Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors

Exploring covalent inhibitors of SARS-CoV-2 main protease: from peptidomimetics to novel scaffolds

Peptidomimetic inhibitors mimic natural peptide substrates, employing electrophilic warheads to covalently interact with the catalytic Cys145 of Mpro. Examples include aldehydes, α-ketoamides, and aza-peptides, with discussions on their mechanisms of action, potency, and structural insights. Non-peptidomimetic inhibitors utilise diverse scaffolds and mechanisms, achieving covalent modification of Mpro.

A deep learning model for structure-based bioactivity optimization and its application in the bioactivity optimization of a SARS-CoV-2 main protease inhibitor

Bioactivity optimization is a crucial and technical task in the early stages of drug discovery, traditionally carried out through iterative substituent optimization, a process that is often both time-consuming and expensive. To address this challenge, we present Pocket-StrMod, a deep-learning model tailored for structure-based bioactivity optimization. Pocket-StrMod employs an autoregressive flow-based architecture, optimizing molecules within a specific protein binding pocket while explicitly incorporating chemical expertise. It synchronously optimizes all substituents by generating atoms and covalent bonds at designated sites within a molecular scaffold nestled inside a protein pocket. We applied this model to optimize the bioactivity of Hit1, an inhibitor of the SARS-CoV-2 main protease (Mpro) with initially poor bioactivity (IC50 : 34.56 μM). Following two rounds of optimization, six compounds were selected for synthesis and bioactivity testing. This led to the discovery of C5, a potent compound with an IC50 value of 33.6 nM, marking a remarkable 1028-fold improvement over Hit1. Furthermore, C5 demonstrated promising in vitro antiviral activity against SARS-CoV-2. Collectively, these findings underscore the great potential of deep learning in facilitating rapid and cost-effective bioactivity optimization in the early phases of drug development.

Expanding the utilization of binding pockets proves to be effective for noncovalent small molecule inhibitors against SARS-CoV-2 Mpro

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in millions of deaths and continues to pose serious threats to global public health. The main protease (Mpro) of SARS-CoV-2 is crucial for viral replication and its conservation, making it an attractive drug target. Here, we employed a structure-based drug design strategy to develop and optimize novel inhibitors targeting SARS-CoV-2 Mpro. By fully exploring occupation of the S1, S2, and S3/S4 binding pockets, we identified eight promising inhibitors with half-maximal inhibitory concentration (IC50) values below 20 nM. The cocrystal structure of Mpro with compound 10 highlighted the crucial roles of the interactions within the S3/S4 pockets in inhibitor potency enhancement. These findings demonstrated that expanding the utilization of these binding pockets was an effective strategy for developing noncovalent small molecule inhibitors that target SARS-CoV-2 Mpro. Compound 4 demonstrated outstanding in vitro antiviral activity against wild-type SARS-CoV-2 with an EC50 of 9.4 nM. Moreover, oral treatment with compounds 1 and 9 exhibited excellent antiviral potency and substantially ameliorated virus-induced tissue damage in the lungs of Omicron BA.5-infected K18-human ACE2 (K18-hACE2) transgenic mice, indicating that these novel noncovalent inhibitors could be potential oral agents for the treatment of COVID-19.

The efficiency of high-throughput screening (HTS) and in-silico data analysis during medical emergencies: Identification of effective antiviral 3CLpro inhibitors

The COVID-19 pandemic highlighted the importance of accelerating the drug discovery process. The 3-chymotrypsin-like protease (3CLpro) is a critical enzyme in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral replication process and was quickly identified as a prime target for drug development. This study leverages High-Throughput Screening (HTS) to identify novel 3CLpro inhibitors. We screened a different library of 325,000 compounds, leading to the discovery of two new chemical scaffolds with selective inhibitory activity against 3CLpro. In-silico analysis and further experimental validation, elucidated the binding modes and mechanisms of action, revealing a covalent inhibitor targeting the catalytic pocket and two allosteric inhibitors affecting the monomer/dimer equilibrium of 3CLpro. The identified compounds demonstrated significant antiviral activity in vitro, reducing SARS-CoV-2 replication in VeroE6 and Calu-3 cell lines. This study highlights the potential of combining HTS and computational approaches to accelerate the discovery of effective antiviral agents, suggesting a workflow to support the research and the design of effective therapeutic strategies.

Chondroitin sulfate binds to main protease of SARS-CoV-2 and efficaciously inhibits its activity

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is constantly mutating and spreading globally, posing a great threat to people's lives and health. The main protease of SARS-CoV-2 (Mpro, also called 3CLpro) is an attractive drug target for SARS-CoV-2, due to its crucial role in processing the viral replication. Here, we showed that chondroitin sulfate (CS) from pig, cattle and shark efficaciously inhibits Mpro activity of SARS-CoV-2 with half maximal inhibitory concentrations (IC50) of 0.148, 0.121 and 0.119 μM, respectively, through a fluorescence resonance energy transfer (FRET) assay. The inhibition pattern of CSs against Mpro activity is competitive inhibition, with inhibition constants (Ki) of CSs derived from pig, bovine and shark are 0.111, 0.096, and 0.107 μM, respectively, indicating significant inhibitory effects of CSs on Mpro activity. Protein fluorescence quenching demonstrated that porcine, bovine and shark CSs strongly bind to Mpro protein with dissociation constants (KD) of 28.31, 28.47 and 20.66 μM at 25 °C at a physiological condition, respectively, mainly through van der Waals and hydrogen bond interactions. Molecular docking and dynamics analysis provides an insight into structural information of the binding of the CSs with Mpro protein. Our findings suggested that CSs from different origins might be a promising food ingredient for the prevention of the SARS-CoV-2 infection.

Peptides designed based on 3C substrates exhibit antiviral efficacy in vivo

Enteroviruses are a large group of positive-sense single-stranded RNA viruses including numerous human pathogens such as enterovirus A71 (EV-A71), coxsackieviruses, and echoviruses. The diseases caused by these enteroviruses pose a significant threat to global public health. The 3C protein is a crucial protease in enteroviruses, responsible for cleaving the viral polyprotein into individual active proteins. This process is essential for viral replication and pathogenesis, making 3C an attractive target for the development of anti-enteroviral drugs. In this study, we designed and screened peptides based on the sequences of several substrates of the 3C protease, aiming to impact the function of the 3C protease and thereby exert antiviral effects. Ultimately, we obtained a peptide with good antiviral activity at the cellular level, which we named vp23. This peptide effectively disrupted the protease activity of 3C, provided significant in vivo protection against EV-A71, and possessed strong antiviral effects against multiple enteroviruses such as EV-A71, Coxsackievirus A16 (CV-A16), and Echovirus 11 (Echo 11). Taken together, our results suggest that targeting 3C proteases using rationally designed peptides is an effective antiviral strategy against enteroviruses.

Identification of potential SARS-CoV-2 inhibitors among well-tolerated drugs using drug repurposing and in vitro approaches

The 3C-like protease (3CLpro) is essential in the SARS-CoV-2 life cycle and a promising target for antiviral drug discovery, as no similar proteases exist in humans. This study aimed to identify effective SARS-CoV-2 inhibitors among FDA-approved drugs. Previous computational analysis revealed several drugs with high binding affinity to the 3CLpro active site. In vitro enzymatic assays confirmed that ten of these drugs effectively inhibited the enzyme. To evaluate their impact on viral replication, we used non-infectious SARS-CoV-2 sub-genomic replicons in lung and intestinal cells. Amcinonide, eltrombopag, lumacaftor, candesartan, and nelfinavir inhibited replication at low micromolar concentrations. Lumacaftor showed IC50 values of 964 nM in Caco-2 cells and 458 nM in Calu-3 cells, while candesartan had IC50 values of 714 nM and 1.05 µM, respectively. Furthermore, dual combination experiments revealed that amcinonide, pimozide, lumacaftor, and eltrombopag acted as potent inhibitors at nanomolar concentrations when combined with candesartan. This study highlights lumacaftor, candesartan, and nelfinavir as effective inhibitors of SARS-CoV-2 replication in vitro and emphasizes their potential for repurposing as antiviral treatments. These findings support future clinical trials and may lead to breakthroughs in COVID-19 treatment strategies.

Development of Peptidomimetic PROTACs as Potential Degraders of 3-Chymotrypsin-like Protease of SARS-CoV-2

3CL protease (3CLpro), a key enzyme of SARS-CoV-2 replication, is one of the most selective targets of antivirals, as no homologous protease has been recognized in the human body. As proteolysis-targeting chimeras (PROTACs) are superior to traditional inhibitors, based on the reported cereblon (CRBN) ligands thalidomide and lenalidomide, 3CLpro ligands of peptidomimetic inhibitors, and suitable linkers, we aimed to develop novel PROTACs that may trigger efficient intracellular 3CLpro degradation through a balance of hydrophilicity and lipophilicity. In brief, we designed and synthesized 5 PROTAC molecules. The 3CLpro degradation efficiency of the PROTACs was assayed in stable SARS-CoV-2 3CLpro expression HEK293 cell models and evaluated by Western blot. All compounds showed prominent 3CLpro degradation activity with tolerable HEK293 cytotoxicity. The most prominent PROTAC compounds, 15 and 16, have DC50 values of approximately 1 µM, and Dmax of 89.3% and 75% respectively, indicating good potential for further application.

Discriminating High from Low Energy Conformers of Druglike Molecules: An Assessment of Machine Learning Potentials and Quantum Chemical Methods

Accurate and efficient prediction of high energy ligand conformations is important in structure-based drug discovery for the exclusion of unrealistic structures in docking-based virtual screening and de novo design approaches. In this work, we constructed a database of 140 solution conformers from 20 druglike molecules of varying size and chemical complexity, with energetics evaluated at the DLPNO-CCSD(T)/complete basis set (CBS) level. We then assessed a selection of machine learning potentials and semiempirical quantum mechanical models for their ability to predict conformational energetics. The GFN2-xTB tight binding density functional method correlates with reference conformer energies, yielding a Kendall's τ of 0.63 and mean absolute error of 2.2 kcal/mol. As putative internal energy filters for screening, we find that the GFN2-xTB, ANI-2x and MACE-OFF23(L) models perform well in identifying low energy conformer geometries, with sensitivities of 95 %, 89 % and 95 % respectively, but display a reduced ability to exclude high energy conformers, with respective specificities of 80 %, 61 % and 63 %. The GFN2-xTB method therefore exhibited the best overall performance and appears currently the most suitable of the three methods to act as an internal energy filter for integration into drug discovery workflows. Enrichment of high energy conformers in the training of machine learning potentials could improve their performance as conformational filters.

A phycobiliprotein-based reporter assay for the evaluation of SARS-CoV-2 main protease activity

SARS-CoV-2 Mpro is crucial for viral replication and transcription and is highly conserved. Therefore, it is an ideal target for developing broad-spectrum antiviral drugs. To address resistance to existing drugs caused by mutations, a simple and sensitive method for detecting the activity of Mpro is needed. Considering the excellent fluorescence properties of phycobiliproteins, this study developed a phycobiliprotein-based reporter assay to evaluate Mpro activity. An engineered lyase was generated by inserting the Mpro recognition sequence between the phycobiliprotein lyases CpcF and CpcE. To ensure that the binding of CpcE and CpcF depended on the linker, a series of truncated forms were constructed. Among them, the activity of CpcE/F-10 was significantly reduced in the presence of Mpro; however, both genetic and chemical inhibition of Mpro activity reversed these results. These data indicated that the fluorescence of phycobiliproteins was negatively correlated with Mpro activity. The reporter assay developed here will contribute to determining the impact of Mpro mutations and screening for new inhibitors.

Scutellaria barbata D. Don extracts alleviate SARS-CoV-2 induced acute lung injury by inhibiting virus replication and bi-directional immune modulation

The emergence of SARS-CoV-2 variants and drug-resistant mutants emphasizes the urgent need to develop novel antiviral agents. In the present study, we examined the therapeutic effect of the Chinese medicinal herb, Scutellaria barbata D. Don (SBD), against SARS-CoV-2 infection both in vitro and in vivo. Using a viral replicon particle (VRP)-based mouse model of SARS-CoV-2 infection, our study revealed that SBD extracts can reduce viral load in mouse lungs and alleviate the viral induced pneumonia. In vitro antiviral determination further validated the direct acting antiviral efficacy of SBD extracts against SARS-CoV-2 replication. Mechanistic studies demonstrated that SBD can act against SARS-CoV-2 replication by targeting both 3-chymotrypsin-like and papain-like cysteine proteases, via a combination of multiple active constituents. Moreover, SBD can modulate the host inflammation response in a bi-directional manner, which also contribute to the mitigation of viral induced acute lung injury. In summary, our study provides SBD as a promising therapeutic agent to combat SARS-CoV-2 infections that merit further development.

The interface hydrophilic-hydrophobic integration of fluorinated defective graphene towards biomedical applications

In biomedical fields, rational design of novel two-dimensional (2D) biomedical nanomaterials aims to precisely manipulate biomolecules, including efficient capture, structural-functional transformation, directional movement, and self-assembly. In this work, we innovatively proposed new graphene nanosheets and selected two representative proteins to explore their binding mechanisms, structural-functional transformation of proteins, and biological effects of the materials. Fluorinated defective graphene (FDG) exhibited highly efficient capture and structural-functional transformation for the receptor binding domain (RBD), and we observed its collapse phenomenon in 2D materials for the first time. For the main protease (Mpro), FDG achieved an optimal balance between efficient capture, immobilization, and structural disruption. Further studies showed that fluorination on oxygen-containing defect graphene significantly enhanced variances in water distribution, surface properties, and hydrogen bond networks on the material surface. This allowed amino acids to be confined to specific areas, achieving efficient capture and directional movement. Additionally, the adsorption behavior and interaction strength of peptides and deoxynucleotides on FDG further validated the possibility of self-assembly. In summary, we highlight FDG as an excellent biomedical material with hydrophilic-hydrophobic integration.

Antiviral potential of Melissa officinalis extracts against influenza and emerging coronaviruses

Melissa officinalis is a perennial medicinal plant traditionally used for its diverse biological activities, including antiviral properties. This study investigates the antiviral efficacy of various extracts, including water, acetone, alkaloid, non-alkaloid, ethanol, and methanol extracts, against influenza A (H1N1), SARS-CoV-2, and MERS-CoV. The water extract demonstrated significant inhibitory effects on SARS-CoV-2 (IC50 = 421.9 µg/mL) and MERS-CoV (IC50 = 222.1 µg/mL) in Vero E6 cells (an African green monkey kidney cell line), with a CC50 of 4221 µg/mL, indicating a favorable selectivity index. Additionally, it exhibited strong activity against H1N1 in Madin-Darby canine kidney cell line (MDCK cells) (IC50 = 57.30 µg/mL, CC50 = 3073 µg/mL). Among all the extracts, the methanol extract showed the highest antiviral activity. It has IC50 = 2.549 µg/ml and selectivity index (SI) = 230 against H1N1.While it showed IC50 = 10.83 µg/ml against SARS-CoV-2 and 9.82 µg/ml against MERS-CoV with SI values of 54.2 and 59.77, respectively. Molecular docking studies revealed that 5-Methyl-5 H-naphtho[2,3-c]carbazole,7 H-Dibenzo[b, g]carbazole, 7-methyl, hesperidin, luteolin-7-glucoside-3'-glucuronide, Melitric acid A, and other compounds exhibited high binding affinities to the receptor-binding domains (RBDs) of SARS-CoV-2 and MERS-CoV spike glycoproteins, suggesting their potential to interfere with viral entry. Furthermore, GC-MS-identified bioactive compounds, including docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), paromomycin, and phenolic acids, demonstrated additional antiviral potential. These results underscore the potential of M. officinalis extracts as natural antiviral agents, offering a foundation for further in vitro and in vivo validation and potential therapeutic applications against respiratory viral infections, including coronaviruses and influenza viruses.

A Reflection on the Use of Molecular Simulation to Respond to SARS-CoV-2 Pandemic Threats

Molecular simulations play important roles in understanding the lifecycle of the SARS-CoV-2 virus and contribute to the design and development of antiviral agents and diagnostic tests for COVID. Here, we discuss the insights that such simulations have provided and the challenges involved, focusing on the SARS-CoV-2 main protease (Mpro) and the spike glycoprotein. Mpro is the leading target for antivirals, while the spike glycoprotein is the target for vaccine design. Finally, we reflect on lessons from this pandemic for the simulation community. Data sharing initiatives and collaborations across the international research community contributed to advancing knowledge and should be built on to help in future pandemics and other global challenges such as antimicrobial resistance.

Development of a highly sensitive luciferase assay for intracellular evaluation of coronavirus Mpro activity

COVID-19, caused by SARS-CoV-2 virus, has emerged as a global threat to human health. The main protease (Mpro) of SARS-CoV-2 is an excellent target for the development of antiviral drugs against COVID-19, and various protease biosensors have been developed to evaluate anti-coronavirus drugs. However, the application of these protease biosensors was limited due to high background fluorescence, poor signal-to-noise ratios, and constraints in enzyme activity thresholds for accessing live viruses. In this study, we rationally designed a highly conserved Mpro cleavage site sequence among different coronaviruses (CoVs) with high proteolytic activity, and described an intracellular coronavirus Mpro proteolytic (ICMP) reporter system that takes advantage of virus-encoded Mpro expressed in infected cells to reform the NanoBiT fluorescent protein. The system can be used to visualize and identify cells infected with coronavirus, and demonstrated high compatibility with various Mpro proteins from 13 different mammalian coronaviruses (covering α, β, γ, and δ CoVs), exhibiting at least a 1,030-fold increase in luminescence. Stronger Nluc signals were detectable with CoV 229E virus infection at a MOI of 0.001. Additionally, the system proved suitable for evaluating and screening of antiviral compounds, including lufotrelvir, GC376, Nirmatrelvir, X77, MG-101, and the potential inhibitor Cynaroside. The ICMP system is not only an invaluable tool for the detection of live coronaviruses, but also for the discovery of antivirals against current and future pandemic coronaviruses.

Natural sapogenins as potential inhibitors of aquaporins for targeted cancer therapy: computational insights into binding and inhibition mechanism

Aquaporins (AQPs) are membrane proteins that facilitate the transport of water and other small molecules across biological membranes. AQPs are involved in various physiological processes and pathological conditions, including cancer, making them as potential targets for anticancer therapy. However, the development of selective and effective inhibitors of AQPs remains a challenge. In this study, we explored the possibility of using natural sapogenins, a class of plant-derived aglycones of saponins with diverse biological activities, as potential inhibitors of AQPs. We performed molecular docking, dynamics simulation and binding energy calculation to investigate the binding and inhibition mechanism of 19 sapogenins against 13 AQPs (AQP0-AQP13) that are overexpressed in various cancers. Our results showed that out of 19 sapogenins, 8 (Diosgenin, Gitogenin, Tigogenin, Ruscogenin, Yamogenin, Hecogenin, Sarsasapogenin and Smilagenin) exhibited acceptable drug-like characteristics. These sapogenin also exhibited favourable binding affinities in the range of -7.6 to -13.4 kcal/mol, and interactions within the AQP binding sites. Furthermore, MD simulations provided insights into stability and dynamics of the sapogenin-AQP complexes. Most of the fluctuations in binding pocket were observed for AQP0-Gitogenin and AQP4-Diosgenin. However, remaining protein-ligand complex showed stable root mean square deviation (RMSD) plots, strong hydrogen bonding interactions, stable solvent-accessible surface area (SASA) values and minimum distance to the receptor. These observations suggest that natural sapogenin hold promise as novel inhibitors of AQPs, offering a basis for the development of innovative therapeutic agents for cancer treatment. However, further validation of the identified compounds through experiments is essential for translating these findings into therapeutic applications.

Exploring the antiviral activity of α-ketoamides compounds through electronic structure calculations: a structure-activity relationship study

In recent years, the scientific community has worked intensively in the search and development of new drugs to suppress viral infections, such as COVID-19. In fact, a number of active compounds have been tested; however, the absence of significant structure-activity relationships hinders the production of optimized drugs. In this study, molecular modeling techniques were employed to investigate the electronic, structural and chemical reactivity properties of a set α-ketoamides whose antiviral activities have been reported in the literature, aiming to propose new promising derivatives. The local reactivity of the compounds was evaluated via condensed-to-atoms Fukui indexes and molecular electrostatic potential. Multivariate data analysis and random forests machine learning techniques were employed to correlate the antiviral properties and electronic and structural descriptors and identify relevant variables. A series of new derivatives were then proposed and evaluated via density functional theory-based calculations, and docking/molecular dynamics with the target protein of the virus. The results suggest that active derivatives present reduced reactivity towards electrophilic agents on the central core of the molecules and high reactivity on R1 ligands. Derivatives with higher predicted antiviral activities were proposed based on simple electronic descriptors, and their efficacies are reinforced by docking and molecular dynamics simulations.

Synthesis, biological evaluation and molecular docking studies of flavonol-3-O-β-D-glycoside as a potential inhibitor of SARS-CoV-2 main protease (3CLpro) in drug development for COVID-19

The COVID-19 pandemic began in March 2020 and has affected many countries and infected over a million people. It has had a serious impact on people's physical and mental health, daily life and the global economy. Today, many drugs show limited efficacy in the treatment of COVID-19 and studies to develop effective drugs continue. Here, we aim to the synthesise and characterise of the flavonol-3-O-glycoside derivatives, the following and evaluated molecular docking studies with antimicrobial activity, inhibition of SARS-CoV-2 main protease enzyme (3CLpro) and nuclease activity. Molecular docking simulations of the synthesized flavonol-3-O-glycoside derivatives, especially compounds 5a, 5d, 5h, 5i and 5m, showed a stronger interaction with SARS-CoV-2 3CLpro in the active site. Two compounds from the target compounds, 5h and 5m, were found to be specifically effective against M. smegmatis and yeasts. In particular, compounds 5a, 5d, 5h, 5i and 5m, which exhibited high activity against the SARS-CoV-2 main protease enzyme, were found to be effective at low concentrations. We determined the IC50 values for the compounds that showed an inhibitory effect as well as their nuclease activities, which further emphasising the potential of our results. Among these, compound 5d showed a significant competitive inhibitor of 3CLpro. Furthermore, nuclease activity studies identified compound 5d as the most potent. The above results suggest that the flavonol-3-O-glycoside derivatives could be promising new antiviral agents for the development of 3CLpro inhibitors to combat COVID-19.

In silico evaluation of S-adenosyl-L-homocysteine analogs as inhibitors of nsp14-viral cap N7 methyltranferase and PLpro of SARS-CoV-2: synthesis, molecular docking, physicochemical data, ADMET and molecular dynamics simulations studies

A series of S-adenosyl-L-homosysteine (SAH) analogs, with modification in the base and sugar moiety, have been designed, synthesized and screened as nsp14 and PLpro inhibitors of severe acute respiratory syndrome corona virus (SARS-CoV-2). The outcomes of ADMET (Adsorption, Distribution, Metabolism, Excretion, and Toxicity) studies demonstrated that the physicochemical properties of all analogs were permissible for development of these SAH analogs as antiviral agents. All molecules were screened against different SARS-CoV-2 targets using molecular docking. The docking results revealed that the SAH analogs interacted well in the active site of nsp14 protein having H-bond interactions with the amino acid residues Arg289, Val290, Asn388, Arg400, Phe401 and π-alkyl interactions with Arg289, Val290 and Phe426 of Nsp14-MTase site. These analogs also formed stable H-bonds with Leu163, Asp165, Arg167, Ser246, Gln270, Tyr274 and Asp303 residues of PLpro proteins and found to be quite stable complexes therefore behaved as probable nsp14 and PLpro inhibitors. Interestingly, analog 3 showed significant in silico activity against the nsp14 N7 methyltransferase of SARS-CoV-2. The molecular dynamics (MD) and post-MD results of analog 3 unambiguously established the higher stability of the nsp14 (N7 MTase):3 complex and also indicated its behavior as probable nsp14 inhibitor like the reference sinefungin. The docking and MD simulations studies also suggested that sinefungin did act as SARS-CoV-2 PLpro inhibitor as well. This study's findings not only underscore the efficacy of the designed SAH analogs as potent inhibitors against crucial SARS-CoV-2 proteins but also pinpoint analog 3 as a particularly promising candidate. All the study provides valuable insights, paving the way for potential advancements in antiviral drug development against SARS-CoV-2.

Mechanistic Characterization of Covalent Enzyme Inhibition by Isothermal Titration Calorimetry Kinetic Competition (ITC-KC)

Covalent enzyme inhibitors can offer high potency and specificity and are increasingly sought after in drug discovery. They typically inhibit in two steps: noncovalent binding followed by covalent bond formation. Rational optimization requires quantitative information on both steps. Current methods for measuring these steps are technically demanding, time-consuming, and are not well suited for routine insertion into drug discovery pipelines. We have developed a new approach, using isothermal titration calorimetry kinetic competition (ITC-KC), that overcomes many of these challenges. ITC-KC measures enzyme activity directly, via the heat flow generated during catalysis, making it a sensitive and nearly universal approach. We performed extensive numerical simulations in which ITC-KC outperformed current methods with 3- to 10-fold greater accuracy. We applied ITC-KC to a library of 19 inhibitors of the protease 3CLpro from SARS-CoV-2 and found that the reactive warheads and noncovalent binding portions of these molecules influenced the two-step inhibition mechanism in complex and unpredictable ways. This highlights the need for detailed mechanistic information in the development of covalent inhibitors, information that ITC-KC can provide rapidly, accurately, and essentially universally.

In vitro enzymatic and cell culture assays for SARS-CoV-2 main protease interaction with ambenonium

The 2019 pandemic of coronavirus disease (COVID-19) caused by SARS-CoV-2 led to millions of deaths worldwide since its emergence. The viral genomic material can code structural and non-structural proteins including the main protease or 3CLpro, a cysteine protease that cleavages the viral polyprotein generating 11 proteins that participate in viral pre-replication. Thus, 3CLpro is a promising therapeutic target for SARS-CoV-2 inhibition by new drugs or drug repositioning because 3CLpro is dissimilar to human proteases. We conducted in vitro assays demonstrating the modulation activity of ambenonium, a drug already used in Myasthenia gravis that acts by inhibiting the action of acetylcholinesterase, and had its potential inhibitory activity against viral replication pointed out in a previous in silico study. In concentrations of 100 µM, 50 µM, 25 µM, 10 µM, and 1 µM there was no inhibition in the formation of lysis plates, with a slight increase in the genome copy number at the higher concentrations evaluated. However, in the concentrations of 0,1 µM and 0,01 µM, there was a reduction in the number of lysis plates. This behavior suggests that the ambenonium acts as a modulator of viral activity in vitro. To investigate potential conformational changes in the protein between dimeric and monomeric forms in the presence of the compound, a local docking analysis was performed. Results indicated this conformational shift is possible, though further studies are needed to confirm these findings.

Inhibitory efficacy and structural insights of Bofutrelvir against SARS-CoV-2 Mpro mutants and MERS-CoV Mpro

The COVID-19 pandemic has caused significant global health and economic disruption. Mutations E166N, E166R, E166N, S144A and His163A in the SARS-CoV-2 main protease (Mpro) have been implicated in reducing the efficacy of certain antiviral treatments. Bofutrelvir, a promising inhibitor, has shown effectiveness against SARS-CoV-2 Mpro. This study aims to evaluate the inhibitory effects of Bofutrelvir on the E166N, E166R, His163A, E166V and S144A mutants of SARS-CoV-2 Mpro, as well as on MERS-CoV Mpro. Our findings indicate a substantial reduction in the inhibitory potency of Bofutrelvir against these mutants and MERS-CoV, with IC50 values significantly higher than those for the wild-type SARS-CoV-2 Mpro. Specifically, the E166N, E166R, E166V, S144A, and H163A mutations significantly reduce the binding affinity and inhibitory effectiveness of Bofutrelvir due to disrupted hydrogen bonds, altered binding site stability, and reduced enzyme activity. Structural analysis of the crystal complexes showed that changes in interactions at the S1 subsite in the mutants and the loss of hydrogen bonds at the S4 subsite in MERS-CoV Mpro are critical factors contributing to the diminished inhibitory activity. These insights reveal the necessity of ongoing structural analysis to adapt therapeutic strategies.

The SARS-CoV-2 3CL protease inhibits pyroptosis through the cleavage of gasdermin D

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of novel coronavirus disease 2019, can cause acute respiratory symptoms and even death globally. However, the immune escape mechanism and viral pathogenesis remain poorly understood. Here, we report that the SARS-CoV-2 3C-like (3CL) protease specifically cleaves gasdermin D (GSDMD) at Q29 and Q193, producing two N-terminal fragments, GSDMD1-29 and GSDMD1-193. We also found that SARS-CoV-2 infection induced the cleavage of GSDMD. Then, we demonstrated that the ability to cleave GSDMD was dependent on the protease activity of the 3CL protease. Interestingly, unlike the GSDMD1-275 fragment cleaved by caspase-1, GSDMD1-29 and GSDMD1-193 did not trigger pyroptosis or inhibit SARS-CoV-2 replication. Additionally, various RNA viral proteases display different preferences for cleaving GSDMD at Q29 and Q193. Our findings reveal a mechanism by which SARS-CoV-2 and other RNA viruses inhibit pyroptosis, highlighting the critical role of the 3CL protease in immune evasion and viral replication.

Design, Synthesis, and Biological Evaluation of 5,8-Dimethyl Shikonin Oximes as SARS-CoV-2 Mpro Inhibitors

We have designed, synthesized, and characterized a small library of shikonin derivatives and demonstrated their inhibitory activity against the main protease, Mpro, of SARS-CoV-2. One analog, 5,8-dimethyl shikonin oxime (15), exhibited the highest activity against SARS-CoV-2 Mpro with an IC50 value of 12.53 ± 3.59 μM. It exhibited much less toxicity as compared with the parent compound, shikonin, in both in vitro and in vivo models. Structure-activity relationship analysis indicated that the oxime moieties on the naphthalene ring and the functional groups attached to the oxygen atom on the side chain play a pivotal role in enzymatic inhibitory activity. Molecular docking results implied that the inhibitor 15 is perfectly settled in the core of the substrate-binding pocket of Mpro by possibly interacting with three catalytic residues, His41, Cys145, and Met165. Overall, the shikonin oxime derivative 15 deserves further investigation as an antiviral agent against SARS-CoV-2.

Structural Virology: The Key Determinants in Development of Antiviral Therapeutics

Structural virology has emerged as the foundation for the development of effective antiviral therapeutics. It is pivotal in providing crucial insights into the three-dimensional frame of viruses and viral proteins at atomic-level or near-atomic-level resolution. Structure-based assessment of viral components, including capsids, envelope proteins, replication machinery, and host interaction interfaces, is instrumental in unraveling the multiplex mechanisms of viral infection, replication, and pathogenesis. The structural elucidation of viral enzymes, including proteases, polymerases, and integrases, has been essential in combating viruses like HIV-1 and HIV-2, SARS-CoV-2, and influenza. Techniques including X-ray crystallography, Nuclear Magnetic Resonance spectroscopy, Cryo-electron Microscopy, and Cryo-electron Tomography have revolutionized the field of virology and significantly aided in the discovery of antiviral therapeutics. The ubiquity of chronic viral infections, along with the emergence and reemergence of new viral threats necessitate the development of novel antiviral strategies and agents, while the extensive structural diversity of viruses and their high mutation rates further underscore the critical need for structural analysis of viral proteins to aid antiviral development. This review highlights the significance of structure-based investigations for bridging the gap between structure and function, thus facilitating the development of effective antiviral therapeutics, vaccines, and antibodies for tackling emerging viral threats.

Molecular docking, pharmacological profiling, and MD simulations of glycolytic inhibitors targeting novel SARS CoV-2 main protease and spike protein

Abstract

Coronavirus infection (COVID-19), designated a global health emergency by the World Health Organization in 2020, continues to spur the search for effective therapeutics. The causative agent, SARS-CoV-2, depends on viral proteins and host metabolic reprogramming for replication. This study explores the potential of glycolytic inhibitors as dual-action agents against SARS-CoV-2, explicitly targeting the main protease and the spike protein due to their critical roles in viral replication and cellular entry. These inhibitors disrupt the activity of viral proteins and host cell glycolysis, thereby preventing viral propagation. Through a combination of virtual screening, molecular docking, and molecular dynamics simulations, fluoro-deoxy-glucose folate (FDGF) and N-(2-fluoro-3-(6-O-glucosylpropyl-azomycin)) were identified as potent candidates. The docking results showed strong binding affinities, with scores of -8.6 and -7.1 kcal/mol for main protease and -9.9 and - 7.5 kcal/mol for spike receptor-binding domain bound to ACE2. Further molecular dynamic simulations confirmed the stability of the FDGF complexes, with RMSD fluctuations consistently remained within 1.6-2.9 Å over a 100 ns trajectory. Additionally, MM-GBSA binding free energy calculations revealed favorable binding energies, underscoring the stability and potential efficacy of these compounds. Overall, the findings suggest that FDGF and N-(2-fluoro-3-(6-O-glucosylpropyl-azomycin)) show promise as SARS-CoV-2 therapeutics, warranting further in vitro and in vivo validation to confirm their antiviral potential.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-025-00336-2.

Biochemical Screening of Phytochemicals and Identification of Scopoletin as a Potential Inhibitor of SARS-CoV-2 Mpro, Revealing Its Biophysical Impact on Structural Stability

The main protease (Mpro or 3CLpro or nsp5) of SARS-CoV-2 is crucial to the life cycle and pathogenesis of SARS-CoV-2, making it an attractive drug target to develop antivirals. This study employed the virtual screening of a few phytochemicals, and the resultant best compound, Scopoletin, was further investigated by a FRET-based enzymatic assay, revealing an experimental IC50 of 15.75 µM. The impact of Scopoletin on Mpro was further investigated by biophysical and MD simulation studies. Fluorescence spectroscopy identified a strong binding constant of 3.17 × 104 M⁻1 for Scopoletin binding to Mpro, as demonstrated by its effective fluorescence quenching of Mpro. Additionally, CD spectroscopy showed a significant reduction in the helical content of Mpro upon interaction with Scopoletin. The findings of thermodynamic measurements using isothermal titration calorimetry (ITC) supported the spectroscopic data, indicating a tight binding of Scopoletin to Mpro with a KA of 2.36 × 103 M-1. Similarly, interaction studies have also revealed that Scopoletin forms hydrogen bonds with the amino acids nearest to the active site, and this has been further supported by molecular dynamics simulation studies. These findings indicate that Scopoletin may be developed as a potential antiviral treatment for SARS-CoV-2 by targeting Mpro.

SARS-CoV-2 Mpro Dihedral Angles Reveal Allosteric Signaling

In allosteric proteins, identifying the pathways that signals take from allosteric ligand-binding sites to enzyme active sites or binding pockets and interfaces remains challenging. This avenue of research is motivated by the goals of understanding particular macromolecular systems of interest and creating general methods for their study. An especially important protein that is the subject of many investigations in allostery is the SARS-CoV-2 main protease (Mpro), which is necessary for coronaviral replication. It is both an attractive drug target and, due to intense interest in it for the development of pharmaceutical compounds, a gauge of the state of the art approaches in studying protein inhibition. Here we develop a computational method for characterizing protein allostery and use it to study Mpro. We propose a role of the protein's C-terminal tail in allosteric modulation and warn of unintuitive traps that can plague studies of the role of protein dihedral angles in transmitting allosteric signals.

Molecular Modeling Studies of Similar Molecules to Selective Estrogen Receptor Degrader Elacestrant as Inhibitors of SARS-COV-2

Coronavirus 2019 (COVID-19) is a disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) strain. Many anticancer compounds have been repurposed as effective anti-coronavirus agents and are currently in a clinical trial to be evaluated for treatment. Elacestrant is a novel selective estrogen receptor degrader (SERD). A fingerprint Tanimoto-based 2-dimensional similarity search was performed in the PubChem database using elacestrant as a prototype. The chemical compounds were downloaded, and virtual screening, molecular docking, and molecular dynamics were further used to identify the most active molecules in the binding pocket SARS-COV-2 main protease. Eight compounds with superior docking score, gscore, and glide binding energy were identified. Molecular dynamic simulations (MD) were performed at 100 ns to remove the false interactions between the receptor and the active ligands. The results showed that all the compounds displayed good stability. Further, the ADMET results showed that compounds CID58023104 was observed to be deemed a hit compound; hence, CID58023104 and could be optimize, derivatize, and explore for further development as an anti-coronavirus agent targeting SARS-COV-2 main protease.

Cys44 of SARS-CoV-2 3CLpro affects its catalytic activity

SARS-CoV-2 encodes a 3C-like protease (3CLpro) that is essential for viral replication. This cysteine protease cleaves viral polyproteins to release functional nonstructural proteins, making it a prime target for antiviral drug development. We investigated the inhibitory effects of halicin, a known c-Jun N-terminal kinase inhibitor, on 3CLpro. Mass spectrometry and crystallographic analysis revealed that halicin covalently binds to several cysteine residues in 3CLpro. As expected, Cys145, the catalytic residue, was found to be the most targeted residue by halicin. Secondly, Cys44 was found to be modified, suggesting a potential inhibitory role of this residue. A mutant protease (Cys44Ala) was generated to further understand the function of Cys44. In silico and enzymatic assays showed that the mutation significantly reduced the stability and activity of 3CLpro, indicating the importance of Cys44 in maintaining the active conformation of the protease. Differential scanning fluorimetry assays confirmed this evidence, showing a reduced thermal stability of the mutant compared to the wild-type protease. Our results highlight the potential of halicin as a multi-target inhibitor of 3CLpro and underline the importance of Cys44 in the function of the protease. These findings contribute to the development of effective antiviral therapies against COVID-19 by targeting critical residues in 3CLpro.

Precision spatiotemporal analysis of large-scale compound-protein interactions through molecular dynamics simulation

Biological systems are composed of and regulated by intricate and diverse biomolecular interactions. Experimental and computational approaches have been developed to elucidate the mechanisms of these interactions; however, owing to cost, time, and accuracy issues, large-scale spatiotemporal analyses of molecular pairs remain challenging. Thus, the molecular recognition mechanisms underlying these diverse interactions remain unclear. We successfully simulated the large-scale molecular dynamics (MD) of 4,275 protein-compound pairs by combining a method to accelerate the MD simulations with the supercomputer Fugaku. Our spatiotemporal analysis of generated big MD data revealed universal features underlying molecular recognition and binding processes. This study expands our understanding of the concept of MD simulations from a technique to investigate the dynamic properties of individual protein-drug pairs to an approach to perform large-scale spatiotemporal analysis and compound screening. This study opens an avenue in biological research for subsequent drug discovery.

Transformative approaches in SARS-CoV-2 management: Vaccines, therapeutics and future direction

The global healthcare and economic challenges caused by the pandemic of COVID-19 reinforced the urgent demand for quick and effective therapeutic and preventative interventions. While vaccines served as the frontline of defense, antivirals emerged as adjunctive countermeasures, especially for people who developed infection, were immunocompromised, or were reluctant to be vaccinated. Beyond the serious complications of SARS-CoV-2 infection, the threats of long-COVID and the potential for zoonotic spillover continue to be significant health concerns that cannot be overlooked. Moreover, the incessant viral evolution, clinical safety issues, waning immune responses, and the emergence of drug-resistant variants pinpoint towards more severe viral threats in the future and call for broad-spectrum innovative therapies as a pre-pandemic preparedness measure. The present review provides a comprehensive up-to-date overview of the strategies utilized in the development of classical and next-generation vaccines against SARS-CoV-2, the clinical and experimental data obtained from clinical trials, while addressing safety risks that may arise. Besides vaccines, the review also covers recent breakthroughs in anti-SARS-CoV-2 drug discovery, emphasizing druggable viral and host targets, virus- and host-targeting antivirals, and highlighting mechanistically representative molecules that are either approved or are under clinical investigation. In conclusion, the integration of both vaccines and antiviral therapies, along with swift innovative strategies to address viral evolution and drug resistance is crucial to strengthen our preparedness against future viral outbreaks.

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.

A comprehensive review of current insights into the virulence factors of SARS-CoV-2

The evolution of SARS-CoV-2 pathogenicity has been a major focus of attention. However, the determinants of pathogenicity are still unclear. Various hypotheses have attempted to elucidate the mechanisms underlying the evolution of viral pathogenicity, but a definitive conclusion has yet to be reached. Here, we review the potential impact of all proteins in SARS-CoV-2 on the viral pathogenic process and analyze the effects of their mutations on pathogenicity evolution. We aim to summarize which virus-encoded proteins are crucial in influencing viral pathogenicity, defined as disease severity following infection. Mutations in these key proteins, which are the virulence factors in SARS-CoV-2, may be the driving forces behind the evolution of viral pathogenicity. Mutations in the S protein can impact viral entry and fusogenicity. Mutations in proteins such as NSP2, NSP5, NSP14, and ORF7a can alter the virus's ability to suppress host protein synthesis and innate immunity. Mutations in NSP3, NSP4, NSP6, N protein, NSP5, and NSP12 may alter viral replication efficiency. The combined effects of mutations in the S protein and NSP6 can significantly reduce viral replication. In addition, various viral proteins, including ORF3a, ORF8, NSP4, Spike protein, N protein, and E protein, directly participate in the inflammatory process. Mutations in these proteins can modulate the levels of inflammation following infection. Collectively, these viral protein mutations can influence SARS-CoV-2 pathogenicity by impacting viral immune evasion, replication capacity, and the level of inflammation mediated by infection. In conclusion, the evolution of SARS-CoV-2 pathogenicity is likely determined by multiple virulence factors.

Evaluating the structure-based virtual screening performance of SARS-CoV-2 main protease: A benchmarking approach and a multistage screening example against the wild-type and Omicron variants

COVID-19 still poses a worldwide health threat due to continuous viral mutations and potential resistance to vaccination. SARS-CoV-2 viral multiplication hindrance by inhibiting the viral main protease (Mpro) deemed propitious. Structure-based virtual screening (SBVS) is a conventional strategy for discovering new inhibitors. Nonetheless, the SBVS efforts against Mpro variants needed to be benchmarked. Herein, in the first stage of the study, we evaluated four docking tools (FRED, PLANTS, AutoDock Vina and CDOCKER) via an in-depth benchmarking approach against SARS-CoV2 Mpro of both the wild type (WTMpro) and the deadly Omicron P132H variant (OMpro). We started by compiling an active dataset of non-covalent small molecule inhibitors of the WTMpro from literature and the COVID-Moonshot database along with generating a high-quality benchmark set via DEKOIS 2.0. pROC-Chemotype plots revealed superior performance for AutoDock Vina against WTMpro, while both FRED and AutoDock Vina demonstrated excellent performance for OMPro. In the second stage, VS was performed on a focused library of 636 compounds transformed from the early-enriched cluster related to perampanel via a scaffold hopping approach. Subsequently, molecular dynamics (MD) simulation and MM GBSA calculations validated the binding potential of the recommended hits against both explored targets. This study provides an example of how to conduct an in-depth benchmarking approach for both WTMPro and OMPro variants and offering an evaluated SBVS protocol for them both.

Dihydropyrimidine-2-thione derivatives as SARS-CoV-2 main protease inhibitors: synthesis, SAR and in vitro profiling

Despite the passage of approximately five years since the outbreak, an efficacious remedy for SARS-CoV-2 remains elusive, highlighting the urgent imperative for developing SARS-CoV-2 potent inhibitors. In our current study, we have unmasked the hitherto unrealized potential of dihydropyrimidine-2-thiones against the Main Protease (Mpro) of SARS-CoV-2. Employing a predictive docking tool, we identified promising lead compounds and optimized them via comprehensive Structural Activity Relationship (SAR) studies. Key design elements included proton donor/acceptor groups, six-membered rings, and fluorinated moieties to enhance interactions. These leads underwent in vitro inhibition assays to enhance their interaction with key Mpro amino acid residues. Our findings indicated that all synthesized compounds exhibited significant inhibition of the Mpro. Compounds 12j (IC50 = 0.063 μM), and 12l (IC50 = 0.054 μM) displayed exceptional in vitro binding affinities. In addition to their string inhibitory activity, CC50 values were assessed, confirming acceptable cytotoxicity profiles for potent compounds. Molecular dynamic simulation substantiated the binding mechanism revealing that compound 12l maintains robust stability with the target protein. Furthermore, compounds predicted to have minimal oral toxicity and high intestinal absorption make them promising candidates for drug development. These findings paved the way for the potent clinical application of these dihydropyrimidine-2-thiones as efficient SARS-CoV-2 therapeutics.

Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (Mpro) with Noncovalent Preclinical Candidate, Mpro61

SARS-CoV-2 Mpro inhibitors, such as nirmatrelvir, have proven efficacy in clinical use. Nirmatrelvir was developed in a target-based approach against wild-type Mpro, with the anticipation that prolonged usage may cause enrichment of drug-resistant mutations and persistence of COVID infections. Although globally prevalent drug-resistant mutations have not yet been observed, individual cases have recently been reported among patients following treatment with Paxlovid-a formulation of nirmatrelvir. Mutations E166V and E166A have been detected in these drug-resistant clinical isolates, consistent with predictions from in vitro viral passage experiments and therefore necessitate ongoing drug development. In this study, we selected seven Mpro variants (T21I, L50F, E166V, A173V, T190I, E166V/L50F, and A173V/L50F), which have been repeatedly found in viral passage experiments. We investigated their kinetic and structural properties, as well as resistance level to Mpro inhibitors: nirmatrelvir, GC376-a similar peptidomimetic for feline COVID infections, and our in-house-developed nonpeptidomimetic inhibitor Mpro61. Mpro61 maintains potency against the single variants (except for E166V) and the A173/L50F double variant, with K i values similar to those of the wild type. In contrast, while nirmatrelvir and GC376 were still effective against the A173V/L50F double variant, their K i values significantly increased up to 10-fold. None of the inhibitors appeared to be potent against E166V-containing variants. Our structural analysis revealed a significant movement of Ser1 residue in all E166V-containing variants in the presence or absence of an inhibitor. The new orientation of the Ser1 suggested potential strategies for medicinal chemistry modifications of Mpro61 to enhance hydrogen-bonding interactions between these variants and Mpro61 derivatives. These studies provide critical insights into guiding the future design of additional Mpro61 derivatives that would potentially inhibit variants with the pan-drug-resistant E166V mutation.

Structure-Based Optimization of Pyridone α-Ketoamides as Inhibitors of the SARS-CoV-2 Main Protease

The main protease Mpro is a clinically validated target to treat infections by the coronavirus SARS-CoV-2. Among the first reported Mpro inhibitors was the peptidomimetic α-ketoamide 13b, whose cocrystal structure with Mpro paved the way for multiple lead-finding studies. We established structure-activity relationships for the 13b series by modifying residues at the P1', P3, and P4 sites. Guided by cocrystal structures, we reduced the P1' substituent size to better fill the pocket and added a fluorine substituent to the pyridone ring, enabling a new hydrogen bond with Gln189 in P3. Among 22 novel analogues, 6d and 12d inhibited Mpro with IC50s of 110 nM and 40 nM, improving the potency of 13b by up to 9.5-fold. Compound 6d had pronounced antiviral activity with an EC50 of 1.6 μM and was stable in plasma and microsomes. The study illustrates the potential of structure-based design to systematically improve peptidomimetic α-ketoamides.

Decoding SARS-CoV-2 Inhibition: Insights From Molecular Dynamics Simulation of Condensed Amino Thiourea Scaffold Small Molecules

The main protease (Mpro) of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) plays a crucial role in viral replication. In this study, the binding modes and inhibitory mechanisms of eight condensed amino thiourea scaffold inhibitors of Mpro in proteins were investigated using a combination of molecular docking, molecular dynamics simulations, and MM/PBSA binding free energy calculations. The results indicated that the para-hydroxyl group on the benzene ring at the head of the inhibitor has a decisive influence on the initial docking pose and binding free energy strength of the inhibitor. Additionally, the position and length of the hydrophobic side chain on the tail six-membered ring significantly impacted the final binding pose of the inhibitor. The presence of a long hydrophobic side chain in the ortho position of this ring, through its interaction with the P4 hydrophobic pocket, led to an opposite binding mode in the protein compared with when it was present with or without the para-side chain. Different lengths of para-substituted side chains affected the positioning of the inhibitors in the enzyme. These different binding modes led to variations in the binding free energy between the inhibitor and the protein, which in turn gave rise to differences in inhibitory capability.

Discovery of Severe Acute Respiratory Syndrome Coronavirus 2 Main Protease Inhibitors through Rational Design of Novel Fluorinated 1,3,4-oxadiazole Amide Derivatives: An In-Silico Study

As severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) variants continue to emerge, there is an urgent need to develop more effective antiviral drugs capable of combating the COVID-19 pandemic. The main protease (Mpro) of SARS-CoV-2 is an evolutionarily conserved drug discovery target. The present study mainly focused on chemoinformatics computational methods to investigate the efficacy of our newly designed trifluoromethyl-1,3,4-oxadiazole amide derivatives as SARS-CoV-2 Mpro inhibitors. Drug-likeness absorption, distribution, metabolism, excretion, and toxicity analysis, molecular docking simulation, density functional theory (DFT), and molecular dynamics simulation methods were included. A comprehensive drug-likeness analysis was performed on the 14 newly designed compounds (1a-1n), and this series of small molecule inhibitors showed potential anti-SARS-CoV-2 activity. In order to reveal the mechanism of drug interaction, these novel compounds were classified by structure, and molecular docking simulations were performed. The results showed good interactions and identified the key amino acid residue GLY-143. Further DFT analysis using B3LYP-D3BJ functional and 6-311 + + G (d, p) basis set was performed to optimize the optimal configuration of the Mpro inhibitors, and the infrared spectrum of the vibration frequency was analyzed to clearly understand the structure and stability of the drug. The electrostatic potential map was analyzed to predict the reactivity of functional groups and protein-substrate interactions. The frontier molecular orbital analysis and density of states map showed the reactivity level and stability of the drug itself, among which 1i had the smallest energy gap difference (ΔEgap = 3.64 ev), showing good reactivity. The analysis of global reactivity descriptors such as electrophilic index (ω) and chemical potential (μ) also showed that our newly designed Mpro inhibitors had stronger interactions. Molecular dynamics simulation further revealed the stable binding of the Mpro inhibitors in a solvent environment. The binding free energy results calculated by Molecular Mechanics / Poisson Boltzmann Surface Area (MM/PBSA) all exceeded the Food and Drug Administration-approved standard reference drug (Nirmatrelvir), and the free energy landscape and principal component analysis also further described the energy sites formed during the binding process between the drug molecule and the ligand-protein and the changes in conformation. These new series of small molecule inhibitors studied in this work will provide the necessary theoretical basis for the synthesis and activity evaluation of novel SARS-CoV-2 Mpro inhibitors.

Identification of promising SARS-CoV-2 main protease inhibitor through molecular docking, dynamics simulation, and ADMET analysis

The COVID-19 pandemic caused by SARS-CoV-2 continues to pose a major challenge to global health. Targeting the main protease of the virus (Mpro), which is essential for viral replication and transcription, offers a promising approach for therapeutic intervention. In this study, advanced computational techniques such as molecular docking and molecular dynamics simulations were used to screen a series of antiviral compounds for their potential inhibitory effect on the SARS-CoV-2 Mpro. A comprehensive analysis of compounds from the ChemDiv and PubChem databases was performed. The physicochemical properties, pharmacokinetics, and ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) profiles were evaluated to determine drug similarity and safety. Compound 4896 - 4038 proved to be the most promising candidate. It exhibited a favorable balance between molecular weight (491.06) and lipophilicity (logP 3.957), high intestinal absorption (92.119%), and broad tissue distribution (VDss of 0.529), indicating good oral bioavailability and therapeutic potential. Molecular docking studies showed that 4896 - 4038 has a strong binding affinity to the active site of Mpro and forms key interactions, such as hydrogen bonds, carbon-hydrogen bonds, pi-sulfur, and multiple van der Waals and pi-pi stacked bonds. The binding energy was comparable to that of the reference drug X77, indicating potential efficacy. Molecular dynamics simulations over 300 ns confirmed the stability of the Mpro/4896 - 4038 complex of protein-ligand. Free energy landscape mapping and MM/PBSA calculations further substantiated the favorable binding and stability of the complex. Importantly, 4896 - 4038 exhibited a comparatively favorable safety profile. In summary, compound 4896 - 4038 shows significant potential as a potent SARS-CoV-2 Mpro inhibitor, combining potent inhibitory activity with favorable pharmacokinetic and safety profiles. These results support the further development of 4896 - 4038 as a promising therapeutic agent in the fight against COVID-19 that warrants experimental validation and clinical investigation.

Quantum-computing-enhanced algorithm unveils potential KRAS inhibitors

We introduce a quantum-classical generative model for small-molecule design, specifically targeting KRAS inhibitors for cancer therapy. We apply the method to design, select and synthesize 15 proposed molecules that could notably engage with KRAS for cancer therapy, with two holding promise for future development as inhibitors. This work showcases the potential of quantum computing to generate experimentally validated hits that compare favorably against classical models.

Research Progress on the Structure and Function, Immune Escape Mechanism, Antiviral Drug Development Methods, and Clinical Use of SARS-CoV-2 Mpro

The three-year COVID-19 pandemic 'has' caused a wide range of medical, social, political, and financial implications. Since the end of 2020, various mutations and variations in SARS-CoV-2 strains, along with the immune escape phenomenon, have emerged. There is an urgent need to identify a relatively stable target for the development of universal vaccines and drugs that can effectively combat both SARS-CoV-2 strains and their mutants. Currently, the main focus in treating SARS-CoV-2 lies in disrupting the virus's life cycle. The main protease (Mpro) is closely associated with virus replication and maturation and plays a crucial role in the early stages of infection. Consequently, it has become an important target for the development of SARS-CoV-2-specific drugs. This review summarizes the recent research progress on the novel coronavirus's main proteases, including the pivotal role of Mpro in the virus's life cycle, the structure and catalytic mechanism of Mpro, the self-maturation mechanism of Mpro, the role of Mpro in virus immune escape, the current methods of developing antiviral drugs targeting Mpro, and the key drugs that have successfully entered clinical trials. The aim is to provide researchers involved in the development of antiviral drugs targeting Mpro with systematic and comprehensive information.

Dual Inhibitors of SARS-CoV-2 3CL Protease and Human Cathepsin L Containing Glutamine Isosteres Are Anti-CoV-2 Agents

SARS-CoV-2 3CL protease (Main protease) and human cathepsin L are proteases that play unique roles in the infection of human cells by SARS-CoV-2, the causative agent of COVID-19. Both proteases recognize leucine and other hydrophobic amino acids at the P2 position of a peptidomimetic inhibitor. At the P1 position, cathepsin L accepts many amino acid side chains, with a partial preference for phenylalanine, while 3CL-PR protease has a stringent specificity for glutamine or glutamine analogues. We have designed, synthesized, and evaluated peptidomimetic aldehyde dual-target (dual-acting) inhibitors using two peptide scaffolds based on those of two Pfizer 3CL-PR inhibitors, Nirmatrelvir, and PF-835321. Our inhibitors contain glutamine isosteres at the P1 position, including 2-pyridon-3-yl-alanine, 3-pyridinyl-alanine, and 1,3-oxazo-4-yl-alanine groups. Inhibition constants for these new inhibitors ranged from Ki = 0.6-18 nM (cathepsin L) and Ki = 2.6-124 nM (3CL-PR), for which inhibitors with the 2-pyridon-3-yl-alanal substituent were the most potent for 3CL-PR. The anti-CoV-2 activity of these inhibitors ranged from EC50 = 0.47-15 μM. X-ray structures of the peptidomimetic aldehyde inhibitors of 3CL-PR with similar scaffolds all demonstrated the formation of thiohemiacetals with Cys145, and hydrogen-bonding interactions with the heteroatoms of the pyridon-3-yl-alanyl group, as well as the nitrogen of the N-terminal indole and its appended carbonyl group at the P3 position. The absence of these hydrogen bonds for the inhibitors containing the 3-pyridinyl-alanyl and 1,3-oxazo-4-yl-alanyl groups was reflected in the less potent inhibition of the inhibitors with 3CL-PR. In summary, our studies demonstrate the value of a second generation of cysteine protease inhibitors that comprise a single agent that acts on both human cathepsin L and SARS-CoV-2 3CL protease. Such dual-target inhibitors will provide anti-COVID-19 drugs that remain active despite the development of resistance due to mutation of the viral protease. Such dual-target inhibitors are more likely to remain useful therapeutics despite the emergence of inactivating mutations in the viral protease because the human cathepsin L will not develop resistance. This particular dual-target approach is innovative since one of the targets is viral (3CL-PR) required for viral protein maturation and the other is human (hCatL) which enables viral infection.

Optimization of SARS-CoV-2 Mpro Inhibitors by a Structure-Based Multilevel Virtual Screening Method

With the aim of developing novel anti-SARS-CoV-2 drugs to address the ongoing evolution and emergence of drug-resistant strains, the reported SARS-CoV-2 Mpro inhibitor WU-04 was selected as a lead to find novel, highly potent, and broad-spectrum inhibitors. Using a fragment-based multilevel virtual screening strategy, 15 hit compounds were identified and subsequently synthesized. Among them, A5 (IC50 = 1.05 μM), A6 (IC50 = 1.08 μM), and A9 (IC50 = 0.154 μM) demonstrated potent SARS-CoV-2 Mpro inhibition comparable to or slightly weaker than WU-04. Antiviral activity evaluations revealed that compound A9 exhibited the strongest antiviral activity with an EC50 value of 0.18 μM, quite comparable to the marketed drug Nirmatrelvir (EC50 = 0.123 μM) and inferior to WU-04 (EC50 = 0.042 μM). Molecular dynamics simulations elucidated the key interactions between compounds A5, A6, A9, and the binding pocket of SARS-CoV-2 Mpro, providing valuable insights into their mechanisms of action. These findings identify compound A9 as a promising lead for anti-SARS-CoV-2 drug development.

Computational Assessment of Clinical Drugs against SARS-CoV-2: Foreseeing Molecular Mechanisms and Potent Mpro Inhibitors

The emergence of new SARS-CoV-2 variants of concern (VOC) is a propulsion for accelerated potential therapeutic discovery. SARS-CoV-2's main protease (Mpro), essential for host cell viral replication, is a pre-eminent druggable protein target. Here, we perform extensive drug re-profiling of the comprehensive Excelra database, which compiles various under-trial drug candidates for COVID-19 treatment. For mechanistic understanding, the most promising screened-out molecules with targets are subjected to molecular dynamics (MD) simulations. Post-MD analyses demonstrate Darunavir, Ponatinib, and Tomivosertib forming a stable complex with Mpro, characterized by less fluctuation of Cα atoms, smooth and stable root-mean-square deviation (RMSD), and robust contact with the active site residues. Likewise, they all have lower binding free energy with Mpro, demonstrating strong affinity. In free energy landscape profiles, the distances from His41 and Cys145 exhibit a single energy minima basin, implying their preponderance in proximity to Mpro's catalytic dyad. Overall, the computational assessment earmarks promising candidates from the Excelra database, emphasizing on carrying out exhaustive biochemical experiments along with clinical trials. The work lays the foundation for potential therapeutic interventions in treating COVID-19.

Recognition and cleavage of human tRNA methyltransferase TRMT1 by the SARS-CoV-2 main protease

The SARS-CoV-2 main protease (Mpro or Nsp5) is critical for production of viral proteins during infection and, like many viral proteases, also targets host proteins to subvert their cellular functions. Here, we show that the human tRNA methyltransferase TRMT1 is recognized and cleaved by SARS-CoV-2 Mpro. TRMT1 installs the N2,N2-dimethylguanosine (m2,2G) modification on mammalian tRNAs, which promotes cellular protein synthesis and redox homeostasis. We find that Mpro can cleave endogenous TRMT1 in human cell lysate, resulting in removal of the TRMT1 zinc finger domain. Evolutionary analysis shows the TRMT1 cleavage site is highly conserved in mammals, except in Muroidea, where TRMT1 is likely resistant to cleavage. TRMT1 proteolysis results in reduced tRNA binding and elimination of tRNA methyltransferase activity. We also determined the structure of an Mpro-TRMT1 peptide complex that shows how TRMT1 engages the Mpro active site in an uncommon substrate binding conformation. Finally, enzymology and molecular dynamics simulations indicate that kinetic discrimination occurs during a later step of Mpro-mediated proteolysis following substrate binding. Together, these data provide new insights into substrate recognition by SARS-CoV-2 Mpro that could help guide future antiviral therapeutic development and show how proteolysis of TRMT1 during SARS-CoV-2 infection impairs both TRMT1 tRNA binding and tRNA modification activity to disrupt host translation and potentially impact COVID-19 pathogenesis or phenotypes.

The Conformational Space of the SARS-CoV-2 Main Protease Active Site Loops Is Determined by Ligand Binding and Interprotomer Allostery

The main protease (Mpro) of SARS-CoV-2 is essential for viral replication and is, therefore, an important drug target. Here, we investigate two flexible loops in Mpro that play a role in catalysis. Using all-atom molecular dynamics simulations, we analyze the structural ensemble of Mpro in an apo state and substrate-bound state. We find that the flexible loops can adopt open, intermediate (partly open), and closed conformations in solution, which differs from the partially closed state observed in crystal structures of Mpro. When the loops are in closed or intermediate states, the catalytic residues are more likely to be in close proximity, which is crucial for catalysis. Additionally, we find that substrate binding to one protomer of the homodimer increases the frequency of intermediate states in the bound protomer while also affecting the structural propensity of the apo protomer's flexible loops. Using dynamic network analysis, we identify multiple allosteric pathways connecting the two active sites of the homodimer. Common to these pathways is an allosteric hotspot involving the N-terminus, a critical region that comprises part of the binding pocket. Taken together, the results of our simulation study provide detailed insight into the relationships between the flexible loops and substrate binding in a prime drug target for COVID-19.

Discovery of peptidomimetic spiropyrrolidine derivatives as novel 3CLpro inhibitors against SARS-CoV -2

Given the high pathogenicity and rapid mutation rates of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), it is imperative to sustain efforts in drug research and development. Herein, we present the design, synthesis, and evaluation of peptidomimetic spiropyrrolidine derivatives as potent 3CLpro inhibitors against SARS-CoV-2. Among the synthesized derivatives, several compounds exhibited high potency in inhibiting 3CLpro, with IC50 values ranging from 21 nM to 53 nM. Notably, compounds 9b and 9h displayed improved enzymatic inhibition (IC50 = 25 nM and 21 nM, respectively) compared to nirmatrelvir (47 nM). Compound 9b showed enhanced stability in human and mouse liver microsomes compared to nirmatrelvir, whereas 9h exhibited similar stability to nirmatrelvir in both species. Furthermore, compound 9h displayed exceptional potency in cellular assays targeting the SARS-CoV-2 replicon within Huh7 cells, with a single-digit nanomolar activity that is 5.6 times better than that of nirmatrelvir. In a pharmacokinetic study in mice (PO, 20 mg/kg), compound 9h exhibited a prolonged plasma half-life (T1/2 = 2.58 h) compared to nirmatrelvir (T1/2 = 0.51 h) and demonstrated an AUC(0-t) value (1106 h∗ng/mL) equivalent to that of nirmatrelvir (1023 h∗ng/mL). These findings indicate that compound 9h is a promising lead for developing a novel 3CLpro inhibitor against SARS-CoV-2.

Unveiling the mechanism of action of a novel natural dual inhibitor of SARS-CoV-2 Mpro and PLpro with molecular dynamics simulations

In the twenty-first century, we have witnessed multiple coronavirus pandemics. Despite declining SARS-CoV-2 cases, continued research remains vital. We report the discovery of sydowiol B, a natural product, as a dual inhibitor of SARS-CoV-2 main protease (Mpro) and papain-like protease (PLpro). Sydowiol B interacts with the nano-channel at the Mpro dimer interface and the PLpro active site. Molecular dynamics simulations suggest that sydowiol B inhibits Mpro by limiting active site expansion rather than inducing collapse. Furthermore, sydowiol B binding may amplify the fluctuation of two loops coordinating with the structural Zn2+ in PLpro, displacing Zn2+ from the zinc finger domain to the S2 helix. Sydowiol B and its analogue, violaceol I, exhibit broad-spectrum antiviral activity against homologous coronaviruses. Given the conservation of Mpro and PLpro, sydowiol B and violaceol I are promising leads for designing and developing anti-coronavirus therapies.