No abstract

Estrogen circulating in blood has been proved to be a strong biomarker for breast cancer. A β-glucuronidase enzyme (GUS) from human gastrointestinal tract (GIT) microbiota including probiotics has significant involvement in enhancing the estrogen concentration in blood through deconjugation of glucuronidated estrogens. The present project has been designed to explore GIT microbiome-encoded GUS enzymes (GUSOME) repertoire in normal human and breast cancer patients. For this purpose, a total of nineteen GUS enzymes from human GIT microbes, i.e., seven from healthy and twelve from breast cancer patients have been focused on. Protein sequences of enzymes retrieved from UniProt database were subjected to ProtParam, CELLO2GO, SOPMA (secondary structure prediction method), PDBsum (Protein Database summaries), PHYRE2 (Protein Homology/AnalogY Recognition Engine), SAVES v6.0 (Structure Validation Server), MEME version 5.4.1 (Multiple Em for Motif Elicitation), Caver Web server v 1.1, Interproscan and Predicted Antigenic Peptides tool. Analysis revealed the number of amino acids, isoelectric point, extinction coefficient, instability index and aliphatic index of GUS enzymes in the range of 586–795, 4.91–8.92, 89980–155075, 25.88–40.93 and 71.01–88.10, respectively. Sub-cellular localization of enzyme was restricted to cytoplasm and inner-membrane in case of breast cancer patients’ bacteria as compared to periplasmic space, outer membrane and extracellular space in normal GIT bacteria. The 2-D structure analysis showed α helix, extended strand, β turn and random coil in the range of 27.42–22.66%, 22.04–25.91%, 5.39–8.30% and 41.75–47.70%, respectively. The druggability score was found to be 0.05–0.45 and 0.06–0.80 in normal and breast cancer patients GIT, respectively. The radius, length and curvature of catalytic sites were observed to be 1.1–2.8 Å, 1.4–15.9 Å and 0.65–1.4, respectively. Ten conserved protein motifs with p < 0.05 and width 25–50 were found. Antigenic propensity-associated sequences were 20–29. Present study findings hint about the use of the bacterial GUS enzymes against breast cancer tumors after modifications via site-directed mutagenesis of catalytic sites involved in the activation of estrogens and through destabilization of these enzymes.

No abstract

Cytochrome P450s (P450ome) constitute an extended superfamily group of heme-thiolate enzymes identified in all biological domains. P450omes play a critical role in the oxidation of steroids and fatty acids, xenobiotic degradation of hydrophobic compounds, biosynthesis of hormones, and primary and secondary metabolism in organisms. Aspergillus species are among the most economically important fungal organisms in human medicine, industry, and agriculture worldwide. Exploring insight on the genome-wide annotations of cytochrome P450s in Aspergillus species is necessary for their biosynthetic applications. In this present study, we report the identification of 306 cytochrome P450s and their robust profiling in eight notable Aspergillus species (A. carbonarius, A. clavatus, A. flavus, A. fumigatus, A. nidulans, A. niger, A. oryzae, and A. terreus). Based on the evolutionary relationship, the Aspergillus P450s families clustered into 15 clades, with clades V, I, and XIII recording higher percentages (17.3%, 15.00%, and 14.71%, respectively) of Cyp families. Cyps were classified into 120 families 64 clans, and their putative functions were also elucidated. P450s were predicted to be located in 13 subcellular components, but the endoplasm reticulum was the dominant location across the eight Aspergillus species. Cyps genes of Aspergillus species were associated with seven secondary metabolism-related gene clusters. Elucidating the genome-wide annotations of P450s enzymes in Aspergillus species will form vital potential biotechnological tools that could be harnessed for industrial, pharmaceutical, and agricultural use.

The novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a pathogenic virus responsible for the coronavirus disease 2019 (COVID-19) outbreak. The virus has rapidly spread worldwide and caused serious global health and economic issues. The World Health Organization has declared COVID-19 a pandemic and suggested that all countries should take extreme countermeasures to stop it from spreading. SARS-CoV-2 targets the angiotensin-converting enzyme 2 (ACE2) receptor on human lung cells through receptor binding domain on the spike proteins (S-RBD) via N487, Y489, and G496 residues as previously reported. The virus uses ACE2 to inoculate mRNA and to replicate inside the cells, which results in a severe respiratory syndrome. Patients might experience serious symptoms including fever, cough, inability to taste, shortness of breath, and sometimes respiratory failure. Therefore, developing a vaccine is highly necessary to control the outbreak, which led to our goal in this study to identify antigenic peptide sequences on the S-RBD domain that may induce the immune response to provide protection from the virus. We virtually analyzed S-RBD protein structure by multiple sequence alignment (MSA) via CLUSTAL OMEGA to study the homology of the S-RBD domain in both strains (SARS-CoV and SARS-CoV-2), and the results showed 76% identical shared amino acids. Moreover, the S-RBD sequence for SARS-CoV-2 was blasted against the sequence “486-FNCYFPLQSYGFQ-498” on Drugbank database with a penalty of -1 for each indel, -3 for the mismatch, and with an expected value of 8 to screen for potential molecules that might interact with the target sequence. The blast results showed a possible alignment with complement component 4A (C4-A) protein, a protein involved in autoimmunity and antibody signaling, on the residues F490, C488, P491, Y495, G496, F497, and Q498. Lastly, a molecular docking analysis was performed by ClusPro 2.0 docking system to analyze the binding affinity of C4-A protein to the S-RBD-protein, and the results of the docking analysis showed 30 different bindings with different weighted energy coefficient scores. The top 10 binding conformations were chosen based on the coefficient score values between -856.2 to -985.4. The highest binding affinity of C4-A protein was observed on the target sequence, which might be a therapeutic approach for a possible COVID-19 vaccine. Further experiments are required to synthesize recombinant peptides for S-RBD protein and test it on animal models to check if it will induce C4-A production in response to recombinant S-RBD peptide and antibodies signaling to counter SARS-CoV-2 virus and, hopefully, competing with ACE2 binding to S-protein. Citation Format: Majid Al-Zahrani. A computational approach to identify a possible SARS-CoV-2 vaccine from receptor binding domain peptide sequence on spike glycoproteins [abstract]. In: Proceedings of the AACR Virtual Meeting: COVID-19 and Cancer; 2020 Jul 20-22. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(18_Suppl):Abstract nr S03-03.