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The Role of Natural Products in Drug Discovery
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The Role of Natural Products in Drug Discovery

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

Deadline for manuscript submissions: 31 May 2025 | Viewed by 2938

Special Issue Editors

Prof. Dr. Luciana Scotti

E-Mail Website
Guest Editor
Laboratório de Tecnologia Farmacêutica, Federal University of Paraíba, Campus I, João Pessoa 58051-970, PB, Brazil
Interests: molecular modeling; cheminformatic; natural products
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Marcus Tullius Scotti

E-Mail Website
Guest Editor
Department of Chemistry, Federal University of Paraíba, João Pessoa, Brazil
Interests: natural products database; cheminformatics; virtual screening; chemotaxonomy; natural product drug discovery; machine learning; molecular descriptors
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Natural products often result from an optimized evolutionary process in which chemicals have been under the selective forces of coevolution, where organisms produce substances in the presence of their predators. These natural compounds have been utilized by humans since ancient times to treat and cure their diseases. Of the existing plants in the world, most of which are unknown from a scientific point of view, only about 5% of the approximately 250,000-500,000 species have been biologically studied and evaluated. Natural products are often phenolic compounds, flavonoids, alkaloids, or terpenes—secondary plant metabolites that may provide several benefits to our health. These benefits include cosmetic action, cardioprotective effects, anti-inflammatory activity, the treatment of cancer, etc.

More than half of the world's population uses medicines of natural origin, and approximately half of the commercially available drugs are of natural origin or based on natural pharmacophores. There is a popular illusion that a natural compound is both effective and completely safe. Pharmaceutical industries find fertile ground in this untruth and exploit the lack of mass knowledge. In addition, the rich chemical universe associated with more advantageous physicochemical properties for the medicinal use of natural products makes them more attractive than purely synthetic ones. Despite the difficulties in the extraction, isolation, and characterization of their molecular structure, and although the sources (mainly the marine ones) are not always abundantly available, the pharmaceutical market generates billions of dollars selling natural drugs. In recent decades, this profit has shown growth. On the other hand, the planet's natural sources have immense wealth that is still unexplored. This issue will consist of articles that report different studies carried out in relation to natural drug research in order to provide relevant information on new drug candidate compounds that use bioactive natural products.

Prof. Dr. Luciana Scotti
Prof. Dr. Marcus Tullius Scotti
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

  • natural product
  • medicinal chemistry
  • drug design
  • drug discovery
  • pharmacy
  • chemistry

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Published Papers (4 papers)

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Research

21 pages, 6365 KiB  
Article
Network Pharmacology and Molecular Dynamics Identified Potential Androgen Receptor-Targeted Metabolites in Crocus alatavicus
by Zhen Ding, Yuanfeng Lu, Jichen Zhao, Daoyuan Zhang and Bei Gao
Int. J. Mol. Sci. 2025, 26(8), 3533; https://doi.org/10.3390/ijms26083533 - 9 Apr 2025
Viewed by 438
Abstract
The objective of this study is to identify the active components of Crocus alatavicus and potential targets through a combination of network pharmacology, molecular docking technology combined with molecular dynamics simulation, and binding free energy analyses. A total of 253 active ingredients from [...] Read more.
The objective of this study is to identify the active components of Crocus alatavicus and potential targets through a combination of network pharmacology, molecular docking technology combined with molecular dynamics simulation, and binding free energy analyses. A total of 253 active ingredients from C. alatavicus were screened, and 1360 associated targets were predicted through systematic searches conducted using TCMSP, SwissDrugDesign, and SymMap, which were integrated to construct a pharmacological network to dissect the relationships among active components, targets, diseases, and pathways; we found prostate cancer-related genes were significantly enriched among the targets. Subsequently, the core prostate cancer-related targets were identified in the network, and the binding interactions between protein targets and active components were evaluated using molecular docking technology. Furthermore, molecular dynamics simulation and binding free energy analyses were performed to verify the binding stability of the most promising complex. Then, protein–protein interaction network analysis was conducted to evaluate the core target sites, leading to the identification of nine target proteins with significant correlations, providing potential targets for cancer treatment. Furthermore, these targets were found to be associated with 20 signaling pathways, including neuroactive ligand–receptor interactions, prostate cancer, lipid metabolism and atherosclerosis, as well as calcium signaling pathways. The active component–target–disease–pathway network diagram suggests that Capillarisin, Eugenol, 1-(4-Methoxyphenyl)-1-propanol, 2,4,2′,4′-tetrahydroxy-3′-prenylchalcone, and 4-Hydroxymandelonitrile may serve as key components targeting prostate cancer. Molecular docking analyses demonstrated that Capillarisin has a high affinity for the androgen receptor (AR), and molecular dynamics simulation was performed to further verify the binding stability, indicating that Capillarisin may exert its pharmacological effects in prostate cancer. Based on the integrated strategies of network pharmacology, molecular docking, molecular dynamics simulation, and binding free energy analysis, this study generated novel insights into the active components of C. alatavicus and potential targets related to prostate cancer, thus providing valuable biological resources for future drug research and development. Full article
(This article belongs to the Special Issue The Role of Natural Products in Drug Discovery)
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19 pages, 2119 KiB  
Article
4-Hydroxycoumarin Exhibits Antinociceptive and Anti-Inflammatory Effects Through Cytokine Modulation: An Integrated In Silico and In Vivo Study
by Diogo Vilar da Fonsêca, Juliana Sousa Rocha, Pablo R. da Silva, Hugo Natan de Sá Novaes Pereira, Lucas Vinicius Novaes dos Santos, Melquisedec Abiaré Dantas de Santana, Alan F. Alves, Adiel H. O. Pontes, Joás de Souza Gomes, Cícero F. Bezerra Felipe, Damião Pergentino de Sousa, Marcus T. Scotti and Luciana Scotti
Int. J. Mol. Sci. 2025, 26(6), 2788; https://doi.org/10.3390/ijms26062788 - 19 Mar 2025
Cited by 1 | Viewed by 464
Abstract
Chronic pain significantly impacts quality of life and is often accompanied by inflammation, a natural bodily response that can become harmful when excessive. The orofacial region is commonly affected, making effective treatment crucial. However, current drugs often cause undesirable side effects, highlighting the [...] Read more.
Chronic pain significantly impacts quality of life and is often accompanied by inflammation, a natural bodily response that can become harmful when excessive. The orofacial region is commonly affected, making effective treatment crucial. However, current drugs often cause undesirable side effects, highlighting the need for new pharmacological alternatives. 4-hydroxycoumarin (4-HC), a natural compound, has shown promising antinociceptive and anti-inflammatory effects, but studies confirming its specific properties are limited. In silico analyses suggest that 4-HC exhibits favorable pharmacokinetic characteristics, not interacting with P-glycoprotein and successfully crossing the blood–brain barrier. Molecular docking studies indicate that its effects may be mediated through NMDAR or by inhibiting iNOS. Our study assessed the antinociceptive and anti-inflammatory effects of 4-HC in animal models at doses of 25, 50, and 75 mg/kg. 4-HC significantly reduced abdominal contortions induced by acetic acid and decreased nociceptive rubbing in orofacial pain models induced by formalin, glutamate, and capsaicin. Interactions with opioid receptors were not observed, suggesting that 4-HC’s antinociceptive effect does not involve this pathway. Additionally, 4-HC reduced paw edema induced by carrageenan and significantly decreased leukocyte migration and TNF-α levels. These findings highlight the therapeutic potential of 4-HC and warrant further investigation into its mechanisms. Full article
(This article belongs to the Special Issue The Role of Natural Products in Drug Discovery)
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19 pages, 1482 KiB  
Article
Exploring the In Vitro Photoprotective Effect of a Combination of Aspalathus linearis Natural Extracts: First Steps in Developing New Technologies for Photoprotection Strategies
by Irene Cáceres Estévez, Luisa Haya Rodriguez, Elena Haro Perdiguero, Francisco Javier Moreno Tovar, David Montalvo Lobo, Luis Nieto Botella, Salvador González and Ana López Sánchez
Int. J. Mol. Sci. 2025, 26(5), 2330; https://doi.org/10.3390/ijms26052330 - 5 Mar 2025
Viewed by 723
Abstract
There is a need for new technologies in photoprotection. The negative effects of solar exposure on the skin have been amply demonstrated and there is an urgency for the development of alternative photoprotective approaches. In this respect, natural extracts represent the most interesting [...] Read more.
There is a need for new technologies in photoprotection. The negative effects of solar exposure on the skin have been amply demonstrated and there is an urgency for the development of alternative photoprotective approaches. In this respect, natural extracts represent the most interesting and promising source. Among them, Aspalathus linearis extracts appear to be an excellent candidate due to supporting evidence, their multiple beneficial biological effects, and their robust toxicological profile. Here, we first explored the photoprotective properties of two different Aspalathus linearis extracts (fermented and unfermented) individually, and then in combination, in a simplified model assessing Normal Human Dermal Fibroblast survival after UVB radiation. Surprisingly, we found the fermented extract to be more photoprotective than the unfermented one. In addition, a specific combination of the two extracts showed a synergistic effect. By HPLC and FRAP analyses, we observed that the photoprotective effect did not correlate with the amount of Aspalathus linearis main characteristic metabolites nor with the antioxidant capacity of the ingredients. Finally, an additional photoprotective effect was observed when Aspalathus linearis extracts were combined with a Polypodium leucotomos extract (Fernblock®), a well-known botanical ingredient with demonstrated photoprotection activities. Thus, this work provides a solid scientific basis for the inclusion of this technology in future topical and systemic photoprotective strategies. Full article
(This article belongs to the Special Issue The Role of Natural Products in Drug Discovery)
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9 pages, 1858 KiB  
Communication
Role of Human DNA Ligases in Mediating Pharmacological Activities of Flavonoids
by Daekyu Sun and Vijay Gokhale
Int. J. Mol. Sci. 2025, 26(4), 1456; https://doi.org/10.3390/ijms26041456 - 10 Feb 2025
Viewed by 566
Abstract
Dietary flavonoids are a group of polyphenol compounds originating from plants that have drawn much attention in the last few decades. Flavonoid-rich foods and dietary supplements are used worldwide due to their health benefits, including antioxidative, anti-inflammatory, immunity-enhancing, anticarcinogenic, estrogenic, and favorable cardiovascular [...] Read more.
Dietary flavonoids are a group of polyphenol compounds originating from plants that have drawn much attention in the last few decades. Flavonoid-rich foods and dietary supplements are used worldwide due to their health benefits, including antioxidative, anti-inflammatory, immunity-enhancing, anticarcinogenic, estrogenic, and favorable cardiovascular effects. The main objective of our study was to explore the molecular targets of flavonoids to gain insight into the mechanism of action behind their biological effects. In this study, a novel class of resorcinol-based flavonoid compounds was identified as a potent inhibitor of human DNA ligase activity. Human DNA ligases are crucial in the maintenance of genetic integrity and cell fate determination. Thus, our results strongly suggest that this activity against human DNA ligases is responsible, at least in part, for the cellular effects of flavonoid compounds. We anticipate that the results from our studies will improve our understanding of how interactions with human DNA ligases cascade into the recognized health benefits of flavonoids, particularly their wide variety of anticancer effects. Full article
(This article belongs to the Special Issue The Role of Natural Products in Drug Discovery)
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