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From Biomolecules to Therapies: Bridging the Gap with Molecular Mechanisms, Computational Design, and Drug Delivery

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

Deadline for manuscript submissions: closed (30 April 2025) | Viewed by 5417

Special Issue Editors

Prof. Dr. Jesús Vicente de Julián-Ortiz

E-Mail Website
Guest Editor
Department of Physical Chemistry, Faculty of Pharmacy, University of Valencia, Valencia, Spain
Interests: computational chemistry; medicinal chemistry; QSAR; QSTR
Special Issues, Collections and Topics in MDPI journals
Dr. Francisco Torrens

E-Mail Website
Guest Editor
Institut Universitari de Ciencia Molecular, Edifici d’Instituts de Paterna, P. O. Box 22085, E-46071 Valencia, Spain
Interests: theoretical chemistry; physical chemistry; mathematical chemistry; computational chemistry; molecular modelling; simulation and design; computer-aided drug design and development; molecular graphics and representation of molecular properties
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Gloria Castellano

E-Mail Website
Guest Editor
Centro de Investigación Traslacional San Alberto Magno (CITSAM), Catholic University of Valencia San Vicente Mártir, 46001 Valencia, Spain
Interests: natural products; organic chemistry; phytochemistry; medicinal plant chemistry; food chemistry
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This special issue highlights the biologically important integration of biomolecular research, computational modeling, and drug delivery approaches. It seeks to reduce the gap between fundamental research into biomolecules and their development into clinically useful therapeutic agents. The articles in this issue will reveal the structure of the biological processes and pathologies mentioned above, along with the molecular structure that define them. The issue would include chemical simulations, cutting-edge computational methods for exploration of these molecular mechanisms, as well as the analyses to generate new therapy approaches. In addition to the above topics, the issue will cover the innovative drug delivery systems to maximize the bioavailability and specificity of the therapeutic agents. Some of the topics in this category will include strategies of bypassing the biological barriers and targeting of the drugs to a specific tissue or cell type. The special issue has been designed to cover a wide array of research fields to demonstrate the disruptive potential of holistic drug discovery and development. This issue will further emphasize that when a deep understanding of the biomolecules, their interactions and their specific delivery systems combine with the advanced computational tools, it will lead to a new era of life-saving treatments.

Prof. Dr. Jesús Vicente de Julián-Ortiz
Dr. Francisco Torrens
Prof. Dr. Gloria Castellano
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.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • biomolecules
  • molecular mechanisms
  • computational studies
  • drug delivery
  • xenobiotics

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

Published Papers (3 papers)

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Research

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15 pages, 2385 KiB  
Article
Eleutherin and Isoeleutherin Activity against Staphylococcus aureus and Escherichia coli Strain’s: Molecular Docking and Antibacterial Evaluation
by Mírian Letícia Carmo Bastos, Houéfa Egidia Fallon Adido, Ananda Karolyne Martins de Brito, Cristian Kallahan Silva Chagas, Ana Laura Gadelha Castro, Gleison Gonçalves Ferreira, Pedro Henrique Costa Nascimento, Walice Rans da Silva Padilha, Rosana Moura Sarmento, Viviane Vasconcelos Garcia, Andrey Moacir do Rosario Marinho, Patrícia Santana Barbosa Marinho, Johnatt Allan Rocha de Oliveira, Valdicley Vieira Vale, Sandro Percário and Maria Fâni Dolabela
Int. J. Mol. Sci. 2024, 25(23), 12583; https://doi.org/10.3390/ijms252312583 - 23 Nov 2024
Viewed by 1329
Abstract
Naphthoquinones eleutherin and isoeleutherin have demonstrated promising antibacterial activity, probably due to their quinone structure, which can generate reactive oxygen species. The study examines the activities of pathogens, such as Staphylococcus aureus and Escherichia coli, associated with antimicrobial resistance and explores their [...] Read more.
Naphthoquinones eleutherin and isoeleutherin have demonstrated promising antibacterial activity, probably due to their quinone structure, which can generate reactive oxygen species. The study examines the activities of pathogens, such as Staphylococcus aureus and Escherichia coli, associated with antimicrobial resistance and explores their potential mechanisms of action. The MIC, IC50, and MBC were determined. PharmMapper 2017 server and GOLD 2020.1 software were utilized for molecular docking to identify protein targets and interaction mechanisms. The docking predictions were verified by redocking, focusing on structures with RMSD below 2 Å. The molecular docking revealed a significant affinity of eleutherin for the peptide, transcriptional regulator QacR, and regulatory protein BlaR1 with better interactions with BlaR1 than the crystallographic ligand (benzylpenicillin). Isoeleutherin demonstrated specific interactions with methionine aminopeptidase, indicating specificity and affinity. In summary, the difference in naphthoquinones activities may be related to structural differences. Eleutherin exhibits potential as a therapeutic adjuvant to reverse bacterial resistance in S. aureus, suggesting this molecule interferes with the antibiotic resistance mechanism. The absence of homologous proteins or variations in the structure of the target proteins could be the cause of the inactivity against E. coli. Full article
(This article belongs to the Special Issue From Biomolecules to Therapies: Bridging the Gap with Molecular Mechanisms, Computational Design, and Drug Delivery)
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23 pages, 7831 KiB  
Article
Biosynthesis and Characterization of Aeonium arboreum-Derived Silver Nanoparticles: Antimicrobial Activity, Biofilm Inhibition, Antihemolytic Activity, and In Silico Studies
by Marwah M. Alfeqy, Seham S. El-Hawary, Ali M. El-Halawany, Mohamed A. Rabeh, Saad A. Alshehri, Usama Ramadan Abdelmohsen, Nesreen A. Safwat, Aya M. Serry, Heba A. Fahmy and Marwa I. Ezzat
Int. J. Mol. Sci. 2024, 25(15), 8039; https://doi.org/10.3390/ijms25158039 - 23 Jul 2024
Viewed by 1532
Abstract
Environmentally friendly biosynthesis of silver nanoparticles (AgNPs) from Aeonium arboreum (L.) Webb & Berthel is reported for the first time. The synthesized AgNPs were characterized using UV-Vis, FTIR, TEM, Zeta potential, and XRD analysis, revealing high stability (−29.1 mV), spherical shape, and an [...] Read more.
Environmentally friendly biosynthesis of silver nanoparticles (AgNPs) from Aeonium arboreum (L.) Webb & Berthel is reported for the first time. The synthesized AgNPs were characterized using UV-Vis, FTIR, TEM, Zeta potential, and XRD analysis, revealing high stability (−29.1 mV), spherical shape, and an average size of 100 nm. The antimicrobial activity levels of both A. arboreum extract and biosynthesized AgNPs were evaluated against five uropathogens (Staphylococcus aureus, Enterococcus faecalis, Escherichia coli, Pseudomonas aeruginosa, and Candida albicans). Both the extract and the AgNPs exhibited significant efficacy, particularly against E. coli, with inhibition zones of 27 mm and 30 mm, respectively. LC-MS analysis tentatively identified 11 secondary metabolites in the extract, including quercetin-3-O-glucoside, quercetin-3-O-rhamnoside, myricetin 3-glucoside, and daphneresinol. In silico docking studies revealed promising binding affinities of these metabolites in relation to key enzymes involved in bacterial folate synthesis (dihydrofolate reductase (DHFR) and dihydropteroate synthase (DHPS)) and DNA replication (DNA gyrase). These findings demonstrate the potential of A. arboreum-based AgNPs and their associated metabolites as a novel therapeutic approach for combating urinary tract infections. Their antimicrobial, antihemolytic, and antibiofilm properties warrant further investigation. Full article
(This article belongs to the Special Issue From Biomolecules to Therapies: Bridging the Gap with Molecular Mechanisms, Computational Design, and Drug Delivery)
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Review

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40 pages, 4101 KiB  
Review
Computational Strategies for Assessing Adverse Outcome Pathways: Hepatic Steatosis as a Case Study
by Rita Ortega-Vallbona, Martina Palomino-Schätzlein, Laia Tolosa, Emilio Benfenati, Gerhard F. Ecker, Rafael Gozalbes and Eva Serrano-Candelas
Int. J. Mol. Sci. 2024, 25(20), 11154; https://doi.org/10.3390/ijms252011154 - 17 Oct 2024
Cited by 1 | Viewed by 1722
Abstract
The evolving landscape of chemical risk assessment is increasingly focused on developing tiered, mechanistically driven approaches that avoid the use of animal experiments. In this context, adverse outcome pathways have gained importance for evaluating various types of chemical-induced toxicity. Using hepatic steatosis as [...] Read more.
The evolving landscape of chemical risk assessment is increasingly focused on developing tiered, mechanistically driven approaches that avoid the use of animal experiments. In this context, adverse outcome pathways have gained importance for evaluating various types of chemical-induced toxicity. Using hepatic steatosis as a case study, this review explores the use of diverse computational techniques, such as structure–activity relationship models, quantitative structure–activity relationship models, read-across methods, omics data analysis, and structure-based approaches to fill data gaps within adverse outcome pathway networks. Emphasizing the regulatory acceptance of each technique, we examine how these methodologies can be integrated to provide a comprehensive understanding of chemical toxicity. This review highlights the transformative impact of in silico techniques in toxicology, proposing guidelines for their application in evidence gathering for developing and filling data gaps in adverse outcome pathway networks. These guidelines can be applied to other cases, advancing the field of toxicological risk assessment. Full article
(This article belongs to the Special Issue From Biomolecules to Therapies: Bridging the Gap with Molecular Mechanisms, Computational Design, and Drug Delivery)
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