X-ray Structure-Guided Discovery of a Potent, Orally Bioavailable, Dual Human Indoleamine/Tryptophan 2,3-Dioxygenase (hIDO/hTDO) Inhibitor That Shows Activity in a Mouse Model of Parkinson’s Disease

Abstract

Human indoleamine 2,3-dioxygenase 1 (hIDO1) and tryptophan 2,3-dioxygenase (hTDO) have been closely linked to the pathogenesis of Parkinson's disease (PD); nevertheless, development of dual hIDO1 and hTDO inhibitors to evaluate their potential efficacy against PD is still lacking. Here, we report biochemical, biophysical, and computational analyses revealing that 1H-indazole-4-amines inhibit both hIDO1 and hTDO by a mechanism involving direct coordination with the heme ferrous and ferric states. Crystal structure-guided optimization led to 23, which manifested IC 50 values of 0.64 and 0.04 μM to hIDO1 and hTDO, respectively, and had good pharmacokinetic properties and brain penetration in mice. 23 showed efficacy against the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-induced mouse motor coordination deficits, comparable to Madopar, an anti-PD medicine. Further studies revealed that different from Madopar, 23 likely has specific anti-PD mechanisms involving lowering IDO1 expression, alleviating dopaminergic neurodegeneration, reducing inflammatory cytokines and quinolinic acid in mouse brain, and increasing kynurenic acid in mouse blood.

Structure and Plasticity of Indoleamine 2,3-Dioxygenase 1 (IDO1)

“…The influence of the sulfur–bromine halogen bond can be estimated from the potencies of the indazole ligands 12 (PDB ID 7e0s) and 13 (PDB ID 7e0t), which differ only in the bromine position. The IC 50 value of the ligand with the sulfur–bromine halogen bond is only better by a factor of two (0.64 versus 1.23 μM) . As manifest by the methyl substituent also frequently found in this position, hydrophobic ligand–protein contacts certainly contribute to increasing the binding affinity of substituted ligands.…”

“…The IC 50 value of the ligand with the sulfur−bromine halogen bond is only better by a factor of two (0.64 versus 1.23 μM). 43 As manifest by the methyl substituent also frequently found in this position, hydrophobic ligand−protein contacts certainly contribute to increasing the binding affinity of substituted ligands. Additionally, the influence of the aromatic substituents on the electronic structure of the heme binding group can modulate the binding affinity.…”

“…All of them have been determined by X-ray crystallography, and there are no NMR or electron microscopy structures available. Besides six structures with mutations close to the active site (PDB IDs 4u72, 4u74, 5wmw, 5wmx, 6cxu, and 6cxv), , there are seven ligand-free holo-IDO1 structures (PDB IDs 6azu, 6dpq chain A, 6dpr-A, 6e44, 6e45, 6mq6-A, and 7a62), ,,, three with cyanide and substrate l -Trp (PDB IDs 5wmu, 5wmv, and 6e35), 11 with imidazole inhibitors (PDB IDs 2d0t, 4pk6, 5ek2, 5ek3, 5ek4, 6e42, 6kof, 6kps, 6kw7, 6o3i, and 7m7d), ,,− six with triazole inhibitors (PDB IDs 4pk5, 6f0a, 6r63, 7ah4, 7ah5, and 7ah6), ,, six with indazole inhibitors (PDB IDs 7e0o, 7e0p, 7e0q, 7e0s, 7e0t, and 7e0u), five with hydroxyamidine inhibitors (PDB IDs 5wn8, 5xe1, 6e40, 6e41, and 6pu7), ,,, and two with the indole inhibitor EOS200271 (PDB IDs 5whr and 6pz1). , In addition, there are eight heme-free apo-IDO1 structures bound to type iv ligands (PDB IDs 6azv, 6azw, 6e43, 6v52, 6wjy, 6wpe, 6x5y, and 7m63) ,,,…”

Structure-based optimization of type III indoleamine 2,3-dioxygenase 1 (IDO1) inhibitors

“…Indazoles are also known haem binders, and the indazol-4-amine scaffold developed by IOmet Pharma 54 yielded selective nanomolar TDO inhibitors and dual IDO1/TDO inhibitors 55–57 . X-ray structures of the complexes between IDO1 and some indazol-4-amines such as compound 8 have recently been resolved 57 . These compounds provide access to pocket B while preserving a LE of up to 0.47 kcal/mol/HA.…”

Discovery of the First Potent IDO1/IDO2 Dual Inhibitors: A Promising Strategy for Cancer Immunotherapy

“…In addition, the growth of 4T1 breast cancer is initially inhibited by selective IDO1 blockade, but resistance develops, with elevated levels of Kyn, suggesting alternate mechanisms involving IDO2 and/or TDO . Thus, cotargeting IDO1/2 and TDO by developing dual or pan-inhibitors is a reasonable strategy. , …”