1
|
Acebrón-García-de-Eulate M, Mayol-Llinàs J, Holland MTO, Kim SY, Brown KP, Marchetti C, Hess J, Di Pietro O, Mendes V, Abell C, Floto RA, Coyne AG, Blundell TL. Discovery of Novel Inhibitors of Uridine Diphosphate- N-Acetylenolpyruvylglucosamine Reductase (MurB) from Pseudomonas aeruginosa, an Opportunistic Infectious Agent Causing Death in Cystic Fibrosis Patients. J Med Chem 2022; 65:2149-2173. [PMID: 35080396 PMCID: PMC7614804 DOI: 10.1021/acs.jmedchem.1c01684] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pseudomonas aeruginosa is of major concern for cystic fibrosis patients where this infection can be fatal. With the emergence of drug-resistant strains, there is an urgent need to develop novel antibiotics against P. aeruginosa. MurB is a promising target for novel antibiotic development as it is involved in the cell wall biosynthesis. MurB has been shown to be essential in P. aeruginosa, and importantly, no MurB homologue exists in eukaryotic cells. A fragment-based drug discovery approach was used to target Pa MurB. This led to the identification of a number of fragments, which were shown to bind to MurB. One fragment, a phenylpyrazole scaffold, was shown by ITC to bind with an affinity of Kd = 2.88 mM (LE 0.23). Using a structure guided approach, different substitutions were synthesized and the initial fragment was optimized to obtain a small molecule with Kd = 3.57 μM (LE 0.35).
Collapse
Affiliation(s)
| | - Joan Mayol-Llinàs
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Matthew T O Holland
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - So Yeon Kim
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Karen P Brown
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular Biology, University of Cambridge, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K.,Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, CB23 3RE, UK
| | - Chiara Marchetti
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Jeannine Hess
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Ornella Di Pietro
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Vitor Mendes
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Chris Abell
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - R Andres Floto
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular Biology, University of Cambridge, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K.,Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, CB23 3RE, UK
| | - Anthony G Coyne
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, U.K
| |
Collapse
|
2
|
Jukič M, Hrast M, Patin D, Ogorevc E, Barreteau H, Gobec S. Virtual screening approach and biochemical evaluation on MurB. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.cdc.2019.100276] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
3
|
Ewing TA, Fraaije MW, Mattevi A, van Berkel WJ. The VAO/PCMH flavoprotein family. Arch Biochem Biophys 2017; 632:104-117. [DOI: 10.1016/j.abb.2017.06.022] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 06/26/2017] [Accepted: 06/29/2017] [Indexed: 01/15/2023]
|
4
|
Auldridge ME, Cao H, Sen S, Franz LP, Bingman CA, Yennamalli RM, Phillips GN, Mead D, Steinmetz EJ. LucY: A Versatile New Fluorescent Reporter Protein. PLoS One 2015; 10:e0124272. [PMID: 25906065 PMCID: PMC4408115 DOI: 10.1371/journal.pone.0124272] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 03/12/2015] [Indexed: 01/07/2023] Open
Abstract
We report on the discovery, isolation, and use of a novel yellow fluorescent protein. Lucigen Yellow (LucY) binds one FAD molecule within its core, thus shielding it from water and maintaining its structure so that fluorescence is 10-fold higher than freely soluble FAD. LucY displays excitation and emission spectra characteristic of FAD, with 3 excitation peaks at 276 nm, 377 nm, and 460 nm and a single emission peak at 530 nm. These excitation and emission maxima provide the large Stokes shift beneficial to fluorescence experimentation. LucY belongs to the MurB family of UDP-N-acetylenolpyruvylglucosamine reductases. The high resolution crystal structure shows that in contrast to other structurally resolved MurB enzymes, LucY does not contain a potentially quenching aromatic residue near the FAD isoalloxazine ring, which may explain its increased fluorescence over related proteins. Using E. coli as a system in which to develop LucY as a reporter, we show that it is amenable to circular permutation and use as a reporter of protein-protein interaction. Fragmentation between its distinct domains renders LucY non-fluorescent, but fluorescence can be partially restored by fusion of the fragments to interacting protein domains. Thus, LucY may find application in Protein-fragment Complementation Assays for evaluating protein-protein interactions.
Collapse
Affiliation(s)
| | - Hongnan Cao
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
| | - Saurabh Sen
- Lucigen Corp., Middleton, WI, United States of America
| | | | - Craig A. Bingman
- Department of Biochemistry, University of Wisconsin, Madison, WI, United States of America
| | - Ragothaman M. Yennamalli
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
| | - George N. Phillips
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
- Department of Biochemistry, University of Wisconsin, Madison, WI, United States of America
| | - David Mead
- Lucigen Corp., Middleton, WI, United States of America
| | | |
Collapse
|
5
|
Moraes GL, Gomes GC, Monteiro de Sousa PR, Alves CN, Govender T, Kruger HG, Maguire GEM, Lamichhane G, Lameira J. Structural and functional features of enzymes of Mycobacterium tuberculosis peptidoglycan biosynthesis as targets for drug development. Tuberculosis (Edinb) 2015; 95:95-111. [PMID: 25701501 DOI: 10.1016/j.tube.2015.01.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 01/13/2015] [Accepted: 01/19/2015] [Indexed: 10/24/2022]
Abstract
Tuberculosis (TB) is the second leading cause of human mortality from infectious diseases worldwide. The WHO reported 1.3 million deaths and 8.6 million new cases of TB in 2012. Mycobacterium tuberculosis (M. tuberculosis), the infectious bacteria that causes TB, is encapsulated by a thick and robust cell wall. The innermost segment of the cell wall is comprised of peptidoglycan, a layer that is required for survival and growth of the pathogen. Enzymes that catalyse biosynthesis of the peptidoglycan are essential and are therefore attractive targets for discovery of novel antibiotics as humans lack similar enzymes making it possible to selectively target bacteria only. In this paper, we have reviewed the structures and functions of enzymes GlmS, GlmM, GlmU, MurA, MurB, MurC, MurD, MurE and MurF from M. tuberculosis that are involved in peptidoglycan biosynthesis. In addition, we report homology modelled 3D structures of those key enzymes from M. tuberculosis of which the structures are still unknown. We demonstrated that natural substrates can be successfully docked into the active sites of the GlmS and GlmU respectively. It is therefore expected that the models and the data provided herein will facilitate translational research to develop new drugs to treat TB.
Collapse
Affiliation(s)
- Gleiciane Leal Moraes
- Laboratório de Planejamento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, CEP 66075-110 Belém, PA, Brazil
| | - Guelber Cardoso Gomes
- Laboratório de Planejamento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, CEP 66075-110 Belém, PA, Brazil; Instituto de Ciências Biológicas, Universidade Federal do Pará, CEP 66075-110 Belém, PA, Brazil
| | - Paulo Robson Monteiro de Sousa
- Laboratório de Planejamento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, CEP 66075-110 Belém, PA, Brazil
| | - Cláudio Nahum Alves
- Laboratório de Planejamento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, CEP 66075-110 Belém, PA, Brazil
| | - Thavendran Govender
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, South Africa
| | - Hendrik G Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, South Africa
| | - Glenn E M Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, South Africa
| | - Gyanu Lamichhane
- Johns Hopkins University School of Medicine, Taskforce to Study Resistance Emergence & Antimicrobial Development Technology, 1503 E. Jefferson St, Baltimore, MD 21231, USA
| | - Jerônimo Lameira
- Laboratório de Planejamento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, CEP 66075-110 Belém, PA, Brazil; Instituto de Ciências Biológicas, Universidade Federal do Pará, CEP 66075-110 Belém, PA, Brazil.
| |
Collapse
|
6
|
Chen MW, Lohkamp B, Schnell R, Lescar J, Schneider G. Substrate Channel Flexibility in Pseudomonas aeruginosa MurB Accommodates Two Distinct Substrates. PLoS One 2013; 8:e66936. [PMID: 23805286 PMCID: PMC3689657 DOI: 10.1371/journal.pone.0066936] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 05/10/2013] [Indexed: 12/03/2022] Open
Abstract
Biosynthesis of UDP-N-acetylmuramic acid in bacteria is a committed step towards peptidoglycan production. In an NADPH- and FAD-dependent reaction, the UDP-N-acetylglucosamine-enolpyruvate reductase (MurB) reduces UDP-N-acetylglucosamine-enolpyruvate to UDP-N-acetylmuramic acid. We determined the three-dimensional structures of the ternary complex of Pseudomonas aeruginosa MurB with FAD and NADP+ in two crystal forms to resolutions of 2.2 and 2.1 Å, respectively, to investigate the structural basis of the first half-reaction, hydride transfer from NADPH to FAD. The nicotinamide ring of NADP+ stacks against the si face of the isoalloxazine ring of FAD, suggesting an unusual mode of hydride transfer to flavin. Comparison with the structure of the Escherichia coli MurB complex with UDP-N-acetylglucosamine-enolpyruvate shows that both substrates share the binding site located between two lobes of the substrate-binding domain III, consistent with a ping pong mechanism with sequential substrate binding. The nicotinamide and the enolpyruvyl moieties are strikingly well-aligned upon superimposition, both positioned for hydride transfer to and from FAD. However, flexibility of the substrate channel allows the non-reactive parts of the two substrates to bind in different conformations. A potassium ion in the active site may assist in substrate orientation and binding. These structural models should help in structure-aided drug design against MurB, which is essential for cell wall biogenesis and hence bacterial survival.
Collapse
Affiliation(s)
- Ming Wei Chen
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Bernhard Lohkamp
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Robert Schnell
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Gunter Schneider
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
| |
Collapse
|
7
|
Gautam A, Vyas R, Tewari R. Peptidoglycan biosynthesis machinery: a rich source of drug targets. Crit Rev Biotechnol 2010; 31:295-336. [PMID: 21091161 DOI: 10.3109/07388551.2010.525498] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The range of antibiotic therapy for the control of bacterial infections is becoming increasingly limited because of the rapid rise in multidrug resistance in clinical bacterial isolates. A few diseases, such as tuberculosis, which were once thought to be under control, have re-emerged as serious health threats. These problems have resulted in intensified research to look for new inhibitors for bacterial pathogens. Of late, the peptidoglycan (PG) layer, the most important component of the bacterial cell wall has been the subject of drug targeting because, first, it is essential for the survivability of eubacteria and secondly, it is absent in humans. The last decade has seen tremendous inputs in deciphering the 3-D structures of the PG biosynthetic enzymes. Many inhibitors against these enzymes have been developed using virtual and high throughput screening techniques. This review discusses the mechanistic and structural properties of the PG biosynthetic enzymes and inhibitors developed in the last decade.
Collapse
Affiliation(s)
- Ankur Gautam
- Department of Biotechnology, Panjab University, Chandigarh, India
| | | | | |
Collapse
|
8
|
Barreteau H, Kovac A, Boniface A, Sova M, Gobec S, Blanot D. Cytoplasmic steps of peptidoglycan biosynthesis. FEMS Microbiol Rev 2008; 32:168-207. [PMID: 18266853 DOI: 10.1111/j.1574-6976.2008.00104.x] [Citation(s) in RCA: 479] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The biosynthesis of bacterial cell wall peptidoglycan is a complex process that involves enzyme reactions that take place in the cytoplasm (synthesis of the nucleotide precursors) and on the inner side (synthesis of lipid-linked intermediates) and outer side (polymerization reactions) of the cytoplasmic membrane. This review deals with the cytoplasmic steps of peptidoglycan biosynthesis, which can be divided into four sets of reactions that lead to the syntheses of (1) UDP-N-acetylglucosamine from fructose 6-phosphate, (2) UDP-N-acetylmuramic acid from UDP-N-acetylglucosamine, (3) UDP-N-acetylmuramyl-pentapeptide from UDP-N-acetylmuramic acid and (4) D-glutamic acid and dipeptide D-alanyl-D-alanine. Recent data concerning the different enzymes involved are presented. Moreover, special attention is given to (1) the chemical and enzymatic synthesis of the nucleotide precursor substrates that are not commercially available and (2) the search for specific inhibitors that could act as antibacterial compounds.
Collapse
Affiliation(s)
- Hélène Barreteau
- Laboratoire des Enveloppes Bactériennes et Antibiotiques, Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Univ Paris-Sud, Orsay, France
| | | | | | | | | | | |
Collapse
|