Benzylaminoethyureido-Tailed Benzenesulfonamides: Design, Synthesis, Kinetic and X-ray Investigations on Human Carbonic Anhydrases.

A drug design strategy of carbonic anhydrase inhibitors (CAIs) belonging to sulfonamides incorporating ureidoethylaminobenzyl tails is presented. A variety of substitution patterns on the ring and the tails, located on para- or meta- positions with respect to the sulfonamide warheads were incorporated in the new compounds. Inhibition of human carbonic anhydrases (hCA) isoforms I, II, IX and XII, involving various pathologies, was assessed with the new compounds. Selective inhibitory profile towards hCA II was observed, the most active compounds being low nM inhibitors (KIs of 2.8-9.2 nM, respectively). Extensive X-ray crystallographic analysis of several sulfonamides in an adduct with hCA I allowed an in-depth understanding of their binding mode and to lay a detailed structure-activity relationship.

1. Introduction

Carbonic anhydrases (CA, EC 4.2.1.1) are a ubiquitous superfamily of metalloenzymes present in all living organisms. So far fifteen carbonic anhydrase isozymes have been characterized in humans and they all mainly differ for their catalytic activities, subcellular localizations and tissue distributions [1,2,3,4]. The abnormal expression of one or multiple CA isoforms in humans usually is associated to various pathologies [4,5,6]. Therefore the use of proper CA modulators (i.e., traditionally CA inhibitors, CAIs) represented the winning strategy for the management of various diseases such as glaucoma, altitude sickness, epilepsy and obesity [4,5,6]. A contribute of this kind is the recently reported sulfonamide CAI, named SLC-0111, which entered Phase II clinical trials in association with Gemcitabine for the treatment of metastatic pancreatic ductal cancer in patients overexpressing the CA IX isoform [7,8,9,10]. New evidences in the field strongly support the involvement of CA isoforms in other pathologies, such as neuropathic pain, arthritis, cerebral ischemia and thus pave the way for the use of CAIs in their management [11,12,13,14].

CAs structural architectures have been intensively studied mainly by the use of X-ray crystallographic experiments [15]. They all report quite similar features such as the conical shaped cleft, which bears the catalytic metal ion at the bottom end [15]. As for the human expressed CAs, which are considered in this manuscript, the catalytically active isoform all share the same enzymatic cluster formed by a Zn (II) ion tetrahedrally coordinated to three His-residues and a hydroxide ion/water molecule [16,17,18,19,20].

All clinically used CAIs, which mainly belong to the sulfonamides or sulfamate classes, do present modest and general undesired side-effects after administration, which usually are ascribed to the non-selective interference with CAs other than the desired one/ones [4]. In this contest the “tail approach” proved to be the most successful strategy within the field of Medicinal Chemistry on targeting specific CA isoforms. Such an approach makes use of the interactions occurring between the chemical moieties inserted in the CAIs tails and the amino acid residues located at the rim of the enzymatic cavity, which have the lowest homology sequences among the CA isoforms of the α-class [17,21,22,23,24,25,26,27]. An important structural consideration is the role of the linker connecting the tail and the warhead sections within CAI molecules in order to make use of the tail strategy. The ureidic moiety was demonstrated to be particularly suitable as it allows the entire molecule to assume the best conformation when allocated within the enzyme cavity and at the same time to contribute to the stabilization of the enzyme–inhibitor complex by means of hydrogen bonds [8,9,10,28,29,30]. Subsequently, various CAI moieties bearing ureido linkers were reported [28,29,30,31,32,33,34]. Noteworthy are the N’phenyl-N-hydroxyureas, the N-aryl-N′-ureido-O-sulfamates [14,35,36] in which the ureidic tether was merged into the CAI moiety or alternatively molecules having the ureido moiety being part of tail section such as the GABA or the N-substituted piperazinyl moiety [31,32,37].

In this study we further extended our research by means of designing and synthesizing sulfonamide based CAIs possessing the benzylaminoethylureido-tails, not reported yet, and we investigated their inhibition profiles in vitro against the physiologically dominant cytosolic hCA I and II and the tumor associated isoforms hCA IX and XII with the aim to set the basis for a preliminary structure-activity relationship (SAR) worthy of future development.

2. Results and Discussion

2.1. Chemistry

Our drug design strategy was based on a multistep synthesis, based on the methodology previously reported for obtaining 4-N-substituted piperazinyl-ureido benzene sulfonamides [32]. Sulfanilamide (SA, 1a) and metanilamide (MA, 1b) were reacted with phenylchloroformate in mild conditions to afford the phenylcarbamate derivatives 2a–b in high yields and purities, in agreement with previous literature reports [32]. 2a–b were coupled with N-boc-ethylene diamine 3 to afford Boc-aminoethylureidobenzene sulfonamide derivatives 4a–b in high yields. Then Boc-protecting groups were removed by trifluoroacetic acid to obtain the key intermediates possessing terminal primary amino groups 5a–b. The final step involved reaction of 5a–b with a series of commercially available benzaldehydes 6–15 to form the corresponding Schiff bases, thereafter reduced in situ with sodium borohydride to afford the desired products 26–35 (Scheme 1).

Scheme 1

General synthetic scheme for the synthesis of sulfonamides 16-35.

2.2. Carbonic Anhydrase Inhibition

The inhibitory activity of the novel sulfonamides 16-35 on four physiological relevant human (h) CA isoforms; hCA I, II (cytosolic isoforms) and hCA IX and XII (tumor associated membrane bound) reported here was obtained by means of the stopped flow CO2 hydrase assay [38]. Inhibition constants of reported compounds and reference drug acetazolamide (AAZ) are shown in Table 1.

Table 1

Inhibition data of human CA isoforms hCA I, II, IX and IXI with 16-35 reported here and the standard sulfonamide inhibitor acetazolamide (AAZ) by a stopped flow CO2 hydrase assay [38].

KI (nM) *
Compound	R	hCA I	hCA II	hCA IX	hCA XII
16		552.4	350.1	1350	54.5
17	4-Cl	582.1	126.9	458.3	32
18	4-F	724.7	9.2	30.1	53.2
19	2-F	24.6	3.9	20.3	58.3
20	4-OH	781	267	974.2	75.8
21	4-NO2	526.9	96.1	317.1	77.5
22	4-Me2N	1506	73.2	342.8	264.1
23	4-NO2, 2-MeO	788.4	82.4	290.6	53.6
24	4-Br, 2-OH	138.4	5.3	115.6	97.6
25	4-C6H5	781.7	63.2	1150	63.7
26	-	928.3	76.3	>10,000	772.1
27	4-Cl	702.4	36.9	3378	228.1
28	4-F	867.5	53.8	4212	71.3
29	2-F	728	33.4	>10,000	478.8
30	4-OH	6250	166.4	3511	317.1
31	4-NO2	5851	168.4	2325	60.7
32	4-Me2N	8906	564.9	1199	78
33	4-NO2, 2-MeO	>10,000	90.2	2606	53.1
34	4-Br, 2-OH	653.8	2.8	1915	7.2
35	4-C6H5	>10,000	456.3	>10,000	688
AAZ		250	12.1	25.8	5.7

* Mean from 3 different assays, by a stopped flow technique (errors were in the range of ± 5%–10% of the reported values).

The following structure activity relationship (SAR) can be observed from the data reported in Table 1.

hCA I was inhibited by all these sulfonamides with a variety of potencies. The most potent inhibitor was the 4-F substituted SA derivative 18 with a KI of 24.6 nM. Followed by 4-Br, the 2-OH substituted SA derivative 24 showed medium potency with a KI of 138.4 nM. The remaining SA derivatives 16–18, 20–23 and 25 were weak inhibitors with KIs spanning between 526.9 and 1506 nM. The MA derivatives of the series 26–35 were poor to ineffective inhibitors of the cytosolic widespread hCA I. 26–32 and 34 were weak inhibitors with KIs spanning between 653.8 and 6250 nM. 33 and 35 showed ineffective inhibition of hCA I whereas clinically used drug AAZ was medium potency inhibitor with a KI of 250 nM (Table 1).

The series of sulfonamides 16–35 showed nanomolar range inhibitory potencies on the physiologically dominant cytosolic isoform hCA II with KIs spanning between 2.8 and 564.9 nM. The compounds 18–19, 24–25, 27–29 and 34 were effective inhibitors with KIs in the range of 2.8–63 nM. The most effective inhibitor of the series was 4-Br, 2-OH substituted MA derivative 34 with a KI of 2.8 nM, also its SA derivative 24 was the third most effective inhibitor reported here with a KI of 5.3 nM. 2-F derivative of SA 19 was the second most potent inhibitor with a KI of 3.9 nM and its MA derivative 29 inhibited this isoform effectively with a KI of 53.8 (8.6-fold less potent). When the fluorine substitution pattern of 19 shifted from the ortho- to para- position to afford 18 resulted as a slight reduction of the inhibition constant (0.4-fold) to 9.2 nM. MA derivative 28 was a less effective inhibitor compared to its SA counterpart 18 with a KI of 53.8 nM (5.8-fold less potent). The last high potency inhibitor of this isoform was 4-Cl substituted MA derivative 27 with a KI of 36.9 nM whereas its SA warhead possessing derivative 17 showed medium potency with 3.4-fold decrease compared to 27 with a KI of 126.9 nM. SA derivatives 21–23, 25 and MA derivatives 26, 33 were medium potency inhibitors with KIs spanning between 63.2–96.1 nM and 76.3–90.2 nM, respectively. The remaining SA derivatives 16, 20, and MA derivatives 30–32, 35 were weak to ineffective inhibitors of hCA II with KIs of 267–350 nM and 166.4–564.9 nM, respectively.

The tumor associated transmembrane isoform hCA IX was effectively inhibited only by two SA derivatives with fluoro substitutions, 18 in–para and 19 in–ortho positions with KIs of 30.1 and 20.3 nM, respectively. Their inhibition levels are in comparison with clinically used drug AAZ (KI 25.8 nM). Compounds 17 and 21–24 were medium potency inhibitors with KIs spanning between 115.6 and 458.3 nM. The remaining ones 16, 20, 25, 27, 28 and 30–34 were low micromolar KI values obtained and comprised between 0.97 and 4.21 µM. The remaining of the series 26, 29 and 35 were not inhibitors of the hCA IX.

The second extracellular tumor associated isoform hCA XII was inhibited by 16-35 more effectively (except 18 and 19) compared to the other tumor associated isoform hCA IX investigated here. The 4-bromo-2-hydroxyphenyl substituted derivative 35 was the most potent inhibitor of this isoform with a KI of 7.2 nM. 35 showed a comparable KI with AAZ (KI of 5.7 nM). Compounds 16-21, 23–25, 28, 31 and 32–33 were potent inhibitors with KIs between 32 and 97.6 nM. Compounds 22, 27 and 30 showed medium potency inhibition of this isoform with KIs spanning between 228.1 and 317.1 nM whereas compounds 26, 29 and 35 showed lower inhibitory effects with inhibition constants between 478.8 and 772.1 nM. The comparison of two subset reported here showed us the derivatives of SA were more potent inhibitors versus MA derivatives. Whereas 4-nitro substituted 31, 4-dimethylamino substituted 32 and 4-bromo-2-hydroxy substituted 34 were more potent compare to their SA derivatives (1.3, 3.4 and 13.6-folds, respectively). 4-nitro-2-methoxy substituted derivatives 23 and 33 showed very similar inhibition activities on this isoform with KIs of 53.6 and 53.1 nM, respectively.

Overall, the series showed selective inhibition of the cytosolic isoform hCA II and the membrane bound isoform hCA XII over the hCA I and the tumor associated hCA IX. In particular compounds 18, 21, 23–25, 28, 33 and 34 were the most representative of such a kinetic profile.

2.3. Structure of hCA I/Inhibitor Complexes

The crystal structure of six different inhibitors in the complex with hCA I was determined at a resolution ranging from 1.37 to 1.66 Å. Two monomers virtually equivalent (the r.m.s.d. between monomers A and B ranges from 0.197 to 0.25 Å) were present in the asymmetric unit. In all structures, the polypeptide chain was clearly visible from residue 4 to 260 in both monomers. The r.m.s.d. between the monomers A and B of our structure at the highest resolution and that of the apo enzyme in a different crystal form was 0.35 Å and 0.32 Å, respectively, indicating that the binding of the ligand did not induce any significant conformational differences in the protein.

In all complexes the inhibitor was bound in a similar way, with the nitrogen of the benzenesulfonamide group interacting with the Zn2+ ion present in the active site. The coordination of Zn2+ ion is tetrahedral, with three corners of the tetrahedron corresponding to three histidines of the enzyme (His 94, 96 and 119), and the fourth corner to the N atom of sulfonamide (Figure 1). In addition, an oxygen atom of sulfonamide forms a H-bond with the main-chain nitrogen of Thr199. In all cases, the benzenesulfonamide group was clearly visible in the electron density map and was oriented in the same way in all six complexes, whilst significant differences were observed in the rest of the inhibitor molecule. In particular, the amino-ethyl-ureido chain was less clearly visible in some of the complexes, indicating a flexible conformation in the crystal.

Figure 1

Ribbon drawing of the monomer of hCA I (cyan) present in the asymmetric unit of the P212121 space group, with compound 29 (PDB code: 6Y00) in the active site. The Zn2+ ion is shown as a red sphere.

In the 3-benzene substituted compounds, in the three structures determined that the ligand bound assumed a bent conformation (Figure 2A) and the benzylamino group was accommodated in the hydrophobic portion of hCAI catalytic site. In 34 (Figure 2B) structure, N11 and N14 formed a potential H-bond with Ne2 of His 200 and with carbonyl oxygen of Pro 201. In compound 26, the carbonyl oxygen formed a H-bond with a side chain nitrogen of Gln 92, whilst in compound 29 the amino-ethyl-ureido chain did not form any specific H-bond interaction with the protein.

Figure 2

(A) Conformations of compounds 26 (magenta, PDB accession code 6XZX), 29 (green, PDB accession code 6XZY) and 34 (cyan, PDB accession code 6Y00) in the active site of monomer B. The conformation and the interactions with the protein are essentially the same for monomer A. Residues surrounding the ligand are shown. (B) The active site of compound 34, with interactions explicitly shown. In both figures the Zn2+ ion is depicted as a red sphere.

In the 4-benzene substituted inhibitors, the geometry of the binding of the benzenesulfonamide group and the interactions with the enzyme were identical to those described above. On the contrary, compound 24 was present in the active site in a nearly extended conformation (Figure 3A). Since the complexes were obtained by soaking the compound inside a solution containing the crystals, in the complex containing compound 24 only one ligand was present in the active site of the two monomers, since, owing to the crystal packing, the compound protruded from the active site in the solvent and partially obstructed the binding of the same compound in the active site of the second monomer. Consequently, the occupancy of each of the two ligands in this case was close to 0.50.

Figure 3

Cartoon view (left) of the two monomers of hCA I with compounds 18 (orange, PDB access code 6XZS), 19 (green, PDB access code 6XZE) and 24 (yellow, PDB access code 6XZO) in the active sites of the enzyme. Compounds 18, 19 and 24 are present in two different conformations in the two active sites of the enzyme (the two sites differ only for the environment in the crystal, but they are conformationally identical, and so they are in solution). In site A the compound is present in an extended conformation, (better illustrated in the right side), whilst in site B the same conformation is not possible owing to the steric hindrance generated by the presence of the same compound in site A, and the compounds folds in a way similar to compounds 26, 29 and 34 (as in A, the right side of B shows the folded conformations. See text for more details).

In compound 18 and 19 complexes, the ligand present in molecule B of the crystal assumed a bent conformation, similarly to the 3-substituted ones, whilst they presented a more extended conformation in site A (Figure 3A,B). In this case the nearly extended conformation did not prevent the binding of the same inhibitor to the other site, but probably in this second site the ligand, to avoid clashes with the ligand bound in site B of a symmetry-related molecule, must assume a bent conformation.

In all cases, the amino-ethyl-ureido chain of compounds 4-substitued did not form any direct H-bond or hydrophilic interaction with the enzyme, and eventually some were indirect mediated by water molecules.

3. Conclusions

Herein we reported a series of benzenesulfonamides incorporating ureido moieties. Compounds 16-35 were assayed in vitro as inhibitors of four hCA isoforms of pharmacological relevance, the cytosolic isoforms hCA I, II and the tumor associated transmembrane isoform hCA IX and XII. Interestingly the in vitro results showed a preferential inhibition of the cytosolic isoform hCA II and most potent inhibitors of this isoform were 18, 19, 24 and 34 with low nanomolar inhibition constants. We determined the binding modes of compounds 18, 19, 24, 26, 29 and 34 within adduct of hCA I isoform by means of X-ray crystallography techniques

4. Experimental Protocols

4.1. Chemistry

All the reagents and solvents used in this study were purchased from Sigma-Aldrich. Moisture sensitive reactions were performed under nitrogen flow using anhydrous solvents and dried glassware. Nuclear magnetic resonance (1H-NMR, 13C-NMR and 19F-NMR) spectra were recorded on a Bruker Avance III 400 MHZ spectrometer using deuterated DMSO as a solvent and TMS (tetramethylsaline) as an internal standard. Chemical shifts (δ) are reported in parts per million (ppm) scale and coupling constants (J values) are given in Hertz (Hz). Splitting patterns are designated by: s (singlet); d (doublet); t (triplet); q (quartet); m (multiplet); brs (broad singlet) and dd (doublet of doublets). The exchangeable protons (NH and OH) were confirmed by D2O. Analytical thin-layer chromatography (TLC) was carried out on Merck Silica gel F-254 plates. Purification was carried out through crystallization and flash chromatography. Methanol/Dicholoromethane were used as a mobile phase (eluent) and Merck Silica gel 60 (230-400 mesh ASTM) as a stationary phase during flash chromatography. The high-resolution mass spectrometry (HRMS) analysis was performed with a Thermo Finnigan LTQ Orbitrap mass spectrometer coupled with an electrospray ionization source (ESI). The analysis was carried out in positive ion mode [M+H]+, and it was used a proper dwell time acquisition to achieve 60,000 units of resolution at full width at half maximum (fwhm). Melting points were determined in open capillary tubes with a Gallenkamp MPD350.BM3.5 apparatus and are uncorrected.

1. General Procedure for the Synthesis of Compound 5a-b

2. Synthesis of intermediates 4a–b. A Solution of 2a–b (2.5 g, 1.0 eq) was treated with tert-butyl (2-aminoethyl) carbamate (1.0 eq) in acetonitrile (10 mL) and refluxed until the consumption of the starting materials (TLC monitoring). The reaction mixture was cooled to room temperature (r.t.) rt. Obtained precipitate was filtered-off, washed with Et2O (3 × 5 mL) and dried under vacuum to afford 4a–b as a white solid.

3. tert-butyl (2-(3-(4-sulfamoylphenyl)ureido)ethyl)carbamate (4a): white solid; yield 80%; mp 173–174 °C; δH (400 MHz, DMSO-d6) 1.42 (9H, s), 3.05 (2H, q, J 5.8), 3.17 (2H, q, J 5.8), 6.33 (1H, t, J 5.8), 6.89 (2H, t, J 5.8), 7.17 (2H, s, exchange with D2O, SO2NH2), 7.56 (2H, d, J 8.8) 7.70 (2H, d, J 8.8), 8.97 (1H, s, exchange with D2O, NH); δC (100 MHz, DMSO-d6) 29.1, 40.0, 41.1, 78.5, 117.7, 127.6, 136.9, 144.5, 155.8, 156.6.

4. tert-butyl (2-(3-(3-sulfamoylphenyl)ureido)ethyl)carbamate (4b): white solid; yield 79%; mp 160–161 °C; TLC Rf 0.1 (EtOAc/n-hexane 70% v/v); δH (400 MHz, DMSO-d6) 1.42 (9H, s), 3.05 (2H, q, J 5.8), 3.17 (2H, q, J 5.8), 6.25 (1H, t, J 5.8), 6.89 (1H, t, J 5.8), 7.31 (2H, s, exchange with D2O, SO2NH2), 7.37 (1H, d, J 7.8), 7.43 (1H, t, 7.8), 7.55 (1H, d, J 7.8), 8.01 (1H, d, J 7.8), 8.90 (1H, s, exchange with D2O, NH); δC (100 MHz, DMSO-d6) 29.1, 41.2, 78.6, 115.4, 118.9, 121.3, 130.1, 141.9, 145.5, 155.9, 156.6.

5. Synthesis of intermediates 5a–b. A solution of 4a–b (1 eq) in DCM was treated with fuming trifluoroacetic acid (6 eq), the reaction continued until the consumption of the starting material (TLC monitoring). Then the solvents were removed under reduced pressure to obtain a residue that was triturated from Et2O to obtain intermediates as 5a–b as white solid.

6. 2-(3-(4-sulfamoylphenyl)ureido)ethan-1-aminium 2,2,2-trifluoroacetate (5a): white solid; yield 74%; mp 165–166 °C; δH (400 MHz, DMSO-d6) 2.95 (2H, m), 3.37 (2H, m), 6.94 (1H, t, J 5.8), 7.19 (2H, s, exchange with D2O, SO2NH2), 7.60 (2H, d, J 8.8) 7.71 (2H, d, J 8.8), 8.88 (3H, s, exchange with D2O, NH3), 9.45 (1H, s, exchange with D2O, NH); δC (100 MHz, DMSO-d6) 38.1, 40.2, 117.5, 127.6, 137.2, 144.5, 156.3; δF (376 MHz, DMSO-d6) -73.8.

7. 2-(3-(3-sulfamoylphenyl)ureido)ethan-1-aminium 2,2,2-trifluoroacetate (5b): white solid; yield 69%; mp 158–159 °C; δH (400 MHz, DMSO-d6) 2.96 (2H, m), 3.37 (2H, m), 6.87 (1H, t, J 6.8, exchange with D2O, NH), 7.33 (2H, s, exchange with D2O, SO2NH2), 7.39-7.47 (2H, m), 7.57 (1H, d, J 8), 7.88 (3H, s, exchange with D2O, NH3), 8.08 (1H, m), 9.36 (1H, s, exchange with D2O, NH); δC (100 MHz, DMSO-d6) 38.2, 40.2, 115.6, 119.2, 121.6, 130.2, 141.8, 145.5, 156.5; δF (376 MHz, DMSO-d6) -73.6.

8. General Procedure for the Synthesis of compound 16-35. A solution of 5a-b (0.2 g, 1.0 eq) in dry MeOH was treated with Et3N (1 eq) then the reaction mixture was cooled to 0 °C and benzaldehyde 6-15 (1 eq) was added. The reaction was continued for 2 h at 0 °C, followed by addition of sodium borohydride (4 eq) and reaction continued until the consumption of starting materials (TLC monitoring). The solvents were removed under reduced pressure and the title compounds were either obtained from filtration of the precipitates formed after addition of 5-10 mL of ice-cold water, followed by washing with Et2O (3 × 5 mL) (21, 26, 33) or extracted from ethyl acetate. In the latter the combined organic layers were washed with H2O (3 × 20 mL), dried over Na2SO4, filtered and concentrated in vacuum to give a residue that was crystallized from EtOH-Water (1:1) (17, 22, 25, 34) or purified by silica gel column chromatography by eluting with 10%MeOH in DCM as the mobile phase (16, 18–20, 23–24, 27–30, 35).

9. 4-(3-(2-(benzylamino)ethyl)ureido) benzenesulfonamide (16): white solid; yield 41%; mp 176–177 °C; TLC Rf 0.12 (MeOH/DCM 10% v/v); δH (400 MHz, DMSO-d6) 2.22 (1H, t, J 5.8, exchange with D2O, NH), 2.63 (2H, q, J 5.8), 3.22 (2H, q, J 5.8), 3.74 (2H, d, J 5.8), 6.49 (1H, brt, J 5.8, exchange with D2O, NH), 7.15 (2H, s, exchange with D2O, SO2NH2), 7.25 (1H, t, J 7.2), 7.32-7.39 (4H, m), 7.56 (2H, d, J 8.8), 7.69 (2H, d, J 8.8), 9.15 (1H, s, exchange with D2O, NH); δC (100 MHz, DMSO-d6) 40.1, 49.3, 53.6, 117.6, 127.4, 127.6, 128.9, 129.0, 137.0, 141.8, 144.7, 155.9; m/z (ESI positive) 349.1 [M+H]+.

10. 4-(3-(2-((4-chlorobenzyl)amino)ethyl)ureido) benzenesulfonamide (17): white solid; yield 44%; mp 20–-205 °C; TLC Rf 0.10 (MeOH/DCM 10% v/v); δH (400 MHz, DMSO-d6) 2.60 (2H, t, J 6), 3.21 (2H, q, J 6), 3.73 (2H, brs), 6.42 (1H, t, J 6, exchange with D2O, NH), 7.19 (2H, s, exchange with D2O, SO2NH2), 7.40 (4H, m), 7.56 (2H, d, J 8.8), 7.69 (2H, d, J 8.8), 9.09 (1H, s, exchange with, D2O, NH); δC (100 MHz, DMSO-d6) 39.8, 49.2, 52.8, 117.6, 127.7, 128.9, 130.7, 131.9,136.8, 140.9, 144.6, 155.8; m/z (ESI positive) 383.0 [M+H]+.

11. 4-(3-(2-((4-fluorobenzyl)amino)ethyl)ureido) benzenesulfonamide (18): Pale yellow solid; yield 30%; mp 191–192 °C; TLC Rf 0.10 (MeOH/DCM 10% v/v); δH (400 MHz, DMSO-d6) 2.75 (2H, t, J 5.8), 3.26 (2H, q, J 5.8), 3.89 (2H, brs), 6.41 (1H, t, J 5.8, exchange with D2O, NH), 7.19-7.24 (4H, m, 2H exchange with D2O, SO2NH2), 7.48 (2H, m), 7.55 (2H, d, J 8.8), 7.70 (2H, d, J 8.8), 9.16 (1H, s, exchange with D2O, NH); δC (100 MHz, DMSO-d6) 38.8, 48.6, 51.8, 115.9 (d, 2JC-F 21), 117.7, 127.7, 131.7 (d, 3JC-F 8), 134.6 (d, 4JC-F 3), 136.9, 144.6, 156.1, 162.5 (d, 1JC-F 242), δF (376 MHz, DMSO-d6) -115.1 (1F, s); m/z (ESI positive) 367.1 [M+H]+.

12. 4-(3-(2-((2-fluorobenzyl)amino)ethyl)ureido) benzenesulfonamide (19): White solid; yield 41%; mp 156–157 °C; TLC Rf 0.10 (MeOH/DCM 10% v/v); δH (400 MHz, DMSO-d6) 2.71 (2H, t, J 5.8), 3.26 (2H, q, J 5.8), 3.86 (2H, brs), 6.42 (1H, t, J 5.8, exchange with D2O, NH), 7.19 (2H, s, exchange with D2O, SO2NH2), 7.19-7.24 (2H, m), 7.35 (1H, m), 7.52-7.58 (3H, m), 7.70 (2H, d, J 8.8), 9.09 (1H, s, exchange with D2O, NH); δC (100 MHz, DMSO-d6) 39.4, 46.1 (d, J 3.3), 49.1, 116.0 (d, JC-F 22), 116.1, 117.6, 125.2 (d, JC-F 3.5), 127.6, 130.0 (d, JC-F 8.7), 131.6 (d, JC-F 4.4), 136.9, 144.7, 155.9, 161.4 (d, JC-F 243); δF (376 MHz, DMSO-d6) -118.9 (1F, s); m/z (ESI positive) 367.1 [M+H]+.

13. 4-(3-(2-((4-hydroxybenzyl)amino)ethyl)ureido) benzenesulfonamide (20): Pale yellow solid; yield 28%; mp 134–135 °C; TLC Rf 0.10 (MeOH/DCM 10% v/v); δH (400 MHz, DMSO-d6) 2.60 (2H, t, J 6), 3.20 (2H, q, J 6), 3.62 (2H, brs), 6.39 (1H, t, J 6, exchange with D2O, NH), 6.72 (2H, d, J 8.5), 7.15 (4H, m, 2H exchange with D2O, SO2NH2), 7.55 (2H, d, J 8.8), 7.69 (2H, d, J 8.8), 9.08 (1H, s, exchange with D2O, NH), 9.23 (1H, s, exchange with D2O, OH); δC (100 MHz, DMSO-d6) 40.1, 49.2, 53.3, 115.9, 117.7, 127.8, 130.2, 131.8, 136.9, 144.8, 155.9, 157.0; m/z (ESI positive) 365.1 [M+H]+.

14. 4-(3-(2-((4-nitrobenzyl)amino)ethyl)ureido) benzenesulfonamide (21): White solid, yield 38%; mp 191–192 °C; TLC Rf 0.11 (MeOH/DCM 10% v/v); δH (400 MHz, DMSO-d6) 2.63 (2H, t, J 6.2), 3.23 (2H, q, J 6.2), 3.88 (2H, brs), 6.41 (1H, t, J 6.2, exchange with D2O, NH), 7.19 (2H, s, exchange with D2O, SO2NH2), 7.55 (2H, d, J 8.5), 7.68 (4H, m), 8.22 (2H, d, J 7.9), 9.06 (1H, s, exchange with D2O, NH); δC (100 MHz, DMSO-d6) 40.1, 49.4, 52.9, 117.7, 124.2, 127.7, 129.8, 136.9, 144.7, 147.2, 150.4, 155.8; m/z (ESI positive) 394.1 [M+H]+.

15. 4-(3-(2-((4-(dimethylamino)benzyl)amino)ethyl)ureido) benzenesulfonamide (22): White solid, yield 24%; mp 162–163 °C; TLC Rf 0.13 (MeOH/DCM 10% v/v); δH (400 MHz, DMSO-d6) 2.60 (2H, t, J 6), 2.89 (6H, s), 3.21 (2H, q, J 6), 3.62 (2H, brs), 6.41 (1H, t, J 6, exchange with D2O, NH), 6.70 (2H, d, J 8.5), 7.18 (4H, m, 2H exchange with D2O, SO2NH2), 7.56 (2H, d, J 8.8), 7.70 (2H, d, J 8.8), 9.09 (1H, s, exchange with D2O, NH); δC (100 MHz, DMSO-d6) 40.0, 41.3, 49.1, 53.2, 113.2, 117.6, 127.6, 129.2, 129.7, 136.8, 144.7, 150.4, 155.9; m/z (ESI negative) 436.0 [M+HCOO]−

16. 4-(3-(2-((2-methoxy-4-nitrobenzyl)amino)ethyl)ureido)benzenesulfonamide (23): Pale yellow solid, yield 31%; mp 199–200 °C; TLC Rf 0.12 (MeOH/DCM 10% v/v); δH (400 MHz, DMSO-d6) 2.66 (2H, t, J 6), 3.24 (2H, q, J 6), 3.81 (2H, brs), 3.96 (3H, s), 6.38 (1H, t, J 6, exchange with D2O, NH), 7.18 (2H, s, exchange with D2O, SO2NH2), 7.56 (2H, d, J 8.9), 7.70 (3H, m), 7.77 (1H, d, J 2.1), 7.88 (1H, dd, J 2.1, 8.3), 9.03 (1H, s, exchange with D2O, NH); δC (100 MHz, DMSO-d6) 39.7, 47.5, 49.4, 57.0, 106.1, 116.3, 117.6, 127.6, 130.3, 137.0, 144.7, 148.5, 156.0, 158.2; m/z (ESI positive) 424.1 [M+H]+.

17. 4-(3-(2-((4-bromo-2-hydroxybenzyl)amino)ethyl)ureido) benzenesulfonamide (24): White solid, yield 23%; mp 164–165 °C; TLC Rf 0.11 (MeOH/DCM 10% v/v); δH (400 MHz, DMSO-d6) 2.71 (2H, t, J 5.8), 3.27 (2H, q, J 5.8), 3.85 (2H, brs), 6.44 (1H, t, J 5.8, exchange with D2O, NH), 6.97 (2H, m), 7.17 (3H, m, 2H exchange with D2O, SO2NH2), 7.56 (2H, d, J 8.8), 7.69 (2H, d, J 8.8), 9.07 (1H, s, exchange with D2O, NH); δC (100 MHz, DMSO-d6) 39.4, 48.9, 49.4, 117.7, 118.8, 121.2, 122.2, 124.5, 127.7, 131.7, 137.0, 144.7, 156.0, 159.0; m/z (ESI positive) 442.9 [M+H]+.

18. 4-(3-(2-(([1,1′-biphenyl]-4-ylmethyl)amino)ethyl)ureido) benzenesulfonamide (25): White solid, yield 37%; mp 197–198 °C; TLC Rf 0.13 (MeOH/DCM 10% v/v); δH (400 MHz, DMSO-d6) 2.66 (2H, t, J 6.1), 3.24 (2H, q, J 6.1), 3.79 (2H, brs), 6.41 (1H, brt, J 6.1, exchange with D2O, NH), 7.18 (2H, s, exchange with D2O, SO2NH2), 7.38 (1H, t, J 7.4), 7.49 (4H, m), 7.56 (2H, d, J 8.8), 7.63-7.70 (6H, m), 9.07 (1H, s, exchange with D2O, NH); δC (100 MHz, DMSO-d6) 39.6, 49.3, 53.3, 117.7, 127.4, 127.5, 127.7, 128.2, 129.5, 129.8, 136.9, 139.4, 141.0, 141.1, 144.7, 155.9; m/z (ESI positive) 425.1 [M+H]+.

19. 3-(3-(2-(benzylamino)ethyl)ureido)benzenesulfonamide (26): Pale yellow solid, yield 16%; mp 109–110 °C; TLC Rf 0.12 (MeOH/DCM 10% v/v); δH (400 MHz, DMSO-d6) 2.63 (2H, t, J 6), 3.22 (2H, q, J 6), 3.75 (2H, brs), 6.29 (1H, t, J 6, exchange with D2O, NH), 7.25 (1H, t, J 7), 7.32-7.44 (8H, m, 2H exchange with D2O, SO2NH2), 7.54 (1H, d, J 7.9), 8.00 (1H, brt, J 1.6), 8.97 (1H, s, exchange with D2O, NH); δC (100 MHz, DMSO-d6) 39.8, 49.3, 53.6, 115.3, 118.8, 121.2, 127.5, 128.9, 129.0, 130.1, 141.7, 142.0, 145.5, 156.0; m/z (ESI positive) 349.1 [M+H]+.

20. 3-(3-(2-((4-chlorobenzyl)amino)ethyl)ureido) benzenesulfonamide (27): Pale yellow solid, yield 10%; mp 102–103 °C; TLC Rf 0.11 (MeOH/DCM 10% v/v); δH (400 MHz, DMSO-d6) 2.67 (2H, t, J 6), 3.24 (2H, q, J 6), 3.79 (2H, brs), 6.32 (1H, t, J 6, exchange with D2O, NH), 7.32 (2H, s, exchange with D2O, SO2NH2), 7.36-7.44 (6H, m), 7.54 (1H, d, J 7.8), 8.00 (1H, s), 8.98 (1H, s, exchange with D2O, NH); δC (100 MHz, DMSO-d6) 39.7, 49.2, 52.5, 115.5, 119.0, 121.4, 129.1, 130.2, 131.0, 132.4, 139.8, 142.0, 145.6, 156.2; m/z (ESI positive) 383.1 [M+H]+.

21. 3-(3-(2-((4-fluorobenzyl)amino)ethyl)ureido) benzenesulfonamide (28): Pale yellow solid, yield 35%; mp 104–105 °C; TLC Rf 0.11 (MeOH/DCM 10% v/v); δH (400 MHz, DMSO-d6) 2.68 (2H, t, J 6), 3.25 (2H, q, J 6), 3.80 (2H, brs), 6.38 (1H, t, J 6, exchange with D2O, NH), 7.18 (2H, m), 7.33 (2H, s, exchange with D2O, SO2NH2), 7.37-7.47 (4H, m), 7.55 (1H, d, J 8.0), 8.02 (1H, d, J 1.8), 9.05 (1H, s, exchange with D2O, NH); δC (100 MHz, DMSO-d6) 39.6, 49.1, 52.4, 115.4, 115.8 (d, 2JC-F 23), 118.9, 121.3, 130.2, 131.1 (d, 3JC-F 8), 136.8, 142.0, 145.5, 156.1, 162.2 (d, 1JC-F 240); δF (376 MHz, DMSO-d6) -116.1 (1F, s); m/z (ESI positive) 367.1 [M+H]+.

22. 3-(3-(2-((2-fluorobenzyl)amino)ethyl)ureido) benzenesulfonamide (29): Pale yellow solid, yield 15%; mp 155–156 °C; TLC Rf 0.12 (MeOH/DCM 10% v/v); δH (400 MHz, DMSO-d6) 2.72 (2H, t, J 6), 3.27 (2H, q, J 6), 3.87 (2H, brs), 6.34 (1H, t, J 6, exchange with D2O, NH), 7.22 (2H, m), 7.32 (2H, s, exchange with D2O, SO2NH2), 7.34-7.45 (3H, m), 7.55 (2H, m), 8.01 (1H, brt, J 1.8), 9.00 (1H, s, exchange with D2O, NH); δC (100 MHz, DMSO-d6) 39.5, 46.2 (d, J 3.4), 49.2, 115.5, 116.0 (d, J 22), 119.0, 121.4, 125.3 (d, JC-F 3.6), 126.9 (d, J 14.7), 130.1 (d, J 8), 130.2, 131.7 (d, J 5), 142.0, 145.5, 156.2, 161.3 (d, J 243); δF (395 MHz, DMSO-d6) -118.7 (1F, s); m/z (ESI positive) 367.1 [M+H]+.

23. 3-(3-(2-((4-hydroxybenzyl)amino)ethyl)ureido) benzenesulfonamide (30): Orange solid, yield 15%; mp 133–134 °C; TLC Rf 0.10 (MeOH/DCM 10% v/v); δH (400 MHz, DMSO-d6) 2.59 (2H, t, J 6), 3.20 (2H, q, J 6), 3.61 (2H, brs), 6.36 (1H, brt, J 6, exchange with D2O, NH), 6.72 (2H, d, J 8.4), 7.15 (2H, d, J 8.4), 7.34-7.44 (3H, m, 2H exchange with D2O, SO2NH2), 7.42 (1H, t, J 7.9), 7.53 (1H, d, J 7.9), 8.01 (1H, brt, J 1.8), 9.06 (1H, s, exchange with D2O, NH), 9.27 (1H, s, exchange with D2O, OH); δC (100 MHz, DMSO-d6) 39.2, 49.5, 53.5, 116.5, 116.7, 120.3, 123.0, 131.3, 132.0, 142.2, 145.6, 157.3, 157.4; m/z (ESI positive) 365.1 [M+H]+.

24. 3-(3-(2-((4-nitrobenzyl)amino)ethyl)ureido) benzenesulfonamide (31): Pale yellow solid, yield 10%; mp 109–110 °C; TLC Rf 0.11 (MeOH/DCM 10% v/v); δH (400 MHz, DMSO-d6) 2.62 (2H, t, J 6), 3.24 (2H, q, J 6), 3.91 (2H, brs), 6.33 (1H, t, J 6, exchange with D2O, NH), 7.33-7.45 (4H, m, 2H, s, exchange with D2O, SO2NH2), 7.54 (1H, d, J 8.0), 7.68 (2H, d, J 8.6), 8.01 (1H, t, J 2), 8.23 (2H, d, J 8.6), 8.99 (1H, s, exchange with D2O, NH); δC (100 MHz, DMSO-d6) 39.8, 49.4, 52.8, 115.6, 119.3, 121.7, 124.5, 130.3, 130.5, 142.0, 145.5. 147.6, 149.9, 156.3; m/z (ESI positive) 394.0 [M+H]+.

25. 3-(3-(2-((4-(dimethylamino)benzyl)amino)ethyl)ureido) benzenesulfonamide (32): Pale brown solid, yield 10%; mp 101–103 °C; TLC Rf 0.13 (MeOH/DCM 10% v/v); δH (400 MHz, DMSO-d6) 2.64 (2H, t, J 5.8), 2.89 (6H, s), 3.23 (2H, q, J 5.8), 3.66 (2H, brs), 6.31 (1H, t, J 5.8, exchange with D2O, NH), 6.71 (2H, d, J 8.6), 7.19 (2H, d, J 8.6), 7.32-7.38 (3H, m, 2H exchange with D2O, SO2NH2), 7.43 (1H, t, J 7.8), 7.54 (1H, d, J 7.8), 8.00 (1H, t, J 1.8), 9.00 (1H, s, exchange with D2O, NH); δC (100 MHz, DMSO-d6) 39.8, 41.2, 48.9, 52.9, 113.2, 115.4, 118.9, 121.3, 129.9, 130.2, 142.0, 145.5, 150.5, 156.1; m/z (ESI negative) 436.0 [M+HCOO]−.

26. 3-(3-(2-((2-methoxy-4-nitrobenzyl)amino)ethyl)ureido)benzenesulfonamide (33): Yellow solid, yield 42%; mp 103–105 °C; TLC Rf 0.12 (MeOH/DCM 10% v/v); δH (400 MHz, DMSO-d6) 2.66 (2H, t, J 5.8), 3.25 (2H, q, J 5.8), 3.81 (2H, brs), 3.96 (3H, s), 6.33 (1H, t, J 6.8, exchange with D2O, NH), 7.33 (2H, s, exchange with D2O, SO2NH2), 7.40-7.48 (2H, m), 7.58 (1H, m), 7.76 (1H, d, J 8.4), 7.89 (1H, d, J 2.2), 7.97 (1H, dd, J 8.4, 2.2), 8.01 (1H, t, J 2), 8.99 (1H, s, exchange with D2O, NH); δC (100 MHz, DMSO-d6) 40.1, 47.7, 49.6, 57.0, 105.9, 115.4, 116.3, 118.9, 121.3, 129.8, 130.2, 138.1, 142.0, 145.5, 148.1, 156.0, 158.1; m/z (ESI positive) 424.1 [M+H]+.

27. 3-(3-(2-((4-bromo-2-hydroxybenzyl)amino)ethyl)ureido) benzenesulfonamide (34): Pale yellow solid, yield 13%, mp 113–114 °C; TLC Rf 0.11 (MeOH/DCM 10% v/v); δH (400 MHZ, DMSO-d6) 2.65 (2H, t, J 6), 3.22 (2H, q, J 6), 3.78 (2H, brs), 6.30 (1H, t, J 6, exchange with D2O, NH), 6.95 (2H, m), 7.12 (1H, d, J 7.8), 7.32 (2H, s, exchange with D2O, SO2NH2), 7.35-7.38 (1H, m), 7.43 (1H, t, J 7.8), 7.55 (1H, m), 8.01 (1H, t, J 2), 8.94 (1H, s, exchange with D2O, NH): δC (100 MHz, DMSO-d6) 39.7, 49.1, 49.9, 115.4, 118.8, 118.9, 120.8, 121.3, 122.1, 125.2, 130.1, 131.3, 141.9, 145.5. 155.9, 159.1; m/z (ESI negative) 440.9 [M-H]−.

28. 3-(3-(2-(([1,1’-biphenyl]-4-ylmethyl)amino)ethyl)ureido) benzenesulfonamide (35): White solid, yield 17%; mp 116–117 °C; TLC Rf 0.13 (MeOH/DCM 10% v/v); δH (400 MHz, DMSO-d6) 2.76 (2H, t, J 6), 3.30 (2H, q, J 6), 3.90 (2H, brs), 6.39 (1H, t, J 6, exchange with D2O, NH), 7.33 (2H, s, exchange with D2O, SO2NH2), 7.36-7.45 (3H, m), 7.48-7.57 (5H, m), 7.66-7.70 (4H, m), 8.02 (1H, t, J 2), 9.06 (1H, s, exchange with D2O, NH); δC (100 MHz, DMSO-d6) 39.4, 49.1, 52.7, 115.7, 119.4, 121.8, 127.7, 128.6, 130.2, 130.3, 130.5, 132.7, 138.8, 140.3, 141.1, 141.9, 145.5, 156.4; m/z (ESI positive) 425.1 [M+H]+.

4.2. CA Inhibition

An applied photophysics stopped-flow instrument measuring CA catalyzed CO2 hydration by a spectrophotometric method [38] was employed for obtaining the inhibition constants of the new compounds reported here. The used indicator was phenol red (0.2 mM), the buffer was HEPES (20 mM, pH 7.5) and ionic strength was maintained constant by the use of 20 mM Na2SO4. CO2 hydration rates were followed for 10–100 s, using CO2 concentrations in the range of 1.7–17 mM. Each inhibitor was tested in triplicate, in serial dilutions starting from 0.01 to 0.1 mM. An incubation time of 15 min between inhibitor and enzyme has been used, as reported earlier, in order to be sure that the enzyme–inhibitor complex has been formed [2,25,27,39,40,41,42,43,44,45,46,47,48,49,50]. The inhibition constants were obtained by using the Cheng–Prusoff equation [39,51,52,53] and are the mean from three determinations. The employed CA isoforms were recombinant proteins obtained by us as reported in earlier publications [39,51,52].

4.3. Crystallization, Data Collection and Structure Determination

Crystals of hCAI were obtained using the sitting drop vapor diffusion method in 96 well SWISSCI MRC 2 plate. A solution of 0.5 µL of 10 mg ml−1 of hCAI (purchased from Sigma-Aldrich) in 50 mM Tris-HCl pH 8.7 was mixed with 0.5 µL of a solution of 200 mM Na-acetate, 30% PEG 4000, 100 mM Tris-HCl pH 9. Single crystals were obtained in about one week of incubation at 20 °C. Crystals of hCAI in complex with inhibitors (compounds 18, 19, 24, 26, 29 and 34) were prepared by soaking 0.2 µL of 10 mM inhibitor solution (150 mM NaCl, 10% DMSO, 50 mM Tris pH 7) in a drop containing crystals of the hCAI apoenzyme. Frames with an oscillation of 0.1° each were collected at the I03 MX beamline of Diamond Light Source (Didcot, UK). All the crystals belong to the space group P212121, with two monomers in the asymmetric unit. Datasets were processed automatically with the xia2 expert system (https://xia2.github.io/index.html) and scaled with Aimless [54]. The space group resulted in being isomorphous with the native apo hCA I and the structure of hCA I in a complex with the inhibitor famotidine (PDB ID 6g3v) was used as a starting points for the refinement [55]. The structure was refined using the software package Phenix [56]. After a few cycles, a clear density in the active site was clearly visible and a model of the appropriate inhibitor was manually fitted and refined. Map visualization and manual adjustment of the models were performed using the Coot graphic interface [57]. Statistics on data collection and refinement are reported in Supporting Information Table S1.