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Mandal SK, Rehman MDMU, Katyal A, Rajvanshi K, Kannan M, Garg M, Murugesan S, Deepa P. In silico anti-viral assessment of phytoconstituents in a traditional (Siddha Medicine) polyherbal formulation - Targeting Mpro and pan-coronavirus post-fusion Spike protein. J Tradit Complement Med 2024; 14:55-69. [PMID: 38223813 PMCID: PMC10785248 DOI: 10.1016/j.jtcme.2023.07.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 06/16/2023] [Accepted: 07/06/2023] [Indexed: 01/16/2024] Open
Abstract
Background and aim Novel nature of the viral pathogen SARS-CoV-2 and the absence of standard drugs for treatment, have been a major challenge to combat this deadly infection. Natural products offer safe and effective remedy, for which traditional ethnic medicine can provide leads. An indigenous poly-herbal formulation, Kabasura Kudineer from Siddha system of medicine was evaluated here using a combination of computational approaches, to identify potential inhibitors against two anti-SARS-CoV-2 targets - post-fusion Spike protein (structural protein) and main protease (Mpro, non-structural protein). Experimental procedure We docked 32 phytochemicals from the poly-herbal formulation against viral post-fusion Spike glycoprotein and Mpro followed by molecular dynamics using Schrodinger software. Drug-likeness analysis was performed using machine learning (ML) approach and pkCSM. Results The binding affinity of the phytochemicals in Kabasura Kudineer revealed the following top-five bioactives: Quercetin > Luteolin > Chrysoeriol > 5-Hydroxy-7,8-Dimethoxyflavone > Scutellarein against Mpro target, and Gallic acid > Piperlonguminine > Chrysoeriol > Elemol > Piperine against post-fusion Spike protein target. Quercetin and Gallic acid exhibited binding stability in complexation with their respective viral-targets and favourable free energy change as revealed by the molecular dynamics simulations and MM-PBSA analysis. In silico predicted pharmacokinetic profiling of these ligands revealed appropriate drug-likeness properties. Conclusion These outcomes provide: (a) potential mechanism for the anti-viral efficacy of the indigenous Siddha formulation, targeting Mpro and post-fusion Spike protein (b) top bioactive lead-molecules that may be developed as natural product-based anti-viral pharmacotherapy and their pleiotropic protective effects may be leveraged to manage co-morbidities associated with COVID-19.
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Affiliation(s)
- Sumit Kumar Mandal
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS Pilani), Pilani Campus, Pilani, 333031, Rajasthan, India
| | - MD Muzaffar-Ur Rehman
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani, 333031, Rajasthan, India
| | - Ashish Katyal
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS Pilani), Pilani Campus, Pilani, 333031, Rajasthan, India
| | - Kanishk Rajvanshi
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS Pilani), Pilani Campus, Pilani, 333031, Rajasthan, India
| | - Manoj Kannan
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS Pilani), Pilani Campus, Pilani, 333031, Rajasthan, India
- Plaksha University, SAS Nagar, Mohali, 140306, Punjab, India
| | - Mohit Garg
- Department of Chemical Engineering, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani, 333031, Rajasthan, India
| | - Sankaranarayanan Murugesan
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani, 333031, Rajasthan, India
| | - P.R. Deepa
- Department of Biological Sciences, Birla Institute of Technology & Science (BITS Pilani), Pilani Campus, Pilani, 333031, Rajasthan, India
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Wang C, Liu X, Guo S. Network pharmacology-based strategy to investigate the effect and mechanism of α-solanine against glioma. BMC Complement Med Ther 2023; 23:371. [PMID: 37865727 PMCID: PMC10589944 DOI: 10.1186/s12906-023-04215-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 10/13/2023] [Indexed: 10/23/2023] Open
Abstract
BACKGROUND An anti-tumour activity has been demonstrated for α-solanine, a bioactive compound extracted from the traditional Chinese herb Solanum nigrum L. However, its efficacy in the treatment of gliomas and the underlying mechanisms remain unclear. The aim of this study was to investigate the inhibitory effects of α-solanine on glioma and elucidate its mechanisms and targets using network pharmacology, molecular docking, and molecular biology experiments. METHODS Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) was utilized to predict the potential targets of α-solanine. GeneCards was used to gather glioma-related targets, and the STRING online database was used to analyze protein-protein interaction (PPI) networks for the shared targets. Hub genes were identified from the resulting PPI network and further investigated using Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Additionally, prognostic and gene set enrichment analyses (GSEA) were carried out to identify potential therapeutic targets and their underlying mechanisms of action in relation to the prognosis of gliomas. In vitro experiments were conducted to verify the findings from the network pharmacology analysis. RESULTS A total of 289 α-solanine targets and 1149 glioma-related targets were screened, of which 78 were common targets. 11 hub genes were obtained, including SRC, HRAS, HSP90AA1, IGF1, MAPK1, MAPK14, KDR, STAT1, JAK2, MAP2K1, and IGF1R. The GO and KEGG pathway analyses unveiled that α-solanine was strongly associated with several signaling pathways, including positive regulation of MAP kinase activity and PI3K-Akt. Moreover, α-solanine (10 µM and 15 µM) inhibited the proliferation and migration but promoted the apoptosis of glioma cells. Finally, STAT1 was identified as a potential mediator of the effect of α-solanine on glioma prognosis. CONCLUSION α-Solanine can inhibit the proliferation and migration of gliomas by regulating multiple targets and signalling pathways. These findings lay the foundation for the creation of innovative clinical anti-glioma agents.
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Affiliation(s)
- ChunPeng Wang
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710000, China
| | - XiaoHui Liu
- Department of Medical Oncology, Anyang Cancer Hospital, An Yang, 455000, China
| | - ShiWen Guo
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710000, China.
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Sharma R, Jadhav M, Choudhary N, Kumar A, Rauf A, Gundamaraju R, AlAsmari AF, Ali N, Singla RK, Sharma R, Shen B. Deciphering the impact and mechanism of Trikatu, a spices-based formulation on alcoholic liver disease employing network pharmacology analysis and in vivo validation. Front Nutr 2022; 9:1063118. [PMID: 36466417 PMCID: PMC9709420 DOI: 10.3389/fnut.2022.1063118] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 10/28/2022] [Indexed: 07/30/2023] Open
Abstract
Trikatu Churna (TC) comprising Zingiber officinale rhizome, Piper longum, and Piper nigrum fruit, is effective in treating liver diseases and has high nutraceutical values. However, the efficacy of TC in treating alcoholic liver disease (ALD) and its mechanism remain largely unknown. This study evaluated the hepatoprotective effects of different doses of TC as well as to identify the bioactive components and determine their mechanism of action against ethanol-induced ALD. A compound-target network analysis model of TC was established to identify its potential bioactive compounds and pathways that might regulate its hepatoprotective effects. Further, in-vivo studies were performed to validate the potential of TC (200 mg/kg and 400 mg/kg b.w.) in the treatment and management of ALD. The study revealed that both the dosages of TC demonstrate significant (p > 0.0001) hepatoprotective effects by improving body weight, total bilirubin, serum glutamic oxaloacetic transaminase (SGOT), serum glutamic pyruvic transaminase (SGPT), serum alkaline phosphate (ALP), total cholesterol, total protein, globulin, albumin, and liver morphology. The High-performance thin-layer chromatography (HPTLC) fingerprinting of TC showed the presence of piperine. Network pharmacology identifies the role of TC in regulating various signaling processes including Advanced glycation end products-receptor for advanced glycation end products (AGE-RAGE), Hypoxia-inducible factors (HIF-1), Nuclear factor kappa-light-chain-enhancer of activated B cells (NF-Kappa B), and Phosphatidylinositol 3-kinase/protein kinase B (PI3K/Akt) signaling to exert its anti-inflammatory, antioxidant and anti-apoptotic role in managing ALD. Based on the bioinformatics analysis, some of the key targets of TC were found to be Prostaglandin-Endoperoxide Synthase 2 (PTGS2) or Cyclooxygenase-2 (COX-2), Sirtuin 1 (SRT1), and caspase-3. These effects may serve as a novel therapeutic option for the treatment of ALD. These preclinical validation studies for the ethnopharmacological potential of TC in ALD treatment further paved the way for researchers to perform next-level translational and clinical studies. Further, in-depth experimental studies for the validation of these bioinformatics-based results will give a clearer picture of mechanisms.
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Affiliation(s)
- Ruchi Sharma
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Sciences, BHU, Varanasi, Uttar Pradesh, India
| | - Mangala Jadhav
- Department of Rasa Shastra and Bhaishajya Kalpana, R. A. Podar Ayurvedic Medical College, Mumbai, India
| | - Neha Choudhary
- Centre for Computational Biology and Bioinformatics, Central University of Himachal Pradesh, Dharamsala, Himachal Pradesh, India
| | - Arun Kumar
- Institute of Nuclear Medicine and Allied Sciences (INMAS), Defence Research and Development Organisation (DRDO), New Delhi, India
| | - Abdur Rauf
- Department of Chemistry, University of Swabi, Anbar, Pakistan
| | - Rohit Gundamaraju
- ER Stress and Mucosal Immunology Lab, School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, TAS, Australia
| | - Abdullah F. AlAsmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Nemat Ali
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Rajeev K. Singla
- Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Rohit Sharma
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Sciences, BHU, Varanasi, Uttar Pradesh, India
| | - Bairong Shen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
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Data Mining and Network Pharmacology Analysis of Kidney-Tonifying Herbs on the Treatment of Renal Osteodystrophy Based on the Theory of "Kidney Governing Bones" in Traditional Chinese Medicine. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:1116923. [PMID: 36238608 PMCID: PMC9552684 DOI: 10.1155/2022/1116923] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 08/07/2022] [Accepted: 08/11/2022] [Indexed: 11/06/2022]
Abstract
Background Renal osteodystrophy (ROD) secondary to chronic kidney disease is closely associated with osteoporosis and fractures. Based on the theory of “kidney governing bones” in traditional Chinese medicine (TCM), treating bone diseases from the perspective of the kidney has become a basic principle of treating ROD. However, there are many kidney-tonifying herbs and their mechanisms of treating ROD are not clear. Therefore, our study intends to use data mining and network pharmacology to study the commonly used kidney-tonifying herbs, as well as their active ingredients and mechanisms of treating ROD. Methods We established a clinical ROD database by searching PubMed, CNKI, and other databases and screened out a core herbal combination of treating ROD. Furthermore, by using databases such as Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform and GeneCards, we obtained active ingredients and targets of the core herbal combination and ROD targets. The STRING website and Cytoscape software were then used to obtain information on key active ingredients and key targets. Finally, we conducted GO and KEGG analyses using the Metascape website and molecular docking using the AutoDock Vina software. Results Our study eventually included 58 prescriptions and 116 herbs of treating ROD. Through data mining, we found that yin-yang-huo, du-zhong, and bu-gu-zhi (YDB) constituted a core herbal combination to treat ROD. Network pharmacology showed that YDB mainly acted on targets such as estrogen receptor alpha through active ingredients such as quercetin by mitogen-activated protein kinase and other signaling pathways. Conclusion Many ingredients, targets, and pathways are involved in the treatment of YDB for ROD. Specifically, the flavonoids contained in YDB have great potential for ROD treatment.
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