Computational protocol: Mechanism of thioamide drug action against tuberculosis and leprosy

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Protocol publication

[…] Data were collected at 121 K using cryoprotection solution containing reservoir solution with an additional 30% MPD. Crystals of M. tuberculosis InhA:ETH-NAD and M. leprae InhA:PTH-NAD diffracted x rays to 2.2 and 1.8 Å using the beamline 23-ID at the Advanced Photon Source (Argonne National Laboratory, Argonne, IL). Diffraction data were collected from a single crystal with 1° oscillation widths for a range of 120°. Crystals of M. tuberculosis InhA:PTH-NAD were diffracted to 2.5 Å using a Raxis image plate detector coupled to a Rigaku x-ray generator using a copper rotating anode (CuKα, λ = 1.54 Å). The data were integrated and reduced using HKL-2000 (HKL Research, Inc.; Table S1) (). [...] Crystals produced from InhA in complex with ETH-NAD were isomorphous to those of the native enzyme. Initial phases were obtained by molecular replacement using the apo-InhA structure (1ENY) and refined with CNS software (Table S1) (). Fo – Fc and 2Fo – Fc electron density maps were calculated, and an additional density resembling the inhibitor was found. The ligand was fit into the additional density, and the whole model was rebuilt using XtalView (). During the final cycles of the refinement, water molecules were added into peaks above 3 σ of the Fo − Fc electron density maps that were within hydrogen-bonding distances from the appropriate protein atoms. The final refinement statistics are listed in Table S1. […]

Pipeline specifications

Software tools SHELX, HKL-2000, CNS
Application Protein structure analysis
Organisms Mycobacterium avium, Mycobacterium tuberculosis, Mycobacterium leprae
Diseases Leprosy, Tuberculosis
Chemicals Ethionamide, NAD, Prothionamide, Thioamides