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Probing the Effects of Pyrimidine Functional Group Switches on Acyclic Fleximer Analogues for Antiviral Activity. Molecules 2019; 24:molecules24173184. [PMID: 31480658 PMCID: PMC6749450 DOI: 10.3390/molecules24173184] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 08/30/2019] [Accepted: 08/31/2019] [Indexed: 01/29/2023] Open
Abstract
Due to their ability to inhibit viral DNA or RNA replication, nucleoside analogues have been used for decades as potent antiviral therapeutics. However, one of the major limitations of nucleoside analogues is the development of antiviral resistance. In that regard, flexible nucleoside analogues known as “fleximers” have garnered attention over the years due to their ability to survey different amino acids in enzyme binding sites, thus overcoming the potential development of antiviral resistance. Acyclic fleximers have previously demonstrated antiviral activity against numerous viruses including Middle East Respiratory Syndrome coronavirus (MERS-CoV), Ebola virus (EBOV), and, most recently, flaviviruses such as Dengue (DENV) and Yellow Fever Virus (YFV). Due to these interesting results, a Structure Activity Relationship (SAR) study was pursued in order to analyze the effect of the pyrimidine functional group and acyl protecting group on antiviral activity, cytotoxicity, and conformation. The results of those studies are presented herein.
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Negi I, Kathuria P, Sharma P, Wetmore SD. How do hydrophobic nucleobases differ from natural DNA nucleobases? Comparison of structural features and duplex properties from QM calculations and MD simulations. Phys Chem Chem Phys 2018; 19:16365-16374. [PMID: 28657627 DOI: 10.1039/c7cp02576a] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Computational (DFT and MD simulation) methods are employed to systematically characterize the structural and energetic properties of five hydrophobic nucleobases (FEMO, MMO2, NaM, 5SICS and TPT3) that constitute four unnatural base pairs (FEMO:5SICS, MMO2:5SICS, NaM:5SICS and TPT3:NaM). These hydrophobic bases have been recently shown to be replicated when present between natural bases in DNA duplexes, with the highest replication fidelity and efficiency occuring for the TPT3:NaM pair. Our QM calculations suggest that the preferred (anti) glycosidic orientations of nucleosides containing hydrophobic bases are similar to the natural DNA nucleosides despite differences in their chemical structures. However, due to the inability to form interbase hydrogen bonds, hydrophobic base pairs intrinsically prefer nonplanar, distorted geometries, many of which are stabilized through π-π stacking interactions. Furthermore, the intrinsic stacking potential between a hydrophobic and a natural base is similar to that between two natural bases, indicating that the strength of stacking interactions in DNA duplexes containing hydrophobic bases is likely comparable to natural DNA. However, in contrast to the isolated base-pair geometries, our MD simulations suggest that the hydrophobic base pairs adopt variable geometries within DNA, which range from stacked (5SICS:FEMO) to nearly planar (5SICS:NaM and SICS:MMO2) to planar (TPT3:NaM). As a result, the duplex structural features at the site of modification depend on the identity of the hydrophobic base pair, where the TPT3:NaM pair causes the least structural changes compared to natural DNA. Overall, the structural insight obtained from our calculations on DNA containing hydrophobic base pairs explains the experimentally-observed higher fidelity and efficiency during replication of TPT3:NaM compared to other hydrophobic nucleobase pairs. By providing valuable structural information that explains the intrinsic and duplex properties of this class of unnatural nucleobases, the present work may aid the future design of improved hydrophobic analogues.
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Affiliation(s)
- Indu Negi
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India.
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Chen Z, Ku TC, Seley-Radtke KL. Thiophene-expanded guanosine analogues of Gemcitabine. Bioorg Med Chem Lett 2015; 25:4274-6. [PMID: 26316465 PMCID: PMC4579529 DOI: 10.1016/j.bmcl.2015.07.086] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 07/24/2015] [Accepted: 07/27/2015] [Indexed: 12/23/2022]
Abstract
The chemotherapeutic drug Gemcitabine, 2',2'-difluoro-2'-deoxycytidine, has long been the standard of care for a number of cancers. Gemcitabine's chemotherapeutic properties stem from its 2',2'-difluoro-2'-deoxyribose sugar, which mimics the natural nucleoside, but also disrupts nucleic acid synthesis, leading to cell death. As a result, numerous analogues have been prepared to further explore the biological implications for this structural modification. In that regard, a thieno-expanded guanosine analogue was of interest due to biological activity previously observed for the tricyclic heterobase scaffold. Several analogues were prepared, including the McGuigan ProTide, however the parent nucleoside exhibited the best chemotherapeutic activity, specifically against breast cancer cell lines (89.53% growth inhibition).
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Affiliation(s)
- Zhe Chen
- University of Maryland, Baltimore County, Department of Chemistry & Biochemistry, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Therese C Ku
- University of Maryland, Baltimore County, Department of Chemistry & Biochemistry, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Katherine L Seley-Radtke
- University of Maryland, Baltimore County, Department of Chemistry & Biochemistry, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
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Chen Z, Jochmans D, Ku T, Paeshuyse J, Neyts J, Seley-Radtke KL. Bicyclic and Tricyclic "Expanded" Nucleobase Analogues of Sofosbuvir: New Scaffolds for Hepatitis C Therapies. ACS Infect Dis 2015; 1:357-66. [PMID: 27624884 DOI: 10.1021/acsinfecdis.5b00029] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Given the impressive success of Gilead's Sofosbuvir, many laboratories, including ours, have explored the unique 2'-sugar modification (2'-Me, 2'-F) of nucleoside analogues in the hopes of exploiting the biological activity that this unique modification has imparted to the nucleoside scaffold. In that regard, we have combined our tricyclic "expanded" purine base motif with the 2'-Me, 2'-F sugar modification. Although the synthesis of these complex molecules proved to be nontrivial, with the best results coming from a linear approach, the overall strategy resulted in highly promising biological results for several of the target compounds, including their corresponding McGuigan ProTides. Modest activity against HCV was observed with inhibitory concentrations of as low as 20 μM.
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Affiliation(s)
- Zhe Chen
- Department of Chemistry & Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
| | - Dirk Jochmans
- Rega Institute, University of Leuven (KU Leuven), Leuven, Belgium
| | - Therese Ku
- Department of Chemistry & Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
| | - Jan Paeshuyse
- Rega Institute, University of Leuven (KU Leuven), Leuven, Belgium
| | - Johan Neyts
- Rega Institute, University of Leuven (KU Leuven), Leuven, Belgium
| | - Katherine L. Seley-Radtke
- Department of Chemistry & Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
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5
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Zhang L, Zhou L, Tian J, Li X. Hetero-ring-expansion design for purine analogs: A theoretical study on the structural, electronic, and excited-state properties. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.02.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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6
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Zhang L, Zhou L, Tian J, Li X. Structural, electronic, and photophysical properties of thieno-expanded tricyclic purine analogs: a theoretical study. Phys Chem Chem Phys 2014; 16:4338-49. [DOI: 10.1039/c3cp54505a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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7
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Sharma P, Lait LA, Wetmore SD. yDNA versus yyDNA pyrimidines: computational analysis of the effects of unidirectional ring expansion on the preferred sugar-base orientation, hydrogen-bonding interactions and stacking abilities. Phys Chem Chem Phys 2013; 15:2435-48. [PMID: 23303174 DOI: 10.1039/c2cp43910g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The properties of natural, y- and yy-pyrimidines are compared using computational (B3LYP, MP2) methods. Ring expansion upon incorporation of benzene or naphthalene into the natural pyrimidines affects the preferred orientation of the base about the glycosidic bond in the corresponding nucleoside to a similar extent. Specifically, although the natural pyrimidines preferentially adopt the anti orientation with respect to the 2'-deoxyribose moiety, the expanded analogues will likely display (anti/syn) conformational heterogeneity, which may lead to alternate hydrogen-bonding modes in double-stranded duplexes. Nevertheless, the A:T Watson-Crick hydrogen-bond strengths do not significantly change upon base expansion, while the G:C interaction energy is slightly strengthened upon incorporation of either expanded pyrimidine. The largest effect of base expansion occurs in the stacking energies. Specifically, the maximum (most negative) stacking energies in isolated dimers formed by aligning the nucleobase centers of mass can be increased up to 45% by inclusion of a single y-pyrimidine and up to 55% by consideration of a yy-pyrimidine. Similar increases in the stacking interactions are found when a simplified duplex model composed of two stacked (hydrogen-bonded) base pairs is considered, where both the intrastrand and interstrand stacking interactions can be increased and the effects are more pronounced for the yy-pyrimidines. Moreover, the total stability (sum of all hydrogen-bonding and stacking interactions) is greater for duplexes containing expanded yy-pyrimidines compared to y-pyrimidines, which is mainly due to enhanced stacking interactions. Thus, our calculations suggest that multiple unidirectional increases in the size of the nucleobase spacer can continuously enhance the stability of expanded duplexes.
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Affiliation(s)
- Purshotam Sharma
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
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Robaldo L, Pontiggia R, Di Lella S, Estrin DA, Engels JW, Iribarren AM, Montserrat JM. Conformational States of 2′-C-Methylpyrimidine Nucleosides in Single and Double Nucleic Acid Stranded Structures. J Phys Chem B 2012; 117:57-69. [DOI: 10.1021/jp3081645] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Laura Robaldo
- INGEBI (CONICET), Vuelta de Obligado 2490, Buenos Aires
(1428), Argentina
| | - Rodrigo Pontiggia
- INGEBI (CONICET), Vuelta de Obligado 2490, Buenos Aires
(1428), Argentina
| | - Santiago Di Lella
- Departamento
de Química
Inorgánica, Analítica y Química Física-INQUIMAE,
Fac. de Cs. Exactas y Naturales, UBA, Ciudad
Universitaria, Cap. Fed., Argentina
| | - Darío A. Estrin
- Departamento
de Química
Inorgánica, Analítica y Química Física-INQUIMAE,
Fac. de Cs. Exactas y Naturales, UBA, Ciudad
Universitaria, Cap. Fed., Argentina
| | - Joachim W. Engels
- Institute for Organic Chemistry,
and Chemical Biology, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Adolfo M. Iribarren
- INGEBI (CONICET), Vuelta de Obligado 2490, Buenos Aires
(1428), Argentina
- Laboratorio de Biotransformaciones, Universidad Nacional de Quilmes, Roque Saenz Peña
352 (1876) Bernal, Prov. de Bs. As., Argentina
| | - Javier M. Montserrat
- INGEBI (CONICET), Vuelta de Obligado 2490, Buenos Aires
(1428), Argentina
- Instituto de Ciencias, Universidad Nacional de Gral. Sarmiento, J. M. Gutierrez
1150, Los Polvorines (B1613GSX), Prov. de Bs. As., Argentina
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Johnson AT, Schlegel MK, Meggers E, Essen LO, Wiest O. On the structure and dynamics of duplex GNA. J Org Chem 2011; 76:7964-74. [PMID: 21838272 DOI: 10.1021/jo201469b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Glycol nucleic acid (GNA), with a nucleotide backbone comprising of just three carbons and the stereocenter derived from propylene glycol (1,2-propanediol), is a structural analog of nucleic acids with intriguing biophysical properties, such as formation of highly stable antiparallel duplexes with high Watson-Crick base pairing fidelity. Previous crystallographic studies of double stranded GNA (dsGNA) indicated two forms of backbone conformations, an elongated M-type (containing metallo-base pairs) and the condensed N-type (containing brominated base pairs). A herein presented new crystal structure of a GNA duplex at 1.8 Å resolution from self-complementary 3'-CTC(Br)UAGAG-2' GNA oligonucleotides reveals an N-type conformation with alternating gauche-anti torsions along its (O3'-C3'-C2'-O2') backbone. To elucidate the conformational state of dsGNA in solution, molecular dynamic simulations over a period of 20 ns were performed with the now available repertoire of structural information. Interestingly, dsGNA adopts conformational states in solution intermediate between experimentally observed backbone conformations: simulated dsGNA shows the all-gauche conformation characteristic of M-type GNA with the higher helical twist common to N-type GNA structures. The so far counterintuitive, smaller loss of entropy upon duplex formation as compared to DNA can be traced back to the conformational flexibility inherent to dsGNA but missing in dsDNA. Besides extensive interstrand base stacking and conformational preorganization of single strands, this flexibility contributes to the extraordinary thermal stability of GNA.
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Affiliation(s)
- Andrew T Johnson
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556-5670, United States
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Millen AL, Manderville RA, Wetmore SD. Conformational Flexibility of C8-Phenoxyl-2′-deoxyguanosine Nucleotide Adducts. J Phys Chem B 2010; 114:4373-82. [DOI: 10.1021/jp911993f] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Andrea L. Millen
- Department of Chemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4, Department of Chemistry, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Richard A. Manderville
- Department of Chemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4, Department of Chemistry, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Stacey D. Wetmore
- Department of Chemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4, Department of Chemistry, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
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Sharma P, Sharma S, Mitra A, Singh H. A Theoretical Study on Interaction of Small Gold Clusters Aun(n = 4, 6, 8) with xDNA Base Pairs. J Biomol Struct Dyn 2009; 27:65-82. [DOI: 10.1080/07391102.2009.10507297] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Zhang Z, Wauchope OR, Seley-Radtke KL. Mechanistic studies in the synthesis of a series of thieno-expanded xanthosine and guanosine nucleosides. Tetrahedron 2008; 64:10791-10797. [PMID: 19946353 PMCID: PMC2629406 DOI: 10.1016/j.tet.2008.09.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
During the synthetic pursuit of guanosine (triG) and xanthosine (triX) tricyclic nucleosides analogues, an interesting side product was discovered. In an effort to uncover the mechanistic factors leading to this result, a series of reaction conditions were investigated. It was found that by varying the conditions, the appearance of the side product could be controlled. In addition, the yield of the desired products could be manipulated to afford either a 50:50 mix of both triG and triX, or a majority of one or the other. To demonstrate the broad utility of the method, it was also adapted to the synthesis of guanosine and xanthosine from 5-amino-1-beta-D-ribofuranosyl-4-imidazolecarboxyamide (AICAR). The mechanistic details surrounding the synthetic efforts are reported herein.
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Affiliation(s)
- Zhibo Zhang
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore Co.,, Baltimore, MD 21250
| | - Orrette R. Wauchope
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore Co.,, Baltimore, MD 21250
| | - Katherine L. Seley-Radtke
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore Co.,, Baltimore, MD 21250
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