David A. Spiegel

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Name: Spiegel, David A.

Organization: Yale University , USA

Department: Department of Chemistry

Title: (PhD)

Chemicals
References

Neutralization of Pathogenic Fungi with Small-Molecule Immunotherapeutics

Co-reporter:Dr. Egor Chirkin;Dr. Viswanathan Muthusamy;Paul Mann;Dr. Terry Roemer;Dr. Philippe G. Nantermet; Dr. David A. Spiegel

Angewandte Chemie 2017 Volume 129(Issue 42) pp:13216-13220

Publication Date(Web):2017/10/09

DOI:10.1002/ange.201707536

AbstractSystemic fungal infections represent an important public health concern, and new antifungal agents are highly desirable. Herein, we describe the design, synthesis, and biological evaluation of a novel class of antifungal compounds called antibody-recruiting molecules targeting fungi (ARM-Fs). Our approach relies on the use of non-peptidic small molecules, which selectively bind fungal cells and recruit endogenous antibodies to their surfaces, resulting in immune-mediated clearance. Using the opportunistic fungal pathogen Candida albicans as a model, we identified a highly specific bifunctional molecule able to mediate the engulfment and phagocytosis of C. albicans cells by human immune cells in biologically relevant functional assays. This work represents a novel therapeutic approach to treating fungal illness with significant potential to complement and/or combine with existing treatment strategies.

Neutralization of Pathogenic Fungi with Small-Molecule Immunotherapeutics

Co-reporter:Dr. Egor Chirkin;Dr. Viswanathan Muthusamy;Paul Mann;Dr. Terry Roemer;Dr. Philippe G. Nantermet; Dr. David A. Spiegel

Angewandte Chemie International Edition 2017 Volume 56(Issue 42) pp:13036-13040

Publication Date(Web):2017/10/09

DOI:10.1002/anie.201707536

Peptidines: glycine-amidine-based oligomers for solution- and solid-phase synthesis

Co-reporter:Julian Vastl, Rendy Kartika, Kichul Park, Art E. Cho and David A. Spiegel

Chemical Science 2016 vol. 7(Issue 5) pp:3317-3324

Publication Date(Web):16 Feb 2016

DOI:10.1039/C5SC03882K

Efforts to emulate biological oligomers have given rise to a host of useful technologies, ranging from solid-phase peptide and nucleic acid synthesis to various peptidomimetic platforms. Herein we introduce a novel class of peptide-like oligomers called “peptidines” wherein each carbonyl O-atom within poly-N-alkyl glycine oligomers is replaced with a functionalized N-atom. Compared to peptoids or peptides, the presence of this amidine N-substituent in peptidines effectively doubles the number of diversification sites per monomeric unit, and can decrease their overall conformational flexibility. We have developed iterative solution- and solid-phase protocols for the straightforward assembly of peptidines containing diverse backbone and amidine substituents, derived from readily available primary and secondary amines. We have also performed crystallographic and computational studies, which demonstrate a strong preference for the trans (E) amidine geometry. Given their straightforward synthetic preparation and high functional group density, peptidines have the potential to serve as useful tools for library generation, peptide mimicry, and the identification of biologically active small molecules.

Re-engineering the Immune Response to Metastatic Cancer: Antibody-Recruiting Small Molecules Targeting the Urokinase Receptor

Co-reporter:Dr. Anthony F. Rullo;Kelly J. Fitzgerald;Dr. Viswanathan Muthusamy;Min Liu;Dr. Cai Yuan;Dr. Mingdong Huang;Minsup Kim;Dr. Art E. Cho;Dr. David A. Spiegel

Angewandte Chemie 2016 Volume 128( Issue 11) pp:3706-3710

Publication Date(Web):

DOI:10.1002/ange.201510866

Abstract

Developing selective strategies to treat metastatic cancers remains a significant challenge. Herein, we report the first antibody-recruiting small molecule (ARM) that is capable of recognizing the urokinase-type plasminogen activator receptor (uPAR), a uniquely overexpressed cancer cell-surface marker, and facilitating the immune-mediated destruction of cancer cells. A co-crystal structure of the ARM-U2/uPAR complex was obtained, representing the first crystal structure of uPAR complexed with a non-peptide ligand. Finally, we demonstrated that ARM-U2 substantially suppresses tumor growth in vivo with no evidence of weight loss, unlike the standard-of-care agent doxorubicin. This work underscores the promise of antibody-recruiting molecules as immunotherapeutics for treating cancer.

Re-engineering the Immune Response to Metastatic Cancer: Antibody-Recruiting Small Molecules Targeting the Urokinase Receptor

Co-reporter:Dr. Anthony F. Rullo;Kelly J. Fitzgerald;Dr. Viswanathan Muthusamy;Min Liu;Dr. Cai Yuan;Dr. Mingdong Huang;Minsup Kim;Dr. Art E. Cho;Dr. David A. Spiegel

Angewandte Chemie International Edition 2016 Volume 55( Issue 11) pp:3642-3646

Publication Date(Web):

DOI:10.1002/anie.201510866

Abstract

An Activity-Based Probe for Studying Crosslinking in Live Bacteria

Co-reporter:Dr. Samir Gautam;Dr. Taehan Kim;Dr. Takuji Shoda;Dr. Sounok Sen;Deeksha Deep;Ragini Luthra;Maria Teresa Ferreira;Dr. Mariana G. Pinho;Dr. David A. Spiegel

Angewandte Chemie International Edition 2015 Volume 54( Issue 36) pp:10492-10496

Publication Date(Web):

DOI:10.1002/anie.201503869

Abstract

Penicillin-binding proteins (PBPs) catalyze the crosslinking of peptidoglycan (PG), an essential process for bacterial growth and survival, and a common antibiotic target. Yet, despite its importance, little is known about the spatiotemporal aspects of crosslinking—largely because of a lack of experimental tools for studying the reaction in live bacteria. Here we introduce such a tool: an activity-based probe that enables visualization and relative quantitation of crosslinking in vivo. In Staphylococcus aureus, we show that fluorescent mimics of the natural substrate of PBPs (PG stem peptide) are covalently incorporated into the cell wall, installing fluorophores in place of natural crosslinks. These fluorescent stem peptide mimics (FSPMs) are selectively recognized by a single PBP in S. aureus: PBP4. Thus, we were able to use FSPM pulse-labeling to localize PBP4 activity in live cells, showing that it is recruited to the septum in a manner dependent on wall teichoic acid.

Co-reporter:Tina Wang;Cristian Draghici

Science 2015 Volume 350(Issue 6258) pp:

Publication Date(Web):

DOI:10.1126/science.aac9655

Getting a handle on a cross-linking motif

Although protein backbones consist exclusively of amino acids, various other molecules in the cell often get latched on afterward in a process termed posttranslational modification. In one such motif, called glucosepane, the side chains of lysine and arginine form a condensed cross-link through a reaction sequence with glucose. Formation of this cross-link is of interest in diabetes research. Draghici et al. now report a chemical synthesis of glucosepane outside the broader environment of a surrounding protein (see the Perspective by Boger). This synthesis should facilitate more precise characterization of the structure and function of the motif in vivo.

Science, this issue p. 294; see also p. 275

An Activity-Based Probe for Studying Crosslinking in Live Bacteria

Co-reporter:Dr. Samir Gautam;Dr. Taehan Kim;Dr. Takuji Shoda;Dr. Sounok Sen;Deeksha Deep;Ragini Luthra;Maria Teresa Ferreira;Dr. Mariana G. Pinho;Dr. David A. Spiegel

Angewandte Chemie 2015 Volume 127( Issue 36) pp:10638-10642

Publication Date(Web):

DOI:10.1002/ange.201503869

Abstract

Illuminating HIV gp120-ligand recognition through computationally-driven optimization of antibody-recruiting molecules

Co-reporter:Christopher G. Parker, Markus K. Dahlgren, Ran N. Tao, Don T. Li, Eugene F. Douglass, Takuji Shoda, Navneet Jawanda, Krasimir A. Spasov, Sangil Lee, Nannan Zhou, Robert A. Domaoal, Richard E. Sutton, Karen S. Anderson, Mark Krystal, William L. Jorgensen and David A. Spiegel

Chemical Science 2014 vol. 5(Issue 6) pp:2311-2317

Publication Date(Web):02 Apr 2014

DOI:10.1039/C4SC00484A

Here we report on the structure-based optimization of antibody-recruiting molecules targeting HIV gp120 (ARM-H). These studies have leveraged a combination of medicinal chemistry, biochemical and cellular assay analysis, and computation. Our findings have afforded an optimized analog of ARM-H, which is ∼1000 fold more potent in gp120-binding and MT-2 antiviral assays than our previously reported derivative. Furthermore, computational analysis, taken together with experimental data, provides evidence that azaindole- and indole-based attachment inhibitors bind gp120 at an accessory hydrophobic pocket beneath the CD4-binding site and can also adopt multiple distinct binding modes in interacting with gp120. These results are likely to prove enabling in the development of novel HIV attachment inhibitors, and more broadly, they suggest novel applications for ARMs as probes of conformationally flexible systems.

A Comprehensive Mathematical Model for Three-Body Binding Equilibria

Co-reporter:Eugene F. Douglass, Jr., Chad J. Miller, Gerson Sparer, Harold Shapiro, and David A. Spiegel

Journal of the American Chemical Society 2013 Volume 135(Issue 16) pp:6092-6099

Publication Date(Web):April 1, 2013

DOI:10.1021/ja311795d

Three-component systems are often more complex than their two-component counterparts. Although the reversible association of three components in solution is critical for a vast array of chemical and biological processes, no general physical picture of such systems has emerged. Here we have developed a general, comprehensive framework for understanding ternary complex equilibria, which relates directly to familiar concepts such as EC50 and IC50 from simpler (binary complex) equilibria. Importantly, application of our model to data from the published literature has enabled us to achieve new insights into complex systems ranging from coagulation to therapeutic dosing regimens for monoclonal antibodies. We also provide an Excel spreadsheet to assist readers in both conceptualizing and applying our models. Overall, our analysis has the potential to render complex three-component systems—which have previously been characterized as “analytically intractable”—readily comprehensible to theoreticians and experimentalists alike.

Exploring Binding and Effector Functions of Natural Human Antibodies Using Synthetic Immunomodulators

Co-reporter:Charles E. Jakobsche, Christopher G. Parker, Ran N. Tao, Mariya D. Kolesnikova, Eugene F. Douglass Jr., and David A. Spiegel

ACS Chemical Biology 2013 Volume 8(Issue 11) pp:2404

Publication Date(Web):September 20, 2013

DOI:10.1021/cb4004942

The ability to profile the prevalence and functional activity of endogenous antibodies is of vast clinical and diagnostic importance. Serum antibodies are an important class of biomarkers and are also crucial elements of immune responses elicited by natural disease-causing agents as well as vaccines. In particular, materials for manipulating and/or enhancing immune responses toward disease-causing cells or viruses have exhibited significant promise for therapeutic applications. Antibody-recruiting molecules (ARMs), bifunctional organic molecules that redirect endogenous antibodies to pathological targets, thereby increasing their recognition and clearance by the immune system, have proven particularly interesting. Notably, although ARMs capable of hijacking antibodies against oligosaccharides and electron-poor aromatics have proven efficacious, systematic comparisons of the prevalence and effectiveness of natural anti-hapten antibody populations have not appeared in the literature. Herein we report head-to-head comparisons of three chemically simple antigens, which are known ligands for endogenous antibodies. Thus, we have chemically synthesized bifunctional molecules containing 2,4-dinitrophenyl (DNP), phosphorylcholine (PC), and rhamnose. We have then used a combination of ELISA, flow cytometry, and cell-viability assays to compare these antigens in terms of their abilities both to recruit natural antibody from human serum and also to direct serum-dependent cytotoxicity against target cells. These studies have revealed rhamnose to be the most efficacious of the synthetic antigens examined. Furthermore, analysis of 122 individual serum samples has afforded comprehensive insights into population-wide prevalence and isotype distributions of distinct anti-hapten antibody populations. In addition to providing a general platform for comparing and studying anti-hapten antibodies, these studies serve as a useful starting point for the optimization of antibody-recruiting molecules and other synthetic strategies for modulating human immunity.

Antibody-Recruiting Molecules: An Emerging Paradigm for Engaging Immune Function in Treating Human Disease

Co-reporter:Patrick J. McEnaney, Christopher G. Parker, Andrew X. Zhang, and David A. Spiegel

ACS Chemical Biology 2012 Volume 7(Issue 7) pp:1139

Publication Date(Web):July 3, 2012

DOI:10.1021/cb300119g

Synthetic immunology, the development of synthetic systems capable of modulating and/or manipulating immunological functions, represents an emerging field of research with manifold possibilities. One focus of this area has been to create low molecular weight synthetic species, called antibody-recruiting molecules (ARMs), which are capable of enhancing antibody binding to disease-relevant cells or viruses, thus leading to their immune-mediated clearance. This article provides a thorough discussion of contributions in this area, beginning with the history of small-molecule-based technologies for modulating antibody recognition, followed by a systematic review of the various applications of ARM-based strategies. Thus, we describe ARMs capable of targeting cancer, bacteria, and viral pathogens, along with some of the scientific discoveries that have resulted from their development. Research in this area underscores the many exciting possibilities at the interface of organic chemistry and immunobiology and is positioned to advance both basic and clinical science in the years to come.

Reprogramming Urokinase into an Antibody-Recruiting Anticancer Agent

Co-reporter:Charles E. Jakobsche, Patrick J. McEnaney, Andrew X. Zhang, and David A. Spiegel

ACS Chemical Biology 2012 Volume 7(Issue 2) pp:316

Publication Date(Web):November 18, 2011

DOI:10.1021/cb200374e

Synthetic compounds for controlling or creating human immunity have the potential to revolutionize disease treatment. Motivated by challenges in this arena, we report herein a strategy to target metastatic cancer cells for immune-mediated destruction by targeting the urokinase-type plasminogen activator receptor (uPAR). Urokinase-type plasminogen activator (uPA) and uPAR are overexpressed on the surfaces of a wide range of invasive cancer cells and are believed to contribute substantially to the migratory propensities of these cells. The key component of our approach is an antibody-recruiting molecule that targets the urokinase receptor (ARM-U). This bifunctional construct is formed by selectively, covalently attaching an antibody-binding small molecule to the active site of the urokinase enzyme. We demonstrate that ARM-U is capable of directing antibodies to the surfaces of target cancer cells and mediating both antibody-dependent cellular phagocytosis (ADCP) and antibody-dependent cellular cytotoxicity (ADCC) against multiple human cancer cell lines. We believe that the reported strategy has the potential to inform novel treatment options for a variety of deadly, invasive cancers.

A Remote Arene-Binding Site on Prostate Specific Membrane Antigen Revealed by Antibody-Recruiting Small Molecules

Co-reporter:Andrew X. Zhang ; Ryan P. Murelli ; Cyril Barinka ; Julien Michel ; Alexandra Cocleaza ; William L. Jorgensen ; Jacek Lubkowski

Journal of the American Chemical Society 2010 Volume 132(Issue 36) pp:12711-12716

Publication Date(Web):August 20, 2010

DOI:10.1021/ja104591m

Prostate specific membrane antigen (PSMA) is a membrane-bound glutamate carboxypeptidase overexpressed in many forms of prostate cancer. Our laboratory has recently disclosed a class of small molecules, called ARM-Ps (antibody-recruiting molecule targeting prostate cancer) that are capable of enhancing antibody-mediated immune recognition of prostate cancer cells. Interestingly, during the course of these studies, we found ARM-Ps to exhibit extraordinarily high potencies toward PSMA, compared to previously reported inhibitors. Here, we report in-depth biochemical, crystallographic, and computational investigations which elucidate the origin of the observed affinity enhancement. These studies reveal a previously unreported arene-binding site on PSMA, which we believe participates in an aromatic stacking interaction with ARMs. Although this site is composed of only a few amino acid residues, it drastically enhances small molecule binding affinity. These results provide critical insights into the design of PSMA-targeted small molecules for prostate cancer diagnosis and treatment; more broadly, the presence of similar arene-binding sites throughout the proteome could prove widely enabling in the optimization of small molecule−protein interactions.

A Biosynthetic Strategy for Re-engineering the Staphylococcus aureus Cell Wall with Non-native Small Molecules

Co-reporter:James W. Nelson, Alexander G. Chamessian, Patrick J. McEnaney, Ryan P. Murelli, Barbara I. Kazmiercak, and David A. Spiegel

ACS Chemical Biology 2010 Volume 5(Issue 12) pp:1147

Publication Date(Web):October 5, 2010

DOI:10.1021/cb100195d

Staphylococcus aureus (S. aureus) is a Gram-positive bacterial pathogen that has emerged as a major public health threat. Here we report that the cell wall of S. aureus can be covalently re-engineered to contain non-native small molecules. This process makes use of endogenous levels of the bacterial enzyme sortase A (SrtA), which ordinarily functions to incorporate proteins into the bacterial cell wall. Thus, incubation of wild-type bacteria with rationally designed SrtA substrates results in covalent incorporation of functional molecular handles (fluorescein, biotin, and azide) into cell wall peptidoglycan. These conclusions are supported by data obtained through a variety of experimental techniques (epifluorescence and electron microscopy, biochemical extraction, and mass spectrometry), and cell-wall-incorporated azide was exploited as a chemical handle to perform an azide–alkyne cycloaddition reaction on the bacterial cell surface. This report represents the first example of cell wall engineering of S. aureus or any other pathogenic Gram-positive bacteria and has the potential for widespread utility.

An Antibody-Recruiting Small Molecule That Targets HIV gp120

Co-reporter:Christopher G. Parker ; Robert A. Domaoal ; Karen S. Anderson

Journal of the American Chemical Society 2009 Volume 131(Issue 45) pp:16392-16394

Publication Date(Web):October 19, 2009

DOI:10.1021/ja9057647

HIV/AIDS is a global pandemic for which new treatment strategies are desperately needed. We have designed a novel small molecule, designated as ARM-H, that has the potential to interfere with HIV survival through two mechanisms: (1) by recruiting antibodies to gp120-expressing virus particles and infected human cells, thus enhancing their uptake and destruction by the human immune system, and (2) by binding the viral glycoprotein gp120, inhibiting its interaction with the human protein CD4 and preventing virus entry. Here we demonstrate that ARM-H is capable of simultaneously binding gp120, a component of the Env surface viral glycoprotein (found on the surface of both HIV and virus-infected cells) and anti-2,4-dinitrophenyl antibodies (already present in the human bloodstream). The ternary complex formed between the antibody, ARM-H, and gp120 is immunologically active and leads to the complement-mediated destruction of Env-expressing cells. Furthermore, ARM-H prevents virus entry into human T-cells and should therefore be capable of inhibiting virus replication through two mutually reinforcing mechanisms (inhibition of virus entry and antibody-mediated killing). These studies demonstrate the viable anti-HIV activity of antibody-recruiting small molecules and have the potential to initiate novel paradigms in HIV treatment.

Chemical Control over Immune Recognition: A Class of Antibody-Recruiting Small Molecules That Target Prostate Cancer

Co-reporter:Ryan P. Murelli ; Andrew X. Zhang ; Julien Michel ; William L. Jorgensen

Journal of the American Chemical Society 2009 Volume 131(Issue 47) pp:17090-17092

Publication Date(Web):November 4, 2009

DOI:10.1021/ja906844e

Prostate cancer is the second leading cause of cancer-related death among the American male population, and society is in dire need of new approaches to treat this disease. Here we report the design, synthesis, and biological evaluation of a class of bifunctional small molecules called antibody-recruiting molecules targeting prostate cancer (ARM-Ps) that enhance the recognition of prostate cancer cells by the human immune system. ARM-P derivatives were designed rationally via the computational analysis of crystallographic data, and we demonstrate here that these materials are able to (1) bind prostate-specific membrane antigen (PSMA) with high affinity (high pM to low nM), (2) template the formation of ternary complexes of anti-DNP antibodies, ARM-P, and LNCaP human prostate cancer cells, and (3) mediate the antibody-dependent killing of LNCaP cells in the presence of human effector cells. This manuscript describes the application of fundamental chemical principles to the design of a novel class of molecules with high therapeutic potential. We believe that this general small-molecule-based strategy could give rise to novel directions in treating cancer and other diseases.

Exterior design: strategies for redecorating the bacterial surface with small molecules

Co-reporter:Samir Gautam, Thomas J. Gniadek, Taehan Kim, David A. Spiegel

Trends in Biotechnology (April 2013) Volume 31(Issue 4) pp:258-267

Publication Date(Web):1 April 2013

DOI:10.1016/j.tibtech.2013.01.012

Recombinant techniques for expressing heterologous proteins and sugars on the surface of bacteria have been known since the 1980s, and have proven useful in a variety of settings from biocatalysis to vaccinology. The past decade has also seen the emergence of novel methods that allow modification of bacterial surfaces with small non-biological compounds. Such technologies enable researchers to harness the unique properties of synthetic materials on a live bacterial platform, opening the door to an exciting new set of applications. Here we review strategies for bacterial surface display and describe how they have been applied thus far. We believe that chemical surface display holds great potential for advancing research in basic bacteriology and applied fields of biotechnology and biomedicine.Highlights► New methods allow installation of small molecules on the surface of live bacteria. ► Bacterial chemical display allows applications that were not previously possible. ► Fields of basic research, biotechnology, and medicine have already felt the impact.

Peptidines: glycine-amidine-based oligomers for solution- and solid-phase synthesis

Co-reporter:Julian Vastl, Rendy Kartika, Kichul Park, Art E. Cho and David A. Spiegel

Chemical Science (2010-Present) 2016 - vol. 7(Issue 5) pp:NaN3324-3324

Publication Date(Web):2016/02/16

DOI:10.1039/C5SC03882K

Illuminating HIV gp120-ligand recognition through computationally-driven optimization of antibody-recruiting molecules

Chemical Science (2010-Present) 2014 - vol. 5(Issue 6) pp:NaN2317-2317

Publication Date(Web):2014/04/02

DOI:10.1039/C4SC00484A