ReviewKeynoteTargeting isocitrate lyase for the treatment of latent tuberculosis
Introduction
Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis 1, 2. M. tuberculosis can live inside the human body for years without causing disease – resulting in a syndrome that is known as latent TB. TB has a latency period that is longer than any other infectious disease 3, 4, 5. It is estimated that at least a quarter of the world’s population is infected by the bacteria [6], of which around 5–15% will develop active TB in their lifetime, a probability that increases dramatically if the infected individual becomes immunocompromised.
The World Health Organisation End TB Strategy aims to reduce the mortality rate by 90% and the incidence rate by 80% by 2030 [7]. Treatment of latent TB infection, especially for people from high-risk groups such as those who are infected by HIV, is a viable strategy to control the disease because M. tuberculosis can only spread from people who have developed active pulmonary TB 8, 9, 10. Current medication regimens used to treat latent TB infection require high patient compliance, which typically involves regular (sometimes daily) intake of antimicrobial drugs for up to 9 months 11, 12. In addition, these drugs can induce severe hepatotoxicity and other unpleasant side effects [13]. The development of more-effective and less toxic drugs to treat latent TB infection is therefore required if the goals set out by the WHO are to be met.
Section snippets
ICL in M. tuberculosis
Isocitrate lyase (ICL) is an Mg2+-dependent enzyme that catalyses the reversible lysis of a CC bond of d-isocitrate to form glyoxylate and succinate (Fig. 1a) [14]. ICL is present in bacteria (including mycobacteria), fungi and plants, but not in humans or animals [15]. In M. tuberculosis there are two known isoforms of ICL: ICL1 and ICL2, which are encoded by the genes icl1 and aceA (also known as icl2), respectively 16, 17. Exceptions can be found in some mycobacterial species including M.
ICL and the glyoxylate cycle
One of the most well-known roles of ICL is its involvement as the first enzyme in the glyoxylate cycle, which was first identified from cell-free extracts of Pseudomonas aeruginosa in 1953 [24]. The glyoxylate cycle is an alternative pathway to the tricarboxylic acid (TCA) cycle (Fig. 2) 25, 26. The early steps of the glyoxylate cycle resemble those in the TCA cycle, in which acetyl-coenzyme A (CoA) is converted into d-isocitrate via citrate and cis-aconitate. The major point of difference
ICL and the methylcitrate cycle
During infection, the pools of carbon that M. tuberculosis can utilise include fatty acids from the host as well as the bacteria’s internal lipid reserves [39]. Although natural animal fatty acids are composed of an even number of carbons, bacteria including mycobacteria possess the ability to synthesise odd-chain fatty acids [40]. However, β-oxidation of odd-chain fatty acids is potentially harmful to the bacteria, because the process generates propionyl CoA and propionate 41, 42, 43, both of
ICL and its potential role in antibiotic tolerance of M. tuberculosis
Recently, ICL was linked to the development of antibiotic resistance in M. tuberculosis. By using metabolomics and gene expression analyses it was demonstrated that ICL was activated when M. tuberculosis was subjected to sublethal doses of three different anti-TB drugs: rifampicin, streptomycin or isoniazid [50]. M. tuberculosis with an icl1 deletion showed a 100-fold increase in sensitivity to these antibiotics [50]. Furthermore, studies that used a M. tuberculosis mutant complemented with a
Structure and catalytic mechanism of ICL
The exact mechanism by which ICL converts isocitrate into glyoxylate and succinate is not fully understood, but a retro Claisen-type condensation pathway has been inferred (Fig. 1b) [52]. The first step involves deprotonation of the isocitrate hydroxyl group followed by fragmentation of the isocitrate to form glyoxylate and succinate 53, 54. Mutagenesis and bioinformatics studies showed that the highly conserved KKCGH sequence motif at the enzyme active site (residues 189–193 in ICL1, also
Inhibitors of ICL
Given the central role ICL has in the glyoxylate and methylisocitrate cycles, ICL is a current inhibition target for antimicrobial applications including (but not limited to) latent TB. However, despite considerable efforts by academia and industry, no compounds have progressed through to the clinical trial stage. There are three major challenges in targeting ICLs: (i) the polar nature of the ICL binding pocket; (ii) the small size of the natural substrates; and (iii) the need to target ICL1
Concluding remarks
ICL is an attractive inhibition target for the treatment of latent TB because it is vital for bacterial survival and, in addition, humans do not possess this enzyme. Existing ICL inhibitors are mimics of the native substrate (or products) that keeps the enzyme in the closed confirmation, as observed in the inhibitor-bound structures of ICL1. The inherent toxicity of these inhibitors is probably caused by their binding to other human enzymes, for example those that take isocitrate or succinate
Acknowledgement
We thank the University of Auckland for a Doctoral Scholarship (R.P.B) and the Maurice and Phyllis Paykel Trust for funding.
Ram Bhusal is carrying out PhD research under the supervision of Dr Ivanhoe Leung and A/Prof. Jonathan Sperry at the University of Auckland. His PhD is focused on the structural, mechanistic and inhibition studies of Mycobacterium tuberculosis isocitrate lyase. Before joining the University of Auckland, he obtained his undergraduate degree in Pharmacy from Pokhara University, Nepal, and his MSc in Medicinal Chemistry from Wonkwang University, South Korea. He also has experience working as a
References (92)
Tuberculosis control and elimination 2010–50: cure, care, and social development
Lancet
(2010)Identification of genes of Mycobacterium tuberculosis upregulated during anaerobic persistence by fluorescence and kanamycin resistance selection
Tuberculosis
(2008)A deviation from the conventional tricarboxylic acid cycle in Pseudomonas aeruginosa
Biochim. Biophys. Acta
(1953)- et al.
Determination of flux through the branch point of two metabolic cycles. The tricarboxylic acid cycle and the glyoxylate shunt
J. Biol. Chem.
(1984) Metabolomics of Mycobacterium tuberculosis reveals compartmentalized co-catabolism of carbon substrates
Chem. Biol.
(2010)Mycobacterium tuberculosis wears what it eats
Cell Host Microbe
(2010)Role of the Mce1 transporter in the lipid homeostasis of Mycobacterium tuberculosis
Tuberculosis
(2014)Intracellular Mycobacterium tuberculosis exploits host-derived fatty acids to limit metabolic stress
J. Biol. Chem.
(2013)- et al.
Odd-numbered very-long-chain fatty acids from the microbial, animal and plant kingdoms
Prog. Lipid Res.
(2009) Cholesterol catabolism by Mycobacterium tuberculosis requires transcriptional and metabolic adaptations
Chem. Biol.
(2012)
Pathway profiling in Mycobacterium tuberculosis: elucidation of cholesterol-derived catabolite and enzymes that catalyze its metabolism
J. Biol. Chem.
Cholesterol plays a larger role during Mycobacterium tuberculosis in vitro dormancy and reactivation than previously suspected
Tuberculosis
Insight into the structural flexibility and function of Mycobacterium tuberculosis isocitrate lyase
Biochimie
Reactivation by a bacteria acetate: enzyme ligase of plant glyoxysomal isocitrate lyase
FEBS Lett.
Succinylome analysis reveals the involvement of lysine succinylation in metabolism in pathogenic Mycobacterium tuberculosis
Mol. Cell. Proteomics
Proteome-wide lysine acetylation profiling of the human pathogen Mycobacterium tuberculosis
Int. J. Biochem. Cell. Biol.
Alkylation of isocitrate lyase from Escherichia coli by 3-bromopyruvate
Arch. Biochem. Biophys.
Pharmacology of itaconic acid and its sodium, magnesium, and calcium salts
J. Am. Pharm. Assoc.
The inhibitory effects of itaconic acid in vitro and in vivo
J. Biol. Chem.
3-Nitropropionic acid exacerbates N-methyl-d-aspartate toxicity in striatal culture by multiple mechanisms
Neuroscience
Advanced cancers: eradication in all cases using 3-bromopyruvate therapy to deplete ATP
Biochem. Biophys. Res. Commun.
High-throughput screening for inhibitors of Mycobacterium tuberculosis H37Rv
Tuberculosis
Identification of a novel inhibitor of isocitrate lyase as a potent antitubercular agent against both active and non-replicating Mycobacterium tuberculosis
Tuberculosis
Synthesis and in vitro antimycobacterial and isocitrate lyase inhibition properties of novel 2-methoxy-2′-hydroxybenzanilides, their thioxo analogues and benzoxazoles
Eur. J. Med. Chem.
Synthesis and in vitro antimycobacterial activity of 2-methoxybenzanilides and their thioxo analogues
Eur. J. Med. Chem.
Salicylanilide derivatives block Mycobacterium tuberculosis through inhibition of isocitrate lyase and methionine aminopeptidase
Tuberculosis
Synthesis and biological activity of new salicylanilide NN-disubstituted carbamates and thiocarbamates
Bioorg. Med. Chem.
Salicylanilide pyrazinoates inhibit in vitro multidrug-resistant Mycobacterium tuberculosis strains, atypical mycobacteria and isocitrate lyase
Eur. J. Pharm. Sci.
Synthesis of various 3-nitropropionamides as Mycobacterium tuberculosis isocitrate lyase inhibitor
Bioorg. Med. Chem. Lett.
5-Nitro-2-furoic acid hydrazones: design, synthesis and in vitro antimycobacterial evaluation against log and starved phase cultures
Bioorg. Med. Chem. Lett.
Novel isatinyl derivatives as potential molecule in the crusade against HIV-TB co-infection
Eur. J. Med. Chem.
Tuberculosis
Nat. Rev. Dis. Primers
Tuberculosis
N. Engl. J. Med.
Understanding latent tuberculosis: a moving target
J. Immunol.
Latent Mycobacterium tuberculosis infection
N. Engl. J. Med.
The ongoing challenge of latent tuberculosis
Phil. Trans. R. Soc. B
The global burden of latent tuberculosis infection: a re-estimation using mathematical modelling
PLoS Med.
Global Tuberculosis Report 2016
Management of latent Mycobacterium tuberculosis infection: WHO guidelines for low tuberculosis burden countries
Eur. Respir. J.
Recent developments in the diagnosis and management of tuberculosis
NPJ Prim. Care Respir. Med
Current management options for latent tuberculosis: a review
Infect. Drug Resist
The use of anti-tuberculosis therapy for latent TB infection
Infect. Drug Resist
An official ATS statement: hepatotoxicity of antituberculosis therapy
Am. J. Respir. Crit. Care Med.
Characterization of activity and expression of isocitrate lyase in Mycobacterium avium and Mycobacterium tuberculosis
J. Bacteriol.
Evolution of glyoxylate cycle enzymes in Metazoa: evidence of multiple horizontal transfer events and pseudogene formation
Biol. Direct
Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
Nature
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Ram Bhusal is carrying out PhD research under the supervision of Dr Ivanhoe Leung and A/Prof. Jonathan Sperry at the University of Auckland. His PhD is focused on the structural, mechanistic and inhibition studies of Mycobacterium tuberculosis isocitrate lyase. Before joining the University of Auckland, he obtained his undergraduate degree in Pharmacy from Pokhara University, Nepal, and his MSc in Medicinal Chemistry from Wonkwang University, South Korea. He also has experience working as a lecturer and pharmacist in his home country, Nepal. His long-term interest is in teaching and research.
Ghader Bashiri received his PhD in structural biology at the University of Auckland in 2009. He is currently a Sir Charles Hercus Fellow, awarded through the Health Research Council of New Zealand. His research investigates proteins of biomedical significance, with a focus on bacterial biochemistry and physiology. As part of the Maurice Wilkins Centre, a national Centre of Research Excellence, he utilises a structure-based drug discovery approach with the ultimate goal of developing a new generation of anti-TB agents.
Jonathan Sperry obtained his BSc (Hons) in biological and medicinal chemistry in 2002 from the University of Exeter, UK. He conducted his PhD under the supervision of Professor Chris Moody at the same institution, before moving to New Zealand where he spent 3.5 years as a postdoctoral researcher with Distinguished Professor Margaret Brimble at the University of Auckland. He took up a lectureship at the same institution in 2009, where he is currently an Associate Professor and a Royal Society of New Zealand Rutherford Discovery Fellow.
Ivanhoe Leung attained his MChem in Chemistry in 2007 from the University of Oxford, UK, as a member of St Peter’s College. He completed a DPhil in the laboratories of Profs Christopher J. Schofield FRS and Timothy D.W. Claridge at the same institution. After his DPhil he spent a further 2 years in the same groups as a postdoctoral research assistant. He joined the School of Chemical Sciences at the University of Auckland in September 2014, where he is currently a senior lecturer. His research focuses on the application of biophysical techniques to a variety of problems in chemistry and biology.