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Protein-Protein Interactions as Druggable Targets: Recent Advances
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Protein-Protein Interactions as Druggable Targets: Recent Advances

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Pharmacology".

Deadline for manuscript submissions: closed (30 November 2023) | Viewed by 4067

Special Issue Editors

Prof. Dr. Stefano Alcaro

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Guest Editor
1. Dipartimento di Scienze della Salute, Università “Magna Græcia” di Catanzaro, 88100 Catanzaro, Italy
2. Net4Science Academic Spin-off, Università “Magna Græcia” di Catanzaro, 88100 Catanzaro, Italy
3. Associazione CRISEA: Centro di Ricerca e Servizi per l’innovazione Rurale, Condoleo di Belcastro (CZ), 88055 Belcastro, CZ, Italy
Interests: medicinal chemistry; computational chemistry; multi-target rational drug design; CADD; structural bioinformatics; chemical databases; drug discovery
Dr. Isabella Romeo

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Guest Editor
1. Dipartimento di Scienze della Salute, Università “Magna Græcia” di Catanzaro, 88100 Catanzaro, Italy
2. Net4Science Academic Spin-Off, Università “Magna Græcia” di Catanzaro, 88100 Catanzaro, Italy
Interests: computational chemistry; medicinal chemistry; infectiouse disease; drug repurposing; virtual screening; molecular dynamics; antioxidant activity
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The classification of protein–protein interactions (PPIs) as druggable targets is fairly new. Considering “druggability” as the capability to modulate the therapeutic target with small molecules as antagonists of PPI, the first structural insights into it date from 2000. PPIs are more abundant in human cells than single proteins and play numerous crucial roles in cellular processes, including diseases. Therefore, molecules that prevent the formation of these protein complexes could represent a good strategy to treat different diseases. Due to the structural diversity of protein interfaces, one of the main goals in drug discovery is to identify these interfaces and to explore their properties to make promising drugs. Several efforts have been undertaken in the last decade in both industry and academia, but finding a small molecule able to inhibit the interaction in a protein–protein complex remains a hard task. Natural compounds could be an interesting starting point for this purpose. Because of its inherent challenges, new technologies and strategies must be adopted to overcome the many difficulties in the research of finding safe and efficacious drugs for these targets. In this Special Issue, we encourage authors to submit manuscripts in the form of research papers, reviews, or communications that improve the knowledge in this field, contributing to efficient advances in drug discovery research.

Prof. Dr. Stefano Alcaro
Dr. Isabella Romeo
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 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 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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

  • protein–protein interactions
  • PPI
  • antagonist PPI
  • PPI drugs
  • drug discovery
  • interface motifs
  • protein interface clustering
  • hot regions
  • natural bioactive compounds

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Published Papers (2 papers)

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Research

10 pages, 1466 KiB  
Communication
Gibbs Energy and Gene Expression Combined as a New Technique for Selecting Drug Targets for Inhibiting Specific Protein–Protein Interactions
by Edward A. Rietman, Hava T. Siegelmann, Giannoula Lakka Klement and Jack A. Tuszynski
Int. J. Mol. Sci. 2023, 24(19), 14648; https://doi.org/10.3390/ijms241914648 - 27 Sep 2023
Viewed by 1099
Abstract
One of the most important aspects of successful cancer therapy is the identification of a target protein for inhibition interaction. Conventionally, this consists of screening a panel of genes to assess which is mutated and then developing a small molecule to inhibit the [...] Read more.
One of the most important aspects of successful cancer therapy is the identification of a target protein for inhibition interaction. Conventionally, this consists of screening a panel of genes to assess which is mutated and then developing a small molecule to inhibit the interaction of two proteins or to simply inhibit a specific protein from all interactions. In previous work, we have proposed computational methods that analyze protein–protein networks using both topological approaches and thermodynamic quantification provided by Gibbs free energy. In order to make these approaches both easier to implement and free of arbitrary topological filtration criteria, in the present paper, we propose a modification of the topological–thermodynamic analysis, which focuses on the selection of the most thermodynamically stable proteins and their subnetwork interaction partners with the highest expression levels. We illustrate the implementation of the new approach with two specific cases, glioblastoma (glioma brain tumors) and chronic lymphatic leukoma (CLL), based on the publicly available patient-derived datasets. We also discuss how this can be used in clinical practice in connection with the availability of approved and investigational drugs. Full article
(This article belongs to the Special Issue Protein-Protein Interactions as Druggable Targets: Recent Advances)
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17 pages, 4731 KiB  
Article
HSV-1 Glycoprotein D and Its Surface Receptors: Evaluation of Protein–Protein Interaction and Targeting by Triazole-Based Compounds through In Silico Approaches
by Roberta Bivacqua, Isabella Romeo, Marilia Barreca, Paola Barraja, Stefano Alcaro and Alessandra Montalbano
Int. J. Mol. Sci. 2023, 24(8), 7092; https://doi.org/10.3390/ijms24087092 - 11 Apr 2023
Cited by 4 | Viewed by 2172
Abstract
Protein–protein interactions (PPI) represent attractive targets for drug design. Thus, aiming at a deeper insight into the HSV-1 envelope glycoprotein D (gD), protein–protein docking and dynamic simulations of gD-HVEM and gD-Nectin-1 complexes were performed. The most stable complexes and the pivotal key residues [...] Read more.
Protein–protein interactions (PPI) represent attractive targets for drug design. Thus, aiming at a deeper insight into the HSV-1 envelope glycoprotein D (gD), protein–protein docking and dynamic simulations of gD-HVEM and gD-Nectin-1 complexes were performed. The most stable complexes and the pivotal key residues useful for gD to anchor human receptors were identified and used as starting points for a structure-based virtual screening on a library of both synthetic and designed 1,2,3-triazole-based compounds. Their binding properties versus gD interface with HVEM and Nectin-1 along with their structure-activity relationships (SARs) were evaluated. Four [1,2,3]triazolo[4,5-b]pyridines were identified as potential HSV-1 gD inhibitors, for their good theoretical affinity towards all conformations of HSV-1 gD. Overall, this study suggests promising basis for the design of new antiviral agents targeting gD as a valuable strategy to prevent viral attachment and penetration into the host cell. Full article
(This article belongs to the Special Issue Protein-Protein Interactions as Druggable Targets: Recent Advances)
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