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Ren R, Wang X, Leas DA, Scheurer C, Hoevel S, Cal M, Chen G, Zhong L, Katneni K, Pham T, Patil R, Sil D, Walters MJ, Schulze TT, Neville AJ, Dong Y, Wittlin S, Kaiser M, Davis PH, Charman SA, Vennerstrom JL. Antimalarial Dibenzannulated Medium-Ring Keto Lactams. ACS Infect Dis 2023; 9:1964-1980. [PMID: 37695781 PMCID: PMC10860121 DOI: 10.1021/acsinfecdis.3c00245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
We discovered dibenzannulated medium-ring keto lactams (11,12-dihydro-5H-dibenzo[b,g]azonine-6,13-diones) as a new antimalarial chemotype. Most of these had chromatographic LogD7.4 values ranging from <0 to 3 and good kinetic solubilities (12.5 to >100 μg/mL at pH 6.5). The more polar compounds in the series (LogD7.4 values of <2) had the best metabolic stability (CLint values of <50 μL/min/mg protein in human liver microsomes). Most of the compounds had relatively low cytotoxicity, with IC50 values >30 μM, and there was no correlation between antiplasmodial activity and cytotoxicity. The four most potent compounds had Plasmodium falciparum IC50 values of 4.2 to 9.4 nM and in vitro selectivity indices of 670 to >12,000. They were more than 4 orders-of-magnitude less potent against three other protozoal pathogens (Trypanosoma brucei rhodesiense, Trypanosoma cruzi, and Leishmania donovani) but did have relatively high potency against Toxoplasma gondii, with IC50 values ranging from 80 to 200 nM. These keto lactams are converted into their poorly soluble 4(1H)-quinolone transannular condensation products in vitro in culture medium and in vivo in mouse blood. The similar antiplasmodial potencies of three keto lactam-quinolone pairs suggest that the quinolones likely contribute to the antimalarial activity of the lactams.
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Affiliation(s)
- Rongguo Ren
- College of Pharmacy, University of Nebraska Medical Center, 986125 Nebraska Medical Center, Omaha, Nebraska 68198-6125, United States
| | - Xiaofang Wang
- College of Pharmacy, University of Nebraska Medical Center, 986125 Nebraska Medical Center, Omaha, Nebraska 68198-6125, United States
| | - Derek A Leas
- College of Pharmacy, University of Nebraska Medical Center, 986125 Nebraska Medical Center, Omaha, Nebraska 68198-6125, United States
| | - Christian Scheurer
- Department of Medical Parasitology and Infection Biology, Swiss Tropical Institute, Kreuzstrasse 2, CH-4123 Allschwil, Switzerland
- University of Basel, CH-4003 Basel, Switzerland
| | - Sarah Hoevel
- Department of Medical Parasitology and Infection Biology, Swiss Tropical Institute, Kreuzstrasse 2, CH-4123 Allschwil, Switzerland
- University of Basel, CH-4003 Basel, Switzerland
| | - Monica Cal
- Department of Medical Parasitology and Infection Biology, Swiss Tropical Institute, Kreuzstrasse 2, CH-4123 Allschwil, Switzerland
- University of Basel, CH-4003 Basel, Switzerland
| | - Gong Chen
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Longjin Zhong
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Kasiram Katneni
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Thao Pham
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Rahul Patil
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Diptesh Sil
- College of Pharmacy, University of Nebraska Medical Center, 986125 Nebraska Medical Center, Omaha, Nebraska 68198-6125, United States
| | - Matthias J Walters
- Department of Biology, University of Nebraska at Omaha, 6001 Dodge St., Omaha, Nebraska 68182, United States
| | - Thomas T Schulze
- Department of Biology, University of Nebraska at Omaha, 6001 Dodge St., Omaha, Nebraska 68182, United States
- Department of Pathology and Microbiology, University of Nebraska Medical Center, 985900 Nebraska Medical Center, Omaha, Nebraska 68198-5900, United States
| | - Andrew J Neville
- Department of Biology, University of Nebraska at Omaha, 6001 Dodge St., Omaha, Nebraska 68182, United States
| | - Yuxiang Dong
- College of Pharmacy, University of Nebraska Medical Center, 986125 Nebraska Medical Center, Omaha, Nebraska 68198-6125, United States
| | - Sergio Wittlin
- Department of Medical Parasitology and Infection Biology, Swiss Tropical Institute, Kreuzstrasse 2, CH-4123 Allschwil, Switzerland
- University of Basel, CH-4003 Basel, Switzerland
| | - Marcel Kaiser
- Department of Medical Parasitology and Infection Biology, Swiss Tropical Institute, Kreuzstrasse 2, CH-4123 Allschwil, Switzerland
- University of Basel, CH-4003 Basel, Switzerland
| | - Paul H Davis
- Department of Biology, University of Nebraska at Omaha, 6001 Dodge St., Omaha, Nebraska 68182, United States
| | - Susan A Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Jonathan L Vennerstrom
- College of Pharmacy, University of Nebraska Medical Center, 986125 Nebraska Medical Center, Omaha, Nebraska 68198-6125, United States
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Schulze TT, Neville AJ, Chapman RC, Davis PH. Mouse splenocyte enrichment strategies via negative selection for broadened single-cell transcriptomics. STAR Protoc 2022; 3:101402. [PMID: 35600930 PMCID: PMC9120244 DOI: 10.1016/j.xpro.2022.101402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Mammalian splenic tissue is rich in functional immune cells, primarily lymphocytes which can mask low-abundance populations in downstream analyses. This protocol enriches minority immune cell populations from mouse spleen via immunomagnetic negative depletion to generate an untouched enriched cell fraction. Enriched cells are then spiked with untouched splenocytes in a controlled repopulation, validated by flow cytometry and results in a single-cell transcriptomic clustering analysis with a broadened cellular landscape.
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Affiliation(s)
- Thomas T. Schulze
- Department of Biology, University of Nebraska at Omaha, Omaha, NE 68182, USA
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68106, USA
| | - Andrew J. Neville
- Department of Biology, University of Nebraska at Omaha, Omaha, NE 68182, USA
| | - Ryan C. Chapman
- Department of Biology, University of Nebraska at Omaha, Omaha, NE 68182, USA
| | - Paul H. Davis
- Department of Biology, University of Nebraska at Omaha, Omaha, NE 68182, USA
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Abstract
Increased technological methods have enabled the investigation of biology at nanoscale levels. Such systems require the use of computational methods to comprehend the complex interactions that occur. The dynamics of metabolic systems have been traditionally described utilizing differential equations without fully capturing the heterogeneity of biological systems. Stochastic modeling approaches have recently emerged with the capacity to incorporate the statistical properties of such systems. However, the processing of stochastic algorithms is a computationally intensive task with intrinsic limitations. Alternatively, the queueing theory approach, historically used in the evaluation of telecommunication networks, can significantly reduce the computational power required to generate simulated results while simultaneously reducing the expansion of errors. We present here the application of queueing theory to simulate stochastic metabolic networks with high efficiency. With the use of glycolysis as a well understood biological model, we demonstrate the power of the proposed modeling methods discussed herein. Furthermore, we describe the simulation and pharmacological inhibition of glycolysis to provide an example of modeling capabilities.
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Affiliation(s)
- Emalie J. Clement
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska, USA
| | - Thomas T. Schulze
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Ghada A. Soliman
- Graduate School of Public Health and Health Policy, City University of New York, New York, USA
| | - Beata J. Wysocki
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska, USA
| | - Paul H. Davis
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska, USA
| | - Tadeusz A. Wysocki
- Department of Electrical and Computer Engineering, University of Nebraska – Lincoln, Omaha, Nebraska, USA
- UTP University, Bydgoszcz, Poland
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Ali JM, Montecinos A, Schulze TT, Allmon LG, Kallenbach AT, Watson GF, Davis PH, Snow DD, Bertin A, Gouin N, Kolok AS. Assessment of Gene Expression Biomarkers in the Chilean Pencil Catfish, Trichomycterus areolatus, from the Choapa River Basin, Coquimbo Chile. Arch Environ Contam Toxicol 2020; 78:137-148. [PMID: 31646361 DOI: 10.1007/s00244-019-00678-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 10/03/2019] [Indexed: 06/10/2023]
Abstract
The objective of this study was to describe changes in the gene expression in the Chilean catfish, Trichomycterus areolatus, based on their geographic location within the Choapa River. Genes of choice included those that are biomarkers of exposure to metals, oxidative stress, and endocrine disruption. Male and female T. areolatus were sampled from four sites in January 2015 differently impacted by human activities. In males, but not females, hepatic gene expression of heat shock protein (HSP70) and cytochrome P450 1A (CYP1A) were significantly elevated at the site adjacent to the small city of Salamanca, relative to the other sites. In females, hepatic HSP70, the aryl hydrocarbon receptor (AHR), and the estrogen responsive genes, vitellogenin (VTG) and estrogen receptor alpha (ERα), were significantly lower at the site located furthest downstream. A similar downstream pattern of lower expression levels also was found in ovarian tissue for the genes, HSP70 and ERα. Gill gene expression showed a unique pattern in females as levels of metallothionein were elevated at the site furthest downstream. While analytical chemistry of water samples provided limited evidence of agrichemical contamination, the gene expression data are consistent with an exposure to agrichemicals and metals. T. areolatus may be a valuable sentinel organism and its use as a bioindicator species in some rivers within Chile can provide considerable insight, particularly in situations analytical chemistry is limited by environmental constraints.
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Affiliation(s)
- Jonathan M Ali
- Department of Environmental, Agricultural and Occupational Health, University of Nebraska - Medical Center, Omaha, NE, 68198-6805, USA
| | - Angela Montecinos
- Departamento de Biología, Universidad de La Serena, Raúl Bitrán 1305, La Serena, Chile
| | - Thomas T Schulze
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, 68182-0040, USA
| | - Luke G Allmon
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, 68182-0040, USA
| | - Alex T Kallenbach
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, 68182-0040, USA
| | - Gabrielle F Watson
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, 68182-0040, USA
| | - Paul H Davis
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, 68182-0040, USA
| | - Daniel D Snow
- School of Natural Resources, University of Nebraska-Lincoln, Lincoln, NE, 68583-0844, USA
| | - Angéline Bertin
- Departamento de Biología, Universidad de La Serena, Raúl Bitrán 1305, La Serena, Chile
| | - Nicolas Gouin
- Departamento de Biología, Universidad de La Serena, Raúl Bitrán 1305, La Serena, Chile
- Centro de Estudios Avanzados en Zonas Aridas (CEAZA), Raúl Bitrán 1305, La Serena, Chile
- Instituto de Investigación Multidisciplinar en Ciencia y Tecnología, Universidad de La Serena, La Serena, Chile
| | - Alan S Kolok
- Idaho Water Resources Research Institute, University of Idaho, 875 Perimeter Drive, MS 3002, Moscow, ID, 83844-3002, USA.
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Won HI, Schulze TT, Clement EJ, Watson GF, Watson SM, Warner RC, Ramler EAM, Witte EJ, Schoenbeck MA, Rauter CM, Davis PH. De novo Assembly of the Burying Beetle Nicrophorus orbicollis (Coleoptera: Silphidae) Transcriptome Across Developmental Stages with Identification of Key Immune Transcripts. J Genomics 2018; 6:41-52. [PMID: 29707046 PMCID: PMC5916875 DOI: 10.7150/jgen.24228] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 03/17/2018] [Indexed: 11/05/2022] Open
Abstract
Burying beetles (Nicrophorus spp.) are among the relatively few insects that provide parental care while not belonging to the eusocial insects such as ants or bees. This behavior incurs energy costs as evidenced by immune deficits and shorter life-spans in reproducing beetles. In the absence of an assembled transcriptome, relatively little is known concerning the molecular biology of these beetles. This work details the assembly and analysis of the Nicrophorus orbicollis transcriptome at multiple developmental stages. RNA-Seq reads were obtained by next-generation sequencing and the transcriptome was assembled using the Trinity assembler. Validation of the assembly was performed by functional characterization using Gene Ontology (GO), Eukaryotic Orthologous Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Differential expression analysis highlights developmental stage-specific expression patterns, and immunity-related transcripts are discussed. The data presented provides a valuable molecular resource to aid further investigation into immunocompetence throughout this organism's sexual development.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Paul H. Davis
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska
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Sanford AG, Schulze TT, Potluri LP, Hemsley RM, Larson JJ, Judge AK, Zach SJ, Wang X, Charman SA, Vennerstrom JL, Davis PH. Novel Toxoplasma gondii inhibitor chemotypes. Parasitol Int 2018; 67:107-111. [PMID: 29081387 DOI: 10.1016/j.parint.2017.10.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 10/24/2017] [Accepted: 10/24/2017] [Indexed: 11/18/2022]
Abstract
We profiled three novel T. gondii inhibitors identified from an antimalarial phenotypic high throughput screen (HTS) campaign: styryl 4-oxo-1,3-benzoxazin-4-one KG3, tetrahydrobenzo[b]pyran KG7, and benzoquinone hydrazone KG8. These compounds inhibit T. gondii in vitro with IC50 values ranging from 0.3 to 2μM, comparable to that of 0.25 to 1.5μM for the control drug pyrimethamine. KG3 had no measurable cytotoxicity against five mammalian cell lines, whereas KG7 and KG8 inhibited the growth of 2 of 5 cell lines with KG8 being the least selective for T. gondii. None of the compounds were mutagenic in an Ames assay. Experimental gLogD7.4 and calculated PSA values for the three compounds were well within the ranges predicted to be favorable for good ADME, even though each compound had relatively low aqueous solubility. All three compounds were metabolically unstable, especially KG3 and KG7. Multiple IP doses of 5mg/kg KG7 and KG8 increased survival in a T. gondii mouse model. Despite their liabilities, we suggest that these compounds are useful starting points for chemical prospecting, scaffold-hopping, and optimization.
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Affiliation(s)
- A G Sanford
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, USA
| | - T T Schulze
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, USA
| | - L P Potluri
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, USA
| | - R M Hemsley
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, USA
| | - J J Larson
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, USA
| | - A K Judge
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, USA
| | - S J Zach
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, USA
| | - X Wang
- College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, USA
| | - S A Charman
- Centre for Drug Candidate Optimization, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - J L Vennerstrom
- College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, USA
| | - P H Davis
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, USA.
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Schulze TT, Ali JM, Bartlett ML, McFarland MM, Clement EJ, Won HI, Sanford AG, Monzingo EB, Martens MC, Hemsley RM, Kumar S, Gouin N, Kolok AS, Davis PH. De novo Assembly and Analysis of the Chilean Pencil Catfish Trichomycterus areolatus Transcriptome. J Genomics 2016; 4:29-41. [PMID: 27672404 PMCID: PMC5033730 DOI: 10.7150/jgen.16885] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Trichomycterus areolatus is an endemic species of pencil catfish that inhabits the riffles and rapids of many freshwater ecosystems of Chile. Despite its unique adaptation to Chile's high gradient watersheds and therefore potential application in the investigation of ecosystem integrity and environmental contamination, relatively little is known regarding the molecular biology of this environmental sentinel. Here, we detail the assembly of the Trichomycterus areolatus transcriptome, a molecular resource for the study of this organism and its molecular response to the environment. RNA-Seq reads were obtained by next-generation sequencing with an Illumina® platform and processed using PRINSEQ. The transcriptome assembly was performed using TRINITY assembler. Transcriptome validation was performed by functional characterization with KOG, KEGG, and GO analyses. Additionally, differential expression analysis highlights sex-specific expression patterns, and a list of endocrine and oxidative stress related transcripts are included.
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Affiliation(s)
- Thomas T Schulze
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska 68182, USA
| | - Jonathan M Ali
- Department of Environmental, Agricultural and Occupational Health, University of Nebraska - Medical Center, Omaha, NE, 68198-6805, United States
| | - Maggie L Bartlett
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska 68182, USA
| | - Madalyn M McFarland
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska 68182, USA
| | - Emalie J Clement
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska 68182, USA
| | - Harim I Won
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska 68182, USA
| | - Austin G Sanford
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska 68182, USA
| | - Elyssa B Monzingo
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska 68182, USA
| | - Matthew C Martens
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska 68182, USA
| | - Ryan M Hemsley
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska 68182, USA
| | - Sidharta Kumar
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska 68182, USA
| | - Nicolas Gouin
- Departamento de Biología, Universidad de La Serena, La Serena, Chile;; Centro de Estudios Avanzados en Zonas Aridas, La Serena, Chile;; Instituto de Investigación Multidisciplinar en Ciencia y Tecnología, Universidad de La Serena, La Serena, Chile
| | - Alan S Kolok
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska 68182, USA;; Center for Environmental Health and Toxicology, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA
| | - Paul H Davis
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska 68182, USA
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