Listar por autoría "e5e236f4-e792-464f-8365-1c6cc0d2445b"
Mostrando ítems 1-20 de 59
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A Molecular Modeling Approach to Identify Novel Inhibitors of the Major Facilitator Superfamily of Efflux Pump Transporters
Zárate Villarroel, Sandra Giovana; Morales, Paula; Świderek, Katarzyna; Bolanos-Garcia, Victor M.; Bastida, Agatha MDPI (2019)Multidrug efflux systems play a prominent role in medicine, as they are important contributors to bacterial antibiotic resistance. NorA is an efflux pump transporter from the major facilitator superfamily that expels ... -
A theoretical study of carbon–carbon bond formation by a Michael-type addition
Świderek, Katarzyna; Pabis, Anna; Moliner, Vicent Royal Society of Chemistry (2012)A theoretical study of the Michael-type addition of 1,3-dicarbonyl compounds to α,β-unsaturated carbonyl compounds has been performed in the gas phase by means of the AM1 semiempirical method and by density functional ... -
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 ... -
Binding Analysis of Some Classical Acetylcholinesterase Inhibitors: Insights for a Rational Design Using Free Energy Perturbation Method Calculations with QM/MM MD Simulations
Nascimento, Érica C. M.; Oliva, Mónica; Świderek, Katarzyna; Martins, João B. L.; Andres, Juan American Chemical Society (2017-04)In the present study, the binding free energy of some classical inhibitors (DMT, DNP, GNT, HUP, THA) with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation (FEP) method based on hybrid ... -
Binding Isotope Effects as a Tool for Distinguishing Hydrophobic and Hydrophilic Binding Sites of HIV-1 RT
Krzemińska, Agnieszka; Paneth, Piotr; Moliner, Vicent; Świderek, Katarzyna American Chemical Society (2014-08)The current treatment for HIV-1 infected patients consists of a cocktail of inhibitors, in an attempt to improve the potency of the drugs by adding the possible effects of each supplied compound. In this contribution, nine ... -
Catalytic enantioselective epoxidation of nitroalkenes
Vidal-Albalat, Andreu; Świderek, Katarzyna; Izquierdo Ferrer, Javier; Rodríguez, Santiago; Moliner, Vicent; González, Florenci Royal Society of Chemistry (2016)Nitroepoxides are potentially exploitable as synthons with vicinal electrophilic centers. Nevertheless, although advances have been made in the field, enantioselective epoxidation of nitroalkenes is still a challenging ... -
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 ... -
Combined Theoretical and Experimental Study to Unravel the Differences in Promiscuous Amidase Activity of Two Nonhomologous Enzymes
Galmés, Miquel À; Nödling, Alexander; Luk, Louis Y. P.; Świderek, Katarzyna; Moliner, Vicent American Chemical Society (2021-07-16)Convergent evolution has resulted in nonhomologous enzymes that contain similar active sites that catalyze the same primary and secondary reactions. Comparing how these enzymes achieve their reaction promiscuity can yield ... -
Computational design of an amidase by combining the best electrostatic features of two promiscuous hydrolases
Galmes, Miquel Angel; Nödling, Alexander; He, Kaining; Luk, Louis Yu Pan; Świderek, Katarzyna; Moliner, Vicent The Royal Society of Chemistry (2022-03-15)While there has been emerging interest in designing new enzymes to solve practical challenges, computer-based options to redesign catalytically active proteins are rather limited. Here, a rational QM/MM molecular dynamics ... -
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 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 ... -
Covalent Inhibition of the Human 20S Proteasome with Homobelactosin C Inquired by QM/MM Studies
Serrano Aparicio, Natalia; Ferrer, Silvia; Świderek, Katarzyna MDPI (2022)20S proteasome is a main player in the protein degradation pathway in the cytosol, thus intervening in multiple pivotal cellular processes. Over the years the proteasome has emerged as a crucial target for the treatment ... -
Discovery of a Histidine‐Based Scaffold as an Inhibitor of Gut Microbial Choline Trimethylamine‐Lyase
Gabr, Moustafa; Świderek, Katarzyna Wiley (2020-08-22)Anaerobic choline metabolism by human gut microbiota to produce trimethylamine (TMA) has recently evolved as a potential therapeutic target because of its association with chronic kidney disease and increased cardiovascular ... -
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 ... -
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 ... -
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 ... -
Engineering a Highly Regioselective Fungal Peroxygenase for the Synthesis of Hydroxy Fatty Acids
González-Benjumea, Alejandro; Gomez de Santos, Patricia; Fernández-García, Ángela; Aranda Oliden, María del Carmen; Wu, Yinqi; But, Andrada; Molina-Espeja, Patricia; Mate, Diana; Gonzalez-Perez, David; Zhang, Wuyuan; Kiebist, Jan; Scheibner, Katrin; Hofrichter, Martin; Świderek, Katarzyna; Moliner, Vicent; Sanz-Aparicio, Julia; Hollmann, Frank; Gutiérrez, Ana; Alcalde, Miguel John Wiley & Sons (2023-02-20)The hydroxylation of fatty acids is an appealing reaction in synthetic chemistry, although the lack of selective catalysts hampers its industrial implementation. In this study, we have engineered a highly regioselective ...