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Cheminformatics in Drug Discovery and Green Synthesis
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Cheminformatics in Drug Discovery and Green Synthesis

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 July 2025 | Viewed by 5643

Special Issue Editor

Dr. Ana Amić

E-Mail Website
Guest Editor
Department of Chemistry, Josip Juraj Strossmayer University of Osijek, Ulica Cara Hadrijana 8A, 31000 Osijek, Croatia
Interests: computational chemistry; mechanisms of antioxidant activity; antiradical potential of polyphenolic compounds; DFT; molecular simulations; molecular docking; cheminformatics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue aims to provide an overview of the impact of cheminformatics methods in drug discovery and green synthesis. Some aspects of interest are data mining integrated in cheminformatics (descriptor computations, structural similarity matrices, etc.), virtual libraries, building molecular databases for drug screening, in silico methods for data curation, optimisation of candidate drug molecules, visualisation and analysis of candidate drug molecule for better understanding of compound structure and prediction of compound bioactivity, toxicity or safety profiles, molecular docking for finding drug targets, etc. The part related to green synthesis focuses on novel environmentally friendly approaches for drug synthesis and the role of cheminformatics in these approaches. Drug synthesis is in most cases connected with negative impact on the environment, especially nowadays when the situation is additionally worsened due to the ever-growing population and environmental damage caused by various industries. Hence, the design of environmentally acceptable methods and technologies has a lot to offer, making green chemistry a very useful and significant tool for drug development. Future directions of cheminformatics and their impact on drug discovery and green synthesis are of interest as well.

Dr. Ana Amić
Guest Editor

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.

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Keywords

  • cheminformatics
  • drug discovery
  • databases
  • in silico methods
  • green chemistry

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Published Papers (5 papers)

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Research

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22 pages, 7438 KiB  
Article
Bacillibactin, a Potential Bacillus-Based Antibacterial Non-Ribosomal Peptide: In Silico Studies for Targeting Common Fish Pathogens
by Evgeniya Prazdnova, Anna Zaikina, Alexey Neurov, Maria Mazanko, Anuj Ranjan and Dmitry Rudoy
Int. J. Mol. Sci. 2025, 26(12), 5811; https://doi.org/10.3390/ijms26125811 - 17 Jun 2025
Viewed by 486
Abstract
Aquaculture is one of the fastest-growing sectors in food production. The widespread use of antibiotics in fish farming has been identified as a driver for the development of antibiotic resistance. One of the promising approaches to solving this problem is the use of [...] Read more.
Aquaculture is one of the fastest-growing sectors in food production. The widespread use of antibiotics in fish farming has been identified as a driver for the development of antibiotic resistance. One of the promising approaches to solving this problem is the use of probiotics. There are many promising aquaculture probiotics in the Bacillus genus, which produces non-ribosomal peptides (NRPs). NRPs are known as antimicrobial agents, although evidence is gradually accumulating that they may have other effects, especially at lower (subinhibitory) concentrations. The mechanisms of action of many NRPs remain unexplored, and molecular docking and molecular dynamics studies are invaluable tools for studying such mechanisms. The purpose of this study was to investigate the in silico inhibition of crucial bacterial targets by NRPs. Molecular docking analyses were conducted to assess the binding affinities of the NRPs of Bacillus for protein targets. Among the complexes evaluated, bacillibactin with glutamine synthetase, dihydrofolate reductase, and proaerolysin exhibited the lowest docking scores. Consequently, these complexes were selected for further investigation through molecular dynamics simulations. As a result, three additional potential mechanisms of action for bacillibactin were identified through in silico analyses, including the inhibition of glutamine synthetase, dihydrofolate reductase, and proaerolysin, which are critical bacterial enzymes and considered as the potential antibacterial targets. These findings were further supported by in vitro antagonism assays using bacillibactin-producing Bacillus velezensis strains MT55 and MT155, which demonstrated strong inhibitory activity against Pseudomonas aeruginosa and Aeromonas veronii. Full article
(This article belongs to the Special Issue Cheminformatics in Drug Discovery and Green Synthesis)
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20 pages, 2187 KiB  
Article
The 8-Hydroxyquinoline Derivatives of 1,4-Naphthoquinone: Synthesis, Computational Analysis, and Anticancer Activity
by Arkadiusz Sokal, Roman Wrzalik, Małgorzata Latocha and Monika Kadela-Tomanek
Int. J. Mol. Sci. 2025, 26(11), 5331; https://doi.org/10.3390/ijms26115331 - 1 Jun 2025
Viewed by 722
Abstract
Anticancer drug design has been reformed by the creation of heterocyclic hybrids. The introduction of a quinoline scaffold affects the activity, toxicity, and bioavailability of new compounds. The aim of this study was to synthesize and evaluate the biological activity of hybrids of [...] Read more.
Anticancer drug design has been reformed by the creation of heterocyclic hybrids. The introduction of a quinoline scaffold affects the activity, toxicity, and bioavailability of new compounds. The aim of this study was to synthesize and evaluate the biological activity of hybrids of 1,4-naphthoquinone with the 8-hydroxyquinoline moiety. The structure of the new compounds was characterized using spectroscopic methods, such as HR-MS, NMR, and IR. The analysis was supplemented by calculated NMR and IR spectra. The physicochemical properties and bioavailability of the compounds were examined using in silico methods. An analysis of reactivity descriptors showed that the compounds are good electron acceptors and exhibit high reactivity. Bioavailability properties confirm that hybrids could be good oral administration drugs. The biological potential of hybrids was examined by designation of the enzymatic conversion rate of the NQO1 protein and in vitro against cancer cell lines with overexpression of the gene encoding the NQO1 protein. The possibility of interaction between the tested ligand and the NQO1 protein was examined by molecular docking methods. Full article
(This article belongs to the Special Issue Cheminformatics in Drug Discovery and Green Synthesis)
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17 pages, 6609 KiB  
Article
Rational Method for Structural Simplification as Key Step in Hit Discovery: The Case of FGFR2 and IGF1R Dual Inhibitors
by Endika Torres-Urtizberea, José I. Borrell, Raimon Puig de la Bellacasa and Roger Estrada-Tejedor
Int. J. Mol. Sci. 2025, 26(9), 4457; https://doi.org/10.3390/ijms26094457 - 7 May 2025
Viewed by 426
Abstract
In the classic medicinal chemistry hit discovery procedure, large virtual libraries undergo different filtering and prediction steps until a small group of molecules is selected for their subsequent synthesis and biological testing. The starting molecular libraries can easily be composed of millions of [...] Read more.
In the classic medicinal chemistry hit discovery procedure, large virtual libraries undergo different filtering and prediction steps until a small group of molecules is selected for their subsequent synthesis and biological testing. The starting molecular libraries can easily be composed of millions of molecules, hindering the selection of the most representative and promising compounds. Moreover, the resulting molecular systems tend to be overcomplex structures, hardly attainable, and often involve extrapolations of the prediction models used. We present a rational-based method to reduce the structural complexity of molecular candidates without compromising their biological activity, improving the attainability and efficiency of hit discovery. This approach has been successfully applied to identify potential tyrosine kinase dual inhibitors against Fibroblast Growth Factor Receptor 2 (FGFR2) and Insulin-Like Growth Factor 1 Receptor (IGF1R), a set of overexpressed proteins in different cancers, such as pancreatic ductal adenocarcinoma (PDAC). Full article
(This article belongs to the Special Issue Cheminformatics in Drug Discovery and Green Synthesis)
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25 pages, 4644 KiB  
Article
Design and Synthesis of New 5-Methylisatin Derivatives as Potential CDK2 Inhibitors
by Przemysław Czeleń, Agnieszka Skotnicka, Beata Szefler, Janina Kabatc-Borcz and Paweł Sutkowy
Int. J. Mol. Sci. 2025, 26(5), 2144; https://doi.org/10.3390/ijms26052144 - 27 Feb 2025
Cited by 1 | Viewed by 725
Abstract
Cancer remains one of the leading causes of death globally, driving the need for effective therapies. Targeting cyclin-dependent kinase 2 (CDK2), a critical cell cycle regulator, is a promising approach for cancer treatment. This study developed a new group of 5-methylisatin derivatives with [...] Read more.
Cancer remains one of the leading causes of death globally, driving the need for effective therapies. Targeting cyclin-dependent kinase 2 (CDK2), a critical cell cycle regulator, is a promising approach for cancer treatment. This study developed a new group of 5-methylisatin derivatives with strong binding potential to CDK2. By combining the isatin core with various benzoylhydrazide substituents, the design process was guided by molecular docking, dynamic simulations, and ADMET analysis. Thirty-one derivatives were modelled, and a subset was synthesised and characterised for their physicochemical and spectroscopic properties. The analysis suggested that substitutions at R2 and R3 positions improved binding affinity, while modifications at R4 were less favourable. Hydrogen bonds with GLU81 and LEU83, along with hydrophobic interactions, were key to stabilising the complexes. A comparison with a reference molecule (RM) 3-((2,6-Dichlorobenzylidene)hydrazono)indolin-2-one, showing inhibitory activity similar to doxorubicin, revealed several advantages for the new derivatives. The multidimensional comparative analysis highlighted significant improvements in active site affinity, conformational stability, and fit. ADMET analysis confirmed comparable performance in most areas, with superior bioavailability observed in derivatives 1, 2a, 2b, 3h, 3b, and 3e. These results suggest that 5-methylisatin derivatives could be promising CDK2 inhibitors. Full article
(This article belongs to the Special Issue Cheminformatics in Drug Discovery and Green Synthesis)
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Review

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32 pages, 26719 KiB  
Review
Importance of Advanced Detection Methodologies from Plant Cells to Human Microsystems Targeting Anticancer Applications
by Mostafa M. Gouda, Eman R. Elsharkawy, Yong He and Xiaoli Li
Int. J. Mol. Sci. 2025, 26(10), 4691; https://doi.org/10.3390/ijms26104691 - 14 May 2025
Cited by 1 | Viewed by 2585
Abstract
The growing global demand for phytochemicals as bioactive sources is prompting scientists to develop methods that link their sensory properties to their mechanisms of action in cancer treatment. Recent techniques for tracking the actions of small plant metabolites (SPMs) from single-cell plant sources [...] Read more.
The growing global demand for phytochemicals as bioactive sources is prompting scientists to develop methods that link their sensory properties to their mechanisms of action in cancer treatment. Recent techniques for tracking the actions of small plant metabolites (SPMs) from single-cell plant sources to their molecular anticancer biomarkers could provide valuable insights in this field. Among the critical methods discussed in this review are the real-time tracking of cell components through stable isotope probing (Sis) and microspectroscopy, which has attracted the attention of biotechnologists. Additionally, the precise pathways required for studying new insights into functional materials are discussed, based on high-resolution and accurate technologies, which could aid their functional categorization. Notably, the molecules under study have recently garnered attention for their anticancer applications due to advancements in effective evaluation techniques that surpass traditional methods. In December 2020, the Food and Drug Administration (FDA) authorized 89 SPMs as safe anticancer natural molecules. In conclusion, by combining spatiotemporal techniques and SPMs’ mechanisms, they could facilitate the development of more exceptional, bio-efficient materials. Full article
(This article belongs to the Special Issue Cheminformatics in Drug Discovery and Green Synthesis)
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