Displaying publications 1 - 20 of 30 in total

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  1. A decision tree model for the prediction of homodimer folding mechanism
    Suresh A, Karthikraja V, Lulu S, Kangueane U, Kangueane P
    Bioinformation, 2009 Nov 17;4(5):197-205.
    PMID: 20461159
    The formation of protein homodimer complexes for molecular catalysis and regulation is fascinating. The homodimer formation through 2S (2 state), 3SMI (3 state with monomer intermediate) and 3SDI (3 state with dimer intermediate) folding mechanism is known for 47 homodimer structures. Our dataset of forty-seven homodimers consists of twenty-eight 2S, twelve 3SMI and seven 3SDI. The dataset is characterized using monomer length, interface area and interface/total (I/T) residue ratio. It is found that 2S are often small in size with large I/T ratio and 3SDI are frequently large in size with small I/T ratio. Nonetheless, 3SMI have a mixture of these features. Hence, we used these parameters to develop a decision tree model. The decision tree model produced positive predictive values (PPV) of 72% for 2S, 58% for 3SMI and 57% for 3SDI in cross validation. Thus, the method finds application in assigning homodimers with folding mechanism.
  2. Fulltext A review on the nutritional, medicinal, molecular and genome attributes of Durian (Durio zibethinus L.), the King of fruits in Malaysia
    Husin NA, Rahman S, Karunakaran R, Bhore SJ
    Bioinformation, 2018;14(6):265-270.
    PMID: 30237671 DOI: 10.6026/97320630014265
    Durian (Durio zibethinus L.; Family Bombacaceae) is an iconic tropical fruit plant cultivated in Malaysia and the Southeast Asian countries. In Malaysia, durian is recognised as the King of fruits and well known as a rich source of volatile sulphur compounds that make it unique. Fruit pulp of this fruit is an excellent source of nutrients as it contains proteins, dietary fat, fibers, and carbohydrates. Durian leaf and root decoctions are known to have a febrifuge and anti-malarial properties. The understanding of this plant's molecular biology will help breeders to develop a strategy for its further improvements. Hence, there is a need to identify and understand the genes necessary for the quality improvement of the durian fruits. Its genome contains about 46,000 genes which is almost double that of humans (Homo sapiens). The understanding of durian genes will be useful not only in the molecular breeding but also in the microbial production of novel proteins and or enzymes. This review highlights nutritional and medicinal attributes of durian. The molecular studies including the importance of undertaking transcriptomics work and the insights from the most recently reported genome draft are also highlighted.
  3. An improved hybrid of SVM and SCAD for pathway analysis
    Misman MF, Mohamad MS, Deris S, Abdullah A, Hashim SZ
    Bioinformation, 2011;7(4):169-75.
    PMID: 22102773
    Pathway analysis has lead to a new era in genomic research by providing further biological process information compared to traditional single gene analysis. Beside the advantage, pathway analysis provides some challenges to the researchers, one of which is the quality of pathway data itself. The pathway data usually defined from biological context free, when it comes to a specific biological context (e.g. lung cancer disease), typically only several genes within pathways are responsible for the corresponding cellular process. It also can be that some pathways may be included with uninformative genes or perhaps informative genes were excluded. Moreover, many algorithms in pathway analysis neglect these limitations by treating all the genes within pathways as significant. In previous study, a hybrid of support vector machines and smoothly clipped absolute deviation with groups-specific tuning parameters (gSVM-SCAD) was proposed in order to identify and select the informative genes before the pathway evaluation process. However, gSVM-SCAD had showed a limitation in terms of the performance of classification accuracy. In order to deal with this limitation, we made an enhancement to the tuning parameter method for gSVM-SCAD by applying the B-Type generalized approximate cross validation (BGACV). Experimental analyses using one simulated data and two gene expression data have shown that the proposed method obtains significant results in identifying biologically significant genes and pathways, and in classification accuracy.
  4. Fulltext Analysis of MAP kinase MPK4/MEKK1/MKK genes of Carica papaya L. comparative to other plant homologues
    Hamid MH, Rozano L, Yeong WC, Abdullah JO, Saidi NB
    Bioinformation, 2017;13(2):31-41.
    PMID: 28642634 DOI: 10.6026/97320630013031
    Mitogen-activated protein kinase 4 (MPK4) interacts with the (Mitogen-activated protein kinase kinase kinase 1) MEKK1/ Mitogenactivated protein kinase kinase 1 (MKK1)/ Mitogen-activated protein kinase kinase 2 (MKK2) complex to affect its function in plant development or against pathogen attacks. The KEGG (Kyoto Encyclopedia of Genes and Genomes) network analysis of Arabidopsis thaliana revealed close interactions between those four genes in the same plant-pathogen interaction pathway, which warrants further study of these genes due to their evolutionary conservation in different plant species. Through targeting the signature sequence in MPK4 of papaya using orthologs from Arabidopsis, the predicted sequence of MPK4 was studied using a comparative in silico approach between different plant species and the MAP cascade complex of MEKK1/MKK1/MKK2. This paper reported that MPK4 was highly conserved in papaya with 93% identical across more than 500 bases compared in each species predicted. Slight variations found in the MEKK1/MKK1/MKK2 complex nevertheless still illustrated sequence similarities between most of the species. Localization of each gene in the cascade network was also predicted, potentiating future functional verification of these genes interactions using knock out or/and gene silencing tactics.
  5. Fulltext Anticancer effects and lysosomal acidification in A549 cells by Astaxanthin from Haematococcus lacustris
    Ramamoorthy K, Raghunandhakumar S, Anand RS, Paramasivam A, Kamaraj S, Nagaraj S, et al.
    Bioinformation, 2020;16(11):965-973.
    PMID: 34803274 DOI: 10.6026/97320630016965
    Astaxanthin (AXN) is known to have health benefits by epidemiological studies. Therefore, it is of interest to assess the effect of AXN (derived from indigenous unicellular green alga Haematococcus lacustris) to modulate cell cycle arrest, lysosomal acidification and eventually apoptosis using in vitro in A549 lung cancer cells. Natural extracts of astaxanthin were obtained by standardized methods as reported earlier and characterized by standard HPLC and MS. Treatment of A549 cells with AXN (purified fraction) showed significant reduction in cell viability (about 50%) as compared to crude extract at 50µM concentration. Thus, we show the anticancer effects and lysosomal acidification in A549 cells by Astaxanthin from Haematococcus lacustris for further consideration. Together, our results demonstrated the anticancer potential of AXN from Haematococcus lacustris, which is found to be mediated via its ability to induce cell cycle arrest, lysosomal acidification and apoptotic induction.
  6. Fulltext Antimicrobial, antioxidant and anti-inflammatory activities of seeds from emblica officinalis (Gaertn.)
    G Singh P, S Jain A, B Sridhara Setty P, Bv S, S Patil S, P A, et al.
    Bioinformation, 2022;18(8):683-691.
    PMID: 37323557 DOI: 10.6026/97320630018683
    There is a shred of evidence to suggest that Emblica officinalis Gaertn, the botanical name for amla seeds, has greater medicinal potential than amla fruit. We conducted this work to assess the anti-inflammatory, antibacterial, and antioxidant capacities of E. officinalis seed extracts. The bioactive components from the seeds were fractionated using chloroform, hexane, methanol, and diethyl ether, according to the polarity of the solvents. The total amount of phenolic and flavonoid was estimated. Both the reducing power and antioxidant capacities of the extracts were evaluated using the DPPH (1,1-diphenyl-2-picryl-hydrazyl) technique. 15-lipoxygenase (LOX) was inhibited by seed extracts at doses ranging from 5 to 25 micrograms. In silico docking was employed to assess the results. Some human pathogenic microorganisms were tested for their antibacterial activity using the agar disc diffusion method. Escherichia coli, Proteus vulgaris, and Klebsiella pneumonia were inhibited by a methanolic extract with an IC50 value of 58g, making it the most common organic solvent extract. Methanolic extracts also showed good antioxidant and antibacterial activity. Our investigation led us to discover that amla seeds have anti-inflammatory, antioxidant, and antibacterial effects.
  7. Fulltext Artificial signal peptide prediction by a hidden markov model to improve protein secretion via Lactococcus lactis bacteria
    Razmara J, Deris SB, Illias RB, Parvizpour S
    Bioinformation, 2013;9(7):345-8.
    PMID: 23750078 DOI: 10.6026/97320630009345
    A hidden Markov model (HMM) has been utilized to predict and generate artificial secretory signal peptide sequences. The strength of signal peptides of proteins from different subcellular locations via Lactococcus lactis bacteria correlated with their HMM bit scores in the model. The results show that the HMM bit score +12 are determined as the threshold for discriminating secreteory signal sequences from the others. The model is used to generate artificial signal peptides with different bit scores for secretory proteins. The signal peptide with the maximum bit score strongly directs proteins secretion.
  8. Bioinformatics in molecular immunology laboratories demonstrated: Modeling an anti-CMV scFv antibody
    Heng CK, Othman RY
    Bioinformation, 2006 Mar 27;1(4):118-20.
    PMID: 17597869
    A scFv (single chain variable fragment) antibody clone from anti-CMV (anti-cucumber mosaic virus) was successfully constructed from immunized mouse and the DNA sequence was submitted to GenBank (AY337618 and AY337619). The expression of a 32 kDa recombinant antibody in bacteria was verified using ELISA (enzyme-linked immunoassay) and western blot. However, elucidation of specific anti-CMV scFv function requires detailed and time consuming immuno-assays. Alternatively, useful functional information on anti-CMV scFV antibody can be obtained using available Bioinformatics tools and techniques without performing tedious assays. Here, we use the commonly used Bioinformatics tools and databases such as BLAST (basic local alignment search tool), GenBank, PDB (protein databank), KABAT numbering, SWISS-MODEL and Insight II to gain specific functional insights into anti-CMV scFv.
  9. Fulltext Comparative sequence-structure analysis of Aves insulin
    Islam MM, Aktaruzzaman M, Mohamed Z
    Bioinformation, 2015;11(2):67-72.
    PMID: 25848166 DOI: 10.6026/97320630011067
    Normal blood glucose level depends on the availability of insulin and its ability to bind insulin receptor (IR) that regulates the downstream signaling pathway. Insulin sequence and blood glucose level usually vary among animals due to species specificity. The study of genetic variation of insulin, blood glucose level and diabetics symptoms development in Aves is interesting because of its optimal high blood glucose level than mammals. Therefore, it is of interest to study its evolutionary relationship with other mammals using sequence data. Hence, we compiled 32 Aves insulin from GenBank to compare its sequence-structure features with phylogeny for evolutionary inference. The analysis shows long conserved motifs (about 14 residues) for functional inference. These sequences show high leucine content (20%) with high instability index (>40). Amino acid position 11, 14, 16 and 20 are variable that may have contribution to binding to IR. We identified functionally critical variable residues in the dataset for possible genetic implication. Structural models of these sequences were developed for surface analysis towards functional representation. These data find application in the understanding of insulin function across species.
  10. Fulltext Computational analysis of common bean (Phaseolus vulgaris L., genotype BAT93) lycopene β-cyclase and β-carotene hydroxylase gene's cDNA
    Bhore SJ, Amelia K, Wang E, Priyadharsini S, Shah FH
    Bioinformation, 2013;9(4):197-206.
    PMID: 23519320 DOI: 10.6026/97320630009197
    The identification of genes and understanding of genes' expression and regulation in common bean (Phaseolus vulgaris L.) is necessary in order to strategize its improvement using genetic engineering techniques. Generation of expressed sequence tags (ESTs) is useful in rapid isolation, identification and characterization of the genes. To study the gene expression in P. vulgaris pods tissue, ESTs generation work was initiated. Early stage and late stage bean-pod-tissues cDNA libraries were constructed using CloneMiner cDNA library construction kit. In total, 5972 EST clones were isolated using random method of gene isolation. While processing ESTs, we found lycopene β-cyclase (PvLCY-β) and β-carotene hydroxylase (PvCHY-β) gene's cDNA. In carotenoid biosynthesis pathway, PvLCY-β catalyzes the production of carotene; and PvCHY-β is known to function as a catalyst in the production of lutein and zeaxanthin. To understand more about PvLCY-β and PvCHY-β, both strands of both cDNA clones were sequenced using M13 forward and reverse primers. Nucleotide and deduced protein sequences were analyzed and annotated using online bioinformatics tools. Results showed that PvLCY-β and PvCHY-β cDNAs are 1639 and 1107 bp in length, respectively. Analysis results showed that PvLCY-β and PvCHY-β gene's cDNA contains an open reading frame (ORF) that encodes for 502 and 305 amino acid residues, respectively. The deduced protein sequence analysis results also showed the presence of conserved domains needed for PvLCY-β and PvCHY-β functions. The phylogenetic analysis of both PvLCY-β and PvCHY-β proteins showed it's closeness with the LCY-β and CHY-β proteins from Glycine max, respectively. The nucleotide sequence of PvLCY-β and PvCHY-β gene's cDNA and it's annotation is reported in this paper.
  11. Fulltext Computer aided analysis of disease linked protein networks
    Sabetian S, Shamsir MS
    Bioinformation, 2019;15(7):513-522.
    PMID: 31485137 DOI: 10.6026/97320630015513
    Proteins can interact in various ways, ranging from direct physical relationships to indirect interactions in a formation of protein-protein interaction network. Diagnosis of the protein connections is critical to identify various cellular pathways. Today constructing and analyzing the protein interaction network is being developed as a powerful approach to create network pharmacology toward detecting unknown genes and proteins associated with diseases. Discovery drug targets regarding therapeutic decisions are exciting outcomes of studying disease networks. Protein connections may be identified by experimental and recent new computational approaches. Due to difficulties in analyzing in-vivo proteins interactions, many researchers have encouraged improving computational methods to design protein interaction network. In this review, the experimental and computational approaches and also advantages and disadvantages of these methods regarding the identification of new interactions in a molecular mechanism have been reviewed. Systematic analysis of complex biological systems including network pharmacology and disease network has also been discussed in this review.
  12. Fulltext Cytotoxic potentials of silibinin assisted silver nanoparticles on human colorectal HT-29 cancer cells
    Jackson K, Devaraj E, Lakshmi T, Rajeshkumar S, Dua K, Chellappan DK, et al.
    Bioinformation, 2020;16(11):817-827.
    PMID: 34803254 DOI: 10.6026/97320630016817
    It is of interest to study the cytotoxicity of silibinin assisted silver nanoparticles in human colorectal (HT-29) cancer cells. Silver nanoparticles were synthesized using silibinin as a reducing agent. The synthesized silibinin assisted silver nanoparticles ( SSNPs) were characterized and analyzed using a transmission electron microscope and spectrophotometer. The SSNPs synthesized in this study are spherical and their size ranges from 10 to 80 nm. HT-29 cells were treated with different concentrations (2, 4, 6, 8 and 10 ng/mL) of SSNPs and cytotoxicity was evaluated. The apoptosis was using flow cytometry. p53 protein expression using western blot. SSNPs are induced a decrease in viability and increased concentration-dependent cytotoxicity in HT-29 cells. SSNPs treatment also caused apoptosis-related morphological changes. SSNPs treatments at 8 and 16 ng/ml showed a prominent apoptotic change i.e., 70.3% and 83.6% respectively, and decreased viability of HT-29 cells 20% and 11.2% respectively as compared to control cells. SSNPs treatments induced p53 expression in HT-29 cells. Data shows that SSNPs have the potential to induce apoptosis in colorectal cancer cells. This provides insights for the further evaluation of SSNPs in fighting colon cancer.
  13. Fulltext D-carvone induced ROS mediated apoptotic cell death in human leukemic cell lines (Molt-4)
    Iyappan P, Bala MD, Sureshkumar M, Veeraraghavan VP, Palanisamy A
    Bioinformation, 2021;17(1):171-180.
    PMID: 34393434 DOI: 10.6026/97320630017171
    The immature lymphoid cells with chromosomal structural and numerical abnormalities cause the acute lymphoblastic leukemia (ALL). This hematologic disorder constitutes about 25% of cancer prognosis among children and adolescents. D-Carvone, a monocyclic monoterpene obtained from the essential oils extracted from plants is reported to possess the various biological activities. The present study was aimed to investigate the anticancer potential of D-Carvone against the human leukemic Molt-4 cells. The cytotoxicity of DCarvone was analyzed by MTT assay. The level of lipid peroxidation and antioxidants were determined. The intracellular ROS, MMP and apoptosis were demonstrated by fluorescent staining techniques. The MTT assay revealed that the D-Carvone treatment suppressed the viability of Molt-4 cells and the IC50 was determined at 20 µM/ml. The D-Carvone treatment was increased the oxidative stress and reduced the level of antioxidants in the Molt-4 cell lines. The increased intracellular ROS, apoptotic cell death, and diminished MMP was noted in the D-Carvone treatment. In the Molt-4 cells, D-carvone induced the apoptosis in a time and dose dependent manner by the activation of caspases-8, -9 and -3. Thus, data provide insights for the clinical application of D-Carvone in the treatment of blood cancer Molt-4 cells. Our study suggests the therapeutic potential D-Carvone for the treatment of leukemia in future.
  14. Fulltext Data on known anti-virals in combating CoVid-19
    Akshayaa L, Lakshmi T, Devaraj E, Roy A, Raghunandhakumar S, Sivaperumal P, et al.
    Bioinformation, 2020;16(11):878-881.
    PMID: 34803262 DOI: 10.6026/97320630016878
    Design and development of effective anti-virals in combating CoVid-19 is a great challenge worldwide. Known drugs such as chloroquine, lopinavir, favipiravir and remdesivir are used in the management of CoVid - 19. It is known that Ivermectin and remdesivir both are effective against filoviruses, paramyxo viruses. Available data also shows that ivermectin and remedesivir repress the replication of SARS-CoV-2. Thus, we document the potential use of ivermectin and remdesivir in the management of CoVid -19.
  15. EuDBase: An online resource for automated EST analysis pipeline (ESTFrontier) and database for red seaweed Eucheuma denticulatum
    Hussein ZA, Loke KK, Abidin RA, Othman R
    Bioinformation, 2011;7(4):157-62.
    PMID: 22102771
    Functional genomics has proven to be an efficient tool in identifying genes involved in various biological functions. However the availability of commercially important seaweed Eucheuma denticulatum functional resources is still limited. EuDBase is the first seaweed online repository that provides integrated access to ESTs of Eucheuma denticulatum generated from samples collected from Kudat and Semporna in Sabah, Malaysia. The database stored 10,031 ESTs that are clustered and assembled into 2,275 unique transcripts (UT) and 955 singletons. Raw data were automatically processed using ESTFrontier, an in-house automated EST analysis pipeline. Data was collected in MySQL database. Web interface is implemented using PHP and it allows browsing and querying EuDBase through search engine. Data is searchable via BLAST hit, domain search, Gene Ontology or KEGG Pathway. A user-friendly interface allows the identification of sequences either using a simple text query or similarity search. The development of EuDBase is initiated to store, manage and analyze the E. denticulatum ESTs and to provide accumulative digital resources for the use of global scientific community. EuDBase is freely available from http://www.inbiosis.ukm.my/eudbase/.
  16. Evolutionary trace analysis at the ligand binding site of laccase
    Mohamad SB, Ong AL, Ripen AM
    Bioinformation, 2008 Jun 18;2(9):369-72.
    PMID: 18795108
    Laccase belongs to the family of blue multi-copper oxidases and are capable of oxidizing a wide range of aromatic compounds. Laccases have industrial applications in paper pulping or bleaching and hydrocarbon bioremediation as a biocatalyst. We describe the design of a laccase with broader substrate spectrum in bioremediation. The application of evolutionary trace (ET) analysis of laccase at the ligand binding site for optimal design of the enzyme is described. In this attempt, class specific sites from ET analysis were mapped onto known crystal structure of laccase. The analysis revealed 162PHE as a critical residue in structure function relationship studies.
  17. Fulltext Fucoxanthin induced apoptotic cell death in oral squamous carcinoma (KB) cells
    Iyappan P, Bala MD, Sureshkumar M, Veeraraghavan VP, Palanisamy A
    Bioinformation, 2021;17(1):181-191.
    PMID: 34393435 DOI: 10.6026/97320630017181
    Fucoxanthin (Fx) is an active compound commonly found in the many types of seaweed with numerous biological activities. The main goal of this investigation is to explore the effect of Fx against the cell proliferation, apoptotic induction and oxidative stress in the oral squamous (KB) cell line. Cytotoxicity of Fx was determined by MTT assay. The intracellular ROS production, mitochondrial membrane potential (MMP) and apoptosis induction in KB cells were examined through DCFH-DA, Rhodamine-123 and DAPI, and dual staining techniques. Effect of Fx on the antioxidant enzymes and lipid peroxidation in the KB cells was studied through the standard procedures. Fx treated KB cells showed morphological changes and reduced cell survival, which is exhibited by the cytotoxic activity of 50 µM/ml (IC50) Fx against the KB cells. The Fx treatment considerably induced the apoptotosis cells (EB/AO) and decreased the MMP (Rh-123) in KB cells. Further, it was pointed out that there was an increased lipid peroxidation (LPO) with decreased antioxidants (CAT, SOD and GSH). These results concluded that Fx has the cytotoxic effect against KB cells and has the potential to induce the apoptosis via increased oxidative stress. Hence, the Fx can be a promising agent for the treatment of oral cancer and it may lead to the development of cancer therapeutics.
  18. Highlights of Biosafety and Biosecurity Month (BBM)at the AIMST University and Perspectives on Biorisk Management
    Bhore SJ
    Bioinformation, 2019;15(8):568-571.
    PMID: 31719766 DOI: 10.6026/97320630015568
    The innovations and developments in microbiology, biomedical sciences, and biotechnology come along with the challenges of biological risk (biorisk). Biorisk is defined as the "combination of the probability of occurrence of harm and the severity of that harm where the source of harm is a biological agent or toxin." Biorisk is a borderless challenge to the global community. Hence, all universities, colleges, centers of bio-excellence, and institutions of higher learning can and should do their bit to educate technical members, academicians, students and stakeholders (LASS) for the efficient and comprehensive biorisk management (BRM) for our and future generations safety and sustainability.
  19. Insights from the GC content analysis of 76genome survey sequences (GSS) from Elaeisoleifera
    Bhore SJ, Kassim A, Shah FH
    Bioinformation, 2010 Sep 20;5(4):141-5.
    PMID: 21364775
    South American oil-palm (Elaeis oleifera) is not cultivated in tropical countries like Malaysia on large scale due to low yield of palm oil derived from its fruit mesocarp. However, its fruit mesocarp oil contains about 68.6 % oleic acid (C(18:1)) which is more than double in comparison to commercially cultivated oilpalm, E. guineensis Jacq Tenera (hybrid of Dura (♀) x Pisifera (♂)). It is also known that E. oleifera is a good source of tocotrienols and carotenoids. Therefore, it is of interest to know the genome sequence of E. oleifera. The objective of this study is to generate genome survey sequences (GSS) to get GC content insight in the E. oleifera genome. The nuclear genomic DNA isolated from young leaf-tissues was digested with EcoRI and NdeI/DraI restriction enzymes; and three genomic DNA libraries were constructed using Lambda ZAP-II, pGEM®-T Easy, and pDONR 222™ as cloning vectors. Generated 76 GSSs were analyzed by using Bioinformatics tools. The analysis result indicates that the adenine, cytosine, guanine and thymine content in generated GSSs are 30%, 20%, 20%, and 30% respectively. In conclusion, based on the precise GC content analysis of the randomly isolated 76 GSSs by using Bioinformatics tools we hypothesize that GC content in E. oleifera genome is 40%. The hypothesized 40% GC content in E. oleifera genome is expected to remain close to the GC content based on the whole genome analysis.(ψ)The nucleotide sequence data reported in this paper have been submitted to dbGSS division of the international DNA database (GenBank/DDBJ/EMBL) under accession numbers: DX575945- DX575972 and EI798032-EI798079.

    ABBREVIATIONS: gDNA - Nuclear genomic DNA, GSSs - Genome survey sequences K12, SAOP - South American oil-palm Db1.

  20. Fulltext Insights from the docking and molecular dynamics simulation of the Phosphopantetheinyl transferase (PptT) structural model from Mycobacterium tuberculosis
    Rohini K, Srikumar PS
    Bioinformation, 2013;9(13):685-9.
    PMID: 23930020 DOI: 10.6026/97320630009685
    A great challenge is posed to the treatment of tuberculosis due to the evolution of multidrug-resistant (MDR) and extensively drugresistant (XDR) strains of Mycobacterium tuberculosis in recent times. The complex cell envelope of the bacterium contains unusual structures of lipids which protects the bacterium from host enzymes and escape immune response. To overcome the drug resistance, targeting "drug targets" which have a critical role in growth and virulence factor is a novel approach for better tuberculosis treatment. The enzyme Phosphopantetheinyl transferase (PptT) is an attractive drug target as it is primarily involved in post translational modification of various types-I polyketide synthases and assembly of mycobactin, which is required for lipid virulence factors. Our in silico studies reported that the structural model of M.tuberculosis PptT characterizes the structure-function activity. The refinement of the model was carried out with molecular dynamics simulations and was analyzed with root mean square deviation (RMSD), and radius of gyration (Rg). This confirmed the structural behavior of PptT in dynamic system. Molecular docking with substrate coenzyme A (CoA) identified the binding pocket and key residues His93, Asp114 and Arg169 involved in PptT-CoA binding. In conclusion, our results show that the M.tuberculosis PptT model and critical CoA binding pocket initiate the inhibitor design of PptT towards tuberculosis treatment.
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