Fragment-based approach to identify IDO1 inhibitor building blocks

Abstract

Indoleamine 2,3-dioxygenase 1 (IDO1) is attracting a great deal of interest as drug target in immune-oncology being highly expressed in cancer cells and participating to the tumor immune-editing process. Although several classes of IDO1 inhibitors have been reported in literature and patent applications, only few compounds have proved optimal pharmacological profile in preclinical studies to be advanced in clinical trials. Accordingly, the quest for novel structural classes of IDO1 inhibitors is still open. In this paper, we report a fragment-based screening campaign that combines Water-LOGSY NMR experiments and microscale thermophoresis approach to identify fragments that may be helpful for the development of novel IDO1 inhibitors as therapeutic agents in immune-oncology disorders.

Tracking Hidden Binding Pockets Along the Molecular Recognition Path of l‐Trp to Indoleamine 2,3‐Dioxygenase 1

“…[43] Unmodified rhIDO1 and NT647-rhIDO1 were also checked in biochemical assay for their catalytic activity, using the experimental protocol reported elsewhere. [24] Both protein samples proved catalytically active, yielding K M of 99.6 μM and Vmax of 135 μM/h for the unmodified rhIDO1 and K M of 79.0 μM and Vmax of 125 μM/h for the NT647-rhIDO1 ( Figure S1 of supporting information). l-Trp pre-dilutions were prepared for MST experiments by 16-fold 1 : 1 serial dilutions in assay buffer containing 4 % DMSO in PCR tubes supplied by NanoTemper Technologies to yield final volumes of 10 μL.…”

“…The stability of NT647‐rhIDO1, NT647‐apo‐rhIDO1, and unmodified rhIDO1 and apo‐rhIDO1 proteins was checked using circular dichroism (Table S1 of supporting information) . Unmodified rhIDO1 and NT647‐rhIDO1 were also checked in biochemical assay for their catalytic activity, using the experimental protocol reported elsewhere . Both protein samples proved catalytically active, yielding K M of 99.6 μM and Vmax of 135 μM/h for the unmodified rhIDO1 and K M of 79.0 μM and Vmax of 125 μM/h for the NT647‐rhIDO1 (Figure S1 of supporting information).…”

“…Moreover, disappointing results have been very recently reported for the most advanced IDO1 inhibitor, i. e. epacadostat ( 4 ), and compound 6 and 7 have also been withdrawn from the clinic . Additional studies have sought to better understand the complex biology of the enzyme and aid the design and development of next‐generation IDO1 inhibitors . In the current report, we investigated the molecular recognition path of l ‐Trp ( 1 ) to human IDO1 through a synergic approach based on microscale thermophoresis, supervised molecular dynamics (SuMD) and mutagenesis experiments.…”

“…[22] Additional studies have sought to better understand the complex biology of the enzyme and aid the design and development of next-generation IDO1 inhibitors. [23][24][25] In the current report, we investigated the molecular recognition path of l-Trp (1) to human IDO1 through a synergic approach based on microscale thermophoresis, supervised molecular dynamics (SuMD) and mutagenesis experiments. Results have allowed disclosing for the first time high and low dissociation constants (K d ) of l-Trp to IDO1, as well as the presence of a metastable interaction site located close to the C-terminal part of the JK-loop and defined by Lys238.…”

New Insights from Crystallographic Data: Diversity of Structural Motifs and Molecular Recognition Properties between Groups of IDO1 Structures

“…Since the disclosure of the first crystal structure in 2006, applications of SBDD approaches to IDO1 have been fostered by the ever increasing number of entries in the PDB database (Figure ; Table S1 in the Supporting Information) . However, only few of these entries have hitherto been used for SBDD screening campaigns (33 %, Figure ) …”