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Ultrahigh resolution crystal structures of human carbonic anhydrases I and II complexed with "two-prong" inhibitors reveal the molecular basis of high affinity.

Jude KM, Banerjee AL, Haldar MK, Manokaran S, Roy B, Mallik S, Srivastava DK, Christianson DW
J Am Chem Soc 128 3011-8 (2006)
Related entries: 2foq, 2fos, 2fou, 2fov

Cited: 34 times
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Abstract

The atomic-resolution crystal structures of human carbonic anhydrases I and II complexed with "two-prong" inhibitors are reported. Each inhibitor contains a benzenesulfonamide prong and a cupric iminodiacetate (IDA-Cu(2+)) prong separated by linkers of different lengths and compositions. The ionized NH(-) group of each benzenesulfonamide coordinates to the active site Zn(2+) ion; the IDA-Cu(2+) prong of the tightest-binding inhibitor, BR30, binds to H64 of CAII and H200 of CAI. This work provides the first evidence verifying the structural basis of nanomolar affinity measured for two-prong inhibitors targeting the carbonic anhydrases.

Reviews - 2foy mentioned but not cited (1)

  1. Carbonic anhydrase as a model for biophysical and physical-organic studies of proteins and protein-ligand binding. Krishnamurthy VM, Kaufman GK, Urbach AR, Gitlin I, Gudiksen KL, Weibel DB, Whitesides GM. Chem Rev 108 946-1051 (2008)

Articles - 2foy mentioned but not cited (4)

  1. Ultrahigh resolution crystal structures of human carbonic anhydrases I and II complexed with "two-prong" inhibitors reveal the molecular basis of high affinity. Jude KM, Banerjee AL, Haldar MK, Manokaran S, Roy B, Mallik S, Srivastava DK, Christianson DW. J Am Chem Soc 128 3011-3018 (2006)
  2. Structural analysis of charge discrimination in the binding of inhibitors to human carbonic anhydrases I and II. Srivastava DK, Jude KM, Banerjee AL, Haldar M, Manokaran S, Kooren J, Mallik S, Christianson DW. J Am Chem Soc 129 5528-5537 (2007)
  3. Identification of a Potential Target of Capsaicin by Computational Target Fishing. Ye XY, Ling QZ, Chen SJ. Evid Based Complement Alternat Med 2015 983951 (2015)
  4. Ridge regression estimated linear probability model predictions of O-glycosylation in proteins with structural and sequence data. Gana R, Vasudevan S. BMC Mol Cell Biol 20 21 (2019)


Reviews citing this publication (8)

  1. How many carbonic anhydrase inhibition mechanisms exist? Supuran CT. J Enzyme Inhib Med Chem 31 345-360 (2016)
  2. Application of metal coordination chemistry to explore and manipulate cell biology. Haas KL, Franz KJ. Chem Rev 109 4921-4960 (2009)
  3. Targeting proteins with metal complexes. Meggers E. Chem Commun (Camb) 1001-1010 (2009)
  4. Exploiting the hydrophobic and hydrophilic binding sites for designing carbonic anhydrase inhibitors. De Simone G, Alterio V, Supuran CT. Expert Opin Drug Discov 8 793-810 (2013)
  5. Structure, function and applications of carbonic anhydrase isozymes. Imtaiyaz Hassan M, Shajee B, Waheed A, Ahmad F, Sly WS. Bioorg Med Chem 21 1570-1582 (2013)
  6. The design of inhibitors for medicinally relevant metalloproteins. Jacobsen FE, Lewis JA, Cohen SM. ChemMedChem 2 152-171 (2007)
  7. Fragment-based lead discovery: a chemical update. Erlanson DA. Curr Opin Biotechnol 17 643-652 (2006)
  8. Thermodynamic, kinetic, and structural parameterization of human carbonic anhydrase interactions toward enhanced inhibitor design. Linkuvienė V, Zubrienė A, Manakova E, Petrauskas V, Baranauskienė L, Zakšauskas A, Smirnov A, Gražulis S, Ladbury JE, Matulis D. Q Rev Biophys 51 e10 (2018)

Articles citing this publication (21)

  1. Insights towards sulfonamide drug specificity in α-carbonic anhydrases. Aggarwal M, Kondeti B, McKenna R. Bioorg Med Chem 21 1526-1533 (2013)
  2. Carbonic anhydrase inhibitors. The X-ray crystal structure of human isoform II in adduct with an adamantyl analogue of acetazolamide resides in a less utilized binding pocket than most hydrophobic inhibitors. Avvaru BS, Wagner JM, Maresca A, Scozzafava A, Robbins AH, Supuran CT, McKenna R. Bioorg Med Chem Lett 20 4376-4381 (2010)
  3. [(Cp-R)M(CO)3] (M=Re or 99mTc) Arylsulfonamide, arylsulfamide, and arylsulfamate conjugates for selective targeting of human carbonic anhydrase IX. Can D, Spingler B, Schmutz P, Mendes F, Raposinho P, Fernandes C, Carta F, Innocenti A, Santos I, Supuran CT, Alberto R. Angew Chem Int Ed Engl 51 3354-3357 (2012)
  4. Human carbonic anhydrase II as a host for piano-stool complexes bearing a sulfonamide anchor. Monnard FW, Heinisch T, Nogueira ES, Schirmer T, Ward TR. Chem Commun (Camb) 47 8238-8240 (2011)
  5. Binding of uridine 5'-diphosphate in the "basic patch" of the zinc deacetylase LpxC and implications for substrate binding. Gennadios HA, Christianson DW. Biochemistry 45 15216-15223 (2006)
  6. Metal complexes as "protein surface mimetics". Hewitt SH, Wilson AJ. Chem Commun (Camb) 52 9745-9756 (2016)
  7. The first example of a significant active site conformational rearrangement in a carbonic anhydrase-inhibitor adduct: the carbonic anhydrase I-topiramate complex. Alterio V, Monti SM, Truppo E, Pedone C, Supuran CT, De Simone G. Org Biomol Chem 8 3528-3533 (2010)
  8. Carbonic anhydrase inhibitors: copper(II) complexes of polyamino-polycarboxylamido aromatic/heterocyclic sulfonamides are very potent inhibitors of the tumor-associated isoforms IX and XII. Rami M, Winum JY, Innocenti A, Montero JL, Scozzafava A, Supuran CT. Bioorg Med Chem Lett 18 836-841 (2008)
  9. Characterization of the Copper(II) Binding Sites in Human Carbonic Anhydrase II. Nettles WL, Song H, Farquhar ER, Fitzkee NC, Emerson JP. Inorg Chem 54 5671-5680 (2015)
  10. Amphipathic benzoic acid derivatives: synthesis and binding in the hydrophobic tunnel of the zinc deacetylase LpxC. Shin H, Gennadios HA, Whittington DA, Christianson DW. Bioorg Med Chem 15 2617-2623 (2007)
  11. Inhibition pattern of sulfamide-related compounds in binding to carbonic anhydrase isoforms I, II, VII, XII and XIV. Gavernet L, Gonzalez Funes JL, Palestro PH, Bruno Blanch LE, Estiu GL, Maresca A, Barrios I, Supuran CT. Bioorg Med Chem 21 1410-1418 (2013)
  12. In Vivo Evaluation of Selective Carbonic Anhydrase Inhibitors as Potential Anticonvulsant Agents. Bruno E, Buemi MR, De Luca L, Ferro S, Monforte AM, Supuran CT, Vullo D, De Sarro G, Russo E, Gitto R. ChemMedChem 11 1812-1818 (2016)
  13. Synthesis of sulfonamide conjugates of Cu(II), Ga(III), In(III), Re(V) and Zn(II) complexes: carbonic anhydrase inhibition studies and cellular imaging investigations. Dilworth JR, Pascu SI, Waghorn PA, Vullo D, Bayly SR, Christlieb M, Sun X, Supuran CT. Dalton Trans 44 4859-4873 (2015)
  14. Thermodynamics of binding of structurally similar ligands to histone deacetylase 8 sheds light on challenges in the rational design of potent and isozyme-selective inhibitors of the enzyme. Singh RK, Suzuki T, Mandal T, Balsubramanian N, Haldar M, Mueller DJ, Strode JA, Cook G, Mallik S, Srivastava DK. Biochemistry 53 7445-7458 (2014)
  15. Enantiopure Cryptophane-129Xe Nuclear Magnetic Resonance Biosensors Targeting Carbonic Anhydrase. Taratula O, Bai Y, D'Antonio EL, Dmochowski IJ. Supramol Chem 27 65-71 (2015)
  16. A strategy for designing "multi-prong" enzyme inhibitors by incorporating selective ligands to the liposomal surface. Elegbede AI, Haldar MK, Manokaran S, Kooren J, Roy BC, Mallik S, Srivastava DK. Chem Commun (Camb) 3377-3379 (2007)
  17. Combined enzyme and substrate design: grafting of a cooperative two-histidine catalytic motif into a protein targeted at the scissile bond in a designed ester substrate. Höst GE, Razkin J, Baltzer L, Jonsson BH. Chembiochem 8 1570-1576 (2007)
  18. Module assembly for protein-surface recognition: geranylgeranyltransferase I bivalent inhibitors for simultaneous targeting of interior and exterior protein surfaces. Machida S, Usuba K, Blaskovich MA, Yano A, Harada K, Sebti SM, Kato N, Ohkanda J. Chemistry 14 1392-1401 (2008)
  19. Toxic Metal Species and 'Endogenous' Metalloproteins at the Blood-Organ Interface: Analytical and Bioinorganic Aspects. Bridle TG, Kumarathasan P, Gailer J. Molecules 26 3408 (2021)
  20. Recognition of isozymes via lanthanide ion incorporated polymerized liposomes. Elegbede AI, Haldar MK, Manokaran S, Mallik S, Srivastava DK. Chem Commun (Camb) 4495-4497 (2007)
  21. Stabilization of anionic and neutral forms of a fluorophoric ligand at the active site of human carbonic anhydrase I. Manokaran S, Banerjee J, Mallik S, Srivastava DK. Biochim Biophys Acta 1804 1965-1973 (2010)


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