Quantitative structure–activity relationships (QSARs) in CYP3A4 inhibitors: The importance of lipophilic character and hydrogen bonding

Figures & data

Table I.  Statins inhibiting CYP3A4-mediated mexazolam hydroxylation

Compound	log D7.0	Ki (μM)	ΔGpart	ΔGinh
1. Pravastatin	2.42	115	− 3.4327	− 5.5878
2. Simvastatin	4.40	2.13	− 6.2413	− 8.0450
3. Lovastatin	3.91	2.98	− 5.5462	− 7.8381
4. Fluvastatin	3.65	7.10	− 5.1774	− 7.3033
5. Atorvastatin	4.20	2.54	− 5.9576	− 7.9366
6. Cerivastatin	4.24	2.18	− 6.0143	− 8.0307
QSAR expressions	n	s	R	F
1. ΔGinh = 0.914 ΔGpart − 2.527 ( ± 0.084)	5	0.1847	0.9877	119.71
2. ΔGinh = 0.915 ΔGpart − 2.522 ( ± 0.069)	6	0.1600	0.9887	174.00

These statins are all present as the lactone form, apart from Cerivastatin which is likely to exist partially in the acid form also. This has a bearing on the log D_7.0 value listed above for Cerivastatin where a weighted average has been taken, based on the reported experimental log D_7.0 values [11]. Cerivastatin was omitted from the analysis shown in Equation (1). n = number of observations; s = standard error; R = correlation coefficient; F = variance ratio. In the ΔG subscripts, inh refers to inhibition and part refers to partitioning as follows: ΔG_inh = RT ln K_i where K_i is the equilibrium constant for inhibition of CYP3A4-mediated activity and ΔG_part = − RT ln P where P is the octanol–water partition coefficient. R = gas constant (1.9872 cal deg^{− 1}mol^{− 1}); T = absolute temperature (310K). Reference to K_i and log D_7.0 data: Ishigami et al. 2001 [11].

Table II.  CYP3A4 mixed inhibitors*

Compound	log P	IC50 (μM)	ΔGpart	ΔGinh
1. Clotrimazole	5.71^c	0.002	− 8.0994	− 12.3392
2. Nicardipine	4.96	0.008	− 7.0356	− 11.4852
3. Cisapride	3.65^d	0.038	− 5.1774	− 10.5253
4. Verapamil	3.79	0.12	− 5.3760	− 9.8169
5. Cyclosporin	2.92	0.46	− 4.1419	− 8.9892
6. Midazolam	3.27	0.46	− 4.6384	− 8.9892
7. Erythromycin	2.48	1.8	− 3.5178	− 8.1487
8. Astemizole	3.17	0.59	− 4.4965	− 8.8358
9. Mibefradil	6.22^d	0.006	− 8.8229	− 11.6624
10. Nifedipine	2.86	6.6	− 4.0568	− 7.3483
11. Nimodipine	4.18	0.62	− 5.9292	− 8.8053
12. Terfenadine	4.00	1.4	− 5.6739	− 8.3035
13. Troleandomycin	4.26^c	0.36	− 6.0427	− 9.1402
14. Ketoconazole	3.73	0.016	− 5.2909	− 11.9582
QSAR expressions	n	s	R	F
1. ΔGinh = 0.927 ΔGpart − 3.391 ( ± 0.074)	5	0.2558	0.991	155.65
2. ΔGinh = 0.919 ΔGpart − 5.012 ( ± 0.091)	8	0.3691	0.972	101.00
3. ΔGinh = 0.926 ΔGpart − 4.990 ( ± 0.055)	13	0.3047	0.981	279.73
4. ΔGinh = 0.924 ΔGpart − 5.024 ( ± 0.055)	14	0.3011	0.980	285.15

c = calculated value (Pallas Software, CompuDrug Limited, Budapest); d = calculated value (ClogP Software, BioByte Corporation, Pomona, California);* = compounds in this dataset exhibit mixed types of inhibition with respect to the mode of inhibition although they would not be regarded as reversible mixed inhibitors in the classical sense. Reference to IC₅₀ data: Ekins et al. 2003 [13].

Table III.  Structurally diverse CYP3A4 inhibitors^†

Compound	log P	IC50 (μM)	ΔGpart	ΔGinh	Compound Type
1. Erythromycin	2.54*	132	− 2.6951	− 5.5028	Amine
2. Chloroquine	1.23	350	− 1.7447	− 4.9021	Amine/quinoline
3. Diltiazem	2.80	217	− 3.9717	− 5.1966	Amine/diazepine
4. Verapamil	3.79	76	− 5.3760	− 5.8429	Amine/cyano
5. Bromocriptine	2.37	3	− 3.3618	− 7.8340	Azole
6. Dihydroergotamine	2.40^c	3	− 3.4043	− 7.8340	Azole
7. Troleandomycin	4.16	8	− 5.9008	− 7.2298	Azole
8. Sulfamethizole	0.54	836	− 0.7660	− 4.3657	Azole
9. Timoprazole	1.33	309	− 1.8866	− 4.9789	Azole
10. Piroxicam	1.98	1000	− 2.8086	− 4.2554	Pyridine
11. Tazanolast	1.39	290	− 1.9719	− 5.0180	Azole
12. Cimetidine	0.40	1000	− 0.5674	− 4.2554	Azole
13. Nifedipine	2.86	47	− 4.0568	− 6.1390	Pyridine
14. Omeprazole	2.23	78	− 3.1632	− 5.8269	Azole
15. 1-Methylimidazole	− 0.06	2700	0.0851	− 3.6435	Azole
16. 2-Methylimidazole	0.24	1252	− 0.3404	− 4.1169	Azole
17. 3-Hydroxypyridine	0.52	768	− 0.7376	− 4.4180	Pyridine
18. 2-Anilinopyridine	2.75	431	− 3.9008	− 4.7739	Pyridine
19. AZ-2	3.80	43	− 5.3902	− 6.1938	Not known
20. Thioperamide	2.41	6.1	− 2.5958	− 7.3968	Azole
21. Triadimefon	2.77	9.3	− 2.7944	− 7.1370	Azole
22. Propiconazole	3.50	1.04	− 4.4823	− 8.4866	Azole
23. Ketoconazole	3.73	0.2	− 5.2909	− 9.5023	Azole
24. Metyrapone	1.78	4.93	− 2.5249	− 7.5280	Pyridine
25. Glipizide	1.91	7.44	− 2.7093	− 7.2745	Pyrazine
26. Miconazole	5.70	0.85	− 8.0853	− 8.6109	Azole
27. Clotrimazole	5.48	0.05	− 7.7732	− 10.3563	Azole
28. Fluconazole	0.50	25	− 0.7092	− 6.5279	Azole
29. Econazole	5.51	0.43	− 7.8157	− 9.0307	Azole
30. AZ-1	4.00	3.5	− 5.6739	− 7.7391	Not known

c = calculated value obtained using the Pallas System (CompuDrug Limited, Budapest). *The log D_7.4 value is 1.26 for this compound and the ΔG_part figure shown above represents an average of the log P and log D_7.4 - derived values, thus allowing for the effect of ionization. ^†Correlations for this dataset are presented in Table IV and it should be recognized that the mechanisms of inhibition actually differ within the group listed above. Notes: 1. Econazole and AZ-1 are weak outliers of expression (2), in Table IV; both being about − 0.9 kcal mol^{− 1} above the line, thus indicating the possible presence of an additional π–π stacking interaction within the CYP3A4 active site. However, they can be included in the dataset satisfactorily with an allowance for the − 0.9 kcal mol^{− 1} energy difference. 2. Although the inhibitors contain nitrogenous functions which may act as heme ligands, AZ-1 and AZ-2 are AstraZeneca compounds of unknown chemical structure, thus restricting their analysis in terms of potential CYP3A4 active site interactions. However, it is found that AZ-2 conforms well with one of the lipophilicity relationships shown by the other compounds in the group. Reference to IC₅₀ values and some of the experimental log P data: Riley et al. 2001 [14].

Table IV.  Results of QSAR analysis for three groups of CYP3A4 inhibitors

	n	s	R	F
1. Statins (5 congeners)
a) ΔGinh = 0.914 ΔGpart − 2.527 ( ± 0.084)	5	0.1847	0.988	119.71
b) ΔGinh = 0.915 ΔGpart − 2.522 ( ± 0.069)	6	0.1600	0.989	174.00
2. Mixed inhibitors (13 compounds)
a) ΔGinh = 0.901 ΔGpart − 5.155 ( ± 0.093)	7	0.3753	0.974	90.61
b) ΔGinh = 0.927 ΔGpart − 3.391 ( ± 0.074)	5	0.2558	0.990	155.65
c) ΔGinh = 0.919 ΔGpart − 5.012 ( ± 0.091)	8	0.3691	0.971	101.90
d) ΔGinh = 0.926 ΔGpart − 4.990 ( ± 0.055)	13	0.3047	0.980	279.73
e) ΔGinh = 0.924 ΔGpart − 5.024 ( ± 0.055)	14	0.3011	0.978	285.15
3. Structurally diverse inhibitors (28 compounds)
a) ΔGinh = 0.590 ΔGpart − 5.973 ( ± 0.045)	9	0.2623	0.979	157.56
b) ΔGinh = 0.580 ΔGpart − 5.894 ( ± 0.049)	10	0.2835	0.973	142.73
c) ΔGinh = 0.579 ΔGpart − 3.889 ( ± 0.011)	13	0.0873	0.998	304.73
d) ΔGinh = 0.694 ΔGpart − 2.275 ( ± 0.095)	5	0.2081	0.973	53.94
e) ΔGinh = 0.600 ΔGpart − 3.827 ( ± 0.018)	28	0.2149	0.988	1073.0

n = number of observations; s = standard error; R = correlation coefficient; F = variance ratio. In the ΔG subscripts, inh refers to inhibition and part refers to partitioning as follows: ΔG_inh = RT ln K_i where K_i is the equilibrium constant for inhibition of CYP3A4-mediated activity, ΔG_part = − RT ln P where P is the octanol-water partition coefficient. R = gas constant (1.9872 cal deg^{− 1}mol^{− 1}); T = absolute temperature (310K).

Figure 1 Lipophilicity relationships for a series of statins showing CYP3A4 inhibitory activity. The ΔG_inh value is plotted against ΔG_part for log D_7.0 data and indicates a single hydrogen bond interaction with the CYP3A4 enzyme active site.

Figure 2 Lipophilicity relationships within a group of 14 structurally diverse CYP3A4 inhibitors. The ΔG_inh value is plotted against ΔG_part for log P data and indicates that the difference between the two lines is equivalent to an average hydrogen bond energy of − 1.5 kcal mol^{− 1}.

Figure 3 Lipophilicity relationships within a group of 28 structurally diverse CYP3A4 inhibitors. The ΔG_inh value is plotted against ΔG_part for log P data and indicates that the difference between two of the lines is equivalent to an average hydrogen bond energy of − 1.6 kcal mol^{− 1}. However, the difference between the two upper lines is equivalent to an average hydrogen bond energy of − 2 kcal mol^{− 1}.

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