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Das A, Dasgupta S, Pathak T. Crescent-shaped meta-Substituted Benzene Derivatives as a New Class of Non-Nucleoside Ribonuclease A Inhibitors. Bioorg Med Chem 2022; 71:116888. [DOI: 10.1016/j.bmc.2022.116888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 06/15/2022] [Accepted: 06/15/2022] [Indexed: 11/29/2022]
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Das A, Dasgupta S, Pathak T. Design of configuration-restricted triazolylated β-d-ribofuranosides: a unique family of crescent-shaped RNase A inhibitors. Org Biomol Chem 2020; 18:6340-6356. [PMID: 32766618 DOI: 10.1039/d0ob01286f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Seven new carbohydrate-bistriazole hybrid molecules were designed taking into consideration the crescent shaped active site of ribonuclease A (RNase A). In this case, the β-d-ribofuranose structure was used as the basic building unit; both the C1 and C4 arms protruding out towards the β-face of the tetrahydrofuran moiety of the ribose sugar provided an overall "U" shape to the basic building block. Several combinations of bistriazole moieties were constructed on the two arms of this basic building block. These mono- and/or bis-substituted 1,2,3-triazole units were linked to acidic functional groups because of the overall basic nature of the hydrolytic site of RNase A. All these compounds were efficient competitive inhibitors of RNase A with inhibition constants (Ki) in the micromolar range. In contrast to the carboxylic acid-modified hybrid molecules, molecules carrying sulfonic acids were found to be more potent because of the stronger interactions with the positively charged active site. The most efficient inhibitor of the series was the disulfonic acid-functionalized carbohydrate-bis-triazole hybrid molecule. Docking studies disclosed that the molecule, because of its well defined "U" shape with flexible arms, fits effectively in the active site; moreover, in all cases, besides the acid groups, the triazole and sugar rings also actively participated in creating the hydrogen bonding network in the cavity of the enzyme active site.
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Affiliation(s)
- Ashrukana Das
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721 302, West Bengal, India.
| | - Swagata Dasgupta
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721 302, West Bengal, India.
| | - Tanmaya Pathak
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721 302, West Bengal, India.
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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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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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Chatzileontiadou DSM, Parmenopoulou V, Manta S, Kantsadi AL, Kylindri P, Griniezaki M, Kontopoulou F, Telopoulou A, Prokova H, Panagopoulos D, Boix E, Balatsos NAA, Komiotis D, Leonidas DD. Triazole double-headed ribonucleosides as inhibitors of eosinophil derived neurotoxin. Bioorg Chem 2015; 63:152-65. [PMID: 26551065 DOI: 10.1016/j.bioorg.2015.10.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/26/2015] [Accepted: 10/30/2015] [Indexed: 02/01/2023]
Abstract
Eosinophil derived neurotoxin (EDN) is an eosinophil secretion protein and a member of the Ribonuclease A (RNase A) superfamily involved in the immune response system and inflammatory disorders. The pathological actions of EDN are strongly dependent on the enzymatic activity and therefore, it is of significant interest to discover potent and specific inhibitors of EDN. In this framework we have assessed the inhibitory potency of triazole double-headed ribonucleosides. We present here an efficient method for the heterologous production and purification of EDN together with the synthesis of nucleosides and their biochemical evaluation in RNase A and EDN. Two groups of double-headed nucleosides were synthesized by the attachment of a purine or a pyrimidine base, through a triazole group at the 3'-C position of a pyrimidine or a purine ribonucleoside, respectively. Based on previous data with mononucleosides these compounds were expected to improve the inhibitory potency for RNase A and specificity for EDN. Kinetics data revealed that despite the rational, all but one, double-headed ribonucleosides were less potent than the respective mononucleosides while they were also more specific for ribonuclease A than for EDN. Compound 11c (9-[3'-[4-[(cytosine-1-yl)methyl]-1,2,3-triazol-1-yl]-β-d-ribofuranosyl]adenine) displayed a stronger preference for EDN than for ribonuclease A and a Ki value of 58μM. This is the first time that an inhibitor is reported to have a better potency for EDN than for RNase A. The crystal structure of EDN-11c complex reveals the structural basis of its potency and selectivity providing important guidelines for future structure-based inhibitor design efforts.
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Affiliation(s)
| | - Vanessa Parmenopoulou
- Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Str., 41221 Larissa, Greece
| | - Stella Manta
- Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Str., 41221 Larissa, Greece
| | - Anastassia L Kantsadi
- Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Str., 41221 Larissa, Greece
| | - Paroula Kylindri
- Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Str., 41221 Larissa, Greece
| | - Marianna Griniezaki
- Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Str., 41221 Larissa, Greece
| | - Filitsa Kontopoulou
- Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Str., 41221 Larissa, Greece
| | - Aikaterini Telopoulou
- Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Str., 41221 Larissa, Greece
| | - Helena Prokova
- Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Str., 41221 Larissa, Greece
| | - Dimitrios Panagopoulos
- Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Str., 41221 Larissa, Greece
| | - Ester Boix
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Spain
| | - Nikolaos A A Balatsos
- Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Str., 41221 Larissa, Greece
| | - Dimitri Komiotis
- Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Str., 41221 Larissa, Greece.
| | - Demetres D Leonidas
- Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Str., 41221 Larissa, Greece.
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Chakraborty K, Dasgupta S, Pathak T. Carboxylated acyclonucleosides: synthesis and RNase A inhibition. Molecules 2015; 20:5924-41. [PMID: 25854756 PMCID: PMC6272279 DOI: 10.3390/molecules20045924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 03/20/2015] [Accepted: 03/20/2015] [Indexed: 11/17/2022] Open
Abstract
Strategically designed carboxylated acyclonucleosides have been probed as a new class of RNase A inhibitors. Several experimental and theoretical studies have been performed to compile relevant qualitative and quantitative information regarding the nature and extent of inhibition. The inhibition constant (Ki) values were determined using a UV-based kinetics experiment. The changes in the secondary structure of the enzyme upon binding with the inhibitors were obtained from circular dichroism studies. The binding constants for enzyme-inhibitor interactions were determined with the help of fluorescence spectroscopy. Docking studies were performed to reveal the possible binding sites of the inhibitors within the enzyme. The cytosine analogues were found to possess better inhibitory properties in comparison to the corresponding uracil derivatives. An increment in the number of carboxylic acid groups (-COOH) in the inhibitor backbone was found to result in better inhibition.
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Affiliation(s)
- Kaustav Chakraborty
- 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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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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Debnath J, Dasgupta S, Pathak T. Amino and carboxy functionalized modified nucleosides: a potential class of inhibitors for angiogenin. Bioorg Chem 2013; 52:56-61. [PMID: 24362350 DOI: 10.1016/j.bioorg.2013.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 11/16/2013] [Accepted: 11/19/2013] [Indexed: 10/26/2022]
Abstract
The 3'-amino and carboxy functionalize thymidines execute their ribonucleolytic inhibition activity for angiogenin. These modified nucleosidic molecules inhibit the ribonucleolytic activity of angiogenin in a competitive manner like the other conventional nucleotidic inhibitors, which have been confirmed from kinetic experiments. The improved inhibition constant (Ki) values 427 ± 7, 775 ± 6 μM clearly indicate modified nucleosides are an obvious option for the designing of inhibitors of angiogenesis process. The chorioallantoic membrane (CAM) assay qualitatively suggests that amino functionalized nucleosides have an effective potency to inhibited angiogenin-induced angiogenesis. Docking studies further demonstrate the interaction of their polar amino group with the P1 site residues of angiogenin, i.e., His-13 and His-114 residues.
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Affiliation(s)
- Joy Debnath
- School of Chemical and Biotechnology, SASTRA University, Thanjavur, Tamil Nadu 613401, 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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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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Samanta A, Dasgupta S, Pathak T. 5′-Modified pyrimidine nucleosides as inhibitors of ribonuclease A. Bioorg Med Chem 2011; 19:2478-84. [DOI: 10.1016/j.bmc.2010.08.059] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 08/27/2010] [Accepted: 08/28/2010] [Indexed: 10/19/2022]
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Debnath J, Dasgupta S, Pathak T. Comparative inhibitory activity of 3′- and 5′-functionalized nucleosides on ribonuclease A. Bioorg Med Chem 2010; 18:8257-63. [DOI: 10.1016/j.bmc.2010.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Revised: 10/03/2010] [Accepted: 10/05/2010] [Indexed: 10/19/2022]
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