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Datta D, Dasgupta S, Pathak T. Sulfonic nucleic acids (SNAs): a new class of substrate mimics for ribonuclease A inhibition. Org Biomol Chem 2019; 17:7215-7221. [PMID: 31322157 DOI: 10.1039/c9ob01250h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sulfonic nucleic acids were identified as inhibitors of ribonuclease A (RNase A). The incorporation of a strongly acidic group (sulfonic, -SO3H) at the 3'-end of pyrimidine nucleosides thymidine and uridine was prompted by the low inhibition constant (Ki) values recorded for carboxymethylsulfonyl (-SO2CH2CO2H) and -CO2H functionalized nucleosides. It was envisaged that the sulfonic acid-modified pyrimidines would bind effectively with the positively charged P1 site of ribonuclease A. Typical harsh conditions used for SO3H incorporation were replaced with milder reaction conditions. The uridine analogue showing a Ki value of 0.96 μM elicited a better result than the thymidine-modified inhibitor. Notably, it was also the best result among all modified non-phosphate acidic nucleosides reported and screened so far as RNase A inhibitors.
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Affiliation(s)
- Dhrubajyoti Datta
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
| | - Swagata Dasgupta
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
| | - Tanmaya Pathak
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
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Hoang TT, Tanrikulu IC, Vatland QA, Hoang TM, Raines RT. A Human Ribonuclease Variant and ERK-Pathway Inhibitors Exhibit Highly Synergistic Toxicity for Cancer Cells. Mol Cancer Ther 2018; 17:2622-2632. [PMID: 30282811 DOI: 10.1158/1535-7163.mct-18-0724] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 08/15/2018] [Accepted: 09/27/2018] [Indexed: 12/20/2022]
Abstract
Pancreatic-type ribonucleases (ptRNases) are prevalent secretory enzymes that catalyze the cleavage of RNA. Ribonuclease inhibitor (RI) is a cytosolic protein that has femtomolar affinity for ptRNases, affording protection from the toxic catalytic activity of ptRNases, which can invade human cells. A human ptRNase variant that is resistant to inhibition by RI is a cytotoxin that is undergoing a clinical trial as a cancer chemotherapeutic agent. We find that the ptRNase and protein kinases in the ERK pathway exhibit strongly synergistic toxicity toward lung cancer cells (including a KRASG12C variant) and melanoma cells (including BRAFV600E variants). The synergism arises from inhibiting the phosphorylation of RI and thereby diminishing its affinity for the ptRNase. These findings link seemingly unrelated cellular processes, and suggest that the use of a kinase inhibitor to unleash a cytotoxic enzyme could lead to beneficial manifestations in the clinic.
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Affiliation(s)
- Trish T Hoang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin
| | - I Caglar Tanrikulu
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Quinn A Vatland
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin
| | - Trieu M Hoang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin
| | - Ronald T Raines
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin. .,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin
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Kayet A, Datta D, Das A, Dasgupta S, Pathak T. 1,5-Disubstituted 1,2,3-triazole linked disaccharides: Metal-free syntheses and screening of a new class of ribonuclease A inhibitors. Bioorg Med Chem 2018; 26:455-462. [DOI: 10.1016/j.bmc.2017.12.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 11/28/2017] [Accepted: 12/02/2017] [Indexed: 10/18/2022]
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Datta D, Mondal P, Dasgupta S, Pathak T. Acidic-Amino-Acid-Conjugated Dinucleosides as Ribonuclease A Inhibitors: Rational Design and Effect of Backbone Chirality on Enzyme Inhibition. ChemistrySelect 2017. [DOI: 10.1002/slct.201700253] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Dhrubajyoti Datta
- Department of Chemistry; Indian Institute of Technology Kharagpur (IIT Kharagpur); Kharagpur 721302 India
| | - Pampa Mondal
- Department of Chemistry; Indian Institute of Technology Kharagpur (IIT Kharagpur); Kharagpur 721302 India
| | - Swagata Dasgupta
- Department of Chemistry; Indian Institute of Technology Kharagpur (IIT Kharagpur); Kharagpur 721302 India
| | - Tanmaya Pathak
- Department of Chemistry; Indian Institute of Technology Kharagpur (IIT Kharagpur); Kharagpur 721302 India
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Winton VJ, Aldrich C, Kiessling LL. Carboxylate Surrogates Enhance the Antimycobacterial Activity of UDP-Galactopyranose Mutase Probes. ACS Infect Dis 2016; 2:538-43. [PMID: 27626294 DOI: 10.1021/acsinfecdis.6b00021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Uridine diphosphate galactopyranose mutase (UGM also known as Glf) is a biosynthetic enzyme required for construction of the galactan, an essential mycobacterial cell envelope polysaccharide. Our group previously identified two distinct classes of UGM inhibitors; each possesses a carboxylate moiety that is crucial for potency yet likely detrimental for cell permeability. To enhance the antimycobacterial potency, we sought to replace the carboxylate with a functional group mimic-an N-acylsulfonamide group. We therefore synthesized a series of N-acylsulfonamide analogs and tested their ability to inhibit UGM. For each inhibitor scaffold tested, the N-acylsulfonamide group functions as an effective carboxylate surrogate. Although the carboxylates and their surrogates show similar activity against UGM in a test tube, several N-acylsulfonamide derivatives more effectively block the growth of Mycobacterium smegmatis. These data suggest that the replacement of a carboxylate with an N-acylsulfonamide group could serve as a general strategy to augment antimycobacterial activity.
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Affiliation(s)
- Valerie J. Winton
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706-1322, United States
| | - Claudia Aldrich
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706-1322, United States
| | - Laura L. Kiessling
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706-1322, United States
- Department
of Biochemistry, University of Wisconsin—Madison, 433 Babcock Drive, Madison, Wisconsin 53706-1544, United States
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Datta D, Dasgupta S, Pathak T. Carboxymethylsulfonylated Ribopyrimidines: Rational Design of Ribonuclease A Inhibitors Employing Chemical Logic. ChemMedChem 2016; 11:620-8. [PMID: 26945688 DOI: 10.1002/cmdc.201600007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Indexed: 11/11/2022]
Abstract
Hydrolysis of RNA by ribonuclease A crucially depends on the participation of the 2'-OH group as well as the positioning of the internucleotide bond at two different sites of the enzyme. Therefore, ribopyrimidines were modified with -SO2CH2CO2H, an acidic functional group, which was expected to interact with the phosphate binding site. These ribonucleosides were designed to understand the influence of the 2'-OH group of these inhibitors on ribonuclease A inhibition along with the effect of the -SO2CH2CO2H group. The "down" configuration of the 2'-OH group enhanced the inhibitory properties (Ki =1.75 μm) and also imparted important Val43 H-bonding with the furanose oxygen atom of the inhibitors. One of the most important aspects of this work is that there was no serendipitous discovery of the inhibitors. The inhibitors reported in this manuscript were obtained by design by employing chemical logic.
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Affiliation(s)
- Dhrubajyoti Datta
- Department of Chemistry, Indian Institute of Technology (IIT)-Kharagpur, Kharagpur, 721302, India
| | - Swagata Dasgupta
- Department of Chemistry, Indian Institute of Technology (IIT)-Kharagpur, Kharagpur, 721302, India.
| | - Tanmaya Pathak
- Department of Chemistry, Indian Institute of Technology (IIT)-Kharagpur, Kharagpur, 721302, India.
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Datta D, Dasgupta S, Pathak T. Ribonuclease A inhibition by carboxymethylsulfonyl-modified xylo- and arabinopyrimidines. ChemMedChem 2014; 9:2138-49. [PMID: 25125220 DOI: 10.1002/cmdc.201402179] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Indexed: 11/10/2022]
Abstract
A group of acidic nucleosides were synthesized to develop a new class of ribonuclease A (RNase A) inhibitors. Our recent study on carboxymethylsulfonyl-modified nucleosides revealed some interesting results in RNase A inhibition. This positive outcome triggered an investigation of the role played by secondary sugar hydroxy groups in inhibiting RNase A activity. Uridines and cytidines modified with SO2 CH2 COOH groups at the 2'- and 3'-positions show good inhibitory properties with low inhibition constant (Ki ) values in the range of 109-17 μM. The present work resulted in a set of inhibitors that undergo more effective interactions with the RNase A active site, as visualized by docking studies.
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Affiliation(s)
- Dhrubajyoti Datta
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur (India), Fax: (+91) 3222-255303
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Datta D, Samanta A, Dasgupta S, Pathak T. 3′-Oxo-, amino-, thio- and sulfone-acetic acid modified thymidines: Effect of increased acidity on ribonuclease A inhibition. Bioorg Med Chem 2013; 21:4634-45. [DOI: 10.1016/j.bmc.2013.05.047] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 05/13/2013] [Accepted: 05/14/2013] [Indexed: 01/13/2023]
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Triazole pyrimidine nucleosides as inhibitors of Ribonuclease A. Synthesis, biochemical, and structural evaluation. Bioorg Med Chem 2012; 20:7184-93. [DOI: 10.1016/j.bmc.2012.09.067] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 09/21/2012] [Accepted: 09/24/2012] [Indexed: 11/22/2022]
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Debnath J, Dasgupta S, Pathak T. Dinucleosides with Non-Natural Backbones: A New Class of Ribonuclease A and Angiogenin Inhibitors. Chemistry 2012; 18:1618-27. [DOI: 10.1002/chem.201102816] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Indexed: 11/11/2022]
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