Machine Learning to Predict Enzyme-Substrate Interactions in Elucidation of Synthesis Pathways: A Review.

Enzyme-substrate interactions play a fundamental role in elucidating synthesis pathways and synthetic biology, as they allow for the understanding of important aspects of a reaction. Establishing the interaction experimentally is a slow and costly process, which is why this problem has been addressed using computational methods such as molecular dynamics, molecular docking, and Monte Carlo simulations. Nevertheless, this type of method tends to be computationally slow when dealing with a large search space. Therefore, in recent years, methods based on artificial intelligence, such as support vector machines, neural networks, or decision trees, have been implemented, significantly reducing the computing time and covering vast search spaces. These methods significantly reduce the computation time and cover broad search spaces, rapidly reducing the number of interacting candidates, as they allow repetitive processes to be automated and patterns to be extracted, are adaptable, and have the capacity to handle large amounts of data. This article analyzes these artificial intelligence-based approaches, presenting their common structure, advantages, disadvantages, limitations, challenges, and future perspectives.

Interaction models between peptide substrate and Alphavirus Protease nsP2 of Chikungunya and Mayaro and implications to the mechanism of action.

The Arbovirus (Arthropod-borne virus) is a group which comprises viruses whose transmission is carried out by arthropod vectors infecting vertebrates. Some arboviruses related to human diseases have been given considerable relevance as Chikungunya and Mayaro of the family Togaviridae, genus Alphavirus. The lack of proper specific treatment has prompted the requirement for deeper structural studies that could unveil leads to new drugs. Among possible targets, viral proteases are recognized as proteins with big potential. These proteins, termed nsP2 in Alphavirus, have the function of cleaving certain regions of the viral polyprotein, being vital to the viral cycle. In this research, we used docking and molecular dynamics to analyze the contact between the protease nsP2 of Alphavirus Chikungunya and Mayaro and substrates formed by peptides with ten amino acid residues. A model of the Mayaro nsP2 was constructed based on homologous proteases. Our study suggests that the glycine specificity motif, a region where a highly conserved glycine residue in position P2 of the protease substrate is positioned, facilitates the nucleophilic attack by assisting in placing the P1 carbonyl group carbon. Stabilization of different substrate regions maybe explained by relevant contacts with the enzyme. Besides that, the phi and psi angles in the outlier region of the Ramachandran plot found for the P2 glycine of the Chikungunya substrate seems to indicate the necessity of this residue that can accommodate angles not allowed to other residues.Communicated by Ramaswamy H. Sarma.

Probing poly(N-isopropylacrylamide-co-butylacrylate)/cell interactions by atomic force microscopy.

Poly(N-isopropylacrylamide) based hydrogels have been proposed as cell culture supports in cell sheet engineering. Toward this goal, we characterized the poly(N-isopropylacrylamide-co-butylacrylate) copolymer thermo-sensitivity and the cell/copolymer interactions above and below the copolymer lower critical solution temperature. We did that by direct force measurements at different temperatures using an atomic force microscope with either a polystyrene or a glass microbead as probes. We used a copolymer-coated microbead to measure adhesion after a short contact time with a single fibroblast in culture. Statistical analysis of the maximum adhesion force and the mechanical work necessary to separate the probe from the cell surface confirmed the hydrophilic/hydrophobic behavior of poly(N-isopropylacrylamide-co-butylacrylate) as a function of temperature in the range 20-37°C and, consequently, a reversible increase/decrease in cell adhesion with the copolymer. As control experiments we measured interactions between uncoated microbeads with the copolymer hydrogel or cells as well as interaction of the Poly(N-isopropylacrylamide) homopolymer with cells. These results show the potential of an assay based on atomic force microscopy for an in situ and quantitative assessment of cell/substrate interactions and support the use of poly(N-isopropylacrylamide-co-butylacrylate) copolymer as an efficient culture substrate in cell sheet engineering.