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Barden CJ, Wu F, Fernandez-Murray JP, Lu E, Sun S, Taylor MM, Rushton AL, Williams J, Tavasoli M, Meek A, Reddy AS, Doyle LM, Sagamanova I, Sivamuthuraman K, Boudreau RTM, Byers DM, Weaver DF, McMaster CR. Computer-aided drug design to generate a unique antibiotic family. Nat Commun 2024; 15:8317. [PMID: 39333560 PMCID: PMC11436758 DOI: 10.1038/s41467-024-52797-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/23/2024] [Indexed: 09/29/2024] Open
Abstract
The World Health Organization has identified antibiotic resistance as one of the three greatest threats to human health. The need for antibiotics is a pressing matter that requires immediate attention. Here, computer-aided drug design is used to develop a structurally unique antibiotic family targeting holo-acyl carrier protein synthase (AcpS). AcpS is a highly conserved enzyme essential for bacterial survival that catalyzes the first step in lipid synthesis. To the best of our knowledge, there are no current antibiotics targeting AcpS making this drug development program of high interest. We synthesize a library of > 700 novel compounds targeting AcpS, from which 33 inhibit bacterial growth in vitro at ≤ 2 μg/mL. We demonstrate that compounds from this class have stand-alone activity against a broad spectrum of Gram-positive organisms and synergize with colistin to enable coverage of Gram-negative species. We demonstrate efficacy against clinically relevant multi-drug resistant strains in vitro and in animal models of infection in vivo including a difficult-to-treat ischemic infection exemplified by diabetic foot ulcer infections in humans. This antibiotic family could form the basis for several multi-drug-resistant antimicrobial programs.
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Affiliation(s)
- Christopher J Barden
- Krembil Research Institute, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Fan Wu
- Krembil Research Institute, University Health Network, University of Toronto, Toronto, ON, Canada
| | | | - Erhu Lu
- Krembil Research Institute, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Shengguo Sun
- Krembil Research Institute, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Marcia M Taylor
- Krembil Research Institute, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Annette L Rushton
- Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
| | - Jason Williams
- Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
| | - Mahtab Tavasoli
- Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
| | - Autumn Meek
- Krembil Research Institute, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Alla Siva Reddy
- Krembil Research Institute, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Lisa M Doyle
- Krembil Research Institute, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Irina Sagamanova
- Krembil Research Institute, University Health Network, University of Toronto, Toronto, ON, Canada
| | | | | | - David M Byers
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | - Donald F Weaver
- Krembil Research Institute, University Health Network, University of Toronto, Toronto, ON, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, ON, Canada
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2
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Amudala S, Sumit, Aidhen IS. LpxC inhibition: Potential and opportunities with carbohydrate scaffolds. Carbohydr Res 2024; 537:109057. [PMID: 38402732 DOI: 10.1016/j.carres.2024.109057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/01/2024] [Accepted: 02/08/2024] [Indexed: 02/27/2024]
Abstract
Uridine diphosphate-3-O-(hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) is a key enzyme involved in the biosynthesis of lipid A, an essential building block, for the construction and assembly of the outer membrane (OM) of Gram-negative bacteria. The enzyme is highly conserved in almost all Gram-negative bacteria and hence has emerged as a promising target for drug discovery in the fight against multi-drug resistant Gram-negative infections. Since the first nanomolar LpxC inhibitor, L-161,240, an oxazoline-based hydroxamate, the two-decade-long ongoing search has provided valuable information regarding essential features necessary for inhibition. Although the design and structure optimization for arriving at the most efficacious inhibitor of this enzyme has made good use of different heterocyclic moieties, the use of carbohydrate scaffold is scant. This review briefly covers the advancement and progress made in LpxC inhibition. The field awaits the use of potential associated with carbohydrate-based scaffolds for LpxC inhibition and the discovery of anti-bacterial agents against Gram-negative infections.
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Affiliation(s)
- Subramanyam Amudala
- Department of Chemistry, Indian Institute of Technology Madras, Chennai, 600036, India.
| | - Sumit
- Department of Chemistry, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Indrapal Singh Aidhen
- Department of Chemistry, Indian Institute of Technology Madras, Chennai, 600036, India.
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3
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Gotsko MD, Saliy IV, Ushakov IA, Sobenina LN, Trofimov BA. Functionalized 2,3'-Bipyrroles and Pyrrolo[1,2- c]imidazoles from Acylethynylpyrroles and Tosylmethylisocyanide. Molecules 2024; 29:885. [PMID: 38398639 PMCID: PMC10893325 DOI: 10.3390/molecules29040885] [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: 12/15/2023] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024] Open
Abstract
An efficient method for the synthesis of pharmaceutically prospective but still rare functionalized 2,3'-bipyrroles (in up to 80% yield) by the cycloaddition of easily available acylethynylpyrroles with tosylmethylisocyanide (TosMIC) has been developed. The reaction proceeds under reflux (1 h) in the KOH/THF system. In the t-BuONa/THF system, TosMIC acts in two directions: along with 2,3'-bipyrroles, the unexpected formation of pyrrolo[1,2-c]imidazoles is also observed (products ratio~1:1).
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Affiliation(s)
| | | | | | | | - Boris A. Trofimov
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch, Russian Academy of Sciences, 1 Favorsky Str., 664033 Irkutsk, Russia; (M.D.G.); (I.V.S.); (I.A.U.); (L.N.S.)
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4
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Kamal El-Sagheir AM, Abdelmesseh Nekhala I, Abd El-Gaber MK, Aboraia AS, Persson J, Schäfer AB, Wenzel M, Omar FA. Rational design, synthesis, molecular modeling, biological activity, and mechanism of action of polypharmacological norfloxacin hydroxamic acid derivatives. RSC Med Chem 2023; 14:2593-2610. [PMID: 38099058 PMCID: PMC10718593 DOI: 10.1039/d3md00309d] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/11/2023] [Indexed: 12/17/2023] Open
Abstract
Fluoroquinolones are broad-spectrum antibiotics that target gyrase and topoisomerase IV, involved in DNA compaction and segregation. We synthesized 28 novel norfloxacin hydroxamic acid derivatives with additional metal-chelating and hydrophobic pharmacophores, designed to enable interactions with additional drug targets. Several compounds showed equal or better activity than norfloxacin against Gram-positive, Gram-negative, and mycobacteria, with MICs as low as 0.18 μM. The most interesting derivatives were selected for in silico, in vitro, and in vivo mode of action studies. Molecular docking, enzyme inhibition, and bacterial cytological profiling confirmed inhibition of gyrase and topoisomerase IV for all except two tested derivatives (10f and 11f). Further phenotypic analysis revealed polypharmacological effects on peptidoglycan synthesis for four derivatives (16a, 17a, 17b, 20b). Interestingly, compounds 17a, 17b, and 20b, showed never seen before effects on cell wall synthetic enzymes, including MreB, MurG, and PonA, suggesting a novel mechanism of action, possibly impairing the lipid II cycle.
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Affiliation(s)
| | - Ireny Abdelmesseh Nekhala
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology 412 96 Gothenburg Sweden
| | | | - Ahmed S Aboraia
- Medicinal Chemistry Department, Faculty of Pharmacy, Assiut University Assiut 71526 Egypt
| | - Jonatan Persson
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology 412 96 Gothenburg Sweden
- Center for Antibiotic Resistance Research in Gothenburg (CARe) Gothenburg Sweden
| | - Ann-Britt Schäfer
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology 412 96 Gothenburg Sweden
- Center for Antibiotic Resistance Research in Gothenburg (CARe) Gothenburg Sweden
| | - Michaela Wenzel
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology 412 96 Gothenburg Sweden
- Center for Antibiotic Resistance Research in Gothenburg (CARe) Gothenburg Sweden
| | - Farghaly A Omar
- Medicinal Chemistry Department, Faculty of Pharmacy, Assiut University Assiut 71526 Egypt
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5
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Theuretzbacher U, Blasco B, Duffey M, Piddock LJV. Unrealized targets in the discovery of antibiotics for Gram-negative bacterial infections. Nat Rev Drug Discov 2023; 22:957-975. [PMID: 37833553 DOI: 10.1038/s41573-023-00791-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2023] [Indexed: 10/15/2023]
Abstract
Advances in areas that include genomics, systems biology, protein structure determination and artificial intelligence provide new opportunities for target-based antibacterial drug discovery. The selection of a 'good' new target for direct-acting antibacterial compounds is the first decision, for which multiple criteria must be explored, integrated and re-evaluated as drug discovery programmes progress. Criteria include essentiality of the target for bacterial survival, its conservation across different strains of the same species, bacterial species and growth conditions (which determines the spectrum of activity of a potential antibiotic) and the level of homology with human genes (which influences the potential for selective inhibition). Additionally, a bacterial target should have the potential to bind to drug-like molecules, and its subcellular location will govern the need for inhibitors to penetrate one or two bacterial membranes, which is a key challenge in targeting Gram-negative bacteria. The risk of the emergence of target-based drug resistance for drugs with single targets also requires consideration. This Review describes promising but as-yet-unrealized targets for antibacterial drugs against Gram-negative bacteria and examples of cognate inhibitors, and highlights lessons learned from past drug discovery programmes.
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Affiliation(s)
| | - Benjamin Blasco
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Maëlle Duffey
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Laura J V Piddock
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland.
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6
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Zou S, Li X, Huang Y, Zhang B, Tang H, Xue Y, Zheng Y. Properties and biotechnological applications of microbial deacetylase. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12613-1. [PMID: 37326683 DOI: 10.1007/s00253-023-12613-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/25/2023] [Accepted: 05/31/2023] [Indexed: 06/17/2023]
Abstract
Deacetylases, a class of enzymes that can catalyze the hydrolysis of acetylated substrates to remove the acetyl group, used in producing various products with high qualities, are one of the most influential industrial enzymes. These enzymes are highly specific, non-toxic, sustainable, and eco-friendly biocatalysts. Deacetylases and deacetylated compounds have been widely applicated in pharmaceuticals, medicine, food, and the environment. This review synthetically summarizes deacetylases' sources, characterizations, classifications, and applications. Moreover, the typical structural characteristics of deacetylases from different microbial sources are summarized. We also reviewed the deacetylase-catalyzed reactions for producing various deacetylated compounds, such as chitosan-oligosaccharide (COS), mycothiol, 7-aminocephalosporanic acid (7-ACA), glucosamines, amino acids, and polyamines. It is aimed to expound on the advantages and challenges of deacetylases in industrial applications. Moreover, it also serves perspectives on obtaining promising and innovative biocatalysts for enzymatic deacetylation. KEYPOINTS: • The fundamental properties of microbial deacetylases of various microorganisms are presented. • The biochemical characterizations, structures, and catalyzation mechanisms of microbial deacetylases are summarized. • The applications of microbial deacetylases in food, pharmaceutical, medicine, and the environment were discussed.
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Affiliation(s)
- Shuping Zou
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Xia Li
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Yinfeng Huang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Bing Zhang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Heng Tang
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Yaping Xue
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.
| | - Yuguo Zheng
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
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7
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Di Leo R, Cuffaro D, Rossello A, Nuti E. Bacterial Zinc Metalloenzyme Inhibitors: Recent Advances and Future Perspectives. Molecules 2023; 28:molecules28114378. [PMID: 37298854 DOI: 10.3390/molecules28114378] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/18/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Human deaths caused by Gram-negative bacteria keep rising due to the multidrug resistance (MDR) phenomenon. Therefore, it is a priority to develop novel antibiotics with different mechanisms of action. Several bacterial zinc metalloenzymes are becoming attractive targets since they do not show any similarities with the human endogenous zinc-metalloproteinases. In the last decades, there has been an increasing interest from both industry and academia in developing new inhibitors against those enzymes involved in lipid A biosynthesis, and bacteria nutrition and sporulation, e.g., UDP-[3-O-(R)-3-hydroxymyristoyl]-N-acetylglucosamine deacetylase (LpxC), thermolysin (TLN), and pseudolysin (PLN). Nevertheless, targeting these bacterial enzymes is harder than expected and the lack of good clinical candidates suggests that more effort is needed. This review gives an overview of bacterial zinc metalloenzyme inhibitors that have been synthesized so far, highlighting the structural features essential for inhibitory activity and the structure-activity relationships. Our discussion may stimulate and help further studies on bacterial zinc metalloenzyme inhibitors as possible novel antibacterial drugs.
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Affiliation(s)
- Riccardo Di Leo
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Doretta Cuffaro
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Armando Rossello
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Elisa Nuti
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
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8
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Kumar Pal S, Kumar S. LpxC (UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase) inhibitors: A long path explored for potent drug design. Int J Biol Macromol 2023; 234:122960. [PMID: 36565833 DOI: 10.1016/j.ijbiomac.2022.12.179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Microbial infections are becoming resistant to traditional antibiotics. As novel resistance mechanisms are developed and disseminated across the world, our ability to treat the most common infectious diseases is becoming increasingly compromised. As existing antibiotics are losing their effectiveness, especially treatment of bacterial infections, is difficult. In order to combat this issue, it is of utmost importance to identify novel pharmacological targets or antibiotics. LpxC, a zinc-dependent metalloamidase that catalyzes the committed step in the biosynthesis of lipid A (endotoxin) in bacteria, is a prime candidate for drug/therapeutic target. So far, the rate-limiting metallo-amidase LpxC has been the most-targeted macromolecule in the Raetz pathway. This is because it is important for the growth of these bacterial infections. This review showcases on the research done to develop efficient drugs in this area before and after the 2015.
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Affiliation(s)
- Sudhir Kumar Pal
- Centre for Bio-Separation Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India.
| | - Sanjit Kumar
- Centre for Bio-Separation Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India.
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9
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Niu Z, Lei P, Wang Y, Wang J, Yang J, Zhang J. Small molecule LpxC inhibitors against gram-negative bacteria: Advances and future perspectives. Eur J Med Chem 2023; 253:115326. [PMID: 37023679 DOI: 10.1016/j.ejmech.2023.115326] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/18/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023]
Abstract
Uridine diphosphate-3-O-(hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) is a metalloenzyme with zinc ions as cofactors and is a key enzyme in the essential structural outer membrane lipid A synthesis commitment step of gram-negative bacteria. As LpxC is extremely homologous among different Gram-negative bacteria, it is conserved in almost all gram-negative bacteria, which makes LpxC a promising target. LpxC inhibitors have been reported extensively in recent years, such as PF-5081090 and CHIR-090 were found to have broad-spectrum antibiotic activity against P. aeruginosa and E. coli. They are mainly classified into hydroxamate inhibitors and non-hydroxamate inhibitors based on their structure, but no LpxC inhibitors have been marketed due to safety and activity issues. This review, therefore, focuses on small molecule inhibitors of LpxC against gram-negative pathogenic bacteria and covers recent advances in LpxC inhibitors, focusing on their structural optimization process, structure-activity relationships, and future directions, with the aim of providing ideas for the development of LpxC inhibitors and clinical research.
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10
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Romano K, Hung D. Targeting LPS biosynthesis and transport in gram-negative bacteria in the era of multi-drug resistance. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119407. [PMID: 36543281 PMCID: PMC9922520 DOI: 10.1016/j.bbamcr.2022.119407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 11/09/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022]
Abstract
Gram-negative bacteria pose a major threat to human health in an era fraught with multi-drug resistant bacterial infections. Despite extensive drug discovery campaigns over the past decades, no new antibiotic target class effective against gram-negative bacteria has become available to patients since the advent of the carbapenems in 1985. Antibiotic discovery efforts against gram-negative bacteria have been hampered by limited intracellular accumulation of xenobiotics, in large part due to the impermeable cell envelope comprising lipopolysaccharide (LPS) in the outer leaflet of the outer membrane, as well as a panoply of efflux pumps. The biosynthesis and transport of LPS are essential to the viability and virulence of most gram-negative bacteria. Thus, both LPS biosynthesis and transport are attractive pathways to target therapeutically. In this review, we summarize the LPS biosynthesis and transport pathways and discuss efforts to find small molecule inhibitors against targets within these pathways.
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Affiliation(s)
- K.P. Romano
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA, USA,The Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
| | - D.T. Hung
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA,Department of Genetics, Harvard Medical School, Boston, MA, USA,Corresponding author at: The Broad Institute of MIT and Harvard, Cambridge, MA, USA. (D.T. Hung)
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11
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Oparina LA, Kolyvanov NA, Ushakov IA, Nikitina LP, Petrova OV, Sobenina LN, Petrushenko KB, Trofimov BA. Contributing to Biochemistry and Optoelectronics: Pyrrolo[1',2':2,3]imidazo[1,5- a]indoles and Cyclohepta[4,5]pyrrolo[1,2- c]pyrrolo[1,2- a]imidazoles via [3+2] Annulation of Acylethynylcycloalka[ b]pyrroles with Δ 1-Pyrrolines. Int J Mol Sci 2023; 24:ijms24043404. [PMID: 36834813 PMCID: PMC9959468 DOI: 10.3390/ijms24043404] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/02/2023] [Accepted: 02/05/2023] [Indexed: 02/11/2023] Open
Abstract
Available pyrrolylalkynones with tetrahydroindolyl, cycloalkanopyrrolyl, and dihydrobenzo[g]indolyl moieties, acylethynylcycloalka[b]pyrroles, are readily annulated with Δ1-pyrrolines (MeCN/THF, 70 °C, 8 h) to afford a series of novel pyrrolo[1',2':2,3]imidazo[1,5-a]indoles and cyclohepta[4,5]pyrrolo[1,2-c]pyrrolo[1,2-a]imidazoles functionalized with an acylethenyl group in up to an 81% yield. This original synthetic approach contributes to the arsenal of chemical methods promoting drug discovery. Photophysical studies show that some of the synthesized compounds, e.g., benzo[g]pyrroloimidazoindoles, are prospective candidates for TADF emitters of OLED.
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12
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Wei T, Li D, Zhang Y, Tang Y, Zhou H, Liu H, Li X. Thiophene-2,3-Dialdehyde Enables Chemoselective Cyclization on Unprotected Peptides, Proteins, and Phage Displayed Peptides. SMALL METHODS 2022; 6:e2201164. [PMID: 36156489 DOI: 10.1002/smtd.202201164] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/12/1912] [Indexed: 06/16/2023]
Abstract
Ortho-phthalaldehyde has recently found wide potentials for protein bioconjugation and peptide cyclization. Herein, the second-generation dialdehyde-based peptide cyclization method is reported. The thiophene-2,3-dialdehyde (TDA) reacts specifically with the primary amine (from Lys side chain or peptide N-terminus) and thiol (from Cys side chain) within unprotected peptides to generate a highly stable thieno[2,3-c]pyrrole-bridged cyclic structure, while it does not react with primary amine alone. This reaction is carried out in the aqueous buffer and features tolerance of diverse functionalities, rapid and clean transformation, and operational simplicity. The features allow TDA to be used for protein stapling and phage displayed peptide cyclization.
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Affiliation(s)
- Tongyao Wei
- Department of Chemistry, State Key Laboratory of Synthetic Organic Chemistry, The University of Hong Kong, Hong Kong, SAR, P. R. China
| | - Dongfang Li
- Department of Chemistry, State Key Laboratory of Synthetic Organic Chemistry, The University of Hong Kong, Hong Kong, SAR, P. R. China
| | - Yue Zhang
- Department of Chemistry, State Key Laboratory of Synthetic Organic Chemistry, The University of Hong Kong, Hong Kong, SAR, P. R. China
| | - Yubo Tang
- Department of Chemistry, State Key Laboratory of Synthetic Organic Chemistry, The University of Hong Kong, Hong Kong, SAR, P. R. China
| | - Haiyan Zhou
- Department of Chemistry, State Key Laboratory of Synthetic Organic Chemistry, The University of Hong Kong, Hong Kong, SAR, P. R. China
- Chemistry and Chemical Engineering Guangdong Laboratory, Shantou, 515063, P. R. China
| | - Han Liu
- Department of Chemistry, State Key Laboratory of Synthetic Organic Chemistry, The University of Hong Kong, Hong Kong, SAR, P. R. China
| | - Xuechen Li
- Department of Chemistry, State Key Laboratory of Synthetic Organic Chemistry, The University of Hong Kong, Hong Kong, SAR, P. R. China
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13
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Basak S, Li Y, Tao S, Daryaee F, Merino J, Gu C, Delker SL, Phan JN, Edwards TE, Walker SG, Tonge PJ. Structure-Kinetic Relationship Studies for the Development of Long Residence Time LpxC Inhibitors. J Med Chem 2022; 65:11854-11875. [PMID: 36037447 PMCID: PMC10182817 DOI: 10.1021/acs.jmedchem.2c00974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) is a promising drug target in Gram-negative bacteria. Previously, we described a correlation between the residence time of inhibitors on Pseudomonas aeruginosa LpxC (paLpxC) and the post-antibiotic effect (PAE) caused by the inhibitors on the growth of P. aeruginosa. Given that drugs with prolonged activity following compound removal may have advantages in dosing regimens, we have explored the structure-kinetic relationship for paLpxC inhibition by analogues of the pyridone methylsulfone PF5081090 (1) originally developed by Pfizer. Several analogues have longer residence times on paLpxC than 1 (41 min) including PT913, which has a residence time of 124 min. PT913 also has a PAE of 4 h, extending the original correlation observed between residence time and PAE. Collectively, the studies provide a platform for the rational modulation of paLpxC inhibitor residence time and the potential development of antibacterial agents that cause prolonged suppression of bacterial growth.
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Affiliation(s)
- Sneha Basak
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Yong Li
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Suyuan Tao
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Fereidoon Daryaee
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Jonathan Merino
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Chendi Gu
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | | | - Jenny N. Phan
- McGill University Montreal, Quebec H3A 0G4, Canada Canada
| | | | - Stephen G. Walker
- Department of Oral Biology and Pathology, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Peter J. Tonge
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Department of Radiology, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, USA
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14
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Fernández Álvaro E, Voong Vinh P, de Cozar C, Willé DR, Urones B, Cortés A, Price A, Tran Do Hoang N, Ha Thanh T, McCloskey M, Shaheen S, Dayao D, Martinot A, de Mercado J, Castañeda P, García-Perez A, Singa B, Pavlinac P, Walson J, Martínez-Martínez MS, Arnold SLM, Tzipori S, Ballell Pages L, Baker S. The repurposing of Tebipenem pivoxil as alternative therapy for severe gastrointestinal infections caused by extensively drug-resistant Shigella spp. eLife 2022; 11:e69798. [PMID: 35289746 PMCID: PMC8959600 DOI: 10.7554/elife.69798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 03/09/2022] [Indexed: 11/18/2022] Open
Abstract
Background Diarrhoea remains one of the leading causes of childhood mortality globally. Recent epidemiological studies conducted in low-middle income countries (LMICs) identified Shigella spp. as the first and second most predominant agent of dysentery and moderate diarrhoea, respectively. Antimicrobial therapy is often necessary for Shigella infections; however, we are reaching a crisis point with efficacious antimicrobials. The rapid emergence of resistance against existing antimicrobials in Shigella spp. poses a serious global health problem. Methods Aiming to identify alternative antimicrobial chemicals with activity against antimicrobial resistant Shigella, we initiated a collaborative academia-industry drug discovery project, applying high-throughput phenotypic screening across broad chemical diversity and followed a lead compound through in vitro and in vivo characterisation. Results We identified several known antimicrobial compound classes with antibacterial activity against Shigella. These compounds included the oral carbapenem Tebipenem, which was found to be highly potent against broadly susceptible Shigella and contemporary MDR variants for which we perform detailed pre-clinical testing. Additional in vitro screening demonstrated that Tebipenem had activity against a wide range of other non-Shigella enteric bacteria. Cognisant of the risk for the development of resistance against monotherapy, we identified synergistic behaviour of two different drug combinations incorporating Tebipenem. We found the orally bioavailable prodrug (Tebipenem pivoxil) had ideal pharmacokinetic properties for treating enteric pathogens and was effective in clearing the gut of infecting organisms when administered to Shigella-infected mice and gnotobiotic piglets. Conclusions Our data highlight the emerging antimicrobial resistance crisis and shows that Tebipenem pivoxil (licenced for paediatric respiratory tract infections in Japan) should be accelerated into human trials and could be repurposed as an effective treatment for severe diarrhoea caused by MDR Shigella and other enteric pathogens in LMICs. Funding Tres Cantos Open Lab Foundation (projects TC239 and TC246), the Bill and Melinda Gates Foundation (grant OPP1172483) and Wellcome (215515/Z/19/Z).
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Affiliation(s)
| | - Phat Voong Vinh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research UnitHo Chi Minh CityViet Nam
| | | | | | | | | | - Alan Price
- GSK Global Health, Tres CantosMadridSpain
| | - Nhu Tran Do Hoang
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research UnitHo Chi Minh CityViet Nam
| | - Tuyen Ha Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research UnitHo Chi Minh CityViet Nam
| | - Molly McCloskey
- Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Diseases University of Washington School of MedicineSeattleUnited States
| | - Shareef Shaheen
- Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Diseases University of Washington School of MedicineSeattleUnited States
| | - Denise Dayao
- Department of Infectious Disease and Global Health, Tufts University Cummings School of Veterinary MedicineNorth GraftonUnited States
| | - Amanda Martinot
- Department of Infectious Disease and Global Health, Tufts University Cummings School of Veterinary MedicineNorth GraftonUnited States
| | | | | | | | | | - Patricia Pavlinac
- Department of Global Health, University of WashingtonSeattleUnited States
| | - Judd Walson
- Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Diseases University of Washington School of MedicineSeattleUnited States
| | | | - Samuel LM Arnold
- Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Diseases University of Washington School of MedicineSeattleUnited States
| | - Saul Tzipori
- Department of Infectious Disease and Global Health, Tufts University Cummings School of Veterinary MedicineNorth GraftonUnited States
| | | | - Stephen Baker
- University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
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15
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16
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Schlimpen F, Plaçais C, Starck E, Bénéteau V, Pale P, Chassaing S. α-Tertiary Propargylamine Synthesis via KA 2-Type Coupling Reactions under Solvent-Free Cu I-Zeolite Catalysis. J Org Chem 2021; 86:16593-16613. [PMID: 34806367 DOI: 10.1021/acs.joc.1c01893] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The potential of copper(I)-zeolite catalysis was evaluated in the three-component KA2-coupling mediated synthesis of α-tertiary propargylamines. Our archetypal copper(I)-doped zeolite CuI-USY proved to be efficient under ligand- and solvent-free conditions at 80 °C. Usable up to four times, this catalytic material enables the coupling of diverse ketones, alkynes, and amines with a broad functional group tolerance. A decarboxylative and a desilylative version, respectively, involving an alkynoic acid and trimethylsilylacetylene as alkyne surrogates, was also set up to bypass selectivity issues and/or to access α-tertiary propargylamines that are unattainable under standard KA2 conditions. Interestingly, the KA2-type coupling reactions were successfully linked to other CuI-catalyzed reactions, thus resulting in sequential one-pot processes under full CuI-USY catalysis.
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Affiliation(s)
- Fabian Schlimpen
- Laboratoire de Synthèse, Réactivité Organique et Catalyse (LASYROC), Institut de Chimie, CNRS-UMR7177, Université de Strasbourg, 4 rue Blaise Pascal, Strasbourg 67070, France
| | - Clotilde Plaçais
- Laboratoire de Synthèse, Réactivité Organique et Catalyse (LASYROC), Institut de Chimie, CNRS-UMR7177, Université de Strasbourg, 4 rue Blaise Pascal, Strasbourg 67070, France
| | - Eliot Starck
- Laboratoire de Synthèse, Réactivité Organique et Catalyse (LASYROC), Institut de Chimie, CNRS-UMR7177, Université de Strasbourg, 4 rue Blaise Pascal, Strasbourg 67070, France
| | - Valérie Bénéteau
- Laboratoire de Synthèse, Réactivité Organique et Catalyse (LASYROC), Institut de Chimie, CNRS-UMR7177, Université de Strasbourg, 4 rue Blaise Pascal, Strasbourg 67070, France
| | - Patrick Pale
- Laboratoire de Synthèse, Réactivité Organique et Catalyse (LASYROC), Institut de Chimie, CNRS-UMR7177, Université de Strasbourg, 4 rue Blaise Pascal, Strasbourg 67070, France
| | - Stefan Chassaing
- Laboratoire de Synthèse, Réactivité Organique et Catalyse (LASYROC), Institut de Chimie, CNRS-UMR7177, Université de Strasbourg, 4 rue Blaise Pascal, Strasbourg 67070, France
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17
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Guest RL, Rutherford ST, Silhavy TJ. Border Control: Regulating LPS Biogenesis. Trends Microbiol 2021; 29:334-345. [PMID: 33036869 PMCID: PMC7969359 DOI: 10.1016/j.tim.2020.09.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/20/2022]
Abstract
The outer membrane (OM) is a defining feature of Gram-negative bacteria that serves as a permeability barrier and provides rigidity to the cell. Critical to OM function is establishing and maintaining an asymmetrical bilayer structure with phospholipids in the inner leaflet and the complex glycolipid lipopolysaccharide (LPS) in the outer leaflet. Cells ensure this asymmetry by regulating the biogenesis of lipid A, the conserved and essential anchor of LPS. Here we review the consequences of disrupting the regulatory components that control lipid A biogenesis, focusing on the rate-limiting step performed by LpxC. Dissection of these processes provides critical insights into bacterial physiology and potential new targets for antibiotics able to overcome rapidly spreading resistance mechanisms.
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Affiliation(s)
- Randi L Guest
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Steven T Rutherford
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Thomas J Silhavy
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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18
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Troudi A, Pagès JM, Brunel JM. Chemical Highlights Supporting the Role of Lipid A in Efficient Biological Adaptation of Gram-Negative Bacteria to External Stresses. J Med Chem 2021; 64:1816-1834. [PMID: 33538159 DOI: 10.1021/acs.jmedchem.0c02185] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The outer membrane (OM) of Gram-negative bacteria provides an efficient barrier against external noxious compounds such as antimicrobial agents. Associated with drug target modification, it contributes to the overall failure of chemotherapy. In the complex OM architecture, Lipid A plays an essential role by anchoring the lipopolysaccharide in the membrane and ensuring the spatial organization between lipids, proteins, and sugars. Currently, the targets of almost all antibiotics are intracellularly located and require translocation across membranes. We report herein an integrated view of Lipid A synthesis, membrane assembly, a structure comparison at the molecular structure level of numerous Gram-negative bacterial species, as well as its recent use as a target for original antibacterial molecules. This review paves the way for a new vision of a key membrane component that acts during bacterial adaptation to environmental stresses and for the development of new weapons against microbial resistance to usual antibiotics.
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Affiliation(s)
- Azza Troudi
- UMR-MD1, U1261, Aix Marseille Université, INSERM, SSA, MCT, 13385 Marseille, France.,Laboratory of Microorganisms and Active Biomolecules, Department of Biology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis 1008, Tunisia
| | - Jean Marie Pagès
- UMR-MD1, U1261, Aix Marseille Université, INSERM, SSA, MCT, 13385 Marseille, France
| | - Jean Michel Brunel
- UMR-MD1, U1261, Aix Marseille Université, INSERM, SSA, MCT, 13385 Marseille, France
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19
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Ushiyama F, Takashima H, Matsuda Y, Ogata Y, Sasamoto N, Kurimoto-Tsuruta R, Ueki K, Tanaka-Yamamoto N, Endo M, Mima M, Fujita K, Takata I, Tsuji S, Yamashita H, Okumura H, Otake K, Sugiyama H. Lead optimization of 2-hydroxymethyl imidazoles as non-hydroxamate LpxC inhibitors: Discovery of TP0586532. Bioorg Med Chem 2020; 30:115964. [PMID: 33385955 DOI: 10.1016/j.bmc.2020.115964] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 11/19/2022]
Abstract
Infectious diseases caused by resistant Gram-negative bacteria have become a serious problem, and the development of therapeutic drugs with a novel mechanism of action and that do not exhibit cross-resistance with existing drugs has been earnestly desired. UDP-3-O-acyl-N-acetylglucosamine deacetylase (LpxC) is a drug target that has been studied for a long time. However, no LpxC inhibitors are available on the market at present. In this study, we sought to create a new antibacterial agent without a hydroxamate moiety, which is a common component of the major LpxC inhibitors that have been reported to date and that may cause toxicity. As a result, a development candidate, TP0586532, was created that is effective against carbapenem-resistant Klebsiella pneumoniae and does not pose a cardiovascular risk.
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Affiliation(s)
- Fumihito Ushiyama
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan.
| | - Hajime Takashima
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Yohei Matsuda
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Yuya Ogata
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Naoki Sasamoto
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | | | - Kaori Ueki
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | | | - Mayumi Endo
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Masashi Mima
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Kiyoko Fujita
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Iichiro Takata
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Satoshi Tsuji
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Haruhiro Yamashita
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Hirotoshi Okumura
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Katsumasa Otake
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Hiroyuki Sugiyama
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
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20
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Furuya T, Shapiro AB, Comita-Prevoir J, Kuenstner EJ, Zhang J, Ribe SD, Chen A, Hines D, Moussa SH, Carter NM, Sylvester MA, Romero JAC, Vega CV, Sacco MD, Chen Y, O'Donnell JP, Durand-Reville TF, Miller AA, Tommasi RA. N-Hydroxyformamide LpxC inhibitors, their in vivo efficacy in a mouse Escherichia coli infection model, and their safety in a rat hemodynamic assay. Bioorg Med Chem 2020; 28:115826. [PMID: 33160146 DOI: 10.1016/j.bmc.2020.115826] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 10/22/2020] [Indexed: 11/30/2022]
Abstract
UDP-3-O-(R-3-hydroxyacyl)-N-acetylglucosamine deacetylase (LpxC), the zinc metalloenzyme catalyzing the first committed step of lipid A biosynthesis in Gram-negative bacteria, has been a target for antibacterial drug discovery for many years. All inhibitor chemotypes reaching an advanced preclinical stage and clinical phase 1 have contained terminal hydroxamic acid, and none have been successfully advanced due, in part, to safety concerns, including hemodynamic effects. We hypothesized that the safety of LpxC inhibitors could be improved by replacing the terminal hydroxamic acid with a different zinc-binding group. After choosing an N-hydroxyformamide zinc-binding group, we investigated the structure-activity relationship of each part of the inhibitor scaffold with respect to Pseudomonas aeruginosa and Escherichia coli LpxC binding affinity, in vitro antibacterial potency and pharmacological properties. We identified a novel, potency-enhancing hydrophobic binding interaction for an LpxC inhibitor. We demonstrated in vivo efficacy of one compound in a neutropenic mouse E. coli infection model. Another compound was tested in a rat hemodynamic assay and was found to have a hypotensive effect. This result demonstrated that replacing the terminal hydroxamic acid with a different zinc-binding group was insufficient to avoid this previously recognized safety issue with LpxC inhibitors.
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Affiliation(s)
- Takeru Furuya
- Entasis Therapeutics, 35 Gatehouse Dr., Waltham, MA 02451, USA.
| | - Adam B Shapiro
- Entasis Therapeutics, 35 Gatehouse Dr., Waltham, MA 02451, USA
| | | | | | - Jing Zhang
- Entasis Therapeutics, 35 Gatehouse Dr., Waltham, MA 02451, USA
| | - Seth D Ribe
- Entasis Therapeutics, 35 Gatehouse Dr., Waltham, MA 02451, USA
| | - April Chen
- Entasis Therapeutics, 35 Gatehouse Dr., Waltham, MA 02451, USA
| | - Daniel Hines
- Entasis Therapeutics, 35 Gatehouse Dr., Waltham, MA 02451, USA
| | - Samir H Moussa
- Entasis Therapeutics, 35 Gatehouse Dr., Waltham, MA 02451, USA
| | - Nicole M Carter
- Entasis Therapeutics, 35 Gatehouse Dr., Waltham, MA 02451, USA
| | | | - Jan A C Romero
- Entasis Therapeutics, 35 Gatehouse Dr., Waltham, MA 02451, USA
| | - Camilo V Vega
- Entasis Therapeutics, 35 Gatehouse Dr., Waltham, MA 02451, USA
| | - Michael D Sacco
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida 12901 Bruce B. Downs Blvd, MDC 07, Tampa, FL 33612, USA
| | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida 12901 Bruce B. Downs Blvd, MDC 07, Tampa, FL 33612, USA
| | | | | | - Alita A Miller
- Entasis Therapeutics, 35 Gatehouse Dr., Waltham, MA 02451, USA
| | - Ruben A Tommasi
- Entasis Therapeutics, 35 Gatehouse Dr., Waltham, MA 02451, USA.
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21
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Pascual S, Planas A. Carbohydrate de-N-acetylases acting on structural polysaccharides and glycoconjugates. Curr Opin Chem Biol 2020; 61:9-18. [PMID: 33075728 DOI: 10.1016/j.cbpa.2020.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/06/2020] [Accepted: 09/08/2020] [Indexed: 12/14/2022]
Abstract
Deacetylation of N-acetylhexosamine residues in structural polysaccharides and glycoconjugates is catalyzed by different families of carbohydrate esterases that, despite different structural folds, share a common metal-assisted acid/base mechanism with the metal cation coordinated with a conserved Asp-His-His triad. These enzymes serve diverse biological functions in the modification of cell-surface polysaccharides in bacteria and fungi as well as in the metabolism of hexosamines in the biosynthesis of cellular glycoconjugates. Focusing on carbohydrate de-N-acetylases, this article summarizes the background of the different families from a structural and functional viewpoint and covers advances in the characterization of novel enzymes over the last 2-3 years. Current research is addressed to the identification of new deacetylases and unravel their biological functions as they are candidate targets for the design of antimicrobials against pathogenic bacteria and fungi. Likewise, some families are also used as biocatalysts for the production of defined glycostructures with diverse applications.
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Affiliation(s)
- Sergi Pascual
- Laboratory of Biochemistry, Institut Químic de Sarrià, University Ramon Llull, 08017, Barcelona, Spain
| | - Antoni Planas
- Laboratory of Biochemistry, Institut Químic de Sarrià, University Ramon Llull, 08017, Barcelona, Spain.
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22
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Abe M, Picard B, De Paolis M. Convergent Synthesis of 2-Oxazolone-4-carboxylates Esters by Reaction of Aldehydes with Ambivalent N-Cbz-α-Tosylglycinate Ester. Org Lett 2020; 22:4864-4867. [PMID: 32519551 DOI: 10.1021/acs.orglett.0c01703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
N-Cbz-α-tosylglycinate ester was combined with aldehydes in a redox-neutral sequence leading to 2-oxazolone-4-carboxylates with high functional group tolerance. While the scope of the method was delineated to primary and secondary aliphatic aldehydes as well as aromatics, no racemization occurred with chiral aldehydes such as Garner's. Hitherto unknown, this process relies on the ambivalent role of N-Cbz-α-tosylglycinate ester acting as a pronucleophile.
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Affiliation(s)
- Masahiro Abe
- Normandie Univ, UNIROUEN, COBRA, INSA Rouen, CNRS, COBRA, 76000 Rouen, France
| | - Baptiste Picard
- Normandie Univ, UNIROUEN, COBRA, INSA Rouen, CNRS, COBRA, 76000 Rouen, France
| | - Michaël De Paolis
- Normandie Univ, UNIROUEN, COBRA, INSA Rouen, CNRS, COBRA, 76000 Rouen, France
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23
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Naveen, Kumar Tittal R, Vikas GD, Rani P, Lal K, Kumar A. Synthesis, Antimicrobial Activity, Molecular Docking and DFT Study: Aryl‐Carbamic Acid 1‐Benzyl‐1
H
‐[1,2,3]Triazol‐4‐ylmethyl Esters. ChemistrySelect 2020. [DOI: 10.1002/slct.202001547] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Naveen
- Department of ChemistryNational Institute of Technology, Kurukshetra Haryana 136119 India
| | - Ram Kumar Tittal
- Department of ChemistryNational Institute of Technology, Kurukshetra Haryana 136119 India
| | - Ghule D. Vikas
- Department of ChemistryNational Institute of Technology, Kurukshetra Haryana 136119 India
| | - Poonam Rani
- Department of ChemistryGJUS&T, Hisar Haryana 125001 India
| | - Kashmiri Lal
- Department of ChemistryGJUS&T, Hisar Haryana 125001 India
| | - Ashwani Kumar
- Department of Pharmaceutical Sciences, GJUS&T Hisar Haryana 12500 India
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24
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Panchaud P, Surivet JP, Diethelm S, Blumstein AC, Gauvin JC, Jacob L, Masse F, Mathieu G, Mirre A, Schmitt C, Enderlin-Paput M, Lange R, Gnerre C, Seeland S, Herrmann C, Locher HH, Seiler P, Ritz D, Rueedi G. Optimization of LpxC Inhibitor Lead Compounds Focusing on Efficacy and Formulation for High Dose Intravenous Administration. J Med Chem 2019; 63:88-102. [DOI: 10.1021/acs.jmedchem.9b01605] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Philippe Panchaud
- Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | | | - Stefan Diethelm
- Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | | | | | - Loïc Jacob
- Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Florence Masse
- Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Gaëlle Mathieu
- Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Azely Mirre
- Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Christine Schmitt
- Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | | | - Roland Lange
- Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Carmela Gnerre
- Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Swen Seeland
- Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Charlyse Herrmann
- Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Hans H. Locher
- Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Peter Seiler
- Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Daniel Ritz
- Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Georg Rueedi
- Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
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