The Scientific Observer Issue 29

How a CRISPR-Like System Was Discovered in Eukaryotes Cicadas Could Help Us Develop Future Self-Cleaning Everyday Surfaces PSYCHEDELIC PSYCHEDELIC ISSUE 29, AUGUST 2023 THE POWER OF PLACEBO IN THE POWER OF PLACEBO IN TRIALS TRIALS 2 CONTENT FEATURE The Power of Placebo in Psychedelic Trials Ruairi Mackenzie FROM THE NEWSROOM 04 ARTICLE How a CRISPRLike System Was Discovered in Eukaryotes 06 Molly Campbell ARTICLE Cicadas Could Help Us Develop Future Self-Cleaning Everyday Surfaces 10 Sreehari Perumanath ARTICLE The Power of Placebo in Psychedelic Trials 12 Ruairi J Mackenzie ARTICLE Fragment-Based Drug Discovery Enters the Mainstream 20 Alison Halliday 06 20 12 3 EDITORS’ NOTE Welcome to issue 29 of The Scientific Observer, the monthly magazine brought to you by Technology Networks. Each month, our newsroom team brings you a handpicked selection of our favorite scientific news stories from the previous month. In this issue, we’re delighted to highlight further advances in the exciting field of ancient DNA analysis, where researchers have discovered that Sambaqui societies were genetically diverse groups. Over at the Massachusetts Institute of Technology, a pioneering study reveals how general anesthetics affect our brain waves, insights that might aid our voyage into the unknowns of human unconsciousness. In “The Power of Placebo in Psychedelic Trials”, Ruairi J Mackenzie embarks on a journey into the enigmatic interplay between perception and healing. The astonishing influence of placebo in the realm of psychedelic clinical trials presents an array of challenges for both investigators and patients. In this feature article, leading experts in the psychedelics space describe their experiences with patients and their theories on why this phenomenon occurs. Also in issue 29, Dr. Feng Zhang – a trailblazer in the field of genome editing – sits down with Molly Campbell to discuss his laboratory's journey to discovering a novel CRISPR-like system in eukaryotes. “Fanzor” carries many advantages over CRISPR-Cas9, but will it replace it? This, and much more in issue 29. We hope you enjoy this issue of The Scientific Observer. Subscribe to make sure you never miss an issue. The Technology Networks Editorial Team Have an idea for a story? If you would like to contribute to The Scientific Observer, please feel free to email our friendly editorial team. CONTRIBUTORS Alison Halliday, PhD Dr. Halliday is as an award-winning freelance science communications specialist with 20+ years of experience across academia and industry. Molly Campbell Molly Campbell is a senior science writer at Technology Networks. Ruairi J Mackenzie Ruairi J Mackenzie is a senior science writer at Technology Networks. Sreehari Perumanath, PhD Dr. Perumanath is a Leverhulme Early Career Research Fellow at the University of Warwick. 4 From the Newsroom FROM THE NEWSROOM André Strauss, Victor Freitas / Unsplash, Jon Tyson/Unsplash DNA analysis of ancient remains, obtained across four different parts of Brazil, reveal new insights into the ancient communities that occupied eastern South America thousands of years ago. JOURNAL: Nature Ecology and Evolution. Ancient Sambaqui Societies Were Genetically Diverse MOLLY CAMPBELL The benefits of exercise on human health are numerous, but how different types of training can impact the health of our skin isn’t yet clear. A new study suggests that resistance training can improve skin elasticity and dermal thickness in women. JOURNAL: Scientific Reports. How Resistance Training Helps To “Rejuvenate” Aging Skin MOLLY CAMPBELL A new study has constructed an “aging clock” for the female body – information missing from previous studies of aging. The research mapped four domains of biological aging – chronic inflammation, hormonal regulation, tissue fitness and lipid metabolism – that can together accurately measure female biological age. JOURNAL: Med. Points in Life Where Women Age Fastest Identified Using Biological Clocks RUAIRI J MACKENZIE 5 FROM THE NEWSROOM 5 iStock. Gregory Pappas/Unsplash, danilo.alvesd/Unsplash Want to learn more? Check out the Technology Networks newsroom. Spelunking the depths of unconsciousness may have gotten a notch easier, as researchers from MIT unveil a pioneering study on how general anesthetics affect our brain waves. JOURNAL: Proceedings of the National Academy of Sciences. Brain Wave Study Reveals Secrets of Unconsciousness RUAIRI J MACKENZIE A study has found that changes to our sleeping patterns – such as getting up early on weekdays and lying in on the weekend, known as “social jet lag” – are associated with harmful bacteria in the gut. JOURNAL: The European Journal of Nutrition Disrupted Sleeping Patterns Are Associated With Harmful Gut Bacteria SARAH WHELAN The first oral pill specifically for treating postpartum depression – Zurzuvae™ (zuranolone) – has been approved by the FDA. Data from two Phase 3 clinical trials show that a 2-week course of daily zuranolone provided rapid improvements in PPD symptoms. First Pill for Postpartum Depression Approved by FDA SARAH WHELAN 6 iStock modified At the McGovern Institute for Brain Research of MIT, Professor Feng Zhang’s laboratory discovers and develops gene-editing systems that can be harnessed as research tools and potential therapeutics. Renowned for his innovative approaches to science and technology, Zhang is considered a leading scientist in the CRISPR research field. After the discovery and characterization of CRISPR-Cas systems in prokaryotic organisms over a decade ago, CRISPR-based genome editing is utilized across an ever-growing list of applications, from basic research to gene therapy development and modern agriculture. Zhang has long wondered whether a similar system could exist in other kingdoms of life. Now, he has an answer. A CRISPR-LIKE SYSTEM IN EUKARYOTES Last month, Zhang’s lab published what he describes as “the most comprehensive study we have reported in a single paper to date” in Nature. The paper outlines the team’s discovery and characterization of the first programmable RNA-guided system in eukaryotes, which centers around an RNA-guided endonuclease named Fanzor. Many scientists had been doubtful that such systems could exist in complex life forms. “It's typical cleverness from the Zhang lab, proving them wrong," says geneticist Ethan Bier, who was not involved in the research. Fanzor is encoded within transposable elements of the eukaryotic genome. “We have known about eukaryotic Fanzor proteins for many years now (the protein sequences were discovered by others many years ago), but the first time we suspected that they might How a CRISPR-Like System Was Discovered in Eukaryotes MOLLY CAMPBELL 7 iStock modified be RNA-guided nucleases is when we were studying the ancestry of proteins like Cas9 and Cas12 a few years ago,” says Zhang. A LIKENESS BETWEEN EUKARYOTIC AND PROKARYOTIC NUCLEASES In 2021, Zhang and colleagues were exploring the evolution and functions of IscB proteins in bacteria. IscB proteins are nucleases encoded in a family of “jumping genes” called IS200/IS605. At that point, the function and interactions of IscB had not been fully characterized. Zhang and colleagues discovered that IscB, and another IS200/IS605 transposon-encoded protein – TnpB, likely gave rise to Cas9 and Cas12. In Science, they called this class of transposon-encoded RNA-guided nucleases “OMEGA”, an acronym for obligate mobile element–guided activity. The researchers hypothesized that TnpB may be the ancestor of the eukaryotic enzyme Fanzor, because of similarities between the two. This further drove Zhang’s conviction that eukaryotes may also have a CRISPRCas-like system, he describes: “Because of the conservations between TnpB and Fanzor, we had a good reason to think that Fanzor is most likely also an RNA-guided OMEGA nuclease. So, after we finished the OMEGA study on IscB and TnpB, we focused on studying Fanzor.” Zhang and colleagues think that Fanzors could have evolved from TnpB proteins that moved from bacteria to eukaryotes in a genetic “shuffling” of sorts. Transposable elements containing TnpB may have “jumped” to these new genomes via horizontal gene transfer. “We found Fanzors in a number of eukaryotic organisms that live in symbiotic relationships with prokaryotes that contain the related TnpB proteins. We also found evidence that Fanzors spread between eukaryotes,” he says. FANZOR IS GUIDED BY RNA The current Nature paper outlines the extensive work undertaken by the McGovern Institute team to understand Fanzor’s function, which included bioinformatic evolutionary analysis, biochemical and genetic studies, engineering and optimization of an enzyme for enhanced gene editing in human cells, and CryoEM structure determination. The first step for the team was to address the question of whether Fanzor is actually RNA-guided. This wasn’t an easy feat, Zhang recalls, “Unlike CRISPR and OMEGA systems, the WHAT ARE TRANSPOSABLE ELEMENTS? Transposable elements are DNA sequences that can change their position within the genome, earning them the nickname of “jumping” genes. “We are quite excited about this paper […] Typically, a single paper would just cover one aspect of an enzyme system. For example, we have published papers that just described the biochemical characterization of a protein, or a paper that described the engineering of an enzyme for genome editing, or a paper that described the study of a protein’s structure. This Fanzor paper is like four papers combined into a single comprehensive paper — we have bioinformatic evolutionary analysis, biochemical and genetic studies, engineering and optimization of an enzyme for enhanced gene editing in human cells, and CryoEM structure determination. It is very satisfying to be able to report so comprehensively at once,” says Zhang. 8 iStock modified, Courtesy of the Zhang lab, Broad Institute of MIT and Harvard/McGovern Institute for Brain Research at MIT. non-coding RNA for Fanzor was not easy to predict based on just looking at the genomic sequence. We had to empirically look for the guide RNA.” Because Fanzor is eukaryotic, it had to be studied in a eukaryotic system, adding further complexity to the work. “The model organism Saccharomyces cerevisiae (baker’s yeast) was used instead of the bacteria Escherichia coli, which is well established for testing the function of CRISPR proteins. We had to develop new assays in S. cerevisiae to study Fanzors. The team discovered that Fanzor shares similarities with CRISPR in that it does interact with a guide RNA – a molecule called omegaRNA, or ωRNA. “The Fanzor protein is a kind of molecular scissors that can cut DNA. Fanzor interacts very closely with a special piece of RNA, called an omegaRNA, and this omegaRNA contains a section, called the guide. When the guideRNA sequence and the target DNA match up, they ‘zip together’ and Fanzor can then recognize and cut that specific piece of DNA,” says Zhang. “Once we had found the non-coding RNA and had a system we could work in, from there, we were able to demonstrate the RNA-guided activity and begin engineering the system,” he adds. A VALUABLE NEW TECHNOLOGY FOR HUMAN GENOME EDITING Fanzor’s efficiency as a genome-editing tool was initially lower than that of CRISPR-Cas systems when applied in human cells. It was successful ~12% of the time, but with genome engineering enhancements, this efficiency could be increased. “We made changes to both the Fanzor protein and the omegaRNA. For the protein, we changed amino acids that we predicted were important for interacting with either the target DNA or the omegaRNA to try and increase the strength of those interaction[s],” explains Zhang. “For the omegaRNA, we tested several different variations to increase its stability in human cells. These optimizations boosted activity ~10 fold, and we are continuing to work on engineering the system for enhanced and extended function in human cells.” Technology Networks asks Zhang the big question – does he envision that Fanzor could one day be a superior tool to CRISPR-Cas genome-editing, or will it offer a complementary approach? He emphasizes that Fanzor proteins are more compact than CRISPR proteins, which is certainly appealing from a delivery perspective; the sheer size of the CRISPR system is considered the most challenging barrier to its in vivo use. “Further refinements to improve their targeting efficiency could make them [Fanzor proteins] a valuable new technology for human genome editing,” Zhang says. “We are excited to see how the trajectory unfolds, and we are continuing to work to develop Fanzor into a valuable new technology for human genome editing. Going forward, we are continuing to study the biology of Fanzor proteins and exploring ways that we can engineer them for use as molecular technologies.” ⚫ Reference: 1. Saito M, Xu P, Faure G, et al. Fanzor is a eukaryotic programmable RNA-guided endonuclease. Nature. 2023. doi: 10.1038/s41586- 023-06356-2 A Cryo-EM map of a Fanzor protein (gray, yellow, light blue and pink) in complex with omegaRNA (purple) and its target DNA (red). Non-target DNA strand in blue. 9 iStock Disseminate Your Research With Us We know how important it is to disseminate your findings when working in research, but also what a challenge it can be to find opportunities beyond the conference hall. We want to address this! Technology Networks is spearheading a project to help researchers raise the profile of their work to a wider audience and increase coverage of the fantastic research papers out there that may not get the media attention they deserve. There is a lot of great research output and a very engaged audience that wants to hear about it, so share your work with us! Find Out More 10 Cicadas Could Help Us Develop Future Self-Cleaning Everyday Surfaces Sreehari Perumanath, PhD RESEARCH SPOTLIGHT In a multi-institutional study led by the University of Warwick, we investigated a model surface that mimics cicada wings to understand precisely how the insects get rid of contaminants from them. If you are thinking “don’t cicadas just shake the dust off their wings?”, the answer is surprisingly no. Cicadas don’t even move a bit to clean their wings because nature does it for them using condensing water droplets. Our study was published in Nano Letters. The Author's Take iStock 11 IS SELF-CLEANING SPECIFIC TO WATER DROPLETS? Self-cleaning surfaces like cicada wings, gecko skin and lotus leaves have a unique property called “super-hydrophobicity” that makes them extremely repellent to water. Due to this, when water droplets do fall on them, or condense under humid conditions, they will assume a spherical shape. These bead-like droplets will either roll down the surfaces due to gravity or “jump” off them upon merging with neighbors. In the process, they “pick up” contaminants, removing them from the surface. This has been observed in recent experiments. However, so far there have been no theories that completely describe how self-cleaning surfaces work in nature. Once formulated and systematically validated, a complete theory would help researchers predict which liquids can remove specific contaminants from a given surface without any external intervention. A UNIFIED THEORY OF SELFCLEANING SURFACES In our study, we formulated such a theory, which explains self-cleaning of various surfaces observed in previous experiments conducted at micro-to-millimeter scale. This new theory also remarkably explains the results of our molecular simulations conducted at nanoscale. In our simulations, we placed a nanoparticle underneath one droplet sitting on a super-hydrophobic surface and pushed a second droplet towards the first. They came together, coalesced and jumped away from the surface, carrying away the particle. Upon carefully investigating various forces involved in the system, we identified the important parameters that influenced the process. It turns out that, prior to removing contaminants from a surface, the droplet with a contaminant underneath will resemble a hot-air balloon that is about to take-off from the ground. The key findings of the paper were: • The new theory can be depicted in a phase diagram that gives a comprehensive idea about when and how self-cleaning occurs. • The pulling force experienced by the nanoparticle/contaminant is at its highest when the droplet is in the hot-air balloon shape. • The size of the droplet relative to that of the contaminant underneath must be within a particular range for self-cleaning to occur. • The system parameters can be fine-tuned to inhibit self-cleaning, if desired, and to encourage transport of nanoparticles on super-hydrophobic surfaces. HIGH-PERFORMANCE SELF-CLEANING SURFACES IN OUR DAY-TO-DAY LIVES Our results show that water droplets can only remove a certain class of contaminants from various surfaces. Furthermore, those contaminants cannot be too small compared to the size of the droplet, which is counterintuitive. The application ambit of our improved understanding of the process includes manufacturing of windowpanes and automobile surfaces that do not require our attention to clean, and in the design of biosensors that trap macromolecules between accurately placed functionalized nanoparticles. Self-cleaning surfaces typically have anti-icing properties too. While the new theory reasonably explains results of experiments and simulations, it is not devoid of assumptions. We have only validated the theory in scenarios where water droplets try to remove contaminants from various surfaces. Water is the most used fluid in our daily lives as well as in some industries. However, self-cleaning characteristics of other liquids might be of interest elsewhere. MORE EXPERIMENTS REQUIRED FOR A COMPLETE THEORY The assumptions made in deriving the equations that govern the self-cleaning process must be investigated further to develop a more general theory. Moreover, there are some predictions made by the current theory that can only be validated by performing experiments at the millimeter scale, which is inaccessible to molecular simulations. ⚫ iStock 11 iStock 12 iStock 13 iStock Envato Elements, iStock PSYCHEDELIC THE POWER OF PLACEBO IN TRIALS RUAIRI MACKENZIE I t’s a story that launched a thousand research grants. A patient suffering from treatment-resistant depression – a stubborn, chronic loss of joy that has seen off multiple traditional interventions – takes one dose of a drug and their world opens up. Boris Heifets, a professor of anesthesiology, perioperative and pain medicine at Stanford University, recently ran a trial of the rapidly acting antidepressant ketamine. Heifets, who is also a by courtesy professor in Stanford’s department of psychiatry and brain sciences, is telling me about a patient on the trial. Their response to treatment was remarkable, but familiar to those seen in response to other psychedelic and psychedelic-adjacent drugs: “She says she’s never felt like this before; she's talking to old friends. I can only describe it as a psychological transformation.” To Heifets, this was a clear-cut example of ketamine’s power. There was just one problem: the patient had been injected with plain old saline. 14 ACHIEVING THE DOUBLE BLIND Heifets’s trial, currently in print ahead of full publication, had a unique design. Virtually all clinical trials of novel antidepressants, like psilocybin, DMT and ketamine, dance around a nonsensical conceit. All split their patients into two groups – one receiving the active, game-changing treatment of the day, and the other a blank pill or inert injection. This study design, the randomized controlled trial (RCT) approach, is intended to rule out any contributions from the placebo effect by shielding participants from the knowledge of which treatment they received. Of course, the curtain drops away after the treatments are given. Heifets calls this “the moment of affirmation” for those given a drug, and the “moment of betrayal” for those in the control group, who applied to go on a trial with a revolutionary psychedelic and instead find themselves sitting on a couch, “trapped in their own head." Heifets’s approach promised the first fully “double-blinded” psychedelic study. There would be no affirmation or betrayal; patients would genuinely have no idea which treatment they received. That’s because they would be fully unconscious for the duration of the intervention. The team hoped that this would answer a long-standing question in the field: is a conscious, subjective experience required to mediate these drugs’ effects? Heifets’s work as an anesthesiologist gave him access to what he calls a “population of convenience” – people booked in for surgery that would be conducted under general anesthesia. Working with such a vulnerable group meant patient selection was important – they recruited 40 participants, none of whom were undergoing brain or cardiac surgery, and all of whom had moderate-to-severe, treatment-resistant depression. Privately, Heifets had confident predictions about the experiment’s outcome. The placebo group, he had forecasted, “would do what placebo groups have done in anesthesia trials before, which is get worse.” This is due, he says, to the stress of an operation and the subsequent recovery. He was equally confident that patients given ketamine would get better without even knowing that they received it, as the body responded to neurobiological effects that the drug induces. Looking at the data post-experiment, Heifets noted that the ketamine group did get better – much better. Their scores on the widely used Montgomery-Åsberg Depression Rating Scale (MADRS) depression scale halved on average – an improvement on par with that achieved in other ketamine studies with awake patients. The problem was that patients receiving placebo got better at the same rate. PLACEBOS: EVERYTHING BUT A BLANK PILL The placebo effect has fascinated and frustrated clinicians for decades. Henry Beecher’s influential 1955 paper, The Powerful Placebo, reflected that these inert substances have “doubtless been used for centuries by wise physicians as well as by quacks.” In the 20th century, our ability to effectively treat disease raced forward, and the use of placebos to heal fell away. Instead, Beecher championed them as a tool that could tease out the pharmacological effects of a new drug. Chloé Pronovost-Morgan, a researcher at Maastricht University’s Department of Neuropsychology and Psychopharmacology, argues that in his enthusiasm to promote placebos, Beecher made a jump in logic that has sowed much confusion about what they actually are. “You still have people that are saying the placebo is an improvement caused by an inert pill,” she says. Pronovost-Morgan and Heifets both explain the same thing: the real placebo effect, also called a non-specific effect, comes from everything but the pill. When a clinician sits down with a patient, the placebo effect takes in the room they are in, the tone of voice the doctor uses and the words they choose to describe the intervention. In a clinical trial, there are dozens of treatment-related factors that have nothing to do with what is in the pill being trialed – all of these come under “the single most reproducible effect in clinical medicine, period" Boris Heifets FEATURE Envato Elements, iStock 15 the banner of placebo. Those effects add up and are found in many more trials than just the ones testing psychedelics. The placebo effect is “the single most reproducible effect in clinical medicine, period,” says Heifets. “When we talk about the placebo effect, that's really how we should conceptualize it – something that is powerful and long-lasting,” Gerard Sanacora, George D. and Esther S. Gross Professor of Psychiatry at Yale University, draws on a neat analogy to summarize placebo. “If for 40 years of your life you take an ibuprofen when you have a headache, and the headache goes away, at a certain point, you can take any pill and it's going to generate that same set of physiologic responses, that are going to cause your headache to go away.” In many areas of modern medicine, however, placebo has become a dirty word. “In biomedical sciences, I think that there's quite a negative, pejorative connotation to the concept of placebo,” says Pronovost-Morgan. In a new review paper, co-authored with Maastricht Professor Jan Ramaekers, she argues that psychedelic science, and the way it has embraced non-specific effects, can provide a route to reassessing the placebo. SET AND SETTING For thousands of years, psychedelic drugs were used as part of rituals by Indigenous peoples around the globe. The writers, researchers and free-love hippies that spearheaded the wave of Western psychedelic enthusiasm in the 1950s and 60s did so with little understanding of the unique culture in which these rituals originally occurred. What they did realize was the need to create a safe external setting and internal mindset of openness and relaxation for those embarking on psychedelic experiences. These factors don’t change the drug itself – they are part of the placebo effect. Importantly, these effects are embraced, not rejected, by the field. “In psychedelics, set and setting are not taboo. It's just common knowledge, even within the lay public, that it is important to pay attention to these variables,” says Pronovost-Morgan. These details are even more important in the context of the drugs’ effects on the brain. They're thought of as consciousness amplifiers, says Pronovost-Morgan: “They can put people in a more suggestible state where they're more responsive to the cues around them.” The biomedical approach to placebo has been one of identification and elimination. As early as 1955, Beecher was totting up “total treatment effect” as a sum of specific and placebo effects. The difference between the two totals remains the key factor in assessments of RCT performance. At the same time, the field has been aware for decades that placebo and treatment effect interact. “It's possible that the placebo effect is enhanced if you realize that you are taking the active pill,” Pronovost-Morgan points out. “This means that the placebo effect would not be the same in the placebo group as in the treatment group. You can't simply pull them apart – because they're interacting.” When dealing with psychedelic drugs and their blind-breaking potential, that possibility is almost guaranteed. Ramaekers and Pronovost-Morgan suggest that a different type of trial design that reflects this interaction might have a benefit for psychedelic research and beyond. This alternative model is called a “balanced placebo” design. Instead of two groups, there are four: one where a participant receives a placebo and is told they have received a placebo, one where a participant receives a drug and is told they have received a drug, and two more groups where the participants 16 are lied to – receiving a drug and being told it is a placebo and receiving a placebo and being told it is a drug. This type of study design is unusual: while not telling participants what drug they are getting is standard in clinical trials, outright deception is more controversial. Additionally, four-armed trials require more participants. When each patient goes through hours of aftercare, and each dose of the drug is heavily regulated and extortionately priced, it is little surprise that this approach is so rare. “MISSING THE FOREST FOR THE TREES” Heifets’s study provides what is perhaps a window onto how powerful the psychedelic placebo effect can be. What Heifets regrets is not measuring expectancy, another facet of the placebo effect with an outsize effect in psychedelics. His view is that these expectations of getting better are what drove his patients’ recoveries. His data hints at this – people whose scores recovered thought they had received ketamine, while non-responders assumed they had received a placebo. “Why would they think that, unless they had some prior belief about the value of ketamine?” Heifets points out. But without having asked patients prior to the trial how much they expected to benefit from participation, this theory cannot be causally proved. In the absence of this neat explanation, alternative theories have sprung up from around the field. Perhaps ketamine’s inherent effects were blocked by general anesthetic, goes one idea, leaving only the expectation-driven benefit. Heifets says that this “doesn’t really fit the data.” If some of ketamine’s effect had been dulled, his patients’ recoveries might have been impaired in comparison to other trials of the drug. But the effects seen were just as strong. Additionally, if general anesthetic impaired ketamine’s action more generally, Heifets points out, the generations of anesthetists who used it every day probably would have noticed. “It has been studied for decades in other contexts, and somehow no one has ever complained about ketamine no longer being an opioid-sparing analgesic or being good for chronic pain when it's given under anesthesia.” It is possible that only the antidepressant qualities of the drug are blocked by general anesthetic, says Heifets, but it “isn’t a parsimonious explanation of the data.” Other responses have, in Heifets’s words, “missed the forest for the trees.” One argument goes that Heifets’s paper has merely identified that general anesthetics themselves are antidepressants. There’s no evidence of such an effect being previously recorded with the doses and drugs Heifets used, but he wasn’t entirely surprised to hear these arguments. “Part of it is, I think, the cognitive bias created by our mental health system,” he says. “It’s like there has to be a light switch somewhere; you give a drug, and you turn the depression on and off. If it wasn’t the ketamine, it must have been the propofol.” The medical model of mental health puts all the power in the pill. What Heifets is most eager to say is that his data doesn’t suggest ketamine is ineffective. He points to a recent review authored by his postdoctoral fellow, Dr. Tuuli Hietamies. This looked at thousands of case reports of people visiting ketamine clinics and reporting recovery. What he suggests instead is that ketamine, like many other medical treatments, works by tapping into that placebo. Our medical model has put all the power in the pill, and that bleeds into patients’ expectations. As Sanacora sums up, “People hear that nonspecific effects are so important, but the corollary of that is, well, the drug doesn't really work. It's just all fake. That’s not the case. It's just that a large part of this effect is nonspecific, but you don't get any of it if you don't actually take the drug.” CUTTING OUT PLACEBO That mindset has now extended into psychedelic science as well. A commentary paper was recently coauthored by some of the leadership team at Compass Pathways. This drug developer is leading a Phase 3 clinical trial of psilocybin-derived The medical model of mental health puts all the power in the pill. Envato Elements, iStock 17 iStock drug COMP360. The paper proposes that psychedelic drugs should be evaluated alone, without the trappings of psychotherapy. To Ramaekers, this argument is driven by a need to comply with the United States Food and Drug Administration (FDA) regulations: “They're changing their perspective because the FDA may make them change their perspective. The FDA is trained to develop drugs. They're not trained to understand how psychotherapy works. They have no means of evaluating psychotherapy.” Heifets predicts that this approach will reduce the placebo effect, and with it, dull these drugs’ efficacies, risking a mighty drop-off in performance post-trial. That’s an effect seen across psychiatric drugs and is not unique to psychedelics. But given how central the powerful placebo has been to psychedelic clinical trials up until now, what remains might not be the revolution in mental health foreseen by so many. “As soon as you strip away everything else, all of the human attachment and support and the validation and the being seen, and all that stuff that we intuitively know is important but is very difficult to get intellectual property on and to sell and to reimburse, what you'll be left with is very transactional,” says Heifets. “Go to a clinic, take your trip, then leave and do the [therapy] app. The field is at a crossroads will it embrace placebo, using different trial designs and formal definitions of set and setting or remove these factors altogether.” Regardless of the route that the field decides to take, it will have to acknowledge the power of placebo. “I wish I could be more hopeful about decriminalization and commercialization of psychedelics,” he concludes. “I don't think they're going to reimburse the right things.” ⚫ 18 iStock Novel psychoactive substances (NPS) are compounds that are designed to mimic the effects of established illicit drugs. Many NPS emerged during the early- to mid-2000s and the number of new substances being reported continues to rise. Their use and misuse have swiftly increased, posing a significant risk to public health. Potential side effects include agitation, aggression, paranoia, psychosis and seizures, as well as possible NPS dependence. In this infographic, we will explore various NPS, highlight ways to analyze them and consider challenges associated with their detection. ! Download to learn more We combine our scientific expertise with creativity to transform your ideas into standout pieces. WORK WITH US Articles eBooks Podcasts Infographics Online Events Videos SEO Services 20 iStock iStock S mall molecule drug discovery is plagued by high attrition rates along the development pathway. Many promising drug candidates identified during initial screening programs are discarded at a later stage and in many cases, these failures can be traced back to the quality of the initial chemical leads. Employing alternative approaches, such as fragment-based drug discovery (FBDD), could help to increase the chances of success as well as open new opportunities to tackle previously intractable biological targets. “You use very small compounds that are promiscuous, which allows you to find some chemical starting points from which you can then go on and assemble properly potent molecules,” says Frank von Delft, professor of structural chemical biology at the University of Oxford. FBDD typically employs very sensitive biophysical methods to rapidly screen a small library of low molecular weight fragments to identify initial “hits” that bind – albeit weakly – to a target protein. As these chemical starting points are small and typically soluble, they are more likely to have Fragment-Based Drug Discovery Enters the Mainstream ALISON HALLIDAY, PHD DRUG HUNTERS ARE INCREASINGLY TURNING TO FRAGMENT-BASED SCREENING TO SEARCH FOR HIGH-QUALITY CHEMICAL STARTING POINTS FOR EARLY-STAGE DRUG DISCOVERY. 21 iStock better drug-like properties, improving the likelihood of eventually producing a viable drug. “Because the fragments are so small, there are so many ways you could then build them up to a full-sized drug molecule, so screening a library of a few thousand compounds is representative of a vast amount of chemical space,” explains Andy Merritt, associate director of chemistry at LifeArc, a UK-based medical research charity that supports translational research. In 2011, the targeted cancer treatment vemurafenib was the first fragment-derived drug to be approved by the US Federal Drug Administration (FDA). Since then, dozens more drug candidates derived from fragments have entered the clinic – with further approvals and many currently in latestage trials. TRADITIONAL DRUG DISCOVERY The process of drug discovery usually kicks off with the identification of a biologically important target, such as a protein that plays a critical role in disease. Medicinal chemists will then begin the hunt for a compound that can bind to the target and modify its activity. Traditionally, the search will often start with high-throughput screening (HTS), which involves testing libraries containing hundreds of thousands – or even millions – of drug-sized chemical compounds (< 500 Daltons [Da]) to narrow down a list of “hits" with promising activity against the target. These initial candidates can then be further refined through subsequent rounds of development to improve potency and refine their “drug-like” properties – such as non-toxicity, solubility and stability – which are also essential for clinical success. “These screens take a lot of effort and are expensive, and while they can test a lot of compounds, it’s a relatively small number compared to the vastness of the potential chemical space,” says Merritt. An early estimate put the number of possible small drug-like molecules at 1063, making even the largest compound libraries look tiny in comparison. And so, finding the rare ones that are a good fit for the target will extrapolate to exploring a staggeringly wide range of molecules – especially due to the probable high number of “near misses”. “Intuitively, you might think by having more complicated and bigger molecules will improve the odds of finding a good candidate in your initial screening experiment,” says Merritt. “But if just one of those interactions is wrong, it won’t bind to the target at all.” A SMARTER APPROACH Rather than physically screening increasingly high numbers of drugsized compounds, FBDD instead begins by testing much smaller collections containing just hundreds or thousands of fragments. While individual fragments are too small (< 300 Da) to have strong interactions with the target, they are still capable of binding into lots of tiny crevices in its structure. “Due to their small size, these fragments have much less decoration than drug-sized molecules,” describes Merritt. “So you’re much less likely to hit detrimental interactions – increasing your chances of finding something that binds to the target.” Since each fragment has so few interactions with the target protein, the binding affinities are typically in the high micromolar to the millimolar region – which is much lower than for larger molecules. “A big disadvantage is you have to start from very low potency, which can be very disconcerting for your typical medicinal chemist,” says von Delft. “As the signal of binding is weak, fragment-based screening requires sensitive and robust assays so you can differentiate appropriate fragments from false positives.” Biophysical methods – including nuclear magnetic resonance (NMR) spectroscopy, surface plasmon resonance (SPR) and X-ray crystallography – are the most commonly used techniques for FBDD. Of these, X-ray crystallography offers the advantage that the 3D structures show exactly how each fragment binds. “You can see the position of the atoms,” explains von Delft. “That’s enormously powerful because it cuts out a lot of the guesswork.” Medicinal chemists can then take clues from these structural data, which will help them to piece together larger, more potent drug-like molecules for onward development. BOOSTING EFFICIENCY While the throughput of FBDD is generally lower than other screening methods, the introduction of automation in crystal handling and data analysis has improved this issue. At the Diamond Light Source, the UK national synchrotron, the XChem facility has streamlined the process of fragment-based screening using X-ray Fragment-based drug discovery could help to increase the chances of success as well as open new opportunities to tackle previously intractable biological targets. 22 iStock crystallography, enabling academic and industrial researchers to screen up to 1,000 compounds in less than a week. “We’ve made it possible to run the X-ray crystallography many hundreds of times in 24 hours without interference,” enthuses von Delft. “So users can come and perform this gold-standard experiment, and by the end of it, they will have some strong data to take away and build on.” A powerful example of how fragment-based screening can help accelerate drug discovery comes from the COVID Moonshot, a spontaneous global collaboration that came together in early 2020 to urgently design an effective new antiviral treatment. The search was kicked off with an XChem experiment of over 1,250 unique fragments to probe a key protein of the SARS-CoV-2 virus, identifying 74 initial hits. “It was quite mind-blowing at the time – we were all taken aback by it,”reflects von Delft. “We had very interesting data, and we decided to put it out to the world to ask medicinal chemists for ideas of how to take these fragments forward.” This crowdsourcing effort had attracted more than 4,000 suggestions for improved, more potent compounds within two weeks – and all contributions were submitted with no intellectual property attached. “We found a company in Ukraine who committed to synthesizing some of the most promising compounds at cost,” says von Delft. “If everything goes well, we’re expecting to have drugs that are ready for Phase I clinical testing by early next year.” A CHANGING TIDE After decades of development, fragment-based screening is now becoming one of the mainstream approaches in small molecule drug discovery. Due to its lower initial costs, it has opened the possibility of lead discovery to smaller companies and academic researchers. “In the past, it was very difficult to get traction as people didn’t start drug programs based on millimolar binding affinities,” says Merritt. “But we now have the right tools as well as computational and structural support to drive these projects forward.” Because of its higher hit rates, it has also opened new opportunities for drug discoverers to crack more challenging targets such as protein–protein interactions. “It’s become part of the arsenal now,” concludes Merritt. “It’s a technique that everybody will use at the early stages of small molecule drug discovery.” ⚫ It’s simple, just choose the groups and click the bubble. Our Facebook groups allow you to keep up to date with the latest news and research and share content with like-minded professionals. With three diverse groups there is something for everyone. Hi. How are you? 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