Table 2. Docking Scores and in Vitro IC₅₀ (nM) of 47 MMP-9 Inhibitors (Protonated and Deprotonated) against Four Model Proteins.

		protonated ligand models				deprotonated ligand models
entry ID	MMP9	E402_Zn	E402_woZn	Q402_Zn	Q402_woZn	E402_Zn	E402_woZn	Q402_Zn	Q402_woZn
1	58	−9.66	−7.95	−4.73	−9.8	−9.57	−4.87	−12.42	−2.67
2	11	−9.39	−9.02	−5.94	−9.46	−10.29	−8.71	−10.74	−8.68
3	13	−8.99	−9.94	−9.31	−10.59	−10.76	−9.4	−6.21	−9.12
4	107	−7.92	−7.11	−7.83	−8.24	−9.31	−8.18	−9.79	−8.1
5	11	−7.21	−3.06	−3.28	−3.18	−9.95	−3.35	−8.36	−7.79
6	83	−5.59	−7.16	−7.34	−6.86	−9.3	−3.18	−8.79	−1.37
7	120	−5.37	−5.19	−6.6	−2.19	−10.23	−5.17	−7.41	−5.88
8	63	−5.48	−9.1	−3.99	−3.42	−3.41	−3.03	−8.16	−6.4
9	9	−4.99	−8.8	−6.72	−7.29	−3.31	−2.2	−5.61	−4.94
10	38	−6.95	−5.68	−5.44	−7.32	−8.49	−2.96	−7.46	−8.06
11	141	−5.21	−6.95	−7.63	−5.41	−7.83	−5.54	−9.69	−7.9
12	9	−6.96	−6.15	−7.66	−8.37	−8.77	−7.74	−5.77	−6.16
13	16	−8.68	−8.34	−4.05	−6.34	−9.52	−8.39	−9.85	−3.17
14	35	−5.08	−7.51	−5.56	−7.75	−8.25	−5.74	−10.31	−7.48
15	0.5	−7.98	−7.2	−3.5	−5.8	−9.2	−5.04	−8.31	−6.96
16	11	−3.97	−5.04	−5.91	−8.15	−10.04	−5.81	−9.75	−7.46
17	23	−7.32	−7.25	−6.58	−5.64	−6.72	−7.69	−9.4	−6.36
18	8	−2.57	−5.79	−7.89	−7.2	−10.39	−3.12	−10.87	−7.17
19	197	−8.56	−7.85	−5.17	−7.68	−9.25	−4.56	−12.7	−9.51
20	1.1	−7.55	−7.03	−6.98	−7.22	−9.91	1.03	−8.91	−5.09
21	1.1	−7.43	−9.44	−5.67	−2.76	−9.62	−6.41	−7.96	−8.63
22	2	−8.81	−9.87	−7.68	−8.09	−11.2	−8.01	−9.07	−7.61
23	0.79	−8.17	−9.84	−7.71	−5.14	−10.58	−2.15	−11.09	−5.59
24	2	−7.37	−2.42	−5.91	−7.69	−6.42	−1.14	−6.73	−3.12
25	2	−8.04	−7.92	−6.7	−9.07	−11.03	−3.46	−10.29	−7.09
26	1.7	−6.95	−9.11	−7.17	−10.67	−10.79	−4.76	−8.94	−4.98
27	0.092	−8.39	−6.37	−7.12	−7.3	−9.75	−8.21	−9.02	−4.71
28	0.49	−6.32	−7.24	−7.1	−10.09	−12.07	−4.02	−8.66	−4.48
29	0.3	−6.74	−2.92	−7.94	−4.2	−9.55	−7.71	−10.52	−4.58
30	0.9	−6.98	−9.69	−7.04	−7.75	−9.3	−6.2	−8.6	−8.4
31	0.26	−6.98	−2.93	−6.83	−7.12	−7.82	0.4	−8.69	−3.86
32	1.7	−7.03	−7.96	−6.81	−4.24	−9.53	−1.19	−8.76	−4.82
33	0.9	−7.18	−9.48	−7.05	−8.05	−9.42	−3.87	−8.68	−4.38
34	0.53	−8.42	−6.997	−8.59	−9.48	−11.1	−2.29	−9.41	−5.43
35	0.98	−8.48	−9.47	−9.01	−10.75	−11.28	−9.31	−12.69	−6.81
36	37	−8.45	−11.61	−9.11	−9.94	−9.96	−5	−9.51	−5.85
37	2.2	−7.86	−3.42	−7.73	−7.31	−11.36	2.06	−10.83	−4.19
38	4.1	−7.98	−4.83	−7.17	−4.66	−10.49	−1.5	−9.51	−10.49
39	0.5	−7.55	−5.09	−6.93	−8.38	−9.54	−2.88	−8.87	−4.47
40	1.4	−7.34	−8.65	−6.95	0.51	−6.22	−4.96	−5.65	−0.68
41	0.34	−8.76	−8.39	−9.01	−9.77	−10.24	−4.85	−8.09	−8.82
42	1.4	−7.97	−5.37	−7.51	−7.64	−10.06	−0.28	−9.63	−4.29
43	1.8	−7.64	−8.3	−7.43	−8.52	−9.24	−6.72	−8.46	−6.34
44	37	−7.73	−6.68	−7.06	−8.02	−8.79	−5.83	−9.9	−6.69
45	3.9	−7.08	−7.19	−7.44	−7.52	−6.82	−5.83	−8.14	−7.05
46	2	−7.17	−5.58	−7.35	−4.67	−8.73	−6.84	−7.75	−4.8
47	4.1	−7.95	−10.75	−8.93	−8.8	−10.59	−8.62	−11.07	−4.12