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AbstractIn this study, attempts have been made to identify novel inhibitor(s) of SdiA (a homolog of LuxR transcription regulator) of Klebseilla pneumoniaeusing various computational techniques. 4LFU was used as a template to model the structure of SdiA. ProCheck, Verify3D, Ramachandran plot scores and ProSA-Web confirmed the good quality of the model as the root mean square deviation (RMSD) between SdiA model, and 4LFU template was estimated to be 0.21 Å. The secondary structural contents of SdiA model were predicted using PDBsum. The only binding site of SdiA was identified (area = 523.083 Å2and volume = 351.044 Å3) using CASTp. Molecular docking at three different levels [high throughput virtual screening, standard-precision (SP) and extra-precision (XP) dockings] with increasingly stringent conditions was performed using Glide on Selleck’s express pick library (L3600). A total of 61 ligands were found to bind with high affinities to the active site of SdiA. Further, the effect of solvent on protein-ligand interaction was evaluated by performing molecular mechanics-general born surface area (Prime/MM-GBSA). On the basis of Prime/MM-GBSA score, molecular dynamics simulation (50 ns) was performed on the ligand (WAY-390139-A) showing lowest binding energy to confirm the stability of protein-ligand complex. Docking energy and the corresponding binding affinity of WAY-390139-A towards SdiA were estimated to be –13.005 kcal mol–1and 3.46 × 109M−1, respectively. Our results confirm that WAY-390139-A binds at the autoinducer binding site of SdiA with high affinity and stability and can be further exploited as potential drug against K. pneumoniaeafter experimental validation.Communicated by Ramaswamy H. Sarma

The widespread burden of Dengue was amplified over the last three decades and almost half of the world population is estimated to be at the risk of Dengue fever, Dengue Hemorrhagic Fever (DHF) and Dengue Shock Syndrome (DSS) which has increased drastically in recent times. Therefore, it has been a major concern of public health world wide. The genome of dengue virus encodes a single polyprotein; having both the functional and non-functional region. The predicted motif involved in regulation, activity and stability of virus and protein sub cellular localization of all structural regions of dengue virus variants were plasma membrane. Eight significant motifs like cAMP & cGMP dependent protein kinase, N-Glycosylation, N-Myristoylation, Protein kinase C, Casein kinase 2, GTP-Binding Elongation Factor Signature, Tyrosine kinase and Glycosaminoglycan were predicted in dengue variants. These finding might be used to distinguish the proteome function for targeting or designing the antiviral inhibitors against the motifs of Dengue virus. Keywords: Dengue, sub cellular localization, motifs, antiviral drugs, Table of Contents Abstract Introduction Material And Methods Results And Discussion References Introduction Dengue virus genome contains a positive strand RNA with one open reading frame coding for polyprotein. The [...]

Hexachlorocyclohexane (HCH) is a non-degradable compound extensively used against agricultural pests and various public health programs for controlling mosquitoes. It imbibes into the food chain from crop to animals; biodegradable enzymes present in the genes of some bacteria degrade HCH in soil. Mainly, two genes linA and linB encode dehydrochlorinase and dehalogenase enzymes involved in degradation of HCH. Bioinformatics strategies were used to find other homologous genes and proteins, which can also degrade HCH present in various bacteria for controlling of pollution and offer clue to prevent its entry in the food chain. Total 38 nucleotides and 36 proteins sequences of linA and linB were used for constructing the phylogeny. In addition, analysis on culture dependent and culture independent bacteria were done, which might play a vital role in the degradation of the non-degradable compounds. These bacteria possibly will facilitate in the safety of soil pollution, improving fertility of the soil and prevent entry of HCH in the food chain. Keywords: Hexachlorocyclohexane, linA, linB, homologous, degradation, Table of Contents Abstract Introduction Material And Methods Results And Discussion References Introduction Xenobiotics are chemicals, which did not exist in nature. These are synthetic compounds viz. pesticides, fungicides, herbicides, [...]

The avian influenza is an important infectious disease of birds. Its genome consists of negative sense single stranded segmented RNA which encodes 8 structural proteins (HA, NA, PB1, PB2, PA, M1, M2, NP). The most significant surface proteins of influenza A virus subtype H5N1 are hemagglutinin and neuraminidase for pathogenicity in birds to human. The neighbor-joining method with jukes and cantor algorithm was used for predicting the thirty-six hemagglutinin and thirty-seven neuraminidase nucleotide sequences that were used. The phylogenetic analysis with nucleotide sequences showed proximity between different sources of virus in the same country. It was observed that distribution of almost analogous influenza virus infecting different animals in same country. Therefore, the genome of virus encoded the eight structural proteins, which is important for propagation and infection in the host. We have predicted the sub cellular localization of all proteins in the virus targeting the host. These proteins were located in the plasma membrane and host nucleus interacts with DNA. We have also identified the nine motifs viz. N-glycosylation site, N- myristoylation site, protein kinase C phosphrylation site, casein kinase 2 phosphorylation site, cAMP and cGMP dependent protein kinase phosphorylation site, amidation, cell attachment sequences (RGD), tyrosine kinase, and prokaryotic membrane lipoprotein lipid attachment site in the proteins. These motifs were involved in regulation, activity and stability of virus. This computational study may be easy to understand the proteome function useful for targeting the antiviral drugs against these motifs. Keywords: Avian influenza, hemagglutinin, motifs, neuraminidase, phylogenetic tree, subcellular localization, Table of Contents Abstract Introduction Material And Methods Results And Discussion References Introduction Avian influenza is an important infectious disease of birds ranged from mild to severe form of illness, [...]

Vibrio cholerae have evolved mechanism to become pathogenic to humans with a potential to cause the severe life-threatening diarrhea disease, cholera. Cholera can emerge as explosive outbreaks in the human population. V. cholerae illness is produced primarily through the expression of a potent toxin within the human intestine. Several proteins are involved in the pathogenesis and regulation of bacterial cell activity. The insilico prediction of protein subcellular localization was used to distinguish the actual location in the cells. Total 52 V. cholerae proteins were analyzed with the help of PSLPred. The subcellular localization of these proteins was five in the cells like cytoplasm, periplasm, inner membrane, outer membrane and extracellular space. They have widespread applications in function of proteins in the host cell and in designing the drugs. Keywords: Vibrio cholerae, Cholera, pathogenesis, subcellular localization, drugs, Table of Contents Abstract Introduction Materials And Methods Results And Discussion References Introduction Worldwide 1.3 billion cases of acute diarrhea occur in children below 5 years annually of which more [...]

Dengue has reemerged significantly from the past two decades for the public health problems. Clinicians require a diagnostic test with high sensitivity, which is applicable during early symptomatic phase. PCR is a specific and sensitive molecular technique to detect the gene for monitoring possible Dengue outbreaks and circulating viral serotypes. Bioinformatics tools were used to design and verify the novel Dengue subtype specific primers. In this investigation, 24 primers targeting the structural region of four variants of dengue virus were designed through in silico. There is no cross reactivity found with the primers designed with any other virus. All these sets of primers of dengue were highly specific and may perhaps be helpful for the molecular diagnostic of Dengue viruses. Keywords: Dengue, primers, structural region, Table of Contents Abstract Introduction Material And Methods Results And Discussion References Introduction Dengue fever (DF), dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS) are a major public health [...]

There is a constant need for assessment of potential allergenic and their patterns of cross-reactivity of genetically modified food (GMF) and pharmaceutical; in which novel proteins are introduced into the human food chain. The aspect for its identification is still in its nascent stage, which includes detection of motifs commonly, occurred in many allergens but rare in ordinary proteins. Transgenic proteins were used by GMF are evaluated on the basis of potential allergenic properties, identification of short identical amino acid sequences were detected from transgenic proteins In this study, bioinformatics approach had been used to detect the potential allergens motifs in amino acid sequences. The purpose of the analysis is to suggest a guideline for food safety, which will aid in human welfare and thereby, controlling the extra use of allergen based transgene introduced into the transgenic foods. Therefore, computationally predicted IgE epitopes from GMF allergen might be an ideal peptide-based novel candidate for immunotherapy. Keywords: Allergens, Epitopes, IgE Genetically modified foods, Motifs, Table of Contents Abstract Introduction Materials And Methods Results And Discussion References Introduction In most nations assessment before authorities is required for the safety of genetically engineered foods prior to [...]

Table of Contents Abstract Introduction Materials And Methods Results And Discussion References Abstract Mycobacterium tuberculosis is a facultative intracellular pathogen that has evolved the ability to survive and multiply within [...]