Use of DNA-specific anthraquinone dyes to directly reveal cytoplasmic and nuclear boundaries in live and fixed cells

Antimalarial Imidazopyridines Incorporating an Intramolecular Hydrogen Bonding Motif: Medicinal Chemistry and Mechanistic Studies

We previously identified a novel class of antimalarial benzimidazoles incorporating an intramolecular hydrogen bonding motif. The frontrunner of the series, analogue A, showed nanomolar activity against the chloroquine-sensitive NF54 and multi-drug-resistant K1 strains of Plasmodium falciparum (PfNF54 IC₅₀ = 0.079 μM; PfK1 IC₅₀ = 0.335 μM). Here, we describe a cell-based medicinal chemistry structure-activity relationship study using compound A as a basis. This effort led to the identification of novel antimalarial imidazopyridines with activities of <1 μM, favorable cytotoxicity profiles, and good physicochemical properties. Analogue 14 ( PfNF54 IC₅₀ = 0.08 μM; PfK1 IC₅₀ = 0.10 μM) was identified as the frontrunner of the series. Preliminary mode of action studies employing molecular docking, live-cell confocal microscopy, and a cellular heme fractionation assay revealed that 14 does not directly inhibit the conversion of heme to hemozoin, although it could be involved in other processes in the parasite's digestive vacuole.

Novel 3-Trifluoromethyl-1,2,4-oxadiazole Analogues of Astemizole with Multi-stage Antiplasmodium Activity and In Vivo Efficacy in a Plasmodium berghei Mouse Malaria Infection Model

Iterative medicinal chemistry optimization of an ester-containing astemizole (AST) analogue 1 with an associated metabolic instability liability led to the identification of a highly potent 3-trifluoromethyl-1,2,4-oxadiazole analogue 23 (PfNF54 IC₅₀ = 0.012 μM; PfK1 IC₅₀ = 0.040 μM) displaying high microsomal metabolic stability (HLM CL_int < 11.6 μL·min^-1·mg^-1) and > 1000-fold higher selectivity over hERG compared to AST. In addition to asexual blood stage activity, the compound also shows activity against liver and gametocyte life cycle stages and demonstrates in vivo efficacy in Plasmodium berghei-infected mice at 4 × 50 mg·kg^-1 oral dose. Preliminary interrogation of the mode of action using live-cell microscopy and cellular heme speciation revealed that 23 could be affecting multiple processes in the parasitic digestive vacuole, with the possibility of a novel target at play in the organelles associated with it.

Intrinsic fluorescence properties of antimalarial pyrido[1,2-a]benzimidazoles facilitate subcellular accumulation and mechanistic studies in the human malaria parasite Plasmodium falciparum

The intrinsic fluorescence properties of two related pyrido[1,2-a]benzimidazole antimalarial compounds suitable for the cellular imaging of the human malaria parasite Plasmodium falciparum without the need to attach extrinsic fluorophores are described. Although these compounds are structurally related, they have been shown by confocal microscopy to not only accumulate selectively within P. falciparum but to also accumulate differently in the organelles investigated. Localization to the digestive vacuole and nearby neutral lipids was observed for compound 2 which was shown to inhibit hemozoin formation using a cellular fractionation assay indicating that this is a contributing mechanism of action. By contrast, compound 1, which differs from compound 2 by the replacement of the imidazole[1,2-a:4,5-b']dipyridine core with the benzimidazole core as well as the presence of Cl substituents, shows very different localisation patterns and shows no evidence of hemozoin inhibition, suggesting a different mechanism of antimalarial action. Docking profiles of both compounds on the hemozoin surface further provided insight into their mechanisms of action.

Synthesis of Anthraquinones by Iridium-Catalyzed [2 + 2 + 2] Cycloaddition of a 1,2-Bis(propiolyl)benzene Derivative with Alkynes

[2 + 2 + 2] cycloaddition of a 1,2-bis(propiolyl)benzene derivative with terminal and internal alkynes takes place in the presence of [Ir(cod)Cl]2 (cod = 1,5-cyclooctadiene) combined with bis(diphenylphosphino)ethane (DPPE) to give anthraquinones in 42% to 93% yields with a simple experimental procedure. A fluorenone derivative can also be synthesized by iridium-catalyzed [2 + 2 + 2] cycloaddition of a benzene-linked ketodiyne with an internal alkyne to give a 94% yield.

Ir-Catalyzed C-H Amidation and Borylation of Anthraquinones

A mild, regioselective, iridium-catalyzed C-H amidation and borylation of anthraquinones to the o-sulfonamide and m-borylated products has been developed. The anthraquinone carbonyl moieties direct the C-H amidation with high selectivity to afford the ortho-substituted products in modest to high yields.

Probing cytochrome P450 bioactivation and fluorescent properties with morpholinyl-tethered anthraquinones

Structural features from the anticancer prodrug nemorubicin (MMDX) and the DNA-binding molecule DRAQ5™ were used to prepare anthraquinone-based compounds, which were assessed for their potential to interrogate cytochrome P450 (CYP) functional activity and localisation. 1,4-disubstituted anthraquinone 8 was shown to be 5-fold more potent in EJ138 bladder cancer cells after CYP1A2 bioactivation. In contrast, 1,5-bis((2-morpholinoethyl)amino) substituted anthraquinone 10 was not CYP-bioactivated but was shown to be fluorescent and subsequently photo-activated by a light pulse (at a bandwidth 532-587 nm), resulting in punctuated foci accumulation in the cytoplasm. It also showed low toxicity in human osteosarcoma cells. These combined properties provide an interesting prospective approach for opto-tagging single or a sub-population of cells and seeking their location without the need for continuous monitoring.

Anti-Vascular Endothelial Growth Factor Targeting by Curcumin and Thalidomide in Acute Myeloid Leukemia Cells

Acute myeloid leukemias (AMLs) are blood disorders that exhibit uncontrolled growth and reduction of apoptosis rates. As with other malignancies, progression may be result of induction and formation of new blood vessels influenced by disease conditions. Cancer cells produce a variety of factors which play important roles in angiogenesis. Vascular endothelial growth factor (VEGF) is critical for many malignancies, including AMLs. Curcumin, as a natural compound, is able to enhance apoptosis via a mechanism affecting regulatory genes. As a new strategy we here evaluated anti-VEGF properties of curcumin, alone and in combination with thalidomide, in leukemic cell lines. Growth inhibitory effects were assessed by MTT assay and apoptosis was detected by annexin/PI staining in U937 and KG-1 cell lines. mRNA expression levels of VEGF isoforms were evaluated by qRT-PCR. Curcumin inhibited proliferation and induced apoptosis in both KG-1 and U937 cells and this effect was stronger in combination with thalidomide. In KG-1 cells, the level of VEGF (A, B, C and D) mRNA was decreased in curcumin-treated as compared to untreated cells. Maximum effects were obtained at the concentration of 40 μM curcumin in U937 cells. Taken together, the results indicate that the VEGF autocrine loop may have an impact on AML development and progression and could be considered as a therapeutic target. Thalidomide as a VEGF inhibitor in combination with curcumin appears to have a synergistic impact on inhibition of cell proliferation and promotion of apoptosis.

Evaluation of Compound Optical Interference in High-Content Screening

Compound optical interference remains an inherent problem in chemical screening and has been well documented for biochemical assays and less so for automated microscopy-based assays. It has also been the assumption that the latter should not suffer from such interference because of the washing steps involved in the process, thus eliminating the residual nonspecific compound effects. Instead, these compounds may have no relevance to the actual target, and as such, compound optical interference contributes to a number of false-positives, resulting in a high attrition rate during subsequent follow-up studies. In this report, we analyze the outcome of a high-content screen using enhanced green fluorescent protein as a reporter in a gain-of-function cell-based assay in search of modulators of the micro RNA (miRNA) biogenesis pathway. Using a previously validated image-based biosensor, we screened a diverse library collection of ~315,000 compounds covering natural and synthetic derivatives in which 1130 positives were identified to enhance green fluorescence expression. Lateral confirmation and dose-response studies revealed that all of these compounds were the result of optical interference and not specific inhibition of miRNA biogenesis. Here, we highlight the chemical classes that are susceptible to compound optical interference and discuss their implications in automated microscopy-based assays.

A Novel Fluorescent Labeling Method Enables Monitoring of Spatio-Temporal Dynamics of Developing Microsporidia

The microsporidium, Anncaliia algerae (Brachiola algerae), is a eukaryotic obligate intracellular parasite first isolated from mosquitoes and is an important opportunistic human pathogen that can cause morbidity and mortality among immune-compromised individuals including patients with AIDS and those undergoing chemotherapy. There is little known about the Microsporidia-host cell interface in living host cells, due to current approaches being limited by the lack of fluorescent reporters for detecting the parasite lifecycle. Here, we have developed and applied novel vital fluorescent parasite labeling methodologies in conjunction with fluorescent protein-tagged reporters to track simultaneously the dynamics of both parasite and host cell specific components, including the secretory and endocytic trafficking pathways, during the entire infection time period. We have found dramatic changes in the dynamics of host secretory trafficking organelles during the course of infection. The Golgi compartment is gradually disassembled and regenerated into mini-Golgi structures in parallel with cellular microtubule depolymerization. Importantly, we find that Microsporidia progeny are associated with these de novo formed mini-Golgi structures. These host structures appear to create a membrane bound niche environment for parasite development. Our studies presented here provide novel imaging tools and methodologies that will facilitate in understanding the biology of microsporidial parasites in the living host.

Modified annexin V/propidium iodide apoptosis assay for accurate assessment of cell death

Studies of cellular apoptosis have been significantly impacted since the introduction of flow cytometry-based methods. Propidium iodide (PI) is widely used in conjunction with Annexin V to determine if cells are viable, apoptotic, or necrotic through differences in plasma membrane integrity and permeability^1,2. The Annexin V/ PI protocol is a commonly used approach for studying apoptotic cells³. PI is used more often than other nuclear stains because it is economical, stable and a good indicator of cell viability, based on its capacity to exclude dye in living cells ^4,5. The ability of PI to enter a cell is dependent upon the permeability of the membrane; PI does not stain live or early apoptotic cells due to the presence of an intact plasma membrane ^1,2,6. In late apoptotic and necrotic cells, the integrity of the plasma and nuclear membranes decreases^7,8, allowing PI to pass through the membranes, intercalate into nucleic acids, and display red fluorescence ^1,2,9. Unfortunately, we find that conventional Annexin V/ PI protocols lead to a significant number of false positive events (up to 40%), which are associated with PI staining of RNA within the cytoplasmic compartment¹⁰. Primary cells and cell lines in a broad range of animal models are affected, with large cells (nuclear: cytoplasmic ratios <0.5) showing the highest occurrence¹⁰. Herein, we demonstrate a modified Annexin V/ PI method that provides a significant improvement for assessment of cell death compared to conventional methods. This protocol takes advantage of changes in cellular permeability during cell fixing to promote entry of RNase A into cells following staining. Both the timing and concentration of RNase A have been optimized for removal of cytoplasmic RNA. The result is a significant improvement over conventional Annexin V/ PI protocols (< 5% events with cytoplasmic PI staining).

Short exposure to the DNA intercalator DRAQ5 dislocates the transcription machinery and induces cell death

The fluorescent probe DRAQ5 which rapidly permeates cells and binds to DNA is potentially useful for functional studies of molecular dynamics and interactions in living nuclei. Within minutes after the incubation of human osteosarcoma U2OS cells with 5μm DRAQ5, the distributions of RNA polymerase II and some of its associated regulatory proteins HEXIM and cyclin T1 in the nucleus are severely impaired, and transcription is inhibited. Furthermore, 30min exposure to DRAQ5 induces death of U2OS cells 24h later. Incubation with Hoechst 33342 under similar conditions does not induce these effects. These results emphasize the importance of carefully examining the functional consequences of labeling DNA with intercalating fluorescent dyes before use.

Study of cytotoxic and therapeutic effects of stable and purified silver nanoparticles on tumor cells

We have synthesized and purified silver nanoparticles (Ag NPs) (11.3+/-2.3 nm) that are stable (non-aggregated) in cell culture medium and inside single living cells. We have developed new imaging methods to characterize sizes and number of single NPs in the medium and in single living cells in real-time and determine their stability (non-aggregation) in the medium and in single living cells at single NP resolution. These new approaches allow us to study toxic and therapeutic effects of single Ag NPs on tumor cells (L929, mouse fibroblast cells) with determined sizes and concentrations (doses) of NPs over time at single NP and single cell resolution. We found that Ag NPs inhibited the growth and division of tumor cells and their nuclei, in a dose and time dependent manner, showing significant inhibitory effects and abnormal cells with giant undivided nuclei or multiple nuclei beyond 12 h incubation. The results show that Ag NPs inhibited the segregation of chromosomes, but not their replication. Intracellular Ag NPs were well distributed in the cell population, and located in the nuclei and cytoplasm with higher numbers in the cytoplasm. This study demonstrates the possibility of using Ag NPs to inhibit the growth and division of tumor cells and using their cytotoxicity for potential therapeutic treatments. This study offers a new method to count the number of single NPs in the medium for characterization of their concentration and stability at single NP resolution over time.

The use of DRAQ5 to monitor intracellular DNA in Escherichia coli by flow cytometry

Flow cytometry provides a rapid and high-content multiparameter analysis of individual microorganisms within a population. In the past years, several fluorescent stains were developed in order to monitor DNA content distribution and cell-cycle phases, mainly in eukaryotic cells. Recently, due to its low detection limits, several of these fluorescent stains were also applied to prokaryotic cells. In this study, the ability of a novel far-red fluorescent stain DRAQ5 in assessing intracellular DNA content distribution in Escherichia coli DH5alpha was evaluated. The results showed that a DRAQ5-labelled live E. coli suspension can be obtained by incubation of 1 x 10(6) cells/mL with 5 microM DRAQ5 in PBS buffer supplemented with EDTA (pH = 7.4) during 30 min at 37 degrees C. Flow cytometric analysis of fixed E. coli cells revealed that ethanol should be used in detriment of glutaraldehyde for DRAQ5 labelling. After the analysis of RNase and DNase digested samples, DRAQ5 was proven to be a specific DNA labelling stain. The present study demonstrates that the use of DRAQ5 as a DNA-labelling stain provides an easy assessment of intracellular DNA content and cell-cycle phases in gram-negative bacteria such as E. coli.

Discovery of a green DNA probe for live-cell imaging

We discovered a DNA-selective probe, and demonstrated its potentials for nucleus imaging and DNA quantification.