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Computational Chemical Biology 2021

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Chemical Biology".

Deadline for manuscript submissions: closed (31 March 2022) | Viewed by 9171

Special Issue Editors


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Guest Editor
Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua, Chih 31136, Mexico
Interests: conceptual DFT; computational peptidology; bioavailability; bioactivity scores; ADME

E-Mail Website
Guest Editor
Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua, Chih 31136, Mexico
Interests: molecular modeling; molecular docking; DFT; binding energy; bioavailability; bioactivity scores

Special Issue Information

Dear Colleagues,

The development of efficient computer equipment, computing cluster growth, high-speed networks, and high-performance software have allowed increasing the precision of the prediction of properties for a wide range of applications on organic materials and biological systems.

Molecular modeling tools are extremely helpful in predicting properties and supplying important explanations that allow a complex comprehension of biological systems. The use of simulation techniques leads to an easier discovery of interactions and interaction types between molecular systems. For example, computational chemistry techniques significantly improve the prediction of active sites and finding of groups of geometric and electronic properties for optimal interaction with specific biological targets and an adequate biological response.

These interactions are related to the reactivity properties of the molecular systems involved. Particularly, the conceptual density functional theory has shown an accurate reproduction of interesting properties through the application of different combinations of algorithms, functionals, and theory levels that allow reducing the deviation between desire and expected results.

We invite authors to submit original research that contributes to the development of new methodologies for the improvement of prediction of properties, theoretical features to understand biological systems, and the exploration of biological functions.

Potential topics include but are not limited to:

  • Computational structure–activity relationship;
  • Development of calculations of reactivity properties of ligands and targets;
  • Development of methodologies to improve the properties prediction in biological systems;
  • The role of simulation in biological systems properties prediction;
  • Molecular docking;
  • Molecular dynamics.

Prof. Dr. Daniel Glossman-Mitnik
Dr. Norma Flores-Holguín
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • molecular docking
  • conceptual DFT
  • bioavailability
  • bioactivity scores

Published Papers (3 papers)

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Research

22 pages, 6238 KiB  
Article
Quantum Computational Investigation of (E)-1-(4-methoxyphenyl)-5-methyl-N′-(3-phenoxybenzylidene)-1H-1,2,3-triazole-4-carbohydrazide
by Halil Gökce, Fatih Şen, Yusuf Sert, Bakr F. Abdel-Wahab, Benson M. Kariuki and Gamal A. El-Hiti
Molecules 2022, 27(7), 2193; https://doi.org/10.3390/molecules27072193 - 28 Mar 2022
Cited by 58 | Viewed by 2525
Abstract
The title compound was synthesized and structurally characterized. Theoretical IR, NMR (with the GIAO technique), UV, and nonlinear optical properties (NLO) in four different solvents were calculated for the compound. The calculated HOMO–LUMO energies using time-dependent (TD) DFT revealed that charge transfer occurs [...] Read more.
The title compound was synthesized and structurally characterized. Theoretical IR, NMR (with the GIAO technique), UV, and nonlinear optical properties (NLO) in four different solvents were calculated for the compound. The calculated HOMO–LUMO energies using time-dependent (TD) DFT revealed that charge transfer occurs within the molecule, and probable transitions in the four solvents were identified. The in silico absorption, distribution, metabolism, and excretion (ADME) analysis was performed in order to determine some physicochemical, lipophilicity, water solubility, pharmacokinetics, drug-likeness, and medicinal properties of the molecule. Finally, molecular docking calculation was performed, and the results were evaluated in detail. Full article
(This article belongs to the Special Issue Computational Chemical Biology 2021)
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23 pages, 10510 KiB  
Article
Novel and Potential Small Molecule Scaffolds as DYRK1A Inhibitors by Integrated Molecular Docking-Based Virtual Screening and Dynamics Simulation Study
by Mir Mohammad Shahroz, Hemant Kumar Sharma, Abdulmalik S. A. Altamimi, Mubarak A. Alamri, Abuzer Ali, Amena Ali, Safar Alqahtani, Ali Altharawi, Alhumaidi B. Alabbas, Manal A. Alossaimi, Yassine Riadi, Ahmad Firoz and Obaid Afzal
Molecules 2022, 27(4), 1159; https://doi.org/10.3390/molecules27041159 - 9 Feb 2022
Cited by 10 | Viewed by 3432
Abstract
The dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) is a novel, promising and emerging biological target for therapeutic intervention in neurodegenerative diseases, especially in Alzheimer’s disease (AD). The molMall database, comprising rare, diverse and unique compounds, was explored for molecular docking-based virtual screening [...] Read more.
The dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) is a novel, promising and emerging biological target for therapeutic intervention in neurodegenerative diseases, especially in Alzheimer’s disease (AD). The molMall database, comprising rare, diverse and unique compounds, was explored for molecular docking-based virtual screening against the DYRK1A protein, in order to find out potential inhibitors. Ligands exhibiting hydrogen bond interactions with key amino acid residues such as Ile165, Lys188 (catalytic), Glu239 (gk+1), Leu241 (gk+3), Ser242, Asn244, and Asp307, of the target protein, were considered potential ligands. Hydrogen bond interactions with Leu241 (gk+3) were considered key determinants for the selection. High scoring structures were also docked by Glide XP docking in the active sites of twelve DYRK1A related protein kinases, viz. DYRK1B, DYRK2, CDK5/p25, CK1, CLK1, CLK3, GSK3β, MAPK2, MAPK10, PIM1, PKA, and PKCα, in order to find selective DYRK1A inhibitors. MM/GBSA binding free energies of selected ligand–protein complexes were also calculated in order to remove false positive hits. Physicochemical and pharmacokinetic properties of the selected six hit ligands were also computed and related with the proposed limits for orally active CNS drugs. The computational toxicity webserver ProTox-II was used to predict the toxicity profile of selected six hits (molmall IDs 9539, 11352, 15938, 19037, 21830 and 21878). The selected six docked ligand–protein systems were exposed to 100 ns molecular dynamics (MD) simulations to validate their mechanism of interactions and stability in the ATP pocket of human DYRK1A kinase. All six ligands were found to be stable in the ATP binding pocket of DYRK1A kinase. Full article
(This article belongs to the Special Issue Computational Chemical Biology 2021)
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16 pages, 3481 KiB  
Article
Theoretical Study of the Structural Stability, Chemical Reactivity, and Protein Interaction for NMP Compounds as Modulators of the Endocannabinoid System
by Maricruz Rangel-Galván, María Eugenia Castro, Jose Manuel Perez-Aguilar, Norma A. Caballero, Alejandro Rangel-Huerta and Francisco J. Melendez
Molecules 2022, 27(2), 414; https://doi.org/10.3390/molecules27020414 - 9 Jan 2022
Cited by 7 | Viewed by 2470
Abstract
The cannabinoid receptors (CB1/CB2) and the T-type calcium channels are involved in disorders associated with both physiological pain and depressive behaviors. Valuable pharmacological species carbazole derivatives such as the NMP-4, NMP-7, and NMP-181 (Neuro Molecular Production) regulate both biological entities. In this work, [...] Read more.
The cannabinoid receptors (CB1/CB2) and the T-type calcium channels are involved in disorders associated with both physiological pain and depressive behaviors. Valuable pharmacological species carbazole derivatives such as the NMP-4, NMP-7, and NMP-181 (Neuro Molecular Production) regulate both biological entities. In this work, DFT calculations were performed to characterize theoretically their structural and chemical reactivity properties using the BP86/cc-pVTZ level of theory. The molecular orbital contributions and the chemical reactivity analysis reveal that a major participation of the carbazole group is in the donor-acceptor interactions of the NMP compounds. The DFT analysis on the NMP compounds provides insights into the relevant functional groups involved during the ligand-receptor interactions. Molecular docking analysis is used to reveal possible sites of interaction of the NMP compounds with the Cav3.2 calcium channel. The interaction energy values and reported experimental evidence indicate that the site denominated as “Pore-blocking”, which is formed mainly by hydrophobic residues and the T586 residue, is a probable binding site for the NMP compounds. Full article
(This article belongs to the Special Issue Computational Chemical Biology 2021)
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