1
|
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.
Collapse
|
2
|
Abstract
Over the past few years, nucleosides have maintained a prominent role as one of the cornerstones of antiviral and anticancer therapeutics, and many approaches to nucleoside drug design have been pursued. One such approach involves flexibility in the sugar moiety of nucleosides, for example, in the highly successful anti-HIV and HBV drug tenofovir. In contrast, introduction of flexibility to the nucleobase scaffold has only more recently gained significance with the invention of our fleximers. The history, development, and some biological relevance for this innovative class of nucleosides are detailed herein.
Collapse
|
3
|
Yates MK, Seley-Radtke KL. The evolution of antiviral nucleoside analogues: A review for chemists and non-chemists. Part II: Complex modifications to the nucleoside scaffold. Antiviral Res 2019; 162:5-21. [PMID: 30529089 PMCID: PMC6349489 DOI: 10.1016/j.antiviral.2018.11.016] [Citation(s) in RCA: 150] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/24/2018] [Accepted: 11/30/2018] [Indexed: 12/13/2022]
Abstract
This is the second of two invited articles reviewing the development of nucleoside analogue antiviral drugs, written for a target audience of virologists and other non-chemists, as well as chemists who may not be familiar with the field. As with the first paper, rather than providing a chronological account, we have chosen to examine particular examples of structural modifications made to nucleoside analogues that have proven fruitful as various antiviral, anticancer, and other therapeutics. The first review covered the more common, and in most cases, single modifications to the sugar and base moieties of the nucleoside scaffold. This paper focuses on more recent developments, especially nucleoside analogues that contain more than one modification to the nucleoside scaffold. We hope that these two articles will provide an informative historical perspective of some of the successfully designed analogues, as well as many candidate compounds that encountered obstacles.
Collapse
Affiliation(s)
- Mary K Yates
- Department of Chemistry & Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, USA
| | - Katherine L Seley-Radtke
- Department of Chemistry & Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, USA.
| |
Collapse
|
4
|
Antiviral activity spectrum of phenoxazine nucleoside derivatives. Antiviral Res 2019; 163:117-124. [PMID: 30684562 DOI: 10.1016/j.antiviral.2019.01.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/14/2019] [Accepted: 01/17/2019] [Indexed: 12/13/2022]
Abstract
The phenoxazine scaffold is widely used to stabilize nucleic acid duplexes, as a part of fluorescent probes for the study of nucleic acid structure, recognition, and metabolism, etc. Here we present the synthesis of phenoxazine-based nucleoside derivatives and their antiviral activity against a panel of structurally diverse viruses: enveloped DNA herpesviruses varicella zoster virus (VZV) and human cytomegalovirus, enveloped RNA tick-borne encephalitis virus (TBEV), and non-enveloped RNA enteroviruses. Studied compounds were effective against DNA and RNA viruses reproduction in cell culture. 3-(2'-Deoxy-β-D-ribofuranosyl)-1,3-diaza-2-oxophenoxazine proved to be a potent inhibitor of VZV replication with superior activity against wild type than thymidine kinase deficient strains (EC50 0.06 and 10 μM, respectively). This compound did not show cytotoxicity on all the studied cell lines. Several compounds showed promising activity against TBEV (EC50 0.35-0.91 μM), but the activity was accompanied by pronounced cytotoxicity. These compounds may be considered as a good starting point for further structure optimization as antiherpesviral or antiflaviviral compounds.
Collapse
|
5
|
Seley-Radtke KL, Yates MK. The evolution of nucleoside analogue antivirals: A review for chemists and non-chemists. Part 1: Early structural modifications to the nucleoside scaffold. Antiviral Res 2018; 154:66-86. [PMID: 29649496 PMCID: PMC6396324 DOI: 10.1016/j.antiviral.2018.04.004] [Citation(s) in RCA: 307] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/22/2018] [Accepted: 04/04/2018] [Indexed: 02/07/2023]
Abstract
This is the first of two invited articles reviewing the development of nucleoside-analogue antiviral drugs, written for a target audience of virologists and other non-chemists, as well as chemists who may not be familiar with the field. Rather than providing a simple chronological account, we have examined and attempted to explain the thought processes, advances in synthetic chemistry and lessons learned from antiviral testing that led to a few molecules being moved forward to eventual approval for human therapies, while others were discarded. The present paper focuses on early, relatively simplistic changes made to the nucleoside scaffold, beginning with modifications of the nucleoside sugars of Ara-C and other arabinose-derived nucleoside analogues in the 1960's. A future paper will review more recent developments, focusing especially on more complex modifications, particularly those involving multiple changes to the nucleoside scaffold. We hope that these articles will help virologists and others outside the field of medicinal chemistry to understand why certain drugs were successfully developed, while the majority of candidate compounds encountered barriers due to low-yielding synthetic routes, toxicity or other problems that led to their abandonment.
Collapse
Affiliation(s)
- Katherine L Seley-Radtke
- 1000 Hilltop Circle, Department of Chemistry & Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, USA.
| | - Mary K Yates
- 1000 Hilltop Circle, Department of Chemistry & Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, USA
| |
Collapse
|
6
|
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).
Collapse
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.
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Jahnz-Wechmann Z, Framski G, Januszczyk P, Boryski J. Bioactive fused heterocycles: Nucleoside analogs with an additional ring. Eur J Med Chem 2015; 97:388-96. [DOI: 10.1016/j.ejmech.2014.12.026] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 12/05/2014] [Accepted: 12/17/2014] [Indexed: 11/25/2022]
|
9
|
Zhang L, Zhang Z, Ren T, Tian J, Wang M. New size-expanded RNA nucleobase analogs: a detailed theoretical study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 140:407-415. [PMID: 25617981 DOI: 10.1016/j.saa.2015.01.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 12/20/2014] [Accepted: 01/05/2015] [Indexed: 06/04/2023]
Abstract
Fluorescent nucleobase analogs have attracted much attention in recent years due to their potential applications in nucleic acids research. In this work, four new size-expanded RNA base analogs were computationally designed and their structural, electronic, and optical properties are investigated by means of DFT calculations. The results indicate that these analogs can form stable Watson-Crick base pairs with natural counterparts and they have smaller ionization potentials and HOMO-LUMO gaps than natural ones. Particularly, the electronic absorption spectra and fluorescent emission spectra are calculated. The calculated excitation maxima are greatly red-shifted compared with their parental and natural bases, allowing them to be selectively excited. In gas phase, the fluorescence from them would be expected to occur around 526, 489, 510, and 462 nm, respectively. The influences of water solution and base pairing on the relevant absorption spectra of these base analogs are also examined.
Collapse
Affiliation(s)
- Laibin Zhang
- School of Physics and Engineering, Qufu Normal University, Qufu 273165, PR China.
| | - Zhenwei Zhang
- Linyi Academy of Technology Cooperation and Application, Linyi 276001, PR China
| | - Tingqi Ren
- School of Physics and Engineering, Qufu Normal University, Qufu 273165, PR China
| | - Jianxiang Tian
- School of Physics and Engineering, Qufu Normal University, Qufu 273165, PR China.
| | - Mei Wang
- School of Physics and Engineering, Qufu Normal University, Qufu 273165, PR China
| |
Collapse
|
10
|
Martinčič R, Venko K, Župerl Š, Novič M. Chemometrics approach for the prediction of structure-activity relationship for membrane transporter bilitranslocase. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2014; 25:853-872. [PMID: 25337672 DOI: 10.1080/1062936x.2014.962082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Membrane transport proteins are essential for cellular uptake of numerous salts, nutrients and drugs. Bilitranslocase is a transporter, specific for water-soluble organic anions, and is the only known carrier of nucleotides and nucleotide-like compounds. Experimental data of bilitranslocase ligand specificity for 120 compounds were used to construct classification models using counter-propagation artificial neural networks (CP-ANNs) and support vector machines (SVMs). A subset of active compounds with experimentally determined transport rates was used to build predictive QSAR models for estimation of transport rates of unknown compounds. Several modelling methods and techniques were applied, i.e. CP-ANN, genetic algorithm, self-organizing mapping and multiple linear regression method. The best predictions were achieved using CP-ANN coupled with a genetic algorithm, with the external validation parameter QV(2) of 0.96. The applicability domains of the models were defined to determine the chemical space in which reliable predictions can be obtained. The models were applied for the estimation of bilitranslocase transport activity for two sets of pharmaceutically interesting compounds, antioxidants and antiprions. We found that the relative planarity and a high potential for hydrogen bond formation are the common structural features of anticipated substrates of bilitranslocase. These features may serve as guidelines in the design of new pharmaceuticals transported by bilitranslocase.
Collapse
Affiliation(s)
- R Martinčič
- a Laboratory of Chemometrics , National Institute of Chemistry , Ljubljana , Slovenia
| | | | | | | |
Collapse
|
11
|
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]
|
12
|
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]
|
13
|
Effects of substitutions at the 4' and 2 positions on the bioactivity of 4'-ethynyl-2-fluoro-2'-deoxyadenosine. Antimicrob Agents Chemother 2013; 57:6254-64. [PMID: 24100493 DOI: 10.1128/aac.01703-13] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Nucleos(t)ide reverse transcriptase inhibitors (NRTIs) form the backbone of most anti-HIV therapies. We have shown that 4'-ethynyl-2-fluoro-2'-deoxyadenosine (EFdA) is a highly effective NRTI; however, the reasons for the potent antiviral activity of EFdA are not well understood. Here, we use a combination of structural, computational, and biochemical approaches to examine how substitutions in the sugar or adenine rings affect the incorporation of dA-based NRTIs like EFdA into DNA by HIV RT and their susceptibility to deamination by adenosine deaminase (ADA). Nuclear magnetic resonance (NMR) spectroscopy studies of 4'-substituted NRTIs show that ethynyl or cyano groups stabilize the sugar ring in the C-2'-exo/C-3'-endo (north) conformation. Steady-state kinetic analysis of the incorporation of 4'-substituted NRTIs by RT reveals a correlation between the north conformation of the NRTI sugar ring and efficiency of incorporation into the nascent DNA strand. Structural analysis and the kinetics of deamination by ADA demonstrate that 4'-ethynyl and cyano substitutions decrease the susceptibility of adenosine-based compounds to ADA through steric interactions at the active site. However, the major determinant for decreased susceptibility to ADA is the 2-halo substitution, which alters the pKa of N1 on the adenine base. These results provide insight into how NRTI structural attributes affect their antiviral activities through their interactions with the RT and ADA active sites.
Collapse
|
14
|
Zhou J, Sayre DA, Wang J, Pahadi N, Sintim HO. Endo-S-c-di-GMP analogues-polymorphism and binding studies with class I riboswitch. Molecules 2012; 17:13376-89. [PMID: 23143150 PMCID: PMC6269045 DOI: 10.3390/molecules171113376] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 10/30/2012] [Accepted: 11/01/2012] [Indexed: 11/17/2022] Open
Abstract
C-di-GMP, a cyclic guanine dinucleotide, has been shown to regulate biofilm formation as well as virulence gene expression in a variety of bacteria. Analogues of c-di-GMP have the potential to be used as chemical probes to study c-di-GMP signaling and could even become drug leads for the development of anti-biofilm compounds. Herein we report the synthesis and biophysical studies of a series of c-di-GMP analogues, which have both phosphate and sugar moieties simultaneously modified (called endo-S-c-di-GMP analogues). We used computational methods to predict the relative orientation of the guanine nucleobases in c-di-GMP and analogues. DOSY NMR of the endo-S-c-di-GMP series showed that the polymorphism of c-di-GMP can be tuned with conservative modifications to the phosphate and sugar moieties (conformational steering). Binding studies with Vc2 RNA (a class I c-di-GMP riboswitch) revealed that conservative modifications to the phosphate and 2'-positions of c-di-GMP dramatically affected binding to class I riboswitch.
Collapse
Affiliation(s)
| | | | | | | | - Herman O. Sintim
- Author to whom correspondence should be addressed; ; Tel.: +1-301-405-0633; Fax: +1-301-314-9121
| |
Collapse
|
15
|
An efficient and convenient one-pot multicomponent synthesis of novel pyrimidine derivatives: N-(4-aryl-6-(pyridin-2-yl)pyrimidin-2-yl)cyanamides. RESEARCH ON CHEMICAL INTERMEDIATES 2012. [DOI: 10.1007/s11164-012-0724-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
16
|
Wauchope OR, Velasquez M, Seley-Radtke K. Synthetic Routes to a Series of Proximal and Distal 2'-Deoxy Fleximers. SYNTHESIS-STUTTGART 2012; 44:3496-3504. [PMID: 24465059 PMCID: PMC3898542 DOI: 10.1055/s-0032-1316791] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Two series of innovative 2'-deoxy nucleoside analogues have been designed where the nucleobase has been split into its imidazole and pyrimidine subunits. This structural modification serves to introduce flexibility into the nucleobase scaffold while still retaining the elements required for recognition. The synthetic efforts to realize these analogues are described within.
Collapse
Affiliation(s)
- Orrette R. Wauchope
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA Fax +1(410)4552608
| | - Melvin Velasquez
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA Fax +1(410)4552608
| | - Katherine Seley-Radtke
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA Fax +1(410)4552608
| |
Collapse
|