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Official websites use. Share sensitive information only on official, secure websites. Designed ankyrin repeat proteins DARPins are antibody mimetics with high and mostly unexplored potential in drug development. By using in silico analysis and a rationally guided Ala scanning, we identified position 17 of the N-terminal capping repeat to play a key role in overall protein thermostability. We then transferred the Asp17Leu mutation to various backgrounds, including clinically validated DARPin domains, such as the vascular endothelial growth factor-binding domain of the DARPin abicipar pegol. Molecular dynamics simulations showed that the Asp17Leu mutation reduces electrostatic repulsion and improves van-der-Waals packing, rendering the DARPin domain less flexible and more stable. Overall, such N-terminal capping repeats with increased thermostability seem to be beneficial for the development of innovative drugs based on DARPins. Keywords: designed ankyrin repeat protein, DARPin, drug development, ensovibep, abicipar pegol, thermostability, N-terminal capping repeat, drug engineering, molecular dynamics. Designed ankyrin repeat proteins DARPins are a class of antibody mimetics that have been conceived and developed about two decades ago at the University of Zurich 1 , 2 , 3. Their application as research tool and protein therapeutic was recently reviewed 4. The DARPin scaffold was shown to serve as an alternative 5 , as a complementation, 6 and as an expansion of what is possible with binders derived from immunoglobulins 7 , 8. Translation of academic research in DARPin technology toward pharmaceutical benefits has been predominantly steered by Molecular Partners, who provided the fundamental clinical validation of the scaffold 9. However, in light of the long generation cycles in drug development—especially in the case of biologics that typically require 10 years from concept to drug approval—the DARPin technology can still be regarded as young and emerging, and the full potential of DARPins as a class of biologics has yet to be realized. The recent development of ensovibep 10 , a multi-specific anti-SARS-CoV-2 DARPin, which has entered clinical trials in November in less than 9 months after initial research and development activities had commenced, reinforces this high potential 11 , DARPins are based on natural ankyrin repeat proteins 13 that have evolved to mediate various kinds of protein-protein interactions in all kingdoms of life Their structure is simpler than that of immunoglobulins. Immunoglobulins naturally consist of four polypeptide chains and unite more than four chains in recombinant formats like T-cell bispecifics 15 , whereas a single polypeptide chain is sufficient to form a multispecific DARPin DARPins are built from solenoid protein domains, which possess a modular architecture that was derived by a consensus design approach 2 , 17 , 18 : a stack of internal ankyrin repeats, each composed of 33 amino acids, flanked by N- and C-terminal capping repeats N- and C-Caps that function to seal the hydrophobic core of the protein domain Fig. Together, these structural units form an elongated ankyrin repeat domain. Amino acids present at defined positions at the surface of the internal repeats form a paratope, enabling the binding to target proteins with high affinity and specificity 3 , 19 , These positions are randomized in DARPin libraries, which are used as starting point for in vitro selection, most prominently by means of ribosome display 21 , to generate highly specific target-binding molecules. Despite the clinical validation, most of the amino acid sequence of these original caps was not optimized, indicating that there may be room for further improvements, in particular, for those that increase DARPin thermostability. Generic DARPin representation. A , schematic representation of a DARPin domain. The designed N- and C-terminal capping repeats and designed self-compatible repeat modules are the building blocks that stack via compatible interfaces. B , the repeat modules stack together forming a continuous hydrophobic core, which is sealed by an N-Cap green and a C-Cap cyan. The repeat domains display variable molecular surfaces randomized positions, depicted in red , which are potential target-binding sites 1 , 2. C , structure of a DARPin PDB ID: 2XEE 25 in ribbon representation with the same color scheme as above: helices of the N-terminal capping repeat, the internal repeat modules, and the C-terminal capping repeat are colored green , blue , and cyan , respectively. The side chains of randomized positions are displayed as red sticks. DARPin, designed ankyrin repeat protein. In general, we identify three major motivations that fuel the quest for increased thermostability of biologics: i reduction of aggregation and thus reduction of immunogenicity risk, ii simplification of chemistry, manufacturing, and controls processes, thus bringing down the manufacturing costs and reduction of cold chain drug storage requirements, and iii increase of degrees of freedom for protein engineering to allow for mode-of-action design, for example, advanced multispecificity 11 , receptor fine-tuning 22 , and proximity-based activation When this improved mut5 C-Cap was compared with the original C-Cap 2 , a rigid-body movement of the C-Cap toward the internal repeat was observed, as evidenced by crystallographic data This movement results in an increased buried surface area and a superior complementarity of the interface between the internal repeat and the C-Cap, which explains the improved thermostability. It is likely that this improvement mainly arises from the Met24Leu-mutation present in N02, which removes the only methionine besides the methionine encoded by the start codon from the original DARPin sequence, and thereby also removes this hotspot for oxidation. Amino acids in N02, N03, and N04 that are identical to the one present in N01 are indicated as dots. The sequence numbering is shown as used in the text. N01, the original N-Cap, as described by Binz et al. N03, an N-Cap where 12 out of the 32 amino acids are changed in comparison to N The choice of this DARPin model has a 3-fold motivation. Third, because DARPins get more stable with increasing number of IRs, we choose to have only one internal repeat and thus a low starting thermostability 26 such that stability improvements are readily observable. For a comprehensive list of amino acid sequences of all domain variants used, see Table S1. By visual analysis of the DARPin structure, we identified four residues within the N-Cap to be of potential importance for the repeat stacking and thereby also for the overall domain stability. Alanine scanning of residues four and five showed no improvement in thermostability, with Leu4Ala lowering the T m value from However, the Asp17Ala mutation showed a strong improvement of the T m value from All amino acid substitutions tested excluding e. These results show that Asp is an exceptionally unfavorable amino acid at position 17, and that there are many alternative residues resulting in a strong thermostability gain. Of these alternative residues, Asp17Leu provided one of the largest improvements, which we investigated further. The side chains of N-Cap residues Leu4, Gly5, Asp17, and Met24 are displayed as spheres and sticks , and the surrounding side chains are displayed as lines. To test if the improvements derived from mutating the N-Cap Asp17 are generic and independent of the N02 background, we transferred the Asp17Leu mutation onto the original N01 N-Cap and the N03 N-Cap that differs in nine amino acids from N Further, we were interested in whether our observed stability improvement based on the N-Cap and the stability improvement based on the mut5 C-Cap 24 would be additive. Indicates T m measurements in 2 M GdmCl. Starting from the homology models, three independent simulations were carried out for each system, two at K and one at K, for a total sampling of 1. Three conclusions can be drawn from the MD simulations Fig. First, the substitution of Asp at position 17 with Leu leads in all instances to improved interaction energies with the surrounding Table 5. Second, the analysis focused on the protein flexibility at high temperatures K and on two different timescales 5 ns and ns revealed that the systems containing Leu at position 17 systematically show lower fluctuations than their Asp17 counterparts Fig. The effects of the Asp17Leu mutation are more pronounced on the ns timescale Fig. The profiles along the full protein sequences show the least fluctuations in the helical segments and the highest flexibility at the loops. The higher rigidity of the helical segments of the Leu17 mutants lower fluctuations is relevant for enthalpic stabilization. The differences in the fluctuations of the loops are less relevant as their flexibility contributes to entropic stabilization. The localized stability may be related to the stabilizing Met24Leu mutation of N These findings further support our hypothesis that position 17 is an Achilles heel with respect to the N-Cap and thus the overall DARPin domain thermostability. RMSF profiles of the proteins at K. Compared are the Asp17 light gray with the Leu17 black constructs in the Nbackground top , the Nbackground middle , and the Nbackground combined with the mut5 C-Cap bottom. Two different timescales are shown comprising a fluctuations over 5 ns and b ns. The RMSF profiles on the 5 ns timescale were calculated as the average over 30 independent 5-ns profiles. The four independent profiles for the ns timescales show the fluctuations over the first and the last ns of the production simulations that is, the last ns of the ns run. The fluctuations were calculated about the average structure determined from the corresponding 5 ns or ns intervals. The helical regions of the secondary structure are indicated by red boxes below the residue index. Overall, the described significant gain in thermostability of the Asp17Leu mutation proved to be generic and is transferable to different N- and C-Cap backgrounds and different library members selected for high affinity, including clinically validated DARPin domains. The importance of the capping repeats as a prerequisite for the high stability and robustness of the DARPin-fold has been known since the first description of this antibody mimetic 26 , The contribution of the capping repeats to the overall stability of the DARPin domain is central The architecture of solenoid repeat protein domains does not rely on long-range interactions distant in sequence , which is a fundamental difference to globular proteins. In repeat proteins, stabilizing and structure-determining interactions are formed within a repeat and between neighboring repeats. In contrast to IRs, the capping repeats have only one stabilizing neighboring repeat Fig. Both natural 30 and designed ankyrin repeat proteins 26 have been shown to unfold in a sequential manner starting with the capping repeats. An unfolded cap leads to an internal repeat losing a stabilizing neighbor resulting in destabilization of the whole repeat domain. Because Met possesses a larger side chain than Leu, it might not optimally fit into the confined space at the interface between the N-Cap and the adjacent internal repeat. This mutation has the additional advantage that it eliminates an oxidation hotspot from the DARPin domain; unwanted oxidation of Met and its negative impact on the bioactivity of biologics is well documented We now performed a detailed analysis of the N-Cap, searching for additional mutations that may improve the overall DARPin domain stability. Following in silico analyses, we used equilibrium thermal denaturation experiments of DARPins harboring different N-Cap mutations. Although Interlandi et al. Throughout nature, the negatively charged amino acids are found at the N-terminal turn of helices as they support helix formation during protein folding 32 , which rationalizes the placement of Asp at position The known DARPin crystal structures show that the side chain of Asp17 can either face inward and be buried in the interface between N-Cap and IR1, or face outward into the surrounding solvent. If Asp17 is facing inward, it is involved in van-der-Waals contacts with IR1 i. If facing outward, Asp17 shields the hydrophobic interface from the solvent, but experiences repulsive forces to the equally negatively charged IR1 Glu19 Fig. The different rotamers in different structures are consistent with the lack of favorable interactions of Asp17 with the rest of the protein Table 5. Side chain orientation s and interaction s of Asp17 and Leu17 with surrounding residues. A , inward and B outward facing Asp17 present in 2V4H The average structures of the systems equilibrated at K with C outward facing Asp17 and D inward facing Leu The analyses of equilibrated, energy-minimized average MD structures at K and associated interactions between the N-Cap residue 17 and its surrounding at K show that although in our starting model, Asp17 faced inward, during the course of the simulation, Asp17 Fig. The improved interactions of Leu17 are consistent with the strong increase in thermostability observed by CD measurements. Second, the Asp17Leu mutation was also beneficial in the context of the improved mut5 C-Cap. This general transferability of the Asp17Leu mutation may be because of the fact that all DARPin domains are based on a quasi-identical framework embedding the randomized positions The underlying reason for this similarity of the framework is the consensus design of DARPins, resulting in the stacking of self-compatible IRs 1 , 2 , This indicates that this single amino acid change may also be beneficial for DARPin domains comprising framework mutations; in particular, when these mutations have a negative effect on the domain stability. Position 17 is located outside of these known paratope regions, and our MD based structural analyses indicate that the overall alteration of the domain structure through the Asp17Leu mutation is marginal. Incorporation of the Asp17Leu mutation into existing DARPin binders could increase their thermostability without significantly impacting their target-binding properties. The benefit obtained by this novel N-Cap i. Thus, our discovered Asp17Leu improvement adds substantially to other capping repeat improvements described previously. We see the modular, solenoid structure of DARPins as the origin for making the observed modular addition of thermostability improvements possible. They are stabilized by interactions with their folded immediate neighboring repeats, and thus each repeat individually contributes to the overall domain stability DARPins unify a plethora of key characteristics beneficial for drug development from discovery to preclinical and clinical development and manufacturing. For example, their low molecular weight, high solubility, high expression level, picomolar affinities, multispecific potential, and especially the high stability offer drug developers access to huge versatility 9. With their simple modular structure, multispecific DARPins 16 can be easily constructed with a single polypeptide chain and different molecular formats, as the binding domains are freely combinable. Their high solubility and high expression level awards them with unparalleled high-throughput capabilities, and their excellent biophysical properties are the origin for low attrition rates. Their high thermostability, in particular, positively influences low aggregation and associated immunogenicity risks, allows for low-cost manufacturing and makes them very amenable to protein engineering to generate molecules with novel modes of action, such as receptor fine-tuning With these characteristics, DARPins complement existing therapeutic antibodies and will also expand the scope of innovative drugs via the multitude of advanced formats and applications that can be conceived and realized with this scaffold. All mentioned characteristics build on the stability of this versatile scaffold. Thus, an increased thermostability as presented in this study will have a positive impact on many levels. A recent example of drug development at unparalleled speed is the development of the multi-specific, highly efficacious anti-SARS-CoV-2 DARPin ensovibep that went from first selection of binders to entry into the clinic in less than 9 months This not only gives clinical validation to the Asp17Leu mutation, but also underscores the importance and reach of the findings outlined here. These beneficial properties are especially remarkable as this COVID antiviral drug is composed of five distinct DARPin domains with four different specificities on a single polypeptide chain. In our view, an immunoglobulin-based drug with similar properties would require extensive engineering to be generated, if feasible at all. Together, it does not surprise that Molecular Partners is speculating that ensovibep has the potential to bypass cold storage, and that it provides a superior alternative to monoclonal antibody cocktails for global supply These two domains are identical to aHSA of our study. Furthermore, aVEGF of our study corresponds to the ankyrin repeat domain of abicipar pegol that is a first generation DARPin drug to treat patients with neovascular age-related macular degeneration. Two randomized phase 3 clinical trials CEDAR and SEQUOIA demonstrated that quarterly applied abicipar pegol is noninferior to monthly applied ranibizumab, but showed a higher level of intraocular inflammation typically mild or moderate in severity than ranibizumab The authors of these phase 3 studies mentioned that the used abicipar pegol was further purified to reduce host cell proteins with the goal to minimize the incidence of intraocular inflammation. A correspondingly improved abicipar pegol would be amenable to more stringent purification processes that may result in much lower contaminations with host cell proteins. Our results further provide evidence for the importance of the capping repeats for the robustness and reliability of this solenoid scaffold. Combining our N-Cap improvement with the cap enhancements described by Interlandi et al. Such thermodynamically stabilized antibody mimetics could pave the way for the future development of innovative drugs. First, increased thermostability of biologics is known to correlate with a reduced aggregation propensity Second, the improved thermostability will make DARPins even more amenable to protein engineering. We believe that this is of high importance when the biological activity of a drug needs to be optimized, for example, to fine-tune the activation of receptors Third, the increased thermostability will translate into more efficient preclinical development and chemistry, manufacturing, and controls processes, low-cost manufacturing, and may even help to bypass the cold storage of biologics. The recent development of the DARPin ensovibep comprising the N-Cap Asp17Leu mutation in less than 9 months from idea conception to entry into the clinics underlines this huge potential 11 , Along the same lines, we speculate that a high thermostability may facilitate the development of aerosol or dry powder inhaler formulations of DARPin drugs; something that may also be of interest for the pulmonary delivery of ensovibep for the treatment of COVID patients. In conclusion, future drug development asks for more robust and very versatile biologics, and we believe that DARPins would be the ideal scaffold for this. At an absorbance of about 1. The ankyrin repeat domains were purified over a Ni-nitrilotriacetic acid column 2. Up to mg of highly soluble ankyrin repeat domains were purified from 1 L of E. The melting temperature values were derived, as described by Consalvi et al. Importantly, all constructs assessed in CD ran as monomeric peaks in analytical size-exclusion chromatography aSEC. The sequences of the proteins are shown in Supplementary Table S1. These models were used as the structural basis of this study. Three independent simulations with different initial random velocities were carried out for each repeat protein, two at K and one at K, cumulating 1. To reproduce neutral pH conditions, standard protonation states were used for the ionizable side chains, the N-terminus was positively charged, and the C-terminus was negatively charged. Each protein was solvated in a cubic box edge length of 6. For the production simulations, temperature and pressure were maintained constant at K or K and 1 atm, by using the modified Berendsen thermostat 0. The short-range interactions were cutoff beyond a distance of 1. The Particle Mesh Ewald technique 43 with a cubic interpolation order, a real space cut-off of 1. In all simulations, the time step was fixed to 4 fs, enabled through the use of virtual sites for all hydrogen atoms. Periodic boundary conditions were applied, and the snapshots were saved every 50 ps. The elevated temperature is used to enhance the sampling; the density of water is kept at the value corresponding to K to perturb the free energy surface as little as possible The authors declare that they have no conflicts of interest with the contents of this article. The authors would like to thank Dr Lorenz Kallenbach, Dr Nora Guidotti, and Dr Philipp Wild for critical reading and helpful comments during preparation and revision of the article. All other aspects of this study were funded by Athebio AG, Switzerland. Schilling, C. Schnabl, A. Schnabl, O. Schnabl, R. Schnabl, and R. Schilling and J. Schnabl, visualization; C. This section collects any data citations, data availability statements, or supplementary materials included in this article. As a library, NLM provides access to scientific literature. J Biol Chem. Find articles by Johannes Schilling. Find articles by Christian Jost. Find articles by Ioana Mariuca Ilie. Find articles by Joachim Schnabl. Find articles by Oralea Buechi. Find articles by Rohan S Eapen. Find articles by Rafaela Truffer. Find articles by Amedeo Caflisch. Find articles by Patrik Forrer. Open in a new tab. T m values of N1C variants having various amino acids at position Similar articles. Add to Collections. Create a new collection. Add to an existing collection. Choose a collection Unable to load your collection due to an error Please try again. Add Cancel.
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From traditional residence halls to apartment and house-style living, Loras offers a variety of living and learning options. While conveniently located, our housing provides independence and easy access to recreation spaces, community kitchens, social lounges, and free laundry services. Located on the lower campus, Beckman Hall houses a mix of coed, first-year through senior students within single, double, and triple rooms. Recent renovations were made to the kitchens, common areas, and a chapel. First-year through senior students choose between single and double rooms. These rooms share a private bath between two rooms with four students. A limited number of suites are also available. These share a private bathroom between the four roommates. First-year through senior residents living in this coed hall with single, double, and quad occupancy rooms. 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Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs
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