| Literature DB >> 32936638 |
Magdalena Konieczny1, Bogdan Musielak1, Justyna Kocik1, Lukasz Skalniak1, Dominik Sala1, Miroslawa Czub1, Katarzyna Magiera-Mularz1, Ismael Rodriguez1, Maja Myrcha1, Malgorzata Stec2, Maciej Siedlar2, Tad A Holak1, Jacek Plewka1.
Abstract
Immune checkpoint blockade is one of the most promising strategies of cancer immunotherapy. However, unlike classical targeted therapies, it is currently solely based on expensive monoclonal antibodies, which often inflict immune-related adverse events. Herein, we propose a novel small-molecule inhibitor targeted at the most clinically relevant immune checkpoint, PD-1/PD-L1. The compound is capable of disrupting the PD-1/PD-L1 complex by antagonizing PD-L1 and, therefore, restores activation of T cells similarly to the antibodies, while being cheap in production and possibly nonimmunogenic. The final compound is significantly smaller than others reported in the literature while being nontoxic to cells even at high concentrations. The scaffold was designed using a structure-activity relationship screening cascade based on a new antagonist-induced dissociation NMR assay, called the weak-AIDA-NMR. Weak-AIDA-NMR finds true inhibitors, as opposed to only binders to the target protein, in early steps of lead compound development, and this process makes it less time and cost consuming.Entities:
Year: 2020 PMID: 32936638 PMCID: PMC7584369 DOI: 10.1021/acs.jmedchem.0c01260
Source DB: PubMed Journal: J Med Chem ISSN: 0022-2623 Impact factor: 7.446
Figure 1Comparison of selected short biphenyl-based initial scaffolds. BA stands for binding affinity.
Figure 2w-AIDA-NMR HSQC (A–D) and 1D NMR spectra (E). (A) N66A-PD-1 w-AIDA, five groups of characteristic peaks are boxed in green; (B) N66A-PD-1/PD-L1 complex, part of the PD-1 peaks disappeared, boxed in red; (C) N66A-PD-1/PD-L1 complex + 1a, after addition of compound 1a the spectrum of N66A-PD-1/PD-L1 complex resembles spectrum A; all PD-1 peaks are restored indicating the displacement of PD-L1 from the complex (peaks boxed in green); (D) N66A-PD-1/PD-L1 complex + 1c spectrum resembles spectrum A; all PD-1 peaks are restored indicating the displacement of PD-L1 from the complex; (E) aliphatic part of the 1D NMR spectrum: blue, a characteristic spectrum of N66A-PD-1 is highlighted with gray bars; red, PD-L1spectrum, peaks in highlighted regions differ; green, spectrum of N66A-PD-1/PD-L1 complex, spectrum becomes flattened due to complex formation; purple, N66A-PD-1/PD-L1 complex + 1a, restoration of characteristic PD-1 peaks due to addition of 1a inhibitor; orange, N66A-PD-1/PD-L1 complex + 1c, restoration of characteristic PD-1 peaks due to addition of 1c inhibitor.
General Pathway for the Synthesis of Bromo Mono-Substituted Compoundsb
(A) Methyl 3-bromo-4-hydroxybenzoate, K2CO3, DMF, rt, overnight (45% for 2e); (B) amine component R3, DBU (25% for 2f).
Reagents and conditions: (A) substituted 4-hydroxybenzaldehde, K2CO3, DMF, rt, overnight (43% for 2a, 39% for 2b, 38% for 2c, and 52% for 2d); (B) amine component, NaBH3CN, AcOH, DMF, rt, overnight (53% for 2g, 65% for 2h, 56% for 2i, 72% for 2j, and 51% for 2k).
General Pathway for the Synthesis of Extended 2-Bromo-3-(bromomethyl)-1,1′-biphenyl (1a) and [1,1′:2′,1″-Terphenyl]-3′-ylmethanol (1b)-Based Compounds 3b–d, 3fa
Reagents and conditions: (A) for compound 1a where X is −Br, 5-chloro-2,4-dihydroxybenzaldehyde, NaHCO3, ACN/DMF, rt, overnight (54% for 3a); for compound 1b where X is −OH, 5-chloro-2,4-dihydroxybenzaldehyde, PPh3, DIAD, THF, rt, overnight (20% for 3e); (B) picolinonitrile/benzonitrile component, K2CO3, DMF, rt, overnight (63% for 3b, 87% for 3c, and 90% for 3f); (C) amine component, NaBH3CN, AcOH, DMF, rt, overnight (for 3d).
General Pathway for the Synthesis of 6-(2-Bromo-3-(bromomethyl)phenyl)-2,3-dihydrobenzo[b][1,4]dioxine (1g), 1,1′:2′,1″-Terphenyl (1b), 6-(3-(Bromomethyl)-2-fluorophenyl)-2,3-dihydrobenzo[b][1,4]dioxine (1d), [1,1′:2′,1″-Terphenyl]-3′-ylmethanol, 2-Bromo-3-(bromomethyl)-3′-fluoro-1,1′-biphenyl (1f), and 2′-Bromo-3′-(bromomethyl)-[1,1′-biphenyl]-4-carbonitrile (1e)-Based Compounds 4a–na
Reagents and conditions: (A) for compounds 1e–g where X is −Br, substituted 4-hydroxybenzaldehde, K2CO3, DMF, rt, overnight (88% for 4a, 61% for 4g, 57% for 4i, and 52% for 4m); for compounds 1b, 1d where X is −OH, (1) SOCl2, DCM, 40 °C, (2) substituted 4-hydroxybenzaldehde, K2CO3, DMF, rt, overnight (30% for 4c and 60% for 4e); (B) for compounds 4a,c,e,g,i, amine component, NaBH3CN, AcOH, DMF, rt, overnight (43% for 4b, 61% for 4d, 37% for 4f, 26% for 4h, 44% for 4j, 67% for 4k, and 33% for 4l); for compounds 4m, (1) SOCl2, DCM, 40 °C, (2) amine component, K2CO3, DMF, rt, overnight (29% for 4n).
Figure 3Activity of modified bromo compounds in PD-1/PD-L1 immune checkpoint blockade cell-based assay. Activities of the reference anti-PD-L1 antibody durvalumab and tested compounds in alleviating the effect of PD-1/PD-L1 checkpoint on TCR-mediated effector Jurkat T cells are expressed as fold induction of the luciferase activity, the expression of which is TCR-inducible (for details, please see the Experimental Section). The graphs present relative luminescence normalized to DMSO-treated controls and are mean ± SEM values from 4 to 7 independent experiments.
Figure 4Compound 2k blocks the PD-L1/PD-1 immune checkpoint in primary human T cells, as evidenced by the increased expression of the late activation and exhaustion marker, PD-1. Peripheral blood mononuclear cells (PBMCs) were seeded on the preseeded hPD-L1 aAPCs and cultured for 48 h alone or in the presence of 2k, DMSO (as a solvent for 2k), or atezolizumab (atezo., an anti-PD-L1 therapeutic antibody). The expression of PD-1 was tested with flow cytometry. (A) Exemplary histograms, presenting the increased expression of PD-1 on either the CD4+ or the CD8+ T cells. (B) The analysis of the expression of PD-1 on CD4+ or CD8+ T cells under control conditions and in the presence of PD-L1-blocking molecules, the antibody atezolizumab, and compound 2k. Graphs present mean ± SD values calculated for three independent experiments performed with the engagement of different donors. Statistical significance was analyzed with the Student’s t test: *p < 0.05, **p < 0.01.
Figure 5Interactions between PD-L1 and 3b (top) and 2k (bottom) from modeled complexes (compounds were docked on PD-L1 taken from PDB ID: 5NIX). Both compounds are involved in a number of hydrophobic interactions (gray dashed lines) with residues Ile54A Tyr56A and B, Gln66B, Met115B, Ala121A for 3b and Ala121B for 2h, and Tyr123A. There is strong conserved stabilizing π-stacking (green dashed line) between the distal phenyl ring from the biphenyl moiety and Tyr56A and the phenyl from phenoxymethyl with Tyr56B. The major differences are in the hydrogen bonds (blue solid line), which for 2k are between the Tyr56B hydroxyl group and the tertiary amine in piperidine solubilizer and the Asn63B amide nitrogen and oxygen from the carboxylic group of the solubilizer. For 3b, hydrogen bonds are between the cyanopyridine nitrogen with Arg125A nitrogen and the nitrile group nitrogen with Asn63B nitrogen.