1
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Hagedoorn PL, Pabst M, Hanefeld U. The metal cofactor: stationary or mobile? Appl Microbiol Biotechnol 2024; 108:391. [PMID: 38910188 PMCID: PMC11194214 DOI: 10.1007/s00253-024-13206-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/22/2024] [Accepted: 05/27/2024] [Indexed: 06/25/2024]
Abstract
Metal cofactors are essential for catalysis and enable countless conversions in nature. Interestingly, the metal cofactor is not always static but mobile with movements of more than 4 Å. These movements of the metal can have different functions. In the case of the xylose isomerase and medium-chain dehydrogenases, it clearly serves a catalytic purpose. The metal cofactor moves during substrate activation and even during the catalytic turnover. On the other hand, in class II aldolases, the enzymes display resting states and active states depending on the movement of the catalytic metal cofactor. This movement is caused by substrate docking, causing the metal cofactor to take the position essential for catalysis. As these metal movements are found in structurally and mechanistically unrelated enzymes, it has to be expected that this metal movement is more common than currently perceived. KEY POINTS: • Metal ions are essential cofactors that can move during catalysis. • In class II aldolases, the metal cofactors can reside in a resting state and an active state. • In MDR, the movement of the metal cofactor is essential for substrate docking.
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Affiliation(s)
- Peter-Leon Hagedoorn
- Afdeling Biotechnologie, Technische Universiteit Delft, Van der Maasweg 9, Delft, 2629 HZ, The Netherlands
| | - Martin Pabst
- Afdeling Biotechnologie, Technische Universiteit Delft, Van der Maasweg 9, Delft, 2629 HZ, The Netherlands
| | - Ulf Hanefeld
- Afdeling Biotechnologie, Technische Universiteit Delft, Van der Maasweg 9, Delft, 2629 HZ, The Netherlands.
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2
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Wang G. Thermal Ring-Based Heat Switches in Hyperthermophilic Class II Bacterial Fructose Aldolase. ACS OMEGA 2023; 8:24624-24634. [PMID: 37457467 PMCID: PMC10339327 DOI: 10.1021/acsomega.3c03001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 05/24/2023] [Indexed: 07/18/2023]
Abstract
Both thermophilic and hyperthermophilic enzymes in bacterial and archaeal species are activated above a specific temperature threshold but inactivated at another higher temperature. However, the underlying structural basis for these two heat switches is still unresolved. Here, graph theory was used to test if the temperature-dependent noncovalent interactions and metal bridges as identified in a series of crystal structures of the class II bacterial fructose 1,6-bisphosphate aldolase homodimer or homotetramer with or without natural substrates and products bound could form systematic fluidic grid-like mesh networks with topological grids as thermal rings to regulate their structural thermostability and functional thermoactivity. The results indicated that the second biggest grid in the Thermus aquaticus fructose 1,6-diphosphate aldolase dimer may control the specific temperature threshold to release the swapping flexible active sites at the dimeric interface for heat-evoked activation. Meanwhile, the third biggest grid may serve as a necessary structural motif against heat inactivation. Finally, the smallest grid may act as a stiff thermostable anchor. Its dissociation at the maximal melting temperature threshold may stop the catalytic activity. Taken as a whole, this computational study may render the structural motifs for the optimal growth temperature and the extreme heat stability of hyperthermophiles.
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3
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Balkenhol J, Bencurova E, Gupta SK, Schmidt H, Heinekamp T, Brakhage A, Pottikkadavath A, Dandekar T. Prediction and validation of host-pathogen interactions by a versatile inference approach using Aspergillus fumigatus as a case study. Comput Struct Biotechnol J 2022; 20:4225-4237. [PMID: 36051885 PMCID: PMC9399266 DOI: 10.1016/j.csbj.2022.07.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 11/03/2022] Open
Abstract
Biological networks are characterized by diverse interactions and dynamics in time and space. Many regulatory modules operate in parallel and are interconnected with each other. Some pathways are functionally known and annotated accordingly, e.g., endocytosis, migration, or cytoskeletal rearrangement. However, many interactions are not so well characterized. For reconstructing the biological complexity in cellular networks, we combine here existing experimentally confirmed and analyzed interactions with a protein-interaction inference framework using as basis experimentally confirmed interactions from other organisms. Prediction scoring includes sequence similarity, evolutionary conservation of interactions, the coexistence of interactions in the same pathway, orthology as well as structure similarity to rank and compare inferred interactions. We exemplify our inference method by studying host-pathogen interactions during infection of Mus musculus (phagolysosomes in alveolar macrophages) with Aspergillus fumigatus (conidia, airborne, asexual spores). Three of nine predicted critical host-pathogen interactions could even be confirmed by direct experiments. Moreover, we suggest drugs that manipulate the host-pathogen interaction.
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Affiliation(s)
| | - Elena Bencurova
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Shishir K Gupta
- Evolutionary Genomics Group, Center for Computational and Theoretical Biology, University of Würzburg, 97078 Würzburg, Germany
| | - Hella Schmidt
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745 Jena, Germany
| | - Thorsten Heinekamp
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745 Jena, Germany
| | - Axel Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745 Jena, Germany
| | - Aparna Pottikkadavath
- Department of Structural Biology, Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, 97074 Würzburg, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
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Wen W, Cao H, Huang Y, Tu J, Wan C, Wan J, Han X, Chen H, Liu J, Rao L, Su C, Peng C, Sheng C, Ren Y. Structure-Guided Discovery of the Novel Covalent Allosteric Site and Covalent Inhibitors of Fructose-1,6-Bisphosphate Aldolase to Overcome the Azole Resistance of Candidiasis. J Med Chem 2022; 65:2656-2674. [PMID: 35099959 DOI: 10.1021/acs.jmedchem.1c02102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fructose-1,6-bisphosphate aldolase (FBA) represents an attractive new antifungal target. Here, we employed a structure-based optimization strategy to discover a novel covalent binding site (C292 site) and the first-in-class covalent allosteric inhibitors of FBA from Candida albicans (CaFBA). Site-directed mutagenesis, liquid chromatography-mass spectrometry, and the crystallographic structures of APO-CaFBA, CaFBA-G3P, and C157S-2a4 revealed that S268 is an essential pharmacophore for the catalytic activity of CaFBA, and L288 is an allosteric regulation switch for CaFBA. Furthermore, most of the CaFBA covalent inhibitors exhibited good inhibitory activity against azole-resistant C. albicans, and compound 2a11 can inhibit the growth of azole-resistant strains 103 with the MIC80 of 1 μg/mL. Collectively, this work identifies a new covalent allosteric site of CaFBA and discovers the first generation of covalent inhibitors for fungal FBA with potent inhibitory activity against resistant fungi, establishing a structural foundation and providing a promising strategy for the design of potent antifungal drugs.
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Affiliation(s)
- Wuqiang Wen
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Hongxuan Cao
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Yunyuan Huang
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Jie Tu
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Chen Wan
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Jian Wan
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Xinya Han
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Han Chen
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Jiaqi Liu
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Li Rao
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Chen Su
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai 201210, China
| | - Chao Peng
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai 201210, China
| | - Chunquan Sheng
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Yanliang Ren
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
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Joshi H, Kandari D, Bhatnagar R. Insights into the molecular determinants involved in Mycobacterium tuberculosis persistence and their therapeutic implications. Virulence 2021; 12:2721-2749. [PMID: 34637683 PMCID: PMC8565819 DOI: 10.1080/21505594.2021.1990660] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/17/2021] [Accepted: 10/05/2021] [Indexed: 01/08/2023] Open
Abstract
The establishment of persistent infections and the reactivation of persistent bacteria to active bacilli are the two hurdles in effective tuberculosis treatment. Mycobacterium tuberculosis, an etiologic tuberculosis agent, adapts to numerous antibiotics and resists the host immune system causing a disease of public health concern. Extensive research has been employed to combat this disease due to its sheer ability to persist in the host system, undetected, waiting for the opportunity to declare itself. Persisters are a bacterial subpopulation that possesses transient tolerance to high doses of antibiotics. There are certain inherent mechanisms that facilitate the persister cell formation in Mycobacterium tuberculosis, some of those had been characterized in the past namely, stringent response, transcriptional regulators, energy production pathways, lipid metabolism, cell wall remodeling enzymes, phosphate metabolism, and proteasome protein degradation. This article reviews the recent advancements made in various in vitro persistence models that assist to unravel the mechanisms involved in the persister cell formation and to hunt for the possible preventive or treatment measures. To tackle the persister population the immunodominant proteins that express specifically at the latent phase of infection can be used for diagnosis to distinguish between the active and latent tuberculosis, as well as to select potential drug or vaccine candidates. In addition, we discuss the genes engaged in the persistence to get more insights into resuscitation and persister cell formation. The in-depth understanding of persistent cells of mycobacteria can certainly unravel novel ways to target the pathogen and tackle its persistence.
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Affiliation(s)
- Hemant Joshi
- Molecular Biology and Genetic Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Divya Kandari
- Molecular Biology and Genetic Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Rakesh Bhatnagar
- Molecular Biology and Genetic Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
- Amity University of Rajasthan, Jaipur, Rajasthan, India
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6
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Pirovich DB, Da’dara AA, Skelly PJ. Multifunctional Fructose 1,6-Bisphosphate Aldolase as a Therapeutic Target. Front Mol Biosci 2021; 8:719678. [PMID: 34458323 PMCID: PMC8385298 DOI: 10.3389/fmolb.2021.719678] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/31/2021] [Indexed: 01/01/2023] Open
Abstract
Fructose 1,6-bisphosphate aldolase is a ubiquitous cytosolic enzyme that catalyzes the fourth step of glycolysis. Aldolases are classified into three groups: Class-I, Class-IA, and Class-II; all classes share similar structural features but low amino acid identity. Apart from their conserved role in carbohydrate metabolism, aldolases have been reported to perform numerous non-enzymatic functions. Here we review the myriad "moonlighting" functions of this classical enzyme, many of which are centered on its ability to bind to an array of partner proteins that impact cellular scaffolding, signaling, transcription, and motility. In addition to the cytosolic location, aldolase has been found the extracellular surface of several pathogenic bacteria, fungi, protozoans, and metazoans. In the extracellular space, the enzyme has been reported to perform virulence-enhancing moonlighting functions e.g., plasminogen binding, host cell adhesion, and immunomodulation. Aldolase's importance has made it both a drug target and vaccine candidate. In this review, we note the several inhibitors that have been synthesized with high specificity for the aldolases of pathogens and cancer cells and have been shown to inhibit classical enzyme activity and moonlighting functions. We also review the many trials in which recombinant aldolases have been used as vaccine targets against a wide variety of pathogenic organisms including bacteria, fungi, and metazoan parasites. Most of such trials generated significant protection from challenge infection, correlated with antigen-specific cellular and humoral immune responses. We argue that refinement of aldolase antigen preparations and expansion of immunization trials should be encouraged to promote the advancement of promising, protective aldolase vaccines.
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Affiliation(s)
- David B. Pirovich
- Molecular Helminthology Laboratory, Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, United States
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FBPAII and rpoBC, the Two Novel Secreted Proteins Identified by the Proteomic Approach from a Comparative Study between Antibiotic-Sensitive and Antibiotic-Resistant Helicobacter pylori-Associated Gastritis Strains. Infect Immun 2021; 89:IAI.00053-21. [PMID: 33782154 DOI: 10.1128/iai.00053-21] [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: 01/28/2021] [Accepted: 03/17/2021] [Indexed: 11/20/2022] Open
Abstract
Helicobacter pylori infection is the leading cause of chronic gastritis, which can develop into gastric cancer. Eliminating H. pylori infection with antibiotics achieves the prevention of gastric cancer. Currently, the prevalence of H. pylori resistance to clarithromycin and metronidazole, and the dual resistance to metronidazole and clarithromycin (C_R, M_R, and C/M_R, respectively), remains at a high level worldwide. As a means of exploring new candidate proteins for the management of H. pylori infection, secreted proteins from antibiotic-susceptible and antibiotic-resistant H. pylori-associated gastritis strains were obtained by in-solution tryptic digestion coupled with nano-liquid chromatography tandem mass spectrometry (nano-LC-MS/MS). A total of 583, 582, 590, and 578 differential expressed proteins were identified from C_R, M_R, C/M_R, and antibiotic-sensitive strain (S_S) samples, respectively. Of these, 23 overlapping proteins were found by Venn diagram analysis. Based on heat map analyses, the most and least differing protein expressions were observed from C/M_R strains and S_S strains, respectively. Of the proteins secreted by the S_S strain, only nine were found. After predicting the protein interaction with metronidazole and clarithromycin via the STITCH database, the two most interesting proteins were found to be rpoBC and FBPAII. After quantitative real-time reverse transcription PCR (qRT-PCR) analysis, a downregulation of rpoB from M_R strains was observed, suggesting a relationship of rpoB to metronidazole sensitivity. Inversely, an upregulation of fba from C_R, M_R, and C/M_R strains was noticed, suggesting the paradoxical expression of FBPAII and the fba gene. This report is the first to demonstrate the association of these two novel secreted proteins, namely, rpoBC and FBPAII, with antibiotic-sensitive H. pylori -associated gastritis strains.
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8
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Chen X, Zhang Z, Chen Z, Li Y, Su S, Sun S. Potential Antifungal Targets Based on Glucose Metabolism Pathways of Candida albicans. Front Microbiol 2020; 11:296. [PMID: 32256459 PMCID: PMC7093590 DOI: 10.3389/fmicb.2020.00296] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 02/10/2020] [Indexed: 01/04/2023] Open
Abstract
In recent years, fungal infections have become a serious health problem. Candida albicans are considered as the fourth most common isolates associated with approximately 40% mortality in bloodstream infections among hospitalized patients. Due to various limitations of classical antifungals used currently, such as limited kinds of drugs, inevitable toxicities, and high price, there is an urgent need to explore new antifungal agents based on novel targets. Generally, nutrient metabolism is involved with fungal virulence, and glucose is one of the important nutrients in C. albicans. C. albicans can obtain and metabolize glucose through a variety of pathways; in theory, many enzymes in these pathways can be potential targets for developing new antifungal agents, and several studies have confirmed that compounds which interfere with alpha-glucosidase, acid trehalase, trehalose-6-phosphate synthase, class II fructose bisphosphate aldolases, and glucosamine-6-phosphate synthase in these pathways do have antifungal activities. In this review, the glucose metabolism pathways in C. albicans, the potential antifungal targets based on these pathways, and some compounds which have antifungal activities by inhibiting several enzymes in these pathways are summarized. We believe that our review will be helpful to the exploration of new antifungal drugs with novel antifungal targets.
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Affiliation(s)
- Xueqi Chen
- Department of Pharmacy, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, China
- School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Zewen Zhang
- Department of Imaging Medicine and Nuclear Medicine, Qilu Medical College, Shandong University, Jinan, China
| | - Zuozhong Chen
- Department of Pharmacy, Zibo Central Hospital, Zibo, China
| | - Yiman Li
- School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Shan Su
- School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Shujuan Sun
- Department of Clinical Pharmacy, The First Affiliated Hospital of Shandong First Medical University, Jinan, China
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9
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Méndez ST, Castillo-Villanueva A, Martínez-Mayorga K, Reyes-Vivas H, Oria-Hernández J. Structure-based identification of a potential non-catalytic binding site for rational drug design in the fructose 1,6-biphosphate aldolase from Giardia lamblia. Sci Rep 2019; 9:11779. [PMID: 31409864 PMCID: PMC6692403 DOI: 10.1038/s41598-019-48192-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 07/30/2019] [Indexed: 12/15/2022] Open
Abstract
Giardia lamblia is the causal agent of giardiasis, one of the most prevalent parasitosis in the world. Even though effective pharmacotherapies against this parasite are available, the disadvantages associated with its use call for the development of new antigiardial compounds. Based on the Giardia dependence on glycolysis as a main energy source, glycolytic enzymes appear to be attractive targets with antiparasitic potential. Among these, fructose 1,6-biphosphate aldolase (GlFBPA) has been highlighted as a promising target for drug design. Current efforts are based on the design of competitive inhibitors of GlFBPA; however, in the kinetic context of metabolic pathways, competitive inhibitors seem to have low potential as therapeutic agents. In this work, we performed an experimental and in silico structure-based approach to propose a non-catalytic binding site which could be used as a hot spot for antigardial drug design. The druggability of the selected binding site was experimentally tested; the alteration of the selected region by site directed mutagenesis disturbs the catalytic properties and the stability of the enzyme. A computational automated search of binding sites supported the potential of this region as functionally relevant. A preliminary docking study was performed, in order to explore the feasibility and type of molecules to be able to accommodate in the proposed binding region. Altogether, the results validate the proposed region as a specific molecular binding site with pharmacological potential.
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Affiliation(s)
- Sara-Teresa Méndez
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Insurgentes Sur 3700-C, Col. Insurgentes Cuicuilco, Alcaldía Coyoacán, CP 04530, Ciudad de México, Mexico
| | - Adriana Castillo-Villanueva
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Insurgentes Sur 3700-C, Col. Insurgentes Cuicuilco, Alcaldía Coyoacán, CP 04530, Ciudad de México, Mexico
| | - Karina Martínez-Mayorga
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Alcaldía Coyoacán, C.P. 04510, Ciudad de México, Mexico
| | - Horacio Reyes-Vivas
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Insurgentes Sur 3700-C, Col. Insurgentes Cuicuilco, Alcaldía Coyoacán, CP 04530, Ciudad de México, Mexico.
| | - Jesús Oria-Hernández
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Insurgentes Sur 3700-C, Col. Insurgentes Cuicuilco, Alcaldía Coyoacán, CP 04530, Ciudad de México, Mexico.
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10
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Elhag M, Abubaker M, Ahmad NM, Haroon EM, Alaagib RM, Abd albagi SO, Hassan MA. Immunoinformatics Prediction of Epitope Based Peptide Vaccine Against Listeria Monocytogenes Fructose Bisphosphate Aldolase Protein.. [DOI: 10.1101/649111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
AbstractListeria Monocytogenesrepresents an important food-borne pathogen worldwide that can cause life-threatening listeriosis disease especially in pregnant women, fetuses, elderly people, and immuno-compromised individuals with high mortality rates. Moreover, no vaccine against it exists. This study predicts an effective epitope-based vaccine against Fructose 1,6 Bisphosphate Aldolase (FBA) enzyme of Listeria Monocytogenes using immunoinformatics approaches. The sequences were retrieved from NCBI and several prediction tests were conducted to analyze possible epitopes for B-cell, T-cell MHC class I and II. 3D structure of the promising epitopes was obtained. Two epitopes showed high binding affinity for B-cells, while four epitopes showed high binding affinity for MHCI and MHCII. The results were promising to formulate a vaccine with more than 98% population coverage. We hope that these promising epitopes serves as a preventive measure for the disease in the future and recommend invivo and invitro studies.
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11
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Chen AY, Adamek RN, Dick BL, Credille CV, Morrison CN, Cohen SM. Targeting Metalloenzymes for Therapeutic Intervention. Chem Rev 2019; 119:1323-1455. [PMID: 30192523 PMCID: PMC6405328 DOI: 10.1021/acs.chemrev.8b00201] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes are central to a wide range of essential biological activities, including nucleic acid modification, protein degradation, and many others. The role of metalloenzymes in these processes also makes them central for the progression of many diseases and, as such, makes metalloenzymes attractive targets for therapeutic intervention. Increasing awareness of the role metalloenzymes play in disease and their importance as a class of targets has amplified interest in the development of new strategies to develop inhibitors and ultimately useful drugs. In this Review, we provide a broad overview of several drug discovery efforts focused on metalloenzymes and attempt to map out the current landscape of high-value metalloenzyme targets.
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Affiliation(s)
- Allie Y Chen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Rebecca N Adamek
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Benjamin L Dick
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Cy V Credille
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Christine N Morrison
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Seth M Cohen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
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12
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de Amorim AL, de Lima AVM, Rosário ACDAD, Souza ÉTDS, Ferreira JV, Hage-Melim LIDS. Molecular modeling of inhibitors against fructose bisphosphate aldolase from Candida albicans. In Silico Pharmacol 2018; 6:2. [PMID: 30607315 PMCID: PMC6314639 DOI: 10.1007/s40203-018-0040-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 03/02/2018] [Indexed: 10/17/2022] Open
Abstract
Candida albicans is an opportunistic pathogen that causes from vulvovaginal and oropharyngeal candidiasis to systemic infections. The enzyme 1,6-fructose bisphosphate aldolase class II (FBA II), is a macromolecule existing only in lower organisms, being essential for the survival of the pathogen due to its function of maintaining the glycolysis process. The aim of this paper was to evaluate the inhibitors of FBA II regarding their physicochemical, pharmacokinetic and toxicological properties and apply concepts of rational drug development to propose new compounds for the treatment of fungal infections of C. albicans. Physicochemical (HyperChem software and the webserver cactus) and ADME/Tox (PreADMET webserver) properties were calculated to four inhibitors described in the literature and three analogues. None of the compounds presented in this study violated RO5, however all inhibitors demonstrated low or moderate human intestinal absorption (HIA), as well as low or moderate permeability in Caco-2 and MDCK, poor plasma proteins binding (PPB) and low permeability of the blood-brain barrier (BBB); however, Compound 4 is the exception for BBB permeability, being also the only non-mutagenic compound, and therefore, used as a lead compound. Analogues B and C presented high HIA, weak PPB and low BBB permeability, as well as a positive prediction for carcinogenicity in rats and mouse and non-mutagenicity in the Ames test. Through the evaluations carried out, it was concluded that the analogues B and C have proved to be promising candidates for oral administration drugs in the treatment of fungal infections of the genus Candida.
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Affiliation(s)
- Andréia Lima de Amorim
- Grupo de Biocatálise e Biotransformação de Compostos Orgânicos, Universidade Federal do Amapá, Macapá, Amapá Brazil
| | - Alan Vitor Morais de Lima
- Laboratório de Química Farmacêutica e Medicinal (PharMedChem), Universidade Federal do Amapá, Macapá, Amapá Brazil
| | | | | | - Jaderson Vieira Ferreira
- Laboratório de Química Farmacêutica e Medicinal (PharMedChem), Universidade Federal do Amapá, Macapá, Amapá Brazil
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13
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Li D, Luong TTM, Dan WJ, Ren Y, Nien HX, Zhang AL, Gao JM. Natural products as sources of new fungicides (IV): Synthesis and biological evaluation of isobutyrophenone analogs as potential inhibitors of class-II fructose-1,6-bisphosphate aldolase. Bioorg Med Chem 2017; 26:386-393. [PMID: 29248352 DOI: 10.1016/j.bmc.2017.10.046] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 10/24/2017] [Accepted: 10/30/2017] [Indexed: 11/19/2022]
Abstract
Several recently identified antifungal compounds share the backbone structure of acetophenones. The aim of the present study was to develop new isobutyrophenone analogs as new antifungal agents. A series of new 2,4-dihydroxy-5-methyl isobutyrophenone derivatives were prepared and characterized by 1H, 13C NMR and MS spectroscopic data. These products were evaluated for in vitro antifungal activities against seven plant fungal pathogens by the mycelial growth inhibitory rate assay. Compounds 3, 4a, 5a, 5b, 5e, 5f and 5g showed a broad-spectrum high antifungal activity. On the other hand, for the first time, these compounds were also assayed as potential inhibitors against Class II fructose-1,6-bisphosphate aldolase (Fba) from the rice blast fungus, Magnaporthe grisea. Compounds 5e and 5g were found to exhibit the inhibition constants (Ki) for 15.12 and 14.27 μM, respectively, as the strongest competitive inhibitors against Fba activity. The possible binding-modes of compounds 5e and 5g were further analyzed by molecular docking algorithms. The results strongly suggested that compound 5g could be a promising lead for the discovery of new fungicides via targeting Class II Fba.
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Affiliation(s)
- Ding Li
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, Shaanxi Engineering Center of Bioresource Chemistry & Sustainable Utilization, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China
| | - Tuong Thi Mai Luong
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, Shaanxi Engineering Center of Bioresource Chemistry & Sustainable Utilization, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China; Institute of Scientific Research and Technological Development, Thu Dau Mot University, Binh Duong, Viet Nam
| | - Wen-Jia Dan
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, Shaanxi Engineering Center of Bioresource Chemistry & Sustainable Utilization, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China
| | - Yanliang Ren
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China.
| | - Hoang Xuan Nien
- Institute of Scientific Research and Technological Development, Thu Dau Mot University, Binh Duong, Viet Nam
| | - An-Ling Zhang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, Shaanxi Engineering Center of Bioresource Chemistry & Sustainable Utilization, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China
| | - Jin-Ming Gao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, Shaanxi Engineering Center of Bioresource Chemistry & Sustainable Utilization, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China.
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14
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Han X, Zhu X, Hong Z, Wei L, Ren Y, Wan F, Zhu S, Peng H, Guo L, Rao L, Feng L, Wan J. Structure-Based Rational Design of Novel Inhibitors Against Fructose-1,6-Bisphosphate Aldolase from Candida albicans. J Chem Inf Model 2017; 57:1426-1438. [DOI: 10.1021/acs.jcim.6b00763] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Xinya Han
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Xiuyun Zhu
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Zongqin Hong
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Lin Wei
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Yanliang Ren
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Fen Wan
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Shuaihua Zhu
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Hao Peng
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Li Guo
- Hubei Environmental
Monitoring Central Station, Wuhan 430072, Hubei China
| | - Li Rao
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Lingling Feng
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Jian Wan
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
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15
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Tran HT, Lee SH, Ho TH, Hong SH, Huynh KH, Ahn YJ, Oh DK, Kang LW. Crystallographic snapshots of active site metal shift in E. coli fructose 1,6-bisphosphate aldolase. BMB Rep 2016; 49:681-686. [PMID: 27733232 PMCID: PMC5346313 DOI: 10.5483/bmbrep.2016.49.12.132] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 08/30/2016] [Accepted: 10/10/2016] [Indexed: 11/30/2022] Open
Abstract
Fructose 1,6-bisphosphate aldolase (FBA) is important for both glycolysis and gluconeogenesis in life. Class II (zinc dependent) FBA is an attractive target for the development of antibiotics against protozoa, bacteria, and fungi, and is also widely used to produce various high-value stereoisomers in the chemical and pharmaceutical industry. In this study, the crystal structures of class II Escherichia coli FBA (EcFBA) were determined from four different crystals, with resolutions between 1.8 Å and 2.0 Å. Native EcFBA structures showed two separate sites of Zn1 (interior position) and Zn2 (active site surface position) for Zn2+ ion. Citrate and TRIS bound EcFBA structures showed Zn2+ position exclusively at Zn2. Crystallographic snapshots of EcFBA structures with and without ligand binding proposed the rationale of metal shift at the active site, which might be a hidden mechanism to keep the trace metal cofactor Zn2+ within EcFBA without losing it. [BMB Reports 2016; 49(12): 681-686].
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Affiliation(s)
- Huyen-Thi Tran
- Department of Biological Sciences, Konkuk University, Seoul 05029,
Korea
- Department of Biotechnology and Food Technology, Industrial University of Ho Chi Minh City, 12 Nguyen Van Bao Street, Ward 4, Go Vap District, Ho Chi Minh City,
Vietnam
| | - Seon-Hwa Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029,
Korea
| | - Thien-Hoang Ho
- Department of Biological Sciences, Konkuk University, Seoul 05029,
Korea
| | - Seung-Hye Hong
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029,
Korea
| | - Kim-Hung Huynh
- Department of Biological Sciences, Konkuk University, Seoul 05029,
Korea
| | - Yeh-Jin Ahn
- Department of Life Science, Sangmyung University, Seoul 03016,
Korea
| | - Deok-Kun Oh
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029,
Korea
| | - Lin-Woo Kang
- Department of Biological Sciences, Konkuk University, Seoul 05029,
Korea
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16
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Fructose 1,6-Bisphosphate Aldolase, a Novel Immunogenic Surface Protein on Listeria Species. PLoS One 2016; 11:e0160544. [PMID: 27489951 PMCID: PMC4973958 DOI: 10.1371/journal.pone.0160544] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 07/21/2016] [Indexed: 12/12/2022] Open
Abstract
Listeria monocytogenes is a ubiquitous food-borne pathogen, and its presence in food or production facilities highlights the importance of surveillance. Increased understanding of the surface exposed antigens on Listeria would provide potential diagnostic and therapeutic targets. In the present work, using mass spectrometry and genetic cloning, we show that fructose-1,6-bisphosphate aldolase (FBA) class II in Listeria species is the antigen target of the previously described mAb-3F8. Western and dot blot assays confirmed that the mAb-3F8 could distinguish all tested Listeria species from close-related bacteria. Localization studies indicated that FBA is present in every fraction of Listeria cells, including supernatant and the cell wall, setting Listeria spp. as one of the few bacteria described to have this protein on their cell surface. Epitope mapping using ORFeome display and a peptide membrane revealed a 14-amino acid peptide as the potential mAb-3F8 epitope. The target epitope in FBA allowed distinguishing Listeria spp. from closely-related bacteria, and was identified as part of the active site in the dimeric enzyme. However, its function in cell surface seems not to be host cell adhesion-related. Western and dot blot assays further demonstrated that mAb-3F8 together with anti-InlA mAb-2D12 could differentiate pathogenic from non-pathogenic Listeria isolated from artificially contaminated cheese. In summary, we report FBA as a novel immunogenic surface target useful for the detection of Listeria genus.
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17
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Shams F, Oldfield NJ, Lai SK, Tunio SA, Wooldridge KG, Turner DPJ. Fructose-1,6-bisphosphate aldolase of Neisseria meningitidis binds human plasminogen via its C-terminal lysine residue. Microbiologyopen 2016; 5:340-50. [PMID: 26732512 PMCID: PMC4831477 DOI: 10.1002/mbo3.331] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 11/10/2015] [Accepted: 11/24/2015] [Indexed: 11/23/2022] Open
Abstract
Neisseria meningitidis is a leading cause of fatal sepsis and meningitis worldwide. As for commensal species of human neisseriae, N. meningitidis inhabits the human nasopharynx and asymptomatic colonization is ubiquitous. Only rarely does the organism invade and survive in the bloodstream leading to disease. Moonlighting proteins perform two or more autonomous, often dissimilar, functions using a single polypeptide chain. They have been increasingly reported on the surface of both prokaryotic and eukaryotic organisms and shown to interact with a variety of host ligands. In some organisms moonlighting proteins perform virulence‐related functions, and they may play a role in the pathogenesis of N. meningitidis. Fructose‐1,6‐bisphosphate aldolase (FBA) was previously shown to be surface‐exposed in meningococci and involved in adhesion to host cells. In this study, FBA was shown to be present on the surface of both pathogenic and commensal neisseriae, and surface localization and anchoring was demonstrated to be independent of aldolase activity. Importantly, meningococcal FBA was found to bind to human glu‐plasminogen in a dose‐dependent manner. Site‐directed mutagenesis demonstrated that the C‐terminal lysine residue of FBA was required for this interaction, whereas subterminal lysine residues were not involved.
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Affiliation(s)
- Fariza Shams
- School of Life Sciences, Molecular Bacteriology and Immunology Group, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Neil J Oldfield
- School of Life Sciences, Molecular Bacteriology and Immunology Group, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Si Kei Lai
- School of Life Sciences, Molecular Bacteriology and Immunology Group, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Sarfraz A Tunio
- School of Life Sciences, Molecular Bacteriology and Immunology Group, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Karl G Wooldridge
- School of Life Sciences, Molecular Bacteriology and Immunology Group, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - David P J Turner
- School of Life Sciences, Molecular Bacteriology and Immunology Group, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
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18
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Affiliation(s)
- Tai-Ni Lu
- Department of Chemistry, Fu Jen Catholic University, 510 Zhongzheng Road, Xinzhuang
District, New Taipei City 24205, Taiwan Republic of China
| | - Che-Chien Chang
- Department of Chemistry, Fu Jen Catholic University, 510 Zhongzheng Road, Xinzhuang
District, New Taipei City 24205, Taiwan Republic of China
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19
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Han X, Zhu X, Zhu S, Wei L, Hong Z, Guo L, Chen H, Chi B, Liu Y, Feng L, Ren Y, Wan J. A Rational Design, Synthesis, Biological Evaluation and Structure--Activity Relationship Study of Novel Inhibitors against Cyanobacterial Fructose-1,6-bisphosphate Aldolase. J Chem Inf Model 2015; 56:73-81. [PMID: 26669534 DOI: 10.1021/acs.jcim.5b00618] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the present study, a series of novel maleimide derivatives were rationally designed and optimized, and their inhibitory activities against cyanobacteria class-II fructose-1,6-bisphosphate aldolase (Cy-FBA-II) and Synechocystis sp. PCC 6803 were further evaluated. The experimental results showed that the introduction of a bigger group (Br, Cl, CH3, or C6H3-o-F) on the pyrrole-2',5'-dione ring resulted in a decrease in the Cy-FBA-II inhibitory activity of the hit compounds. Generally, most of the hit compounds with high Cy-FBA-II inhibitory activities could also exhibit high in vivo activities against Synechocystis sp. PCC 6803. Especially, compound 10 not only shows a high Cy-FBA-II activity (IC50 = 1.7 μM) but also has the highest in vivo activity against Synechocystis sp. PCC 6803 (EC50 = 0.6 ppm). Thus, compound 10 was selected as a representative molecule, and its probable interactions with the surrounding important residues in the active site of Cy-FBA-II were elucidated by the joint use of molecular docking, molecular dynamics simulations, ONIOM calculations, and enzymatic assays to provide new insight into the binding mode of the inhibitors and Cy-FBA-II. The positive results indicate that the design strategy used in the present study is very likely to be a promising way to find novel lead compounds with high inhibitory activities against Cy-FBA-II in the future. The enzymatic and algal inhibition assays suggest that Cy-FBA-II is very likely to be a promising target for the design, synthesis, and development of novel specific algicides to solve cyanobacterial harmful algal blooms.
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Affiliation(s)
- Xinya Han
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University , Wuhan, Hubei 430079, China
| | - Xiuyun Zhu
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University , Wuhan, Hubei 430079, China
| | - Shuaihua Zhu
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University , Wuhan, Hubei 430079, China
| | - Lin Wei
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University , Wuhan, Hubei 430079, China
| | - Zongqin Hong
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University , Wuhan, Hubei 430079, China
| | - Li Guo
- Hubei Environmental Monitoring Central Station , Wuhan, Hubei 430072, China
| | - Haifeng Chen
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University , Wuhan, Hubei 430079, China
| | - Bo Chi
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University , Wuhan, Hubei 430079, China
| | - Yan Liu
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University , Wuhan, Hubei 430079, China
| | - Lingling Feng
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University , Wuhan, Hubei 430079, China
| | - Yanliang Ren
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University , Wuhan, Hubei 430079, China
| | - Jian Wan
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University , Wuhan, Hubei 430079, China
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20
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Capodagli GC, Lee SA, Boehm KJ, Brady KM, Pegan SD. Structural and functional characterization of methicillin-resistant Staphylococcus aureus's class IIb fructose 1,6-bisphosphate aldolase. Biochemistry 2014; 53:7604-14. [PMID: 25390935 PMCID: PMC4263427 DOI: 10.1021/bi501141t] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
![]()
Staphylococcus aureus is one of the most common
nosocomial sources of soft-tissue and skin infections and has more
recently become prevalent in the community setting as well. Since
the use of penicillins to combat S. aureus infections
in the 1940s, the bacterium has been notorious for developing resistances
to antibiotics, such as methicillin-resistant Staphylococcus
aureus (MRSA). With the persistence of MRSA as well as many
other drug resistant bacteria and parasites, there is a growing need
to focus on new pharmacological targets. Recently, class II fructose
1,6-bisphosphate aldolases (FBAs) have garnered attention to fill
this role. Regrettably, scarce biochemical data and no structural
data are currently available for the class II FBA found in MRSA (SaFBA).
With the recent finding of a flexible active site zinc-binding loop
(Z-Loop) in class IIa FBAs and its potential for broad spectrum class
II FBA inhibition, the lack of information regarding this feature
of class IIb FBAs, such as SaFBA, has been limiting for further Z-loop
inhibitor development. Therefore, we elucidated the crystal structure
of SaFBA to 2.1 Å allowing for a more direct structural analysis
of SaFBA. Furthermore, we determined the KM for one of SaFBA’s substrates, fructose 1,6-bisphosphate,
as well as performed mode of inhibition studies for an inhibitor that
takes advantage of the Z-loop’s flexibility. Together the data
offers insight into a class IIb FBA from a pervasively drug resistant
bacterium and a comparison of Z-loops and other features between the
different subtypes of class II FBAs.
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Affiliation(s)
- Glenn C Capodagli
- Department of Chemistry and Biochemistry, University of Denver , Denver, Colorado 80208, United States
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21
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Puckett S, Trujillo C, Eoh H, Marrero J, Spencer J, Jackson M, Schnappinger D, Rhee K, Ehrt S. Inactivation of fructose-1,6-bisphosphate aldolase prevents optimal co-catabolism of glycolytic and gluconeogenic carbon substrates in Mycobacterium tuberculosis. PLoS Pathog 2014; 10:e1004144. [PMID: 24851864 PMCID: PMC4031216 DOI: 10.1371/journal.ppat.1004144] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 04/11/2014] [Indexed: 11/19/2022] Open
Abstract
Metabolic pathways used by Mycobacterium tuberculosis (Mtb) to establish and maintain infections are important for our understanding of pathogenesis and the development of new chemotherapies. To investigate the role of fructose-1,6-bisphosphate aldolase (FBA), we engineered an Mtb strain in which FBA levels were regulated by anhydrotetracycline. Depletion of FBA resulted in clearance of Mtb in both the acute and chronic phases of infection in vivo, and loss of viability in vitro when cultured on single carbon sources. Consistent with prior reports of Mtb's ability to co-catabolize multiple carbon sources, this in vitro essentiality could be overcome when cultured on mixtures of glycolytic and gluconeogenic carbon sources, enabling generation of an fba knockout (Δfba). In vitro studies of Δfba however revealed that lack of FBA could only be compensated for by a specific balance of glucose and butyrate in which growth and metabolism of butyrate were determined by Mtb's ability to co-catabolize glucose. These data thus not only evaluate FBA as a potential drug target in both replicating and persistent Mtb, but also expand our understanding of the multiplicity of in vitro conditions that define the essentiality of Mtb's FBA in vivo. The development of new chemotherapies targeting Mycobacterium tuberculosis (Mtb) will benefit from genetic evaluation of potential drug targets and a better understanding of the pathways required by Mtb to establish and maintain chronic infections. We employed a genetic approach to investigate the essentiality of fructose-1,6-bisphosphate aldolase (FBA) for growth and survival of Mtb in vitro and in mice. A conditional fba mutant revealed that Mtb requires FBA for growth in the acute phase and for survival in the chronic phase of mouse infections. In vitro essentiality of fba was strictly condition-dependent. An FBA deletion mutant (Δfba) required a balanced combination of carbon substrates entering metabolism above and below the FBA-catalyzed reaction for growth and died in media with single carbon sources and in mouse lungs. Death of Δfba in vitro was associated with the perturbation of intracellular metabolites. These studies highlight how a conditional fba mutant helped identify conditions in which FBA is dispensable for growth of Mtb, evaluate FBA as a potential target for eliminating persistent bacilli and offer insight into metabolic regulation of carbon co-catabolism in Mtb.
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Affiliation(s)
- Susan Puckett
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Carolina Trujillo
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Hyungjin Eoh
- Department of Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Joeli Marrero
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - John Spencer
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - Kyu Rhee
- Department of Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
- * E-mail:
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22
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Bäsell K, Otto A, Junker S, Zühlke D, Rappen GM, Schmidt S, Hentschker C, Macek B, Ohlsen K, Hecker M, Becher D. The phosphoproteome and its physiological dynamics in Staphylococcus aureus. Int J Med Microbiol 2014; 304:121-32. [DOI: 10.1016/j.ijmm.2013.11.020] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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23
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Capodagli GC, Sedhom WG, Jackson M, Ahrendt KA, Pegan SD. A noncompetitive inhibitor for Mycobacterium tuberculosis's class IIa fructose 1,6-bisphosphate aldolase. Biochemistry 2014; 53:202-13. [PMID: 24325645 PMCID: PMC4167715 DOI: 10.1021/bi401022b] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Class II fructose 1,6-bisphosphate aldolase (FBA) is an enzyme critical for bacterial, fungal, and protozoan glycolysis/gluconeogenesis. Importantly, humans lack this type of aldolase, having instead a class I FBA that is structurally and mechanistically distinct from class II FBAs. As such, class II FBA is considered a putative pharmacological target for the development of novel antibiotics against pathogenic bacteria such as Mycobacterium tuberculosis, the causative agent for tuberculosis (TB). To date, several competitive class II FBA substrate mimic-styled inhibitors have been developed; however, they lack either specificity, potency, or properties that limit their potential as possible therapeutics. Recently, through the use of enzymatic and structure-based assisted screening, we identified 8-hydroxyquinoline carboxylic acid (HCA) that has an IC50 of 10 ± 1 μM for the class II FBA present in M. tuberculosis (MtFBA). As opposed to previous inhibitors, HCA behaves in a noncompetitive manner, shows no inhibitory properties toward human and rabbit class I FBAs, and possesses anti-TB properties. Furthermore, we were able to determine the crystal structure of HCA bound to MtFBA to 2.1 Å. HCA also demonstrates inhibitory effects for other class II FBAs, including pathogenic bacteria such as methicillin-resistant Staphylococcus aureus. With its broad-spectrum potential, unique inhibitory characteristics, and flexibility of functionalization, the HCA scaffold likely represents an important advancement in the development of class II FBA inhibitors that can serve as viable preclinical candidates.
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Affiliation(s)
- Glenn C. Capodagli
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Wafik G. Sedhom
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Kateri A. Ahrendt
- Department of Chemistry, Regis University, Denver, Colorado 80221, United States,Corresponding Authors Department of Chemistry, Regis University, 3333 Regis Blvd., Denver, CO 80221. . Telephone: (303) 964-5088. Eleanor Roosevelt Institute and Department of Chemistry and Biochemistry, University of Denver, 2190 E. Iliff Ave., Olin 202, Denver, CO 80208. . Telephone: (303) 871-2533
| | - Scott D. Pegan
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States,Eleanor Roosevelt Institute, University of Denver, Denver, Colorado 80208, United States,Corresponding Authors Department of Chemistry, Regis University, 3333 Regis Blvd., Denver, CO 80221. . Telephone: (303) 964-5088. Eleanor Roosevelt Institute and Department of Chemistry and Biochemistry, University of Denver, 2190 E. Iliff Ave., Olin 202, Denver, CO 80208. . Telephone: (303) 871-2533
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24
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Li D, Han X, Tu Q, Feng L, Wu D, Sun Y, Chen H, Li Y, Ren Y, Wan J. Structure-based design and synthesis of novel dual-target inhibitors against cyanobacterial fructose-1,6-bisphosphate aldolase and fructose-1,6-bisphosphatase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:7453-7461. [PMID: 23889687 DOI: 10.1021/jf401939h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Cyanobacteria class II fructose-1,6-bisphoshate aldolase (Cy-FBA-II) and cyanobacteria fructose-1,6-bisphosphatase (Cy-FBPase) are two neighboring key regulatory enzymes in the Calvin cycle of the cyanobacteria photosynthesis system. Each of them might be taken as a potential target for designing novel inhibitors to chemically control harmful algal blooms (HABs). In the present paper, a series of novel inhibitors were rationally designed, synthesized, and optimized based upon the structural and interactional information of both Cy-FBA-II and Cy-FBPase, and their inhibitory activities were examined in vitro and in vivo. The experimental results showed that compounds L19e-L19g exhibited moderate inhibitory activities (IC50 = 28.1-103.2 μM) against both Cy-FBA-II and Cy-FBPase; compounds L19a-L19d, L19h, L20a-L20d exhibited high Cy-FBA-II inhibitory activities (IC50 = 2.3-16.9 μM) and moderate Cy-FBPase inhibitory activities (IC50 = 31.5-141.2 μM); however, compounds L20e-L20h could potently inhibit both Cy-FBA-II and Cy-FBPase with IC50 values less than 30 μM, which demonstrated more or less dual-target inhibitor's feature. Moreover, most of them exhibited potent algicide activity (EC50 = 0.8-22.3 ppm) against cyanobacteria Synechocystis sp. PCC 6803.
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Affiliation(s)
- Ding Li
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
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Chim N, Owens CP, Contreras H, Goulding CW. Withdrawn. Infect Disord Drug Targets 2012:CDTID-EPUB-20121116-2. [PMID: 23167715 PMCID: PMC3695056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Withdrawn by the publisher.
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Affiliation(s)
- Nicholas Chim
- Department of Molecular Biology and Biochemistry, University of California, Irvine CA 92697, USA
| | - Cedric P. Owens
- Department of Molecular Biology and Biochemistry, University of California, Irvine CA 92697, USA
| | - Heidi Contreras
- Department of Molecular Biology and Biochemistry, University of California, Irvine CA 92697, USA
| | - Celia W. Goulding
- Department of Molecular Biology and Biochemistry, University of California, Irvine CA 92697, USA
- Department of Pharmaceutical Sciences, University of California, Irvine CA 92697, USA
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Ma’ayeh SY, Brook-Carter PT. Representational difference analysis identifies specific genes in the interaction of Giardia duodenalis with the murine intestinal epithelial cell line, IEC-6. Int J Parasitol 2012; 42:501-9. [DOI: 10.1016/j.ijpara.2012.04.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Revised: 03/30/2012] [Accepted: 04/02/2012] [Indexed: 10/28/2022]
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Labbé G, Krismanich AP, de Groot S, Rasmusson T, Shang M, Brown MDR, Dmitrienko GI, Guillemette JG. Development of metal-chelating inhibitors for the Class II fructose 1,6-bisphosphate (FBP) aldolase. J Inorg Biochem 2012; 112:49-58. [PMID: 22546686 DOI: 10.1016/j.jinorgbio.2012.02.032] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 02/26/2012] [Accepted: 02/26/2012] [Indexed: 11/19/2022]
Abstract
It has long been suggested that the essential and ubiquitous enzyme fructose 1,6-bisphosphate (FBP) aldolase could be a good drug target against bacteria and fungi, since lower organisms possess a metal-dependant (Class II) FBP aldolase, as opposed to higher organisms which possess a Schiff-base forming (Class I) FBP aldolase. We have tested the capacity of derivatives of the metal-chelating compound dipicolinic acid (DPA), as well a thiol-containing compound, to inhibit purified recombinant Class II FBP aldolases from Mycobacterium tuberculosis, Pseudomonas aeruginosa, Bacillus cereus, Bacillus anthracis, and from the Rice Blast causative agent Magnaporthe grisea. The aldolase from M. tuberculosis was the most sensitive to the metal-chelating inhibitors, with an IC(50) of 5.2 μM with 2,3-dimercaptopropanesulfonate (DMPS) and 28 μM with DPA. DMPS and the synthesized inhibitor 6-(phosphonomethyl)picolinic acid inhibited the enzyme in a time-dependent, competitive fashion, with second order rate constants of 273 and 270 M(-1) s(-1) respectively for the binding of these compounds to the M. tuberculosis aldolase's active site in the presence of the substrate FBP (K(M) 27.9 μM). The most potent first generation inhibitors were modeled into the active site of the M. tuberculosis aldolase structure, with results indicating that the metal chelators tested cannot bind the catalytic zinc in a bidentate fashion while it remains in its catalytic location, and that most enzyme-ligand interactions involve the phosphate binding pocket residues.
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Affiliation(s)
- Geneviève Labbé
- Department of Chemistry, University of Waterloo, 200 University Ave. W, Waterloo, ON, Canada N2L 3G1
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Desvergnes S, Courtiol-Legourd S, Daher R, Dabrowski M, Salmon L, Therisod M. Synthesis and evaluation of malonate-based inhibitors of phosphosugar-metabolizing enzymes: class II fructose-1,6-bis-phosphate aldolases, type I phosphomannose isomerase, and phosphoglucose isomerase. Bioorg Med Chem 2012; 20:1511-20. [PMID: 22269276 DOI: 10.1016/j.bmc.2011.12.050] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 12/20/2011] [Accepted: 12/22/2011] [Indexed: 11/29/2022]
Abstract
In the design of inhibitors of phosphosugar metabolizing enzymes and receptors with therapeutic interest, malonate has been reported in a number of cases as a good and hydrolytically-stable surrogate of the phosphate group, since both functions are dianionic at physiological pH and of comparable size. We have investigated a series of malonate-based mimics of the best known phosphate inhibitors of class II (zinc) fructose-1,6-bis-phosphate aldolases (FBAs) (e.g., from Mycobacterium tuberculosis), type I (zinc) phosphomannose isomerase (PMI) from Escherichia coli, and phosphoglucose isomerase (PGI) from yeast. In the case of FBAs, replacement of one phosphate by one malonate on a bis-phosphorylated inhibitor (1) led to a new compound (4) still showing a strong inhibition (K(i) in the nM range) and class II versus class I selectivity (up to 8×10(4)). Replacement of the other phosphate however strongly affected binding efficiency and selectivity. In the case of PGI and PMI, 5-deoxy-5-malonate-D-arabinonohydroxamic acid (8) yielded a strong decrease in binding affinities when compared to its phosphorylated parent compound 5-phospho-D-arabinonohydroxamic acid (2). Analysis of the deposited 3D structures of the kinetically evaluated enzymes complexed to the phosphate-based inhibitors indicate that malonate could be a good phosphate surrogate only if phosphate is not tightly bound at the enzyme active site, such as in position 7 of compound 1 for FBAs. These observations are of importance for further design of inhibitors of phosphorylated-compounds metabolizing enzymes with therapeutic interest.
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Affiliation(s)
- Stéphanie Desvergnes
- Univ. Paris-Sud, Laboratoire de Chimie Bioorganique et Bioinorganique, ICMMO, UMR8182, LabEx LERMIT, Orsay F-91405, France
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de la Paz Santangelo M, Gest PM, Guerin ME, Coinçon M, Pham H, Ryan G, Puckett SE, Spencer JS, Gonzalez-Juarrero M, Daher R, Lenaerts AJ, Schnappinger D, Therisod M, Ehrt S, Sygusch J, Jackson M. Glycolytic and non-glycolytic functions of Mycobacterium tuberculosis fructose-1,6-bisphosphate aldolase, an essential enzyme produced by replicating and non-replicating bacilli. J Biol Chem 2011; 286:40219-31. [PMID: 21949126 PMCID: PMC3220552 DOI: 10.1074/jbc.m111.259440] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 09/09/2011] [Indexed: 12/29/2022] Open
Abstract
The search for antituberculosis drugs active against persistent bacilli has led to our interest in metallodependent class II fructose-1,6-bisphosphate aldolase (FBA-tb), a key enzyme of gluconeogenesis absent from mammalian cells. Knock-out experiments at the fba-tb locus indicated that this gene is required for the growth of Mycobacterium tuberculosis on gluconeogenetic substrates and in glucose-containing medium. Surface labeling and enzymatic activity measurements revealed that this enzyme was exported to the cell surface of M. tuberculosis and produced under various axenic growth conditions including oxygen depletion and hence by non-replicating bacilli. Importantly, FBA-tb was also produced in vivo in the lungs of infected guinea pigs and mice. FBA-tb bound human plasmin(ogen) and protected FBA-tb-bound plasmin from regulation by α(2)-antiplasmin, suggestive of an involvement of this enzyme in host/pathogen interactions. The crystal structures of FBA-tb in the native form and in complex with a hydroxamate substrate analog were determined to 2.35- and 1.9-Å resolution, respectively. Whereas inhibitor attachment had no effect on the plasminogen binding activity of FBA-tb, it competed with the natural substrate of the enzyme, fructose 1,6-bisphosphate, and substantiated a previously unknown reaction mechanism associated with metallodependent aldolases involving recruitment of the catalytic zinc ion by the substrate upon active site binding. Altogether, our results highlight the potential of FBA-tb as a novel therapeutic target against both replicating and non-replicating bacilli.
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Affiliation(s)
- Maria de la Paz Santangelo
- From the Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682
- Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas-Instituto Nacional de Tecnología Agropecuaria, 1686 Buenos Aires, Argentina
| | - Petra M. Gest
- From the Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682
| | - Marcelo E. Guerin
- Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas-Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC-UPV/EHU), Barrio Sarriena s/n, Leioa, 48940 Bizkaia, Spain
- Departamento de Bioquímica, Universidad del País Vasco, Aptdo. 644, 48080 Bilbao, Spain
- IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
| | - Mathieu Coinçon
- Département de Biochimie, Université de Montréal, CP 6128, Station centre-ville, Montréal PQ H3C 3J7, Canada
| | - Ha Pham
- From the Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682
| | - Gavin Ryan
- From the Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682
| | - Susan E. Puckett
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065
| | - John S. Spencer
- From the Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682
| | - Mercedes Gonzalez-Juarrero
- From the Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682
| | - Racha Daher
- Laboratoire de Chimie Bioorganique et Bioinorganique-Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR 8182, Université Paris Sud, 91405 Orsay, France and
| | - Anne J. Lenaerts
- From the Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065
| | - Michel Therisod
- Laboratoire de Chimie Bioorganique et Bioinorganique-Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR 8182, Université Paris Sud, 91405 Orsay, France and
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065
| | - Jurgen Sygusch
- Département de Biochimie, Université de Montréal, CP 6128, Station centre-ville, Montréal PQ H3C 3J7, Canada
| | - Mary Jackson
- From the Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523-1682
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