Encoding and display technologies for combinatorial libraries in drug discovery: The coming of age from biology to therapy

Abstract

Drug discovery is a sophisticated process that incorporates scientific innovations and cutting-edge technologies. Compared to traditional bioactivity-based screening methods, encoding and display technologies for combinatorial libraries have recently advanced from proof-of-principle experiments to promising tools for pharmaceutical hit discovery due to their high screening efficiency, throughput, and resource minimization. This review systematically summarizes the development history, typology, and prospective applications of encoding and displayed technologies, including phage display, ribosomal display, mRNA display, yeast cell display, one-bead one-compound, DNA-encoded, peptide nucleic acid-encoded, and new peptide-encoded technologies, and examples of preclinical and clinical translation. We discuss the progress of novel targeted therapeutic agents, covering a spectrum from small-molecule inhibitors and nonpeptidic macrocycles to linear, monocyclic, and bicyclic peptides, in addition to antibodies. We also address the pending challenges and future prospects of drug discovery, including the size of screening libraries, advantages and disadvantages of the technology, clinical translational potential, and market space. This review is intended to establish a comprehensive high-throughput drug discovery strategy for scientific researchers and clinical drug developers.

Keywords: Clinical drugs; DNA-encoded chemical libraries; Drug screening; Peptide-encoded chemical libraries; Phage display.

Graphical abstract

Figure 1

Encoding and display technologies for combinatorial libraries in drug discovery development timeline, pros and cons in drug discovery.

Figure 2

Overview of the representative drug screening strategies using display technology. (A) Schematic illustration of the phage display workflow for drug discovery. (B) Schematic illustration of the ribosome display workflow for drug discovery. (C) Schematic illustration of the mRNA display workflow for drug discovery. (D) Schematic illustration of the yeast surface display workflow for drug discovery.

Figure 3

Overview of the representative drug screening strategies using encoding technology. (A) Schematic illustration of the OBOC workflow for drug discovery. (B) Schematic illustration of the DEL workflow for drug discovery. (C) Schematic illustration of the PNA-encoded chemical libraries workflow for drug discovery. (D) Schematic illustration of the PEL workflow for drug discovery.

Figure 4

Application of encoding and display technologies for combinatorial libraries in the drug discovery of small molecule compounds. (A) The strategy of cell-based DEL selection. (B) Structures of the identified compounds. (C) Example of the selection of a 30.42-million DEL against the folate receptor on live cells. (D) Analysis of potential inhibitors H1 and H2 through fluorescence polarization and fluorescent cell imaging. Reproduced with permission from Ref. . Copyright ©2021 Springer Nature.

Figure 5

Application of encoding and display technologies for combinatorial libraries in the drug discovery of non-peptidic macrocycles. (A) Design of a non-peptidic macrocycle library construction using a split-and-pool strategy. (B) Enrichments and dissociation constants of synthesized compounds. (C) High-throughput DNA sequencing plot and fluorescence polarization measurements of selected combinations against human serum albumin (HSA) and alpha-1 acid glycoprotein (AGP). Reproduced with permission from Ref. . Copyright ©2018 Springer Nature.

Figure 6

Application of encoding and display technologies for combinatorial libraries in linear peptide drug discovery. (A) Schematic illustration of the sequential screening strategy for screening potent antifungal linear peptide. (B) A potent antifungal linear peptide K-oLBF127 from the OBOC combinatorial linear peptide library with the reduction in lung fungal burden. Reproduced with permission from Ref. . Copyright ©2022 ACS Publications.

Figure 7

Application of encoding and display technologies for combinatorial libraries in the drug discovery of monocyclic peptides. (A) Workflow for the discovery of potent monocyclic peptides against MAGE-A4 using combination of tyrosinase-mediated cyclization with mRNA display methods. (B) The chemical structure of the monocyclic peptides. Reproduced with permission from Ref. . Copyright ©2023 ACS Publications.

Figure 8

Application of encoding and display technologies for combinatorial libraries in drug discovery of bicyclic peptides. (A) Schematic diagram of phage-encoded chemical libraries for screening bicyclic peptide inhibitors of NODAL. (B) The chemical structure of 19b. (C) Cell viability assay of TYK-nu cell line transfected with rhNODAL and treated with 19b at various peptide concentrations. Reproduced with permission from Ref. . Copyright ©2021 Royal Society of Chemistry.

Figure 9

Application of encoding and display technologies for combinatorial libraries in antibody drug discovery. (A) Schematic illustration of the ribosome display screening strategy for antibody discovery. (B) Rapid discovery of high-affinity antibodies via massively parallel sequencing, ribosome display. Reproduced with permission from Ref. . Copyright ©2023 Springer Nature.