Structure-Based Discovery of the SARS-CoV-2 Main Protease Noncovalent Inhibitors from Traditional Chinese Medicine

Journal of Chemical Information and Modeling, Journal Year: 2024, Volume and Issue: 64(4), P. 1319 - 1330

Published: Feb. 12, 2024

Traditional Chinese medicine (TCM) has been extensively employed for the treatment of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome 2 (SARS-CoV-2). However, there is demand discovering more SARS-CoV-2 Mpro inhibitors with diverse scaffolds to optimize anti-SARS-CoV-2 lead compounds. In this study, comprehensive in silico and vitro assays were utilized determine potential from TCM compounds against Mpro, which an important therapeutic target SARS-CoV-2. The ensemble docking analysis 18263 15 conformations identified 19 as promising candidates. Further testing validated three showed IC50 values 4.64 ± 0.11, 7.56 0.78, 11.16 0.26 μM, EC50 12.25 1.68, 15.58 0.77, 29.32 1.25 respectively. Molecular dynamics (MD) simulations indicated that complexes remained stable over last 100 ns production run. An binding mode revealed active occupy different subsites (S1, S2, S3, S4) site via specific poses through noncovalent interactions key amino acids (e.g., HIS 41, ASN 142, GLY 143, MET 165, GLU 166, or GLN 189). Overall, study provides evidence indicating natural products obtained could be further used anti-COVID-19 research, justifying investigation herbal medicinal ingredients bioactive constituents targets.

Language: Английский

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Nanobody engineering for SARS-CoV-2 neutralization and detection

Microbiology Spectrum, Journal Year: 2024, Volume and Issue: 12(4)

Published: Feb. 16, 2024

ABSTRACT In response to the ongoing COVID-19 pandemic, quest for coronavirus inhibitors has inspired research on a variety of small proteins beyond conventional antibodies, including robust single-domain antibody fragments, i.e., “nanobodies.” Here, we explore potential nanobody engineering in development antivirals and diagnostic tools. Through fusion domains that target distinct binding sites, engineered multimodular constructs neutralize wild-type SARS-CoV-2 Alpha Delta variants at high potency, with IC 50 values as low pM. Despite simultaneous epitopes, Beta Omicron were more resistant neutralization by nanobodies, which highlights importance accounting antigenic drift design biologics. To further applications outbreak management, present an assay based fusions nanobodies fragments NanoLuc luciferase can detect sub-nanomolar quantities spike protein single step. Our work showcases combat emerging infectious diseases. IMPORTANCE Nanobodies, binders derived from camelid antibody, are highly potent respiratory viruses offer several advantages over antibodies candidates specific therapies, stability production costs. this work, leverage unique properties apply them building blocks new therapeutic We report ultra-potent inhibition comprising multiple modules structure-guided combinations develop carry signal molecules, allowing rapid detection protein. results highlight effective countermeasures, both diagnostic, manage outbreaks viruses.

Language: Английский

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Conformational and Stability Analysis of SARS-CoV-2 Spike Protein Variants by Molecular Simulation

Pathogens, Journal Year: 2025, Volume and Issue: 14(3), P. 274 - 274

Published: March 12, 2025

We performed a comprehensive structural analysis of the conformational space several spike (S) protein variants using molecular dynamics (MD) simulations. Specifically, we examined four well-known (Delta, BA.1, XBB.1.5, and JN.1) alongside wild-type (WT) form SARS-CoV-2. The states each variant were characterized by analyzing their distributions within selected collective variables (CVs), such as inter-domain distances between receptor-binding domain (RBD) N-terminal (NTD). Our primary focus was to identify relevant potential transitions determine set native contacts (NCs) that stabilize these conformations. results reveal genetically more distant variants, JN.1, tend adopt compact compared WT. Additionally, exhibit novel NC profiles, an increased number specific distributed among ionic, polar, nonpolar residues. further analyzed impact mutations, including T478K, N500Y, Y504H. These mutations not only enhance interactions with human host receptor but also alter inter-chain stability introducing additional NCs Consequently, may influence accessibility certain regions neutralizing antibodies. Overall, findings contribute deeper understanding functional variations S variants.

Language: Английский

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Genomic surveillance of SARS-CoV-2 variants in Guangzhou, China, from April 2023 to March 2024

Infection Genetics and Evolution, Journal Year: 2025, Volume and Issue: unknown, P. 105747 - 105747

Published: April 1, 2025

After the relaxation of stringent control measures, nationwide large-scale SARS-CoV-2 surveillance was gradually phased out post-2023, transitioning to focused monitoring Influenza-like Illness (ILI) through sentinel hospitals and laboratory networks. Nationally, respiratory pathogens performed via random sampling, resulting in a lack microbial results Guangzhou China. A crucial area scientific inquiry is whether current cases are attributable emergence novel variant. Throat swab samples were obtained from 1478 outpatients 337 hospitalized patients with fever (temperature ≥ 38 °C) cough or sore throat detect SARS-CoV-2. The positive subjected viral whole-genome sequencing phylogenetic analysis. Respiratory pathogen multiplex PCR tests on stratified samples. detected 517 (28.48 %) patients. There higher rates infection among women, older those who hospitalized. total 299 high-quality sequences obtained, including 12 clades 71 pango lineages. advantageous evolved over three peak periods infection, BA.5 (April 2023) XBB (June July then JN.1 (February 2024). 590 distinct amino acid mutations identified across sequences. highest prevalence observed for spike protein mutations, more than 50 % epidemic peaks detected. Epidemiological profiles interactions between other exhibit considerable variation different seasons, tendency toward suppression within each. Surveillance by Eighth People's Hospital provides snapshot Guangzhou, which consistent national offers important data understanding spread southern

Language: Английский

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Discrimination of SARS-CoV-2 omicron variant and its lineages by rapid detection of immune-escape mutations in spike protein RBD using asymmetric PCR-based melting curve analysis

Virology Journal, Journal Year: 2023, Volume and Issue: 20(1)

Published: Aug. 25, 2023

Abstract Background The SARS-CoV-2 Omicron strain has multiple immune-escape mutations in the spike protein receptor-binding domain (RBD). Rapid detection of these to identify and its lineages is essential for guiding public health strategies patient treatments. We developed a two-tube, four-color assay employing asymmetric polymerase chain reaction (PCR)-based melting curve analysis detect discriminate BA.1, BA.2, BA.4/5, BA.2.75 lineages. Methods presented technique involves combinatory six fluorescent probes targeting L452R, N460K, E484A, F486V, Q493R, Q498R, Y505H within one amplicon RBD ORF1ab N genes. After protocol optimization, analytical performance was evaluated using plasmid templates. Sensitivity assessed based on limit (LOD), reliability by calculating intra- inter-run precision temperatures (T m s). Specificity pseudotyped lentivirus common human respiratory pathogens genomic DNA. used analyze 40 SARS-CoV-2–positive clinical samples (including 36 BA.2 4 BA.4/5 samples) lentiviruses wild-type BA.1 viral RNA control materials, as well 20 SARS-CoV-2–negative samples, accuracy comparing results with those sequencing. Results All genotypes were sensitively identified method LOD 39.1 copies per reaction. coefficients variation T s ≤ 0.69% 0.84%, standard deviations 0.38 °C 0.41 °C, respectively. Validation known demonstrated ability correctly targeted preliminarily characterize Conclusion can provide accurate, reliable, rapid, simple low-cost located variant lineages, use be easily generalized laboratories PCR platform.

Language: Английский

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Genomic surveillance and sequencing of SARS-CoV-2 in Malaysia

Asia-Pacific Journal of Molecular Biology and Biotechnology, Journal Year: 2024, Volume and Issue: unknown, P. 71 - 83

Published: April 16, 2024

This manuscript offers an in-depth review of the genomic surveillance SARS-CoV-2 variants in Malaysia, emphasizing integral role this understanding virus's evolution and informing public health responses. Leveraging platforms like GISAID, Nextstrain, Pangolin classification system, researchers Malaysia their global counterparts share genome sequences clinical data SARS-CoV-2. These tools, particularly Nextstrain for real-time tracking visualization viral evolution, lineage have advanced significant mutations, such as D614G N501Y, impact on virus transmissibility pathogenicity. The study emergence vital insights into its evolutionary trajectories, aiding effective pandemic management. Malaysia's Genomic Surveillance Program, aligned with national immunization efforts, plays a key identifying controlling COVID-19 spread. program integrates molecular, epidemiological, that helps authorities making decision leads to intervention policymaking. details significance monitoring variants, strategies responses, preparing future infectious disease challenges effectively.

Language: Английский

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Neutralizing Antibodies against 10 SARS-CoV-2 Variants at Two Years Post-COVISHIELD Vaccination with Special Reference to Omicron Subvariants and Booster Administration

Vaccines, Journal Year: 2024, Volume and Issue: 12(9), P. 1039 - 1039

Published: Sept. 11, 2024

To study the durability of neutralizing antibodies (NAbs) against ten SARS-CoV-2 variants among COVISHIELD vaccine recipients from Pune, India, 184 vaccinee samples with (pre-positives) or without (pre-negatives) prior antibody positivity were evaluated. estimate NAb levels, a validated ten-plex MSD ACE2 neutralization assay was used. NAbs Alpha, Beta, Delta, and Omicron/subvariants assessed at 1 month (PD2-1) 6 months (PD2-6) post-vaccination, post-booster dose, 2 years (2Y) post-vaccination. In pre-negatives, seropositivity declined PD2-1 to PD2-6 for all (Omicron variants: 14-54% 0%; non-Omicron 66-100% 8-44%). pre-positives, decline in seen only Omicron (14-39%). At PD2-6, significant reduction levels observed vaccinees variants. Irrespective exposure, diminished anti-variant increased significantly following administration booster. conclusion, booster dose did provide cross-neutralizing broad-range improved up [16 (15-18)] two

Language: Английский

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Benchmark Investigation of SARS-CoV-2 Mutants’ Immune Escape with 2B04 Murine Antibody: A Step Towards Unraveling a Larger Picture

Current Issues in Molecular Biology, Journal Year: 2024, Volume and Issue: 46(11), P. 12550 - 12573

Published: Nov. 6, 2024

Even though COVID-19 is no longer the primary focus of global scientific community, its high mutation rate (nearly 30 substitutions per year) poses a threat potential comeback. Effective vaccines have been developed and administered to population, ending pandemic. Nonetheless, reinfection by newly emerging subvariants, particularly latest JN.1 strain, remains common. The rapid this virus demands fast response from community in case an emergency. While immune escape earlier variants was extensively investigated, one still needs comprehensive understanding how specific mutations, especially newest influence antigenic pathogen. Here, we tested silico approaches identify methods for accurate prediction antibody neutralization various mutants. As benchmark, modeled complexes murine 2B04, which neutralizes infection preventing SARS-CoV-2 spike glycoprotein's association with angiotensin-converting enzyme (ACE2). Complexes wild-type, B.1.1.7 Alpha, B.1.427/429 Epsilon were used as positive controls, while B.1.351 Beta, P.1 Gamma, B.1.617.2 Delta, B.1.617.1 Kappa, BA.1 Omicron, Omicron decoys. Three essentially different algorithms employed: forced placement based on template, followed two steps extended molecular dynamics simulations; protein-protein docking utilizing PIPER (an FFT-based method use pairwise interaction potentials); AlphaFold 3.0 model complex structure prediction. Homology modeling assess 3D emerged subvariant, whose crystallographic not yet available Protein Database. After careful comparison these three approaches, able pros cons each method. Protein-protein yielded false-positive results, manual reinforced produced false negative. In contrast, resulted only doubtful result higher overall accuracy-to-time ratio. reasons inaccuracies pitfalls are carefully explained. addition comparative analysis methods, some mechanisms elucidated herein. This provides critical foundation improving predictive accuracy vaccine efficacy against new viral introducing methodologies, pinpointing challenges.

Language: Английский

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Neutralization of Different Variants of SARS-CoV-2 by a F(ab’)2 Preparation from Sera of Horses Immunized with the Viral Receptor Binding Domain

Published: Sept. 8, 2023

The Receptor Binding Domain (RBD) of SARS-CoV-2, the virus responsible for COVID-19 pandemic, is functional region viral Spike protein (S), which involved in cell attachment to target cells. has accumulated progressively mutations its genome, particularly RBD region, many them associated with immune evasion host neutralizing antibodies. Some lineages derived from this evolution, have been classified as Variant Interest (VOI) or Concern (VOC). capacity a F(ab’)2 preparation sera horses immunized was evaluated, by lytic plaque reduction assay, against different SARS-CoV-2 variants. A an hyperimmune serum 15 immunizations RBD, exhibited high titer antibodies ancestral-like strain (1/18,528). title observed variants tested. highest Omicron VOC (4.7 fold), followed Mu VOI (2.6), Delta (1.8 fold) and Gamma (1.5). Even if progressive evaluated observed, still significant titer, (1/7113 1/3918 respectively), strains most resistant neutralization.

Language: Английский

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Neutralization of Different Variants of SARS-CoV-2 by a F(ab′)2 Preparation from Sera of Horses Immunized with the Viral Receptor Binding Domain

Antibodies, Journal Year: 2023, Volume and Issue: 12(4), P. 80 - 80

Published: Dec. 7, 2023

The Receptor Binding Domain (RBD) of SARS-CoV-2, the virus responsible for COVID-19 pandemic, is functional region viral Spike protein (S), which involved in cell attachment to target cells. has accumulated progressively mutations its genome, particularly RBD region, many them associated with immune evasion host neutralizing antibodies. Some lineages derived from this evolution have been classified as Variant Interest (VOI) or Concern (VOC). capacity a F(ab′)2 preparation sera horses immunized was evaluated by lytic plaque reduction assay against different SARS-CoV-2 variants. A hyperimmune serum after nine immunizations exhibited high titer antibodies ancestral-like strain (1/18,528). F(ab’)2 observed variants tested compared activity strain. highest neutralization Omicron VOC (4.7-fold), followed Mu VOI (2.6), Delta (1.8-fold), and Gamma (1.5). Even if progressive observed, still (1/7113 1/3918, respectively), strains most resistant neutralization. Therefore, retained all tested.

Language: Английский

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