Fig 1.
The structure of LCAT with compound 1b bound to the allosteric site.
The α/β hydrolase domain is colored as purple, the cap domain as gray, and the membrane-binding domain as green. The a1-a2 region of the MBD (amino acids 63–75) is marked with orange. The protein is rendered as a cartoon secondary structure representation and the compound as blue sticks. The compound (hued blue) and the amino acids ASN78, ASP63, TYR51, and MET49 are rendered with sticks and colored according to the element types. Carbon atoms are cyan, oxygen red, nitrogen blue, fluorine pink, and sulfur yellow.
Fig 2.
(A) The chemical structures of the compounds studied. (B) The docking poses of the compounds bound (hued purple) in the MBD cleft of LCAT and the co-crystallized compound 1b (PDB accession code 6MVD; hued blue) compared to its position docked back the structure (hued red). The allosteric site of LCAT is rendered as a cartoon secondary structure representation and shown as green. The compounds and the significant amino acids are rendered as sticks and are colored according to different elements. Carbon atoms are cyan, oxygen red, nitrogen blue, fluorine pink, and sulfur yellow.
Table 1.
The calculated binding free energies for the compounds docked either to the X-ray structure or the simulated structure of LCAT (after 1 us).
Fig 3.
(A) The average number of hydrogen bonds formed between the MBD amino acids and drug compounds during the whole simulation trajectory. (B) The average number of hydrophobic interactions between drugs and amino acids showing the most variation for compound 8 relative to other compounds. (C) Visualization of the primary hydrogen bonding pairs between compounds and LCAT. Snapshots from Drug-1B (Top) and Drug-2A (Bottom) simulations showing the conformations of compounds 1b and 2a in the cleft of MBD. The hydrogen bonds between drugs and amino acids are marked with black dashed lines. Compounds 1b and 2a are rendered as sticks and are colored according to the element types. Compound 1b is hued purple and 2a orange. The MBD cleft is rendered as a cartoon representation and colored green. Amino acids forming hydrogen bonds with compounds are rendered as sticks and colored according to the element types. Carbon atoms are cyan, oxygen red, nitrogen blue, fluorine pink, and sulfur yellow.
Fig 4.
(A) The average distances between the relevant residues mapped as a distance matrix plot. Drug 2a is used as an example as the rest of the compounds induced a similar change. (B) The distance between the α-carbon atoms of M66 and I231 as a function of time in Drug-2a and Nodrug-2 simulations (Left). The average distances between the α-carbon atoms of M66 and I231 for all simulated systems (Right). (C) Snapshots from Drug-2a and Nodrug-2 simulation showing the maxima and minima of the detected conformational change. The proteins are rendered as cartoons and the marker residues’ α-carbons as red spheres. (D) The distance plot derived from the simulation where compound 2a was removed from the allosteric site after 800 ns (Left). Two simulation snapshots superimposed showing the orientation of the MBD domain before (0 ns; green) and after the removal of compound 2a (120 ns; blue) (Right).
Fig 5.
(Left) Spatial energetics of the MBD. The free energy profiles as a function of the distance between M66 and I231 α-carbon atoms with and without compound 2a. (Right) A blue cartoon presentation of LCAT showing the ILE231 and MET66 Cα atoms (red spheres) that were used to determine the conformational free energy as a function of distance.
Fig 6.
(Left) Steered molecular dynamics analysis showing the distance of the α-carbon atom of MET66 from the initial position as a function of time. (Right) Superimposed snapshots illustrating the pulling pathway of the lid loop. The light red and blue cartoon or van der Waals renderings mark the lid loop’s open and closed states, respectively. The rest of the LCAT enzyme is rendered as a grey cartoon representation. The black arrow indicates the movement of the lid loop during the pulling simulations. The active site tunnel opening is marked with a yellow sphere.