1
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Capponi S, Wang S. AI in cellular engineering and reprogramming. Biophys J 2024:S0006-3495(24)00245-5. [PMID: 38576162 DOI: 10.1016/j.bpj.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/19/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024] Open
Abstract
During the last decade, artificial intelligence (AI) has increasingly been applied in biophysics and related fields, including cellular engineering and reprogramming, offering novel approaches to understand, manipulate, and control cellular function. The potential of AI lies in its ability to analyze complex datasets and generate predictive models. AI algorithms can process large amounts of data from single-cell genomics and multiomic technologies, allowing researchers to gain mechanistic insights into the control of cell identity and function. By integrating and interpreting these complex datasets, AI can help identify key molecular events and regulatory pathways involved in cellular reprogramming. This knowledge can inform the design of precision engineering strategies, such as the development of new transcription factor and signaling molecule cocktails, to manipulate cell identity and drive authentic cell fate across lineage boundaries. Furthermore, when used in combination with computational methods, AI can accelerate and improve the analysis and understanding of the intricate relationships between genes, proteins, and cellular processes. In this review article, we explore the current state of AI applications in biophysics with a specific focus on cellular engineering and reprogramming. Then, we showcase a couple of recent applications where we combined machine learning with experimental and computational techniques. Finally, we briefly discuss the challenges and prospects of AI in cellular engineering and reprogramming, emphasizing the potential of these technologies to revolutionize our ability to engineer cells for a variety of applications, from disease modeling and drug discovery to regenerative medicine and biomanufacturing.
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Affiliation(s)
- Sara Capponi
- IBM Almaden Research Center, San Jose, California; Center for Cellular Construction, San Francisco, California.
| | - Shangying Wang
- Bay Area Institute of Science, Altos Labs, Redwood City, California.
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2
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McCorkindale W, Filep M, London N, Lee AA, King-Smith E. Deconvoluting low yield from weak potency in direct-to-biology workflows with machine learning. RSC Med Chem 2024; 15:1015-1021. [PMID: 38516605 PMCID: PMC10953487 DOI: 10.1039/d3md00719g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 02/12/2024] [Indexed: 03/23/2024] Open
Abstract
High throughput and rapid biological evaluation of small molecules is an essential factor in drug discovery and development. Direct-to-biology (D2B), whereby compound purification is foregone, has emerged as a viable technique in time efficient screening, specifically for PROTAC design and biological evaluation. However, one notable limitation is the prerequisite of high yielding reactions to ensure the desired compound is indeed the compound responsible for biological activity. Herein, we report a machine learning based yield-assay deconfounder capable of deconvoluting low yield from low potency to identify false negatives. We validated this approach by identifying promising SARS-CoV-2 main protease inhibitors with nanomolar activity that rivaled potency observed from the standard D2B workflow. Furthermore, we show how our framework can be utilized in a broad, in silico screen to produce compounds of similar potency as a D2B assay.
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Affiliation(s)
| | - Mihajlo Filep
- Department of Chemical and Structural Biology, The Weizmann Institute of Science Israel
| | - Nir London
- Department of Chemical and Structural Biology, The Weizmann Institute of Science Israel
| | - Alpha A Lee
- Cavendish Laboratory, University of Cambridge UK
| | - Emma King-Smith
- Yusuf Hamied Department of Chemistry, University of Cambridge UK
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3
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Huang CY, Metz A, Lange R, Artico N, Potot C, Hazemann J, Müller M, Dos Santos M, Chambovey A, Ritz D, Eris D, Meyer S, Bourquin G, Sharpe M, Mac Sweeney A. Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket. Acta Crystallogr D Struct Biol 2024; 80:123-136. [PMID: 38289714 PMCID: PMC10836397 DOI: 10.1107/s2059798324000329] [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: 11/20/2023] [Accepted: 01/09/2024] [Indexed: 02/01/2024] Open
Abstract
To identify starting points for therapeutics targeting SARS-CoV-2, the Paul Scherrer Institute and Idorsia decided to collaboratively perform an X-ray crystallographic fragment screen against its main protease. Fragment-based screening was carried out using crystals with a pronounced open conformation of the substrate-binding pocket. Of 631 soaked fragments, a total of 29 hits bound either in the active site (24 hits), a remote binding pocket (three hits) or at crystal-packing interfaces (two hits). Notably, two fragments with a pose that was sterically incompatible with a more occluded crystal form were identified. Two isatin-based electrophilic fragments bound covalently to the catalytic cysteine residue. The structures also revealed a surprisingly strong influence of the crystal form on the binding pose of three published fragments used as positive controls, with implications for fragment screening by crystallography.
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Affiliation(s)
- Chia Ying Huang
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Alexander Metz
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | - Roland Lange
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | - Nadia Artico
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | - Céline Potot
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | | | - Manon Müller
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | | | | | - Daniel Ritz
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | - Deniz Eris
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Solange Meyer
- Idorsia Pharmaceuticals Ltd, 4123 Allschwil, Switzerland
| | | | - May Sharpe
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
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4
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Janin YL. On the origins of SARS-CoV-2 main protease inhibitors. RSC Med Chem 2024; 15:81-118. [PMID: 38283212 PMCID: PMC10809347 DOI: 10.1039/d3md00493g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 10/13/2023] [Indexed: 01/30/2024] Open
Abstract
In order to address the world-wide health challenge caused by the COVID-19 pandemic, the 3CL protease/SARS-CoV-2 main protease (SARS-CoV-2-Mpro) coded by its nsp5 gene became one of the biochemical targets for the design of antiviral drugs. In less than 3 years of research, 4 inhibitors of SARS-CoV-2-Mpro have actually been authorized for COVID-19 treatment (nirmatrelvir, ensitrelvir, leritrelvir and simnotrelvir) and more such as EDP-235, FB-2001 and STI-1558/Olgotrelvir or five undisclosed compounds (CDI-988, ASC11, ALG-097558, QLS1128 and H-10517) are undergoing clinical trials. This review is an attempt to picture this quite unprecedented medicinal chemistry feat and provide insights on how these cysteine protease inhibitors were discovered. Since many series of covalent SARS-CoV-2-Mpro inhibitors owe some of their origins to previous work on other proteases, we first provided a description of various inhibitors of cysteine-bearing human caspase-1 or cathepsin K, as well as inhibitors of serine proteases such as human dipeptidyl peptidase-4 or the hepatitis C protein complex NS3/4A. This is then followed by a description of the results of the approaches adopted (repurposing, structure-based and high throughput screening) to discover coronavirus main protease inhibitors.
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Affiliation(s)
- Yves L Janin
- Structure et Instabilité des Génomes (StrInG), Muséum National d'Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université 75005 Paris France
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5
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Song L, Gao S, Ye B, Yang M, Cheng Y, Kang D, Yi F, Sun JP, Menéndez-Arias L, Neyts J, Liu X, Zhan P. Medicinal chemistry strategies towards the development of non-covalent SARS-CoV-2 M pro inhibitors. Acta Pharm Sin B 2024; 14:87-109. [PMID: 38239241 PMCID: PMC10792984 DOI: 10.1016/j.apsb.2023.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/10/2023] [Accepted: 08/02/2023] [Indexed: 01/22/2024] Open
Abstract
The main protease (Mpro) of SARS-CoV-2 is an attractive target in anti-COVID-19 therapy for its high conservation and major role in the virus life cycle. The covalent Mpro inhibitor nirmatrelvir (in combination with ritonavir, a pharmacokinetic enhancer) and the non-covalent inhibitor ensitrelvir have shown efficacy in clinical trials and have been approved for therapeutic use. Effective antiviral drugs are needed to fight the pandemic, while non-covalent Mpro inhibitors could be promising alternatives due to their high selectivity and favorable druggability. Numerous non-covalent Mpro inhibitors with desirable properties have been developed based on available crystal structures of Mpro. In this article, we describe medicinal chemistry strategies applied for the discovery and optimization of non-covalent Mpro inhibitors, followed by a general overview and critical analysis of the available information. Prospective viewpoints and insights into current strategies for the development of non-covalent Mpro inhibitors are also discussed.
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Affiliation(s)
- Letian Song
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Shenghua Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Shenzhen Research Institute of Shandong University, Shenzhen 518057, China
| | - Bing Ye
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Mianling Yang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Yusen Cheng
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Fan Yi
- The Key Laboratory of Infection and Immunity of Shandong Province, Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan 250012, China
| | - Jin-Peng Sun
- Key Laboratory Experimental Teratology of the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Luis Menéndez-Arias
- Centro de Biología Molecular “Severo Ochoa” (Consejo Superior de Investigaciones Científicas & Autonomous University of Madrid), Madrid 28049, Spain
| | - Johan Neyts
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven 3000, Belgium
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
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6
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Boby ML, Fearon D, Ferla M, Filep M, Koekemoer L, Robinson MC, Chodera JD, Lee AA, London N, von Delft A, von Delft F. Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors. Science 2023; 382:eabo7201. [PMID: 37943932 PMCID: PMC7615835 DOI: 10.1126/science.abo7201] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 10/09/2023] [Indexed: 11/12/2023]
Abstract
We report the results of the COVID Moonshot, a fully open-science, crowdsourced, and structure-enabled drug discovery campaign targeting the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease. We discovered a noncovalent, nonpeptidic inhibitor scaffold with lead-like properties that is differentiated from current main protease inhibitors. Our approach leveraged crowdsourcing, machine learning, exascale molecular simulations, and high-throughput structural biology and chemistry. We generated a detailed map of the structural plasticity of the SARS-CoV-2 main protease, extensive structure-activity relationships for multiple chemotypes, and a wealth of biochemical activity data. All compound designs (>18,000 designs), crystallographic data (>490 ligand-bound x-ray structures), assay data (>10,000 measurements), and synthesized molecules (>2400 compounds) for this campaign were shared rapidly and openly, creating a rich, open, and intellectual property-free knowledge base for future anticoronavirus drug discovery.
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Affiliation(s)
- Melissa L. Boby
- Pharmacology Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
- Program in Chemical Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Program in Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Daren Fearon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
| | - Matteo Ferla
- Oxford Biomedical Research Centre, National Institute for Health Research, University of Oxford, Oxford, UK
| | - Mihajlo Filep
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel, 7610001
| | - Lizbé Koekemoer
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - The COVID Moonshot Consortium
- Pharmacology Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
- Program in Chemical Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Program in Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
- Oxford Biomedical Research Centre, National Institute for Health Research, University of Oxford, Oxford, UK
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel, 7610001
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- PostEra Inc., 1 Broadway, 14th Floor,Cambridge, MA 02142, USA
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
| | - John D. Chodera
- Program in Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alpha A Lee
- PostEra Inc., 1 Broadway, 14th Floor,Cambridge, MA 02142, USA
| | - Nir London
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel, 7610001
| | - Annette von Delft
- Oxford Biomedical Research Centre, National Institute for Health Research, University of Oxford, Oxford, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Frank von Delft
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
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7
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Puhl AC, Godoy AS, Noske GD, Nakamura AM, Gawriljuk VO, Fernandes RS, Oliva G, Ekins S. Discovery of PL pro and M pro Inhibitors for SARS-CoV-2. ACS OMEGA 2023; 8:22603-22612. [PMID: 37387790 PMCID: PMC10275482 DOI: 10.1021/acsomega.3c01110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 06/01/2023] [Indexed: 07/01/2023]
Abstract
There are very few small-molecule antivirals for SARS-CoV-2 that are either currently approved (or emergency authorized) in the US or globally, including remdesivir, molnupiravir, and paxlovid. The increasing number of SARS-CoV-2 variants that have appeared since the outbreak began over three years ago raises the need for continual development of updated vaccines and orally available antivirals in order to fully protect or treat the population. The viral main protease (Mpro) and the papain-like protease (PLpro) are key for viral replication; therefore, they represent valuable targets for antiviral therapy. We herein describe an in vitro screen performed using the 2560 compounds from the Microsource Spectrum library against Mpro and PLpro in an attempt to identify additional small-molecule hits that could be repurposed for SARS-CoV-2. We subsequently identified 2 hits for Mpro and 8 hits for PLpro. One of these hits was the quaternary ammonium compound cetylpyridinium chloride with dual activity (IC50 = 2.72 ± 0.09 μM for PLpro and IC50 = 7.25 ± 0.15 μM for Mpro). A second inhibitor of PLpro was the selective estrogen receptor modulator raloxifene (IC50 = 3.28 ± 0.29 μM for PLpro and IC50 = 42.8 ± 6.7 μM for Mpro). We additionally tested several kinase inhibitors and identified olmutinib (IC50 = 0.54 ± 0.04 μM), bosutinib (IC50 = 4.23 ± 0.28 μM), crizotinib (IC50 = 3.81 ± 0.04 μM), and dacominitinib (IC50 = IC50 3.33 ± 0.06 μM) as PLpro inhibitors for the first time. In some cases, these molecules have also been tested by others for antiviral activity for this virus, or we have used Calu-3 cells infected with SARS-CoV-2. The results suggest that approved drugs can be identified with promising activity against these proteases, and in several cases we or others have validated their antiviral activity. The additional identification of known kinase inhibitors as molecules targeting PLpro may provide new repurposing opportunities or starting points for chemical optimization.
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Affiliation(s)
- Ana C. Puhl
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Andre S. Godoy
- Sao
Carlos Institute of Physics, University
of Sao Paulo, Av. Joao
Dagnone, 1100—Jardim Santa Angelina, Sao Carlos 13563-120, Brazil
| | - Gabriela D. Noske
- Sao
Carlos Institute of Physics, University
of Sao Paulo, Av. Joao
Dagnone, 1100—Jardim Santa Angelina, Sao Carlos 13563-120, Brazil
| | - Aline M. Nakamura
- Sao
Carlos Institute of Physics, University
of Sao Paulo, Av. Joao
Dagnone, 1100—Jardim Santa Angelina, Sao Carlos 13563-120, Brazil
| | - Victor O. Gawriljuk
- Sao
Carlos Institute of Physics, University
of Sao Paulo, Av. Joao
Dagnone, 1100—Jardim Santa Angelina, Sao Carlos 13563-120, Brazil
| | - Rafaela S. Fernandes
- Sao
Carlos Institute of Physics, University
of Sao Paulo, Av. Joao
Dagnone, 1100—Jardim Santa Angelina, Sao Carlos 13563-120, Brazil
| | - Glaucius Oliva
- Sao
Carlos Institute of Physics, University
of Sao Paulo, Av. Joao
Dagnone, 1100—Jardim Santa Angelina, Sao Carlos 13563-120, Brazil
| | - Sean Ekins
- Collaborations
Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
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8
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Chenthamarakshan V, Hoffman SC, Owen CD, Lukacik P, Strain-Damerell C, Fearon D, Malla TR, Tumber A, Schofield CJ, Duyvesteyn HME, Dejnirattisai W, Carrique L, Walter TS, Screaton GR, Matviiuk T, Mojsilovic A, Crain J, Walsh MA, Stuart DI, Das P. Accelerating drug target inhibitor discovery with a deep generative foundation model. SCIENCE ADVANCES 2023; 9:eadg7865. [PMID: 37343087 DOI: 10.1126/sciadv.adg7865] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/17/2023] [Indexed: 06/23/2023]
Abstract
Inhibitor discovery for emerging drug-target proteins is challenging, especially when target structure or active molecules are unknown. Here, we experimentally validate the broad utility of a deep generative framework trained at-scale on protein sequences, small molecules, and their mutual interactions-unbiased toward any specific target. We performed a protein sequence-conditioned sampling on the generative foundation model to design small-molecule inhibitors for two dissimilar targets: the spike protein receptor-binding domain (RBD) and the main protease from SARS-CoV-2. Despite using only the target sequence information during the model inference, micromolar-level inhibition was observed in vitro for two candidates out of four synthesized for each target. The most potent spike RBD inhibitor exhibited activity against several variants in live virus neutralization assays. These results establish that a single, broadly deployable generative foundation model for accelerated inhibitor discovery is effective and efficient, even in the absence of target structure or binder information.
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Affiliation(s)
| | - Samuel C Hoffman
- IBM Research, Thomas J. Watson Research Center, Yorktown Heights, New York, NY, USA
| | - C David Owen
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, OX11 0FA Didcot, UK
| | - Petra Lukacik
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, OX11 0FA Didcot, UK
| | - Claire Strain-Damerell
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, OX11 0FA Didcot, UK
| | - Daren Fearon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, OX11 0FA Didcot, UK
| | - Tika R Malla
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, UK
| | - Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK
| | - Wanwisa Dejnirattisai
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Loic Carrique
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK
| | - Thomas S Walter
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK
| | - Gavin R Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | | | | | - Jason Crain
- IBM Research Europe, Hartree Centre, Daresbury WA4 4AD, UK
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Martin A Walsh
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, OX11 0FA Didcot, UK
| | - David I Stuart
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, UK
- Division of Structural Biology, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK
| | - Payel Das
- IBM Research, Thomas J. Watson Research Center, Yorktown Heights, New York, NY, USA
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9
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The Potential of Stilbene Compounds to Inhibit M pro Protease as a Natural Treatment Strategy for Coronavirus Disease-2019. Curr Issues Mol Biol 2022; 45:12-32. [PMID: 36661488 PMCID: PMC9857500 DOI: 10.3390/cimb45010002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/05/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
COVID-19 disease has had a global impact on human health with increased levels of morbidity and mortality. There is an unmet need to design and produce effective antivirals to treat COVID-19. This study aimed to explore the potential ability of natural stilbenes to inhibit the Mpro protease, an acute respiratory syndrome coronavirus-2 (SARS-CoV-2) enzyme involved in viral replication. The binding affinities of stilbene compounds against Mpro were scrutinized using molecular docking, prime molecular mechanics-generalized Born surface area (MM-GBSA) energy calculations, and molecular dynamic simulations. Seven stilbene molecules were docked with Mpro and compared with GC376 and N3, antivirals with demonstrated efficacy against Mpro. Ligand binding efficiencies and polar and non-polar interactions between stilbene compounds and Mpro were analyzed. The binding affinities of astringin, isorhapontin, and piceatannol were -9.319, -8.166, and -6.291 kcal/mol, respectively, and higher than either GC376 or N3 at -6.976 and -6.345 kcal/mol, respectively. Prime MM-GBSA revealed that these stilbene compounds exhibited useful ligand efficacy and binding affinity to Mpro. Molecular dynamic simulation studies of astringin, isorhapontin, and piceatannol showed their stability at 300 K throughout the simulation time. Collectively, these results suggest that stilbenes such as astringin, isorhapontin, and piceatannol could provide useful natural inhibitors of Mpro and thereby act as novel treatments to limit SARS-CoV-2 replication.
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10
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Viral proteases as therapeutic targets. Mol Aspects Med 2022; 88:101159. [PMID: 36459838 PMCID: PMC9706241 DOI: 10.1016/j.mam.2022.101159] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 11/30/2022]
Abstract
Some medically important viruses-including retroviruses, flaviviruses, coronaviruses, and herpesviruses-code for a protease, which is indispensable for viral maturation and pathogenesis. Viral protease inhibitors have become an important class of antiviral drugs. Development of the first-in-class viral protease inhibitor saquinavir, which targets HIV protease, started a new era in the treatment of chronic viral diseases. Combining several drugs that target different steps of the viral life cycle enables use of lower doses of individual drugs (and thereby reduction of potential side effects, which frequently occur during long term therapy) and reduces drug-resistance development. Currently, several HIV and HCV protease inhibitors are routinely used in clinical practice. In addition, a drug including an inhibitor of SARS-CoV-2 main protease, nirmatrelvir (co-administered with a pharmacokinetic booster ritonavir as Paxlovid®), was recently authorized for emergency use. This review summarizes the basic features of the proteases of human immunodeficiency virus (HIV), hepatitis C virus (HCV), and SARS-CoV-2 and discusses the properties of their inhibitors in clinical use, as well as development of compounds in the pipeline.
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11
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Ray D, Quijano RN, Andricioaei I. Point mutations in SARS-CoV-2 variants induce long-range dynamical perturbations in neutralizing antibodies. Chem Sci 2022; 13:7224-7239. [PMID: 35799828 PMCID: PMC9214918 DOI: 10.1039/d2sc00534d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 05/23/2022] [Indexed: 01/02/2023] Open
Abstract
Monoclonal antibodies are emerging as a viable treatment for the coronavirus disease 19 (COVID-19). However, newly evolved variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can reduce the efficacy of currently available antibodies and can diminish vaccine-induced immunity. Here, we demonstrate that the microscopic dynamics of neutralizing monoclonal antibodies can be profoundly modified by the mutations present in the spike proteins of the SARS-COV-2 variants currently circulating in the world population. The dynamical perturbations within the antibody structure, which alter the thermodynamics of antigen recognition, are diverse and can depend both on the nature of the antibody and on the spatial location of the spike mutation. The correlation between the motion of the antibody and that of the spike receptor binding domain (RBD) can also be changed, modulating binding affinity. Using protein-graph-connectivity networks, we delineated the mutant-induced modifications in the information-flow along allosteric pathway throughout the antibody. Changes in the collective dynamics were spatially distributed both locally and across long-range distances within the antibody. On the receptor side, we identified an anchor-like structural element that prevents the detachment of the antibodies; individual mutations there can significantly affect the antibody binding propensity. Our study provides insight into how virus neutralization by monoclonal antibodies can be impacted by local mutations in the epitope via a change in dynamics. This realization adds a new layer of sophistication to the efforts for rational design of monoclonal antibodies against new variants of SARS-CoV2, taking the allostery in the antibody into consideration. Mutations in the new variants of SARS-CoV-2 spike protein modulates the dynamics of the neutralizing antibodies. Capturing such modulations from MD simulations and graph network model identifies the role of mutations in facilitating immune evasion.![]()
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Affiliation(s)
- Dhiman Ray
- Department of Chemistry, University of California Irvine Irvine CA 92697 USA
| | | | - Ioan Andricioaei
- Department of Chemistry, University of California Irvine Irvine CA 92697 USA .,Department of Physics and Astronomy, University of California Irvine Irvine CA 92697 USA
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12
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Rickert CA, Lieleg O. Machine learning approaches for biomolecular, biophysical, and biomaterials research. BIOPHYSICS REVIEWS 2022; 3:021306. [PMID: 38505413 PMCID: PMC10914139 DOI: 10.1063/5.0082179] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 05/12/2022] [Indexed: 03/21/2024]
Abstract
A fluent conversation with a virtual assistant, person-tailored news feeds, and deep-fake images created within seconds-all those things that have been unthinkable for a long time are now a part of our everyday lives. What these examples have in common is that they are realized by different means of machine learning (ML), a technology that has fundamentally changed many aspects of the modern world. The possibility to process enormous amount of data in multi-hierarchical, digital constructs has paved the way not only for creating intelligent systems but also for obtaining surprising new insight into many scientific problems. However, in the different areas of biosciences, which typically rely heavily on the collection of time-consuming experimental data, applying ML methods is a bit more challenging: Here, difficulties can arise from small datasets and the inherent, broad variability, and complexity associated with studying biological objects and phenomena. In this Review, we give an overview of commonly used ML algorithms (which are often referred to as "machines") and learning strategies as well as their applications in different bio-disciplines such as molecular biology, drug development, biophysics, and biomaterials science. We highlight how selected research questions from those fields were successfully translated into machine readable formats, discuss typical problems that can arise in this context, and provide an overview of how to resolve those encountered difficulties.
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13
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Abstract
![]()
One application area
of computational methods in drug discovery
is the automated design of small molecules. Despite the large number
of publications describing methods and their application in both retrospective
and prospective studies, there is a lack of agreement on terminology
and key attributes to distinguish these various systems. We introduce
Automated Chemical Design (ACD) Levels to clearly define the level
of autonomy along the axes of ideation and decision making. To fully
illustrate this framework, we provide literature exemplars and place
some notable methods and applications into the levels. The ACD framework
provides a common language for describing automated small molecule
design systems and enables medicinal chemists to better understand
and evaluate such systems.
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Affiliation(s)
- Brian Goldman
- Relay Therapeutics, 399 Binney Street, Cambridge, Massachusetts 02139, United States
| | - Steven Kearnes
- Relay Therapeutics, 399 Binney Street, Cambridge, Massachusetts 02139, United States
| | - Trevor Kramer
- Relay Therapeutics, 399 Binney Street, Cambridge, Massachusetts 02139, United States
| | - Patrick Riley
- Relay Therapeutics, 399 Binney Street, Cambridge, Massachusetts 02139, United States
| | - W Patrick Walters
- Relay Therapeutics, 399 Binney Street, Cambridge, Massachusetts 02139, United States
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14
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Pavan M, Bassani D, Sturlese M, Moro S. Bat coronaviruses related to SARS-CoV-2: what about their 3CL proteases (MPro)? J Enzyme Inhib Med Chem 2022; 37:1077-1082. [PMID: 35418253 PMCID: PMC9037175 DOI: 10.1080/14756366.2022.2062336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Despite a huge effort by the scientific community to determine the animal reservoir of SARS-CoV-2, which led to the identification of several SARS-CoV-2-related viruses both in bats and in pangolins, the origin of SARS-CoV-2 is still not clear. Recently, Temmam et al. reported the discovery of bat coronaviruses with a high degree of genome similarity with SARS-CoV-2, especially concerning the RBDs of the S protein, which mediates the capability of such viruses to enter and therefore infect human cells through a hACE2-dependent pathway. These viruses, especially the one named BANAL-236, showed a higher affinity for the hACE2 compared to the original strain of SARS-CoV-2. In the present work, we analyse the similarities and differences between the 3CL protease (main protease, Mpro) of these newly reported viruses and SARS-CoV-2, discussing their relevance relative to the efficacy of existing therapeutic approaches against COVID-19, particularly concerning the recently approved orally available Paxlovid, and the development of future ones.
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Affiliation(s)
- Matteo Pavan
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences University of Padova, Padova, Italy
| | - Davide Bassani
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences University of Padova, Padova, Italy
| | - Mattia Sturlese
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences University of Padova, Padova, Italy
| | - Stefano Moro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences University of Padova, Padova, Italy
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15
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El Khoury L, Jing Z, Cuzzolin A, Deplano A, Loco D, Sattarov B, Hédin F, Wendeborn S, Ho C, El Ahdab D, Jaffrelot Inizan T, Sturlese M, Sosic A, Volpiana M, Lugato A, Barone M, Gatto B, Macchia ML, Bellanda M, Battistutta R, Salata C, Kondratov I, Iminov R, Khairulin A, Mykhalonok Y, Pochepko A, Chashka-Ratushnyi V, Kos I, Moro S, Montes M, Ren P, Ponder JW, Lagardère L, Piquemal JP, Sabbadin D. Computationally driven discovery of SARS-CoV-2 M pro inhibitors: from design to experimental validation. Chem Sci 2022; 13:3674-3687. [PMID: 35432906 PMCID: PMC8966641 DOI: 10.1039/d1sc05892d] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 02/03/2022] [Indexed: 11/21/2022] Open
Abstract
We report a fast-track computationally driven discovery of new SARS-CoV-2 main protease (Mpro) inhibitors whose potency ranges from mM for the initial non-covalent ligands to sub-μM for the final covalent compound (IC50 = 830 ± 50 nM). The project extensively relied on high-resolution all-atom molecular dynamics simulations and absolute binding free energy calculations performed using the polarizable AMOEBA force field. The study is complemented by extensive adaptive sampling simulations that are used to rationalize the different ligand binding poses through the explicit reconstruction of the ligand–protein conformation space. Machine learning predictions are also performed to predict selected compound properties. While simulations extensively use high performance computing to strongly reduce the time-to-solution, they were systematically coupled to nuclear magnetic resonance experiments to drive synthesis and for in vitro characterization of compounds. Such a study highlights the power of in silico strategies that rely on structure-based approaches for drug design and allows the protein conformational multiplicity problem to be addressed. The proposed fluorinated tetrahydroquinolines open routes for further optimization of Mpro inhibitors towards low nM affinities. The dominant binding mode of the QUB-00006-Int-07 main protease inhibitor during absolute binding free energy simulations.![]()
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Affiliation(s)
- Léa El Khoury
- Qubit Pharmaceuticals, Incubateur Paris Biotech Santé 24 Rue du Faubourg Saint Jacques 75014 Paris France
| | - Zhifeng Jing
- Qubit Pharmaceuticals, Incubateur Paris Biotech Santé 24 Rue du Faubourg Saint Jacques 75014 Paris France
| | - Alberto Cuzzolin
- Chiesi Farmaceutici S.p.A, Nuovo Centro Ricerche Largo Belloli 11a 43122 Parma Italy
| | - Alessandro Deplano
- Pharmacelera, Torre R, 4a planta Despatx A05, Parc Cientific de Barcelona, Baldiri Reixac 8 08028 Barcelona Spain
| | - Daniele Loco
- Qubit Pharmaceuticals, Incubateur Paris Biotech Santé 24 Rue du Faubourg Saint Jacques 75014 Paris France
| | - Boris Sattarov
- Qubit Pharmaceuticals, Incubateur Paris Biotech Santé 24 Rue du Faubourg Saint Jacques 75014 Paris France
| | - Florent Hédin
- Qubit Pharmaceuticals, Incubateur Paris Biotech Santé 24 Rue du Faubourg Saint Jacques 75014 Paris France
| | - Sebastian Wendeborn
- University of Applied Sciences and Arts Northwestern Switzerland, School of LifeSciences Hofackerstrasse 30 CH-4132 Muttenz Switzerland
| | - Chris Ho
- Qubit Pharmaceuticals, Incubateur Paris Biotech Santé 24 Rue du Faubourg Saint Jacques 75014 Paris France
| | - Dina El Ahdab
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS 75005 Paris France
| | - Theo Jaffrelot Inizan
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS 75005 Paris France
| | - Mattia Sturlese
- Molecular Modeling Section, Department of Pharmaceutical and Pharmacological Sciences, University of Padua via F. Marzolo 5 35131 Padova Italy
| | - Alice Sosic
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5 35131 Padova Italy
| | - Martina Volpiana
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5 35131 Padova Italy
| | - Angela Lugato
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5 35131 Padova Italy
| | - Marco Barone
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5 35131 Padova Italy
| | - Barbara Gatto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5 35131 Padova Italy
| | - Maria Ludovica Macchia
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5 35131 Padova Italy
| | - Massimo Bellanda
- Department of Chemistry, University of Padova via Marzolo 1 35131 Padova Italy
| | - Roberto Battistutta
- Department of Chemistry, University of Padova via Marzolo 1 35131 Padova Italy
| | - Cristiano Salata
- Department of Molecular Medicine, University of Padua via Gabelli 63 35121 Padova Italy
| | | | - Rustam Iminov
- Enamine Ltd 78 Chervonotkats'ka Str. Kyiv 02094 Ukraine
| | | | | | | | | | - Iaroslava Kos
- Enamine Ltd 78 Chervonotkats'ka Str. Kyiv 02094 Ukraine
| | - Stefano Moro
- Molecular Modeling Section, Department of Pharmaceutical and Pharmacological Sciences, University of Padua via F. Marzolo 5 35131 Padova Italy
| | - Matthieu Montes
- Laboratoire GBCM, EA7528, Conservatoire National des Arts et Métiers, Hesam Université 2 Rue Conte 75003 Paris France
| | - Pengyu Ren
- University of Texas at Austin, Department of Biomedical Engineering TX 78712 USA
| | - Jay W Ponder
- Department of Chemistry, Washington University in Saint Louis MO 63130 USA.,Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine MO 63110 USA
| | - Louis Lagardère
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS 75005 Paris France
| | - Jean-Philip Piquemal
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS 75005 Paris France .,Institut Universitaire de France 75005 Paris France
| | - Davide Sabbadin
- Qubit Pharmaceuticals, Incubateur Paris Biotech Santé 24 Rue du Faubourg Saint Jacques 75014 Paris France
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16
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Floresta G, Zagni C, Gentile D, Patamia V, Rescifina A. Artificial Intelligence Technologies for COVID-19 De Novo Drug Design. Int J Mol Sci 2022; 23:ijms23063261. [PMID: 35328682 PMCID: PMC8949797 DOI: 10.3390/ijms23063261] [Citation(s) in RCA: 12] [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: 02/28/2022] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 12/16/2022] Open
Abstract
The recent covid crisis has provided important lessons for academia and industry regarding digital reorganization. Among the fascinating lessons from these times is the huge potential of data analytics and artificial intelligence. The crisis exponentially accelerated the adoption of analytics and artificial intelligence, and this momentum is predicted to continue into the 2020s and beyond. Drug development is a costly and time-consuming business, and only a minority of approved drugs generate returns exceeding the research and development costs. As a result, there is a huge drive to make drug discovery cheaper and faster. With modern algorithms and hardware, it is not too surprising that the new technologies of artificial intelligence and other computational simulation tools can help drug developers. In only two years of covid research, many novel molecules have been designed/identified using artificial intelligence methods with astonishing results in terms of time and effectiveness. This paper reviews the most significant research on artificial intelligence in de novo drug design for COVID-19 pharmaceutical research.
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17
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Edwards AM, Baric RS, Saphire EO, Ulmer JB. Stopping pandemics before they start: Lessons learned from SARS-CoV-2. Science 2022; 375:1133-1139. [PMID: 35271333 DOI: 10.1126/science.abn1900] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The vaccine and drug discovery responses to COVID-19 have worked far better than could have been imagined. Yet by the end of 2021, more than 5 million people had died, and the pandemic continues to evolve and rage globally. This Review will describe how each of the vaccines, antibody therapies, and antiviral drugs that have been approved to date were built on decades of investment in technology and basic science. We will caution that the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has so far proven a straightforward test of our pandemic preparedness, and we will recommend steps we should undertake now to prepare for, to minimize the effects of, and ideally to prevent future pandemics. Other Reviews in this series describe the interactions of SARS-CoV-2 with the immune system and those therapies that target the host response to infection.
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Affiliation(s)
- Aled M Edwards
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Ralph S Baric
- Rapidly Emerging Antiviral Drug Development Initiative (READDI), Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Erica Ollmann Saphire
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA.,Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Jeffrey B Ulmer
- TechImmune, Newport Beach, CA 92660, USA.,Immorna Biotherapeutics, Durham, NC 27703, USA
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18
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Clyde A, Galanie S, Kneller DW, Ma H, Babuji Y, Blaiszik B, Brace A, Brettin T, Chard K, Chard R, Coates L, Foster I, Hauner D, Kertesz V, Kumar N, Lee H, Li Z, Merzky A, Schmidt JG, Tan L, Titov M, Trifan A, Turilli M, Van Dam H, Chennubhotla SC, Jha S, Kovalevsky A, Ramanathan A, Head MS, Stevens R. High-Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Noncovalent Inhibitor. J Chem Inf Model 2022; 62:116-128. [PMID: 34793155 PMCID: PMC8610012 DOI: 10.1021/acs.jcim.1c00851] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Indexed: 12/27/2022]
Abstract
Despite the recent availability of vaccines against the acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the search for inhibitory therapeutic agents has assumed importance especially in the context of emerging new viral variants. In this paper, we describe the discovery of a novel noncovalent small-molecule inhibitor, MCULE-5948770040, that binds to and inhibits the SARS-Cov-2 main protease (Mpro) by employing a scalable high-throughput virtual screening (HTVS) framework and a targeted compound library of over 6.5 million molecules that could be readily ordered and purchased. Our HTVS framework leverages the U.S. supercomputing infrastructure achieving nearly 91% resource utilization and nearly 126 million docking calculations per hour. Downstream biochemical assays validate this Mpro inhibitor with an inhibition constant (Ki) of 2.9 μM (95% CI 2.2, 4.0). Furthermore, using room-temperature X-ray crystallography, we show that MCULE-5948770040 binds to a cleft in the primary binding site of Mpro forming stable hydrogen bond and hydrophobic interactions. We then used multiple μs-time scale molecular dynamics (MD) simulations and machine learning (ML) techniques to elucidate how the bound ligand alters the conformational states accessed by Mpro, involving motions both proximal and distal to the binding site. Together, our results demonstrate how MCULE-5948770040 inhibits Mpro and offers a springboard for further therapeutic design.
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Affiliation(s)
- Austin Clyde
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Stephanie Galanie
- Biosciences Division, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Daniel W. Kneller
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Heng Ma
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Yadu Babuji
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Ben Blaiszik
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Alexander Brace
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Thomas Brettin
- Computing Environment and Life Sciences Directorate,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Kyle Chard
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Ryan Chard
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Ian Foster
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Darin Hauner
- Computational Biology Group, Biological Science Division,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Vlimos Kertesz
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Neeraj Kumar
- Computational Biology Group, Biological Science Division,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Hyungro Lee
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Zhuozhao Li
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Andre Merzky
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Jurgen G. Schmidt
- Bioscience Division, Los Alamos National
Laboratory, Los Alamos, New Mexico 87545, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Li Tan
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Mikhail Titov
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Anda Trifan
- University of Illinois at
Urbana-Champaign, Champaign, Illinois 61820, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Matteo Turilli
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- Computational Science Initiative,
Brookhaven National Laboratory, Upton, New York 11973,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Hubertus Van Dam
- Computational Science Initiative,
Brookhaven National Laboratory, Upton, New York 11973,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Srinivas C. Chennubhotla
- Department of Computational and Systems
Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
15260, United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Shantenu Jha
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- Computational Science Initiative,
Brookhaven National Laboratory, Upton, New York 11973,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Andrey Kovalevsky
- Second Target Station, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Arvind Ramanathan
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Martha S. Head
- Joint Institute for Biological Sciences,
Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Rick Stevens
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- Computing Environment and Life Sciences Directorate,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
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19
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Asada K, Komatsu M, Shimoyama R, Takasawa K, Shinkai N, Sakai A, Bolatkan A, Yamada M, Takahashi S, Machino H, Kobayashi K, Kaneko S, Hamamoto R. Application of Artificial Intelligence in COVID-19 Diagnosis and Therapeutics. J Pers Med 2021; 11:886. [PMID: 34575663 PMCID: PMC8471764 DOI: 10.3390/jpm11090886] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/01/2021] [Accepted: 09/02/2021] [Indexed: 12/12/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic began at the end of December 2019, giving rise to a high rate of infections and causing COVID-19-associated deaths worldwide. It was first reported in Wuhan, China, and since then, not only global leaders, organizations, and pharmaceutical/biotech companies, but also researchers, have directed their efforts toward overcoming this threat. The use of artificial intelligence (AI) has recently surged internationally and has been applied to diverse aspects of many problems. The benefits of using AI are now widely accepted, and many studies have shown great success in medical research on tasks, such as the classification, detection, and prediction of disease, or even patient outcome. In fact, AI technology has been actively employed in various ways in COVID-19 research, and several clinical applications of AI-equipped medical devices for the diagnosis of COVID-19 have already been reported. Hence, in this review, we summarize the latest studies that focus on medical imaging analysis, drug discovery, and therapeutics such as vaccine development and public health decision-making using AI. This survey clarifies the advantages of using AI in the fight against COVID-19 and provides future directions for tackling the COVID-19 pandemic using AI techniques.
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Affiliation(s)
- Ken Asada
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan; (K.A.); (M.K.); (R.S.); (K.T.); (N.S.); (A.B.); (S.T.); (H.M.); (K.K.); (S.K.)
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (A.S.); (M.Y.)
| | - Masaaki Komatsu
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan; (K.A.); (M.K.); (R.S.); (K.T.); (N.S.); (A.B.); (S.T.); (H.M.); (K.K.); (S.K.)
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (A.S.); (M.Y.)
| | - Ryo Shimoyama
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan; (K.A.); (M.K.); (R.S.); (K.T.); (N.S.); (A.B.); (S.T.); (H.M.); (K.K.); (S.K.)
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (A.S.); (M.Y.)
| | - Ken Takasawa
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan; (K.A.); (M.K.); (R.S.); (K.T.); (N.S.); (A.B.); (S.T.); (H.M.); (K.K.); (S.K.)
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (A.S.); (M.Y.)
| | - Norio Shinkai
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan; (K.A.); (M.K.); (R.S.); (K.T.); (N.S.); (A.B.); (S.T.); (H.M.); (K.K.); (S.K.)
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (A.S.); (M.Y.)
- Department of NCC Cancer Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Akira Sakai
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (A.S.); (M.Y.)
- Department of NCC Cancer Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Amina Bolatkan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan; (K.A.); (M.K.); (R.S.); (K.T.); (N.S.); (A.B.); (S.T.); (H.M.); (K.K.); (S.K.)
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (A.S.); (M.Y.)
| | - Masayoshi Yamada
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (A.S.); (M.Y.)
- Department of Endoscopy, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Satoshi Takahashi
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan; (K.A.); (M.K.); (R.S.); (K.T.); (N.S.); (A.B.); (S.T.); (H.M.); (K.K.); (S.K.)
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (A.S.); (M.Y.)
| | - Hidenori Machino
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan; (K.A.); (M.K.); (R.S.); (K.T.); (N.S.); (A.B.); (S.T.); (H.M.); (K.K.); (S.K.)
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (A.S.); (M.Y.)
| | - Kazuma Kobayashi
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan; (K.A.); (M.K.); (R.S.); (K.T.); (N.S.); (A.B.); (S.T.); (H.M.); (K.K.); (S.K.)
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (A.S.); (M.Y.)
| | - Syuzo Kaneko
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan; (K.A.); (M.K.); (R.S.); (K.T.); (N.S.); (A.B.); (S.T.); (H.M.); (K.K.); (S.K.)
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (A.S.); (M.Y.)
| | - Ryuji Hamamoto
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan; (K.A.); (M.K.); (R.S.); (K.T.); (N.S.); (A.B.); (S.T.); (H.M.); (K.K.); (S.K.)
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (A.S.); (M.Y.)
- Department of NCC Cancer Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
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