In silico anti-viral assessment of phytoconstituents in a traditional (Siddha Medicine) polyherbal formulation – Targeting Mpro and pan-coronavirus post-fusion Spike protein
Sumit Kumar Mandal, Md Muzaffar-Ur Rehman, Ashish Katyal, Kanishk Rajvanshi, Manoj Kannan, Mohit Garg, Sankaranarayanan Murugesan, P R Deepa
Journal of Traditional and Complementary Medicine, doi:10.1016/j.jtcme.2023.07.004
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Conflict of Interest The authors declare no conflict of interest J o u r n a l P r e -p r o o f
References
Aljindan, Al-Subaie, Ohali, Kamaraj, Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach, Comput Biol Med,
doi:10.1016/j.compbiomed.2021.104654Banks, Beard, Cao, Integrated modeling program, applied chemical theory J o u r n a l P r e -p r o o f (IMPACT), J Comput Chem
Bellik, Hammoudi, Abdellah, Iguer-Ouada, Boukraa, None, Phytochemicals to J o u r n a l P r e -p r o o f Prevent Inflammation and Allergy. Recent Pat Inflamm Allergy Drug Discov,
doi:10.2174/187221312800166886Burkard, Verheije, Wicht, Coronavirus Cell Entry Occurs through the Endo-/Lysosomal Pathway in a Proteolysis-Dependent Manner, PLoS Pathog,
doi:10.1371/journal.ppat.1004502Cheng, Zhang, Liang, Antiinflammatory and antioxidant flavonoids and phenols from Cardiospermum halicacabum (倒地鈴 Dào Dì Líng), J Tradit Complement Med,
doi:10.1016/S2225-4110(16)30165-1Cornélio Favarin, Teixeira, De Andrade, Anti-inflammatory effects of ellagic acid on acute lung injury induced by acid in mice, Mediators Inflamm,
doi:10.1155/2013/164202Delaney, ESOL: Estimating aqueous solubility directly from molecular structure, J Chem Inf Comput Sci,
doi:10.1021/ci034243xDivya, Vijayakumar, Chen, Vaseeharan, Ef, South Indian medicinal plants can combat deadly viruses along with COVID-19? -A review, Microb Pathog. J o u r n a l P r e -p r o o f,
doi:10.1016/j.micpath.2020.104277Duan, Zheng, Zhang, Niu, Lou et al., The SARS-CoV-2 Spike Glycoprotein J
Duquerroy, Vigouroux, Rottier, Rey, Bosch, Central ions and lateral asparagine/glutamine zippers stabilize the post-fusion hairpin conformation of the SARS coronavirus spike glycoprotein, Virology,
doi:10.1016/j.virol.2005.02.022Ekberg, Ryde, On the use of interaction entropy and related methods to estimate binding entropies, J Chem Theory Comput,
doi:10.1021/acs.jctc.1c00374Govea-Salas, Rivas-Estilla, Rodríguez-Herrera, Gallic acid decreases hepatitis C virus expression through its antioxidant capacity, Exp Ther Med,
doi:10.3892/etm.2015.2923Hcvpred, A web server for predicting the bioactivity of hepatitis C virus NS5B inhibitors, J Comput Chem,
doi:10.1002/jcc.26223Huang, Zhang, Zhou, Reverse screening methods to search for the protein targets of chemopreventive compounds, Front Chem,
doi:10.3389/fchem.2018.00138Jabaris, Sl, Kabasura kudineer, a siddha medicine against COVID-19 infection: scope and future perspective, Int J Complement Altern Med,
doi:10.15406/ijcam.2021.14.00554Jain, Narayanan, Chaturvedi, Pai, Sunil, In Vivo Evaluation of Withania somnifera-Based Indian Traditional Formulation (Amukkara Choornam), Against Chikungunya Virus-Induced Morbidity and Arthralgia, J Evidence-Based Integr Med,
doi:10.1177/2156587218757661Jose, Anti-inflammatory effect of Kaba Sura Kudineer (AYUSH approved COVID-19 drug)-A Siddha poly-herbal formulation against lipopolysaccharide induced inflammatory response in RAW-264.7 macrophages cells, J Ethnopharmacol,
doi:10.1016/j.jep.2021.114738Kannan, Sathiyarajeswaran, Sasikumar, Safety and Efficacy of a Siddha Medicine Fixed Regimen for the treatment of Asymptomatic and Mild COVID-19 patients, J Ayurveda Integr Med. Published online,
doi:10.1016/j.jaim.2022.100589Khalifa, Nawaz, Sobhy, Althawb, Barakat, Polyacylated anthocyanins constructively network with catalytic dyad residues of 3CLpro of 2019-nCoV than monomeric anthocyanins: A structural-relationship activity study with 10 anthocyanins using in-silico approaches, J Mol Graph Model,
doi:10.1016/j.jmgm.2020.107690Kiran, Karthik, Devi, In Silico computational screening of Kabasura Kudineer -Official Siddha Formulation and JACOM against SARS-CoV-2 spike protein, J Ayurveda Integr Med,
doi:10.1016/j.jaim.2020.05.009Kirchdoerfer, Wang, Pallesen, Erratum to: Stabilized coronavirus spikes are resistant to conformational changes induced by receptor recognition or proteolysis, Sci Rep,
doi:10.1038/s41598-018-34171-7Kumar, Rai, Khan, Role of herbal medicines in the management of patients with COVID-19: A systematic review and meta-analysis of randomized controlled trials, J Tradit Complement Med
Liu, Wang, Potential inhibitors against 2019-nCoV coronavirus M protease from clinically approved medicines, J Genet Genomics,
doi:10.1016/j.jgg.2020.02.001Malik, Phanus-Umporn, Schaduangrat, Shoombuatong, Isarankura-Na-Ayudhya, None
Manandhar, Mehta, Nayak, Pai, Structure-based docking, pharmacokinetic evaluation, and molecular dynamics-guided evaluation of traditional formulation against SARS-CoV-2 spike protein receptor bind domain and ACE2 receptor complex, Chem Pap,
doi:10.1007/s11696-021-01917-zMandal, Kumar, Sharma, Murugesan, Deepa, In silico and in vitro analysis of PPAR -α / γ dual agonists: Comparative evaluation of potential phytochemicals with antiobesity drug orlistat, Comput Biol Med,
doi:10.1016/j.compbiomed.2022.105796Mandal, Puri, Kumar, Targeting lipid-sensing nuclear receptors PPAR (α, γ, β/δ): HTVS and molecular docking/dynamics analysis of pharmacological ligands as potential pan-PPAR agonists, Mol Divers,
doi:10.1007/s11030-023-10666-yMhatre, Srivastava, Naik, Patravale, Antiviral activity of green tea and black tea polyphenols in prophylaxis and treatment of COVID-19: A review, Phytomedicine,
doi:10.1016/j.phymed.2020.153286Miller, Br, Jr, Swails, Homeyer et al., MMPBSA. py: an efficient program for end-state free energy calculations, J Chem Theory Comput,
doi:10.1021/ct300418hNutt, Smith, Molecular dynamics simulations of proteins: Can the explicit water model be varied?, J Chem Theory Comput,
doi:10.1021/ct700053uOtvos, Still, Somsen, Smit, Kool, Drug Discovery on Natural Products: From Ion Channels to nAChRs, from Nature to Libraries, from Analytics to Assays, SLAS Discov,
doi:10.1177/2472555218822098Ounissi, Rachedi, Targeting the SARS-CoV-2 Main protease: in silico study contributed to exploring potential natural compounds as candidate inhibitors, J Comput Biophys Chem,
doi:10.1142/s2737416522500272Petrillo, Orrù, Fais, Fantini, Quercetin and its derivates as antiviral potentials: A comprehensive review, Phyther Res,
doi:10.1002/ptr.7309Pires, Blundell, Ascher, pkCSM: Predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures, J Med Chem,
doi:10.1021/acs.jmedchem.5b00104Sd, Singh, vitro Antiviral Activity of Kabasura Kudineer -Siddha Polyherbal Formulation Against Novel Coronavirus (SARS-CoV-2),
doi:10.2139/ssrn.3842077Sen, Chakraborty, Revival, modernization and integration of Indian traditional herbal medicine in clinical practice: Importance, challenges and future, J Tradit Complement Med,
doi:10.1016/j.jtcme.2016.05.006Shah, Modi, Trivedi, Pharmacophore-based virtual screening, 3D-QSAR, molecular docking approach for identification of potential dipeptidyl peptidase IV inhibitors, J Biomol Struct Dyn,
doi:10.1080/07391102.2020.1750485Shirts, Klein, Swails, Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset, J Comput Aided Mol Des,
doi:10.1007/s10822-016-9977-1Siddha, SYSTEM OF MEDICINE SIDDHA SYSTEM OF MEDICINE SIDDHA SYSTEM OF MEDICINE SIDDHA SYSTEM OF MEDICINE The Science of Holistic Health
Singh, Bhardwaj, Purohit, Inhibition of nonstructural protein 15 of SARS-CoV-2 by golden spice: A computational insight, Cell Biochem Funct. Published online,
doi:10.1002/cbf.3753Singh, Bhardwaj, Sharma, Kumar, Purohit, Identification of potential plant bioactive as SARS-CoV-2 Spike protein and human ACE2 fusion inhibitors, Comput Biol J o u r n a l P r e -p r o o f Med,
doi:10.1016/j.compbiomed.2021.104631Singh, Bhardwaj, Sharma, Purohit, Kumar, In-silico evaluation of bioactive compounds from tea as potential SARS-CoV-2 nonstructural protein 16 inhibitors, J Tradit Complement Med,
doi:10.1016/j.jtcme.2021.05.005Song, Gui, Wang, Xiang, Cryo-EM structure of the SARS coronavirus spike glycoprotein in complex with its host cell receptor ACE2, PLoS Pathog,
doi:10.1371/journal.ppat.1007236Srivastava, Rengaraju, Srivastava, Efficacy of two siddha polyherbal decoctions, Nilavembu Kudineer and Kaba Sura Kudineer, along with standard allopathy treatment in the management of mild to moderate symptomatic COVID-19 patients-a double-blind, placebo-controlled, clinical trial, Trials,
doi:10.1186/s13063-021-05478-0JValdés-Tresanco, Valdés-Tresanco, Valiente, Moreno, gmx_MMPBSA: a new tool to perform end-state free energy calculations with GROMACS, J Chem Theory Comput,
doi:10.1021/acs.jctc.1c00645Vincent, Arokiyaraj, Saravanan, Dhanraj, Molecular docking studies on the antiviral effects of compounds from kabasura kudineer on SARS-CoV-2 3CLpro. Front Mol Biosci,
doi:10.3389/fmolb.2020.613401Wang, Xia, Zhu, Lu, Jiang, Pan-coronavirus fusion inhibitors as the hope for today and tomorrow, Protein Cell
Wong, Tap, Hashim, Dual actions of gallic acid and andrographolide trigger AdipoR1 to stimulate insulin secretion in a streptozotocin-induced diabetes rat model, J Tradit Complement Med,
doi:10.1016/j.jtcme.2022.09.002Wu, Gong, Qin, In silico analysis of the potential mechanism of a preventive Chinese medicine formula on coronavirus disease 2019, J Ethnopharmacol,
doi:10.1016/j.jep.2021.114098Xia, Lan, Zhu, Structural and functional basis for pan-CoV fusion inhibitors against SARS-CoV-2 and its variants with preclinical evaluation, Signal Transduct Target Ther,
doi:10.1038/s41392-021-00712-2Xia, Liu, Wang, Inhibition of SARS-CoV-2 (previously 2019-nCoV) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion, Cell Res,
doi:10.1038/s41422-020-0305-xZysk, Some Reflections on Siddha Medicine in Tamilnadu, Indian J Hist Sci
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'author': 'Singh',
'year': '2022',
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'author': 'Bellik',
'year': '2012',
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'first-page': '1',
'article-title': 'Safety and efficacy of a siddha medicine fixed regimen for the '
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'author': 'Kannan',
'year': '2022',
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'DOI': '10.1016/j.jep.2021.114738',
'article-title': 'Anti-inflammatory effect of Kaba Sura Kudineer (AYUSH approved COVID-19 '
'drug)-A Siddha poly-herbal formulation against lipopolysaccharide '
'induced inflammatory response in RAW-264.7 macrophages cells',
'volume': '283',
'author': 'Jose',
'year': '2022',
'journal-title': 'J Ethnopharmacol'},
{ 'key': '10.1016/j.jtcme.2023.07.004_bib26',
'doi-asserted-by': 'crossref',
'DOI': '10.1016/j.compbiomed.2021.104654',
'article-title': 'Investigation of nonsynonymous mutations in the spike protein of '
'SARS-CoV-2 and its interaction with the ACE2 receptor by molecular '
'docking and MM/GBSA approach',
'volume': '135',
'author': 'Aljindan',
'year': '2021',
'journal-title': 'Comput Biol Med'},
{ 'key': '10.1016/j.jtcme.2023.07.004_bib27',
'doi-asserted-by': 'crossref',
'article-title': 'Inhibition of nonstructural protein 15 of SARS‐CoV‐2 by golden spice: a '
'computational insight',
'author': 'Singh',
'year': '2022',
'journal-title': 'Cell Biochem Funct',
'DOI': '10.1002/cbf.3753'},
{ 'key': '10.1016/j.jtcme.2023.07.004_bib28',
'doi-asserted-by': 'crossref',
'DOI': '10.1016/j.compbiomed.2021.104631',
'article-title': 'Identification of potential plant bioactive as SARS-CoV-2 Spike protein '
'and human ACE2 fusion inhibitors',
'volume': '136',
'author': 'Singh',
'year': '2021',
'journal-title': 'Comput Biol Med'},
{ 'issue': '1',
'key': '10.1016/j.jtcme.2023.07.004_bib29',
'doi-asserted-by': 'crossref',
'first-page': '288',
'DOI': '10.1038/s41392-021-00712-2',
'article-title': 'Structural and functional basis for pan-CoV fusion inhibitors against '
'SARS-CoV-2 and its variants with preclinical evaluation',
'volume': '6',
'author': 'Xia',
'year': '2021',
'journal-title': 'Signal Transduct Targeted Ther'},
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'key': '10.1016/j.jtcme.2023.07.004_bib30',
'doi-asserted-by': 'crossref',
'first-page': '2021',
'DOI': '10.1080/07391102.2020.1750485',
'article-title': 'Pharmacophore- based virtual screening, 3D- QSAR, molecular docking '
'approach for identification of potential dipeptidyl peptidase IV '
'inhibitors',
'volume': '39',
'author': 'Shah',
'year': '2021',
'journal-title': 'J Biomol Struct Dyn'},
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'key': '10.1016/j.jtcme.2023.07.004_bib31',
'doi-asserted-by': 'crossref',
'first-page': '1479',
'DOI': '10.1007/s43440-020-00155-6',
'article-title': 'Drug repurposing approach to fight COVID-19',
'volume': '72',
'author': 'Singh',
'year': '2020',
'journal-title': 'Pharmacol Rep'},
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'doi-asserted-by': 'crossref',
'first-page': '1',
'DOI': '10.3389/fchem.2018.00138',
'article-title': 'Reverse screening methods to search for the protein targets of '
'chemopreventive compounds',
'volume': '6',
'author': 'Huang',
'year': '2018',
'journal-title': 'Front Chem'},
{ 'issue': '6',
'key': '10.1016/j.jtcme.2023.07.004_bib33',
'doi-asserted-by': 'crossref',
'first-page': '663',
'DOI': '10.1142/S2737416522500272',
'article-title': 'Targeting the SARS-CoV-2 Main protease: in silico study contributed to '
'exploring potential natural compounds as candidate inhibitors',
'volume': '21',
'author': 'Ounissi',
'year': '2022',
'journal-title': 'J Comput Biophys Chem'},
{ 'issue': '2',
'key': '10.1016/j.jtcme.2023.07.004_bib34',
'doi-asserted-by': 'crossref',
'first-page': '146',
'DOI': '10.1111/j.1747-0285.2007.00483.x',
'article-title': 'New method for fast and accurate binding-site identification and '
'analysis',
'volume': '69',
'author': 'Halgren',
'year': '2007',
'journal-title': 'Chem Biol Drug Des'},
{ 'issue': '2',
'key': '10.1016/j.jtcme.2023.07.004_bib35',
'doi-asserted-by': 'crossref',
'first-page': '65',
'DOI': '10.1016/B978-0-12-821471-8.00005-2',
'article-title': 'Molecular dynamics simulations',
'volume': '12',
'author': 'Arya',
'year': '2021',
'journal-title': 'Des Dev Nov Drugs Vaccines Princ Protoc'},
{ 'issue': '4',
'key': '10.1016/j.jtcme.2023.07.004_bib36',
'doi-asserted-by': 'crossref',
'first-page': '1550',
'DOI': '10.1021/ct700053u',
'article-title': 'Molecular dynamics simulations of proteins: can the explicit water '
'model be varied?',
'volume': '3',
'author': 'Nutt',
'year': '2007',
'journal-title': 'J Chem Theor Comput'},
{ 'issue': '16',
'key': '10.1016/j.jtcme.2023.07.004_bib37',
'doi-asserted-by': 'crossref',
'first-page': '1752',
'DOI': '10.1002/jcc.20292',
'article-title': 'Integrated modeling program, applied chemical theory (IMPACT)',
'volume': '26',
'author': 'Banks',
'year': '2005',
'journal-title': 'J Comput Chem'},
{ 'key': '10.1016/j.jtcme.2023.07.004_bib38',
'doi-asserted-by': 'crossref',
'article-title': 'Targeting lipid-sensing nuclear receptors PPAR (α, γ, β/δ): HTVS and '
'molecular docking/dynamics analysis of pharmacological ligands as '
'potential pan-PPAR agonists',
'author': 'Mandal',
'year': '2023',
'journal-title': 'Mol Divers',
'DOI': '10.1007/s11030-023-10666-y'},
{ 'issue': '10',
'key': '10.1016/j.jtcme.2023.07.004_bib39',
'doi-asserted-by': 'crossref',
'first-page': '6281',
'DOI': '10.1021/acs.jctc.1c00645',
'article-title': 'A new tool to perform end-state free energy calculations with GROMACS',
'volume': '17',
'author': 'Valdés-Tresanco',
'year': '2021',
'journal-title': 'J Chem Theor Comput'},
{ 'issue': '9',
'key': '10.1016/j.jtcme.2023.07.004_bib40',
'doi-asserted-by': 'crossref',
'first-page': '3314',
'DOI': '10.1021/ct300418h',
'article-title': 'MMPBSA. py: an efficient program for end-state free energy calculations',
'volume': '8',
'author': 'Miller',
'year': '2012',
'journal-title': 'J Chem Theor Comput'},
{ 'key': '10.1016/j.jtcme.2023.07.004_bib41',
'doi-asserted-by': 'crossref',
'first-page': '147',
'DOI': '10.1007/s10822-016-9977-1',
'article-title': 'Lessons learned from comparing molecular dynamics engines on the SAMPL5 '
'dataset',
'volume': '31',
'author': 'Shirts',
'year': '2017',
'journal-title': 'J Comput Aided Mol Des'},
{ 'issue': '8',
'key': '10.1016/j.jtcme.2023.07.004_bib42',
'doi-asserted-by': 'crossref',
'first-page': '5379',
'DOI': '10.1021/acs.jctc.1c00374',
'article-title': 'On the use of interaction entropy and related methods to estimate '
'binding entropies',
'volume': '17',
'author': 'Ekberg',
'year': '2021',
'journal-title': 'J Chem Theor Comput'},
{ 'issue': '9',
'key': '10.1016/j.jtcme.2023.07.004_bib43',
'doi-asserted-by': 'crossref',
'first-page': '4066',
'DOI': '10.1021/acs.jmedchem.5b00104',
'article-title': 'pkCSM: predicting small-molecule pharmacokinetic and toxicity '
'properties using graph-based signatures',
'volume': '58',
'author': 'Pires',
'year': '2015',
'journal-title': 'J Med Chem'},
{ 'issue': '3',
'key': '10.1016/j.jtcme.2023.07.004_bib44',
'doi-asserted-by': 'crossref',
'first-page': '1000',
'DOI': '10.1021/ci034243x',
'article-title': 'ESOL: estimating aqueous solubility directly from molecular structure',
'volume': '44',
'author': 'Delaney',
'year': '2004',
'journal-title': 'J Chem Inf Comput Sci'},
{ 'issue': '20',
'key': '10.1016/j.jtcme.2023.07.004_bib45',
'doi-asserted-by': 'crossref',
'first-page': '1820',
'DOI': '10.1002/jcc.26223',
'article-title': 'HCVpred: a web server for predicting the bioactivity of hepatitis C '
'virus NS5B inhibitors',
'volume': '41',
'author': 'Malik',
'year': '2020',
'journal-title': 'J Comput Chem'},
{ 'issue': '1',
'key': '10.1016/j.jtcme.2023.07.004_bib46',
'doi-asserted-by': 'crossref',
'first-page': '48',
'DOI': '10.4103/0975-8453.83439',
'article-title': 'Fundamental aspect and basic concept of siddha medicines',
'volume': '2',
'author': 'Shukla',
'year': '2011',
'journal-title': 'Sys Rev Pharm'},
{ 'key': '10.1016/j.jtcme.2023.07.004_bib47',
'series-title': 'In Vitro Antiviral Activity of Kabasura Kudineer - Siddha Polyherbal '
'Formulation against Novel Coronavirus (SARS-CoV-2)',
'author': 'Ms',
'year': '2021'},
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'doi-asserted-by': 'crossref',
'first-page': '149',
'DOI': '10.1002/9781118742785.ch8',
'article-title': 'Chemoinformatics in lead optimization',
'author': 'Green',
'year': '2013',
'journal-title': 'Chemoinformatics Drug Discov'},
{ 'key': '10.1016/j.jtcme.2023.07.004_bib49',
'doi-asserted-by': 'crossref',
'first-page': '1',
'DOI': '10.1177/2156587218757661',
'article-title': 'In vivo evaluation of withania somnifera–based Indian traditional '
'formulation (amukkara choornam), against chikungunya virus–induced '
'morbidity and arthralgia',
'volume': '23',
'author': 'Jain',
'year': '2018',
'journal-title': 'J Evidence-Based Integr Med.'},
{ 'key': '10.1016/j.jtcme.2023.07.004_bib50',
'doi-asserted-by': 'crossref',
'DOI': '10.1016/j.jep.2021.114098',
'article-title': 'In silico analysis of the potential mechanism of a preventive Chinese '
'medicine formula on coronavirus disease 2019',
'volume': '275',
'author': 'Wu',
'year': '2021',
'journal-title': 'J Ethnopharmacol'},
{ 'issue': '1',
'key': '10.1016/j.jtcme.2023.07.004_bib51',
'doi-asserted-by': 'crossref',
'first-page': '1',
'DOI': '10.1016/j.jaim.2020.05.009',
'article-title': 'In silico computational screening of kabasura kudineer - official '
'siddha formulation and JACOM against SARS-CoV-2 spike protein',
'volume': '13',
'author': 'Kiran',
'year': '2022',
'journal-title': 'J Ayurveda Integr Med'},
{ 'key': '10.1016/j.jtcme.2023.07.004_bib52',
'first-page': '434',
'article-title': 'Molecular docking studies on the anti-viral effects of compounds from '
'kabasura kudineer on SARS-CoV-2 3CLpro',
'author': 'Vincent',
'year': '2020',
'journal-title': 'Front Mol Biosci'},
{ 'key': '10.1016/j.jtcme.2023.07.004_bib53',
'first-page': '1',
'article-title': 'Multi-scale mechanism of antiviral drug-alike phytoligands from '
'Ayurveda in managing COVID-19 and associated metabolic comorbidities: '
'insights from network pharmacology',
'author': 'Choudhary',
'year': '2022',
'journal-title': 'Mol Divers'},
{ 'issue': '2',
'key': '10.1016/j.jtcme.2023.07.004_bib54',
'doi-asserted-by': 'crossref',
'first-page': '1063',
'DOI': '10.1007/s11696-021-01917-z',
'article-title': 'Structure-based docking, pharmacokinetic evaluation, and molecular '
'dynamics-guided evaluation of traditional formulation against '
'SARS-CoV-2 spike protein receptor bind domain and ACE2 receptor complex',
'volume': '76',
'author': 'Manandhar',
'year': '2022',
'journal-title': 'Chem Pap'},
{ 'issue': '1',
'key': '10.1016/j.jtcme.2023.07.004_bib55',
'doi-asserted-by': 'crossref',
'first-page': '266',
'DOI': '10.1002/ptr.7309',
'article-title': 'Quercetin and its derivates as antiviral potentials: a comprehensive '
'review',
'volume': '36',
'author': 'Di Petrillo',
'year': '2022',
'journal-title': 'Phyther Res'},
{ 'issue': '1',
'key': '10.1016/j.jtcme.2023.07.004_bib56',
'doi-asserted-by': 'crossref',
'first-page': '33',
'DOI': '10.1016/S2225-4110(16)30165-1',
'article-title': 'Antiinflammatory and antioxidant flavonoids and phenols from '
'Cardiospermum halicacabum (倒地鈴 Dào Dì Líng)',
'volume': '3',
'author': 'Cheng',
'year': '2013',
'journal-title': 'J Tradit Complement Med'},
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'doi-asserted-by': 'crossref',
'DOI': '10.1016/j.compbiomed.2022.105796',
'article-title': 'In silico and in vitro analysis of PPAR – α/γ dual agonists: '
'comparative evaluation of potential phytochemicals with anti-obesity '
'drug orlistat',
'volume': '147',
'author': 'Mandal',
'year': '2022',
'journal-title': 'Comput Biol Med'},
{ 'issue': '2',
'key': '10.1016/j.jtcme.2023.07.004_bib58',
'doi-asserted-by': 'crossref',
'first-page': '619',
'DOI': '10.3892/etm.2015.2923',
'article-title': 'Gallic acid decreases hepatitis C virus expression through its '
'antioxidant capacity',
'volume': '11',
'author': 'Govea-Salas',
'year': '2016',
'journal-title': 'Exp Ther Med'},
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'doi-asserted-by': 'crossref',
'DOI': '10.1016/j.phymed.2020.153286',
'article-title': 'Antiviral activity of green tea and black tea polyphenols in '
'prophylaxis and treatment of COVID-19: a review',
'volume': '85',
'author': 'Mhatre',
'year': '2021',
'journal-title': 'Phytomedicine'},
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'key': '10.1016/j.jtcme.2023.07.004_bib60',
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'first-page': '11',
'DOI': '10.1016/j.jtcme.2022.09.002',
'article-title': 'Dual actions of gallic acid and andrographolide trigger AdipoR1 to '
'stimulate insulin secretion in a streptozotocin-induced diabetes rat '
'model',
'volume': '13',
'author': 'Wong',
'year': '2023',
'journal-title': 'J Tradit Complement Med'},
{ 'issue': '1',
'key': '10.1016/j.jtcme.2023.07.004_bib61',
'first-page': '1',
'article-title': 'Efficacy of two siddha polyherbal decoctions, Nilavembu Kudineer and '
'Kaba Sura Kudineer, along with standard allopathy treatment in the '
'management of mild to moderate symptomatic COVID-19 patients—a '
'double-blind, placebo-controlled, clinical trial',
'volume': '22',
'author': 'Srivastava',
'year': '2021',
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