Welcome to the Recombinant Antibody Network

@article{pmid42476294,

title = {Epitope-guided detection of a molecular glue-induced ternary complex using engineered synthetic antibody fragments},

author = {Kelly M O'Leary and Tomasz Slezak and Duc Anh Le and Anthony A Kossiakoff},

doi = {10.1016/j.jmb.2026.169953},

issn = {1089-8638},

year  = {2026},

date = {2026-07-01},

urldate = {2026-07-01},

journal = {J Mol Biol},

pages = {169953},

abstract = {Molecular glues represent a class of small molecules that enable the modulation of proteins lacking traditional ligand-binding pockets. A defining feature of molecular glues is their ability to bind cooperatively at weak or neomorphic protein-protein interfaces. Despite growing interest in these compounds, tools for selectively isolating native molecular glue-induced protein assemblies from heterogeneous populations in cells remain limited. Here, synthetic antibody fragment (Fab) reporters were generated by phage display to enable selective detection of the rapamycin-induced FKBP12-mTOR ternary complex as a model molecular glue-induced protein assembly. Crystallographic studies revealed the structural basis for three distinctive epitope recognition mechanisms to monitor the molecular glue activity of rapamycin using synthetic binders. Fab-1A and Fab-2C reported ternary complex formation with low to moderate precision by exploiting rapamycin-induced allosteric and interaction-gated epitopes, respectively. Fab-4R exhibited superior accuracy as a molecular glue reporter by sensing a rapamycin-gated junctional epitope that bridges the FKBP12-rapamycin-mTOR architecture. Structure-guided mutagenesis showed that the paratope of Fab-4R confers specificity for the ternary complex through hot spot interactions positioned directly across the conditional interface formed between FKBP12 and mTOR. Cell-based immunoprecipitation assays demonstrated that both Fab-4R and scFv-4R function as versatile molecular probes to report FKBP12-dependent mTOR inhibition by rapamycin with high fidelity and picomolar sensitivity. Taken together, these findings delineate the recognition properties for multiple antibody-based molecular glue reporters and highlight the versatility of synthetic binders for sensing conditionally formed epitopes within the proteome.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid42178617,

title = {Dual targeting of inhibitory EGFR epitopes with synthetic antibodies in therapeutic-resistant cancers},

author = {Jarrett J Adams and Evan Mallette and Max London and Ryan J Liang and Dewald van Dyk and Zvezdan Pavlovic and Isabelle Pot and C Ronald Geyer and Heather A Bruce and Levi L Blazer and Craig A Hokanson and Michael D L Suits and Alexander U Singer and Sachdev S Sidhu},

doi = {10.1002/pro.70645},

issn = {1469-896X},

year  = {2026},

date = {2026-06-01},

urldate = {2026-06-01},

journal = {Protein Sci},

volume = {35},

number = {6},

pages = {e70645},

abstract = {Therapeutic antibodies that inhibit the epidermal growth factor receptor (EGFR) are limited to a subset of EGFR-driven cancers. This is in part due to resistance mechanisms that attenuate efficacy. All approved therapeutic antibodies target the closed form of EGFR and compete with the ligand. However, tumors can be desensitized to these antibodies by upregulation of EGFR ligands or through EGFR mutations that uncouple kinase activity from ligand binding. We sought to overcome these resistance mechanisms by developing antibodies targeting alternative epitopes of EGFR. Using phage-displayed libraries, we developed two distinct antibodies, one that competed with EGF and another that did not. Crystal structures revealed that the competitive antibody bound to a site that overlapped the EGF-binding site, whereas the other antibody bound to the arm that induces receptor dimerization. Because the libraries used a common light chain, we were able to assemble a biparatopic antibody that incorporated both antigen-binding sites and thus targeted both epitopes on EGFR. We showed that the antibody that targeted the dimerization arm inhibited the growth of cancer cell lines that were resistant to the antibody that targeted the EGF-binding site. Moreover, the biparatopic antibody was more potent than the monoparatopic antibodies. Our results suggest that antibodies that target the dimerization arm of EGFR may be effective across a broader range of cancers than antibodies that target the EGF-binding site, and that a biparatopic antibody targeting both epitopes may be the most effective therapeutic for inhibiting aberrant EGFR signaling in cancer.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid42239335,

title = {Extending structural surfaceomics to identify aberrant conformations of tumor surface proteins as potential immunotherapy targets},

author = {Audrey Kishishita and Sabine Cismoski and Tianna Grant and Rucha Deo and Sanjana Prudhvi and Catherine Sue and Abhilash Barpanda and Clinton Yu and Sanjyot Shenoy and Sarah Berman and Audrey G Reeves and Haolong Li and Tianyi Liu and Akul Naik and Deeptarup Biswas and Fenglong Jiao and Yi He and Matthew Hancock and Radhika Dalal and Arthur Zalevsky and Michael R Hoopmann and Chun Jimmie Ye and Rosa I Viner and Felix Feng and Kamal Mandal and Robert L Moritz and Ignacia Echeverria Riesco and Andrej Sali and James A Wells and Sanjeeva Srivastava and Lan Huang and Arun P Wiita},

doi = {10.64898/2026.05.15.721813},

issn = {2692-8205},

year  = {2026},

date = {2026-05-01},

urldate = {2026-05-01},

journal = {bioRxiv},

abstract = {The complement of tumor cell surface proteins, or "surfaceome", is a rich source of potential immunotherapy targets. To move beyond expression-based target discovery, we previously described "structural surfaceomics," combining crosslinking mass spectrometry (XL-MS) with surface protein biotinylation to identify conformation-selective targets. In our prior work, we applied this method to a single model of acute myeloid leukemia (AML), identifying active integrin beta-2 as a promising target. Here, we expand structural surfaceomics to identify additional immunotherapy targets and surface protein biology across additional models of AML, multiple myeloma, and prostate cancer, as well as donor peripheral blood mononuclear cells. Utilizing these models and different chemical crosslinkers, we compile an extensive database of 5,209 crosslinks. We characterize both shared and unique crosslink-based features, identifying 1,612 disease model-specific crosslinks, including 212 potentially defining tumor-specific conformations based on distance constraint violations relative to AlphaFold predictions. We further implement a suite of emerging modeling tools to predict tumor-specific protein structures. We probe crosslinking patterns suggesting multiple myeloma-specific CD48 and AML-specific integrin α1/β4 heterodimer conformations. This work establishes a resource for cancer structural biology by implementation of structural surfaceomics. Our findings also point toward more realistic protein design models, potentially enabling systematic detection of targetable cancer-specific epitopes for next-generation immunotherapies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}