Zobrazeno 1 - 10
of 11
pro vyhledávání: '"Carlos A. Ramos-Guzmán"'
Autor:
Kirill Zinovjev, Paul Guénon, Carlos A. Ramos-Guzmán, J. Javier Ruiz-Pernía, Damien Laage, Iñaki Tuñón
Publikováno v:
Nature Communications, Vol 15, Iss 1, Pp 1-12 (2024)
Abstract Protein loop dynamics have recently been recognized as central to enzymatic activity, specificity and stability. However, the factors controlling loop opening and closing kinetics have remained elusive. Here, we combine molecular dynamics si
Externí odkaz:
https://doaj.org/article/8ddd2ac61fd549b694633d361c28dae6
Publikováno v:
ACS Catalysis. 13:4348-4361
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::40f77edf23b17e99c8c79c1a438b8faf
https://doi.org/10.1021/acscatal.3c00037
https://doi.org/10.1021/acscatal.3c00037
Publikováno v:
Angewandte Chemie (International Ed. in English)
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 complex the carbonyl oxygen atom of the warhead is placed in the oxyanio
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::130d628c80b60c97a8fbeafddd3ea32a
https://doi.org/10.1002/ange.202110027
https://doi.org/10.1002/ange.202110027
Publikováno v:
ACS Catalysis
We here investigate the mechanism of SARS-CoV-2 3CL protease inhibition by one of the most promising families of inhibitors, those containing an aldehyde group as a warhead. These compounds are covalent inhibitors that inactivate the protease, formin
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::851f2a5d8229adb66a6c9824f45b9a41
http://europepmc.org/articles/PMC8008790
http://europepmc.org/articles/PMC8008790
Publikováno v:
ACS Catalysis
We present a detailed theoretical analysis of the reaction mechanism of proteolysis catalyzed by the main protease of SARS-CoV-2. Using multiscale simulation methods, we have characterized the interactions established by a peptidic substrate in the a
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d130fe4ae91b79d99ae138f9c679775a
http://europepmc.org/articles/PMC7556163
http://europepmc.org/articles/PMC7556163
Publikováno v:
Chemical communications (Cambridge, England). 57(72)
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 free energy calculations suggest that positions P3 and P4 could be susce
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::625ff208f7f5dc4b7d7c916afbfd08a4
https://pubmed.ncbi.nlm.nih.gov/34498651
https://pubmed.ncbi.nlm.nih.gov/34498651
We present a detailed analysis of the binding mode and reactivity of the novel oral inhibitor PF-07321332 developed against SARS-CoV-2 3CL protease. Classical and QM/MM Molecular Dynamics simulations are used to quantify the contributions to the bind
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7249a7e6e4e01b9a9ff6bf34e1a03b10
https://doi.org/10.26434/chemrxiv-2021-tndbs
https://doi.org/10.26434/chemrxiv-2021-tndbs
We present the results of combined classical and QM/MM simulations for the inhibition of SARS-CoV-2 3CL protease by a recently proposed ketone-based covalent inhibitor, PF-00835231, that is under clinical trial. In the noncovalent complex formed afte
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::66b7f2be7379db15a011e0284e811522
https://doi.org/10.26434/chemrxiv.13340939
https://doi.org/10.26434/chemrxiv.13340939
Publikováno v:
Chemical Science
The irreversible inhibition of the main protease of SARS-CoV-2 by a Michael acceptor known as N3 has been investigated using multiscale methods. The noncovalent enzyme–inhibitor complex was simulated using classical molecular dynamics techniques an
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ee5af5e39765029b119833adf2f751cb
https://doi.org/10.26434/chemrxiv.12895064.v1
https://doi.org/10.26434/chemrxiv.12895064.v1
We present a detailed theoretical analysis of the reaction mechanism of proteolysis catalyzed by the main protease of SARS-CoV-2. Using multiscale simulation methods, we have characterized the interactions stablished by a peptidic substrate in the ac
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1433eaf2acff760331974768baa153fb
https://doi.org/10.26434/chemrxiv.12501734.v2
https://doi.org/10.26434/chemrxiv.12501734.v2