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How Are New Drugs Discovered and What Are Some of the Current Challenges in Drug Development?

Posted By Arun Kumar
Tags: Drug Discovery

Core Concepts in the Drug Discovery Process

Developing a new drug, whether it is a new chemical entity or a biologic therapeutic, is a very complex process which can take many years and can be very costly. Drug discovery involves the identification of new target candidates for testing in humans for efficacy and safety. Clinical testing is part of the development process where potential new drugs are selected for clinical trials. Theoretically, from this point it could either fail or succeed based on its own merit that will be determined in the clinical development program and biopharmaceutics evaluations. Each step of the process from early discovery through production and delivery must be fully explored, characterized, and understood. Drug discovery and development is long, complex and expensive involving iterative improvement cycle. Many biological targets must be considered for every new medicine eventually approved for clinical use and new research tools are needed to investigate each new target.

What is a target?

A target is a broad term which can be applied to a range of biological entities which may include proteins, genes and RNA. A good target needs to be efficacious, safe, and meet clinical and commercial needs. Selection of molecular targets based on disease understanding is a dominant paradigm in drug discovery.


Drug discovery has evolved different strategies based on the available knowledge of the disease. Enzo offers a line of products and services that can accelerate your drug discovery program. Choose from an extensive range of assay kits, enzymes, substrates and compound libraries for primary and secondary screening, immunodetection assays for reliable biomarker detection, and cytotoxicity assays for in vitro drug safety assessment. Our aim is to deliver innovative tools that make drug development more efficient, more cost-effective and more successful.


Figure 1: Enzo offers a line of products to accelerate your drug discovery program


Target-based Drug Discovery

There are broadly two different approaches to drug discovery. Drugs typically act by engaging a molecular target. In the past three decades, target-based drug (TBD) discovery has been the dominant approach employed in drug discovery in the pharmaceutical industry. This has been the method of choice in drug discovery but phenotypic screening can also be used. Let us review advantages and applications of both. Defining a specific target is the first step and by far, the richest source of targets for drugs are protein targets which play a key role in disease pathogenesis. This approach involves screening of compounds for specific activity against known targets associated with disease pathogenesis. Enzo Life Sciences has a long and successful track record in identifying, synthesizing, and commercializing valuable known bioactives for use as research tools. Our small molecules are available as either stand-alone products or curated libraries, offering ultimate flexibility and value. Our longstanding, flagship SCREEN-WELL® Compound Library product family offers an easy, ready-to-use method for compound screening.

A key advantage of TBD screening is that it utilizes straightforward biochemical assays that can be carried out either with a simple format or on an automated, rapid screening system of thousands of different compounds. Target-based assays, in general, are less time consuming to implement but sometimes are challenged by standard readouts such as enzymatic activity. The strength of the target based approach lies in the ability to apply molecular and chemical knowledge to investigate spe¬cific molecular hypotheses. For example, it is advantageous to have the ability to apply both small-molecule screening strategies using high-throughput formats and biologic-based approaches, such as identifying monoclonal anti¬bodies. Tremendous advances have been made in the develop¬ment of new tools to identify targets and compounds that interact with these targets. A case in point is high-throughput target-based screening assays that are applicable to key protein fami¬lies such as G protein-coupled receptors and kinases. Computational modelling and screening tools have also aided lead identification and optimization of targets.

Our decades of experience in the design and manufacture of active enzymes and their substrates supports development of an ever-expanding portfolio of biochemical assays. Our menu of scalable enzyme activity assays is anchored by our FLUOR DE LYS® deacetylase assay platform, featuring kits for screening modulators of HDAC and Sirtuin activity. We also offer FRET-based assays for matrix metalloproteinases (MMPs) and caspase activity, as well as phospho-specific antibody-based kinase assays. These assays exemplify the synergy of Enzo’s capabilities, assembling small peptides, active recombinant protein synthesis, fluorescent labeling and detection technologies, and antibody development into robust, reproducible assay kits.


Figure 2: Fluorescent emission spectra of small molecule drug camptothecin (light blue), OE33 cells (dark blue), MMP GREEN substrate (green), and MMP RED substrate (red), showing that the MMP GREEN and RED substrates avoid the interference caused by small molecules and cells.


Figure 3: Analysis of purified active PKA activity (ADI-EKS-390A). Varying quantities of purified active PKA were assayed using the PKA substrate microtiter plate. Assays were incubated for 60 min at 30°C.



Challenges of Target-based Drug Discovery

Despite the power of these tools to identify potential drug candidates, R&D productivity remains a crucial challenge for the pharmaceutical industry, which raises questions about the possible limitations of a tar¬get-centric approach to drug discovery. A recent analysis of all first-in-class small molecule medications points to reduced success and higher attrition rates for target-based approaches. A disadvantage of the target-based approach is that the specific molecular hypotheses may not be relevant to the disease pathogenesis. The study also showed that the contribution of phenotypic screening to the discovery of first-in-class drugs exceeded that of target based approaches. The target selection is also one of the most important determinants of attrition and overall R&D productivity.


Phenotypic Screening

Phenotypic screening is a strategy for the identification of molecules with particular biological effects in cell-based assays or animal models. Before the introduction of target-based approaches, drug dis¬covery was driven primarily by phenotypic assays, often with limited knowledge of the molecular mechanisms of disease. Here there is no preconceived idea of the molecular mechanism of action and the target. As a result, bioactive molecules identified in phenotypic screens have higher in vivo therapeutic impact. Phenotypic screening hits constitute better starting points for optimization as they must be cell permeable and engage their targets with sufficient affinity to displace endogenous interacting metabolites or proteins. Interest in phenotypic screening as a means for small molecule drug discovery has continued to increase in recent years. A successful phenotypic screen is based on selecting suitable biomarkers e.g. antibodies, chemical dyes or genetically encoded fluorescent tags whose phenotypic profiles can classify a set of known drugs in a single pass.


Limitations of Phenotypic Screening

Despite increased adoption, researchers interested in implementing phenotypic screening assays have encountered several challenges. Phenotypic screening assays have lower throughput and access to relevant cell models presents a major challenge. The greatest challenge is the identification of molecular targets of bioactive small molecules. Current phenotypic screenings are based on either too specific or broad readouts and this does not effectively distinguish modes of action in a single-pass screen.


Identifying Unwanted Drug Toxicity Sooner

Toxicity continues to be responsible for more than 30% of compound attrition during the drug development process. This remains one of the major causes for drugs being withdrawn after their approval. The other key cause of attrition is a lack of efficacy, accounting for some 30% of drug development failures. Today’s drug discovery strategies require candidate compounds to fail early and cheaply in the discovery stage, rather than late and expensively in the clinical phase. Testing compounds in physiologically relevant model systems and leveraging information from image-based screens are ways to focus on those compounds that give rise to the right phenotypic changes without undesirable effects on the system. The drug development industry has undertaken significant efforts to identify toxic events at the earliest opportunity during the development process. The growth in such Early Safety Assessment Initiatives has driven the need for more reliable, cost-effective, high throughput in vitro toxicity assays capable of predicting toxic liabilities prior to investment in more costly pre-clinical and clinical trials. Enzo Life Sciences has developed a panel of fluorescence-based live cell assays designed to assess the impact of toxic agents on overall cell function. Increasing the understanding of the cell signaling networks involved in a disease process can decrease the amount of clinical failures by identifying factors contributing to unexpected activity, toxicities and lack of efficacy. The next generation of phenotypic screening would benefit from advances in 3D culture model particularly in early drug discovery screening, drug efficacy and safety assessment. In addition, the whole field of organs-on-chips are new tools to model disease and facilitate drug development.


From our long-standing, flagship SCREEN-WELL® Compound library product family to our complex CELLESTIAL® portfolio of fluorescent probes and assay kits for cellular analysis, Enzo Life Sciences provides a wide variety of products for your drug discovery needs. Our decades of experience in the design and manufacture of active enzymes and their substrates supports development of an ever-expanding portfolio of biochemical assays. Please check out our Successful Research Tips or feel free to contact our Technical Support Service for further assistance.

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