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Journal : Indonesian Journal of Pharmaceutical Science and Technology

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 Abidi, Subhan R Aflit Nuryulia Praswati Afzalur Rahman Agustina, Rinna Ahmad, Farhand Ahsaninnisa, Azizah Alfarizky, Mustaqim Ananta, Karunia Dinda Andi Suhendi Annisa Wifa Rizqi Madjid Arifa Nursayyida Aulia Rahman Aulia Rahman Auliya, Dhiyahul Bella Permatasani Bintari, Iin Chintika Irianti Dani Cantika Nukitasari Choirulisa, Nur Dwi Dedi Hanwar Dedy Priyatama Dewi, Monarita Puspita Dewi, Triana Ariska Diah Mukti Sari Dimas Satrio Utomo Diva Ratna Shabrina Erwinda Kusumaningtyas Fabiola Irianty Atmaja Fakhmi, Nurul Farras, Naufal Fauzi Ahmad Muda Fauziyah Ardli Oktavianingrum Fitri Kusvila Aziz Fortuna, Tista Ayu Ghiyats Ramadhan Hafid Nugroho Hanidya Fidela Ulayya Haryoto Haryoto Haryoto, H Hidayah Karuniawati Iin Chintika Irianti Dani Bintari Ika Trisharyanti Dian Kusumowati Karisma Enggar Saputri Karunia Dinda Ananta Kasful Asra Sakika Keisya, Aulita Kusumaningtyas, Erwinda Lestari, Susi Indah Lita Windy Aryati M. Kuswandi M. Kuswandi, M. Madjid, Annisa Wifa Rizqi Monarita Puspita Dewi Muhammad Haqqi Hidayatullah Mustaqim Alfarizky Mustika, Yurnanda Ambar Naufal Farras Nur Cholis Endriyatno Nur Dwi Choirulisa Nurul Fakhmi Permatasani, Bella Prastiwi Wulaning Tyas Priyatama, Dedy Pujiastuti, Nurkholifah Rahman, Afzalur Ramadhan, Ghiyats Rani Wulandari Rani Wulandari Ratna Yuliani Ratna Yuliani Rinna Agustina Riyanto, R Rizkiananda Wardani Saputri, Karisma Enggar Sari, Diah Mukti Shabrina, Diva Ratna Subhan R Abidi Susi Indah Lestari Tyas, Prastiwi Wulaning Utomo, Dimas Satrio Wardani, Rizkiananda Wathony, Al Y Yuliansah Yuliansah, Y Yurnanda Ambar Mustika Zafarani Azzuhra, Alifia