Predicting anti-COVID-19 potential: in silico analysis of Mauritine compound from Ziziphus- spina christi as a promising papain-like protease (PLpro) inhibitor

Fakih, Taufik Muhammad and Darusman, Fitrianti and Apriliani, Riry and Prahayati, Syifa and Ramadhan, Dwi Syah Fitra and Hidayat, Aulia Fikri and Rizkita, Aden Dhana and Yuniarta, Tegar Achsendo (2024) Predicting anti-COVID-19 potential: in silico analysis of Mauritine compound from Ziziphus- spina christi as a promising papain-like protease (PLpro) inhibitor. Journal of Biomolecular Structure and Dynamics.

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Abstract

The COVID-19 pandemic caused by the SARS-CoV-2 virus, recognized by the World Health Organization (WHO), has led to 164,523,894 confirmed cases and 3,412,032 deaths globally as of May 20, 2021. SARS-CoV-2 encodes crucial proteases for its replication cycle, including the papain-like pro- tease (PLpro), presenting a potential target for developing COVID-19 treatments. Mauritine, a cyclopep- tide alkaloid found in the Ziziphus-spina christi plant, exhibits antiviral properties and was investigated for its affinity and toxicity towards PLpro using molecular docking through MGLTools 1.5.6 with Autodock Tools 4.2. Preceding this, toxicity and ADME prediction were performed via Toxtree 3.1.0 software and SwissADME servers. Results from molecular docking revealed free binding energy values of −8.58; −7.73; −8.36; −6.07; −6.67; −7.83; −7.67; −7.40; and −6.87 Kcal/mol for Mauritine-A, Mauritine-B, Mauritine-C, Mauritine-D, Mauritine-F, Mauritine-H, Mauritine-J, Mauritine-L, and Mauritine- M, respectively. Correspondingly, inhibition constants were 0.51724; 2.14; 0.7398; 35.43; 12.95; 1.83; 2.38; 3.80; and 9.17 mM, respectively. Interactions observed included hydrogen bonds, hydrophobic interactions, and electrostatic interactions between the Mauritine compounds and the receptor. Mauritine-A and Mauritine-C emerged as a promising anti-COVID-19 candidate due to its superior affinity compared to other derivatives, as indicated by research findings. Interestingly, Mauritine-A and Mauritine-C exhibits notable stability as depicted by the RMSD and RMSF graphs, along with a consid- erable MM-PBSA binding free energy value of −162.431 and −137.500 kJ/mol, respectively.

Item Type:	Article
Uncontrolled Keywords:	In silico approach; papain- like protease (PLpro); COVID-19; Mauritine; Ziziphus-spina christi
Subjects:	Q Science > QD Chemistry
Divisions:	Faculty of Pharmacy > Department of Pharmacy
Depositing User:	TEGAR ACHSENDO YUNIARTA
Date Deposited:	27 Mar 2024 08:04
Last Modified:	27 Mar 2024 08:04
URI:	http://repository.ubaya.ac.id/id/eprint/46126

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