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Special Issue "Molecular Modeling in Drug Design"

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

Deadline for manuscript submissions: 31 May 2018

Special Issue Editors

Guest Editor
Prof. Dr. Rebecca Wade

Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, Heidelberg, Germany
Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Im Neuenheimer Feld 282, Heidelberg, Germany
Website | E-Mail
Interests: molecular modelling and simulation; structure-based drug design; bioinformatics; molecular systems biology; molecular recognition; protein-ligand interactions
Guest Editor
Prof. Dr. Outi Salo-Ahen

Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, Biocity, Tykistökatu 6A, FI 20520 Turku, Finland
Website | E-Mail
Interests: computer-aided drug design; molecular dynamics simulations; anti-virulence agents; antibacterials; natural compounds

Special Issue Information

Dear Colleagues,

Since the first attempts at structure-based drug design about four decades ago, molecular modelling techniques for drug design have developed enormously, along with the increasing computational power and structural and biological information on active compounds and potential target molecules. Currently, molecular modeling can be considered an integral component of the contemporary drug discovery and development process. Rational target-based drug development projects benefit significantly from understanding the essential ligand-receptor interactions for designing a potent and efficacious drug to the desired target.

Although current modeling techniques can give important insights and speed up the drug discovery and design stages significantly, there are still many challenges in, for example, predicting accurate ligand binding energies, considering protein flexibility upon ligand binding, or mapping off-target effects of designed compounds. Nowadays, there is also a need for modelling bigger entities, such as antibodies and nanoparticles, as well as targeting macromolecular interfaces.     

The aim of this Special Issue is to present a contemporary overview of recent developments in the field of molecular modeling in the context of modern drug design. Reviews, full papers, and short communications, covering the methodological and theoretical aspects of the current trends in molecular modeling are all welcome. The submission of papers addressing the topics listed below is particularly encouraged.

Prof. Dr. Rebecca Wade
Prof. Dr. Outi Salo-Ahen
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. Molecules 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 1800 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.


  • Advanced molecular simulation techniques
  • Big data analysis
  • Molecular dynamics simulations
  • Quantum mechanics
  • Chemoinformatics
  • Water in binding sites
  • Cryptic binding pockets
  • Drug binding kinetics
  • Covalent inhibitors
  • Off-target prediction
  • Protein-protein interaction inhibitors
  • Antibody design
  • Nanoparticles

Published Papers (1 paper)

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Open AccessArticle Discovery of Potential Inhibitors of Squalene Synthase from Traditional Chinese Medicine Based on Virtual Screening and In Vitro Evaluation of Lipid-Lowering Effect
Molecules 2018, 23(5), 1040; https://doi.org/10.3390/molecules23051040
Received: 19 March 2018 / Revised: 19 April 2018 / Accepted: 25 April 2018 / Published: 28 April 2018
PDF Full-text (4702 KB) | HTML Full-text | XML Full-text | Supplementary Files
Squalene synthase (SQS), a key downstream enzyme involved in the cholesterol biosynthetic pathway, plays an important role in treating hyperlipidemia. Compared to statins, SQS inhibitors have shown a very significant lipid-lowering effect and do not cause myotoxicity. Thus, the paper aims to discover
[...] Read more.
Squalene synthase (SQS), a key downstream enzyme involved in the cholesterol biosynthetic pathway, plays an important role in treating hyperlipidemia. Compared to statins, SQS inhibitors have shown a very significant lipid-lowering effect and do not cause myotoxicity. Thus, the paper aims to discover potential SQS inhibitors from Traditional Chinese Medicine (TCM) by the combination of molecular modeling methods and biological assays. In this study, cynarin was selected as a potential SQS inhibitor candidate compound based on its pharmacophoric properties, molecular docking studies and molecular dynamics (MD) simulations. Cynarin could form hydrophobic interactions with PHE54, LEU211, LEU183 and PRO292, which are regarded as important interactions for the SQS inhibitors. In addition, the lipid-lowering effect of cynarin was tested in sodium oleate-induced HepG2 cells by decreasing the lipidemic parameter triglyceride (TG) level by 22.50%. Finally. cynarin was reversely screened against other anti-hyperlipidemia targets which existed in HepG2 cells and cynarin was unable to map with the pharmacophore of these targets, which indicated that the lipid-lowering effects of cynarin might be due to the inhibition of SQS. This study discovered cynarin is a potential SQS inhibitor from TCM, which could be further clinically explored for the treatment of hyperlipidemia. Full article
(This article belongs to the Special Issue Molecular Modeling in Drug Design)

Figure 1a

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: Theoretical Model of EphA2-Ephrin A1 Inhibition
Authors: Wiktoria Jedwabny 1, Alessio Lodola 2 and Edyta Dyguda-Kazimierowicz *,1
Affiliation: 1 Department of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
2 Department of Food and Drug, Universita di Parma, Parma, Italy
Email: sokalski@pwr.wroc.pl
Abstract: This work aims at the theoretical description of EphA2-ephrinA1 inhibition by small molecules. Recently proposed ab initio-based scoring models, comprising long-range components of interaction energy, is tested on lithocholic acid class inhibitors of this protein-protein interaction (PPI) against common empirical descriptors. We show that although limited to compounds with similar solvation energy, the ab initio model is able to rank the set of selected inhibitors more effectively than empirical scoring functions, aiding the design of novel compounds.


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