Discovering novel carbonic anhydrase type IX (CA IX) inhibitors from seven million compounds using virtual screening and in vitro analysis

Figures & data

Figure 1. Chemical structure of acetazolamide (AZM) exists in each monomer.

Figure 2. A snapshot picture taken from the simulation box: Protein (CA IX-dimer in yellow, inhibitor (inside the protein), water (as quick surface) and K⁺, Cl⁻ ions (cyan and brown colored spheres).

Figure 3. Cognate docking poses alignment with the co-crystallized ligand conformation using different methods.

Figure 4. Superimposition of selected ligands from docking simulations in the active site.

Table 1. 2D chemical structures and their corresponding docking scores for selected top-docking scored compounds.

Compound	Chemical structures	Glide/XP scores (kcal/mole)	Compound	Chemical structures	Glide/XP scores (kcal/mole)
ZINC20464003		−9.80	ZINC67956012		−9.42
ZINC72421916		−9.66	ZINC11935360		−9.41
ZINC67805921		−9.47	ZINC67433231		−9.30
ZINC01592824		−9.45	ZINC67433435		−9.10
ZINC67714195		−9.43	ZINC67458868		−8.69
ZINC12291144		−8.67	ZINC58328414		−8.30
ZINC58327836		−8.61	ZINC32533143		−8.22
ZINC67850016		−8.38	ZINC72438236		−8.22
ZINC40528234		−8.38	ZINC19376149		−8.11

Figure 5. 3D and 2D ligand interaction diagrams for the ligands, ZINC20464003 (upper panel) and ZINC72421916 (lower panel).

Table 2. Selected compounds with their ADME properties.

Compound	mol MW^a	QplogP o/w^b	QPPCaco^c	QploghERG^d	Percent human oral absorption^e	Rule of five
ZINC20464003	385.46	0.61	68.54	−6.02	63.39	+
ZINC72421916	352.44	1.60	128.29	−4.21	74.04	+
ZINC67805921	371.44	1.89	318.28	−4.73	82.83	+
ZINC01592824	215.18	−2.30	3.43	−2.04	23.04	+
ZINC67714195	341.36	0.58	44.33	−2.64	59.83	+
ZINC67956012	399.44	4.13	678.67	−4.83	100.00	+
ZINC11935360	364.39	2.82	302.50	−4.54	87.86	+
ZINC67433231	383.49	2.68	354.23	−4.51	88.25	+
ZINC67433435	377.49	3.58	263.38	−4.95	91.20	+
ZINC67458868	387.50	4.11	873.75	−4.35	100.00	+
ZINC12291144	316.44	2.37	398.16	−5.12	87.34	+
ZINC58327836	302.38	2.08	290.27	−5.62	83.22	+
ZINC67850016	341.40	2.15	227.63	−4.79	81.70	+
ZINC40528234	282.77	0.40	74.90	−3.57	62.86	+
ZINC58328414	314.43	2.69	263.47	−5.18	86.00	+
ZINC32533143	315.86	3.03	671.66	−4.84	95.31	+
ZINC72438236	342.44	2.53	351.71	−5.20	87.35	+

^aMolecular weight (reasonable value < 500).

^bPredicted octanol/water partition coefficient (reasonable value from −2.0 to 6.5).

^cPredicted apparent Caco-2 cell permeability in nm/s (reasonable value > 25).

^dPredicted blockage of hERG K + channel (reasonable value < −7).

^ePercentage of human oral absorption (<25% is weak and >80% is strong).

Figure 6. 3D docking poses of selected compounds at the active site of CA-IX.

Figure 7. 2D ligand interaction diagrams of selected compounds into the active site of CA-IX.

Table 3. hCA IX inhibition data of selected compounds.

		Determined Ki (μM)*	Predicted Ki (μM)**
Compound	Chemical structures	hCA IX	hCA IX
ZINC67714195		0.85	0.227
ZINC11935360		1.03	0.231
ZINC67458868		1.58	0.750

*Mean from at least three determinations. Errors in the range of 1–3% of the reported value (data not shown).

**Converted from top-docking scores.