Virtual Screening in Novel Drug Discovery cHiPSet CS 1 Final Report Vilnius March 2829 201 9 Speaker Drug discovery is Important one could go as far as to assess our development as a society by the coverage of diseases that can b ID: 806396
Download The PPT/PDF document "Cloud- B ased High Performance" is the property of its rightful owner. Permission is granted to download and print the materials on this web site for personal, non-commercial use only, and to display it on your personal computer provided you do not modify the materials and that you retain all copyright notices contained in the materials. By downloading content from our website, you accept the terms of this agreement.
Slide1
Cloud-Based High Performance Virtual Screening in Novel Drug DiscoverycHiPSet – CS1 Final Report
Vilnius, March 28-29, 2019
Speaker
Slide2Drug discovery is...Important – one could go as far as to assess our development as a society by the coverage of diseases that can be treatedDiverseevery patient is differentmolecular understanding required for tailoring treatments to genetically different individualsConsiderable fraction of patients has a rare disease that lacks causative treatmentHeterogeneousMany different tools are to be integrated at different stages of drug developmentFlexible: Researchers differ significantly over ‘what is the right workflow´DemandingRegular drugs are not affordable to develop – promising leads are sold to big pharmaRare diseases big pharma cannot address – the expertise with biological models of the disorder is with academic settingsComputational effort requiredChallengingRepeated interaction of IT modeling and biological findings/validationsRare disorders are investigated by clinical groups with little or no access to IT resources
Slide3Drug Discovery
Slide4Challenge: Enable Pre-Clinical Research to perform Virtual Drug ScreeningTargets Identification and ValidationVirtual drug screening
Evaluation in vitroAdjustment of search parameters
HTS
Surprises
Adjustment of sequence
databases
Monitoring and Visualization
Slide5Addressed ProblemFinding a developable hit molecule / drug candidateComputational needsInfrastructureSoftwareMethod validationComplexity of big data intertwined with diverse tools of analysis.Security concerns (public/private cloud)
Slide6Adressed ProblemDrug discovery and development requires the integration of multiple scientific and technological disciplines in chemistry and biology and extensive use of information technology. Virtual screening(VS) is one of the methods used in rational drug design and development studies. It may be applied in early stages of drug discovery pipeline.The number of modular and scalable computational cloud based web platforms are increasing. Such platforms are being developed to try to help researchers during the drug discovery and development pipeline. They are designed to efficiently perform VS, aimed to identify commercially available lead-like and drug-like compounds to be acquired and tested. Chemical datasets can be built, library analysis and profiling, receptor preparation can be done to be used for a molecular docking based VS using cloud technologies. Such platforms could also be adapted to be included in different stages of the R&D process to rationalize the needs.
Slide7Existing Partial Solutions(The rule of 5C)Cloud-based (Evias Cloud, Achilles Blind Docking Server, Scripps, mCule)Commercial databases (ZINC, Molport, eMolecules ..)Chemical vendors (Enamine, Life Chemicals ..)Computational Methods (Schrödinger, AutoDock ..)Clouds (AWS, BOiNC, OpenStack [public or private clouds], HPC servers ..)
Slide8Proposed SolutionDevelopment of a Rule Based System is required. This system may include an architecture, as described below:USER: describes the needs of the simulation and the state of analysisWORKFLOW: describes steps taken (or to be taken) in the simulation( and/or analysis)SYSTEM: describes rules/constrains/prioritisation to get from a well defined current state into another state that is yet unknown but somehow promising, since this is where the research with a particular tool has been performed. There will be different rules to select the compounds to screen.EX-SYSTEM: Information that is contributed from the literature or in vitro experiments that better describe the current state of the analysis.
Slide9Case Study TeamidName
institution (type*)Contact e-mail
Related WG
1
Abdurrahman Olğaç
Gazi
University
, TR (A)
Evias
Pharmaceutical R&D Ltd., TR
(I
)
aolgac@evias.com.tr
WG3
2
Steffen Möller
Rostock University, DE (A)
steffen.moeller@uni-rostock.de
WG3
1
Andrea Carotti
University of Perugia, IT (A)
andrea.carotti@unipg.it
WG3
2
Jean Remy Marchand
Novartis, CH (I)
jean-remy.marchand@novartis.com
WG3
3
Horacio
Pérez-Sánchez
Catholic University of Murcia
,
ES (A)
hperez@ucam.edu
WG3
4
José
Pedro Cerón Carrasco
Catholic University of Murcia, ES (A)
jpceron@ucam.edu
WG3
5
Marco
Aldinucci
University of Turin, IT (A)
aldinuc@di.unito.it WG26Andrea Bracciali University of Stirling, UK (A) abb@cs.stir.ac.uk WG37Cevdet Aykanat Bilkent University, TR (A) aykanat@gmail.com WG28Roberto NutiEvias Pharmaceutical R&D Ltd., IT (I)roberto.nuti@evias.com.trWG39Qian WangAthlone Institute of Technology, IR (A)qwang@research.ait.ieWG210Sandra GesingUniversity of Notre Dame, Indiana, USA (A)sandra.gesing@nd.eduWG3,WG411Simla OlğaçGazi University, TR(A)csimla@gazi.edu.trWG312Aslı TüreMarmara University, TR (A)asli.demirci@marmara.edu.trWG3