Vellore Institute of Technology (VIT) is a private university located in&nbsp;Tamil Nadu, India. Founded in 1984, as Vellore Engineering College, the institution offers 20 undergraduate, 34 postgraduate, four integrated and four research programs. It has campuses in Vellore, Amravati, Bhopal and Chennai.

VIT is one of the top ranked private universities in India according to NIRF, THE and QS Rankings.&nbsp;Govt. of India has recognized&nbsp;VIT, Vellore as an&nbsp;Institution of Eminence. This has allowed VIT to take independent quality initiatives and move up in world ranking.

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VIT University

Department of Biotechnology

β-Catenin, a key transcriptional factor involved in the canonical Wnt signaling pathway, is regulated by a cascade of phosphorylations and plays a major role in the progression of triple-negative breast cancer (TNBC). However, the phosphorylation induced conformational changes in a β-Catenin is still poorly understood. Hence, we adopted a conventional molecular dynamics approach to study phosphorylations present in a sequence motif Ser 552 675 and Tyr670 of the β-Catenin domain and analyzed in terms of structural transitions, bond formation, and folding-misfolding conformations. Our results unveil the β-Catenin linear motif 549–555 (RRTSMGG) of armadillo repeats domain prefers order to disorder state. In contrast, helix C associated with 670–678 (YKKRLSVEL) motif prefers disorder to order upon phosphorylation of Ser 552 675 and Tyr670. In addition, the crucial secondary structural transition from α-helix to coil induced by phospho Ser552 and phospho Tyr670 of β-Catenin ARM domain connecting helix C modifies conformational diversity and binding affinities of the complex interaction in functional regulation significantly. Moreover, the post phosphorylation disrupted the hydrogen bond interactions (Ser552-Arg549, Arg550-Asp546 and Ser675-Lys672) and abolished the residual alliance with hydrophobic interactions (Tyr670-Leu674) that easily interrupt in secondary structure packing as well as folding conformations connecting ARM and helix C (R10, 12 &amp; R1C) compared to unphosphorylation. Our integrated computational analysis may help in shedding light on understanding the induced folding and unfolding pattern due to motif phosphorylations. Overall, our results provide an atomistic structural description of the way phosphorylation facilitates conformational and dynamic changes in β-Catenin, a fundamental molecular switch mechanism in triple-negative breast cancer pathogenesis. © 2020 Elsevier Inc.

World University root node

School of Bio Sciences and Technology

Vellore Campus

Archives of Biochemistry and Biophysics

Exploring the structural significance of molecular switch mechanism alias motif phosphorylation in Wnt/β-catenin and their crucial role in triple-negative breast cancer

Diabetes Mellitus is a complex metabolic disorder with one of the highest prevalence rates in the world. The present study probes into the Thr-Ala 642 mutation of Akt substrate of 160 kDa (AS160) which has been implicated in diabetes by the dysregulation of glucose transported vesicle 4 (GLUT4) translocation. Our study provides a possible evidence on structural basis dysfunction of AS160 and how the association of phosphorylated AS160 with 14-3-3, a downstream binding partner regulating GLUT4 translocation got disrupted due to T642A mutation. We initially derived the disease-causing mutation (Thr642Ala) among others through in-silico based statistical analysis. Subsequently, we interpreted the perturbation induced in the structural arrangement and their impaired interaction in core regions. Due to mutation, the key interfacial interactions between AS160-14-3-3 were changing from Thr642-Asp756, Thr642-Asp757, and Thr642-Lys659 for phosphorylated form, to Ala642-Val681 for mutant. Further, for phosphorylated AS160 the hotspot residues observed were Glu-629, Gln-635, His-641, Lys-653 and Arg-842 which changed to Arg-637, His-641 for mutant. Eventually, the molecular dynamics analysis revealed that local region for phosphorylation site of AS160 is reducing the flexibility, whereas mutation is making the region more flexible. Principal component analysis and Free energy landscape analysis together reveals phosphorylated AS160 is occupying less phase space with more stable landscape when compared to mutant. Our study strongly confers the destabilizing effect of the point mutation at a conserved site providing novel insights right down to the residual level of the conformational dysregulation of AS160 implicating deadly disease. © 2020 Informa UK Limited, trading as Taylor & Francis Group.

Journal of Biomolecular Structure and Dynamics

Delineating the folding perturbations and molecular mechanisms of Thr-Ala 642 mutation in Rab-GTPase activating protein Akt substrate of 160kDa and its impact on the aetiology of diabetes

Parkinson’s disease (PD) is a progressive neurodegenerative disease affecting the ventral midbrain dopaminergic neurons, resulting in motor defects mainly tremor, rigidity, and bradykinesia along with a wide array of non-motor symptoms. The current study is focused on determining the potential druggable targets of PD by consolidating gene expression profiling and network methodology. Initially, the differentially expressed genes were established from which the central network was constructed by assimilating the interacting partners. Investigating the topological parameters of the network, the genes SYT1, CXCR4, CDC42, KIT, RET, DRD2, NTN1, PRKACB, KDR, NR4A2, SLC18A2, CCK, TH, KCNJ6, and TAC1 were identified as the hub genes and can be explored as potential candidate genes for PD therapeutics. Gene ontology and cluster analysis of the hub genes has provided further insights about the pathophysiology of the disease. Among the hub genes, PRKACB is observed in relatively all the enriched pathways which are modulated by G protein-coupled receptors through protein kinases. Further, we noticed SYT1 as a novel biomarker for PD. Moreover, the regulatory network was constructed with the hub genes as seed nodes with associated transcription factors (TFs) and microRNA (miRNAs). In this analysis, we identified MYC as the major TF and the miRNAs miR-21, miR-155, miR-7, and miR26A1 have a significant role in modulating the hub genes. Briefly, these significant hub genes and their enriched pathways, TFs, and miRNAs have aided in the better understanding of molecular mechanisms underlying PD and its potential core target genes. © 2020, Springer Science+Business Media, LLC, part of Springer Nature.

Journal of Molecular Neuroscience

Integrative Analysis of Gene Expression and Regulatory Network Interaction Data Reveals the Protein Kinase C Family of Serine/Threonine Receptors as a Significant Druggable Target for Parkinson’s Disease

Background: Marine bacteria serve as excellent sources of therapeutic enzymes, metabolites and natural products, which possess novel therapeutic properties. Increasing death rates due to cardiovascular diseases urge for cost-effective production of the fibrinolytic enzyme. Methods: In this study, marine sponge samples were screened for potent fibrinolytic producing bacteria. The primary screening was done for protease production, and clot lysis activity. The secondary screening was done for casein plasminogen activity and fibrinolytic activity. The strain which had potent fibrinolytic activity among them was further subjected to morphological, biochemical and molecular characterization. Media optimization was carried out to enhance enzyme production. The enzyme produced was subjected to purification using ammonium sulfate precipitation, gel filtration and characterized using HPLC and FTIR analysis Results: Sponge was identified to be Desmapsamma anchorata. Thirteen bacterial isolates were isolated from the sponge sample. The 16S rRNA sequencing revealed that the potential strain had 99% similarity with Bacillus licheniformis. Amongst the isolates, most were found to be morphologically identical to the Bacillus genus. Gram’s staining and SEM analysis of the potent isolate were performed to identify the spore formation and rod-shaped morphology of the bacteria. The optimal temperature and pH for the production of the enzyme were 37°C and 8, respectively. The carbon source maltose and nitrogen sources were malt extract and yeast extract that were found to be optimal. The optimum incubation time was found to be 4 to 5 days. The crude supernatant was purified with ammonium sulfate precipitation and gel filtration chromatography. The retention time of 11.3 min and the presence of functional groups show the purity of the enzyme. The partially purified enzyme showed 96.4% clot lysis in artificial clot lysis activity. Conclusion: Although the secretion of fibrinolytic enzymes from Bacillus species is not new, based on our investigation, there are no reports regarding Bacillus licheniformis being isolated from marine sponges. However, there are reports of Bacillus licheniformis secreting fibrinolytic enzymes isolated from fermented food samples. This study identifies the marine environment as a potential source of new exploration for drug discovery. © 2021 Bentham Science Publishers.

Current Bioactive Compounds

Production of fibrinolytic protease from a halobacterium bacillus licheniformis vitlms isolated from marine sponges of rameshwaram coast, india

Though numerous proteases have been isolated and screened for the dehairing purpose, their use in the leather industry is limited mainly due to high cost, the need for expertise, and control during unit operation and alterations in the quality of leather due to lack of the right kind of substrate specificity of the enzymes used. This paper deals with the comparative specificity and dehairing efficiency of proteases isolated from Bacillus cereus VITSP01 (PE2) and Brevibacterium luteolum VITSP02 (PE). PE2 and PE were found to be trypsin-like and elastase-like serine proteases respectively. The protease of VITSP02 degraded the proteoglycans efficiently in comparison to that of VITSP01. The results suggest that the possible targets of the studied proteases might be skin proteoglycans, including those cementing the hair root bulb. Hence, an in-depth study on the substrate specificity of the dehairing proteases would help in designing an improved screening method for isolating potent dehairing enzymes. © 2021 Elsevier B.V.

International Journal of Biological Macromolecules

Insights into substrate specificity of proteases for screening efficient dehairing enzymes

Objectives: Parkinson’s disease (PD) is the second most common neurodegenerative disorder which resists around 10 million people worldwide. It develops when nerve cells in a region of the brain that regulates movement become damaged; the symptoms usually begin gradually and become critical over time. In this study, we proposed to investigate the topological properties of functional brain networks within healthy controls (HCs) and PD patients. Also, we evaluated the gender difference among PD patients through graph theoretical approach. Materials and Methods: The rs-fMRI (resting-state functional magnetic resonance imaging) data of fifty-one PD patients and healthy controls was applied to generate the brain functional connectome. The functional whole-brain connectome was constructed by thresholding partial correlation matrices of 160 regions from Dosenbach brain atlas. From the graph theory approach, global and nodal metrics were analysed, and we observed considerable changes in PD patients in comparison with healthy controls. Results: Findings suggest that there is a significant difference in the topological characteristics of PD patients, and this was found to be evident in the default mode network (DMN) and occipital regions. Conclusion: This study provides essential insights from network changes to the clinically relevant information for the PD progression. © 2020 Informa UK Limited, trading as Taylor & Francis Group.

International Journal of Neuroscience

Global and regional connectivity analysis of resting-state function MRI brain images using graph theory in Parkinson’s disease

Rapidly evolving sequencing technologies have enabled efficient sequencing of complex genomes and metagenomes. Here, we have presented our metagenomic analysis of rat faeces isolated DNA, sequenced using long-read sequencing technology. The microbiome changes in the rat faeces after sixteen weeks of prolonged administration of subcutaneous 1,2 dimethylhydrazine to induce colon carcinogenesis and oral carotenoid-rich whole-cell lyophilised Dunaliella salina supplement. The faecal pellets were aseptically collected, and DNA was isolated and sequenced subsequently. The post-sequencing analysis revealed that the rat gut microbiome is highly complex and diverse. There was a significant difference between the microbiome of rats that received Dunaliella salina supplement in comparison with rats treated with 1,2 dimethylhydrazine and control rats. We observed the dominance of Bacteroidetes over Firmicutes in both cases of administration. The dominance was notably contributed by individuals like B. vulgatus, B. dorei, B. fragilis, P. ruminicola, and P. copri. The presence of protozoans like Trypanosoma, Trichomonas, and Leishmania was also identified among other commensal eukaryotes. Moreover, there was an abundant presence of bacteriophages targeting probiotic organisms like Lactobacillus among the identified DNA viruses. © 2020, Association of Microbiologists of India.

Indian Journal of Microbiology

Metagenomic Analysis of the Faecal Microbiome of Rats with 1, 2-Dimethylhydrazine Induced Colon Cancer and Prophylactic Whole-Cell Carotenoid Intervention

Zingiber officinale (ZO) and Terminalia chebula (TC) are plants used for the treatment of diverse illnesses in traditional medicine. The present study investigates the preventive effect of Zingiber officinale–Terminalia chebula extract (ZOTC) against DMBA-induced breast cancer in a rat model. Bioactive compounds from ZO (6-gingerol, 6-shogaol) and TC (gallic acid, ellagic acid, corilagin, chebulinic acid, and chebulagic acid) were detected using high-performance liquid chromatography. Mammary carcinogenesis was induced in rats with a single subcutaneous injection of 7,12-Dimethylbenz[a]anthracene (DMBA). Oral administration of ZOTC ameliorated the antioxidant status in mammary tissues, serum lipid levels, and serum cytokines. Histological analysis of the mammary tissue (normal and tumor) was carried out to obtain pathological alterations due to ZOTC treatment. The effect of ZOTC on the mechanistic target of rapamycin (mTOR) gene and accumulation of corresponding gene product was also investigated. mTOR plays a central role in cell metabolism and proliferation in normal and cancer cells. Transcriptional and immunohistochemical analysis showed the downregulation of mTOR expression in the mammary tissues of ZOTC-treated rats. In conclusion, the results obtained suggest that ZOTC can suppress tumor progression in DMBA-induced breast cancer rats via inhibition of the mTOR pathway. © 2021 Taylor &amp; Francis Group, LLC.

Nutrition and Cancer

Preventive Effect of Combined Zingiber officinale and Terminalia chebula against DMBA-Induced Breast Cancer Rats via mTOR Inhibition

Epimerase-deficiency galactosemia (EDG) is caused by mutations in the UDP-galactose 4’-epimerase enzyme, encoded by gene GALE. Catalyzing the last reaction in the Leloir pathway, UDP-galactose-4-epimerase catalyzes the interconversion of UDP-galactose and UDP-glucose. This study aimed to use in-depth computational strategies to prioritize the pathogenic missense mutations in GALE protein and investigate the systemic behavior, conformational spaces, atomic motions, and cross-correlation matrix of the GALE protein. We searched four databases (dbSNP, ClinVar, UniProt, and HGMD) and major biological literature databases (PubMed, Science Direct, and Google Scholar), for missense mutations that are associated with EDG patients, our search yielded 190 missense mutations. We applied a systematic computational prediction pipeline, including pathogenicity, stability, biochemical, conservational, protein residue contacts, and structural analysis, to predict the pathogenicity of these mutations. We found three mutations (p.K161N, p.R239W, and p.G302D) with a severe phenotype in patients with EDG that correlated with our computational prediction analysis; thus, they were selected for further structural and simulation analyses to compute the flexibility and stability of the mutant GALE proteins. The three mutants were subjected to molecular dynamics simulation (MDS) with native protein for 200 ns using GROMACS. The MDS demonstrated that these mutations affected the beta-sheets and helical region that are responsible for the catalytic activity; subsequently, affects the stability and flexibility of the mutant proteins along with a decrease and more deviations in compactness when compared to that of a native. Also, three mutations created major variations in the combined atomic motions of the catalytic and C-terminal regions. The network analysis of the residues in the native and three mutant protein structures showed disturbed residue contacts occurred owing to the missense mutations. Our findings help to understand the structural behavior of a protein owing to mutation and are intended to serve as a platform for prioritizing mutations, which could be potential targets for drug discovery and development of targeted therapeutics. © 2021, The Author(s), under exclusive licence to Springer Science+Business Media, LLC part of Springer Nature.

Department of Integrative Biology

Cell Biochemistry and Biophysics

Molecular dynamics, residue network analysis, and cross-correlation matrix to characterize the deleterious missense mutations in GALE causing galactosemia III

Proteus mirabilis is one among the most frequently identified pathogen in patients with the urinary tract infection. The multidrug resistance exhibited by P. mirabilis renders the treatment ineffective, and new progressive strategies are needed to overcome the antibiotic resistance (AR). We have analyzed the evolutionary relationship of 29 P. mirabilis strains available in the National Center for Biotechnology Information-Genome database. The antimicrobial resistance genes of P. mirabilis along with the enriched pathways and the Gene Ontology terms are analyzed using gene networks to understand the molecular basis of AR. The genes rpoB, tufB, rpsl, fusA, and rpoA could be exploited as potential drug targets as they are involved in regulating the vital functions within the bacterium. The drug targets reported in the present study will aid researchers in developing new strategies to combat multidrug-resistant P. mirabilis. © 2020 Wiley Periodicals LLC