ACE2 Peptide Fragment Interaction with Different S1 Protein Sites

Effect of Nasal Irrigation in Children With Omicron Variant of COVID-19 Infection

Objective: To explore the effect of nasal irrigation on the disappearance of symptoms and nucleic acid conversion in children with Omicron variant. Methods: This quasi-experimental study included children diagnosed with asymptomatic, mild, and moderate Omicron variant infection during the isolation observation period in the Shandong Public Health Clinical Center between April 1, 2022 and May 1, 2022. The children were divided into a routine group (received Lianhua Qingwen (LhQw) Granules), isotonic saline group (received LhQw Granules combined with isotonic saline nasal irrigation), and hypertonic saline group (received LhQw Granules combined with 3% hypertonic saline nasal irrigation), respectively. The primary outcomes were the time of symptom disappearance and nucleic acid conversion time. The secondary outcomes were peripheral white blood cell count (WBC), lymphocyte count (LYM), neutrophil count (NEU), and C-reactive protein (CRP) levels. Results: A total of 60 children (7.26 ± 3.15 years old) were included (20 per group). The average time of nucleic acid conversion in the 2 saline nasal irrigation groups was significantly reduced compared with the routine group (all P < 0.001), while the fever time and cough duration among the 3 groups were comparable (all P > 0.05). LYM count in the 2 saline nasal irrigation groups was significantly increased after treatment compared to before treatment and was significantly higher than in the routine group (all P < 0.05). There was no significant difference in LYM count between the isotonic and hypertonic saline groups (P = 0.76). Additionally, all children in the saline group well tolerated the treatment, and no adverse events occurred in the isotonic saline group. Conclusions: Timely use of saline nasal irrigation may promote nucleic acid conversion in children with Omicron virus infection.

Design of protein-binding peptides with controlled binding affinity: the case of SARS-CoV-2 receptor binding domain and angiotensin-converting enzyme 2 derived peptides

The development of methods able to modulate the binding affinity between proteins and peptides is of paramount biotechnological interest in view of a vast range of applications that imply designed polypeptides capable to impair or favour Protein-Protein Interactions. Here, we applied a peptide design algorithm based on shape complementarity optimization and electrostatic compatibility and provided the first experimental in vitro proof of the efficacy of the design algorithm. Focusing on the interaction between the SARS-CoV-2 Spike Receptor-Binding Domain (RBD) and the human angiotensin-converting enzyme 2 (ACE2) receptor, we extracted a 23-residues long peptide that structurally mimics the major interacting portion of the ACE2 receptor and designed in silico five mutants of such a peptide with a modulated affinity. Remarkably, experimental KD measurements, conducted using biolayer interferometry, matched the in silico predictions. Moreover, we investigated the molecular determinants that govern the variation in binding affinity through molecular dynamics simulation, by identifying the mechanisms driving the different values of binding affinity at a single residue level. Finally, the peptide sequence with the highest affinity, in comparison with the wild type peptide, was expressed as a fusion protein with human H ferritin (HFt) 24-mer. Solution measurements performed on the latter constructs confirmed that peptides still exhibited the expected trend, thereby enhancing their efficacy in RBD binding. Altogether, these results indicate the high potentiality of this general method in developing potent high-affinity vectors for hindering/enhancing protein-protein associations.

Effect of nasal irrigation in adults infected with Omicron variant of COVID-19: A quasi-experimental study

Objective

To investigate the effect of nasal irrigation on the duration of symptoms and nucleic acid conversion in adults infected with the Omicron variant of COVID-19.

Methods

This quasi-experimental study enrolled patients diagnosed with asymptomatic, mild, or moderate Omicron infection at the Shandong Public Health Clinical Center between April 1, 2022 and May 1, 2022. Patients were divided into two groups to receive Lianhua Qingwen granules and traditional Chinese medicine (TCM) prescriptions (conventional group) and 3% hypertonic saline nasal irrigation based on conventional treatment (nasal irrigation groups), respectively. Primary outcomes were symptom disappearance time and nucleic acid negative conversion time. Secondary outcomes were peripheral blood white blood cell (WBC), lymphocyte (LYM) count, neutrophil (NEU) count, C-reactive protein (CRP) level, and chest CT examination findings.

Results

Eighty patients were included (40 patients/group). Multiple linear regression analysis showed that, after adjustment for comorbidities, smoking history, LYM count, and Ct values of N gene, the patients in the nasal irrigation group were more likely to get lower nucleic acid negative conversion time (β = -11.052, 95% CI: -8.277-13.827, P < 0.001) compared with the conventional group. The symptom disappearance time showed no significant improvement (P > 0.05). Subgroup analysis for treatment-naïve patients in the nasal irrigation group showed similar nucleic acid negative conversion time improvement (P = 0.038).

Conclusion

Early nasal irrigation shortens the nucleic acid negative conversion time in adults infected with the Omicron variant but without improvements in symptom disappearance time.

Inhibition of SARS-CoV-2 pathogenesis by potent peptides designed by the mutation of ACE2 binding region

The outbreak of COVID-19 has resulted in millions of deaths. Despite all attempts that have been made to combat the pandemic, the re-emergence of new variants complicated SARS-CoV-2 eradication. The ongoing global spread of COVID-19 demands the incessant development of novel agents in vaccination, diagnosis, and therapeutics. Targeting receptor-binding domain (RBD) of spike protein by which the virus identifies host receptor, angiotensin-converting enzyme (ACE2), is a promising strategy for curbing viral infection. This study aims to discover novel peptide inhibitors against SARS-CoV-2 entry using computational approaches. The RBD binding domain of ACE2 was extracted and docked against the RBD. MMPBSA calculations revealed the binding energies of each residue in the template. The residues with unfavorable binding energies were considered as mutation spots by OSPREY. Binding energies of the residues in RBD-ACE2 interface was determined by molecular docking. Peptide inhibitors were designed by the mutation of RBD residues in the virus-receptors complex which had unfavorable energies. Peptide tendency for RBD binding, safety, and allergenicity were the criteria based on which the final hits were screened among the initial library. Molecular dynamics simulations also provided information on the mechanisms of inhibitory action in peptides. The results were finally validated by molecular docking simulations to make sure the peptides are capable of hindering virus-host interaction. Our results introduce three peptides P7 (RAWTFLDKFNHEAEDLRYQSSLASWN), P13 (RASTFLDKFNHEAEDLRYQSSLASWN), and P19 (RADTFLDKFNHEAEDLRYQSSLASWN) as potential effective inhibitors of SARS-CoV-2 entry which could be considered in drug development for COVID-19 treatment.

Virtual and biochemical screening to identify the inhibitors of binding between SARS-CoV-2 spike protein and human angiotensin-converting enzyme 2

Severe acute respiratory syndrome coronavirus (SARS-CoV-2) appeared as a new viral pathogen and caused the COVID-19 pandemic worldwide. Since the antiviral medicines effective for the treatment of COVID-19 are rare, it is necessary to identify the new candidate molecules for chemotherapy. The glycosylated Spike protein (S-protein) of SARS-CoV-2 plays a critical role in entering into the host cell through a direct interaction with human angiotensin-converting enzyme 2 (ACE2). For this reason, S-protein has served as one of the most effective therapeutic targets for discovering the antiviral medicines for COVID-19. In this work, we report the new small-molecule inhibitors of the interaction between the S-protein of SARS-CoV-2 and human ACE2, which were discovered through the structure-based virtual screening and in vitro biochemical binding assays. As a consequence of combining the computational and experimental validations, three novel inhibitors against the binding of S-protein and ACE2 were found with the associated IC₅₀ values ranging from 50 to 100 μM. Although the biochemical potencies are moderate, the newly found inhibitors are worth being considered for further investigation by structure-activity relationship analysis to maximize the antiviral activity because of the low molecular weights and good physicochemical properties as a drug candidate. The interaction patterns of the new inhibitors in the ACE2-binding region of S-protein are addressed in detail.