Visualitza INAM_Articles per paraule clau "QM/MM"
Ara mostrant els elements 1-11 d 11
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Combined Theoretical and Experimental Study to Unravel the Differences in Promiscuous Amidase Activity of Two Nonhomologous Enzymes
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 ... -
Elucidating the Dual Mode of Action of Dipeptidyl Enoates in the Inhibition of Rhodesain Cysteine Proteases
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 ... -
Enzymatic Δ1-Dehydrogenation of 3-Ketosteroids—Reconciliation of Kinetic Isotope Effects with the Reaction Mechanism
American Chemical Society (2021-07-02)Δ1-Dehydrogenation of 3-ketosteroids catalyzed by flavin adenine dinucleotide (FAD)-dependent 3-ketosteroid dehydrogenases (Δ1-KSTD) is a crucial step in steroid degradation and synthesis of several steroid drugs. The ... -
Impact of the Recognition Part of Dipeptidyl Nitroalkene Compounds on the Inhibition Mechanism of Cysteine Proteases Cruzain and Cathepsin L
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 the Warhead of Dipeptidyl Keto Michael Acceptors on the Inhibition Mechanism of Cysteine Protease Cathepsin L
American Chemical Society (2023-10-03)Cathepsin L (CatL) is a lysosomal cysteine protease whose activity has been related to several human pathologies. However, although preclinical trials using CatL inhibitors were promising, clinical trials have been ... -
Impact of Warhead Modulations on the Covalent Inhibition of SARS-CoV2 Mpro Explored by QM\/MM Simulations
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 ... -
Nature of Irreversible Inhibition of Human 20S Proteasome by Salinosporamide A. The Critical Role of Lys–Asp Dyad Revealed from Electrostatic Effects Analysis
American Chemical Society (2021-03-05)20S proteasome is the enzymatic core engine involved in the processes of cellular protein regulation, thus becoming a promising target inter alia in the therapy of many diseases. In this work, the mechanism of the irreversible ... -
On the Origin of the Different Reversible Characters of Salinosporamide A and Homosalinosporamide A in the Covalent Inhibition of the Human 20S Proteasome
American Chemical Society (2021-09-17)Covalent inhibition of the 20S proteasome is one of the strategies used in the fight against cancer, Chagas’ disease, malaria, tuberculosis, or neurodegenerative disorders. In this work, studies based on quantum ... -
QM/MM Study of the Enzymatic Biodegradation Mechanism of Polyethylene Terephthalate
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 ... -
Theoretical Studies of the Self Cleavage Pistol Ribozyme Mechanism
Springer (2021-08-25)Ribozymes are huge complex biological catalysts composed of a combination of RNA and proteins. Nevertheless, there is a reduced number of small ribozymes, the self-cleavage ribozymes, that are formed just by RNA and, ... -
Unveiling the Mechanistic Singularities of Caspases: A Computational Analysis of the Reaction Mechanism in Human Caspase-1
American Chemical Society (2023-04-07)Caspases are cysteine proteases in charge of breaking a peptide bond next to an aspartate residue. Caspases constitute an important family of enzymes involved in cell death and inflammatory processes. A plethora of diseases, ...