1
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Guo CJ, Zhang Z, Lu JL, Zhong J, Wu YF, Guo SY, Liu JL. Structural basis of bifunctional CTP/dCTP synthase. J Mol Biol 2024:168750. [PMID: 39173734 DOI: 10.1016/j.jmb.2024.168750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 08/16/2024] [Accepted: 08/17/2024] [Indexed: 08/24/2024]
Abstract
The final step in the de novo synthesis of cytidine 5'-triphosphate (CTP) is catalyzed by CTP synthase (CTPS), which can form cytoophidia in all three domains of life. Recently, we have discovered that CTPS binds to ribonucleotides (NTPs) to form filaments, and have successfully solved the structures of Drosophila melanogaster CTPS bound with NTPs. Previous biochemical studies have shown that CTPS can bind to deoxyribonucleotides (dNTPs) to produce 2'-deoxycytidine-5'-triphosphate (dCTP). However, the structural basis of CTPS binding to dNTPs is still unclear. In this study, we find that Drosophila CTPS can also form filaments with dNTPs. Using cryo-electron microscopy, we are able to solve the structure of Drosophila melanogaster CTPS bound to dNTPs with a resolution of up to 2.7 Å. By combining these structural findings with biochemical analysis, we compare the binding and reaction characteristics of NTPs and dNTPs with CTPS. Our results indicate that the same enzyme can act bifunctionally as CTP/dCTP synthase in vitro, and provide a structural basis for these activities.
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Affiliation(s)
- Chen-Jun Guo
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zherong Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Jia-Li Lu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jiale Zhong
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yu-Fen Wu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Shu-Ying Guo
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom.
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2
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Coombs KM, Glover KKM, Russell R, Kaspler P, Roufaiel M, Graves D, Pelka P, Kobasa D, DuMoulin-White R, Mandel A. Nanomolar concentrations of the photodynamic compound TLD-1433 effectively inactivate numerous human pathogenic viruses. Heliyon 2024; 10:e32140. [PMID: 38882312 PMCID: PMC11176859 DOI: 10.1016/j.heliyon.2024.e32140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/18/2024] Open
Abstract
The anti-viral properties of a small (≈1 kDa), novel Ru(II) photo dynamic compound (PDC), referred to as TLD-1433 (Ruvidar™), are presented. TLD-1433 had previously been demonstrated to exert strong anti-bacterial and anti-cancer properties. We evaluated the capacity of TLD-1433 to inactivate several human pathogenic viruses. TLD-1433 that was not photo-activated was capable of effectively inactivating 50 % of influenza H1N1 virus (ID50) at a concentration of 117 nM. After photo-activation, the ID50 was reduced to <10 nM. The dose of photo-activated TLD-1433 needed to reduce H1N1 infectivity >99 % (ID99) was approximately 170 nM. Similarly, the ID99 of photo-activated TLD-1433 was determined to range from about 20 to 120 nM for other tested enveloped viruses; specifically, a human coronavirus, herpes simplex virus, the poxvirus Vaccinia virus, and Zika virus. TLD-1433 also inactivated two tested non-enveloped viruses; specifically, adenovirus type 5 and mammalian orthoreovirus, but at considerably higher concentrations. Analyses of TLD-1433-treated membranes suggested that lipid peroxidation was a major contributor to enveloped virus inactivation. TLD-1433-mediated virus inactivation was temperature-dependent, with approximately 10-fold more efficient virucidal activity when viruses were treated at 37 °C than when treated at room temperature (∼22 °C). The presence of fetal bovine serum and virus solution turbidity reduced TLD-1433-mediated virucidal efficiency. Immunoblots of TLD-1433-treated human coronavirus indicated the treated spike protein remained particle-associated.
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Affiliation(s)
- Kevin M Coombs
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, R3E 0J9, Canada
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, Manitoba, R3E 3P4, Canada
| | - Kathleen K M Glover
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, R3E 0J9, Canada
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, Manitoba, R3E 3P4, Canada
| | - Raquel Russell
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, R3E 0J9, Canada
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, Manitoba, R3E 3P4, Canada
| | - Pavel Kaspler
- Theralase® Technologies Inc., 41 Hollinger Road, Toronto, Ontario, M4B 3G4, Canada
| | - Mark Roufaiel
- Theralase® Technologies Inc., 41 Hollinger Road, Toronto, Ontario, M4B 3G4, Canada
| | - Drayson Graves
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Peter Pelka
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Darwyn Kobasa
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, R3E 3R2, Canada
| | - Roger DuMoulin-White
- Theralase® Technologies Inc., 41 Hollinger Road, Toronto, Ontario, M4B 3G4, Canada
| | - Arkady Mandel
- Theralase® Technologies Inc., 41 Hollinger Road, Toronto, Ontario, M4B 3G4, Canada
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3
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Guo C, Wang Z, Liu J. Filamentation and inhibition of prokaryotic CTP synthase with ligands. MLIFE 2024; 3:240-250. [PMID: 38948148 PMCID: PMC11211670 DOI: 10.1002/mlf2.12119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/18/2024] [Accepted: 02/06/2024] [Indexed: 07/02/2024]
Abstract
Cytidine triphosphate synthase (CTPS) plays a pivotal role in the de novo synthesis of cytidine triphosphate (CTP), a fundamental building block for RNA and DNA that is essential for life. CTPS is capable of directly binding to all four nucleotide triphosphates: adenine triphosphate, uridine triphosphate, CTP, and guanidine triphosphate. Furthermore, CTPS can form cytoophidia in vivo and metabolic filaments in vitro, undergoing regulation at multiple levels. CTPS is considered a potential therapeutic target for combating invasions or infections by viral or prokaryotic pathogens. Utilizing cryo-electron microscopy, we determined the structure of Escherichia coli CTPS (ecCTPS) filament in complex with CTP, nicotinamide adenine dinucleotide (NADH), and the covalent inhibitor 6-diazo-5-oxo- l-norleucine (DON), achieving a resolution of 2.9 Å. We constructed a phylogenetic tree based on differences in filament-forming interfaces and designed a variant to validate our hypothesis, providing an evolutionary perspective on CTPS filament formation. Our computational analysis revealed a solvent-accessible ammonia tunnel upon DON binding. Through comparative structural analysis, we discern a distinct mode of CTP binding of ecCTPS that differs from eukaryotic counterparts. Combining biochemical assays and structural analysis, we determined and validated the synergistic inhibitory effects of CTP with NADH or adenine on CTPS. Our results expand our comprehension of the diverse regulatory aspects of CTPS and lay a foundation for the design of specific inhibitors targeting prokaryotic CTPS.
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Affiliation(s)
- Chenjun Guo
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Zixuan Wang
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Ji‐Long Liu
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
- Shanghai Clinical Research and Trial CenterShanghaiChina
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4
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McGary LC, Regan GL, Bearne SL. Reactive architecture profiling with a methyl acyl phosphate electrophile. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140945. [PMID: 37536394 DOI: 10.1016/j.bbapap.2023.140945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 08/05/2023]
Abstract
Activity-based protein profiling has facilitated the study of the activity of enzymes in proteomes, inhibitor development, and identification of enzymes that share mechanistic and active-site architectural features. Since methyl acyl phosphate monoesters act as electrostatically selective anionic electrophiles for the covalent modification of nucleophiles that reside adjacent to cationic sites in proteins, we synthesized methyl hex-5-ynoyl phosphate (MHP) to broadly target such protein architectures. After treating the soluble proteome of Paucimonas lemoignei with MHP, biotinylating the resulting acylated proteins using click chemistry, enriching the protein adducts using streptavidin, and analyzing the proteins by LC-MS/MS, a set of 240 enzymes and 132 non-enzyme proteins were identified for a wide spectrum of biological processes and from all 7 enzyme classes. Among those enzymes identified, β-hydroxybutyrate dehydrogenase (PlHBDH) and CTP synthase (E. coli orthologue, EcCTPS) were purified as recombinant enzymes and their rates of inactivation and sites of modification by MHP and methyl acetyl phosphate (MAP) were characterized. MHP reacted more slowly with these proteins than MAP but exhibited greater specificity, despite its lack of multiple binding determinants. Generally, MAP modified more surface residues than MHP. MHP specifically modified Ser 146, Lys 156, and Lys 163 at the active site of PlHBDH. MHP and MAP modified numerous residues of EcCTPS with CTP furnishing the greatest level of protection against MHP- and MAP-dependent modification and inactivation, respectively, followed by ATP and glutamine. Overall, MHP served as an effective probe to identify proteins that are potentially amenable to inhibition by methyl acyl phosphates.
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Affiliation(s)
- Laura C McGary
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Gemma L Regan
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Stephen L Bearne
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Department of Chemistry, Dalhousie University, Halifax, NS B3H 4R2, Canada.
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5
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Kciuk M, Mujwar S, Rani I, Munjal K, Gielecińska A, Kontek R, Shah K. Computational Bioprospecting Guggulsterone against ADP Ribose Phosphatase of SARS-CoV-2. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238287. [PMID: 36500379 PMCID: PMC9739500 DOI: 10.3390/molecules27238287] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 11/29/2022]
Abstract
Coronavirus Disease-2019 (COVID-19) is a highly contagious disease caused by Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2). The World Health Organization (WHO) classified the disease a as global public health hazard on 11 March 2020. Currently, there are no adequate measures to combat viral infections, including COVID-19, and the medication guidelines for the management of COVID-19 are dependent on previous findings from SARS-CoV and MERS-CoV research. Natural products have achieved widespread acceptance around the world as a means of enhancing healthcare and disease prevention. Plants are a potential source of antiviral factors such as flavonoids, phenolic acids, terpenoids, and others. Some of these agents exhibit a broad spectrum of antiviral activity. This study aimed to screen herbal leads for possible inhibitors of the SARS-CoV-2 ADP Ribose Phosphatase enzyme (ARP). Guggulsterone was found to be highly stabilized within the active site of the viral ARP enzyme by molecular dynamic simulation with very little fluctuation throughout the simulation timeframe of 100 ns. Thus, guggulsterone can be further used to develop a safe and competent medication for evolving therapy against SARS-CoV-2 in post-preclinical and clinical trials.
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Affiliation(s)
- Mateusz Kciuk
- Department of Molecular Biotechnology and Genetics, University of Lodz, 90-237 Lodz, Poland
- Doctoral School of Exact and Natural Sciences, University of Lodz, 90-237 Lodz, Poland
- Correspondence:
| | - Somdutt Mujwar
- Chitkara College of Pharmacy, Chitkara University, Chandigarh 140401, Punjab, India
| | - Isha Rani
- Spurthy College of Pharmacy, Marasur Gate, Bengaluru 562106, Karnataka, India
| | - Kavita Munjal
- Department of Pharmacognosy, M.M. College of Pharmacy, Maharishi Markandeshwar (Deemed to Be University) Mullana, Ambala 133207, Haryana, India
| | - Adrianna Gielecińska
- Department of Molecular Biotechnology and Genetics, University of Lodz, 90-237 Lodz, Poland
| | - Renata Kontek
- Department of Molecular Biotechnology and Genetics, University of Lodz, 90-237 Lodz, Poland
| | - Kamal Shah
- Institute of Pharmaceutical Research, GLA University, Mathura 281406, Uttar Pradesh, India
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6
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Gillis TD, Bearne SL. Effects of the 5'-Triphosphate Metabolites of Ribavirin, Sofosbuvir, Vidarabine, and Molnupiravir on CTP Synthase Catalysis and Filament Formation: Implications for Repurposing Antiviral Agents against SARS-CoV-2. ChemMedChem 2022; 17:e202200399. [PMID: 36184568 PMCID: PMC9538051 DOI: 10.1002/cmdc.202200399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/22/2022] [Indexed: 01/14/2023]
Abstract
Repurposing of antiviral drugs affords a rapid and effective strategy to develop therapies to counter pandemics such as COVID-19. SARS-CoV-2 replication is closely linked to the metabolism of cytosine-containing nucleotides, especially cytidine-5'-triphosphate (CTP), such that the integrity of the viral genome is highly sensitive to intracellular CTP levels. CTP synthase (CTPS) catalyzes the rate-limiting step for the de novo biosynthesis of CTP. Hence, it is of interest to know the effects of the 5'-triphosphate (TP) metabolites of repurposed antiviral agents on CTPS activity. Using E. coli CTPS as a model enzyme, we show that ribavirin-5'-TP is a weak allosteric activator of CTPS, while sofosbuvir-5'-TP and adenine-arabinofuranoside-5'-TP are both substrates. β-d-N4 -Hydroxycytidine-5'-TP is a weak competitive inhibitor relative to CTP, but induces filament formation by CTPS. Alternatively, sofosbuvir-5'-TP prevented CTP-induced filament formation. These results reveal the underlying potential for repurposed antivirals to affect the activity of a critical pyrimidine nucleotide biosynthetic enzyme.
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Affiliation(s)
- Thomas D. Gillis
- Dalhousie UniversityDepartment of Biochemistry & Molecular Biology5850 College St.Tupper Medical Building, 9JB3H 4R2HalifaxCANADA
| | - Stephen L. Bearne
- Dalhousie UniversityBiochemistry & Molecular Biology5850 College StreetTupper Medical BuildingB3H 4R2HalifaxCANADA
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7
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GTP-Dependent Regulation of CTP Synthase: Evolving Insights into Allosteric Activation and NH3 Translocation. Biomolecules 2022; 12:biom12050647. [PMID: 35625575 PMCID: PMC9138612 DOI: 10.3390/biom12050647] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/21/2022] [Accepted: 04/21/2022] [Indexed: 12/24/2022] Open
Abstract
Cytidine-5′-triphosphate (CTP) synthase (CTPS) is the class I glutamine-dependent amidotransferase (GAT) that catalyzes the last step in the de novo biosynthesis of CTP. Glutamine hydrolysis is catalyzed in the GAT domain and the liberated ammonia is transferred via an intramolecular tunnel to the synthase domain where the ATP-dependent amination of UTP occurs to form CTP. CTPS is unique among the glutamine-dependent amidotransferases, requiring an allosteric effector (GTP) to activate the GAT domain for efficient glutamine hydrolysis. Recently, the first cryo-electron microscopy structure of Drosophila CTPS was solved with bound ATP, UTP, and, notably, GTP, as well as the covalent adduct with 6-diazo-5-oxo-l-norleucine. This structural information, along with the numerous site-directed mutagenesis, kinetics, and structural studies conducted over the past 50 years, provide more detailed insights into the elaborate conformational changes that accompany GTP binding at the GAT domain and their contribution to catalysis. Interactions between GTP and the L2 loop, the L4 loop from an adjacent protomer, the L11 lid, and the L13 loop (or unique flexible “wing” region), induce conformational changes that promote the hydrolysis of glutamine at the GAT domain; however, direct experimental evidence on the specific mechanism by which these conformational changes facilitate catalysis at the GAT domain is still lacking. Significantly, the conformational changes induced by GTP binding also affect the assembly and maintenance of the NH3 tunnel. Hence, in addition to promoting glutamine hydrolysis, the allosteric effector plays an important role in coordinating the reactions catalyzed by the GAT and synthase domains of CTPS.
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8
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Abstract
Cytidine triphosphate synthase (CTPS), which comprises an ammonia ligase domain and a glutamine amidotransferase domain, catalyzes the final step of de novo CTP biosynthesis. The activity of CTPS is regulated by the binding of four nucleotides and glutamine. While glutamine serves as an ammonia donor for the ATP-dependent conversion of UTP to CTP, the fourth nucleotide GTP acts as an allosteric activator. Models have been proposed to explain the mechanisms of action at the active site of the ammonia ligase domain and the conformational changes derived by GTP binding. However, actual GTP/ATP/UTP binding modes and relevant conformational changes have not been revealed fully. Here, we report the discovery of binding modes of four nucleotides and a glutamine analog 6-diazo-5-oxo-L-norleucine in Drosophila CTPS by cryo-electron microscopy with near-atomic resolution. Interactions between GTP and surrounding residues indicate that GTP acts to coordinate reactions at both domains by directly blocking ammonia leakage and stabilizing the ammonia tunnel. Additionally, we observe the ATP-dependent UTP phosphorylation intermediate and determine interacting residues at the ammonia ligase. A noncanonical CTP binding at the ATP binding site suggests another layer of feedback inhibition. Our findings not only delineate the structure of CTPS in the presence of all substrates but also complete our understanding of the underlying mechanisms of the allosteric regulation and CTP synthesis.
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9
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Bianculli RH, Mase JD, Schulz MD. Antiviral Polymers: Past Approaches and Future Possibilities. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c01273] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Rachel H. Bianculli
- Department of Chemistry, Macromolecules Innovation Institute (MII), Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Jonathan D. Mase
- Department of Chemistry, Macromolecules Innovation Institute (MII), Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Michael D. Schulz
- Department of Chemistry, Macromolecules Innovation Institute (MII), Virginia Tech, Blacksburg, Virginia 24061, United States
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10
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Saftić D, Žinić B, Glavaš-Obrovac L, Studzińska M, Paradowska E, Leśnikowski ZJ. Synthesis and in vitro evaluation of antiviral and cytostatic properties of novel 8-triazolyl acyclovir derivatives. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2018; 37:397-414. [PMID: 30449256 DOI: 10.1080/15257770.2018.1485932] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
As a part of the research aimed on identification of new nucleobase derivatives with improved biological properties, a series of novel 8-substituted acyclovir derivatives were synthesized. The 8-azidoguanosine 4 and novel 8-azidoacyclovir 9 were synthesized from commercially available guanosine 1 and acyclovir 6 which were transformed into 8-bromopurine derivatives 2 and 7 and hydrazine derivatives 3 and 8, respectively. 8-Triazolylguanosine 5 and 8-triazolylacyclovir analogs 10-12 were successfully synthesized via the Cu(I) catalyzed 1,3-dipolar cycloaddition reaction of azides 4 and 9 with propargyl alcohol, 4-pentyn-1-ol and 5-hexyn-1-ol. The novel 1,4-disubstituted 1,2,3-triazolyl compounds 5, 10-12 were evaluated for antiviral activity against selected DNA and RNA viruses and cytostatic activity against normal Madine Darby canine kidney (MDCK I) cells, and seven tumor cell lines (HeLa, CaCo-2, NCI-H358, Jurkat, K562, Raji and HuT78). While tested compounds exerted no antiviral activity at nontoxic concentrations, the 8-triazolyl acyclovir derivative 10, with the shortest alkyl substituent at the C-4 of triazole ring, was found to be the most active against the CaCo-2 cell line.
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Affiliation(s)
- Dijana Saftić
- a Division of Organic Chemistry and Biochemistry , Ruđer Bošković Institute , Zagreb , Croatia
| | - Biserka Žinić
- a Division of Organic Chemistry and Biochemistry , Ruđer Bošković Institute , Zagreb , Croatia
| | - Ljubica Glavaš-Obrovac
- b Department of Chemistry, Biochemistry and Clinical Chemistry, Faculty of Medicine , Osijek , Croatia
| | - Mirosława Studzińska
- c Laboratory of Molecular Virology and Biological Chemistry , Institute of Medical Biology of the Polish Academy of Sciences , Łódź , Poland
| | - Edyta Paradowska
- c Laboratory of Molecular Virology and Biological Chemistry , Institute of Medical Biology of the Polish Academy of Sciences , Łódź , Poland
| | - Zbigniew J Leśnikowski
- c Laboratory of Molecular Virology and Biological Chemistry , Institute of Medical Biology of the Polish Academy of Sciences , Łódź , Poland
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McCluskey GD, Bearne SL. "Pinching" the ammonia tunnel of CTP synthase unveils coordinated catalytic and allosteric-dependent control of ammonia passage. Biochim Biophys Acta Gen Subj 2018; 1862:2714-2727. [PMID: 30251661 DOI: 10.1016/j.bbagen.2018.08.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/20/2018] [Accepted: 08/06/2018] [Indexed: 01/10/2023]
Abstract
Molecular gates within enzymes often play important roles in synchronizing catalytic events. We explored the role of a gate in cytidine-5'-triphosphate synthase (CTPS) from Escherichia coli. This glutamine amidotransferase catalyzes the biosynthesis of CTP from UTP using either l-glutamine or exogenous NH3 as a substrate. Glutamine is hydrolyzed in the glutaminase domain, with GTP acting as a positive allosteric effector, and the nascent NH3 passes through a gate located at the end of a ~25-Å tunnel before entering the synthase domain where CTP is generated. Substitution of the gate residue Val 60 by Ala, Cys, Asp, Trp, or Phe using site-directed mutagenesis and subsequent kinetic analyses revealed that V60-substitution impacts glutaminase activity, nucleotide binding, salt-dependent inhibition, and inter-domain NH3 transport. Surprisingly, the increase in steric bulk present in V60F perturbed the local structure consistent with "pinching" the tunnel, thereby revealing processes that synchronize the transfer of NH3 from the glutaminase domain to the synthase domain. V60F had a slightly reduced coupling efficiency at maximal glutaminase activity that was ameliorated by slowing down the glutamine hydrolysis reaction, consistent with a "bottleneck" effect. The inability of V60F to use exogenous NH3 was overcome in the presence of GTP, and more so if CTPS was covalently modified by 6-diazo-5-oxo-l-norleucine. Use of NH2OH by V60F as an alternative bulkier substrate occurred most efficiently when it was concomitant with the glutaminase reaction. Thus, the glutaminase activity and GTP-dependent activation act in concert to open the NH3 gate of CTPS to mediate inter-domain NH3 transport.
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Affiliation(s)
- Gregory D McCluskey
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Stephen L Bearne
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Department of Chemistry, Dalhousie University, Halifax, NS B3H 4R2, Canada.
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12
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Biophysical Analysis of Bacterial CTP Synthase Filaments Formed in the Presence of the Chemotherapeutic Metabolite Gemcitabine-5'-triphosphate. J Mol Biol 2018; 430:1201-1217. [PMID: 29501573 DOI: 10.1016/j.jmb.2018.02.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 02/16/2018] [Accepted: 02/23/2018] [Indexed: 11/21/2022]
Abstract
While enzyme activity is often regulated by a combination of substrate/effector availability and quaternary structure, many cytosolic enzymes may be further regulated through oligomerization into filaments. Cytidine-5'-triphosphate (CTP) synthase (CTPS) forms such filaments-a process that is promoted by the product CTP. The CTP analog and active chemotherapeutic metabolite gemcitabine-5'-triphosphate (dF-dCTP) is a potent inhibitor of CTPS; however, its effect on the enzyme's ability to form filaments is unknown. Alongside electron microscopy studies, dynamic light scattering showed that dF-dCTP induces Escherichia coli CTPS (EcCTPS) to form filaments in solution with lengths ≥30 nm in the presence of CTP or dF-dCTP. The substrate UTP blocks formation of filaments and effects their disassembly. EcCTPS variants were constructed to investigate the role of CTP-binding determinants in CTP- and dF-dCTP-dependent filament formation. Substitution of Glu 149 (i.e., E149D), which interacts with the ribose of CTP, caused reduced affinity for both CTP and dF-dCTP, and obviated filament formation. Phe 227 appears to interact with CTP through an edge-on interaction with the cytosine ring, yet the F227A and F227L variants bound CTP and dF-dCTP. F227A EcCTPS did not form filaments, while F227L EcCTPS formed shorter filaments in the presence of CTP or dF-dCTP. Hence, Phe 227 plays a role in filament formation, although replacement by a bulky hydrophobic amino acid is sufficient for limited filament formation. That dF-dCTP can induce filament formation highlights the fact that nucleotide analogs employed as chemotherapeutic agents may affect the filamentous states of enzymes and potentially alter their regulation in vivo.
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Gucci A, Lafrate E, Manzini S, Giochetti A. Mechanism of Antiviral Action of (E)-5-(2-Bromovinyl)-2′-Deoxyuridine (BVDU): Direct Evidence with [14C]BVDU in Herpes Simplex Virus-Infected Cells. ACTA ACUST UNITED AC 2017. [DOI: 10.1177/095632029700800611] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- A Gucci
- Department of Pharmacology, Menarmi Ricerche SpA, Via Tito Speri 10, 00040 Pomezia, Rome, Italy
| | - Em Lafrate
- Department of Pharmacology, Menarmi Ricerche SpA, Via Tito Speri 10, 00040 Pomezia, Rome, Italy
| | - S Manzini
- Department of Pharmacology, Menarmi Ricerche SpA, Via Tito Speri 10, 00040 Pomezia, Rome, Italy
| | - A Giochetti
- Department of Pharmacology, Menarmi Ricerche SpA, Via Tito Speri 10, 00040 Pomezia, Rome, Italy
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Ordonez P, Kunzelmann S, Groom HCT, Yap MW, Weising S, Meier C, Bishop KN, Taylor IA, Stoye JP. SAMHD1 enhances nucleoside-analogue efficacy against HIV-1 in myeloid cells. Sci Rep 2017; 7:42824. [PMID: 28220857 PMCID: PMC5318888 DOI: 10.1038/srep42824] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 01/16/2017] [Indexed: 11/17/2022] Open
Abstract
SAMHD1 is an intracellular enzyme that specifically degrades deoxynucleoside triphosphates into component nucleoside and inorganic triphosphate. In myeloid-derived dendritic cells and macrophages as well as resting T-cells, SAMHD1 blocks HIV-1 infection through this dNTP triphosphohydrolase activity by reducing the cellular dNTP pool to a level that cannot support productive reverse transcription. We now show that, in addition to this direct effect on virus replication, manipulating cellular SAMHD1 activity can significantly enhance or decrease the anti-HIV-1 efficacy of nucleotide analogue reverse transcription inhibitors presumably as a result of modulating dNTP pools that compete for recruitment by viral polymerases. Further, a variety of other nucleotide-based analogues, not normally considered antiretrovirals, such as the anti-herpes drugs Aciclovir and Ganciclovir and the anti-cancer drug Clofarabine are now revealed as potent anti-HIV-1 agents, under conditions of low dNTPs. This in turn suggests novel uses for nucleotide analogues to inhibit HIV-1 in differentiated cells low in dNTPs.
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Affiliation(s)
- Paula Ordonez
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, London, UK
| | - Simone Kunzelmann
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
| | - Harriet C. T. Groom
- Infection and Replication of Retroviruses Laboratory, The Francis Crick Institute, London, UK
| | - Melvyn W. Yap
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, London, UK
| | - Simon Weising
- Organic Chemistry, Department of Chemistry, Faculty of Sciences, University of Hamburg, Germany
| | - Chris Meier
- Organic Chemistry, Department of Chemistry, Faculty of Sciences, University of Hamburg, Germany
| | - Kate N. Bishop
- Infection and Replication of Retroviruses Laboratory, The Francis Crick Institute, London, UK
| | - Ian A. Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, London, UK
| | - Jonathan P. Stoye
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, London, UK
- Faculty of Medicine, Imperial College London, London, UK
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15
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McCluskey GD, Mohamady S, Taylor SD, Bearne SL. Exploring the Potent Inhibition of CTP Synthase by Gemcitabine-5'-Triphosphate. Chembiochem 2016; 17:2240-2249. [PMID: 27643605 DOI: 10.1002/cbic.201600405] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Indexed: 11/10/2022]
Abstract
CTP synthase (CTPS) catalyzes the conversion of UTP to CTP and is a target for the development of antiviral, anticancer, antiprotozoal, and immunosuppressive agents. Exposure of cell lines to the antineoplastic cytidine analogue gemcitabine causes depletion of intracellular CTP levels, but the direct inhibition of CTPS by its metabolite gemcitabine-5'-triphosphate (dF-dCTP) has not been demonstrated. We show that dF-dCTP is a potent competitive inhibitor of Escherichia coli CTPS with respect to UTP [Ki =(3.0±0.1) μm], and that its binding affinity exceeds that of CTP ≈75-fold. Site-directed mutagenesis studies indicated that Glu149 is an important binding determinant for both CTP and dF-dCTP. Comparison of the binding affinities of the 5'-triphosphates of 2'-fluoro-2'-deoxycytidine and 2'-fluoro-2'-deoxyarabinocytidine revealed that the 2'-F-arabino group contributes markedly to the strong binding of dF-dCTP. Geminal 2'-F substitution on UTP (dF-dUTP) did not result in an increase in binding affinity with CTPS. Remarkably, CTPS catalyzed the conversion of dF-dUTP into dF-dCTP, thus suggesting that dF-dCTP might be regenerated in vivo from its catabolite dF-dUTP.
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Affiliation(s)
- Gregory D McCluskey
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Samy Mohamady
- Faculty of Pharmacy, The British University in Egypt, 11837, Cairo, Egypt
| | - Scott D Taylor
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Stephen L Bearne
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada.,Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
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16
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Affiliation(s)
- Loredana Elena Vîjan
- Department of Natural Sciences, Faculty of Science, University of Pitesti, Pitesti, Romania
| | - Carmen Mihaela Topală
- Department of Natural Sciences, Faculty of Science, University of Pitesti, Pitesti, Romania
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17
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Herdewijn PAMM. 5-Substituted-2′-deoxyuridines as anti-HSV-1 Agents: Synthesis and Structure Activity Relationship. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029400500301] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Nucleoside and pyrophosphate analogues are currently in use to treat infection with Human herpesvirus 1 (HSV-1). Both series of compounds exert their activity by inhibition of the viral DNA polymerase either directly, or after anabolic phosphorylation. As the X-ray structure of the viral-specific DNA polymerase is not known, it is difficult to design a nucleoside or non-nucleoside antiviral agent which specifically inhibits this enzyme. Therefore, alternative strategies have relied on extensive structure activity relationship studies of anti-HSV-1 agents in an endeavour to understand the essential structural requirements for activity and hence the design of drugs with increased selectivity. A virus-specific enzyme which plays a crucial role in the selective activation of nucleoside analogues is thymidine kinase. Present knowledge regarding the specificity of herpesvirus thymidine kinase for its 5-substituted-2′-deoxyuridine substrates is reviewed herein.
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Affiliation(s)
- P. A. M. M. Herdewijn
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
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18
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Graci JD, Cameron CE. Challenges for the Development of Ribonucleoside Analogues as Inducers of Error Catastrophe. ACTA ACUST UNITED AC 2016; 15:1-13. [PMID: 15074710 DOI: 10.1177/095632020401500101] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
RNA viruses are responsible for numerous human diseases; some of these viruses are also potential agents of bioterrorism. In general, the replication of RNA viruses results in the incorporation of at least one mutation per round of replication, leading to a heterogeneous population, termed a qua-sispecies. The antiviral nucleoside ribavirin has been shown to cause an increase in the mutation frequency of RNA viruses. This increase in mutation frequency leads to a loss of viability due to error catastrophe. In this article, we review lethal mutagenesis as an antiviral strategy, emphasizing the challenges remaining for the development of lethal mutagenesis into a practical clinical approach.
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Affiliation(s)
- Jason D Graci
- Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, Pa., USA
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19
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Zhang Q, Mi Z, Huang Y, Ma L, Ding J, Wang J, Zhang Y, Chen Y, Zhou J, Guo F, Li X, Cen S. 2-thio-6-azauridine inhibits Vpu mediated BST-2 degradation. Retrovirology 2016; 13:13. [PMID: 26935098 PMCID: PMC4776379 DOI: 10.1186/s12977-016-0247-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 02/25/2016] [Indexed: 12/31/2022] Open
Abstract
Backgroud
BST-2 is an interferon-induced host restriction factor that inhibits the release of diverse mammalian enveloped viruses from infected cells by physically trapping the newly formed virions onto the host cell surface. Human Immunodeficiency Virus-1 (HIV-1) encodes an accessory protein Vpu that antagonizes BST-2 by down-regulating BST-2 from the cell surface. Results Using a cell-based ELISA screening system, we have discovered a lead compound, 2-thio-6-azauridine, that restores cell surface BST-2 level in the presence of Vpu. This compound has no effect on the expression of BST-2 and Vpu, but inhibits Vpu-mediated BST-2 down-regulation and exerts no effect on Vpu-induced down-regulation of CD4 or KSHV K5 protein induced BST-2 down-regulation. 2-thio-6-azauridine suppresses HIV-1 production in a BST-2-dependent manner. Further results indicate that 2-thio-6-azauridine does not interrupt the interaction of BST-2 with Vpu and β-TrCP2, but decreases BST-2 ubiquitination. Conclusion Our study demonstrates the feasibility of using small molecules to target Vpu function and sensitize wild type HIV-1 to BST-2-mediated host restriction. Electronic supplementary material The online version of this article (doi:10.1186/s12977-016-0247-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Quan Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Zeyun Mi
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China. .,Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin, China.
| | - Yuming Huang
- Beijing Ditan Hospital, Capital Medical University, Beijing, China.
| | - Ling Ma
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Jiwei Ding
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Jing Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Yongxin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Yang Chen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Jinming Zhou
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Fei Guo
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Xiaoyu Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
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20
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Coen N, Duraffour S, Snoeck R, Andrei G. KSHV targeted therapy: an update on inhibitors of viral lytic replication. Viruses 2014; 6:4731-59. [PMID: 25421895 PMCID: PMC4246246 DOI: 10.3390/v6114731] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 11/07/2014] [Accepted: 11/17/2014] [Indexed: 01/01/2023] Open
Abstract
Kaposi’s sarcoma-associated herpesvirus (KSHV) is the causative agent of Kaposi’s sarcoma, primary effusion lymphoma and multicentric Castleman’s disease. Since the discovery of KSHV 20 years ago, there is still no standard treatment and the management of virus-associated malignancies remains toxic and incompletely efficacious. As the majority of tumor cells are latently infected with KSHV, currently marketed antivirals that target the virus lytic cycle have shown inconsistent results in clinic. Nevertheless, lytic replication plays a major role in disease progression and virus dissemination. Case reports and retrospective studies have pointed out the benefit of antiviral therapy in the treatment and prevention of KSHV-associated diseases. As a consequence, potent and selective antivirals are needed. This review focuses on the anti-KSHV activity, mode of action and current status of antiviral drugs targeting KSHV lytic cycle. Among these drugs, different subclasses of viral DNA polymerase inhibitors and compounds that do not target the viral DNA polymerase are being discussed. We also cover molecules that target cellular kinases, as well as the potential of new drug targets and animal models for antiviral testing.
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Affiliation(s)
- Natacha Coen
- Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium.
| | - Sophie Duraffour
- Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium.
| | - Robert Snoeck
- Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium.
| | - Graciela Andrei
- Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium.
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21
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Mudhasani R, Kota KP, Retterer C, Tran JP, Tritsch SR, Zamani R, Whitehouse CA, Bavari S. High-content image-based screening of a signal transduction pathway inhibitor small-molecule library against highly pathogenic RNA viruses. ACTA ACUST UNITED AC 2014; 20:141-52. [PMID: 25342145 DOI: 10.1177/1087057114556253] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
High-content image-based screening was developed as an approach to test a small-molecule library of compounds targeting signal transduction pathways for antiviral activity against multiple highly pathogenic RNA viruses. Of the 2843 compounds screened, 120 compounds exhibited ≥60% antiviral activity. Four compounds (E225-0969, E528-0039, G118-0778, and G544-0735), which were most active against Rift Valley fever virus (RVFV) and showed broad-spectrum antiviral activity, were selected for further evaluation for their concentration-response profile and cytotoxicity. These compounds did not show any visible cytotoxicity at the highest concentration of compound tested (200 µM). All four of these compounds were more active than ribavirin against several viruses. One compound, E225-0969, had the lowest effective concentration (EC50 = 1.9-8.92 µM) for all the viruses tested. This compound was 13- and 43-fold more inhibitory against RVFV and Chikungunya virus (CHIKV), respectively, than ribavirin. The highest selectivity index (>106.2) was for E225-0969 against CHIKV. Time-of-addition assays suggested that all four lead compounds targeted early steps in the viral life cycle (entry and/or replication) but not virus egress. Overall, this work demonstrates that high-content image analysis can be used to screen chemical libraries for new antivirals against highly pathogenic viruses.
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Affiliation(s)
- Rajini Mudhasani
- Therapeutic Discovery Center, Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Krishna P Kota
- Therapeutic Discovery Center, Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Cary Retterer
- Therapeutic Discovery Center, Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Julie P Tran
- Therapeutic Discovery Center, Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Sarah R Tritsch
- Therapeutic Discovery Center, Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Rouzbeh Zamani
- Therapeutic Discovery Center, Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Chris A Whitehouse
- Therapeutic Discovery Center, Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Sina Bavari
- Therapeutic Discovery Center, Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
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22
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Głowacka IE, Balzarini J, Andrei G, Snoeck R, Schols D, Piotrowska DG. Design, synthesis, antiviral and cytostatic activity of ω-(1H-1,2,3-triazol-1-yl)(polyhydroxy)alkylphosphonates as acyclic nucleotide analogues. Bioorg Med Chem 2014; 22:3629-41. [PMID: 24906510 PMCID: PMC7127666 DOI: 10.1016/j.bmc.2014.05.020] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 05/12/2014] [Accepted: 05/12/2014] [Indexed: 11/24/2022]
Abstract
The efficient synthesis of a new series of polyhydroxylated dibenzyl ω-(1H-1,2,3-triazol-1-yl)alkylphosphonates as acyclic nucleotide analogues is described starting from dibenzyl ω-azido(polyhydroxy)alkylphosphonates and selected alkynes under microwave irradiation. Selected O,O-dibenzylphosphonate acyclonucleotides were transformed into the respective phosphonic acids. All compounds were evaluated in vitro for activity against a broad variety of DNA and RNA viruses and for cytostatic activity against murine leukemia L1210, human T-lymphocyte CEM and human cervix carcinoma HeLa cells. Compound (1S,2S)-16b exhibited antiviral activity against Influenza A H3N2 subtype (EC50=20μM-visual CPE score; EC50=18μM-MTS method; MCC >100μM, CC50 >100μM) in Madin Darby canine kidney cell cultures (MDCK), and (1S,2S)-16k was active against vesicular stomatitis virus and respiratory syncytial virus in HeLa cells (EC50=9 and 12μM, respectively). Moreover, compound (1R,2S)-16l showed activity against both herpes simplex viruses (HSV-1, HSV-2) in HEL cell cultures (EC50=2.9 and 4μM, respectively) and feline herpes virus in CRFK cells (EC50=4μM) but at the same time it exhibited cytotoxicity toward uninfected cell (MCC⩾4μM). Several other compounds have been found to inhibit proliferation of L1210, CEM as well as HeLa cells with IC50 in the 4-50μM range. Among them compounds (1S,2S)- and (1R,2S)-16l were the most active (IC50 in the 4-7μM range).
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Affiliation(s)
- Iwona E Głowacka
- Bioorganic Chemistry Laboratory, Faculty of Pharmacy, Medical University of Łódź, Muszyńskiego 1, 90-151 Łódź, Poland.
| | - Jan Balzarini
- Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Graciela Andrei
- Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Robert Snoeck
- Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Dominique Schols
- Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Dorota G Piotrowska
- Bioorganic Chemistry Laboratory, Faculty of Pharmacy, Medical University of Łódź, Muszyńskiego 1, 90-151 Łódź, Poland
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23
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Rostirolla DC, Milech de Assunção T, Bizarro CV, Basso LA, Santos DS. Biochemical characterization of Mycobacterium tuberculosis IMP dehydrogenase: kinetic mechanism, metal activation and evidence of a cooperative system. RSC Adv 2014. [DOI: 10.1039/c4ra02142h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Proposed kinetic mechanism forMtIMPDH in the presence of K+.
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Affiliation(s)
- Diana Carolina Rostirolla
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF)
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB)
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)
- Porto Alegre, Brazil
- Programa de Pós-Graduação em Medicina e Ciências da Saúde
| | | | - Cristiano Valim Bizarro
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF)
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB)
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)
- Porto Alegre, Brazil
| | - Luiz Augusto Basso
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF)
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB)
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)
- Porto Alegre, Brazil
- Programa de Pós-Graduação em Medicina e Ciências da Saúde
| | - Diogenes Santiago Santos
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF)
- Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB)
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)
- Porto Alegre, Brazil
- Programa de Pós-Graduação em Medicina e Ciências da Saúde
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24
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Kibenge FS, Godoy MG, Fast M, Workenhe S, Kibenge MJ. Countermeasures against viral diseases of farmed fish. Antiviral Res 2012; 95:257-81. [DOI: 10.1016/j.antiviral.2012.06.003] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 06/01/2012] [Accepted: 06/09/2012] [Indexed: 12/24/2022]
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Shetty M, Maiti B, Shivakumar Santhosh K, Venugopal MN, Karunasagar I. Betanodavirus of marine and freshwater fish: distribution, genomic organization, diagnosis and control measures. INDIAN JOURNAL OF VIROLOGY : AN OFFICIAL ORGAN OF INDIAN VIROLOGICAL SOCIETY 2012; 23:114-23. [PMID: 23997435 PMCID: PMC3550751 DOI: 10.1007/s13337-012-0088-x] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 06/29/2012] [Indexed: 10/28/2022]
Abstract
The family Nodaviridae include the genera Alphanodavirus and the Betanodavirus which are non-enveloped, single stranded RNA viruses. Alphanodavirus include the insect viruses while betanodavirus include species that are responsible for causing disease outbreaks in hatchery-reared larvae and juveniles of a wide variety of marine and freshwater fish throughout the world and has impacted fish culture over the last decade. According to International Committee on Taxonomy of Viruses, the genus Betanodavirus comprises four recognized species viz barfin flounder nervous necrosis virus, red-spotted grouper nervous necrosis virus (RGNNV), striped jack nervous necrosis virus and tiger puffer nervous necrosis virus with the RGNNV being the most common. The viruses are distributed worldwide having been recorded in Southeast Asia, Mediterranean countries, United Kingdom, North America and Australia. The disease has been reported by different names such as viral nervous necrosis, fish encephalitis, viral encephalopathy and retinopathy by various investigators. The virus is composed of two segments designated RNA1 and RNA2 and sometimes possesses an additional segment designated RNA3. However, genome arrangement of the virus can vary from strain to strain. The virus is diagnosed by microscopy and other rapid and sensitive molecular methods as well as immunological assays. Several cell lines have been developed for the virus propagation and study of infection mechanism. Control of nodavirus infection is a serious issue in aquaculture industry since it is responsible for huge economic losses. In combination with other management practices, vaccination of fish would be a useful strategy to control the disease.
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Affiliation(s)
- Mahesh Shetty
- Department of Fishery Microbiology, College of Fisheries, Karnataka Veterinary, Animal and Fisheries Sciences University, Mangalore, 575 002 India
| | - Biswajit Maiti
- Department of Fishery Microbiology, College of Fisheries, Karnataka Veterinary, Animal and Fisheries Sciences University, Mangalore, 575 002 India
| | - Kogaluru Shivakumar Santhosh
- Department of Fishery Microbiology, College of Fisheries, Karnataka Veterinary, Animal and Fisheries Sciences University, Mangalore, 575 002 India
| | - Moleyur Nagarajappa Venugopal
- Department of Fishery Microbiology, College of Fisheries, Karnataka Veterinary, Animal and Fisheries Sciences University, Mangalore, 575 002 India
| | - Indrani Karunasagar
- Department of Fishery Microbiology, College of Fisheries, Karnataka Veterinary, Animal and Fisheries Sciences University, Mangalore, 575 002 India
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Jia Y, Polunovsky V, Bitterman PB, Wagner CR. Cap-dependent translation initiation factor eIF4E: an emerging anticancer drug target. Med Res Rev 2012; 32:786-814. [PMID: 22495651 PMCID: PMC7168506 DOI: 10.1002/med.21260] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Cancer cells tend to be more highly dependent on cap‐dependent translation than normal tissues. Thus, proteins involved in the initiation of cap‐dependent translation have emerged as potential anti‐cancer drug targets. Cap‐dependent translation is initiated by the binding of the factor eIF4E to the cap domain of mRNA. Detailed x‐ray crystal and NMR structures are available for eIF4E in association with cap‐analogs, as well as domains of other initiation factors. This review will summarize efforts to design potential antagonist of eIF4E that could be used as new pharmacological tools and anti‐cancer agents and. Insights drawn from these studies should aid in the design of future inhibitors of eIF4E dependent translation initiation. © 2012 Wiley Periodicals, Inc. Med Res Rev., 32, No. 4, 786‐814, 2012
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Affiliation(s)
- Yan Jia
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
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27
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Salazar M, Yun NE, Poussard AL, Smith JN, Smith JK, Kolokoltsova OA, Patterson MJ, Linde J, Paessler S. Effect of ribavirin on junin virus infection in guinea pigs. Zoonoses Public Health 2012; 59:278-85. [PMID: 22212688 DOI: 10.1111/j.1863-2378.2011.01447.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Junin virus (JUNV) is the aetiological agent of Argentine haemorrhagic fever. The pathogenesis of the infection is not well understood, no licensed vaccines exist and no specific antiviral therapy is available. Previous studies have demonstrated the ability of ribavirin to delay and reduce JUNV disease and virus burden in guinea pigs without preventing death. Based on available data, we performed three different studies to determine the efficacy of ribavirin against JUNV in the guinea pig model with a focus on survival. Different doses and treatment schedules of ribavirin were tested in a lethal model of JUNV infection. Our results show that prolonged treatment with high doses of ribavirin significantly reduces the mortality in guinea pigs infected with JUNV. These results may be useful in future experimental studies or clinical testing.
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Affiliation(s)
- M Salazar
- Galveston National Laboratory and Institute for Human Infections and Immunity, Department of Pathology, Sealy Vaccine Center, University of Texas Medical Branch, Galveston, TX, USA
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Iyidogan P, Anderson KS. Lethal Mutagenesis as an Unconventional Approach to Combat HIV. ANTIVIRAL DRUG STRATEGIES 2011. [DOI: 10.1002/9783527635955.ch11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Kim WH, Park AY, Kang JA, Kim J, Kim JA, Lee HR, Chun P, Choi J, Lee CK, Jeong LS, Moon HR. First synthesis of 2′-oxabicyclo[3.1.0]hexyl nucleosides with a north conformation. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.01.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Roy AC, Lunn FA, Bearne SL. Inhibition of CTP synthase from Escherichia coli by xanthines and uric acids. Bioorg Med Chem Lett 2009; 20:141-4. [PMID: 20004571 DOI: 10.1016/j.bmcl.2009.11.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2009] [Revised: 11/05/2009] [Accepted: 11/05/2009] [Indexed: 10/20/2022]
Abstract
CTP synthase (CTPS) catalyzes the conversion of UTP to CTP and is a recognized target for the development of anticancer, antiviral, and antiprotozoal agents. Xanthine and related compounds inhibit CTPS activity (IC(50)=0.16-0.58mM). The presence of an 8-oxo function (i.e., uric acids) enhances inhibition (IC(50)=0.060-0.121mM). An intact purine ring with anionic character favors inhibition. In general, methylation of the purine does not significantly affect inhibition.
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Affiliation(s)
- Alexander C Roy
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 1X5
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31
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Ruebsam F, Murphy DE, Tran CV, Li LS, Zhao J, Dragovich PS, McGuire HM, Xiang AX, Sun Z, Ayida BK, Blazel JK, Kim SH, Zhou Y, Han Q, Kissinger CR, Webber SE, Showalter RE, Shah AM, Tsan M, Patel RA, Thompson PA, Lebrun LA, Hou HJ, Kamran R, Sergeeva MV, Bartkowski DM, Nolan TG, Norris DA, Khandurina J, Brooks J, Okamoto E, Kirkovsky L. Discovery of tricyclic 5,6-dihydro-1H-pyridin-2-ones as novel, potent, and orally bioavailable inhibitors of HCV NS5B polymerase. Bioorg Med Chem Lett 2009; 19:6404-12. [PMID: 19818610 DOI: 10.1016/j.bmcl.2009.09.045] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2009] [Revised: 09/13/2009] [Accepted: 09/14/2009] [Indexed: 11/27/2022]
Abstract
A novel series of non-nucleoside small molecules containing a tricyclic dihydropyridinone structural motif was identified as potent HCV NS5B polymerase inhibitors. Driven by structure-based design and building on our previous efforts in related series of molecules, we undertook extensive SAR studies, in which we identified a number of metabolically stable and very potent compounds in genotype 1a and 1b replicon assays. This work culminated in the discovery of several inhibitors, which combined potent in vitro antiviral activity against both 1a and 1b genotypes, metabolic stability, good oral bioavailability, and high C(12) (PO)/EC(50) ratios.
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Affiliation(s)
- Frank Ruebsam
- Department of Medicinal Chemistry, Anadys Pharmaceuticals, Inc., 5871 Oberlin Drive, Suite 200, San Diego, CA 92121, USA.
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32
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Ellis DA, Blazel JK, Tran CV, Ruebsam F, Murphy DE, Li LS, Zhao J, Zhou Y, McGuire HM, Xiang AX, Webber SE, Zhao Q, Han Q, Kissinger CR, Lardy M, Gobbi A, Showalter RE, Shah AM, Tsan M, Patel RA, LeBrun LA, Kamran R, Bartkowski DM, Nolan TG, Norris DA, Sergeeva MV, Kirkovsky L. 5,5'- and 6,6'-dialkyl-5,6-dihydro-1H-pyridin-2-ones as potent inhibitors of HCV NS5B polymerase. Bioorg Med Chem Lett 2009; 19:6047-52. [PMID: 19796938 DOI: 10.1016/j.bmcl.2009.09.051] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Revised: 09/09/2009] [Accepted: 09/14/2009] [Indexed: 11/16/2022]
Abstract
The discovery of 5,5'- and 6,6'-dialkyl-5,6-dihydro-1H-pyridin-2-ones as potent inhibitors of the HCV RNA-dependent RNA polymerase (NS5B) is described. Several of these agents also display potent antiviral activity in cell culture experiments (EC50 <0.10 microM). In vitro DMPK data for selected compounds as well as crystal structures of representative inhibitors complexed with the NS5B protein are also disclosed.
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Affiliation(s)
- David A Ellis
- Anadys Pharmaceuticals, Inc., 3115 Merryfield Row, San Diego, CA 92121, USA
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33
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Wang X, Zhang L. Physicochemical properties and antitumor activities for sulfated derivatives of lentinan. Carbohydr Res 2009; 344:2209-16. [PMID: 19733344 DOI: 10.1016/j.carres.2009.04.033] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 04/21/2009] [Accepted: 04/22/2009] [Indexed: 10/20/2022]
Abstract
Five fractions of lentinan, a beta-(1-->3)-D-glucan bearing beta-(1-->6)-d-glucopyranosyl branches, were treated with chlorosulfonic acid for 90 min at 60 degrees C in pyridine medium to synthesize water-soluble sulfated derivatives having the substitution degree of 1.44-1.76. The (13)C NMR spectra of the sulfated beta-glucans indicated that the C-6 position was preferentially substituted by the sulfate groups. The values of the weight-average molecular weight (M(w)), radius of gyration (s(2)(z)(1/2)), and intrinsic viscosity ([eta]) of the sulfated lentinan fractions were determined by size-exclusion chromatography with multi-angle laser light scattering (SEC-MALLS) and viscometry in 0.15 M aq NaCl at 25 degrees C, respectively. The dependence of [eta] on M(w) for the sulfated lentinan was found to be [eta]=8.93 x 10(-3)M(w)(0.73+/-0.02) (mL/g) in 0.15 M aq NaCl (for M(w) ranging from 14.6 x 10(4) to 50.4 x 10(4)). On the basis of the Yamakawa-Fujii-Yoshizaki (YFY) theory, the conformational parameters of the sulfated lentinan were calculated as 950 nm(-1) for the molar mass per unit contour length (M(L)), 4.8 nm for the persistence length (q), and 13.9 for the characteristic ratio (C(infinity)), indicating relatively extended single flexible chains in solution. The sulfated glucan fractions exhibited in vitro antiproliferative activities against sarcoma 180 (S-180) cells, and their inhibition ratios were lower than that of the triple-helix lentinan, but higher than that for the one with single random-coil lentinan chains.
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Affiliation(s)
- Xiaohua Wang
- Department of Chemistry, Wuhan University, Wuhan 430072, China
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34
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Novel antiviral agent DTriP-22 targets RNA-dependent RNA polymerase of enterovirus 71. Antimicrob Agents Chemother 2009; 53:2740-7. [PMID: 19414569 DOI: 10.1128/aac.00101-09] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Enterovirus 71 (EV71) has emerged as an important virulent neurotropic enterovirus in young children. DTriP-22 (4{4-[(2-bromo-phenyl)-(3-methyl-thiophen-2-yl)-methyl]-piperazin-1-yl}-1-pheny-1H-pyrazolo[3,4-d]pyrimidine) was found to be a novel and potent inhibitor of EV71. The molecular target of this compound was identified by analyzing DTriP-22-resistant viruses. A substitution of lysine for Arg163 in EV71 3D polymerase rendered the virus drug resistant. DTriP-22 exhibited the ability to inhibit viral replication by reducing viral RNA accumulation. The compound suppressed the accumulated levels of both positive- and negative-stranded viral RNA during virus infection. An in vitro polymerase assay indicated that DTriP-22 inhibited the poly(U) elongation activity, but not the VPg uridylylation activity, of EV71 polymerase. These findings demonstrate that the nonnucleoside analogue DTriP-22 acts as a novel inhibitor of EV71 polymerase. DTriP-22 also exhibited a broad spectrum of antiviral activity against other picornaviruses, which highlights its potential in the development of antiviral agents.
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35
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Taylor SD, Lunn FA, Bearne SL. Ground state, intermediate, and multivalent nucleotide analogue inhibitors of cytidine 5'-triphosphate synthase. ChemMedChem 2009; 3:1853-7. [PMID: 18988211 DOI: 10.1002/cmdc.200800236] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Scott D Taylor
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L3G1, Canada.
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36
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A recombinant, infectious human parainfluenza virus type 3 expressing the enhanced green fluorescent protein for use in high-throughput antiviral assays. Antiviral Res 2009; 82:12-21. [PMID: 19189850 DOI: 10.1016/j.antiviral.2009.01.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Revised: 01/05/2009] [Accepted: 01/12/2009] [Indexed: 11/22/2022]
Abstract
The ability to rescue an infectious, recombinant, negative-stranded, RNA virus from a complementary DNA (cDNA) clone, has led to new opportunities for measuring viral replication from a viral expressed reporter gene. In this study, the enhanced green fluorescent protein (EGFP) gene was inserted into the human parainfluenza virus type 3 (HPIV-3) antigenome and a recombinant, infectious virus was rescued. Maximum EGFP expression levels, measured by fluorescence, were seen at day 3. Comparison of a 3-day, viral expressed EGFP fluorescence assay to a 7-day, neutral red assay, based on complete cell destruction in virus infected MA-104 cells, yielded Z'-factor values of 0.83 and 0.70, respectively. A 3-day, endpoint EGFP-based antiviral assay and a 7-day, endpoint neutral red based antiviral assay were run in parallel to establish antiviral sensitivity profiles of 23 compounds based on selective index (SI) values. Using an SI threshold of 10, the EGFP-based antiviral assay had a sensitivity of 100% and a specificity of 54%. Thus, the use of an EGFP-based antiviral assay for testing potential antiviral compounds against HPIV-3 in a high-throughput format may be justified.
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37
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Ruebsam F, Tran CV, Li LS, Kim SH, Xiang AX, Zhou Y, Blazel JK, Sun Z, Dragovich PS, Zhao J, McGuire HM, Murphy DE, Tran MT, Stankovic N, Ellis DA, Gobbi A, Showalter RE, Webber SE, Shah AM, Tsan M, Patel RA, Lebrun LA, Hou HJ, Kamran R, Sergeeva MV, Bartkowski DM, Nolan TG, Norris DA, Kirkovsky L. 5,6-Dihydro-1H-pyridin-2-ones as potent inhibitors of HCV NS5B polymerase. Bioorg Med Chem Lett 2008; 19:451-8. [PMID: 19054673 DOI: 10.1016/j.bmcl.2008.11.048] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2008] [Revised: 11/12/2008] [Accepted: 11/13/2008] [Indexed: 11/27/2022]
Abstract
5,6-Dihydro-1H-pyridin-2-one analogs were discovered as a novel class of inhibitors of genotype 1 HCV NS5B polymerase. Among these, compound 4ad displayed potent inhibitory activities in biochemical and replicon assays (IC(50) (1b)<10nM; IC(50) (1a)<25nM, EC(50) (1b)=16nM), good in vitro DMPK properties, as well as moderate oral bioavailability in monkeys (F=24%).
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Affiliation(s)
- Frank Ruebsam
- Department of Medicinal Chemistry, Anadys Pharmaceuticals, Inc., 3115 Merryfield Row, San Diego, CA 92121, USA.
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Verma H, Patil PR, Kolhapure RM, Gopalkrishna V. ANTIVIRAL ACTIVITY OF THE INDIAN MEDICINAL PLANT EXTRACT, SWERTIA CHIRATA AGAINST HERPES SIMPLEX VIRUSES: A STUDY BY IN-VITRO AND MOLECULAR APPROACH. Indian J Med Microbiol 2008. [DOI: 10.1016/s0255-0857(21)01807-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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39
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Hexahydro-pyrrolo- and hexahydro-1H-pyrido[1,2-b]pyridazin-2-ones as potent inhibitors of HCV NS5B polymerase. Bioorg Med Chem Lett 2008; 18:5002-5. [DOI: 10.1016/j.bmcl.2008.08.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2008] [Revised: 08/05/2008] [Accepted: 08/06/2008] [Indexed: 11/19/2022]
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40
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Ellis DA, Blazel JK, Webber SE, Tran CV, Dragovich PS, Sun Z, Ruebsam F, McGuire HM, Xiang AX, Zhao J, Li LS, Zhou Y, Han Q, Kissinger CR, Showalter RE, Lardy M, Shah AM, Tsan M, Patel R, LeBrun LA, Kamran R, Bartkowski DM, Nolan TG, Norris DA, Sergeeva MV, Kirkovsky L. 4-(1,1-Dioxo-1,4-dihydro-1λ6-benzo[1,4]thiazin-3-yl)-5-hydroxy-2H-pyridazin-3-ones as potent inhibitors of HCV NS5B polymerase. Bioorg Med Chem Lett 2008; 18:4628-32. [DOI: 10.1016/j.bmcl.2008.07.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2008] [Revised: 07/02/2008] [Accepted: 07/07/2008] [Indexed: 11/29/2022]
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41
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Novel HCV NS5B polymerase inhibitors derived from 4-(1′,1′-dioxo-1′,4′-dihydro-1′λ6-benzo[1′,2′,4′]thiadiazin-3′-yl)-5-hydroxy-2H-pyridazin-3-ones: Part 4. Optimization of DMPK properties. Bioorg Med Chem Lett 2008; 18:3421-6. [DOI: 10.1016/j.bmcl.2008.04.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2008] [Revised: 03/30/2008] [Accepted: 04/01/2008] [Indexed: 10/22/2022]
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42
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Mutational analysis of conserved glycine residues 142, 143 and 146 reveals Gly(142) is critical for tetramerization of CTP synthase from Escherichia coli. Biochem J 2008; 412:113-21. [PMID: 18260824 DOI: 10.1042/bj20071163] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
CTPS (cytidine 5'-triphosphate synthase) catalyses the ATP-dependent formation of CTP from UTP using either ammonia or L-glutamine as the nitrogen source. Binding of the substrates ATP and UTP, or the product CTP, promotes oligomerization of CTPS from inactive dimers to active tetramers. In the present study, site-directed mutagenesis was used to replace the fully conserved glycine residues 142 and 143 within the UTP-binding site and 146 within the CTP-binding site of Escherchia coli CTPS. CD spectral analyses of wild-type CTPS and the glycine mutants showed a slight reduction of approximately 15% in alpha-helical content for G142A and G143A relative to G146A and wild-type CTPS, suggesting some local alterations in structure. Relative to wild-type CTPS, the values of k(cat)/K(m) for ammonia-dependent and glutamine-dependent CTP formation catalysed by G143A were reduced 22- and 16-fold respectively, whereas the corresponding values for G146A were reduced only 1.4- and 1.8-fold respectively. The glutaminase activity (k(cat)) of G146A was similar to that exhibited by the wild-type enzyme, whereas that of G143A was reduced 7.5-fold. G146A exhibited substrate inhibition at high concentrations of ammonia and a partial uncoupling of glutamine hydrolysis from CTP production. Although the apparent affinity (1/[S](0.5)) of G143A and G146A for UTP was reduced approximately 4-fold, G146A exhibited increased co-operativity with respect to UTP. Thus mutations in the CTP-binding site can affect UTP-dependent activity. Surprisingly, G142A was inactive with both ammonia and glutamine as substrates. Gel-filtration HPLC experiments revealed that both G143A and G146A were able to form active tetramers in the presence of ATP and UTP; however, nucleotide-dependent tetramerization of G142A was significantly impaired. Our observations highlight the sensitivity of the structure of CTPS to mutations in the UTP- and CTP-binding sites, with Gly(142) being critical for nucleotide-dependent oligomerization of CTPS to active tetramers. This 'structural sensitivity' may limit the number and/or types of mutations that could be selected for during the development of resistance to cytotoxic pyrimidine nucleotide analogues.
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43
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Pyrrolo[1,2-b]pyridazin-2-ones as potent inhibitors of HCV NS5B polymerase. Bioorg Med Chem Lett 2008; 18:3616-21. [PMID: 18487044 DOI: 10.1016/j.bmcl.2008.04.066] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2008] [Revised: 04/23/2008] [Accepted: 04/28/2008] [Indexed: 11/23/2022]
Abstract
Pyrrolo[1,2-b]pyridazin-2-one analogs were discovered as a novel class of inhibitors of genotype 1 HCV NS5B polymerase. Structure-based design led to the discovery of compound 3 k, which displayed potent inhibitory activities in biochemical and replicon assays (IC(50) (1b)<10nM; EC(50) (1b)=12 nM) as well as good stability towards human liver microsomes (HLM t(1/2)>60 min).
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44
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Li LS, Zhou Y, Murphy DE, Stankovic N, Zhao J, Dragovich PS, Bertolini T, Sun Z, Ayida B, Tran CV, Ruebsam F, Webber SE, Shah AM, Tsan M, Showalter RE, Patel R, Lebrun LA, Bartkowski DM, Nolan TG, Norris DA, Kamran R, Brooks J, Sergeeva MV, Kirkovsky L, Zhao Q, Kissinger CR. Novel HCV NS5B polymerase inhibitors derived from 4-(1',1'-dioxo-1',4'-dihydro-1'lambda(6)-benzo[1',2',4']thiadiazin-3'-yl)-5-hydroxy-2H-pyridazin-3-ones. Part 3: Further optimization of the 2-, 6-, and 7'-substituents and initial pharmacokinetic assessments. Bioorg Med Chem Lett 2008; 18:3446-55. [PMID: 18457949 DOI: 10.1016/j.bmcl.2008.02.072] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2008] [Revised: 02/27/2008] [Accepted: 02/28/2008] [Indexed: 11/30/2022]
Abstract
5-Hydroxy-3(2H)-pyridazinone derivatives were investigated as inhibitors of genotype 1 HCV NS5B polymerase. Lead optimization led to the discovery of compound 3a, which displayed potent inhibitory activities in biochemical and replicon assays [IC(50) (1b)<10nM; IC(50) (1a)=22 nM; EC(50) (1b)=5nM], good stability toward human liver microsomes (HLM t(1/2)>60 min), and high ratios of liver to plasma concentrations 12h after a single oral administration to rats.
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Affiliation(s)
- Lian-Sheng Li
- Anadys Pharmaceuticals, Inc., 3115 Merryfield Row, San Diego, CA 92121, USA
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45
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Nikkels A, Piérard GE. Section Review: Anti-infectives: Current therapies for shingles. Expert Opin Investig Drugs 2008. [DOI: 10.1517/13543784.5.2.185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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46
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Peters GJ, Ackland SP. Leading Article: Oncologic, Endocrine & Metabolic: New antimetabolites in preclinical and clinical development. Expert Opin Investig Drugs 2008. [DOI: 10.1517/13543784.5.6.637] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Godefridus J Peters
- Department of Oncology, Free University Hospital, PO Box 7075, 1007, MB, Amsterdam, The Netherlands
| | - Stephen P Ackland
- Department of Medical Oncology, Newcastle Mater Misericordiae Hospital, Waratah, 2298, Australia
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47
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Lunn FA, MacDonnell JE, Bearne SL. Structural requirements for the activation of Escherichia coli CTP synthase by the allosteric effector GTP are stringent, but requirements for inhibition are lax. J Biol Chem 2007; 283:2010-20. [PMID: 18003612 DOI: 10.1074/jbc.m707803200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Cytidine 5'-triphosphate synthase catalyzes the ATP-dependent formation of CTP from UTP using either NH(3) or l-glutamine (Gln) as the source of nitrogen. GTP acts as an allosteric effector promoting Gln hydrolysis but inhibiting Gln-dependent CTP formation at concentrations of >0.15 mM and NH(3)-dependent CTP formation at all concentrations. A structure-activity study using a variety of GTP and guanosine analogues revealed that only a few GTP analogues were capable of activating Gln-dependent CTP formation to varying degrees: GTP approximately 6-thio-GTP > ITP approximately guanosine 5'-tetraphosphate > O(6)-methyl-GTP > 2'-deoxy-GTP. No activation was observed with guanosine, GMP, GDP, 2',3'-dideoxy-GTP, acycloguanosine, and acycloguanosine monophosphate, indicating that the 5'-triphosphate, 2'-OH, and 3'-OH are required for full activation. The 2-NH(2) group plays an important role in binding recognition, whereas substituents at the 6-position play an important role in activation. The presence of a 6-NH(2) group obviates activation, consistent with the inability of ATP to substitute for GTP. Nucleotide and nucleoside analogues of GTP and guanosine, respectively, all inhibited NH(3)- and Gln-dependent CTP formation (often in a cooperative manner) to a similar extent (IC(50) approximately 0.2-0.5 mM). This inhibition appeared to be due solely to the purine base and was relatively insensitive to the identity of the purine with the exception of inosine, ITP, and adenosine (IC(50) approximately 4-12 mM). 8-Oxoguanosine was the best inhibitor identified (IC(50) = 80 microM). Our findings suggest that modifying 2-aminopurine or 2-aminopurine riboside may serve as an effective strategy for developing cytidine 5'-triphosphate synthase inhibitors.
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Affiliation(s)
- Faylene A Lunn
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 1X5, Canada
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48
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Souza TML, De Souza MCBV, Ferreira VF, Canuto CVBS, Marques IP, Fontes CFL, Frugulhetti ICPP. The chloroxoquinolinic derivative 6-chloro-1,4-dihydro-4-oxo-1-(β-D-ribofuranosyl) quinoline-3-carboxylic acid inhibits HSV-1 adsorption by impairing its adsorption on HVEM. Arch Virol 2007; 152:1417-24. [PMID: 17458622 DOI: 10.1007/s00705-007-0960-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2006] [Accepted: 02/07/2007] [Indexed: 11/24/2022]
Abstract
In this paper, we describe that the oxoquinolinic acid derivative (compound A) inhibited HSV-1 adsorption on Vero cells. This effect was achieved with an EC(50) value of 10 +/- 2.0 microM and with low cytotoxicity, since the CC(50) value for compound A was >1000 microM. Moreover, we demonstrate for the first time that adsorption inhibition was due to the blockage of the interactions between HSV-1 and the cellular receptor herpes virus entry mediator (HVEM). These results show that compound A can prevent HSV-1 infection in Vero cells, encouraging further studies to determine at what level compound A inhibits HSV-1-HVEM interactions.
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Affiliation(s)
- T M L Souza
- Laboratório de Virologia Molecular, Departamento de Biologia Celular e Molecular, Instituto de Biologia, Universidade Federal Fluminense, Niterói, RJ, Brazil
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49
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Prichard MN, Keith KA, Johnson MP, Harden EA, McBrayer A, Luo M, Qiu S, Chattopadhyay D, Fan X, Torrence PF, Kern ER. Selective phosphorylation of antiviral drugs by vaccinia virus thymidine kinase. Antimicrob Agents Chemother 2007; 51:1795-803. [PMID: 17325220 PMCID: PMC1855528 DOI: 10.1128/aac.01447-06] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The antiviral activity of a new series of thymidine analogs was determined against vaccinia virus (VV), cowpox virus (CV), herpes simplex virus, and varicella-zoster virus. Several compounds were identified that had good activity against each of the viruses, including a set of novel 5-substituted deoxyuridine analogs. To investigate the possibility that these drugs might be phosphorylated preferentially by the viral thymidine kinase (TK) homologs, the antiviral activities of these compounds were also assessed using TK-deficient strains of some of these viruses. Some of these compounds were shown to be much less effective in the absence of a functional TK gene in CV, which was unexpected given the high degree of amino acid identity between this enzyme and its cellular homolog. This unanticipated result suggested that the CV TK was important in the mechanism of action of these compounds and also that it might phosphorylate a wider variety of substrates than other type II enzymes. To confirm these data, we expressed the VV TK and human TK1 in bacteria and isolated the purified enzymes. Enzymatic assays demonstrated that the viral TK could efficiently phosphorylate many of these compounds, whereas most of the compounds were very poor substrates for the cellular kinase, TK1. Thus, the specific phosphorylation of these compounds by the viral kinase may be sufficient to explain the TK dependence. This unexpected result suggests that selective phosphorylation by the viral kinase may be a promising new approach in the discovery of highly selective inhibitors of orthopoxvirus replication.
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Affiliation(s)
- Mark N Prichard
- Department of Pediatrics, University of Alabama School of Medicine, Birmingham, AL 35233, USA.
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50
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Sun Y, Chung DH, Chu YK, Jonsson CB, Parker WB. Activity of ribavirin against Hantaan virus correlates with production of ribavirin-5'-triphosphate, not with inhibition of IMP dehydrogenase. Antimicrob Agents Chemother 2006; 51:84-8. [PMID: 17060520 PMCID: PMC1797647 DOI: 10.1128/aac.00790-06] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Ribavirin (RBV) is a broad-spectrum antiviral agent that inhibits the production of infectious Hantaan virus (HTNV). Although the mechanism of action of RBV against HTNV is not understood, RBV is metabolized in human cells to both RBV-5'-monophosphate, which inhibits IMP dehydrogenase, resulting in a decrease in intracellular GTP levels, and RBV-5'-triphosphate (RBV-TP), which could selectively interact with the viral RNA polymerase. To elucidate which activity of RBV was most important to its anti-HTNV activity, the mechanism of action of RBV was studied in Vero E6 cells. Incubation with 10 to 40 mug/ml RBV resulted in a small decrease in GTP levels that was not dose dependent. Increasing the RBV concentration from 10 to 40 mug/ml resulted in a decrease in viral RNA (vRNA) levels and an increase in RBV-TP formation. Mycophenolic acid (MPA), an inhibitor of IMP dehydrogenase, also resulted in a decrease in vRNA levels; however, treatment with MPA resulted in a much greater decrease in GTP levels than that seen with RBV. Treatment with both MPA and RBV resulted in increased reduction of vRNA levels but did not result in enhanced depression of GTP levels. Although guanosine prevented the depression in GTP levels caused by RBV, guanosine only partially prevented the effect of RBV on vRNA levels. These results suggest that the inhibition of IMP dehydrogenase by RBV is of secondary importance to the inhibition of vRNA replication by RBV and that the interaction of RBV-TP with the viral polymerase is the primary action of RBV.
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Affiliation(s)
- Yanjie Sun
- Southern Research Institute, 2000 Ninth Avenue South, Birmingham, AL 35205, USA
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