Docking studies of trifluraline and the dinitroaniline-etherphospholipid hybrids against kinetoplastid alpha-tubulin
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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.
SEEK ID: https://fairdomhub.org/studies/1132
Antiparasitic dinitroaniline-ether phospholipid hybrids
Projects: NMTrypI - New Medicines for Trypanosomatidic Infections
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Created: 16th Feb 2023 at 10:55
Last updated: 24th Apr 2023 at 13:36
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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
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
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...
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...
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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 Trypanosoma brucei 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
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 Trypanosoma brucei 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
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 the M-loop region of a Leishmania donovani alpha-tubulin homology model built on PDB-ID 5ubq. The docking grid was centered on the M-loop region residue Leu286 (T. cruzi numbering). No result was obtained for compound 6.
The docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced Fit docking ...
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
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 donovani 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
SOP describing application of the Induced fit docking workflow to Trypanosoma and Leishmania alpha-tubulin receptors.
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
