Development of the Inhibitors that Target the PD-1/PD-L1 Interaction-A Brief Look at Progress on Small Molecules, Peptides and Macrocycles

Abstract

Cancer immunotherapy based on antibodies targeting the immune checkpoint PD-1/PD-L1 pathway has seen unprecedented clinical responses and constitutes the new paradigm in cancer therapy. The antibody-based immunotherapies have several limitations such as high production cost of the antibodies or their long half-life. Small-molecule inhibitors of the PD-1/PD-L1 interaction have been highly anticipated as a promising alternative or complementary therapeutic to the monoclonal antibodies (mAbs). Currently, the field of developing anti-PD-1/PD-L1 small-molecule inhibitors is intensively explored. In this paper, we review anti-PD-1/PD-L1 small-molecule and peptide-based inhibitors and discuss recent structural and preclinical/clinical aspects of their development. Discovery of the therapeutics based on small-molecule inhibitors of the PD-1/PD-L1 interaction represents a promising but challenging perspective in cancer treatment.

Keywords: PD-1/PD-L1 pathway; cancer immunotherapy; cocrystal structures; lead optimization; peptide-based and small synthetic molecule inhibitors; rational drug design; scaffold hopping; structure-activity relationship.

Figure 1

Structure of AUNP-12 (1)—A 29-residue peptide sequence.

Figure 2

An example of modified heptapeptide (SNTSEFS-NH₂) derived from 1 (modified moiety is coloured with blue).

Figure 3

The structures of BMS peptides 3 (BMS-57) and 4 (BMS-71) with their IC₅₀ values reported in the patent.

Figure 4

Geldanamycin (5) and Rifabutin (6) as the PD-L1 inhibitors.

Figure 5

Representative structures of the Aurigene peptidomimetics 7 and 8. The SAR-affected parts are marked in blue.

Figure 6

Linear 9 and cyclic peptide 10 showing the highest MSPA rates.

Figure 7

Examples of the macrocyclic peptidomimetic compounds 11 and 12 with glycol-derived linker.

Figure 8

Examples of Aurigene’s small-molecule inhibitors.

Figure 9

Modifications of structures 13 and 14 [55,56].

Figure 10

Examples of the small-molecules patented by Aurigene in 2018/2019.

Figure 11

SAR of structures from Aurigene patents [56,57].

Figure 12

General structure and examples of the PD-1/PD-L1 sulfamonomethoxine 24 and sulfamethizole 25 inhibitors [59].

Figure 13

General structures of the compounds disclosed by Bristol-Myers Squibb company and their representative examples [60,61,62,63,64,65].

Figure 14

(A) Crystal structure of the 26/PD-L1 complex. The asymmetric unit contains four molecules of PD-L1 (ribbon representation), which are organized into two dimers (_APD-L1—green, _BPD-L1—purple-blue, _cPD-L1—salmon, _DPD-L1—bright orange). Each dimer binds a single molecule of 26 (yellow) at the dimer interface. (B) Detailed interactions of 26 at the binding cleft of PD-L1 dimer. 26 binds at a hydrophobic cavity formed upon PD-L1 dimerization (PDB: 5J89). Compound 30 cocrystal structure is consistent with structural data for 26.

Figure 15

(A) Detailed interactions of 31 (light yellow) at the binding cleft of PD-L1. Compound 31 binds at a hydrophobic cavity formed upon PD-L1 binding. (B) Detailed interactions of 32 (yellow) at the binding cleft of PD-L1. 32 binds at a hydrophobic tunnel formed upon the PD-L1 dimerization. The movement of the aromatic ring of _ATyr56 is induced by the 2,3-dihydro-1,4-benzdioxine moiety. (C) The movement of _ATyr56 (green) that is induced by the 2,3-dihydro-1,4-benzdioxine group of 32 (yellow) compared with the _ATyr56 (salmon) arrangement in the complex of 31/PD-L1.

Figure 16

Examples of the BMS class compounds, for which structural data were provided. (A, B) 2,3-dihydro-1,4-benzodioxine group of 33 and 34 induced transformation of the binding pocket into the binding tunnel across the transverse vertical axis of the dimer. Both compounds trigger formation of a subpocket binding the benzonitrile moiety [41,43,44]. (C) The binding cleft of 35 is closed from one side by the _AY56 residue. The arrangement of this inhibitor follows patterns for compounds 26, 30, and 31.

Figure 17

(A) Fragment 36 bound to dimeric PD-L1. Detailed interactions of 36 (yellow) at the binding cleft of PD-L1. 36 binds at a hydrophobic tunnel formed upon the PD-L1 dimerization. PDB: 6NM7 (B) Overlay of fragment 36 (yellow), BMS small molecule inhibitor 33 (light pink) and BMS macrocyclic inhibitor 4 (plum) (PDB codes: Fragment 1: 6NM7, BMS small molecule 5NIU: 6NM8, BMS peptide-71: 6NNV).

Figure 18

Examples of hits 36–44 found in the fragment-based screening published by Perry et al. [44]. Fragments were able to displace PD-1 from PD-L1 in the NMR-based AIDA assay [66]. The PD-1 rescue score was estimated on the percent of the G90 signal rescued of the ¹⁵N labeled PD-1 at 800 µM fragment concentration. Score 1 indicates 1–15% signal rescue and score 2 indicates >15% signal rescue (some of the K_d values were not determined due to solubility limits and/or resonance peak broadening).

Figure 19

The general structure and examples of the PD-1/PD-L1 inhibitors (45 and 46) reported by Incyte Corporation. The biphenyl fragment is shown in blue and the fused heteroaromatic system is shown in red. The next figure follows the same color pattern unless stated otherwise.

Figure 20

General structure and examples of PD-1/PD-L1 inhibitors (47–49) reported by Incyte Corporation in the second patent. Aryl ether fragment is shown in green.

Figure 21

General structure and examples of the PD-1/PD-L1 inhibitors (50 and 51) reported by Incyte Corporation [71].

Figure 22

General structure and examples of the PD-1/PD-L1 inhibitors (50 and 51) reported by Incyte Corporation [71].

Figure 23

General structure and examples of the PD-1/PD-L1 inhibitors (54 and 55) reported by Incyte Corporation, based on the fused six-membered heteroaromatic rings linked with the biphenyl scaffold.

Figure 24

General structure and examples of the PD-1/PD-L1 inhibitors (56 and 57) reported by Incyte Corporation, based on the picolinamide-biphenyl scaffold.

Figure 25

General structure and examples of the PD-1/PD-L1 inhibitors (58 and 59) reported by Incyte Corporation and based on the N-methyl-2-pyridone-6-carboxamide moiety (depicted with red).

Figure 26

General structures and examples of the PD-1/PD-L1 inhibitors patented by Incyte Corporation, based on heterocyclic five-membered aromatic rings (60 and 61) and on heterocyclic five-membered aromatic rings fused with piperidine (62 and 63).

Figure 27

General structure and examples of the PD-1/PD-L1 inhibitors patented by Incyte Corporation (64 and 65). The 3′ biphenyl’s substituent is depicted in gold.

Figure 28

The structures of inhibitors 66, 67 disclosed by ChemoCentryx.

Figure 29

Examples of the benzyl phenyl ether derivatives 68 reported by Feng et al., [82]; the resorcinol (69) and isonicotinic acid (70) derivatives reported, respectively, by Li et al. [83] and Sun et al. [84].

Figure 30

Examples of the structures patented by Arising International LLC.

Figure 31

Examples of inhibitors 74–75 designed by Polaris Pharmaceuticals company [86].

Figure 32

Compounds reported by Aktoudianakis et al. [87] (Gilead Sciences).

Figure 33

Examples of the compounds published by Qin et al. [88].

Figure 34

Structures of PD-1 binders reported by Patil and co-workers [89].

Figure 35

General structures 21–24 and examples of compounds 85–88 described by Dömling.

Figure 36

General structure and examples of the PD-1/PD-L1 inhibitors patented by the Maxinovel Corporation (89–91). Biphenyl fragments are shown in blue, phenyl fragments in red, the ethenyl and acetylenyl linkers in green.

Figure 37

The general pattern in the development of PD-L1 inhibitors.