Distributed Drug Discovery Indiana University Purdue University, Indianapolis

  • View
    214

  • Download
    1

Embed Size (px)

Text of Distributed Drug Discovery Indiana University Purdue University, Indianapolis

  • Slide 1

Distributed Drug Discovery Indiana University Purdue University, Indianapolis Slide 2 Introduction: PURPOSE OUTLINE DESIGN IMPLEMENTATION FUTURE WORK Slide 3 Purpose Need for innovative and inexpensive drugs to treat diseases in the developing world. Developed world has the equipment and procedures in the pharmaceutical industry through the economic incentives. Developing countries do not have the required economic incentives for the pharmaceutical industry. Slide 4 Concept Concept of Distributed Drug Discovery is that if simple, inexpensive equipment and procedures are developed for each of the core scientific drug discovery disciplines (computational chemistry, synthetic chemistry and biochemical screening), large research problems can be broken down into manageable smaller units and carried out at multiple academic sites throughout the developing and developed world. The coordinated and recombined results of these resources would inexpensively accelerate the identification of leads in the early stages of the drug discovery process. Slide 5 Procedure A list of potential drug lead candidates could be split up into small batches for synthesis in academic laboratories throughout the world. Then the pooled molecule products can be tested by the distributed screening effort. The summation of these efforts, networked across the three core disciplines, becomes a powerful globally distributed drug lead process and solution. Slide 6 Procedure (contd.) The synthetic laboratory experimental work is done in three main locations around the world including IUPUI. Enumeration software is used to create large sets of potential product molecules called virtual libraries. These in turn are rehearsed by students using a distributed approach theoretically. This distributed project can be made successful with the help of information technology to coordinate the dissemination, recollection and analysis of data. Slide 7 Outline To keep track of the data used and produced, a Distributed Drug Discovery Database is generated. Features oEntry of reagents in database oGeneration of combinatorial products oEntry of synthesized products information Release: oWeb application to enable data entry/searching of D3 database oWorkflow environment to support pipelining of tasks involving D3 database oWeb services to facilitate integration with other resources (e.g. PubChem) Slide 8 Database Database: PostgreSQL User Interface: Java and HTML Tomcat Server and JDBC driver Chemaxon oMarvin Sketch oMarvin View oJChem Reactor Slide 9 Entity-Relationship Diagram Slide 10 Tables 1.Reagents Table 2.Virtual Library Table 3.Rehearsed Library Table 4.Synthesized Library Table 5.Source Table 6.Organization Table Slide 11 Web Interface Created a web interface using Tomcat 5.5, html and JSP. The front end is in HTML and the back end is in JSP. Web interface connects to the backend database using Tomcat 5.5. Slide 12 WORK FLOW FOR INTERFACE Login Page AdministratorStudent Slide 13 Administrator Search the database Update the Database Search the Reagents Search the products Populating the Database Contd. Slide 14 Enumeration Using Chemaxon Reactor Chemaxons Marvin Reactor enables the user to enumerate the virtual library. The Reactor program is embedded in the web application. first the user selects a reaction for the experiment: from a standard set of reactions draw his/her own reaction in Marvin sketch upload using smarts. Second the user selects the reagents involved in the reaction The results are also available in a downloadable format. Slide 15 Selecting a Reaction Slide 16 Selecting the Reaction (contd.) Slide 17 Setting the Reactants Slide 18 Results Slide 19 Student WorkBook integration Student Workbook into the Web application used to populate the synthesized table Moving data from students table to synthesized table is performed by the administrator Also used to grade students Slide 20 Contd. Can be accessed at http://cheminfo.informatics.indiana.edu:8080/ddd/first.html Input based on student name, team number and organization name. Slide 21 Contd. User is given the choice of experimental vessel in which he wishes to input the data as shown below Slide 22 Contd. Next the student enters the data of the experimental work. The user can enter incomplete data and then come back to update the experiment. If the user is not having sufficient data for input, he can input the available data and return back at a later time to enter the remaining data. The interface is capable of retrieving the previous information entered with the authentication of Student last name and team number. Marvin Sketch is embedded to enable users to draw the product structure and copy it as SMILES to enter the data in the database. Since the data entered could be retrieved, the user can always make changes if he realizes that he has entered incorrect data. Slide 23 Contd. Slide 24 Slide 25 Usability Study A usability study is being conducted on the student interface. To study the feasibility and usability of the Web application for the students. Points Considered for Survey Website design i.e., user-friendly, legibility of instructions, size of fields, etc. Use of Marvin Sketch i.e., usefulness, complexity and overall impression. Database Entry i.e., paper Vs. computer, updating/editing information Rating of the overall web application Slide 26 Results Slide 27 Contd. Slide 28 Slide 29 Slide 30 Students were a bit confused in the beginning to use the web application. Though the application needs to be polished, the database is very useful in storing the outcomes of the experiments. Found Marvin Sketch similar to Chemdraw, but were confused why they were using Marvin. Overall the web application was a good one. Slide 31 Administrative Interface Administrator is given a choice of searching the student input by Student Lastname Product Structure Team number Vessel number Slide 32 Slide 33 Interface of Product Structure Input Slide 34 Result Slide 35 Search by Vessel Number Slide 36 Result Slide 37 Contd. Once the administrator checks the experimental results, He can grade the students Check for the correct product structures Omit the ones which are wrong and Input the right ones into the synthesized library Can send these results for further investigation to laboratories Slide 38 Future Work Supporting more popular queries: Extracting the Reagents from Aldrich and storing them in our database. Test and fine tuning of the distributed application Transform popular queries into web services (e.g. combinatorial queries into web services) Slide 39 THANK YOU!