Prediction of SARS-CoV-2 main protease inhibitors in medicinal plant-derived compounds by molecular docking approach

Farabi, Sayma; Saha, Niladri; Hasanuzzaman, Md.; Khan, Nazmul Alam; Haque, M. S.

doi:10.5455/jabet.2020.d159

Cited by 3 publications

(2 citation statements)

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“…In comparison with cluster 2 (Fig. 10B ), just one interaction is preserved: Tyr126, and new ones are formed with residues near to Tyr126 (which seems to be crucial in the binding process of amentoflavone): Val114, Gln128, Cys128, Ser139, and Leu141, residues considered important for ligand recognition [ 65 ], and important for binding of other molecules with inhibitory activity, such as paritaprevir, lopinavir, and epigallocatechin-3-gallate [ 66 ]. In contrast, baicalein in both clusters (Fig.…”

Section: Resultsmentioning

confidence: 99%

In silico evaluation of flavonoids as potential inhibitors of SARS-CoV-2 main nonstructural proteins (Nsps)—amentoflavone as a multitarget candidate

et al. 2022

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Despite the development of vaccines against COVID-19 disease and the multiple efforts to find efficient drugs as treatment for this virus, there are too many social, political, economic, and health inconveniences to incorporate a fully accessible plan of prevention and therapy against SARS-CoV-2. In this sense, it is necessary to find nutraceutical/pharmaceutical drugs as possible COVID-19 preventives/treatments. Based on their beneficial effects, flavonoids are one of the most promising compounds. Therefore, using virtual screening, 478 flavonoids obtained from the KEGG database were evaluated against non-structural proteins Nsp1, Nsp3, Nsp5, Nsp12, and Nsp15, which are essential for the virus-host cell infection, searching for possible multitarget flavonoids. Amentoflavone, a biflavonoid found mainly in Ginkgo biloba , Lobelia chinensis , and Byrsonima intermedia , can interact and bind with the five proteins, suggesting its potential as a multitarget inhibitor. Molecular docking calculations and structural analysis (RMSD, number of H bonds, and clustering) performed from molecular dynamics simulations of the amentoflavone-protein complex support this potential. The results shown here are theoretical evidence of the probable multitarget inhibition of non-structural proteins of SARS-CoV-2 by amentoflavone, which has wide availability, low cost, no side effects, and long history of use. These results are solid evidence for future in vitro and in vivo experiments aiming to validate amentoflavone as an inhibitor of the Nsp1, 3, 5, 12, and 15 of SARS-CoV-2. Graphical Abstract Supplementary Information The online version contains supplementary material available at 10.1007/s00894-022-05391-6.

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Section: Resultsmentioning

confidence: 99%

In silico evaluation of flavonoids as potential inhibitors of SARS-CoV-2 main nonstructural proteins (Nsps)—amentoflavone as a multitarget candidate

et al. 2022

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“…Daun sirih hijau (Piper betle L.) memiliki berbagai efek dermatologis seperti anti-bakteri, anti-jamur, antivirus, antikanker, radikal bebas pemulungan, luka bakar dan penyembuhan luka, penerangan kulit dan pelindung kulit, anti penuaan (Soni, Sharma and Malik, 2020). Senyawa piperitol, euganol, dan chavibetol ialah salah satu dari senyawa metabolit sekunder yang ada dalam daun sirih hijau yang dimana menurut penelitian yang dilakukan oleh Farabi et al, (2020) membuktikan bahwa senyawa piperitol, euganol, dan chavibetol dapat menjadi senyawa yang berfungsi sebagai inhibitor dari Main Protease (Mpro). Cara yang dapat digunakan untuk mengidentifikasi potensial aktivitas antivirus pada senyawa metabolit sekunder dalam daun sirih hijau yaitu pemanfaatan metode penambatan molekuler atau biasa disebut Molecular docking.…”

Section: Pendahuluanunclassified

STUDI IN SILICO SENYAWAhMETABOLIThSEKUNDER DAUN SIRIH HIJAU (Piper betle L) SEBAGAI INHIBITOR ENZIM MAINhPROTEASE (Mpro) PADA SARS-CoV-2

Naja¹,

Andika²,

Mi’rajunnisa³

2022

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Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) adalah virus penyebab COVID-19. Salah satu target potensial untuk pengobatan SARS-CoV-2 ialah Main protease (Mpro). Daun sirih hijau (Piper betle L.) adalah tanaman yang terbukti secara ilmiah mempunyai efek sebagai antibakteri dan antivirus. Bagian dari tanaman sirih (Piper betle L.) seperti akar, biji, dan daun bermanfaat untuk pengobatan, tetapi yang paling umum digunakan adalah bagian daun. Tujuan penelitian ini ialah untuk mengetahui potensi dan interaksi senyawa metabolit sekunder daun sirih hijau sebagai antivirus penghambat Mpro pada SARS-CoV-2 dengan protein ID: 5R84 menggunakan uji penambatan molekul. Pengujian ini meliputi penambatan molekul, pengujian Lipinski dan prediksi ADMET. Metode yang digunakan berbasis oriented docking dengan kompleks protein ligand dibuat semi fleksible docking menggunakan software Autodock4. Hasil secara keseluruhan diperoleh dua puluh lima senyawa uji dari metabolit sekunder daun sirih hijau berpotensi sebagai penghambat Mpro dan senyawa uji yang mempunyai nilai energi binding (energi ikat bebas (?G)) terbaik yang berasal dari Piperine sebesar - 8,27..kcal/mol, disusul oleh Piperlonguminine sebesar..-8,07..kcal/mol serta Kaempferol - 7,95..kcal/mol. Piperine sendiri diprediksi memiliki absorbsi yang bagus, distribusi pada VDss tinggi, tetapi bukan subtrat dan inhibitor dari CYP 450, memiliki total klerens yang tinggi, berpotensi menimbulkan iritasi pada kulit dan toksik pada uji protozoa T.pyriformis. Residu asam amino HIS 41, MET 49, PHE 140, HIS 163, MET 165, GLU 166, ASN 142, ARG 188, dan GLN 189 banyak berkontibusi terbentuk ikatan hydrogen.

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Antiviral Significance of Isoquercetin (Quercetin-3-O-Glucoside) With Special Reference to its Anti-Coronaviral Potential

Agrawal,

Blunden,

Jacob

2024

Natural Product Communications

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Isoquercetin, a naturally occurring dietary flavonoid glycoside, has shown many promising biological activities, such as antioxidant, anti-inflammatory, and anticancer. It also exhibits broad-spectrum antiviral activity, significantly reducing cell infection by influenza, Zika, Ebola, and dengue viruses, among others. Its beneficial effect for mitigating the disease of COVID-19 can be explained due to its inhibitory effects on several stages of the viral life cycle, from entry to replication and virus infectivity, and thus isoquercetin can be a promising anticoronaviral flavonoid to manage severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection and warrants further investigation into its potential use in clinical settings.

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Prediction of SARS-CoV-2 main protease inhibitors in medicinal plant-derived compounds by molecular docking approach

Cited by 3 publications

References 0 publications

In silico evaluation of flavonoids as potential inhibitors of SARS-CoV-2 main nonstructural proteins (Nsps)—amentoflavone as a multitarget candidate

In silico evaluation of flavonoids as potential inhibitors of SARS-CoV-2 main nonstructural proteins (Nsps)—amentoflavone as a multitarget candidate

STUDI IN SILICO SENYAWAhMETABOLIThSEKUNDER DAUN SIRIH HIJAU (Piper betle L) SEBAGAI INHIBITOR ENZIM MAINhPROTEASE (Mpro) PADA SARS-CoV-2

Antiviral Significance of Isoquercetin (Quercetin-3-O-Glucoside) With Special Reference to its Anti-Coronaviral Potential

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