Induced-fit docking studies
Docking results of pteridine-based compounds in different target PTR1 and DHFR receptors and the off-target human DHFR when using an induced fit docking routine with an initial crude ligand placement step, subsequent receptor optimization in response to ligand binding and another docking step into the optimized receptor.
SEEK ID: https://fairdomhub.org/assays/1339
Modelling analysis
Projects: NMTrypI - New Medicines for Trypanosomatidic Infections
Investigation: Pteridines as anti-kinetoplastid folate-pathway protein inhibitors
Study: Docking to PTR1 and DHFR targets and off-targets
Assay position:
Biological problem addressed: Model Analysis Type
Organisms: Leishmania major, Trypanosoma brucei
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Created: 22nd Aug 2020 at 09:50
Last updated: 30th Sep 2020 at 10:03
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Projects: Kinetics on the move - Workshop 2016, COVID-19 Disease Map, NMTrypI - New Medicines for Trypanosomatidic Infections, CoVIDD - Coronavirus interactions in drug discovery - optimization and implementation
Institutions: Kinetics on the move Workshop at HITS, Heidelberg Institute for Theoretical Studies (HITS gGmbH), University of Eastern Finland (UEF)
https://orcid.org/0000-0002-2801-8902
Group Leader, Molecular and Cellular Modeling Group, EML Research, Heidelberg
Projects: NMTrypI - New Medicines for Trypanosomatidic Infections
Web page: https://cordis.europa.eu/programme/id/FP7_HEALTH.2013.2.3.4-2
The New Medicines for Trypanosomatidic Infections - NMTrypI project aimed at obtaining new candidate drugs against Trypanosomatidic infections with appropriate efficiency from the lead phase to the final preclinical phase that are more accessible to patients.
Programme: Drug development for neglected parasitic diseases
Public web page: https://fp7-nmtrypi.eu/
Start date: 1st Feb 2014
End date: 31st Jan 2017
Multidisciplinary development of selective anti-parasitic multi-target inhibitors of PTR1/DHFR based on a pteridine scaffold.
Submitter: Ina Poehner
Studies: Docking to PTR1 and DHFR targets and off-targets, In silico property and correlation analysis
Assays: Compound library preparation, Correlation analysis between PTR1 and DHFR activities and anti-parasitic..., Correlation analysis between predicted ADMET properties and anti-parasit..., Docking receptor preparation, In silico ADMET data prediction, Induced-fit docking studies, PAINS filtering, Rigid-body docking studies
Rigid-body docking studies and induced-fit docking studies of pteridine-based compounds to the target proteins TbPTR1, TbDHFR, LmPTR1, LmDHFR and the off-target hDHFR. For both PTR1 variants and human DHFR, conserved structural water sets were considered. Preparations of compound libraries and docking receptors are also covered.
Zip-archive with induced fit docking results for reference compounds methotrexate and 1b as well as the N10-modified compounds 2a and 2e in their neutral and N1-protonated variants and the PABA-modified compound 3d in neutral form as individual ligand:receptor complex PDB files. The files are ordered as ranked by Glide docking scores. The TbPTR1 receptor was based on PDB-ID 2x9g without additional water molecules. Docking results were obtained by Induced Fit docking with Schrödinger Glide and ...
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Relationship type: Not specified
Zip-archive with induced fit docking results for reference compounds methotrexate and 1b as well as the N10-modified compounds 2a and 2e in their neutral and N1-protonated variants and the N10-modified compound 2c and merged-series compound 5e in neutral form as individual ligand:receptor complex PDB files. The files are ordered as ranked by Glide docking scores. The TbPTR1 receptor was based on PDB-ID 2x9g with explicit conserved structural water molecules. Docking results were obtained by Induced ...
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Relationship type: Not specified
Zip-archive with induced fit docking results for methotrexate in its neutral and N1-protonated variant as individual ligand:receptor complex PDB files. The files are ordered as ranked by Glide docking scores. The TbDHFR receptor was based on PDB-ID 3rg9 without additional water molecules. Docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced Fit docking workflow (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Induced Fit Docking ...
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Relationship type: Not specified
Zip-archive with induced fit docking results for reference compounds methotrexate, 1b and 1c as well as the N10-modified compound 2e in their neutral and N1-protonated variants and the N10-modified compound 2a and Tail-modified compounds 4e, 4f, 4i and 4j in neutral form as individual ligand:receptor complex PDB files. The files are ordered as ranked by Glide docking scores. The LmPTR1 receptor was based on PDB-ID 1e92 without additional water molecules. Docking results were obtained by Induced ...
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Relationship type: Not specified
Zip-archive with induced fit docking results for reference compounds methotrexate, 1b and 1c as well as the N10-modified compound 2e in their neutral and N1-protonated variants and the PABA-modified compound 3e in neutral form as individual ligand:receptor complex PDB files. The files are ordered as ranked by Glide docking scores. The LmPTR1 receptor was based on PDB-ID 1e92 with explicit conserved structural water molecules. Docking results were obtained by Induced Fit docking with Schrödinger ...
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Relationship type: Not specified
Zip-archive with induced fit docking results for methotrexate in its neutral and N1-protonated variant as individual ligand:receptor complex PDB files. The files are ordered as ranked by Glide docking scores. The LmDHFR receptor was based on a published homology model of LmDHFR (Panecka-Hofman et al. (2017) Biochim Biophys Acta Gen Subj. 1861(12), 3215-3230. DOI: 10.1016/j.bbagen.2017.09.012) without additional water molecules. Docking results were obtained by Induced Fit docking with Schrödinger ...
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Relationship type: Not specified
Zip-archive with induced fit docking results for methotrexate in its neutral and N1-protonated variant as individual ligand:receptor complex PDB files. The files are ordered as ranked by Glide docking scores. The hDHFR receptor was based on PDB-ID 1u72 without additional water molecules. Docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced Fit docking workflow (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Induced Fit Docking ...
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Relationship type: Not specified
Zip-archive with induced fit docking results for methotrexate in its neutral and N1-protonated variant as individual ligand:receptor complex PDB files. The files are ordered as ranked by Glide docking scores. The hDHFR receptor was based on PDB-ID 1u72 with explicit conserved structural water molecules. Docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced Fit docking workflow (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Induced ...
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Relationship type: Not specified
This SOP describes the docking of pteridine libraries into PTR1 or DHFR target receptors, using Glide and Prime in Schrödinger Maestro as part of the Induced Fit workflow to allow for receptor side chain reorganization upon ligand binding.
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
