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
    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
    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
    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.
    herg assistant

    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 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.

    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.
    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

    Synthesis

    Name Description
    Synthia analysis Searches for retrosynthetic routes for a given compound.
    Requires separate purchase of Synthia.
    Unlike other plugins, this takes a long time (usually on the order of minutes) to complete its searches.
    Reaxys Runs search in Reaxys and returns compound information and citations.
    Requires separate purchase of Reaxys.
    chemical.ai Searches for retrosynthetic routes for a given compound.
    Requires separate purchase of chemical.ai.
    Results are saved as CDX, SVG and PDF files when selected by users on the chemical.ai interface