@article {1002, title = {Establishment of a 3D-structure Database for Chemical Compounds in Indonesian Sponges}, journal = {Pharmacognosy Journal}, volume = {11}, year = {2019}, month = {October 2019}, pages = {1211-1218}, type = {Original Article}, chapter = {1211}, abstract = {

Objective: Nowadays, There hasn{\textquoteright}t any three-dimensional (3D) chemical structure database yet for biologically active compound in sponges from Indonesian origin. Therefore, this study aimed to create in silico a 3D-structure database of such compound and to evaluate the preferred software for this purpose. Methods: 2D- structure of selected compounds was established using MarvinSketch software. Conversion from 2D- into 3D-structures was evaluated by comparing MarvinSketch, OpenBabel and VegaZZ software packages. Visualization of the respective 3D-structures was perfomed by using PyMOL software. From 68 scientific articles, 212 chemical compounds were selected from 53 Indonesian sponge species. Results: The conversion of 2D-structures of the selected 212 chemical compound into 3D-structures lead to 7118 files, respectively consisting of 2508 files from the MarvinSketch, 1672 files from the OpenBabel and 1051 files from the VegaZZ software. The results based on the extention files were 1043 SDF, 1258 MOL and 2930 PDB format files of the three-dimensional structure. The valid and correct three-dimensional structure of chemical compound were 914 .sdf format files, 916 format .mol files and 72 .pdb format files. From the three-dimensional structures visualization, the database prefers established by using MarvinSketch with SDF or MOL format files since the results is consistent to literature and contain less number of errors.

}, keywords = {2D-and 3D-chemical structures, 3D-database of chemical structures, Evaluation of software packages, Indonesian sponges}, doi = {10.5530/pj.2019.11.188}, author = {Retno Prihatiningtyas and Rezi Riadhi Syahdi and Masteria Yunovilsa Putra and Arry Yanuar} } @article {1001, title = {HerbalDB 2.0: Optimization of Construction of Three-Dimensional Chemical Compound Structures to Update Indonesian Medicinal Plant Database}, journal = {Pharmacognosy Journal}, volume = {11}, year = {2019}, month = {October 2019}, pages = {1189-1194}, type = {Original Article}, chapter = {1189}, abstract = {

Objective: Development of novel drugs is an important challenge in the pharmaceutical world and industry. In-silico methods are often considered in refinement / correction processes of drug design because they may lower the costs. The in-silico drug discovery process requires a three- Dimensional Structure (3DS) of the chemical compounds as input. Computational 3DSs often exhibit structural mismatches thus affecting the validity of the in-silico drug design process. In a previous study, a 3DS database with 1405 of Indonesian herbal compounds was developed, named HerbalDB. In this database, various structural mismatches were identified in some of the 3DSs. Our study aimed to identify and correct the structural mismatches in the herbalDB and to determine the best method in creating correct 3DS of chemical compounds. Methods: Structural mismatches in the herbal database were identified by molecular visualization. Results: The identification process yielded 170 compounds with structural mismatches that were corrected with 10 different parameters using the MarvinSketch and VegaZZ software, evaluated by molecular visualization. Conclusions: based on 3DS of chemical compound visualization, *.mol and *.sdf file format created using Dreiding force fields of MarvinSketch are the best method to construct the proper structure of Indonesian medicinal plant{\textquoteright}s chemical compound database compared with MMFF94, AMBER and CHARMM forcefields.

}, keywords = {Herbal database, MarvinSketch, Three-dimensional structure, VegaZZ}, doi = {10.5530/pj.2019.11.184}, author = {Rezi Riadhi Syahdi and Jasmine Tiara Iqbal and Abdul Munim and Arry Yanuar} } @article {996, title = {In silico Analysis of Flavonoid Glycosides and its Aglycones as Reverse Transcriptase Inhibitor}, journal = {Pharmacognosy Journal}, volume = {11}, year = {2019}, month = {October 2019}, pages = {1252-1255}, type = {Original Article}, chapter = {1252}, abstract = {

Background: HIV continues to be a major global public health issue, having claimed more than 35 million lives so far. In 2016, 1 million people died from HIV-related causes globally. HIV-1 reverse transcriptase is one of HIV{\textquoteright}s vital enzymes for virus reproduction. If the enzyme is inhibited, the virus multiplication could be significantly decreased. There are currently many treatments for HIV, but more effective treatment is always needed because of the possibility of drug resistance and side effects for long-term use. Based on the previous study, there are some natural compounds with high affinity to the HIV-1 reverse transcriptase enzyme. Some of these compounds are flavonoid glycosides. Aims and Method: This study was aimed to learn more about in silico HIV-1 reverse transcriptase inhibitory activities of flavonoid glycosides using docking method. Results: The results showed that the most recommended flavonoid glycosides are those with the lowest binding energy, which were kaempferol-3-O-rhamnoside, myricetin-3-O-rhamnoside and quercetin-3-O-rhamnoside. This was due to the interactions of all three flavonoid rings and sugar moiety with key amino acid residues, which were Leu100, Lys101, Glu138, Tyr181, His235 and Tyr318. Conclusion: Flavonoid glycosides with rhamnose as glycone showed lower binding energy on HIV-1 reverse transcriptase.

}, keywords = {Flavonoid, Glycosides, HIV, Molecular docking, Reverse transcriptase}, doi = {10.5530/pj.2019.11.194}, author = {Stefandi J Wijaya and Arry Yanuar and Rosita Handayani and Rezi Riadhi Syahdi} } @article {999, title = {Virtual Screening of Indonesian Herbal Database as Adenosine A2A Antagonist using AutoDock and AutoDock Vina}, journal = {Pharmacognosy Journal}, volume = {11}, year = {2019}, month = {October 2019}, pages = {1219-1224}, type = {Original Article}, chapter = {1219}, abstract = {

Objective: Previous research found that Adenosine A2A antagonist allows to reduce motor fluctuations, dyskinesia, protect from neurodegenerative disorder in Parkinson{\textquoteright}s disease in the human brain which is chronic progressive of losing dopaminergic neurons. The aim of this study is to explore Indonesian herbal compounds as Adenosine A2A inhibitor using virtual screening method. Methods: In this study, virtual screening of Indonesian herbal database as Adenosine A2A inhibitor was done by AutoDock and AutoDock Vina and was validated by database from A Directory of Useful Decoys: Enhanced (DUD-E). The method was validated by Enrichment Factor (EF) and Area Under Curve (AUC) of Receiver Operating Characteristics (ROC) curve Results: Based on the validation results, grid box that was used in virtual screening using AutoDock is 60 {\texttimes} 60 {\texttimes} 60 with EF1\% 16.5869 and AUC 0.8406. The two compounds Chitranone and 3-O-Methylcalopocarpin with binding energy -10.19 and -9.55 kcal/mol, respectively showing interaction with Adenosine A2A active site at residues ALA63, ILE66, ALA81, LEU85, PHE168, GLU169, MET177, TRP246, LEU249, ASN253 and ILE274. Conclusions:\ This study concludes that Chitranone and 3-O-Methylcalopocarpin could be proposed to be developed as Adenosine A2A antagonists.

}, keywords = {Adenosine A2A antagonist, AutoDock, Autodock vina, Indonesian herbal database, Parkinson{\textquoteright}s disease, Virtual Screening}, doi = {10.5530/pj.2019.11.189}, author = {Nabilah Nurtika Salamah and Widya Dwi Aryati and Arry Yanuar} } @article {998, title = {Virtual Screening of Indonesian Herbal Database as alpha-Amino-3- Hydroxy-5-Methyl-4 Isoxazolepropionic Acid (AMPA) Antagonist}, journal = {Pharmacognosy Journal}, volume = {11}, year = {2019}, month = {October 2019}, pages = {1204-1210}, type = {Original Article}, chapter = {1204}, abstract = {

Objective: Ischemic stroke is one type of circulatory disturbance caused by blood clots that block blood flow to the brain. One of the impact of ischemia is nerve cell damage due to excitotoxicity. Inhibition of the ionotropic glutamate receptor such as the AMPA receptor, becomes an essential approach to the treatment of ischemia. This study aims to explore the possibility of an Indonesian herbal compound as an AMPA receptor antagonist. Methods: In this study, virtual screening of 2233 herbal compounds was performed by docking method using AutoDock to find the antagonist candidate of AMPA receptor from Indonesian herbal database. The virtual screening method was validated by an area under curve (AUC) of the ROC curve and enrichment factor (EF). Lipinski{\textquoteright}s Rule of Five was used to filter the screening result. Results: The validation of virtual screening result showed that AUC was 0.9385 and EF 1\% was 23.5550. The screening result of Indonesian herbal database showed top five compound sanggenol O, blazeispirol X, progesterone, nimolicinol and boeravinone F (-8.51; -8.39; -8.19; -8.17; -8.08 kcal/mol, respectively) and have interaction with TYR61 and THR91 residues of AMPA receptor. Conclusion: Five compounds of the Indonesia herbal database were shown as hits of AMPA receptor antagonist based on the docking method.

}, keywords = {AMPA receptor, AutoDock, Herbal plants, Neuroprotective, Virtual Screening}, doi = {10.5530/pj.2019.11.187}, author = {Rezi Riadhi Syahdi and Chindy Dwi Martinah and Arry Yanuar} } @article {871, title = {Virtual Screening of Indonesian Herbal Database for Discovery of Procaspase-3 Activators Using Autodock and Autodock Vina}, journal = {Pharmacognosy Journal}, volume = {xx}, year = {2019}, pages = {xx-xx}, type = {Original Article}, chapter = {xx}, abstract = {

Objective: Cancer is a disease where body cell grows abnormal, spread to every part of human body. Previous studies have found excessive expression of Procaspase-3 on cancer that must be activated to Caspase-3 to induce apoptotic in cells. Methods: Virtual screening of Indonesian Herbal Database was carried out to discover Procaspase-3 activators. This study was validated using enrichment factor (EF), receiver operating characteristics (ROC) area under curve (AUC) parameters. Among 1412 compounds were screened using Autodock and Autodock Vina software. Results: The virtual screening results using Autodock obtained the best ten compounds with binding energy -8.28 ~ -9.31 kcal/mol and Autodock Vina obtained the best ten compounds with binding energy -8.1 ~ -8.8 kcal/mol. Both virtual screening software showed two compounds in common, i.e., betulinic acid and maslinic acid. Conclusion: Betulinic acid interacts with Leu136A, Lys137A, Tyr195A and Pro201 residues in Autodock and Autodock Vina. While maslinic acid interacts with Leu136A, Lys137A and Pro201 residues in Autodock and Autodock Vina.

}, keywords = {Apoptotic, Cancer, Herbal, Procaspase-3 activator, Virtual Screening}, doi = {10.5530/pj.2019.11xx}, author = {Rezi Riadhi Syahdi and Ayu Annissa and Arry Yanuar} } @article {839, title = {Virtual Screening of Indonesian Herbal Database for Discovery of Procaspase-3 Activators Using Autodock and Autodock Vina}, journal = {Pharmacognosy Journal}, year = {2019}, pages = {xx-xx}, type = {Original Article}, chapter = {xx}, abstract = {

Objective: Cancer is a disease where body cell grows abnormal, spread to every part of human body. Previous studies have found excessive expression of Procaspase-3 on cancer that must be activated to Caspase-3 to induce apoptotic in cells. Methods: Virtual screening of Indonesian Herbal Database was carried out to discover Procaspase-3 activators. This study was validated using enrichment factor (EF), receiver operating characteristics (ROC) area under curve (AUC) parameters. Among 1412 compounds were screened using Autodock and Autodock Vina software. Results: The virtual screening results using Autodock obtained the best ten compounds with binding energy -8.28 ~ -9.31 kcal/mol and Autodock Vina obtained the best ten compounds with binding energy -8.1 ~ -8.8 kcal/mol. Both virtual screening software showed two compounds in common, i.e., betulinic acid and maslinic acid. Conclusion: Betulinic acid interacts with Leu136A, Lys137A, Tyr195A and Pro201 residues in Autodock and Autodock Vina. While maslinic acid interacts with Leu136A, Lys137A and Pro201 residues in Autodock and Autodock Vina

}, keywords = {Apoptotic, Cancer, Herbal, Procaspase-3 activator, Virtual Screening}, doi = {10.5530/pj.2017.4.x}, author = {Rezi Riadhi Syahdi, and Ayu Annissa and Arry Yanuar} } @article {640, title = {Indonesian Herbal SGLT2 Inhibitor Discovery through Pharmacophore-Based Virtual Screening}, journal = {Pharmacognosy Journal}, volume = {10}, year = {2018}, month = {June 2018}, pages = {803-807}, type = {Original Article}, chapter = {803}, abstract = {

Objective: Sodium-glucose cotransporter 2 (SGLT2) inhibitor had been evaluated in clinical trials as the basic strategy of hyperglycemia handling in diabetes. However, because of SGLT2 inhibitors is the new class of oral antidiabetic, it is rare to be found in Indonesia, and it is costly. This study was intended to find compounds from Indonesian herbal database that show capability to be used as SGLT2 inhibitors through a pharmacophore-based virtual screening approach. Methods: The SGLT2 inhibitor pharmacophore models were made from 10 training sets of SGLT2 ligand inhibitors using the Ligand Scout 4.1.5. Ten pharmacophore models which had been made were validated using test set and decoy set methods to know how the performance of pharmacophore model worked. Virtual screening were then applied to the best pharmacophore model. Results: The model-1 pharmacophore was the best model, with values of 0.9080, EF1\% = 56.5, EF5\% = 56.5 and AUC100\% = 0.87 which served as model for virtual screening. Model-1 consisted of one hydrophobic interaction, one aromatic ring, four hydrogen bond donors and five hydrogen bond acceptors. Virtual screening showed three compounds (Hits) with best pharmacophore fit scores according to model-1 among 1377 compounds, they were vitexin = 113.62; cucumerin A = 112.62; and cucumerin B = 113.51. Conclusion: These results showed that vitexin, cucumerin A, and cucumerin B potentially have activity as an SGLT2 inhibitor.

}, keywords = {Diabetes, Pharmacophore, SGLT2 Inhibitor, Virtual Screening}, doi = {10.5530/pj.2018.4.136}, url = {http://fulltxt.org/article/674}, author = {Rezwendy R and Rezi Riadhi Syahdi and Arry Yanuar} } @article {641, title = {Molecular Dynamic Simulation of Hydroxymethylglutaryl-CoA Reductase Inhibitors from Gnetum gnemon L. Seed Extract}, journal = {Pharmacognosy Journal}, volume = {10}, year = {2018}, month = {June 2018}, pages = {793-797}, type = {Original Article}, chapter = {793}, abstract = {

Objective: Gnetum gnemon L. (melinjo) seed extract contained trans-resveratrol which has been shown to inhibit hydroxymethylglutaryl-CoA (HMG-CoA) reductase. Therefore it has a potent activity for lowering blood cholesterol. This study was carried out to determine the molecular dynamics simulation of HMG-CoA reductase inhibitors from Gnetum gnemon L. seed extract. Methods: Molecular dynamics simulation using AMBER was used. The simulation was set at 300 K as default temperature and 310 K, average human body temperature. The main parameters of this study were ligand-residue interaction, binding affinity, root mean square deviation (RMSD), root mean square fluctuation (RMSF), hydrogen bonds analysis, molecular mechanics Poisson Boltzmann surface area (MMPBSA), and molecular mechanics generalized born surface area (MMGBSA). Results: In the simulation study, trans-resveratrol, trans-piceid, gnemonol M, gnemonoside B, viniferin and gnetin C had shown lower energy than HMG (PDB ID: MAH), the substrate of HMG-CoA Reductase. Free energy binding obtained from simulation was between 11.1 to -31.38 kcal/mol. Conclusion: The simulation at 310 K was preferable than 300 K as more interactions were performed and higher affinity was obtained.

}, keywords = {Gnetum gnemon L, Hydroxymethylglutaryl-CoA reductase inhibitor, Molecular dynamics, Trans-resveratrol}, doi = {10.5530/pj.2018.4.134}, url = {http://fulltxt.org/article/672}, author = {Yuditya Artha and Arif Arrahman and Azminah and Arry Yanuar} } @article {738, title = {Virtual Screening of Indonesian Herbal Database as Murine Double Minute-2 (MDM2) Inhibitor}, journal = {Pharmacognosy Journal}, volume = {10}, year = {2018}, month = {August 2018}, pages = {1184-1189}, type = {Original Article}, chapter = {1184}, abstract = {

Background: Murine Double Minute-2 (MDM2) overexpression causes the p53 deficiency, so the role p53 as a cell regulator does not work in the case of cancer. Methods: In this study, virtual screening of Indonesian herbal database to discover MDM2 inhibitors was carried out. Autodock and Autodock Vina validated with Directory of Useful Decoy-Enhanced (DUD-E). Validation parameters were performed with Enrichment Factor, Receiver Operating Characteristics, and Area Under Curve. Results: The validation with the grid box 70x70x70 on Autodock resulting AUC value 0.72, while in Autodock Vina 0.43. Autodock Vina did not fulfilll the standard value but still used for comparison. Based on the virtual screening result, top ten compounds from Autodock are Nimolicinol, Jacoumaric acid, Isoarborinol, Lantic acid, Diosgenin, Theasaponin E1, Taraxasterol, Leucadenone C, Simiarenol, and Alpha-Amyrin were found to have strong interaction with MDM2, with binding energy (\ΔG) ranging from -8.83 to -9.65 kcal/mol. The Autodock Vina screening resulted in the identification of Yuehchukene, Morusin, Cyanidin, Leucadenone C, Roxburghine-B, Ocidentoside, Beta-sitosterol, Curine, Withangulatin, and Jacoumaric acid as potential inhibitors with binding energy (\ΔG) ranging from -8.7 to -9.4 kcal/mol. Conclusion: Jacoumaric acid and Leucadenone C were shown to interact with the active site in MDM2 at residues Leu54, Ile61, Met62, and Ile99.

}, keywords = {Cancer, Docking, Indonesian Herbal, Inhibitor, MDM2, Virtual Screening}, doi = {10.5530/pj.2018.6.203}, author = {Alexander Victory and Rezi Riadhi Syahdi and Arry Yanuar} } @article {256, title = {Application of Ionic Liquid based Microwave-Assisted Extraction of the Secondary Metabolite from Peperomia pellucida (L) Kunth}, journal = {Pharmacognosy Journal}, volume = {9}, year = {2017}, month = {February 2017}, pages = {227-234}, type = {Original Article}, chapter = {227}, abstract = {

Introduction: An ionic liquid (ILs) is a new alternative solvent (containing cations and anions) has the physical and specific solutions properties, and also had proven to be a promising substituent of conventional organic solvents are flammable, volatile and toxic in various processes. The ILS application in separating the secondary metabolites compound from Peperomia pellucida (L) Kunth herbaceous can be carried out using microwaveassisted extraction method (MAE). Objective: The aim of this study was to investigate the effect of ionic liquid based microwave-assisted extraction method for attracting the secondary metabolites compound from P. pellucida compared with a conventional solvent for the enrichment of secondary metabolites (especially polyphenols group) and their HPTLC fingerprinting profile. Methods: The herb dried powder extracted by microwave-assisted extraction using an ionic liquid such us 1-Butyl-3-methylimidazolium chloride ([BMIM]Cl), 1-Butyl-3-methylimidazolium Bromide ([BMIM]Br). The obtained extract solution was partitioned using an organic solvent; the extract was evaporated to obtain a dry extract and determination the HPTLC fingerprinting profile. Results: Based on the research results was obtained from the various types of solvents there are differences in the extraction of secondary metabolite.

}, keywords = {HPTLC profile, Ionic liquid, Microwave-assisted extraction, Peperomia pellucida (L) Kunth, Secondary metabolite.}, doi = {10.5530/pj.2017.2.38}, url = {http://phcogj.com/fulltext/305}, author = {Islamudin Ahmad and Arry Yanuar and Kamarza Mulia and Abdul Mun{\textquoteright}im} }