3-Chymotrypsin-like Protease (3CLpro) of SARS-CoV-2: Validation as a Molecular Target, Proposal of a Novel Catalytic Mechanism, and Inhibitors in Preclinical and Clinical Trials

Viruses, Год журнала: 2024, Номер 16(6), С. 844 - 844

Опубликована: Май 24, 2024

Proteases represent common targets in combating infectious diseases, including COVID-19. The 3-chymotrypsin-like protease (3CLpro) is a validated molecular target for COVID-19, and it key developing potent selective inhibitors inhibiting viral replication of SARS-CoV-2. In this review, we discuss structural relationships diverse subsites 3CLpro, shedding light on the pivotal role dimerization active site architecture substrate recognition catalysis. Our analysis bioinformatics other published studies motivated us to investigate novel catalytic mechanism SARS-CoV-2 polyprotein cleavage by centering triad involving His41-Cys145-Asp187 its indispensable replication. hypothesis that Asp187 may participate modulating pKa His41, which histidine act as an acid and/or base mechanism. Recognizing crucial component process underscores significance fundamental pharmacophoric element drug design. Next, provide overview both covalent non-covalent inhibitors, elucidating advancements development observed preclinical clinical trials. By highlighting various chemical classes their pharmacokinetic profiles, our review aims guide future research directions toward highly underscore 3CLpro therapeutic target, propel progression candidates through phases.

Язык: Английский

---

Subpocket-Based Analysis Approach for the Protein Pocket Dynamics

Journal of Chemical Theory and Computation, Год журнала: 2024, Номер 20(11), С. 4909 - 4920

Опубликована: Май 21, 2024

Structural and dynamic characteristics of protein pockets remarkably influence their biological functions are also important for enzyme engineering new drug research development. To date, several softwares have been developed to analyze the properties pockets. However, due complexity diversity pocket information during kinetic relaxation, further improvement capacity expansion current tools required. Here, we a platform software AlphaTraj in which computational strategy that divides whole into subpockets examines various such as survival time, stability, correlation was proposed implemented. We scoring function well visualize quality pocket. Furthermore, implemented automated conformational search ligand docking optimization. These may help us gain deep understanding accelerate design inhibitors small-molecule drugs. The is freely available at https://github.com/dooo12332/AlphaTraj.git under GNU GPL license.

Язык: Английский

---

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

Journal of Chemical Information and Modeling, Год журнала: 2024, Номер unknown

Опубликована: Ноя. 28, 2024

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

Язык: Английский

---

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

Communications Biology, Год журнала: 2025, Номер 8(1)

Опубликована: Март 25, 2025

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

Язык: Английский

---

3C-like proteases in SARS-CoV-2

Bioscience Reports, Год журнала: 2024, Номер unknown

Опубликована: Июль 22, 2024

Coronaviruses constitute a significant threat to the human population. Severe acute respiratory syndrome coronavirus-2, SARS-CoV-2, is highly pathogenic coronavirus that has caused COVID-19 pandemic. It led global viral outbreak with an exceptional spread and high death toll, highlighting need for effective antiviral strategies. 3-chymotrypsin-like protease (3CLpro), main in plays indispensable role SARS-CoV-2 life cycle by cleaving polyprotein produce eleven individual non-structural proteins necessary replication. 3CLpro one of two proteases function new particles. conserved cysteine identical structural folds all known coronaviruses. Inhibitors binding affinity will prevent cleavage polyproteins, thus impeding Multiple strategies have been implemented screen inhibitors against 3CLpro, including peptide-like small molecule covalently non-covalently bind active site, respectively. In addition, allosteric sites identified molecules could make non-competitive 3CLpro. essence, this review serves as comprehensive guide understanding intricacies functional dynamics emphasizing key findings elucidate its SARS-CoV-2. Notably, critical resource recognizing advancements identifying developing COVID-19, some which are already approved clinical use patients.

Язык: Английский

---

3-Chymotrypsin-like Protease (3CLpro): Validation as a Molecular Target, Proposal of a Novel Catalytic Mechanism, and Inhibitors in Preclinical and Clinical Trials

Опубликована: Май 7, 2024

Proteases represent common targets in combating infectious diseases including COVID-19. The 3-chymotrypsin-like protease (3CLpro) is a validated molecular target for COVID-19 and it key developing potent selective inhibitors inhibiting viral replication of SARS-CoV-2. In this review, we discuss structural relationships diverse subsites 3CLpro, shedding light on the pivotal role dimerization active site architecture substrate recognition catalysis. Our analysis bioinformatics other published studies unveil proposal novel catalytic mechanism SARS-CoV-2 polyprotein cleavage by centering triad involving His41-Cys145-Asp187 its indispensable replication. Recognizing Asp187 as crucial component process underscores significance fundamental pharmacophoric element drug design. Next, provide an overview both covalent non-covalent inhibitors, elucidating advancements development observed preclinical clinical trials. By highlighting various chemical classes their pharmacokinetic profiles, our review aims to guide future research directions toward highly underscore 3CLpro therapeutic target, propel progression candidates through phases.

Язык: Английский

---

Boosting immunity: synergistic antiviral effects of luteolin, vitamin C, magnesium and zinc against SARS-CoV-2 3CLpro

Bioscience Reports, Год журнала: 2024, Номер 44(8)

Опубликована: Июль 24, 2024

SARS-CoV-2 was first discovered in 2019 and has disseminated throughout the globe to pandemic levels, imposing significant health economic burdens. Although vaccines against have been developed, their long-term efficacy specificity not determined, antiviral drugs remain necessary. Flavonoids, which are commonly found plants, fruits, vegetables part of human diet, attracted considerable attention as potential therapeutic agents due antimicrobial activities effects on other biological activities, such inflammation. The present study uses a combination biochemical, cellular, molecular dynamics, docking experiments provide compelling evidence that flavonoid luteolin (2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one) activity 3-chymotrypsin-like protease (3CLpro) is synergistically enhanced by magnesium, zinc, vitamin C. IC50 2 µM 3CLpro 78 decreases 10-fold 7.6 presence Thermodynamic stability analyses revealed minimal structure 3CLpro, whereas metal ions C significantly alter thermodynamic protease. Interactome analysis uncovered host-virus interactions functional clusters associated with activity, supporting relevance this flavone for combating infection. This comprehensive investigation sheds light luteolin's provides insights into its mechanisms action SARS-CoV-2. novel formulation luteolin, may be an effective avenue treating COVID-19 patients.

Язык: Английский

---

Why is the Omicron main protease of SARS-CoV-2 less stable than its wild-type counterpart? A crystallographic, biophysical, and theoretical study

hLife, Год журнала: 2024, Номер 2(8), С. 419 - 433

Опубликована: Июнь 15, 2024

During the continuing evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Omicron variant concern emerged in second half 2021 and has been dominant since November that year. Along with its sublineages, it maintained a prominent role ever since. The Nsp5 main protease (Mpro) virus is characterized by single mutation, P132H. Here we determined X-ray crystal structures P132H mutant (or O-Mpro) as free enzyme complex Mpro inhibitor, alpha-ketoamide 13b-K, conducted enzymological, biophysical well theoretical studies to characterize O-Mpro. We found O-Mpro similar overall structure binding 13b-K; however, displays lower enzymatic activity thermal stability compared WT-Mpro (with "WT" referring prototype strain). Intriguingly, imidazole ring His132 carboxylate plane Glu240 are stacked configuration here. Empirical folding energy calculations suggest dimer destabilized relative due less favorable van der Waals interactions backbone conformations individual protomers. All-atom continuous constant-pH molecular dynamics (MD) simulations reveal display coupled titration. At pH 7, predominantly neutral respect which charged. In order examine whether mutation eases emergence further mutations, also analyzed P132H+T169S double mutant, characteristic BA.1.1.2 lineage. However, little evidence correlation between two sites.

Язык: Английский

---

Mechanistic Insights into the Mutational Landscape of the Main Protease/3CLPro and Its Impact on Long-Term COVID-19/SARS-CoV-2 Management

Опубликована: Июль 8, 2024

The main proteinase (Mpro), or 3CLpro, is a critical enzyme in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lifecycle and responsible for breaking down releasing vital functional viral proteins crucial virus development transmission. As catalytically active dimer, its dimerization interface has become an attractive target antiviral drug development. Recent research extensively investigated enzymatic activity of Mpro, focusing on role regulating replication complex significance maturation infectivity. Computational investigations have identified four druggable pockets, suggesting potential allosteric sites beyond substrate-binding region. Empirical validation through site-directed alanine mutagenesis targeted residues both regions corroborated these predictions. Structural studies can inform therapeutic approaches, with metadynamics simulations shedding light H163 Mpro function providing insights into dynamic equilibrium to wild-type enzyme. Despite efficacy vaccines drugs mitigating SARS-CoV-2 spread, ongoing evolution, selective pressures, continued transmission pose challenges, potentially leading resistance mutations. Phylogenetic analyses indicated existence several variations predating introduction human population, emphasizing likelihood spread. Hydrogen/deuterium-exchange mass spectrometry reveals structural influence mutation, while clinical trials 3CLPro inhibitors underscore reduced offer avenues future exploration. Understanding implications mutations holds promise shaping forthcoming strategies against COVID-19. This review delves factors influencing mutation rates identifies areas warranting further investigation, comprehensive overview mutations, their categorization, terminology. Moreover, we examined associations outcomes, illness severity, unresolved issues, prospects, including impact vaccine targeting.

Язык: Английский

---

Identification of Novel Allosteric Sites of SARS-CoV-2 Papain-Like Protease (PLpro) for the Development of COVID-19 Antivirals

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Май 17, 2023

Abstract Coronaviruses such as SARS-CoV-2 encode a conserved papain-like protease (PLpro) that is crucial for viral replication and immune evasion, making it prime target antiviral drug development. In this study, three surface pockets on PLpro may function sites allosteric inhibition were computationally identified. To evaluate the effects of these proteolytic activity, 52 residues separately mutated to alanine. Pocket 1, located between Ubl thumb domains, introduction alanine at T10, D12, T54, Y72, or Y83 reduced activity <12% WT. 2, situated interface thumb, fingers, palm Q237A, S239A, H275A, S278A inactivated PLpro. Finally, introducing five in 3, fingers PLpro: S212, Y213, Y251, K254, Y305. 1 has higher druggability score than Pockets 2 3. MD simulations showed interactions within domains play critical roles thermal stability. The essential participate combination intra- inter-domain interactions. By contrast, 3 predominantly most promising targets therapeutic development are which have highest largest number residues, respectively. Non-competitive inhibitors targeting be agents against COVID-19 related coronaviruses.

Язык: Английский

---