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Thabit AK, Monogue ML, Newman JV, Nicolau DP. Assessment of in vivo efficacy of eravacycline against Enterobacteriaceae exhibiting various resistance mechanisms: a dose-ranging study and pharmacokinetic/pharmacodynamic analysis. Int J Antimicrob Agents 2018; 51:727-732. [PMID: 29325762 DOI: 10.1016/j.ijantimicag.2018.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 11/07/2017] [Accepted: 01/02/2018] [Indexed: 10/18/2022]
Abstract
After the pharmacokinetic (PK) profile of eravacycline, a novel fluorocycline, was defined, understanding its pharmacodynamic (PD) profile became essential. This study aimed to assess the correlation of the PK/PD index fAUC/MIC (ratio of area under the free drug concentration-time curve to MIC) and its magnitude with eravacycline's efficacy against Enterobacteriaceae using an immunocompetent murine thigh infection model to resemble the immunocompetent environment in eravacycline's clinical trials. Eight Enterobacteriaceae isolates with various resistance mechanisms were tested. Eravacycline doses ranged from 1-10 mg/kg/day and were given either once daily (q24h) or divided into doses every 12 h (q12h) over the 24-h treatment period. Antibacterial efficacy was measured as the change in log10CFU at 24 h compared with 0 h controls. Composite data were modelled using a sigmoid Emax model. Eravacycline MICs ranged from 0.125-0.5 µg/mL. The mean fAUC/MIC magnitudes required for stasis and 1-log reduction for the eight isolates were 2.9 ± 3.1 and 5.6 ± 5.0, respectively. Whilst the humanised eravacycline regimen (2.5 mg/kg q12h) pharmacokinetically achieves an fAUC0-24 that is higher than the fAUC0-24 achieved with the 5 mg/kg q24h dose, the latter was associated with greater efficacy, raising a suggestive correlation of the peak free drug concentration to MIC (fCmax/MIC) ratio with eravacycline's efficacy. This study showed that the magnitudes associated with eravacycline's efficacy in an immunocompetent murine thigh model appear to be close to achievable targets in human. These data support further development of eravacycline for treatment of infections caused by drug-resistant Enterobacteriaceae.
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Affiliation(s)
- Abrar K Thabit
- Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia; Center for Anti-Infective Research and Development, Hartford Hospital, Hartford, CT, USA
| | - Marguerite L Monogue
- Center for Anti-Infective Research and Development, Hartford Hospital, Hartford, CT, USA
| | | | - David P Nicolau
- Center for Anti-Infective Research and Development, Hartford Hospital, Hartford, CT, USA; Division of Infectious Diseases, Hartford Hospital, Hartford, CT, USA.
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2
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Grossman TH, Anderson MS, Drabek L, Gooldy M, Heine HS, Henning LN, Lin W, Newman JV, Nevarez R, Siefkas-Patterson K, Radcliff AK, Sutcliffe JA. The Fluorocycline TP-271 Is Efficacious in Models of Aerosolized Bacillus anthracis Infection in BALB/c Mice and Cynomolgus Macaques. Antimicrob Agents Chemother 2017; 61:e01103-17. [PMID: 28784679 PMCID: PMC5610513 DOI: 10.1128/aac.01103-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 07/28/2017] [Indexed: 01/08/2023] Open
Abstract
The fluorocycline TP-271 was evaluated in mouse and nonhuman primate (NHP) models of inhalational anthrax. BALB/c mice were exposed by nose-only aerosol to Bacillus anthracis Ames spores at a level of 18 to 88 lethal doses sufficient to kill 50% of exposed individuals (LD50). When 21 days of once-daily dosing was initiated at 24 h postchallenge (the postexposure prophylaxis [PEP] study), the rates of survival for the groups treated with TP-271 at 3, 6, 12, and 18 mg/kg of body weight were 90%, 95%, 95%, and 84%, respectively. When 21 days of dosing was initiated at 48 h postchallenge (the treatment [Tx] study), the rates of survival for the groups treated with TP-271 at 6, 12, and 18 mg/kg TP-271 were 100%, 91%, and 81%, respectively. No deaths of TP-271-treated mice occurred during the 39-day posttreatment observation period. In the NHP model, cynomolgus macaques received an average dose of 197 LD50 of B. anthracis Ames spore equivalents using a head-only inhalation exposure chamber, and once-daily treatment of 1 mg/kg TP-271 lasting for 14 or 21 days was initiated within 3 h of detection of protective antigen (PA) in the blood. No (0/8) animals in the vehicle control-treated group survived, whereas all 8 infected macaques treated for 21 days and 4 of 6 macaques in the 14-day treatment group survived to the end of the study (56 days postchallenge). All survivors developed toxin-neutralizing and anti-PA IgG antibodies, indicating an immunologic response. On the basis of the results obtained with the mouse and NHP models, TP-271 shows promise as a countermeasure for the treatment of inhalational anthrax.
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Affiliation(s)
| | | | | | | | - Henry S Heine
- United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
| | | | - Winston Lin
- IIT Research Institute, Chicago, Illinois, USA
| | - Joseph V Newman
- Tetraphase Pharmaceuticals, Inc., Watertown, Massachusetts, USA
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3
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Durand-Réville TF, Guler S, Comita-Prevoir J, Chen B, Bifulco N, Huynh H, Lahiri S, Shapiro AB, McLeod SM, Carter NM, Moussa SH, Velez-Vega C, Olivier NB, McLaughlin R, Gao N, Thresher J, Palmer T, Andrews B, Giacobbe RA, Newman JV, Ehmann DE, de Jonge B, O'Donnell J, Mueller JP, Tommasi RA, Miller AA. ETX2514 is a broad-spectrum β-lactamase inhibitor for the treatment of drug-resistant Gram-negative bacteria including Acinetobacter baumannii. Nat Microbiol 2017; 2:17104. [PMID: 28665414 DOI: 10.1038/nmicrobiol.2017.104] [Citation(s) in RCA: 168] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 05/25/2017] [Indexed: 11/09/2022]
Abstract
Multidrug-resistant (MDR) bacterial infections are a serious threat to public health. Among the most alarming resistance trends is the rapid rise in the number and diversity of β-lactamases, enzymes that inactivate β-lactams, a class of antibiotics that has been a therapeutic mainstay for decades. Although several new β-lactamase inhibitors have been approved or are in clinical trials, their spectra of activity do not address MDR pathogens such as Acinetobacter baumannii. This report describes the rational design and characterization of expanded-spectrum serine β-lactamase inhibitors that potently inhibit clinically relevant class A, C and D β-lactamases and penicillin-binding proteins, resulting in intrinsic antibacterial activity against Enterobacteriaceae and restoration of β-lactam activity in a broad range of MDR Gram-negative pathogens. One of the most promising combinations is sulbactam-ETX2514, whose potent antibacterial activity, in vivo efficacy against MDR A. baumannii infections and promising preclinical safety demonstrate its potential to address this significant unmet medical need.
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Affiliation(s)
| | - Satenig Guler
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | | | - Brendan Chen
- AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | - Neil Bifulco
- AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | - Hoan Huynh
- AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | - Sushmita Lahiri
- AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | - Adam B Shapiro
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | - Sarah M McLeod
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | - Nicole M Carter
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | - Samir H Moussa
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | - Camilo Velez-Vega
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | - Nelson B Olivier
- AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | | | - Ning Gao
- AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | - Jason Thresher
- AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | - Tiffany Palmer
- AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | - Beth Andrews
- AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | | | - Joseph V Newman
- AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | - David E Ehmann
- AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | | | - John O'Donnell
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | - John P Mueller
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | - Rubén A Tommasi
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
| | - Alita A Miller
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, USA
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4
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Kawatkar SP, Keating TA, Olivier NB, Breen JN, Green OM, Guler SY, Hentemann MF, Loch JT, McKenzie AR, Newman JV, Otterson LG, Martínez-Botella G. Antibacterial inhibitors of Gram-positive thymidylate kinase: structure-activity relationships and chiral preference of a new hydrophobic binding region. J Med Chem 2014; 57:4584-97. [PMID: 24828090 DOI: 10.1021/jm500463c] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Thymidylate kinase (TMK), an essential enzyme in bacterial DNA biosynthesis, is an attractive therapeutic target for the development of novel antibacterial agents, and we continue to explore TMK inhibitors with improved potency, protein binding, and pharmacokinetic potential. A structure-guided design approach was employed to exploit a previously unexplored region in Staphylococcus aureus TMK via novel interactions. These efforts produced compound 39, with 3 nM IC50 against S. aureus TMK and 2 μg/mL MIC against methicillin-resistant S. aureus (MRSA). This compound exhibits a striking inverted chiral preference for binding relative to earlier compounds and also has improved physical properties and pharmacokinetics over previously published compounds. An example of this new series was efficacious in a murine S. aureus infection model, suggesting that compounds like 39 are options for further work toward a new Gram-positive antibiotic by maintaining a balance of microbiological potency, low clearance, and low protein binding that can result in lower efficacious doses.
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Affiliation(s)
- Sameer P Kawatkar
- Infection Innovative Medicines and ‡Discovery Sciences, AstraZeneca , 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
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5
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Keating TA, Newman JV, Olivier NB, Otterson LG, Andrews B, Boriack-Sjodin PA, Breen JN, Doig P, Dumas J, Gangl E, Green OM, Guler SY, Hentemann MF, Joseph-McCarthy D, Kawatkar S, Kutschke A, Loch JT, McKenzie AR, Pradeepan S, Prasad S, Martínez-Botella G. In vivo validation of thymidylate kinase (TMK) with a rationally designed, selective antibacterial compound. ACS Chem Biol 2012; 7:1866-72. [PMID: 22908966 DOI: 10.1021/cb300316n] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
There is an urgent need for new antibacterials that pinpoint novel targets and thereby avoid existing resistance mechanisms. We have created novel synthetic antibacterials through structure-based drug design that specifically target bacterial thymidylate kinase (TMK), a nucleotide kinase essential in the DNA synthesis pathway. A high-resolution structure shows compound TK-666 binding partly in the thymidine monophosphate substrate site, but also forming new induced-fit interactions that give picomolar affinity. TK-666 has potent, broad-spectrum Gram-positive microbiological activity (including activity against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus), bactericidal action with rapid killing kinetics, excellent target selectivity over the human ortholog, and low resistance rates. We demonstrate in vivo efficacy against S. aureus in a murine infected-thigh model. This work presents the first validation of TMK as a compelling antibacterial target and provides a rationale for pursuing novel clinical candidates for treating Gram-positive infections through TMK.
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Affiliation(s)
- Thomas A. Keating
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Joseph V. Newman
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Nelson B. Olivier
- AstraZeneca Discovery Sciences, 35 Gatehouse Drive,
Waltham, Massachusetts 02451, United States
| | - Linda G. Otterson
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Beth Andrews
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - P. Ann Boriack-Sjodin
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
- AstraZeneca Discovery Sciences, 35 Gatehouse Drive,
Waltham, Massachusetts 02451, United States
| | - John N. Breen
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
- AstraZeneca Discovery Sciences, 35 Gatehouse Drive,
Waltham, Massachusetts 02451, United States
| | - Peter Doig
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
- AstraZeneca Discovery Sciences, 35 Gatehouse Drive,
Waltham, Massachusetts 02451, United States
| | - Jacques Dumas
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Eric Gangl
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Oluyinka M. Green
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Satenig Y. Guler
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Martin F. Hentemann
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Diane Joseph-McCarthy
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Sameer Kawatkar
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Amy Kutschke
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - James T. Loch
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Andrew R. McKenzie
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Selvi Pradeepan
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Swati Prasad
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Gabriel Martínez-Botella
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
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6
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Martínez-Botella G, Breen JN, Duffy JES, Dumas J, Geng B, Gowers IK, Green OM, Guler S, Hentemann MF, Hernandez-Juan FA, Joseph-McCarthy D, Kawatkar S, Larsen NA, Lazari O, Loch JT, Macritchie JA, McKenzie AR, Newman JV, Olivier NB, Otterson LG, Owens AP, Read J, Sheppard DW, Keating TA. Discovery of Selective and Potent Inhibitors of Gram-Positive Bacterial Thymidylate Kinase (TMK). J Med Chem 2012; 55:10010-21. [DOI: 10.1021/jm3011806] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gabriel Martínez-Botella
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - John N. Breen
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
- AstraZeneca Discovery Sciences, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | | | - Jacques Dumas
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Bolin Geng
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Ian K. Gowers
- BioFocus, Chesterford Research Park, Saffron Walden
CB10 1XL, U.K
| | - Oluyinka M. Green
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Satenig Guler
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Martin F. Hentemann
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | | | - Diane Joseph-McCarthy
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Sameer Kawatkar
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Nicholas A. Larsen
- AstraZeneca Discovery Sciences, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Ovadia Lazari
- BioFocus, Chesterford Research Park, Saffron Walden
CB10 1XL, U.K
| | - James T. Loch
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | | | - Andrew R. McKenzie
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Joseph V. Newman
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Nelson B. Olivier
- AstraZeneca Discovery Sciences, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Linda G. Otterson
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | - Andrew P. Owens
- BioFocus, Chesterford Research Park, Saffron Walden
CB10 1XL, U.K
| | - Jon Read
- AstraZeneca Discovery Sciences, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
| | | | - Thomas A. Keating
- AstraZeneca Infection Innovative Medicines, 35 Gatehouse Drive, Waltham, Massachusetts
02451, United States
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7
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Reck F, Alm RA, Brassil P, Newman JV, Ciaccio P, McNulty J, Barthlow H, Goteti K, Breen J, Comita-Prevoir J, Cronin M, Ehmann DE, Geng B, Godfrey AA, Fisher SL. Novel N-Linked Aminopiperidine Inhibitors of Bacterial Topoisomerase Type II with Reduced pKa: Antibacterial Agents with an Improved Safety Profile. J Med Chem 2012; 55:6916-33. [DOI: 10.1021/jm300690s] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Andrew Aydon Godfrey
- Pharmaceutical
Development, Chemical Sciences, AstraZeneca, Silk Road Business Park, Macclesfield, SK10 4TG Cheshire, England
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8
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Stokes SS, Gowravaram M, Huynh H, Lu M, Mullen GB, Chen B, Albert R, O'Shea TJ, Rooney MT, Hu H, Newman JV, Mills SD. Discovery of bacterial NAD⁺-dependent DNA ligase inhibitors: improvements in clearance of adenosine series. Bioorg Med Chem Lett 2011; 22:85-9. [PMID: 22154350 DOI: 10.1016/j.bmcl.2011.11.071] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 11/16/2011] [Accepted: 11/18/2011] [Indexed: 10/15/2022]
Abstract
Optimization of clearance of adenosine inhibitors of bacterial NAD(+)-dependent DNA ligase is discussed. To reduce Cytochrome P-450-mediated metabolic clearance, many strategies were explored; however, most modifications resulted in compounds with reduced antibacterial activity and/or unchanged total clearance. The alkyl side chains of the 2-cycloalkoxyadenosines were fluorinated, and compounds with moderate antibacterial activity and favorable pharmacokinetic properties in rat and dog were identified.
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Affiliation(s)
- Suzanne S Stokes
- Infection Innovative Medicines Unit, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA.
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9
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Abstract
Enzymes that utilize nicotinamide adenine dinucleotide (NAD) or its 2'-phosphate derivative (NADP) are found throughout the kingdoms of life. These enzymes are fundamental to many biochemical pathways, including central intermediary metabolism and mechanisms for cell survival and defense. The complete genomes of 25 organisms representing bacteria, protists, fungi, plants, and animals, and 811 viruses, were mined to identify and classify NAD(P)-dependent enzymes. An average of 3.4% of the proteins in these genomes was categorized as NAD(P)-utilizing proteins, with highest prevalence in the medium-chain oxidoreductase and short-chain oxidoreductase families. In general, the distribution of these enzymes by oxidoreductase family was correlated to the number of different catalytic mechanisms in each family. Organisms with smaller genomes encoded a larger proportion of NAD(P)-dependent enzymes in their proteome (approximately 6%) as compared to the larger genomes of eukaryotes (approximately 3%). Among viruses, those with large, double-strand DNA genomes were shown to encode oxidoreductases. Gram-positive and gram-negative bacteria showed some differences in the distribution of NAD(P)-dependent proteins. Several organisms such as M. tuberculosis, P. falciparum, and A. thaliana showed unique distributions of oxidoreductases corresponding to some phenotypic features.
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Affiliation(s)
- Richard Kho
- Triad Therapeutics, Inc., 9381 Judicial Drive, San Diego, California 92121, USA
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10
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Abstract
A novel method to organize protein structural information based solely on sequence is presented. The method clusters proteins into families that correlate with the three-dimensional protein structure and the conformation of the bound ligands. This procedure was applied to nicotinamide adenine dinucleotide [NAD(P)]-utilizing enzymes to identify a total of 94 sequence families, 53 of which are structurally characterized. Each of the structurally characterized proteins within a sequence family correlates to a single protein fold and to a common bound conformation of NAD(P). A wide range of structural folds is identified that recognize NAD(P), including Rossmann folds and beta/alpha barrels. The defined sequence families can be used to identify the type and prevalence of NAD(P)-utilizing enzymes in the proteomes of sequenced organisms. The proteome of Mycobacterium tuberculosis was mined to generate a proteome-wide profile of NAD(P)-utilizing enzymes coded by this organism. This enzyme family comprises approximately 6% of the open reading frames, with the largest subgroup being the Rossmann fold, short-chain dehydrogenases. The preponderance of short-chain dehydrogenases correlates strongly with the phenotype of M. tuberculosis, which is characterized as having one of the most complex prokaryotic cell walls.
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Affiliation(s)
- Richard Kho
- Triad Therapeutics, Inc., San Diego, CA 92121, USA
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11
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Mansfield KG, Lin KC, Xia D, Newman JV, Schauer DB, MacKey J, Lackner AA, Carville A. Enteropathogenic Escherichia coli and ulcerative colitis in cotton-top tamarins (Saguinus oedipus). J Infect Dis 2001; 184:803-7. [PMID: 11517446 DOI: 10.1086/322990] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2001] [Revised: 05/24/2001] [Indexed: 12/24/2022] Open
Abstract
The cotton-top tamarin (CTT; Saguinus oedipus) is an endangered New World primate that develops a highly prevalent idiopathic colitis resembling human ulcerative colitis. This study found that enteropathogenic Escherichia coli (EPEC) caused acute colitis in CTTs, which was associated with ulcerative colitis. EPEC clinical isolates revealed localized adherence patterns by HEp-2 assay and were devoid of Shiga-toxin production. Sequencing of the eae gene (GenBank accession no. AF319597) revealed 99.2% identity to sequences of human isolates (GenBank AF116899) and corresponded to the epsilon intimin gene subtype. Detection of intimin sequences by polymerase chain reaction on primary fecal cultures indicated widespread EPEC infection in the CTT colony. Prospective analysis revealed that animals with fecal cultures positive for intimin sequences had a higher frequency of active colitis (75.0% vs. 27.2%; P<.005, chi(2) test) and higher histological scores of colonic inflammation (0.875 vs. 0.455, respectively; P<.05, Mann-Whitney rank sum test).
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Affiliation(s)
- K G Mansfield
- New England Regional Primate Research Center, Harvard Medical School, Southborough, MA 01772-9012, USA.
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12
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Newman JV, Kosaka T, Sheppard BJ, Fox JG, Schauer DB. Bacterial infection promotes colon tumorigenesis in Apc(Min/+) mice. J Infect Dis 2001; 184:227-30. [PMID: 11424022 DOI: 10.1086/321998] [Citation(s) in RCA: 126] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2000] [Revised: 04/05/2001] [Indexed: 12/21/2022] Open
Abstract
The Min mouse, which has a germ line mutation in 1 allele of the Apc tumor suppressor gene, is a model for the early steps in human colorectal cancer. Helicobacter pylori infection, a known risk factor for gastric cancer in humans, causes chronic inflammation and increased epithelial cell proliferation in the stomach. Infection with the bacterium Citrobacter rodentium is known to increase epithelial cell proliferation and to promote chemically initiated tumors in the colon of mice. Min mice infected with C. rodentium at 1 month of age were found to have a 4-fold increase in the number of colonic adenomas at 6 months of age, compared with uninfected Min mice. Most of the colonic adenomas in the infected Min mice were in the distal colon, where C. rodentium-induced hyperplasia occurs. These data demonstrate that bacterial infection promotes colon tumor formation in genetically susceptible mice.
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Affiliation(s)
- J V Newman
- Division of Bioengineering and Environmental Health, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Luperchio SA, Newman JV, Dangler CA, Schrenzel MD, Brenner DJ, Steigerwalt AG, Schauer DB. Citrobacter rodentium, the causative agent of transmissible murine colonic hyperplasia, exhibits clonality: synonymy of C. rodentium and mouse-pathogenic Escherichia coli. J Clin Microbiol 2000; 38:4343-50. [PMID: 11101562 PMCID: PMC87603 DOI: 10.1128/jcm.38.12.4343-4350.2000] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2000] [Accepted: 09/29/2000] [Indexed: 11/20/2022] Open
Abstract
Citrobacter rodentium (formerly Citrobacter freundii biotype 4280 and Citrobacter genomospecies 9) was described on the basis of biochemical characterization and DNA-DNA hybridization data and is the only Citrobacter species known to possess virulence factors homologous to those of the human pathogens enteropathogenic Escherichia coli and enterohemorrhagic E. coli. These virulence factors are encoded on the locus of enterocyte effacement (LEE), a pathogenicity island required for the characteristic attaching and effacing (AE) pathology seen in infection with these three pathogens. C. rodentium, which apparently infects only mice, provides a useful animal model for studying the molecular basis of AE pathology. No work has been done to assess differences in pathogenicity between C. rodentium isolates from diverse sources. Here, we report the examination of 15 C. rodentium isolates using a battery of genetic and biochemical approaches. No differences were observed between the isolates by repetitive-element sequence-based PCR analysis, biochemical analysis, and possession of LEE-specific virulence factors. These data suggest that members of the species are clonal. We further characterized an atypical E. coli strain from Japan called mouse-pathogenic E. coli (MPEC) that, in our hands, caused the same disease as C. rodentium. Applying the same battery of tests, we found that MPEC possesses LEE-encoded virulence factors and is indistinguishable from the previously characterized C. rodentium isolate DBS100. These results demonstrate that MPEC is a misclassified C. rodentium isolate and that members of this species are clonal and represent the only known attaching and effacing bacterial pathogen of mice.
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Affiliation(s)
- S A Luperchio
- Division of Bioengineering and Environmental Health, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Abstract
Citrobacter rodentium is the causative agent of transmissible murine colonic hyperplasia and contains a locus of enterocyte effacement (LEE) similar to that found in enteropathogenic Escherichia coli (EPEC). EPEC espB is necessary for intimate attachment and signal transduction between EPEC and cultured cell monolayers. Mice challenged with wild-type C. rodentium develop a mucosal immunoglobulin A response to EspB. In this study, C. rodentium espB has been cloned and its nucleotide sequence has been determined. C. rodentium espB was found to have 90% identity to EPEC espB. A nonpolar insertion mutation in C. rodentium espB was constructed and used to replace the chromosomal wild-type allele. The C. rodentium espB mutant exhibited reduced cell association and had no detectable fluorescent actin staining activity on cultured cell monolayers. The C. rodentium espB mutant also failed to colonize laboratory mice following experimental inoculation. The espB mutation could be complemented with a plasmid-encoded copy of the gene, which restored both cell association and fluorescent actin staining activity, as well as the ability to colonize laboratory mice. These studies indicate that espB is necessary for signal transduction and for colonization of laboratory mice by C. rodentium.
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Affiliation(s)
- J V Newman
- Division of Bioengineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Abstract
Escherichia coli F-18, a normal human fecal isolate, is an excellent colonizer of the streptomycin-treated mouse large intestine. E. coli F-18 Col-, a derivative of E. coli F-18 that no longer makes the E. coli F-18 colicin, colonizes the mouse large intestine as well as E. coli F-18 when fed alone, but is eliminated when fed together with E. coli F-18. Recently, a random bank of E. coli F-18 DNA was transformed into E. coli F-18 Col-, the resultant population was fed to streptomycin-treated mice, and the intestine was used to select the best colonizer. In this fashion, a 6.5 kb E. coli F-18 DNA fragment was isolated. This fragment was shown to enhance E. coli F-18 Col- mouse large intestinal colonizing ability and survival during stationary phase in intestinal mucus in vitro, as well as stimulate the synthesis of type-1 fimbriae. Here, we present evidence that the gene responsible for the enhanced E. coli F-18 Col- colonizing ability and survival during stationary phase in vitro is leuX. This gene encodes a rare leucine tRNA specific for the UUG codon. In addition, we show that the presence of a functional leuX gene is necessary for E. coli K-12 intestinal colonization and for survival in stationary phase.
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Affiliation(s)
- J V Newman
- Department of Biochemistry, Microbiology and Molecular Genetics, University of Rhode Island, Kingston 02881, USA
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Newman JV, Burghoff RL, Pallesen L, Krogfelt KA, Kristensen CS, Laux DC, Cohen PS. Stimulation of Escherichia coliF-18Col âtype-1 fimbriae synthesis by leuX. FEMS Microbiol Lett 1994. [DOI: 10.1111/j.1574-6968.1994.tb07181.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Newman JV, Burghoff RL, Pallesen L, Krogfelt KA, Kristensen CS, Laux DC, Cohen PS. Stimulation of Escherichia coli F-18Col- type-1 fimbriae synthesis by leuX. FEMS Microbiol Lett 1994; 122:281-7. [PMID: 7988869 DOI: 10.1016/0378-1097(94)00337-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Escherichia coli F-18, a normal human fecal isolate, is an excellent colonizer of the streptomycin-treated mouse large intestine. E. coli F-18Col-, a derivative of E. coli F-18 which no longer makes the E. coli F-18 colicin, colonizes the large intestine as well as E. coli F-18 when fed to mice alone but is eliminated when fed together with E. coli F-18. Recently we randomly cloned E. coli F-18 DNA into E. coli F-18Col- and let the mouse intestine select the best colonizer. In this way, we isolated a 6.5-kb E. coli F-18 DNA sequence that simultaneously stimulated synthesis of type 1 fimbriae and enhanced E. coli F-18Col- colonizing ability. In the present investigation we show that the gene responsible for stimulation of type 1 fimbriae synthesis appears to be leuX, which encodes a tRNA specific for the rare leucine codon UUG. Moreover, it appears that expression of leuX may be regulated by two proteins (22 kDa and 26 kDa) encoded by genes immediately adjacent to leuX.
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Affiliation(s)
- J V Newman
- Department of Biochemistry, Microbiology, and Molecular Genetics, University of Rhode Island, Kingston 02881
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Burghoff RL, Pallesen L, Krogfelt KA, Newman JV, Richardson M, Bliss JL, Laux DC, Cohen PS. Utilization of the mouse large intestine to select an Escherichia coli F-18 DNA sequence that enhances colonizing ability and stimulates synthesis of type 1 fimbriae. Infect Immun 1993; 61:1293-300. [PMID: 8095923 PMCID: PMC281361 DOI: 10.1128/iai.61.4.1293-1300.1993] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Escherichia coli F-18, a normal human fecal isolate, is an excellent colonizer of the streptomycin-treated mouse large intestine. E. coli F-18 Col-, a derivative of E. coli F-18 which no longer makes the E. coli F-18 colicin, colonizes the large intestine as well as E. coli F-18 when fed to mice alone but is eliminated when fed together with E. coli F-18. Random sequences of E. coli F-18 DNA were cloned into pRLB2, a par-B-stabilized derivative of pHC79. The entire gene library was transformed into E. coli F-18 Col- and fed to streptomycin-treated mice. The mouse large intestine selected a predominant clone which contained a recombinant plasmid (pRLB7) that enhanced E. coli F-18 Col- colonizing ability 100-fold but did not stimulate colicin synthesis. Moreover, pRLB7 simultaneously improved the survival of E. coli F-18 Col- in stationary phase in vitro, utilizing nutrients derived from mouse cecal mucus, and stimulated synthesis of both type 1 fimbriae and three E. coli F-18 Col- outer membrane proteins (74, 71, and 69 kDa). The 6.5-kb E. coli F-18 DNA sequence in pRLB7 does not contain either the fim operon or pilG (hns), both known to be involved in type 1 fimbrial synthesis. The sequence encodes six proteins, all smaller than the three E. coli F-18 Col- outer membrane proteins whose synthesis it stimulates. Collectively, the results suggest that the cloned E. coli F-18 DNA sequence contains one or more regulators of E. coli F-18 Col- operons expressed in the mouse large intestine in vivo and in isolated mouse cecal mucus in vitro.
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Affiliation(s)
- R L Burghoff
- Department of Microbiology, University of Rhode Island, Kingston 02881
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