Benzenesulfonamide derivatives as Vibrio cholerae carbonic anhydrases inhibitors: a computational-aided insight in the structural rigidity-activity relationships

Figures & data

Figure 1. Compounds investigated in this work.

Figure 2. Overview of the tail approach and the design strategy used in the current work.

Table 1. Inhibition data of sulfonamides 1–15a–c and reference compound AAZ on hCAs I and II and VchCAs through the stopped-flow CO₂ hydrase assay.

Cpd	Scaffold	Series	R	KI (nM)					SI [$\frac{KI \mathit{hCA}\mathrm{ }\mathrm{I}}{KI\mathrm{ }\mathit{Vch}\mathrm{\alpha }\mathrm{CA}}$]	SI [$\frac{KI \mathit{hCA}\mathrm{ }\mathrm{II}}{KI \mathit{Vch}\alpha \mathrm{CA}}$]
				hCA Ia	hCA II^a	VchαCA	VchβCA	VchγCA
1	a	p-		25.4	7.2	78.1	18 300	n.a.	0.3	0.1
2	a	p-		9.7	3.1	43.1	16 800	39 900	0.2	0.1
3	a	p-		39.0	47.0	27.4	53 800	n.a.	1.4	1.7
4	a	p-		787	646	65.0	136 400	n.a.	12.1	9.9
5	a	p-		939	908	64.1	89 200	n.a.	14.7	14.2
6	a	p-		75.3	8.2	36.2	100 800	73 700	2.1	0.2
7	a	p-		87.0	31.4	37.0	19 000	69 800	2.4	0.9
8	a	p-		169	32.7	23.0	12 400	52 700	7.4	1.4
9	a	p-		538	82.2	78.8	115 000	n.a.	6.8	1.0
10	a	p-		896	338	7.5	12 500	92 900	119.5	45.0
11	a	m-		7.0	4.1	63.0	15 600	n.a.	0.1	0.1
12	a	m-		>1000	901	44.1	173 200	79 000	>22.7	20.4
13	a	m-		346	15.7	75.6	59 200	5600	4.6	0.2
14	a	m-		7.6	3.3	63.5	97 000	n.a.	0.1	0.1
15	a	m-		151	43.2	80.3	56 500	69 300	1.9	0.5
1	b	p-		62.6	3.2	53.0	17 700	49 400	1.2	0.1
2	b	p-		6.6	82.4	43.1	97 000	82 600	0.2	1.9
3	b	p-		16.7	6.0	66.0	116 400	86 900	0.3	0.1
4	b	p-		>1000	909	22.8	157 300	72 500	>43.9	39.9
5	b	p-		29.8	3.0	62.0	47 400	87 700	0.5	0.1
6	b	p-		18.4	4.8	79.0	51 400	93 100	0.2	0.1
7	b	p-		15.3	4.7	17.0	73 100	59 800	0.9	0.3
8	b	p-		26.5	5.0	61.4	53 200	n.a.	0.4	0.1
9	b	p-		160	8.4	78.6	141 400	n.a.	2.0	0.1
10	b	p-		92.0	26.6	36.2	4000	58 300	2.5	0.7
11	b	m-		443	35.5	59.4	132 500	n.a.	7.5	0.6
12	b	m-		86.4	8.2	73.1	120 800	9600	1.2	0.1
13	b	m-		269	32.4	75.5	70 400	n.a.	3.6	0.4
14	b	m-		20.3	86.0	72.3	16 000	72 400	0.3	1.9
15	b	m-		83.7	37.4	66.4	116 400	73 600	1.3	0.6
1	c	p-		54.4	4.3	7.1	134 000	5000	7.7	0.6
2	c	p-		16.1	3.7	27.0	83 600	3500	0.60	0.14
3	c	p-		194	46.3	47.0	106 000	50 200	4.1	1.0
4	c	p-		92.7	13.0	13.0	116 000	72 200	7.1	1.0
5	c	p-		6.2	3.4	47.2	n.a.	73 200	0.1	0.1
6	c	p-		7.8	3.1	9.7	108 000	82 800	0.8	0.3
7	c	p-		54.6	7.2	11.0	122 000	80 200	5.0	0.7
8	c	p-		8.0	3.1	2.6	127 200	8100	3.1	1.2
9	c	p-		604	423	4.7	113 100	54 900	128.4	90.0
10	c	p-		8.5	3.2	9.8	113 200	64 500	0.9	0.3
11	c	m-		60.6	31.1	50.3	100 200	6500	1.2	0.6
12	c	m-		462	500	11.0	n.a.	76 000	42.0	45.5
13	c	m-		30.3	84.1	4.0	121 800	73 700	7.6	21.0
14	c	m-		8.0	54.4	10.0	132 100	81 300	0.8	5.4
15	c	m-		36.3	8.0	47.0	122 000	8000	0.8	0.2
AAZ				250	12.1	6.8	451	473	36.8	1.8

K_I values are reported as means of three independent experiments by a stopped-flow technique. Errors are in the range of ± 5–10% of the reported values. Acetazolamide (AAZ) was used as a reference control in these assays. VchCAs are from V. cholerae species. Selectivity index (SI) values are calculated as indicated in the table. Compounds are presented based on the molecular scaffold (a, amine, b, amide, and c, urea) and the (meta- or para-) position with respect to the benzenesulfonamide core. n.a.: not active at 100 µM.

^aData from Ref. 40.

Table 2. Flexibility properties of compounds 1a–c and 9a–c, selected as representative of the whole library of derivatives, calculated through FAFDrugs4 webtool.

CPD	Structure	Flexibility	Rotable bonds (#)	Rigid bonds (#)
1a		0.30	6	14
1b		0.24	5	16
1c		0.13	3	20
9a		0.50	8	8
9b		0.41	7	10
9c		0.26	5	14

Figure 3. (A, C, E, and G) Predicted 3D binding mode and (B, D, F, and H) corresponding ligand interaction diagram of most selective ligands (A, B) 9c yellow, (C, D) 12c magenta, (E, F) 4b orange, and (G, H) 10a cyan, within VchαCA (light grey). The compounds are represented as sticks, and the protein surface is visualised.

Figure 4. Most representative geometry retrieved after MD simulation for the four studied ligands. (A) 9c yellow, (B) 12c magenta, (C) 4b orange, and (D) 10a cyan in the VchαCA (light grey). The compounds are represented in stick and the protein surface is visualised.

Figure 5. (A, C, E, and G) The 2D representation of most conserved ligand–protein interactions with (B, D, F, and H) the indication of the persistence (%) along the simulation and depiction of frequency and type of ligand-protein interaction along with the MD simulation. (A, B) 9c, (C, D) 12c, (E, F) 4b, and (G, H) 10a.

Figure 6. (A) Predicted 3D binding mode and (B) corresponding ligand interaction diagram of the most selective ligands 9c (yellow) in the hCA I (light salon). The compound is represented as the stick and the protein surface is visualised.

Figure 7. (A) Predicted 3D binding mode and (B) corresponding ligand interaction diagram of the most selective ligand 9c (yellow) in the hCA II (light cyan). The compounds are represented as a stick and the protein surface is visualised.

Figure 8. (A) Predicted 3D binding mode and (B) corresponding ligand interaction diagram of the most selective ligand 9c (yellow) within VchβCA (grey and pink). The compound is represented as a stick and the protein surface is visualised.

Figure 9. (A) Predicted 3D binding mode and (B) corresponding ligand interaction diagram of the most selective ligand 9c (yellow) within VchβCA (grey and pink). The compound is represented as a stick and the protein surface is visualised.

Figure 10. Schematic representation of the ligand contacts producing the selectivity towards VchαCA with respect to hCAs. The compound (9c) is represented as sticks and the VchαCA coil and the short alpha helix hCAII (similar to hCAI) are visualised as cartoon and surface.

Table 3. Physicochemical and pharmacokinetic properties of the studied ligands.

cpd	MW	PSA	Rule of Five	% h Oral Abs	QPP Caco	QP logBB	QP logHERG
9c	297.371	95.123	0	76.996	209.196	−1.454	−4.882
10a	257.35	89.372	0	60.538	67.277	−1.064	−5.688
12c	331.389	93.581	0	80.227	228.807	−1.242	−5.54
14b	384.247	111.98	0	72.068	134.213	−1.639	−6.072
AAZ	222.236	133.243	0	44.375	35.654	−1.802	−3.791

MW: molecular weight; PSA: Van der Waals surface area of polar nitrogen and oxygen atoms and carbonyl carbon atoms (7–200); Rule Of Five: Number of violations of Lipinski rule of five; h Oral Abs: human oral absorption (1, 2, or 3 for low, medium, or high); % h OralAbs: Predicted human oral absorption on a 0–100% scale; QPPCaco: Predicted apparent Caco-2 cell permeability in nm/s. Caco-2 cells are a model for the gut–blood barrier (500 great); QPlogBB: Predicted brain/blood partition coefficient (−3.0 to 1.2); QPlogHERG: Predicted IC₅₀ value for the blockage of HERG K⁺ channels (concern below −5).

Scheme 1. Synthesis of compounds 1-15a–c. Reagents and conditions: (i) chloroacetyl chloride, dry acetone, N₂, 0 °C, 0.5 h; (ii) appropriately substituted aniline, KI, sealed tube, dry THF, N₂, 110 °C, 24 h; or 2-amino-6-methylpyridine, dry TEA, abs EtOH, N₂, ref., 24 h; or benzylamine, dry TEA, dry ACN, N₂, 24 h; or amine, KI, dry THF, N₂, 24 h; (iii) 1 M BH3·THF, dry THF, N₂, r.t., 24 h; or LiAlH₄, dry THF, N₂, 0–70 °C, 24 h; (iv). triphosgene, dry TEA, dry THF, N₂, r.t., 2 h.

Liguori F, Carradori S, Ronca R, Rezzola S, Filiberti S, Carta F, Turati M, Supuran CT. Benzenesulfonamides with different rigidity-conferring linkers as carbonic anhydrase inhibitors: an insight into the antiproliferative effect on glioblastoma, pancreatic, and breast cancer cells. J Enzyme Inhib Med Chem. 2022;37(1):1857–1869.

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