1
|
Guida M, Tammaro C, Quaranta M, Salvucci B, Biava M, Poce G, Consalvi S. Amino Acid Biosynthesis Inhibitors in Tuberculosis Drug Discovery. Pharmaceutics 2024; 16:725. [PMID: 38931847 PMCID: PMC11206623 DOI: 10.3390/pharmaceutics16060725] [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: 04/19/2024] [Revised: 05/15/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
According to the latest World Health Organization (WHO) report, an estimated 10.6 million people were diagnosed with tuberculosis (TB) in 2022, and 1.30 million died. A major concern is the emergence of multi-drug-resistant (MDR) and extensively drug-resistant (XDR) strains, fueled by the length of anti-TB treatment and HIV comorbidity. Innovative anti-TB agents acting with new modes of action are the only solution to counteract the spread of resistant infections. To escape starvation and survive inside macrophages, Mtb has evolved to become independent of the host by synthesizing its own amino acids. Therefore, targeting amino acid biosynthesis could subvert the ability of the mycobacterium to evade the host immune system, providing innovative avenues for drug discovery. The aim of this review is to give an overview of the most recent progress in the discovery of amino acid biosynthesis inhibitors. Among the hits discovered over the past five years, tryptophan (Trp) inhibitors stand out as the most advanced and have significantly contributed to demonstrating the feasibility of this approach for future TB drug discovery. Future efforts should be directed at prioritizing the chemical optimization of these hits to enrich the TB drug pipeline with high-quality leads.
Collapse
Affiliation(s)
| | | | | | | | | | - Giovanna Poce
- Department of Chemistry and Technologies of Drug, Sapienza University of Rome, Piazzale A. Moro, 5, 00185 Rome, Italy; (M.G.); (C.T.); (M.Q.); (B.S.); (M.B.)
| | - Sara Consalvi
- Department of Chemistry and Technologies of Drug, Sapienza University of Rome, Piazzale A. Moro, 5, 00185 Rome, Italy; (M.G.); (C.T.); (M.Q.); (B.S.); (M.B.)
| |
Collapse
|
2
|
Witek W, Sliwiak J, Rawski M, Ruszkowski M. Targeting imidazole-glycerol phosphate dehydratase in plants: novel approach for structural and functional studies, and inhibitor blueprinting. FRONTIERS IN PLANT SCIENCE 2024; 15:1343980. [PMID: 38559763 PMCID: PMC10978614 DOI: 10.3389/fpls.2024.1343980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 03/04/2024] [Indexed: 04/04/2024]
Abstract
The histidine biosynthetic pathway (HBP) is targeted for herbicide design with preliminary success only regarding imidazole-glycerol phosphate dehydratase (IGPD, EC 4.2.1.19), or HISN5, as referred to in plants. HISN5 catalyzes the sixth step of the HBP, in which imidazole-glycerol phosphate (IGP) is dehydrated to imidazole-acetol phosphate. In this work, we present high-resolution cryoEM and crystal structures of Medicago truncatula HISN5 (MtHISN5) in complexes with an inactive IGP diastereoisomer and with various other ligands. MtHISN5 can serve as a new model for plant HISN5 structural studies, as it enables resolving protein-ligand interactions at high (2.2 Å) resolution using cryoEM. We identified ligand-binding hotspots and characterized the features of plant HISN5 enzymes in the context of the HISN5-targeted inhibitor design. Virtual screening performed against millions of small molecules not only revealed candidate molecules but also identified linkers for fragments that were experimentally confirmed to bind. Based on experimental and computational approaches, this study provides guidelines for designing symmetric HISN5 inhibitors that can reach two neighboring active sites. Finally, we conducted analyses of sequence similarity networks revealing that plant HISN5 enzymes derive from cyanobacteria. We also adopted a new approach to measure MtHISN5 enzymatic activity using isothermal titration calorimetry and enzymatically synthesized IGP.
Collapse
Affiliation(s)
- Wojciech Witek
- Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Joanna Sliwiak
- Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Michal Rawski
- Cryo-EM Facility, SOLARIS National Synchrotron Radiation Centre, Krakow, Poland
| | - Milosz Ruszkowski
- Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| |
Collapse
|
3
|
Raguraman V, Chauhan L, Gehlot P, Kongkham B, Hariprasad P. Computational insights into the role of structurally diverse plant secondary metabolites as inhibitors against Imidazole Glycerol Phosphate Dehydratase of Mycobacterium tuberculosis. J Biomol Struct Dyn 2023:1-13. [PMID: 37578041 DOI: 10.1080/07391102.2023.2245486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 07/28/2023] [Indexed: 08/15/2023]
Abstract
Mycobacterium tuberculosis (Mtb) is one of the major causes of death worldwide and there is a pressing need for the development of novel drug leads. The Imidazole Glycerol Phosphate Dehydratase (IGPD) of Mtb is one of the key enzymes in the histidine biosynthesis pathway and has been recognized as the potentially underexploited drug target for anti-tuberculosis treatment. In the present study, 6063 structurally diverse plant secondary metabolites (PSM) were screened for their efficiency in inhibiting the catalytic activity of IGPD through molecular docking. The top 150 PSMs with the lowest binding energy represent the chemical classes, including Tannins (34%), Flavonoid Glycosides (14%), Terpene Glycosides (10%), Steroid Lactones (9.3%), Flavonoids (6.6%), Steroidal Glycosides (4.6%), etc. Bismahanine, Ashwagandhanolide, and Daurisoline form stable IGPD-inhibitor complexes with binding free energies of -291.3 ± 16.5, -279.0 ± 25.0, and -279.8 ± 17.6 KJ/mol, respectively, as determined by molecular dynamics simulations. These PSM demonstrated strong H-bond interactions with the amino acid residues Ile279, Arg281, and Lys276 in the catalytic region of IGPD, as revealed by structural snapshots. On the basis of our findings, these three PSM could be considered as possible leads against IGPD and should be explored in vitro and in vivo.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Vasantharaja Raguraman
- Environmental Biotechnology Laboratory, Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
| | - Leena Chauhan
- Environmental Biotechnology Laboratory, Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
| | - Priyanka Gehlot
- Environmental Biotechnology Laboratory, Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
| | - Bhani Kongkham
- Environmental Biotechnology Laboratory, Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
| | - P Hariprasad
- Environmental Biotechnology Laboratory, Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
| |
Collapse
|
4
|
Wang L, Liu R, Meng Y, Li F, Lu H. Structure and Function of the Refined C-Terminal Loop in Imidazole Glycerol Phosphate Dehydratase from Different Homologs. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:13871-13880. [PMID: 34780187 DOI: 10.1021/acs.jafc.1c04282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
IGPD is an essential metalloenzyme that catalyzes histidine biosynthesis. We found that its C-terminus loop region has a vital role in determining enzyme activity but has been hardly mentioned before. In this work, we focused on the dynamic feature and function of C-Loop in Arabidopsis thaliana and Saccharomyces cerevisiae IGPD (At_IGPD and Sc_IGPD, respectively). Due to the high flexibility of this region, we performed a total of 3.4 μs of accelerated molecular dynamics simulation to enhance sampling. Inhibitor C348 in At-IGPD exhibited instability in the later stage of simulation, while the characteristic sequence in Sc_IGPD reduced solvent interference and significantly restrained the interaction mode. For the C-Loop-assisted ligand-binding process, we proposed a "Lock-Lid" model. Meanwhile, the dissociated ligand in At_IGPD served as a probe, a metastable pocket was determined at the root of C-Loop, and its rationality was proved by theoretical verification and enzyme mutation experiments. This study complemented the important structural features of C-Loop and provided a basis for the design of selective inhibitors. Considering the absence in mammals, we suggested that IGPD could be a promising germicide target.
Collapse
Affiliation(s)
- Leng Wang
- Department of Chemistry, College of Science, China Agricultural University, 100193 Beijing, China
| | - Ruiyuan Liu
- Department of Chemistry, College of Science, China Agricultural University, 100193 Beijing, China
| | - Yue Meng
- Department of Chemistry, College of Science, China Agricultural University, 100193 Beijing, China
| | - Fang Li
- Department of Chemistry, College of Science, China Agricultural University, 100193 Beijing, China
| | - Huizhe Lu
- Department of Chemistry, College of Science, China Agricultural University, 100193 Beijing, China
| |
Collapse
|
5
|
Kumar D, Jha B, Bhatia I, Ashraf A, Dwivedy A, Biswal BK. Characterization of a triazole scaffold compound as an inhibitor of Mycobacterium tuberculosis imidazoleglycerol-phosphate dehydratase. Proteins 2021; 90:3-17. [PMID: 34288118 DOI: 10.1002/prot.26181] [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: 01/07/2021] [Revised: 04/24/2021] [Accepted: 07/11/2021] [Indexed: 11/11/2022]
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of human tuberculosis (TB), employs ten enzymes including imidazoleglycerol-phosphate dehydratase (IGPD) for de novo biosynthesis of histidine. The absence of histidine-biosynthesis in humans combined with its essentiality for Mtb makes the enzymes of this pathway major anti-TB drug targets. We explored the inhibitory potential of a small molecule β-(1,2,4-Triazole-3-yl)-DL-alanine (DLA) against Mtb IGPD. DLA exhibits an in vitro inhibitory efficacy in the lower micromolar range. Higher-resolution crystal structures of native and substrate-bound Mtb IGPD provided additional structural features of this important drug target. Crystal structure of IGPD-DLA complex at a resolution of 1.75 Å, confirmed that DLA locks down the function of the enzyme by binding in the active site pocket of the IGPD mimicking the substrate-binding mode to a high degree. In our biochemical study, DLA showed an efficient inhibition of Mtb IGPD. Furthermore, DLA also showed bactericidal activity against Mtb and Mycobacterium smegmatis and inhibited their growth in respective culture medium. Importantly, owing to the favorable ADME and physicochemical properties, it serves as an important lead molecule for further derivatizations.
Collapse
Affiliation(s)
- Deepak Kumar
- Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi, India.,Department of Zoology, University of Rajasthan, JLN Marg, Jaipur, Rajasthan, India
| | - Bhavya Jha
- Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi, India.,Department of Zoology, GDM Mahavidyalaya, Patliputra University, Kankarbagh, Patna, Bihar, India
| | - Indu Bhatia
- Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi, India
| | - Anam Ashraf
- Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi, India
| | - Abhisek Dwivedy
- Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi, India
| | - Bichitra Kumar Biswal
- Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi, India
| |
Collapse
|
6
|
De novo histidine biosynthesis protects Mycobacterium tuberculosis from host IFN-γ mediated histidine starvation. Commun Biol 2021; 4:410. [PMID: 33767335 PMCID: PMC7994828 DOI: 10.1038/s42003-021-01926-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 03/01/2021] [Indexed: 01/31/2023] Open
Abstract
Intracellular pathogens including Mycobacterium tuberculosis (Mtb) have evolved with strategies to uptake amino acids from host cells to fulfil their metabolic requirements. However, Mtb also possesses de novo biosynthesis pathways for all the amino acids. This raises a pertinent question- how does Mtb meet its histidine requirements within an in vivo infection setting? Here, we present a mechanism in which the host, by up-regulating its histidine catabolizing enzymes through interferon gamma (IFN-γ) mediated signalling, exerts an immune response directed at starving the bacillus of intracellular free histidine. However, the wild-type Mtb evades this host immune response by biosynthesizing histidine de novo, whereas a histidine auxotroph fails to multiply. Notably, in an IFN-γ-/- mouse model, the auxotroph exhibits a similar extent of virulence as that of the wild-type. The results augment the current understanding of host-Mtb interactions and highlight the essentiality of Mtb histidine biosynthesis for its pathogenesis.
Collapse
|
7
|
Qu Q, Wang J, Cui W, Zhou Y, Xing X, Che R, Liu X, Chen X, Bello-Onaghise G, Dong C, Li Z, Li X, Li Y. In vitro activity and In vivo efficacy of Isoliquiritigenin against Staphylococcus xylosus ATCC 700404 by IGPD target. PLoS One 2019; 14:e0226260. [PMID: 31860659 PMCID: PMC6924684 DOI: 10.1371/journal.pone.0226260] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/23/2019] [Indexed: 12/16/2022] Open
Abstract
Staphylococcus xylosus (S. xylosus) is a type of coagulase-negative Staphylococcus, which was previously considered as non-pathogenic. However, recent studies have linked it with cases of mastitis in cows. Isoliquiritigenin (ISL) is a bioactive compound with pharmacological functions including antibacterial activity. In this study, we evaluated the effect of ISL on S. xylosus in vitro and in vivo. The MIC of ISL against S. xylosus was 80 μg/mL. It was observed that sub-MICs of ISL (1/2MIC, 1/4MIC, 1/8MIC) significantly inhibited the formation of S. xylosus biofilm in vitro. Previous studies have observed that inhibiting imidazole glycerol phosphate dehydratase (IGPD) concomitantly inhibited biofilm formation in S. xylosus. So, we designed experiments to target the formation of IGPD or inhibits its activities in S. xylosus ATCC 700404. The results indicated that the activity of IGPD and its histidine content decreased significantly under 1/2 MIC (40 μg/mL) ISL, and the expression of IGPD gene (hisB) and IGPD protein was significantly down-regulated. Furthermore, Bio-layer interferometry experiments showed that ISL directly interacted with IGPD protein (with strong affinity; KD = 234 μM). In addition, molecular docking was used to predict the binding mode of ISL and IGPD. In vivo tests revealed that, ISL significantly reduced TNF-α and IL-6 levels, mitigated the destruction of the mammary glands and reversed the production of inflammatory cells in mice. The results of the study suggest that, ISL may inhibit S. xylosus growth by acting on IGPD, which can be used as a target protein to treat infections caused by S. xylosus.
Collapse
Affiliation(s)
- Qianwei Qu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, P. R. China
| | - Jinpeng Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, P. R. China
| | - Wenqiang Cui
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, P. R. China
| | - Yonghui Zhou
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, P. R. China
| | - Xiaoxu Xing
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, P. R. China
| | - Ruixiang Che
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, P. R. China
| | - Xin Liu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, P. R. China
| | - Xueying Chen
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, P. R. China
| | - God’spower Bello-Onaghise
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, P. R. China
| | - Chunliu Dong
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, P. R. China
| | - Zhengze Li
- Jiangxi University of Traditional Chinese Medicine, Nanchang, Jiangxi, P. R. China
| | - Xiubo Li
- Feed Research Institute Chinese Academy of Agricultural Science, Harbin, Heilongjiang, P. R. China
| | - Yanhua Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, P. R. China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, Heilongjiang, P. R. China
- * E-mail:
| |
Collapse
|
8
|
Dwivedy A, Jha B, Singh KH, Ahmad M, Ashraf A, Kumar D, Biswal BK. Serendipitous crystallization and structure determination of bacterioferritin from Achromobacter. Acta Crystallogr F Struct Biol Commun 2018; 74:558-566. [PMID: 30198888 PMCID: PMC6130420 DOI: 10.1107/s2053230x18009809] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 07/09/2018] [Indexed: 11/10/2022] Open
Abstract
Bacterioferritins (Bfrs) are ferritin-like molecules with a hollow spherical 24-mer complex design that are unique to bacterial and archaeal species. They play a critical role in storing iron(III) within the complex at concentrations much higher than the feasible solubility limits of iron(III), thus maintaining iron homeostasis within cells. Here, the crystal structure of bacterioferritin from Achromobacter (Ach Bfr) that crystallized serendipitously during a crystallization attempt of an unrelated mycobacterial protein is reported at 1.95 Å resolution. Notably, Fe atoms were bound to the structure along with a porphyrin ring sandwiched between the subunits of a dimer. Furthermore, the dinuclear ferroxidase center of Ach Bfr has only a single iron bound, in contrast to the two Fe atoms in other Bfrs. The structure of Ach Bfr clearly demonstrates the substitution of a glutamate residue, which is involved in the interaction with the second Fe atom, by a threonine and the consequent absence of another Fe atom there. The iron at the dinuclear center has a tetravalent coordination, while a second iron with a hexavalent coordination was found within the porphyrin ring, generating a heme moiety. Achromobacter spp. are known opportunistic pathogens; this structure enhances the current understanding of their iron metabolism and regulation, and importantly will be useful in the design of small-molecule inhibitors against this protein through a structure-guided approach.
Collapse
Affiliation(s)
- Abhisek Dwivedy
- Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Bhavya Jha
- Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Khundrakpam Herojit Singh
- Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Mohammed Ahmad
- Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Anam Ashraf
- Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Deepak Kumar
- Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Bichitra Kumar Biswal
- Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| |
Collapse
|
9
|
Ding W, Zhou Y, Qu Q, Cui W, God'spower BO, Liu Y, Chen X, Chen M, Yang Y, Li Y. Azithromycin Inhibits Biofilm Formation by Staphylococcus xylosus and Affects Histidine Biosynthesis Pathway. Front Pharmacol 2018; 9:740. [PMID: 30042679 PMCID: PMC6048454 DOI: 10.3389/fphar.2018.00740] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 06/18/2018] [Indexed: 11/13/2022] Open
Abstract
Staphylococcus xylosus, a coagulase-negative, non-pathogenic bacterium, responsible for opportunistic infections in humans and bovine mastitis, has the ability to form biofilms, which are responsible for persistent infections and antibiotic resistance. In our study, azithromycin significantly inhibited biofilm formation by altering protein expression. Of the 1764 proteins measured by the isobaric Tag for Relative and Absolute Quantification (iTRAQ) technique, only 148 proteins showed significantly different expression between the azithromycin-treated and untreated cells. Most ribosomal proteins were markedly up-regulated, and the expression of the proteins involved in histidine biosynthesis, which, in turn, influence biofilm formation, was down-regulated, particularly imidazole glycerophosphate dehydratase (IGPD). Previously, we had observed that IGPD plays an important role in biofilm formation by S. xylosus. Therefore, hisB expression was studied by real-time PCR, and the interactions between azithromycin and IGPD were predicted by molecular docking analysis. hisB was found to be significantly down-regulated, and six bond interactions were observed between azithromycin and IGPD. Many active atoms of azithromycin did not interact with the biologically active site of IGPD. Surface plasmon resonance analysis used to further study the relationship between IGPD and azithromycin showed minimum interaction between them. Histidine content in the azithromycin-treated and untreated groups was determined. We noted a slight difference, which was not consistent with the expression of the proteins involved in histidine biosynthesis. Therefore, histidine degradation into glutamate was also studied, and we found that all proteins were down-regulated. This could be the reason why histidine content showed little change between the treated and untreated groups. In summary, we found that azithromycin is a potential inhibitor of S. xylosus biofilm formation, and the underlying mechanism was preliminarily elucidated in this study.
Collapse
Affiliation(s)
- Wenya Ding
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Yonghui Zhou
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Qianwei Qu
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Wenqiang Cui
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Bello Onaghise God'spower
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Yanyan Liu
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Xueying Chen
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Mo Chen
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Yanbei Yang
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Yanhua Li
- Department of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| |
Collapse
|
10
|
Structural and functional studies of histidine biosynthesis in Acanthamoeba spp. demonstrates a novel molecular arrangement and target for antimicrobials. PLoS One 2018; 13:e0198827. [PMID: 29969448 PMCID: PMC6029752 DOI: 10.1371/journal.pone.0198827] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 05/26/2018] [Indexed: 01/29/2023] Open
Abstract
Acanthamoeba is normally free-living, but sometimes facultative and occasionally opportunistic parasites. Current therapies are, by necessity, arduous and yet poorly effective due to their inabilities to kill cyst stages or in some cases to actually induce encystation. Acanthamoeba can therefore survive as cysts and cause disease recurrence. Herein, in pursuit of better therapies and to understand the biochemistry of this understudied organism, we characterize its histidine biosynthesis pathway and explore the potential of targeting this with antimicrobials. We demonstrate that Acanthamoeba is a histidine autotroph, but with the ability to scavenge preformed histidine. It is able to grow in defined media lacking this amino acid, but is inhibited by 3-amino-1,2,4-triazole (3AT) that targets Imidazoleglycerol-Phosphate Dehydratase (IGPD) the rate limiting step of histidine biosynthesis. The structure of Acanthamoeba IGPD has also been determined in complex with 2-hydroxy-3-(1,2,4-triazol-1-yl) propylphosphonate [(R)-C348], a recently described novel inhibitor of Arabidopsis thaliana IGPD. This compound inhibited the growth of four Acanthamoeba species, having a 50% inhibitory concentration (IC50) ranging from 250-526 nM. This effect could be ablated by the addition of 1 mM exogenous free histidine, but importantly not by physiological concentrations found in mammalian tissues. The ability of 3AT and (R)-C348 to restrict the growth of four strains of Acanthamoeba spp. including a recently isolated clinical strain, while not inducing encystment, demonstrates the potential therapeutic utility of targeting the histidine biosynthesis pathway in Acanthamoeba.
Collapse
|
11
|
Jha B, Kumar D, Sharma A, Dwivedy A, Singh R, Biswal BK. Identification and structural characterization of a histidinol phosphate phosphatase from Mycobacterium tuberculosis. J Biol Chem 2018; 293:10102-10118. [PMID: 29752410 PMCID: PMC6028948 DOI: 10.1074/jbc.ra118.002299] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 05/10/2018] [Indexed: 01/07/2023] Open
Abstract
The absence of a histidine biosynthesis pathway in humans, coupled with histidine essentiality for survival of the important human pathogen Mycobacterium tuberculosis (Mtb), underscores the importance of the bacterial enzymes of this pathway as major antituberculosis drug targets. However, the identity of the mycobacterial enzyme that functions as the histidinol phosphate phosphatase (HolPase) of this pathway remains to be established. Here, we demonstrate that the enzyme encoded by the Rv3137 gene, belonging to the inositol monophosphatase (IMPase) family, functions as the Mtb HolPase and specifically dephosphorylates histidinol phosphate. The crystal structure of Rv3137 in apo form enabled us to dissect its distinct structural features. Furthermore, the holo-complex structure revealed that a unique cocatalytic multizinc-assisted mode of substrate binding and catalysis is the hallmark of Mtb HolPase. Interestingly, the enzyme-substrate complex structure unveiled that although monomers possess individual catalytic sites they share a common product-exit channel at the dimer interface. Furthermore, target-based screening against HolPase identified several small-molecule inhibitors of this enzyme. Taken together, our study unravels the missing enzyme link in the Mtb histidine biosynthesis pathway, augments our current mechanistic understanding of histidine production in Mtb, and has helped identify potential inhibitors of this bacterial pathway.
Collapse
Affiliation(s)
- Bhavya Jha
- From the Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi 110067, India and
| | - Deepak Kumar
- From the Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi 110067, India and
| | - Arun Sharma
- Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India
| | - Abhisek Dwivedy
- From the Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi 110067, India and
| | - Ramandeep Singh
- Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India
| | - Bichitra Kumar Biswal
- From the Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, Delhi 110067, India and , Recipient of funding from the National Institute of Immunology, New Delhi, India. To whom correspondence should be addressed. Tel.:
91-11-26703705; Fax:
91-11-26742125; E-mail:
| |
Collapse
|
12
|
Zhou YH, Xu CG, Yang YB, Xing XX, Liu X, Qu QW, Ding WY, Bello-Onaghise G, Li YH. Histidine Metabolism and IGPD Play a Key Role in Cefquinome Inhibiting Biofilm Formation of Staphylococcus xylosus. Front Microbiol 2018; 9:665. [PMID: 29675012 PMCID: PMC5896262 DOI: 10.3389/fmicb.2018.00665] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 03/21/2018] [Indexed: 12/20/2022] Open
Abstract
Staphylococcus xylosus (S. xylosus) is an AT-rich and coagulase-negative Staphylococcus (CNS). It is normally regarded as non-pathogenic, however, recent studies have demonstrated that it is related to human opportunistic infections and bovine mastitis. In addition, S. xylosus strains have the ability to form biofilm. Biofilms are also involved in chronic infections and antibiotic resistance, there are only a few reports about cefquinome inhibiting S. xylosus biofilm formation and the protein targets of cefquinome. In our study, we found that sub-MICs of cefquinome were sufficient to inhibit biofilm formation. To investigate the potential protein targets of cefquinome, we used iTRAQ for the analyses of cells at two different conditions: 1/2-MIC (0.125 μg/mL) cefquinome treatment and no treatment. Using iTRAQ technique and KEGG database analysis, we found that proteins differently expression in histidine metabolism pathway may play a role in the process by which 1/2-MIC (0.125 μg/mL) cefquinome inhibits S. xylosus biofilm formation. Interestingly, we found a sharply down-regulated enzyme [A0A068E9J3 imidazoleglycerol-phosphate dehydratase (IGPD)] involved in histidine metabolism pathway in cefquinome-treated cells. We demonstrated the important role of IGPD in sub-MICs cefquinome inhibiting biofilm formation of S. xylosus by gene (hisB) knockout, IGPD enzyme activity and histidine content assays. Thus, our data sheds light on important role of histidine metabolism in S. xylosus biofilm formation; especially, IGPD involved in histidine metabolism might play a crucial role in sub-MICs cefquinome inhibition of biofilm formation of S. xylosus, and we propose IGPD as an attractive protein target of cefquinome.
Collapse
Affiliation(s)
- Yong-Hui Zhou
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Chang-Geng Xu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Yan-Bei Yang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Xiao-Xu Xing
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Xin Liu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Qian-Wei Qu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Wen-Ya Ding
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - God'spower Bello-Onaghise
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Yan-Hua Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| |
Collapse
|
13
|
Abstract
Histidine biosynthesis is a target for herbicide and antibacterial agents, with imidazoleglycerol-phosphate dehydratase (IGPD) a key enzyme within this pathway. As a result, IGPD is the focus of inhibitor design programs, with several potent herbicides in development. Interestingly, the lead inhibitor is more potent against yeast (Saccharomyces) compared with plant (Arabidopsis) IGPD. To understand this change, we have determined their structure by electron microscopy to reveal a possible mechanism behind differences in inhibitor potency, with Saccharomyces IGPD containing a 24-amino acid insert that forms an extended surface loop that stabilizes an inhibitor binding loop. This study provides insights into the IGPD family and demonstrates the power of using an electron microcopy approach to study inhibitor binding. Histidine biosynthesis is an essential process in plants and microorganisms, making it an attractive target for the development of herbicides and antibacterial agents. Imidazoleglycerol-phosphate dehydratase (IGPD), a key enzyme within this pathway, has been biochemically characterized in both Saccharomyces cerevisiae (Sc_IGPD) and Arabidopsis thaliana (At_IGPD). The plant enzyme, having been the focus of in-depth structural analysis as part of an inhibitor development program, has revealed details about the reaction mechanism of IGPD, whereas the yeast enzyme has proven intractable to crystallography studies. The structure–activity relationship of potent triazole-phosphonate inhibitors of IGPD has been determined in both homologs, revealing that the lead inhibitor (C348) is an order of magnitude more potent against Sc_IGPD than At_IGPD; however, the molecular basis of this difference has not been established. Here we have used single-particle electron microscopy (EM) to study structural differences between the At and Sc_IGPD homologs, which could influence the difference in inhibitor potency. The resulting EM maps at ∼3 Å are sufficient to de novo build the protein structure and identify the inhibitor binding site, which has been validated against the crystal structure of the At_IGPD/C348 complex. The structure of Sc_IGPD reveals that a 24-amino acid insertion forms an extended loop region on the enzyme surface that lies adjacent to the active site, forming interactions with the substrate/inhibitor binding loop that may influence inhibitor potency. Overall, this study provides insights into the IGPD family and demonstrates the power of using an EM approach to study inhibitor binding.
Collapse
|
14
|
Podshivalov D, Mandzhieva YB, Sidorov-Biryukov DD, Timofeev VI, Kuranova IP. Discovery of Selective Inhibitors of Imidazoleglycerol-Phosphate Dehydratase from Mycobacterium tuberculosis by Virtual Screening. CRYSTALLOGR REP+ 2018. [DOI: 10.1134/s1063774518010133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
15
|
Chen XR, Wang XT, Hao MQ, Zhou YH, Cui WQ, Xing XX, Xu CG, Bai JW, Li YH. Homology Modeling and Virtual Screening to Discover Potent Inhibitors Targeting the Imidazole Glycerophosphate Dehydratase Protein in Staphylococcus xylosus. Front Chem 2017; 5:98. [PMID: 29177138 PMCID: PMC5686052 DOI: 10.3389/fchem.2017.00098] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 10/30/2017] [Indexed: 01/11/2023] Open
Abstract
The imidazole glycerophosphate dehydratase (IGPD) protein is a therapeutic target for herbicide discovery. It is also regarded as a possible target in Staphylococcus xylosus (S. xylosus) for solving mastitis in the dairy cow. The 3D structure of IGPD protein is essential for discovering novel inhibitors during high-throughput virtual screening. However, to date, the 3D structure of IGPD protein of S. xylosus has not been solved. In this study, a series of computational techniques including homology modeling, Ramachandran Plots, and Verify 3D were performed in order to construct an appropriate 3D model of IGPD protein of S. xylosus. Nine hits were identified from 2,500 compounds by docking studies. Then, these nine compounds were first tested in vitro in S. xylosus biofilm formation using crystal violet staining. One of the potential compounds, baicalin was shown to significantly inhibit S. xylosus biofilm formation. Finally, the baicalin was further evaluated, which showed better inhibition of biofilm formation capability in S. xylosus by scanning electron microscopy. Hence, we have predicted the structure of IGPD protein of S. xylosus using computational techniques. We further discovered the IGPD protein was targeted by baicalin compound which inhibited the biofilm formation in S. xylosus. Our findings here would provide implications for the further development of novel IGPD inhibitors for the treatment of dairy mastitis.
Collapse
Affiliation(s)
- Xing-Ru Chen
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Xiao-Ting Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Mei-Qi Hao
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Yong-Hui Zhou
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Wen-Qiang Cui
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Xiao-Xu Xing
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Chang-Geng Xu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Jing-Wen Bai
- College of Science, Northeast Agricultural University, Harbin, China
| | - Yan-Hua Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| |
Collapse
|
16
|
Xu CG, Yang YB, Zhou YH, Hao MQ, Ren YZ, Wang XT, Chen JQ, Muhammad I, Wang S, Liu D, Li XB, Li YH. Comparative Proteomic Analysis Provides insight into the Key Proteins as Possible Targets Involved in Aspirin Inhibiting Biofilm Formation of Staphylococcus xylosus. Front Pharmacol 2017; 8:543. [PMID: 28871227 PMCID: PMC5566577 DOI: 10.3389/fphar.2017.00543] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 08/04/2017] [Indexed: 01/01/2023] Open
Abstract
Staphylococcus xylosus is an opportunistic pathogen that causes infection in humans and cow mastitis. And S. xylosus possesses a strong ability to form biofilms in vitro. As biofilm formation facilitates resistance to antimicrobial agents, the discovery of new medicinal properties for classic drugs is highly desired. Aspirin, which is the most common active component of non-steroidal anti-inflammatory compounds, affects the biofilm-forming capacity of various bacterial species. We have found that aspirin effectively inhibits biofilm formation of S. xylosus by Crystal violet (CV) staining and scanning electron microscopy analyses. The present study sought to elucidate possible targets of aspirin in suppressing S. xylosus biofilm formation. Based on an isobaric tag for relative and absolute quantitation (iTRAQ) fold-change of >1.2 or <0.8 (P-value < 0.05), 178 differentially expressed proteins, 111 down-regulated and 67 up-regulated, were identified after application of aspirin to cells at a 1/2 minimal inhibitory concentration. Gene ontology analysis indicated enrichment in metabolic processes for the majority of the differentially expressed proteins. We then used the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database to analyze a large number of differentially expressed proteins and identified genes involved in biosynthesis of amino acids pathway, carbon metabolism (pentose phosphate and glycolytic pathways, tricarboxylic acid cycle) and nitrogen metabolism (histidine metabolism). These novel proteins represent candidate targets in aspirin-mediated inhibition of S. xylosus biofilm formation at sub-MIC levels. The findings lay the foundation for further studies to identify potential aspirin targets.
Collapse
Affiliation(s)
- Chang-Geng Xu
- College of Veterinary Medicine, Northeast Agricultural UniversityHarbin, China
| | - Yan-Bei Yang
- College of Veterinary Medicine, Northeast Agricultural UniversityHarbin, China
| | - Yong-Hui Zhou
- College of Veterinary Medicine, Northeast Agricultural UniversityHarbin, China
| | - Mei-Qi Hao
- College of Veterinary Medicine, Northeast Agricultural UniversityHarbin, China
| | - Yong-Zhi Ren
- College of Veterinary Medicine, Northeast Agricultural UniversityHarbin, China
| | - Xiao-Ting Wang
- College of Veterinary Medicine, Northeast Agricultural UniversityHarbin, China
| | - Jian-Qing Chen
- College of Veterinary Medicine, Northeast Agricultural UniversityHarbin, China
| | - Ishfaq Muhammad
- College of Veterinary Medicine, Northeast Agricultural UniversityHarbin, China
| | - Shuai Wang
- College of Veterinary Medicine, Northeast Agricultural UniversityHarbin, China
| | - Di Liu
- Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Xiu-Bo Li
- Feed Research Institute, Chinese Academy of Agricultural SciencesBeijing, China
| | - Yan-Hua Li
- College of Veterinary Medicine, Northeast Agricultural UniversityHarbin, China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical DevelopmentHarbin, China
| |
Collapse
|
17
|
Bisson C, Britton KL, Sedelnikova SE, Rodgers HF, Eadsforth TC, Viner RC, Hawkes TR, Baker PJ, Rice DW. Mirror-Image Packing Provides a Molecular Basis for the Nanomolar Equipotency of Enantiomers of an Experimental Herbicide. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201607185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Claudine Bisson
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology; University of Sheffield; Firth Court Western Bank Sheffield S10 2TN UK
| | - K. Linda Britton
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology; University of Sheffield; Firth Court Western Bank Sheffield S10 2TN UK
| | - Svetlana E. Sedelnikova
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology; University of Sheffield; Firth Court Western Bank Sheffield S10 2TN UK
| | - H. Fiona Rodgers
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology; University of Sheffield; Firth Court Western Bank Sheffield S10 2TN UK
| | - Thomas C. Eadsforth
- Division of Biological Chemistry and Drug Discovery; Wellcome Trust Biocentre; University of Dundee; Dundee DD1 5EH UK
| | - Russell C. Viner
- Syngenta, Jealott's Hill International Research Station; Bracknell RG42 6EY UK
| | - Tim R. Hawkes
- Syngenta, Jealott's Hill International Research Station; Bracknell RG42 6EY UK
| | - Patrick J. Baker
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology; University of Sheffield; Firth Court Western Bank Sheffield S10 2TN UK
| | - David W. Rice
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology; University of Sheffield; Firth Court Western Bank Sheffield S10 2TN UK
| |
Collapse
|
18
|
Bisson C, Britton KL, Sedelnikova SE, Rodgers HF, Eadsforth TC, Viner RC, Hawkes TR, Baker PJ, Rice DW. Mirror-Image Packing Provides a Molecular Basis for the Nanomolar Equipotency of Enantiomers of an Experimental Herbicide. Angew Chem Int Ed Engl 2016; 55:13485-13489. [PMID: 27717128 PMCID: PMC5113775 DOI: 10.1002/anie.201607185] [Citation(s) in RCA: 12] [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: 07/25/2016] [Indexed: 11/26/2022]
Abstract
Programs of drug discovery generally exploit one enantiomer of a chiral compound for lead development following the principle that enantiomer recognition is central to biological specificity. However, chiral promiscuity has been identified for a number of enzyme families, which have shown that mirror-image packing can enable opposite enantiomers to be accommodated in an enzyme's active site. Reported here is a series of crystallographic studies of complexes between an enzyme and a potent experimental herbicide whose chiral center forms an essential part of the inhibitor pharmacophore. Initial studies with a racemate at 1.85 Å resolution failed to identify the chirality of the bound inhibitor, however, by extending the resolution to 1.1 Å and by analyzing high-resolution complexes with the enantiopure compounds, we determined that both enantiomers make equivalent pseudosymmetric interactions in the active site, thus mimicking an achiral reaction intermediate.
Collapse
Affiliation(s)
- Claudine Bisson
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - K Linda Britton
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Svetlana E Sedelnikova
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - H Fiona Rodgers
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Thomas C Eadsforth
- Division of Biological Chemistry and Drug Discovery, Wellcome Trust Biocentre, University of Dundee, Dundee, DD1 5EH, UK
| | - Russell C Viner
- Syngenta, Jealott's Hill International Research Station, Bracknell, RG42 6EY, UK
| | - Tim R Hawkes
- Syngenta, Jealott's Hill International Research Station, Bracknell, RG42 6EY, UK
| | - Patrick J Baker
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK.
| | - David W Rice
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK.
| |
Collapse
|
19
|
Dietl AM, Amich J, Leal S, Beckmann N, Binder U, Beilhack A, Pearlman E, Haas H. Histidine biosynthesis plays a crucial role in metal homeostasis and virulence of Aspergillus fumigatus. Virulence 2016; 7:465-76. [PMID: 26854126 PMCID: PMC4871644 DOI: 10.1080/21505594.2016.1146848] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Aspergillus fumigatus is the most prevalent airborne fungal pathogen causing invasive fungal infections in immunosuppressed individuals. The histidine biosynthetic pathway is found in bacteria, archaebacteria, lower eukaryotes, and plants, but is absent in mammals. Here we demonstrate that deletion of the gene encoding imidazoleglycerol-phosphate dehydratase (HisB) in A. fumigatus causes (i) histidine auxotrophy, (ii) decreased resistance to both starvation and excess of various heavy metals, including iron, copper and zinc, which play a pivotal role in antimicrobial host defense, (iii) attenuation of pathogenicity in 4 virulence models: murine pulmonary infection, murine systemic infection, murine corneal infection, and wax moth larvae. In agreement with the in vivo importance of histidine biosynthesis, the HisB inhibitor 3-amino-1,2,4-triazole reduced the virulence of the A. fumigatus wild type and histidine supplementation partially rescued virulence of the histidine-auxotrophic mutant in the wax moth model. Taken together, this study reveals limited histidine availability in diverse A. fumigatus host niches, a crucial role for histidine in metal homeostasis, and the histidine biosynthetic pathway as being an attractive target for development of novel antifungal therapy approaches.
Collapse
Affiliation(s)
- Anna-Maria Dietl
- a Division of Molecular Biology, Biocenter, Medical University of Innsbruck , Innsbruck , Austria
| | - Jorge Amich
- b IZKF Forschergruppe für Experimentelle Stammzelltransplantation, Medizinische Klinik und Poliklinik II & Universitäts-Kinderklinik , Würzburg , Germany
| | - Sixto Leal
- c Department of Ophthalmology and Visual Sciences , Case Western Reserve University , Cleveland , OH , USA
| | - Nicola Beckmann
- a Division of Molecular Biology, Biocenter, Medical University of Innsbruck , Innsbruck , Austria
| | - Ulrike Binder
- d Division of Hygiene & Medical Microbiology, Medical University of Innsbruck , Innsbruck , Austria
| | - Andreas Beilhack
- b IZKF Forschergruppe für Experimentelle Stammzelltransplantation, Medizinische Klinik und Poliklinik II & Universitäts-Kinderklinik , Würzburg , Germany
| | - Eric Pearlman
- c Department of Ophthalmology and Visual Sciences , Case Western Reserve University , Cleveland , OH , USA
| | - Hubertus Haas
- a Division of Molecular Biology, Biocenter, Medical University of Innsbruck , Innsbruck , Austria
| |
Collapse
|
20
|
Bisson C, Britton KL, Sedelnikova SE, Rodgers HF, Eadsforth TC, Viner RC, Hawkes TR, Baker PJ, Rice DW. Crystal Structures Reveal that the Reaction Mechanism of Imidazoleglycerol-Phosphate Dehydratase Is Controlled by Switching Mn(II) Coordination. Structure 2015; 23:1236-45. [PMID: 26095028 PMCID: PMC4509728 DOI: 10.1016/j.str.2015.05.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 05/01/2015] [Accepted: 05/02/2015] [Indexed: 12/18/2022]
Abstract
Imidazoleglycerol-phosphate dehydratase (IGPD) catalyzes the Mn(II)-dependent dehydration of imidazoleglycerol phosphate (IGP) to 3-(1H-imidazol-4-yl)-2-oxopropyl dihydrogen phosphate during biosynthesis of histidine. As part of a program of herbicide design, we have determined a series of high-resolution crystal structures of an inactive mutant of IGPD2 from Arabidopsis thaliana in complex with IGP. The structures represent snapshots of the enzyme trapped at different stages of the catalytic cycle and show how substrate binding triggers a switch in the coordination state of an active site Mn(II) between six- and five-coordinate species. This switch is critical to prime the active site for catalysis, by facilitating the formation of a high-energy imidazolate intermediate. This work not only provides evidence for the molecular processes that dominate catalysis in IGPD, but also describes how the manipulation of metal coordination can be linked to discrete steps in catalysis, demonstrating one way that metalloenzymes exploit the unique properties of metal ions to diversify their chemistry.
Collapse
Affiliation(s)
- Claudine Bisson
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - K Linda Britton
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Svetlana E Sedelnikova
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - H Fiona Rodgers
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Thomas C Eadsforth
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Russell C Viner
- Syngenta, Jealott's Hill International Research Station, Bracknell RG42 6EY, UK
| | - Tim R Hawkes
- Syngenta, Jealott's Hill International Research Station, Bracknell RG42 6EY, UK
| | - Patrick J Baker
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK.
| | - David W Rice
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK.
| |
Collapse
|
21
|
Bashiri G, Baker EN. Production of recombinant proteins in Mycobacterium smegmatis for structural and functional studies. Protein Sci 2014; 24:1-10. [PMID: 25303009 DOI: 10.1002/pro.2584] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 10/07/2014] [Accepted: 10/08/2014] [Indexed: 11/11/2022]
Abstract
Protein production using recombinant DNA technology has a fundamental impact on our understanding of biology through providing proteins for structural and functional studies. Escherichia coli (E. coli) has been traditionally used as the default expression host to over-express and purify proteins from many different organisms. E. coli does, however, have known shortcomings for obtaining soluble, properly folded proteins suitable for downstream studies. These shortcomings are even more pronounced for the mycobacterial pathogen Mycobacterium tuberculosis, the bacterium that causes tuberculosis, with typically only one third of proteins expressed in E. coli produced as soluble proteins. Mycobacterium smegmatis (M. smegmatis) is a closely related and non-pathogenic species that has been successfully used as an expression host for production of proteins from various mycobacterial species. In this review, we describe the early attempts to produce mycobacterial proteins in alternative expression hosts and then focus on available expression systems in M. smegmatis. The advantages of using M. smegmatis as an expression host, its application in structural biology and some practical aspects of protein production are also discussed. M. smegmatis provides an effective expression platform for enhanced understanding of mycobacterial biology and pathogenesis and for developing novel and better therapeutics and diagnostics.
Collapse
Affiliation(s)
- Ghader Bashiri
- Structural Biology Laboratory, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, 1010, New Zealand
| | | |
Collapse
|