1
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Patel KB, Rajani D, Ahmad I, Patel H, Patel HD, Kumari P. Chrysin based pyrimidine-piperazine hybrids: design, synthesis, in vitro antimicrobial and in silico E. coli topoisomerase II DNA gyrase efficacy. Mol Divers 2024; 28:1377-1392. [PMID: 37318711 DOI: 10.1007/s11030-023-10663-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/19/2023] [Indexed: 06/16/2023]
Abstract
Ten chrysin-based pyrimidine-piperazine hybrids have been evaluated in vitro for antimicrobial activity against eleven bacterial and two fungal strains. All compounds 5a-j exhibited moderate to good inhibition, with MIC values ranging from 6.25 to 250 µg/ml. At 6.25 µg/ml and 12.5 µg/ml MIC values, respectively, compounds 5b and 5h demonstrated the most promising potency against E. coli, outperforming ampicillin, chloramphenicol, and ciprofloxacin. None of the substances had the same level of action as norfloxacin. 5a, 5d, 5g, 5h, and 5i have exhibited superior antifungal efficacy than Griseofulvin against C. albicans with 250 µg/ml MIC. All the compounds were also individually docked into the E. coli DNA gyrase ATP binding site (PDB ID: 1KZN) and CYP51 inhibitor (PDB ID: 5V5Z). The most active compound, 5h and 5g displayed a Glide docking score of - 5.97 kcal/mol and - 10.99 kcal/mol against DNA gyrase and 14α-demethylase enzyme CYP51 respectively. Potent compounds 5b, 5h, and 5g may be used to design new, innovative antimicrobial agents, according to in vitro, ADMET, and in silico biological efficacy analyses.
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Affiliation(s)
- Kajalben B Patel
- Department of Chemistry, Sardar Vallabhbhai National Institute of Technology, Surat, Gujarat, 395007, India
| | | | - Iqrar Ahmad
- Department of Pharmaceutical Chemistry, Prof. Ravindra Nikam College of Pharmacy, Gondur, Dhule, Maharashtra, 424002, India
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, 425405, India
| | - Harun Patel
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, 425405, India
| | - Hitesh D Patel
- Department of Chemistry, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Premlata Kumari
- Department of Chemistry, Sardar Vallabhbhai National Institute of Technology, Surat, Gujarat, 395007, India.
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2
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Kokot M, Minovski N. Dynamic Profiling and Binding Affinity Prediction of NBTI Antibacterials against DNA Gyrase Enzyme by Multidimensional Machine Learning and Molecular Dynamics Simulations. ACS OMEGA 2024; 9:18278-18295. [PMID: 38680300 PMCID: PMC11044241 DOI: 10.1021/acsomega.4c00036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/25/2024] [Accepted: 03/29/2024] [Indexed: 05/01/2024]
Abstract
Bacterial type II topoisomerases are well-characterized and clinically important targets for antibacterial chemotherapy. Novel bacterial topoisomerase inhibitors (NBTIs) are a newly disclosed class of antibacterials. Prediction of their binding affinity to these enzymes would be beneficial for de novo design/optimization of new NBTIs. Utilizing in vitro NBTI experimental data, we constructed two comprehensive multidimensional DNA gyrase surrogate models for Staphylococcus aureus (q2 = 0.791) and Escherichia coli (q2 = 0.806). Both models accurately predicted the IC50s of 26 NBTIs from our recent studies. To investigate the NBTI's dynamic profile and binding to both targets, 10 selected NBTIs underwent molecular dynamics (MD) simulations. The analysis of MD production trajectories confirmed key hydrogen-bonding and hydrophobic contacts that NBTIs establish in both enzymes. Moreover, the binding free energies of selected NBTIs were computed by the linear interaction energy (LIE) method employing an in-house derived set of fitting parameters (α = 0.16, β = 0.029, γ = 0.0, and intercept = -1.72), which are successfully applicable to DNA gyrase of Gram-positive/Gram-negative pathogens. Both methods offer accurate predictions of the binding free energies of NBTIs against S. aureus and E. coli DNA gyrase. We are confident that this integrated modeling approach could be valuable in the de novo design and optimization of efficient NBTIs for combating resistant bacterial pathogens.
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Affiliation(s)
- Maja Kokot
- Laboratory
for Cheminformatics, Theory Department, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
- The
Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Nikola Minovski
- Laboratory
for Cheminformatics, Theory Department, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
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3
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Nammalwar B, Bunce RA. Recent Advances in Pyrimidine-Based Drugs. Pharmaceuticals (Basel) 2024; 17:104. [PMID: 38256937 PMCID: PMC10820437 DOI: 10.3390/ph17010104] [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: 11/27/2023] [Revised: 01/03/2024] [Accepted: 01/07/2024] [Indexed: 01/24/2024] Open
Abstract
Pyrimidines have become an increasingly important core structure in many drug molecules over the past 60 years. This article surveys recent areas in which pyrimidines have had a major impact in drug discovery therapeutics, including anti-infectives, anticancer, immunology, immuno-oncology, neurological disorders, chronic pain, and diabetes mellitus. The article presents the synthesis of the medicinal agents and highlights the role of the biological target with respect to the disease model. Additionally, the biological potency, ADME properties and pharmacokinetics/pharmacodynamics (if available) are discussed. This survey attempts to demonstrate the versatility of pyrimidine-based drugs, not only for their potency and affinity but also for the improved medicinal chemistry properties of pyrimidine as a bioisostere for phenyl and other aromatic π systems. It is hoped that this article will provide insight to researchers considering the pyrimidine scaffold as a chemotype in future drug candidates in order to counteract medical conditions previously deemed untreatable.
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Affiliation(s)
- Baskar Nammalwar
- Vividion Therapeutics, 5820 Nancy Ridge Drive, San Diego, CA 92121, USA;
| | - Richard A. Bunce
- Department of Chemistry, Oklahoma State University, Stillwater, OK 74078, USA
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4
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Piplani P, Kumar A, Kulshreshtha A, Vohra T, Piplani V. Recent Development of DNA Gyrase Inhibitors: An Update. Mini Rev Med Chem 2024; 24:1001-1030. [PMID: 37909434 DOI: 10.2174/0113895575264264230921080718] [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: 06/15/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 11/03/2023]
Abstract
Antibiotic or antimicrobial resistance is an urgent global public health threat that occurs when bacterial or fungal infections do not respond to the drug regimen designed to treat these infections. As a result, these microbes are not evaded and continue to grow. Antibiotic resistance against natural and already-known antibiotics like Ciprofloxacin and Novobiocin can be overcome by developing an agent that can act in different ways. The success of agents like Zodiflodacin and Zenoxacin in clinical trials against DNA gyrase inhibitors that act on different sites of DNA gyrase has resulted in further exploration of this target. However, due to the emergence of bacterial resistance against these targets, there is a great need to design agents that can overcome this resistance and act with greater efficacy. This review provides information on the synthetic and natural DNA gyrase inhibitors that have been developed recently and their promising potential for combating antimicrobial resistance. The review also presents information on molecules that are in clinical trials and their current status. It also analysed the SAR studies and mechanisms of action of enlisted agents.
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Affiliation(s)
- Poonam Piplani
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, 160017, India
| | - Ajay Kumar
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, 160017, India
| | - Akanksha Kulshreshtha
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, 160017, India
| | - Tamanna Vohra
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, 160017, India
| | - Vritti Piplani
- Bhojia Dental College and Hospital, Baddi, 173205, India
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5
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An B, Chen P, Tao Y. The roles of membrane permeability and efflux pumps in the toxicity of bisphenol S analogues (2,4-bisphenol S and bis-(3-allyl-4-hydroxyphenyl) sulfone) to Escherichia coli K12. CHEMOSPHERE 2023; 329:138697. [PMID: 37062394 DOI: 10.1016/j.chemosphere.2023.138697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 05/03/2023]
Abstract
Bisphenol S (BPS) analogues are a group of recently reported emerging contaminants in the environment. Bacteria are important components of food webs. However, the potential risks of BPS analogues in bacteria have not been fully addressed. The toxicity effects and related mechanisms of two BPS analogues with different molecular weights (2,4-bisphenol S (2,4-BPS) and bis-(3-allyl-4-hydroxyphenyl) sulfone (TGSA)) on Escherichia coli K12 were compared. The minimum inhibitory concentration (MIC) of 2,4-BPS in the wild-type of E. coli K12 was lower than that of TGSA. The membrane permeability of the wild-type increased significantly after exposed to the same concentrations (0.5-50 nmol L-1) of 2,4-BPS and TGSA. In addition, 2,4-BPS induced more significant changes in membrane permeability than TGSA. Hormetic effects of 2,4-BPS and TGSA in the wild-type strain were noted in the levels of outer membrane proteins (ompC and ompF), multidrug efflux pump acriflavine resistance B (acrB) and type II topoisomerases. Transcriptomic results indicated these two BPS analogues inhibited the function of ABC transporters. In contrast to TGSA, 2,4-BPS affected DNA replication, tricarboxylic acid cycle, oxidative phosphorylation, and inhibited energy metabolism. Compared with wild-type strain, the ΔacrB mutant strain showed enhanced susceptibility to 2,4-BPS and TGSA with their MICs reduced by 20% and 11%, respectively. Deletion of the acrB affected the growth characteristics and induced stronger oxidative stress than the wild-type strain when exposed to 2,4-BPS or TGSA. The results suggested that 2,4-BPS were more toxic to E. coli K12 than TGSA in the concentration range of 0.5-50 nmol L-1, which was supported by the evidence from their impacts on membrane permeability and efflux pumps.
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Affiliation(s)
- Baihui An
- College of Oceanography, Hohai University, Nanjing, 210024, China
| | - Pengyu Chen
- College of Oceanography, Hohai University, Nanjing, 210024, China
| | - Yuqiang Tao
- College of Oceanography, Hohai University, Nanjing, 210024, China.
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6
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Janin YL. On drug discovery against infectious diseases and academic medicinal chemistry contributions. Beilstein J Org Chem 2022; 18:1355-1378. [PMID: 36247982 PMCID: PMC9531561 DOI: 10.3762/bjoc.18.141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 09/21/2022] [Indexed: 11/23/2022] Open
Abstract
This perspective is an attempt to document the problems that medicinal chemists are facing in drug discovery. It is also trying to identify relevant/possible, research areas in which academics can have an impact and should thus be the subject of grant calls. Accordingly, it describes how hit discovery happens, how compounds to be screened are selected from available chemicals and the possible reasons for the recurrent paucity of useful/exploitable results reported. This is followed by the successful hit to lead stories leading to recent and original antibacterials which are, or about to be, used in human medicine. Then, illustrated considerations and suggestions are made on the possible inputs of academic medicinal chemists. This starts with the observation that discovering a "good" hit in the course of a screening campaign still rely on a lot of luck - which is within the reach of academics -, that the hit to lead process requires a lot of chemistry and that if public-private partnerships can be important throughout these stages, they are absolute requirements for clinical trials. Concerning suggestions to improve the current hit success rate, one academic input in organic chemistry would be to identify new and pertinent chemical space, design synthetic accesses to reach these and prepare the corresponding chemical libraries. Concerning hit to lead programs on a given target, if no new hits are available, previously reported leads along with new structural data can be pertinent starting points to design, prepare and assay original analogues. In conclusion, this text is an actual plea illustrating that, in many countries, academic research in medicinal chemistry should be more funded, especially in the therapeutic area neglected by the industry. At the least, such funds would provide the intensive to secure series of hopefully relevant chemical entities which appears to often lack when considering the results of academic as well as industrial screening campaigns.
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Affiliation(s)
- Yves L Janin
- Structure et Instabilité des Génomes (StrInG), Muséum National d'Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université, 75005 Paris, France
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7
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Frejat FOA, Cao Y, Wang L, Zhai H, Abdelazeem AH, Gomaa HAM, Youssif BGM, Wu C. New 1,2,4-oxadiazole/pyrrolidine hybrids as topoisomerase IV and DNA gyrase inhibitors with promising antibacterial activity. Arch Pharm (Weinheim) 2022; 355:e2100516. [PMID: 35363388 DOI: 10.1002/ardp.202100516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/04/2022] [Accepted: 03/08/2022] [Indexed: 11/09/2022]
Abstract
A series of hybridized pyrrolidine compounds with a 1,2,4-oxadiazole moiety were synthesized to develop effective molecules against the enzymes DNA gyrase and topoisomerase IV (Topo IV). Compounds 8-20 were developed based on a previously disclosed series of compounds from our lab, but with small structural modifications in the hopes of increasing the compounds' biological activity. In comparison to novobiocin, with IC50 = 170 nM, the findings of the DNA gyrase inhibitory assay revealed that compounds 16 and 17 were the most potent of all synthesized derivatives, with IC50 values of 180 and 210 nM, respectively. Compound 17 had the strongest inhibitory effect against Escherichia coli Topo IV of all the synthesized compounds, with an IC50 value of 13 µM, which was comparable to novobiocin (IC50 = 11 µM). Therefore, hybrids 16 and 17 appeared to be potential dual-target inhibitors. In the minimal inhibitory concentration (MIC) assays, compound 17 outperformed ciprofloxacin against E. coli, with an MIC of 55 ng/ml, compared to 60 ng/ml for ciprofloxacin. Finally, the docking study, along with the in vitro experiments, supports our promising approach to effectively develop potent leads for further optimization as dual DNA gyrase and Topo IV inhibitors.
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Affiliation(s)
- Firas O A Frejat
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, People's Republic of China.,Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Zhengzhou, People's Republic of China
| | - Yaquan Cao
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, People's Republic of China.,Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Zhengzhou, People's Republic of China
| | - Lihong Wang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, People's Republic of China.,Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Zhengzhou, People's Republic of China
| | - Hongjin Zhai
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, People's Republic of China.,Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Zhengzhou, People's Republic of China
| | - Ahmed H Abdelazeem
- Department of Medicinal Chemistry, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt.,Pharmacy Department, College of Pharmacy, Riyadh Elm University, Riyadh, Saudi Arabia
| | - Hesham A M Gomaa
- Pharmacology Department, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - Bahaa G M Youssif
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut, Egypt
| | - Chunli Wu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, People's Republic of China.,Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Zhengzhou, People's Republic of China
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8
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Stroganova TA, Vasilin VK, Kanishcheva EA, Dmitrieva IG, Taranenko VV, Tumskiy RS, Tumskaia AV, Aksenov NA, Krapivin GD. Design, Synthesis, and Screening of Pyridothieno[3,2-b]indole and Pyridothieno[3,2-c]cinnoline Derivatives as Potential Biologically Active Molecules. SYNTHESIS-STUTTGART 2022. [DOI: 10.1055/a-1785-7191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
AbstractNew pyridothieno[3,2-b]indole and pyridothieno[3,2-c]cinnoline derivatives are designed and prepared from the corresponding 3-amino-2-arylthieno[2,3-b]pyridines. By a molecular docking method novel potential inhibitors of DNA gyrase B are identified among the thieno[2,3-b]pyridine derivatives. In addition, some of the prepared pyridothienoindoles exhibit in vivo antidote activity against the herbicide 2,4-D.
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Affiliation(s)
- Tatyana A. Stroganova
- Department of Bioorganic Chemistry and Technical Microbiology, Kuban State Technological University
| | - Vladimir K. Vasilin
- Department of Bioorganic Chemistry and Technical Microbiology, Kuban State Technological University
| | - Eugeniya A. Kanishcheva
- Research Institute of Heterocyclic Compounds Chemistry, Kuban State Technological University
| | | | | | - Roman S. Tumskiy
- Institute of Biochemistry and Physiology of Plants and Microorganisms (IBPPM RAS), Russian Academy of Sciences
| | | | | | - Gennady D. Krapivin
- Research Institute of Heterocyclic Compounds Chemistry, Kuban State Technological University
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9
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Flagstad T, Pedersen MT, Jakobsen TH, Felding J, Tolker-Nielsen T, Givskov M, Qvortrup K, Nielsen TE. Solid-phase synthesis and biological evaluation of piperazine-based novel bacterial topoisomerase inhibitors. Bioorg Med Chem Lett 2021; 57:128499. [PMID: 34906671 DOI: 10.1016/j.bmcl.2021.128499] [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: 10/05/2021] [Revised: 12/05/2021] [Accepted: 12/06/2021] [Indexed: 11/28/2022]
Abstract
There is an emerging global need for new and more effective antibiotics against multi-resistant bacteria. This situation has led to massive industrial investigations on novel bacterial topoisomerase inhibitors (NBTIs) that target the vital bacterial enzymes DNA gyrase and topoisomerase IV. However, several of the NBTI compound classes have been associated with inhibition of the hERG potassium channel, an undesired cause of cardiac arrhythmia, which challenges medicinal chemistry efforts through lengthy synthetic routes. We herein present a solid-phase strategy that rapidly facilitates the chemical synthesis of a promising new class of NBTIs. A proof-of-concept library was synthesized with the ability to modulate both hERG affinity and antibacterial activity through scaffold substitutions.
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Affiliation(s)
- Thomas Flagstad
- Department of Chemistry, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Mette T Pedersen
- Department of Chemistry, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Tim H Jakobsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | | | - Tim Tolker-Nielsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Michael Givskov
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore
| | - Katrine Qvortrup
- Department of Chemistry, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Thomas E Nielsen
- Department of Chemistry, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark; Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore.
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10
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Lu Y, Vibhute S, Li L, Okumu A, Ratigan SC, Nolan S, Papa JL, Mann CA, English A, Chen A, Seffernick JT, Koci B, Duncan LR, Roth B, Cummings JE, Slayden RA, Lindert S, McElroy CA, Wozniak DJ, Yalowich J, Mitton-Fry MJ. Optimization of TopoIV Potency, ADMET Properties, and hERG Inhibition of 5-Amino-1,3-dioxane-Linked Novel Bacterial Topoisomerase Inhibitors: Identification of a Lead with In Vivo Efficacy against MRSA. J Med Chem 2021; 64:15214-15249. [PMID: 34614347 DOI: 10.1021/acs.jmedchem.1c01250] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Novel bacterial topoisomerase inhibitors (NBTIs) are among the most promising new antibiotics in preclinical/clinical development. We previously reported dioxane-linked NBTIs with potent antistaphylococcal activity and reduced hERG inhibition, a key safety liability. Herein, polarity-focused optimization enabled the delineation of clear structure-property relationships for both microsomal metabolic stability and hERG inhibition, resulting in the identification of lead compound 79. This molecule demonstrates potent antibacterial activity against diverse Gram-positive pathogens, inhibition of both DNA gyrase and topoisomerase IV, a low frequency of resistance, a favorable in vitro cardiovascular safety profile, and in vivo efficacy in a murine model of methicillin-resistant Staphylococcus aureus infection.
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Affiliation(s)
- Yanran Lu
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sandip Vibhute
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Linsen Li
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Antony Okumu
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Steven C Ratigan
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sheri Nolan
- Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jonathan L Papa
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Chelsea A Mann
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Anthony English
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Anna Chen
- Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Justin T Seffernick
- Department of Chemistry and Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Bryan Koci
- Eurofins Panlabs, St. Charles, Missouri 63304, United States
| | | | - Brieanna Roth
- JMI Laboratories, North Liberty, Iowa 52317, United States
| | - Jason E Cummings
- Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Richard A Slayden
- Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Craig A McElroy
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Daniel J Wozniak
- Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States.,Department of Microbiology, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jack Yalowich
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Mark J Mitton-Fry
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
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11
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Kong Q, Pan W, Xu H, Xue Y, Guo B, Meng X, Luo C, Wang T, Zhang S, Yang Y. Design, Synthesis, and Biological Evaluation of Novel Pyrimido[4,5- b]indole Derivatives Against Gram-Negative Multidrug-Resistant Pathogens. J Med Chem 2021; 64:8644-8665. [PMID: 34080858 DOI: 10.1021/acs.jmedchem.1c00621] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Due to the poor permeability across Gram-negative bacterial membranes and the troublesome bacterial efflux mechanism, only a few GyrB/ParE inhibitors with potent activity against Gram-negative pathogens have been reported. Among them, pyrimido[4,5-b]indole derivatives represented by GP-1 demonstrated excellent broad-spectrum antibacterial activity against both Gram-positive and Gram-negative bacteria but were limited by hERG inhibition and poor pharmacokinetics profile. To improve their drug-like properties, we designed a series of novel pyrimido[4,5-b]indole derivatives based on the tricyclic scaffold of GP-1 and the C-7 moiety of acorafloxacin. These efforts have culminated in the discovery of a promising compound 18r with reduced hERG liability and an improved PK profile. Compound 18r exhibited superior broad-spectrum in vitro antibacterial activity compared to GP-1, including a variety of clinical multidrug G- pathogens, especially Acinetobacter baumannii, and the in vivo efficacy was also demonstrated in a neutropenic mouse thigh model of infection with multidrug-resistant A. baumannii.
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Affiliation(s)
- Qidi Kong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Wei Pan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Heng Xu
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Yaru Xue
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Bin Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xin Meng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Cheng Luo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Ting Wang
- Department of Microbiology, Sichuan Primed Bio-Tech Group Company, Limited, Chengdu 610041, Sichuan Province, China
| | - Shuhua Zhang
- Department of Microbiology, Sichuan Primed Bio-Tech Group Company, Limited, Chengdu 610041, Sichuan Province, China
| | - Yushe Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
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12
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Lapointe G, Skepper CK, Holder LM, Armstrong D, Bellamacina C, Blais J, Bussiere D, Bian J, Cepura C, Chan H, Dean CR, De Pascale G, Dhumale B, Fisher LM, Fulsunder M, Kantariya B, Kim J, King S, Kossy L, Kulkarni U, Lakshman J, Leeds JA, Ling X, Lvov A, Ma S, Malekar S, McKenney D, Mergo W, Metzger L, Mhaske K, Moser HE, Mostafavi M, Namballa S, Noeske J, Osborne C, Patel A, Patel D, Patel T, Piechon P, Polyakov V, Prajapati K, Prosen KR, Reck F, Richie DL, Sanderson MR, Satasia S, Savani B, Selvarajah J, Sethuraman V, Shu W, Tashiro K, Thompson KV, Vaarla K, Vala L, Veselkov DA, Vo J, Vora B, Wagner T, Wedel L, Williams SL, Yendluri S, Yue Q, Yifru A, Zhang Y, Rivkin A. Discovery and Optimization of DNA Gyrase and Topoisomerase IV Inhibitors with Potent Activity against Fluoroquinolone-Resistant Gram-Positive Bacteria. J Med Chem 2021; 64:6329-6357. [PMID: 33929852 DOI: 10.1021/acs.jmedchem.1c00375] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Herein, we describe the discovery and optimization of a novel series that inhibits bacterial DNA gyrase and topoisomerase IV via binding to, and stabilization of, DNA cleavage complexes. Optimization of this series led to the identification of compound 25, which has potent activity against Gram-positive bacteria, a favorable in vitro safety profile, and excellent in vivo pharmacokinetic properties. Compound 25 was found to be efficacious against fluoroquinolone-sensitive Staphylococcus aureus infection in a mouse thigh model at lower doses than moxifloxacin. An X-ray crystal structure of the ternary complex formed by topoisomerase IV from Klebsiella pneumoniae, compound 25, and cleaved DNA indicates that this compound does not engage in a water-metal ion bridge interaction and forms no direct contacts with residues in the quinolone resistance determining region (QRDR). This suggests a structural basis for the reduced impact of QRDR mutations on antibacterial activity of 25 compared to fluoroquinolones.
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Affiliation(s)
- Guillaume Lapointe
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Colin K Skepper
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Lauren M Holder
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Duncan Armstrong
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Cornelia Bellamacina
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Johanne Blais
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Dirksen Bussiere
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Jianwei Bian
- Novartis Global Drug Development, Pudong, Shanghai 201203, China
| | - Cody Cepura
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Helen Chan
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Charles R Dean
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Gianfranco De Pascale
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Bhavesh Dhumale
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - L Mark Fisher
- Molecular and Clinical Sciences Research Institute, St George's, University of London, London SW17 0RE, U.K
| | - Mangesh Fulsunder
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Bhavin Kantariya
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Julie Kim
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Sean King
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Lauren Kossy
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Upendra Kulkarni
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Jay Lakshman
- Novartis Global Drug Development, East Hanover, New Jersey 07936, United States
| | - Jennifer A Leeds
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Xiaolan Ling
- Novartis Global Drug Development, Pudong, Shanghai 201203, China
| | - Anatoli Lvov
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Sylvia Ma
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Swapnil Malekar
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - David McKenney
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Wosenu Mergo
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Louis Metzger
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Keshav Mhaske
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Heinz E Moser
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Mina Mostafavi
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Sunil Namballa
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Jonas Noeske
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Colin Osborne
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Ashish Patel
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Darshit Patel
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Tushar Patel
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Philippe Piechon
- Novartis Institutes for BioMedical Research, Basel 4002, Switzerland
| | - Valery Polyakov
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Krunal Prajapati
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Katherine R Prosen
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Folkert Reck
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Daryl L Richie
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Mark R Sanderson
- Randall Centre for Cell and Molecular Biophysics, King's College, Guy's Campus, London Bridge, London SE1 1UL, U.K
| | - Shailesh Satasia
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Bhautik Savani
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Jogitha Selvarajah
- Molecular and Clinical Sciences Research Institute, St George's, University of London, London SW17 0RE, U.K
| | - Vijay Sethuraman
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Wei Shu
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Kyuto Tashiro
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Katherine V Thompson
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Krishniah Vaarla
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Lakhan Vala
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Dennis A Veselkov
- Randall Centre for Cell and Molecular Biophysics, King's College, Guy's Campus, London Bridge, London SE1 1UL, U.K
| | - Jason Vo
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Bhavesh Vora
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Trixie Wagner
- Novartis Institutes for BioMedical Research, Basel 4002, Switzerland
| | - Laura Wedel
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Sarah L Williams
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Satya Yendluri
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Qin Yue
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Aregahegn Yifru
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Yong Zhang
- Novartis Global Drug Development, Pudong, Shanghai 201203, China
| | - Alexey Rivkin
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
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13
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New dual ATP-competitive inhibitors of bacterial DNA gyrase and topoisomerase IV active against ESKAPE pathogens. Eur J Med Chem 2021; 213:113200. [PMID: 33524686 DOI: 10.1016/j.ejmech.2021.113200] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/10/2020] [Accepted: 01/12/2021] [Indexed: 11/21/2022]
Abstract
The rise in multidrug-resistant bacteria defines the need for identification of new antibacterial agents that are less prone to resistance acquisition. Compounds that simultaneously inhibit multiple bacterial targets are more likely to suppress the evolution of target-based resistance than monotargeting compounds. The structurally similar ATP binding sites of DNA gyrase and topoisomerase Ⅳ offer an opportunity to accomplish this goal. Here we present the design and structure-activity relationship analysis of balanced, low nanomolar inhibitors of bacterial DNA gyrase and topoisomerase IV that show potent antibacterial activities against the ESKAPE pathogens. For inhibitor 31c, a crystal structure in complex with Staphylococcus aureus DNA gyrase B was obtained that confirms the mode of action of these compounds. The best inhibitor, 31h, does not show any in vitro cytotoxicity and has excellent potency against Gram-positive (MICs: range, 0.0078-0.0625 μg/mL) and Gram-negative pathogens (MICs: range, 1-2 μg/mL). Furthermore, 31h inhibits GyrB mutants that can develop resistance to other drugs. Based on these data, we expect that structural derivatives of 31h will represent a step toward clinically efficacious multitargeting antimicrobials that are not impacted by existing antimicrobial resistance.
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14
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Durcik M, Skok Ž, Ilaš J, Zidar N, Zega A, Szili PÉ, Draskovits G, Révész T, Kikelj D, Nyerges A, Pál C, Mašič LP, Tomašič T. Hybrid Inhibitors of DNA Gyrase A and B: Design, Synthesis and Evaluation. Pharmaceutics 2020; 13:pharmaceutics13010006. [PMID: 33374964 PMCID: PMC7822030 DOI: 10.3390/pharmaceutics13010006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/15/2020] [Accepted: 12/19/2020] [Indexed: 11/16/2022] Open
Abstract
The discovery of multi-targeting ligands of bacterial enzymes is an important strategy to combat rapidly spreading antimicrobial resistance. Bacterial DNA gyrase and topoisomerase IV are validated targets for the development of antibiotics. They can be inhibited at their catalytic sites or at their ATP binding sites. Here we present the design of new hybrids between the catalytic inhibitor ciprofloxacin and ATP-competitive inhibitors that show low nanomolar inhibition of DNA gyrase and antibacterial activity against Gram-negative pathogens. The most potent hybrid 3a has MICs of 0.5 µg/mL against Klebsiella pneumoniae, 4 µg/mL against Enterobacter cloacae, and 2 µg/mL against Escherichia coli. In addition, inhibition of mutant E. coli strains shows that these hybrid inhibitors interact with both subunits of DNA gyrase (GyrA, GyrB), and that binding to both of these sites contributes to their antibacterial activity.
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Affiliation(s)
- Martina Durcik
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia; (M.D.); (Ž.S.); (J.I.); (N.Z.); (A.Z.); (D.K.)
| | - Žiga Skok
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia; (M.D.); (Ž.S.); (J.I.); (N.Z.); (A.Z.); (D.K.)
| | - Janez Ilaš
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia; (M.D.); (Ž.S.); (J.I.); (N.Z.); (A.Z.); (D.K.)
| | - Nace Zidar
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia; (M.D.); (Ž.S.); (J.I.); (N.Z.); (A.Z.); (D.K.)
| | - Anamarija Zega
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia; (M.D.); (Ž.S.); (J.I.); (N.Z.); (A.Z.); (D.K.)
| | - Petra Éva Szili
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary; (P.É.S.); (G.D.); (T.R.); (A.N.); (C.P.)
| | - Gábor Draskovits
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary; (P.É.S.); (G.D.); (T.R.); (A.N.); (C.P.)
| | - Tamás Révész
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary; (P.É.S.); (G.D.); (T.R.); (A.N.); (C.P.)
| | - Danijel Kikelj
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia; (M.D.); (Ž.S.); (J.I.); (N.Z.); (A.Z.); (D.K.)
| | - Akos Nyerges
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary; (P.É.S.); (G.D.); (T.R.); (A.N.); (C.P.)
- Department of Genetics, Harvard Medical School, Boston, MA 02215, USA
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary; (P.É.S.); (G.D.); (T.R.); (A.N.); (C.P.)
| | - Lucija Peterlin Mašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia; (M.D.); (Ž.S.); (J.I.); (N.Z.); (A.Z.); (D.K.)
- Correspondence: (L.P.M.); (T.T.); Tel.: +386-1-4769-635 (L.P.M.); +386-1-4769-556 (T.T.)
| | - Tihomir Tomašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia; (M.D.); (Ž.S.); (J.I.); (N.Z.); (A.Z.); (D.K.)
- Correspondence: (L.P.M.); (T.T.); Tel.: +386-1-4769-635 (L.P.M.); +386-1-4769-556 (T.T.)
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15
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Lu Y, Papa JL, Nolan S, English A, Seffernick JT, Shkolnikov N, Powell J, Lindert S, Wozniak DJ, Yalowich J, Mitton-Fry MJ. Dioxane-Linked Amide Derivatives as Novel Bacterial Topoisomerase Inhibitors against Gram-Positive Staphylococcus aureus. ACS Med Chem Lett 2020; 11:2446-2454. [PMID: 33335666 DOI: 10.1021/acsmedchemlett.0c00428] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/14/2020] [Indexed: 12/19/2022] Open
Abstract
In recent years, novel bacterial topoisomerase inhibitors (NBTIs) have been developed as future antibacterials for treating multidrug-resistant bacterial infections. A series of dioxane-linked NBTIs with an amide moiety has been synthesized and evaluated. Compound 3 inhibits DNA gyrase, induces the formation of single strand breaks to bacterial DNA, and achieves potent antibacterial activity against a variety of Gram-positive pathogens, including methicillin-resistant Staphylococcus aureus (MRSA). Optimization of this series of analogues led to the discovery of a subseries of compounds (22-25) with more potent anti-MRSA activity, dual inhibition of DNA gyrase and topoisomerase IV, and the ability to induce double strand breaks through inhibition of S. aureus DNA gyrase.
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16
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Henderson SR, Stevenson CEM, Malone B, Zholnerovych Y, Mitchenall LA, Pichowicz M, McGarry DH, Cooper IR, Charrier C, Salisbury AM, Lawson DM, Maxwell A. Structural and mechanistic analysis of ATPase inhibitors targeting mycobacterial DNA gyrase. J Antimicrob Chemother 2020; 75:2835-2842. [PMID: 32728686 PMCID: PMC7556816 DOI: 10.1093/jac/dkaa286] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 05/28/2020] [Accepted: 05/30/2020] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVES To evaluate the efficacy of two novel compounds against mycobacteria and determine the molecular basis of their action on DNA gyrase using structural and mechanistic approaches. METHODS Redx03863 and Redx04739 were tested in antibacterial assays, and also against their target, DNA gyrase, using DNA supercoiling and ATPase assays. X-ray crystallography was used to determine the structure of the gyrase B protein ATPase sub-domain from Mycobacterium smegmatis complexed with the aminocoumarin drug novobiocin, and structures of the same domain from Mycobacterium thermoresistibile complexed with novobiocin, and also with Redx03863. RESULTS Both compounds, Redx03863 and Redx04739, were active against selected Gram-positive and Gram-negative species, with Redx03863 being the more potent, and Redx04739 showing selectivity against M. smegmatis. Both compounds were potent inhibitors of the supercoiling and ATPase reactions of DNA gyrase, but did not appreciably affect the ATP-independent relaxation reaction. The structure of Redx03863 bound to the gyrase B protein ATPase sub-domain from M. thermoresistibile shows that it binds at a site adjacent to the ATP- and novobiocin-binding sites. We found that most of the mutations that we made in the Redx03863-binding pocket, based on the structure, rendered gyrase inactive. CONCLUSIONS Redx03863 and Redx04739 inhibit gyrase by preventing the binding of ATP. The fact that the Redx03863-binding pocket is distinct from that of novobiocin, coupled with the lack of activity of resistant mutants, suggests that such compounds could have potential to be further exploited as antibiotics.
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Affiliation(s)
- Sara R Henderson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- Norwich Medical School, University of East Anglia, Norwich NR4 7UQ, UK
| | - Clare E M Stevenson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Brandon Malone
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Yelyzaveta Zholnerovych
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Lesley A Mitchenall
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Mark Pichowicz
- Redx Pharma PLC, Mereside, Alderley Park, Alderley Edge SK10 4TG, UK
- Sygnature Discovery, The Discovery Building, Biocity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - David H McGarry
- Redx Pharma PLC, Mereside, Alderley Park, Alderley Edge SK10 4TG, UK
- Globachem Discovery Ltd, Mereside, Alderley Park SK10 4TG, UK
| | - Ian R Cooper
- Redx Pharma PLC, Mereside, Alderley Park, Alderley Edge SK10 4TG, UK
- AMR Centre Ltd, Mereside, Alderley Park SK10 4TG, UK
| | - Cedric Charrier
- Redx Pharma PLC, Mereside, Alderley Park, Alderley Edge SK10 4TG, UK
- IHMA Europe Sàrl, Rte. de I’lle-au-Bois 1A, 1870 Monthey/VS, Switzerland
| | - Anne-Marie Salisbury
- Redx Pharma PLC, Mereside, Alderley Park, Alderley Edge SK10 4TG, UK
- 5D Health Protection Group Ltd, William Henry Duncan Building, West Derby Street, Liverpool L7 8TX, UK
| | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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17
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Ushiyama F, Amada H, Mihara Y, Takeuchi T, Tanaka-Yamamoto N, Mima M, Kamitani M, Wada R, Tamura Y, Endo M, Masuko A, Takata I, Hitaka K, Sugiyama H, Ohtake N. Lead optimization of 8-(methylamino)-2-oxo-1,2-dihydroquinolines as bacterial type II topoisomerase inhibitors. Bioorg Med Chem 2020; 28:115776. [PMID: 33032189 DOI: 10.1016/j.bmc.2020.115776] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/13/2020] [Accepted: 09/15/2020] [Indexed: 11/28/2022]
Abstract
The global increase in multidrug-resistant pathogens has caused severe problems in the treatment of infections. To overcome these difficulties, the advent of a new chemical class of antibacterial drug is eagerly desired. We aimed at creating novel antibacterial agents against bacterial type II topoisomerases, which are well-validated targets. TP0480066 (compound 32) has been identified by using structure-based optimization originated from lead compound 1, which was obtained as a result of our previous lead identification studies. The MIC90 values of TP0480066 against methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococci (VRE), and genotype penicillin-resistant Streptococcus pneumoniae (gPRSP) were 0.25, 0.015, and 0.06 μg/mL, respectively. Hence, TP0480066 can be regarded as a promising antibacterial drug candidate of this chemical class.
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Affiliation(s)
- Fumihito Ushiyama
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan.
| | - Hideaki Amada
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Yasuhiro Mihara
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Tomoki Takeuchi
- 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
| | - Masafumi Kamitani
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Reiko Wada
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
| | - Yunoshin Tamura
- 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
| | - Aiko Masuko
- 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
| | - Kosuke Hitaka
- 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
| | - Norikazu Ohtake
- Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan
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18
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Lu CH, McCloskey A, Chen FR, Nakayasu ES, Zhang LQ, Luo ZQ. Fic Proteins Inhibit the Activity of Topoisomerase IV by AMPylation in Diverse Bacteria. Front Microbiol 2020; 11:2084. [PMID: 32983060 PMCID: PMC7479194 DOI: 10.3389/fmicb.2020.02084] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 08/07/2020] [Indexed: 12/14/2022] Open
Abstract
The Fic (filamentation induced by cyclic AMP) domain is a widely distributed motif with a conserved sequence of HPFx[D/E]GN[G/K]R, some of which regulate cellular activity by catalyzing the transfer of the AMP moiety from ATP to protein substrates. Some Fic proteins, including Fic-1 from the soil bacterium Pseudomonas fluorescens strain 2P24, have been shown to inhibit bacterial DNA replication by AMPylating the subunit B of DNA gyrase (GyrB), but the biochemical activity and cellular target of most Fic proteins remain unknown. Here, we report that Fic-2, which is another Fic protein from strain 2P24 and Fic-1 AMPylate the topoisomerase IV ParE at Tyr109. We also examined Fic proteins from several phylogenetically diverse bacteria and found that those from Yersinia pseudotuberculosis and Staphylococcus aureus AMPylate ParE and GrlB, the counterpart of ParE in Gram-positive bacteria, respectively. Modification by Fic-1 of P. fluorescens and FicY of Y. pseudotuberculosis inhibits the relaxation activity of topoisomerase IV. Consistent with the inhibition of ParE activity, ectopic expression of these Fic proteins causes cell filamentation akin to the canonical par phenotype in which nucleoids are assembled in the center of elongated cells, a process accompanied by the induction of the SOS response. Our results establish that Fic proteins from diverse bacterial species regulate chromosome division and cell separation in bacteria by targeting ParE.
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Affiliation(s)
- Can-Hua Lu
- Yunnan Academy of Tobacco Agriculture Science, Kunming, China.,Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China.,Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
| | - Alix McCloskey
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
| | - Fu-Rong Chen
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Ernesto S Nakayasu
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Li-Qun Zhang
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Zhao-Qing Luo
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
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19
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Recent advances in DNA gyrase-targeted antimicrobial agents. Eur J Med Chem 2020; 199:112326. [DOI: 10.1016/j.ejmech.2020.112326] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 12/16/2022]
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20
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Skepper CK, Armstrong D, Balibar CJ, Bauer D, Bellamacina C, Benton BM, Bussiere D, De Pascale G, De Vicente J, Dean CR, Dhumale B, Fisher LM, Fuller J, Fulsunder M, Holder LM, Hu C, Kantariya B, Lapointe G, Leeds JA, Li X, Lu P, Lvov A, Ma S, Madhavan S, Malekar S, McKenney D, Mergo W, Metzger L, Moser HE, Mutnick D, Noeske J, Osborne C, Patel A, Patel D, Patel T, Prajapati K, Prosen KR, Reck F, Richie DL, Rico A, Sanderson MR, Satasia S, Sawyer WS, Selvarajah J, Shah N, Shanghavi K, Shu W, Thompson KV, Traebert M, Vala A, Vala L, Veselkov DA, Vo J, Wang M, Widya M, Williams SL, Xu Y, Yue Q, Zang R, Zhou B, Rivkin A. Topoisomerase Inhibitors Addressing Fluoroquinolone Resistance in Gram-Negative Bacteria. J Med Chem 2020; 63:7773-7816. [PMID: 32634310 DOI: 10.1021/acs.jmedchem.0c00347] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Since their discovery over 5 decades ago, quinolone antibiotics have found enormous success as broad spectrum agents that exert their activity through dual inhibition of bacterial DNA gyrase and topoisomerase IV. Increasing rates of resistance, driven largely by target-based mutations in the GyrA/ParC quinolone resistance determining region, have eroded the utility and threaten the future use of this vital class of antibiotics. Herein we describe the discovery and optimization of a series of 4-(aminomethyl)quinolin-2(1H)-ones, exemplified by 34, that inhibit bacterial DNA gyrase and topoisomerase IV and display potent activity against ciprofloxacin-resistant Gram-negative pathogens. X-ray crystallography reveals that 34 occupies the classical quinolone binding site in the topoisomerase IV-DNA cleavage complex but does not form significant contacts with residues in the quinolone resistance determining region.
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Affiliation(s)
- Colin K Skepper
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Duncan Armstrong
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Carl J Balibar
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Daniel Bauer
- Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland
| | - Cornelia Bellamacina
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Bret M Benton
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Dirksen Bussiere
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Gianfranco De Pascale
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Javier De Vicente
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Charles R Dean
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Bhavesh Dhumale
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - L Mark Fisher
- Molecular and Clinical Sciences Research Institute, St George's University of London, London SW17 0RE, U.K
| | - John Fuller
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Mangesh Fulsunder
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Lauren M Holder
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Cheng Hu
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Bhavin Kantariya
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Guillaume Lapointe
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Jennifer A Leeds
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Xiaolin Li
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Peichao Lu
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Anatoli Lvov
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Sylvia Ma
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Shravanthi Madhavan
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Swapnil Malekar
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - David McKenney
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Wosenu Mergo
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Louis Metzger
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Heinz E Moser
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Daniel Mutnick
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Jonas Noeske
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Colin Osborne
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Ashish Patel
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Darshit Patel
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Tushar Patel
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Krunal Prajapati
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Katherine R Prosen
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Folkert Reck
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Daryl L Richie
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Alice Rico
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Mark R Sanderson
- Randall Centre for Cell and Molecular Biophysics, King's College, Guy's Campus, London Bridge, London SE1 1UL, U.K
| | - Shailesh Satasia
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - William S Sawyer
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Jogitha Selvarajah
- Molecular and Clinical Sciences Research Institute, St George's University of London, London SW17 0RE, U.K
| | - Nirav Shah
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Kartik Shanghavi
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Wei Shu
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Katherine V Thompson
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Martin Traebert
- Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland
| | - Anand Vala
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Lakhan Vala
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Sarkhej Bavla Highway, Ahmedabad, Gujarat 382213, India
| | - Dennis A Veselkov
- Randall Centre for Cell and Molecular Biophysics, King's College, Guy's Campus, London Bridge, London SE1 1UL, U.K
| | - Jason Vo
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Michael Wang
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Marcella Widya
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Sarah L Williams
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Yongjin Xu
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Qin Yue
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Richard Zang
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Bo Zhou
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Alexey Rivkin
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
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21
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Ushiyama F, Amada H, Takeuchi T, Tanaka-Yamamoto N, Kanazawa H, Nakano K, Mima M, Masuko A, Takata I, Hitaka K, Iwamoto K, Sugiyama H, Ohtake N. Lead Identification of 8-(Methylamino)-2-oxo-1,2-dihydroquinoline Derivatives as DNA Gyrase Inhibitors: Hit-to-Lead Generation Involving Thermodynamic Evaluation. ACS OMEGA 2020; 5:10145-10159. [PMID: 32391502 PMCID: PMC7203957 DOI: 10.1021/acsomega.0c00865] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/09/2020] [Indexed: 05/26/2023]
Abstract
DNA gyrase and topoisomerase IV are well-validated pharmacological targets, and quinolone antibacterial drugs are marketed as their representative inhibitors. However, in recent years, resistance to these existing drugs has become a problem, and new chemical classes of antibiotics that can combat resistant strains of bacteria are strongly needed. In this study, we applied our hit-to-lead (H2L) chemistry for the identification of a new chemical class of GyrB/ParE inhibitors by efficient use of thermodynamic parameters. Investigation of the core fragments obtained by fragmentation of high-throughput screening hit compounds and subsequent expansion of the hit fragment was performed using isothermal titration calorimetry (ITC). The 8-(methylamino)-2-oxo-1,2-dihydroquinoline derivative 13e showed potent activity against Escherichia coli DNA gyrase with an IC50 value of 0.0017 μM. In this study, we demonstrated the use of ITC for primary fragment screening, followed by structural optimization to obtain lead compounds, which advanced into further optimization for creating novel antibacterial agents.
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Affiliation(s)
- Fumihito Ushiyama
- Chemistry
Laboratories, Taisho Pharmaceutical Company
Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Hideaki Amada
- Chemistry
Laboratories, Taisho Pharmaceutical Company
Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Tomoki Takeuchi
- Chemistry
Laboratories, Taisho Pharmaceutical Company
Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Nozomi Tanaka-Yamamoto
- Chemistry
Laboratories, Taisho Pharmaceutical Company
Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Harumi Kanazawa
- Chemistry
Laboratories, Taisho Pharmaceutical Company
Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Koichiro Nakano
- Pharmacology
Laboratories, Taisho Pharmaceutical Company
Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Masashi Mima
- Pharmacology
Laboratories, Taisho Pharmaceutical Company
Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Aiko Masuko
- Pharmacology
Laboratories, Taisho Pharmaceutical Company
Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Iichiro Takata
- Pharmacology
Laboratories, Taisho Pharmaceutical Company
Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Kosuke Hitaka
- Pharmacology
Laboratories, Taisho Pharmaceutical Company
Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Kunihiko Iwamoto
- Pharmacology
Laboratories, Taisho Pharmaceutical Company
Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Hiroyuki Sugiyama
- Pharmacology
Laboratories, Taisho Pharmaceutical Company
Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
| | - Norikazu Ohtake
- Chemistry
Laboratories, Taisho Pharmaceutical Company
Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan
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22
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Radwan MA, Alshubramy MA, Abdel-Motaal M, Hemdan BA, El-Kady DS. Synthesis, molecular docking and antimicrobial activity of new fused pyrimidine and pyridine derivatives. Bioorg Chem 2020; 96:103516. [DOI: 10.1016/j.bioorg.2019.103516] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/10/2019] [Accepted: 12/12/2019] [Indexed: 12/12/2022]
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23
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Antimicrobial screening and pharmacokinetic profiling of novel phenyl-[1,2,4]triazolo[4,3-a]quinoxaline analogues targeting DHFR and E. coli DNA gyrase B. Bioorg Chem 2020; 96:103656. [DOI: 10.1016/j.bioorg.2020.103656] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/21/2020] [Accepted: 02/08/2020] [Indexed: 12/11/2022]
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24
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Kolarič A, Anderluh M, Minovski N. Two Decades of Successful SAR-Grounded Stories of the Novel Bacterial Topoisomerase Inhibitors (NBTIs). J Med Chem 2020; 63:5664-5674. [PMID: 32027491 PMCID: PMC7307926 DOI: 10.1021/acs.jmedchem.9b01738] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The emergence of bacterial resistance against life-saving medicines has forced the scientific community and pharmaceutical industry to take actions in the quest for novel antibacterials. These should not only overcome the existing bacterial resistance but also provide at least interim effective protection against emerging bacterial infections. Research into DNA gyrase and topoisomerase IV inhibitors has become a particular focus, with the description of a new class of bacterial topoisomerase type II inhibitors known as "novel bacterial topoisomerase inhibitors", NBTIs. Elucidation of the key structural modifications incorporated into these inhibitors and the impact these can have on their general physicochemical properties are detailed in this review. This defines novel bacterial topoisomerase inhibitors with promising antibacterial activities and potencies, which thus represent one potential example of the future "drugs for bad bugs", as identified by the World Health Organization.
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Affiliation(s)
- Anja Kolarič
- Laboratory for Cheminformatics, Theory Department, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia.,Chair of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Marko Anderluh
- Chair of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Nikola Minovski
- Laboratory for Cheminformatics, Theory Department, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
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25
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Azam MA, Thathan J, Jupudi S. Pharmacophore modeling, atom based 3D-QSAR, molecular docking and molecular dynamics studies on Escherichia coli ParE inhibitors. Comput Biol Chem 2019; 84:107197. [PMID: 31901788 DOI: 10.1016/j.compbiolchem.2019.107197] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/20/2019] [Accepted: 12/22/2019] [Indexed: 10/25/2022]
Abstract
ATP dependent ParE enzyme is as an attractive target for the development of antibacterial agents. Atom based 3D-QSAR model AADHR.187 was developed based on the thirty eight Escherichia coli ParE inhibitors. The generated model showed statistically significant coefficient of determinations for the training (R2 = 0.985) and test (R2 = 0.86) sets. The cross-validated correlation coefficient (q2) was 0.976. The utility of the generated model was validated by the enrichment study. The model was also validated with structurally diverse external test set of ten compounds. Contour plot analysis of the generated model unveiled the chemical features necessary for the E. coli ParE enzyme inhibition. Extra-precision docking result revealed that hydrogen bonding and ionic interactions play a major role in ParE protein-ligand binding. Binding free energy was computed for the data set inhibitors to validate the binding affinity. A 30-ns molecular dynamics simulation showed high stability and effective binding of inhibitor 34 within the active site of ParE enzyme. Using the best fitted model AADHR.187, pharmacophore-based high-throughput virtual screening was performed to identify virtual hits. Based on the above studies three new molecules are proposed as E. coli ParE inhibitors with high binding affinity and favourable ADME properties.
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Affiliation(s)
- Mohammed Afzal Azam
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Ooty, 643001, Tamil Nadu, India(1).
| | - Janarthanan Thathan
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Ooty, 643001, Tamil Nadu, India(1)
| | - Srikanth Jupudi
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Ooty, 643001, Tamil Nadu, India(1)
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26
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Fois B, Skok Ž, Tomašič T, Ilaš J, Zidar N, Zega A, Peterlin Mašič L, Szili P, Draskovits G, Nyerges Á, Pál C, Kikelj D. Dual
Escherichia coli
DNA Gyrase A and B Inhibitors with Antibacterial Activity. ChemMedChem 2019; 15:265-269. [DOI: 10.1002/cmdc.201900607] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Indexed: 01/11/2023]
Affiliation(s)
- Benedetta Fois
- Faculty of Pharmacy University of Ljubljana Aškerčeva cesta 7 1000 Ljubljana Slovenia
- Faculty of Biology and Pharmacy University of Cagliari Via Ospedale 72 09124 Cagliari Italy
| | - Žiga Skok
- Faculty of Pharmacy University of Ljubljana Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Tihomir Tomašič
- Faculty of Pharmacy University of Ljubljana Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Janez Ilaš
- Faculty of Pharmacy University of Ljubljana Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Nace Zidar
- Faculty of Pharmacy University of Ljubljana Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Anamarija Zega
- Faculty of Pharmacy University of Ljubljana Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Lucija Peterlin Mašič
- Faculty of Pharmacy University of Ljubljana Aškerčeva cesta 7 1000 Ljubljana Slovenia
| | - Petra Szili
- Synthetic and Systems Biology Unit Hungarian Academy of Sciences Szeged 6726 Hungary
- Doctoral School of Multidisciplinary Medical Sciences University of Szeged Szeged 6720 Hungary
| | - Gábor Draskovits
- Synthetic and Systems Biology Unit Hungarian Academy of Sciences Szeged 6726 Hungary
| | - Ákos Nyerges
- Synthetic and Systems Biology Unit Hungarian Academy of Sciences Szeged 6726 Hungary
| | - Csaba Pál
- Synthetic and Systems Biology Unit Hungarian Academy of Sciences Szeged 6726 Hungary
| | - Danijel Kikelj
- Faculty of Pharmacy University of Ljubljana Aškerčeva cesta 7 1000 Ljubljana Slovenia
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27
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Synthesis, Docking Studies, and In Vitro Evaluation of Some Novel Thienopyridines and Fused Thienopyridine-Quinolines as Antibacterial Agents and DNA Gyrase Inhibitors. Molecules 2019; 24:molecules24203650. [PMID: 31658631 PMCID: PMC6832920 DOI: 10.3390/molecules24203650] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/03/2019] [Accepted: 10/06/2019] [Indexed: 01/05/2023] Open
Abstract
A series of novel thienopyridines and pyridothienoquinolines (3a,b–14) was synthesized, starting with 2-thioxo-1,2-dihydropyridine-3-carbonitriles 1a and 1b. All compounds were evaluated for their in vitro antimicrobial activity against six bacterial strains. Compounds 3a,b, 4a, 5b, 6a,b, 7a, 9b, 12b, and 14 showed significant growth inhibition activity against both Gram-positive and Gram-negative bacteria compared with the reference drug. The most active compounds (4a, 7a, 9b, and 12b) against Staphylococcus aureus were also tested for their in vitro inhibitory action on methicillin-resistant Staphylococcus aureus (MRSA). The tested compounds showed promising inhibition activity, with the performance of 12b being equal to gentamicin and that of 7a exceeding it. Moreover, the most promising compounds were also screened for their Escherichia coli DNA gyrase inhibitory activity, compared with novobiocin as a reference DNA gyrase inhibitor. The results revealed that compounds (3a, 3b, 4a, 9b, and 12b) had the highest inhibitory capacity, with IC50 values of 2.26–5.87 µM (that of novobiocin is equal to 4.17 µM). Docking studies were performed to identify the mode of binding of the tested compounds to the active site of E. coli DNA gyrase B.
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28
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Masci D, Hind C, Islam MK, Toscani A, Clifford M, Coluccia A, Conforti I, Touitou M, Memdouh S, Wei X, La Regina G, Silvestri R, Sutton JM, Castagnolo D. Switching on the activity of 1,5-diaryl-pyrrole derivatives against drug-resistant ESKAPE bacteria: Structure-activity relationships and mode of action studies. Eur J Med Chem 2019; 178:500-514. [DOI: 10.1016/j.ejmech.2019.05.087] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 05/29/2019] [Accepted: 05/29/2019] [Indexed: 12/13/2022]
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29
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Li L, Okumu AA, Nolan S, English A, Vibhute S, Lu Y, Hervert-Thomas K, Seffernick JT, Azap L, Cole SL, Shinabarger D, Koeth LM, Lindert S, Yalowich JC, Wozniak DJ, Mitton-Fry MJ. 1,3-Dioxane-Linked Bacterial Topoisomerase Inhibitors with Enhanced Antibacterial Activity and Reduced hERG Inhibition. ACS Infect Dis 2019; 5:1115-1128. [PMID: 31041863 DOI: 10.1021/acsinfecdis.8b00375] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The development of new therapies to treat methicillin-resistant Staphylococcus aureus (MRSA) is needed to counteract the significant threat that MRSA presents to human health. Novel inhibitors of DNA gyrase and topoisomerase IV (TopoIV) constitute one highly promising approach, but continued optimization is required to realize the full potential of this class of antibiotics. Herein, we report further studies on a series of dioxane-linked derivatives, demonstrating improved antistaphylococcal activity and reduced hERG inhibition. A subseries of analogues also possesses enhanced inhibition of the secondary target, TopoIV.
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Affiliation(s)
- Linsen Li
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, 500 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Antony A. Okumu
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, 500 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Sheri Nolan
- Microbial Infection and Immunity, The Ohio State University, 460 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Anthony English
- Division of Pharmacology, The Ohio State University, 500 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Sandip Vibhute
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, 500 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Yanran Lu
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, 500 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Katherine Hervert-Thomas
- Department of Chemistry, Ohio Wesleyan University, 61 South Sandusky Street, Delaware, Ohio 43015, United States
| | - Justin T. Seffernick
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Lovette Azap
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, 500 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Serena L. Cole
- Micromyx, 4717 Campus Drive, Kalamazoo, Michigan 49008, United States
| | - D. Shinabarger
- Micromyx, 4717 Campus Drive, Kalamazoo, Michigan 49008, United States
| | - Laura M. Koeth
- Laboratory Specialists, Inc., 26214 Center Ridge Road, Westlake, Ohio 44145, United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Jack C. Yalowich
- Division of Pharmacology, The Ohio State University, 500 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Daniel J. Wozniak
- Microbial Infection and Immunity, The Ohio State University, 460 West 12th Avenue, Columbus, Ohio 43210, United States
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Mark J. Mitton-Fry
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, 500 West 12th Avenue, Columbus, Ohio 43210, United States
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Jones JA, Hevener KE. Crystal structure of the 65-kilodalton amino-terminal fragment of DNA topoisomerase I from the gram-positive model organism Streptococcus mutans. Biochem Biophys Res Commun 2019; 516:333-338. [PMID: 31204053 DOI: 10.1016/j.bbrc.2019.06.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 06/07/2019] [Indexed: 01/06/2023]
Abstract
Herein we report the first structure of topoisomerase I determined from the gram-positive bacterium, S. mutans. Bacterial topoisomerase I is an ATP-independent type 1A topoisomerase that uses the inherent torsional strain within hyper-negatively supercoiled DNA as an energy source for its critical function of DNA relaxation. Interest in the enzyme has gained momentum as it has proven to be essential in various bacterial organisms. In order to aid in further biochemical characterization, the apo 65-kDa amino-terminal fragment of DNA topoisomerase I from the gram-positive model organism Streptococcus mutans was crystalized and a three-dimensional structure was determined to 2.06 Å resolution via x-ray crystallography. The overall structure illustrates the four classic major domains that create the traditional topoisomerase I "lock" formation comprised of a sizable toroidal aperture atop what is considered to be a highly dynamic body. A catalytic tyrosine residue resides at the interface between two domains and is known to form a 5' phosphotyrosine DNA-enzyme intermediate during transient single-stranded cleavage required for enzymatic relaxation of hyper negative DNA supercoils. Surrounding the catalytic tyrosine residue is the remainder of the highly conserved active site. Within 5 Å from the catalytic center, only one dissimilar residue is observed between topoisomerase I from S. mutans and the gram-negative model organism E. coli. Immediately adjacent to the conserved active site, however, S. mutans topoisomerase I displays a somewhat unique nine residue loop extension not present in any bacterial topoisomerase I structures previously determined other than that of an extremophile.
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Affiliation(s)
- Jesse A Jones
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, 38163, United States
| | - Kirk E Hevener
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, 38163, United States.
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Sonawane AD, Kubota Y, Koketsu M. Iron-Promoted Intramolecular Cascade Cyclization for the Synthesis of Selenophene-Fused, Quinoline-Based Heteroacenes. J Org Chem 2019; 84:8602-8614. [DOI: 10.1021/acs.joc.9b01061] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amol D. Sonawane
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Gifu 501-1193, Japan
| | - Yasuhiro Kubota
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Gifu 501-1193, Japan
| | - Mamoru Koketsu
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Gifu 501-1193, Japan
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Bioactivity Profile of the Diterpene Isosteviol and its Derivatives. Molecules 2019; 24:molecules24040678. [PMID: 30769819 PMCID: PMC6412665 DOI: 10.3390/molecules24040678] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 02/03/2019] [Accepted: 02/06/2019] [Indexed: 12/24/2022] Open
Abstract
Steviosides, rebaudiosides and their analogues constitute a major class of naturally occurring biologically active diterpene compounds. The wide spectrum of pharmacological activity of this group of compounds has developed an interest among medicinal chemists to synthesize, purify, and analyze more selective and potent isosteviol derivatives. It has potential biological applications and improves the field of medicinal chemistry by designing novel drugs with the ability to cope against resistance developing diseases. The outstanding advancement in the design and synthesis of isosteviol and its derivative has proved its effectiveness and importance in the field of medicinal chemical research. The present review is an effort to integrate recently developed novel drugs syntheses from isosteviol and potentially active pharmacological importance of the isosteviol derivatives covering the recent advances.
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Huang X, Guo J, Liu Q, Gu Q, Xu J, Zhou H. Identification of an auxiliary druggable pocket in the DNA gyrase ATPase domain using fragment probes. MEDCHEMCOMM 2018; 9:1619-1629. [PMID: 30429968 DOI: 10.1039/c8md00148k] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 07/03/2018] [Indexed: 12/21/2022]
Abstract
Discovery of new drug binding sites on well-established targets is of great interest as it facilitates the design of new mechanistic inhibitors to overcome the acquired drug resistance. Small chemical fragments can easily enter and bind to the cavities on the protein surface. Thus, they can be used to probe new druggable pockets in proteins. DNA gyrase plays indispensable roles in DNA replication, and both its GyrA and GyrB subunits are clinically validated antibacterial targets. New mechanistic GyrB inhibitors are urgently desired since the withdrawal of novobiocin from the market by the FDA due to its reduced efficiency and other reasons. Here, a fragment library was screened against the E. coli GyrB ATPase domain by combining affinity- and bioactivity-based approaches. The following X-ray crystallographic efforts were made to determine the cocrystal structures of GyrB with ten fragment hits, and three different binding modes were disclosed. Fortunately, a hydrophobic pocket which is previously unknown was identified by two fragments. Fragments that bind to this pocket were shown to inhibit the ATPase activity as well as the DNA topological transition activity of DNA gyrase in vitro. A set of fragment analogs were screened to explore the binding capacity of this pocket and identify the better starting fragments for lead development. Phylogenetic analysis revealed that this pocket is conserved in most Gram-negative and also many Gram-positive human pathogenic bacteria, implying a broad-spectrum antibacterial potential and a lower risk of mutation. Thus, the novel druggable pocket and the starting fragments provide a novel basis for designing new GyrB-targeting therapeutics.
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Affiliation(s)
- Xiaojie Huang
- Research Center for Drug Discovery , School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , China .
| | - Junsong Guo
- Research Center for Drug Discovery , School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , China .
| | - Qi Liu
- Research Center for Drug Discovery , School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , China .
| | - Qiong Gu
- Research Center for Drug Discovery , School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , China .
| | - Jun Xu
- Research Center for Drug Discovery , School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , China .
| | - Huihao Zhou
- Research Center for Drug Discovery , School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , China .
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Abstract
New antibacterials that modulate less explored targets are needed to fight the emerging bacterial resistance. DNA gyrase and topoisomerase IV are attractive targets in this search. These are both type II topoisomerases that can cleave both DNA strands, and can thus alter DNA topology during replication or similar processes. Currently, there are no ATP-competitive inhibitors of these two enzymes on the market, as the only aminocoumarin representative, novobiocin, was withdrawn due to safety concerns. The search for novel ATP-competitive inhibitors is a focus of ongoing industrial and academical research. This review summarizes the recent efforts in the design, synthesis and evaluation of GyrB/ParE inhibitors. The various approaches to achieve improved antibacterial activities are described, with particular reference to Gram-negative bacteria.
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36
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Badshah SL, Ullah A. New developments in non-quinolone-based antibiotics for the inhibiton of bacterial gyrase and topoisomerase IV. Eur J Med Chem 2018; 152:393-400. [DOI: 10.1016/j.ejmech.2018.04.059] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 04/23/2018] [Accepted: 04/29/2018] [Indexed: 01/06/2023]
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Jeannot F, Taillier T, Despeyroux P, Renard S, Rey A, Mourez M, Poeverlein C, Khichane I, Perrin MA, Versluys S, Stavenger RA, Huang J, Germe T, Maxwell A, Cao S, Huseby DL, Hughes D, Bacqué E. Imidazopyrazinones (IPYs): Non-Quinolone Bacterial Topoisomerase Inhibitors Showing Partial Cross-Resistance with Quinolones. J Med Chem 2018; 61:3565-3581. [PMID: 29596745 DOI: 10.1021/acs.jmedchem.7b01892] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In our quest for new antibiotics able to address the growing threat of multidrug resistant infections caused by Gram-negative bacteria, we have investigated an unprecedented series of non-quinolone bacterial topoisomerase inhibitors from the Sanofi patrimony, named IPYs for imidazopyrazinones, as part of the Innovative Medicines Initiative (IMI) European Gram Negative Antibacterial Engine (ENABLE) organization. Hybridization of these historical compounds with the quinazolinediones, a known series of topoisomerase inhibitors, led us to a novel series of tricyclic IPYs that demonstrated potential for broad spectrum activity, in vivo efficacy, and a good developability profile, although later profiling revealed a genotoxicity risk. Resistance studies revealed partial cross-resistance with fluoroquinolones (FQs) suggesting that IPYs bind to the same region of bacterial topoisomerases as FQs and interact with at least some of the keys residues involved in FQ binding.
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Affiliation(s)
- Frédéric Jeannot
- Therapeutic Area Infectious Diseases , Sanofi R&D , 1541 Avenue Marcel Mérieux , 69280 Marcy L'Etoile , France
| | - Thomas Taillier
- Therapeutic Area Infectious Diseases , Sanofi R&D , 1541 Avenue Marcel Mérieux , 69280 Marcy L'Etoile , France
| | - Pierre Despeyroux
- Therapeutic Area Infectious Diseases , Sanofi R&D , 1541 Avenue Marcel Mérieux , 69280 Marcy L'Etoile , France
| | - Stéphane Renard
- Therapeutic Area Infectious Diseases , Sanofi R&D , 1541 Avenue Marcel Mérieux , 69280 Marcy L'Etoile , France
| | - Astrid Rey
- Therapeutic Area Infectious Diseases , Sanofi R&D , 1541 Avenue Marcel Mérieux , 69280 Marcy L'Etoile , France
| | - Michaël Mourez
- Therapeutic Area Infectious Diseases , Sanofi R&D , 1541 Avenue Marcel Mérieux , 69280 Marcy L'Etoile , France
| | - Christoph Poeverlein
- R&D, Integrated Drug Discovery , Sanofi-Aventis Deutschland GmbH , Industriepark Hoechst , 65926 Frankfurt am Main , Germany
| | - Imène Khichane
- LGCR, Analytical Sciences , Sanofi R&D , 13 Quai Jules Guesde , 94400 Vitry sur Seine , France
| | - Marc-Antoine Perrin
- LGCR, Analytical Sciences , Sanofi R&D , 13 Quai Jules Guesde , 94400 Vitry sur Seine , France
| | - Stéphanie Versluys
- Evotec France , 195 Route d'Espagne , BP 13669, 31036 Toulouse Cedex 1, France
| | - Robert A Stavenger
- Antibacterial DPU , GlaxoSmithKline , 1250 Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | - Jianzhong Huang
- Antibacterial DPU , GlaxoSmithKline , 1250 Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | - Thomas Germe
- Department of Biological Chemistry , John Innes Centre , Norwich Research Park , Norwich NR4 7UH , U.K
| | - Anthony Maxwell
- Department of Biological Chemistry , John Innes Centre , Norwich Research Park , Norwich NR4 7UH , U.K
| | - Sha Cao
- Department of Medical Biochemistry and Microbiology, Biomedical Center , Uppsala University , Box 582, Uppsala S-751 23 , Sweden
| | - Douglas L Huseby
- Department of Medical Biochemistry and Microbiology, Biomedical Center , Uppsala University , Box 582, Uppsala S-751 23 , Sweden
| | - Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, Biomedical Center , Uppsala University , Box 582, Uppsala S-751 23 , Sweden
| | - Eric Bacqué
- Therapeutic Area Infectious Diseases , Sanofi R&D , 1541 Avenue Marcel Mérieux , 69280 Marcy L'Etoile , France
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38
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Kolaric A, Minovski N. Structure-based design of novel combinatorially generated NBTIs as potential DNA gyrase inhibitors against various Staphylococcus aureus mutant strains. MOLECULAR BIOSYSTEMS 2018; 13:1406-1420. [PMID: 28590495 DOI: 10.1039/c7mb00168a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Although intercalating agents such as quinolones have had proven therapeutic success as antibacterial agents for more than 40 years, new forms of quinolone-based resistance in bacteria are continually emerging. To alleviate this problem, a new class of antibacterials is urgently needed; recently, novel bacterial topoisomerase inhibitors (NBTIs) have been found to be particularly important. Based on 67 experimentally evaluated NBTIs against wild-type (WT) DNA gyrase originating from Staphylococcus aureus, a predictive QSAR model was initially constructed and validated and was later used for in silico prediction of biological activities for an in house designed compound library of 548 novel drug-like NBTI combinatorial analogs. To evaluate the influence of gyrA alterations on NBTI resistance, various mutant homology models were constructed; meanwhile, their resistance profiles were assessed and validated relative to that of WT enzyme by structure-based virtual screening (VS) of known NBTIs. Surprisingly, the M121K mutant model was recognized as the most selective due to an additional established cation-π interaction between K121-NH3+ (not found in the WT) and the aromatic moiety of the NBTI right-hand site (RHS) fragment; this finding was additionally supported by VS of our combinatorially generated NBTIs. Moreover, we identified several attractive, synthetically feasible RHS building blocks that may enable the development of new NBTIs.
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Affiliation(s)
- Anja Kolaric
- Department of Cheminformatics, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.
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Franco-Ulloa S, La Sala G, Miscione GP, De Vivo M. Novel Bacterial Topoisomerase Inhibitors Exploit Asp83 and the Intrinsic Flexibility of the DNA Gyrase Binding Site. Int J Mol Sci 2018; 19:ijms19020453. [PMID: 29401640 PMCID: PMC5855675 DOI: 10.3390/ijms19020453] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 01/29/2018] [Accepted: 01/30/2018] [Indexed: 11/19/2022] Open
Abstract
DNA gyrases are enzymes that control the topology of DNA in bacteria cells. This is a vital function for bacteria. For this reason, DNA gyrases are targeted by widely used antibiotics such as quinolones. Recently, structural and biochemical investigations identified a new class of DNA gyrase inhibitors called NBTIs (i.e., novel bacterial topoisomerase inhibitors). NBTIs are particularly promising because they are active against multi-drug resistant bacteria, an alarming clinical issue. Structural data recently demonstrated that these NBTIs bind tightly to a newly identified pocket at the dimer interface of the DNA–protein complex. In the present study, we used molecular dynamics (MD) simulations and docking calculations to shed new light on the binding of NBTIs to this site. Interestingly, our MD simulations demonstrate the intrinsic flexibility of this binding site, which allows the pocket to adapt its conformation and form optimal interactions with the ligand. In particular, we examined two ligands, AM8085 and AM8191, which induced a repositioning of a key aspartate (Asp83B), whose side chain can rotate within the binding site. The conformational rearrangement of Asp83B allows the formation of a newly identified H-bond interaction with an NH on the bound NBTI, which seems important for the binding of NBTIs having such functionality. We validated these findings through docking calculations using an extended set of cognate oxabicyclooctane-linked NBTIs derivatives (~150, in total), screened against multiple target conformations. The newly identified H-bond interaction significantly improves the docking enrichment. These insights could be helpful for future virtual screening campaigns against DNA gyrase.
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Affiliation(s)
- Sebastian Franco-Ulloa
- COBO Computational Bio-Organic Chemistry Bogotá, Chemistry Department, Universidad de los Andes, Cra 1 No 18A-12, 111711 Bogotá, Colombia.
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy.
| | - Giuseppina La Sala
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy.
| | - Gian Pietro Miscione
- COBO Computational Bio-Organic Chemistry Bogotá, Chemistry Department, Universidad de los Andes, Cra 1 No 18A-12, 111711 Bogotá, Colombia.
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy.
- IAS-5/INM-9 Computational Biomedicine Forschungszentrum Jülich Wilhelm-Johnen-Straße, 52428 Jülich, Germany.
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40
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Delgado JL, Hsieh CM, Chan NL, Hiasa H. Topoisomerases as anticancer targets. Biochem J 2018; 475:373-398. [PMID: 29363591 PMCID: PMC6110615 DOI: 10.1042/bcj20160583] [Citation(s) in RCA: 264] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 12/14/2017] [Accepted: 12/21/2017] [Indexed: 12/15/2022]
Abstract
Many cancer type-specific anticancer agents have been developed and significant advances have been made toward precision medicine in cancer treatment. However, traditional or nonspecific anticancer drugs are still important for the treatment of many cancer patients whose cancers either do not respond to or have developed resistance to cancer-specific anticancer agents. DNA topoisomerases, especially type IIA topoisomerases, are proved therapeutic targets of anticancer and antibacterial drugs. Clinically successful topoisomerase-targeting anticancer drugs act through topoisomerase poisoning, which leads to replication fork arrest and double-strand break formation. Unfortunately, this unique mode of action is associated with the development of secondary cancers and cardiotoxicity. Structures of topoisomerase-drug-DNA ternary complexes have revealed the exact binding sites and mechanisms of topoisomerase poisons. Recent advances in the field have suggested a possibility of designing isoform-specific human topoisomerase II poisons, which may be developed as safer anticancer drugs. It may also be possible to design catalytic inhibitors of topoisomerases by targeting certain inactive conformations of these enzymes. Furthermore, identification of various new bacterial topoisomerase inhibitors and regulatory proteins may inspire the discovery of novel human topoisomerase inhibitors. Thus, topoisomerases remain as important therapeutic targets of anticancer agents.
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Affiliation(s)
- Justine L Delgado
- Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, 115 S Grand Ave., S321 Pharmacy Building, Iowa City, IA 52242, U.S.A
| | - Chao-Ming Hsieh
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei City 100, Taiwan
| | - Nei-Li Chan
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei City 100, Taiwan
| | - Hiroshi Hiasa
- Department of Pharmacology, University of Minnesota Medical School, 6-120 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455, U.S.A.
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41
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Durcik M, Tammela P, Barančoková M, Tomašič T, Ilaš J, Kikelj D, Zidar N. Synthesis and Evaluation of N-Phenylpyrrolamides as DNA Gyrase B Inhibitors. ChemMedChem 2018; 13:186-198. [PMID: 29206345 DOI: 10.1002/cmdc.201700549] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 12/01/2017] [Indexed: 01/05/2023]
Abstract
ATP-competitive inhibitors of DNA gyrase and topoisomerase IV are among the most interesting classes of antibacterial drugs that are unrepresented in the antibacterial pipeline. We developed 32 new N-phenylpyrrolamides and evaluated them against DNA gyrase and topoisomerase IV from E. coli and Staphylococcus aureus. Antibacterial activities were studied against Gram-positive and Gram-negative bacterial strains. The most potent compound displayed an IC50 of 47 nm against E. coli DNA gyrase, and a minimum inhibitory concentration (MIC) of 12.5 μm against the Gram-positive Enterococcus faecalis. Some compounds displayed good antibacterial activities against an efflux-pump-deficient E. coli strain (MIC=6.25 μm) and against wild-type E. coli in the presence of efflux pump inhibitor PAβN (MIC=3.13 μm). Here we describe new findings regarding the structure-activity relationships of N-phenylpyrrolamide DNA gyrase B inhibitors and investigate the factors that are important for the antibacterial activity of this class of compounds.
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Affiliation(s)
- Martina Durcik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, Viikinkaari 5E, Helsinki, 00014, Finland
| | - Michaela Barančoková
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Tihomir Tomašič
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Janez Ilaš
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Danijel Kikelj
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Nace Zidar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
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42
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Abstract
DNA topoisomerases are proven therapeutic targets of antibacterial agents. Quinolones, especially fluoroquinolones, are the most successful topoisomerase-targeting antibacterial drugs. These drugs target type IIA topoisomerases in bacteria. Recent structural and biochemical studies on fluoroquinolones have provided the molecular basis for both their mechanism of action, as well as the molecular basis of bacterial resistance. Due to the development of drug resistance, including fluoroquinolone resistance, among bacterial pathogens, there is an urgent need to discover novel antibacterial agents. Recent advances in topoisomerase inhibitors may lead to the development of novel antibacterial drugs that are effective against fluoroquinolone-resistant pathogens. They include type IIA topoisomerase inhibitors that either interact with the GyrB/ParE subunit or form nick-containing ternary complexes. In addition, several topoisomerase I inhibitors have recently been identified. Thus, DNA topoisomerases remain important targets of antibacterial agents.
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43
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Tomašič T, Barančoková M, Zidar N, Ilaš J, Tammela P, Kikelj D. Design, synthesis, and biological evaluation of 1-ethyl-3-(thiazol-2-yl)urea derivatives as Escherichia coli
DNA gyrase inhibitors. Arch Pharm (Weinheim) 2017; 351. [DOI: 10.1002/ardp.201700333] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 11/22/2017] [Accepted: 11/24/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Tihomir Tomašič
- Faculty of Pharmacy; University of Ljubljana; Ljubljana Slovenia
| | | | - Nace Zidar
- Faculty of Pharmacy; University of Ljubljana; Ljubljana Slovenia
| | - Janez Ilaš
- Faculty of Pharmacy; University of Ljubljana; Ljubljana Slovenia
| | - Päivi Tammela
- Division of Pharmaceutical Biosciences; Faculty of Pharmacy; University of Helsinki; Helsinki Finland
| | - Danijel Kikelj
- Faculty of Pharmacy; University of Ljubljana; Ljubljana Slovenia
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44
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Cheng B, Müller R, Trauner D. Total Syntheses of Cystobactamids and Structural Confirmation of Cystobactamid 919‐2. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201705387] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Bichu Cheng
- Department of Chemistry University of Munich Butenandtstrasse 5–13, Haus F 81377 Munich Germany
- Department of Chemistry New York University 100 Washington Square East, Room 712 New York NY 10003 USA
| | - Rolf Müller
- Department of Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland Helmholtz Center for Infection Research Saarland University 66123 Saarbrücken Germany
| | - Dirk Trauner
- Department of Chemistry University of Munich Butenandtstrasse 5–13, Haus F 81377 Munich Germany
- Department of Chemistry New York University 100 Washington Square East, Room 712 New York NY 10003 USA
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45
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Cheng B, Müller R, Trauner D. Total Syntheses of Cystobactamids and Structural Confirmation of Cystobactamid 919-2. Angew Chem Int Ed Engl 2017; 56:12755-12759. [PMID: 28731542 DOI: 10.1002/anie.201705387] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Indexed: 12/21/2022]
Abstract
The cystobactamids are a family of antibacterial natural products with unprecedented chemical scaffolds that are active against both Gram-positive and Gram-negative pathogens. Herein, we describe the first total synthesis of cystobactamid 919-2 from three fragments. Our convergent synthesis enabled both the confirmation of the correct structure and the determination of the absolute configuration of cystobactamid 919-2.
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Affiliation(s)
- Bichu Cheng
- Department of Chemistry, University of Munich, Butenandtstrasse 5-13, Haus F, 81377, Munich, Germany.,Department of Chemistry, New York University, 100 Washington Square East, Room 712, New York, NY, 10003, USA
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Center for Infection Research, Saarland University, 66123, Saarbrücken, Germany
| | - Dirk Trauner
- Department of Chemistry, University of Munich, Butenandtstrasse 5-13, Haus F, 81377, Munich, Germany.,Department of Chemistry, New York University, 100 Washington Square East, Room 712, New York, NY, 10003, USA
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46
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Walker SS, Labroli M, Painter RE, Wiltsie J, Sherborne B, Murgolo N, Sher X, Mann P, Zuck P, Garlisi CG, Su J, Kargman S, Xiao L, Scapin G, Salowe S, Devito K, Sheth P, Buist N, Tan CM, Black TA, Roemer T. Antibacterial small molecules targeting the conserved TOPRIM domain of DNA gyrase. PLoS One 2017; 12:e0180965. [PMID: 28700746 PMCID: PMC5507300 DOI: 10.1371/journal.pone.0180965] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 06/23/2017] [Indexed: 12/21/2022] Open
Abstract
To combat the threat of antibiotic-resistant Gram-negative bacteria, novel agents that circumvent established resistance mechanisms are urgently needed. Our approach was to focus first on identifying bioactive small molecules followed by chemical lead prioritization and target identification. Within this annotated library of bioactives, we identified a small molecule with activity against efflux-deficient Escherichia coli and other sensitized Gram-negatives. Further studies suggested that this compound inhibited DNA replication and selection for resistance identified mutations in a subunit of E. coli DNA gyrase, a type II topoisomerase. Our initial compound demonstrated weak inhibition of DNA gyrase activity while optimized compounds demonstrated significantly improved inhibition of E. coli and Pseudomonas aeruginosa DNA gyrase and caused cleaved complex stabilization, a hallmark of certain bactericidal DNA gyrase inhibitors. Amino acid substitutions conferring resistance to this new class of DNA gyrase inhibitors reside exclusively in the TOPRIM domain of GyrB and are not associated with resistance to the fluoroquinolones, suggesting a novel binding site for a gyrase inhibitor.
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Affiliation(s)
- Scott S. Walker
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
- * E-mail:
| | - Marc Labroli
- Merck & Co., Inc., West Point, Pennsylvania, United States of America
| | | | - Judyann Wiltsie
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Brad Sherborne
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Nicholas Murgolo
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Xinwei Sher
- Merck & Co., Inc., Boston, Massachusetts, United States of America
| | - Paul Mann
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Paul Zuck
- Merck & Co., Inc., West Point, Pennsylvania, United States of America
| | | | - Jing Su
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Stacia Kargman
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Li Xiao
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Giovanna Scapin
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Scott Salowe
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Kristine Devito
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Payal Sheth
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Nichole Buist
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | | | - Todd A. Black
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Terry Roemer
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
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47
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Panchaud P, Bruyère T, Blumstein AC, Bur D, Chambovey A, Ertel EA, Gude M, Hubschwerlen C, Jacob L, Kimmerlin T, Pfeifer T, Prade L, Seiler P, Ritz D, Rueedi G. Discovery and Optimization of Isoquinoline Ethyl Ureas as Antibacterial Agents. J Med Chem 2017; 60:3755-3775. [DOI: 10.1021/acs.jmedchem.6b01834] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Philippe Panchaud
- Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Thierry Bruyère
- Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | | | - Daniel Bur
- Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Alain Chambovey
- Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Eric A. Ertel
- Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Markus Gude
- Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | | | - Loïc Jacob
- Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Thierry Kimmerlin
- Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Thomas Pfeifer
- Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Lars Prade
- Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Peter Seiler
- Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Daniel Ritz
- Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Georg Rueedi
- Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
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48
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Surivet JP, Zumbrunn C, Bruyère T, Bur D, Kohl C, Locher HH, Seiler P, Ertel EA, Hess P, Enderlin-Paput M, Enderlin-Paput S, Gauvin JC, Mirre A, Hubschwerlen C, Ritz D, Rueedi G. Synthesis and Characterization of Tetrahydropyran-Based Bacterial Topoisomerase Inhibitors with Antibacterial Activity against Gram-Negative Bacteria. J Med Chem 2017; 60:3776-3794. [PMID: 28406300 DOI: 10.1021/acs.jmedchem.6b01831] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
There is an urgent unmet medical need for novel antibiotics that are effective against a broad range of bacterial species, especially multidrug resistant ones. Tetrahydropyran-based inhibitors of bacterial type II topoisomerases (DNA gyrase and topoisomerase IV) display potent activity against Gram-positive pathogens and no target-mediated cross-resistance with fluoroquinolones. We report our research efforts aimed at expanding the antibacterial spectrum of this class of molecules toward difficult-to-treat Gram-negative pathogens. Physicochemical properties (polarity and basicity) were considered to guide the design process. Dibasic tetrahydropyran-based compounds such as 6 and 21 are potent inhibitors of both DNA gyrase and topoisomerase IV, displaying antibacterial activities against Gram-positive and Gram-negative pathogens (Staphylococcus aureus, Enterobacteriaceae, Pseudomonas aeruginosa, and Acinetobacter baumannii). Compounds 6 and 21 are efficacious in clinically relevant murine infection models.
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Affiliation(s)
- Jean-Philippe Surivet
- Actelion Pharmaceuticals Limited , Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Cornelia Zumbrunn
- Actelion Pharmaceuticals Limited , Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Thierry Bruyère
- Actelion Pharmaceuticals Limited , Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Daniel Bur
- Actelion Pharmaceuticals Limited , Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Christopher Kohl
- Actelion Pharmaceuticals Limited , Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Hans H Locher
- Actelion Pharmaceuticals Limited , Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Peter Seiler
- Actelion Pharmaceuticals Limited , Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Eric A Ertel
- Actelion Pharmaceuticals Limited , Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Patrick Hess
- Actelion Pharmaceuticals Limited , Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Michel Enderlin-Paput
- Actelion Pharmaceuticals Limited , Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | | | | | - Azely Mirre
- Actelion Pharmaceuticals Limited , Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | | | - Daniel Ritz
- Actelion Pharmaceuticals Limited , Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
| | - Georg Rueedi
- Actelion Pharmaceuticals Limited , Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
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49
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Discovery of substituted oxadiazoles as a novel scaffold for DNA gyrase inhibitors. Eur J Med Chem 2017; 130:171-184. [DOI: 10.1016/j.ejmech.2017.02.046] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 02/13/2017] [Accepted: 02/17/2017] [Indexed: 01/06/2023]
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50
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Stereo-Electronic, Molecular Connectivity, and Geometric Configuration Approaches towards Designing Antibacterial Agents from 1, 3, 4-Thiadiazole as the Starting Molecular Template. ChemistrySelect 2017. [DOI: 10.1002/slct.201601137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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