A team of scientists headed by researchers at Technische Universität (TU) Dresden has used computer modeling and simulations to design novel bio-inspired molecules to enhance bone regeneration in mice. The new molecules are based on glycosaminoglycans (GAGs)—which are long-chained sugars such as hyaluronic acid or heparin—and can be incorporated into biomaterials and applied locally to bone defects. They suggest that the newly designed molecules could potentially be used to turn off the proteins that block bone regeneration and lead to the development of novel, more effective treatments for bone fractures and other bone-related conditions.

“Thanks to our group’s work and the work of other researchers, we know a distinct molecular pathway that regulates bone formation and repair,” explained TU Dresden medical faculty professor Lorenz Hofbauer, PhD. “In fact, we can narrow it down to two proteins that work together to block bone regeneration, sclerostin and dickkopf-1. The big challenge for developing drugs that improve bone healing is to efficiently turn off both of these proteins, which act as brake signals, at the same time.”

The team: Maria Teresa Pisabarro, PhD, Gloria Ruiz Gómez, PhD, Juliane Salbach-Hirsch, and Lorenz Hofbauer, PhD [© TUD/Magdalena Gonciarz]

Hofbauer is senior and co-corresponding author of the researchers’ published paper in Biomaterials, titled “Rational engineering of glycosaminoglycan-based Dickkopf-1 scavengers to improve bone regeneration.” In their report, the team concluded, “… rationally engineered GAG variants may represent an innovative strategy to develop novel therapeutic approaches for regenerative medicine.”

As people age, their ability to regenerate bones decreases, and osteoporosis-related bone fragility, and bone defects add to what the authors describe as “emerging medical challenges of skeletal health of the aging population,” which result in an increasing socioeconomic burden for society. Scientists are working to develop new therapeutic approaches that can improve bone regeneration. “To date, anti-resorptive therapies that target enhanced bone resorption have become standard of care,” the authors wrote. “More recently, osteo-anabolic approaches that stimulate bone formation have been implemented.”

The canonical WNT signaling pathway is a complex regulatory pathway consisting of ligands, receptors, and inhibitors that serve essential functions for the regulation of bone formation and skeletal strength during homeostasis and bone repair, the team noted. “A comprehensive understanding of the function, interactions, and redundancies of this pathway is required for developing specific therapeutic approaches.”

Sclerostin and Dickkopf-1 (DKK1) are endogenous inhibitors of the WNT pathway. And, as the team further noted, “Functional alterations of WNT ligands and inhibitors are associated with a variety of bone diseases that affect bone fragility and result in a high medical and socioeconomic burden. Hence, this cellular pathway has emerged as a novel target for bone-protective therapies, e.g., in osteoporosis.”

An interdisciplinary approach was key to the team’s challenge, to disable both sclerostin and DKK1. The collaboration combined the expertise of bone expert Hofbauer with the knowhow of the structural bioinformatics group led by Maria Teresa Pisabarro, PhD, at the Biotechnology Center (BIOTEC) of TU Dresden, and the functional biomaterials group led by Vera Hintze, PhD, at the Max Bergmann Center of Biomaterials (MBC), Institute of Materials Science of TU Dresden.

An artistic depiction of computer-aided structure-based rational design. The green arrows symbolize the innovative strategy to introduce new chemical properties in the hyaluronic acid molecule (green and red sticks) to develop Rationally Engineered GAG (REGAG) molecules that act as hijackers of bone regeneration blocking proteins. Dickkopf-1, a protein blocking bone formation, is shown in grey, and its receptor in beige. The colored spheres represent a set of properties that mimic the interactions between dickkopf-1 and its receptor. [© Gloria Ruiz Gómez]

The multidisciplinary team used rational drug design to create novel molecules with tailored properties, and minimal side effects. By using computational methods to predict and refine the properties of the designed molecules, the team was able to develop a series of candidates with the greatest potential for turning off the proteins that block bone regeneration.

The Pisabarro group’s expertise allowed the thorough analysis of the 3D structures of the two proteins that block bone regeneration. With that knowledge, the researchers were able to model the proteins’ interactions with their receptors in 3D and identify hot spots, the specific physicochemical and dynamic properties that are essential for the biological interaction to occur. “In a multidisciplinary approach we applied in silico structure-based de novo design strategies and molecular dynamics simulations combined with synthetic chemistry and surface plasmon resonance spectroscopy to Rationally Engineer oligomeric Glycosaminoglycan derivatives (REGAG) with improved neutralizing properties for DKK1,” the investigators stated.

“For several years, we have harnessed the power of computer simulations to investigate how proteins regulating bone formation interact with their receptors,” Pisabarro said. “All this to design new molecules that can efficiently interfere with these interactions. We used molecular modeling to design new structures that mimic relevant receptor interactions with both proteins. We wanted this binding to be stronger than their natural interactions. In this way, our novel molecules would simultaneously hijack the proteins and effectively turn them off to turn the bone regeneration on.”

Hintze further explained, “The molecules designed by Pisabarro’s group were synthesized by our colleagues at the Free University of Berlin and then analyzed regarding their protein binding properties via biophysical interaction analysis. For each of the molecules we were able to measure the binding strength of the proteins and their interference with natural receptor binding of the proteins. Thus, we could reveal empirically how effective each of the small molecules could be at turning off the inhibitory proteins.”

The team in Hofbauer’s bone lab then loaded the new molecules into a biomaterial, and tested them on bone defects in mice to evaluate their effectiveness. The group found that materials containing the novel molecules outperformed the standard biomaterial and enhanced bone healing by up to 50%, indicating the potential for their future use in improving bone regeneration The authors noted in their published paper, “In vitro and in vivo assays show that the GAG modification to obtain REGAG translated into increased WNT pathway activity and improved bone regeneration in a mouse calvaria defect model with critical size bone lesions. Importantly, the developed REGAG outperformed polymeric high-sulfated hyaluronan (sHA3) in enhancing bone healing up to 50% due to their improved DKK1 binding properties.” Pisabarro added, “We worked in tandem between the computer and the bench, designing new molecules and testing them, feeding the results back to our molecular models, and learning more about the molecular properties required for our goal.”

The results of such iterative testing are a valuable asset that enhances the current molecular models of the Pisabarro group, and can be used to guide the development of novel and better molecules in the future. Such an approach also ensures that animal research is minimized and enters the project only in its final phase. “In this study, we combined computational de novo design studies with biophysical as well as in vitro and in vivo analyses to create a GAG-based refined structure-based engineering strategy superior to classical blind drug screening,” the authors summarised in their paper. “While the classical approaches amount to years of screening and rescreening of drug candidates, our in silico structure-based rational design approach has been key to markedly reduce the time, resources, and necessary animal experiments to select a final target as lead for WNT signaling regulation.”

They stated that their studies demonstrated the potential of chemically sulfated glucosaminoglycan (sGAG) variants to enhance regenerative processes in the bone microenvironment via targeted interference with mediators of the canonical WNT signaling pathway. “Here, we provide proof-of-concept that fine-tuning of the sGAG structure via rational design enhances binding selectivity and improves scavenging inhibitors such as DKK1 and sclerostin to promote bone regeneration in vivo.

The researchers are continuing to work together. “We are applying for funding for a preclinical study that will further develop the molecules and biomaterial-based bone booster to lay the ground for studies in humans,” Hofbauer noted.

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