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Andreu JM, Huecas S, Araújo-Bazán L, Vázquez-Villa H, Martín-Fontecha M. The Search for Antibacterial Inhibitors Targeting Cell Division Protein FtsZ at Its Nucleotide and Allosteric Binding Sites. Biomedicines 2022; 10:biomedicines10081825. [PMID: 36009372 PMCID: PMC9405007 DOI: 10.3390/biomedicines10081825] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/18/2022] [Accepted: 07/25/2022] [Indexed: 11/18/2022] Open
Abstract
The global spread of bacterial antimicrobial resistance is associated to millions of deaths from bacterial infections per year, many of which were previously treatable. This, combined with slow antibiotic deployment, has created an urgent need for developing new antibiotics. A still clinically unexploited mode of action consists in suppressing bacterial cell division. FtsZ, an assembling GTPase, is the key protein organizing division in most bacteria and an attractive target for antibiotic discovery. Nevertheless, developing effective antibacterial inhibitors targeting FtsZ has proven challenging. Here we review our decade-long multidisciplinary research on small molecule inhibitors of bacterial division, in the context of global efforts to discover FtsZ-targeting antibiotics. We focus on methods to characterize synthetic inhibitors that either replace bound GTP from the FtsZ nucleotide binding pocket conserved across diverse bacteria or selectively bind into the allosteric site at the interdomain cleft of FtsZ from Bacillus subtilis and the pathogen Staphylococcus aureus. These approaches include phenotype screening combined with fluorescence polarization screens for ligands binding into each site, followed by detailed cytological profiling, and biochemical and structural studies. The results are analyzed to design an optimized workflow to identify effective FtsZ inhibitors, and new approaches for the discovery of FtsZ-targeting antibiotics are discussed.
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Affiliation(s)
- José M. Andreu
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain; (S.H.); (L.A.-B.)
- Correspondence: (J.M.A.); (M.M.-F.)
| | - Sonia Huecas
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain; (S.H.); (L.A.-B.)
| | - Lidia Araújo-Bazán
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain; (S.H.); (L.A.-B.)
| | - Henar Vázquez-Villa
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040 Madrid, Spain;
| | - Mar Martín-Fontecha
- Departamento de Química Orgánica, Facultad de Óptica y Optometría, Universidad Complutense de Madrid, Avda. Complutense s/n, 28040 Madrid, Spain
- Correspondence: (J.M.A.); (M.M.-F.)
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2
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Huecas S, Canosa-Valls AJ, Araújo-Bazán L, Ruiz FM, Laurents DV, Fernández-Tornero C, Andreu JM. Nucleotide-induced folding of cell division protein FtsZ from Staphylococcus aureus. FEBS J 2020; 287:4048-4067. [PMID: 31997533 DOI: 10.1111/febs.15235] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 12/12/2019] [Accepted: 01/09/2020] [Indexed: 11/29/2022]
Abstract
The essential bacterial division protein FtsZ uses GTP binding and hydrolysis to assemble into dynamic filaments that treadmill around the Z-ring, guiding septal wall synthesis and cell division. FtsZ is a structural homolog of tubulin and a target for discovering new antibiotics. Here, using FtsZ from the pathogen S. aureus (SaFtsZ), we reveal that, prior to assembly, FtsZ monomers require nucleotide binding for folding; this is possibly relevant to other mesophilic FtsZs. Apo-SaFtsZ is essentially unfolded, as assessed by nuclear magnetic resonance and circular dichroism. Binding of GTP (≥ 1 mm) dramatically shifts the equilibrium toward the active folded protein. Supportingly, SaFtsZ refolded with GDP crystallizes in a native structure. Apo-SaFtsZ also folds with 3.4 m glycerol, enabling high-affinity GTP binding (KD 20 nm determined by isothermal titration calorimetry) similar to thermophilic stable FtsZ. Other stabilizing agents that enhance nucleotide binding include ethylene glycol, trimethylamine N-oxide, and several bacterial osmolytes. High salt stabilizes SaFtsZ without bound nucleotide in an inactive twisted conformation. We identified a cavity behind the SaFtsZ-GDP nucleotide-binding pocket that harbors different small compounds, which is available for extended nucleotide-replacing inhibitors. Furthermore, we devised a competition assay to detect any inhibitors that overlap the nucleotide site of SaFtsZ, or Escherichia coli FtsZ, employing osmolyte-stabilized apo-FtsZs and the specific fluorescence anisotropy change in mant-GTP upon dissociation from the protein. This robust assay provides a basis to screening for high-affinity GTP-replacing ligands, which combined with structural studies and phenotypic profiling should facilitate development of a next generation of FtsZ-targeting antibacterial inhibitors.
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Affiliation(s)
- Sonia Huecas
- Centro de Investigaciones Biológicas Margarita Salas CSIC, Madrid, Spain
| | | | - Lidia Araújo-Bazán
- Centro de Investigaciones Biológicas Margarita Salas CSIC, Madrid, Spain
| | - Federico M Ruiz
- Centro de Investigaciones Biológicas Margarita Salas CSIC, Madrid, Spain
| | | | | | - José M Andreu
- Centro de Investigaciones Biológicas Margarita Salas CSIC, Madrid, Spain
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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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4
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Hahn DF, König G, Hünenberger PH. Overcoming Orthogonal Barriers in Alchemical Free Energy Calculations: On the Relative Merits of λ-Variations, λ-Extrapolations, and Biasing. J Chem Theory Comput 2020; 16:1630-1645. [DOI: 10.1021/acs.jctc.9b00853] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- David F. Hahn
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Gerhard König
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Philippe H. Hünenberger
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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Vidović N, Recca T, Francescato P, Rabuffetti M, Sironi M, Oliva F, Pieraccini S, Speranza G. Conformational Studies on Two FtsZ Targeting Cyclic Peptides. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09962-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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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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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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8
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Huecas S, Ramírez-Aportela E, Vergoñós A, Núñez-Ramírez R, Llorca O, Díaz JF, Juan-Rodríguez D, Oliva MA, Castellen P, Andreu JM. Self-Organization of FtsZ Polymers in Solution Reveals Spacer Role of the Disordered C-Terminal Tail. Biophys J 2017; 113:1831-1844. [PMID: 29045877 DOI: 10.1016/j.bpj.2017.08.046] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 07/28/2017] [Accepted: 08/30/2017] [Indexed: 11/24/2022] Open
Abstract
FtsZ is a self-assembling GTPase that forms, below the inner membrane, the mid-cell Z-ring guiding bacterial division. FtsZ monomers polymerize head to tail forming tubulin-like dynamic protofilaments, whose organization in the Z-ring is an unresolved problem. Rather than forming a well-defined structure, FtsZ protofilaments laterally associate in vitro into polymorphic condensates typically imaged on surfaces. We describe here nanoscale self-organizing properties of FtsZ assemblies in solution that underlie Z-ring assembly, employing time-resolved x-ray scattering and cryo-electron microscopy. We find that FtsZ forms bundles made of loosely bound filaments of variable length and curvature. Individual FtsZ protofilaments further bend upon nucleotide hydrolysis, highlighted by the observation of some large circular structures with 2.5-5° curvature angles between subunits, followed by disassembly end-products consisting of highly curved oligomers and 16-subunit -220 Å diameter mini-rings, here observed by cryo-electron microscopy. Neighbor FtsZ filaments in bundles are laterally spaced 70 Å, leaving a gap in between. In contrast, close contact between filament core structures (∼50 Å spacing) is observed in straight polymers of FtsZ constructs lacking the C-terminal tail, which is known to provide a flexible tether essential for FtsZ functions in cell division. Changing the length of the intrinsically disordered C-tail linker modifies the interfilament spacing. We propose that the linker prevents dynamic FtsZ protofilaments in bundles from sticking to one another, holding them apart at a distance similar to the lateral spacing observed by electron cryotomography in several bacteria and liposomes. According to this model, weak interactions between curved polar FtsZ protofilaments through their the C-tails may facilitate the coherent treadmilling dynamics of membrane-associated FtsZ bundles in reconstituted systems, as well as the recently discovered movement of FtsZ clusters around bacterial Z-rings that is powered by GTP hydrolysis and guides correct septal cell wall synthesis and cell division.
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Affiliation(s)
- Sonia Huecas
- Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | | | | | | | - Oscar Llorca
- Centro de Investigaciones Biológicas, CSIC, Madrid, Spain; Spanish National Cancer Research Center, CNIO, Madrid, Spain
| | | | | | - María A Oliva
- Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - Patricia Castellen
- Centro de Investigaciones Biológicas, CSIC, Madrid, Spain; Department of Chemistry, State University of Ponta Grossa, Paraná, Brazil
| | - José M Andreu
- Centro de Investigaciones Biológicas, CSIC, Madrid, Spain.
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Chan KF, Sun N, Yan SC, Wong ILK, Lui HK, Cheung KC, Yuan J, Chan FY, Zheng Z, Chan EWC, Chen S, Leung YC, Chan TH, Wong KY. Efficient Synthesis of Amine-Linked 2,4,6-Trisubstituted Pyrimidines as a New Class of Bacterial FtsZ Inhibitors. ACS OMEGA 2017; 2:7281-7292. [PMID: 30023544 PMCID: PMC6044853 DOI: 10.1021/acsomega.7b00701] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 09/12/2017] [Indexed: 06/08/2023]
Abstract
We have recently identified a new class of filamenting temperature-sensitive mutant Z (FtsZ)-interacting compounds that possess a 2,4,6-trisubstituted pyrimidine-quinuclidine scaffold with moderate antibacterial activity. Employing this scaffold as a molecular template, a compound library of amine-linked 2,4,6-trisubstituted pyrimidines with 99 candidates was successfully established by employing an efficient convergent synthesis designed to explore their structure-activity relationship. The results of minimum inhibitory concentration (MIC) assay against Staphylococcus aureus strains and cytotoxicity assay against the mouse L929 cell line identified those compounds with potent antistaphylococcal properties (MIC ranges from 3 to 8 μg/mL) and some extent of cytotoxicity against normal cells (IC50 ranges from 6 to 27 μM). Importantly, three compounds also exhibited potent antibacterial activities against nine clinically isolated methicillin-resistant S. aureus (MRSA) strains. One of the compounds, 14av_amine16, exhibited low spontaneous frequency of resistance, low toxicity against Galleria mellonella larvae, and the ability to rescue G. mellonella larvae (20% survival rate at a dosage of 100 mg/kg) infected with a lethal dose of MRSA ATCC 43300 strain. Biological characterization of compound 14av_amine16 by saturation transfer difference NMR, light scattering assay, and guanosine triphosphatase hydrolysis assay with purified S. aureus FtsZ protein verified that it interacted with the FtsZ protein. Such a property of FtsZ inhibitors was further confirmed by observing iconic filamentous cell phenotype and mislocalization of the Z-ring formation of Bacillus subtilis. Taken together, these 2,4,6-trisubstituted pyrimidine derivatives represent a novel scaffold of S. aureus FtsZ inhibitors.
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Affiliation(s)
- Kin-Fai Chan
- State Key Laboratory of Chirosciences and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Ning Sun
- State Key Laboratory of Chirosciences and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Siu-Cheong Yan
- State Key Laboratory of Chirosciences and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Iris L K Wong
- State Key Laboratory of Chirosciences and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Hok-Kiu Lui
- State Key Laboratory of Chirosciences and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Kwan-Choi Cheung
- State Key Laboratory of Chirosciences and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Jian Yuan
- State Key Laboratory of Chirosciences and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Fung-Yi Chan
- State Key Laboratory of Chirosciences and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Zhiwei Zheng
- Shenzhen Key Laboratory for Food Biological Safety Control, Food Safety and Technology Research Centre, The Hong Kong PolyU Shenzhen Research Institute, Shenzhen 518057, China
| | - Edward W C Chan
- State Key Laboratory of Chirosciences and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Sheng Chen
- State Key Laboratory of Chirosciences and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
- Shenzhen Key Laboratory for Food Biological Safety Control, Food Safety and Technology Research Centre, The Hong Kong PolyU Shenzhen Research Institute, Shenzhen 518057, China
| | - Yun-Chung Leung
- State Key Laboratory of Chirosciences and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Tak Hang Chan
- State Key Laboratory of Chirosciences and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
- Department of Chemistry, McGill University, Montreal, Quebec H3A 2K6, Canada
| | - Kwok-Yin Wong
- State Key Laboratory of Chirosciences and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
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Zhang W, Gao Q, Wei S, Fu B, Yang Q, Ming X. Synthesis of 8-Substituted 2'-Deoxyisoguanosines via Unprotected 8-Brominated 2-Amino-2'-deoxyadenosine. Chem Biodivers 2017; 15. [PMID: 28853211 DOI: 10.1002/cbdv.201700335] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 08/24/2017] [Indexed: 12/21/2022]
Abstract
A variety of applications of 8-alkynylated nucleosides has prompted the synthesis of new purine analogues. Bromination of unprotected 2-amino-2'-deoxyadenosine with Br2 /AcOH/AcONa gives 2-amino-8-bromo-2'-deoxyadenosine (87%). The brominated derivative is converted to 8-alkynylated 2-amino-2'-deoxyadenosines by palladium-catalyzed Sonogashira cross-coupling reaction via microwave assistance (81 - 95%). The resulting compounds are further transformed to 8-alkynylated 2'-deoxyisoguanosines (52 - 70%). The physical properties of new compounds are investigated.
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Affiliation(s)
- Wen Zhang
- Department of Pharmacy, Chengdu Medical College, No. 783 Xindu Avenue, Chengdu, 610500, P. R. China
| | - Qian Gao
- Department of Pharmacy, Chengdu Medical College, No. 783 Xindu Avenue, Chengdu, 610500, P. R. China
| | - Shuxian Wei
- Department of Pharmacy, Chengdu Medical College, No. 783 Xindu Avenue, Chengdu, 610500, P. R. China
| | - Bicheng Fu
- Department of Pharmacy, Chengdu Medical College, No. 783 Xindu Avenue, Chengdu, 610500, P. R. China
| | - Qian Yang
- Department of Pharmacy, Chengdu Medical College, No. 783 Xindu Avenue, Chengdu, 610500, P. R. China.,Study on the Structure-Specificity Small Molecule Drug in Sichuan Province Colleges Key Laboratory, No. 783 Xindu Avenue, Chengdu, 610500, P. R. China
| | - Xin Ming
- Department of Pharmacy, Chengdu Medical College, No. 783 Xindu Avenue, Chengdu, 610500, P. R. China.,Study on the Structure-Specificity Small Molecule Drug in Sichuan Province Colleges Key Laboratory, No. 783 Xindu Avenue, Chengdu, 610500, P. R. China
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Sridevi D, Sudhakar KU, Ananthathatmula R, Nankar RP, Doble M. Mutation at G103 of MtbFtsZ Altered their Sensitivity to Coumarins. Front Microbiol 2017; 8:578. [PMID: 28428773 PMCID: PMC5382161 DOI: 10.3389/fmicb.2017.00578] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 03/21/2017] [Indexed: 02/02/2023] Open
Abstract
Coumarins are natural polyphenol lactones comprising of fused rings of benzene and α-pyrone. The current study demonstrates the inhibitory effect of coumarins with various substitutions on Mycobacterium smegmatis mc2 155. We also demonstrate the effect of pomegranate (Punica granatum) extract containing ellagic acid, on M. smegmatis as well as their affect on MtbFtsZ (FtsZ from Mycobacterium tuberculosis). The ellagic acid extracts from pomegranate peels inhibit mycobacteria with a MIC of 25 μM and 0.3 to 3.5 mg/mL, respectively, but failed to inhibit the polymerization of MtbFtsZ. However, the coumarins were shown to inhibit the polymerization and GTPase activity of the protein as well as have an inhibitory affect on M. smegmatis mc2 155. Docking of the most active coumarin (7-Dimethyl-4-methyl coumarin with MIC of 38.7 μM) to the GTP binding site suggests that it interacted with the G103 residue. Based on the docking results two mutants of varying activity (G103S and G103A) were constructed to elucidate the interaction of MtbFtsZ and coumarins. Mutation of G103 with Serine (a bulky group) results in an inactive mutant and substitution with alanine produces a variant that retains most of the activity of the wild type. There is a disruption of the protofilament formation of the MtbFtsZ upon interaction with coumarins as demonstrated by TEM. The coumarins increase the length of Mycobacteria five times and MtbFtsZ localization is disturbed. The mutant proteins altered the GTPase and polymerization activity of coumarins as compared to wild type protein. The results here support that coumarins inhibit proliferation of Mycobacteria by targeting the assembly of MtbFtsZ and provide the possible binding site of coumarins on MtbFtsZ. This study may aid in the design of natural products as anti-mycobacterial agents. The currently reported GTP analogs for FtsZ are toxic to the human cell lines; natural coumarins targeting the GTP binding site of MtbFtsZ may hold promise as an important drug lead for tuberculosis treatment.
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Affiliation(s)
- Duggirala Sridevi
- Bioengineering and Drug Design Lab, Department of Biotechnology, Indian Institute of Technology MadrasChennai, India
| | - Karpagam U Sudhakar
- Bioengineering and Drug Design Lab, Department of Biotechnology, Indian Institute of Technology MadrasChennai, India
| | - Ragamanvitha Ananthathatmula
- Bioengineering and Drug Design Lab, Department of Biotechnology, Indian Institute of Technology MadrasChennai, India
| | - Rakesh P Nankar
- Bioengineering and Drug Design Lab, Department of Biotechnology, Indian Institute of Technology MadrasChennai, India
| | - Mukesh Doble
- Bioengineering and Drug Design Lab, Department of Biotechnology, Indian Institute of Technology MadrasChennai, India
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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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Serpi M, Ferrari V, Pertusati F. Nucleoside Derived Antibiotics to Fight Microbial Drug Resistance: New Utilities for an Established Class of Drugs? J Med Chem 2016; 59:10343-10382. [PMID: 27607900 DOI: 10.1021/acs.jmedchem.6b00325] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Novel antibiotics are urgently needed to combat the rise of infections due to drug-resistant microorganisms. Numerous natural nucleosides and their synthetically modified analogues have been reported to have moderate to good antibiotic activity against different bacterial and fungal strains. Nucleoside-based compounds target several crucial processes of bacterial and fungal cells such as nucleoside metabolism and cell wall, nucleic acid, and protein biosynthesis. Nucleoside analogues have also been shown to target many other bacterial and fungal cellular processes although these are not well characterized and may therefore represent opportunities to discover new drugs with unique mechanisms of action. In this Perspective, we demonstrate that nucleoside analogues, cornerstones of anticancer and antiviral treatments, also have great potential to be repurposed as antibiotics so that an old drug can learn new tricks.
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Affiliation(s)
- Michaela Serpi
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University , Redwood Building, King Edward VII Avenue, CF10 3NB Cardiff, United Kingdom
| | - Valentina Ferrari
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University , Redwood Building, King Edward VII Avenue, CF10 3NB Cardiff, United Kingdom
| | - Fabrizio Pertusati
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University , Redwood Building, King Edward VII Avenue, CF10 3NB Cardiff, United Kingdom
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14
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Staker BL, Buchko GW, Myler PJ. Recent contributions of structure-based drug design to the development of antibacterial compounds. Curr Opin Microbiol 2016; 27:133-8. [PMID: 26458180 DOI: 10.1016/j.mib.2015.09.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/09/2015] [Accepted: 09/23/2015] [Indexed: 11/28/2022]
Abstract
According to a Pew Research study published in February 2015, there are 37 antibacterial programs currently in clinical trials in the United States. Protein structure-based methods for guiding small molecule design were used in at least 34 of these programs. Typically, this occurred at an early stage (drug discovery and/or lead optimization) prior to an Investigational New Drug (IND) application, although sometimes in retrospective studies to rationalize biological activity. Recognizing that structure-based methods are resource-intensive and often require specialized equipment and training, the NIAID has funded two Structural Genomics Centers to determine structures of infectious disease species proteins with the aim of supporting individual investigators' research programs with structural biology methods.
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Affiliation(s)
- Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease, United States; Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States.
| | - Garry W Buchko
- Seattle Structural Genomics Center for Infectious Disease, United States; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease, United States; Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), 307 Westlake Ave N, Suite 500, Seattle, WA 98109, United States; Department of Global Health, University of Washington, Seattle, WA 98195, United States; Department of Biomedical Informatics and Health Education, University of Washington, Seattle, WA 98195, United States
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15
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Duggirala S, Napoleon JV, Nankar RP, Senu Adeeba V, Manheri MK, Doble M. FtsZ inhibition and redox modulation with one chemical scaffold: Potential use of dihydroquinolines against mycobacteria. Eur J Med Chem 2016; 123:557-567. [PMID: 27517804 DOI: 10.1016/j.ejmech.2016.07.058] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 07/20/2016] [Accepted: 07/23/2016] [Indexed: 12/15/2022]
Abstract
The dual effect of FtsZ inhibition and oxidative stress by a group of 1,2-dihydroquinolines that culminate in bactericidal effect on mycobacterium strains is demonstrated. They inhibited the non-pathogenic Mycobacterium smegmatis mc(2) 155 with MIC as low as 0.9 μg/mL and induced filamentation. Detailed studies revealed their ability to inhibit polymerization and GTPase activity of MtbFtsZ (Mycobacterial filamentous temperature sensitive Z) with an IC50 value of ∼40 μM. In addition to such target specific effects, these compounds exerted a global cellular effect by causing redox-imbalance that was evident from overproduction of ROS in treated cells. Such multi-targeting effect with one chemical scaffold has considerable significance in this era of emerging drug resistance and could offer promise in the development of new therapeutic agents against tuberculosis.
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Affiliation(s)
- Sridevi Duggirala
- Bioengineering and Drug Design Lab, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, 600 036, India
| | - John Victor Napoleon
- Department of Chemistry, Indian Institute of Technology Madras, Chennai, 600 036, India
| | - Rakesh P Nankar
- Bioengineering and Drug Design Lab, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, 600 036, India
| | - V Senu Adeeba
- Department of Chemistry, Indian Institute of Technology Madras, Chennai, 600 036, India
| | | | - Mukesh Doble
- Bioengineering and Drug Design Lab, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, 600 036, India.
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16
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Abstract
Filamenting temperature-sensitive mutant Z (FtsZ), an essential cell division protein in bacteria, has recently emerged as an important and exploitable antibacterial target. Cytokinesis in bacteria is regulated by the assembly dynamics of this protein, which is ubiquitously present in eubacteria. The perturbation of FtsZ assembly has been found to have a deleterious effect on the cytokinetic machinery and, in turn, upon cell survival. FtsZ is highly conserved among prokaryotes, offering the possibility of broad-spectrum antibacterial agents, while its limited sequence homology with tubulin (an essential protein in eukaryotic mitosis) offers the possibility of selective toxicity. This review aims to summarize current knowledge regarding the mechanism of action of FtsZ, and to highlight existing attempts toward the development of clinically useful inhibitors.
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17
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Kamal A, Nagaseshadri B, Nayak VL, Srinivasulu V, Sathish M, Kapure JS, Suresh Reddy C. Synthesis and biological evaluation of benzimidazole–oxindole conjugates as microtubule-targeting agents. Bioorg Chem 2015; 63:72-84. [DOI: 10.1016/j.bioorg.2015.09.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 09/21/2015] [Accepted: 09/22/2015] [Indexed: 11/25/2022]
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18
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Huecas S, Marcelo F, Perona A, Ruiz-Ávila LB, Morreale A, Cañada FJ, Jiménez-Barbero J, Andreu JM. Beyond a Fluorescent Probe: Inhibition of Cell Division Protein FtsZ by mant-GTP Elucidated by NMR and Biochemical Approaches. ACS Chem Biol 2015; 10:2382-92. [PMID: 26247422 DOI: 10.1021/acschembio.5b00444] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
FtsZ is the organizer of cell division in most bacteria and a target in the quest for new antibiotics. FtsZ is a tubulin-like GTPase, in which the active site is completed at the interface with the next subunit in an assembled FtsZ filament. Fluorescent mant-GTP has been extensively used for competitive binding studies of nucleotide analogs and synthetic GTP-replacing inhibitors possessing antibacterial activity. However, its mode of binding and whether the mant tag interferes with FtsZ assembly function were unknown. Mant-GTP exists in equilibrium as a mixture of C2'- and C3'-substituted isomers. We have unraveled the molecular recognition process of mant-GTP by FtsZ monomers. Both isomers bind in the anti glycosidic bond conformation: 2'-mant-GTP in two ribose puckering conformations and 3'-mant-GTP in the preferred C2' endo conformation. In each case, the mant tag strongly interacts with FtsZ at an extension of the GTP binding site, which is also supported by molecular dynamics simulations. Importantly, mant-GTP binding induces archaeal FtsZ polymerization into inactive curved filaments that cannot hydrolyze the nucleotide, rather than straight GTP-hydrolyzing assemblies, and also inhibits normal assembly of FtsZ from the Gram-negative bacterium Escherichia coli but is hydrolyzed by FtsZ from Gram-positive Bacillus subtilis. Thus, the specific interactions provided by the fluorescent mant tag indicate a new way to search for synthetic FtsZ inhibitors that selectively suppress the cell division of bacterial pathogens.
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Affiliation(s)
- Sonia Huecas
- Centro de Investigaciones
Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Filipa Marcelo
- Centro de Investigaciones
Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
- UCIBIO, REQUIMTE, Dept. de Química, Faculdade de Ciências
e Tecnologia, UNL, 2829-516 Caparica, Portugal
| | - Almudena Perona
- Unidad de Bioinformática,
Centro de Biología Molecular Severo Ochoa, CBMSO−CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Laura B. Ruiz-Ávila
- Centro de Investigaciones
Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Antonio Morreale
- Unidad de Bioinformática,
Centro de Biología Molecular Severo Ochoa, CBMSO−CSIC, Cantoblanco, 28049 Madrid, Spain
| | - F. Javier Cañada
- Centro de Investigaciones
Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Jesús Jiménez-Barbero
- Centro de Investigaciones
Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - José M. Andreu
- Centro de Investigaciones
Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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19
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Souard F, Perrier S, Noël V, Fave C, Fiore E, Peyrin E, Garcia J, Vanhaverbeke C. Optimization of Experimental Parameters to Explore Small-Ligand/Aptamer Interactions through Use of (1) H NMR Spectroscopy and Molecular Modeling. Chemistry 2015; 21:15740-8. [PMID: 26356596 DOI: 10.1002/chem.201501527] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Indexed: 12/25/2022]
Abstract
Aptamers constitute an emerging class of molecules designed and selected to recognize any given target that ranges from small compounds to large biomolecules, and even cells. However, the underlying physicochemical principles that govern the ligand-binding process still have to be clarified. A major issue when dealing with short oligonucleotides is their intrinsic flexibility that renders their active conformation highly sensitive to experimental conditions. To overcome this problem and determine the best experimental parameters, an approach based on the design-of-experiments methodology has been developed. Here, the focus is on DNA aptamers that possess high specificity and affinity for small molecules, L-tyrosinamide, and adenosine monophosphate. Factors such as buffer, pH value, ionic strength, Mg(2+) -ion concentration, and ligand/aptamer ratio have been considered to find the optimal experimental conditions. It was then possible to gain new insight into the conformational features of the two ligands by using ligand-observed NMR spectroscopic techniques and molecular mechanics.
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Affiliation(s)
- Florence Souard
- DPM, Université Grenoble Alpes, Grenoble, 38000 (France). .,DPM, CNRS, Grenoble, 38000 (France).
| | - Sandrine Perrier
- DPM, Université Grenoble Alpes, Grenoble, 38000 (France).,DPM, CNRS, Grenoble, 38000 (France)
| | - Vincent Noël
- ITODYS, UMR 7086 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Paris, 75205 (France)
| | - Claire Fave
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Paris, 75205 (France)
| | - Emmanuelle Fiore
- DPM, Université Grenoble Alpes, Grenoble, 38000 (France).,DPM, CNRS, Grenoble, 38000 (France)
| | - Eric Peyrin
- DPM, Université Grenoble Alpes, Grenoble, 38000 (France).,DPM, CNRS, Grenoble, 38000 (France)
| | - Julian Garcia
- DCM, Université Grenoble Alpes, Grenoble, 38000 (France).,DCM, CNRS, Grenoble, 38000 (France)
| | - Cécile Vanhaverbeke
- DPM, Université Grenoble Alpes, Grenoble, 38000 (France). .,DPM, CNRS, Grenoble, 38000 (France).
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20
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Hybridization Properties of RNA Containing 8-Methoxyguanosine and 8-Benzyloxyguanosine. PLoS One 2015; 10:e0137674. [PMID: 26353054 PMCID: PMC4564172 DOI: 10.1371/journal.pone.0137674] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 08/20/2015] [Indexed: 12/21/2022] Open
Abstract
Modified nucleobase analogues can serve as powerful tools for changing physicochemical and biological properties of DNA or RNA. Guanosine derivatives containing bulky substituents at 8 position are known to adopt syn conformation of N-glycoside bond. On the contrary, in RNA the anti conformation is predominant in Watson-Crick base pairing. In this paper two 8-substituted guanosine derivatives, 8-methoxyguanosine and 8-benzyloxyguanosine, were synthesized and incorporated into oligoribonucleotides to investigate their influence on the thermodynamic stability of RNA duplexes. The methoxy and benzyloxy substituents are electron-donating groups, decreasing the rate of depurination in the monomers, as confirmed by N-glycoside bond stability assessments. Thermodynamic stability studies indicated that substitution of guanosine by 8-methoxy- or 8-benzyloxyguanosine significantly decreased the thermodynamic stability of RNA duplexes. Moreover, the presence of 8-substituted guanosine derivatives decreased mismatch discrimination. Circular dichroism spectra of modified RNA duplexes exhibited patterns typical for A-RNA geometry.
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21
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Ramírez-Aportela E, López-Blanco JR, Andreu JM, Chacón P. Understanding nucleotide-regulated FtsZ filament dynamics and the monomer assembly switch with large-scale atomistic simulations. Biophys J 2015; 107:2164-76. [PMID: 25418101 DOI: 10.1016/j.bpj.2014.09.033] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 09/23/2014] [Accepted: 09/30/2014] [Indexed: 01/08/2023] Open
Abstract
Bacterial cytoskeletal protein FtsZ assembles in a head-to-tail manner, forming dynamic filaments that are essential for cell division. Here, we study their dynamics using unbiased atomistic molecular simulations from representative filament crystal structures. In agreement with experimental data, we find different filament curvatures that are supported by a nucleotide-regulated hinge motion between consecutive FtsZ monomers. Whereas GTP-FtsZ filaments bend and twist in a preferred orientation, thereby burying the nucleotide, the differently curved GDP-FtsZ filaments exhibit a heterogeneous distribution of open and closed interfaces between monomers. We identify a coordinated Mg(2+) ion as the key structural element in closing the nucleotide site and stabilizing GTP filaments, whereas the loss of the contacts with loop T7 from the next monomer in GDP filaments leads to open interfaces that are more prone to depolymerization. We monitored the FtsZ monomer assembly switch, which involves opening/closing of the cleft between the C-terminal domain and the H7 helix, and observed the relaxation of isolated and filament minus-end monomers into the closed-cleft inactive conformation. This result validates the proposed switch between the low-affinity monomeric closed-cleft conformation and the active open-cleft FtsZ conformation within filaments. Finally, we observed how the antibiotic PC190723 suppresses the disassembly switch and allosterically induces closure of the intermonomer interfaces, thus stabilizing the filament. Our studies provide detailed structural and dynamic insights into modulation of both the intrinsic curvature of the FtsZ filaments and the molecular switch coupled to the high-affinity end-wise association of FtsZ monomers.
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Affiliation(s)
- Erney Ramírez-Aportela
- Department of Biological Physical Chemistry, Instituto de Química-Física Rocasolano, CSIC, Madrid, Spain; Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - José Ramón López-Blanco
- Department of Biological Physical Chemistry, Instituto de Química-Física Rocasolano, CSIC, Madrid, Spain
| | - José Manuel Andreu
- Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - Pablo Chacón
- Department of Biological Physical Chemistry, Instituto de Química-Física Rocasolano, CSIC, Madrid, Spain.
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22
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Dow CE, van den Berg HA, Roper DI, Rodger A. Biological Insights from a Simulation Model of the Critical FtsZ Accumulation Required for Prokaryotic Cell Division. Biochemistry 2015; 54:3803-13. [PMID: 26031209 DOI: 10.1021/acs.biochem.5b00261] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A simulation model of prokaryotic Z-ring assembly, based on the observed behavior of FtsZ in vitro as well as on in vivo parameters, is used to integrate critical processes in cell division. According to the model, the cell's ability to divide depends on a "contraction parameter" (χ) that links the force of contraction to the dynamics of FtsZ. This parameter accurately predicts the outcome of division. Evaluating the GTP binding strength, the FtsZ polymerization rate, and the intrinsic GTP hydrolysis/dissociation activity, we find that inhibition of GTP-FtsZ binding is an inefficient antibacterial target. Furthermore, simulations indicate that the temperature sensitivity of the ftsZ84 mutation arises from the conversion of FtsZ to a dual-specificity NTPase. Finally, the sensitivity to temperature of the rate of ATP hydrolysis, over the critical temperature range, leads us to conclude that the ftsZ84 mutation affects the turnover rate of the Z-ring much less strongly than previously reported.
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Affiliation(s)
- Claire E Dow
- †Molecular Organisation and Assembly in Cells Doctoral Training Centre, Senate House, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Hugo A van den Berg
- ‡Mathematics Institute, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - David I Roper
- §School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Alison Rodger
- ∥Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom.,⊥Warwick Analytical Science Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
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23
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Broughton CE, Roper DI, Van Den Berg HA, Rodger A. Bacterial cell division: experimental and theoretical approaches to the divisome. Sci Prog 2015; 98:313-45. [PMID: 26790174 PMCID: PMC10365498 DOI: 10.3184/003685015x14461391862881] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Cell division is a key event in the bacterial life cycle. It involves constriction at the midcell, so that one cell can give rise to two daughter cells. This constriction is mediated by a ring composed offibrous multimers of the protein FtsZ. However a host of additional factors is involved in the formation and dynamics of this "Z-ring" and this complicated apparatus is collectively known as the "divisome". We review the literature, with an emphasis on mathematical modelling, and show how such theoretical efforts have helped experimentalists to make sense of the at times bewildering data, and plan further experiments.
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24
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Wang W, Kong D, Cheng H, Tan L, Zhang Z, Zhuang X, Long H, Zhou Y, Xu Y, Yang X, Ding K. New benzimidazole-2-urea derivates as tubulin inhibitors. Bioorg Med Chem Lett 2014; 24:4250-3. [DOI: 10.1016/j.bmcl.2014.07.035] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 06/20/2014] [Accepted: 07/11/2014] [Indexed: 12/13/2022]
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25
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Duggirala S, Nankar RP, Rajendran S, Doble M. Phytochemicals as Inhibitors of Bacterial Cell Division Protein FtsZ: Coumarins Are Promising Candidates. Appl Biochem Biotechnol 2014; 174:283-96. [DOI: 10.1007/s12010-014-1056-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 07/09/2014] [Indexed: 10/25/2022]
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26
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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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