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Quantitative Structure–Activity Relationships (Qsar) Study on Novel 4-Amidinoquinoline and 10- Amidinobenzonaphthyridine Derivatives As Potent Antimalaria Agent
JCECThe Journal of Engineering and Exact Sciences – JCEC, Vol. 05 N. 03 (2019) journal homepage: https://periodicos.ufv.br/ojs/jcec doi: 10.18540/jcecvl5iss3pp0271-0282 OPEN ACCESS – ISSN: 2527-1075 QUANTITATIVE STRUCTURE–ACTIVITY RELATIONSHIPS (QSAR) STUDY ON NOVEL 4-AMIDINOQUINOLINE AND 10- AMIDINOBENZONAPHTHYRIDINE DERIVATIVES AS POTENT ANTIMALARIA AGENT A. W. MAHMUD1, G. A. SHALLANGWA1 and A. UZAIRU1 1Ahmadu Bello University, Department of Chemistry, Zaria, Kaduna, Nigeria. A R T I C L E I N F O A B S T R A C T Article history: Quantitative structure–activity relationships (QSAR) has been a reliable study in the Received 2019-02-16 development of models that predict biological activities of chemical substances based on Accepted 2019-06-27 Available online 2019-06-30 their structures for the development of novel chemical entities. This study was carried out on 44 compounds of 4-amidinoquinoline and 10-amidinobenzonaphthyridine derivatives to p a l a v r a s - c h a v e develop a model that relates their structures to their activities against Plasmodium QSAR falciparum. Density Functional Theory (DFT) with basis set B3LYP/6-31G was used to ∗ Antimalaria optimize the compounds. Genetic Function Algorithm (GFA) was employed in selecting Plasmodium falciparum descriptors and building the model. Four models were generated and the model with best 4-Amidinoquinolina internal and external validation has internal squared correlation coefficient ( 2) of 0.9288, k e y w o r d s adjusted squared correlation coefficient ( adj) of 0.9103, leave-one-out (LOO) cross- 2 2 QSAR validation coefficient ( cv) value of 0.8924 and external squared correlation coefficient ( ) Antimalaria value of 0.8188. -
Open Babel Documentation Release 2.3.1
Open Babel Documentation Release 2.3.1 Geoffrey R Hutchison Chris Morley Craig James Chris Swain Hans De Winter Tim Vandermeersch Noel M O’Boyle (Ed.) December 05, 2011 Contents 1 Introduction 3 1.1 Goals of the Open Babel project ..................................... 3 1.2 Frequently Asked Questions ....................................... 4 1.3 Thanks .................................................. 7 2 Install Open Babel 9 2.1 Install a binary package ......................................... 9 2.2 Compiling Open Babel .......................................... 9 3 obabel and babel - Convert, Filter and Manipulate Chemical Data 17 3.1 Synopsis ................................................. 17 3.2 Options .................................................. 17 3.3 Examples ................................................. 19 3.4 Differences between babel and obabel .................................. 21 3.5 Format Options .............................................. 22 3.6 Append property values to the title .................................... 22 3.7 Filtering molecules from a multimolecule file .............................. 22 3.8 Substructure and similarity searching .................................. 25 3.9 Sorting molecules ............................................ 25 3.10 Remove duplicate molecules ....................................... 25 3.11 Aliases for chemical groups ....................................... 26 4 The Open Babel GUI 29 4.1 Basic operation .............................................. 29 4.2 Options ................................................. -
Open Data, Open Source, and Open Standards in Chemistry: the Blue Obelisk Five Years On" Journal of Cheminformatics Vol
Oral Roberts University Digital Showcase College of Science and Engineering Faculty College of Science and Engineering Research and Scholarship 10-14-2011 Open Data, Open Source, and Open Standards in Chemistry: The lueB Obelisk five years on Andrew Lang Noel M. O'Boyle Rajarshi Guha National Institutes of Health Egon Willighagen Maastricht University Samuel Adams See next page for additional authors Follow this and additional works at: http://digitalshowcase.oru.edu/cose_pub Part of the Chemistry Commons Recommended Citation Andrew Lang, Noel M O'Boyle, Rajarshi Guha, Egon Willighagen, et al.. "Open Data, Open Source, and Open Standards in Chemistry: The Blue Obelisk five years on" Journal of Cheminformatics Vol. 3 Iss. 37 (2011) Available at: http://works.bepress.com/andrew-sid-lang/ 19/ This Article is brought to you for free and open access by the College of Science and Engineering at Digital Showcase. It has been accepted for inclusion in College of Science and Engineering Faculty Research and Scholarship by an authorized administrator of Digital Showcase. For more information, please contact [email protected]. Authors Andrew Lang, Noel M. O'Boyle, Rajarshi Guha, Egon Willighagen, Samuel Adams, Jonathan Alvarsson, Jean- Claude Bradley, Igor Filippov, Robert M. Hanson, Marcus D. Hanwell, Geoffrey R. Hutchison, Craig A. James, Nina Jeliazkova, Karol M. Langner, David C. Lonie, Daniel M. Lowe, Jerome Pansanel, Dmitry Pavlov, Ola Spjuth, Christoph Steinbeck, Adam L. Tenderholt, Kevin J. Theisen, and Peter Murray-Rust This article is available at Digital Showcase: http://digitalshowcase.oru.edu/cose_pub/34 Oral Roberts University From the SelectedWorks of Andrew Lang October 14, 2011 Open Data, Open Source, and Open Standards in Chemistry: The Blue Obelisk five years on Andrew Lang Noel M O'Boyle Rajarshi Guha, National Institutes of Health Egon Willighagen, Maastricht University Samuel Adams, et al. -
Secondary Structure Propensities in Peptide Folding Simulations: a Systematic Comparison of Molecular Mechanics Interaction Schemes
Biophysical Journal Volume 97 July 2009 599–608 599 Secondary Structure Propensities in Peptide Folding Simulations: A Systematic Comparison of Molecular Mechanics Interaction Schemes Dirk Matthes and Bert L. de Groot* Department of Theoretical and Computational Biophysics, Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, Go¨ttingen, Germany ABSTRACT We present a systematic study directed toward the secondary structure propensity and sampling behavior in peptide folding simulations with eight different molecular dynamics force-field variants in explicit solvent. We report on the combi- national result of force field, water model, and electrostatic interaction schemes and compare to available experimental charac- terization of five studied model peptides in terms of reproduced structure and dynamics. The total simulation time exceeded 18 ms and included simulations that started from both folded and extended conformations. Despite remaining sampling issues, a number of distinct trends in the folding behavior of the peptides emerged. Pronounced differences in the propensity of finding prominent secondary structure motifs in the different applied force fields suggest that problems point in particular to the balance of the relative stabilities of helical and extended conformations. INTRODUCTION Molecular dynamics (MD) simulations are routinely utilized to that study, simulations of relatively short lengths were per- study the folding dynamics of peptides and small proteins as formed and the natively folded state was used as starting well as biomolecular aggregation. The critical constituents of point, possibly biasing the results (13). such molecular mechanics studies are the validity of the under- For folding simulations, such a systematic test has not lyingphysical models together with theassumptionsofclassical been carried out so far, although with growing computer dynamics and a sufficient sampling of the conformational power several approaches toward the in silico folding space. -
Reversal of Multidrug Resistance in Mouse Lymphoma Cells by Extracts and Flavonoids from Pistacia Integerrima
DOI:http://dx.doi.org/10.7314/APJCP.2016.17.1.51 Reversal of Multidrug Resistance in Mouse Lymphoma Cells by Extract and Flavonoids from Pistacia integerrima RESEARCH ARTICLE Reversal of Multidrug Resistance in Mouse Lymphoma Cells by Extracts and Flavonoids from Pistacia integerrima Abdur Rauf1*, Ghias Uddin2, Muslim Raza3, Bashir Ahmad4, Noor Jehan1, Bina S Siddiqui5, Joseph Molnar6, Akos Csonka6, Diana Szabo6 Abstract Phytochemical investigation of Pistacia integerrima has highlighted isolation of two known compounds naringenin (1) and dihydrokaempferol (2). A crude extract and these isolated compounds were here evaluated for their effects on reversion of multidrug resistance (MDR) mediated by P-glycoprotein (P-gp). The multidrug resistance P-glycoprotein is a target for chemotherapeutic drugs from cancer cells. In the present study rhodamine- 123 exclusion screening test on human mdr1 gene transfected mouse gene transfected L5178 and L5178Y mouse T-cell lymphoma cells showed excellent MDR reversing effects in a dose dependent manner. In-silico molecular docking investigations demonstrated a common binding site for Rhodamine123, and compounds naringenin and dihydrokaempferol. Our results showed that the relative docking energies estimated by docking softwares were in satisfactory correlation with the experimental activities. Preliminary interaction profile of P-gp docked complexes were also analysed in order to understand the nature of binding modes of these compounds. Our computational investigation suggested that the compounds interactions with the hydrophobic pocket of P-gp are mainly related to the inhibitory activity. Moreover this study s a platform for the discovery of novel natural compounds from herbal origin, as inhibitor molecules against the P-glycoprotein for the treatment of cancer. -
A Study on Cheminformatics and Its Applications on Modern Drug Discovery
Available online at www.sciencedirect.com Procedia Engineering 38 ( 2012 ) 1264 – 1275 Internatio na l Conference on Modeling Optimisatio n and Computing (ICMOC 2012) A Study on Cheminformatics and its Applications on Modern Drug Discovery B.Firdaus Begama and Dr. J.Satheesh Kumarb aResearch Scholar, Bharathiar University, Coimbatore, India, [email protected] bAssistant Professor, Bharathiar University, Coimbatore, India, [email protected] Abstract Discovering drugs to a disease is still a challenging task for medical researchers due to the complex structures of biomolecules which are responsible for disease such as AIDS, Cancer, Autism, Alzimear etc. Design and development of new efficient anti-drugs for the disease without any side effects are becoming mandatory in the recent history of human life cycle due to changes in various factors which includes food habit, environmental and migration in human life style. Cheminformaticds deals with discovering drugs based in modern drug discovery techniques which in turn rectifies complex issues in traditional drug discovery system. Cheminformatics tools, helps medical chemist for better understanding of complex structures of chemical compounds. Cheminformatics is a new emerging interdisciplinary field which primarily aims to discover Novel Chemical Entities [NCE] which ultimately results in design of new molecule [chemical data]. It also plays an important role for collecting, storing and analysing the chemical data. This paper focuses on cheminformatics and its applications on drug discovery and modern drug discovery techniques which helps chemist and medical researchers for finding solution to the complex disease. © 2012 Published by Elsevier Ltd. Selection and/or peer-review under responsibility of Noorul Islam Centre for Higher Education. -
Molecular Structure Input on the Web Peter Ertl
Ertl Journal of Cheminformatics 2010, 2:1 http://www.jcheminf.com/content/2/1/1 REVIEW Open Access Molecular structure input on the web Peter Ertl Abstract A molecule editor, that is program for input and editing of molecules, is an indispensable part of every cheminfor- matics or molecular processing system. This review focuses on a special type of molecule editors, namely those that are used for molecule structure input on the web. Scientific computing is now moving more and more in the direction of web services and cloud computing, with servers scattered all around the Internet. Thus a web browser has become the universal scientific user interface, and a tool to edit molecules directly within the web browser is essential. The review covers a history of web-based structure input, starting with simple text entry boxes and early molecule editors based on clickable maps, before moving to the current situation dominated by Java applets. One typical example - the popular JME Molecule Editor - will be described in more detail. Modern Ajax server-side molecule editors are also presented. And finally, the possible future direction of web-based molecule editing, based on tech- nologies like JavaScript and Flash, is discussed. Introduction this trend and input of molecular structures directly A program for the input and editing of molecules is an within a web browser is therefore of utmost importance. indispensable part of every cheminformatics or molecu- In this overview a history of entering molecules into lar processing system. Such a program is known as a web applications will be covered, starting from simple molecule editor, molecular editor or structure sketcher. -
A Web-Based 3D Molecular Structure Editor and Visualizer Platform
Mohebifar and Sajadi J Cheminform (2015) 7:56 DOI 10.1186/s13321-015-0101-7 SOFTWARE Open Access Chemozart: a web‑based 3D molecular structure editor and visualizer platform Mohamad Mohebifar* and Fatemehsadat Sajadi Abstract Background: Chemozart is a 3D Molecule editor and visualizer built on top of native web components. It offers an easy to access service, user-friendly graphical interface and modular design. It is a client centric web application which communicates with the server via a representational state transfer style web service. Both client-side and server-side application are written in JavaScript. A combination of JavaScript and HTML is used to draw three-dimen- sional structures of molecules. Results: With the help of WebGL, three-dimensional visualization tool is provided. Using CSS3 and HTML5, a user- friendly interface is composed. More than 30 packages are used to compose this application which adds enough flex- ibility to it to be extended. Molecule structures can be drawn on all types of platforms and is compatible with mobile devices. No installation is required in order to use this application and it can be accessed through the internet. This application can be extended on both server-side and client-side by implementing modules in JavaScript. Molecular compounds are drawn on the HTML5 Canvas element using WebGL context. Conclusions: Chemozart is a chemical platform which is powerful, flexible, and easy to access. It provides an online web-based tool used for chemical visualization along with result oriented optimization for cloud based API (applica- tion programming interface). JavaScript libraries which allow creation of web pages containing interactive three- dimensional molecular structures has also been made available. -
Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development
processes Review Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development Outi M. H. Salo-Ahen 1,2,* , Ida Alanko 1,2, Rajendra Bhadane 1,2 , Alexandre M. J. J. Bonvin 3,* , Rodrigo Vargas Honorato 3, Shakhawath Hossain 4 , André H. Juffer 5 , Aleksei Kabedev 4, Maija Lahtela-Kakkonen 6, Anders Støttrup Larsen 7, Eveline Lescrinier 8 , Parthiban Marimuthu 1,2 , Muhammad Usman Mirza 8 , Ghulam Mustafa 9, Ariane Nunes-Alves 10,11,* , Tatu Pantsar 6,12, Atefeh Saadabadi 1,2 , Kalaimathy Singaravelu 13 and Michiel Vanmeert 8 1 Pharmaceutical Sciences Laboratory (Pharmacy), Åbo Akademi University, Tykistökatu 6 A, Biocity, FI-20520 Turku, Finland; ida.alanko@abo.fi (I.A.); rajendra.bhadane@abo.fi (R.B.); parthiban.marimuthu@abo.fi (P.M.); atefeh.saadabadi@abo.fi (A.S.) 2 Structural Bioinformatics Laboratory (Biochemistry), Åbo Akademi University, Tykistökatu 6 A, Biocity, FI-20520 Turku, Finland 3 Faculty of Science-Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands; [email protected] 4 Swedish Drug Delivery Forum (SDDF), Department of Pharmacy, Uppsala Biomedical Center, Uppsala University, 751 23 Uppsala, Sweden; [email protected] (S.H.); [email protected] (A.K.) 5 Biocenter Oulu & Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7 A, FI-90014 Oulu, Finland; andre.juffer@oulu.fi 6 School of Pharmacy, University of Eastern Finland, FI-70210 Kuopio, Finland; maija.lahtela-kakkonen@uef.fi (M.L.-K.); tatu.pantsar@uef.fi -
Spoken Tutorial Project, IIT Bombay Brochure for Chemistry Department
Spoken Tutorial Project, IIT Bombay Brochure for Chemistry Department Name of FOSS Applications Employability GChemPaint GChemPaint is an editor for 2Dchem- GChemPaint is currently being developed ical structures with a multiple docu- as part of The Chemistry Development ment interface. Kit, and a Standard Widget Tool kit- based GChemPaint application is being developed, as part of Bioclipse. Jmol Jmol applet is used to explore the Jmol is a free, open source molecule viewer structure of molecules. Jmol applet is for students, educators, and researchers used to depict X-ray structures in chemistry and biochemistry. It is cross- platform, running on Windows, Mac OS X, and Linux/Unix systems. For PG Students LaTeX Document markup language and Value addition to academic Skills set. preparation system for Tex typesetting Essential for International paper presentation and scientific journals. For PG student for their project work Scilab Scientific Computation package for Value addition in technical problem numerical computations solving via use of computational methods for engineering problems, Applicable in Chemical, ECE, Electrical, Electronics, Civil, Mechanical, Mathematics etc. For PG student who are taking Physical Chemistry Avogadro Avogadro is a free and open source, Research and Development in Chemistry, advanced molecule editor and Pharmacist and University lecturers. visualizer designed for cross-platform use in computational chemistry, molecular modeling, material science, bioinformatics, etc. Spoken Tutorial Project, IIT Bombay Brochure for Commerce and Commerce IT Name of FOSS Applications / Employability LibreOffice – Writer, Calc, Writing letters, documents, creating spreadsheets, tables, Impress making presentations, desktop publishing LibreOffice – Base, Draw, Managing databases, Drawing, doing simple Mathematical Math operations For Commerce IT Students Drupal Drupal is a free and open source content management system (CMS). -
Organi &C Biomolecular Chemistry
Organic Biomolecular& Chemistry INDEXED IN MEDLINE Incorporating Acta Chemica Scandinavica Instructions for Authors (2004) Also see www.rsc.org/illustrations and www.rsc.org/electronicfiles CONTENTS 1.0 General Policy 1.0 General Policy Organic & Biomolecular Chemistry is a bimonthly journal 1.1 Articles for the publication of original research papers (articles), 1.2 Communications communications, Emerging Areas and Perspectives focusing on 1.3 Emerging Areas all aspects of synthetic, physical and biomolecular organic 1.4 Perspective Articles chemistry. 1.5 Submission of Articles Authors should note that papers that mainly emphasise the novel properties, applications or potential applications of 2.0 Administration materials may be more suited for submission to Journal of Materials Chemistry. (http://www.rsc.org/materials). 3.0 Notes on the Preparation of Papers There is no page charge for papers published in Organic & 3.1 Organisation of Material Biomolecular Chemistry. 3.2 Artwork Guidelines 3.3 Nomenclature Scope of the Journal 3.4 Deposition of Supplementary Data Organic & Biomolecular Chemistry brings together molecular 3.5 Guidelines on submitting files for proof preparation design, synthesis, structure, function and reactivity in one journal. It publishes fundamental work on synthetic, physical 4.0 Experimental and Characterisation Requirements and biomolecular organic chemistry as well as all organic 4.1 Physical Characteristics of Compounds aspects of: chemical biology, medicinal chemistry, natural 4.2 Characterisation of New Compounds -
Introduction to GROMOS
CSCPB - Introduction to GROMOS Information: Prof. Dr. W.F. van Gunsteren Laboratory of Physical Chemistry, ETH-Z¨urich, 8092 Z¨urich, Switzerland Tel: +41-44-6325501 Fax: +41-44-6321039 e-mail: [email protected] Note: This MD tutorial is still under development. Please report any errors, incon- sistencies, obscurities or suggestions for improvements to [email protected]. Purpose: This molecular dynamics (MD) tutorial serves a number of objectives. These are to obtain experience with: • computer simulation in general • executing and understanding GROMOS • interpreting the results of computer simulations Version: SVN revision December 5, 2007 W.F.v.G., Z.G., J.D., A-P.K., C.C., N.S. 1 Required knowledge: Some knowledge about the following is required: • Computer programming languages: ability to read simple code (C++). • Computer operating system language of the machine on which the tutorial will be carried out: UNIX. Good books on MD are (Frenkel & Smit, 2002) and (Allen & Tildesley, 1987). 2 Contents 1 INTRODUCTION 4 1.1 The Lennard-Jones interaction . 4 1.2 Electrostatic interaction . 5 1.3 Periodic boundary conditions . 5 1.4 Newton’s equations of motion . 6 1.5 The leap-frog integration scheme . 7 1.6 Coupling to a temperature bath . 8 1.7 Pressure and the virial . 9 1.8 Center of mass motion . 9 1.9 Gaussian or Maxwellian distributions . 10 1.10 The radial distribution function g(r).................. 10 1.11 Units . 11 2 INSTALLATION OF GROMOS 12 2.1 System Requirements . 12 2.2 Getting and Installing GROMOSXX . 13 2.3 Getting and Installing GROMOS++ .