Enhancing the Potency of Nalidixic Acid toward a Bacterial DNA Gyrase with Conjugated Peptides

Quinolones and fluoroquinolones are widely used antibacterial agents. Nalidixic acid (NA) is a first-generation quinolone-based antibiotic that has a narrow spectrum and poor pharmacokinetics. Here, we describe a family of peptide–nalidixic acid conjugates featuring different levels of hydrophobicity and molecular charge prepared by solid-phase peptide synthesis that exhibit intriguing improvements in potency. In comparison to NA, which has a low level of potency in <i>S. aureus</i>, the NA peptide conjugates with optimized hydrophobicities and molecular charges exhibited significantly improved antibacterial activity. The most potent NA conjugatefeaturing a peptide containing cyclohexylalanine and arginineexhibited efficient bacterial uptake and, notably, specific inhibition of <i>S. aureus</i> DNA gyrase. A systematic study of peptide–NA conjugates revealed that a fine balance of cationic charge and hydrophobicity in an appendage anchored to the core of the drug is required to overcome the intrinsic resistance of <i>S. aureus</i> DNA gyrase toward this quinolone-based drug

Delivery and Release of Small-Molecule Probes in Mitochondria Using Traceless Linkers

Mitochondria-penetrating peptides (MPPs) are specific targeting vectors for the localization of small molecules to the mitochondrial matrix. Mitochondrial targeting of small molecules has enabled the development of a number of potential therapeutics and chemical probes. However, the need for covalent conjugation of small molecules to MPPs can negatively affect the activity of the appended cargo against its cellular target. Here, we describe cleavable linkers designed for the traceless release of chemical cargo from MPPs following mitochondrial transit. The cleavage kinetics of a number of disulfides were investigated using a fluorescent reporter system in order to optimize linker stability for mitochondrial release. The stability of mono- and disubstituted disulfides was determined to be sufficient during transit through the cytosol while still allowing for release of the cargo within 24 h. This linker system successfully released the compound Luminespib, an HSP90 inhibitor, which was deactivated by direct MPP conjugation. The releasable conjugate regenerated Luminespib activity and induced mitochondrial phenotypes of HSP90 inhibition. This linker may prove useful in expanding the repertoire of small molecules that can be used with mitochondrial targeting vectors

Peptide Targeting of an Antibiotic Prodrug toward Phagosome-Entrapped Mycobacteria

Mycobacterial infections are difficult to treat due to the bacterium’s slow growth, ability to reside in intracellular compartments within macrophages, and resistance mechanisms that limit the effectiveness of conventional antibiotics. Developing antibiotics that overcome these challenges is therefore critical to providing a pipeline of effective antimicrobial agents. Here, we describe the synthesis and testing of a unique peptide–drug conjugate that exhibits high levels of antimicrobial activity against <i>M. smegmatis</i> and <i>M. tuberculosis</i> as well as clearance of intracellular mycobacteria from cultured macrophages. Using an engineered peptide sequence, we deliver a potent DHFR inhibitor and target the intracellular phagosomes where mycobacteria reside and also incorporate a β-lactamase-cleavable cephalosporin linker to enhance the targeting of quiescent intracellular β-lactam-resistant mycobacteria. By using this type of prodrug approach to target intracellular mycobacterial infections, the emergence of antibacterial resistance mechanisms could be minimized

Targeted Delivery of Doxorubicin to Mitochondria

Several families of highly effective anticancer drugs are selectively toxic to cancer cells because they disrupt nucleic acid synthesis in the nucleus. Much less is known, however, about whether interfering with nucleic acid synthesis in the mitochondria would have significant cellular effects. In this study, we explore this with a mitochondrially targeted form of the anticancer drug doxorubicin, which inhibits DNA topoisomerase II, an enzyme that is both in mitochondria and nuclei of human cells. When doxorubicin is attached to a peptide that targets mitochondria, it exhibits significant toxicity. However, when challenged with a cell line that overexpresses a common efflux pump, it does not exhibit the reduced activity of the nuclear-localized parent drug and resists being removed from the cell. These results indicate that targeting drugs to the mitochondria provides a means to limit drug efflux and provide evidence that a mitochondrially targeted DNA topoisomerase poison is active within the organelle

Amplified Micromagnetic Field Gradients Enable High-Resolution Profiling of Rare Cell Subpopulations

Analyzing small collections of cells is challenging because of the need for extremely high levels of sensitivity. We recently reported a new approach, termed magnetic ranking cytometry (MagRC), to profile nanoparticle-labeled cells. Using antibody-functionalized magnetic nanoparticles, we label cells so that each cell’s magnetization is proportional to its surface expression of a selected biomarker. Using a microfluidic device that sorts the cells into 100 different zones based on magnetic labeling levels, we generate profiles that report on the level and distribution of surface expression in small collections of cells. Here, we present a new set of studies investigating in depth parameters such as flow rate and magnetic nanoparticle size that affect device performance using both experiments and modeling. We present a model that further elucidates the mechanism of cell capture and use it to optimize device performance to efficiently capture rare cells. We show that this method has excellent specificity and can be used to characterize rare cells even in the presence of whole blood

Structural Modifications of Mitochondria-Targeted Chlorambucil Alter Cell Death Mechanism but Preserve MDR Evasion

Multidrug resistance (MDR) remains one of the major obstacles in chemotherapy, potentially rendering a multitude of drugs ineffective. Previously, we have demonstrated that mitochondrial targeting of DNA damaging agents is a promising tool for evading a number of common resistance factors that are present in the nucleus or cytosol. In particular, mitochondria-targeted chlorambucil (mt-Cbl) has increased potency and activity against resistant cancer cells compared to the parent compound chlorambucil (Cbl). However, it was found that, due to its high reactivity, mt-Cbl induces a necrotic type of cell death via rapid nonspecific alkylation of mitochondrial proteins. Here, we demonstrate that by tuning the alkylating activity of mt-Cbl via chemical modification, the rate of generation of protein adducts can be reduced, resulting in a shift of the cell death mechanism from necrosis to a more controlled apoptotic pathway. Moreover, we demonstrate that all of the modified mt-Cbl compounds effectively evade MDR resulting from cytosolic GST-μ upregulation by rapidly accumulating in mitochondria, inducing cell death directly from within. In this study, we systematically elucidated the advantages and limitations of targeting alkylating agents with varying reactivity to mitochondria

Biomolecular Steric Hindrance Effects Are Enhanced on Nanostructured Microelectrodes

The availability of rapid approaches for quantitative detection of biomarkers would drastically impact global health by enabling decentralized disease diagnosis anywhere that patient care is administered. A promising new approach, the electrochemical steric hindrance hybridization assay (eSHHA) has been introduced for quantitative detection of large proteins (e.g., antibodies) with a low nanomolar detection limit within 10 min. Here, we report the use of a nanostructured microelectrode (NME) platform for eSHHA that improves the performance of this approach by increasing the efficiency and kinetics of DNA hybridization. We demonstrated that eSHHA on nanostructured microelectrodes leverages three effects: (1) steric hindrance effects at the nanoscale, (2) a size-dependent hybridization rate of DNA complexes, and (3) electrode morphology-dependent blocking effects. As a proof of concept, we showed that the sensitivity of eSHHA toward a model antibody is enhanced using NMEs as scaffolds for this reaction. We improved the detection limit of eSHHA, taking advantage of nanostructured surfaces to allow the use of longer capture strands for detection of proteins. Finally, we concluded that using the eSHHA approach in conjunction with nanostructured microelectrodes is an advantageous alternative to conventional macroelectrodes as the sensitivity and detection limits are enhanced

Proximal Bacterial Lysis and Detection in Nanoliter Wells Using Electrochemistry

Rapid and direct genetic analysis of low numbers of bacteria using chip-based sensors is limited by the slow diffusion of mRNA molecules. Long incubation times are required in dilute solutions in order to collect a sufficient number of molecules at the sensor surface to generate a detectable signal. To overcome this barrier here we present an integrated device that leverages electrochemistry-driven lysis less than 50 μm away from electrochemical nucleic acid sensors to overcome this barrier. Released intracellular mRNA can diffuse the short distance to the sensors within minutes, enabling rapid and sensitive detection. We validate this strategy through direct lysis and detection of E. coli mRNA at concentrations as low as 0.4 CFU/μL in 2 min, a clinically relevant combination of speed and sensitivity for a sample-to-answer molecular analysis approach

Electrochemical DNA-Based Immunoassay That Employs Steric Hindrance To Detect Small Molecules Directly in Whole Blood

The development of a universal sensing mechanism for the rapid and quantitative detection of small molecules directly in whole blood would drastically impact global health by enabling disease diagnostics, monitoring, and treatment at home. We have previously shown that hybridization between a free DNA strand and its complementary surface-bound strand can be sterically hindered when the former is bound to large antibodies. Here, we exploit this effect to design a competitive antibody-based electrochemical assay, called CeSHHA, that enables the quantitative detection of small molecules directly in complex matrices, such as whole blood or soil. We discuss the importance of this inexpensive assay for point-of-care diagnosis and for treatment monitoring applications

Electrochemical Enzyme-Linked Immunosorbent Assay Featuring Proximal Reagent Generation: Detection of Human Immunodeficiency Virus Antibodies in Clinical Samples

We describe a simple electrochemical immunoassay for human immunodeficiency virus (HIV) antibody detection that localizes capture and detection reagents in close proximity to a microelectrode. Antigenic peptides from HIV-1 gp41 or HIV-2 gp36 were covalently attached to a SU-8 substrate that also presented a template for the deposition of three-dimensional microelectrodes. The detection of HIV antibodies was achieved with an electrochemical immunoassay where an alkaline phosphatase conjugated secondary antibody reacts with <i>p</i>-aminophenyl phosphate (<i>p</i>APP) to produce a redox-active product, <i>p</i>-aminophenol. The current derived from the oxidation of the reporter group increased linearly over a wide antibody concentration range (0.001–1 μg mL^–1), with a detection limit of 1 ng mL^–1 (6.7 pM) for both HIV-1 and HIV-2. This level of sensitivity is clinically relevant, and the feasibility of this approach for clinical sample testing was also evaluated with HIV clinical patient samples, with excellent performance observed compared against a commercially available gold standard. This approach was used to develop the first electrochemical enzyme-linked immunosorbent assay (ELISA) to detect HIV in clinical samples, and excellent performance relative to a gold standard test was achieved