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Molecular Docking in Drug Discovery, 2nd Edition
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Molecular Docking in Drug Discovery, 2nd Edition

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

Deadline for manuscript submissions: 31 July 2025 | Viewed by 1092

Special Issue Editor

Dr. Eleni Pontiki

E-Mail Website
Guest Editor
Department of Pharmaceutical Chemistry, School of Pharmacy, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
Interests: medicinal chemistry; natural products; antioxidants; anti-inflammatory activity; pharmacokinetics; drug design; structure–activity relationships
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Molecular docking remains a valuable tool in drug discovery. It is a fast and inexpensive technique for medicinal chemists to predict, identify, and synthesize compounds of potential biological interest, predict ligand-target interactions, or delineate structure–activity relationships (SAR) without the existence of other target modulators. Although initially, it was developed to identify the mechanisms and interactions of a ligand conformation within the binding pocket of a target molecule, many aspects remain challenging, and new approaches are being developed. 

This Special Issue describes traditional applications of molecular docking in drug discovery. Recent developments in molecular docking approaches include machine learning and applications such as drug repurposing, adverse effects, polypharmacology, etc. Examination of the various approaches and methods of molecular docking and an exploration of the techniques used for interpreting and validating docking results can be included.

This Special Issue covers the entire field of molecular docking in drug discovery and can contain reviews, research articles, and methodological papers. Manuscripts using structure-based drug design are welcome for targeted drug discovery rational synthesis of agents. Moreover, newer and emerging approaches and applications of molecular dockings, such as algorithms in fragment-based approaches, available benchmarking sets, consensus methods, and machine learning algorithms, can be submitted.

The scope also encompasses the integration of molecular docking with other computational techniques and all future applications when combined with emergent techniques, such as artificial intelligence.

Dr. Eleni Pontiki
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

  • computer aided drug design
  • drug discovery
  • molecular docking
  • structure–activity relationships
  • drug design

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Related Special Issue

Published Papers (2 papers)

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Research

19 pages, 2360 KiB  
Article
Novel N-Alkyl 3-(3-Benzyloxyquinoxalin-2-yl) Propanamides as Antiproliferative Agents: Design, Synthesis, In Vitro Testing, and In Silico Mechanistic Study
by Samar A. Abubshait
Molecules 2025, 30(14), 3025; https://doi.org/10.3390/molecules30143025 - 18 Jul 2025
Viewed by 148
Abstract
A series of eleven new N-alkyl 3-(3-benzyloxyquinoxalin-2-yl) propanamides were prepared based on the azide coupling of 3-(3-benzyloxyquinoxalin-2-yl) propanhydrazide with a variety of primary and secondary amines and the consequent conjunction of a broad spectrum of lipophile and hydrophile characters to a quinoxaline [...] Read more.
A series of eleven new N-alkyl 3-(3-benzyloxyquinoxalin-2-yl) propanamides were prepared based on the azide coupling of 3-(3-benzyloxyquinoxalin-2-yl) propanhydrazide with a variety of primary and secondary amines and the consequent conjunction of a broad spectrum of lipophile and hydrophile characters to a quinoxaline ring system. 3-(3-benzyloxyquinoxalin-2-yl) propanhydrazide was produced in a two-step reaction of methyl 3-(3-oxo-3,4-dihydroquinoxalin-2-yl) propanoate with benzyl chloride followed by the hydrazinolysis of the corresponding ester. The antiproliferative activity of the compounds was tested in various cancer cell lines, including PC-3, Hela, HCT-116, and MCF-7; they showed a wide spectrum of activity for most of the tested compounds. Compound 6k exhibited the highest activity, which was comparable to that of doxorubicin, with IC50 (µM) values of 12.17 ± 0.9, 9.46 ± 0.7, 10.88 ± 0.8, and 6.93 ± 0.4 µM compared to 8.87 ± 0.6, 5.57 ± 0.4, 5.23 ± 0.3, and 4.17 ± 0.2 µM for doxorubicin against Hela, HCT-116, and MCF-7, respectively. The in silico mechanistic study revealed the inhibition of HDAC-6 through the binding of the unique zinc finger ubiquitin-binding domain (HDAC6 Zf-UBD). The docking results showed a specific binding pattern that emphasized the crucial role of the quinoxaline ring and its substituents. The newly developed derivatives were evaluated for antitumor effects against four cancer cell lines PC-3, HeLa, HCT-116, and MCF-7. This research led to the identification of a quinoxaline-based scaffold exhibiting broad-spectrum antiproliferative activity and a distinct mechanism involving binding to HDAC6 Zf-UBD. The findings highlight its potential for further optimization and preclinical studies to support future anticancer drug development. Full article
(This article belongs to the Special Issue Molecular Docking in Drug Discovery, 2nd Edition)
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18 pages, 1571 KiB  
Article
One-Pot Synthesis of Novel Pyrimidine Derivatives with Potential Antidiabetic Activity Through Dual α-Glucosidase and α-Amylase Inhibitors
by Ohood Al-Shehri, Samar Abubshait, Muhammad Nawaz, Mohamed S. Gomaa and Haya A. Abubshait
Molecules 2025, 30(13), 2857; https://doi.org/10.3390/molecules30132857 - 4 Jul 2025
Viewed by 563
Abstract
This study describes the synthesis of heterocyclic derivatives containing multiple nitrogen atoms serving as important moieties for developing novel antidiabetics through a simple synthetic pathway. We herein describe the synthesis and characterization of novel pyrimidine derivatives using one-pot reactions in a catalyst-free and [...] Read more.
This study describes the synthesis of heterocyclic derivatives containing multiple nitrogen atoms serving as important moieties for developing novel antidiabetics through a simple synthetic pathway. We herein describe the synthesis and characterization of novel pyrimidine derivatives using one-pot reactions in a catalyst-free and efficient manner through a two-stage process involving the synthesis of 2-amino-4-hydrazinyl-6-methoxy pyrimidine, followed by a reaction with phenyl isothiocyanate derivatives. The structures of all the new compounds were confirmed via physical and spectral analysis. Furthermore, we evaluated the synthesized pyrimidine derivatives’ biological activities in relation to their potential roles as novel anti-diabetic agents by testing their activity profiles against the enzymes α-glucosidase and α-amylase. Compound 4 expressed the highest level of activity against α-glucosidase and α-amylase, with a greater inhibitory concentration (IC50 of 12.16 ± 0.12 µM and IC50 11.13 ± 0.12 µM) compared to that of acarbose (IC50 = 10.60 ± 0.17 µM and IC50 = 11.30 ± 0.12 µM), which is widely used as a standard antidiabetic drug. The primary structure activity relationship analysis identified the impact of an electron- withdrawing group, especially with respect to fluorine on inhibitory activity. This was further confirmed in molecular docking studies, which demonstrated that both compounds exhibited similar inhibition patterns and emphasized the significance of incorporating a lipophilic electron-withdrawing substituent on the phenyl ring, along with the 2,4-diaminopyrimidine scaffold. Full article
(This article belongs to the Special Issue Molecular Docking in Drug Discovery, 2nd Edition)
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