1
|
Mackinnon S, Krojer T, Foster WR, Diaz-Saez L, Tang M, Huber KVM, von Delft F, Lai K, Brennan PE, Arruda Bezerra G, Yue WW. Fragment Screening Reveals Starting Points for Rational Design of Galactokinase 1 Inhibitors to Treat Classic Galactosemia. ACS Chem Biol 2021; 16:586-595. [PMID: 33724769 PMCID: PMC8056384 DOI: 10.1021/acschembio.0c00498] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 02/18/2021] [Indexed: 11/28/2022]
Abstract
Classic galactosemia is caused by loss-of-function mutations in galactose-1-phosphate uridylyltransferase (GALT) that lead to toxic accumulation of its substrate, galactose-1-phosphate. One proposed therapy is to inhibit the biosynthesis of galactose-1-phosphate, catalyzed by galactokinase 1 (GALK1). Existing inhibitors of human GALK1 (hGALK1) are primarily ATP-competitive with limited clinical utility to date. Here, we determined crystal structures of hGALK1 bound with reported ATP-competitive inhibitors of the spiro-benzoxazole series, to reveal their binding mode in the active site. Spurred by the need for additional chemotypes of hGALK1 inhibitors, desirably targeting a nonorthosteric site, we also performed crystallography-based screening by soaking hundreds of hGALK1 crystals, already containing active site ligands, with fragments from a custom library. Two fragments were found to bind close to the ATP binding site, and a further eight were found in a hotspot distal from the active site, highlighting the strength of this method in identifying previously uncharacterized allosteric sites. To generate inhibitors of improved potency and selectivity targeting the newly identified binding hotspot, new compounds were designed by merging overlapping fragments. This yielded two micromolar inhibitors of hGALK1 that were not competitive with respect to either substrate (ATP or galactose) and demonstrated good selectivity over hGALK1 homologues, galactokinase 2 and mevalonate kinase. Our findings are therefore the first to demonstrate inhibition of hGALK1 from an allosteric site, with potential for further development of potent and selective inhibitors to provide novel therapeutics for classic galactosemia.
Collapse
Affiliation(s)
- Sabrina
R. Mackinnon
- Structural
Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom, OX3 7DQ
| | - Tobias Krojer
- Structural
Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom, OX3 7DQ
| | - William R. Foster
- Structural
Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom, OX3 7DQ
| | - Laura Diaz-Saez
- Structural
Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom, OX3 7DQ
- Target
Discovery Institute, University of Oxford, Oxford, United Kingdom, OX3 7FZ
| | - Manshu Tang
- Department
of Pediatrics, University of Utah, Salt Lake City, Utah 84108-6500, United States
| | - Kilian V. M. Huber
- Structural
Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom, OX3 7DQ
- Target
Discovery Institute, University of Oxford, Oxford, United Kingdom, OX3 7FZ
| | - Frank von Delft
- Structural
Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom, OX3 7DQ
- Diamond
Light Source, Harwell Science and Innovation
Campus, Didcot, Oxfordshire, United Kingdom, OX11 0DE
| | - Kent Lai
- Department
of Pediatrics, University of Utah, Salt Lake City, Utah 84108-6500, United States
| | - Paul E. Brennan
- Structural
Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom, OX3 7DQ
- Target
Discovery Institute, University of Oxford, Oxford, United Kingdom, OX3 7FZ
| | - Gustavo Arruda Bezerra
- Structural
Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom, OX3 7DQ
| | - Wyatt W. Yue
- Structural
Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom, OX3 7DQ
| |
Collapse
|
2
|
Liu X, Han C, Fang L, Fan Z, Wang Y, Gao X, Shi J, Min W. Mechanism of the feedback-inhibition resistance in aspartate kinase of Corynebacterium pekinense: from experiment to MD simulations. RSC Adv 2020; 11:30-38. [PMID: 35423034 PMCID: PMC8690038 DOI: 10.1039/d0ra09153g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/14/2020] [Indexed: 11/21/2022] Open
Abstract
In microorganisms and plants, aspartate kinase (AK) is the initial committed enzyme of the biosynthesis of the aspartate acid family amino acids and is inhibited by end products. In the paper, we mutated the key allosteric regulatory site A380 around the binding site of the Lys inhibitor in Corynebacterium pekinense AK (CpAK). A single-mutant A380C was obtained with 12.35-fold higher enzyme activity through high-throughput screening. On this basis, T379 as another key allosteric regulatory site was further modified, and the double-mutant T379N/A380C with 22.79-fold higher enzyme activity was obtained. Molecular dynamics (MD) simulations were used to investigate the mechanism of allosteric inhibition by Lys. The results indicated that the binding of Lys with CpAK resulted in conformational changes and a larger distance between the phosphorus atom of ATP and the oxygen atom of Asp, which was detrimental for the catalytic reaction. However, the mutation of allosteric sites opens the "switch" of allosteric regulation and can prevent the conformational transformation. Some key residues such as G168, R203, and D193 play an important role in maintaining the substrate binding with CpAK and further enhance the enzyme activity.
Collapse
Affiliation(s)
- Xiaoting Liu
- College of Food Science and Engineering, National Engineering Laboratory of Wheat and Corn Deep Processing, Jilin Agricultural University Changchun 130118 Jilin People's Republic of China +86-431-8451-7235 +86-139-4491-9697
- National Engineering Laboratory of Wheat and Corn Deep Processing Changchun 130118 Jilin China
| | - Caijing Han
- College of Food Science and Engineering, National Engineering Laboratory of Wheat and Corn Deep Processing, Jilin Agricultural University Changchun 130118 Jilin People's Republic of China +86-431-8451-7235 +86-139-4491-9697
- National Engineering Laboratory of Wheat and Corn Deep Processing Changchun 130118 Jilin China
- School of Public Health, Weifang Medical University Weifang 261042 Shandong China
| | - Li Fang
- College of Food Science and Engineering, National Engineering Laboratory of Wheat and Corn Deep Processing, Jilin Agricultural University Changchun 130118 Jilin People's Republic of China +86-431-8451-7235 +86-139-4491-9697
- National Engineering Laboratory of Wheat and Corn Deep Processing Changchun 130118 Jilin China
| | - Zhanqing Fan
- College of Food Science and Engineering, National Engineering Laboratory of Wheat and Corn Deep Processing, Jilin Agricultural University Changchun 130118 Jilin People's Republic of China +86-431-8451-7235 +86-139-4491-9697
- National Engineering Laboratory of Wheat and Corn Deep Processing Changchun 130118 Jilin China
| | - Yanan Wang
- College of Food Science and Engineering, National Engineering Laboratory of Wheat and Corn Deep Processing, Jilin Agricultural University Changchun 130118 Jilin People's Republic of China +86-431-8451-7235 +86-139-4491-9697
- National Engineering Laboratory of Wheat and Corn Deep Processing Changchun 130118 Jilin China
| | - Xin Gao
- College of Food Science and Engineering, National Engineering Laboratory of Wheat and Corn Deep Processing, Jilin Agricultural University Changchun 130118 Jilin People's Republic of China +86-431-8451-7235 +86-139-4491-9697
- National Engineering Laboratory of Wheat and Corn Deep Processing Changchun 130118 Jilin China
| | - Junhua Shi
- College of Food Science and Engineering, National Engineering Laboratory of Wheat and Corn Deep Processing, Jilin Agricultural University Changchun 130118 Jilin People's Republic of China +86-431-8451-7235 +86-139-4491-9697
- National Engineering Laboratory of Wheat and Corn Deep Processing Changchun 130118 Jilin China
| | - Weihong Min
- College of Food Science and Engineering, National Engineering Laboratory of Wheat and Corn Deep Processing, Jilin Agricultural University Changchun 130118 Jilin People's Republic of China +86-431-8451-7235 +86-139-4491-9697
- National Engineering Laboratory of Wheat and Corn Deep Processing Changchun 130118 Jilin China
| |
Collapse
|
3
|
McClory J, Hui C, Zhang J, Huang M. The phosphorylation mechanism of mevalonate diphosphate decarboxylase: a QM/MM study. Org Biomol Chem 2020; 18:518-529. [PMID: 31854421 DOI: 10.1039/c9ob02254f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mevalonate diphosphate decarboxylase (MDD) catalyses a crucial step of the mevalonate pathway via Mg2+-ATP-dependent phosphorylation and decarboxylation reactions to ultimately produce isopentenyl diphosphate, the precursor of isoprenoids, which is essential to bacterial functions and provides ideal building blocks for the biosynthesis of isopentenols. However, the metal ion(s) in MDD has not been unambiguously resolved, which limits the understanding of the catalytic mechanism and the exploitation of enzymes for the development of antibacterial therapies or the mevalonate metabolic pathway for the biosynthesis of biofuels. Here by analogizing structurally related kinases and molecular dynamics simulations, we constructed a model of the MDD-substrate-ATP-Mg2+ complex and proposed that MDD requires two Mg2+ ions for maintaining a catalytically active conformation. Subsequent QM/MM studies indicate that MDD catalyses the phosphorylation of its substrate mevalonate diphosphate (MVAPP) via a direct phosphorylation reaction, instead of the previously assumed catalytic base mechanism. The results here would shed light on the active conformation of MDD-related enzymes and their catalytic mechanisms and therefore be useful for developing novel antimicrobial therapies or reconstructing mevalonate metabolic pathways for the biosynthesis of biofuels.
Collapse
Affiliation(s)
- James McClory
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Stranmillis Road, Belfast, BT9 5AG, Northern Ireland, UK.
| | | | | | | |
Collapse
|
4
|
McAuley M, Huang M, Timson DJ. Dynamic origins of substrate promiscuity in bacterial galactokinases. Carbohydr Res 2019; 486:107839. [PMID: 31704571 DOI: 10.1016/j.carres.2019.107839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/15/2019] [Accepted: 10/15/2019] [Indexed: 12/21/2022]
Abstract
Galactokinase catalyses the ATP-dependent phosphorylation of galactose and structurally related sugars. The enzyme has attracted interest as a potential biocatalyst for the production of sugar 1-phosphates and several attempts have been made to broaden its specificity. In general, bacterial galactokinases have wider substrate ranges than mammalian ones. The enzymes from Escherichia coli and Lactococcus lactis have received particular attention and a number of variants with increased promiscuity have been identified. Here, we present a molecular dynamics study designed to investigate the molecular causes of the wider substrate ranges of these enzymes and their variants with particular reference to protein mobility. Some regions close to the active site of the enzyme have different structures in the bacterial enzymes compared to the human one. Alterations known to increase the substrate range (e.g. Y371H in the E. coli enzyme), tend to alter the conformation of a key α-helical region (residues 216-232 in the E. coli enzyme). The equivalent helix in the human enzyme has previously been predicted to be altered in variants which affect catalytic activity or protein stability. This helix appears to be a key region in galactokinases from a range of species and may represent an interesting target for future attempts to broaden the specificity of galactokinases.
Collapse
Affiliation(s)
- Margaret McAuley
- School of Biological Sciences Queen's University Belfast, Medical Biology Building, 97 Lisburn Road, Belfast, BT9 7BL, UK
| | - Meilan Huang
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Stranmillis Road, Belfast, BT9 5AG, UK
| | - David J Timson
- School of Biological Sciences Queen's University Belfast, Medical Biology Building, 97 Lisburn Road, Belfast, BT9 7BL, UK; School of Pharmacy and Biomolecular Sciences, University of Brighton, Huxley Building, Lewes Road, Brighton, BN2 4GJ, UK.
| |
Collapse
|
5
|
Abstract
Biocatalysis (the use of biological molecules or materials to catalyse chemical reactions) has considerable potential. The use of biological molecules as catalysts enables new and more specific syntheses. It also meets many of the core principles of “green chemistry”. While there have been some considerable successes in biocatalysis, the full potential has yet to be realised. This results, partly, from some key challenges in understanding the fundamental biochemistry of enzymes. This review summarises four of these challenges: the need to understand protein folding, the need for a qualitative understanding of the hydrophobic effect, the need to understand and quantify the effects of organic solvents on biomolecules and the need for a deep understanding of enzymatic catalysis. If these challenges were addressed, then the number of successful biocatalysis projects is likely to increase. It would enable accurate prediction of protein structures, and the effects of changes in sequence or solution conditions on these structures. We would be better able to predict how substrates bind and are transformed into products, again leading to better enzyme engineering. Most significantly, it may enable the de novo design of enzymes to catalyse specific reactions.
Collapse
|
6
|
McClory J, Lin JT, Timson DJ, Zhang J, Huang M. Catalytic mechanism of mevalonate kinase revisited, a QM/MM study. Org Biomol Chem 2019; 17:2423-2431. [PMID: 30735219 DOI: 10.1039/c8ob03197e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Mevalonate Kinase (MVK) catalyses the ATP-Mg2+ mediated phosphate transfer of mevalonate to produce mevalonate 5-phosphate and is a key kinase in the mevalonate pathway in the biosynthesis of isopentenyl diphosphate, the precursor of isoprenoid-based biofuels. However, the crystal structure in complex with the native substrate mevalonate, ATP and Mg2+ has not been resolved, which has limited the understanding of its reaction mechanism and therefore its application in the production of isoprenoid-based biofuels. Here using molecular docking, molecular dynamics (MD) simulations and a hybrid QM/MM study, we revisited the location of Mg2+ resolved in the crystal structure of MVK and determined a catalytically competent MVK structure in complex with the native substrate mevalonate and ATP. We demonstrated that significant conformational change on a flexible loop connecting the α6 and α7 helix is induced by the substrate binding. Further, we found that Asp204 is coordinated to the Mg2+ ion. Arg241 plays a crucial role in organizing the triphosphoryl tail of ATP for in-line phosphate transfer and stabilizing the negative charge that accumulates at the β,γ-bridging oxygen of ATP upon bond cleavage. Remarkably, we revealed that the phosphorylation of mevalonate catalyzed by MVK occurs via a direct phosphorylation mechanism, instead of the conventionally postulated catalytic base mechanism. The catalytically competent complex structure of MVK as well as the mechanism of reaction will pave the way for the rational engineering of MVK to exploit its applications in the production of biofuels.
Collapse
Affiliation(s)
- James McClory
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Stranmillis Road, Belfast, BT9 5AG, Northern Ireland, UK.
| | | | | | | | | |
Collapse
|
7
|
Abstract
Carbohydrate kinases activate a wide variety of monosaccharides by adding a phosphate group, usually from ATP. This modification is fundamental to saccharide utilization, and it is likely a very ancient reaction. Modern organisms contain carbohydrate kinases from at least five main protein families. These range from the highly specialized inositol kinases, to the ribokinases and galactokinases, which belong to families that phosphorylate a wide range of substrates. The carbohydrate kinases utilize a common strategy to drive the reaction between the sugar hydroxyl and the donor phosphate. Each sugar is held in position by a network of hydrogen bonds to the non-reactive hydroxyls (and other functional groups). The reactive hydroxyl is deprotonated, usually by an aspartic acid side chain acting as a catalytic base. The deprotonated hydroxyl then attacks the donor phosphate. The resulting pentacoordinate transition state is stabilized by an adjacent divalent cation, and sometimes by a positively charged protein side chain or the presence of an anion hole. Many carbohydrate kinases are allosterically regulated using a wide variety of strategies, due to their roles at critical control points in carbohydrate metabolism. The evolution of a similar mechanism in several folds highlights the elegance and simplicity of the catalytic scheme.
Collapse
|
8
|
Miller BR, Kung Y. Structural insight into substrate and product binding in an archaeal mevalonate kinase. PLoS One 2018; 13:e0208419. [PMID: 30521590 PMCID: PMC6283576 DOI: 10.1371/journal.pone.0208419] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 11/18/2018] [Indexed: 12/03/2022] Open
Abstract
Mevalonate kinase (MK) is a key enzyme of the mevalonate pathway, which produces the biosynthetic precursors for steroids, including cholesterol, and isoprenoids, the largest class of natural products. Currently available crystal structures of MK from different organisms depict the enzyme in its unbound, substrate-bound, and inhibitor-bound forms; however, until now no structure has yet been determined of MK bound to its product, 5-phosphomevalonate. Here, we present crystal structures of mevalonate-bound and 5-phosphomevalonate-bound MK from Methanosarcina mazei (MmMK), a methanogenic archaeon. In contrast to the prior structure of a eukaryotic MK bound with mevalonate, we find a striking lack of direct interactions between this archaeal MK and its substrate. Further, these two MmMK structures join the prior structure of the apoenzyme to complete the first suite of structural snapshots that depict unbound, substrate-bound, and product-bound forms of the same MK. With this collection of structures, we now provide additional insight into the catalytic mechanism of this biologically essential enzyme.
Collapse
Affiliation(s)
- Bradley R. Miller
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, PA, United States of America
| | - Yan Kung
- Department of Chemistry, Bryn Mawr College, Bryn Mawr, PA, United States of America
- * E-mail:
| |
Collapse
|
9
|
McAuley M, Huang M, Timson DJ. Modulation of the mobility of a key region in human galactokinase: Impacts on catalysis and stability. Bioorg Chem 2018; 81:649-657. [DOI: 10.1016/j.bioorg.2018.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 08/29/2018] [Accepted: 09/06/2018] [Indexed: 12/28/2022]
|
10
|
Zinsser VL, Cox C, McAuley M, Hoey EM, Trudgett A, Timson DJ. A galactokinase-like protein from the liver fluke Fasciola hepatica. Exp Parasitol 2018; 192:65-72. [PMID: 30040960 DOI: 10.1016/j.exppara.2018.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 05/30/2018] [Accepted: 07/20/2018] [Indexed: 11/25/2022]
Abstract
Galactokinase catalyses the ATP-dependent phosphorylation of galactose. A galactokinase-like sequence was identified in a Fasciola hepatica EST library. Recombinant expression of the corresponding protein in Escherichia coli resulted in a protein of approximately 50 kDa. The protein is monomeric, like galactokinases from higher animals, yeasts and some bacteria. The protein has no detectable enzymatic activity with galactose or N-acetylgalactosamine as a substrate. However, it does bind to ATP. Molecular modelling predicted that the protein adopts a similar fold to galactokinase and other GHMP kinases. However, a key loop in the active site was identified which may influence the lack of activity. Sequence analysis strongly suggested that this protein (and other proteins annotated as "galactokinase" in the trematodes Schistosoma mansoni and Clonorchis sinensis) are closer to N-acetylgalactosamine kinases. No other galactokinase-like sequences appear to be present in the genomes of these three species. This raises the intriguing possibility that these (and possibly other) trematodes are unable to catabolise galactose through the Leloir pathway due to the lack of a functional galactokinase.
Collapse
Affiliation(s)
- Veronika L Zinsser
- School of Biological Sciences, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast, BT9 7BL, UK
| | - Ciara Cox
- School of Biological Sciences, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast, BT9 7BL, UK
| | - Margaret McAuley
- School of Biological Sciences, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast, BT9 7BL, UK
| | - Elizabeth M Hoey
- School of Biological Sciences, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast, BT9 7BL, UK
| | - Alan Trudgett
- School of Biological Sciences, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast, BT9 7BL, UK
| | - David J Timson
- School of Biological Sciences, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast, BT9 7BL, UK; School of Pharmacy and Biomolecular Sciences, University of Brighton, Huxley Building, Lewes Road, Brighton, BN2 4GJ, UK.
| |
Collapse
|
11
|
McAuley M, Mesa-Torres N, McFall A, Morris S, Huang M, Pey AL, Timson DJ. Improving the Activity and Stability of Human Galactokinase for Therapeutic and Biotechnological Applications. Chembiochem 2018; 19:1088-1095. [DOI: 10.1002/cbic.201800025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Margaret McAuley
- School of Biological Sciences; Queen's University; Belfast; Medical Biology Centre; Lisburn Road Belfast BT9 7BL UK
| | - Noel Mesa-Torres
- Department of Physical Chemistry; University of Granada; Av. Fuentenueva s/n 18071 Granada Spain
| | - Aisling McFall
- School of Biological Sciences; Queen's University; Belfast; Medical Biology Centre; Lisburn Road Belfast BT9 7BL UK
| | - Sarah Morris
- School of Biological Sciences; Queen's University; Belfast; Medical Biology Centre; Lisburn Road Belfast BT9 7BL UK
| | - Meilan Huang
- School of Chemistry and Chemical Engineering; Queen's University; Belfast; David Keir Building Stranmillis Road Belfast BT9 5AG UK
| | - Angel L. Pey
- Department of Physical Chemistry; University of Granada; Av. Fuentenueva s/n 18071 Granada Spain
| | - David J. Timson
- School of Biological Sciences; Queen's University; Belfast; Medical Biology Centre; Lisburn Road Belfast BT9 7BL UK
- School of Pharmacy and Biomolecular Sciences; University of Brighton; Huxley Building Lewes Road Brighton BN2 4GJ UK
| |
Collapse
|
12
|
McClory J, Lin JT, Timson DJ, Zhang J, Huang M. Water-mediated network in the resistance mechanism of fosfomycin. Phys Chem Chem Phys 2018; 20:21660-21667. [DOI: 10.1039/c8cp02860e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Resistance mechanism of fosfomycin mediated by a water network.
Collapse
Affiliation(s)
- James McClory
- School of Chemistry and Chemical Engineering
- Queen's University Belfast
- David Keir Building
- Belfast
- UK
| | - Jun-Tang Lin
- Stem Cells and Biotheraphy Engineering Research Centre of Henan
- College of Biomedical Engineering
- Xinxiang Medical University
- Xinxiang 453003
- China
| | - David J. Timson
- School of Pharmacy and Biomolecular Sciences
- The University of Brighton, Huxley Building
- Brighton
- UK
| | - Jian Zhang
- Shanghai Jiaotong University
- Shanghai 200025
- China
| | - Meilan Huang
- School of Chemistry and Chemical Engineering
- Queen's University Belfast
- David Keir Building
- Belfast
- UK
| |
Collapse
|
13
|
McAuley M, Huang M, Timson DJ. Insight into the mechanism of galactokinase: Role of a critical glutamate residue and helix/coil transitions. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:321-328. [PMID: 27789348 DOI: 10.1016/j.bbapap.2016.10.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 10/19/2016] [Accepted: 10/21/2016] [Indexed: 11/24/2022]
Abstract
Galactokinase, the enzyme which catalyses the first committed step in the Leloir pathway, has attracted interest due to its potential as a biocatalyst and as a possible drug target in the treatment of type I galactosemia. The mechanism of the enzyme is not fully elucidated. Molecular dynamics (MD) simulations of galactokinase with the active site residues Arg-37 and Asp-186 altered predicted that two regions (residues 174-179 and 231-240) had different dynamics as a consequence. Interestingly, the same two regions were also affected by alterations in Arg-105, Glu-174 and Arg-228. These three residues were identified as important in catalysis in previous computational studies on human galactokinase. Alteration of Arg-105 to methionine resulted in a modest reduction in activity with little change in stability. When Arg-228 was changed to methionine, the enzyme's interaction with both ATP and galactose was affected. This variant was significantly less stable than the wild-type protein. Changing Glu-174 to glutamine (but not to aspartate) resulted in no detectable activity and a less stable enzyme. Overall, these combined in silico and in vitro studies demonstrate the importance of a negative charge at position 174 and highlight the critical role of the dynamics in to key regions of the protein. We postulate that these regions may be critical for mediating the enzyme's structure and function.
Collapse
Affiliation(s)
- Margaret McAuley
- School of Biological Sciences, Queen's University Belfast, Medical Biology Building, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Meilan Huang
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Stranmillis Road, Belfast BT9 5AG, UK
| | - David J Timson
- School of Biological Sciences, Queen's University Belfast, Medical Biology Building, 97 Lisburn Road, Belfast BT9 7BL, UK; School of Pharmacy and Biomolecular Sciences, University of Brighton, Huxley Building, Lewes Road, Brighton BN2 4GJ, UK.
| |
Collapse
|
14
|
Huang M, Wei K, Li X, McClory J, Hu G, Zou JW, Timson D. Phosphorylation Mechanism of Phosphomevalonate Kinase: Implications for Rational Engineering of Isoprenoid Biosynthetic Pathway Enzymes. J Phys Chem B 2016; 120:10714-10722. [DOI: 10.1021/acs.jpcb.6b08480] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Meilan Huang
- School
of Chemistry and Chemical Engineering, Queen’s University Belfast, David
Keir Building, Stranmillis Road, Belfast, BT9 5AG, Northern Ireland, United Kingdom
| | - Kexin Wei
- School
of Chemistry and Chemical Engineering, Queen’s University Belfast, David
Keir Building, Stranmillis Road, Belfast, BT9 5AG, Northern Ireland, United Kingdom
| | - Xiao Li
- School
of Chemistry and Chemical Engineering, Queen’s University Belfast, David
Keir Building, Stranmillis Road, Belfast, BT9 5AG, Northern Ireland, United Kingdom
| | - James McClory
- School
of Chemistry and Chemical Engineering, Queen’s University Belfast, David
Keir Building, Stranmillis Road, Belfast, BT9 5AG, Northern Ireland, United Kingdom
| | - Guixiang Hu
- School
of Biotechnology and Chemical Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China
| | - Jian-Wei Zou
- School
of Biotechnology and Chemical Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China
| | - David Timson
- School
of Pharmacy and Biomolecular Sciences, The University of Brighton, Huxley Building, Lewes Road, Brighton, BN2 4GJ, United Kingdom
| |
Collapse
|
15
|
Functional analysis of anomeric sugar kinases. Carbohydr Res 2016; 432:23-30. [DOI: 10.1016/j.carres.2016.06.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 06/06/2016] [Accepted: 06/07/2016] [Indexed: 11/19/2022]
|
16
|
Vivoli M, Isupov MN, Nicholas R, Hill A, Scott AE, Kosma P, Prior JL, Harmer NJ. Unraveling the B. pseudomallei Heptokinase WcbL: From Structure to Drug Discovery. ACTA ACUST UNITED AC 2016; 22:1622-32. [PMID: 26687481 PMCID: PMC4691232 DOI: 10.1016/j.chembiol.2015.10.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 10/20/2015] [Accepted: 10/31/2015] [Indexed: 11/25/2022]
Abstract
Gram-negative bacteria utilize heptoses as part of their repertoire of extracellular polysaccharide virulence determinants. Disruption of heptose biosynthesis offers an attractive target for novel antimicrobials. A critical step in the synthesis of heptoses is their 1-O phosphorylation, mediated by kinases such as HldE or WcbL. Here, we present the structure of WcbL from Burkholderia pseudomallei. We report that WcbL operates through a sequential ordered Bi-Bi mechanism, loading the heptose first and then ATP. We show that dimeric WcbL binds ATP anti-cooperatively in the absence of heptose, and cooperatively in its presence. Modeling of WcbL suggests that heptose binding causes an elegant switch in the hydrogen-bonding network, facilitating the binding of a second ATP molecule. Finally, we screened a library of drug-like fragments, identifying hits that potently inhibit WcbL. Our results provide a novel mechanism for control of substrate binding and emphasize WcbL as an attractive anti-microbial target for Gram-negative bacteria.
Collapse
Affiliation(s)
- Mirella Vivoli
- Department of Biosciences, University of Exeter, Henry Wellcome Building, Stocker Road, Exeter EX4 4QD, UK
| | - Michail N Isupov
- Department of Biosciences, University of Exeter, Henry Wellcome Building, Stocker Road, Exeter EX4 4QD, UK
| | - Rebecca Nicholas
- Department of Biosciences, University of Exeter, Henry Wellcome Building, Stocker Road, Exeter EX4 4QD, UK
| | - Andrew Hill
- Department of Biosciences, University of Exeter, Henry Wellcome Building, Stocker Road, Exeter EX4 4QD, UK
| | - Andrew E Scott
- Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire SP4 0JQ, UK
| | - Paul Kosma
- University of Natural Resources and Life Sciences-Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Joann L Prior
- Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire SP4 0JQ, UK
| | - Nicholas J Harmer
- Department of Biosciences, University of Exeter, Henry Wellcome Building, Stocker Road, Exeter EX4 4QD, UK.
| |
Collapse
|
17
|
Jiang Y, Tan H, Zheng J, Li X, Chen G, Jia Z. Phosphoryl transfer reaction catalyzed by membrane diacylglycerol kinase: a theoretical mechanism study. Phys Chem Chem Phys 2016; 17:25228-34. [PMID: 26352441 DOI: 10.1039/c5cp03342j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Diacylglycerol kinase is an integral membrane protein which catalyzes phosphoryl transfer from ATP to diacylglycerol. As the smallest kinase known, it shares no sequence homology with conventional kinases and possesses a distinct trimer structure. Thus far, its catalytic mechanism remains elusive. Using molecular dynamics and quantum mechanics calculations, we investigated the co-factor and the substrate binding and phosphoryl transfer mechanism. Based on the analysis of density functional theory calculations, we reveal that the phosphorylation reaction of diacylglycerol kinase features the same phosphoryl transfer mechanism as other kinases, despite its unique structural properties. Our results further show that the active site is relatively open and able to accommodate ligands in multiple orientations, suggesting that the optimization of binding orientations and conformational changes would occur prior to actual phosphoryl transfer.
Collapse
Affiliation(s)
- Yafei Jiang
- College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | | | | | | | | | | |
Collapse
|
18
|
Abstract
Galactokinase catalyses the first committed step of the Leloir pathway, i.e. the ATP-dependent phosphorylation of α-D-galactose at C1-OH. Reduced galactokinase activity results in the inherited metabolic disease type II galactosaemia. However, inhibition of galactokinase is considered a viable approach to treating more severe forms of galactosaemia (types I and III). Considerable progress has been made in the identification of high affinity, selective inhibitors. Although the structure of galactokinase from a variety of species is known, its catalytic mechanism remains uncertain. Although the bulk of evidence suggests that the reaction proceeds via an active site base mechanism, some experimental and theoretical studies contradict this. The enzyme has potential as a biocatalyst in the production of sugar 1-phosphates. This potential is limited by its high specificity. A variety of approaches have been taken to identify galactokinase variants which are more promiscuous. These have broadened galactokinase's specificity to include a wide range of D- and L-sugars. Initial studies suggest that some of these alterations result in increased flexibility at the active site. It is suggested that modulation of protein flexibility is at least as important as structural modifications in determining the success or failure of enzyme engineering.
Collapse
|
19
|
Abstract
Classic galactosemia is an inherited metabolic disease for which, at present, no therapy is available apart from galactose-restricted diet. However, the efficacy of the diet is questionable, since it is not able to prevent the insurgence of chronic complications later in life. In addition, it is possible that dietary restriction itself could induce negative side effects. Therefore, there is a need for an alternative therapeutic approach that can avert the manifestation of chronic complications in the patients. In this review, the authors describe the development of a novel class of pharmaceutical agents that target the production of a toxic metabolite, galactose-1-phosphate, considered as the main culprit for the cause of the complications, in the patients.
Collapse
|