APLpred: A machine learning-based tool for accurate prediction and characterization of asparagine peptide lyases using sequence-derived optimal features.

Asparagine peptide lyase (APL) is among the seven groups of proteases, also known as proteolytic enzymes, which are classified according to their catalytic residue. APLs are synthesized as precursors or propeptides that undergo self-cleavage through autoproteolytic reaction. At present, APLs are grouped into 10 families belonging to six different clans of proteases. Recognizing their critical roles in many biological processes including virus maturation, and virulence, accurate identification and characterization of APLs is indispensable. Experimental identification and characterization of APLs is laborious and time-consuming. Here, we developed APLpred, a novel support vector machine (SVM) based predictor that can predict APLs from the primary sequences. APLpred was developed using Boruta-based optimal features derived from seven encodings and subsequently trained using five machine learning algorithms. After evaluating each model on an independent dataset, we selected APLpred (an SVM-based model) due to its consistent performance during cross-validation and independent evaluation. We anticipate APLpred will be an effective tool for identifying APLs. This could aid in designing inhibitors against these enzymes and exploring their functions. The APLpred web server is freely available at https://procarb.org/APLpred/.

Identification of High-Affinity Inhibitors of Cyclin-Dependent Kinase 2 Towards Anticancer Therapy.

Cyclin-dependent kinase 2 (CDK2) is an essential protein kinase involved in the cell cycle regulation. The abnormal activity of CDK2 is associated with cancer progression and metastasis. Here, we have performed structure-based virtual screening of the PubChem database to identify potent CDK2 inhibitors. First, we retrieved all compounds from the PubChem database having at least 90% structural similarity with the known CDK2 inhibitors. The selected compounds were subjected to structure-based molecular docking studies to investigate their pattern of interaction and estimate their binding affinities with CDK2. Selected compounds were further filtered out based on their physicochemical and ADMET properties. Detailed interaction analysis revealed that selected compounds interact with the functionally important residues of the active site pocket of CDK2. All-atom molecular dynamics simulation was performed to evaluate conformational changes, stability and the interaction mechanism of CDK2 in-complex with the selected compound. We found that binding of 6-N,6-N-dimethyl-9-(2-phenylethyl)purine-2,6-diamine stabilizes the structure of CDK2 and causes minimal conformational change. Finally, we suggest that the compound (PubChem ID 101874157) would be a promising scaffold to be further exploited as a potential inhibitor of CDK2 for therapeutic management of cancer after required validation.

Protective effects of Emblica officinalis (Amla) on metal-induced lipid peroxidation in human erythrocytes.

The protective potential of Emblica officinalis (amla) was investigated on metal-induced lipid per oxidation in human erythrocytes. Increases in the levels of MDA and catalase activity were assessed as lipid per oxidation. In addition, glutathione peroxidase (GPX), glutathione (GSH), and ascorbic acid levels were assessed as antioxidant indices. Preliminary investigation of the extract exhibited a significant reduction in lipid per oxidation and an increase in antioxidant abilities, such as a decrease in MDA, GPx and GSH (P<0.05). A significant reduction in erythrocyte hemolysis induced by hydrogen peroxide was observed using amla extract (P<0.05). These findings show that amla extract has significant protective potential against lipid per oxidation.

Review-Ulcerative colitis and probiotics: An overview.

Ulcerative colitis is an inflammatory disease of the large intestine whose effects are bloody diarrhea, cramping and bloating. The disease is usually relapsing and remitting. However, the cause of ulcerative colitis is not yet known. Due to this reason, finding an effective treatment has been a great challenge. The suggested medical treatment is usually composed of two portions; keeping the flare up from happening and treating the flare up when it has happened. Active flare ups are treated with corticosteroids. There are several hypothesis which suggest that ulcerative colitis could be due to the micro flora present in gut. For this reason, several researchers tried to modify the gut microflora with probiotics. However, there is no probiotics found that can induce emission faster than the placebo. The ulcerative colitis patients taking probiotics showed fewer and less severe symptoms during the flare up. This means that even though the probiotics did not end up the flare up faster, it slowed up the severity of the symptoms of the patients.