Molecular Docking, ADME Analysis, and Estimation of MM/GBSA Binding-Free Energies of Coumarin Derivatives as Potential Inhibitors of SARS CoV-2 Receptors

Coronavirus Disease (COVID-19) is recently declared pandemic (WHO) caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Currently, there is no speci�c drug for the therapy of COVID-19. In the present study, in silico study have been done to �nd out possible inhibitors of SARS CoV-2. Coumarin derivatives with 2755 compounds were virtually screen against methyltransferase-stimulatory factor complex of NSP16 and NSP10, NSP15 Endoribonuclease, ADP ribose phosphatase (ADRP)of NSP3 and protease enzymes of SARS CoV-2. Docked top �ve compounds showed good docking scores and free energy of binding with the respective receptors. ADME/T analysis of docked compound shows the docked ligands are showing drug-likeness properties.

Currently, we do not have any speci c drugs for the treatment of COVID-2019 patients.Some potential combinations of protease inhibitors like lopinavir/ritonavir commonly used in the treatment of HIV and other antiviral inhibitors like remdesivir, tenofovir disoproxil are using for the treatment of COVID-2019 patient [7].
The outputs of the present study will provide information to other researchers with opportunities to identify the accurate drug to treating COVID-19.

Result And Discussion
In the present study, methyltransferase, endoribonuclease, ADP ribose phosphatase, and protease were evaluated through molecular docking studies with coumarin derivatives, which is an in silico analysis, using Glide module of Schrodinger.

Virtual Screening and Molecular Docking of Coumarin Derivatives
Coumarin derivatives (2755 compound) were docked at the active site of methyltransferase (MTase), endoribonuclease(endoU), ADP ribose phosphatase, and protease and top 5 compounds of each have docking score from -9.00 to -7.97, -8.42 to -6.80, -8.63 to -7.48 and -7.30 to -6.01 kcal/mol respectively (Table 1).Closer view of the interaction of ligands and each SAR CoV-2 proteins/receptors discloses that the oxygen and nitrogen-containing compounds of coumarin derivatives are interacting with active site's amino acids of receptors, H atom of hydroxy groups make coumarin derivatives more suitable to form a hydrogen bond with the target macromolecule and show the good docking score [16] (Figure 1-4 and Table 1).

Estimation of Binding Free Energy
The calculations of MM/GBSA were performed to estimate the relative binding a nity of ligands to the receptor.The top ve compounds of methyltransferase (MTase), endoribonuclease (endoU), ADP ribose phosphatase, and protease binding-free energy values are in table 1. Coumarin derivatives with good docking scores were showed good binding free energy with their respective receptors.So, these coumarin derivatives may be a potent inhibitor of SARS CoV-2.

DME/T properties analysis
In silico pharmacokinetic and pharmacodynamics properties of the coumarin derivatives calculated by the using QikProp utility of Maestro 12.0.The top 5 docked compounds of each enzyme showed the best score.It predicts the drug-likeness feature of ligands.

Lipinski rule of ve
Pharmacodynamic and pharmacokinetic properties of ligands de ne drug-likeness of compounds.Lipinski rule de nes numbers for some parameters compounds which are molecular weight < 500, QPlogPo/w < 5, donorHB ≤ 5, accptHB ≤ 10.The numbers of parameters are in multiples of 5, so, this the rule of ve.The compounds which satisfy these numbers for the same parameters are considered as the drug-likeness [17].ADME/T calculation and rule of ve of the top 5 compounds of each enzyme are given in table 2.
Methyltransferase of SARS CoV-2 involves mRNA capping and cap by 2'-O-ribose methylation to the 5'-cap structure of viral mRNAs.NSP16 is a binding site of the N7-methyl guanosine cap.So, methyltransferase plays an important role in viral mRNAs cap methylation [18].EndoU enzyme of all known CoVs is highly conserved (19,20).EndoU enzyme of coronaviruses is similar to the animal cellular endoribonuclease [21].It plays a role in mRNA maintenances.Adenosine diphosphate ribose phosphatase (ADRP) domain of SARS CoV nsP3 is indeed a phosphatase that removes the terminal 1″ phosphate from Appr-1″-p [22].CoV S (coronavirus spike glycoprotein) proteins are class I viral fusion proteins, and for the fusion with human body cells activation of S protein is required and protease cleavage is required for S protein activation [23].So, all taken enzymes or receptors very actively participate in the replication and infection of SARS CoV-2 and inhibition of these targets may inhibit the infection of SARS CoV-2 or may cure the infected people with COVID-19.In present in silico study, coumarin derivatives actively interact with taken receptors and showed good docking results for methyltransferase (MTase), endoribonuclease(endoU), ADP ribose phosphatase, and protease and top 5 compounds of each have docking score from -9.00 to -7.97, -8.42 to -6.80, -8.63 to -7.48 and -7.30 to -6.01 kcal/mol respectively.All the enzymes showed good results with different compounds, therefore, less chance to be resistant to other targets.So, the combination therapy of the active compounds may be potent inhibitors of SARS CoV-2.

Protein Preparation
The protein structures, namely, 6w61 (methyltransferase-stimulatory factor complex of NSP16 and NSP10), 6vww (NSP15 Endoribonuclease), 6vxs (ADP ribose phosphatase (ADRP)of NSP3) and 6lu7 (protease) were retrieved from protein data bank (https://www.rcsb.org/)as anti-COVID-2019 targets.Retrieved structures were subjected to the protein preparation wizard of Maestro for preparation of the structures.The selected structures were processed for the incorporation of creating zero bond order for metal, assigning proper bond orders, creating disulphide bonds, and the addition of missing hydrogens.Optimization of hydrogen bonds was assigned using sample water orientations and Non-hydrogen atoms of protein structures were energy minimized until the RMSD (root mean square deviation) reaches the value of 0.3Å.Ligand interaction diagram with phosphatase

Figures Figure 1 Page 9
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Table 1 :
docking score and glide parameters

Table 2 :
ADME/T properties of top 5 compounds of each enzymes/receptor.Estimated number of hydrogen bonds that would be accepted by the solute from water molecules in an aqueous solution DonorH = Estimated number of hydrogen bonds that would be donated by the solute to water molecules in an aqueous solution.QPPCaco = Predicted apparent Caco-2 cell permeability in nm/sec.Caco2 cells are a model for the gut-blood barrier QPlogBB = Predicted brain/blood partition coe cient.coumarin derivatives, both naturally derived and chemically derived were found to have good antiviral activity.Based on biological activity 2755 compounds of coumarin derivatives weredownloadedfromthewebsitePubChem (https://pubchem.ncbi.nlm.nih.gov/#query= coumarin), is a chemical database in SDF format.These ligands were prepared using the LigPrep module of Maestro.LigPrep performs 3D low energy structure conversion from 2D with accurate chiralities.Ionization were retained in original states with realistic bond lengths and bond angles, tautomers, ring conformation were generated, using the OPLS-2005 force eld. Some