Tag Archives: drug testing

Human-on-a-chip predicts in vivo results based on in vitro model … for the first time

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If successful the hope is that ‘human-on-a-chip’ will replace most, if not all, animal testing. This July 3, 2019 Hesperos news release (also on EurekAlert) suggests scientists are making serious gains in the drive to replace animal testing (Note: For anyone having difficulty with the terms, pharmacokinetics and pharmacodynamics, there are definitions towards the end of this posting, which may prove helpful),

Hesperos Inc., pioneers* of the “human-on-a-chip” in vitro system has announced the use of its innovative multi-organ model to successfully measure the concentration and metabolism of two known cardiotoxic small molecules over time, to accurately describe the drug behavior and toxic effects in vivo. The findings further support the potential of body-on-a-chip systems to transform the drug discovery process.

In a study published in Nature Scientific Reports, in collaboration with AstraZeneca, Hesperos described how they used a pumpless heart model and a heart:liver system to evaluate the temporal pharmacokinetic/pharmacodynamic (PKPD) relationship for terfenadine, an antihistamine that was banned due to toxic cardiac effects, as well as determine its mechanism of toxicity.

The study found there was a time-dependent, drug-induced response in the heart model. Further experiments were conducted, adding a metabolically competent liver module to the Hesperos Human-on-a-Chip® system to observe what happened when terfenadine was converted to fexofenadine. By doing so, the researchers were able to determine the driver of the pharmacodynamic (PD) effect and develop a mathematical model to predict the effect of terfenadine in preclinical species. This is the first time an in vitro human-on-a-chip system has been shown to predict in vivo outcomes, which could be used to predict clinical trial outcomes in the future.

“The ability to examine PKPD relationships in vitro would enable us to understand compound behavior prior to in vivo testing, offering significant cost and time savings,” said Dr. Shuler, President and CEO, Hesperos, Inc and Professor Emeritus, Cornell University. “We are excited about the potential of this technology to help us ensure that potential new drug candidates have a higher probability of success during the clinical trial process.”

Understanding the inter-relationship between pharmacokinetics (PK), the drug’s time course for absorption, distribution, metabolism and excretion, and PD, the biological effect of a drug, is crucial in drug discovery and development. Scientists have learned that the maximum drug effect is not always driven by the peak drug concentration. In some cases, time is a critical factor influencing drug effect, but often this concentration-effect-time relationship only comes to light during the advanced stages of the preclinical program. In addition, often the data cannot be reliably extrapolated to humans.

“It is costly and time consuming to discover that potential drug candidates may have poor therapeutic qualities preventing their onward progression,” said James Hickman, Chief Scientist at Hesperos and Professor at the University of Central Florida. “Being able to define this during early drug discovery will be a valuable contribution to the optimization of potential new drug candidates.”

As demonstrated with the terfenadine experiment, the PKPD modelling approach was critical for understanding both the flux of compound between compartments as well as the resulting PD response in the context of dynamic exposure profiles of both parent and metabolite, as indicated by Dr. Shuler.

In order to test the viability of their system in a real-world drug discovery setting, the Hesperos team collaborated with scientists at AstraZeneca, to test one of their failed small molecules, known to have a CV [cardiovscular?] risk.

One of the main measurements used to assess the electrical properties of the heart is the QT interval, which approximates the time taken from when the cardiac ventricles start to contract to when they finish relaxing. Prolongation of the QT interval on the electrocardiogram can lead to a fatal arrhythmia known as Torsade de Pointes. Consequently, it is a mandatory requirement prior to first-in-human administration of potential new drug candidates that their ability to inhibit the hERG channel (a biomarker for QT prolongation) is investigated.

In the case of the AstraZeneca molecule, the molecule was assessed for hERG inhibition early on, and it was concluded to have a low potential to cause in vivo QT prolongation up to 100 μM. In later pre-clinical testing, the QT interval increased by 22% at a concentration of just 3 μM. Subsequent investigations found that a major metabolite was responsible. Hesperos was able to detect a clear PD effect at concentrations above 3 μM and worked to determine the mechanism of toxicity of the molecule.

The ability of these systems to assess cardiac function non-invasively in the presence of both parent molecule and metabolite over time, using multiplexed and repeat drug dosing regimes, provides an opportunity to run long-term studies for chronic administration of drugs to study their potential toxic effects.

Hesperos, Inc. is the first company spun out from the Tissue Chip Program at NCATS (National Center for Advancing Translational Sciences), which was established in 2011 to address the long timelines, steep costs and high failure rates associated with the drug development process. Hesperos currently is funded through NCATS’ Small Business Innovation Research program to undertake these studies and make tissue chips technology available as a service based company.

“The application of tissue chip technology in drug testing can lead to advances in predicting the potential effects of candidate medicines in people,” said Danilo Tagle, Ph.D., associate director for special initiatives at NCATS.

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About Hesperos
Hesperos, Inc. is a leader in efforts to characterize an individual’s biology with human-on-a-chip microfluidic systems. Founders Michael L. Shuler and James J. Hickman have been at the forefront of every major scientific discovery in this realm, from individual organ-on-a-chip constructs to fully functional, interconnected multi-organ systems. With a mission to revolutionize toxicology testing as well as efficacy evaluation for drug discovery, the company has created pumpless platforms with serum-free cellular mediums that allow multi-organ system communication and integrated computational PKPD modeling of live physiological responses utilizing functional readouts from neurons, cardiac, muscle, barrier tissues and neuromuscular junctions as well as responses from liver, pancreas and barrier tissues. Created from human stem cells, the fully human systems are the first in vitro solutions that accurately utilize in vitro systems to predict in vivo functions without the use of animal models, as featured in Science. More information is available at http://www.
hesperosinc.com

Years ago I went to a congress focused on alternatives to animal testing (August 22, 2014 posting) and saw a video of heart cells in a petri dish (in vitro) beating in a heartlike rhythm. It was something like this,

ipscira
Published on Oct 17, 2010 https://www.youtube.com/watch?v=BqzW9Jq-OVA

I found it amazing as did the scientist who drew my attention to it. After, it’s just a collection of heart cells. How do they start beating and keep time with each other?

Getting back to the latest research, here’s a link and a citation for the paper,

On the potential of in vitro organ-chip models to define temporal pharmacokinetic-pharmacodynamic relationships by Christopher W. McAleer, Amy Pointon, Christopher J. Long, Rocky L. Brighton, Benjamin D. Wilkin, L. Richard Bridges, Narasimham Narasimhan Sriram, Kristin Fabre, Robin McDougall, Victorine P. Muse, Jerome T. Mettetal, Abhishek Srivastava, Dominic Williams, Mark T. Schnepper, Jeff L. Roles, Michael L. Shuler, James J. Hickman & Lorna Ewart. Scientific Reports volume 9, Article number: 9619 (2019) DOI: https://doi.org/10.1038/s41598-019-45656-4 Published: 03 July 2019

This paper is open access.

I happened to look at the paper and found good definitions of pharmacokinetics and pharmacodynamics. I know it’s not for everyone but if you’ve ever been curious about the difference (from the Introduction of On the potential of in vitro organ-chip models to define temporal pharmacokinetic-pharmacodynamic relationships),

Integrative pharmacology is a discipline that builds an understanding of the inter-relationship between pharmacokinetics (PK), the drug’s time course for absorption, distribution, metabolism and excretion and pharmacodynamics (PD), the biological effect of a drug. In drug discovery, this multi-variate approach guides medicinal chemists to modify structural properties of a drug molecule to improve its chance of becoming a medicine in a process known as “lead optimization”.

…

*More than one person and more than one company and more than one country claims pioneer status where ‘human-on-a-chip’ is concerned.

Predicting drug side effects with guts-on-a-chip

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It’s been a while since I’ve featured a story about a technology that could drastically reduce (or even eliminate) animal testing. Researchers in the Netherlands have announced some guts-on-a-chip research that may do just that. From an Aug. 22, 2017 news item on ScienceDaily,

Research conducted at Leiden has established that guts-on-chips respond in the same way to aspirin as real human organs do. This is a sign that these model organs are good predictors of the effect of medical drugs on the human body.

A method to test medical drugs for efficacy and potential side-effects, but then much cheaper and using the fewest possible lab animals: this is likely to be possible in future thanks to organs-on-chips, miniature model organs on microchips. In these model organs, which are equipped with human organ cells and microfluidic channels, researchers and pharmacists can mimic the working of an organ.

An Aug. 17, 2017 University of Leiden (Universiteit Leiden) press release, which originated the news item, provides more detail,

Leiden researchers, their spin-off company Mimetas and pharmaceutical company Roche have now shown that one type of organ chip experiences the same side-effects from the drug aspirin as the same organ in the human body. This is good news, because it is a sign that these miniature model organs are good predictors of the effect of medical drugs in the human body.

Aspirin

The researchers exposed 357 guts-on-chips for a significant period to the substance acetylsalicylic acid, better known as the analgesic aspirin. It has been known for a long time already that this substance can lead to gastrointestinal perforation, a complication that can be fatal if untreated. ‘We saw exactly the same side-effects occur in our guts-on-chips,’ says Professor of Analytical Biosciences Thomas Hankemeier. ‘In our model guts the gut wall also became more permeable after the drug had been administered.’

Effectiveness of candidate drugs

According to Hankemeier, the research shows that organs-on-chips are suited to testing a medical drug for efficacy and side-effects. This is good news for pharmacists, because the model organs make it easier for them to evaluate whether candidate drugs are effective or harmful. Many substances would be excluded from futher research before a drug entered the lab animal phase. This would help reduce the cost of drug production and mean less animal testing.

Diagnosing diseases

Organs-on-chips have taken off in recent years. They will be increasingly important in the near future, not just in drug development but also in the diagnosis of disease. Leiden researchers are at the forefront of this development. Hankemeier and a number of other groups (Erasmus MC, VUmc, RU Groningen) have been awared a 1.5 million ZonMW grant to research the effect of the body’s micro-organisms in the gut on the development of dementia. Organ-on-a-chip technology will play an important role here. Mimetas is the first company in the world to produce and sell organ chips on a large scale.

Here’s a link to and a citation for the paper,

Membrane-free culture and real-time barrier integrity assessment of perfused intestinal epithelium tubes by Sebastiaan J. Trietsch, Elena Naumovska, Dorota Kurek, Meily C. Setyawati, Marianne K. Vormann, Karlijn J. Wilschut, Henriëtte L. Lanz, Arnaud Nicolas, Chee Ping Ng, Jos Joore, Stefan Kustermann, Adrian Roth, Thomas Hankemeier, Annie Moisan, & Paul Vulto. Nature Communications 8, Article number: 262 (2017) doi:10.1038/s41467-017-00259-3 Published online: 15 August 2017

This paper is open access.

You can find Mimetas here.

Monitoring the life of bacteria in microdroplets

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Trying to establish better ways to test the effect of drugs on bacteria has led the Institute of Physical Chemistry of the Polish Academy of Sciences to develop a new monitoring technique. From a Jan.  11, 2017 news item on Nanowerk,

So far, however, there has been no quick or accurate method of assessing the oxygen conditions in individual microdroplets. This key obstacle has been overcome at the Institute of Physical Chemistry of the Polish Academy of Sciences.

Not in rows of large industrial tanks, nor on shelves laden with test tubes and beakers. The future of chemistry and biology is barely visible to the eye: it’s hundreds and thousands of microdroplets, whizzing through thin tubules of microfluidic devices. The race is on to find technologies that will make it possible to carry out controlled chemical and biological experiments in microdroplets. At the Institute of Physical Chemistry of the Polish Academy of Sciences (IPC PAS) in Warsaw a method of remote, yet rapid and accurate assessment of oxygen consumption by micro-organisms living in individual microdroplets has been demonstrated for the first time.

“Devices for the cultivation of bacteria in microdroplets have the chance to revolutionize work on the development of new antibiotics and the study of mechanisms responsible for the acquisition of drug resistance by bacteria. In one small microfluidic system it is possible to accommodate several hundred or even several thousand microdroplets – and to carry out a different experiment in each of them, for example with different types of microorganisms and at different concentrations of antibiotic in each drop,” describes Prof. Piotr Garstecki (IPC PAS), then explains: “For such studies to be possible, one has to provide the bacteria with conditions for development for even a few weeks. Thus, knowledge about the flow of oxygen to the droplets and the rate of its consumption by the microorganisms becomes extremely important. In our latest system we demonstrate how to read this key information.”

A Jan. 11, 2017 IPC PAS press release on EurekAlert, which originated the  news item, describes the work in more detail,

The bioreactors of the future are water droplets with culture medium suspended in a carrier liquid with which they are immiscible (usually this is oil). In the channel of the microfluidic device each droplet is longer than it is wide and it almost completely fills its lumen; sizes matched in this manner ensure that the drops do not swop places in the channel and throughout the duration of the experiment they can be identified without any problems. At the same time, there has to be a thin layer of oil maintained continuously between each microdroplet and the wall of the channel. Without this, the bacteria would be in direct contact with the walls of the channel so they would be able to settle on them and move from drop to drop. Unfortunately, when the microdroplet is stationary, with time it pushes out the oil separating it from the walls, laying it open to contamination. For this reason the drops must be kept in constant motion – even for weeks.

Growing bacteria need culture medium, and waste products need to be removed from their environment at an appropriate rate. Information about the bacterial oxygen consumption in individual droplets is therefore crucial to the operation of microbioreactors.

“It is immediately obvious where the problem lies. In each of the hundreds of moving droplets measurements need to be carried out at a frequency corresponding to the frequency of division of the bacteria or more, in practice at least once every 15 minutes. In addition, the measurement cannot cause any interference in the microdroplets,” says PhD student Michal Horka (IPC PAS), a co-author of the publication in the journal Analytical Chemistry.

Help was at hand for the Warsaw researchers from chemists from the Austrian Institute of Analytical Chemistry and Food Chemistry at the Graz University of Technology. They provided polymer nanoparticles with a phosphorescent dye, which after excitation emit light for longer the higher the concentration of oxygen in the surrounding solution (the nanoparticles underwent tests at the IPC PAS on bacteria in order to determine their possible toxicity – none was found).

Research on monitoring oxygen consumption in the droplets commenced with the preparation of an aqueous solution with the bacteria, the culture medium and a suitable quantity of nanoparticles. The mixture was injected into the microfluidic system constructed of tubing with Teflon connectors with correspondingly shaped channels. The first module formed droplets with a volume of approx. 4 microlitres, which were directed to the incubation tube wound on a spool. In the middle of its length there was another module, with detectors for measuring oxygen and absorbance.

“In the incubation part in one phase of the cycle the droplets flowed in one direction, in the second – in another, electronically controlled by means of suitable solenoid valves. All this looks seemingly simple enough, but in practice one of the biggest challenges was to ensure a smooth transition between the detection module and the tubing, so that bacterial contamination did not occur at the connections,” explains PhD student Horka.

During their passage through the detection module the droplets flowed under an optical sensor which measured the so-called optical density, which is the standard parameter used to evaluate the number of cells (the more bacteria in the droplets, the less light passes through them). In turn, the measurement of the duration of the phosphorescence of the nanoparticles, evaluating the concentration of oxygen in the microdroplets, was carried out using the Piccolo2 optical detector, provided by the Austrian group. This detector, which looks like a big pen drive, was connected directly to the USB port on the control computer. Comparing information from both sensors, IPC PAS researchers showed that the microfluidic device they had constructed made it possible to regularly and quickly monitor the metabolic activity of bacteria in the individual microdroplets.

“We carried out our tests both with bacteria floating in water singly – this is how the common Escherichia coli bacteria behave – as well as with those having a tendency to stick together in clumps – as is the case for tuberculosis bacilli or others belonging to the same family including Mycobacterium smegmatis which we studied. Evaluation of the rate of oxygen consumption by both species of microorganisms proved to be not only possible, but also reliable,” stresses PhD student Artur Ruszczak (IPC PAS).

The results of the research, funded by the European ERC Starting Grant (Polish side) and the Maria Sklodowska-Curie grant (Austrian side) are an important step in the process of building fully functional microfluidic devices for conducting biological experiments lasting many weeks. A system for culturing bacteria in microdroplets was developed at the IPC PAS a few years ago, however it was constructed on a polycarbonate plate. The maximum dimensions of the plate did not exceed 10 cm, which greatly limited the number of droplets; in addition, as a result of interaction with the polycarbonate, after four days the channels were contaminated with bacteria. Devices of Teflon modules and tubing would not have these disadvantages, and would be suitable for practical applications.

Here’s a link to and a citation for the paper,

Lifetime of Phosphorescence from Nanoparticles Yields Accurate Measurement of Concentration of Oxygen in Microdroplets, Allowing One To Monitor the Metabolism of Bacteria by Michał Horka, Shiwen Sun, Artur Ruszczak, Piotr Garstecki, and Torsten Mayr. Anal. Chem., 2016, 88 (24), pp 12006–12012 DOI: 10.1021/acs.analchem.6b03758 Publication Date (Web): November 23, 2016

Copyright © 2016 American Chemical Society

This paper is behind a paywall.

University of Toronto, ebola epidemic, and artificial intelligence applied to chemistry

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It’s hard to tell much from the Nov. 5, 2014 University of Toronto news release by Michael Kennedy (also on EurekAlert but dated Nov. 10, 2014) about in silico drug testing focused on finding a treatment for ebola,

The University of Toronto, Chematria and IBM are combining forces in a quest to find new treatments for the Ebola virus.

Using a virtual research technology invented by Chematria, a startup housed at U of T’s Impact Centre, the team will use software that learns and thinks like a human chemist to search for new medicines. Running on Canada’s most powerful supercomputer, the effort will simulate and analyze the effectiveness of millions of hypothetical drugs in just a matter of weeks.

“What we are attempting would have been considered science fiction, until now,” says Abraham Heifets (PhD), a U of T graduate and the chief executive officer of Chematria. “We are going to explore the possible effectiveness of millions of drugs, something that used to take decades of physical research and tens of millions of dollars, in mere days with our technology.”

The news release makes it all sound quite exciting,

Chematria’s technology is a virtual drug discovery platform based on the science of deep learning neural networks and has previously been used for research on malaria, multiple sclerosis, C. difficile, and leukemia. [emphases mine]

Much like the software used to design airplanes and computer chips in simulation, this new system can predict the possible effectiveness of new medicines, without costly and time-consuming physical synthesis and testing. [emphasis mine] The system is driven by a virtual brain that teaches itself by “studying” millions of datapoints about how drugs have worked in the past. With this vast knowledge, the software can apply the patterns it has learned to predict the effectiveness of hypothetical drugs, and suggest surprising uses for existing drugs, transforming the way medicines are discovered.

My understanding is that Chematria’s is not the only “virtual drug discovery platform based on the science of deep learning neural networks” as is acknowledged in the next paragraph. In fact, there’s widespread interest in the medical research community as evidenced by such projects as Seurat-1’s NOTOX* and others. Regarding the research on “malaria, multiple sclerosis, C. difficile, and leukemia,” more details would be welcome, e.g., what happened?

A Nov. 4, 2014 article for Mashable by Anita Li does offer a new detail about the technology,

Now, a team of Canadian researchers are hunting for new Ebola treatments, using “groundbreaking” artificial-intelligence technology that they claim can predict the effectiveness of new medicines 150 times faster than current methods.

With the quotes around the word, groundbreaking, Li suggests a little skepticism about the claim.

Here’s more from Li where she seems to have found some company literature,

Chematria describes its technology as a virtual drug-discovery platform that helps pharmaceutical companies “determine which molecules can become medicines.” Here’s how it works, according to the company:

The system is driven by a virtual brain, modeled on the human visual cortex, that teaches itself by “studying” millions of datapoints about how drugs have worked in the past. With this vast knowledge, Chematria’s brain can apply the patterns it perceives, to predict the effectiveness of hypothetical drugs, and suggest surprising uses for existing drugs, transforming the way medicines are discovered.

I was not able to find a Chematria website or anything much more than this brief description on the University of Toronto website (from the Impact Centre’s Current Companies webpage),

Chematria makes software that helps pharmaceutical companies determine which molecules can become medicines. With Chematria’s proprietary approach to molecular docking simulations, pharmaceutical researchers can confidently predict potent molecules for novel biological targets, thereby enabling faster drug development for a fraction of the price of wet-lab experiments.

Chematria’s Ebola project is focused on drugs already available but could be put to a new use (from Li’s article),

In response to the outbreak, Chematria recently launched an Ebola project, using its algorithm to evaluate molecules that have already gone through clinical trials, and have proven to be safe. “That means we can expedite the process of getting the treatment to the people who need it,” Heifets said. “In a pandemic situation, you’re under serious time pressure.”

He cited Aspirin as an example of proven medicine that has more than one purpose: People take it for headaches, but it’s also helpful for heart disease. Similarly, a drug that’s already out there may also hold the cure for Ebola.

I recommend reading Li’s article in its entirety.

The University of Toronto news release provides more detail about the partners involved in this ebola project,

… The unprecedented speed and scale of this investigation is enabled by the unique strengths of the three partners: Chematria is offering the core artificial intelligence technology that performs the drug research, U of T is contributing biological insights about Ebola that the system will use to search for new treatments and IBM is providing access to Canada’s fastest supercomputer, Blue Gene/Q.

“Our team is focusing on the mechanism Ebola uses to latch on to the cells it infects,” said Dr. Jeffrey Lee of the University of Toronto. “If we can interrupt that process with a new drug, it could prevent the virus from replicating, and potentially work against other viruses like Marburg and HIV that use the same mechanism.”

…

The initiative may also demonstrate an alternative approach to high-speed medical research. While giving drugs to patients will always require thorough clinical testing, zeroing in on the best drug candidates can take years using today’s most common methods. Critics say this slow and prohibitively expensive process is one of the key reasons that finding treatments for rare and emerging diseases is difficult.

“If we can find promising drug candidates for Ebola using computers alone,” said Heifets, “it will be a milestone for how we develop cures.”

I hope this effort along with all the others being made around the world prove helpful with Ebola. it’s good to see research into drugs (chemical formulations) that are familiar to the medical community and can be used for a different purpose than originally intended. Drugs that are ‘repurposed’ should be cheaper than new ones and we already have data about side effects.

As for the “milestone for how we develop cures,” this team’s work along with all the international research on this front and on how we assess toxicity should certainly make that milestone possible.

* Full disclosure: I came across Seurat-1’s NOTOX project when I attended (at Seurat-1’s expense) the 9th World Congress on Alternatives to Animal Testing held in Aug. 2014 in Prague.