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Near-Physiological-Temperature Serial Femtosecond X-ray Crystallography Reveals Novel Conformations of SARS-CoV-2 Main Protease Active Site for Improved Drug Repurposing

Serdar Durdagi, Cagdas Dag, Berna Dogan, Merve Yigin, Timucin Avsar, Cengizhan Buyukdag, Ismail Erol, Betul Ertem, Seyma Calis, Gunseli Yildirim, Muge D. Orhan, Omur Guven, Busecan Aksoydan, Ebru Destan, Kader Sahin, Sabri O. Besler, Lalehan Oktay, Alaleh Shafiei, Ilayda Tolu, Esra Ayan, Busra Yuksel, Ayse B. Peksen, Oktay Gocenler, Ali D. Yucel, Ozgur Can, Serena Ozabrahamyan, Alpsu Olkan, Ece Erdemoglu, Fulya Aksit, Gokhan Tanisali, Oleksandr M. Yefanov, Anton Barty, Alexandra Tolstikova, Gihan K. Ketawala, Sabine Botha, E. Han Dao, Brandon Hayes, Mengning Liang, Matthew H. Seaberg, Mark S. Hunter, Alex Batyuk, Valerio Mariani, Zhen Su, Frederic Poitevin, Chun Hong Yoon, Christopher Kupitz, Raymond G. Sierra, Edward Snell, View ORCID ProfileHasan DeMirci
doi: https://doi.org/10.1101/2020.09.09.287987
Serdar Durdagi
1Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, 34734, Istanbul, Turkey
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Cagdas Dag
2Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
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Berna Dogan
1Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, 34734, Istanbul, Turkey
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Merve Yigin
2Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
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Timucin Avsar
3Department of Medical Biology, School of Medicine, Bahcesehir University, 34734, Istanbul, Turkey
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Cengizhan Buyukdag
2Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
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Ismail Erol
1Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, 34734, Istanbul, Turkey
4Department of Chemistry, Gebze Technical University, 41400, Kocaeli, Turkey
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Betul Ertem
2Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
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Seyma Calis
3Department of Medical Biology, School of Medicine, Bahcesehir University, 34734, Istanbul, Turkey
5Department of Molecular Biology - Genetics and Biotechnology, Istanbul Technical University, 34469, Istanbul, Turkey
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Gunseli Yildirim
2Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
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Muge D. Orhan
3Department of Medical Biology, School of Medicine, Bahcesehir University, 34734, Istanbul, Turkey
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Omur Guven
2Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
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Busecan Aksoydan
1Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, 34734, Istanbul, Turkey
6Neuroscience Program, Graduate School of Health Sciences, Bahcesehir University, 34734, Istanbul, Turkey
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Ebru Destan
2Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
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Kader Sahin
1Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, 34734, Istanbul, Turkey
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Sabri O. Besler
2Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
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Lalehan Oktay
1Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, 34734, Istanbul, Turkey
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Alaleh Shafiei
2Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
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Ilayda Tolu
1Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, 34734, Istanbul, Turkey
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Esra Ayan
2Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
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Busra Yuksel
2Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
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Ayse B. Peksen
2Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
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Oktay Gocenler
2Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
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Ali D. Yucel
2Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
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Ozgur Can
2Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
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Serena Ozabrahamyan
2Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
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Alpsu Olkan
1Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, 34734, Istanbul, Turkey
7School of Medicine, Bahcesehir University, 34734, Istanbul, Turkey
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Ece Erdemoglu
1Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, 34734, Istanbul, Turkey
8Faculty of Medicine, Mersin University, 33070, Mersin, Turkey
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Fulya Aksit
2Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
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Gokhan Tanisali
2Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
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Oleksandr M. Yefanov
9Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg Germany
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Anton Barty
9Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg Germany
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Alexandra Tolstikova
9Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg Germany
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Gihan K. Ketawala
10Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
11Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA
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Sabine Botha
10Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
11Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA
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E. Han Dao
12Stanford PULSE Institute, SLAC National Laboratory, 94025, Menlo Park, CA, USA
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Brandon Hayes
13Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd, Menlo Park, 94025, CA, USA
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Mengning Liang
13Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd, Menlo Park, 94025, CA, USA
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Matthew H. Seaberg
13Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd, Menlo Park, 94025, CA, USA
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Mark S. Hunter
13Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd, Menlo Park, 94025, CA, USA
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Alex Batyuk
13Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd, Menlo Park, 94025, CA, USA
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Valerio Mariani
13Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd, Menlo Park, 94025, CA, USA
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Zhen Su
13Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd, Menlo Park, 94025, CA, USA
14Department of Applied Physics, Stanford University, Stanford, CA, USA
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Frederic Poitevin
13Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd, Menlo Park, 94025, CA, USA
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Chun Hong Yoon
13Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd, Menlo Park, 94025, CA, USA
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Christopher Kupitz
13Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd, Menlo Park, 94025, CA, USA
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Raymond G. Sierra
13Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd, Menlo Park, 94025, CA, USA
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Edward Snell
15Hauptman-Woodward Medical Research Institute, 700 Ellicott St, University at Buffalo, Buffalo, NY, USA and Materials Design and Innovation, SUNY at Buffalo, 700 Ellicott St., Buffalo, NY USA
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Hasan DeMirci
2Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
12Stanford PULSE Institute, SLAC National Laboratory, 94025, Menlo Park, CA, USA
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  • ORCID record for Hasan DeMirci
  • For correspondence: hasan_demirci@stanford.edu
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Abstract

The COVID19 pandemic has resulted in 25+ million reported infections and nearly 850.000 deaths. Research to identify effective therapies for COVID19 includes: i) designing a vaccine as future protection; ii) structure-based drug design; and iii) identifying existing drugs to repurpose them as effective and immediate treatments. To assist in drug repurposing and design, we determined two apo structures of Severe Acute Respiratory Syndrome CoronaVirus-2 main protease at ambienttemperature by Serial Femtosecond X-ray crystallography. We employed detailed molecular simulations of selected known main protease inhibitors with the structures and compared binding modes and energies. The combined structural biology and molecular modeling studies not only reveal the dynamics of small molecules targeting main protease but will also provide invaluable opportunities for drug repurposing and structure-based drug design studies against SARS-CoV-2.

One Sentence Summary Radiation-damage-free high-resolution SARS-CoV-2 main protease SFX structures obtained at near-physiological-temperature offer invaluable information for immediate drug-repurposing studies for the treatment of COVID19.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Near-Physiological-Temperature Serial Femtosecond X-ray Crystallography Reveals Novel Conformations of SARS-CoV-2 Main Protease Active Site for Improved Drug Repurposing
Serdar Durdagi, Cagdas Dag, Berna Dogan, Merve Yigin, Timucin Avsar, Cengizhan Buyukdag, Ismail Erol, Betul Ertem, Seyma Calis, Gunseli Yildirim, Muge D. Orhan, Omur Guven, Busecan Aksoydan, Ebru Destan, Kader Sahin, Sabri O. Besler, Lalehan Oktay, Alaleh Shafiei, Ilayda Tolu, Esra Ayan, Busra Yuksel, Ayse B. Peksen, Oktay Gocenler, Ali D. Yucel, Ozgur Can, Serena Ozabrahamyan, Alpsu Olkan, Ece Erdemoglu, Fulya Aksit, Gokhan Tanisali, Oleksandr M. Yefanov, Anton Barty, Alexandra Tolstikova, Gihan K. Ketawala, Sabine Botha, E. Han Dao, Brandon Hayes, Mengning Liang, Matthew H. Seaberg, Mark S. Hunter, Alex Batyuk, Valerio Mariani, Zhen Su, Frederic Poitevin, Chun Hong Yoon, Christopher Kupitz, Raymond G. Sierra, Edward Snell, Hasan DeMirci
bioRxiv 2020.09.09.287987; doi: https://doi.org/10.1101/2020.09.09.287987
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Near-Physiological-Temperature Serial Femtosecond X-ray Crystallography Reveals Novel Conformations of SARS-CoV-2 Main Protease Active Site for Improved Drug Repurposing
Serdar Durdagi, Cagdas Dag, Berna Dogan, Merve Yigin, Timucin Avsar, Cengizhan Buyukdag, Ismail Erol, Betul Ertem, Seyma Calis, Gunseli Yildirim, Muge D. Orhan, Omur Guven, Busecan Aksoydan, Ebru Destan, Kader Sahin, Sabri O. Besler, Lalehan Oktay, Alaleh Shafiei, Ilayda Tolu, Esra Ayan, Busra Yuksel, Ayse B. Peksen, Oktay Gocenler, Ali D. Yucel, Ozgur Can, Serena Ozabrahamyan, Alpsu Olkan, Ece Erdemoglu, Fulya Aksit, Gokhan Tanisali, Oleksandr M. Yefanov, Anton Barty, Alexandra Tolstikova, Gihan K. Ketawala, Sabine Botha, E. Han Dao, Brandon Hayes, Mengning Liang, Matthew H. Seaberg, Mark S. Hunter, Alex Batyuk, Valerio Mariani, Zhen Su, Frederic Poitevin, Chun Hong Yoon, Christopher Kupitz, Raymond G. Sierra, Edward Snell, Hasan DeMirci
bioRxiv 2020.09.09.287987; doi: https://doi.org/10.1101/2020.09.09.287987

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