Maestro suite

MD simulations (60 ns) were performed using Schrödinger (Schrödinger, New York, NY, USA) Desmond software [37 ,38 ]. The starting L–R complexes selected by molecular docking analysis in our previous study [8 (link)] were immersed into a phosphatidylcholine (POPC, 300 K) membrane bilayer and positioned using the PPM web server (http://opm.phar.umich.edu/server.php, accessed 05-01-2019) [39 (link)]. Each system was solvated by water molecules described by the TIP4P potential, and the OPLS3 force field parameters were used for all atoms. Additionally, 0.15 M NaCl was added to mimic the ionic strength inside the cell. All simulations were performed on GPU processors, repeating each system three times. Only one trajectory was used to illustrate the results, showing the lowest variation of XB distance and angle values during the simulation. The output MD trajectories were hierarchically clustered into 10 clusters using trajectory analysis tools from the Maestro Schrödinger Suite. For further analysis, the most populated complex was used. Based on obtained trajectories, the mean geometrical parameters of the selected halogen bonds (distance and angle) were calculated using the Simulation Event Analysis tool in Maestro Schrödinger Suite and further analyzed using in-house scripts written in R.

The crystal structures of FP-2 and FP-3 were obtained from the protein databank (PDB) with the IDs 3BPF and 3BPM, respectively. Co-crystallized water molecules and other heteroatoms were removed, and Hydrogen atoms were added to the structures using the H++ server (Gordon et al., 2005 (link)). The 3D coordinates of the compounds QOD and ICD were collected from the MolPort database in SDF format, protonated, and converted to PDB format using the Schrodinger Maestro suite (Schrödinger, 2022 ). The cleaned-protonated proteins and ligands structures were then used to generate topology in the amber forcefield using AmberTools22 (Case et al., 2017 ). In each case, the ligand (i.e., QOD or ICD) is placed in a random position away from the protein (FP-2 or FP-3) in a cubic simulation box (Figure 2B) and solvated in the TIP3P water model (Price and Brooks, 2004 (link)). The systems were further neutralized with 150 mM NaCl, and ligand parameters were defined using GAFF forcefield (Wang et al., 2004 (link)).

A receptor grid was created around the protein binding residues
(W86, G121, G122, Y124, E202, S203, A204, W236, F295, F297
Y337, F338, and H447). The reference ligand were sketched by
Marvin sketch software and ligand were prepared in LigPrepmodule
of Schrodinger suite, which generates all possible states
with the neutral pH and generated ionized and tautomer state for
the ligands. After protein preparation, Grid generation and
LigPrep preparation, ligands were used for molecular docking
suite Glide version 9.2 in Schrodinger maestro suite with the
extra-precision mode for docking [23 (link)].