On the importance of the distance measures used to train and test knowledge-based potentials for proteins

An In Silico Design of Peptides Targeting the S1/S2 Cleavage Site of the SARS-CoV-2 Spike Protein

SARS-CoV-2, responsible for the COVID-19 pandemic, invades host cells via its spike protein, which includes critical binding regions, such as the receptor-binding domain (RBD), the S1/S2 cleavage site, the S2 cleavage site, and heptad-repeat (HR) sections. Peptides targeting the RBD and HR1 inhibit binding to host ACE2 receptors and the formation of the fusion core. Other peptides target proteases, such as TMPRSS2 and cathepsin L, to prevent the cleavage of the S protein. However, research has largely ignored peptides targeting the S1/S2 cleavage site. In this study, bioinformatics was used to investigate the binding of the S1/S2 cleavage site to host proteases, including furin, trypsin, TMPRSS2, matriptase, cathepsin B, and cathepsin L. Peptides targeting the S1/S2 site were designed by identifying binding residues. Peptides were docked to the S1/S2 site using HADDOCK (High-Ambiguity-Driven protein-protein DOCKing). Nine peptides with the lowest HADDOCK scores and strong binding affinities were selected, which was followed by molecular dynamics simulations (MDSs) for further investigation. Among these peptides, BR582 and BR599 stand out. They exhibited relatively high interaction energies with the S protein at -1004.769 ± 21.2 kJ/mol and -1040.334 ± 24.1 kJ/mol, respectively. It is noteworthy that the binding of these peptides to the S protein remained stable during the MDSs. In conclusion, this research highlights the potential of peptides targeting the S1/S2 cleavage site as a means to prevent SARS-CoV-2 from entering cells, and contributes to the development of therapeutic interventions against COVID-19.

Strain sonoelastography in asymptomatic individuals and individuals with knee osteoarthritis: an evaluation of quadriceps and patellar tendon

An advanced ultrasound imaging technique, sonoelastography (SE) is used to evaluate tissue elasticity. To determine SE potential to detect pathological-related changes, and characteristics related to tendon pathology we aimed to (1) compare quadriceps and patellar tendon findings in individuals with knee osteoarthritis (KOA) and asymptomatic older adults (AC), and (2) explore associations between SE, participant characteristics (age, BMI, and leg circumference) and KOA status. 84 participants (47; KOA and 37; asymptomatic older adults) underwent SE examination of quadriceps (distal) and patellar (distal, proximal) tendon in a supine position with the knee bent at 30°. Colour score (CS) and Elasticity Ratio (ER) analysis were performed by a blinded experienced operator using Esaote Mylab 70 XVG Ultrasound equipment. Significantly reduced elasticity in the distal quadriceps (median (IQR) 2(2), 3(1), p = 0.033 for KOA and AC, respectively) and proximal patellar (3(1), 3(0), p = 0.001) tendons and more elastic distal patellar (1.50 (0.55), 1.87 (0.72), p = 0.034) tendons were observed in the KOA group. Significant associations) were identified between SE and participant BMI (Rs = − 0.249–0.750, p < 0.05) and leg circumference (Rs = − 0.260–0.903, p < 0.05). Age, BMI and KOA status, were independent explanatory variables of SE CS findings at the distal quadriceps tendon patellar tendon, proximal patellar tendon and distal patellar tendon, explaining 66%, 81% and 64% of variance, respectively. Age, BMI and KOA status were independent explanatory variables of SE ER findings at the distal patellar tendon explaining 19% of variance. Potentially clinically relevant altered tendon stiffness were observed between individuals with KOA and asymptomatic controls. Key KOA risk factors and participant characteristics explained variance in tendon stiffness. Findings provide context for future studies to investigate the potential for targeted SE detected early clinical management based on associated participant characteristics.

In Silico Template Selection of Short Antimicrobial Peptide Viscotoxin for Improving Its Antimicrobial Efficiency in Development of Potential Therapeutic Drugs

Rapid increase in antibiotic resistance has posed a worldwide threat, due to increased mortality, morbidity, and expenditure caused by antibiotic-resistant microbes. Recent development of the antimicrobial peptides like viscotoxin (Vt) has been successfully comprehended as a substitute for classical antibiotics. A structurally stable peptide, Vt can enhance antimicrobial property and can be used for various developmental purposes. Thus, structural stability among the antimicrobial peptides, Vt A1 (3C8P), A2 (1JMN), A3 (1ED0), B (1JMP), and C (1ORL) of Viscus album was computationally analyzed. In specific, the static confirmation of VtA3 showed high number of intramolecular interactions, along with an increase in hydrophobicity than others comparatively. Further, conformational sampling was used to analyze various geometrical parameters such as root mean square deviation, root mean square fluctuation, radius of gyration, and ovality which also revealed the structural stability of VtA3. Moreover, the statistically validated contours of surface area, lipophilicity, and distance constraints of disulfide bonds also supported the priority of VtA3 with respect to stability. Finally, the functional activity of peptides was accessed by computing their free energy of membrane association and membrane interactions, which defined VtA3 as functionally stable. Currently, peptide-based antibiotics and nanoparticles have attracted the pharmaceutical industries for their potential therapeutic applications. Thereby, it is proposed that viscotoxin A3 (1ED0) could be used as a preeminent template for scaffolding potentially efficient antimicrobial peptide-based drugs and nanomaterials in future.