Professional Education


  • Doctor of Philosophy, Harvard University (2016)

Stanford Advisors


2020-21 Courses


All Publications


  • Lysosome-targeting chimaeras for degradation of extracellular proteins. Nature Banik, S. M., Pedram, K., Wisnovsky, S., Ahn, G., Riley, N. M., Bertozzi, C. R. 2020

    Abstract

    The majority of therapies that target individual proteins rely on specific activity-modulating interactions with the target protein-for example, enzyme inhibition or ligand blocking. However, several major classes of therapeutically relevant proteins have unknown or inaccessible activity profiles and so cannot be targeted by such strategies. Protein-degradation platforms such as proteolysis-targeting chimaeras (PROTACs)1,2 and others (for example, dTAGs3, Trim-Away4, chaperone-mediated autophagy targeting5 and SNIPERs6) have been developed for proteins that are typically difficult to target; however, these methods involve the manipulation of intracellular protein degradation machinery and are therefore fundamentally limited to proteins that contain cytosolic domains to which ligands can bind and recruit the requisite cellular components. Extracellular and membrane-associated proteins-the products of 40% of all protein-encoding genes7-are key agents in cancer, ageing-related diseases and autoimmune disorders8, and so a general strategy to selectively degrade these proteins has the potential to improve human health. Here we establish the targeted degradation of extracellular and membrane-associated proteins using conjugates that bind both a cell-surface lysosome-shuttling receptor and the extracellular domain of a target protein. These initial lysosome-targeting chimaeras, which we term LYTACs, consist of a small molecule or antibody fused to chemically synthesized glycopeptide ligands that are agonists of the cation-independent mannose-6-phosphate receptor (CI-M6PR). We use LYTACs to develop a CRISPR interference screen that reveals the biochemical pathway for CI-M6PR-mediated cargo internalization in cell lines, and uncover the exocyst complex as a previously unidentified-but essential-component of this pathway. We demonstrate the scope of this platform through the degradation of therapeutically relevant proteins, including apolipoproteinE4, epidermal growth factor receptor, CD71 and programmed death-ligand 1. Our results establish a modular strategy for directing secreted and membrane proteins for lysosomal degradation, with broad implications for biochemical research and for therapeutics.

    View details for DOI 10.1038/s41586-020-2545-9

    View details for PubMedID 32728216

  • Membrane-tethered mucin-like polypeptides sterically inhibit binding and slow fusion kinetics of influenza A virus. Proceedings of the National Academy of Sciences of the United States of America Delaveris, C. S., Webster, E. R., Banik, S. M., Boxer, S. G., Bertozzi, C. R. 2020

    Abstract

    The mechanism(s) by which cell-tethered mucins modulate infection by influenza A viruses (IAVs) remain an open question. Mucins form both a protective barrier that can block virus binding and recruit IAVs to bind cells via the sialic acids of cell-tethered mucins. To elucidate the molecular role of mucins in flu pathogenesis, we constructed a synthetic glycocalyx to investigate membrane-tethered mucins in the context of IAV binding and fusion. We designed and synthesized lipid-tethered glycopolypeptide mimics of mucins and added them to lipid bilayers, allowing chemical control of length, glycosylation, and surface density of a model glycocalyx. We observed that the mucin mimics undergo a conformational change at high surface densities from a compact to an extended architecture. At high surface densities, asialo mucin mimics inhibited IAV binding to underlying glycolipid receptors, and this density correlated to the mucin mimic's conformational transition. Using a single virus fusion assay, we observed that while fusion of virions bound to vesicles coated with sialylated mucin mimics was possible, the kinetics of fusion was slowed in a mucin density-dependent manner. These data provide a molecular model for a protective mechanism by mucins in IAV infection, and therefore this synthetic glycocalyx provides a useful reductionist model for studying the complex interface of host-pathogen interactions.

    View details for DOI 10.1073/pnas.1921962117

    View details for PubMedID 32457151

  • A Plasma Protein Network Regulates PM20D1 and N-Acyl Amino Acid Bioactivity. Cell chemical biology Kim, J. T., Jedrychowski, M. P., Wei, W., Fernandez, D., Fischer, C. R., Banik, S. M., Spiegelman, B. M., Long, J. Z. 2020

    Abstract

    N-acyl amino acids are a family of cold-inducible circulating lipids that stimulate thermogenesis. Their biosynthesis is mediated by a secreted enzyme called PM20D1. The extracellular mechanisms that regulate PM20D1 or N-acyl amino acid activity in the complex environment of blood plasma remains unknown. Using quantitative proteomics, here we show that PM20D1 circulates in tight association with both low- and high-density lipoproteins. Lipoprotein particles are powerful co-activators of PM20D1 activity invitro and N-acyl amino acid biosynthesis invivo. We also identify serum albumin as a physiologic N-acyl amino acid carrier, which spatially segregates N-acyl amino acids away from their sites of production, confers resistance to hydrolytic degradation, and establishes an equilibrium between thermogenic "free" versus inactive "bound" fractions. These data establish lipoprotein particles as principal extracellular sites of N-acyl amino acid biosynthesis and identify a lipoprotein-albumin network that regulates the activity of a circulating thermogenic lipid family.

    View details for DOI 10.1016/j.chembiol.2020.04.009

    View details for PubMedID 32402239

  • Catalytic, Enantioselective 1,2-Difluorination of Cinnamamides ORGANIC LETTERS Haj, M. K., Banik, S. M., Jacobsen, E. N. 2019; 21 (13): 4919–23

    Abstract

    The enantio- and diastereoselective synthesis of 1,2-difluorides via chiral aryl iodide-catalyzed difluorination of cinnamamides is reported. The method uses HF-pyridine as a fluoride source and mCPBA as a stoichiometric oxidant to turn over catalyst, and affords compounds containing vicinal, fluoride-bearing stereocenters. Selectivity for 1,2-difluorination versus a rearrangement pathway resulting in 1,1-difluorination is enforced through anchimeric assistance from a N- tert-butyl amide substituent.

    View details for DOI 10.1021/acs.orglett.9b00938

    View details for Web of Science ID 000474795200001

    View details for PubMedID 30963766

  • Lysosome Targeting Chimeras (LYTACs) for the Degradation of Secreted and Membrane Proteins ChemRxiv Banik, S. M., Pedram, K., Wisnovsky, S., Riley, N. M., Bertozzi, C. R. 2019
  • Catalytic Diastereo- and Enantioselective Fluoroamination of Alkenes JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Mennie, K. M., Banik, S. M., Reichert, E. C., Jacobsen, E. N. 2018; 140 (14): 4797–4802

    Abstract

    The stereoselective synthesis of syn-β-fluoroaziridine building blocks via chiral aryl iodide-catalyzed fluorination of allylic amines is reported. The method employs HF-pyridine as a nucleophilic fluoride source together with mCPBA as a stoichiometric oxidant, and affords access to arylethylamine derivatives featuring fluorine-containing stereocenters in high diastereo- and enantioselectivity. Catalyst-controlled diastereoselectivity in the fluorination of chiral allylic amines enabled the preparation of highly enantioenriched 1,3-difluoro-2-amines bearing three contiguous stereocenters. The enantioselective catalytic method was applied successfully to other classes of multifunctional alkene substrates to afford anti-β-fluoropyrrolidines, as well as a variety of 1,2-oxyfluorinated products.

    View details for DOI 10.1021/jacs.8b02143

    View details for Web of Science ID 000430155800011

    View details for PubMedID 29583001

    View details for PubMedCentralID PMC5902804

  • Lewis acid enhancement by hydrogen-bond donors for asymmetric catalysis Science Banik, S. M., Levina, A., Hyde, A. M., Jacobsen, E. N. 2017; 358: 761-764
  • Catalytic 1,3-Difunctionalization via Oxidative C–C Bond Activation Journal of the American Chemical Society Banik, S. M., Mennie, K. M., Jacobsen, E. N. 2017; 139 (27): 9152-9155
  • Catalytic, asymmetric difluorination of alkenes to generate difluoromethylated stereocenters Science Banik, S. M., Medley, J. W., Jacobsen, E. N. 2016; 353 (6294): 51-54

    View details for DOI 10.1126/science.aaf8078

  • Catalytic, Diastereoselective 1,2-Difluorination of Alkenes Journal of the American Chemical Society Banik, S. M., Medley, J. W., Jacobsen, E. N. 2016; 138 (15): 5000-5003
  • Chemoselective pd-catalyzed oxidation of polyols: synthetic scope and mechanistic studies. Journal of the American Chemical Society Chung, K., Banik, S. M., De Crisci, A. G., Pearson, D. M., Blake, T. R., Olsson, J. V., Ingram, A. J., Zare, R. N., Waymouth, R. M. 2013; 135 (20): 7593-7602

    Abstract

    The regio- and chemoselective oxidation of unprotected vicinal polyols with [(neocuproine)Pd(OAc)]2(OTf)2 (1) (neocuproine = 2,9-dimethyl-1,10-phenanthroline) occurs readily under mild reaction conditions to generate α-hydroxy ketones. The oxidation of vicinal diols is both faster and more selective than the oxidation of primary and secondary alcohols; vicinal 1,2-diols are oxidized selectively to hydroxy ketones, whereas primary alcohols are oxidized in preference to secondary alcohols. Oxidative lactonization of 1,5-diols yields cyclic lactones. Catalyst loadings as low as 0.12 mol % in oxidation reactions on a 10 g scale can be used. The exquisite selectivity of this catalyst system is evident in the chemoselective and stereospecific oxidation of the polyol (S,S)-1,2,3,4-tetrahydroxybutane [(S,S)-threitol] to (S)-erythrulose. Mechanistic, kinetic, and theoretical studies revealed that the rate laws for the oxidation of primary and secondary alcohols differ from those of diols. Density functional theory calculations support the conclusion that β-hydride elimination to give hydroxy ketones is product-determining for the oxidation of vicinal diols, whereas for primary and secondary alcohols, pre-equilibria favoring primary alkoxides are product-determining. In situ desorption electrospray ionization mass spectrometry (DESI-MS) revealed several key intermediates in the proposed catalytic cycle.

    View details for DOI 10.1021/ja4008694

    View details for PubMedID 23659308