Portable BLAST-like algorithm library and its implementations for command line, Python, and R.

Basic local-alignment search tool (BLAST) is a versatile and commonly used sequence analysis tool in bioinformatics. BLAST permits fast and flexible sequence similarity searches across nucleotide and amino acid sequences, leading to diverse applications such as protein domain identification, orthology searches, and phylogenetic annotation. Most BLAST implementations are command line tools which produce output as comma-separated values files. However, a portable, modular and embeddable implementation of a BLAST-like algorithm, is still missing from our toolbox. Here we present nsearch, a command line tool and C++11 library which provides BLAST-like functionality that can easily be embedded in any application. As an example of this portability we present Blaster which leverages nsearch to provide native BLAST-like functionality for the R programming language, as well as npysearch which provides similar functionality for Python. These packages permit embedding BLAST-like functionality into larger frameworks such as Shiny or Django applications. Benchmarks show that nsearch, npysearch, and Blaster are comparable in speed and accuracy to other commonly used modern BLAST implementations such as VSEARCH and BLAST+. We envision similar implementations of nsearch for other languages commonly used in data science such as Julia to facilitate sequence similarity comparisons. Nsearch, Blaster and npysearch are free to use under the BSD 3.0 license and available on Github Conda, CRAN (Blaster) and PyPi (npysearch).

Re-Evaluation of Product Outcomes in the Rh-Catalyzed Ring Expansion of Aziridines with N-Sulfonyl-1,2,3-Triazoles.

N-heterocycles are prevalent in pharmaceuticals and natural products, but traditional methods often do not introduce significant stereochemical complexity into the ring. We previously reported a Rh-catalyzed ring expansion of aziridines and N-sulfonyl-1,2,3-triazoles to furnish dehydropiperazines with excellent diastereocontrol. However, later studies employing ketone-containing carbene precursors showed that [3,9]-bicyclic aziridine formation competes with production of the desired heterocyclic scaffolds. In light of these surprising results, our initial findings were re-examined both experimentally and computationally to reveal how noncovalent interactions and restricted bond rotation in the aziridinium ylide intermediate promote this unexpected reaction pathway.

Use of a Novel Polymer-Coated Steel as an Alternative to Traditional Can Manufacturing in the Food Industry.

Metal containers (both food and beverage cans) are made from huge steel or aluminum coils that are transformed into two- or three-piece products. During the manufacturing process, the metal is sprayed on both sides and the aerosol acts as insulation, but unfortunately produces volatile organic compounds (VOCs). The present work presents a different way to manufacture these containers using a novel prelaminated two-layer polymer steel. It was experimentally possible to verify that the material survives all the involved manufacturing processes. Thus tests were carried out in an ironing simulator to measure roughness, friction coefficient and surface quality. In addition, two theoretical ironing models were developed: upper bound model and artificial neural network. These models are useful for packaging designers and manufacturers.

Digital multiplex ligation assay for highly multiplexed screening of ß-lactamase-encoding genes in bacterial isolates.

Increasing incidence of antibiotic resistance in clinical and environmental settings calls for increased scalability in their surveillance. Current screening technologies are limited by the number of samples and genes that can easily be screened. We demonstrate here digital multiplex ligation assay (dMLA) as a low-cost targeted genomic detection workflow capable of highly-parallel screening of bacterial isolates for multiple target gene regions simultaneously. Here, dMLA is used for simultaneous detection of 1187 ß-lactamase-encoding genes, including extended spectrum ß-lactamase (ESBL) genes, in 74 bacterial isolates. We demonstrate dMLA as a light-weight and cost-efficient workflow which provides a highly scalable tool for antimicrobial resistance surveillance and is also adaptable to genetic screening applications beyond antibiotic resistance.

Intermolecular [3+3] ring expansion of aziridines to dehydropiperi-dines through the intermediacy of aziridinium ylides.

The importance of N-heterocycles in drugs has stimulated diverse methods for their efficient syntheses. Methods that introduce significant stereochemical complexity are attractive for identifying new bioactive amine chemical space. Here, we report a [3 + 3] ring expansion of bicyclic aziridines and rhodium-bound vinyl carbenes to form complex dehydropiperidines in a highly stereocontrolled rearrangement. Mechanistic studies and DFT computations indicate that the reaction proceeds through formation of a vinyl aziridinium ylide; this reactive intermediate undergoes a pseudo-[1,4]-sigmatropic rearrangement to directly furnish heterocyclic products with net retention at the new C-C bond. In combination with asymmetric silver-catalyzed aziridination, enantioenriched scaffolds with up to three contiguous stereocenters are rapidly delivered. The mild reaction conditions, functional group tolerance, and high stereospecificity of this method are well-suited for appending piperidine motifs to natural product and complex molecules. Ultimately, our work establishes the value of underutilized aziridinium ylides as key intermediates for converting small, strained rings to larger N-heterocycles.

Ring Expansion of Bicyclic Methyleneaziridines via Concerted, Near-Barrierless [2,3]-Stevens Rearrangements of Aziridinium Ylides.

The synthesis of densely functionalized azetidinesin a highly stereocontrolled manner is challenging, but interest in the bioactivities of these small heterocycles has stimulated methods for their preparation. We recently reported a one-carbon ring expansion of bicyclic methylene aziridines under dirhodium catalysis capable of delivering enantioenriched azetidines. This work explores this ring expansion using computational and experimental studies. DFT computations indicate that the reaction proceeds through formation of an aziridinium ylide, which is precisely poised for concerted, asynchronous ring-opening/closing to deliver the azetidines in a [2,3]-Stevens-type rearrangement. The concerted nature of this rearrangement is responsible for the stereospecificity of the reaction, where axial chirality from the initial allene substrate is transferred to the azetidine product with complete fidelity. The computed mechanistic pathway highlights the key roles of the olefin and the rigid structure of the methylene aziridine in differentiating our observed ring expansion from competing cheletropic elimination pathways noted with ylides derived from typical aziridines.

A Stereoselective [3+1] Ring Expansion for the Synthesis of Highly Substituted Methylene Azetidines.

The reaction of rhodium-bound carbenes with strained bicyclic methylene aziridines results in a formal [3+1] ring expansion to yield highly substituted methylene azetidines with excellent regio- and stereoselectivity. The reaction appears to proceed through an ylide-type mechanism, where the unique strain and structure of the methylene aziridine promotes a ring-opening/ring-closing cascade that efficiently transfers chirality from substrate to product. The resultant products can be elaborated into new azetidine scaffolds containing vicinal tertiary-quaternary and even quaternary-quaternary stereocenters.

Anti-Endosialin Antibody-Drug Conjugate: Potential in Sarcoma and Other Malignancies.

Endosialin/TEM1/CD248 is a cell surface protein expressed at high levels by the malignant cells of about 50% of sarcomas and neuroblastomas. The antibody-drug conjugate (ADC) anti-endosialin-MC-VC-PABC-MMAE was selectively cytotoxic to endosialin-positive cells in vitro and achieved profound and durable antitumor efficacy in preclinical human tumor xenograft models of endosialin-positive disease. MC-VC-PABC-MMAE was conjugated with anti-endosialin with 3-4 MMAE molecules per ADC. The anti-endosialin-MC-VC-PABC-MMAE conjugate was tested for activity in four human cell lines with varied endosialin levels. The HT-1080 fibrosarcoma cells do not express endosialin, A-673 Ewing sarcoma cells and SK-N-AS neuroblastoma cells are moderate expressers of endosialin, and SJSA-1 osteosarcoma cells express very high levels of endosialin. To determine whether endosialin expression was maintained in vivo, A-673 Ewing sarcoma, SK-N-AS neuroblastoma, and SJSA-1 osteosarcoma cells were grown as xenograft tumors in nude mice. The SK-N-AS neuroblastoma and the A-673 Ewing sarcoma lines were selected for in vivo efficacy testing of the anti-endosialin-MC-VC-PABC-MMAE conjugate. The treatment groups included a vehicle control, unconjugated anti-endosialin, an admix control consisting of anti-endosialin and a dose of free MMAE equivalent to the dose administered as the ADC, and the anti-endosialin-MC-VC-PABC-MMAE conjugate. The unconjugated anti-endosialin had no antitumor activity and resulted in similar tumor growth as the vehicle control. The admix control produced a modest tumor growth delay. Administration of the anti-endosialin-MC-VC-PABC-MMAE conjugate resulted in a marked prolonged tumor response of both xenograts. These proof-of-concept results break new ground and open a promising drug discovery approach to these rare and neglected tumors.

Removal of Metabolic Liabilities Enables Development of Derivatives of Procaspase-Activating Compound 1 (PAC-1) with Improved Pharmacokinetics.

Procaspase-activating compound 1 (PAC-1) is an o-hydroxy-N-acylhydrazone that induces apoptosis in cancer cells by chelation of labile inhibitory zinc from procaspase-3. PAC-1 has been assessed in a wide variety of cell culture experiments and in vivo models of cancer, with promising results, and a phase 1 clinical trial in cancer patients has been initiated (NCT02355535). For certain applications, however, the in vivo half-life of PAC-1 could be limiting. Thus, with the goal of developing a compound with enhanced metabolic stability, a series of PAC-1 analogues were designed containing modifications that systematically block sites of metabolic vulnerability. Evaluation of the library of compounds identified four potentially superior candidates with comparable anticancer activity in cell culture, enhanced metabolic stability in liver microsomes, and improved tolerability in mice. In head-to-head experiments with PAC-1, pharmacokinetic evaluation in mice demonstrated extended elimination half-lives and greater area under the curve values for each of the four compounds, suggesting them as promising candidates for further development.

High speed fracture fixation: assessing resulting fixation stability and fastener withdrawal strength.

A new method of bone fracture fixation has been developed in which fixation darts (small diameter nails/pins) are driven across a fracture site at high velocity with a pneumatically powered gun. When fixation darts are inserted oblique to one another, kinematic constraints prevent fragment motion and allow bone healing to progress. The primary aim of this study is to determine if fixation darts can provide reasonable fixation stability compared to bone screws, which were used as a benchmark since they represent a simple, yet well-established, surgical technique. The first objective was to evaluate macro-level stability using different numbers of darts inserted parallel and oblique to each other; experimental comparisons were undertaken in a bone analog model. Experimental results showed fixation darts could not be substituted for screws on a one-to-one basis, but that a plurality of fixation darts provided comparable fixation to two bone screws while allowing for faster insertion and damaging less bone. A second objective was to evaluate micro-level stability; a finite element model was created in order to provide a detailed look at the stress state surrounding the fixation darts and the evolution of the fracture gap. Even with relatively weak fixation dart configurations, the fracture gap was maintained below physiological thresholds for bone healing. Most failures of the fixed fractures were attributed to fixation dart pullout from the cancellous structure. The final objective of the study was to characterize this mode of failure with separate fixation dart and screw pullout tests conducted in Sawbones® cancellous foam and fresh porcine cancellous bone. The results showed that the cancellous foam was an acceptable substitute for real bone and provided a conservative estimate of the fixation darts' performance relative to bone screws. A final comparison between experimental and numerically predicted pullout strengths provided confirmation that the model and experiments were consistent.

Targeting HER2-positive cancer with dolastatin 15 derivatives conjugated to trastuzumab, novel antibody-drug conjugates.

PURPOSE: Targeting tubulin binders to cancer cells using antibody-drug conjugates (ADCs) has great potential to become an effective cancer treatment with low normal tissue toxicity. The nature of the linker used to tether the tubulin binder to the antibody and the conjugation sites on the antibody and the small molecule are important factors in the ADC stability and effectiveness. METHODS: We explored the use of tubulin-targeting dolastatin 15 derivatives (Dol15) tethered covalently to a representative antibody, trastuzumab, via cleavable and non-cleavable linkers at varying antibody reactive sites (i.e., lysine residues, partially reduced hinge region disulfide bonds) and drug coupling sites (i.e., C-terminus, N-terminus), to investigate which constructs were more effective in killing HER2-positive cells in vitro and in vivo. RESULTS: We found that Dol15 conjugated to trastuzumab via lysine residues at the drug C-terminus using a non-cleavable linker (trastuzumab-amide-C-term-Dol15) produced target-dependent growth inhibition of cells endogenously expressing high HER2 levels (i.e., SK-BR-3, SK-OV-3) in vitro. This ADC was effective at varying doses (i.e., 10 and 20 mg/kg) in the SK-OV-3 human ovarian cancer xenograft. CONCLUSIONS: Tethering Dol15 via partially reduced disulfide bonds at the drug C-terminus via a non-cleavable linker (trastuzumab-MC-C-term-Dol15) resulted in an equally effective ADC in vitro, showing that site of antibody conjugation did not influence ADC activity. However, tethering Dol15 at the drug N-terminus using non-cleavable and cleavable linkers (trastuzumab-MC-N-term-Dol15 and trastuzumab-MC-VC-PABC-N-term-Dol15, respectively) resulted in ineffective ADCs. Thus, Dol15 tethered at the C-terminus may be a useful tubulin-targeting agent for conjugation at various antibody reactive sites.

SCD1 inhibition causes cancer cell death by depleting mono-unsaturated fatty acids.

Increased metabolism is a requirement for tumor cell proliferation. To understand the dependence of tumor cells on fatty acid metabolism, we evaluated various nodes of the fatty acid synthesis pathway. Using RNAi we have demonstrated that depletion of fatty-acid synthesis pathway enzymes SCD1, FASN, or ACC1 in HCT116 colon cancer cells results in cytotoxicity that is reversible by addition of exogenous fatty acids. This conditional phenotype is most pronounced when SCD1 is depleted. We used this fatty-acid rescue strategy to characterize several small-molecule inhibitors of fatty acid synthesis, including identification of TOFA as a potent SCD1 inhibitor, representing a previously undescribed activity for this compound. Reference FASN and ACC inhibitors show cytotoxicity that is less pronounced than that of TOFA, and fatty-acid rescue profiles consistent with their proposed enzyme targets. Two reference SCD1 inhibitors show low-nanomolar cytotoxicity that is offset by at least two orders of magnitude by exogenous oleate. One of these inhibitors slows growth of HCT116 xenograft tumors. Our data outline an effective strategy for interrogation of on-mechanism potency and pathway-node-specificity of fatty acid synthesis inhibitors, establish an unambiguous link between fatty acid synthesis and cancer cell survival, and point toward SCD1 as a key target in this pathway.

Parallel synthesis and biological evaluation of 837 analogues of procaspase-activating compound 1 (PAC-1).

Procaspase-Activating Compound 1 (PAC-1) is an ortho-hydroxy N-acyl hydrazone that enhances the enzymatic activity of procaspase-3 in vitro and induces apoptosis in cancer cells. An analogue of PAC-1, called S-PAC-1, was evaluated in a veterinary clinical trial in pet dogs with lymphoma and found to have considerable potential as an anticancer agent. With the goal of identifying more potent compounds in this promising class of experimental therapeutics, a combinatorial library based on PAC-1 was created, and the compounds were evaluated for their ability to induce death of cancer cells in culture. For library construction, 31 hydrazides were condensed in parallel with 27 aldehydes to create 837 PAC-1 analogues, with an average purity of 91%. The compounds were evaluated for their ability to induce apoptosis in cancer cells, and through this work, six compounds were discovered to be substantially more potent than PAC-1 and S-PAC-1. These six hits were further evaluated for their ability to relieve zinc-mediated inhibition of procaspase-3 in vitro. In general, the newly identified hit compounds are two- to four-fold more potent than PAC-1 and S-PAC-1 in cell culture, and thus have promise as experimental therapeutics for treatment of the many cancers that have elevated expression levels of procaspase-3.

High speed insertion of bone fracture fixation pins: a finite element penetration model with experimental comparisons.

A new method of bone fracture fixation is considered in which small pins/darts are dynamically inserted into bone to prevent translation and rotation at the fracture site. An ABAQUS model was developed to analyze dart penetration in cortical and cancellous bone for varying dart diameter, material, and velocity, and cortical thickness. The method is advocated for bioresorbable darts, so polylactide (PLA) and magnesium are the materials examined in this study. Numerical results showed that magnesium darts can achieve full penetration in bone while suffering little damage. The PLA darts penetrated thin bone well, but substantial deformation was seen as the cortical thickness increased, especially for small diameter darts. As partial validation, prototype PLA fixation darts were fired into cadaveric bone with a custom nailer. As in the model, the PLA darts could penetrate thin cortices but saw gross deformation when impacted against thicker bone.

Endosialin: a novel malignant cell therapeutic target for neuroblastoma.

Endosialin emerged recently as a potential therapeutic target for sarcoma. Since some sarcoma subtypes, such as Ewing's sarcoma, show characteristics of neuroendocrine differentiation, we wondered whether cancers with neuro-endocrine properties and/or neuroectodermal origin, such as neuroblastoma, small cell lung cancer and melanoma, may express endosialin. Endosialin protein expression was surveyed in neuroblastoma, small cell lung cancer and melanoma in human clinical specimens by immunohistochemistry (IHC) and in human cell lines by flow cytometry. Side population cells were examined to determine whether cancer stem cells can express endosialin. Endosialin-expressing neuroblastoma cell lines were implanted in immunodeficient mice and allowed to grow. The xenograft tumors were resected and tested for endosialin expression by IHC. In human clinical specimens, vascular endosialin staining was observed in neuroblastoma, small cell lung cancer and melanoma. Malignant cell staining was strongest in neuroblastoma, weak in melanoma and rare in small cell lung cancer. In human cell lines, endosialin was detected in neuroblastoma cell lines, including cancer stem cell-like side population (SP) cells, but was absent in melanoma and was both rare and weak in small cell lung cancer. Human neuroblastoma xenograft tumors were found to be positive for endosialin. Our work suggests that endosialin may be a suitable therapeutic target for neuroblastoma.

Endosialin is expressed in high grade and advanced sarcomas: evidence from clinical specimens and preclinical modeling.

We previously surveyed the expression of endosialin/ CD248/TEM-1 by immunohistochemistry in human clinical specimens of sarcomas and documented expression in tumor cells, stromal cells and vasculature. In the present study, we completed a retrospective analysis of the diagnostic reports available for these same samples in order to identify high-grade and metastatic disease. Our results show that endosialin can be detected in advanced disease. We screened human sarcoma cell lines in vitro for endosialin expression and developed preclinical human xenograft models of disseminated sarcoma. We found that 22 out of 42 human sarcoma cell lines were positive for endosialin with a positive correlation between mRNA and protein levels. When implanted in vivo, endosialin was expressed at all sites of dissemination. These data provide clinical and preclinical evidence that endosialin can be detected in advanced sarcoma. These results demonstrate for the first time that endosialin is a suitable therapeutic target for poor prognosis and advanced disease.

Genz-644282, a novel non-camptothecin topoisomerase I inhibitor for cancer treatment.

PURPOSE: Genz-644282 [8,9-dimethoxy-5-(2-N-methylaminoethyl)-2,3-methylenedioxy-5H-dibenzo[c,h][1,6]naphthyridin-6-one] has emerged as a promising candidate for antitumor agents. This report describes the bone marrow colony-forming unit, granulocyte macrophage (CFU-GM) and tumor cell CFU activity of topoisomerase I (Top1) inhibitors, such as Genz-644282, topotecan, irinotecan/SN-38, and ARC-111, and examines their activity in several human tumor xenograft models. EXPERIMENTAL DESIGN: Colony-forming assays were conducted with mouse and human bone marrow and eight human tumor cell lines. In addition, 29 human tumor cell lines representing a range of histology and potential resistance mechanisms were assayed for sensitivity to Genz-644282 in a 72-hour exposure assay. The efficacy of Genz-644282 was compared with standard anticancer drugs (i.e., irinotecan, docetaxel, and dacarbazine) in human tumor xenografts of colon cancer, renal cell carcinoma, non-small cell lung cancer, and melanoma. RESULTS: Human bone marrow CFU-GM was more sensitive to the Top1 inhibitors than was mouse bone marrow CFU-GM. The ratio of mouse to human IC(90) values was more than 10 for the camptothecins and less than 10 for Genz-644282, which had more potency as a cytotoxic agent toward human tumor cells in culture than the camptothecins in the colony-forming and 72-hour proliferation assays. Genz-644282 has superior or equal antitumor activity in the human tumor xenografts than the standard drug comparators. CONCLUSIONS: On the basis of preclinical activity and safety, Genz-644282 was selected for development and is currently undergoing phase 1 clinical trial.

Bone marrow CFU-GM and human tumor xenograft efficacy of three antitumor nucleoside analogs.

Nucleoside analogs are rationally designed anticancer agents that disrupt DNA and RNA synthesis. Fludarabine and cladribine have important roles in the treatment of hematologic malignancies. Clofarabine is a next generation nucleoside analog which is under clinical investigation. The bone marrow toxicity, tumor cell cytotoxicity and human tumor xenograft activity of fludarabine, cladribine and clofarabine were compared. Mouse and human bone marrow were subjected to colony forming (CFU-GM) assays over a 5-log concentration range in culture. NCI-60 cell line screening data were compared. In vivo, a range of clofarabine doses was compared with fludarabine for efficacy in several human tumor xenografts. The IC90 concentrations for fludarabine and cladribine for mouse CFU-GM were >30 and 0.93 microM, and for human CFU-GM were 8 and 0.11 microM, giving mouse to human differentials of >3.8- and 8.5-fold. Clofarabine produced IC90s of 1.7 microM in mouse and 0.51 microM in human CFU-GM, thus a 3.3-fold differential between species. In the NCI-60 cell line screen, fludarabine and cladribine showed selective cytotoxicity toward leukemia cell lines while for clofarabine there was no apparent selectivity based upon origin of the tumor cells. In vivo, clofarabine produced a dose-dependent increase in tumor growth delay in the RL lymphoma, the RPMI-8226 multiple myeloma, and HT-29 colon carcinoma models. The PC3 prostate carcinoma was equally responsive to clofarabine and fludarabine. Bringing together bone marrow toxicity data, tumor cell line cytotoxicity data, and human tumor xenograft efficacy provides valuable information for the translation of preclinical findings to the clinic.

Bone marrow CFU-GM and human tumor xenograft efficacy of three tubulin binding agents.

PURPOSE: The dynamic instability of microtubules in cells is one of the key targets of anticancer therapeutics. Microtubule-disrupting agents such as vinca alkaloids and microtubule-stabilizing agents such as taxanes are important antitumor agents. The bone marrow toxicity and human tumor xenograft activity of three tubulin-binding compounds, vincristine, paclitaxel, and tasidotin were compared. METHODS: Mouse and human bone marrow were subjected to colony-forming (CFU-GM) assays over a 5-log concentration range in culture. In vivo, a range of tasidotin doses was compared with vincristine, paclitaxel, and docetaxel for efficacy in several human tumor xenografts. RESULTS: The IC(90) concentrations for vincristine and paclitaxel for mouse CFU-GM were 30 and 27 nM, and for human CFU-GM were 3 and 9 nM, giving mouse to human differentials of ten- and threefold. Tasidotin produced IC(90)s of >300 nM in mouse and 65 nM in human CFU-GM, thus a >4.6-fold differential between species. In vivo, tasidotin resulted in a dose-dependent increase in tumor growth delay in the RL lymphoma, the RPMI 8226 multiple myeloma, and MX-1 breast carcinoma models. Vincristine and tasidotin were also very effective against these tumors. The PC-3 prostate carcinoma was very responsive to full-dose paclitaxel and docetaxel while tasidotin generated a dose dependent effect. CONCLUSIONS: Bringing together bone marrow toxicity data, pharmacokinetic parameters, and human tumor xenograft efficacy provides valuable information for the translation of preclinical findings to the clinic.

Reinforcement of bone cement using zirconia fibers with and without acrylic coating.

Acrylic (polymethylmethacrylate or PMMA) bone cement was modified by the addition of high-strength zirconia fibers with average lengths of 200 microm and diameters of 15 microm or 30 microm. A novel emulsion polymerization process was developed to encapsulate individual fibers in PMMA. Improvements in tensile and compressive properties as well as in fracture toughness were investigated upon incorporation of uncoated and acrylic coated zirconia fibers. Bone cements were reinforced with 2% by volume of the 15 microm diameter and 5% by volume of the 30 microm fibers. Results indicate that elastic modulus and ultimate strength of bone cements reinforced with zirconia fibers were higher than controls, being the largest for cements reinforced with 30 microm diameter fibers. The fracture toughness of the cement increased by 23% and 41% by the addition of 15 microm and 30 microm fibers, respectively. Coating of individual zirconia fibers did not result in improved material properties of bone cements. The use of uncoated or acrylic coated 30 microm fibers is recommended based on the significant increases in ultimate strength and fracture toughness of the cements.