ijms-logo

Journal Browser

Journal Browser

In Silico Methods of Assessing the Therapeutic Potential of Natural Substances

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: 20 June 2025 | Viewed by 1297

Special Issue Editors


E-Mail Website
Guest Editor
1. Department of Economic and Medical Informatics, University of Lodz, 90-214 Lodz, Poland
2. Department of Medical Informatics and Statistics, Medical University of Lodz, 90-645 Lodz, Poland
Interests: in silico screening; natural products; molecular docking; computational drug discovery; QSAR modeling; molecular dynamics simulations; natural compounds; drug-target interactions; virtual screening; structure-activity relationships; computational chemistry; cheminformatics; ADMET prediction; bioinformatics; phytochemicals; machine learning in drug discovery; computer-aided drug design; pharmacophore modeling; natural therapeutics; computational pharmacology
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
1. Department of Economic and Medical Informatics, University of Lodz, 90-214 Lodz, Poland
2. Department of Allergology and Respiratory Rehabilitation, Medical University of Lodz, 90-725 Lodz, Poland
Interests: in silico screening; natural products; molecular docking; computational drug discovery; QSAR modeling; molecular dynamics simulations; natural compounds; drug-target interactions; virtual screening; structure-activity relationships; computational chemistry; cheminformatics; ADMET prediction; bioinformatics; phytochemicals; machine learning in drug discovery; computer-aided drug design; pharmacophore modeling; natural therapeutics; computational pharmacology

Special Issue Information

Dear Colleagues,

The exploration of naturally occurring substances for therapeutic applications has entered a new era with the advancement of computational methods. This Special Issue focuses on cutting-edge in silico approaches for evaluating the therapeutic potential of natural compounds, bringing together research that bridges traditional natural product discovery with modern computational techniques. We welcome studies involving molecular docking, machine learning applications, QSAR modeling, molecular dynamics simulations, and other computational methods that advance our understanding of natural substances' biological activities and drug-like properties. The issue particularly emphasizes research combining multiple computational approaches to predict, analyze, and optimize the therapeutic potential of compounds derived from natural sources, including plants. Original research articles, comprehensive reviews, and methodological papers addressing challenges and innovations in computational assessment of natural products are encouraged. Topics of interest include, but are not limited to, virtual screening of natural compound libraries, prediction of ADMET properties, target identification, and structure-activity relationship analyses. This Special Issue aims to showcase how in silico methods can accelerate the discovery and development of natural substance-based therapeutics while reducing the time and resources required for traditional experimental approaches.

Prof. Dr. Radosław Zajdel
Dr. Anna Merecz-Sadowska
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

  • in silico screening
  • natural products
  • molecular docking
  • computational drug discovery
  • QSAR modeling
  • molecular dynamics simulations
  • natural compounds
  • drug-target interactions
  • virtual screening
  • structure-activity relationships
  • computational chemistry
  • cheminformatics
  • ADMET prediction
  • bioinformatics
  • phytochemicals
  • machine learning in drug discovery
  • computer-aided drug design
  • pharmacophore modeling
  • natural therapeutics
  • computational pharmacology

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 policies can be found here.

Published Papers (2 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

21 pages, 2686 KiB  
Article
In Silico Identification of Putative Allosteric Pockets and Inhibitors for the KRASG13D-SOS1 Complex in Cancer Therapy
by Zehra Sarica, Ozge Kurkcuoglu and Fethiye Aylin Sungur
Int. J. Mol. Sci. 2025, 26(7), 3293; https://doi.org/10.3390/ijms26073293 - 2 Apr 2025
Viewed by 424
Abstract
RAS mutations occur in about 30% of human cancers, leading to enhanced RAS signaling and tumor growth. KRAS is the most commonly mutated oncogene in human tumors, especially lung, pancreatic, and colorectal cancers. Direct targeting of KRAS is difficult due to its highly [...] Read more.
RAS mutations occur in about 30% of human cancers, leading to enhanced RAS signaling and tumor growth. KRAS is the most commonly mutated oncogene in human tumors, especially lung, pancreatic, and colorectal cancers. Direct targeting of KRAS is difficult due to its highly conserved sequence; but, its complex with the guanine nucleotide exchange factor Son of Sevenless (SOS) 1 promises an attractive target for inhibiting RAS-mediated signaling. Here, we first revealed putative allosteric binding sites of the SOS1, KRASG12C-SOS1 complex, and the ternary KRASG13D-SOS1 complex structures using two network-based models, the essential site scanning analysis and the residue interaction network model. The results enabled us to identify two new putative allosteric pockets for the ternary KRASG13D-SOS1 complex. These were then screened together with the known ligand binding site against the natural compounds in the InterBioScreen (IBS) database using the Glide software package developed by Schrödinger, Inc. The docking poses of seven hit compounds were assessed using 400 ns long molecular dynamics (MD) simulations with two independent replicas using Desmond, coupled with thermal MM-GBSA calculations for the estimation of the binding free energy values. The structural skeleton of the seven proposed compounds consists of different functional groups and heterocyclic rings that possess anti-cancer activity and exhibit persistent interactions with key residues in binding pockets throughout the MD simulations. STOCK1N-09823 was determined as the most promising hit that promoted the disruption of the interactions R73 (chain A)/N879 and R73 (chain A)/Y884, which are key for SOS1-mediated KRAS activation. Full article
Show Figures

Figure 1

20 pages, 13101 KiB  
Article
Dalbergia odorifera Trans-Nerolidol Protects Against Myocardial Ischemia via Downregulating Cytochrome- and Caspases-Signaling Pathways in Isoproterenol-Induced Rats
by Canhong Wang, Yulan Wu, Bao Gong, Xiangsheng Zhao, Hui Meng, Junyu Mou, Xiaoling Cheng, Yinfeng Tan and Jianhe Wei
Int. J. Mol. Sci. 2025, 26(5), 2251; https://doi.org/10.3390/ijms26052251 - 3 Mar 2025
Viewed by 608
Abstract
Dalbergia odorifera is widely used to treat cardiovascular diseases. Our research group found that Dalbergia odorifera volatile oil has a good anti-myocardial ischemic effect, and its main pharmacodynamic components are trans-nerolol and its oxides. However, the exact mechanisms underlying this effect have not [...] Read more.
Dalbergia odorifera is widely used to treat cardiovascular diseases. Our research group found that Dalbergia odorifera volatile oil has a good anti-myocardial ischemic effect, and its main pharmacodynamic components are trans-nerolol and its oxides. However, the exact mechanisms underlying this effect have not yet been elucidated. This study aimed to explore the potential myocardial protective effects of trans-nerolol and its underlying molecular mechanisms. Molecular docking was used to predict and visualize the possible mechanism of the anti-apoptotic myocardial protection by trans-nerolol. The myocardial protective effect of trans-nerolol was evaluated by observing pathological injury, myocardial enzyme levels, oxidation, antioxidant levels, and the expression of related proteins. Molecular docking results showed that trans-nerolol binds closely to cytochrome C (Cytc) and apoptosis-related proteins, suggesting that it may play a role in interacting with these target proteins. The results showed that pre-treatment with dose-dependent trans-nerolol significantly mitigated the myocardial histological damage; decreased lactate dehydrogenase (LDH), creatinine kinase (CK), alanine transaminase (ALT), and aspartate transaminase (AST) levels; reduced nitric oxide (NO) production, hydrogen peroxide (H2O2), and lipid peroxide (LPO); and increased the total antioxidant content (T-AOC), glutathione (GSH), catalase (CAT), and superoxide dismutase (SOD) activities compared with the model group. In addition, dose-dependent trans-nerolol significantly increased the Na+-K+-ATPase and Ca2+-Mg2+-ATPase levels. Moreover, trans-nerolol markedly reduced the endogenous and external apoptotic pathways; downregulated the protein expression of Cytc, apoptotic protease activating factor-1 (Apaf1), Fibroblast-associated (Fas), Cysteine-aspartate protease 3 (Caspase3), Cysteine-aspartate protease 8 (Caspase8), and Cysteine-aspartate protease 9 (Caspase9); and upregulated the expression of Heat shock protein 70 (Hsp70) and B-cell lymphoma-2 (Bcl-2). These data indicate that trans-nerolol exerts protective effects against myocardial ischemia (MI), and its mechanism is associated with the suppression of the Cytc- and caspase-signaling pathways. Trans-nerolol has a therapeutic effect on MI, and its mechanism of action is related to its anti-apoptotic effect. These results suggest that Dalbergia odorifera has a potential role to be developed as an MI-promoting therapeutic agent. Full article
Show Figures

Figure 1

Back to TopTop