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Activities of anthropological organisms lead to the production of massive lignocellulosic waste every year and these lignocellulolytic enzymes plays crucial role in developing eco-friendly, sustainable and economical methods for decomposing and pre-treating the biomass to produce biofuels, organic acids, feeds and enzymes. Lignocellulolytic enzymes sustainably hydrolyse the biomass and can be utilized in wide range of applications such as personal care, pharmaceutical, biofuel release, sewage treatment, food and beverage industries. Every year a significant ton of biomass waste is released and insight on these crucial enzymes could establish in all the industries. However, due to the increased demand for compost materials, biomass degradation has resulted in composting processes. Several methods for improving compost amount and quality have been explored, including increasing decomposer inoculums, stimulating microbial activity, and establishing a decomposable environment. All of these prerequisites are met by biotechnological applications. Biotechnological procedures are used to improve the activity of enzymes on biomass. It leads to an adequate supply of compost and base materials for enterprises. In terms of effectiveness and stability during the breakdown process, lignocellulolytic enzymes derived from genetically modified species outperformed naturally derived lignocellulolytic enzymes. It has the potential to increase the quality and output of by-products. This review discussed the development of lignocellulolytic enzyme families and their widespread applications in a variety of industries such as olive oil extraction, carotenoid extraction, waste management, pollution control, second-generation bio-ethanol production, textile and dyeing, pharmaceuticals, pulp and paper, animal feed, food processing industries, detergent, and agricultural industries.

COVID-19, the current global pandemic has caused immense damage to human lives and the global economy. It is instigated by the SARS-CoV-2 virus and there is an immediate need for the identification of effective drugs against this deadly virus. SARS-CoV-2 genome codes for four structural proteins, sixteen non-structural proteins (NSPs) and several accessory proteins for its survival inside the host cells. In the present study, through in silico approaches, we aim to identify compounds that are effective against the four NSPs namely, NSP1, NSP4, NSP6 and NSP13 of SARS-CoV-2. The selection criteria of these four NSP proteins are they are least explored and potential targets. First, we have modeled the 3D structures of these proteins using homology modeling methods. Further, through molecular docking studies, we have screened the FDA-approved compounds against these modeled proteins and reported their docking scores. To gain dynamic insights, molecular dynamics studies have also been carried out for the best scored ligand against the NSPs. This study can further pave way for exposing more number of compounds against these proteins and enhance COVID-19 treatment. Supplementary Information The online version contains supplementary material available at 10.1007/s42485-021-00067-w.

Novel vaccines are required to effectively combat the epidemic spread of tuberculosis. Using in silico approaches, this study focuses on prediction of potential B cell and T cell binding immunogenic epitopes for 30 putative outer membrane proteins of Mtb. Among these, certain immunodominant epitopes of Rv0172, Rv0295c, Rv1006, Rv2264c, and Rv2525c were found, which are capable of binding B-cell and a maximum number of MHC alleles. The selected immunodominant epitopes were screened for their allergenic and antigenic properties, their percentage identity against the human proteome and their structural properties. Further, the binding efficacy of the immunodominant epitopes of Rv0295c and Rv1006 with HLA-DRB1*04:01 was analyzed using molecular docking and molecular dynamics studies. Hence, the in silico-derived immunogenic peptides (epitopes) could potentially be used for the design of subunit vaccines against tuberculosis. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-021-00148-9.

Cold and drought are of the maximum intense threats affecting the boom and productiveness of the Coffea Arabica, proscribing its worldwide spread. Both stress reason osmotic modifications within the cells of the Coffea Arabica through lowering their water ability. To broaden cultivars that are tolerant to each stress, it's far vital to recognize the genetic responses of Coffea Arabica flowers to those stresses, in particular in phrases of the genes concerned. In this examination, we mixed literature records with interspecific transcriptomic analyses (the use of Arabidopsis thaliana and Solanum Lycopersicum) to select genes associated with bloodless tolerance. We recognized forty-five pressure-inducible candidate genes related to bloodless and drought responses in Coffea Arabica flowers primarily based totally on a complete homologous detection method. Of those, 9 have been newly characterized through us, and 36 had formerly been reported. The gene community evaluation found out upregulated expression in ICE1-associated cluster of bHLH elements, HSP70/BAM5 related genes (hexokinases, galactinol synthases, SnRK complex, etc.) indicating their feasible co-expression. Using qRT-PCR we found out that 10 genes have been extensively upregulated in reaction to each bloodless and drought in Coffea Arabica flowers: HSP70, GST, SUS1, DHN1, BMY5, bHLH102, GR-RBP3, ICE1, GOLS1, and GOLS3. SnRK1.2, HXK1/2, bHLH7/43/79/93 have been especially upregulated in bloodless, whilst RHL41, CAU1, Hydrolase22 have been especially upregulated in drought. Interestingly, the expression of CIP changed better within the restoration level of each stress, indicating its probably vital position in plant restoration after pressure. In addition, a few genes, which include DHN3, bHLH79, PEI54, SnRK1.2, SnRK1.3, and Hydrolase22, have been extensively undoubtedly correlated among the bloodless and drought responses. CBF1, GOLS1, HXK2, and HXK3, through contrast, confirmed extensive poor correlations among the bloodless and drought responses. Our outcomes offer precious statistics and sturdy candidate genes for destiny purposeful analyses supposed to enhance the pressure tolerance of the Coffea Arabica and different species., {"references":["1.\tAfzal, A. J., Wood, A. J., and Lightfoot, D. A. (2008). Plant receptor-like serine-threonine kinases: roles in signaling and plant defense. Mol. Plant-Microbe Interact. 21, 507–517. doi: 10.1094/MPMI-21-5-0507 2.\tAmrine, K. C. H., Blanco-Ulate, B., and Cantu, D. (2015). Discovery of core biotic stress-responsive genes in Arabidopsis by weighted gene co-expression network analysis. PLoS ONE 10:e0118731. doi: 10.1371/journal.pone.0118731 3.\tBajji, M., Kinet, J.-M., and Lutts, S. (2001). The use of the electrolyte leakage method for assessing cell membrane stability as a water stress tolerance test in durum wheat. 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The modern-day have a look at received 24,891 collapsed isoforms of full-duration transcripts, and 20,662 have been mapped to recognized annotated genes, consisting of 17, one hundred seventy-five novel transcripts. The modern-day have a look at additionally diagnosed 915 fusion genes, 1794 novel genes, 2435 lengthy non-coding RNAs (lncRNAs), and 20,356 opportunity splicing events. Moreover, evaluation of differentially expressed genes (DEGs) found out that genes concerned in metabolic and molecular proliferation strategies have been notably enriched in up-regulated and down-regulated sets, respectively, in BPH, ate up resistant rice relative to BPH ate up inclined wild kind rice. Furthermore, the FoxO signaling pathway becomes concerned and genes associated with BPH hunger reaction (Nlbmm), apoptosis and autophagy (caspase 8, ATG13, BNIP3, and IAP), energetic oxygen elimination (catalase, MSR, ferritin) and detoxification (GST, CarE) have been up-regulated in BPH responses to resistant rice. The brown planthopper (BPH), Nilaparvatalugens, is one of the principal pests of rice (Oryza sativa). Plant defenses in opposition to insect herbivores had been drastically studied, however, our expertise of insect responses to host flowers��� resistance mechanisms remains limited. The cause of this have a look at is to signify transcripts of BPH and monitor the responses of BPH bugs to resistant rice at transcription stage through the usage of the superior molecular techniques, the next-era sequencing (NGS) and the single-molecule, real-time (SMRT) sequencing., {"references": ["1.\tWar AR, Paulraj MG, Ahmad T, Buhroo AA, Hussain B, Ignacimuthu S, et al. 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Sleep Med. 8, 421\u2013429. doi: 10.5664/jcsm.2038 42.\tChen, Y., Ozturk, N. C., and Zhou, F. C. (2013). DNA methylation program in developing hippocampus and its alteration by alcohol. PLoS ONE 8, 1\u201311. doi: 10.1371/journal.pone.0060503 43.\tSudheer Menon (2021) Advances in Systems biology and immunological data analysis for drug and vaccine development, International Journal of Educational Research and Studies (IJERS), 3 (3), PP 53-64. 44.\tSudheer Menon (2021) Whole genome sequencing and Insilico approaches to understand the genetic basis of Rare Diseases, International Journal of Advanced Scientific Research (IJASR), 6(5), PP 7-13. 45.\tSudheer Menon (2021) Bioinformatics approaches to identify neurodegenerative diseases by Next generation sequencing data, International Journal of Educational Research and Development (IJERD), 3(3), PP 70-74. 46.\tSudheer Menon (2021) Bioinformatics approaches for cross-species liver cancer analysis based single cell RNA sequencing data, International Journal of Molecular Biology and Biochemistry (IJMBB), 3(1), PP 05-13. 47.\tSudheer Menon (2021) Genomic sequence of worldwide strains of SARS-CoV-2: insights the Role of Variants in Disease Epidemiology, International Journal of Advanced Research and Development (IJARD), 6(4), PP 14-21. 48.\tSudheer Menon (2021) Differential Gene expression analysis by Single Cell RNA sequencing reveals insights to genetic diseases, International Journal of Multidisciplinary Education and Research (IJMER), 6(4), PP 1-7. 49.\tCheng, J., Wang, Y., Zhou, K., Wang, L., Li, J., Zhuang, Q., et al. (2014). Male-specific association between dopamine receptor D4 gene methylation and schizophrenia. PLoS ONE 9:e89128. doi: 10.1371/journal.pone.0089128 50.\tChurch, M. W., and Gerkin, K. P. (1988). Hearing disorders in children with fetal alcohol syndrome: findings from case reports. Pediatrics 82, 147\u2013154. 51.\tDadds, M. R., Schollar-Root, O., Lenroot, R., Moul, C., and Hawes, D. J. (2016). Epigenetic regulation of the DRD4 gene and dimensions of attention-deficit/hyperactivity disorder in children. Eur. Child Adolesc. Psychiatry 25, 1081\u20131089. doi: 10.1007/s00787-016-0828-3 52.\tDobbing, J., and Sands, J. (1979). Comparative aspects of the brain growth spurt. Early Hum. Dev. 3, 79\u201383. 53.\tDocherty, S. J., Davis, O. S. P., Haworth, C. M. A., Plomin, R., D'Souza, U., and Mill, J. (2012). A genetic association study of DNA methylation levels in the DRD4 gene region finds associations with nearby SNPs. Behav. Brain Funct. 8:31. doi: 10.1186/1744-9081-8-31 54.\tSudheer Menon (2021) Protein\u2013protein interactions by exploiting evolutionary information insights the genes and conserved regions in the corresponding human and mouse genome, International Journal of Advanced Multidisciplinary Research (IJARM), 8(9), PP 36-55. 55.\tSudheer Menon and Binu Thomas (2021) An insights to Bioinformatics methods in Natural Product Drug Discovery, International Journal of Clinical Biology and Biochemistry (IJCBB), 3(1), PP 26-37. 56.\tSudheer Menon and Binu Thomas (2021) Use of multi omics data in precision medicine and cancer research with applications in tumor subtyping, prognosis, and diagnosis, International Journal of Advanced Education and Research (IJAER), 6(5), PP 19-29. 57.\tSudheer Menon and Binu Thomas (2021) Gene Expression Analysis, Functional Enrichment, and Network Inference in disease prediction, International Journal of Advanced Educational Research (IJAER), 6(5), PP 6-18. 58.\tSudheer Menon and Binu Thomas (2021) Vaccine informatics, systems biology studies on neuro-degenerative diseases, International Journal of Multidisplinary Educational Research IJMER, 10(9-4), PP 85-101. 59.\tSudheer Menon (2021) Computational approaches to understand the role of epigenetics and microRNA in Cancer among different populations, International Journal of Multidisciplinary Research Review (IJMDRR) 7(9), PP 69-81. 60.\tEarnest, D. 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Psychiatry 20, 1438\u20131447. doi: 10.1038/mp.2014.159. 65.\tSudheer Menon and Binu Thomas (2021) Recent advances, methods and opportunities of Deep learning in computational and systems biology International Journal of Applied and Advanced Scientific Research (IJAASR) 6(2), PP 12-25. 66.\tSudheer Menon (2021) Computational genome based studies of Complex Genetic Diseases, International Journal of Multidisciplinary Research and Modern Education (IJMRME) 7(2) PP 28-39. 67.\tSudheer Menon (2021) Transcriptomic and metabolic pathway analysis reveals the mutated genes p53 and TP53 and their role in different types of cancer, International Journal of Engineering Research and Modern Education (IJERME), 6(2) PP 10-33. 68.\tSudheer Menon, Amanda Ramer Tait, Shanmughavel Piramanagakam, Vincent Chi Hang Lui and Paul Kwong Hang Tam (2021) Bisulphite seq data reveals host-microbiota interaction in germfree and conventional mice, International Journal of Bioinformatics and Biological Sciences, 9(1), PP 1-8. 69.\tSudheer Menon (2021) Insilico identification of Transcription End Sites in Eukaryotes,International Journal of Pharmacy and Biological Sciences (IJPBS), 11(3), PP-104-115. 70.\tFransquet, P. 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Mutations in the CDKN2A gene are the extremely common alteration in genetic melanoma, with presence in 40% of families with strong family ancestor. This gene normally encodes the p16 protein, which then at that point inhibits cycling-dependent kinase (CDK) 4 and 6, and the p14ARF protein. Afterwards mutations in CDKN2A bring about hyper phosphorylation of retinoblastoma protein (RB1), releasing the E2F1 transcription factor to produce cell cycle progression from G1 to S phase. Moreover, loss of p14ARF function advances the ubiquitination of p53, meanwhile diminishing cell cycle arrest and apoptosis. Those with the CDKN2A mutation have been displayed to develop multiple melanomas and importantly more dysplastic nevi, including presentations consistent with dysplastic nevus syndrome. Amazingly, one study found CDKN2A penetrance varied with geographic location, postulating a correlation with UV exposure as biggest penetrance by age 80 in families from Australia. Histological look into CDKN2A-mutated familial melanomas revealed a greater association with the superficial spreading subtype as compared with CDKN2A-wild type familial melanomas. In addition, in a Swedish study, familial melanoma cases with the CDKN2A mutation were related with a younger age at onset and worse survival than those without the mutation. That study revealed that deregulation of the cell cycle with CDKN2A mutations may exacerbate mutational load and increase tumor aggression. Approximately 8���12% of melanomas are diagnosed in individuals with a hereditary predisposition. Individuals with minimum one first-degree relative with melanoma have an approximately two-fold increased risk of adopting this disease, and the risk increases with the number of affected relatives. Multiple primary melanomas (MPM) produce in about 5% of sporadic melanoma infectants and in up to 19% of melanoma infectants with a strong positive family history. CDKN2A is well-known high-risk melanoma susceptibility gene, diagnosed about 20 years ago. Germline mutations of the CDKN2A gene are displayed in 20% of familial melanoma (FM) infectants, with the frequency increasing to 40% in families with three or can be more affected members. Recently, the invention of next-generation sequencing methodologies led to the diagnosis of new melanoma susceptibility genes implicated in different unknown pathways. The telomere-shelterin POT1 gene was diagnosed as a new high-penetrance susceptibility gene for FM and the p.S270N germline variant has been noticed as a founder mutation in Italy with a frequency in comparison with that of CDKN2A mutations. Two extra genes encoding proteins of the shelterin complex, ACD and TERF2IP, have been relate with familial melanoma. Moreover, to high-risk susceptibility genes, the importance of intermediate-risk genes, such as MC1R, has been highlighted by candidate gene and genome-wide association studies. MC1R variants are classified as red hair color or ���R��� variants and non-RHC or ���r��� alleles according to the strength of association with the RHC phenotype. MC1R variants have been associated with melanoma risk that appears to be stronger in RHC carriers and in darkly pigmented patients. More recently, the E318K substitution in the MITF-M gene has been reported as conferring an intermediate risk for melanoma and as a susceptibility gene for renal cell carcinoma. Development of MPM, increased nevus count and no blue eye color are clinical characteristics of MITF E318K mutation carriers. Hereditary susceptibility to cutaneous melanoma has been discovered in Italian high-hazardous melanoma patients from various geographical regions. CDKN2A has been seprated in almost all published investigations. In the current study, we did a mutational analysis of the major known melanoma susceptibility genes (CDKN2A, CDK4 exon 2, POT1 p.S270N, MC1R, MITF exon 10, and the TERT promoter) in high-hazardous FM and sump patients from Central Italy and asserted the association of mutational status with the center pathological attributes of patients and tumors. Mutations in the CDKN2A gene are the extremely common alteration in genetic melanoma, with presence in 40% of families with strong family ancestor. This gene normally encodes the p16 protein, which then at that point inhibits cycling-dependent kinase (CDK) 4 and 6, and the p14ARF protein. Afterwards mutations in CDKN2A bring about hyper phosphorylation of retinoblastoma protein (RB1), releasing the E2F1 transcription factor to produce cell cycle progression from G1 to S phase. Moreover, loss of p14ARF function advances the ubiquitination of p53, meanwhile diminishing cell cycle arrest and apoptosis. Those with the CDKN2A mutation have been displayed to develop multiple melanomas and importantly more dysplastic nevi, including presentations consistent with dysplastic nevus syndrome. Amazingly, one study found CDKN2A penetrance varied with geographic location, postulating a correlation with UV exposure as biggest penetrance by age 80 in families from Australia. Histological look into CDKN2A-mutated familial melanomas revealed a greater association with the superficial spreading subtype as compared with CDKN2A-wild type familial melanomas. In addition, in a Swedish study, familial melanoma cases with the CDKN2A mutation were related with a younger age at onset and worse survival than those without the mutation. That study revealed that deregulation of the cell cycle with CDKN2A mutations may exacerbate mutational load and increase tumor aggression. Approximately 8���12% of melanomas are diagnosed in individuals with a hereditary predisposition. Individuals with minimum one first-degree relative with melanoma have an approximately two-fold increased risk of adopting this disease, and the risk increases with the number of affected relatives. Multiple primary melanomas (MPM) produce in about 5% of sporadic melanoma infectants and in up to 19% of melanoma infectants with a strong positive family history. CDKN2A is well-known high-risk melanoma susceptibility gene, diagnosed about 20 years ago. Germline mutations of the CDKN2A gene are displayed in 20% of familial melanoma (FM) infectants, with the frequency increasing to 40% in families with three or can be more affected members. Recently, the invention of next-generation sequencing methodologies led to the diagnosis of new melanoma susceptibility genes implicated in different unknown pathways. The telomere-shelterin POT1 gene was diagnosed as a new high-penetrance susceptibility gene for FM and the p.S270N germline variant has been noticed as a founder mutation in Italy with a frequency in comparison with that of CDKN2A mutations. Two extra genes encoding proteins of the shelterin complex, ACD and TERF2IP, have been relate with familial melanoma. Moreover, to high-risk susceptibility genes, the importance of intermediate-risk genes, such as MC1R, has been highlighted by candidate gene and genome-wide association studies. MC1R variants are classified as red hair color or ���R��� variants and non-RHC or ���r��� alleles according to the strength of association with the RHC phenotype. MC1R variants have been associated with melanoma risk that appears to be stronger in RHC carriers and in darkly pigmented patients. More recently, the E318K substitution in the MITF-M gene has been reported as conferring an intermediate risk for melanoma and as a susceptibility gene for renal cell carcinoma. Development of MPM, increased nevus count and no blue eye color are clinical characteristics of MITF E318K mutation carriers. Hereditary susceptibility to cutaneous melanoma has been discovered in Italian high-hazardous melanoma patients from various geographical regions. CDKN2A has been seprated in almost all published investigations. In the current study, we did a mutational analysis of the major known melanoma susceptibility genes (CDKN2A, CDK4 exon 2, POT1 p.S270N, MC1R, MITF exon 10, and the TERT promoter) in high-hazardous FM and sump patients from Central Italy and asserted the association of mutational status with the center pathological attributes of patients and tumors., {"references":["1.\tMaria Santa Rocca, Giovanni Minervini, Andrea Di Nisio, Maurizio Merico, Maria Bueno Marinas, Luca De Toni, Kalliopi Pilichou, Andrea Garolla, Carlo Foresta, Alberto Ferlin, Identification of Rare LRP5 Variants in a Cohort of Males with Impaired Bone Mass, International Journal of Molecular Sciences, 10.3390/ijms221910834, 22, 19, (10834), (2021). 2.\tMaria Chiara Scaini, Jacopo Pigozzo, Marco Pizzi, Mariangela Manicone, Vanna Chiarion-Sileni, Pamela Zambenedetti, Massimo Rugge, Paola Zanovello, Elisabetta Rossi, Rita Zamarchi, Antonella Facchinetti, Clonal heterogeneity of melanoma in a paradigmatic case study, Melanoma Research, 10.1097/CMR.0000000000000510, 29, 1, (89-94), (2019). 3.\tSudheer Menon (2020) \"Preparation and computational analysis of Bisulphite sequencing in Germfree Mice\" International Journal for Science and Advance Research In Technology, 6(9) PP (557-565). 4.\tSudheer Menon, Shanmughavel Piramanayakam and Gopal Agarwal (2021) \"Computational identification of promoter regions in prokaryotes and Eukaryotes\" EPRA International Journal of Agriculture and Rural Economic Research (ARER), Vol (9) Issue (7) July 2021, PP (21-28). 5.\tSudheer Menon (2021) \"Bioinformatics approaches to understand gene looping in human genome\" EPRA International Journal of Research & Development (IJRD), Vol (6) Issue (7) July 2021, PP (170-173). 6.\tSudheer Menon (2021) \"Insilico analysis of terpenoids in Saccharomyces Cerevisiae\" International Journal of Engineering Applied Sciences and Technology, 2021 Vol. 6, Issue1, ISSN No. 2455-2143, PP(43-52). 7.\tMengqi Cui, Juan Du, XiaoJun Yao, The Binding Mechanism Between Inositol Phosphate (InsP) and the Jasmonate Receptor Complex: A Computational Study, Frontiers in Plant Science, 10.3389/fpls.2018.00963, 9, (2018). 8.\tSudheer Menon (2021) \"Computational analysis of Histone modification and TFBs that mediates gene looping\" Bioinformatics, Pharmaceutical, and Chemical Sciences (RJLBPCS), June 2021, 7(3) PP (53-70). 9.\tSudheer Menon Shanmughavel piramanayakam, Gopal Prasad Agarwal (2021) \"FPMD-Fungal promoter motif database: A database for the Promoter motifs regions in fungal genomes\" EPRA International Journal of Multidisciplinary research,7(7) PP (620-623). 10.\tSudheer Menon, Shanmughavel Piramanayakam and Gopal Agarwal (2021) Computational Identification of promoter regions in fungal genomes, International Journal of Advance Research, Ideas and Innovations in Technology, 7(4) PP (908-914). 11.\tSudheer Menon, Vincent Chi Hang Lui and Paul Kwong Hang Tam (2021) Bioinformatics methods for identifying hirschsprung disease genes, International Journal for Research in Applied Science & Engineering Technology (IJRASET), Volume 9 Issue VII July, PP (2974-2978). 12.\tSudheer Menon, (2021), Bioinformatics approaches to understand the role of African genetic diversity in disease, International Journal Of Multidisciplinary Research In Science, Engineering and Technology (IJMRSET), 4(8), PP 1707-1713. 13.\tVikas Pejaver, Sean D. Mooney, Predrag Radivojac, Missense variant pathogenicity predictors generalize well across a range of function‐specific prediction challenges, Human Mutation, 10.1002/humu.23258, 38, 9, (1092-1108), (2017). 14.\tSudheer Menon (2021) Comparison of High-Throughput Next generation sequencing data processing pipelines, International Research Journal of Modernization in Engineering Technology and Science (IRJMETS), 3(8), PP 125-136. 15.\tSudheer Menon (2021) Evolutionary analysis of SARS-CoV-2 genome and protein insights the origin of the virus, Wuhan, International Journal of Creative Research Thoughts (IJCRT), 9 (8), PP b696-b704. 16.\tPanagiotis Katsonis, Olivier Lichtarge, Objective assessment of the evolutionary action equation for the fitness effect of missense mutations across CAGI‐blinded contests, Human Mutation, 10.1002/humu.23266, 38, 9, (1072-1084), (2017). 17.\tSudheer Menon, Vincent Chi Hang Lui and Paul Kwong Hang Tam (2021) A step-by-step work flow of Single Cell RNA sequencing data analysis, International Journal for Scientific Research and Development (IJSRD), 9(6) PP 1-13. 18.\tSudheer Menon (2021) Computational characterization of Transcription End sites in Human Genome, International Journal of All Research Education and Scientific Methods (IJRESM), 9(8), PP 1043-1048. 19.\tSudheer Sivasankaran Menon and Shanmughavel Piramanayakam (2021) Insilico prediction of gyr A and gyr B in Escherichia coli insights the DNA-Protein interaction in prokaryotes, International Journal of Multidisciplinary Research and Growth Evaluation, (IJMRD), 2(4), PP 709-714. 20.\tWilliam Bruno, Virginia Andreotti, Alessandra Bisio, Lorenza Pastorino, Giuseppe Fornarini, Stefania Sciallero, Giovanna Bianchi-Scarrà, Alberto Inga, Paola Ghiorzo, Functional analysis of a CDKN2A 5'UTR germline variant associated with pancreatic cancer development, PLOS ONE, 10.1371/journal.pone.0189123, 12, 12, (e0189123), (2017). 21.\tSudheer Menon, Vincent Chi Hang Lui and Paul Kwong Hang Tam (2021) Bioinformatics tools and methods to analyze single cell RNA sequencing data, International Journal of Innovative Science and Research Technology, (IJISRT), 6(8), PP 282-288. 22.\tSudheer Menon (2021) Computational genome analysis for identifying Biliary Atresia genes, International Journal of Biotechnology and Microbiology, (IJBM), 3(2), PP 29-33. 23.\tSudheer Menon (2021) Recent Insilco advancements in genome analysis and characteristics of SARS-Cov2. International Journal of Biology Research, (IJBR), 6(3), PP 50-54. 24.\tSudheer Menon (2021) Bioinformatics methods for identifying Human disease genes, International Journal of Biology Sciences, (IJBR), 3(2), PP 1-5. 25.\tSudheer Menon (2021) SARS-CoV-2 Genome structure and protein interaction map, insights to drug discovery, International Journal of Recent Scientific Research, (IJRSR), 12(8), PP 42659-42665. 26.\tDamiano Piovesan, Giovanni Minervini, Silvio C.E. Tosatto, The RING 2.0 web server for high quality residue interaction networks, Nucleic Acids Research, 10.1093/nar/gkw315, 44, W1, (W367-W374), (2016). 27.\tSudheer Menon (2021) Insilico Insights to Mutational and Evolutionary aspects of SARS-Cov2, International Journal of Multidisciplinary Research and Development, (IJMRD) 8(8), 167-172. 28.\tSudheer Menon (2021) Computational biology, machine learning and reverse vaccinology detects the role of conserved Nsp3 Protein and its importance in Covid-19 vaccine development, European Journal of Biotechnology and Bioscience 9(3), PP 95-99. 29.\tSudheer Menon (2021) Protein Evolutionary Analysis of SARS-CoV-2 Delta Plus and C.1.2 Insights Virulence and Host Immunity, International Journal of Multidisciplinary Research and Publications (IJMRAP), 4(2), PP 6-13. 30.\tSudheer Menon (2021) Computing for Genomics and Proteomics in Microbial biotechnology in the identification of SARS COV2 Variants, International Journal of Scientific Engineering and Applied Science (IJSEAS), 7(9), PP 147-175. 31.\tSudheer Menon (2021) Functional Genome analysis and drug screening by Bioinformatics methods in SARS-CoV-2. International Journal of Academic Research and Development (IJARD), 6(5), PP 33-39. 32.\tGiovanni Minervini, Federica Quaglia, Silvio C.E. Tosatto, Insights into the proline hydroxylase (PHD) family, molecular evolution and its impact on human health, Biochimie, 10.1016/j.biochi. 2015.07.009, 116, (114-124), (2015). 33.\tSudheer Menon (2021) Advances in Systems biology and immunological data analysis for drug and vaccine development, International Journal of Educational Research and Studies (IJERS), 3 (3), PP 53-64. 34.\tSudheer Menon (2021) Whole genome sequencing and Insilico approaches to understand the genetic basis of Rare Diseases, International Journal of Advanced Scientific Research (IJASR), 6(5), PP 7-13. 35.\tSudheer Menon (2021) Bioinformatics approaches to identify neurodegenerative diseases by Next generation sequencing data, International Journal of Educational Research and Development (IJERD), 3(3), PP 70-74. 36.\tSudheer Menon (2021) Bioinformatics approaches for cross-species liver cancer analysis based single cell RNA sequencing data, International Journal of Molecular Biology and Biochemistry (IJMBB), 3(1), PP 05-13. 37.\tSudheer Menon (2021) Genomic sequence of worldwide strains of SARS-CoV-2: insights the Role of Variants in Disease Epidemiology, International Journal of Advanced Research and Development (IJARD), 6(4), PP 14-21. 38.\tSudheer Menon (2021) Differential Gene expression analysis by Single Cell RNA sequencing reveals insights to genetic diseases, International Journal of Multidisciplinary Education and Research (IJMER), 6(4), PP 1-7. 39.\tSudheer Menon (2021) Protein–protein interactions by exploiting evolutionary information insights the genes and conserved regions in the corresponding human and mouse genome, International Journal of Advanced Multidisciplinary Research (IJARM), 8(9), PP 36-55. 40.\tSudheer Menon and Binu Thomas (2021) An insights to Bioinformatics methods in Natural Product Drug Discovery, International Journal of Clinical Biology and Biochemistry (IJCBB), 3(1), PP 26-37. 41.\tSudheer Menon and Binu Thomas (2021) Use of multi omics data in precision medicine and cancer research with applications in tumor subtyping, prognosis, and diagnosis, International Journal of Advanced Education and Research (IJAER), 6(5), PP 19-29. 42.\tSudheer Menon and Binu Thomas (2021) Gene Expression Analysis, Functional Enrichment, and Network Inference in disease prediction, International Journal of Advanced Educational Research (IJAER), 6(5), PP 6-18. 43.\tSudheer Menon and Binu Thomas (2021) Vaccine informatics, systems biology studies on neuro-degenerative diseases, International Journal of Multidisplinary Educational Research IJMER, 10(9-4), PP 85-101. 44.\tSudheer Menon (2021) Computational approaches to understand the role of epigenetics and microRNA in Cancer among different populations, International Journal of Multidisciplinary Research Review (IJMDRR) 7(9), PP 69-81. 45.\tSudheer Menon and Binu Thomas (2021) Recent advances, methods and opportunities of Deep learning in computational and systems biology International Journal of Applied and Advanced Scientific Research (IJAASR) 6(2), PP 12-25. 46.\tSudheer Menon (2021) Computational genome based studies of Complex Genetic Diseases, International Journal of Multidisciplinary Research and Modern Education (IJMRME) 7(2) PP 28-39. 47.\tLauren G. Aoude, Michael Gartside, Peter Johansson, Jane M. Palmer, Judith Symmons, Nicholas G. Martin, Grant W. Montgomery, Nicholas K. Hayward, Prevalence of Germline BAP1, CDKN2A, and CDK4 Mutations in an Australian Population-Based Sample of Cutaneous Melanoma Cases, Twin Research and Human Genetics, 10.1017/thg.2015.12, 18, 02, (126-133), (2015). 48.\tSudheer Menon (2021) Transcriptomic and metabolic pathway analysis reveals the mutated genes p53 and TP53 and their role in different types of cancer, International Journal of Engineering Research and Modern Education (IJERME), 6(2) PP 10-33. 49.\tSudheer Menon, Amanda Ramer Tait, Shanmughavel Piramanagakam, Vincent Chi Hang Lui and Paul Kwong Hang Tam (2021) Bisulphite seq data reveals host-microbiota interaction in germfree and conventional mice, International Journal of Bioinformatics and Biological Sciences, 9(1), PP 1-8. 50.\tSudheer Menon (2021) Insilico identification of Transcription End Sites in Eukaryotes, International Journal of Pharmacy and Biological Sciences (IJPBS), 11(3), PP-104-115. 51.\tSudheer Menon (2021) Computational identification of upregulated genes in Breast, Prostate, and Colorectal Cancer and the Cellular Signaling process, Research Journal of Life Sciences, Bioinformatics, Pharmaceutical and Chemical Sciences, (RJLBPCS), 7(5), PP 68-83. 52.\tSudheer Menon (2021) Structural and Functional Characteristics of miRNAs in colon cancer and the identification of targets by Insilco methods, Research Journal of Life Sciences, Bioinformatics, Pharmaceutical and Chemical Sciences, (RJLBPCS), 7(6), PP 86-96. 53.\tPanagiotis Katsonis, Amanda Koire, Stephen Joseph Wilson, Teng‐Kuei Hsu, Rhonald C. Lua, Angela Dawn Wilkins, Olivier Lichtarge, Single nucleotide variations: Biological impact and theoretical interpretation, Protein Science, 10.1002/pro.2552, 23, 12, (1650-1666), (2014)."]}

The growth safe microenvironment is firmly identified with the harmful movement and treatment obstruction of brain tumors. Long non-coding RNA (lncRNA) assumes an administrative part in this interaction. We researched the neurotic components inside the brain tumors microenvironment and potential immunotherapy opposition identified with lncRNAs., {"references":["1.\tZhang, J. E. Price, G. Schackert, K. Itoh, and I. J. Fidler, \"Malignant potential of cells isolated from lymph node or brain metastases of melanoma patients and implications for prognosis,\" Cancer Research, vol. 51, no. 8, pp. 2029–2035, 1991. 2.\tAlizadeh, M. B. Eisen, R. E. Davis et al., \"Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling,\" Nature, vol. 403, no. 6769, pp. 503–511, 2000. 3.\tC. April, B. Klotzle, T. Royce et al., \"Whole-genome gene expression profiling of formalin-fixed, paraffin-embedded tissue samples,\" PLoS One, vol. 4, no. 12, Article ID e8162, 2009 4.\tSudheer Menon (2020) \"Preparation and computational analysis of Bisulphite sequencing in Germfree Mice\" International Journal for Science and Advance Research In Technology, 6(9) PP (557-565). 5.\tSudheer Menon, Shanmughavel Piramanayakam and Gopal Agarwal (2021) \"Computational identification of promoter regions in prokaryotes and Eukaryotes\" EPRA International Journal of Agriculture and Rural Economic Research (ARER), Vol (9) Issue (7) July 2021, PP (21-28). 6.\tSudheer Menon (2021) \"Bioinformatics approaches to understand gene looping in human genome\" EPRA International Journal of Research & Development (IJRD), Vol (6) Issue (7) July 2021, PP (170-173). 7.\tSudheer Menon (2021) \"Insilico analysis of terpenoids in Saccharomyces Cerevisiae\" International Journal of Engineering Applied Sciences and Technology, 2021 Vol. 6, Issue1, ISSN No. 2455-2143, PP(43-52). 8.\tSudheer Menon (2021) \"Computational analysis of Histone modification and TFBs that mediates gene looping\" Bioinformatics, Pharmaceutical, and Chemical Sciences (RJLBPCS), June 2021, 7(3) PP (53-70). 9.\tR. 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Nonaka et al., \"Constitutive ex-pression and costimulatory function of LIGHT/TNFSF14 on human melanoma cells and melanoma-derived micro- vesicles,\" Cancer Research, vol. 65, no. 8, pp. 3428–3436, 2005 10.\tSudheer Menon Shanmughavel piramanayakam, Gopal Prasad Agarwal (2021) \"FPMD-Fungal promoter motif database: A database for the Promoter motifs regions in fungal genomes\" EPRA International Journal of Multidisciplinary research,7(7) PP (620-623). 11.\tSudheer Menon, Shanmughavel Piramanayakam and Gopal Agarwal (2021) Computational Identification of promoter regions in fungal genomes, International Journal of Advance Research, Ideas and Innovations in Technology, 7(4) PP (908-914). 12.\tSudheer Menon, Vincent Chi Hang Lui and Paul Kwong Hang Tam (2021) Bioinformatics methods for identifying hirschsprung disease genes, International Journal for Research in Applied Science & Engineering Technology (IJRASET), Volume 9 Issue VII July, PP (2974-2978). 13.\tSudheer Menon, (2021), Bioinformatics approaches to understand the role of African genetic diversity in disease, International Journal Of Multidisciplinary Research In Science, Engineering and Technology (IJMRSET), 4(8), PP 1707-1713. 14.\tSudheer Menon (2021) Comparison of High-Throughput Next generation sequencing data processing pipelines, International Research Journal of Modernization in Engineering Technology and Science (IRJMETS), 3(8), PP 125-136. 15.\tSudheer Menon (2021) Evolutionary analysis of SARS-CoV-2 genome and protein insights the origin of the virus, Wuhan, International Journal of Creative Research Thoughts (IJCRT), 9 (8), PP b696-b704. 16.\tSudheer Menon, Vincent Chi Hang Lui and Paul Kwong Hang Tam (2021) A step-by-step work flow of Single Cell RNA sequencing data analysis, International Journal for Scientific Research and Development (IJSRD), 9(6) PP 1-13. 17.\tSudheer Menon (2021) Computational characterization of Transcription End sites in Human Genome, International Journal of All Research Education and Scientific Methods (IJRESM), 9(8), PP 1043-1048. 18.\tA. Subramanian, P. Tamayo, V. K. Mootha et al., \"Gene set enrichment analysis: a knowledge-based approach for inter-preting genome-wide expression profiles,\" Proceedings of the National Academy of Sciences, vol. 102, no. 43, pp. 15545–15550, 2005 19.\tSudheer Sivasankaran Menon and Shanmughavel Piramanayakam (2021) Insilico prediction of gyr A and gyr B in Escherichia coli insights the DNA-Protein interaction in prokaryotes, International Journal of Multidisciplinary Research and Growth Evaluation, (IJMRD), 2(4), PP 709-714. 20.\tSudheer Menon, Vincent Chi Hang Lui and Paul Kwong Hang Tam (2021) Bioinformatics tools and methods to analyze single cell RNA sequencing data, International Journal of Innovative Science and Research Technology, (IJISRT), 6(8), PP 282-288. 21.\tSudheer Menon (2021) Computational genome analysis for identifying Biliary Atresia genes, International Journal of Biotechnology and Microbiology, (IJBM), 3(2), PP 29-33. 22.\tSudheer Menon (2021) Recent Insilco advancements in genome analysis and characteristics of SARS-Cov2. International Journal of Biology Research, (IJBR), 6(3), PP 50-54. 23.\tBotti, G., Scognamiglio, G., Aquino, G., Liguori, G., and Cantile, M. (2019). LncRNA HOTAIR in tumor microenvironment: what role? Int. J. Mol. Sci. 20:2279. doi: 10.3390/ijms20092279 24.\tSudheer Menon (2021) Bioinformatics methods for identifying Human disease genes, International Journal of Biology Sciences, (IJBR), 3(2), PP 1-5. 25.\tSudheer Menon (2021) SARS-CoV-2 Genome structure and protein interaction map, insights to drug discovery, International Journal of Recent Scientific Research, (IJRSR), 12(8), PP 42659-42665. 26.\tChen, Q., Gao, J., Zhao, Y., and Hou, R. (2020). Long non-coding RNA LBX2-AS1 enhances glioma proliferation through downregulating microRNA-491-5p. Cancer Cell Int. 20:411. doi: 10.1186/s12935-020-01433-2 27.\tSudheer Menon (2021) Insilico Insights to Mutational and Evolutionary aspects of SARS-Cov2, International Journal of Multidisciplinary Research and Development, (IJMRD) 8(8), 167-172. 28.\tSudheer Menon (2021) Computational biology, machine learning and reverse vaccinology detects the role of conserved Nsp3 Protein and its importance in Covid-19 vaccine development, European Journal of Biotechnology and Bioscience 9(3), PP 95-99. 29.\tSudheer Menon (2021) Protein Evolutionary Analysis of SARS-CoV-2 Delta Plus and C.1.2 Insights Virulence and Host Immunity, International Journal of Multidisciplinary Research and Publications (IJMRAP), 4(2), PP 6-13. 30.\tCui, D., Huang, Z., Liu, Y., and Ouyang, G. (2017). The multifaceted role of periostin in priming the tumor microenvironments for tumor progression. Cell Mol. Life Sci. 74, 4287–4291. doi: 10.1007/s00018-017-2646-2 31.\tSudheer Menon (2021) Computing for Genomics and Proteomics in Microbial biotechnology in the identification of SARS COV2 Variants, International Journal of Scientific Engineering and Applied Science (IJSEAS), 7(9), PP 147-175. 32.\tWang, F., Cao, X., Yin, L., Wang, Q., and He, Z. (2020). Identification of SCARA5 gene as a potential immune-related biomarker for triple-negative breast cancer by integrated analysis. DNA Cell Biol. 39, 1813–1824. doi: 10.1089/dna.2020.5449 33.\tSudheer Menon (2021) Functional Genome analysis and drug screening by Bioinformatics methods in SARS-CoV-2. International Journal of Academic Research and Development (IJARD), 6(5), PP 33-39. 34.\tSudheer Menon (2021) Advances in Systems biology and immunological data analysis for drug and vaccine development, International Journal of Educational Research and Studies (IJERS), 3 (3), PP 53-64. 35.\tSudheer Menon (2021) Whole genome sequencing and Insilico approaches to understand the genetic basis of Rare Diseases, International Journal of Advanced Scientific Research (IJASR), 6(5), PP 7-13. 36.\tSudheer Menon (2021) Bioinformatics approaches to identify neurodegenerative diseases by Next generation sequencing data, International Journal of Educational Research and Development (IJERD), 3(3), PP 70-74. 37.\tGieryng, A., Pszczolkowska, D., Walentynowicz, K. A., Rajan, W. D., and Kaminska, B. (2017). Immune microenvironment of gliomas. Lab Invest. 97, 498–518. doi: 10.1038/labinvest.2017.19 38.\tSudheer Menon (2021) Bioinformatics approaches for cross-species liver cancer analysis based single cell RNA sequencing data, International Journal of Molecular Biology and Biochemistry (IJMBB), 3(1), PP 05-13. 39.\tOstrom, Q. T., Cioffi, G., Gittleman, H., Patil, N., Waite, K., Kruchko, C., et al. (2019). CBTRUS statistical report: primary brain and other central nervous system tumors diagnosed in the United States in 2012-2016. Neuro Oncol. 21(Suppl. 5), v1–v100. doi: 10.1093/neuonc/noz150 40.\tSudheer Menon (2021) Genomic sequence of worldwide strains of SARS-CoV-2: insights the Role of Variants in Disease Epidemiology, International Journal of Advanced Research and Development (IJARD), 6(4), PP 14-21. 41.\tSudheer Menon (2021) Differential Gene expression analysis by Single Cell RNA sequencing reveals insights to genetic diseases, International Journal of Multidisciplinary Education and Research (IJMER), 6(4), PP 1-7. 42.\tSudheer Menon (2021) Protein–protein interactions by exploiting evolutionary information insights the genes and conserved regions in the corresponding human and mouse genome, International Journal of Advanced Multidisciplinary Research (IJARM), 8(9), PP 36-55. 43.\tSudheer Menon and Binu Thomas (2021) An insights to Bioinformatics methods in Natural Product Drug Discovery, International Journal of Clinical Biology and Biochemistry (IJCBB), 3(1), PP 26-37. 44.\tSudheer Menon and Binu Thomas (2021) Use of multi omics data in precision medicine and cancer research with applications in tumor subtyping, prognosis, and diagnosis, International Journal of Advanced Education and Research (IJAER), 6(5), PP 19-29. 45.\tSudheer Menon and Binu Thomas (2021) Gene Expression Analysis, Functional Enrichment, and Network Inference in disease prediction, International Journal of Advanced Educational Research (IJAER), 6(5), PP 6-18. 46.\tSturm, D., Pfister, S. 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NEAT1 long noncoding RNA regulates transcription via protein sequestration within subnuclear bodies. Mol. Biol. Cell 25, 169–183. doi: 10.1091/mbc.E13-09-0558 52.\tSudheer Menon (2021) Transcriptomic and metabolic pathway analysis reveals the mutated genes p53 and TP53 and their role in different types of cancer, International Journal of Engineering Research and Modern Education (IJERME), 6(2) PP 10-33. 53.\tSudheer Menon, Amanda Ramer Tait, Shanmughavel Piramanagakam, Vincent Chi Hang Lui and Paul Kwong Hang Tam (2021) Bisulphite seq data reveals host-microbiota interaction in germfree and conventional mice, International Journal of Bioinformatics and Biological Sciences, 9(1), PP 1-8. 54.\tQuail, D. F., and Joyce, J. A. (2017). The Microenvironmental Landscape of Brain Tumors. 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Mosquito borne diseases are on the rise because of their fast spread worldwide and the lack of effective treatments. Here we are focusing on the development of a novel anti-malarial and virucidal agent with biocidal effects also on its vectors. We have synthesized a new quinoline (4,7-dichloroquinoline) derivative which showed significant larvicidal and pupicidal properties against a malarial and a dengue vector and a lethal toxicity ranging from 4.408 µM/mL (first instar larvae) to 7.958 µM/mL (pupal populations) for Anopheles stephensi and 5.016 µM/mL (larva 1) to 10.669 µM/mL (pupae) for Aedes aegypti. In-vitro antiplasmodial efficacy of 4,7-dichloroquinoline revealed a significant growth inhibition of both sensitive strains of Plasmodium falciparum with IC50 values of 6.7 nM (CQ-s) and 8.5 nM (CQ-r). Chloroquine IC50 values, as control, were 23 nM (CQ-s), and 27.5 nM (CQ-r). In vivo antiplasmodial studies with P. falciparum infected mice showed an effect of 4,7-dichloroquinoline compared to chloroquine. The quinoline compound showed significant activity against the viral pathogen serotype 2 (DENV-2). In vitro conditions and the purified quinoline exhibited insignificant toxicity on the host system up to 100 µM/mL. Overall, 4,7-dichloroquinoline could provide a good anti-vectorial and anti-malarial agent.

Structural genomics involves the advent of three-dimensional structures of the genome encoded proteins through various techniques available. Numerous structural genomics research groups have been developed across the globe and they contribute enormously to the identification of three-dimensional structures of various proteins. In this review, we have discussed the applications of the structural genomics approach towards the discovery of potential lead-like molecules against the genomic drug targets of three vector-borne diseases, namely, Dengue, Chikungunya and Zika. Currently, all these three diseases are associated with the most important global public health problems and significant economic burden in tropical countries. Structural genomics has accelerated the identification of novel drug targets and inhibitors for the treatment of these diseases. We start with the current development status of the drug targets and antiviral drugs against these three diseases and conclude by describing challenges that need to be addressed to overcome the shortcomings in the process of drug discovery.

Successive oxidative stress and biochemical changes results in neuronal death and neuritic plaques growth in Alzheimer's disease (AD). Therefore, it is interest to analyze amyloid-βeta precursor protein (APP), beta-secretase 1 (BACE1), presenilin (PSEN1 and PSEN2) genes from brain tissues to gain insights. Development of potential inhibitors for these targets is of significance. EST sequences of 2898 (APP), 539 (BACE1), 786 (PSEN1) and 314 (PSEN2) genes were analyzed in this study. A contig sequences with APP (contigs 1-4), BACE1 (contigs 5-7), PSEN1 (contigs 8, 9, 10, 11), PSEN2 (contigs 13, 14) except PSEN1 (contigs 10) and PSEN2 (contigs 13) genes were identified. APP (contig 3 without translational error) was further analyzed using molecular modeling and docking to show its binding with curcumin (principal curcuminoid of turmeric) having -7.3 kcal/mol interaction energy for further consideration as a potential inhibitor.

Mycobacterium tuberculosis (Mtb) has the ability to scrounge off the host macrophages and create a cordial environment for its survival. Identification of mechanisms favoring this purpose leads to ...

Trypanosoma brucei brucei (T.b.brucei) is an extra-cellular parasite that causes Animal African Trypanosomiasis (AAT) disease in animals. Till day, this disease is more difficult to treat and control due to lack of efficient vaccines and early diagnosis of the parasite infection. T.b.brucei Excretory/Secretory (ES) proteins were involved in pathogenesis and key for understanding the host-parasite interactions. Functions of T.b.brucei's ES proteins were poorly investigated and experimental identification is expensive and time-consuming. Bioinformatics approaches are cost-effective by facilitating the experimental analysis of potential drug targets for parasitic diseases. Here we applied several bioinformatics tools to predict and functionalize the annotation of 1104 ES proteins and immunoinformatics approaches carried out to predict and evaluate the epitopes in T.b.brucei. Secretory information, functional annotations and potential epitopes of each ES proteins were available at http://tbb.insilico.in . This study provides functional information of T.b.brucei for experimental studies to identify potential targets for diagnosis and therapeutics development.

This study is aimed to determine the 3D structure of a bacterial virulence protein Sortase A (SrtA) and to screen for curcumin analogues with high bioavailability and drug like properties that can target SrtA. SrtA is a membrane anchored protein, crucial for efficient pilus assembly, biofilm formation, and colonization of host tissue. Therefore, in this study SrtA was chosen as an antimicrobial target. However, lack of crystallography structural data of Enterococcus faecalis (E. faecalis) SrtA was a major shortcoming in screening for antimicrobial compounds. Therefore, in this work, we have elucidated the 3D structure of SrtA of E. faecalis using homology modeling. In addition, the molecular docking study confirmed that the curcumin analogue CA51 had better binding activity towards SrtA. Furthermore, the analogue CA51 was bound to the active site of SrtA enzyme in a stable conformation throughout the simulation time scale of 10 ns. From the molecular dynamics results, we propose that the analogue CA51 is a potent inhibitor of E. faecalis SrtA and can be used as novel antimicrobial compound against E. faecalis infections.

Background: Mycoplasmas are cell wall-deficient bacteria which cause respiratory and urogenital infections in human. Mycoplasmas are resistant to many of the available antibiotics because of their high mutation rates and lack of cell wall. Various studies have identified the emergence of treatment-resistant Mycoplasma isolates. Novel drug target identification has become significant for the development of successful antibacterial treatments. Computational genomic analysis plays a significant role in facilitating the identification of potential drug targets in many bacterial pathogens. Methods: In the present study, 12 Mycoplasma genomes were subjected to comparative genomic analysis to reinforce the understanding of their genomic organization and to identify potential drug targets. The distributions of genes under the Clusters of Orthologous Groups of proteins (COG) functional categories were analyzed for all the 12 Mycoplasma genomes. Genes from each functional category that are conserved across all the Mycoplasma genomes were extracted to identify the backbone genome of Mycoplasma species. The genes in the backbone genome were subjected to similarity search against a database of essential genes to validate their essentiality. Essentiality of these genes was further analyzed based on their function and subcellular localization. Results: The 12 Mycoplasma genomes under study were found to exhibit marked similarities in COG functional category distributions. An overall loss of genes in various functional categories has been observed in all the 12 Mycoplasma genomes. In all the 12 Mycoplasma genomes under study, a maximum reduction in the genes involved in the secondary metabolites biosynthesis, transport, and catabolism (Q) is observed. Conclusion: Comparative genomic studies have identified a set of 170 genes which are commonly present all the 12 Mycoplasma genomes. Further analysis of these genes has identified a set of 158 core essential genes which serve as a promising cluster of novel antibacterial targets.

Antimicrobial peptides (AMPs) play a prominent role in drug discovery due to the rapid increase in drug resistant infections. Hence, we report the molecular docking analysis of antimicrobial peptides MREEKKERKRD and MVQGAKRGGRLHRV with the target protein CXCL1 in the context of colorectal cancer for further consideration in drug discovery.

M. tuberculosis proliferates within the macrophages during infection and they are bounded by carbohydrates in the cell wall, called lectins. Despite their surface localization, the studies on exact functions of lectins are unexplored. Hence, in our study, using insilico approaches, 11 potential lectins of Mtb was explored as potential drug targets and vaccine candidates. Initially, a gene interaction network was constructed for the 11 potential lectins and identified its functional partners. A gene ontology analysis was also performed for the 11 mycobacterial lectins along with its functional partners and found most of the proteins are present in the extracellular region of the bacterium and belongs to the PE/PPE family of proteins. Further, molecular docking studies were performed for two of the potential lectins (Rv2075c and Rv1917c). A novel series of quinoxalinone and fucoidan derivatives have been made to dock against these selected lectins. Molecular docking study reveals that quinoxalinone derivatives showed better affinity against Rv2075c, whereas fucoidan derivatives have good binding affinity against Rv1917c. Moreover, the mycobacterial lectins can interact with the host and they are considered as potential vaccine candidates. Hence, immunoinformatics study was carried out for all the 11 potential lectins. B-cell and T-cell binding epitopes were predicted using insilico tools. Further, an immunodominant epitope 1062SIPAIPLSVEV1072 of Rv1917c was identified, which was predicted to bind B-cell and most of the MHC alleles. Thus, the study has explored that mycobacterial lectins could be potentially used as drug targets and vaccine candidates for tuberculosis treatment. Supplementary Information The online version contains supplementary material available at 10.1007/s42485-021-00065-y.

Additional file 1: Table S1. UniprotKB IDs of the putative OMPs of Mtb. Table S2. List of MHC-I and MHC-II alleles employed in the study. Figure S3. Ramachandran plot of IDE of Rv0295c. Figure 4. Ramachandran plot of IDE of Rv1006. Figure S5. Ramachandran plot of IDE of Rv2265.

Hyperglycemia, hyperlipidemia, and atherosclerotic lesions may cause inflammation, which leads to chemokine production and changes in vascular responses. Hyperglycemia can impair normal protein folding by producing reactive oxygen species (ROS) and interacting with various signaling molecules, resulting in the activation of ER stress responses, that stimulates NF-kB, which regulates the expression of numerous genes involved in inflammation and vascular remodeling. Our previous studies have shown that diosgenin has a protective effect against streptozotocin (STZ) - induced oxidative damage in rat aorta. However, the therapeutic role of diosgenin on iRhom2/TACE signaling which has primarily been linked to the endoplasmic reticulum (ER)-stress induced inflammation is unknown. Diosgenin was administered (40 mg/kg b. wt, orally, for 4 weeks) to STZ-induced male albino rats. Fasting plasma glucose, blood pressure, nitrite level, lipid profile, and lipoprotein were assessed. Serum insulin and pro-inflammatory markers were analyzed using ELISA, mRNA and protein expression of iRhom2/TACE signaling molecules were analyzed using RT-PCR and western blotting analysis respectively. In silico study was also performed to find out the possible binding affinity of diosgenin with the ER stress signaling molecules. Through regulation of the iRhom2/TACE signaling molecules, diosgenin lowered dyslipidemia, hypertension, and pro-inflammatory cytokines (TNF-α, IL-1, IL-6, and IL-4) in the aorta of STZ induced diabetic rats. Results of molecular docking analysis also confirmed the potential binding interaction with iRhom2/TACE and TNF- α. These in silico and in vivo results indicated that a change in lipid profile and hypertension led to diabetes-related inflammation by promoting ER stress and, as a result, accelerating the aorta by generating proinflammatory cytokines and lipid deposition. This study concludes that diosgenin attenuates ER stress-induced inflammation in diabetic rat aorta by modulating the expression of pro-inflammatory, iRhom2/TACE mediated mechanism and hence diosgenin can be a therapeutic drug for the treatment of diabetes-induced inflammation.

Typhoid fever is a severe illness in humans, caused by Salmonella typhi, a Gram-negative bacterium. Membrane proteins of S. typhi have strong potential for its use in development of subunit vaccine against typhoid. In current study, peptide-based subunit vaccine constructed from AI-2 import ATP-binding cassette transporter protein (LsrA) against S. typhi. B-cell and T-cell epitopes were identified at fold level with validated 3-D theoretical modelled structure. T-cell epitope from LsrA (LELPGSRPQ) has binds to maximum number (82.93%) of MHC class I and class II alleles. LsrA epitope was docked with HLA-DR4 and contact map were constructed to analyze molecular interaction (docking) studies. Simulation search for the binding site for full flexibility of the peptide from CABS-dock shows the stable interactions. MD simulation analysis reveals that LsrA epitope was binding and interacting firmly with the HLA-DR4. Hence, we are proposing that LsrA epitope would be a prominent epitope vaccine for human specific pathogen of S. typhi, which requires further steps to be elevated as a vaccine drug in near future.

The growing use of short-interfering RNA (siRNA)-based therapeutics for viral diseases reflects the most recent innovations in anti-viral vaccines and drugs. These drugs play crucial roles in the fight against many hitherto incurable diseases, the causes, pathophysiologies, and molecular processes of which remain unknown. Targeted liver drug delivery systems are in clinical trials. The receptor-mediated endocytosis approach involving the abundant asialoglycoprotein receptors (ASGPRs) on the surfaces of liver cells show great promise. We here review N-acetylgalactosamine (GalNAc)-siRNA conjugates that treat viral diseases such as hepatitis B infection, but we also mention that novel, native conjugate-based, targeted siRNA anti-viral drugs may also cure several life-threatening diseases such as hemorrhagic cystitis, multifocal leukoencephalopathy, and severe acute respiratory syndrome caused by coronaviruses and human herpes virus., Graphical abstract

This study focuses on insilico analysis to understand the mechanism between tuberculosis (TB) associated comorbidities such as Human Immunodeficiency Virus (HIV) and lung cancer. Initially, gene expression studies of samples associated with HIV-TB and lung cancer-TB were analyzed and differentially expressed genes were identified. Further, gene networks for the up-regulated genes were constructed and the functionally associated genes were identified. Functional enrichment analysis was also performed for the genes associated. Differentially- regulated genes could be possible drug targets for treatment of TB associated comorbidities. In this regards, Rv2949c which was found to be highly expressed in HIV patients with TB and it could be a candidate drug target for treatment of patients with HIV comorbidity. Similarly, pgsA1 is highly expressed in lung cancer patients with TB, is a candidate drug target for treatment of patients with lung cancer comorbidity. Suitable inhibitors for Rv2949c and pgsA1 have been found through molecular docking studies. Thus the insights gained through this study will be helpful in designing suitable drug candidates for treatment of TB related comorbidities.

Thirty children aged 3-10 years with clinically confirmed or suspected Duchenne Muscular Dystrophy (DMD) were analyzed for chromosomal aberrations using cytological preparations, biochemical change...

Tuberculosis (TB) is a deadly disease, and novel treatment strategies are required to combat it. Repurposing of existing Food and Drug Administration (FDA) approved drugs against Mycobacterium tuberculosis (Mtb) proteins could be beneficial for TB treatment. Protein kinase A (PknA) is one of the Serine/Threonine protein kinases (STPKs) of Mtb, and is an essential drug target, as it phosphorylates a number of proteins important for mycobacterial survival. In this study, through a molecular docking approach, we have screened 3176 FDA approved drugs against PknA and determined binding efficacy. Interestingly, the topmost compounds which have an improved docking score were found to be Vitamin B2 based compounds (ZINC3831425 and ZINC1769096) which can potentially bind and inhibit PknA. Molecular dynamics (MD) studies were performed to evaluate the stability of the docked complexes. Free energy of binding for the compounds docked with PknA was assessed by using the MM/PBSA method. Nutritional supplements have proven to be beneficial in treating TB. Thus, we hypothesize that Riboflavin or Vitamin B2 based compounds may inhibit PknA of Mtb, and could be used as an adjunct for the treatment of TB. Keywords: Mycobacterium tuberculosis, PknA, Molecular docking and dynamics, Riboflavin, Repurposing of drugs, Free energy calculation

Myocardial fibrosis reside a common pathological feature in hypertrophic and dilated cardiomyopathy that results in ventricular dysfunction leading to heart failure. Though several studies reported the role of fibrosis in cardiac diseases, their pathologic mechanisms leading to heart failure remains unclear. A few studies have proposed integrated analysis of microarray information and protein-protein interaction (PPI) systems to discover subnetwork markers related to diagnosis and prognosis of the disease. In addition to PPI networks, we incorporated miRNAs and transcription factors to find the putative miRNAs and transcription factors that might regulate the pathological process and progression of cardiomyopathy and their further progression to heart failure. The important submodules from network revealed the significance of Small Leucine Rich Proteoglycans (SLRPs), Extracellular matrix (ECM) related proteins and complement system in fibrosis. Sequence analysis of different SLRPs suggest that Keratocan and Fibromodulin possesses the same collagen binding site. A predicted mechanism of TGFβ1 shows the involvement of different pathway of HCM and DCM in progression of heart failure.