eprintid: 21773
rev_number: 8
eprint_status: archive
userid: 3858
dir: disk0/00/02/17/73
datestamp: 2023-04-02 10:33:39
lastmod: 2023-04-02 10:33:39
status_changed: 2023-04-02 10:33:39
type: thesis
metadata_visibility: show
creators_name: Nur, Zeta Rukhshah Zam Zamy
creators_name: Rachmania, Rizky Arcinthya
creators_name: Hariyanti, Hariyanti
title: MOLECULAR DOCKING DAN MOLECULAR DYNAMICS SENYAWA
MINYAK ATSIRI HERBA TIMI (Thymus vulgaris) SEBAGAI
ANTITUBERKULOSIS TERHADAP GLUTAMATE RACEMASE (Murl)
ispublished: pub
subjects: R
subjects: RS
divisions: 48201
abstract: Tuberkulosis (TB) merupakan penyakit yang disebabkan oleh bakteri
Mycobacterium tuberkulosis (MTB) yang dapat ditularkan melalui droplet.
Penggunaan herba timi (Thymus vulgaris) merupakan salah satu senyawa tanaman
alam yang sudah diteliti kandungan minyak atsirinya dan memiliki aktivitas
menghambat pertumbuhan bakteri MTB. Tujuan penelitian ini untuk memprediksi
kandidat pada senyawa dalam minyak atsiri dari herba timi terhadap Glutamate
racemase (Murl) pada dinding sel bakteri MTB menggunakan obat pembanding
yaitu ethambutol. Metode penelitian ini menggunakan metode molecular docking
dengan software Autodock untuk memprediksi senyawa dalam minyak atsiri dari
herba timi yang memiliki potensi terbaik sebagai antituberkulosis dilihat dari
energy binding, klaster, dan Ki serta metode molecular dynamics dengan software
GROMACS untuk mengetahui kestabilan melalui analisis energi potensial, RMSD,
RMSF, Girasi, dan energi MMPBSA. Hasil penelitian dengan metode simulasi
molecular docking menunjukkan senyawa Tymoquinone dan γ-Eudesmol
diprediksi memiliki afinitas yang baik dan hasil dari metode simulasi molecular
dynamics berdasarkan parameter energi MMPBSA menunjukan bahwa γ-Eudesmol
menunjukan kestabilan yang baik selama simulasi. Simpulan dari penelitian ini
yaitu senyawa minyak atsiri dari herba timi yakni γ-Eudesmol diprediksi berpotensi
sebagai kandidat obat antituberkulosis.
Kata Kunci: Molecular Docking, Molecular Dynamics, Minyak Atsiri Herba Timi,
Antituberkulosis, dan Glutamate racemase
date: 2020
date_type: completed
full_text_status: public
institution: Universitas Muhammadiyah Prof. DR. HAMKA
department: Fakultas Farmasi dan Sains
thesis_type: bachelor
thesis_name: bphil
referencetext: Alderwick, L. J., Birch, A. K., Mishara, L., Eggelling, & Besra, G. S. (2007).
Structure, Function and Biosynthesis of The Mycobacterium Tuberculosis
Cell Wall: Arabinoglaktan and Lipoarabinomannan Assembly with a View to
Discovering New Drug Targets. Biochemical Society Transactions, 35(5),
1325–1328.
Apol, E., Apostolov, R., Berendsen, H. J. C., Van Buuren, A., & GROMACS
development team. (2016). GROMACS 2016 Reference Manual. Sweden:
The GROMACS development teams at the Royal Institute of Technology and
Uppsala University.
Arba, M. (2019). Buku Ajar Farmasi Komputasi. Yogyakarta: Deepublish.
Bajda, M., Jończyk, J., Malawska, B., & Filipek, S. (2014). Application of
Computational Methods for the Design of BACE-1 Inhibitors : Validation of
in Silico Modelling. International Journal of Molecular Sciences, 15(3),
5128–5139.
Becker, O. M., Jr., A. D. M., Roux, B., & Watanabe, M. (2001). Computational
Biochemistry and Biophysics. New York: Marcel Dekker AG.
Chairunnisa, A., & Runadi, D. (2017). Aktivitas Kalkon terhadap Reseptor
Esterogen β (er-β) Sebagai Antikanker Payudara Secara In Vitro dan In Silico.
Review. Farmaka, 14(2), 1–8.
Depkes RI. (2005). Pharmaceutical Care. Jakarta: Departemen Kesehatan RI.
Depkes RI. (2011). Pedoman Nasional Pengendalian Tuberkulosis. Jakarta:
Kementrian Kesehatan.
Dermawan, D., Sumirtanurdin, R., & Dewantisari, D. (2019). Molecular Dynamics
Simulation of Estrogen Receptor Alpha Against Andrografolid as Anti Breast
Cancer. Indonesian Journal of Pharmaceutical Science and Technology, 6(2),
65–76.
Dizaji, P., Soleimani, Afrugh, & Saedi. (2018). In vitro Antibacterial Activity of
Thymus vulgaris Essential Oil Against Mycobacterium tuberculosis.
Microbiology & Microbial Biotechnology Department, 4(2), 47–51.
Doak, Over, Gioardanetto, & Kihlberg. (2014). Oral Druggable Space beyond the
Rule of 5: Insights from Drugs and Clinical Candidates. Chemistry & Biology,
21(9), 1115–1142.
Fisher, S. L. (2008). Review Glutamate Racemase as a Target for Drug Discovery.
Microbial Biotechnology, 1(5), 345–360.
Glowacki, E., Vladu, M., & Bauer, S. (2013). Hydrogen Bonds in Molecular Solid
From Biological Systems to Organic Electronics. Journal of Materials 
Chemistry B, 1(31), 3742–3753.
Goodman, & Gilman. (2015). Dasar Farmakologi Terapi. Jakarta: EGC.
Gunawan, S. G., & Sulistia, G. (2016). Farmakologi dan Terapi Edisi 6. Jakarta:
UI Press.
Hunter, R. L., Olsen, M. R., Jagannath, C., & Jeffrey, K. A. (2006). Multiple Roles
of Cord Factor in the Pathogenesis of Primary, Secondary, and Cavitary
Tuberculosis, Including a Revised Description of the Pathology of Secondary
Disease. Annals of Clinical and Laboratory Science, 36(4), 371–386.
Irianti, Kuswandi, & Nanang. (2016). Buku Anti-tuberkulosis. Yogyakarta: UGM
Press.
Istyastono, E. P. (2018). Rancangan Obat dan Penapisan Virtual Berbasis Struktur.
Yogyakarta: Sanata Dharma University Press.
Julius, M., Cruse, M. D., Robert, E., & Lewis. (2010). Atlas of Immunology 3th Ed.
New York: CRC Press.
Junaid, M., Muhseen, T. Z., Ullah, A., Wadood, A., Liu, J., & Zhang, H. (2014).
Molecular Modeling and Molecular Dynamics Simulation Study of the
Human Rab9 and RhoBTB3 C-terminus Complex. Bioinformation, 10(12),
757–763.
Kaboli, P. J., Ismail, P., & Ling, K. H. (2018). Molecular Dynamics (MD)
Simulations. Drug Discovery, 12(4), 1–13.
Kaitin, K. I., & Dimasi, J. A. (2011). Pharmaceutical innovation in the 21st century:
new drug approvals in the first decade 2000-2009. Clinical Pharmacology
and Therapeutics, 89(2), 183–188.
Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (1997).
Experimental and Computational Approaches to Estimate Solubility and
Permeability in Drug Discovery and Development Settings. Advance Drug
Delivery Reviews, 23(1–3), 3–25.
Maitra, A., Munshi, T., Healy, J., Martin, L. T., Vollmer, W., Keep, N. H., &
Bhakta, S. (2019). Cell wall peptidoglycan in Mycobacterium tuberculosis :
An Achilles ’ heel for the TB-causing pathogen. FEMS Microbiology
Reviews, 43(5), 548–575.
Manna, A., Dian, M., Hudiyanti, D., & Siahaan, P. (2017). Molecular Docking of
Interaction between E-Cadherin Protein and Conformational Structure of
Cyclic Peptide ADTC3 (Ac-CADTPC-NH2). Jurnal Kimia Sains Dan
Aplikasi, 20(1), 30–36.
Mishra, S., Ojha, K. K., Pandey, P. N., & Shukla, A. (2018). Trends in
Bioinformatics In silico Studies for Potential Natural Inhibitors for Isocitrate 
Dehydrogenase Type II of Mycobacterium tuberculosis ( H37Rv ). Trends in
Bioinformatics, 11(1), 7–16.
Morris, G. M., Goodsell, D. S., Piqeu, M. E., Heuy, R., & Olson, A. (2012).
AutoDock Version 4.2. Citeseer, 1–66.
Mukesh, & Rakesh. (2011). Molecular Docking: A Review Internasional. Journal
of Research in Ayurveda and Pharmacy, 2(6), 1746–1751.
Muttaqin, F. Z., Pratama, M. F., & Kurniawan, F. (2019). Molecular Docking And
Molecular Dynamic Studies Of Stilbene Derivative Compounds As Sirtuin-3
(Sirt3) Histone Deacetylase Inhibitor On Melanoma Skin Cancer And Their
Toxicities Prediction. Journal of Pharmacopolium, 2(2), 112–121.
Paissoni, C., Spiliotopoulos, D., Musco, G., & Spitaleri, A. (2014). GMXPBSA 2.0:
A GROMACS tool to perform MM/PBSA and computational alanine
scanning. Computer Physics Communications, 185(11), 2920–2929.
Pawar, A., Jha, P., Konwar, C., Chaudhry, U., Chopra, M., & Saluja, D. (2018).
Ethambutol targets the glutamate racemase of Mycobacterium tuberculosis
an enzyme involved in peptidoglycan biosynthesis. Applied Microbiology
and Biotechnology, 103(2), 843–851.
Poeloengan, Komala, & Noor. (2007). Bahaya dan Penanganan Tuberkulosis.
Balai Penelitian Veteriner Bogor: Lokakarya Nasional Zoonosis.
Porcelli, S. A. (2008). Tuberculosis: Shrewd Survival Strategy. Nature, 454(7205),
702–703.
Purnomo, H. (2013). Kimia Komputasi untuk Farmasi dan Ilmu Terkait.
Yogyakarta: Pustaka Pelajar.
Purwanto, & Hardjono. (2016). Kimia Medisinal Edition 2: Hubungan Struktur
Ikatan Kimia dan Aktivitas Biologi Obat. Surabaya: Airlangga University
Press.
Putra, R. K. E. (2019). Penentuan Energi Bebas Gibbs Antara Ligan Natural
Dengan Protein Pf Pk7 Sebagai Indikator Awal Potensi Antimalaria. Bogor
Agrucultural : Institut Pertanian Bogor.
Rafflesia, U. (2014). Model Penyebaran Penyakit Tuberkulosis (TBC). Jurnal
Gradien, 10(2), 983–986.
Reddy, P., & Biotech, V. (2016). Review on Thymus vulgaris Traditional Uses and
Pharmacological Properties Medicinal & Aromatic Plants Review on Thymus
vulgaris Traditional Uses and Pharmacological Properties. Medical and
Aromatic Plants, 3(3), 1–4.
Rollando. (2017). Pengantar Kimia Medisinal. Malang: CV. Seribu Bintang.
Ruswanto. (2015). Molecular Docking Empat Turunan Isonicotinohydrazide Pada
Mycobacterium Tuberculosis Enoyl-Acyl Carrier Protein Reductase (Inha).
Jurnal Kesehatan Bakti Tunas Husada, 13(1), 135–141.
Ruswanto, Ratnasari, A., & Tuslinah, L. (2015). Sintesis Senyawa N-(3,5-
Dinitrobenzoyl)-Isonicotinohydrazide dan Studi Interaksinya pada
Mycobacterium Tuberculosis Enoyl Acyl Carrier Protein Reductase (InhA).
Jurnal Kesehatan Bakti Tunas Husada, 14(1), 63–73.
Ryan, K. J., & Ray, C. G. (2010). Sherris Medical Microbiology (5th ed.). United
State of America: McGraw-Hill.
Sadiki, M., Farah, A., Saad, & Koraichi, I. (2014). Characterization and
Antibacterial Activity of The Essential Oil from Thymus vulgaris cultuvated
in morocco (taounat) against ten Bacteria. Journal of Pharmaceutical
Research, 4(5), 314–325.
Samantray, S., Schumann, W., Illig, A.-M., Carballo-Pacheco, M., Paul, A., Barz,
B., & Strodel, B. (2020). Molecular dynamics simulations of protein
aggregation: protocols for simulation setup and analysis with Markov state
models and transition networks. Biorxiv, 1–34.
Thomas. (2004). Fundamental of Medicinal Chemistry 1st Edition. England: Wiley.
Wesołowska, A., & Jadczak, D. (2019). Comparison of the Chemical Composition
of Essential Oils Isolated from Two Thyme (Thymus vulgaris L.) Cultivars.
Notulae Botanicae Horti Agrobotanici Cluj-Napoca, 47(3), 829–835.
World Health Organization (WHO). (2018). Global Tuberculosis Report 2018.
Geneva: CC BY-NC-SA 3.0 IGO.
Yanuar, A. (2012). Penambatan Molekular Praktek dan Aplikasi pada Virtual
Screening. Depok: UI Press.
citation:   Nur, Zeta Rukhshah Zam Zamy dan Rachmania, Rizky Arcinthya dan Hariyanti, Hariyanti  (2020) MOLECULAR DOCKING DAN MOLECULAR DYNAMICS SENYAWA MINYAK ATSIRI HERBA TIMI (Thymus vulgaris) SEBAGAI ANTITUBERKULOSIS TERHADAP GLUTAMATE RACEMASE (Murl).  Bachelor thesis, Universitas Muhammadiyah Prof. DR. HAMKA.   
document_url: http://repository.uhamka.ac.id/id/eprint/21773/1/FS03-220037.pdf