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Pharmacological Activities and Mechanisms of Action of Natural Products

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A special issue of Current Issues in Molecular Biology (ISSN 1467-3045). This special issue belongs to the section "Bioorganic Chemistry and Medicinal Chemistry".

Deadline for manuscript submissions: 31 July 2025 | Viewed by 7181

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Special Issue Editors

Dr. Shining Loo

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Wisdom Lake Academy of Pharmacy, Xi’an Jiaotong-Liverpool University, Wuzhong No.111, Renai Road, Suzhou 215123, China
Interests: precision medicine; peptide drug discovery and design; mass spectrometry; proteomics-based target-identification, functional and structural characterization; high-throughput drug screening and validation; peptide and protein chemistry; molecular pharmacology; targeted protein modifiers; targeted drug delivery; natural products
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Dr. Antony Kam

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Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Wuzhong No. 111, Renai Road, Suzhou 215123, China
Interests: peptide; drug discovery; molecular pharmacology; natural products; chemical biology
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Lee Simon Ming-Yuen

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Guest Editor

1. State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
2. Department of Pharmacological Sciences, Faculty of Health Sciences, University of Macau, Macao, China
Interests: cardiovascular; neurodegenerative diseases and brain disorders; molecular pharmacology; mitochondrial functions; systems biology; genome; transcriptome; proteome; protein interaction network; natural product chemistry; Chinese medicine; peptide chemistry
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Natural products are small molecules biosynthesized by living organisms that have evolved to modulate biochemical pathways and biological processes. This Special Issue focuses on understanding the molecular mechanisms by which natural products exert their pharmacological activities and therapeutic effects. For centuries, natural products have been invaluable sources of medicinal agents, exemplified by antibiotics, antimalarials, analgesics, and anticancer drugs like penicillin, artemisinin, ziconotide, and paclitaxel, respectively. Unraveling their molecular targets, modes of binding, and regulatory roles can unlock new therapeutic strategies.

This SI welcomes original research elucidating the structural basis of natural products’ bioactivity through techniques like X-ray crystallography, NMR spectroscopy, computational modeling, and pharmacological assays. Also of interest are investigations into natural products’ interactions with proteins, nucleic acids, lipids, and other biomolecules, underlying their pharmacological effects, and mechanistic studies dissecting their impact on cellular signaling pathways, gene expression, enzyme activities, and other molecular processes. Additionally, this Issue aims to showcase cutting-edge strategies for natural product isolation, derivatization, and molecular target deconvolution to accelerate drug discovery. Through an enhanced understanding of natural products’ mechanisms of action, this Special Issue strives to enrich the pipeline for molecular probes and therapeutic leads.

Dr. Shining Loo
Dr. Antony Kam
Prof. Dr. Lee Simon Ming-Yuen
Guest Editors

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Keywords

natural products
pharmacological activity
molecular mechanisms
therapeutic targets
structure–activity relationships
protein–ligand interactions
cell signaling pathways
enzyme inhibition/activation
molecular targets

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Published Papers (7 papers)

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Research

14 pages, 1469 KiB

Open AccessArticle

Lychee Peel Extract Ameliorates Hyperuricemia by Regulating Uric Acid Production and Excretion in Mice

by Zhenwang Guo, Li Zhang, Jinlei Liu and Ziming Yang

Curr. Issues Mol. Biol. 2025, 47(2), 76; https://doi.org/10.3390/cimb47020076 - 25 Jan 2025

Viewed by 317

Abstract

Lychee peel generated during the industrial processing of lychee fruit are currently disposed of as agricultural waste. This study investigates the primary components of lychee peel extract (LPE) and the regulatory mechanisms of LPE on reducing uric acid (UA). Mice were injected with hypoxanthine and potassium oxonate to induce hyperuricemia and concurrently orally administered LPE. The analysis of the LPE composition reveals a predominance of polyphenolic compounds, including (-)-epicatechin, (-)-epigallocatechin, and procyanidin A2. In vitro tests have demonstrated that the LPE significantly inhibits the activity of xanthine oxidase (XOD). In vivo studies showed that LPE can reduce UA levels in hyperuricemia mice. Further mechanistic insights indicate that LPE inhibits hepatic XOD activity, thereby reducing UA synthesis within the organism. It also decreases the protein expression of urate transporter 1 (URAT1) and glucose transporter 9 (GLUT9), which leads to diminished UA reabsorption and increased excretion of UA. Additionally, LPE enhances the activity of superoxide dismutase (SOD) while simultaneously reducing malondialdehyde (MDA) contents, thereby improving antioxidant capacity in mice. Our findings indicate that LPE not only inhibits the production of UA but also promotes its elimination, positioning it as a promising candidate for UA-lowering agents. Full article

(This article belongs to the Special Issue Pharmacological Activities and Mechanisms of Action of Natural Products)

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16 pages, 7196 KiB

Open AccessArticle

Notoginsenoside R1 Attenuates H/R Injury in H9c2 Cells by Maintaining Mitochondrial Homeostasis

by Yuanbo Xu, Piao Wang, Ting Hu, Ke Ning and Yimin Bao

Curr. Issues Mol. Biol. 2025, 47(1), 44; https://doi.org/10.3390/cimb47010044 - 10 Jan 2025

Viewed by 844

Abstract

Mitochondrial homeostasis is crucial for maintaining cellular energy production and preventing oxidative stress, which is essential for overall cellular function and longevity. Mitochondrial damage and dysfunction often occur concomitantly in myocardial ischemia–reperfusion injury (MIRI). Notoginsenoside R1 (NGR1), a unique saponin from the traditional Chinese medicine Panax notoginseng, has been shown to alleviate MIRI in previous studies, though its precise mechanism remains unclear. This study aimed to elucidate the mechanisms of NGR1 in maintaining mitochondrial homeostasis in hypoxia/reoxygenation (H/R) H9c2 cells. The results showed that NGR1 pretreatment effectively increased cell survival rates post-H/R, reduced lactate dehydrogenase (LDH) leakage, and mitigated cell damage. Further investigation into mitochondria revealed that NGR1 alleviated mitochondrial structural damage, improved mitochondrial membrane permeability transition pore (mPTP) persistence, and prevented mitochondrial membrane potential (Δψm) depolarization. Additionally, NGR1 pretreatment enhanced ATP levels, increased the activity of mitochondrial respiratory chain complexes I–V after H/R, and reduced excessive mitochondrial reactive oxygen species (mitoROS) production, thereby protecting mitochondrial function. Further analysis indicated that NGR1 upregulated the expression of mitochondrial biogenesis-related proteins (PGC-1α, Nrf1, Nrf2) and mitochondrial fusion proteins (Opa1, Mfn1, Mfn2), while downregulating mitochondrial fission proteins (Fis1, Drp1) and reducing mitochondrial autophagy (mitophagy) levels, as well as the expression of mitophagy-related proteins (Pink1, Parkin, BNIP3) post-H/R. Therefore, this study showed that NGR1 can maintain mitochondrial homeostasis by regulating mitophagy, mitochondrial fission–fusion dynamics, and mitochondrial biogenesis, thereby alleviating H9c2 cell H/R injury and protecting cardiomyocytes. Full article

(This article belongs to the Special Issue Pharmacological Activities and Mechanisms of Action of Natural Products)

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9 pages, 793 KiB

Open AccessArticle

Abrin Toxin Paradoxically Increases Protein Synthesis in Stimulated CD4⁺ T-Cells While Decreasing Protein Synthesis in Kidney Cells

by Bradley Hernlem and Reuven Rasooly

Curr. Issues Mol. Biol. 2024, 46(12), 13970-13978; https://doi.org/10.3390/cimb46120835 - 11 Dec 2024

Viewed by 795

Abstract

Abrin, a toxin of the rosary pea plant (Abras precatorius), has been implicated as causing an autoimmune demyelinating disease in humans, but the exact mechanisms responsible for the induction of these demyelinating conditions are still unknown. Certain superantigen microbial toxins such as Staphylococcus enterotoxin type A, type D, type E or streptococcal pyrogenic exotoxin type C also lead to various diseases including autoimmune disorders of the nervous system. Here, the effect of abrin toxin on the immune reaction was studied in human CD4⁺ T-cell lines, and its inhibition of protein synthesis in kidney cells. It is shown for the first time that low concentrations of abrin toxin up to as high as 1 to 10 ng/mL amplifies superantigen activity in stimulated T-cells, leading to excessive NFAT pathway activation and secretion of cytokines, e.g., interleukin-2 (IL-2) and interferon-γ (INFγ), in a dose-dependent manner. This behavior, except at high concentration, is contrary to the effect on other cell types. Abrin’s inhibition of protein synthesis was demonstrated with Vero (kidney) cells and milk was observed to competitively reduce this effect. This new concept in the behavior of abrin in amplifying superantigen activity may explain the mechanism by which abrin toxin triggers autoimmune demyelinating disease in people exposed to low doses of the toxin via the excessive secretion of cytokines which may create excessive inflammation leading to loss of immune tolerance and triggering an immune response against self-antigens. Full article

(This article belongs to the Special Issue Pharmacological Activities and Mechanisms of Action of Natural Products)

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15 pages, 2242 KiB

Open AccessArticle

Curcumin Mitigates Muscle Atrophy Potentially by Attenuating Calcium Signaling and Inflammation in a Spinal Nerve Ligation Model

by Casey Appell, Nigel C. Jiwan, Chwan-Li Shen and Hui-Ying Luk

Curr. Issues Mol. Biol. 2024, 46(11), 12497-12511; https://doi.org/10.3390/cimb46110742 - 5 Nov 2024

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Abstract

Denervation-induced calcium/calmodulin-dependent protein kinase II (CaMKII) activation and inflammation can result in muscle atrophy. Curcumin and bisdemethoxycurcumin are well known to exhibit an anti-inflammatory effect. In addition, curcumin has been shown to attenuate CaMKII activation in neuronal cells. This study aimed to examine the effect of curcumin or bisdemethoxycurcumin on CaMKII activation, inflammation, and muscle cross-sectional area (CSA) in spinal nerve ligated rats. Sixteen female rats were assigned to sham (CON), spinal nerve ligation (SNL), SNL+ curcumin 100 mg/kg BW (100CUR), and SNL+ bisdemethoxycurcumin 50 mg/kg BW (50CMO) for 4 weeks. Ipsilateral (surgical) soleus and tibialis anterior (TA) muscles was stained for dystrophin to measure CSA. Ipsilateral and contralateral (non-surgical) plantaris muscles were analyzed for protein content for acetylcholine receptor (AChR), CaMKII, CaMKII^Thr286, nuclear factor-κB (NF-κB), NF-κB^Ser536, and interleukin-1β (IL-1β) and normalized to α-tubulin and then CON. A significant (p < 0.050) group effect was observed for TA CSA where CON (11,082.25 ± 1617.68 μm²; p < 0.001) and 100CUR (9931.04 ± 2060.87 μm²; p = 0.018) were larger than SNL (4062.25 ± 151.86 μm²). In the ipsilateral plantaris, the SNL (4.49 ± 0.69) group had greater CaMKII activation compared to CON (1.00 ± 0.25; p = 0.010), 100CUR (1.12 ± 0.45; p = 0.017), and 50CMO (0.78 ± 0.19; p = 0.009). The ipsilateral plantaris (2.11 ± 0.66) had greater IL-1β protein content than the contralateral leg (0.65 ± 0.14; p = 0.041) in the SNL group. In plantaris, the SNL (1.65 ± 0.51) group had greater NF-κB activation compared to CON (1.00 ± 0.29; p = 0.021), 100CUR (0.61 ± 0.10; p = 0.003), 50CMO (0.77 ± 0.25; p = 0.009) groups. The observed reduction in Ca²⁺ signaling and inflammation in type II plantaris muscle fibers might reflect the changes within the type II TA muscle fibers which may contribute to the mitigation of TA mass loss with curcumin supplementation. Full article

(This article belongs to the Special Issue Pharmacological Activities and Mechanisms of Action of Natural Products)

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19 pages, 7937 KiB

Open AccessArticle

Exploring the Benefits of Herbal Medicine Composite 5 (HRMC5) for Skin Health Enhancement

by Rira Ha, Won Kyong Cho, Euihyun Kim, Sung Joo Jang, Ju-Duck Kim, Chang-Geun Yi and Sang Hyun Moh

Curr. Issues Mol. Biol. 2024, 46(11), 12133-12151; https://doi.org/10.3390/cimb46110720 - 29 Oct 2024

Viewed by 1008

Abstract

The skin, as the body’s largest organ, is vital for protecting against environmental stressors, regulating temperature, and preventing water loss. Here, we examined the potential of a mixture of five traditional Korean herbal extracts—Cimicifuga racemosa, Paeonia lactiflora, Phellodendron amurense, Rheum rhaponticum, and Scutellaria baicalensis—referred to as herbal medicine composite 5 (HRMC5) for enhancing skin health and managing menopausal symptoms. High-performance liquid chromatography identified 14 bioactive compounds, including flavonoids, phenolic acids, anthraquinones, and alkaloids. In vitro studies revealed an optimal concentration of 0.625 g/L for cell survival and UV protection, with the mixture demonstrating significant wound-healing properties comparable to epidermal growth factor. HRMC5 exhibited anti-inflammatory effects by downregulating COX2 expression and upregulating the key skin barrier proteins. A 4-week clinical trial involving 20 postmenopausal women showed significant improvements in skin redness, hemoglobin concentration, and skin moisture content. Visual analog scale assessments indicated substantial reductions in facial flushing severity and the associated sweating. The topical application of HRMC5 cream offered potential advantages over ingested phytoestrogens by reducing the systemic side effects. These findings suggest that HRMC5 is a promising non-invasive treatment for vasomotor symptoms in menopausal women and overall skin health, warranting further research on its long-term efficacy and safety in larger populations. Full article

(This article belongs to the Special Issue Pharmacological Activities and Mechanisms of Action of Natural Products)

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13 pages, 3017 KiB

Open AccessArticle

Platycladus orientalis Leaf Extract Promotes Hair Growth via Non-Receptor Tyrosine Kinase ACK1 Activation

by Jaeyoon Kim, Jang Ho Joo, Juhyun Kim, Heena Rim, Jae young Shin, Yun-Ho Choi, Kyoungin Min, So Young Lee, Seung-Hyun Jun and Nae-Gyu Kang

Curr. Issues Mol. Biol. 2024, 46(10), 11207-11219; https://doi.org/10.3390/cimb46100665 - 5 Oct 2024

Viewed by 1465

Abstract

Platycladus orientalis is a traditional oriental herbal medicinal plant that is widely used as a component of complex prescriptions for alopecia treatment in Eastern Asia. The effect of PO on hair growth and its underlying mechanism, however, have not been demonstrated or clarified. In this study, we investigated the hair-growth-promoting effect of PO in cultured human dermal papilla cells (hDPCs). Platycladus orientalis leaf extract (POLE) was found to stimulate the proliferation of hDPCs. POLE with higher quercitrin concentration, especially, showed a high level of cellular viability. In the context of cellular senescence, POLE decreased the expression of p16 (CDKN2A) and p21(CDKN1A), which resulted in enhanced proliferation. In addition, growth factor receptors, FGFR1 and VEGFR2/3, and non-receptor tyrosine kinases, ACK1 and HCK, were significantly activated. In addition, LEF1, a transcription factor of Wnt/β-catenin signaling, was enhanced, but DKK1, an inhibitor of Wnt/β-catenin signaling, was downregulated by POLE treatment in cultured hDPCs. As a consequence, the expression of growth factors such as bFGF, KGF, and VEGF were also increased by POLE. We further investigated the hair-growth-promoting effect of topically administered POLE over a 12-week period. Our data suggest that POLE could support terminal hair growth by stimulating proliferation of DPCs and that enhanced production of growth factors, especially KGF, occurred as a result of tyrosine kinase ACK1 activation. Full article

(This article belongs to the Special Issue Pharmacological Activities and Mechanisms of Action of Natural Products)

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20 pages, 3780 KiB

Open AccessArticle

Quercetin as a Modulator of PTPN22 Phosphomonoesterase Activity: A Biochemical and Computational Evaluation

by Abdulhakeem Olarewaju Sulyman, Tafa Ndagi Akanbi Yusuf, Jamiu Olaseni Aribisala, Kamaldeen Sanni Ibrahim, Emmanuel Oladipo Ajani, Abdulfatai Temitope Ajiboye, Saheed Sabiu and Karishma Singh

Curr. Issues Mol. Biol. 2024, 46(10), 11156-11175; https://doi.org/10.3390/cimb46100662 - 3 Oct 2024

Viewed by 1010

Abstract

Cancer, a group of diseases characterized by uncontrollable cell proliferation and metastasis, remains a global health challenge. This study investigates quercetin, a natural compound found in many fruits and vegetables, for its potential to inhibit the phosphomonoesterase activity of protein tyrosine phosphatase nonreceptor type 22 (PTPN22), a key immune response regulator implicated in cancer and autoimmune diseases. We started by screening seven (7) natural compounds against the activities of PTPN22 in vitro. The initial screening identified quercetin with the highest percentage inhibition (81%) among the screened compounds when compared with ursolic acid that has 84%. After the identification of quercetin, we proceeded by investigating the effect of increasing concentrations of the compound on the activity of PTPN22. In vitro studies showed that quercetin inhibited PTPN22 with an IC₅₀ of 29.59 μM, outperforming the reference standard ursolic acid, which had an IC₅₀ of 37.19 μM. Kinetic studies indicated a non-competitive inhibition by quercetin with a Ki of 550 μM. In silico analysis supported these findings, showing quercetin’s better binding affinity (ΔGbind −24.56 kcal/mol) compared to ursolic acid, attributed to its higher reactivity and electron interaction capabilities at PTPN22′s binding pocket. Both quercetin and ursolic acid improved the structural stability of PTPN22 during simulations. These results suggest quercetin’s potential as an anticancer agent, meriting further research. However, in vivo studies and clinical trials are necessary to fully assess its efficacy and safety, and to better understand its mechanisms of action. Full article

(This article belongs to the Special Issue Pharmacological Activities and Mechanisms of Action of Natural Products)

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