Table 1.
Validation of models before and after MDS by profile-3D.
Table 2.
Validation of models before and after MDS by ProSA analysis.
Figure 1.
Constitutional formulae of four inhibitor compounds used for investigating binding poses with LPL, HL and EL.
Table 3.
Inhibitors used in the docking investigation.
Figure 2.
Sequence alignment between each lipase and their respective template.
1 LPA_B (Homo sapiens) and 1 GPL_A (Cavia porcellus) were used as templates for LPL (a), and EL (c) or HL (b). Red indicates identical amino acids, yellow indicates similar amino acids, and light blue designates somewhat similar amino acids. The amino acid sequences of lid elements of these lipases are marked with a red box.
Figure 3.
Multiple alignment of LPL, HL, and EL against the PL sequence.
Red indicates identical amino acids, yellow indicates similar amino acids, and light blue designates somewhat similar amino acids. Amino acids are numbered according to convention, beginning with the first residue of the secreted protein. The predicted sites of signal peptide cleavage are marked with a solid line between amino acid residues. The GXSXG lipase motif containing the active serine is marked with black box. The amino acids of the catalytic triad are marked with an asterisk (Ser132, Asp156, and His241 in LPL, Ser146, Asp172, and His257 in HL, and Ser151, Asp175, and His256 in EL). The amino acid sequences of lid elements of the three lipases are marked with red boxes.
Figure 4.
Ramachandran plot of the LPL, HL, and EL models.
The different color codes indicate most favored (red), generously allowed (dark yellow), additionally allowed (light yellow), and disallowed (white) regions. For LPL, 84.5% of the residues were in the most favored regions, 12.4% in additionally allowed regions, 2.1% in generously allowed regions, and 1.0% in disallowed regions. In the case of HL, 84.7% of residues were in the most favored regions, 13.9% in additionally allowed regions, 1.2% in generously allowed regions, and 0.2% in disallowed regions. Similarly for EL, 87.3% of residues were in the most favored regions, 10.4% in additionally allowed regions, 1.5% in generously allowed regions, and 0.7% in disallowed regions.
Figure 5.
LPL, HL, and EL plots show the variation in potential energy throughout the system for a period of 4 ns. X-axis: time (ps). Y-axis: the potential energy (KJ/mol).
Figure 6.
Graphical representation of the root mean square deviation (RMSD) plot.
Backbone RMSD for LPL, HL, and EL from the initial structures throughout the simulation of 4 ns, as a function of time. X-axis: time (ps). Y-axis: RMSD (ns).
Figure 7.
Views of putative binding pockets of LPL, HL, and EL.
Predicted pockets of (a) LPL, (b) HL, and (c) EL are shown. The binding pocket information is created by Cavity. The key catalytic residues previously identified are all located in pocket 1. The graphics are generated using PyMOL program (http://www.pymol.org).
Figure 8.
The pharmacophore features of (a) LPL, (b) HL, and (c) EL created by the Cavity approach.
The red ball represents a “Hydrogen bond acceptor”, the blue ball represents a “Hydrogen bond donor”, and the gray ball represents a Van Der Waals and hydrophobic contact. Pharmacophore features located in binding pockets, and their corresponding residues, have been marked and labeled. The graphics are generated using the PyMOL program (http://www.pymol.org).
Figure 9.
The triangles formed by the catalytic triad before and after MDS.
From top to bottom on the left side: the structure and spatial triangle formed by catalytic triad residues before MDS. (a) LPL, (c) HL, and (e) EL. From top to bottom on the right side: the structure and spatial triangle formed by catalytic triad residues after MDS. (b) LPL, (d) HL, and (f) EL.
Figure 10.
Binding modes and interactions of LPL with its inhibitors, CHEMBL339297 and CHEMBL485946.
The pictures on the left side are of LPL complexed with (a) CHEMBL339297, and (c) CHEMBL485946. The protein surface and binding pocket is colored, with blue representing the positively charged region, red representing the negatively charged region, green representing the hydrophobic region, and gray representing the protein backbone. The pictures on the right side were created by LigPlot+ [48] for the representation of the interactions with (b) CHEMBL339297 and (d) CHEMBL485946, showing the inhibitors (purple), residues involved in hydrogen bonding with the ligand (brown), along with their hydrogen bonds (green), and residues involved in non-bonded interactions (red spikes).
Figure 11.
Binding modes and interactions of HL with its inhibitors, CHEMBL339297 and CHEMBL133897.
The pictures on the left side are of HL complexed with (a) CHEMBL339297 and (c) CHEMBL133897. The protein surface and binding pocket is colored, with blue representing positively charged region, red representing the negatively charged region, green representing the hydrophobic region, and gray representing the protein backbone. The pictures on the right side were created by LigPlot+ to represent the interactions with (b) CHEMBL339297 and (d) CHEMBL133897, showing the inhibitors (purple), residues involved in hydrogen bonding with the ligand (brown), along with their hydrogen bonds (green), and the residues involved in non-bonded interactions (red spikes).
Figure 12.
Binding modes and interactions of EL with its inhibitors, CHEMBL467023 and CHEMBL485946.
The pictures on the left side are the EL complexed with (a) CHEMBL467023 and (c) CHEMBL485946. The protein surface and binding pocket is colored, with blue representing positively charged region, red representing the negatively charged region, green representing the hydrophobic region and gray representing the protein backbone. The pictures on the right side were created by LigPlot+ to represent the interactions with (b) CHEMBL467023 and (d) CHEMBL485946, showing the inhibitors (purple), residues involved in hydrogen bonding with the ligand (brown), along with their hydrogen bonds (green), and residues involved in non-bonded interactions (red spikes).