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Analisis in silico interaksi senyawa kurkuminoid terhadap enzim main protease 6LU7 dari SARS-CoV-2

Winih Kinasih et al., Duta Pharma Journal, doi:10.47701/djp.v3i1.2904

Jun 2023

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Curcumin for COVID-19

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In Silico study of the interaction between curcumin and its derivatives with the main protease enzyme from SARS-CoV-2. The compounds tested were curcumin, bisdemethoxycurcumin, and demethoxycurcumin. All compounds met the requirements of Lipinski's Rule of Five, indicating they have drug-like properties. Bisdemethoxycurcumin had the highest binding affinity (lowest docking score of -6.7 kcal/mol) to the protease, suggesting it is the most potent inhibitor of the enzyme. Bisdemethoxycurcumin shared the most amino acid residues with the reference ligand favipiravir. This suggests bisdemethoxycurcumin has potential as an antiviral agent against SARS-CoV-2 by inhibiting its main protease enzyme.

48 preclinical studies support the efficacy of curcumin for COVID-19:

24 In Silico studies1-24

23 In Vitro studies1,5,7,11,17,21,25-41

1 In Vivo animal study5

In Silico studies predict inhibition of SARS-CoV-2 with curcumin or metabolites via binding to the spikeA,5,10,12,18,21 (and specifically the receptor binding domainB,8,11,14), M^proC,5,7,9-11,13,14,16,19,21,22,24,38, RNA-dependent RNA polymeraseD,11,20, ACE2E,12,13,15, nucleocapsidF,6,23, nsp10G,23, and helicaseH,27 proteins. In Vitro studies demonstrate inhibition of the spikeA,32 (and specifically the receptor binding domainB,41), M^proC,17,32,38,40, ACE2E,41, and TMPRSS2I,41 proteins, and inhibition of spike-ACE2 interactionJ,25. In Vitro studies demonstrate efficacy in Calu-3K,39, A549L,32, 293TM,1, HEK293-hACE2N,17,30, 293T/hACE2/TMPRSS2O,31, Vero E6P,7,11,21,30,32,34,35,37,39, and SH-SY5YQ,29 cells. Curcumin is predicted to inhibit the interaction between the SARS-CoV-2 spike protein receptor binding domain and the human ACE2 receptor for the delta and omicron variants8, decreases pro-inflammatory cytokines induced by SARS-CoV-2 in peripheral blood mononuclear cells37, alleviates SARS-CoV-2 spike protein-induced mitochondrial membrane damage and oxidative stress1, may limit COVID-19 induced cardiac damage by inhibiting the NF-κB signaling pathway which mediates the profibrotic effects of the SARS-CoV-2 spike protein on cardiac fibroblasts42, and inhibits SARS-CoV-2 ORF3a ion channel activity, which contributes to viral pathogenicity and cytotoxicity33.

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1. Zhang et al., Computational Discovery of Mitochondrial Dysfunction Biomarkers in Severe SARS-CoV-2 Infection: Facilitating Pytomedicine Screening, Phytomedicine, doi:10.1016/j.phymed.2024.155784.sciencedirect.com, doi.org.

2. Öztürkkan et al., In Silico investigation of the effects of curcuminoids on the spike protein of the omicron variant of SARS-CoV-2, Baku State University Journal of Chemistry and Material Sciences, 1:2, bsuj.bsu.edu.az/uploads/pdf/ec4204d62f7802de54e6092bf7860029.pdf.edu.az.

3. Yunze et al., Therapeutic effect and potential mechanism of curcumin, an active ingredient in Tongnao Decoction, on COVID-19 combined with stroke: a network pharmacology study and GEO database mining, Research Square, doi:10.21203/rs.3.rs-4329762/v1.researchsquare.com, doi.org.

4. Agamah et al., Network-based multi-omics-disease-drug associations reveal drug repurposing candidates for COVID-19 disease phases, ScienceOpen, doi:10.58647/DRUGARXIV.PR000010.v1.scienceopen.com, doi.org.

5. Boseila et al., Throat spray formulated with virucidal Pharmaceutical excipients as an effective early prophylactic or treatment strategy against pharyngitis post-exposure to SARS CoV-2, European Journal of Pharmaceutics and Biopharmaceutics, doi:10.1016/j.ejpb.2024.114279.sciencedirect.com, doi.org.

6. Hidayah et al., Bioinformatics study of curcumin, demethoxycurcumin, bisdemethoxycurcumin and cyclocurcumin compounds in Curcuma longa as an antiviral agent via nucleocapsid on SARS-CoV-2 inhibition, International Conference on Organic and Applied Chemistry, doi:10.1063/5.0197724.aip.org, doi.org.

7. Singh et al., Unlocking the potential of phytochemicals in inhibiting SARS-CoV-2 M Pro protein - An in-silico and cell-based approach, Research Square, doi:10.21203/rs.3.rs-3888947/v1.researchsquare.com, doi.org.

8. Kant et al., Structure-based drug discovery to identify SARS-CoV2 spike protein–ACE2 interaction inhibitors, Journal of Biomolecular Structure and Dynamics, doi:10.1080/07391102.2023.2300060.tandfonline.com, doi.org.

9. Naderi Beni et al., In silico studies of anti-oxidative and hot temperament-based phytochemicals as natural inhibitors of SARS-CoV-2 Mpro, PLOS ONE, doi:10.1371/journal.pone.0295014.plos.org, doi.org.

10. Moschovou et al., Exploring the Binding Effects of Natural Products and Antihypertensive Drugs on SARS-CoV-2: An In Silico Investigation of Main Protease and Spike Protein, International Journal of Molecular Sciences, doi:10.3390/ijms242115894.mdpi.com, doi.org.

11. Eleraky et al., Curcumin Transferosome-Loaded Thermosensitive Intranasal in situ Gel as Prospective Antiviral Therapy for SARS-Cov-2, International Journal of Nanomedicine, doi:10.2147/IJN.S423251.dovepress.com, doi.org.

12. Singh (B) et al., Computational studies to analyze effect of curcumin inhibition on coronavirus D614G mutated spike protein, The Seybold Report, doi:10.17605/OSF.IO/TKEXJ.ac.in, doi.org.

13. Thapa et al., In-silico Approach for Predicting the Inhibitory Effect of Home Remedies on Severe Acute Respiratory Syndrome Coronavirus-2, Makara Journal of Science, doi:10.7454/mss.v27i3.1609.ac.id, doi.org.

14. Srivastava et al., Paradigm of Well-Orchestrated Pharmacokinetic Properties of Curcuminoids Relative to Conventional Drugs for the Inactivation of SARS-CoV-2 Receptors: An In Silico Approach, Stresses, doi:10.3390/stresses3030043.mdpi.com, doi.org.

15. Alkafaas et al., A study on the effect of natural products against the transmission of B.1.1.529 Omicron, Virology Journal, doi:10.1186/s12985-023-02160-6.biomedcentral.com, doi.org.

16. Winih Kinasih et al., Analisis in silico interaksi senyawa kurkuminoid terhadap enzim main protease 6LU7 dari SARS-CoV-2, Duta Pharma Journal, doi:10.47701/djp.v3i1.2904.ac.id, doi.org.

17. Wu et al., Potential Mechanism of Curcumin and Resveratrol against SARS-CoV-2, Research Square, doi:10.21203/rs.3.rs-2780614/v1.researchsquare.com, doi.org.

18. Nag et al., Curcumin inhibits spike protein of new SARS-CoV-2 variant of concern (VOC) Omicron, an in silico study, Computers in Biology and Medicine, doi:10.1016/j.compbiomed.2022.105552.sciencedirect.com, doi.org.

19. Rampogu et al., Molecular Docking and Molecular Dynamics Simulations Discover Curcumin Analogue as a Plausible Dual Inhibitor for SARS-CoV-2, International Journal of Molecular Sciences, doi:10.3390/ijms23031771.mdpi.com, doi.org.

20. Singh (C) et al., Potential of turmeric-derived compounds against RNA-dependent RNA polymerase of SARS-CoV-2: An in-silico approach, Computers in Biology and Medicine, doi:10.1016/j.compbiomed.2021.104965.sciencedirect.com, doi.org.

21. Kandeil et al., Bioactive Polyphenolic Compounds Showing Strong Antiviral Activities against Severe Acute Respiratory Syndrome Coronavirus 2, Pathogens, doi:10.3390/pathogens10060758.mdpi.com, doi.org.

22. 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.

23. Suravajhala et al., Comparative Docking Studies on Curcumin with COVID-19 Proteins, Preprints, doi:10.20944/preprints202005.0439.v3.preprints.org, doi.org.

24. Sekiou et al., In-Silico Identification of Potent Inhibitors of COVID-19 Main Protease (Mpro) and Angiotensin Converting Enzyme 2 (ACE2) from Natural Products: Quercetin, Hispidulin, and Cirsimaritin Exhibited Better Potential Inhibition than Hydroxy-Chloroquine Against COVID-19 Main Protease Active Site and ACE2, ChemRxiv, doi:10.26434/chemrxiv.12181404.v1.chemrxiv.org, doi.org.

25. Emam et al., Establishment of in-house assay for screening of anti-SARS-CoV-2 protein inhibitors, AMB Express, doi:10.1186/s13568-024-01739-8.springeropen.com, doi.org.

26. Van Tin et al., Spike Protein of SARS-CoV-2 Activates Cardiac Fibrogenesis through NLRP3 Inflammasomes and NF-κB Signaling, Cells, doi:10.3390/cells13161331.mdpi.com, doi.org.

27. Li et al., Thermal shift assay (TSA)-based drug screening strategy for rapid discovery of inhibitors against the Nsp13 helicase of SARS-CoV-2, Animals and Zoonoses, doi:10.1016/j.azn.2024.06.001.sciencedirect.com, doi.org.

28. Kamble et al., Nanoparticulate curcumin spray imparts prophylactic and therapeutic properties against SARS-CoV-2, Emergent Materials, doi:10.1007/s42247-024-00754-6.springer.com, doi.org.

29. Nicoliche et al., Antiviral, anti-inflammatory and antioxidant effects of curcumin and curcuminoids in SH-SY5Y cells infected by SARS-CoV-2, Scientific Reports, doi:10.1038/s41598-024-61662-7.nature.com, doi.org.

30. Nittayananta et al., A novel film spray containing curcumin inhibits SARS-CoV-2 and influenza virus infection and enhances mucosal immunity, Virology Journal, doi:10.1186/s12985-023-02282-x.biomedcentral.com, doi.org.

31. Septisetyani et al., Curcumin and turmeric extract inhibited SARS-CoV-2 pseudovirus cell entry and Spike mediated cell fusion, bioRxiv, doi:10.1101/2023.09.28.560070.biorxiv.org, doi.org.

32. 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.

33. Fam et al., Channel activity of SARS-CoV-2 viroporin ORF3a inhibited by adamantanes and phenolic plant metabolites, Scientific Reports, doi:10.1038/s41598-023-31764-9.nature.com, doi.org.

34. Teshima et al., Antiviral activity of curcumin and its analogs selected by an artificial intelligence-supported activity prediction system in SARS-CoV-2-infected VeroE6 cells, Natural Product Research, doi:10.1080/14786419.2023.2194647.tandfonline.com, doi.org.

35. Leka et al., In vitro antiviral activity against SARS-CoV-2 of common herbal medicinal extracts and their bioactive compounds, Phytotherapy Research, doi:10.1002/ptr.7463.wiley.com, doi.org.

36. Goc et al., Inhibitory effects of specific combination of natural compounds against SARS-CoV-2 and its Alpha, Beta, Gamma, Delta, Kappa, and Mu variants, European Journal of Microbiology and Immunology, doi:10.1556/1886.2021.00022.akjournals.com, doi.org.

37. Marín-Palma et al., Curcumin Inhibits In Vitro SARS-CoV-2 Infection In Vero E6 Cells through Multiple Antiviral Mechanisms, Molecules, doi:10.3390/molecules26226900.mdpi.com, doi.org.

38. Bahun et al., Inhibition of the SARS-CoV-2 3CLpro main protease by plant polyphenols, Food Chemistry, doi:10.1016/j.foodchem.2021.131594.sciencedirect.com, doi.org.

39. Bormann et al., Turmeric Root and Its Bioactive Ingredient Curcumin Effectively Neutralize SARS-CoV-2 In Vitro, Viruses, doi:10.3390/v13101914.mdpi.com, doi.org.

40. Guijarro-Real et al., Potential In Vitro Inhibition of Selected Plant Extracts against SARS-CoV-2 Chymotripsin-Like Protease (3CLPro) Activity, Foods, doi:10.3390/foods10071503.mdpi.com, doi.org.

41. Goc (B) et al., Phenolic compounds disrupt spike-mediated receptor-binding and entry of SARS-CoV-2 pseudo-virions, PLOS ONE, doi:10.1371/journal.pone.0253489.plos.org, doi.org.

42. Van Tin (B) et al., Spike Protein of SARS-CoV-2 Activates Cardiac Fibrogenesis through NLRP3 Inflammasomes and NF-κB Signaling, Cells, doi:10.3390/cells13161331.mdpi.com, doi.org.

a. The trimeric spike (S) protein is a glycoprotein that mediates viral entry by binding to the host ACE2 receptor, is critical for SARS-CoV-2's ability to infect host cells, and is a target of neutralizing antibodies. Inhibition of the spike protein prevents viral attachment, halting infection at the earliest stage.

b. The receptor binding domain is a specific region of the spike protein that binds ACE2 and is a major target of neutralizing antibodies. Focusing on the precise binding site allows highly specific disruption of viral attachment with reduced potential for off-target effects.

c. The main protease or M^pro, also known as 3CL^pro or nsp5, is a cysteine protease that cleaves viral polyproteins into functional units needed for replication. Inhibiting M^pro disrupts the SARS-CoV-2 lifecycle within the host cell, preventing the creation of new copies.

d. RNA-dependent RNA polymerase (RdRp), also called nsp12, is the core enzyme of the viral replicase-transcriptase complex that copies the positive-sense viral RNA genome into negative-sense templates for progeny RNA synthesis. Inhibiting RdRp blocks viral genome replication and transcription.

e. The angiotensin converting enzyme 2 (ACE2) protein is a host cell transmembrane protein that serves as the cellular receptor for the SARS-CoV-2 spike protein. ACE2 is expressed on many cell types, including epithelial cells in the lungs, and allows the virus to enter and infect host cells. Inhibition may affect ACE2's physiological function in blood pressure control.

f. The nucleocapsid (N) protein binds and encapsulates the viral genome by coating the viral RNA. N enables formation and release of infectious virions and plays additional roles in viral replication and pathogenesis. N is also an immunodominant antigen used in diagnostic assays.

g. Non-structural protein 10 (nsp10) serves as an RNA chaperone and stabilizes conformations of nsp12 and nsp14 in the replicase-transcriptase complex, which synthesizes new viral RNAs. Nsp10 disruption may destabilize replicase-transcriptase complex activity.

h. The helicase, or nsp13, protein unwinds the double-stranded viral RNA, a crucial step in replication and transcription. Inhibition may prevent viral genome replication and the creation of new virus components.

i. Transmembrane protease serine 2 (TMPRSS2) is a host cell protease that primes the spike protein, facilitating cellular entry. TMPRSS2 activity helps enable cleavage of the spike protein required for membrane fusion and virus entry. Inhibition may especially protect respiratory epithelial cells, buy may have physiological effects.

j. The interaction between the SARS-CoV-2 spike protein and the human ACE2 receptor is a primary method of viral entry, inhibiting this interaction can prevent the virus from attaching to and entering host cells, halting infection at an early stage.

k. Calu-3 is a human lung adenocarcinoma cell line with moderate ACE2 and TMPRSS2 expression and SARS-CoV-2 susceptibility. It provides a model of the human respiratory epithelium, but many not be ideal for modeling early stages of infection due to the moderate expression levels of ACE2 and TMPRSS2.

l. A549 is a human lung carcinoma cell line with low ACE2 expression and SARS-CoV-2 susceptibility. Viral entry/replication can be studied but the cells may not replicate all aspects of lung infection.

m. 293T is a human embryonic kidney cell line that can be engineered for high ACE2 expression and SARS-CoV-2 susceptibility. 293T cells are easily transfected and support high protein expression.

n. HEK293-hACE2 is a human embryonic kidney cell line with high ACE2 expression and SARS-CoV-2 susceptibility. Cells have been transfected with a plasmid to express the human ACE2 (hACE2) protein.

o. 293T/hACE2/TMPRSS2 is a human embryonic kidney cell line engineered for high ACE2 and TMPRSS2 expression, which mimics key aspects of human infection. 293T/hACE2/TMPRSS2 cells are very susceptible to SARS-CoV-2 infection.

p. Vero E6 is an African green monkey kidney cell line with low/no ACE2 expression and high SARS-CoV-2 susceptibility. The cell line is easy to maintain and supports robust viral replication, however the monkey origin may not accurately represent human responses.

q. SH-SY5Y is a human neuroblastoma cell line that exhibits neuronal phenotypes. It is commonly used as an in vitro model for studying neurotoxicity, neurodegenerative diseases, and neuronal differentiation.

Winih Kinasih et al., 30 Jun 2023, peer-reviewed, 3 authors. Contact: ahone.far02@gmail.com.

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

This Paper Curcumin All

ANALISIS IN SILICO INTERAKSI SENYAWA KURKUMINOID TERHADAP ENZIM MAIN PROTEASE 6LU7 DARI SARS-COV-2

Angkininta Ayu, Winih Kinasih, Fadilah Qonitah

Covid-19 merupakan penyakit yang disebabkan coronavirus jenis baru (SARS-CoV-2) di akhir tahun 2019. Sampai saat ini tidak ada obat khusus yang tersedia untuk mengobati penyakit ini. Pengobatan tradisional telah memainkan peran positif dalam memerangi Covid-19. Beberapa senyawa aktif mulai dilakukan penelitian untuk menangkal virus Covid-19 salah satunya adalah senyawa kurkumin. Kurkumin merupakan senyawa aktif dari tanaman kunyit dan temulawak. Berdasarkan penelitian dilaporkan kurkumin dapat menghambat agregasi trombosit, antidiabetes, antitumor, efek antiinflamasi, efek antioksidan, dan antivirus. Penelitian ini bertujuan untuk mengetahui interaksi antara senyawa kurkuminoid terhadap enzim main protease 6LU7 dari SARS CoV-2 serta senyawa kurkuminoid yang dapat berikatan dengan enzim main protease 6LU7 dari SARS CoV-2. Penelitian ini termasuk jenis penelitian eksperimental secara in silico. Hasil penelitian ini diperoleh senyawa uji kurkumin dan turunannya yaitu kurkumin, bisdemetoksikurkumin, dan demetoksikurkumin telah memenuhi syarat hukum Lipinksi Rule of Five. Bisdemetoksikurkumin memiliki kemampuan sebagai antivirus SARS-CoV-2 karena memiliki persamaan residu asam amino paling banyak dengan ligan pembanding (Favipiravir) yaitu residu ASN A

DAFTAR PUSTAKA

{ 'indexed': {'date-parts': [[2023, 8, 1]], 'date-time': '2023-08-01T04:25:10Z', 'timestamp': 1690863910582}, 'reference-count': 0, 'publisher': 'Universitas Duta Bangsa Surakarta', 'issue': '1', 'license': [ { 'start': { 'date-parts': [[2023, 6, 30]], 'date-time': '2023-06-30T00:00:00Z', 'timestamp': 1688083200000}, 'content-version': 'unspecified', 'delay-in-days': 0, 'URL': 'https://creativecommons.org/licenses/by/4.0'}], 'content-domain': {'domain': [], 'crossmark-restriction': False}, 'abstract': 'Covid-19 merupakan penyakit yang disebabkan coronavirus jenis baru (SARS-CoV-2) di ' 'akhir tahun 2019. Sampai saat ini tidak ada obat khusus yang tersedia untuk mengobati ' 'penyakit ini. Pengobatan tradisional telah memainkan peran positif dalam memerangi Covid-19. ' 'Beberapa senyawa aktif mulai dilakukan penelitian untuk menangkal virus Covid-19 salah ' 'satunya adalah senyawa kurkumin. Kurkumin merupakan senyawa aktif dari tanaman kunyit dan ' 'temulawak. Berdasarkan penelitian dilaporkan kurkumin dapat menghambat agregasi trombosit, ' 'antidiabetes, antitumor, efek antiinflamasi, efek antioksidan, dan antivirus. Penelitian ini ' 'bertujuan untuk mengetahui interaksi antara senyawa kurkuminoid terhadap enzim main protease ' '6LU7 dari SARS CoV-2 serta senyawa kurkuminoid yang dapat berikatan dengan enzim main ' 'protease 6LU7 dari SARS CoV-2. Penelitian ini termasuk jenis penelitian eksperimental secara ' 'in silico. Hasil penelitian ini diperoleh senyawa uji kurkumin dan turunannya yaitu kurkumin, ' 'bisdemetoksikurkumin, dan demetoksikurkumin telah memenuhi syarat hukum Lipinksi Rule of ' 'Five. Bisdemetoksikurkumin memiliki kemampuan sebagai antivirus SARS-CoV-2 karena memiliki ' 'persamaan residu asam amino paling banyak dengan ligan pembanding (Favipiravir) yaitu residu ' 'ASN A:142; GLY A:143; CYS A:145; HIS A:163; HIS A:172; LEU A:141; SER A:144; GLU A:166; PHE ' 'A:140 dengan docking score sebesar -6,7 kkal/mol.', 'DOI': '10.47701/djp.v3i1.2904', 'type': 'journal-article', 'created': {'date-parts': [[2023, 7, 31]], 'date-time': '2023-07-31T05:14:10Z', 'timestamp': 1690780450000}, 'source': 'Crossref', 'is-referenced-by-count': 0, 'title': 'ANALISIS IN SILICO INTERAKSI SENYAWA KURKUMINOID TERHADAP ENZIM MAIN PROTEASE 6LU7 DARI ' 'SARS-COV-2', 'prefix': '10.47701', 'volume': '3', 'author': [ {'given': 'Ahwan', 'family': 'Abdul', 'sequence': 'first', 'affiliation': []}, { 'given': 'Angkininta Ayu', 'family': 'Winih Kinasih', 'sequence': 'additional', 'affiliation': []}, {'given': 'Fadilah', 'family': 'Qonitah', 'sequence': 'additional', 'affiliation': []}], 'member': '27561', 'published-online': {'date-parts': [[2023, 6, 30]]}, 'container-title': 'Duta Pharma Journal', 'original-title': [], 'link': [ { 'URL': 'https://ojs.udb.ac.id/index.php/DJP/article/download/2904/2115', 'content-type': 'application/pdf', 'content-version': 'vor', 'intended-application': 'text-mining'}, { 'URL': 'https://ojs.udb.ac.id/index.php/DJP/article/download/2904/2115', 'content-type': 'unspecified', 'content-version': 'vor', 'intended-application': 'similarity-checking'}], 'deposited': { 'date-parts': [[2023, 7, 31]], 'date-time': '2023-07-31T05:14:11Z', 'timestamp': 1690780451000}, 'score': 1, 'resource': {'primary': {'URL': 'https://ojs.udb.ac.id/index.php/DJP/article/view/2904'}}, 'subtitle': [], 'short-title': [], 'issued': {'date-parts': [[2023, 6, 30]]}, 'references-count': 0, 'journal-issue': {'issue': '1', 'published-online': {'date-parts': [[2023, 6, 30]]}}, 'URL': 'http://dx.doi.org/10.47701/djp.v3i1.2904', 'relation': {}, 'ISSN': ['2829-811X', '2830-7054'], 'container-title-short': 'DJP', 'published': {'date-parts': [[2023, 6, 30]]}}

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