Affinity-Directed Site-Specific Protein Labeling and Its Application to Antibody-Drug Conjugates

Polypeptide-protein conjugation: A new paradigm for therapeutic protein delivery

Protein therapeutics have emerged as a potent and highly targeted treatment for a wide range of diseases, including cancer, immune disorders, and genetic conditions. However, their clinical applications are often constrained by challenges such as low stability, short circulation half-life, immunogenic responses, and high manufacturing expenses. The rapid development of biodegradable and biocompatible polypeptide materials provides innovative strategies to address these limitations. In particular, polypeptide-protein conjugation, the covalent linkage of a polypeptide chain to therapeutic proteins, has emerged as a promising strategy for enhancing specific delivery of therapeutic proteins. Leveraging the unique properties of polypeptides, these conjugates significantly improve the stability, solubility, and bioavailability of therapeutic proteins, thereby enhancing their therapeutic efficacy and reducing side effects. This review comprehensively summarizes the recent progress in this field, discussing the current obstacles faced by therapeutic proteins in clinical applications, fundamental design principles, and methodologies for constructing well-defined polypeptide-protein conjugates. Key advancements discussed include innovations in polypeptide synthesis, protein modification, bioorthogonal reactions for precise conjugation, techniques for conjugate purification and characterization. The review further summarizes recent progresses of various polypeptide-protein conjugates for therapeutic protein delivery. Current obstacles and future research directions are also highlighted, underscoring the potential of polypeptide-protein conjugation to propel further advancement in therapeutic protein delivery.

Directed evolution of aminoacyl-tRNA synthetases through in vivo hypermutation

Genetic code expansion (GCE) is a critical approach to the site-specific incorporation of non-canonical amino acids (ncAAs) into proteins. Central to GCE is the development of orthogonal aminoacyl-tRNA synthetase (aaRS)/tRNA pairs wherein engineered aaRSs recognize chosen ncAAs and charge them onto tRNAs that decode blank codons (e.g., the amber stop codon). However, evolving new aaRS/tRNA pairs traditionally relies on a labor-intensive process that often yields aaRSs with suboptimal ncAA incorporation efficiencies. Here, we present an OrthoRep-mediated strategy for aaRS evolution, which we demonstrate in 8 independent aaRS evolution campaigns, yielding multiple aaRSs that incorporate an overall range of 13 ncAAs tested. Some evolved systems enable ncAA-dependent translation at single amber codons with similar efficiency as natural translation at sense codons. Additionally, we discover an aaRS that regulated its own expression to enhance ncAA dependency. These findings demonstrate the potential of OrthoRep-driven aaRS evolution platforms to advance the field of GCE.

Enhancing theranostic potential of anti-mesothelin sdAb through site-specific labeling at a unique conserved lysine by molecular engineering

BACKGROUND

Mesothelin is a 40 kDa glycoprotein overexpressed in several cancers, including triple-negative breast cancer (TNBC). The anti-mesothelin single-domain antibody (sdAb, or nanobody) A1 can serve as a radio-theranostic agent, but random DOTA conjugation on lysines yields heterogeneous products.

RESULTS

We reengineered A1-His by directed mutagenesis to produce four single-lysine variants (A1K1-His, A1K2-His, A1K3-His, and A1K4-His). Each was site-specifically conjugated with p-SCN-Bn-DOTA, radiolabeled with 68Ga, and evaluated by PET imaging in mice bearing HCC70 TNBC xenografts, followed by ex vivo biodistribution at 1 h post-injection. All mutants were successfully produced and site-specifically conjugated. A1K1-His showed lower conjugation efficiency and increased liver/spleen retention, whereas A1K3-His exhibited reduced stability. A1K2-His and A1K4-His performed best overall. Removing the His-tag and administering gelofusin further lowered renal uptake. Notably, A1K2 displayed tumor-to-kidney and tumor-to-liver ratios 2.4 and 1.9 times higher, respectively, than A1K4 (p < 0.01).

CONCLUSIONS

For the first time, site-specific DOTA conjugation using sdAb derivatives containing a single lysine was achieved, avoiding the production of mixed final compounds. These findings identify 68Ga-DOTA-A1K2 as the leading candidate for mesothelin-expressing tumor imaging with minimal off-target uptake. Ongoing studies will assess its therapeutic utility with 177Lu-DOTA-A1K2. Since these four lysines are conserved in many sdAbs, this strategy may be broadly applicable for site-specific sdAb labeling.

Enhancing the Protein Stability of an Anticancer VHH-Fc Heavy Chain Antibody through Computational Modeling and Variant Design

VHHs (also known as nanobodies) are important therapeutic antibodies. To prolong their half-life in bloodstream, VHHs are usually fused to the Fc fragment of full-length antibodies. However, stability is often the main challenge for their commercialization, and methods to improve stability are still lacking. Here, an in silico pipeline is developed for analyzing the stability of an anticancer VHH-Fc fusion antibody (VFA01) and designing its stable variants. Computational modeling is used to analyze the VFA01 structure and evaluate its conformational stability, disulfide bond reduction state, and aggregation and degradation tendency. By building mechanistic models of aggregation and degradation, the hotspot residues affecting stability: C130, F57, Y106, L120, and W111 are identified. Based on them, a series of VFA01 variants are designed and obtained a variant M11 (C130S/W111F/F57K) whose stability is significantly enhanced compared to VFA01: there are no visible particles in solution, and the change rate of DLS average hydrodynamic size, SEC HMW%, and CE-SDS purity are improved by 6.2-, 3.4-, and 1.5-fold, respectively. Both antigen-binding activity and production yield are also improved by about 1.5-fold. The results show that our computational pipeline is a very promising approach for improving the protein stability of therapeutic VHH-Fc fusion antibodies.

A review of conjugation technologies for antibody drug conjugates

Antibody-drug conjugates (ADCs) have gained significant attention in biotherapeutics after several years of steady development. Among the multiple factors influencing ADC design, the conjugation method is one of the most critical parameters. This review classifies conjugation strategies into three categories: non-specific, site-specific but non-selective, and fully site-specific and selective methods. The characteristics; advantages and disadvantages; chemistry, manufacturing, and controls (CMC) potential; and clinical status of each conjugation strategy are discussed in detail. The site-specific and selective methods will yield more homogeneous ADC, which may influence the stability and pharmacokinetics (PK) profile of the ADC and then influence the final therapeutic outcome. Additionally, the review also explores challenges and future directions for developing novel conjugation strategies. This review presents the most prevalent conjugation techniques, providing a valuable resource for researchers in selecting conjugation technologies and advancing ADC development.

Formation of mono- and dual-labelled antibody fragment conjugates via reversible site-selective disulfide modification and proximity induced lysine reactivity

Many protein bioconjugation strategies focus on the modification of lysine residues owing to the nucleophilicity of their amine side-chain, the generally high abundance of lysine residues on a protein's surface and the ability to form robustly stable amide-based bioconjugates. However, the plethora of solvent accessible lysine residues, which often have similar reactivity, is a key inherent issue when searching for regioselectivity and/or controlled loading of an entity. A relevant example is the modification of antibodies and/or antibody fragments, whose conjugates offer potential for a wide variety of applications. Thus, research in this area for the controlled loading of an entity via reaction with lysine residues is of high importance. In this article, we present an approach to achieve this by exploiting the quantitative and reversible site-selective modification of disulfides using pyridazinediones, which facilitates near-quantitative proximity-induced reactions with lysines to enable controlled loading of an entity. The strategy was appraised on several clinically relevant antibody fragments and enabled the formation of mono-labelled lysine-modified antibody fragment conjugates via the formation of stable amide bonds and the use of click chemistry for modular modification. Furthermore, through the use of multiple cycles of this novel strategy, an orthogonally bis-labelled lysine-modified antibody fragment conjugate was also furnished.

N-Acyl-N-alkyl/aryl Sulfonamide Chemistry Assisted by Proximity for Modification and Covalent Inhibition of Endogenous Proteins in Living Systems

Selective chemical modification of endogenous proteins in living systems with synthetic small molecular probes is a central challenge in chemical biology. Such modification has a variety of applications important for biological and pharmaceutical research, including protein visualization, protein functionalization, proteome-wide profiling of enzyme activity, and irreversible inhibition of protein activity. Traditional chemistry for selective protein modification in cells largely relies on the high nucleophilicity of cysteine residues to ensure target-selectivity and site-specificity of modification. More recently, lysine residues, which are more abundant on protein surfaces, have attracted attention for the covalent modification of proteins. However, it has been difficult to efficiently modify the ε-amino groups of lysine side-chains, which are mostly (∼99.9%) protonated and thus exhibit low nucleophilicity at physiological pH. Our group revealed that N-acyl-N-alkyl sulfonamide (NASA) moieties can rapidly and efficiently acylate noncatalytic (i.e., less reactive) lysine residues in proteins by leveraging a reaction acceleration effect via proximity. The excellent reaction kinetics and selectivity for lysine of the NASA chemistry enable covalent modification of natural intracellular and cell-surface proteins, which is intractable using conventional chemistries. Moreover, recently developed N-acyl-N-aryl sulfonamide (ArNASA) scaffolds overcome some problems faced by the first-generation NASA compounds. In this Account, we summarize our recent works in the development of NASA/ArNASA chemistry and several applications reported by ourselves and other groups. First, we characterize the basic properties of NASA/ArNASA chemistry, including the labeling kinetics, amino acid preference, and biocompatibility, and compare this approach with other ligand-directed chemistries. This section also describes the principles of nucleophilic organocatalyst-mediated protein acylation, another important protein labeling strategy using the NASA reactive group, and its application to neurotransmitter receptor labeling in brain slices. Second, we highlight various recent examples of protein functionalization using NASA/ArNASA chemistry, such as visualization of membrane proteins including therapeutically important G-protein coupled receptors, gel-based ligand screening assays, photochemical control of protein activity, and targeted protein degradation. Third, we survey covalent inhibition of proteins by NASA/ArNASA-based lysine-targeting. The unprecedented reactivity of NASA/ArNASA toward lysine allows highly potent, irreversible inhibition of several drug targets for the treatment of cancer, including HSP90, HDM2-p53 protein-protein interaction, and a Bruton's tyrosine kinase mutant that has developed resistance to cysteine-targeted covalent-binding drugs. Finally, current limitations of, and future perspectives on, this research field are discussed. The new chemical labeling techniques offered by NASA/ArNASA chemistry and its derivatives create a valuable molecular toolbox for studying numerous biomolecules in living cells and even in vivo.

Directed evolution of aminoacyl-tRNA synthetases through in vivo hypermutation

Genetic code expansion (GCE) has become a critical tool in biology by enabling the site-specific incorporation of non-canonical amino acids (ncAAs) into proteins. Central to GCE is the development of orthogonal aminoacyl-tRNA synthetase (aaRS)/tRNA pairs wherein engineered aaRSs recognize chosen ncAAs and charge them onto tRNAs that decode blank codons ( e.g ., the amber stop codon). Many orthogonal aaRS/tRNA pairs covering a wide range of ncAAs have been generated by directed evolution, yet the evolution of new aaRS/tRNA pairs by standard strategies remains a labor-intensive process that often produces aaRS/tRNA pairs with suboptimal ncAA incorporation efficiencies. In this study, we present a strategy for evolving aaRSs that leverages OrthoRep to drive their continuous hypermutation in yeast. We demonstrate our strategy in 8 independent aaRS evolution campaigns starting from 4 different aaRS/tRNA parents targeting 7 distinct ncAAs. We observed the rapid evolution of multiple novel aaRSs capable of incorporating an overall range of 13 ncAAs tested into proteins in response to the amber codon. Some evolved systems reached efficiencies for amber codon-specified ncAA-dependent translation comparable to translation with natural amino acids specified by sense codons in yeast. Additionally, we discovered a surprising aaRS that evolved to self-regulate its own expression for greater dependency on ncAAs for translation. These findings demonstrate the potential of OrthoRep-driven aaRS evolution platforms in supporting the continued growth of GCE technologies.

AJICAP-M: Traceless Affinity Peptide Mediated Conjugation Technology for Site-Selective Antibody-Drug Conjugate Synthesis

A traceless site-selective conjugation method, "AJICAP-M", was developed for native antibodies at sites using Fc-affinity peptides, focusing on Lys248 or Lys288. It produces antibody-drug conjugates (ADCs) with consistent drug-to-antibody ratios, enhanced stability, and simplified manufacturing. Comparative in vivo assessment demonstrated AJICAP-M's superior stability over traditional ADCs. This technology has been successfully applied to continuous-flow manufacturing, marking the first achievement in site-selective ADC production. This manuscript outlines AJICAP-M's methodology and its effectiveness in ADC production.