Computational Antibody Papers
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TitleKey points
- They introduce six molecular descriptors (MolDesk) that perform better than the therapeutic antibody profiler (TAP) and MOE.
- The method used for calculating hydrophobicity and the specific scale employed can have a notable influence on the evaluation of antibody developability characteristics, as highlighted by Waibl et al. in 2022.
- They use APBS (Adaptive Poisson-Boltzmann Solver) to calculate electrostatic potential of the molecules.
- They calculate the values generated by a conformational ensemble using MD.
- Their calculation of hydrophobicity showed sensitivity to the hydrophobicity definition.
- Their measure of CDR negative charge outperforms other methods on viscosity experimental dataset.
- They used a dataset of 64 antibodies with determined clearance and showed that hydrophobicity base descriptors do not discriminate between fast clearance and slow clearance whereas CDR_APBS_pos does.
- They tested the effect of the model on the calculation of properties - they achieve broadly similar results.
- After molecular dynamic simulations of the models, the results between the models are blurred, showing the importance of conformational sampling.
- Their final set of metrics: “These descriptors include CDR_APBS_neg, a significant factor influencing viscosity and colloidal stability (Figure 3), CDR_APBS_pos, a major driver of PK clearance and polyspecificity (Figure 4), CDR_HPATCH_WW, which plays a key role in SEC, HMW, and HIC (Figure 5), CDR_HPATCH_BM which correlated the best with HIC, as well as total CDR length and APBS charge asymmetry (APBS_CAP) as two additional descriptors to align with the type of descriptors considered in the TAP metrics”
- They compared TAP and MolDesk on the basis of whether molecules progressed or regressed in the tests. MolDesk performed better on showing less critical flags for the approved and progressed molecules.
2024-07-16
Human-likeness of antibody biologics determined by back-translation and comparison with large antibody variable gene repertoires
- developability
- numbering/annotation
- They create a tool to do back translation and provide single nucleotide frequencies (SNFs) for antibody variable regions from large-scale NGS study.
- They use the Soto et al. dataset, which was ~326m antibody sequences.
- They create position and gene specific scoring matrix (pgssm) using the gene and CDR-H3 length matches.
- They can back-translate amino acid sequences to obtain plausible codons.
- Their PGSSMVJ score is the average of single nucleotide frequencies.
- Their naturalness score distinguishes between human and non-human sequences.
- They benchmarked the back-translation on 181k sequences from GenBank.
2024-07-16
Computational optimization of antibody humanness and stability by systematic energy-based ranking
- developability
- They employed Rosetta to show that energy-based ranking of constructs is superior to homology based approaches.
- In certain instances, the most successful humanized design achieved through experimentation originates from human framework genes that lack significant similarity to the corresponding animal antibodies. This observation underscores the potential efficacy of an energy-based humanization approach over the conventional homology-based humanization method.
- They make all the V-J combinations that are free of liabilities such as n-glycosylation and extra cysteines, making a set of frameworks.
- Mouse CDRs are grafted onto the artificial frameworks, modeled and energy minimized using Rosetta.
2024-07-09
The immunogenicity of human-origin therapeutic antibodies are associated with V gene usage
- developability
- annotation/numbering
- They demonstrate that germline usage and distance from the germline are correlated with ADA.
- They use OAS as a reference for natural NGS sequences, but they exclude studies that focus on single isotopes such as IgM, IgG.
- They collected ADA points from therapeutics from IMGT and related these to FDA labels in the first instance and heterogenous search second.
- If they had multiple values for ADA, they then take the maximum value.
- There are 14 amino acid differences between the IGHV4-34*10 and IGHV4-34*11 alleles, a 14.4% sequence difference.
- Healthy donors have similar gene usages as diseased ones.
- They show that V gene usage has correlation with ADA just as the number of mutations.
2024-06-25
Identifying developability risks for clinical progression of antibodies using high-throughput in vitro and in silico approaches
- developability
- They benchmarked a range of experimental and computational measures to see which ones correlated with therapeutics moving it through the clinical trials.
- Table 2 - cheat sheet of experimental methods and what they do.
- Some of the experimental results are highly correlated with one another (The retention time on the FcRn column was highly correlated with the affinity-capture self-interaction nanoparticle spectroscopy (AC-SINS), polyspecificity reagent (PSR), clone self-interaction using bio-layer interferometry (CSI) and cross-interaction chromatography (CIC) assays, which constituted one of the polyspecificity clusters in our prior work)
- For each experimental assay they update the 90% intervals wrt to their previous experimental recommendations.
- Table 4 shows the descriptors that need to be calculated for developability assessments.
- Some of the in silico metrics also correlate with one another, forming conceptual groups (e.g. charge calculations)
- They notice that there is a slight trend for mabs that progress in trials to have less violations of their experimental descriptors than those that were regressed.
2024-03-13
Protein language models enable prediction of polyreactivity of monospecific, bispecific, and heavy-chain-only antibodies
- language models
- developability
- Using language models to predict polyreactivity.
- Polyspecificity and polyreactivity are cognate, however the first is thought to be driven by factors such as overlapping epitopes whereas polyreactivity by excess charge or hydrophobicity.
- Baculovirus particles assay (BVP) is often used to test polyreactivity. mAbs are added at high-concentrations to BVP coated plates.
- They generated a dataset of polyreactive antibodies (~300 antibodies) that was heterogeneous in terms of antibodies/nanobodies, monospecific and formats.
- They tested different concentrations (from 6.67nM to 667 nM) and well coating types (percentage BVP) - this was aimed at reducing noise from experimental conditions.
- They tested two prediction modes, language models and structural descriptors. For language models, PROT5, ESM2 and Antiberty were used. Descriptors were calculated using Alphafold2-multimer. The language model predictions were superior to those calculated from AF2-multimer ones.
- Review on developability methods, very good reference for what are the problems afflicting antibodies, what assays are used and it gives perspective where computational might have an impact.
- Specific binding high on-target binding and low off-target and non-specific binding is important to reduce the risks of abnormal pharmacokinetics and fast antibody clearance.
- Polyspecificity. For nonspecific binding ELISA can be used to check non-specific binding for non-targets. Polyspecificify particle assay (PSP) checks binding to complex antigen mixtures. Polyspecificity reagent (PSR) is similar to PSP. In Cross interaction Chromatography (CIC) non-specific protein interactions, such as monoclonal antibodies interacting with immobilized polyclonal antibodies, are detected via their relative retention times. Standup monolayer chromatography (SMAC), instead detects non-specific interactions between monoclonal antibodies and the column.
- Colloidal stability, self-association. Self interaction Chromatography (SIC). AC-SINS, affinity-capture self-interaction nanoparticle spectroscopy and charge-stabilized self-interaction nanoparticle spectroscopy (CS-SINS). Also HIC.
- Folding stability. Differential scanning calorimetry or differential scanning fluorimetry.
- Ideally antibodies would have a shelf-life of several years which requires stability engineering.
- Assays can be performed in formulation (pH 6, 10 mM histidine) or physiological conditions (pH 7.4, phosphate-buffered saline).
- Generally, the isoelectric point of therapeutic antibodies is between 6 and 9. However, various developability challenges have been reported for some antibodies with relatively low (pI <6.5-7) or high (pI >8.5-9) isoelectric points
- Computational assays can include: naturalness prediction, MHC class II, ptm liabilities, isoelectric point (pI), charge, hydrophobic imbalance, surface areas buried at the VH-VL interface along with molecular surface patches
- Antibodies are flexible & crystallization might not reflect well the actual dominant structure adopted.
- T-cell epitope assay: This may be addressed in vitro by the use of immune cell activation assays, where pooled peripheral blood mononuclear cells are exposed to candidate biologics to reveal the presence of activating T cell epitopes.
- Antibodies have quite a long half-life (3 weeks) because they can engage the FcRn receptor which rescues the ligands from cellular recycling. The efficiency by which different biologics undergo this process has an enormous impact on their pharmacokinetic properties and biodistribution
- There are some raging differences between humans and mice for the animal to be used as a model organism:
- While being a potent vascular endothelial growth factor (VEGF)-blocker in humans, the widely used anti-VEGF human IgG1 bevacizumab is unable to block mouse VEGF, implying that mice could not have been used in its development.
- Our understanding of FcRn biology has revealed major differences that must be taken into consideration when conventional mice are used. This is due to large differences in ligand binding to mouse and human FcRn, where mouse IgG binds very weakly to the human form, and human IgG binds stronger to mouse FcRn than to the human counterpart.
- Most antibodies are IV, but there are some experiments with abs targeting infections in the GI tract and these are oral.