Steven Banik

All Publications

• Molecular glues and induced proximity: An evolution of tools and discovery. Cell chemical biology Robinson, S. A., Co, J. A., Banik, S. M. 2024

  Abstract

  Small molecule molecular glues can nucleate protein complexes and rewire interactomes. Molecular glues are widely used as probes for understanding functional proximity at a systems level, and the potential to instigate event-driven pharmacology has motivated their application as therapeutics. Despite advantages such as cell permeability and the potential for low off-target activity, glues are still rare when compared to canonical inhibitors in therapeutic development. Their often simple structure and specific ability to reshape protein-protein interactions pose several challenges for widespread, designer applications. Molecular glue discovery and design campaigns can find inspiration from the fields of synthetic biology and biophysics to mine chemical libraries for glue-like molecules.

  View details for DOI 10.1016/j.chembiol.2024.04.001

  View details for PubMedID 38688281

• Elucidating the cellular determinants of targeted membrane protein degradation by lysosome-targeting chimeras. Science (New York, N.Y.) Ahn, G., Riley, N. M., Kamber, R. A., Wisnovsky, S., Moncayo von Hase, S., Bassik, M. C., Banik, S. M., Bertozzi, C. R. 2023; 382 (6668): eadf6249

  Abstract

  Targeted protein degradation can provide advantages over inhibition approaches in the development of therapeutic strategies. Lysosome-targeting chimeras (LYTACs) harness receptors, such as the cation-independent mannose 6-phosphate receptor (CI-M6PR), to direct extracellular proteins to lysosomes. In this work, we used a genome-wide CRISPR knockout approach to identify modulators of LYTAC-mediated membrane protein degradation in human cells. We found that disrupting retromer genes improved target degradation by reducing LYTAC recycling to the plasma membrane. Neddylated cullin-3 facilitated LYTAC-complex lysosomal maturation and was a predictive marker for LYTAC efficacy. A substantial fraction of cell surface CI-M6PR remains occupied by endogenous M6P-modified glycoproteins. Thus, inhibition of M6P biosynthesis increased the internalization of LYTAC-target complexes. Our findings inform design strategies for next-generation LYTACs and elucidate aspects of cell surface receptor occupancy and trafficking.

  View details for DOI 10.1126/science.adf6249

  View details for PubMedID 37856615

• An exercise-inducible metabolite that suppresses feeding and obesity. Nature Li, V. L., He, Y., Contrepois, K., Liu, H., Kim, J. T., Wiggenhorn, A. L., Tanzo, J. T., Tung, A. S., Lyu, X., Zushin, P. H., Jansen, R. S., Michael, B., Loh, K. Y., Yang, A. C., Carl, C. S., Voldstedlund, C. T., Wei, W., Terrell, S. M., Moeller, B. C., Arthur, R. M., Wallis, G. A., van de Wetering, K., Stahl, A., Kiens, B., Richter, E. A., Banik, S. M., Snyder, M. P., Xu, Y., Long, J. Z. 2022

  Abstract

  Exercise confers protection against obesity, type 2 diabetes and other cardiometabolic diseases1-5. However, the molecular and cellular mechanisms that mediate the metabolic benefits of physical activity remain unclear6. Here we show that exercise stimulates the production of N-lactoyl-phenylalanine (Lac-Phe), a blood-borne signalling metabolite that suppresses feeding and obesity. The biosynthesis of Lac-Phe from lactate and phenylalanine occurs in CNDP2+ cells, including macrophages, monocytes and other immune and epithelial cells localized to diverse organs. In diet-induced obese mice, pharmacological-mediated increases in Lac-Phe reduces food intake without affecting movement or energy expenditure. Chronic administration of Lac-Phe decreases adiposity and body weight and improves glucose homeostasis. Conversely, genetic ablation of Lac-Phe biosynthesis in mice increases food intake and obesity following exercise training. Last, large activity-inducible increases in circulating Lac-Phe are also observed in humans and racehorses, establishing this metabolite as a molecular effector associated with physical activity across multiple activity modalities and mammalian species. These data define a conserved exercise-inducible metabolite that controls food intake and influences systemic energy balance.

  View details for DOI 10.1038/s41586-022-04828-5

  View details for PubMedID 35705806

• CRISPR-Suppressor Scanning Unsticks Molecular Glues. ACS central science Robinson, S. A., Banik, S. M. 2022; 8 (4): 408-411

  View details for DOI 10.1021/acscentsci.2c00216

  View details for PubMedID 35505876

• Recent advances in induced proximity modalities. Current opinion in chemical biology Ng, C. S., Banik, S. M. 1800; 67: 102107

  Abstract

  Challenging disease targets necessitate new approaches for therapeutic intervention. Rewiring protein-biomolecule interactions with proximity-inducing agents extends intervention opportunities beyond target agonism or inhibition. Spanning varied molecular phenotypes and diverse target classes, proximity-inducing agents demonstrate immense potential across target degradation, cleavage, and post-translational editing. Here, we review a selection of exciting developments in the concepts and mechanisms of induced proximity-driven strategies from the last two years. Key technological advances that enable these discoveries and expand the scope of targets and machinery for induced-proximity modalities are highlighted.

  View details for DOI 10.1016/j.cbpa.2021.102107

  View details for PubMedID 35033823

• Taming transcription factors with TRAFTACs. Cell chemical biology Ng, C. S., Banik, S. M. 2021; 28 (5): 588-590

  Abstract

  Transcription factors play central roles in numerous diseases yet are notoriously challenging targets for drug development. In this issue of Cell Chemical Biology, Samarasinghe etal. (2021) describe a modular approach to targeting transcription factors for degradation with TRAFTACs, without the need for extensive ligand development campaigns.

  View details for DOI 10.1016/j.chembiol.2021.04.016

  View details for PubMedID 34019844

• LYTACs that engage the asialoglycoprotein receptor for targeted protein degradation. Nature chemical biology Ahn, G., Banik, S. M., Miller, C. L., Riley, N. M., Cochran, J. R., Bertozzi, C. R. 2021

  Abstract

  Selective protein degradation platforms have afforded new development opportunities for therapeutics and tools for biological inquiry. The first lysosome-targeting chimeras (LYTACs) targeted extracellular and membrane proteins for degradation by bridging a target protein to the cation-independent mannose-6-phosphate receptor (CI-M6PR). Here, we developed LYTACs that engage the asialoglycoprotein receptor (ASGPR), a liver-specific lysosome-targeting receptor, to degrade extracellular proteins in a cell-type-specific manner. We conjugated binders to a triantenerrary N-acetylgalactosamine (tri-GalNAc) motif that engages ASGPR to drive the downregulation of proteins. Degradation of epidermal growth factor receptor (EGFR) by GalNAc-LYTAC attenuated EGFR signaling compared to inhibition with an antibody. Furthermore, we demonstrated that a LYTAC consisting of a 3.4-kDa peptide binder linked to a tri-GalNAc ligand degrades integrins and reduces cancer cell proliferation. Degradation with a single tri-GalNAc ligand prompted site-specific conjugation on antibody scaffolds, which improved the pharmacokinetic profile of GalNAc-LYTACs in vivo. GalNAc-LYTACs thus represent an avenue for cell-type-restricted protein degradation.

  View details for DOI 10.1038/s41589-021-00770-1

  View details for PubMedID 33767387

• Degradation from the outside in: targeting extracellular and membrane proteins for degradation through the endolysosomal pathway. Cell chemical biology Ahn, G., Banik, S. M., Bertozzi, C. R. 2021

  Abstract

  Targeted protein degradation (TPD) is a promising strategy to remove deleterious proteins for therapeutic benefit and to probe biological pathways. The past two decades have witnessed a surge in the development of technologies that rely on intracellular machinery to degrade challenging cytosolic targets. However, these TPD platforms leave the majority of extracellular and membrane proteins untouched. To enable degradation of these classes of proteins, internalizing receptors can be co-opted to traffic extracellular proteins to the lysosome. Sweeping antibodies and Seldegs use Fc receptors in conjunction with engineered antibodies to degrade soluble proteins. Recently, lysosome-targeting chimeras (LYTACs) have emerged as a strategy to degrade both secreted and membrane-anchored targets. Together with other newcomer technologies, including antibody-based proteolysis-targeting chimeras, modalities that degrade extracellular proteins have promising translational potential. This perspective will give an overview of TPD platforms that degrade proteins via outside-in approaches and focus on the recent development of LYTACs.

  View details for DOI 10.1016/j.chembiol.2021.02.024

  View details for PubMedID 33770486

• Spreading of a mycobacterial cell surface lipid into host epithelial membranes promotes infectivity. eLife Cambier, C. J., Banik, S. M., Buonomo, J. A., Bertozzi, C. R. 2020; 9

  Abstract

  Several virulence lipids populate the outer cell wall of pathogenic mycobacteria (Jackson, 2014). Phthiocerol dimycocerosate (PDIM), one of the most abundant outer membrane lipids (Anderson, 1929), plays important roles in both defending against host antimicrobial programs (Camacho et al., 2001; Cox et al., 1999; Murry et al., 2009) and in evading these programs altogether (Cambier et al., 2014a; Rousseau et al., 2004). Immediately following infection, mycobacteria rely on PDIM to evade Myd88-dependent recruitment of microbicidal monocytes which can clear infection (Cambier et al., 2014b). To circumvent the limitations in using genetics to understand virulence lipids, we developed a chemical approach to track PDIM during Mycobacterium marinum infection of zebrafish. We found that PDIM's methyl-branched lipid tails enabled it to spread into host epithelial membranes to prevent immune activation. Additionally, PDIM's affinity for cholesterol promoted this phenotype; treatment of zebrafish with statins, cholesterol synthesis inhibitors, decreased spreading and provided protection from infection. This work establishes that interactions between host and pathogen lipids influence mycobacterial infectivity and suggests the use of statins as tuberculosis preventive therapy by inhibiting PDIM spread.

  View details for DOI 10.7554/eLife.60648

  View details for PubMedID 33226343

• 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

  View details for DOI 10.26434/chemrxiv.7927061.v1

• 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