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Virtual screening of compounds from the patchouli oil of Pogostemon herba for COX-1 inhibition.

ABSTRACT: Our interest is to identify compounds from the patchouli oil of Pogostemon herba to inhibit the cyclooxygenase-1 (COX-1) enzyme activity. The data for the major compounds (alpha-patchouli alcohol isomer (CD521903, CD442384, and/or CD6432585), alphabulnusene, seychellene and alpha-guaiene) of patchouli oil were explored from the PubChem database. The compounds to COX-1 interactions were studied using the molecular docking tools Hex 6.12 and LeadIT2 Bisolve. The interactions were further visualized using the Chimera 1.7s viewer software tool. The analysis of the major compounds of patchouli oil showed that alpha-Patchouli alcohol (CD521903) binds to COX-1 at many active sites including: Leu223B, Asp228B, Leu237B, Arg332B, Trp138A, Glu139A, Ser142A, and Asn143A. Further analysis revealed that these binding sites are maintained by hydrogen bonds with Ser142A, Glu139A, and Asp228B. The interaction energy between COX-1 and alpha-patchouli alcohol (CD521903) is -6 kJ/mol (without solvent) and -15 kJ/ mol (with solvent DMSO). These theoretical data suggests alpha-patchouli alcohol as a potential inhibitor of the COX-1 enzyme. However, these observations should be investigated and confirmed using experimental evidence.

SUBMITTER: Raharjo SJ

PROVIDER: S-EPMC3607192 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Virtual screening of compounds from the patchouli oil of Pogostemon herba for COX-1 inhibition.

Raharjo Sentot Joko SJ Fatchiyah Fatchiyah F

Bioinformation 20130319 6

Our interest is to identify compounds from the patchouli oil of Pogostemon herba to inhibit the cyclooxygenase-1 (COX-1) enzyme activity. The data for the major compounds (alpha-patchouli alcohol isomer (CD521903, CD442384, and/or CD6432585), alphabulnusene, seychellene and alpha-guaiene) of patchouli oil were explored from the PubChem database. The compounds to COX-1 interactions were studied using the molecular docking tools Hex 6.12 and LeadIT2 Bisolve. The interactions were further visualize ...[more]

PMID: 23559751

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Project description:Pogostemon cablin, a medicinally and economically important perennial herb, is cultivated around the world due to its medicinal and aromatic properties. Different P. cablin cultivars exhibit different morphological traits and patchouli oil components and contents (especially patchouli alcohol (PA) and pogostone (PO)). According to the signature constituent of the leaf, P. cablin was classified into two different chemotypes, including PA-type and PO-type. To better understand the molecular mechanisms of PA biosynthesis, the transcriptomes of Chinese-cultivated P. cablin cv. PA-type "Nanxiang" (NX) and PO-type "Paixiang" (PX) were analyzed and compared with ribonucleic acid sequencing (RNA-Seq) technology. We obtained a total of 36.83 G clean bases from the two chemotypes, compared them with seven databases and revealed 45,394 annotated unigenes. Thirty-six candidate unigenes participating in the biosynthesis of PA were found in the P. cablin transcriptomes. Overall, 8,390 differentially expressed unigenes were identified between the chemotypes, including 2,467 upregulated and 5,923 downregulated unigenes. Furthermore, six and nine differentially expressed genes (DEGs) were mapped to the terpenoid backbone biosynthetic and sesquiterpenoid and triterpenoid biosynthetic pathways, respectively. One key sesquiterpene synthase gene involved in the sesquiterpenoid and triterpenoid biosynthetic pathways, encoding patchoulol synthase variant 1, was significantly upregulated in NX. Additionally, GC-MS analysis of the two chemotypes in this study showed that the content of PA in NX was significantly higher than that of PX, while the content of PO showed the opposite phenotype. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed that the DEG expression tendency was consistent with the transcriptome sequencing results. Overall, 23 AP2/ERF, 13 bHLH, 11 MYB, 11 NAC, three Trihelix, 10 WRKY and three bZIP genes that were differentially expressed may act as regulators of terpenoid biosynthesis. Altogether, 8,314 SSRs were recognized within 6,825 unigenes, with a distribution frequency of 18.32%, among which 1,202 unigenes contained more than one SSR. The transcriptomic characteristics of the two P. cablin chemotypes are comprehensively reported in this study, and these results will contribute to a better understanding of the molecular mechanism of PA biosynthesis. Our transcriptome data also provide a valuable genetic resource for further studies on P. cablin.

Dataset Information

Virtual screening of compounds from the patchouli oil of Pogostemon herba for COX-1 inhibition.

Publications

Virtual screening of compounds from the patchouli oil of Pogostemon herba for COX-1 inhibition.

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