Distal protein-protein interactions contribute to nirmatrelvir resistance

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Feb. 1, 2025

SARS-CoV-2 main protease, Mpro, is responsible for processing the viral polyproteins into individual proteins, including protease itself. Mpro a key target of anti-COVID-19 therapeutics such as nirmatrelvir (the active component Paxlovid). Resistance mutants identified clinically and in passage assays contain combination site mutations (e.g., E166V, E166A, L167F), which reduce inhibitor binding enzymatic activity, non-active P252L, T21I, L50F), restore fitness replication. To probe role rescue, here we use an triple mutant (L50F/E166A/L167F) that confers drug resistance with level similar to wild-type. By comparing peptide full-length protein substrates, demonstrate substrate involves more than residues site. Particularly, L50F other can enhance dimer-dimer interactions help place nsp5-6 at enzyme catalytic center. The structural activity data L50F, L50F/E166A/L167F, others underscore importance considering whole studying interactions, offers important insights function, development, design.

Language: Английский

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M49L and other drug resistance mutations emerging in individuals after administration of ensitrelvir in Japanese clinical settings

Antiviral Research, Journal Year: 2025, Volume and Issue: 236, P. 106118 - 106118

Published: Feb. 17, 2025

Language: Английский

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An Investigation of Nirmatrelvir (Paxlovid) Resistance in SARS-CoV-2 M^pro

ACS Bio & Med Chem Au, Journal Year: 2024, Volume and Issue: 4(6), P. 280 - 290

Published: Oct. 8, 2024

The high throughput YESS 2.0 platform was used to screen a large library of SARS-CoV-2 Mpro variants in the presence nirmatrelvir. Of 100 individual most prevalent mutations identified and reported here, common were E166V, L27V, N142S, A173V, Y154N, along with their various combinations. In vitro analysis revealed that resistance nirmatrelvir for these mutations, as well all combinations we analyzed, accompanied by decreased catalytic activity native substrate. Importantly, have not appeared significantly enriched sequences isolated from COVID-19 patients following introduction We also analyzed three been seen recently, only measured increase when more recently appearing A285V is added both P132H K90R. Taken together, our results predict will be slower develop than expected based on experience other viral protease inhibitors, perhaps due part close structural correspondence between Mpro's preferred substrates.

Language: Английский

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CAR-NK cell therapy: a potential antiviral platform

Science Bulletin, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Language: Английский

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

ACS Bio & Med Chem Au, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 27, 2025

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

Language: Английский

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Effects of organic salts of virucidal and antiviral compounds from Nelumbo nucifera and Kaempferia parviflora against SARS-CoV-2

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: Feb. 21, 2025

The present work investigates virucidal and antiviral compounds in the extracts of seed embryos a lotus, Nelumbo nucifera, Thai ginseng, Kaempferia parviflora. Separation led to identification against SARS-CoV-2. Neferine (1) nuciferine (3) from N. as well their respective HCl salts (2 4), exhibited activities Virucidal activity neferine salt (2) (EC50 4.78 µM) was 7.5 times better than its free-base, 36.01 µM), also improved selectivity index (SI), showing less cytotoxicity 1. This demonstrates that organic have an impact on biological activities. A crude extract K. parviflora rhizomes displayed 42.11 µg/mL) 39.28 µg/mL). Isolation nine flavonoids (5–13). Among these flavonoids, only 5,7,4'-trimethoxyflavone (8) found show 437.90 50.97 However, (5–13) did not inhibit SARS-CoV-2 3CLpro enzyme at concentrations 10 µM 100 µM. In conclusion, our data underscores therapeutic potential nucifera derived bioactive

Language: Английский

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Phase 2‐3 Trial: Prevention of the Progression to Moderate and Severe COVID‐19 in SARS‐CoV‐2‐Infected Non‐Hospitalized Adults With Inhaled siRNA‐Based MIR 19

Allergy, Journal Year: 2025, Volume and Issue: unknown

Published: March 3, 2025

ABSTRACT Background COVID‐19 continues to be a major global health challenge. Inhaled siRNA‐based MIR 19 has been shown reduce the time clinical improvement in patients hospitalized with moderate COVID‐19. Methods We conducted an open‐label, randomized, controlled multicenter phase 2b‐3 trial (NCT05783206) evaluating safety and efficacy of inhaled siR‐7‐EM/KK‐46 (MIR 19) (5.55 mg/day) comparison standard care (control group) outpatients mild ( N = 492 for each group). The primary endpoint was proportion who developed or severe by 28th day randomization. Results Moderate course disease detected 14 (2.85%) 34 (6.91%) mg) therapy groups, respectively (the difference proportions −4.107% [95% CI: −7.28% −1.03%] p 0.002)). Adverse events (AE) were reported 77 (15.65%) from group, while group AEs registered 100 (20.33%) patients. No severe, treatment‐related observed group. Conclusions siR‐7‐EM/KK‐46, SARS‐CoV‐2‐specific RNAi‐based drug, well‐tolerated significantly decreased progression moderate/severe

Language: Английский

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

Communications Biology, Journal Year: 2025, Volume and Issue: 8(1)

Published: March 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

Language: Английский

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Deep learning in the discovery of antiviral peptides and peptidomimetics: databases and prediction tools

Molecular Diversity, Journal Year: 2025, Volume and Issue: unknown

Published: March 28, 2025

Language: Английский

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Molecular mechanisms of drug resistance and compensation in SARS-CoV-2 main protease: the interplay between E166 and L50

mBio, Journal Year: 2025, Volume and Issue: unknown

Published: April 4, 2025

The SARS-CoV-2 main protease (Mpro) is essential for viral replication and a primary target COVID-19 antivirals. Direct-acting antivirals such as nirmatrelvir, the active component of Paxlovid, Mpro site to block polyprotein cleavage thus replication. However, drug resistance mutations at residue Glu166 (E166) have emerged during in vitro selection studies, raising concerns about durability current antiviral strategies. Here, we investigate molecular basis conferred by E166A E166V against nirmatrelvir related PF-00835231, individually combination with distal mutation L50F. We found that E166 reduce potency up 3,000-fold while preserving substrate cleavage, catalytic efficiency reduced only twofold. This loss was compensated addition L50F double-mutant variants. determined three cocrystal structures variants (E166A, E166V, E166V/L50F) bound PF-00835231. Comparison these wild-type enzyme demonstrated crucial dimerization shaping substrate-binding S1 pocket. Our findings highlight mutability E166, prime inhibitors leverage direct interactions this position, potential emergence highly resistant compensatory These insights support design conserved features avoid side-chain minimize susceptibility resistance. Drug remains great challenge modern medicine. study investigates which confer can retain considerable enzymatic activity through For single- variant enzymes, assessed efficiency, measured its analog cocrystallized caused mutations. results contribute toward understanding mechanisms combinations mutations, pushes resistance-thwarting inhibitor design. principles also apply broadly many quickly evolving targets infectious diseases.

Language: Английский

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