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All Journal JURNAL KIMIA SAINS DAN APLIKASI Bulletin of Chemical Reaction Engineering & Catalysis Indonesian Journal of Chemistry Indonesian Journal of Natural Pigments Journal of Multidisciplinary Applied Natural Science Makara Journal of Science Molekul: Jurnal Ilmiah Kimia Bioactivities Bulletin of Chemical Reaction Engineering & Catalysis
Kurniawan, Yehezkiel Steven
Department Of Chemistry, Faculty Of Mathematics And Natural Sciences, Universitas Gadjah Mada
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Energy Engineering Environmental Science Immunology & microbiology Materials Science & Nanotechnology Mathematics Medicine & Pharmacology Physics Other

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Design of Hydroxyxanthone Derivatives as Breast Cancer Inhibitors: A QSAR Modeling, Molecular Docking, Molecular Dynamics, MM-PBSA and ADMET Prediction Fatmasari, Nela; Hermawan, Faris; Jumina, Jumina; Kurniawan, Yehezkiel Steven; Pranowo, Harno Dwi; Puspitasari, Anita Dwi; Hastuti, Lathifah Puji; Marlina, Lala Adetia; Putra, Nicky Rahmana
Journal of Multidisciplinary Applied Natural Science Articles in Press
Publisher : Pandawa Institute

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.47352/jmans.2774-3047.283

Abstract

A comprehensive QSAR analysis, in conjunction with molecular docking, molecular dynamics simulations, MM-PBSA binding energy estimations, and ADMET profiling, was conducted to facilitate the development of novel anticancer agents based on hydroxyxanthone derivatives. Molecular and electronic descriptors were calculated using the DFT method with the 3-21G basis set. The best QSAR model identified several descriptors that significantly influence anticancer activity, including the atomic charges at positions C1, C3, C4a, and C7, as well as the highest occupied molecular orbital (HOMO), surface area (SA), molecular volume (VOL), and molecular weight (MW). This model was used to design novel hydroxyxanthone derivatives (X27 to X47). The docking result showed that compounds 7-bromo-3-hydroxy-1-(methylamino)-9H-xanthen-9-one (X43), 6-hydroxy-8-(methylamino)-9-oxo-9H-xanthene-2-carbonitrile (X44), and 3-hydroxy-7-mercapto-1-(methylamino)-9H-xanthen-9-one (X45) had stronger binding energy values than gefitinib as a native ligand. Gefitinib had a binding energy of -6.84 kcal/mol, while those compounds had values of -6.92, -7.12, and -6.92 kcal/mol, respectively. In a molecular dynamics simulation of 100 ns, compounds X43, X44, and X45 exhibited stability comparable to that of gefitinib against the EGFR protein. Additionally, the binding energy MM-PBSA of compound X43 was the lowest (-29.18 kcal/mol), followed by X44 (-27.11 kcal/mol), gefitinib (-26.06 kcal/mol), and X45 (-25.21 kcal/mol). Furthermore, these compounds met Lipinski's rule parameters and the minimal standard parameters in terms of ADMET characteristics, as predicted by physicochemical properties. In conclusion, compounds X43, X44, and X45 are potential anticancer agents for MDA-MB-231 breast cancer cells.
Anticancer and Antimalarial Assays of Xanthone-Fatty Acid Hybrids: Integrative In Vitro and In Silico Evaluation Kurniawan, Yehezkiel Steven; Harizal, Harizal; Yudha, Ervan; Gurning, Kasta; Pranowo, Harno Dwi; Sholikhah, Eti Nurwening; Jumina, Jumina
Indonesian Journal of Chemistry Vol 25, No 4 (2025)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.106816

Abstract

Cancer and malaria are two fatal diseases found in Indonesia over the past several years. Therefore, researchers are trying their best to find new anticancer and antimalarial agents. In the present work, we evaluated five xanthone-fatty acid hybrids, i.e., xanthyl laurate (XL), xanthyl myristate (XM), xanthyl palmitate (XP), xanthyl stearate (XS), and xanthyl oleate (XO), as novel anticancer and antimalarial agents. The cytotoxicity assay towards NIH3T3 reveals that xanthone-fatty acid hybrids showed a selectivity index up to 282.08, demonstrating their non-toxic profile. The MTT assay found that XO yielded stronger breast anticancer activity than doxorubicin as the positive control. All xanthone-fatty acid hybrids exhibited moderate antimalarial activity with IC50 values of 24.24–87.57 µM, lower than that of chloroquine diphosphate as the positive control (4.26 µM). As the best anticancer agent for breast cancer, the mode of action of XO was further studied by computational studies. The molecular docking results showed the binding energy against the HER2 protein was −45.73 kJ/mol through a hydrogen bond with Lys753. This hydrogen bond remained stable until the end of the molecular dynamics simulations for 100 ns. These findings highlight the potential application of XO as a new drug candidate for breast cancer treatment.
Synthesis, Molecular Docking, and In Vitro Activity Test of Thioxanthenol and Nitrothioxanthone Derivatives As Anticancer Agents Anggraeni, Putri Dian; Jumina, Jumina; Anwar, Chairil; Kurniawan, Yehezkiel Steven
Molekul Vol 20 No 2 (2025)
Publisher : Universitas Jenderal Soedirman

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20884/1.jm.2025.20.2.10089

Abstract

ABSTRACT. This research aimed to compare, synthesise, study molecular docking, and test the anticancer activity of thioxanthenol, 1-hydroxythioxanthone, 4-nitrothioxanthone, and 2-nitrothioxanthone compounds through in silico and in vitro assays, highlighting their selective cytotoxicity and potential as novel anticancer scaffolds. These four compounds were obtained through reduction and nitration reactions of the thioxanthone. Thioxanthenol compound was obtained through the reduction of thioxanthone using sodium borohydride. The 1-hydroxythioxanthone, 4-nitrothioxanthone, and 2-nitrothioxanthone compounds were obtained from the nitration of thioxanthone compounds. The compounds were characterised using FTIR, GC-MS, 1H-NMR, and 13C-NMR. In vitro cytotoxicity tests were performed using microtetrazolium (MTT) assays against T47D, WiDr, and Hela cancer cell lines and the Vero cell line as normal cells. The molecular docking process was studied to determine the in silico activity of the compounds with protein targets. The reduction reaction produced the thioxanthenol compound as a yellowish-white solid in 40.63% yield. The nitration reaction produced 1-hydroxythioxanthone, 4-nitrothioxanthone, and 2-nitrothioxanthone compounds as light-yellow solids in 33.54%; 29.27%; and 31.71% yield, respectively. The synthesized compounds demonstrated selective anticancer activity against certain cancer cells. Thioxanthenol compound showed an IC50 value of 17.46 µg mL-1 on the WiDr cell line and nitrotioxanthone compound showed an IC50 value of 6.05 µg mL-1 on the T47D cell line. Molecular docking showed that the thioxanthone derivatives might act as the anticancer agent through inhibition of epidermal growth factor receptor (EGFR), P-glycoprotein, and Erα functions. Keywords: anticancer, nitrothioxanthone, thioxanthenol, thioxanthone
Co-Authors Abdul Karim Zulkarnain Adhi Dwi Hatmanto Adhiwibawa, Marcelinus Alfasisurya Setya Agus Dwi Ananto, Agus Agustinus Winarno Ahmad Bikharudin Alfanaar, Rokiy Amrulloh, Hanif Anggit Fitria Anggraeni, Putri Dian Anita Dwi Puspitasari Arif Cahyo Imawan Arif Cahyo Imawan Awalul Fatiqin Bambang Purwono Chairil Anwar Christyowati Primi Sagita Citrariana, Shesanthi Danny Nur Wahyu Hidayat Diah Kartika Sari Dita Ariyanti Dwi Rahmasari Fatmawati Dwi Siswanta Dyah Iswantini Edi Setiyono Ervan Yudha Ervan Yudha Eti Nurwening Sholikhah Eti Nurwening Sholikhah Eti Nurwening Sholikhah Eti Nurwening Sholikhah Fahmi, Muhammad Riza Ghulam Faris Hermawan Faris Hermawan, Faris Fatimi, Hana Anisa Fatmasari, Nela Fitria, Anggit Gerry Nugraha Ghozali, Ali Aulia Hana Anisa Fatimi Harizal Harizal Harno Dwi Pranowo Harno Dwi Pranowo Harno Dwi Pranowo Harno Dwi Pranowo Hefni Effendi Hendra Hendra Hendrik Oktendy Lintang Hidetaka Kawakita Iksen Iksen Indriana Kartini Jeffry Julianus Johan Syafri Mahathir Ahmad Joko Waluyo Jumina Jumina Jumina Jumina Jumina Jumina Jumina Jumina Jumina Jumina Jumina Jumina Kasta Gurning Keisuke Ohto Keisuke Ohto Kesuma, Ruth Febriana Kevin Thomas Krisfian Tata Aneka Priyangga Krisfian Tata Aneka Priyangga Krisfian Tata Aneka Priyangga Krisfian Tata Aneka Priyangga Krisfian Tata Aneka Priyangga Langit Cahya Adi Lathifah Puji Hastuti Leny Yuliati Limpat Nulandaya Lintang, Hendrik Oktendy Marlina, Lala Adetia Masatoshi Maeki Masaya Miyazaki Mizuki Ryu Muhammad Fernadi Lukman Muhammad Idham Darussalam Mardjan Mu’afa Purwa Arsana Nela Fatmasari Nela Fatmasari Nisa, Siti Astika Novik Nurhidayat Nursofia, Baiq Ike Philip Anggo Krisbiantoro Priastomo, Yoga Priyangga, Krisfian Tata Aneka Purnomo, Tantyo Ardy Bintoro Purwantiningsih Sugita Putra, Nicky Rahmana Rahman, Sudarman Ramachandra Rao Sathuluri Rizky Riyami Putri Rizky Riyami Putri Rokiy Alfanaar Shintaro Morisada Tantiana Indriani Thathit Suprayogi Triyono Triyono Tutik Dwi Wahyuningsih Tutik Dwi Wahyuningsih Tutik Dwi Wahyuningsih Vina Aida Roza Wataru Iwasaki Wibowo, Susalit Setya Yahya Febrianto Yudha Ramanda Yudha, Ervan