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Recent Advances in Computer-Aided Drug Design and Drug Discovery

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

Deadline for manuscript submissions: 31 December 2024 | Viewed by 492

Special Issue Editors


E-Mail Website
Guest Editor
School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
Interests: computer-aided drug design; computational biology; multi-scale modelling

E-Mail Website
Guest Editor
NYU-ECU Center for Computational Chemistry, NYU Shanghai, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
Interests: computational chemistry; MD simulation; computational drug design; protein–protein interaction; free energy calculation

Special Issue Information

Dear Colleagues,

Computer-Aided Drug Designing (CADD) has gained wide popularity among biologists and chemists as a part of an interdisciplinary drug discovery approach. It plays a vital role in the discovery, design and analysis of drugs in the pharmaceutical industry. It is extensively used to reduce costs and time and speed up the early-stage development of biologically new active molecules. Several approved drugs have been developed with the aid of CADD. In this Special Issue, we will present manuscripts on the following types of CADD: Structure-Based Drug Designing (SBDD) including molecular docking and molecular dynamic simulations, Ligand-Based Drug Designing (LBDD) including quantitative structure–activity relationship (QSAR) modelling, Pharmacophore-based drug designing (PBDD), and Fragment-Based Drug Designing (FBDD), in addition to the theory, including artificial intelligence (AI), behind the types of CADD and their applications.

Dr. **** Lei
Prof. Dr. John Zhang
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at mdpi.longhoe.net 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

  • computer-aided drug design
  • structure-based drug design
  • ligand-based drug design
  • fragment-based drug design
  • pharmacophore
  • QSAR
  • molecular modelling
  • artificial intelligence

Published Papers (1 paper)

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Research

20 pages, 32505 KiB  
Article
Unraveling the Binding Mode of Cyclic Adenosine–Inosine Monophosphate (cAIMP) to STING through Molecular Dynamics Simulations
by Meiting Wang, Baoyi Fan, Wenfeng Lu, Ulf Ryde, Yuxiao Chang, Di Han, Jiarui Lu, Taigang Liu, Qinghe Gao, Changpo Chen and Yongtao Xu
Molecules 2024, 29(11), 2650; https://doi.org/10.3390/molecules29112650 - 4 Jun 2024
Viewed by 378
Abstract
The stimulator of interferon genes (STING) plays a significant role in immune defense and protection against tumor proliferation. Many cyclic dinucleotide (CDN) analogues have been reported to regulate its activity, but the dynamic process involved when the ligands activate STING remains unclear. In [...] Read more.
The stimulator of interferon genes (STING) plays a significant role in immune defense and protection against tumor proliferation. Many cyclic dinucleotide (CDN) analogues have been reported to regulate its activity, but the dynamic process involved when the ligands activate STING remains unclear. In this work, all-atom molecular dynamics simulations were performed to explore the binding mode between human STING (hSTING) and four cyclic adenosine–inosine monophosphate analogs (cAIMPs), as well as 2′,3′-cGMP-AMP (2′,3′-cGAMP). The results indicate that these cAIMPs adopt a U-shaped configuration within the binding pocket, forming extensive non-covalent interaction networks with hSTING. These interactions play a significant role in augmenting the binding, particularly in interactions with Tyr167, Arg238, Thr263, and Thr267. Additionally, the presence of hydrophobic interactions between the ligand and the receptor further contributes to the overall stability of the binding. In this work, the conformational changes in hSTING upon binding these cAIMPs were also studied and a significant tendency for hSTING to shift from open to closed state was observed after binding some of the cAIMP ligands. Full article
(This article belongs to the Special Issue Recent Advances in Computer-Aided Drug Design and Drug Discovery)
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