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Figure S5

March 2012

License
CC BY 4.0

Authors:

Dr Reetu Sharma

Indian Institute of Chemical Technology

Roopa Kothapalli

Uppsala University

Antonius M Vandongen

Duke University

Binding poses of known inhibitors/ligands. The known inhibitors or ligands are shown as thick ball and stick. Atoms are colored as: H: white, C: green, N: blue, O: red and S: yellow. The interacting MtbADC residues are drawn as thin wireframe with the same color scheme and are labeled. Hydrogen bond interactions are shown as dotted yellow lines, along with the distance between donor and acceptor atoms. (TIFF)

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Chemoinformatic Identification of Novel Inhibitors against Mycobacterium tuberculosis L-aspartate α-decarboxylase

Article

March 2012

Dr Reetu Sharma · Roopa Kothapalli · Antonius M Vandongen · Kunchithapadam Swaminathan

Project

Data Science and AI approaches to advance the understanding of lifestyle related diseases

Dr Reetu Sharma

1. Employed data science-driven approaches to identify the patterns associated with the structural and functional aspect of certain marketed medicines and diseases. 2. Decision rules to predict dru g-induced adverse effect in advance are suggested comparing machine learning algorithms. 3. Improvised k-means, an unsupervised machine learning approach and employed it to cluster the marketed anti-hypertensives to identify the biomarkers (pattern) within a group. 4. Implemented novel network medicine based approaches reveal disease-disease relationships. Recently, she has identified how hypertension is related to selective diseases, highlighting the interplay among market available anti-hypertensives target coding genes. 5. Our work suggests that hypertension is deeply connected to certain diseases through common genes. 6. Deciphered how Covid-19 led to high mortality of comorbid patients from clinical trial datasets through a network of common genes. ... [more]

Project

Elucidating thermal stability of industrially significant proteins

Dr Reetu Sharma

Goals: 1) Deciphering the Dynamics of Non-Covalent Interactions Affecting Thermal Stability of a Protein 2)Elucidating the Preference of Protein Oligomerization for Thermal Stability

Project

Ion channel selectivity filter is also the "gate"

Antonius M Vandongen

Data

Full-text available

S35 Fig

June 2018

Ligands ZINC12671898 and ZINC17353914 that prefer GNP-bound Rab11a. The figure shows the interactions of the ligands (labeled) with the residues of the Rab11 structures in which they scored the best (see Table 3). The ligand and Rab11 side chains are shown in ball-and-stick representation. Black circles denote carbon atoms, red circles denote oxygen atoms and blue circles denote nitrogen atoms. ... [Show full abstract] The ligand bonds are colored in purple. Residues in Rab11 interacting with the ligand are labeled. Hydrogen bonds are shown as green dotted lines. The Rab11 residues making nonbonded contacts with the ligand are shown as spoked arcs. Figures are generated using LigPlot+ [66][67]. (TIF)

Data

Full-text available

S31 Fig

June 2018

Ligands ZINC00084617 and ZINC13208966 that prefer GDP-bound Rab11a. The figure shows the interactions of the ligands (labeled) with the residues of PDB entry 1OIV_A. The ligand and Rab11 side chains are shown in ball-and-stick representation. Black circles denote carbon atoms, red circles denote oxygen atoms, and blue circles denote nitrogen atoms. The ligand bonds are colored in purple. Residues ... [Show full abstract] in Rab11 interacting with the ligand are labeled. Hydrogen bonds are shown as green dotted lines. The Rab11 residues making nonbonded contacts with the ligand are shown as spoked arcs. Figures are generated using LigPlot+ [66][67]. (TIF)

Data

Full-text available

Figure S2

March 2012

Fumarate binding in ADC. (a) The superimposed view of the TthADC:fumarate crystal structure (red) and MtbADC:fumarate docking model (blue) is shown. The processed model for MtbADC was generated from the crystal structure of unprocessed protein and docking of fumarate was achieved using the Glide Extra Precision mode. The interacting conserved residues are labelled for MtbADC and the interactions ... [Show full abstract] between the protein and fumarate are shown as dashed lines in the corresponding colors. (b) Surface diagram around the substrate binding cavity in the same orientation of panel A. The interacting protein residues are also shown in faint trace. (TIFF)

Data

Full-text available

Table S2

March 2012

The ADMET properties of the 28 ligands. The ligands that interact with Pyr25 are in bold. The entries of Table 2 are underlined. The definitions of the properties are as in Table 2. (DOCX)

Data

Full-text available

Table S1

March 2012

The 28 ligand hits from the Maybridge, NCI and FDA databases which interact with at least one of the conserved functional residues of MtbADC residues involved in substrate binding and their glide score (kcal/mol). The ligands are ranked according to their glide scores in their respective databases. The ligands that interact with Pyr25 are in bold. The entries of Table 1 are underlined. (DOCX)

Data

Full-text available

Table S3

March 2012

Interactions of selected known inhibitors/ligands with MtbADC as verified by Glide XP. (DOCX)

Data

Full-text available

Figure S4

March 2012

Ligands docked to monomeric MtbADC. The structures of the top three hits, obtained by docking the Maybridge, NCI and FDA databases with the processed monomeric MtbADC structure. These molecules are big and cannot be genuine inhibitors as the actual active site is formed in the cleft of a dimer with relatively smaller volume and only molecules of small size can bind in the pocket. (TIFF)