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in silico drug target identification

However, these transmembrane proteins are involved in lipid polysaccharide synthesis (kdtA), ubiquinone-terpenoid-quinone biosynthesis (ubiA), bacterial chemotaxis (fliN, cheA, mcp)as well as part of flagellar assembly (fliN) and two component system (mcp, cheA). KIF11, CCNB1, PTTG1, PRC1, and KIF23 belong to ‘Mitotic Roles of Polo-Like Kinase’ pathway, whose inhibition can reduce the NE of luminal B of 2% (PCI). We believe that in silico methods based on PCI could offer valuable approaches to identifying more tailored and effective treatments in particular in heterogeneous cancer diseases. Yes University School of Information, Communication & Technology, Guru Gobind Singh Indraprastha University, New Delhi, India, Affiliation Privacy Furthermore, considering FDA-approved drugs, our study confirms that tamoxifen is the drug with the best action on pathway network since it is able to inhibit ‘Human Embryonic Stem Cell Pluripotency’. CC made substantial contributions to conception and design of the work, in data analysis and drafting the manuscript. we quantified the percentage activity of the subtype pathway network that is inhibited, defined as PCI [6]. In contrast, gene thiL found to be important in conversion of thiamine monophosphate to thiamine pyrophosphate which is essential for pathogen survival [52].

140 0 obj endobj Bernards R. A missing link in genotype-directed cancer therapy. Surface view of cobA is showing a deep binding pocket while thiL represented Gln23, Thr24, Asp25, Asp26, Asp39, Asp68, Arg140, Asp207, Thr209 and Asp210 as key residues in their binding pocket (Fig 4). The metabolic network reconstruction of L. borgpetersenii serovar Hardjo-bovis str.

The considered FDA approved drugs for BC do not seem to act on ‘EIF2 Signaling’ and ‘Mismatch Repair in Eukaryotes’, pathways that, according to our findings, could be interesting potential drug targets. The efficiency of the pathway network in HER2 was 0.3492. Moreover, we focused our study on BC, but we suggest the application of our approach also to other complex and heterogeneous diseases, in which pathway cross-talk is likely to cooperate important functions. PubMed  Additional file 1 shows nNE values in the luminal A network after inhibition of individual and pairs pathway(s).

Nascimento et al., 2004 and Ren et al., 2003 reported the genomic size of L. interrogans i.e. Complete amino acid sequence (*.faa) of sixteen serovars were successfully retrieved from NCBI-FTP server and subjected to TiD software. For each BC subtype, we selected those cross-talking pathways from the network, that, if inhibited, caused nNE < NE, thus building a potential DTPN. Introduction. Liaw A, Wiener M. Classification and regression by randomforest. Methodology, Cell. The inhibition of this pathway can reduce the NE of luminal A of 1% (PCI). Trends Pharmacol Sci. 2 and 5 If nNE < NE the inhibited pathway could be a potential drug target.

The authors declare that they have no competing interests. The ‘Triacylglycerol Degradation Pathway’, if inhibited, reduces the NE of 0.4% and it is target of capecitabine. PubMed Central  Conceptualization, <>/Font<>/ProcSet[/PDF/Text]>>/Type/Page>> Select this link to jump to content. Then, for each BC subtype, we generated a network-based model of BC subtype pathways (5. 2009;5:290. https://doi.org/10.1038/msb.2009.47.

In addition, genome scale metabolic network reconstruction and choke point analysis revealed cobA (porphyrin and chlorophyll metabolism) and thiL (thiamine metabolism) as chokepoints in their respective metabolic pathways. In the present study, L. weilii serovar Topaz str. Select this link to jump to navigation, In navigation section. Drug target pathway network. The cobA with an EC: participated in cobalamin biosynthesis pathway. Cava, C., Bertoli, G. & Castiglioni, I. It is confirmed that the inhibition of couples of pathways of the pathway network reduces the efficiency more than individual pathway. Hence, these complex set of genes involved in endoflagellum and its basal rotor system formation play critical role in the motility and virulence to cause Leptospirosis. The inhibition of couples of pathways is confirmed to reduce the efficiency more than individual pathway. These reconstructed models were used for choke point analysis.

2097 genes which are non-homologous to human genome. In addition, the details of cell-specific information or clinical data of samples are not always available [32,33,34]. Carcinogenesis. The ‘Epithelial Adherens Junction Signaling Pathway’, if inhibited, reduces the NE of 2.3% and it is target of docetaxel. https://doi.org/10.3322/caac.21254. uuid:f70d41bc-1dd1-11b2-0a00-1e0000000000 https://doi.org/10.1371/journal.pone.0221446.g003, https://doi.org/10.1371/journal.pone.0221446.t002. The inhibition of 416/903 combinations of pathways reduces the NE of the pathway network with values that ranges from 0.2148 to 0.3445 (Fig. (KEGG) pathways database, revealed 87 enzymes of A. hydrophila that may H��WYo�~ׯIs��i��C�F�n��ׁ��b��z���B/y�_O�&���- 6Ls����:>��H��T)�6��(&��S�M����o�?�n�.�>��ӟA'>�qt�� &r���Q����i�g�����?�����?�� -5D�BX�=M�`S�4WE�{�a�66����h�_�v������ ��J��,_フE��A2�H��P4�#7&���P���Y\��! It routinely reorganizes the drug discovery method by incorporating vast data encrypted in our genome.

We have performed subtractive genomic and comparative genomics analyses with network analysis of 16 pathogenic strains of Leptospira and identified 8 common drug targets that can be potential targets for drug designing and vaccine development.

Multiple sequence alignment was performed for cobA and thiL gene within the pathogenic Leptospira strain (Table 1). �+ݖ$�̉�@n�b��H�&�E%CE���D˪�u�U�q�5�PH(��#(��Cg �;ԇK����-� S;�"���j��}�5L��Δ�M1Íϒa���d�y�Ǟ���\郁��QM�K�ڗ�������!L`=}��O/{�v��c]�8��í��g��wɕ�����ĢN A�6�X�p����`�h5�@`^�F�"�ʤ4�D� ��֡�(f����@߭2"�|�S��(�N��9�:�i>� �֛���6��Z application/pdf Fax: +86 10 8446 7947

These can be https://doi.org/10.1186/bcr3443.

In this study, a comprehensive in silico target identification pipeline was performed on members of the family Legionellaceae to identify the best targets. Of these, 15 Among these common hub proteins, 8 are novel in at least 10 strains, 5 are virulent while 2 are novel as well as common drug targets (Figs 6 and 7). All 16 hubs are similarly connecting with one another with the degree of 13 to 15. Although, the significance level of these putative targets need to be validated through experimental approach to ensure them as real one and can be the best against pathogenic strains of Leptospira. Oncogene. endobj from the pathways that are common to both human and the bacteria. In silico and in vitro target identification research to cure leptospirosis, till date, have been more focused towards most pathogenic L. interrogans serovars named Lai and Copenhagani [20,46–47].

PLOS ONE promises fair, rigorous peer review, Shows the network efficiency after inhibition of individual and combined pathway(s) in basal BC. E2F3 belongs to ‘Role of BRCA1 in DNA Damage Response’ pathway. Aeromonas hydrophila infections are known to cause gastroenteritis and wound In particular, tamoxifen acting on 4 pathways reduces the NE of 8.59%, thus it is very effective.

Among the drug target pathways found in our DTPN, we found 5/34 pathways that were ranked as part of the top 10 pathways, playing the major role in the reduction of NE. A gene-expression signature as a predictor of survival in breast cancer. Yes Extended network added ribB, ribC, cysl, cysH, cysD, cobA and cysG genes which are responsible for riboflavin biosynthesis, microbial metabolism in diverse environment, sulfur metabolism porhyrin and cholorophyll metabolism (Tables 4 and 5). 2097 genes which are non-homologous to human genome. The ‘Regulation of the Salvage Pathways of Pyrimidine Deoxyribonucleotides’, if inhibited, reduces the NE of 0.2% and it is target of fluoracil, and methotrexate. Cite this article.

We obtained 6 drugs (fluoracil, capecitabine, fulvestrant, methotrexate, raloxifene and tamoxifen) that interact with the DTPN in basal BC (Table 4).

Yes In this context, several studies examined the effects of drugs considering protein network approaches [2]. Writing – review & editing, Affiliation DTPN of Luminal A was built considering only the 34 pathways of the network that if inhibited, reduced the NE (nNE < NE).

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