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All Journal Jurnal Zeolit Indonesia Jurnal Pendidikan Kimia (JPKim) Indonesian Journal of Chemistry Journal of Multidisciplinary Applied Natural Science Makara Journal of Science Molekul: Jurnal Ilmiah Kimia
Harno Dwi Pranowo
Faculty of Mathematics and Natural Sciences, University Gadjah Mada, Yogyakarta
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Education Energy Environmental Science Immunology & microbiology Materials Science & Nanotechnology Mathematics Physics

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THE KINETIC OF CYCLIZATION-ACETYLATION (R)-(+)-CITRONELLAL WITH ANHYDRIDE ACETIC ACID WHICH CATALYZED OF Zn2+-NATURAL ZEOLITE Cahyono, Edy; Muchalal, M.; Triyono, Triyono; Pranowo, Harno Dwi
Jurnal Zeolit Indonesia Vol 8, No 1 (2009)
Publisher : Jurnal Zeolit Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (131.024 KB)

Abstract

Reaction kinetic of acetylation-cyclization (R)- (+)-citronellal with acetic acid anhydride which catalyzed Zn2+-zeolite (Zn2+-Za) was analyzed by Langmuir- Hinshelwood Models. (R)-(+)-citronellal isolated from lemongrass oil with fractionation distillation reduced pressure and analyzed anantiomer ratio with GC chiral column β- DEX 225. Catalyst preparation of Zn2+-Za conducted by acid activation on natural zeolite Malang 100 mesh using 1% HF and 6 M HCl, then soaked on 0,1 M NH4Cl. Calcination was done at 450oC during 1 hour with N2 flow to achieved H-natural zeolite (HZa). Cation exchange H-Za with 0,1 M ZnCl2 conducted to obtain Zn2+-natural zeolit (Zn2+-Za). Reactions of Cyclization-acetylation (R )-(+)- citronellal using a catalyst of Zn2+-Za was done by varying molar ratio of (R )-(+)- citronellal with acetic acid anhydride, namely 0.25, 0.5, 1.0; 1 , 25; 1.5. During the reaction, into system, samples were taken each 1 mL of reaction with duration 10, 20, 30, 60, 120, 180 minutes. Reaction product was extracted with n-hexana. Structure elucidation was done by GC-MS, FTIR spectrophotometer, and 1H-NMR spectrometer. The result showed a greater molar ratio (R)-(+)-citronellal against quantity of acetic acid anhydride acetic, pulegil total was decline. Acetylation-cyclization catalyzed with Zn2+-Za on duration of 30 minutes and 80°C has k of 30.964 to 47.619 mmol (minute.gram catalyst)-1 and KSIT/KAA of 7.09.
Quantitative Structure-Activity Relationship Analysis of Organophosphate Insecticides Using Electronic and Molecular Parameters Wibowo, Yari Mukti; Mudasir,; Pranowo, Harno Dwi
Makara Journal of Science Vol. 21, No. 3
Publisher : UI Scholars Hub

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Abstract

Quantitative Structure-Activity Relationship (QSAR) analysis of organophosphate derivatives, and their insecticide activities, was performed using electronic and molecular parameters. The series of organophosphate derivatives and their activities were obtained from literature. The semi-empirical AM1 method was used to model the structure of organophosphate derivatives and calculate the parameters of QSAR. Multiple linear regression (MLR) analysis was performed on the electronic and molecular parameters as well as the activities of the organophosphate insecticides to derive the QSAR model. The best QSAR equation model was used to design, in silico, new insecticide molecules of organophosphate derivatives with higher insecticidal activity. A new insecticide molecule, 4-(diethoxy phosphoryloxy) benzene sulfonic acid, -Log LD50 = 7.344, had the highest insecticidal activity. Lastly, we recommend synthesizing and testing the new insecticide molecule further in the laboratory.
Exploring The Inhibition of SARS-COV-2 PLpro: Docking and Molecular Dynamics Simulation of Flavonoid in Red Fruit Papua and Its Derivatives Ananto, Agus Dwi; Pranowo, Harno Dwi; Haryadi, Winarto; Prasetyo, Niko
Molekul Vol 19 No 3 (2024)
Publisher : Universitas Jenderal Soedirman

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20884/1.jm.2024.19.3.11717

Abstract

In early 2024, Covid-19 witnessed a substantial decline in cases. Nevertheless, with lingering cases and fatalities persisting, it remains crucial to focus on research to develop patented medicines to inhibit the spread of this virus effectively. This study focuses on the Papain-like protease (PLpro) of SARS-CoV-2 because of its crucial role in the viral life cycle, where it is vital for processing precursor proteins into functional components required for viral replication and propagation. This study investigated the inhibitory potential of flavonoid compounds derived from red fruit (Pandanus conoideus Lam) and their derivatives against SARS-CoV-2 PLpro. Employing an in silico approach through molecular docking and MD simulation, internal validation was conducted by redocking the native ligand 100 times, resulting in an average RMSD of 0.228. The Molecular Docking stage conducted for all flavonoid compounds found in red fruit revealed that Quercetin 3′-glucoside exhibited a binding energy of -8.2440 Kcal/mol, surpassing its comparators, remdesivir and paxlovid, which recorded binding energies of -8.2590 Kcal/mol and -7.2170 Kcal/mol, respectively. Consequently, Quercetin 3′-glucoside was selected as a reference compound for identifying derivative compounds. Subsequently, a derivative compound coded DN5 (2-hydroxy-5-(3,5,7-trihydroxy-4-oxo-4H-chromen-2-yl)phenyl 2-methoxybenzoate) was obtained, demonstrating a higher binding energy than the reference compound, remdesivir, and paxlovid, with a value of -8.9300 Kcal/mol. Molecular dynamic simulations over 100 ns at 300 K further validated the stability of DN5's structure, supported by the presence of hydrogen bonds, van der Waals bonds, and several other bonds, underscoring its potential to inhibit SARS-CoV-2 PLpro and positioning it as a promising candidate for drug development. Keywords: Docking, MD Simulation, red fruit, SARS-CoV-2 PLpro
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.
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.
Investigation of New 4-Benzyloxy-2-trichloromethylquinazoline Derivatives as Plasmodium falciparum Dihydrofolate Reductase-thymidylate Synthase Inhibitors: QSAR, ADME, Drug-likeness, Toxicity, Molecular Docking and Molecular Dynamics Simulation Yogaswara, Radite; Pranowo, Harno Dwi; Prasetyo, Niko; Pulung, Maria Ludya
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.2774-3047.258

Abstract

Plasmonium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) is one of the most crucial antimalarial targets. Mutations in the binding pocket of this target lead to resistance to the antifolate. The mutations influence the amino acid residues at points 51, 59, 108 and 164 and contribute significantly to malaria not being treated well. Priority should therefore be given to the development of antifolate-resistance drugs. These studies aim to investigate new 4-benzyloxy-2-trichloromethylquinazoline derivatives as PfDHFR-TS inhibitors using QSAR, ADME, drug-likeness, toxicity, molecular docking studies, and molecular dynamics simulations. The best equation model from the QSAR analysis used MLR and PLS statistics to show that the pIC50 is linearly related to GATS4e, SpMax AEA(ed), and Mor28e, but inverted when compared to ATS6m and ATSC7m. The predictive ability of the model was confirmed by internal and external validation. In addition, the Y-randomization validation showed that the QSAR model was reliable, robust, and stable, with a cRp2 score of over 0.5. ADME and drug-likeness predictions confirmed the new QSAR design for molecules S10, S23 and S64. Based on the toxicity results, three molecules are expected to have moderate and non-toxic properties, starting with S23 and then S10 and S64. Molecular docking studies show that all three molecules have high binding energies, 9.869, 9.589, and 9.565 kcal/mol. The amino acid residues Leu46, Asp54, Ser111, and Thr185 play a major role in ligand-receptor interaction in the binding pocket of quadruple mutant PfDHFR-TS. Furthermore, an evaluation of molecular dynamics simulations of three complexes S10-3JSU, S23-3JSU and S64-3JSU demonstrated stable interactions over 100 ns.
Synthesis of (3E,5E)-1-benzil-3,5 bis (3 (benziloksi)benziliden)piperidin-4-on curcumin analogues and their potential as breast anticancer agents: Assessment using MTT test and molecular docking Astuti, Endang; Kultsum, Jihan Alfiyah; Aulia, Zarah; Rahmawari, Frika; Gurning, Kasta; Triono, Sugeng; Haryadi, Winarto; Pranowo, Harno Dwi
Jurnal Pendidikan Kimia Vol. 16 No. 3 (2024): J. Pendidik. Kim : December 2024
Publisher : Pascasarjana Universitas Negeri Medan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24114/jpkim.v16i3.65150

Abstract

Breast cancer is a serious disease that occurs in women and contributes to the highest mortality compared to other types of cancer. This study aims to synthesize curcumin analog compounds ((3E,5E)-1-benzyl-3,5 bis (3 (benzyloxy)benzylidene) piperidin-4-one), test them in vitro against various breast cancer cells (T47D, HER-2, MCF-7, and 4T1) and normal cells (vero cells), and study their molecular docking. Synthesis was carried out by reacting 3-benzyloxybenzaldehyde with N-benzyl-4-piperidone catalyzed by 5% KOH at room temperature; in vitro testing was carried out using the Microculture Tetrazolium Technique Assay method, ADMET analysis with an online database server, and molecular docking studies in Autodoc Vina. The synthesis results obtained yellow solid powder with a yield of 65.85%, characterization with TLC gave black fluorescence (Rf 0.63), melting point 114-116oC, TLC scanner one peak (100%), retention time 0.65 minutes, 1H &13C-NMR analysis showed the molecular formula C40H35NO3, moderate activity against 4T1 breast cancer cells and inactivity on T47D, HER-2, and MCF-7 cancer cells, and did not show cytotoxicity to normal cells (vero cells). ADMET predictions from Lipinski's five rules contained two parameters that did not meet, namely molecular weight and log P value. Molecular docking studies were carried out on estrogen receptor protein (ER)-α (PDB ID: 2ERT), which showed a binding affinity energy of -8.7 kcal/mol and -7.1 kcal/mol of the native ligand. Further research and development is needed on synthetic curcumin analog compounds to increase their activity value against breast cancer by paying attention to Lipinski's five rules to obtain compounds with better potential activity and ADMET.
Unlocking the Potential of Papuan Red Fruit (Pandanus conoideus Lamk): A Comprehensive Exploration of Its Role in COVID-19 Inhibition Through Molecular Docking and Molecular Dynamics Simulation Ananto, Agus Dwi; Pranowo, Harno Dwi; Haryadi, Winarto; Prasetyo, Niko
Indonesian Journal of Chemistry Vol 25, No 3 (2025)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.99486

Abstract

Indonesia's rich flora has long been used in traditional herbal medicine, and scientific research is now confirming the health benefits of these plants. Among them, Papuan Red Fruit is gaining attention for its potential in treating various ailments, including COVID-19, due to its antioxidant and antibacterial properties. This study focuses on using in silico methods to investigate how Papuan Red Fruit might inhibit COVID-19, specifically by targeting the papain-like protease (PLpro), a key protein in viral replication. Molecular docking and molecular dynamics (MD) simulations were used to assess the binding affinity and stability of compounds from the fruit. The compound quercetin 3'-glucoside showed the lowest binding energy, indicating strong interactions with PLpro. MD simulations at 300 K for 100 ns confirmed the stability of the quercetin 3'-glucoside-PLpro complex, revealing hydrogen bonds with residues like GLN169. The simulations showed an average delta RMSD of 0.2702 Å, indicating the complex's stability. Overall, this research highlights the potential of Papuan Red Fruit as a natural treatment for COVID-19, opening the door for further studies in drug development.
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 Agus Dwi Ananto, Agus Anita Dwi Puspitasari Aulia, Zarah Aziz, Hafiz Aji Edy Cahyono Endang Astuti Eti Nurwening Sholikhah Faris Hermawan, Faris Fatimi, Hana Anisa Fatmasari, Nela Fitria, Anggit Harizal Harizal Jeffry Julianus Jumina Jumina Kasta Gurning Kuamit, Thanawit Kultsum, Jihan Alfiyah Kurniawan, Yehezkiel Steven Lathifah Puji Hastuti M. Muchalal Marlina, Lala Adetia Mudasir, Mulya, Fadjar Nursofia, Baiq Ike Prasetyo, Niko Priastomo, Yoga Priyangga, Krisfian Tata Aneka Pulung, Maria Ludya Putra, Nicky Rahmana Rahmawari, Frika Triono, Sugeng Triyono Triyono Wibowo, Susalit Setya Winarto Haryadi Yari Mukti Wibowo Yogaswara, Radite Yudha, Ervan