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Murphy-Benenato KE, Gingipalli L, Boriack-Sjodin PA, Martinez-Botella G, Carcanague D, Eyermann CJ, Gowravaram M, Harang J, Hale MR, Ioannidis G, Jahic H, Johnstone M, Kutschke A, Laganas VA, Loch JT, Miller MD, Oguto H, Patel SJ. Negishi cross-coupling enabled synthesis of novel NAD(+)-dependent DNA ligase inhibitors and SAR development. Bioorg Med Chem Lett 2015; 25:5172-7. [PMID: 26463129 DOI: 10.1016/j.bmcl.2015.09.075] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Revised: 09/28/2015] [Accepted: 09/30/2015] [Indexed: 01/17/2023]
Abstract
Two novel compounds, pyridopyrimidines (1) and naphthyridines (2) were identified as potent inhibitors of bacterial NAD(+)-dependent DNA ligase (Lig) A in a fragment screening. SAR was guided by molecular modeling and X-ray crystallography. It was observed that the diaminonitrile pharmacophore made a key interaction with the ligase enzyme, specifically residues Glu114, Lys291, and Leu117. Synthetic challenges limited opportunities for diversification of the naphthyridine core, therefore most of the SAR was focused on a pyridopyrimidine scaffold. The initial diversification at R(1) improved both enzyme and cell potency. Further SAR developed at the R(2) position using the Negishi cross-coupling reaction provided several compounds, among these compounds 22g showed good enzyme potency and cellular potency.
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Affiliation(s)
- Kerry E Murphy-Benenato
- Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA
| | - Lakshmaiah Gingipalli
- Oncology Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA
| | - P Ann Boriack-Sjodin
- Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA
| | - Gabriel Martinez-Botella
- Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA
| | - Dan Carcanague
- Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA
| | - Charles J Eyermann
- Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA
| | - Madhu Gowravaram
- Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA
| | - Jenna Harang
- Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA
| | - Michael R Hale
- Oncology Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA
| | - Georgine Ioannidis
- Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA
| | - Harris Jahic
- Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA
| | - Michele Johnstone
- Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA
| | - Amy Kutschke
- Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA
| | - Valerie A Laganas
- Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA
| | - James T Loch
- Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA
| | - Matthew D Miller
- Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA
| | - Herbert Oguto
- Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA
| | - Sahil Joe Patel
- Discovery Sciences, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA
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Laganas VA, Dunn EF, McLaughlin RE, Tiong-Yip CL, Yuzhakov O, Isabella VM, Hill P, Yu Q. Characterization of novel respiratory syncytial virus inhibitors identified by high throughput screen. Antiviral Res 2014; 115:71-4. [PMID: 25542974 DOI: 10.1016/j.antiviral.2014.12.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 12/12/2014] [Accepted: 12/15/2014] [Indexed: 10/24/2022]
Abstract
Respiratory Syncytial Virus (RSV) is a major cause of lower respiratory tract infections with no effective treatment available. Finding novel inhibitors of RSV is an important first step towards developing an efficacious RSV therapy. Here we report the characterization of three novel classes of RSV replication inhibitors identified through a high throughput RSV replicon screen of ∼1million compounds in the AstraZeneca compound collection. These inhibitors, cpd 1, 2, and 3, specifically targeted RSV and were not active against other viruses tested. Resistance selection in RSV A2 with cpd 1 identified escape viruses with mutations mapped to the RSV L protein, an RNA-dependent RNA polymerase (Y1631C and I1413T). Recombinant RSV containing the L Y1631C substitution conferred resistance towards cpd 1, suggesting that the RSV polymerase is the target of this inhibitor. Interestingly, cpd 3, a nucleoside analog, induced a single resistant mutation in the P protein (D231V), indicating a novel mode of action not previously reported. cpd 2 affected host cell cycle and no frequent mutation was isolated following resistance selection, suggesting its possible involvement of a host-targeted mechanism. Taken together, we have identified three novel RSV inhibitors with different modes of action, providing new chemistry starting points for the discovery and development of future RSV therapeutic treatment.
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Affiliation(s)
- Valerie A Laganas
- Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, United States
| | - Ewan F Dunn
- Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, United States
| | - Robert E McLaughlin
- Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, United States
| | - Choi Lai Tiong-Yip
- Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, United States
| | - Olga Yuzhakov
- Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, United States
| | - Vincent M Isabella
- Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, United States
| | - Pamela Hill
- Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, United States
| | - Qin Yu
- Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, United States.
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Abibi A, Ferguson AD, Fleming PR, Gao N, Hajec LI, Hu J, Laganas VA, McKinney DC, McLeod SM, Prince DB, Shapiro AB, Buurman ET. The role of a novel auxiliary pocket in bacterial phenylalanyl-tRNA synthetase druggability. J Biol Chem 2014; 289:21651-62. [PMID: 24936059 DOI: 10.1074/jbc.m114.574061] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The antimicrobial activity of phenyl-thiazolylurea-sulfonamides against Staphylococcus aureus PheRS are dependent upon phenylalanine levels in the extracellular fluids. Inhibitor efficacy in animal models of infection is substantially diminished by dietary phenylalanine intake, thereby reducing the perceived clinical utility of this inhibitor class. The search for novel antibacterial compounds against Gram-negative pathogens led to a re-evaluation of this phenomenon, which is shown here to be unique to S. aureus. Inhibition of macromolecular syntheses and characterization of novel resistance mutations in Escherichia coli demonstrate that antimicrobial activity of phenyl-thiazolylurea-sulfonamides is mediated by PheRS inhibition, validating this enzyme as a viable drug discovery target for Gram-negative pathogens. A search for novel inhibitors of PheRS yielded three novel chemical starting points. NMR studies were used to confirm direct target engagement for phenylalanine-competitive hits. The crystallographic structure of Pseudomonas aeruginosa PheRS defined the binding modes of these hits and revealed an auxiliary hydrophobic pocket that is positioned adjacent to the phenylalanine binding site. Three viable inhibitor-resistant mutants were mapped to this pocket, suggesting that this region is a potential liability for drug discovery.
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Affiliation(s)
| | - Andrew D Ferguson
- the Department of Structure and Biophysics, Discovery Sciences, AstraZeneca R&D Boston, Waltham, Massachusetts 02451
| | | | - Ning Gao
- From the Departments of Biosciences and
| | | | - Jun Hu
- the Department of Structure and Biophysics, Discovery Sciences, AstraZeneca R&D Boston, Waltham, Massachusetts 02451
| | | | | | | | - D Bryan Prince
- the Department of Structure and Biophysics, Discovery Sciences, AstraZeneca R&D Boston, Waltham, Massachusetts 02451
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Buurman ET, Laganas VA, Liu CF, Manchester JI. Antimicrobial Activity of Adenine-Based Inhibitors of NAD(+)-Dependent DNA Ligase. ACS Med Chem Lett 2012; 3:663-7. [PMID: 24900527 DOI: 10.1021/ml300169x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 07/12/2012] [Indexed: 01/28/2023] Open
Abstract
The relationship between enzyme inhibition and antimicrobial potency of adenine-based NAD(+)-dependent DNA ligase (LigA) inhibitors was investigated using a strain of the Gram-negative pathogen Haemophilus influenzae lacking its major AcrAB-TolC efflux pump and the Gram-positive pathogen Streptococcus pneumoniae. To this end, biochemical inhibitors not mediating their antibacterial mode of action (MOA) via LigA were removed from the analysis. In doing so, a significant number of compounds were identified that acted via inhibition of LigA in S. pneumoniae but not in H. influenzae, despite being inhibitors of both isozymes. Deviations from the line correlating antimicrobial and biochemical potencies of LigA inhibitors with the correct MOA were observed for both species. These deviations, usually corresponding to higher MIC/IC50 ratios, were attributed to varying compound permeance into the cell.
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Affiliation(s)
- Ed T. Buurman
- Departments of †Bioscience and ‡Chemistry, AstraZeneca R&D Boston, Infection Innovative Medicines Unit, Waltham, Massachusetts 02451, United States
| | - Valerie A. Laganas
- Departments of †Bioscience and ‡Chemistry, AstraZeneca R&D Boston, Infection Innovative Medicines Unit, Waltham, Massachusetts 02451, United States
| | - Ce Feng Liu
- Departments of †Bioscience and ‡Chemistry, AstraZeneca R&D Boston, Infection Innovative Medicines Unit, Waltham, Massachusetts 02451, United States
| | - John I. Manchester
- Departments of †Bioscience and ‡Chemistry, AstraZeneca R&D Boston, Infection Innovative Medicines Unit, Waltham, Massachusetts 02451, United States
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