The objective of the present study is to identify a suitable ligand to interact with the different target proteins of the novel corona virus COVID-19. The study was carried out with virtual screening of the molecules using Schrodinger Maestro v11.9.011. The viral proteins targeted to have therapeutic value are 3CLpro (PDB ID: 6LU7), PLpro (PDB ID: 3E9S) & SPIKE (PDB ID: 6M0J) of nCOVID-19. These proteins have definite function like protease activity, which helps the virus RNA transcription, translation, protein synthesis, and replication. SPIKE protein help in fusion and entry of virus into the host cell. Targeting these proteins were mediated through the binding pockets involving amino acids 3CLpro (Cys 145, HID 41, Gly 143, Asn 142, HID 163, Glu 166,Thr 190, Arg 188, Ser 144, Gln 189) ; PLpro ( Gly 164, Gln 270, Tyr 274, Asp 303, Gly 267, Asp 165, Glu 168, Arg 167, Ala 247, Tyr 269, Pro 248, Pro 249) ; SPIKE ( Tyr 449, Gln 498, Thr 500, Val 445, Lys 417, Asn 501, Gly 446, Gly 502,Tyr 505, Leu 455, Gln 493,Gln 506, Lys 444, Phe 486, Ser 477, Tyr 473,Arg 403,Gly 496,Tyr 453). Our study revealed that chemical molecules having flavonoid nucleus, namely saponarin, mangiferin, & hesperidin, had better binding scores with 3CLpro protein (PDB ID: 6LU7). Similarly, for the target SPIKE protein (PDB ID: 6M0J), chemical molecules like diphyllin & tuberculatin showed better G-scores than the standard drugs and these molecules are from the plants Mukia maderaspatana, Justicia adhatoda, and Mangifera indica. While for the target PLpro (PDB ID: 3E9S), chemical molecules like mangiferin& aspartame showed good G-scores.
FNQ3 naptho-quinone derivatives have shown antiviral property against Japanese encephalitis virus through inhibition of viral replication by blocking viral RNA and transcriptional activities . One of our hit compound diphyllin has also been reported to have antiviral property. Glycosylated diphyllin prevented zika virus during fusion with host cell, preventing the release of viral RNA into the target cells. This effect was attributed to acidification of the cytoplasmic content by glycosylated diphyllin. So, these results support that the napthofuran molecules like diphyllin may exhibit antiviral property by blocking structural protein (SPIKE protein) .
Quercetin, a flavone derivative, has shown antiviral property against enterovirus 71(EV71). Quercetin exhibited antiviral property by preventing the early post attachment, inhibition of protease enzymes, RNA polymerase. Quercetin also has shown to bind with the substrate binding pocket of enterovirus 3Cpro .However, in the present study we did not observe any interaction of quercetin with the targets. It might be protein specific. Another flavone mangiferin has shown antiviral property in clinical strains of HIV1. It was also found to be effective against resistant HIV1 strain through inhibition of peptide protease. It also possesses HIV protease enzyme inhibition in HIV strain . The significant role of flavonoids for antiviral property has been reviewed recently by . So, these observations also support the present finding that flavonoids can block the protease enzyme activity of COVID-19.
Interestingly, the phytoconstituents from neem, tulsi & andrographis (Nila-Vembu) did not show any binding scores with these protein targets. Likewise, other chemical molecules studied include curcumin, liquitrigenin, iso-liquitrigenin, glabridin, piperine, glycyrrhizic acid, vasicine & vascinone and these showed no or low binding scores. The clinically used protease inhibitors, anti-viral drugs, ivermectin & chloroquine were also docked with these proteins; the results show lower G-scores comparatively with saponarin, mangiferin, hesperidin, diphyllin, and tuberculatin. Hydroxychloroquine and remedesivir showed better G-scores for 3CLpro & PLpro, but these two drugs showed lesser G-scores for SPIKE protein in comparison to diphyllin & tuberculatin. 6M0J can also be targeted, being it a SPIKE protein. But, as the binding site is quite large it is difficult to block it with small molecules and it would be better if it can be blocked with larger molecules with better g-scores and binding affinity, However, this target can be tried for prophylactic purpose.
Formulations of traditional system of medicine contain multiple herbs and generally natural products act on either additive or synergistic mechanism to elicit the poly-pharmacological action . The current work was designed based on the hypothesis on antiviral activities of these compounds from selected herbs. However, compounds like curcumin (from Curcurma longa) and azadirachtin (from Azadirachta indica) are well-documented for their immuno-modulatory responses, including its effect on lymphoid cell populations, antigen presentation, humoral and cell-mediated immunity, and cytokine production [24, 25]. Hence, studying the effect of these compounds on immune modulation targets is also needed to elucidate the complete potential of these compounds.
It can be concluded, that the molecules having flavone scaffolds show better binding affinity with protease proteins 3CLpro and PLpro. SPIKE protein scaffold is different and showed better binding affinity with molecules having napthofuran ring. The traditionally used plant phytoconstituents did not exhibit good binding affinity; however, we believe that a combination of these herbs might induce human immune system against microbial infection.