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Special Issue "Molecular Simulations Applications in Biochemistry and Molecular Biology"

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

Deadline for manuscript submissions: 31 March 2021.

Special Issue Editors

Prof. Dr. Angelo Facchiano
Guest Editor
Nazionale delle Ricerche, Institute of Food Science, Avellino, Italy
Interests: protein structure and function; computational chemistry and biology; bioinformatics
Prof. Dr. Anna Marabotti
Guest Editor
Dipartimento di Chimica e Biologia “A. Zambelli”, Università degli Studi di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy
Interests: structure-dynamics-function relationships of proteins; proteins involved in rare pathologies; characterization; biocomputational techniques

Special Issue Information

Dear Colleagues,

Molecular simulation applications in biochemistry and molecular biology offer powerful opportunities to investigate the structural and functional aspects of molecules, towards the interpretation of biochemical mechanisms and the identification of novel functional compounds. Several approaches have been developed over recent decades, and many applications are reported in the literature. The most recent years have been characterized by the availability of large data sets, the fairification of data, the increase of computational power, and the development of open science. All these aspects together now make it possible to define novel approaches and applications. In particular, novel technologies offer the opportunity to generate large data sets or new types of experimental data, both requiring novel tools for their management, analysis and interpretation.

This Special Issue will include research articles that describe the development of novel molecular simulation approaches and the applications of current methods to unexplained aspects of biochemical mechanisms, with the opportunity to present purely computational studies, as well as computational studies with experimental validations. The Special Issue will includes also articles from the 15th edition of the Bioinformatics and Computational Biology Conference (, Naples, Italy, November 16–18th, 2020.

Prof. Dr. Angelo Facchiano
Prof. Dr. Anna Marabotti
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at 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 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 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.


  • Molecular dynamics
  • Docking
  • Bioactive molecules
  • Protein-ligand interactions
  • Protein modelling

Published Papers (1 paper)

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Open AccessArticle
Computational Study of C-X-C Chemokine Receptor (CXCR)3 Binding with Its Natural Agonists Chemokine (C-X-C Motif) Ligand (CXCL)9, 10 and 11 and with Synthetic Antagonists: Insights of Receptor Activation towards Drug Design for Vitiligo
Molecules 2020, 25(19), 4413; - 25 Sep 2020
Vitiligo is a hypopigmentary skin pathology resulting from the death of melanocytes due to the activity of CD8+ cytotoxic lymphocytes and overexpression of chemokines. These include CXCL9, CXCL10, and CXCL11 and its receptor CXCR3, both in peripheral cells of the immune system [...] Read more.
Vitiligo is a hypopigmentary skin pathology resulting from the death of melanocytes due to the activity of CD8+ cytotoxic lymphocytes and overexpression of chemokines. These include CXCL9, CXCL10, and CXCL11 and its receptor CXCR3, both in peripheral cells of the immune system and in the skin of patients diagnosed with vitiligo. The three-dimensional structure of CXCR3 and CXCL9 has not been reported experimentally; thus, homology modeling and molecular dynamics could be useful for the study of this chemotaxis-promoter axis. In this work, a homology model of CXCR3 and CXCL9 and the structure of the CXCR3/Gαi/0βγ complex with post-translational modifications of CXCR3 are reported for the study of the interaction of chemokines with CXCR3 through all-atom (AA-MD) and coarse-grained molecular dynamics (CG-MD) simulations. AA-MD and CG-MD simulations showed the first activation step of the CXCR3 receptor with all chemokines and the second activation step in the CXCR3-CXCL10 complex through a decrease in the distance between the chemokine and the transmembrane region of CXCR3 and the separation of the βγ complex from the α subunit in the G-protein. Additionally, a general protein–ligand interaction model was calculated, based on known antagonists binding to CXCR3. These results contribute to understanding the activation mechanism of CXCR3 and the design of new molecules that inhibit chemokine binding or antagonize the receptor, provoking a decrease of chemotaxis caused by the CXCR3/chemokines axis. Full article
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