Supramolecular Chemistry: Playing with Diverse Identities
Ivan Huc’s office is decorated with four pictures of iconic mountain peaks, summits that he himself has either stood on or very nearly conquered. He tackled the Matterhorn together with his father. “We were forced to turn back near the summit,” he recalls, “when it began to snow – in the middle of August!” He shows me where the decision was made, shrugs his shoulders and laughs. Huc’s research has much in common with mountain-climbing. One aims for a distant goal, encounters expected and unanticipated obstacles, and cannot be assured of success until one reaches one’s objective. Learning to overcome natural barriers is good training for a budding chemist.
Indeed, in his scientific work, nature is an immediate inspiration. Huc creates synthetic analogs of biomolecules that have been shaped by evolution. He joined LMU in 2017 and he and his research group explore the potential of what he calls ‘biomimetic supramolecular chemistry’. Using a kind of origami based on the principles of synthetic chemistry, he constructs molecules that exhibit the functional capacities of biological macromolecules. He refers to these mimics as foldamers. “The expertise we have acquired gives us precise control over the shape of biological-like molecules,” he says. This is crucial, “because the basic principle of biology is that shape determines function”. The ability to control molecular shape provides access to what endows a given structure with specific properties – its chemical identity, so to speak – and allows one to probe the elements that confer this identity.
Earlier in his career, when he was based at the Institut Européen de Chimie et Biologie in Bordeaux, it was not clear where this approach might lead, or whether it would ever yield meaningful results. But Huc was not deterred. He studied the binding properties of non-natural amino acids inspired by the basic constituents of proteins and other reactive molecules, and found ways to iron out their curves and kinks. This then allowed him to connect subunits in a linear fashion and modulate the angles between them. In this way, he began to design chemical building-blocks modeled on nature’s biological toolbox. Now, some 20 years later, he can control the chemical assembly of over 20 constituent components to yield the desired product. He created geometric shapes such as closed molecular rings with defined radii and helical molecules that mimic the spiral-like strands of the DNA double helix. Having crafted a library of reactive components, he and his team assemble these parts in any given sequence to yield morphologically complex macromolecules. “It’s like playing with Lego bricks. We are curious to know what can be built with these modules.”
“The ability to imitate leads to understanding”
But it’s much more than an amusing game. Huc uses his synthetic imitations of natural macromolecules to dissect in detail how enzymes and other proteins work. Slavishly copying nature’s designs is not the objective: “mimicking is not copying”. The subtle differences between model and mimic are what allow Huc and his team to elucidate the mechanisms that underpin the complexity of biological systems. “We play with identities to see what happens,” he says. The goal is to understand how enzymes act as catalysts to promote chemical reactions, how DNA can store genetic information with remarkable fidelity. In more general terms, this requires a detailed knowledge of how biomolecules selectively recognize and bind to one another. “The ability to imitate leads to understanding,” says Huc. “One cannot understand a system unless it can be reconstructed.” Reconstruction tells one what’s important for function.
"Folding is nature's most powerful tool, every biopolymer is subject to this mechanism": Ivan Huc and Céline Douat in protein analysis. Photo: Jan Greune / LMU
In the design of his mimics, Huc exploits a basic property of biological macromolecules – their ability to fold. “Folding is the most powerful tool that nature possesses,” he says. Virtually every biopolymer can fold autonomously into a stable structure, often during its own synthesis. “The most remarkable self-organizing molecules in cells are proteins with their specialized, hierarchical folding patterns,” says Huc. Enzymes are proteins that have catalytic functions. They mediate the myriad of chemical transformations that make up human metabolism. Proteins regulate sugar levels, transport oxygen in the blood, and control the immune system. Molecular factories called ribosomes – themselves conglomerates of proteins and RNAs – synthesize all proteins, in accordance with the genetic instructions encoded in each cell’s DNA. A protein is basically a chain of amino acids that progressively folds into a particular spatial conformation. Its shape is mainly determined by its amino-acid sequence, and defines its biological function. Huc’s models shed light on the mechanisms that drive the folding process, and control the spatial geometry and functional properties of each protein. “Some medical disorders result from defects in protein folding,” he points out. An understanding of the folding process yields insight into why errors occur, and how to correct them.
On the desk in his office on LMU’s campus in Grosshadern, is a strange-looking object made of interlinked stainless-steel hinges sourced from a hardware store, which are held together by small screws. “Nature also makes use of combinations of fixed and flexible joints,” Huc remarks – and the shape of the final structure is often determined by a small number of fixed angles and folds. Huc pulls on one end of the object and rotates a few hinges, converting the object into a sinuously coiled shape. The set of adjustable joints can be readily reconfigured into a helical shape or a succession of folded domains reminiscent of protein conformations. Altering the angle of a single hinge can transform the morphology of the whole thing. “In principle, possible folds are innumerable,” he says, but nature utilizes special shapes that molecules can spontaneously adopt.
Some proteins even imitate the double helix
Huc’s remodeling efforts focus primarily on the structural backbones of biological macromolecules, like the well-known double helix that characterizes the genetic material in cells. “The DNA is subjected to ceaseless manipulation by proteins. These interactions define which genes are activated in each cell type in an organism, for instance,” he explains. In order to do so, these proteins must recognize DNA sequences, especially their overall shape and their specific surface contours. Some proteins even imitate the double helix, acting as decoys to detach other proteins from DNA. Huc also applies this principle in the construction of his foldamers. “We too can imitate the shape and surface features of DNA so as to deceive proteins that naturally bind to the real thing.”
He recently succeeded in doing just that, thus demonstrating the immense potential of his synthetic mimics. He and his colleagues not only ‘reproduced’ the overall structure of the DNA double helix, but replicated its surface contours so convincingly that a viral protein bound to the imitation. In this case, Huc used doubly negatively charged groups attached to the subunits that make up each strand instead of the singly charged phosphates that do the same job in real DNA. Such minimal changes are often sufficient to alter the functional characteristics of the entire polymer, as subsequent experiments showed.
“The novel charged groups in the backbone of the double helix were not deleterious to protein binding to the foldamer,” Huc explains. On the contrary, some proteins preferentially bound to the DNA mimic in the presence of natural DNA. In the paper that was published in the journal Nature Chemistry, Huc demonstrated that his ‘false’ DNA had a higher affinity for two enzymes of pharmaceutical significance, and prevented them from binding to cellular DNA. One of the enzymes was the HIV integrase, which is responsible for integration of the viral DNA that causes AIDS into the genome of infected cells.
More attractive than real DNA
The ability of the mimic to serve as an efficient decoy implies that it is more attractive than real DNA. “If enzymes interact preferentially with the foldamer under competitive conditions, the imitation must be a better binder than the original,” Huc notes. And measurements confirmed that the HIV integrase bound more strongly to the foldamer. “Although designed to look like DNA, the foldamer owes its most valuable properties to the ways in which it differs from the model.” This feature opens up a new approach to drug development.
In principle, the potential of the foldamer strategy seems virtually unlimited. But Huc has learned from his expeditions in the Alps that it pays to take one step at a time. In research, this means dividing big problems into smaller, soluble segments that can be tackled one by one. He is well aware that progress can be painfully slow. “For us, the real bottleneck, and our know-how, is synthetic chemistry,” he says. “We can construct lots of structures, but most of what we do involves manual work in the lab – and that takes time.” This aspect of scientific investigation is often omitted from popular depictions of research, in which persons in white coats are shown mixing solutions, and a sudden color change reveals the formation of the desired reaction product. It looks like magic. “We are able to link over 20 molecular building-blocks together in arbitrary sequences,” Huc says, and we continue to extend the limits of what we can do in this respect. His job as leader of a research group is to keep an eye on everything, and coordinate the activities so that they all contribute to a common goal. “Here, everyone in the team strikes the same anvil.” Many other research groups tackle different problems in parallel.
As a chemist, Huc does all he can to expand the capabilities of technical developments in the field of chemical synthesis. He mentions a new apparatus that can link amino acids together in any given sequence. “At the moment, the machine is no faster than a laboratory technician – but it doesn’t need any sleep!” So it will allow him to increase the output of new foldamers.
Meanwhile, a different class of natural biopolymers has attracted his attention – polysaccharides, which are made up of sugars. How do these sugars work in biological systems? Why do particular sugars play important roles, while others with very similar structures do not? Being able to recognize and discriminate sugars could help to answer such questions. Last year, Huc’s group designed a molecule that recognizes a specific disaccharide, consisting of two sugar subunits. The compound takes the shape of a helical chamber which specifically encapsulates the disaccharide xylobiose. It therefore acts as a specific sugar receptor. At the moment, his group is modifying the structure so that the binding interaction also works in aqueous solution. This step is essential to enable the receptor to serve as a sensor that can detect and bind saccharides in biological media.
Hence this new departure may also lead to mimics that are of practical use. The components required to tailor the required contours and charge distributions can be found among those 20 components that constitute his molecular mimicry toolbox. But like a climbing expedition, this operation must be carefully planned if the envisaged goal is to be attained. “We have to resist the temptation to overdo the design,” he says. The pictures on the wall remind him of the perils of overreaching.
Prof. Dr. Ivan Huc holds the Chair of Chemical Biology for Drug Research in the Department of Pharmacy at LMU. Huc (b. 1969) studied Chemistry at the Ecole Normale Supérieure (ENS) in Paris. He did the work for his PhD at the ENS and the Massachusetts Institute of Technology (MIT) in Cambridge, USA. On his return to France, he took a post at the Université Louis Pasteur in Strasbourg, before moving to the Institut Européen de Chimie et Biologie (IECB) in Bordeaux. He subsequently served as Co-Director of both the ICEB and the Institut de Chimie & Biologie des Membranes & des Nano-objets in Bordeaux, before he took up his current position at LMU in 2017