Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
7.4
4.2
Journals
Molecules
Special Issues
Molecular Modelling in Drug Design for the Identification of New...
molecules-logo
Submit to Molecules Review for Molecules Propose a Special Issue

Journal Menu

► Journal Menu

Journal Browser

► Journal Browser
share announcement

Molecular Modelling in Drug Design for the Identification of New Protein Targets and Their Signalling Pathways

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

Deadline for manuscript submissions: closed (15 March 2024) | Viewed by 3579

Special Issue Editors

Dr. Simone Ronsisvalle

E-Mail Website
Guest Editor
Department of Drug and Health Sciences, University of Catania, Catania, Italy
Interests: pharmaceutical chemistry; molecular modelling; molecular docking; molecular dynamics; drug discovery; analytical chemistry; UPLC-MS/MS
Special Issues, Collections and Topics in MDPI journals
Dr. Salvatore Guccione

E-Mail Website
Guest Editor
Department of Drug and Health Sciences, University of Catania, Catania, Italy
Interests: molecular modelling; drug discovery; pharmaceutical chemistry; computational chemistry; proteins
Dr. Matteo Pappalardo

E-Mail Website
Guest Editor
Department of Drug and Health Sciences, University of Catania, Catania, Italy
Interests: molecular dynamics; phospholipidic membrane; proteins; drug discovery; computational chemistry

Special Issue Information

Dear Colleagues,

The complex networks of proteins and their signalling pathways are critical for proper cellular functioning. Any alteration in this system can lead to a diseased state. Currently, bioactive molecules are studied to manage altered protein signalling networks and maintain the health of individuals. Unfortunately, the number of known proteins represents only a small percentage of the total proteins involved in such a complex mechanism, limiting the diversification of new therapeutics. On the other hand, the recent pandemic has highlighted the catastrophic impacts of viruses on human health and the world economy. In addition to vaccine development, antiviral drug treatment has become an essential means to overcome these issues. To efficiently discover active molecules, it is necessary to identify key target proteins in the development of disease, screen active molecules, and develop methods for the identification and characterization of target proteins based on the active ingredients of drugs. In this long process, that is, drug discovery, computational chemistry is critical to reduce the cost and time of research.

This Special Issue aims to gather scientific research on the identification of new protein targets and their signalling pathways using computational techniques. Peer-reviewed original research articles and critical reviews will be considered.

Dr. Simone Ronsisvalle
Dr. Salvatore Guccione
Dr. Matteo Pappalardo
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. 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 2700 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.

Keywords

  • molecular modelling
  • computational chemistry
  • drug discovery
  • protein targets

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

Further information on MDPI's Special Issue polices can be found here.

Published Papers (2 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

12 pages, 2352 KiB  
Article
A Computational Workflow to Predict Biological Target Mutations: The Spike Glycoprotein Case Study
by Pietro Cozzini, Federica Agosta, Greta Dolcetti and Alessandro Dal Palù
Molecules 2023, 28(20), 7082; https://doi.org/10.3390/molecules28207082 - 14 Oct 2023
Cited by 2 | Viewed by 1766
Abstract
The biological target identification process, a pivotal phase in the drug discovery workflow, becomes particularly challenging when mutations affect proteins’ mechanisms of action. COVID-19 Spike glycoprotein mutations are known to modify the affinity toward the human angiotensin-converting enzyme ACE2 and several antibodies, compromising [...] Read more.
The biological target identification process, a pivotal phase in the drug discovery workflow, becomes particularly challenging when mutations affect proteins’ mechanisms of action. COVID-19 Spike glycoprotein mutations are known to modify the affinity toward the human angiotensin-converting enzyme ACE2 and several antibodies, compromising their neutralizing effect. Predicting new possible mutations would be an efficient way to develop specific and efficacious drugs, vaccines, and antibodies. In this work, we developed and applied a computational procedure, combining constrained logic programming and careful structural analysis based on the Structural Activity Relationship (SAR) approach, to predict and determine the structure and behavior of new future mutants. “Mutations rules” that would track statistical and functional types of substitutions for each residue or combination of residues were extracted from the GISAID database and used to define constraints for our software, having control of the process step by step. A careful molecular dynamics analysis of the predicted mutated structures was carried out after an energy evaluation of the intermolecular and intramolecular interactions using the HINT (Hydrophatic INTeraction) force field. Our approach successfully predicted, among others, known Spike mutants. Full article
(This article belongs to the Special Issue Molecular Modelling in Drug Design for the Identification of New Protein Targets and Their Signalling Pathways)
►▼ Show Figures

Graphical abstract

22 pages, 5195 KiB  
Article
Different In Silico Approaches Using Heterocyclic Derivatives against the Binding between Different Lineages of SARS-CoV-2 and ACE2
by Federica Sipala, Gianfranco Cavallaro, Giuseppe Forte, Cristina Satriano, Alessandro Giuffrida, Aurore Fraix, Angelo Spadaro, Salvatore Petralia, Carmela Bonaccorso, Cosimo Gianluca Fortuna and Simone Ronsisvalle
Molecules 2023, 28(9), 3908; https://doi.org/10.3390/molecules28093908 - 5 May 2023
Cited by 1 | Viewed by 1452
Abstract
Over the last few years, the study of the SARS-CoV-2 spike protein and its mutations has become essential in understanding how it interacts with human host receptors. Since the crystallized structure of the spike protein bound to the angiotensin-converting enzyme 2 (ACE2) receptor [...] Read more.
Over the last few years, the study of the SARS-CoV-2 spike protein and its mutations has become essential in understanding how it interacts with human host receptors. Since the crystallized structure of the spike protein bound to the angiotensin-converting enzyme 2 (ACE2) receptor was released (PDB code 6M0J), in silico studies have been performed to understand the interactions between these two proteins. Specifically, in this study, heterocyclic compounds with different chemical characteristics were examined to highlight the possibility of interaction with the spike protein and the disruption of the interaction between ACE2 and the spike protein. Our results showed that these compounds interacted with the spike protein and interposed in the interaction zone with ACE2. Although further studies are needed, this work points to these heterocyclic push–pull compounds as possible agents capable of interacting with the spike protein, with the potential for the inhibition of spike protein–ACE2 binding. Full article
(This article belongs to the Special Issue Molecular Modelling in Drug Design for the Identification of New Protein Targets and Their Signalling Pathways)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-2
Back to TopTop