克曼吉β-谷甾醇作为口腔细菌MurA酶抑制剂的生物机制预测:体外和硅细胞研究

Q2 Biochemistry, Genetics and Molecular Biology
Advances and Applications in Bioinformatics and Chemistry Pub Date : 2021-06-23 eCollection Date: 2021-01-01 DOI:10.2147/AABC.S301488
Ida Ayu Evangelina, Yetty Herdiyati, Avi Laviana, Rasmi Rikmasari, Cucu Zubaedah, Anisah, Dikdik Kurnia
{"title":"克曼吉β-谷甾醇作为口腔细菌MurA酶抑制剂的生物机制预测:体外和硅细胞研究","authors":"Ida Ayu Evangelina,&nbsp;Yetty Herdiyati,&nbsp;Avi Laviana,&nbsp;Rasmi Rikmasari,&nbsp;Cucu Zubaedah,&nbsp;Anisah,&nbsp;Dikdik Kurnia","doi":"10.2147/AABC.S301488","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>Dental caries is a widespread disease that causes dental tissue destruction and leads to local and general complications. Gram-positive bacteria including <i>Streptococcus mutans</i>, <i>Streptococcus sanguinis</i>, and <i>Enterococcus faecalis</i> take part in dental caries formation. Gram-positive bacteria have cell walls that consistof a thick layer of peptidoglycan which maintains the strength and rigidity of the bacteria, as well as bacteria guard from internal osmotic pressure. The biosynthesis of peptidoglycan involves many enzymes, including the Mur family, penicillin binding protein (PBP), and sortases.</p><p><strong>Purpose: </strong>This research has the intention to screen and examine the antibacterial compound of edible plant Kemangi (<i>Ocimum basilicum</i> L.) in terms of how it fights against some oral pathogenic bacteria of <i>E. faecalis</i> ATCC 29212, <i>S. mutans</i> ATCC 25175, and <i>S. sanguinis</i> ATCC 10566.</p><p><strong>Materials and methods: </strong>The <i>O. basilicum</i> L. was macerated by several organic solvents to obtain the extracts, before then being purified using several combinations of chromatography methods and the compound was discovered via spectroscopic methods. For the assay against bacteria, the extracts and compounds were tested using agar well diffusion and microdilution assay.</p><p><strong>Results: </strong>The isolated compound was identified as β-sitosterol. The compound activity against bacteria was evaluated by in vitro assay against <i>S. sanguinis</i> ATCC 10566 and <i>E. faecalis</i> ATCC 29212 with the MIC and MBC value of 25,000 and 50,000 ppm, respectively. The compound was also tested by in silico study using the molecular docking method. The molecular interaction between β-sitosterol and the protein target showed a lower binding affinity value than the native ligand and other positive controls for each protein. Based on the amino acid residue bound to the ligands, β-sitosterol on MurA and SrtA is not competitive to the positive control, showing potential as a natural antibacterial agent. Meanwhile, on the MurB and PBP, β-sitosterol and positive control do compete with each other.</p><p><strong>Conclusion: </strong>The compound, isolated from <i>O. basilicum</i> L. leaf, was determined as β-sitosterol, which has the molecular formula C<sub>29</sub>H<sub>50</sub>O. The antibacterial activity of β-sitosterol by in vitro assay showed weak antibacterial activity, yet exhibited the potential to inhibit the biosynthesis of peptidoglycan and prevent bacteria cell wall formation by inhibiting MurA and SrtA activity via docking simulation.</p>","PeriodicalId":53584,"journal":{"name":"Advances and Applications in Bioinformatics and Chemistry","volume":"14 ","pages":"103-115"},"PeriodicalIF":0.0000,"publicationDate":"2021-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/37/e7/aabc-14-103.PMC8236250.pdf","citationCount":"13","resultStr":"{\"title\":\"Bio-Mechanism Inhibitory Prediction of β-Sitosterol from Kemangi (<i>Ocimum basilicum</i> L.) as an Inhibitor of MurA Enzyme of Oral Bacteria: In vitro and in silico Study.\",\"authors\":\"Ida Ayu Evangelina,&nbsp;Yetty Herdiyati,&nbsp;Avi Laviana,&nbsp;Rasmi Rikmasari,&nbsp;Cucu Zubaedah,&nbsp;Anisah,&nbsp;Dikdik Kurnia\",\"doi\":\"10.2147/AABC.S301488\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>Dental caries is a widespread disease that causes dental tissue destruction and leads to local and general complications. Gram-positive bacteria including <i>Streptococcus mutans</i>, <i>Streptococcus sanguinis</i>, and <i>Enterococcus faecalis</i> take part in dental caries formation. Gram-positive bacteria have cell walls that consistof a thick layer of peptidoglycan which maintains the strength and rigidity of the bacteria, as well as bacteria guard from internal osmotic pressure. The biosynthesis of peptidoglycan involves many enzymes, including the Mur family, penicillin binding protein (PBP), and sortases.</p><p><strong>Purpose: </strong>This research has the intention to screen and examine the antibacterial compound of edible plant Kemangi (<i>Ocimum basilicum</i> L.) in terms of how it fights against some oral pathogenic bacteria of <i>E. faecalis</i> ATCC 29212, <i>S. mutans</i> ATCC 25175, and <i>S. sanguinis</i> ATCC 10566.</p><p><strong>Materials and methods: </strong>The <i>O. basilicum</i> L. was macerated by several organic solvents to obtain the extracts, before then being purified using several combinations of chromatography methods and the compound was discovered via spectroscopic methods. For the assay against bacteria, the extracts and compounds were tested using agar well diffusion and microdilution assay.</p><p><strong>Results: </strong>The isolated compound was identified as β-sitosterol. The compound activity against bacteria was evaluated by in vitro assay against <i>S. sanguinis</i> ATCC 10566 and <i>E. faecalis</i> ATCC 29212 with the MIC and MBC value of 25,000 and 50,000 ppm, respectively. The compound was also tested by in silico study using the molecular docking method. The molecular interaction between β-sitosterol and the protein target showed a lower binding affinity value than the native ligand and other positive controls for each protein. Based on the amino acid residue bound to the ligands, β-sitosterol on MurA and SrtA is not competitive to the positive control, showing potential as a natural antibacterial agent. Meanwhile, on the MurB and PBP, β-sitosterol and positive control do compete with each other.</p><p><strong>Conclusion: </strong>The compound, isolated from <i>O. basilicum</i> L. leaf, was determined as β-sitosterol, which has the molecular formula C<sub>29</sub>H<sub>50</sub>O. The antibacterial activity of β-sitosterol by in vitro assay showed weak antibacterial activity, yet exhibited the potential to inhibit the biosynthesis of peptidoglycan and prevent bacteria cell wall formation by inhibiting MurA and SrtA activity via docking simulation.</p>\",\"PeriodicalId\":53584,\"journal\":{\"name\":\"Advances and Applications in Bioinformatics and Chemistry\",\"volume\":\"14 \",\"pages\":\"103-115\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2021-06-23\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/37/e7/aabc-14-103.PMC8236250.pdf\",\"citationCount\":\"13\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Advances and Applications in Bioinformatics and Chemistry\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.2147/AABC.S301488\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2021/1/1 0:00:00\",\"PubModel\":\"eCollection\",\"JCR\":\"Q2\",\"JCRName\":\"Biochemistry, Genetics and Molecular Biology\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Advances and Applications in Bioinformatics and Chemistry","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.2147/AABC.S301488","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2021/1/1 0:00:00","PubModel":"eCollection","JCR":"Q2","JCRName":"Biochemistry, Genetics and Molecular Biology","Score":null,"Total":0}
引用次数: 13

摘要

背景:龋齿是一种广泛存在的疾病,可导致牙齿组织破坏并导致局部和全身并发症。革兰氏阳性细菌包括变形链球菌、血链球菌和粪肠球菌参与龋齿的形成。革兰氏阳性细菌的细胞壁由一层厚厚的肽聚糖组成,肽聚糖维持细菌的强度和刚性,并保护细菌免受内部渗透压的影响。肽聚糖的生物合成涉及多种酶,包括Mur家族、青霉素结合蛋白(PBP)和分选酶。目的:筛选和研究食用植物克曼基(Ocimum basilicum L.)抗菌化合物对粪肠杆菌(E. faecalis) ATCC 29212、变形链球菌(S. mutans) ATCC 25175、血链球菌(S. sanguinis) ATCC 10566等口腔致病菌的抑菌作用。材料和方法:用几种有机溶剂浸泡得到basilicum L.提取物,然后用几种色谱方法组合纯化,通过光谱方法发现化合物。采用琼脂孔扩散法和微量稀释法对提取物和化合物进行抑菌试验。结果:分离得到的化合物鉴定为β-谷甾醇。在MIC和MBC分别为25000 ppm和50000 ppm的条件下,对血链球菌ATCC 10566和粪链球菌ATCC 29212进行体外抑菌试验。并用分子对接法对该化合物进行了硅研究。β-谷甾醇与靶蛋白的分子相互作用显示出比天然配体和其他阳性对照蛋白更低的结合亲和力值。基于与配体结合的氨基酸残基,MurA和SrtA上的β-谷甾醇与阳性对照没有竞争关系,显示出作为天然抗菌剂的潜力。同时,在MurB和PBP上,β-谷甾醇与阳性对照存在竞争关系。结论:该化合物从basilicum L.叶片中分离得到,为β-谷甾醇,分子式为C29H50O。体外实验结果显示,β-谷甾醇的抑菌活性较弱,但通过对接模拟显示,β-谷甾醇可能通过抑制MurA和SrtA活性,抑制肽聚糖的生物合成,阻止细菌细胞壁的形成。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Bio-Mechanism Inhibitory Prediction of β-Sitosterol from Kemangi (<i>Ocimum basilicum</i> L.) as an Inhibitor of MurA Enzyme of Oral Bacteria: In vitro and in silico Study.

Bio-Mechanism Inhibitory Prediction of β-Sitosterol from Kemangi (<i>Ocimum basilicum</i> L.) as an Inhibitor of MurA Enzyme of Oral Bacteria: In vitro and in silico Study.

Bio-Mechanism Inhibitory Prediction of β-Sitosterol from Kemangi (<i>Ocimum basilicum</i> L.) as an Inhibitor of MurA Enzyme of Oral Bacteria: In vitro and in silico Study.

Bio-Mechanism Inhibitory Prediction of β-Sitosterol from Kemangi (Ocimum basilicum L.) as an Inhibitor of MurA Enzyme of Oral Bacteria: In vitro and in silico Study.

Background: Dental caries is a widespread disease that causes dental tissue destruction and leads to local and general complications. Gram-positive bacteria including Streptococcus mutans, Streptococcus sanguinis, and Enterococcus faecalis take part in dental caries formation. Gram-positive bacteria have cell walls that consistof a thick layer of peptidoglycan which maintains the strength and rigidity of the bacteria, as well as bacteria guard from internal osmotic pressure. The biosynthesis of peptidoglycan involves many enzymes, including the Mur family, penicillin binding protein (PBP), and sortases.

Purpose: This research has the intention to screen and examine the antibacterial compound of edible plant Kemangi (Ocimum basilicum L.) in terms of how it fights against some oral pathogenic bacteria of E. faecalis ATCC 29212, S. mutans ATCC 25175, and S. sanguinis ATCC 10566.

Materials and methods: The O. basilicum L. was macerated by several organic solvents to obtain the extracts, before then being purified using several combinations of chromatography methods and the compound was discovered via spectroscopic methods. For the assay against bacteria, the extracts and compounds were tested using agar well diffusion and microdilution assay.

Results: The isolated compound was identified as β-sitosterol. The compound activity against bacteria was evaluated by in vitro assay against S. sanguinis ATCC 10566 and E. faecalis ATCC 29212 with the MIC and MBC value of 25,000 and 50,000 ppm, respectively. The compound was also tested by in silico study using the molecular docking method. The molecular interaction between β-sitosterol and the protein target showed a lower binding affinity value than the native ligand and other positive controls for each protein. Based on the amino acid residue bound to the ligands, β-sitosterol on MurA and SrtA is not competitive to the positive control, showing potential as a natural antibacterial agent. Meanwhile, on the MurB and PBP, β-sitosterol and positive control do compete with each other.

Conclusion: The compound, isolated from O. basilicum L. leaf, was determined as β-sitosterol, which has the molecular formula C29H50O. The antibacterial activity of β-sitosterol by in vitro assay showed weak antibacterial activity, yet exhibited the potential to inhibit the biosynthesis of peptidoglycan and prevent bacteria cell wall formation by inhibiting MurA and SrtA activity via docking simulation.

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
Advances and Applications in Bioinformatics and Chemistry
Advances and Applications in Bioinformatics and Chemistry Biochemistry, Genetics and Molecular Biology-Biochemistry, Genetics and Molecular Biology (miscellaneous)
CiteScore
6.50
自引率
0.00%
发文量
7
审稿时长
16 weeks
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信