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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 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Bennett JM, Ward KE, Muir RK, Kabeche S, Yoo E, Yeo T, Lam G, Zhang H, Almaliti J, Berger G, Faucher FF, Lin G, Gerwick WH, Yeh E, Fidock DA, Bogyo M. Covalent Macrocyclic Proteasome Inhibitors Mitigate Resistance in Plasmodium falciparum. ACS Infect Dis 2023; 9:2036-2047. [PMID: 37712594 PMCID: PMC10591878 DOI: 10.1021/acsinfecdis.3c00310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
The Plasmodium proteasome is a promising antimalarial drug target due to its essential role in all parasite lifecycle stages. Furthermore, proteasome inhibitors have synergistic effects when combined with current first-line artemisinin and related analogues. Linear peptides that covalently inhibit the proteasome are effective at killing parasites and have a low propensity for inducing resistance. However, these scaffolds generally suffer from poor pharmacokinetics and bioavailability. Here we describe the development of covalent, irreversible, macrocyclic inhibitors of the Plasmodium falciparum proteasome. We identified compounds with excellent potency and low cytotoxicity; however, the first generation suffered from poor microsomal stability. Further optimization of an existing macrocyclic scaffold resulted in an irreversible covalent inhibitor carrying a vinyl sulfone electrophile that retained high potency and low cytotoxicity and had acceptable metabolic stability. Importantly, unlike the parent reversible inhibitor that selected for multiple mutations in the proteasome, with one resulting in a 5,000-fold loss of potency, the irreversible analogue only showed a 5-fold loss in potency for any single point mutation. Furthermore, an epoxyketone analogue of the same scaffold retained potency against a panel of known proteasome mutants. These results confirm that macrocycles are optimal scaffolds to target the malarial proteasome and that the use of a covalent electrophile can greatly reduce the ability of the parasite to generate drug resistance mutations.
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Affiliation(s)
- John M Bennett
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Kurt E Ward
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, New York 10032, United States
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, New York 10032, United States
| | - Ryan K Muir
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Stephanie Kabeche
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Euna Yoo
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, United States
| | - Tomas Yeo
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, New York 10032, United States
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, New York 10032, United States
| | - Grace Lam
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, California 94304, United States
| | - Hao Zhang
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| | - Jehad Almaliti
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Gabriel Berger
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Franco F Faucher
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Gang Lin
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| | - William H Gerwick
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92037, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Ellen Yeh
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94304, United States
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, New York 10032, United States
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, New York 10032, United States
- Division of Infectious Diseases, Columbia University Medical Center, New York, New York 10032, United States
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92037, United States
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Faucher FF, Abegg D, Ipock P, Adibekian A, Lovell S, Bogyo M. Solid Phase Synthesis of Fluorosulfate Containing Macrocycles for Chemoproteomic Workflows. Isr J Chem 2023. [DOI: 10.1002/ijch.202300020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Affiliation(s)
| | - Daniel Abegg
- Department of Chemistry University of Illinois Chicago Chicago, Illinois 60607 USA
| | - Phillip Ipock
- Department of Chemistry Stanford University Stanford 94305 CA
| | - Alexander Adibekian
- Department of Chemistry University of Illinois Chicago Chicago, Illinois 60607 USA
| | - Scott Lovell
- Department of Life Sciences University of Bath Bath BA2 7AX U.K
- Department of Pathology Stanford University School of Medicine Stanford 94305 CA
| | - Matthew Bogyo
- Department of Pathology Stanford University School of Medicine Stanford 94305 CA
- Department of Chemical and Systems Biology Stanford University School of Medicine Stanford 94305 CA
- Department of Microbiology and Immunology Stanford University School of Medicine Stanford 94305 CA
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Faucher FF, Abegg D, Ipock P, Adibekian A, Lovell S, Bogyo M. Solid Phase Synthesis of Fluorosulfate Containing Macrocycles for Chemoproteomic Workflows. bioRxiv 2023:2023.02.17.529022. [PMID: 36824748 PMCID: PMC9949109 DOI: 10.1101/2023.02.17.529022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Macrocyclic peptides are attractive for chemoproteomic applications due to their modular synthesis and potential for high target selectivity. We describe a solid phase synthesis method for the efficient generation of libraries of small macrocycles that contain an electrophile and alkyne handle. The modular synthesis produces libraries that can be directly screened using simple SDS-PAGE readouts and then optimal lead molecules applied to proteomic analysis. We generated a library of 480 macrocyclic peptides containing the weakly reactive fluorosulfate (OSF) electrophile. Initial screening of a subset of the library containing each of the various diversity elements identified initial molecules of interest. The corresponding positional and confirmational isomers were then screened to select molecules that showed specific protein labeling patterns that were dependent on the probe structure. The most promising hits were applied to standard chemoproteomic workflows to identify protein targets. Our results demonstrate the feasibility of rapid, on-resin synthesis of diverse macrocyclic electrophiles to generate new classes of covalent ligands.
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Affiliation(s)
| | - Daniel Abegg
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, USA
| | | | - Alexander Adibekian
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, USA
| | - Scott Lovell
- Current Address: Department of Life Sciences, University of Bath, Bath BA2 7AX, U.K
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
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Ye R, Zhao J, Yuan B, Liu WC, Rodrigues De Araujo J, Faucher FF, Chang M, Deraedt CV, Toste FD, Somorjai GA. New Insights into Aldol Reactions of Methyl Isocyanoacetate Catalyzed by Heterogenized Homogeneous Catalysts. Nano Lett 2017; 17:584-589. [PMID: 27966991 DOI: 10.1021/acs.nanolett.6b04827] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The Hayashi-Ito aldol reaction of methyl isocyanoacetate (MI) and benzaldehydes, a classic homogeneous Au(I)-catalyzed reaction, was studied with heterogenized homogeneous catalysts. Among dendrimer encapsulated nanoparticles (NPs) of Au, Pd, Rh, or Pt loaded in mesoporous supports and the homogeneous analogues, the Au NPs led to the highest yield and highest diastereoselectivity of products in toluene at room temperature. The Au catalyst was stable and was recycled for at least six runs without substantial deactivation. Moreover, larger pore sizes of the support and the use of a hydrophobic solvent led to a high selectivity for the trans diastereomer of the product. The activation energy is sensitive to neither the size of Au NPs nor the support. A linear Hammett plot was obtained with a positive slope, suggesting an increased electron density on the carbonyl carbon atom in the rate-limiting step. IR studies revealed a strong interaction between MI and the gold catalyst, supporting the proposed mechanism, in which rate-limiting step involves an electrophilic attack of the aldehyde on the enolate formed from the deprotonated MI.
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Affiliation(s)
- Rong Ye
- Department of Chemistry and ‡Kavli Energy NanoScience Institute, University of California , Berkeley, California 94720, United States
- Chemical Science Division and ∥Materials Science Division, Lawrence Berkeley National Laboratory , 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Jie Zhao
- Department of Chemistry and ‡Kavli Energy NanoScience Institute, University of California , Berkeley, California 94720, United States
- Chemical Science Division and ∥Materials Science Division, Lawrence Berkeley National Laboratory , 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Bing Yuan
- Department of Chemistry and ‡Kavli Energy NanoScience Institute, University of California , Berkeley, California 94720, United States
- Chemical Science Division and ∥Materials Science Division, Lawrence Berkeley National Laboratory , 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Wen-Chi Liu
- Department of Chemistry and ‡Kavli Energy NanoScience Institute, University of California , Berkeley, California 94720, United States
- Chemical Science Division and ∥Materials Science Division, Lawrence Berkeley National Laboratory , 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Joyce Rodrigues De Araujo
- Department of Chemistry and ‡Kavli Energy NanoScience Institute, University of California , Berkeley, California 94720, United States
- Chemical Science Division and ∥Materials Science Division, Lawrence Berkeley National Laboratory , 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Franco F Faucher
- Department of Chemistry and ‡Kavli Energy NanoScience Institute, University of California , Berkeley, California 94720, United States
- Chemical Science Division and ∥Materials Science Division, Lawrence Berkeley National Laboratory , 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Matthew Chang
- Department of Chemistry and ‡Kavli Energy NanoScience Institute, University of California , Berkeley, California 94720, United States
- Chemical Science Division and ∥Materials Science Division, Lawrence Berkeley National Laboratory , 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Christophe V Deraedt
- Department of Chemistry and ‡Kavli Energy NanoScience Institute, University of California , Berkeley, California 94720, United States
- Chemical Science Division and ∥Materials Science Division, Lawrence Berkeley National Laboratory , 1 Cyclotron Road, Berkeley, California 94720, United States
| | - F Dean Toste
- Department of Chemistry and ‡Kavli Energy NanoScience Institute, University of California , Berkeley, California 94720, United States
- Chemical Science Division and ∥Materials Science Division, Lawrence Berkeley National Laboratory , 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Gabor A Somorjai
- Department of Chemistry and ‡Kavli Energy NanoScience Institute, University of California , Berkeley, California 94720, United States
- Chemical Science Division and ∥Materials Science Division, Lawrence Berkeley National Laboratory , 1 Cyclotron Road, Berkeley, California 94720, United States
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