Tag: Noncovalent Interactions

Controlling Intramolecular Interactions in the Design of Selective, High-Affinity, Ligands for the CREBBP Bromodomain.

Brand, M.; Clayton, J.; Moroglu, M. ; Schiedel, M.; Picaud, S.; Bluck, J. P.; Skwarska,A.; Chan, A. K. N.; Laurin, C. M. C.; Scorah, A. R.; See, L.; Rooney, T. P. C.; Fedorov, O.; Perell, G.; Cortopassi, W. A.; Christensen, K. E.; Cooper, R. I.; Paton, R. S.; Pomerantz, W. C. K.; Biggin, P. C.; Hammond, E. M.; Filippakopoulos, P.; Conway, S. J. J. Med. Chem. 2021, 64, 10102–10123

wSterimol.

A program to generate Boltzmann-weighted Sterimol Steric Parameters for conformationally-flexible substituents that integrates with PyMol. The program contains an automated computational workflow which computes multidimensional Sterimol parameters. For flexible molecules or substituents, the program will generate & optimize a conformational ensemble, and produce Boltzmann-weighted Sterimol parameters. It has been developed as a PyMol plugin and can be run from within the graphical user interface. The wSterimol code is described in more detail in Conformational Effects on Physical-Organic Descriptors – the Case of Sterimol Steric Parameters

[Zenodo] [GitHub]
Comparison of Molecular Recognition of Trimethyllysine and Trimethylthialysine by Epigenetic Reader Proteins.

Hintzen, J. C. J.; Poater, J.; Kumar, K.; Al Temimi, A. H. K.; Pieters, B. J. G. E.; Paton, R. S.; Bickelhaupt, F. M.; Mecinović, J. Molecules 2020, 25, 1918

Mechanism of biomolecular recognition of trimethyllysine by the fluorinated aromatic cage of KDM5A PHD3 finger.

Pieters, B. J. G. E., Wuts, M. H. M., Poater, J.; Kumar, K.; White, P. B.; Kamps, J. J. A. G.; Sherman, W; Pruijn, G. J. M.; Paton, R. S.; Beuming, T.; Bickelhaupt, F. M.; Mecinović, J. Commun. Chem. 2020, 3, 69

Cation–Pi Interactions in Protein-Ligand Binding: Theory and Data-Mining Reveal Different Roles for Lysine and Arginine.

Kumar, K.; Woo, S. M.; Siu, T.; Cortopassi, W. A.; Duarte, F.; Paton, R. S. Chem. Sci. 2018, 9, 2655–2665

A Series of Potent CREBBP Bromodomain Ligands Reveals an Induced Fit Pocket Stabilized by a Cation-Pi Interaction.

Rooney, T. P. C.; Filippakopoulos, P.; Fedorov, O.; Picaud, S.; Cortopassi, W. A.; Hay, D. A.; Martin, S.; Tumber, A.; Rogers, C. M.; Philpott, M.; Wang, M.; Thompson, A. L.; Heightman, T. D.; Pryde, D. C.; Cook, A.; Paton, R. S.; Müller-Knapp, S.; Knapp, S.; Brennan, P. E.; Conway, S. J. Angew. Chem. Int. Ed. 2014, 126, 6240–6244

Dissecting Non-Covalent Interactions In Oxazaborolidinium Catalyzed Cycloadditions of Maleimides.

Paton, R. S. Org. Biomol. Chem. 2014, 12, 1717–1720

Hydrogen Bonding and Pi-Stacking: How Reliable Are Force Fields? A Critical Evaluation of Force Field Descriptions of Non-Bonded Interactions.

Paton, R. S.; Goodman, J. M. J. Chem. Inf. Model. 2009, 49, 944–955

Tag: Noncovalent Interactions

Controlling Intramolecular Interactions in the Design of Selective, High-Affinity, Ligands for the CREBBP Bromodomain.

Brand, M.; Clayton, J.; Moroglu, M. ; Schiedel, M.; Picaud, S.; Bluck, J. P.; Skwarska,A.; Chan, A. K. N.; Laurin, C. M. C.; Scorah, A. R.; See, L.; Rooney, T. P. C.; Fedorov, O.; Perell, G.; Cortopassi, W. A.; Christensen, K. E.; Cooper, R. I.; Paton, R. S.; Pomerantz, W. C. K.; Biggin, P. C.; Hammond, E. M.; Filippakopoulos, P.; Conway, S. J. J. Med. Chem. 2021, 64, 10102–10123

wSterimol.

A program to generate Boltzmann-weighted Sterimol Steric Parameters for conformationally-flexible substituents that integrates with PyMol. The program contains an automated computational workflow which computes multidimensional Sterimol parameters. For flexible molecules or substituents, the program will generate & optimize a conformational ensemble, and produce Boltzmann-weighted Sterimol parameters. It has been developed as a PyMol plugin and can be run from within the graphical user interface. The wSterimol code is described in more detail in Conformational Effects on Physical-Organic Descriptors – the Case of Sterimol Steric Parameters

[Zenodo] [GitHub]
Comparison of Molecular Recognition of Trimethyllysine and Trimethylthialysine by Epigenetic Reader Proteins.

Hintzen, J. C. J.; Poater, J.; Kumar, K.; Al Temimi, A. H. K.; Pieters, B. J. G. E.; Paton, R. S.; Bickelhaupt, F. M.; Mecinović, J. Molecules 2020, 25, 1918

Mechanism of biomolecular recognition of trimethyllysine by the fluorinated aromatic cage of KDM5A PHD3 finger.

Pieters, B. J. G. E., Wuts, M. H. M., Poater, J.; Kumar, K.; White, P. B.; Kamps, J. J. A. G.; Sherman, W; Pruijn, G. J. M.; Paton, R. S.; Beuming, T.; Bickelhaupt, F. M.; Mecinović, J. Commun. Chem. 2020, 3, 69

Cation–Pi Interactions in Protein-Ligand Binding: Theory and Data-Mining Reveal Different Roles for Lysine and Arginine.

Kumar, K.; Woo, S. M.; Siu, T.; Cortopassi, W. A.; Duarte, F.; Paton, R. S. Chem. Sci. 2018, 9, 2655–2665

A Series of Potent CREBBP Bromodomain Ligands Reveals an Induced Fit Pocket Stabilized by a Cation-Pi Interaction.

Rooney, T. P. C.; Filippakopoulos, P.; Fedorov, O.; Picaud, S.; Cortopassi, W. A.; Hay, D. A.; Martin, S.; Tumber, A.; Rogers, C. M.; Philpott, M.; Wang, M.; Thompson, A. L.; Heightman, T. D.; Pryde, D. C.; Cook, A.; Paton, R. S.; Müller-Knapp, S.; Knapp, S.; Brennan, P. E.; Conway, S. J. Angew. Chem. Int. Ed. 2014, 126, 6240–6244

Dissecting Non-Covalent Interactions In Oxazaborolidinium Catalyzed Cycloadditions of Maleimides.

Paton, R. S. Org. Biomol. Chem. 2014, 12, 1717–1720

Hydrogen Bonding and Pi-Stacking: How Reliable Are Force Fields? A Critical Evaluation of Force Field Descriptions of Non-Bonded Interactions.

Paton, R. S.; Goodman, J. M. J. Chem. Inf. Model. 2009, 49, 944–955