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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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Lu L, Li J, Wei R, Guidi I, Cozzuto L, Ponomarenko J, Prats-Ejarque G, Boix E. Selective cleavage of ncRNA and antiviral activity by RNase2/EDN in THP1-induced macrophages. Cell Mol Life Sci 2022; 79:209. [PMID: 35347428 PMCID: PMC8960563 DOI: 10.1007/s00018-022-04229-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 02/21/2022] [Accepted: 03/03/2022] [Indexed: 12/11/2022]
Abstract
AbstractRNase2 is the member of the RNaseA family most abundant in macrophages. Here, we knocked out RNase2 in THP-1 cells and analysed the response to Respiratory Syncytial Virus (RSV). RSV induced RNase2 expression, which significantly enhanced cell survival. Next, by cP-RNAseq sequencing, which amplifies the cyclic-phosphate endonuclease products, we analysed the ncRNA population. Among the ncRNAs accumulated in WT vs KO cells, we found mostly tRNA-derived fragments (tRFs) and second miRNAs. Differential sequence coverage identified tRFs from only few parental tRNAs, revealing a predominant cleavage at anticodon and d-loops at U/C (B1) and A (B2) sites. Selective tRNA cleavage was confirmed in vitro using the recombinant protein. Likewise, only few miRNAs were significantly more abundant in WT vs RNase2-KO cells. Complementarily, by screening of a tRF & tiRNA array, we identified an enriched population associated to RNase2 expression and RSV exposure. The results confirm the protein antiviral action and provide the first evidence of its cleavage selectivity on ncRNAs.
Graphical abstract
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Affiliation(s)
- Lu Lu
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China.
| | - Jiarui Li
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Ranlei Wei
- National Frontier Center of Disease Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Irene Guidi
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Luca Cozzuto
- Bioinformatic Unit, Centre de Regulació Genòmica (CRG), Barcelona, Spain
| | - Julia Ponomarenko
- Bioinformatic Unit, Centre de Regulació Genòmica (CRG), Barcelona, Spain
| | - Guillem Prats-Ejarque
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Ester Boix
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.
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Shepard SM, Windsor IW, Raines RT, Cummins CC. Nucleoside Tetra- and Pentaphosphates Prepared Using a Tetraphosphorylation Reagent Are Potent Inhibitors of Ribonuclease A. J Am Chem Soc 2019; 141:18400-18404. [PMID: 31651164 DOI: 10.1021/jacs.9b09760] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Adenosine and uridine 5'-tetra- and 5'-pentaphosphates were synthesized from an activated tetrametaphosphate ([PPN]2[P4O11], [PPN]2[1], PPN = bis(triphenylphosphine)iminium) and subsequently tested for inhibition of the enzymatic activity of ribonuclease A (RNase A). Reagent [PPN]2[1] reacts with unprotected uridine and adenosine in the presence of a base under anhydrous conditions to give nucleoside tetrametaphosphates. Ring opening of these intermediates with tetrabutylammonium hydroxide ([TBA][OH]) yields adenosine and uridine tetraphosphates (p4A, p4U) in 92% and 85% yields, respectively, from the starting nucleoside. Treatment of ([PPN]2[1]) with AMP or UMP yields nucleoside-monophosphate tetrametaphosphates (cp4pA, cp4pU) having limited aqueous stability. Ring opening of these ultraphosphates with [TBA][OH] yields p5A and p5U in 58% and 70% yield from AMP and UMP, respectively. We characterized inorganic and nucleoside-conjugated linear and cyclic oligophosphates as competitive inhibitors of RNase A. Increasing the chain length in both linear and cyclic inorganic oligophosphates resulted in improved binding affinity. Increasing the length of oligophosphates on the 5' position of adenosine beyond three had a deleterious effect on binding. Conversely, uridine nucleotides bearing 5' oligophosphates saw progressive increases in binding with chain length. We solved X-ray cocrystal structures of the highest affinity binders from several classes. The terminal phosphate of p5A binds in the P1 enzymic subsite and forces the oligophosphate to adopt a convoluted conformation, while the oligophosphate of p5U binds in several extended conformations, targeting multiple cationic regions of the active-site cleft.
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Affiliation(s)
- Scott M Shepard
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge Massachusetts 02139 , United States
| | - Ian W Windsor
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge Massachusetts 02139 , United States
| | - Ronald T Raines
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge Massachusetts 02139 , United States
| | - Christopher C Cummins
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge Massachusetts 02139 , United States
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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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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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Bakan A, Dutta A, Mao W, Liu Y, Chennubhotla C, Lezon TR, Bahar I. Evol and ProDy for bridging protein sequence evolution and structural dynamics. Bioinformatics 2014; 30:2681-3. [PMID: 24849577 DOI: 10.1093/bioinformatics/btu336] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
UNLABELLED Correlations between sequence evolution and structural dynamics are of utmost importance in understanding the molecular mechanisms of function and their evolution. We have integrated Evol, a new package for fast and efficient comparative analysis of evolutionary patterns and conformational dynamics, into ProDy, a computational toolbox designed for inferring protein dynamics from experimental and theoretical data. Using information-theoretic approaches, Evol coanalyzes conservation and coevolution profiles extracted from multiple sequence alignments of protein families with their inferred dynamics. AVAILABILITY AND IMPLEMENTATION ProDy and Evol are open-source and freely available under MIT License from http://prody.csb.pitt.edu/.
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Affiliation(s)
- Ahmet Bakan
- Department of Computational and Systems Biology, and Clinical & Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Anindita Dutta
- Department of Computational and Systems Biology, and Clinical & Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Wenzhi Mao
- Department of Computational and Systems Biology, and Clinical & Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Ying Liu
- Department of Computational and Systems Biology, and Clinical & Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Chakra Chennubhotla
- Department of Computational and Systems Biology, and Clinical & Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Timothy R Lezon
- Department of Computational and Systems Biology, and Clinical & Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Ivet Bahar
- Department of Computational and Systems Biology, and Clinical & Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
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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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Thiyagarajan N, Smith BD, Raines RT, Acharya KR. Functional and structural analyses of N-acylsulfonamide-linked dinucleoside inhibitors of RNase A. FEBS J 2011; 278:541-9. [PMID: 21205197 PMCID: PMC3039443 DOI: 10.1111/j.1742-4658.2010.07976.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Molecular probes are useful for both studying and controlling the functions of enzymes and other proteins. The most useful probes have high affinity for their target, along with small size and resistance to degradation. Here, we report on new surrogates for nucleic acids that fulfill these criteria. Isosteres in which phosphoryl [R–O–P(O2−)–O–R′] groups are replaced with N-acylsulfonamidyl [R–C(O)–N−–S(O2)–R′] or sulfonimidyl [R–S(O2)–N−–S(O2)–R′] groups increase the number of nonbridging oxygens from two (phosphoryl) to three (N-acylsulfonamidyl) or four (sulfonimidyl). Six such isosteres were found to be more potent inhibitors of catalysis by bovine pancreatic RNase A than are parent compounds containing phosphoryl groups. The atomic structures of two RNase A·N-acylsulfonamide complexes were determined at high resolution by X-ray crystallography. The N-acylsulfonamidyl groups were observed to form more hydrogen bonds with active site residues than did the phosphoryl groups in analogous complexes. These data encourage the further development and use of N-acylsulfonamides and sulfonimides as antagonists of nucleic acid-binding proteins.
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Formoso E, Matxain JM, Lopez X, York DM. Molecular dynamics simulation of bovine pancreatic ribonuclease A-CpA and transition state-like complexes. J Phys Chem B 2010; 114:7371-82. [PMID: 20455590 PMCID: PMC2892782 DOI: 10.1021/jp909004y] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mechanisms of enzymes are intimately connected with their overall structure and dynamics in solution. Experimentally, it is considerably challenging to provide detailed atomic level information about the conformational events that occur at different stages along the chemical reaction path. Here, theoretical tools may offer new potential insights that complement those obtained from experiments that may not yield an unambiguous mechanistic interpretation. In this study, we apply molecular dynamics simulations of bovine pancreatic ribonuclease A, an archetype ribonuclease, to study the conformational dynamics, structural relaxation, and differential solvation that occur at discrete stages of the transesterification and cleavage reaction. Simulations were performed with explicit solvation with rigorous electrostatics and utilize recently developed molecular mechanical force field parameters for transphosphorylation and hydrolysis transition state analogues. Herein, we present results for the enzyme complexed with the dinucleotide substrate cytidilyl-3',5'-adenosine (CpA) in the reactant, and transphosphorylation and hydrolysis transition states. A detailed analysis of active site structures and hydrogen-bond patterns is presented and compared. The integrity of the overall backbone structure is preserved in the simulations and supports a mechanism whereby His12 stabilizes accumulating negative charge at the transition states through hydrogen-bond donation to the nonbridge oxygens. Lys41 is shown to be highly versatile along the reaction coordinate and can aid in the stabilization of the dianionic transition state, while being poised to act as a general acid catalyst in the hydrolysis step.
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Affiliation(s)
- Elena Formoso
- Kimika Fakultatea, Euskal Herriko Unibertsitatea and Donostia International Physics Center (DIPC), P.K. 1072, 20080 Donostia, Euskadi, Spain.
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