Sortase A Enzyme-Mediated Generation of Site-Specifically Conjugated Antibody-Drug Conjugates

A Recognition Tag of Human Origin for Bioorthogonal Generation of Antibody-Drug Conjugates using Microbial Biotin Ligase

The use of enzymes, such as microbial transglutaminase, lipoate protein ligase A, or sortase A, for the generation of antibody-drug conjugates has proven to be a powerful tool for the site-specific payload conjugation to tumor-specific antibodies. Herein, the extension of this enzymatic toolbox by Pyrococcus horikoshii biotin ligase is reported. To this end, the therapeutic antibody trastuzumab is equipped with p67, the 67 amino acid carboxyl-terminal domain of human propionyl-CoA carboxylase α subunit, at the C-terminus of either the light or heavy chain (Trz-LC:p67 and Trz-HC:p67). Upon incubation with PhBL, the azide-bearing linker desthiobiotin azide is site-specifically coupled to the p67 domains at the antibody. Subsequent strain-promoted azide-alkyne cycloaddition with DBCO-AF488 and DBCO-Val-Cit-PAB-MMAE yielded conjugates near to full conversion. In cellular assays, these constructs exhibit single-digit nanomolar EC50 values in cellular proliferation assays on SK-BR-3 and A431 cells, where no significant difference in the performance between the two variants Trz-LC:p67-MMAE and Trz-HC:p67-MMAE is observed. On high Fc-γIIIa receptor expressing Jurkat cells, Trz-HC:p67-MMAE exhibits higher potency than Trz-LC:p67-MMAE, indicating an Fc-blocking effect of p67 when fused to the light chain.

Enzymatic protein fusions with 100% product yield

The protein ligase Connectase can be used to fuse proteins to small molecules, solid carriers, or other proteins. Compared to other protein ligases, it offers greater substrate specificity, higher catalytic efficiency, and catalyzes no side reactions. However, its reaction is reversible, resulting in only 50% fusion product from two equally abundant educts. Here, we present a simple method to reliably obtain 100% fusion product in 1:1 conjugation reactions. This method is efficient for protein-protein or protein-peptide fusions at the N- or C-termini. It enables the generation of defined and completely labeled antibody conjugates with one fusion partner on each chain. The reaction requires short incubation times with small amounts of enzyme and is effective even at low substrate concentrations and at low temperatures. With these characteristics, it presents a valuable new tool for bioengineering.

Present Scenario and Future Landscape of Payloads for ADCs: Focus on DNA-Interacting Agents

ADCs have emerged as a promising class of therapeutics, combining the targeting specificity of monoclonal antibodies with the cytotoxic potency of small-molecule drugs. Although the majority of approved ADCs are still based on microtubule binder payloads, the recent success of topoisomerase I inhibitors has revitalized interest in the identification of novel agents overcoming present limitations in the field including narrow therapeutic window and chemoresistance. The success of DNA binders as payload for ADCs has been very limited, up to now, due, among other factors, to high hydrophobicity and planar chemical structures resulting in most cases in ADCs with a strong tendency to aggregate, poor plasma stability, and limited therapeutic index. Some of these molecules, however, continue to be of interest due to their favorable properties in terms of cytotoxic potency even in chemoresistant settings, bystander and immunogenic cell death effects, and known combinability with approved drugs. We critically evaluated several clinically tested ADCs containing DNA binders, focusing on payload physicochemical properties, cytotoxic potency, and obtained clinical results. Our analysis suggests that further exploration of certain chemical classes, specifically anthracyclines and duocarmycins, based on the optimization of physicochemical parameters, reduction of cytotoxic potency, and careful design of targeting molecules is warranted. This approach will possibly result in a novel generation of payloads overcoming the limitations of clinically validated ADCs.

Emerging conjugation strategies and protein engineering technologies aim to improve ADCs in the fight against cancer

Antibody drug conjugates are an exciting therapeutic modality that combines the targeting specificity of antibodies with potent cytotoxins to selectively kill cancer cells. The targeting component improves efficacy and protects non-target cells from the harmful effects of the payload. To date 15 ADCs have been approved by regulatory agencies for commercial use and shown to be valuable tools in the treatment of cancer.The assembly of an ADC requires the chemical ligation of a linker-payload to an antibody. Conventional conjugation methods targeting accessible lysines and cysteines have produced all the ADCs currently on the market. While successful, technologies aiming to improve the homogeneity and stability of ADCs are being developed and tested.Here we provide a review of developing methods for ADC construction. These include enzymatic methods, oligosaccharide remodelling, and technologies using genetic code expansion techniques. The virtues and limitations of each technology are discussed.Emerging conjugation technologies are being applied to produce new formats of ADCs with enhanced functionality including bispecific ADCs, dual-payload ADCs, and nanoparticles for targeted drug delivery. The benefits of these novel formats are highlighted.

Sortases: structure, mechanism, and implications for protein engineering

Sortase enzymes are critical cysteine transpeptidases on the surface of bacteria that attach proteins to the cell wall and are involved in the construction of bacterial pili. Due to their ability to recognize specific substrates and covalently ligate a range of reaction partners, sortases are widely used in protein engineering applications via sortase-mediated ligation (SML) strategies. In this review, we discuss recent structural studies elucidating key aspects of sortase specificity and the catalytic mechanism. We also highlight select recent applications of SML, including examples where fundamental studies of sortase structure and function have informed the continued development of these enzymes as tools for protein engineering.

An overview of site-specific methods for achieving antibody drug conjugates with homogenous drug to antibody ratio

INTRODUCTION

Antibody drug conjugates (ADCs) have emerged as a potent tool in cancer treatment, where cytotoxic drugs are linked to antibodies targeting specific antigens. While conventional ADC synthesis methods have seen success as commercials therapeutics, there is a growing interest in next-generation ADCs, looking at homogeneity of the drug-to-antibody ratio.

AREAS COVERED

The article provides a high-level overview for achieving said homogeneity by site-directed conjugations via encompassing engineered amino acids, enzyme-mediated strategies, peptide sequences, affinity peptides, and beyond. As the field rapidly evolves with multiple ADCs in clinical trials and the advent of biosimilars, the article explores the benefits and challenges in both conventional and non-platform ADC technologies.

EXPERT OPINION

The choice of site selection approach must be based on multiple criteria as discussed in this report. Two ADCs made from conjugation to engineered cysteines have been approved by regulatory agencies which have contributed to the excitement in this space. For the others, though successful as proof-of-concept, the true test of merit will be determined as these technologies advance into the clinic. The promise of improving the therapeutics index and decreasing toxicities will continue to drive progress in this area.

Nature-inspired protein ligation and its applications

The ability to manipulate the chemical composition of proteins and peptides has been central to the development of improved polypeptide-based therapeutics and has enabled researchers to address fundamental biological questions that would otherwise be out of reach. Protein ligation, in which two or more polypeptides are covalently linked, is a powerful strategy for generating semisynthetic products and for controlling polypeptide topology. However, specialized tools are required to efficiently forge a peptide bond in a chemoselective manner with fast kinetics and high yield. Fortunately, nature has addressed this challenge by evolving enzymatic mechanisms that can join polypeptides using a diverse set of chemical reactions. Here, we summarize how such nature-inspired protein ligation strategies have been repurposed as chemical biology tools that afford enhanced control over polypeptide composition.

Recent advances in nanoscale targeted therapy of HER2-positive breast cancer

Breast cancer is the second leading cause of death among women with high mortality rates worldwide. The exceptionally fast rate of metastasis, the emergence of drug-resistant mechanisms, and the occurrence of inadvertent side effects by cytotoxic chemotherapies often make conventional chemotherapy and immunotherapy treatments ineffective. Similar to other solid tumors, breast cancer can develop unique cellular and molecular characteristics forming an atypical permissive tumor microenvironment (TME). Due to the unique features of TME, cancer cells can further proliferate and coadapt with the stromal cells and evade immunosurveillance. aberrantly abundantly express various pieces of molecular machinery (the so-called oncomarkers) in favor of their survival, progression, metastasis, and further invasion. Such overexpressed oncomarkers can be exploited in the targeted therapy of cancer. Among breast cancer oncomarkers, epidermal growth factor receptors, particularly HER2, are considered as clinically valid molecular targets not only for the thorough diagnosis but also for the targeted therapy of the disease using different conventional and advanced nanoscale treatment modalities. This review aims to elaborate on the recent advances in the targeted therapy of HER2-positive breast cancer, and discuss various types of multifunctional nanomedicines/theranostics, and antibody-/aptamer-drug conjugates.

Intrinsically Fluorescent Oligomeric Cytotoxic Conjugates Toxic for FGFR1-Overproducing Cancers

Fibroblast growth factor receptor 1 (FGFR1) is an integral membrane protein that transmits prolife signals through the plasma membrane. Overexpression of FGFR1 has been reported in various tumor types, and therefore, this receptor constitutes an attractive molecular target for selective anticancer therapies. Here, we present a novel system for generation of intrinsically fluorescent, self-assembling, oligomeric cytotoxic conjugates with high affinity and efficient internalization targeting FGFR1. In our approach, we employed FGF1 as an FGFR1 recognizing molecule and genetically fused it to green fluorescent protein polygons (GFPp), a fluorescent oligomerization scaffold, resulting in a set of GFPp_FGF1 oligomers with largely improved receptor binding. To validate the applicability of using GFPp_FGF1 oligomers as cancer probes and drug carriers in targeted therapy of cancers with aberrant FGFR1, we selected a trimeric variant from generated GFPp_FGF1 oligomers and further engineered it by introducing FGF1-stabilizing mutations and by incorporating the cytotoxic drug monomethyl auristatin E (MMAE) in a site-specific manner. The resulting intrinsically fluorescent, trimeric cytotoxic conjugate 3xGFPp_FGF1E_LPET_MMAE exhibits nanomolar affinity for the receptor and very high stability. Notably, the intrinsic fluorescence of 3xGFPp_FGF1E_LPET_MMAE allows for tracking the cellular transport of the conjugate, demonstrating that 3xGFPp_FGF1E_LPET_MMAE is efficiently and selectively internalized into cells expressing FGFR1. Importantly, we show that 3xGFPp_FGF1E_LPET_MMAE displays very high cytotoxicity against a panel of different cancer cells overproducing FGFR1 while remaining neutral toward cells devoid of FGFR1 expression. Our data implicate that the engineered fluorescent conjugates can be used for imaging and targeted therapy of FGFR1-overproducing cancers.

Perspectives on the development of antibody-drug conjugates targeting ROR1 for hematological and solid cancers

Antibody–drug conjugates (ADCs) are targeted therapeutics generated by conjugation of cytotoxic small molecules to monoclonal antibodies (mAbs) via chemical linkers. Due to their selective delivery of toxic payloads to antigen-positive cancer cells, ADCs demonstrate wider therapeutic indexes compared with conventional chemotherapy. After decades of intensive research and development, significant advances have been made in the field, leading to a total of 10 U.S. food and drug administration (FDA)-approved ADCs to treat cancer patients. Currently, ~80 ADCs targeting different antigens are under clinical evaluation for treatment of either hematological or solid malignancies. Notably, three ADCs targeting the same oncofetal protein, receptor tyrosine kinase like orphan receptor 1 (ROR1), have attracted considerable attention when they were acquired or licensed successively in the fourth quarter of 2020 by three major pharmaceutical companies. Apparently, ROR1 has emerged as an attractive target for cancer therapy. Since all the components of ADCs, including the antibody, linker and payload, as well as the conjugation method, play critical roles in ADC’s efficacy and performance, their choice and combination will determine how far they can be advanced. This review summarizes the design and development of current anti-ROR1 ADCs and highlights an emerging trend to target ROR1 for cancer therapy.

EGFR binding Fc domain-drug conjugates: stable and highly potent cytotoxic molecules mediate selective cell killing

The exposition of cancer cells to cytotoxic doses of payload is fundamental for the therapeutic efficacy of antibody drug conjugates (ADCs) in solid cancers. To maximize payload exposure, tissue penetration can be increased by utilizing smaller-sized drug conjugates which distribute deeper into the tumor. Our group recently explored small human epidermal growth factor receptor 2 (HER2) targeting Fc antigen binding fragments (Fcabs) for ADC applications in a feasibility study. Here, we expand this concept using epidermal growth factor receptor (EGFR) targeting Fcabs for the generation of site-specific auristatin-based drug conjugates. In contrast to HER2-targeting Fcabs, we identified novel conjugation sites in the EGFR-targeting Fcab scaffold that allowed for higher DAR enzymatic conjugation. We demonstrate feasibility of resultant EGFR-targeting Fcab-drug conjugates that retain binding to half-life prolonging neonatal Fc receptor (FcRn) and EGFR and show high serum stability as well as target receptor mediated cell killing at sub-nanomolar concentrations. Our results emphasize the applicability of the Fcab format for the generation of drug conjugates designed for increased penetration of solid tumors and potential FcRn-driven antibody-like pharmacokinetics.

Efficient Labeling of Native Human IgG by Proximity-Based Sortase-Mediated Isopeptide Ligation

Antibody-drug conjugates (ADCs) have demonstrated great therapeutic potential due to their ability to target the delivery of potent cytotoxins. However, the heterogeneous nature of conventional drug conjugation strategies can affect the safety, efficacy, and stability of ADCs. Site-specific conjugations can resolve these issues, but often require genetic modification of Immunoglobulin G (IgG), which can impact yield or cost of production, or require undesirable chemical linkages. Here, we describe a near-traceless conjugation method that enables the efficient modification of native IgG, without the need for genetic engineering or glycan modification. This method utilizes engineered variants of sortase A to catalyze noncanonical isopeptide ligation. Sortase A was fused to an antibody-binding domain to improve ligation efficiency. Antibody labeling is limited to five lysine residues on the heavy chain and one on the light chain of human IgG1. The ADCs exhibit conserved antigen and Fc-receptor interactions, as well as potent cytolytic activity.

Sortase-Mediated Site-Specific Modification of Interleukin-2 for the Generation of a Tumor-Targeting Acetazolamide-Cytokine Conjugate

Small ligands specific to tumor-associated antigens can be used as alternatives to antibodies for the delivery of small payloads such as radionuclides, cytotoxic drugs, and fluorophores. Their use as a delivery moiety of bioactive proteins such as cytokines remains largely unexplored. Here, we describe the preparation and in vivo characterization of the first small molecule-cytokine conjugate targeting carbonic anhydrase IX (CAIX), a marker of renal cell carcinoma and hypoxia. Site-specific conjugation between interleukin-2 and acetazolamide was obtained by sortase A-mediated transpeptidation. Binding of the conjugate to the cognate CAIX antigen was confirmed by surface plasmon resonance. The in vivo targeting of structures expressing carbonic anhydrase IX was assessed by biodistribution experiments in tumor-bearing mice. Optimization of manufacturability and tumor-targeting performance of acetazolamide-cytokine products will be required in order to enable industrial applications.

Efficient Sortase-Mediated Ligation Using a Common C-Terminal Fusion Tag

Sortase-mediated ligation is a powerful method for generating site-specifically modified proteins. However, this process is limited by the inherent reversibility of the ligation reaction. To address this, here we report the continued development and optimization of an experimentally facile strategy for blocking reaction reversibility. This approach, which we have termed metal-assisted sortase-mediated ligation (MA-SML), relies on the use of a solution additive (Ni2+) and a C-terminal tag (LPXTGGHH5) that is widely used for converting protein targets into sortase substrates. In a series of model systems utilizing a 1:1 molar ratio of sortase substrate and glycine amine nucleophile, we find that MA-SML consistently improves the extent of ligation. This enables the modification of proteins with fluorophores, PEG, and a bioorthogonal cyclooctyne moiety without the need to use precious reagents in excess. Overall, these results demonstrate the potential of MA-SML as a general strategy for improving reaction efficiency in a broad range of sortase-based protein engineering applications.