Publications by authors named "Steven C Zimmerman"

103 Publications

Versatile Target-Guided Screen for Discovering Bidirectional Transcription Inhibitors of a Trinucleotide Repeat Disease.

ACS Med Chem Lett 2021 Jun 21;12(6):935-940. Epub 2021 May 21.

Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.

Myotonic dystrophy type 1 originates from d(CTG·CAG) repeats that undergo aberrant expansion during normal processing because the d(CTG) repeat forms stable hairpin structures. Bidirectional transcription of d(CTG·CAG) yields two RNA transcripts that undergo repeat-associated non-ATG (RAN) translation to form homopolymeric proteins. Thus, both the r(CUG) transcript and the r(CAG) transcript are known to be toxic. We report a pairwise fragment-based, target-guided approach to screen for proximity-induced click dimers formed on the nucleic acid template. This screen uses an azide/alkyne clickable fragment library of nucleic acid-binding ligands incubated in parallel, pairwise reactions as an alternative to our previously reported one-pot screening method. MALDI-TOF mass spectroscopy was used to detect template assisted click products. Hit compounds inhibited the transcription of d(CTG·CAG) bidirectionally with IC values in the low micromolar range. This approach may be broadly applicable to other trinucleotide repeat diseases and in targeting other disease-associated nucleic acid sequences.
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http://dx.doi.org/10.1021/acsmedchemlett.1c00064DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8201509PMC
June 2021

A Novel Minor Groove Binder as a Potential Therapeutic Agent for Myotonic Dystrophy Type 1.

ChemMedChem 2021 Sep 10;16(17):2638-2644. Epub 2021 Jun 10.

Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, 61801, Urbana, IL, USA.

Myotonic dystrophy type 1 (DM1) is a multisystemic neuromuscular disorder that is inherited in an autosomal dominant manner. DM1 originates in a (CTG⋅CAG) repeat expansion in the 3'-UTR of the dystrophia myotonic protein kinase (DMPK) gene on chromosome 19. One of the transcripts, r(CUG) , is toxic in various ways. Herein we report a rationally designed small molecule with a thiazole peptidomimetic unit that can serve as a minor groove binder for the nucleic acid targets. This peptide unit linked to two triaminotriazine recognition units selectively binds to d(CTG) to inhibit the transcription process, and also targets r(CUG) selectively to improve representative DM1 pathological molecular features, including foci formation and pre-mRNA splicing defects in DM1 model cells. As such, it represents a new structure type that might serve as a lead compound for future structure-activity optimization.
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http://dx.doi.org/10.1002/cmdc.202100243DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8429064PMC
September 2021

CAG RNAs induce DNA damage and apoptosis by silencing expression in polyglutamine degeneration.

Proc Natl Acad Sci U S A 2021 May;118(19)

Laboratory of Drosophila Research, The Chinese University of Hong Kong, Hong Kong, China;

DNA damage plays a central role in the cellular pathogenesis of polyglutamine (polyQ) diseases, including Huntington's disease (HD). In this study, we showed that the expression of untranslatable expanded CAG RNA per se induced the cellular DNA damage response pathway. By means of RNA sequencing (RNA-seq), we found that expression of the () gene was down-regulated in mutant CAG RNA-expressing cells. The loss of NUDT16 function results in a misincorporation of damaging nucleotides into DNAs and leads to DNA damage. We showed that small CAG (sCAG) RNAs, species generated from expanded CAG transcripts, hybridize with CUG-containing mRNA and form a CAG-CUG RNA heteroduplex, resulting in gene silencing of and leading to the DNA damage and cellular apoptosis. These results were further validated using expanded CAG RNA-expressing mouse primary neurons and in vivo R6/2 HD transgenic mice. Moreover, we identified a bisamidinium compound, DB213, that interacts specifically with the major groove of the CAG RNA homoduplex and disfavors the CAG-CUG heteroduplex formation. This action subsequently mitigated RNA-induced silencing complex (RISC)-dependent silencing in both in vitro cell and in vivo mouse disease models. After DB213 treatment, DNA damage, apoptosis, and locomotor defects were rescued in HD mice. This work establishes NUDT16 deficiency by CAG repeat RNAs as a pathogenic mechanism of polyQ diseases and as a potential therapeutic direction for HD and other polyQ diseases.
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http://dx.doi.org/10.1073/pnas.2022940118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8126783PMC
May 2021

A polymeric approach toward resistance-resistant antimicrobial agent with dual-selective mechanisms of action.

Sci Adv 2021 Jan 27;7(5). Epub 2021 Jan 27.

Institute of Chemical Biology and Nanomedicine, Hunan University, Changsha, Hunan 410082, China.

Antibiotic resistance is now a major threat to human health, and one approach to combating this threat is to develop resistance-resistant antibiotics. Synthetic antimicrobial polymers are generally resistance resistant, having good activity with low resistance rates but usually with low therapeutic indices. Here, we report our solution to this problem by introducing dual-selective mechanisms of action to a short amidine-rich polymer, which can simultaneously disrupt bacterial membranes and bind to bacterial DNA. The oligoamidine shows unobservable resistance generation but high therapeutic indices against many bacterial types, such as ESKAPE strains and clinical isolates resistant to multiple drugs, including colistin. The oligomer exhibited excellent effectiveness in various model systems, killing extracellular or intracellular bacteria in the presence of mammalian cells, removing all bacteria from , and rescuing mice with severe infections. This "dual mechanisms of action" approach may be a general strategy for future development of antimicrobial polymers.
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http://dx.doi.org/10.1126/sciadv.abc9917DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7840121PMC
January 2021

Expanded DNA and RNA Trinucleotide Repeats in Myotonic Dystrophy Type 1 Select Their Own Multitarget, Sequence-Selective Inhibitors.

Biochemistry 2020 09 10;59(37):3463-3472. Epub 2020 Sep 10.

Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.

There are few methods available for the rapid discovery of multitarget drugs. Herein, we describe the template-assisted, target-guided discovery of small molecules that recognize d(CTG) in the expanded d(CTG·CAG) sequence and its r(CUG) transcript that cause myotonic dystrophy type 1. A positive cross-selection was performed using a small library of 30 monomeric alkyne- and azide-containing ligands capable of producing >5000 possible di- and trimeric click products. The monomers were incubated with d(CTG) or r(CUG) under physiological conditions, and both sequences showed selectivity in the proximity-accelerated azide-alkyne [3+2] cycloaddition click reaction. The limited number of click products formed in both selections and the even smaller number of common products suggests that this method is a useful tool for the discovery of single-target and multitarget lead therapeutic agents.
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http://dx.doi.org/10.1021/acs.biochem.0c00472DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7793557PMC
September 2020

Nonionic Surfactant Properties of Amphiphilic Hyperbranched Polyglycerols.

Langmuir 2020 09 18;36(34):10103-10109. Epub 2020 Aug 18.

Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.

The surfactant properties of amphiphilic hyperbranched polyglycerols (HPGs) were investigated. The HPGs were prepared by ring-opening multibranching polymerization of glycidol using hydrophobic initiators of varying size and structure. The cloud points for all HPG surfactants were found to be >80 °C in deionized water with >1 wt % NaCl. The HPG surfactants with hydrophilic-lipophilic balance values between 16 and 18 were found to form stable octanol/water (o/w) emulsions within a 24 h period. Several surface properties, including critical micelle concentration (CMC), efficiency of surface tension reduction (p), effectiveness of surface tension reduction (γ), surface excess concentration at the CMC (Γ), minimum area/molecule at the interface (), and the CMC/ ratio of the HPG surfactants were measured in deionized water at 22.6 °C. In general, increasing HPG size was marked by an increase in minimum surface area per molecule () at the aqueous liquid/air interface. This increase in size also led to lower CMC and greater p values of HPG surfactants prepared with Tergitol 15-S-7 initiator (), a commercially available ethylene glycol oligomer with a branched hydrophobic tail.
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http://dx.doi.org/10.1021/acs.langmuir.0c01349DOI Listing
September 2020

A Bioorthogonal Small Molecule Selective Polymeric "Clickase".

J Am Chem Soc 2020 08 28;142(32):13966-13973. Epub 2020 Jul 28.

Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States.

Synthetic polymer scaffolds may serve as gatekeepers preventing the adhesion of biomacromolecules. Herein, we use gating to develop a copper-containing single-chain nanoparticle (SCNP) catalyst as an artificial "clickase" that operates selectively on small molecules that are able to penetrate the polymeric shell. Whereas the analogous clickase with surface ammonium groups performs highly efficient copper(I)-catalyzed alkyne-azide cycloaddition (CuAAC) reactions on both alkynylated proteins and small molecule substrates, the new SCNP clickase with polyethylene glycol (PEG) groups is only active on small molecules. Further, the new SCNP resists uptake by cells allowing extracellular click chemistry to be performed. We describe two proof of principle applications that illustrate the utility of the bioorthogonal activity. First, the SCNP catalyst is able to screen for ligands that bind proteins, including proteolysis targeting chimera (PROTAC)-like molecules. Second, the nonmembrane permeable SCNP can efficiently catalyze the click reaction extracellularly, thereby enabling in situ anticancer drug synthesis and screening without the catalyst perturbing intracellular functions.
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http://dx.doi.org/10.1021/jacs.0c06553DOI Listing
August 2020

Structural Basis for Targeting T:T Mismatch with Triaminotriazine-Acridine Conjugate Induces a U-Shaped Head-to-Head Four-Way Junction in CTG Repeat DNA.

J Am Chem Soc 2020 06 16;142(25):11165-11172. Epub 2020 Jun 16.

Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.

The potent DNA-binding compound triaminotriazine-acridine conjugate (Z1) functions by targeting T:T mismatches in CTG trinucleotide repeats that are responsible for causing neurological diseases such as myotonic dystrophy type 1, but its binding mechanism remains unclear. We solved a crystal structure of Z1 in a complex with DNA containing three consecutive CTG repeats with three T:T mismatches. Crystallographic studies revealed that direct intercalation of two Z1 molecules at both ends of the CTG repeat induces thymine base flipping and DNA backbone deformation to form a four-way junction. The core of the complex unexpectedly adopts a U-shaped head-to-head topology to form a crossover of each chain at the junction site. The crossover junction is held together by two stacked G:C pairs at the central core that rotate with respect to each other in an X-shape to form two nonplanar minor-groove-aligned G·C·G·C tetrads. Two stacked G:C pairs on both sides of the center core are involved in the formation of pseudo-continuous duplex DNA. Four metal-mediated base pairs are observed between the N7 atoms of G and Co, an interaction that strongly preserves the central junction site. Beyond revealing a new type of ligand-induced, four-way junction, these observations enhance our understanding of the specific supramolecular chemistry of Z1 that is essential for the formation of a noncanonical DNA superstructure. The structural features described here serve as a foundation for the design of new sequence-specific ligands targeting mismatches in the repeat-associated structures.
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http://dx.doi.org/10.1021/jacs.0c03591DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7837310PMC
June 2020

Intramolecularly Cross-Linked Polymers: From Structure to Function with Applications as Artificial Antibodies and Artificial Enzymes.

Acc Chem Res 2020 06 22;53(6):1244-1256. Epub 2020 May 22.

Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.

Cross-linking of polymers significantly alters their physical properties, greatly expanding their everyday utility. Indeed, the polymeric networks resulting from linkages between polymer chains are found in everyday materials from soft contact lenses and automobile tires to enamel coatings and high-performance adhesives. In contrast, intramolecularly cross-linked polymers have received far less attention until recent years, in large part because they are synthetically more challenging to prepare. In this Account, we trace our own efforts to develop the chemistry of intramolecularly cross-linked macromolecules, starting with dendrimers. Dendrimers provided an excellent starting point for investigating intramolecular cross-linking because they are single molecular entities. We showed that the end groups of dendrimers can be extensively cross-linked using the ring-closing metathesis reaction and that the discrete structure of the dendrimer provides unique opportunities for characterizing the number and location of the cross-links as well as some physical properties of the macromolecule such as its size and rigidity. Increasing the number of ring-closing metathesis reactions correlated with a reduction in size and an increase in rigidity. The general strategy applied to dendrimers was extended to star polymers and hyperbranched polyglycerols. Each of these macromolecules has a core or an initiating group from which the branches emanate. Linking the end groups or branches of these polymers presents a unique opportunity to chemically remove the core of the cross-linked macromolecule in a process that is reminiscent of that used to produce covalent molecular imprinted polymers. Recognizing this analogy, we sought a compelling application for cross-linked dendrimers, the first example of unimolecular imprinting, where a single polymer contains a single molecular imprint. The quality of the imprinting was mixed but pointed to an alternative general strategy for molecular imprinting in polymers. The effort also focused attention on synthetic antibodies and the general biomimicry provided by this class of macromolecules. Indeed, cross-linking of polymers either covalently or non-covalently bears a loose resemblance to folding of proteins into defined three-dimensional shapes. The synthesis and study of cross-linked linear polymers, often called single-chain nanoparticles (SCNPs), has emerged as a very active area of research in the past few years. Our experience with the cross-linking of branched polymers combined with an interest in performing organic synthesis within living cells led us to develop copper-containing SCNPs as artificial clickases. These polymeric clickases exhibit all of the hallmarks of enzymatic catalysis. One clickase containing a polyacrylamide backbone performs low-concentration copper-assisted alkyne-azide click reactions at unprecedented rates. Another performs click reactions within living cells. Other organic transformations can be performed intracellularly, and some of the most advanced SCNPs engage in concurrent and tandem catalysis with a naturally occurring biocatalyst. By tracing our own efforts, this Account provides a few entry points into the broader literature and also points to both the remaining challenges and overall promising future envisioned for this unique class of functional macromolecules.
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http://dx.doi.org/10.1021/acs.accounts.0c00178DOI Listing
June 2020

Base-triggered self-amplifying degradable polyurethanes with the ability to translate local stimulation to continuous long-range degradation.

Chem Sci 2020 Mar 3;11(12):3326-3331. Epub 2020 Mar 3.

Department of Chemistry, University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA

A new type of base-triggered self-amplifying degradable polyurethane is reported that degrades under mild conditions, with the release of increasing amounts of amine product leading to self-amplified degradation. The polymer incorporates a base-sensitive Fmoc-derivative into every repeating unit to enable highly sensitive amine amplified degradation. A sigmoidal degradation curve for the linear polymer was observed consistent with a self-amplifying degradation mechanism. An analogous cross-linked polyurethane gel was prepared and also found to undergo amplified breakdown. In this case, a trace amount of localized base initiates the degradation, which in turn propagates through the material in an amplified manner. The results demonstrate the potential utility of these new generation polyurethanes in enhanced disposability and as stimuli responsive materials.
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http://dx.doi.org/10.1039/c9sc06582bDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8152679PMC
March 2020

Single-Chain Nanoparticle Delivers a Partner Enzyme for Concurrent and Tandem Catalysis in Cells.

J Am Chem Soc 2020 03 28;142(10):4565-4569. Epub 2020 Feb 28.

Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States.

Combining synthetic chemistry and biocatalysis is a promising but underexplored approach to intracellular catalysis. We report a strategy to codeliver a single-chain nanoparticle (SCNP) catalyst and an exogenous enzyme into cells for performing bioorthogonal reactions. The nanoparticle and enzyme reside in endosomes, creating engineered artificial organelles that manufacture organic compounds intracellularly. This system operates in both concurrent and tandem reaction modes to generate fluorophores or bioactive agents. The combination of SCNP and enzymatic catalysts provides a versatile tool for intracellular organic synthesis with applications in chemical biology.
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http://dx.doi.org/10.1021/jacs.9b13997DOI Listing
March 2020

Independent control over size, valence, and elemental composition in the synthesis of DNA-nanoparticle conjugates.

Chem Sci 2020 Jan 2;11(6):1564-1572. Epub 2020 Jan 2.

Department of Chemistry, University of Illinois at Urbana-Champaign Urbana IL 61801 USA

DNA-nanoparticle conjugates have found widespread use in sensing, imaging, and as components of devices. However, their synthesis remains relatively complicated and empirically based, often requiring specialized protocols for conjugates of different size, valence, and elemental composition. Here we report a novel, bottom-up approach for the synthesis of DNA-nanoparticle conjugates, based on ring-opening metathesis polymerization (ROMP), intramolecular crosslinking, and template synthesis. Using size, valence, and elemental composition as three independent synthetic parameters, various conjugates can be obtained using a facile and universal procedure. Examples are given to show the usefulness of these conjugates as sensing probes, building blocks for self-assembly, and as model particles for structure-property relationship studies.
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http://dx.doi.org/10.1039/c9sc05656dDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8148076PMC
January 2020

Structure of an RNA helix with pyrimidine mismatches and cross-strand stacking.

Acta Crystallogr F Struct Biol Commun 2019 Oct 24;75(Pt 10):652-656. Epub 2019 Sep 24.

Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.

The structure of a 22-base-pair RNA helix with mismatched pyrimidine base pairs is reported. The helix contains two symmetry-related CUG sequences: a triplet-repeat motif implicated in myotonic dystrophy type 1. The CUG repeat contains a U-U mismatch sandwiched between Watson-Crick pairs. Additionally, the center of the helix contains a dimerized UUCG motif with tandem pyrimidine (U-C/C-U) mismatches flanked by U-G wobble pairs. This region of the structure is significantly different from previously observed structures that share the same sequence and neighboring base pairs. The tandem pyrimidine mismatches are unusual and display sheared, cross-strand stacking geometries that locally constrict the helical width, a type of stacking previously associated with purines in internal loops. Thus, pyrimidine-rich regions of RNA have a high degree of structural diversity.
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http://dx.doi.org/10.1107/S2053230X19012172DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6777134PMC
October 2019

Polymeric "Clickase" Accelerates the Copper Click Reaction of Small Molecules, Proteins, and Cells.

J Am Chem Soc 2019 06 4;141(24):9693-9700. Epub 2019 Jun 4.

Institute for Molecular Engineering , The University of Chicago , Chicago , Illinois 60637 , United States.

Recent work has shown that polymeric catalysts can mimic some of the remarkable features of metalloenzymes by binding substrates in proximity to a bound metal center. We report here an unexpected role for the polymer: multivalent, reversible, and adaptive binding to protein surfaces allowing for accelerated catalytic modification of proteins. The catalysts studied are a group of copper-containing single-chain polymeric nanoparticles (Cu-SCNP) that exhibit enzyme-like catalysis of the copper-mediated azide-alkyne cycloaddition reaction. The Cu-SCNP use a previously observed "uptake mode", binding small-molecule alkynes and azides inside a water-soluble amphiphilic polymer and proximal to copper catalytic sites, but with unprecedented rates. Remarkably, a combined experimental and computational study shows that the same Cu-SCNP perform a more efficient click reaction on modified protein surfaces and cell surface glycans than do small-molecule catalysts. The catalysis occurs through an "attach mode" where the SCNPs reversibly bind protein surfaces through multiple hydrophobic and electrostatic contacts. The results more broadly point to a wider capability for polymeric catalysts as artificial metalloenzymes, especially as it relates to bioapplications.
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http://dx.doi.org/10.1021/jacs.9b04181DOI Listing
June 2019

Development of novel macrocyclic small molecules that target CTG trinucleotide repeats.

Bioorg Med Chem 2019 07 14;27(13):2978-2984. Epub 2019 May 14.

Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, United States. Electronic address:

We describe the molecular design, synthesis, and investigation of a series of acridine-triaminotriazine macrocycles that selectively bind to CTG trinucleotide repeats in DNA with minimal nonspecific binding. The limited conformational flexibility enforces the stacking of the triaminotriazine and acridine units. Isothermal titration calorimetry studies and Job plot analyses revealed that the ligands bound to d(CTG) mismatched sites. The acridine and triaminotriazine units were shown to intramolecularly π-stack in aqueous solutions. Compared to a noncyclic analog, the macrocycles showed an almost 10-fold lower cytotoxicity in HeLa cells and up to 4-fold higher transcription inhibition of d(CTG·CAG).
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http://dx.doi.org/10.1016/j.bmc.2019.05.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6592636PMC
July 2019

Intrinsically cell-penetrating multivalent and multitargeting ligands for myotonic dystrophy type 1.

Proc Natl Acad Sci U S A 2019 04 11;116(18):8709-8714. Epub 2019 Apr 11.

Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801;

Developing highly active, multivalent ligands as therapeutic agents is challenging because of delivery issues, limited cell permeability, and toxicity. Here, we report intrinsically cell-penetrating multivalent ligands that target the trinucleotide repeat DNA and RNA in myotonic dystrophy type 1 (DM1), interrupting the disease progression in two ways. The oligomeric ligands are designed based on the repetitive structure of the target with recognition moieties alternating with bisamidinium groove binders to provide an amphiphilic and polycationic structure, mimicking cell-penetrating peptides. Multiple biological studies suggested the success of our multivalency strategy. The designed oligomers maintained cell permeability and exhibited no apparent toxicity both in cells and in mice at working concentrations. Furthermore, the oligomers showed important activities in DM1 cells and in a DM1 liver mouse model, reducing or eliminating prominent DM1 features. Phenotypic recovery of the climbing defect in adult DM1 was also observed. This design strategy should be applicable to other repeat expansion diseases and more generally to DNA/RNA-targeted therapeutics.
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http://dx.doi.org/10.1073/pnas.1820827116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6500145PMC
April 2019

Acid-Triggered, Acid-Generating, and Self-Amplifying Degradable Polymers.

J Am Chem Soc 2019 02 6;141(7):2838-2842. Epub 2019 Feb 6.

We describe the 3-iodopropyl acetal moiety as a simple cleavable unit that undergoes acid catalyzed hydrolysis to liberate HI (p K ∼ -10) and acrolein stoichiometrically. Integrating this unit into linear and network polymers gives a class of macromolecules that undergo a new mechanism of degradation with an acid amplified, sigmoidal rate. This trigger-responsive self-amplified degradable polymer undergoes accelerated rate of degradation and agent release.
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http://dx.doi.org/10.1021/jacs.8b07705DOI Listing
February 2019

AQAMAN, a bisamidine-based inhibitor of toxic protein inclusions in neurons, ameliorates cytotoxicity in polyglutamine disease models.

J Biol Chem 2019 02 28;294(8):2757-2770. Epub 2018 Dec 28.

From the Laboratory of Drosophila Research,

Polyglutamine (polyQ) diseases are a group of dominantly inherited neurodegenerative disorders caused by the expansion of an unstable repeat in the coding region of the affected genes. Hallmarks of polyQ diseases include the accumulation of misfolded protein aggregates, leading to neuronal degeneration and cell death. PolyQ diseases are currently incurable, highlighting the urgent need for approaches that inhibit the formation of disaggregate cytotoxic polyQ protein inclusions. Here, we screened for bisamidine-based inhibitors that can inhibit neuronal polyQ protein inclusions. We demonstrated that one inhibitor, AQAMAN, prevents polyQ protein aggregation and promotes de-aggregation of self-assembled polyQ proteins in several models of polyQ diseases. Using immunocytochemistry, we found that AQAMAN significantly reduces polyQ protein aggregation and specifically suppresses polyQ protein-induced cell death. Using a recombinant and purified polyQ protein (thioredoxin-Huntingtin-Q46), we further demonstrated that AQAMAN interferes with polyQ self-assembly, preventing polyQ aggregation, and dissociates preformed polyQ aggregates in a cell-free system. Remarkably, AQAMAN feeding of expressing expanded polyQ disease protein suppresses polyQ-induced neurodegeneration In addition, using inhibitors and activators of the autophagy pathway, we demonstrated that AQAMAN's cytoprotective effect against polyQ toxicity is autophagy-dependent. In summary, we have identified AQAMAN as a potential therapeutic for combating polyQ protein toxicity in polyQ diseases. Our findings further highlight the importance of the autophagy pathway in clearing harmful polyQ proteins.
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http://dx.doi.org/10.1074/jbc.RA118.006307DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6393596PMC
February 2019

Enzyme-like Click Catalysis by a Copper-Containing Single-Chain Nanoparticle.

J Am Chem Soc 2018 10 20;140(42):13695-13702. Epub 2018 Sep 20.

Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.

A major challenge in performing reactions in biological systems is the requirement for low substrate concentrations, often in the micromolar range. We report that copper cross-linked single-chain nanoparticles (SCNPs) are able to significantly increase the efficiency of copper(I)-catalyzed alkyne-azide cycloaddition (CuAAC) reactions at low substrate concentration in aqueous buffer by promoting substrate binding. Using a fluorogenic click reaction and dye uptake experiments, a structure-activity study is performed with SCNPs of different size and copper content and substrates of varying charge and hydrophobicity. The high catalytic efficiency and selectivity are attributed to a mechanism that involves an enzyme-like substrate binding process. Saturation-transfer difference (STD) NMR spectroscopy, 2D-NOESY NMR, kinetic analyses with varying substrate concentrations, and computational simulations are consistent with a Michaelis-Menten, two-substrate, random-sequential enzyme-like kinetic profile. This general approach may prove useful for developing more-sustainable catalysts and agents for biomedicine and chemical biology.
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http://dx.doi.org/10.1021/jacs.8b06875DOI Listing
October 2018

Designed transition metal catalysts for intracellular organic synthesis.

Chem Soc Rev 2018 Mar;47(5):1811-1821

Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.

The development of synthetic, metal-based catalysts to perform intracellular bioorthogonal reactions represents a relatively new and important area of research that combines transition metal catalysis and chemical biology. The ability to perform reactions in cellulo, especially those transformations without a natural counterpart, offers a versatile tool for medicinal chemists and chemical biologists. With proper modification of the metal catalysts, it is even possible to direct a reaction to certain intracellular sites. This review highlights advances in this new area, from early work on intracellular functional group conversions to recent advances in intracellular synthesis of drugs, including cytotoxic agents. Both the fundamental and applied aspects of this approach to intracellular synthesis are reviewed.
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http://dx.doi.org/10.1039/c7cs00447hDOI Listing
March 2018

Engineering the Surface of Therapeutic "Living" Cells.

Chem Rev 2018 02 16;118(4):1664-1690. Epub 2018 Jan 16.

Department of Prosthodontics and Dental Research Institute, School of Dentistry, Seoul National University , Seoul 110-749, Korea.

Biological cells are complex living machines that have garnered significant attention for their potential to serve as a new generation of therapeutic and delivery agents. Because of their secretion, differentiation, and homing activities, therapeutic cells have tremendous potential to treat or even cure various diseases and injuries that have defied conventional therapeutic strategies. Therapeutic cells can be systemically or locally transplanted. In addition, with their ability to express receptors that bind specific tissue markers, cells are being studied as nano- or microsized drug carriers capable of targeted transport. Depending on the therapeutic targets, these cells may be clustered to promote intercellular adhesion. Despite some impressive results with preclinical studies, there remain several obstacles to their broader development, such as a limited ability to control their transport, engraftment, secretion and to track them in vivo. Additionally, creating a particular spatial organization of therapeutic cells remains difficult. Efforts have recently emerged to resolve these challenges by engineering cell surfaces with a myriad of bioactive molecules, nanoparticles, and microparticles that, in turn, improve the therapeutic efficacy of cells. This review article assesses the various technologies developed to engineer the cell surfaces. The review ends with future considerations that should be taken into account to further advance the quality of cell surface engineering.
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http://dx.doi.org/10.1021/acs.chemrev.7b00157DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8243527PMC
February 2018

Bottom-Up Strategy To Prepare Nanoparticles with a Single DNA Strand.

J Am Chem Soc 2017 03 6;139(10):3623-3626. Epub 2017 Mar 6.

Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.

We describe the preparation of cross-linked, polymeric organic nanoparticles (ONPs) with a single, covalently linked DNA strand. The structure and functionalities of the ONPs are controlled by the synthesis of their parent linear block copolymers that provide monovalency, fluorescence and narrow size distribution. The ONP can also guide the deposition of chloroaurate ions allowing gold nanoparticles (AuNPs) to be prepared using the ONPs as templates. The DNA strand on AuNPs is shown to preserve its functions.
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http://dx.doi.org/10.1021/jacs.7b00065DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5831407PMC
March 2017

Patterning Three-Dimensional Hydrogel Microenvironments Using Hyperbranched Polyglycerols for Independent Control of Mesh Size and Stiffness.

Biomacromolecules 2017 04 9;18(4):1393-1400. Epub 2017 Mar 9.

Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign , 1206 West Gregory Drive, Urbana, Illinois 61801, United States.

The extracellular matrix is an environment rich with structural, mechanical, and molecular signals that can impact cell biology. Traditional approaches in hydrogel biomaterial design often rely on modifying the concentration of cross-linking groups to adjust mechanical properties. However, this strategy provides limited capacity to control additional important parameters in 3D cell culture such as microstructure and molecular diffusivity. Here we describe the use of multifunctional hyperbranched polyglycerols (HPGs) to manipulate the mechanical properties of polyethylene glycol (PEG) hydrogels while not altering biomolecule diffusion. This strategy also provides the ability to separately regulate spatial and temporal distribution of biomolecules tethered within the hydrogel. The functionalized HPGs used here can also react through a copper-free click chemistry, allowing for the encapsulation of cells and covalently tethered biomolecules within the hydrogel. Because of the hyperbranched architecture and unique properties of HPGs, their addition into PEG hydrogels affords opportunities to locally alter hydrogel cross-linking density with minimal effects on global network architecture. Additionally, photocoupling chemistry allows micropatterning of bioactive cues within the three-dimensional gel structure. This approach therefore enables us to tailor mechanical and diffusive properties independently while further allowing for local modulation of biomolecular cues to create increasingly complex cell culture microenvironments.
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http://dx.doi.org/10.1021/acs.biomac.7b00118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5444810PMC
April 2017

Proton transfer dynamics dictate quinone speciation at lipid-modified electrodes.

Phys Chem Chem Phys 2017 Mar;19(10):7086-7093

Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA. and International Institute for Carbon Neutral Energy Research (WPI-I2CNER), Kyushu University, Fukuoka 819-0395, Japan.

Proton-coupled electron transfer (PCET) reactions are ubiquitous in biochemistry and alternative energy schemes. Natural enzymes utilize quinones in proton transfer chains and energy conversion processes. Here, we utilize a bio-inspired hybrid bilayer membrane system to control the reaction mechanism of a quinone molecule covalently bound to an electrode surface. In particular, by impeding proton access to the quinone moiety, we change the reaction pathway from a PCET process to a pure electron transfer step. We further alter the reaction pathway to a stepwise PCET process by controlling the proton flux through the use of an alkyl proton carrier incorporated in the lipid membrane. By modulating proton availability, we control the quinone reaction pathway without changing the molecular structure of the redox species. This work provides unique insight into PCET reactions and a novel electrochemical platform for interrogating them.
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http://dx.doi.org/10.1039/c6cp07586jDOI Listing
March 2017

Worm-Like Superparamagnetic Nanoparticle Clusters for Enhanced Adhesion and Magnetic Resonance Relaxivity.

ACS Appl Mater Interfaces 2017 Jan 6;9(2):1219-1225. Epub 2017 Jan 6.

Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.

Nanosized bioprobes that can highlight diseased tissue can be powerful diagnostic tools. However, a major unmet need is a tool with adequate adhesive properties and contrast-to-dose ratio. To this end, this study demonstrates that targeted superparamagnetic nanoprobes engineered to present a worm-like shape and hydrophilic packaging enhance both adhesion efficiency to target substrates and magnetic resonance (MR) sensitivity. These nanoprobes were prepared by the controlled self-assembly of superparamagnetic iron oxide nanoparticles (SPIONs) into worm-like superstructures using glycogen-like amphiphilic hyperbranched polyglycerols functionalized with peptides capable of binding to defective vasculature. The resulting worm-like SPION clusters presented binding affinity to the target substrate 10-fold higher than that of spherical ones and T molar MR relaxivity 3.5-fold higher than that of conventional, single SPIONs. The design principles discovered for these nanoprobes should be applicable to a range of other diseases where improved diagnostics are needed.
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http://dx.doi.org/10.1021/acsami.6b10891DOI Listing
January 2017

A Highly Efficient Single-Chain Metal-Organic Nanoparticle Catalyst for Alkyne-Azide "Click" Reactions in Water and in Cells.

J Am Chem Soc 2016 09 26;138(35):11077-80. Epub 2016 Aug 26.

Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.

We show that copper-containing metal-organic nanoparticles (MONPs) are readily synthesized via Cu(II)-mediated intramolecular cross-linking of aspartate-containing polyolefins in water. In situ reduction with sodium ascorbate yields Cu(I)-containing MONPs that serve as highly efficient supramolecular catalysts for alkyne-azide "click chemistry" reactions, yielding the desired 1,4-adducts at low parts per million catalyst levels. The nanoparticles have low toxicity and low metal loadings, making them convenient, green catalysts for alkyne-azide "click" reactions in water. The Cu-MONPs enter cells and perform efficient, biocompatible click chemistry, thus acting as intracellular nanoscale molecular synthesizers.
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http://dx.doi.org/10.1021/jacs.6b04477DOI Listing
September 2016

Integrating Display and Delivery Functionality with a Cell Penetrating Peptide Mimic as a Scaffold for Intracellular Multivalent Multitargeting.

J Am Chem Soc 2016 08 20;138(30):9498-507. Epub 2016 Jul 20.

Laboratory of Drosophila Research and School of Life Sciences, The Chinese University of Hong Kong , Shatin, New Territories, Hong Kong SAR, China.

The construction of a multivalent ligand is an effective way to increase affinity and selectivity toward biomolecular targets with multiple-ligand binding sites. Adopting this strategy, we used a known cell-penetrating peptide (CPP) mimic as a scaffold to develop a series of multivalent ligand constructs that bind to the expanded dCTG (CTG(exp)) and rCUG nucleotide repeats (CUG(exp)) known to cause myotonic dystrophy type I (DM1), an incurable neuromuscular disease. By assembling this polyvalent construct, the hydrophobic ligands are solubilized and delivered into cell nuclei, and their enhanced binding affinity leads to the inhibition of ribonuclear foci formation and a reversal of splicing defects, all at low concentrations. Some of the multivalent ligands are shown to inhibit selectively the in vitro transcription of (CTG·CAG)74, to reduce the concentration of the toxic CUG RNA in DM1 model cells, and to show phenotypic improvement in vivo in a Drosophila model of DM1. This strategy may be useful in drug design for other trinucleotide repeat disorders and more broadly for intracellular multivalent targeting.
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http://dx.doi.org/10.1021/jacs.6b03697DOI Listing
August 2016

Supramolecular chemistry at the interface of biology, materials and medicine.

Beilstein J Org Chem 2016 31;12:1101-2. Epub 2016 May 31.

Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.

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http://dx.doi.org/10.3762/bjoc.12.105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4901886PMC
June 2016

The Flip-Flop Diffusion Mechanism across Lipids in a Hybrid Bilayer Membrane.

Biophys J 2016 06;110(11):2451-2462

Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois; International Institute for Carbon Neutral Energy Research (WPI-I2CNER), Kyushu University, Fukuoka, Japan. Electronic address:

In this study, we examine the mechanism of flip-flop diffusion of proton carriers across the lipid layer of a hybrid bilayer membrane (HBM). The HBM consists of a lipid monolayer appended on top of a self-assembled monolayer containing a Cu-based O2 reduction catalyst on a Au electrode. The flip-flop diffusion rates of the proton carriers dictate the kinetics of O2 reduction by the electrocatalyst. By varying both the tail lengths of the proton carriers and the lipids, we find the combinations of lengths that maximize the flip-flop diffusion rate. These experimental results combined with biophysical modeling studies allow us to propose a detailed mechanism for transmembrane flip-flop diffusion in HBM systems, which involves the bending of the alkyl tail of the proton carrier as the rate-determining step. Additional studies with an unbendable proton carrier further validate these mechanistic findings.
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http://dx.doi.org/10.1016/j.bpj.2016.04.041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4922581PMC
June 2016

A Potent Inhibitor of Protein Sequestration by Expanded Triplet (CUG) Repeats that Shows Phenotypic Improvements in a Drosophila Model of Myotonic Dystrophy.

ChemMedChem 2016 07 1;11(13):1428-35. Epub 2016 Jun 1.

Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL, 61801, USA.

Myotonic dystrophy is the most common form of adult-onset muscular dystrophy, originating in a CTG repeat expansion in the DMPK gene. The expanded CUG transcript sequesters MBNL1, a key regulator of alternative splicing, leading to the misregulation of numerous pre-mRNAs. We report an RNA-targeted agent as a possible lead compound for the treatment of myotonic dystrophy type 1 (DM1) that reveals both the promise and challenges for this type of small-molecule approach. The agent is a potent inhibitor of the MBNL1-rCUG complex with an inhibition constant (Ki ) of 25±8 nm, and is also relatively nontoxic to HeLa cells, able to dissolve nuclear foci, and correct the insulin receptor splicing defect in DM1 model cells. Moreover, treatment with this compound improves two separate disease phenotypes in a Drosophila model of DM1: adult external eye degeneration and larval crawling defect. However, the compound has a relatively low maximum tolerated dose in mice, and its cell uptake may be limited, providing insight into directions for future development.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5074844PMC
http://dx.doi.org/10.1002/cmdc.201600081DOI Listing
July 2016
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