The Art of Finding the Right Drug Target: Emerging Methods and Strategies

Abstract

Drug targets are specific molecules in biological tissues and body fluids that interact with drugs. Drug target discovery is a key component of drug discovery and is essential for the development of new drugs in areas such as cancer therapy and precision medicine. Traditional in vitro or in vivo target discovery methods are time-consuming and labor-intensive, limiting the pace of drug discovery. With the development of modern discovery methods, the discovery and application of various emerging technologies have greatly improved the efficiency of drug discovery, shortened the cycle time, and reduced the cost. This review provides a comprehensive overview of various emerging drug target discovery strategies, including computer-assisted approaches, drug affinity response target stability, multiomics analysis, gene editing, and nonsense-mediated mRNA degradation, and discusses the effectiveness and limitations of the various approaches, as well as their application in real cases. Through the review of the aforementioned contents, a general overview of the development of novel drug targets and disease treatment strategies will be provided, and a theoretical basis will be provided for those who are engaged in pharmaceutical science research. SIGNIFICANCE STATEMENT: Target-based drug discovery has been the main approach to drug discovery in the pharmaceutical industry for the past three decades. Traditional drug target discovery methods based on in vivo or in vitro validation are time-consuming and costly, greatly limiting the development of new drugs. Therefore, the development and selection of new methods in the drug target discovery process is crucial.

Fig. 1

Summary of drug target screening methods for drugs. Drug-centered drug target screening methods: (A) DARTS for drug target discovery and identification. The specific steps can be divided into five steps: sample preparation, small molecule or drug treatment, protease treatment, protein stability analysis, and target protein identification. (B) Network-based and machine learning-based methods for predicting drug targets. The specific steps can be divided into three steps: data collection and preprocessing, similarity analysis of known drug components and similarity analysis of known proteins, and prediction of unknown DTIs. Disease-centered drug target screening: (C) gene editing methods applied to drug target discovery (CRISPR–Cas9 library screening). The process can be divided into four steps: selection of CRISPR libraries and design and construction of gRNA libraries, delivery of CRISPR libraries and selection and drug treatment, creation of polymerase chain reaction libraries, and single-cell sequencing and analysis. (D) Posttranscriptional regulation (NMD)-based screening of cancer drug targets. Cellular NMD activity target identification methods: endogenous assays, such as plasmid reporter gene assays, determine intracellular NMD activity by transcriptional analysis of reporter genes. Exogenous assays, based on real-time fluorescent quantitative PCR, determine intracellular NMD activity by comparing the individual abundance of NMD-sensitive isoforms and their non-NMD counterparts. (E) Multiomics approach for drug target discovery.

Fig. 2

Mechanisms by which NMD promotes or inhibits the onset of disease. (A) Mechanisms by which inhibition of NMD can inhibit the progression of the disease, Downregulation of drug or UPF1 splicing factor expression inhibits the NMD pathway, affecting downstream genes or signaling pathways and thus suppressing disease. (B) Mechanisms by which NMD promotes disease progression. The PIWIL1 gene can interact with splicing factors to promote NMD in disease-suppressor genes leading to their degradation and thus promoting disease.