Problems with generating the combinatorial pharmacophore library

[josegomide]

Dear David,

I hope this message finds you well.

I am encountering problems while generating the combinatorial pharmacophore library. I have successfully acquired the super_pharmacophore.pml file using the trajectory_pharmacophore_combo.cfg and analyzed the pharmacophore features with LigandScout (the image bellow represents the pharmacophore points selected after the ligandscout analysis. 16 points in total):

However, when I run the command pyrod library.cfg, I receive the following message:

"(pyrod) lammol@lammol:~/pyrod/nsp2$ pyrod library.cfg
/home/lammol/miniconda3/envs/pyrod/lib/python3.8/site-packages/Bio/Application/init.py:40: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.
Due to the ongoing maintenance burden of keeping command line application wrappers up to date, we have decided to deprecate and eventually remove these modules. We instead now recommend building your command line and invoking it directly with the subprocess module.
warnings.warn(

                                                                                  |X|                                                                                        
                                                                                   )__)                                                                                      
                                                                              ))  )__) ))                                                                                  
                                                                             )_) )_)))                                                                                 
                                                                        _    )_)_))_)                                                                                
                                                                         \---_|_/|_|_-----                                                                           
                                                                 ~~~\   oo  oo  oo  oo  /~~~                                                                     
                                                                   ~~~~~~     ~~    ~~                                                                       
                                                                     ~~    PyRod v0.7.5     ~~~                                                                          
                                                                            ~~     ~    ~~~                                                                              
                                                                  Tracing water molecules in molecular dynamics simulations.                                                                              

Starting library generation.
The given pharmacophore contains incomplete hydrogen bonding features. Feature type is hd2 but only one interaction partner was found. Either create a new pharmacophore without splitting ha2, hd2 and hda features or set pyrod pharmacophore to false."

I noticed that the super_pharmacophore obtained by the trajectory_pharmacophore_combo.cfg did not return any acceptor points, making it impossible to create a new pharmacophore without splitting the ha2, hd2, and hda features. The only option left was to set the pharmacophore option to false, but, after modifying it, pyrod library.cfg returned:

"(pyrod) lammol@lammol:~/pyrod/nsp2$ pyrod library.cfg
/home/lammol/miniconda3/envs/pyrod/lib/python3.8/site-packages/Bio/Application/init.py:40: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.
Due to the ongoing maintenance burden of keeping command line application wrappers up to date, we have decided to deprecate and eventually remove these modules. We instead now recommend building your command line and invoking it directly with the subprocess module.
warnings.warn(

                                                                                  |X|                                                                                        
                                                                                   )__)                                                                                      
                                                                              ))  )__) ))                                                                                  
                                                                             )_) )_)))                                                                                 
                                                                        _    )_)_))_)                                                                                
                                                                         \---_|_/|_|_-----                                                                           
                                                                 ~~~\   oo  oo  oo  oo  /~~~                                                                     
                                                                   ~~~~~~     ~~    ~~                                                                       
                                                                     ~~    PyRod v0.7.5     ~~~                                                                          
                                                                            ~~     ~    ~~~                                                                              
                                                                  Tracing water molecules in molecular dynamics simulations.                                                                              

Starting library generation.
0 pharmacophores will be written, taking about 0 B of space."
As a result, the library.cfg file does not produce any output containing the combinatorial pharmacophore library. The only file generated is template_pharmacophore.pml, which is identical to the input pharmacophore file processed after the LigandScout analysis.

Could you please advise why this is happening and how I might resolve this issue?

Thank you for your time and assistance.

Best regards,
José Gomide

[schallerdavid]

Dear José,

thanks for reaching out and your interest in using PyRod!

I noticed that the super_pharmacophore obtained by the trajectory_pharmacophore_combo.cfg did not return any acceptor points, making it impossible to create a new pharmacophore without splitting the ha2, hd2, and hda features.

This is quite worrying, since every protein binding pocket should allow for some acceptor points in the default super_pharmacophore.pml generated by PyRod. Do you have more details on the MD software/force field being used or was there recently a LigandScout update? Please be aware that PyRod was developed years ago and software updates may lead to incompatibilities at some point.

Could you please advise why this is happening and how I might resolve this issue?

I could imagine that the library.cfg contains settings that prevent generation of any valid pharmacophore. Could you paste the content here?

Best regards,
David

[josegomide]

Dear David,

I am rerunning the trajectory-pharmacophore combination with a larger grid to verify if the socket truly lacks acceptor regions. As requested, the current library.cfg settings I am using are shown below:

###############################################################################

This is a config-file for PyRod. Please do not modify the original

version. Create and change a new copy for each run to avoid errors.

###############################################################################

[directory]
###############################################################################

Section for defining the path to the output directory. If no path is

specified, the output will be saved in a directory named pyrod in the

current working directory.

###############################################################################
directory:/home/lammol/pyrod/test2/

[library parameters]
###############################################################################

Section for defining parameters for pharmacophore library generation

based on an input pharmacophore. Currently only pml and pdb-like

pharmacophores (from pyrod) are supported for in- and output. Mandatory

features will be present in each pharmacophore. Optional features will

be added in a combinatorial fashion based on specified parameters

below. If the pharmacophore was not generated by pyrod set pyrod

pharmacophore false.

###############################################################################
pharmacophore path: /home/lammol/pyrod/test2/pharmacophores/super_pharmacophore.pml
output format: pml
minimal features: 3
maximal features: 6
minimal hydrogen bonds: 1
maximal hydrogen bonds: 4
minimal hydrophobic interactions: 1
maximal hydrophobic interactions: 3
minimal aromatic interactions: 0
maximal aromatic interactions: 2
minimal ionizable interactions: 0
maximal ionizable interactions: 1
library name: library
pyrod pharmacophore: true

The pharmacophore generated from the superpharmacophore analysis using LigandScout includes 7 hydrophobic interactions, 1 positive ionizable region, 2 aromatic rings, and 4 hydrogen bond donors. This pharmacophore serves as the input for the library configuration file.

Best regards,
José