Figure 1.
A biochemical reaction catalyzed by HMGR.
HMG-CoA is converted to mevalonte using two molecules of NADPH. The reaction proceeds by two successive hydride transfers.
Figure 2.
Functional domain and 3D structures of the human HMGR.
(A) Human HMGR consists of 888 amino acids and is divided into three domains: membrane anchor domain, linker domain, and catalytic domain. In the catalytic domain, further separated into three subdomain named as N domain, L domain, and S domain. Cis-loop which acts as HMG binding pocket is present between S and L domain. (B) Crystal structure of the human HMGR monomer with NAD (P), cofactor (PDB ID: 1DQA). The protein was represented as cartoon model and this figure was prepared using PyMOL.
Figure 3.
The chemical structures of human HMGR inhibitors used in pharmacophore model generation along with their IC50 values.
Figure 4.
The generated pharmacophore model with their inter-feature distance constraints.
HBA, HBD, and HYP features are displayed in green, magenta, and cyan, respectively.
Table 1.
The results of the common feature pharmacophore model generation and validation.
Figure 5.
The best pharmacophore model aligned with the retrieved hit compounds obtained from virtual screening.
(A) Hit1 (B) Hit2 (C) Hit3 (D) Hit4. HBA, HBD, and HYP features are displayed in green, magenta, and cyan, respectively. Hit compounds are represented in stick model.
Figure 6.
The RMSD and potential energy plots for six complex structures.
(A) The RMSD for backbone atoms of the protein. (B) The potential energy of the system. These plots are calculated during 10 ns MD simulations for each complex. Blue, red, green, purple, cyan, and orange lines represent Inh1 (rosuvastatin), Inh2 (atorvastatin), Hit1, Hit2, Hit3, and Hit4, respectively.
Figure 7.
The binding modes of reference and four hit compounds.
All compounds in their representative structures were superimposed (left) and enlarged (right). The dimeric structure of HMGR is shown by cartoon model and each monomer is displayed in cyan and salmon color. All compounds are represented as stick model and in the same colors described in Fig. 6. Only polar hydrogen atoms were shown for clarify.
Table 2.
The details of six systems used for MD simulations.
Figure 8.
The binding orientations and hydrogen bonding interactions of reference and four hit compounds in the active site of HMGR.
(A) Inh1 (B) Inh2 (C) Hit1 (D) Hit2 (E) Hit3 (F) Hit4. All compounds and interacting residues belong to both monomers (called ‘a’ and ‘b’) are represented as pink stick model. Hydrogen bond interactions between compounds and proteins are shown as gray dotted line. Only polar hydrogen atoms were shown for clarify.
Table 3.
Molecular interactions between compound and protein.
Figure 9.
The number of hydrogen bonds between compound and protein during 10 ns MD simulations.
Blue, red, green, purple, cyan, and orange colors represent Inh1 (rosuvastatin), Inh2 (atorvastatin), Hit1, Hit2, Hit3, and Hit4, respectively.
Figure 10.
2D structures of final hit compounds.
Hit1 and Hit4 were obtained from ASINEX database and the other hits were identified from Maybridge database.