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Bergman ME, Kortbeek RWJ, Gutensohn M, Dudareva N. Plant terpenoid biosynthetic network and its multiple layers of regulation. Prog Lipid Res 2024:101287. [PMID: 38906423 DOI: 10.1016/j.plipres.2024.101287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 06/23/2024]
Abstract
Terpenoids constitute one of the largest and most chemically diverse classes of primary and secondary metabolites in nature with an exceptional breadth of functional roles in plants. Biosynthesis of all terpenoids begins with the universal five‑carbon building blocks, isopentenyl diphosphate (IPP) and its allylic isomer dimethylallyl diphosphate (DMAPP), which in plants are derived from two compartmentally separated but metabolically crosstalking routes, the mevalonic acid (MVA) and methylerythritol phosphate (MEP) pathways. Here, we review the current knowledge on the terpenoid precursor pathways and highlight the critical hidden constraints as well as multiple regulatory mechanisms that coordinate and homeostatically govern carbon flux through the terpenoid biosynthetic network in plants.
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Affiliation(s)
- Matthew E Bergman
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Ruy W J Kortbeek
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Michael Gutensohn
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, United States
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States; Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States; Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States.
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2
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Azman AA, Muhd Noor ND, Leow ATC, Mohd Noor SA, Mohamad Ali MS. Identification and characterization of a promiscuous metallohydrolase in metallo-β-lactamase superfamily from a locally isolated organophosphate-degrading Bacillus sp. strain S3wahi. Int J Biol Macromol 2024; 271:132395. [PMID: 38761915 DOI: 10.1016/j.ijbiomac.2024.132395] [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: 12/20/2023] [Revised: 04/23/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024]
Abstract
In this present study, characteristics and structure-function relationship of an organophosphate-degrading enzyme from Bacillus sp. S3wahi were described. S3wahi metallohydrolase, designated as S3wahi-MH (probable metallohydrolase YqjP), featured the conserved αβ/βα metallo-β-lactamase-fold (MBL-fold) domain and a zinc bimetal at its catalytic site. The metal binding site of S3wahi-MH also preserves the H-X-H-X-D-H motif, consisting of specific amino acids at Zn1 (Asp69, His70, Asp182, and His230) and Zn2 (His65, His67, and His137). The multifunctionality of S3wahi-MH was demonstrated through a steady-state kinetic study, revealing its highest binding affinity (KM) and catalytic efficiency (kcat/KM) for OP compound, paraoxon, with values of 8.09 × 10-6 M and 4.94 × 105 M-1 s-1, respectively. Using OP compound, paraoxon, as S3wahi-MH native substrate, S3wahi-MH exhibited remarkable stability over a broad temperature range, 20 °C - 60 °C and a broad pH tolerance, pH 6-10. Corresponded to S3wahi-MH thermal stability characterization, the estimated melting temperature (Tm) was found to be 72.12 °C. S3wahi-MH was also characterized with optimum catalytic activity at 30 °C and pH 8. Additionally, the activity of purified S3wahi-MH was greatly enhanced in the presence of 1 mM and 5 mM of manganese (Mn2+), showing relative activities of 1323.68 % and 2073.68 %, respectively. The activity of S3wahi-MH was also enhanced in the presence of DMSO and DMF, showing relative activities of 270.37 % and 307.41 %, respectively. The purified S3wahi-MH retained >60 % residual activity after exposure to non-ionic Tween series surfactants. Nevertheless, the catalytic activity of S3wahi-MH was severely impacted by the treatment of SDS, even at low concentrations. Considering its enzymatic properties and promiscuity, S3wahi-MH emerges as a promising candidate as a bioremediation tool in wide industrial applications, including agriculture industry.
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Affiliation(s)
- Ameera Aisyah Azman
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Noor Dina Muhd Noor
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Adam Thean Chor Leow
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Siti Aminah Mohd Noor
- Center for Defence Foundation Studies, National Defence University of Malaysia, Kem Perdana Sungai Besi, Kuala Lumpur 57000, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia.
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Chen X, Zhao H, Wang C, Hamed M, Shang Q, Yang Y, Diao X, Sun X, Hu W, Jiang X, Zhang Y, Hirsch AKH, Wu D, Zhuang J. Two natural compounds as potential inhibitors against the Helicobacter pylori and Acinetobacter baumannii IspD enzymes. Int J Antimicrob Agents 2024; 63:107160. [PMID: 38537721 DOI: 10.1016/j.ijantimicag.2024.107160] [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: 12/30/2023] [Revised: 02/27/2024] [Accepted: 03/21/2024] [Indexed: 04/21/2024]
Abstract
In a vast majority of bacteria, protozoa and plants, the methylerythritol phosphate (MEP) pathway is utilized for the synthesis of isopentenyl diphosphate (IDP) and dimethylallyl diphosphate (DMADP), which are precursors for isoprenoids. Isoprenoids, such as cholesterol and coenzyme Q, play a variety of crucial roles in physiological activities, including cell-membrane formation, protein degradation, cell apoptosis, and transcription regulation. In contrast, humans employ the mevalonate (MVA) pathway for the production of IDP and DMADP, rendering proteins in the MEP pathway appealing targets for antimicrobial agents. This pathway consists of seven consecutive enzymatic reactions, of which 4-diphosphocytidyl-2C-methyl-D-erythritol synthase (IspD) and 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) catalyze the third and fifth steps, respectively. In this study, we characterized the enzymatic activities and protein structures of Helicobacter pylori IspDF and Acinetobacter baumannii IspD. Then, using the direct interaction-based thermal shift assay, we conducted a compound screening of an approved drug library and identified 27 hit compounds potentially binding to AbIspD. Among them, two natural products, rosmarinic acid and tanshinone IIA sodium sulfonate, exhibited inhibitory activities against HpIspDF and AbIspD, by competing with one of the substrates, MEP. Moreover, tanshinone IIA sodium sulfonate also demonstrated certain antibacterial effects against H. pylori. In summary, we identified two IspD inhibitors from approved ingredients, broadening the scope for antibiotic discovery targeting the MEP pathway.
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Affiliation(s)
- Xiaoyu Chen
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Huilin Zhao
- Department of Pathogenic Biology, College of Basic Medicine, Binzhou Medical University, Yantai, China
| | - Chuandong Wang
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Mostafa Hamed
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Saarbrücken, Germany
| | - Qinghong Shang
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yating Yang
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xiaotong Diao
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xiangnan Sun
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Wei Hu
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xukai Jiang
- National Glycoengineering Research Center, Shandong University, Qingdao, China
| | - Youming Zhang
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Saarbrücken, Germany; Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Dalei Wu
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
| | - Jingjing Zhuang
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China; Marine College, Shandong University, Weihai, China.
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Wang J, Wu W, Zhou Y, Han M, Zhou X, Sun Y, Zhang A. Design, synthesis and activity evaluation of pseudilin analogs against cyanobacteria as IspD inhibitors. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2024; 199:105769. [PMID: 38458678 DOI: 10.1016/j.pestbp.2024.105769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/27/2023] [Accepted: 01/05/2024] [Indexed: 03/10/2024]
Abstract
The discovery of safe, effective, and selective chemical algicides is the stringent need for the algicides development, and it is also one of the effective routes to control cyanobacteria harmful algal blooms and to meet the higher requirements of environmental and ecological. In this work, a series of novel bromo-N-phenyl-5-o-hydroxyphenylpyrazole-3-carboxyamides were rationally designed as pseudilin analogs by bioisosteric replacement and molecular hybridization strategies, in which the pyrrole unit of pseudilin was replaced with pyrazole and further combined with the dominant structural fragments of algicide diuron. The synthesis was carried out by a facile four-step routeincluding cyclization, amidation, transanulation, and halogenation. The biological activity evaluation on AtIspD, EcIspD, Synechocystis sp. PCC6803 and Microcystis aeruginosa FACHB905 revealed that most compounds had good EcIspD and excellent cyanobacteria inhibitory activity. In particular, compound 6bb exhibited potent algicidal activity against PCC6803 and FACHB905 with EC50 = 1.28 μM and 0.37 μM, respectively, 1.4-fold and 4.0-fold enhancement compared to copper sulfate (EC50 = 1.79 and 1.49 μM, respectively), and it also showed the best inhibitory activity of EcIspD. The binding of 6bb to EcIspD was explored by molecular docking, and it was confirmed that 6bb could bind to the EcIspD active site. Compound 6bb was proven to be a potential structure for the further development of novel algicides that targets IspD in the MEP pathway.
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Affiliation(s)
- Jili Wang
- College of Chemical and Environmental engineering, Hanjiang Normal University, Shiyan 442000, China
| | - Wenhai Wu
- College of Chemical and Environmental engineering, Hanjiang Normal University, Shiyan 442000, China
| | - Yaqing Zhou
- College of Chemical and Environmental engineering, Hanjiang Normal University, Shiyan 442000, China
| | - Mengying Han
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Xin Zhou
- College of Chemical and Environmental engineering, Hanjiang Normal University, Shiyan 442000, China
| | - Yong Sun
- College of Chemical and Environmental engineering, Hanjiang Normal University, Shiyan 442000, China.
| | - Aidong Zhang
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan 430079, China.
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The Multifaceted MEP Pathway: Towards New Therapeutic Perspectives. Molecules 2023; 28:molecules28031403. [PMID: 36771066 PMCID: PMC9919496 DOI: 10.3390/molecules28031403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 01/27/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
Isoprenoids, a diverse class of natural products, are present in all living organisms. Their two universal building blocks are synthesized via two independent pathways: the mevalonate pathway and the 2-C-methyl-ᴅ-erythritol 4-phosphate (MEP) pathway. The presence of the latter in pathogenic bacteria and its absence in humans make all its enzymes suitable targets for the development of novel antibacterial drugs. (E)-4-Hydroxy-3-methyl-but-2-enyl diphosphate (HMBPP), the last intermediate of this pathway, is a natural ligand for the human Vγ9Vδ2 T cells and the most potent natural phosphoantigen known to date. Moreover, 5-hydroxypentane-2,3-dione, a metabolite produced by Escherichia coli 1-deoxy-ᴅ-xylulose 5-phosphate synthase (DXS), the first enzyme of the MEP pathway, structurally resembles (S)-4,5-dihydroxy-2,3-pentanedione, a signal molecule implied in bacterial cell communication. In this review, we shed light on the diversity of potential uses of the MEP pathway in antibacterial therapies, starting with an overview of the antibacterials developed for each of its enzymes. Then, we provide insight into HMBPP, its synthetic analogs, and their prodrugs. Finally, we discuss the potential contribution of the MEP pathway to quorum sensing mechanisms. The MEP pathway, providing simultaneously antibacterial drug targets and potent immunostimulants, coupled with its potential role in bacterial cell-cell communication, opens new therapeutic perspectives.
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Li FKK, Gale RT, Petrotchenko EV, Borchers CH, Brown ED, Strynadka NCJ. Crystallographic analysis of TarI and TarJ, a cytidylyltransferase and reductase pair for CDP-ribitol synthesis in Staphylococcus aureus wall teichoic acid biogenesis. J Struct Biol 2021; 213:107733. [PMID: 33819634 DOI: 10.1016/j.jsb.2021.107733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 11/18/2022]
Abstract
The cell wall of many pathogenic Gram-positive bacteria contains ribitol-phosphate wall teichoic acid (WTA), a polymer that is linked to virulence and regulation of essential physiological processes including cell division. CDP-ribitol, the activated precursor for ribitol-phosphate polymerization, is synthesized by a cytidylyltransferase and reductase pair known as TarI and TarJ, respectively. In this study, we present crystal structures of Staphylococcus aureus TarI and TarJ in their apo forms and in complex with substrates and products. The TarI structures illustrate the mechanism of CDP-ribitol synthesis from CTP and ribitol-phosphate and reveal structural changes required for substrate binding and catalysis. Insights into the upstream step of ribulose-phosphate reduction to ribitol-phosphate is provided by the structures of TarJ. Furthermore, we propose a general topology of the enzymes in a heterotetrameric form built using restraints from crosslinking mass spectrometry analysis. Together, our data present molecular details of CDP-ribitol production that may aid in the design of inhibitors against WTA biosynthesis.
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Affiliation(s)
- Franco K K Li
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Robert T Gale
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3ZS, Canada
| | - Evgeniy V Petrotchenko
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada; Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada; Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia; Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8N 3ZS, Canada
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.
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Chen WQ, Yin MM, Song PJ, He XH, Liu Y, Jiang FL. Thermodynamics, Kinetics and Mechanisms of Noncompetitive Allosteric Inhibition of Chymotrypsin by Dihydrolipoic Acid-Coated Gold Nanoclusters. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:6447-6457. [PMID: 32460493 DOI: 10.1021/acs.langmuir.0c00699] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Enzymes are an important class of biomacromolecules which catalyze many metabolic processes in living systems. Nanomaterials can be synthesized with tailored sizes as well as desired surface modifications, thus acting as promising enzyme regulators. Fluorescent gold nanoclusters (AuNCs) are a representative class of ultrasmall nanoparticles (USNPs) with sizes of ∼2 nm, smaller than most of proteins including enzymes. In this work, we chose α-chymotrypsin (ChT) and AuNCs as the model system. Activity assays and inhibition kinetics studies showed that dihydrolipoic acid (DHLA)-coated AuNCs (DHLA-AuNCs) had a high inhibitory potency (IC50 = 3.4 μM) and high inhibitory efficacy (>80%) on ChT activity through noncompetitive inhibition mechanism. In distinct contrast, glutathione (GSH)-coated AuNCs (GSH-AuNCs) had no significant inhibition effects. Fluorescence spectroscopy, agarose gel electrophoresis and circular dichroism (CD) spectroscopy were conducted to explore the underlying mechanisms. A two-step interaction model was proposed. First, both DHLA-AuNCs and GSH-AuNCs might be bound to the positively charged sites of ChT through electrostatic forces. Second, further hydrophobic interactions occurred between three tyrosine residues of ChT and the hydrophobic carbon chain of DHLA, leading to a significant structural change thus to deactivate ChT on the allosteric site. On the contrary, no such interactions occurred with GSH of zwitterionic characteristic, which explained no inhibitory effect of GSH-AuNCs on ChT. To the best of our knowledge, this is the first example of the allosteric inhibition of ChT by nano regulators. These findings provide a fundamental basis for the design and development of nano regulators.
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Affiliation(s)
- Wen-Qi Chen
- Sauvage Center for Molecular Sciences, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Miao-Miao Yin
- Sauvage Center for Molecular Sciences, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Peng-Jun Song
- Sauvage Center for Molecular Sciences, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Xiao-Hang He
- Sauvage Center for Molecular Sciences, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Yi Liu
- Sauvage Center for Molecular Sciences, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
- Hubei Province Key Laboratory for Coal Conversion and New Carbon Materials, School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, P. R. China
- Guangxi Key Laboratory of Natural Polymer Chemistry, College of Chemistry and Materials Science, Nanning Normal University, Nanning 530001, P. R. China
| | - Feng-Lei Jiang
- Sauvage Center for Molecular Sciences, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
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Wang J, Zhou Y, Wang X, Duan L, Duan J, Li W, Zhang A. Synthesis and Evaluation of Halogenated 5-(2-Hydroxyphenyl)pyrazoles as Pseudilin Analogues Targeting the Enzyme IspD in the Methylerythritol Phosphate Pathway. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:3071-3078. [PMID: 32078770 DOI: 10.1021/acs.jafc.9b08057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
This work reports halogenated 5-(2-hydroxyphenyl)pyrazoles as pseudilin analogues with the potential to target the enzyme IspD in the methylerythritol phosphate (MEP) pathway. Such analogues were designed using the bioisosteric replacement of the pseudilin core structure and synthesized via an efficient three-step route. With AtIspD-based screening and pre- and post-emergence herbicidal tests, these compounds were demonstrated to have considerable activities against AtIspD, with IC50 up to 3.27 μM, and against model plants rape and barnyard grass, with moderate to excellent activities. At a rate of 150 g/ha in the greenhouse test, three compounds exhibited higher or comparable herbicidal activities than pseudilin. Molecular docking of representative compounds into the allosteric site of AtIspD revealed a binding mode similar to that of pseudilin. The established bioisosterism and synthesis method in this work may serve as an important tool for the development of new herbicides and antimicrobials targeting IspD in the MEP pathway.
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Affiliation(s)
- Jili Wang
- Key Laboratory of Pesticides & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Yaqing Zhou
- Key Laboratory of Pesticides & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Xiuwen Wang
- Key Laboratory of Pesticides & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Lixia Duan
- Key Laboratory of Pesticides & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Jiang Duan
- Key Laboratory of Pesticides & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Weiguo Li
- Key Laboratory of Pesticides & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Aidong Zhang
- Key Laboratory of Pesticides & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
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De Gasparo R, Halgas O, Harangozo D, Kaiser M, Pai EF, Krauth‐Siegel RL, Diederich F. Targeting a Large Active Site: Structure‐Based Design of Nanomolar Inhibitors of
Trypanosoma brucei
Trypanothione Reductase. Chemistry 2019; 25:11416-11421. [DOI: 10.1002/chem.201901664] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/03/2019] [Indexed: 01/16/2023]
Affiliation(s)
- Raoul De Gasparo
- Laboratorium für Organische ChemieETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Ondrej Halgas
- Departments of Biochemistry and Medical BiophysicsUniversity of Toronto Medical Sciences Building, 5318, 1 King's College Circle Toronto ON M5S 1A8 Canada
- The Campbell Family Institute for Cancer ResearchUniversity Health Network 101 College Street Toronto ON M5G 1L7 Canada
| | - Dora Harangozo
- Laboratorium für Organische ChemieETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute Socinstrasse 57 4002 Basel Switzerland
- University of Basel Petersplatz 1 4003 Basel Switzerland
| | - Emil F. Pai
- Departments of Biochemistry and Medical BiophysicsUniversity of Toronto Medical Sciences Building, 5318, 1 King's College Circle Toronto ON M5S 1A8 Canada
- The Campbell Family Institute for Cancer ResearchUniversity Health Network 101 College Street Toronto ON M5G 1L7 Canada
| | - R. Luise Krauth‐Siegel
- Biochemie-Zentrum Heidelberg (BZH)Universität Heidelberg Im Neuenheimer Feld 328 69120 Heidelberg Germany
| | - François Diederich
- Laboratorium für Organische ChemieETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
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Bjij I, Khan S, Betz R, Cherqaoui D, Soliman MES. Exploring the Structural Mechanism of Covalently Bound E3 Ubiquitin Ligase: Catalytic or Allosteric Inhibition? Protein J 2019; 37:500-509. [PMID: 30232697 DOI: 10.1007/s10930-018-9795-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Covalent inhibition has recently gained a resurgence of interest in several drug discovery areas. The expansion of this approach is based on evidence elucidating the selectivity and potency of covalent inhibitors when bound to particular amino acids of a biological target. The Nedd4-1, an E3 ubiquitin ligase, is characterized by two covalent binding sites, of which catalytic Cyscat and allosteric Cysallo are enclosed. This enzyme has demonstrated inhibition at both the above-mentioned binding sites; however, a detailed molecular understanding of the structural mechanism of inhibition upon Cyscat and Cysallo binding remains vague. This prompted us to provide the first account of investigating the preferential covalent binding mode and the underlying structural and molecular dynamic implications. Based on the molecular dynamic analyses, it was evident that although both catalytic and allosteric covalent binding led to greater stability of the enzyme, a preferential covalent mechanism of inhibition was seen in the allosteric-targeted system. This was supported by a more favorable binding energy in the allosteric site compared to the catalytic site, in addition to the larger number of residue interactions and stabilizing hydrogen bonds occurring in the allosteric covalent bound complex. The fundamental dynamic analysis presented in this report compliments, as well as adds to previous experimental findings, thus leading to a crucial understanding of the structural mechanism by which Nedd4-1 is inhibited. The findings from this study may assist in the design of more target-specific Nedd4-1 covalent inhibitors exploring the surface-exposed cysteine residues.
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Affiliation(s)
- Imane Bjij
- Molecular Bio-Computation & Drug Design Lab, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, 4000, South Africa.,Département de Chimie, Faculté des Sciences Semlalia, Université Cadi Ayyad, Av. My Abdellah, BP2390, Marrakech, Morocco
| | - Shama Khan
- Molecular Bio-Computation & Drug Design Lab, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, 4000, South Africa
| | - Robin Betz
- Biophysics Program, Stanford University, Stanford, CA, 94305, USA
| | - Driss Cherqaoui
- Département de Chimie, Faculté des Sciences Semlalia, Université Cadi Ayyad, Av. My Abdellah, BP2390, Marrakech, Morocco
| | - Mahmoud E S Soliman
- Molecular Bio-Computation & Drug Design Lab, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, 4000, South Africa.
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11
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Fischer G. Recent advances in 1,2,4-triazolo[1,5-a]pyrimidine chemistry. ADVANCES IN HETEROCYCLIC CHEMISTRY 2019. [DOI: 10.1016/bs.aihch.2018.10.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Root K, Barylyuk K, Schwab A, Thelemann J, Illarionov B, Geist JG, Gräwert T, Bacher A, Fischer M, Diederich F, Zenobi R. Aryl bis-sulfonamides bind to the active site of a homotrimeric isoprenoid biosynthesis enzyme IspF and extract the essential divalent metal cation cofactor. Chem Sci 2018; 9:5976-5986. [PMID: 30079212 PMCID: PMC6050538 DOI: 10.1039/c8sc00814k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 06/17/2018] [Indexed: 12/22/2022] Open
Abstract
Characterizing the mode of action of non-covalent inhibitors in multisubunit enzymes often presents a great challenge. Most of the conventionally used methods are based on ensemble measurements of protein-ligand binding in bulk solution. They often fail to accurately describe multiple binding processes occurring in such systems. Native electrospray ionization mass spectrometry (ESI-MS) of intact protein complexes is a direct, label-free approach that can render the entire distribution of ligand-bound states in multimeric protein complexes. Here we apply native ESI-MS to comprehensively characterize the isoprenoid biosynthesis enzyme IspF from Arabidopsis thaliana, an example of a homomeric protein complex with multiple binding sites for several types of ligands, including a metal cofactor and a synthetic inhibitor. While standard biophysical techniques failed to reveal the mode of action of recently discovered aryl-sulfonamide-based inhibitors of AtIspF, direct native ESI-MS titrations of the protein with the ligands and ligand competition assays allowed us to accurately capture the solution-phase protein-ligand binding equilibria in full complexity and detail. Based on these combined with computational modeling, we propose a mechanism of AtIspF inhibition by aryl bis-sulfonamides that involves both the competition with the substrate for the ligand-binding pocket and the extraction of Zn2+ from the enzyme active site. This inhibition mode is therefore mixed competitive and non-competitive, the latter exerting a key inhibitory effect on the enzyme activity. The results of our study deliver a profound insight into the mechanisms of AtIspF action and inhibition, open new perspectives for designing inhibitors of this important drug target, and demonstrate the applicability and value of the native ESI-MS approach for deep analysis of complex biomolecular binding equilibria.
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Affiliation(s)
- Katharina Root
- Department of Chemistry and Applied Biosciences , ETH Zurich , Zurich , Switzerland .
| | - Konstantin Barylyuk
- Department of Chemistry and Applied Biosciences , ETH Zurich , Zurich , Switzerland .
| | - Anatol Schwab
- Department of Chemistry and Applied Biosciences , ETH Zurich , Zurich , Switzerland .
| | - Jonas Thelemann
- Department of Chemistry and Applied Biosciences , ETH Zurich , Zurich , Switzerland .
| | - Boris Illarionov
- Hamburg School of Food Science , University of Hamburg , Hamburg , Germany
| | - Julie G Geist
- Department of Chemistry and Applied Biosciences , ETH Zurich , Zurich , Switzerland .
| | - Tobias Gräwert
- Hamburg School of Food Science , University of Hamburg , Hamburg , Germany
| | - Adelbert Bacher
- Department of Chemistry , Technical University of Munich , Garching , Germany
| | - Markus Fischer
- Hamburg School of Food Science , University of Hamburg , Hamburg , Germany
| | - François Diederich
- Department of Chemistry and Applied Biosciences , ETH Zurich , Zurich , Switzerland .
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences , ETH Zurich , Zurich , Switzerland .
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Gropp C, Quigley BL, Diederich F. Molecular Recognition with Resorcin[4]arene Cavitands: Switching, Halogen-Bonded Capsules, and Enantioselective Complexation. J Am Chem Soc 2018; 140:2705-2717. [DOI: 10.1021/jacs.7b12894] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Cornelius Gropp
- Laboratory of Organic Chemistry,
Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg
3, 8093 Zürich, Switzerland
| | - Brendan L. Quigley
- Laboratory of Organic Chemistry,
Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg
3, 8093 Zürich, Switzerland
| | - François Diederich
- Laboratory of Organic Chemistry,
Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg
3, 8093 Zürich, Switzerland
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