The ATPases: A new family for a family-based drug design approach

Expert Opinion on Therapeutic Targets

Volumn 7, Issue 3, 2003, Pages 453-461

  Chène, Patrick ^a  

^a NOVARTIS PHARMA AG   (Switzerland)

Author keywords

AAA ATPases; ABC transporters; Heat shock proteins (hsps); Helicases; Kinesins; P ATPases; V ATPases

Indexed keywords

ABC TRANSPORTER; ADENOSINE TRIPHOSPHATASE; ADENOSINE TRIPHOSPHATASE (POTASSIUM SODIUM); ADENOSINE TRIPHOSPHATASE INHIBITOR; CIPROFLOXACIN; DIGOXIN; DNA TOPOISOMERASE (ATP HYDROLYSING); GYRASE INHIBITOR; HEAT SHOCK PROTEIN; HEAT SHOCK PROTEIN 90; HELICASE; HYDROGEN POTASSIUM ADENOSINE TRIPHOSPHATASE; IMATINIB; KINESIN; NEW DRUG; OMEPRAZOLE; PROTEIN INHIBITOR; PROTEIN KINASE; PROTEIN KINASE INHIBITOR; PROTEOME;

APOPTOSIS; COMPETITIVE INHIBITION; DRUG DESIGN; DRUG TARGETING; ENZYME ACTIVITY; ENZYME INHIBITION; GENE LIBRARY; HUMAN; NONHUMAN; NUCLEOTIDE BINDING SITE; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN TARGETING; REVIEW; STRUCTURE ACTIVITY RELATION;

EID: 0037702997     PISSN: 14728222     EISSN: None     Source Type: Journal    
DOI: 10.1517/14728222.7.3.453     Document Type: Review

References (120)

1. HOPKINS AL, GROOM CR: The druggable genome. Nat. Rev. Drug Discov. (2002) 1:727-730.
2. SCAPIN G: Structural biology in drug design: selective protein kinase inhibitors. Drug Discov. Today (2002) 7:601-611.
3. COHEN P: Protein kinases - the major drug targets of the twenty-first century? Nat. Rev. Drug Discov. (2002) 1:309-315.
4. CAPDEVILLE R, BUCHDUNGER E, ZIMMERMANN J, MATTER A: Glivec (STI-571, imatinib), a rationally developed targeted anticancer drug. Nat. Rev. Drug Discov. (2002) 1:493-502.
5. DEAN M, RZHETSKY A, ALLIKMETS R: The human ATP-binding cassette (ABC) transporter superfamily. Genome Res. (2001) 11:1156-1166.
6. SAIER MH: A functional-phylogenetic classification system for transmembrane solute transporters. Microbiol. Mol. Biol. Rev. (2000) 64:354-411.
7. KERR ID: Structure and association of ATP-binding cassette transporter nucleotide-binding domains. Biochim. Biophys. Acta. (2002) 1561:47-64
8. SCHNEIDER E, HUNKE S: ATP-binding cassette (ABC) transport systems: functional and structural aspects of the ATP-hydrolyzing subunits/domains. FEMS Microbiol. Rev. (1998) 22:1-20.
9. JONES PM, GEORGE AM: Mechanism of ABC transporters: a molecular dynamics simulation of a well characterized nucleotide-binding subunit. Proc. Natl. Acad. Sci. USA (2002) 99:12639-12644.
10. SHAROM FJ: The P-glycoprotein efflux pump: how does it transport drugs? J. Membr. Biol. (1997) 160:161-175.
11. SENIOR AE, AL-SHAWI MK, URBATSCH IL: The catalytic cycle of P-glycoprotein. FEBS Lett. (1995) 377:285-289.
12. BORST P, OUDE ELFERINK R: Mammalian ABC transporters in health and disease. Annu. Rev. Biochem. (2002) 71:537-592.
13. EFFERTH T: The human ATP-binding cassette transporter genes: from the bench to the bedside. Curr. Mol. Med. (2001) 1:45-65.
14. LEHNE G: P-glycoprotein as a drug target in the treatment of multidrug resistant cancer. Curr. Drug Targets (2000) 1:85-99.
15. LOO TP, CLARKE DM: Rapid purification of human P-glycoprotein mutants expressed transiently in HEK 293 cells by nickel-chelate chromatography and characterization of their drug-stimulated ATPase activities. J. Biol. Chem. (1995) 270:21449-21452.
16. AZZARIA M, SCHURR E, GROS P: Discrete mutations introduced in the predicted nucleotide-binding sites of the mdr1 gene abolish its ability to confer multidrug resistance. Mol. Cell. Biol. (1989) 9:5289-5297.
17. AVENDANO C, MENENDEZ JC: Inhibitors of multidrug resistance to antitumor agents (MDR). Curr. Med. Chem. (2002) 9:159-193.
18. DASSA E, BOUIGE P: The ABC of ABCS: a phylogenetic and functional classification of ABC systems in living organisms. Res. Microbiol. (2001) 152:211-229.
19. AXELSEN KB, PALMGREN MG: Evolution of substrate specificities in the P-type ATPase superfamily. J. Mol. Evol. (1998) 46:84-101.
20. DUNBAR LA, CAPLAN MJ: The cell biology of ion pumps: sorting and regulation. Eur. J. Cell Biol. (2000) 79:557-563.
21. MOLLER JV, JUUL B, MAIRE M: Structural organization, ion transport, and energy transduction of P-type ATPases. Biochim. Biophys. Acta (1996) 1286:1-51.
22. LEE AG: A calcium pump made visible. Curr. Opin. Struct. Biol. (2002) 12:547-554.
23. TOYOSHIMA C, NOMURA H: Structural changes in the calcium pump accompanying the dissociation of calcium. Nature (2002) 418:605-611.
24. SCARBOROUGH GA: Structure and function of the P-type ATPases. Curr. Opin. Cell Biol. (1999) 11:517-522.
25. TOYOSHIMA C, NAKASAKO M, NOMURA H, OGAWA H: Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 A resolution. Nature (2000) 405:647-655.
26. 2+-ATPase produces pumps defective in ATP binding. J. Biol. Chem. (1996) 271:25778-25789.
27. KJELDSEN K, NORGAARD A, GHEORGHIADE M: Myocardial Na,K-ATPase: the molecular basis for the hemodynamic effect of digoxin therapy in congestive heart failure. Cardiovasc. Res. (2002) 55:710-713.
28. +ATPase inhibition. Eur. J. Clin. Invest. (2001) 31(Suppl. 2):1-4.
29. HORN J: The proton-pump inhibitors: similarities and differences. Clin. Ther. (2000) 22:266-280.
30. 2+-ATPases 2B involvement in human prostate cancer cell growth control. J. Biol Chem. (2001) 276:47608-47614.
31. KRISHNA S, ECKSTEIN-LUDWIG U, JOET T et al.: Transport processes in Plasmodium falciparum-infected erythrocytes: potential as new drug targets. Int. J. Parasitol. (2002) 32:1567-1573.
32. +)-ATPases - nature's most versatile proton pumps. Nature Rev. Mol. Cell. Biol. (2002) 3:94-103.
33. GRUBER G, WIECZOREK H, HARVEY WR, MULLER V: Structure-function relationships of A-, F- and V-ATPases. J. Exp. Biol. (2001) 204:2597-2605.
34. +)-ATPases. FEBS Lett. (1998) 440:258-263.
35. +-ATPase. Curr. Pharm. Des. (2002) 8:2033-2048.
36. +-ATPase: functional mechanisms and potential as a target for cancer therapy. Anticancer Drugs (2002) 13:237-243.
37. MIKI H, SITOU M, KANESHIRO K, HIROKAWA N: All kinesin superfamily protein, KIF, genes in mouse and human. Proc. Natl. Acad. Sci. USA (2001) 98:7004-7011.
38. VERHEY KJ, RAPOPORT TA: Kinesin carries the signal. Trends Biochem. Sci. (2001) 26:545-549.
39. HIROKAWA N, NODA Y, OKADA Y: Kinesin and dynein superfamily proteins in organelle transport and cell division. Curr. Opin. Cell Biol. (1998) 10:60-73.
40. HIROSE K, AMOS LA: Three-dimensional structure of motor molecules. Cell. Mol. Life Sci. (1999) 56:184-199.
41. VALE RD, FLETTERICK RJ: The design plan of kinesin motors. Annu. Rev. Cell Dev. Biol. (1997) 13:745-777.
42. WOEHLKE G, RUBY AK, HART CL, LY B, HOM-BOOHER N, VALE RD: Microtubule interaction site of the kinesin motor. Cell (2000) 90:207-216.
43. SINDELAR CV, BUDNY MJ, RICE S, NABER N, FLETTERICK R, COOKE R: Two conformations in the human kinesin power stroke defined by X-ray crystallography and EPR spectroscopy. Nature Struct. Biol. (2002) 9:844-848.
44. CROSS RA: Molecular motors: kinesin's string variable. Curr. Biol. (2001) 11:R147-R149.
45. FARRELL CM, MACKEY AT, KLUMPP LM, GILBERT SP: The role of ATP hydrolysis for kinesin processivity. J. Biol. Chem. (2002) 277:17079-17087.
46. YUN M, ZHANG X, PARK CG, PARK HW, ENDOW SA. A structural pathway for activation of the kinesin motor ATPase. EMBO J. (2001) 20:2611-2618.
47. KIKKAWA M, SABLIN EP, OKADA Y, YAJIMA H, FLETTERICK RJ, HIROKAWA N: Switch-based mechanism of kinesin motors. Nature (2001) 411:439-445.
48. RICE S, LIN AW, SAFER D et al.: A structural change in the kinesin motor protein that drives motility. Nature (1999) 402:778-784.
49. BLANGY A, LANE HA, D'HERIN P, HARPER M, KRESS M, NIGG EA: Phosphorylation by p34cdc2 regulates spindle association of human Eg5, a kinesin-related motor essential for bipolar spindle formation in vivo. Cell (1995) 83:1159-1169.
50. WOOD KW, CORNWELL WD, JACKSON JR: Past and future of the mitotic spindle as an oncology target. Curr. Opin. Pharmacol. (2001) 1:370-377.
51. SAKOWICZ R, BERDELIS MS, RAY K et al.: A marine natural product inhibitor of kinesin motors. Science (1998) 280:292-295.
52. MAYER TU, KAPOOR TM, HAGGARTY SJ, KING RW, SCHREIBER SL, MITCHISON TJ: Small molecule inhibitor of mitotic spindle bipolarity identified in a phenotype-based screen. Science (1999) 286:971-974.
53. WOOD KW, BERAUD C, CHABALA JC et al.: Inhibitors of the mitotic kinesin KSP: discovery and proof of principle antitumor activity. Proc. Am. Assoc. Cancer Res. (2002) 43:665.
54. SOULTANAS P, WIGLEY DB: Unwinding the 'Gordian knot' of helicase action. Trends Biochem Sci. (2001) 26:47-54.
55. CARUTHERS JM, MCKAY DB: Helicase structure and mechanism. Curr. Opin. Struct. Biol (2002) 12:123-133.
56. TANNER NK, LINDER P: DExD/H box helicases: from generic motors to specific dissociation functions. Mol. Cell (2001) 8:251-262.
57. SCHWER B: A new twist on RNA helicases: DExH/D box proteins as RNPases. Nature Struct. Biol (2001) 8:113-116.
58. HALL MC, MATSON SW: Helicase motifs: the engine that powers DNA unwinding. Mol. Microbiol. (1999) 34:867-877.
59. GORBALENYA AE, KOONIN EV: Helicases: amino acid sequence comparisons and structure-function relationships. Curr. Biol. (1993) 3:419-429.
60. VON HIPPEL PH, DELAGOUTTE E: A general model for nucleic acid helicases and their coupling within macromolecular machines. Cell (2001) 104:177-190.
61. SOULTANAS P, WIGLEY DB: DNA helicases: 'inching forward'. Curr. Opin. Struct. Biol. (2000) 10:124-128.
62. VELANKAR SS, SOULTANAS P, DILLINGHAM MS, SUBRAMANYA HS, WIGLEY DB: Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate and inchworm mechanism. Cell (1999) 97:75-84.
63. DILLINGHAM MS, WIGLEY DB, WEBB MR: Demonstration of unidirectional single-stranded DNA translocation by PcrA helicase: measurement of step size and translocation speed. Biochemistry (2000) 39:205-212.
64. CAUSEVIC M, HISLOP RG, KERNOHAN NM et al.: Overexpression and poly-ubiquitylation of the DEAD-box RNA helicase p68 in colorectal tumours. Oncogene (2001) 20:7734-7743.
65. ISHIGURO H, SHIMOKAWA T, TSUNODA T et al.: Isolation of HELAD1, a novel human helicase gene up-regulated in colorectal carcinomas. Oncogene (2002) 21:6387-6394.
66. HASHIMOTO K, NAKAGAWA Y, MORIKAWA H et al.: Co-overexpression of DEAD box protein rck/p54 and c-myc protein in human colorectal adenomas and the relevance of their expression in cultured cell lines. Carcinogenesis (2001) 22:1965-1970.
67. GODBOUT R, PACKER M, BIE W: Overexpression of DEAD box protein (DDX1) in neuroblastoma and retinoblastoma cell lines. J. Biol. Chem. (1998) 273:21161-21168.
68. TANEJA P, GU J, PENG R et al.: A dominant-negative mutant of human DNA helicase B blocks the onset of chromosomal DNA replication. J. Biol. Chem (2002) 277:40853-40861.
69. WOOD MA, MCMAHON SB, COLE MD: An ATPase/helicase complex is an essential cofactor for oncogenic transformation by c-Myc. Mol. Cell. (2000) 5:321-330.
70. LUN L, SUN PM, TRUBEY CM, BACHUR NR: Antihelicase action of CI-958, a new drug for prostate cancer. Cancer Chemother. Pharmacol. (1998) 42:447-453.
71. CRUTE JJ, GRYGON CA, HARGRAVE KD et al.: Herpes simplex virus helicase-primase inhibitors are active in animal models of human disease. Nat. Med. (2002) 8:386-391.
72. BETZ UAK, FISCHER R, KLEYMANN G, HENDRIX M, RUBSAMEN-WAIGMANN H: Potent in vivo antiviral activity of the herpes simplex virus primase-helicase inhibitor BAY 57-1293. Antimicrob. Agents Chemother. (2002) 46:1766-1772.
73. BOROWSKI P, SCHALINSKI S, SCHMITZ H: Nucleotide triphosphatase/helicase of hepatitis C virus as a target for antiviral therapy. Antiviral Res. (2002) 55:397-412.
74. MORIMOTO RI: Cells in stress: transcriptional activation of heat shock genes. Science (1993) 259:1409-1410.
75. FELDMAN DE, FRYDMAN J: Protein folding in vivo: the importance of molecular chaperones. Curr. Opin. Struct. Biol. (2000) 10:26-33.
76. SLAVOTINEK AM, BIESECKER LG: Unfolding the role of chaperones and chaperonins in human disease. Trends Genet. (2001) 17:528-535.
77. BUKAU B, HORWICH AL: The hsp70 and hsp60 chaperone machines. Cell (1998) 92:351-366.
78. PEARL LH, PRODROMOU C: Structure and in vivo function of hsp90. Curr. Opin. Struct. Biol. (2000) 10:46-51.
79. LEE-YOON D, EASTON D, MURAWSKI M, BURD R, SUBJECK JR: Identification of major subfamily of a large hsp70-like proteins through the cloning of the mammalian 110-kDa heat shock protein. J. Biol. Chem. (1995) 270:15725-15733.
80. OBERMANN WM, SONDERMANN H, RUSSO AA, PAVLETICH NP, HARTL FU: In vivo function of Hsp90 is dependent on ATP binding and ATP hydrolysis. J. Cell Biol. (1998) 143:901-910.
81. BREHMER D, RUDIGER S, GASSLER CS et al.: Tuning of chaperone activity of hsp70 proteins by modulation of nucleotide exchange. Nature Struct. Biol. (2001) 8:427-432.
82. MAYER MP, SCHRODER H, RUDIGER S, PAAL K, LAUFEN T, BUKAU B: Multistep mechanism of substrate binding determines chaperone activity of hsp70. Nature Struct. Biol. (2000) 7:586-593.
83. PANARETOU B, PRODROMOU C, ROE SM et al.: ATP binding and hydrolysis are essential to the function of the hsp90 molecular chaperone in vivo. EMBO J. (1998) 17:4829-4836.
84. GARRIDO C, GURBUXANI S, RAVAGNAN L, KROEMER G: Heat shock proteins: endogenous modulators of apoptotic cell death. Biochem. Biophys. Res. Commun. (2001) 286:433-442.
85. XANTHOUDAKIS S, NICHOLSON DW: Heat-shock proteins as death determinants. Nature Cell Biol. (2000) 2:E163-E165.
86. JOLLY C, MORIMOTO RI: Role of the heat shock response and molecular chaperones in oncogenesis and cell death. J. Natl. Cancer Inst. (2000) 92:1564-1572.
87. BLAGOSKLONNY MV: Hsp-90-associated oncoproteins: multiple targets of geldanamycin and its analogs. Leukemia (2002) 16:455-462.
88. BEERE HM, GREEN DR: Stress management - heat shock protein-70 and the regulation of apoptosis. Trends Cell Biol. (2001) 11:6-10.
89. NECKERS L: Hsp90 inhibitors as novel cancer chemotherapeutic agents. Trends Mol. Med. (2002) 8:S55-S61.
90. SOGA S, SHARMA SV, SHIOTSU Y et al.: Stereospecific antitumor activity of radicicol oxime derivatives. Cancer Chemother. Pharmacol. (2001) 48:435-445.
91. CHIOSIS G, TIMAUL MN, LUCAS B et al.: A small molecule designed to bind to the adenine nucleotide pocket of Hsp90 causes Her2 degradation and the growth arrest and differentiation of breast cancer cells. Chem. Biol. (2001) 8:289-299.
92. NYLANDSTED J, ROHDE M, BRAND K, BASTHOLM L, ELLING F, JAATTELA M: Selective depletion of heat shock protein 70 (hsp70) activates a tumor-specific death program that is independent of caspases and bypasses bcl-2. Proc. Natl. Acad. Sci. USA (2000) 97:7871-7876.
93. KAUR J, KAUR J, RALHAN R: Induction of apoptosis by abrogation of hsp70 expression in human oral cancer cells. Int. J. Cancer (2000) 85:1-5.
94. ROBERTSON JD, DATTA KB, BISWAL SS, KEHRER JP: Heat-shock protein 70 antisense oligomers enhance proteasome inhibitor-induced apoptosis. Biochem. J. (1999) 344:477-485.
95. MALONEY A, WORKMAN P: HSP90 as a new therapeutic target for cancer therapy: the story unfolds. Expert Opin. Biol. Ther. (2002) 2:3-24.
96. VALE RD: AAA proteins: lords of the ring. J. Cell Sci. (2000) 150:F13-F19.
97. PATEL S, LATTERICH M: The AAA team: related ATPases with diverse function. Trends Cell Biol. (1998) 8:65-71.
98. BEYER A: Sequence analysis of the AAA protein family. Protein Sci. (1997) 6:2043-2058.
99. DOUGAN DA, MOGK A, ZETH K, TURGAY K, BUKAU B: AAA+ proteins and substrate recognition, it all depends on their partner crime. FEBS Lett. (2002) 529:6-10.
100. NEUWALD AF, ARAVIND L, SPOUGE JL, KOONIN EV: AAA+: a class of chaperone-like ATPases associated with the assembly, operation and disassembly of protein complexes. Genome Res. (1999) 9:27-43.
101. SINGH SK, GUO F, MAURIZI MR: ClpA and ClpP remain associated during multiple rounds of ATP-dependent protein degradation by ClpAP protease. Biochemistry (1999) 38:14906-14915.
102. HARTMAN JJ, VALE RD: Microtubule disassembly by ATP-dependent oligomerization of the AAA enzyme katanin. Science (1999) 286:782-785.
103. ADAMS J: Proteasome inhibitors as new anticancer drugs. Curr. Opin. Oncol. (2002) 14:628-634.
104. CHENE P: ATPases as drug targets: learning from their structure. Nat. Rev. Drug Discov. (2002) 1:665-673.
105. DUTTA R, INOUYE M: GHKL, an emergent ATPase/kinase superfamily. Trends Biochem. Sci. (2000) 25:24-28.
106. GUARNE A, JUNOP MS, YANG W: Structure and function of the N-terminal 40 kDa fragment of human PMS2: a monomeric GHL ATPase. EMBO J. (2001) 20:5521-5531.
107. BAN C, YANG W: Crystal structure and ATPase activity of MutL: implications for DNA repair and mutagenesis. Cell (1998) 95:541-552.
108. BERGERAT A, DE MASSY N, GADELLE D, VAROUTAS PC, NICOLAS A, FORTERRE P: An atypical topoisomerase II from archea with implications for meiotic recombination. Nature (1997) 386:414-417.
109. BORK P, SANDER C, VALENCIA A: An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins. Proc. Natl. Acad. Sci. USA (1992) 89:7290-7294.
110. FLAHERTY KM, MCKAY DB, KABSCH W, HOLMES KC: Similarity of the three-dimensional structures of actin and the ATPase fragment of a 70-kDa heat shock cognate protein. Proc. Natl. Acad. Sci. USA (1991) 88:5041-5045.
111. +-ATPase. Nature (2002) 297:1692-1696.
112. SMITH CA, RAYMENT I: Active site comparisons highlight structural similarities between myosin and other P-loop proteins. Biophys. J. (1996) 70:1590-1602.
113. SARASTE M, SIBBALD PR, WITTINGHOFER A: The P-loop-α common motif in ATP- and GTP-binding proteins. Trends Biochem. Sci. (1990) 15:430-434.
114. WALKER JE, SARASTE M, RUNSWICK MJ, GAY NJ: Distantly related sequences in the α- and β-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. (1982) 1:945-951.
115. VETTER IR, WITTINGHOFER A: Nucleoside triphosphate-binding proteins: different scaffolds to achieve phosphoryl transfer. Q. Rev. Biophys. (1999) 32:1-56.
116. ROE SM, PRODROMOU C, O'BRIEN R, LADBURY JE, PIPER PW, PEARL LH: Structural basis for inhibition of the Hsp90 molecular chaperone by the antitumor antibiotics radicicol and geldanamycin. J. Med. Chem. (1999) 42:260-266.
117. GARCIA-ECHEVERRIA C, CHENE P, BLOMMERS MJ, FURET P: Discovery of potent antagonists of the interaction between human double minute 2 and tumor suppressor p53. J. Med. Chem. (2000) 43:3205-3208.
118. BOEHM HJ, BOEHRINGER M, BUR D et al.: Novel inhibitors of DNA gyrase: 3D structure based biased needle screening, hit validation by biophysical methods, and 3D guided optimization. A promising alternative to random screening. J. Med. Chem. (2000) 43:2664-2674.
119. +-ATPase by flavonoids: a structure-activity study. J. Enzym. Inhib. (1999) 14:151-166.
120. CHEEK S, ZHANG H, GRISHIN NV: Sequence and structure classification of kinases. J. Mol. Biol. (2002) 320:855-881.