Bioinformatics techniques for efficient structure prediction of SARS-CoV-2 protein ORF7a via structure prediction approaches (preprint)

Protein is the building block for all organisms. Protein structure prediction is always a complicated task in the field of proteomics. DNA and protein databases can find the primary sequence of the peptide chain and even similar sequences in different proteins. Mainly, there are two methodologies based on the presence or absence of a template for Protein structure prediction. Template-based structure prediction (threading and homology modeling) and Template-free structure prediction (ab initio). Numerous web-based servers that either use templates or do not can help us forecast the structure of proteins. In this current study, ORF7a, a transmembrane protein of the SARS-coronavirus, is predicted using Phyre2, IntFOLD, and Robetta. The protein sequence is straightforwardly entered into the sequence bar on all three web servers. Their findings provided information on the domain, the region with the disorder, the global and local quality score, the predicted structure, and the estimated error plot. Our study presents the structural details of the SARS-CoV protein ORF7a. This immunomodulatory component binds to immune cells and induces severe inflammatory reactions.

The Impact of COVID-19 on the Psychological Well-Being of Surgeons in Pakistan: A Multicenter Cross-Sectional Study

Introduction The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic left a profound and pervasive impact on the healthcare infrastructure on a global scale. Since its onset, the pattern of reported cases and its associated mortality had shown variability with intermittent peaks causing a significant effect on the psychological well-being of the surgeons of Pakistan. The aim of this study was to assess the effects of the COVID-19 pandemic on the mental well-being of surgeons in Pakistan. Methods This multicenter cross-sectional study was carried out to assess the impact of COVID-19 on the psychological well-being of surgeons in Pakistan. The validated Self-Reporting Questionnaire-20 (SRQ-20) tool was circulated electronically via Google Forms (Google, Inc., Mountain View, CA, USA) in the practicing surgical fraternity across all five regions of Pakistan, i.e., Sindh, Punjab, Baluchistan, Khyber Pakhtunkhwa (KPK), and Azad Jammu and Kashmir (AJK). Results This study showed that the female gender, having fewer years of working experience, non-satisfaction with the available personal protective equipment (PPE), and working in the public sector were the factors affecting the psychological well-being of surgeons during the pandemic. Conclusion Considering the continuous rise in new cases during the ongoing pandemic, the mental health of surgeons working in low- and middle-income countries (LMIC) such as Pakistan has been significantly affected. There is an undeniable need to pay close attention to their psychological well-being. Measures need to be undertaken to ensure their physical and mental health and wellness.

Vaccine Design from the Ensemble of Surface Glycoprotein Epitopes of SARS-CoV-2: An Immunoinformatics Approach.

The present study aimed to work out a peptide-based multi-epitope vaccine against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We predicted different B-cell and T-cell epitopes by using the Immune Epitopes Database (IEDB). Homology modeling of the construct was done using SWISS-MODEL and then docked with different toll-like-receptors (TLR4, TLR7, and TLR8) using PatchDock, HADDOCK, and FireDock, respectively. From the overlapped epitopes, we designed five vaccine constructs C1-C5. Based on antigenicity, allergenicity, solubility, different physiochemical properties, and molecular docking scores, we selected the vaccine construct 1 (C1) for further processing. Docking of C1 with TLR4, TLR7, and TLR8 showed striking interactions with global binding energy of -43.48, -65.88, and -60.24 Kcal/mol, respectively. The docked complex was further simulated, which revealed that both molecules remain stable with minimum RMSF. Activation of TLRs induces downstream pathways to produce pro-inflammatory cytokines against viruses and immune system simulation shows enhanced antibody production after the booster dose. In conclusion, C1 was the best vaccine candidate among all designed constructs to elicit an immune response SARS-CoV-2 and combat the coronavirus disease (COVID-19).