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5W2S

Crystal Structure of Mycobacterium Tuberculosis KasA in complex with KMG

Summary for 5W2S
Entry DOI10.2210/pdb5w2s/pdb
Related2WGD 2WGE 2WGF 2WGG 4C6U 4C6V 4C6W 4C6X 4C6Z 4C70 4C71 4C72 4C73 5LD8 5W2O 5W2P 5W2Q
Descriptor3-oxoacyl-[acyl-carrier-protein] synthase 1, SODIUM ION, ISOPROPYL ALCOHOL, ... (6 entities in total)
Functional Keywordsbeta ketoacyl synthase i, lipid synthesis, fatty acid biosynthesis, transferase
Biological sourceMycobacterium tuberculosis (strain ATCC 35801 / TMC 107 / Erdman)
Total number of polymer chains1
Total formula weight46323.25
Authors
Capodagli, G.C.,Neiditch, M.B. (deposition date: 2017-06-06, release date: 2018-12-05, Last modification date: 2023-10-04)
Primary citationKumar, P.,Capodagli, G.C.,Awasthi, D.,Shrestha, R.,Maharaja, K.,Sukheja, P.,Li, S.G.,Inoyama, D.,Zimmerman, M.,Ho Liang, H.P.,Sarathy, J.,Mina, M.,Rasic, G.,Russo, R.,Perryman, A.L.,Richmann, T.,Gupta, A.,Singleton, E.,Verma, S.,Husain, S.,Soteropoulos, P.,Wang, Z.,Morris, R.,Porter, G.,Agnihotri, G.,Salgame, P.,Ekins, S.,Rhee, K.Y.,Connell, N.,Dartois, V.,Neiditch, M.B.,Freundlich, J.S.,Alland, D.
Synergistic Lethality of a Binary Inhibitor of Mycobacterium tuberculosis KasA.
MBio, 9:-, 2018
Cited by
PubMed Abstract: We report GSK3011724A (DG167) as a binary inhibitor of β-ketoacyl-ACP synthase (KasA) in Genetic and biochemical studies established KasA as the primary target. The X-ray crystal structure of the KasA-DG167 complex refined to 2.0-Å resolution revealed two interacting DG167 molecules occupying nonidentical sites in the substrate-binding channel of KasA. The binding affinities of KasA to DG167 and its analog, 5g, which binds only once in the substrate-binding channel, were determined, along with the KasA-5g X-ray crystal structure. DG167 strongly augmented the activity of isoniazid (INH), leading to synergistic lethality, and also synergized in an acute mouse model of infection. Synergistic lethality correlated with a unique transcriptional signature, including upregulation of oxidoreductases and downregulation of molecular chaperones. The lead structure-activity relationships (SAR), pharmacokinetic profile, and detailed interactions with the KasA protein that we describe may be applied to evolve a next-generation therapeutic strategy for tuberculosis (TB). Cell wall biosynthesis inhibitors have proven highly effective for treating tuberculosis (TB). We discovered and validated members of the indazole sulfonamide class of small molecules as inhibitors of KasA-a key component for biosynthesis of the mycolic acid layer of the bacterium's cell wall and the same pathway as that inhibited by the first-line antitubercular drug isoniazid (INH). One lead compound, DG167, demonstrated synergistic lethality in combination with INH and a transcriptional pattern consistent with bactericidality and loss of persisters. Our results also detail a novel dual-binding mechanism for this compound as well as substantial structure-activity relationships (SAR) that may help in lead optimization activities. Together, these results suggest that KasA inhibition, specifically, that shown by the DG167 series, may be developed into a potent therapy that can synergize with existing antituberculars.
PubMed: 30563908
DOI: 10.1128/mBio.02101-17
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (2.399 Å)
Structure validation

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