Khairunnisa, Amalia and Prof. Dr. Ir. Abdul Latief Abadi, MS. and Muhammad Akhid Syib’li,, SP., MP., Ph.D. (2024) Pengaruh Senyawa Anti Jamur Ekstrak Cengkeh Terhadap Dinamika Molekuler dan Aktivitas Enzim Kutinase Fusarium oxysporum f.sp. lycopersici. Magister thesis, Universitas Brawijaya.
Abstract
Fusarium oxysporum f.sp. lycopersici merupakan ancaman yang signifikan bagi tanaman tomat karena aktivitas hidrolitik enzim kutinasenya, yang memfasilitasi penetrasi jaringan akar tanaman. Oleh karena itu, mengurangi aktivitas kutinase melalui penggunaan cengkeh sebagai inhibitor menawarkan alternatif ramah lingkungan dibandingkan dengan fungisida kimia berbahaya, menunjukkan potensi besar dalam mengendalikan penyakit layu Fusarium, terutama dengan menargetkan enzim kutinase dari Fusarium oxysporum. Studi ini bertujuan untuk mensimulasikan mengenai potensi serta mekanisme dari senyawa alami cengkeh sebagai inhibitor enzim kutinase untuk meminimalisir terjadinya penetrasi patogen Fusarium oxysporum f.sp. lycopersici pada tanaman tomat. Oleh karena itu, diperlukan pemanfaatan metode penelitian, baik simulasi komputasional (molecular docking dan molecular dynamic) maupun in vitro guna memahami potensi serta mekanisme tersebut. Penelitian ini melibatkan beberapa metode yang mencakup in silico dan in vitro. Tahapan penelitian terdiri dari karakterisasi jamur patogen Fusarium oxysporum, uji kandungan senyawa ekstrak cengkeh menggunakan GC-MS, simulasi molecular docking dan molecular dynamic pada senyawa antijamur terpilih, uji penghambatan aktivitas enzim kutinase, serta analisis FTIR. Uji in vitro dilakukan menggunakan 4 perlakuan (0%, 1%, 2%, dan 3%) cengkeh dan 5 ulangan. Analisis GC-MS mengindikasikan bahwa terdapat 685 senyawa yang terkandung di dalam ekstrak cengkeh, dengan total 138 senyawa antijamur (20%). Virtual screening menggunakan molecular docking menunjukkan bahwa senyawa antijamur terpilih dari ekstrak cengkeh mampu mereduksi aktivitas hidrolitik enzim kutinase dimana terdapat 7 dari 10 senyawa terpilih yang memiliki interaksi dengan enzim kutinase, yaitu eugenol (-4,5 kcal/mol), 7-Methoxy-3-(4-methoxyphenyl)-4- methylcoumarin (-2,1 kcal/mol), Methylamine (-2,1 kcal/mol), Methyl alcohol (-2,1 kcal/mol), Chavicol (-0,7 kcal/mol), Hexadecanoic acid (-3,5 kcal/mol), serta 9,12- Octadecadienoic acid (Z,Z)- (-3,7 kcal/mol) dan 2 diantaranya berinteraksi dengan sisi aktif, yaitu eugenol dan chavicol. Hasil simulasi molecular dynamic menunjukkan bahwa senyawa antijamur terpilih (eugenol, 7-Methoxy-3-(4- methoxyphenyl)-4-methylcoumarin, Methylamin, Methyl alcohol, Chavicol, Hexadecanoic acid, 9,12-Octadecadienoic acid (Z,Z)-) mengakibatkan adanya perubahan posisi struktur enzim kutinase sehingga berpotensi menurunkan aktivitas enzim kutinase. Ekstrak cengkeh mampu menurunkan aktivitas enzim kutinase pada uji in vitro mengguanakan media uji ROA, ditunjukkan dengan adanya penurunan intensitas fluoresensi oranye seiring dengan penambahan persentase ekstrak cengkeh pada media uji. Analisis FTIR mengindikasikan adanya penurunan aktivitas enzim kutinase akibat penambahan ekstrak cengkeh pada media uji ROA, ditunjukkan dengan adanya perubahan pola spektral FTIR dengan intensitas gugus fungsi ikatan ester yang tinggi dan gugus fungsi hidroksilalkil yang rendah pada perlakuan ekstrak cengkeh.
English Abstract
Fusarium oxysporum f.sp. lycopersici is a significant threat to tomato plants due to the hydrolytic activity of its cutinase enzyme, which facilitates the penetration of plant root tissues. Therefore, reducing cutinase activity through the use of cloves as inhibitors offers an environmentally friendly alternative compared to hazardous chemical fungicides, showing great potential in controlling Fusarium wilt disease, particularly by targeting the cutinase enzyme of Fusarium oxysporum. This study aims to simulate the potential and mechanism of clove's natural compounds as cutinase enzyme inhibitors to minimize the penetration of the Fusarium oxysporum f.sp. lycopersici pathogen in tomato plants. Consequently, research methods, including both computational simulations (molecular docking and molecular dynamics) and in vitro studies, are needed to understand this potential and mechanism. This research involves several methods encompassing both in silico and in vitro approaches. The research stages include the characterization of the pathogenic fungus Fusarium oxysporum, analysis of clove extract compounds using GC-MS, molecular docking and molecular dynamics simulations of selected antifungal compounds, inhibition assays of cutinase enzyme activity, and FTIR analysis. In vitro tests were conducted using four treatments (0%, 1%, 2%, and 3%) of clove extract and five replicates. GC-MS analysis indicated that there are 685 compounds in the clove extract, with a total of 138 antifungal compounds (20%). Virtual screening using molecular docking showed that selected antifungal compounds from clove extract could reduce the hydrolytic activity of the cutinase enzyme, with 7 out of 10 selected compounds interacting with the cutinase enzyme, namely eugenol (-4.5 kcal/mol), 7-Methoxy-3-(4-methoxyphenyl)-4-methylcoumarin (-2.1 kcal/mol), methylamine (- 2.1 kcal/mol), methyl alcohol (-2.1 kcal/mol), chavicol (-0.7 kcal/mol), hexadecanoic acid (-3.5 kcal/mol), and 9,12-octadecadienoic acid (Z,Z)- (-3.7 kcal/mol). Among these, two compounds interacted with the active site, specifically eugenol and chavicol. Molecular dynamics simulations showed that the selected antifungal compounds (eugenol, 7-Methoxy-3-(4-methoxyphenyl)-4- methylcoumarin, methylamine, methyl alcohol, chavicol, hexadecanoic acid, 9,12- octadecadienoic acid (Z,Z)-) caused structural changes in the cutinase enzyme, potentially reducing its activity. Clove extract was able to reduce cutinase enzyme activity in in vitro tests using ROA test media, as indicated by a decrease in orange fluorescence intensity with increasing concentrations of clove extract in the test media. FTIR analysis indicated a reduction in cutinase enzyme activity due to the addition of clove extract in ROA test media, as shown by changes in the FTIR spectral patterns with high ester bond functional group intensity and low hydroxylalkyl functional group intensity in clove extract treatments.
| Item Type: | Thesis (Magister) |
|---|---|
| Identification Number: | 042405 |
| Divisions: | S2/S3 > Magister Ilmu Tanaman, Fakultas Pertanian |
| Depositing User: | Unnamed user with username nova |
| Date Deposited: | 05 Sep 2024 06:59 |
| Last Modified: | 05 Sep 2024 06:59 |
| URI: | http://repository.ub.ac.id/id/eprint/227484 |
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