Subtractive proteomics to identify novel targets for paptide based vaccine development against Enterococcus faecium

Project Title

Subtractive proteomics to identify novel targets for paptide based vaccine development against Enterococcus faecium

Project Area of Specialization Artificial IntelligenceProject Summary

The objective of the project is to find the drug target  of the Enterococcus faecium strains using subtractive genomics approach so comparative research between strains can be conducted.This identification of drug targets  will enable to design drug against lethal human pathogen Enterococcus faecium.In this project, we will use subtractive proteomics approach to identify suitable non-human homologous targets for vaccine development. The procedure of this project is follow as:

1:Retrieval of proteome in FASTA form from UniProt: List of all available Enterococcus faecium strains in Fasta format and excel sheet will be retrieved from the Uniprot server. Various geno-species have been filtered out from the list and used for further analysis. /

2:Paralog elimination using CDHIT : Paralogous protein sequences with a cut-off value of 0.6 (60 percent) will be removed using CD-HIT.

3:Homologous elimination against host proteom: Use BLASTp against RefSe to remove homologous proteins from non-paralogous pathogen sequences

4:Essential pathogen gene Discovering: Database of Essential Gene (DEG) will be used to determine the integral pathogen genes because this database includes curated information about proteins expressed by essential genes

5:Host and Pathogen Track Analysis Database of the Kyoto Encyclopedia of Genes and Genomes (KEGG) will be used to find human and pathogen metabolic pathways.For this purpose, KEGG Automated Annotation Server (KAAS) will be used, achieving results in the form of KEGG Orthology List Assignment, Enzyme Commission (EC) number, etc.

6:Localization of proteins and functional family prediction :The pathogenspecific protein involved in the pathogen's basic metabolic pathway and not reveal in humans would be further used to locate and determine functional families. Localization would be used to determine the type of drug that is going to be vaccine or medicine.

7:Identification of drug targets  :Drug targets will be checked against the DrugBank database in the selected list of proteins using BLASTp. After reviewing their potency, the protein to be further used for drug design will be selected

8:Construction of the structure / model :RCSB Protein Data Bank (PDB) will search for the three-dimensional (3D) structure of the selected drug target. If there is no 3D structure, we will use Homology Modeling, Ab-Initio and Threading to predict 3D protein model.

9:Prediction of the active site :Different machine learning methods were developed to discover protein's local secondary structures and to illustrate active site residues. One such technique is multiple sequence alignment (MSA) to be used along with literature survey in our study.

10:Docking with ligands of the drug target: Drug target is docked with ligands library to find the best docked ligand using various tools like AutoDcok.

Project Objectives

Project Objective:

The project is designed for following objectives:

1. Better insight into disease mechanism of human pathogen

2. Better understanding of multiple drug resistance mechanism of pathogen.

3. Finding of plausible druggable targets for pathogen.

4. Drug designing against pathogen.

5. Vaccine target identification.

Project Implementation Method

Druggable targets will be further used for pathogen drug development. The drug developed will be further used for laboratory and clinical testing purposes.

Benefits of the Project

This project will achieve the following benefits: 

1:The disease mechanism of pathogen against host will be better understandable.

2:Explanations of pathogen's multiple drug resistance will also be studied well.

3:Drug targets can identified through this study will be essential proteins for the pathogen.

4:Drugs that are harmless to the human host are designed in such a way that they can act on pathogen affectively without causing any harm to host.

5:The proteins which will be membranous would come out to be better option for vaccine targets.

6:This project will allowed for the design of vaccines consisting of selected epitopes free from irrelevant or unwanted structures.

7:By this project we will be abled for the perdictions of antigenic proteins.

8:Identification of epitope perdictions can be done by this project.

9:We were able for the identification of virulence factors.

Technical Details of Final Deliverable

1:The drug targets: identify the essential pathogen proteins that will be present in the pathogen's unique pathway. These targets will serve as binding drug sites. 2:Designed drug: these drugs will be identified from the ligands library as best docked ligands. For laboratory and clinical trials, these drugs can be further developed. 3:Vaccine targets: essential pathogen membrane proteins present in a unique metabolic pathway will also be used as targets for the vaccine.

Final Deliverable of the Project HW/SW integrated systemType of Industry Others Technologies Artificial Intelligence(AI)Sustainable Development Goals Good Health and Well-Being for PeopleRequired Resources

Item Name	Type	No. of Units	Per Unit Cost (in Rs)	Total (in Rs)
			Total in (Rs)	80000
Simulation Fee	Equipment	3	3000	9000
PyRx	Equipment	1	45500	45500
Internet availability	Equipment	4	1500	6000
Stationary Items	Miscellaneous	10	100	1000
Office Files	Miscellaneous	10	200	2000
Paper rim	Miscellaneous	10	700	7000
Tera Byte device	Equipment	1	9500	9500