Nature is our best inventor: our lab is interested in the development of cutting-edge mass spectrometry-based proteomics technologies for the analysis of biomolecules and macromolecular assemblies. Recently, fascinated by the exciting biomedical potentials of camelid single-chain VHH antibodies (so-called nanobodies), we have begun to develop methods and informatics to revolutionize the discovery and characterizations of nanobodies.  In parallel, we are harnessing these tools that we developed and biomolecules from nature for biomedical applications, disease diagnosis, and treatment. Through collaboration with structural biologists and modelers, we are also interested in understanding the mechanisms of antigen-antibody binding. 

Currently, the lab is working towards the following directions: 

1. Development of novel nanobody-based SARS-Cov-2 therapeutics. We have recently discovered thousands of potent SARS-CoV-2 neutralizing nanobodies. We discovered multiple elite Nbs with up to femtomolar affinities (the strongest binders that have ever known in nature) that inhibit viral infection at sub-ng/ml concentration, more potent than some of the best human neutralizing antibodies. We determined a crystal structure of such an elite neutralizing Nb in complex with RBD. Structural proteomics and integrative modeling revealed multiple distinct and non-overlapping epitopes and indicated an array of potential neutralization mechanisms. Structural characterization facilitated the bioengineering of novel multivalent Nb constructs into multi-epitope cocktails that achieved ultrahigh neutralization potency (IC50s as low as 0.058 ng/ml- the most potent biotherapeutics to date) and may prevent mutational escape. Our thermostable Nbs can be rapidly produced in bulk from microbes and resist lyophilization, and aerosolization. These promising agents are readily translated into efficient, cost-effective, and convenient therapeutics to help end this once-in-a-century health crisis.

We are employing bioengineering and structural biology to better understand the mechanisms of these amazing neutralizers. We are evaluating the preclinical efficacy of our Nb drugs towards clinical trials soon. 


2. Tools and informatics for large-scale, quantitative analysis of nanobody proteomes. Recently, we developed a proteomic strategy to survey, at an unprecedented scale, the landscapes of antigen-engaged, serum-circulating repertoires of camelid heavy-chain antibodies (hcAbs). The sensitivity and robustness of this technology were validated using three antigens spanning orders of magnitude in immune response; thousands of divergent, high-affinity hcAb families were confidently 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-antibody complexes.  In collaboration with Dina Schneidman's group, we have made some really interesting discoveries about how mammalian circulating antibodies recognize an antigen. This is the coolest paper that we have published by far!!

Check this out:

Currently, we are exploring new directions to develop AI-based algorithms to facilitate the proteomic discovery of antibodies.  We are developing tools to facilitate nanobody humanization.  We are also interested in developing novel methods for high-throughput Nb productions.

3. Development of novel nanobody therapeutics for human diseases. 

Nanobody-based drug delivery and the Durakeukin technology: Therapeutic and diagnostic efficacies of numerous small biomolecules, nanobodies, and chemical compounds are hampered by the short half-lives. Here we developed a repertoire of diverse, high-affinity albumin-nanobodies (NbHSA) to facilitate drug delivery. By integrating biophysics, and hybrid structural biology, we have systematically characterized the Nb-HSA for albumin binding, mapped the epitopes, and resolved the architecture of a tetrameric Nb-albumin complex. We employed quantitative proteomics for accurate, multiplex Nb pharmacokinetic analysis. Using a humanized albumin mouse model, we found that the Nb-HSA has outstanding pharmacokinetics; the most stable Nb-HSA has a 771-fold T1/2 improvement compared with a control Nb. Interestingly, the pharmacokinetics of Nb-HSA is related to their biophysical and structural properties. To demonstrate the utility of NbHSA, we developed a highly stable Nb-HSA-hIL-2 cytokine conjugate “Duraleukin” and confirmed its improved anticancer properties than hIL-2 alone. We envision that this high-quality Nb resource will advance research into novel biotherapeutics.

Check out technology preprint here:

Currently, we are developing novel GPCR nanobodies and agents to penetrate the blood-brain barrier 

We'd like to thank the supports from 

© 2016-2019 by the Shi Lab University of Pittsburgh Pittsburgh PA 15213

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