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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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Anuran diversity and community structure in Lesti upriver across buffer zone habitat in Bromo Tengger Semeru National Park Fathoni, Muhammad; Hakim, Luchman; Kurniawan, Nia
Biotropika: Journal of Tropical Biology Vol. 10 No. 1 (2022)
Publisher : Universitas Brawijaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.biotropika.2022.010.01.10

Abstract

In Bromo Tengger Semeru National Park (BTSNP), buffer zone areas, one of which is the Lesti upstream rivers, play a critical role in sustaining biodiversity and community life. Frogs serve as a bioindicator of environmental change, particularly in the upstream rivers of the Lesti. The present study examines the diversity and community structure of Anura in the upstream rivers of Lesti, which are included in the BTSNP buffer zones. Throughout the surveys, up to 14 anuran species were encountered in four sites adjacent to the BTSNP border and crossed by the Lesti rivers. This study suggests that buffer zones may support herpetofaunal diversity by allowing humans to interact with them and sustainably utilize the resources in the areas. Urban development and conservation in these areas must be kept current in order to minimize environmental disruption caused by humans.
Identification of Mudskipper Species in Mangrove Area of Luwu Timur, Luwu Utara, and Wajo South Sulawesi Indonesia Darojat, Annisa Zakiyah; Marhendra, Agung Pramana Warih; Kurniawan, Nia
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.2023.011.02.02

Abstract

Mudskipper is amphibious fish that inhabited sandy beaches, mudflat, and mangrove areas. This fish is euryhaline because of its tolerance to varying salinity as well as pH, temperature, conductivity, and dissolved oxygen. This study aimed to identify the taxonomy status of mudskipper in Banua Pangka Mangrove Ecotourism, Seta-Seta Beach, and Masiae River, it was expected to be additional information used as a basis for management and benefaction in taxonomic and ecological aspects. The sampling method of this study was purposive sampling. Morphological identification was carried out by observing morphometric and meristic character. The result found two mudskipper species from three sampling sites, namely Periophthalmus argentilineatus and Periophthalmodon freycineti. Water quality parameter values at three sampling locations were within the optimal range for mudskipper species according to the previous study. The temperatures ranged from 28-33 Celsius, the dissolved oxygen ranged from 2.04-6.74 mg/L, the pH ranged from 6.57-7.1, conductivity ranged from 3.47-41.2 mS/cm, and the salinity ranged from 1.7-2.58 per-mille.
In silico Exploration of Bioactive Compounds from Withania somnifera as Inhibitor for Alpha Delta Bungarotoxin of Bungarus candidus Venom Prabasari, Kartika; Kurnianingsih, Nia; Kurniawan, Nia
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.2023.011.02.01

Abstract

The antivenom for Malayan krait (Bungarus candidus) venom has not yet been available in Indonesia, leading to many fatal snakebite cases. Alternative treatment approaches using medicinal plants are needed to be explored. This study investigated the potential of medicinal plants’ natural bioactive compounds as toxic alpha-delta bungarotoxin protein inhibitors in B. candidus venom. The approach taken is using the 3D structure of the alpha-delta protein of bungarotoxin B. candidus predicted by SWISS-MODEL. Knapsack Family Database and PubChem were used for bioactive compounds datamining. ADME analysis and drug-likeness of the compounds were carried out with SWISS-ADME. Docking between alpha-delta-Bungarotoxin protein and bioactive compounds was carried out with Pyrx 0.9.5. Visualization of docking results was performed with PyMOL and Discovery Studio 2016 was used to evaluate docking interactions. The docking results showed that a compound with the potential inhibitor of alpha-delta bungarotoxin came from Ashwagandha (Withania somnifera) with a binding energy ranging from -6.6 to -6.9. The compound with the best inhibitor potential, namely withanolide D, was seen from the stability of the interaction based on hydrogen bonding at three amino acid residues: THR59, SER62, and THR63. The evaluation is supported by the results of molecular dynamics simulations which show stability in almost all aspects. Our results suggest the potential for exploratory research in the field of bioinformatics related to bioactive compounds from herbal plants as an alternative to antivenom.
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 Muhammad Fathoni, Muhammad Mumpuni Mumpuni Narwasthu, Sekararum Nashi Widodo Nasirudin, Mohamad 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