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Hasil In Silico Senyawa Z12501572, Z00321025, SCB5631028 dan SCB13970547 dibandingkan Turunan Zerumbon terhadap Human Liver Glycogen Phosphorylase (1l5Q) sebagai Antidiabetes Fitri Kusvila Aziz; Cantika Nukitasari; Fauziyah Ardli Oktavianingrum; Lita Windy Aryati; Broto Santoso
Jurnal Kimia Valensi Jurnal Kimia VALENSI Volume 2, No. 2, November 2016
Publisher : Syarif Hidayatullah State Islamic University

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (843.026 KB) | DOI: 10.15408/jkv.v2i2.4170

Abstract

Abstrak Human Liver Glycogen Phosphorylase (HLGP), suatu katalis glikogen yang mengontrol pelepasan glukosa-1-fosfat glikogen dari hati. Enzim ini mempunyai peran sentral dalam luaran glukosa hati sehingga menjadi target obat antidiabetik. Kajian docking dilakukan pada komputer dengan prosesor Intel Pentium, RAM 1 GB dan Windows 7. Ligan yang digunakan adalah senyawa obat (Z12501572, Z00321025, SCB5631028 dan SCB13970547), dataset pembanding aktif glycogen phosphorylase outer dimer site (PYGL-out) dan decoysdari www.dekois.com dan turunan zerumbon. Protein dipisahkan dari ligan nativ dan semua ligan beserta protein dikonversi menggunakan PyRx. Visualisasi interaksi ligan-protein dihasilkan dengan program Protein-Ligand Interaction Profiler (PLIP) dan PyMOL. Senyawa ZER11 memiliki binding energy terbaik, yaitu -7.11 kkal/mol (untuk metode LGA dan GA) dan -4.08 kkal/mol untuk metode SA. Nilai binding energy tersebut lebih rendah dari pada nilai untuk ligan native dan satu dari keempat senyawa obat, terlebih jika dibandingkan dengan bindingaffinity dari dataset dan decoys. Interaksi ligan-protein pada ketiga metode tersebut ditemukan sangat bervariasi. Hal berbeda terjadi untuk metode Vina, bindingenergy ZER11 (-9.9 kkal/mol) lebih baik dibandingkan dengan ligan native dan keempat senyawa obat. Senyawa ZER11 memiliki residu interaksi yang sama dengan ligan native pada TRP67 dan LYS191 untuk metode Vina. Kata kunci: PDBID-1L5Q, AutoDock, docking molekuler, vina, antidiabetes   Abstract Human Liver Glycogen Phosphorylase (HLGP) can catalyze glycogen and control the release of glucose-1-phosphate of glycogen from the liver. This enzyme has a central role in output rule of liver glucose as it can be used as an antidiabetic drug targets. Docking studies were carried out on PC with Intel Pentium, 1 GB RAM, in environment of Windows 7. Ligands used are drug compounds (Z12501572, Z00321025, SCB5631028 and SCB13970547), the active dataset comparator wasglycogenphosphorylase outer dimer site (PYGL-out) and decoys from www.dekois.com andzerumbonederivates. Protein was separated from its native ligand and all ligands including the protein were converted to pdbqt using PyRx. The interaction of protein-ligand was visualized using software of PLIP and PyMOL. Compound of ZER11 had the best binding energy were -7.11 kcal/mol (LGA and GA) and -4.08 kcal/mol (SA). The binding energy value was lower than the ligand native and one of the four drug compounds, especially compared with the binding affinity of dataset and decoys. Vice versa, for Vina method, the value of ligand binding protein for ZER11 (-9.9 kcal/mol) was better than the ligand native and all of the fourth drugcompounds. Vina result showed that ZER11 had the same residual interaction as the ligand native, which are TRP67 and LYS191. Keyword: PDBID-1L5Q, AutoDock, molecular docking, vina, antidiabetic DOI: http://dx.doi.org/10.15408/jkv.v0i0.4170
PENGARUH pH PADA SINTESIS 4-[N-(4-hidroksifenil)karboksimidoil]-2-metoksifenol MELALUI REAKSI ADISI-ELIMINASI M. Kuswandi; Nur Dwi Choirulisa; Broto Santoso
Chimica et Natura Acta Vol 4, No 1 (2016)
Publisher : Departemen Kimia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (464.781 KB) | DOI: 10.24198/cna.v4.n1.10446

Abstract

Modifikasi molekul obat telah banyak dilakukan dan ditujukan untuk meningkatkan aktivitas atau menurunkan efek sampingnya. Penelitian in silico 4-[N-(4-hidroksifenil)karboksimidoil]-2-metoksifenol diperoleh nilai aktivitas yang lebih baik dibandingkan parasetamol sehingga diduga memiliki potensi analgetik yang lebih baik. Penelitian ini bertujuan untuk mendapatkan senyawa 4-[N-(4-hidroksifenil)karboksimidoil]-2-metoksifenol melalui reaksi p-aminofenol dengan vanilin dengan variasi pH awal. Kondisi pH terpilih ditandai dengan jumlah rendemen maksimal. Percobaan telah dilakukan dengan mereaksikan p-aminofenol dan vanilin dengan penambahan HCl 2 N untuk memperoleh kondisi awal pH 2, 3 dan 4 di atas penangas air dengan suhu 100°C terkendali selama 5 menit. Produk yang terbentuk didinginkan untuk mendapatkan kristal berwarna kuning. Hasil sintesis telah dilakukan uji kromatografi lapis tipis (KLT), titik lebur, kelarutan dan gugus fungsional dengan menggunakan Fourier transform infrared spectroscopy (FTIR). Rendemen dan nilai Rf KLT produk pada pH 2, 3, 4 secara berurutan adalah 71% (0,50), 14% (0,42), dan 49% (0,56) dengan eluen kloroform : metanol (9:1). Kondisi pH terbaik untuk pembentukan produk adalah pH 2 dan produk larut dalam metanol. Spektrum FTIR produk memberikan informasi terbentuknya gugus imina (-C=N-) yang ditunjukkan adanya puncak pada bilangan gelombang 1651 cm-1. Produk perlu dilakukan pemurnian dan uji NMR untuk meyakinkan struktur kimia produk.
DOCKING MOLEKULAR POTENSI ANTI DIABETES MELITUS TIPE 2 TURUNAN ZERUMBON SEBAGAI INHIBITOR ALDOSA REDUKTASE DENGAN AUTODOCK-VINA Karisma Enggar Saputri; Nurul Fakhmi; Erwinda Kusumaningtyas; Dedy Priyatama; Broto Santoso
Chimica et Natura Acta Vol 4, No 1 (2016)
Publisher : Departemen Kimia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (688.748 KB) | DOI: 10.24198/cna.v4.n1.10443

Abstract

Obat anti-diabetes yang telah dipasarkan seperti Epalrestat, Ponalrestat, Pioglitazone dan Sitagliptin serta turunan zerumbon pada penelitian sebelumnya memiliki aktivitas anti diabetes, perlu diketahui bagaimana mekanisme interaksinya terhadap protein target aldosa reduktase (2HV5). Protein target aldosa reduktase dipreparasi menggunakan UCSF Chimera. Penelitian ini telah dilakukan dengan menggunakan ligan uji termasuk empat senyawa tersebut, yaitu ligan dataset (50 senyawa) dan decoys dari dude.docking.org, dan 25 senyawa turunan zerumbon. Semua ligan dilakukan docking molekular menggunakan Program PyRx  dengan program Vina dan AutoDock (Lamarckian Genetic Algorithm (LGA), Genetic Algorithm (GA) dan Monte Carlo Simulated Annealing (SA)). Hasil yang diperoleh berupa nilai binding affinity (kkal/mol) ligan terhadap protein. Program PyMOL dan PLIP (Protein Ligand Interaction Profiler) digunakan untuk memvisualisasikan konformasi 3D molekul dan interaksi ligan-protein. Perangkat keras yang digunakan komputer personal dengan spesifikasi prosesor Intel® Atom(™) CPUN2600 @ 1,60 GHz, RAM 2GB, Windows 7. Hasil docking didapatkan bahwa ZER (SA, -6,99 kkal/mol), ZER08 (vina, -10,9 kkal/mol) dan ZER11 (LGA, -11,26 kkal/mol dan GA, -11,17 kkal/mol) mempunyai nilai binding affinity lebih baik dibandingkan dengan keempat senyawa obat tetapi, nilai ini tidak lebih baik dibandingkan dengan ligan natif, dataset dan decoys. Hasil interaksi ligan-protein yang terjadi melibatkan residu PHE-122 dan VAL-47, dan hal ini ditemukan sama untuk ketiga senyawa turunan zerumbon tersebut dengan ligan natif. Ketiga turunan zerumbon ini dapat dilanjutkan uji aktivitas in vitro di laboratorium.
In Silico Study of Weight-selected Molecules of Sea Cucumber as Antimitotic through PyRx-Vina Approach Broto Santoso
Indonesian Journal of Pharmaceutical Science and Technology Suppl. 2, No. 2 (2019)
Publisher : Indonesian Journal of Pharmaceutical Science and Technology

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (854.894 KB) | DOI: 10.24198/ijpst.v1i2.20210

Abstract

Active ligands usually have low molecular weights (MW). However, paclitaxel, a natural anticancer, has high MW. Some compounds (MW = 750-1000 dalton) in Sea cucumber from TCMSP database have anticancer activity. The objective of study is to obtain docking profile of selected compounds compared to taxol as native. Three of human kinesin-8, were collected from the RCSB database and regenerated by adding hydrogen atoms and charge using the Dock Prep in Chimera. These proteins and selected compounds were prepared to fulfil PyRx's requirement. Molecular docking was performed based on mass center value and grid-box volume from previous studies and resulted vina-score (kcal/mol). Docking data and their 3D conformation were analyzed using PyMOL, PoseView, and PLIP. The native alignment results between docked and original conformation showed that their RMSD value is less than one and only one that has the same three-dimensional conformation. Holothurinoside D, desholothurin B, and 2,4-dehydroechinoside B have a binding affinity of -9.7, -9.4, and -9.3 kcal/mol, respectively. Their value is better or at least the same as the native (-9.3 kcal/mol). Hydrophobic interactions between proteins and ligands occurred at residue of F272, V23, and P360. These results confirm that the anticancer mechanism of these compounds may be through inhibition of kinesin-8. Key words: in silico, sea cucumber, antimitotic, PyRx-vina
PREDIKSI 3D-MOLEKULAR AKTIVITAS TURUNAN SENYAWA POLIHIDROKSI ZERUMBON TERHADAP GLIKOGEN SINTASE KINASE-3 BETA (GSK-3) MENGGUNAKAN DOCK6 Broto Santoso; Dedi Hanwar; Andi Suhendi
PROSIDING SEMINAR NASIONAL & INTERNASIONAL 2015: Prosiding Bidang MIPA dan Kesehatan The 2nd University Research Colloquium
Publisher : Universitas Muhammadiyah Semarang

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (559.645 KB)

Abstract

Insulin resistance causes 90% of type 2 diabetes mellitus (DM) cases and this is due to an increase in the activity of glycogen synthase kinase-3 (GSK-3). Dephosphorylation and activation of glycogen synthase prevent type 2 diabetes by inhibiting the work of GSK-3 beta isoform primarily. The study was done in unix (mac and linux) operating system with the sequence of steps were optimization of geometry of ligand, ligand and protein preparation, validation of docking methods, molecular docking and analysis, and 3D modeling of ligand-protein interactions. Optimization of target ligand geometry using Gaussian showed that molecular docking score increased 62.5% compared with geometry optimization using MarvinSpace. Polyhydroxy compound zerumbon derivats: ZER04, ZER05 and ZER06 potential to be tested further in the laboratory as an anti- type 2 diabetes both in vitro and in vivo. This is based on the ability of the compounds in term of molecular interactions that better than the native ligand of target protein 4PTE, 4AFJ, 3ZRK, 3GB2, 3DU8 and 1Q3W (60% of the total protein targets tested) as an inhibitor of glycogen synthase kinase- 3 types of beta (GSK-3b).Keywords: polyhydroxyzerumbone, glycogen synthase kinase-3 beta, docking molecular, DOCK6
ANALISIS KROMATOGRAFI LAPIS TIPIS (KLT) DAN AKTIVITAS PENANGKAPAN RADIKAL BEBAS (PRB) EKSTRAK ETANOL LEMPUYANG EMPRIT (Zingiber americans) HASIL MASERASI SEKALI DAN MASERASI BERULANG Susi Indah Lestari; Broto Santoso
Biomedika Vol 13, No 1 (2021): Biomedika Februari 2021
Publisher : Universitas Muhamadiyah Surakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23917/biomedika.v13i1.11439

Abstract

ABSTRAKMetode ekstraksi menjadi penting dan dapat mempengaruhi ekstrak yang diperoleh. Rendemen hasil metode maserasi berulang didapatkan lebih tinggi dibandingkan maserasi. Penelitian ini ditujukan untuk membandingkan hasil analisis kromatografi lapis tipis (KLT) dan aktivitas penangkapan radikal bebas (PRB) ekstrak etanol rimpang lempuyang emprit (Zingiber americans) hasil maserasi sekali dan maserasi berulang. Simplisia diekstraksi dengan pelarut etanol 96% (rasio 10:75) menggunakan metode maserasi dan maserasi berulang masing-masing sebanyak empat kali replikasi. Setiap ekstrak dilakukan analisis kromatografi lapis tipis silika gel GF254 menggunakan eluen heksana:etil asetat (9:1), dan dilanjutkan dengan uji penangkapan radikal bebas DPPH. Rendemen hasil maserasi dan maserasi berulang adalah 4,37% dan 6,83% (p 0,05) berturut-turut, sedangkan persen PRB-nya 21,63% dan 32,68% (p 0,05) secara berturut-turut. Hasil kromatogram menampakkan perbedaan intensitas bercak dan nilai Rf.  Bercak yang tidak terelusi menunjukkan kemampuan dalam menangkap radikal bebas, dimana sebagian bercak menunjukkan bahwa ekstrak mengandung golongan senyawa terpenoid, flavonoid, dan alkaloid, namun tidak fenolik. Kesimpulan penelitian ini bahwa maserasi dan masersi berulang memiliki aktivitas PRB yang tidak berbeda, dengan kandungan terpenoid, flavonoid, dan alkaloid yang lebih tinggi pada maserasi berulang.Kata Kunci: Lempuyang Emprit, Maserasi, Maserasi Berulang, Aktivitas Penangkapan Radikal Bebas, Kromatografi Lapis Tipis ABSTRACTExtraction method is important because has high impact to the final result of extract.  The repeated maceration yield (rMAC) is higher than maceration (MAC) method. The aim of the research was to compare the results of chromatogram profile and free radical scavenging activity of ethanol extracts of lempuyang emprit (Zingiber americans) between both of methods. Crude material was extracted using 96% ethanol (ratio 10:75) four times for each method. Extracts were analyzed using TLC plate of silica gel GF254 as stationary phase and hexane-ethyl acetate (9:1) as mobile phase. Their radical scavenging activity were done using DPPH method. The yield of maceration repeated maceration results was 4.37% and 21.63% (p 0.05), respectively, while the percentage of PRB was 6.83% and 32.68% (p 0.05), respectively. The chromatogram results showed the difference in spot intensity and the Rf value. The uneluted spots showed the activity of radical scavenging. The spots reveal that terpenoid, flavonoid, and alkaloid groups but not phenolic were found in both of extract. Further purification needed to be done to confirm the% PRB value that did not differ from the two extractsKeywords: Lempuyang Emprit, Maceration, Repeated Maceration, Radical Scavenging Activity, Thin Layer Chromatography
EXPLORING 3D MOLECULAR STUDIES OF DIKETOPIPERAZINE ANALOGUES ON Staphylococcus aureus DEHYDROSQUALENE SYNTHASE USING GLIDE-XP Broto Santoso
Pharmacon: Jurnal Farmasi Indonesia Vol 13, No 2 (2012)
Publisher : Universitas Muhammadiyah Surakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23917/pharmacon.v13i2.14

Abstract

There is a strong correlation between 3D molecular docking result with dehydrosqualene synthase protein and antibacterial activity against Staphylococcus aureus (S. aureus) of the pyrazoline analogues. The enzyme has been known as important protein for the synthesis of staphyloxanthin in S. aureus. Diketopiperazine analogues have similar structure to pyrazoline. Glide-XP, Schrodinger application that seeks for molecular docking screening between ligand and protein target is designed for speed, efficiency, and accuracy to conduct discovery efforts. The research report the three-dimension molecular studies diketopiperazine analogues for their antibacterial activity on dehydrosqualene synthase of S. aureus using Glide-XP. Analogues compound of diketopiperazine and curcumin has been calculated their geometry optimization using Gaussian-Density Functional Theory method. These 3D-optimized ligands along with reference ligands obtained from bindingDB database, MIMICs fingerprint shape screening and the compound from previous research were performed on dehydrosqualene synthase (2ZCO) for their docking score. The lowest values docking score were analyzed with multiple linear regressions. The results suggest that the diketopiperazine framework is a prospective template for modification and optimization to accomplish better potency of antibacterial activity in laboratory testing. Keywords: diketopiperazine, Glide-XP, docking score, Staphylococcus aureus, multiple linear regression.
DOCKING ANALOG KURKUMIN TURUNAN PIPERAZINDION DENGAN TUBULIN (1TUB) RANTAI  MENGGUNAKAN VINA DAN AUTODOCK1 Broto Santoso
Pharmacon: Jurnal Farmasi Indonesia Vol 12, No 1 (2011)
Publisher : Universitas Muhammadiyah Surakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23917/pharmacon.v12i1.43

Abstract

Program Autodock mampu memprediksi energi bebas dan konformasi ikatan antara fleksibel ligan dan makromolekul target yang telah diketahui. Senyawa turunan dan analog kurkumin adalah ligan yang telah banyak dihasilkan dan diuji aktivitasnya. Beberapa diantaranya memiliki khasiat yang lebih baik dari kurkumin. Enam senyawa turunan piperazindion, kurkumin, PGV-0, dan PGV-1 dihitung energi optimasi geometrinya menggunakan density functional theory (DFT) – Gaussian. Ligan hasil optimasi dicari energi ikatan ligan dengan reseptor 1TUB rantai b melalui docking menggunakan Vina dan Autodock dengan metode Lamarckian Genetic Algorithm (LGA), traditional Genetic Algorithm (tGA), dan Simulated Annealing (SA) Monte Carlo. Data energi ikatan (affinitas) terbaik yang diperoleh dianalisis dengan Anova: Two-Factor Without Replication (P=0,01). Hasil docking dengan semua metode menunjukkan bahwa senyawa analog kurkumin turunan piperazindion mempunyai potensi ikatan lebih baik dibanding senyawa induknya Kata Kunci: 1TUB, Autodock, docking, kurkumin, piperazindionage:IN'Kata kunci: Citrus reticulata, antiproliferatif, DMBA, AgNOR, c-Myc. 
Hasil Skrining Aktivitas Sitotoksik Ekstrak Etanol Daun Kelengkeng (Dimocarpus longan), Daun Kersen (Muntingia calabura), dan Daun Alpukat (Persea americana) terhadap Sel T47D Dan WiDr Ratna Yuliani; Broto Santoso; Bella Permatasani; Diah Mukti Sari
Pharmacon: Jurnal Farmasi Indonesia Vol 16, No 2 (2019)
Publisher : Universitas Muhammadiyah Surakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23917/pharmacon.v16i2.9050

Abstract

Cancer treatments usually cause adverse drug reactions. Therefore, safe anticancer drugs are needed in the treatment of cancer. One source of medicine that can be explored is plant. Extracts of longan leaves (Dimocarpus longan), jamaican cherry leaves (Muntingia calabura), and avocado leaves (Persea americana) have been tested for cytotoxic activity against several cancer cell lines. This study aims to determine the cytotoxic activity of ethanolic extract of longan leaves, jamaican cherry leaves, and avocado leaves against T47D and WiDr cells and to identify secondary metabolites in the extracts which have the highest activity. Ethanolic extract of longan leaves, jamaican cherry leaves, and avocado leaves were tested for their cytotoxic activity using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) method. Identification of secondary metabolites in the ethanolic extract of avocado leaves was carried out by thin layer chromatography method using silica gel GF254 as the stationary phase and a mixture of n-hexane and acetone (6:4) as the mobile phase. Cytotoxic test results show that ethanolic extract of longan leaves and cherry leaves with concentration of up to 1600 μg/mL do not reduce the T47D and WiDr living cells to 50%. Avocado leaf extract decreases the percentage of living T47D cells and WiDr with IC50 values of  790.679 µg/mL and 1072.2 µg/mL, respectively. The ethanolic extract of avocado leaves contains flavonoid, phenolic, and terpenoid. Ethanolic extract of longan leaves, cherry leaves and avocado leaves do not have cytotoxic activity against T47D and WiDr cells.
3D-MOLECULAR SCREENING OF DIKETOPIPERAZINE DERIVATES ON Staphylococcus aureus DEHYDROSQUALENE SYNTHASE USING VINA Broto Santoso
Pharmacon: Jurnal Farmasi Indonesia Vol 13, No 1 (2012)
Publisher : Universitas Muhammadiyah Surakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.23917/pharmacon.v13i1.23

Abstract

Dehydrosqualene synthase enzyme has been used as protein target model for exploring docking simulation of pyrazoline analogues. One of diketopiperazine derivates that have similar structure to pyrazoline has antibacterial activity against Staphylococcus aureus (S. aureus). Vina is AutoDock- improved program that capable for molecular screening based on free-energy and binding conformation prediction between ligand and protein target. The aim of these studies is to screen diketopiperazine derivates on dehydrosqualene synthase of S. aureus using Vina. Diketopiperazine derivates, curcumin analogues, curcumin, pentagammavunon derivates (PGV-0 and PGV-1) were calculated for their geometry optimization energy using Gaussian-Density Functional Theory method. 3D-optimized ligands along with reference ligands were screened for their binding energy with dehydrosqualene synthase (2ZCO) by docking using Vina. The lowest values of binding energy were analyzed with statistic method. The results showed that top thirteen ligands of docking binding energy with receptor are diketopiperazine derivates (31%), curcumin analogues (31%), and reference ligands (38%). The new compounds of diketopiperazine derivates and curcumin analogues have better potency of binding energy than curcurmin as lead compound. Keywords: diketopiperazine, Vina, docking, Staphylococcus aureus, curcumin.