Schrodinger suite 2009

To predict the PA docking poses, we performed docking simulations with Glide^{41 (link)} in Schrodinger Suite 2009 (Schrödinger, LLC, NY, USA). The binding poses for ornithine, putrescine, spermidine, and spermine were generated in Glide SP (standard precision) mode. The binding free energy (ΔG) for each pose was estimated with the molecular mechanics energies combined with the generalized Born and surface area continuum solvation (MM/GBSA) method using Prime^{42 (link)} in Schrodinger Suite 2009 (Schrödinger, LLC). For each ligand, we selected binding poses with the lowest MM/GBSA score. In the docking simulations, we took the LSD1 protein coordinate (PDB ID: 2H94) from the Protein Data Bank (PDB).

The three-dimensional (3D) structure models of single-chain variable-fragment antibodies (scFvs) were built via homology modeling using the Schrodinger Suite 2009 (Schrödinger, LLC, New York, NY, USA). The Gromacs program, a versatile package in Schrodinger software to perform molecular dynamics, was used to optimize the structure of m5E12scFv in silico and make it closer to the conformation in the natural environment Subsequently, the qualities of the constructed models were evaluated by Ramachandran Plot within Discovery Studio software v2.5 (Accelrys Software Inc., San Diego, CA, USA). Root mean square deviation (RMSD) is a statistic to assess the deviation degree between resulting and target conformations, which here was used to estimate the model deviation of the constructed models. Thus, the RMSD values of the main chain atoms (C-α, C, N, O) in CDRs between the models were also calculated by Molecular Operating Environment (MOE) software (Chemical Computing Group, Montreal, Quebec, Canada).