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Mondal P, Dasgupta S, Pathak T. Carboxymethyl tethered poly(disubstituted)triazoles built on nucleoside skeletons: A unique class of ribonuclease A inhibitors designed using chemical logic. Bioorg Med Chem 2022; 76:117065. [PMID: 36436488 DOI: 10.1016/j.bmc.2022.117065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 09/22/2022] [Accepted: 10/11/2022] [Indexed: 01/05/2023]
Abstract
Molecular docking of N-1,4-disubstituted-1,2,3-triazole tethered carboxymethylated thymidine and uridine with ribonuclease A, indicated their possible binding with the P1, B1 and P2 subsites with varied efficiencies. This theoretical study in combination of our earlier experimental observations was used as the guiding principles for designing a range of 1,4-disubstituted 1, 2, 3- triazole tethered carboxymethylated pyrimidine nucleosides. Triazoles are biologically important molecules and at the same time easily accessible through less complicated synthetic routes as reported about two decades back in the context of "click" reactions. Regioselective propargylation of the nucleosides under controlled conditions followed by the use of CuAAC strategy afforded mono-, bis-, tris- and tetratriazolyl pyrimidine nucleosides. Although the characteristics of nucleosides were lost in these densely functionalized polyheterocycles, the catalytic efficiency of ribonuclease A was significantly reduced by these molecules which were investigated experimentally and by docking studies. Triazoles as linkers helped one or more acidic groups to reach the P1 subsite of ribonuclease A. Enzyme kinetics showed that the efficiency of inhibition reached the highest point with an optimum number of functional groups and were not linearly dependent on the number of triazole tethered carboxymethyl groups. The location of the triazole ring in the molecule affected the efficiency and nature of inhibition which were the result of the overall structure of the modified nucleosides. Thus, the tris-triazolylated thymidine derivative (T-3', 5', N-tris-CH2TzCH2COOH) as opposed to tetra-triazolylated uridine (U-2', 3', 5', N-tetrakis-CH2TzCH2COOH) emerged as the best inhibitor with an inhibition constant value of 2.3 ± 0.05 µM.
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Affiliation(s)
- Pampa Mondal
- 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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Tang Y, Ren F, Cong X, Kong Y, Tian Y, Xu Y, Fan J. Overexpression of ribonuclease inhibitor induces autophagy in human colorectal cancer cells via the Akt/mTOR/ULK1 pathway. Mol Med Rep 2019; 19:3519-3526. [PMID: 30896869 PMCID: PMC6472130 DOI: 10.3892/mmr.2019.10030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 03/06/2019] [Indexed: 12/18/2022] Open
Abstract
Ribonuclease inhibitor (RI), also termed angiogenin inhibitor, acts as the inhibitor of ribonucleolytic activity of RNase A and angiogenin. The expression of RI has been investigated in melanoma and bladder cancer cells. However, the precise role of RI in tumorigenesis, in addition to RI‑induced autophagy, remains poorly understood. In the present study, it was demonstrated that RI positively regulated autophagy in human colorectal cancer (CRC) cells as indicated by an increase in light chain 3 (LC3)‑II levels. Furthermore, RI regulated cell survival in HT29 cells. In addition, autophagy‑associated proteins, including beclin‑1 and autophagy‑related protein 13, were increased in response to RI‑induced autophagy, and the protein kinase B (Akt)/mechanistic target of rapamycin (mTOR)/Unc‑51 like autophagy activating kinase (ULK1) pathway may be involved in the activation of autophagy induced by RI overexpression. Taken together, the evidence of the present study indicated that the overexpression of RI induced ATG‑dependent autophagy in CRC cells via the Akt/mTOR/ULK1 pathway, suggesting that the upregulation of RI activity may constitute a novel approach for the treatment of human colorectal carcinoma.
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Affiliation(s)
- Ying Tang
- Department of Pathology, The Second Affiliated Hospital of Dalian Medical University, Dalian, Liaoning 116023, P.R. China
| | - Feng Ren
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Xi Cong
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Ying Kong
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Yuxiang Tian
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Yuefei Xu
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Jianhui Fan
- Department of Biochemistry and Molecular Biology, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
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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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Zhuang X, Lv M, Zhong Z, Zhang L, Jiang R, Chen J. Interplay between intergrin-linked kinase and ribonuclease inhibitor affects growth and metastasis of bladder cancer through signaling ILK pathways. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2016; 35:130. [PMID: 27576342 PMCID: PMC5006283 DOI: 10.1186/s13046-016-0408-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 08/17/2016] [Indexed: 12/29/2022]
Abstract
Background Integrin-linked kinase (ILK) is a multifunctional adaptor protein which is involved with protein signalling within cells to modulate malignant (cancer) cell movement, cell cycle, metastasis and epithelial–mesenchymal transition (EMT). Our previous experiment demonstrated that ILK siRNA inhibited the growth and induced apoptosis of bladder cancer cells as well as increased the expression of Ribonuclease inhibitor (RI), an important cytoplasmic protein with many functions. We also reported that RI overexpression inhibited ILK and phosphorylation of AKT and GSK3β. ILK and RI gene both locate on chromosome 11p15 and the two genes are always at the adjacent position of same chromosome during evolution, which suggest that ILK and RI could have some relationship. However, underlying interacting mechanisms remain unclear between them. Here, we postulate that RI might regulate ILK signaling pathway via interacting with ILK. Methods Co-immunoprecipitation, GST pull-down and co-localization under laser confocal microscope assay were used to determine the interaction between ILK and RI exogenously and endogenously. Furthermore, we further verified that there is a direct binding between the two proteins by fluorescence resonance energy transfer (FRET) in cells. Next, The effects of interplay between ILK and RI on the key target protein expressions of PI3K/AKT/mTOR signaling pathway were determined by western blot, immunohistochemistry and immunofluorescence assay in vivo and in vitro. Finally, the interaction was assessed using nude mice xenograft model. Results We first found that ILK could combine with RI both in vivo and in vitro by GST pull-down, co-immunoprecipitation (Co-IP) and FRET. The protein levels of ILK and RI revealed a significant inverse correlation in vivo and in vitro. Subsequently, The results showed that up-regulating ILK could increase cell proliferation, change cell morphology and regulate cell cycle. We also demonstrated that the overexpression of ILK remarkably promoted EMT and expressions of target molecules of ILK signaling pathways in vitro and in vivo. Finally, we found that ILK overexpression significantly enhanced growth, metastasis and angiogenesis of xenograft tumor; Whereas, RI has a contrary role compared to ILK in vivo and in vitro. Conclusions Our findings, for the first time, directly proved that the interplay between ILK and RI regulated EMT via ILK/PI3K/AKT signaling pathways for bladder cancer, which highlights the possibilities that ILK/RI could be valuable markers together for the therapy and diagnosis of human carcinoma of urinary bladder.
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Affiliation(s)
- Xiang Zhuang
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, 400016, China
| | - Mengxin Lv
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, 400016, China
| | - Zhenyu Zhong
- The First Clinical College, Chongqing Medical University, Chongqing, 400016, China
| | - Luyu Zhang
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, 400016, China
| | - Rong Jiang
- Laboratory of Stem Cells and Tissue Engineering, Chongqing Medical University, Chongqing, China
| | - Junxia Chen
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, 400016, China.
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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, Bera RK, Jana S, Manna B, Roy D, Anoop A, Raj CR, Pathak T. A Rationally Designed Thymidine-Based Self-Assembled Monolayer on a Gold Electrode for Electroanalytical Applications. Chem Asian J 2015; 10:1554-60. [DOI: 10.1002/asia.201500045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Revised: 04/13/2015] [Indexed: 11/12/2022]
Affiliation(s)
- Dhrubajyoti Datta
- Department of Chemistry; Indian Institute of Technology Kharagpur; Kharagpur 721302 India
| | - Raj Kumar Bera
- Department of Chemistry; Indian Institute of Technology Kharagpur; Kharagpur 721302 India
| | - Saibal Jana
- Department of Chemistry; Indian Institute of Technology Kharagpur; Kharagpur 721302 India
| | - Bhaskar Manna
- Department of Chemistry; Indian Institute of Technology Kharagpur; Kharagpur 721302 India
| | - Debayan Roy
- Department of Chemistry; Indian Institute of Technology Kharagpur; Kharagpur 721302 India
| | - Anakuthil Anoop
- Department of Chemistry; Indian Institute of Technology Kharagpur; Kharagpur 721302 India
| | - C. Retna Raj
- 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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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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Comparison of the ribonucleolytic activity of the dityrosine cross-linked Ribonuclease A dimer with its monomer in the presence of inhibitors. Int J Biol Macromol 2014; 63:107-13. [DOI: 10.1016/j.ijbiomac.2013.10.033] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 10/24/2013] [Indexed: 11/18/2022]
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Datta D, Samanta A, Dasgupta S, Pathak T. Synthesis of 5′-carboxymethylsulfonyl-5′-deoxyribonucleosides under mild hydrolytic conditions: a new class of acidic nucleosides as inhibitors of ribonuclease A. RSC Adv 2014. [DOI: 10.1039/c3ra45084h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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