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Khurshid R, Schulz JM, Hu J, Snowden TS, Reynolds RC, Schürer SC. Targeted degrader technologies as prospective SARS-CoV-2 therapies. Drug Discov Today 2024; 29:103847. [PMID: 38029836 PMCID: PMC10836335 DOI: 10.1016/j.drudis.2023.103847] [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] [Received: 09/30/2023] [Revised: 11/10/2023] [Accepted: 11/23/2023] [Indexed: 12/01/2023]
Abstract
COVID-19 remains a severe public health threat despite the WHO declaring an end to the public health emergency in May 2023. Continual development of SARS-CoV-2 variants with resistance to vaccine-induced or natural immunity necessitates constant vigilance as well as new vaccines and therapeutics. Targeted protein degradation (TPD) remains relatively untapped in antiviral drug discovery and holds the promise of attenuating viral resistance development. From a unique structural design perspective, this review covers antiviral degrader merits and challenges by highlighting key coronavirus protein targets and their co-crystal structures, specifically illustrating how TPD strategies can refine existing SARS-CoV-2 3CL protease inhibitors to potentially produce superior protease-degrading agents.
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Affiliation(s)
- Rabia Khurshid
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Joseph M Schulz
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Jiaming Hu
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Timothy S Snowden
- The University of Alabama, Department of Chemistry and Biochemistry and Center for Convergent Bioscience and Medicine, 250 Hackberry Lane, Tuscaloosa, AL 35487-0336, USA
| | - Robert C Reynolds
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35205, USA
| | - Stephan C Schürer
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; Institute for Data Science & Computing, University of Miami, Coral Gables, FL 33146, USA.
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Gibbons GS, Chakraborty A, Grigsby SM, Umeano AC, Liao C, Moukha-Chafiq O, Pathak V, Mathew B, Lee YT, Dou Y, Schürer SC, Reynolds RC, Snowden TS, Nikolovska-Coleska Z. Identification of DOT1L inhibitors by structure-based virtual screening adapted from a nucleoside-focused library. Eur J Med Chem 2020; 189:112023. [PMID: 31978781 DOI: 10.1016/j.ejmech.2019.112023] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/27/2019] [Accepted: 12/29/2019] [Indexed: 02/07/2023]
Abstract
Disruptor of Telomeric Silencing 1-Like (DOT1L), the sole histone H3 lysine 79 (H3K79) methyltransferase, is required for leukemogenic transformation in a subset of leukemias bearing chromosomal translocations of the Mixed Lineage Leukemia (MLL) gene, as well as other cancers. Thus, DOT1L is an attractive therapeutic target and discovery of small molecule inhibitors remain of high interest. Herein, we are presenting screening results for a unique focused library of 1200 nucleoside analogs originally produced under the aegis of the NIH Pilot Scale Library Program. The complete nucleoside set was screened virtually against DOT1L, resulting in 210 putative hits. In vitro screening of the virtual hits resulted in validation of 11 compounds as DOT1L inhibitors clustered into two distinct chemical classes, adenosine-based inhibitors and a new chemotype that lacks adenosine. Based on the developed DOT1L ligand binding model, a structure-based design strategy was applied and a second-generation of non-nucleoside DOT1L inhibitors was developed. Newly synthesized compound 25 was the most potent DOT1L inhibitor in the new series with an IC50 of 1.0 μM, showing 40-fold improvement in comparison with hit 9 and exhibiting reasonable on target effects in a DOT1L dependent murine cell line. These compounds represent novel chemical probes with a unique non-nucleoside scaffold that bind and compete with the SAM binding site of DOT1L, thus providing foundation for further medicinal chemistry efforts to develop more potent compounds.
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Affiliation(s)
- Garrett S Gibbons
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA; Molecular and Cellular Pathology Graduate Program, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Amarraj Chakraborty
- Department of Chemistry and Biochemistry, The University of Alabama, 250 Hackberry Lane, Tuscaloosa, AL, 35487, USA
| | - Sierrah M Grigsby
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA; Molecular and Cellular Pathology Graduate Program, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Afoma C Umeano
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
| | - Chenzhong Liao
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Omar Moukha-Chafiq
- Southern Research Institute, Drug Discovery Division, Birmingham, AL, 35205, USA
| | - Vibha Pathak
- Southern Research Institute, Drug Discovery Division, Birmingham, AL, 35205, USA
| | - Bini Mathew
- Southern Research Institute, Drug Discovery Division, Birmingham, AL, 35205, USA
| | - Young-Tae Lee
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Yali Dou
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Stephan C Schürer
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA; Center for Computational Science, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA; Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
| | - Robert C Reynolds
- Division of Hematology and Oncology, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Timothy S Snowden
- Department of Chemistry and Biochemistry, The University of Alabama, 250 Hackberry Lane, Tuscaloosa, AL, 35487, USA.
| | - Zaneta Nikolovska-Coleska
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA; Molecular and Cellular Pathology Graduate Program, University of Michigan Medical School, Ann Arbor, MI, 48109, USA; Rogel Cancer Center at University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
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Moukha-Chafiq O, Reynolds RC, Wilson JC, Snowden TS. Parallel Solution Phase Synthesis and Preliminary Biological Activity of a 5'-Substituted Cytidine Analog Library. ACS Comb Sci 2019; 21:628-634. [PMID: 31365223 DOI: 10.1021/acscombsci.9b00072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A 109-membered library of 5'-substituted cytidine analogs was synthesized, via funding through the NIH Roadmap Initiative and the Pilot Scale Library (PSL) Program. Reaction core compounds contained -NH2 (2) and -COOH (44 and 93) groups that were coupled to a diversity of reactants in a parallel, solution phase format to produce the target library. The assorted reactants included -NH2, -CHO, -SO2Cl, and -COOH functional groups, and condensation with the intermediate core materials 2 and 44 followed by acidic hydrolysis produced 3-91 in good yields and high purity. Linkage of the amino terminus of d-phenylalanine methyl ester to the free 5'-COOH of 44 and NaOH treatment led to core library -COOH precursor 93. In a libraries from libraries approach, compound 93 served as the vital building block for our unique library of dipeptidyl cytidine analogs 94-114 through amide coupling of the -COOH group with numerous commercial amines followed by acidic deprotection. Initial screening of the complete final library through the MLPCN program revealed a modest number of hits over diverse biological processes. These hits might be considered as starting points for hit-to-lead optimization and development studies.
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Affiliation(s)
- Omar Moukha-Chafiq
- Chemistry Department, Drug Discovery Division, Southern Research, 2000 Ninth Avenue South, Birmingham, Alabama 35205, United States
| | - Robert C. Reynolds
- Department of Medicine, Division of Hematology and Oncology, University of Alabama at Birmingham, NP 2540 J, 1720 Second Avenue South, Birmingham, Alabama 35294-3300, United States
| | - Jacob C. Wilson
- Department of Chemistry and Biochemistry, The University of Alabama, 250 Hackberry Lane, Tuscaloosa, Alabama 35487-0336, United States
| | - Timothy S. Snowden
- Department of Chemistry and Biochemistry, The University of Alabama, 250 Hackberry Lane, Tuscaloosa, Alabama 35487-0336, United States
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Mathew B, Snowden TS, Connelly MC, Guy RK, Reynolds RC. A small diversity library of α-methyl amide analogs of sulindac for probing anticancer structure-activity relationships. Bioorg Med Chem Lett 2018; 28:2136-2142. [PMID: 29776741 DOI: 10.1016/j.bmcl.2018.05.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/06/2018] [Accepted: 05/09/2018] [Indexed: 12/21/2022]
Abstract
Non-steroidal anti-inflammatory drugs (NSAIDs) have a variety of potential indications that include management of pain and inflammation as well as chemoprevention and/or treatment of cancer. Furthermore, a specific form of ibuprofen, dexibuprofen or the S-(+) form, shows interesting neurological activities and has been proposed for the treatment of Alzheimer's disease. In a continuation of our work probing the anticancer activity of small sulindac libraries, we have prepared and screened a small diversity library of α-methyl substituted sulindac amides in the profen class. Several compounds of this series displayed promising activity compared with a lead sulindac analog.
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Affiliation(s)
- Bini Mathew
- Drug Discovery Division, Southern Research Institute, 2000 Ninth Avenue South, Birmingham, AL 35205, USA
| | - Timothy S Snowden
- Department of Chemistry and Biochemistry, The University of Alabama, 250 Hackberry Lane, Tuscaloosa, AL 35487, USA
| | - Michele C Connelly
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Mailstop 1000, Memphis, TN 38105-3678, USA
| | - R Kiplin Guy
- The University of Kentucky College of Pharmacy, 214H BioPharm Complex, Lexington, KY 40536-0596, USA
| | - Robert C Reynolds
- Division of Hematology and Oncology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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Li Z, Gupta MK, Snowden TS. One-Carbon Homologation of Primary Alcohols and the Reductive Homologation of Aldehydes Involving a Jocic-Type Reaction. European J Org Chem 2015. [DOI: 10.1002/ejoc.201501089] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Bhattarai BT, Adhikari S, Kimball EA, Moore JN, Shaughnessy KH, Snowden TS, Fronczek FR, Dolliver DD. Palladium-catalyzed ortho-halogenation of diaryl oxime ethers. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.06.080] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Affiliation(s)
- Manoj K. Gupta
- Department of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Zhexi Li
- Department of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Timothy S. Snowden
- Department of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336, United States
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Dolliver DD, Bhattarai BT, Pandey A, Lanier ML, Bordelon AS, Adhikari S, Dinser JA, Flowers PF, Wills VS, Schneider CL, Shaughnessy KH, Moore JN, Raders SM, Snowden TS, McKim AS, Fronczek FR. Stereospecific Suzuki, Sonogashira, and Negishi Coupling Reactions of N-Alkoxyimidoyl Iodides and Bromides. J Org Chem 2013; 78:3676-87. [DOI: 10.1021/jo400179u] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Debra D. Dolliver
- Department of Chemistry and Physics, Southeastern Louisiana University, SLU 10878, Hammond, Louisiana
70402, United States
| | - Bijay T. Bhattarai
- Department of Chemistry and Physics, Southeastern Louisiana University, SLU 10878, Hammond, Louisiana
70402, United States
| | - Arjun Pandey
- Department of Chemistry and Physics, Southeastern Louisiana University, SLU 10878, Hammond, Louisiana
70402, United States
| | - Megan L. Lanier
- Department of Chemistry and Physics, Southeastern Louisiana University, SLU 10878, Hammond, Louisiana
70402, United States
| | - Amber S. Bordelon
- Department of Chemistry and Physics, Southeastern Louisiana University, SLU 10878, Hammond, Louisiana
70402, United States
| | - Sarju Adhikari
- Department of Chemistry and Physics, Southeastern Louisiana University, SLU 10878, Hammond, Louisiana
70402, United States
| | - Jordan A. Dinser
- Department of Chemistry and Physics, Southeastern Louisiana University, SLU 10878, Hammond, Louisiana
70402, United States
| | - Patrick F. Flowers
- Department of Chemistry and Physics, Southeastern Louisiana University, SLU 10878, Hammond, Louisiana
70402, United States
| | - Veronica S. Wills
- Department of Chemistry and Physics, Southeastern Louisiana University, SLU 10878, Hammond, Louisiana
70402, United States
| | - Caroline L. Schneider
- Department of Chemistry and Physics, Southeastern Louisiana University, SLU 10878, Hammond, Louisiana
70402, United States
| | - Kevin H. Shaughnessy
- Department of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336,
United States
| | - Jane N. Moore
- Department of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336,
United States
| | - Steven M. Raders
- Department of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336,
United States
| | - Timothy S. Snowden
- Department of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336,
United States
| | - Artie S. McKim
- Gaylord Chemical Company, 106 Galaria
Blvd., Slidell, Louisiana 70459-1209, United States
| | - Frank R. Fronczek
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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Ganta A, Shamshina JL, Cafiero LR, Snowden TS. Stereoselective synthesis of cis- or trans-2,4-disubstituted butyrolactones from Wynberg lactone. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.04.107] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Affiliation(s)
- Manoj K. Gupta
- Department of Chemistry, The University of Alabama, P.O. Box 870336, Tuscaloosa, Alabama 35487-0336,
United States
| | - Zhexi Li
- Department of Chemistry, The University of Alabama, P.O. Box 870336, Tuscaloosa, Alabama 35487-0336,
United States
| | - Timothy S. Snowden
- Department of Chemistry, The University of Alabama, P.O. Box 870336, Tuscaloosa, Alabama 35487-0336,
United States
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Ganta A, Snowden TS. Carbocupration−Functionalization of Arynes: Rapid Access to Variably Ortho-Substituted ((E)-3-Phenylprop-1-enyl)silanes. Org Lett 2008; 10:5103-6. [DOI: 10.1021/ol8021885] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ashok Ganta
- Department of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336
| | - Timothy S. Snowden
- Department of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336
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Affiliation(s)
- Lauren R. Cafiero
- Department of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336
| | - Timothy S. Snowden
- Department of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336
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Cafiero LR, Snowden TS. tert-Butyldimethylsilyloxytrichloromethylmethane—readily accessible and robust protecting group for (hetero)aryl aldehydes. Tetrahedron Lett 2008. [DOI: 10.1016/j.tetlet.2008.02.072] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
The reaction of alkenyl trichloromethyl carbinols with various nucleophiles under protic basic conditions reveals that mercaptans participate by alpha-substitution (S(N)2) of the intermediate alkenyl gem-dichloroepoxides. Conversely, hydroxide results in preferential gamma-substitution with stereoselective allylic transposition (S(N)2'). Regioselectivity with alkoxides depends upon the level of alkene substitution. [reaction: see text]
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Affiliation(s)
- Julia L Shamshina
- Department of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, AL 34587-0336, USA
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Zhong Z, Snowden TS, Best MD, Anslyn EV. Rate of Enolate Formation Is Not Very Sensitive to the Hydrogen Bonding Ability of Donors to Carboxyl Oxygen Lone Pair Acceptors; A Ramification of the Principle of Non-Perfect Synchronization for General-Base-Catalyzed Enolate Formation. J Am Chem Soc 2004; 126:3488-95. [PMID: 15025476 DOI: 10.1021/ja0306011] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Two series of structures (1 and 2) possessing intramolecular hydrogen bonds to the lone-pair electrons of carbonyl oxygens have been examined to reveal the influence of the pK(a) of the hydrogen-bond donor on the rate of general-base-catalyzed enolate formation. The geometry of the hydrogen bonds is well accepted to be appropriate for intramolecular hydrogen-bond formation. Yet, as revealed by Brønsted plots, both series show very little dependence of the rate of enolate formation on the hydrogen-bond donor ability. The intramolecular hydrogen bonds give rate enhancements only on the order of 10-100-fold, and corrected Brønsted alpha-values are slightly below 0.1. The results can be understood by interpreting them in light of the Principle of Non-Perfect Synchronization. The results are consistent with the proton transfer occurring through an asynchronous transition state with the developing negative charge localized on carbon. We postulate that catalysts of enolate formation will be most effective if the binding groups are focused on stabilizing negative charge that is forming on the enolate carbon rather than on the enolate oxygen.
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Affiliation(s)
- Zhenlin Zhong
- Department of Chemistry and Biochemistry, 1 University Station, A5300, The University of Texas at Austin, Austin, Texas 78712, USA
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Abstract
Abiotic receptors used to enolize carbonyl compounds or to shift substrate pK(a) values are reviewed. These systems exhibit disparate frameworks and several approaches to binding and anion stabilization. Detailed emphasis is placed on a bicyclic cyclophane that induces pK(a) shifts in active methylene compounds through NH-pi hydrogen bonding with the resultant enolates.
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Affiliation(s)
- T S Snowden
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, TX 78712, USA
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Abstract
Important contributions to the field of anion sensing include electrochemical lipophilic uranyl salophene receptors incorporated into membranes that act as fluoride-selective potentiometric microsensors. A promising optical-based sensor, selective for cyclic AMP, involves a preorganized, molecularly imprinted polymer employing an intrinsic fluorophore. Competition methods using ensembles of recognition units and external indicators have been used to sense citrate in highly competitive media and micromolar concentrations of inositol(tris)phosphate in water. In addition, DNA dendrimers immobilized on a quartz-crystal microbalance acted as an elegant biosensor for Cryptosporidium DNA. These designs display the varied methods of anion detection currently being pursued.
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Affiliation(s)
- T S Snowden
- Department of Chemistry and Biochemistry, University of Texas at Austin, TX 78712, USA
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Affiliation(s)
- Timothy S. Snowden
- The Department of Chemistry and Biochemistry The University of Texas at Austin Austin, Texas 78712
| | - Adrian P. Bisson
- The Department of Chemistry and Biochemistry The University of Texas at Austin Austin, Texas 78712
| | - Eric V. Anslyn
- The Department of Chemistry and Biochemistry The University of Texas at Austin Austin, Texas 78712
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