Steven Banik’s research interests center on rewiring mammalian biology and chemical biotechnology development using molecular design and construction. Projects in the Banik lab combine chemical biology, organic chemistry, protein engineering, cell and molecular biology to precisely manipulate the biological machines present in mammalian cells. Projects broadly aim to perform new functions that shed light on regulatory machinery and the potential scope of mammalian biology. A particular focus is the study of biological mechanisms that can be coopted by synthetic molecules (both small molecules and proteins). These concepts are applied to develop new therapeutic strategies for treating aging-related disorders, genetic diseases, and cancer.
Prior to joining the faculty at Stanford, Steven was a NIH and Burroughs CASI postdoctoral fellow advised by Prof. Carolyn Bertozzi at Stanford. His postdoctoral research developed approaches for targeted protein degradation from the extracellular space with lysosome targeting chimeras (LYTACs). He received his Ph.D. from Harvard University in 2016, where he worked with Prof. Eric Jacobsen on synthetic methods for the selective, catalytic difluorination of organic molecules and new approaches for generating and controlling reactive cationic intermediates in asymmetric catalysis.
Faculty Fellow, Stanford ChEM-H (2021 - Present)
Postdoc, Stanford University, Chemical Biology
B.S., University of Wisconsin–Madison, Chemistry (2011)
Ph.D., Harvard University, Chemistry (2017)
- The Chemical Principles of Life II
CHEM 143 (Spr)
- Independent Studies (5)
Prior Year Courses
- Exploring Chemical Research at Stanford
CHEM 91 (Win)
- Exploring Chemical Research at Stanford
LYTACs that engage the asialoglycoprotein receptor for targeted protein degradation.
Nature chemical biology
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
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.
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.
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
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
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
2019; 21 (13): 4919–23
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
View details for DOI 10.26434/chemrxiv.7927061.v1
Catalytic Diastereo- and Enantioselective Fluoroamination of Alkenes
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
2018; 140 (14): 4797–4802
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 2017; 358: 761-764
- Catalytic 1,3-Difunctionalization via Oxidative C–C Bond Activation Journal of the American Chemical Society 2017; 139 (27): 9152-9155
Catalytic, asymmetric difluorination of alkenes to generate difluoromethylated stereocenters
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 2016; 138 (15): 5000-5003
Chemoselective pd-catalyzed oxidation of polyols: synthetic scope and mechanistic studies.
Journal of the American Chemical Society
2013; 135 (20): 7593-7602
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