| Literature DB >> 25247142 |
Vadlapudi Kumar1, Chethan S Kumar1, Gajula Hari1, Nayana K Venugopal1, Poornima D Vijendra1, Giridhara Basappa B1.
Abstract
Centella asiatica is a well-known medicinal plant, produces large amount of triterpenoid saponins, collectively known as centelloids, with a wide-spectrum of pharmacological applications. Various strategies have been developed for the production of plant secondary metabolites in cell and tissue cultures; one of these is modular metabolic engineering, in which one of the competitive metabolic pathways is selectively suppressed to channelize precursor molecules for the production of desired molecules by another route. In plants the precursor 2,3-oxidosqualene is shared in between two competitive pathways involved with two isoforms of oxidosqualene cyclases. One is primary metabolic route for the synthesis of phytosterol like cycloartenol by cycloartenol synthase; another is secondary metabolic route for the synthesis of triterpenoid like β-amyrin by β-amyrin synthase. The present work is envisaged to evaluate specific negative modulators for cycloartenol synthase, to channelize the precursor molecule for the production of triterpenoids. As there are no experimentally determined structures for these enzymes reported in the literature, we have modeled the protein structures and were docked with a panel of ligands. Of the various modulators tested, ketoconazole has been evaluated as the negative modulator of primary metabolism that inhibits cycloartenol synthase specifically, while showing no interaction with β-amyrin synthase. Amino acid substitution studies confirmed that, ketoconazole is specific modulator for cycloartenol synthase, LYS728 is the key amino acid for the interaction. Our present study is a novel approach for identifying a suitable specific positive modulator for the over production of desired triterpenoid secondary metabolites in the cell cultures of plants.Entities:
Keywords: Cycloartenol synthase; Docking studies; Oxidosqualene cyclases; Protein modeling; β-amyrin synthase
Year: 2013 PMID: 25247142 PMCID: PMC4169231 DOI: 10.1186/2193-1801-2-189
Source DB: PubMed Journal: Springerplus ISSN: 2193-1801
Figure 1A simplified scheme of triterpenoid biosynthesis in Farensyl diphosphate synthase (FPS) isomerizes isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) to farensyl diphosphate (FPP), which squalene synthase (SQS) converts to squalene. Squalene epoxidase (SQE) oxidises squalene to 2,3-oxidosqualene. Oxidosqualene cyclase (OSC) enzymes cyclize 2,3-oxidosqualene through cationic intermendiates (e.g. dammarenyl cation) to one or more cyclic triterpene skeletons. Other enzymes involved include α/β-amyrin synthases (α/β-AS) which can also form the lupenyl cation but further ring expansion and rearrangements are required before the deprotonation to α/β-amyrin, the precursors of the sapogenins, to generate the products.
Figure 2Alignment of amino acid residues of cycloartenol synthase and β-amyrin synthase. QW motifs are shown in single underline and DCTAE motifs in double underline.
Retrieved sequences from the databases
| Source | OSC | Accession no | Sequence length | ||
|---|---|---|---|---|---|
| Nucleotide | Protein | Nucleotide | Protein | ||
|
| Cycloartenol synthase | AY520819 | AAS01524 | 2547 bp | 757 aa |
|
| β-amyrin synthase | AY520818 | AASO1523 | 2562 bp | 760 aa |
Results of protein modeling using SWISS-MODEL
| Template PDB ID | Target | Sequence identity | QMEAN4 Score |
|---|---|---|---|
| 1W6JA | Cycloartenol synthase | 42.27% | 0.42 |
| 1W6JA | β-amyrin synthase | 36.31% | 0.45 |
Figure 3Modelled structures of two enzymes of . a) Cycloartenol synthase and b) β-amyrin synthase.
Results of structure validation using RAMPAGE
| Assessment | Cycloartenol synthase | β-amyrin synthase |
|---|---|---|
| Favored region | 92.90% | 90.09% |
| Allowed region | 4.50% | 5.30% |
| Outlier region | 2.50% | 3.70% |
Figure 4Modelled structures of reciprocally amino acid substituted enzymes of a) Cycloartenol synthase and b) β-amyrin synthase.
Results of reciprocal studies of protein modeling using SWISS-MODEL
| Template PDB ID | Target | Sequence Identity | QMEAN4 Score |
|---|---|---|---|
| 1W6JA | Cycloartenol synthase with VAL 728 for LYS 728 | 42.14% | 0.424 |
| 1W6JA | β-amyrin synthase with LYS 728 for VAL 728 | 36.18% | 0.405 |
Results of reciprocal studies of structure validation using RAMPAGE
| Assessment | Cycloartenol synthase with VAL 728 for LYS 728 | β-amyrin synthase with LYS 728 for VAL 728 |
|---|---|---|
| Favored region | 92.90% | 90.09% |
| Allowed region | 4.50% | 5.30% |
| Outlier region | 2.50% | 3.70% |
| Structure Accuracy with non-substituted structures | 99.9% | 99.9% |
Figure 5Ramachandran Maps of CAS and β-AS generated by Rampage. Dark blue and dark orange are favored regions. Light blue and light orange are allowed regions. a) Cycloartenol synthase and b) β-amyrin synthase.
Figure 6Ramachandran Maps of CAS and β-AS generated by Rampage for reciprocally amino acid substituted enzymes of . Dark blue and dark orange are favored regions. Light blue and light orange are allowed regions. a) Cycloartenol synthase and b) β-amyrin synthase.
Modulators for cycloartenol synthase and β-amyrin synthase
| Sl. No. | Modulators used in the present study |
|---|---|
| 1 | 2-aza-2,3-dihydrosqualenea |
| 2 | 3-β-(2-Diethylaminoethoxy) androsteroneandrosteroneb |
| 3 | 4-hydroxypiperidinec |
| 4 | 8-azadecalinc |
| 5 | Benzenesulfonic acidd |
| 6 | Fluconazolee |
| 7 | Itraconazolee |
| 8 | Ketoconazolee |
| 9 | Methyl jasmonatef |
| 10 | NEM (N-ethylmaleimide)g |
| 11 | Sodium deoxycholateh |
| 12 | N-[(1,5,9)-Trimethyl-decayl]-4α, 10-dimethyl-8-aza-trans-decal-3β-oli |
| 13 | N-lauryl-N-dimethylamino-N-oxidej |
| 14 | Pectin/Oligogalacturonic acidk |
a Ref : (Delprino et al. 1983).
b Ref : (Fenner & Raphiou 1995).
c Ref : (Taton et al. 1992).
d Ref : (Abe et al. 1993).
e Ref : (Goldman et al. 1996).
f Ref : (Kim et al. 2005).
g Ref : (Abe et al. 1992).
h Ref : (Beastall et al. 1971).
i Ref : (Taton et al. 1986).
j Ref : (Schmitt et al. 1987).
k Ref : (Flores-Sanchez et al. 2002; Hu et al. 2003).
Figure 7Structures of the modulators considered for the study.
Predicted ligand binding site of CAS and β-AS using Q-SiteFinder
| Cycloartenol synthase | β-amyrin synthase | ||
|---|---|---|---|
| Residues | Residue number | Residues | Residue number |
| TYR | 118 | PRO | 124 |
| PRO | 121 | PHE | 127 |
| LEU | 124 | TRP | 258 |
| TRP | 255 | CYS | 259 |
| CYS | 256 | TYR | 260 |
| HIS | 257 | ILE | 368 |
| CYS | 258 | GLY | 369 |
| ILE | 365 | CYS | 370 |
| GLY | 366 | VAL | 771 |
| PRO | 367 | GLN | 411 |
| VAL | 368 | SER | 412 |
| GLY | 409 | TRP | 418 |
| TYR | 410 | PHE | 474 |
| TRP | 479 | VAL | 483 |
| ILE | 481 | ASP | 485 |
| THR | 531 | CYS | 486 |
| TYR | 532 | ILE | 534 |
| GLU | 533 | TRP | 535 |
| PHE | 550 | CYS | 565 |
| ILE | 553 | TRP | 613 |
| ASP | 556 | TYR | 619 |
| TYR | 559 | *VAL | *728 |
| SER | 609 | TYR | 729 |
| TRP | 610 | LEU | 735 |
| VAL | 725 | TYR | 737 |
| PHE | 726 | TYR | 740 |
| ASN | 727 | ||
| *LYS | *728 | ||
| CYS | 730 | ||
| ILE | 732 | ||
*Amino acid residue changes between two enzymes at ketoconazole binding site of cycloartenol synthase (LYS 728).
Docking results of CAS and BAS using Argus Lab
| Ligands | Best ligand pose (E = kcal/mol) | |
|---|---|---|
| Cycloartenol synthase | β-amyrin synthase | |
| 2-Aza-2,3-dihydrosqualene | −19.1334 | −19.4249 |
| 3-β-(2-Diethylaminoethoxy) androsteroneandrosterone | ---* | −13.1427 |
| 4-hydroxypiperidine | - 6.96723 | - 7.01001 |
| 8-Azadecalin | - 9.3033 | - 10.027 |
| Benzenesulfonic acid | - 9.19979 | - 10.1391 |
| Fluconazole | - 9.44939 | - 10.1095 |
| Itraconazole | ---* | ---* |
| Ketoconazole | - 8.82927 | ---* |
| NEM (N-ethylmaleimide) | - 6.36966 | - 6.89406 |
| Sodium deoxycholate | ---* | - 14.3559 |
| N-[(1,5,9)-Trimethyl-decayl]-4alpha, 10-dimethyl-8-aza-trans-decal-3beta-ol | - 15.4413 | - 15.4102 |
| N-Lauryl-N-dimethylamino-N-oxide | - 11.4094 | - 12.2249 |
| Pectin/Oligogalacturonic acid | - 7.60546 | - 7.48043 |
| Methyl jasmonate | - 11.2485 | - 11.2796 |
---* No acceptable ligand poses were found.
Figure 8Interaction between CAS and ketoconazole in cartoon and solid representation. (a) Interaction between amino acid residue 728 and hydrogen atom of ketoconazole. (b) Interaction between amino residue LYS 728 of CAS and hydrogen atom of ketoconazole. (c) Interaction between hydrogen atom of CAS and oxygen atom of ketoconazole. (d) Binding surface of CAS.
Figure 9Interaction between reciprocally amino acid substituted enzymes of . (a) Non-substituted CAS with LYS 728 and ketoconazole. (b) Substituted CAS with VAL 728 for LYS 728 and ketoconazole. (c) Non-substituted BAS with VAL 728 and ketoconazole. (d) Substituted BAS with LYS 728 for VAL 728 and ketoconazole. *Ligand and amino acids at 728 position in modeled protein structures are shown in rectangle/square.