Investigating the binding affinity of andrographolide against human SARS-CoV-2 spike receptor-binding domain through docking and molecular dynamics simulations

Bhattarai et al., Journal of Biomolecular Structure and Dynamics, doi:10.1080/07391102.2023.2174596

Feb 2023

Source PDF All Studies Meta AnalysisMeta

In Silico study showing that andrographolide binds strongly to the SARS-CoV-2 spike protein receptor-binding domain (RBD). Authors used molecular docking and dynamics simulations to demonstrate that andrographolide forms stable non-covalent interactions with the RBD, leading to conformational changes that stabilize the complex. The ligand-bound RBD showed reduced conformational fluctuations compared to the unbound form, suggesting potential interference with ACE2 receptor binding and viral entry.

22 preclinical studies support the efficacy of andrographolide for COVID-19:

12 In Silico studies1-12

8 In Vitro studies1,13-19

2 In Vivo animal studies16,19

Important missing comments or errors? Let us know.

1. Zhang et al., Effects and Mechanisms of Andrographolide for COVID-19: A Network Pharmacology-Based and Experimentally Validated Study, Natural Product Communications, doi:10.1177/1934578X241288428.sagepub.com, doi.org.

2. Thomas et al., Cheminformatics approach to identify andrographolide derivatives as dual inhibitors of methyltransferases (nsp14 and nsp16) of SARS-CoV-2, Scientific Reports, doi:10.1038/s41598-024-58532-7.nature.com, doi.org.

3. Bhattarai et al., Investigating the binding affinity of andrographolide against human SARS-CoV-2 spike receptor-binding domain through docking and molecular dynamics simulations, Journal of Biomolecular Structure and Dynamics, doi:10.1080/07391102.2023.2174596.tandfonline.com, doi.org.

4. Nguyen et al., The Potential of Ameliorating COVID-19 and Sequelae From Andrographis paniculata via Bioinformatics, Bioinformatics and Biology Insights, doi:10.1177/11779322221149622.sagepub.com, doi.org.

5. Dassanayake et al., Molecular Docking and In-Silico Analysis of Natural Biomolecules against Dengue, Ebola, Zika, SARS-CoV-2 Variants of Concern and Monkeypox Virus, International Journal of Molecular Sciences, doi:10.3390/ijms231911131.mdpi.com, doi.org.

6. Ningrum et al., Potency Of Andrographolide, L-Mimosine And Asiaticoside Compound As Antiviral For Covid-19 Based On In Silico Method, Proceedings Universitas Muhammadiyah Yogyakarta Undergraduate Conference, doi:10.18196/umygrace.v2i2.418.ac.id, doi.org.

7. Ravichandran et al., Identification of Potential Semisynthetic Andrographolide Derivatives to Combat COVID-19 by Targeting the SARS-COV-2 Spike Protein and Human ACE2 Receptor– An In-silico Approach, Biointerface Research in Applied Chemistry, doi:10.33263/BRIAC132.155.biointerfaceresearch.com, doi.org.

8. Saeheng et al., In Silico Prediction of Andrographolide Dosage Regimens for COVID-19 Treatment, The American Journal of Chinese Medicine, doi:10.1142/S0192415X22500732.worldscientific.com, doi.org.

9. Khanal et al., Combination of system biology to probe the anti-viral activity of andrographolide and its derivative against COVID-19, RSC Advances, doi:10.1039/D0RA10529E.rsc.org, doi.org.

10. Rehan et al., A Computational Approach Identified Andrographolide as a Potential Drug for Suppressing COVID-19-Induced Cytokine Storm, Frontiers in Immunology, doi:10.3389/fimmu.2021.648250.frontiersin.org, doi.org.

11. Rajagopal et al., Activity of phytochemical constituents of Curcuma longa (turmeric) and Andrographis paniculata against coronavirus (COVID-19): an in silico approach, Future Journal of Pharmaceutical Sciences, doi:10.1186/s43094-020-00126-x.springeropen.com, doi.org.

12. Dey et al., The role of andrographolide and its derivative in COVID-19 associated proteins and immune system, Research Square, doi:10.21203/rs.3.rs-35800/v1.researchsquare.com, doi.org.

13. Chaopreecha et al., Proteomic Analysis Identifies the Glutathione Synthesizing Enzyme Gclc as an Andrographolide Target and a Protective Factor Against Sars-Cov-2 Infection, Elsevier BV, doi:10.2139/ssrn.4876852.ssrn.com, doi.org.

14. Li et al., Andrographolide suppresses SARS-CoV-2 infection by downregulating ACE2 expression: A mechanistic study, Antiviral Therapy, doi:10.1177/13596535241259952.sagepub.com, doi.org.

15. Low et al., The wide spectrum anti-inflammatory activity of andrographolide in comparison to NSAIDs: a promising therapeutic compound against the cytokine storm, bioRxiv, doi:10.1101/2024.02.21.581396.biorxiv.org, doi.org.

16. Wan et al., Synergistic inhibition effects of andrographolide and baicalin on coronavirus mechanisms by downregulation of ACE2 protein level, Scientific Reports, doi:10.1038/s41598-024-54722-5.nature.com, doi.org.

17. Siridechakorn et al., Inhibitory efficiency of Andrographis paniculata extract on viral multiplication and nitric oxide production, Scientific Reports, doi:10.1038/s41598-023-46249-y.nature.com, doi.org.

18. Mohd Abd Razak et al., In Vitro Anti-SARS-CoV-2 Activities of Curcumin and Selected Phenolic Compounds, Natural Product Communications, doi:10.1177/1934578X231188861.sagepub.com, doi.org.

19. Pu et al., The effects and mechanisms of the anti-COVID-19 traditional Chinese medicine, Dehydroandrographolide from Andrographis paniculata (Burm.f.) Wall, on acute lung injury by the inhibition of NLRP3-mediated pyroptosis, Phytomedicine, doi:10.1016/j.phymed.2023.154753.sciencedirect.com, doi.org.

Bhattarai et al., 10 Feb 2023, peer-reviewed, 3 authors.

In Silico studies are an important part of preclinical research, however results may be very different in vivo.

This Paper Andrographol..All

{ 'indexed': {'date-parts': [[2024, 3, 5]], 'date-time': '2024-03-05T19:10:40Z', 'timestamp': 1709665840476}, 'reference-count': 63, 'publisher': 'Informa UK Limited', 'issue': '22', 'content-domain': {'domain': ['www.tandfonline.com'], 'crossmark-restriction': True}, 'published-print': {'date-parts': [[2023, 12, 29]]}, 'DOI': '10.1080/07391102.2023.2174596', 'type': 'journal-article', 'created': {'date-parts': [[2023, 2, 11]], 'date-time': '2023-02-11T02:20:36Z', 'timestamp': 1676082036000}, 'page': '13438-13453', 'update-policy': 'http://dx.doi.org/10.1080/tandf_crossmark_01', 'source': 'Crossref', 'is-referenced-by-count': 2, 'title': 'Investigating the binding affinity of andrographolide against human SARS-CoV-2 spike ' 'receptor-binding domain through docking and molecular dynamics simulations', 'prefix': '10.1080', 'volume': '41', 'author': [ { 'given': 'Anil', 'family': 'Bhattarai', 'sequence': 'first', 'affiliation': [ { 'name': 'Bioinformatics Programming Laboratory, Department of ' 'Biotechnology, School of Bio-Sciences and Technology, Vellore ' 'Institute of Technology, VIT, Vellore, Tamil Nadu, India'}]}, { 'given': 'Annadurai', 'family': 'Priyadharshini', 'sequence': 'additional', 'affiliation': [ { 'name': 'Bioinformatics Programming Laboratory, Department of ' 'Biotechnology, School of Bio-Sciences and Technology, Vellore ' 'Institute of Technology, VIT, Vellore, Tamil Nadu, India'}]}, { 'ORCID': 'http://orcid.org/0000-0003-4212-0927', 'authenticated-orcid': False, 'given': 'Isaac Arnold', 'family': 'Emerson', 'sequence': 'additional', 'affiliation': [ { 'name': 'Bioinformatics Programming Laboratory, Department of ' 'Biotechnology, School of Bio-Sciences and Technology, Vellore ' 'Institute of Technology, VIT, Vellore, Tamil Nadu, India'}]}], 'member': '301', 'published-online': {'date-parts': [[2023, 2, 10]]}, 'reference': [ { 'key': 'e_1_3_3_2_1', 'doi-asserted-by': 'publisher', 'DOI': '10.3109/14756366.2014.979345'}, {'key': 'e_1_3_3_3_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1016/j.softx.2015.06.001'}, {'key': 'e_1_3_3_4_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1007/s00894-020-04599-8'}, { 'key': 'e_1_3_3_5_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1080/07391102.2021.1900916'}, { 'key': 'e_1_3_3_6_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1371/journal.pcbi.1000544'}, {'key': 'e_1_3_3_7_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1093/nar/gky318'}, { 'key': 'e_1_3_3_8_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1080/07391102.2018.1444511'}, {'key': 'e_1_3_3_9_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1021/j100142a004'}, {'key': 'e_1_3_3_10_1', 'doi-asserted-by': 'publisher', 'DOI': '10.3389/fimmu.2020.552925'}, {'key': 'e_1_3_3_11_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1002/prot.22922'}, { 'key': 'e_1_3_3_12_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1128/JVI.77.16.8801-8811.2003'}, { 'key': 'e_1_3_3_13_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1093/bioinformatics/btx349'}, { 'key': 'e_1_3_3_14_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1080/22221751.2020.1725399'}, { 'key': 'e_1_3_3_15_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1080/22221751.2020.1737364'}, {'key': 'e_1_3_3_16_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1038/s41579-018-0118-9'}, { 'key': 'e_1_3_3_17_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1016/j.toxicon.2021.02.015'}, {'key': 'e_1_3_3_18_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1063/1.464397'}, { 'key': 'e_1_3_3_19_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1021/acs.jmedchem.5b01684'}, {'key': 'e_1_3_3_20_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1093/nar/gku401'}, { 'key': 'e_1_3_3_21_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1007/978-1-4939-2438-7_1'}, { 'key': 'e_1_3_3_22_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1016/0040-4020(80)80168-2'}, {'key': 'e_1_3_3_23_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1002/elps.1150181505'}, { 'key': 'e_1_3_3_24_1', 'article-title': 'Avogadro: An advanced semantic chemical editor, visualization, and ' 'analysis platform', 'author': 'Hanwell M. D.', 'year': '2018', 'unstructured': 'Hanwell, M. D., Curtis, D. E., Lonie, D. C., Vandermeersch, T., Zurek, ' 'E., & Hutchison, G. R. (2018). Avogadro: An advanced semantic chemical ' 'editor, visualization, and analysis platform. Journal of Cheminformatics ' '4(1), 1-17.', 'journal-title': 'Journal of Cheminformatics 4(1), 1-17.'}, { 'key': 'e_1_3_3_25_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H'}, {'key': 'e_1_3_3_26_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1038/s41579-020-00459-7'}, {'key': 'e_1_3_3_27_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1002/jcc.23354'}, {'key': 'e_1_3_3_28_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1038/nmeth.4067'}, {'key': 'e_1_3_3_29_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1107/S090744490200985X'}, {'key': 'e_1_3_3_30_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1002/prot.340110305'}, { 'key': 'e_1_3_3_31_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1103/PhysRevLett.94.078102'}, {'key': 'e_1_3_3_32_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1155/2013/846740'}, {'key': 'e_1_3_3_33_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1038/189771a0'}, {'key': 'e_1_3_3_34_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1038/nsb0902-646'}, {'key': 'e_1_3_3_35_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1038/347631a0'}, {'key': 'e_1_3_3_36_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1021/ci500020m'}, { 'key': 'e_1_3_3_37_1', 'first-page': '16', 'article-title': 'Influence of logBB cut-off on the prediction of blood-brain barrier ' 'permeability', 'author': 'Kunwittaya S.', 'year': '2013', 'unstructured': 'Kunwittaya, S., Nantasenamat, C., Treeratanapiboon, L., Srisarin, A., ' 'Isarankura-Na-Ayudhya, C., & Prachayasittikul, V. (2013). Influence of ' 'logBB cut-off on the prediction of blood-brain barrier permeability. ' 'Biomedical and Applied Technology Journal, 1, 16–34.', 'journal-title': 'Biomedical and Applied Technology Journal, 1'}, { 'key': 'e_1_3_3_38_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1016/S1875-5364(20)60016-4'}, {'key': 'e_1_3_3_39_1', 'doi-asserted-by': 'publisher', 'DOI': '10.3390/ph13090209'}, {'key': 'e_1_3_3_40_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1038/s41564-020-0688-y'}, {'key': 'e_1_3_3_41_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1002/prot.22711'}, { 'key': 'e_1_3_3_42_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1016/j.ddtec.2004.11.007'}, {'key': 'e_1_3_3_43_1', 'doi-asserted-by': 'publisher', 'DOI': '10.15171/apb.2017.041'}, {'key': 'e_1_3_3_44_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1016/j.str.2011.03.010'}, { 'key': 'e_1_3_3_45_1', 'first-page': '283', 'article-title': 'Andrographis paniculata (Kalmegh). A Review', 'author': 'Mishra S. K.', 'year': '2007', 'unstructured': 'Mishra, S. K., Sangwan, N. S., & Sangwan, R. S. (2007). Andrographis ' 'paniculata (Kalmegh). A Review. Pharmacognosy Reviews, 1(2), 283–298.', 'journal-title': 'Pharmacognosy Reviews, 1'}, { 'key': 'e_1_3_3_46_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B'}, {'key': 'e_1_3_3_47_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1002/cbic.202000047'}, {'key': 'e_1_3_3_48_1', 'doi-asserted-by': 'publisher', 'DOI': '10.3390/v13050828'}, { 'key': 'e_1_3_3_49_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1016/j.chempr.2021.07.015'}, {'key': 'e_1_3_3_50_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1016/j.tibs.2021.06.001'}, {'key': 'e_1_3_3_51_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1021/jp5013544'}, {'key': 'e_1_3_3_52_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1021/acsomega.2c00844'}, {'key': 'e_1_3_3_53_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1007/s15010-020-01486-5'}, { 'key': 'e_1_3_3_54_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1021/acs.jnatprod.0c01324'}, {'key': 'e_1_3_3_55_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1021/jacs.0c01718'}, {'key': 'e_1_3_3_56_1', 'doi-asserted-by': 'publisher', 'DOI': '10.3389/fmolb.2020.599079'}, {'key': 'e_1_3_3_57_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1002/jcc.21334'}, {'key': 'e_1_3_3_58_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1163/_q3_SIM_00374'}, {'key': 'e_1_3_3_59_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1002/jcc.20035'}, {'key': 'e_1_3_3_60_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1038/s41401-021-00735-z'}, {'key': 'e_1_3_3_61_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1016/j.cell.2020.03.045'}, {'key': 'e_1_3_3_62_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1002/cpbi.3'}, {'key': 'e_1_3_3_63_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1016/j.apsb.2021.06.016'}, {'key': 'e_1_3_3_64_1', 'doi-asserted-by': 'publisher', 'DOI': '10.1002/jcc.21816'}], 'container-title': 'Journal of Biomolecular Structure and Dynamics', 'original-title': [], 'language': 'en', 'link': [ { 'URL': 'https://www.tandfonline.com/doi/pdf/10.1080/07391102.2023.2174596', 'content-type': 'unspecified', 'content-version': 'vor', 'intended-application': 'similarity-checking'}], 'deposited': { 'date-parts': [[2024, 3, 5]], 'date-time': '2024-03-05T18:37:15Z', 'timestamp': 1709663835000}, 'score': 1, 'resource': {'primary': {'URL': 'https://www.tandfonline.com/doi/full/10.1080/07391102.2023.2174596'}}, 'subtitle': [], 'short-title': [], 'issued': {'date-parts': [[2023, 2, 10]]}, 'references-count': 63, 'journal-issue': {'issue': '22', 'published-print': {'date-parts': [[2023, 12, 29]]}}, 'alternative-id': ['10.1080/07391102.2023.2174596'], 'URL': 'http://dx.doi.org/10.1080/07391102.2023.2174596', 'relation': {}, 'ISSN': ['0739-1102', '1538-0254'], 'subject': [], 'container-title-short': 'Journal of Biomolecular Structure and Dynamics', 'published': {'date-parts': [[2023, 2, 10]]}, 'assertion': [ { 'value': 'The publishing and review policy for this title is described in its Aims & ' 'Scope.', 'order': 1, 'name': 'peerreview_statement', 'label': 'Peer Review Statement'}, { 'value': 'http://www.tandfonline.com/action/journalInformation?show=aimsScope&journalCode=tbsd20', 'URL': 'http://www.tandfonline.com/action/journalInformation?show=aimsScope&journalCode=tbsd20', 'order': 2, 'name': 'aims_and_scope_url', 'label': 'Aim & Scope'}, { 'value': '2022-09-19', 'order': 0, 'name': 'received', 'label': 'Received', 'group': {'name': 'publication_history', 'label': 'Publication History'}}, { 'value': '2023-01-24', 'order': 1, 'name': 'accepted', 'label': 'Accepted', 'group': {'name': 'publication_history', 'label': 'Publication History'}}, { 'value': '2023-02-10', 'order': 2, 'name': 'published', 'label': 'Published', 'group': {'name': 'publication_history', 'label': 'Publication History'}}]}

Download Image

Please send us corrections, updates, or comments. c19early involves the extraction of 100,000+ datapoints from thousands of papers. Community updates help ensure high accuracy. Treatments and other interventions are complementary. All practical, effective, and safe means should be used based on risk/benefit analysis. No treatment or intervention is 100% available and effective for all current and future variants. We do not provide medical advice. Before taking any medication, consult a qualified physician who can provide personalized advice and details of risks and benefits based on your medical history and situation. FLCCC and WCH provide treatment protocols.

Submit

Post

@CovidAnalysis

FAQ

Public domain CC0 1.0