Computational Approaches in Drug Discovery and Design
A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Computational and Theoretical Chemistry".
Deadline for manuscript submissions: 15 June 2024 | Viewed by 4144
Special Issue Editor
Interests: protein-ligand interaction; scoring function; force field parameter; gaussian basis set; QSAR; quantum chemical computation; molecular dynamics simulation; molecular docking
Special Issue Information
Dear Colleagues,
Various computational methods have been applied to medicinal chemistry for drug design and discovery, continuously enhancing the performance of computer-aided drug design (CADD). The calculations of protein–ligand bindings, relying on the three-dimensional structure of the target protein, are associated with structure-based drug design which uses molecular docking, molecular dynamics simulation, and quantum chemistry. The searching and design of similar molecular structures based on well-identified ligand forms another category, called ligand-based drug design which is linked to quantitative structure–activity relationship (QSAR) and pharmacophore modeling. Computations were also applied to further validate drug molecules for absorption, distribution, metabolism, excretion, and toxicity (ADMET), as well as druglikeness and pan-assay interference compounds (PAINS). With the help of available information and well-built databases, machine learning methods can be used in any stage of drug design and development. This Special Issue welcomes the submission of any study on the development of computational methods and algorithms, databases, and informatics, as well as approaches combining or integrating multiple computational treatments used in drug design and discovery. Case studies using any new methods or combined approaches are also welcome.
Prof. Dr. Shijun Zhong
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. 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
- combined and integrated approaches in CADD
- QM/MM and quantum chemical computations for protein–ligand binding
- scoring function
- binding free energy
- target identification
- molecular docking molecular dynamics simulation
- machine learning or deep learning
- data fitting
- database
- pattern recognition
- druglikeness
- drug design or drug discovery
Planned Papers
The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.
Title: Structure-based virtual screening for MTase inhibitors of SARS-CoV-2 nsp14 and nsp16
Authors: Kejue Wu; Yinfeng Guo; Tiefeng Xu; Weifeng Huang; Deyin Guo; Liu Cao; Jinping Lei
Affiliation: Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, P. R. China
Abstract: The ongoing COVID-19 pandemic still threats human health over the world. The methyltransferase (MTase) of SARS-CoV-2, specifically nsp14 and nsp16, play crucial roles in the methylation of the N7 and 2'-O positions of viral RNA, making them promising targets for the development of antiviral drugs. In this work, we performed the structure-based virtual screening for nsp14 and nsp16 using the rigorous screening workflow (HTVS, SP, XP) of Schrödinger software, and carried out biochemical assays for identification of potential MTase inhibitors. For nsp14, we screened 239,000 molecules, leading to the identification of 3 hits (Y207-3841, ZINC000009481760, D306-0032) showing N7-MTase inhibition rates greater than 60% under a concentration of 50 µM. For nsp16, the screening of 210,000 molecules from ZINC15 led to the discovery of 3 hit compounds (ZINC55183218, ZINC4073149, ZINC95190922) exhibiting more than 45% 2'-O-MTase inhibition under 50 µM. These 6 compounds with moderate MTase inhibitory activities could be used as novel candidates for further development of anti-SARS-CoV-2 drugs.
