Main Protease Inhibitors Research Articles

Pyrrolidines as Main Protease Inhibitors for Treating Viral Infections, in Particular, Coronavirus Infections

Pyrrolidines as Main Protease Inhibitors for Treating Viral Infections, in Particular, Coronavirus Infections

Fragment-based Drug Discovery Strategy and its Application to the Design of SARS-CoV-2 Main Protease Inhibitor.

Severe Acute Respiratory Syndrome Coronavirus Type 2 (SARS-CoV-2) emerged at the end of 2019, causing a highly infectious and pathogenic disease known as 2019 coronavirus disease. This disease poses a serious threat to human health and public safety. The SARS-CoV-2 main protease (Mpro) is a highly sought-after target for developing drugs against COVID-19 due to its exceptional specificity. Its crystal structure has been extensively documented. Numerous strategies have been employed in the investigation of Mpro inhibitors. This paper is primarily concerned with Fragment-based Drug Discovery (FBDD), which has emerged as an effective approach to drug design in recent times. Here, we summarize the research on the approach of FBDD and its application in developing inhibitors for SARS-CoV-2 Mpro.

Identification of catechin as main protease inhibitor of SARS-CoV-2 Omicron variant using molecular docking, molecular dynamics, PCA, DCCM, MM/GBSA and ADMET profiling

The Omicron variant of SARS-CoV-2 spreads more rapidly than other variants and can affect even vaccinated individuals. The Omicron variant main protease (Mpro), crucial for viral replication and transcription, is an attractive target for antiviral drug discovery. This research aims to investigate non-toxic flavonoids that follow Lipinski’s rule of five (RO5) and inhibit the Omicron variant Mpro. Molecular docking was performed on 35 flavonoids screened by analysing their medicinal values and adherence to RO5. Catechin (2-(3,4-dihydroxyphenol) chroman-3,5,7-triol), a non-toxic natural compound having predicted toxicity class 6 and LD50 value 10,000 mg/kg, exhibited a docking score of −7.1 kcal/mol with Mpro. The Mpro-catechin complex remained stable during 250 ns MD simulations. The post-MD free energy (MM/GBSA) calculations showed a binding energy of −20.5 kcal/mol, indicating strong interactions with the active amino acid residues. These findings suggest that catechin is a promising drug candidate against the Omicron variant.

Inhibitory Effects of Mangifera indica Secondary Metabolites and Their Synthetic Derivatives against SARS-CoV-2 Mpro and NS2B/NS3 (ZIKV and DENV-2).

Chemical studies of Mangifera indica twigs yielded two compounds, identified as taraxerol (1) and methyl gallate (2). The galloyl moiety was suggested as a potential scaffold that can interfere with proteases by previous biological investigations on SARS-CoV-2 main protease (Mpro) inhibitors in combination with docking studies. Therefore, a series of 13 gallate esters were prepared by treating gallic acid with natural and non-natural alcohols. Their inhibitory effects were evaluated against Mpro and NS2B/NS3 of Zika and Dengue viruses. Among the obtained compounds, 2e and 2i were the most potent against Mpro with IC50 values of 2.60 and 4.0 μM, respectively. Compounds 2f and 2g were more potent than others against ZIKV protease with IC50 values of 2.7 and 1.9 μM, respectively. The bioactivity profile against DENV NS2B/NS3 was different with 2e and 2f showing moderate inhibition with IC50 values of 66.0 and 59.29 μM, respectively. It was found that 2f and 2g inhibited ZIKV NS2B/NS3 via a noncompetitive mechanism. The study also showed that 2e and 2f could exert noncompetitive inhibition at the previously described allosteric pocket of flaviviral NS2B/NS3 proteases. Molecular docking revealed different types of interactions among the most prominent were hydrogen bonding with the galloyl moiety.

Design, Synthesis, Biological Evaluation and Molecular Docking Studies of New Thiazolidinone Derivatives as NNRTIs and SARS-CoV-2 Main Protease Inhibitors.

HIV-1 remains a major health problem worldwide since the virus has developed drug-resistant strains, so, the need for novel agents is urgent. The protein reverse transcriptase plays fundamental role in the viruses' replication cycle. FDA approved Delavirdine bearing a sulfonamide moiety, while thiazolidinone has demonstrated significant anti-HIV activity as a core heterocycle or derivative of substituted heterocycles. In this study, thirty new thiazolidinone derivatives (series A, B and C) bearing sulfonamide group were designed, synthesized and evaluated for their HIV-1 RT inhibition activity predicted by computer program PASS taking into account the best features of available NNRTIs as well as against SARS-COV-2 main protease. Seven compounds showed good anti-HIV inhibitory activity, with two of them, C1 and C2 being better (IC50 0.18 μΜ & 0.12 μΜ respectively) than the reference drug nevirapine (IC50 0.31 μΜ). The evaluation of molecules to inhibit the main protease revealed that 6 of the synthesized compounds exhibited excellent to moderate activity with two of them (B4 and B10) having better IC50 values (0.15 & 0.19 μΜ respectively) than the reference inhibitor GC376 (IC50 0.439 μΜ). The docking studies is coincides with experimental results, showing good binding mode to both enzymes.

A computational biology approach for the identification of potential SARS-CoV-2 main protease inhibitors from natural essential oil compounds.

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has fomented a climate of fear worldwide due to its rapidly spreading nature, and high mortality rate. The World Health Organization (WHO) declared it as a global pandemic on 11th March, 2020. Many endeavors have been made to find appropriate medications to restrain the SARS CoV-2 infection from spreading but there is no specific antiviral therapy to date. However, a computer-aided drug design approach can be an alternative to identify probable drug candidates within a short time. SARS-CoV-2 main protease is a proven drug target, and it plays a pivotal role in viral replication and transcription. Methods: In this study, we identified a total of 114 essential oil compounds as a feasible anti-SARS-CoV-2 agent from several online reservoirs. These compounds were screened by incorporating ADMET profiling, molecular docking, and 50 ns of molecular dynamics simulation to identify potential drug candidates against the SARS-CoV-2 main protease. The crystallized SARS-CoV-2 main protease structure was collected from the RCSB PDB database (PDB ID 6LU7). Results: According to the results of the ADMET study, none of the compounds have any side effects that could reduce their druglikeness or pharmacokinetic properties. Out of 114 compounds, we selected bisabololoxide B, eremanthin, and leptospermone as our top drug candidates based on their higher binding affinity scores, and strong interaction with the Cys 145-His 41 catalytic dyad. Finally, the molecular dynamics simulation was implemented to evaluate the structural stability of the ligand-receptor complex. MD simulations disclosed that all the hits showed conformational stability compared to the positive control α-ketoamide. Conclusions: Our study showed that the top three hits might work as potential anti-SARS-CoV-2 agents, which can pave the way for discovering new drugs, but for experimental validation, they will require more in vivo trials.

Flavonoids as potential SARS-CoV-2 main protease inhibitors: In vitro activity evaluation, molecular docking, 3D-QSAR investigation and synthesis

The damage to public health posed by the COVID-19 epidemic remains non-negligible, and research into highly effective antiviral drugs is key to addressing the epidemic. The main protease (Mpro) is critical for SARS-CoV-2 replication and acts as an effective target for drug development. To date, many flavonoid compounds have been reported to exhibit inhibition of Mpro, and flavonoid structures are informative for the development of new inhibitors. In the present study, we first evaluated the ability of 35 flavonoid compounds to bind Mpro and found that the hydrophobic interaction generated between the benzene ring and the residues may be the main source of binding force. The in vitro inhibitory activity of these compounds was tested by the FRET method, and most of them showed significant inhibition of Mpro. Preliminary analysis revealed that the presence of the glycosidic group was detrimental to the activity of the compounds, in addition the position of the hydroxyl substituent had an effect on the activity of the compounds. Reliable and predictive CoMFA (q2 = 0.541, r2 = 0.998, SEE = 0.039) and CoMISA (q2 = 0.554, r2 = 0.999, SEE = 0.034) models were developed, and the compounds were analyzed by 3D-QSAR with modeled steric, electrostatic, hydrogen bond donor, and hydrophobic fields. A series of compounds were synthesized and characterized, which showed similar experimental and predicted activities, with the activity of 15d (IC50 = 0.74 ± 0.04 uM) exceeding that of the template molecule 15 (0.98 ± 0.13 uM). Subsequently, molecular docking revealed the binding mode of 15d to Mpro and verified the predictions of steric, hydrogen bond donor, and hydrophobic field. In conclusion, these findings provide ideas for subsequent structural studies of flavonoids that could be used in the development of flavonoid-type SARS-CoV-2 Mpro inhibitors.

Identification of Potent, Broad-Spectrum Coronavirus Main Protease Inhibitors for Pandemic Preparedness.

The COVID-19 pandemic highlights the ongoing risk of zoonotic transmission of coronaviruses to global health. To prepare for future pandemics, it is essential to develop effective antivirals targeting a broad range of coronaviruses. Targeting the essential and clinically validated coronavirus main protease (Mpro), we constructed a structurally diverse Mpro panel by clustering all known coronavirus sequences by Mpro active site sequence similarity. Through screening, we identified a potent covalent inhibitor that engaged the catalytic cysteine of SARS-CoV-2 Mpro and used structure-based medicinal chemistry to develop compounds in the pyrazolopyrimidine sulfone series that exhibit submicromolar activity against multiple Mpro homologues. Additionally, we solved the first X-ray cocrystal structure of Mpro from the human-infecting OC43 coronavirus, providing insights into potency differences among compound-target pairs. Overall, the chemical compounds described in this study serve as starting points for the development of antivirals with broad-spectrum activity, enhancing our preparedness for emerging human-infecting coronaviruses.

Evaluation of inhibition effect and interaction mechanism of antiviral drugs on main protease of novel coronavirus: Molecular docking and molecular dynamics studies

The outbreak of pneumonia caused by the novel coronavirus (SARS-CoV-2) has presented a challenge to public health. The identification and development of effective antiviral drugs is essential. The main protease (3CLpro) plays an important role in the viral replication of SARS-CoV-2 and is considered to be an effective therapeutic target. In this study, according to the principle of drug repurposing, a variety of antiviral drugs commonly used were studied by molecular docking and molecular dynamics (MD) simulations to obtain potential inhibitors of main proteases. 24 antiviral drugs were docked with 5 potential action sites of 3CLpro, and the drugs with high binding strength were further simulated by MD and the molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) binding free energy calculations. The results showed that the drugs with high flexibility could bind to 3CLpro better than those with low flexibility. The interaction mechanism between antiviral drugs and main protease was analyzed in detail by calculating the root mean square displacement (RMSD), root mean square fluctuation (RMSF) and interaction residues properties. The results showed that the six drugs with high flexibility (Remdesivir, Simnotrelvir, Sofosbuvir, Ledipasvir, Indinavir and Raltegravir) had strong binding strength with 3CLpro, and the last four antiviral drugs can be used as potential candidates for main protease inhibitors.

Design and synthesis of novel main protease inhibitors of COVID-19: quinoxalino[2,1-b]quinazolin-12-ones.

The COVID-19 pandemic represents a substantial global challenge, being a significant cause of mortality in numerous countries. Thus, it is imperative to conduct research to develop effective therapies to combat COVID-19. The primary aim of this study is to employ a two-step tandem reaction involving 2,3-dichloroquinoxaline and 2-amino-N-substituted benzamides in alkaline media/DMF at an elevated temperature to design and synthesize a series of polycyclic derivatives endowed with quinoxalino[2,1-b]quinazolin-12-one framework. Following synthesis, the newly synthesized heterocycles were evaluated for their potential as inhibitors of the main protease of SARS-CoV-2 by means of molecular docking and dynamic simulation techniques. The in silico investigation demonstrated that all tested compounds effectively establish stable binding interactions, primarily through multiple hydrogen bonding and hydrophobic interactions, at the active site of the enzyme. These findings offer crucial structural insights that can be employed in future endeavors toward designing potent inhibitors targeting the main protease (Mpro). Among the investigated compounds, the p-tolylamino-substituted quinoxalino[2,1-b]quinazolinone derivative exhibited the most promise as an inhibitor of the main protease in COVID-19. Consequently, it warrants further investigation both in vitro and in vivo to identify it as a prospective candidate for anti-SARS-CoV-2 drug development.

Design of novel and highly selective SARS-CoV-2 main protease inhibitors.

We have synthesized a novel and highly selective severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease peptide mimetic inhibitor mimicking the replicase 1ab recognition sequence -Val-Leu-Gln- and utilizing a cysteine selective acyloxymethyl ketone as the electrophilic warhead to target the active site Cys145. Utilizing a constrained cyclic peptide that locks the conformation between the P3 (Val) and P2 (Leu) residues, we identified a highly selective inhibitor that fills the P2 pocket occupied by the leucine residue sidechain of PF-00835231 and the dimethyl-3-azabicyclo-hexane motif in nirmatrelvir (PF-07321332). This strategy resulted in potent and highly selective Mpro inhibitors without inhibiting essential host cathepsin cysteine or serine proteases. The lead prototype compound 1 (MPro IC50 = 230 ± 18 nM) also inhibits the replication of multiple SARS-CoV-2 variants in vitro, including SARS-CoV-2 variants of concern, and can synergize at lower concentrations with the viral RNA polymerase inhibitor, remdesivir, to inhibit replication. It also reduces SARS-CoV-2 replication in SARS-CoV-2 Omicron-infected Syrian golden hamsters without obvious toxicities, demonstrating in vivo efficacy. This novel lead structure provides the basis for optimization of improved agents targeting evolving SARS-CoV-2 drug resistance that can selectively act on Mpro versus host proteases and are less likely to have off-target effects due to non-specific targeting. Developing inhibitors against the active site of the main protease (Mpro), which is highly conserved across coronaviruses, is expected to impart a higher genetic barrier to evolving SARS-CoV-2 drug resistance. Drugs that selectively inhibit the viral Mpro are less likely to have off-target effects warranting efforts to improve this therapy.

Model informed dose regimen optimizing in development of leritrelvir for the treatment of mild or moderate COVID-19.

Leritrelvir (RAY1216) acts as a main protease inhibitor that hinders the cleavage of viral precursor proteins, thereby inhibiting virus replication of SARS-CoV-2). This antiviral mechanism has shown significant efficacy against the novel coronavirus. Preclinical studies have demonstrated the potent antiviral activity and favorable safety profile of this compound. This study aims to develop a pharmacokinetic model for leritrelvir, with and without ritonavir as a pharmacokinetic enhancer and to evaluate the necessity of co-administration with ritonavir and to investigate different dosage regimens. The model establishment was based on plasma concentration data from a phase I trial involving 72 subjects in single-ascending dose (SAD), multiple-ascending dose (MAD), and a food effect cohort. Analysis was conducted using a nonlinear mixed-effects model, and clinical trial simulations were carried out. The findings of this study demonstrate a favorable safety profile for leritrelvir. With simulation suggests that a 400mg thrice-daily (TID) regimen may be optimal to maintain the trough concentrations (Ctrough) above levels required for inhibiiting viral replication. While ritonavir was found to enhance exposure, it was deemed unnecessary. Gender and food consumption were identified as significant covariates affecting pharmacokinetic parameters, however, no dose adjustments were deemed necessary. This findings supported by subsequent phase II and phase III trials validated the appropriateness of a 400mg TID regimen for the administration of leritrelvir.

Synthesis, Spectroscopic Characterization, DFT, Molecular Docking, Catechol Oxidase Activity, and Anti-SARS-CoV-2 of Acylhydrazone Derivatives

In the present work, five pyrazole-hydrazone biomolecule ligands (L1–L5) were synthesized by condensation between 1H-pyrazole-3-carbohydrazide (2) and aromatic benzaldehydes. Their corresponding structures were elucidated employing NMR and FT-IR spectra and ESI-MS data. Li-Cu(II) complexes (i = 1–5) were evaluated for catecholase activity in situ at standard conditions. The findings disclose that the catecholase oxidation rate varies with the substituted functional groups in ligand and the anion type in the copper (II) salt. Catecholase activity results showed that the L(i = 1–5) -Cu(II)SO4 complexes exhibited efficient catalytic activity, and a maximum activity of 105 ± 42 µM.min−1 is obtained with L5-Cu(II)SO4. DFT and NBO calculations have been carried out to identify the global reactivity and the strength of interaction bonds between the donors and acceptors in L1–L5. The optimized structure of L1–L3 and L5 were found planar, while that of L4 is out of the molecular plan and forms a torsion angle of 18 degrees due to the presence of methoxy and hydroxyl group at meta and para. In L4, the 5-methyl-1H-pyrazole moiety. NBO findings show that the strongest interactions in L1–L5 are those involved in the electronic transition from π-bonding → π*-antibonding and LP → π*- antibonding molecular orbitals. Further, the anti-SARS-CoV-2 of L1–L5 are investigated by estimating their binding affinities into its binding. The docking results reveal that L1–L5 may act as SARS-CoV-2 main protease inhibitors with estimated binding energies in the −6.00 to −8.0 kcal.mol−1 range.

Discovery of potent SARS-CoV-2 nsp3 macrodomain inhibitors uncovers lack of translation to cellular antiviral response.

A strategy for pandemic preparedness is the development of antivirals against a wide set of viral targets with complementary mechanisms of action. SARS-CoV-2 nsp3-mac1 is a viral macrodomain with ADP-ribosylhydrolase activity, which counteracts host immune response. Targeting the virus' immunomodulatory functionality offers a differentiated strategy to inhibit SARS-CoV-2 compared to approved therapeutics, which target viral replication directly. Here we report a fragment-based lead generation campaign guided by computational approaches. We discover tool compounds which inhibit nsp3-mac1 activity at low nanomolar concentrations, and with responsive structure-activity relationships, high selectivity, and drug-like properties. Using our inhibitors, we show that inhibition of nsp3-mac1 increases ADP-ribosylation, but surprisingly does not translate to demonstrable antiviral activity in cell culture and iPSC-derived pneumocyte models. Further, no synergistic activity is observed in combination with interferon gamma, a main protease inhibitor, nor a papain-like protease inhibitor. Our results question the extent to which targeting modulation of innate immunity-driven ADP-ribosylation can influence SARS-CoV-2 replication. Moreover, these findings suggest that nsp3-mac1 might not be a suitable target for antiviral therapeutics development.

An automated positive selection screen in yeast provides support for boron-containing compounds as inhibitors of SARS-CoV-2 main protease.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus continues to cause severe disease and deaths in many parts of the world, despite massive vaccination efforts. Antiviral drugs to curb an ongoing infection remain a priority. The virus-encoded 3C-like main protease (MPro; nsp5) is seen as a promising target. Here, with a positive selection genetic system engineered in Saccharomyces cerevisiae using cleavage and release of MazF toxin as an indicator, we screened in a robotized setup small molecule libraries comprising ~2,500 compounds for MPro inhibitors. We detected eight compounds as effective against MPro expressed in yeast, five of which are characterized proteasome inhibitors. Molecular docking indicates that most of these bind covalently to the MPro catalytically active cysteine. Compounds were confirmed as MPro inhibitors in an in vitro enzymatic assay. Among those were three previously only predicted in silico; the boron-containing proteasome inhibitors bortezomib, delanzomib, and ixazomib. Importantly, we establish reaction conditions in vitro preserving the MPro-inhibitory activity of the boron-containing drugs. These differ from the standard conditions, which may explain why boron compounds have gone undetected in screens based on enzymatic in vitro assays. Our screening system is robust and can find inhibitors of a specific protease that are biostable, able to penetrate a cell membrane, and are not generally toxic. As a cellular assay, it can detect inhibitors that fail in a screen based on an in vitro enzymatic assay using standardized conditions, and now give support for boron compounds as MPro inhibitors. This method can also be adapted for other viral proteases.IMPORTANCEThe coronavirus disease 2019 (COVID-19) pandemic triggered the realization that we need flexible approaches to find treatments for emerging viral threats. We implemented a genetically engineered platform in yeast to detect inhibitors of the virus's main protease (MPro), a promising target to curb severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. Screening molecule libraries, we identified candidate inhibitors and verified them in a biochemical assay. Moreover, the system detected boron-containing molecules as MPro inhibitors. Those were previously predicted computationally but never shown effective in a biochemical assay. Here, we demonstrate that they require a non-standard reaction buffer to function as MPro inhibitors. Hence, our cell-based method detects protease inhibitors missed by other approaches and provides support for the boron-containing molecules. We have thus demonstrated that our platform can screen large numbers of chemicals to find potential inhibitors of a viral protease. Importantly, the platform can be modified to detect protease targets from other emerging viruses.

The Influence of Chitosan Derivatives in Combination with Bacillus subtilis Bacteria on the Development of Systemic Resistance in Potato Plants with Viral Infection and Drought.

Viral diseases of potatoes are among the main problems causing deterioration in the quality of tubers and loss of yield. The growth and development of potato plants largely depend on soil moisture. Prevention strategies require comprehensive protection against pathogens and abiotic stresses, including modeling the beneficial microbiome of agroecosystems combining microorganisms and immunostimulants. Chitosan and its derivatives have great potential for use in agricultural engineering due to their ability to induce plant immune responses. The effect of chitosan conjugate with caffeic acid (ChCA) in combination with Bacillus subtilis 47 on the transcriptional activity of PR protein genes and changes in the proteome of potato plants during potato virus Y (PVY) infection and drought was studied. The mechanisms of increasing the resistance of potato plants to PVY and lack of moisture are associated with the activation of transcription of genes encoding PR proteins: the main protective protein (PR-1), chitinase (PR-3), thaumatin-like protein (PR-5), protease inhibitor (PR-6), peroxidase (PR-9), and ribonuclease (PR-10), as well as qualitative and quantitative changes in the plant proteome. The revealed activation of the expression of marker genes of systemic acquired resistance and induced systemic resistance under the influence of combined treatment with B. subtilis and chitosan conjugate indicate that, in potato plants, the formation of resistance to viral infection in drought conditions proceeds synergistically. By two-dimensional electrophoresis of S. tuberosum leaf proteins followed by MALDI-TOF analysis, 10 proteins were identified, the content and composition of which differed depending on the experiment variant. In infected plants treated with ChCA, the synthesis of proteinaceous RNase P 1 and oxygen-evolving enhancer protein 2 was enhanced in conditions of normal humidity, and 20 kDa chaperonin and TMV resistance protein N-like was enhanced in conditions of lack of moisture. The virus coat proteins were detected, which intensively accumulated in the leaves of plants infected with potato Y-virus. ChCA treatment reduced the content of these proteins in the leaves, and in plants treated with ChCA in combination with Bacillus subtilis, viral proteins were not detected at all, both in conditions of normal humidity and lack of moisture, which suggests the promising use of chitosan derivatives in combination with B. subtilis bacteria in the regulation of plant resistance.

Hierarchical Virtual Screening of SARS-CoV-2 Main Protease Potential Inhibitors: Similarity Search, Pharmacophore Modeling, and Molecular Docking Study

Background: The outbreak of COVID-19 caused by severe acute respiratory syndrome coronavirus2 (SARS-CoV-2) resulted in a widespread pandemic. Various approaches involved the repositioning of antiviral remedies and other medications. Several therapies, including oral antiviral treatments, represent some approaches to adapting to the long existence of the COVID-19 pandemic. In silico studies provide valuable insights throughout drug discovery and development in compliance with global efforts to overcome the pandemic. The main protease is an essential target in the viral cycle. Computer-aided drug design accelerates the identification of potential treatments, including oral therapy. Aims: This work aims to identify potential SARS-CoV-2 main protease inhibitors using different aspects of in silico approaches. Methods: In this work, we conducted a hierarchical virtual screening of SARS-CoV-2 main protease inhibitors. A similarity search was conducted to screen molecules similar to the inhibitor PF-07321332. Concurrently, structure-based pharmacophores, besides ligand-based pharmacophores, were derived. A drug-likeness filter filtered the compounds retrieved from similarity search and pharmacophore modeling before being subjected to molecular docking. The candidate molecules that showed higher affinity to the main protease than the reference inhibitor were further filtered by absorption, distribution, metabolism, and excretion (ADME) parameters. Results: According to binding affinity and ADME analysis, four molecules (CHEMBL218022, PubChem163362029, PubChem166149100, and PubChem 162396459) were prioritized as promising hits. The compounds above were not reported before; no previous experimental studies and bioactive assays are available. Conclusion: Our time-saving approach represents a strategy for discovering novel SARS-CoV- 2 main protease inhibitors. The ultimate hits may be nominated as leads in discovering novel SARS-CoV-2 main protease inhibitors.

Discovery of Natural Compounds as SARS-CoV-2’s Main Protease Inhibitors by Docking-based Virtual Screening

Introduction: The novel coronavirus disease (COVID-19) is a viral disease caused by severe acute respiratory syndrome coronavirus 2 (SAR-CoV-2). The development of antiviral drugs has enhaced treatment of COVID-19. SARS-CoV-2 main protease (Mpro) is a key enzyme responsible for viral replication and transcription. This study aimed to identify new natural structures for the design of SARS-CoV-2 Mpro inhibitors. Methods: In this present work, The CDOCKER protocol and scoring functions were validated. The validated docking-based virtual screening approach was then employed to search the in-house database of natural compounds for potential lead compounds as SARS-CoV-2 Mpro inhibitors. The top 3 compounds were further biologically evaluated in vitro. Results and Discussion: Docking studies of the known ligand GC-376 led to results consistent with cocrystallized data (PDB ID: 7D1M). Additionally, the effectiveness of docking scoring functions was validated by using the training set consisting of 15 active compounds and 15 inactive compounds. Then, the in-house database of natural compounds (overall 34,439 natural compounds) was subjected to dockingbased virtual screening resulting in the identification of the top 100 compounds having relatively better docking scores. Among them, the highest ranking 3 compounds (W-1, W-2, and W-3) were biologically evaluated in vitro for their inhibitory activity against SARS-CoV-2 Mpro, and compound W-1 was identified as the most potent SARS-CoV-2 Mpro inhibitor with an IC50 value of 63 ± 3 μM. Interestingly, it appeared that the in vitro activities of compounds W-1, W-2, and W-3 were in agreement with their molecular modeling data. Conclusion: Our results provided a useful reference for the discovery of novel natural SARS-CoV-2 Mpro inhibitors by virtual screening.

Ensemble docking based virtual screening of SARS-CoV-2 main protease inhibitors.

During the first years of COVID-19 pandemic, X-ray structures of the coronavirus drug targets were acquired at an unprecedented rate, giving hundreds of PDB depositions in less than a year. The main protease (Mpro) of severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) is the primary validated target of direct-acting antivirals. The selection of the optimal ensemble of structures of Mpro for the docking-driven virtual screening campaign was thus non-trivial and required a systematic and automated approach. Here we report a semi-automated active site RMSD based procedure of ensemble selection from the SARS-CoV-2 Mpro crystallographic data and virtual screening of its inhibitors. The procedure was compared with other approaches to ensemble selection and validated with the help of hand-picked and peer-reviewed activity-annotated libraries. Prospective virtual screening of non-covalent Mpro inhibitors resulted in a new chemotype of thienopyrimidinone derivatives with experimentally confirmed enzyme inhibition.

De novo design of SARS-CoV-2 main protease inhibitors with characteristic binding modes

The coronavirus disease 2019 (COVID-19) is caused by a novel coronavirus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which spreads rapidly all over the world. The main protease (Mpro) is significant to the replication and transcription of viruses, making it an attractive drug target against coronaviruses. Here, we introduce a series of novel inhibitors which are designed de novo through structure-based drug design approach that have great potential to inhibit SARS-CoV-2 Mproinvitro. High-resolution structures show that these inhibitors form covalent bonds with the catalytic cysteine through the novel dibromomethyl ketone (DBMK) as a reactive warhead. At the same time, the designed phenyl group beside the DBMK warhead inserts into the cleft between H41 and C145 through π-π stacking interaction, splitting the catalytic dyad and disrupting proton transfer. This unique binding model provides novel clues for the cysteine protease inhibitor development of SARS-CoV-2 as well as other pathogens.