key: cord-0830741-3o2f2x1q
authors: Andrianov, Alexander M.; Kornoushenko, Yuri V.; Karpenko, Anna D.; Bosko, Ivan P.; Tuzikov, Alexander V.
title: Computational discovery of small drug-like compounds as potential inhibitors of SARS-CoV-2 main protease
date: 2020-07-14
journal: Journal of biomolecular structure & dynamics
DOI: 10.1080/07391102.2020.1792989
sha: b4b8b39afa1154cc53aff0a761ae7147a3620139
doc_id: 830741
cord_uid: 3o2f2x1q

A computational approach to in silico drug discovery was carried out to identify small drug-like compounds able to show structural and functional mimicry of the high affinity ligand X77, potent non-covalent inhibitor of SARS-COV-2 main protease (M(Pro)). In doing so, the X77-mimetic candidates were predicted based on the crystal X77-M(Pro) structure by a public web-oriented virtual screening platform Pharmit. Models of these candidates bound to SARS-COV-2 M(Pro) were generated by molecular docking, quantum chemical calculations and molecular dynamics simulations. At the final point, analysis of the interaction modes of the identified compounds with M(Pro) and prediction of their binding affinity were carried out. Calculation revealed 5 top-ranking compounds that exhibited a high affinity to the active site of SARS-CoV-2 M(Pro). Insights into the ligand − M(Pro) models indicate that all identified compounds may effectively block the binding pocket of SARS-CoV-2 M(Pro), in line with the low values ​​of binding free energy and dissociation constant. Mechanism of binding of these compounds to M(Pro) is mainly provided by van der Waals interactions with the functionally important residues of the enzyme, such as His-41, Met-49, Cys-145, Met-165, and Gln-189 that play a role of the binding hot spots assisting the predicted molecules to effectively interact with the M(Pro) active site. The data obtained show that the identified X77-mimetic candidates may serve as good scaffolds for the design of novel antiviral agents able to target the active site of SARS-CoV-2 M(Pro). Communicated by Ramaswamy H. Sarma

The recent outbreak of coronavirus infection in China caused by the SARS-CoV-2 virus associated with COVID-19 has become a matter of serious concern to the world community, as the number of infected people is constantly increasing with significant geographical spread. As of the beginning of June 2020, the World Health Organization reports over 6.9 million confirmed cases of infection and over 400 thousand deaths. Numerous attempts are being made to develop an effective antiviral vaccine and find new therapeutic agents against COVID-19. Studies of various aspects of SARS-CoV-2, including structure, mechanism of action, epidemiology and genome sequencing, have provided important information about the new virus (Boopathi et al., 2020; Chan et al., 2020; Lu et al., 2020) . According to the data obtained (Chan et al., 2020; Lu et al., 2020) , SARS-CoV-2 belongs to a large family of coronaviruses that infect humans and other animal species, causing many widespread and serious diseases, such as Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) (De Wit et al., 2016) . The SARS-CoV-2 coronavirus genome is positive-sense, single-stranded RNA and consists of $ 30,000 nucleotides, and its replicase gene encodes two overlapping polyproteins, pp1a and pp1ab, required for virus replication and transcription . These polyproteins undergo extensive proteolytic processing by two cysteine proteases, namely papainlike protease PLpro and 3-chymotrypsin-like protease 3CLpro (also known as the main protease M Pro ) which is essential for mediating viral replication and transcription (Anand et al., 2002; Yang et al., 2003) . The main protease digests polyprotein at no less than 11 conserved sites, starting with the autolytic cleavage of this enzyme itself from pp1a and pp1ab (Hegyi & Ziebuhr, 2002) . This indicates the extremely important role of M Pro in the life virus cycle and makes this enzyme one of the most attractive targets for the development of effective antiviral drugs (Pillaiyar et al., 2016) .

In the newest studies, SARS-CoV-2 M Pro has been used as a target for screening clinically approved drugs as potential virus inhibitors in the hope of identifying drugs that are effective against COVID-19 (e.g. Adeoye et al., 2020; Babadaei et al., 2020; Enmozhi et al., 2020; Hendaus, 2020; Muralidharan et al., 2020; Rismanbaf, 2020; Yan et al., 2020; Zhijian et al., 2020; Zhou et al., 2020) . Since the safety profiles of these drugs are well-documented, such an approach combining the structural design of drugs with virtual screening and molecular modeling methods can significantly facilitate and accelerate the detection of antiviral compounds with clinical potential in order to re-profile them for the treatment of patients infected with a new type of coronavirus. However, taking into account SARS-CoV-2 mutations (Forster et al., 2020; Khailany et al., 2020; Pachetti et al., 2020; Yao et al., 2020) , studies on the development of novel antiviral compounds capable of blocking the functionally important sites of the viral proteins are also extremely significant.

Determination of the high-resolution X-ray structures of SARS-CoV-2 main protease (M Pro ) in ligand-bound and unbound states (Berman et al., 2000;  http://www.rcsb.org/pdb/) laid the foundation not only for understanding the function and molecular mechanism of the enzyme action, but also for developing novel effective SARS-CoV-2 inhibitors by direct methods of computer-aided drug design (e.g. Bhardwaj et al., 2020; Fischer et al., 2020; Gupta et al., 2020; Islam et al., 2020; Jin et al., 2020; Joshi et al., 2020; Olubiyi et al., 2020; Pant et al., 2020; Sarma et al., 2020; Ton et al., 2020; Vega-Valdez et al., 2020; Wahedi et al., 2020; Zhang et al., 2020) . In particular, SARS-CoV-2 M Pro structure in the complex with the high affinity ligand X77 that is potent non-covalent inhibitor of SARS-COV-2 M Pro was recently deposited in the Protein Data Bank (PDB ID: 6W63, http://www.rcsb.org/pdb/).

In this study, an integrated computational approach to in silico drug discovery was carried out to discover small drug-like compounds able to show structural and functional mimicry of the inhibitor X77. This computer-based approach included i) generation of pharmacophore model representing 3 D-arrangements of chemical functionalities that make X77 active towards the active site of SARS-CoV-2 M Pro , (ii) shape/pharmacophore-based identification of the X77-mimetic candidates by a web-oriented virtual screening platform Pharmit (http://pharmit.csb.pitt.edu) allowing one to search for small molecules based on their structural and chemical similarity to another small molecule (Sunseri & Koes, 2016) , iii) identification of compounds satisfying the Lipinski's "rule of five" (Lipinski et al., 2001 ) that recognizes molecules with drug-like properties, iv) molecular docking of these drug-like compounds with the enzyme active site, v) prediction of the interaction modes dominating the binding; vi) calculation of the values of binding free energy and dissociation constant (K d ) for the docking ligand À M Pro models, vii) optimization of these models using the semiempirical quantum chemical method PM7 (Stewart, 2013) , viii) molecular dynamics (MD) simulations of the identified compounds bound to M Pro , ix) calculation of the values of binding energy for the PM7-based and dynamic ligand À M Pro models, and x) selection of molecules most promising for biochemical assays.

As a result, an ensemble of hit compounds that bind to the active site of SARS-CoV-2 M Pro and specifically interact with the functionally important residues of the enzyme was identified. These compounds are suggested to form good scaffolds for the development of novel, potent and broad drugs against COVID-19.

The Pharmit server software (Sunseri & Koes, 2016 ; http:// pharmit.csb.pitt.edu) was used to generate the X77 pharmacophore model based on the X77 À M Pro complex in crystal (PDB ID: 6w63; https://www.rcsb. org). This model (Table 1) was applied for virtual screening of small-molecule compounds able to block the X77-binding site of SARS-CoV-2 M Pro . Virtual screening was performed in the 9 Pharmit molecular libraries containing over 213.5 million chemical structures (Sunseri & Koes, 2016 ; http://pharmit.csb.pitt.edu), resulting in a set of compounds that satisfied the X77 pharmacophore model (Table 1 ) and Lipinski's "rule of five" (Lipinski et al., 2001) . These molecules were further screened by molecular docking and quantum chemical calculations to evaluate the affinity of their binding to SARS-CoV-2 M Pro and identify molecules most promising for biochemical assays. Table 4 ).

Molecular docking of the predicted compounds with SARS-CoV-2 M Pro was carried out by the QuickVina 2 program (Alhossary et al., 2015) in the approximation of rigid receptor and flexible ligands. The X77 inhibitor ( Figure 1 ) was used in the calculations as a positive control. The 3 D structure of this compound was isolated from the crystal X77 À M Pro complex (the PDB ID: 6W63; http://www.rcsb.org/pdb/). The SARS-CoV-2 M Pro and ligand structures were prepared by adding hydrogen atoms with the Open Babel software (http://openbabel.org/wiki/Main_Page) followed by their optimization in the UFF force field (Rappe et al., 1992) . The ligands were docked to the crystal SARS-CoV-2 M Pro structure using QuickVina 2 (Alhossary et al., 2015). The grid box included the X77-binding site of SARS-CoV-2 M Pro and had the following parameters:

that is, the box volume was 19 Â 21 Â 23 ¼ 9177 Å 3 . The value of "exhaustiveness" parameter defining number of individual sampling "runs" was set to 1000 (Alhossary et al., 2015) .

The quantum chemical optimization of the docked ligand À M Pro structures was carried out using the semiempirical quantum chemical method PM7 (Stewart, 2013) associated with the MOPAC2016 software package (http:// OpenMOPAC.net). Before the calculations, the ligand À M Pro complexes were supplemented with hydrogen atoms and optimized in the UFF force field (Rappe et al., 1992) . For this purpose, the Open Babel program (http://openbabel.org/ wiki/Main_Page) was used. The calculations were performed in the COSMO solvation model (COnductor-like Screening MOdel) approximation (Klamt, 2005; Klamt et al., 2015; Klamt & Sch€ u€ urmann, 1993) (Stewart, 2013) was applied. The value of RMS gradient was set to 10 kcal/mol/ Å.

The classical dynamics of the ligand À M Pro complexes in water was made with the implementation of Amber18 using the Amber ff14SB force field (Case et al., 2020) . The Antechamber module was employed to set the Gasteiger atomic partial charges (Case et al., 2020) . To prepare the force field parameters, the general Amber GAFF force field (Wang et al., 2004) was used. Hydrogen atoms were added to M Pro by the tleap program of the AmberTools18 package (Case et al., 2020) . Initially, the ligand À M Pro complexes were each placed in a cubical box with periodic boundary conditions. In addition to the ligand À M Pro complex, the box for the MD simulations included TIP3P water (Jorgensen et al., 1983) as an explicit solvent, Na þ and Cl À ions providing overall salt concentration of 0.10 M. After setting up the system, an energy minimization was performed using 500 steps of the steepest descent algorithm followed by 500 steps of the conjugate-gradient method. The backbone atoms of the complex assembly were then fixed by an additional harmonic potential with the force constant of 2.0 kcal/mol and the system was subject to the equilibration phase. The system equilibration was carried out in three consecutive stages: 1) the system was gradually heated from 0 K to 310 K for 1 ns in NVT ensemble using a Langevin thermostat with a collision frequency of 2.0 ps À1 (Case et al., 2020) ; 2) pressure equilibration was made for 1 ns at 1.0 bar in NPT ensemble using Berendsen barostat with a 2.0 ps characteristic time (Case et al., 2020) ; 3) the constraints on the complex assembly were removed and the system was equilibrated again at 310 K over 0.5 ns under constant volume conditions. After equilibration was achieved, the MD simulations were carried out for 50 ns in NPT ensemble at temperature T ¼ 310 K and p ¼ 1 bar. Bonds involving hydrogen atoms were constrained using SHAKE algorithm (Ryckaert et al., 1977) to achieve the integration time-step of 2 ps. Long-range electrostatic interactions were calculated using Particle Mesh Ewald (PME) algorithm (Essmann et al., 1995) . Coulomb interactions and van der Waals interactions were truncated at 8 Å.

The binding modes of the predicted compounds to SARS-CoV-2 M Pro , namely hydrogen bonds, salt bridges, van der Waals contacts, and p-p interactions were identified by the BINANA program . The ligand poses in the docking ligand À M Pro models were visualized with the program UCSF Chimera (Pettersen et al., 2004) . To visualize van der Waals contacts, the program LigPlot (McDonald & Thornton, 1994) was employed. The values of K d for the ligand À M Pro structures were calculated using a neural-network-based scoring function NNScore 2.0 . The values of binding free energy were estimated from those of K d by the formula DG ¼ R Â T Â ln(K d ) (where DG is the binding free energy, R is the universal gas constant, T is the absolute temperature equal to 310 K) (Sharma & First, 2009) . For the PM7-based complexes, the ligand-binding affinity was estimated in terms of the values of binding enthalpy DH calculated as the differences between the heats of formation of the ligand À M Pro complexes and heats of formation of the ligand and M Pro in the unbound states (Stewart, 2013;  http://OpenMOPAC.net). Quantum chemical calculations of the ligand and M Pro structures in the unbound states were performed using the computational protocol described above for the docking ligand À M Pro models.

In the case of dynamic ligand À M Pro models, the values of binding energy were calculated with Amber18 (Case et al., 2020) using the MM/GBSA method (Genheden & Ryde, 2015; Sun et al., 2014; Xu et al., 2013) . The calculations were made for 200 snapshots extracted from the final 40 ns of the MD trajectories, by keeping the snapshots every 0.2 ns. The polar solvation energies were computed in continuum solvent using Poisson-Boltzmann continuum-solvation model with ionic strength of 0.10. The non-polar terms were estimated using solvent accessible surface areas (Case et al., 2020) . Analysis of the MD trajectories was performed by the CPPTRAJ module of AmberTools 18 (Case et al., 2020) .

Shape/Pharmacophore-based virtual screening of the Pharmit databases resulted in 24 molecules that exhibited favorable binding energies (< À6 kcal/mol) and the values of rootmean-square deviations between the query features and the hit compound features less than 2 Å (Sunseri & Koes, 2016) . Molecular docking of these molecules with the active site of M Pro followed by quantum chemical calculations and MD simulations identified 5 top-ranking compounds (Figure 2 ) that showed a high-affinity binding in terms of K d , binding free energy, and binding enthalpy (Table 2 ). This allowed one to consider these compounds as the most probable X77-mimetic candidates. Inspection of the physicochemical parameters of the predicted compounds (Table 3) providing such important characteristics for a potential drug as absorption, distribution, metabolism and excretion indicates that these molecules fully satisfy the requirements of the Lipinski's "rule of five" (Lipinski et al., 2001) .

Insights into the docking ligand À M Pro models (Figure 3 ) show that all identified X77-mimetic candidates form a wide network of intermolecular interactions involving amino acid residues of the binding pocket of M Pro . In particular, compound I exhibiting the lower values of K d and binding free energy compared to the other predicted molecules and X77 (Table 2) (Table 4 ). In addition to these direct interatomic contacts, compound I is also involved in specific p-p interaction with His-41 which is a part of the catalytic dyad of M Pro formed by this residue and Cys-145 (Chang, 2010; Qamar et al., 2020) . Examination of the intermolecular interaction profile calculated for the other identified compounds indicates ( Table 4 ) that these molecules exhibit the modes of binding to SARS-CoV-2 M Pro similar to those predicted for compound I. According to the data obtained, these binding modes are provided by hydrogen bonds, van der Waals contacts, salt bridges (compounds I and III) and p-p interactions between p-conjugated systems of the ligands and the side chain of His-41 (compounds I, III and IV) (Table 4, Figure 4 ). Among these binding modes, intermolecular van der Waals interactions are the major contributors to the ligand À M Pro interface including significant residues of the enzyme active pocket (Table 4, Figure 4 ).

The efficiency of the intermolecular interactions of the X77-mimetic candidates with SARS-CoV-2 M Pro is supported by the low values of K d (0.006 lM À 2.56 lM) and binding free energies (DG À7.9 kcal/mol), indicating their high affinity with the catalytic site of the enzyme ( Table 2) . Analysis of the values of K d and binding free energy calculated for the identified compounds shows that, given the calculation errors, they are comparable with those obtained for X77 using the identical computational protocol (Table 2) .

So, the data of molecular docking show that all identified compounds (Figure 2 ) may effectively block the key residues of the M Pro catalytic site, which is confirmed by the low values of binding free energy and K d calculated for the docking ligand À M Pro models (Table 2) . This is also supported by the data of quantum chemical calculations which show that, excluding compound V, the values of binding enthalpy of the analyzed molecules to M Pro are lower than that predicted for the control inhibitor X77 by the same computational parameters (Table 2) .

In general, the data of MD simulations are in agreement with the principal conclusions made from the analysis of the static ligand À M Pro complexes. These complexes are relatively stable within the MD simulations, as evidenced by the averages of binding energies and corresponding standard T25 (2) deviations (Table 2) . Given the MM/GBSA method errors (Genheden & Ryde, 2015; Sun et al., 2014; Xu et al., 2013) , one can suggest that the dynamic ligand À M Pro structures exhibit the averages of binding energy comparable with the value calculated for X77 by the identical computational protocol (Table 2 ). In favor of the relative stability of the dynamic ligand À M Pro structures is also evidence of the data on the time dependence of the root-mean square deviations (RMSD) of the atomic positions for the dynamic and static models of the predicted compounds bound to M Pro ( Figure  5 ). Analysis of Figure 5 indicates that these complexes do not undergo significant structural rearrangements on the MD trajectories, which is confirmed by the averages of the RMSD calculated for the dynamic models of the identified molecules in the complexes with M Pro . The mean values of RMSD and standard deviations, which are 2.54 ± 0.45 Å (compound I), 2.15 ± 0.33 Å (compound II), 1.59 ± 0.39 Å (compound III), 1.81 ± 0.32 Å (compound IV), and 2.13 ± 0.34 Å (compound V), are close to those of 1.54 ± 0.23 Å obtained for the SARS-CoV-2 inhibitor X77 ( Figure 5) . Examination of the data on the contributions of individual M Pro amino-acid residues into the binding energy reveals the residues dominating the ligand À M Pro interaction profile. Table 5 shows that these residues are His-41, Met-49 (excluding compound I), Cys-145, Met-165, and Gln-189. Importantly, it is those residues that are the major contributors to the X77 À M Pro interaction (Table 5) . Among these residues, it should first be noted the highly important His-41 and Cys-145 forming the catalytic dyad of SARS-CoV-2 M pro (Chang, 2010; Qamar et al., 2020) . These data indicate that, despite the unbound SARS-CoV-2 M pro shows the higher mobility than a highly similar SARS-CoV M pro (Bz owka et al., 2020), there are a number of the key anchoring residues assisting the identified compounds and X77 to effectively interact with the active site of the enzyme. Figure 6 casts shed on the values of root-mean-square fluctuations (RMSF) of the individual residues of M Pro indicating the flexibility of each amino acid during the MD simulations. Analysis of Figure 6 reveals that the majority of the M Pro residues are positionally restrained on the MD trajectories, including the key anchoring residues His-41, Cys-145, Met-165, and Gln-189. The values of RMSF given for these binding hot spots in Table 6 testify to the quite small internal motions of these residues, in line with the data on their contributions into the binding energy (Table 5 ). The exception is Met-49 exhibiting the higher atomic fluctuations in the complexes with compound V and X77 compared with the other residues of the binding pocket of M Pro (Figure 6 , Table 6 ).

So, the findings of molecular docking, quantum chemical calculations and MD simulations suggest that the analyzed anti-SARS-CoV-2 (COVID-19) drug candidates expose the interaction modes and binding affinity profiles similar to those calculated for X77, potent, broad-spectrum inhibitor of coronavirus main protease including SARS-CoV-2 (PDB ID: 6W63, http://www.rcsb.org/pdb/).

Certainly, when analyzing the obtained data, it is necessary to keep in mind that all computational approaches for modeling ligand À protein complexes and estimating the binding affinity involve various approximations. They vary from simplified forms of the first-principles equations that are easier or faster to solve, to approximations limiting the size of the system, to fundamental approximations to the underlying equations that are required to achieve any solution to them at all. Nevertheless, the findings of comparative analysis of the X77 À M Pro complexes constructed by the X- Thus, the data on the intermolecular interaction network (Tables 4 and 5) are in line with the results of binding affinity prediction obtained for the ligand À M Pro complexes using molecular docking, quantum chemical calculations and MD simulations ( Table 2) . From the data of Table 2 , the analyzed complexes show the low values of K d and binding energies, suggesting strong attachment of the identified X77-mimetic candidates to SARS-CoV-2 M Pro . These small drug-like molecules are therefore promising candidates for further detailed experimental evaluation. However, it is clear that, despite promising in silico profile, the analyzed compounds are only starting points for the development of new highly potent drug candidates. In this connection, before biochemical assays, these compounds should go through a lead optimization, iterative process of altering the molecule structure to identify their chemical modifications with improved antiviral potency and ADMET parameters. For this purpose, the modern QSAR methods commonly used as a lead optimization approach in drug discovery may be applied (Golbraikh et al., 2017; Kuseva et al., 2019; Schultz et al., 2018) .

Shape/Pharmacophore-based virtual screening combined with molecular docking, quantum chemical calculation and MD simulations revealed 5 top-ranking compounds that exhibited a high affinity to the catalytic site of SARS-CoV-2 M Pro , allowing one to consider these small drug-like molecules as the most promising X77-mimetic candidates. Insights into the ligand À M Pro models indicate that all identified compounds may specifically and effectively block the active site of SARS-CoV-2 M Pro , in line with the low values of dissociation constants and binding energies. Mechanism of binding of these compounds to M Pro is mainly provided by van der Waals interactions with the functionally important residues of the enzyme, such as His-41, Met-49, Cys-145, Met-165, and Gln-189 that play a role of the binding hot spots assisting the predicted molecules to effectively interact with the M Pro active site. Taken together, the data obtained show that the identified X77-mimetic candidates may serve as good scaffolds for the design of novel antiviral agents able to target the active pocket of SARS-CoV-2 M Pro .

No potential conflict of interest was reported by the author(s).

This study was funded by grants from the State Program of Scientific Research "Convergence 2020" (subprogram "Consolidation", project 3.08) and the Belarusian Republican Foundation for Fundamental Research (project X20-006). . Superposition of the X77 À M Pro complexes constructed using X-ray crystallography and molecular docking. The root-mean-square deviation between the atomic coordinates of the X77 inhibitor in the calculated and experimental structures is 0.63 Å. Residues of M Pro forming direct interatomic contacts with X77 are marked by a wire model.

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