In this work, the potential use of medicinal plants and more than 16 500 of their constituents was investigated within two suggested therapeutic strategies in the ﬁght against SARS-CoV-2 including prevention of SARS-CoV-2 RNA synthesis and replication, through targeting vital proteins and enzymes as well as modulation of the host's immunity through production of virulence factors. Molecular docking studies on the viral enzymes 3Clpro, PLpro and RdRp suggested rocymosin B, verbascoside, rutin, caftaric acid, luteolin 7-rutinoside, fenugreekine and cyanidin 3-(600 -malonylglucoside) as promising molecules for further drug development. Meanwhile, the medicinal plants Glycyrrhiza glabra, Hibiscus sabdariﬀa, Cichorium intybus, Chrysanthemum coronarium, Nigella sativa, Anastatica hierochuntica, Euphorbia species, Psidium guajava and Epilobium hirsutum were enriched in compounds with the multi-targets PTGS2, IL2, IL1b, VCAM1 and TNF such as quercetin, ursolic acid, kaempferol, isorhamnetin, luteolin, glycerrhizin and apigenin. Enriched pathways of the molecular targets included cytokine–cytokine receptor interaction, TNF signaling pathway, NOD-like receptor signaling pathway, Toll-like receptor signaling pathway, NF- kappa B signaling pathway and JAK-STAT3 signaling pathway which are all closely related to inﬂammatory, innate and adaptive immune responses. The present study identiﬁed natural compounds targeting SARS-CoV-2 for further in vitro and in vivo studies and emphasizes the potential role of medicinal plants in the mitigation of SARS-CoV-2.
Results and discussion
Identifying potential medicinal plants constituents against viral targets
A medicinal plant/natural products library comprised of 10 823 phytoconstituents was screened in silico via molecular docking against three proven protein targets in SARS-CoV-2 striving for potent anti-COVID-19 natural compounds. 3-Chymotrypsin-like protease (3CLpro), papain-like protease (PLpro) and RNA-dependent RNA polymerase (RdRp) are elemental for viral replication and therefore, impending targets for anti-coronaviruses screening. Lopinavir, nelfinavir and remdesivir are commonly used antiviral drugs acting on viral proteins that are presently available in the market and undergoing clinical trials for repurposing in treatment of SARS-CoV-2 infection. These drugs were also analyzed against the three selected key protein targets. Meanwhile, other drugs like hydroxychloroquine and dexamathasone don't act on the viral proteins but rather on the immune system reaction caused by the viral infection so they were not involved in the docking study.
Molecular docking against 3-chymotrypsin-like protease (3CLpro)
The main protease (Mp) or 3-chymotrypsin-like protease (3CLpro) or Nsp5 has a critical role in cleavage of the polyprotein at eleven distinct sites to generate various Nsps that are essential for viral replication.30 The maturation of Nsps, which is crucial in the virus life cycle is directly mediated via 3CLpro. The detailed inspection on catalytic mechanism of 3CLpro makes it an attractive target for anti-COVID-19 drug development.
Virtual screening of our database using Glide Xp protocol against 3CLpro crystalline structure (5R7Y) deposited in March in complex with co-crystallized ligand disclosed that rutin from Anastatica hierochuntica, Glycyrrhiza glabra and Allium myrianthum followed by rocymosin b from Glycyrrhiza glabra and subsequently verbascoside from Cichorium intybus, Olea europaea and Marrubium vulgare were the top three scoring compounds (Table 1) which endorsed us to investigate their binding modes. The compounds bound to the Cys–His catalytic dyad (Cys-145 and His-41)32 along with the other residues, with notable docking scores (Table 1). It was discerned that the active site of the main protease in which the three top scoring compounds bind enclosed hydrophobic residues such as Met49, Leu141, Cys145, Met165, Leu167 and Pro168 in addition to amino acids polar contributions such as Thr25, Thr26, His41, Asn142, Ser144, His163 and Hie164. Hydrogen bonding with Leu141 and Glu166 also stabilized their conformations
Molecular docking against papain-like protease (PLpro)
PLpro is the proteolytic enzyme that cleaves the N-terminus of viral replicase poly-protein at three sites to release mature Nsp1, 2 and 3. This process is fundamental for correcting virus replication.18 Moreover, PLpro also has a critical role in antagonizing the host's innate immunity.33 As a result of its imperative function in the process of coronavirus replication and host infection, PLpro has emerged as a prevalent target for coronavirus inhibitors. However, no PLpro inhibitor has reached the FDA marketing approval till this moment.
After conducting the extra precision Glide docking protocol on our database and the three chosen antiviral repurposed drugs, the interactions between the three top scoring constituents and PLpro crystalline structure (PDB ID: 6W9C) released on first of April 2020, were analyzed (Fig. 2 and S2†). It was observed that the specific pocket in which the top scoring compounds bind contained non-polar amino acids like Leu162, Val202, Met206, Met208 and Ile222 in addition to amino acids polar contributions such as Ser170 and Asn156.
Verbascoside from Cichorium intybus, Olea europaea and Marrubium vulgare which achieved the highest XP docking score (Table 1) was furthermore bound to PLpro active site through hydrogen bonding with Glu167, Tyr171, Met208, Tyr268, Tyr273 and Thr301 and additionally through charged negative interactions with Glh203 and Asp164 (Fig. 2A).It was also discerned that verbascoside had bound to the two selected proteases PLpro and 3CLpro with high XP docking scores. These dual targets inhibition advocates verbascoside as a potential druggable anti-COVID-19.
The second active top scoring compound against PLpro; luteolin-7-rutinoside from Cynara scolymus (Table1) interacted with numerous hydrogen bonds with the amino acids Asn156, Gly163, Ser170, Tyr268, Tyr273 and Thr301 as well as π–π stacking interaction with Arg166 and negatively charged interactions with Glh161, Asp164, Glh203 and Asp302 (Fig. 2B).
Analysis of binding modes of caftaric acid; the third top scoring compound, with PLpro revealed that besides the polar and non-polar amino acids contributions in the active site, caftaric acid exhibited four H-bonding with Leu162, Tyr207, Met208 and Lys232
Many of the medicinal plants and their constituents have a potential for use in the mitigation of the new SARS-CoV-2 infection. Herein, a database comprised of more than 16 500 compounds was screened against the three viral targets 3CLpro, PLpro and RdRp, and several constituents identified may inhibit SARS-CoV-2 activity through inhibition of virus replication. A network pharmacology analysis was performed for all the plants constituents and revealed that several compounds possessed multi-targets and enriched pathways of the molecular targets including cytokine–cytokine receptor interaction, TNF signaling pathway, Toll-like receptor signaling pathway, NF-kappa B signaling pathway, and JAK-STAT3 signaling pathway. These results suggest a potential role of medicinal plants in the management of the current SARS-CoV-2 infection. A special emphasis is paid to the plant Glycyrrhiza glabra (liquorice) which has a long history of use in treatment of several viral infections. In fact, randomized controlled trials confirmed that the Glycyrrhiza glabra demonstrated a reduction of mortality and viral activity in SARS-CoV-2 related coronavirus.Meanwhile, the plants Hibiscus sabdariffa and Cichorium intybus are rich sources of caffeic acid derivatives which have been widely investigated concerning their antiviral potential
The performed network pharmacology analysis revealed the synergistic nature of the compounds within each medicinal plant as shown in Fig. 6 and 7. Combination of the most enriched plants in the created network i.e. Glycyrrhiza glabra (liquorice), Hibiscus sabdariffa, Cichorium intybus, could be chosen for mitigation of SARS-CoV-2.
Further molecular dynamic simulation studies, in vitro and in vivo analyses are required to confirm the results of our study, however, the insights provided by the present study may substantiate valuable exploration and development of anti-SARS-CoV-2 therapeutic agents from natural origin.
Reference & Source information: https://pubs.rsc.org/
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