Center for Protein Engineering and Therapeutics
Department of Pharmacological Sciences
Icahn School of Medicine at Mount Sinai
Welcome! Our lab is interested in developing hybrid proteomic techniques for the analysis of biomolecules. We are also interested in protein engineering and translational sciences.
Fascinated by the exciting potential of nanobodies, we have recently developed powerful proteomic technologies to deconvolute the repertoire of serum-circulating antigen-binding nanobodies. Using this approach, thousands of highly specific and multiepitope nanobodies often with unprecedented affinity can be identified for drug development.
We are also interested in harnessing nanobodies for translational sciences. Through collaborations with structure biologists and modellers, we are investigating the structural basis of ultrahigh-affinity nanobody binding to the disease targets. Another active area of our lab is to develop hybrid techniques to facilitate the design of miniprotein binders.
Finally, we are interested in developing new technique to identify new targets against challenging diseases for future pharmacological interventions.
Integrative proteomics identifies thousands of distinct, multi-epitope, and high-affinity nanobodies
The antibody immune response is essential for the survival of mammals. However, we still lack a systematic understanding of the antibody repertoire. Here, we developed a proteomic strategy to survey, at an unprecedented scale, the landscape of antigen-engaged, circulating camelid heavy-chain antibodies, whose minimal binding fragments are called VHH antibodies or nanobodies. The sensitivity and robustness of this approach were validated with three antigens spanning orders of magnitude in immune responses; thousands of distinct, high-affinity nanobody families were reliably identified and quantified. Using high-throughput structural modeling, cross-linking mass spectrometry, mutagenesis, and deep learning, we mapped and analyzed the epitopes of >100,000 antigen-nanobody complexes. Our results revealed a surprising diversity of ultrahigh-affinity camelid nanobodies for specific antigen binding on various dominant epitope clusters. Nanobodies utilize both shape and charge complementarity to enable highly selective antigen binding. Interestingly, we found that nanobody-antigen binding can mimic conserved intracellular protein-protein interactions. A record of this paper's Transparent Peer Review process is included in the Supplemental information.