Targeting SARS-CoV-2 main protease for treatment of COVID-19: covalent inhibitors structure–activity relationship insights and evolution perspectives

G La Monica, A Bono, A Lauria… - Journal of medicinal …, 2022 - ACS Publications
The viral main protease is one of the most attractive targets among all key enzymes involved
in the SARS-CoV-2 life cycle. Covalent inhibition of the cysteine145 of SARS-CoV-2 MPRO …

Applications of density functional theory in COVID-19 drug modeling

N Ye, Z Yang, Y Liu - Drug discovery today, 2022 - Elsevier
The rapidly evolving Coronavirus 2019 (COVID-19) pandemic has led to millions of deaths
around the world, highlighting the pressing need to develop effective antiviral …

Benchmarking the ability of common docking programs to correctly reproduce and score binding modes in SARS-CoV-2 protease Mpro

S Zev, K Raz, R Schwartz, R Tarabeh… - Journal of Chemical …, 2021 - ACS Publications
The coronavirus SARS-CoV-2 main protease, Mpro, is conserved among coronaviruses with
no human homolog and has therefore attracted significant attention as an enzyme drug …

Methodology-centered review of molecular modeling, simulation, and prediction of SARS-CoV-2

K Gao, R Wang, J Chen, L Cheng, J Frishcosy… - Chemical …, 2022 - ACS Publications
Despite tremendous efforts in the past two years, our understanding of severe acute
respiratory syndrome coronavirus 2 (SARS-CoV-2), virus–host interactions, immune …

SERS-PCR assays of SARS-CoV-2 target genes using Au nanoparticles-internalized Au nanodimple substrates

Y Wu, H Dang, SG Park, L Chen, J Choo - Biosensors and Bioelectronics, 2022 - Elsevier
The reverse transcription-polymerase chain reaction (RT-PCR) method has been adopted
worldwide to diagnose severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) …

Michael acceptor molecules in natural products and their mechanism of action

ST Liang, C Chen, RX Chen, R Li, WL Chen… - Frontiers in …, 2022 - frontiersin.org
Purpose: Michael receptor molecules derived from plants are biologically active due to
electrophilic groups in their structure. They can target nucleophilic residues on disease …

Computational simulations on the binding and reactivity of a nitrile inhibitor of the SARS-CoV-2 main protease

CA Ramos-Guzmán, JJ Ruiz-Pernía… - Chemical …, 2021 - pubs.rsc.org
We present a detailed computational analysis of the binding mode and reactivity of the novel
oral inhibitor PF-07321332 developed against the SARS-CoV-2 3CL protease. Alchemical …

Exploring the mechanism of covalent inhibition: simulating the binding free energy of α-ketoamide inhibitors of the main protease of SARS-CoV-2

D Mondal, A Warshel - Biochemistry, 2020 - ACS Publications
The development of reliable ways of predicting the binding free energies of covalent
inhibitors is a challenge for computer-aided drug design. Such development is important, for …

Multiscale simulations of the covalent inhibition of the SARS-CoV-2 main protease: Four compounds and three reaction mechanisms

BL Grigorenko, IV Polyakov, MG Khrenova… - Journal of the …, 2023 - ACS Publications
We report the results of computational modeling of the reactions of the SARS-CoV-2 main
protease (MPro) with four potential covalent inhibitors. Two of them, carmofur and …

Inhibition mechanism of SARS‐CoV‐2 main protease with ketone‐based inhibitors unveiled by multiscale simulations: insights for improved designs

CA Ramos‐Guzmán, JJ Ruiz‐Pernía… - Angewandte Chemie …, 2021 - Wiley Online Library
We present the results of classical and QM/MM simulations for the inhibition of SARS‐CoV‐2
3CL protease by a hydroxymethylketone inhibitor, PF‐00835231. In the noncovalent …