title: Increasing the structural coverage of tuberculosis drug targets.
abstract: High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus "homolog-rescue" strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. Of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structures would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Cα RMSD <1 Å, >85% side chain identity, and ≥80% PSAPF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases.
authors.affiliation: Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States.
authors.forename: Loren
authors.initials: L
authors.lastname: Baugh
authors.affiliation: Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Phan
authors.affiliation: Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States.
authors.forename: Darren W
authors.initials: DW
authors.lastname: Begley
authors.affiliation: Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States.
authors.forename: Matthew C
authors.initials: MC
authors.lastname: Clifton
authors.affiliation: Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States.
authors.forename: Brianna
authors.initials: B
authors.lastname: Armour
authors.affiliation: Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States.
authors.forename: David M
authors.initials: DM
authors.lastname: Dranow
authors.affiliation: Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States.
authors.forename: Brandy M
authors.initials: BM
authors.lastname: Taylor
authors.affiliation: Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States.
authors.forename: Marvin M
authors.initials: MM
authors.lastname: Muruthi
authors.affiliation: Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States.
authors.forename: Jan
authors.initials: J
authors.lastname: Abendroth
authors.affiliation: Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States.
authors.forename: James W
authors.initials: JW
authors.lastname: Fairman
authors.affiliation: Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States.
authors.forename: David
authors.initials: D
authors.lastname: Fox
authors.affiliation: Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States.
authors.forename: Shellie H
authors.initials: SH
authors.lastname: Dieterich
authors.affiliation: Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States.
authors.forename: Bart L
authors.initials: BL
authors.lastname: Staker
authors.affiliation: Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States; EMD Serono Research & Development Institute, Inc., 45A Middlesex Turnpike, Billerica, MA 01821, United States.
authors.forename: Anna S
authors.initials: AS
authors.lastname: Gardberg
authors.affiliation: Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States.
authors.forename: Ryan
authors.initials: R
authors.lastname: Choi
authors.affiliation: Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States.
authors.forename: Stephen N
authors.initials: SN
authors.lastname: Hewitt
authors.affiliation: Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States.
authors.forename: Alberto J
authors.initials: AJ
authors.lastname: Napuli
authors.affiliation: Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States.
authors.forename: Janette
authors.initials: J
authors.lastname: Myers
authors.affiliation: Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States.
authors.forename: Lynn K
authors.initials: LK
authors.lastname: Barrett
authors.affiliation: Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States.
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States.
authors.forename: Micah
authors.initials: M
authors.lastname: Ferrell
authors.affiliation: Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Mundt
authors.affiliation: Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States.
authors.forename: Katie
authors.initials: K
authors.lastname: Thompkins
authors.affiliation: Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States.
authors.forename: Ngoc
authors.initials: N
authors.lastname: Tran
authors.affiliation: Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States.
authors.forename: Sally
authors.initials: S
authors.lastname: Lyons-Abbott
authors.affiliation: Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States.
authors.forename: Ariel
authors.initials: A
authors.lastname: Abramov
authors.affiliation: Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States.
authors.forename: Aarthi
authors.initials: A
authors.lastname: Sekar
authors.affiliation: Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States.
authors.forename: Dmitri
authors.initials: D
authors.lastname: Serbzhinskiy
authors.affiliation: Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States.
authors.forename: Don
authors.initials: D
authors.lastname: Lorimer
authors.affiliation: Seattle Structural Genomics Center for Infectious Disease, United States; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, United States.
authors.forename: Garry W
authors.initials: GW
authors.lastname: Buchko
authors.affiliation: Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States.
authors.forename: Robin
authors.initials: R
authors.lastname: Stacy
authors.affiliation: Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States; Institute for Protein Design, University of Washington, Box 357350, Seattle, WA 98195, United States.
authors.forename: Lance J
authors.initials: LJ
authors.lastname: Stewart
authors.affiliation: Seattle Structural Genomics Center for Infectious Disease, United States; Beryllium, 7869 NE Day Road West, Bainbridge Island, WA 98110, United States.
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Edwards
authors.affiliation: Seattle Structural Genomics Center for Infectious Disease, United States; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, 750 Republican Street, E-701, Box 358061, Seattle, WA 98109, United States; Department of Global Health, University of Washington, Box 359931, Seattle, WA, 98195, United States; Department of Microbiology, University of Washington, Box 357735, Seattle, WA 98195, United States.
authors.forename: Wesley C
authors.initials: WC
authors.lastname: Van Voorhis
authors.affiliation: Seattle Structural Genomics Center for Infectious Disease, United States; Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States; Department of Global Health, University of Washington, Box 359931, Seattle, WA, 98195, United States; Department of Biomedical Informatics and Medical Education, University of Washington, Box 358047, Seattle, WA 98195, United States. Electronic address: peter.myler@seattlebiomed.org.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Myler
mesh_terms: D000995:Antitubercular Agents / Q000737:chemistry / Q000494:pharmacology*; D001426:Bacterial Proteins / Q000737:chemistry; D019295:Computational Biology / Q000379:methods; D018360:Crystallography, X-Ray / Q000379:methods; D030562:Databases, Protein; D015195:Drug Design; D004789:Enzyme Activation; D023281:Genomics / Q000379:methods; D006801:Humans; D008958:Models, Molecular; D058990:Molecular Targeted Therapy / Q000379:methods*; D009161:Mycobacterium / Q000145:classification / Q000201:enzymology / Q000235:genetics; D009169:Mycobacterium tuberculosis / Q000187:drug effects* / Q000201:enzymology / Q000235:genetics; D021281:Quantitative Structure-Activity Relationship; D013045:Species Specificity
chemical_list: D000995:Antitubercular Agents; D001426:Bacterial Proteins
keywords: Drug discovery; Enzyme active site; Homolog-rescue; Structural genomics