Table S1. Table 1 contain inhibitors of class I HDAC, 2D view of data set with IC50 value.

Table1: Table 1 contain inhibitors of class I HDAC, 2D view of data set with IC50 value.

S.No. / Structures / IC50 Value / S.No. / Structures / IC50 Value
1st / / 0.103 / 2nd / / 0.0714
3rd / / 1.5 / 4th / / 0.5
5th / / 0.065 / 6th / / 0.135
7th / / 0.45 / 8th / / 0.035
9th / / 0.153 / 10th / / 0.095
11th / / 0.015 / 12th / / 0.045
13th / / 0.045 / 14th / / 0.005
15th / / 0.0085 / 16th / / 0.004
17th / / 0.008 / 18th / / 0.002
19th / / 0.0095 / 20th / / 0.0045
21st / / 0.6 / 22nd / / 0.006
23rd / / 0.025 / 24th / / 0.035
25th / / 0.9 / 26th / / 1
27th / / 0.1 / 28th / / 0.2
29th / / 2 / 30th / / 17
31st / / 0.6 / 32nd / / 0.075
33rd / / 0.1 / 34th / / 0.3
35th / / 0.6 / 36th / / 0.1
37th / / 0.3 / 38th / / 0.1
39th / / 0.1 / 40th / / 0.6
41st / / 0.06 / 42nd / / 0.09
43rd / / 52.56 / 44th / / 12.25
45th / / 9.65 / 46th / / 11.25
47th / / 2.4 / 48th / / 0.84
49th / / 2.0 / 50th / / 1.0
51st / / 4.8 / 52nd / / >100
53rd / / >100 / 54th / / >100
55th / / >100 / 56th / / 2.2
57th / / >100 / 58th / / >100
59th / / 44 / 60th / / 40
61st / / 2.8 / 62nd / / 4.6
63rd / / 7.7 / 64th / / 6.0
65th / / 0.59+-
0.2 / 66th / / 0.02+-0.06
67th / / 0.46+-0.14 / 68th / / 1.7+-0.064
69th / / >5 / 70th / / 0.32+-0.024

Table S2. Similarity (identity) matrix of SmHDAC1 and Human class I HDACs. SmHDAC1 shows greater than 50% sequence similarity (identity) with class I members of HDACs except HsHDAC8 which have 37.78% (36.60%) similarity (identity) respectively.

IDENTITY MATRIX
HsHDAC1 / 100%
HsHDAC2 / 86.09% / 100%
SmHDAC1 / 65.67% / 65.08% / 100%
HsHDAC3 / 58.41% / 58.41% / 51.63% / 100%
HsHDAC8 / 39.25% / 39.52% / 36.60% / 39.25% / 100%
HsHDAC1 / HsHDAC2 / SmHDAC1 / HsHDAC3 / HsHDAC8
SIMILARITY MATRIX
HsHDAC1 / 100%
HsHDAC2 / 91.98% / 100%
SmHDAC1 / 69.46% / 69.08% / 100%
HsHDAC3 / 66.03% / 64.50% / 53.62% / 100%
HsHDAC8 / 47.90% / 46.56% / 37.78% / 56.67% / 100%
HsHDAC1 / HsHDAC2 / SmHDAC1 / HsHDAC3 / HsHDAC8

Table S3. Comparative binding energy of inhibitors with HsHDAC1 and model structure SmHDAC1. Values which are bold were ligand no. 24th. Ligand 24th has been selected for downstream analysis.

Ligand / Binding Energy of HsHDAC1(kcal/mol) / Binding Energy of SmHDAC1 (kcal/mol)
10th / -5.9 / -6.4
11th / -6 / -5.6
12th / -6.7 / -6.1
13th / -6.1 / -6.6
14th / -6 / -5.4
15th / -7.7 / -7
16th / -8.4 / -6.7
17th / -6 / -6.6
18th / -7.6 / -5.9
19th / -6.9 / -6.3
20th / -7.2 / -5
21st / -6.5 / -6.7
22nd / -7.1 / -7.3
23rd / -6 / -6.7
24rth / -6.4 / -8.1
25th / -7.2 / -7.1
26th / -7.1 / -7.1
27th / -6.8 / -7.1
29th / -7 / -6.7
2nd / -6.6 / -6.8
30th / -6.8 / -6.5
31st / -6.9 / -6.8
32nd / -7.1 / -6.7
33rd / -7.3 / -7.1
34rth / -6.8 / -6.4
35th / -7.3 / -6.4
36th / -8 / -7
37th / -8.1 / -7.1
38th / -7.6 / -7.2
39th / -7.5 / -7.2
3rd / -6.7 / -6.2
40th / -7.1 / -6.4
41th / -7.3 / -6.3
42nd / -7.3 / -6.1
43rd / -7.6 / -6.3
44rth / -6 / -6.1
45th / -5.4 / -5.5
46th / -6.4 / -5.8
47th / -6.3 / -5.8
48th / -6.6 / -6.8
49th / -7.7 / -5.7
4rth / -6.4 / -6.5
50th / -6.9 / -4.9
51st / -6.8 / -6.3
52nd / -7.7 / -7.3
53rd / -8.8 / -7.5
54rth / -8.2 / -7.1
55th / -7 / -7.7
56th / -8 / -7.8
57th / -8.9 / -7.4
58th / -7.4 / -7.4
59th / -6.8 / -7.9
5th / -5.8 / -6.5
60th / -6.8 / -7.7
61st / -6.8 / -7.7
62nd / -7.3 / -8.2
63rd / -7.4 / -7.8
64rth / -7.6 / -7.3
65th / -7.5 / -7.3
66th / -8.3 / -7.6
67th / -8.2 / -6.9
68th / -8.3 / -7
69th / -7.8 / -7.5
6th / -5.9 / -6.4
70th / -7.4 / -7.7
71st / -8.6 / -7.5
7th / -6.4 / -6.4
8th / -7.2 / -6.9
9th / -6.5 / -5.9
First / -6.7 / -6.9

Table S4. Conservation of Zn++ binding residues throughout the human class I HDAC. Table has drowned from available pdb structures in RCSB protein data base in PyMol.

Protein / Metal binding residue with their positions / Distance from Zn++ (Angstrom) / PDB ID
Hm_HDAC1 / ASP-176 / 1.963 / 4BKXB
HIS- 178 / 2.277
ASP-264 / 1.949
Sm_HDAC1 / ASP-126 / 2.033 / Modeled
HIS-128 / 2.262
ASP-214 / 1.944
Hs_HDAC2 / ASP-181 / 1.998 / 4LXZB
HIS- 183 / 2.068
ASP-269 / 1.902
Hs_HDAC3 / ASP-170 / 2.720 / 4A69A
HIS-172 / 3.066
ASP-259 / 2.966
Hs_HDAC8 / ASP-178 / 2.131 / 1T69A
HIS-180 / 1.789
ASP-267 / 1.908