Functional assignment to JEV proteins using SVM

A Review of miRNA Regulation in Japanese Encephalitis (JEV) Virus Infection

Japanese encephalitis (JE) is a mosquito-borne disease that causes neuronal damage and inflammation of microglia, and in severe cases, it can be fatal. JE infection can resist cellular immune responses and survive in host cells. Japanese encephalitis virus (JEV) infects macrophages and peripheral blood lymphocytes. In addition to regulating biological signaling pathways, microRNAs in cells also influence virus-host interactions. Under certain circumstances, viruses can change microRNA production. These changes affect the replication and spread of the virus. Host miRNAs can contain viral pathogenicity by downregulating the antiviral immune response pathways. Simultaneous profiling of miRNA and messenger RNA (mRNA) could help us detect pathogenic factors, and dual RNA detection is possible. This work highlights important miRNAs involved in human JE infection. In this study, we have shown the important miRNAs that play significant roles in JEV infection. We found that during JEV infection, miRNA-155, miRNA-29b, miRNA-15b, miRNA-146a, miRNA-125b-5p, miRNA-30la, miRNA-19b-3p, and miRNA-124, cause upregulation of human genes whereas miRNA-432, miRNA-370, miRNA- 33a-5p, and miRNA-466d-3p are responsible for downregulation of human genes respectively. Further, these miRNAs are also responsible for the inflammatory effects. Although several other miRNAs critical to the JEV life cycle are yet unknown, there is currently no evidence for the role of miRNAs in persistence.

Molecular docking studies of chloroquine and its derivatives against P23pro-zbd domain of chikungunya virus: Implication in designing of novel therapeutic strategies

The arthropod-transmitted chikungunya virus has emerged as an epidemic menace that causes debilitating polyarthritis. With this life-threatening impact on humans, the possible treatment requires to cure the viral infectivity. But, devoid of any vaccine against the chikungunya virus (CHIKV), there is a need to develop a novel chemotherapeutic strategy to treat this noxious infection. CHIKV carries highly compact P23^pro-zbd structure that possesses potential RNA-binding surface domains which extremely influences the use of RNA template during genome replication at the time of infection and pathogenesis. Therefore, computational approaches were used to explore the novel small molecule inhibitors targeting P23^pro-zbd domain. The tertiary structure was modeled and optimized using in silico approaches. The results obtained from PROCHECK (93.1% residues in favored regions), ERRAT (87.480 overall model quality) and ProSA (Z-score: -11.72) revealed the reliability of the proposed model. Interestingly, a previously reported inhibitor, chloroquine possesses good binding affinities with the target domain. In-depth analysis revealed that chloroquine derivatives such as didesethyl chloroquine hydroxyacetamide, cletoquine, hydroxychloroquine exhibited a better binding affinity. Notably, MD simulation analysis exhibited that Thr1312, Ala1355, Ala1356, Asn1357, Asp1364, Val1366, Cys1367, Ala1401, Gly1403, Ser1443, Tyr1444, Gly1445, Asn1459, and Thr1463 residues are the key amino acid responsible for stable ligand-protein interaction. The results obtained from this study provide new insights and advances the understanding to develop a new approach to consider effective and novel drug against chikungunya. However, a detailed in vivo study is required to explore its drug likeliness against this life-threatening disease.

Biomarkers in Japanese encephalitis: a review

JE is a flavivirus generated dreadful CNS disease which causes high mortality in various pediatric groups. JE disease is currently diagnosed by measuring the level of viral antigens and virus neutralization IgM antibodies in blood serum and CSF by ELISA. However, it is not possible to measure various disease-identifying molecules, structural and molecular changes occurred in tissues, and cells by using such routine methods. However, few important biomarkers such as cerebrospinal fluid, plasma, neuro-imaging, brain mapping, immunotyping, expression of nonstructural viral proteins, systematic mRNA profiling, DNA and protein microarrays, active caspase-3 activity, reactive oxygen species and reactive nitrogen species, levels of stress-associated signaling molecules, and proinflammatory cytokines could be used to confirm the disease at an earlier stage. These biomarkers may also help to diagnose mutant based environment specific alterations in JEV genotypes causing high pathogenesis and have immense future applications in diagnostics. There is an utmost need for the development of new more authentic, appropriate, and reliable physiological, immunological, biochemical, biophysical, molecular, and therapeutic biomarkers to confirm the disease well in time to start the clinical aid to the patients. Hence, the present review aims to discuss new emerging biomarkers that could facilitate more authentic and fast diagnosis of JE disease and its related disorders in the future.

CPDB: cysteine protease annotation database in Leishmania species

There has been a revival of interest in Cysteine protease for Visceral Leishmaniasis (VL) attributed to massive outbreaks of leishmaniasis in the tropical region. The cysteine protease database (CPDB) was designed to find data related to cysteine protease (CP) of different species of Leishmania and Trypanosoma brucei in a single platform. This has reflected in substantial increase in the submission of Leishmania genome sequences to NCBI (National Center for Biotechnology Information) database. The CPDB database aims to provide a summary of data analysis, such as physiochemical and molecular properties, proteolytic cleavage sites, classification into functional families using SVMProt and other ExPASy tools. The main aim of this database is to provide different protein inhibitors of cysteine protease groups that were collected from literature and make available their 3-D structures through JMol with JAVA platform. These CP inhibitors are freely downloadable and also have added links for functional analyses of other proteins, which is helpful for users. All this information in CPDB, a single platform, will prove to be of great help for researchers who are involved in drug discovery and analysis of other physiochemical and molecular properties of the protein.

AVAILABILITY

the database is available for free at.

Analysis of sequence, structure of GAPDH of Leishmania donovani and its interactions

Drug resistance acquired by Leishmania donovani (Ldv) is a major problem in the treatment and control of visceral leishmaniasis (VL). Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a major glycolytic enzyme has been targeted as is found in other protozoan which cause diseases like sleeping sickness. GAPDH gene of Ldv (AG83 strain) was amplified, sequenced, and modeled on the basis of crystal structure of Leishmania mexicana. The model of the Ldv GAPDH exhibited NAD-binding domain with Rossmann folding. Virtual screening of different experimentally proved compounds with the crystal and the modeled structures of GAPDH of Leishmania strains revealed diverse binding affinities of different compounds. Comparison of binding affinities (based on different programs) of compounds revealed that discovery studio v2.5 (Ligandfit) was able to predict the most hit compounds, the best hit compounds against GAPDH of Leishmania strains are hydrazine, vetrazine, and benzyl carbazate. It is predicted that patients suffering from both VL and cardiac disorders (atrial fibrillation) may benefit if they are treated with warfarin in conjunction with first-line antileishmanial therapies such as miltefosine and AmBisome.

A comparative protein function analysis databaseof different Leishmania strains

A complete understanding of different protein functional families and template information opens new avenues for novel drug development. Protein identification and analysis software performs a central role in the investigation of proteins and leads to the development of refined database for description of proteins of different Leishmania strains. There are certain databases for different strains that lack template information and functional family annotation. Rajendra Memorial Research Institute of Medical Sciences (RMRIMS) has developed a web-based unique database to provide information about functional families of different proteins and its template information in different Leishmania species. Based on the template information users can model the tertiary structure of protein. The database facilitates significant relationship between template information and possible protein functional families assigned to different proteins by SVMProt. This database is designed to provide comprehensive descriptions of certain important proteins found in four different species of Leishmania i.e. L. donovani, L. infantum, L. major and L. braziliensis. A specific characterization information table provides information related to species and specific functional families. This database aims to be a resource for scientists working on proteomics. The database is freely available at http://biomedinformri.org/calp/.

Comparative domain modeling of human EGF-like module EMR2 and study of interaction of the fourth domain of EGF with chondroitin 4-sulphate

EMR2 is an EGF-like module containing mucin-like hormone receptor-2 precursor, a G-protein coupled receptor (G-PCR). Mutation in EMR2 causes complicated disorders like polycystic kidney disease (PKD). The structure of EMR2 shows that the fifth domain is comprised of EGF-TM7 helices. Functional assignment of EMR2 by support vector machine (SVM) revealed that along with transporter activity, several novel functions are predicted. A twenty amino acid sequence "MGGRVFLVFLAFCVWLTLPG" acts as the signal peptide responsible for posttranslational transport. Eight amino acids are involved in N-glycosylation sites and two cleavage sites are Leu517 and Ser518 in EMR2. The residue Arg241 is responsible for interaction with glycosaminoglycan and chondroitin sulfate. On the basis of structure, function and ligand binding sites, competitive EMR2 inhibitors designed may decrease the rate of human diseases like Usher's syndrome, bilateral frontoparietal polymicrogyria and PKD.

Computational identification of post-translational modification sites and functional families reveal possible moonlighting role of rotaviral proteins

Rotavirus (RV) diarrhoea causes huge number deaths in children less than 5 years of age. In spite of available vaccines, it has been difficult to combat RV due to large number of antigenically distinct genotypes, high mutation rates, generation of reassortant viruses due to segmented genome. RV is an eukaryotic virus which utilizes host cell machinery for its propagation. Since RV only encodes 12 proteins, post­translational modification (PTM) is important mechanism for modification, which consequently alters their function. A single protein exhibiting different functions in different locations or in different subcellular sites, are known to be ’moonlighting‘. So there is a possibility that viral proteins moonlight in separate location and in different time to exhibit diverse cellular effects. Based on the primary sequence, the putative behaviour of proteins in cellular environment can be predicted, which helps to classify them into different functional families with high reliability score. In this study, sites for phosphorylation, glycosylation and SUMOylation of the six RV structural proteins (VP1, VP2, VP3, VP4, VP6 & VP7) & five non­structural proteins (NSP1, NSP2,NSP3,NSP4 & NSP5) and the functional families were predicted. As NSP6 is a very small protein and not required for virus growth & replication, it was not included in the study. Classification of RV proteins revealed multiple putative functions of each structural protein and varied number of PTM sites, indicating that RV proteins may also moonlight depending on requirements during viral life cycle. Targeting the crucial PTM sites on RV structural proteins may have implications in developing future anti­rotaviral strategies.

CHPVDB--a sequence annotation database for Chandipura virus

Databases containing proteomic information have become indispensable for virology studies. As the gap between the amount of sequence information and functional characterization widens, increasing efforts are being directed to the development of databases. For virologist, it is therefore desirable to have a single data collection point which integrates research related data from different domains. CHPVDB is our effort to provide virologist such a one-step information center. We describe herein the creation of CHPVDB, a new database that integrates information of different proteins in to a single resource. For basic curation of protein information, the database relies on features from other selected databases, servers and published reports. This database facilitates significant relationship between molecular analysis, cleavage sites, possible protein functional families assigned to different proteins of Chandipura virus (CHPV) by SVMProt and related tools.

AVAILABILITY

The database is freely available at http://chpvdb.biomedinformri.org/.