Pathway based therapeutic targets identification and development of an interactive database CampyNIBase of Campylobacter jejuni RM1221 through non-redundant protein dataset

Abstract

The bacterial species Campylobacter jejuni RM1221 (CjR) is the primary cause of campylobacteriosis which poses a global threat for human health. Over the years the efficacy of antibiotic treatment is becoming more fruitless due to the development of multiple drug resistant strains. Therefore, identification of new drug targets is a valuable tool for the development of new treatments for affected patients and can be obtained by targeting essential protein(s) of CjR. We conducted this in silico study in order to identify therapeutic targets by subtractive CjR proteome analysis. The most important proteins of the CjR proteome, which includes chokepoint enzymes, plasmid, virulence and antibiotic resistant proteins were annotated and subjected to subtractive analyses to filter out the CjR essential proteins from duplicate or human homologous proteins. Through the subtractive and characterization analysis we have identified 38 eligible therapeutic targets including 1 potential vaccine target. Also, 12 potential targets were found in interactive network, 5 targets to be dealt with FDA approved drugs and one pathway as potential pathway based drug target. In addition, a comprehensive database ‘CampyNIBase’ has also been developed. Besides the results of this study, the database is enriched with other information such as 3D models of the identified targets, experimental structures and Expressed Sequence Tag (EST) sequences. This study, including the database might be exploited for future research and the identification of effective therapeutics against campylobacteriosis. URL: (http://nib.portal.gov.bd/site/page/4516e965-8935-4129-8c3f-df95e754c562#Banner).

Efficacy of Plant Growth-Promoting Bacteria Bacillus cereus YN917 for Biocontrol of Rice Blast

“…B. cereus YN917 genomic DNA was extracted using CTAB method, and whole genome sequencing was performed using the PacBio platform and Illumina HiSeq platform at Majorbio Bio-Pharm Technology Co., Ltd. (Shanghai, China). Six databases were used for general function annotation: GO (Gene Ontology) ( Moura et al, 2009 ), KEGG (Kyoto Encyclopedia of Genes and Genomes) ( Kanehisa and Goto, 2000 ), COG (Clusters of Orthologous Groups) ( Juhl et al, 2008 ), NR (Non-Redundant Protein database) ( Hossain et al, 2018 ), Swiss-Prot ( Bairoch and Apweiler, 2000 ), and Pfam ( Mistry et al, 2021 ).…”

Recognition of plausible therapeutic agents to combat COVID-19: An omics data based combined approach

“…7, Supplementary Fig. 5, Supplementary Data 9,10,11,12,13,14,15,16 and 17). We then identi ed the Interferon stimulating genes KPNA4, IRF7, OAS3, CAMK2G, IFITM1, IFIT1, EGR1, MX1 and IFNAR2 from the upregulated immunoregulatory genes and TRIM8, VCAM1, IFNGR2, JAK1 from the downregulated immunoregulatory genes (Fig.…”

“…In silico approaches are the most suitable way to execute this type of research in a short time with nearly zero cost. Powerful computational methods such as subtractive proteomics, comparative genomics or virtual screening can determine therapeutic targets and help develop drugs against bacteria, fungi or non-communicable diseases ( Hossain et al, 2018 , Abadio et al, 2011 , Bhattacharjee et al, 2020 ). Unfortunately, for viral infections, this type of combined rational approach is hardly seen.…”

“…Powerful computational methods such as subtractive proteomics, comparative genomics or virtual screening can disclose therapeutic targets and drugs against bacteria, fungi or non-communicable diseases 15,16,17 .…”

Novel Approaches for Systems Biology of Metabolism-Oriented Pathogen-Human Interactions: A Mini-Review

“…The structure-based methods such as homology modeling, molecular docking and molecular dynamics simulations are used to classify the candidate enzymes in terms of structure and function, as reviewed below. Hossain et al (2018) presented a very interesting application of the subtractive genomics method on a bacterial species Campylobacter jejuni RM1221 (CjR). The bacteria CjR is now resistant to many antibiotics.…”