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. 2021 Apr 12;26(8):2210.
doi: 10.3390/molecules26082210.

Efficacy of Phytochemicals Derived from Avicennia officinalis for the Management of COVID-19: A Combined In Silico and Biochemical Study

Shafi Mahmud  1 , Gobindo Kumar Paul  1 , Mirola Afroze  2 , Shirmin Islam  1 , Swagota Briti Ray Gupt  3 , Mamudul Hasan Razu  2 , Suvro Biswas  3 , Shahriar Zaman  1 , Md Salah Uddin  1 , Mala Khan  2 , Nunzio Antonio Cacciola  4 , Talha Bin Emran  5 , Md Abu Saleh  1 , Raffaele Capasso  6 , Jesus Simal-Gandara  7
Affiliations

Efficacy of Phytochemicals Derived from Avicennia officinalis for the Management of COVID-19: A Combined In Silico and Biochemical Study

Shafi Mahmud et al. Molecules. .

Abstract

The recent coronavirus disease 2019 (COVID-19) pandemic is a global threat for healthcare management and the economic system, and effective treatments against the pathogenic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus responsible for this disease have not yet progressed beyond the developmental phases. As drug refinement and vaccine progression require enormously broad investments of time, alternative strategies are urgently needed. In this study, we examined phytochemicals extracted from Avicennia officinalis and evaluated their potential effects against the main protease of SARS-CoV-2. The antioxidant activities of A. officinalis leaf and fruit extracts at 150 µg/mL were 95.97% and 92.48%, respectively. Furthermore, both extracts displayed low cytotoxicity levels against Artemia salina. The gas chromatography-mass spectroscopy analysis confirmed the identifies of 75 phytochemicals from both extracts, and four potent compounds, triacontane, hexacosane, methyl linoleate, and methyl palminoleate, had binding free energy values of -6.75, -6.7, -6.3, and -6.3 Kcal/mol, respectively, in complexes with the SARS-CoV-2 main protease. The active residues Cys145, Met165, Glu166, Gln189, and Arg188 in the main protease formed non-bonded interactions with the screened compounds. The root-mean-square difference (RMSD), root-mean-square fluctuations (RMSF), radius of gyration (Rg), solvent-accessible surface area (SASA), and hydrogen bond data from a molecular dynamics simulation study confirmed the docked complexes' binding rigidity in the atomistic simulated environment. However, this study's findings require in vitro and in vivo validation to ensure the possible inhibitory effects and pharmacological efficacy of the identified compounds.

Keywords: Avicennia officinalis; GC-MS; SARS-CoV-2; antioxidant; main protease; molecular dynamics simulation.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Antioxidant and cytotoxic activity of A. officinalis leaves and fruits extract. (a) DPPH scavenging activity of both leaves and fruits, and (b) mortality percentage of brine shrimp for cytotoxicity test where different significance letter indicates significant differences between mean ± SD of replication (n = 3) at a p < 0.05 significance level.
Figure 2
Figure 2
Total ionic chromatogram of A. officinalis methanolic extract of (a) leaves and (b) fruits by GC-MS.
Figure 3
Figure 3
Binding interaction of the hydrocinnamic acid and main protease enzyme, (a) 2D representation of binding interaction, (b) 3D representation, and (c) surface view.
Figure 4
Figure 4
The non-bonded interaction of phenethyl alcohol and main protease from SARS-CoV-2. (a) 2D interaction pattern of main protease from SARS-CoV-2 and hexacosane, (b) 3D binding interaction, and (c) surface view of the docked complex.
Figure 5
Figure 5
The interaction of dihydroartemisinin and main protease enzyme, (a) 2D interaction obtained from Discovery Studio, (b) 3D view, and (c) surface view.
Figure 6
Figure 6
The molecular dynamics simulation. (a) Root mean square deviation of the control and four docked complexes, (b) solvent accessible surface area, (c) radius of gyration, (d) hydrogen bond of the docked and control complexes, and (e) root mean square fluctuation.
Figure 7
Figure 7
The superimposition between pre- and post-MD structure where lesser degrees of deviation were observed. The figures were prepared in the Pymol and Discovery Studio software (a–c).
Figure 8
Figure 8
The simulation snapshots of hydrocinnamic acid and main protease complex acquired from the trajectories where rigid profiles of the ligand-protein complex were observed in the same binding pockets. The snapshots were (a–e) taken after 0, 25, 50, 75, and 100 ns intervals, respectively.
Figure 9
Figure 9
The dynamics snapshots (a–e) of phenethyl alcohol and main protease complex after 0, 25, 50, 75, and 100 ns, respectively.
Figure 10
Figure 10
The simulation snapshots of dihydroartemisinin and main protease (a–e) after 0, 25, 50, 75, and 100 ns, respectively.
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