Recent Advances in Structure-Based Inhibitor/Drug Design

A special issue of Biomolecules (ISSN 2218-273X).

Deadline for manuscript submissions: 31 March 2027 | Viewed by 1372

Editors


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Guest Editor
1. National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Chinese Academy of Agriculture Science, Nanning 530004, China
2. Rocky Mount Life Sciences Institute, Rocky Mount, NC 27804, USA
Interests: structural and dynamic studies of protein and DNA by solution NMR spectroscopy; computer modeling of protein-DNA, protein-drug complex, bioinformatics, as well as interactions of protein-protein, and protein-drug; the studies of introduction of graphic methods into biological systems
Special Issues, Collections and Topics in MDPI journals

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Guest Editor Assistant
Guangxi Academy of Agricultural Sciences, Nanning, China
Interests: structural biology; NMR spectroscopy; molecular docking and ligand interaction

Special Issue Information

Dear Colleagues,

This Special Issue aims to report recent progress in the field of structure-based inhibitor and drug design, a pivotal approach that relies on the precise three-dimensional structures of therapeutic targets to rationally develop potent and selective compounds. By elucidating biomolecular interactions and the structures and functions of biomolecules through techniques such as X-ray crystallography, NMR, and molecular dynamics simulations, this strategy enables the rational design of molecules that selectively bind and modulate target functions. Additionally, the integration of bioinformatics, Artificial Intelligence (AI), Machine Learning (ML), and Deep Learning (DL) is accelerating the prediction and optimization of drug candidates. This Special Issue will collect the latest research and review papers focused on these advances, providing valuable insights to promote future drug discovery and development.

Submissions may include original research, comprehensive reviews, or perspectives.

Prof. Dr. Guoping Zhou
Guest Editor

Dr. Si‑Ming Liao
Guest Editor Assistant

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 250 words) can be sent to the Editorial Office for assessment.

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-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomolecules is an international peer-reviewed open access monthly 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

  • biomolecular interactions
  • structures and functions of biomolecules
  • nuclear magnetic resonance (NMR)
  • X-ray crystallography
  • bioinformatics
  • structural studies using Artificial Intelligence (AI)
  • machine learning (ML)
  • deep learning (DL)
  • molecular dynamics simulation (MDS)

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Published Papers (1 paper)

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Review

23 pages, 2612 KB  
Review
Epigallocatechin Gallate as a State-Dependent Modulator of Amyloid-β: Molecular Simulation-Guided Mechanistic Synthesis for Structure-Based Inhibitor Design
by Budimir S. Ilić
Biomolecules 2026, 16(5), 734; https://doi.org/10.3390/biom16050734 - 17 May 2026
Viewed by 548
Abstract
Amyloid-β (Aβ) aggregation is a central mechanistic feature of Alzheimer’s disease, involving heterogeneous conformational ensembles that evolve through monomeric, oligomeric, and fibrillar states. Understanding how small molecules modulate these state-dependent processes remains a major challenge in medicinal chemistry. This review [...] Read more.
Amyloid-β (Aβ) aggregation is a central mechanistic feature of Alzheimer’s disease, involving heterogeneous conformational ensembles that evolve through monomeric, oligomeric, and fibrillar states. Understanding how small molecules modulate these state-dependent processes remains a major challenge in medicinal chemistry. This review examines the molecular mechanisms by which (-)-epigallocatechin-3-gallate (EGCG) perturbs Aβ aggregation, with a focus on insights derived from molecular dynamics (MD) simulations integrated with experimental data. MD studies employing structural, dynamical, and interaction-based descriptors (e.g., β-sheet content, contact maps, and salt bridge persistence) reveal that EGCG acts as a state-dependent modulator: it redistributes monomeric ensembles by masking aggregation-prone regions, induces topology switching in oligomers that suppresses seeding competence, and destabilizes protofibrillar β-sheet networks through interfacial and node-targeting interactions. Methodological analysis highlights the importance of force field selection, sampling depth, and aggregate model dependence, leading to a hierarchy of mechanistic confidence that distinguishes well-supported trends from model-specific observations. From a medicinal chemistry perspective, EGCG is best interpreted as a mechanistic probe rather than as a lead compound, informing the design of biostable modulators through principles such as bioisosteric replacement, topology control, and interfacial targeting. Collectively, this work provides a framework for translating the state-dependent aggregation mechanisms into rational therapeutic strategies. Full article
(This article belongs to the Special Issue Recent Advances in Structure-Based Inhibitor/Drug Design)
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