Binding properties of the anti-TB drugs bedaquiline and TBAJ-876 to a mycobacterial F-ATP synthase
Tài liệu tham khảo
Abraham, 2015, GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers, SoftwareX, 1–2, 19, 10.1016/j.softx.2015.06.001
Andries, 2005, A diarylquinoline drug active on the ATP synthase of Mycobacterium tuberculosis, Science, 307, 223, 10.1126/science.1106753
Andries, 2014, Acquired resistance of Mycobacterium tuberculosis to bedaquiline, PLoS One, 9, 10.1371/journal.pone.0102135
Bennett, 1976, Efficient estimation of free energy differences from Monte Carlo data, J. Comput. Phys., 22, 245, 10.1016/0021-9991(76)90078-4
Bussi, 2007, Canonical sampling through velocity rescaling, J. Chem. Phys., 126
Cook, 2014, Energetics of respiration and oxidative phosphorylation in mycobacteria, Microbiol. Spectr., 2, 10.1128/microbiolspec.MGM2-0015-2013
Demmer, 2022, Structure of ATP synthase from ESKAPE pathogen Acinetobacter baumannii, Sci. Adv., 8, 10.1126/sciadv.abl5966
FDA, 2012. SIRTUROTM (bedaquiline). [WWW Document]. URL https://www.accessdata.fda.gov/drugsatfda_docs/label/2013/204384s002lbl.pdf.
Fillingame, 2014, Half channels mediating H(+) transport and the mechanism of gating in the Fo sector of Escherichia coli F1Fo ATP synthase, Biochim. Biophys. Acta, 1837, 1063, 10.1016/j.bbabio.2014.03.005
Gohlke, 2012, Resolving the negative potential side (n-side) water-accessible proton pathway of F-type ATP synthase by molecular dynamics simulations, J. Biol. Chem., 287, 36536, 10.1074/jbc.M112.398396
Guo, 2021, Structure of mycobacterial ATP synthase bound to the tuberculosis drug bedaquiline, Nature, 589, 143, 10.1038/s41586-020-3004-3
Haagsma, 2011, Probing the interaction of the diarylquinoline TMC207 with its target mycobacterial ATP synthase, PLoS One, 6, 10.1371/journal.pone.0023575
Hards, 2018, Ionophoric effects of the antitubercular drug bedaquiline, Proc. Natl. Acad. Sci., 115, 7326, 10.1073/pnas.1803723115
Hards, 2015, Bactericidal mode of action of bedaquiline, J. Antimicrob. Chemother., 111, 10580
Harikishore, 2022, Mutational analysis of mycobacterial F-ATP synthase subunit δ leads to a potent δ enzyme inhibitor, ACS Chem. Biol., 17, 529, 10.1021/acschembio.1c00766
Hess, 1997, LINCS: a linear constraint solver for molecular simulations, J. Comput. Chem., 18, 1463, 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
Huang, 2016, CHARMM36m: an improved force field for folded and intrinsically disordered proteins, Nat. Methods, 14, 71, 10.1038/nmeth.4067
Humphrey, 1996, VMD: visual molecular dynamics, J. Mol. Graph., 14, 33, 10.1016/0263-7855(96)00018-5
Jo, 2008, CHARMM-GUI: a web-based graphical user interface for CHARMM, J. Comput. Chem., 29, 1859, 10.1002/jcc.20945
Jorgensen, 1983, Comparison of simple potential functions for simulating liquid water, J. Chem. Phys., 79, 926, 10.1063/1.445869
Kamariah, 2019, Structure and subunit arrangement of Mycobacterial F1FO ATP synthase and novel features of the unique mycobacterial subunit δ, J. Struct. Biol., 207, 199, 10.1016/j.jsb.2019.05.008
Klauda, 2010, Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types, J. Phys. Chem. B, 114, 7830, 10.1021/jp101759q
Koul, 2008, Diarylquinolines are bactericidal for dormant mycobacteria as a result of disturbed ATP homeostasis, J. Biol. Chem., 283, 25273, 10.1074/jbc.M803899200
Krah, 2020, Characterizing the hydration properties of proton binding sites in the ATP synthase c-rings of Bacillus species, J. Phys. Chem. B, 124, 7176, 10.1021/acs.jpcb.0c03896
Krah, 2010, On the structure of the proton-binding site in the fo rotor of chloroplast ATP synthases, J. Mol. Biol., 395, 20, 10.1016/j.jmb.2009.10.059
Kubo, 2020, Molecular dynamics simulation of proton-transfer coupled rotations in ATP synthase FO motor, Sci. Rep., 10, 8225, 10.1038/s41598-020-65004-1
Laskowski, 2011, LigPlot+: multiple ligand–protein interaction diagrams for drug discovery, J. Chem. Inf. Model., 51, 2778, 10.1021/ci200227u
Luo, 2020, Bedaquiline inhibits the yeast and human mitochondrial ATP synthases, Commun. Biol., 3, 452, 10.1038/s42003-020-01173-z
McNeil, 2020, Transcriptional inhibition of the F1F0 -type ATP synthase has bactericidal consequences on the viability of mycobacteria, Antimicrob. Agents Chemother., 64, e00492, 10.1128/AAC.00492-20
Meier, 2001, The central plug in the reconstituted undecameric c cylinder of a bacterial ATP synthase consists of phospholipids, FEBS Lett., 505, 353, 10.1016/S0014-5793(01)02837-X
Mitome, 2010, Essential arginine residue of the Fo - a subunit in FoF1 -ATP synthase has a role to prevent the proton shortcut without c -ring rotation in the Fo proton channel, Biochem. J., 430, 171, 10.1042/BJ20100621
Montgomery, 2021, Structure of the ATP synthase from Mycobacterium smegmatis provides targets for treating tuberculosis, Proc. Natl. Acad. Sci., 118, 10.1073/pnas.2111899118
Paramo, 2014, Efficient characterization of protein cavities within molecular simulation trajectories: trj_cavity, J. Chem. Theor. Comput., 10, 2151, 10.1021/ct401098b
Parrinello, 1981, Polymorphic transitions in single crystals: a new molecular dynamics method, J. Appl. Phys., 52, 7182, 10.1063/1.328693
Pogoryelov, 2010, Microscopic rotary mechanism of ion translocation in the Fo complex of ATP synthases, Nat. Chem. Biol., 6, 891, 10.1038/nchembio.457
Preiss, 2015, Structure of the mycobacterial ATP synthase Fo rotor ring in complex with the anti-TB drug bedaquiline, Sci. Adv., 1, 10.1126/sciadv.1500106
Rao, 2008, The protonmotive force is required for maintaining ATP homeostasis and viability of hypoxic, nonreplicating Mycobacterium tuberculosis, Proc. Natl. Acad. Sci. U. S. A., 105, 11945, 10.1073/pnas.0711697105
Sanguinetti, 2006, hERG potassium channels and cardiac arrhythmia, Nature, 440, 463, 10.1038/nature04710
Sarathy, 2020, TBAJ-876, a 3,5-dialkoxypyridine analogue of bedaquiline, is active against Mycobacterium abscessus, Antimicrob. Agents Chemother., 64, 10.1128/AAC.02404-19
Sarathy, 2020, TBAJ-876 displays bedaquiline-like mycobactericidal potency without retaining the parental drug's uncoupler activity, Antimicrob. Agents Chemother., 64, 10.1128/AAC.01540-19
Sarathy, 2019, TBAJ-876 retains bedaquiline’s activity against subunits c and ε of Mycobacterium tuberculosis F-ATP synthase, Antimicrob. Agents Chemother., 63, 10.1128/AAC.01191-19
Saw, 2019, Disrupting coupling within mycobacterial F-ATP synthases subunit ε causes dysregulated energy production and cell wall biosynthesis, Sci. Rep., 9, 10.1038/s41598-019-53107-3
Sebald, 1980, N,N’-dicyclohexylcarbodiimide binds specifically to a single glutamyl residue of the proteolipid subunit of the mitochondrial adenosinetriphosphatases from Neurospora crassa and Saccharomyces cerevisiae, Proc. Natl. Acad. Sci. U.S.A., 77, 785, 10.1073/pnas.77.2.785
Sutherland, 2019, 3,5-Dialkoxypyridine analogues of bedaquiline are potent antituberculosis agents with minimal inhibition of the hERG channel, Bioorg. Med. Chem., 27, 1292, 10.1016/j.bmc.2019.02.026
Sutherland, 2018, Structure-activity relationships for analogs of the tuberculosis drug bedaquiline with the naphthalene unit replaced by bicyclic heterocycles, Bioorg. Med. Chem., 26, 1797, 10.1016/j.bmc.2018.02.026
Tantry, 2017, Discovery of imidazo[1,2-a]pyridine ethers and squaramides as selective and potent inhibitors of mycobacterial adenosine triphosphate (ATP) synthesis, J. Med. Chem., 60, 1379, 10.1021/acs.jmedchem.6b01358
Vanommeslaeghe, 2010, CHARMM general force field: a force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields, J. Comput. Chem., 31, 671, 10.1002/jcc.21367
Vestergaard, 2022, Targeting the ATP synthase in bacterial and fungal pathogens: beyond Mycobacterium tuberculosis, J. Glob. Antimicrob. Resist., 29, 29, 10.1016/j.jgar.2022.01.026
Wang, 2006, Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials, Biophys. J., 91, 2798, 10.1529/biophysj.106.084301
Wu, 2014, CHARMM-GUI Membrane Builder toward realistic biological membrane simulations, J. Comput. Chem., 35, 1997, 10.1002/jcc.23702
Zhao, 2003, Fast calculation of van der Waals volume as a sum of atomic and bond contributions and its application to drug compounds, J. Org. Chem., 68, 7368, 10.1021/jo034808o
