A minireview on the perturbation effects of polar groups to direct nanoscale hydrophobic interaction and amphiphilic peptide assembly

Whiteleg shrimp-derived Cryptides induce mitochondrial-mediated cytotoxicity in human breast Cancer

Breast cancer remains the most prevalent cancer in females. The triple negative subtype of breast cancer is associated with higher recurrence rates and poorer prognosis, lack of effective targeted therapy options, and frequently becoming unresponsive to chemotherapy. This study investigates the in vitro anti-cancer potential of our previously in silico-discovered cryptides, from Penaeus vannamei, against MCF-7, MCF-7-CR, and MDA-MB-231 cancer cell lines. Five cryptides-AD4, AD7, AD8, AD11, and AD12-were tested using the MTT assay, revealing selective toxicity against cancer cells. The lowest and highest calculated IC50 values were for AD12 against MCF-7-CR (∼4.6 μM) and MDA-MB-231 (∼20 μM), respectively. Mechanistic studies showed that the cytotoxicity mediated by cryptides, AD7 and AD8, induced loss of mitochondrial membrane potential, release of mitochondrial cytochrome C, and cleavage of caspases that were associated with BAX activation in MCF-7 and MDA-MB-231 cells. Furthermore, our results showed that both MCF-7 and MDA-MB-231 cells treated with AD7 or AD8 exhibited nuclei condensation, activation of Caspase 3/7, leading to apoptotic cell death associated with intrinsic apoptotic cell signaling mechanism. However, further investigation showed that both AD7 and AD8 peptides promoted up-regulation of FAS and p53 in MCF-7 cells while down-regulated the expression of both FAS and p53 in MDA-MB-231 cells, suggesting cell-type dependent apoptotic cell signaling mechanisms. Moreover, both AD7 and AD8 demonstrated cytotoxic and disintegration effects in 3D cancer model. This study highlights the anticancer potential of marine-derived cryptides against challenging breast cancer subtypes, including triple-negative breast cancer (TNBC), with selective cytotoxicity and potential to overcome resistance and recurrence.

Application of Hierarchical Clustering to Analyze Solvent-Accessible Surface Area Patterns in Amycolatopsis lipases

Simple Summary

Solvent-Accessible Surface Area (SASA) as the one dimensional structure property of the protein considers as the measuring the exposure of an amino acid residue to the solvent in one protein. It is an important structural property as the active sites of proteins are mostly located on the protein surfaces. The aim of this paper is to provide the clear information on different Amycolatopsis eburnea lipases based on the SASA patterns. This information could help in recognizing the structural stability and conformation as well as precise clustering them for revealing lipase evolution.

Abstract

The wealth of biological databases provides a valuable asset to understand evolution at a molecular level. This research presents the machine learning approach, an unsupervised agglomerative hierarchical clustering analysis of invariant solvent accessible surface areas and conserved structural features of Amycolatopsis eburnea lipases to exploit the enzyme stability and evolution. Amycolatopsis eburnea lipase sequences were retrieved from biological database. Six structural conserved regions and their residues were identified. Total Solvent Accessible Surface Area (SASA) and structural conserved-SASA with unsupervised agglomerative hierarchical algorithm were clustered lipases in three distinct groups (99/96%). The minimum SASA of nucleus residues was related to Lipase-4. It is clearly shown that the overall side chain of SASA was higher than the backbone in all enzymes. The SASA pattern of conserved regions clearly showed the evolutionary conservation areas that stabilized Amycolatopsis eburnea lipase structures. This research can bring new insight in protein design based on structurally conserved SASA in lipases with the help of a machine learning approach.