COMPUTATIONAL MOLECULAR DOCKING AND IN SILICO ADMET PREDICTION STUDIES OF PYRAZOLE DERIVATIVES AS COVID-19 MAIN PROTEASE (M PRO ) AND PAPAIN-LIKE PROTEASE (PL PRO ) INHIBITORS

. The inhibition of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (M pro ) and papain-like protease (PL pro ) prevents viral multiplications. Molecular docking, absorption, distribution, metabolism, excretion, and toxicity (ADMET) studies of pyrazole-indole molecules 6a, b, Schiff bases 8a, b, and pyrazolo[1,5-a ]pyrimidines 10a, b were performed and done. Based on the molecular docking study verified that the presented structures ( 6a , 6b , 8a , 8b , 10a , and 10b ) give promised attached bonds with the active site in the COVID-19 main protease (M pro ). The results of in silico ADMET prediction study revealed that these compounds may be considered candidates for the discovery or development of new series of COVID-19 drugs.

Among many disease outbreaks caused by RNA viruses, coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the deadliest of all. Since its initiation in December 2019, COVID-19 has afflicted humans worldwide. Viral enzymes such as the main protease (M pro ) and papain-like protease (PL pro ) are significantly responsible for the replication of SARS-CoV-2. As inhibition of M pro and PL pro prevents viral multiplication, they have been recognized as the most promising targets for anti-SARS-CoV-2 drugs [14].
Nowadays, molecular modeling study is considered an important study because it provides a more accurate picture of biologically active molecules at the atomic level and plays a major role in the drug designing process [15]. Molecular docking simulation is considered the simplified form of molecular dynamic (MD) simulation that safe time and money spent and common component of drug discovery because traditional experimental methods for drug discovery take a long time [16]. Docking study can also be defined as a computational procedure that studies how ligand and protein fit both energetically and geometrically to give us a complete figure to predict the binding-conformation of small drug-like molecules to target proteins [17]. Molecular docking simulation was used to predict the possible binding mode as well as the active conformation of these derivatives inside the target enzyme. Additionally, the preferring structure selected from one to another in the docking study related to the highest binding affinity between the ligand and the protein [18].

2-(4-Methoxyphenylamino)-N,7-diphenylpyrazolo[1,5-a]pyrimidine-3-carboxamide
(10a). Yellow crystals, m.p. 218-220 °C. IR (KBr) νmax/cm -1 3346 (NH), 1658 (C=O). 1  Docking protocol molecular docking protocols are widely used for predicting the binding affinities for a number of ligands. In the current work, our aim was to examine the possibility of an existing relationship between the experimental bioactivities of the inhibitors under study and the docking scores. In order to get accurate results, all the docking experiments were performed with the default parameters. The time to dock one ligand was approximately 1-2 min. Docking with AutoDock/Vina, GOLD, and FRED was performed on a Linux workstation (openSUSE11. 4) with an Intel Pentium D processor (3.0 GHz) and 1 GB of RAM whereas FlexX was run on windows 7 equipped with an Intel® Atom™ processor (1.67 GHz) and 1GB of RAM.

Molecular docking study
Molecular docking validations were done to predict the binding between active sites in the COVID-19 main protease (M pro ) as a targeting enzyme docked by pyrazoles. The result was obtained by comparison with hydroxychloroquine as a reference molecule. Hydroxychloroquine during the last few months was considered a promised candidate drug for Covid-19 [32]. The inhibition of M pro presents a unique challenge in which the active site pocket is characteristically and in continuation of our work [33] to discover new drug enzyme interaction we presented this study.

In silico ADMET prediction
The absorption, distribution, metabolism, excretion, and toxicity (ADMET) prediction properties of pyrazole-indole molecules 6a,b, Schiff bases 8a,b, and pyrazolo[1,5-a]pyrimidines 10a,b were predicted using pkCSM web (http://biosig.unimelb.edu.au/pkcsm/prediction) [31]. The results properties are shown in Table 3. Absorption properties, P-gps substrate or enzymes (P-glycoprotein substrate, P-glycoprotein I inhibitor, and P-glycoprotein II inhibitor) are the keys to estimating active efflux through biological membranes and are known as the most important member of ATP-binding cassette transporters or ABC-transporters used to protect the central nervous system (CNS) from xenobiotics. From the result, we can conclude that all the molecules 6a, 6b, 8a, 8b, 10a, and 10b are inhibitors for P-glycoprotein substrate, P-glycoprotein I enzyme, and P-glycoprotein II enzyme. The distribution properties are including the blood-brain barrier (BBB) Permeability, central nervous system (CNS) Permeability, and volume of distribution (VDss) [34]. The BBB permeability values, the four compounds, pyrazole-indole molecules 6a,b, and Schiff bases 8a,b, have lower values of log BB (log BB < -1, ranging between -1.47 to -1.624) referring to these compounds are poorly distributed to the brain and have not the ability to pass the blood-brain barrier (BBB). But, pyrazolo[1,5-a]pyrimidines 10a and 10b have values of log BB -0.073 and -0.234, respectively, which refer to these compounds are moderately distributed. The six  compounds 6a, 6b, 8a, 8b, 10a, and 10b have CNS permeability of more than -2; therefore, these compounds have the ability to penetrate the central nervous system (CNS). The volume of distribution (VDss) predicted that all the molecules 6a, 6b, 8a, 8b, 10a, and 10b have lower values of VDss (log VDss < -0.15, ranging between -0.832 to -0.319) refer to the compounds are contained in plasma rather than in tissues.
Inhibition of the five major CYP isoforms (CYP1A2, CYP2C19, CYP2C9, CYP2D6, and CYP3A4) is certainly one major cause of pharmacokinetics-related drug-drug interactions leading to toxic or other unwanted adverse effects due to the lower clearance and accumulation of the drug or its metabolites [35]. All the molecules 6a, 6b, 8a, 8b, 10a, and 10b are inhibitors of the CYP1A2, CYP2C19, and CYP2C9 enzymes. But, are non-inhibitors of the CYP2D6 enzyme. The four molecules 8a, 8b, 10a, and 10b are inhibitors of the CYP3A4 enzyme, but, the two compounds 6a and 6b are non-inhibitors.
Hepatotoxicity (from hepatic toxicity) implies chemical-driven liver damage. Drug-induced liver injury is a cause of acute and chronic liver disease caused specifically by medications. The five compounds 6a, 8a, 8b, 10a, and 10b are inhibitors for the compounds that caused hepatic toxicity except for 6b. hERG I and II inhibitors: inhibition of the potassium channels encoded by hERG (human ether-a-go-go-related gene) is the principal cause for the development of acquiring long QT syndrome-leading to fatal ventricular arrhythmia. All the molecules are non-inhibitors of the hERG I enzyme but are inhibitors of the hERG II enzyme.

CONCLUSION
The aim of this manuscript was to study the molecular docking of pyrazole-indole molecules 6a,b, Schiff bases 8a,b, and pyrazolo[1,5-a]pyrimidines 10a,b as COVID-19 main protease (M pro ) and papain-like protease (PL pro ) inhibitors. Also, study in silico absorption, distribution, metabolism, excretion, and toxicity (ADMET) prediction properties. The molecular docking study verified that the presented structures (6a, 6b, 8a, 8b, 10a, and 10b) give promised attached bonds with the active site in the COVID-19 main protease (M pro ). In silico ADMET prediction study revealed that all the molecules 6a, 6b, 8a, 8b, 10a, and 10b are inhibitors for P-glycoprotein substrate, Pglycoprotein I enzyme, and P-glycoprotein II enzyme, have CNS permeability of more than -2, have lower values of VDss (log VDss < -0.15, ranged between -0.832 to -0.319), and are inhibitors of the CYP1A2, CYP2C19, CYP2C9, and hERG II enzymes but are non-inhibitors of the CYP2D6, renal organic cation transporter 2 (OCT2), and hERG I enzymes. (ii) The four compounds, 6a, 6b, 8a, and 8b, have lower values of log BB (log BB < -1, ranging between -1.47 to -1.624). But, pyrazolo[1,5-a]pyrimidines 10a and 10b have values of log BB -0.073 and -0.234, respectively. (iii) The four molecules 8a, 8b, 10a, and 10b are inhibitors of the CYP3A4 enzyme, but, the two compounds 6a and 6b are non-inhibitors. (iv) The five compounds 6a, 8a, 8b, 10a, and 10b are inhibitors for the compounds that caused hepatic toxicity except for 6b. In the future, this study could be valuable in the discovery of new series of COVID-19 drugs by modification the structure of the molecules.