Insights on the mutational landscape of the SARS-CoV-2 Omicron variant

The SARS-COV2 Omicron variant has sparked global concern due to the possibility of enhanced transmissibility and escape from vaccines and therapeutics. In this study, we describe the mutational landscape of the Omicron variant using amino acid interaction (AAI) networks. AAI network analysis is particularly well suited for interrogating the impact of constellations of mutations as occur on Omicron that may function in an epistatic manner. Our analyses suggest that as compared to previous variants of concern, the Omicron variant has increased antibody escape breadth due to mutations in class 3 and 4 antibody epitopes as well as increased escape depth due to accumulated mutations in class 1 antibody epitopes. We note certain RBD mutations that might further enhance Omicron escape, and in particular advise careful surveillance of two subclades bearing R346S/K mutations. Further, AAI network analysis suggests that the function of certain therapeutic monoclonal antibodies may be disrupted by Omicron mutations as a result of the cumulative indirect perturbations to the epitope surface properties, despite point-mutation analyses suggesting these antibodies are tolerant of the set of Omicron mutations in isolation. Finally, for several Omicron mutations that do not appear to contribute meaningfully to antibody escape, we find evidence for a plausible role in enhanced transmissibility via disruption of RBD-down conformational stability at the RBD-RBD interface.

Anti-Obesity Properties of Black Pepper (Piper nigrum): Completing Puzzle using Computational Analysis

Pepper (Piper nigrum) is one of the most common spices found in almost every food. Current knowledge informed that pepper regulates physiological activity in obesity. However, the exact mechanism is still poorly understood. This study determined the potential of piperine and piperidine as major compounds in pepper as GHSR-Ghrelin inhibitors due to over-activity of Ghrelin as appetite hormone in obesity. Molecular docking was performed to simulate the binding pattern of piperine and piperidine as GHSR-Ghrelin antagonist. The result showed that piperidine has a lower potential as GHSR-Ghrelin antagonist than piperine based on binding energy calculation and amino acid interaction. Further, piperine binding to GHSR could shift the Ghrelin binding site to the GHSR. In conclusion, piperine may act as an inhibitor of GHSR-Ghrelin interaction to prevent appetite behavior resulting in bodyweight loss in obesity.

Structure-based virtual screening of bioherbicide candidates for weeds in sugarcane plantation using in silico approaches

Weeds in sugarcane have negatively affected the sugar yield rate. Several approaches have been carried out to overcome the weeds, including the usage of diuron as synthetic herbicide. However, the long-term usage of diuron is known to have a negative effect leads to the production of 3,4- Dichloroaniline responsible for soil leach and bioaccumulation. Therefore, this study aimed to find a potential natural herbicide. By mimicking the diuron's mode of action which inhibits the process of photosynthesis through blocking the Photosystem II protein D1 (psbA) of the weeds, fourteen compounds as potential candidate bioherbicides were virtually docked by PyRx v0.9.5 software to the specific site. Three important species of the weeds were chosen including Eleusine indica, Praxelis clematidea, and Momordica charantia. The binding affinity score was further calculated and ranked to screen the top six compounds as bioherbicide candidates. Interaction of each complex and the biological activity prediction were then performed by Discovery Studio software and PASS server, respectively. Aurachin P, Aurachin A, and Cyanobacterin were placed in the top ranked compounds with high binding affinity score around -6 to -9 kcal mol-1 toward the psbA. The amino acid interaction involved in the complex shows 50-90% similar to the control, psbA and diuron complex. Besides, the biological activity prediction of Aurachin P, Aurachin A, and Cyanobacterin exhibits the terms related to the inhibition of photosynthesis process via enzymatic pathway. Thus, the active compounds might have inhibition action in the photosynthesis process and control the weeds in sugarcane.

Amino acid adsorption on tetraphenyl porphyrin films

In this work, metal free, zinc and copper tetraphenyl porphyrin thin films were employed as substrates to study their interaction with glycine, serine, glutamate, lysine and argynine amino acids in order to investigate the effect of the metallic center and the amino acid characteristics in the adsorption phenomena. The amount of amino acid adsorbed on the films was quantified by using the Ruhemann method. Adsorption isotherms were obtained and analyzed in order to predict the adsorption mechanism for each case. In addition, the morphology of the films was investigated before and after the amino acid immersion by using scanning electron and atomic force microscopies. On the other hand, dynamic contact angle measurements were performed to monitor the spreading phenomena and changes in the hydrophobic nature of the surfaces after the amino acid interaction. From the results, it was observed that the largest deposited amino acid on all three surfaces corresponded to the positively charged compounds, while serine was the lowest adsorbed amino acid in all cases. These results can be attributed to electronic interactions between the amino acids’ lateral chains and the electronic [Formula: see text] distribution of the porphyrin macrocycle ring, and they provide important information regarding the amino acid selectivity of adsorption on tetraphenyl porphyrin films.