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Harisna AH, Nurdiansyah R, Syaifie PH, Nugroho DW, Saputro KE, Firdayani, Prakoso CD, Rochman NT, Maulana NN, Noviyanto A, Mardliyati E. In silico investigation of potential inhibitors to main protease and spike protein of SARS-CoV-2 in propolis. Biochem Biophys Rep 2021; 26:100969. [PMID: 33681482 PMCID: PMC7914023 DOI: 10.1016/j.bbrep.2021.100969] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 12/16/2022] Open
Abstract
Docking analysis of propolis's natural compound was successfully performed against SARS-CoV-2 main protease (Mpro) and spike protein subunit 2 (S2). Initially, the propolis's protein was screened using chromatography analysis and successfully identified 22 compounds in the propolis. Four compounds were further investigated, i.e., neoblavaisoflavone, methylophiopogonone A, 3'-Methoxydaidzin, and genistin. The binding affinity of 3'-Methoxydaidzin was -7.7 kcal/mol, which is similar to nelfinavir (control), while the others were -7.6 kcal/mol. However, we found the key residue of Glu A:166 in the methylophiopogonone A and genistin, even though the predicted binding energy slightly higher than nelfinavir. In contrast, the predicted binding affinity of neoblavaisoflavone, methylophiopogonone A, 3'-Methoxydaidzin, and genistin against S2 were -8.1, -8.2, -8.3, and -8.3 kcal/mol, respectively, which is far below of the control (pravastatin, -7.3 kcal/mol). Instead of conventional hydrogen bonding, the π bonding influenced the binding affinity against S2. The results reveal that this is the first report about methylophiopogonone A, 3'-Methoxydaidzin, and genistin as candidates for anti-viral agents. Those compounds can then be further explored and used as a parent backbone molecule to develop a new supplementation for preventing SARS-CoV-2 infections during COVID-19 outbreaks.
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Affiliation(s)
- Azza Hanif Harisna
- Nano Center Indonesia, Jl. PUSPIPTEK, South Tangerang, Banten, 15314, Indonesia
| | - Rizky Nurdiansyah
- Department of Bioinformatics, Indonesia International Institute for Life Sciences, Jakarta, 13210, Indonesia
| | - Putri Hawa Syaifie
- Nano Center Indonesia, Jl. PUSPIPTEK, South Tangerang, Banten, 15314, Indonesia
| | - Dwi Wahyu Nugroho
- Nano Center Indonesia, Jl. PUSPIPTEK, South Tangerang, Banten, 15314, Indonesia
| | | | - Firdayani
- Center for Pharmaceutical and Medical Technology, Agency for the Assessment and Application of Technology, PUSPIPTEK, South Tangerang, Banten, 15314, Indonesia
| | - Chandra Dwi Prakoso
- Nano Center Indonesia, Jl. PUSPIPTEK, South Tangerang, Banten, 15314, Indonesia
| | - Nurul Taufiqu Rochman
- Research Center for Metallurgy and Materials, Indonesian Institute of Sciences, PUSPIPTEK, South Tangerang, Banten, 15314, Indonesia
| | | | - Alfian Noviyanto
- Nano Center Indonesia, Jl. PUSPIPTEK, South Tangerang, Banten, 15314, Indonesia
- Department of Mechanical Engineering, Mercu Buana University, Jl. Meruya Selatan, Kebun Jeruk, Jakarta, 11650, Indonesia
| | - Etik Mardliyati
- Nano Center Indonesia, Jl. PUSPIPTEK, South Tangerang, Banten, 15314, Indonesia
- Center for Pharmaceutical and Medical Technology, Agency for the Assessment and Application of Technology, PUSPIPTEK, South Tangerang, Banten, 15314, Indonesia
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Pei L, Li DZ, Zhang LJ. Theoretical insights into the hydrogen bonding interaction in the complexation of epinephrine with uracil. J Mol Model 2019; 25:252. [PMID: 31353431 DOI: 10.1007/s00894-019-4123-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/04/2019] [Indexed: 11/28/2022]
Abstract
The present study is aimed at probing the hydrogen bonding interaction between epinephrine and uracil by means of density functional theory calculations concerning their complexation's geometries, interaction energies, and vibrational frequencies. Geometry optimization was carried out giving 19 stable geometries of epinephrine-uracil complex with interaction energies in a range of - 21.51 to - 62.37 kJ mol-1 using the basis set superposition error (BSSE) correction. The analysis of structure and vibration shows that the hydrogen bonding elongates the length of corresponding bond O(N)-H and decreases the symmetric stretching vibrational frequency, which indicates red-shifted H-bonding interactions in all the geometries. Additionally, the analysis with theories of natural bond orbital (NBO), atoms in molecules (AIM), and the reduced density gradient (RDG) of hydrogen bonding properties and characteristics of the 19 geometries suggests that the hydrogen bonding in all the optimized structures of epinephrine-uracil complex is kind of a closed-shell interaction and mainly electrostatic dominant.
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Affiliation(s)
- Ling Pei
- Department of Chemical Engineering and Safety, Binzhou University, Binzhou, 256603, Shandong, People's Republic of China.
| | - Da-Zhi Li
- Department of Chemical Engineering and Safety, Binzhou University, Binzhou, 256603, Shandong, People's Republic of China
| | - Li-Juan Zhang
- Department of Chemical Engineering and Safety, Binzhou University, Binzhou, 256603, Shandong, People's Republic of China
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