key: cord-308786-e6rv5csl authors: Alamri, Mubarak A.; Tahir ul Qamar, Muhammad; Mirza, Muhammad Usman; Alqahtani, Safar M.; Froeyen, Matheus; Chen, Ling-Ling title: Discovery of human coronaviruses pan-papain-like protease inhibitors using computational approaches date: 2020-08-28 journal: J Pharm Anal DOI: 10.1016/j.jpha.2020.08.012 sha: doc_id: 308786 cord_uid: e6rv5csl The papain-like protease (PL(pro)) is vital for the replication of coronaviruses (CoVs), as well as for escaping innate-immune responses of the host. Hence, it has emerged as an attractive antiviral drug-target. In this study, computational approaches were employed, mainly the structure-based virtual screening coupled with all-atom molecular dynamics (MD) simulations to computationally identify specific inhibitors of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) PL(pro), that can be further developed as potential pan-PL(pro) based broad-spectrum antiviral drugs. The sequence, structure, and functional conserveness of most deadly human CoVs PL(pro) were exploited, and it was revealed that functionally important catalytic triad residues are well conserved among SARS-CoV, SARS-CoV-2, and middle east respiratory syndrome coronavirus (MERS-CoV). The subsequent screening of a focused protease inhibitors database composed of ∼7000 compounds resulted in the identification of three candidate compounds, ADM_13083841, LMG_15521745, and SYN_15517940. These three compounds established conserved interactions which were further explored through MD simulations, free energy calculations, and residual energy contribution estimated by MM-PB(GB)SA method. All these compounds showed stable conformation and interacted well with the active residues of SARS-CoV-2 PL(pro) and showed consistent interaction profile with SARS-CoV PL(pro) and MERS-CoV PL(pro) as well. Conclusively, the reported SARS-CoV-2 PL(pro) specific compounds could serve as seeds for developing potent pan-PL(pro) based broad-spectrum antiviral drugs against deadly human coronaviruses. Moreover, the presented information related to binding site residual energy contribution could lead to further optimization of these compounds. In order to estimate the decisive role of interacting residues towards ligand's binding, per-159 residue energy decomposition analysis was performed using the MM-GBSA method, and 160 binding energy were calculated as ΔG residue using the following equation. The sequence alignment of SARS-CoV-2 PL pro protein sequence displayed an identity of 169 82.80% and only 30.00% with SARS-CoV PL pro and MERS-CoV PL pro , respectively (Fig. 1) . 170 However, the sequence alignment revealed that PL pro crucial catalytic triad residues of CoVs 171 PL pro are well conserved amongst SARS-CoV-2 (Cys111-His272-Asp286), SARS-CoV as same as the PL pro of SARS-CoV and MERS-CoV (Fig. 2B) . Interestingly, the functionally 176 well-conserved catalytic triad residues within the catalytic pockets of PL pro among SARS- 183 Integrated computational methods comprising virtual high throughput screening, molecular 184 docking, and MD simulation are a significant approach for the exploration of potential 185 inhibitors against a target protein [22, 28, 78, 86] . In order to find out potential pan-PL pro 186 based anti-SARS-CoV-2 inhibitors, the structure-based screening was carried out against a 187 virtual library of ~7000 protease inhibitors. By applying a docking score cutoff of lower than 188 -8.5 kcal/mol, three potential hits (Fig. 3) were selected with maximum scores, which were 189 found interacted well with the active site residues. These include ADM_13083841 ((S)-4- (2-(5-methyl-7-oxo-6,7-dihydropyrazolo[1,5-a]pyrimidin-2-yl)pyrrolidin-1-yl)-2- with binding energy score of -8.9, -8.7, -8.7 kcal/mol, respectively, and considered as 196 potential inhibitors of SARS-CoV-2 PL pro (Table 1) . These three hit compounds were used to 199 In order to understand the binding mode and mechanism of interaction of these compounds ADMET-based drug scan tool at the SwissADME server [74] was used to evaluate the drug- Table 2 ). For further validation of the drug likeliness capability of target compounds, all these 235 compounds were subjected to the PreADMET and pkCSM server, that have five main 236 parameters (absorption, distribution, metabolism, excretion, and toxicity) to assess them. These five parameters were then assessed according to the number of thresholds. All the three 238 compounds successfully passed the criteria of drug-ability (Table 3) . 247 Potential binding energy 248 The RMSD computes the direct changes in the atoms of superimposed proteins and an scores ranged from -8.7 to -7.9 kcal/mol (Fig. 10) . However, the binding energy scores of 376 these compounds were low in the case of MERS-CoV, ranged from -5.9 to -6.7 kcal/mol, indicating that their activity toward SARS-CoV might be greater than the activity against 378 MERS-CoV (Fig.11 ). This could be because of the structural difference of MERS-CoV This comprehensive study offers an integrated computational approach towards the 394 discovery of three novel hit compounds, screened from a focused library of ~7000 J o u r n a l P r e -p r o o f Note: ∆G bind is the sum of molecular mechanics energy (∆E MM ) which is the gas term, and solvation free energy (∆G sol ). Both ∆E MM and ∆G sol are further divided into internal energy (∆E int ), electrostatic energy (∆E ele ), and van der Waals (∆E vdw ) energy, and polar (∆G p ) and non-polar (∆G np ) contributions to the solvation free energy. Solvation term were included from both MM/PBSA and MM/GBSA methods. These calculations were executed with the incorporation of entropic term (T∆S) by the following equation: ∆G bind (MM-PB(GB)SA) = ∆E MM + ∆G sol -T∆S. J o u r n a l P r e -p r o o f Bat-to-human: spike features determining 'host jump Severe acute respiratory syndrome Pharmacoinformatics and molecular dynamic simulation studies to 624 identify potential small-molecule inhibitors of WNK-SPAK/OSR1 signaling that mimic the 625 RFQV motifs of WNK kinases Tools for integrated sequence-structure 627 analysis with UCSF Chimera MMPBSA. py: an efficient program 629 for end-state free energy calculations Inhibition of Oncogenic Kinases: An In 631 Vitro Validated Computational Approach Identified Potential Multi-Target Anticancer 632 Compounds In silico Structure-based Identification of Novel 634 Acetylcholinesterase Inhibitors Against Alzheimer's Disease, CNS & Neurological 635 Disorders-Drug Targets (Formerly Current Drug Targets-CNS & Neurological Disorders Assessing the performance of the MM/PBSA and 638 MM/GBSA methods. 1. 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