Encapsulation of copper phenanthroline within horse spleen apoferritin: characterisation, cytotoxic activity and ability to retain temozolomide

Protein capsules are promising drug delivery vehicles for cancer research therapies. Apoferritin (AFt) is a self-assembling 12 nm diameter hollow nanocage with many desirable features for drug delivery, however, control of drug retention inside the protein cage remains challenging. Here we report the encapsulation of copper(ii)-1,10-phenanthroline (Cu(phen)) within the horse spleen AFt (HSAFt) nanocage, by diffusion of the metal through the pores between the protein subunits. Transmission electron microscopy revealed the formation of organised copper adducts inside HSAFt, without affecting protein integrity. These structures proved stable during storage (>4 months at -20 °C). Exposure to physiologically relevant conditions (37 °C) showed some selectivity in cargo release after 24 h at pH 5.5, relevant to the internalisation of AFt within the endosome (60% release), compared to pH 7.4, relevant to the bloodstream (40% release). Co-encapsulation of temozolomide, a prodrug used to treat glioblastoma multiforme, and Cu(phen) enabled entrapment of an average of 339 TMZ molecules per cage. In vitro results from MTT and clonogenic assays identified cytotoxic activity of the Cu(phen), HSAFt-Cu(phen) and HSAFt-Cu(phen)-TMZ adducts against colorectal cancer cells (HCT-116) and glioblastoma cells (U373V, U373M). However, the presence of the metal also contributed to more potent activity toward healthy MRC5 fibroblasts, a result that requires further investigation to assess the clinical viability of this system.

Correction to "Apoferritin-Encapsulated Jerantinine A for Transferrin Receptor Targeting and Enhanced Selectivity in Breast Cancer Therapy"

[This corrects the article DOI: 10.1021/acsomega.2c00997.].

Optimizing Excipient Properties to Prevent Aggregation in Biopharmaceutical Formulations

Excipients are included within protein biotherapeutic solution formulations to improve colloidal and conformational stability but are generally not designed for the specific purpose of preventing aggregation and improving cryoprotection in solution. In this work, we have explored the relationship between the structure and antiaggregation activity of excipients by utilizing coarse-grained molecular dynamics modeling of protein-excipient interaction. We have studied human serum albumin as a model protein, and we report the interaction of 41 excipients (polysorbates, fatty alcohol ethoxylates, fatty acid ethoxylates, phospholipids, glucosides, amino acids, and others) in terms of the reduction of solvent accessible surface area of aggregation-prone regions, proposed as a mechanism of aggregation prevention. Polyoxyethylene sorbitan had the greatest degree of interaction with aggregation-prone regions, decreasing the solvent accessible surface area of APRs by 20.7 nm2 (40.1%). Physicochemical descriptors generated by Mordred are employed to probe the structure-property relationship using partial least-squares regression. A leave-one-out cross-validated model had a root-mean-square error of prediction of 4.1 nm2 and a mean relative error of prediction of 0.077. Generally, longer molecules with a large number of alcohol-terminated PEG units tended to interact more, with qualitatively different protein interactions, wrapping around the protein. Shorter or less ethoxylated compounds tend to form hemimicellar clusters at the protein surface. We propose that an improved design would feature many short chains of 5 to 10 PEG units in many distinct branches and at least some hydrophobic content in the form of medium-length or greater aliphatic chains (i.e., six or more carbon atoms). The combination of molecular dynamics simulation and quantitative modeling is an important first step in an all-purpose protein-independent model for the computer-aided design of stabilizing excipients.

Near-infrared PbS quantum dots functionalized with affibodies and ZnPP for targeted imaging and therapeutic applications

We report a new theranostic device based on lead sulfide quantum dots (PbS QDs) with optical emission in the near infrared wavelength range decorated with affibodies (small 6.5 kDa protein-based antibody replacements) specific to the cancer biomarker human epidermal growth factor receptor 2 (HER2), and zinc(II) protoporphyrin IX (ZnPP) to combine imaging, targeting and therapy within one nanostructure. Colloidal PbS QDs were synthesized in aqueous solution with a nanocrystal diameter of ∼5 nm and photoluminescence emission in the near infrared wavelength range. The ZHER2:432 affibody, mutated through the introduction of two cysteine residues at the C-terminus (Afb2C), was used as capping ligand to form Afb2C-PbS QDs that have a high binding affinity for HER2, which is overexpressed in several types of cancer including breast cancer. Afb2C-PbS QDs were further modified by conjugation with ZnPP, which acts as an anticancer agent. The biological activity of these QDs was tested against SKBR3 (HER2-positive) and MDA-MB-231 (HER2-normal) breast cancer cells, with results showing that ZnPP-Afb2C-functionalized PbS QDs were successfully targeted to the HER2-overexpressing cancer cells and induced cell apoptosis thanks to the conjugation with ZnPP. These results expand the use of the QD nanoplatform with the formulation of novel nanomaterials for targeted delivery and combined imaging and therapy via direct surface-protein interaction.

Quantitative Bioreactor Monitoring of Intracellular Bacterial Metabolites in Clostridium autoethanogenum Using Liquid Chromatography-Isotope Dilution Mass Spectrometry

We report a liquid chromatography-isotope dilution mass spectrometry method for the simultaneous quantification of 131 intracellular bacterial metabolites of Clostridium autoethanogenum. A comprehensive mixture of uniformly ¹³C-labeled internal standards (U-¹³C IS) was biosynthesized from the closely related bacterium Clostridium pasteurianum using 4% ¹³C-glucose as a carbon source. The U-¹³C IS mixture combined with ¹²C authentic standards was used to validate the linearity, precision, accuracy, repeatability, limits of detection, and quantification for each metabolite. A robust-fitting algorithm was employed to reduce the weight of the outliers on the quantification data. The metabolite calibration curves were linear with R ² ≥ 0.99, limits of detection were ≤1.0 μM, limits of quantification were ≤10 μM, and precision/accuracy was within RSDs of 15% for all metabolites. The method was subsequently applied for the daily monitoring of the intracellular metabolites of C. autoethanogenum during a CO gas fermentation over 40 days as part of a study to optimize biofuel production. The concentrations of the metabolites were estimated at steady states of different pH levels using the robust-fitting mathematical approach, and we demonstrate improved accuracy of results compared to conventional regression. Metabolic pathway analysis showed that reactions of the incomplete (branched) tricarboxylic acid "cycle" were the most affected pathways associated with the pH shift in the bioreactor fermentation of C. autoethanogenum and the concomitant changes in ethanol production.

Inhibition of Mycobacterium tuberculosis InhA: Design, synthesis and evaluation of new di-triclosan derivatives

Multi-drug resistant tuberculosis (MDR-TB) represents a growing problem for global healthcare systems. In addition to 1.3 million deaths in 2018, the World Health Organisation reported 484,000 new cases of MDR-TB. Isoniazid is a key anti-TB drug that inhibits InhA, a crucial enzyme in the cell wall biosynthesis pathway and identical in Mycobacterium tuberculosis and M. bovis. Isoniazid is a pro-drug which requires activation by the enzyme KatG, mutations in KatG prevent activation and confer INH-resistance. 'Direct inhibitors' of InhA are attractive as they would circumvent the main clinically observed resistance mechanisms. A library of new 1,5-triazoles, designed to mimic the structures of both triclosan molecules uniquely bound to InhA have been synthesised. The inhibitory activity of these compounds was evaluated using isolated enzyme assays with 2 (5-chloro-2-(4-(5-(((4-(4-chloro-2-hydroxyphenoxy)benzyl)oxy)methyl)-1H-1,2,3-triazol-1-yl)phenoxy)phenol) exhibiting an IC₅₀ of 5.6 µM. Whole-cell evaluation was also performed, with 11 (5-chloro-2-(4-(5-(((4-(cyclopropylmethoxy)benzyl)oxy)methyl)-1H-1,2,3-triazol-1-yl)phenoxy)phenol) showing the greatest potency, with an MIC₉₉ of 12.9 µM against M. bovis.

Cyclo(RGDfK) Functionalized Spider Silk Cell Scaffolds: Significantly Improved Performance in Just One Click

Recombinant spider silk has the potential to provide a new generation of biomaterial scaffolds as a result of its degree of biocompatibility and lack of immunogenicity. These recombinant biomaterials are, however, reported to exhibit poor cellular adhesion which limits their potential for use in applications such as tissue engineering and regenerative medicine. In this study, a simple chemical functionalization approach is described that specifically addresses this issue and significantly improves the adhesion of human mesenchymal stem cells (CiMSCs) to a recombinant spider silk biomaterial. This utilizes copper-catalyzed or strain-promoted azide-alkyne cycloaddition (CuAAC/SPAAC) "click" chemistry to covalently attach cyclo(RGDfK) peptides to the azide group of l-azidohomoalanine, a methionine analogue previously site specifically incorporated into the primary sequence of a thioredoxin (TRX)-tagged silk fusion protein, TRX-4RepCT, to give TRX^3Aha -4RepCT^3Aha . This method is used to produce cyclo(RGDfK) functionalized films and macroscopic fibers. Over 24 h, cyclo(RGDfK) functionalized TRX^3Aha -4RepCT^3Aha  films and 4RepCT^3Aha  fibers display significantly improved performance in CiMSC culture, yielding far greater cell numbers than the controls. This approach circumvents the previously observed lack of cell adhesion, thus allowing spider silk derived biomaterials to be used where such adhesion is critical, in tissue engineering, regenerative medicine and wound healing.

Abstract 1727: Challenging resistance to temozolomide in glioblastoma by drug encapsulation in apoferritin

Background: Temozolomide (TMZ) is a DNA alkylating prodrug used for the treatment of malignant, glioblastoma multiforme (GBM) tumors. Yet, TMZ therapy is blighted by resistance systems in GBM that thwart eradication of all cancer cells remaining after surgery and radiotherapy. Resistance mechanisms include drug efflux by P-glycoprotein 1 (Pgp), present on the blood brain barrier (BBB) and on GBM cells, overexpression of O6-methylguanine DNA-methyltransferase (MGMT), which removes cytotoxic O6-methylated guanine (O6-MeG) lesions caused by TMZ, and deficiency in mismatch repair (MMR), which leads to tolerance of O6-MeG lesions. Nanoscale delivery systems are proposed as a strategy to enhance drug targeting and accumulation under systemically tolerable conditions. Apoferritin (AFt), a hollow protein capsule, has been used to deliver anticancer agents. Transferrin receptor 1 (TfR1) binding sites on the AFt cage has reportedly been shown to allow AFt to cross the BBB and accumulate in GBM cells, as both BBB endothelial and GBM (but not glial) cells express TfR1. Thus, we use AFt for targeted delivery, specific uptake and controlled release of TMZ in GBM.

Methods: TMZ was encapsulated into AFt via molecular diffusion through the channels in the AFt cage. Encapsulation efficiency and stability for this formulation were assessed by dynamic light scattering (DLS) and UV-vis spectroscopy. In vitro assays were conducted (MTT, live cell count, clonogenic, flow cytometry and ELISA) against isogenic GBM cell lines, U373V (vector control) and U373M (MGMT overexpressing), as well as MMR deficient and Pgp overexpressing HCT116 (colorectal carcinoma) and healthy MRC-5 (lung fibroblasts) cells. Environmental scanning electron microscopy (ESEM) and confocal microscopy were further employed to assess morphological changes to the cells after treatment.

Results: Encapsulation of > 500 molecules of TMZ per AFt cage was achieved, with encapsulation efficiency > 70%. MTT assays demonstrated significantly increased activity of AFt-TMZ compared to TMZ alone in all cancer cell lines, with 50% growth inhibition (GI50) in resistant cancer cell lines at < 15 μM, compared to > 200 μM for TMZ alone. Clonogenic and flow cytometric cell cycle and DNA damage analyses further corroborate these findings. Additionally, ELISA quantification demonstrated significantly (P < 0.001) elevated O6-MeG levels following treatment of U373V and U373M cells with AFt-TMZ compared to naked TMZ, correlating with enhanced γ-H2AX burden in cells following exposure to AFt-TMZ. Against MRC-5, lower activity was observed, with GI50 for AFt-TMZ > 70 μM. Furthermore, cell shrinkage and blebbing were observed in GBM cells following 24 h treatment with AFt-TMZ.

Conclusions: TMZ delivered by AFt demonstrated enhanced potency. Overcoming resistance by enhancing TMZ intracellular accumulation, may prove to be a turning point in enhancing drug efficacy in GBM.

Citation Format: Kaouthar Bouzinab, Neil R. Thomas, Lyudmila Turyanska, Pavel Gershkovich, Nicola Weston, Marianne B. Ashford, Tracey D. Bradshaw. Challenging resistance to temozolomide in glioblastoma by drug encapsulation in apoferritin [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1727.

Delivery of Temozolomide and N3-Propargyl Analog to Brain Tumors Using an Apoferritin Nanocage

Glioblastoma multiforme (GBM) is a grade IV astrocytoma, which is the most aggressive form of brain tumor. The standard of care for this disease includes surgery, radiotherapy and temozolomide (TMZ) chemotherapy. Poor accumulation of TMZ at the tumor site, tumor resistance to drug, and dose-limiting bone marrow toxicity eventually reduce the success of this treatment. Herein, we have encapsulated >500 drug molecules of TMZ into the biocompatible protein nanocage, apoferritin (AFt), using a "nanoreactor" method (AFt-TMZ). AFt is internalized by transferrin receptor 1-mediated endocytosis and is therefore able to facilitate cancer cell uptake and enhance drug efficacy. Following encapsulation, the protein cage retained its morphological integrity and surface charge; hence, its cellular recognition and uptake are not affected by the presence of this cargo. Additional benefits of AFt include maintenance of TMZ stability at pH 5.5 and drug release under acidic pH conditions, encountered in lysosomal compartments. MTT assays revealed that the encapsulated agents displayed significantly increased antitumor activity in U373V (vector control) and, remarkably, the isogenic U373M (MGMT expressing TMZ-resistant) GBM cell lines, with GI₅₀ values <1.5 μM for AFt-TMZ, compared to 35 and 376 μM for unencapsulated TMZ against U373V and U373M, respectively. The enhanced potency of AFt-TMZ was further substantiated by clonogenic assays. Potentiated G2/M cell cycle arrest following exposure of cells to AFt-TMZ indicated an enhanced DNA damage burden. Indeed, increased O6-methylguanine (O6-MeG) adducts in cells exposed to AFt-TMZ and subsequent generation of γH2AX foci support the hypothesis that AFt significantly enhances the delivery of TMZ to cancer cells in vitro, overwhelming the direct O6-MeG repair conferred by MGMT. We have additionally encapsulated >500 molecules of the N3-propargyl imidazotetrazine analog (N3P), developed to combat TMZ resistance, and demonstrated significantly enhanced activity of AFt-N3P against GBM and colorectal carcinoma cell lines. These studies support the use of AFt as a promising nanodelivery system for targeted delivery, lysosomal drug release, and enhanced imidazotetrazine potency for treatment of GBM and wider-spectrum malignancies.

Synthesis of folic acid functionalized gold nanoclusters for targeting folate receptor-positive cells

We report on the synthesis of water-soluble gold nanoclusters capped with polyethylene glycol (PEG)-based ligands and further functionalized with folic acid for specific cellular uptake. The dihydrolipoic acid-PEG-based ligands terminated with -OMe, -NH₂ and -COOH functional groups are produced and used for surface passivation of Au nanoclusters (NCs) with diameters <2 nm. The produced sub 2 nm Au NCs possess long-shelf life and are stable in physiologically relevant environments (temperature and pH), are paramagnetic and biocompatible. The paramagnetism of Au NCs in solution is also reported. The functional groups on the capping ligands are used for direct conjugation of targeting molecules onto Au NCs without the need for post synthesis modification. Folic acid (FA) is attached via an amide group and effectively target cells expressing the folate receptor. The combination of targeting ability, biocompatibility and paramagnetism in FA-functionalized Au NCs is of relevance for their exploitation in nanomedicine for targeted imaging.

Protein Encapsulation of Experimental Anticancer Agents 5F 203 and Phortress: Towards Precision Drug Delivery

INTRODUCTION

Advancement of novel anticancer drugs into clinical use is frequently halted by their lack of solubility, reduced stability under physiological conditions, and non-specific uptake by normal tissues, causing systemic toxicity. Their progress to use in the clinic could be accelerated by the development of new formulations employing suitable and complementary drug delivery vehicles.

METHODS

A robust method for apoferritin (AFt)-encapsulation of antitumour benzothiazoles has been developed for enhanced activity against and drug delivery to benzothiazole-sensitive cancers.

RESULTS

More than 70 molecules of benzothiazole 5F 203 were encapsulated per AFt cage. Post-encapsulation, the size and integrity of the protein cages were retained as evidenced by dynamic light scattering. ToF-SIMS depth profiling using an argon cluster beam confirmed 5F 203 exclusively within the AFt cavity. Improved encapsulation of benzothiazole lysyl-amide prodrugs was achieved (~130 molecules of Phortress per AFt cage). Transferrin receptor 1, TfR1, was detected in lysates prepared from most cancer cell lines studied, contributing to enhanced anticancer potency of the AFt-encapsulated benzothiazoles (5F 203, Phortress, GW 610, GW 608-Lys). Nanomolar activity was demonstrated by AFt-formulations in breast, ovarian, renal and gastric carcinoma cell lines, whereas GI50 >50 µM was observed in non-tumourigenic MRC-5 fibroblasts. Intracellular 5F 203, a potent aryl hydrocarbon receptor (AhR) ligand, and inducible expression of cytochrome P450 (CYP) 1A1 were detected following exposure of sensitive cells to AFt-5F 203, confirming that the activity of benzothiazoles was not compromised following encapsulation.

CONCLUSION

Our results show enhanced potency and selectivity of AFt-encapsulated 5F 203 against carcinomas derived from breast, ovarian, renal, colorectal as well as gastric cancer models, and offer realistic prospects for potential refinement of tumour-targeting and treatment, and merit further in vivo investigations.

Targeting brain tumours: apoferritin nanocage for delivery of novel analogues of temozolomide

Treatment for glioblastoma multiforme (GBM) consists of surgery, radiotherapy and temozolomide (TMZ) chemotherapy. Nevertheless, patient prognosis remains poor; in England 5-year survival is < 10%. Resistance to TMZ is a major obstacle thwarting successful treatment, due to overexpression of the O6-methylguanine DNA-methyltransferase (MGMT) and deficiency in mismatch repair (MMR). To overcome resistance, novel N3-substituted analogues of TMZ have been developed. An N3-propargyl analogue, T3, has promising activity irrespective of MGMT or MMR status. However, poor brain drug bioavailability and systemic toxicity remain to be resolved. We use apoferritin (AFt) as a biocompatible nano-delivery system for encapsulation of therapeutic agents via molecular diffusion, through channels in the AFt cage. Around 520 molecules of TMZ and T3 per AFt cage were encapsulated. AFt`s small size (diameter: 12 nm) and numerous transferrin receptor recognition sites on its surface; alongside enhanced expression of transferrin receptors (TfR1; which sequester AFt) on the membranes of cancer cells, offer a dual targeting approach towards greater cancer-selectivity. The encapsulated agents have demonstrated significantly increased anti-tumour activity in brain cancer GBM cell lines, U373V (vector control) and U373M (MGMT over-expressing), with growth inhibition GI50 values < 1 μM, compared to > 30 μM for naked drugs. Clonogenic and cell cycle analyses further corroborate these findings. Hence, the AFt nano-delivery system offers a promising route for enhanced specificity, selectivity and potency of TMZ analogues.

Hybrid light emitting diodes based on stable, high brightness all-inorganic CsPbI3 perovskite nanocrystals and InGaN

Despite important advances in the synthesis of inorganic perovskite nanocrystals (NCs), the long-term instability and degradation of their quantum yield (QY) over time need to be addressed to enable the further development and exploitation of these nanomaterials. Here we report stable CsPbI3 perovskite NCs and their use in hybrid light emitting diodes (LEDs), which combine in one system the NCs and a blue GaN-based LED. Nanocrystals with improved morphological and optical properties are obtained by optimizing the post-synthesis replacement of oleic acid ligands with iminodibenzoic acid: the NCs have a long shelf-life (>2 months), stability under different environmental conditions, and a high QY, of up to 90%, in the visible spectral range. Ligand replacement enables the engineering of the morphological and optical properties of the NCs. Furthermore, the NCs can be used to coat the surface of a GaN-LED to realize a stable diode where they are excited by blue light from the LED under low current injection conditions, resulting in emissions at distinct wavelengths in the visible range. The high QY and fluorescence lifetime in the nanosecond range are key parameters for visible light communication, an emerging technology that requires high-performance visible light sources for secure, fast energy-efficient wireless transmission.

In search of effective therapies to overcome resistance to Temozolomide in brain tumours

Glioblastoma multiforme is the most common and lethal brain tumour-type. The current standard of care includes Temozolomide (TMZ) chemotherapy. However, inherent and acquired resistance to TMZ thwart successful treatment. The direct repair protein methylguanine DNA methyltransferase (MGMT) removes the cytotoxic O6-methylguanine (O6-MeG) lesion delivered by TMZ and so its expression by tumours confers TMZ-resistance. DNA mismatch repair (MMR) is essential to process O6-MeG adducts and MMR-deficiency leads to tolerance of lesions, resistance to TMZ and further DNA mutations. In this article, two strategies to overcome TMZ resistance are discussed: (1) synthesis of imidazotetrazine analogues - designed to retain activity in the presence of MGMT or loss of MMR; (2) preparation of imidazotetrazine-nanoparticles to deliver TMZ preferably to the brain and tumour site. Our promising results encourage belief in a future where better prognoses exist for patients diagnosed with this devastating disease.

Antibiotic Spider Silk: Site-Specific Functionalization of Recombinant Spider Silk Using "Click" Chemistry

In a new, versatile approach to fun-ction-alizing recombinant spider silk, L-azidohomoalanine is introduced residue-specifically in the minispidroin protein 4RepCT through expression in an E. coli methionine auxotroph. Both fluorophores and the antibiotic levofloxacin are attached to this bio-orthogonal amino acid using copper-catalyzed click chemistry, either before or after the silk fibers are self-assembled.

Probe-Specific Procedure to Estimate Sensitivity and Detection Limits for 19F Magnetic Resonance Imaging

Due to low fluorine background signal in vivo, 19F is a good marker to study the fate of exogenous molecules by magnetic resonance imaging (MRI) using equilibrium nuclear spin polarization schemes. Since 19F MRI applications require high sensitivity, it can be important to assess experimental feasibility during the design stage already by estimating the minimum detectable fluorine concentration. Here we propose a simple method for the calibration of MRI hardware, providing sensitivity estimates for a given scanner and coil configuration. An experimental "calibration factor" to account for variations in coil configuration and hardware set-up is specified. Once it has been determined in a calibration experiment, the sensitivity of an experiment or, alternatively, the minimum number of required spins or the minimum marker concentration can be estimated without the need for a pilot experiment. The definition of this calibration factor is derived based on standard equations for the sensitivity in magnetic resonance, yet the method is not restricted by the limited validity of these equations, since additional instrument-dependent factors are implicitly included during calibration. The method is demonstrated using MR spectroscopy and imaging experiments with different 19F samples, both paramagnetically and susceptibility broadened, to approximate a range of realistic environments.

Developing Mn-doped lead sulfide quantum dots for MRI labels

Magnetic interactions of Mn²⁺ ions in lead sulfide (PbS) nanocrystals with protons in water are probed by NMR and MRI.

An Apoferritin-based Drug Delivery System for the Tyrosine Kinase Inhibitor Gefitinib

Anticancer drug Gefitinib encapsulated within human heavy chain apoferritin by diffusion allows pH-controlled sustained release of cargo. The combination of increased cellular uptake, and potent and enhanced antitumor activity against the HER2 overexpressing SKBR3 cell line compared to Gefitinib alone, makes it a promising carrier for delivery of drugs to tumor sites.

Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium

Background

Clostridium autoethanogenum is an acetogenic bacterium capable of producing high value commodity chemicals and biofuels from the C1 gases present in synthesis gas. This common industrial waste gas can act as the sole energy and carbon source for the bacterium that converts the low value gaseous components into cellular building blocks and industrially relevant products via the action of the reductive acetyl-CoA (Wood-Ljungdahl) pathway. Current research efforts are focused on the enhancement and extension of product formation in this organism via synthetic biology approaches. However, crucial to metabolic modelling and directed pathway engineering is a reliable and comprehensively annotated genome sequence.

Results

We performed next generation sequencing using Illumina MiSeq technology on the DSM10061 strain of Clostridium autoethanogenum and observed 243 single nucleotide discrepancies when compared to the published finished sequence (NCBI: GCA_000484505.1), with 59.1 % present in coding regions. These variations were confirmed by Sanger sequencing and subsequent analysis suggested that the discrepancies were sequencing errors in the published genome not true single nucleotide polymorphisms. This was corroborated by the observation that over 90 % occurred within homopolymer regions of greater than 4 nucleotides in length. It was also observed that many genes containing these sequencing errors were annotated in the published closed genome as encoding proteins containing frameshift mutations (18 instances) or were annotated despite the coding frame containing stop codons, which if genuine, would severely hinder the organism’s ability to survive. Furthermore, we have completed a comprehensive manual curation to reduce errors in the annotation that occur through serial use of automated annotation pipelines in related species. As a result, different functions were assigned to gene products or previous functional annotations rejected because of missing evidence in various occasions.

Conclusions

We present a revised manually curated full genome sequence for Clostridium autoethanogenum DSM10061, which provides reliable information for genome-scale models that rely heavily on the accuracy of annotation, and represents an important step towards the manipulation and metabolic modelling of this industrially relevant acetogen.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2287-5) contains supplementary material, which is available to authorized users.

Crystal structure of the antimicrobial peptidase lysostaphin from Staphylococcus simulans

Staphylococcus simulans biovar staphylolyticus lysostaphin efficiently cleaves Staphylococcus aureus cell walls. The protein is in late clinical trials as a topical anti-staphylococcal agent, and can be used to prevent staphylococcal growth on artificial surfaces. Moreover, the gene has been both stably engineered into and virally delivered to mice or livestock to obtain resistance against staphylococci. Here, we report the first crystal structure of mature lysostaphin and two structures of its isolated catalytic domain at 3.5, 1.78 and 1.26 Å resolution, respectively. The structure of the mature active enzyme confirms its expected organization into catalytic and cell-wall-targeting domains. It also indicates that the domains are mobile with respect to each other because of the presence of a highly flexible peptide linker. The high-resolution structures of the catalytic domain provide details of Zn²⁺ coordination and may serve as a starting point for the engineering of lysostaphin variants with improved biotechnological characteristics.

Cooperativity and site selectivity in the ileal lipid binding protein

The ileal lipid binding protein (ILBP or I-BABP) binds bile salts with positive cooperativity and has unusual site selectivity, whereby cholic acid binds preferentially in one site and chenodeoxycholic in another, despite both sites having an affinity for both ligands and the ligands only differing by a single hydroxyl group. Previous studies of the human variant have assumed that the ligand/protein binding ratio is 2:1, but we show, using electrospray ionization mass spectroscopy, that human ILBP binds bile acids with a 3:1 ratio, even at low protein and ligand concentrations. Docking calculations and molecular dynamics (MD) simulations identify an allosterically active binding site on the protein exterior that induces a change from a closed conformation to an open one, characterized by a movement of one of the α-helices by ~10° with respect to the β-clam shell. Additional independent MD simulations of several hundred nanoseconds implicate the change between conformations in the mechanisms of both cooperativity and ligand site selectivity.

Injection locking of violet laser diodes with a 3.2 GHz offset frequency for driving Raman transitions in 43Ca+

Two cw single-mode violet (397 nm) diode lasers are locked to a single external-cavity master diode laser by optical injection locking. A double-pass 1.6 GHz acousto-optic modulator is used to provide a 3.2 GHz offset frequency between the two slave lasers. We achieve up to 20 mW usable output in each slave beam, with as little as 25 μW of injection power at room temperature. An optical heterodyne measurement of the beat note between the two slave beams gives a linewidth of ≤10 Hz at 3.2 GHz. We also estimate the free-running linewidth of the master laser to be approximately 3 MHz by optical heterodyning with a similar device.

Identification of Novel Inhibitors of UDP-Galactopyranose Mutase by Structure-Based Virtual Screening

UDP-galactopyranose mutase (UGM) is a flavo-enzyme involved in the bacterial cell wall biosynthesis. UGM catalyzes the reversible isomerization of UDP-galactopyranose (UDP-Galp) to UDP-galactofuranose (UDP-Galf). UDP-Galf is the activated precursor of galactofuranose (Galf) residues that are essential components of the cell wall of certain pathogenic bacteria such as Klebsiella pneumoniae and Mycobacterium tuberculosis. Neither UGM nor Galf residues are found in humans, making Galf biosynthesis a potential drug target for developing antibacterial agents. We report the identification of novel inhibitors of UGM by in silico docking of the LeadQuest compound database against UGM from Escherichia coli. The 13 most promising inhibitors were then evaluated against K. pneumonia and M. tuberculosis UGMs by enzyme inhibition studies. Two inhibitors were identified with IC50 values of ∼1 µM and subsequently these compounds were docked into the recently solved X-ray structure of Deinococcus radiodurans UGM. The structure-activity relationships of the initial 13 compounds evaluated as inhibitors are discussed.

Chemoenzymatic synthesis, inhibition studies, and X-ray crystallographic analysis of the phosphono analog of UDP-Galp as an inhibitor and mechanistic probe for UDP-galactopyranose mutase

UDP (uridine diphosphate) galactopyranose mutase (UGM) is involved in the cell wall biosynthesis of many pathogenic microorganisms. UGM catalyzes the reversible conversion of UDP-α-D-galactopyranose into UDP-α-D-galactofuranose, with the latter being the precursor of galactofuranose (Galf) residues in cell walls. Glycoconjugates of Galf are essential components in the cell wall of various pathogenic bacteria, including Mycobacterium tuberculosis, the causative agent of tuberculosis. The absence of Galf in humans and its bacterial requirement make UGM a potential target for developing novel antibacterial agents. In this article, we report the synthesis, inhibitory activity, and X-ray crystallographic studies of UDP-phosphono-galactopyranose, a nonhydrolyzable C-glycosidic phosphonate. This is the first report on the synthesis of a phosphonate analog of UDP-α-D-galactopyranose by a chemoenzymatic phosphoryl coupling method. The phosphonate was evaluated against three bacterial UGMs and showed only moderate inhibition. We determined the crystal structure of the phosphonate analog bound to Deinococcus radiodurans UGM at 2.6 Å resolution. The phosphonate analog is bound in a novel conformation not observed in UGM-substrate complex structures or in other enzyme-sugar nucleotide phosphonate complexes. This complex structure provides a structural basis for the observed micromolar inhibition towards UGM. Steric clashes, loss of electrostatic stabilization between an active-site arginine (Arg305) and the phosphonate analog, and a 180° flip of the hexose moiety account for the differences in the binding orientations of the isosteric phosphonate analog and the physiological substrate. This provides new insight into the ability of a sugar-nucleotide-binding enzyme to orient a substrate analog in an unexpected geometry and should be taken into consideration in designing such enzyme inhibitors.

Abstract 1462: Triterpene extract of Ganoderma lucidum inhibits proliferation of premalignant human prostate cells by regulation of epithelial mesenchymal transition

Background: Prostate cancer is the leading cancer diagnosed in men. Ganoderma lucidum (GL), a well known medicinal fungus, has been widely used in the treatment and prevention of many diseases, including cancer, in Asian countries. The triterpene extract of GL, has been identified as an important active ingredient possessing anti-cancer activities, through, as yet an unknown mechanism of action. The aims of our current research were to characterise the inhibitory activity of triterpene extracts of GL in pre-malignant prostate cell lines (PINs) as a potential model of chemoprevention and to investigate the mechanism of action of triterpene.

Materials and methods: Effects on growth of PIN cell lines were measured using an “in vitro” fluorometric cell viability assay and “in vivo” growth assays. Invasive behaviour of PIN was assessed “in vitro” by using a wound healing assay, and cell branching, in a matrigel invasion assay. The effect on angiogenesis was assessed by measuring formation of tubules by human endothelial cells. To identify the cellular targets of triterpene, two-dimensional gel electrophoresis was used, and proteins showing differential expression were identified by mass spectrometry. Effects on protein expression and gene regulation were further confirmed by western blotting, quantitative RT-PCR and luciferase reporter assay.

Results: The triterpene extract of GL inhibited the “in vitro” proliferation of PINs with an IC50 ranging from 38.8μg/ml to 118.8μg/ml and inhibited the volume of PIN xenografts by 30% (p&lt;0.05; 77mg/ml). In addition, triterpene (at the IC25) significantly suppressed angiogenesis (&gt;95% inhibition, p&lt;0.0001), migration (76% inhibition, p&lt;0.001) and invasion of PIN (p&lt;0.001). From proteomic analysis, two potential target proteins identified included the epithelial-mesenchymal transition (EMT) marker vimentin and the glycolytic enzyme enolase α. The down-regulation of vimentin and up-regulation of enolase α were further confirmed by western blotting. The possible role of triterpene in regulation of EMT markers including vimentin, E-cadherin, N-cadherin and slug was also demonstrated by quantitative RT-PCR of PIN cells collected from a cell branching assay. Additionally, triterpene was found to down-regulate the protooncogene c-myc, a downstream target of enolase α, which plays an important role in the cell cycle, cell proliferation and apoptosis.

Conclusion: These findings suggest that the triterpene extract of GL could be a promising new agent in prevention of prostate cancer by regulation of EMT and c-myc.

Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1462.

The UDP-Galp mutase catalyzed isomerization: synthesis and evaluation of 1,4-anhydro-beta-D-galactopyranose and its [2.2.2] methylene homologue

The synthesis of 1,4-anhydro-beta-D-galactopyranose (1,5-anhydro-alpha-D-galactofuranose), a proposed intermediate in the ring contraction isomerisation catalyzed by UDP-galactopyranose mutase, together with its [2.2.2] bicyclic methylene homologue, synthesised as a possible competitive inhibitor or alternative substrate, are reported. Neither compound was found to be an inhibitor or substrate for UDP-galactopyranose mutase from Klebsiella pneumoniae.

Tailoring the physical properties of thiol-capped PbS quantum dots by thermal annealing

We show that the thermal annealing of thiol-capped PbS colloidal quantum dots provides a means of narrowing the nanoparticle size distribution, increasing the size of the quantum dots and facilitating their coalescence preferentially along the 100 crystallographic axes. We exploit these phenomena to tune the photoluminescence emission of an ensemble of dots and to narrow the optical linewidth to values that compare with those reported at room temperature for single PbS quantum dots. We probe the influence of annealing on the electronic properties of the quantum dots by temperature dependent studies of the photoluminescence and magneto-photoluminescence.

Enzyme-catalyzed synthesis of isosteric phosphono-analogues of sugar nucleotides

Efficient enzymatic syntheses of isosteric phosphono analogues of sugar nucleotides have been accomplished using a thymidylyltransferase.

Acyl derivatives of coenzyme A inhibit platelet function via antagonism at P2Y1 and P2Y12 receptors: a new finding that may influence the design of anti-thrombotic agents

We have performed a detailed investigation of the effects on platelet function of coenzyme A (CoA) and several acyl-CoAs. Platelet aggregation was measured by turbidimetry and by platelet counting; platelet shape change was measured using light scattering; P-selectin, Ca2+ mobilization and vasodilator-stimulated phosphoprotein (VASP) phosphorylation were measured by flow cytometry. The compounds investigated inhibited ADP-induced platelet aggregation; those with saturated acyl groups containing 16-18 carbons were most effective. The effects of palmitoyl-CoA (16:0) were studied in depth. It inhibited platelet shape change and Ca2+ mobilization brought about by ADP (but not other agonists) indicating antagonism at P2Y(1) receptors, and also inhibited ADP-induced P-selectin expression. Effects of palmitoyl-CoA on the platelet aggregation and Ca2+ mobilization induced by several different agonists and agonist combinations were compared with those of MRS 2179 (a P2Y(1) antagonist) and AR-C69931 (a P2Y(12) antagonist), and were consistent with palmitoyl-CoA acting mainly at P2Y(1) but also with partial antagonism at P2Y(12) receptors. Antagonism at P2Y(12) receptors was confirmed in studies of VASP-phosphorylation. Palmitoyl-CoA did not act as an antagonist at P2X(1) receptors. The results are discussed in relation to the possibility that acyl-CoAs may contribute as endogenous modulators of platelet function and might serve as lead compounds for the design of novel antithrombotics.

Stable colloidal dispersions of a lipase-perfluoropolyether complex in liquid and supercritical carbon dioxide

The technique of hydrophobic ion pairing was used to solubilize the lipase from Candida rugosa in a fluorinated solvent, perfluoromethylcyclohexane (PFMC), in complex with a perfluoropolyether (PFPE) surfactant, KDP 4606. The enzyme-surfactant complex was determined to have a hydrodynamic diameter of 6.5 nm at atmospheric pressure by dynamic light scattering (DLS), indicating that a single lipase molecule is stabilized by surrounding surfactant molecules. The complex formed a highly stable colloidal dispersion in both liquid and supercritical carbon dioxide at high CO2 densities (>0.92 and 0.847 g/mL, respectively), with 4% by volume PFMC as a cosolvent, yielding a fluid that was orange, optically translucent, and very nearly transparent. DLS demonstrated aggregation of the enzyme-surfactant complexes in CO2 at 25 and 40 degrees C and various pressures (2000-5000 psia) with hydrodynamic diameters ranging from 50 to 200 nm. The mechanism by which the enzyme-surfactant particles aggregate was shown to be via condensation due to very low polydispersities as characterized by the size distribution moments. Interparticle interactions were investigated with respect to density and temperature, and it was shown that on decreasing the CO2 density, the particle size increased, and the stability against settling decreased. Particle size also decreased as the temperature was increased to 40 degrees C, at constant CO2 density. Nanoparticle aggregates of an enzyme-surfactant complex in CO2, which are nearly optically transparent and stable to settling, are a promising new alternative to previous types of dispersions of proteins in CO2 that either required water/CO2 microemulsions or were composed of large particles unstable to settling.

Bile Acid Interactions with Rabbit Ileal Lipid Binding Protein and an Engineered Helixless Variant Reveal Novel Ligand Binding Properties of a Versatile β-Clam Shell Protein Scaffold

The intracellular ileal lipid binding proteins (ILBPs) are involved in the transport and enterohepatic circulation of bile acids. ILBPs from different species show high sequence and structural homology and have been shown to bind multiple bile acid ligands with differing degrees of selectivity and positive co-operativity. Human ILBP binds bile acid derivatives in a well-characterised 2:1 ligand:protein complex, however, we show that the highly homologous rabbit ILBP (82% sequence identity) with seven conservative substitutions preferentially binds multiple conjugated deoxycholate ligands in a novel 3:1 binding mode essentially within the same beta-clam shell structure. We have extended these studies to investigate the role of the alpha-helical capping motif (residues 9-35) in controlling the dimensions of the binding cavity and ligand uptake. Substituting the alpha-helical motif (residues 9-35) with a short Gly-Gly-Ser-Gly linker dramatically affects the protein stability such that under physiological conditions the mutant (Deltaalpha-ILBP) is highly disordered. However, we show that the inability of the mutant to adopt a stable three-dimensional structure under these conditions is no barrier to binding ligands with near-native affinity. These structural modifications not only demonstrate the possibility of strong coupling between ligand binding and protein folding, but result in changes in bile acid selectivity and binding stoichiometry, which we characterise in detail using isothermal calorimetry and mass spectrometry.

Long-lived mesoscopic entanglement outside the Lamb-Dicke regime

We create entangled states of the spin and motion of a single 40Ca+ ion in a linear ion trap. We theoretically study and experimentally observe the behavior outside the Lamb-Dicke regime, where the trajectory in phase space is modified and the motional coherent states become squeezed. We directly observe the modification of the return time of the trajectory, and infer the squeezing. The mesoscopic entanglement is observed up to Deltaalpha=5.1 with coherence time 170 micros and mean phonon excitation n = 16.

Coupling ligand recognition to protein folding in an engineered variant of rabbit ileal lipid binding protein

We have engineered a variant of the beta-clam shell protein ILBP which lacks the alpha-helical motif that caps the central binding cavity; the mutant protein is sufficiently destabilised that it is unfolded under physiological conditions, however, it unexpectedly binds its natural bile acid substrates with high affinity forming a native-like beta-sheet rich structure and demonstrating strong thermodynamic coupling between ligand binding and protein folding.

The high-resolution structure of (+)-epi-biotin bound to streptavidin

(+)-Epi-biotin differs from (+)-biotin in the configuration of the chiral center at atom C2. This could lead to a difference in the mode of binding of (+)-epi-biotin to streptavidin, a natural protein receptor for (+)-biotin. Diffraction data were collected to a maximum of 0.85 Angstrom resolution for structural analysis of the complex of streptavidin with a sample of (+)-epi-biotin and refinement was carried out at both 1.0 and 0.85 Angstrom resolution. The structure determination shows a superposition of two ligands in the binding site, (+)-biotin and (+)-epi-biotin. The molecules overlap in the model for the complex except for the position of S1 in the tetrahydrothiophene ring. Differences in the conformation of the ring permits binding of each molecule to streptavidin with little observable difference in the protein structures at this high resolution.

Internally quenched peptides for the study of lysostaphin: an antimicrobial protease that kills Staphylococcus aureus

Lysostaphin (EC. 3.4.24.75) is a protein secreted by Staphylococcus simulans biovar staphylolyticus and has been shown to be active against methicillin resistant S. aureus (MRSA). The design and synthesis of three internally quenched substrates for lysostaphin based on the peptidoglycan crossbridges of S. aureus, and their use in fluorescence resonance energy transfer (FRET) assays is reported. These substrates enabled the gathering of information about the endopeptidase activity of lysostaphin and the effect that mutations have on its enzymatic ability. Significant problems with the inner filter effect and substrate aggregation were encountered; their minimisation and the subsequent estimation of the kinetic parameters for the interaction of lysostaphin with the substrates is described, as well as a comparison of substrates incorporating two FRET pairs: Abz-EDDnp and DABCYL-EDANS. In addition to this, the points of cleavage caused by lysostaphin in Abz-pentaglycine-EDDnp have been determined by HPLC and mass spectrometry analysis to be between glycines 2 and 3(approximately 60%) and glycines 3 and 4 (approximately 40%).

Synthesis of a Carbasugar Analogue of a Putative Intermediate in the UDP-Galp-Mutase Catalyzed Isomerization

[reaction: see text] The synthesis of the carbasugar analogue of 1,4-anhydro-beta-d-galactopyranose, a proposed intermediate in the reaction catalyzed by uridine diphosphate-alpha-d-Galp mutase, in racemic form via Diels-Alder and Barton decarboxylation chemistry is reported. This compound was found not to inhibit the mutase from Mycobacterium tuberculosis, indicating that the enzyme does not possess a 1,4-anhydro-beta-d-galactopyranose binding pocket.

A Rapid Synthesis of Hexofuranose-like Iminosugars Using Ring-Closing Metathesis

Two new 1-N-iminosugars have been prepared as hexofuranose analogues in an efficient manner by an RCM-based route. Both 3,4-disubstituted pyrrolidines display moderate inhibitory activity against Mycobacterium smegmatis galactan biosynthesis. [structure: see text]

Mutation in myosin heavy chain 6 causes atrial septal defect

Atrial septal defect is one of the most common forms of congenital heart malformation. We identified a new locus linked with atrial septal defect on chromosome 14q12 in a large family with dominantly inherited atrial septal defect. The underlying mutation is a missense substitution, I820N, in alpha-myosin heavy chain (MYH6), a structural protein expressed at high levels in the developing atria, which affects the binding of the heavy chain to its regulatory light chain. The cardiac transcription factor TBX5 strongly regulates expression of MYH6, but mutant forms of TBX5, which cause Holt-Oram syndrome, do not. Morpholino knock-down of expression of the chick MYH6 homolog eliminates the formation of the atrial septum without overtly affecting atrial chamber formation. These data provide evidence for a link between a transcription factor, a structural protein and congenital heart disease.