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Molecular Docking Method and Application
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Molecular Docking Method and Application

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: 20 July 2026 | Viewed by 2467

Special Issue Editor

Dr. Yigui Wang

E-Mail Website
Guest Editor
Department of Chemistry and Biochemistry, Southern Connecticut State University, New Haven, CT 06515, USA
Interests: biophysics; molecular docking; drug discovery

Special Issue Information

Dear Colleagues,

Molecular docking has become an integral part of drug discovery. Traditional drug candidates can be rapidly evaluated using molecular docking to obtain docking scores and gain insights into molecular interactions. Molecular docking is also used in biochemistry classrooms as an effective tool for teaching biochemistry. With the availability of large compound databases and crystal structures of biological drug targets, ligand-based virtual screening (LBVS) and structure-based virtual screening (SBVS), together with molecular docking approaches, are widely employed to find identify potential drug leads or hits. Fast and reliable docking algorithms continue to be developed to meet the growing demands of both industrial and academic communities. The contribution of ligand conformations or poses can be estimated using pose scores, and target flexibility can also be considered through various approaches, among which molecular dynamics simulations are commonly used. Recently, machine learning (ML) has gained momentum as a complementary approach for predicting potential drug structures.

This Special Issue, “Molecular Docking Method and Application”, covers all aspects of molecular docking advancements.

Dr. Yigui Wang
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 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-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.

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Keywords

  • drug discovery
  • docking scores
  • docking poses
  • traditional methods of drug discovery
  • ligand-based virtual screening (LBVS)
  • structure-based virtual screening (SBVS)
  • machine learning (ML)

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Published Papers (3 papers)

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Research

24 pages, 5382 KB  
Article
Computational Identification of Triphala-Derived Sterol Compounds as Putative Agonists of the Human Takeda G Protein-Coupled Receptor (TGR5)
by Yathindra Maruthi Prasad, Sneha Ramaiah Gowda, Nandita Shantamurthy, Allwin Ebinesar Jacob Samuel Sehar, Sirajunnisa Abdul Razack, Somdet Srichairatanakool and Yuvaraj Ravikumar
Int. J. Mol. Sci. 2026, 27(7), 3130; https://doi.org/10.3390/ijms27073130 - 30 Mar 2026
Viewed by 485
Abstract
The presence of an unbalanced gut microbiome and the dysregulation of bile acid signalling are considered pivotal causes of various inflammation-based diseases. The Takeda G protein-coupled receptor (TGR5), TGR5 is a bile acid-responsive receptor that modulates inflammatory signalling pathways, making it an enticing [...] Read more.
The presence of an unbalanced gut microbiome and the dysregulation of bile acid signalling are considered pivotal causes of various inflammation-based diseases. The Takeda G protein-coupled receptor (TGR5), TGR5 is a bile acid-responsive receptor that modulates inflammatory signalling pathways, making it an enticing molecular target for the discovery of novel anti-inflammatory agents. Herein, a comprehensive in silico approach was employed to identify potential TGR5 agonists from sterol-rich phytocompounds present in Triphala, a traditional polyherbal formulation. Using in silico computational methods, such as molecular docking and molecular dynamics simulations (MDS), we screened the putative agonistic potential of 10 phytocompounds obtained from Terminalia chebula, Terminalia bellirica, and Phyllanthus emblica against the crystal structure of human TGR5 (PDB ID: 7XTQ). Based on binding energy and molecular interactions, ergosterol (−12.34 ± 0.17 kcal/mol) and stigmasterol (−10.35 ± 0.04 kcal/mol) were predicted to be the top and best compounds. Furthermore, the stability of these two compounds in the docked complex was analysed using MDS for 200 ns. The mean Cα RMSD values were 0.22 ± 0.02 nm for both ergosterol- and stigmasterol-bound complexes, compared to 0.21 ± 0.02 nm for the unbound apo protein. Further, the molecular mechanics/Poisson–Boltzmann surface area (MMPBSA) analysis revealed that ergosterol exhibited binding free energy (−139.868 ± 12.318 kJ/mol) comparable to that of the co-crystallised ligand R399 −93.424 ± 8.919 kJ/mol. In silico ADMET predictions indicated acceptable drug-like properties and low toxicity for both compounds. Collectively, these computational findings suggest that ergosterol is a promising putative TGR5 agonist, warranting further experimental validation of its potential role in modulating inflammation-related pathways. Full article
(This article belongs to the Special Issue Molecular Docking Method and Application)
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31 pages, 9688 KB  
Article
Integration of Network Pharmacology and Molecular Docking Together with an In Vitro Nitric Oxide Inhibition for the Insight for Antipyretic Effects of Benjalokawichian, the Thai Traditional Polyherbal Remedy
by Chinnaphat Chaloemram, Ruchilak Rattarom, Anake Kijjoa and Somsak Nualkaew
Int. J. Mol. Sci. 2026, 27(6), 2697; https://doi.org/10.3390/ijms27062697 - 16 Mar 2026
Viewed by 1156
Abstract
Benjalokawichian (BLW) is a classic antipyretic polyherbal remedy used in Thai traditional medicine (TTM) to reduce toxic fever (TF). This study aimed to shed light on the mechanisms of action and identify bioactive components of BLW responsible for TF treatment. The methods that [...] Read more.
Benjalokawichian (BLW) is a classic antipyretic polyherbal remedy used in Thai traditional medicine (TTM) to reduce toxic fever (TF). This study aimed to shed light on the mechanisms of action and identify bioactive components of BLW responsible for TF treatment. The methods that combine network pharmacology, molecular docking, and the inhibition of nitric oxide (NO) production in LPS-induced RAW 264.7 were employed for these objectives. Network pharmacology served as a means to identify 15 potential bioactive compounds, 88 possible therapeutic targets, and 4 hub genes related to BLW. Among the significant targets, TNF, PTGS2, STAT3, and NFKB1 were closely linked to the metabolic pathways of phenylalanine, arachidonic acid, and tyrosine, which are vital in managing infections, inflammation, proliferation, and apoptosis in the TF microenvironment. Additionally, molecular docking analysis indicated that core compounds displayed strong binding affinities for the key targets, with binding energies ranging between −4.5 and −11.1 kcal/mol. The in vitro assay demonstrated that BLW extract significantly inhibited NO production in LPS-activated RAW 264.7 macrophages, presenting an IC50 value of 69.10 μg/mL, and no cytotoxic effects on RAW 264.7 macrophages. Furthermore, the biomarker compounds of BLW extract, viz., perforatic acid and peucenin-7-methyl ether were found to decrease NO production in a dose-dependent manner. In summary, this research indicates that BLW provides therapeutic benefits for TF via a complex interplay of different compounds, targets, and pathways. These findings serve as a foundation for further research into the mechanisms of action of a polyherbal remedy toward TF to provide scientific evidences for its clinical use. Full article
(This article belongs to the Special Issue Molecular Docking Method and Application)
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25 pages, 2462 KB  
Article
Artificial Neural Network-Guided Discovery of Antioxidant Peptides from Peony (Paeonia ostii) Seed Meal: Peptidomics, Molecular Mechanism, and Cellular Validation
by Tianrong Zhang, Xin Wang, Peng Ye, Yuhan Liu, Ming Zhao, Ziyan Liu, Yuan Zhao, Jinling Fan and Bin Zhang
Int. J. Mol. Sci. 2026, 27(5), 2364; https://doi.org/10.3390/ijms27052364 - 3 Mar 2026
Viewed by 488
Abstract
Peony seed meal (PSM), a protein-rich by-product of oil extraction from Paeonia ostii, represents an underutilized resource with significant potential for functional ingredient development. In this study, an integrated strategy combining artificial neural network (ANN)-guided hydrolysis, peptidomics, molecular simulation, and cellular validation [...] Read more.
Peony seed meal (PSM), a protein-rich by-product of oil extraction from Paeonia ostii, represents an underutilized resource with significant potential for functional ingredient development. In this study, an integrated strategy combining artificial neural network (ANN)-guided hydrolysis, peptidomics, molecular simulation, and cellular validation was employed to identify antioxidant peptides from PSM. Neutrase was selected as the optimal protease, and hydrolysis conditions were optimized using a backpropagation ANN model (R = 0.9935), yielding a hydrolysate with strong radical-scavenging activity (DPPH• IC50 = 0.30 mg/mL; ABTS•+ IC50 = 0.07 mg/mL). LC–MS/MS identified 364 peptides, predominantly low-molecular-weight sequences. In silico screening highlighted four candidates (FRF, WQFR, FEFR, and RWL) with favorable binding toward ABTS•+, DPPH•, and Keap1. Molecular docking and 100 ns molecular dynamics simulations confirmed stable peptide–Keap1 interactions, particularly for FRF. Cellular assays demonstrated that FRF and RWL significantly protected HepG2 cells against H2O2-induced oxidative damage by restoring antioxidant enzyme activities (SOD, CAT, and GSH-Px). Collectively, this study establishes a systematic workflow for discovering plant-derived antioxidant peptides and supports the sustainable valorization of PSM as a functional food ingredient. Full article
(This article belongs to the Special Issue Molecular Docking Method and Application)
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