One of the main obstacles in prevention and treatment of COVID-19 is the rapid evolution of the SARS-CoV-2 Spike protein. Given that Spike is the main target of common treatments of COVID-19, mutations occurring at this virulent factor can affect the effectiveness of treatments. The B.1.617.2 lineage of SARS-CoV-2, being characterized by many Spike mutations inside and outside of its receptor-binding domain (RBD), shows high infectivity and relative resistance to existing cures. Here, utilizing a wide range of computational biology approaches, such as immunoinformatics, molecular dynamics (MD), analysis of intrinsically disordered regions (IDRs), protein-protein interaction analyses, residue scanning, and free energy calculations, we examine the structural and biological attributes of the B.1.617.2 Spike protein. Furthermore, the antibody design protocol of Rosetta was implemented for evaluation the stability and affinity improvement of the Bamlanivimab (LY-CoV55) antibody, which is not capable of interactions with the B.1.617.2 Spike. We observed that the detected mutations in the Spike of the B1.617.2 variant of concern can cause extensive structural changes compatible with the described variation in immunogenicity, secondary and tertiary structure, oligomerization potency, Furin cleavability, and drug targetability. Compared to the Spike of Wuhan lineage, the B.1.617.2 Spike is more stable and binds to the Angiotensin-converting enzyme 2 (ACE2) with higher affinity.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9683856 | PMC |
| http://dx.doi.org/10.1016/j.ijbiomac.2022.11.227 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Robotic Waterjet Resection for Men with Prostate Cancer Suffering from Lower Urinary Tract Symptoms.
Urology
January 2025
S.H. Ho Urology Centre, Department of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong.
Objectives: To evaluate the impact of Aquablation on circulating tumor cells (CTCs) in men with localized prostate cancer.
Methods: This prospective study included subjects with biopsy-positive mpMRI visible lesions (PIRADS ≥ 3) who underwent Aquablation. Ten ml blood samples were collected before, during and after the procedure to measure CTC counts using an immunofluorescence assay.
Spiking-PhysFormer: Camera-based remote photoplethysmography with parallel spike-driven transformer.
Neural Netw
January 2025
Tsinghua University, Beijing, China. Electronic address:
Artificial neural networks (ANNs) can help camera-based remote photoplethysmography (rPPG) in measuring cardiac activity and physiological signals from facial videos, such as pulse wave, heart rate and respiration rate with better accuracy. However, most existing ANN-based methods require substantial computing resources, which poses challenges for effective deployment on mobile devices. Spiking neural networks (SNNs), on the other hand, hold immense potential for energy-efficient deep learning owing to their binary and event-driven architecture.
View Article and Find Full Text PDFVaccination against SARS-CoV-2 provides low-level cross-protection against common cold coronaviruses in mouse and non-human primate animal models.
J Virol
January 2025
Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada.
The common cold coronaviruses are a source of ongoing morbidity and mortality particularly among elderly and immunocompromised individuals. While cross-reactive immune responses against multiple coronaviruses have been described following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and vaccination, it remains unclear if these confer any degree of cross-protection against the common cold coronaviruses. A recombinant fowl adenovirus vaccine expressing the SARS-CoV-2 spike protein (FAdV-9-S19) was generated, and protection from SARS-CoV-2 challenge was shown in K18-hACE2 mice.
View Article and Find Full Text PDFLongitudinal Follow-Up of the Specific Antibody Response to SARS-CoV-2 Vaccination in Colombia.
J Med Virol
January 2025
Centro Internacional de Vacunas, Cali, Colombia.
A total of 5011 adult volunteers attending vaccination centers in different regions of Colombia were enrolled in a 1-year prospective observational cohort study to evaluate the immunogenicity and effectiveness of SARS-CoV-2-based vaccines as part of a National Vaccine Program established to contain the COVID-19 pandemic. Following informed consent, 5,011 participants underwent a sociodemographic survey and PCR testing to assess SARS-CoV-2 infection. Blood samples were collected, and serum fractions were obtained from a participant subsample (n = 3441) at six-time points to assess virus-specific IgG responses to the Spike protein, its Receptor Binding Domain, and the Nucleoprotein by ELISA.
View Article and Find Full Text PDFExploring the Key Indicators for Off-Flavor in Industrial Osmanthus Absolute through Sensomics and Chemometric Approaches.
J Agric Food Chem
January 2025
Zhengzhou Tobacco Research Institute of CNTC, Fengyang Street #2, Zhengzhou, Henan 450001, PR China.
The occurrence of off-flavor in osmanthus absolutes has emerged as a significant concern that could hinder its broad market acceptance and associated economic development. In this study, key off-flavor molecules in industrial osmanthus absolute were identified through sensomics and chemometric approaches. A group of 10 off-flavor (OF) samples, eliciting smoky/phenolic, sweaty/sour, and spicy odors, were compared with 10 pleasant aroma (PA) samples through various analyses, including overall aroma assessment, comprehensive chemical profiling, aroma extract dilution analysis (AEDA), and orthogonal partial least-squares-discriminant analysis (OPLS-DA).
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!