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All Journal Indonesian Journal of Cancer Chemoprevention Data Science: Journal of Computing and Applied Informatics Stannum : Jurnal Sains dan Terapan Kimia Jurnal Buana Farma Helium: Journal of Science and Applied Chemistry Jurnal Pengabdian Masyarakat Bangsa Diteksi : Jurnal Pengabdian Kepada Masyarakat Helium: Journal of Science and Applied Chemistry
Muhammad Yogi Saputra
Chemistry Department, Institut Teknologi Sumatera, South Lampung, Lampung, 35365
Agriculture, Biological Sciences & Forestry Arts Humanities Automotive Engineering Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Civil Engineering, Building, Construction & Architecture Computer Science & IT Control & Systems Engineering Economics, Econometrics & Finance Education Energy Environmental Science Health Professions Immunology & microbiology Industrial & Manufacturing Engineering Languange, Linguistic, Communication & Media Law, Crime, Criminology & Criminal Justice Materials Science & Nanotechnology Mathematics Medicine & Pharmacology Nursing Physics Public Health Social Sciences

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In Silico Analysis of Cucurbitacin IIa and Cucurbitacin IIb as Potential Modulators of Oxidative Stress Regulatory Proteins Sarmoko, Sarmoko; Suprahman, Nisa Yulianti; Putri, Refsya Azanti; Hakim, Ahmad Zammi Autadan; Cahyadi, Dzaky Raihan; Saputra, Muhammad Yogi
Indonesian Journal of Cancer Chemoprevention Vol 15, No 3 (2024)
Publisher : Indonesian Society for Cancer Chemoprevention

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14499/indonesianjcanchemoprev15iss3pp224-236

Abstract

Oxidative stress, resulting from imbalance between rective oxygen species (ROS) production and antioxidant defenses, contributes significantly to numerous pathological conditions, including inflammation, cancer and neurodegeneration. Natural compounds with antioxidant properties offer promising therapeutic potential. This study aims to investigate the potential of Cucurbitacin IIa and IIb to modulate oxidative stress regulatory proteins (NOS2, Lipoxygenase, KEAP1, and Xanthine oxidase) using molecular docking approaches. Target protein structures were retrieved from the RSCB Protein Data Bank. Ligand geometries were constructed and optimized using density functional theory. Molecular docking was performed using AutoDock 1.5.6 with a validated docking protocol (RPMS<2Å). Our results demonstrated favorable binding energies for both compounds with NOS2 (-9.75 and -9.57 kcal/mol) and KEAP1 (-8.52 and -9.34 kcal/mol), approaching the affinities of their respective native ligands. Moderate binding was observed with Lipoxygenase (-6.14 and -5.54 kcal/mol), while both compounds showed incompatibility with Xanthine oxidase, as evidenced by highly positive binding energies. The interaction between Cucurbitacins with NOS2, KEAP1 and Lipoxygenase was mediated through hydrogen and hydrophobic interaction. These findings provide mechanistic insight into their bioactivity and support further experimental studies for therapeutic development in oxidative stress-related disorders.Keywords: Cucurbitacin, Molecular docking, Oxidative stress, NOS2, KEAP1.
The Potential of Isoniazid Derivatives as Anti-Tuberculosis Drugs targeting 6MA8: In Silico Study Saputra, Muhammad Yogi; Ivansyah, Atthar Luqman; Maharani, Nabila Aprilia; Kurniawan, Rahmat; Putri, Refsya Azanti; Abshar, Irham Fauzi
Helium: Journal of Science and Applied Chemistry Vol. 5 No. 1 (2025): Helium: Journal of Science and Applied Chemistry
Publisher : Study Program of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Pakuan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33751/helium.v5i1.13

Abstract

Tuberculosis (TB) is a contagious disease caused by Mycobacterium tuberculosis. Isoniazid, a synthetic antimicrobial agent, remains one of the most crucial first-line medications in TB therapy. Enhancing TB treatment strategies can be achieved through structural modifications of existing drugs. This study investigates the potential of isoniazid derivatives as anti-tuberculosis agents targeting the CYP3A4 protein complexed with a small-molecule inhibitor (PDB ID: 6MA8) and evaluates their toxicity profiles using in silico methods. The ligands analyzed include isoniazid derivatives 1–5, with isoniazid as a reference compound and protoporphyrin as the native ligand. The structure of ligands was prepared using Avogadro software and optimized with ORCA software. The crystal structures of 6MA8 were retrieved from the PDB database and further validated using YASARA. In silico methods such as molecular docking and ProTox prediction were employed to evaluate the potential of these isoniazid derivatives as anti-TB drugs. The interactions were visualized using Biovia Discovery to assess the interaction between the isoniazid derivatives and the receptor. The results showed derivative 4 exhibited the lowest binding affinity (-71.56 kcal/mol) compared to isoniazid (-65.90 kcal/mol), derivative 1 (-63.65 kcal/mol), derivative 2 (-67.01 kcal/mol), derivative 3 (-67.37 kcal/mol), derivative 5 (-69.02 kcal/mol), and native ligand (-182.68 kcal/mol). Biovia Discovery Studio simulations indicated that the isoniazid derivatives interacted with 6MA8 via conventional hydrogen bonds, carbon-hydrogen bonds, and other interactions. The toxicity analysis showed that the derivatives had safe LD50 values, supporting their safety profiles. These results suggest that isoniazid derivatives have promising potential as anti-tuberculosis agents targeting 6MA8.
Co-Authors A.L, Ihza Adzkiya Mubarak Abshar, Irham Fauzi Aji, Abdul Alrando, Raja Aksana Andika Setiawan, Andika Arif Ashari Arif Azhari Arrafi, Muhammad Zhafran Atthar Luqman Ivansyah Ayuwulanda, Aditya Cahyadi, Dzaky Raihan Clara L.A, Cindy Moyna Debora Silalahi Demi Dama Yanti Enggelina, Nia Natalia Ghifari, M. Alvien Habeahan, Angelina Hakim, Ahmad Zammi Autadan Hamdiyah Fuola Zeri Hasibuan Handrizal Hangger Gahara Mawandha Hanifa, Milla Hasna, Naurah Rosyidah Hawa Purnama Celala Ary Cane I Putu Mahendra Indarto Indarto Indriyanto, Anatasya Irawan, Siti Azara Nayla Krisnawati, Linda Maharani, Nabila Aprilia Mario, Frisel Mariska, Soraya Mariyam Mariyam Mohammad Andri Budiman Muhammad Raffi Zakaria N.S, Yonatan Adi Nirwanto Nirwanto, Nirwanto Nisa Yulianti Suprahman Pastina, Henggis Rahmadi, Muhammad Zaki Ammar Rahman, M. Arief Rahmat Kurniawan Rahmat Kurniawan Rahmatulllah, Ilham Refsya Azanti Putri Rohadi, Rahmat Saeli, Pinka Mustika Sarmoko Sarmoko Sena Maulana Sukrasno Sukrasno Swandari, Tantri Syaikhul Aziz Tantri Liris Nareswari Tuta, Gabriell Vanes Sabat Welldone Sartika Windari, Nurul Irna Windasari, Liska Yesi, Litri Yoga Anjas Pratama