Introductory Chapter: High-Throughput Screening - A New Tool for Precision Medicine

1. Introduction

High-Throughput Screening (HTS) is a programmed process that can rapidly identify active compounds (chemical /biological), antibodies, genes, or one or more candidates based on specific criteria [1]. In the pharmaceutical industry, HTS has been applied for novel drug discovery to overcome the conventional “trial and error” strategies to discover new therapeutic targets or validate their biological effects. Thus, a large number of biological effectors and modulators can be screened against specific targets in a short period using HTS technology during humanitarian emergencies [2]. HTS can also be used to evaluate pharmacological targets and pharmacological profile of agonists and antagonists for various receptors such as G-protein-coupled receptors (GPCRs) and enzymes. In recent years, a large number of drugs in clinical trials have come through HTS campaigns, establishing HTS as a reliable hit-finding technique. HTS has recently emerged as one of the important methods in the area of drug and vaccine design [3, 4, 5, 6]. It also allows the immediate incorporation of broad screening collections such as GPCR, kinase, and ion channel-based libraries, as well as the use of client-supplied libraries, into an HTS campaign [7]. Over the past decades, HTS mainly focused on several fundamental technologies like homogeneous assays, high-density microplates, high-performance microliter dispensers, imaging, laboratory automation, and combinatorial chemistry and genomics [8]. The success of HTS is dependent on the identification of meaningful assay systems. HTS is mainly performed using in silico methods (ligand-based drug design and structure-based drug design) in vitro methods (cell-based assays and biochemical assays), in-vivo methods (whole organism-based assays) [9].

Recently, with a rising need to store, access, and compute more sequencing reads and other biological data, HTS technology is becoming more important in the therapeutic context [10]. High-throughput biochemical measures of new variation, thorough health records, and open data sharing will improve our capacity to read individual genomics and understand exactly human health and diseases. The availability of HTS has surpassed current procedures for reporting on data analysis techniques. Lower prices and better accessibility led to an influx of data and related studies, which helped to progress bioinformatics. Innovative, dependable, and accurate omics-based study (i.e., genomics, transcriptomics, and proteomics) would aid novel drug development and precision medicine research [11].

This book also provides an in-depth look at the technologies utilized to detect biological reactions in HTS bioassays, such as fluorescence, luminescence, and atomic absorbance. In the context of anti-infective drug design, discovery, and development, the applications of HTS, reverse pharmacology, present obstacles, and future views of HTS in the pharmaceutical and biotechnology industries are explored. In this book, we describe a novel, multiplex immuno-assay platform based on high-throughput flow cytometry technology and advanced computational algorithms for data analysis. The assay simultaneously measures T cell dynamics including phenotype, time-dependent expression of activation markers, secreted effector cytokines, and proliferation. Further, this book covers the recent advances that use high-throughput methods to move towards the generation of a comprehensive network of extracellular protein-protein interactions (ePPIs) in humans for future targeted drug discovery. Furthermore, the book focuses on the advancement of technologies in HTS methods and research advances in three major technology areas including miniaturization, automation and robotics, and artificial intelligence, which promises to help speed up the discovery of medicines and their development process. At last, this book provides comprehensive knowledge about the use of various machine-learning algorithms for the screening of Aryl hydrocarbon receptor (AhR) modulators that have minimum errors compared with structure-based methods.

Precision medicine has gained a lot of attention in recent years due to its unique approach i.e., “to target the right treatments to the right patients at the right time”. According to the National Institutes of Health (NIH), precision medicine is a new therapy and preventative strategy based on knowledge about an individual’s genes, environment, and lifestyle [12, 13]. Precision medicine aims to give accurate and personalized treatment to patients by using genomes, proteomics, and other related technologies to evaluate and identify biomarkers in huge sample groups for specific diseases [14]. Precision medicine attempts to limit medical expenses while achieving an optimal treatment impact by bringing humanism, ethics, economics, sociology, and other knowledge factors together [15]. Precision medicine is a new medical concept for gaining a comprehensive knowledge of a patient’s genetic and genomic data to estimate disease and make better preventive, diagnostic, and treatment decisions [16]. Medical oncology has progressed through three stages: cytotoxic chemical treatment, gene-driven precision medicine, and personalized molecule-targeted treatment (Figure 1) [17]. Precision medicine has entered a new phase in clinical practice today. Its overall purpose is to minimize mortality, morbidity, and disability from serious diseases, improve healthcare service quality (Table 1) [18, 19].

Figure 1.

Applications of precision medicine in cancer management, therapeutic drug monitoring, drug discovery and delivery.

Area	Biomarkers	Treatment	Disease
Infectious diseases	CD4 + T cells, HIV viral load	Highly active antiretroviral therapy	HIV/AIDS
Cancer	BCR-ABL1	Blinatumomab, Bosutinib, Busulfan, Imatinib, Nilotinib	CML
	EML4-ALK	Crizotinib, Brigatinib, Alectinib	Lung cancer
Cardiovascular disease	CYP2C19	Citalopram, Clobazam, Doxepin, Clopidogrel, Carisoprodol	Coronary artery disease (CAD)
Pulmonary disease	G551D	Ivacaftor	Cystic fibrosis
Endocrine disease	RET	Prophylactic thyroidectomy, Carbozantinib	Multiple endocrine neoplasia type 2
Hematology	Factor V Leiden	Avoid prothrombotic drugs	Thrombosis
	Hepatitis C viral load	Direct-acting antiviral agents	Hepatitis C
Metabolic disease	LDL cholesterol	Statins	Hyperlipidemia
Neurology	CXCL13	Immunotherapy	Autoimmune encephalitis
Psychiatry	GRIK1	Topiramate	Alcohol use disorder
Renal disease	Urinary gene signature	Antirejection drugs	Transplant rejection
Ophthalmology	RPE65	Gene therapy	Leber’s congenital amaurosis
Pharmacogenomics	CYP2A6	Varenicline	Smoking cessation

Table 1.

Examples of precision medicine applications for the management of various clinical conditions.

2. Applications of high throughput screening (HTS) in precision medicine

Improvements in sequencing technology over the last 10 years have allowed several high-throughput sequencing platforms to provide novel insights to design personalized medicine [20]. Modern sequencing technology (Ion, Illumina, Torrent, Oxford Nanopore Technologies, pacific biosciences, etc.) created new paths for HTS in the area of medicine. Epigenetic applications, Genomic (DNA-seq), and transcriptomic (RNA-seq), are all part of HTS. To determine genomic variants (insertion or deletion, single nucleotide variants, copy number alterations, and fundamental changes) from biological samples, whole-genome sequencing (WGS), and whole-exome sequencing (WES) is used (Figure 2) [21, 22]. Identification of new transcripts, characterization of gene expression profiles, alternative splicing, RNA editing, and fusion transcripts are all feasible using RNA-seq. [23]. Similarly, next-generation sequencing (NGS) may quickly identify or “sequence” huge parts of a person’s genome and are significant advancements in precision medicine clinical applications. These tests can assist patients, doctors, and researchers uncover genetic variations that can help them diagnose, treat, and know more about human disease. Apart from this, NGS techniques can also be applied in the area of metagenomics, RNAseq, ribosome profiling, targeted sequencing, and minor variant reconstruction, as well as a wide range of post-pipeline studies that combine genomic, clinical, epidemiological, and ecological data [24, 25].

Figure 2.

Scheme for the high-throughput screening based development of personalized/precision medicine. Samples collected from the patients are subjected to DNA isolation and sequencing (NGS) for pharmacogenomics. Based on the analysis of sequencing (NGS) data, high-throughput screening (HTS) of the compound library is performed to identify the drug(s) of choice. Patient treatment with these drug(s) is monitored for its therapeutic and ADME profile. Based on the therapeutic effect of the drug(s), multi-population genome-wide association studies (GWAS) study may lead to development of personalized/precision medicine.

HTS has mostly been applied to specific areas of the genome or in the context of identifying microscopic pathogens. Prenatal assays intended to identify chromosomal abnormalities in cell-free DNA from maternal blood are clinically accessible [26]. Targeted HTS of clinically actionable mutations is also being used to guide illness diagnosis and therapy [27]. HTS has also been used in clinical settings to track pathogen outbreaks like methicillin-resistant Staphylococcus aureus infections. The development and usage of these specialized assays will continue to grow, but precision medicine depends on the potential therapeutic use of more extensive methods like WGS, which is still facing complications. WGS is the most comprehensive technique for potential therapeutic use since that marks the next stage in the path to a complete understanding of the genetic determinants of a patient’s heritable character [28]. Additional genome sequencing, and data from large-scale genomics efforts like ENCODE and GTEx, which allow the development of even more extensive datasets, will help interpret the variations. Community resources for correlating phenotypes to sequences will be provided through open access programs including the Personal Genomes Project and integrated Personal Omics Profiling [29].

3. Few prime areas of high throughput screening (HTS) for precision medicine

3.1 Management of infectious diseases

Efforts have recently been made to combine these technologies with bioinformatics and epidemiology to improve public health surveillance, investigations, and control of infectious diseases [30]. The previous 40 years had a substantial influence on the knowledge of infectious diseases. A broad spectrum of medically important viruses, bacteria, parasites, fungus, and other pathogens have been studied using next-generation sequencing [31]. Many of these pathogens are directly important to the development and assessment of vaccinations, medicines, infection control, and a variety of nonmedical pandemic countermeasures [32].

3.2 Management of cancer

Recently HTS has been coupled with various sequencing techniques in the design of precision medicine for the treatment of various types of cancers like multiple myeloma, glioblastoma, and pediatric cancers. A wide range of FDA approved drugs such as temsirolimus (mTOR inhibitor), ceritinib (ALK inhibitor), and BI2536 (PLK1 inhibitor), panobinostat, bortezomib, ixazomib, carfilzomib, and selinexor, bortezomib (proteasome inhibitor), Bcl-2 inhibitor ABT-263 with the mTOR inhibitor AZD-8055 have been tested as precision therapy for multiple myeloma, glioblastoma, and pediatric cancer [33, 34, 35].

4. Conclusions

In clinical and preclinical research, there have been a few attempts to integrate throughput screening technologies with precision medicine. The relevance of high-throughput screening approaches in identifying and designing precision therapies for the treatment of various diseases is highlighted in this chapter. Over the last ten years, advances in sequencing technology have enabled several high-throughput sequencing platforms to bring unique insights into the creation of customized medicine. The sequencing technologies of the present day (Ion, Illumina, Torrent, Oxford Nanopore Technologies, pacific biosciences) created a new roadmap for HTS technologies to identify and design precision therapeutics.

5. Future perspectives

The development of a single definition for precision medicine will aid transdisciplinary areas with a shared understanding of concepts and enhance collaborative ideas. Standardization of HTS and analytical methods will make it easier to validate and replicate findings in clinically relevant timeframes. This, along with interdisciplinary cooperation, will allow it to be fully integrated into patient care and treatment via the development of novel diagnostic, predictive, and prognostic tests. The creation of broad conceptual frameworks that address the underlying drivers of health across specialized areas will be facilitated by the establishment of a shared precision medicine definition, which will promote collaboration between the transdisciplinary domains that make up precision medicine. It may be beneficial to establish a set of recommendations in the next 5–10 years to assist in deciding whether or not research activities or therapies fit precision medicine requirements. These principles might determine if the endeavor should include efforts to personalize therapies, a focus on genetics/biology, the environment, nutrition, and/or lifestyle, as well as the amount to which these distinct variables interact.