Coumarin carbonic anhydrase inhibitors from natural sources

Figures & data

Figure 1. The simplest coumarin, compound 1, its hydrolysis product 2, and the natural product coumarin 3 (and its hydrolysis product 4) for which the CA inhibitory activity was first reported⁶.

Figure 2. CA inhibition mechanisms (A–D) and the CA activation mechanism (E). The CA modulators of activity incorporate various scaffolds and tails in their molecule, as well as characteristic functionalities for all category: (A) the zinc binders possess a zinc-binding group (ZBG) which is coordinated to the metal ion; (B) the compounds which anchor to the zinc-coordinated water incorporate an anchoring group (AG) which hydrogen bonds with the water coordinated to the metal and the OH of Thr199; (C) AGs are also present in compounds which occlude the entrance of the active site cavity; (D) some inhibitors which bind out of the active site; (E) the activators incorporate proton-shuttling moieties (PSMs) and bind in the same active site region as the inhibitors shown at (C). Only α-class CAs are considered here (as they are the enzymes present in mammals, including humans^12,14) although these mechanisms may be valid to other CA classes.

Figure 3. X-ray crystal structure of adducts of coumarins 1¹⁰ and 3⁶ bound to hCA II. The hydrolysis products of the two coumarins, cis-2-hydroxycinnamic acid 2 (in yellow) and trans-2-hydroxy-cinnamic acid 4 (in magenta) were observed bound wat the entrance of the CA active site. The catalytic Zn(II) ion is the central violet sphere, its three protein ligands (His94, 96 and 119, CPK colors) and the proton shuttle residue His64 (in red) are evidenced. The hCA II backbone is shown as the green ribbon, with its various α-helices, β-sheets, and loops represented in a canonical manner.

Figure 4. Natural product coumarins 5–35 investigated as CAIs.

Table 1. Inhibition data against six CA isoforms (hCA I, II, VII, IX, XII, and XIII) with coumarins 5–35⁹.

	KI (µM)
Compound	hCA I	hCA II	hCA VII	hCA IX	hCA XII	hCA XIII
5	7.66	>100	0.65	0.62	0.79	45.0
6	8.46	>100	8.98	0.78	0.77	29.3
7	9.31	50.7	8.87	0.83	0.81	21.0
8	59.2	63.4	9.03	0.89	0.60	27.4
9	9.75	>100	7.82	0.60	0.83	9.62
10	9.21	49.3	9.31	0.86	8.35	>100
11	9.89	>100	5.56	0.85	7.84	95.7
12	4.86	94.3	4.32	0.61	7.70	9.73
13	5.04	>100	3.87	0.37	7.45	9.80
14	10.56	>100	8.71	0.96	4.05	17.8
15	5.93	>100	9.11	8.72	0.78	8.43
16	9.11	>100	8.85	8.12	7.44	8.89
17	9.7 nM	>100	9.28	6.58	18.2	4.24
18	8.43	>100	29.7	3.35	8.91	4.75
19	6.45	>100	14.5	3.22	9.07	4.63
20	21.5	>100	9.18	7.51	25.7	8.36
21	14.0	>100	23.8	7.37	4.14	5.27
22	5.84	>100	>100	0.67	7.39	4.06
23	7.41	>100	>100	0.68	0.76	3.28
24	6.55	>100	78.4	3.27	1.79	4.24
25	8.32	>100	4.15	8.38	0.87	6.26
26	40.1	>100	58.3	6.33	8.51	3.70
27	5.60	>100	8.11	3.50	9.10	5.91
28	4.31	9.65	7.01	0.76	0.83	3.32
29	7.71	>100	6.27	0.74	0.96	3.15
30	2.07	>100	3.34	7.85	0.84	3.48
31	7.81	>100	3.69	4.03	0.70	6.10
32	7.52	78.9	6.92	9.75	0.77	6.35
33	36.4	>100	4.53	0.85	9.12	7.26
34	68.2	>100	8.79	79.8	8.15	4.24
35	44.1	>100	8.58	17.4	7.42	5.97

Figure 5. NPCs from the Sardinian plant Magydaris pastinacea investigated as CAIs.

Table 2. hCA I, II, IX, and XII inhibition with NPCs 36–50.

NPC	KI (nM)
	hCA I	hCA II	hCA IX	hCA XII
36	>10,000	>10,000	1953	855.1
37	>10,000	>10,000	194.8	876.3
38	>10,000	>10,000	159.8	590.1
39	>10,000	>10,000	2339	550.0
40	>10,000	>10,000	1501	63.5
41	>10,000	>10,000	221.4	832.9
42	>10,000	>10,000	201.9	786.9
43	>10,000	>10,000	162.5	835.6
44	>10,000	>10,000	27.5	813.8
45	>10,000	>10,000	192.5	>10,000
46	>10,000	>10,000	150.9	623.0
47	>10,000	>10,000	2471	74.5
48	>10,000	>10,000	1888	>10,000
49	>10,000	>10,000	>10,000	290.9
50	>10,000	>10,000	266.4	5.8
AAZ	250.0	12.1	25.8	5.7

The standard sulphonamide inhibitor acetazolamide (AAZ) is also included.

Table 3. Coumarins and psoralens 51–58 and their hCA I, II, IX, and XII inhibitory action.

NPC	R	KI (nM)
		hCA I	hCA II	hCA IX	hCA XII
51	Cl	>10,000	>10,000	23.6	446.6
52	Me	>10,000	>10,000	122.8	56.6
53	H	>10,000	>10,000	89.7	72.5
54	F	>10,000	>10,000	84.7	250.0
55	Cl	>10,000	>10,000	94.7	9.3
56	Me	>10,000	>10,000	23.0	9.1
57	H	>10,000	>10,000	17.5	9.4
58	F	>10,000	>10,000	17.7	7.4

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