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Computational Studies in Drug Design and Discovery

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Informatics".

Deadline for manuscript submissions: 31 July 2024 | Viewed by 940

Special Issue Editor


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Guest Editor
Department of Pharmacy, University of Genoa, Viale Benedetto XV, 16132 Genoa, Italy
Interests: medicinal chemistry; GPCR; enzyme; neuroprotective agents; cystic fibrosis; cancer; molecular modeling; virtual screening; homology modeling; repositioning
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Special Issue Information

Dear Colleagues,

Molecular modelling approaches in drug design, such as ligand- and structure-based computational methods, represent widely exploited tools to guide the discovery of novel bioactive molecules.

The identification of novel putative drugs requires experimental assays to validate the therapeutic effectiveness as well as the safety profile of the newly developed compounds. In this context, computational studies represent an intriguing opportunity to accelerate the hit-to-lead and lead optimization process and to lower the costs of drug discovery.

The rapid development of new approaches to better explore novel druggable targets has uncovered new promising perspectives for the rational design and optimization of drug candidates. Structure-based strategies including homology modelling and molecular dynamics techniques as well as ligand-based methods are known exploited tools in the modern medicinal chemistry scenario. Drug repositioning also has emerged as a promising approach to accelerate the drug design and development process. This kind of strategy offers a cost-effective and time-efficient solution for the identification of novel bioactive compounds endowed with a broader spectrum of activity with respect to those already known or described in the literature.

This Special Issue will cover all different aspects of computational methods in drug design leading to the identification of novel hit compounds or optimized analogues, as confirmed by following experimental data. This Special Issue invites both reviews and original articles that shed light on the rational design and hit-to-lead optimization process aided by molecular modelling techniques. Experimental assays validating the whole study are required, giving strong support to the applied strategy. This Special Issue aims to summarize the state of the art, and the latest findings published in medicinal chemistry thanks to the computer-assisted drug design. 

Dr. Elena Cichero
Guest Editor

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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
  • homology modeling
  • repositioning
  • virtual screening
  • QSAR
  • molecular dynamics
  • ADME prediction
 

Published Papers (1 paper)

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Research

23 pages, 10610 KiB  
Article
Rationally Designed Novel Antimicrobial Peptides Targeting Chitin Synthase for Combating Soybean Phytophthora Blight
by Yue Ran, Kiran Shehzadi, Jian-Hua Liang and Ming-Jia Yu
Int. J. Mol. Sci. 2024, 25(6), 3512; https://doi.org/10.3390/ijms25063512 - 20 Mar 2024
Viewed by 627
Abstract
Soybean phytophthora blight is a severe menace to global agriculture, causing annual losses surpassing USD 1 billion. Present crop loss mitigation strategies primarily rely on chemical pesticides and disease-resistant breeding, frequently surpassed by the pathogens’ quick adaptive evolution. In this urgent scenario, our [...] Read more.
Soybean phytophthora blight is a severe menace to global agriculture, causing annual losses surpassing USD 1 billion. Present crop loss mitigation strategies primarily rely on chemical pesticides and disease-resistant breeding, frequently surpassed by the pathogens’ quick adaptive evolution. In this urgent scenario, our research delves into innovative antimicrobial peptides characterized by low drug resistance and environmental friendliness. Inhibiting chitin synthase gene activity in Phytophthora sojae impairs vital functions such as growth and sporulation, presenting an effective method to reduce its pathogenic impact. In our study, we screened 16 previously tested peptides to evaluate their antimicrobial effects against Phytophthora using structure-guided drug design, which involves molecular docking, saturation mutagenesis, molecular dynamics, and toxicity prediction. The in silico analysis identified AMP_04 with potential inhibitory activity against Phytophthora sojae’s chitin synthase. Through three rounds of saturation mutagenesis, we pin-pointed the most effective triple mutant, TP (D10K, G11I, S14L). Molecular dynamic simulations revealed TP’s stability in the chitin synthase-TP complex and its transmembrane mechanism, employing an all-atom force field. Our findings demonstrate the efficacy of TP in occupying the substrate-binding pocket and translocation catalytic channel. Effective inhibition of the chitin synthase enzyme can be achieved. Specifically, the triple mutant demonstrates enhanced antimicrobial potency and decreased toxicity relative to the wild-type AMP_04, utilizing a mechanism akin to the barrel-stave model during membrane translocation. Collectively, our study provides a new strategy that could be used as a potent antimicrobial agent in combatting soybean blight, contributing to sustainable agricultural practices. Full article
(This article belongs to the Special Issue Computational Studies in Drug Design and Discovery)
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