Special Issue "Pharmacophore Modeling and Applications in Drug Discovery: Challenges and Recent Advances"

A special issue of Pharmaceuticals (ISSN 1424-8247). This special issue belongs to the section "Medicinal Chemistry".

Deadline for manuscript submissions: 28 February 2022.

Special Issue Editors

Dr. Pavel Polishchuk
E-Mail Website
Guest Editor
Institute of Molecular and Translational Medicine, Palacky University, 771 47 Olomouc, Czech Republic
Interests: cheminformatics; machine learning; molecular and drug design; medicinal chemistry.
Dr. Thomas Seidel
E-Mail Website
Guest Editor
Department of Pharmaceutical Sciences, University of Vienna, 1010 Vienna, Austria
Interests: cheminformatics; algorithm development; medicinal chemistry; computer-aided drug design

Special Issue Information

Dear Colleagues,

Pharmacophores are widely used in drug design due to their simplicity and the high level of abstraction enabling a fast screening of chemical libraries and the identification of potential hits bearing new scaffolds. The concept of pharmacophores opened a well established research field with many achievements in the past and is still undergoing a rapid further development. Recent advancements mainly concern the extended application of pharmacophores to retrieve and refine information obtained from molecular dynamics simulations of protein-ligand complexes. This can improve performance of virtual screening, help to explain observed structure-property relationships, or derive pharmacophores for apo-protein sites. More recently, application of deep learning demonstrated the ability to generate structures for a particular pharmacophore model that substantially expands the applicability of pharmacophores to the design of novel promising ligands with tailored properties.

This Special Issue will cover a wide range of topics related to pharmacophore modeling to summarize recent advances and future challenges in the field. This includes but is not limited to new applications of pharmacophores, newly developed methods and their retrospective and prospective validation, application of pharmacophores in machine learning and de novo design. In addition, there will be space for “success stories” in drug design where pharmacophore-based approaches played a key role to achieve substantial advancements in the exploration of novel targets, newly discovered binding sites or targets where other methods failed.

Dr. Pavel Polishchuk
Dr. Thomas Seidel
Guest Editors

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 papers will be 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. Pharmaceuticals 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 2000 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.


  • ligand-based pharmacophores
  • structure-based pharmacophores
  • virtual screening
  • drug design
  • machine learning
  • molecular dynamics
  • de novo design

Published Papers

This special issue is now open for submission.
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