Fig 1.
The four general alkaloid classes include the mitragynine congeners (1–10), pyran-fused mitragynine congeners (11–12), oxindole congeners (13–21), and the pyran-fused oxindole congeners (22–25). The chiral centers that are addressed in this manuscript are indicated by wavy bonds and asterisks (*), and the locations of varying side chains are marked as R1, R2 and R3. A complete description of the structure and stereochemistry of alkaloids is presented in the supporting information.
Table 1.
Structural similarity analysis of the kratom alkaloids with respect to (w.r.t) mitragynine and the controlled substance database.
The MACCS166 molecular fingerprint only considers two-dimensional structure. Therefore, the 25 alkaloids under consideration map to 12 unique chemical structures.
Table 2.
Alkaloid binding predictions at the opioid receptors.
Compounds that were included in each model training set are reported as ‘T’, while compounds that are predicted to have a binding affinity > 10 μM are reported as ‘-‘. Clarity and SEAware use different metrics associated with probability of binding to respective drug targets. For positive predictions of binding, Clarity confidence scores and SEAWare p-values are provided.
Table 3.
Alkaloid binding predictions at the adrenergic and serotonin receptors.
Compounds that were included in each model training set are marked ‘T’, while compounds that are predicted to have a binding affinity > 10 μM are marked ‘-‘. Clarity and SEAware use different metrics associated with probability of binding to the respective drug targets. For positive predictions of binding, Clarity confidence scores and SEAWare p-values are provided.
Fig 2.
Molecular docking evaluation of the alkaloids at the mu opioid receptor.
(A) The docking score of the mitragynine congeners (red), pyran-fused mitragynine congeners (blue), oxindole congeners (white), and the pyran-fused oxindole congeners (gray) normalized to mitragynine. (B) Crystal structure of the mu opioid receptor in complex with the agonist, BU72. (C-E) Lowest energy docking configuration of mitragynine (1), 7-hydroxymitragynine (7), and ajmalicine (11) with the mu opioid receptor. In panels B-E, the negatively charged sidechain of Asp147 that forms the salt bridge with the positively charged amine of each opioid is highlighted by the red mesh surface, and the aromatic sidechain of His297 is represented by the blue mesh surface.
Table 4.
Evaluation of the opioid receptor binding predictions.
Compounds that were included in the model training sets are marked as ‘T’, compounds predicted to have sub 10 μM binding affinity are marked as ‘+’, and compounds predicted to have > 10 μM binding affinity are marked as ‘-‘. The predictions from Clarity and SEAware are presented on the left and right, respectively. Cells that are shaded green indicate that the two software predictions are in agreement and correct. Cells that are shaded red indicate that the two software predictions are in agreement and incorrect. Finally, cells that are not shaded indicate that the two software platforms have conflicting predictions.
Table 5.
Evaluation of the adrenergic and serotonin receptor binding predictions.
Compounds that were included in the model training sets are marked as ‘T’, compounds predicted to have sub 10 μM binding affinity are marked as ‘+’, and compounds predicted to have > 10 μM binding affinity are marked as ‘-‘. The predictions from Clarity and SEAware are presented on the left and right, respectively. Cells that are shaded green indicate that the two software predictions agree and are correct. Cells that are shaded red indicate that the two software predictions are in agreement and incorrect. Finally, cells that are not shaded indicate that the two software platforms have conflicting predictions.
Fig 3.
Binding affinity predictions using the mu opioid regression model.
The model predictivity interval is shown by the error bars, while the experimentally determined binding affinities are presented as symbols in panel A. The measured binding affinities of fentanyl and carfentanil are presented, for comparison, as the black squares and the normalized mitragynine binding affinity is presented as the black diamond. Panel A also presents the measured binding affinities of the remaining eight kratom alkaloids. The green diamonds indicate the experimentally measured binding affinities, while the purple greater than symbol indicates that no binding occurred below 10 μM.