionable guidance for female computational chemists at early career stages to bring visibility to their impacts, and ascent to senior positions.
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Affiliation(s)
- Yue Qian
- Viva Biotech (Shanghai) Limited, 735 Ziping Road, Pudong New District, Shanghai 201318, P. R. China
| | - Le Li
- Viva Biotech (Shanghai) Limited, 735 Ziping Road, Pudong New District, Shanghai 201318, P. R. China
| | - Yanning Liu
- Viva Biotech (Shanghai) Limited, 735 Ziping Road, Pudong New District, Shanghai 201318, P. R. China
| | - Piaopiao Zhao
- Viva Biotech (Shanghai) Limited, 735 Ziping Road, Pudong New District, Shanghai 201318, P. R. China
| | - Zhuwei Xie
- Viva Biotech (Shanghai) Limited, 735 Ziping Road, Pudong New District, Shanghai 201318, P. R. China
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Breznik M, Ge Y, Bluck JP, Briem H, Hahn DF, Christ CD, Mortier J, Mobley DL, Meier K. Prioritizing Small Sets of Molecules for Synthesis through in-silico Tools: A Comparison of Common Ranking Methods. ChemMedChem 2023; 18:e202200425. [PMID: 36240514 PMCID: PMC9868080 DOI: 10.1002/cmdc.202200425] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/10/2022] [Indexed: 01/26/2023]
Abstract
Prioritizing molecules for synthesis is a key role of computational methods within medicinal chemistry. Multiple tools exist for ranking molecules, from the cheap and popular molecular docking methods to more computationally expensive molecular-dynamics (MD)-based methods. It is often questioned whether the accuracy of the more rigorous methods justifies the higher computational cost and associated calculation time. Here, we compared the performance on ranking the binding of small molecules for seven scoring functions from five docking programs, one end-point method (MM/GBSA), and two MD-based free energy methods (PMX, FEP+). We investigated 16 pharmaceutically relevant targets with a total of 423 known binders. The performance of docking methods for ligand ranking was strongly system dependent. We observed that MD-based methods predominantly outperformed docking algorithms and MM/GBSA calculations. Based on our results, we recommend the application of MD-based free energy methods for prioritization of molecules for synthesis in lead optimization, whenever feasible.
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Affiliation(s)
- Marko Breznik
- Computational Molecular Design, Pharmaceuticals, R&D, Bayer AG, 13342 Berlin, Germany
| | - Yunhui Ge
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA
| | - Joseph P. Bluck
- Computational Molecular Design, Pharmaceuticals, R&D, Bayer AG, 13342 Berlin, Germany
| | - Hans Briem
- Computational Molecular Design, Pharmaceuticals, R&D, Bayer AG, 13342 Berlin, Germany
| | - David F. Hahn
- Computational Chemistry, Janssen Research & Development, Turnhoutseweg 30, Beerse B-2340, Belgium
| | - Clara D. Christ
- Molecular Design, Pharmaceuticals, R&D, Bayer AG, 13342 Berlin, Germany
| | - Jérémie Mortier
- Computational Molecular Design, Pharmaceuticals, R&D, Bayer AG, 13342 Berlin, Germany
| | - David L. Mobley
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA,Department of Chemistry, University of California, Irvine, CA 92697, USA
| | - Katharina Meier
- Computational Life Science Technology Functions, Crop Science, R&D, Bayer AG, 40789 Monheim, Germany
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3
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Pekel H, Ilter M, Sensoy O. Inhibition of SARS-CoV-2 main protease: a repurposing study that targets the dimer interface of the protein. J Biomol Struct Dyn 2022; 40:7167-7182. [PMID: 33847241 PMCID: PMC8054500 DOI: 10.1080/07391102.2021.1910571] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 02/28/2021] [Indexed: 11/22/2022]
Abstract
Coronavirus disease-2019 (COVID-19) was firstly reported in Wuhan, China, towards the end of 2019, and emerged as a pandemic. The spread and lethality rates of the COVID-19 have ignited studies that focus on the development of therapeutics for either treatment or prophylaxis purposes. In parallel, drug repurposing studies have also come into prominence. Herein, we aimed at having a holistic understanding of conformational and dynamical changes induced by an experimentally characterized inhibitor on main protease (Mpro) which would enable the discovery of novel inhibitors. To this end, we performed molecular dynamics simulations using crystal structures of apo and α-ketoamide 13b-bound Mpro homodimer. Analysis of trajectories pertaining to apo Mpro revealed a new target site, which is located at the homodimer interface, next to the catalytic dyad. Thereafter, we performed ensemble-based virtual screening by exploiting the ZINC and DrugBank databases and identified three candidate molecules, namely eluxadoline, diosmin, and ZINC02948810 that could invoke local and global conformational rearrangements which were also elicited by α-ketoamide 13b on the catalytic dyad of Mpro. Furthermore, ZINC23881687 stably interacted with catalytically important residues Glu166 and Ser1 and the target site throughout the simulation. However, it gave positive binding energy, presumably, due to displaying higher flexibility that might dominate the entropic term, which is not included in the MM-PBSA method. Finally, ZINC20425029, whose mode of action was different, modulated dynamical properties of catalytically important residue, Ala285. As such, this study presents valuable findings that might be used in the development of novel therapeutics against Mpro.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hanife Pekel
- Department of Pharmacy Services, Vocational School of Health Services, Istanbul Medipol University, Istanbul, Turkey
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
| | - Metehan Ilter
- Graduate School of Engineering and Natural Sciences, Istanbul Medipol University, Istanbul, Turkey
| | - Ozge Sensoy
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
- Department of Computer Engineering, School of Engineering and Natural Sciences, Istanbul Medipol University, Istanbul, Turkey
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Cox PB, Gupta R. Contemporary Computational Applications and Tools in Drug Discovery. ACS Med Chem Lett 2022; 13:1016-1029. [DOI: 10.1021/acsmedchemlett.1c00662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Philip B. Cox
- Drug Discovery Science and Technology, AbbVie, 1 North Waukegan Road, North Chicago, Illinois 60064-6217, United States
| | - Rishi Gupta
- Drug Discovery Science and Technology, AbbVie, 1 North Waukegan Road, North Chicago, Illinois 60064-6217, United States
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Onawole AT, Sulaiman KO, Kolapo TU, Akinde FO, Adegoke RO. COVID-19: CADD to the rescue. Virus Res 2020; 285:198022. [PMID: 32417181 PMCID: PMC7228740 DOI: 10.1016/j.virusres.2020.198022] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/30/2020] [Accepted: 05/11/2020] [Indexed: 12/13/2022]
Abstract
The recent outbreak of the deadly COVID-19 disease, being caused by the novel coronavirus (SARS-CoV-2), has put the world on red alert as it keeps spreading and recording more fatalities. Research efforts are being carried out to curtail the disease from spreading as it has been declared as of global health emergency. Hence, there is an exigent need to identify and design drugs that are capable of curing the infection and hinder its continual spread across the globe. Herein, a computer-aided drug design tool known as the virtual screening method was used to screen a database of 44 million compounds to find compounds that have the potential to inhibit the surface glycoprotein responsible for virus entry and binding. The consensus scoring approach selected three compounds with promising physicochemical properties and favorable molecular interactions with the target protein. These selected compounds can undergo lead optimization to be further developed as drugs that can be used in treating the COVID-19 disease.
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Affiliation(s)
- Abdulmujeeb T Onawole
- Department of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran, 31261 Saudi Arabia
| | - Kazeem O Sulaiman
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, Saskatchewan S7N 5C9, Canada.
| | - Temitope U Kolapo
- Department of Veterinary Parasitology and Entomology, University of Ilorin,P.M.B. 1515, Ilorin, Nigeria; Department of Veterinary Microbiology, University of Saskatchewan, 52 Campus Drive, Saskatoon, Saskatchewan S7N 5B4, Canada
| | - Fatimo O Akinde
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, China
| | - Rukayat O Adegoke
- Department of Pure and Applied Biology, Ladoke Akintola University of Technology, P.M.B. 4000, Ogbomoso, Nigeria
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Green DVS, Pickett S, Luscombe C, Senger S, Marcus D, Meslamani J, Brett D, Powell A, Masson J. BRADSHAW: a system for automated molecular design. J Comput Aided Mol Des 2020; 34:747-765. [PMID: 31637565 PMCID: PMC7292824 DOI: 10.1007/s10822-019-00234-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 10/05/2019] [Indexed: 12/18/2022]
Abstract
This paper introduces BRADSHAW (Biological Response Analysis and Design System using an Heterogenous, Automated Workflow), a system for automated molecular design which integrates methods for chemical structure generation, experimental design, active learning and cheminformatics tools. The simple user interface is designed to facilitate access to large scale automated design whilst minimising software development required to introduce new algorithms, a critical requirement in what is a very fast moving field. The system embodies a philosophy of automation, best practice, experimental design and the use of both traditional cheminformatics and modern machine learning algorithms.
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Affiliation(s)
- Darren V S Green
- Department of Molecular Design, Data and Computational Sciences, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK.
| | - Stephen Pickett
- Department of Molecular Design, Data and Computational Sciences, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Chris Luscombe
- Department of Molecular Design, Data and Computational Sciences, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Stefan Senger
- Department of Molecular Design, Data and Computational Sciences, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - David Marcus
- Department of Molecular Design, Data and Computational Sciences, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Jamel Meslamani
- Department of Molecular Design, Data and Computational Sciences, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA, 19426, USA
| | - David Brett
- Tessella Ltd, Walkern Road, Stevenage, Hertfordshire, SG1 3QP, UK
| | - Adam Powell
- Tessella Ltd, Walkern Road, Stevenage, Hertfordshire, SG1 3QP, UK
| | - Jonathan Masson
- Tessella Ltd, Walkern Road, Stevenage, Hertfordshire, SG1 3QP, UK
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Athanasiou C, Cournia Z. From Computers to Bedside: Computational Chemistry Contributing to FDA Approval. BIOMOLECULAR SIMULATIONS IN STRUCTURE-BASED DRUG DISCOVERY 2018. [DOI: 10.1002/9783527806836.ch7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Christina Athanasiou
- Biomedical Research Foundation; Academy of Athens; 4 Soranou Ephessiou 11527 Athens Greece
| | - Zoe Cournia
- Biomedical Research Foundation; Academy of Athens; 4 Soranou Ephessiou 11527 Athens Greece
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Pogány P, Arad N, Genway S, Pickett SD. De Novo Molecule Design by Translating from Reduced Graphs to SMILES. J Chem Inf Model 2018; 59:1136-1146. [DOI: 10.1021/acs.jcim.8b00626] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Peter Pogány
- Computational and Modeling Sciences, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts SG1 2NY, United Kingdom
| | - Navot Arad
- GlaxoSmithKline-Tessella Analytics Partnership, Tessella Ltd, Walkern Road, Stevenage, Herts SG1 3QP, United Kingdom
| | - Sam Genway
- GlaxoSmithKline-Tessella Analytics Partnership, Tessella Ltd, Walkern Road, Stevenage, Herts SG1 3QP, United Kingdom
| | - Stephen D. Pickett
- Computational and Modeling Sciences, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts SG1 2NY, United Kingdom
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Implementing WebGL and HTML5 in Macromolecular Visualization and Modern Computer-Aided Drug Design. Trends Biotechnol 2017; 35:559-571. [DOI: 10.1016/j.tibtech.2017.03.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 03/16/2017] [Accepted: 03/17/2017] [Indexed: 11/21/2022]
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