Author: Ken Doyle

NanoLuc® Luciferase: Brighter Days Ahead for In Vivo Imaging

Posted on by Ken Doyle
nanoluc in vivo imaging

The development of NanoLuc® luciferase technology has provided researchers with new and better tools to study endogenous biology: how proteins behave in their native environments within cells and tissues. This small (~19kDa) luciferase enzyme, derived from the deep-sea shrimp Oplophorus gracilirostris, offers several advantages over firefly or Renilla luciferase. For an overview of NanoLuc® luciferase applications, see: NanoLuc® Luciferase Powers More than Reporter Assays.

The small size of NanoLuc® luciferase, as well the lack of a requirement for ATP to generate a bioluminescent signal, make it particularly attractive as a reporter for in vivo bioluminescent imaging, both in cells and live animals. Expression of a small reporter molecule as a fusion protein is less likely to interfere with the biological function of the target protein. NanoLuc® Binary Technology (NanoBiT®) takes this approach a step further by creating a complementation reporter system where one subunit is just 11 amino acids in length. This video explains how the high-affinity version of NanoBiT® complementation (HiBiT) works:

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New Uses for Old Drugs: Remdesivir and COVID-19

Posted on by Ken Doyle

With the COVID-19 pandemic far from over in the United States and worldwide, the battle against the disease continues to intensify. Much hope has been pinned on vaccine development. However, vaccines are a long-term, preventative strategy. The immediate need for drugs to fight COVID-19 has accelerated efforts for a variety of potential treatments (see The Race to Develop New Therapeutics Against Coronaviruses).

The Remdesivir Origin Story

3d model of coronavirus

One drug that has received widespread attention is remdesivir. It was developed from research by Gilead Sciences that began in 2009, originally targeting hepatitis C virus (HCV) and respiratory syncytial virus (RSV) (1). At present, remdesivir is classified as an investigational new drug (IND) and has not been approved for therapeutic use anywhere in the world.

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Designing BET(ter) Inhibitors to Guide Therapy for Cancer and Inflammatory Diseases

Posted on by Ken Doyle
bet proteins brd nanoluc

Transcriptional activation of genes within the nucleus of eukaryotic cells occurs by a variety of mechanisms. Typically, these mechanisms rely on the interaction of regulatory proteins (transcriptional activators or repressors) with specific DNA sequences that control gene expression. Upon DNA binding, regulatory proteins also interact with other proteins that are part of the RNA polymerase II transcriptional complex.

One type of transcriptional activation relies on inducing a conformational change in chromatin, the DNA-protein complex that makes up each chromosome within a cell. In a broad sense, “extended” or loosely wound chromatin is more accessible to transcription factors and can signify an actively transcribed gene. In contrast, “condensed” chromatin hinders access to transcription factors and is characteristic of a transcriptionally inactive state. Acetylation of lysine residues in histones—the primary constituents of the chromatin backbone—results in opening up the chromatin and consequent gene activation. Disruption of histone acetylation pathways is implicated in many types of cancer (1).

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Which Came First: The Virus or the Host?

Posted on by Ken Doyle

They existed 3.5 billion years before humans evolved on Earth. They’re neither dead nor alive. Their genetic material is embedded in our own DNA, constituting close to 10% of the human genome. They can attack most forms of life on our planet, from bacteria to plants to animals. And yet, if it wasn’t for them, humans might never have existed.

3D structure of a coronavirus
A depiction of the shape of coronavirus as well as the cross-sectional view. The image shows the major elements including glycoproteins, viral envelope and helical RNA. This file is licensed under the Creative Commons Attribution-Share Alike 4.0 International license.

No, that’s not the blurb for a new Hollywood blockbuster, although recent developments have proven, once again, that truth is decidedly more bizarre than fiction. Now that “coronavirus” has become a household word, the level of interest in all things virus-related is growing at an unprecedented rate. At the time of writing, coronavirus and COVID-19 topics dominated search traffic on Google, as well as trends on social media. A recent FAQ on this blog addresses many of the questions we hear on these topics.

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Targeted Protein Degradation: A Bright Future for Drug Discovery

Posted on by Ken Doyle
targeted protein degradation and protacs

Our cells have evolved multiple mechanisms for “taking out the trash”—breaking down and disposing of cellular components that are defective, damaged or no longer required. Within a cell, these processes are balanced by the synthesis of new components, so that DNA, RNA and proteins are constantly undergoing turnover.

Proteins are degraded by two major components of the cellular machinery. The discovery of the lysosome in the mid-1950s provided considerable insight into the first of these degradation mechanisms for extracellular and cytosolic proteins. Over the next several decades, details of a second protein degradation mechanism emerged: the ubiquitin-proteasome system (UPS). Ubiquitin is a small, highly conserved polypeptide that is used to selectively tag proteins for degradation within the cell. Multiple ubiquitin tags are generally attached to a single targeted protein. This ill-fated, ubiquitinated protein is then recognized by the proteasome, a large protein complex with proteolytic activity. Ubiquitination is a multistep process, involving several specialized enzymes. The final step in the process is mediated by a family of ubiquitin ligases, known as E3.

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CRISPR/Cas9 Knock-In Tagging: Simplifying the Study of Endogenous Biology

Posted on by Ken Doyle

Understanding the expression, function and dynamics of proteins in their native environment is a fundamental goal that’s common to diverse aspects of molecular and cell biology. To study a protein, it must first be labeled—either directly or indirectly—with a “tag” that allows specific and sensitive detection.

Using a labeled antibody to the protein of interest is a common method to study native proteins. However, antibody-based assays, such as ELISAs and Western blots, are not suitable for use in live cells. These techniques are also limited by throughput and sensitivity. Further, suitable antibodies may not be available for the target protein of interest.

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The 30th International Symposium on Human Identification: Elevating DNA Forensics

Posted on by Ken Doyle

Thirty Years of ISHI

30 years of ISHI

In the fall of 1989, a small group of forensic scientists, law enforcement officials and representatives from Promega Corporation gathered in Madison, Wisconsin, for the very first International Symposium on Human Identification (ISHI). At the time, DNA typing was in its infancy and had not yet been validated as a forensic method. The available technology consisted of two methods: detection of restriction fragment length polymorphisms (RFLPs) and variable number of tandem repeats (VNTRs). Promega had developed products based on both analytical methods, which essentially provide a DNA “fingerprint” or profile for each individual tested.

Among the attendees at that first symposium was Tom Callaghan, then a graduate student. That experience made a significant impact on his career path. Last week, at ISHI 30, he presented a session on rapid DNA testing. Dr. Callaghan currently serves as a Senior Biometric Scientist for the FBI. In 1999, he was instrumental in launching the FBI’s Combined DNA Index System (CODIS) and in 2003, he became the first CODIS Unit Chief.

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CRISPR/Cas9, NanoBRET and GPCRs: A Bright Future for Drug Discovery

Posted on by Ken Doyle

GPCRs

G protein-coupled receptors (GPCRs) are a large family of receptors that traverse the cell membrane seven times. Functionally, GPCRs are extremely diverse, yet they contain highly conserved structural regions. GPCRs respond to a variety of signals, from small molecules to peptides and large proteins. Many GPCRs are involved in disease pathways and, not surprisingly, they present attractive targets for both small-molecule and biologic drugs.

In response to a signal, GPCRs undergo a conformational change, triggering an interaction with a G protein—a specialized protein that binds GDP in its inactive state or GTP when activated. Typically, the GPCR exchanges the G protein-bound GDP molecule for a GTP molecule, causing the activated G protein to dissociate into two subunits that remain anchored to the cell membrane. These subunits relay the signal to various other proteins that interact with or produce second-messenger molecules. Activation of a single G protein can result, ultimately, in the generation of thousands of second messengers.

Given the complexity of GPCR signaling pathways and their importance to human health, a considerable amount of research has been devoted to GPCR interactions, both with specific ligands and G proteins. Continue reading “CRISPR/Cas9, NanoBRET and GPCRs: A Bright Future for Drug Discovery”

Obesity: Can Simple Approaches Reduce Complex Risks?

Posted on by Ken Doyle

Obesity Prevalance 2017
Prevalence of Self-Reported Obesity Among U.S. Adults by State and Territory, Behavioral Risk Factor Surveillance System (BRFSS) 2017. Prevalence estimates reflect BRFSS methodological changes started in 2011. These estimates should not be compared to prevalence estimates before 2011. Source: BRFSS, Centers for Disease Control and Prevention

The Obesity Epidemic

For over a decade, obesity has been called an “epidemic”, both in the popular and scientific literature. Traditionally, the term “epidemic” is associated with a highly contagious disease that carries with it a significant risk of mortality. A comprehensive review of observational studies (1) suggested that obesity did not fit this definition, despite the use of the term in a widely disseminated report by the World Health Organization in 2002.

Regardless of the etymological fine points, the worldwide prevalence of obesity and its associated health risks are clear. These risks include type 2 diabetes, hypertension, several cancers, gall bladder disease, coronary artery disease and stroke (2). Yet, the debate over obesity and options for reducing its risks has become increasingly polarized. As a result, some health researchers are advocating a “health at every size” (HAES) approach to address the social, cultural and lifestyle implications of obesity (2).

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When Proteins Get Together: Shedding (Blue) Light on Cellular LOV

Posted on by Ken Doyle

NanoBRETNo protein is an island. Within a cell, protein-protein interactions (PPIs) are involved in highly regulated and specific pathways that control gene expression and cell signaling. The disruption of PPIs can lead to a variety of disease states, including cancer.

Two general approaches are commonly used to study PPIs. Real-time assays measure PPI activity in live cells using fluorescent or luminescent tags. A second approach includes methods that measure a specific PPI “after the fact”; popular examples include a reporter system, such as the classic yeast two-hybrid system.

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