1
|
Jovanovic D, Tremmel P, Pallan PS, Egli M, Richert C. The Enzyme‐Free Release of Nucleotides from Phosphoramidates Depends Strongly on the Amino Acid. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Dejana Jovanovic
- Institut für Organische Chemie Universität Stuttgart 70569 Stuttgart Germany
| | - Peter Tremmel
- Institut für Organische Chemie Universität Stuttgart 70569 Stuttgart Germany
| | - Pradeep S. Pallan
- Department of Biochemistry Vanderbilt University School of Medicine Nashville TN 37232 USA
| | - Martin Egli
- Department of Biochemistry Vanderbilt University School of Medicine Nashville TN 37232 USA
| | - Clemens Richert
- Institut für Organische Chemie Universität Stuttgart 70569 Stuttgart Germany
| |
Collapse
|
2
|
Jovanovic D, Tremmel P, Pallan PS, Egli M, Richert C. The Enzyme-Free Release of Nucleotides from Phosphoramidates Depends Strongly on the Amino Acid. Angew Chem Int Ed Engl 2020; 59:20154-20160. [PMID: 32757352 PMCID: PMC7436718 DOI: 10.1002/anie.202008665] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/04/2020] [Indexed: 12/23/2022]
Abstract
Phosphoramidates composed of an amino acid and a nucleotide analogue are critical metabolites of prodrugs, such as remdesivir. Hydrolysis of the phosphoramidate liberates the nucleotide, which can then be phosphorylated to become the pharmacologically active triphosphate. Enzymatic hydrolysis has been demonstrated, but a spontaneous chemical process may also occur. We measured the rate of enzyme-free hydrolysis for 17 phosphoramidates of ribonucleotides with amino acids or related compounds at pH 7.5. Phosphoramidates of proline hydrolyzed fast, with a half-life time as short as 2.4 h for Pro-AMP in ethylimidazole-containing buffer at 37 °C; 45-fold faster than Ala-AMP and 120-fold faster than Phe-AMP. Crystal structures of Gly-AMP, Pro-AMP, βPro-AMP and Phe-AMP bound to RNase A as crystallization chaperone showed how well the carboxylate is poised to attack the phosphoramidate, helping to explain this reactivity. Our results are significant for the design of new antiviral prodrugs.
Collapse
Affiliation(s)
- Dejana Jovanovic
- Institut für Organische ChemieUniversität Stuttgart70569StuttgartGermany
| | - Peter Tremmel
- Institut für Organische ChemieUniversität Stuttgart70569StuttgartGermany
| | - Pradeep S. Pallan
- Department of BiochemistryVanderbilt UniversitySchool of MedicineNashvilleTN37232USA
| | - Martin Egli
- Department of BiochemistryVanderbilt UniversitySchool of MedicineNashvilleTN37232USA
| | - Clemens Richert
- Institut für Organische ChemieUniversität Stuttgart70569StuttgartGermany
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
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]
|
6
|
Doucet N, Jayasundera TB, Simonović M, Loria JP. The crystal structure of ribonuclease A in complex with thymidine-3'-monophosphate provides further insight into ligand binding. Proteins 2010; 78:2459-68. [PMID: 20602460 DOI: 10.1002/prot.22754] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Thymidine-3'-monophosphate (3'-TMP) is a competitive inhibitor analogue of the 3'-CMP and 3'-UMP natural product inhibitors of bovine pancreatic ribonuclease A (RNase A). Isothermal titration calorimetry experiments show that 3'-TMP binds the enzyme with a dissociation constant (K(d)) of 15 microM making it one of the strongest binding members of the five natural bases found in nucleic acids (A, C, G, T, and U). To further investigate the molecular properties of this potent natural affinity, we have determined the crystal structure of bovine pancreatic RNase A in complex with 3'-TMP at 1.55 A resolution and we have performed NMR binding experiments with 3'-CMP and 3'-TMP. Our results show that binding of 3'-TMP is very similar to other natural and non-natural pyrimidine ligands, demonstrating that single nucleotide affinity is independent of the presence or absence of a 2'-hydroxyl on the ribose moiety of pyrimidines and suggesting that the pyrimidine binding subsite of RNase A is not a significant contributor of inhibitor discrimination. Accumulating evidence suggests that very subtle structural, chemical, and potentially motional variations contribute to ligand discrimination in this enzyme.
Collapse
Affiliation(s)
- Nicolas Doucet
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | | | | | | |
Collapse
|
7
|
Rlepokura K, Petrus R. Nucleotide-amino acid interactions in the L-His-IMP.MeOH.H(2)O complex. Acta Crystallogr C 2010; 66:o265-9. [PMID: 20522942 DOI: 10.1107/s0108270110014381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2010] [Accepted: 04/19/2010] [Indexed: 11/10/2022] Open
Abstract
In the crystal structure of the methanol-solvated monohydrated complex of L-histidine (His) with inosine 5'-monophosphate (IMP), namely L-histidinium inosine-5'-phosphate methanol solvate monohydrate, C(6)H(10)N(3)O(2)(+).C(10)H(12)N(4)O(8)P(-).CH(3)OH.H(2)O, most of the interactions between IMP anions (anti/C3'-endo/gauche-gauche conformers) are realized between the riboses and hypoxanthine bases in a trans sugar-edge/sugar-edge geometry, and between the phosphate groups. The base Watson-Crick edge is involved in additional methanol-mediated IMP...MeOH...IMP contacts. Specific and nonspecific nucleotide-amino acid (IMP...His) interactions engage the Hoogsteen edges of the base and phosphate group, respectively. Additional stabilization of His...IMP contacts is provided by pi-pi stacking between the imidazolium ring of His and the hypoxanthine base of IMP. The results may indicate the possible recognition mechanism between His and IMP.
Collapse
Affiliation(s)
- Katarzyna Rlepokura
- Faculty of Chemistry, University of Wrocław, 14 Joliot-Curie Street, 50-383 Wrocław, Poland.
| | | |
Collapse
|
8
|
Larson SB, Day JS, Nguyen C, Cudney R, McPherson A. Structure of bovine pancreatic ribonuclease complexed with uridine 5'-monophosphate at 1.60 A resolution. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:113-20. [PMID: 20124705 PMCID: PMC2815675 DOI: 10.1107/s174430910905194x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Accepted: 12/02/2009] [Indexed: 11/11/2022]
Abstract
Bovine pancreatic ribonuclease A (RNase A) was crystallized from a mixture of small molecules containing basic fuchsin, tobramycin and uridine 5'-monophosphate (U5P). Solution of the crystal structure revealed that the enzyme was selectively bound to U5P, with the pyrimidine ring of U5P residing in the pyrimidine-binding site at Thr45. The structure was refined to an R factor of 0.197 and an R(free) of 0.253.
Collapse
Affiliation(s)
- Steven B. Larson
- Department of Molecular Biology and Biochemistry, The University of California, Irvine, CA 92697-3900, USA
| | - John S. Day
- Department of Molecular Biology and Biochemistry, The University of California, Irvine, CA 92697-3900, USA
| | | | | | - Alexander McPherson
- Department of Molecular Biology and Biochemistry, The University of California, Irvine, CA 92697-3900, USA
| |
Collapse
|
9
|
Holloway DE, Chavali GB, Leonidas DD, Baker MD, Acharya KR. Influence of naturally-occurring 5'-pyrophosphate-linked substituents on the binding of adenylic inhibitors to ribonuclease a: an X-ray crystallographic study. Biopolymers 2009; 91:995-1008. [PMID: 19191310 PMCID: PMC2816359 DOI: 10.1002/bip.21158] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2008] [Revised: 01/26/2009] [Accepted: 01/27/2009] [Indexed: 11/22/2022]
Abstract
Ribonuclease A is the archetype of a functionally diverse superfamily of vertebrate-specific ribonucleases. Inhibitors of its action have potential use in the elucidation of the in vivo roles of these enzymes and in the treatment of pathologies associated therewith. Derivatives of adenosine 5'-pyrophosphate are the most potent nucleotide-based inhibitors known. Here, we use X-ray crystallography to visualize the binding of four naturally-occurring derivatives that contain 5'-pyrophosphate-linked extensions. 5'-ATP binds with the adenine occupying the B(2) subsite in the manner of an RNA substrate but with the gamma-phosphate at the P(1) subsite. Diadenosine triphosphate (Ap(3)A) binds with the adenine in syn conformation, the beta-phosphate as the principal P(1) subsite ligand and without order beyond the gamma-phosphate. NADPH and NADP(+) bind with the adenine stacked against an alternative rotamer of His119, the 2'-phosphate at the P(1) subsite, and without order beyond the 5'-alpha-phosphate. We also present the structure of the complex formed with pyrophosphate ion. The structural data enable existing kinetic data on the binding of these compounds to a variety of ribonucleases to be rationalized and suggest that as the complexity of the 5'-linked extension increases, the need to avoid unfavorable contacts places limitations on the number of possible binding modes.
Collapse
Affiliation(s)
- Daniel E Holloway
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | | | | | | | | |
Collapse
|
10
|
Tsirkone VG, Dossi K, Drakou C, Zographos SE, Kontou M, Leonidas DD. Inhibitor design for ribonuclease A: the binding of two 5'-phosphate uridine analogues. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:671-7. [PMID: 19574636 PMCID: PMC2705631 DOI: 10.1107/s1744309109021423] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2009] [Accepted: 06/05/2009] [Indexed: 11/10/2022]
Abstract
In the quest for the rational design of selective and potent inhibitors for members of the pancreatic ribonuclease A (RNase A) family of biomedical interest, the binding of uridine 5'-phosphate (U5P) and uridine 5'-diphosphate (UDP) to RNase A have been investigated using kinetic studies and X-ray crystallography. Both nucleotides are competitive inhibitors of the enzyme, with K(i) values of 4.0 and 0.65 mM, respectively. They bind to the active site of the enzyme by anchoring two molecules connected to each other by hydrogen bonds and van der Waals interactions. While the first of the inhibitor molecules binds with its nucleobase in the pyrimidinyl-binding subsite, the second is bound at the purine-preferring subsite. The unexpected binding of a pyrimidine at the purine-binding subsite has added new important elements to the rational design approach for the discovery of new potent inhibitors of the RNase A superfamily.
Collapse
Affiliation(s)
- Vicky G. Tsirkone
- Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, 11635 Athens, Greece
| | - Kyriaki Dossi
- Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, 11635 Athens, Greece
| | - Christina Drakou
- Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, 11635 Athens, Greece
| | - Spyros E. Zographos
- Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, 11635 Athens, Greece
| | - Maria Kontou
- Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos St., 41221 Larissa, Greece
| | - Demetres D. Leonidas
- Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, 11635 Athens, Greece
| |
Collapse
|
11
|
Samanta A, Leonidas DD, Dasgupta S, Pathak T, Zographos SE, Oikonomakos NG. Morpholino, Piperidino, and Pyrrolidino Derivatives of Pyrimidine Nucleosides as Inhibitors of Ribonuclease A: Synthesis, Biochemical, and Crystallographic Evaluation,. J Med Chem 2009; 52:932-42. [DOI: 10.1021/jm800724t] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anirban Samanta
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India, and Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, 11635 Athens, Greece
| | - Demetres D. Leonidas
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India, and Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, 11635 Athens, Greece
| | - Swagata Dasgupta
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India, and Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, 11635 Athens, Greece
| | - Tanmaya Pathak
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India, and Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, 11635 Athens, Greece
| | - Spyros E. Zographos
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India, and Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, 11635 Athens, Greece
| | - Nikos G. Oikonomakos
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India, and Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, 11635 Athens, Greece
| |
Collapse
|
12
|
Larson SB, Day JS, Cudney R, McPherson A. A new crystal form of bovine pancreatic RNase A in complex with 2'-deoxyguanosine-5'-monophosphate. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:728-33. [PMID: 17768339 PMCID: PMC2376308 DOI: 10.1107/s1744309107039565] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2007] [Accepted: 08/09/2007] [Indexed: 11/11/2022]
Abstract
The structure of bovine pancreatic RNase A has been determined in complex with 2'-deoxyguanosine-5'-monophosphate (dGMP) at 1.33 A resolution at room temperature in a previously unreported unit cell belonging to space group P3(1). There are two molecules of nucleotide per enzyme molecule, one of which lies in the active-site cleft in the productive binding mode, whilst the guanine base of the other dGMP occupies the pyrimidine-specific binding site in a nonproductive mode such that it forms hydrogen bonds to the phosphate group of the first dGMP. This is the first RNase A structure containing a guanine base in the B2 binding site. Each dGMP molecule is involved in intermolecular interactions with adjacent RNase A molecules in the lattice and the two nucleotides appear to direct the formation of the crystal lattice. Because GMP may be produced during degradation of RNA, this association could represent an inhibitor complex and thereby affect the observed enzyme kinetics.
Collapse
Affiliation(s)
- Steven B. Larson
- Department of Molecular Biology and Biochemistry, The University of California, Irvine, CA 92697-3900, USA
| | - John S. Day
- Department of Molecular Biology and Biochemistry, The University of California, Irvine, CA 92697-3900, USA
| | | | - Alexander McPherson
- Department of Molecular Biology and Biochemistry, The University of California, Irvine, CA 92697-3900, USA
- Correspondence e-mail:
| |
Collapse
|
13
|
Polydoridis S, Leonidas DD, Oikonomakos NG, Archontis G. Recognition of ribonuclease A by 3'-5'-pyrophosphate-linked dinucleotide inhibitors: a molecular dynamics/continuum electrostatics analysis. Biophys J 2007; 92:1659-72. [PMID: 17142283 PMCID: PMC1796809 DOI: 10.1529/biophysj.106.093419] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2006] [Accepted: 11/01/2006] [Indexed: 11/18/2022] Open
Abstract
The proteins of the pancreatic ribonuclease A (RNase A) family catalyze the cleavage of the RNA polymer chain. The development of RNase inhibitors is of significant interest, as some of these compounds may have a therapeutic effect in pathological conditions associated with these proteins. The most potent low molecular weight inhibitor of RNase reported to date is the compound 5'-phospho-2'-deoxyuridine-3-pyrophosphate (P-->5)-adenosine-3-phosphate (pdUppA-3'-p). The 3',5'-pyrophosphate group of this compound increases its affinity and introduces structural features which seem to be unique in pyrophosphate-containing ligands bound to RNase A, such as the adoption of a syn conformation by the adenosine base at RNase subsite B(2) and the placement of the 5'-beta-phosphate of the adenylate (instead of the alpha-phosphate) at subsite P(1) where the phosphodiester bond cleavage occurs. In this work, we study by multi-ns molecular dynamics simulations the structural properties of RNase A complexes with the ligand pdUppA-3'-p and the related weaker inhibitor dUppA, which lacks the 3' and 5' terminal phosphate groups of pdUppA-3'-p. The simulations show that the adenylate 5'-beta-phosphate binding position and the adenosine syn orientation constitute robust structural features in both complexes, stabilized by persistent interactions with specific active-site residues of subsites P(1) and B(2). The simulation structures are used in conjunction with a continuum-electrostatics (Poisson-Boltzmann) model, to evaluate the relative binding affinity of the two complexes. The computed relative affinity of pdUppA-3'-p varies between -7.9 kcal/mol and -2.8 kcal/mol for a range of protein/ligand dielectric constants (epsilon(p)) 2-20, in good agreement with the experimental value (-3.6 kcal/mol); the agreement becomes exact with epsilon(p) = 8. The success of the continuum-electrostatics model suggests that the differences in affinity of the two ligands originate mainly from electrostatic interactions. A residue decomposition of the electrostatic free energies shows that the terminal phosphate groups of pdUppA-3'-p make increased interactions with residues Lys(7) and Lys(66) of the more remote sites P(2) and P(0), and His(119) of site P(1).
Collapse
|
14
|
|
15
|
Leonidas DD, Maiti TK, Samanta A, Dasgupta S, Pathak T, Zographos SE, Oikonomakos NG. The binding of 3′-N-piperidine-4-carboxyl-3′-deoxy-ara-uridine to ribonuclease A in the crystal. Bioorg Med Chem 2006; 14:6055-64. [PMID: 16730994 DOI: 10.1016/j.bmc.2006.05.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2006] [Revised: 04/28/2006] [Accepted: 05/03/2006] [Indexed: 10/24/2022]
Abstract
The binding of a moderate inhibitor, 3'-N-piperidine-4-carboxyl-3'-deoxy-ara-uridine, to ribonuclease A has been studied by X-ray crystallography at 1.7A resolution. Two inhibitor molecules are bound in the central RNA binding cavity of RNase A exploiting interactions with residues from peripheral binding sites rather than from the active site of the enzyme. The uracyl moiety of the first inhibitor molecule occupies the purine-preferring site of RNase A, while the rest of the molecule projects to the solvent. The second inhibitor molecule binds with the carboxyl group at the pyrimidine recognition site and the uridine moiety exploits interactions with RNase A residues Lys66, His119 and Asp121. Comparative structural analysis of the 3'-N-piperidine-4-carboxyl-3'-deoxy-ara-uridine complex with other RNase A-ligand complexes provides a structural explanation of its potency. The crystal structure of the RNase A-3'-N-piperidine-4-carboxyl-3'-deoxy-ara-uridine complex provides evidence of a novel ligand-binding pattern in RNase A for 3'-N-aminonucleosides that was not anticipated by modelling studies, while it also suggests ways to improve the efficiency and selectivity of such compounds to develop pharmaceuticals against pathologies associated with RNase A homologues.
Collapse
Affiliation(s)
- Demetres D Leonidas
- Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, 11635 Athens, Greece.
| | | | | | | | | | | | | |
Collapse
|