Staff

Abstract:
Rational design of novel antibody therapeutics against viral infections such as coronavirus relies on surface complementarity and high affinity for their effectiveness. Here, we explore an additional property of protein complexes, the intrinsic mechanical stability, in SARS-CoV-2 variants when complexed with a potent antibody. In this study, we utilized a recent implementation of the GōMartini 3 approach to investigate large conformational changes in protein complexes with a focus on the mechanostability of the receptor-binding domain (RBD) from WT, Alpha, Delta, and XBB.1.5 variants in complex with the H11-H4 nanobody. The analysis revealed moderate differences in mechanical stability among these variants. Also, we identified crucial residues in both the RBD and certain protein segments in the nanobody that contribute to this property. By performing pulling simulations and monitoring the presence of specific native and non-native contacts across the protein complex interface, we provided mechanistic insights into the dissociation process. Force-displacement profiles indicate a tensile force clamp mechanism associated with the type of protein complex. Our computational approach not only highlights the key mechanostable interactions that are necessary to maintain overall stability, but it also paves the way for the rational design of potent antibodies that are mechanostable and effective against emergent SARS-CoV-2 variants.

Keywords:
SARS-CoV-2, GōMartini 3, Nanomechanics, Protein complexes, protein engineering, MD, native contacts

Abstract:
Argopecten purpuratus, a mollusk very cultivated in Peru, is a species whose ecological relations with respect to the epibionts that colonize it are not well known. For that reason, the objective of this research was to determine the effect of epibionts on valvar growth, total weight, gonad weight, adductor muscle weight, and survival of this cultured species in Samanco Bay. Four lanterns of 2 m and 10 floors were placed with 25 organisms, of 7 cm each, per floor, in two treatments: with epibiont removal (T1) and without removal (T2). The data was obtained after harvest, and the epibiont species on the right and left valves were identified and quantified in T1 and T2. In addition, the Absolute Growth Rate (AGR) was calculated for the meristic records, and the t Student test was applied to compare averages. Furthermore, mortality was recorded at harvest. The analyses allowed the identification of 43 epibiont species, 3 of them endolithic. The greatest biomass is of filter feeders: 70.1% in T1 and 90.9% in T2, and concentrated in 4 species, with limited development in T1. The biomass on the right valve at T1 and T2 represented 80.7 and 151.8% of the weight of the organism, respectively, and on the left valve 89.3 and 95.1%. All Absolute Growth Rates at T1 were higher than at T2, although without statistical significance. Mortality at T1 and T2 was negligible. This research has determined that the epibionts S. patagonicus, C. intestinalis, Hidroydes sp., and B. neritina, qualified as engineered species, are the predominant species on A. purpuratus in suspended cultures. Likewise, treatments with epibiont removal showed a lower development of these and 39 other associated species of lesser importance in terms of number and biomass. Our results allow us to infer that the development of epibionts can generate important stress in A. purpuratus, resulting in losses in the profitability of companies dedicated to this activity.

Keywords:
Argopecten purpuratus, Aquaculture, Epibiosis, Biofouling, Bivalve

Abstract:
Context
SARS-CoV-2, responsible for COVID-19, has led to over 500 million infections and more than 6 million deaths globally. There have been limited effective treatments available. The study aims to find a drug that can prevent the virus from entering host cells by targeting specific sites on the virus’s spike protein.

Method
We examined 13,397 compounds from the Malaria Box library against two specific sites on the spike protein: the receptor-binding domain (RBD) and a predicted cryptic pocket. Using virtual screening, molecular docking, molecular dynamics, and MMPBSA techniques, they evaluated the stability of two compounds. TCMDC-124223 showed high stability and binding energy in the RBD, while TCMDC-133766 had better binding energy in the cryptic pocket. The study also identified that the interacting residues are conserved, which is crucial for addressing various virus variants. The findings provide insights into the potential of small molecules as drugs against the spike protein.

Keywords:
SARS-CoV-2, Molecular docking, Spike protein, Cryptic pocket, MMPBSA