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.
    calculated properties    		 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.
    topological descriptors    		 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).
    sweet spot
    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.
    clogd    		 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).
    cns mpo    		 MPO Score: 1.68
    BBB Calculates and displays a radar plot of Gupta, Mayuri et al's BBB score.
    Calculations are performed using BBB Score tool
    Citation: J. Med. Chem. 2019, 62(21), 9824–9836.
    bbb    		 BBB Score: 4.66
    Toxpredict Runs toxtree predictions using toxpredict.net.
    Requires online access to opentox.net
    toxpredict
    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.
    herg    		 pAct: 5.33
    Error: 0.71
    hERG assistant Return suggested transformations to reduce hERG liability using MMP knowledge base. Dataset is based on ChEMBL published data curated by Chemaxon.
    herg assistant
    Local models Returns the predicted classification or continuous value of a compound using a machine learning model trained on your experimental data
    Calculations are performed using Trainer Engine. Requires separate subscription!
    permeability    		 Permeability: 1
    Confidence: 0.74

    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    		 structural alerts 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
    pains    		 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
    shared compounds    		 Exact matches: 1

    3D Models

    Name Description Example Spreadsheet results
    RDock This demonstration tool submits the compound to an external RDock docking service with ligand preparation and docking protocols.
    Requires per-project configuration and desktop applications.
    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.
    rdock    		 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.
    Only available in AWS environments hosted by Chemaxon.
    Calculations are performed using Chemaxon calculators
    alignment    		 3DTanimoto: 0.94
    Conformers Generates lowest energy conformer of a molecule.
    Calculations are performed using Chemaxon calculators
    conformers

    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.
    enamine real    		 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.
    enamine store    		 Matches: 3
    eMolecules Run searches in the eMolecules catalog.
    emolecules    		 Matches: 3
    Molport Runs screening compound and starting material search in Molport.
    Requires online access to Molport involving your query structure.
    molport    		 Matches: 3
    Mcule Runs similarity searches in the Mcule online catalog.
    Requires online access to Mcule involving your query structure.
    mcule    		 Matches: 3

    Literature

    Name Description Example Spreadsheet results
    SureChEMBL Runs similarity search across SureChEMBL.
    Searches are performed using Chemaxon search tools
    surechembl    		 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.
    ChEMBL    		 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