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Hot Trends in Computational Drug Design

A special issue of Molecules (ISSN 1420-3049).

Deadline for manuscript submissions: 30 April 2026 | Viewed by 817

Special Issue Editor


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Guest Editor
Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, Lublin, Poland
Interests: computer-aided drug design; medicinal chemistry; molecular modeling; CNS agents; GPCRs
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Special Issue Information

Dear Colleagues,

Computer-aided drug design has rapidly evolved over the past decade due to outstanding progress in artificial intelligence, big data analytics, and structural biology. These breakthroughs have revolutionized the way we see biological systems and design modern drugs. Approaches such as machine learning, quantum computing, and multiscale simulations facilitate and speed up drug discovery pipelines. Moreover, computer-aided drug design techniques are able to reduce the costs of drug design and discovery up to 50%.

This Special Issue aims to highlight recent progress and novel methodologies in computational drug design. We welcome contributions focusing on novel theoretical frameworks, algorithmic innovations, and practical applications in drug discovery and development.

In this Special Issue, original research articles and reviews are welcome. Research areas may include (but are not limited to) the following:

  • AI and machine learning in drug discovery;
  • Molecular dynamics and docking simulations;
  • Structure-based and ligand-based drug design;
  • QSAR and cheminformatics;
  • Virtual screening and pharmacophore modeling;
  • De novo drug design techniques;
  • Multi-target drug design and polypharmacology.

We look forward to receiving your contributions.

Prof. Dr. Agnieszka A. Kaczor
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. 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

  • AI in drug discovery
  • cheminformatics
  • computational drug design
  • machine learning
  • molecular docking
  • molecular dynamics simulations
  • molecular modeling
  • pharmacophore
  • QSAR
  • structure-based design
  • virtual screening

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Published Papers (1 paper)

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Research

25 pages, 3646 KB  
Article
SERAAK2 as a Serotonin Receptor Ligand: Structural and Pharmacological In Vitro and In Vivo Evaluation
by Agnieszka A. Kaczor, Agata Zięba, Tadeusz Karcz, Michał K. Jastrzębski, Katarzyna Szczepańska, Tuomo Laitinen, Marián Castro and Ewa Kędzierska
Molecules 2025, 30(23), 4633; https://doi.org/10.3390/molecules30234633 - 2 Dec 2025
Viewed by 503
Abstract
Serotonin receptors, in particular 5-HT1A and 5-HT2A receptors, are important molecular targets for the central nervous system (CNS) disorders, such as schizophrenia, depression, anxiety disorders, memory deficits, and many others. Here, we present structural and pharmacological evaluation of a serotonin receptor [...] Read more.
Serotonin receptors, in particular 5-HT1A and 5-HT2A receptors, are important molecular targets for the central nervous system (CNS) disorders, such as schizophrenia, depression, anxiety disorders, memory deficits, and many others. Here, we present structural and pharmacological evaluation of a serotonin receptor ligand, SERAAK2, identified in a structure-based virtual screening campaign. Molecular docking studies revealed that SERAAK2 binds with its molecular targets via Asp3.32 as the main anchoring point, which is typical for orthosteric ligands of aminergic GPCRs. Molecular dynamics simulations confirmed the stability of the ligand binding poses in the studied receptors. MMGBSA calculations were in accordance with the receptor in vitro binding affinity studies, which indicated that SERAAK2 is a potent ligand of 5-HT1A and 5-HT2A receptors. It was also found that SERAAK2 displays favorable ADMET parameters. The demonstrated anxiolytic- and antidepressant-like effects of SERAAK2 in animal models, which may involve its interaction with 5-HT1A receptors, warrant further studies to confirm these activities and elucidate the underlying mechanisms. Full article
(This article belongs to the Special Issue Hot Trends in Computational Drug Design)
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