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A Comprehensive Mapping of the Druggable Cavities within the SARS-CoV-2 Therapeutically Relevant Proteins by Combining Pocket and Docking Searches as Implemented in Pockets 2.0

Computational Studies of SARS-CoV-2 3CLpro: Insights from MD Simulations

Department HPC, CINECA, via dei Tizii 6, 00185 Roma, Italy
Department HPC, CINECA, via Magnanelli 6/3, 40033 Casalecchio di Reno (BO), Italy
Dompé Farmaceutici SpA, via Campo di Pile, 67100 L’Aquila, Italy
Department Physical Chemistry, R&D, Eni SpA, via Maritano 27, 20097 San Donato Milanese (MI), Italy
Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, 17165 Solna, Sweden
Department of Pharmacy, University of Napoli “Federico II”, via D. Montesano 49, 80131 Napoli, Italy
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Int. J. Mol. Sci. 2020, 21(15), 5346;
Received: 23 July 2020 / Revised: 24 July 2020 / Accepted: 25 July 2020 / Published: 28 July 2020
Given the enormous social and health impact of the pandemic triggered by severe acute respiratory syndrome 2 (SARS-CoV-2), the scientific community made a huge effort to provide an immediate response to the challenges posed by Coronavirus disease 2019 (COVID-19). One of the most important proteins of the virus is an enzyme, called 3CLpro or main protease, already identified as an important pharmacological target also in SARS and Middle East respiratory syndrome virus (MERS) viruses. This protein triggers the production of a whole series of enzymes necessary for the virus to carry out its replicating and infectious activities. Therefore, it is crucial to gain a deeper understanding of 3CLpro structure and function in order to effectively target this enzyme. All-atoms molecular dynamics (MD) simulations were performed to examine the different conformational behaviors of the monomeric and dimeric form of SARS-CoV-2 3CLpro apo structure, as revealed by microsecond time scale MD simulations. Our results also shed light on the conformational dynamics of the loop regions at the entry of the catalytic site. Studying, at atomic level, the characteristics of the active site and obtaining information on how the protein can interact with its substrates will allow the design of molecules able to block the enzymatic function crucial for the virus. View Full-Text
Keywords: SARS-CoV-2; COVID-19; protease; molecular dynamics; 3CLpro SARS-CoV-2; COVID-19; protease; molecular dynamics; 3CLpro
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MDPI and ACS Style

Grottesi, A.; Bešker, N.; Emerson, A.; Manelfi, C.; Beccari, A.R.; Frigerio, F.; Lindahl, E.; Cerchia, C.; Talarico, C. Computational Studies of SARS-CoV-2 3CLpro: Insights from MD Simulations. Int. J. Mol. Sci. 2020, 21, 5346.

AMA Style

Grottesi A, Bešker N, Emerson A, Manelfi C, Beccari AR, Frigerio F, Lindahl E, Cerchia C, Talarico C. Computational Studies of SARS-CoV-2 3CLpro: Insights from MD Simulations. International Journal of Molecular Sciences. 2020; 21(15):5346.

Chicago/Turabian Style

Grottesi, Alessandro, Neva Bešker, Andrew Emerson, Candida Manelfi, Andrea R. Beccari, Francesco Frigerio, Erik Lindahl, Carmen Cerchia, and Carmine Talarico. 2020. "Computational Studies of SARS-CoV-2 3CLpro: Insights from MD Simulations" International Journal of Molecular Sciences 21, no. 15: 5346.

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