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Izquierdo M, Lin D, O'Neill S, Webster LA, Paterson C, Thomas J, Aguado ME, Colina Araújo E, Alpízar-Pedraza D, Joji H, MacLean L, Hope A, Gray DW, Zoltner M, Field MC, González-Bacerio J, De Rycker M. Identification of a potent and selective LAPTc inhibitor by RapidFire-Mass Spectrometry, with antichagasic activity. PLoS Negl Trop Dis 2024; 18:e0011956. [PMID: 38359089 PMCID: PMC10901353 DOI: 10.1371/journal.pntd.0011956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 02/28/2024] [Accepted: 01/31/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND Chagas disease is caused by the protozoan parasite Trypanosoma cruzi and leads to ~10,000 deaths each year. Nifurtimox and benznidazole are the only two drugs available but have significant adverse effects and limited efficacy. New chemotherapeutic agents are urgently required. Here we identified inhibitors of the acidic M17 leucyl-aminopeptidase from T. cruzi (LAPTc) that show promise as novel starting points for Chagas disease drug discovery. METHODOLOGY/PRINCIPAL FINDINGS A RapidFire-MS screen with a protease-focused compound library identified novel LAPTc inhibitors. Twenty-eight hits were progressed to the dose-response studies, from which 12 molecules inhibited LAPTc with IC50 < 34 μM. Of these, compound 4 was the most potent hit and mode of inhibition studies indicate that compound 4 is a competitive LAPTc inhibitor, with Ki 0.27 μM. Compound 4 is selective with respect to human LAP3, showing a selectivity index of >500. Compound 4 exhibited sub-micromolar activity against intracellular T. cruzi amastigotes, and while the selectivity-window against the host cells was narrow, no toxicity was observed for un-infected HepG2 cells. In silico modelling of the LAPTc-compound 4 interaction is consistent with the competitive mode of inhibition. Molecular dynamics simulations reproduce the experimental binding strength (-8.95 kcal/mol), and indicate a binding mode based mainly on hydrophobic interactions with active site residues without metal cation coordination. CONCLUSIONS/SIGNIFICANCE Our data indicates that these new LAPTc inhibitors should be considered for further development as antiparasitic agents for the treatment of Chagas disease.
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Affiliation(s)
- Maikel Izquierdo
- Centre for Protein Studies, Faculty of Biology, University of Havana, La Habana, Cuba
| | - De Lin
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, United Kingdom
| | - Sandra O'Neill
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, United Kingdom
| | - Lauren A Webster
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, United Kingdom
| | - Christy Paterson
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, United Kingdom
| | - John Thomas
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, United Kingdom
| | - Mirtha Elisa Aguado
- Centre for Protein Studies, Faculty of Biology, University of Havana, La Habana, Cuba
| | - Enrique Colina Araújo
- Department of Biochemistry, Faculty of Biology, University of Havana, La Habana, Cuba
| | | | - Halimatu Joji
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, United Kingdom
| | - Lorna MacLean
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, United Kingdom
| | - Anthony Hope
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, United Kingdom
| | - David W Gray
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, United Kingdom
| | - Martin Zoltner
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
- Department of Parasitology, Faculty of Science, Charles University in Prague, Biocev, Vestec, Czech Republic
| | - Mark C Field
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
- Biology Centre, Czech Academy of Sciences, Institute of Parasitology, České Budějovice, Czech Republic
| | - Jorge González-Bacerio
- Centre for Protein Studies, Faculty of Biology, University of Havana, La Habana, Cuba
- Department of Biochemistry, Faculty of Biology, University of Havana, La Habana, Cuba
| | - Manu De Rycker
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, United Kingdom
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Aguado ME, Izquierdo M, González-Matos M, Varela AC, Méndez Y, Del Rivero MA, Rivera DG, González-Bacerio J. Parasite Metalo-aminopeptidases as Targets in Human Infectious Diseases. Curr Drug Targets 2023; 24:416-461. [PMID: 36825701 DOI: 10.2174/1389450124666230224140724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/25/2022] [Accepted: 01/02/2023] [Indexed: 02/25/2023]
Abstract
BACKGROUND Parasitic human infectious diseases are a worldwide health problem due to the increased resistance to conventional drugs. For this reason, the identification of novel molecular targets and the discovery of new chemotherapeutic agents are urgently required. Metalo- aminopeptidases are promising targets in parasitic infections. They participate in crucial processes for parasite growth and pathogenesis. OBJECTIVE In this review, we describe the structural, functional and kinetic properties, and inhibitors, of several parasite metalo-aminopeptidases, for their use as targets in parasitic diseases. CONCLUSION Plasmodium falciparum M1 and M17 aminopeptidases are essential enzymes for parasite development, and M18 aminopeptidase could be involved in hemoglobin digestion and erythrocyte invasion and egression. Trypanosoma cruzi, T. brucei and Leishmania major acidic M17 aminopeptidases can play a nutritional role. T. brucei basic M17 aminopeptidase down-regulation delays the cytokinesis. The inhibition of Leishmania basic M17 aminopeptidase could affect parasite viability. L. donovani methionyl aminopeptidase inhibition prevents apoptosis but not the parasite death. Decrease in Acanthamoeba castellanii M17 aminopeptidase activity produces cell wall structural modifications and encystation inhibition. Inhibition of Babesia bovis growth is probably related to the inhibition of the parasite M17 aminopeptidase, probably involved in host hemoglobin degradation. Schistosoma mansoni M17 aminopeptidases inhibition may affect parasite development, since they could participate in hemoglobin degradation, surface membrane remodeling and eggs hatching. Toxoplasma gondii M17 aminopeptidase inhibition could attenuate parasite virulence, since it is apparently involved in the hydrolysis of cathepsin Cs- or proteasome-produced dipeptides and/or cell attachment/invasion processes. These data are relevant to validate these enzymes as targets.
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Affiliation(s)
- Mirtha E Aguado
- Center for Protein Studies, Faculty of Biology, University of Havana, Calle 25 #455 Entre I y J, 10400, Vedado, La Habana, Cuba
| | - Maikel Izquierdo
- Center for Protein Studies, Faculty of Biology, University of Havana, Calle 25 #455 Entre I y J, 10400, Vedado, La Habana, Cuba
| | - Maikel González-Matos
- Center for Protein Studies, Faculty of Biology, University of Havana, Calle 25 #455 Entre I y J, 10400, Vedado, La Habana, Cuba
| | - Ana C Varela
- Center for Protein Studies, Faculty of Biology, University of Havana, Calle 25 #455 Entre I y J, 10400, Vedado, La Habana, Cuba
| | - Yanira Méndez
- Center for Natural Products Research, Faculty of Chemistry, University of Havana, Zapata y G, 10400, La Habana, Cuba
| | - Maday A Del Rivero
- Center for Protein Studies, Faculty of Biology, University of Havana, Calle 25 #455 Entre I y J, 10400, Vedado, La Habana, Cuba
| | - Daniel G Rivera
- Center for Natural Products Research, Faculty of Chemistry, University of Havana, Zapata y G, 10400, La Habana, Cuba
| | - Jorge González-Bacerio
- Center for Protein Studies, Faculty of Biology, University of Havana, Calle 25 #455 Entre I y J, 10400, Vedado, La Habana, Cuba
- Department of Biochemistry, Faculty of Biology, University of Havana, calle 25 #455 entre I y J, 10400, Vedado, La Habana, Cuba
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KBE009: A Bestatin-Like Inhibitor of the Trypanosoma cruzi Acidic M17 Aminopeptidase with In Vitro Anti-Trypanosomal Activity. Life (Basel) 2021; 11:life11101037. [PMID: 34685408 PMCID: PMC8540442 DOI: 10.3390/life11101037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 09/21/2021] [Accepted: 09/28/2021] [Indexed: 11/17/2022] Open
Abstract
Chagas disease, caused by the kinetoplastid parasite Trypanosoma cruzi, is a human tropical illness mainly present in Latin America. The therapies available against this disease are far from ideal. Proteases from pathogenic protozoan have been considered as good drug target candidates. T. cruzi acidic M17 leucyl-aminopeptidase (TcLAP) mediates the major parasite’s leucyl-aminopeptidase activity and is expressed in all parasite stages. Here, we report the inhibition of TcLAP (IC50 = 66.0 ± 13.5 µM) by the bestatin-like peptidomimetic KBE009. This molecule also inhibited the proliferation of T. cruzi epimastigotes in vitro (EC50 = 28.1 ± 1.9 µM) and showed selectivity for the parasite over human dermal fibroblasts (selectivity index: 4.9). Further insight into the specific effect of KBE009 on T. cruzi was provided by docking simulation using the crystal structure of TcLAP and a modeled human orthologous, hLAP3. The TcLAP-KBE009 complex is more stable than its hLAP3 counterpart. KBE009 adopted a better geometrical shape to fit into the active site of TcLAP than that of hLAP3. The drug-likeness and lead-likeness in silico parameters of KBE009 are satisfactory. Altogether, our results provide an initial insight into KBE009 as a promising starting point compound for the rational design of drugs through further optimization.
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Aguado ME, González-Matos M, Izquierdo M, Quintana J, Field MC, González-Bacerio J. Expression in Escherichia coli, purification and kinetic characterization of LAPLm, a Leishmania major M17-aminopeptidase. Protein Expr Purif 2021; 183:105877. [PMID: 33775769 DOI: 10.1016/j.pep.2021.105877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 12/21/2022]
Abstract
The Leishmania major leucyl-aminopeptidase (LAPLm), a member of the M17 family of proteases, is a potential drug target for treatment of leishmaniasis. To better characterize enzyme properties, recombinant LAPLm (rLAPLm) was expressed in Escherichia coli. A LAPLm gene was designed, codon-optimized for expression in E. coli, synthesized and cloned into the pET-15b vector. Production of rLAPLm in E. coli Lemo21(DE3), induced for 4 h at 37 °C with 400 μM IPTG and 250 μM l-rhamnose, yielded insoluble enzyme with a low proportion of soluble and active protein, only detected by an anti-His antibody-based western-blot. rLAPLm was purified in a single step by immobilized metal ion affinity chromatography. rLAPLm was obtained with a purity of ~10% and a volumetric yield of 2.5 mg per liter, sufficient for further characterization. The aminopeptidase exhibits optimal activity at pH 7.0 and a substrate preference for Leu-p-nitroanilide (appKM = 30 μM, appkcat = 14.7 s-1). Optimal temperature is 50 °C, and the enzyme is insensitive to 4 mM Co2+, Mg2+, Ca2+ and Ba2+. However, rLAPLm was activated by Zn2+, Mn2+ and Cd2+ but is insensitive towards the protease inhibitors PMSF, TLCK, E-64 and pepstatin A, being inhibited by EDTA and bestatin. Bestatin is a potent, non-competitive inhibitor of the enzyme with a Ki value of 994 nM. We suggest that rLAPLm is a suitable target for inhibitor identification.
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Affiliation(s)
- Mirtha Elisa Aguado
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana, Calle 25 #455 Entre I y J, Vedado, 10400, Havana, Cuba.
| | - Maikel González-Matos
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana, Calle 25 #455 Entre I y J, Vedado, 10400, Havana, Cuba.
| | - Maikel Izquierdo
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana, Calle 25 #455 Entre I y J, Vedado, 10400, Havana, Cuba.
| | - Juan Quintana
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, DD1 5EH, Dundee, Scotland, UK.
| | - Mark C Field
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, DD1 5EH, Dundee, Scotland, UK; Institute of Parasitology, Czech Academy of Sciences, 37005, Ceske Budejovice, Czech Republic.
| | - Jorge González-Bacerio
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana, Calle 25 #455 Entre I y J, Vedado, 10400, Havana, Cuba.
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Izquierdo M, Lin D, O'Neill S, Zoltner M, Webster L, Hope A, Gray DW, Field MC, González-Bacerio J. Development of a High-Throughput Screening Assay to Identify Inhibitors of the Major M17-Leucyl Aminopeptidase from Trypanosoma cruzi Using RapidFire Mass Spectrometry. SLAS DISCOVERY 2020; 25:1064-1071. [PMID: 32400260 DOI: 10.1177/2472555220923367] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Leucyl aminopeptidases (LAPs) are involved in multiple cellular functions, which, in the case of infectious diseases, includes participation in the pathogen-host cell interface and pathogenesis. Thus, LAPs are considered good candidate drug targets, and the major M17-LAP from Trypanosoma cruzi (LAPTc) in particular is a promising target for Chagas disease. To exploit LAPTc as a potential target, it is essential to develop potent and selective inhibitors. To achieve this, we report a high-throughput screening method for LAPTc. Two methods were developed and optimized: a Leu-7-amido-4-methylcoumarin-based fluorogenic assay and a RapidFire mass spectrometry (RapidFire MS)-based assay using the LSTVIVR peptide as substrate. Compared with a fluorescence assay, the major advantages of the RapidFire MS assay are a greater signal-to-noise ratio as well as decreased consumption of enzyme. RapidFire MS was validated with the broad-spectrum LAP inhibitors bestatin (IC50 = 0.35 μM) and arphamenine A (IC50 = 15.75 μM). We suggest that RapidFire MS is highly suitable for screening for specific LAPTc inhibitors.
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Affiliation(s)
- Maikel Izquierdo
- Centre for Protein Studies, Faculty of Biology, University of Havana, La Habana, Cuba
| | - De Lin
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | - Sandra O'Neill
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | - Martin Zoltner
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK.,Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Lauren Webster
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | - Anthony Hope
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | - David W Gray
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | - Mark C Field
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Jorge González-Bacerio
- Centre for Protein Studies, Faculty of Biology, University of Havana, La Habana, Cuba.,Department of Biochemistry, Faculty of Biology, University of Havana, La Habana, Cuba
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High-Level Expression in Escherichia coli, Purification and Kinetic Characterization of LAPTc, a Trypanosoma cruzi M17-Aminopeptidase. Protein J 2019; 38:167-180. [DOI: 10.1007/s10930-019-09823-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Structural Characterization of Acidic M17 Leucine Aminopeptidases from the TriTryps and Evaluation of Their Role in Nutrient Starvation in Trypanosoma brucei. mSphere 2017; 2:mSphere00226-17. [PMID: 28815215 PMCID: PMC5557676 DOI: 10.1128/msphere.00226-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 07/24/2017] [Indexed: 11/20/2022] Open
Abstract
Leucine aminopeptidases (LAPs) catalyze the hydrolysis of the N-terminal amino acid of peptides and are considered potential drug targets. They are involved in multiple functions ranging from host cell invasion and provision of essential amino acids to site-specific homologous recombination and transcription regulation. In kinetoplastid parasites, there are at least three distinct LAPs. The availability of the crystal structures provides important information for drug design. Here we report the structure of the acidic LAPs from three kinetoplastids in complex with different inhibitors and explore their role in Trypanosoma brucei survival under various nutrient conditions. Importantly, the acidic LAP is dispensable for growth both in vitro and in vivo, an observation that questions its use as a specific drug target. While LAP-A is not essential, leucine depletion and subcellular localization studies performed under starvation conditions suggest a possible function of LAP-A in the response to nutrient restriction. Leucine aminopeptidase (LAP) is found in all kingdoms of life and catalyzes the metal-dependent hydrolysis of the N-terminal amino acid residue of peptide or amino acyl substrates. LAPs have been shown to participate in the N-terminal processing of certain proteins in mammalian cells and in homologous recombination and transcription regulation in bacteria, while in parasites, they are involved in host cell invasion and provision of essential amino acids for growth. The enzyme is essential for survival in Plasmodium falciparum, where its drug target potential has been suggested. We report here the X-ray structures of three kinetoplastid acidic LAPs (LAP-As from Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major) which were solved in the metal-free and unliganded forms, as well as in a number of ligand complexes, providing insight into ligand binding, metal ion requirements, and oligomeric state. In addition, we analyzed mutant cells defective in LAP-A in Trypanosoma brucei, strongly suggesting that the enzyme is not required for the growth of this parasite either in vitro or in vivo. In procyclic cells, LAP-A was equally distributed throughout the cytoplasm, yet upon starvation, it relocalizes in particles that concentrate in the perinuclear region. Overexpression of the enzyme conferred a growth advantage when parasites were grown in leucine-deficient medium. Overall, the results suggest that in T. brucei, LAP-A may participate in protein degradation associated with nutrient depletion. IMPORTANCE Leucine aminopeptidases (LAPs) catalyze the hydrolysis of the N-terminal amino acid of peptides and are considered potential drug targets. They are involved in multiple functions ranging from host cell invasion and provision of essential amino acids to site-specific homologous recombination and transcription regulation. In kinetoplastid parasites, there are at least three distinct LAPs. The availability of the crystal structures provides important information for drug design. Here we report the structure of the acidic LAPs from three kinetoplastids in complex with different inhibitors and explore their role in Trypanosoma brucei survival under various nutrient conditions. Importantly, the acidic LAP is dispensable for growth both in vitro and in vivo, an observation that questions its use as a specific drug target. While LAP-A is not essential, leucine depletion and subcellular localization studies performed under starvation conditions suggest a possible function of LAP-A in the response to nutrient restriction.
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