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Natural Bioactive Compounds from Plants: Progress in Phytochemistry, Computational Approaches...
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Natural Bioactive Compounds from Plants: Progress in Phytochemistry, Computational Approaches and Biomedical Applications

A Special Issue of Pharmaceuticals (ISSN 1424-8247) belonging to the section "Natural Products".

Deadline for manuscript submissions: 31 December 2026 | Viewed by 2623

Editors

Dr. Maira Huerta-Reyes

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Guest Editor
Unidad de Investigación Médica en Enfermedades Nefrológicas, Hospital de Especialidades “Dr. Bernardo Sepúlveda Gutiérrez”, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Cuauhtémoc, Ciudad de México 06720, Mexico
Interests: pharmacognosy; botany; medicinal chemistry; patents in plants; chronic diseases
Special Issues, Collections and Topics in MDPI journals
Dr. Gil Alfonso Magos-Guerrero

E-Mail Website
Guest Editor
Department of Pharmacology, Faculty of Medicine, University National Autonomous of Mexico (UNAM), Mexico City 04510, Mexico
Interests: medicinal chemistry; cardiovascular diseases; pharmacology; cheminformatics
Special Issues, Collections and Topics in MDPI journals
Dr. Oscar Barrera-Vázquez

E-Mail Website
Guest Editor
Department of Pharmacology, Faculty of Medicine, University National Autonomous of Mexico (UNAM), Mexico City 04510, Mexico
Interests: natural products; cheminformatics; network pharmacology; fingerprints
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Natural bioactive compounds have been used for centuries in the management of human diseases. Natural products from plants continue to represent a cornerstone in drug discovery and development, offering a vast and chemically diverse reservoir of novel therapeutic agents. A substantial body of preclinical, clinical and computational evidence highlights the therapeutic potential of natural products from plants in the prevention and treatment of several human conditions.

This Special Issue invites innovative and high-quality contributions exploring standardized medicinal plant extracts and natural products as sources of bioactive compounds with biomedical applications. We welcome original research articles and comprehensive reviews addressing phytochemicals with biological activities, the biochemical and molecular mechanisms underlying their therapeutic effects and computational approaches.

Submissions incorporating comprehensive insights into the biomedical potential of natural products and supporting their translation into effective and safe therapeutic strategies are strongly encouraged.

Dr. Maira Huerta-Reyes
Dr. Gil Alfonso Magos-Guerrero
Dr. Oscar Barrera-Vázquez
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-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Pharmaceuticals is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2900 CHF (Swiss Francs). 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 products
  • medicinal plants
  • biomedical
  • computational
  • in silico

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Published Papers (5 papers)

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Research

Jump to: Review

16 pages, 3534 KB  
Article
A New Flavonoid Glycoside from the Stem Bark of Albizia saponaria: Isolation, Structural Elucidation, and In Silico Evaluation as a Potent α-Glucosidase Inhibitor
by Emma Julin Pongoh and Rymond Jusuf Rumampuk
Pharmaceuticals 2026, 19(9), 1391; https://doi.org/10.3390/ph19091391 - 2 Sep 2026
Viewed by 269
Abstract
Background/Objectives: In the search for potent non-sugar α-glucosidase inhibitors with improved safety profiles, a novel flavonoid glycoside was isolated for the first time from the stem bark of Albizia saponaria (Fabaceae). The objective of this study was to elucidate its chemical structure [...] Read more.
Background/Objectives: In the search for potent non-sugar α-glucosidase inhibitors with improved safety profiles, a novel flavonoid glycoside was isolated for the first time from the stem bark of Albizia saponaria (Fabaceae). The objective of this study was to elucidate its chemical structure and evaluate its therapeutic potential as an anti-hyperglycemic agent compared to known related flavonoids and a standard clinical drug. Methods: Comprehensive structural elucidation was performed using high-resolution mass spectrometry and multidimensional 1D/2D NMR (1H, 13C, HSQC-DEPT, COSY, and CIGAR). To assess its inhibitory efficacy and pharmacokinetic profiles, an in silico comparative study was conducted against a database of related flavonoids (Quercitrin, Hyperoside, and Isoquercitrin) and the clinical drug Acarbose. This involved molecular docking simulations against human intestinal maltase-glucoamylase (PDB ID: 3TOP) alongside integrated ADMET modeling and toxicological screening. Results: The compound was successfully identified as 4′,7-dihydroxyflavan-3′-O-β-D-glucoside (1). Molecular docking revealed that Compound 1 exhibited a superior predicted binding affinity of −9.5 kcal/mol, outperforming Quercitrin (−9.3 kcal/mol), Hyperoside (−8.3 kcal/mol), Isoquercitrin (−7.9 kcal/mol), and Acarbose (−7.2 kcal/mol). This strong thermodynamic stability is driven by a robust conventional hydrogen-bonding network with key active site residues (Arg1377, Gln1372, and Gly1365), successfully overriding a localized electrostatic strain at Asp1279. Furthermore, ADMET modeling demonstrated a highly desirable local pharmacokinetic framework; its low Caco-2 permeability (−6.432) and low human intestinal absorption (HIA = 0.120) favor targeted luminal retention in the gastrointestinal tract, mirroring Acarbose while minimizing systemic exposure. Crucially, toxicological screening unveiled a significant safety advantage for Compound 1, marked by negligible CYP3A4 interaction (0.004) and a remarkably low risk of Drug-Induced Liver Injury (DILI = 0.213) compared to the high-risk hepatotoxic profile of Acarbose (DILI = 0.882) and the reference flavonoids (DILI > 0.69). Conclusions: These predictive findings establish Compound 1 as a highly promising, low-toxicity natural scaffold for anti-hyperglycemic drug development. Its superior binding affinity and minimized hepatotoxicity risk warrant subsequent in vitro and in vivo functional validation. Full article
(This article belongs to the Special Issue Natural Bioactive Compounds from Plants: Progress in Phytochemistry, Computational Approaches and Biomedical Applications)
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26 pages, 17413 KB  
Article
Pharmacological Effects of Wenjing Decoction in a Rat Model of Cold Coagulation and Blood Stasis Primary Dysmenorrhea: An Integrated Analysis of Serum Pharmacochemistry, Network Pharmacology and Metabolomics
by Junge Li, Yuxin Liu, Xin Shao, Yuanlu Zhang, Zhidong Qiu, Yongchun Wang, Feiran Qi, Qiuzhu Tang and Ailing Jia
Pharmaceuticals 2026, 19(9), 1385; https://doi.org/10.3390/ph19091385 - 1 Sep 2026
Viewed by 294
Abstract
Background: Primary dysmenorrhea (PD) is a prevalent gynecological condition that significantly compromises the quality of life in adolescents and women of reproductive age. Within traditional Chinese medicine (TCM), Cold Coagulation and Blood Stasis Primary Dysmenorrhea (CCBS-PD) represents the most frequently observed syndrome [...] Read more.
Background: Primary dysmenorrhea (PD) is a prevalent gynecological condition that significantly compromises the quality of life in adolescents and women of reproductive age. Within traditional Chinese medicine (TCM), Cold Coagulation and Blood Stasis Primary Dysmenorrhea (CCBS-PD) represents the most frequently observed syndrome pattern of PD. Wenjing Decoction (WJD), a classical TCM formulation, has been extensively employed for the treatment of CCBS-PD. However, given the multi-component and complex nature of WJD, the potential mechanisms underpinning its therapeutic effect have yet to be elucidated. Methods: A rat model of CCBS-PD was induced through ice-water bath stimulation in conjunction with estradiol benzoate and oxytocin. The pharmacological effects of WJD were evaluated by writhing response, hemorheological parameters, uterine index, histopathological examination, and biochemical assays. Serum-exposed constituents of WJD were characterized using UPLC-Orbitrap Exploris 120 MS. To study the mechanisms of WJD, methods from network pharmacology, molecular docking, and off-target metabolomics were used. Western blot analysis examined representative proteins in the signaling pathways predicted by network pharmacology. Network pharmacology and metabolomics were integrated to construct a pathway–metabolite–target–compound network, and representative targets were analyzed by RT-qPCR. Results: WJD treatment reduced writhing responses, improved hemorheological abnormalities, and alleviated uterine pathological changes in CCBS-PD rats. Serum pharmacochemistry identified 62 WJD-derived constituents. Metabolomics analysis indicated that WJD was associated with alterations in nitrogen metabolism, valine/leucine/isoleucine biosynthesis and arginine biosynthesis. Network pharmacology and molecular docking suggested several candidate compounds and targets, including Robinetin, Levistolide A, Pratol, 7,4′-dihydroxyflavone, EGFR, AKT1, ESR1, MMP9, MAPK3, and TNF. RT-qPCR showed that selected genes, including AKT1, EGFR, MAPK3, TNF, ESR1, MMP9 and CASP3, were changed in the model group and partially restored following WJD improvement. Western blot analysis demonstrated that WJD treatment decreased the phosphorylation levels of AKT, ERK1/2, and NF-κB, and down-regulated the protein expression of COX-2. Conclusions: WJD showed beneficial effects in a CCBS-PD rat model. Synthesized assessments indicate a potential link to the actions of serum-exposed constituents, alterations in amino acid metabolism, and modulation of inflammation-related signaling pathways. This research offers initial indications suggesting the multi-component and multi-target pharmacological actions of WJD, although the underlying mechanisms remain to be validated through targeted metabolomics and functional studies. Full article
(This article belongs to the Special Issue Natural Bioactive Compounds from Plants: Progress in Phytochemistry, Computational Approaches and Biomedical Applications)
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28 pages, 3415 KB  
Article
Natural Bioactive Compounds from Delonix regia Seeds Revealed Through Integrated Phytochemical, Biomedical and In Silico Evaluation
by Husam Qanash, Aisha M. H. Al-Rajhi, Abdulrahman S. Bazaid, Manar F. Alghassab, Fahad Almarshadi, Walid Alesefir, Waleed Hakami, Amro Duhduh and Abdu Aldarhami
Pharmaceuticals 2026, 19(8), 1272; https://doi.org/10.3390/ph19081272 - 12 Aug 2026
Viewed by 401
Abstract
Background/Objectives: Delonix regia seeds contain phytochemicals with therapeutic potential, but their activity against Helicobacter pylori and biomedical properties remain incompletely characterized. This study aimed to characterize the phenolic and amino acid composition of D. regia seed extract (DRSE) and evaluate its anticancer, [...] Read more.
Background/Objectives: Delonix regia seeds contain phytochemicals with therapeutic potential, but their activity against Helicobacter pylori and biomedical properties remain incompletely characterized. This study aimed to characterize the phenolic and amino acid composition of D. regia seed extract (DRSE) and evaluate its anticancer, wound-healing, anti-inflammatory, anticoagulant, antibacterial, antibiofilm and urease-targeted docking activities. Methods: DRSE was analyzed by high-performance liquid chromatography (HPLC) and amino acid analysis. Biological effects were assessed using MTT cytotoxicity, scratch wound-healing, bovine serum albumin (BSA) denaturation, prothrombin time (PT) and partial thromboplastin time (PTT), antibacterial and crystal violet antibiofilm assays. Gallic acid and vanillin were docked against H. pylori urease (PDB ID: 1E9Y). Results: Gallic acid was the predominant phenolic compound (1417.90 µg/g), while aspartic and glutamic acids dominated the amino acid fraction. DRSE showed preferential cytotoxicity toward A431 carcinoma cells (IC50 = 108.97 ± 0.68 µg/mL) compared with HFB4 fibroblasts (IC50 = 318.56 ± 2.06 µg/mL), yielding a selectivity index of 2.92. Scratch closure was comparable to the control (81.71% versus 80.85%), although the migration rate increased to 16.12 µm. DRSE inhibited protein denaturation by 91.20% (IC50 = 6.39 ± 0.19 µg/mL) and prolonged PT and PTT to 27.37 and 90.50 s, respectively. It inhibited H. pylori with minimum inhibitory and bactericidal concentrations of 31.25 µg/mL and suppressed biofilm formation by 95.39%. Gallic acid and vanillin showed comparable urease docking scores of −4.72 and −4.71 kcal/mol. Conclusions: DRSE showed selective anticancer, anti-H. pylori, antibiofilm, anti-inflammatory, anticoagulant, and moderate pro-migratory activities. Mechanistic, safety and in vivo studies are warranted. Full article
(This article belongs to the Special Issue Natural Bioactive Compounds from Plants: Progress in Phytochemistry, Computational Approaches and Biomedical Applications)
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17 pages, 14930 KB  
Article
1,8-Cineole Potentiates the Antibacterial Activity of Amoxicillin/Clavulanic Acid Against an ESBL-Producing Escherichia coli Strain: An In Vitro and In Silico Investigation
by Mounia Oukhouia, Assia Houiat, Samira Oukhouia, Chaymae Moubachir, Mohd Yasir Khan, Farah Maarfi, Mohammed Cherkaoui and Adnane Remmal
Pharmaceuticals 2026, 19(7), 1094; https://doi.org/10.3390/ph19071094 - 16 Jul 2026
Viewed by 473
Abstract
Background/Objectives: Antibiotic resistance in bacteria poses a major health problem worldwide. Therefore, to counteract this life-threatening problem, we sought to investigate in the present study the possible potentiation of the efficacy of amoxicillin (AMX) and clavulanic acid (CA) by 1,8-cineole (CN), a [...] Read more.
Background/Objectives: Antibiotic resistance in bacteria poses a major health problem worldwide. Therefore, to counteract this life-threatening problem, we sought to investigate in the present study the possible potentiation of the efficacy of amoxicillin (AMX) and clavulanic acid (CA) by 1,8-cineole (CN), a candidate resistance-modulating agent. The approach seeks to investigate, in vitro and in silico, the interactions among these three molecules. Methods: The antibacterial activity was determined against resistant Escherichia coli (E. coli) using microdilution methods, synergy tests, and time-kill assays for AMX, CA, and CN, used either separately or in combinations: AMX–CA, AMX–CN, CA–CN, and AMX–CA–CN. Furthermore, an in silico drug design methodology was employed, utilizing an integrated workflow that combines Density Functional Theory (DFT) for ligand optimization with molecular docking simulations to evaluate binding energies and interactions between the penicillin-binding protein (PBP) and ligands. Results: In vitro synergy experiments and time-kill assays revealed substantial antibacterial efficacy of the AMX–CA–CN combination. In silico analyses, performed under the simplifying assumption of a pre-assembled multi-ligand entity, were consistent with these findings: within our docking model, the AMX–CA–CN combination exhibited the most favorable computed binding affinity to a representative penicillin-binding protein (PBP3, PDB 7ONW). Conclusions: 1,8-cineole can potentiate the antibacterial effects of AMX–CA, indicating that the AMX–CA–CN combination warrants further evaluation as a candidate adjunctive strategy against ESBL-producing E. coli. Full article
(This article belongs to the Special Issue Natural Bioactive Compounds from Plants: Progress in Phytochemistry, Computational Approaches and Biomedical Applications)
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Review

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45 pages, 7515 KB  
Review
Past, Present, and Future of Plant-Derived Extracellular Vesicles in Biomedical Applications
by Yilixiati Wusiman, Xiaoxiao Qiu, Nazhakaiti Yusufujiang, Yipaerguli Paerhati, Alifeiye Aikebaier, Dilihuma Dilimulati, Alhar Baishan and Wenting Zhou
Pharmaceuticals 2026, 19(8), 1156; https://doi.org/10.3390/ph19081156 - 24 Jul 2026
Viewed by 639
Abstract
Plant-derived extracellular vesicles (PDEVs) have emerged as promising natural nanocarriers for biomedical applications owing to their distinctive ability to facilitate intercellular communication and transport bioactive molecules. In this review, we employ bibliometric analysis to identify research hotspots and trends, providing a comprehensive overview [...] Read more.
Plant-derived extracellular vesicles (PDEVs) have emerged as promising natural nanocarriers for biomedical applications owing to their distinctive ability to facilitate intercellular communication and transport bioactive molecules. In this review, we employ bibliometric analysis to identify research hotspots and trends, providing a comprehensive overview of these core themes. The bibliometric results reveal a sustained increase in annual publications in this field, with keyword analysis identifying drug delivery, cross-kingdom regulation, immunomodulation, engineering modification, and gut microbiota as five major research themes. The focus of research has evolved from early basic biological characteristics into engineered smart delivery platforms, with the application areas expanding from intestinal inflammation to neurological, metabolic, dermatological, and oncological diseases. This review systematically examines the core directions in this field. It compares the strengths and limitations of mainstream isolation methods and highlights the value of multi-omics integration, covering the molecular mechanisms of ferroptosis and gut microbiota regulation by PDEVs along with engineering strategies such as drug loading, surface modification, and membrane fusion. It also discusses the latest progress in frontier therapeutic applications of PDEVs, including cancer, inflammatory diseases, tissue regeneration and aesthetics, and neurological disorders. Finally, this review summarizes the key challenges confronting the field, including the lack of standardized protocols, production bottlenecks, and engineering obstacles. It also delineates future directions, including establishing international standardization definitions, advancing multi-omics and AI-driven mechanistic elucidation, developing scalable and efficient purification technologies, and executing systematic preclinical safety and pharmacokinetic evaluations to facilitate clinical translation. Full article
(This article belongs to the Special Issue Natural Bioactive Compounds from Plants: Progress in Phytochemistry, Computational Approaches and Biomedical Applications)
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