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Wang L, Xie Z, Ruan W, Lan F, Qin Q, Tu Y, Zhu W, Zhao J, Zheng P. In silico method and bioactivity evaluation to discover novel antimicrobial agents targeting FtsZ protein: Machine learning, virtual screening and antibacterial mechanism study. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024:10.1007/s00210-024-03276-4. [PMID: 39043879 DOI: 10.1007/s00210-024-03276-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 07/02/2024] [Indexed: 07/25/2024]
Abstract
This research paper utilizes a fused-in-silico approach alongside bioactivity evaluation to identify active FtsZ inhibitors for drug discovery. Initially, ROC-guided machine learning was employed to obtain almost 13182 compounds from three libraries. After conducting virtual screening to assess the affinity of 2621 acquired compounds, cluster analysis and bonding model analysis led to the discovery of five hit compounds. Additionally, antibacterial activity assays and time-killing kinetics revealed that T3995 could eliminate Staphylococcus aureus ATCC6538 and Bacillus subtilis ATCC9732, with MIC values of 32 and 2 μg/mL. Further morphology and FtsZ polymerization assays indicated that T3995 could be an antimicrobial inhibitor by targeting FtsZ protein. Moreover, hemolytic toxicity evaluation demonstrated that T3995 is safe at or below 16 ug/mL concentration. Additionally, bonding model analysis explained how the compound T3995 can display antimicrobial activity by targeting the FtsZ protein. In conclusion, this study presents a promising FtsZ inhibitor that was discovered through a fused computer method and bioactivity evaluation.
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Affiliation(s)
- Linxiao Wang
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science &Technology, Normal University, Nanchang, 330013, China.
| | - Zhouling Xie
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science &Technology, Normal University, Nanchang, 330013, China
| | - Wei Ruan
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science &Technology, Normal University, Nanchang, 330013, China
| | - Feixiang Lan
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science &Technology, Normal University, Nanchang, 330013, China
| | - Qi Qin
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science &Technology, Normal University, Nanchang, 330013, China
| | - Yuanbiao Tu
- Cancer Research Center, Jiangxi University of Traditional Chinese Medicine, Nanchang, 330004, China
| | - Wufu Zhu
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science &Technology, Normal University, Nanchang, 330013, China
| | - Jing Zhao
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science &Technology, Normal University, Nanchang, 330013, China
| | - Pengwu Zheng
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science &Technology, Normal University, Nanchang, 330013, China.
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2
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Zhao X, Cao X, Qiu H, Liang W, Jiang Y, Wang Q, Wang W, Li C, Li Y, Han B, Tang K, Zhao L, Zhang X, Wang X, Liang H. Rational molecular design converting fascaplysin derivatives to potent broad-spectrum inhibitors against bacterial pathogens via targeting FtsZ. Eur J Med Chem 2024; 270:116347. [PMID: 38552428 DOI: 10.1016/j.ejmech.2024.116347] [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: 02/05/2024] [Revised: 03/06/2024] [Accepted: 03/17/2024] [Indexed: 04/21/2024]
Abstract
The filamentous temperature-sensitive mutant Z protein (FtsZ), a key player in bacterial cell division machinery, emerges as an attractive target to tackle the plight posed by the ever growing antibiotic resistance over the world. Therefore in this regard, agents with scaffold diversities and broad-spectrum antibacterial activity against Gram-positive and Gram-negative pathogens are highly needed. In this study, a new class of marine-derived fascaplysin derivatives has been designed and synthesized by Suzuki-Miyaura cross-coupling. Some compounds exhibited potent bactericidal activities against a panel of Gram-positive (MIC = 0.024-6.25 μg/mL) and Gram-negative (MIC = 1.56-12.5 μg/mL) bacteria including methicillin-resistant S. aureus (MRSA). They exerted their effects by dual action mechanism via disrupting the integrity of the bacterial cell membrane and targeting FtsZ protein. These compounds stimulated polymerization of FtsZ monomers and bundling of the polymers, and stabilized the resulting polymer network, thus leading to the dysfunction of FtsZ in cell division. In addition, these agents showed negligible hemolytic activity and low cytotoxicity to mammalian cells. The studies on docking and molecular dynamics simulations suggest that these inhibitors bind to the hydrophilic inter-domain cleft of FtsZ protein and the insights obtained in this study would facilitate the development of potential drugs with broad-spectrum bioactivities.
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Affiliation(s)
- Xing Zhao
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China; Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Xuanyu Cao
- Health Science Center, Ningbo University, Ningbo, 315211, China; Institute of Drug Discovery Technology, Ningbo University, Ningbo, 315211, China
| | - Hongda Qiu
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China
| | - Weida Liang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China
| | - Yinli Jiang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China
| | - Qiang Wang
- Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Weile Wang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China
| | - Chengxi Li
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China
| | - Yang Li
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, 315211, China
| | - Bowen Han
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, 315211, China
| | - Keqi Tang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China
| | - Lingling Zhao
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China
| | - Xuan Zhang
- Health Science Center, Ningbo University, Ningbo, 315211, China; Institute of Drug Discovery Technology, Ningbo University, Ningbo, 315211, China.
| | - Xiao Wang
- Health Science Center, Ningbo University, Ningbo, 315211, China.
| | - Hongze Liang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China.
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Xie Z, Ruan W, Guo J, Li Y, Zhou S, Zhao J, Wan L, Xu S, Tang Q, Zheng P, Wang L, Zhu W. T5S1607 identified as a antibacterial FtsZ inhibitor:Virtual screening combined with bioactivity evaluation for the drug discovery. Comput Biol Chem 2024; 108:108006. [PMID: 38142532 DOI: 10.1016/j.compbiolchem.2023.108006] [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: 09/28/2023] [Revised: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 12/26/2023]
Abstract
Due to antibiotic overuse, many bacteria have developed resistance, creating an urgent need for novel antimicrobial agents. It has been established that the filamentous temperature-sensitive mutant Z (FtsZ) of the bacterial cell division protein is an effective and promising antibacterial target. In this study, the optimal proteins were assessed by early recognition ability and the processed compound libraries were virtually screened using Vina. This effort resulted in the identification of 14 potentially active antimicrobial compounds. Among them, the compound T5S1607 demonstrated remarkable antibacterial efficacy against Bacillus subtilis ATCC9732 (MIC = 1 μg/mL) and Staphylococcus aureus ATC5C6538 (MIC = 4 μg/mL). Furthermore, in vitro experiments demonstrated that the selected compound T5S1607 rapidly killed bacteria and induced FtsZ protein aggregation, preventing bacterial division and leading to bacterial death. Additionally, cell toxicity and hemolysis experiments indicate that compound T5S1607 exhibits minimal toxicity to LO2 cells and shows no significant hemolytic effects on mammalian cells in vitro at the MIC concentration range. All the results indicate that compound T5S1607 is a promising antibacterial agent and a potential FtsZ inhibitor. In conclusion, this work successfully discovered FtsZ inhibitors with good activity through the virtual screening drug discovery process.
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Affiliation(s)
- Zhouling Xie
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi 330013, China
| | - Wei Ruan
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi 330013, China
| | - Jiaojiao Guo
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi 330013, China
| | - Yan Li
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi 330013, China
| | - Siqi Zhou
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi 330013, China
| | - Jing Zhao
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi 330013, China
| | - Li Wan
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi 330013, China
| | - Shan Xu
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi 330013, China
| | - Qidong Tang
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi 330013, China
| | - Pengwu Zheng
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi 330013, China
| | - Linxiao Wang
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi 330013, China.
| | - Wufu Zhu
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi 330013, China.
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Ruggieri F, Compagne N, Antraygues K, Eveque M, Flipo M, Willand N. Antibiotics with novel mode of action as new weapons to fight antimicrobial resistance. Eur J Med Chem 2023; 256:115413. [PMID: 37150058 DOI: 10.1016/j.ejmech.2023.115413] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/09/2023] [Accepted: 04/22/2023] [Indexed: 05/09/2023]
Abstract
Antimicrobial resistance (AMR) is a major public health issue, causing 5 million deaths per year. Without any action plan, AMR will be in a near future the leading cause of death ahead of cancer. AMR comes from the ability of bacteria to rapidly develop and share resistance mechanisms towards current antibiotics, rendering them less effective. To circumvent this issue and avoid the phenomenon of cross-resistance, new antibiotics acting on novel targets or with new modes of action are required. Today, the pipeline of potential new treatments with these characteristics includes promising compounds such as gepotidacin, zoliflodacin, ibezapolstat, MGB-BP-3, CRS-3123, afabicin and TXA-709, which are currently in clinical trials, and lefamulin, which has been recently approved by FDA and EMA. In this review, we report the chemical synthesis, mode of action, structure-activity relationships, in vitro and in vivo activities as well as clinical data of these eight small molecules listed above.
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Affiliation(s)
- Francesca Ruggieri
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Nina Compagne
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Kevin Antraygues
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Maxime Eveque
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Marion Flipo
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Nicolas Willand
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000, Lille, France.
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5
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Importance of the 2,6-Difluorobenzamide Motif for FtsZ Allosteric Inhibition: Insights from Conformational Analysis, Molecular Docking and Structural Modifications. Molecules 2023; 28:molecules28052055. [PMID: 36903302 PMCID: PMC10003973 DOI: 10.3390/molecules28052055] [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: 01/31/2023] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 02/25/2023] Open
Abstract
A conformational analysis and molecular docking study comparing 2,6-difluoro-3-methoxybenzamide (DFMBA) with 3-methoxybenzamide (3-MBA) has been undertaken for investigating the known increase of FtsZ inhibition related anti S. aureus activity due to fluorination. For the isolated molecules, the calculations reveal that the presence of the fluorine atoms in DFMBA is responsible for its non-planarity, with a dihedral angle of -27° between the carboxamide and the aromatic ring. When interacting with the protein, the fluorinated ligand can thus more easily adopt the non-planar conformation found in reported co-crystallized complexes with FtsZ, than the non-fluorinated one. Molecular docking studies of the favored non-planar conformation of 2,6-difluoro-3-methoxybenzamide highlights the strong hydrophobic interactions between the difluoroaromatic ring and several key residues of the allosteric pocket, precisely between the 2-fluoro substituent and residues Val203 and Val297 and between the 6-fluoro group and the residues Asn263. The docking simulation in the allosteric binding site also confirms the critical importance of the hydrogen bonds between the carboxamide group with the residues Val207, Leu209 and Asn263. Changing the carboxamide functional group of 3-alkyloxybenzamide and 3-alkyloxy-2,6-difluorobenzamide to a benzohydroxamic acid or benzohydrazide led to inactive compounds, confirming the importance of the carboxamide group.
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Deng J, Zhang T, Li B, Xu M, Wang Y. Design, synthesis and biological evaluation of biphenyl-benzamides as potent FtsZ inhibitors. Eur J Med Chem 2022; 239:114553. [PMID: 35763867 DOI: 10.1016/j.ejmech.2022.114553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 06/14/2022] [Accepted: 06/16/2022] [Indexed: 11/04/2022]
Abstract
The rapid emergence of antibiotic resistance has become a prevalent threat to public health, thereby development of new antibacterial agents having novel mechanisms of action is in an urgent need. Targeting at the cytoskeletal cell division protein filamenting temperature-sensitive mutant Z (FtsZ) has been validated as an effective and promising approach for antibacterial drug discovery. In this study, a series of novel biphenyl-benzamides as FtsZ inhibitors has been rationally designed, synthesized and evaluated for their antibacterial activities against various Gram-positive bacteria strains. In particular, the most promising compound 30 exhibited excellent antibacterial activities, especially against four different Bacillus subtilis strains, with an MIC range of 0.008 μg/mL to 0.063 μg/mL. Moreover, compound 30 also showed good pharmaceutical properties with low cytotoxicity (CC50 > 20 μg/mL), excellent human metabolic stability (T1/2 = 111.98 min), moderate pharmacokinetics (T1/2 = 2.26 h, F = 61.2%) and in vivo efficacy, which can be identified as a promising FtsZ inhibitor worthy of further profiling.
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Affiliation(s)
- Jingjing Deng
- Department of Molecular Genetics, University of Groningen, Groningen, Netherlands
| | - Tao Zhang
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health - Guangdong Laboratory),Guangzhou, 510530, PR China
| | - Baiqing Li
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health - Guangdong Laboratory),Guangzhou, 510530, PR China
| | - Mingyuan Xu
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health - Guangdong Laboratory),Guangzhou, 510530, PR China
| | - Yuanze Wang
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health - Guangdong Laboratory),Guangzhou, 510530, PR China.
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Gurnani M, Chauhan A, Ranjan A, Tuli HS, Alkhanani MF, Haque S, Dhama K, Lal R, Jindal T. Filamentous Thermosensitive Mutant Z: An Appealing Target for Emerging Pathogens and a Trek on Its Natural Inhibitors. BIOLOGY 2022; 11:624. [PMID: 35625352 PMCID: PMC9138142 DOI: 10.3390/biology11050624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/18/2022] [Accepted: 04/01/2022] [Indexed: 12/14/2022]
Abstract
Antibiotic resistance is a major emerging issue in the health care sector, as highlighted by the WHO. Filamentous Thermosensitive mutant Z (Fts-Z) is gaining significant attention in the scientific community as a potential anti-bacterial target for fighting antibiotic resistance among several pathogenic bacteria. The Fts-Z plays a key role in bacterial cell division by allowing Z ring formation. Several in vitro and in silico experiments have demonstrated that inhibition of Fts-Z can lead to filamentous growth of the cells, and finally, cell death occurs. Many natural compounds that have successfully inhibited Fts-Z are also studied. This review article intended to highlight the structural-functional aspect of Fts-Z that leads to Z-ring formation and its contribution to the biochemistry and physiology of cells. The current trend of natural inhibitors of Fts-Z protein is also covered.
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Affiliation(s)
- Manisha Gurnani
- Amity Institute of Environmental Science, Amity University, Noida 201301, India;
| | - Abhishek Chauhan
- Amity Institute of Environmental Toxicology, Safety and Management, Amity University, Noida 201303, India;
| | - Anuj Ranjan
- Academy of Biology and Biotechnology, Southern Federal University, 344006 Rostov-on-Don, Russia
| | - Hardeep Singh Tuli
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Ambala 133207, India;
| | - Mustfa F. Alkhanani
- Emergency Service Department, College of Applied Sciences, AlMaarefa University, Riyadh 11597, Saudi Arabia;
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan 45142, Saudi Arabia;
- Faculty of Medicine, Görükle Campus, Bursa Uludağ University, Nilüfer, Bursa 16059, Turkey
| | - Kuldeep Dhama
- Division of Pathology, ICAR—Indian Veterinary Research Institute, Bareilly 243122, India;
| | - Rup Lal
- Department of Zoology, University of Delhi, Delhi 110021, India;
| | - Tanu Jindal
- Amity Institute of Environmental Toxicology, Safety and Management, Amity University, Noida 201303, India;
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Ihsan A, Khera RA, Iqbal J, Asgher M. Binding interaction of benzamide derivatives as inhibitors of DNA gyrase and Sec14p using Molegro Virtual Docker based on binding free energy. Z PHYS CHEM 2022. [DOI: 10.1515/zpch-2021-3119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The docking simulation of benzamide derivatives as ligands and protein targets (DNA–gyrase) was performed and Sec14p binding mode interaction was predicted based on binding free energy analysis. Software Molegro Virtual Docking (MVD) was used to visualize the ligand–protein binding interactions. The results indicated the prevalence of steric or hydrophobic interactions among all the benzamide ligands besides hydrogen bonding or electrostatic interactions. The compounds B2, B4 against DNA gyrase, and compounds B3, B5 against Sec14p showed an uncompetitive pattern of inhibition as compared with the reference molecule. While compounds B1, B5 exhibited the best MolDock scores, i.e., −109.736 and −114.391 kcal/mol respectively for DNA gyrase, also compounds B1 and B2 against Sec14p displayed −100.105 and −119.451 kcal/mol sequentially. It was evident from the comparison of MolDock score for both the bacterial and fungal protein receptors that all the ligands were found to be more potent against DNA gyrase than Sec14p. However, only compound B2 with MolDock score −119.451 kcal/mol showed exceptional activity against Sec14p and was predicted to have potency as a lead compound to find a new anti-fungal therapeutic agent. Docking studies further highlighted the unique interactions such as tail-end hydrophobic rings of benzamide inhibitors with catalytically important amino acid residues, allowing flexibility in binding to both the receptors different from other inhibitors. These findings showed us that B1, B2 against Staphylococcus aureus and B5 against Saccharomyces cerevisiae could be leading compounds to discover new multidrug-resistant strains.
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Affiliation(s)
- Anaum Ihsan
- Department of Chemistry , University of Agriculture , Faisalabad , 38000 , Pakistan
| | - Rasheed Ahmad Khera
- Department of Chemistry , University of Agriculture , Faisalabad , 38000 , Pakistan
| | - Javed Iqbal
- Department of Chemistry , University of Agriculture , Faisalabad , 38000 , Pakistan
| | - Muhammad Asgher
- Department of Biochemistry , University of Agriculture , Faisalabad , 38000 , Pakistan
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Milani G, Cavalluzzi MM, Solidoro R, Salvagno L, Quintieri L, Di Somma A, Rosato A, Corbo F, Franchini C, Duilio A, Caputo L, Habtemariam S, Lentini G. Molecular Simplification of Natural Products: Synthesis, Antibacterial Activity, and Molecular Docking Studies of Berberine Open Models. Biomedicines 2021; 9:452. [PMID: 33922200 PMCID: PMC8146520 DOI: 10.3390/biomedicines9050452] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 02/08/2023] Open
Abstract
Berberine, the main bioactive component of many medicinal plants belonging to various genera such as Berberis, Coptis, and Hydrastis is a multifunctional compound. Among the numerous interesting biological properties of berberine is broad antimicrobial activity including a range of Gram-positive and Gram-negative bacteria. With the aim of identifying berberine analogues possibly endowed with higher lead-likeness and easier synthetic access, the molecular simplification approach was applied to the secondary metabolite and a series of analogues were prepared and screened for their antimicrobial activity against Gram-positive and Gram-negative bacterial test species. Rewardingly, the berberine simplified analogues displayed 2-20-fold higher potency with respect to berberine. Since our berberine simplified analogues may be easily synthesized and are characterized by lower molecular weight than the parent compound, they are further functionalizable and should be more suitable for oral administration. Molecular docking simulations suggested FtsZ, a well-known protein involved in bacterial cell division, as a possible target.
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Affiliation(s)
- Gualtiero Milani
- Department of Pharmacy–Pharmaceutical Sciences, University of Bari Aldo Moro, via E. Orabona n. 4, 70126 Bari, Italy; (G.M.); (R.S.); (L.S.); (A.R.); (F.C.); (C.F.); (G.L.)
| | - Maria Maddalena Cavalluzzi
- Department of Pharmacy–Pharmaceutical Sciences, University of Bari Aldo Moro, via E. Orabona n. 4, 70126 Bari, Italy; (G.M.); (R.S.); (L.S.); (A.R.); (F.C.); (C.F.); (G.L.)
| | - Roberta Solidoro
- Department of Pharmacy–Pharmaceutical Sciences, University of Bari Aldo Moro, via E. Orabona n. 4, 70126 Bari, Italy; (G.M.); (R.S.); (L.S.); (A.R.); (F.C.); (C.F.); (G.L.)
| | - Lara Salvagno
- Department of Pharmacy–Pharmaceutical Sciences, University of Bari Aldo Moro, via E. Orabona n. 4, 70126 Bari, Italy; (G.M.); (R.S.); (L.S.); (A.R.); (F.C.); (C.F.); (G.L.)
| | - Laura Quintieri
- Institute of Sciences of Food Production (CNR-ISPA) National Council of Research, Via G. Amendola, 122/O, 70126 Bari, Italy; (L.Q.); (L.C.)
| | - Angela Di Somma
- Department of Chemical Sciences, University of Naples “Federico II” Via Cinthia 4, 80126 Napoli, Italy; (A.D.S.); (A.D.)
| | - Antonio Rosato
- Department of Pharmacy–Pharmaceutical Sciences, University of Bari Aldo Moro, via E. Orabona n. 4, 70126 Bari, Italy; (G.M.); (R.S.); (L.S.); (A.R.); (F.C.); (C.F.); (G.L.)
| | - Filomena Corbo
- Department of Pharmacy–Pharmaceutical Sciences, University of Bari Aldo Moro, via E. Orabona n. 4, 70126 Bari, Italy; (G.M.); (R.S.); (L.S.); (A.R.); (F.C.); (C.F.); (G.L.)
| | - Carlo Franchini
- Department of Pharmacy–Pharmaceutical Sciences, University of Bari Aldo Moro, via E. Orabona n. 4, 70126 Bari, Italy; (G.M.); (R.S.); (L.S.); (A.R.); (F.C.); (C.F.); (G.L.)
| | - Angela Duilio
- Department of Chemical Sciences, University of Naples “Federico II” Via Cinthia 4, 80126 Napoli, Italy; (A.D.S.); (A.D.)
| | - Leonardo Caputo
- Institute of Sciences of Food Production (CNR-ISPA) National Council of Research, Via G. Amendola, 122/O, 70126 Bari, Italy; (L.Q.); (L.C.)
| | - Solomon Habtemariam
- Pharmacognosy Research Laboratories & Herbal Analysis Services, University of Greenwich, Chatham-Maritime, Kent ME4 4TB, UK;
| | - Giovanni Lentini
- Department of Pharmacy–Pharmaceutical Sciences, University of Bari Aldo Moro, via E. Orabona n. 4, 70126 Bari, Italy; (G.M.); (R.S.); (L.S.); (A.R.); (F.C.); (C.F.); (G.L.)
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10
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Comparison of Proteomic Responses as Global Approach to Antibiotic Mechanism of Action Elucidation. Antimicrob Agents Chemother 2020; 65:AAC.01373-20. [PMID: 33046497 PMCID: PMC7927858 DOI: 10.1128/aac.01373-20] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/25/2020] [Indexed: 12/21/2022] Open
Abstract
New antibiotics are urgently needed to address the mounting resistance challenge. In early drug discovery, one of the bottlenecks is the elucidation of targets and mechanisms. To accelerate antibiotic research, we provide a proteomic approach for the rapid classification of compounds into those with precedented and unprecedented modes of action. We established a proteomic response library of Bacillus subtilis covering 91 antibiotics and comparator compounds, and a mathematical approach was developed to aid data analysis. New antibiotics are urgently needed to address the mounting resistance challenge. In early drug discovery, one of the bottlenecks is the elucidation of targets and mechanisms. To accelerate antibiotic research, we provide a proteomic approach for the rapid classification of compounds into those with precedented and unprecedented modes of action. We established a proteomic response library of Bacillus subtilis covering 91 antibiotics and comparator compounds, and a mathematical approach was developed to aid data analysis. Comparison of proteomic responses (CoPR) allows the rapid identification of antibiotics with dual mechanisms of action as shown for atypical tetracyclines. It also aids in generating hypotheses on mechanisms of action as presented for salvarsan (arsphenamine) and the antirheumatic agent auranofin, which is under consideration for repurposing. Proteomic profiling also provides insights into the impact of antibiotics on bacterial physiology through analysis of marker proteins indicative of the impairment of cellular processes and structures. As demonstrated for trans-translation, a promising target not yet exploited clinically, proteomic profiling supports chemical biology approaches to investigating bacterial physiology.
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Chai WC, Whittall JJ, Song D, Polyak SW, Ogunniyi AD, Wang Y, Bi F, Ma S, Semple SJ, Venter H. Antimicrobial Action and Reversal of Resistance in MRSA by Difluorobenzamide Derivatives Targeted at FtsZ. Antibiotics (Basel) 2020; 9:E873. [PMID: 33291418 PMCID: PMC7762090 DOI: 10.3390/antibiotics9120873] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/26/2020] [Accepted: 11/28/2020] [Indexed: 01/21/2023] Open
Abstract
The bacterial cell division protein, FtsZ, has been identified as a target for antimicrobial development. Derivatives of 3-methoxybenzamide have shown promising activities as FtsZ inhibitors in Gram-positive bacteria. We sought to characterise the activity of five difluorobenzamide derivatives with non-heterocyclic substituents attached through the 3-oxygen. These compounds exhibited antimicrobial activity against methicillin resistant Staphylococcus aureus (MRSA), with an isopentyloxy-substituted compound showing modest activity against vancomycin resistant Enterococcus faecium (VRE). The compounds were able to reverse resistance to oxacillin in highly resistant clinical MRSA strains at concentrations far below their MICs. Three of the compounds inhibited an Escherichia coli strain lacking the AcrAB components of a drug efflux pump, which suggests the lack of Gram-negative activity can partly be attributed to efflux. The compounds inhibited cell division by targeting S. aureus FtsZ, producing a dose-dependent increase in GTPase rate which increased the rate of FtsZ polymerization and stabilized the FtsZ polymers. These compounds did not affect the polymerization of mammalian tubulin and did not display haemolytic activity or cytotoxicity. These derivatives are therefore promising compounds for further development as antimicrobial agents or as resistance breakers to re-sensitive MRSA to beta-lactam antibiotics.
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Affiliation(s)
- Wern Chern Chai
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, SA 5000 Adelaide, Australia; (W.C.C.); (J.J.W.); (S.W.P.); (S.J.S.)
| | - Jonathan J. Whittall
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, SA 5000 Adelaide, Australia; (W.C.C.); (J.J.W.); (S.W.P.); (S.J.S.)
| | - Di Song
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China; (D.S.); (Y.W.); (F.B.); (S.M.)
| | - Steven W. Polyak
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, SA 5000 Adelaide, Australia; (W.C.C.); (J.J.W.); (S.W.P.); (S.J.S.)
| | - Abiodun D. Ogunniyi
- Australia Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy Campus, SA 5371 Roseworthy, Australia;
| | - Yinhu Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China; (D.S.); (Y.W.); (F.B.); (S.M.)
- School of Pharmacy, Liaocheng University, Liaocheng 252000, China
| | - Fangchao Bi
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China; (D.S.); (Y.W.); (F.B.); (S.M.)
| | - Shutao Ma
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China; (D.S.); (Y.W.); (F.B.); (S.M.)
| | - Susan J. Semple
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, SA 5000 Adelaide, Australia; (W.C.C.); (J.J.W.); (S.W.P.); (S.J.S.)
- Quality Use of Medicines and Pharmacy Research Centre, Clinical and Health Sciences, University of South Australia, SA 5000 Adelaide, Australia
| | - Henrietta Venter
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, SA 5000 Adelaide, Australia; (W.C.C.); (J.J.W.); (S.W.P.); (S.J.S.)
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12
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Silber N, Matos de Opitz CL, Mayer C, Sass P. Cell division protein FtsZ: from structure and mechanism to antibiotic target. Future Microbiol 2020; 15:801-831. [DOI: 10.2217/fmb-2019-0348] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Antimicrobial resistance to virtually all clinically applied antibiotic classes severely limits the available options to treat bacterial infections. Hence, there is an urgent need to develop and evaluate new antibiotics and targets with resistance-breaking properties. Bacterial cell division has emerged as a new antibiotic target pathway to counteract multidrug-resistant pathogens. New approaches in antibiotic discovery and bacterial cell biology helped to identify compounds that either directly interact with the major cell division protein FtsZ, thereby perturbing the function and dynamics of the cell division machinery, or affect the structural integrity of FtsZ by inducing its degradation. The impressive antimicrobial activities and resistance-breaking properties of certain compounds validate the inhibition of bacterial cell division as a promising strategy for antibiotic intervention.
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Affiliation(s)
- Nadine Silber
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology & Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, Tübingen 72076, Germany
| | - Cruz L Matos de Opitz
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology & Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, Tübingen 72076, Germany
| | - Christian Mayer
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology & Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, Tübingen 72076, Germany
| | - Peter Sass
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology & Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, Tübingen 72076, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen 72076, Germany
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13
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Straniero V, Suigo L, Casiraghi A, Sebastián-Pérez V, Hrast M, Zanotto C, Zdovc I, De Giuli Morghen C, Radaelli A, Valoti E. Benzamide Derivatives Targeting the Cell Division Protein FtsZ: Modifications of the Linker and the Benzodioxane Scaffold and Their Effects on Antimicrobial Activity. Antibiotics (Basel) 2020; 9:antibiotics9040160. [PMID: 32260339 PMCID: PMC7235863 DOI: 10.3390/antibiotics9040160] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 01/21/2023] Open
Abstract
Filamentous temperature-sensitive Z (FtsZ) is a prokaryotic protein with an essential role in the bacterial cell division process. It is widely conserved and expressed in both Gram-positive and Gram-negative strains. In the last decade, several research groups have pointed out molecules able to target FtsZ in Staphylococcus aureus, Bacillus subtilis and other Gram-positive strains, with sub-micromolar Minimum Inhibitory Concentrations (MICs). Conversely, no promising derivatives active on Gram-negatives have been found up to now. Here, we report our results on a class of benzamide compounds, which showed comparable inhibitory activities on both S. aureus and Escherichia coli FtsZ, even though they proved to be substrates of E. coli efflux pump AcrAB, thus affecting the antimicrobial activity. These surprising results confirmed how a single molecule can target both species while maintaining potent antimicrobial activity. A further computational study helped us decipher the structural features necessary for broad spectrum activity and assess the drug-like profile and the on-target activity of this family of compounds.
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Affiliation(s)
- Valentina Straniero
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Luigi Mangiagalli, 25, 20133 Milano, Italy; (L.S.); (A.C.)
- Correspondence: (V.S.); (E.V.); Tel.: +39-0250319361 (V.S.); +39-0250319334 (E.V.)
| | - Lorenzo Suigo
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Luigi Mangiagalli, 25, 20133 Milano, Italy; (L.S.); (A.C.)
| | - Andrea Casiraghi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Luigi Mangiagalli, 25, 20133 Milano, Italy; (L.S.); (A.C.)
| | - Victor Sebastián-Pérez
- Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain;
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, UK
| | - Martina Hrast
- Pharmacy Faculty, University of Ljubljana, Aškerčeva cesta, 7, 1000 Ljubljana, Slovenia;
| | - Carlo Zanotto
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via Vanvitelli, 32, 20129 Milano, Italy; (C.Z.); (A.R.)
| | - Irena Zdovc
- Veterinary Faculty, University of Ljubljana, Gerbičeva, 60, 1000 Ljubljana, Slovenia;
| | - Carlo De Giuli Morghen
- Department of Chemical – Pharmaceutical and Biomolecular Technologies, Catholic University “Our Lady of Good Counsel”, Rr. Dritan Hoxha, 1025 Tirana, Albania;
| | - Antonia Radaelli
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via Vanvitelli, 32, 20129 Milano, Italy; (C.Z.); (A.R.)
| | - Ermanno Valoti
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Luigi Mangiagalli, 25, 20133 Milano, Italy; (L.S.); (A.C.)
- Correspondence: (V.S.); (E.V.); Tel.: +39-0250319361 (V.S.); +39-0250319334 (E.V.)
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15
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Casiraghi A, Suigo L, Valoti E, Straniero V. Targeting Bacterial Cell Division: A Binding Site-Centered Approach to the Most Promising Inhibitors of the Essential Protein FtsZ. Antibiotics (Basel) 2020; 9:E69. [PMID: 32046082 PMCID: PMC7167804 DOI: 10.3390/antibiotics9020069] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/31/2020] [Accepted: 01/31/2020] [Indexed: 11/16/2022] Open
Abstract
Binary fission is the most common mode of bacterial cell division and is mediated by a multiprotein complex denominated the divisome. The constriction of the Z-ring splits the mother bacterial cell into two daughter cells of the same size. The Z-ring is formed by the polymerization of FtsZ, a bacterial protein homologue of eukaryotic tubulin, and it represents the first step of bacterial cytokinesis. The high grade of conservation of FtsZ in most prokaryotic organisms and its relevance in orchestrating the whole division system make this protein a fascinating target in antibiotic research. Indeed, FtsZ inhibition results in the complete blockage of the division system and, consequently, in a bacteriostatic or a bactericidal effect. Since many papers and reviews already discussed the physiology of FtsZ and its auxiliary proteins, as well as the molecular mechanisms in which they are involved, here, we focus on the discussion of the most compelling FtsZ inhibitors, classified by their main protein binding sites and following a medicinal chemistry approach.
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Affiliation(s)
| | | | | | - Valentina Straniero
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via Luigi Mangiagalli, 25, 20133 Milano, Italy; (A.C.); (L.S.); (E.V.)
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16
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Kadari L, Erb W, Roisnel T, Radha Krishna P, Mongin F. Iodoferrocene as a partner in N-arylation of amides. NEW J CHEM 2020. [DOI: 10.1039/d0nj03470c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A general copper-promoted amidation of iodoferrocene is described toward original scaffolds that can be further functionalized by cross-coupling reactions.
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Affiliation(s)
- Lingaswamy Kadari
- Univ Rennes
- CNRS
- ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226
- F-35000 Rennes
- France
| | - William Erb
- Univ Rennes
- CNRS
- ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226
- F-35000 Rennes
- France
| | - Thierry Roisnel
- Univ Rennes
- CNRS
- ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226
- F-35000 Rennes
- France
| | - Palakodety Radha Krishna
- Organic Synthesis and Process Chemistry Division
- CSIR-Indian Institute of Chemical Technology
- Hyderabad
- India
| | - Florence Mongin
- Univ Rennes
- CNRS
- ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226
- F-35000 Rennes
- France
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17
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Straniero V, Sebastián-Pérez V, Hrast M, Zanotto C, Casiraghi A, Suigo L, Zdovc I, Radaelli A, De Giuli Morghen C, Valoti E. Benzodioxane-Benzamides as Antibacterial Agents: Computational and SAR Studies to Evaluate the Influence of the 7-Substitution in FtsZ Interaction. ChemMedChem 2019; 15:195-209. [PMID: 31750973 DOI: 10.1002/cmdc.201900537] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/08/2019] [Indexed: 01/24/2023]
Abstract
FtsZ is a crucial prokaryotic protein involved in bacterial cell replication. It recently arose as a promising target in the search for antimicrobial agents able to fight antimicrobial resistance. In this work, going on with our structure-activity relationship (SAR) study, we developed variously 7-substituted 1,4-benzodioxane compounds, linked to the 2,6-difluorobenzamide by a methylenoxy bridge. Compounds exhibit promising antibacterial activities not only against multidrug-resistant Staphylococcus aureus, but also on mutated Escherichia coli strains, thus enlarging their spectrum of action toward Gram-negative bacteria as well. Computational studies elucidated, through a validated FtsZ binding protocol, the structural features of new promising derivatives as FtsZ inhibitors.
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Affiliation(s)
- Valentina Straniero
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Luigi Mangiagalli 25, 20133, Milano, Italy
| | | | - Martina Hrast
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Carlo Zanotto
- Department of Medical Biotechnologies and Translational Medicine, Università degli Studi di Milano, Via Vanvitelli 32, 20129, Milano, Italy
| | - Andrea Casiraghi
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Luigi Mangiagalli 25, 20133, Milano, Italy
| | - Lorenzo Suigo
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Luigi Mangiagalli 25, 20133, Milano, Italy
| | - Irena Zdovc
- Faculty of Veterinary Medicine, University of Ljubljana, Gerbičeva 60, 1000, Ljubljana, Slovenia
| | - Antonia Radaelli
- Department of Medical Biotechnologies and Translational Medicine, Università degli Studi di Milano, Via Vanvitelli 32, 20129, Milano, Italy
| | | | - Ermanno Valoti
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Luigi Mangiagalli 25, 20133, Milano, Italy
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18
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Carro L. Recent Progress in the Development of Small-Molecule FtsZ Inhibitors as Chemical Tools for the Development of Novel Antibiotics. Antibiotics (Basel) 2019; 8:E217. [PMID: 31717975 PMCID: PMC6963470 DOI: 10.3390/antibiotics8040217] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/26/2019] [Accepted: 11/05/2019] [Indexed: 01/20/2023] Open
Abstract
Antibiotics are potent pharmacological weapons against bacterial pathogens, nevertheless their efficacy is becoming compromised due to the worldwide emergence and spread of multidrug-resistant bacteria or "superbugs". Antibiotic resistance is rising to such dangerous levels that the treatment of bacterial infections is becoming a clinical challenge. Therefore, urgent action is needed to develop new generations of antibiotics that will help tackle this increasing and serious public health problem. Due to its essential role in bacterial cell division, the tubulin-like protein FtsZ has emerged as a promising target for the development of novel antibiotics with new mechanisms of action. This review highlights the medicinal chemistry efforts towards the identification of small-molecule FtsZ inhibitors with antibacterial activity in the last three years.
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Affiliation(s)
- Laura Carro
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain;
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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19
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FtsZ inhibitors as a new genera of antibacterial agents. Bioorg Chem 2019; 91:103169. [PMID: 31398602 DOI: 10.1016/j.bioorg.2019.103169] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 07/28/2019] [Accepted: 07/29/2019] [Indexed: 11/21/2022]
Abstract
The continuous emergence and rapid spread of a multidrug-resistant strain of bacterial pathogens have demanded the discovery and development of new antibacterial agents. A highly conserved prokaryotic cell division protein FtsZ is considered as a promising target by inhibiting bacterial cytokinesis. Inhibition of FtsZ assembly restrains the cell-division complex known as divisome, which results in filamentation, leading to lysis of the cell. This review focuses on details relating to the structure, function, and influence of FtsZ in bacterial cytokinesis. It also summarizes on the recent perspective of the known natural and synthetic inhibitors directly acting on FtsZ protein, with prominent antibacterial activities. A series of benzamides, trisubstituted benzimidazoles, isoquinolene, guanine nucleotides, zantrins, carbonylpyridine, 4 and 5-Substituted 1-phenyl naphthalenes, sulindac, vanillin analogues were studied here and recognized as FtsZ inhibitors that act either by disturbing FtsZ polymerization and/or GTPase activity. Doxorubicin, from a U.S. FDA, approved drug library displayed strong interaction with FtsZ. Several of the molecules discussed, include the prodrugs of benzamide based compound PC190723 (TXA-709 and TXA707). These molecules have exhibited the most prominent antibacterial activity against several strains of Staphylococcus aureus with minimal toxicity and good pharmacokinetics properties. The evidence of research reports and patent documentations on FtsZ protein has disclosed distinct support in the field of antibacterial drug discovery. The pressing need and interest shall facilitate the discovery of novel clinical molecules targeting FtsZ in the upcoming days.
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20
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Discovery of 1,3,4-oxadiazol-2-one-containing benzamide derivatives targeting FtsZ as highly potent agents of killing a variety of MDR bacteria strains. Bioorg Med Chem 2019; 27:3179-3193. [DOI: 10.1016/j.bmc.2019.06.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/29/2019] [Accepted: 06/05/2019] [Indexed: 11/24/2022]
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21
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Lui HK, Gao W, Cheung KC, Jin WB, Sun N, Kan JW, Wong IL, Chiou J, Lin D, Chan EW, Leung YC, Chan TH, Chen S, Chan KF, Wong KY. Boosting the efficacy of anti-MRSA β-lactam antibiotics via an easily accessible, non-cytotoxic and orally bioavailable FtsZ inhibitor. Eur J Med Chem 2019; 163:95-115. [DOI: 10.1016/j.ejmech.2018.11.052] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/05/2018] [Accepted: 11/21/2018] [Indexed: 11/30/2022]
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Abstract
Ligand efficiency is a widely used design parameter in drug discovery. It is calculated by scaling affinity by molecular size and has a nontrivial dependency on the concentration unit used to express affinity that stems from the inability of the logarithm function to take dimensioned arguments. Consequently, perception of efficiency varies with the choice of concentration unit and it is argued that the ligand efficiency metric is not physically meaningful nor should it be considered to be a metric. The dependence of ligand efficiency on the concentration unit can be eliminated by defining efficiency in terms of sensitivity of affinity to molecular size and this is illustrated with reference to fragment-to-lead optimizations. Group efficiency and fit quality are also examined in detail from a physicochemical perspective. The importance of examining relationships between affinity and molecular size directly is stressed throughout this study and an alternative to ligand efficiency for normalization of affinity with respect to molecular size is presented.![]()
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Affiliation(s)
- Peter W Kenny
- Berwick-on-Sea, North Coast Road, Blanchisseuse, Saint George, Trinidad and Tobago.
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Erlanson DA, Davis BJ, Jahnke W. Fragment-Based Drug Discovery: Advancing Fragments in the Absence of Crystal Structures. Cell Chem Biol 2018; 26:9-15. [PMID: 30482678 DOI: 10.1016/j.chembiol.2018.10.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 07/12/2018] [Accepted: 09/28/2018] [Indexed: 01/08/2023]
Abstract
Fragment-based drug discovery typically requires an interplay between screening methods, structural methods, and medicinal chemistry. X-ray crystallography is generally the method of choice to obtain three-dimensional structures of the bound ligand/protein complex, but this can sometimes be difficult, particularly for early, low-affinity fragment hits. In this Perspective, we discuss strategies to advance and evolve fragments in the absence of crystal structures of protein-fragment complexes, although the structure of the unliganded protein may be available. The strategies can involve other structural techniques, such as NMR spectroscopy, molecular modeling, or a variety of chemical approaches. Often, these strategies are aimed at guiding evolution of initial fragment hits to a stage where crystal structures can be obtained for further structure-based optimization.
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Affiliation(s)
- Daniel A Erlanson
- Carmot Therapeutics, Inc., 740 Heinz Avenue, Berkeley, CA 94710, USA.
| | - Ben J Davis
- Vernalis (R&D) Ltd, Granta Park, Cambridge, UK.
| | - Wolfgang Jahnke
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Novartis Campus, Basel, Switzerland.
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Synthesis of pyrazolo-1,2,4-triazolo[4,3-a]quinoxalines as antimicrobial agents with potential inhibition of DHPS enzyme. Future Med Chem 2018; 10:2155-2175. [PMID: 30088415 DOI: 10.4155/fmc-2018-0082] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
AIM The development of a new class of antimicrobial agents is the optimal lifeline to scrap the escalating jeopardy of drug resistance. EXPERIMENTAL This study aims to design and synthesize a series of pyrazolo-1,2,4-triazolo[4,3-a]quinoxalines, to develop agents having antimicrobial activity through potential inhibition of dihyropteroate synthase enzyme. The target compounds have been evaluated for their in-vitro antimicrobial activity. RESULTS & DISCUSSION Compounds 5b, 5c were equipotent (minimal inhibitory concentration = 12.5 μg/ml) to ampicillin. The docking patterns of 5b and 5c demonstrated that both fit into Bacillus Anthracis dihydropteroate synthase pterin and p-amino benzoic acid-binding pockets. Moreover, their physicochemical properties and pharmacokinetic profiles recommend that they can be considered drug-like candidates. The results highlight some significant information for the future design of lead compounds as antimicrobial agents.
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25
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Lamoree B, Hubbard RE. Using Fragment-Based Approaches to Discover New Antibiotics. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2018; 23:495-510. [PMID: 29923463 PMCID: PMC6024353 DOI: 10.1177/2472555218773034] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 03/16/2018] [Accepted: 04/05/2018] [Indexed: 12/29/2022]
Abstract
Fragment-based lead discovery has emerged over the past two decades as a successful approach to generate novel lead candidates in drug discovery programs. The two main advantages over conventional high-throughput screening (HTS) are more efficient sampling of chemical space and tighter control over the physicochemical properties of the lead candidates. Antibiotics are a class of drugs with particularly strict property requirements for efficacy and safety. The development of novel antibiotics has slowed down so much that resistance has now evolved against every available antibiotic drug. Here we give an overview of fragment-based approaches in screening and lead discovery projects for new antibiotics. We discuss several successful hit-to-lead development examples. Finally, we highlight the current challenges and opportunities for fragment-based lead discovery toward new antibiotics.
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Affiliation(s)
- Bas Lamoree
- YSBL, Department of Chemistry, University of York, Heslington, York, UK
| | - Roderick E. Hubbard
- YSBL, Department of Chemistry, University of York, Heslington, York, UK
- Vernalis Research, Granta Park, Abington, Cambridge, UK
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26
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Bi F, Ji S, Venter H, Liu J, Semple SJ, Ma S. Substitution of terminal amide with 1H-1,2,3-triazole: Identification of unexpected class of potent antibacterial agents. Bioorg Med Chem Lett 2018; 28:884-891. [PMID: 29433923 DOI: 10.1016/j.bmcl.2018.02.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 12/25/2017] [Accepted: 02/01/2018] [Indexed: 11/15/2022]
Abstract
3-Methoxybenzamide (3-MBA) derivatives have been identified as novel class of potent antibacterial agents targeting the bacterial cell division protein FtsZ. As one of isosteres for the amide group, 1,2,3-triazole can mimic the topological and electronic features of the amide, which has gained increasing attention in drug discovery. Based on these considerations, we prepared a series of 1H-1,2,3-triazole-containing 3-MBA analogues via isosteric replacement of the terminal amide with triazole, which had increased antibacterial activity. This study demonstrated the possibility of developing the 1H-1,2,3-triazole group as a terminal amide-mimetic element which was capable of both keeping and modulating amide-related bioactivity. Surprisingly, a different action mode of these new 1H-1,2,3-triazole-containing analogues was observed, which could open new opportunities for the development of antibacterial agents.
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Affiliation(s)
- Fangchao Bi
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Shengli Ji
- ReaLi Tide Biological Technology (Weihai) Co. Ltd., East Longhai Road & South Yangguang Road, Nanhai New District, Weihai 264207, China
| | - Henrietta Venter
- School of Pharmacy & Medical Sciences, Sansom Institute for Health Research, University of South Australia, GPO Box 2471, Adelaide 5001, Australia
| | - Jingru Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, China
| | - Susan J Semple
- School of Pharmacy & Medical Sciences, Sansom Institute for Health Research, University of South Australia, GPO Box 2471, Adelaide 5001, Australia
| | - Shutao Ma
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, Jinan 250012, China.
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27
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Ballu S, Itteboina R, Sivan SK, Manga V. Structural insights of Staphylococcus aureus FtsZ inhibitors through molecular docking, 3D-QSAR and molecular dynamics simulations. J Recept Signal Transduct Res 2018; 38:61-70. [DOI: 10.1080/10799893.2018.1426607] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Srilata Ballu
- Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
| | - Ramesh Itteboina
- Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
| | - Sree Kanth Sivan
- Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
| | - Vijjulatha Manga
- Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
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28
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Brengel C, Thomann A, Schifrin A, Allegretta G, Kamal AAM, Haupenthal J, Schnorr I, Cho SH, Franzblau SG, Empting M, Eberhard J, Hartmann RW. Biophysical Screening of a Focused Library for the Discovery of CYP121 Inhibitors as Novel Antimycobacterials. ChemMedChem 2017; 12:1616-1626. [DOI: 10.1002/cmdc.201700363] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/04/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Christian Brengel
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Andreas Thomann
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Alexander Schifrin
- Department of Biochemistry; Saarland University; Campus B2.2 66123 Saarbrücken Germany
| | - Giuseppe Allegretta
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Ahmed A. M. Kamal
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Jörg Haupenthal
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Isabell Schnorr
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Sang Hyun Cho
- Institute for Tuberculosis Research; College of Pharmacy; University of Illinois at Chicago; 833 S. Wood Street Chicago IL 60612-7231 USA
| | - Scott G. Franzblau
- Institute for Tuberculosis Research; College of Pharmacy; University of Illinois at Chicago; 833 S. Wood Street Chicago IL 60612-7231 USA
| | - Martin Empting
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Jens Eberhard
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Rolf W. Hartmann
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
- Department of Pharmacy; Pharmaceutical and Medicinal Chemistry; Saarland University; Campus C2.3 66123 Saarbrücken Germany
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29
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Straniero V, Zanotto C, Straniero L, Casiraghi A, Duga S, Radaelli A, De Giuli Morghen C, Valoti E. 2,6-Difluorobenzamide Inhibitors of Bacterial Cell Division Protein FtsZ: Design, Synthesis, and Structure-Activity Relationships. ChemMedChem 2017; 12:1303-1318. [PMID: 28586174 DOI: 10.1002/cmdc.201700201] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/30/2017] [Indexed: 11/08/2022]
Abstract
A wide variety of drug-resistant microorganisms are continuously emerging, restricting the therapeutic options for common bacterial infections. Antimicrobial agents that were originally potent are now no longer helpful, due to their weak or null activity toward these antibiotic-resistant bacteria. In addition, none of the recently approved antibiotics affect innovative targets, resulting in a need for novel drugs with innovative antibacterial mechanisms of action. The essential cell division protein filamentous temperature-sensitive Z (FtsZ) has emerged as a possible target, thanks to its ubiquitous expression and its homology to eukaryotic β-tubulin. In the latest years, several compounds were shown to interact with this prokaryotic protein and selectively inhibit bacterial cell division. Recently, our research group developed interesting derivatives displaying good antibacterial activities against methicillin-resistant Staphylococcus aureus, as well as vancomycin-resistant Enterococcus faecalis and Mycobacterium tuberculosis. The aim of the present study was to summarize the structure-activity relationships of differently substituted heterocycles, linked by a methylenoxy bridge to the 2,6-difluorobenzamide, and to validate FtsZ as the real target of this class of antimicrobials.
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Affiliation(s)
- Valentina Straniero
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, via Mangiagalli 25, 20133, Milano, Italy
| | - Carlo Zanotto
- Department of Medical Biotechnologies and Translational Medicine, Università degli Studi di Milano, via Vanvitelli 32, 20129, Milano, Italy
| | - Letizia Straniero
- Department of Biomedical Sciences, Humanitas University, via Manzoni 113, 2, 0089, Rozzano-Milano, Italy
| | - Andrea Casiraghi
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, via Mangiagalli 25, 20133, Milano, Italy
| | - Stefano Duga
- Department of Biomedical Sciences, Humanitas University, via Manzoni 113, 2, 0089, Rozzano-Milano, Italy.,Humanitas Clinical and Research Center, via Manzoni 56, 20089, Rozzano-Milano, Italy
| | - Antonia Radaelli
- Department of Pharmacological and Biomolecular Science, Università degli Studi di Milano, via Balzaretti 9, 20133, Milano, Italy.,Cellular and Molecular Pharmacology Section, National Research Council (CNR), Institute of Neurosciences, Università degli Studi di Milano, via Vanvitelli 32, 20129, Milano, Italy
| | | | - Ermanno Valoti
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, via Mangiagalli 25, 20133, Milano, Italy
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30
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Hu Z, Zhang S, Zhou W, Ma X, Xiang G. Synthesis and antibacterial activity of 3-benzylamide derivatives as FtsZ inhibitors. Bioorg Med Chem Lett 2017; 27:1854-1858. [DOI: 10.1016/j.bmcl.2017.02.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 02/05/2017] [Accepted: 02/15/2017] [Indexed: 11/26/2022]
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31
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Saeloh D, Wenzel M, Rungrotmongkol T, Hamoen LW, Tipmanee V, Voravuthikunchai SP. Effects of rhodomyrtone on Gram-positive bacterial tubulin homologue FtsZ. PeerJ 2017; 5:e2962. [PMID: 28168121 PMCID: PMC5292029 DOI: 10.7717/peerj.2962] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/05/2017] [Indexed: 12/15/2022] Open
Abstract
Rhodomyrtone, a natural antimicrobial compound, displays potent activity against many Gram-positive pathogenic bacteria, comparable to last-defence antibiotics including vancomycin and daptomycin. Our previous studies pointed towards effects of rhodomyrtone on the bacterial membrane and cell wall. In addition, a recent molecular docking study suggested that the compound could competitively bind to the main bacterial cell division protein FtsZ. In this study, we applied a computational approach (in silico), in vitro, and in vivo experiments to investigate molecular interactions of rhodomyrtone with FtsZ. Using molecular simulation, FtsZ conformational changes were observed in both (S)- and (R)-rhodomyrtone binding states, compared with the three natural states of FtsZ (ligand-free, GDP-, and GTP-binding states). Calculations of free binding energy showed a higher affinity of FtsZ to (S)-rhodomyrtone (−35.92 ± 0.36 kcal mol−1) than the GDP substrate (−23.47 ± 0.25 kcal mol−1) while less affinity was observed in the case of (R)-rhodomyrtone (−18.11 ± 0.11 kcal mol−1). In vitro experiments further revealed that rhodomyrtone reduced FtsZ polymerization by 36% and inhibited GTPase activity by up to 45%. However, the compound had no effect on FtsZ localization in Bacillus subtilis at inhibitory concentrations and cells also did not elongate after treatment. Higher concentrations of rhodomyrtone did affect localization of FtsZ and also affected localization of its membrane anchor proteins FtsA and SepF, showing that the compound did not specifically inhibit FtsZ but rather impaired multiple divisome proteins. Furthermore, a number of cells adopted a bean-like shape suggesting that rhodomyrtone possibly possesses further targets involved in cell envelope synthesis and/or maintenance.
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Affiliation(s)
- Dennapa Saeloh
- Excellence Research Laboratory on Natural Products, Faculty of Science and Natural Product Research Center of Excellence, Prince of Songkla University, Hat Yai, Thailand; Department of Microbiology, Faculty of Science, Prince of Songkla University, Hat Yai, Thailand
| | - Michaela Wenzel
- Bacterial Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam , Amsterdam , Netherlands
| | - Thanyada Rungrotmongkol
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand; Center of Innovative Nanotechnology, Chulalongkorn University, Bongkok, Thailand
| | - Leendert Willem Hamoen
- Bacterial Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam , Amsterdam , Netherlands
| | - Varomyalin Tipmanee
- Excellence Research Laboratory on Natural Products, Faculty of Science and Natural Product Research Center of Excellence, Prince of Songkla University, Hat Yai, Thailand; Department of Biomedical Science, Faculty of Medicine, Prince of Songkla University, Hat Yai, Thailand
| | - Supayang Piyawan Voravuthikunchai
- Excellence Research Laboratory on Natural Products, Faculty of Science and Natural Product Research Center of Excellence, Prince of Songkla University, Hat Yai, Thailand; Department of Microbiology, Faculty of Science, Prince of Songkla University, Hat Yai, Thailand
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32
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Artola M, Ruíz-Avila LB, Ramírez-Aportela E, Martínez RF, Araujo-Bazán L, Vázquez-Villa H, Martín-Fontecha M, Oliva MA, Martín-Galiano AJ, Chacón P, López-Rodríguez ML, Andreu JM, Huecas S. The structural assembly switch of cell division protein FtsZ probed with fluorescent allosteric inhibitors. Chem Sci 2017; 8:1525-1534. [PMID: 28616148 PMCID: PMC5460597 DOI: 10.1039/c6sc03792e] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 10/19/2016] [Indexed: 11/21/2022] Open
Abstract
FtsZ is a widely conserved tubulin-like GTPase that directs bacterial cell division and a new target for antibiotic discovery. This protein assembly machine cooperatively polymerizes forming single-stranded filaments, by means of self-switching between inactive and actively associating monomer conformations. The structural switch mechanism was proposed to involve a movement of the C-terminal and N-terminal FtsZ domains, opening a cleft between them, allosterically coupled to the formation of a tight association interface between consecutive subunits along the filament. The effective antibacterial benzamide PC190723 binds into the open interdomain cleft and stabilizes FtsZ filaments, thus impairing correct formation of the FtsZ ring for cell division. We have designed fluorescent analogs of PC190723 to probe the FtsZ structural assembly switch. Among them, nitrobenzoxadiazole probes specifically bind to assembled FtsZ rather than to monomers. Probes with several spacer lengths between the fluorophore and benzamide moieties suggest a binding site extension along the interdomain cleft. These probes label FtsZ rings of live Bacillus subtilis and Staphylococcus aureus, without apparently modifying normal cell morphology and growth, but at high concentrations they induce impaired bacterial division phenotypes typical of benzamide antibacterials. During the FtsZ assembly-disassembly process, the fluorescence anisotropy of the probes changes upon binding and dissociating from FtsZ, thus reporting open and closed FtsZ interdomain clefts. Our results demonstrate the structural mechanism of the FtsZ assembly switch, and suggest that the probes bind into the open clefts in cellular FtsZ polymers preferably to unassembled FtsZ in the bacterial cytosol.
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Affiliation(s)
- Marta Artola
- Dept. Química Orgánica I , Facultad de Ciencias Químicas , UCM , 28040 Madrid , Spain
| | - Laura B Ruíz-Avila
- Centro de Investigaciones Biológicas , CSIC , Ramiro de Maeztu 9 , 28040 Madrid , Spain . ;
| | - Erney Ramírez-Aportela
- Centro de Investigaciones Biológicas , CSIC , Ramiro de Maeztu 9 , 28040 Madrid , Spain . ;
- Instituto de Química-Física Rocasolano , CSIC , Serrano 119 , 20006 Madrid , Spain
| | - R Fernando Martínez
- Dept. Química Orgánica I , Facultad de Ciencias Químicas , UCM , 28040 Madrid , Spain
| | - Lidia Araujo-Bazán
- Centro de Investigaciones Biológicas , CSIC , Ramiro de Maeztu 9 , 28040 Madrid , Spain . ;
| | - Henar Vázquez-Villa
- Dept. Química Orgánica I , Facultad de Ciencias Químicas , UCM , 28040 Madrid , Spain
| | - Mar Martín-Fontecha
- Dept. Química Orgánica I , Facultad de Ciencias Químicas , UCM , 28040 Madrid , Spain
| | - María A Oliva
- Centro de Investigaciones Biológicas , CSIC , Ramiro de Maeztu 9 , 28040 Madrid , Spain . ;
| | | | - Pablo Chacón
- Instituto de Química-Física Rocasolano , CSIC , Serrano 119 , 20006 Madrid , Spain
| | | | - José M Andreu
- Centro de Investigaciones Biológicas , CSIC , Ramiro de Maeztu 9 , 28040 Madrid , Spain . ;
| | - Sonia Huecas
- Centro de Investigaciones Biológicas , CSIC , Ramiro de Maeztu 9 , 28040 Madrid , Spain . ;
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33
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Design, synthesis and biological activity evaluation of novel 2,6-difluorobenzamide derivatives through FtsZ inhibition. Bioorg Med Chem Lett 2017; 27:958-962. [DOI: 10.1016/j.bmcl.2016.12.081] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 12/19/2016] [Accepted: 12/29/2016] [Indexed: 11/20/2022]
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34
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Kobayashi K, Honda Y. An Efficient One-Pot Synthesis of 4-Hydroxyisoquinoline-1,3(2H,4H)-diones from N-Alkylbenzamides and α-Keto Esters. HETEROCYCLES 2017. [DOI: 10.3987/com-17-13666] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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35
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Haranahalli K, Tong S, Ojima I. Recent advances in the discovery and development of antibacterial agents targeting the cell-division protein FtsZ. Bioorg Med Chem 2016; 24:6354-6369. [PMID: 27189886 PMCID: PMC5157688 DOI: 10.1016/j.bmc.2016.05.003] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Revised: 04/29/2016] [Accepted: 05/03/2016] [Indexed: 01/21/2023]
Abstract
With the emergence of multidrug-resistant bacterial strains, there is a dire need for new drug targets for antibacterial drug discovery and development. Filamentous temperature sensitive protein Z (FtsZ), is a GTP-dependent prokaryotic cell division protein, sharing less than 10% sequence identity with the eukaryotic cell division protein, tubulin. FtsZ forms a dynamic Z-ring in the middle of the cell, leading to septation and subsequent cell division. Inhibition of the Z-ring blocks cell division, thus making FtsZ a highly attractive target. Various groups have been working on natural products and synthetic small molecules as inhibitors of FtsZ. This review summarizes the recent advances in the development of FtsZ inhibitors, focusing on those in the last 5years, but also includes significant findings in previous years.
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Affiliation(s)
| | - Simon Tong
- Department of Chemistry, Stony Brook University, Stony Brook, NY, USA
| | - Iwao Ojima
- Department of Chemistry, Stony Brook University, Stony Brook, NY, USA; Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY, USA.
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36
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Araújo-Bazán L, Ruiz-Avila LB, Andreu D, Huecas S, Andreu JM. Cytological Profile of Antibacterial FtsZ Inhibitors and Synthetic Peptide MciZ. Front Microbiol 2016; 7:1558. [PMID: 27752253 PMCID: PMC5045927 DOI: 10.3389/fmicb.2016.01558] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 09/16/2016] [Indexed: 11/26/2022] Open
Abstract
Cell division protein FtsZ is the organizer of the cytokinetic ring in almost all bacteria and a target for the discovery of new antibacterial agents that are needed to counter widespread antibiotic resistance. Bacterial cytological profiling, using quantitative microscopy, is a powerful approach for identifying the mechanism of action of antibacterial molecules affecting different cellular pathways. We have determined the cytological profile on Bacillus subtilis cells of a selection of small molecule inhibitors targeting FtsZ on different binding sites. FtsZ inhibitors lead to long undivided cells, impair the normal assembly of FtsZ into the midcell Z-rings, induce aberrant ring distributions, punctate FtsZ foci, membrane spots and also modify nucleoid length. Quantitative analysis of cell and nucleoid length combined, or the Z-ring distribution, allows categorizing FtsZ inhibitors and to distinguish them from antibiotics with other mechanisms of action, which should be useful for identifying new antibacterial FtsZ inhibitors. Biochemical assays of FtsZ polymerization and GTPase activity combined explain the cellular effects of the FtsZ polymer stabilizing agent PC190723 and its fragments. MciZ is a 40-aminoacid endogenous inhibitor of cell division normally expressed during sporulation in B. subtilis. Using FtsZ cytological profiling we have determined that exogenous synthetic MciZ is an effective inhibitor of B. subtilis cell division, Z-ring formation and localization. This finding supports our cell-based approach to screen for FtsZ inhibitors and opens new possibilities for peptide inhibitors of bacterial cell division.
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Affiliation(s)
- Lidia Araújo-Bazán
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas Madrid, Spain
| | - Laura B Ruiz-Avila
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas Madrid, Spain
| | - David Andreu
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra Barcelona, Spain
| | - Sonia Huecas
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas Madrid, Spain
| | - José M Andreu
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas Madrid, Spain
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37
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Abstract
After 20 years of sometimes quiet growth, fragment-based drug discovery (FBDD) has become mainstream. More than 30 drug candidates derived from fragments have entered the clinic, with two approved and several more in advanced trials. FBDD has been widely applied in both academia and industry, as evidenced by the large number of papers from universities, non-profit research institutions, biotechnology companies and pharmaceutical companies. Moreover, FBDD draws on a diverse range of disciplines, from biochemistry and biophysics to computational and medicinal chemistry. As the promise of FBDD strategies becomes increasingly realized, now is an opportune time to draw lessons and point the way to the future. This Review briefly discusses how to design fragment libraries, how to select screening techniques and how to make the most of information gleaned from them. It also shows how concepts from FBDD have permeated and enhanced drug discovery efforts.
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Conti R, Chagas FO, Caraballo-Rodriguez AM, Melo WGDP, do Nascimento AM, Cavalcanti BC, de Moraes MO, Pessoa C, Costa-Lotufo LV, Krogh R, Andricopulo AD, Lopes NP, Pupo MT. Endophytic Actinobacteria from the Brazilian Medicinal Plant Lychnophora ericoides Mart. and the Biological Potential of Their Secondary Metabolites. Chem Biodivers 2016; 13:727-36. [PMID: 27128202 DOI: 10.1002/cbdv.201500225] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 01/14/2016] [Indexed: 12/25/2022]
Abstract
Endophytic actinobacteria from the Brazilian medicinal plant Lychnophora ericoides were isolated for the first time, and the biological potential of their secondary metabolites was evaluated. A phylogenic analysis of isolated actinobacteria was accomplished with 16S rRNA gene sequencing, and the predominance of the genus Streptomyces was observed. All strains were cultured on solid rice medium, and ethanol extracts were evaluated with antimicrobial and cytotoxic assays against cancer cell lines. As a result, 92% of the extracts showed a high or moderate activity against at least one pathogenic microbial strain or cancer cell line. Based on the biological and chemical analyses of crude extracts, three endophytic strains were selected for further investigation of their chemical profiles. Sixteen compounds were isolated, and 3-hydroxy-4-methoxybenzamide (9) and 2,3-dihydro-2,2-dimethyl-4(1H)-quinazolinone (15) are reported as natural products for the first time in this study. The biological activity of the pure compounds was also assessed. Compound 15 displayed potent cytotoxic activity against all four tested cancer cell lines. Nocardamine (2) was only moderately active against two cancer cell lines but showed strong activity against Trypanosoma cruzi. Our results show that endophytic actinobacteria from L. ericoides are a promising source of bioactive compounds.
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Affiliation(s)
- Raphael Conti
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café s/n, 14040-903, Ribeirão Preto, SP, Brazil.,CEPID-CIBFar - Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, FAPESP, São Paulo, SP, Brazil
| | - Fernanda Oliveira Chagas
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café s/n, 14040-903, Ribeirão Preto, SP, Brazil.,CEPID-CIBFar - Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, FAPESP, São Paulo, SP, Brazil
| | - Andrés Mauricio Caraballo-Rodriguez
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café s/n, 14040-903, Ribeirão Preto, SP, Brazil.,CEPID-CIBFar - Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, FAPESP, São Paulo, SP, Brazil
| | - Weilan Gomes da Paixão Melo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café s/n, 14040-903, Ribeirão Preto, SP, Brazil.,CEPID-CIBFar - Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, FAPESP, São Paulo, SP, Brazil
| | | | | | | | - Cláudia Pessoa
- Faculdade de Medicina, Universidade Federal do Ceará, Fortaleza, CE, Brazil.,Fundação Oswaldo Cruz (Fiocruz), Fortaleza, CE, Brazil
| | | | - Renata Krogh
- CEPID-CIBFar - Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, FAPESP, São Paulo, SP, Brazil.,Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Adriano Defini Andricopulo
- CEPID-CIBFar - Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, FAPESP, São Paulo, SP, Brazil.,Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Norberto Peporine Lopes
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café s/n, 14040-903, Ribeirão Preto, SP, Brazil
| | - Mônica Tallarico Pupo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café s/n, 14040-903, Ribeirão Preto, SP, Brazil. .,CEPID-CIBFar - Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, FAPESP, São Paulo, SP, Brazil.
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39
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Zhang L, Geng Y, Jin Z. Transition-Metal-Free Synthesis of N-Aryl Hydroxamic Acids via Insertion of Arynes. J Org Chem 2016; 81:3542-52. [DOI: 10.1021/acs.joc.6b00111] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lanlan Zhang
- State Key Laboratory of Elementoorganic
Chemistry, Nankai University, Tianjin 300071, China
| | - Yu Geng
- State Key Laboratory of Elementoorganic
Chemistry, Nankai University, Tianjin 300071, China
| | - Zhong Jin
- State Key Laboratory of Elementoorganic
Chemistry, Nankai University, Tianjin 300071, China
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40
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Straniero V, Pallavicini M, Chiodini G, Zanotto C, Volontè L, Radaelli A, Bolchi C, Fumagalli L, Sanguinetti M, Menchinelli G, Delogu G, Battah B, De Giuli Morghen C, Valoti E. 3-(Benzodioxan-2-ylmethoxy)-2,6-difluorobenzamides bearing hydrophobic substituents at the 7-position of the benzodioxane nucleus potently inhibit methicillin-resistant Sa and Mtb cell division. Eur J Med Chem 2016; 120:227-43. [PMID: 27191617 DOI: 10.1016/j.ejmech.2016.03.068] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/09/2016] [Accepted: 03/25/2016] [Indexed: 11/26/2022]
Abstract
Lipophilic substituents at benzodioxane C (7) of 3-(benzodioxan-2-ylmethoxy)-2,6-difluorobenzamide improve the antibacterial activity against methicillin-resistant Staphylococcus aureus strains to MIC values in the range of 0.2-2.5 μg/mL, whereas hydrophilic substituents at the same position and modifications at the benzodioxane substructure, excepting for replacement with 2-cromanyl, are deleterious. Some of the lead compounds also exhibit good activity against Mtb. Parallel SARs to those of 3-(2-benzothiazol-2-ylmethoxy)-2,6-difluorobenzamide, well known FtsZ inhibitor, and cells alterations typical of FtsZ inhibition indicate such a protein as the target of these potent antibacterial benzodioxane-benzamides.
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Affiliation(s)
- Valentina Straniero
- Dipartimento di Scienze Farmaceutiche, Università di Milano, via Mangiagalli 25, I-20133 Milano, Italy
| | - Marco Pallavicini
- Dipartimento di Scienze Farmaceutiche, Università di Milano, via Mangiagalli 25, I-20133 Milano, Italy
| | - Giuseppe Chiodini
- Dipartimento di Scienze Farmaceutiche, Università di Milano, via Mangiagalli 25, I-20133 Milano, Italy
| | - Carlo Zanotto
- Department of Medical Biothechnologies and Translational Medicine, Università di Milano, via Vanvitelli 32, I-20129 Milano, Italy
| | - Luca Volontè
- Department of Medical Biothechnologies and Translational Medicine, Università di Milano, via Vanvitelli 32, I-20129 Milano, Italy
| | - Antonia Radaelli
- Department of Pharmacological and Biomolecular Sciences, Università di Milano, via Balzaretti 9, I-2013 Milano, Italy; CNR Institute of Neurosciences, Cellular and Molecular Pharmacology Section, Università di Milano, via Vanvitelli 32, I-20129 Milano, Italy
| | - Cristiano Bolchi
- Dipartimento di Scienze Farmaceutiche, Università di Milano, via Mangiagalli 25, I-20133 Milano, Italy
| | - Laura Fumagalli
- Dipartimento di Scienze Farmaceutiche, Università di Milano, via Mangiagalli 25, I-20133 Milano, Italy
| | - Maurizio Sanguinetti
- Institute of Microbiology, Università Cattolica del Sacro Cuore, largo Gemelli 8, I-00168 Rome, Italy
| | - Giulia Menchinelli
- Institute of Microbiology, Università Cattolica del Sacro Cuore, largo Gemelli 8, I-00168 Rome, Italy
| | - Giovanni Delogu
- Institute of Microbiology, Università Cattolica del Sacro Cuore, largo Gemelli 8, I-00168 Rome, Italy
| | - Basem Battah
- Institute of Microbiology, Università Cattolica del Sacro Cuore, largo Gemelli 8, I-00168 Rome, Italy
| | - Carlo De Giuli Morghen
- Department of Medical Biothechnologies and Translational Medicine, Università di Milano, via Vanvitelli 32, I-20129 Milano, Italy; CNR Institute of Neurosciences, Cellular and Molecular Pharmacology Section, Università di Milano, via Vanvitelli 32, I-20129 Milano, Italy
| | - Ermanno Valoti
- Dipartimento di Scienze Farmaceutiche, Università di Milano, via Mangiagalli 25, I-20133 Milano, Italy.
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Hurley KA, Santos TMA, Nepomuceno GM, Huynh V, Shaw JT, Weibel DB. Targeting the Bacterial Division Protein FtsZ. J Med Chem 2016; 59:6975-98. [DOI: 10.1021/acs.jmedchem.5b01098] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Katherine A. Hurley
- Department of Pharmaceutical Sciences, University of Wisconsin—Madison, 777 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Thiago M. A. Santos
- Department
of Biochemistry, University of Wisconsin—Madison, 440 Henry Mall, Madison, Wisconsin 53706, United States
| | - Gabriella M. Nepomuceno
- Department of Chemistry, University of California—Davis, One Shields Avenue, Davis, California 95616, United States
| | - Valerie Huynh
- Department of Chemistry, University of California—Davis, One Shields Avenue, Davis, California 95616, United States
| | - Jared T. Shaw
- Department of Chemistry, University of California—Davis, One Shields Avenue, Davis, California 95616, United States
| | - Douglas B. Weibel
- Department
of Biochemistry, University of Wisconsin—Madison, 440 Henry Mall, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
- Department of Biomedical Engineering, University of Wisconsin—Madison, 1550 Engineering Drive, Madison, Wisconsin 53706, United States
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Chen X, Zhang B, Xiao J, Ju F, Li S, Ren C, An L, Chen T, Liu G, Facey P, Mullins JG, Dyson P. RfiA, a novel PAP2 domain-containing polytopic membrane protein that confers resistance to the FtsZ inhibitor PC190723. Future Microbiol 2016; 10:325-35. [PMID: 25812456 DOI: 10.2217/fmb.14.131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND As an essential protein for bacterial cell division, the tubulin-like FtsZ protein has been selected as a target for development of next generation antimicrobials. PC190723 is a fluoride-containing benzamide compound developed as a FtsZ inhibitor that selectively inhibits growth of multidrug resistant Gram-positive bacteria. AIM Our aim was to investigate the mechanism of resistance to PC109723 conferred by over-expression of a gene, rfiA, in an environmental bacterium Arthrobacter A3. MATERIALS & METHODS The investigations included analysis of the effect of PC109723 on wild-type Arthrobacter A3 and a recombinant strain over-expressing rfiA, in vivo localization of RfiA, in vitro measurements of fluorine release from PC109723 by membrane extracts from the over-expression strain combined with mass spectrophotometric analysis of reaction products, and modelling of RfiA structure. RESULTS We describe a novel protein, RfiA, from Arthrobacter A3 that confers PC190723 resistance. RfiA is a PAP2 domain-containing polytopic transmembrane protein that can modify the fluoridated benzamide ring that is critical for high affinity binding of PC190723 with FtsZ. CONCLUSION RfiA-mediated modification of PC190723 is the first reported instance of resistance to this antibiotic involving a change to its structure. We predict that adoption of PC190723 or related benzamides as antimicrobials in clinical practice will lead to the acquisition by resistant pathogens of a gene encoding this subfamily of proteins.
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Affiliation(s)
- Ximing Chen
- Key Laboratory of Extreme Environmental Microbial Resources & Engineering of Gansu Province, Lanzhou University, Lanzhou, Gansu, China
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Adams DW, Wu LJ, Errington J. A benzamide-dependent ftsZ mutant reveals residues crucial for Z-ring assembly. Mol Microbiol 2015; 99:1028-42. [PMID: 26601800 PMCID: PMC4832351 DOI: 10.1111/mmi.13286] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2015] [Indexed: 12/14/2022]
Abstract
In almost all bacteria, cell division is co-ordinated by the essential tubulin homologue FtsZ and represents an attractive but as yet unexploited target for new antibiotics. The benzamides, e.g. PC190723, are potent FtsZ inhibitors that have the potential to yield an important new class of antibiotic. However, the evolution of resistance poses a challenge to their development. Here we show that a collection of PC190723-resistant and -dependent strains of Staphylococcus aureus exhibit severe growth and morphological defects, questioning whether these ftsZ mutations would be clinically relevant. Importantly, we show that the most commonly isolated substitution remains sensitive to the simplest benzamide 3-MBA and likely works by occluding compound binding. Extending this analysis to Bacillus subtilis, we isolated a novel benzamide-dependent strain that divides using unusual helical division events. The ftsZ mutation responsible encodes the substitution of a highly conserved residue, which lies outside the benzamide-binding site and forms part of an interface between the N- and C-terminal domains that we show is necessary for normal FtsZ function. Together with an intragenic suppressor mutation that mimics benzamide binding, the results provide genetic evidence that benzamides restrict conformational changes in FtsZ and also highlights their utility as tools to probe bacterial division.
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Affiliation(s)
- David William Adams
- Centre for Bacterial Cell Biology, Baddiley-Clark Building, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Baddiley-Clark Building, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Baddiley-Clark Building, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
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44
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Andrades J, Campanini J, Vásquez D, Silvestri C, Morales C, Romero J, Mella J. A combined CoMFA and CoMSIA 3D-QSAR study of benzamide type antibacterial inhibitors of the FtsZ protein in drug-resistant Staphylococcus aureus. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2015; 26:925-942. [PMID: 26505124 DOI: 10.1080/1062936x.2015.1095798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A major problem today is bacterial resistance to antibiotics and the small number of new therapeutic agents approved in recent years. The development of new antibiotics capable of acting on new targets is urgently required. The filamenting temperature-sensitive Z (FtsZ) bacterial protein is a key biomolecule for bacterial division and survival. This makes FtsZ an attractive new pharmacological target for the development of antibacterial agents. There have been several attempts to develop ligands able to inhibit FtsZ. Despite the large number of synthesized compounds that inhibit the FtsZ protein, there are no quantitative structure-activity relationships (QSAR) that allow for the rational design and synthesis of promising new molecules. We present the first 3D-QSAR study of a large and diverse set of molecules that are able to inhibit the FtsZ bacterial protein. We summarize a set of chemical changes that can be made in the steric, electrostatic, hydrophobic and donor/acceptor hydrogen-bonding properties of the pharmacophore, to generate new bioactive molecules against FtsZ. These results provide a rational guide for the design and synthesis of promising new antibacterial agents, supported by the strong statistical parameters obtained from CoMFA (r(2)(pred) = 0.974) and CoMSIA (r(2)(pred) = 0.980) analyses.
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Affiliation(s)
- J Andrades
- a Departamento de Química Farmacológica y Toxicológica , Universidad de Chile , Santiago , Chile
| | - J Campanini
- a Departamento de Química Farmacológica y Toxicológica , Universidad de Chile , Santiago , Chile
| | - D Vásquez
- a Departamento de Química Farmacológica y Toxicológica , Universidad de Chile , Santiago , Chile
| | - C Silvestri
- b Department of Bioengineering , Imperial College London , London , England
| | - C Morales
- c Departamento de Ciencias Químicas y Biológicas , Universidad Bernardo O Higgins , Santiago , Chile
| | - J Romero
- d Department of Pharmacy , Pontificia Universidad Católica de Chile , Santiago , Chile
| | - J Mella
- e Instituto de Química y Bioquímica, Universidad de Valparaíso , Valparaíso , Chile
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Qiang S, Wang C, Venter H, Li X, Wang Y, Guo L, Ma R, Ma S. Synthesis and Biological Evaluation of Novel FtsZ-targeted 3-arylalkoxy-2,6-difluorobenzamides as Potential Antimicrobial Agents. Chem Biol Drug Des 2015; 87:257-64. [PMID: 26348110 DOI: 10.1111/cbdd.12658] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 06/09/2015] [Accepted: 08/18/2015] [Indexed: 12/01/2022]
Affiliation(s)
- Shengsheng Qiang
- Department of Medicinal Chemistry; Key Laboratory of Chemical Biology (Ministry of Education); School of Pharmaceutical Sciences; Shandong University; 44, West Culture Road Jinan 250012 China
| | - Changde Wang
- Department of Medicinal Chemistry; Key Laboratory of Chemical Biology (Ministry of Education); School of Pharmaceutical Sciences; Shandong University; 44, West Culture Road Jinan 250012 China
| | - Henrietta Venter
- School of Pharmacy & Medical Sciences; Sansom Institute for Health Research; University of South Australia; GPO Box 2471 Adelaide SA 5001 Australia
| | - Xin Li
- Department of Medicinal Chemistry; Key Laboratory of Chemical Biology (Ministry of Education); School of Pharmaceutical Sciences; Shandong University; 44, West Culture Road Jinan 250012 China
| | - Yi Wang
- Department of Medicinal Chemistry; Key Laboratory of Chemical Biology (Ministry of Education); School of Pharmaceutical Sciences; Shandong University; 44, West Culture Road Jinan 250012 China
| | - Liwei Guo
- Department of Medicinal Chemistry; Key Laboratory of Chemical Biology (Ministry of Education); School of Pharmaceutical Sciences; Shandong University; 44, West Culture Road Jinan 250012 China
| | - Ruixin Ma
- Affiliated Hospital of Medical College; Qingdao University; Qingdao 266003 China
| | - Shutao Ma
- Department of Medicinal Chemistry; Key Laboratory of Chemical Biology (Ministry of Education); School of Pharmaceutical Sciences; Shandong University; 44, West Culture Road Jinan 250012 China
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Mikuni S, Kodama K, Sasaki A, Kohira N, Maki H, Munetomo M, Maenaka K, Kinjo M. Screening for FtsZ Dimerization Inhibitors Using Fluorescence Cross-Correlation Spectroscopy and Surface Resonance Plasmon Analysis. PLoS One 2015; 10:e0130933. [PMID: 26154290 PMCID: PMC4496089 DOI: 10.1371/journal.pone.0130933] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/01/2015] [Indexed: 01/16/2023] Open
Abstract
FtsZ is an attractive target for antibiotic research because it is an essential bacterial cell division protein that polymerizes in a GTP-dependent manner. To find the seed chemical structure, we established a high-throughput, quantitative screening method combining fluorescence cross-correlation spectroscopy (FCCS) and surface plasmon resonance (SPR). As a new concept for the application of FCCS to polymerization-prone protein, Staphylococcus aureus FtsZ was fragmented into the N-terminal and C-terminal, which were fused with GFP and mCherry (red fluorescent protein), respectively. By this fragmentation, the GTP-dependent head-to-tail dimerization of each fluorescent labeled fragment of FtsZ could be observed, and the inhibitory processes of chemicals could be monitored by FCCS. In the first round of screening by FCCS, 28 candidates were quantitatively and statistically selected from 495 chemicals determined by in silico screening. Subsequently, in the second round of screening by FCCS, 71 candidates were also chosen from 888 chemicals selected via an in silico structural similarity search of the chemicals screened in the first round of screening. Moreover, the dissociation constants between the highest inhibitory chemicals and Staphylococcus aureus FtsZ were determined by SPR. Finally, by measuring the minimum inhibitory concentration, it was confirmed that the screened chemical had antibacterial activity against Staphylococcus aureus, including methicillin-resistant Staphylococcus aureus (MRSA).
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Affiliation(s)
- Shintaro Mikuni
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Kota Kodama
- Creative Research Institution, Hokkaido University, Sapporo, Japan
| | - Akira Sasaki
- Bio-Analytical Research Group, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan
| | - Naoki Kohira
- Discovery Research Laboratory for Core Therapeutic Areas, Shionogi & Co., Ltd., Toyonaka, Osaka, Japan
| | - Hideki Maki
- Discovery Research Laboratory for Core Therapeutic Areas, Shionogi & Co., Ltd., Toyonaka, Osaka, Japan
| | - Masaharu Munetomo
- Information Initiative Center and Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Japan
| | - Katsumi Maenaka
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Science, Hokkaido University, Sapporo, Japan
| | - Masataka Kinjo
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
- * E-mail:
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47
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Chiodini G, Pallavicini M, Zanotto C, Bissa M, Radaelli A, Straniero V, Bolchi C, Fumagalli L, Ruggeri P, De Giuli Morghen C, Valoti E. Benzodioxane-benzamides as new bacterial cell division inhibitors. Eur J Med Chem 2014; 89:252-65. [PMID: 25462242 DOI: 10.1016/j.ejmech.2014.09.100] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Revised: 09/09/2014] [Accepted: 09/15/2014] [Indexed: 11/30/2022]
Abstract
A SAR study was performed on 3-substituted 2,6-difluorobenzamides, known inhibitors of the essential bacterial cell division protein FtsZ, through a series of modifications first of 2,6-difluoro-3-nonyloxybenzamide and then of its 3-pyridothiazolylmethoxy analogue PC190723. The study led to the identification of chiral 2,6-difluorobenzamides bearing 1,4-benzodioxane-2-methyl residue at the 3-position as potent antistaphylococcal compounds.
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Affiliation(s)
- Giuseppe Chiodini
- Dipartimento di Scienze Farmaceutiche, Università di Milano, Via Mangiagalli 25, I-20133 Milano, Italy
| | - Marco Pallavicini
- Dipartimento di Scienze Farmaceutiche, Università di Milano, Via Mangiagalli 25, I-20133 Milano, Italy
| | - Carlo Zanotto
- Department of Medical Biothechnologies and Translational Medicine, Università di Milano, Via Vanvitelli 32, I-20129 Milano, Italy
| | - Massimiliano Bissa
- Department of Pharmacological and Biomolecular Sciences, Università di Milano, Via Balzaretti 9, I-2013 Milano, Italy
| | - Antonia Radaelli
- Department of Pharmacological and Biomolecular Sciences, Università di Milano, Via Balzaretti 9, I-2013 Milano, Italy; CNR Institute of Neurosciences, Cellular and Molecular Pharmacology Section, Università di Milano, Via Vanvitelli 32, I-20129 Milano, Italy
| | - Valentina Straniero
- Dipartimento di Scienze Farmaceutiche, Università di Milano, Via Mangiagalli 25, I-20133 Milano, Italy
| | - Cristiano Bolchi
- Dipartimento di Scienze Farmaceutiche, Università di Milano, Via Mangiagalli 25, I-20133 Milano, Italy
| | - Laura Fumagalli
- Dipartimento di Scienze Farmaceutiche, Università di Milano, Via Mangiagalli 25, I-20133 Milano, Italy
| | - Paola Ruggeri
- Dipartimento di Scienze Farmaceutiche, Università di Milano, Via Mangiagalli 25, I-20133 Milano, Italy
| | - Carlo De Giuli Morghen
- Department of Medical Biothechnologies and Translational Medicine, Università di Milano, Via Vanvitelli 32, I-20129 Milano, Italy; CNR Institute of Neurosciences, Cellular and Molecular Pharmacology Section, Università di Milano, Via Vanvitelli 32, I-20129 Milano, Italy
| | - Ermanno Valoti
- Dipartimento di Scienze Farmaceutiche, Università di Milano, Via Mangiagalli 25, I-20133 Milano, Italy.
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Bellale E, Naik M, VB V, Ambady A, Narayan A, Ravishankar S, Ramachandran V, Kaur P, McLaughlin R, Whiteaker J, Morayya S, Guptha S, Sharma S, Raichurkar A, Awasthy D, Achar V, Vachaspati P, Bandodkar B, Panda M, Chatterji M. Diarylthiazole: An Antimycobacterial Scaffold Potentially Targeting PrrB-PrrA Two-Component System. J Med Chem 2014; 57:6572-82. [DOI: 10.1021/jm500833f] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Eknath Bellale
- Department
of Medicinal Chemistry, IMED Infection, AstraZeneca, Bellary
Road, Hebbal, Bangalore 560024, India
| | - Maruti Naik
- Department
of Medicinal Chemistry, IMED Infection, AstraZeneca, Bellary
Road, Hebbal, Bangalore 560024, India
| | - Varun VB
- Department
of Medicinal Chemistry, IMED Infection, AstraZeneca, Bellary
Road, Hebbal, Bangalore 560024, India
| | - Anisha Ambady
- Department
of Biosciences, IMED Infection, AstraZeneca, Bellary Road, Hebbal, Bangalore 560024, India
| | - Ashwini Narayan
- Department
of Biosciences, IMED Infection, AstraZeneca, Bellary Road, Hebbal, Bangalore 560024, India
| | - Sudha Ravishankar
- Department
of Biosciences, IMED Infection, AstraZeneca, Bellary Road, Hebbal, Bangalore 560024, India
| | - Vasanthi Ramachandran
- Department
of Biosciences, IMED Infection, AstraZeneca, Bellary Road, Hebbal, Bangalore 560024, India
| | - Parvinder Kaur
- Department
of Biosciences, IMED Infection, AstraZeneca, Bellary Road, Hebbal, Bangalore 560024, India
| | - Robert McLaughlin
- Infection
IMED, AstraZeneca, GHP, Waltham, Massachusetts 02451, United States
| | - James Whiteaker
- Infection
IMED, AstraZeneca, GHP, Waltham, Massachusetts 02451, United States
| | - Sapna Morayya
- Department
of Biosciences, IMED Infection, AstraZeneca, Bellary Road, Hebbal, Bangalore 560024, India
| | - Supreeth Guptha
- Department
of Biosciences, IMED Infection, AstraZeneca, Bellary Road, Hebbal, Bangalore 560024, India
| | - Sreevalli Sharma
- Department
of Biosciences, IMED Infection, AstraZeneca, Bellary Road, Hebbal, Bangalore 560024, India
| | - Anandkumar Raichurkar
- Department
of Medicinal Chemistry, IMED Infection, AstraZeneca, Bellary
Road, Hebbal, Bangalore 560024, India
| | - Disha Awasthy
- Department
of Biosciences, IMED Infection, AstraZeneca, Bellary Road, Hebbal, Bangalore 560024, India
| | - Vijayshree Achar
- Department
of Medicinal Chemistry, IMED Infection, AstraZeneca, Bellary
Road, Hebbal, Bangalore 560024, India
| | - Prakash Vachaspati
- DMPK
and Animal Sciences, IMED Infection, AstraZeneca, Bellary Road, Hebbal, Bangalore 560024, India
| | - Balachandra Bandodkar
- Department
of Medicinal Chemistry, IMED Infection, AstraZeneca, Bellary
Road, Hebbal, Bangalore 560024, India
| | - Manoranjan Panda
- Department
of Medicinal Chemistry, IMED Infection, AstraZeneca, Bellary
Road, Hebbal, Bangalore 560024, India
| | - Monalisa Chatterji
- Department
of Biosciences, IMED Infection, AstraZeneca, Bellary Road, Hebbal, Bangalore 560024, India
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Sun N, Chan FY, Lu YJ, Neves MAC, Lui HK, Wang Y, Chow KY, Chan KF, Yan SC, Leung YC, Abagyan R, Chan TH, Wong KY. Rational design of berberine-based FtsZ inhibitors with broad-spectrum antibacterial activity. PLoS One 2014; 9:e97514. [PMID: 24824618 PMCID: PMC4019636 DOI: 10.1371/journal.pone.0097514] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 04/17/2014] [Indexed: 02/07/2023] Open
Abstract
Inhibition of the functional activity of Filamenting temperature-sensitive mutant Z (FtsZ) protein, an essential and highly conserved bacterial cytokinesis protein, is a promising approach for the development of a new class of antibacterial agents. Berberine, a benzylisoquinoline alkaloid widely used in traditional Chinese and native American medicines for its antimicrobial properties, has been recently reported to inhibit FtsZ. Using a combination of in silico structure-based design and in vitro biological assays, 9-phenoxyalkyl berberine derivatives were identified as potent FtsZ inhibitors. Compared to the parent compound berberine, the derivatives showed a significant enhancement of antibacterial activity against clinically relevant bacteria, and an improved potency against the GTPase activity and polymerization of FtsZ. The most potent compound 2 strongly inhibited the proliferation of Gram-positive bacteria, including methicillin-resistant S. aureus and vancomycin-resistant E. faecium, with MIC values between 2 and 4 µg/mL, and was active against the Gram-negative E. coli and K. pneumoniae, with MIC values of 32 and 64 µg/mL respectively. The compound perturbed the formation of cytokinetic Z-ring in E. coli. Also, the compound interfered with in vitro polymerization of S. aureus FtsZ. Taken together, the chemical modification of berberine with 9-phenoxyalkyl substituent groups greatly improved the antibacterial activity via targeting FtsZ.
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Affiliation(s)
- Ning Sun
- Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Fung-Yi Chan
- Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Yu-Jing Lu
- Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
- School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, China
| | - Marco A. C. Neves
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Hok-Kiu Lui
- Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Yong Wang
- Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Ka-Yan Chow
- Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Kin-Fai Chan
- Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Siu-Cheong Yan
- Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Yun-Chung Leung
- Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Ruben Abagyan
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
- Molsoft L.L.C, San Diego, California, United States of America
| | - Tak-Hang Chan
- Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
| | - Kwok-Yin Wong
- Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
- * E-mail:
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Bacterial cell division proteins as antibiotic targets. Bioorg Chem 2014; 55:27-38. [PMID: 24755375 DOI: 10.1016/j.bioorg.2014.03.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 03/20/2014] [Accepted: 03/24/2014] [Indexed: 11/21/2022]
Abstract
Proteins involved in bacterial cell division often do not have a counterpart in eukaryotic cells and they are essential for the survival of the bacteria. The genetic accessibility of many bacterial species in combination with the Green Fluorescence Protein revolution to study localization of proteins and the availability of crystal structures has increased our knowledge on bacterial cell division considerably in this century. Consequently, bacterial cell division proteins are more and more recognized as potential new antibiotic targets. An international effort to find small molecules that inhibit the cell division initiating protein FtsZ has yielded many compounds of which some are promising as leads for preclinical use. The essential transglycosylase activity of peptidoglycan synthases has recently become accessible to inhibitor screening. Enzymatic assays for and structural information on essential integral membrane proteins such as MraY and FtsW involved in lipid II (the peptidoglycan building block precursor) biosynthesis have put these proteins on the list of potential new targets. This review summarises and discusses the results and approaches to the development of lead compounds that inhibit bacterial cell division.
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