Tuning Proton Transfer Thermodynamics in SARS-CoV-2 Main Protease: Implications for Catalysis and Inhibitor Design

Conformational heterogeneity and protonation equilibria shape the photocycle branching in channelrhodopsin-2

Channelrhodopsin-2 is a photoactive membrane protein serving as an ion channel, gathering significant interest for its applications in optogenetics. Despite extensive investigation, several aspects of its photocycle remain elusive and continue to be subjects of ongoing debate. Of particular interest are the localization of the P480 intermediate within the photocycle and the timing of the deprotonation of glutamic acid E90, a critical residue for ChR2 functioning. In this study, we explore the possibility of an early-P480 state, formed directly upon photoillumination of the dark-adapted state, where E90 is deprotonated, as hypothesized in a previous work [Kuhne et al. Proc. Natl. Acad. Sci. 116.19 (2019): 9380]. Employing extended molecular dynamics simulations, deprotonation free energy calculations, and the computation of the infrared band associated with E90, we provide support to the photocycle model proposed by Kuhne et al. Furthermore, our findings show that E90 protonation state is influenced by diverse interconnected variables and provide molecular detail insights that connect E90 interaction pattern with its deprotonation propensity. Our data demonstrate in fact that both protonated and deprotonated E90 are possible in P480 depending on E90 hydrogen bonding pattern and explaining the molecular mechanism at the basis of P480 accumulation under continuous illumination.

Revealing the impact of active site residues in modeling the inhibition mechanism of SARS-Cov-2 main protease by GC373

Main protease (Mpro) is a cysteine protease enzyme crucial for the replication of SARS-CoV-2, the etiological agent of COVID-19 and thus considered as a viable target for antiviral development. The GC373 compound, an aldehyde-containing inhibitor, is one of the most effective inhibitors that retards the catalytic function of Mpro. A deeper understanding of the inhibitory action of GC373 by providing precise mechanistic details, is pivotal toward developing more potent inhibitors against Mpro. In this work, we provide novel insights into the inhibition mechanism considering different models and possible pathways using a combination of molecular dynamics and hybrid quantum mechanical/molecular mechanical (QM/MM) methodologies. Our study reveals the impact of key residues on both the binding of the GC373 inhibitor and its inhibition mechanism. Together with the oxyanion hole residues, G143, S144 and C145, we note that H163, and E166 residues play a crucial role in the binding of the inhibitor. Further, our exploration of two pathways namely, water-assisted and direct inhibition mechanisms, using three differently sized QM/MM models shows consistent and distinguishable trends in catalytic pathways and rate-limiting steps, respectively. Our results highlight the importance of treating more representative active site residues in the QM layer enabling a more accurate description of the inhibition mechanism. More importantly, we propose that designing novel inhibitors that could afford stronger interaction with the underlying essential residues is a promising strategy to guide the efforts toward optimizing efficient inhibitors against Mpro.

How Polyproline Type II Conformation at P2 Residues Influences the Success of Proline-Based Peptidyl Inhibitors Against Coronavirus Main Protease

In the wake of the pandemic, peptidyl protease inhibitors with Pro-based rigid Leu mimetics at the P2 position have emerged as potent drug candidates against the SARS-CoV-2 main protease. This success is intuitively attributed to the enhanced hydrophobic interactions and rigidity of Pro-based rigid Leu mimetics in the literature. However, the tertiary amide of proline P2 derivatives, which hinders the formation of a critical hydrogen bond with the enzyme active site, and the constrained PPII conformation, which contradicts the protease preferred β-strand conformation, represent two overlooked disadvantages associated with these inhibitors over traditional inhibitors and, theoretically, should adversely affect their potency. Interestingly, despite these major disadvantages, they maintain or display improved potency compared to traditional peptidyl protease inhibitors. In this study, we uncover a previously unnoticed preference for P2 residues of the protease inhibitors to adopt the PPII conformation, regardless of residue identity, in the main protease-bound form of key RNA viruses, deviating from the traditional β-strand conformation. We also demonstrate that Pro-based rigid Leu mimetics at P2 enhance binding affinity by favoring the enzyme-preferred PPII conformation and significantly reducing configurational entropy loss upon binding, comparable to that of a typical hydrogen bond. This work also highlights the importance of a multidisciplinary approach to enhance the understanding of structure-activity relationships beyond traditional medicinal chemistry intuition. We believe these findings provide new, deep insights and address a major knowledge gap in the area of peptidyl protease inhibitor design, identifying key drivers behind the success of Pro-based peptidyl protease inhibitors beyond mere rigidity and hydrophobicity.

Potency Prediction of Covalent Inhibitors against SARS-CoV-2 3CL-like Protease and Multiple Mutants by Multiscale Simulations

3-Chymotrypsin-like protease (3CLpro) is a prominent target against pathogenic coronaviruses. Expert knowledge of the cysteine-targeted covalent reaction mechanism is crucial to predict the inhibitory potency of approved inhibitors against 3CLpros of SARS-CoV-2 variants and perform structure-based drug design against newly emerging coronaviruses. We carried out an extensive array of classical and hybrid QM/MM molecular dynamics simulations to explore covalent inhibition mechanisms of five well-characterized inhibitors toward SARS-CoV-2 3CLpro and its mutants. The calculated binding affinity and reactivity of the inhibitors are highly consistent with experimental data, and the predicted inhibitory potency of the inhibitors against 3CLpro with L167F, E166V, or T21I/E166V mutant is in full agreement with IC50s determined by the accompanying enzymatic assays. The explored mechanisms unveil the impact of residue mutagenesis on structural dynamics that communicates to change not only noncovalent binding strength but also covalent reaction free energy. Such a change is inhibitor dependent, corresponding to varied levels of drug resistance of these 3CLpro mutants against nirmatrelvir and simnotrelvir and no resistance to the 11a compound. These results together suggest that the present simulations with a suitable protocol can efficiently evaluate the reactivity and potency of covalent inhibitors along with the elucidated molecular mechanisms of covalent inhibition.

Excitation landscape of the CP43 photosynthetic antenna complex from multiscale simulations

Photosystem II (PSII), the principal enzyme of oxygenic photosynthesis, contains two integral light harvesting proteins (CP43 and CP47) that bind chlorophylls and carotenoids. The two intrinsic antennae play crucial roles in excitation energy transfer and photoprotection. CP43 interacts most closely with the reaction center of PSII, specifically with the branch of the reaction center (D1) that is responsible for primary charge separation and electron transfer. Deciphering the function of CP43 requires detailed atomic-level insights into the properties of the embedded pigments. To advance this goal, we employ a range of multiscale computational approaches to determine the site energies and excitonic profile of CP43 chlorophylls, using large all-atom models of a membrane-bound PSII monomer. In addition to time-dependent density functional theory (TD-DFT) used in the context of a quantum-mechanics/molecular-mechanics setup (QM/MM), we present a thorough analysis using the perturbed matrix method (PMM), which enables us to utilize information from long-timescale molecular dynamics simulations of native PSII-complexed CP43. The excited state energetics and excitonic couplings have both similarities and differences compared with previous experimental fits and theoretical calculations. Both static TD-DFT and dynamic PMM results indicate a layered distribution of site energies and reveal specific groups of chlorophylls that have shared contributions to low-energy excitations. Importantly, the contribution to the lowest energy exciton does not arise from the same chlorophylls at each system configuration, but rather changes as a function of conformational dynamics. An unexpected finding is the identification of a low-energy charge-transfer excited state within CP43 that involves a lumenal (C2) and the central (C10) chlorophyll of the complex. The results provide a refined basis for structure-based interpretation of spectroscopic observations and for further deciphering excitation energy transfer in oxygenic photosynthesis.

Prediction of Binding Pose and Affinity of Nelfinavir, a SARS-CoV-2 Main Protease Repositioned Drug, by Combining Docking, Molecular Dynamics, and Fragment Molecular Orbital Calculations

A novel in silico drug design procedure is described targeting the Main protease (Mpro) of the SARS-CoV-2 virus. The procedure combines molecular docking, molecular dynamics (MD), and fragment molecular orbital (FMO) calculations. The binding structure and properties of Mpro were predicted for Nelfinavir (NFV), which had been identified as a candidate compound through drug repositioning, targeting Mpro. Several poses of the Mpro and NFV complexes were generated by docking, from which four docking poses were selected by scoring with FMO energy. Then, each pose was subjected to MD simulation, 100 snapshot structures were sampled from each of the generated MD trajectories, and the structures were evaluated by FMO calculations to rank the pose based on binding energy. Several residues were found to be important in ligand recognition, including Glu47, Asp48, Glu166, Asp187, and Gln189, all of which interacted strongly with NFV. Asn142 is presumably regarded to form hydrogen bonds or CH/π interaction with NFV; however, in the present calculation, their interactions were transient. Moreover, the tert-butyl group of NFV had no interaction with Mpro. Identifying such strong and weak interactions provides candidates for maintaining and substituting ligand functional groups and important suggestions for drug discovery using drug repositioning. Besides the interaction between NFV and the amino acid residues of Mpro, the desolvation effect of the binding pocket also affected the ranking order. A similar procedure of drug design was applied to Lopinavir, and the calculated interaction energy and experimental inhibitory activity value trends were consistent. Our approach provides a new guideline for structure-based drug design starting from a candidate compound whose complex crystal structure has not been obtained.

The H163A mutation unravels an oxidized conformation of the SARS-CoV-2 main protease

The main protease of SARS-CoV-2 (Mpro) is an important target for developing COVID-19 therapeutics. Recent work has highlighted Mpro's susceptibility to undergo redox-associated conformational changes in response to cellular and immune-system-induced oxidation. Despite structural evidence indicating large-scale rearrangements upon oxidation, the mechanisms of conformational change and its functional consequences are poorly understood. Here, we present the crystal structure of an Mpro point mutant (H163A) that shows an oxidized conformation with the catalytic cysteine in a disulfide bond. We hypothesize that Mpro adopts this conformation under oxidative stress to protect against over-oxidation. Our metadynamics simulations illustrate a potential mechanism by which H163 modulates this transition and suggest that this equilibrium exists in the wild type enzyme. We show that other point mutations also significantly shift the equilibrium towards this state by altering conformational free energies. Unique avenues of SARS-CoV-2 research can be explored by understanding how H163 modulates this equilibrium.

Multiscale Simulations of the Covalent Inhibition of the SARS-CoV-2 Main Protease: Four Compounds and Three Reaction Mechanisms

We report the results of computational modeling of the reactions of the SARS-CoV-2 main protease (MPro) with four potential covalent inhibitors. Two of them, carmofur and nirmatrelvir, have shown experimentally the ability to inhibit MPro. Two other compounds, X77A and X77C, were designed computationally in this work. They were derived from the structure of X77, a non-covalent inhibitor forming a tight surface complex with MPro. We modified the X77 structure by introducing warheads capable of reacting with the catalytic cysteine residue in the MPro active site. The reaction mechanisms of the four molecules with MPro were investigated by quantum mechanics/molecular mechanics (QM/MM) simulations. The results show that all four compounds form covalent adducts with the catalytic cysteine Cys 145 of MPro. From the chemical perspective, the reactions of these four molecules with MPro follow three distinct mechanisms. The reactions are initiated by a nucleophilic attack of the thiolate group of the deprotonated cysteine residue from the catalytic dyad Cys145-His41 of MPro. In the case of carmofur and X77A, the covalent binding of the thiolate to the ligand is accompanied by the formation of the fluoro-uracil leaving group. The reaction with X77C follows the nucleophilic aromatic substitution SNAr mechanism. The reaction of MPro with nirmatrelvir (which has a reactive nitrile group) leads to the formation of a covalent thioimidate adduct with the thiolate of the Cys145 residue in the enzyme active site. Our results contribute to the ongoing search for efficient inhibitors of the SARS-CoV-2 enzymes.

Unraveling the catalytic mechanism of SARS-CoV-2 papain-like protease with allosteric modulation of C270 mutation using multiscale computational approaches

Papain-like protease (PL^pro) is a promising therapeutic target against SARS-CoV-2, but its restricted S1/S2 subsites pose an obstacle in developing active site-directed inhibitors. We have recently identified C270 as a novel covalent allosteric site for SARS-CoV-2 PL^pro inhibitors. Here we present a theoretical investigation of the proteolysis reaction catalyzed by the wild-type SARS-CoV-2 PL^pro as well as the C270R mutant. Enhanced sampling MD simulations were first performed to explore the influence of C270R mutation on the protease dynamics, and sampled thermodynamically favorable conformations were then submitted to MM/PBSA and QM/MM MD simulations for thorough characterization of the protease-substrate binding and covalent reactions. The disclosed proteolysis mechanism of PL^pro, as characterized by the occurrence of proton transfer from the catalytic C111 to H272 prior to the substrate binding and with deacylation being the rate-determining step of the whole proteolysis process, is not completely identical to that of the 3C-like protease, another key cysteine protease of coronaviruses. The C270R mutation alters the structural dynamics of the BL2 loop that indirectly impairs the catalytic function of H272 and reduces the binding of the substrate with the protease, ultimately showing an inhibitory effect on PL^pro. Together, these results provide a comprehensive understanding at the atomic level of the key aspects of SARS-CoV-2 PL^pro proteolysis, including the catalytic activity allosterically regulated by C270 modification, which is crucial to the follow-up inhibitor design and development.

Estimating the binding energetics of reversible covalent inhibitors of the SARS-CoV-2 main protease: an in silico study

The main protease (M^pro) of the SARS-CoV-2 virus is an attractive therapeutic target for developing antivirals to combat COVID-19. M^pro is essential for the replication cycle of the SARS-CoV-2 virus, so inhibiting M^pro blocks a vital piece of the cell replication machinery of the virus. A promising strategy to disrupt the viral replication cycle is to design inhibitors that bind to the active site cysteine (Cys145) of the M^pro. Cysteine targeted covalent inhibitors are gaining traction in drug discovery owing to the benefits of improved potency and extended drug-target engagement. An interesting aspect of these inhibitors is that they can be chemically tuned to form a covalent, but reversible bond, with their targets of interest. Several small-molecule cysteine-targeting covalent inhibitors of the M^pro have been discovered-some of which are currently undergoing evaluation in early phase human clinical trials. Understanding the binding energetics of these inhibitors could provide new insights to facilitate the design of potential drug candidates against COVID-19. Motivated by this, we employed rigorous absolute binding free energy calculations and hybrid quantum mechanical/molecular mechanical (QM/MM) calculations to estimate the energetics of binding of some promising reversible covalent inhibitors of the M^pro. We find that the inclusion of enhanced sampling techniques such as replica-exchange algorithm in binding free energy calculations can improve the convergence of predicted non-covalent binding free energy estimates of inhibitors binding to the M^pro target. In addition, our results indicate that binding free energy calculations coupled with multiscale simulations can be a useful approach to employ in ranking covalent inhibitors to their targets. This approach may be valuable in prioritizing and refining covalent inhibitor compounds for lead discovery efforts against COVID-19 and other coronavirus infections.

Hit Expansion of a Noncovalent SARS-CoV-2 Main Protease Inhibitor

Inhibition of the SARS-CoV-2 main protease (M^pro) is a major focus of drug discovery efforts against COVID-19. Here we report a hit expansion of non-covalent inhibitors of M^pro. Starting from a recently discovered scaffold (The COVID Moonshot Consortium. Open Science Discovery of Oral Non-Covalent SARS-CoV-2 Main Protease Inhibitor Therapeutics. bioRxiv 2020.10.29.339317) represented by an isoquinoline series, we searched a database of over a billion compounds using a cheminformatics molecular fingerprinting approach. We identified and tested 48 compounds in enzyme inhibition assays, of which 21 exhibited inhibitory activity above 50% at 20 μM. Among these, four compounds with IC₅₀ values around 1 μM were found. Interestingly, despite the large search space, the isoquinolone motif was conserved in each of these four strongest binders. Room-temperature X-ray structures of co-crystallized protein–inhibitor complexes were determined up to 1.9 Å resolution for two of these compounds as well as one of the stronger inhibitors in the original isoquinoline series, revealing essential interactions with the binding site and water molecules. Molecular dynamics simulations and quantum chemical calculations further elucidate the binding interactions as well as electrostatic effects on ligand binding. The results help explain the strength of this new non-covalent scaffold for M^pro inhibition and inform lead optimization efforts for this series, while demonstrating the effectiveness of a high-throughput computational approach to expanding a pharmacophore library.

Insights into the binding and covalent inhibition mechanism of PF-07321332 to SARS-CoV-2 Mpro

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been causing the COVID-19 pandemic, resulting in several million deaths being reported. Numerous investigations have been carried out to discover a compound that can inhibit the biological activity of the SARS-CoV-2 main protease, which is an enzyme related to the viral replication. Among these, PF-07321332 (Nirmatrelvir) is currently under clinical trials for COVID-19 therapy. Therefore, in this work, atomistic and electronic simulations were performed to unravel the binding and covalent inhibition mechanism of the compound to Mpro. Initially, 5 μs of steered-molecular dynamics simulations were carried out to evaluate the ligand-binding process to SARS-CoV-2 Mpro. The successfully generated bound state between the two molecules showed the important role of the PF-07321332 pyrrolidinyl group and the residues Glu166 and Gln189 in the ligand-binding process. Moreover, from the MD-refined structure, quantum mechanics/molecular mechanics (QM/MM) calculations were carried out to unravel the reaction mechanism for the formation of the thioimidate product from SARS-CoV-2 Mpro and the PF-07321332 inhibitor. We found that the catalytic triad Cys145-His41-Asp187 of SARS-CoV-2 Mpro plays an important role in the activation of the PF-07321332 covalent inhibitor, which renders the deprotonation of Cys145 and, thus, facilitates further reaction. Our results are definitely beneficial for a better understanding of the inhibition mechanism and designing new effective inhibitors for SARS-CoV-2 Mpro.

Characterization of the non-covalent interaction between the PF-07321332 inhibitor and the SARS-CoV-2 main protease

We have studied the non-covalent interaction between PF-07321332 and SARS-CoV-2 main protease at the atomic level using a computational approach based on extensive molecular dynamics simulations with explicit solvent. PF-07321332, whose chemical structure has been recently disclosed, is a promising oral antiviral clinical candidate with well-established anti-SARS-CoV-2 activity in vitro. The drug, currently in phase III clinical trials in combination with ritonavir, relies on the electrophilic attack of a nitrile warhead to the catalytic cysteine of the protease. Nonbonded interaction between the inhibitor and the residues of the binding pocket, as well as with water molecules on the protein surface, have been characterized using two different force fields and the two possible protonation states of the main protease catalytic dyad HIS41-CYS145. When the catalytic dyad is in the neutral state, the non-covalent binding is likely to be stronger. Molecular dynamics simulations seems to lend support for an inhibitory mechanism in two steps: a first non-covalent addition with the dyad in neutral form and then the formation of the thiolate-imidazolium ion pair and the ligand relocation for finalising the electrophilic attack.

Characterization of Phytochemicals in Ulva intestinalis L. and Their Action Against SARS-CoV-2 Spike Glycoprotein Receptor-Binding Domain

Coronavirus disease-2019 (COVID-19) has caused a severe impact on almost all aspects of human life and economic development. Numerous studies are being conducted to find novel therapeutic strategies to overcome COVID-19 pandemic in a much effective way. Ulva intestinalis L. (Ui), a marine microalga, known for its antiviral property, was considered for this study to determine the antiviral efficacy against severe acute respiratory syndrome-associated Coronavirus-2 (SARS-CoV-2). The algal sample was dried and subjected to ethanolic extraction, followed by purification and analysis using gas chromatography-coupled mass spectrometry (GC-MS). Forty-three known compounds were identified and docked against the S1 receptor binding domain (RBD) of the spike (S) glycoprotein. The compounds that exhibited high binding affinity to the RBD of S1 protein were further analyzed for their chemical behaviour using conceptual density-functional theory (C-DFT). Finally, pharmacokinetic properties and drug-likeliness studies were carried out to test if the compounds qualified as potential leads. The results indicated that mainly phenols, polyenes, phytosteroids, and aliphatic compounds from the extract, such as 2,4-di-tert-butylphenol (2,4-DtBP), doconexent, 4,8,13-duvatriene-1,3-diol (DTD), retinoyl-β-glucuronide 6',3'-lactone (RBGUL), and retinal, showed better binding affinity to the target. Pharmacokinetic validation narrowed the list to 2,4-DtBP, retinal and RBGUL as the possible antiviral candidates that could inhibit the viral spike protein effectively.

The Se-S Bond Formation in the Covalent Inhibition Mechanism of SARS-CoV-2 Main Protease by Ebselen-like Inhibitors: A Computational Study

The inhibition mechanism of the main protease (Mpro) of SARS-CoV-2 by ebselen (EBS) and its analog with a hydroxyl group at position 2 of the benzisoselenazol-3(2H)-one ring (EBS-OH) was studied by using a density functional level of theory. Preliminary molecular dynamics simulations on the apo form of Mpro were performed taking into account both the hydrogen donor and acceptor natures of the Nδ and Nε of His41, a member of the catalytic dyad. The potential energy surfaces for the formation of the Se-S covalent bond mediated by EBS and EBS-OH on Mpro are discussed in detail. The EBS-OH shows a distinctive behavior with respect to EBS in the formation of the noncovalent complex. Due to the presence of canonical H-bonds and noncanonical ones involving less electronegative atoms, such as sulfur and selenium, the influence on the energy barriers and reaction energy of the Minnesota hybrid meta-GGA functionals M06, M06-2X and M08HX, and the more recent range-separated hybrid functional wB97X were also considered. The knowledge of the inhibition mechanism of Mpro by the small protease inhibitors EBS or EBS-OH can enlarge the possibilities for designing more potent and selective inhibitor-based drugs to be used in combination with other antiviral therapies.

A computational study of cooperative binding to multiple SARS-CoV-2 proteins

Structure-based drug design targeting the SARS-CoV-2 virus has been greatly facilitated by available virus-related protein structures. However, there is an urgent need for effective, safe small-molecule drugs to control the spread of the virus and variants. While many efforts are devoted to searching for compounds that selectively target individual proteins, we investigated the potential interactions between eight proteins related to SARS-CoV-2 and more than 600 compounds from a traditional Chinese medicine which has proven effective at treating the viral infection. Our original ensemble docking and cooperative docking approaches, followed by a total of over 16-micorsecond molecular simulations, have identified at least 9 compounds that may generally bind to key SARS-CoV-2 proteins. Further, we found evidence that some of these compounds can simultaneously bind to the same target, potentially leading to cooperative inhibition to SARS-CoV-2 proteins like the Spike protein and the RNA-dependent RNA polymerase. These results not only present a useful computational methodology to systematically assess the anti-viral potential of small molecules, but also point out a new avenue to seek cooperative compounds toward cocktail therapeutics to target more SARS-CoV-2-related proteins.

Dinitrosyl iron complexes (DNICs) as inhibitors of the SARS-CoV-2 main protease

By repurposing DNICs designed for other medicinal purposes, the possibility of protease inhibition was investigated in silico using AutoDock 4.2.6 (AD4) and in vitro via a FRET protease assay. AD4 was validated as a predictive computational tool for coordinatively unsaturated DNIC binding using the only known crystal structure of a protein-bound DNIC, PDB- (calculation RMSD = 1.77). From the in silico data the dimeric DNICs TGTA-RRE, [(μ-S-TGTA)Fe(NO)₂]₂ (TGTA = 1-thio-β-d-glucose tetraacetate) and TG-RRE, [(μ-S-TG)Fe(NO)₂]₂ (TG = 1-thio-β-d-glucose) were identified as promising leads for inhibition via coordinative inhibition at Cys-145 of the SARS-CoV-2 Main Protease (SC2M^pro). In vitro studies indicate inhibition of protease activity upon DNIC treatment, with an IC₅₀ of 38 ± 2 μM for TGTA-RRE and 33 ± 2 μM for TG-RRE. This study presents a simple computational method for predicting DNIC-protein interactions; the in vitro study is consistent with in silico leads.

Olive-Derived Triterpenes Suppress SARS COV-2 Main Protease: A Promising Scaffold for Future Therapeutics

SARS CoV-2 pandemic is still considered a global health disaster, and newly emerged variants keep growing. A number of promising vaccines have been recently developed as a protective measure; however, cost-effective treatments are also of great importance to support this critical situation. Previously, betulinic acid has shown promising antiviral activity against SARS CoV via targeting its main protease. Herein, we investigated the inhibitory potential of this compound together with three other triterpene congeners (i.e., ursolic acid, maslinic acid, and betulin) derived from olive leaves against the viral main protease (Mpro) of the currently widespread SARS CoV-2. Interestingly, betulinic, ursolic, and maslinic acids showed significant inhibitory activity (IC50 = 3.22-14.55 µM), while betulin was far less active (IC50 = 89.67 µM). A comprehensive in-silico analysis (i.e., ensemble docking, molecular dynamic simulation, and binding-free energy calculation) was then performed to describe the binding mode of these compounds with the enzyme catalytic active site and determine the main essential structural features required for their inhibitory activity. Results presented in this communication indicated that this class of compounds could be considered as a promising lead scaffold for developing cost-effective anti-SARS CoV-2 therapeutics.