Docking results
Compounds Alprazolam, A1, A2, A3, A4, A5, A6, A7, A8, A9, A10 and their interactions with binding affinities to 6X3X were described in Table 2, ligands A3, A8 and A9 shown greater binding affinity than other compounds, their interactions with receptor were displayed in Fig. 1[A], [B]; Fig. 2[A], [B]; Fig. 3[A], [B] and Fig. 4[A], [B].
Table 2
The docking scores of the title compounds possessing best in-vivo inhibition activity and their interactions with the active site of GABAA receptor crystal structure (PDB ID: 6X3X)
Compound | B.A. (k.cal/ mol) | Hydrogen Interactions | Hydrophobic Interactions | Unfav-oured Bonds |
C- H-bond | C-H Bond | Π-Cation | Π-DHB | Π-Sigma | Π-Alkyl | Alkyl |
Alprazolam | -7.7 | E THR 146 | - | D LYS 105 | E THR 73 E THR 146 | E THR 73 | D LYS 105 D LYS 106 D LYS 105 | D LYS 105 D LYS 106 D ARG 136 | - |
A1 | -7.0 | E THR 146 E THR 197 | - | D LYS 105 | E THR 73 | E THR 73 | E PRO 64 E LYS 118 | - | - |
A2(1) | -7.4 | E THR 197 | - | D LYS 105 | E THR 146 | - | D LYS 105 D LYS 106 | D LYS 105 D LYS 106 D LYS 106 D ARG 136 | - |
A2(2) | -7.4 | E THR 146 | - | D LYS 105 | E THR 73 E THR 146 | - | D LYS 105 D LYS 106 D LYS 105 | D LYS 105 D LYS 106 D LYS 106 D ARG 136 E PRO 64 | - |
A3 | -8.1 | D LYS 105 E THR 146 E ARG 197 E ARG 197 | - | D LYS 105 | E THR 73 E THR 146 | - | D LYS 105 D LYS 106 D LYS 105 | D LYS 105 D LYS 106 D ARG 136 | - |
A4 | -7.6 | E THR 146 | - | D LYS 105 | E THR 146 | - | D LYS 105 D LYS 106 D LYS 105 E PRO 64 | D LYS 105 D LYS 106 D ARG 136 | - |
A5 | -7.2 | E THR 146 | E GLU 71 | D LYS 105 | E THR 73 E THR 146 | E THR 73 | D LYS 105 D LYS 106 D LYS 105 | D LYS 105 D LYS 106 D ARG 136 | - |
A6 | -7.6 | E THR 146 | - | D LYS 105 | E THR 73 E THR 146 | E THR 73 | D LYS 105 D LYS 106 D LYS 105 | D LYS 105 D LYS 106 D ARG 136 E PRO 64 | - |
A7(1) | -7.6 | E THR 197 | - | D LYS 105 | E THR 146 | - | D LYS 105 D LYS 106 | - | D LYS 105 |
A7(2) | -7.6 | E THR 146 E THR 73 | - | D LYS 105 | E THR 73 E THR 146 | E THR 73 | D LYS 105 D LYS 106 D LYS 105 | D LYS 105 D LYS 106 D ARG 136 | - |
A8 | -8.2 | E THR 146 | - | D LYS 105 | E THR 73 E THR 146 | E THR 73 | D LYS 105 D LYS 106 D LYS 105 | D LYS 105 D LYS 106 D ARG 136 | - |
A9 | -8.0 | E THR 146 E THR 146 | E THR 146 | D LYS 105 | E THR 146 | - | D LYS 105 D LYS 106 D LYS 105 | D LYS 105 D LYS 106 D LYS 105 | - |
A10 | -7.4 | E THR 146 | - | D LYS 105 | E THR 73 E THR 146 | - | D LYS 105 D LYS 106 D LYS 105 | D LYS 105 D LYS 106 D ARG 136 | - |
B.A.-Binding Affinity; K. Cal/mol- Kilo Calorie per mole; C-H-Bond – Conventional Hydrogen Bond; C-H bond- Carbon Hydrogen bond; Π- Cation- Pi Cation; Π-DHB- Pi Donor Hydrogen Bond; Π-Sigma – Pi Sigma; Π-Alkyl- Pi Alkyl |
*A2 and A7 ligands exhibited two poses named as A2(1), A2(2), A7(1), and A7(2) of same binding affinities respectively. |
The determined docking score of Alprazolam was − 7.7 kcal/mol, surrounded by E THR 146, DLYS 105, E THR73, D LYS 106, and D ARG 136 amino acid residues of the receptor active site. Hydrogen bond interactions, E THR 146 donates hydrogen to the acceptor at the nitrogen atom of the ligand to make a conventional hydrogen bond. D LYS 105 donates hydrogen to the pi orbitals of the ligand to form pi cation interactions. E THR 73 and E THR 146 on donating the hydrogen to the pi orbitals of the ligand to form pi donor hydrogen bonds. Hydrophobic interactions, E THR 73, C-H site interacts with pi orbitals of the ligand to make a pi sigma bond. Alkyl groups of D LYS 105, D LYS 106, and D LYS 105 interact with pi orbitals of the ligand to make pi alkyl interaction. D LYS 105, D LYS 106, and D ARG 136 of alkyl groups interact with the 8-chloro position of the ligand.
The determined docking score of A3 was − 8.1 kcal/mol, surrounded by D LYS 105, E THR 146, E ARG 197, E THR73, D LYS 106, and D ARG 136 amino acid residues of the receptor active site. In hydrogen bond interactions, D LYS 105, and E ARG 197 (NH1 and NH2) donate hydrogen to the acceptor at the oxygen atom and E THR 146 donates hydrogen to make a conventional hydrogen bond. D LYS 105 donates hydrogen to the pi orbitals of the ligand to form pi cation interactions. E THR 73 and E THR 146 on donating the hydrogen to the pi orbitals of the ligand to form pi donor hydrogen bonds. Hydrophobic interactions, Alkyl groups of D LYS 105, D LYS 106, D LYS 105 interact with pi orbitals of the ligand to form pi alkyl interaction. D LYS 105, D LYS 106, and D ARG 136 of alkyl groups interact with the 8-chloro position of the ligand to form alkyl interactions.
The determined docking score of A8 was − 8.2 kcal/mol, surrounded by E THR 146, D LYS 105, E THR73, D LYS 106, and D ARG 136 amino acid residues of the receptor active site. In hydrogen bond interactions, E THR 146 donates hydrogen to the acceptor at the nitrogen atom of the ligand to form a conventional hydrogen bond. D LYS 105 donates hydrogen to the pi orbitals of the ligand to form pi cation interactions. E THR 73 and E THR 146 on donating the hydrogen to the pi orbitals of the ligand to form pi donor hydrogen bonds. Hydrophobic interactions, E THR 73, make a pi sigma bond on the interaction of the C-H site with pi orbitals of the ligand. Alkyl groups of D LYS 105, D LYS 106, and D LYS 105 interact with pi orbitals of the ligand to form pi alkyl interaction. D LYS 105, D LYS 106, and D ARG 136 of alkyl groups interact with the 8-chloro position of the ligand to form alkyl interactions.
The determined docking score of A9 was − 8.0 kcal/mol, surrounded by E THR 146, DLYS 105, D LYS 106, and D ARG 136 amino acid residues of the receptor active site. In Hydrogen bond interactions, E THR 146 donates hydrogen to the acceptor at the nitrogen and oxygen atom of the ligand to make a conventional hydrogen bond. E THR 146 forms a carbon-hydrogen bond with the ligand. D LYS 105 donates hydrogen to the pi orbitals of the ligand to form pi cation interactions. E THR 146 on donating the hydrogen to the pi orbitals of the ligand to form pi donor hydrogen bonds. Hydrophobic interactions, Alkyl groups of D LYS 105, D LYS 106, D LYS 105 interact with pi orbitals of the ligand to form pi alkyl interaction. D LYS 105, D LYS 106, and D ARG 136 of alkyl groups interact with the 8-chloro position of the ligand to form alkyl interactions.
Admet Results
Nine descriptors associated with the ADME attributes of the ligands were evaluated using SWISS ADME (http://www.swissadme.ch/), displayed in Table 3, based on Lipinski’s rule of five, that is, molecular weight [MW] < 500 g/mol, Hydrogen bond acceptors [HBA] ≤ 5, Hydrogen bond donors [HBD] ≤ 10, and Octane/Water partition [log PO/W] ranges − 2 to 5 (Lipinski CA 2004). The topological polar surface of less than 120[AO]2/mol are orally active drug transport root, and less than 100[AO]2/mol is good brain penetration of CNS drug (Ertl P et al. 2000). PMDCK value of less than 25 indicates poor cell permeability and more than 500, for high cell permeability (Irvine JD et al. 1999). Apparent solubility ranges from − 6 to -0.5 (Lipinski CA 2000).
Table 3
ADME properties of the tittle compounds using SWISS ADME (http://www.swissadme.ch/)
Compound | MW (gm/mol) | HBA | HBD | Log PO/W | TPSA | Log S | PMDCK | BBB | Violation |
Alprazolam | 308.76 | 3 | 0 | 2.12 | 43.07 | -3.60 | High | Yes | 0 |
A1 | 324.76 | 3 | 0 | 1.56 | 59.46 | -2.42 | High | Yes | 0 |
A2 | 354.86 | 3 | 0 | 3.32 | 68.37 | -3.27 | High | Yes | 0 |
A3 | 401.87 | 5 | 1 | 1.93 | 97.62 | -2.29 | High | No | 0 |
A4 | 384.86 | 3 | 0 | 3.68 | 43.07 | -4.27 | High | Yes | 0 |
A5 | 395.89 | 5 | 0 | 2.65 | 55.54 | -2.25 | High | Yes | 0 |
A6 | 322.79 | 3 | 0 | 3.31 | 43.07 | -3.10 | High | Yes | 0 |
A7 | 338.79 | 4 | 1 | 2.49 | 63.30 | -2.26 | High | Yes | 0 |
A8 | 322.79 | 3 | 0 | 3.41 | 43.07 | -3.07 | High | Yes | 0 |
A9 | 395.84 | 5 | 1 | 2.59 | 95.39 | -3.20 | High | No | 0 |
A10 | 323.78 | 3 | 1 | 3.10 | 50.41 | -4.00 | High | Yes | 0 |
ADME– Absorption, Distribution, Metabolism, and Excretion; MW– Molecular weight; gm/mol- gram per molecule; HBA – Hydrogen Bond Acceptors; HBD– Hydrogen Bond Donors; TPSA– Topological Polar Surface Area; Log S– Logarithm of Solubility; Log Po/W– Logarithm of Octane/ Water partition; PMDCK– Permeability Maden Darby Canine Kidney; BBB- Blood Brain Barrier |
The MW of the analogue compounds was between 401.87 (A3) and 395.89 (A5). The MW values of A1-10 and Alprazolam were < 500 which obeys Lipinski’s rule of five. HBA of Alprazolam was determined as 3, which was taken as a reference ligand. Compounds A1, A2, A4, A6, A8, and A10 with 3 hydrogen bond acceptors; A7 (4) and A3, A4 (5) of HBA. All the compounds matched, without violating Lipinski’s rule of five. HBD of the A1, A2, A4, A5, A6, and A8 have no hydrogen donors; A3, A7, A9, and A10 have one hydrogen donor. Alprazolam does not have any hydrogen donor. All the analogues and Alprazolam obey Lipinski’s rule of five.
The log P0/W value ranges between 1.56(A1) and 3.68(A4). Compounds A2, A3, A6-10 values determined as 3.32, 1.92, 2.65, 3.31, 2.49, 3.41, 2.59, and 3.10. Alprazolam is a reference compound valued at 2.12 and matched to the values of drug-likeness.
TPSA values that are elucidated range between 97.62[AO]2/mol (A3) and 43.07[AO]2/mol (A4, A6, and A8). Compounds A1, A2, A5, A7, A9, and A10 were determined as 59.46[AO]2/mol, 68.37[AO]2/mol, 55.54[AO]2/mol, 63.30[AO]2/mol, 95.39[AO]2/mol, and 50.41[AO]2/mol. Alprazolam has TPSA of 43.07[AO]2/mol. The compounds' solubility (log S) values were between − 4.27(A4) and − 2.25(A5). Furthermore, the Alprazolam value of -3.60. The solubility of all compounds matched the drug-likeness values. PMDCK of all the compounds A1-10 compounds, including the reference compound exhibited high PMDCK.
The BOILED-Egg model (Dania A and Zoete V 2016) in Fig. 5 had shown that all the ligands are passively absorbed by the gastrointestinal tract in the white region referred to as Human Intestinal Absorption (HIA). Compounds molecule (A3), and molecule 10 (A9) does not cross the BBB. The rest of the ligands A1, A2, A4-8, A10, and Alprazolam exhibited the ability of crossing BBB. All the ligands showed permeability to the glycoproteins that effluated from the central nervous system (blue dots). A3 and A9 analogue ligands do not show blood-brain barrier penetration. The rest of the compounds including Alprazolam displayed an ability to cross BBB. None of the ligands not effluated from the CNS (red dots) as shown in Fig. 5 BOILED-Egg model.
The OSIRIS server identified that none of the compounds are irritant, tumorigenic, mutagenic, and do not exhibit reproductive toxicity.