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All Journal Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences The Journal of Experimental Life Sciences (JELS) Journal of Indonesian Tourism and Development Studies Biotropika Jurnal Pembangunan dan Alam Lestari AGRIVITA, Journal of Agricultural Science Journal of Tropical Biodiversity and Biotechnology TREUBIA JSMARTech : Journal of Smart Bioprospecting and Technology Proceeding Biology Education Conference RISTEC : Research in Information Systems and Technology Edubiotik : Jurnal Pendidikan, Biologi dan Terapan
Nia Kurniawan
Brawijaya University
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Civil Engineering, Building, Construction & Architecture Computer Science & IT Control & Systems Engineering Decision Sciences, Operations Research & Management Economics, Econometrics & Finance Education Environmental Science Immunology & microbiology Materials Science & Nanotechnology Medicine & Pharmacology Neuroscience Public Health Social Sciences

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Journal : Biotropika

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Study of Flavonoid in Apium graveolens L. as a Kirsten Rat Sarcoma Protein Inhibitor in Colorectal Cancer Based on In Silico Study Abdullah, Abdullah; Putri, Nenis Try Melani; Rosyadah, Nuraini; Ramadhani, Putri; Putri, Siti Aqila Kharisma; Widyananda, Muhammad Hermawan; Kurniawan, Nia; Fatchiyah, Fatchiyah
Biotropika: Journal of Tropical Biology Vol. 11 No. 2 (2023)
Publisher : Universitas Brawijaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.biotropika.2023.011.02.07

Abstract

Colorectal cancer (CRC) is considered the second deadliest cancer, mainly caused by the mutation of Kirsten Rat Sarcoma (KRAS) type G12D; it’s still undruggable. Flavonoids are secondary metabolites in celery, consisting of apigenin, luteolin, quercetin, and kaempferol. This study aims to analyse the most potential flavonoid compounds in Apium graveolens L. as KRAS inhibitors in CRC with in-silico. This study starts by collecting the 3D structure, Compound ID, formula, and canonical SMILES of compounds from PubChem and the 3D structure of KRAS G12D from the RCSB-PDB. Ligand and protein preparations using OpenBabel PyRx and Biovia Discovery Studio 2019. The SwissADME web server is used to analyse drug-likeness, the PassOnline web server is used to analyse biological activity, docked using PyRx VinaWizard, and visualisation by Biovia Discovery Studio 2019. RMSD and RMSF values were obtained by analysing binding stability with the YASARA application. The molecular docking test showed that chrysoeriol, luteolin, and apigenin have the highest binding affinity and advance to molecular dynamic test. Results of the molecular dynamic showed that chrysoeriol could potentially inhibit the KRAS protein drug in CRC since it also had the lowest toxicity and the strongest binding affinity to the KRAS.
Computational Design of a Truncated Javan Spitting Cobra (Naja sputatrix) Venom Cardiotoxin Analogue as a Promising Insulinotropic Agent Dinana, Ichda Arini; Widodo, Widodo; Kurniawan, Nia
Biotropika: Journal of Tropical Biology Vol. 11 No. 3 (2023)
Publisher : Universitas Brawijaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.biotropika.2023.011.03.03

Abstract

Treatment options for diabetes may vary widely, however, around 50% of all diabetic patients do not reach the minimum glycemic target. Therefore, drugs that are able to lower glucose levels through unconventional targets are still needed for the treatment of type 2 diabetes. This study aimed to investigate the activity of cardiotoxins from Naja sputatrix towards Kv channels as potential targets for glucose level reduction. Molecular docking analysis was conducted using the ClusPro web server, and the resulting protein-ligand interactions were visualized using BioVia Discovery Studio and LigPlus v.4.5.3. The stability of the docking structures was further examined through molecular dynamics simulations. The CTX-1, CTX-3, CTX-4, CTX-5, and CTX-KJC3 sequences from N. sputatrix were aligned and modeled, focusing on the 62-81 amino acid residues. The CTX-3, CTX-4, and CTX-5 models demonstrated interactions with the binding site of the KcsA receptor. Additionally, substituting the Val73 residue in the CTX62-81 fragment with Lys73 resulted in reduced binding energy and mitigated the cytotoxic effects of CTX while maintaining its insulinotropic activity.
Co-Authors Abdullah Abdullah Achmad Dadang Burhanuddin Adityas Arifianto Agung Pramana W.M Agung Pramana W.M Agung Pramana Warih Marhendra Agung Pramana Warih Marhendra, Agung Pramana Warih Agung S. Kurnianto Agung Sih Kurnianto Agung Sih Kurnianto Agung Sih Kurnianto Agus Nurrofik Agus Suryanto Aguung Sih Kurnianto Ahmad Muammar Kadafi Alvionita, Cicin Vinolia Amin Setyo Leksono AMIR HAMIDY Amir Hamidy Andri Maulidi Andri Maulidi Andyni, Regina Shania Anggun Sausan Firdaus Aninnas, Afina Ardiansyah, Franky Ardiantoro, Ari Ardyah Ramadhina Irsanti Putri Arief Sugiharto Arifianto, Adityas Asmaul Khusnah Asmaul Khusnah Assiddiqy, Miftah Farid Azrianingzih, Rodiyati Azrianingzih, Rodliyati Badiul Ulum Badiul Ulum Bagus Priambodo Bagyo Yanuwiadi Bayu Hendra Prakosa Catur Retnaningdyah Darojat, Annisa Zakiyah Dinana, Ichda Arini Djong Hon Tjong Dwi Anggorowati Rahayu Eldi Mulyana, Eldi Elsa Mufti Endik Deni Nugroho Estri Laras Arumingtyas Fahmi, Muhamad Faldy Alifianto fatchiyah . Fauzi, Muhammad Alif Firdaus, Anggun Sausan Firmansyah, Richo Fitra Arya Dwi Nugraha Fitra Arya Dwi Nugraha Franky Ardiansyah Gigih Setia Wibawa Haryanti Haryanti Haryono Haryono Herlin Aprilia Kartini Herlin Aprilia Kartini Hermanto, Feri Eko Imti Yazil Wafa Karina hanum wardany Karina hanum wardany Karuniawan Puji Wicaksono Kholilah, Tsaniyah Nur Kurnianingsih, Nia Kurnianto, Aguung Sih Lekatompessy, Vanela Chatrin Lingga Nugraha Luchman Hakim Lutfita Fitriana Lutviyana Rahman Lutviyana Rahman Maharani, Tri Mahmudul Hasan, Mahmudul Maisuroh, Dalilatul Masayuki Sumida, Masayuki Mohamad Nasirudin Muhammad Fathoni, Muhammad Mumpuni Mumpuni Narwasthu, Sekararum Nashi Widodo Nobukazu Nakagoshi Nopharipaldi Rohman, Slamet Nugraha, Yopi Nugroho, Agung Nurrofik, Agus Prabasari, Kartika Pramudya, Muhammad Alif Imam Putri Ramadhani, Putri Putri, Nenis Try Melani Putri, Siti Aqila Kharisma Qothrun Izza Qothrun Izza Ramadani, Shima Rijalullah, Muhammad Asyraf Rikardo, Novy Kurnia Riyanto, Awal Robiatul Adawiyah Rodiyati Azrianingsih Rosyada, Nabila Nur Rosyadah, Nuraini Rudi Candra Aditama Rudi Candra Aditama Septiadi, Luhur Shahroni, Abdul Mutholib Smith, Eric Nelson SRI RAHAYU Sugiharto, Arief Suharjono, Suharjono Suparno, Kelik Supriyatna, Asep Takeshi Igawa, Takeshi Tesri Maideliza Tetep Tri Maharani Triani Widyanti, Triani Vendy Adrinanda Vendy Adrinanda Wibi Riawan Widodo Widodo Widyananda, Muhammad Hermawan Zain, Dhiyaa Syahlaa Bianca Febrinnisa