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CONSTRUCTION AND OPTIMIZATION OF STRUCTURE-BASED VIRTUAL SCREENING PROTOCOLS TO IDENTIFY CYCLOOXYGENASE-1 INHIBITORS USING OPEN BABEL, SPORES AND PLANTS Enade Perdana Istyastono
Indonesian Journal of Chemistry Vol 12, No 2 (2012)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (259.913 KB) | DOI: 10.22146/ijc.21354

Abstract

Structure-Based Virtual Screening (SBVS) protocols to identify cyclooxygenase-1 (COX-1) inhibitors have been constructed and optimized based on their Root Mean Square Deviation (RMSD) values of the docked pose and the crystal structure pose of the reference ligand. Employing a COX-1 structure obtained from the Protein Data Bank (pdb) with code 2OYE as the reference protein and PLANTS1.2 as the molecular docking simulation program, the SBVS protocols were mainly built. The preparation steps involved SPORES and Open Babel, while the results analysis involved PyMOL to calculate the RMSD and R computational statistics software to perform the statistics calculations. The results show that these construction and optimization processes could provide an SBVS protocol to identify COX-1 inhibitors that is accurately able to redock the reference ligand with the RMSD value of 0.633 Å.
DOCKING OF 1-PHENYLSULFONAMIDE-3-TRIFLUOROMETHYL-5-PARABROMOPHENYL-PYRAZOLE TO CYCLOOXYGENASE-2 USING PLANTS Stefanus Layli Prasojo; Fajar Agung Dwi Hartanto; Nunung Yuniarti; Zullies Ikawati; Enade Perdana Istyastono
Indonesian Journal of Chemistry Vol 10, No 3 (2010)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (166.937 KB) | DOI: 10.22146/ijc.21441

Abstract

The docking protocols to virtually screen selective cyclooxygenase-2 (COX-2) ligands using PLANTS docking software were developed and validated. The crystal structure of 1-phenylsulfonamide-3-trifluoromethyl-5-parabromophenyl-pyrazole (S58) binds to cyclooxygenase-2 (COX-2) was used as the reference structure. The developed protocols could predict the binding pose of S58 to COX-2 accurately (RMSD is 1.2 Ǻ).
THE APPLICABILITY OF THE CRYSTAL STRUCTURE OF TERMOTOGA MARITIMA 4-α-GLUCANOTRANSFERASE AS THE TEMPLATE FOR SULOCHRIN AS α-GLUCOSIDASE INHIBITORS Rizna Triana Dewi; Yulia Anita; Enade Perdana Istyastono; Akhmad Darmawan; Muhamad Hanafi
Indonesian Journal of Chemistry Vol 9, No 3 (2009)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (235.731 KB) | DOI: 10.22146/ijc.21520

Abstract

Interaction of sulochrin to active site of glucosidase enzyme of Termotoga maritime has been studied by employing docking method using Molecular Operating Environment (MOE), in comparison with those are reports of established inhibitor α-glucosidase such as acarbose, miglitol and voglibose, and salicinol, as reference compounds. The crystal structure T. maritima α-glucanotransferase (PDB code: 1LWJ) can be employed to serve as the template in the virtual screening of S. cerevisiae α-glucosidase. The comparison between the binding pocket residues of Thermotoga maritima α-glucanotransferase and Saccharomyces cerevisiae α-glucosidase show a high sequence identity and similarity. The result showed that sulochrin could be located in the binding pocket and formed some interactions with the binding residues. The ligands showed proper predicted binding energy (-6.74 - -4.13 kcal/mol) and predicted Ki values (0.011 - 0.939 mM). Sulochrin has a possibility to serve as a lead compound in the development of new α-glucosidase inhibitor.
DOCKING STUDIES OF CURCUMIN AS A POTENTIAL LEAD COMPOUND TO DEVELOP NOVEL DIPEPTYDYL PEPTIDASE-4 INHIBITORS Enade Perdana Istyastono
Indonesian Journal of Chemistry Vol 9, No 1 (2009)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (962.362 KB) | DOI: 10.22146/ijc.21574

Abstract

Interaction of curcumin to dipeptydyl peptidase-4 (DPP-4) has been studied by employing docking method using Molecular Operating Environment (MOE) and AutoDock as the docking software applications. Although MOE can sample more conformational spaces that represent the original interaction poses than AutoDock, both softwares serve as valid and acceptable docking applications to study the interactions of small compound to DPP-4. The calculated free energy of binding (DGbinding)results from MOE and AutoDock shows that curcumin is needed to be optimized to reach similar or better DGbinding compare to the reference compound. Curcumin can be considered as a good lead compound in the development of new DPP-4 inhibitor. The results of these studies can serve as an initial effort of the further study.
ACTIVITY OF PROPYL p-BENZOYLOXYBENZOATE AS A GLUTATHIONE S-TRANSFERASE(S) INHIBITOR: THE COMPARISON BETWEEN COMPUTATIONAL CHEMISTRY APPROACH AND EMPIRICAL OBSERVATION Enade Perdana Istyastono; Agnes Nora Iska Harnita; Sudibyo Martono
Indonesian Journal of Chemistry Vol 6, No 1 (2006)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (250.6 KB) | DOI: 10.22146/ijc.21781

Abstract

The activity of propyl p-benzoyloxybenzoate as a glutathione S-transferase(s) (GSTs) inhibitor has been examined through computational chemistry based theoretical approach and laboratory experiment. This research was related to the nature of GSTs as multifunctional enzymes, which play an important role in the detoxification of electrophilic compounds, the process of inflammation and the effectivities of anticancer compounds. Quantitative Structure-Activity Relationship (QSAR) study, which was established on curcumin and its derivatives using computational chemistry approach, was used to examine the theoretical activity of p-benzoyloxybenzoate as a GSTs inhibitor. Empirical observation on GSTs inhibition was examined using formation reaction model of GS-CNB conjugate through conjugation of 1-chloro-2,4-dinitrobenzene (CDNB) and glutathione (GSH) with GSTs (prepared from rat's liver) as catalysts. The result showed that the difference between the activities of propyl p-benzoyloxybenzoate as a GSTs inhibitor obtained from the computational chemistry approach and the empirical observation were not statistically significant at 95% level of confidence.
SYNTHESIS AND PHYSICOCHEMISTRY PROPERTIES PREDICTION OF A NEW POTENTIAL ANTI-INFLAMMATORY AGENT: DIACETYL PENTAGAMAVUNON-1 Supardjan A. Margono; Pudjono Pudjono; St. Layli Prasojo; Jeffry Julianus; Enade Perdana Istyastono
Indonesian Journal of Chemistry Vol 6, No 1 (2006)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (252.964 KB) | DOI: 10.22146/ijc.21782

Abstract

Synthesis and physicochemistry properties prediction of a potential anti-inflammatory agent, diacetyl pentagamavunon-1 (diacetyl PGV-1), has been done. The synthesis was using pentagamavunon-1 (PGV-1) (2,87x10-3 mole) and anhydride acetic acid (26x10-3 mole; 37x10-3 mole; 49x10-3 mole) as starting materials and NaOH ethanolic as a catalyst. The AM1 semiempirical quantum-chemical calculations using the computational chemistry approach was used to predict and compare the physicochemisty properties of diacetyl PGV-1 to PGV-1. Odorless, light-yellow powder has been obtained. The powder was 0.8512-0.9602 g (2.02 x10-3 - 2.22x10-3 mole; 70.4-77.4%) and the purity of the powder was 92.4%. The purity of the product has been examined by high performance liquid chromatography (HPLC), while the structure elucidation has been done using IR (Infra Red), 1H-NMR (Nuclear Magnetic Resonance) and MS (Mass Spectroscopy). The physicochemisty properties prediction showed that diacetyl PGV-1 was more hydrophobic than PGV-1.
SYNTHESIS NEW POTENTIAL ANTI-INFLAMMATORY AGENT SODIUM SALT OF PENTAGAMAVUNON-0 Enade Perdana Istyastono; Rr. Sri Untari Siwi S.M.P; Andreas Asdi Utama; Supardjan A.M
Indonesian Journal of Chemistry Vol 4, No 3 (2004)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (230.281 KB) | DOI: 10.22146/ijc.21850

Abstract

Inflammation is the response of living tissues to injury. The process affects physiological changes such as erythema, edema, asthma and fever. Non-steroid Anti-inflammatory Drugs (NSAIDs) have been developed since they could inhibit inflammation process because of its ability to inhibit biosynthesis of prostaglandin, one of inflammation mediators, through inhibition of cyclooxigenase (COX) enzymes. Molecules, which have been reported having anti-inflammatory activity, for example, are curcumin, some curcumin derivatives and curcumin analogues. One of curcumin analogues that has been  developed is pentagamavunon-0 (PGV-0) whose IUPAC name is 2,5-bis(4'-hidroxy-3'-methoxy-benzylidene)cyclo-pentanone. But PGV-0, which is like curcumin, practically insoluble in water, so it causes problems in the development. The aim of this research is to synthesize a derivative of PGV-0, a natrium salt of PGV-0 (natrium pentagamavunonate-0/Na-pentagamavunonate-0), which is hoped to have a better anti-inflammatory activity and solubility in water than PGV-0. PGV-0 was synthesized by reacting vanillin and cyclopentanone catalized by acid. Na-pentagamavunonate-0 was synthesized with PGV-0 as a starting material using an appropriate method. This research was able to synthesize new compound that was estimated as a natrium salt of PGV-0 (natrium pentagamavunonate-0/Na-pentagamavunonate-0).
QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP ANALYSIS OF CURCUMIN AND ITS DERIVATIVES AS GST INHIBITORS BASED ON COMPUTATIONAL CHEMISTRY CALCULATION Enade Perdana Istyastono; Sudibyo Martono; Harno Dwi Pranowo; Iqmal Tahir
Indonesian Journal of Chemistry Vol 3, No 3 (2003)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (66.597 KB) | DOI: 10.22146/ijc.21886

Abstract

The Quantitative Structure-Activity Relationship (QSAR) study was established on curcumin and its derivatives as glutathione S-transferase(s) (GSTs) inhibitors using atomic net charges as the descriptors. The charges were resulted by semiempirical AM1 and PM3 quantum-chemical calculations using computational chemistry approach. The inhibition activity was expressed as the concentration that gave 50% inhibition of GSTs activity (IC50). The selection of the best QSAR equation models was determined by multiple linear regression analysis. This research was related to the nature of GSTs as multifunctional enzymes, which play an important role in the detoxification of electrophilic compounds, the process of inflammation and the effectivity of anticancer compounds.The result showed that AM1 semiempirical method gave better descriptor for the construction of QSAR equation model than PM3 did. The best QSAR equation model was described by :log 1/IC50 = -2,238 - 17,326 qC2' + 1,876 qC4' + 9,200 qC6'The equation was significant at 95% level with statistical parameters : n = 10, m = 3, r­ = 0,839, SE = 0,254, F = 4,764, F/Ftable = 1,001.
Binary Quantitative Structure-Activity Relationship Analysis to Increase the Predictive Ability of Structure-Based Virtual Screening Campaigns Targeting Cyclooxygenase-2 Enade Perdana Istyastono
Indonesian Journal of Chemistry Vol 17, No 2 (2017)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (286.833 KB) | DOI: 10.22146/ijc.24172

Abstract

Structure-Based Virtual Screening (SBVS) campaigns employing Protein-Ligand Interaction Fingerprints (PLIF) identification have served as a powerful strategy in fragments and ligands identification, both retro- and prospectively. Most of the SBVS campaigns employed PLIF by comparing them to a reference PLIF to calculate the Tanimoto-coefficient. Since the approach was reference dependent, it could lead to a very different discovery path if a different reference was used. In this article, references independent approach, i.e. decision trees construction using docking score and PLIF as the descriptors to increase the predictive ability of the SBVS campaigns in the identification of ligands for cyclooxygenase-2 is presented. The results showed that the binary Quantitative-Structure Activity Relationship (QSAR) analysis could significantly increase the predictive ability of the SBVS campaign. Moreover, the selected decision tree could also pinpoint the molecular determinants of the ligands binding to cyclooxygenase-2.
Analytical Method Validation and Determination of Free Drug Content of 4-n-Butylresorcinol in Complex Lipid Nanoparticles Using RP-HPLC Method Rini Dwiastuti; Marchaban Marchaban; Enade Perdana Istyastono; Florentinus Dika Octa Riswanto
Indonesian Journal of Chemistry Vol 18, No 3 (2018)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (333.512 KB) | DOI: 10.22146/ijc.28919

Abstract

Lipid nanoparticles, one of nanoparticle technology results has been developed both as a drug delivery system and as a research object. Complex lipid nanoparticle, in the drug delivery system development, has an advantage due to its less toxicity. It is important to develop a validated analytical method to determine the drug content in the system of nanoparticle lipid. This research aimed to develop a valid RP-HPLC method to determine free drug content of 4-n-butylresorcinol in the liposome matrix followed by the determination of the encapsulation efficiency (EE%). A system of the RP-HPLC method has been developed using a column of C18 and methanol-redistilled water-glacial acetic acid 79:20:1 (v/v) as the mobile phase with pH maintained at 2.1–2.6. This method was validated in the parameters of selectivity, sensitivity, linearity, accuracy, and precision. During 30 days of storage, the complex lipid nanoparticle system showed the increase in the EE% value during storage time.
Co-Authors ., Jumina Abdul Mutholib Aditya Asyhar Agnes Mutiara Kurniawan Agnes Nora Iska Harnita Agnes Nora Iska Harnita Agung Endro Nugroho Agustina Setiawati Akhmad Darmawan Andreas Asdi Utama ARGUN WIDARSA ARIEF NURROCHMAD As'ari Nawawi Berlina, Violita Yessi Bonifacius Ivan Wiranata Bonifacius Ivan Wiranata Bonifacius Ivan Wiranata Chrisanti, Marcella Widya Chrisologus Ivan Prasetyo David Chandra Putra Dewi Setyaningsih Dina Christin Ayuning Putri Dita Maria Virginia Eko Yuliyanto Eko Yuliyanto, Eko Esti Mumpuni Evy Fenny Veronica Fajar Agung Dwi Hartanto Fajar Ira Juwita Farach Khanifah Felicia Felicia Felicia Fraulein Setiawan Fitria Fatichatul Hidayah Fitria Fatichatul Hidayah Fitria Fatichatul Hidayah Florentinus D.O. Riswanto Florentinus Dika Octa Riswanto Florentinus Dika Octa Riswanto Florentinus Dika Octa Riswanto Florentinus Dika Octa Riswanto Fransiscus Deddy Riandono Fransiska Kurniawan Gani, Michael Gatot Nugroho Susanto Gerry Nugraha Glory Ivana Ardine Harno Dwi Pranowo Harno Dwi Pranowo Harno Dwi Pranowo Herluin Sekar Krisantia I Gusti Ayu Intan Puspita Dewi Ignasius Widya Parahita Putranto Ignatius Yulius Kristio Budiasmoro Iqmal Tahir Iwan J. P. de Esch Jeffry Julianus Julyus Jason Mark Jutti Levita Liana Roh Widiyani Liliana Liliana Lukman Hakim Marchaban Marchaban Marchaban Marchaban Marchaban Marchaban Maria Ludya Pulung Maywan Hariono Maywan Hariono Michael Raharja Gani Michael Raharja Gani Michael Raharja Gani Michael Resta Surya Yanuar Muhamad Hanafi MUHAMMAD RADIFAR Muhammad Radifar Muhammad Radifar Muhammad Radifar Natalia Kristina Nugraha, Gerry Nunung Priyatni Nunung Yuniarti Nunung Yuniarti Nunung Yuniarti Nunung Yuniarti Nunung Yuniarti Nunung Yuniarti Nunung Yuniarti Octa Riswanto , Florentinus Dika OISAN OISAN Oka, Mitsue Perdana Adhi Nugroho Pramono, Zita Dhirani Primana, Mala Hikmawan Pudjono Pudjono Radite Yogaswara Rekso, Putri Ayu Dharmo reza eka putra Riandono, Fransiscus Deddy Rini Dwiastuti Rizna Triana Dewi Roy Gunawan Wicaksono Rr. Sri Untari Siwi S.M.P Sardjiman Sardjiman Slamet Ibrahim - Sri Hartati Yuliani Sri Noegrohati Sri Noegrohati St. Layli Prasojo Stefanus Layli Prasojo Stephanus Satria Wira Waskitha Sudibyo Martono Sudibyo Martono Sudibyo Martono Sudibyo Martono Sudibyo Martono Supardjan . Supardjan . Supardjan A. Margono Supardjan A. Margono Supardjan A.M Supardjan A.M. Supardjan AM Tasia Amelia Titien Siwi Hartayu Umar Anggara Jenie Vivitri Dewi Prasasty Waskitha, Stephanus Satria Wira Widayati, Aris Windah, Axl Laurens Lukas Wira Waskitha, Stephanus Satria Wiranata, Bonifacius Ivan YANTI SUSILAWATI Yohanes Eko Adi Prasetyanto Yosef Wijoyo Yosef Wijoyo Yosef Wijoyo, Yosef Yosi Bayu Murti Yulia Anita YUMI RAHMADANI Yuniarti, Nunung Zullies Ikawati Zullies Ikawati