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.
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Created: 19th Aug 2020 at 12:30
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/0000-0002-2801-8902Group 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
Snapshots: Snapshot 1
Compound data, library construction schemes and preparation routine for small drug-like molecules as ligands in docking and for further analysis.
Submitter: Ina Poehner
Biological problem addressed: Model Analysis Type
Investigation: Pteridines as anti-kinetoplastid folate-pathway...
Organisms: No organisms
Models: No Models
SOPs: Ligand 3D structure preparation SOP
Data files: Fragments used for construction of the in silic..., SDF files of protonated pteridine compounds, SMILES strings for resynthesized and newly desi...
Snapshots: No snapshots
Prepared target (parasite PTR1, DHFR) and off-target (human DHFR) protein receptors for docking studies, in part with conserved structural water sets, and the corresponding preparation routine.
Submitter: Ina Poehner
Biological problem addressed: Model Analysis Type
Investigation: Pteridines as anti-kinetoplastid folate-pathway...
Organisms: Leishmania major, Trypanosoma brucei
Models: No Models
SOPs: Protein receptor preparation SOP for docking
Data files: LmDHFR docking receptor without water molecules, LmPTR1 docking receptor with conserved structur..., LmPTR1 docking receptor without water molecules, TbDHFR docking receptor without water molecules, TbPTR1 docking receptor with conserved structur..., TbPTR1 docking receptor without water molecules, hDHFR docking receptor with conserved structura..., hDHFR docking receptor without water
Snapshots: No snapshots
Docking results of pteridine-based compounds in different target PTR1 and DHFR receptors and the off-target human DHFR when treating ligands as flexible and the protein receptors as a rigid-body.
Submitter: Ina Poehner
Biological problem addressed: Model Analysis Type
Investigation: Pteridines as anti-kinetoplastid folate-pathway...
Organisms: Leishmania major, Trypanosoma brucei
Models: No Models
SOPs: Rigid-body XP docking with Glide
Data files: PDB files of pteridine docking results in LmDHF..., PDB files of pteridine docking results in LmPTR..., PDB files of pteridine docking results in LmPTR..., PDB files of pteridine docking results in TbDHF..., PDB files of pteridine docking results in TbPTR..., PDB files of pteridine docking results in TbPTR..., PDB files of pteridine docking results in hDHFR..., PDB files of pteridine docking results in hDHFR...
Snapshots: No snapshots
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.
Submitter: Ina Poehner
Biological problem addressed: Model Analysis Type
Investigation: Pteridines as anti-kinetoplastid folate-pathway...
Organisms: Leishmania major, Trypanosoma brucei
Models: No Models
SOPs: Induced fit docking with Glide and Prime as par...
Data files: PDB files of induced fit docking results for se..., PDB files of induced fit docking results for se..., PDB files of induced fit docking results for se..., PDB files of induced fit docking results for se..., PDB files of induced fit docking results for th..., PDB files of induced fit docking results for th..., PDB files of induced fit docking results for th..., PDB files of induced fit docking results for th...
Snapshots: No snapshots
Zip-archive with results for reference and all designed pteridines in their neutral and N1-protonated variant as multi-model PDB files, ordered as ranked by Glide docking scores, in the TbPTR1 receptor based on PDB-ID 2x9g without explicit water molecules. Docking results obtained by rigid-body XP docking with Schrödinger Glide (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Glide v6.9). For further details and naming conventions also refer to the README file.
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Rigid-body docking studies
Zip-archive with results for reference and all designed pteridines in their neutral and N1-protonated variant as multi-model PDB files, ordered as ranked by Glide docking scores, in the TbPTR1 receptor based on PDB-ID 2x9g with explicit conserved structural water molecules. Docking results obtained by rigid-body XP docking with Schrödinger Glide (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Glide v6.9). For further details and naming conventions also refer to the README file. ...
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Rigid-body docking studies
Zip-archive with results for reference and all designed pteridines in their neutral and N1-protonated variant as multi-model PDB files, ordered as ranked by Glide docking scores, in the TbDHFR receptor based on PDB-ID 3rg9 without explicit water molecules. Docking results obtained by rigid-body XP docking with Schrödinger Glide (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Glide v6.9). For further details and naming conventions also refer to the README file.
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Rigid-body docking studies
Zip-archive with results for reference and all designed pteridines in their neutral and N1-protonated variant as multi-model PDB files, ordered as ranked by Glide docking scores, in the LmPTR1 receptor based on PDB-ID 1e92 without explicit water molecules. Docking results obtained by rigid-body XP docking with Schrödinger Glide (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Glide v6.9). For further details and naming conventions also refer to the README file.
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Rigid-body docking studies
Zip-archive with results for reference and all designed pteridines in their neutral and N1-protonated variant as multi-model PDB files, ordered as ranked by Glide docking scores, in the LmPTR1 receptor based on PDB-ID 1e92 with explicit conserved structural water molecules. Docking results obtained by rigid-body XP docking with Schrödinger Glide (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Glide v6.9). For further details and naming conventions also refer to the README file. ...
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Rigid-body docking studies
Zip-archive with results for reference and all designed pteridines in their neutral and N1-protonated variant as multi-model PDB files, ordered as ranked by Glide docking scores, in the LmDHFR receptor based on the 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 explicit water molecules. Docking results obtained by rigid-body XP docking with Schrödinger Glide (Schrödinger, LLC, New York, ...
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Rigid-body docking studies
Zip-archive with results for reference and all designed pteridines in their neutral and N1-protonated variant as multi-model PDB files, ordered as ranked by Glide docking scores, in the hDHFR receptor based on PDB-ID 1u72 without explicit water molecules. Docking results obtained by rigid-body XP docking with Schrödinger Glide (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Glide v6.9). For further details and naming conventions also refer to the README file.
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Rigid-body docking studies
Zip-archive with results for reference and all designed pteridines in their neutral and N1-protonated variant as multi-model PDB files, ordered as ranked by Glide docking scores, in the hDHFR receptor based on PDB-ID 1u72 with explicit conserved structural water molecules. Docking results obtained by rigid-body XP docking with Schrödinger Glide (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Glide v6.9). For further details and naming conventions also refer to the README file. ...
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Rigid-body docking studies
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
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Induced-fit docking studies
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
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Induced-fit docking studies
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
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Induced-fit docking studies
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
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Induced-fit docking studies
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
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Induced-fit docking studies
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
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Induced-fit docking studies
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
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Induced-fit docking studies
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
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Induced-fit docking studies
Compound SMILES of resynthesized or newly designed pteridine compounds 1b, 1c, 2a-e, 3a-e, 4a-j and 5a-f used for ligand preparation within Maestro (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Maestro.). SMILES strings and compound identifiers are comma-separated and can be readily imported in Maestro.
Creators: Ina Poehner, Antonio Quotadamo
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Compound library preparation
Zip archive of N1 protonated reference and newly synthesized pteridines (series 1-5) in SDF format.
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Compound library preparation
PDB file of the prepared human dihydrofolate reductase docking receptor based on chain A of PDB-ID 1u72 with a conserved set of structural waters.
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Docking receptor preparation
PDB file of the prepared human dihydrofolate reductase docking receptor based on chain A of PDB-ID 1u72 without additional water molecules.
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Docking receptor preparation
This SOP describes the preparation of pteridine ligand 3D structures from SMILES or other input formats with the LigPrep routine as embedded in Schrödinger Maestro for usage in docking runs and in silico ADME-Tox property prediction.
Creators: Ina Poehner, Rebecca Wade, Joanna Panecka-Hofman
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Compound library preparation
This SOP describes the docking receptor preparation of PTR1 and DHFR receptor PDB files, performed with the Maestro Protein PrepWizard and the Glide grid generation routine. The optional identification and integration of conserved structural water molecules with the WatCH tool is also covered.
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Docking receptor preparation
This SOP describes the docking of pteridine libraries into PTR1 or DHFR target receptors, using Glide in Schrödinger Maestro with the XP (eXtra Precision) protocol.
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Rigid-body docking studies
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
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: Docking to PTR1 and DHFR targets and off-targets
Assays: Induced-fit docking studies