Listar por autoría "adde8949-fe5b-4451-bfc1-985325e26fcb"
Mostrando ítems 1-11 de 11
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A QM/MM study on the origin of retro-aldolase activity of a catalytic antibody
de Raffele, daria; Martí, Sergio; Moliner, Vicent The Royal Society of Chemistry (2021-04-26)The retro-aldolase mechanism of methodol catalysed by the catalytic antibody 33F12 is described based on the exploration of the free energy landscape obtained with QM/MM methods. The amino acids involved in the reaction ... -
Are Heme-Dependent Enzymes Always Using a Redox Mechanism? A Theoretical Study of the Kemp Elimination Catalyzed by a Promiscuous Aldoxime Dehydratase
Martí, Sergio; Tuñón, Iñaki; Moliner, Vicent; Bertran, Joan American Chemical Society (2020-09-03)The design of biocatalysts is a goal to improve the rate, selectivity and environmental friendship of chemical processes in biotechnology. In this regard, the use of computational techniques has provided valuable assistance ... -
Assessment of the PETase conformational changes induced bypoly(ethylene terephthalate) binding
Costa, Clauber Henrique Souza da; dos Santos, lberto M.; Nahum Alves, Cláudio; Martí, Sergio; Moliner, Vicent; Santana, Kauê; Lameira, Jerônimo Wiley (2021-06-02)Recently, a bacterium strain of Ideonella sakaiensis was identified with the uncommon ability to degrade the poly(ethylene terephthalate) (PET). The PETase from I. sakaiensis strain 201-F6 (IsPETase) catalyzes the hydrolysis ... -
Computational Study of the Inhibition of RgpB Gingipain, a Promising Target for the Treatment of Alzheimer’s Disease
Movilla Núñez, Santiago; Martí, Sergio; Roca, Maite; Moliner, Vicent American Chemical Society (2023-01-17)Alzheimer’s disease represents one of the most ambitious challenges for biomedical sciences due to the growing number of cases worldwide in the elderly population and the lack of efficient treatments. One of the recent ... -
Examination of the performance of semiempirical methods in QM/MM studies of the SN2-like reaction of an adenylyl group transfer catalysed by ANT4′
Martí, Sergio; Moliner, Vicent; Świderek, Katarzyna Springer Berlin Heidelberg (2019)Quantum mechanical (QM) semiempirical methods (SMs), combined with molecular mechanics (MM) force fields, are extensively used in theoretical studies of enzymatic reactions. Despite being several orders of magnitude faster ... -
Impact of Warhead Modulations on the Covalent Inhibition of SARS-CoV2 Mpro Explored by QM\/MM Simulations
Martí, Sergio; Arafet Cruz, Kemel; Lodola, Alessio; Mulholland, Adrian; Świderek, Katarzyna; Moliner, Vicent American Chemical Society (2021-12-26)The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus-2, SARS-CoV-2, shows the need for effective antiviral treatments. Here, we present a simulation study of the inhibition of the SARS-CoV-2 ... -
Mechanistic Modeling of Lys745 Sulfonylation in EGFR C797S Reveals Chemical Determinants for Inhibitor Activity and Discriminates Reversible from Irreversible Agents
Arafet Cruz, Kemel; Scalvini, Laura; Galvani, Francesca; Martí, Sergio; Moliner, Vicent; Mor, Marco; Lodola, Alessio American Chemical Society (2023-02-10)Targeted covalent inhibitors hold promise for drug discovery, particularly for kinases. Targeting the catalytic lysine of epidermal growth factor receptor (EGFR) has attracted attention as a new strategy to overcome ... -
Peptidyl nitroalkene inhibitors of main protease rationalized by computational and crystallographic investigations as antivirals against SARS-CoV-2
Medrano Martin, Francisco Javier; de la hoz rodriguez, Sergio; Martí, Sergio; Arafet Cruz, Kemel; Schirmeister, Tanja; Hammerschmidt, Stefan Josef; Müller-Ruttloff, Christin; González-Martínez, Águeda; Santillana Heras, Elena; Ziebuhr, John; Romero Garrido, Antonio; Zimmer, Collin; Weldert, Annabelle Carolin; Zimmermann, Robert; Lodola, Alessio; Świderek, Katarzyna; Moliner, Vicent; González, Florenci Springer Nature (2024-01-18)The coronavirus disease 2019 (COVID-19) pandemic continues to represent a global public health issue. The viral main protease (Mpro) represents one of the most attractive targets for the development of antiviral drugs. ... -
QMCube (QM3): An all‐purpose suite for multiscale QM/MM calculations
Martí, Sergio Wiley (2020-12-18)QMCube (QM3) is a suite written in the Python programming language, initially focused on multiscale QM/MM simulations of biological systems, but open enough to address other kinds of problems. It allows the user to combine ... -
Understanding the Directed Evolution of De Novo Retro-Aldolases from QM/MM Studies
De Raffele, Daria; Martí, Sergio; Moliner, Vicent American Chemical Society (2020-05-15)In an era in which climatic change puts the planet at risk, the study and development of alternative green chemistry which can help and improve our life can play an essential role. In this context, the use of artificial ... -
Unrevealing the Proteolytic Activity of RgpB Gingipain from Computational Simulations
Movilla Núñez, Santiago; Martí, Sergio; Roca, Maite; Moliner, Vicent American Chemical Society (2021-09-02)Alzheimer’s disease represents one of the greatest medical concerns for today’s population and health services. Its multifactorial inherent nature represents a challenge for its treatment and requires the development of a ...