Identification of membrane associated drug targets in Borrelia burgdorferi ZS7- subtractive genomics approach

Novel vaccine design based on genomics data analysis: A review

Modification of pathogenic strains with the passage of time is responsible for evolution in the timeline of vaccine development for last 30 years. Recent advancements in computational vaccinology on the one hand and genome sequencing approaches on the other have generated new hopes in vaccine development. The aim of this review was to discuss the evolution of vaccines, their characteristics and limitations. In this review, we highlighted the evolution of vaccines, from first generation to the current status, pointing out how different vaccines have emerged and different approaches that are being followed up in the development of more rational vaccines against a wide range of diseases. Data were collected using Google Scholar, Web of Science, Science Direct, Web of Knowledge, Scopus and Science Hub, whereas computational tools such as NCBI, GeneMANIA and STRING were used to analyse the pathways of vaccine action. Innovative tools, such as computational tools, recombinant technologies and intra-dermal devices, are currently being investigated in order to improve the immunological response. New technologies enlightened the interactions of host proteins with pathogenic proteins for vaccine candidate development, but still there is a need of integrating transcriptomic and proteomic approaches. Although immunization with genomics data is a successful approach, its advantages must be assessed case by case and its applicability depends on the nature of the agent to be immunized, the nature of the antigen and the type of immune response required to achieve effective protection.

Identification of Therapeutic Drug Target of Stenotrophomonas maltophilia Through Subtractive Genomic Approach and in-silico Screening Based on 2D Similarity Filtration and Molecular Dynamic Simulation

Background:

Stenotrophomonas maltophilia is a multi-drug resistant, gram-negative bacterium that causes opportunistic infections and is associated with high morbidity and mortality in severely immunocompromised individuals.

Aim:

The study aimed to find out the drug target and a novel inhibitor for Stenotrophomonas maltophilia.

Objectives:

The current study focused on identifying specific drug targets by subtractive genomes analysis to determine the novel inhibitor for the specified target protein by virtual screening, molecular docking, and molecular simulation approach.

Materials and Methods:

In this study, we performed a subtractive genomics approach to identify the novel drug target for S.maltophilia. After obtaining the specific target, the next step was to identify inhibitors that include calculating 2D similarity search, molecular docking, and molecular simulation for drug development for S.maltophilia.

Results:

With an efficient subtractive genomic approach, five unique targets as the impressive therapeutics founded out of 4386 protein genes. In which UDP-D-acetylmuramic (murF) was the most remarkable target. Further virtual screening, docking, and dynamics resulted in the identification of seven novel inhibitors.

Conclusion:

Further, in vitro and in vivo bioassay of the identified novel inhibitors could facilitate effective drug use against S.maltophilia.

Modeling Novel Putative Drugs and Vaccine Candidates against Tick-Borne Pathogens: A Subtractive Proteomics Approach

Ticks and tick-borne pathogens (TBPs) continuously causing substantial losses to the public and veterinary health sectors. The identification of putative drug targets and vaccine candidates is crucial to control TBPs. No information has been recorded on designing novel drug targets and vaccine candidates based on proteins. Subtractive proteomics is an in silico approach that utilizes extensive screening for the identification of novel drug targets or vaccine candidates based on the determination of potential target proteins available in a pathogen proteome that may be used effectively to control diseases caused by these infectious agents. The present study aimed to investigate novel drug targets and vaccine candidates by utilizing subtractive proteomics to scan the available proteomes of TBPs and predict essential and non-host homologous proteins required for the survival of these diseases causing agents. Subtractive proteome analysis revealed a list of fifteen essential, non-host homologous, and unique metabolic proteins in the complete proteome of selected pathogens. Among these therapeutic target proteins, three were excluded due to the presence in host gut metagenome, eleven were found to be highly potential drug targets, while only one was found as a potential vaccine candidate against TBPs. The present study may provide a foundation to design potential drug targets and vaccine candidates for the effective control of infections caused by TBPs.

New approaches and omics tools for mining of vaccine candidates against vector-borne diseases

Vector-borne diseases (VBDs) present a major threat to human and animal health, as well as place a substantial burden on livestock production. As a way of sustainable VBD control, focus is set on vaccine development. Advances in genomics and other "omics" over the past two decades have given rise to a "third generation" of vaccines based on technologies such as reverse vaccinology, functional genomics, immunomics, structural vaccinology and the systems biology approach. The application of omics approaches is shortening the time required to develop the vaccines and increasing the probability of discovery of potential vaccine candidates. Herein, we review the development of new generation vaccines for VBDs, and discuss technological advancement and overall challenges in the vaccine development pipeline. Special emphasis is placed on the development of anti-tick vaccines that can quell both vectors and pathogens.

Essential proteins and possible therapeutic targets of Wolbachia endosymbiont and development of FiloBase--a comprehensive drug target database for Lymphatic filariasis

Lymphatic filariasis (Lf) is one of the oldest and most debilitating tropical diseases. Millions of people are suffering from this prevalent disease. It is estimated to infect over 120 million people in at least 80 nations of the world through the tropical and subtropical regions. More than one billion people are in danger of getting affected with this life-threatening disease. Several studies were suggested its emerging limitations and resistance towards the available drugs and therapeutic targets for Lf. Therefore, better medicine and drug targets are in demand. We took an initiative to identify the essential proteins of Wolbachia endosymbiont of Brugia malayi, which are indispensable for their survival and non-homologous to human host proteins. In this current study, we have used proteome subtractive approach to screen the possible therapeutic targets for wBm. In addition, numerous literatures were mined in the hunt for potential drug targets, drugs, epitopes, crystal structures, and expressed sequence tag (EST) sequences for filarial causing nematodes. Data obtained from our study were presented in a user friendly database named FiloBase. We hope that information stored in this database may be used for further research and drug development process against filariasis. URL: http://filobase.bicpu.edu.in.

Sexually transmitted diseases putative drug target database: a comprehensive database of putative drug targets of pathogens identified by comparative genomics

Objective:

Sexually transmitted diseases (STD) are the serious public health problems and also impose a financial burden on the economy. Sexually transmitted infections are cured with single or multiple antibiotics. However, in many cases the organism showed persistence even after treatment. In the current study, the set of druggable targets in STD pathogens have been identified by comparative genomics.

Materials and Methods:

The subtractive genomics scheme exploits the properties of non-homology, essentiality, membrane localization and metabolic pathway uniqueness in identifying the drug targets. To achieve the effective use of data and to understand properties of drug target under single canopy, an integrated knowledge database of drug targets in STD bacteria was created. Data for each drug targets include biochemical pathway, function, cellular localization, essentiality score and structural details.

Results:

The proteome of STD pathogens yielded 44 membrane associated proteins possessing unique metabolic pathways when subjected to the algorithm. The database can be accessed at http://biomedresearchasia.org/index.html.

Conclusion:

Diverse data merged in the common framework of this database is expected to be valuable not only for basic studies in clinical bioinformatics, but also for basic studies in immunological, biotechnological and clinical fields.

Clostridium-DT(DB): a comprehensive database for potential drug targets of Clostridium difficile

Clostridium difficile is considered to be one of the most important causes of health care-associated infections currently. The prevalence and severity of C. difficile infection have increased significantly worldwide in the past decade which has led to the increased research interest. Here, using comparative genomics strategy coupled with bioinformatics tools we have identified potential drug targets in C. difficile and determined their three-dimensional structures in order to develop a database, named Clostridium-DT(DB). Currently, the database comprises the potential drug targets with their structural information from three strains of C. difficile, namely hypervirulent PCR-ribotype 027 strain R20291, PCR-ribotype 012 strain 630, and PCR-ribotype 027 strain CD196.

Vaccine Development Against Leishmania donovani

Visceral leishmaniasis (VL) caused by Leishmania donovani and Leishmania infantum/chagasi represents the second most challenging infectious disease worldwide, leading to nearly 500,000 new cases and 60,000 deaths annually. Zoonotic VL caused by L. infantum is a re-emergent canid zoonoses which represents a complex epidemiological cycle in the New world where domestic dogs serve as a reservoir host responsible for potentially fatal human infection and where dog culling is the only measure for reservoir control. Life-long immunity to VL has motivated development of prophylactic vaccines against the disease but very few have progressed beyond the experimental stage. No licensed vaccine is available till date against any form of leishmaniasis. High toxicity and increasing resistance to the current chemotherapeutic regimens have further complicated the situation in VL endemic regions of the world. Advances in vaccinology, including recombinant proteins, novel antigen-delivery systems/adjuvants, heterologous prime-boost regimens and strategies for intracellular antigen presentation, have contributed to recent advances in vaccine development against VL. Attempts to develop an effective vaccine for use in domestic dogs in areas of canine VL should be pursued for preventing human infection. Studies in animal models and human patients have revealed the pathogenic mechanisms of disease progression and features of protective immunity. This review will summarize the accumulated knowledge of pathogenesis, immune response, and prerequisites for protective immunity against human VL. Authors will discuss promising vaccine candidates, their developmental status and future prospects in a quest for rational vaccine development against the disease. In addition, several challenges such as safety issues, renewed and coordinated commitment to basic research, preclinical studies and trial design will be addressed to overcome the problems faced in developing prophylactic strategies for protection against this lethal infection.