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Harno Dwi Pranowo

Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Sekip Utara, Yogyakarta 55281, Indonesia

Author-ID : 3960363

Chemical Engineering, Chemistry & Bioengineering Chemistry

Published : 8 Documents Claim Missing Document

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Articles

QMCF-MD Simulation and NBO Analysis of K(I) Ion in Liquid Ammonia Yuniawan Hidayat; Ria Armunanto; Harno Dwi Pranowo
Indonesian Journal of Chemistry Vol 18, No 2 (2018)
Publisher : Universitas Gadjah Mada

Ab initio of Quantum Mechanics Charge Field Molecular Dynamic (QMCF-MD) of K(I) ion in liquid ammonia has been studied. A Hartree-Fock level of theory was coupled with LANL2DZ ECP basis set for K(I) ion and DZP (Dunning) for ammonia. Two regions as first and second solvation shell were observed. In the first solvation shell at distance 3.7 (Å), K(I) ion was coordinated by four to eight ammonia molecules dominated by K(NH3)6+ species. Second shell of solvation was ranging between 3.7 Å to 7.3 Å. Within simulation time of 20 ps, the frequent exchange processes of ligands indicating for a very labile solvation structure. Four mechanism types of ligand exchange between first and second solvation shell were observed. Mean residence time of ligand is less than 2 ps confirming weak in ion-ligand interaction. Evaluation of K(NH3)6+ using natural bond orbital analysis shows that the Wiberg bond Index is less than 0.05 indicating weak electrostatic interaction of K-N.

Hydrogen Bond Stability of Quinazoline Derivatives Compounds in Complex against EGFR using Molecular Dynamics Simulation Herlina Rasyid; Bambang Purwono; Thomas S Hofer; Harno Dwi Pranowo
Indonesian Journal of Chemistry Vol 19, No 2 (2019)
Publisher : Universitas Gadjah Mada

Lung cancer was a second common cancer case due to the high cigarette smoking activity both in men and women. One of protein receptor which plays an important role in the growth of the tumor is Epidermal Growth Factor Receptor (EGFR). EGFR protein is the most frequent protein mutation in cancer and promising target to inhibit the cancer growth. In this work, the stability of the hydrogen bond as the main interaction in the inhibition mechanism of cancer will be evaluated using molecular dynamics simulation. There were two compounds (A1 and A2) as new potential inhibitors that were complexed against the EGFR protein. The dynamic properties of each complexed were compared with respect to erlotinib against EGFR. The result revealed that both compounds had an interaction in the main catalytic area of protein receptor which is at methionine residue. Inhibitor A1 showed additional interactions during simulation time but the interactions tend to be weak. Inhibitor A2 displayed a more stable interaction. Following dynamics simulation, binding free energy calculation was performed by two scoring techniques MM/GB(PB)SA method and gave a good correlation with the stability of the complex. Furthermore, potential inhibitor A2 had a lower binding free energy as a direct consequence of the stability of hydrogen bond interaction.

Docking of New Designed Compounds Derived from 1,6-Dihydro-1,3,5-triazine-2,4-diamine Toward Quadruple Mutant Plasmodium Dihydrofolate Reductase Imam Siswanto; Harno Dwi Pranowo; Mudasir Mudasir
Indonesian Journal of Chemistry Vol 19, No 3 (2019)
Publisher : Universitas Gadjah Mada

Resistance to the traditional antifolates is now widespread in Plasmodium falciparum and Plasmodium vivax. To find the interaction model of some compounds derived from 1,6-dihydro-1,3,5-triazine-2,4-diamine, molecular docking technique was carried out using these compounds ligand and pDHFR as the receptor. Complex ligand and the receptor from Protein Data Bank (PDB ID 1J3K) were chosen as an interaction model between a ligand and its receptor. Each compound was optimized using ab initio methods with 6-311G basis set. Partial charges of ligand were added using AM1-BCC methods. Each ligand was docked to the receptor utilizing Dock6 software. Theoretical prediction based on the binding energy between these compounds as the ligand with pDHFR as receptor resulted in 1 compound, namely 6,6-dimethyl-1-[3-(2-chloro-4,5-dibromophenoxy)propoxy]-1,6-dihydro-1,3,5-triazine-2,4-diamine possessing binding affinity better than that of WR99210 which was known to have good antimalarial activity.

Synthesis of Pyridine Derivative-based Chemosensor for Formaldehyde Detection Nurul Hidayah; Bambang Purwono; Beta Achromi Nurohmah; Harno Dwi Pranowo
Indonesian Journal of Chemistry Vol 19, No 4 (2019)
Publisher : Universitas Gadjah Mada

Compound of 3,3'-(4-(2-amino-4,5-dimethoxyphenyl)pyridine-2,6-diyl)dianiline (CHP) has been synthesized via three-step synthetic procedure from veratraldehyde as starting material and 4-(4,5-dimethoxy-2-nitrophenyl)-2,6-bis(3-nitrophenyl)pyridine (CHP-1) as an intermediate compound. The CHP-1 was reduced using hydrazine hydrate catalyzed by 10% Pd/C to the final target of CHP. The spectroscopic study revealed that CHP in acetonitrile could detect formaldehyde through fluorescence enhancement and showed color change from yellow to blue under the 365 nm portable ultraviolet lamp as a response. Based on the fluorescence spectra, the emission wavelength of CHP in acetonitrile was shifted from 526 to 480 nm after addition of formaldehyde. Limit detection (LOD), selectivity, sensitivity, and computational study geometry of CHP as a chemosensor for formaldehyde has also been investigated. CHP could also be applied as a test paper for the detection of formaldehyde qualitatively.

Stability, Hydrogen Bond Occupancy Analysis and Binding Free Energy Calculation from Flavonol Docked in DAPK1 Active Site Using Molecular Dynamic Simulation Approaches Adi Tiara Zikri; Harno Dwi Pranowo; Winarto Haryadi
Indonesian Journal of Chemistry Vol 21, No 2 (2021)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.56087

Stability and hydrogen bond occupancy analysis of flavonol derivative docked in DAPK1 have been carried out using molecular dynamics simulation approach. Six flavonol derivatives were docked in DAPK1 as protein target, then continued with molecular dynamics simulation. NVT and NPT ensembles were used to equilibrate the system, followed by 20 ns sampling time for each system. Structural stability and hydrogen bond occupancy analyses were carried out at the NVT ensemble, while free binding energy analysis was done at NPT ensemble. From all compounds used in this work, compound B (5,7-dihydroxy-2-(4-hydroxyphenyl)-6-methoxy-4H-chromen-4-one) has a similar interaction with reference ligands (quercetin, kaempferol, and fisetin), and the most stable complex system has the maximum RMSD around 2 Å. Compound C complex has -48.06 kJ/mol binding free energy score, and it was slightly different from quercetin, kaempferol, and fisetin complexes. Even though complex C has similar binding free energy with the reference compound, complex B shows more stable interactions due to their hydrogen bond and occupancy.

Design of New Quinazoline Derivative as EGFR (Epidermal Growth Factor Receptor) Inhibitor through Molecular Docking and Dynamics Simulation Herlina Rasyid; Bambang Purwono; Harno Dwi Pranowo
Indonesian Journal of Chemistry Vol 21, No 1 (2021)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.57012

Erlotinib, Afatinib, and WZ4002 are quinazoline derivative compounds and classified as first, second, and third-generation EGFR inhibitor. All inhibitors have been given directly to cancer patients for many years but find some resistance. These three compounds are candidates as the lead compound in designing a new inhibitor. This work aims to design a new potential quinazoline derivative as an EGFR inhibitor focused on the molecular docking result of the lead compound. The research method was started in building a pharmacophore model of the lead compound then used to design a new potential inhibitor by employing the AutoDock 4.2 program. Molecular dynamics simulation evaluates the interaction of all complexes using the Amber15 program. There are three new potential compounds (A1, B1, and C1) whose hydrogen bond interaction in the main catalytic area (Met769 residue). The Molecular Mechanics Generalized Born Surface Area (MM-GBSA) binding energy calculation shows that B1 and C1 compounds have lower binding energies than erlotinib as a positive control, which indicates that B1 and C1 are potential as EGFR inhibitor.

Synthesis of Calix[4]resorcinarene Derivatives as Antimalarial Agents through Heme Polymerization Inhibition Assay Rizky Riyami Putri; Harno Dwi Pranowo; Yehezkiel Steven Kurniawan; Hana Anisa Fatimi; Jumina Jumina
Indonesian Journal of Chemistry Vol 23, No 4 (2023)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.81452

Malaria is an endemic disease in tropical countries, including Indonesia, with a high annual mortality rate. Because of that, serious attention shall be given to find new antimalarial agents that are highly active for medical treatment. In this work, we designed and synthesized three calix[4]resorcinarene derivatives and evaluated them as antimalarial agents through in vitro heme polymerization inhibitory assay. The calix[4]resorcinarenes were prepared from resorcinol and corresponding aldehyde derivatives in ethanol media through a cyclo-condensation reaction. The calix[4]resorcinarene products were obtained in 31.1–85.1% yield. The synthesized compounds were subjected to structure elucidation using spectroscopy techniques. The antimalarial activity of calix[4]resorcinarene with aromatic substituent (IC50 = 0.198 mg/mL) was higher than the aliphatic ones (IC50 = 0.282–0.814 mg/mL). It was found that all calix[4]resorcinarenes in this work exhibited stronger antimalarial activity than chloroquine diphosphate as the positive control (IC50 = 1.157 mg/mL). The calix[4]resorcinarenes could interact with hydrogen bonding, thus inhibiting the heme polymerization process. These findings demonstrate that calix[4]resorcinarene derivatives are potential antimalarial agents to be developed for effective medical treatment in the near future.

Energy Efficiency of the Carbonate Hydroxyapatite Nanoparticle Synthesis Using Microwave Heating Treatment and Its Effect on Material Characteristics Saifuddin Aziz; Harno Dwi Pranowo; Ika Dewi Ana; Yusril Yusuf
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.88155

This work aimed to study the energy efficiency of the synthesis process of carbonated hydroxyapatite (CHA) nanoparticles using microwave heating treatment and its effect on material characteristics. Microwaves can provide heat quickly, so it is expected to increase the efficiency of CHA synthesis through the heat provided. The CHA nanoparticles were synthesized using precipitation and heated using a microwave oven. The unheated and hydrothermal-heated precipitation methods were also conducted for comparison purposes. The microwave-heated precipitations were done at 270 W for 0.05, 0.10, and 0.15 h, while the hydrothermal-heated precipitations were done at 100 °C for 1, 2, and 3 h. The CHA materials were characterized using an infrared spectrophotometer, X-ray diffractometer, and electron microscope. The X-ray diffractogram and infrared spectra confirmed that the synthesized materials had a hydroxyapatite crystal phase with a CO32− functional group in their spectra. Microscopic images revealed that the materials were nanometer-sized grain aggregates. The heat treatment and duration increased the material characteristics, i.e., crystallinity, crystallite, and grain size. The CHA with microwave heat treatment had the highest crystallinity and crystallite size. The electrical energy calculation revealed microwave heating had better energy efficiency than hydrothermal heating.

Co-Authors Adi Tiara Zikri Bambang Purwono Beta Achromi Nurohmah Hana Anisa Fatimi Herlina Rasyid Ika Dewi Ana Imam Siswanto Jumina Jumina Mudasir Mudasir Nurul Hidayah Ria Armunanto Rizky Riyami Putri Saifuddin Aziz Thomas S Hofer Winarto Haryadi Yehezkiel Steven Kurniawan Yuniawan Hidayat Yusril Yusuf

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