Exploring non-toxic co-evolutionary docking

27 September 2023, Version 1
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

Drug-spaces of nine crystallographic protein / ligand models have been comparatively explored by including Toxicity Risk assessment during computational co-evolution. Tens of thousands children were randomly generated from parent ligands and iteratively selected for higher affinities, increased specificities and low Toxicity Risk using DataWarrior / Build Evolutionary Library algorithms, mimicking natural evolution. Only a few hours of co-evolution increased ~ 2-fold the numbers of non-toxic children. Top-leads predicted drug-like properties, nanoMolar affinities (confirmed by AutoDockVina), higher specificities, absence of known toxicities, and similar docking to their initial binding cavities. Tables were provided with multi-threshold-adjustable filters for alternative in silico explorations of this new "co-evolutionary docking" tool.

Keywords

co-evolutionary docking
novel antibiotics
anticancerigens
antidiabetes
rodenticides
heart diseases
antifibrosis

Supplementary materials

Title
Description
Actions
Title
FtsZ.dwar
Description
These *.dwar DW tables contain 100 DW top-leads selected as NTN children corresponding to nine target / parent pairs. They are provided with threshold slider-filters to their DW and ADV docking-scores, Molecular weights and clogP properties. By moving the slider-filters located at the right of the DW Table, the best fitting children to particular threshold combinations could be selected and further studied. Each *.dwar file can be opened by downloading DW free access at https://openmolecules.org/datawarrior/download.htm. The *.dwar files can be also saved as special *.sdf (vs3) files, maintaining their 3D protein cavity docked to children conformers so that they can be opened in PyMol using its split-states command (more details at the DW forum from February 3th, 2023, https://openmolecules.org/forum/index.php?t=msg&th=632&start=0&).
Actions
Title
Hsp47.dwar
Description
These *.dwar DW tables contain 100 DW top-leads selected as NTN children corresponding to nine target / parent pairs. They are provided with threshold slider-filters to their DW and ADV docking-scores, Molecular weights and clogP properties. By moving the slider-filters located at the right of the DW Table, the best fitting children to particular threshold combinations could be selected and further studied. Each *.dwar file can be opened by downloading DW free access at https://openmolecules.org/datawarrior/download.htm. The *.dwar files can be also saved as special *.sdf (vs3) files, maintaining their 3D protein cavity docked to children conformers so that they can be opened in PyMol using its split-states command (more details at the DW forum from February 3th, 2023, https://openmolecules.org/forum/index.php?t=msg&th=632&start=0&).
Actions
Title
LolEC.dwar
Description
These *.dwar DW tables contain 100 DW top-leads selected as NTN children corresponding to nine target / parent pairs. They are provided with threshold slider-filters to their DW and ADV docking-scores, Molecular weights and clogP properties. By moving the slider-filters located at the right of the DW Table, the best fitting children to particular threshold combinations could be selected and further studied. Each *.dwar file can be opened by downloading DW free access at https://openmolecules.org/datawarrior/download.htm. The *.dwar files can be also saved as special *.sdf (vs3) files, maintaining their 3D protein cavity docked to children conformers so that they can be opened in PyMol using its split-states command (more details at the DW forum from February 3th, 2023, https://openmolecules.org/forum/index.php?t=msg&th=632&start=0&).
Actions
Title
Nkcc1.dwar
Description
These *.dwar DW tables contain 100 DW top-leads selected as NTN children corresponding to nine target / parent pairs. They are provided with threshold slider-filters to their DW and ADV docking-scores, Molecular weights and clogP properties. By moving the slider-filters located at the right of the DW Table, the best fitting children to particular threshold combinations could be selected and further studied. Each *.dwar file can be opened by downloading DW free access at https://openmolecules.org/datawarrior/download.htm. The *.dwar files can be also saved as special *.sdf (vs3) files, maintaining their 3D protein cavity docked to children conformers so that they can be opened in PyMol using its split-states command (more details at the DW forum from February 3th, 2023, https://openmolecules.org/forum/index.php?t=msg&th=632&start=0&).
Actions
Title
P2x3r.dwar
Description
These *.dwar DW tables contain 100 DW top-leads selected as NTN children corresponding to nine target / parent pairs. They are provided with threshold slider-filters to their DW and ADV docking-scores, Molecular weights and clogP properties. By moving the slider-filters located at the right of the DW Table, the best fitting children to particular threshold combinations could be selected and further studied. Each *.dwar file can be opened by downloading DW free access at https://openmolecules.org/datawarrior/download.htm. The *.dwar files can be also saved as special *.sdf (vs3) files, maintaining their 3D protein cavity docked to children conformers so that they can be opened in PyMol using its split-states command (more details at the DW forum from February 3th, 2023, https://openmolecules.org/forum/index.php?t=msg&th=632&start=0&).
Actions
Title
Sglt1.dwar
Description
These *.dwar DW tables contain 100 DW top-leads selected as NTN children corresponding to nine target / parent pairs. They are provided with threshold slider-filters to their DW and ADV docking-scores, Molecular weights and clogP properties. By moving the slider-filters located at the right of the DW Table, the best fitting children to particular threshold combinations could be selected and further studied. Each *.dwar file can be opened by downloading DW free access at https://openmolecules.org/datawarrior/download.htm. The *.dwar files can be also saved as special *.sdf (vs3) files, maintaining their 3D protein cavity docked to children conformers so that they can be opened in PyMol using its split-states command (more details at the DW forum from February 3th, 2023, https://openmolecules.org/forum/index.php?t=msg&th=632&start=0&).
Actions
Title
Sglt2.dwar
Description
These *.dwar DW tables contain 100 DW top-leads selected as NTN children corresponding to nine target / parent pairs. They are provided with threshold slider-filters to their DW and ADV docking-scores, Molecular weights and clogP properties. By moving the slider-filters located at the right of the DW Table, the best fitting children to particular threshold combinations could be selected and further studied. Each *.dwar file can be opened by downloading DW free access at https://openmolecules.org/datawarrior/download.htm. The *.dwar files can be also saved as special *.sdf (vs3) files, maintaining their 3D protein cavity docked to children conformers so that they can be opened in PyMol using its split-states command (more details at the DW forum from February 3th, 2023, https://openmolecules.org/forum/index.php?t=msg&th=632&start=0&).
Actions
Title
Vegfr.dwar
Description
These *.dwar DW tables contain 100 DW top-leads selected as NTN children corresponding to nine target / parent pairs. They are provided with threshold slider-filters to their DW and ADV docking-scores, Molecular weights and clogP properties. By moving the slider-filters located at the right of the DW Table, the best fitting children to particular threshold combinations could be selected and further studied. Each *.dwar file can be opened by downloading DW free access at https://openmolecules.org/datawarrior/download.htm. The *.dwar files can be also saved as special *.sdf (vs3) files, maintaining their 3D protein cavity docked to children conformers so that they can be opened in PyMol using its split-states command (more details at the DW forum from February 3th, 2023, https://openmolecules.org/forum/index.php?t=msg&th=632&start=0&).
Actions
Title
Vkorc1.dwar
Description
These *.dwar DW tables contain 100 DW top-leads selected as NTN children corresponding to nine target / parent pairs. They are provided with threshold slider-filters to their DW and ADV docking-scores, Molecular weights and clogP properties. By moving the slider-filters located at the right of the DW Table, the best fitting children to particular threshold combinations could be selected and further studied. Each *.dwar file can be opened by downloading DW free access at https://openmolecules.org/datawarrior/download.htm. The *.dwar files can be also saved as special *.sdf (vs3) files, maintaining their 3D protein cavity docked to children conformers so that they can be opened in PyMol using its split-states command (more details at the DW forum from February 3th, 2023, https://openmolecules.org/forum/index.php?t=msg&th=632&start=0&).
Actions
Title
NoToxiNasty.dwam
Description
- NoToxiNasty.dwam. A DW macro *.dwam file developed to save, label and eliminate any children molecules co-evolutionary generated by the DW-BEL containing Toxicity (Mutagenesis, Tumorigenicity, Reproductive Interference, Irritant) and/or Nasty Functions (see Nasty_functions.dwar). This macro labels and retains the children having no detectable risks. The macro uses *.sdf or *.dwar files as inputs, user-renamed the input *.dwar file and renamed and saved the corresponding NTN *.dwar and toxic-labelled *.sdf files (they require filtering outside DW). More than ~ 3000 traded drugs were employed as low toxicity example data (https://github.com/thsa/datawarrior/blob/master/src/html/ properties/properties.html. Additional information on DW Toxicity can be found at the Registry of Toxic Effects of Chemical Substances (RTECS data base) (https://www.cdc.gov/niosh/docs/97-119/default.html).
Actions
Title
Nasty_functions.dwar
Description
- Nasty_functions.dwar. List of previously defined DW Nasty functions of small chemical fragments having known physiological interference problems, kindly supplied by Dr.T.Sander of DW (https://openmolecules.org/forum/ index.php?t=msg&th=662&start=0&).
Actions
Title
FtsZ.pse
Description
The DW-BEL best and 9 additional top-lead children complexes with their corresponding protein targets can be visualized in PyMol vs2.5.3. by opening their corresponding *.pse files (best top-lead children compared to initial ligands represented in their target proteins in Figure S3).
Actions
Title
Hdp47.pse
Description
The DW-BEL best and 9 additional top-lead children complexes with their corresponding protein targets can be visualized in PyMol vs2.5.3. by opening their corresponding *.pse files (best top-lead children compared to initial ligands represented in their target proteins in Figure S3).
Actions
Title
LolCE.pse
Description
The DW-BEL best and 9 additional top-lead children complexes with their corresponding protein targets can be visualized in PyMol vs2.5.3. by opening their corresponding *.pse files (best top-lead children compared to initial ligands represented in their target proteins in Figure S3).
Actions
Title
Nkcc1.pse
Description
The DW-BEL best and 9 additional top-lead children complexes with their corresponding protein targets can be visualized in PyMol vs2.5.3. by opening their corresponding *.pse files (best top-lead children compared to initial ligands represented in their target proteins in Figure S3).
Actions
Title
P2x3r.pse
Description
The DW-BEL best and 9 additional top-lead children complexes with their corresponding protein targets can be visualized in PyMol vs2.5.3. by opening their corresponding *.pse files (best top-lead children compared to initial ligands represented in their target proteins in Figure S3).
Actions
Title
Sglt1.pse
Description
The DW-BEL best and 9 additional top-lead children complexes with their corresponding protein targets can be visualized in PyMol vs2.5.3. by opening their corresponding *.pse files (best top-lead children compared to initial ligands represented in their target proteins in Figure S3).
Actions
Title
Sglt2.pse
Description
The DW-BEL best and 9 additional top-lead children complexes with their corresponding protein targets can be visualized in PyMol vs2.5.3. by opening their corresponding *.pse files (best top-lead children compared to initial ligands represented in their target proteins in Figure S3).
Actions
Title
Vegfr.pse
Description
The DW-BEL best and 9 additional top-lead children complexes with their corresponding protein targets can be visualized in PyMol vs2.5.3. by opening their corresponding *.pse files (best top-lead children compared to initial ligands represented in their target proteins in Figure S3).
Actions
Title
Vkorc1.pse
Description
The DW-BEL best and 9 additional top-lead children complexes with their corresponding protein targets can be visualized in PyMol vs2.5.3. by opening their corresponding *.pse files (best top-lead children compared to initial ligands represented in their target proteins in Figure S3).
Actions

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