Human carbonic anhydrase IX (CA IX), a protein specifically expressed on the surface of solid tumour cells, represents a validated target both for anticancer therapy and diagnostics. We recently identified sulfonamide dicarbaboranes as promising inhibitors of CA IX with favourable activities both in vitro and in vivo. To explain their selectivity and potency, we performed detailed X-ray structural analysis of their interactions within the active sites of CA IX and CA II. Series of compounds bearing various aliphatic linkers between the dicarbaborane cluster and sulfonamide group were examined. Preferential binding towards the hydrophobic part of the active site cavity was observed. Selectivity towards CA IX lies in the shape complementarity of the dicarbaborane cluster with a specific CA IX hydrophobic patch containing V131 residue. The bulky side chain of F131 residue in CA II alters the shape of the catalytic cavity, disrupting favourable interactions of the spherical dicarbaborane cluster.

Chemistry Department Apigenex s r o Prague Czech Republic

Deparment of Structural Biology Institute of Molecular Genetics of the Czech Academy of Sciences Prague Czech Republic

Deparment of Structural Biology Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Prague Czech Republic

Department of Syntheses Institute of Inorganic Chemistry of the Czech Academy of Sciences Řež Czech Republic

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Supuran CT. Carbonic anhydrases as drug targets. Current Pharm Des 2008;14:601–2. PubMed

Supuran CT. Carbonic anhydrases: novel therapeutic applications for inhibitors and activators. Nat Rev Drug Discov 2008;7:168–81. PubMed

Pastorekova S, Parkkila S, Parkkila AK, et al. . Carbonic anhydrase IX, MN/CA IX: Analysis of stomach complementary DNA sequence and expression in human and rat alimentary tracts. Gastroenterology 1997;112:398–408. PubMed

Mahon BP, Pinard MA, McKenna R.. Targeting carbonic anhydrase IX activity and expression. Molecules 2015;20:2323–48. PubMed PMC

Warburg O. On respiratory impairment in cancer cells. Science 1956;124:269–70. PubMed

Moulder JE, Rockwell S.. Tumor hypoxia: Its impact on cancer therapy. Cancer Metastasis Rev 1987;5:313–41. PubMed

Hockel M, Vaupel P.. Tumor hypoxia: definitions and current clinical, biologic, and molecular aspects. J Natl Cancer Inst 2001;93:266–76. PubMed

Neri D, Supuran CT.. Interfering with pH regulation in tumours as a therapeutic strategy. Nat Rev Drug Discov 2011;10:767–77. PubMed

Peskin BS, Carter MJ.. Chronic cellular hypoxia as the prime cause of cancer: What is the de-oxygenating role of adulterated and improper ratios of polyunsaturated fatty acids when incorporated into cell membranes? Med Hypotheses 2008;70:298–304. PubMed

Sadri N, Zhang PJ.. Hypoxia-inducible factors: Mediators of cancer progression; prognostic and therapeutic targets in soft tissue sarcomas. Cancers (Basel) 2013;5:320–33. PubMed PMC

Lou YM, McDonald PC, Oloumi A, et al. . Targeting tumor hypoxia: suppression of breast tumor growth and metastasis by novel carbonic anhydrase IX inhibitors. Cancer Res 2011;71:3364–76. PubMed

Ward C, Meehan J, Mullen P, Supuran C, et al. . Evaluation of carbonic anhydrase IX as a therapeutic target for inhibition of breast cancer invasion and metastasis using a series of in vitro breast cancer models. Oncotarget 2015;6:24856–70. PubMed PMC

Parks SK, Cormerais Y, Pouyssegur J.. Hypoxia and cellular metabolism in tumour pathophysiology. J Physiol (Lond) 2017;595:2439–50. PubMed PMC

De Simone G, Alterio V, Supuran CT.. Exploiting the hydrophobic and hydrophilic binding sites for designing carbonic anhydrase inhibitors. Exp Opin Drug Discov 2013;8:793–810. PubMed

Pinard MA, Mahon B, McKenna R.. Probing the surface of human carbonic anhydrase for clues towards the design of isoform specific inhibitors. Biomed Res Int 2015;2015:453543. PubMed PMC

Aggarwal M, McKenna R.. Update on carbonic anhydrase inhibitors: a patent review (2008 - 2011). Expert Opin Ther Pat 2012;22:903–15. PubMed

Supuran CT. Structure-based drug discovery of carbonic anhydrase inhibitors. J Enzyme Inhibit Med Chem 2012;27:759–72. PubMed

Lomelino CL, Supuran CT, McKenna R.. Non-classical inhibition of carbonic anhydrase. Int J Mol Sci 2016;17:1150. PubMed PMC

Hou Z, Lin B, Bao Y, et al. . Dual-tail approach to discovery of novel carbonic anhydrase IX inhibitors by simultaneously matching the hydrophobic and hydrophilic halves of the active site. Eur J Med Chem 2017;132:1–10. PubMed

Yang J, Koruza K, Fisher Z, et al. . Improved molecular recognition of carbonic anhydrase IX by polypeptide conjugation to acetazolamide. Bioorg Med Chem 2017;25:5838–48. PubMed

Brynda J, Mader P, Šícha V, et al. . Carborane-based carbonic anhydrase inhibitors. Angew Chem Int Ed Engl 2013;52:13760–3. PubMed

Grüner B, Brynda J, Das V, et al. . Metallacarborane sulfamides: unconventional, specific, and highly selective inhibitors of carbonic anhydrase IX. J Med Chem 2019;62:9560–75. PubMed

Grimes RN. Carboranes. 2nd ed. London- Amsterdam- Burlington- San Diego- Oxford: Academic Press Publications (Elsevier, Inc.); 2011.

Lesnikowski ZJ. Challenges and opportunities for the application of boron clusters in drug design. J Med Chem 2016;59:7738–58. PubMed

Grimes RN. Boron clusters come of age. J Chem Educ 2004;81:657–72.

Valliant JF, Guenther KJ, King AS, et al. . The medicinal chemistry of carboranes. Coordination Chem Rev 2002;232:173–230.

Lesnikowski ZJ. Boron units as pharmacophores - new applications and opportunities of boron cluster chemistry. Collection Czech Chem Commun 2007;72:1646–58.

Sivaev IB, Bregadze VI.. Polyhedral boranes for medical applications: current status and perspectives. Eur J Inorg Chem 2009;2009:1433–50.

Satapathy R, Dash BP, Maguire JA, Hosmane NS.. New developments in the medicinal chemistry of carboranes. Collection Czech Chem Commun 2010;75:995–1022.

Issa F, Kassiou M, Rendina M.. Boron in drug discovery: carboranes as unique pharmacophores in biologically active compounds. Chem Rev 2011;111:5701–22. PubMed

Scholz M, Hey-Hawkins E.. Carbaboranes as pharmacophores: properties, synthesis, and application strategies. Chem Rev 2011;111:7035–62. PubMed

Frank R, Ahrens VM, Boehnke S, et al. . Charge-compensated metallacarborane building blocks for conjugation with peptides. Chembiochem 2016;17:308–17. PubMed

Bregadze VI, Glazun SA.. Metal containing carboranes with antitumor activity. Russ Chem Bull Intl Ed 2007;56:643–59.

Sibrian-Vazquez M, Hao E, Jensen TJ, Vicente MGH.. Enhanced cellular uptake with a cobaltacarborane-porphyrin-HIV-1 Tat 48-60 conjugate. Bioconjug Chem 2006;17:928–34. PubMed

Dvořanová J, Kugler M, Holub J, et al. . Sulfonamido carboranes as highly selective inhibitors of cancer specific carbonic anhydrase IX. Eur J Med Chem 2020;200:112460. [Accepted 11 May 2020]. PubMed

Pace RJ, Williams J, Williams R4.. Boron hydride derivatives. Part VII. The characterisation of some decaborane derivatives of the type, b10h12,2m. J Chem Soc (Resumed) 1961;2196–204.

Pinard MA, Boone CD, Rife BD, et al. . Structural study of interaction between brinzolamide and dorzolamide inhibition of human carbonic anhydrases. Bioorg Med Chem 2013;21:7210–5. PubMed

Pospíšilová K, Knedlík T, Šácha P, et al. . Inhibitor–polymer conjugates as a versatile tool for detection and visualization of cancer-associated carbonic anhydrase isoforms. ACS Omega 2019;4:6746–56.

Khalifah RG. Carbon dioxide hydration activity of carbonic anhydrase.1. Stop-flow kinetic studies on native human isoenzyme-b and isoenzyme-c. J Biol Chem 1971;246:2561–73. PubMed

Morrisson JWM, Williams JF.. The kinetics of reversible tight-binding inhibition. Methods Enzymol 1979;63:437–67. PubMed

Williams JW, Morrison JF.. The kinetics of reversible tight-binding inhibition. In: Purich DE, ed. Methods in enzymology. Amsterdam, Netherlands: Elsevier; 1979;63: 437−67. PubMed

Yung-Chi C, Prusoff WH.. Relationship between the inhibition constant (Ki) and the concentration of inhibitor which causes 50 per cent inhibition (I50) of an enzymatic reaction. Biochem Pharmacol 1973;22:3099–108. PubMed

Innocenti A, Scozzafava A, Parkkila S, et al. . Investigations of the esterase, phosphatase, and sulfatase activities of the cytosolic mammalian carbonic anhydrase isoforms I, II, and XIII with 4-nitrophenyl esters as substrates. Bioorgan Med Chem Lett 2008;18:2267–71. PubMed

Hilvo M, Baranauskiene L, Salzano AM, et al. . Biochemical characterization of ca IX, one of the most active carbonic anhydrase isozymes. J Biol Chem 2008;283:27799–809. PubMed

Mueller U, Förster R, Hellmig M, et al. . The macromolecular crystallography beamlines at BESSY II of the Helmholtz-Zentrum Berlin: current status and perspectives. Eur Phys J Plus 2015;130:141.

Kabsch W. XDS. Acta Crystallogr D Biol Crystallogr 2010;66:125–32. PubMed PMC

Kabsch W. Integration, scaling, space-group assignment and post-refinement. Acta Crystallogr. D Biol Crystallogr 2010;66:133–44. PubMed PMC

Mader P, Brynda J, Gitto R, et al. . Structural basis for the interaction between carbonic anhydrase and 1,2,3,4-tetrahydroisoquinolin-2-ylsulfonamides. J Med Chem 2011;54:2522–6. PubMed

Ahlrichs R, Bär M, Häser M, et al. . Electronic structure calculations on workstation computers: the program system Turbomole. Chem Phys Lett 1989;162:165–9.

Jurecka P, Cerny J, Hobza P, Salahub DR.. Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations. J Comput Chem 2007;28:555–69. PubMed

Vagin AA, Murshudov GN, Strokopytov BV.. Blanc: the program suite for protein crystallography. J Appl Crystallogr 1998;31:98–102.

Emsley P, Cowtan K.. Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 2004;60:2126–32. PubMed

Murshudov GN, Vagin AA, Dodson EJ.. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 1997;53:240–55. PubMed

Chen VB, Arendall WB, 3rd, Headd JJ, et al. . Molprobity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 2010;66:12–21. PubMed PMC

Schrodinger LLC . (New York, USA) The Pymol molecular graphics system, version 1.8. In: The Pymol molecular graphics system, version 1.8; November; 2015.

Winn MD, Ballard CC, Cowtan KD, Dodson EJ, et al. . Overview of the CCP4 suite and current developments. Acta Crystallogr D Biol Crystallogr 2011;67:235–42. PubMed PMC

Krissinel E, Henrick K.. Inference of macromolecular assemblies from crystalline state. J Mol Biol 2007;372:774–97. PubMed

Mujumdar P, Teruya K, Tonissen KF, et al. . An unusual natural product primary sulfonamide: synthesis, carbonic anhydrase inhibition, and protein X-ray structures of psammaplin c. J Med Chem 2016;59:5462–70. PubMed

Eriksson AE, Kylsten PM, Jones TA, Liljas A.. Crystallographic studies of inhibitor binding sites in human carbonic anhydrase II: a pentacoordinated binding of the SCN- ion to the zinc at high pH. Proteins: Struct Funct Bioinform 1988;4:283–93. PubMed

Mahon BP, Lomelino CL, Ladwig J, et al. . Mapping selective inhibition of the cancer-related carbonic anhydrase IX using structure-activity relationships of glucosyl-based sulfamates. J Med Chem 2015;58:6630–8. PubMed

Bhatt A, Mahon BP, Cruzeiro VWD, et al. . Structure-activity relationships of benzenesulfonamide-based inhibitors towards carbonic anhydrase isoform specificity. ChemBioChem 2017;18:213–22. PubMed

Identification of specific carbonic anhydrase inhibitors via in situ click chemistry, phage-display and synthetic peptide libraries: comparison of the methods and structural study