Abdus Shukur Imran

Emerging multidrug‐resistant (MDR) strains are the main challenges to the progression of new drug discovery. To diminish infectious disease–causing pathogens, new antibiotics are required while the drying pipeline of potent antibiotics is adding to the severity. Plant secondary metabolites or phytochemicals including alkaloids, phenols, flavonoids, and terpenes have successfully demonstrated their inhibitory potential against the drug‐resistant pathogens. In quest of potential phytochemicals, we selected tea (Camellia sinensis) and agarwood (Aquilaria malaccensis) leaves for antimicrobial activity. Fresh tea leaves were collected in three varieties, namely, BT‐6, BT‐7, and BT‐8, including green tea (nonfermented tea), black tea (fully fermented tea), and agarwood leaves collected from Sylhet region of Bangladesh. This study is aimed at analyzing the phytochemical constituency and antimicrobial activity of tea and agarwood leaf extracts and analyzing if there is a combined effect or synergistic activity against multidrug‐resistant pathogens. The antimicrobial activity of tea and agarwood leaf extracts was analyzed against MDR pathogenic bacteria and fungus. Qualitative and quantitative phytochemical constituency profiling of these six leaf extracts was evaluated, and preliminary screening exhibited that most of the leaves contained diverse groups of metabolites (alkaloids, tannin, flavonoids, glycosides, saponins, etc.). The highest amounts of TPC (total phenolic content) (110.16 ± 0.48 μg/mg) were found in BT‐7 in ethanol extracts, and BT‐8 in methanol extracts possessed the highest (128.1 ± 0.43 μg/mg) TFC (total flavonoid content). Notably, green tea showed remarkable results in TPC and TFC. In antioxidant scavenging activity, BT‐7 and green tea showed significant IC₅₀ values which were 13.23 and 20.75 mg/mL, respectively. In antimicrobial assays, both 50 μL of each tea and agarwood leaf extract antimicrobial activities were examined against 50 μL of each bacterial and fungal culture. In synergistic activity, 50 μL of each type of leaf extracts was poured over the commercial antibiotics to evaluate their synergism, additive, or antagonism activity against the multidrug‐resistant pathogens. In the antimicrobial activity test, green tea showed a maximum diameter (22.0 ± 1.1 mm) zone of inhibition against Klebsiella pneumoniae whereas BT‐8 showed 22.0 ± 2.5 mm against Pseudomonas aeruginosa. Indeed, fresh tea BT‐6 and BT‐7 both showed remarkable zone of inhibition against the selected microbes including Gram‐negative and Gram‐positive bacteria. Besides, leaf extract also showed antimicrobial activity against pathogenic fungus Mucor circinelloides. Aiming to increase antibiotic resistance efficacy, synergistic activities were evaluated among leaf extracts and antibiotics against the selected pathogens where synergism, antagonism, and additive results were noted. Combination of BT‐8 extracts with antibiotics (ceftiofur) showed the highest synergism nearly 36 mm of the zone of inhibition against Escherichia coli. Additionally, green tea with gentamicin and erythromycin also showed remarkable synergism 35 and 33 mm against Mucor circinelloides and E. coli, respectively. Tea and agarwood leaves grown in Bangladesh possess high antioxidant activity, promising antibacterial and antifungal activity, thus might provide a potential source for drug discovery.

The common octopus is a cephalopod species subject to active fisheries, with great potential in the aquaculture and food industry, and which serves as a model species for biomedical and behavioral studies. The analysis of the skin mucus allows us to study their health in a non-invasive way, by using a hardly exploited discard of octopus in the fishing sector. A shotgun proteomics approach combined with liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) using an Orbitrap-Elite instrument was used to create a reference dataset from octopus skin mucus. The final proteome compilation was investigated by integrated in-silico studies, including Gene Ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, network studies, and prediction and characterization analysis of potential bioactive peptides. This work presents the first proteomic analysis of the common octopus skin mucus proteome. This library was created by merging 5937 identified spectra of 2038 different peptides. A total of 510 non-redundant proteins were identified. Obtained results show proteins closely related to the defense, which highlight the role of skin mucus as the first barrier of defense and the interaction with the environment. Finally, the potential of the bioactive peptides with antimicrobial properties, and their possible application in biomedicine, pharmaceutical, and nutraceutical industry was addressed.

The common octopus (Octopus vulgaris) is nowadays the most demanded cephalopod species for human consumption. This species was also postulated for aquaculture diversification to supply its increasing demand in the market worldwide, which only relies on continuously declining field captures. In addition, they serve as model species for biomedical and behavioral studies. Body parts of marine species are usually removed before reaching the final consumer as by-products in order to improve preservation, reduce shipping weight, and increase product quality. These by-products have recently attracted increasing attention due to the discovery of several relevant bioactive compounds. Particularly, the common octopus ink has been described as having antimicrobial and antioxidant properties, among others. In this study, the advanced proteomics discipline was applied to generate a common octopus reference proteome to screen potential bioactive peptides from fishing discards and by-products such as ink. A shotgun proteomics approach by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) using an Orbitrap Elite instrument was used to create a reference dataset from octopus ink. A total of 1432 different peptides belonging to 361 non-redundant annotated proteins were identified. The final proteome compilation was investigated by integrated in silico studies, including gene ontology (GO) term enrichment, pathways, and network studies. Different immune functioning proteins involved in the innate immune system, such as ferritin, catalase, proteasome, Cu/Zn superoxide dismutase, calreticulin, disulfide isomerase, heat shock protein, etc., were found in ink protein networks. Additionally, the potential of bioactive peptides from octopus ink was addressed. These bioactive peptides can exert beneficial health properties such as antimicrobial, antioxidant, antihypertensive, and antitumoral properties and are therefore considered lead compounds for developing pharmacological, functional foods or nutraceuticals.

Multidrug-resistant Vibrio parahaemolyticus has become a significant public health concern. The development of effective drugs and vaccines against Vibrio parahaemolyticus is the current research priority. Thus, we aimed to find out effective drug and vaccine targets using a comprehensive genome-based analysis. A total of 4822 proteins were screened from V. parahaemolyticus proteome. Among 16 novel cytoplasmic proteins, ‘VIBPA Type II secretion system protein L’ and ‘VIBPA Putative fimbrial protein Z’ were subjected to molecular docking with 350 human metabolites, which revealed that Eliglustat, Simvastatin and Hydroxocobalamin were the top drug molecules considering free binding energy. On the contrary, ‘Sensor histidine protein kinase UhpB’ and ‘Flagellar hook-associated protein of 25 novel membrane proteins were subjected to T-cell and B-cell epitope prediction, antigenicity testing, transmembrane topology screening, allergenicity and toxicity assessment, population coverage analysis and molecular docking analysis to generate the most immunogenic epitopes. Three subunit vaccines were constructed by the combination of highly antigenic epitopes along with suitable adjuvant, PADRE sequence and linkers. The designed vaccine constructs (V1, V2, V3) were analyzed by their physiochemical properties and molecular docking with MHC molecules- results suggested that the V1 is superior. Besides, the binding affinity of human TLR-1/2 heterodimer and construct V1 could be biologically significant in the development of the vaccine repertoire. The vaccine-receptor complex exhibited deformability at a minimum level that also strengthened our prediction. The optimized codons of the designed construct was cloned into pET28a(+) vector of E. coli strain K12. However, the predicted drug molecules and vaccine constructs could be further studied using model animals to combat V. parahaemolyticus associated infections.

Corchorus capsularis, commonly known as jute occupies the leading position in the production of natural fibre and fibre based products alongside lower environmental threat. Nowadays, the study of lignin biosynthesis pathways with other molecular basis of fibres formation are being more focused for its economic perspective. Small noncoding ∼21 to 24 nt nucleotides long microRNAs play significant roles in regulating the gene expression as well as different functions in cellular growth and development. Here, the study adopted a comprehensive in silico approach to identify and characterize the conserved miRNAs in the genome of C. capsularis including specific gene targets involved in the crucial cellular process. Expressed Sequence Tags (ESTs) based homology search of 3350 known miRNAs of dicotyledons were allowed against 763 non-redundant ESTs of jute genome resulted in the prediction of 5 potential miRNA candidates belonging five different miRNA families (miR1536, miR9567-3p, miR4391, miR11300, and miR8689). The putative miRNAs were 18 nucleotide length, within a range of -0.49 to -1.56 MFEI values and 55% to 61% of (A+U) content of their correspondence pre-miRNAs. A total of 1052 gene targets of putative miRNAs were identified and their functions were extensively analyzed. Most of the gene targets were involved in plant growth, cell cycle regulation, organelle synthesis, developmental process and environmental responses. The five gene targets, namely, NAC Domain Containing Protein, WRKY DNA binding protein, 3-dehydroquinate synthase, S-adenosyl-L-Met–dependent methyl transferase and Vascular-related NAC-Domain were found to be involved in the lignin biosynthesis, phenylpropanoid pathways and secondary wall formation which could play significant roles in the overall fibre biogenesis. The characterization of conserved miRNAs and their functional annotation of specific gene targets might enhance the more miRNA discovery, strengthening the complete understanding of miRNAs association in the cellular basis of lignin biosynthesis towards the production of high standard jute products.

Multidrug-resistant Vibrio parahaemolyticus has become a significant threat to human health as well as aquaculture, prioritizing the development of effective drug and vaccine candidates. Hence, the study was designed to identify novel therapeutics using a comprehensive genome-based analysis of V. parahaemolyticus. From V. parahaemolyticus proteome, a total of 4822 proteins were investigated in order to find out effective drug and vaccine targets. A range of diverse subtractive proteomics approaches – namely, identification of human non-homologous and pathogen-specific essential proteins, druggability and ‘anti-target’ analysis, prediction of subcellular localization, human microbiome non-homology screening, analysis of virulence factors, protein-protein interactions studies. Among 16 novel cytoplasmic proteins, ‘VIBPA Type II secretion system protein L’ and ‘VIBPA Putative fimbrial protein Z’ were allowed to molecular docking with 350 human metabolites, which revealed that Eliglustat, Simvastatin and Hydroxocobalamin were the top drug molecules considering free binding energy. On the contrary, ‘Sensor histidine protein kinase UhpB’ and ‘Flagellar hook-associated protein of 25 novel membrane proteins were subjected to T and B cell epitope prediction, antigenicity testing, transmembrane topology screening, allergenicity and toxicity assessment, population coverage analysis and molecular docking were adopted to generate the most immunogenic epitopes. Three subunit vaccines were constructed by the combination of highly antigenic epitopes along with suitable adjuvant, PADRE sequence and linkers. The designed vaccine constructs (V1, V2, V3) were analyzed by their physiochemical properties and molecular docking with MHC molecules that suggested the superiority of construct V1. Besides, the binding affinity of human TLR1/2 heterodimer and construct V1 was also biologically significant. The vaccine-receptor complex exhibited deformability at a minimum level that also strengthened our prediction. The optimized codons of the designed construct was cloned into pET28a(+) vector of E. coli strain K12. However, the predicted drug molecules and vaccine constructs could be further studied to combat V. parahaemolyticus associated infections.