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Durand-Réville TF, Comita-Prevoir J, Zhang J, Wu X, May-Dracka TL, Romero JAC, Wu F, Chen A, Shapiro AB, Carter NM, McLeod SM, Giacobbe RA, Verheijen JC, Lahiri SD, Sacco MD, Chen Y, O'Donnell JP, Miller AA, Mueller JP, Tommasi RA. Discovery of an Orally Available Diazabicyclooctane Inhibitor (ETX0282) of Class A, C, and D Serine β-Lactamases. J Med Chem 2020; 63:12511-12525. [PMID: 32658473 PMCID: PMC7927146 DOI: 10.1021/acs.jmedchem.0c00579] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
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Multidrug
resistant Gram-negative bacterial infections are an increasing
public health threat due to rapidly rising resistance toward β-lactam
antibiotics. The hydrolytic enzymes called β-lactamases are
responsible for a large proportion of the resistance phenotype. β-Lactamase
inhibitors (BLIs) can be administered in combination with β-lactam
antibiotics to negate the action of the β-lactamases, thereby
restoring activity of the β-lactam. Newly developed BLIs offer
some advantage over older BLIs in terms of enzymatic spectrum but
are limited to the intravenous route of administration. Reported here
is a novel, orally bioavailable diazabicyclooctane (DBO) β-lactamase
inhibitor. This new DBO, ETX1317, contains an endocyclic carbon–carbon
double bond and a fluoroacetate activating group and exhibits broad
spectrum activity against class A, C, and D serine β-lactamases.
The ester prodrug of ETX1317, ETX0282, is orally bioavailable and,
in combination with cefpodoxime proxetil, is currently in development
as an oral therapy for multidrug resistant and carbapenem-resistant Enterobacterales infections.
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Affiliation(s)
| | | | - Jing Zhang
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Xiaoyun Wu
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Tricia L May-Dracka
- Infection Discovery, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | | | - Frank Wu
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - April Chen
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Adam B Shapiro
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Nicole M Carter
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Sarah M McLeod
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Robert A Giacobbe
- Infection Discovery, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Jeroen C Verheijen
- Infection Discovery, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Sushmita D Lahiri
- Infection Discovery, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Michael D Sacco
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States
| | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States
| | - John P O'Donnell
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Alita A Miller
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - John P Mueller
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Rubén A Tommasi
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
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2
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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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3
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Greenspan PD, Clark KL, Tommasi RA, Cowen SD, McQuire LW, Farley DL, van Duzer JH, Goldberg RL, Zhou H, Du Z, Fitt JJ, Coppa DE, Fang Z, Macchia W, Zhu L, Capparelli MP, Goldstein R, Wigg AM, Doughty JR, Bohacek RS, Knap AK. Identification of dipeptidyl nitriles as potent and selective inhibitors of cathepsin B through structure-based drug design. J Med Chem 2001; 44:4524-34. [PMID: 11741472 DOI: 10.1021/jm010206q] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cathepsin B is a member of the papain superfamily of cysteine proteases and has been implicated in the pathology of numerous diseases, including arthritis and cancer. As part of an effort to identify potent, reversible inhibitors of this protease, we examined a series of dipeptidyl nitriles, starting with the previously reported Cbz-Phe-NH-CH(2)CN (19, IC(50) = 62 microM). High-resolution X-ray crystallographic data and molecular modeling were used to optimize the P(1), P(2), and P(3) substituents of this template. Cathepsin B is unique in its class in that it contains a carboxylate recognition site in the S(2)' pocket of the active site. Inhibitor potency and selectivity were enhanced by tethering a carboxylate functionality from the carbon alpha to the nitrile to interact with this region of the enzyme. This resulted in the identification of compound 10, a 7 nM inhibitor of cathepsin B, with excellent selectivity over other cysteine cathepsins.
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Affiliation(s)
- P D Greenspan
- Arthritis and Bone Metabolism Research, Novartis Pharmaceuticals Corporation, 556 Morris Avenue, Summit, New Jersey 07901, USA.
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4
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Affiliation(s)
- R A Tommasi
- Novartis Pharmaceuticals Corporation, 556 Morris Avenue, Summit, New Jersey 07901, USA
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5
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Turner SR, Strohbach JW, Tommasi RA, Aristoff PA, Johnson PD, Skulnick HI, Dolak LA, Seest EP, Tomich PK, Bohanon MJ, Horng MM, Lynn JC, Chong KT, Hinshaw RR, Watenpaugh KD, Janakiraman MN, Thaisrivongs S. Tipranavir (PNU-140690): a potent, orally bioavailable nonpeptidic HIV protease inhibitor of the 5,6-dihydro-4-hydroxy-2-pyrone sulfonamide class. J Med Chem 1998; 41:3467-76. [PMID: 9719600 DOI: 10.1021/jm9802158] [Citation(s) in RCA: 207] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A broad screening program previously identified phenprocoumon (1) as a small molecule template for inhibition of HIV protease. Subsequent modification of this lead through iterative cycles of structure-based design led to the activity enhancements of pyrone and dihydropyrone ring systems (II and V) and amide-based substitution (III). Incorporation of sulfonamide substitution within the dihydropyrone template provided a series of highly potent HIV protease inhibitors, with structure-activity relationships described in this paper. Crystallographic studies provided further information on important binding interactions responsible for high enzymatic binding. These studies culminated in compound VI, which inhibits HIV protease with a Ki value of 8 pM and shows an IC90 value of 100 nM in antiviral cell culture. Clinical trials of this compound (PNU-140690, Tipranavir) for treatment of HIV infection are currently underway.
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Affiliation(s)
- S R Turner
- Department of Structural, Analytical & Medicinal Chemistry, Pharmacia & Upjohn, Inc., 301 Henrietta Street, Kalamazoo, Michigan 49001, USA
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Janakiraman MN, Watenpaugh KD, Tomich PK, Chong KT, Turner SR, Tommasi RA, Thaisrivongs S, Strohbach JW. Non-peptidic HIV protease inhibitors: C2-symmetry-based design of bis-sulfonamide dihydropyrones. Bioorg Med Chem Lett 1998; 8:1237-42. [PMID: 9871742 DOI: 10.1016/s0960-894x(98)00197-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Potent, non-peptidic, dihydropyrone sulfonamide HIV protease inhibitors have been previously described. Crystallographic analysis of dihydropyrone sulfonamide inhibitor/HIV protease complexes suggested incorporation of a second, C2 symmetry-related sulfonamide group. Selected bis-sulfonamide dihydropyrone analogues display high HIV protease inhibitory activity.
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7
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Thaisrivongs S, Romero DL, Tommasi RA, Janakiraman MN, Strohbach JW, Turner SR, Biles C, Morge RR, Johnson PD, Aristoff PA, Tomich PK, Lynn JC, Horng MM, Chong KT, Hinshaw RR, Howe WJ, Finzel BC, Watenpaugh KD. Structure-based design of HIV protease inhibitors: 5,6-dihydro-4-hydroxy-2-pyrones as effective, nonpeptidic inhibitors. J Med Chem 1996; 39:4630-42. [PMID: 8917652 DOI: 10.1021/jm960228q] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
From a broad screening program, the 4-hydroxycoumarin phenprocoumon (I) was previously identified as a lead template with HIV protease inhibitory activity. The crystal structure of phenprocoumon/HIV protease complex initiated a structure-based design effort that initially identified the 4-hydroxy-2-pyrone U-96988 (II) as a first-generation clinical candidate for the potential treatment of HIV infection. Based upon the crystal structure of the 4-hydroxy-2-pyrone III/HIV protease complex, a series of analogues incorporating a 5,6-dihydro-4-hydroxy-2-pyrone template were studied. It was recognized that in addition to having the required pharmacophore (the 4-hydroxy group with hydrogen-bonding interaction with the two catalytic aspartic acid residues and the lactone moiety replacing the ubiquitous water molecule in the active site), these 5,6-dihydro-4-hydroxy-2-pyrones incorporated side chains at the C-6 position that appropriately extended into the S1' and S2' subsites of the enzyme active site. The crystal structures of a number of representative 5,6-dihydro-4-hydroxy-2-pyrones complexed with the HIV protease were also determined to provide better understanding of the interaction between the enzyme and these inhibitors to aid the structure-based drug design effort. The crystal structures of the ligands in the enzyme active site did not always agree with the conformations expected from experience with previous pyrone inhibitors. This is likely due to the increased flexibility of the dihydropyrone ring. From this study, compound XIX exhibited reasonably high enzyme inhibitory activity (Ki = 15 nM) and showed antiviral activity (IC50 = 5 microM) in the cell-culture assay. This result provided a research direction which led to the discovery of active 5,6-dihydro-4-hydroxy-2-pyrones as potential agents for the treatment of HIV infection.
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Affiliation(s)
- S Thaisrivongs
- Medicinal Chemistry Research, Pharmacia & Upjohn, Inc., Kalamazoo, Michigan 49001, USA
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8
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Thaisrivongs S, Skulnick HI, Turner SR, Strohbach JW, Tommasi RA, Johnson PD, Aristoff PA, Judge TM, Gammill RB, Morris JK, Romines KR, Chrusciel RA, Hinshaw RR, Chong KT, Tarpley WG, Poppe SM, Slade DE, Lynn JC, Horng MM, Tomich PK, Seest EP, Dolak LA, Howe WJ, Howard GM, Watenpaugh KD. Structure-based design of HIV protease inhibitors: sulfonamide-containing 5,6-dihydro-4-hydroxy-2-pyrones as non-peptidic inhibitors. J Med Chem 1996; 39:4349-53. [PMID: 8893827 DOI: 10.1021/jm960541s] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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