The sulfonamide function is used extensively as a general building block in various inhibitory scaffolds and, more specifically, as a zinc-binding group (ZBG) of metalloenzyme inhibitors. Here, we provide biochemical, structural, and computational characterization of a metallopeptidase in complex with inhibitors, where the mono- and bisubstituted sulfamide functions are designed to directly engage zinc ions of a bimetallic enzyme site. Structural data showed that while monosubstituted sulfamides coordinate active-site zinc ions via the free negatively charged amino group in a canonical manner, their bisubstituted counterparts adopt an atypical binding pattern divergent from expected positioning of corresponding tetrahedral reaction intermediates. Accompanying quantum mechanics calculations revealed that electroneutrality of the sulfamide function is a major factor contributing to the markedly lower potency of bisubstituted compounds by considerably lowering their interaction energy with the enzyme. Overall, while bisubstituted uncharged sulfamide functions can bolster favorable pharmacological properties of a given inhibitor, their use as ZBGs in metalloenzyme inhibitors might be less advantageous due to their suboptimal metal-ligand properties.

Department of Chemistry Washington State University Pullman Washington 99163 United States

Forensic Laboratory of Biologically Active Substances University of Chemistry and Technology Prague Technická 3 166 28 Prague 6 Czech Republic

Institute of Biotechnology of the Czech Academy of Sciences BIOCEV Prumyslova 595 252 50 Vestec Czech Republic

Zobrazit více v PubMed

Zhao C.; Rakesh K. P.; Ravidar L.; Fang W. Y.; Qin H. L. Pharmaceutical and medicinal significance of sulfur (S(VI))-Containing motifs for drug discovery: A critical review. Eur. J. Med. Chem. 2019, 162, 679–734. 10.1016/j.ejmech.2018.11.017. PubMed DOI PMC

Winum J. Y.; Scozzafava A.; Montero J. L.; Supuran C. T. The sulfamide motif in the design of enzyme inhibitors. Expert Opin. Ther. Pat. 2006, 16, 27–47. 10.1517/13543776.16.1.27. PubMed DOI

Akbaba Y.; Bastem E.; Topal F.; Gulcin I.; Maras A.; Goksu S. Synthesis and carbonic anhydrase inhibitory effects of novel sulfamides derived from 1-aminoindanes and anilines. Arch. Pharm. 2014, 347, 950–957. 10.1002/ardp.201400257. PubMed DOI

Casini A.; Winum J. Y.; Montero J. L.; Scozzafava A.; Supuran C. T. Carbonic anhydrase inhibitors: inhibition of cytosolic isozymes I and II with sulfamide derivatives. Bioorg. Med. Chem. Lett. 2003, 13, 837–840. 10.1016/S0960-894X(03)00028-3. PubMed DOI

Rami M.; Dubois L.; Parvathaneni N. K.; Alterio V.; van Kuijk S. J.; Monti S. M.; Lambin P.; De Simone G.; Supuran C. T.; Winum J. Y. Hypoxia-targeting carbonic anhydrase IX inhibitors by a new series of nitroimidazole-sulfonamides/sulfamides/sulfamates. J. Med. Chem. 2013, 56, 8512–8520. 10.1021/jm4009532. PubMed DOI

Winum J. Y.; Temperini C.; El Cheikh K.; Innocenti A.; Vullo D.; Ciattini S.; Montero J. L.; Scozzafava A.; Supuran C. T. Carbonic anhydrase inhibitors: clash with Ala65 as a means for designing inhibitors with low affinity for the ubiquitous isozyme II, exemplified by the crystal structure of the topiramate sulfamide analogue. J. Med. Chem. 2006, 49, 7024–7031. 10.1021/jm060807n. PubMed DOI

Park J. D.; Kim D. H.; Kim S. J.; Woo J. R.; Ryu S. E. Sulfamide-based inhibitors for carboxypeptidase A. Novel type transition state analogue inhibitors for zinc proteases. J. Med. Chem. 2002, 45, 5295–5302. 10.1021/jm020258v. PubMed DOI

Jones W.; Griffiths K.; Barata P. C.; Paller C. J. PSMA theranostics: review of the current status of PSMA-targeted imaging and radioligand therapy. Cancers 2020, 12, 136710.3390/cancers12061367. PubMed DOI PMC

Evans J. C.; Malhotra M.; Cryan J. F.; O’Driscoll C. M. The therapeutic and diagnostic potential of the prostate specific membrane antigen/glutamate carboxypeptidase II (PSMA/GCPII) in cancer and neurological disease. Br. J. Pharmacol. 2016, 173, 3041–3079. 10.1111/bph.13576. PubMed DOI PMC

Šácha P.; Zamecnik J.; Barinka C.; Hlouchova K.; Vicha A.; Mlcochova P.; Hilgert I.; Eckschlager T.; Konvalinka J. Expression of glutamate carboxypeptidase II in human brain. Neuroscience 2007, 144, 1361–1372. 10.1016/j.neuroscience.2006.10.022. PubMed DOI

El Fakiri M.; Geis N. M.; Ayada N.; Eder M.; Eder A. C. PSMA-targeting radiopharmaceuticals for prostate cancer therapy: recent developments and future perspectives. Cancers 2021, 13, 396710.3390/cancers13163967. PubMed DOI PMC

Kopka K.; Benesova M.; Barinka C.; Haberkorn U.; Babich J. Glu-ureido-based inhibitors of prostate-specific membrane antigen: lessons learned during the development of a novel class of low-molecular-weight theranostic radiotracers. J. Nucl. Med. 2017, 58, 17S–26S. 10.2967/jnumed.116.186775. PubMed DOI

Rais R.; Vavra J.; Tichy T.; Dash R. P.; Gadiano A. J.; Tenora L.; Monincova L.; Barinka C.; Alt J.; Zimmermann S. C.; Slusher C. E.; Wu Y.; Wozniak K.; Majer P.; Tsukamoto T.; Slusher B. S. Discovery of a para-acetoxy-benzyl ester prodrug of a hydroxamate-based glutamate carboxypeptidase II inhibitor as oral therapy for neuropathic pain. J. Med. Chem. 2017, 60, 7799–7809. 10.1021/acs.jmedchem.7b00825. PubMed DOI PMC

Blank B. R.; Alayoglu P.; Engen W.; Choi J. K.; Berkman C. E.; Anderson M. O. N-substituted glutamyl sulfonamides as inhibitors of glutamate carboxypeptidase II (GCP2). Chem. Biol. Drug Des. 2011, 77, 241–247. 10.1111/j.1747-0285.2011.01085.x. PubMed DOI PMC

Choy C. J.; Fulton M. D.; Davis A. L.; Hopkins M.; Choi J. K.; Anderson M. O.; Berkman C. E. Rationally designed sulfamides as glutamate carboxypeptidase II inhibitors. Chem. Biol. Drug Des. 2013, 82, 612–619. 10.1111/cbdd.12174. PubMed DOI

Matier W. L.; Comer W. T.; Deitchman D. Sulfamoyl azides - hydrolysis rates and hypotensive activity. J. Med. Chem. 1972, 15, 538–541. 10.1021/jm00275a025. PubMed DOI

Borghese A.; Antoine L.; Van Hoeck J. P.; Mockel A.; Merschaert A. Mild and safer preparative method for nonsymmetrical sulfamides via N-sulfamoyloxazolidinone derivatives: Electronic effects affect the transsulfamoylation reactivity. Org. Process Res. Dev 2006, 10, 770–775. 10.1021/op0600106. DOI

Barinka C.; Hlouchova K.; Rovenska M.; Majer P.; Dauter M.; Hin N.; Ko Y. S.; Tsukamoto T.; Slusher B. S.; Konvalinka J.; Lubkowski J. Structural basis of interactions between human glutamate carboxypeptidase II and its substrate analogs. J. Mol. Biol. 2008, 376, 1438–1450. 10.1016/j.jmb.2007.12.066. PubMed DOI PMC

Jackson P. F.; Tays K. L.; Maclin K. M.; Ko Y. S.; Li W.; Vitharana D.; Tsukamoto T.; Stoermer D.; Lu X. C.; Wozniak K.; Slusher B. S. Design and pharmacological activity of phosphinic acid based NAALADase inhibitors. J. Med. Chem. 2001, 44, 4170–4175. 10.1021/jm0001774. PubMed DOI

Liu T.; Toriyabe Y.; Kazak M.; Berkman C. E. Pseudoirreversible inhibition of prostate-specific membrane antigen by phosphoramidate peptidomimetics. Biochemistry 2008, 47, 12658–12660. 10.1021/bi801883v. PubMed DOI

Barinka C.; Byun Y.; Dusich C. L.; Banerjee S. R.; Chen Y.; Castanares M.; Kozikowski A. P.; Mease R. C.; Pomper M. G.; Lubkowski J. Interactions between human glutamate carboxypeptidase II and urea-based inhibitors: structural characterization. J. Med. Chem. 2008, 51, 7737–7743. 10.1021/jm800765e. PubMed DOI PMC

Klusák V.; Barinka C.; Plechanovova A.; Mlcochova P.; Konvalinka J.; Rulisek L.; Lubkowski J. Reaction mechanism of glutamate carboxypeptidase II revealed by mutagenesis, X-ray crystallography, and computational methods. Biochemistry 2009, 48, 4126–4138. 10.1021/bi900220s. PubMed DOI PMC

Mesters J. R.; Barinka C.; Li W.; Tsukamoto T.; Majer P.; Slusher B. S.; Konvalinka J.; Hilgenfeld R. Structure of glutamate carboxypeptidase II, a drug target in neuronal damage and prostate cancer. EMBO J. 2006, 25, 1375–1384. 10.1038/sj.emboj.7600969. PubMed DOI PMC

Williams C. J.; Headd J. J.; Moriarty N. W.; Prisant M. G.; Videau L. L.; Deis L. N.; Verma V.; Keedy D. A.; Hintze B. J.; Chen V. B.; Jain S.; Lewis S. M.; Arendall W. B. 3rd; Snoeyink J.; Adams P. D.; Lovell S. C.; Richardson J. S.; Richardson D. C. MolProbity: More and better reference data for improved all-atom structure validation. Protein Sci. 2018, 27, 293–315. 10.1002/pro.3330. PubMed DOI PMC

Chen A. Y.; Adamek R. N.; Dick B. L.; Credille C. V.; Morrison C. N.; Cohen S. M. Targeting metalloenzymes for therapeutic intervention. Chem. Rev. 2019, 119, 1323–1455. 10.1021/acs.chemrev.8b00201. PubMed DOI PMC

Jiang Z. S.; You Q. D.; Zhang X. J. Medicinal chemistry of metal chelating fragments in metalloenzyme active sites: A perspective. Eur. J. Med. Chem. 2019, 165, 172–197. 10.1016/j.ejmech.2019.01.018. PubMed DOI

Kanamori K.; Roberts J. D. Nitrogen-15 nuclear magnetic resonance study of benzenesulfonamide and cyanate binding to carbonic anhydrase. Biochemistry 1983, 22, 2658–2664. 10.1021/bi00280a011. PubMed DOI

Halland N.; Czech J.; Czechtizky W.; Evers A.; Follmann M.; Kohlmann M.; Schreuder H. A.; Kallus C. Sulfamide as zinc binding motif in small molecule inhibitors of activated thrombin activatable fibrinolysis inhibitor (TAFIa). J. Med. Chem. 2016, 59, 9567–9573. 10.1021/acs.jmedchem.6b01276. PubMed DOI

Winum J. Y.; Scozzafava A.; Montero J. L.; Supuran C. T. Therapeutic potential of sulfamides as enzyme inhibitors. Med. Res. Rev. 2006, 26, 767–792. 10.1002/med.20068. PubMed DOI

Hlouchova K.; Barinka C.; Konvalinka J.; Lubkowski J. Structural insight into the evolutionary and pharmacologic homology of glutamate carboxypeptidases II and III. FEBS J. 2009, 276, 4448–4462. 10.1111/j.1742-4658.2009.07152.x. PubMed DOI

Majer P.; Jackson P. F.; Delahanty G.; Grella B. S.; Ko Y. S.; Li W.; Liu Q.; Maclin K. M.; Polakova J.; Shaffer K. A.; Stoermer D.; Vitharana D.; Wang E. Y.; Zakrzewski A.; Rojas C.; Slusher B. S.; Wozniak K. M.; Burak E.; Limsakun T.; Tsukamoto T. Synthesis and biological evaluation of thiol-based inhibitors of glutamate carboxypeptidase II: discovery of an orally active GCP II inhibitor. J. Med. Chem. 2003, 46, 1989–1996. 10.1021/jm020515w. PubMed DOI

Stoermer D.; Liu Q.; Hall M. R.; Flanary J. M.; Thomas A. G.; Rojas C.; Slusher B. S.; Tsukamoto T. Synthesis and biological evaluation of hydroxamate-based inhibitors of glutamate carboxypeptidase II. Bioorg. Med. Chem. Lett. 2003, 13, 2097–2100. 10.1016/S0960-894X(03)00407-4. PubMed DOI

Neres J.; Labello N. P.; Somu R. V.; Boshoff H. I.; Wilson D. J.; Vannada J.; Chen L.; Barry C. E. 3rd; Bennett E. M.; Aldrich C. C. Inhibition of siderophore biosynthesis in Mycobacterium tuberculosis with nucleoside bisubstrate analogues: structure-activity relationships of the nucleobase domain of 5′-O-[N-(salicyl)sulfamoyl]adenosine. J. Med. Chem. 2008, 51, 5349–5370. 10.1021/jm800567v. PubMed DOI PMC

Somu R. V.; Boshoff H.; Qiao C. H.; Bennett E. M.; Barry C. E.; Aldrich C. C. Rationally designed nucleoside antibiotics that inhibit siderophore biosynthesis of Mycobacterium tuberculosis. J. Med. Chem. 2006, 49, 31–34. 10.1021/jm051060o. PubMed DOI

Di Fiore A.; Maresca A.; Alterio V.; Supuran C. T.; De Simone G. Carbonic anhydrase inhibitors: X-ray crystallographic studies for the binding of N-substituted benzenesulfonamides to human isoform II. Chem. Commun. 2011, 47, 11636–11638. 10.1039/c1cc14575d. PubMed DOI

Köhler K.; Hillebrecht A.; Wischeler J. S.; Innocenti A.; Heine A.; Supuran C. T.; Klebe G. Saccharin inhibits carbonic anhydrases: Possible explanation for its unpleasant metallic aftertaste. Angew. Chem., Int. Ed. 2007, 46, 7697–7699. 10.1002/anie.200701189. PubMed DOI

Nocentini A.; Vullo D.; Bartolucci G.; Supuran C. T. N-Nitrosulfonamides: A new chemotype for carbonic anhydrase inhibition. Bioorg. Med. Chem. 2016, 24, 3612–3617. 10.1016/j.bmc.2016.05.072. PubMed DOI

Novakova Z.; Cerny J.; Choy C. J.; Nedrow J. R.; Choi J. K.; Lubkowski J.; Berkman C. E.; Barinka C. Design of composite inhibitors targeting glutamate carboxypeptidase II: the importance of effector functionalities. FEBS J. 2016, 283, 130–143. 10.1111/febs.13557. PubMed DOI PMC

Mäder P.; Kattner L. Sulfoximines as rising stars in modern drug discovery? Current status and perspective on an emerging functional group in medicinal chemistry. J. Med. Chem. 2020, 63, 14243–14275. 10.1021/acs.jmedchem.0c00960. PubMed DOI

Barinka C.; Ptacek J.; Richter A.; Novakova Z.; Morath V.; Skerra A. Selection and characterization of Anticalins targeting human prostate-specific membrane antigen (PSMA). Protein Eng. Des. Sel. 2016, 29, 105–115. 10.1093/protein/gzv065. PubMed DOI

Zhang J.; Rakhimbekova A.; Duan X.; Yin Q.; Foss C. A.; Fan Y.; Xu Y.; Li X.; Cai X.; Kutil Z.; Wang P.; Yang Z.; Zhang N.; Pomper M. G.; Wang Y.; Barinka C.; Yang X. A prostate-specific membrane antigen activated molecular rotor for real-time fluorescence imaging. Nat. Commun. 2021, 12, 546010.1038/s41467-021-25746-6. PubMed DOI PMC

Battye T. G. G.; Kontogiannis L.; Johnson O.; Powell H. R.; Leslie A. G. W. iMOSFLM: a new graphical interface for diffraction-image processing with MOSFLM. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2011, 67, 271–281. 10.1107/S0907444910048675. PubMed DOI PMC

Kabsch W. Xds. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2010, 66, 125–132. 10.1107/S0907444909047337. PubMed DOI PMC

Sparta K. M.; Krug M.; Heinemann U.; Mueller U.; Weiss M. S. Xdsapp2.0. J. Appl. Crystallogr. 2016, 49, 1085–1092. 10.1107/S1600576716004416. DOI

Barinka C.; Starkova J.; Konvalinka J.; Lubkowski J. A high-resolution structure of ligand-free human glutamate carboxypeptidase II. Acta Crystallogr., Sect. F: Struct. Biol. Cryst. Commun. 2007, 63, 150–153. 10.1107/S174430910700379X. PubMed DOI PMC

Schüttelkopf A. W.; van Aalten D. M. F. PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2004, 60, 1355–1363. 10.1107/S0907444904011679. PubMed DOI

Emsley P.; Lohkamp B.; Scott W. G.; Cowtan K. Features and development of Coot. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2010, 66, 486–501. 10.1107/S0907444910007493. PubMed DOI PMC

Murshudov G. N.; Skubak P.; Lebedev A. A.; Pannu N. S.; Steiner R. A.; Nicholls R. A.; Winn M. D.; Long F.; Vagin A. A. REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr., Sect. D: Biol. Crystallogr. 2011, 67, 355–367. 10.1107/S0907444911001314. PubMed DOI PMC

Gore S.; Garcia E. S.; Hendrickx P. M. S.; Gutmanas A.; Westbrook J. D.; Yang H. W.; Feng Z. K.; Baskaran K.; Berrisford J. M.; Hudson B. P.; Ikegawa Y.; Kobayashi N.; Lawson C. L.; Mading S.; Mak L.; Mukhopadhyay A.; Oldfield T. J.; Patwardhan A.; Peisach E.; Sahni G.; Sekharan M. R.; Sen S.; Shao C. H.; Smart O. S.; Ulrich E. L.; Yamashita R.; Quesada M.; Young J. Y.; Nakamura H.; Markley J. L.; Berman H. M.; Burley S. K.; Velankar S.; Kleywegt G. J. Validation of structures in the Protein Data Bank. Structure 2017, 25, 1916–1927. 10.1016/j.str.2017.10.009. PubMed DOI PMC

Berman H.; Henrick K.; Nakamura H. Announcing the worldwide Protein Data Bank. Nat. Struct. Mol. Biol. 2003, 10, 980.10.1038/nsb1203-980. PubMed DOI

Eichkorn K.; Treutler O.; Ohm H.; Haser M.; Ahlrichs R. Auxiliary basis-sets to approximate coulomb potentials. Chem. Phys. Lett. 1995, 240, 283–289. 10.1016/0009-2614(95)00621-A. DOI

Grimme S.; Antony J.; Ehrlich S.; Krieg H. A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. J. Chem. Phys. 2010, 132, 15410410.1063/1.3382344. PubMed DOI

Klamt A.; Schuurmann G. Cosmo - a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient. J. Chem. Soc., Perkin Trans. 2 1993, 799–805. 10.1039/P29930000799. DOI

Balasubramani S. G.; Chen G. P.; Coriani S.; Diedenhofen M.; Frank M. S.; Franzke Y. J.; Furche F.; Grotjahn R.; Harding M. E.; Hattig C.; Hellweg A.; Helmich-Paris B.; Holzer C.; Huniar U.; Kaupp M.; Khah A. M.; Khani S. K.; Muller T.; Mack F.; Nguyen B. D.; Parker S. M.; Perlt E.; Rappoport D.; Reiter K.; Roy S.; Ruckert M.; Schmitz G.; Sierka M.; Tapavicza E.; Tew D. P.; van Wullen C.; Voora V. K.; Weigend F.; Wodynski A.; Yu J. M. TURBOMOLE: Modular program suite for ab initio quantum-chemical and condensed-matter simulations. J. Chem. Phys. 2020, 152, 18410710.1063/5.0004635. PubMed DOI PMC

Contreras-García J.; Johnson E. R.; Keinan S.; Chaudret R.; Piquemal J. P.; Beratan D. N.; Yang W. T. NCIPLOT: A program for plotting noncovalent interaction regions. J. Chem. Theory Comput 2011, 7, 625–632. 10.1021/ct100641a. PubMed DOI PMC

Johnson E. R.; Keinan S.; Mori-Sanchez P.; Contreras-Garcia J.; Cohen A. J.; Yang W. T. Revealing noncovalent interactions. J. Am. Chem. Soc. 2010, 132, 6498–6506. 10.1021/ja100936w. PubMed DOI PMC