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Pemodelan Dan Simulasi Dinamika

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Pemodelan Dan Simulasi Dinamika PLAGIAT MERUPAKAN TINDAKAN TIDAK TERPUJI PEMODELAN DAN SIMULASI DINAMIKA MOLEKUL HUMAN MATRIX METALLOPROTEINASE 9 (hMMP9) UTUH SEBAGAI TARGET VIRTUAL PENEMUAN LIGAN PADA CATALYTIC SITE MAUPUN HEMOPEXIN-LIKE DOMAIN TESIS Diajukan untuk Memenuhi Salah Satu Syarat Memperoleh Gelar Magister Farmasi (M.Farm.) Program Studi Magister Farmasi Diajukan oleh: Roy Gunawan Wicaksono, S.Farm. Nomor Induk Mahasiswa: 188122101 FAKULTAS FARMASI UNIVERSITAS SANATA DHARMA YOGYAKARTA 2020 PLAGIAT MERUPAKAN TINDAKAN TIDAK TERPUJI PEMODELAN DAN SIMULASI DINAMIKA MOLEKUL HUMAN MATRIX METALLOPROTEINASE 9 (hMMP9) UTUH SEBAGAI TARGET VIRTUAL PENEMUAN LIGAN PADA CATALYTIC SITE MAUPUN HEMOPEXIN-LIKE DOMAIN TESIS Diajukan untuk Memenuhi Salah Satu Syarat Memperoleh Gelar Magister Farmasi (M.Farm.) Program Studi Magister Farmasi Diajukan oleh: Roy Gunawan Wicaksono, S.Farm. Nomor Induk Mahasiswa: 188122101 FAKULTAS FARMASI UNIVERSITAS SANATA DHARMA YOGYAKARTA 2020 PLAGIAT MERUPAKAN TINDAKAN TIDAK TERPUJI }ERSETUJUAN PEMBIMBING PEMODELAN DAN SIMULASI DINAMIKA MIOLF]KTJL HUMAN MATRD( METALLOPROTEINASE 9 (hMNTPg) IITUH SEBAGAT TARGET VTRTUAL PENEMUAN LIGAN PADA CATALYTIC SITEiMAI|PIITN HEMOPEXIN DOfuLAIN Tesis yang diajukan oleh: Roy Crunawan Wicaksono, S.Farm. (f 88122101) T€lah disetujui tar.ggdZr 19 ot"t, Dosen ing Utarna Enade Ph.D., Apt. o,lPP/NrD 1969/050608790 I ) PLAGIAT MERUPAKAN TINDAKAN TIDAK TERPUJI PENGESAIIAN TESIS BERJUDT]L PEMODELAIT DAN SIMULASI DINAMIKA MOLEKIJL HUMAN MATRD( METALLOPROTEINASE 9 (htvfrvfp9) UTUH SEBAGAI TARGET VIRTUAL PENEMUAN LIGA}I PADA CITALYTIC SITE MAUI{JN HEMOPHfiN-LIEE DOMAIN oleh: Roy Gunawan Wicaksono, S.Farm. (188122101) Dipertahankan di hadapan panitia penguji tesis Fakultas Farmasi Universitas Sanata Dharma Pada tanggal 23 lanuai 2020 Mengetahui Fakultas Farmasi Universitas Sanata Dharma tr!? ,: utl >-_ | {'2-_ Hartini, Apt. Panitia Penguji: l. Enade Perdana Istyastono, Ph.D., Apt 2. Dr. Rini Dwiastuti, Apt. 3. Maywan Hariono, Ph.D., Apt. PLAGIAT MERUPAKAN TINDAKAN TIDAK TERPUJI HALAMAN PERSEMBAHAN Tesis ini dipersembahkan untuk Tuhan Yesus Kristus, Ibu, Bapak, Kakak , Adik, Novia Yosin dan teman-teman sehingga dapat menyelesaikan tesis ini denga n baik. iii PLAGIAT MERUPAKAN TINDAKAN TIDAK TERPUJI PERNYATAAN KEASLLA.N KARYA Saya merryatakan dengan sesungguhnya bahrva tesis yang saya tulis iui tidak memuat karya atau bagian karya orang lain, kecuali yang telah disebutkan dalam kutipan dan daftar pustaka, sebagaimaru layaknya karya ilmiah. Apabila di kemudian hari ditemukan indikasi plagiarisme dalam naskah ini, maka saya bersedia menanggung segala sanksi sesuai peraturan perundang-undangan yang berlaku. s/.10 Y ogyal(arta, ..../1. Roy Gunawan Wicaksono, S.Faul. iv PLAGIAT MERUPAKAN TINDAKAN TIDAK TERPUJI LEMBAR PERNYATAAN PERSETUJUAN PUBLIKASI IGRYA ILML{H UNTUK KEPENTINGAN AKADEIUIS Yang bertanda tangan di bawah ini, saya mahasiswa Universitas Sanata Dharma: Nama : Roy Gunawan Wicaksono. S.Farm. Nomor Mahasiswa : 188122101 Demi pengembangan ilmu pengekhuan, saya memberikan kepada perpustakaan Universitas Sanata Dharma karya ilmiah saya yang be{udul "PEMODELAN DAN .SIMULASI DINAMIKA MOLEKUL ITUMAN MATRIX 'METALLOhROTEINASE 9 (hMMpg) UTUH SEBAGAI TARGET I'IRTUAL PENEMUAN LIG,{N PADA CATALYTIC SITE MAUPUN HEMOPEXIN DOMAIN" beserta perangkat yang diperlukan (bila ada). Dengan demikian saya memberikan kepada Perpustakaan Universitas Sanata Dharma hak untuk menyimpan, mengalihkan dalam bentuk lain, mengelolanya dalam bentuk pangkalan data, mendish'ibusikan secara terbatas, dan mempubli kasikannya di intemet atau media lain untuk kepentingan akademis tanpa perlu meminta izin saya atau memberi royal4t kepada saya selama tetap mencantumkan nama saya sebagai penulis. Demikian pernyataan ini saya buat dengan sebenar-benamya. Dibuat di Yogyakarta Pada tang!;al ,/t, .19 Yang menyatakan, )tt €elftM-t Roy Gunawan Wicaksono, S.Farm. PLAGIAT MERUPAKAN TINDAKAN TIDAK TERPUJI PRAKATA Puji dan syukur penulis haturkan ke hadirat Tuhan Yang Maha Esa karena atas berkat dan rahmat kasih-Nya penulis dapat menyelesaikan tesis yang berjudul “PEMODELAN DAN SIMULASI DINAMIKA MOLEKUL HUMAN MATRIX METALLOPROTEINASE 9 (hMMP9) UTUH SEBAGAI TARGET VIRTUAL PENEMUAN LIGAN PADA CATALYTIC SITE MAUPUN HEMOPEXIN-LIKE DOMAIN” dengan baik dan lancar. Tesis ini disusun sebagai salah satu syarat memperoleh gelar Magister Farmasi (M.Farm.) Program Studi Magister Farmasi. Penulis berharap agar tesis ini dapat berguna bagi para pembaca, menjadi sumber pengetahuan tentang dinamika molekul pada MMP-9 dan menjadi inspirasi untuk melakukan penelitian yang lebih berkembang nantinya. Penulis tesis ini tidak lepas dari banyak bantuan, dukungan, semangat, dan saran dari berbagai pihak. Oleh karena itu, penulis ingin mengucapkan terima kasih kepada: 1. Ibu Dr. Yustina Sri Hartini, Apt. selaku Dekan Fakultas Farmasi Universitas Santa Dharma. 2. Ibu Aris Widayati, M.Si., Ph.D., Apt. selaku Kaprodi Magister Farmasi Fakultas Farmasi Universitas Sanata Dharma. 3. Bapak Enade Perdana Istyastono, Ph.D., Apt. selaku dosen pembimbing yang telah memberikan ilmu, saran dan bimbingan dengan sabar dalam penelitian ini. 4. Ibu Dr. Rini Dwiastuti, Apt. selaku dosen penguji yang telah bersedia memberikan saran bagi penelitian ini. 5. Bapak Maywan Hariono, Ph.D., Apt. selaku dosen penguji yang telah bersedia memberikan saran bagi penelitian ini. 6. Keluarga penulis yang telah memberikan doa, semangat dan dukungan. 7. Mas F.A Ottok yang telah membantu kelancaran dalam penelitian tesis. 8. Teman-teman Magister Farmasi yang telah memberika ilmu dan saran. 9. Novia Yosin Parura yang selalu memberi dukungan dan semangat kepada penulis selama kuliah dan selalu mendampingin saat penulis membutuhkan bantuan. vi PLAGIAT MERUPAKAN TINDAKAN TIDAK TERPUJI membangun dari para pembaca. Akhir kata, semoga tesis ini dapat bermanfaat dan selamat membaca. 9/ c.o YogJlakarta, /r . 4+Penulis, Roy Gunawan Wicaksono. S.Farm. v PLAGIAT MERUPAKAN TINDAKAN TIDAK TERPUJI DAFTAR ISI PERSETUJUAN PEMBIMBING......................................................................................i HALAMAN PENGESAHAN...........................................................................................ii HALAMAN PERSEMBAHAN.......................................................................................iii PERNYATAAN KEASLIAN KARYA...........................................................................iv LEMBAR PERNYATAAN PUBLIKASI.........................................................................v PRAKATA.......................................................................................................................vi DAFTAR ISI..................................................................................................................viii DAFTAR GAMBAR.........................................................................................................x DAFTAR LAMPIRAN....................................................................................................xi INTISARI........................................................................................................................xii ABSTRACT.....................................................................................................................xiii 1. PENDAHULUAN.........................................................................................................1 2. TINJAUAN PUSTAKA................................................................................................2 2.1 Matrix Metalloproteinase 9.........................................................................................2 2.2 Catalytic Site dan Hemopexin Domain........................................................................3 2.3 MMP-9 Sebagai Target Molekul Dalam Penyembuh Luka........................................4 2.4 MMP-9 Sebagai Target Molekul Dalam Terapi Kanker.............................................5 3. METODE PENELITIAN..............................................................................................7 3.1 Bahan dan Instrumen...................................................................................................7 3.1.1 Bahan........................................................................................................................7 3.1.2 Instrumen..................................................................................................................7 3.2 Tahapan Simulasi........................................................................................................7 3.2.1 Preparasi...................................................................................................................7 3.3.2 Analisis Hasil............................................................................................................8 4. HASIL DAN PEMBAHASAN.....................................................................................8 4.1 Kualitas Hasil Pemodelan Homologi..........................................................................9 4.2 Stabilitas MMP-9 Terhadapat Ligan.........................................................................10 4.3 The Free Energy of Binding (ΔG bind).....................................................................11 4.4 Penambatan Ulang Ligan ..........................................................................................11 viii PLAGIAT MERUPAKAN TINDAKAN TIDAK TERPUJI 5. KESIMPULAN DAN SARAN...................................................................................12 6. DAFTAR PUSTAKA..................................................................................................13
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