1
|
Eurtivong C, Leung E, Sharma N, Leung IKH, Reynisson J. Phosphatidylcholine-Specific Phospholipase C as a Promising Drug Target. Molecules 2023; 28:5637. [PMID: 37570610 PMCID: PMC10420013 DOI: 10.3390/molecules28155637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/12/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
Phosphatidylcholine-specific phospholipase C (PC-PLC) is an enzyme that catalyzes the formation of the important secondary messengers phosphocholine and diacylglycerol (DAG) from phosphatidylcholine. Although PC-PLC has been linked to the progression of many pathological conditions, including cancer, atherosclerosis, inflammation and neuronal cell death, studies of PC-PLC on the protein level have been somewhat neglected with relatively scarce data. To date, the human gene expressing PC-PLC has not yet been found, and the only protein structure of PC-PLC that has been solved was from Bacillus cereus (PC-PLCBc). Nonetheless, there is evidence for PC-PLC activity as a human functional equivalent of its prokaryotic counterpart. Additionally, inhibitors of PC-PLCBc have been developed as potential therapeutic agents. The most notable classes include 2-aminohydroxamic acids, xanthates, N,N'-hydroxyureas, phospholipid analogues, 1,4-oxazepines, pyrido[3,4-b]indoles, morpholinobenzoic acids and univalent ions. However, many medicinal chemistry studies lack evidence for their cellular and in vivo effects, which hampers the progression of the inhibitors towards the clinic. This review outlines the pathological implications of PC-PLC and highlights current progress and future challenges in the development of PC-PLC inhibitors from the literature.
Collapse
Affiliation(s)
- Chatchakorn Eurtivong
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Mahidol University, 447 Si Ayutthaya Road, Ratchathewi, Bangkok 10400, Thailand
| | - Euphemia Leung
- Auckland Cancer Society Research Centre, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand;
| | - Nabangshu Sharma
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand;
- Scion (New Zealand Forest Research Institute), Te Papa Tipu Innovation Park, 49 Sala Street, Rotorua 3010, New Zealand
| | - Ivanhoe K. H. Leung
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Rd, Parkville, VIC 3052, Australia;
| | - Jóhannes Reynisson
- School of Pharmacy and Bioengineering, Keele University, Newcastle-under-Lyme ST5 5BG, UK;
| |
Collapse
|
2
|
Huang EYW, Kwai BXC, Bhusal RP, Bashiri G, Leung IKH. Mycobacterium tuberculosis Rv1916 is an Acetyl-CoA-Binding Protein. Chembiochem 2023:e202300162. [PMID: 37211532 DOI: 10.1002/cbic.202300162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/15/2023] [Accepted: 05/20/2023] [Indexed: 05/23/2023]
Abstract
Isocitrate lyase (ICL) isoform 2 is an essential enzyme for some clinical Mycobacterium tuberculosis (Mtb) strains during infection. In the laboratory Mtb strain H37Rv, the icl2 gene encodes two distinct gene products - Rv1915 and Rv1916 - due to a frameshift mutation. This study aims to characterise these two gene products to understand their structure and function. While we were unable to produce Rv1915 recombinantly, soluble Rv1916 was obtained with sufficient yield for characterisation. Kinetic studies using UV-visible spectrophotometry and 1H-NMR spectroscopy showed that recombinant Rv1916 does not possess isocitrate lyase activity, while waterLOGSY binding experiments demonstrated that it could bind acetyl-CoA. Finally, X-ray crystallography revealed structural similarities between Rv1916 and the C-terminal domain of ICL2. Considering the probable differences between full-length ICL2 and the gene products Rv1915 and Rv1916, care must be taken when using Mtb H37Rv as a model organism to study central carbon metabolism.
Collapse
Affiliation(s)
| | - Brooke X C Kwai
- Monash University, Monash Institute of Pharmaceutical Sciences, AUSTRALIA
| | - Ram Prasad Bhusal
- Monash University, Monash Biomedicine Discovery Institute, AUSTRALIA
| | - Ghader Bashiri
- The University of Auckland, School of Biological Sciences, NEW ZEALAND
| | - Ivanhoe K H Leung
- The University of Melbourne, School of Chemistry, The University of Melbourne, School of Chemistry, Parkville, 3052, Melbourne, AUSTRALIA
| |
Collapse
|
3
|
Chan YY, Mbenza NM, Chan MC, Leung IKH. Assays to Study Hypoxia-Inducible Factor Prolyl Hydroxylase Domain 2 (PHD2), a Key Human Oxygen Sensing Protein. Methods Mol Biol 2023; 2648:187-206. [PMID: 37039992 DOI: 10.1007/978-1-0716-3080-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Molecular oxygen is essential for all multicellular life forms. In humans, the hypoxia-inducible factor (HIF) prolyl hydroxylase domain-containing enzymes (PHDs) serve as important oxygen sensors by regulating the activity of HIF, the master regulator that mediates cellular oxygen homeostasis, in an oxygen-dependent manner. In normoxia, PHDs catalyze the prolyl hydroxylation of HIF, which leads to its degradation and prevents cellular hypoxic response to be triggered. PHDs are current inhibition targets for the potential treatments of a number of diseases. In this chapter, we discuss in vitro and cell-based methods to study the modulation of PHD2, the most important human PHD isoform in normoxia and mild hypoxia. These include the production and purification of recombinant PHD2, the use of mass spectrometry to follow PHD2-catalyzed reactions and the studies of HIF stabilization in cells by immunoblotting.
Collapse
Affiliation(s)
- Yan Ying Chan
- Department of Molecular Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Naasson M Mbenza
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Mun Chiang Chan
- Department of Molecular Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
- GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Ivanhoe K H Leung
- School of Chemistry and the Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia.
| |
Collapse
|
4
|
Zhang S, De Leon Rodriguez LM, Li FF, Huang R, Leung IKH, Harris PWR, Brimble MA. A novel tyrosine hyperoxidation enables selective peptide cleavage. Chem Sci 2022; 13:2753-2763. [PMID: 35356671 PMCID: PMC8890263 DOI: 10.1039/d1sc06216f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 02/10/2022] [Indexed: 11/21/2022] Open
Abstract
A novel tyrosine hyperoxidation enabling selective peptide cleavage is reported. The scission of the N-terminal amide bond of tyrosine was achieved with Dess–Martin periodinane under mild conditions, generating a C-terminal peptide fragment bearing the unprecedented hyperoxidized tyrosine motif, 4,5,6,7-tetraoxo-1H-indole-2-carboxamide, along with an intact N-terminal peptide fragment. This reaction proceeds with high site-selectivity for tyrosine and exhibits broad substrate scope for various peptides, including those containing post-translational modifications. More importantly, this oxidative cleavage was successfully applied to enable sequencing of three naturally occurring cyclic peptides, including one depsipeptide and one lipopeptide. The linearized peptides generated from the cleavage reaction significantly simplify cyclic peptide sequencing by MS/MS, thus providing a robust tool to facilitate rapid sequence determination of diverse cyclic peptides containing tyrosine. Furthermore, the highly electrophilic nature of the hyperoxidized tyrosine unit disclosed in this work renders it an important electrophilic target for the selective bioconjugation or synthetic manipulation of peptides containing this unit. A Tyr-selective peptide cleavage was reported using Dess–Martin periodinane. The cleavage generates an unprecedented hyperoxidized tyrosine motif in the C-terminal fragment and showed excellent site-specificity and broad scope for various peptides.![]()
Collapse
Affiliation(s)
- Shengping Zhang
- School of Chemical Sciences, The University of Auckland 23 Symonds St Auckland 1010 New Zealand .,School of Biological Sciences, The University of Auckland 3A Symonds St Auckland 1010 New Zealand
| | | | - Freda F Li
- School of Chemical Sciences, The University of Auckland 23 Symonds St Auckland 1010 New Zealand
| | - Renjie Huang
- School of Chemical Sciences, The University of Auckland 23 Symonds St Auckland 1010 New Zealand
| | - Ivanhoe K H Leung
- School of Chemical Sciences, The University of Auckland 23 Symonds St Auckland 1010 New Zealand .,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 1142 New Zealand
| | - Paul W R Harris
- School of Chemical Sciences, The University of Auckland 23 Symonds St Auckland 1010 New Zealand .,School of Biological Sciences, The University of Auckland 3A Symonds St Auckland 1010 New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 1142 New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences, The University of Auckland 23 Symonds St Auckland 1010 New Zealand .,School of Biological Sciences, The University of Auckland 3A Symonds St Auckland 1010 New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland 1142 New Zealand
| |
Collapse
|
5
|
Shishodia S, Demetriades M, Zhang D, Tam NY, Maheswaran P, Clunie-O’Connor C, Tumber A, Leung IKH, Ng YM, Leissing TM, El-Sagheer AH, Salah E, Brown T, Aik WS, McDonough MA, Schofield CJ. Structure-Based Design of Selective Fat Mass and Obesity Associated Protein (FTO) Inhibitors. J Med Chem 2021; 64:16609-16625. [PMID: 34762429 PMCID: PMC8631710 DOI: 10.1021/acs.jmedchem.1c01204] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Indexed: 01/09/2023]
Abstract
FTO catalyzes the Fe(II) and 2-oxoglutarate (2OG)-dependent modification of nucleic acids, including the demethylation of N6-methyladenosine (m6A) in mRNA. FTO is a proposed target for anti-cancer therapy. Using information from crystal structures of FTO in complex with 2OG and substrate mimics, we designed and synthesized two series of FTO inhibitors, which were characterized by turnover and binding assays, and by X-ray crystallography with FTO and the related bacterial enzyme AlkB. A potent inhibitor employing binding interactions spanning the FTO 2OG and substrate binding sites was identified. Selectivity over other clinically targeted 2OG oxygenases was demonstrated, including with respect to the hypoxia-inducible factor prolyl and asparaginyl hydroxylases (PHD2 and FIH) and selected JmjC histone demethylases (KDMs). The results illustrate how structure-based design can enable the identification of potent and selective 2OG oxygenase inhibitors and will be useful for the development of FTO inhibitors for use in vivo.
Collapse
Affiliation(s)
- Shifali Shishodia
- The
Chemistry Research Laboratory, Department of Chemistry and the Ineos
Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Marina Demetriades
- The
Chemistry Research Laboratory, Department of Chemistry and the Ineos
Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Dong Zhang
- The
Chemistry Research Laboratory, Department of Chemistry and the Ineos
Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Nok Yin Tam
- Department
of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong
SAR 999077, China
| | - Pratheesh Maheswaran
- The
Chemistry Research Laboratory, Department of Chemistry and the Ineos
Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Caitlin Clunie-O’Connor
- The
Chemistry Research Laboratory, Department of Chemistry and the Ineos
Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Anthony Tumber
- The
Chemistry Research Laboratory, Department of Chemistry and the Ineos
Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Ivanhoe K. H. Leung
- The
Chemistry Research Laboratory, Department of Chemistry and the Ineos
Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Yi Min Ng
- Department
of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong
SAR 999077, China
| | - Thomas M. Leissing
- The
Chemistry Research Laboratory, Department of Chemistry and the Ineos
Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Afaf H. El-Sagheer
- The
Chemistry Research Laboratory, Department of Chemistry and the Ineos
Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
- Chemistry
Branch Department of Science and Mathematics, Suez University, Suez 43721, Egypt
| | - Eidarus Salah
- The
Chemistry Research Laboratory, Department of Chemistry and the Ineos
Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Tom Brown
- The
Chemistry Research Laboratory, Department of Chemistry and the Ineos
Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Wei Shen Aik
- Department
of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong
SAR 999077, China
| | - Michael A. McDonough
- The
Chemistry Research Laboratory, Department of Chemistry and the Ineos
Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Christopher J. Schofield
- The
Chemistry Research Laboratory, Department of Chemistry and the Ineos
Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| |
Collapse
|
6
|
Sharma N, Leung IKH. Characterisation and optimisation of a novel laccase from Sulfitobacter indolifex for the decolourisation of organic dyes. Int J Biol Macromol 2021; 190:574-584. [PMID: 34506861 DOI: 10.1016/j.ijbiomac.2021.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 08/19/2021] [Accepted: 09/01/2021] [Indexed: 11/25/2022]
Abstract
Laccases are multi‑copper oxidases that possess the potential for industrial wastewater treatments. In this study, a putative laccase from Sulfitobacter indolifex was recombinantly produced and characterised. The enzyme was found to be stable and active at low to ambient temperature and across a range of pH conditions. The ability of the putative bacterial laccase to catalyse the decolourisation of seven common industrial dyes was also examined. Our results showed that the putative laccase could efficiently decolourise Indigo Carmine, Coomassie Brilliant Blue R-250, Congo Red, Malachite Green and Alizarin in the presence of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) as a redox mediator. Furthermore, the use of enzyme immobilisation technology to improve the operational stability and reusability of the putative laccase was also investigated. We found that immobilising the enzyme through the cross-linked enzyme aggregate method significantly improved its tolerance towards extreme pH as well as the presence of organic solvents. This work expands the arsenal of bacterial laccases available for the bioremediation of dye-containing wastewater.
Collapse
Affiliation(s)
- Nabangshu Sharma
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - Ivanhoe K H Leung
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand; Centre for Green Chemical Science, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand; School of Chemistry, The University of Melbourne, Parkville, VIC 3010, Australia; Bio21 Molecular Science & Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia.
| |
Collapse
|
7
|
Mbenza NM, Nasarudin N, Vadakkedath PG, Patel K, Ismail AZ, Hanif M, Wright LJ, Sarojini V, Hartinger CG, Leung IKH. Carbon Monoxide is an Inhibitor of HIF Prolyl Hydroxylase Domain 2. Chembiochem 2021; 22:2521-2525. [PMID: 34137488 DOI: 10.1002/cbic.202100181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/16/2021] [Indexed: 11/11/2022]
Abstract
Hypoxia-inducible factor prolyl hydroxylase domain 2 (PHD2) is an important oxygen sensor in animals. By using the CO-releasing molecule-2 (CORM-2) as an in situ CO donor, we demonstrate that CO is an inhibitor of PHD2. This report provides further evidence about the emerging role of CO in oxygen sensing and homeostasis.
Collapse
Affiliation(s)
- Naasson M Mbenza
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand.,School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
| | - Nawal Nasarudin
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - Praveen G Vadakkedath
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand.,The MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
| | - Kamal Patel
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - A Z Ismail
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand.,Department of Chemistry, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Muhammad Hanif
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag, 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - L James Wright
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - Vijayalekshmi Sarojini
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand.,The MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
| | - Christian G Hartinger
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag, 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - Ivanhoe K H Leung
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag, 92019, Victoria Street West, Auckland, 1142, New Zealand.,School of Chemistry, The University of Melbourne, Parkville, VIC 3010, Australia.,Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| |
Collapse
|
8
|
Leung E, Patel J, Hollywood JA, Zafar A, Tomek P, Barker D, Pilkington LI, van Rensburg M, Langley RJ, Helsby NA, Squire CJ, Baguley BC, Denny WA, Reynisson J, Leung IKH. Validating TDP1 as an Inhibition Target for the Development of Chemosensitizers for Camptothecin-Based Chemotherapy Drugs. Oncol Ther 2021; 9:541-556. [PMID: 34159519 PMCID: PMC8593127 DOI: 10.1007/s40487-021-00158-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/03/2021] [Indexed: 12/01/2022] Open
Abstract
Cancer chemotherapy sensitizers hold the key to maximizing the potential of standard anticancer treatments. We have a long-standing interest in developing and validating inhibitors of the DNA repair enzyme tyrosyl-DNA phosphodiesterase 1 (TDP1) as chemosensitizers for topoisomerase I poisons such as topotecan. Herein, by using thieno[2,3-b]pyridines, a class of TDP1 inhibitors, we showed that the inhibition of TDP1 can restore sensitivity to topotecan, results that are supported by TDP1 knockout cell experiments using CRISPR/Cas9. However, we also found that the restored sensitivity towards topoisomerase I inhibitors is likely regulated by multiple complementary DNA repair pathways. Our results showed that one of these pathways is likely modulated by PARP1, although it is also possible that other redundant and partially overlapping pathways may be involved in the DNA repair process. Our work thus raises the prospect of targeting multiple DNA repair pathways to increase the sensitivity to topoisomerase I inhibitors.
Collapse
Affiliation(s)
- Euphemia Leung
- Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand. .,Department of Molecular Medicine and Pathology, School of Medical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand. .,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand.
| | - Jinal Patel
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - Jennifer A Hollywood
- Department of Molecular Medicine and Pathology, School of Medical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - Ayesha Zafar
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - Petr Tomek
- Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - David Barker
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand.,The MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
| | - Lisa I Pilkington
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - Michelle van Rensburg
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - Ries J Langley
- Department of Molecular Medicine and Pathology, School of Medical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - Nuala A Helsby
- Department of Molecular Medicine and Pathology, School of Medical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - Christopher J Squire
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand.,School of Biological Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - Bruce C Baguley
- Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - William A Denny
- Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - Jóhannes Reynisson
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand. .,School of Pharmacy and Bioengineering, Keele University, Staffordshire, ST5 5BG, UK.
| | - Ivanhoe K H Leung
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand. .,School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand. .,School of Chemistry, The University of Melbourne, Parkville, VIC, 3010, Australia. .,Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia.
| |
Collapse
|
9
|
Mak OW, Sharma N, Reynisson J, Leung IKH. Discovery of novel Hsp90 C-terminal domain inhibitors that disrupt co-chaperone binding. Bioorg Med Chem Lett 2021; 38:127857. [PMID: 33609661 DOI: 10.1016/j.bmcl.2021.127857] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/29/2021] [Accepted: 02/05/2021] [Indexed: 12/20/2022]
Abstract
Heat shock protein 90 (Hsp90) is an essential molecular chaperone that performs vital stress-related and housekeeping functions in cells and is a current therapeutic target for diseases such as cancers. Particularly, the development of Hsp90 C-terminal domain (CTD) inhibitors is highly desirable as inhibitors that target the N-terminal nucleotide-binding domain may cause unwanted biological effects. Herein, we report on the discovery of two drug-like novel Hsp90 CTD inhibitors by using virtual screening and intrinsic protein fluorescence quenching binding assays, paving the way for future development of new therapies that employ molecular chaperone inhibitors.
Collapse
Affiliation(s)
- Oi Wei Mak
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - Nabangshu Sharma
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - Jóhannes Reynisson
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand; School of Pharmacy and Bioengineering, Hornbeam Building, Keele University, Keele, Staffordshire ST5 5BG, United Kingdom.
| | - Ivanhoe K H Leung
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand.
| |
Collapse
|
10
|
Sharma N, Langley RJ, Eurtivong C, Leung E, Dixon RJ, Paulin EK, Rees SWP, Pilkington LI, Barker D, Reynisson J, Leung IKH. An optimised MALDI-TOF assay for phosphatidylcholine-specific phospholipase C. Anal Methods 2021; 13:491-496. [PMID: 33432952 DOI: 10.1039/d0ay02208j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The Bacillus cereus phosphatidylcholine-specific phospholipase C (PC-PLCBc) is an enzyme that catalyses the hydrolysis of phosphatidylcholines into phosphocholine and 1,2-diacylglycerols. PC-PLCBc has found applications in both the food industry and in medicinal chemistry. Herein, we report our work in the development and optimisation of a matrix assisted laser desorption ionisation time-of-flight (MALDI-TOF) mass spectrometry-based assay to monitor PC-PLCBc activity. The use of one-phase and two-phase reaction systems to assess the inhibition of PC-PLCBc with different structural classes of inhibitors was compared. We also highlighted the advantage of our assay over the commonly used commercially available Amplex Red assay. This method will also be applicable to work on the activity and inhibition of other phospholipases.
Collapse
Affiliation(s)
- Nabangshu Sharma
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand.
| | - Ries J Langley
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand and Department of Molecular Medicine and Pathology, School of Medical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - Chatchakorn Eurtivong
- Program in Chemical Sciences, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok 10210, Thailand and Center of Excellence on Environmental Health and Toxicology (EHT), Commission on Higher Education (CHE), Ministry of Education, Bangkok 10400, Thailand
| | - Euphemia Leung
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand and Department of Molecular Medicine and Pathology, School of Medical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand and Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - Ryan Joseph Dixon
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand.
| | - Emily K Paulin
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand.
| | - Shaun W P Rees
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand.
| | - Lisa I Pilkington
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand.
| | - David Barker
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand. and Centre for Green Chemical Science, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand and The MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand
| | - Jóhannes Reynisson
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand. and School of Pharmacy and Bioengineering, Keele University, Staffordshire ST5 5BG, UK
| | - Ivanhoe K H Leung
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand. and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand and Centre for Green Chemical Science, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| |
Collapse
|
11
|
Kwai BXC, Collins AJ, Middleditch MJ, Sperry J, Bashiri G, Leung IKH. Itaconate is a covalent inhibitor of the Mycobacterium tuberculosis isocitrate lyase. RSC Med Chem 2021; 12:57-61. [PMID: 34046597 PMCID: PMC8130629 DOI: 10.1039/d0md00301h] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 10/07/2020] [Indexed: 12/20/2022] Open
Abstract
Itaconate is a mammalian antimicrobial metabolite that inhibits the isocitrate lyases (ICLs) of Mycobacterium tuberculosis. Herein, we report that ICLs form a covalent adduct with itaconate through their catalytic cysteine residue. These results reveal atomic details of itaconate inhibition and provide insights into the catalytic mechanism of ICLs.
Collapse
Affiliation(s)
- Brooke X C Kwai
- School of Chemical Sciences, The University of Auckland Private Bag 92019, Victoria Street West Auckland 1142 New Zealand
| | - Annabelle J Collins
- School of Chemical Sciences, The University of Auckland Private Bag 92019, Victoria Street West Auckland 1142 New Zealand
| | - Martin J Middleditch
- School of Biological Sciences, The University of Auckland Private Bag 92019, Victoria Street West Auckland 1142 New Zealand
- Auckland Science Analytical Services, The University of Auckland Private Bag 92019, Victoria Street West Auckland 1142 New Zealand
| | - Jonathan Sperry
- School of Chemical Sciences, The University of Auckland Private Bag 92019, Victoria Street West Auckland 1142 New Zealand
| | - Ghader Bashiri
- School of Biological Sciences, The University of Auckland Private Bag 92019, Victoria Street West Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland Private Bag 92019, Victoria Street West Auckland 1142 New Zealand
| | - Ivanhoe K H Leung
- School of Chemical Sciences, The University of Auckland Private Bag 92019, Victoria Street West Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland Private Bag 92019, Victoria Street West Auckland 1142 New Zealand
| |
Collapse
|
12
|
Affiliation(s)
| | - Ivanhoe K. H. Leung
- School of Chemical Sciences, The University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
- Centre for Green Chemical Science, The University of Auckland, Auckland, New Zealand
| |
Collapse
|
13
|
Mozhaitsev ES, Zakharenko AL, Suslov EV, Korchagina DV, Zakharova OD, Vasil'eva IA, Chepanova AA, Black E, Patel J, Chand R, Reynisson J, Leung IKH, Volcho KP, Salakhutdinov NF, Lavrik OI. Novel Inhibitors of DNA Repair Enzyme TDP1 Combining Monoterpenoid and Adamantane Fragments. Anticancer Agents Med Chem 2020; 19:463-472. [PMID: 30523770 DOI: 10.2174/1871520619666181207094243] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 11/06/2018] [Accepted: 11/20/2018] [Indexed: 01/30/2023]
Abstract
BACKGROUND AND OBJECTIVE The DNA repair enzyme tyrosyl-DNA-phosphodiesterase 1 (TDP1) is a current inhibition target to improve the efficacy of cancer chemotherapy. Previous studies showed that compounds combining adamantane and monoterpenoid fragments are active against TDP1 enzyme. This investigation is focused on the synthesis of monoterpenoid derived esters of 1-adamantane carboxylic acid as TDP1 inhibitors. METHODS New esters were synthesized by the interaction between 1-adamantane carboxylic acid chloride and monoterpenoid alcohols. The esters were tested against TDP1 and its binding to the enzyme was modeling. RESULTS 13 Novel ester-based TDP1 inhibitors were synthesized with yields of 21-94%; of these, nine esters had not been previously described. A number of the esters were found to inhibit TDP1, with IC50 values ranging from 0.86-4.08 µM. Molecular modelling against the TDP1 crystal structure showed a good fit of the active esters in the catalytic pocket, explaining their potency. A non-toxic dose of ester, containing a 3,7- dimethyloctanol fragment, was found to enhance the cytotoxic effect of topotecan, a clinically used anti-cancer drug, against the human lung adenocarcinoma cell line A549. CONCLUSION The esters synthesized were found to be active against TDP1 in the lower micromolar concentration range, with these findings being corroborated by molecular modeling. Simultaneous action of the ester synthesized from 3,7-dimethyloctanol-1 and topotecan revealed a synergistic effect.
Collapse
Affiliation(s)
- Evgenii S Mozhaitsev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of Russian Academy of Sciences, 9, Lavrentiev Ave., Novosibirsk, 630090, Russian Federation
| | - Alexandra L Zakharenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Ave., Novosibirsk, 630090, Russian Federation
| | - Evgeniy V Suslov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of Russian Academy of Sciences, 9, Lavrentiev Ave., Novosibirsk, 630090, Russian Federation
| | - Dina V Korchagina
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of Russian Academy of Sciences, 9, Lavrentiev Ave., Novosibirsk, 630090, Russian Federation
| | - Olga D Zakharova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Ave., Novosibirsk, 630090, Russian Federation
| | - Inna A Vasil'eva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Ave., Novosibirsk, 630090, Russian Federation
| | - Arina A Chepanova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Ave., Novosibirsk, 630090, Russian Federation
| | - Ellena Black
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - Jinal Patel
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - Raina Chand
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - Jóhannes Reynisson
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - Ivanhoe K H Leung
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - Konstantin P Volcho
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of Russian Academy of Sciences, 9, Lavrentiev Ave., Novosibirsk, 630090, Russian Federation.,Novosibirsk State University, 2, Pirogova Str., Novosibirsk, 630090, Russian Federation
| | - Nariman F Salakhutdinov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of Russian Academy of Sciences, 9, Lavrentiev Ave., Novosibirsk, 630090, Russian Federation.,Novosibirsk State University, 2, Pirogova Str., Novosibirsk, 630090, Russian Federation
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Ave., Novosibirsk, 630090, Russian Federation.,Novosibirsk State University, 2, Pirogova Str., Novosibirsk, 630090, Russian Federation
| |
Collapse
|
14
|
Correddu D, Sharma N, Kaur S, Varnava KG, Mbenza NM, Sarojini V, Leung IKH. An investigation into the effect of ribosomal protein S15 phosphorylation on its intermolecular interactions by using phosphomimetic mutant. Chem Commun (Camb) 2020; 56:7857-7860. [DOI: 10.1039/d0cc01618g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An investigation using recombinant ribosomal proteins and synthetic peptide models was conducted to uncover the effect of the introduction of a negative charge at the C-terminal tail of ribosomal protein S15.
Collapse
Affiliation(s)
- Danilo Correddu
- School of Chemical Sciences
- The University of Auckland
- Auckland 1142
- New Zealand
| | - Nabangshu Sharma
- School of Chemical Sciences
- The University of Auckland
- Auckland 1142
- New Zealand
| | - Simranjeet Kaur
- School of Chemical Sciences
- The University of Auckland
- Auckland 1142
- New Zealand
| | - Kyriakos G. Varnava
- School of Chemical Sciences
- The University of Auckland
- Auckland 1142
- New Zealand
| | - Naasson M. Mbenza
- School of Chemical Sciences
- The University of Auckland
- Auckland 1142
- New Zealand
| | - Vijayalekshmi Sarojini
- School of Chemical Sciences
- The University of Auckland
- Auckland 1142
- New Zealand
- The MacDiarmid Institute for Advanced Materials and Nanotechnology
| | - Ivanhoe K. H. Leung
- School of Chemical Sciences
- The University of Auckland
- Auckland 1142
- New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery
| |
Collapse
|
15
|
Khomenko TM, Zakharenko AL, Chepanova AA, Ilina ES, Zakharova OD, Kaledin VI, Nikolin VP, Popova NA, Korchagina DV, Reynisson J, Chand R, Ayine-Tora DM, Patel J, Leung IKH, Volcho KP, Salakhutdinov NF, Lavrik OI. Promising New Inhibitors of Tyrosyl-DNA Phosphodiesterase I (Tdp 1) Combining 4-Arylcoumarin and Monoterpenoid Moieties as Components of Complex Antitumor Therapy. Int J Mol Sci 2019; 21:ijms21010126. [PMID: 31878088 PMCID: PMC6982354 DOI: 10.3390/ijms21010126] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/19/2019] [Accepted: 12/20/2019] [Indexed: 12/26/2022] Open
Abstract
Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is an important DNA repair enzyme in humans, and a current and promising inhibition target for the development of new chemosensitizing agents due to its ability to remove DNA damage caused by topoisomerase 1 (Top1) poisons such as topotecan and irinotecan. Herein, we report our work on the synthesis and characterization of new Tdp1 inhibitors that combine the arylcoumarin (neoflavonoid) and monoterpenoid moieties. Our results showed that they are potent Tdp1 inhibitors with IC50 values in the submicromolar range. In vivo experiments with mice revealed that compound 3ba (IC50 0.62 µM) induced a significant increase in the antitumor effect of topotecan on the Krebs-2 ascites tumor model. Our results further strengthen the argument that Tdp1 is a druggable target with the potential to be developed into a clinically-potent adjunct therapy in conjunction with Top1 poisons.
Collapse
Affiliation(s)
- Tatyana M. Khomenko
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, 9 acad. Lavrentjev ave., 630090 Novosibirsk, Russia; (T.M.K.); (D.V.K.); (N.F.S.)
| | - Alexandra L. Zakharenko
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, 8, acad. Lavrentjev ave., 630090 Novosibirsk, Russia; (A.L.Z.); (A.A.C.); (E.S.I.); (O.D.Z.); (O.I.L.)
| | - Arina A. Chepanova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, 8, acad. Lavrentjev ave., 630090 Novosibirsk, Russia; (A.L.Z.); (A.A.C.); (E.S.I.); (O.D.Z.); (O.I.L.)
| | - Ekaterina S. Ilina
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, 8, acad. Lavrentjev ave., 630090 Novosibirsk, Russia; (A.L.Z.); (A.A.C.); (E.S.I.); (O.D.Z.); (O.I.L.)
| | - Olga D. Zakharova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, 8, acad. Lavrentjev ave., 630090 Novosibirsk, Russia; (A.L.Z.); (A.A.C.); (E.S.I.); (O.D.Z.); (O.I.L.)
| | - Vasily I. Kaledin
- Institute of Cytology and Genetics, 10, acad. Lavrentjev Ave., 630090 Novosibirsk, Russian; (V.I.K.); (V.P.N.); (N.A.P.)
| | - Valeriy P. Nikolin
- Institute of Cytology and Genetics, 10, acad. Lavrentjev Ave., 630090 Novosibirsk, Russian; (V.I.K.); (V.P.N.); (N.A.P.)
| | - Nelly A. Popova
- Institute of Cytology and Genetics, 10, acad. Lavrentjev Ave., 630090 Novosibirsk, Russian; (V.I.K.); (V.P.N.); (N.A.P.)
- Novosibirsk State University, V. Zelman Institute for Medicine and Psychology and Department of Natural Sciences, 2, Pirogova str., 630090 Novosibirsk, Russia
| | - Dina V. Korchagina
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, 9 acad. Lavrentjev ave., 630090 Novosibirsk, Russia; (T.M.K.); (D.V.K.); (N.F.S.)
| | - Jóhannes Reynisson
- School of Pharmacy and Bioengineering, Keele University, Hornbeam Building, Staffordshire ST5 5BG, UK;
| | - Raina Chand
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, 1142 Auckland, New Zealand; (R.C.); (D.M.A.-T.); (J.P.); (I.K.H.L.)
| | - Daniel M. Ayine-Tora
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, 1142 Auckland, New Zealand; (R.C.); (D.M.A.-T.); (J.P.); (I.K.H.L.)
| | - Jinal Patel
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, 1142 Auckland, New Zealand; (R.C.); (D.M.A.-T.); (J.P.); (I.K.H.L.)
| | - Ivanhoe K. H. Leung
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, 1142 Auckland, New Zealand; (R.C.); (D.M.A.-T.); (J.P.); (I.K.H.L.)
| | - Konstantin P. Volcho
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, 9 acad. Lavrentjev ave., 630090 Novosibirsk, Russia; (T.M.K.); (D.V.K.); (N.F.S.)
- Novosibirsk State University, V. Zelman Institute for Medicine and Psychology and Department of Natural Sciences, 2, Pirogova str., 630090 Novosibirsk, Russia
- Correspondence:
| | - Nariman F. Salakhutdinov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, 9 acad. Lavrentjev ave., 630090 Novosibirsk, Russia; (T.M.K.); (D.V.K.); (N.F.S.)
- Novosibirsk State University, V. Zelman Institute for Medicine and Psychology and Department of Natural Sciences, 2, Pirogova str., 630090 Novosibirsk, Russia
| | - Olga I. Lavrik
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, 8, acad. Lavrentjev ave., 630090 Novosibirsk, Russia; (A.L.Z.); (A.A.C.); (E.S.I.); (O.D.Z.); (O.I.L.)
- Novosibirsk State University, V. Zelman Institute for Medicine and Psychology and Department of Natural Sciences, 2, Pirogova str., 630090 Novosibirsk, Russia
- Department of Physical and Chemical Biology and Biotechnology, Altai State University, 61, Lenina Ave., 656049 Barnaul, Russia
| |
Collapse
|
16
|
Correddu D, Montaño López JDJ, Angermayr SA, Middleditch MJ, Payne LS, Leung IKH. Effect of consecutive rare codons on the recombinant production of human proteins in
Escherichia coli. IUBMB Life 2019; 72:266-274. [DOI: 10.1002/iub.2162] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 08/26/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Danilo Correddu
- School of Chemical SciencesThe University of Auckland Auckland New Zealand
| | - José de Jesús Montaño López
- School of Chemical SciencesThe University of Auckland Auckland New Zealand
- Facultad de IngenieríaUniversidad Nacional Autónoma de México, Ciudad Universitaria Coyoacán Mexico
| | | | - Martin J. Middleditch
- School of Biological SciencesThe University of Auckland Auckland New Zealand
- Auckland Science Analytical ServicesThe University of Auckland Auckland New Zealand
| | - Leo S. Payne
- School of Biological SciencesThe University of Auckland Auckland New Zealand
- Auckland Science Analytical ServicesThe University of Auckland Auckland New Zealand
| | - Ivanhoe K. H. Leung
- School of Chemical SciencesThe University of Auckland Auckland New Zealand
- Maurice Wilkins Centre for Molecular BiodiscoveryThe University of Auckland Auckland New Zealand
| |
Collapse
|
17
|
Correddu D, Montaño López JDJ, Vadakkedath PG, Lai A, Pernes JI, Watson PR, Leung IKH. An improved method for the heterologous production of soluble human ribosomal proteins in Escherichia coli. Sci Rep 2019; 9:8884. [PMID: 31222068 PMCID: PMC6586885 DOI: 10.1038/s41598-019-45323-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 05/31/2019] [Indexed: 11/11/2022] Open
Abstract
Human ribosomal proteins play important structural and functional roles in the ribosome and in protein synthesis. An efficient method to recombinantly produce and purify these proteins would enable their full characterisation. However, the production of human ribosomal proteins can be challenging. The only published method about the recombinant production of human ribosomal proteins involved the recovery of proteins from inclusion bodies, a process that is tedious and may lead to significant loss of yield. Herein, we explored the use of different Escherichia coli competent cells and fusion protein tags for the recombinant production of human ribosomal proteins. We found that, by using thioredoxin as a fusion protein, soluble ribosomal protein could be obtained directly from cell lysates, thus leading to an improved method to recombinantly produce these proteins.
Collapse
Affiliation(s)
- Danilo Correddu
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - José de Jesús Montaño López
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand.,Facultad de Ingeniería, Universidad Nacional Autónoma de México, Av. Universidad 3000, Ciudad Universitaria, Coyoacán, Cd. Mx., CP 04510, Mexico
| | - Praveen G Vadakkedath
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand.,The MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
| | - Amy Lai
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - Jane I Pernes
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand.,School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, BS8 1TD, United Kingdom
| | - Paris R Watson
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand.,School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
| | - Ivanhoe K H Leung
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand. .,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand.
| |
Collapse
|
18
|
Zakharenko AL, Luzina OA, Sokolov DN, Kaledin VI, Nikolin VP, Popova NA, Patel J, Zakharova OD, Chepanova AA, Zafar A, Reynisson J, Leung E, Leung IKH, Volcho KP, Salakhutdinov NF, Lavrik OI. Novel tyrosyl-DNA phosphodiesterase 1 inhibitors enhance the therapeutic impact of topoteсan on in vivo tumor models. Eur J Med Chem 2018; 161:581-593. [PMID: 30396105 DOI: 10.1016/j.ejmech.2018.10.055] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/18/2018] [Accepted: 10/22/2018] [Indexed: 02/07/2023]
Abstract
The druggability of the tyrosyl-DNA phosphodiesterase 1 (Tdp1) enzyme was investigated in conjunction with topoisomerase 1 inhibition. A novel class of thiazole, aminothiazole and hydrazonothiazole usnic acid derivatives was synthesized and evaluated as Tdp1 inhibitors and their ability to sensitize tumors to topotecan, a topoisomerase inhibitor in clinical use. Of all the compounds tested, four hydrazinothiazole derivatives, 20c, 20d, 20h and 20i, inhibited the enzyme in the nanomolar range. The activity of the compounds was verified by affinity experiments as well as supported by molecular modelling. The most effective Tdp1 inhibitor, 20d, was ton-toxic and increased the effect of topotecan both in vitro and in vivo in the Lewis lung carcinoma model. Furthermore, 20d showed significant increase in the antitumor and antimetastatic effect of topotecan in mice. The results presented here justify compound 20d to be considered as a drug lead for antitumor therapy.
Collapse
Affiliation(s)
- A L Zakharenko
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk, 630090, Russian Federation
| | - O A Luzina
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk, 630090, Russian Federation
| | - D N Sokolov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk, 630090, Russian Federation
| | - V I Kaledin
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10, Akademika Lavrentieva Ave., Novosibirsk, 630090, Russian Federation
| | - V P Nikolin
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10, Akademika Lavrentieva Ave., Novosibirsk, 630090, Russian Federation
| | - N A Popova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10, Akademika Lavrentieva Ave., Novosibirsk, 630090, Russian Federation; Novosibirsk State University, Pirogova str. 1, Novosibirsk, 630090, Russian Federation
| | - J Patel
- School of Chemical Sciences, The University of Auckland, New Zealand
| | - O D Zakharova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk, 630090, Russian Federation
| | - A A Chepanova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk, 630090, Russian Federation
| | - A Zafar
- School of Chemical Sciences, The University of Auckland, New Zealand
| | - J Reynisson
- School of Chemical Sciences, The University of Auckland, New Zealand
| | - E Leung
- Auckland Cancer Society Research Centre and Department of Molecular Medicine and Pathology, The University of Auckland, New Zealand
| | - I K H Leung
- School of Chemical Sciences, The University of Auckland, New Zealand
| | - K P Volcho
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk, 630090, Russian Federation; Novosibirsk State University, Pirogova str. 1, Novosibirsk, 630090, Russian Federation
| | - N F Salakhutdinov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk, 630090, Russian Federation; Novosibirsk State University, Pirogova str. 1, Novosibirsk, 630090, Russian Federation
| | - O I Lavrik
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk, 630090, Russian Federation; Novosibirsk State University, Pirogova str. 1, Novosibirsk, 630090, Russian Federation.
| |
Collapse
|
19
|
Li-Zhulanov NS, Zakharenko AL, Chepanova AA, Patel J, Zafar A, Volcho KP, Salakhutdinov NF, Reynisson J, Leung IKH, Lavrik OI. A Novel Class of Tyrosyl-DNA Phosphodiesterase 1 Inhibitors That Contains the Octahydro-2 H-chromen-4-ol Scaffold. Molecules 2018; 23:E2468. [PMID: 30261631 PMCID: PMC6222798 DOI: 10.3390/molecules23102468] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 09/21/2018] [Accepted: 09/22/2018] [Indexed: 11/25/2022] Open
Abstract
Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is a DNA repair enzyme that mends topoisomerase 1-mediated DNA damage. Tdp1 is a current inhibition target for the development of improved anticancer treatments, as its inhibition may enhance the therapeutic effect of topoisomerase 1 poisons. Here, we report a study on the development of a novel class of Tdp1 inhibitors that is based on the octahydro-2H-chromene scaffold. Inhibition and binding assays revealed that these compounds are potent inhibitors of Tdp1, with IC50 and KD values in the low micromolar concentration range. Molecular modelling predicted plausible conformations of the active ligands, blocking access to the enzymatic machinery of Tdp1. Our results thus help establish a structural-activity relationship for octahydro-2H-chromene-based Tdp1 inhibitors, which will be useful for future Tdp1 inhibitor development work.
Collapse
Affiliation(s)
- Nikolai S Li-Zhulanov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia.
- Department of Natural Sciences and Institute of Medicine and Psychology, Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russia.
| | - Alexandra L Zakharenko
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia.
| | - Arina A Chepanova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia.
| | - Jinal Patel
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand.
| | - Ayesha Zafar
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand.
| | - Konstantin P Volcho
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia.
- Department of Natural Sciences and Institute of Medicine and Psychology, Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russia.
| | - Nariman F Salakhutdinov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia.
- Department of Natural Sciences and Institute of Medicine and Psychology, Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russia.
| | - Jóhannes Reynisson
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand.
| | - Ivanhoe K H Leung
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand.
| | - Olga I Lavrik
- Department of Natural Sciences and Institute of Medicine and Psychology, Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russia.
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia.
| |
Collapse
|
20
|
Abboud MI, Chowdhury R, Leung IKH, Lippl K, Loenarz C, Claridge TDW, Schofield CJ. Studies on the Substrate Selectivity of the Hypoxia-Inducible Factor Prolyl Hydroxylase 2 Catalytic Domain. Chembiochem 2018; 19:2262-2267. [PMID: 30144273 DOI: 10.1002/cbic.201800246] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Indexed: 12/19/2022]
Abstract
In animals, the response to chronic hypoxia is mediated by upregulation of the α,β-heterodimeric hypoxia-inducible factors (HIFs). Levels of HIFα isoforms, but not HIFβ, are regulated by their post-translational modification as catalysed by prolyl hydroxylase domain enzymes (PHDs). Different roles for the human HIF-1/2α isoforms and their two oxygen-dependent degradation domains (ODDs) are proposed. We report kinetic and NMR analyses of the ODD selectivity of the catalytic domain of wild-type PHD2 (which is conserved in nearly all animals) and clinically observed variants. Studies using Ala scanning and "hybrid" ODD peptides imply that the relatively rigid conformation of the (hydroxylated) proline plays an important role in ODD binding. They also reveal differential roles in binding for the residues on the N- and C-terminal sides of the substrate proline. The overall results indicate how the PHDs achieve selectivity for HIFα ODDs and might be of use in identifying substrate-selective PHD inhibitors.
Collapse
Affiliation(s)
- Martine I Abboud
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Rasheduzzaman Chowdhury
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.,Present address: Department of Molecular and Cellular Physiology, University of Stanford, Stanford, CA, 94305-5345, USA
| | - Ivanhoe K H Leung
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.,Present address: School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Kerstin Lippl
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.,Present address: Roche Innovation Center Munich, Roche Diagnostics GmbH, Nonnenwald 2, 82377, Penzberg, Germany
| | - Christoph Loenarz
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.,Present address: Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, 79104, Freiburg, Germany
| | - Timothy D W Claridge
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | | |
Collapse
|
21
|
Abstract
WaterLOGSY is a ligand-observed NMR method that is widely used for the studies of protein-small molecule interactions. The basis of waterLOGSY relies on the transfer of magnetization between water molecules, proteins, and small molecules via the nuclear Overhauser effect and chemical exchange. WaterLOGSY is used extensively for the screening of protein ligands, as it is a robust, relatively high-throughput, and reliable method to identify small molecules that bind proteins with a binding affinity (KD) in the μM to mM region. WaterLOGSY also enables the determination of KD via ligand titration, although careful optimization of the experimental setup is required to avoid overestimation of binding constants. Finally, waterLOGSY allows the water-accessible ligand protons of protein-bound ligands to be identified, thus providing structural information of the ligand binding orientation. In this chapter, we introduce and describe the waterLOGSY method, and provide a practical guide for ligand screening and KD determination. The use of waterLOGSY to study water accessibility is also discussed.
Collapse
Affiliation(s)
- Renjie Huang
- School of Chemical Sciences, The University of Auckland, Auckland, New Zealand
| | - Ivanhoe K H Leung
- School of Chemical Sciences, The University of Auckland, Auckland, New Zealand.
| |
Collapse
|
22
|
McAllister TE, Yeh TL, Abboud MI, Leung IKH, Hookway ES, King ONF, Bhushan B, Williams ST, Hopkinson RJ, Münzel M, Loik ND, Chowdhury R, Oppermann U, Claridge TDW, Goto Y, Suga H, Schofield CJ, Kawamura A. Non-competitive cyclic peptides for targeting enzyme-substrate complexes. Chem Sci 2018; 9:4569-4578. [PMID: 29899950 PMCID: PMC5969509 DOI: 10.1039/c8sc00286j] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/23/2018] [Indexed: 01/19/2023] Open
Abstract
Affinity reagents are of central importance for selectively identifying proteins and investigating their interactions. We report on the development and use of cyclic peptides, identified by mRNA display-based RaPID methodology, that are selective for, and tight binders of, the human hypoxia inducible factor prolyl hydroxylases (PHDs) - enzymes crucial in hypoxia sensing. Biophysical analyses reveal the cyclic peptides to bind in a distinct site, away from the enzyme active site pocket, enabling conservation of substrate binding and catalysis. A biotinylated cyclic peptide captures not only the PHDs, but also their primary substrate hypoxia inducible factor HIF1-α. Our work highlights the potential for tight, non-active site binding cyclic peptides to act as promising affinity reagents for studying protein-protein interactions.
Collapse
Affiliation(s)
- T E McAllister
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - T-L Yeh
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - M I Abboud
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - I K H Leung
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
- School of Chemical Sciences , The University of Auckland , Private Bag 92019 , Auckland 1142 , New Zealand
| | - E S Hookway
- Botnar Research Centre , NIHR Oxford Biomedical Research Unit , University of Oxford , Windmill Road , Oxford , OX3 7LD , UK
| | - O N F King
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - B Bhushan
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
- Division of Cardiovascular Medicine , Radcliffe Department of Medicine , University of Oxford , Wellcome Trust Centre for Human Genetics , Roosevelt Drive , Oxford OX3 7BN , UK
| | - S T Williams
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - R J Hopkinson
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - M Münzel
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - N D Loik
- Department of Chemistry , Graduate School of Science , The University of Tokyo , Tokyo 113-0033 , Japan
| | - R Chowdhury
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - U Oppermann
- Botnar Research Centre , NIHR Oxford Biomedical Research Unit , University of Oxford , Windmill Road , Oxford , OX3 7LD , UK
| | - T D W Claridge
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - Y Goto
- Department of Chemistry , Graduate School of Science , The University of Tokyo , Tokyo 113-0033 , Japan
| | - H Suga
- Department of Chemistry , Graduate School of Science , The University of Tokyo , Tokyo 113-0033 , Japan
- JST , CREST , The University of Tokyo , Tokyo 113-0033 , Japan
| | - C J Schofield
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - A Kawamura
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
- Division of Cardiovascular Medicine , Radcliffe Department of Medicine , University of Oxford , Wellcome Trust Centre for Human Genetics , Roosevelt Drive , Oxford OX3 7BN , UK
| |
Collapse
|
23
|
Zhang S, De Leon Rodriguez LM, Leung IKH, Cook GM, Harris PWR, Brimble MA. Inside Back Cover: Total Synthesis and Conformational Study of Callyaerin A: Anti-Tubercular Cyclic Peptide Bearing a Rare Rigidifying ( Z
)-2,3- Diaminoacrylamide Moiety (Angew. Chem. Int. Ed. 14/2018). Angew Chem Int Ed Engl 2018. [DOI: 10.1002/anie.201801945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Shengping Zhang
- School of Chemical Sciences; The University of Auckland; 23 Symonds St Auckland 1142 New Zealand
| | - Luis M. De Leon Rodriguez
- Maurice Wilkins Centre for Molecular Biodiscovery; The University of Auckland; Auckland 1142 New Zealand
| | - Ivanhoe K. H. Leung
- School of Chemical Sciences; The University of Auckland; 23 Symonds St Auckland 1142 New Zealand
| | - Gregory M. Cook
- Maurice Wilkins Centre for Molecular Biodiscovery; The University of Auckland; Auckland 1142 New Zealand
- Department of Microbiology and Immunology; University of Otago; Dunedin 9054 New Zealand
| | - Paul W. R. Harris
- School of Chemical Sciences; The University of Auckland; 23 Symonds St Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery; The University of Auckland; Auckland 1142 New Zealand
| | - Margaret A. Brimble
- School of Chemical Sciences; The University of Auckland; 23 Symonds St Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery; The University of Auckland; Auckland 1142 New Zealand
| |
Collapse
|
24
|
Zhang S, De Leon Rodriguez LM, Leung IKH, Cook GM, Harris PWR, Brimble MA. Innenrücktitelbild: Total Synthesis and Conformational Study of Callyaerin A: Anti-Tubercular Cyclic Peptide Bearing a Rare Rigidifying ( Z
)-2,3- Diaminoacrylamide Moiety (Angew. Chem. 14/2018). Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Shengping Zhang
- School of Chemical Sciences; The University of Auckland; 23 Symonds St Auckland 1142 New Zealand
| | - Luis M. De Leon Rodriguez
- Maurice Wilkins Centre for Molecular Biodiscovery; The University of Auckland; Auckland 1142 New Zealand
| | - Ivanhoe K. H. Leung
- School of Chemical Sciences; The University of Auckland; 23 Symonds St Auckland 1142 New Zealand
| | - Gregory M. Cook
- Maurice Wilkins Centre for Molecular Biodiscovery; The University of Auckland; Auckland 1142 New Zealand
- Department of Microbiology and Immunology; University of Otago; Dunedin 9054 New Zealand
| | - Paul W. R. Harris
- School of Chemical Sciences; The University of Auckland; 23 Symonds St Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery; The University of Auckland; Auckland 1142 New Zealand
| | - Margaret A. Brimble
- School of Chemical Sciences; The University of Auckland; 23 Symonds St Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery; The University of Auckland; Auckland 1142 New Zealand
| |
Collapse
|
25
|
Abboud MI, McAllister TE, Leung IKH, Chowdhury R, Jorgensen C, Domene C, Mecinović J, Lippl K, Hancock RL, Hopkinson RJ, Kawamura A, Claridge TDW, Schofield CJ. 2-Oxoglutarate regulates binding of hydroxylated hypoxia-inducible factor to prolyl hydroxylase domain 2. Chem Commun (Camb) 2018. [PMID: 29522057 PMCID: PMC5885369 DOI: 10.1039/c8cc00387d] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The binding of prolyl-hydroxylated HIF-α to PHD2 is hindered by prior 2OG binding; likely, leading to the inhibition of HIF-α degradation under limiting 2OG conditions.
Prolyl hydroxylation of hypoxia inducible factor (HIF)-α, as catalysed by the Fe(ii)/2-oxoglutarate (2OG)-dependent prolyl hydroxylase domain (PHD) enzymes, has a hypoxia sensing role in animals. We report that binding of prolyl-hydroxylated HIF-α to PHD2 is ∼50 fold hindered by prior 2OG binding; thus, when 2OG is limiting, HIF-α degradation might be inhibited by PHD binding.
Collapse
Affiliation(s)
- Martine I Abboud
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Tom E McAllister
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Ivanhoe K H Leung
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK. and School of Chemical Sciences, The University of Auckland, New Zealand
| | - Rasheduzzaman Chowdhury
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | | | - Carmen Domene
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK. and Department of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Jasmin Mecinović
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK. and Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Kerstin Lippl
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Rebecca L Hancock
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Richard J Hopkinson
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK. and Leicester Institute of Structural and Chemical Biology and Department of Chemistry, University of Leicester, Leicester, LE1 7RH, UK
| | - Akane Kawamura
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Timothy D W Claridge
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Christopher J Schofield
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| |
Collapse
|
26
|
Zhang S, De Leon Rodriguez LM, Leung IKH, Cook GM, Harris PWR, Brimble MA. Total Synthesis and Conformational Study of Callyaerin A: Anti-Tubercular Cyclic Peptide Bearing a Rare Rigidifying (Z
)-2,3- Diaminoacrylamide Moiety. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712792] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Shengping Zhang
- School of Chemical Sciences; The University of Auckland; 23 Symonds St Auckland 1142 New Zealand
| | - Luis M. De Leon Rodriguez
- Maurice Wilkins Centre for Molecular Biodiscovery; The University of Auckland; Auckland 1142 New Zealand
| | - Ivanhoe K. H. Leung
- School of Chemical Sciences; The University of Auckland; 23 Symonds St Auckland 1142 New Zealand
| | - Gregory M. Cook
- Maurice Wilkins Centre for Molecular Biodiscovery; The University of Auckland; Auckland 1142 New Zealand
- Department of Microbiology and Immunology; University of Otago; Dunedin 9054 New Zealand
| | - Paul W. R. Harris
- School of Chemical Sciences; The University of Auckland; 23 Symonds St Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery; The University of Auckland; Auckland 1142 New Zealand
| | - Margaret A. Brimble
- School of Chemical Sciences; The University of Auckland; 23 Symonds St Auckland 1142 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery; The University of Auckland; Auckland 1142 New Zealand
| |
Collapse
|
27
|
Zhang S, De Leon Rodriguez LM, Leung IKH, Cook GM, Harris PWR, Brimble MA. Total Synthesis and Conformational Study of Callyaerin A: Anti-Tubercular Cyclic Peptide Bearing a Rare Rigidifying (Z)-2,3- Diaminoacrylamide Moiety. Angew Chem Int Ed Engl 2018; 57:3631-3635. [PMID: 29345033 DOI: 10.1002/anie.201712792] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Indexed: 11/11/2022]
Abstract
The first synthesis of the anti-TB cyclic peptide callyaerin A (1), containing a rare (Z)-2,3-diaminoacrylamide bridging motif, is reported. Fmoc-formylglycine-diethylacetal was used as a masked equivalent of formylglycine in the synthesis of the linear precursor to 1. Intramolecular cyclization between the formylglycine residue and the N-terminal amine in the linear peptide precursor afforded the macrocyclic natural product 1. Synthetic 1 possessed potent anti-TB activity (MIC100 =32 μm) while its all-amide congener was inactive. Variable-temperature NMR studies of both the natural product and its all-amide analogue revealed the extraordinary rigidity imposed by this diaminoacrylamide unit on peptide conformation. The work reported herein pinpoints the intrinsic role that the (Z)-2,3-diaminoacrylamide moiety confers on peptide bioactivity.
Collapse
Affiliation(s)
- Shengping Zhang
- School of Chemical Sciences, The University of Auckland, 23 Symonds St, Auckland, 1142, New Zealand
| | - Luis M De Leon Rodriguez
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, 1142, New Zealand
| | - Ivanhoe K H Leung
- School of Chemical Sciences, The University of Auckland, 23 Symonds St, Auckland, 1142, New Zealand
| | - Gregory M Cook
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, 1142, New Zealand.,Department of Microbiology and Immunology, University of Otago, Dunedin, 9054, New Zealand
| | - Paul W R Harris
- School of Chemical Sciences, The University of Auckland, 23 Symonds St, Auckland, 1142, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, 1142, New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences, The University of Auckland, 23 Symonds St, Auckland, 1142, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, 1142, New Zealand
| |
Collapse
|
28
|
Zhang S, De Leon Rodriguez LM, Huang R, Leung IKH, Harris PWR, Brimble MA. Total synthesis of the proposed structure of talarolide A. Org Biomol Chem 2018; 16:5286-5293. [DOI: 10.1039/c8ob01230j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The proposed structure of talarolide A, a cycloheptapeptide featuring a hydroxamate moiety within the peptide backbone, was successfully synthesized.
Collapse
Affiliation(s)
- Shengping Zhang
- School of Chemical Sciences
- The University of Auckland
- Auckland
- New Zealand
| | | | - Renjie Huang
- School of Chemical Sciences
- The University of Auckland
- Auckland
- New Zealand
| | | | - Paul W. R. Harris
- School of Chemical Sciences
- The University of Auckland
- Auckland
- New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery
| | - Margaret A. Brimble
- School of Chemical Sciences
- The University of Auckland
- Auckland
- New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery
| |
Collapse
|
29
|
Affiliation(s)
- Yu Li
- School of Chemical Sciences; The University of Auckland, Private Bag 92019; Victoria Street West Auckland 1142 New Zealand
| | - Ayesha Zafar
- School of Chemical Sciences; The University of Auckland, Private Bag 92019; Victoria Street West Auckland 1142 New Zealand
| | - Paul A. Kilmartin
- School of Chemical Sciences; The University of Auckland, Private Bag 92019; Victoria Street West Auckland 1142 New Zealand
| | - Jóhannes Reynisson
- School of Chemical Sciences; The University of Auckland, Private Bag 92019; Victoria Street West Auckland 1142 New Zealand
| | - Ivanhoe K. H. Leung
- School of Chemical Sciences; The University of Auckland, Private Bag 92019; Victoria Street West Auckland 1142 New Zealand
| |
Collapse
|
30
|
Yeh TL, Leissing TM, Abboud MI, Thinnes CC, Atasoylu O, Holt-Martyn JP, Zhang D, Tumber A, Lippl K, Lohans CT, Leung IKH, Morcrette H, Clifton IJ, Claridge TDW, Kawamura A, Flashman E, Lu X, Ratcliffe PJ, Chowdhury R, Pugh CW, Schofield CJ. Molecular and cellular mechanisms of HIF prolyl hydroxylase inhibitors in clinical trials. Chem Sci 2017; 8:7651-7668. [PMID: 29435217 PMCID: PMC5802278 DOI: 10.1039/c7sc02103h] [Citation(s) in RCA: 164] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 09/07/2017] [Indexed: 02/06/2023] Open
Abstract
Inhibition of the human 2-oxoglutarate (2OG) dependent hypoxia inducible factor (HIF) prolyl hydroxylases (human PHD1-3) causes upregulation of HIF, thus promoting erythropoiesis and is therefore of therapeutic interest. We describe cellular, biophysical, and biochemical studies comparing four PHD inhibitors currently in clinical trials for anaemia treatment, that describe their mechanisms of action, potency against isolated enzymes and in cells, and selectivities versus representatives of other human 2OG oxygenase subfamilies. The 'clinical' PHD inhibitors are potent inhibitors of PHD catalyzed hydroxylation of the HIF-α oxygen dependent degradation domains (ODDs), and selective against most, but not all, representatives of other human 2OG dependent dioxygenase subfamilies. Crystallographic and NMR studies provide insights into the different active site binding modes of the inhibitors. Cell-based results reveal the inhibitors have similar effects on the upregulation of HIF target genes, but differ in the kinetics of their effects and in extent of inhibition of hydroxylation of the N- and C-terminal ODDs; the latter differences correlate with the biophysical observations.
Collapse
Affiliation(s)
- Tzu-Lan Yeh
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
- Target Discovery Institute (TDI) , Nuffield Department of Medicine , University of Oxford , NDMRB Roosevelt Drive , Oxford OX3 7FZ , UK
| | - Thomas M Leissing
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
- Ludwig Institute for Cancer Research , Nuffield Department of Clinical Medicine , University of Oxford , Oxford OX3 7DQ , UK
| | - Martine I Abboud
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Cyrille C Thinnes
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Onur Atasoylu
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - James P Holt-Martyn
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Dong Zhang
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Anthony Tumber
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
- Structural Genomics Consortium (SGC) , University of Oxford , Oxford OX3 7DQ , UK
| | - Kerstin Lippl
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Christopher T Lohans
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Ivanhoe K H Leung
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Helen Morcrette
- Radcliffe Department of Medicine , Division of Cardiovascular Medicine , BHF Centre of Research Excellence , Wellcome Trust Centre for Human Genetics , Roosevelt Drive , Oxford OX3 7BN , UK
| | - Ian J Clifton
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Timothy D W Claridge
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Akane Kawamura
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
- Radcliffe Department of Medicine , Division of Cardiovascular Medicine , BHF Centre of Research Excellence , Wellcome Trust Centre for Human Genetics , Roosevelt Drive , Oxford OX3 7BN , UK
| | - Emily Flashman
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Xin Lu
- Ludwig Institute for Cancer Research , Nuffield Department of Clinical Medicine , University of Oxford , Oxford OX3 7DQ , UK
| | - Peter J Ratcliffe
- Target Discovery Institute (TDI) , Nuffield Department of Medicine , University of Oxford , NDMRB Roosevelt Drive , Oxford OX3 7FZ , UK
- The Francis Crick Institute , 1 Midland Road , London NW1 1AT , UK
| | - Rasheduzzaman Chowdhury
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Christopher W Pugh
- Target Discovery Institute (TDI) , Nuffield Department of Medicine , University of Oxford , NDMRB Roosevelt Drive , Oxford OX3 7FZ , UK
| | - Christopher J Schofield
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| |
Collapse
|
31
|
Bhusal RP, Patel K, Kwai BXC, Swartjes A, Bashiri G, Reynisson J, Sperry J, Leung IKH. Development of NMR and thermal shift assays for the evaluation of Mycobacterium tuberculosis isocitrate lyase inhibitors. Medchemcomm 2017; 8:2155-2163. [PMID: 30108733 PMCID: PMC6072051 DOI: 10.1039/c7md00456g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 10/16/2017] [Indexed: 12/17/2022]
Abstract
The enzymes isocitrate lyase (ICL) isoforms 1 and 2 are essential for Mycobacterium tuberculosis survival within macrophages during latent tuberculosis (TB). As such, ICLs are attractive therapeutic targets for the treatment of tuberculosis. However, there are few biophysical assays that are available for accurate kinetic and inhibition studies of ICL in vitro. Herein we report the development of a combined NMR spectroscopy and thermal shift assay to study ICL inhibitors for both screening and inhibition constant (IC50) measurement. Operating this new assay in tandem with virtual high-throughput screening has led to the discovery of several new ICL1 inhibitors.
Collapse
Affiliation(s)
- Ram Prasad Bhusal
- School of Chemical Sciences , The University of Auckland , Private Bag 92019, Victoria Street West , Auckland 1142 , New Zealand . (JS) ; (IKHL)
| | - Krunal Patel
- School of Chemical Sciences , The University of Auckland , Private Bag 92019, Victoria Street West , Auckland 1142 , New Zealand . (JS) ; (IKHL)
| | - Brooke X C Kwai
- School of Chemical Sciences , The University of Auckland , Private Bag 92019, Victoria Street West , Auckland 1142 , New Zealand . (JS) ; (IKHL)
| | - Anne Swartjes
- School of Chemical Sciences , The University of Auckland , Private Bag 92019, Victoria Street West , Auckland 1142 , New Zealand . (JS) ; (IKHL)
- Institute for Molecules and Materials , Radboud University , Heyendaalseweg 135 , 6525 AJ , Nijmegen , The Netherlands
| | - Ghader Bashiri
- School of Biological Sciences , The University of Auckland , Private Bag 92019, Victoria Street West , Auckland 1142 , New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery , The University of Auckland , Private Bag 92019, Victoria Street West , Auckland 1142 , New Zealand
| | - Jóhannes Reynisson
- School of Chemical Sciences , The University of Auckland , Private Bag 92019, Victoria Street West , Auckland 1142 , New Zealand . (JS) ; (IKHL)
| | - Jonathan Sperry
- School of Chemical Sciences , The University of Auckland , Private Bag 92019, Victoria Street West , Auckland 1142 , New Zealand . (JS) ; (IKHL)
| | - Ivanhoe K H Leung
- School of Chemical Sciences , The University of Auckland , Private Bag 92019, Victoria Street West , Auckland 1142 , New Zealand . (JS) ; (IKHL)
| |
Collapse
|
32
|
Mbenza NM, Vadakkedath PG, McGillivray DJ, Leung IKH. NMR studies of the non-haem Fe(II) and 2-oxoglutarate-dependent oxygenases. J Inorg Biochem 2017; 177:384-394. [PMID: 28893416 DOI: 10.1016/j.jinorgbio.2017.08.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 08/21/2017] [Accepted: 08/30/2017] [Indexed: 01/13/2023]
Abstract
The non-haem Fe(II) and 2-oxoglutarate (2OG)-dependent oxygenases belong to a superfamily of structurally-related enzymes that play important biological roles in plants, microorganisms and animals. Structural, mechanistic and functional studies of 2OG oxygenases require efficient and effective biophysical tools. Nuclear magnetic resonance (NMR) spectroscopy is a useful tool to study this enzyme superfamily. It has been applied to obtain information about enzyme kinetics, identify and characterise 2OG oxygenase-catalysed oxidation products, elucidate the catalytic mechanism, monitor ligand binding and study protein dynamics. This review summarises the types of information that NMR spectroscopy can provide in the studies of 2OG oxygenases, highlights the advantages of the technique and describes its drawbacks.
Collapse
Affiliation(s)
- Naasson M Mbenza
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - Praveen G Vadakkedath
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand.; MacDiarmid Institute for Advanced Materials and Nanotechnology, PO Box 600, Wellington 6140, New Zealand
| | - Duncan J McGillivray
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand.; MacDiarmid Institute for Advanced Materials and Nanotechnology, PO Box 600, Wellington 6140, New Zealand
| | - Ivanhoe K H Leung
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand..
| |
Collapse
|
33
|
Bhusal RP, Bashiri G, Kwai BXC, Sperry J, Leung IKH. Targeting isocitrate lyase for the treatment of latent tuberculosis. Drug Discov Today 2017; 22:1008-1016. [PMID: 28458043 DOI: 10.1016/j.drudis.2017.04.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 03/04/2017] [Accepted: 04/20/2017] [Indexed: 01/11/2023]
Abstract
Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis that can remain dormant for many years before becoming active. One way to control and eliminate TB is the identification and treatment of latent TB, preventing infected individuals from developing active TB and thus eliminating the subsequent spread of the disease. Isocitrate lyase (ICL) is involved in the mycobacterial glyoxylate and methylisocitrate cycles. ICL is important for the growth and survival of M. tuberculosis during latent infection. ICL is not present in humans and is therefore a potential therapeutic target for the development of anti-TB agents. Here, we explore the evidence linking ICL to persistent survival of M. tuberculosis. The structure, mechanism and inhibition of the enzyme is also discussed.
Collapse
Affiliation(s)
- Ram Prasad Bhusal
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - Ghader Bashiri
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - Brooke X C Kwai
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - Jonathan Sperry
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand.
| | - Ivanhoe K H Leung
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand.
| |
Collapse
|
34
|
Santoso B, Yanaranop P, Kang H, Leung IKH, Jin J. A Critical Update on the Synthesis of Carboxylated Polymers of Intrinsic Microporosity (C-PIMs). Macromolecules 2017. [DOI: 10.1021/acs.macromol.7b00344] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Bagus Santoso
- School of Chemical Sciences, The University of Auckland, Auckland 1142, New Zealand
| | - Paam Yanaranop
- School of Chemical Sciences, The University of Auckland, Auckland 1142, New Zealand
| | - Hong Kang
- School of Chemical Sciences, The University of Auckland, Auckland 1142, New Zealand
| | - Ivanhoe K. H. Leung
- School of Chemical Sciences, The University of Auckland, Auckland 1142, New Zealand
| | - Jianyong Jin
- School of Chemical Sciences, The University of Auckland, Auckland 1142, New Zealand
| |
Collapse
|
35
|
Hanauer T, Hopkinson RJ, Patel K, Li Y, Correddu D, Kawamura A, Sarojini V, Leung IKH, Gruber T. Selective recognition of the di/trimethylammonium motif by an artificial carboxycalixarene receptor. Org Biomol Chem 2017; 15:1100-1105. [PMID: 28091667 DOI: 10.1039/c6ob02616h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2024]
Abstract
Chemical tools that recognise post-translational modifications have promising applications in biochemistry and in therapy. We report a simple carboxycalixarene that selectively binds molecules containing di/trimethylammonium moieties in isolation, in cell lysates and when incorporated in histone peptides. Our findings reveal the potential of using carboxycalixarene-based receptors to study epigenetic regulation.
Collapse
Affiliation(s)
- Thomas Hanauer
- Institute of Organic Chemistry, Technische Universität Bergakademie Freiberg, Leipziger Strasse 29, Freiberg, Sachsen, Germany.
| | - Richard J Hopkinson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Kamal Patel
- School of Chemical Sciences and Centre for Green Chemical Science, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - Yu Li
- School of Chemical Sciences and Centre for Green Chemical Science, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - Danilo Correddu
- School of Chemical Sciences and Centre for Green Chemical Science, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Vijayalekshmi Sarojini
- School of Chemical Sciences and Centre for Green Chemical Science, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - Ivanhoe K H Leung
- School of Chemical Sciences and Centre for Green Chemical Science, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - Tobias Gruber
- Institute of Organic Chemistry, Technische Universität Bergakademie Freiberg, Leipziger Strasse 29, Freiberg, Sachsen, Germany.
| |
Collapse
|
36
|
Abstract
Synthetic antifreeze peptides based on the hyperactive antifreeze protein modify the shape of ice crystals and show enhanced antifreeze activity with the addition of a small molecule.
Collapse
Affiliation(s)
- Charles H. Z. Kong
- School of Chemical Sciences
- The University of Auckland
- Auckland
- New Zealand
| | | | | |
Collapse
|
37
|
Harris PWR, Cook GM, Leung IKH, Brimble MA. An Efficient Chemical Synthesis of Lassomycin Enabled by an On-Resin Lactamisation–Off-Resin Methanolysis Strategy and Preparation of Chemical Variants. Aust J Chem 2017. [DOI: 10.1071/ch16499] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
An efficient synthesis of the naturally occurring cyclic peptide lassomycin that bears a unique Asp–Gly isopeptide bond and a C-terminal methyl ester is described. On-resin cyclisation between 1Gly and side chain 8Asp and a subsequent solution-phase transesterification reaction afforded synthetic lassomycin in high yield. Several analogues were also prepared using the optimised methodology. None of the cyclised peptides, including the synthetic natural product, exhibited any significant activity against Mycobacterium tuberculosis. Comparison of the spectroscopic data for synthetic lassomycin with naturally occurring lassomycin concluded they were otherwise identical.
Collapse
|
38
|
Zhang S, De Leon Rodriguez LM, Lacey E, Piggott AM, Leung IKH, Brimble MA. Cyclization of Linear Tetrapeptides Containing N
-Methylated Amino Acids by using 1-Propanephosphonic Acid Anhydride. European J Org Chem 2016. [DOI: 10.1002/ejoc.201601016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Shengping Zhang
- School of Chemical Sciences; The University of Auckland; 23 Symonds St 1142 Auckland New Zealand
| | - Luis M. De Leon Rodriguez
- Maurice Wilkins Centre for Molecular Biodiscovery; The University of Auckland; 1142 Auckland New Zealand
| | - Ernest Lacey
- Microbial Screening Technologies; Building C; 28-54 Percival Rd. 2164 Smithfield NSW Australia
| | - Andrew M. Piggott
- Department of Chemistry and Biomolecular Sciences; Macquarie University; 2109 NSW Australia
| | - Ivanhoe K. H. Leung
- School of Chemical Sciences; The University of Auckland; 23 Symonds St 1142 Auckland New Zealand
| | - Margaret A. Brimble
- School of Chemical Sciences; The University of Auckland; 23 Symonds St 1142 Auckland New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery; The University of Auckland; 1142 Auckland New Zealand
| |
Collapse
|
39
|
Affiliation(s)
- Ashley C. Lindsay
- School of Chemical Sciences, University of Auckland, 23 Symonds Street, Auckland 1000, New Zealand
| | - Ivanhoe K. H. Leung
- School of Chemical Sciences, University of Auckland, 23 Symonds Street, Auckland 1000, New Zealand
| | - Jonathan Sperry
- School of Chemical Sciences, University of Auckland, 23 Symonds Street, Auckland 1000, New Zealand
| |
Collapse
|
40
|
Chowdhury R, Leung IKH, Tian YM, Abboud MI, Ge W, Domene C, Cantrelle FX, Landrieu I, Hardy AP, Pugh CW, Ratcliffe PJ, Claridge TDW, Schofield CJ. Structural basis for oxygen degradation domain selectivity of the HIF prolyl hydroxylases. Nat Commun 2016; 7:12673. [PMID: 27561929 PMCID: PMC5007464 DOI: 10.1038/ncomms12673] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 07/21/2016] [Indexed: 02/06/2023] Open
Abstract
The response to hypoxia in animals involves the expression of multiple genes regulated by the αβ-hypoxia-inducible transcription factors (HIFs). The hypoxia-sensing mechanism involves oxygen limited hydroxylation of prolyl residues in the N- and C-terminal oxygen-dependent degradation domains (NODD and CODD) of HIFα isoforms, as catalysed by prolyl hydroxylases (PHD 1-3). Prolyl hydroxylation promotes binding of HIFα to the von Hippel-Lindau protein (VHL)-elongin B/C complex, thus signalling for proteosomal degradation of HIFα. We reveal that certain PHD2 variants linked to familial erythrocytosis and cancer are highly selective for CODD or NODD. Crystalline and solution state studies coupled to kinetic and cellular analyses reveal how wild-type and variant PHDs achieve ODD selectivity via different dynamic interactions involving loop and C-terminal regions. The results inform on how HIF target gene selectivity is achieved and will be of use in developing selective PHD inhibitors.
Collapse
Affiliation(s)
- Rasheduzzaman Chowdhury
- Chemistry Research Laboratory, Department of Chemistry, Oxford Centre for Integrative Systems Biology, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Ivanhoe K. H. Leung
- Chemistry Research Laboratory, Department of Chemistry, Oxford Centre for Integrative Systems Biology, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Ya-Min Tian
- Nuffield Department of Clinical Medicine, University of Oxford, Henry Wellcome Building for Molecular Physiology, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Martine I. Abboud
- Chemistry Research Laboratory, Department of Chemistry, Oxford Centre for Integrative Systems Biology, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Wei Ge
- Chemistry Research Laboratory, Department of Chemistry, Oxford Centre for Integrative Systems Biology, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Carmen Domene
- Chemistry Research Laboratory, Department of Chemistry, Oxford Centre for Integrative Systems Biology, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | | | | | - Adam P. Hardy
- Chemistry Research Laboratory, Department of Chemistry, Oxford Centre for Integrative Systems Biology, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Christopher W. Pugh
- Nuffield Department of Clinical Medicine, University of Oxford, Henry Wellcome Building for Molecular Physiology, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Peter J. Ratcliffe
- Nuffield Department of Clinical Medicine, University of Oxford, Henry Wellcome Building for Molecular Physiology, Roosevelt Drive, Oxford OX3 7BN, UK
- Ludwig Institute for Cancer Research, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Timothy D. W. Claridge
- Chemistry Research Laboratory, Department of Chemistry, Oxford Centre for Integrative Systems Biology, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department of Chemistry, Oxford Centre for Integrative Systems Biology, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| |
Collapse
|
41
|
Hopkinson RJ, Leung IKH, Smart TJ, Rose NR, Henry L, Claridge TDW, Schofield CJ. Studies on the Glutathione-Dependent Formaldehyde-Activating Enzyme from Paracoccus denitrificans. PLoS One 2015; 10:e0145085. [PMID: 26675168 PMCID: PMC4682968 DOI: 10.1371/journal.pone.0145085] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 11/26/2015] [Indexed: 12/15/2022] Open
Abstract
Formaldehyde is a toxin and carcinogen that is both an environmental pollutant and an endogenous metabolite. Formaldehyde metabolism, which is probably essential for all aerobic cells, likely proceeds via multiple mechanisms, including via a glutathione-dependent pathway that is widely conserved in bacteria, plants and animals. However, it is unclear whether the first step in the glutathione-dependent pathway (i.e. formation of S-hydroxymethylglutathione (HMG)) is enzyme-catalysed. We report studies on glutathione-dependent formaldehyde-activating enzyme (GFA) from Paracoccus denitrificans, which has been proposed to catalyse HMG formation from glutathione and formaldehyde on the basis of studies using NMR exchange spectroscopy (EXSY). Although we were able to replicate the EXSY results, time course experiments unexpectedly imply that GFA does not catalyse HMG formation under standard conditions. However, GFA was observed to bind glutathione using NMR and mass spectrometry. Overall, the results reveal that GFA binds glutathione but does not directly catalyse HMG formation under standard conditions. Thus, it is possible that GFA acts as a glutathione carrier that acts to co-localise glutathione and formaldehyde in a cellular context.
Collapse
Affiliation(s)
- Richard J. Hopkinson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Ivanhoe K. H. Leung
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
- School of Chemical Sciences, The University of Auckland, Auckland, New Zealand
| | - Tristan J. Smart
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Nathan R. Rose
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Luc Henry
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Timothy D. W. Claridge
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
42
|
Chan MC, Atasoylu O, Hodson E, Tumber A, Leung IKH, Chowdhury R, Gómez-Pérez V, Demetriades M, Rydzik AM, Holt-Martyn J, Tian YM, Bishop T, Claridge TDW, Kawamura A, Pugh CW, Ratcliffe PJ, Schofield CJ. Potent and Selective Triazole-Based Inhibitors of the Hypoxia-Inducible Factor Prolyl-Hydroxylases with Activity in the Murine Brain. PLoS One 2015; 10:e0132004. [PMID: 26147748 PMCID: PMC4492579 DOI: 10.1371/journal.pone.0132004] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 06/09/2015] [Indexed: 01/01/2023] Open
Abstract
As part of the cellular adaptation to limiting oxygen availability in animals, the expression of a large set of genes is activated by the upregulation of the hypoxia-inducible transcription factors (HIFs). Therapeutic activation of the natural human hypoxic response can be achieved by the inhibition of the hypoxia sensors for the HIF system, i.e. the HIF prolyl-hydroxylases (PHDs). Here, we report studies on tricyclic triazole-containing compounds as potent and selective PHD inhibitors which compete with the 2-oxoglutarate co-substrate. One compound (IOX4) induces HIFα in cells and in wildtype mice with marked induction in the brain tissue, revealing that it is useful for studies aimed at validating the upregulation of HIF for treatment of cerebral diseases including stroke.
Collapse
Affiliation(s)
- Mun Chiang Chan
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, United Kingdom
| | - Onur Atasoylu
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Emma Hodson
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, United Kingdom
| | - Anthony Tumber
- Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Ivanhoe K. H. Leung
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Rasheduzzaman Chowdhury
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Verónica Gómez-Pérez
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Marina Demetriades
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Anna M. Rydzik
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - James Holt-Martyn
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Ya-Min Tian
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, United Kingdom
| | - Tammie Bishop
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, United Kingdom
| | - Timothy D. W. Claridge
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Christopher W. Pugh
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, United Kingdom
| | - Peter J. Ratcliffe
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, United Kingdom
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
43
|
Rydzik AM, Leung IKH, Kochan GT, Loik ND, Henry L, McDonough MA, Claridge TDW, Schofield CJ. Comparison of the substrate selectivity and biochemical properties of human and bacterial γ-butyrobetaine hydroxylase. Org Biomol Chem 2015; 12:6354-8. [PMID: 25030770 DOI: 10.1039/c4ob01167h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
2-Oxoglutarate and iron dependent oxygenases have potential for the stereoselective hydroxylation of amino acids and related compounds. The biochemical and kinetic properties of recombinant γ-butyrobetaine hydroxylase from human and Pseudomonas sp. AK1 were compared. The results reveal differences between the two BBOXs, including in their stimulation by ascorbate. Despite their closely related sequences, the two enzymes also display different substrate selectivities, including for the production of (di)hydroxylated betaines, implying use of engineered BBOXs for biocatalytic purposes may be productive.
Collapse
Affiliation(s)
- Anna M Rydzik
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom.
| | | | | | | | | | | | | | | |
Collapse
|
44
|
Tarhonskaya H, Chowdhury R, Leung IKH, Loik ND, McCullagh JSO, Claridge TDW, Schofield CJ, Flashman E. Investigating the contribution of the active site environment to the slow reaction of hypoxia-inducible factor prolyl hydroxylase domain 2 with oxygen. Biochem J 2014; 463:363-72. [PMID: 25120187 DOI: 10.1042/bj20140779] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2024]
Abstract
The prolyl hydroxylase domain proteins (PHDs) catalyse the post-translational hydroxylation of the hypoxia-inducible factor (HIF), a modification that regulates the hypoxic response in humans. The PHDs are Fe(II)/2-oxoglutarate (2OG) oxygenases; their catalysis is proposed to provide a link between cellular HIF levels and changes in O2 availability. Transient kinetic studies have shown that purified PHD2 reacts slowly with O2 compared with some other studied 2OG oxygenases, a property which may be related to its hypoxia-sensing role. PHD2 forms a stable complex with Fe(II) and 2OG; crystallographic and kinetic analyses indicate that an Fe(II)-co-ordinated water molecule, which must be displaced before O2 binding, is relatively stable in the active site of PHD2. We used active site substitutions to investigate whether these properties are related to the slow reaction of PHD2 with O2. While disruption of 2OG binding in a R383K variant did not accelerate O2 activation, we found that substitution of the Fe(II)-binding aspartate for a glutamate residue (D315E) manifested significantly reduced Fe(II) binding, yet maintained catalytic activity with a 5-fold faster reaction with O2. The results inform on how the precise active site environment of oxygenases can affect rates of O2 activation and provide insights into limiting steps in PHD catalysis.
Collapse
Affiliation(s)
- Hanna Tarhonskaya
- *Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Rasheduzzaman Chowdhury
- *Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Ivanhoe K H Leung
- *Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Nikita D Loik
- *Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - James S O McCullagh
- *Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Timothy D W Claridge
- *Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Christopher J Schofield
- *Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Emily Flashman
- *Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K
| |
Collapse
|
45
|
Rydzik AM, Leung IKH, Kochan GT, McDonough MA, Claridge TDW, Schofield CJ. Oxygenase-catalyzed desymmetrization of N,N-dialkyl-piperidine-4-carboxylic acids. Angew Chem Int Ed Engl 2014; 53:10925-7. [PMID: 25164544 PMCID: PMC4497603 DOI: 10.1002/anie.201406125] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Indexed: 12/14/2022]
Abstract
γ-Butyrobetaine hydroxylase (BBOX) is a 2-oxoglutarate dependent oxygenase that catalyzes the final hydroxylation step in the biosynthesis of carnitine. BBOX was shown to catalyze the oxidative desymmetrization of achiral N,N-dialkyl piperidine-4-carboxylates to give products with two or three stereogenic centers.
Collapse
Affiliation(s)
- Anna M Rydzik
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory12 Mansfield Road, Oxford OX1 3TA (UK)
| | - Ivanhoe K H Leung
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory12 Mansfield Road, Oxford OX1 3TA (UK)
| | - Grazyna T Kochan
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosvelt DriveHeadington OX3 7DQ, United Kingdom
| | - Michael A McDonough
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory12 Mansfield Road, Oxford OX1 3TA (UK)
| | - Timothy D W Claridge
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory12 Mansfield Road, Oxford OX1 3TA (UK)
| | - Christopher J Schofield
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory12 Mansfield Road, Oxford OX1 3TA (UK)
| |
Collapse
|
46
|
Rydzik AM, Leung IKH, Kochan GT, McDonough MA, Claridge TDW, Schofield CJ. Oxygenase-Catalyzed Desymmetrization ofN,N-Dialkyl-piperidine-4-carboxylic Acids. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201406125] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
47
|
Tarhonskaya H, Szöllössi A, Leung IKH, Bush JT, Henry L, Chowdhury R, Iqbal A, Claridge TDW, Schofield CJ, Flashman E. Studies on Deacetoxycephalosporin C Synthase Support a Consensus Mechanism for 2-Oxoglutarate Dependent Oxygenases. Biochemistry 2014; 53:2483-93. [DOI: 10.1021/bi500086p] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Hanna Tarhonskaya
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Andrea Szöllössi
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Ivanhoe K. H. Leung
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Jacob T. Bush
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Luc Henry
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Rasheduzzaman Chowdhury
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Aman Iqbal
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Timothy D. W. Claridge
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Christopher J. Schofield
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Emily Flashman
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| |
Collapse
|
48
|
Lingard H, Han JT, Thompson AL, Leung IKH, Scott RTW, Thompson S, Hamilton AD. Cover Picture: Diphenylacetylene-Linked Peptide Strands Induce Bidirectional β-Sheet Formation (Angew. Chem. Int. Ed. 14/2014). Angew Chem Int Ed Engl 2014. [DOI: 10.1002/anie.201401099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
49
|
Lingard H, Han JT, Thompson AL, Leung IKH, Scott RTW, Thompson S, Hamilton AD. Titelbild: Diphenylacetylene-Linked Peptide Strands Induce Bidirectional β-Sheet Formation (Angew. Chem. 14/2014). Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201401099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
50
|
Tarhonskaya H, Rydzik AM, Leung IKH, Loik ND, Chan MC, Kawamura A, McCullagh JSO, Claridge TDW, Flashman E, Schofield CJ. Non-enzymatic chemistry enables 2-hydroxyglutarate-mediated activation of 2-oxoglutarate oxygenases. Nat Commun 2014; 5:3423. [PMID: 24594748 PMCID: PMC3959194 DOI: 10.1038/ncomms4423] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 02/10/2014] [Indexed: 01/08/2023] Open
Abstract
Accumulation of (R)-2-hydroxyglutarate in cells results from mutations to isocitrate dehydrogenase that correlate with cancer. A recent study reports that (R)-, but not (S)-2-hydroxyglutarate, acts as a co-substrate for the hypoxia-inducible factor prolyl hydroxylases via enzyme-catalysed oxidation to 2-oxoglutarate. Here we investigate the mechanism of 2-hydroxyglutarate-enabled activation of 2-oxoglutarate oxygenases, including prolyl hydroxylase domain 2, the most important human prolyl hydroxylase isoform. We observe that 2-hydroxyglutarate-enabled catalysis by prolyl hydroxylase domain 2 is not enantiomer-specific and is stimulated by ferrous/ferric ion and reducing agents including L-ascorbate. The results reveal that 2-hydroxyglutarate is oxidized to 2-oxoglutarate non-enzymatically, likely via iron-mediated Fenton-chemistry, at levels supporting in vitro catalysis by 2-oxoglutarate oxygenases. Succinic semialdehyde and succinate are also identified as products of 2-hydroxyglutarate oxidation. Overall, the results rationalize the reported effects of 2-hydroxyglutarate on catalysis by prolyl hydroxylases in vitro and suggest that non-enzymatic 2-hydroxyglutarate oxidation may be of biological interest.
Collapse
Affiliation(s)
- Hanna Tarhonskaya
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Anna M. Rydzik
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Ivanhoe K. H. Leung
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Nikita D. Loik
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Mun Chiang Chan
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Akane Kawamura
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - James S. O. McCullagh
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Timothy D. W. Claridge
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Emily Flashman
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | | |
Collapse
|