Carbon- versus sulphur-based zinc binding groups for carbonic anhydrase inhibitors?

Figures & data

Figure 1. Clinically used sulphonamides/sulphamates with CA inhibitory action (A–S) and SLC-0111 (T) in phase II clinical trials as an antitumour/antimetastatic agent^18,19.

Figure 2. General scheme showing CAIs belonging to the zinc binders class (sulphonamides, sulphamates, sulphamides, carboxylates, hydroxamates, phosphonates, borols, etc.) in interaction with an α-CA^1,3. The ZBG is coordinated to the metal ion and makes hydrogen bonds with the gate keeper residues Thr199–Glu106, conserved in all α-CAs^1–3. The scaffold of the inhibitor may occupy either the hydrophylic or hydrophobic (or both) halves of the active site¹², whereas the tails are orientated towards the exit of the cavity where the most variable amino acid residues among the different mammalian CAs are located^26–28. The interactions between the scaffold/tail with the enzyme are not shown.

Table 1. Inhibition of CA isozymes I–XV (of human = h, and murine = m origin) with compounds 1–10.

		KI (μM)^a^,^b
No.	X	hCA I	hCA II	hCA III	hCA IV	hCA VA	hCA VB	hCA VI	hCA VII	hCA IX^c	hCA XII^c	mCA XIII	hCA XIV	mCA XV
1	OH	8.65	9.30	6.63	9.10	80.9	79.8	8.80	7.93	9.55	6.45	8.72	8.79	8.03
2	NH2	0.086	0.101	2.26	7.96	1.68	8.82	0.097	0.095	0.097	0.090	0.100	0.092	0.100
3	NHNH2	9.8	5.31	6.28	78.4	7.75	95.2	74.4	8.56	51.7	2.42	5.96	3.81	5.16
4	NHOH	2.73	5.47	4.42	24.6	5.28	67.9	86.2	8.73	60.3	1.53	4.97	1.66	7.17
5	NHOMe	>1000	8.96	5.72	39.5	6.70	10.7	27.0	9.56	64.3	8.32	6.21	1.57	7.84
6	OH	730	30.1	35.7	434	7.12	9.60	91.6	92.2	66.5	20.4	44.8	0.98	72.8
7	NH2	324	93.2	35.7	381	46.8	83.1	82.6	76.8	3.67	11.2	45.1	27.0	85.5
8	NHNH2	91.2	231	40.2	335	59.3	75.9	63.5	76.7	48.4	45.0	44.4	0.99	94.2
9	NHOH	83.1	179	44.8	84.7	67.4	53.6	78.1	70.7	45.9	9.51	23.0	0.94	79.9
10	NHOMe	72.5	341	37.3	111	89.1	57.3	89.9	72.2	57.5	28.5	63.3	10.0	106

^aErrors in the range of ±5% of the reported data from three different assays.

^bh = human; m = murine isozyme.

^cCatalytic domain.

Figure 3. Superimposition of the hCA II – 2 adduct (blue, PDB code 2WEJ⁴²) with the hCA II – 4 adduct (violet, PDB code 3T5U³⁷), the hCA II – 5 adduct (silver, PDB code 3T5Z³⁷) and the hCA II – hydroxamate 9 adduct (green, PDB code 4FL7³⁸).

Table 2. hCA I, II, IX, and XII inhibition data with compounds 2, 2a, 2b, 7, and 7a.

	KI (µM)^c
Compound	hCA I	hCA II	hCA IX	hCA XII
2	0.086	0.101	0.097	0.090
2a	0.002^a	0.0013^a	0.063^a	0.008
2b	0.013^b	0.012^b	0.071	0.014
7	324	93.2	3.67	11.2
7a	720	110	10.1	2.81

^aFrom ref.^43a

^bFrom ref.^43b

^cErrors in the range of ±5% of the reported data from three different assays.

(a) Monti SM, Supuran CT, De Simone G. Anticancer carbonic anhydrase inhibitors: a patent review (2008–2013). Expert Opin Ther Pat 2013;2:737–49. (b) Lou Y, 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;7:3364–76. (c) Pettersen EO, Ebbesen P, Gieling RG, et al. Targeting tumour hypoxia to prevent cancer metastasis. From biology, biosensing and technology to drug development: the METOXIA Consortium. J Enzyme Inhib Med Chem 2015;30:689–721.

 Web of Science ®Google Scholar

(a) Supuran CT. Carbonic anhydrase inhibition and the management of hypoxic tumors. Metabolites 2017;7:E48. (b) Federici C, Lugini L, Marino ML, et al. Lansoprazole and carbonic anhydrase IX inhibitors sinergize against human melanoma cells. J Enzyme Inhib Med Chem 2016;31(Suppl.1):119–25. (c) Kusuzaki K, Matsubara T, Murata H, et al. Natural extracellular nanovesicles and photodynamic molecules: is there a future for drug delivery? J Enzyme Inhib Med Chem 2017;3:908–16. (d) Bragagni M, Carta F, Osman SM, et al. Synthesis of an acridine orange sulfonamide derivative with potent carbonic anhydrase IX inhibitory action. J Enzyme Inhib Med Chem 2017;32:701–6.

 PubMed Web of Science ®Google Scholar

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

 PubMed Web of Science ®Google Scholar

(a) Supuran CT. How many carbonic anhydrase inhibition mechanisms exist? J Enzyme Inhib Med Chem 2016;31:345–60. (b) Supuran CT. Advances in structure-based drug discovery of carbonic anhydrase inhibitors. Expert Opin Drug Discov 2017;12:61–88.

 PubMed Web of Science ®Google Scholar

(a) Alterio V, Di Fiore A, D’Ambrosio K, et al. Multiple binding modes of inhibitors to carbonic anhydrases: how to design specific drugs targeting 15 different isoforms? Chem Rev 2012;1:4421–68. (b) De Simone G, Alterio V, Supuran CT. Exploiting the hydrophobic and hydrophilic binding sites for designing carbonic anhydrase inhibitors. Expert Opin Drug Discov 2013;8:793–810. (c) De Simone G, Langella E, Esposito D, et al. Insights into the binding mode of sulphamates and sulphamides to hCA II: crystallographic studies and binding free energy calculations. J Enzyme Inhib Med Chem 2017;32:1002–11. (d) Di Fiore A, De Simone G, Alterio V, et al. The anticonvulsant sulfamide JNJ-26990990 and its S,S-dioxide analog strongly inhibit carbonic anhydrases: solution and X-ray crystallographic studies. Org Biomol Chem 2016;14:4853–8.

 Web of Science ®Google Scholar

Scott AD, Phillips C, Alex A, et al. Thermodynamic optimisation in drug discovery: a case study using carbonic anhydrase inhibitors. ChemMedChem 2009;4:1985–9.

 PubMed Web of Science ®Google Scholar

Di Fiore A, Maresca A, Alterio V, et al. Carbonic anhydrase inhibitors: X-ray crystallographic studies for the binding of N-substituted benzenesulfonamides to human isoform II. Chem Commun (Camb) 2011;47:11636–8.

 PubMed Web of Science ®Google Scholar

Di Fiore A, Maresca A, Supuran CT, De Simone G. Hydroxamate represents a versatile zinc binding group for the development of new carbonic anhydrase inhibitors. Chem Commun (Camb) 2012;48:8838–40.

 PubMed Web of Science ®Google Scholar

(a) Winum JY, Vullo D, Casini A, et al. Carbonic anhydrase inhibitors. Inhibition of cytosolic isozymes I and II and transmembrane, tumor-associated isozyme IX with sulfamates including EMATE also acting as steroid sulfatase inhibitors. J Med Chem 2003;4:2197–204. (b) Casini A, Winum JY, Montero JL, et al. Carbonic anhydrase inhibitors: inhibition of cytosolic isozymes I and II with sulfamide derivatives. Bioorg Med Chem Lett 2003;1:837–40. (c) Winum JY, Temperini C, El Cheikh K, et al. 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;4:7024–31. (d) Casini A, Antel J, Abbate F, et al. Carbonic anhydrase inhibitors: SAR and X-ray crystallographic study for the interaction of sugar sulfamates/sulfamides with isozymes I, II and IV. Bioorg Med Chem Lett 2003;13:841–5.

 Web of Science ®Google Scholar