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25th Anniversary of IJMS: Updates and Advances in Molecular Informatics

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: 31 December 2025 | Viewed by 2463

Special Issue Editors

Dr. M. Natália D.S. Cordeiro

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Guest Editor
LAQV-REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
Interests: theoretical and computational chemistry; electronic structure theory; quantum theory of atoms in molecules; catalysis; materials science; molecular modelling and simulations; machine learning tools
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Giulio Vistoli

E-Mail Website
Guest Editor
Department of Pharmaceutical Sciences, Università degli Studi di Milano, via Mangiagalli 25, 20133 Milano, Italy
Interests: computational chemistry; drug design; cheminformatics; molecular docking; ADME predictions; lipophilicity
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue commemorates the 25th anniversary of the International Journal of Molecular Sciences (IJMS), celebrating a quarter-century of pioneering research in the molecular sciences. We invite submissions that reflect on major advances in molecular informatics over this period and highlight emerging directions for the field. As molecular data continues to grow exponentially, molecular informatics plays a critical role in decoding complex biological and chemical systems, accelerating discovery, and fostering innovation.

This Special Issue aims to provide a comprehensive overview of current methodologies, applications, and theoretical developments. We encourage contributions that demonstrate the impact of molecular informatics across a wide range of areas, including drug discovery, materials science, systems biology, and the integration of artificial intelligence in molecular research. Join us in celebrating this milestone by sharing your innovative work and shaping the future of molecular informatics.

Dr. M. Natália D.S. Cordeiro
Prof. Dr. Giulio Vistoli
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 250 words) can be sent to the Editorial Office for assessment.

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

  • AI-guided drug repurposing
  • virtual screening in personalized medicine
  • machine learning for toxicity prediction
  • network-based biomarkers in complex diseases
  • in silico pharmacokinetics and ADMET profiling
  • data-driven materials design
  • deep learning for molecular property prediction
  • AI-assisted nanomaterial synthesis
  • systems biology models for metabolic engineering

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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

19 pages, 2897 KB  
Article
Functional Analysis of Hyaluronidase-like Genes in Ovarian Development of Macrobrachium nipponense and Comparative Evaluation with Other Key Regulatory Genes
by Zhiming Wang, Hao Dong, Hui Qiao, Wenyi Zhang, Shubo Jin, Yiwei Xiong, Zhenghao Ye, Yan Gong, Sufei Jiang and Hongtuo Fu
Int. J. Mol. Sci. 2025, 26(21), 10748; https://doi.org/10.3390/ijms262110748 - 5 Nov 2025
Viewed by 391
Abstract
This study conducted a bioinformatic analysis of two Hyaluronidase-like isoforms (Mn-HyaL1 and Mn-HyaL2) in Macrobrachium nipponense and investigated their phylogenetic relationships. The open reading frames of Mn-HyaL1 and Mn-HyaL2 were 1101 bp (encoding 366 amino acids) and 1164 bp (encoding 387 [...] Read more.
This study conducted a bioinformatic analysis of two Hyaluronidase-like isoforms (Mn-HyaL1 and Mn-HyaL2) in Macrobrachium nipponense and investigated their phylogenetic relationships. The open reading frames of Mn-HyaL1 and Mn-HyaL2 were 1101 bp (encoding 366 amino acids) and 1164 bp (encoding 387 amino acids), respectively. Both isoforms exhibited similar conserved domains, with an amino acid sequence similarity of 60.21%. Quantitative PCR analysis revealed that the expression levels of Mn-HyaL1 and Mn-HyaL2 increased during the mid-to-late phase of each developmental stage, were higher during the reproductive season than in the non-reproductive season, and were more abundant in the hepatopancreas than in other tissues. RNA interference experiments targeting both genes simultaneously demonstrated that knockdown of Mn-HyaL2 significantly accelerated ovarian development in M. nipponense, indicating that Mn-HyaL genes function as negative regulators of ovarian maturation. A comparative analysis of multiple genes revealed the following descending order of potency in promoting ovarian development in M. nipponense: Mn-Cholesterol 7-desaturase > Mn-Cathepsin L1. The order of potency in inhibiting ovarian development in M. nipponense, from strongest to weakest, was determined to be Mn-Gonad-inhibiting hormone > Mn-HyaL2. Full article
(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Informatics)
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13 pages, 1868 KB  
Article
Deep Sequencing Analysis of Hepatitis C Virus Subtypes and Resistance-Associated Substitutions in Genotype 4 Patients Resistant to Direct-Acting Antiviral (DAA) Treatment in Egypt
by Damir Garcia-Cehic, Asmaa Mosbeh, Heba A. Gad, Asmaa Ibrahim Gomaa, Marta Ibañez Lligoña, Josep Gregori, Sergi Colomer-Castell, Carolina Campos, Francisco Rodriguez-Frias, Juan Ignacio Esteban, Mohamed S. Kohla, Mohamed Helmy Abdel-Rahman and Josep Quer
Int. J. Mol. Sci. 2025, 26(21), 10649; https://doi.org/10.3390/ijms262110649 - 31 Oct 2025
Viewed by 529
Abstract
Egypt has the highest global prevalence of hepatitis C virus (HCV), with genotype 4 (G4) in over 94% of cases. Direct-acting antivirals (DAAs) yield sustained virologic response (SVR) rates above 95%. Second-generation DAAs are recommended for patients with virological failure, achieving over 90% [...] Read more.
Egypt has the highest global prevalence of hepatitis C virus (HCV), with genotype 4 (G4) in over 94% of cases. Direct-acting antivirals (DAAs) yield sustained virologic response (SVR) rates above 95%. Second-generation DAAs are recommended for patients with virological failure, achieving over 90% eradication. This study aimed to classify and evaluate the pattern of HCV resistance-associated substitutions (RASs) in patients who failed DAA treatment in Egypt. A total of 1778 chronically infected HCV patients from Egypt’s Nile Delta were enrolled (2016–2018). Among them, 37 relapsed, and high-quality serum samples from 22 patients were available, including 6 cases with pre- and post-treatment samples. Next-generation sequencing (NGS) was performed for HCV subtyping and RAS identification. Among the 22 analyzed cases, 21 (95.4%) were G4: 11 were classified as subtype G4a, seven G4o, and three G4m. One patient (4.5%) was identified as G1g. One case shifted from G4a pre- to G4o post-treatment, suggesting reinfection. The RAS pattern in rare G4 subtypes (G4m/G4o) differs from the G4a subtype. The combination of L28M/L30S mutations was detected in 8/11 G4a samples; in contrast, RASs in G4o were characterized by T30S or Y93C/H/N/S substitutions. Notably, some substitutions identified as RASs may represent fixed polymorphisms in regional viral populations, such as those in Egypt’s Nile Delta. HCV subtypes significantly influence the RAS pattern, particularly within the NS5A region, after DAA-treatment failure. The RAS pattern differs among G4 subtypes, particularly in rare ones, predisposing patients to resistance and underscoring the importance of NGS in regional populations to optimize treatment strategies. Full article
(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Informatics)
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23 pages, 4383 KB  
Article
Gaussian Accelerated Molecular Dynamics Simulations Combined with NRIMD to Explore the Mechanism of Substrate Selectivity of Cid1 Polymerase for Different Nucleoside Triphosphates
by Hanwen Liu, Xue Zhou, Haohao Wang, Fuyan Cao and Weiwei Han
Int. J. Mol. Sci. 2025, 26(19), 9325; https://doi.org/10.3390/ijms26199325 - 24 Sep 2025
Viewed by 680
Abstract
Cid1 protein is a crucial component in the RNA interference pathway and abnormal nuclear RNA turnover processes, primarily responsible for adding uridine to the 3′ end of RNA. Cid1 exhibits selective polymerization of UTP over other nucleoside triphosphates. To explore the mechanism of [...] Read more.
Cid1 protein is a crucial component in the RNA interference pathway and abnormal nuclear RNA turnover processes, primarily responsible for adding uridine to the 3′ end of RNA. Cid1 exhibits selective polymerization of UTP over other nucleoside triphosphates. To explore the mechanism of this selectivity, five systems: free-Cid1, Cid1-ATP, Cid1-UTP, Cid1-CTP, and Cid1-GTP with 500 ns Gaussian accelerated molecular dynamics (GaMD) simulations were performed to investigate conformational changes and binding affinities between substrates and Cid1. The results showed that UTP formed stronger and more numerous non-covalent interactions with Cid1 compared to the other three substrates. The Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) binding energy analysis revealed a substrate preference for Cid1 polymerase in the order of UTP, followed by ATP, CTP, and GTP. These findings provide theoretical insights into the substrate selectivity mechanism of Cid1 and provide theoretical clues for the design and modification of Cid1 polymerase. Full article
(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Informatics)
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