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All Journal JURNAL KIMIA SAINS DAN APLIKASI 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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Molecular Docking and Molecular Dynamic Investigations of Xanthone-Chalcone Derivatives against Epidermal Growth Factor Receptor for Preliminary Discovery of Novel Anticancer Agent Yehezkiel Steven Kurniawan; Ervan Yudha; Gerry Nugraha; Nela Fatmasari; Harno Dwi Pranowo; Jumina Jumina; Eti Nurwening Sholikhah
Indonesian Journal of Chemistry Vol 24, No 1 (2024)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.88449

Abstract

Epidermal growth factor receptor (EGFR) is found to be overexpressed in cancer cells as it controls angiogenesis, cell signaling, and proliferation mechanisms. Therefore, EGFR has been known as a common target for the initial screening of new anticancer agents. Either xanthone or chalcone has been evaluated as the anticancer agents, and their activity strongly depends on the type and position of the attached functional group. Therefore, molecular hybridization between xanthone and chalcone could yield novel anticancer agents through the EGFR inhibition mechanism. Herein, a series of xanthone-chalcone derivatives with hydrogen-bond-acceptor or hydrogen-bond-donor substituents at ortho, meta, and para positions was evaluated as the EGFR inhibitor. Thirty-seven xanthone-chalcones were designed and docked in the active site of EGFR. Compared to the native ligand, pristine xanthone-chalcone gave a 1.215× stronger binding energy and a 13.97× lower binding constant. Compound 3SH was found to be the most promising candidate due to its strongest binding energy (−9.71 kcal/mol) and the lowest binding constant (0.08 µM). Furthermore, molecular dynamic studies demonstrated that complex EGFR-3SH was stable for 100 ns simulation. These in silico investigations show that the xanthone-chalcone derivative is a promising novel anticancer agent to be examined through in vitro and in vivo assays.
Synthesis, Activity Test and Molecular Docking of Novel Nitrophenylcalix[4]-2-methylresorcinarene Derivatives as Antimalarial Agent Nisa, Siti Astika; Jumina, Jumina; Mardjan, Muhammad Idham Darussalam; Kurniawan, Yehezkiel Steven
Molekul Vol 18 No 3 (2023)
Publisher : Universitas Jenderal Soedirman

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20884/1.jm.2023.18.3.7866

Abstract

This research involved the synthesis, antimalarial assay and molecular docking of novel nitrophenylcalix[4]-2-methylresorcinarene derivatives. Calix[4]-2-methylresorcinarene derivatives, i.e., 2N, 3N and 4N, were synthesized in a one-step reaction through the cyclo-condensation reaction between resorcinol and aldehydes, i.e., 2-nitrobenzaldehyde, 3-nitrobenzaldehyde and 4-nitrobenzaldehyde, respectively. The reaction was carried out through the reflux method with ethanol and hydrochloric acid 37% as the solvent and catalyst, respectively. The synthetic products were characterized using FTIR, 1H-NMR, 13C-NMR, and LC-MS spectrometers. Furthermore, the in vitro antimalarial assay was carried out against Plasmodium falciparum strain 3D7. The results showed that the 2N, 3N and 4N compounds were successfully synthesized in 86.4, 78.6 dan 95.7% yield, respectively. The antimalarial activity test of 2N, 3N and 4N gave IC50 values of 2.35, 1.68 and 1.79 µM, therefore, these compounds are classified as active antimalarial agents. Molecular docking performed against the PfLDH receptor showed that the 2N, 3N and 4N compounds had negative binding affinity values of -5.1, -6.1, and -6.0 kcal/mol and had specific interactions in the form of hydrogen bonds to the amino acid residues Arg109, Thr101 and Lys102 in the active site of the receptor. The molecular docking results agreed with the experimental antimalarial assay demonstrating the mechanism of action of nitrophenylcalix[4]-2-methylresorcinarenes as active antimalarial agents happened through the inhibition of the PfLDH receptor.
One-Pot Synthesis and In Vitro Studies of Calix[4]-2-methylresorcinarene Derivatives as Antimalarial Agents Against Plasmodium falciparum Chloroquine-Resistant Strain FCR-3 Nursofia, Baiq Ike; Kurniawan, Yehezkiel Steven; Jumina, Jumina; Pranowo, Harno Dwi; Sholikhah, Eti Nurwening; Julianus, Jeffry; Wibowo, Susalit Setya; Fatimi, Hana Anisa; Priastomo, Yoga; Priyangga, Krisfian Tata Aneka
Indonesian Journal of Chemistry Vol 24, No 6 (2024)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.94885

Abstract

Malaria is an endemic disease in Indonesia caused by infection from the Plasmodium parasite. Recently, antimalarial resistance significantly contributed to the decline in the cure rate of malaria sufferers. In this work, three calix[4]resorcinarenes have been synthesized from 2-methylresorcinol and different benzaldehyde derivatives, i.e., 4-chlorobenzaldehyde, 4-methoxybenzaldehyde, and 4-dimethylaminobenzaldehyde through the one-pot synthesis procedure. The calix[4]resorcinarenes synthesis was done through a cyclo-condensation reaction by using HCl 37% as the catalyst and ethanol as the solvent in an one-pot reaction. The structures of the synthesized products were confirmed using Fourier transform infrared, proton-nuclear magnetic resonance, and liquid chromatography-mass spectrometry techniques. The antimalarial activity assay was evaluated against the Plasmodium falciparum FCR-3 strain through an in vitro study. Three synthesized compounds, i.e., C-4-chlorophenylcalix[4]-2-methylresorcinarene, C-4-methoxyphenylcalix[4]-2-methylresorcinarene and C-4-dimethylaminophenylcalix[4]-2-methylresorcinarene have been successfully synthesized in up to 97% yield. The C-4-chlorophenylcalix[4]-2-methylresorcinerene exhibited the most potent antimalarial activity with a half-maximal inhibitory concentration (IC50) value of 2.66 µM against P. falciparum FCR-3 while the C-4-methoxyphenylcalix[4]-2-methylresorcinarene and C-4-dimethylaminophenylcalix[4]-2-methylresorcinarene gave the IC50 values of 23.63 and 13.82 µM, respectively. From the results, it could be concluded that the antimalarial activity of calix[4]-2-methylresorcinarenes was influenced by the type of substituent of aromatic rings at the para position.
Fight for Cancer Diseases using Natural Compounds and Their Semisynthetic Derivatives Yehezkiel Steven Kurniawan; Kasta Gurning; Iksen Iksen; Ahmad Bikharudin
Bioactivities Vol. 2 No. 2 (2024): Bioactivities
Publisher : Pandawa Institute

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.47352/bioactivities.2963-654X.221

Abstract

Cancer stands as one of the deadliest diseases afflicting contemporary human societies, encompassing over 100 distinct forms, including oral, salivary glands, oropharynx, nasopharynx, hypopharynx, colorectal, liver, pancreas, lung, skin, breast, cervix, ovary, prostate, kidney, brain, thyroid, and leukemia cancers. At the cellular level, the uncontrolled growth of cancerous cells can disrupt the body's normal functions. Chemotherapy, a widely recognized cancer treatment, utilizes anticancer agents to target specific cancer cell lines effectively. Natural compounds are favored for their compatibility with the body, minimal harm to healthy cells, and easy extraction from natural sources. These natural compounds and their derivatives hold promise for cancer therapy, boasting diverse structural and pharmacological characteristics. Additionally, chemical modifications can enhance their anticancer properties. This review explores the anticancer potential of terpenoids, flavonoids, alkaloids, xanthones, and epoxides, as well as elucidates their molecular mechanisms, such as their antiproliferative, apoptotic, antiangiogenic, and antimetastatic actions. Furthermore, the effect of the functional group on the anticancer activity through the structure-activity relationship will be discussed in detail, supported by molecular docking and molecular dynamic simulations. Combining experimental in vitro and in vivo assays with computational in silico assays significantly helps us understand how we shall fight cancer diseases in the modern era.
Evaluation of The Anticancer Activity of Hydroxyxanthones Against Human Liver Carcinoma Cell Line Yehezkiel Steven Kurniawan; Nela Fatmasari; Jumina Jumina; Harno Dwi Pranowo; Eti Nurwening Sholikhah
Journal of Multidisciplinary Applied Natural Science Vol. 4 No. 1 (2024): Journal of Multidisciplinary Applied Natural Science
Publisher : Pandawa Institute

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.47352/jmans.2774-3047.165

Abstract

Nowadays, cancer is one of the most fatal diseases in developed and developing countries. Therefore, it is an urgent need to find more effective anticancer drugs among the recent commercially available standard drugs. Xanthone derivatives have been researched as anticancer drugs due to their ease of synthesis and structure modification, as well as their excellent anticancer activity. In this work, the in vitro anticancer activity of hydroxyxanthones against the human liver carcinoma cell line (HepG2) was evaluated. Among the twenty-two hydroxyxanthones, 1,3,6,8-tetrahydroxyxanthone was found as the most active anticancer agent with an IC50 value of 9.18 μM, which was better than doxorubicin as the standard drug. From the molecular docking studies against topoisomeraseIIα and two c-KIT protein kinases, 1,3,6,8-tetrahydroxyxanthone yielded strong binding energy in a range of -25.48 to -30.42 kJ/mol. The 1,3,6,8-tetrahydroxyxanthone could bind on the active site of these protein receptors through hydrogen bonds with key amino acid residues (Glu640, Cys673, Gln767, Met769, Asp810, and Asp831), as well as nitrogen bases (Adenine12 and Guanine13), thus leading to the death of HepG2 cancer cells through the apoptosis mechanism.
Catalytic Reduction of 4-Nitrophenol and Methylene Blue with Silver Nanoparticles Decorated with Drymoglossum piloselloides Extract Awalul Fatiqin; Rokiy Alfanaar; Sudarman Rahman; Yahya Febrianto; Shesanthi Citrariana; Mu’afa Purwa Arsana; Thathit Suprayogi; Yehezkiel Steven Kurniawan
Journal of Multidisciplinary Applied Natural Science Vol. 4 No. 2 (2024): Journal of Multidisciplinary Applied Natural Science
Publisher : Pandawa Institute

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.47352/jmans.2774-3047.210

Abstract

Drymoglossum piloselloides is one of the epiphytic plants that is commonly found in Southeast Asia region. In this study, the ethanol extract of D. piloselloides plant has been used in the green synthesis of silver nanoparticles. The synthesized silver nanoparticles were characterized by ultraviolet-visible (UV-Vis) spectrophotometry, X-ray diffraction (XRD),Fourier-transform infrared (FTIR) spectroscopy, and transmission electron microscopy (TEM) measurements. The UV-Vis spectrum of silver nanoparticles showed a maximum wavelength at 453 nm. The XRD measurement showed the silver nanoparticles peaks at 38.38°, 44.60°, 64.76°, and 77.62°. The FTIR spectra provided evidence of the interaction between silver and chemicals in the plant extract as a weak signal at 682 cm-1. Meanwhile, TEM revealed an average size of 12.63nm. The synthesised silver nanoparticles were utilised for the reduction of 4-nitrophenol with a conversion percentage of up to 100% with a reduction reaction rate constant of 7.104 s-1. In addition, methylene blue was also successfully reduced with the synthesised silver nanoparticles as the catalyst with a reduction reaction rate constant (k) of 21.150 s-1. This study highlights the superior advantage of utilizing ethanolic extract of D. piloselloides to prepare silver nanoparticles with promising catalytic reduction purposes.
Evaluation of Xanthone and Cinnamoylbenzene as Anticancer Agents for Breast Cancer Cell Lines through In Vitro and In Silico Assays Yehezkiel Steven Kurniawan; Hanif Amrulloh; Ervan Yudha; Nela Fatmasari; Faris Hermawan; Anggit Fitria; Harno Dwi Pranowo; Eti Nurwening Sholikhah; Jumina Jumina
Journal of Multidisciplinary Applied Natural Science Vol. 5 No. 1 (2025): Journal of Multidisciplinary Applied Natural Science
Publisher : Pandawa Institute

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.47352/jmans.2774-3047.231

Abstract

Breast cancer is a severe global disease for women as the number of deaths increases annually. Therefore, attempts to find new anticancer agents are critical and inevitable. In this work, we report the investigation on the anticancer activity of xanthone and cinnamoylbenzene compounds against two breast cancer cell lines, i.e., T47D and MCF-7, through experimental in vitro and theoretical in silico assays. Xanthone and cinnamoylbenzene exhibit anticancer activity with a half-maximal inhibitory concentration (IC50) of 136.7–194.3 and 235.8–262.4 µg/mL against T47D and MCF-7 cancer cells, respectively. Cinnamoylbenzene generates less cytotoxicity to normal Vero cells with a selectivity index of 1.095–2.102. The molecular docking studies agree with the experimental data in which cinnamoylbenzene is more active against T47D with an IC50 of 136.7 µg/mL due to Topoisomerase II inhibition through π-π stacked interactions with Adenine12 and Guanine13 nitrogen bases. Meanwhile, xanthone is more active against MCF-7 with an IC50 of 235.8 µg/mL due to EGFR inhibition through van der Waals interaction and hydrogen bond with Glutamic acid767 and Methionine769 amino acid residues, respectively. Additionally, the pharmacokinetic parameters of xanthone and cinnamoylbenzene are predicted through absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis, and they show better suitability than doxorubicin as the commercial anticancer drug.
Allyl-Modified of Calix[4]resorcinarene Derivatives for HER2 Inhibition Agents: An In Silico Study Fitria, Anggit; Kurniawan, Yehezkiel Steven; Ananto, Agus Dwi; Jumina, Jumina; Sholikhah, Eti Nurwening; Pranowo, Harno Dwi
Journal of Multidisciplinary Applied Natural Science Vol. 5 No. 2 (2025): Journal of Multidisciplinary Applied Natural Science
Publisher : Pandawa Institute

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.47352/jmans.2774-3047.250

Abstract

Breast cancer is one of the deathliest cancer diseases for women, with high mortality cases. Since breast cancer cells overexpressed HER2 receptors, a computerized structure-based screening was conducted to identify potential HER2 inhibitors as an anti-breast cancer agent. This method can investigate the potency of proposed compounds as potential protein inhibitors. Researchers were interested in studying some synthetic macromolecules, i.e., allyl-modified calix[4]resorcinarenes, through in silico studies as HER2 inhibitors using molecular docking studies. Prospective protein-ligand complexes for HER2 inhibition were further investigated by molecular dynamics simulations for 200 ns on different binding pockets. The allyloxycalix[4]resorcinarene derivative (5A) was identified as the most potential HER2 inhibitor through a computational approach, including molecular docking studies and molecular dynamics simulations. The HER2-5A complex was relatively stable during the 200 ns molecular dynamics run. In addition, the hydrogen bonds formed between blind docking and molecular dynamics simulations are almost unchanged for the HER2-5A complex. The HER2-5A formed with two crucial amino acid residues, i.e., Asp845 and Asn850. Moreover, the data of the molecular dynamics simulations of compounds 5A and 2A demonstrate the stability of both complexes in different binding sites of HER2. These computational results are preliminary data for further synthesis and in vitro evaluation.
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.
Co-Authors Abdul Karim Zulkarnain Adhi Dwi Hatmanto Adhiwibawa, Marcelinus Alfasisurya Setya Agus Dwi Ananto, Agus Agustinus Winarno Ahmad Bikharudin Alfanaar, Rokiy Amrulloh, Hanif Andini, Vicka 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 Devi Ratnawati 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 Evi Maryanti 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, Risky Hadi Wibowo, Susalit Setya Yahya Febrianto Yudha Ramanda Yudha, Ervan