ArticleStructure (London, England : 1993)2021
Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing.
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Article in Structure (London, England : 1993), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18citing papers in PubMed
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18 citing papers in PubMed, 44 citations in OpenAlex.
- Characterization of an unusual SARS-CoV-2 main protease natural variant exhibiting resistance to nirmatrelvir and ensitrelvir.Communications biology · 2025Article
- Unlocking the potential of phytochemicals in inhibiting SARS-CoV-2 MScientific reports · 2025Article
- FDA-approved drugs as potential covalent inhibitors of key SARS-CoV-2 proteins: an in silico approach.Turkish journal of biology = Turk biyoloji dergisi · 2025Article
- X-ray crystallographic and hydrogen deuterium exchange studies confirm alternate kinetic models for homolog insulin monomers.PloS one · 2025Article
- Machine learning combines atomistic simulations to predict SARS-CoV-2 Mpro inhibitors from natural compounds.Molecular diversity · 2024Article
- Sensitive detection of SARS-CoV-2 main protease 3CLProtein science : a publication of the Protein Society · 2024Article
- Guide to serial synchrotron crystallography.Current research in structural biology · 2024Review
- Review of serial femtosecond crystallography including the COVID-19 pandemic impact and future outlook.Structure (London, England : 1993) · 2023Review
- Bayesian Inference Elucidates the Catalytic Competency of the SARS-CoV-2 Main Protease 3CLAnalytical chemistry · 2023Article
- Accelerating drug target inhibitor discovery with a deep generative foundation model.Science advances · 2023Article
- Cryogenic X-ray crystallographic studies of biomacromolecules at Turkish Light Source "Turkish journal of biology = Turk biyoloji dergisi · 2023Article
- Understanding Cysteine Chemistry Using Conventional and Serial X-Ray Protein Crystallography.Crystals · 2022Article
- xia2.multiplex: a multi-crystal data-analysis pipeline.Acta crystallographica. Section D, Structural biology · 2022Article
- Multiple protonation states in ligand-free SARS-CoV-2 main protease revealed by large-scale quantum molecular dynamics simulations.Chemical physics letters · 2022Article
- Protocol for structure determination of SARS-CoV-2 main protease at near-physiological-temperature by serial femtosecond crystallography.STAR protocols · 2022Article
- The neutralization effect of montelukast on SARS-CoV-2 is shown by multiscale in silico simulations and combined in vitro studies.Molecular therapy : the journal of the American Society of Gene Therapy · 2022Article
- Hit and Indexing Rate in Serial Crystallography: Incomparable Statistics.Frontiers in molecular biosciences · 2022Article
- Structural Basis of Potential Inhibitors Targeting SARS-CoV-2 Main Protease.Frontiers in chemistry · 2021Review
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Authors and funding
49 authors at 7 institutions in 3 countries.
Serdar DurdagiComputational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey. Electronic address: serdar.durdagi@bahcesehir.edu.tr.
Çağdaş DağDepartment of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey.
Berna DoganComputational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey.
Merve YiginDepartment of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey.
Timucin AvsarDepartment of Medical Biology, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey.
Cengizhan BuyukdagDepartment of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey.
Ismail ErolComputational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey; Department of Chemistry, Gebze Technical University, Kocaeli 41400, Turkey.
Fatma Betul ErtemDepartment of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey.
Seyma CalisDepartment of Medical Biology, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey; Department of Molecular Biology - Genetics and Biotechnology, Istanbul Technical University, Istanbul 34469, Turkey.
Gunseli YildirimDepartment of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey.
Muge D OrhanDepartment of Medical Biology, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey.
Omur GuvenDepartment of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey.
Busecan AksoydanComputational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey; Neuroscience Program, Graduate School of Health Sciences, Bahcesehir University, Istanbul 34734, Turkey.
Ebru DestanDepartment of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey.
Kader SahinComputational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey.
Sabri O BeslerDepartment of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey.
Lalehan OktayComputational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey.
Alaleh ShafieiDepartment of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey.
Ilayda ToluComputational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey.
Esra AyanDepartment of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey.
Busra YukselDepartment of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey.
Ayse B PeksenDepartment of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey.
Oktay GocenlerDepartment of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey.
Ali D YucelDepartment of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey.
Ozgur CanDepartment of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey.
Serena OzabrahamyanDepartment of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey.
Alpsu OlkanComputational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey; School of Medicine, Bahcesehir University, Istanbul 34734, Turkey.
Ece ErdemogluComputational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34734, Turkey; Faculty of Medicine, Mersin University, Mersin 33070, Turkey.
Fulya AksitDepartment of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey.
Gokhan TanisaliDepartment of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey.
Oleksandr M YefanovDeutsches Elektronen-Synchrotron, Notkestrasse 85, Hamburg 22607, Germany.
Anton BartyDeutsches Elektronen-Synchrotron, Notkestrasse 85, Hamburg 22607, Germany.
Alexandra TolstikovaDeutsches Elektronen-Synchrotron, Notkestrasse 85, Hamburg 22607, Germany.
Gihan K KetawalaDepartment of Physics, Arizona State University, Tempe, AZ 85287-1504, USA; Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA.
Sabine BothaDepartment of Physics, Arizona State University, Tempe, AZ 85287-1504, USA; Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA.
E Han DaoStanford PULSE Institute, SLAC National Laboratory, Menlo Park, CA 94025, USA.
Brandon HayesLinac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.
Mengning LiangLinac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.
Matthew H SeabergLinac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.
Mark S HunterLinac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.
Alex BatyukLinac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.
Valerio MarianiLinac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.
Zhen SuLinac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA; Department of Applied Physics, Stanford University, Stanford, CA, USA.
Frederic PoitevinLinac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.
Chun Hong YoonLinac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.
Christopher KupitzLinac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.
Raymond G SierraLinac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.
Edward H SnellHauptman-Woodward Medical Research Institute, University at Buffalo, 700 Ellicott St, Buffalo, NY, USA; Materials Design and Innovation, SUNY at Buffalo, 700 Ellicott St., Buffalo, NY, USA.
Hasan DeMirciDepartment of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey; Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, CA 94025, USA; Koc University Isbank Center for Infectious Diseases (KUISCID), 34450, Istanbul, Turkey. Electronic address: hdemirci@ku.edu.tr.
Koç University · TRSLAC National Accelerator Laboratory · USBahçeşehir University · TRDeutsches Elektronen-Synchrotron DESY · DEArizona State University · USGebze Technical University · TRHauptman-Woodward Medical Research Institute · US
Funding
No grant is acknowledged in the PubMed record.
Abstract
The COVID-19 pandemic has resulted in 198 million reported infections and more than 4 million deaths as of July 2021 (covid19.who.int). Research to identify effective therapies for COVID-19 includes: (1) designing a vaccine as future protection; (2) de novo drug discovery; and (3) identifying existing drugs to repurpose them as effective and immediate treatments. To assist in drug repurposing and design, we determine two apo structures of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease at ambient temperature by serial femtosecond X-ray crystallography. We employ detailed molecular simulations of selected known main protease inhibitors with the structures and compare binding modes and energies. The combined structural and molecular modeling studies not only reveal the dynamics of small molecules targeting the main protease but also provide invaluable opportunities for drug repurposing and structure-based drug design strategies against SARS-CoV-2.
Indexed as
COVID-19 Drug TreatmentDrug DesignDrug RepositioningSARS-CoV-2Catalytic DomainComputer SimulationCoronavirus 3C ProteasesCrystallography, X-RayDimerizationMolecular ConformationMolecular Docking SimulationPrincipal Component AnalysisProtein ConformationRecombinant ProteinsTemperature3C-like proteinase, SARS-CoV-2Coronavirus 3C ProteasesRecombinant Proteinsambient temperaturedrug repurposingmain proteaseSARS-CoV-2SFX
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