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
SEEK ID: https://fairdomhub.org/projects/199
Public web page: https://fp7-nmtrypi.eu/
Organisms: Trypanosoma brucei, Leishmania donovani, Leishmania infantum, Leishmania major, Trypanosoma cruzi
FAIRDOM PALs: No PALs for this Project
Project start date: 1st Feb 2014
Project end date: 31st Jan 2017
Related items
- People (8)
- Programmes (1)
- Institutions (4)
- Investigations (3+1)
- Studies (6+1)
- Assays (18)
- Data files (76+1)
- SOPs (9)
- Publications (24)
Projects: SysMO DB, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, de.NBI-SysBio, Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF - Pillar III), Early Metabolic Injury (LiSyM-EMI - Pillar I), Chronic Liver Disease Progression (LiSyM-DP - Pillar II), LiSyM Core Infrastructure and Management (LiSyM-PD), Liver Function Diagnostics (LiSyM-LiFuDi - Pillar IV), Molecular Steatosis - Imaging & Modeling (LiSyM-MSIM), Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), Model Guided Pharmacotherapy In Chronic Liver Disease (LiSyM-MGP), The Hedgehog Signalling Pathway (LiSyM-JGMMS), Kinetics on the move - Workshop 2016, Example use cases, SBEpo - Systems Biology of Erythropoietin, FAIRDOM & LiSyM & de.NBI Data Structuring Training, MESI-STRAT, INCOME, EnzymeML, PoLiMeR - Polymers in the Liver: Metabolism and Regulation, MS_DILI, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", COMBINE Multicellular Modelling, COVID-19 Disease Map, COVID-19 related studies and tools in Germany, nfdi4health - German National Research Data Infrastructure for Personal Health Data, NMTrypI - New Medicines for Trypanosomatidic Infections, ModeleXchange initiative, SNAPPER: Synergistic Neurotoxicology APP for Environmental Regulation, BioCreative VII, SDBV ephemeral data exchanges, The BeeProject, SDBV/HITS, MESI-STRAT Review, MESI-Review 2024, DeepCurate
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)
https://orcid.org/0000-0002-4980-3512I am group leader of the SDBV (Scientific Databases and Visualisation) group at the HITS gGmbH, the Heidelberg Institute for Theoretical Studies.
I am interested in finding data. Starting with my master's thesis I have always worked on how to store data in a way that you can find it, and how to make sense out of data that has been stored.
Within FAIRDOM I find interesting to help people to store their data in a way that they make sense even after years.
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: de.NBI-SysBio, Kinetics on the move - Workshop 2016, Example use cases, SBEpo - Systems Biology of Erythropoietin, FAIRDOM & LiSyM & de.NBI Data Structuring Training, FAIRDOM, EnzymeML, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", FAIRDOM Community Workers, MIX-UP, COVID-19 Disease Map, ERNEST Mapping Group Pilot Study, NMTrypI - New Medicines for Trypanosomatidic Infections, Standardization of enzyme-catalyzed reaction measurement, Standardization of enzyme-catalyzed reaction modelling, ModeleXchange initiative, CoVIDD - Coronavirus interactions in drug discovery - optimization and implementation, Mass spectrometry proteomics for biomarker discovery, Thymidylate synthase dimer dissociation, WG1 - Compound libraries coordination and integration of compound design, WG2 - Integration of early phase studies and low environmental impact actions, WG3 - Coordination of in vitro-to-in vivo translation of OneHealth leads and candidates, WG4 - Integration of R&D process-environmental studies and translation in informed whitepaper, WG5 - Promote dissemination, WG6 - Promote the transfer of knowledge, SABIO-VIS, SDBV/HITS
Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)
https://orcid.org/0000-0002-9077-5664Expertise: Biochemistry, Databases, Data Management, Curation
Projects: NMTrypI - New Medicines for Trypanosomatidic Infections
Web page: https://cordis.europa.eu/programme/id/FP7_HEALTH.2013.2.3.4-2
Design, synthesis, computational studies and biological evaluation of antiparasitic dinitroaniline-ether phospholipid hybrids
Submitter: Ina Poehner
Studies: Computational identification of potential dinitroaniline binding sites i..., Docking studies of trifluraline and the dinitroaniline-etherphospholipid...
Assays: Comparative electrostatic analysis of dinitroaniline-sensitive and -resi..., Induced-fit docking studies, Multiple sequence alignment, Preparation of multimeric tubulin docking receptors
Snapshots: Snapshot 1
Submitter: Pasquale Linciano
Studies: Chemical characterization, and biological evaluation of the SECONDARY HITS, Ty-Box chemical characterization, properties and biological evaluation
Assays: Antimicobacterium, Antiparasitic and in vitro toxicity for Ty-Box library, Biological characterization for Secondary Hits, Molecular Formula STRING excel, MolecularFormula Strings Spreadsheet_Ty, Secondary Hits Characterization, Ty-Box library characterization
Snapshots: No snapshots
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
Induced fit docking studies of the dinitroaniline parent trifluraline and the newly designed dinitroaniline-etherphospholipid hybrids against different potential binding sites in monomeric and multimeric kinetoplastid tubulin receptors.
Submitter: Ina Poehner
Investigation: Antiparasitic dinitroaniline-ether phospholipid...
Assays: Induced-fit docking studies, Preparation of multimeric tubulin docking receptors
Snapshots: No snapshots
Sequence and electrostatic potential analyses to identify sites in tubulins that differ between dinitroaniline-sensitive and dinitroaniline-resistant species.
Submitter: Ina Poehner
Investigation: Antiparasitic dinitroaniline-ether phospholipid...
Assays: Comparative electrostatic analysis of dinitroaniline-sensitive and -resi..., Multiple sequence alignment
Snapshots: No snapshots
Submitter: Pasquale Linciano
Investigation: Phenotypic and machine learning approaches for ...
Assays: Biological characterization for Secondary Hits, Molecular Formula STRING excel, Secondary Hits Characterization
Snapshots: No snapshots
Chemical structures, physicochemical properties and biological results for the compounds of the Ty-Box library
Submitter: Pasquale Linciano
Investigation: Phenotypic and machine learning approaches for ...
Assays: Antimicobacterium, Antiparasitic and in vitro toxicity for Ty-Box library, MolecularFormula Strings Spreadsheet_Ty, Ty-Box library characterization
Snapshots: No snapshots
Computational prediction of physicochemical and advanced descriptors related to ADME-Tox and PAINS assessment. Potential correlations of the computed descriptors with experimentally determined anti-parasitic activities and correlations between experimentally determined levels of target protein inhibition (PTR1, DHFR) with the anti-parasitic activity were also studied.
Submitter: Ina Poehner
Investigation: Pteridines as anti-kinetoplastid folate-pathway...
Assays: Correlation analysis between PTR1 and DHFR activities and anti-parasitic..., Correlation analysis between predicted ADMET properties and anti-parasit..., In silico ADMET data prediction, PAINS filtering
Snapshots: No snapshots
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.
Submitter: Ina Poehner
Investigation: Pteridines as anti-kinetoplastid folate-pathway...
Assays: Compound library preparation, Docking receptor preparation, Induced-fit docking studies, Rigid-body docking studies
Snapshots: No snapshots
Computational prediction of physicochemical and advanced descriptors related to ADME-Tox.
Submitter: Ina Poehner
Biological problem addressed: Model Analysis Type
Investigation: Pteridines as anti-kinetoplastid folate-pathway...
Organisms: No organisms
Models: No Models
SOPs: ADMET-property prediction SOP with QikProp
Data files: QikProp data for merged series compounds (serie..., QikProp data for pteridine in silico library, QikProp data for reference pteridines and N10-,...
Snapshots: No snapshots
Assessment of possible linear correlations between predicted ADMET descriptors from QikProp (Schrödinger, LLC, New York, NY) runs and experimentally determined activities against T. brucei brucei bloodstream forms with the help of a Python script.
Submitter: Ina Poehner
Biological problem addressed: Model Analysis Type
Investigation: Pteridines as anti-kinetoplastid folate-pathway...
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: Python module for calculating pairwise correlat...
Snapshots: No snapshots
Assessment of the possible multiple correlation between experimentally determined TbPTR1 and TbDHFR inhibition values and corresponding anti-parasitic activities against T. brucei brucei bloodstream forms using a Python script.
Submitter: Ina Poehner
Biological problem addressed: Model Analysis Type
Investigation: Pteridines as anti-kinetoplastid folate-pathway...
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: Python module for calculating trivariate statis...
Snapshots: No snapshots
In silico check and filtering for potential Pan-assay interference compounds.
Submitter: Ina Poehner
Biological problem addressed: Model Analysis Type
Investigation: Pteridines as anti-kinetoplastid folate-pathway...
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: FAF-Drugs4 PAINS filtering results and addition...
Snapshots: No snapshots
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
Compound data and computational prediction of physicochemical properties
Submitter: Pasquale Linciano
Biological problem addressed: Chemical characterization
Investigation: Phenotypic and machine learning approaches for ...
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: Predicted Physichcemical Properties for Ty-Box ..., SDF file of Ty-Box compounds, SMILES string for Ty-Box Library components
Snapshots: No snapshots
Submitter: Pasquale Linciano
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Phenotypic and machine learning approaches for ...
Organisms: No organisms
SOPs: No SOPs
Data files: Table S1a. Activity and toxicity profile of the..., Table S1b. In vitro early toxicity profiles (IC...
Snapshots: No snapshots
Submitter: Pasquale Linciano
Biological problem addressed: Chemical characterization
Investigation: Phenotypic and machine learning approaches for ...
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: NMR_spectra_of_the_secondary_hits, SDF file of Secondary Hits, SMILES string for Secondary Hits
Snapshots: No snapshots
Submitter: Pasquale Linciano
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Phenotypic and machine learning approaches for ...
Organisms: No organisms
SOPs: No SOPs
Data files: Table S10. Predicted according to the elaborate..., Table S9. Predicted antiparasitic activity acco...
Snapshots: No snapshots
Prepared multimeric tubulin protein receptors for docking studies, generated by alignment of two identical models of alpha-tubulin on alpha-tubulin chains of two neighboring protofilaments.
Submitter: Ina Poehner
Biological problem addressed: Model Analysis Type
Investigation: Antiparasitic dinitroaniline-ether phospholipid...
Organisms: Trypanosoma cruzi, Trypanosoma brucei, Leishmania donovani, Leishmania infantum
Models: No Models
SOPs: No SOPs
Data files: L. donovani alpha-tubulins from neighboring pro..., L. infantum alpha-tubulins from neighboring pro..., T. brucei alpha-tubulins from neighboring proto..., T. cruzi alpha-tubulins from neighboring protof...
Snapshots: No snapshots
Docking results of trifluraline and dinitroaniline-etherphospholipid hybrids against different kinetoplastid alpha-tubulin receptors with an induced fit docking routine. The docking protocol involves 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: Antiparasitic dinitroaniline-ether phospholipid...
Organisms: Trypanosoma cruzi, Trypanosoma brucei, Leishmania donovani, Leishmania infantum
Models: No Models
SOPs: SOP Induced fit docking
Data files: L. donovani alpha-tubulin M-loop top complexes ..., L. donovani alpha-tubulin MN-loop interface top..., L. donovani alpha-tubulin N-loop top complexes ..., L. infantum alpha-tubulin M-loop top complexes ..., L. infantum alpha-tubulin MN-loop interface top..., L. infantum alpha-tubulin N-loop top complexes ..., T. brucei alpha-tubulin M-loop top complexes fr..., T. brucei alpha-tubulin MN-loop interface top c..., T. brucei alpha-tubulin N-loop top complexes fr..., T. cruzi alpha-tubulin Blume site top complexes..., T. cruzi alpha-tubulin Consensus site top compl..., T. cruzi alpha-tubulin Consensus site top compl..., T. cruzi alpha-tubulin M-loop top complexes fro..., T. cruzi alpha-tubulin MN-loop interface top co..., T. cruzi alpha-tubulin N-loop top complexes fro..., T. cruzi alpha-tubulin pironetin site top compl..., T. cruzi alpha-tubulin top complexes from induc..., T. cruzi alpha-tubulin top complexes from induc..., T. cruzi alpha-tubulin top complexes from induc..., T. cruzi alpha-tubulin top complexes from induc..., T. cruzi alpha-tubulin top complexes from induc...
Snapshots: No snapshots
Alignments of various alpha-tubulin and beta-tubulin sequences from dinitroaniline-sensitive and dinitroaniline-resistant species. Sequences were retrieved from UniProt with the identifiers listed below and subjected to a multiple sequence alignment using ClustalOmega (ebi.ac.uk/Tools/msa/clustalo/; ClustalOmega webserver, last accessed 16-02-23):
alpha-tubulin:
- [dinitroaniline sensitive] T. cruzi - Q27352; T. brucei brucei - Q4GYY5; L. infantum - ...
Submitter: Ina Poehner
Biological problem addressed: Model Analysis Type
Investigation: Antiparasitic dinitroaniline-ether phospholipid...
Organisms: Trypanosoma cruzi, Trypanosoma brucei, Leishmania infantum, Leishmania donovani, Leishmania major
Models: No Models
SOPs: No SOPs
Data files: Multiple sequence alignment of selected alpha-t..., Multiple sequence alignment of selected beta-tu...
Snapshots: No snapshots
Creation of homology models of various tubulins from dinitroaniline-sensitive and -resistant species, and a comparative analysis of their electrostatic potential grids overall and in putative binding site regions using PIPSA (Protein Interaction Property Similarity Analysis).
Submitter: Ina Poehner
Biological problem addressed: Model Analysis Type
Investigation: Antiparasitic dinitroaniline-ether phospholipid...
Organisms: Trypanosoma cruzi, Trypanosoma brucei, Leishmania infantum, Leishmania donovani, Leishmania major
Models: No Models
SOPs: SOP Homology modeling of alpha-tubulins, SOP PIPSA, SOP tubulin protein preparation
Data files: Archive of PIPSA results, Archive of alpha-tubulin homology models
Snapshots: No snapshots
Submitter: Pasquale Linciano
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Phenotypic and machine learning approaches for ...
Organisms: No organisms
SOPs: No SOPs
Data files: Molecular Formula STRING, Molecular Formula STRING
Snapshots: No snapshots
Submitter: Pasquale Linciano
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Phenotypic and machine learning approaches for ...
Creator: Pasquale Linciano
Submitter: Pasquale Linciano
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Creator: Pasquale Linciano
Submitter: Pasquale Linciano
Investigations: Phenotypic and machine learning approaches for ...
Studies: Chemical characterization, and biological evalu...
Assays: Molecular Formula STRING excel
Creator: Pasquale Linciano
Submitter: Pasquale Linciano
Investigations: Phenotypic and machine learning approaches for ...
Studies: Chemical characterization, and biological evalu...
Assays: Molecular Formula STRING excel
Creator: Pasquale Linciano
Submitter: Pasquale Linciano
Investigations: Phenotypic and machine learning approaches for ...
Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compound, compound 1-9, docked to the resulting complex of reference compound trifluralin to the N-loop region of a Trypanosoma cruzi alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on the trifluralin reference compound (T. cruzi numbering).
The docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced ...
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Investigations: Antiparasitic dinitroaniline-ether phospholipid...
Studies: Docking studies of trifluraline and the dinitro...
Assays: Induced-fit docking studies
Zip-archive with top-ranked (by IFDScore) induced fit docking results for dinitroaniline etherphospholipid hybrid compounds 1-4 and 7-8 docked to the resulting complex of reference compound trifluralin in the pironetin site of a Trypanosoma cruzi alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on the trifluralin reference compound (T. cruzi numbering). No results were obtained for compounds 5, 6 and 9.
The docking results were obtained by Induced Fit docking with ...
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Investigations: Antiparasitic dinitroaniline-ether phospholipid...
Studies: Docking studies of trifluraline and the dinitro...
Assays: Induced-fit docking studies
Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compounds 1, 4, 8 and reference compound trifluraline, docked to the Consensus site (Delye, Mitra & Sept) of a Trypanosoma cruzi alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on site residue Thr239 (T. cruzi numbering).
The docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced Fit docking workflow ...
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Investigations: Antiparasitic dinitroaniline-ether phospholipid...
Studies: Docking studies of trifluraline and the dinitro...
Assays: Induced-fit docking studies
Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compounds 1, 2, 4, 8 and reference compound trifluraline, docked to the pironetin site of a Trypanosoma cruzi alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on site residue Leu238 (T. cruzi numbering).
The docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced Fit docking workflow (Schrödinger, LLC, ...
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Investigations: Antiparasitic dinitroaniline-ether phospholipid...
Studies: Docking studies of trifluraline and the dinitro...
Assays: Induced-fit docking studies
Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compounds 1-2, 4-5 and 7-8, docked to the resulting complex of reference compound trifluralin in the Blume site of a Trypanosoma cruzi alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on the trifluralin reference compound (T. cruzi numbering). No results were obtained for compounds 3, 6 and 9.
The docking results were obtained by Induced Fit docking ...
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Investigations: Antiparasitic dinitroaniline-ether phospholipid...
Studies: Docking studies of trifluraline and the dinitro...
Assays: Induced-fit docking studies
Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compounds 1-5 and 7-8, docked to the resulting complex of reference compound trifluralin in the Consensus site of a Trypanosoma cruzi alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on the trifluralin reference compound (T. cruzi numbering). No results were obtained for compounds 6 and 9.
The docking results were obtained by Induced Fit docking ...
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Investigations: Antiparasitic dinitroaniline-ether phospholipid...
Studies: Docking studies of trifluraline and the dinitro...
Assays: Induced-fit docking studies
Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compound, compound 1-9, docked to the resulting complex of reference compound trifluralin to the M-loop region of a Trypanosoma cruzi alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on the trifluralin reference compound (T. cruzi numbering).
The docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced ...
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Investigations: Antiparasitic dinitroaniline-ether phospholipid...
Studies: Docking studies of trifluraline and the dinitro...
Assays: Induced-fit docking studies
Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compound, compound 1-5 and 7-9, docked to the interface region between two neighboring alpha-tubulin monomers of Trypanosoma brucei; alpha-tubulin homology models were built on PDB-ID 5ubq and two monomeric models were aligned to neighboring protofilamentsof the original PDB-ID 5ubq to construct an interface-model receptor. The docking grid was centered on the M-loop region residue ...
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Investigations: Antiparasitic dinitroaniline-ether phospholipid...
Studies: Docking studies of trifluraline and the dinitro...
Assays: Induced-fit docking studies
Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compound, compound 1-9, and reference compound trifluraline, docked to the M-loop region of a Trypanosoma cruzi alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on the M-loop region residue Leu286 (T. cruzi numbering).
The docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced Fit docking workflow ...
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Investigations: Antiparasitic dinitroaniline-ether phospholipid...
Studies: Docking studies of trifluraline and the dinitro...
Assays: Induced-fit docking studies
Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compound, compound 1-9, and reference compound trifluralin, docked to the N-loop region of a Trypanosoma cruzi alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on the N-loop region residue Phe49 (T. cruzi numbering).
The docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced Fit docking workflow ...
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Investigations: Antiparasitic dinitroaniline-ether phospholipid...
Studies: Docking studies of trifluraline and the dinitro...
Assays: Induced-fit docking studies
Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compound, compound 1-5 and 7-9, docked to the interface region between two neighboring alpha-tubulin monomers of Trypanosoma cruzi; alpha-tubulin homology models were built on PDB-ID 5ubq and two monomeric models were aligned to neighboring protofilaments of the original PDB-ID 5ubq to construct an interface-model receptor. The docking grid was centered on the M-loop region residue ...
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Investigations: Antiparasitic dinitroaniline-ether phospholipid...
Studies: Docking studies of trifluraline and the dinitro...
Assays: Induced-fit docking studies
Zip-archive with top-ranked (by IFDScore) induced fit docking results for dinitroaniline etherphospholipid hybrid compounds 1, 2, 4, 5 and 9 and reference compound trifluraline, docked to the Blume site of a Trypanosoma cruzi alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on site residue Ala4 (T. cruzi numbering). No results were obtained with compounds 3 and 6-8.
The docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the ...
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Investigations: Antiparasitic dinitroaniline-ether phospholipid...
Studies: Docking studies of trifluraline and the dinitro...
Assays: Induced-fit docking studies
Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compounds 1, 4, 8 and reference compound trifluraline, docked to the Consensus site (Delye, Mitra & Sept) of a Trypanosoma cruzi alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on site residue Thr239 (T. cruzi numbering).
The docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced Fit docking workflow ...
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Investigations: Antiparasitic dinitroaniline-ether phospholipid...
Studies: Docking studies of trifluraline and the dinitro...
Assays: Induced-fit docking studies
Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compound, compound 1-9, docked to the M-loop region of a Leishmania infantum alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on the M-loop region residue Leu286 (T. cruzi numbering).
The 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 ...
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Investigations: Antiparasitic dinitroaniline-ether phospholipid...
Studies: Docking studies of trifluraline and the dinitro...
Assays: Induced-fit docking studies
Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compound, compound 1-9, docked to the N-loop region of a Leishmania infantum alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on the N-loop region residue Phe49 (T. cruzi numbering).
The 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 ...
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Investigations: Antiparasitic dinitroaniline-ether phospholipid...
Studies: Docking studies of trifluraline and the dinitro...
Assays: Induced-fit docking studies
Zip-archive with top-ranked (by IFDScore) induced fit docking results for each dinitroaniline etherphospholipid hybrid compound, compound 1-5 and 7-9, docked to the interface region between two neighboring alpha-tubulin monomers of Leishmania infantum; alpha-tubulin homology models were built on PDB-ID 5ubq and two monomeric models were aligned to neighboring protofilaments of the original PDB-ID 5ubq to construct an interface-model receptor. The docking grid was centered on the M-loop region ...
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Investigations: Antiparasitic dinitroaniline-ether phospholipid...
Studies: Docking studies of trifluraline and the dinitro...
Assays: Induced-fit docking studies
SOP describing application of the Induced fit docking workflow to Trypanosoma and Leishmania alpha-tubulin receptors.
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Investigations: Antiparasitic dinitroaniline-ether phospholipid...
Studies: Docking studies of trifluraline and the dinitro...
Assays: Induced-fit docking studies
General SOP for the webPIPSA workflow to study electrostatic potential differences of full alpha-tubulin homology models and various putative binding site regions
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
General SOP for alpha-tubulin homology model building
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
SOP for protein preparation steps performed for alpha-tubulin homology models (hydrogen addition, hydrogen bonding network optimization and energy minimization)
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
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 in silico ADME-Tox property prediction with QikProp for prepared pteridine ligands.
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Investigations: Pteridines as anti-kinetoplastid folate-pathway...
Studies: In silico property and correlation analysis
Assays: In silico ADMET data prediction
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
Abstract (Expand)
Authors: Marina Roussaki, George E. Magoulas, Theano Fotopoulou, Nuno Santarem, Emile Barrias, Ina Pöhner, Sara Luelmo, Pantelis Afroudakis, Kalliopi Georgikopoulou, Paloma Tejera Nevado, Julia Eick, Eugenia Bifeld, María J. Corral, María Dolores Jiménez-Antón, Bernhard Ellinger, Maria Kuzikov, Irini Fragiadaki, Effie Scoulica, Sheraz Gul, Joachim Clos, Kyriakos C. Prousis, Juan J. Torrado, José María Alunda, Rebecca C. Wade, Wanderley de Souza, Anabela Cordeiro da Silva, Theodora Calogeropoulou
Date Published: 1st Sep 2023
Publication Type: Journal
DOI: 10.1016/j.bioorg.2023.106615
Citation: Bioorganic Chemistry 138:106615
Abstract (Expand)
Authors: P. Linciano, G. Cullia, C. Borsari, M. Santucci, S. Ferrari, G. Witt, S. Gul, M. Kuzikov, B. Ellinger, N. Santarem, A. Cordeiro da Silva, P. Conti, M. L. Bolognesi, M. Roberti, F. Prati, F. Bartoccini, M. Retini, G. Piersanti, A. Cavalli, L. Goldoni, S. M. Bertozzi, F. Bertozzi, E. Brambilla, V. Rizzo, D. Piomelli, A. Pinto, T. Bandiera, M. P. Costi
Date Published: 1st Mar 2020
Publication Type: Journal
PubMed ID: 31982652
Citation: Eur J Med Chem. 2020 Mar 1;189:112047. doi: 10.1016/j.ejmech.2020.112047. Epub 2020 Jan 10.
Abstract (Expand)
Authors: D. Vanossi, M. Caselli, G. Pavesi, C. Borsari, P. Linciano, M. P. Costi, G. Ponterini
Date Published: 1st Sep 2019
Publication Type: Journal
PubMed ID: 30900698
Citation: Photochem Photobiol Sci. 2019 Sep 1;18(9):2270-2280. doi: 10.1039/c9pp00026g. Epub 2019 Mar 22.
Abstract
Authors: Venkatesan Jayaprakash, Daniele Castagnolo, Yusuf Özkay
Date Published: 15th Aug 2019
Publication Type: Book
Citation: CRC Press
Abstract (Expand)
Authors: G. Landi, P. Linciano, C. Borsari, C. P. Bertolacini, C. B. Moraes, A. Cordeiro-da-Silva, S. Gul, G. Witt, M. Kuzikov, M. P. Costi, C. Pozzi, S. Mangani
Date Published: 12th Jul 2019
Publication Type: Journal
PubMed ID: 31012301
Citation: ACS Infect Dis. 2019 Jul 12;5(7):1105-1114. doi: 10.1021/acsinfecdis.8b00358. Epub 2019 May 1.
Abstract (Expand)
Authors: P. Linciano, C. Pozzi, L. D. Iacono, F. di Pisa, G. Landi, A. Bonucci, S. Gul, M. Kuzikov, B. Ellinger, G. Witt, N. Santarem, C. Baptista, C. Franco, C. B. Moraes, W. Muller, U. Wittig, R. Luciani, A. Sesenna, A. Quotadamo, S. Ferrari, I. Pohner, A. Cordeiro-da-Silva, S. Mangani, L. Costantino, M. P. Costi
Date Published: 25th Apr 2019
Publication Type: Journal
PubMed ID: 30908048
Citation: J Med Chem. 2019 Apr 25;62(8):3989-4012. doi: 10.1021/acs.jmedchem.8b02021. Epub 2019 Apr 9.
Abstract (Expand)
Authors: C. Borsari, N. Santarem, S. Macedo, M. D. Jimenez-Anton, J. J. Torrado, A. I. Olias-Molero, M. J. Corral, A. Tait, S. Ferrari, L. Costantino, R. Luciani, G. Ponterini, S. Gul, M. Kuzikov, B. Ellinger, B. Behrens, J. Reinshagen, J. M. Alunda, A. Cordeiro-da-Silva, M. P. Costi
Date Published: 11th Apr 2019
Publication Type: Journal
PubMed ID: 30996791
Citation: ACS Med Chem Lett. 2019 Jan 29;10(4):528-533. doi: 10.1021/acsmedchemlett.8b00565. eCollection 2019 Apr 11.
Abstract (Expand)
Authors: C. B. Moraes, G. Witt, M. Kuzikov, B. Ellinger, T. Calogeropoulou, K. C. Prousis, S. Mangani, F. Di Pisa, G. Landi, L. D. Iacono, C. Pozzi, L. H. Freitas-Junior, B. Dos Santos Pascoalino, C. P. Bertolacini, B. Behrens, O. Keminer, J. Leu, M. Wolf, J. Reinshagen, A. Cordeiro-da-Silva, N. Santarem, A. Venturelli, S. Wrigley, D. Karunakaran, B. Kebede, I. Pohner, W. Muller, J. Panecka-Hofman, R. C. Wade, M. Fenske, J. Clos, J. M. Alunda, M. J. Corral, E. Uliassi, M. L. Bolognesi, P. Linciano, A. Quotadamo, S. Ferrari, M. Santucci, C. Borsari, M. P. Costi, S. Gul
Date Published: 21st Feb 2019
Publication Type: Journal
PubMed ID: 30784368
Citation: SLAS Discov. 2019 Mar;24(3):346-361. doi: 10.1177/2472555218823171.
Abstract (Expand)
Authors: M. D. Jimenez-Anton, E. Garcia-Calvo, C. Gutierrez, M. D. Escribano, N. Kayali, J. L. Luque-Garcia, A. I. Olias-Molero, M. J. Corral, M. P. Costi, J. J. Torrado, J. M. Alunda
Date Published: 30th Aug 2018
Publication Type: Journal
PubMed ID: 29883726
Citation: Eur J Pharm Sci. 2018 Aug 30;121:281-286. doi: 10.1016/j.ejps.2018.06.002. Epub 2018 Jun 5.
Abstract (Expand)
Authors: E. Uliassi, L. Piazzi, F. Belluti, A. Mazzanti, M. Kaiser, R. Brun, C. B. Moraes, L. H. Freitas-Junior, S. Gul, M. Kuzikov, B. Ellinger, C. Borsari, M. P. Costi, M. L. Bolognesi
Date Published: 6th Apr 2018
Publication Type: Journal
PubMed ID: 29451361
Citation: ChemMedChem. 2018 Apr 6;13(7):678-683. doi: 10.1002/cmdc.201700786. Epub 2018 Feb 16.
Abstract (Expand)
Authors: P. Linciano, C. B. Moraes, L. M. Alcantara, C. H. Franco, B. Pascoalino, L. H. Freitas-Junior, S. Macedo, N. Santarem, A. Cordeiro-da-Silva, S. Gul, G. Witt, M. Kuzikov, B. Ellinger, S. Ferrari, R. Luciani, A. Quotadamo, L. Costantino, M. P. Costi
Date Published: 25th Feb 2018
Publication Type: Journal
PubMed ID: 29407968
Citation: Eur J Med Chem. 2018 Feb 25;146:423-434. doi: 10.1016/j.ejmech.2018.01.043. Epub 2018 Jan 31.
Abstract
Authors: Chiara Borsari, Antonio Quotadamo, Stefania Ferrari, Alberto Venturelli, Anabela Cordeiro-da-Silva, Nuno Santarem, Maria Paola Costi
Date Published: 2018
Publication Type: InBook
DOI: 10.1016/bs.armc.2018.08.002
Citation: Neglected Diseases: Extensive Space for Modern Drug Discovery 51:39-95,Elsevier
Abstract (Expand)
Authors: F. C. Herrmann, N. Sivakumar, J. Jose, M. P. Costi, C. Pozzi, T. J. Schmidt
Date Published: 6th Dec 2017
Publication Type: Journal
PubMed ID: 29211037
Citation: Molecules. 2017 Dec 6;22(12). pii: molecules22122166. doi: 10.3390/molecules22122166.
Abstract (Expand)
Authors: E. Uliassi, G. Fiorani, R. L. Krauth-Siegel, C. Bergamini, R. Fato, G. Bianchini, J. Carlos Menendez, M. T. Molina, E. Lopez-Montero, F. Falchi, A. Cavalli, S. Gul, M. Kuzikov, B. Ellinger, G. Witt, C. B. Moraes, L. H. Freitas-Junior, C. Borsari, M. P. Costi, M. L. Bolognesi
Date Published: 1st Dec 2017
Publication Type: Journal
PubMed ID: 29031061
Citation: Eur J Med Chem. 2017 Dec 1;141:138-148. doi: 10.1016/j.ejmech.2017.10.005. Epub 2017 Oct 3.
Abstract (Expand)
Authors: P. Linciano, A. Dawson, I. Pohner, D. M. Costa, M. S. Sa, A. Cordeiro-da-Silva, R. Luciani, S. Gul, G. Witt, B. Ellinger, M. Kuzikov, P. Gribbon, J. Reinshagen, M. Wolf, B. Behrens, V. Hannaert, P. A. M. Michels, E. Nerini, C. Pozzi, F. di Pisa, G. Landi, N. Santarem, S. Ferrari, P. Saxena, S. Lazzari, G. Cannazza, L. H. Freitas-Junior, C. B. Moraes, B. S. Pascoalino, L. M. Alcantara, C. P. Bertolacini, V. Fontana, U. Wittig, W. Muller, R. C. Wade, W. N. Hunter, S. Mangani, L. Costantino, M. P. Costi
Date Published: 30th Sep 2017
Publication Type: Journal
PubMed ID: 28983525
Citation: ACS Omega. 2017 Sep 30;2(9):5666-5683. doi: 10.1021/acsomega.7b00473. Epub 2017 Sep 11.
Abstract (Expand)
Authors: J. Panecka-Hofman, I. Pohner, F. Spyrakis, T. Zeppelin, F. Di Pisa, L. Dello Iacono, A. Bonucci, A. Quotadamo, A. Venturelli, S. Mangani, M. P. Costi, R. C. Wade
Date Published: 25th Sep 2017
Publication Type: Journal
PubMed ID: 28939533
Citation: Biochim Biophys Acta Gen Subj. 2017 Dec;1861(12):3215-3230. doi: 10.1016/j.bbagen.2017.09.012. Epub 2017 Sep 20.
Abstract (Expand)
Authors: W. Jedwabny, J. Panecka-Hofman, E. Dyguda-Kazimierowicz, R. C. Wade, W. A. Sokalski
Date Published: 9th Jul 2017
Publication Type: Journal
PubMed ID: 28688090
Citation: J Comput Aided Mol Des. 2017 Aug;31(8):715-728. doi: 10.1007/s10822-017-0035-4. Epub 2017 Jul 7.
Abstract (Expand)
Authors: A. Stank, D. B. Kokh, M. Horn, E. Sizikova, R. Neil, J. Panecka, S. Richter, R. C. Wade
Date Published: 3rd Jul 2017
Publication Type: Journal
PubMed ID: 28431137
Citation: Nucleic Acids Res. 2017 Jul 3;45(W1):W325-W330. doi: 10.1093/nar/gkx277.
Abstract (Expand)
Authors: R. J. Pierce, J. MacDougall, R. Leurs, M. P. Costi
Date Published: 23rd May 2017
Publication Type: Journal
PubMed ID: 28529130
Citation: Trends Parasitol. 2017 Aug;33(8):581-583. doi: 10.1016/j.pt.2017.04.007. Epub 2017 May 18.
Abstract (Expand)
Authors: F. Di Pisa, G. Landi, L. Dello Iacono, C. Pozzi, C. Borsari, S. Ferrari, M. Santucci, N. Santarem, A. Cordeiro-da-Silva, C. B. Moraes, L. M. Alcantara, V. Fontana, L. H. Freitas-Junior, S. Gul, M. Kuzikov, B. Behrens, I. Pohner, R. C. Wade, M. P. Costi, S. Mangani
Date Published: 8th Mar 2017
Publication Type: Journal
PubMed ID: 28282886
Citation: Molecules. 2017 Mar 8;22(3). pii: molecules22030426. doi: 10.3390/molecules22030426.