Development of a Non-IgG PD-1/PD-L1 Inhibitor by in Silico Mutagenesis and an In-Cell Protein–Protein Interaction Assay

Abstract

Inhibiting the programmed death-1 (PD-1)/programmed death ligand 1 (PD-L1) axis by monoclonal antibodies (mAbs) is a successful cancer immunotherapy. However, mAbbased drugs have various disadvantages including high production costs and large molecular sizes, which motivated us to develop a smaller alternative drug. Since PD-L1 binds PD-1 with moderate affinity, a higher affinity PD-1 variant should serve as a competitive inhibitor of the wild-type PD-1/PD-L1 interaction. In this report, we conducted in silico point mutagenesis of PD-1 to identify potent PD-1 variants with a higher affinity toward PD-L1 and refined the in silico results using a luciferase-based in-cell protein−protein interaction (PPI) assay. As a result, a PD-1 variant was developed that had two mutated amino acids (T76Y, A132V), termed 2-PD-1. 2-PD-1 could bind with PD-L1 at a dissociation constant of 12.74 nM. Moreover, 2-PD-1 successfully inhibited the PD-1/PD-L1 interaction with a half maximal inhibitory concentration of 19.15 nM and reactivated the T cell with a half maximal effective concentration of 136.1 nM. These results show that in silico mutagenesis combined with an in-cell PPI assay verification strategy successfully prepared a non-IgG inhibitor of the PD-1/PD-L1 interaction.

Evaluation of the Binding Kinetics of RHEB with mTORC1 by In-Cell and In Vitro Assays

“…Since the ∆ATP domain of mTOR (aa 2148-2300) is highly conserved in the PI3K family [10,22], it is possible that RHEB regulates the kinase activity of mTOR upon the binding to ∆ATP domain. Based on the NanoBiT results, we further quantitatively measured the binding kinetics of RHEB with the mTOR fragments of ∆N-FAT-M, ∆N, and ∆ATP by the BLItz system (FortéBio, Fremont, CA, USA) [15]. For the measurements, we overexpressed the mTOR fragments by pET15b/BL21(DE3) E. coli system and purified them by Ni-NTA and Superdex-200 columns (GE Healthcare, USA) (Figures S6-S8).…”

“…On the lysosome surface, two RHEB-GTP complexes cooperatively activate mTORC1 to phosphorylate 4E-BP1 [4]. The stoichiometry obtained, however, did not involve the kinetics of RHEB binding to mTOR by means of protein-protein interaction (PPI) assays [15,16]. Therefore, in this study we aimed to reveal the kinetics of RHEB to mTOR, which can inform the development of new anti-cancer drugs.…”

Evaluation of the Binding Kinetics of RHEB with mTORC1 by In-cell and In vitro Assays

“…Since the ∆ATP domain of mTOR (2148-2300) is highly conserved in the PI3K family [10,17], it is possible that RHEB regulates the kinase activity of mTOR upon the binding to ∆ATP domain. Based on the NanoBiT results, we further quantitatively measured the binding kinetics of RHEB with the mTOR fragments of ∆N-FAT-M, ∆N and ∆ATP by the BLItz system (FortéBio, USA) [15]. For the measurements, we overexpressed the mTOR fragments by pET15b/BL21(DE3) E. coli system and purified them by Ni-NTA and Superdex-200 columns (GE Healthcare, USA) (Figure S6-S8).…”

“…Here we studied the binding details of RHEB to whole mTOR and the truncated mTOR fragments [4,10]. In the assays, we used the in-cell and in vitro assays to facilitate the measurements [18]. RHEB bound to whole mTOR with 5 times weaker affinity in the presence of GTP than that of GTP absence.…”

“…The stoichiometry obtained, however, did not involve the binding kinetics of the RHEB to mTOR protein-protein interaction (PPI). Therefore, we aimed in this study to reveal the kinetics of the RHEB to mTOR by using the in-cell and in vitro PPI methods [15].…”