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Hao Y, Li B, Huang D, Wu S, Wang T, Fu L, Liu X. Developing a Semi-Supervised Approach Using a PU-Learning-Based Data Augmentation Strategy for Multitarget Drug Discovery. Int J Mol Sci 2024; 25:8239. [PMID: 39125808 PMCID: PMC11312053 DOI: 10.3390/ijms25158239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 07/26/2024] [Accepted: 07/26/2024] [Indexed: 08/12/2024] Open
Abstract
Multifactorial diseases demand therapeutics that can modulate multiple targets for enhanced safety and efficacy, yet the clinical approval of multitarget drugs remains rare. The integration of machine learning (ML) and deep learning (DL) in drug discovery has revolutionized virtual screening. This study investigates the synergy between ML/DL methodologies, molecular representations, and data augmentation strategies. Notably, we found that SVM can match or even surpass the performance of state-of-the-art DL methods. However, conventional data augmentation often involves a trade-off between the true positive rate and false positive rate. To address this, we introduce Negative-Augmented PU-bagging (NAPU-bagging) SVM, a novel semi-supervised learning framework. By leveraging ensemble SVM classifiers trained on resampled bags containing positive, negative, and unlabeled data, our approach is capable of managing false positive rates while maintaining high recall rates. We applied this method to the identification of multitarget-directed ligands (MTDLs), where high recall rates are critical for compiling a list of interaction candidate compounds. Case studies demonstrate that NAPU-bagging SVM can identify structurally novel MTDL hits for ALK-EGFR with favorable docking scores and binding modes, as well as pan-agonists for dopamine receptors. The NAPU-bagging SVM methodology should serve as a promising avenue to virtual screening, especially for the discovery of MTDLs.
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Affiliation(s)
- Yang Hao
- Wisdom Lake Academy of Pharmacy, Xi’an Jiaotong-Liverpool University, Suzhou 215123, China; (Y.H.); (B.L.); (S.W.); (T.W.); (L.F.)
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZX, UK
| | - Bo Li
- Wisdom Lake Academy of Pharmacy, Xi’an Jiaotong-Liverpool University, Suzhou 215123, China; (Y.H.); (B.L.); (S.W.); (T.W.); (L.F.)
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZX, UK
| | - Daiyun Huang
- Wisdom Lake Academy of Pharmacy, Xi’an Jiaotong-Liverpool University, Suzhou 215123, China; (Y.H.); (B.L.); (S.W.); (T.W.); (L.F.)
- School of Life Sciences, Fudan University, Shanghai 200092, China
| | - Sijin Wu
- Wisdom Lake Academy of Pharmacy, Xi’an Jiaotong-Liverpool University, Suzhou 215123, China; (Y.H.); (B.L.); (S.W.); (T.W.); (L.F.)
| | - Tianjun Wang
- Wisdom Lake Academy of Pharmacy, Xi’an Jiaotong-Liverpool University, Suzhou 215123, China; (Y.H.); (B.L.); (S.W.); (T.W.); (L.F.)
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZX, UK
| | - Lei Fu
- Wisdom Lake Academy of Pharmacy, Xi’an Jiaotong-Liverpool University, Suzhou 215123, China; (Y.H.); (B.L.); (S.W.); (T.W.); (L.F.)
| | - Xin Liu
- Wisdom Lake Academy of Pharmacy, Xi’an Jiaotong-Liverpool University, Suzhou 215123, China; (Y.H.); (B.L.); (S.W.); (T.W.); (L.F.)
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Abbas A, Barkhouse A, Hackenberger D, Wright GD. Antibiotic resistance: A key microbial survival mechanism that threatens public health. Cell Host Microbe 2024; 32:837-851. [PMID: 38870900 DOI: 10.1016/j.chom.2024.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/13/2024] [Accepted: 05/17/2024] [Indexed: 06/15/2024]
Abstract
Antibiotic resistance (AMR) is a global public health threat, challenging the effectiveness of antibiotics in combating bacterial infections. AMR also represents one of the most crucial survival traits evolved by bacteria. Antibiotics emerged hundreds of millions of years ago as advantageous secondary metabolites produced by microbes. Consequently, AMR is equally ancient and hardwired into the genetic fabric of bacteria. Human use of antibiotics for disease treatment has created selection pressure that spurs the evolution of new resistance mechanisms and the mobilization of existing ones through bacterial populations in the environment, animals, and humans. This integrated web of resistance elements is genetically complex and mechanistically diverse. Addressing this mode of bacterial survival requires innovation and investment to ensure continued use of antibiotics in the future. Strategies ranging from developing new therapies to applying artificial intelligence in monitoring AMR and discovering new drugs are being applied to manage the growing AMR crisis.
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Affiliation(s)
- Amna Abbas
- David Braley Center for Antibiotic Discovery, Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Alexandra Barkhouse
- David Braley Center for Antibiotic Discovery, Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Dirk Hackenberger
- David Braley Center for Antibiotic Discovery, Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Gerard D Wright
- David Braley Center for Antibiotic Discovery, Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.
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Bolz SN, Schroeder M. Promiscuity in drug discovery on the verge of the structural revolution: recent advances and future chances. Expert Opin Drug Discov 2023; 18:973-985. [PMID: 37489516 DOI: 10.1080/17460441.2023.2239700] [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: 06/09/2023] [Accepted: 07/19/2023] [Indexed: 07/26/2023]
Abstract
INTRODUCTION Promiscuity denotes the ability of ligands and targets to specifically interact with multiple binding partners. Despite negative aspects like side effects, promiscuity is receiving increasing attention in drug discovery as it can enhance drug efficacy and provides a molecular basis for drug repositioning. The three-dimensional structure of ligand-target complexes delivers exclusive insights into the molecular mechanisms of promiscuity and structure-based methods enable the identification of promiscuous interactions. With the recent breakthrough in protein structure prediction, novel possibilities open up to reveal unknown connections in ligand-target interaction networks. AREAS COVERED This review highlights the significance of structure in the identification and characterization of promiscuity and evaluates the potential of protein structure prediction to advance our knowledge of drug-target interaction networks. It discusses the definition and relevance of promiscuity in drug discovery and explores different approaches to detecting promiscuous ligands and targets. EXPERT OPINION Examination of structural data is essential for understanding and quantifying promiscuity. The recent advancements in structure prediction have resulted in an abundance of targets that are well-suited for structure-based methods like docking. In silico approaches may eventually completely transform our understanding of drug-target networks by complementing the millions of predicted protein structures with billions of predicted drug-target interactions.
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Affiliation(s)
- Sarah Naomi Bolz
- Biotechnology Center (BIOTEC), CMCB, Technische Universität Dresden, Dresden, Germany
| | - Michael Schroeder
- Biotechnology Center (BIOTEC), CMCB, Technische Universität Dresden, Dresden, Germany
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Dobričić V, Savić J, Tomašič T, Durcik M, Zidar N, Mašič LP, Ilaš J, Kikelj D, Čudina O. High-performance liquid chromatography evaluation of lipophilicity and QSRR modeling of a series of dual DNA gyrase and topoisomerase IV inhibitors. ACTA CHROMATOGR 2022. [DOI: 10.1556/1326.2022.01096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
AbstractBacterial DNA gyrase and topoisomerase IV control the topological state of DNA during replication and represent important antibacterial drug targets. To be successful as drug candidates, newly synthesized compounds must possess optimal lipophilicity, which enables efficient delivery to the site of action. In this study, retention behavior of twenty-three previously synthesized dual DNA gyrase and topoisomerase IV inhibitors was tested in RP-HPLC system, consisting of C8 column and acetonitrile/phosphate buffer (pH 5.5 and pH 7.4) mobile phase. logD was calculated at both pH values and the best correlation with logD was obtained for retention parameter φ0, indicating that this RP-HPLC system could be used as an alternative to the shake-flask determination of lipophilicity. Subsequent QSRR analysis revealed that intrinsic lipophilicity (logP) and molecular weight (bcutm13) have a positive, while solubility (bcutp3) has a negative influence on this retention parameter.
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Affiliation(s)
- Vladimir Dobričić
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11000 Belgrade, Serbia
| | - Jelena Savić
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11000 Belgrade, Serbia
| | - Tihomir Tomašič
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Martina Durcik
- 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
| | - Lucija Peterlin Mašič
- 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
| | - Olivera Čudina
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11000 Belgrade, Serbia
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Perveen S, Sharma R. Screening approaches and therapeutic targets: The two driving wheels of tuberculosis drug discovery. Biochem Pharmacol 2022; 197:114906. [PMID: 34990594 DOI: 10.1016/j.bcp.2021.114906] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/28/2021] [Accepted: 12/28/2021] [Indexed: 12/21/2022]
Abstract
Tuberculosis (TB) is an infectious disease, infecting a quarter of world's population. Drug resistant TB further exacerbates the grim scenario of the drying TB drug discovery pipeline. The limited arsenal to fight TB presses the need for thorough efforts for identifying promising hits to combat the disease. The review highlights the efforts in the field of tuberculosis drug discovery, with an emphasis on massive drug screening campaigns for identifying novel hits against Mtb in both industry and academia. As an intracellular pathogen, mycobacteria reside in a complicated intracellular environment with multiple factors at play. Here, we outline various strategies employed in an effort to mimic the intracellular milieu for bringing the screening models closer to the actual settings. The review also focuses on the novel targets and pathways that could aid in target-based drug discovery in TB. The recent high throughput screening efforts resulting in the identification of potent hits against Mtb has been summarized in this article. There is a pressing need for effective screening strategies and approaches employing innovative tools and recent technologies; including nanotechnology, gene-editing tools such as CRISPR-cas system, host-directed bacterial killing and high content screening to augment the TB drug discovery pipeline with safer and shorter drug regimens.
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Affiliation(s)
- Summaya Perveen
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rashmi Sharma
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Polypharmacology: The science of multi-targeting molecules. Pharmacol Res 2022; 176:106055. [PMID: 34990865 DOI: 10.1016/j.phrs.2021.106055] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/23/2021] [Accepted: 12/31/2021] [Indexed: 12/28/2022]
Abstract
Polypharmacology is a concept where a molecule can interact with two or more targets simultaneously. It offers many advantages as compared to the conventional single-targeting molecules. A multi-targeting drug is much more efficacious due to its cumulative efficacy at all of its individual targets making it much more effective in complex and multifactorial diseases like cancer, where multiple proteins and pathways are involved in the onset and development of the disease. For a molecule to be polypharmacologic in nature, it needs to possess promiscuity which is the ability to interact with multiple targets; and at the same time avoid binding to antitargets which would otherwise result in off-target adverse effects. There are certain structural features and physicochemical properties which when present would help researchers to predict if the designed molecule would possess promiscuity or not. Promiscuity can also be identified via advanced state-of-the-art computational methods. In this review, we also elaborate on the methods by which one can intentionally incorporate promiscuity in their molecules and make them polypharmacologic. The polypharmacology paradigm of "one drug-multiple targets" has numerous applications especially in drug repurposing where an already established drug is redeveloped for a new indication. Though designing a polypharmacological drug is much more difficult than designing a single-targeting drug, with the current technologies and information regarding different diseases and chemical functional groups, it is plausible for researchers to intentionally design a polypharmacological drug and unlock its advantages.
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Estrada FGA, Miccoli S, Aniceto N, García-Sosa AT, Guedes RC. Exploring EZH2-Proteasome Dual-Targeting Drug Discovery through a Computational Strategy to Fight Multiple Myeloma. Molecules 2021; 26:5574. [PMID: 34577052 PMCID: PMC8468724 DOI: 10.3390/molecules26185574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 11/29/2022] Open
Abstract
Multiple myeloma is an incurable plasma cell neoplastic disease representing about 10-15% of all haematological malignancies diagnosed in developed countries. Proteasome is a key player in multiple myeloma and proteasome inhibitors are the current first-line of treatment. However, these are associated with limited clinical efficacy due to acquired resistance. One of the solutions to overcome this problem is a polypharmacology approach, namely combination therapy and multitargeting drugs. Several polypharmacology avenues are currently being explored. The simultaneous inhibition of EZH2 and Proteasome 20S remains to be investigated, despite the encouraging evidence of therapeutic synergy between the two. Therefore, we sought to bridge this gap by proposing a holistic in silico strategy to find new dual-target inhibitors. First, we assessed the characteristics of both pockets and compared the chemical space of EZH2 and Proteasome 20S inhibitors, to establish the feasibility of dual targeting. This was followed by molecular docking calculations performed on EZH2 and Proteasome 20S inhibitors from ChEMBL 25, from which we derived a predictive model to propose new EZH2 inhibitors among Proteasome 20S compounds, and vice versa, which yielded two dual-inhibitor hits. Complementarily, we built a machine learning QSAR model for each target but realised their application to our data is very limited as each dataset occupies a different region of chemical space. We finally proceeded with molecular dynamics simulations of the two docking hits against the two targets. Overall, we concluded that one of the hit compounds is particularly promising as a dual-inhibitor candidate exhibiting extensive hydrogen bonding with both targets. Furthermore, this work serves as a framework for how to rationally approach a dual-targeting drug discovery project, from the selection of the targets to the prediction of new hit compounds.
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Affiliation(s)
- Filipe G. A. Estrada
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal; (F.G.A.E.); (S.M.)
- Department of Pharmaceutical Sciences and Medicines, Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal
- Institute of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - Silvia Miccoli
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal; (F.G.A.E.); (S.M.)
- Department of Drug Science and Technology, University of Turin, Via Verdi 8, 10124 Torino, Italy
| | - Natália Aniceto
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal; (F.G.A.E.); (S.M.)
- Department of Pharmaceutical Sciences and Medicines, Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | | | - Rita C. Guedes
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal; (F.G.A.E.); (S.M.)
- Department of Pharmaceutical Sciences and Medicines, Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal
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Surur AS, Sun D. Macrocycle-Antibiotic Hybrids: A Path to Clinical Candidates. Front Chem 2021; 9:659845. [PMID: 33996753 PMCID: PMC8120311 DOI: 10.3389/fchem.2021.659845] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/15/2021] [Indexed: 12/21/2022] Open
Abstract
The tale of abate in antibiotics continued defense mechanisms that chaperone the rise of drug-defying superbugs—on the other hand, the astray in antibacterial drug discovery and development. Our salvation lies in circumventing the genesis of resistance. Considering the competitive advantages of antibacterial chemotherapeutic agents equipped with multiple warheads against resistance, the development of hybrids has rejuvenated. The adoption of antibiotic hybrid paradigm to macrocycles has advanced novel chemical entities to clinical trials. The multi-targeted TD-1792, for instance, retained potent antibacterial activities against multiple strains that are resistant to its constituent, vancomycin. Moreover, the antibiotic conjugation of rifamycins has provided hybrid clinical candidates with desirable efficacy and safety profiles. In 2020, the U.S. FDA has granted an orphan drug designation to TNP-2092, a conjugate of rifamycin and fluoroquinolone, for the treatment of prosthetic joint infections. DSTA4637S is a pioneer antibacterial agent under clinical development and represents a novel class of bacterial therapy, that is, antibody–antibiotic conjugates. DSTA4637S is effective against the notorious persistent S. aureus bacteremia, a revelation of the abracadabra potential of antibiotic hybrid approaches.
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Affiliation(s)
- Abdrrahman Shemsu Surur
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawai'i at Hilo, Hilo, HI, United States
| | - Dianqing Sun
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawai'i at Hilo, Hilo, HI, United States
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Kowalczyk A, Paneth A, Trojanowski D, Paneth P, Zakrzewska-Czerwińska J, Stączek P. Thiosemicarbazide Derivatives Decrease the ATPase Activity of Staphylococcus aureus Topoisomerase IV, Inhibit Mycobacterial Growth, and Affect Replication in Mycobacterium smegmatis. Int J Mol Sci 2021; 22:ijms22083881. [PMID: 33918623 PMCID: PMC8069432 DOI: 10.3390/ijms22083881] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/01/2021] [Accepted: 04/06/2021] [Indexed: 11/16/2022] Open
Abstract
Compounds targeting bacterial topoisomerases are of interest for the development of antibacterial agents. Our previous studies culminated in the synthesis and characterization of small-molecular weight thiosemicarbazides as the initial prototypes of a novel class of gyrase and topoisomerase IV inhibitors. To expand these findings with further details on the mode of action of the most potent compounds, enzymatic studies combined with a molecular docking approach were carried out, the results of which are presented herein. The biochemical assay for 1-(indol-2-oyl)-4-(4-nitrophenyl) thiosemicarbazide (4) and 4-benzoyl-1-(indol-2-oyl) thiosemicarbazide (7), showing strong inhibitory activity against Staphylococcus aureus topoisomerase IV, confirmed that these compounds reduce the ability of the ParE subunit to hydrolyze ATP rather than act by stabilizing the cleavage complex. Compound 7 showed better antibacterial activity than compound 4 against clinical strains of S. aureus and representatives of the Mycobacterium genus. In vivo studies using time-lapse microfluidic microscopy, which allowed for the monitoring of fluorescently labelled replisomes, revealed that compound 7 caused an extension of the replication process duration in Mycobacterium smegmatis, as well as the growth arrest of bacterial cells. Despite some similarities to the mechanism of action of novobiocin, these compounds show additional, unique properties, and can thus be considered a novel group of inhibitors of the ATPase activity of bacterial type IIA topoisomerases.
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Affiliation(s)
- Aleksandra Kowalczyk
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland;
| | - Agata Paneth
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Lublin, Chodźki 4a, 20-093 Lublin, Poland
- Correspondence: (A.P.); (P.S.)
| | - Damian Trojanowski
- Department of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland; (D.T.); (J.Z.-C.)
| | - Piotr Paneth
- Institute of Applied Radiation Chemistry, Łódź University of Technology, Żeromskiego 116, 90-924 Łódź, Poland;
- International Centre for Research on Innovative Biobased Materials (ICRI-BioM)—International Research Agenda, Łódź University of Technology, Żeromskiego 116, 90-924 Łódź, Poland
| | - Jolanta Zakrzewska-Czerwińska
- Department of Molecular Microbiology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland; (D.T.); (J.Z.-C.)
| | - Paweł Stączek
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland;
- Correspondence: (A.P.); (P.S.)
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Hrast M, Frlan R, Knez D, Zdovc I, Barreteau H, Gobec S. Mur ligases inhibitors with azastilbene scaffold: Expanding the structure-activity relationship. Bioorg Med Chem Lett 2021; 40:127966. [PMID: 33744441 DOI: 10.1016/j.bmcl.2021.127966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/06/2021] [Accepted: 03/10/2021] [Indexed: 11/28/2022]
Abstract
Antibiotic resistance represents one of the biggest public health challenges in the last few years. Mur ligases (MurC-MurF) are involved in the synthesis of UDP-N-acetylmuramyl-pentapeptide, the main building block of bacterial peptidoglycan polymer. They are essential for the survival of bacteria and therefore important antibacterial targets. We report herein the synthesis and structure-activity relationships of Mur ligases inhibitors with an azastilbene scaffold. Several compounds showed promising inhibitory potencies against multiple ligases and one compound also possessed moderate antibacterial activity. These results represent a solid ground for further development and optimization of structurally novel antimicrobial agents to combat the rising bacterial resistance.
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Affiliation(s)
- Martina Hrast
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia.
| | - Rok Frlan
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Damijan Knez
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Irena Zdovc
- Veterinary Faculty, University of Ljubljana, Gerbičeva ulica 60, SI-1000 Ljubljana, Slovenia
| | - Hélène Barreteau
- Bacterial Cell Envelopes and Antibiotics Group, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia.
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Kim S, Jo S, Kim MS, Shin DH. A triple-targeting inhibitory activity of Rose Bengal on polysaccharide biosynthesis of Burkholderia pseudomallei. Arch Pharm (Weinheim) 2021; 354:e2000360. [PMID: 33555065 DOI: 10.1002/ardp.202000360] [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: 09/22/2020] [Revised: 12/31/2020] [Accepted: 01/15/2021] [Indexed: 11/08/2022]
Abstract
Sugar nucleotidyltransferases (SNTs) participate in various biosynthesis pathways constructing polysaccharides in Gram-negative bacteria. In this study, a triple-targeting inhibitory activity of Rose Bengal against SNTs such as d-glycero-α-d-manno-heptose-1-phosphate guanylyltransferase (HddC), d-glycero-β-d-manno-heptose-1-phosphate adenylyltransferase (HldC), and 3-deoxy-d-manno-oct-2-ulosonic acid cytidylyltransferase (KdsB) from Burkholderia pseudomallei is provided. Rose Bengal effectively suppresses the nucleotidyltransferase activity of the three SNTs, and its IC50 values are 10.42, 0.76, and 5.31 µM, respectively. Interestingly, Rose Bengal inhibits the three enzymes regardless of their primary, secondary, tertiary, and quaternary structural differences. The experimental results indicate that Rose Bengal possesses the plasticity to shape its conformation suitable to interact with the three SNTs. As HddC functions in the formation of capsular polysaccharides and HldC and KdsB produce building blocks to constitute the inner core of lipopolysaccharide, Rose Bengal is a potential candidate to design antibiotics in a new category. In particular, it can be developed as a specific antimelioidosis agent. As the mortality rate of the infected people caused by B. pseudomallei is quite high, there is an urgent need for specific antimelioidosis agents. Therefore, a further study is being carried out with derivatives of Rose Bengal.
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Affiliation(s)
- Suwon Kim
- Department of Pharmacy, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Seri Jo
- Department of Pharmacy, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Mi-Sun Kim
- Department of Pharmacy, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Dong H Shin
- Department of Pharmacy, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, Republic of Korea
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Profiling of gene expression in methicillin-resistant Staphylococcus aureus in response to cyclo-(L-Val-L-Pro) and chloramphenicol isolated from Streptomyces sp., SUK 25 reveals gene downregulation in multiple biological targets. Arch Microbiol 2020; 202:2083-2092. [PMID: 32494868 DOI: 10.1007/s00203-020-01896-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 04/08/2020] [Accepted: 05/11/2020] [Indexed: 01/21/2023]
Abstract
Chloramphenicol (CAP) and cyclo-(L-Val-L-Pro) were previously isolated from Streptomyces sp., SUK 25 which exhibited a high potency against methicillin-resistant Staphylococcus aureus (MRSA). This study aimed to profile gene expression of MRSA treated with CAP and cyclo-(L-Val-L-Pro) compounds using DNA microarray. Treatment of MRSA with CAP resulted in upregulation of genes involved in protein synthesis, suggesting the coping mechanism of MRSA due to the inhibition of protein synthesis effect from CAP. Most upregulated genes in cyclo-(L-Val-L-Pro) were putative genes with unknown functions. Interestingly, genes encoding ribosomal proteins, cell membrane synthesis, DNA metabolism, citric acid cycle and virulence were downregulated in MRSA treated with cyclo-(L-Val-L-Pro) compound, suggesting the efficacy of this compound in targeting multiple biological pathways. Contrary to CAP, with only a single target, cyclo-(L-Val-L-Pro) isolated from this study had multiple antimicrobial targets that can delay antibiotic resistance and hence is a potential antimicrobial agent of MRSA.
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Multitargeting Compounds: A Promising Strategy to Overcome Multi-Drug Resistant Tuberculosis. Molecules 2020; 25:molecules25051239. [PMID: 32182964 PMCID: PMC7179463 DOI: 10.3390/molecules25051239] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 02/28/2020] [Accepted: 03/08/2020] [Indexed: 12/18/2022] Open
Abstract
Tuberculosis is still an urgent global health problem, mainly due to the spread of multi-drug resistant M. tuberculosis strains, which lead to the need of new more efficient drugs. A strategy to overcome the problem of the resistance insurgence could be the polypharmacology approach, to develop single molecules that act on different targets. Polypharmacology could have features that make it an approach more effective than the classical polypharmacy, in which different drugs with high affinity for one target are taken together. Firstly, for a compound that has multiple targets, the probability of development of resistance should be considerably reduced. Moreover, such compounds should have higher efficacy, and could show synergic effects. Lastly, the use of a single molecule should be conceivably associated with a lower risk of side effects, and problems of drug–drug interaction. Indeed, the multitargeting approach for the development of novel antitubercular drugs have gained great interest in recent years. This review article aims to provide an overview of the most recent and promising multitargeting antitubercular drug candidates.
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14
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Hybrid molecules of scutellarein and tertramethylpyrazine's active metabolites for ischemic stroke. Bioorg Med Chem Lett 2019; 29:126608. [PMID: 31444086 DOI: 10.1016/j.bmcl.2019.08.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 07/24/2019] [Accepted: 08/06/2019] [Indexed: 12/15/2022]
Abstract
A series of hybrid molecules of scutellarein and tertramethylpyrazine's active metabolites have been synthesized. Compared to the original compound, these prepared compounds exhibited higher water solubility, more appropriate logP and better stability. Importantly, compounds 11b, 11d and 11e showed improved neuroprotective activity against the H2O2-induced cell death in PC12 cells, and better antithrombosis activity. The optimized compound 11b was further evaluated by cerebral ischemia/ reperfusion in the middle cerebral artery occlusion (MCAO) model, the results showed that the compound could significantly reduce the infarct area and decrease the neuronal cell damage in CA1 pyramidal neurons. Overall, we demonstrated that the twin drug strategy could be applied in the development of agents for the treatment of ischemic stroke.
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15
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Magarò G, Prati F, Garofalo B, Corso G, Furlotti G, Apicella C, Mangano G, D'Atanasio N, Robinson D, Di Giorgio FP, Ombrato R. Virtual Screening Approach and Investigation of Structure-Activity Relationships To Discover Novel Bacterial Topoisomerase Inhibitors Targeting Gram-Positive and Gram-Negative Pathogens. J Med Chem 2019; 62:7445-7472. [PMID: 31276392 DOI: 10.1021/acs.jmedchem.9b00394] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacterial resistance is increasing rapidly, requiring urgent identification of new antibacterial drugs that are effective against multidrug-resistant pathogens. Novel bacterial topoisomerase inhibitors (NBTIs) provide a new strategy for investigating the well-validated DNA gyrase and topoisomerase IV targets while preventing cross-resistance issues. On this basis, starting from a virtual screening campaign and subsequent structure-based hit optimization guided by X-ray studies, a novel class of piperazine-like NBTIs with outstanding enzymatic activity against Staphylococcus aureus and Escherichia coli DNA gyrase and topoisomerase IV was identified. Notably, compounds (±)-33, (±)-35, and (±)-36 with potent and balanced multitarget enzymatic profiles exhibited excellent efficacy against selected Gram-positive and Gram-negative pathogens, as well as clinically relevant resistant strains. Overall, the new NBTI chemotype described herein, owing to the broad-spectrum antibacterial activity and favorable in vitro safety profile, might serve as a basis for the development of novel treatments against serious infections.
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Affiliation(s)
- Gabriele Magarò
- Angelini RR&D (Research, Regulatory & Development) , Angelini S.p.A. , Piazzale della Stazione SNC, S. Palomba-Pomezia , Rome 00071 , Italy
| | - Federica Prati
- Angelini RR&D (Research, Regulatory & Development) , Angelini S.p.A. , Piazzale della Stazione SNC, S. Palomba-Pomezia , Rome 00071 , Italy
| | - Barbara Garofalo
- Angelini RR&D (Research, Regulatory & Development) , Angelini S.p.A. , Piazzale della Stazione SNC, S. Palomba-Pomezia , Rome 00071 , Italy
| | - Gaia Corso
- Angelini RR&D (Research, Regulatory & Development) , Angelini S.p.A. , Piazzale della Stazione SNC, S. Palomba-Pomezia , Rome 00071 , Italy
| | - Guido Furlotti
- Angelini RR&D (Research, Regulatory & Development) , Angelini S.p.A. , Piazzale della Stazione SNC, S. Palomba-Pomezia , Rome 00071 , Italy
| | - Claudia Apicella
- Angelini RR&D (Research, Regulatory & Development) , Angelini S.p.A. , Piazzale della Stazione SNC, S. Palomba-Pomezia , Rome 00071 , Italy
| | - Giorgina Mangano
- Angelini RR&D (Research, Regulatory & Development) , Angelini S.p.A. , Piazzale della Stazione SNC, S. Palomba-Pomezia , Rome 00071 , Italy
| | - Noemi D'Atanasio
- Angelini RR&D (Research, Regulatory & Development) , Angelini S.p.A. , Piazzale della Stazione SNC, S. Palomba-Pomezia , Rome 00071 , Italy
| | - Daniel Robinson
- Schrodinger , 120 West 45th Street , New York , New York 10036 , United States
| | - Francesco Paolo Di Giorgio
- Angelini RR&D (Research, Regulatory & Development) , Angelini S.p.A. , Piazzale della Stazione SNC, S. Palomba-Pomezia , Rome 00071 , Italy
| | - Rosella Ombrato
- Angelini RR&D (Research, Regulatory & Development) , Angelini S.p.A. , Piazzale della Stazione SNC, S. Palomba-Pomezia , Rome 00071 , Italy
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16
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González-Hernández E, Aparicio R, Garayoa M, Montero MJ, Sevilla MÁ, Pérez-Melero C. Dihydropyrimidine-2-thiones as Eg5 inhibitors and L-type calcium channel blockers: potential antitumour dual agents. MEDCHEMCOMM 2019; 10:1589-1598. [PMID: 31673316 DOI: 10.1039/c9md00108e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 06/29/2019] [Indexed: 11/21/2022]
Abstract
The use of multitarget drugs has evolved as an alternative to "magic bullets" for the treatment of complex diseases such as cancer, in order to affect simultaneously several targets relevant to the disease. We have designed and synthesized a series of dual agents as both Eg5 inhibitors and calcium channel blockers, bearing a 4-aryldihydropyrimidine core. Compound 2 (aryl: 3-nitrophenyl) was selected as potential dual agent due to displaying both activities: it is a vasorelaxant agent (>90% relaxation at 10-5 M in KCl-precontracted aorta rings), it decreases the response to calcium and it is cytotoxic to MCF-7 (breast), HCT-116 (colon) and A-549 (lung) cancer cell lines. The dual mechanism of action was confirmed by blocking (-)-BAY K8644-induced vascular contraction and production of monopolar spindles, typical of Eg5 inhibition. Docking suggests that both (R) and (S)-enantiomers could bind Eg5.
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Affiliation(s)
- Elena González-Hernández
- Pharmaceutical Sciences Department , School of Pharmacy , University of Salamanca , Campus Miguel de Unamuno , 37007 Salamanca , Spain .
| | - Rubén Aparicio
- Physiology and Pharmacology Department , School of Pharmacy , University of Salamanca , Campus Miguel de Unamuno , 37007 Salamanca , Spain . .,Institute of Biomedical Research of Salamanca (IBSAL) , University Hospital of Salamanca , Paseo de San Vicente, 58-182 , 37007 Salamanca , Spain
| | - Mercedes Garayoa
- Institute of Biomedical Research of Salamanca (IBSAL) , University Hospital of Salamanca , Paseo de San Vicente, 58-182 , 37007 Salamanca , Spain.,Cancer Research Center , University of Salamanca-CSIC , Campus Miguel de Unamuno , 37007 Salamanca , Spain
| | - M José Montero
- Physiology and Pharmacology Department , School of Pharmacy , University of Salamanca , Campus Miguel de Unamuno , 37007 Salamanca , Spain . .,Institute of Biomedical Research of Salamanca (IBSAL) , University Hospital of Salamanca , Paseo de San Vicente, 58-182 , 37007 Salamanca , Spain
| | - M Ángeles Sevilla
- Physiology and Pharmacology Department , School of Pharmacy , University of Salamanca , Campus Miguel de Unamuno , 37007 Salamanca , Spain . .,Institute of Biomedical Research of Salamanca (IBSAL) , University Hospital of Salamanca , Paseo de San Vicente, 58-182 , 37007 Salamanca , Spain
| | - Concepción Pérez-Melero
- Pharmaceutical Sciences Department , School of Pharmacy , University of Salamanca , Campus Miguel de Unamuno , 37007 Salamanca , Spain . .,Institute of Biomedical Research of Salamanca (IBSAL) , University Hospital of Salamanca , Paseo de San Vicente, 58-182 , 37007 Salamanca , Spain.,Centre for Research on Tropical Diseases (CIETUS) , University of Salamanca , Spain
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17
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Islam MA, Pillay TS. Identification of promising anti-DNA gyrase antibacterial compounds using de novo design, molecular docking and molecular dynamics studies. J Biomol Struct Dyn 2019; 38:1798-1809. [PMID: 31084271 DOI: 10.1080/07391102.2019.1617785] [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] [Indexed: 01/09/2023]
Abstract
The rapidly increasing rate of antibiotic resistance is of great concern. Approximately two million deaths result annually from bacterial infections worldwide. Therefore, there is a paramount requirement to develop innovative and novel antibacterial agents with new mechanisms of action and activity against resistant bacterial strains. For this purpose, a set of benzothiazole and N-phenylpyrrolamides derivatives reported as DNA Gyrase B (GyrB) inhibitors were collected from the literature and docked inside the receptor cavity of DNA Gyrase B (PDB ID: 5L3J). The best 10 docked complexes were used to identify novel antibacterial chemical agents through a de novo design approach. Out of initial 300 chemical analogues, the best six analogues were identified using screening with a set of criteria followed by pharmacokinetic analysis. The binding interactions of the best six analogues revealed that all molecules formed a number of critical interactions with catalytic amino residues of DNA Gyrase B with high binding energy. The predicted inhibitory constant biological activity based on binding energy supported the potential of the molecules as DNA Gyrase B ligands. The RMSD, RMSF, and radius of gyration parameters obtained from the 100 ns molecular dynamics simulation study clearly demonstrated that all six analogues were efficient enough to form stable complexes with DNA Gyrase B. High negative binding energy of all ligands obtained from MM-GBSA approach undoubtedly explained the strong affinity toward the DNA Gyrase B. Therefore, the proposed de novo designed molecules can be considered as promising antibacterial chemical agents subject to experimental validation, in vitro.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Md Ataul Islam
- Department of Chemical Pathology, Faculty of Health Sciences, University of Pretoria and National Health Laboratory Service Tshwane Academic Division, Pretoria, South Africa.,School of Health Sciences, University of Kwazulu-Natal, Durban, South Africa.,Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Tahir S Pillay
- Department of Chemical Pathology, Faculty of Health Sciences, University of Pretoria and National Health Laboratory Service Tshwane Academic Division, Pretoria, South Africa.,Division of Chemical Pathology, University of Cape Town, Cape Town, South Africa
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18
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Kartsev V, Shikhaliev KS, Geronikaki A, Medvedeva SM, Ledenyova IV, Krysin MY, Petrou A, Ciric A, Glamoclija J, Sokovic M. Appendix A. dithioloquinolinethiones as new potential multitargeted antibacterial and antifungal agents: Synthesis, biological evaluation and molecular docking studies. Eur J Med Chem 2019; 175:201-214. [PMID: 31078867 DOI: 10.1016/j.ejmech.2019.04.046] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/11/2019] [Accepted: 04/16/2019] [Indexed: 01/23/2023]
Abstract
Herein we report the design, synthesis, molecular docking study and evaluation of antimicrobial activity of ten new dithioloquinolinethiones. The structures of compounds were confirmed by 1H NMR, 13C NMR and HPLC-HRMS. Before evaluation of their possible antimicrobial activity prediction of toxicity was performed. All compounds showed antibacterial activity against eight Gram positive and Gram negative bacterial species. All compounds appeared to be more active than ampicillin and almost all than streptomycin. The best antibacterial activity was observed for compound 8c 4,4,8-trimethyl-5-{[(4-phenyl-5-thioxo-4,5-dihydro-1,3,4-thiadiazol-2-yl)thio]acetyl}-4,5-dihydro-1H-[1,2]dithiolo[3,4c]quino lone-1-thione). The most sensitive bacterium En.cloacae followed by S. aureus, while L.monocytogenes was the most resistant. All compounds were tested for antifungal activity also against eight fungal species. The best activity was expressed by compound 8d (5-[(4,5-Dihydro-1,3-thiazol-2-ylthio)acetyl]-4,4-dimethyl-4,5-dihydro-1H-[1,2]dithiolo[3,4-c]quinoline-1-thione). The most sensitive fungal was T. viride, while P. verrucosum var. cyclopium was the most resistant one. All compounds were more potent as antifungal agent than reference compound bifonazole and ketoconazole. The docking studies indicated a probable involvement of E. coli DNA GyrB inhibition in the anti-bacterial mechanism, while CYP51ca inhibition is probably responsible for antifungal activity of tested compounds. It is interesting to mention that docking results coincides with experimental.
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Affiliation(s)
| | - Khidmet S Shikhaliev
- Department of organic chemistry, Faculty of chemistry, Voronezh State University, Voronezh, 394018, Russian Federation
| | - A Geronikaki
- Aristotle University, School of Pharmacy, Thessaloniki, 54124, Greece.
| | - Svetlana M Medvedeva
- Department of organic chemistry, Faculty of chemistry, Voronezh State University, Voronezh, 394018, Russian Federation
| | - Irina V Ledenyova
- Department of organic chemistry, Faculty of chemistry, Voronezh State University, Voronezh, 394018, Russian Federation
| | - Mikhail Yu Krysin
- Department of organic chemistry, Faculty of chemistry, Voronezh State University, Voronezh, 394018, Russian Federation
| | - A Petrou
- Aristotle University, School of Pharmacy, Thessaloniki, 54124, Greece
| | - A Ciric
- Mycological Laboratory, Department of Plant Physiology, Institute for Biological Research, Siniša Stanković, University of Belgrade, Bulevar Despota Stefana, Serbia
| | - J Glamoclija
- Mycological Laboratory, Department of Plant Physiology, Institute for Biological Research, Siniša Stanković, University of Belgrade, Bulevar Despota Stefana, Serbia
| | - M Sokovic
- Mycological Laboratory, Department of Plant Physiology, Institute for Biological Research, Siniša Stanković, University of Belgrade, Bulevar Despota Stefana, Serbia
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19
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QSAR of 1,4-benzoxazin-3-one antimicrobials and their drug design perspectives. Bioorg Med Chem 2018; 26:6105-6114. [PMID: 30471830 DOI: 10.1016/j.bmc.2018.11.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/05/2018] [Accepted: 11/12/2018] [Indexed: 11/23/2022]
Abstract
Synthetic derivatives of 1,4-benzoxazin-3-ones have been shown to possess promising antimicrobial activity, whereas their natural counterparts were found lacking in this respect. In this work, quantitative structure-activity relationships (QSAR) of natural and synthetic 1,4-benzoxazin-3-ones as antimicrobials were established. Data published in literature were curated into an extensive dataset of 111 compounds. Descriptor selection was performed by a genetic algorithm. QSAR models revealed differences in requirements for activity against fungi, gram-positive and gram-negative bacteria. Shape, VolSurf, and H-bonding property descriptors were frequently picked in all models. The models obtained for gram-positive and gram-negative bacteria showed good predictive power (Q2Ext 0.88 and 0.85, respectively). Based on the models generated, an additional set of 1,4-benzoxazin-3-ones, for which no antimicrobial activity had been determined in literature, were evaluated in silico. Additionally, newly designed lead compounds with a 1,4-benzoxazin-3-one scaffold were generated in silico by varying the positions and combinations of substituents. Two of these were predicted to be up to 5 times more active than any of the compounds in the current dataset. The 1,4-benzoxazin-3-one scaffold was concluded to possess potential for the design of new antimicrobial compounds with potent antibacterial activity, a multitarget mode of action, and possibly reduced susceptibility to gram negatives' efflux pumps.
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20
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Dean CR, Barkan DT, Bermingham A, Blais J, Casey F, Casarez A, Colvin R, Fuller J, Jones AK, Li C, Lopez S, Metzger LE, Mostafavi M, Prathapam R, Rasper D, Reck F, Ruzin A, Shaul J, Shen X, Simmons RL, Skewes-Cox P, Takeoka KT, Tamrakar P, Uehara T, Wei JR. Mode of Action of the Monobactam LYS228 and Mechanisms Decreasing In Vitro Susceptibility in Escherichia coli and Klebsiella pneumoniae. Antimicrob Agents Chemother 2018; 62:e01200-18. [PMID: 30061293 PMCID: PMC6153799 DOI: 10.1128/aac.01200-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 07/25/2018] [Indexed: 12/14/2022] Open
Abstract
The monobactam scaffold is attractive for the development of new agents to treat infections caused by drug-resistant Gram-negative bacteria because it is stable to metallo-β-lactamases (MBLs). However, the clinically used monobactam aztreonam lacks stability to serine β-lactamases (SBLs) that are often coexpressed with MBLs. LYS228 is stable to MBLs and most SBLs. LYS228 bound purified Escherichia coli penicillin binding protein 3 (PBP3) similarly to aztreonam (derived acylation rate/equilibrium dissociation constant [k2/Kd ] of 367,504 s-1 M-1 and 409,229 s-1 M-1, respectively) according to stopped-flow fluorimetry. A gel-based assay showed that LYS228 bound mainly to E. coli PBP3, with weaker binding to PBP1a and PBP1b. Exposing E. coli cells to LYS228 caused filamentation consistent with impaired cell division. No single-step mutants were selected from 12 Enterobacteriaceae strains expressing different classes of β-lactamases at 8× the MIC of LYS228 (frequency, <2.5 × 10-9). At 4× the MIC, mutants were selected from 2 of 12 strains at frequencies of 1.8 × 10-7 and 4.2 × 10-9 LYS228 MICs were ≤2 μg/ml against all mutants. These frequencies compared favorably to those for meropenem and tigecycline. Mutations decreasing LYS228 susceptibility occurred in ramR and cpxA (Klebsiella pneumoniae) and baeS (E. coli and K. pneumoniae). Susceptibility of E. coli ATCC 25922 to LYS228 decreased 256-fold (MIC, 0.125 to 32 μg/ml) after 20 serial passages. Mutants accumulated mutations in ftsI (encoding the target, PBP3), baeR, acrD, envZ, sucB, and rfaI These results support the continued development of LYS228, which is currently undergoing phase II clinical trials for complicated intraabdominal infection and complicated urinary tract infection (registered at ClinicalTrials.gov under identifiers NCT03377426 and NCT03354754).
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Affiliation(s)
- Charles R Dean
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - David T Barkan
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Alun Bermingham
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Johanne Blais
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Fergal Casey
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Anthony Casarez
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Richard Colvin
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, USA
| | - John Fuller
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Adriana K Jones
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Cindy Li
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Sara Lopez
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Louis E Metzger
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Mina Mostafavi
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Ramadevi Prathapam
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Dita Rasper
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Folkert Reck
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Alexey Ruzin
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Jacob Shaul
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Xiaoyu Shen
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Robert L Simmons
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Peter Skewes-Cox
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Kenneth T Takeoka
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Pramila Tamrakar
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Tsuyoshi Uehara
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
| | - Jun-Rong Wei
- Novartis Institutes for BioMedical Research, Emeryville, California, USA
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21
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Proschak E, Stark H, Merk D. Polypharmacology by Design: A Medicinal Chemist's Perspective on Multitargeting Compounds. J Med Chem 2018; 62:420-444. [PMID: 30035545 DOI: 10.1021/acs.jmedchem.8b00760] [Citation(s) in RCA: 276] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Multitargeting compounds comprising activity on more than a single biological target have gained remarkable relevance in drug discovery owing to the complexity of multifactorial diseases such as cancer, inflammation, or the metabolic syndrome. Polypharmacological drug profiles can produce additive or synergistic effects while reducing side effects and significantly contribute to the high therapeutic success of indispensable drugs such as aspirin. While their identification has long been the result of serendipity, medicinal chemistry now tends to design polypharmacology. Modern in vitro pharmacological methods and chemical probes allow a systematic search for rational target combinations and recent innovations in computational technologies, crystallography, or fragment-based design equip multitarget compound development with valuable tools. In this Perspective, we analyze the relevance of multiple ligands in drug discovery and the versatile toolbox to design polypharmacology. We conclude that despite some characteristic challenges remaining unresolved, designed polypharmacology holds enormous potential to secure future therapeutic innovation.
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Affiliation(s)
- Ewgenij Proschak
- Institute of Pharmaceutical Chemistry , Goethe University Frankfurt , Max-von-Laue-Strasse 9 , D-60438 Frankfurt , Germany
| | - Holger Stark
- Institute of Pharmaceutical and Medicinal Chemistry , Heinrich Heine University Düsseldorf , Universitaetsstrasse 1 , D-40225 , Duesseldorf , Germany
| | - Daniel Merk
- Institute of Pharmaceutical Chemistry , Goethe University Frankfurt , Max-von-Laue-Strasse 9 , D-60438 Frankfurt , Germany.,Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences , Swiss Federal Institute of Technology (ETH) Zürich , Vladimir-Prelog-Weg 4 , CH-8093 Zürich , Switzerland
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22
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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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23
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Optimization of novel monobactams with activity against carbapenem-resistant Enterobacteriaceae - Identification of LYS228. Bioorg Med Chem Lett 2018; 28:748-755. [PMID: 29336873 DOI: 10.1016/j.bmcl.2018.01.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 01/02/2018] [Accepted: 01/03/2018] [Indexed: 11/23/2022]
Abstract
Metallo-β-lactamases (MBLs), such as New Delhi metallo-β-lactamase (NDM-1) have spread world-wide and present a serious threat. Expression of MBLs confers resistance in Gram-negative bacteria to all classes of β-lactam antibiotics, with the exception of monobactams, which are intrinsically stable to MBLs. However, existing first generation monobactam drugs like aztreonam have limited clinical utility against MBL-expressing strains because they are impacted by serine β-lactamases (SBLs), which are often co-expressed in clinical isolates. Here, we optimized novel monobactams for stability against SBLs, which led to the identification of LYS228 (compound 31). LYS228 is potent in the presence of all classes of β-lactamases and shows potent activity against carbapenem-resistant isolates of Enterobacteriaceae (CRE).
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24
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Batson S, de Chiara C, Majce V, Lloyd AJ, Gobec S, Rea D, Fülöp V, Thoroughgood CW, Simmons KJ, Dowson CG, Fishwick CWG, de Carvalho LPS, Roper DI. Inhibition of D-Ala:D-Ala ligase through a phosphorylated form of the antibiotic D-cycloserine. Nat Commun 2017; 8:1939. [PMID: 29208891 PMCID: PMC5717164 DOI: 10.1038/s41467-017-02118-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 11/08/2017] [Indexed: 11/11/2022] Open
Abstract
D-cycloserine is an antibiotic which targets sequential bacterial cell wall peptidoglycan biosynthesis enzymes: alanine racemase and D-alanine:D-alanine ligase. By a combination of structural, chemical and mechanistic studies here we show that the inhibition of D-alanine:D-alanine ligase by the antibiotic D-cycloserine proceeds via a distinct phosphorylated form of the drug. This mechanistic insight reveals a bimodal mechanism of action for a single antibiotic on different enzyme targets and has significance for the design of future inhibitor molecules based on this chemical structure. The antibiotic D-cycloserine (DCS) targets the peptidoglycan biosynthesis enzyme D-Ala-D-Ala ligase (Ddl). Here the authors reveal the DCS inhibitory mechanism by determining the structure of E. coli DdlB with a phosphorylated DCS molecule in the active site that formed in crystallo and mimics the D-alanyl phosphate intermediate.
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Affiliation(s)
- Sarah Batson
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Cesira de Chiara
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, NW1 1AT, London, UK
| | - Vita Majce
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Adrian J Lloyd
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Stanislav Gobec
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Dean Rea
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Vilmos Fülöp
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | | | | | | | | | - Luiz Pedro S de Carvalho
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, NW1 1AT, London, UK.
| | - David I Roper
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.
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25
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Cardona ST, Choy M, Hogan AM. Essential Two-Component Systems Regulating Cell Envelope Functions: Opportunities for Novel Antibiotic Therapies. J Membr Biol 2017; 251:75-89. [DOI: 10.1007/s00232-017-9995-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 10/20/2017] [Indexed: 01/22/2023]
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26
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Thomas SE, Mendes V, Kim SY, Malhotra S, Ochoa-Montaño B, Blaszczyk M, Blundell TL. Structural Biology and the Design of New Therapeutics: From HIV and Cancer to Mycobacterial Infections: A Paper Dedicated to John Kendrew. J Mol Biol 2017; 429:2677-2693. [PMID: 28648615 DOI: 10.1016/j.jmb.2017.06.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 06/19/2017] [Indexed: 10/19/2022]
Abstract
Interest in applications of protein crystallography to medicine was evident, as the first high-resolution structures emerged in the 50s and 60s. In Cambridge, Max Perutz and John Kendrew sought to understand mutations in sickle cell and other genetic diseases related to hemoglobin, while in Oxford, the group of Dorothy Hodgkin became interested in long-lasting zinc-insulin crystals for treatment of diabetes and later considered insulin redesign, as synthetic insulins became possible. The use of protein crystallography in structure-guided drug discovery emerged as enzyme structures allowed the identification of potential inhibitor-binding sites and optimization of interactions of hits using the structure of the target protein. Early examples of this approach were the use of the structure of renin to design antihypertensives and the structure of HIV protease in design of AIDS antivirals. More recently, use of structure-guided design with fragment-based drug discovery, which reduces the size of screening libraries by decreasing complexity, has improved ligand efficiency in drug design and has been used to progress three oncology drugs through clinical trials to FDA approval. We exemplify current developments in structure-guided target identification and fragment-based lead discovery with efforts to develop new antimicrobials for mycobacterial infections.
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Affiliation(s)
- Sherine E Thomas
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK
| | - Vitor Mendes
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK
| | - So Yeon Kim
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK
| | - Sony Malhotra
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK
| | - Bernardo Ochoa-Montaño
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK
| | - Michal Blaszczyk
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK.
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27
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Singh SB, Young K, Silver LL. What is an “ideal” antibiotic? Discovery challenges and path forward. Biochem Pharmacol 2017; 133:63-73. [DOI: 10.1016/j.bcp.2017.01.003] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/09/2017] [Indexed: 01/24/2023]
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28
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Charrier C, Salisbury AM, Savage VJ, Duffy T, Moyo E, Chaffer-Malam N, Ooi N, Newman R, Cheung J, Metzger R, McGarry D, Pichowicz M, Sigerson R, Cooper IR, Nelson G, Butler HS, Craighead M, Ratcliffe AJ, Best SA, Stokes NR. Novel Bacterial Topoisomerase Inhibitors with Potent Broad-Spectrum Activity against Drug-Resistant Bacteria. Antimicrob Agents Chemother 2017; 61:e02100-16. [PMID: 28223393 PMCID: PMC5404544 DOI: 10.1128/aac.02100-16] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 01/27/2017] [Indexed: 12/30/2022] Open
Abstract
The novel bacterial topoisomerase inhibitor class is an investigational type of antibacterial inhibitor of DNA gyrase and topoisomerase IV that does not have cross-resistance with the quinolones. Here, we report the evaluation of the in vitro properties of a new series of this type of small molecule. Exemplar compounds selectively and potently inhibited the catalytic activities of Escherichia coli DNA gyrase and topoisomerase IV but did not block the DNA breakage-reunion step. Compounds showed broad-spectrum inhibitory activity against a wide range of Gram-positive and Gram-negative pathogens, including biodefence microorganisms and Mycobacterium tuberculosis No cross-resistance with fluoroquinolone-resistant Staphylococcus aureus and E. coli isolates was observed. Measured MIC90 values were 4 and 8 μg/ml against a panel of contemporary multidrug-resistant isolates of Acinetobacter baumannii and E. coli, respectively. In addition, representative compounds exhibited greater antibacterial potency than the quinolones against obligate anaerobic species. Spontaneous mutation rates were low, with frequencies of resistance typically <10-8 against E. coli and A. baumannii at concentrations equivalent to 4-fold the MIC. Compound-resistant E. coli mutants that were isolated following serial passage were characterized by whole-genome sequencing and carried a single Arg38Leu amino acid substitution in the GyrA subunit of DNA gyrase. Preliminary in vitro safety data indicate that the series shows a promising therapeutic index and potential for low human ether-a-go-go-related gene (hERG) inhibition (50% inhibitory concentration [IC50], >100 μM). In summary, the compounds' distinct mechanism of action relative to the fluoroquinolones, whole-cell potency, low potential for resistance development, and favorable in vitro safety profile warrant their continued investigation as potential broad-spectrum antibacterial agents.
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Affiliation(s)
| | | | | | - Thomas Duffy
- Redx Pharma, Alderley Park, Cheshire, United Kingdom
| | - Emmanuel Moyo
- Redx Pharma, Alderley Park, Cheshire, United Kingdom
| | | | - Nicola Ooi
- Redx Pharma, Alderley Park, Cheshire, United Kingdom
| | | | | | | | - David McGarry
- Redx Pharma, Alderley Park, Cheshire, United Kingdom
| | | | | | - Ian R Cooper
- Redx Pharma, Alderley Park, Cheshire, United Kingdom
| | - Gary Nelson
- Redx Pharma, Alderley Park, Cheshire, United Kingdom
| | | | | | | | - Stuart A Best
- Redx Pharma, Alderley Park, Cheshire, United Kingdom
| | - Neil R Stokes
- Redx Pharma, Alderley Park, Cheshire, United Kingdom
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29
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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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30
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Ahmad MJ, Hassan SF, Nisa RU, Ayub K, Nadeem MS, Nazir S, Ansari FL, Qureshi NA, Rashid U. Synthesis, in vitro potential and computational studies on 2-amino-1, 4-dihydropyrimidines as multitarget antibacterial ligands. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1613-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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31
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Gokgoz NB, Akbulut BS. Proteomics Evidence for the Activity of the Putative Antibacterial Plant Alkaloid (-)-Roemerine: Mainstreaming Omics-Guided Drug Discovery. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 19:478-89. [PMID: 26230533 DOI: 10.1089/omi.2015.0056] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Discovery of new antibacterials with novel mechanisms is important to counteract the ingenious resistance mechanisms of bacteria. In this connection, omics-guided drug discovery offers a rigorous method in the quest of new antibacterials. (-)-Roemerine is a plant alkaloid that has been reported to possess putative antibacterial activity against Escherichia coli, Bacillus subtilis, and Salmonella typhimurium. The aim of the present study was to characterize the activity of (-)-roemerine in Escherichia coli TB1 using proteomics tools. With (-)-roemerine treatment, we found limited permeability through the outer membrane and repression of transport proteins involved in carbohydrate metabolism, resulting in poor carbon source availability. The shortfall of intracellular carbon sources in turn led to impaired cell growth. The reduction in the abundance of proteins related to translational machinery, amino acid biosynthesis, and metabolism was accompanied by a nutrient-limited state. The latter finding could suggest a metabolic shutdown in E. coli cells. High osmolarity was clearly not one of the reasons of bacterial death by (-)-roemerine. These observations collectively attest to the promise of plant omics and profiling of putative drug candidates using proteomics tools. Omics-guided drug discovery deserves greater attention in mainstream pharmacology so as to better understand the plants' medicinal potentials.
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32
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Hughes RE, Nikolic K, Ramsay RR. One for All? Hitting Multiple Alzheimer's Disease Targets with One Drug. Front Neurosci 2016; 10:177. [PMID: 27199640 PMCID: PMC4842778 DOI: 10.3389/fnins.2016.00177] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 04/06/2016] [Indexed: 12/12/2022] Open
Abstract
HIGHLIGHTS Many AD target combinations are being explored for multi-target drug design.New databases and models increase the potential of computational drug designLiraglutide and other antidiabetics are strong candidates for repurposing to AD.Donecopride a dual 5-HT/AChE inhibitor shows promise in pre-clinical studies Alzheimer's Disease is a complex and multifactorial disease for which the mechanism is still not fully understood. As new insights into disease progression are discovered, new drugs must be designed to target those aspects of the disease that cause neuronal damage rather than just the symptoms currently addressed by single target drugs. It is becoming possible to target several aspects of the disease pathology at once using multi-target drugs (MTDs). Intended as an introduction for non-experts, this review describes the key MTD design approaches, namely structure-based, in silico, and data-mining, to evaluate what is preventing compounds progressing through the clinic to the market. Repurposing current drugs using their off-target effects reduces the cost of development, time to launch, and the uncertainty associated with safety and pharmacokinetics. The most promising drugs currently being investigated for repurposing to Alzheimer's Disease are rasagiline, originally developed for the treatment of Parkinson's Disease, and liraglutide, an antidiabetic. Rational drug design can combine pharmacophores of multiple drugs, systematically change functional groups, and rank them by virtual screening. Hits confirmed experimentally are rationally modified to generate an effective multi-potent lead compound. Examples from this approach are ASS234 with properties similar to rasagiline, and donecopride, a hybrid of an acetylcholinesterase inhibitor and a 5-HT4 receptor agonist with pro-cognitive effects. Exploiting these interdisciplinary approaches, public-private collaborative lead factories promise faster delivery of new drugs to the clinic.
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Affiliation(s)
- Rebecca E Hughes
- School of Biology, BMS Building, University of St Andrews St Andrews, UK
| | - Katarina Nikolic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade Belgrade, Serbia
| | - Rona R Ramsay
- School of Biology, BMS Building, University of St Andrews St Andrews, UK
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33
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Feng X, Zhu W, Schurig-Briccio LA, Lindert S, Shoen C, Hitchings R, Li J, Wang Y, Baig N, Zhou T, Kim BK, Crick DC, Cynamon M, McCammon JA, Gennis RB, Oldfield E. Antiinfectives targeting enzymes and the proton motive force. Proc Natl Acad Sci U S A 2015; 112:E7073-82. [PMID: 26644565 PMCID: PMC4697371 DOI: 10.1073/pnas.1521988112] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
There is a growing need for new antibiotics. Compounds that target the proton motive force (PMF), uncouplers, represent one possible class of compounds that might be developed because they are already used to treat parasitic infections, and there is interest in their use for the treatment of other diseases, such as diabetes. Here, we tested a series of compounds, most with known antiinfective activity, for uncoupler activity. Many cationic amphiphiles tested positive, and some targeted isoprenoid biosynthesis or affected lipid bilayer structure. As an example, we found that clomiphene, a recently discovered undecaprenyl diphosphate synthase inhibitor active against Staphylococcus aureus, is an uncoupler. Using in silico screening, we then found that the anti-glioblastoma multiforme drug lead vacquinol is an inhibitor of Mycobacterium tuberculosis tuberculosinyl adenosine synthase, as well as being an uncoupler. Because vacquinol is also an inhibitor of M. tuberculosis cell growth, we used similarity searches based on the vacquinol structure, finding analogs with potent (∼0.5-2 μg/mL) activity against M. tuberculosis and S. aureus. Our results give a logical explanation of the observation that most new tuberculosis drug leads discovered by phenotypic screens and genome sequencing are highly lipophilic (logP ∼5.7) bases with membrane targets because such species are expected to partition into hydrophobic membranes, inhibiting membrane proteins, in addition to collapsing the PMF. This multiple targeting is expected to be of importance in overcoming the development of drug resistance because targeting membrane physical properties is expected to be less susceptible to the development of resistance.
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Affiliation(s)
- Xinxin Feng
- Department of Chemistry, University of Illinois, Urbana, IL 61801
| | - Wei Zhu
- Department of Chemistry, University of Illinois, Urbana, IL 61801
| | | | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210
| | - Carolyn Shoen
- Central New York Research Corporation, Veterans Affairs Medical Center, Syracuse, NY 13210
| | - Reese Hitchings
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523
| | - Jikun Li
- Department of Chemistry, University of Illinois, Urbana, IL 61801
| | - Yang Wang
- Department of Chemistry, University of Illinois, Urbana, IL 61801
| | - Noman Baig
- Department of Chemistry, University of Illinois, Urbana, IL 61801
| | - Tianhui Zhou
- Department of Chemistry, University of Illinois, Urbana, IL 61801
| | - Boo Kyung Kim
- Department of Chemistry, University of Illinois, Urbana, IL 61801
| | - Dean C Crick
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523
| | - Michael Cynamon
- Central New York Research Corporation, Veterans Affairs Medical Center, Syracuse, NY 13210
| | - J Andrew McCammon
- Department of Pharmacology and Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA 92093; Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093; National Biomedical Computation Resource, University of California San Diego, La Jolla, CA 92093;
| | - Robert B Gennis
- Department of Chemistry, University of Illinois, Urbana, IL 61801; Department of Biochemistry, University of Illinois, Urbana, IL 61801; Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Eric Oldfield
- Department of Chemistry, University of Illinois, Urbana, IL 61801; Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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34
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Paneth A, Stączek P, Plech T, Strzelczyk A, Dzitko K, Wujec M, Kuśmierz E, Kosikowska U, Grzegorczyk A, Paneth P. Biological evaluation and molecular modelling study of thiosemicarbazide derivatives as bacterial type IIA topoisomerases inhibitors. J Enzyme Inhib Med Chem 2015; 31:14-22. [PMID: 25792505 DOI: 10.3109/14756366.2014.1003214] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In the present article, we describe the inhibitory potency of nine thiosemicarbazide derivatives against bacterial type IIA topoisomerases, their antibacterial profile and molecular modelling evaluation. We found that one of the tested compounds, compound 7, significantly inhibits activity of Staphylococcus aureus DNA gyrase with an IC(50) below 15 μM. Besides, this compound displays antibacterial activity on reference Staphylococuss spp. and Enterococcus faecalis strains as well as clinical S. aureus isolates at non-cytotoxic concentrations in mammalian cells with MIC values ranging from 16 to 32 μg/mL thereby indicating, in some cases, equipotent or even more effective action than standard drugs such as vancomycin, ampicillin and nitrofurantoin. The computational studies showed that both molecular geometry and the electron density distribution have a great impact on antibacterial activity of thiosemicarbazide derivatives.
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Affiliation(s)
- Agata Paneth
- a Department of Organic Chemistry , Medical University of Lublin , Poland .,e Institute of Applied Radiation Chemistry, Lodz University of Technology , Poland
| | | | - Tomasz Plech
- a Department of Organic Chemistry , Medical University of Lublin , Poland
| | | | - Katarzyna Dzitko
- c Department of Immunoparasitology , University of Łódź , Poland
| | - Monika Wujec
- a Department of Organic Chemistry , Medical University of Lublin , Poland
| | - Edyta Kuśmierz
- a Department of Organic Chemistry , Medical University of Lublin , Poland
| | - Urszula Kosikowska
- d Department of Pharmaceutical Microbiology , Medical University of Lublin , Poland , and
| | - Agnieszka Grzegorczyk
- d Department of Pharmaceutical Microbiology , Medical University of Lublin , Poland , and
| | - Piotr Paneth
- e Institute of Applied Radiation Chemistry, Lodz University of Technology , Poland
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35
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Gooyit M, Tricoche N, Javor S, Lustigman S, Janda KD. Exploiting the Polypharmacology of ß-Carbolines to Disrupt O. volvulus Molting. ACS Med Chem Lett 2015; 6:339-43. [PMID: 25815157 DOI: 10.1021/ml500516r] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 01/20/2015] [Indexed: 01/22/2023] Open
Abstract
Onchocerciasis is an infection caused by the filarial worm Onchocerca volvulus, which can eventually result in blindness. The lack of an effective macrofilaricide and the possible development of ivermectin-resistant strains of O. volvulus necessitate the need for alternative treatment strategies. We have shown that targeting the L3-stage-specific chitinase OvCHT1 impairs the shedding of the filarial cuticle. In our continued efforts to discover OvCHT1 inhibitors, we identified the β-carboline alkaloid scaffolding as a chitinase inhibitor that is capable of penetrating the worm cuticle. Herein, we disclose the rich polypharmacology of the β-carboline class of compounds as an approach to abrogate the molting of the parasite and thus the initiation of infection in the human host.
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Affiliation(s)
- Major Gooyit
- Departments
of Chemistry and Immunology and Microbial Science, The Skaggs Institute
for Chemical Biology, and The Worm Institute of Research and Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Nancy Tricoche
- Lindsley
F. Kimball Research Institute, New York Blood Center, New York, New York 10065, United States
| | - Sacha Javor
- Departments
of Chemistry and Immunology and Microbial Science, The Skaggs Institute
for Chemical Biology, and The Worm Institute of Research and Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Sara Lustigman
- Lindsley
F. Kimball Research Institute, New York Blood Center, New York, New York 10065, United States
| | - Kim D. Janda
- Departments
of Chemistry and Immunology and Microbial Science, The Skaggs Institute
for Chemical Biology, and The Worm Institute of Research and Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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36
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Abstract
Antibiotics are essential for both treating and preventing infectious diseases. Paradoxically, despite their importance as pillars of modern medicine, we are in danger of losing antibiotics because of the evolution and dissemination of resistance mechanisms throughout all pathogenic microbes. This fact, coupled with an inability to bring new drugs to market at a pace that matches resistance, has resulted in a crisis of global proportion. Solving this crisis requires the actions of many stakeholders, but chemists, chemical biologists, and microbiologists must drive the scientific innovation that is required to maintain our antibiotic arsenal. This innovation requires (1) a deep understanding of the evolution and reservoirs of resistance; (2) full knowledge of the molecular mechanisms of antibiotic action and resistance; (3) the discovery of chemical and genetic probes of antibiotic action and resistance; (4) the integration of systems biology into antibiotic discovery; and (5) the discovery of new antimicrobial chemical matter. Addressing these pressing scientific gaps will ensure that we can meet the antibiotic crisis with creativity and purpose.
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Affiliation(s)
- Gerard D. Wright
- Michael G. DeGroote Institute
for Infectious Disease Research, Department of Biochemistry and Biomedical
Sciences, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
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37
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Small-molecule inhibitors of Staphylococcus aureus RnpA-mediated RNA turnover and tRNA processing. Antimicrob Agents Chemother 2015; 59:2016-28. [PMID: 25605356 DOI: 10.1128/aac.04352-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
New agents are urgently needed for the therapeutic treatment of Staphylococcus aureus infections. In that regard, S. aureus RNase RnpA may represent a promising novel dual-function antimicrobial target that participates in two essential cellular processes, RNA degradation and tRNA maturation. Accordingly, we previously used a high-throughput screen to identify small-molecule inhibitors of the RNA-degrading activity of the enzyme and showed that the RnpA inhibitor RNPA1000 is an attractive antimicrobial development candidate. In this study, we used a series of in vitro and cellular assays to characterize a second RnpA inhibitor, RNPA2000, which was identified in our initial screening campaign and is structurally distinct from RNPA1000. In doing so, it was found that S. aureus RnpA does indeed participate in 5'-precursor tRNA processing, as was previously hypothesized. Further, we show that RNPA2000 is a bactericidal agent that inhibits both RnpA-associated RNA degradation and tRNA maturation activities both in vitro and within S. aureus. The compound appears to display specificity for RnpA, as it did not significantly affect the in vitro activities of unrelated bacterial or eukaryotic ribonucleases and did not display measurable human cytotoxicity. Finally, we show that RNPA2000 exhibits antimicrobial activity and inhibits tRNA processing in efflux-deficient Gram-negative pathogens. Taken together, these data support the targeting of RnpA for antimicrobial development purposes, establish that small-molecule inhibitors of both of the functions of the enzyme can be identified, and lend evidence that RnpA inhibitors may have broad-spectrum antimicrobial activities.
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38
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Surivet JP, Zumbrunn C, Rueedi G, Bur D, Bruyère T, Locher H, Ritz D, Seiler P, Kohl C, Ertel EA, Hess P, Gauvin JC, Mirre A, Kaegi V, Dos Santos M, Kraemer S, Gaertner M, Delers J, Enderlin-Paput M, Weiss M, Sube R, Hadana H, Keck W, Hubschwerlen C. Novel tetrahydropyran-based bacterial topoisomerase inhibitors with potent anti-gram positive activity and improved safety profile. J Med Chem 2014; 58:927-42. [PMID: 25494934 DOI: 10.1021/jm501590q] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Novel antibacterial drugs that are effective against infections caused by multidrug resistant pathogens are urgently needed. In a previous report, we have shown that tetrahydropyran-based inhibitors of bacterial type II topoisomerases (DNA gyrase and topoisomerase IV) display potent antibacterial activity and exhibit no target-mediated cross-resistance with fluoroquinolones. During the course of our optimization program, lead compound 5 was deprioritized due to adverse findings in cardiovascular safety studies. In the effort of mitigating these findings and optimizing further the pharmacological profile of this class of compounds, we have identified a subseries of tetrahydropyran-based molecules that are potent DNA gyrase and topoisomerase IV inhibitors and display excellent antibacterial activity against Gram positive pathogens, including clinically relevant resistant isolates. One representative of this class, compound 32d, elicited only weak inhibition of hERG K(+) channels and hNaV1.5 Na(+) channels, and no effects were observed on cardiovascular parameters in anesthetized guinea pigs. In vivo efficacy in animal infection models has been demonstrated against Staphylococcus aureus and Streptococcus pneumoniae strains.
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Affiliation(s)
- Jean-Philippe Surivet
- Actelion Pharmaceuticals Limited , Gewerbestrasse 16, CH-4123 Allschwil, Switzerland
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39
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Brown P, Dawson MJ. A perspective on the next generation of antibacterial agents derived by manipulation of natural products. PROGRESS IN MEDICINAL CHEMISTRY 2014; 54:135-84. [PMID: 25727704 DOI: 10.1016/bs.pmch.2014.10.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Natural products have been a major source of anti-infective drugs for many decades. With urgent need for new antibacterial agents to combat drug-resistant bacteria, the investigation of both new and existing classes of natural products has once again become an important focus. In this review, we highlight how a medicinal chemistry/semi-synthetic approach to natural product manipulation continues to offer a valuable strategy to overcome limitations in current therapy. Approaches to address toxicity and to improve the solubility, bioavailability and the spectrum of activity are demonstrated. Examples are drawn from aminoglycosides, glycopeptides, tetracyclines, macrolides, thiazolyl peptides, pleuromutilins and polymyxins and are taken from the current literature, patents and abstracts of symposia. In many cases, this approach has led to drug candidates currently in late stages of clinical development.
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Affiliation(s)
- Pamela Brown
- Cantab Anti-infectives, Welwyn Garden City, Hertfordshire, United Kingdom
| | - Michael J Dawson
- Cantab Anti-infectives, Welwyn Garden City, Hertfordshire, United Kingdom
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40
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Resistance-resistant antibiotics. Trends Pharmacol Sci 2014; 35:664-74. [PMID: 25458541 DOI: 10.1016/j.tips.2014.10.007] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 10/10/2014] [Accepted: 10/14/2014] [Indexed: 01/27/2023]
Abstract
New antibiotics are needed because drug resistance is increasing while the introduction of new antibiotics is decreasing. We discuss here six possible approaches to develop 'resistance-resistant' antibiotics. First, multitarget inhibitors in which a single compound inhibits more than one target may be easier to develop than conventional combination therapies with two new drugs. Second, inhibiting multiple targets in the same metabolic pathway is expected to be an effective strategy owing to synergy. Third, discovering multiple-target inhibitors should be possible by using sequential virtual screening. Fourth, repurposing existing drugs can lead to combinations of multitarget therapeutics. Fifth, targets need not be proteins. Sixth, inhibiting virulence factor formation and boosting innate immunity may also lead to decreased susceptibility to resistance. Although it is not possible to eliminate resistance, the approaches reviewed here offer several possibilities for reducing the effects of mutations and, in some cases, suggest that sensitivity to existing antibiotics may be restored in otherwise drug-resistant organisms.
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41
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Silvers MA, Robertson GT, Taylor CM, Waldrop GL. Design, Synthesis, and Antibacterial Properties of Dual-Ligand Inhibitors of Acetyl-CoA Carboxylase. J Med Chem 2014; 57:8947-59. [DOI: 10.1021/jm501082n] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Molly A. Silvers
- Division
of Biochemistry and Molecular Biology, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Gregory T. Robertson
- Department
of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Carol M. Taylor
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Grover L. Waldrop
- Division
of Biochemistry and Molecular Biology, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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42
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Gopal P, Dick T. Reactive dirty fragments: implications for tuberculosis drug discovery. Curr Opin Microbiol 2014; 21:7-12. [DOI: 10.1016/j.mib.2014.06.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 06/19/2014] [Accepted: 06/29/2014] [Indexed: 01/01/2023]
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43
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Kouidmi I, Levesque RC, Paradis-Bleau C. The biology of Mur ligases as an antibacterial target. Mol Microbiol 2014; 94:242-53. [DOI: 10.1111/mmi.12758] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2014] [Indexed: 01/19/2023]
Affiliation(s)
- Imène Kouidmi
- Department of Microbiology, Infectiology and Immunology; Université de Montreal; Montreal Quebec Canada
| | - Roger C. Levesque
- Institut de biologie intégrative et des systèmes; Université Laval; Montreal Quebec Canada
| | - Catherine Paradis-Bleau
- Department of Microbiology, Infectiology and Immunology; Université de Montreal; Montreal Quebec Canada
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44
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Basarab GS, Hill PJ, Garner CE, Hull K, Green O, Sherer BA, Dangel PB, Manchester JI, Bist S, Hauck S, Zhou F, Uria-Nickelsen M, Illingworth R, Alm R, Rooney M, Eakin AE. Optimization of pyrrolamide topoisomerase II inhibitors toward identification of an antibacterial clinical candidate (AZD5099). J Med Chem 2014; 57:6060-82. [PMID: 24959892 DOI: 10.1021/jm500462x] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
AZD5099 (compound 63) is an antibacterial agent that entered phase 1 clinical trials targeting infections caused by Gram-positive and fastidious Gram-negative bacteria. It was derived from previously reported pyrrolamide antibacterials and a fragment-based approach targeting the ATP binding site of bacterial type II topoisomerases. The program described herein varied a 3-piperidine substituent and incorporated 4-thiazole substituents that form a seven-membered ring intramolecular hydrogen bond with a 5-position carboxylic acid. Improved antibacterial activity and lower in vivo clearances were achieved. The lower clearances were attributed, in part, to reduced recognition by the multidrug resistant transporter Mrp2. Compound 63 showed notable efficacy in a mouse neutropenic Staphylococcus aureus infection model. Resistance frequency versus the drug was low, and reports of clinical resistance due to alteration of the target are few. Hence, 63 could offer a novel treatment for serious issues of resistance to currently used antibacterials.
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Affiliation(s)
- Gregory S Basarab
- Infection Innovative Medicines, AstraZeneca R&D Boston , 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
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45
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Biological evaluation of benzothiazole ethyl urea inhibitors of bacterial type II topoisomerases. Antimicrob Agents Chemother 2013; 57:5977-86. [PMID: 24041906 DOI: 10.1128/aac.00719-13] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The type II topoisomerases DNA gyrase (GyrA/GyrB) and topoisomerase IV (ParC/ParE) are well-validated targets for antibacterial drug discovery. Because of their structural and functional homology, these enzymes are amenable to dual targeting by a single ligand. In this study, two novel benzothiazole ethyl urea-based small molecules, designated compound A and compound B, were evaluated for their biochemical, antibacterial, and pharmacokinetic properties. The two compounds inhibited the ATPase activity of GyrB and ParE with 50% inhibitory concentrations of <0.1 μg/ml. Prevention of DNA supercoiling by DNA gyrase was also observed. Both compounds potently inhibited the growth of a range of bacterial organisms, including staphylococci, streptococci, enterococci, Clostridium difficile, and selected Gram-negative respiratory pathogens. MIC90s against clinical isolates ranged from 0.015 μg/ml for Streptococcus pneumoniae to 0.25 μg/ml for Staphylococcus aureus. No cross-resistance with common drug resistance phenotypes was observed. In addition, no synergistic or antagonistic interactions between compound A or compound B and other antibiotics, including the topoisomerase inhibitors novobiocin and levofloxacin, were detected in checkerboard experiments. The frequencies of spontaneous resistance for S. aureus were <2.3 × 10(-10) with compound A and <5.8 × 10(-11) with compound B at concentrations equivalent to 8× the MICs. These values indicate a multitargeting mechanism of action. The pharmacokinetic properties of both compounds were profiled in rats. Following intravenous administration, compound B showed approximately 3-fold improvement over compound A in terms of both clearance and the area under the concentration-time curve. The measured oral bioavailability of compound B was 47.7%.
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46
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Surivet JP, Zumbrunn C, Rueedi G, Hubschwerlen C, Bur D, Bruyère T, Locher H, Ritz D, Keck W, Seiler P, Kohl C, Gauvin JC, Mirre A, Kaegi V, Dos Santos M, Gaertner M, Delers J, Enderlin-Paput M, Boehme M. Design, Synthesis, and Characterization of Novel Tetrahydropyran-Based Bacterial Topoisomerase Inhibitors with Potent Anti-Gram-Positive Activity. J Med Chem 2013; 56:7396-415. [DOI: 10.1021/jm400963y] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | - Cornelia Zumbrunn
- Actelion Pharmaceuticals Ltd, Gewerbestrasse
16, CH-4123 Allschwil, Switzerland
| | - Georg Rueedi
- Actelion Pharmaceuticals Ltd, Gewerbestrasse
16, CH-4123 Allschwil, Switzerland
| | | | - Daniel Bur
- Actelion Pharmaceuticals Ltd, Gewerbestrasse
16, CH-4123 Allschwil, Switzerland
| | - Thierry Bruyère
- Actelion Pharmaceuticals Ltd, Gewerbestrasse
16, CH-4123 Allschwil, Switzerland
| | - Hans Locher
- Actelion Pharmaceuticals Ltd, Gewerbestrasse
16, CH-4123 Allschwil, Switzerland
| | - Daniel Ritz
- Actelion Pharmaceuticals Ltd, Gewerbestrasse
16, CH-4123 Allschwil, Switzerland
| | - Wolfgang Keck
- Actelion Pharmaceuticals Ltd, Gewerbestrasse
16, CH-4123 Allschwil, Switzerland
| | - Peter Seiler
- Actelion Pharmaceuticals Ltd, Gewerbestrasse
16, CH-4123 Allschwil, Switzerland
| | - Christopher Kohl
- Actelion Pharmaceuticals Ltd, Gewerbestrasse
16, CH-4123 Allschwil, Switzerland
| | | | - Azely Mirre
- Actelion Pharmaceuticals Ltd, Gewerbestrasse
16, CH-4123 Allschwil, Switzerland
| | - Verena Kaegi
- Actelion Pharmaceuticals Ltd, Gewerbestrasse
16, CH-4123 Allschwil, Switzerland
| | - Marina Dos Santos
- Actelion Pharmaceuticals Ltd, Gewerbestrasse
16, CH-4123 Allschwil, Switzerland
| | - Mika Gaertner
- Actelion Pharmaceuticals Ltd, Gewerbestrasse
16, CH-4123 Allschwil, Switzerland
| | - Jonathan Delers
- Actelion Pharmaceuticals Ltd, Gewerbestrasse
16, CH-4123 Allschwil, Switzerland
| | | | - Maria Boehme
- Actelion Pharmaceuticals Ltd, Gewerbestrasse
16, CH-4123 Allschwil, Switzerland
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47
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Affiliation(s)
- Jens-Uwe Peters
- F. Hoffmann-La Roche Ltd., pRED, Pharma Research and Early Development, Discovery
Chemistry,
CH-4070 Basel, Switzerland
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48
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Abstract
The United States GAIN (Generating Antibiotic Incentives Now) Act is a call to action for new antibiotic discovery and development that arises from a ground swell of concern over declining activity in this therapeutic area in the pharmaceutical sector. The GAIN Act aims to provide economic incentives for antibiotic drug discovery in the form of market exclusivity and accelerated drug approval processes. The legislation comes on the heels of nearly two decades of failure using the tools of modern drug discovery to find new antibiotic drugs. The lessons of failure are examined herein as are the prospects for a renewed effort in antibiotic drug discovery and development stimulated by new investments in both the public and private sector.
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Affiliation(s)
- Eric D. Brown
- Department of Biochemistry and Biomedical Sciences, and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
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