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Cheuka PM, Njaria P, Mayoka G, Funjika E. Emerging Drug Targets for Antimalarial Drug Discovery: Validation and Insights into Molecular Mechanisms of Function. J Med Chem 2024; 67:838-863. [PMID: 38198596 DOI: 10.1021/acs.jmedchem.3c01828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Approximately 619,000 malaria deaths were reported in 2021, and resistance to recommended drugs, including artemisinin-combination therapies (ACTs), threatens malaria control. Treatment failure with ACTs has been found to be as high as 93% in northeastern Thailand, and parasite mutations responsible for artemisinin resistance have already been reported in some African countries. Therefore, there is an urgent need to identify alternative treatments with novel targets. In this Perspective, we discuss some promising antimalarial drug targets, including enzymes involved in proteolysis, DNA and RNA metabolism, protein synthesis, and isoprenoid metabolism. Other targets discussed are transporters, Plasmodium falciparum acetyl-coenzyme A synthetase, N-myristoyltransferase, and the cyclic guanosine monophosphate-dependent protein kinase G. We have outlined mechanistic details, where these are understood, underpinning the biological roles and hence druggability of such targets. We believe that having a clear understanding of the underlying chemical interactions is valuable to medicinal chemists in their quest to design appropriate inhibitors.
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Affiliation(s)
- Peter Mubanga Cheuka
- Department of Chemistry, School of Natural Sciences, University of Zambia, P.O. Box 32379, Lusaka 10101, Zambia
| | - Paul Njaria
- Department of Pharmacognosy and Pharmaceutical Chemistry, Kenyatta University, P.O. Box 14548-00400, Nairobi 00100, Kenya
| | - Godfrey Mayoka
- Department of Pharmacology and Pharmacognosy, School of Pharmacy, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi 00100, Kenya
| | - Evelyn Funjika
- Department of Chemistry, School of Natural Sciences, University of Zambia, P.O. Box 32379, Lusaka 10101, Zambia
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Counihan NA, Chernih HC, de Koning-Ward TF. Post-translational lipid modifications in Plasmodium parasites. Curr Opin Microbiol 2022; 69:102196. [PMID: 36037636 DOI: 10.1016/j.mib.2022.102196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/15/2022] [Accepted: 07/27/2022] [Indexed: 11/26/2022]
Abstract
Most eukaryotic proteins undergo post-translational modifications (PTMs) that significantly alter protein properties, regulate diverse cellular processes and increase proteome complexity. Among these PTMs, lipidation plays a unique and key role in subcellular trafficking, signalling and membrane association of proteins through altering substrate function, and hydrophobicity via the addition and removal of lipid groups. Three prevalent classes of lipid modifications in Plasmodium parasites include prenylation, myristoylation, and palmitoylation that are important for regulating parasite-specific molecular processes. The enzymes that catalyse these lipid attachments have also been explored as potential drug targets for antimalarial development. In this review, we discuss these lipidation processes in Plasmodium spp. and the methodologies that have been used to identify these modifications in the deadliest species of malaria parasite, Plasmodium falciparum. We also discuss the development status of inhibitors that block these pathways.
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Affiliation(s)
- Natalie A Counihan
- School of Medicine, Deakin University, Geelong, Victoria, Australia; The Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, Victoria, Australia
| | - Hope C Chernih
- School of Medicine, Deakin University, Geelong, Victoria, Australia; The Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, Victoria, Australia
| | - Tania F de Koning-Ward
- School of Medicine, Deakin University, Geelong, Victoria, Australia; The Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, Victoria, Australia.
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Impact of a conserved N-terminal proline-rich region of the α-subunit of CAAX-prenyltransferases on their enzyme properties. Cell Commun Signal 2022; 20:118. [PMID: 35941619 PMCID: PMC9358863 DOI: 10.1186/s12964-022-00929-w] [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: 03/30/2022] [Accepted: 07/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The CAAX-prenyltransferases farnesyltransferase (FTase) and geranylgeranyltransferase I (GGTase I) are heterodimers with a common α- (FTα) and unique β-subunits. Recently, α-subunits of species (e.g., human) that harbour an N-terminal proline-rich region (PRR) showed different dimerization behaviours than α-subunits without PRR (e.g., yeast). However, the specific function of the PRR has not been elucidated so far. METHODS To determine whether the PRR is a conserved motif throughout eukaryotes, we performed phylogenetics. Elucidating the impact of the PRR on enzyme properties, we cloned human as well as rat PRR deficient FTα, expressed them heterologously and compared protein-protein interaction by pull-down as well as crosslinking experiments. Substrate binding, enzyme activity and sensitivity towards common FTase inhibitors of full length and PRR-deletion α-subunits and their physiological partners was determined by continuous fluorescence assays. RESULTS The PRR is highly conserved in mammals, with an exception for marsupials harbouring a poly-alanine region instead. The PRR shows similarities to canonical SH3-binding domains and to profilin-binding domains. Independent of the PRR, the α-subunits were able to dimerize with the different physiological β-subunits in in vitro as well as in yeast two-hybrid experiments. FTase and GGTase I with truncated FTα were active. The KM values for both substrates are in the single-digit µM range and show no significant differences between enzymes with full length and PRR deficient α-subunits within the species. CONCLUSIONS Our data demonstrate that an N-terminal PRR of FTα is highly conserved in mammals. We could show that the activity and inhibitability is not influenced by the truncation of the N-terminal region. Nevertheless, this region shows common binding motifs for other proteins involved in cell-signalling, trafficking and phosphorylation, suggesting that this PRR might have other or additional functions in mammals. Our results provide new starting points due to the relevant but only partly understood role of FTα in eukaryotic FTase and GGTase I. Video Abstract.
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Mathews ES, Jezewski AJ, Odom John AR. Protein Prenylation and Hsp40 in Thermotolerance of Plasmodium falciparum Malaria Parasites. mBio 2021; 12:e0076021. [PMID: 34182772 PMCID: PMC8262983 DOI: 10.1128/mbio.00760-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/01/2021] [Indexed: 12/31/2022] Open
Abstract
During its complex life cycle, the malaria parasite survives dramatic environmental stresses, including large temperature shifts. Protein prenylation is required during asexual replication of Plasmodium falciparum, and the canonical heat shock protein 40 protein (HSP40; PF3D7_1437900) is posttranslationally modified with a 15-carbon farnesyl isoprenyl group. In other organisms, farnesylation of Hsp40 orthologs controls their localization and function in resisting environmental stress. In this work, we find that plastidial isopentenyl pyrophosphate (IPP) synthesis and protein farnesylation are required for malaria parasite survival after cold and heat shock. Furthermore, loss of HSP40 farnesylation alters its membrane attachment and interaction with proteins in essential pathways in the parasite. Together, this work reveals that farnesylation is essential for parasite survival during temperature stress. Farnesylation of HSP40 may promote thermotolerance by guiding distinct chaperone-client protein interactions.
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Affiliation(s)
- Emily S. Mathews
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Andrew J. Jezewski
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Audrey R. Odom John
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Division of Infectious Disease, Department of Pediatrics, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Yang T, Ottilie S, Istvan ES, Godinez-Macias KP, Lukens AK, Baragaña B, Campo B, Walpole C, Niles JC, Chibale K, Dechering KJ, Llinás M, Lee MCS, Kato N, Wyllie S, McNamara CW, Gamo FJ, Burrows J, Fidock DA, Goldberg DE, Gilbert IH, Wirth DF, Winzeler EA. MalDA, Accelerating Malaria Drug Discovery. Trends Parasitol 2021; 37:493-507. [PMID: 33648890 PMCID: PMC8261838 DOI: 10.1016/j.pt.2021.01.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 12/24/2022]
Abstract
The Malaria Drug Accelerator (MalDA) is a consortium of 15 leading scientific laboratories. The aim of MalDA is to improve and accelerate the early antimalarial drug discovery process by identifying new, essential, druggable targets. In addition, it seeks to produce early lead inhibitors that may be advanced into drug candidates suitable for preclinical development and subsequent clinical testing in humans. By sharing resources, including expertise, knowledge, materials, and reagents, the consortium strives to eliminate the structural barriers often encountered in the drug discovery process. Here we discuss the mission of the consortium and its scientific achievements, including the identification of new chemically and biologically validated targets, as well as future scientific directions.
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Affiliation(s)
- Tuo Yang
- Department of Pediatrics, School of Medicine, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Sabine Ottilie
- Department of Pediatrics, School of Medicine, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Eva S Istvan
- Department of Internal Medicine, Division of Infectious Diseases, Washington University School of Medicine, Saint Louis, MO 63130, USA; Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63130, USA
| | - Karla P Godinez-Macias
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - Amanda K Lukens
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Beatriz Baragaña
- Wellcome Center for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, UK
| | - Brice Campo
- Medicines for Malaria Venture, 1215 Geneva 15, Switzerland
| | - Chris Walpole
- Structural Genomics Consortium, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Jacquin C Niles
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Building 56-341, 77 Massachusetts Avenue, Cambridge MA 02139-4307, USA
| | - Kelly Chibale
- Drug Discovery and Development Centre (H3D), University of Cape Town, Rondebosch 7701, South Africa; South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
| | | | - Manuel Llinás
- Department of Biochemistry and Molecular Biology and Department of Chemistry, Huck Center for Malaria Research, The Pennsylvania State University, University Park, PA 16082, USA
| | - Marcus C S Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Nobutaka Kato
- Global Health Drug Discovery Institute, Zhongguancun Dongsheng International Science Park, 1 North Yongtaizhuang Road, Beijing 100192, China
| | - Susan Wyllie
- Wellcome Center for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, UK
| | - Case W McNamara
- Calibr, a division of The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Francisco Javier Gamo
- Tres Cantos Medicines Development Campus, Diseases of the Developing World, GlaxoSmithKline, Tres Cantos, 28760, Madrid, Spain
| | - Jeremy Burrows
- Medicines for Malaria Venture, 1215 Geneva 15, Switzerland
| | - David A Fidock
- Department of Microbiology and Immunology and Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Daniel E Goldberg
- Department of Internal Medicine, Division of Infectious Diseases, Washington University School of Medicine, Saint Louis, MO 63130, USA; Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63130, USA
| | - Ian H Gilbert
- Wellcome Center for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, UK
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Elizabeth A Winzeler
- Department of Pediatrics, School of Medicine, University of California, San Diego (UCSD), La Jolla, CA 92093, USA.
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Phan TN, Baek KH, Lee N, Byun SY, Shum D, No JH. In Vitro and in Vivo Activity of mTOR Kinase and PI3K Inhibitors Against Leishmania donovani and Trypanosoma brucei. Molecules 2020; 25:molecules25081980. [PMID: 32340370 PMCID: PMC7221892 DOI: 10.3390/molecules25081980] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/02/2020] [Accepted: 04/21/2020] [Indexed: 11/16/2022] Open
Abstract
Kinetoplastid parasites, including Leishmania and Trypanosoma spp., are life threatening pathogens with a worldwide distribution. Next-generation therapeutics for treatment are needed as current treatments have limitations, such as toxicity and drug resistance. In this study, we examined the activities of established mammalian target of rapamycin (mTOR)/phosphoinositide 3-kinase (PI3K) inhibitors against these tropical diseases. High-throughput screening of a library of 1742 bioactive compounds against intracellular L. donovani was performed, and seven mTOR/PI3K inhibitors were identified. Dose-dilution assays revealed that these inhibitors had half maximal effective concentration (EC50) values ranging from 0.14 to 13.44 μM for L. donovani amastigotes and from 0.00005 to 8.16 μM for T. brucei. The results of a visceral leishmaniasis mouse model indicated that treatment with Torin2, dactolisib, or NVP-BGT226 resulted in reductions of 35%, 53%, and 54%, respectively, in the numbers of liver parasites. In an acute T. brucei mouse model using NVP-BGT226 parasite numbers were reduced to under the limits of detection by five consecutive days of treatment. Multiple sequence and structural alignment results indicated high similarities between mTOR and kinetoplastid TORs; the inhibitors are predicted to bind in a similar manner. Taken together, these results indicated that the TOR pathways of parasites have potential for the discovery of novel targets and new potent inhibitors.
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Affiliation(s)
- Trong-Nhat Phan
- Leishmania Research Laboratory, Institut Pasteur Korea, 696 Sampyeong-dong, Bundang-gu, Seongnam-si, Gyeonggi-do 463–400, Korea; (T.-N.P.); (K.-H.B.)
| | - Kyung-Hwa Baek
- Leishmania Research Laboratory, Institut Pasteur Korea, 696 Sampyeong-dong, Bundang-gu, Seongnam-si, Gyeonggi-do 463–400, Korea; (T.-N.P.); (K.-H.B.)
| | - Nakyung Lee
- Screening Development Platform, Institut Pasteur Korea, 696 Sampyeong-dong, Bundang-gu, Seongnam-si, Gyeonggi-do 463–400, Korea; (N.L.); (S.Y.B.); (D.S.)
| | - Soo Young Byun
- Screening Development Platform, Institut Pasteur Korea, 696 Sampyeong-dong, Bundang-gu, Seongnam-si, Gyeonggi-do 463–400, Korea; (N.L.); (S.Y.B.); (D.S.)
| | - David Shum
- Screening Development Platform, Institut Pasteur Korea, 696 Sampyeong-dong, Bundang-gu, Seongnam-si, Gyeonggi-do 463–400, Korea; (N.L.); (S.Y.B.); (D.S.)
| | - Joo Hwan No
- Leishmania Research Laboratory, Institut Pasteur Korea, 696 Sampyeong-dong, Bundang-gu, Seongnam-si, Gyeonggi-do 463–400, Korea; (T.-N.P.); (K.-H.B.)
- Correspondence:
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Cowell AN, Winzeler EA. Advances in omics-based methods to identify novel targets for malaria and other parasitic protozoan infections. Genome Med 2019; 11:63. [PMID: 31640748 PMCID: PMC6805675 DOI: 10.1186/s13073-019-0673-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 09/13/2019] [Indexed: 01/23/2023] Open
Abstract
A major advance in antimalarial drug discovery has been the shift towards cell-based phenotypic screening, with notable progress in the screening of compounds against the asexual blood stage, liver stage, and gametocytes. A primary method for drug target deconvolution in Plasmodium falciparum is in vitro evolution of compound-resistant parasites followed by whole-genome scans. Several of the most promising antimalarial drug targets, such as translation elongation factor 2 (eEF2) and phenylalanine tRNA synthetase (PheRS), have been identified or confirmed using this method. One drawback of this method is that if a mutated gene is uncharacterized, a substantial effort may be required to determine whether it is a drug target, a drug resistance gene, or if the mutation is merely a background mutation. Thus, the availability of high-throughput, functional genomic datasets can greatly assist with target deconvolution. Studies mapping genome-wide essentiality in P. falciparum or performing transcriptional profiling of the host and parasite during liver-stage infection with P. berghei have identified potentially druggable pathways. Advances in mapping the epigenomic regulation of the malaria parasite genome have also enabled the identification of key processes involved in parasite development. In addition, the examination of the host genome during infection has identified novel gene candidates associated with susceptibility to severe malaria. Here, we review recent studies that have used omics-based methods to identify novel targets for interventions against protozoan parasites, focusing on malaria, and we highlight the advantages and limitations of the approaches used. These approaches have also been extended to other protozoan pathogens, including Toxoplasma, Trypanosoma, and Leishmania spp., and these studies highlight how drug discovery efforts against these pathogens benefit from the utilization of diverse omics-based methods to identify promising drug targets.
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Affiliation(s)
- Annie N Cowell
- Division of Infectious Diseases and Global Health, Department of Medicine, University of California, San Diego, Gilman Drive, La Jolla, CA, 92093, USA.
| | - Elizabeth A Winzeler
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, Gilman Drive, La Jolla, CA, 92093, USA
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Gisselberg JE, Herrera Z, Orchard LM, Llinás M, Yeh E. Specific Inhibition of the Bifunctional Farnesyl/Geranylgeranyl Diphosphate Synthase in Malaria Parasites via a New Small-Molecule Binding Site. Cell Chem Biol 2017; 25:185-193.e5. [PMID: 29276048 DOI: 10.1016/j.chembiol.2017.11.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 09/24/2017] [Accepted: 11/22/2017] [Indexed: 12/19/2022]
Abstract
The bifunctional farnesyl/geranylgeranyl diphosphate synthase (FPPS/GGPPS) is a key branchpoint enzyme in isoprenoid biosynthesis in Plasmodium falciparum (malaria) parasites. PfFPPS/GGPPS is a validated, high-priority antimalarial drug target. Unfortunately, current bisphosphonate drugs that inhibit FPPS and GGPPS enzymes by acting as a diphosphate substrate analog show poor bioavailability and selectivity for PfFPPS/GGPPS. We identified a new non-bisphosphonate compound, MMV019313, which is highly selective for PfFPPS/GGPPS and showed no activity against human FPPS or GGPPS. Inhibition of PfFPPS/GGPPS by MMV019313, but not bisphosphonates, was disrupted in an S228T variant, demonstrating that MMV019313 and bisphosphonates have distinct modes of inhibition. Molecular docking indicated that MMV019313 did not bind previously characterized substrate sites in PfFPPS/GGPPS. Our finding uncovers a new, selective small-molecule binding site in this important antimalarial drug target with superior druggability compared with the known inhibitor site and sets the stage for the development of Plasmodium-specific FPPS/GGPPS inhibitors.
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Affiliation(s)
- Jolyn E Gisselberg
- Department of Biochemistry, Stanford Medical School, Stanford University, Stanford, CA 94305, USA
| | - Zachary Herrera
- Department of Biochemistry, Stanford Medical School, Stanford University, Stanford, CA 94305, USA
| | - Lindsey M Orchard
- Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA; Huck Center for Malaria Research, Pennsylvania State University, University Park, PA 16802, USA
| | - Manuel Llinás
- Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA; Huck Center for Malaria Research, Pennsylvania State University, University Park, PA 16802, USA; Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - Ellen Yeh
- Department of Biochemistry, Stanford Medical School, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford Medical School, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford Medical School, Stanford University, Stanford, CA 94305, USA.
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Istvan ES, Mallari JP, Corey VC, Dharia NV, Marshall GR, Winzeler EA, Goldberg DE. Esterase mutation is a mechanism of resistance to antimalarial compounds. Nat Commun 2017; 8:14240. [PMID: 28106035 PMCID: PMC5263872 DOI: 10.1038/ncomms14240] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 12/12/2016] [Indexed: 11/09/2022] Open
Abstract
Pepstatin is a potent peptidyl inhibitor of various malarial aspartic proteases, and also has parasiticidal activity. Activity of pepstatin against cultured Plasmodium falciparum is highly variable depending on the commercial source. Here we identify a minor contaminant (pepstatin butyl ester) as the active anti-parasitic principle. We synthesize a series of derivatives and characterize an analogue (pepstatin hexyl ester) with low nanomolar activity. By selecting resistant parasite mutants, we find that a parasite esterase, PfPARE (P. falciparum Prodrug Activation and Resistance Esterase) is required for activation of esterified pepstatin. Parasites with esterase mutations are resistant to pepstatin esters and to an open source antimalarial compound, MMV011438. Recombinant PfPARE hydrolyses pepstatin esters and de-esterifies MMV011438. We conclude that (1) pepstatin is a potent but poorly bioavailable antimalarial; (2) PfPARE is a functional esterase that is capable of activating prodrugs; (3) Mutations in PfPARE constitute a mechanism of antimalarial resistance. Pepstatin is a known inhibitor of malarial proteases, but its activity varies between sources. Here, Istvan et al. identify a pepstatin ester as the active component of pepstatin preparations and show that this prodrug is activated by a Plasmodium esterase, mutation of which can confer resistance to pepstatin and other compounds.
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Affiliation(s)
- Eva S Istvan
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, Saint Louis, Missouri 63110, USA.,Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA
| | - Jeremy P Mallari
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, Saint Louis, Missouri 63110, USA.,Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA
| | - Victoria C Corey
- Department of Pediatrics, School of Medicine, University of California San Diego School of Medicine, La Jolla, California 92093, USA
| | - Neekesh V Dharia
- Department of Pediatrics, School of Medicine, University of California San Diego School of Medicine, La Jolla, California 92093, USA
| | - Garland R Marshall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, USA
| | - Elizabeth A Winzeler
- Department of Pediatrics, School of Medicine, University of California San Diego School of Medicine, La Jolla, California 92093, USA
| | - Daniel E Goldberg
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, Saint Louis, Missouri 63110, USA.,Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA
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10
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Gisselberg JE, Zhang L, Elias JE, Yeh E. The Prenylated Proteome of Plasmodium falciparum Reveals Pathogen-specific Prenylation Activity and Drug Mechanism-of-action. Mol Cell Proteomics 2016; 16:S54-S64. [PMID: 28040698 DOI: 10.1074/mcp.m116.064550] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 12/01/2016] [Indexed: 11/06/2022] Open
Abstract
Plasmodium parasites contain several unique membrane compartments in which prenylated proteins may play important roles in pathogenesis. Protein prenylation has also been proposed as an antimalarial drug target because farnesyltransferase inhibitors cause potent growth inhibition of blood-stage Plasmodium However, the specific prenylated proteins that mediate antimalarial activity have yet to be identified. Given the potential for new parasite biology and elucidating drug mechanism-of-action, we performed a large-scale identification of the prenylated proteome in blood-stage P. falciparum parasites using an alkyne-labeled prenyl analog to specifically enrich parasite prenylated proteins. Twenty high-confidence candidates were identified, including several examples of pathogen-specific prenylation activity. One unique parasite prenylated protein was FYVE-containing coiled-coil protein (FCP), which is only conserved in Plasmodium and related Apicomplexan parasites and localizes to the parasite food vacuole. Targeting of FCP to this parasite-specific compartment was dependent on prenylation of its CaaX motif, as mutation of the prenylation site caused cytosolic mislocalization. We also showed that PfRab5b, which lacks C-terminal cysteines that are the only known site of Rab GTPase modification, is prenylated. Finally, we show that the THQ class of farnesyltransferase inhibitors abolishes FCP prenylation and causes its mislocalization, providing the first demonstration of a specific prenylated protein disrupted by antimalarial farnesyl transferase inhibitors. Altogether, these findings identify prenylated proteins that reveal unique parasite biology and are useful for evaluating prenyltransferase inhibitors for antimalarial drug development.
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Affiliation(s)
| | - Lichao Zhang
- ‖Chemical and Systems Biology, Stanford Medical School, Stanford University, Stanford, California 94025
| | - Joshua E Elias
- ‖Chemical and Systems Biology, Stanford Medical School, Stanford University, Stanford, California 94025
| | - Ellen Yeh
- From the ‡Department of Biochemistry, .,§Pathology.,¶Microbiology and Immunology, and
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Moorthy NSHN, Sousa SF, Ramos MJ, Fernandes PA. Binding mode of conformations and structure-based pharmacophore development for farnesyltransferase inhibitors. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1578-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Soni R, Sharma D, Patel S, Sharma B, Bhatt TK. Structure-based binding between protein farnesyl transferase and PRL-PTP of malaria parasite: an interaction study of prenylation process in Plasmodium. J Biomol Struct Dyn 2016; 34:2667-2678. [PMID: 26727035 DOI: 10.1080/07391102.2015.1126533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Protein prenylation is a post-translational modification critical for many cellular processes such as DNA replication, signaling, and trafficking. It is mediated by protein farnesyltransferase by recognizing 'CAAX' motif on protein substrate. Plasmodium falciparum also possesses many such proteins with 'CAAX' motif, involved in various pathways of the parasite. The interaction studies of PfPFT with its substrate were carried out using synthetic peptides but not with full protein. Therefore, in this study, we have modeled both PfPFT and its substrate protein tyrosine phosphatase (PfPRL-PTP) followed by interaction studies using protein-protein docking and molecular dynamics simulation. Our findings provided a clear picture of interactions at atomic level between prenyltransferase and its protein substrate. We are assured that this piece of information can be extended to many other proteins of parasite containing 'CAAX' motif and that it may also lead to the development of anti-malarials based on the inhibition of prenylation-dependent pathways of parasite..
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Affiliation(s)
- Rani Soni
- a Department of Biotechnology , Central University of Rajasthan , NH-8, Bandarsindri , Rajasthan 305801 , India
| | - Drista Sharma
- a Department of Biotechnology , Central University of Rajasthan , NH-8, Bandarsindri , Rajasthan 305801 , India
| | - Sachin Patel
- a Department of Biotechnology , Central University of Rajasthan , NH-8, Bandarsindri , Rajasthan 305801 , India
| | - Bhaskar Sharma
- a Department of Biotechnology , Central University of Rajasthan , NH-8, Bandarsindri , Rajasthan 305801 , India
| | - Tarun Kumar Bhatt
- a Department of Biotechnology , Central University of Rajasthan , NH-8, Bandarsindri , Rajasthan 305801 , India
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Moorthy NSHN, Sousa SF, Ramos MJ, Fernandes PA. Molecular dynamic simulations and structure-based pharmacophore development for farnesyltransferase inhibitors discovery. J Enzyme Inhib Med Chem 2016; 31:1428-42. [PMID: 26887913 DOI: 10.3109/14756366.2016.1144593] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Farnesyltransferase is one of the enzyme targets for the development of drugs for diseases, including cancer, malaria, progeria, etc. In the present study, the structure-based pharmacophore models have been developed from five complex structures (1LD7, 1NI1, 2IEJ, 2ZIR and 2ZIS) obtained from the protein data bank. Initially, molecular dynamic (MD) simulations were performed for the complexes for 10 ns using AMBER 12 software. The conformers of the complexes (75) generated from the equilibrated protein were undergone protein-ligand interaction fingerprint (PLIF) analysis. The results showed that some important residues, such as LeuB96, TrpB102, TrpB106, ArgB202, TyrB300, AspB359 and TyrB361, are predominantly present in most of the complexes for interactions. These residues form side chain acceptor and surface (hydrophobic or π-π) kind of interactions with the ligands present in the complexes. The structure-based pharmacophore models were generated from the fingerprint bits obtained from PLIF analysis. The pharmacophore models have 3-4 pharmacophore contours consist of acceptor and metal ligation (Acc & ML), hydrophobic (HydA) and extended acceptor (Acc2) features with the radius ranging between 1-3 Å for Acc & ML and 1-2 Å for HydA. The excluded volumes of the pharmacophore contours radius are between 1-2 Å. Further, the distance between the interacting groups, root mean square deviation (RMSD), root mean square fluctuation (RMSF) and radial distribution function (RDF) analysis were performed for the MD-simulated proteins using PTRAJ module. The generated pharmacophore models were used to screen a set of natural compounds and database compounds to select significant HITs. We conclude that the developed pharmacophore model can be a significant model for the identification of HITs as FTase inhibitors.
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Affiliation(s)
- N S Hari Narayana Moorthy
- a UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Universidade do Porto , 687, Rua do Campo Alegre , Porto , Portugal
| | - Sergio F Sousa
- a UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Universidade do Porto , 687, Rua do Campo Alegre , Porto , Portugal
| | - Maria J Ramos
- a UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Universidade do Porto , 687, Rua do Campo Alegre , Porto , Portugal
| | - Pedro A Fernandes
- a UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Universidade do Porto , 687, Rua do Campo Alegre , Porto , Portugal
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Rodriguez JB, Falcone BN, Szajnman SH. Approaches for Designing new Potent Inhibitors of Farnesyl Pyrophosphate Synthase. Expert Opin Drug Discov 2016; 11:307-20. [DOI: 10.1517/17460441.2016.1143814] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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15
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White J, Mascarenhas A, Pereira L, Dash R, Walke JT, Gawas P, Sharma A, Manoharan SK, Guler JL, Maki JN, Kumar A, Mahanta J, Valecha N, Dubhashi N, Vaz M, Gomes E, Chery L, Rathod PK. In vitro adaptation of Plasmodium falciparum reveal variations in cultivability. Malar J 2016; 15:33. [PMID: 26794408 PMCID: PMC4722725 DOI: 10.1186/s12936-015-1053-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Accepted: 12/15/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Culture-adapted Plasmodium falciparum parasites can offer deeper understanding of geographic variations in drug resistance, pathogenesis and immune evasion. To help ground population-based calculations and inferences from culture-adapted parasites, the complete range of parasites from a study area must be well represented in any collection. To this end, standardized adaptation methods and determinants of successful in vitro adaption were sought. METHODS Venous blood was collected from 33 P. falciparum-infected individuals at Goa Medical College and Hospital (Bambolim, Goa, India). Culture variables such as whole blood versus washed blood, heat-inactivated plasma versus Albumax, and different starting haematocrit levels were tested on fresh blood samples from patients. In vitro adaptation was considered successful when two four-fold or greater increases in parasitaemia were observed within, at most, 33 days of attempted culture. Subsequently, parasites from the same patients, which were originally cryopreserved following blood draw, were retested for adaptability for 45 days using identical host red blood cells (RBCs) and culture media. RESULTS At a new endemic area research site, ~65% of tested patient samples, with varied patient history and clinical presentation, were successfully culture-adapted immediately after blood collection. Cultures set up at 1% haematocrit and 0.5% Albumax adapted most rapidly, but no single test condition was uniformly fatal to culture adaptation. Success was not limited by low patient parasitaemia nor by patient age. Some parasites emerged even after significant delays in sample processing and even after initiation of treatment with anti-malarials. When 'day 0' cryopreserved samples were retested in parallel many months later using identical host RBCs and media, speed to adaptation appeared to be an intrinsic property of the parasites collected from individual patients. CONCLUSIONS Culture adaptation of P. falciparum in a field setting is formally shown to be robust. Parasites were found to have intrinsic variations in adaptability to culture conditions, with some lines requiring longer attempt periods for successful adaptation. Quantitative approaches described here can help describe phenotypic diversity of field parasite collections with precision. This is expected to improve population-based extrapolations of findings from field-derived fresh culture-adapted parasites to broader questions of public health importance.
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Affiliation(s)
- John White
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA.
| | - Anjali Mascarenhas
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA. .,Department of Medicine, Goa Medical College and Hospital, Bambolim, 403202, Goa, India.
| | - Ligia Pereira
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA. .,Department of Medicine, Goa Medical College and Hospital, Bambolim, 403202, Goa, India.
| | - Rashmi Dash
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA. .,Department of Medicine, Goa Medical College and Hospital, Bambolim, 403202, Goa, India.
| | - Jayashri T Walke
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA. .,Department of Medicine, Goa Medical College and Hospital, Bambolim, 403202, Goa, India.
| | - Pooja Gawas
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA. .,Department of Medicine, Goa Medical College and Hospital, Bambolim, 403202, Goa, India.
| | - Ambika Sharma
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA. .,Department of Medicine, Goa Medical College and Hospital, Bambolim, 403202, Goa, India.
| | - Suresh Kumar Manoharan
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA. .,Department of Medicine, Goa Medical College and Hospital, Bambolim, 403202, Goa, India.
| | - Jennifer L Guler
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA. .,Department of Biology, University of Virginia, Charlottesville, VA, 22904, USA.
| | - Jennifer N Maki
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA.
| | - Ashwani Kumar
- National Institute of Malaria Research (ICMR), Panaji, 403001, Goa, India.
| | - Jagadish Mahanta
- Regional Medical Research Centre (NE), Dibrugarh, 786001, Assam, India.
| | - Neena Valecha
- National Institute of Malaria Research (ICMR), New Delhi, 110077, India.
| | - Nagesh Dubhashi
- Department of Medicine, Goa Medical College and Hospital, Bambolim, 403202, Goa, India.
| | - Marina Vaz
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA. .,Department of Medicine, Goa Medical College and Hospital, Bambolim, 403202, Goa, India.
| | - Edwin Gomes
- Department of Medicine, Goa Medical College and Hospital, Bambolim, 403202, Goa, India.
| | - Laura Chery
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA.
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Guggisberg AM, Amthor RE, Odom AR. Isoprenoid biosynthesis in Plasmodium falciparum. EUKARYOTIC CELL 2014; 13:1348-59. [PMID: 25217461 PMCID: PMC4248697 DOI: 10.1128/ec.00160-14] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Malaria kills nearly 1 million people each year, and the protozoan parasite Plasmodium falciparum has become increasingly resistant to current therapies. Isoprenoid synthesis via the methylerythritol phosphate (MEP) pathway represents an attractive target for the development of new antimalarials. The phosphonic acid antibiotic fosmidomycin is a specific inhibitor of isoprenoid synthesis and has been a helpful tool to outline the essential functions of isoprenoid biosynthesis in P. falciparum. Isoprenoids are a large, diverse class of hydrocarbons that function in a variety of essential cellular processes in eukaryotes. In P. falciparum, isoprenoids are used for tRNA isopentenylation and protein prenylation, as well as the synthesis of vitamin E, carotenoids, ubiquinone, and dolichols. Recently, isoprenoid synthesis in P. falciparum has been shown to be regulated by a sugar phosphatase. We outline what is known about isoprenoid function and the regulation of isoprenoid synthesis in P. falciparum, in order to identify valuable directions for future research.
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Affiliation(s)
- Ann M Guggisberg
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Rachel E Amthor
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Audrey R Odom
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
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Peptide chemistry applied to a new family of phenothiazine-containing inhibitors of human farnesyltransferase. Bioorg Med Chem Lett 2014; 24:3180-5. [DOI: 10.1016/j.bmcl.2014.04.102] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 04/23/2014] [Accepted: 04/25/2014] [Indexed: 02/02/2023]
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18
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Thillainayagam M, Pandian L, Murugan KK, Vijayaparthasarathi V, Sundaramoorthy S, Anbarasu A, Ramaiah S. In silicoanalysis reveals the anti-malarial potential of quinolinyl chalcone derivatives. J Biomol Struct Dyn 2014; 33:961-77. [DOI: 10.1080/07391102.2014.920277] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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19
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Expression of functional Plasmodium falciparum enzymes using a wheat germ cell-free system. EUKARYOTIC CELL 2013; 12:1653-63. [PMID: 24123271 DOI: 10.1128/ec.00222-13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
One decade after the sequencing of the Plasmodium falciparum genome, 95% of malaria proteins in the genome cannot be expressed in traditional cell-based expression systems, and the targets of the best new leads for antimalarial drug discovery are either not known or not available in functional form. For a disease that kills up to 1 million people per year, routine expression of recombinant malaria proteins in functional form is needed both for the discovery of new therapeutics and for identification of targets of new drugs. We tested the general utility of cell-free systems for expressing malaria enzymes. Thirteen test enzyme sequences were reverse amplified from total RNA, cloned into a plant-like expression vector, and subjected to cell-free expression in a wheat germ system. Protein electrophoresis and autoradiography confirmed the synthesis of products of expected molecular masses. In rare problematic cases, truncated products were avoided by using synthetic genes carrying wheat codons. Scaled-up production generated 39 to 354 μg of soluble protein per 10 mg of translation lysate. Compared to rare proteins where cell-based systems do produce functional proteins, the cell-free yields are comparable or better. All 13 test products were enzymatically active, without failure. This general path to produce functional malaria proteins should now allow the community to access new tools, such as biologically active protein arrays, and lead to the discovery of new chemical functions, structures, and inhibitors of previously inaccessible malaria gene products.
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20
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VPS37 isoforms differentially modulate the ternary complex formation of ALIX, ALG-2, and ESCRT-I. Biosci Biotechnol Biochem 2013; 77:1715-21. [PMID: 23924735 DOI: 10.1271/bbb.130280] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The endosomal sorting complex required for transport (ESCRT) system comprises a series of protein complexes that play essential roles in multivesicular body (MVB) sorting of ubiquitylated membrane proteins, enveloped RNA virus budding, and cytokinesis in mammalian cells. The complex, named ESCRT-I, consists of four subunits (TSG101, VPS28, VPS37, and MVB12). There are four VPS37 isoforms. We have reported that ALIX (an ALG-2-interacting protein and accessory protein in the ESCRT system) is physically linked with TSG101 by ALG-2 in a Ca²⁺-dependent manner, but the role of ALG-2 as an adaptor protein for the ESCRT-I complex remains unknown. To characterize this adaptor function, initially we investigated the binding of ALG-2 to ESCRT-I complexes containing each one of the four different VPS37 isoforms by two approaches: first, Far-Western blot analysis with biotin-labeled ALG-2 probe, and second, a pulldown assay to determine the binding of the four recombinant ESCRT-I complexes to Strep-tagged ALG-2 after co-expression in HEK293T cells. VPS37B and VPS37C appeared to interact with ALG-2 in a stronger manner than TSG101 does. The results of in vitro binding assays using purified recombinant proteins indicated that ALG-2 functions as a Ca²⁺-dependent adaptor protein that bridges ALIX and ESCRT-I to form a ternary complex, ESCRT-I/ALIX/ALG-2.
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Guler JL, Freeman DL, Ahyong V, Patrapuvich R, White J, Gujjar R, Phillips MA, DeRisi J, Rathod PK. Asexual populations of the human malaria parasite, Plasmodium falciparum, use a two-step genomic strategy to acquire accurate, beneficial DNA amplifications. PLoS Pathog 2013; 9:e1003375. [PMID: 23717205 PMCID: PMC3662640 DOI: 10.1371/journal.ppat.1003375] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 04/05/2013] [Indexed: 11/18/2022] Open
Abstract
Malaria drug resistance contributes to up to a million annual deaths. Judicious deployment of new antimalarials and vaccines could benefit from an understanding of early molecular events that promote the evolution of parasites. Continuous in vitro challenge of Plasmodium falciparum parasites with a novel dihydroorotate dehydrogenase (DHODH) inhibitor reproducibly selected for resistant parasites. Genome-wide analysis of independently-derived resistant clones revealed a two-step strategy to evolutionary success. Some haploid blood-stage parasites first survive antimalarial pressure through fortuitous DNA duplications that always included the DHODH gene. Independently-selected parasites had different sized amplification units but they were always flanked by distant A/T tracks. Higher level amplification and resistance was attained using a second, more efficient and more accurate, mechanism for head-to-tail expansion of the founder unit. This second homology-based process could faithfully tune DNA copy numbers in either direction, always retaining the unique DNA amplification sequence from the original A/T-mediated duplication for that parasite line. Pseudo-polyploidy at relevant genomic loci sets the stage for gaining additional mutations at the locus of interest. Overall, we reveal a population-based genomic strategy for mutagenesis that operates in human stages of P. falciparum to efficiently yield resistance-causing genetic changes at the correct locus in a successful parasite. Importantly, these founding events arise with precision; no other new amplifications are seen in the resistant haploid blood stage parasite. This minimizes the need for meiotic genetic cleansing that can only occur in sexual stage development of the parasite in mosquitoes. Malaria parasites kill up to a million people around the world every year. Emergence of resistance to drugs remains a key obstacle against elimination of malaria. In the laboratory, parasites can efficiently acquire resistance to experimental antimalarials by changing DNA at the target locus. This happens efficiently even for an antimalarial that the parasite has never encountered in a clinical setting. In this study, we formally demonstrate how parasites achieve this feat: first, individual parasites in a population of millions randomly amplify large regions of DNA between short sequence repeats of adenines (A) or thymines (T) that are peppered throughout the malaria parasite genome. The rare lucky parasite that amplifies DNA coding for the target of the antimalarial, along with dozens of its neighboring genes, gains an evolutionary advantage and survives. In a second step, to withstand increasing drug pressure and to achieve higher levels of resistance, each parasite line makes additional copies of this region. This second expansion does not rely on the random A/T-based DNA rearrangements but, instead, a more precise amplification mechanism that retains the unique signature of co-amplified genes created earlier in each parasite. Generation of multiple copies of the target genes in the parasite genome may be the beginning of other beneficial changes for the parasite, including the future acquisition of mutations.
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Affiliation(s)
- Jennifer L. Guler
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington, United States of America
| | - Daniel L. Freeman
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington, United States of America
| | - Vida Ahyong
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California, United States of America
| | - Rapatbhorn Patrapuvich
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington, United States of America
| | - John White
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington, United States of America
| | - Ramesh Gujjar
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington, United States of America
| | - Margaret A. Phillips
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Joseph DeRisi
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California, United States of America
| | - Pradipsinh K. Rathod
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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Jouvenet N. Dynamics of ESCRT proteins. Cell Mol Life Sci 2012; 69:4121-33. [PMID: 22669260 PMCID: PMC11114710 DOI: 10.1007/s00018-012-1035-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Revised: 05/11/2012] [Accepted: 05/16/2012] [Indexed: 10/28/2022]
Abstract
Proteins of the ESCRT (endosomal sorting complex required for transport) complex function in membrane fission processes, such as multivesicular body (MVBs) formation, the terminal stages of cytokinesis, and separation of enveloped viruses from the plasma membrane. In mammalian cells, the machinery consists of a network of more than 20 proteins, organized into three complexes (ESCRT-I, -II, and -III), and other associated proteins such as the ATPase vacuolar protein sorting 4 (Vps4). Early biochemical studies of MVBs biogenesis in yeast support a model of sequential recruitment of ESCRT complexes on membranes. Live-cell imaging of ESCRT protein dynamics during viral budding and cytokinesis now reveal that this long-standing model of sequential assembly and disassembly holds true in mammalian cells.
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Ghinet A, Rigo B, Dubois J, Farce A, Hénichart JP, Gautret P. Discovery of ferrocene-containing farnesyltransferase inhibitors. Investigation of bulky lipophilic groups for the A2 binding site of farnesyltransferase. MEDCHEMCOMM 2012. [DOI: 10.1039/c2md20138k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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McNamara C, Winzeler EA. Target identification and validation of novel antimalarials. Future Microbiol 2011; 6:693-704. [PMID: 21707315 DOI: 10.2217/fmb.11.45] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
It has been recognized that new antimalarials with a novel mode of action are critical to combat the continued emergence and dissemination of drug-resistant parasites that threaten the efficacy of current malaria treatments. Thus, recent high-throughput screening campaigns have been initiated using asexual intraerythrocytic stage cell-based assays of Plasmodium falciparum. These have led to the unprecedented identification of over 10,000 new antimalarial compounds. Inherently, novel compounds identified by cell-based assays will have poorly defined modes of action. While some of these compounds may have recognizable targets, the majority of cell-based hits are comprised of unique chemical scaffolds usually lacking cross-resistance with known drugs. It is likely that these novel antimalarial scaffolds will reveal new targets. A challenge for the community will be to assign these small molecules to their targets. In this article, we review methodologies to assist in the determination of a compound's mode of action.
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Affiliation(s)
- Case McNamara
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
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25
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Diaz-Gonzalez R, Kuhlmann FM, Galan-Rodriguez C, da Silva LM, Saldivia M, Karver CE, Rodriguez A, Beverley SM, Navarro M, Pollastri MP. The susceptibility of trypanosomatid pathogens to PI3/mTOR kinase inhibitors affords a new opportunity for drug repurposing. PLoS Negl Trop Dis 2011; 5:e1297. [PMID: 21886855 PMCID: PMC3160303 DOI: 10.1371/journal.pntd.0001297] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2011] [Accepted: 07/19/2011] [Indexed: 12/20/2022] Open
Abstract
Background Target repurposing utilizes knowledge of “druggable” targets obtained in one organism and exploits this information to pursue new potential drug targets in other organisms. Here we describe such studies to evaluate whether inhibitors targeting the kinase domain of the mammalian Target of Rapamycin (mTOR) and human phosphoinositide-3-kinases (PI3Ks) show promise against the kinetoplastid parasites Trypanosoma brucei, T. cruzi, Leishmania major, and L. donovani. The genomes of trypanosomatids encode at least 12 proteins belonging to the PI3K protein superfamily, some of which are unique to parasites. Moreover, the shared PI3Ks differ greatly in sequence from those of the human host, thereby providing opportunities for selective inhibition. Methodology/Principal Findings We focused on 8 inhibitors targeting mTOR and/or PI3Ks selected from various stages of pre-clinical and clinical development, and tested them against in vitro parasite cultures and in vivo models of infection. Several inhibitors showed micromolar or better efficacy against these organisms in culture. One compound, NVP-BEZ235, displayed sub-nanomolar potency, efficacy against cultured parasites, and an ability to clear parasitemia in an animal model of T. brucei rhodesiense infection. Conclusions/Significance These studies strongly suggest that mammalian PI3/TOR kinase inhibitors are a productive starting point for anti-trypanosomal drug discovery. Our data suggest that NVP-BEZ235, an advanced clinical candidate against solid tumors, merits further investigation as an agent for treating African sleeping sickness. In our study we describe the potency of established phosphoinositide-3-kinase (PI3K) and mammalian Target of Rapamycin (mTOR) kinase inhibitors against three trypanosomatid parasites: Trypanosoma brucei, T. cruzi, and Leishmania sp., which are the causative agents for African sleeping sickness, Chagas disease, and leishmaniases, respectively. We noted that these parasites and humans express similar kinase enzymes. Since these similar human targets have been pursued by the drug industry for many years in the discovery of cellular growth and proliferation inhibitors, compounds developed as human anti-cancer agents should also have effect on inhibiting growth and proliferation of the parasites. With that in mind, we selected eight established PI3K and mTOR inhibitors for profiling against these pathogens. Among these inhibitors is an advanced clinical candidate against cancer, NVP-BEZ235, which we demonstrate to be a highly potent trypanocide in parasite cultures, and in a mouse model of T. brucei infection. Additionally, we describe observations of these inhibitors' effects on parasite growth and other cellular characteristics.
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Affiliation(s)
- Rosario Diaz-Gonzalez
- Instituto de Parasitología y Biomedicina “López-Neyra” Consejo Superior de Investigaciones Cientificas, Granada, Spain
| | - F. Matthew Kuhlmann
- Department of Medicine-Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Cristina Galan-Rodriguez
- Division of Medical Parasitology, Department of Microbiology, New York University School of Medicine, New York, New York, United States of America
| | - Luciana Madeira da Silva
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Manuel Saldivia
- Instituto de Parasitología y Biomedicina “López-Neyra” Consejo Superior de Investigaciones Cientificas, Granada, Spain
| | - Caitlin E. Karver
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Ana Rodriguez
- Division of Medical Parasitology, Department of Microbiology, New York University School of Medicine, New York, New York, United States of America
| | - Stephen M. Beverley
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Miguel Navarro
- Instituto de Parasitología y Biomedicina “López-Neyra” Consejo Superior de Investigaciones Cientificas, Granada, Spain
| | - Michael P. Pollastri
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
- * E-mail:
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Deshpande S, Jaiswal S, Katti SB, Prabhakar YS. CoMFA and CoMSIA analysis of tetrahydroquinolines as potential antimalarial agents. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2011; 22:473-488. [PMID: 21598193 DOI: 10.1080/1062936x.2011.569945] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were used on a dataset of compounds, some of them having been reported to inhibit Plasmodium falciparum protein, farnesyltransferase. The co-crystal structure of the lead molecule, BMS-214662 bound to Rat-PFT was used as a template. CoMFA yielded a good model, with r²(ncv) = 0.909, r²(cv) = 0.617 and was validated using an external set r²(pred) = 0.748). It compared favourably with CoMSIA. In the CoMFA model the steric and electrostatic fields exerted an almost equal influence on activity. The contour maps indicated the necessity for sterically large electropositive groups with electronegative tail to be present in these molecules for activity, and sterically large electronegative moieties on the sulfonamide linker. By incorporating these features some new compounds have been identified for further investigation.
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Affiliation(s)
- S Deshpande
- Medicinal and Process Chemistry Division, Central Drug Research Institute, CSIR, Lucknow, India
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Fletcher S, Keaney EP, Cummings CG, Blaskovich MA, Hast MA, Glenn MP, Chang SY, Bucher CJ, Floyd RJ, Katt WP, Gelb MH, Van Voorhis WC, Beese LS, Sebti SM, Hamilton AD. Structure-based design and synthesis of potent, ethylenediamine-based, mammalian farnesyltransferase inhibitors as anticancer agents. J Med Chem 2010; 53:6867-88. [PMID: 20822181 DOI: 10.1021/jm1001748] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A potent class of anticancer, human farnesyltransferase (hFTase) inhibitors has been identified by "piggy-backing" on potent, antimalarial inhibitors of Plasmodium falciparum farnesyltransferase (PfFTase). On the basis of a 4-fold substituted ethylenediamine scaffold, the inhibitors are structurally simple and readily derivatized, facilitating the extensive structure-activity relationship (SAR) study reported herein. Our most potent inhibitor is compound 1f, which exhibited an in vitro hFTase IC(50) value of 25 nM and a whole cell H-Ras processing IC(50) value of 90 nM. Moreover, it is noteworthy that several of our inhibitors proved highly selective for hFTase (up to 333-fold) over the related prenyltransferase enzyme geranylgeranyltransferase-I (GGTase-I). A crystal structure of inhibitor 1a co-crystallized with farnesyl pyrophosphate (FPP) in the active site of rat FTase illustrates that the para-benzonitrile moiety of 1a is stabilized by a π-π stacking interaction with the Y361β residue, suggesting a structural explanation for the observed importance of this component of our inhibitors.
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Affiliation(s)
- Steven Fletcher
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06511, USA
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Abstract
Macrophages have been postulated to play an important role in the pathogenesis of HIV-1 infection. Their ability to cross the blood-brain barrier and their resistance to virus-induced cytopathic effects allows them to serve as reservoirs for long-term infection. Thus, exploring the mechanisms of virus transmission from macrophages to target cells such as other macrophages or T lymphocytes is central to our understanding of HIV-1 pathogenesis and progression to AIDS, and is vital to the development of vaccines and novel antiretroviral therapies. This review provides an overview of the current understanding of cell-cell transmission in macrophages.
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Nzila A, Mwai L. In vitro selection of Plasmodium falciparum drug-resistant parasite lines. J Antimicrob Chemother 2009; 65:390-8. [PMID: 20022938 PMCID: PMC2818104 DOI: 10.1093/jac/dkp449] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The in vitro selection of antimicrobial resistance in important pathogens can provide critical information on the genetic basis of drug resistance, and such information can be used to predict, anticipate and even contain the spread of resistance in clinical practice. For instance, the discovery of the role of pfmdr1 in mefloquine resistance in malaria parasites resulted from in vitro studies. However, the in vitro selection of resistance is difficult, challenging and time consuming. In this review, we discuss the key parameters that impact on the efficiency of the in vitro selection of resistance, and propose strategies to improve and streamline this process.
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Affiliation(s)
- Alexis Nzila
- Kenya Medical Research Institute (KEMRI)/Wellcome Trust Collaborative Research Program, PO Box 230, 80108 Kilifi, Kenya.
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30
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XIE AIHUA, CLARK SHAWNAR, PRASANNA SIVAPRAKASAM, DOERKSEN ROBERTJ. Three-dimensional quantitative structure-farnesyltransferase inhibition analysis for some diaminobenzophenones. J Enzyme Inhib Med Chem 2009; 24:1220-8. [PMID: 19912055 PMCID: PMC10725738 DOI: 10.3109/14756360902781389] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
A 3D-QSAR investigation of 95 diaminobenzophenone yeast farnesyltransferase (FT) inhibitors selected from the work of Schlitzer et al. showed that steric, electrostatic, and hydrophobic properties play key roles in the bioactivity of the series. A CoMFA/CoMSIA combined model using the steric and electrostatic fields of CoMFA together with the hydrophobic field of CoMSIA showed significant improvement in prediction compared with the CoMFA steric and electrostatic fields model. The similarity of the 3D-QSAR field maps for yeast FT inhibition activity (from this work) and for antimalarial activity data (from previous work) and the correlation between those activities are discussed.
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Affiliation(s)
- AIHUA XIE
- Department of Medicinal Chemistry, School of Pharmacy, University of Mississippi, University, MS, 38677-1848, USA
| | - SHAWNA R. CLARK
- Department of Medicinal Chemistry, School of Pharmacy, University of Mississippi, University, MS, 38677-1848, USA
- Tougaloo College, Jackson, MS, 39174
| | - SIVAPRAKASAM PRASANNA
- Department of Medicinal Chemistry, School of Pharmacy, University of Mississippi, University, MS, 38677-1848, USA
| | - ROBERT J. DOERKSEN
- Department of Medicinal Chemistry, School of Pharmacy, University of Mississippi, University, MS, 38677-1848, USA
- Research Institute of Pharmaceutical Sciences, School of Pharmacy, University of Mississippi
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31
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Hast MA, Fletcher S, Cummings CG, Pusateri EE, Blaskovich MA, Rivas K, Gelb MH, Van Voorhis WC, Sebti SM, Hamilton AD, Beese LS. Structural basis for binding and selectivity of antimalarial and anticancer ethylenediamine inhibitors to protein farnesyltransferase. ACTA ACUST UNITED AC 2009; 16:181-92. [PMID: 19246009 DOI: 10.1016/j.chembiol.2009.01.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2008] [Revised: 01/21/2009] [Accepted: 01/26/2009] [Indexed: 11/24/2022]
Abstract
Protein farnesyltransferase (FTase) catalyzes an essential posttranslational lipid modification of more than 60 proteins involved in intracellular signal transduction networks. FTase inhibitors have emerged as a significant target for development of anticancer therapeutics and, more recently, for the treatment of parasitic diseases caused by protozoan pathogens, including malaria (Plasmodium falciparum). We present the X-ray crystallographic structures of complexes of mammalian FTase with five inhibitors based on an ethylenediamine scaffold, two of which exhibit over 1000-fold selective inhibition of P. falciparum FTase. These structures reveal the dominant determinants in both the inhibitor and enzyme that control binding and selectivity. Comparison to a homology model constructed for the P. falciparum FTase suggests opportunities for further improving selectivity of a new generation of antimalarial inhibitors.
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Affiliation(s)
- Michael A Hast
- Department of Biochemistry, Duke University Medical Center, Box 3711, Durham, NC 27710, USA
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32
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Sousa SF, Fernandes PA, Ramos MJ. Molecular dynamics simulations on the critical states of the farnesyltransferase enzyme. Bioorg Med Chem 2009; 17:3369-78. [DOI: 10.1016/j.bmc.2009.03.055] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2008] [Revised: 03/16/2009] [Accepted: 03/20/2009] [Indexed: 10/20/2022]
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Witkowski B, Berry A, Benoit-Vical F. Resistance to antimalarial compounds: Methods and applications. Drug Resist Updat 2009; 12:42-50. [DOI: 10.1016/j.drup.2009.01.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2008] [Revised: 01/22/2009] [Accepted: 01/31/2009] [Indexed: 11/29/2022]
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34
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Fletcher S, Cummings CG, Rivas K, Katt WP, Hornéy C, Buckner FS, Chakrabarti D, Sebti SM, Gelb MH, Van Voorhis WC, Hamilton AD. Potent, Plasmodium-selective farnesyltransferase inhibitors that arrest the growth of malaria parasites: structure-activity relationships of ethylenediamine-analogue scaffolds and homology model validation. J Med Chem 2008; 51:5176-97. [PMID: 18686940 DOI: 10.1021/jm800113p] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
New chemotherapeutics are urgently needed to combat malaria. We previously reported on a novel series of antimalarial, ethylenediamine-based inhibitors of protein farnesyltransferase (PFT). In the current study, we designed and synthesized a series of second generation inhibitors, wherein the core ethylenediamine scaffold was varied in order to examine both the homology model of Plasmodium falciparum PFT (PfPFT) and our predicted inhibitor binding mode. We identified several PfPFT inhibitors (PfPFTIs) that are selective for PfPFT versus the mammalian isoform of the enzyme (up to 136-fold selectivity), that inhibit the malarial enzyme with IC50 values down to 1 nM, and that block the growth of P. falciparum in infected whole cells (erythrocytes) with ED50 values down to 55 nM. The structure-activity data for these second generation, ethylenediamine-inspired PFT inhibitors were rationalized by consideration of the X-ray crystal structure of mammalian PFT and the homology model of the malarial enzyme.
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Affiliation(s)
- Steven Fletcher
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06511, USA
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35
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Moreno SNJ, Li ZH. Anti-infectives targeting the isoprenoid pathway of Toxoplasma gondii. Expert Opin Ther Targets 2008; 12:253-63. [PMID: 18269336 DOI: 10.1517/14728222.12.3.253] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Isoprenoids are an extensive group of natural products with diverse structures consisting of various numbers of five carbon isopentenyl diphosphate (IPP) units. OBJECTIVE We review here what is known about the isoprenoid pathway in T. gondii. METHODS Recent primary literature is reviewed. RESULTS/CONCLUSION Genomic evidence points toward the presence of a 1-deoxy-D-xylulose 5-phosphate/2-C-methyl-D-erythritol 4-phosphate (DOXP/MEP) pathway, similar to the one found in plants, which will produce isopentenyl diphosphate (IPP). The DOXP/MEP pathway has been validated as a target in the related Apicomplexan parasite Plasmodium. The DOXP/MEP pathway in Toxoplasma has not been characterized. Downstream in the pathway, the enzyme farnesyl diphosphate synthase (FPPS) has a central role in forming important intermediates since farnesyl diphosphate (FPP) is a precursor of critical molecules with fundamental biological function such as dolichols, heme a, cholesterol, farnesylated proteins and others. Strong evidence indicates that this enzyme is a valid target for drugs since bisphosphonates, which are specific FPPS inhibitors, inhibited parasite growth in vitro and in vivo. Our hypothesis is that the isoprenoid pathway constitutes a major novel target for the treatment of toxoplasmosis.
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Affiliation(s)
- Silvia N J Moreno
- University of Georgia, Department of Cellular Biology and Center for Tropical and Emerging Global Diseases, 500 D. W. Brooks Dr, Athens, Georgia 30602, USA.
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36
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Gupta MK, Prabhakar YS. QSAR study on tetrahydroquinoline analogues as plasmodium protein farnesyltransferase inhibitors: a comparison of rationales of malarial and mammalian enzyme inhibitory activities for selectivity. Eur J Med Chem 2008; 43:2751-67. [PMID: 18329140 DOI: 10.1016/j.ejmech.2008.01.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2007] [Revised: 01/14/2008] [Accepted: 01/14/2008] [Indexed: 11/27/2022]
Abstract
The quantitative structure-activity relationships of Plasmodium falciparum and Rat protein farnesyltransferase (PFT) inhibitory activities of 6-cyano-1-(3-methyl-3H-imidazoly-4-ylmethyl)-3-substituted-1,2,3,4-tetrahydroquinoline (THQ) analogues are investigated in order to explore the similarities/deviations between the two enzymes for these analogues. The structure space of a ligand (BMS-214662) bound to Rat-PFT (PDB code 1SA5) has been used as the conformational space of the compounds under investigation. The study has been carried out using the combinatorial protocol in multiple linear regression with several 2D- and 3D-descriptors from molecular operating environment (MOE) representing the physicochemical and electronic features of the compounds. The molecular potential energy and partially charged van der Waals surface areas have taken part in the PFT models. They suggested in favor of molecular arrangement with minimum energy and low positively/negatively charged surfaces for optimum Pf-PFT inhibitory activity. Furthermore, less hydrophobic compounds are preferred for the activity. The Rat-PFT inhibitory activity models suggested in favor of more negatively as well as more positively charged surface area descriptors for the better activity. The PLS analysis carried out on the descriptors of the Pf-PFT and Rat-PFT models suggested that among the parameters, the partially charged surface areas in the range -0.20 to -0.15 (PEOE_VSA-3) and -0.30 to -0.25 (PEOE_VSA-5), hydrophobicity (a_hyd, logP(o/w) and SlogP_VSA4), and electronic energy (PM3_Eele) of the molecules hold promise for modulating the Pf-PFT/R-PFT inhibitory activities of the compounds. This suggested the possibility of modulating the Pf-PFT/R-PFT inhibitory activities and bringing about selectivity in the THQ analogues for the malarial parasite enzyme.
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Affiliation(s)
- Manish K Gupta
- Medicinal and Process Chemistry Division, Central Drug Research Institute, Lucknow 226001, India
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37
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Gelb MH. Drug discovery for malaria: a very challenging and timely endeavor. Curr Opin Chem Biol 2007; 11:440-5. [PMID: 17761335 PMCID: PMC1993815 DOI: 10.1016/j.cbpa.2007.05.038] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Revised: 04/19/2007] [Accepted: 05/04/2007] [Indexed: 11/17/2022]
Abstract
The prevalence of resistance to known antimalarial drugs has resulted in the expansion of antimalarial drug discovery efforts. Academic and nonprofit institutions are partnering with the pharmaceutical industry to develop new antimalarial drugs. Several new antimalarial agents are undergoing clinical trials, mainly those resurrected from previous antimalarial drug discovery programs. Novel antimalarials are being advanced through the drug development process, of course, with the anticipated high failure rate typical of drug discovery. Many of these are summarized in this review. Mechanisms for funding antimalarial drug discovery and genomic information to aid drug target selection have never been better. It remains to be seen whether ongoing efforts will be sufficient for reducing malaria burden in the developing world.
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Affiliation(s)
- Michael H Gelb
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA.
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38
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Yokoyama K, Gillespie JR, Van Voorhis WC, Buckner FS, Gelb MH. Protein geranylgeranyltransferase-I of Trypanosoma cruzi. Mol Biochem Parasitol 2007; 157:32-43. [PMID: 17996962 DOI: 10.1016/j.molbiopara.2007.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2007] [Revised: 09/24/2007] [Accepted: 09/26/2007] [Indexed: 10/22/2022]
Abstract
Protein geranylgeranyltransferase type I (PGGT-I) and protein farnesyltransferase (PFT) occur in many eukaryotic cells. Both consist of two subunits, the common alpha subunit and a distinct beta subunit. In the gene database of protozoa Trypanosoma cruzi, the causative agent of Chagas' disease, a putative protein that consists of 401 amino acids with approximately 20% amino acid sequence identity to the PGGT-I beta of other species was identified, cloned, and characterized. Multiple sequence alignments show that the T. cruzi ortholog contains all three of the zinc-binding residues and several residues uniquely conserved in the beta subunit of PGGT-I. Co-expression of this protein and the alpha subunit of T. cruzi PFT in Sf9 insect cells yielded a dimeric protein that forms a tight complex selectively with [(3)H]geranylgeranyl pyrophosphate, indicating a key characteristic of a functional PGGT-I. Recombinant T. cruzi PGGT-I ortholog showed geranylgeranyltransferase activity with distinct specificity toward the C-terminal CaaX motif of protein substrates compared to that of the mammalian PGGT-I and T. cruzi PFT. Most of the CaaX-containing proteins with X=Leu are good substrates of T. cruzi PGGT-I, and those with X=Met are substrates for both T. cruzi PFT and PGGT-I, whereas unlike mammalian PGGT-I, those with X=Phe are poor substrates for T. cruzi PGGT-I. Several candidates for T. cruzi PGGT-I or PFT substrates containing the C-terminal CaaX motif are found in the T. cruzi gene database. Among five C-terminal peptides of those tested, a peptide of a Ras-like protein ending with CVLL was selectively geranylgeranylated by T. cruzi PGGT-I. Other peptides with CTQQ (Tcj2 DNAJ protein), CAVM (TcPRL-1 protein tyrosine phosphatase), CHFM (a small GTPase like protein), and CQLF (TcRho1 GTPase) were specific substrates for T. cruzi PFT but not for PGGT-I. The mRNA and protein of the T. cruzi PGGT-I beta ortholog were detected in three life-cycle stages of T. cruzi. Cytosol fractions from trypomastigotes (infectious mammalian stage) and epimastigotes (insect stage) were shown to contain levels of PGGT-I activity that are approximately 100-fold lower than PFT activity. The CaaX mimetics known as PGGT-I inhibitors show very low potency against T. cruzi PGGT-I compared to the mammalian enzyme, suggesting the potential to develop selective inhibitors against the parasite enzyme.
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Affiliation(s)
- Kohei Yokoyama
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA.
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39
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Abstract
Widespread parasitic resistance has led to an urgent need for the development and implementation of new drugs for the treatment of Plasmodium falciparum malaria. Artemisinin and its derivatives are becoming increasingly important, used preferably in combination with a second antimalarial agent to increase the efficacy and slow the development of resistance. However, cost, production and pharmacological issues associated with artemisinin derivatives and potential partner drugs are hindering the implementation of combination therapies. This article reviews the molecular basis of the action of, and resistance to, different antimalarials and examines the prospects for the next generation of drugs to combat this potentially lethal human pathogen.
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Affiliation(s)
- Leann Tilley
- Department of Biochemistry, La Trobe University, Melbourne, Victoria, Australia.
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40
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Bendale P, Olepu S, Suryadevara PK, Bulbule V, Rivas K, Nallan L, Smart B, Yokoyama K, Ankala S, Pendyala PR, Floyd D, Lombardo LJ, Williams DK, Buckner FS, Chakrabarti D, Verlinde CLMJ, Van Voorhis WC, Gelb MH. Second generation tetrahydroquinoline-based protein farnesyltransferase inhibitors as antimalarials. J Med Chem 2007; 50:4585-605. [PMID: 17722901 PMCID: PMC2894570 DOI: 10.1021/jm0703340] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Substituted tetrahydroquinolines (THQs) have been previously identified as inhibitors of mammalian protein farnesyltransferase (PFT). Previously we showed that blocking PFT in the malaria parasite led to cell death and that THQ-based inhibitors are the most potent among several structural classes of PFT inhibitors (PFTIs). We have prepared 266 THQ-based PFTIs and discovered several compounds that inhibit the malarial enzyme in the sub- to low-nanomolar range and that block the growth of the parasite (P. falciparum) in the low-nanomolar range. This body of structure-activity data can be rationalized in most cases by consideration of the X-ray structure of one of the THQs bound to mammalian PFT together with a homology structural model of the malarial enzyme. The results of this study provide the basis for selection of antimalarial PFTIs for further evaluation in preclinical drug discovery assays.
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Affiliation(s)
- Pravin Bendale
- Department of Chemistry, University of Washington, Seattle, Washington 98195
| | - Srinivas Olepu
- Department of Chemistry, University of Washington, Seattle, Washington 98195
| | | | - Vivek Bulbule
- Department of Chemistry, University of Washington, Seattle, Washington 98195
| | - Kasey Rivas
- Department of Medicine, University of Washington, Seattle, Washington 98195
- Department of Pathobiology, University of Washington, Seattle, Washington 98195
| | - Laxman Nallan
- Department of Chemistry, University of Washington, Seattle, Washington 98195
| | - Brian Smart
- Department of Chemistry, University of Washington, Seattle, Washington 98195
| | - Kohei Yokoyama
- Department of Chemistry, University of Washington, Seattle, Washington 98195
| | - Sudha Ankala
- Department of Chemistry, University of Washington, Seattle, Washington 98195
| | - Prakash Rao Pendyala
- Department of Molecular Biology and Microbiology, University of Central Florida, Orlando, Florida 32826
| | - David Floyd
- Pharmacopeia Drug Discovery, Princeton, New Jersey
| | - Louis J. Lombardo
- Bristol-Myers Squibb Pharmaceutical Research Institute, Princeton, New Jersey 08543-4000
| | - David K. Williams
- Bristol-Myers Squibb Pharmaceutical Research Institute, Princeton, New Jersey 08543-4000
| | - Frederick S. Buckner
- Department of Medicine, University of Washington, Seattle, Washington 98195
- Department of Pathobiology, University of Washington, Seattle, Washington 98195
| | - Debopam Chakrabarti
- Department of Molecular Biology and Microbiology, University of Central Florida, Orlando, Florida 32826
| | | | - Wesley C. Van Voorhis
- Department of Medicine, University of Washington, Seattle, Washington 98195
- Department of Pathobiology, University of Washington, Seattle, Washington 98195
| | - Michael H. Gelb
- Department of Chemistry, University of Washington, Seattle, Washington 98195
- Department of Biochemistry, University of Washington, Seattle, Washington 98195
- To whom correspondence should be addressed. Phone: 206-543-7142. Fax: 206-685-8665.
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41
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Van Voorhis WC, Rivas KL, Bendale P, Nallan L, Hornéy C, Barrett LK, Bauer KD, Smart BP, Ankala S, Hucke O, Verlinde CLMJ, Chakrabarti D, Strickland C, Yokoyama K, Buckner FS, Hamilton AD, Williams DK, Lombardo LJ, Floyd D, Gelb MH. Efficacy, pharmacokinetics, and metabolism of tetrahydroquinoline inhibitors of Plasmodium falciparum protein farnesyltransferase. Antimicrob Agents Chemother 2007; 51:3659-71. [PMID: 17606674 PMCID: PMC2043286 DOI: 10.1128/aac.00246-07] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
New antimalarials are urgently needed. We have shown that tetrahydroquinoline (THQ) protein farnesyltransferase (PFT) inhibitors (PFTIs) are effective against the Plasmodium falciparum PFT and are effective at killing P. falciparum in vitro. Previously described THQ PFTIs had limitations of poor oral bioavailability and rapid clearance from the circulation of rodents. In this paper, we validate both the Caco-2 cell permeability model for predicting THQ intestinal absorption and the in vitro liver microsome model for predicting THQ clearance in vivo. Incremental improvements in efficacy, oral absorption, and clearance rate were monitored by in vitro tests; and these tests were followed up with in vivo absorption, distribution, metabolism, and excretion studies. One compound, PB-93, achieved cure when it was given orally to P. berghei-infected rats every 8 h for a total of 72 h. However, PB-93 was rapidly cleared, and dosing every 12 h failed to cure the rats. Thus, the in vivo results corroborate the in vitro pharmacodynamics and demonstrate that 72 h of continuous high-level exposure to PFTIs is necessary to kill plasmodia. The metabolism of PB-93 was demonstrated by a novel technique that relied on double labeling with a radiolabel and heavy isotopes combined with radiometric liquid chromatography and mass spectrometry. The major liver microsome metabolite of PB-93 has the PFT Zn-binding N-methyl-imidazole removed; this metabolite is inactive in blocking PFT function. By solving the X-ray crystal structure of PB-93 bound to rat PFT, a model of PB-93 bound to malarial PFT was constructed. This model suggests areas of the THQ PFTIs that can be modified to retain efficacy and protect the Zn-binding N-methyl-imidazole from dealkylation.
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Affiliation(s)
- Wesley C Van Voorhis
- Department of Medicine, University of Washington, Room I-104-E, Health Sciences Building, Seattle, WA 98195-7185, USA.
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42
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Raz T, Nardi V, Azam M, Cortes J, Daley GQ. Farnesyl transferase inhibitor resistance probed by target mutagenesis. Blood 2007; 110:2102-9. [PMID: 17536018 PMCID: PMC1976354 DOI: 10.1182/blood-2006-12-064907] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Mutation in the target oncoprotein is a common mechanism of resistance to tyrosine kinase inhibitors, as exemplified by the many BCR/ABL mutations that thwart imatinib activity in patients with chronic myelogenous leukemia. It remains unclear whether normal cellular protein targets of chemotherapeutics will evolve drug resistance via mutation to a similar extent. We conducted an in vitro screen for resistance to lonafarnib, a farnesyl protein transferase inhibitor that blocks prenylation of a number of proteins important in cell proliferation, and identified 9 mutations clustering around the lonafarnib binding site. In patients treated with a combination of imatinib and lonafarnib, we identified farnesyl protein transferase mutations in residues identified in our screen. Substitutions at Y361 were found in patients prior to treatment initiation, suggesting that these mutants might confer a proliferative advantage to leukemia cells, which we were able to confirm in cell culture. In vitro mutagenesis of normal cellular enzymes can be exploited to identify mutations that confer chemotherapy resistance to novel agents.
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MESH Headings
- Animals
- Antineoplastic Combined Chemotherapy Protocols/pharmacology
- Apoptosis
- Benzamides
- Cell Proliferation/drug effects
- Drug Resistance, Neoplasm
- Enzyme Inhibitors/pharmacology
- Farnesyltranstransferase/antagonists & inhibitors
- Farnesyltranstransferase/genetics
- Humans
- Imatinib Mesylate
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/enzymology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Mice
- Mutagenesis
- Mutagenesis, Site-Directed
- Mutation/genetics
- Pilot Projects
- Piperazines/administration & dosage
- Piperidines/administration & dosage
- Protein Conformation
- Protein Prenylation
- Pyridines/administration & dosage
- Pyrimidines/administration & dosage
- Tumor Cells, Cultured
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Affiliation(s)
- Tal Raz
- Division of Hematology/Oncology, Children's Hospital Boston, and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
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43
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Sousa SF, Fernandes PA, Ramos MJ. Theoretical studies on farnesyl transferase: Evidence for thioether product coordination to the active-site zinc sphere. J Comput Chem 2007; 28:1160-8. [PMID: 17342704 DOI: 10.1002/jcc.20577] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Farnesyltransferase (FTase), an interesting zinc metaloenzyme, has been the subject of great attention in anticancer research over the last decade. However, despite the major accomplishments in the field, some very pungent questions on the farnesylation mechanism still persist. In this study, the authors have analyzed a mechanistic paradox that arises from the existence of several contradicting and inconclusive experimental evidence regarding the existence of direct coordination between the active-site zinc cation and the thioether from the farnesylated peptide product, which include UV-vis spectroscopy data on a Co(2+)-substituted FTase, two X-ray crystallographic structures of the FTase-product complex, and extended X-ray absorption fine structure results. Using high-level theoretical calculations on two models of different sizes, and QM/MM calculations on the full enzyme, the authors have shown that the farnesylated product is Zn coordinated, and that a subsequent step where this Zn bond is broken is coherent with the available kinetic results. Furthermore, an explanation for the contradicting experimental evidence is suggested.
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Affiliation(s)
- Sérgio Filipe Sousa
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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44
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Eastman RT, White J, Hucke O, Yokoyama K, Verlinde CLMJ, Hast MA, Beese LS, Gelb MH, Rathod PK, Van Voorhis WC. Resistance mutations at the lipid substrate binding site of Plasmodium falciparum protein farnesyltransferase. Mol Biochem Parasitol 2006; 152:66-71. [PMID: 17208314 PMCID: PMC2875941 DOI: 10.1016/j.molbiopara.2006.11.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2006] [Revised: 11/30/2006] [Accepted: 11/30/2006] [Indexed: 11/23/2022]
Abstract
The post-translational farnesylation of proteins serves to anchor a subset of intracellular proteins to membranes in eukaryotic organisms and also promotes protein-protein interactions. This enzymatic reaction is carried out by protein farnesyltransferase (PFT), which catalyzes the transfer of a 15-carbon isoprenoid lipid unit, a farnesyl group, from farnesyl pyrophosphate to the C-termini of proteins containing a CaaX motif. Inhibition of PFT is lethal to the pathogenic protozoa Plasmodium falciparum. Previously, we have shown that parasites resistant to a tetrahydroquinoline (THQ)-based PFT inhibitor BMS-388891 have mutations leading to amino acid substitutions in PFT that map to the peptide substrate binding domain. We now report the selection of parasites resistant to another THQ PFT inhibitor BMS-339941. In whole cell assays sensitivity to BMS-339941 was reduced by 33-fold in a resistant clone, and biochemical analysis demonstrated a corresponding 33-fold increase in the BMS-339941 K(i) for the mutant PFT enzyme. More detailed kinetic analysis revealed that the mutant enzyme required higher concentration of peptide and farnesyl pyrophosphate substrates for optimum catalysis. Unlike previously characterized parasites resistant to BMS-388891, the resistant parasites have a mutation which is predicted to be in a distinct location of the enzymatic pocket, near the farnesyl pyrophosphate binding pocket. This is the first description of a mutation from any species affecting the farnesyl pyrophosphate binding pocket with reduced efficacy of PFT inhibitors. These data provide further support that PFT is the target of THQ inhibitors in P. falciparum and suggest that PFT inhibitors should be combined with other antimalarial agents to minimize the development of resistant parasites.
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Affiliation(s)
| | - John White
- Department of Pathobiology, University of Washington, Seattle, WA, USA
| | - Oliver Hucke
- Biochemistry, University of Washington, Seattle, WA, USA
| | | | | | - Michael A. Hast
- Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Lorena S. Beese
- Biochemistry, Duke University Medical Center, Durham, NC, USA
| | | | - Pradipsinh K. Rathod
- Department of Pathobiology, University of Washington, Seattle, WA, USA
- Chemistry, University of Washington, Seattle, WA, USA
| | - Wesley C. Van Voorhis
- Department of Pathobiology, University of Washington, Seattle, WA, USA
- Medicine, University of Washington, Seattle, WA, USA
- Corresponding author: Wesley C. Van Voorhis, Dept. of Medicine, University of Washington, Box 357185, 1959 N.E. Pacific, Seattle, WA 98195-7185, Tel.: + 1-206-543-2447; fax: + 1-206-685-8681, E. mail addresses:
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45
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Gelb MH, Brunsveld L, Hrycyna CA, Michaelis S, Tamanoi F, Van Voorhis WC, Waldmann H. Therapeutic intervention based on protein prenylation and associated modifications. Nat Chem Biol 2006; 2:518-28. [PMID: 16983387 PMCID: PMC2892741 DOI: 10.1038/nchembio818] [Citation(s) in RCA: 156] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In eukaryotic cells, a specific set of proteins are modified by C-terminal attachment of 15-carbon farnesyl groups or 20-carbon geranylgeranyl groups that function both as anchors for fixing proteins to membranes and as molecular handles for facilitating binding of these lipidated proteins to other proteins. Additional modification of these prenylated proteins includes C-terminal proteolysis and methylation, and attachment of a 16-carbon palmitoyl group; these modifications augment membrane anchoring and alter the dynamics of movement of proteins between different cellular membrane compartments. The enzymes in the protein prenylation pathway have been isolated and characterized. Blocking protein prenylation is proving to be therapeutically useful for the treatment of certain cancers, infection by protozoan parasites and the rare genetic disease Hutchinson-Gilford progeria syndrome.
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Affiliation(s)
- Michael H Gelb
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA.
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46
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Xie A, Sivaprakasam P, Doerksen RJ. 3D-QSAR analysis of antimalarial farnesyltransferase inhibitors based on a 2,5-diaminobenzophenone scaffold. Bioorg Med Chem 2006; 14:7311-23. [PMID: 16837204 DOI: 10.1016/j.bmc.2006.06.041] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2006] [Revised: 06/20/2006] [Accepted: 06/21/2006] [Indexed: 01/30/2023]
Abstract
With annual death tolls in the millions and emerging resistance to existing drugs, novel therapies are needed against malaria. Wiesner et al. recently developed a novel class of antimalarials derived from farnesyltransferase inhibitors based on a 2,5-diaminobenzophenone scaffold. The compounds displayed a wide range of activity, including submicromolar, against the multi-drug resistant Plasmodium falciparum strain Dd2. In order to investigate quantitatively the local physicochemical properties involved in the interaction between drug and biotarget, we used the 3D-QSAR methods CoMFA and CoMSIA to study some of the series, including the screened lead compound 2,5-bis-acylaminobenzophenone, 28 cinnamic acid derivatives, 29 N-(3-benzoyl-4-tolylacetylaminophenyl)-3-(5-aryl-2-furyl)acrylic acid amides, and 34 N-(4-substituted-amino-3-benzoylphenyl)-[5-(4-nitrophenyl)-2-furyl]acrylic acid amides. We found that steric, electrostatic, and hydrophobic properties of substituent groups play key roles in the bioactivity of the series of compounds, while hydrogen bonding interactions show no obvious impact. We built several highly predictive 3D-QSAR models, including a CoMSIA one composed of steric, electrostatic, and hydrophobic fields, with r(2)=0.94, q(2)=0.63, and r(pred)(2)=0.63. The results provide insight for optimization of this class of antimalarials for better activity and may prove helpful for further lead optimization.
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Affiliation(s)
- Aihua Xie
- Department of Medicinal Chemistry, School of Pharmacy, University of Mississippi, 38677-1848, USA
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47
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Sousa SF, Fernandes PA, Ramos MJ. Theoretical studies on farnesyltransferase: The distances paradox explained. Proteins 2006; 66:205-18. [PMID: 17068802 DOI: 10.1002/prot.21219] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In spite of the enormous interest that has been devoted to its study, the mechanism of the enzyme farnesyltransferase (FTase) remains the subject of several crucial doubts. In this article, we shed a new light in one of the most fundamental dilemmas that characterize the mechanism of this puzzling enzyme commonly referred to as the "distances paradox", which arises from the existence of a large 8-A distance between the two reactive atoms in the reaction catalyzed by this enzyme: a Zn-bound cysteine sulphur atom from a peptidic substrate and the farnesyldiphosphate (FPP) carbon 1. This distance must be overcome for the reaction to occur. In this study, the two possible alternatives were evaluated by combining molecular mechanics (AMBER) and quantum chemical calculations (B3LYP). Basically, our results have shown that an activation of the Zn-bound cysteine thiolate with subsequent displacement from the zinc coordination sphere towards the FPP carbon 1 is not a realistic hypothesis of overcoming the large distance reported in the crystallographic structures of the ternary complexes between the two reactive atoms, but that a rotation involving the FPP molecule can bring the two atoms closer with moderate energetic cost, coherent with previous experimental data. This conclusion opens the door to an understanding of the chemical step in the farnesylation reaction.
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Affiliation(s)
- Sérgio Filipe Sousa
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
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48
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Glenn MP, Chang SY, Hornéy C, Rivas K, Yokoyama K, Pusateri EE, Fletcher S, Cummings CG, Buckner FS, Pendyala PR, Chakrabarti D, Sebti SM, Gelb M, Van Voorhis WC, Hamilton AD. Structurally simple, potent, Plasmodium selective farnesyltransferase inhibitors that arrest the growth of malaria parasites. J Med Chem 2006; 49:5710-27. [PMID: 16970397 PMCID: PMC2728208 DOI: 10.1021/jm060081v] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Third world nations require immediate access to inexpensive therapeutics to counter the high mortality inflicted by malaria. Here, we report a new class of antimalarial protein farnesyltransferase (PFT) inhibitors, designed with specific emphasis on simple molecular architecture, to facilitate easy access to therapies based on this recently validated antimalarial target. This novel series of compounds represents the first Plasmodium falciparum selective PFT inhibitors reported (up to 145-fold selectivity), with lead inhibitors displaying excellent in vitro activity (IC(50) < 1 nM) and toxicity to cultured parasites at low concentrations (ED(50) < 100 nM). Initial studies of absorption, metabolism, and oral bioavailability are reported.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Andrew D. Hamilton
- To whom correspondence should be addressed. Phone: (203) 432-5570. Fax: (203) 432-3221. E-mail:
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49
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Sousa SF, Fernandes PA, Ramos MJ. Effective tailor-made force field parameterization of the several Zn coordination environments in the puzzling FTase enzyme: opening the door to the full understanding of its elusive catalytic mechanism. Theor Chem Acc 2006. [DOI: 10.1007/s00214-006-0170-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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50
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Rathore D, McCutchan TF, Sullivan M, Kumar S. Antimalarial drugs: current status and new developments. Expert Opin Investig Drugs 2006; 14:871-83. [PMID: 16022576 DOI: 10.1517/13543784.14.7.871] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Malaria continues to be a major threat in the developing world, with > 1 million clinical episodes and 3000 deaths every day. In the last century, malaria claimed between 150 and 300 million lives, accounting for 2 - 5% of all deaths. Currently approximately 40% of the world population resides in areas of active malaria transmission. The disease symptoms are most severe in young children and pregnant women. A total of 90% of the disease-associated mortality occurs in Subsaharan Africa, despite the fact that malaria is indigenous to most tropical regions. A licensed vaccine for malaria has not become a reality and antimalarial drugs are the only available method of treatment. Although chloroquine, the first synthetically developed antimalarial, proved to be an almost magical cure for > 30 years, the emergence and spread of chloroquine-resistant parasites has made it virtually ineffective in most parts of the world. Currently, artemisinin, a plant-derived antimalarial, is the only available drug that is globally effective against the parasite. Although several new drugs have been introduced in the past 30 years, widespread or isolated cases of resistance indicate that their window of effectiveness will be limited. Thus, there is an urgent need to develop new therapeutics and regimens for malaria control. This article presents an overview of the currently available antimalarial chemotherapy options and the efforts being undertaken to develop new drugs based on both the recent technological advances and modifications to the old remedies, and on combination therapies.
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Affiliation(s)
- Dharmendar Rathore
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Washington Street, Blacksburg, VA 24061, USA
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