1
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Mahanta PJ, Lhouvum K. Plasmodium falciparum proteases as new drug targets with special focus on metalloproteases. Mol Biochem Parasitol 2024; 258:111617. [PMID: 38554736 DOI: 10.1016/j.molbiopara.2024.111617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 02/15/2024] [Accepted: 03/10/2024] [Indexed: 04/02/2024]
Abstract
Malaria poses a significant global health threat particularly due to the prevalence of Plasmodium falciparum infection. With the emergence of parasite resistance to existing drugs including the recently discovered artemisinin, ongoing research seeks novel therapeutic avenues within the malaria parasite. Proteases are promising drug targets due to their essential roles in parasite biology, including hemoglobin digestion, merozoite invasion, and egress. While exploring the genomic landscape of Plasmodium falciparum, it has been revealed that there are 92 predicted proteases, with only approximately 14 of them having been characterized. These proteases are further distributed among 26 families grouped into five clans: aspartic proteases, cysteine proteases, metalloproteases, serine proteases, and threonine proteases. Focus on metalloprotease class shows further role in organelle processing for mitochondria and apicoplasts suggesting the potential of metalloproteases as viable drug targets. Holistic understanding of the parasite intricate life cycle and identification of potential drug targets are essential for developing effective therapeutic strategies against malaria and mitigating its devastating global impact.
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Affiliation(s)
| | - Kimjolly Lhouvum
- Department of Biotechnology, National Institute of Technology, Arunachal Pradesh, India.
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2
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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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3
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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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4
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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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5
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Marapaka AK, Sankoju P, Zhang G, Ding Y, Ma C, Pillalamarri V, Sudhakar R, Reddi B, Sijwali PS, Zhang Y, Addlagatta A. Development of peptidomimetic hydroxamates as PfA-M1 and PfA-M17 dual inhibitors: Biological evaluation and structural characterization by cocrystallization. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.09.102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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6
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Bala S, Yellamanda KV, Kadari A, Ravinuthala VSU, Kattula B, Singh OV, Gundla R, Addlagatta A. Selective inhibition of Helicobacter pylori methionine aminopeptidase by azaindole hydroxamic acid derivatives: Design, synthesis, in vitro biochemical and structural studies. Bioorg Chem 2021; 115:105185. [PMID: 34329997 DOI: 10.1016/j.bioorg.2021.105185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/04/2021] [Accepted: 07/14/2021] [Indexed: 12/27/2022]
Abstract
Methionine aminopeptidases (MetAPs) are an important class of enzymes that work co-translationally for the removal of initiator methionine. Chemical inhibition or gene knockdown is lethal to the microbes suggesting that they can be used as antibiotic targets. However, sequence and structural similarity between the microbial and host MetAPs has been a challenge in the identification of selective inhibitors. In this study, we have analyzed several thousands of MetAP sequences and established a pattern of variation in the S1 pocket of the enzyme. Based on this knowledge, we have designed a library of 17 azaindole based hydroxamic acid derivatives which selectively inhibited the MetAP from H. pylori compared to the human counterpart. Structural studies provided the molecular basis for the selectivity.
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Affiliation(s)
- Sandeepchowdary Bala
- Division of Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201 002, India
| | - Kalisha Vali Yellamanda
- Department of Chemistry, School of Science, GITAM Deemed to be University, Hyderabad 502 102, Telangana, India
| | - Anilkumar Kadari
- Department of Chemistry, School of Science, GITAM Deemed to be University, Hyderabad 502 102, Telangana, India
| | - Venkata S U Ravinuthala
- Division of Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, Telangana, India
| | - Bhavita Kattula
- Division of Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201 002, India
| | - Om V Singh
- Department of Chemistry, School of Science, GITAM Deemed to be University, Hyderabad 502 102, Telangana, India
| | - Rambabu Gundla
- Department of Chemistry, School of Science, GITAM Deemed to be University, Hyderabad 502 102, Telangana, India.
| | - Anthony Addlagatta
- Division of Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201 002, India.
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7
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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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8
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Harsági N, Keglevich G. The Hydrolysis of Phosphinates and Phosphonates: A Review. Molecules 2021; 26:molecules26102840. [PMID: 34064764 PMCID: PMC8150351 DOI: 10.3390/molecules26102840] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/04/2021] [Accepted: 05/06/2021] [Indexed: 11/21/2022] Open
Abstract
Phosphinic and phosphonic acids are useful intermediates and biologically active compounds which may be prepared from their esters, phosphinates and phosphonates, respectively, by hydrolysis or dealkylation. The hydrolysis may take place both under acidic and basic conditions, but the C-O bond may also be cleaved by trimethylsilyl halides. The hydrolysis of P-esters is a challenging task because, in most cases, the optimized reaction conditions have not yet been explored. Despite the importance of the hydrolysis of P-esters, this field has not yet been fully surveyed. In order to fill this gap, examples of acidic and alkaline hydrolysis, as well as the dealkylation of phosphinates and phosphonates, are summarized in this review.
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9
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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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10
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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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11
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Gao H, Pauphilet J, Struble TJ, Coley CW, Jensen KF. Direct Optimization across Computer-Generated Reaction Networks Balances Materials Use and Feasibility of Synthesis Plans for Molecule Libraries. J Chem Inf Model 2020; 61:493-504. [PMID: 33331158 DOI: 10.1021/acs.jcim.0c01032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The synthesis of thousands of candidate compounds in drug discovery and development offers opportunities for computer-aided synthesis planning to simplify the synthesis of molecule libraries by leveraging common starting materials and reaction conditions. We develop an optimization-based method to analyze large organic chemical reaction networks and design overlapping synthesis plans for entire molecule libraries so as to minimize the overall number of unique chemical compounds needed as either starting materials or reaction conditions. We consider multiple objectives, including the number of starting materials, the number of catalysts/solvents/reagents, and the likelihood of success of the overall syntheses plan, to select an optimal reaction network to access the target molecules. The library synthesis planning task was formulated as a network flow optimization problem, and we design an efficient decomposition scheme that reduces solution time by a factor of 5 and scales to instance with 48 target molecules and nearly 8000 intermediate reactions within hours. In four case studies of pharmaceutical compounds, the approach reduces the number of starting materials and catalysts/solvents/reagents needed by 32.2 and 66.0% on average and up to 63.2 and 80.0% in the best cases. The code implementation can be found at https://github.com/Coughy1991/Molecule_library_synthesis.
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Affiliation(s)
- Hanyu Gao
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jean Pauphilet
- London Business School, Regent's Park, London NW1 4SA, U.K
| | - Thomas J Struble
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Connor W Coley
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Klavs F Jensen
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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12
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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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13
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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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14
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Wanat W, Talma M, Dziuk B, Kafarski P. Synthesis and Inhibitory Studies of Phosphonic Acid Analogues of Homophenylalanine and Phenylalanine towards Alanyl Aminopeptidases. Biomolecules 2020; 10:E1319. [PMID: 32938014 PMCID: PMC7565091 DOI: 10.3390/biom10091319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/08/2020] [Accepted: 09/12/2020] [Indexed: 11/17/2022] Open
Abstract
A library of novel phosphonic acid analogues of homophenylalanine and phenylalanine, containing fluorine and bromine atoms in the phenyl ring, have been synthesized. Their inhibitory properties against two important alanine aminopeptidases, of human (hAPN, CD13) and porcine (pAPN) origin, were evaluated. Enzymatic studies and comparison with literature data indicated the higher inhibitory potential of the homophenylalanine over phenylalanine derivatives towards both enzymes. Their inhibition constants were in the submicromolar range for hAPN and the micromolar range for pAPN, with 1-amino-3-(3-fluorophenyl) propylphosphonic acid (compound 15c) being one of the best low-molecular inhibitors of both enzymes. To the best of our knowledge, P1 homophenylalanine analogues are the most active inhibitors of the APN among phosphonic and phosphinic derivatives described in the literature. Therefore, they constitute interesting building blocks for the further design of chemically more complex inhibitors. Based on molecular modeling simulations and SAR (structure-activity relationship) analysis, the optimal architecture of enzyme-inhibitor complexes for hAPN and pAPN were determined.
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Affiliation(s)
- Weronika Wanat
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland; (M.T.); (P.K.)
| | - Michał Talma
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland; (M.T.); (P.K.)
| | - Błażej Dziuk
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland;
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Paweł Kafarski
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland; (M.T.); (P.K.)
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15
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Rut W, Groborz K, Zhang L, Modrzycka S, Poreba M, Hilgenfeld R, Drag M. Profiling of flaviviral NS2B-NS3 protease specificity provides a structural basis for the development of selective chemical tools that differentiate Dengue from Zika and West Nile viruses. Antiviral Res 2020; 175:104731. [PMID: 32014497 DOI: 10.1016/j.antiviral.2020.104731] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 01/14/2020] [Accepted: 01/30/2020] [Indexed: 12/11/2022]
Abstract
West Nile virus (WNV) and Dengue virus (DENV) are mosquito-borne pathogenic flaviviruses. The NS2B-NS3 proteases found in these viruses are responsible for polyprotein processing and are therefore considered promising medical targets. Another ortholog of these proteases is found in Zika virus (ZIKV). In this work, we applied a combinatorial chemistry approach - Hybrid Combinatorial Substrate Library (HyCoSuL), to compare the substrate specificity profile at the P4-P1 positions of the NS2B-NS3 proteases found in all three viruses. The obtained data demonstrate that Zika and West Nile virus NS2B-NS3 proteases display highly overlapping substrate specificity in all binding pockets, while the Dengue ortholog has slightly different preferences toward natural and unnatural amino acids at the P2 and P4 positions. We used this information to extract specific peptide sequences recognized by the Dengue NS2B-NS3 protease. Next, we applied this knowledge to design a selective substrate and activity-based probe for the Dengue NS2B-NS3 protease. Our work provides a structural framework for the design of inhibitors, which could be used as a lead structure for drug development efforts.
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Affiliation(s)
- Wioletta Rut
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland.
| | - Katarzyna Groborz
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Linlin Zhang
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany; German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, 23562, Lübeck, Germany
| | - Sylwia Modrzycka
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Marcin Poreba
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Rolf Hilgenfeld
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany; German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, 23562, Lübeck, Germany
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland.
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16
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Rut W, Nielsen NV, Czarna J, Poreba M, Kanse SM, Drag M. Fluorescent activity-based probe for the selective detection of Factor VII activating protease (FSAP) in human plasma. Thromb Res 2019; 182:124-132. [PMID: 31479940 DOI: 10.1016/j.thromres.2019.08.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 07/28/2019] [Accepted: 08/17/2019] [Indexed: 12/21/2022]
Abstract
The zymogen form of circulating Factor VII activating protease (FSAP) is activated by histones that are released as a consequence of tissue damage or excessive inflammation. This is likely to have consequences in a number of disease conditions such as stroke, atherosclerosis, liver fibrosis, thrombosis and cancer. To investigate the existence, as well as the concentration of active FSAP (FSAPa) in complex biological systems an active site probe is needed. We used Hybrid Combinatorial Substrate Library (HyCoSuL) to screen for natural and unnatural amino acids that specifically bind to P4-P2 pockets of FSAPa. This information was used to designing a fluorogenic substrate (Ac-Pro-DTyr-Lys-Arg-ACC) as well as an irreversible, fluorogenic activity-based probe Cy5-6-Ahx-Pro-DTyr-Lys-ArgP(OPh)2. In normal human plasma the probe showed very low non-specific reactivity with some plasma proteins but upon activation of pro-FSAP with histones, strong labelling of FSAPa was observed. This labelling could be inhibited by aprotinin and was not found in the plasma of a subject that was homozygous for a polymorphism, which leads to loss of activity, or in plasma that was depleted of FSAP by antibodies. This 2nd generation substrate exhibited 6-fold higher catalytic efficiency than the 1st generation substrate and a much higher selectivity for FSAPa over other plasma proteases. This substrate and probe can be useful to detect and localize FSAPa in normal and pathological tissue and plasma to gain more insight into its functions.
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Affiliation(s)
- Wioletta Rut
- 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 Poreba
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland; NCI-designated Cancer Center, Sanford-Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Sandip M Kanse
- Oslo University Hospital and University of Oslo, Norway.
| | - 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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17
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Lee J, Vinh NB, Drinkwater N, Yang W, Kannan Sivaraman K, Schembri LS, Gazdik M, Grin PM, Butler GS, Overall CM, Charman SA, McGowan S, Scammells PJ. Novel Human Aminopeptidase N Inhibitors: Discovery and Optimization of Subsite Binding Interactions. J Med Chem 2019; 62:7185-7209. [PMID: 31251594 DOI: 10.1021/acs.jmedchem.9b00757] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Aminopeptidase N (APN/CD13) is a zinc-dependent M1 aminopeptidase that contributes to cancer progression by promoting angiogenesis, metastasis, and tumor invasion. We have previously identified hydroxamic acid-containing analogues that are potent inhibitors of the APN homologue from the malarial parasite Plasmodium falciparum M1 aminopeptidase (PfA-M1). Herein, we describe the rationale that underpins the repurposing of PfA-M1 inhibitors as novel APN inhibitors. A series of novel hydroxamic acid analogues were developed using a structure-based design approach and evaluated their inhibition activities against APN. N-(2-(Hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro-[1,1'-biphenyl]-4-yl)ethyl)-4-(methylsulfonamido)benzamide (6ad) proved to be an extremely potent inhibitor of APN activity in vitro, selective against other zinc-dependent enzymes such as matrix metalloproteases, and possessed limited cytotoxicity against Ad293 cells and favorable physicochemical and metabolic stability properties. The combined results indicate that compound 6ad may be a useful lead for the development of anticancer agents.
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Affiliation(s)
| | | | - Nyssa Drinkwater
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology , Monash University , Clayton Campus , Clayton , VIC 3800 , Australia
| | - Wei Yang
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology , Monash University , Clayton Campus , Clayton , VIC 3800 , Australia
| | - Komagal Kannan Sivaraman
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology , Monash University , Clayton Campus , Clayton , VIC 3800 , Australia
| | | | | | | | | | | | | | - Sheena McGowan
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology , Monash University , Clayton Campus , Clayton , VIC 3800 , Australia
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18
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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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19
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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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20
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Yang W, Riley BT, Lei X, Porebski BT, Kass I, Buckle AM, McGowan S. Mapping the Pathway and Dynamics of Bestatin Inhibition of the
Plasmodium falciparum
M1 Aminopeptidase
Pf
A‐M1. ChemMedChem 2018; 13:2504-2513. [DOI: 10.1002/cmdc.201800563] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/04/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Wei Yang
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery InstituteMonash University Clayton VIC 3800 Australia
| | - Blake T. Riley
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash University Clayton VIC 3800 Australia
| | - Xiangyun Lei
- School of Chemical and Biomolecular EngineeringGeorgia Institute of Technology Atlanta GA USA
| | - Benjamin T. Porebski
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash University Clayton VIC 3800 Australia
- Current address: Medical Research Council Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK
| | - Itamar Kass
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash University Clayton VIC 3800 Australia
- Victorian Life Sciences Computation CentreMonash University Clayton VIC 3800 Australia
| | - Ashley M. Buckle
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash University Clayton VIC 3800 Australia
| | - Sheena McGowan
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery InstituteMonash University Clayton VIC 3800 Australia
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21
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Salomon E, Schmitt M, Marapaka AK, Stamogiannos A, Revelant G, Schmitt C, Alavi S, Florent I, Addlagatta A, Stratikos E, Tarnus C, Albrecht S. Aminobenzosuberone Scaffold as a Modular Chemical Tool for the Inhibition of Therapeutically Relevant M1 Aminopeptidases. Molecules 2018; 23:molecules23102607. [PMID: 30314342 PMCID: PMC6222927 DOI: 10.3390/molecules23102607] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 10/08/2018] [Accepted: 10/10/2018] [Indexed: 01/22/2023] Open
Abstract
The synthesis of racemic substituted 7-amino-5,7,8,9-tetrahydrobenzocyclohepten-6-one hydrochlorides was optimized to enhance reproducibility and increase the overall yield. In order to investigate their specificity, series of enzyme inhibition assays were carried out against a diversity of proteases, covering representative members of aspartic, cysteine, metallo and serine endopeptidases and including eight members of the monometallic M1 family of aminopeptidases as well as two members of the bimetallic M17 and M28 aminopeptidase families. This aminobenzosuberone scaffold indeed demonstrated selective inhibition of M1 aminopeptidases to the exclusion of other tested protease families; it was particularly potent against mammalian APN and its bacterial/parasitic orthologues EcPepN and PfAM1.
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Affiliation(s)
- Emmanuel Salomon
- Laboratoire d'Innovation Moléculaire et Applications, Université de Haute-Alsace, Université de Strasbourg, CNRS, 68093 Mulhouse, France.
| | - Marjorie Schmitt
- Laboratoire d'Innovation Moléculaire et Applications, Université de Haute-Alsace, Université de Strasbourg, CNRS, 68093 Mulhouse, France.
| | - Anil Kumar Marapaka
- Centre for Chemical Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India.
- Academy of Scientific and Innovative Research (AcSIR), Rafi Marg, New Dehli 110001, India.
| | - Athanasios Stamogiannos
- Protein Chemistry Laboratory, INRASTES, National Centre for Scientific Research Demokritos, Agia Paraskevi, 15310 Athens, Greece.
| | - Germain Revelant
- Laboratoire d'Innovation Moléculaire et Applications, Université de Haute-Alsace, Université de Strasbourg, CNRS, 68093 Mulhouse, France.
| | - Céline Schmitt
- Laboratoire d'Innovation Moléculaire et Applications, Université de Haute-Alsace, Université de Strasbourg, CNRS, 68093 Mulhouse, France.
| | - Sarah Alavi
- Laboratoire d'Innovation Moléculaire et Applications, Université de Haute-Alsace, Université de Strasbourg, CNRS, 68093 Mulhouse, France.
| | - Isabelle Florent
- Molécules de Communication et Adaptation des Micro-organismes, Muséum National d'Histoire Naturelle, CNRS, 75231 Paris, France.
| | - Anthony Addlagatta
- Centre for Chemical Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India.
- Academy of Scientific and Innovative Research (AcSIR), Rafi Marg, New Dehli 110001, India.
| | - Efstratios Stratikos
- Protein Chemistry Laboratory, INRASTES, National Centre for Scientific Research Demokritos, Agia Paraskevi, 15310 Athens, Greece.
| | - Céline Tarnus
- Laboratoire d'Innovation Moléculaire et Applications, Université de Haute-Alsace, Université de Strasbourg, CNRS, 68093 Mulhouse, France.
| | - Sébastien Albrecht
- Laboratoire d'Innovation Moléculaire et Applications, Université de Haute-Alsace, Université de Strasbourg, CNRS, 68093 Mulhouse, France.
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22
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Assiri MA, Ali TE, Ali MM, Yahia IS. Synthesis and anticancer activity of some novel diethyl {(chromonyl/pyrazolyl) [(4-oxo-2-phenyl-quinazolin-3(4H)-yl)amino]methyl}phosphonates. PHOSPHORUS SULFUR 2018. [DOI: 10.1080/10426507.2018.1487969] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Mohammed A. Assiri
- Advanced Materials and Green Chemistry Chemistry Department Faculty of Science, King Khalid University, Abha, Saudi Arabia
- Research Center for Advanced Materials Science, King Khalid University, Abha, Saudi Arabia
| | - Tarik E. Ali
- Advanced Materials and Green Chemistry Chemistry Department Faculty of Science, King Khalid University, Abha, Saudi Arabia
- Department of Chemistry Faculty of Education, Ain Shams University Roxy, Cairo, Egypt
| | - Mamdouh M. Ali
- Department of Biochemistry Division of Genetic Engineering and Biotechnology, National Research Centre, Dokki Giza, Egypt
| | - I. S. Yahia
- Advanced Functional Materials & Optoelectronic Laboratory Department of Physics Faculty of Science, King Khalid University, Abha, Saudi Arabia
- Nanoscience Laboratory for Environmental and Biomedical Applications, Semiconductor Lab, Department of Physics Faculty of Education, Ain Shams University, Roxy, Cairo, Egypt
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23
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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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24
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Perfluorophenyl phosphonate analogues of aromatic amino acids: Synthesis, X-ray and DFT studies. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.01.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Sevrain CM, Berchel M, Couthon H, Jaffrès PA. Phosphonic acid: preparation and applications. Beilstein J Org Chem 2017; 13:2186-2213. [PMID: 29114326 PMCID: PMC5669239 DOI: 10.3762/bjoc.13.219] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 09/19/2017] [Indexed: 12/26/2022] Open
Abstract
The phosphonic acid functional group, which is characterized by a phosphorus atom bonded to three oxygen atoms (two hydroxy groups and one P=O double bond) and one carbon atom, is employed for many applications due to its structural analogy with the phosphate moiety or to its coordination or supramolecular properties. Phosphonic acids were used for their bioactive properties (drug, pro-drug), for bone targeting, for the design of supramolecular or hybrid materials, for the functionalization of surfaces, for analytical purposes, for medical imaging or as phosphoantigen. These applications are covering a large panel of research fields including chemistry, biology and physics thus making the synthesis of phosphonic acids a determinant question for numerous research projects. This review gives, first, an overview of the different fields of application of phosphonic acids that are illustrated with studies mainly selected over the last 20 years. Further, this review reports the different methods that can be used for the synthesis of phosphonic acids from dialkyl or diaryl phosphonate, from dichlorophosphine or dichlorophosphine oxide, from phosphonodiamide, or by oxidation of phosphinic acid. Direct methods that make use of phosphorous acid (H3PO3) and that produce a phosphonic acid functional group simultaneously to the formation of the P-C bond, are also surveyed. Among all these methods, the dealkylation of dialkyl phosphonates under either acidic conditions (HCl) or using the McKenna procedure (a two-step reaction that makes use of bromotrimethylsilane followed by methanolysis) constitute the best methods to prepare phosphonic acids.
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Affiliation(s)
- Charlotte M Sevrain
- CEMCA UMR CNRS 6521, Université de Brest, IBSAM. 6 Avenue Victor Le Gorgeu, 29238 Brest, France
| | - Mathieu Berchel
- CEMCA UMR CNRS 6521, Université de Brest, IBSAM. 6 Avenue Victor Le Gorgeu, 29238 Brest, France
| | - Hélène Couthon
- CEMCA UMR CNRS 6521, Université de Brest, IBSAM. 6 Avenue Victor Le Gorgeu, 29238 Brest, France
| | - Paul-Alain Jaffrès
- CEMCA UMR CNRS 6521, Université de Brest, IBSAM. 6 Avenue Victor Le Gorgeu, 29238 Brest, France
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26
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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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27
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Qian R, Kuliszewska E, Macoratti E, Hammerschmidt F. Chemoenzymatic Synthesis of Racemic and Enantiomerically Pure Phosphaaspartic Acid and Phosphaarginine. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700948] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Renzhe Qian
- Institut für Organische Chemie; Universität Wien; Wien Austria
| | | | - Elena Macoratti
- Institut für Organische Chemie; Universität Wien; Wien Austria
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Yang W, Riley BT, Lei X, Porebski BT, Kass I, Buckle AM, McGowan S. Generation of AMBER force field parameters for zinc centres of M1 and M17 family aminopeptidases. J Biomol Struct Dyn 2017; 36:2595-2604. [DOI: 10.1080/07391102.2017.1364669] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Wei Yang
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Blake T. Riley
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Xiangyun Lei
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive N.W., Atlanta, GA, 30332-0100, USA
| | - Benjamin T. Porebski
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Itamar Kass
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Victorian Life Sciences Computation Centre, Monash University, Clayton 3800, Victoria, Australia
| | - Ashley M. Buckle
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Sheena McGowan
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
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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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Drinkwater N, Lee J, Yang W, Malcolm TR, McGowan S. M1 aminopeptidases as drug targets: broad applications or therapeutic niche? FEBS J 2017; 284:1473-1488. [PMID: 28075056 PMCID: PMC7164018 DOI: 10.1111/febs.14009] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 12/12/2016] [Accepted: 01/09/2017] [Indexed: 12/30/2022]
Abstract
M1 aminopeptidase enzymes are a diverse family of metalloenzymes characterized by conserved structure and reaction specificity. Excluding viruses, M1 aminopeptidases are distributed throughout all phyla, and have been implicated in a wide range of functions including cell maintenance, growth and development, and defense. The structure and catalytic mechanism of M1 aminopeptidases are well understood, and make them ideal candidates for the design of small‐molecule inhibitors. As a result, many research groups have assessed their utility as therapeutic targets for both infectious and chronic diseases of humans, and many inhibitors with a range of target specificities and potential therapeutic applications have been developed. Herein, we have aimed to address these studies, to determine whether the family of M1 aminopeptidases does in fact present a universal target for the treatment of a diverse range of human diseases. Our analysis indicates that early validation of M1 aminopeptidases as therapeutic targets is often overlooked, which prevents the enzymes from being confirmed as drug targets. This validation cannot be neglected, and needs to include a thorough characterization of enzymes’ specific roles within complex physiological pathways. Furthermore, any chemical probes used in target validation must be carefully designed to ensure that specificity over the closely related enzymes has been achieved. While many drug discovery programs that target M1 aminopeptidases remain in their infancy, certain inhibitors have shown promise for the treatment of a range of conditions including malaria, hypertension, and cancer.
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Affiliation(s)
- Nyssa Drinkwater
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, Vic., Australia
| | - Jisook Lee
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Vic., Australia
| | - Wei Yang
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, Vic., Australia
| | - Tess R Malcolm
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, Vic., Australia
| | - Sheena McGowan
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Melbourne, Vic., Australia
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31
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Ogungbe IV, Setzer WN. The Potential of Secondary Metabolites from Plants as Drugs or Leads against Protozoan Neglected Diseases-Part III: In-Silico Molecular Docking Investigations. Molecules 2016; 21:E1389. [PMID: 27775577 PMCID: PMC6274513 DOI: 10.3390/molecules21101389] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 10/06/2016] [Accepted: 10/12/2016] [Indexed: 12/11/2022] Open
Abstract
Malaria, leishmaniasis, Chagas disease, and human African trypanosomiasis continue to cause considerable suffering and death in developing countries. Current treatment options for these parasitic protozoal diseases generally have severe side effects, may be ineffective or unavailable, and resistance is emerging. There is a constant need to discover new chemotherapeutic agents for these parasitic infections, and natural products continue to serve as a potential source. This review presents molecular docking studies of potential phytochemicals that target key protein targets in Leishmania spp., Trypanosoma spp., and Plasmodium spp.
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Affiliation(s)
- Ifedayo Victor Ogungbe
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39217, USA.
| | - William N Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
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32
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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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33
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Drinkwater N, Vinh NB, Mistry SN, Bamert RS, Ruggeri C, Holleran JP, Loganathan S, Paiardini A, Charman SA, Powell AK, Avery VM, McGowan S, Scammells PJ. Potent dual inhibitors of Plasmodium falciparum M1 and M17 aminopeptidases through optimization of S1 pocket interactions. Eur J Med Chem 2016; 110:43-64. [DOI: 10.1016/j.ejmech.2016.01.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 01/11/2016] [Accepted: 01/11/2016] [Indexed: 10/22/2022]
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34
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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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35
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Aneja B, Kumar B, Jairajpuri MA, Abid M. A structure guided drug-discovery approach towards identification of Plasmodium inhibitors. RSC Adv 2016. [DOI: 10.1039/c5ra19673f] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
This article provides a comprehensive review of inhibitors from natural, semisynthetic or synthetic sources against key targets ofPlasmodium falciparum.
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Affiliation(s)
- Babita Aneja
- Medicinal Chemistry Lab
- Department of Biosciences
- Jamia Millia Islamia (A Central University)
- New Delhi 110025
- India
| | - Bhumika Kumar
- Medicinal Chemistry Lab
- Department of Biosciences
- Jamia Millia Islamia (A Central University)
- New Delhi 110025
- India
| | - Mohamad Aman Jairajpuri
- Protein Conformation and Enzymology Lab
- Department of Biosciences
- Jamia Millia Islamia (A Central University)
- New Delhi 110025
- India
| | - Mohammad Abid
- Medicinal Chemistry Lab
- Department of Biosciences
- Jamia Millia Islamia (A Central University)
- New Delhi 110025
- India
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36
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Ramírez-Marroquín OA, Romero-Estudillo I, Viveros-Ceballos JL, Cativiela C, Ordóñez M. Convenient Synthesis of Cyclic α-Aminophosphonates by Alkylation-Cyclization Reaction of Iminophosphoglycinates Using Phase-Transfer Catalysis. European J Org Chem 2015. [DOI: 10.1002/ejoc.201501203] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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37
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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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38
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Design of a Selective Substrate and Activity Based Probe for Human Neutrophil Serine Protease 4. PLoS One 2015; 10:e0132818. [PMID: 26172376 PMCID: PMC4501687 DOI: 10.1371/journal.pone.0132818] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 06/18/2015] [Indexed: 12/11/2022] Open
Abstract
Human neutrophil serine protease 4 (NSP4), also known as PRSS57, is a recently discovered fourth member of the neutrophil serine proteases family. Although its biological function is not precisely defined, it is suggested to regulate neutrophil response and innate immune reactions. To create optimal substrates and visualization probes for NSP4 that distinguish it from other NSPs we have employed a Hybrid Combinatorial Substrate Library approach that utilizes natural and unnatural amino acids to explore protease subsite preferences. Library results were validated by synthesizing individual substrates, leading to the identification of an optimal substrate peptide. This substrate was converted to a covalent diphenyl phosphonate probe with an embedded biotin tag. This probe demonstrated high inhibitory activity and stringent specificity and may be suitable for visualizing NSP4 in the background of other NSPs.
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39
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Ordóñez M, Viveros-Ceballos JL, Cativiela C, Sayago FJ. An update on the stereoselective synthesis of α-aminophosphonic acids and derivatives. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.01.029] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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40
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Drinkwater N, Bamert RS, Sivaraman KK, Paiardini A, McGowan S. X-ray crystal structures of an orally available aminopeptidase inhibitor, Tosedostat, bound to anti-malarial drug targets P
f
A-M1 and P
f
A-M17. Proteins 2015; 83:789-95. [DOI: 10.1002/prot.24771] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 01/16/2015] [Accepted: 01/20/2015] [Indexed: 01/23/2023]
Affiliation(s)
- Nyssa Drinkwater
- Department of Biochemistry and Molecular Biology; Monash University; Melbourne Victoria 3800 Australia
| | - Rebecca S. Bamert
- Department of Biochemistry and Molecular Biology; Monash University; Melbourne Victoria 3800 Australia
| | - Komagal Kannan Sivaraman
- Department of Biochemistry and Molecular Biology; Monash University; Melbourne Victoria 3800 Australia
| | - Alessandro Paiardini
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”; Sapienza University of Rome; Rome Italy
| | - Sheena McGowan
- Department of Biochemistry and Molecular Biology; Monash University; Melbourne Victoria 3800 Australia
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Paiardini A, Bamert RS, Kannan-Sivaraman K, Drinkwater N, Mistry SN, Scammells PJ, McGowan S. Screening the Medicines for Malaria Venture "Malaria Box" against the Plasmodium falciparum aminopeptidases, M1, M17 and M18. PLoS One 2015; 10:e0115859. [PMID: 25700165 PMCID: PMC4336144 DOI: 10.1371/journal.pone.0115859] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 12/02/2014] [Indexed: 12/12/2022] Open
Abstract
Malaria is a parasitic disease that remains a global health burden. The ability of the parasite to rapidly develop resistance to therapeutics drives an urgent need for the delivery of new drugs. The Medicines for Malaria Venture have compounds known for their antimalarial activity, but not necessarily the molecular targets. In this study, we assess the ability of the “MMV 400” compounds to inhibit the activity of three metalloaminopeptidases from Plasmodium falciparum, PfA-M1, PfA-M17 and PfM18 AAP. We have developed a multiplex assay system to allow rapid primary screening of compounds against all three metalloaminopeptidases, followed by detailed analysis of promising compounds. Our results show that there were no PfM18AAP inhibitors, whereas two moderate inhibitors of the neutral aminopeptidases PfA-M1 and PfA-M17 were identified. Further investigation through structure-activity relationship studies and molecular docking suggest that these compounds are competitive inhibitors with novel binding mechanisms, acting through either non-classical zinc coordination or independently of zinc binding altogether. Although it is unlikely that inhibition of PfA-M1 and/or PfA-M17 is the primary mechanism responsible for the antiplasmodial activity reported for these compounds, their detailed characterization, as presented in this work, pave the way for their further optimization as a novel class of dual PfA-M1/PfA-M17 inhibitors utilising non-classical zinc binding groups.
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Affiliation(s)
- Alessandro Paiardini
- Dipartmento di Scienze biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, Roma, Italy
| | - Rebecca S. Bamert
- Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Komagal Kannan-Sivaraman
- Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Nyssa Drinkwater
- Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - Shailesh N. Mistry
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville Campus, Melbourne, Victoria, Australia
| | - Peter J. Scammells
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville Campus, Melbourne, Victoria, Australia
| | - Sheena McGowan
- Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne, Victoria, Australia
- * E-mail:
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42
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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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Substrate profiling of Finegoldia magna SufA protease, inhibitor screening and application to prevent human fibrinogen degradation and bacteria growth in vitro. Biochimie 2014; 103:137-43. [DOI: 10.1016/j.biochi.2014.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 05/12/2014] [Indexed: 11/21/2022]
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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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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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McGowan S. Working in concert: the metalloaminopeptidases from Plasmodium falciparum. Curr Opin Struct Biol 2013; 23:828-35. [PMID: 23948130 DOI: 10.1016/j.sbi.2013.07.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 07/24/2013] [Accepted: 07/24/2013] [Indexed: 01/05/2023]
Abstract
Malaria remains the world's most prevalent human parasitic disease. Because of the rapid spread of drug resistance in parasites, there is an urgent need to identify diverse new drug targets. One group of proteases that are emerging as targets for novel antimalarials are the metalloaminopeptidases. These enzymes catalyze the removal of the N-terminal amino acids from proteins and peptides. Given the restricted specificities of each of these enzymes for different N-terminal amino acids, it is thought that they act in concert to facilitate protein turnover. Here we review recent structure and functional data relating to the development of the Plasmodium falciparum metalloaminopeptidases as drug targets.
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Affiliation(s)
- Sheena McGowan
- Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne, Victoria 3800, Australia.
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