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All Journal VALENSI PROSIDING SEMINAR NASIONAL Jurnal Ilmu Dasar Indonesian Journal of Pharmaceutical Science and Technology Jurnal Ilmu Farmasi dan Farmasi Klinik (Journal of Pharmaceutical Science and Clinical Pharmacy) Biomedika Pharmacon Chimica et Natura Acta JKPK (Jurnal Kimia dan Pendidikan Kimia) Urecol Journal. Part C: Health Sciences Prosiding University Research Colloquium Journal of Pharmaceutical and Sciences. Medical Sains : Jurnal Ilmiah Kefarmasian
Broto Santoso
Universitas Muhammadiyah Surakarta
Agriculture, Biological Sciences & Forestry Humanities Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Computer Science & IT Control & Systems Engineering Dentistry Education Environmental Science Health Professions Immunology & microbiology Law, Crime, Criminology & Criminal Justice Materials Science & Nanotechnology Mathematics Medicine & Pharmacology Nursing Public Health Veterinary

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Journal : Indonesian Journal of Pharmaceutical Science and Technology

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In Silico Study of Weight-selected Molecules of Sea Cucumber as Antimitotic through PyRx-Vina Approach Broto Santoso
Indonesian Journal of Pharmaceutical Science and Technology Suppl. 2, No. 2 (2019)
Publisher : Indonesian Journal of Pharmaceutical Science and Technology

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (854.894 KB) | DOI: 10.24198/ijpst.v1i2.20210

Abstract

Active ligands usually have low molecular weights (MW). However, paclitaxel, a natural anticancer, has high MW. Some compounds (MW = 750-1000 dalton) in Sea cucumber from TCMSP database have anticancer activity. The objective of study is to obtain docking profile of selected compounds compared to taxol as native. Three of human kinesin-8, were collected from the RCSB database and regenerated by adding hydrogen atoms and charge using the Dock Prep in Chimera. These proteins and selected compounds were prepared to fulfil PyRx's requirement. Molecular docking was performed based on mass center value and grid-box volume from previous studies and resulted vina-score (kcal/mol). Docking data and their 3D conformation were analyzed using PyMOL, PoseView, and PLIP. The native alignment results between docked and original conformation showed that their RMSD value is less than one and only one that has the same three-dimensional conformation. Holothurinoside D, desholothurin B, and 2,4-dehydroechinoside B have a binding affinity of -9.7, -9.4, and -9.3 kcal/mol, respectively. Their value is better or at least the same as the native (-9.3 kcal/mol). Hydrophobic interactions between proteins and ligands occurred at residue of F272, V23, and P360. These results confirm that the anticancer mechanism of these compounds may be through inhibition of kinesin-8. Key words: in silico, sea cucumber, antimitotic, PyRx-vina
Co-Authors Aflit Nuryulia Praswati Afzalur Rahman Ahsaninnisa, Azizah Al Wathony Andi Suhendi Annisa Wifa Rizqi Madjid Arifa Nursayyida Aulia Rahman Aulita Keisya Bella Permatasani Cantika Nukitasari Choirulisa, Nur Dwi Dedi Hanwar Dedy Priyatama Dhiyahul Auliya Diah Mukti Sari Dimas Satrio Utomo Diva Ratna Shabrina Erwinda Kusumaningtyas Fabiola Irianty Atmaja Fakhmi, Nurul Farhand Ahmad Fauzi Ahmad Muda Fauziyah Ardli Oktavianingrum Fitri Kusvila Aziz Ghiyats Ramadhan Hafid Nugroho Hanidya Fidela Ulayya Haryoto Haryoto Hidayah Karuniawati Iin Chintika Irianti Dani Bintari Ika Trisharyanti Dian Kusumowati Karisma Enggar Saputri Karunia Dinda Ananta Kasful Asra Sakika Kusumaningtyas, Erwinda Lestari, Susi Indah Lita Windy Aryati M. Kuswandi M. Kuswandi, M. Monarita Puspita Dewi Muhammad Haqqi Hidayatullah Mustaqim Alfarizky Naufal Farras Nur Cholis Endriyatno Nur Dwi Choirulisa Nurkholifah Pujiastuti Nurul Fakhmi Permatasani, Bella Prastiwi Wulaning Tyas Priyatama, Dedy R Riyanto Rani Wulandari Ratna Yuliani Ratna Yuliani Rinna Agustina Rizkiananda Wardani Saputri, Karisma Enggar Sari, Diah Mukti Subhan R Abidi Susi Indah Lestari Tista Ayu Fortuna Triana Ariska Dewi Y Yuliansah Yurnanda Ambar Mustika Zafarani Azzuhra, Alifia