Design Hub Plugin Catalogue

This page describes plugins available in Design Hub subscription services.

Phys-chem

Name	Description	Example	Spreadsheet results
Calculated Properties	Calculates molecular descriptors and basic med-chem properties. Calculations are performed using Chemaxon calculators Lipophilicity, pKa and solubility are key descriptors in drug design, important to both pharmacokinetic exposure (ADME) and pharmacodynamic response (effect on target and off-targets). Use these calculations for instance to filter out design ideas with risk of poor solubility, increase the fraction of sp3 carbons to "escape flatland" or apply your own Lipinski type of rules on your compound libraries.		Mass: 426.44 cLogP: 0.76 TPSA: 121.8 Solubility: -5.4 H-bond acceptors: 6 H-bond donors: 3 pKa (str. basic): -3.77 pKa (str. acidic): -2.21
Topological descriptors	Calculates simple molecular descriptors. Calculations are performed using Chemaxon calculators Lipophilicity, pKa and solubility are key descriptors in drug design, important to both pharmacokinetic exposure (ADME) and pharmacodynamic response (effect on target and off-targets). Use these calculations for instance to filter out design ideas with risk of poor solubility, increase the fraction of sp3 carbons to "escape flatland" or apply your own Lipinski type of rules on your compound libraries.		Heavy atom count: 13 Aromatic ring count: 1 Rotatable bond count: 3 FSP3: 0.11
Sweet Spot	Displays a gradient colored scatter plot of mass and logP values showing the sweet spot (for obtaining oral bioavailability for your drug) Calculations are performed using Chemaxon calculators Citation: Hann, M., Keserü, G. Finding the sweet spot: the role of nature and nurture in medicinal chemistry. Nat Rev Drug Discov 11, 355–365 (2012).
cLogD	Calculates and displays a pH-logD chart. Calculations are performed using Chemaxon calculators Lipophilicity is usually measured by the octanol/water partitioning coefficient. Highly lipophilic compounds have an increased risk of being poorly soluble, quickly metabolized and promiscuous binders, whereas more polar compounds often are less permeable. Thus, lipophilicity is an important parameter for all ADMET properties of a drug, and a rule of thumb for an orally available drug is to keep it between 1-3, however the optimal interval can be different for different chemical series.		pH1.5: 4.1088 pH5.0: 5.0327 pH6.5: 5.1607 pH7.4: 5.1652

ADMET

Name	Description	Example	Spreadsheet results
CNS MPO	Calculates and displays a radar plot of Pfizer CNS MPO scoring. Calculations are performed using Chemaxon calculators Citation: ACS Chem. Neurosci. 2010, 1, 6, 435–449 Brain permeability is important irrespective of whether your drug is supposed to enter the brain - or not. Thus, the current coloring of the score depends on your goal. To decrease the risk of CNS side-effects, you want a drug with low BBB permeability (Blood Brain Barrier).		MPO Score: 1.68
Toxpredict	Runs toxtree predictions using toxpredict.net. Requires online access to opentox.net
hERG	Returns the predicted pIC50 value of a compound using a machine learning model trained on electrophysiological assays for hERG inhibition Calculations are performed using Chemaxon calculators To avoid side-effects from hitting the hERG channel, the predicted pAct value should be as low as possible.		pAct: 5.33 Error: 0.71
Permeability (beta)	Returns the predicted low/high classification of PAMPA permeability of a compound using a machine learning model trained on publicly available data Calculations are performed using Trainer Engine, separate subscription required.		Permeability: 1 Confidence: 0.74
hERG assistant	Return suggested transformations to reduce hERG liability using MMP knowledge base. Dataset is based on ChEMBL published data curated by Chemaxon.

Structure Check

Name	Description	Example	Spreadsheet results
Structural Alerts	Checks substructure patterns to find problematic substructure features that relate to reactive metabolite formation. Citation: Chem. Res. Toxicol. 2018, 31, 6, 389–411		Count: 3.
PAINS	Checks the compound against substructure rules associated with the Pan-Assay Interference of Compounds publication. Citation: J. Med. Chem. 2015, 58, 5, 2091–2113		Issues: 3
Compliance Checker	Fetches legislative references for a molecule. Analysis performed by Chemaxon Compliance Checker, separate subscription required.		Issues: 0 Last checked: 2021-11-04
Structure Checker	Checks the drawing quality of molecules and offers fixing them. Checks configured using Chemaxon Structure Checker		Issues: 1
Design Hub shared compounds	Check the provided query molecule within Design Hub to novelty. Coverage is subject to compound access permissions and project members. Options include: substructure, similarity, and exact search. For substructure search, Ignore stereo option is available corresponding to the following two options: Ignore tetrahedral stereo search, Stereo search on marked double bond only		Exact matches: 1

3D Models

Name	Description	Example	Spreadsheet results
RDock	This submits the compound to an external RDock docking service with ligand preparation and docking protocols. Requires per-project configuration. Ligand preparation performed using Chemaxon calculators Unlike other plugins, this takes a long time (usually on the order of minutes) to complete its calculations. Docking scores are reported as negative values, mimicking the free energy of binding.		Score: -21.479
Alignment	Provides a display of a protein and reference ligand of choice from the PDB, and attempts to overlay the designed compound on the ligand. Requires online access to PDB to download crystal structure files. Calculations are performed using Chemaxon calculators		3DTanimoto: 0.94
Conformers	Generates lowest energy conformer of a molecule. Calculations are performed using Chemaxon calculators

Commercial compounds

Name	Description	Example	Spreadsheet results
Enamine REAL	Runs substructure and similarity search across the Enamine REAL database. Searches are performed using Chemaxon search tools as a substructure search or a fingerprint similarity search. Higher similar values represent higher degree of similarity.		Matches: 31 Highest similarity: 0.93
Mcule Ultimate	Runs similarity searches in the Mcule Ultimate database. Requires online access to Mcule involving query structure.		Matches: 31 Highest similarity: 0.93
Enamine Store	Run searches in the Enamine Store SCR and BB catalog. Requires online access to Enamine Store involving your query structure.		Matches: 3
eMolecules	Run searches in the eMolecules catalog.		Matches: 3
Molport	Runs screening compound and starting material search in Molport. Requires online access to Molport involving your query structure.		Matches: 3
Mcule	Runs similarity searches in the Mcule online catalog. Requires online access to Mcule involving your query structure.		Matches: 3

Literature

Name	Description	Example	Spreadsheet results
SureChEMBL	Runs similarity search across SureChEMBL. Searches are performed using Chemaxon search tools		Matches: 31 Highest similarity: 0.93
ChEMBL	Returns molecules and activity values from ChEMBL (sim search, high p_chembl value). Requires online access to ChEMBL hosted at ebi.ac.uk involving your query structure.		Matches: 31 Highest similarity: 0.93 p_chembl: 4.6
PubChem	Returns substructure matches through PubChem's PUG interface. Requires online access to PubChem hosted at nih.gov involving your query structure		Matches: 3

Synthesis