PDB Format Research Articles

Web-ARM: A Web-Based Interface for the Automatic Construction of QM/MM Models of Rhodopsins.

This article introduces Web-ARM, a specialized tool, online available, designed to build quantum mechanical/molecular mechanical models of rhodopsins, a widely spread family of light-responsive proteins. Web-ARM allows the rapidly building of models of rhodopsins with a documented quality and the prediction of trends in UV-vis absorption maximum wavelengths, based on their excitation energies computed at the CASPT2//CASSCF/Amber level of theory. Web-ARM builds upon the recently reported, python-based a-ARM protocol [J. Chem. Theory Comput., 2019, 15, 3134-3152] and, as such, necessitates only a crystallographic structure or a comparative model in PDB format and a very basic knowledge of the studied rhodopsin system. The user-friendly web interface uses such input to generate congruous, gas-phase models of rhodopsins and, if requested, their mutants. We present two possible applications of Web-ARM, which showcase how the interface can be employed to assist both research and educational activities in fields at the interface between chemistry and biology. The first application shows how, through Web-ARM, research projects (e.g., rhodopsin and rhodopsin mutant screening) can be carried out in significantly less time with respect to using the required computational photochemistry tools via a command line. The second application documents the use of Web-ARM in a real-life educational/training activity, through a hands-on experience illustrating the concepts of rhodopsin color tuning.

RNA CoSSMos 2.0: an improved searchable database of secondary structure motifs in RNA three-dimensional structures.

The RNA Characterization of Secondary Structure Motifs, RNA CoSSMos, database is a freely accessible online database that allows users to identify secondary structure motifs among RNA 3D structures and explore their structural features. RNA CoSSMos 2.0 now requires two closing base pairs for all RNA loop motifs to create a less redundant database of secondary structures. Furthermore, RNA CoSSMos 2.0 represents an upgraded database with new features that summarize search findings and aid in the search for 3D structural patterns among RNA secondary structure motifs. Previously, users were limited to viewing search results individually, with no built-in tools to compare search results. RNA CoSSMos 2.0 provides two new features, allowing users to summarize, analyze and compare their search result findings. A function has been added to the website that calculates the average and representative structures of the search results. Additionally, users can now view a summary page of their search results that reports percentages of each structural feature found, including sugar pucker, glycosidic linkage, hydrogen bonding patterns and stacking interactions. Other upgrades include a newly embedded NGL structural viewer, the option to download the clipped structure coordinates in *.pdb format and improved NMR structure results. RNA CoSSMos 2.0 is no longer simply a search engine for a structure database; it now has the capability of analyzing, comparing and summarizing search results.Database URL: http://rnacossmos.com

Establishment of a 3D-structure Database for Chemical Compounds in Indonesian Sponges

Objective: Nowadays, There hasn’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.

The CELLmicrocosmos Tools: A Small History of Java-Based Cell and Membrane Modelling Open Source Software Development.

For more than one decade, CELLmicrocosmos tools are being developed. Here, we discus some of the technical and administrative hurdles to keep a software suite running so many years. The tools were being developed during a number of student projects and theses, whereas main developers refactored and maintained the code over the years. The focus of this publication is laid on two Java-based Open Source Software frameworks. Firstly, the CellExplorer with the PathwayIntegration combines the mesoscopic and the functional level by mapping biological networks onto cell components using database integration. Secondly, the MembraneEditor enables users to generate membranes of different lipid and protein compositions using the PDB format. Technicalities will be discussed as well as the historical development of these tools with a special focus on group-based development. In this way, university-associated developers of Integrative Bioinformatics applications should be inspired to go similar ways. All tools discussed in this publication can be downloaded and installed from https://www.CELLmicrocosmos.org.

Knot_pull-python package for biopolymer smoothing and knot detection.

The biggest hurdle in studying topology in biopolymers is the steep learning curve for actually seeing the knots in structure visualization. Knot_pull is a command line utility designed to simplify this process-it presents the user with a smoothing trajectory for provided structures (any number and length of protein, RNA or chromatin chains in PDB, CIF or XYZ format), and calculates the knot type (including presence of any links, and slipknots when a subchain is specified). Knot_pull works under Python >=2.7 and is system independent. Source code and documentation are available at http://github.com/dzarmola/knot_pull under GNU GPL license and include also a wrapper script for PyMOL for easier visualization. Examples of smoothing trajectories can be found at: https://www.youtube.com/watch?v=IzSGDfc1vAY. Supplementary data are available at Bioinformatics online.

Abstract 1661: Molecular modeling of an emerging chemopreventive agent wedelolactone against multiple targets in oncogenetic pathway

Abstract Targeting multiple pathways involved either in drug resistance or/and in intact cancer cell survival are promising strategies. Epigenetics is being immensely recognized as exciting frontier in cancer research. Kinases have direct and indirect epigenetic impacts. Kinases are among the popular discovery targets and kinase inhibitors represent one of the key classes of drugs in the last two decades of oncology research. Braf kinases and cyclin dependent protein kinases exert their role as key mediators of signal transduction, apoptosis and overall intercellular communications. Topoisomerase II inhibitors including etoposide, tinoposide are important drugs used in breast cancer, sarcomas and lymphomas while inhibitors of dihydrofolatereductase, a key enzyme in the synthesis of DNA, are also clinically useful antagonists/inhibitors of ERα and aromatases have the potential to be therapeutically significant towards estrogen mediated breast, ovarian and uterine (endometrium) cancers. Wedelolactone is emerging as a small molecule with cytotoxic potential. Auto Dock Vina program was used for docking study .Affinity of best docked pose of ligand and protein target complex was determined by E-value (Kcal/mol).3D-structures of target proteins were taken from http://www.rcsb.org/pdb/home/home.do. The target proteins include dihydrofolatereductase, braf kinase, cyclin dependent protein kinase, nuclear factor kappa b, topoisomerase II, aromatase, estrogen receptor alpha and alkaline phosphatase (PDB ID: 2C2T, PDB ID: 3Q4C, PDB ID: 1HCL, PDB ID: 1NFK, PDB ID: 5B58, PDB ID: 3S7S, PDB ID: 3ERT, PDB ID: 1ANI). The structures (wedelolactone and standard drugs) were downloaded in.xml format and converted to PDB format via Open Babel JUI software. PDB form of wedelolactone, EGCG, reference drugs and target proteins were converted to PDBQT via AutoDock Tools (Version1.5.6 Sep_17_14). Discovery studio visualizer was used for post docking interactions for number of Hydrogen bonds (classical and non-classical), π-π bonds and other hydrophobic interactions by binding amino acid residues. The cell survival fraction was determined using the MTT reduction assay. The order of binding affinity of wedelolactone was found as: estrogen receptor alpha >dihydrofolate reductase>braf kinase > topoisomerase II > CDPK > aromatase > alkaline phosphatase >Nfkb. We identified wedelolactone as a cytotoxic agent in breast and ovarian tumor models with the potential to inhibit multiple targets in oncogenic as depicted through its In-silico study. Further research should be encouraged to investigate different aspects of wedelolactone. Note: This abstract was not presented at the meeting. Citation Format: sadia sarwar, Tauqeer Ahmed, Jun Q. Yu, Fazlul Huq. Molecular modeling of an emerging chemopreventive agent wedelolactone against multiple targets in oncogenetic pathway [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1661.

VoroMQA web server for assessing three-dimensional structures of proteins and protein complexes.

The VoroMQA (Voronoi tessellation-based Model Quality Assessment) web server is dedicated to the estimation of protein structure quality, a common step in selecting realistic and most accurate computational models and in validating experimental structures. As an input, the VoroMQA web server accepts one or more protein structures in PDB format. Input structures may be either monomeric proteins or multimeric protein complexes. For every input structure, the server provides both global and local (per-residue) scores. Visualization of the local scores along the protein chain is enhanced by providing secondary structure assignment and information on solvent accessibility. A unique feature of the VoroMQA server is the ability to directly assess protein-protein interaction interfaces. If this type of assessment is requested, the web server provides interface quality scores, interface energy estimates, and local scores for residues involved in inter-chain interfaces. VoroMQA, the underlying method of the web server, was extensively tested in recent community-wide CASP and CAPRI experiments. During these experiments VoroMQA showed outstanding performance both in model selection and in estimation of accuracy of local structural regions. The VoroMQA web server is available at http://bioinformatics.ibt.lt/wtsam/voromqa.

GAG Builder: a web-tool for modeling 3D structures of glycosaminoglycans.

Here we report the launch of a web-tool (the GLYCAM-Web GAG Builder, www.glycam.org/gag) for the rapid and straightforward prediction of 3D structural models for glycosaminoglycans (GAGs). The tool provides the user with coordinate files (PDB format) for use in visualization, as well as files for performing MD simulation with the AMBER software package. Counter ions and water may also be added as desired. The tool is designed with the non-expert in mind, and as such has implemented typical default values for structural parameters, which the user may change if desired. Multiple GAG types are supported, including Heparin/Heparan Sulfate, Chondroitin Sulfate, Dermatan Sulfate, Keratan Sulfate, and Hyaluronan; however, the user may alter the default sulfation patterns to create novel sequences. The common non-natural unsaturated uronic acid (ΔUA) and its sulfated derivative are also supported.

Molecular docking studies of salubrinal and its analogs as inhibitors of the GADD34:PP1 enzyme.

The phenomenon of the endoplasmic reticulum (ER) stress as a molecular pathophysiological process underlies diseases as cancer, diabetes mellitus, myocardial infarction, neurodegenerative disorders, diseases of the urinary system, disorders associated with bone integrity, etc. To prevent ER stress, salubrinal, which is a phosphatase inhibitor of the eukaryotic translation initiation factor - GADD34:PP1, is currently being intensively studied. The aim of this work is to search for new analogues of this drug using molecular docking methods. Optimization of the geometry of the studied structures and molecular docking was carried out using the ArgusLab 4.0.1 software package. The three-dimensional crystal structure of the GADD34: PP1 enzyme (PDB ID: 4XPN) was loaded in the PDB format from the protein molecule data bank. The model of the binding site was created on the basis of the phosphoric acid residue (403 PO4). The dimensions of the binding site were set manually and were 40.000 Å along the X-axis, 40.000 Å - the Y-axis and 40.000 Å - the Z-axis. The docking was done with a flexible ligand, and the semi-empirical AScore function was used for the scoring procedure. It was shown that for the salubrinal molecule the most favorable was the conformation stabilized by the intramolecular hydrogen bond formed between the hydrogen atom of the thiourea fragment and the oxygen atom of the amide fragment. According to molecular docking data, six compounds from the fifty-four analyzed analogues of salubrinal exceed it in the stability of the complex formed with GADD34:PP1. The results of this work can be used to create new phosphatase inhibitors of the eukaryotic translation initiation factor GADD34:PP1.

Molecular docking analysis of nuclear factor-κB and genistein interaction in the context of breast cancer.

Nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) is a transcription factor and it contributes to breast cancer growth and metastasis. Hence, NF-κB is considered as a target for anti-breast cancer drugs. NF-κB was retrieved from the UniProtKB Data Base with UniProt ID P19838, its energy was minimized and subjected to molecular dynamic simulations using Gromacs v5.0.7 software with GROMOS96 43A1 force field implementing the steepest descent algorithm. The structure of genistein was retrieved from NCBI PubChem database in .sdf format and convert to .pdb format. The genistein compound was docked into the active site of NF-κB proteins with AutoDock tools 1.5. The genistein compound displayed the best binding energies at -6.29 (NF-κB) kcal/mol correspondingly. The binding interactions of this compound with the active site of NF-κB proteins suggested that amino acid residues (Lys52, Ser243, Asp274, Lys, 275) might play a key role in anti-breast cancer activity. Genistein also inhibited the translocation and expression of NF-κB in the nucleus of both breast cancer cell lines. These findings might increase our understanding of the molecular and functional role of NF-κB in breast cancer. It could also help in developing additional druggable NF-κB inhibitors with high potency, specificity and outstanding bioavailability.

Using SMOG 2 to Simulate Complex Biomolecular Assemblies.

Over the last 20 years, the application of structure-based (Gō-like) models has ranged from protein folding with coarse-grained models to all-atom representations of large-scale molecular assemblies. While there are many variants that may be employed, the common feature of these models is that some (or all) of the stabilizing energetic interactions are defined based on the knowledge of a particular experimentally obtained conformation. With the generality of this approach, there was a need for a versatile computational platform for designing and implementing this class of models. To this end, the SMOG 2 software package provides an easy-to-use interface, where the user has full control of the model parameters. This software allows the user to edit XML-formatted files in order to provide definitions of new structure-based models. SMOG 2 reads these "template" files and maps the interactions onto specific structures, which are provided in PDB format. The force field files produced by SMOG 2 may then be used to perform simulations with a variety of popular molecular dynamics suites. In this chapter, we describe some of the key features of the SMOG 2 package, while providing examples and strategies for applying these techniques to complex (often large-scale) molecular assemblies, such as the ribosome.

COMPUTATIONAL STUDY OF BUTYL AND NAPHTHYL AMINE DERIVATIVE OF PERYLENE DIIMIDES TARGETTING TELOMERASE ENZYME FOR ANTICANCER ACTIVITY

Objective: Telomeres are protective caps present at the end of the chromosomes and it contains genetic information. From the literature survey, we selected perylene diimides which interact with the telomerase enzyme and possess anticancer activity. Telomestatin a macrocyclic chemical compound that inhibits telomerase activity as well it induces the formation of G-Quadruplex structures in the telomeric region. The main objective of the study was to find the binding affinity of butyl and naphthyl amine derivative of perylene ligands targeting telomerase enzyme for anticancer activity. Telomerase enzyme is responsible for maintaining the length of telomeres and keeping the chromosomes intact longer. Telomeres will become increasingly common with age. Perylene diimides and its derivatives show good biological activity and also in vitro studies possess efficient anticancer agent. The butyl and naphthyl amine derivatives are screened by computational techniques to study regarding binding energy and ligand interactions with respect to the targets.Methods: Butyl and naphthyl amine derivative of perylene diimides is drawn using Accelrys Draw. The structures are retrieved from the previous study. The structures are converted to pdb formats using Discovery Studio Visualizer 4.1. The study was to investigate the binding energy values of butyl and naphthyl amine derivatives of perylene diimides. Auto Dock 4.2 was used to dock the ligand with the targets. The target selected for docking was 3CE5 and 4B18. The results are visualized by Discovery Studio Visualizer 4.1. The results are compared with the standard drug N,N’-bis-(2-(1- piperidino)ethyl)-3,4,9,10-perylene tetracarboxylic acid diimide (PIPER).Results: From the results, butylamine derivative of perylene diimide possesses good binding energy when compared with standard drug PIPER. This result shows that the butylamine will be effective for anticancer therapy. In future, in vivo studies of butylamine derivative of perylene diimide will be carried out.

34. A study on molecular docking of HBV core protein against selected active compounds of traditional herbal drugs of northeast India

Background and Aims: A large population in India and North East India in particular depends on folk medicine to treat any type of jaundice. Off late many incidence of drug induced liver disease has been reported. There is an urgent need to elucidate the scientific merit for the use of such traditional medicines. Methods: Bioinformatics software's have been applied to model 30 sequences [JQ038375-414] of HBV core protein that were previously submitted and to evaluate that docking pattern with 15 selected active compounds which are used in folk medicine. The protein sequences as well as the structures were first converted to PDB format using Open Babel. These sequences were submitted to Gene Bank under the accession number [AFD32897- AFD32961]. The sequences were analyzed by RaptorX & PROTPARAM for structure and chemical compositions. The Ramachandran plots were constructed for understanding the stability using RAMPAGE. Molecular Docking was carried out by PATCHDOCK. The results were visualized using Rasmol. PASS was carried out for toxicity while ADME was also performed. Results: Stable protein structures of HBV core protein were confirmed. The stability was well supported by the analysis of Ramachandran Plot. The docking profile for all the active compounds showed significant compatibility with little or no variation across the studied sequences. However, the best results were found for Bael against sequence ID AFD32924. Promising results were documented for β-carotene, Solasonine & Emblicanin against sequence ID AFD32957. Conclusions: Aegelin (Bael) as active compound was found to be the most effective. The active compounds studied can be further evaluated for large-scale commercial use based on the results at animal studies and human trials. Molecular docking can be an important and cheaper tool for screening and documentation of scientific merit of the traditional herbal drugs used in North East India. The authors have none to declare. Table 1Tabled 1Common nameActive compoundScientific nameProtein idBest resultsLiquoriceGlycyrrhizinGlycyrrhiza glabraAFD329574554AmlaEmblicaninPhyllanthus emblica L.AFD329574568TurmericCurcuminCurcumae longaAFD329343592Dandelion rootβ CaroteneTaraxacum officinaleAFD329575664NeemAzadirachtinAzadirachta indicaAFD329344560KatukiKutkinPicrorhiza kurroaAFD329574092Reishi MushroomGanoderic acidGanoderma lucidumAFD329343742KakmachiSolasonineSolanum indicumAFD329574612Milk ThistleSilymarinSilybum marianumAFD329573994StonebreakerPhyllanthinPhyllanthus niruriAFD329344340Worm woodAbsinthinArtemisia absinthiumAFD329076662Green teaCatechinCamellia sinesisAFD329075032BaelAegelineAegle marmelosAFD329248876India mulberryMoranlineMorinda citrifoliaAFD328972438 Open table in a new tab

PDB2ENTROPY and PDB2TRENT: Conformational and Translational-Rotational Entropy from Molecular Ensembles.

Entropy calculation is an important step in the postprocessing of molecular dynamics trajectories or predictive models. In recent years the nearest neighbor method has emerged as a powerful method to deal in a flexible way with the dimensionality of the problem. Here we provide two programs, PBD2ENTROPY and PDB2TRENT that compute the conformational and translational-rotational entropy, respectively, based on the nearest neighbor method. PDB2ENTROPY takes in input two files containing the following: (1) conformational ensembles of the same molecule(s) in PDB format and (2) definitions of torsion angles (a default file is provided where additional user definitions can be easily implemented). PDB2TRENT takes in a file containing samples of the complexed molecules, a string specifying atoms providing the reference framework to superimpose samples, and a string specifying atoms used to compute rotation and translation of one molecule with respect to the other. The C programs and sample demonstration data are available on the GitHub repository (URL: http://github.com/federico-fogolari/pdb2entropy and http://github.com/federico-fogolari/pdb2trent ).

KymoKnot: A web server and software package to identify and locate knots in trajectories of linear or circular polymers

.The KymoKnot software package and web server identifies and locates physical knots or proper knots in a series of polymer conformations. It is mainly intended as an analysis tool for trajectories of linear or circular polymers, but it can be used on single instances too, e.g. protein structures in PDB format. A key element of the software package is the so-called minimally interfering chain closure algorithm that is used to detect physical knots in open chains and to locate the knotted region in both open and closed chains. The web server offers a user-friendly graphical interface that identifies the knot type and highlights the knotted region on each frame of the trajectory, which the user can visualize interactively from various viewpoints. The dynamical evolution of the knotted region along the chain contour is presented as a kymograph. All data can be downloaded in text format. The KymoKnot package is licensed under the BSD 3-Clause licence. The server is publicly available at http://kymoknot.sissa.it/kymoknot/interactive.php.Graphical abstract

MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update).

MOLEonline is an interactive, web-based application for the detection and characterization of channels (pores and tunnels) within biomacromolecular structures. The updated version of MOLEonline overcomes limitations of the previous version by incorporating the recently developed LiteMol Viewer visualization engine and providing a simple, fully interactive user experience. The application enables two modes of calculation: one is dedicated to the analysis of channels while the other was specifically designed for transmembrane pores. As the application can use both PDB and mmCIF formats, it can be leveraged to analyze a wide spectrum of biomacromolecular structures, e.g. stemming from NMR, X-ray and cryo-EM techniques. The tool is interconnected with other bioinformatics tools (e.g., PDBe, CSA, ChannelsDB, OPM, UniProt) to help both setup and the analysis of acquired results. MOLEonline provides unprecedented analytics for the detection and structural characterization of channels, as well as information about their numerous physicochemical features. Here we present the application of MOLEonline for structural analyses of α-hemolysin and transient receptor potential mucolipin 1 (TRMP1) pores. The MOLEonline application is freely available via the Internet at https://mole.upol.cz.

Computational Toolset for Glycoconjugate Modeling and Simulation

Characterizing glycoconjugates and protein-glycan interactions in the context of three-dimensional structures is important in understanding glycan's biological roles and develop efficient therapeutic agents. However, it is challenging to achieve this goal due to limitations in available experimental approaches and computational tools. To tackle this problem, we have developed GlycanStructure.ORG, a web portal to provide various computational tools. (1) Glycan Reader has been developed for automatic detection and annotation of carbohydrates, their chemical derivatives, and glycosidic linkages from PDB files (both in the PDB and mmCIF formats). Molecular system and input generations for the glycoconjugate simulation are available through CHARMM-GUI, http://www.charmm-gui.org. (2) The glycan fragment database (GFDB) provides an intuitive glycan sequence search tool that allows users to search for complex glycan structures in the PDB. After a glycan search, each selected glycosidic torsion angle distribution can be displayed and clustering analysis is used to provide most populated glycan structures, which can be useful for glycan structure modeling. (3) GS-align is an algorithm to identify the best structural alignment between glycan structure pairs and to provide a length-independent score of the structural similarity. This tool is useful to study the relationship between multiple glycoforms and biological functions, and glycan structure prediction. (4) Glycan Modeler is a template-based method to predict glycan structures from a given sequence using the PDB glycan structures as fragment template. After templates are identified by the random forest algorithm, Glycan Modeler provides two conformational sampling approaches that are assembly of rigid bodies and satisfaction of spatial restraints using by conformational space annealing (CSA).

EzMol: A Web Server Wizard for the Rapid Visualization and Image Production of Protein and Nucleic Acid Structures

EzMol is a molecular visualization Web server in the form of a software wizard, located at http://www.sbg.bio.ic.ac.uk/ezmol/. It is designed for easy and rapid image manipulation and display of protein molecules, and is intended for users who need to quickly produce high-resolution images of protein molecules but do not have the time or inclination to use a software molecular visualization system. EzMol allows the upload of molecular structure files in PDB format to generate a Web page including a representation of the structure that the user can manipulate. EzMol provides intuitive options for chain display, adjusting the color/transparency of residues, side chains and protein surfaces, and for adding labels to residues. The final adjusted protein image can then be downloaded as a high-resolution image. There are a range of applications for rapid protein display, including the illustration of specific areas of a protein structure and the rapid prototyping of images.

ConfBuster: Open-Source Tools for Macrocycle Conformational Search and Analysis

Macrocycles are cyclic macromolecules that have gained an increased interest in drug development. To our knowledge, the current bioinformatics tools that are available to investigate and predict macrocycles 3D conformations are limited in their availability. In this paper, we introduce ConfBuster, a suite of tools written in Python with the goal of sampling the lower energy conformations of macrocycles. The suite also includes tools for the analysis and visualisation of the conformational search results. Coordinate sets of single molecules in MOL2 or PDB format are required as input, and a set of lower energy conformation coordinates is returned as output, as well as PyMOL script and graphics for results analysis. In addition to Python and the optional R programming languages with freely available packages, the tools require Open Babel and PyMOL to work properly. For several examples, ConfBuster found macrocycle conformations that are within few tenths of Å of the experimental structures in minutes. To our knowledge, this is the only open-source tools for macrocycle conformational search available to the scientific community

The interaction of the active compounds of Labisia pumila on RANK–RANKL–OPG system

Summary The objective of this research was to analyze the interaction of the active ingredients in Labisia pumila (kaempferol, rutin, apigenin, caffeic acid, pyrogallol and gallic acid) against RANK–RANKL–OPG system in context of osteoporosis. This is an in silico research. The three-dimensional structure in .sdf file is converted to PDB format using the Open Babel 2.3.1 software. The three-dimensional structure model of RCSB RANK–RANKL and RANKL–OPG was obtained from http://www.rcsb.org/pdb. The ligand–protein docking and visualization analysis was carried out with Hex8.0 and Discovery Studio Client 3.5 software. RANK–RANKL or RANKL–OPG complex has the easiest interaction with rutin. In conclusion, flavonoid compounds (rutin, apigenin, kaempferol) more easily interact with RANK–RANKL and RANKL–OPG systems than isofavonoid groups (caffeic acid, pyrogallol, gallic acid). This opens the opportunity for the utilization of flavonoid from L. pumila as antiosteoporosis.