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Journal : Indonesian Journal of Biotechnology

Simultaneous clustering analysis with molecular docking in network pharmacology for type 2 antidiabetic compounds Nur Azizah Komara Rifai; Farit Mochamad Afendi; I Made Sumertajaya
Indonesian Journal of Biotechnology Vol 22, No 1 (2017)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (655.479 KB) | DOI: 10.22146/ijbiotech.27334

Abstract

The database of drug compounds and human proteins plays a very important role in identifying the protein target and the compound in drug discovery. Recently, a network pharmacology approach was established by updating the research paradigm from the current “one disease-one target-one drug” to a new “drug-target-disease network”. Ligand-protein interactions can be analyzed quantitatively using simultaneous clustering and molecular docking. The docking method offers the ability to quickly and cheaply predict the ligand-protein binding free energy (DG) in structure-based virtual screening. Meanwhile, simultaneous clustering was used to find subgroups of compounds that exhibit a high correlation with subgroups of target proteins. This study is focused on the interaction between the 306 compounds from medicinal plants (brotowali Tinospora crispa, ginger Zingiber officinale, pare Momordica charantia, sembung Blumea balsamifera, synthetic drugs (FDA-approved) and the 21 significant human proteins associated with type 2 diabetes. We found that brotowali (B018), sembung (S031), pare (P231), and ginger (J036, J033) were close to the synthetic drugs and can possibly be developed as antidiabetic drug candidates. Likewise, the proteins AKT1, WFS1, APOE, EP300, PTH, GCG, and UBC which assemble each other and which have a high association with INS can be seen as target proteins that play a role in type 2 diabetes.
Co-Authors A Kurnia A. A. Mattjik AA Mattjik Abd. Rasyid Syamsuri Abdu Alifah Abdul Aziz Nurussadad Ade Gusalinda Adelia Putri Pangestika Agus Mohamad Soleh Agustin Faradila Ahmad Anshori Mattjik Ahmad Ansori Matjjik Ahmad Ansori Mattjik Ahmad Ansori Mattjik Aidi, Muhammad N Aini, Febri Nur Aji Hamim Wigena Akbar Rizki Alfian Futuhul Hadi Alwani, Nadira Nisa Amanda Permata Dewi Anang Kurnia Andi Setiawan Andina Fahriya Andrew Donda Munthe Anggraini Sukmawati Anik Djuraidah Arina, Faula Aropah, Vina Da'watul Aropah, Vina Da’watul ASEP SAEFUDDIN Astari, Reka Agustia Azagi, Ilham Alifa Azis, Irfani Bagus Sartono Budi Susetyo Choirun Nisa Chrisinta, Debora Cici Suhaeni Cynthia Wulandari Dede Dirgahayu Domiri Dede Dirgahayu Domiri, Dede Dirgahayu Dian Kusumaningrum Dian Kusumaningrum Diki Akhwan Mulya Doni Suhartono Dwi Agustin Nuriani Sirodj Dwi Yulianti Embay Rohaeti Emeylia Safitri Erfiani Erfiani Erfiani Erfiani, Erfiani Erwina Erwina Evita Choiriyah Fadilah, Anggita Rizky FAHREZAL ZUBEDI Faqih Udin dan Jono M. Munandar Meivita Amelia Farit M Afendi Farit Mochamad Afendi Fitria Hasanah Fitrianto, Anwar Halimatus Sa'diyah Hari Wijayanto Haryastuti, Rizqi Hengki Muradi Hidayat, Agus Sofian Eka Hilda Zaikarina Huda, Usep Firdaus Humairoh, Andi Zahira Al I Gede Nyoman Mindra Jaya Ilma Nabila Ilmani, Erdanisa Aghnia Imam Adiyana Indahwati Indonesian Journal of Statistics and Its Applications IJSA Iqbal, Teuku Achmad Irfani Azis Irfani Azis Ismah, Ismah Isti Rochayati Itasia Dina Sulvianti Jamaluddin Rabbani Harahap Jasiulewicz, Anna Khairil Anwar Notodiputro Kurnia, A Kusdaniyama, Nunung Kusman Sadik Laradea Marifni Lestari P, Merryanty Linda Sakinah M. Syamsul Maarif Ma'mun Sarma Manuel Leonard Sirait Manuel Leonard Sirait Manuel Leonard Sirait Mattjik, AA Maulida, Annisaturrahmah Mega Pradita Pangestika Meilania, Gusti Tasya Merryanty Lestari P Mintarto Mundandar, Jono Muhamad Nur Aidi Muhammad Amirullah Yusuf Albasia Muhammad N Aidi Muhammad Nur Aidi Muhammad Ulinnuha Mulianto Raharjo Munanda, Jono Mintarto Muradi, Hengki Newton Newton Nina Valentika Ningsih, Wiwik Andriyani Lestari Noercahyo, Unggul Sentanu Novi Hidayat Pusponegoro Nunung Kusdaniyama Nunung Kusdaniyama Nur Hikmah Nurlia Eka Damayanti Nurus Sabani Pasaribu, Sahat M. Pepi Novianti Pika Silvianti Pratiwi, Windy Ayu Pratiwi, Windy Ayu Pudji Muljono Purwaningsih, Siti Samsiyah Puspasari, Novia Rahardiantoro, Septian Rahma Anisa Rahma Anisa Rhesa Adisty, Mohamad Risnawati, I'lmisukma Rizqi Haryastuti Sahat M. Pasaribu Sarah Fadhlia Sarma, Ma’mun Satria Yudha Herawan SATRIYAS ILYAS Setyono Setyono Setyono Sirait, Manuel Leonard Siti Samsiyah Purwaningsih Sri Surjani Tjahjawati Sunardi Sunardi Sunardi Suruddin, Adzkar Adlu Hasyr Sutomo, Valantino A Syafitri, Utami Syella Sumampouw Tsabitah, Dhiya Tsabitah, Dhiya Ulayya Ulfah Sulistyowati Utami Dyah Syafitri Valantino A Sutomo Valentika, Nina Wibowo, Dwi Yoga Ari Winda Nurpadilah Windi D.Y Putri Wiwik Andriyani Lestari Ningsih Yenni Angraini Yoga, Ibnu Abi Zulkarnain, Rizky