| Literature DB >> 26170618 |
Shih-Hung Lin1, Kao-Jean Huang2, Ching-Feng Weng1, David Shiuan1.
Abstract
Cholesterol plays an important role in living cells. However, a very high level of cholesterol may lead to atherosclerosis. HMG-CoA (3-hydroxy-3-methylglutaryl coenzyme A) reductase is the key enzyme in the cholesterol biosynthesis pathway, and the statin-like drugs are inhibitors of human HMG-CoA reductase (hHMGR). The present study aimed to virtually screen for potential hHMGR inhibitors from natural product to discover hypolipidemic drug candidates with fewer side effects and lesser toxicities. We used the 3D structure 1HWK from the PDB (Protein Data Bank) database of hHMGR as the target to screen for the strongly bound compounds from the traditional Chinese medicine database. Many interesting molecules including polyphenolic compounds, polisubstituted heterocyclics, and linear lipophilic alcohols were identified and their ADMET (absorption, disrtibution, metabolism, excretion, toxicity) properties were predicted. Finally, four compounds were obtained for the in vitro validation experiments. The results indicated that curcumin and salvianolic acid C can effectively inhibit hHMGR, with IC50 (half maximal inhibitory concentration) values of 4.3 µM and 8 µM, respectively. The present study also demonstrated the feasibility of discovering new drug candidates through structure-based virtual screening.Entities:
Keywords: HMG-CoA reductase; curcumin; salvianolic acid C; virtual screening
Mesh:
Substances:
Year: 2015 PMID: 26170618 PMCID: PMC4492635 DOI: 10.2147/DDDT.S84641
Source DB: PubMed Journal: Drug Des Devel Ther ISSN: 1177-8881 Impact factor: 4.162
Figure 1Identification of the ligand-binding sites of hHMGR.
Notes: (A) The tetrameric structure of hHMGR (PDB 1HWK). (B) The dimeric hHMGRs displaying subunit a (red), subunit B (green), and atorvastatin (yellow). (C) The active site from PDB site record. (D) analysis of the ligand–receptor interactions.
Abbreviations: hHMGR, human HMG-CoA reductase; PDB, Protein Data Bank.
Figure 2The 2D structures of the known statin molecules and their IC50 values against hHMGR.
Abbreviations: 2D, two dimensional; hHMGR, human HMG-CoA reductase; IC50, half maximal inhibitory concentration.
The docking scores, basic properties, and IC50 of the known statins
| Statins | Formula | –PMF | DOCK | MW | IC50 (nM) | |
|---|---|---|---|---|---|---|
| Atorvastatin | C33H33FN2O5 | 87 | 54 | 558 | 5.0 | 8 |
| Cerivastatin | C26H34FNO5 | 84 | 62 | 459 | 3.6 | 10 |
| Simvastatin | C25H38O5 | 78 | 42 | 411 | 4.7 | 11 |
| Mevastatin | C23H34O5 | 73 | 43 | 390 | 3.9 | 23 |
| Fluvastatin | C24H26FNO4 | 71 | 60 | 411 | 3.5 | 28 |
Abbreviations: IC50, half maximal inhibitory concentration; MW, molecular weight; –PMF, potential of mean force; x Log P, predicted octanol/water distribution.
The docking scores, physicochemical properties, and the number of hydrogen bonds between the selected ten compounds and hHMGR
| Compound number | –PMF | DOCK | MW | HBD | HBA | H-bond | |
|---|---|---|---|---|---|---|---|
| 1 | 146.0 | 81.0 | 492.4 | 4.1 | 6 | 10 | 3 |
| 2 | 138.8 | 77.0 | 548.4 | 0.1 | 8 | 14 | 2 |
| 3 | 129.0 | 63.0 | 368.3 | 3.2 | 2 | 6 | 2 |
| 4 | 117.9 | 73.0 | 496.4 | 0.3 | 7 | 12 | 2 |
| 5 | 114.6 | 70.7 | 458.0 | 1.2 | 8 | 11 | 2 |
| 6 | 110.7 | 66.6 | 486.5 | −2.3 | 7 | 11 | 1 |
| 7 | 103.3 | 74.4 | 369.4 | 3.8 | 3 | 6 | 2 |
| 8 | 98.3 | 44.0 | 326.6 | 8.8 | 1 | 1 | 1 |
| 9 | 88.6 | 35.0 | 354.6 | 9.3 | 1 | 1 | 1 |
| 10 | 74.5 | 131.9 | 441.3 | −0.2 | 6 | 9 | 1 |
Note:
Potential H-bond between the compound and hHMGR.
Abbreviations: HBA, hydrogen bond acceptor; HBD, hydrogen bond donor; hHMGR, human HMG-CoA reductase; MW, molecular weight; -PMF, potential of mean force; x Log P, predicted octanol/water distribution.
Figure 3The 2D structures of the selected top ten compounds.
Abbreviation: 2D, two dimensional.
The plant origins and IUPAC names of the selected ten compounds
| Compound | Plant origin | IUPAC name |
|---|---|---|
| 1. Salvianolic acid c (C26H20O10) | (2r)-3-(3,4-dihydroxyphenyl)-2-[(E)-3-[2-(3,4-dihydroxyphenyl)-7-hydroxy-1-benzofuran-4-yl]prop-2-enoyl] oxypropanoic acid | |
| 2. Quercetin-3- | 3-[[(2R,3S,4S,5R,6S)-6-[2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4-oxochromen-3-yl]oxy-3,4,5-trihydroxyoxan-2-yl]methoxy]-3-oxopropanoic acid | |
| 3. Curcumin (C21H20O6) | (1E,6E)-1,7-bis(4-hydroxy-3-methoxyphenyl)-1,6-heptadiene-3, 5-dione | |
| 4. Ampelopsisin (C23H28O12) | [(2R,3S,4R,5R,6S)-3,4,5-trihydroxy-6-[4-(1-hydroxypropan-2-yl)-2-methoxyphenoxy]oxan2-yl] methyl 3,4,5-trihydroxybenzoate | |
| 5. Epigallocatechin-3-gallate (C22H18O11) | cis-3,3′,4′,5,5′,7-Hexahydroxy-flavane-3-gallate, (−)-cis-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-1(2h)-benzopyran-3,5,7-triol 3-gallate | |
| 6. | 1(3H)-isobenzofuranone, 3-butylidene | |
| 7. Tenellin (C21H23NO5) | 3-[(2E,4E)-4,6-dimethyl-2,4-octadienoyl]-1,4-dihydroxy-5-(4-hydroxyphenyl)-2(1H)pyridinone | |
| 8. Docosanol (C22H46O) | Docosan-1-ol | |
| 9. Tetracosanol (C24H50O) | Tetracosan-1-ol | |
| 10. Folic acid (C19H19N7O6) | (2S)-2-[(4-{[(2-amino-4-hydroxypteridin-6-yl)methyl] amino} phenyl) formamido] pentanedioic acid |
Abbreviation: IUPAC, international Union of Pure and Applied Chemistry.
Figure 4Inhibition on hHMGR enzyme activities by (A) salvianolic acid c, (B) curcumin, and (C) docosanol.
Abbreviation: hHMGR, human HMG-CoA reductase.
Figure 5Potential cytotoxic activities of the selected compounds: salvianolic acid C (gray), curcumin (blank column), and docosanol (horizontal lines).
Note: atorvastatin (black) was used as the positive control.
Figure 6The ligand–protein interaction analyses of salvianolic acid C with hHMGR.
Notes: (A) The overall ribbon structure. (B) The 3D hydrophobicity surface plot at the binding site. (C) The interaction analyses in 2D. (D) The predicted H-bonds between the ligand and the nearby binding site residues.
Abbreviations: 2D, two dimensional; 3D, three dimensional; hHMGR, human HMG-CoA reductase.
ADMET predictions of the ten selected compounds and statins
| Compound name | –PMF | A | D | M | E | T-H | |
|---|---|---|---|---|---|---|---|
| 1 | 146 | 3 very low | 2 yes, low | 4 undefined | 0 noninhibitor | 1 binding is >90% | 0 N-T |
| 2 | 138.8 | 3 very low | 2 yes, low | 4 undefined | 0 noninhibitor | 0 binding is <90% | 0 N-T |
| 3 | 129 | 3 very low | 3 yes, good | 4 undefined | 0 noninhibitor | 0 binding is <90% | 0 N-T |
| 4 | 117.9 | 3 very low | 3 yes, good | 4 undefined | 0 noninhibitor | 0 binding is <90% | 0 N-T |
| 5 | 114.6 | 3 very low | 1 no, low | 4 undefined | 0 noninhibitor | 0 binding is <90% | 0 N-T |
| 6 | 110.7 | 0 good | 3 yes, good | 4 undefined | 0 noninhibitor | 0 binding is <90% | 0 N-T |
| 7 | 103.3 | 0 good | 3 yes, good | 4 undefined | 0 noninhibitor | 1 binding is >90% | 0 N-T |
| 8 | 98.3 | 3 very low | 1 no, low | 4 undefined | 1 inhibitor | 2 binding is >95% | 0 N-T |
| 9 | 88.6 | 3 very low | 1 no, low | 4 undefined | 1 inhibitor | 2 binding is >95% | 0 N-T |
| 10 | 74.5 | 3 very low | 3 yes, good | 4 undefined | 0 noninhibitor | 0 binding is <90% | 0 N-T |
| A | 87 | 2 low | 2 yes, low | 4 undefined | 0 noninhibitor | 2 binding is >95% | 1 T |
| C | 84 | 0 good | 2 yes, low | 4 undefined | 0 noninhibitor | 1 binding is >90% | 1 T |
| S | 78 | 0 good | 2 yes, low | 1 high | 0 noninhibitor | 1 binding is >90% | 0 N-T |
| M | 73 | 0 good | 2 yes, low | 2 medium | 0 noninhibitor | 1 binding is >90% | 1 T |
| F | 71 | 0 good | 2 yes, low | 2 medium | 0 noninhibitor | 0 binding is <90% | 0 N-T |
Notes:
The following numerals and alphabets represent: 1, salvianolic acid C; 2, quercetin-3-O-(6′-malonyl) glucoside; 3, curcumin; 4, ampelopsisin; 5, epigallocatechin-3-gallate; 6, Z-ligustilide-SG1a; 7, tenellin; 8, docosanol; 9, tetracosanol; 10, folic acid; A, atorvastatin; C, cerivastatin; S, simvastatin; M, mevastatin; F, fuvastatin.
Absorption: intestinal absorption.
Distribution: aqueous solubility blood–brain barrier penetration.
Metabolism: YPA2D6.
Excretion: plasma protein binding;
Toxicity: hepatotoxicity.
Abbreviation: ADMET, absorption, distribution, metabolism, excretion, toxicity; N-T, nontoxic.