BP International: molecular modeling

Showing posts with label molecular modeling. Show all posts

Friday, 7 March 2025

Interactions between Dihydroorotate Dehydrogenase and a Series of Inhibitors of Pyrrole Derivatives for Malaria Treatment: A Study Using Molecular Docking | Chapter 5 | Chemical and Materials Sciences: Research Findings Vol. 1

Despite the efforts and resources devoted to the fight against malaria, also the knowledge acquired on the various species of plasmodium, of which Plasmodium faciparum is the most common in humans, malaria remains the world's leading parasitic endemic. Malaria, although a curable disease, continues to be the most important infectious disease in terms of incidence and mortality worldwide. It is a potentially fatal disease caused by parasites transmitted to people through the bites of infected female Anopheles mosquitoes. This disease affects more than 216 million people and kills a million, mainly children and pregnant women. Anti-malaria therapy finds itself confronted with drug-resistant strains, hence the urgency of finding new targets and new anti-infectious agents. Dihydroorotate dehydrogenase (DHODH) is an essential enzyme for the design of new antimalarial drugs. Using a Computer Aided Molecular Design (CAMD) reaction approach, a series of 17 molecules from the pyrrole family, inhibitors of (DHODH) was designed within the protein (PDB code: 6VTN). These molecules with known IC₅₀ were selected to build an RQSAR model presenting a linear correlation between the Gibbs energy (∆∆G), the complexes formed and the experimental inhibition potential (pIC₅₀^exp): pIC₅₀^exp = - 0.2909 × ∆∆G + 7.7715 ; R² = 0,97. we subsequently carried out a study on the catalytic residues (interaction by residue) in order to exploit the different interactions (enzyme: inhibitor). The predictive power of the QSAR model was validated by the generation of 3D-QSAR pharmacophores (PH4): pIC₅₀^exp=0.9939 × pIC₅₀^est+0.0421; R² = 0.92. The different methods used, namely molecular docking, interaction energy per residue and the pharmacophore model, allowed us to establish the correlation between biological activity and a set of real numbers called descriptors, to predict the mode of binding of the ligands, the free energies of formation of the different complexes.

Author (s) Details

Niaré Adama
Fundamental and Applied Physics Laboratory (FAPL), University of Nangui Abrogoua, Abidjan 02, Côte d’Ivoire.

Attia Yapo John Alex
Fundamental and Applied Physics Laboratory (FAPL), University of Nangui Abrogoua, Abidjan 02, Côte d’Ivoire.

Djako Akassa Marius Bernard
Fundamental and Applied Physics Laboratory (FAPL), University of Nangui Abrogoua, Abidjan 02, Côte d’Ivoire.

Kambiré Sobamfou Marius
General Chemistry Laboratory (GCL), University of Péléforo Gon Coulibaly, BP 1328 Korhogo, Côte d’Ivoire.

Dembélé Georges Stéphane
Laboratory of Thermodynamics and Physico-chemistry of the Environment, UFR SFA, Nangui University 02 BP 801Abidjan 02, Côte-d’Ivoire.

Kouadio Assandé Moise
Fundamental and Applied Physics Laboratory (FAPL), University of Nangui Abrogoua, Abidjan 02, Côte d’Ivoire.

Koné Mamadou Guy-Richard
Laboratory of Thermodynamics and Physico-chemistry of the Environment, UFR SFA, Nangui University 02 BP 801Abidjan 02, Côte-d’Ivoire.

Yves Kily Hervé Fagnidi
Department of Science and Technology, University Alassane Ouattara, Bouaké 1801, Côte d’Ivoire.

Soro Doh
Laboratory of Thermodynamics and Physico-chemistry of the Environment, UFR SFA, Nangui University
02 BP 801Abidjan 02, Côte-d’Ivoire.

Please see the book here:- https://doi.org/10.9734/bpi/cmsrf/v1/4608

Monday, 4 September 2023

Some New Aspects in the Structure and Functional Activity of Sea Anemone Neurotoxins | Chapter 5 | Novel Aspects on Chemistry and Biochemistry Vol. 6

The aim concerning this work was to rehash the literature and our own experimental dossier obtained over ancient times four decades on the structure-working relationships of all surf anemone neurotoxins described to date, particularly interacting accompanying various subtypes of physical ability-gated sodium channels (VGSCs/NaVs). Disruption of the working activity of these biological aims causes many severe pathologies, while everyday toxins, containing those of sea anemones, concede possibility prove to be a hopeful tool in pharmacological research, in addition to in the study of the molecular arrangement and mechanisms of NaVs functioning. The review likewise focuses on the several type 2 neurotoxins from the sea growth Heteractis crispa, five structurally homologous, and individual unique double-chain neurotoxin that we first labeled in sea anemones. Due to the misfortune of the functionally significant Arg14 residue, this peptide homolog of the staying Heteractis neurotoxins completely extinct its toxicity, but employed the ability to modulate various subtypes of NaVs, which is characteristic of type 2 neurotoxins. The review examines the results of in vivo, in vitro, and in silico studies of the interplay of neurotoxins with their organic targets, sodium channels of several NaV subtypes.

Author(s) Details:

Margarita Monastyrnaya,
G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Science, 690022 Vladivostok, Russia.

Rimma Kalina,
G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Science, 690022 Vladivostok, Russia.

Emma Kozlovskaya,
G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Science, 690022 Vladivostok, Russia.

Please see the link here: https://stm.bookpi.org/NACB-V6/article/view/11717

Sunday, 12 September 2021

Determining the Informatics and Conceptual DFT Study of Pigments Derived from Carotenoids of Marine Origin | Chapter 11 | New Innovations in Chemistry and Biochemistry Vol. 1

The goal of this study was to evaluate the behaviour of five density functionals, CAM-B3LYP, LC-HPBE, MN12SX, N12SX, and B97XD, when used in conjunction with the Def2TZVP basis set and the SMD solvation model to calculate the molecular properties, chemical reactivities, and solubilities of some pigments derived from Astaxanthin, -Cryptoxanthin, Fucoxant (hexane, methanol, ethanol and water). Concep- tual Density Functional Theory was used to calculate all of the chemical reactivity characteristics for the systems (CDFT). Finally, the prospective bioavailability and druggability of the marine carotenoid pigments, as well as the bioactivity scores, were predicted using several methods already reported in the literature and previously verified during the research of other natural products originating from marine sources.

Author (S) Details

Norma Flores-Holguin
Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energia, Centro de Investigacion en Materiales Avanzados, Chihuahua, Chih 31136, Mexico.

Juan Frau
Departament de Quimica, Facultad de Ciencias, Universitat de les Illes Balears, Palma de Mallorca, E-07122, Spain.

Daniel Glossman-Mitnik
Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energia, Centro de Investigacion en Materiales Avanzados, Chihuahua, Chih 31136, Mexico.

View Book :- https://stm.bookpi.org/NICB-V1/article/view/3354

Study on the Computational Nutraceutics of a Citrus Flavonoid: An Approach Using Conceptual Density Functional Theory (CDFT) | Chapter 10 | New Innovations in Chemistry and Biochemistry Vol. 1

The goal of this study is to evaluate the M06 density functional family for calculating the molecular structure and characteristics of the Naringin flavonoid, as well as the chemical reactivity descriptors, using the Conceptual DFT (CDFT) technique. Using the Fukui function indices and the dual descriptor f(2), the active sites for nucleophilic and electrophilic assaults have been found (r). As a last verification of the validity of the previous technique, the descriptors produced using vertical energy values were compared to those derived using the Koopmans' theorem approximation.

Study on the Molecular Reactivity of the Dansylglycine in Water and Dioxane Estimated through Conceptual DFT | Chapter 9 | New Innovations in Chemistry and Biochemistry Vol. 1

The structure, molecular properties, and chemical reactivity of the M8 intermediate melanoidin pigment in the presence of water and dioxane were computed using a fixed long-range corrected range-separated hybrid (RSH) density functional associated with the Def2TZVP basis set and the SMD solvation model. The electrophilic and nucleophilic Parr functions, Fukui function indices, and condensed Dual Descriptor, which are chemical reactivity descrip- tors derived from Conceptual Density Functional Theory, are used to link the active sites relevant to radical, nucleophilic, and electrophilic assaults. The results of this study back up previous findings that the MN12SX density functional is the best at predicting the chemical reactivity of this molecule in both solvents.

About the Computational Prediction of the Maximum Absorption Wavelengths of Indigo in Different Solvents with the Minnesota Family of Density Functionals | Chapter 8 | New Innovations in Chemistry and Biochemistry Vol. 1

The results of using the Minnesota family of density functionals (M05, M05-2X, M06, M06L, M06-2X, and M06-HF) for the calculation of the UV-Vis of the Indigo molecule in different polarity solvents using Time-Dependent Density Functional Theory (TD-DFT) and the Polarized Continuum Model are presented in this paper (PCM). The projected maximum absorption wavelengths for each density functional on each solvent were compared to experimental data.

Monday, 16 August 2021

The Reactivity Sites of Amyloid -Peptides A40 and A42 in Alzheimer's Disease: Computational Prediction | Chapter 6 | Challenges and Advances in Chemical Science Vol. 2

Alzheimer's disease is a degenerative nervous system ailment caused by extracellular senile plaques. Extracellular senile plaques are usually made up of 40-42 residues of -peptides, which are amino acid-containing polypeptides. The Theory of Chemical Reactivity, MEDT (Molecular Electron Density Theory), and Conceptual DFT were used to find descriptors that allowed QM:MM calculations with the ONIOM methodology to predict the sites of reactivity of the Alzheimer amyloid β-peptides Aβ40 and Aβ42.

Author (S) Details

Juan Frau
Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain.

Daniel Glossman-Mitnik
Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Laboratorio Virtual Nanocosmos, Chihuahua, Chih 31136, Mexico.

View Book :- https://stm.bookpi.org/CACS-V2/article/view/2655

Revisiting the Validation of the KID Methodology through CDFT Descriptors of Fluorescent DNA Staining Dyes | Chapter 5 | Challenges and Advances in Chemical Science Vol.

The calculation of numerous global descriptors originating from Conceptual DFT is used to verify the fulfilment of the "Koopmans' theorem in DFT" or KID technique. They were estimated using the HOMO and LUMO frontier orbitals, as well as a (triangle)SCF technique. Three fluorescent DNA staining dyes, Hoechst 33258, Hoechst 33342, and Hoechst 34580, were investigated as part of the latest Minnesota family of density functionals. A set of descriptors has been established based on the acquired Conceptual DFT indices in order to determine the accuracy of each model chemical used in the verification of the given theorem. It is demonstrated that only range-separated hybrids (RSH) density functionals are suitable for this purpose, whereas local density functionals are useless.

Author (S) Details

Daniel Glossman-Mitnik
Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energ´?a, Centro de Investigacion en Materiales Avanzados, Chihuahua, Chih 31136, Mexico.

View Book :- https://stm.bookpi.org/CACS-V2/article/view/2654

A Short Update on Cheminformatics for Prompting the Process of Drug Design and Discovery | Chapter 4 | Challenges and Advances in Chemical Science Vol. 2

Cheminformatics is one of the newest topics in science, bringing cutting-edge state-of-the-art knowledge to the table. This paper provides an updated report on new publications in Cheminformatics and related topics that may be useful throughout the drug design and discovery process, as well as the development of therapeutic medications.