Structure-guided and phage-assisted evolution of a therapeutic anti-EGFR antibody to reverse acquired resistance

The physiological limits of bispecific monoclonal antibody tissue targeting specificity

Bispecific monoclonal antibodies (bsmAbs) are expected to provide targeted drug delivery that overcomes the dose-limiting toxicities often accompanying antibody-drug conjugates (ADC) in clinical practice. Much attention has been paid in the past to target selection, mAb affinities and the payload linker design, but challenges remain. Here, we demonstrate, by physiologically based pharmacokinetic (PBPK) in silico modeling and simulation, that the tissue-targeting accuracy of mono- and bispecific antibody therapeutics is substantially limited by normal physiological characteristics like organ volumes, blood flow rates, lymphatic circulation, and rates of extravasation. Only a small fraction of blood flows through solid tumor, where the diffusion-driven extravasation is relatively slow compared with many other organs. EGFR and HER2 are used as model antigens based on their experimentally measured tissue and tumor expression levels, but the approach is generic and can account for the cellular expression variation of targets. The model confirms experimental observations that only about 0.1-1% of the dosed mAb is likely to reach the tumor, while the rest ends up in healthy tissues due to target-mediated internalization and nonspecific uptake. The model suggests that the dual-positive tumor cell targeting specificity with bispecific antibodies is likely to be higher at lower drug concentrations and doses. However, this can be offset by elevated drug exposure in more accessible healthy tissues, primarily endothelium. The balance of exposure can be shifted toward tumor cells by using higher doses, albeit at the expense of more extensive target engagement elsewhere in the body, suggesting the need to adapt the toxicity of the payload if ADCs are considered. We suggest that PBPK modeling can guide and support biologics and bsmAb development, from target evaluation and drug optimization to therapeutic dose selection.

Physical insights guided rational design of anti-EGFR antibody to reverse the acquired resistance

Cetuximab (Ctx), a monoclonal antibody targeting the epidermal growth factor receptor (EGFR) for colorectal cancer treatment, often faces diminished clinical efficacy due to acquired resistance driven by EGFR mutations. Here, we investigated the molecular mechanisms underlying this mutation-induced drug resistance and developed a mechanism-based strategy to restore the binding affinity of Ctx to EGFR mutants. Through molecular dynamics simulations and free energy perturbation calculations, we discovered that most resistant mutations primarily alter the electrostatic properties of the binding interface. Focusing on two key mutations, EGFR K489E and I491M, we rationally designed two Ctx variants-CtxD103R for EGFRK489E and CtxD103E_E105D for EGFRI491M-using electrostatic compensation and steric hindrance adjustment strategies. Surface plasmon resonance measurements verified that the two designed Ctx variants exhibit improved binding affinity to the corresponding EGFR mutants compared with wild-type Ctx. Additionally, western blot experiments using HEK-293T cells showed that the designed CtxD103R effectively inhibits EGF-stimulated phosphorylation of EGFRK489E. Our findings highlight a rational design approach, empowered by interaction landscape at atomic detail, as a promising and cost-effective strategy to combat mutation-driven resistance in antibody therapies.

Combined delivery of IL12 and an IL18 mutant without IL18BP-binding activity by an adenoviral vector enhances tumor specific immunity

Cytokines play pivotal roles in anticancer immune response. We previously reported that adenovirus armed with an IL18 variant (DR18) that overcomes IL18BP neutralizing effect displayed powerful therapeutic effects in local and distant tumors when delivered intratumorally. Here, we tested a combined delivery of IL12 and DR18 in tumor models since IL12 and IL18 are known to act synergistically in potentiating IFNγ production and antitumor immunity. To minimize adverse effects associated with systemic delivery, we constructed oncolytic adenoviruses (oAd) harboring DR18 and IL12 (oAd.DR18/IL12). IL12 was expressed as a single chain IL12 (scIL12) peptide composed of the IL12/p40 and IL12/p35 subunits. Intratumoral administration of oAd.DR18/IL12, oAd-expressing DR18 (oAd.DR18), or oAd-expressing IL12 (oAd.IL12) showed antitumor effect in syngeneic colorectal tumor models. Compared to oAd.DR18 or oAd.IL12, administration of oAd.DR18/IL12 improved the antitumor effects as well as increased survival rate in these models. We detected enhanced tumor infiltrating T lymphocytes and NK cells in oAd.DR18/IL12-treated mice than those from mock-treated or individually treated groups. Moreover, mice received oAd.DR18/IL12 had more robust tumor-specific cytotoxicity. Importantly, mice that had tumor regression after oAd.DR18/IL12 treatment established anti-tumor specific immune memory. These results show that adenovirus armed with engineered cytokines boosts tumor specific immunity and antitumor effect.

Computational-aided rational mutation design of pertuzumab to overcome active HER2 mutation S310F through antibody-drug conjugates

Recurrent missense mutations in the human epidermal growth factor receptor 2 (HER2) have been identified across various human cancers. Among these mutations, the active S310F mutation in the HER2 extracellular domain stands out as not only oncogenic but also confers resistance to pertuzumab, an antibody drug widely used in clinical cancer therapy, by impeding its binding. In this study, we have successfully employed computational-aided rational design to undertake directed evolution of pertuzumab, resulting in the creation of an evolved pertuzumab variant named Ptz-SA. This variant, with only two mutations (T30S/D31A) located on its heavy chain, effectively reinstates binding to the mutated antigen, at the expense of a 35-fold reduction in binding affinity to HER2 (S310F) compared to the wild-type pair. Subsequently, Ptz-SA demonstrates potent killing capacity through antigen-dependent cytotoxicity. Moreover, upon engineering Ptz-SA into antibody-drug conjugates, such as Ptz-SA-MMAE, it manifests notable in vitro and in vivo antitumor efficacy by efficiently delivering cytotoxic payload into tumor cells expressing HER2 (S310F). Cryoelectron microscopy studies elucidate the molecular mechanism underlying the restored binding ability of Ptz-SA toward the S310F mutation. The steric hindrance induced by the S310F mutation is efficiently circumvented by the T30S and D31A mutations, which provides adequate space to accommodate the larger phenylalanine. Additionally, Ptz-SA also exhibits binding capacity to HER2 (S310Y), another mutation occurring at the S310 site of HER2 with high frequency. The computational-aided evolution of pertuzumab provides an alternative strategy for overcoming point mutation-mediated resistance to therapeutic antibodies.

The effect of Fc region affinity of protein-based antibody-recruiting molecules on antibody-dependent cellular cytotoxicity

Previously, we reported anticancer molecules, Fc-binding antibody-recruiting molecules (Fc-ARMs), which crosslink proteins on cancer cells with endogenous immunoglobulin Gs (IgGs) via their Fc region. The mobilized IgGs on cancer cells can accommodate natural killer cells to induce antibody-dependent cellular cytotoxicity (ADCC). Because previous Fc-ARMs utilized Fc-binding peptides, their affinity to IgGs is weak, which resulted in the limited induction capability of ADCC. Previous Fc-ARMs also unitized small molecular ligands to cancer cells, which limited their universal applicability to any cancer cells. A recent study reported that protein-based Fc-ARMs might overcome the issues associated with non-proteinous Fc-ARMs. Here, we examined the universality of a protein-based Fc-ARM by replacing its tumor-binding domain with a human epidermal growth factor receptor 2 (HER2)-specific affibody (ZHER2:342). We also examined the requirement of its Fc-binding domain affinity. We found that the Fc-ARMs accepted an affibody as a tumor-binding domain to induce ADCC. Furthermore, the required residence time of the complex between Fc-ARM and IgG was ∼102 min, which was comparable to that when monoclonal antibodies bind to their specific antigens. However, we found that the extent of ADCC induced by Fc-ARM was lower than that of conventional IgG-mediated ADCC, indicating that further enhancement of the affinity of the antibody-binding terminus and tumor-binding terminus of Fc-ARM may be needed to achieve ADCC equivalent to that of conventional IgG-mediated ADCC.

Highly drug/target-tolerant neutralizing antibody (NAb) assay development through target-based drug depletion and drug-based NAb extraction for an anti-EGFR therapeutic monoclonal antibody

The reduction of immunogenicity is fundamental for the development of biobetter Erbitux, given that the development of an immune response reduces treatment efficacy and may lead to potential side effects. One of the requirements for the clinical research of a Erbitux biobetter candidate (CMAB009) is to develop a neutralizing antibody (NAb) assay, and sufficient drug and target tolerance for the assay is necessary. Here, we describe the development of a competitive ligand binding (CLB) assay for CMAB009 with high drug and target tolerance through target-based drug depletion and drug-based NAb extraction, the integrated experimental strategy was implemented to simultaneously mitigate drug interference and enhance target tolerance. Following troubleshooting and optimization, the NAb assay was validated for clinical sample analysis with the sensitivity of 92 ng/mL, drug tolerance of 70 μg/mL and target tolerance of 798 ng/mL. The innovative drug depletion and NAb extraction achieved though the combination of drug and target beads would enable the development of reliable NAb assays for many other therapeutics that overcome drug and its target interference for more precise and sensitive NAb assessment.

Multivalent Rhamnose-Modified EGFR-Targeting Nanobody Gains Enhanced Innate Fc Effector Immunity and Overcomes Cetuximab Resistance via Recruitment of Endogenous Antibodies

Cetuximab resistance is a significant challenge in cancer treatment, requiring the development of novel therapeutic strategies. In this study, a series of multivalent rhamnose (Rha)-modified nanobody conjugates are synthesized and their antitumor activities and their potential to overcome cetuximab resistance are investigated. Structure-activity relationship studies reveal that the multivalent conjugate D5, bearing sixteen Rha haptens, elicits the most potent innate fragment crystallizable (Fc) effector immunity in vitro and exhibits an excellent in vivo pharmacokinetics by recruiting endogenous antibodies. Notably, it is found that the optimal conjugate D5 represents a novel entity capable of reversing cetuximab-resistance induced by serine protease (PRSS). Moreover, in a xenograft mouse model, conjugate D5 exhibits significantly improved antitumor efficacy compared to unmodified nanobodies and cetuximab. The findings suggest that Rha-Nanobody (Nb) conjugates hold promise as a novel therapeutic strategy for the treatment of cetuximab-resistant tumors by enhancing the innate Fc effector immunity and enhancing the recruitment of endogenous antibodies to promote cancer cell clearance by innate immune cells.

Structure-Guided and Phage-Assisted Evolution of Therapeutic Antibodies to Reverse On-Target Point Mutation-Mediated Resistance

Resistance to therapeutic antibodies caused by on-target point mutations is a major obstacle in anticancer therapy, creating an "unmet clinical need." To tackle this problem, researchers are developing new generations of antibody drugs that can overcome the resistance mechanisms of existing agents. We have previously reported a structure-guided and phage-assisted evolution (SGAPAE) approach to evolve cetuximab, a therapeutic antibody, to effectively reverse the resistance driven by EGFRS492R or EGFRG465R mutations, without changing the binding epitope or compromising the antibody efficacy. In this protocol, we provide detailed instructions on how to use the SGAPAE approach to evolve cetuximab, which can also be applied to other therapeutic antibodies for reversing on-target point mutation-mediated resistance. The protocol consists of four steps: structure preparation, computational prediction, phage display library construction, and antibody candidate selection.

Accelerating antibody discovery and design with artificial intelligence: Recent advances and prospects

Therapeutic antibodies are the largest class of biotherapeutics and have been successful in treating human diseases. However, the design and discovery of antibody drugs remains challenging and time-consuming. Recently, artificial intelligence technology has had an incredible impact on antibody design and discovery, resulting in significant advances in antibody discovery, optimization, and developability. This review summarizes major machine learning (ML) methods and their applications for computational predictors of antibody structure and antigen interface/interaction, as well as the evaluation of antibody developability. Additionally, this review addresses the current status of ML-based therapeutic antibodies under preclinical and clinical phases. While many challenges remain, ML may offer a new therapeutic option for the future direction of fully computational antibody design.

Structure of the Major G-Quadruplex in the Human EGFR Oncogene Promoter Adopts a Unique Folding Topology with a Distinctive Snap-Back Loop

EGFR tyrosine kinase inhibitors have made remarkable success in targeted cancer therapy. However, therapeutic resistance inevitably occurred and EGFR-targeting therapy has been demonstrated to have limited efficacy or utility in glioblastoma, colorectal cancer, and hepatocellular carcinoma. Therefore, there is a high demand for the development of new targets to inhibit EGFR signaling. Herein, we found that the EGFR oncogene proximal promoter sequence forms a unique type of snap-back loop containing G-quadruplex (G4), which can be targeted by small molecules. For the first time, we determined the NMR solution structure of this snap-back EGFR-G4, a three-tetrad-core, parallel-stranded G4 with naturally occurring flanking residues at both the 5'-end and 3'-end. The snap-back loop located at the 3'-end region forms a stable capping structure through two stacked G-triads connected by multiple potential hydrogen bonds. Notably, the flanking residues are consistently absent in reported snap-back G4s, raising the question of whether such structures truly exist under in vivo conditions. The resolved EGFR-G4 structure has eliminated the doubt and showed distinct structural features that distinguish it from the previously reported snap-back G4s, which lack the flanking residues. Furthermore, we found that the snap-back EGFR-G4 structure is highly stable and can form on an elongated DNA template to inhibit DNA polymerase. The unprecedented high-resolution EGFR-G4 structure has thus contributed a promising molecular target for developing alternative EGFR signaling inhibitors in cancer therapeutics. Meanwhile, the two stacked triads may provide an attractive site for specific small-molecule targeting.

Mechanisms of Action and Limitations of Monoclonal Antibodies and Single Chain Fragment Variable (scFv) in the Treatment of Cancer

Monoclonal antibodies are among the most effective tools for detecting tumor-associated antigens. The U.S. Food and Drug Administration (FDA) has approved more than 36 therapeutic antibodies for developing novel alternative therapies that have significant success rates in fighting cancer. However, some functional limitations have been described, such as their access to solid tumors and low interaction with the immune system. Single-chain variable fragments (scFv) are versatile and easy to produce, and being an attractive tool for use in immunotherapy models. The small size of scFv can be advantageous for treatment due to its short half-life and other characteristics related to the structural and functional aspects of the antibodies. Therefore, the main objective of this review was to describe the current situation regarding the mechanisms of action, applications, and limitations of monoclonal antibodies and scFv in the treatment of cancer.

Targeted Therapies in Colorectal Cancer: Recent Advances in Biomarkers, Landmark Trials, and Future Perspectives

In 2022, approximately 600,000 cancer deaths were expected; more than 50,000 of those deaths would be from colorectal cancer (CRC). The CRC mortality rate in the US has decreased in recent decades, with a 51% drop between 1976 and 2014. This drop is attributed, in part, to the tremendous therapeutic improvements, especially after the 2000s, in addition to increased social awareness regarding risk factors and diagnostic improvement. Five-fluorouracil, irinotecan, capecitabine, and later oxaliplatin were the mainstays of mCRC treatment from the 1960s to 2002. Since then, more than a dozen drugs have been approved for the disease, betting on a new chapter in medicine, precision oncology, which uses patient and tumor characteristics to guide the therapeutic choice. Thus, this review will summarize the current literature on targeted therapies, highlighting the molecular biomarkers involved and their pathways.

The Dawn of a New Era: Targeting the "Undruggables" with Antibody-Based Therapeutics

The high selectivity and affinity of antibodies toward their antigens have made them a highly valuable tool in disease therapy, diagnosis, and basic research. A plethora of chemical and genetic approaches have been devised to make antibodies accessible to more "undruggable" targets and equipped with new functions of illustrating or regulating biological processes more precisely. In this Review, in addition to introducing how naked antibodies and various antibody conjugates (such as antibody-drug conjugates, antibody-oligonucleotide conjugates, antibody-enzyme conjugates, etc.) work in therapeutic applications, special attention has been paid to how chemistry tools have helped to optimize the therapeutic outcome (i.e., with enhanced efficacy and reduced side effects) or facilitate the multifunctionalization of antibodies, with a focus on emerging fields such as targeted protein degradation, real-time live-cell imaging, catalytic labeling or decaging with spatiotemporal control as well as the engagement of antibodies inside cells. With advances in modern chemistry and biotechnology, well-designed antibodies and their derivatives via size miniaturization or multifunctionalization together with efficient delivery systems have emerged, which have gradually improved our understanding of important biological processes and paved the way to pursue novel targets for potential treatments of various diseases.