Browsing by Author "b4142568-0480-4843-a58f-543a27f10279"
Now showing items 1-16 of 16
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Benchmarking Quantum Mechanics/Molecular Mechanics (QM/MM) Methods on the Thymidylate Synthase-Catalyzed Hydride Transfer
Świderek, Katarzyna; Arafet Cruz, Kemel; Kohen, Amnon; Moliner, Vicent American Chemical Society (2017-02)Given the ubiquity of hydride-transfer reactions in enzyme-catalyzed processes, identifying the appropriate computational method for evaluating such biological reactions is crucial to perform theoretical studies of these ... -
Caught in Action: X-ray Structure of Thymidylate Synthase with Noncovalent Intermediate Analog
Kholodar, Svetlana; Finer-Moore, Janet; Świderek, Katarzyna; Arafet Cruz, Kemel; Moliner, Vicent; Stroud, Robert M.; Kohen, Amnon American Chemical Society (2021-04-08)Methylation of 2-deoxyuridine-5′-monophosphate (dUMP) at the C5 position by the obligate dimeric thymidylate synthase (TSase) in the sole de novo biosynthetic pathway to thymidine 5′-monophosphate (dTMP) proceeds by forming ... -
Computational Study of the Catalytic Mechanism of the Cruzain Cysteine Protease
Arafet Cruz, Kemel; Ferrer Castillo, Silvia; Moliner, Vicent American Chemical Society (2017)Cysteine proteases of the papain family are involved in many diseases, making them attractive targets for developing drugs. In this paper, different catalytic mechanisms of cruzain cysteine protease have been studied on ... -
Computational Study of the Michaelis Complex Formation and the Effect on the Reaction Mechanism of Cruzain Cysteine Protease
Arafet Cruz, Kemel; Świderek, Katarzyna; Moliner, Vicent American Chemical Society (2018)Cruzain, a cysteine protease of the papain family, is essential in the development of the protozoan Trypanosoma cruzi, the etiologic agent of Chagas disease, making it an attractive target for developing new drugs. The ... -
Digital Twins in Solar Farms: An Approach through Time Series and Deep Learning
Arafet Cruz, Kemel; Berlanga Llavori, Rafael MDPI (2021-05-18)The generation of electricity through renewable energy sources increases every day, with solar energy being one of the fastest-growing. The emergence of information technologies such as Digital Twins (DT) in the field of ... -
Elucidating the Dual Mode of Action of Dipeptidyl Enoates in the Inhibition of Rhodesain Cysteine Proteases
Arafet Cruz, Kemel; González, Florenci; Moliner, Vicent Wiley (2021-04-14)A computational study of the two possible inhibition mechanisms of rhodesain cysteine protease by the dipeptidyl enoate Cbz-Phe-Leu-CH=CH−CO2C2H5 has been carried out by means of molecular dynamics simulations with hybrid ... -
First Quantum Mechanics/Molecular Mechanics Studies of the Inhibition Mechanism of Cruzain by Peptidyl Halomethyl Ketones
Arafet Cruz, Kemel; Ferrer Castillo, Silvia; Moliner, Vicent ACS Publications (2015-05-12)Cruzain is a primary cysteine protease expressed by the protozoan parasite Trypanosoma cruzi during Chagas disease infection, and thus, the development of inhibitors of this protein is a promising target for designing ... -
Gemelo Digital en Parques Solares: enfoque mediante series temporales y aprendizaje profundo
Arafet Cruz, Kemel Universitat Jaume I (2020-11-13)Cada día aumenta la presencia de la generación mediante fuentes renovables de energía, siendo la energía solar una de las de mayor crecimiento. El surgimiento de tecnologías como los Gemelos Digitales dentro del marco de ... -
Impact of the Recognition Part of Dipeptidyl Nitroalkene Compounds on the Inhibition Mechanism of Cysteine Proteases Cruzain and Cathepsin L
Arafet Cruz, Kemel; Royo, Santiago; Schirmeister, Tanja; Barthels, Fabian; González, Florenci; Moliner, Vicent American Chemical Society (2023-05-05)Cysteine proteases (CPs) are an important class of enzymes, many of which are responsible for several human diseases. For instance, cruzain of protozoan parasite Trypanosoma cruzi is responsible for the Chagas disease, ... -
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 ... -
Mechanism of inhibition of SARS-CoV-2 Mpro by N3 peptidyl Michael acceptor explained by QM/MM simulations and design of new derivatives with tunable chemical reactivity
Arafet Cruz, Kemel; Serrano Aparicio, Natalia; Lodola, Alessio; Mulholland, Adrian J.; González, Florenci; Świderek, Katarzyna; Moliner, Vicent Royal Society of Chemistry (2021)The SARS-CoV-2 main protease (Mpro) is essential for replication of the virus responsible for the COVID-19 pandemic, and one of the main targets for drug design. Here, we simulate the inhibition process of SARS-CoV-2 Mpro ... -
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 ... -
QM/MM Study of the Enzymatic Biodegradation Mechanism of Polyethylene Terephthalate
Boneta, Sergio; Arafet Cruz, Kemel; Moliner, Vicent American Chemical Society (2021-06-04)The environmental problems derived from the generalized plastic consumption and disposal could find a friendly solution in enzymatic biodegradation. Recently, two hydrolases from Ideonella sakaiensis 201-F6 and the ... -
Quantum mechanics/molecular mechanics studies of the mechanism of cysteine protease inhibition by peptidyl-2,3-epoxyketones
Arafet Cruz, Kemel; Ferrer Castillo, Silvia; González, Florenci; Moliner, Vicent Royal Society of Chemistry (2017)Cysteine proteases are the most abundant proteases in parasitic protozoa and they are essential enzymes to the life cycle of several of them, thus becoming attractive therapeutic targets for the development of new ... -
Quantum Mechanics/Molecular Mechanics Studies of the Mechanism of Cysteine Proteases Inhibition by Dipeptidyl Nitroalkenes
Arafet Cruz, Kemel; González, Florenci; Moliner, Vicent Wiley (2020-02-11)In this work a computational study of the mechanism of inhibition of cruzain, rhodesain, and cathepsin L cysteine proteases by the dipeptidyl nitroalkene Cbz‐Phe‐Ala‐CH=CH‐NO2 has been carried out by means of molecular ... -
Quantum Mechanics/Molecular Mechanics Studies of the Mechanism of Falcipain-2 Inhibition by the Epoxysuccinate E64
Arafet Cruz, Kemel; Ferrer Castillo, Silvia; Martí Forés, Sergio; Moliner, Vicent American Chemical Society (2014-05)Because of the increasing resistance of malaria parasites to antimalarial drugs, the lack of highly effective vaccines, and an inadequate control of mosquito vectors, the problem is growing, especially in the developing ...