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Molecular Docking and Conceptual DFT-Based Study of Some Potential SARS-CoV-2 Inhibitors

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Computational Molecular Bioscience 2020年第4期10卷 111-128页

作者： Norma Flores-Holguín daniel glossman-mitnik Laboratorio Virtual NANOCOSMOS Departamento de Medio Ambiente y Energía Centro de Investigación en Materiales Avanzados Miguel de Cervantes 120 Complejo Industrial Chihuahua Chihuahua Mexico

Nowadays, the main effort of the scientific community is focused on the search of specific drugs for the inhibition of the Severe Acute Respiratory Syndrome—Coronavirus 2 (SARS-CoV-2), which is responsible for the Coro-navirus Disease 19 or COVID-19. With the same objective in mind, a Molecular Docking study was performed in this work in order to discover information about some antiviral drugs of common use as protease inhibitors. As a complement of this research, a chemical reactivity study of these potential drugs was done with the aim of finding a relationship between the inhibition ability and the chemical reactivity. The results presented in this research constitute one of the first predictions aimed to identify the best potential compounds for this purpose while at the same time verifying the validity of the employed theoretical and computational methodology. By means of the analysis of the number of hydrogen bonds as well as the binding energies coming from the Molecular Docking study, it can be said that Telaprevir, Nelfinavir and Indinavir have the highest probability of success as potential inhibitors of SARS-CoV-2.

关键词： SARS-CoV-2 Molecular Docking DFT Binding Energy Conceptual DFT

Computational Chemistry and Molecular Modeling Techniques for the Study of Micropeptin EI-964: Insights into Its Chemical Reactivity and Potential Pharmaceutical Properties

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Computational Molecular Bioscience 2023年第3期13卷 35-47页

作者： Norma Flores-Holguín Juan Frau daniel glossman-mitnik Laboratorio Virtual NANOCOSMOS Departamento de Medio Ambiente y Energía Centro de Investigación en Materiales Avanzados Chihuahua Mexico Departament de Química Facultat de Ciències Universitat de les Illes Balears Palma de Mallorca Spain

Micropeptin EI-964 is a cyclic peptide compound isolated from a marine cyanobacterium with potent inhibitory activity against serine proteases, particularly chymotrypsin and trypsin. It has shown promising activity against various cancer cell lines, making it a candidate for drug development. The unique structure and activity of Micropeptin EI-964 make it a promising lead compound for the development of novel serine protease inhibitors and anti-cancer drugs. Computational Chemistry and Molecular Modeling techniques can provide valuable insights into the chemical reactivity and pharmaceutical properties of Micropeptin EI-964, guiding the design and development of new compounds with enhanced bioactivity and improved drug-like properties.

关键词： Micropeptin EI-964 Chemical Reactivity Conceptual DFT Computational Pharmacokinetics Pharmaceutical Drugs

Conceptual Density Functional Theory Study of the Chemical Reactivity Properties and Bioactivity Scores of the Leu-Enkephalin Opioid Peptide Neurotransmitter

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Computational Molecular Bioscience 2019年第1期9卷 13-26页

作者： Juan Frau Norma Flores-Holguín daniel glossman-mitnik Departament de Química Universitat de les Illes Balears Palma de Mallorca Spain Laboratorio Virtual NANOCOSMOS Departamento de Medio Ambiente y Energía Centro de Investigación en Materiales Avanzados Chihuahua Mexico

The SMD solvation model (Solvation Model based on the Density) and eight density functionals, CAM-B3LYP, LC-ωPBE, M11, MN12SX, N12SX, ωB97, ωB97X, and ωB97XD, were assessed in link with the Def2TZVP basis set for the calculation of the structure of the Leu-Enkephalin Opioid Peptide Neurotransmitter as well as their molecular properties. Through the Conceptual Density Functional Theory (CDFT), the entire chemical descriptors for the system were calculated. The active regions of the molecules necessary for electrophilic, nucleophilic and radical attacks were chosen through linking them with the corresponding Fukui functions. Furthermore, the prediction of the pKa value for the peptide is done with great accuracy as well as the ability of the studied molecule in acting as an efficient inhibitor of the formation of Advanced Glycation Endproducts (AGEs), which comprises of a useful knowledge for the development of drugs for preventing Alzheimer, Diabetes and Parkinson diseases. Lastly, the bioactivity scores for the studied peptides are predicted via various methodologies.

关键词： Leu-Enkephalin Opioid Neurotransmitters Computational Chemistry Conceptual DFT Bioactivity Scores

Chemical Reactivity Theory (CRT) Study of the Melanoidin M8: Local Conceptual Density Functional Theory Descriptors

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Computational Molecular Bioscience 2018年第2期8卷 80-90页

This study evaluated a fixed long-range corrected range-separated hybrid (RSH) density functional associated with the Def2TZVP basis set alongside the Solvation Model based on Density (SMD) for the computation of the structure, molecular properties and chemical reactivity of the M8 intermediate melanoidin pigment. The preference of the active sites pertinent to radical, nucleophilic and electrophilic attacks is made through linking them with the electrophilic and nucleophilic Parr functions, Fukui function indices, and condensed Dual Descriptor. This study showed that the MN12SX density functional is the most suitable one for predicting the chemical reactivity of this system.

关键词： Melanoidin M8 Conceptual DFT Chemical Reactivity Dual Descriptor Parr Function

Chemical Reactivity Properties, Drug-Likeness Features and Bioactivity Scores of the Cholecystokinin Peptide Hormone

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Computational Molecular Bioscience 2019年第2期9卷 41-47页

作者： Norma Flores-Holguín Juan Frau daniel glossman-mitnik Laboratorio Virtual NANOCOSMOS Departamento de Medio Ambiente y Energía Centro de Investigación en Materiales Avanzados Chihuahua Mexico Departament de Química Universitat de les Illes Balears Palma de Mallorca Spain

Five density functionals, CAM-B3LYP, LC-ωPBE, MN12SX, N12SX and ωB97XD, in connection with the Def2TZVP basis set were assessed together with the SMD solvation model for the calculation of the molecular and chemical reactivity properties of the Cholecystokinin peptide hormone (CCK-8) in the presence of water. All the chemical reactivity descriptors for the systems were calculated via Conceptual Density Functional Theory (CDFT). The potential bioavailability and druggability as well as the bioactivity scoresfor CCK-8 were predicted through different methodologies already reported in the literature which have been previously validated during the study of different peptidic systems. The conclusion was that the CCK-8 peptide will be moderately bioactive regarding all the interactions.

关键词： Cholecystokinin Peptide Hormone (CCK-8) Conceptual DFT Chemical Reactivity Drug-likeness Features Bioactivity Scores

Computational Study of the Chemical Reactivity and Bioactivity Rates of Marine Peptides Hemiasterlin and Its A and B Derivatives Used in the Cancer Treatment through Conceptual Density Functional Theory

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Computational Molecular Bioscience 2019年第4期9卷 95-107页

作者： Norma Flores-Holguín Juan Frau daniel glossman-mitnik Laboratorio Virtual NANOCOSMOS Departamento de Medio Ambiente y EnergíaCentro de Investigación en Materiales AvanzadosMiguel de Cervantes 120Complejo Industrial ChihuahuaChihuahua ChihMexico Departament de Química Universitat de les Illes BalearsPalma de MallorcaSpain

This study involved the assessment of the MNI2SX/Def2TZVP/H2O model chemistry to enhance the understanding of the structural composition of the marine peptide Hemiasterlin and its derivatives A and B used in cancer treatment. The Conceptual Density Functional theory was used in the calculation of molecular properties of the system chemical descriptors during the study. Integration of the active molecular regions into their respective Fukui functions was used in the selection of electrophilic and nucleophilic attacks. Additionally, the proposed correlation between global hardness and the pKa was used as the basis of deriving accurate predictions for the pKa values while a homology technique was used in the prediction of bioactivity and bioavailability scores of the peptides under investigation.

关键词： Hemiasterlins Computational Chemistry Conceptual DFT Bioavailability Bioactivity Scores