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Special Issue "Protein-Protein Interactions"

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

Deadline for manuscript submissions: 30 March 2018

Special Issue Editors

Guest Editor
Prof. Dr. Alessio Ciulli

Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, UK
Website | E-Mail
Interests: structural and chemical biology of protein–protein interactions; chemical probe development; ubiquitin–proteasome system; targeted protein degradation (PROTACs); chromatin-reader domains; fragment-based drug discovery
Guest Editor
Dr. Carles Galdeano

Facultat de Farmàcia i Ciències de l'Alimentació, Institut de Biomedicina (IBUB), Universitat de Barcelona. Av. Joan XXIII 27–31, 08028 Barcelona, Spain
Website | E-Mail
Interests: drug discovery of protein–protein interactions; fragment-based drug discovery; E3 ubiquitin ligases; computational techniques; neurodegenerative disorders; personalized medicine

Special Issue Information

Dear Colleagues,

It is indisputable that there is a need to expand the druggable genome since only a small portion of it is pharmaceutically accessible to classical drug discovery approaches. Transcription factors, scaffolding proteins, pharmacological chaperones and multi-subunit enzymes have in major part been considered no go targets. These target classes rarely present deep active sites that can bind small molecules with high affinity, and in contrast function via formation of specific protein–protein interactions (PPIs). These interactions are considered difficult, due to the often large and flat surface areas that need to be targeted. Ligandability challenges, combined with historic failures of early high-throughput screening campaigns by the pharmaceutical industry against PPI targets, rapidly contributed to perceiving PPIs as “undruggable” space.

In recent years, however, these perceptions and misconceptions about targeting protein–protein interactions are beginning to break. Dozens of drug-like small molecules and peptides that target different protein-protein interactions have entered clinical trials or even they are approved (e.g., tirofiban, Merck). Many chemical probes that intervene onto specific PPIs have been developed by industry and academia, opening tremendous new opportunities to explore biology. Targeting protein-protein interaction is, nowadays, a highly rewarding scientific endeavour, providing many opportunities to modalities of chemical intervention other than conventional inhibition, and beyond traditional Rule-of-5 compliant chemical space.

Researchers in the field of chemical biology and drug discovery of protein-protein interactions are cordially invited to contribute with original papers and reviews to this Special Issue of Molecules, which report on the design and synthesis, evaluation and development of new small molecules or peptides that target to protein–protein interactions or new computational and biophysical approaches and technologies to target protein–protein interactions.

Prof. Dr. Alessio Ciulli
Dr. Carles Galdeano
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.


  • Protein–protein interactions
  • Rational design: Structure-based
  • drug discovery
  • Fragment-based drug discovery
  • Computational approaches
  • Biophysical techniques
  • High-throughput screening

Published Papers (1 paper)

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Open AccessArticle Binding Direction-Based Two-Dimensional Flattened Contact Area Computing Algorithm for Protein–Protein Interactions
Molecules 2017, 22(10), 1722; doi:10.3390/molecules22101722
Received: 31 August 2017 / Revised: 6 October 2017 / Accepted: 12 October 2017 / Published: 13 October 2017
PDF Full-text (1253 KB) | HTML Full-text | XML Full-text
Interactions between protein molecules are essential for the assembly, function, and regulation of proteins. The contact region between two protein molecules in a protein complex is usually complementary in shape for both molecules and the area of the contact region can be used
[...] Read more.
Interactions between protein molecules are essential for the assembly, function, and regulation of proteins. The contact region between two protein molecules in a protein complex is usually complementary in shape for both molecules and the area of the contact region can be used to estimate the binding strength between two molecules. Although the area is a value calculated from the three-dimensional surface, it cannot represent the three-dimensional shape of the surface. Therefore, we propose an original concept of two-dimensional contact area which provides further information such as the ruggedness of the contact region. We present a novel algorithm for calculating the binding direction between two molecules in a protein complex, and then suggest a method to compute the two-dimensional flattened area of the contact region between two molecules based on the binding direction. Full article
(This article belongs to the Special Issue Protein-Protein Interactions)

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