Omics-informed drug target discovery in combating emerging infectious diseases
The catastrophic consequences of ever-increasing rates of death from infectious diseases demands new experimental strategies for drug target selection and drug design. Over the last decade, the pharmaceutical industry has been wounded by several issues including failure of drug-development programmes, burgeoning cost of drug development, increasing regulatory control, lack of innovation and declining productivity of therapeutic drugs in the market.
Given the multifaceted riddle posed to drug discovery, traditional methods alone are certainly not sufficient and are likely to shift focus to the integration of different areas of biology, allowing researchers to comprehend the bigger picture in drug discovery. Integrating ‘omics’ sciences – genomics, transcriptomics, proteomics and metabolomics – is having a significant impact on the drug discovery process, providing a new perspective for addressing problems in clinical and translational medicine. The coming of age of omics-based technologies could offer a solution to major bottlenecks in drug discovery and could foster the acceleration of target selection for the rational design of new drugs that can interfere with specific pathways associated with infectious diseases. In future, omics-based technologies should enable us to develop innovative approaches that will be predictive, preventive and personalised.
For most of human history, infectious diseases have often led to unexplained critical illness and death. The drug discovery breakthroughs of the last decade have contributed enormously to the progress of medicine that has saved hundreds of millions of people from infectious diseases.1 However, the rapid emergence of drug-resistant pathogens along with a shrinking therapeutic arsenal is serving to frustrate decades of progress in infection medicine. The current drug discovery pipeline is a long, tedious, expensive and time-consuming process, entrenched with a higher level of uncertainty that a drug will actually enter human clinical testing, get approved, and reach the market. Rising drug development costs against a backdrop of decline in productivity also negatively affects the sustainability of the pharmaceutical industry.2 As we now stand on the edge of a global crisis in infectious diseases, there is a strong need for innovative approaches that can overcome limitations in the traditional drug discovery process and accelerate the development of new, safe and effective medicines.
The advent of molecular biology is having a profound effect on drug discovery, as it enables us to determine the most accurate point of attack to overcome the hurdles in new drug development pipelines, thereby expanding the number of potential therapeutic options. The main promise of drug discovery lies in understanding disease mechanisms at the molecular level and identifying potential molecular targets for drug intervention.3 Robust validated drug targets are needed to improve therapeutic response and guide development of more safe and targeted therapies for infectious diseases. While several types of molecular targets have been impacting the field of drug discovery, the process of identifying and validating specific disease targets has been quite challenging. To achieve the most successful treatment of infectious diseases and tailor medical treatment to the individual characteristics of each patient, it is essential to monitor the molecular basis of early initiation and progression of diseases to provide important consideration and guide future directions to develop successful drug candidates.4 Recent advances in ‘omics’ approaches (genomics, transcriptomics, proteomics and metabolomics) have made it possible to accelerate the discovery of potential targets for safe and more effective drug intervention.5 However, there are several challenges that still need to be addressed, but current efforts regarding target selection and validation will assist in the development of effective drugs to treat infectious diseases and pave way for the execution of personalised therapies for the benefit of patients, medical providers and pharmaceutical companies.
An important step towards identification of infectious pathogens is to determine the differences in the structure and function of microbial communities between diseased and non-diseased individuals. This can be achieved through community-wide high-throughput amplicon sequencing of the whole microbial community in healthy and diseased individuals.6 Furthermore, the functional capacities of the microbial community can be studied by additional techniques such as shotgun metagenomics, metatranscriptomics, proteomics and metabolomics.5 This article outlines an effective mitigation strategy for identification of disease targets based on omics data that would maximise the probability of finding causative agents and the factors that contribute to disease initiation and progression. These approaches will also enhance our understanding of disease mechanisms and provide promising avenues for drug target selection towards effective treatment of infectious diseases.
16S/18S Amplicon sequencing
The identification of pathogenic microbes is critical for drug target selection, to ultimately maximise the efficacy of treatment for serious infections. Current diagnostic approaches are incapable of uncovering the full spectrum of pathogenic microbes in patients, which restricts our ability to identify the most relevant therapeutic targets for successful treatments.7 Community-wide high-throughput amplicon sequencing of the 16S/18S rRNA gene would enable us to detect the full array of pathogens in patient specimens, which would help achieve maximum therapeutic outcome in clinical practice. The amplicon sequencing approach can be used to identify bacterial and fungal compositions that are most persistent on hosts. This method is often desirable to quantify and characterise specific microbial populations in terms of abundance, composition and diversity.6 By providing information about the microbial strain involved in specific infections, amplicon sequencing can help target the isolation of potential pathogens in pure culture. If pure cultures are available, then physiological, metabolic and genomic analysis of these strains can inform about the potential targets of drug intervention.8 Furthermore, prior knowledge about strain interactions, searching for genes associated with antibiotic resistance, and host-microbe interactions could increase the chance of selecting appropriate drug candidates for successful antimicrobial therapy.9
Shotgun metagenomics is the untargeted sequencing of metagenomes that can potentially catalogue all microbes – including bacteria, fungi and viruses – that are present in a sample. This method is performed to determine the diversity and abundance of microbes with additional functional analysis that would enable us to explore large unknown parts of the microbiome with relation to health, disease and treatment intervention. Shotgun methods are less biased, and allow us to identify genes or genetic pathways associated with specific functions, thereby providing valuable insight into novel drug targets for potential therapeutic benefits.10 Furthermore, shotgun methods can also interrogate accessory genome, an important driver of pathogens that persist in particular environments. Identifying specific accessory genes in pathogens would facilitate rational design of potential drugs for better treatment against infectious diseases. Shotgun methods also provide greater taxonomic resolution and can distinguish species and strains with distinct biological functions. It also provides opportunity to gain insight into the functional alterations that accompany the conversion of a normal microbiome to one of a disease-driving configuration.11 Thus, understanding the biological origin of disease and characterising specific strains of microbial communities offers great promise for novel target selection and innovative ways to design new drugs for more effective treatment.
Recent advances in massively parallel RNA-sequencing have presented exciting opportunities in the area of transcriptome analysis, providing insight into new sources of drug discovery. Metatranscriptomics is a community-wide RNA-sequencing approach that provides a snapshot of a transcriptome profile that corresponds to the discrete environmental microbial population. This method is rapidly growing in popularity and provides an opportunity to gain more insight into the functionality of microbial communities.12 During the course of microbial infection, a dynamic cascade of events is initiated that triggers alteration of global gene expression patterns between the host and the interacting pathogen. The metatranscriptome approach is relevant for identifying genes and pathways that are differentially regulated in response to pathogen infection and also uncovers functional responses involved in host-microbe interaction. Moreover, recent methods such as the ‘Dual-RNA-seq’ profile – the expression levels of genes simultaneously in an infected bacterium and its infected host – enable us to determine the interactions between the host and the colonising extracellular pathogens.13 The dual-RNA-seq approach also allows rapid discovery of virulence-related factors and regulatory processes that drive pathogenesis.14 Application of this high-throughput approach would allow genome-wide infection-linked transcriptome profiling to unravel concealed gene functions in pathogens that are critical for survival in different host niches and could help identify potential drug targets for improved treatments.
In recent years, several innovative strategies have been developed that facilitate the process of drug discovery either by identifying the mode of action of a drug, by understanding off-target interactions, or by finding potential therapeutic benefit for an existing drug.15 Advances in proteomics technology offers great promise in understanding the molecular pathogenic mechanisms and therapeutic options for infectious diseases. Many different proteomic methods have been introduced that have enabled scientists to screen large numbers of proteins from clinically-relevant samples to aid discovery of disease-specific biomarkers, identify drug targets and design more effective drugs. Functional proteomics constitutes an emerging research area in the proteomics field, which explores pathway components and the frequency of pathway dysregulation associated with pathologies. This approach would allow us to develop strategies that can target multiple pathways using combinations of pathway-specific drugs, which can reduce the spread of antibiotic resistance.16 Chemical proteomics is another multidisciplinary research area integrating cell biology and biochemistry with organic synthesis and mass spectrometry. This approach has been widely used to screen drug-protein interactions and can lead to identification of new drug targets.15 Clinical proteomics offers both quantitative and qualitative profiling of proteins in clinically relevant materials and can help in clinical decision making.17 A range of techniques – including one- or two-dimensional gel electrophoresis, high-performance liquid chromatography (HPLC), fast performance liquid chromatography (FPLC), and mass spectrometry (MS) – has been successfully used in identification and separation of protein targets from complex mixtures. Due to exquisite speed and sensitivity, MS-based methods are becoming the most powerful tool of choice in drug target discovery. The emerging multiplexing technology of protein chips and arrays is also expected to enhance the throughput of drug target selection in the near future.
Metabolomics is the emerging ‘omics’ science that involves comprehensive characterisation of metabolites for understanding biological systems. Metabolomics has been increasingly used in disease diagnosis, characterisation of disease mechanisms, drug target discovery and drug treatments.18 Metabolomics enables scientists to identify both endogenous metabolites (gene-derived metabolites) and exogenous metabolites (environment-derived metabolites) that would provide deeper insight into the fundamental causes of infectious diseases for therapeutic intervention. The growing accessibility of metabolomics has led to a new approach known as ‘personalised metabolic phenotyping’ that can customise an individual’s medical treatment and help advance the field of precision medicine.19 Several analytical methods have been used to collect data on the metabolite composition of biological samples, which includes mass spectrometry (MS), liquid chromatography-mass spectrometry (LC-MS), nuclear magnetic resonance spectroscopy (NMR), vibrational spectroscopy and mass spectral imaging techniques.20 Recent advancement in metabolomics offers promise to identify more informative disease targets for rational design of drugs and improved therapeutics. On a population level, metabolomics is accelerating drug discovery and development, and on an individual level, metabolomics is advancing the field of precision medicine.
To conclude, integrating ‘omics’ sciences – genomics, transcriptomics, proteomics and metabolomics – is the most powerful approach to providing deeper insight into the molecular basis of early initiation and progression of infectious diseases. Whether it’s being used in the clinic or in the pharmaceutical industry, omics approaches are becoming vital tools for target selection, drug discovery and therapeutics. As we look to the future, it is in the context of infectious disease research that omics technologies will likely impact novel target selection for therapeutic intervention.
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- Muthuirulan P. (2016). Chasing new drugs against infectious diseases: a herculean task. J Clin Case Rep, 6(859), 2.
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- Torkamani A, Andersen KG, Steinhubl SR, Topol EJ. (2017). High-definition medicine. Cell, 170(5), 828-843.
- Muthuirulan P. (2016). Integrating Omics Technologies for Prospective Antimicrobial Drug Development. 1-7 J Cell Biol Mol Sci, 1(1).
- Zhou J, Wu L, Deng Y, Zhi X, Jiang YH, Tu Q, et al. (2011). Reproducibility and quantitation of amplicon sequencing-based detection. The ISME journal, 5(8), 1303.
- Liu A, Wang C, Liang Z, Zhou ZW, Wang L, Ma Q, et al. (2015). High-throughput sequencing of 16S rDNA amplicons characterizes bacterial composition in cerebrospinal fluid samples from patients with purulent meningitis. Drug design, development and therapy, 9, 4417.
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- Laudadio I, Fulci V, Palone F, Stronati L, Cucchiara S, Carissimi C. (2018). Quantitative Assessment of Shotgun Metagenomics and 16S rDNA Amplicon Sequencing in the Study of Human Gut Microbiome. Omics: a journal of integrative biology, 22(4), 248-254.
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- Ishii SI, Suzuki S, Tenney A, Nealson KH, Bretschger O. (2018). Comparative metatranscriptomics reveals extracellular electron transfer pathways conferring microbial adaptivity to surface redox potential changes. The ISME journal, 1.
- Westermann AJ, Vogel J. (2018). Host-Pathogen Transcriptomics by Dual RNA-Seq. In Bacterial Regulatory RNA(pp. 59-75). Humana Press, New York, NY.
- Nuss AM, Beckstette M, Pimenova M, Schmühl, C, Opitz W, Pisano F, et al. (2017). Tissue dual RNA-seq allows fast discovery of infection-specific functions and riboregulators shaping host–pathogen transcriptomes.Proceedings of the National Academy of Sciences, 114(5), E791-E800.
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Pushpanathan Muthuirulan is currently a Research Associate at Harvard University studying the developmental and genetic basis of human height variations using functional genomics approaches. Previously, he worked as a postdoctoral researcher at the National Institutes of Health, where his research focused on developing state-of-the-art technologies using CRISPR-cas9 and super-resolution microscopy to map neural circuits that involves visual motion information processing in Drosophila.
He obtained his PhD in Microbiology from the Department of Genetics, School of Biological Sciences at Madurai Kamaraj University, India where he identified a novel antifungal peptide, MMGP1, from the marine metagenome and characterised its discrete antifungal mechanisms with an ultimate goal to combat opportunistic human fungal infections such as candidiasis and aspergillosis. He gained his Bachelors and Master’s degree in Zoology (specialisation Biotechnology) at the American College, India and subsequently gained industry experience as Project Assistant (2006) in Strides Arcolab R&D project towards the development and production of antifungal agents, Capsofungin acetate against Candidiasis. His expertise lies in omics technologies, drug discovery, neuroscience and developmental and evolutionary genetics.