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Edgar RCS, Malcolm TR, Siddiqui G, Giannangelo C, Counihan NA, Challis M, Duffy S, Chowdhury M, Marfurt J, Dans M, Wirjanata G, Noviyanti R, Daware K, Suraweera CD, Price RN, Wittlin S, Avery VM, Drinkwater N, Charman SA, Creek DJ, de Koning-Ward TF, Scammells PJ, McGowan S. On-target, dual aminopeptidase inhibition provides cross-species antimalarial activity. mBio 2024; 15:e0096624. [PMID: 38717141 DOI: 10.1128/mbio.00966-24] [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: 03/31/2024] [Accepted: 04/08/2024] [Indexed: 06/13/2024] Open
Abstract
To combat the global burden of malaria, development of new drugs to replace or complement current therapies is urgently required. Here, we show that the compound MMV1557817 is a selective, nanomolar inhibitor of both Plasmodium falciparum and Plasmodium vivax aminopeptidases M1 and M17, leading to inhibition of end-stage hemoglobin digestion in asexual parasites. MMV1557817 can kill sexual-stage P. falciparum, is active against murine malaria, and does not show any shift in activity against a panel of parasites resistant to other antimalarials. MMV1557817-resistant P. falciparum exhibited a slow growth rate that was quickly outcompeted by wild-type parasites and were sensitized to the current clinical drug, artemisinin. Overall, these results confirm MMV1557817 as a lead compound for further drug development and highlights the potential of dual inhibition of M1 and M17 as an effective multi-species drug-targeting strategy.IMPORTANCEEach year, malaria infects approximately 240 million people and causes over 600,000 deaths, mostly in children under 5 years of age. For the past decade, artemisinin-based combination therapies have been recommended by the World Health Organization as the standard malaria treatment worldwide. Their widespread use has led to the development of artemisinin resistance in the form of delayed parasite clearance, alongside the rise of partner drug resistance. There is an urgent need to develop and deploy new antimalarial agents with novel targets and mechanisms of action. Here, we report a new and potent antimalarial compound, known as MMV1557817, and show that it targets multiple stages of the malaria parasite lifecycle, is active in a preliminary mouse malaria model, and has a novel mechanism of action. Excitingly, resistance to MMV15578117 appears to be self-limiting, suggesting that development of the compound may provide a new class of antimalarial.
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Affiliation(s)
- Rebecca C S Edgar
- School of Medicine, Deakin University, Geelong, Australia
- The Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, Australia
| | - Tess R Malcolm
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Ghizal Siddiqui
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Carlo Giannangelo
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Natalie A Counihan
- School of Medicine, Deakin University, Geelong, Australia
- The Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, Australia
| | - Matthew Challis
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Sandra Duffy
- Discovery Biology, Centre for Cellular Phenomics, Griffith University, Nathan, Queensland, Australia
| | - Mrittika Chowdhury
- School of Medicine, Deakin University, Geelong, Australia
- The Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, Australia
| | - Jutta Marfurt
- Global Health and Tropical Medicine Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Madeline Dans
- School of Medicine, Deakin University, Geelong, Australia
- The Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, Australia
| | - Grennady Wirjanata
- Global Health and Tropical Medicine Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | | | - Kajal Daware
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Chathura D Suraweera
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Ric N Price
- Global Health and Tropical Medicine Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Vicky M Avery
- School of Environment and Science, Griffith Sciences, Griffith University, Nathan, Queensland, Australia
| | - Nyssa Drinkwater
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Susan A Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Darren J Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Tania F de Koning-Ward
- School of Medicine, Deakin University, Geelong, Australia
- The Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, Australia
| | - Peter J Scammells
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Sheena McGowan
- Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
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Creek D, Giannangelo C, Challis M, Siddiqui G, Edgar R, Malcolm T, Webb C, Drinkwater N, Vinh N, MacRaild C, Counihan N, Duffy S, Wittlin S, Devine S, Avery V, de Koning-Ward T, Scammells P, McGowan S. Chemoproteomics validates selective targeting of Plasmodium M1 alanyl aminopeptidase as an antimalarial strategy. RESEARCH SQUARE 2024:rs.3.rs-3251230. [PMID: 38746424 PMCID: PMC11092810 DOI: 10.21203/rs.3.rs-3251230/v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
New antimalarial drug candidates that act via novel mechanisms are urgently needed to combat malaria drug resistance. Here, we describe the multi-omic chemical validation of Plasmodium M1 alanyl metalloaminopeptidase as an attractive drug target using the selective inhibitor, MIPS2673. MIPS2673 demonstrated potent inhibition of recombinant Plasmodium falciparum ( Pf A-M1) and Plasmodium vivax ( Pv A-M1) M1 metalloaminopeptidases, with selectivity over other Plasmodium and human aminopeptidases, and displayed excellent in vitro antimalarial activity with no significant host cytotoxicity. Orthogonal label-free chemoproteomic methods based on thermal stability and limited proteolysis of whole parasite lysates revealed that MIPS2673 solely targets Pf A-M1 in parasites, with limited proteolysis also enabling estimation of the binding site on Pf A-M1 to within ~5 Å of that determined by X-ray crystallography. Finally, functional investigation by untargeted metabolomics demonstrated that MIPS2673 inhibits the key role of Pf A-M1 in haemoglobin digestion. Combined, our unbiased multi-omic target deconvolution methods confirmed the on-target activity of MIPS2673, and validated selective inhibition of M1 alanyl metalloaminopeptidase as a promising antimalarial strategy.
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Ouali R, Bousbata S. Unveiling the Peptidase Network Orchestrating Hemoglobin Catabolism in Rhodnius prolixus. Mol Cell Proteomics 2024; 23:100775. [PMID: 38663568 PMCID: PMC11135036 DOI: 10.1016/j.mcpro.2024.100775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/29/2024] [Accepted: 04/21/2024] [Indexed: 05/23/2024] Open
Abstract
Chagas disease is transmitted to humans by obligatory hematophagous insects of Triatominae subfamily, which feeds on various hosts to acquire their nutritional sustenance derived from blood proteins. Hemoglobin (Hb) digestion is a pivotal metabolic feature of triatomines, representing a key juncture in their competence toward Trypanosoma cruzi; however, it remains poorly understood. To explore the Hb digestion pathway in Rhodnius prolixus, a major Chagas disease vector, we employed an array of approaches for activity profiling of various midgut-associated peptidases using specific substrates and inhibitors. Dissecting the individual contribution of each peptidase family in Hb digestion has unveiled a predominant role played by aspartic proteases and cathepsin B-like peptidases. Determination of peptidase-specific cleavage sites of these key hemoglobinases, in conjunction with mass spectrometry-based identification of in vivo Hb-derived fragments, has revealed the intricate network of peptidases involved in the Hb digestion pathway. This network is initiated by aspartic proteases and subsequently sustained by cysteine proteases belonging to the C1 family. The process is continued simultaneously by amino and carboxypeptidases. The comprehensive profiling of midgut-associated aspartic proteases by quantitative proteomics has enabled the accurate revision of gene annotations within the A1 family of the R. prolixus genome. Significantly, this study also serves to illuminate a potentially important role of the anterior midgut in blood digestion. The expanded repertoire of midgut-associated proteases presented in this study holds promise for the identification of novel targets aimed at controlling the transmission of Chagas disease.
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Affiliation(s)
- Radouane Ouali
- Laboratory of Vector-Pathogen Biology, Proteomic Platform, Department of Molecular Biology, Université Libre de Bruxelles, Gosselies, Belgium.
| | - Sabrina Bousbata
- Laboratory of Vector-Pathogen Biology, Proteomic Platform, Department of Molecular Biology, Université Libre de Bruxelles, Gosselies, Belgium.
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Goettig P, Koch NG, Budisa N. Non-Canonical Amino Acids in Analyses of Protease Structure and Function. Int J Mol Sci 2023; 24:14035. [PMID: 37762340 PMCID: PMC10531186 DOI: 10.3390/ijms241814035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/18/2023] [Accepted: 08/20/2023] [Indexed: 09/29/2023] Open
Abstract
All known organisms encode 20 canonical amino acids by base triplets in the genetic code. The cellular translational machinery produces proteins consisting mainly of these amino acids. Several hundred natural amino acids serve important functions in metabolism, as scaffold molecules, and in signal transduction. New side chains are generated mainly by post-translational modifications, while others have altered backbones, such as the β- or γ-amino acids, or they undergo stereochemical inversion, e.g., in the case of D-amino acids. In addition, the number of non-canonical amino acids has further increased by chemical syntheses. Since many of these non-canonical amino acids confer resistance to proteolytic degradation, they are potential protease inhibitors and tools for specificity profiling studies in substrate optimization and enzyme inhibition. Other applications include in vitro and in vivo studies of enzyme kinetics, molecular interactions and bioimaging, to name a few. Amino acids with bio-orthogonal labels are particularly attractive, enabling various cross-link and click reactions for structure-functional studies. Here, we cover the latest developments in protease research with non-canonical amino acids, which opens up a great potential, e.g., for novel prodrugs activated by proteases or for other pharmaceutical compounds, some of which have already reached the clinical trial stage.
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Affiliation(s)
- Peter Goettig
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, Strubergasse 21, 5020 Salzburg, Austria
| | - Nikolaj G. Koch
- Biocatalysis Group, Technische Universität Berlin, 10623 Berlin, Germany;
- Bioanalytics Group, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany;
| | - Nediljko Budisa
- Bioanalytics Group, Institute of Biotechnology, Technische Universität Berlin, 10623 Berlin, Germany;
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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Structure-based development of potent Plasmodium falciparum M1 and M17 aminopeptidase selective and dual inhibitors via S1'-region optimisation. Eur J Med Chem 2023; 248:115051. [PMID: 36634455 DOI: 10.1016/j.ejmech.2022.115051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/13/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022]
Abstract
Malaria remains a global health threat and growing resistance to artemisinin-based therapies calls for therapeutic agents with novel mechanisms of action. The Plasmodium spp M1 and M17 metalloaminopeptidases have been identified as attractive new antimalarial drug targets as inhibition of these enzymes results in antiplasmodial activity. Previously identified novel hydroxamic acid 2 as a moderate inhibitor of PfA-M1 and PfA-M17 and a potent inhibitor of P. falciparum. This study has sought to improve the enzymatic inhibitory properties in addition to increasing the drug-likeness of this scaffold by introducing polar moieties into the S1' region of the active site. Structural biology studies on the co-crystallised structures of potent dual-inhibitor 9aa bound to PfA-M1 and PfA-M17 have revealed that there are few direct interactions between the inhibitor and the S1' domain of these enzymes. Structure-based compound design led to the identification of a variety of novel hydroxamic acids that show improved inhibitory activity against PfA-M1 and PfA-M17, in addition to displaying antiplasmodial activity. Notably, compounds with substitutions on the aniline ring resulted in a loss of potency (Ki > 500 nM) toward PfA-M1 and PfA-M17. ioisosteric replacement of the S1-region biaryl ring system with a bromophenyl moiety resulted in increased potency compared to parent 9aa. Elaboration of 9aa to bioisosterically replace the S1 moiety with an aryl bromide, combined with substituted anilines has resulted in potent selective PfA-M1 inhibitors which show strong activity against Pf-3D7, with meta- and para-fluoroaniline groups of 15ag and 15ah forming hydrogen-bonds with residues within the active site. These findings establish the importance of the previously under-utilised S1' domain and will aid the design of future PfA-M1 and PfA-M17 inhibitors.
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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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Edgar RCS, Siddiqui G, Hjerrild K, Malcolm TR, Vinh NB, Webb CT, Holmes C, MacRaild CA, Chernih HC, Suen WW, Counihan NA, Creek DJ, Scammells PJ, McGowan S, de Koning-Ward TF. Genetic and chemical validation of Plasmodium falciparum aminopeptidase PfA-M17 as a drug target in the hemoglobin digestion pathway. eLife 2022; 11:80813. [PMID: 36097817 PMCID: PMC9470162 DOI: 10.7554/elife.80813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/02/2022] [Indexed: 11/18/2022] Open
Abstract
Plasmodium falciparum, the causative agent of malaria, remains a global health threat as parasites continue to develop resistance to antimalarial drugs used throughout the world. Accordingly, drugs with novel modes of action are desperately required to combat malaria. P. falciparum parasites infect human red blood cells where they digest the host’s main protein constituent, hemoglobin. Leucine aminopeptidase PfA-M17 is one of several aminopeptidases that have been implicated in the last step of this digestive pathway. Here, we use both reverse genetics and a compound specifically designed to inhibit the activity of PfA-M17 to show that PfA-M17 is essential for P. falciparum survival as it provides parasites with free amino acids for growth, many of which are highly likely to originate from hemoglobin. We further show that loss of PfA-M17 results in parasites exhibiting multiple digestive vacuoles at the trophozoite stage. In contrast to other hemoglobin-degrading proteases that have overlapping redundant functions, we validate PfA-M17 as a potential novel drug target. Malaria is a disease spread by mosquitoes. When infected insects bite the skin, they inject parasites called Plasmodium into the host. The symptoms of the disease then develop when Plasmodium infect host red blood cells. These parasites cannot make the raw materials to build their own proteins, so instead, they digest haemoglobin – the protein used by red blood cells to carry oxygen – and use its building blocks to produce proteins. Blocking the digestion of haemoglobin can stop malaria infections in their tracks, but it is unclear how exactly Plasmodium parasites break down the protein. Researchers think that a group of four enzymes called aminopeptidases are responsible for the final stage in this digestion, releasing the amino acids that make up haemoglobin. However, the individual roles of each of these aminopeptidases are not yet known. To start filling this gap, Edgar et al. set out to study one of these aminopeptidases, called PfA-M17. First, they genetically modified Plasmodium falciparum parasites so that the levels of this aminopeptidase were reduced during infection. Without the enzyme, the parasites were unable to grow. The next step was to confirm that this was because PfA-M17 breaks down haemoglobin, and not for another reason. To test this, Edgar et al. designed a new molecule that could stop PfA-M17 from releasing amino acids. This molecule, which they called ‘compound 3’, had the same effect as reducing the levels of PfA-M17. Further analysis showed that the amino acids that PfA- M17 releases match the amino acids found in haemoglobin. Malaria causes hundreds of thousands of deaths per year. Although there are treatments available, the Plasmodium parasites are starting to develop resistance. Confirming the role of PfA-M17 provides a starting point for new studies by parasitologists, biologists, and drug developers. This could lead to the development of chemicals that block this enzyme, forming the basis for new treatments.
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Affiliation(s)
- Rebecca C S Edgar
- School of Medicine, Deakin University, Geelong, Australia.,The Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, Australia
| | - Ghizal Siddiqui
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | | | - Tess R Malcolm
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia.,Centre to Impact AMR, Monash University, Melbourne, Australia
| | - Natalie B Vinh
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Chaille T Webb
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia.,Centre to Impact AMR, Monash University, Melbourne, Australia
| | - Clare Holmes
- CSIRO Australian Centre for Disease Preparedness, Geelong, Australia
| | - Christopher A MacRaild
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Hope C Chernih
- School of Medicine, Deakin University, Geelong, Australia.,The Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, Australia
| | - Willy W Suen
- CSIRO Australian Centre for Disease Preparedness, Geelong, Australia
| | - Natalie A Counihan
- School of Medicine, Deakin University, Geelong, Australia.,The Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, Australia
| | - Darren J Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Peter J Scammells
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Sheena McGowan
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia.,Centre to Impact AMR, Monash University, Melbourne, Australia
| | - Tania F de Koning-Ward
- School of Medicine, Deakin University, Geelong, Australia.,The Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, Australia
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Bąchor R. Peptidyl-Resin Substrates as a Tool in the Analysis of Caspase Activity. Molecules 2022; 27:molecules27134107. [PMID: 35807352 PMCID: PMC9268085 DOI: 10.3390/molecules27134107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 02/04/2023] Open
Abstract
Caspases, proteolytic enzymes belonging to the group of cysteine proteases, play a crucial role in apoptosis. Understanding their activity and substrate specificity is extremely important. Fluorescence-based approaches, including fluorogenic substrates, are generally used to confirm cleavage preferences. Here we present a new method of substrate specificity and activity analysis based on the application of fix-charge tagged peptides located on the resin. The proteolysis of peptide bond on the resin, occurring even with low efficiency, results in the formation of N-terminal fragments of model peptide containing ionization enhancers in the form of quaternary ammonium groups, allowing for ultrasensitive and reliable analysis by LC-MS/MS. The possibility of application of the proposed solution was tested through the analysis of substrate specificity and activity of caspase 3 or 7. The obtained results confirm the known substrate specificity of executioner caspases. Our solution also allowed us to observe that caspases can hydrolyze peptides shorter than those presented to date in the scientific literature.
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Affiliation(s)
- Remigiusz Bąchor
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wrocław, Poland
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9
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Edgar RCS, Counihan NA, McGowan S, de Koning-Ward TF. Methods Used to Investigate the Plasmodium falciparum Digestive Vacuole. Front Cell Infect Microbiol 2022; 11:829823. [PMID: 35096663 PMCID: PMC8794586 DOI: 10.3389/fcimb.2021.829823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 12/22/2021] [Indexed: 11/13/2022] Open
Abstract
Plasmodium falciparum malaria remains a global health problem as parasites continue to develop resistance to all antimalarials in use. Infection causes clinical symptoms during the intra-erythrocytic stage of the lifecycle where the parasite infects and replicates within red blood cells (RBC). During this stage, P. falciparum digests the main constituent of the RBC, hemoglobin, in a specialized acidic compartment termed the digestive vacuole (DV), a process essential for survival. Many therapeutics in use target one or multiple aspects of the DV, with chloroquine and its derivatives, as well as artemisinin, having mechanisms of action within this organelle. In order to better understand how current therapeutics and those under development target DV processes, techniques used to investigate the DV are paramount. This review outlines the involvement of the DV in therapeutics currently in use and focuses on the range of techniques that are currently utilized to study this organelle including microscopy, biochemical analysis, genetic approaches and metabolomic studies. Importantly, continued development and application of these techniques will aid in our understanding of the DV and in the development of new therapeutics or therapeutic partners for the future.
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Affiliation(s)
- Rebecca C. S. Edgar
- School of Medicine, Deakin University, Geelong, VIC, Australia
- The Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC, Australia
| | - Natalie A. Counihan
- School of Medicine, Deakin University, Geelong, VIC, Australia
- The Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC, Australia
| | - Sheena McGowan
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia
- Centre to Impact AMR, Monash University, Monash University, Clayton, VIC, Australia
| | - Tania F. de Koning-Ward
- School of Medicine, Deakin University, Geelong, VIC, Australia
- The Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC, Australia
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10
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Veni, Vidi, Vici: Immobilized Peptide-Based Conjugates as Tools for Capture, Analysis, and Transformation. CHEMOSENSORS 2022. [DOI: 10.3390/chemosensors10010031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Analysis of peptide biomarkers of pathological states of the organism is often a serious challenge, due to a very complex composition of the cell and insufficient sensitivity of the current analytical methods (including mass spectrometry). One of the possible ways to overcome this problem is sample enrichment by capturing the selected components using a specific solid support. Another option is increasing the detectability of the desired compound by its selective tagging. Appropriately modified and immobilized peptides can be used for these purposes. In addition, they find application in studying the specificity and activity of proteolytic enzymes. Immobilized heterocyclic peptide conjugates may serve as metal ligands, to form complexes used as catalysts or analytical markers. In this review, we describe various applications of immobilized peptides, including selective capturing of cysteine-containing peptides, tagging of the carbonyl compounds to increase the sensitivity of their detection, enrichment of biological samples in deoxyfructosylated peptides, and fishing out of tyrosine–containing peptides by the formation of azo bond. Moreover, the use of the one-bead-one-compound peptide library for the analysis of substrate specificity and activity of caspases is described. Furthermore, the evolution of immobilization from the solid support used in peptide synthesis to nanocarriers is presented. Taken together, the examples presented here demonstrate immobilized peptides as a multifunctional tool, which can be successfully used to solve multiple analytical problems.
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Hoff CC, Azevedo MF, Thurler AB, Maluf SEC, Melo PMS, del Rivero MA, González-Bacerio J, Carmona AK, Budu A, Gazarini ML. Overexpression of Plasmodium falciparum M1 Aminopeptidase Promotes an Increase in Intracellular Proteolysis and Modifies the Asexual Erythrocytic Cycle Development. Pathogens 2021; 10:pathogens10111452. [PMID: 34832608 PMCID: PMC8618464 DOI: 10.3390/pathogens10111452] [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: 09/11/2021] [Revised: 11/05/2021] [Accepted: 11/06/2021] [Indexed: 11/16/2022] Open
Abstract
Plasmodium falciparum, the most virulent of the human malaria parasite, is responsible for high mortality rates worldwide. We studied the M1 alanyl-aminopeptidase of this protozoan (PfA-M1), which is involved in the final stages of hemoglobin cleavage, an essential process for parasite survival. Aiming to help in the rational development of drugs against this target, we developed a new strain of P. falciparum overexpressing PfA-M1 without the signal peptide (overPfA-M1). The overPfA-M1 parasites showed a 2.5-fold increase in proteolytic activity toward the fluorogenic substrate alanyl-7-amido-4-methylcoumarin, in relation to the wild-type group. Inhibition studies showed that overPfA-M1 presented a lower sensitivity against the metalloaminopeptidase inhibitor bestatin and to other recombinant PfA-M1 inhibitors, in comparison with the wild-type strain, indicating that PfA-M1 is a target for the in vitro antimalarial activity of these compounds. Moreover, overPfA-M1 parasites present a decreased in vitro growth, showing a reduced number of merozoites per schizont, and also a decrease in the iRBC area occupied by the parasite in trophozoite and schizont forms when compared to the controls. Interestingly, the transgenic parasite displays an increase in the aminopeptidase activity toward Met-, Ala-, Leu- and Arg-7-amido-4-methylcoumarin. We also investigated the potential role of calmodulin and cysteine proteases in PfA-M1 activity. Taken together, our data show that the overexpression of PfA-M1 in the parasite cytosol can be a suitable tool for the screening of antimalarials in specific high-throughput assays and may be used for the identification of intracellular molecular partners that modulate their activity in P. falciparum.
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Affiliation(s)
- Carolina C. Hoff
- Department of Biosciences, Federal University of São Paulo, Santos 11015-020, Brazil; (C.C.H.); (M.F.A.)
| | - Mauro F. Azevedo
- Department of Biosciences, Federal University of São Paulo, Santos 11015-020, Brazil; (C.C.H.); (M.F.A.)
| | - Adriana B. Thurler
- Department of Biophysics, Federal University of São Paulo, São Paulo 04039-032, Brazil; (A.B.T.); (S.E.C.M.); (P.M.S.M.); (A.K.C.)
| | - Sarah El Chamy Maluf
- Department of Biophysics, Federal University of São Paulo, São Paulo 04039-032, Brazil; (A.B.T.); (S.E.C.M.); (P.M.S.M.); (A.K.C.)
| | - Pollyana M. S. Melo
- Department of Biophysics, Federal University of São Paulo, São Paulo 04039-032, Brazil; (A.B.T.); (S.E.C.M.); (P.M.S.M.); (A.K.C.)
| | - Maday Alonso del Rivero
- Center for Protein Studies, Faculty of Biology, University of Havana, Vedado, La Habana 10400, Cuba; (M.A.d.R.); (J.G.-B.)
| | - Jorge González-Bacerio
- Center for Protein Studies, Faculty of Biology, University of Havana, Vedado, La Habana 10400, Cuba; (M.A.d.R.); (J.G.-B.)
| | - Adriana K. Carmona
- Department of Biophysics, Federal University of São Paulo, São Paulo 04039-032, Brazil; (A.B.T.); (S.E.C.M.); (P.M.S.M.); (A.K.C.)
| | - Alexandre Budu
- Department of Biophysics, Federal University of São Paulo, São Paulo 04039-032, Brazil; (A.B.T.); (S.E.C.M.); (P.M.S.M.); (A.K.C.)
- Correspondence: (A.B.); (M.L.G.)
| | - Marcos L. Gazarini
- Department of Biosciences, Federal University of São Paulo, Santos 11015-020, Brazil; (C.C.H.); (M.F.A.)
- Correspondence: (A.B.); (M.L.G.)
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12
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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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13
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Mapping the substrate specificity of the Plasmodium M1 and M17 aminopeptidases. Biochem J 2021; 478:2697-2713. [PMID: 34133730 PMCID: PMC8286833 DOI: 10.1042/bcj20210172] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/14/2021] [Accepted: 06/16/2021] [Indexed: 02/02/2023]
Abstract
During malarial infection, Plasmodium parasites digest human hemoglobin to obtain free amino acids for protein production and maintenance of osmotic pressure. The Plasmodium M1 and M17 aminopeptidases are both postulated to have an essential role in the terminal stages of the hemoglobin digestion process and are validated drug targets for the design of new dual-target anti-malarial compounds. In this study, we profiled the substrate specificity fingerprints and kinetic behaviors of M1 and M17 aminopeptidases from Plasmodium falciparum and Plasmodium vivax, and the mouse model species, Plasmodium berghei. We found that although the Plasmodium M1 aminopeptidases share a largely similar, broad specificity at the P1 position, the P. falciparum M1 displays the greatest diversity in specificity and P. berghei M1 showing a preference for charged P1 residues. In contrast, the Plasmodium M17 aminopeptidases share a highly conserved preference for hydrophobic residues at the P1 position. The aminopeptidases also demonstrated intra-peptide sequence specificity, particularly the M1 aminopeptidases, which showed a definitive preference for peptides with fewer negatively charged intrapeptide residues. Overall, the P. vivax and P. berghei enzymes had a faster substrate turnover rate than the P. falciparum enzymes, which we postulate is due to subtle differences in structural dynamicity. Together, these results build a kinetic profile that allows us to better understand the catalytic nuances of the M1 and M17 aminopeptidases from different Plasmodium species.
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14
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Mills B, Isaac RE, Foster R. Metalloaminopeptidases of the Protozoan Parasite Plasmodium falciparum as Targets for the Discovery of Novel Antimalarial Drugs. J Med Chem 2021; 64:1763-1785. [PMID: 33534577 DOI: 10.1021/acs.jmedchem.0c01721] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Malaria poses a significant threat to approximately half of the world's population with an annual death toll close to half a million. The emergence of resistance to front-line antimalarials in the most lethal human parasite species, Plasmodium falciparum (Pf), threatens progress made in malaria control. The prospect of losing the efficacy of antimalarial drugs is driving the search for small molecules with new modes of action. Asexual reproduction of the parasite is critically dependent on the recycling of amino acids through catabolism of hemoglobin (Hb), which makes metalloaminopeptidases (MAPs) attractive targets for the development of new drugs. The Pf genome encodes eight MAPs, some of which have been found to be essential for parasite survival. In this article, we discuss the biological structure and function of each MAP within the Pf genome, along with the drug discovery efforts that have been undertaken to identify novel antimalarial candidates of therapeutic value.
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Affiliation(s)
- Belinda Mills
- School of Chemistry, University of Leeds, Leeds, U.K., LS2 9JT
| | - R Elwyn Isaac
- School of Biology, University of Leeds, Leeds, U.K., LS2 9JT
| | - Richard Foster
- School of Chemistry, University of Leeds, Leeds, U.K., LS2 9JT
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15
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Mathew R, Wunderlich J, Thivierge K, Cwiklinski K, Dumont C, Tilley L, Rohrbach P, Dalton JP. Biochemical and cellular characterisation of the Plasmodium falciparum M1 alanyl aminopeptidase (PfM1AAP) and M17 leucyl aminopeptidase (PfM17LAP). Sci Rep 2021; 11:2854. [PMID: 33536500 PMCID: PMC7858622 DOI: 10.1038/s41598-021-82499-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 01/18/2021] [Indexed: 01/30/2023] Open
Abstract
The Plasmodium falciparum M1 alanyl aminopeptidase and M17 leucyl aminopeptidase, PfM1AAP and PfM17LAP, are potential targets for novel anti-malarial drug development. Inhibitors of these aminopeptidases have been shown to kill malaria parasites in culture and reduce parasite growth in murine models. The two enzymes may function in the terminal stages of haemoglobin digestion, providing free amino acids for protein synthesis by the rapidly growing intra-erythrocytic parasites. Here we have performed a comparative cellular and biochemical characterisation of the two enzymes. Cell fractionation and immunolocalisation studies reveal that both enzymes are associated with the soluble cytosolic fraction of the parasite, with no evidence that they are present within other compartments, such as the digestive vacuole (DV). Enzyme kinetic studies show that the optimal pH of both enzymes is in the neutral range (pH 7.0-8.0), although PfM1AAP also possesses some activity (< 20%) at the lower pH range of 5.0-5.5. The data supports the proposal that PfM1AAP and PfM17LAP function in the cytoplasm of the parasite, likely in the degradation of haemoglobin-derived peptides generated in the DV and transported to the cytosol.
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Affiliation(s)
- Rency Mathew
- grid.14709.3b0000 0004 1936 8649Institute of Parasitology, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, Québec, H9X 3V9 Canada ,grid.4777.30000 0004 0374 7521School of Biological Sciences, Queen’s University Belfast, Belfast, Northern Ireland UK
| | - Juliane Wunderlich
- grid.14709.3b0000 0004 1936 8649Institute of Parasitology, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, Québec, H9X 3V9 Canada ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Notkestraße 85, 22607 Hamburg, Germany
| | - Karine Thivierge
- grid.14709.3b0000 0004 1936 8649Institute of Parasitology, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, Québec, H9X 3V9 Canada ,grid.434819.30000 0000 8929 2775Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC Canada
| | - Krystyna Cwiklinski
- grid.4777.30000 0004 0374 7521School of Biological Sciences, Queen’s University Belfast, Belfast, Northern Ireland UK ,grid.6142.10000 0004 0488 0789Centre for One Health & Ryan Institute, School of Natural Sciences, NUI Galway, Galway, Republic of Ireland
| | - Claire Dumont
- grid.1008.90000 0001 2179 088XDepartment of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, VIC Australia
| | - Leann Tilley
- grid.1008.90000 0001 2179 088XDepartment of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, VIC Australia
| | - Petra Rohrbach
- grid.14709.3b0000 0004 1936 8649Institute of Parasitology, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, Québec, H9X 3V9 Canada
| | - John P. Dalton
- grid.14709.3b0000 0004 1936 8649Institute of Parasitology, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, Québec, H9X 3V9 Canada ,grid.4777.30000 0004 0374 7521School of Biological Sciences, Queen’s University Belfast, Belfast, Northern Ireland UK ,grid.6142.10000 0004 0488 0789Centre for One Health & Ryan Institute, School of Natural Sciences, NUI Galway, Galway, Republic of Ireland
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16
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Schipper S, Wu H, Furdui CM, Poole LB, Delahunty CM, Park R, Yates JR, Becker K, Przyborski JM. Identification of sulfenylation patterns in trophozoite stage Plasmodium falciparum using a non-dimedone based probe. Mol Biochem Parasitol 2021; 242:111362. [PMID: 33513391 DOI: 10.1016/j.molbiopara.2021.111362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/31/2020] [Accepted: 01/18/2021] [Indexed: 10/22/2022]
Abstract
Plasmodium falciparum causes the deadliest form of malaria. Adequate redox control is crucial for this protozoan parasite to overcome oxidative and nitrosative challenges, thus enabling its survival. Sulfenylation is an oxidative post-translational modification, which acts as a molecular on/off switch, regulating protein activity. To obtain a better understanding of which proteins are redox regulated in malaria parasites, we established an optimized affinity capture protocol coupled with mass spectrometry analysis for identification of in vivo sulfenylated proteins. The non-dimedone based probe BCN-Bio1 shows reaction rates over 100-times that of commonly used dimedone-based probes, allowing for a rapid trapping of sulfenylated proteins. Mass spectrometry analysis of BCN-Bio1 labeled proteins revealed the first insight into the Plasmodium falciparum trophozoite sulfenylome, identifying 102 proteins containing 152 sulfenylation sites. Comparison with Plasmodium proteins modified by S-glutathionylation and S-nitrosation showed a high overlap, suggesting a common core of proteins undergoing redox regulation by multiple mechanisms. Furthermore, parasite proteins which were identified as targets for sulfenylation were also identified as being sulfenylated in other organisms, especially proteins of the glycolytic cycle. This study suggests that a number of Plasmodium proteins are subject to redox regulation and it provides a basis for further investigations into the exact structural and biochemical basis of regulation, and a deeper understanding of cross-talk between post-translational modifications.
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Affiliation(s)
- Susanne Schipper
- Department of Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, Giessen, Germany
| | - Hanzhi Wu
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Cristina M Furdui
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Leslie B Poole
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Claire M Delahunty
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Robin Park
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Katja Becker
- Department of Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, Giessen, Germany
| | - Jude M Przyborski
- Department of Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, Giessen, Germany.
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17
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Malcolm TR, Belousoff MJ, Venugopal H, Borg NA, Drinkwater N, Atkinson SC, McGowan S. Active site metals mediate an oligomeric equilibrium in Plasmodium M17 aminopeptidases. J Biol Chem 2020; 296:100173. [PMID: 33303633 PMCID: PMC7948507 DOI: 10.1074/jbc.ra120.016313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 01/14/2023] Open
Abstract
M17 leucyl aminopeptidases are metal-dependent exopeptidases that rely on oligomerization to diversify their functional roles. The M17 aminopeptidases from Plasmodium falciparum (PfA-M17) and Plasmodium vivax (Pv-M17) function as catalytically active hexamers to generate free amino acids from human hemoglobin and are drug targets for the design of novel antimalarial agents. However, the molecular basis for oligomeric assembly is not fully understood. In this study, we found that the active site metal ions essential for catalytic activity have a secondary structural role mediating the formation of active hexamers. We found that PfA-M17 and Pv-M17 exist in a metal-dependent dynamic equilibrium between active hexameric species and smaller inactive species that can be controlled by manipulating the identity and concentration of metals available. Mutation of residues involved in metal ion binding impaired catalytic activity and the formation of active hexamers. Structural resolution of Pv-M17 by cryoelectron microscopy and X-ray crystallography together with solution studies revealed that PfA-M17 and Pv-M17 bind metal ions and substrates in a conserved fashion, although Pv-M17 forms the active hexamer more readily and processes substrates faster than PfA-M17. On the basis of these studies, we propose a dynamic equilibrium between monomer ↔ dimer ↔ tetramer ↔ hexamer, which becomes directional toward the large oligomeric states with the addition of metal ions. This sophisticated metal-dependent dynamic equilibrium may apply to other M17 aminopeptidases and underpin the moonlighting capabilities of this enzyme family.
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Affiliation(s)
- Tess R Malcolm
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Matthew J Belousoff
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Hariprasad Venugopal
- Ramacciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, Victoria, Australia
| | - Natalie A Borg
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia; Immunity and Immune Evasion Laboratory, Chronic Infectious and Inflammatory Diseases Research, School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria, Australia
| | - Nyssa Drinkwater
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Sarah C Atkinson
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia; Immunity and Immune Evasion Laboratory, Chronic Infectious and Inflammatory Diseases Research, School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria, Australia
| | - Sheena McGowan
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia.
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18
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Pascual Alonso I, Rivera Méndez L, Valdés-Tresanco ME, Bounaadja L, Schmitt M, Arrebola Sánchez Y, Alvarez Lajonchere L, Charli JL, Florent I. Biochemical evidences for M1-, M17- and M18-like aminopeptidases in marine invertebrates from Cuban coastline. Z NATURFORSCH C 2020; 75:397-407. [PMID: 32609656 DOI: 10.1515/znc-2019-0169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 06/01/2020] [Indexed: 11/15/2022]
Abstract
Metallo-aminopeptidases (mAPs) control many physiological processes. They are classified in different families according to structural similarities. Neutral mAPs catalyze the cleavage of neutral amino acids from the N-terminus of proteins or peptide substrates; they need one or two metallic cofactors in their active site. Information about marine invertebrate's neutral mAPs properties is scarce; available data are mainly derived from genomics and cDNA studies. The goal of this work was to characterize the biochemical properties of the neutral APs activities in eight Cuban marine invertebrate species from the Phyla Mollusca, Porifera, Echinodermata, and Cnidaria. Determination of substrate specificity, optimal pH and effects of inhibitors (1,10-phenanthroline, amastatin, and bestatin) and cobalt on activity led to the identification of distinct neutral AP-like activities, whose biochemical behaviors were similar to those of the M1 and M17 families of mAPs. Additionally, M18-like glutamyl AP activities were detected. Thus, marine invertebrates express biochemical activities likely belonging to various families of metallo-aminopeptidases.
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Affiliation(s)
- Isel Pascual Alonso
- Center for Protein Studies, Faculty of Biology, University of Havana, Havana, Cuba
| | - Laura Rivera Méndez
- Center for Protein Studies, Faculty of Biology, University of Havana, Havana, Cuba
| | - Mario E Valdés-Tresanco
- Center for Protein Studies, Faculty of Biology, University of Havana, Havana, Cuba.,Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Lotfi Bounaadja
- Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR 7245), Muséum National d'Histoire Naturelle, CNRS, Paris, France
| | - Marjorie Schmitt
- Laboratoire d'Innovation Moléculaire et Applications - Université de Haute-Alsace, Université de Strasbourg, CNRS, LIMA UMR7042, Mulhouse, France
| | | | - Luis Alvarez Lajonchere
- Museum of Natural History Felipe Poey, Faculty of Biology, University of Havana, Havana, Cuba
| | - Jean-Louis Charli
- Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Mexico
| | - Isabelle Florent
- Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR 7245), Muséum National d'Histoire Naturelle, CNRS, Paris, France
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19
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Driving antimalarial design through understanding of target mechanism. Biochem Soc Trans 2020; 48:2067-2078. [PMID: 32869828 PMCID: PMC7609028 DOI: 10.1042/bst20200224] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/23/2020] [Accepted: 07/27/2020] [Indexed: 11/17/2022]
Abstract
Malaria continues to be a global health threat, affecting approximately 219 million people in 2018 alone. The recurrent development of resistance to existing antimalarials means that the design of new drug candidates must be carefully considered. Understanding of drug target mechanism can dramatically accelerate early-stage target-based development of novel antimalarials and allows for structural modifications even during late-stage preclinical development. Here, we have provided an overview of three promising antimalarial molecular targets, PfDHFR, PfDHODH and PfA-M1, and their associated inhibitors which demonstrate how mechanism can inform drug design and be effectively utilised to generate compounds with potent inhibitory activity.
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20
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X-ray crystal structure and specificity of the Toxoplasma gondii ME49 TgAPN2. Biochem J 2020; 477:3819-3832. [PMID: 32926129 PMCID: PMC7557147 DOI: 10.1042/bcj20200569] [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: 07/18/2020] [Revised: 09/03/2020] [Accepted: 09/14/2020] [Indexed: 11/21/2022]
Abstract
Toxoplasmosis is a parasitic disease caused by infection with Toxoplasma gondii that currently has few therapeutic options. The M1 aminopeptidase enzymes have been shown to be attractive targets for anti-parasitic agents and/or vaccine candidates, suggesting potential to re-purpose inhibitors between parasite M1 aminopeptidase targets. The M1 aminopeptidase TgAPN2 has been suggested to be a potential new drug target for toxoplasmosis. Here we investigate the structure and function of TgAPN2, a homologue of the antimalarial drug target PfA-M1, and evaluate the capacity to use inhibitors that target PfA-M1 against TgAPN2. The results show that despite a similar overall fold, the TgAPN2 has a unique substrate specificity and inhibition profile. Sequence and structure differences are investigated and show how comparative structure-activity relationships may provide a route to obtaining potent inhibitors of TgAPN2.
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21
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Chen S, Yim JJ, Bogyo M. Synthetic and biological approaches to map substrate specificities of proteases. Biol Chem 2020; 401:165-182. [PMID: 31639098 DOI: 10.1515/hsz-2019-0332] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/11/2019] [Indexed: 02/07/2023]
Abstract
Proteases are regulators of diverse biological pathways including protein catabolism, antigen processing and inflammation, as well as various disease conditions, such as malignant metastasis, viral infection and parasite invasion. The identification of substrates of a given protease is essential to understand its function and this information can also aid in the design of specific inhibitors and active site probes. However, the diversity of putative protein and peptide substrates makes connecting a protease to its downstream substrates technically difficult and time-consuming. To address this challenge in protease research, a range of methods have been developed to identify natural protein substrates as well as map the overall substrate specificity patterns of proteases. In this review, we highlight recent examples of both synthetic and biological methods that are being used to define the substrate specificity of protease so that new protease-specific tools and therapeutic agents can be developed.
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Affiliation(s)
- Shiyu Chen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joshua J Yim
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
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22
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Tibon NS, Ng CH, Cheong SL. Current progress in antimalarial pharmacotherapy and multi-target drug discovery. Eur J Med Chem 2019; 188:111983. [PMID: 31911292 DOI: 10.1016/j.ejmech.2019.111983] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 12/09/2019] [Accepted: 12/16/2019] [Indexed: 12/13/2022]
Abstract
Discovery and development of antimalarial drugs have long been dominated by single-target therapy. Continuous effort has been made to explore and identify different targets in malaria parasite crucial for the malaria treatment. The single-target drug therapy was initially successful, but it was later supplanted by combination therapy with multiple drugs to overcome drug resistance. Emergence of resistant strains even against the combination therapy has warranted a review of current antimalarial pharmacotherapy. This has led to the development of the new concept of covalent biotherapy, in which two or more pharmacophores are chemically bound to produce hybrid antimalarial drugs with multi-target functionalities. Herein, the review initially details the current pharmacotherapy for malaria as well as the conventional and novel targets of importance identified in the malaria parasite. Then, the rationale of multi-targeted therapy for malaria, approaches taken to develop the multi-target antimalarial hybrids, and the examples of hybrid molecules are comprehensively enumerated and discussed.
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Affiliation(s)
- Natasha Stella Tibon
- Department of Pharmaceutical Chemistry, School of Pharmacy, International Medical University, No. 126, Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Kuala Lumpur, Malaysia
| | - Chew Hee Ng
- Department of Pharmaceutical Chemistry, School of Pharmacy, International Medical University, No. 126, Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Kuala Lumpur, Malaysia.
| | - Siew Lee Cheong
- Department of Pharmaceutical Chemistry, School of Pharmacy, International Medical University, No. 126, Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Kuala Lumpur, Malaysia.
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Localization and enzyme kinetics of aminopeptidase N3 from Toxoplasma gondii. Parasitol Res 2019; 119:357-364. [PMID: 31836922 DOI: 10.1007/s00436-019-06512-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 10/15/2019] [Indexed: 10/25/2022]
Abstract
Aminopeptidase N is an important metalloenzyme from the M1 zinc metallopeptidase family, which is present in numerous apicomplexan parasites, including Plasmodium, Eimeria, and Cryptosporidium. Aminopeptidase N is a potential drug target, and hence, its properties have been widely investigated. In the current study, the cellular localization and enzyme characteristics of Toxoplasma gondii aminopeptidase N3 (TgAPN3) were evaluated in vitro. Cellular localization analysis revealed that TgAPN3 and GRA protein were co-located in the organelle and parasitophorous vacuole of T. gondii. The secretion assay showed that TgAPN3 could be co-secreted from the tachyzoites with GRA protein. A functional recombinant Toxoplasma aminopeptidase N3 (rTgAPN3) was produced in Escherichia coli. The enzyme activity was first determined using a fluorogenic H-Ala-MCA substrate. Some activity of rTgAPN3 was observed between pH 3.0 and 8.0, with a peak at pH 7.0. The activity was significantly enhanced in the presence of Co2+ ions. Substrate specificity of rTgAPN3 was then evaluated. The enzyme showed a preference for substrates containing N-terminal Ala residues, followed by Tyr and Cys. The rTgAPN3 activity was significantly inhibited by bestatin and phebestatin. In general, TgAPN3 was a structurally conserved member of the M1 family, although it also displayed unique biochemical characteristics. These results lay the foundation for a functional study of TgAPN3 and constitute its putative identification as a drug target.
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Drinkwater N, Malcolm TR, McGowan S. M17 aminopeptidases diversify function by moderating their macromolecular assemblies and active site environment. Biochimie 2019; 166:38-51. [DOI: 10.1016/j.biochi.2019.01.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/10/2019] [Indexed: 12/24/2022]
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25
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Maluch I, Czarna J, Drag M. Applications of Unnatural Amino Acids in Protease Probes. Chem Asian J 2019; 14:4103-4113. [PMID: 31593336 DOI: 10.1002/asia.201901152] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 10/01/2019] [Indexed: 12/11/2022]
Abstract
Since proteases are involved in a wide range of physiological and disease states, the development of novel tools for imaging proteolytic enzyme activity is attracting increasing interest from scientists. Peptide substrates containing proteinogenic amino acids are often the first line of defining enzyme specificity. This Minireview outlines examples of major recent advances in probing proteases using unnatural amino acid residues, which greatly expands the possibilities for designing substrate probes and inhibitory activity-based probes. This approach already yielded innovative probes that selectively target only one active protease within the group of enzymes exhibiting similar specificity both in cellular assays and in bioimaging research.
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Affiliation(s)
- Izabela Maluch
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw, University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Justyna Czarna
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw, University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Marcin Drag
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw, University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
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26
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de Vries LE, Sanchez MI, Groborz K, Kuppens L, Poreba M, Lehmann C, Nevins N, Withers-Martinez C, Hirst DJ, Yuan F, Arastu-Kapur S, Horn M, Mares M, Bogyo M, Drag M, Deu E. Characterization of P. falciparum dipeptidyl aminopeptidase 3 specificity identifies differences in amino acid preferences between peptide-based substrates and covalent inhibitors. FEBS J 2019; 286:3998-4023. [PMID: 31177613 PMCID: PMC6851853 DOI: 10.1111/febs.14953] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 04/12/2019] [Accepted: 06/06/2019] [Indexed: 12/31/2022]
Abstract
Malarial dipeptidyl aminopeptidases (DPAPs) are cysteine proteases important for parasite development thus making them attractive drug targets. In order to develop inhibitors specific to the parasite enzymes, it is necessary to map the determinants of substrate specificity of the parasite enzymes and its mammalian homologue cathepsin C (CatC). Here, we screened peptide-based libraries of substrates and covalent inhibitors to characterize the differences in specificity between parasite DPAPs and CatC, and used this information to develop highly selective DPAP1 and DPAP3 inhibitors. Interestingly, while the primary amino acid specificity of a protease is often used to develop potent inhibitors, we show that equally potent and highly specific inhibitors can be developed based on the sequences of nonoptimal peptide substrates. Finally, our homology modelling and docking studies provide potential structural explanations of the differences in specificity between DPAP1, DPAP3, and CatC, and between substrates and inhibitors in the case of DPAP3. Overall, this study illustrates that focusing the development of protease inhibitors solely on substrate specificity might overlook important structural features that can be exploited to develop highly potent and selective compounds.
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Affiliation(s)
- Laura E de Vries
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mateo I Sanchez
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA
| | - Katarzyna Groborz
- Division of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology, Wroclaw, Poland
| | - Laurie Kuppens
- Chemical Biology Approaches to Malaria Laboratory, The Francis Crick Institute, London, UK
| | - Marcin Poreba
- Division of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology, Wroclaw, Poland
| | - Christine Lehmann
- Chemical Biology Approaches to Malaria Laboratory, The Francis Crick Institute, London, UK
| | - Neysa Nevins
- Computational Sciences, GlaxoSmithKline, Collegeville, PA, USA
| | | | - David J Hirst
- Crick-GSK Biomedical LinkLabs, GlaxoSmithKline, Stevenage, UK
| | - Fang Yuan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Shirin Arastu-Kapur
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Martin Horn
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Michael Mares
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Marcin Drag
- Division of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology, Wroclaw, Poland
| | - Edgar Deu
- Chemical Biology Approaches to Malaria Laboratory, The Francis Crick Institute, London, UK
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Wang F, Hu X, Zhou B. Structural characterization of plasmodial aminopeptidase: a combined molecular docking and QSAR-based in silico approaches. Mol Divers 2019; 23:965-984. [DOI: 10.1007/s11030-019-09921-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 01/18/2019] [Indexed: 11/24/2022]
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28
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Vinh NB, Drinkwater N, Malcolm TR, Kassiou M, Lucantoni L, Grin PM, Butler GS, Duffy S, Overall CM, Avery VM, Scammells PJ, McGowan S. Hydroxamic Acid Inhibitors Provide Cross-Species Inhibition of Plasmodium M1 and M17 Aminopeptidases. J Med Chem 2018; 62:622-640. [DOI: 10.1021/acs.jmedchem.8b01310] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Natalie B. Vinh
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Melbourne, VIC 3052, Australia
| | - Nyssa Drinkwater
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Melbourne, VIC 3800, Australia
| | - Tess R. Malcolm
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Melbourne, VIC 3800, Australia
| | - Michael Kassiou
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
| | - Leonardo Lucantoni
- Discovery Biology, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia
| | | | | | - Sandra Duffy
- Discovery Biology, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia
| | | | - Vicky M. Avery
- Discovery Biology, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia
| | - Peter J. Scammells
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Melbourne, VIC 3052, Australia
| | - Sheena McGowan
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Melbourne, VIC 3800, Australia
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Fitness Loss under Amino Acid Starvation in Artemisinin-Resistant Plasmodium falciparum Isolates from Cambodia. Sci Rep 2018; 8:12622. [PMID: 30135481 PMCID: PMC6105667 DOI: 10.1038/s41598-018-30593-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/31/2018] [Indexed: 11/09/2022] Open
Abstract
Artemisinin is the most rapidly effective drug for Plasmodium falciparum malaria treatment currently in clinical use. Emerging artemisinin-resistant parasites pose a great global health risk. At present, the level of artemisinin resistance is still relatively low with evidence pointing towards a trade-off between artemisinin resistance and fitness loss. Here we show that artemisinin-resistant P. falciparum isolates from Cambodia manifested fitness loss, showing fewer progenies during the intra-erythrocytic developmental cycle. The loss in fitness was exacerbated under the condition of low exogenous amino acid supply. The resistant parasites failed to undergo maturation, whereas their drug-sensitive counterparts were able to complete the erythrocytic cycle under conditions of amino acid deprivation. The artemisinin-resistant phenotype was not stable, and loss of the phenotype was associated with changes in the expression of a putative target, Exp1, a membrane glutathione transferase. Analysis of SNPs in haemoglobin processing genes revealed associations with parasite clearance times, suggesting changes in haemoglobin catabolism may contribute to artemisinin resistance. These findings on fitness and protein homeostasis could provide clues on how to contain emerging artemisinin-resistant parasites.
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Escotte-Binet S, Huguenin A, Aubert D, Martin AP, Kaltenbach M, Florent I, Villena I. Metallopeptidases of Toxoplasma gondii: in silico identification and gene expression. ACTA ACUST UNITED AC 2018; 25:26. [PMID: 29737275 PMCID: PMC5939537 DOI: 10.1051/parasite/2018025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 04/16/2018] [Indexed: 12/17/2022]
Abstract
Metallopeptidases are a family of proteins with domains that remain highly conserved throughout evolution. These hydrolases require divalent metal cation(s) to activate the water molecule in order to carry out their catalytic action on peptide bonds by nucleophilic attack. Metallopeptidases from parasitic protozoa, including Toxoplasma, are investigated because of their crucial role in parasite biology. In the present study, we screened the T. gondii database using PFAM motifs specific for metallopeptidases in association with the MEROPS peptidase Database (release 10.0). In all, 49 genes encoding proteins with metallopeptidase signatures were identified in the Toxoplasma genome. An Interpro Search enabled us to uncover their domain/motif organization, and orthologs with the highest similarity by BLAST were used for annotation. These 49 Toxoplasma metallopeptidases clustered into 15 families described in the MEROPS database. Experimental expression analysis of their genes in the tachyzoite stage revealed transcription for all genes studied. Further research on the role of these peptidases should increase our knowledge of basic Toxoplasma biology and provide opportunities to identify novel therapeutic targets. This type of study would also open a path towards the comparative biology of apicomplexans.
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Affiliation(s)
- Sandie Escotte-Binet
- EA 7510, ESCAPE, Laboratory of Parasitology-Mycology, University of Reims Champagne-Ardenne, 51100 Reims, France - Laboratory of Parasitology-Mycology, Toxoplasmosis National Reference Center, Toxoplasma Biological Resource Center, Maison Blanche Hospital, 51100 Reims, France
| | - Antoine Huguenin
- EA 7510, ESCAPE, Laboratory of Parasitology-Mycology, University of Reims Champagne-Ardenne, 51100 Reims, France - Laboratory of Parasitology-Mycology, Toxoplasmosis National Reference Center, Toxoplasma Biological Resource Center, Maison Blanche Hospital, 51100 Reims, France
| | - Dominique Aubert
- EA 7510, ESCAPE, Laboratory of Parasitology-Mycology, University of Reims Champagne-Ardenne, 51100 Reims, France - Laboratory of Parasitology-Mycology, Toxoplasmosis National Reference Center, Toxoplasma Biological Resource Center, Maison Blanche Hospital, 51100 Reims, France
| | - Anne-Pascaline Martin
- EA 7510, ESCAPE, Laboratory of Parasitology-Mycology, University of Reims Champagne-Ardenne, 51100 Reims, France
| | - Matthieu Kaltenbach
- EA 7510, ESCAPE, Laboratory of Parasitology-Mycology, University of Reims Champagne-Ardenne, 51100 Reims, France
| | - Isabelle Florent
- UMR7245 CNRS-MNHN, National Museum of Natural History, Department Adaptations of the Living, 75005 Paris, France
| | - Isabelle Villena
- EA 7510, ESCAPE, Laboratory of Parasitology-Mycology, University of Reims Champagne-Ardenne, 51100 Reims, France - Laboratory of Parasitology-Mycology, Toxoplasmosis National Reference Center, Toxoplasma Biological Resource Center, Maison Blanche Hospital, 51100 Reims, France
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31
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Bounaadja L, Schmitt M, Albrecht S, Mouray E, Tarnus C, Florent I. Selective inhibition of PfA-M1, over PfA-M17, by an amino-benzosuberone derivative blocks malaria parasites development in vitro and in vivo. Malar J 2017; 16:382. [PMID: 28934959 PMCID: PMC5609037 DOI: 10.1186/s12936-017-2032-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 09/18/2017] [Indexed: 01/09/2023] Open
Abstract
Background Plasmodium falciparum M1 family aminopeptidase is currently considered as a promising target for anti-malarial chemotherapy. Several series of inhibitors developed by various research groups display IC50/Ki values down to nM range on native PfA-M1 or recombinant forms and block the parasite development in culture at µM to sub-µM concentrations. A handful of these inhibitors has been tested on murine models of malaria and has shown anti plasmodial in vivo activity. However, most of these inhibitors do also target the other neutral malarial aminopeptidase, PfA-M17, often with lower Ki values, which questions the relative involvement and importance of each enzyme in the parasite biology. Results An amino-benzosuberone derivative from a previously published collection of chemicals targeting specifically the M1-aminopeptidases has been identified; it is highly potent on PfA-M1 (Ki = 50 nM) and devoid of inhibitory activity on PfA-M17 (no inhibition up to 100 µM). This amino-benzosuberone derivative (T5) inhibits, in the µM range, the in vitro growth of two P. falciparum strains, 3D7 and FcB1, respectively chloroquino-sensitive and resistant. Evaluated in vivo, on the murine non-lethal model of malaria Plasmodium chabaudi chabaudi, this amino-benzosuberone derivative was able to reduce the parasite burden by 44 and 40% in a typical 4-day Peters assay at a daily dose of 12 and 24 mg/kg by intraperitoneal route of administration. Conclusions The evaluation of a highly selective inhibitor of PfA-M1, over PfA-M17, active on Plasmodium parasites in vitro and in vivo, highlights the relevance of PfA-M1 in the biological development of the parasite as well as in the list of promising anti-malarial targets to be considered in combination with current or future anti-malarial drugs. Electronic supplementary material The online version of this article (doi:10.1186/s12936-017-2032-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lotfi Bounaadja
- Molécules de Communication et Adaptation des Microorganismes, (MCAM, UMR7245), Muséum National Histoire Naturelle, Sorbonne Universités, CNRS, CP 52, 57 Rue Cuvier, 75005, Paris, France
| | - Marjorie Schmitt
- Laboratoire de Chimie Moléculaire, CNRS-UMR7509, Université de Strasbourg, 67037, Strasbourg Cedex 2, France
| | - Sébastien Albrecht
- Laboratoire de Chimie Organique et Bioorganique, EA4566, Université de Haute Alsace, 68093, Mulhouse Cedex, France
| | - Elisabeth Mouray
- Molécules de Communication et Adaptation des Microorganismes, (MCAM, UMR7245), Muséum National Histoire Naturelle, Sorbonne Universités, CNRS, CP 52, 57 Rue Cuvier, 75005, Paris, France
| | - Céline Tarnus
- Laboratoire de Chimie Organique et Bioorganique, EA4566, Université de Haute Alsace, 68093, Mulhouse Cedex, France
| | - Isabelle Florent
- Molécules de Communication et Adaptation des Microorganismes, (MCAM, UMR7245), Muséum National Histoire Naturelle, Sorbonne Universités, CNRS, CP 52, 57 Rue Cuvier, 75005, Paris, France.
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Rosati M, Dalal S, Klemba M. Two cap residues in the S1 subsite of a Plasmodium falciparum M1-family aminopeptidase promote broad specificity and enhance catalysis. Mol Biochem Parasitol 2017; 217:7-12. [PMID: 28811124 DOI: 10.1016/j.molbiopara.2017.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/04/2017] [Accepted: 08/05/2017] [Indexed: 12/22/2022]
Abstract
The aminopeptidase PfA-M1 is a key contributor to peptide catabolism in the human malaria parasite Plasmodium falciparum. PfA-M1 substrate specificity is shaped by the cylindrical S1 subsite, which accommodates the sidechain of the substrate P1 residue. At the top of the S1 subsite are two "cap" residues, E572 and M1034, that are positioned to influence S1 subsite specificity. In this study, we have mutated the cap residues, individually and together, and have evaluated the effects on PfA-M1 specificity and catalytic efficiency. When the P1 residue was too small to engage the cap residues, the mutations had no effect on catalysis. Hydrolysis of dipeptide substrates with a basic P1 residue was significantly impaired in the E572A mutant, most likely due to the loss of a stabilizing salt bridge between E572 and the P1 sidechain. With M1034A, a substantial reduction in catalytic efficiency was observed when the P1 sidechain was large and non-polar. The double E572A/M1034A exhibited significant decreases in catalytic efficiency for most substrates. This effect was not reversed with the polar substitutions E572N/M1034Q, which replaced the PfA-M1 cap residues with those of Escherichia coli aminopeptidase N. Both E572 and M1034 contributed to the binding of the competitive aminopeptidase inhibitor bestatin.
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Affiliation(s)
- Matthew Rosati
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
| | - Seema Dalal
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
| | - Michael Klemba
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA.
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Deu E. Proteases as antimalarial targets: strategies for genetic, chemical, and therapeutic validation. FEBS J 2017; 284:2604-2628. [PMID: 28599096 PMCID: PMC5575534 DOI: 10.1111/febs.14130] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 04/29/2017] [Accepted: 06/06/2017] [Indexed: 01/17/2023]
Abstract
Malaria is a devastating parasitic disease affecting half of the world's population. The rapid emergence of resistance against new antimalarial drugs, including artemisinin-based therapies, has made the development of drugs with novel mechanisms of action extremely urgent. Proteases are enzymes proven to be well suited for target-based drug development due to our knowledge of their enzymatic mechanisms and active site structures. More importantly, Plasmodium proteases have been shown to be involved in a variety of pathways that are essential for parasite survival. However, pharmacological rather than target-based approaches have dominated the field of antimalarial drug development, in part due to the challenge of robustly validating Plasmodium targets at the genetic level. Fortunately, over the last few years there has been significant progress in the development of efficient genetic methods to modify the parasite, including several conditional approaches. This progress is finally allowing us not only to validate essential genes genetically, but also to study their molecular functions. In this review, I present our current understanding of the biological role proteases play in the malaria parasite life cycle. I also discuss how the recent advances in Plasmodium genetics, the improvement of protease-oriented chemical biology approaches, and the development of malaria-focused pharmacological assays, can be combined to achieve a robust biological, chemical and therapeutic validation of Plasmodium proteases as viable drug targets.
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Affiliation(s)
- Edgar Deu
- Chemical Biology Approaches to Malaria LaboratoryThe Francis Crick InstituteLondonUK
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Li Q, Jia H, Cao S, Zhang Z, Zheng J, Zhang Y. Biochemical characterization of aminopeptidase N2 from Toxoplasma gondii. J Vet Med Sci 2017; 79:1404-1411. [PMID: 28701624 PMCID: PMC5573830 DOI: 10.1292/jvms.17-0119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Aminopeptidase N (APN) is a member of the highly conserved M1 family of metalloproteases, and is considered to be a valuable target for the treatment of a variety of diseases, e.g., cancer, malaria, and coccidiosis. In this study, we identified an APN gene (TgAPN2) in the Toxoplasma gondii genome, and performed a biochemical characterization of the recombinant TgAPN2 (rTgAPN2) protein. Active rTgAPN2 was first produced and purified in Escherichia coli. The catalytic activity of the enzyme was verified using a specific fluorescent substrate, H-Ala-MCA; the rTgAPN2 was relatively active in the absence of added metal ions. The addition of some metal ions, especially Zn2+, inhibited the activity of the recombinant enzyme. The activity of rTgAPN2 was reduced in the presence of the EDTA chelator in the absence of added metal ions. The optimum pH for enzyme activity was 8.0; the enzyme was active in the 3-10 pH range. The substrate preference of rTgAPN2 was evaluated. The enzyme showed a preference for substrates containing N-terminal Ala and Arg residues. Finally, bestatin and amastatin were shown to inhibit the activity of the enzyme. In conclusion, rTgAPN2 shared general characteristics with the M1 family of aminopeptidases but also had some unique characteristics. This provides a basis for the function of aminopeptidases and the study of drug targets.
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Affiliation(s)
- Qingwei Li
- Department of Gastrointestinal Medical Oncology, The Affiliated Tumor Hospital of Harbin Medical University, Harbin 150001, China
| | - Honglin Jia
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Shinuo Cao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Zhaoxia Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Jun Zheng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Yanqiao Zhang
- Department of Gastrointestinal Medical Oncology, The Affiliated Tumor Hospital of Harbin Medical University, Harbin 150001, China
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35
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González-Bacerio J, Maluf SEC, Méndez Y, Pascual I, Florent I, Melo PMS, Budu A, Ferreira JC, Moreno E, Carmona AK, Rivera DG, Alonso Del Rivero M, Gazarini ML. KBE009: An antimalarial bestatin-like inhibitor of the Plasmodium falciparum M1 aminopeptidase discovered in an Ugi multicomponent reaction-derived peptidomimetic library. Bioorg Med Chem 2017; 25:4628-4636. [PMID: 28728898 DOI: 10.1016/j.bmc.2017.06.047] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 06/23/2017] [Accepted: 06/27/2017] [Indexed: 10/19/2022]
Abstract
Malaria is a global human parasitic disease mainly caused by the protozoon Plasmodium falciparum. Increased parasite resistance to current drugs determines the relevance of finding new treatments against new targets. A novel target is the M1 alanyl-aminopeptidase from P. falciparum (PfA-M1), which is essential for parasite development in human erythrocytes and is inhibited by the pseudo-peptide bestatin. In this work, we used a combinatorial multicomponent approach to produce a library of peptidomimetics and screened it for the inhibition of recombinant PfA-M1 (rPfA-M1) and the in vitro growth of P. falciparum erythrocytic stages (3D7 and FcB1 strains). Dose-response studies with selected compounds allowed identifying the bestatin-based peptidomimetic KBE009 as a submicromolar rPfA-M1 inhibitor (Ki=0.4μM) and an in vitro antimalarial compound as potent as bestatin (IC50=18μM; without promoting erythrocyte lysis). At therapeutic-relevant concentrations, KBE009 is selective for rPfA-M1 over porcine APN (a model of these enzymes from mammals), and is not cytotoxic against HUVEC cells. Docking simulations indicate that this compound binds PfA-M1 without Zn2+ coordination, establishing mainly hydrophobic interactions and showing a remarkable shape complementarity with the active site of the enzyme. Moreover, KBE009 inhibits the M1-type aminopeptidase activity (Ala-7-amido-4-methylcoumarin substrate) in isolated live parasites with a potency similar to that of the antimalarial activity (IC50=82μM), strongly suggesting that the antimalarial effect is directly related to the inhibition of the endogenous PfA-M1. These results support the value of this multicomponent strategy to identify PfA-M1 inhibitors, and make KBE009 a promising hit for drug development against malaria.
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Affiliation(s)
- Jorge González-Bacerio
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana, Calle 25 #455 entre I y J, 10400, Vedado, La Habana, Cuba.
| | - Sarah El Chamy Maluf
- Departamento de Biofísica, Universidade Federal de São Paulo, Rua Pedro de Toledo, 669, 7 andar, 04039-032, Vila Mariana, São Paulo, Brazil.
| | - Yanira Méndez
- Centro de Estudio de Productos Naturales, Facultad de Química, Universidad de La Habana, Zapata y G, 10400 La Habana, Cuba.
| | - Isel Pascual
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana, Calle 25 #455 entre I y J, 10400, Vedado, La Habana, Cuba.
| | - Isabelle Florent
- Unité Molécules de Communication et Adaptation des Microorganismes, (MCAM, UMR 7245), Sorbonne Universités, Muséum National Histoire Naturelle, CNRS, CP 52, 57 Rue Cuvier, 75005 Paris, France.
| | - Pollyana M S Melo
- Departamento de Biofísica, Universidade Federal de São Paulo, Rua Pedro de Toledo, 669, 7 andar, 04039-032, Vila Mariana, São Paulo, Brazil.
| | - Alexandre Budu
- Departamento de Biofísica, Universidade Federal de São Paulo, Rua Pedro de Toledo, 669, 7 andar, 04039-032, Vila Mariana, São Paulo, Brazil.
| | - Juliana C Ferreira
- Departamento de Biofísica, Universidade Federal de São Paulo, Rua Pedro de Toledo, 669, 7 andar, 04039-032, Vila Mariana, São Paulo, Brazil.
| | - Ernesto Moreno
- Centro de Inmunología Molecular, Calle 15 esq. 216, Siboney, Playa, La Habana, Cuba; Universidad de Medellín, Carrera 87 #30-65, Medellín, Colombia.
| | - Adriana K Carmona
- Departamento de Biofísica, Universidade Federal de São Paulo, Rua Pedro de Toledo, 669, 7 andar, 04039-032, Vila Mariana, São Paulo, Brazil.
| | - Daniel G Rivera
- Centro de Estudio de Productos Naturales, Facultad de Química, Universidad de La Habana, Zapata y G, 10400 La Habana, Cuba.
| | - Maday Alonso Del Rivero
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de La Habana, Calle 25 #455 entre I y J, 10400, Vedado, La Habana, Cuba.
| | - Marcos L Gazarini
- Departamento de Biociências, Universidade Federal de São Paulo, R. Silva Jardim, 136, 11015-020, Vila Mathias, Santos, São Paulo, Brazil.
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36
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Kasperkiewicz P, Poreba M, Groborz K, Drag M. Emerging challenges in the design of selective substrates, inhibitors and activity-based probes for indistinguishable proteases. FEBS J 2017; 284:1518-1539. [PMID: 28052575 PMCID: PMC7164106 DOI: 10.1111/febs.14001] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Revised: 12/02/2016] [Accepted: 01/03/2017] [Indexed: 12/31/2022]
Abstract
Proteases are enzymes that hydrolyze the peptide bond of peptide substrates and proteins. Despite significant progress in recent years, one of the greatest challenges in the design and testing of substrates, inhibitors and activity‐based probes for proteolytic enzymes is achieving specificity toward only one enzyme. This specificity is particularly important if the enzyme is present with other enzymes with a similar catalytic mechanism and substrate specificity but completely different functionality. The cross‐reactivity of substrates, inhibitors and activity‐based probes with other enzymes can significantly impair or even prevent investigations of a target protease. In this review, we describe important concepts and the latest challenges, focusing mainly on peptide‐based substrate specificity techniques used to distinguish individual enzymes within major protease families.
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Affiliation(s)
- Paulina Kasperkiewicz
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Poland
| | - Marcin Poreba
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Poland
| | - Katarzyna Groborz
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Poland
| | - Marcin Drag
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Poland
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37
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Structure and substrate fingerprint of aminopeptidase P from Plasmodium falciparum. Biochem J 2016; 473:3189-204. [DOI: 10.1042/bcj20160550] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 07/26/2016] [Indexed: 12/18/2022]
Abstract
Malaria is one of the world's most prevalent parasitic diseases, with over 200 million cases annually. Alarmingly, the spread of drug-resistant parasites threatens the effectiveness of current antimalarials and has made the development of novel therapeutic strategies a global health priority. Malaria parasites have a complicated lifecycle, involving an asymptomatic ‘liver stage’ and a symptomatic ‘blood stage’. During the blood stage, the parasites utilise a proteolytic cascade to digest host hemoglobin, which produces free amino acids absolutely necessary for parasite growth and reproduction. The enzymes required for hemoglobin digestion are therefore attractive therapeutic targets. The final step of the cascade is catalyzed by several metalloaminopeptidases, including aminopeptidase P (APP). We developed a novel platform to examine the substrate fingerprint of APP from Plasmodium falciparum (PfAPP) and to show that it can catalyze the removal of any residue immediately prior to a proline. Further, we have determined the crystal structure of PfAPP and present the first examination of the 3D structure of this essential malarial enzyme. Together, these analyses provide insights into potential mechanisms of inhibition that could be used to develop novel antimalarial therapeutics.
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38
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Palomo V, Díaz SA, Stewart MH, Susumu K, Medintz IL, Dawson PE. 3,4-Dihydroxyphenylalanine Peptides as Nonperturbative Quantum Dot Sensors of Aminopeptidase. ACS NANO 2016; 10:6090-9. [PMID: 27206058 PMCID: PMC4968404 DOI: 10.1021/acsnano.6b01682] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Fluorescence-based assays for hydrolases that cleave within the substrate (endopeptidases) are common, while developing substrates for proteases that selectively cleave from peptide termini (exopeptidases) is more challenging, since the termini are specifically recognized by the enzyme and cannot be modified to facilitate a Förster resonance energy transfer (FRET)-based approach. The development of a robust system that enables the quenching of fluorescent particles by simple amino acid side chains would find broad utility for peptide sensors and would be advantageous for exopeptidases. Here we describe a quantum dot (QD)-based electron transfer (ET) sensor that is able to allow direct, quantitative monitoring of both exopeptidase and endopeptidase activity. The incorporation of 3,4-dihydroxyphenylalanine (DOPA) into the sequence of a peptide allows for the quenching of QD photoluminescence through an ET mechanism. DOPA is a nonproteinogenic amino acid that can replace a phenylalanine or tyrosine residue in a peptide sequence without severely altering structural properties, allowing for its introduction at multiple positions within a biologically active peptide substrate. Consequently, the quenching system presented here is ideally suited for incorporation into diverse peptide substrates for enzyme recognition, digestion, and activity sensing. Our findings suggest a broad utility of a small ET-capable amino acid side chain in detecting enzyme activity through ET-mediated QD luminescence quenching.
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Affiliation(s)
- Valle Palomo
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, 92037 (USA)
| | - Sebastián A. Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375 (USA)
| | - Michael H. Stewart
- Optical Sciences Division, Code 5611, U.S. Naval Research Laboratory, Washington, D.C., 20375 (USA)
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5611, U.S. Naval Research Laboratory, Washington, D.C., 20375 (USA)
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375 (USA)
| | - Philip E. Dawson
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, 92037 (USA)
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Węglarz-Tomczak E, Berlicki Ł, Pawełczak M, Nocek B, Joachimiak A, Mucha A. A structural insight into the P1S1 binding mode of diaminoethylphosphonic and phosphinic acids, selective inhibitors of alanine aminopeptidases. Eur J Med Chem 2016; 117:187-96. [PMID: 27100031 DOI: 10.1016/j.ejmech.2016.04.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 04/04/2016] [Accepted: 04/06/2016] [Indexed: 10/22/2022]
Abstract
N'-substituted 1,2-diaminoethylphosphonic acids and 1,2-diaminoethylphosphinic dipeptides were explored to unveil the structural context of the unexpected selectivity of these inhibitors of M1 alanine aminopeptidases (APNs) versus M17 leucine aminopeptidase (LAP). The diaminophosphonic acids were obtained via aziridines in an improved synthetic procedure that was further expanded for the phosphinic pseudodipeptide system. The inhibitory activity, measured for three M1 and one M17 metalloaminopeptidases of different sources (bacterial, human and porcine), revealed several potent compounds (e.g., Ki = 65 nM of 1u for HsAPN). Two structures of an M1 representative (APN from Neisseria meningitidis) in complex with N-benzyl-1,2-diaminoethylphosphonic acid and N-cyclohexyl-1,2-diaminoethylphosphonic acid were determined by the X-ray crystallography. The analysis of these structures and the models of the phosphonic acid complexes of the human ortholog provided an insight into the role of the additional amino group and the hydrophobic substituents of the ligands within the S1 active site region.
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Affiliation(s)
- Ewelina Węglarz-Tomczak
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | | | - Bogusław Nocek
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, USA
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, USA
| | - Artur Mucha
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
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Berenstein AJ, Magariños MP, Chernomoretz A, Agüero F. A Multilayer Network Approach for Guiding Drug Repositioning in Neglected Diseases. PLoS Negl Trop Dis 2016; 10:e0004300. [PMID: 26735851 PMCID: PMC4703370 DOI: 10.1371/journal.pntd.0004300] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 11/21/2015] [Indexed: 12/16/2022] Open
Abstract
Drug development for neglected diseases has been historically hampered due to lack of market incentives. The advent of public domain resources containing chemical information from high throughput screenings is changing the landscape of drug discovery for these diseases. In this work we took advantage of data from extensively studied organisms like human, mouse, E. coli and yeast, among others, to develop a novel integrative network model to prioritize and identify candidate drug targets in neglected pathogen proteomes, and bioactive drug-like molecules. We modeled genomic (proteins) and chemical (bioactive compounds) data as a multilayer weighted network graph that takes advantage of bioactivity data across 221 species, chemical similarities between 1.7 105 compounds and several functional relations among 1.67 105 proteins. These relations comprised orthology, sharing of protein domains, and shared participation in defined biochemical pathways. We showcase the application of this network graph to the problem of prioritization of new candidate targets, based on the information available in the graph for known compound-target associations. We validated this strategy by performing a cross validation procedure for known mouse and Trypanosoma cruzi targets and showed that our approach outperforms classic alignment-based approaches. Moreover, our model provides additional flexibility as two different network definitions could be considered, finding in both cases qualitatively different but sensible candidate targets. We also showcase the application of the network to suggest targets for orphan compounds that are active against Plasmodium falciparum in high-throughput screens. In this case our approach provided a reduced prioritization list of target proteins for the query molecules and showed the ability to propose new testable hypotheses for each compound. Moreover, we found that some predictions highlighted by our network model were supported by independent experimental validations as found post-facto in the literature. Neglected tropical diseases are human infectious diseases that are often associated with poverty. Historically, lack of interest from the pharmaceutical industry resulted in the lack of good drugs to combat the majority of the pathogens that cause these diseases. Recently, the availability of open chemical information has increased with the advent of public domain chemical resources and the release of data from high throughput screening assays. Our aim in this work was to make use of data from extensively studied organisms like human, mouse, E. coli and yeast, among others, to prioritize and identify candidate drug targets in neglected pathogen proteomes, and drug-like bioactive molecules to foster drug development against neglected diseases. Our approach to the problem relied on applying bioinformatics and computational biology strategies to model large datasets spanning complete proteomes and extensive chemical information from publicly available sources. As a result, we were able to prioritize drug targets and identify potential targets for orphan bioactive drugs.
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Affiliation(s)
- Ariel José Berenstein
- Laboratorio de Bioinformática, Fundación Instituto Leloir, Buenos Aires, Argentina
- Departamento de Física, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María Paula Magariños
- Laboratorio de Genómica y Bioinformática, Instituto de Investigaciones Biotecnológicas–Instituto Tecnológico de Chascomús, Universidad de San Martín–CONICET, Sede San Martín, San Martín, Buenos Aires, Argentina
| | - Ariel Chernomoretz
- Laboratorio de Bioinformática, Fundación Instituto Leloir, Buenos Aires, Argentina
- Departamento de Física, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Fernán Agüero
- Laboratorio de Genómica y Bioinformática, Instituto de Investigaciones Biotecnológicas–Instituto Tecnológico de Chascomús, Universidad de San Martín–CONICET, Sede San Martín, San Martín, Buenos Aires, Argentina
- * E-mail: ,
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41
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Modak JK, Rut W, Wijeyewickrema LC, Pike RN, Drag M, Roujeinikova A. Structural basis for substrate specificity of Helicobacter pylori M17 aminopeptidase. Biochimie 2015; 121:60-71. [PMID: 26616008 DOI: 10.1016/j.biochi.2015.11.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 11/20/2015] [Indexed: 11/25/2022]
Abstract
The M17 aminopeptidase from the carcinogenic gastric bacterium Helicobacter pylori (HpM17AP) is an important housekeeping enzyme involved in catabolism of endogenous and exogenous peptides. It is implicated in H. pylori defence against the human innate immune response and in the mechanism of metronidazole resistance. Bestatin inhibits HpM17AP and suppresses H. pylori growth. To address the structural basis of catalysis and inhibition of this enzyme, we have established its specificity towards the N-terminal amino acid of peptide substrates and determined the crystal structures of HpM17AP and its complex with bestatin. The position of the D-phenylalanine moiety of the inhibitor with respect to the active-site metal ions, bicarbonate ion and with respect to other M17 aminopeptidases suggested that this residue binds to the S1 subsite of HpM17AP. In contrast to most characterized M17 aminopeptidases, HpM17AP displays preference for L-Arg over L-Leu residues in peptide substrates. Compared to very similar homologues from other bacteria, a distinguishing feature of HpM17AP is a hydrophilic pocket at the end of the S1 subsite that is likely to accommodate the charged head group of the L-Arg residue of the substrate. The pocket is flanked by a sodium ion (not present in M17 aminopeptidases that show preference for L-Leu) and its coordinating water molecules. In addition, the structure suggests that variable loops at the entrance to, and in the middle of, the substrate-binding channel are important determinants of substrate specificity of M17 aminopeptidases.
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Affiliation(s)
- Joyanta K Modak
- Infection and Immunity Program, Monash Biomedical Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Wioletta Rut
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology, Wroclaw, Poland
| | - Lakshmi C Wijeyewickrema
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Robert N Pike
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Marcin Drag
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology, Wroclaw, Poland
| | - Anna Roujeinikova
- Infection and Immunity Program, Monash Biomedical Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.
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Ruggeri C, Drinkwater N, Sivaraman KK, Bamert RS, McGowan S, Paiardini A. Identification and Validation of a Potent Dual Inhibitor of the P. falciparum M1 and M17 Aminopeptidases Using Virtual Screening. PLoS One 2015; 10:e0138957. [PMID: 26406322 PMCID: PMC4583420 DOI: 10.1371/journal.pone.0138957] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 09/04/2015] [Indexed: 01/19/2023] Open
Abstract
The Plasmodium falciparum PfA-M1 and PfA-M17 metalloaminopeptidases are validated drug targets for the discovery of antimalarial agents. In order to identify dual inhibitors of both proteins, we developed a hierarchical virtual screening approach, followed by in vitro evaluation of the highest scoring hits. Starting from the ZINC database of purchasable compounds, sequential 3D-pharmacophore and molecular docking steps were applied to filter the virtual 'hits'. At the end of virtual screening, 12 compounds were chosen and tested against the in vitro aminopeptidase activity of both PfA-M1 and PfA-M17. Two molecules showed significant inhibitory activity (low micromolar/nanomolar range) against both proteins. Finally, the crystal structure of the most potent compound in complex with both PfA-M1 and PfA-M17 was solved, revealing the binding mode and validating our computational approach.
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Affiliation(s)
- Chiara Ruggeri
- Dipartimento di Scienze biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Roma, Italy
| | - Nyssa Drinkwater
- Department of Microbiology, Monash University, Clayton Campus, Melbourne, Victoria, 3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne, Victoria, 3800, Australia
| | - Komagal Kannan Sivaraman
- Department of Microbiology, Monash University, Clayton Campus, Melbourne, Victoria, 3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne, Victoria, 3800, Australia
| | - Rebecca S. Bamert
- Department of Microbiology, Monash University, Clayton Campus, Melbourne, Victoria, 3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne, Victoria, 3800, Australia
| | - Sheena McGowan
- Department of Microbiology, Monash University, Clayton Campus, Melbourne, Victoria, 3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne, Victoria, 3800, Australia
- * E-mail: (SM); (AP)
| | - Alessandro Paiardini
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185, Roma, Italy
- * E-mail: (SM); (AP)
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43
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Bestatin induces specific changes in Trypanosoma cruzi dipeptide pool. Antimicrob Agents Chemother 2015; 59:2921-5. [PMID: 25712359 DOI: 10.1128/aac.05046-14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Accepted: 02/16/2015] [Indexed: 11/20/2022] Open
Abstract
Proteases and peptidases in Trypanosoma cruzi are considered potential targets for antichagasic chemotherapy. We monitored changes in low-mass metabolites in T. cruzi epimastigotes treated with bestatin, a dipeptide metalloaminopeptidase inhibitor. After treatment, multiple dipeptides were shown to be increased, confirming in situ inhibition of the leucine aminopeptidase of T. cruzi (LAPTc) and probably other peptidases.
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44
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High-level expression in Escherichia coli, purification and kinetic characterization of Plasmodium falciparum M1-aminopeptidase. Protein Expr Purif 2014; 104:103-14. [DOI: 10.1016/j.pep.2014.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 08/03/2014] [Accepted: 08/05/2014] [Indexed: 12/20/2022]
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45
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Mistry SN, Drinkwater N, Ruggeri C, Sivaraman KK, Loganathan S, Fletcher S, Drag M, Paiardini A, Avery VM, Scammells PJ, McGowan S. Two-Pronged Attack: Dual Inhibition of Plasmodium falciparum M1 and M17 Metalloaminopeptidases by a Novel Series of Hydroxamic Acid-Based Inhibitors. J Med Chem 2014; 57:9168-83. [DOI: 10.1021/jm501323a] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shailesh N. Mistry
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Nyssa Drinkwater
- Department
of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Chiara Ruggeri
- Department
of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- Dipartmento
di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Universita di Roma, 00185 Roma, Italy
| | - Komagal Kannan Sivaraman
- Department
of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Sasdekumar Loganathan
- Discovery
Biology, Eskitis Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Sabine Fletcher
- Discovery
Biology, Eskitis Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Marcin Drag
- Division
of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Alessandro Paiardini
- Dipartmento
di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Universita di Roma, 00185 Roma, Italy
| | - Vicky M. Avery
- Discovery
Biology, Eskitis Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Peter J. Scammells
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Sheena McGowan
- Department
of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
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Vassiliou S, Węglarz-Tomczak E, Berlicki Ł, Pawełczak M, Nocek B, Mulligan R, Joachimiak A, Mucha A. Structure-guided, single-point modifications in the phosphinic dipeptide structure yield highly potent and selective inhibitors of neutral aminopeptidases. J Med Chem 2014; 57:8140-51. [PMID: 25192493 PMCID: PMC4331105 DOI: 10.1021/jm501071f] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Seven crystal structures of alanyl aminopeptidase from Neisseria meningitides (the etiological agent of meningitis, NmAPN) complexed with organophosphorus compounds were resolved to determine the optimal inhibitor-enzyme interactions. The enantiomeric phosphonic acid analogs of Leu and hPhe, which correspond to the P1 amino acid residues of well-processed substrates, were used to assess the impact of the absolute configuration and the stereospecific hydrogen bond network formed between the aminophosphonate polar head and the active site residues on the binding affinity. For the hPhe analog, an imperfect stereochemical complementarity could be overcome by incorporating an appropriate P1 side chain. The constitution of P1'-extended structures was rationally designed and the lead, phosphinic dipeptide hPhePψ[CH2]Phe, was modified in a single position. Introducing a heteroatom/heteroatom-based fragment to either the P1 or P1' residue required new synthetic pathways. The compounds in the refined structure were low nanomolar and subnanomolar inhibitors of N. meningitides, porcine and human APNs, and the reference leucine aminopeptidase (LAP). The unnatural phosphinic dipeptide analogs exhibited a high affinity for monozinc APNs associated with a reasonable selectivity versus dizinc LAP. Another set of crystal structures containing the NmAPN dipeptide ligand were used to verify and to confirm the predicted binding modes; furthermore, novel contacts, which were promising for inhibitor development, were identified, including a π-π stacking interaction between a pyridine ring and Tyr372.
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Affiliation(s)
- Stamatia Vassiliou
- Laboratory of Organic Chemistry, Department of Chemistry, University of Athens , Panepistimiopolis, Zografou, 15701 Athens, Greece
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Abstract
Despite a century of control and eradication campaigns, malaria remains one of the world's most devastating diseases. Our once-powerful therapeutic weapons are losing the war against the Plasmodium parasite, whose ability to rapidly develop and spread drug resistance hamper past and present malaria-control efforts. Finding new and effective treatments for malaria is now a top global health priority, fuelling an increase in funding and promoting open-source collaborations between researchers and pharmaceutical consortia around the world. The result of this is rapid advances in drug discovery approaches and technologies, with three major methods for antimalarial drug development emerging: (i) chemistry-based, (ii) target-based, and (iii) cell-based. Common to all three of these approaches is the unique ability of structural biology to inform and accelerate drug development. Where possible, SBDD (structure-based drug discovery) is a foundation for antimalarial drug development programmes, and has been invaluable to the development of a number of current pre-clinical and clinical candidates. However, as we expand our understanding of the malarial life cycle and mechanisms of resistance development, SBDD as a field must continue to evolve in order to develop compounds that adhere to the ideal characteristics for novel antimalarial therapeutics and to avoid high attrition rates pre- and post-clinic. In the present review, we aim to examine the contribution that SBDD has made to current antimalarial drug development efforts, covering hit discovery to lead optimization and prevention of parasite resistance. Finally, the potential for structural biology, particularly high-throughput structural genomics programmes, to identify future targets for drug discovery are discussed.
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Aminopeptidase N1 (EtAPN1), an M1 metalloprotease of the apicomplexan parasite Eimeria tenella, participates in parasite development. EUKARYOTIC CELL 2014; 13:884-95. [PMID: 24839124 DOI: 10.1128/ec.00062-14] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Aminopeptidases N are metalloproteases of the M1 family that have been reported in numerous apicomplexan parasites, including Plasmodium, Toxoplasma, Cryptosporidium, and Eimeria. While investigating the potency of aminopeptidases as therapeutic targets against coccidiosis, one of the most important avian diseases caused by the genus Eimeria, we identified and characterized Eimeria tenella aminopeptidase N1 (EtAPN1). Its inhibition by bestatin and amastatin, as well as its reactivation by divalent ions, is typical of zinc-dependent metalloproteases. EtAPN1 shared a similar sequence, three-dimensional structure, and substrate specificity and similar kinetic parameters with A-M1 from Plasmodium falciparum (PfA-M1), a validated target in the treatment of malaria. EtAPN1 is synthesized as a 120-kDa precursor and cleaved into 96-, 68-, and 38-kDa forms during sporulation. Further, immunolocalization assays revealed that, similar to PfA-M1, EtAPN1 is present during the intracellular life cycle stages in both the parasite cytoplasm and the parasite nucleus. The present results support the hypothesis of a conserved role between the two aminopeptidases, and we suggest that EtAPN1 might be a valuable target for anticoccidiosis drugs.
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Carroll RK, Veillard F, Gagne DT, Lindenmuth JM, Poreba M, Drag M, Potempa J, Shaw LN. The Staphylococcus aureus leucine aminopeptidase is localized to the bacterial cytosol and demonstrates a broad substrate range that extends beyond leucine. Biol Chem 2014; 394:791-803. [PMID: 23241672 DOI: 10.1515/hsz-2012-0308] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 12/12/2012] [Indexed: 12/31/2022]
Abstract
Staphylococcus aureus is a potent pathogen of humans exhibiting a broad disease range, in part due to an extensive repertoire of secreted virulence factors, including proteases. Recently, we identified the first example of an intracellular protease (leucine aminopeptidase, LAP) that is required for virulence in S. aureus. Disruption of pepZ, the gene encoding LAP, had no affect on the growth rate of bacteria; however, in systemic and localized infection models the pepZ mutant had significantly attenuated virulence. Recently, a contradictory report was published suggesting that LAP is an extracellular enzyme and it is required for growth in S. aureus. Here, we investigate these results and confirm our previous findings that LAP is localized to the bacterial cytosol and is not required for growth. In addition, we conduct a biochemical investigation of purified recombinant LAP, identifying optimal conditions for enzymatic activity and substrate preference for hydrolysis. Our results show that LAP has a broad substrate range, including activity against the dipeptide cysteine-glycine, and that leucine is not the primary target of LAP.
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Affiliation(s)
- Ronan K Carroll
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA
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Byzia A, Haeggström JZ, Salvesen GS, Drag M. A remarkable activity of human leukotriene A4 hydrolase (LTA4H) toward unnatural amino acids. Amino Acids 2014; 46:1313-20. [PMID: 24573245 PMCID: PMC3984412 DOI: 10.1007/s00726-014-1694-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 02/06/2014] [Indexed: 12/01/2022]
Abstract
Leukotriene A4 hydrolase (LTA4H––EC 3.3.2.6) is a bifunctional zinc metalloenzyme, which processes LTA4 through an epoxide hydrolase activity and is also able to trim one amino acid at a time from N-terminal peptidic substrates via its aminopeptidase activity. In this report, we have utilized a library of 130 individual proteinogenic and unnatural amino acid fluorogenic substrates to determine the aminopeptidase specificity of this enzyme. We have found that the best proteinogenic amino acid recognized by LTA4H is arginine. However, we have also observed several unnatural amino acids, which were significantly better in terms of cleavage rate (kcat/Km values). Among them, the benzyl ester of aspartic acid exhibited a kcat/Km value that was more than two orders of magnitude higher (1.75 × 105 M−1 s−1) as compared to l-Arg (1.5 × 103 M−1 s−1). This information can be used for design of potent inhibitors of this enzyme, but may also suggest yet undiscovered functions or specificities of LTA4H.
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Affiliation(s)
- Anna Byzia
- Division of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, 50-370, Wrocław, Poland
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