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Bennett JM, Narwal SK, Kabeche S, Abegg D, Thathy V, Hackett F, Yeo T, Li VL, Muir R, Faucher F, Lovell S, Blackman MJ, Adibekian A, Yeh E, Fidock DA, Bogyo M. Mixed alkyl/aryl phosphonates identify metabolic serine hydrolases as antimalarial targets. Cell Chem Biol 2024; 31:1714-1728.e10. [PMID: 39137783 DOI: 10.1016/j.chembiol.2024.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 06/20/2024] [Accepted: 07/15/2024] [Indexed: 08/15/2024]
Abstract
Malaria, caused by Plasmodium falciparum, remains a significant health burden. One major barrier for developing antimalarial drugs is the ability of the parasite to rapidly generate resistance. We previously demonstrated that salinipostin A (SalA), a natural product, potently kills parasites by inhibiting multiple lipid metabolizing serine hydrolases, a mechanism that results in a low propensity for resistance. Given the difficulty of employing natural products as therapeutic agents, we synthesized a small library of lipidic mixed alkyl/aryl phosphonates as bioisosteres of SalA. Two constitutional isomers exhibited divergent antiparasitic potencies that enabled the identification of therapeutically relevant targets. The active compound kills parasites through a mechanism that is distinct from both SalA and the pan-lipase inhibitor orlistat and shows synergistic killing with orlistat. Our compound induces only weak resistance, attributable to mutations in a single protein involved in multidrug resistance. These data suggest that mixed alkyl/aryl phosphonates are promising, synthetically tractable antimalarials.
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Affiliation(s)
- John M Bennett
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Sunil K Narwal
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA; Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY, USA
| | - Stephanie Kabeche
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel Abegg
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
| | - Vandana Thathy
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA; Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY, USA
| | - Fiona Hackett
- Malaria Biochemistry Laboratory, Francis Crick Institute, London NW1 1AT, UK
| | - Tomas Yeo
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA; Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY, USA
| | - Veronica L Li
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Ryan Muir
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Franco Faucher
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Scott Lovell
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael J Blackman
- Malaria Biochemistry Laboratory, Francis Crick Institute, London NW1 1AT, UK; Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Ellen Yeh
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA; Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY, USA; Division of Infectious Diseases, Columbia University Medical Center, New York, NY 10032, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
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2
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Sundararaman SA, Miller JJ, Daley EC, O'Brien KA, Kasak P, Daniels AM, Edwards RL, Heidel KM, Bague DA, Wilson MA, Koelper AJ, Kourtoglou EC, White AD, August SA, Apple GA, Rouamba RW, Durand AJ, Esteb JJ, Muller FL, Johnson RJ, Hoops GC, Dowd CS, Odom John AR. Prodrug activation in malaria parasites mediated by an imported erythrocyte esterase, acylpeptide hydrolase (APEH). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.30.610542. [PMID: 39257815 PMCID: PMC11383709 DOI: 10.1101/2024.08.30.610542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
The continued emergence of antimalarial drug resistance highlights the need to develop new antimalarial therapies. Unfortunately, new drug development is often hampered by poor drug-like properties of lead compounds. Prodrugging temporarily masks undesirable compound features, improving bioavailability and target penetration. We have found that lipophilic diester prodrugs of phosphonic acid antibiotics, such as fosmidomycin, exhibit significantly higher antimalarial potency than their parent compounds (1). However, the activating enzymes for these prodrugs were unknown. Here, we show that an erythrocyte enzyme, acylpeptide hydrolase (APEH) is the major activating enzyme of multiple lipophilic ester prodrugs. Surprisingly, this enzyme is taken up by the malaria parasite, Plasmodium falciparum, where it localizes to the parasite cytoplasm and retains enzymatic activity. Using a novel fluorogenic ester library, we characterize the structure activity relationship of APEH, and compare it to that of P. falciparum esterases. We show that parasite-internalized APEH plays an important role in the activation of substrates with branching at the alpha carbon, in keeping with its exopeptidase activity. Our findings highlight a novel mechanism for antimicrobial prodrug activation, relying on a host-derived enzyme to yield activation at a microbial target. Mutations in prodrug activating enzymes are a common mechanism for antimicrobial drug resistance (2-4). Leveraging an internalized host enzyme would circumvent this, enabling the design of prodrugs with higher barriers to drug resistance.
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Affiliation(s)
- S A Sundararaman
- Department of Pediatrics, Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - J J Miller
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - E C Daley
- Department of Pediatrics, Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - K A O'Brien
- Department of Pediatrics, Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - P Kasak
- College of Health Professions, Thomas Jefferson University, Philadelphia, PA, USA
| | - A M Daniels
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, USA
| | - R L Edwards
- Department of Pediatrics, Washington University School of Medicine, Saint Louis, Missouri, USA
- Omniose, Saint Louis, MO, USA
| | - K M Heidel
- Department of Chemistry, George Washington University, 800 22nd Street NW, Washington DC, USA
| | - D A Bague
- Department of Chemistry, George Washington University, 800 22nd Street NW, Washington DC, USA
| | - M A Wilson
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave, Indianapolis, IN, USA
| | - A J Koelper
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave, Indianapolis, IN, USA
| | - E C Kourtoglou
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave, Indianapolis, IN, USA
| | - A D White
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave, Indianapolis, IN, USA
| | - S A August
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave, Indianapolis, IN, USA
| | - G A Apple
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave, Indianapolis, IN, USA
| | - R W Rouamba
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave, Indianapolis, IN, USA
| | - A J Durand
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave, Indianapolis, IN, USA
| | - J J Esteb
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave, Indianapolis, IN, USA
| | - F L Muller
- Lindonlight Collective, Houston, TX, USA
| | - R J Johnson
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave, Indianapolis, IN, USA
| | - G C Hoops
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave, Indianapolis, IN, USA
| | - C S Dowd
- Department of Chemistry, George Washington University, 800 22nd Street NW, Washington DC, USA
| | - A R Odom John
- Department of Pediatrics, Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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3
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Liu J, Fike KR, Dapper C, Klemba M. Metabolism of host lysophosphatidylcholine in Plasmodium falciparum-infected erythrocytes. Proc Natl Acad Sci U S A 2024; 121:e2320262121. [PMID: 38349879 PMCID: PMC10895272 DOI: 10.1073/pnas.2320262121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 01/09/2024] [Indexed: 02/15/2024] Open
Abstract
The human malaria parasite Plasmodium falciparum requires exogenous fatty acids to support its growth during the pathogenic, asexual erythrocytic stage. Host serum lysophosphatidylcholine (LPC) is a significant fatty acid source, yet the metabolic processes responsible for the liberation of free fatty acids from exogenous LPC are unknown. Using an assay for LPC hydrolysis in P. falciparum-infected erythrocytes, we have identified small-molecule inhibitors of key in situ lysophospholipase activities. Competitive activity-based profiling and generation of a panel of single-to-quadruple knockout parasite lines revealed that two enzymes of the serine hydrolase superfamily, termed exported lipase (XL) 2 and exported lipase homolog (XLH) 4, constitute the dominant lysophospholipase activities in parasite-infected erythrocytes. The parasite ensures efficient exogenous LPC hydrolysis by directing these two enzymes to distinct locations: XL2 is exported to the erythrocyte, while XLH4 is retained within the parasite. While XL2 and XLH4 were individually dispensable with little effect on LPC hydrolysis in situ, loss of both enzymes resulted in a strong reduction in fatty acid scavenging from LPC, hyperproduction of phosphatidylcholine, and an enhanced sensitivity to LPC toxicity. Notably, growth of XL/XLH-deficient parasites was severely impaired when cultured in media containing LPC as the sole exogenous fatty acid source. Furthermore, when XL2 and XLH4 activities were ablated by genetic or pharmacologic means, parasites were unable to proliferate in human serum, a physiologically relevant fatty acid source, revealing the essentiality of LPC hydrolysis in the host environment and its potential as a target for anti-malarial therapy.
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Affiliation(s)
- Jiapeng Liu
- Department of Biochemistry, Virginia Tech, Blacksburg, VA24061
| | | | - Christie Dapper
- Department of Biochemistry, Virginia Tech, Blacksburg, VA24061
| | - Michael Klemba
- Department of Biochemistry, Virginia Tech, Blacksburg, VA24061
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Bennett JM, Narwal SK, Kabeche S, Abegg D, Hackett F, Yeo T, Li VL, Muir RK, Faucher FF, Lovell S, Blackman MJ, Adibekian A, Yeh E, Fidock DA, Bogyo M. Mixed Alkyl/Aryl Phosphonates Identify Metabolic Serine Hydrolases as Antimalarial Targets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.11.575224. [PMID: 38260474 PMCID: PMC10802587 DOI: 10.1101/2024.01.11.575224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Malaria, caused by Plasmodium falciparum, remains a significant health burden. A barrier for developing anti-malarial drugs is the ability of the parasite to rapidly generate resistance. We demonstrated that Salinipostin A (SalA), a natural product, kills parasites by inhibiting multiple lipid metabolizing serine hydrolases, a mechanism with a low propensity for resistance. Given the difficulty of employing natural products as therapeutic agents, we synthesized a library of lipidic mixed alkyl/aryl phosphonates as bioisosteres of SalA. Two constitutional isomers exhibited divergent anti-parasitic potencies which enabled identification of therapeutically relevant targets. We also confirm that this compound kills parasites through a mechanism that is distinct from both SalA and the pan-lipase inhibitor, Orlistat. Like SalA, our compound induces only weak resistance, attributable to mutations in a single protein involved in multidrug resistance. These data suggest that mixed alkyl/aryl phosphonates are a promising, synthetically tractable anti-malarials with a low-propensity to induce resistance.
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Affiliation(s)
- John M Bennett
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Sunil K Narwal
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY, USA
| | - Stephanie Kabeche
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel Abegg
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
| | - Fiona Hackett
- Malaria Biochemistry Laboratory, Francis Crick Institute, London NW1 1AT, UK
| | - Tomas Yeo
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY, USA
| | - Veronica L Li
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Ryan K Muir
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Scott Lovell
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael J Blackman
- Malaria Biochemistry Laboratory, Francis Crick Institute, London NW1 1AT, UK
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Ellen Yeh
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY, USA
- Division of Infectious Diseases, Columbia University Medical Center, New York, NY 10032 USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
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Ramanathan R, Hatzios SK. Activity-based Tools for Interrogating Host Biology During Infection. Isr J Chem 2023; 63:e202200095. [PMID: 37744997 PMCID: PMC10512441 DOI: 10.1002/ijch.202200095] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Indexed: 02/18/2023]
Abstract
Host cells sense and respond to pathogens by dynamically regulating cell signaling. The rapid modulation of signaling pathways is achieved by post-translational modifications (PTMs) that can alter protein structure, function, and/or binding interactions. By using chemical probes to broadly profile changes in enzyme function or side-chain reactivity, activity-based protein profiling (ABPP) can reveal PTMs that regulate host-microbe interactions. While ABPP has been widely utilized to uncover microbial mechanisms of pathogenesis, in this review, we focus on more recent applications of this technique to the discovery of host PTMs and enzymes that modulate signaling within infected cells. Collectively, these advances underscore the importance of ABPP as a tool for interrogating the host response to infection and identifying potential targets for host-directed therapies.
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Affiliation(s)
- Renuka Ramanathan
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520 USA
- Microbial Sciences Institute, Yale University, West Haven, CT 06516 USA
| | - Stavroula K. Hatzios
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520 USA
- Microbial Sciences Institute, Yale University, West Haven, CT 06516 USA
- Department of Chemistry, Yale University, New Haven, CT 06520 USA
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