Synthesis, biological activity and multiscale molecular modeling studies for coumaryl-carboxamide derivatives as selective carbonic anhydrase IX inhibitors

Figures & data

Scheme 1. Synthesis of new thiourea substituted coumaryl-carboxamid derivatives. Reaction conditions: (i) H₂O, reflux, 10 h; (ii) SOCl₂, 80 °C, 4 h; (iii) KSCN, CH₃CN, 70 °C, 30 min.; (iv) RNH₂, 70 °C, 4 h.

Table 1. Carbonic anhydrase inhibitions of synthesized thiourea substituted coumaryl-carboxamid derivatives.

		Ki (nM)*
Compound	R	hCA I	hCA II	hCA VII	hCA IX
e1		>10,000	>10,000	>10,000	322.9
e2		>10,000	>10,000	>10,000	286.4
e3		>10,000	>10,000	>10,000	376.2
e4		>10,000	>10,000	>10,000	351.4
e5		>10,000	>10,000	>10,000	115.1
e6		>10,000	>10,000	>10,000	297.5
e7		>10,000	>10,000	>10,000	201.8
e8		>10,000	>10,000	>10,000	128.1
e9		>10,000	>10,000	>10,000	136.5
e10		>10,000	>10,000	>10,000	130.3
e11		>10,000	>10,000	>10,000	107.9
e12		>10,000	>10,000	>10,000	223.8
e13		>10,000	>10,000	>10,000	179.8
e14		>10,000	>10,000	>10,000	196.4
e15		>10,000	>10,000	>10,000	184.5
e16		>10,000	>10,000	>10,000	2589.4
e17		>10,000	>10,000	>10,000	258.9
e18		>10,000	>10,000	>10,000	387.5
e19		>10,000	>10,000	>10,000	249.6
e20		>10,000	>10,000	>10,000	182.2
AAZ		250	12.1	6	25.8

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

Figure 1. Formation of 2-hydroxy-cinnamic acids A1, B1 and e11-h by the CA-mediated hydrolysis of coumarin A, B and e11.

Figure 2. Docking scores (GOLD ChemScore dG) of studied compounds (nonhydrolyzed forms) at the hCA I, II, VII and IX isoforms.

Figure 3. Docking scores (GOLD ChemScore dG) of studied compounds (hydrolyzed forms) at the hCA I, II, VII and IX isoforms.

Table 2. Top-docking scores of compounds e1–e20 (non-hydrolyzed forms) at the hCAI, hCAII, hCA VII and hCA IX isoforms.

Compounds	hCA I (2FW4)	hCA II (5AML)	hCA VII (3MDZ)	hCA IX (3IAI)
e1	−3.128	−1.163	−5.049	−4.605
e2	−4.747	−2.292	−4.400	−8.142
e3	−2.534	−1.996	−5.177	−5.259
e4	−7.622	−2.049	−6.114	−4.788
e5	−5.600	−3.613	−4.832	−4.903
e6	−3.339	−5.502	−5.150	−5.796
e7	−5.885	−1.811	−5.383	−4.591
e8	−3.745	−4.148	−5.370	−6.723
e9	−3.159	−4.798	−6.899	−6.678
e10	−5.625	−5.580	−6.330	−5.345
e11	−4.137	−4.298	−4.604	−8.429
e12	−3.805	−4.322	−6.770	−4.996
e13	−4.907	−1.443	−5.040	−5.491
e14	−1.843	−2.858	−5.397	−5.027
e15	−3.328	−2.898	−4.689	−6.798
e16	−4.407	−3.338	−5.441	−6.687
e17	−4.172	−1.909	−4.497	−4.167
e18	−4.258	−2.075	−4.446	−8.750
e19	−2.744	−1.885	−4.158	−5.103
e20	−1.473	0.138	−4.866	−4.226

Used protein data bank (PDB) IDs of proteins were also highlighted at the table. Docking scores are in kcal/mol.

Table 3. Top-docking scores of compounds e1–e20 (hydrolyzed forms) at the hCAI, hCAII, hCA VII and hCA IX isoforms.

Compounds	hCAI (2FW4)	hCAII (5AML)	hCAVII (3MDZ)	hCAIX (3IAI)
e1	−4.422	−5.837	−5.658	−7.025
e2	−4.980	−6.555	−5.468	−6.878
e3	−4.884	−4.292	−6.166	−7.064
e4	−5.270	−7.194	−4.855	−1.879
e5	−5.617	−5.991	−6.191	−8.287
e6	−4.802	−6.698	−6.690	−7.655
e7	−4.715	−6.375	−5.463	−6.833
e8	−4.441	−3.632	−5.703	−4.146
e9	−5.343	−6.699	−6.724	−7.310
e10	−4.726	−7.553	−7.104	−8.819
e11	−4.587	−5.816	−5.597	−9.006
e12	−5.377	−5.121	−7.164	−8.769
e13	−5.366	−6.667	−5.690	−9.481
e14	−5.554	−5.967	−6.518	−9.238
e15	−4.51	−5.879	−6.036	−9.445
e16	−4.929	−6.322	−6.652	−4.213
e17	−4.642	−5.634	−6.219	−4.123
e18	−5.149	−6.855	−3.487	−2.713
e19	−5.82	−6.421	−7.123	−9.301
e20	−4.507	−5.738	−6.672	−9.096

Used protein data bank (PDB) IDs of proteins were also highlighted at the table. Docking scores are in kcal/mol.

Figure 4. 2D and 3D ligand interaction diagrams of active compound e11 at the binding cavity of hCA IX. (top) hydrolyzed form; (bottom) nonhydrolyzed form.