Molecular modeling and Drug designingMolecular modeling is a widely used computational approach to identify and design molecules for therapeutic use. This method greatly reduces the time and effort for the discovery phase of drug development. This technique helps to identify the relationships between different compounds and their biological activity to specific targets, and offers useful leads about their interaction patterns with target proteins that finally lead to most promising compounds. We are focusing on proteins related to the survival and virulence of pathogenic bacteria (Salmonella, Vibrio, Helicobacter etc.) as potential targets for drug/ vaccine development.
Computational prediction and network analysis of host-pathogen interactions
Human typhoid fever is an important public health problem worldwide with 90% of cases reported from Asia. However, host-pathogen interactions during typhoid fever is incompletely known. Our overall goal is to improve the understanding of the global picture of pathogenesis of typhoid fever¿to identify the active network to evaluate the number of biological processes and the connected sets of genes whose expressions are altered in the disease state. Our approach may reveal the network modules related to Typhoid fever, provide new insight into the cause of this disease and the molecular modules that might be used as potential drug targets. Viral infectious diseases are among the foremost causes of death worldwide. Viral-host protein-protein interactions are crucial for better understanding of the mechanisms that results in disease development. We have taken a systematic approach to predict viral-host (inter-species) protein-protein interactions using diverse biological information like protein sequence, domain-domain associations, disorder regions, degree etc.
A complete genome sequence of an organism can be considered as the ultimate genetic map of that organism. Individual genome sequences give insight into genome structure, but not into genome function. Comparative genomics has contributed significantly to our understanding of bacterial genomic organization, genetic diversity and virulence determinants, antimicrobial drug and vaccine targets and new markers for diagnostics. In the infectious disease research, comparative genomics exploits available genome sequences to perform inter and intra-species comparisons of bacterial genome and those of other model organisms. Genome evaluation of Salmonella spp. will help us to identify the ¿differentially evolved genes¿ including the virulent genes and the possible mode of interaction of these gene products with host proteins that may contribute to pathogenesis.
A web-based knowledge hub of Vibrio cholerae and cholera for researchers around the world. The database will have (1) the sequence, genomic, proteomic experimental and epidemiological data, (2) A literature portal, which will contain PubMed publications, meeting reports, seminar proceedings and posters, recordings of talks and text book materials on cholera and (3) A technique portal.
In the past, our research work mainly focused on comprehensive and critical analysis of DNA, RNA and protein data as well as genomes through different bioinformatics tools and techniques.
- Cholera, the most severe and deadly diarrheal disease, is causing pandemics since 1817. Pandemic Vibrio cholerae strains show an unusual genomic transformation to attain greater fitness. We carried out comparative genome analysis of different Vibrio cholerae strains to understand the evolutionary events, which influence the emergence of their pathogenic traits.
- Leptospirosis has emerged as a major public health problem in the developing countries including India. Leptospirosis continues to occur annually in the Andaman Islands since the early 20th century. We worked jointly with the Regional Medical Research Centre (ICMR), Andaman & Nicobar Islands to study the genetic difference, if any between the strains of pathogenic, non pathogenic and intermediate phenotypic characters and to understand the genetic changes as a repertoire of gene acquisition and loss on an evolutionary timescale.
- Swine flu, as colloquially referred to, is a pandemic caused by a new strain of H1N1 influenza virus in the year 2009. The virus, as proposed by the reassortment theory, is found to contain a combination of genes from swine, avian (bird) and human influenza viruses. Various strains of influenza viruses have caused pandemics since 1918. We had investigated the evolutionary complexities of H1N1 influenza virus to explore the possible etiology of the 2009 flu pandemic, keeping track with the earlier recorded pandemics. We also analyzed how the evolutionary constraints were detrimental in pronouncing the fitness of the organism and thus the severity of the disease.
- ASRDb (Archael Stress Response Database): The word stress has become a very frequently encountered word in our day to day life. Even for microscopic organisms like Archaea, there are not much change in the scenario. We have developed a comprehensive database of Archaeal stress response genes. Such a database will hold immense potential for further downstream works in the relevant fields where in-depth studies of Archaeal stress responsive proteins/genes would be required. This database is likely to provide an instant insight, which would make the researchers¿ job faster and easier. http://188.8.131.52/ASRDb/