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Computational Methods in Drug Design and Food Chemistry II

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

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 3837

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Guest Editor
1. Dipartimento di Scienze della Salute, Università “Magna Græcia” di Catanzaro, 88100 Catanzaro, Italy
2. Net4Science Academic Spin-Off, Università “Magna Græcia” di Catanzaro, 88100 Catanzaro, Italy
Interests: computational chemistry; medicinal chemistry; infectiouse disease; drug repurposing; virtual screening; molecular dynamics; antioxidant activity
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Special Issue Information

Dear Colleagues,

Today, the contribution of computational methodologies to drug discovery is no longer in doubt, and all major world pharmaceutical, academic, and biotechnology companies use computational design tools. Computer-aided drug design includes computational methods and resources that are used to facilitate the design and discovery of new bioactive chemical entities, including natural compounds with potentially nutraceutical activity.

The confirmation of the usefulness of these methodologies came in 2013, when the Nobel prize for chemistry was awarded to Martin Karplus, Michael Levitt, and Arieh Warshel “for the development of multiscale models for complex chemical systems”; thus, from this point of view, chemistry is an experimental science, but theoretical chemists are providing answers to questions about how to design drugs to fit with their target molecules.

In this Special Issue, we encourage authors to submit manuscripts in the form of a research paper, review, or communication that contributes positively in each aspect of medicinal chemistry and drug discovery, from the design of high-throughput screening libraries to providing estimations of the molecular properties required for drug molecules, improving our understanding of how they interact with biological targets of pharmaceutical interest.

This Special Issue will accept original research papers, high-quality reviews, and communications in the field of computational methods in drug design and food chemistry.

Dr. Giosuè Costa
Dr. Isabella Romeo
Guest Editors

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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.

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Keywords

  • Molecular docking and structure-based virtual screening
  • Fragment-based drug design
  • Advances in molecular dynamics simulations and free-energy calculations applicable in drug design
  • QM applications in drug discovery
  • Pharmacophore modeling
  • In silico absorption, distribution, metabolism, and excretion (ADME)
  • Computational methods for drug target profiling and polypharmacology
  • Integrating structure- and ligand-based approaches for computer-aided drug design
  • Multi-target rational drug design
  • Computer-aided drug repurposing
  • In silico toxicology

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Published Papers (1 paper)

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Research

18 pages, 4807 KiB  
Article
Discovery of Potential Antiviral Compounds against Hendra Virus by Targeting Its Receptor-Binding Protein (G) Using Computational Approaches
by Faisal Ahmad, Aqel Albutti, Muhammad Hamza Tariq, Ghufranud Din, Muhammad Tahir ul Qamar and Sajjad Ahmad
Molecules 2022, 27(2), 554; https://doi.org/10.3390/molecules27020554 - 16 Jan 2022
Cited by 16 | Viewed by 3155
Abstract
Hendra virus (HeV) belongs to the paramyxoviridae family of viruses which is associated with the respiratory distress, neurological illness, and potential fatality of the affected individuals. So far, no competitive approved therapeutic substance is available for HeV. For that reason, the current research [...] Read more.
Hendra virus (HeV) belongs to the paramyxoviridae family of viruses which is associated with the respiratory distress, neurological illness, and potential fatality of the affected individuals. So far, no competitive approved therapeutic substance is available for HeV. For that reason, the current research work was conducted to propose some novel compounds, by adopting a Computer Aided Drug Discovery approach, which could be used to combat HeV. The G attachment Glycoprotein (Ggp) of HeV was selected to achieve the primary objective of this study, as this protein makes the entry of HeV possible in the host cells. Briefly, a library of 6000 antiviral compounds was screened for potential drug-like properties, followed by the molecular docking of short-listed compounds with the Protein Data Bank (PDB) structure of Ggp. Docked complexes of top two hits, having maximum binding affinities with the active sites of Ggp, were further considered for molecular dynamic simulations of 200 ns to elucidate the results of molecular docking analysis. MD simulations and Molecular Mechanics Energies combined with the Generalized Born and Surface Area (MMGBSA) or Poisson–Boltzmann and Surface Area (MMPBSA) revealed that both docked complexes are stable in nature. Furthermore, the same methodology was used between lead compounds and HeV Ggp in complex with its functional receptor in human, Ephrin-B2. Surprisingly, no major differences were found in the results, which demonstrates that our identified compounds can also perform their action even when the Ggp is attached to the Ephrin-B2 ligand. Therefore, in light of all of these results, we strongly suggest that compounds (S)-5-(benzylcarbamoyl)-1-(2-(4-methyl-2-phenylpiperazin-1-yl)-2-oxoethyl)-6-oxo-3,6-dihydropyridin-1-ium-3-ide and 5-(cyclohexylcarbamoyl)-1-(2-((2-(3-fluorophenyl)-2-methylpropyl)amino)-2-oxoethyl)-6-oxo-3,6-dihydropyridin-1-ium-3-ide could be considered as potential therapeutic agents against HeV; however, further in vitro and in vivo experiments are required to validate this study. Full article
(This article belongs to the Special Issue Computational Methods in Drug Design and Food Chemistry II)
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