Computational protocol: Enzyme catalysed Pictet-Spengler formation of chiral 1,1'-disubstituted- and spiro-tetrahydroisoquinolines

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Protocol publication

[…] Reaction intermediates were energy optimized using MM2 energy minimization (ChemBio3D, CambridgeSoft). The receptor used was subunit A from the TfNCS crystal structure 2VQ5 (residues 40–191, with ligands removed). Docking was performed using AutoDock Vina (exhaustiveness=10). Docking box parameters (x,y,z): center (22.27, 21.16,-27.51); size (23.56, 17.37, 21.78). The exception to the method was the iminium intermediate of 17—no MM2 minimization was conducted and modified docking box parameters were used: center (22.15, 21.15, −27.94), size (16.61, 16.56, 13.43). For each docking calculation, the nine clusters with the lowest free energy were visualized and their structure analysed. The mechanistically relevant binding modes (corresponding to the dopamine-first mechanism) were selected, and their ranking and predicted affinity was recorded (). Figures of docking results were prepared using UCSF Chimera. […]

Pipeline specifications

Software tools AutoDock Vina, UCSF Chimera
Application Protein interaction analysis
Chemicals Dopamine, Ketones