Listar por autoría "483a8f3c-ddf2-41a0-aa46-da4c14cd9023"
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Computational design of biological catalysts
Martí Forés, Sergio; Andres, Juan; Moliner, Vicent; Silla, Estanislao; Tuñón, Iñaki; Bertrán, Juan Royal Society of Chemistry (2008)The purpose of this tutorial review is to illustrate the way to design new and powerful catalysts. The first possibility to get a biological catalyst for a given chemical process is to use existing enzymes that catalyze ... -
Computational strategies for the design of new enzymatic functions
Świderek, Katarzyna; Tuñón, Iñaki; Moliner, Vicent; Bertrán, Juan Elsevier (2015-09-15)In this contribution, recent developments in the design of biocatalysts are reviewed with particular emphasis in the de novo strategy. Studies based on three different reactions, Kemp elimination, Diels–Alder and Retro-Aldolase, ... -
Computational Studies of Candida Antarctica Lipase B to Test Its Capability as a Starting Point to Redesing New Diels-Alderases
Świderek, Katarzyna; Moliner, Vicent American Chemical Society (2016-03)The design of new biocatalysts is a target that is receiving increasing attention. One of the most popular reactions in this regard is the Diels-Alder cycloaddition due to its applications in organic synthesis and the ... -
Computational Studies Suggest Promiscuous Candida antarctica Lipase B as an Environmentally Friendly Alternative for the Production of Epoxides
Galmés, Miquel À; Świderek, Katarzyna; Moliner, Vicent American Chemical Society (2021-07-26)Environmentally friendly processes are nowadays a trending topic to get highly desired chemical compounds and, in this sense, the use of enzyme-catalyzed routes is becoming a promising alternative to traditional synthetic ... -
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 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 ... -
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 ... -
Computational Study of the Phosphoryl Donor Activity of Dihydroxyacetone Kinase from ATP to Inorganic Polyphosphate
Bordes, Isabel; García-Junceda, Eduardo; Sánchez Moreno, Israel; Castillo, Raquel; Moliner, Vicent Wiley (2017-10)Adenosine triphosphate (ATP) is the main biological phosphoryl donor required in many enzymes including dihydroxyacetone kinases (DHAKs) that convert dihydroxyacetone (Dha) into dihydroxyacetone phosphate (Dha-P), a key ... -
Computational study on hydrolysis of Cefotaxime in gas phase and in aqueous solution
Meliá, Conchín; Ferrer, Silvia; Moliner, Vicent; Tuñón, Iñaki; Beltrán, Juan Wiley-Blackwell (2012)We are presenting a theoretical study of the hydrolysis of a β-lactam antibiotic in gas phase and in aqueous solution by means of hybrid quantum mechanics/molecular mechanics potentials. After exploring the potential energy ... -
Convergence of Theory and Experiment on the Role of Preorganization, Quantum Tunneling, and Enzyme Motions into Flavoenzyme-Catalyzed Hydride Transfer
Delgado, Manuel; Görlich, Stefan; Scrutton, Nigel; Hay, Sam; Moliner, Vicent; Tuñón, Iñaki American Chemical Society (2017)Hydride transfer is one of the most common reactions catalyzed by enzymatic systems, and it has become an object of study because of possible significant quantum tunneling effects. In the present work, we provide a combination ... -
Coupling of the Guanosine Glycosidic Bond Conformation and the Ribonucleotide Cleavage Reaction: Implications for Barnase Catalysis
Moliner, Vicent Wiley-Blackwell (2008)To examine the possible relationship of guanine-dependent GpA conformations with ribonucleotide cleavage, two potential of mean force (PMF) calculations were performed in aqueous solution. In the first calculation, the ... -
Dioxygen Activation by Mononuclear Copper Enzymes: Insights from a Tripodal Ligand Mimicking Their CuM Coordination Sphere
de la LANDE, Aurélien; Salahub, Dennis; Moliner, Vicent; Gérard, Hélène; Piquemal, Jean-Philip; Parisel, Olivier American Chemical Society (2009)A mononuclear cuprous complex is proposed as a novel in silico model for the CuM active site of noncoupled copper monooxygenases. To the best of our knowledge, it is one of the first biomimicking models that allows one to ... -
Discovery of SARS-CoV-2 M-pro peptide inhibitors from modelling substrate and ligand binding
Chan, Henry; Moesser, Marc Alexander; Walters, Rebecca; Malla, Tika; Twidale, Rebecca; John, Tobias; Deeks, Helen M.; Johnston-Wood, Tristan; Mikhailov, Victor; Sessions, Richard; Dawson, William; Salah, Eidarus; Lukacik, Petra; Strain-Damerell, Claire; Owen, David; Nakajima, Takahito; Świderek, Katarzyna; Lodola, Alessio; Moliner, Vicent; Glowacki, David; Walsh, Martin Austin; Schofield, Christopher; Genovese, Luigi; Shoemark, Deborah K.; Mulholland, Adrian; Duarte, Fernanda; Morris, Garrett The Royal Society of Chemistry (2021-09-06)The main protease (Mpro) of SARS-CoV-2 is central to viral maturation and is a promising drug target, but little is known about structural aspects of how it binds to its 11 natural cleavage sites. We used biophysical and ... -
Diseño computacional de catalizadores biológicos
Martí Forés, Sergio; Moliner, Vicent; Andres, Juan; Roca, Maite; López Canut, Violeta; Silla, Estanislao; Tuñón, Iñaki; Bertrán, Juan Real Sociedad Española de Química (2011)Enzymes are a source of inspiration for the design of new and powerful industrial catalysts able to work, in principle, in mild conditions of pressure, temperature and solvents. The Transition State of the reaction is the ... -
Do Dynamic Effects Play a Significant Role in Enzymatic Catalysis? A Theoretical Analysis of Formate Dehydrogenase
Roca, Maite; Oliva, Mónica; Castillo, Raquel; Moliner, Vicent; Tuñón, Iñaki Wiley-VCH (2010)A theoretical study of the protein dynamic effects on the hydride transfer between the formate anion and nicotinamide adenine dinucleotide (NAD+), catalyzed by formate dehydrogenase (FDH), is presented in this paper. The ... -
Do zwitterionic species exist in the non-enzymatic peptide bond formation?
Świderek, Katarzyna; Tuñón, Iñaki; Martí Forés, Sergio; Moliner, Vicent; Bertrán, Juan The Royal Society of Chemistry (2012-09-30)The use of proper computational methods and models has allowed answering the controversial question of whether zwitterionic species exist in the mechanism of peptide bond synthesis in aqueous solution. In fact, the different ... -
Dynamic and Electrostatic Effects on the Reaction Catalyzed by HIV‑1 Protease
Krzemińska, Agnieszka; Moliner, Vicent; Świderek, Katarzyna American Chemical Society (2016-11)HIV-1 Protease (HIV-1 PR) is one of the three enzymes essential for the replication process of HIV-1 virus, which explains why it has been the main target for design of drugs against acquired immunodeficiency syndrome ... -
Dynamic effects on reaction rates in a Michael Addition catalyzed by Chalcone Isomerase. Beyond the frozen environment approach
Ruiz-Pernía, José Javier; Tuñón, Iñaki; Moliner, Vicent; Hynes, James T.; Roca, Maite American Chemical Society (2008)We present a detailed microscopic study of the dynamics of the Michael addition reaction leading from 6′-deoxychalcone to the corresponding flavanone. The reaction dynamics are analyzed for both the uncatalyzed reaction ... -
Electric Field Measurements Reveal the Pivotal Role of Cofactor–Substrate Interaction in Dihydrofolate Reductase Catalysis
Adesina, Aduragbemi S.; Świderek, Katarzyna; Luk, Louis Y. P.; Moliner, Vicent American Chemical Society (2020-07-17)The contribution of ligand–ligand electrostatic interaction to transition state formation during enzyme catalysis has remained unexplored, even though electrostatic forces are known to play a major role in protein functions ... -
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 ...