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Article ; Online: The Potential of Clerodendrum paniculatum Leaves Fraction as a 3-Chymotrypsin-Like (3CL) Protease Inhibitor of SARS-CoV-2

Muhammad Arba / Arfan Arfan / Yamin Yamin / Muhammad Sulaiman Zubair

Indonesian Journal of Chemistry, Vol 23, Iss 3, Pp 770-

2023 Volume 781

Abstract: We described the biological activity of the Clerodendrum paniculatum leaf fraction against the SARS-CoV-2 3-Chymotrypsin-like 3CL protease at the molecular level. This study applied LC-MS/MS to identify bioactive compounds from fractions, computational ... ...

Abstract	We described the biological activity of the Clerodendrum paniculatum leaf fraction against the SARS-CoV-2 3-Chymotrypsin-like 3CL protease at the molecular level. This study applied LC-MS/MS to identify bioactive compounds from fractions, computational studies, and fluorescence resonance energy transfer (FRET) assays to ascertain their inhibitory activity. LC-MS/MS analysis of the three samples revealed that sample 1 contained 18 compound peaks. In samples 2 and 3, there were 23 and 25 compounds with different molecular weights, respectively. Docking's study identified that the alkaloids (komarovicine and roemerine) have lower binding energies than other metabolites and standard compounds, with values of -33.47 and -32.63 kJ/mol, respectively. Roemerine demonstrated excellent stability based on dynamic simulation results and confirmed its affinity for 3CL protease predicted by the MM-PBSA approach of -89.44 kJ/mol. The FRET method for testing 3CL protease activity revealed that sample 2 had an enzyme inhibitory activity of 94.3%, which was close to that of GC376 (98.19%). Meanwhile, samples 1 and 3 yielded satisfactory inhibition activity by 89.64% and 85.24%, respectively. The antiviral activity of C. paniculatum leaves was discovered for the first time by inhibiting the 3CL protease SARS-CoV-2, providing an excellent opportunity for its development as an anti-SARS-CoV-2.
Keywords	clerodendrum paniculatum ; covid-19 ; molecular dynamics simulation ; sars-cov-2 ; 3-chymotrypsin-like protease ; Chemistry ; QD1-999
Subject code	540 ; 500
Language	English
Publishing date	2023-05-01T00:00:00Z
Publisher	Department of Chemistry, Universitas Gadjah Mada
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: The Search for Cyclooxygenase-2 (COX-2) Inhibitors for the Treatment of Inflammation Disease: An in-silico Study.

Ruslin, Ruslin / Yamin, Yamin / Kasmawati, Henny / Mangrura, Samuel / Kadidae, Laode / Alroem, Armid / Arba, Muhammad

Journal of multidisciplinary healthcare

2022 Volume 15, Page(s) 783–791

Abstract: Purpose: Cyclooxygenase (COX-2) has been validated as a molecular target for treating inflammatory diseases. The present work was performed to identify potential COX-2 inhibitors by employing pharmacophore modeling.: Methods: The pharmacophore ... ...

Abstract	Purpose: Cyclooxygenase (COX-2) has been validated as a molecular target for treating inflammatory diseases. The present work was performed to identify potential COX-2 inhibitors by employing pharmacophore modeling. Methods: The pharmacophore features consisted of seven features, ie, three hydrophobic, one negative ion, and three hydrogen bond acceptors, which were developed based on the structure of COX-2 inhibitor, (R)-naproxen. Results: The pharmacophore model was validated with a Goodness of Hit (GH score) of 0.754 and the values of AUC100% 0.51. Screening against the ZINC database retrieved 1675 hits, while the molecular docking procedure identified four best hit molecules in term of binding orientation and binding energies, ie, Lig_1805/ZINC103584272 (E = -11.03 kcal/mol), Lig_553/ZINC408573132 (E = -10.92 kcal/mol), Lig_680/ZINC103584263 (E = -10.90 kcal/mol), and Lig_2006/ZINC19324645 (E = -10.62 kcal/mol). Conclusion: The interactions of the four hits occurred in the binding site as (R)-naproxen did, and interestingly, their binding affinities were stronger than (R)-naproxen, implying their potential as COX-2 inhibitors.
Language	English
Publishing date	2022-04-12
Publishing country	New Zealand
Document type	Journal Article
ZDB-ID	2453343-9
ISSN	1178-2390
ISSN	1178-2390
DOI	10.2147/JMDH.S359429
Database	MEDical Literature Analysis and Retrieval System OnLINE

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