Figure - available from: Scientific Reports
This content is subject to copyright. Terms and conditions apply.
Structural validation of four H3 redesigns. Sequences for design IDs 16_0325, 13_0346, 14_0130 and 12_0327 are shown in Table 3. In light and dark gray are the crystal and predicted structures, respectively, for each prospective design. The experimentally observed conformation of H3 loop is shown in green. The best-scoring Talaris energy-based H3 loop conformation is shown in orange.
Source publication
The design of superior biologic therapeutics, including antibodies and engineered proteins, involves optimizing their specific ability to bind to disease-related molecular targets. Previously, we developed and applied the Assisted Design of Antibody and Protein Therapeutics (ADAPT) platform for virtual affinity maturation of antibodies (Vivcharuk e...
Similar publications
The evolutional development of the RNA translation process that leads to protein synthesis based on naturally occurring amino acids has its continuation via synthetic biology, the so-called rational bioengineering. Genetic code expansion (GCE) explores beyond the natural translational processes to further enhance the structural properties and augme...
Citations
... Also, deep sequencing explorations can help determine the representation of distinct Ab library features associated with antigen interactions. These observations can then be analyzed via computational models to determine Abantigen interactions and molecular docking predictions, ultimately enabling a holistic approach to big data assessments [68,69]. Moreover, such in silico predictive models can offer valuable insights to improve the designs of affinity maturation libraries. ...
Synthetic antibodies (Abs) represent a category of artificial proteins capable of closely emulating the functions of natural Abs. Their in vitro production eliminates the need for an immunological response, streamlining the process of Ab discovery, engineering, and development. These artificially engineered Abs offer novel approaches to antigen recognition, paratope site manipulation, and biochemical/biophysical enhancements. As a result, synthetic Abs are fundamentally reshaping conventional methods of Ab production. This mirrors the revolution observed in molecular biology and genomics as a result of deep sequencing, which allows for the swift and cost-effective sequencing of DNA and RNA molecules at scale. Within this framework, deep sequencing has enabled the exploration of whole genomes and transcriptomes, including particular gene segments of interest. Notably, the fusion of synthetic Ab discovery with advanced deep sequencing technologies is redefining the current approaches to Ab design and development. Such combination offers opportunity to exhaustively explore Ab repertoires, fast-tracking the Ab discovery process, and enhancing synthetic Ab engineering. Moreover, advanced computational algorithms have the capacity to effectively mine big data, helping to identify Ab sequence patterns/features hidden within deep sequencing Ab datasets. In this context, these methods can be utilized to predict novel sequence features thereby enabling the successful generation of de novo Ab molecules. Hence, the merging of synthetic Ab design, deep sequencing technologies, and advanced computational models heralds a new chapter in Ab discovery, broadening our comprehension of immunology and streamlining the advancement of biological therapeutics.
... Polar interactions hardly contributed to drug resistance. For biologics, 5 internal publications yielded 150 antibody mutants with both predicted and experimental binding affinities relative to the respective parental antibodies (Vivcharuk et al., 2017;Sulea et al., 2018;Zwaagstra et al., 2019;Sulea et al., 2020;Corbeil et al., 2021). When compared to the published results for small molecules, the quantitative prediction of relative binding affinity for antibodies is not as successful (S = 0.58, MUE = 0.90 kcal/mol). ...
... Despite the low correlation observed, these predictions still proved useful (Section 4.3). In Corbeil et al. (2021) a mutational engineering endeavor was undertaken by attempting to redesign the entire CDR H3 loop of an antibody. The requirement of predicting the protein loop backbone conformation significantly increased affinity prediction errors. ...
Scoring functions are ubiquitous in structure-based drug design as an aid to predicting binding modes and estimating binding affinities. Ideally, a scoring function should be broadly applicable, obviating the need to recalibrate and refit its parameters for every new target and class of ligands. Traditionally, drugs have been small molecules, but in recent years biologics, particularly antibodies, have become an increasingly important if not dominant class of therapeutics. This makes the goal of having a transferable scoring function, i.e., one that spans the range of small-molecule to protein ligands, even more challenging. One such broadly applicable scoring function is the Solvated Interaction Energy (SIE), which has been developed and applied in our lab for the last 15 years, leading to several important applications. This physics-based method arose from efforts to understand the physics governing binding events, with particular care given to the role played by solvation. SIE has been used by us and many independent labs worldwide for virtual screening and discovery of novel small-molecule binders or optimization of known drugs. Moreover, without any retraining, it is found to be transferrable to predictions of antibody-antigen relative binding affinities and as accurate as functions trained on protein-protein binding affinities. SIE has been incorporated in conjunction with other scoring functions into ADAPT (Assisted Design of Antibody and Protein Therapeutics), our platform for affinity modulation of antibodies. Application of ADAPT resulted in the optimization of several antibodies with 10-to-100-fold improvements in binding affinity. Further applications included broadening the specificity of a single-domain antibody to be cross-reactive with virus variants of both SARS-CoV-1 and SARS-CoV-2, and the design of safer antibodies by engineering of a pH switch to make them more selective towards acidic tumors while sparing normal tissues at physiological pH.
... Conversely, a similar NOAC apixaban is much more rigid and compact, making it easier to be described, but at the same time, it may lose some possibility to bind FXa in alternative patterns as RIV, which may partially explain its lower binding affinity in some mutants, as discussed earlier . From this example, we would again emphasize the recognition of the important influence of the flexibility of both the target protein and the drug molecule, which was often neglected in structurebased drug design and screening using static crystal structures but more and more considered in recent studies, especially in protein and antibody design (Corbeil et al., 2021). Second, here, we used a popular method of clustering to find a representative structure of different binding patterns for illustration. ...
A novel coagulation factor X (FX) Tyr319Cys mutation (Y99C as chymotrypsin numbering) was identified in a patient with severe bleeding. Unlike the earlier reported Y99A mutant, this mutant can bind and cleave its specific chromogenetic substrate at a normal level, suggesting an intact binding pocket. Here, using molecular dynamics simulations and MM-PBSA calculations on a FX-rivaroxaban (RIV) complex, we confirmed a much stronger binding of RIV in Y99C than in Y99A on a molecular level, which is actually the average result of multiple binding poses in dynamics. Detailed structural analyses also indicated the moderate flexibility of the 99-loop and the importance of the flexible side chain of Trp215 in the different binding poses. This case again emphasizes that binding of ligands may not only be a dynamic process but also a dynamic state, which is often neglected in drug design and screening based on static X-ray structures. In addition, the computational results somewhat confirmed our hypothesis on the activated Tyr319Cys FX (Y99C FXa) with an impaired procoagulant function to bind inhibitors of FXa and to be developed into a potential reversal agent for novel oral anticoagulants (NOAC).
