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Zhang Y, Vass M, Shi D, Abualrous E, Chambers JM, Chopra N, Higgs C, Kasavajhala K, Li H, Nandekar P, Sato H, Miller EB, Repasky MP, Jerome SV. Benchmarking Refined and Unrefined AlphaFold2 Structures for Hit Discovery. J Chem Inf Model 2023; 63:1656-1667. [PMID: 36897766 DOI: 10.1021/acs.jcim.2c01219] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
The recently developed AlphaFold2 (AF2) algorithm predicts proteins' 3D structures from amino acid sequences. The open AlphaFold protein structure database covers the complete human proteome. Using an industry-leading molecular docking method (Glide), we investigated the virtual screening performance of 37 common drug targets, each with an AF2 structure and known holo and apo structures from the DUD-E data set. In a subset of 27 targets where the AF2 structures are suitable for refinement, the AF2 structures show comparable early enrichment of known active compounds (avg. EF 1%: 13.0) to apo structures (avg. EF 1%: 11.4) while falling behind early enrichment of the holo structures (avg. EF 1%: 24.2). With an induced-fit protocol (IFD-MD), we can refine the AF2 structures using an aligned known binding ligand as the template to improve the performance in structure-based virtual screening (avg. EF 1%: 18.9). Glide-generated docking poses of known binding ligands can also be used as templates for IFD-MD, achieving similar improvements (avg. EF 1% 18.0). Thus, with proper preparation and refinement, AF2 structures show considerable promise for in silico hit identification.
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Affiliation(s)
- Yuqi Zhang
- Schrödinger Inc., 9868 Scranton Road, Suite3200, San Diego, California 92121, United States
| | - Marton Vass
- Schrödinger Technologies Limited, Nine Hills Road, Cambridge CB2 1GE, United Kingdom
| | - Da Shi
- Schrödinger Inc., 9868 Scranton Road, Suite3200, San Diego, California 92121, United States
| | - Esam Abualrous
- Schrödinger GmbH, Glücksteinallee 25, Mannheim 68159, Germany
| | - Jennifer M Chambers
- Schrödinger Inc., 1540 Broadway, 24th Floor, New York, New York 10036, United States
| | - Nikita Chopra
- Schrödinger Inc., 9868 Scranton Road, Suite3200, San Diego, California 92121, United States
| | - Christopher Higgs
- Schrödinger Inc., 9868 Scranton Road, Suite3200, San Diego, California 92121, United States
| | - Koushik Kasavajhala
- Schrödinger India Private Limited, No: #147, 3rd Floor, Jawaharlal Nehru Main Road, Channasandra 5th Stage Rajarajeswari Nagar, Above State Bank of India, Bengaluru, India 560098
| | - Hubert Li
- Schrödinger Inc., 9868 Scranton Road, Suite3200, San Diego, California 92121, United States
| | - Prajwal Nandekar
- Schrödinger India Private Limited, No: #147, 3rd Floor, Jawaharlal Nehru Main Road, Channasandra 5th Stage Rajarajeswari Nagar, Above State Bank of India, Bengaluru, India 560098
| | - Hideyuki Sato
- Schrödinger KK, 13F Marunouchi Trust Tower North, 1-8-1 Marunouchi, Chiyoda-ku, Tokyo 100-0005, Japan
| | - Edward B Miller
- Schrödinger Inc., 1540 Broadway, 24th Floor, New York, New York 10036, United States
| | - Matthew P Repasky
- Schrödinger Inc., 101 SW Main Street, #1300, Portland, Oregon 97239, United States
| | - Steven V Jerome
- Schrödinger Inc., 9868 Scranton Road, Suite3200, San Diego, California 92121, United States
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Atkinson ST, Cale D, Pinder A, Chambers JM, Halse SA, Robson BJ. Substantial long-term loss of alpha and gamma diversity of lake invertebrates in a landscape exposed to a drying climate. Glob Chang Biol 2021; 27:6263-6279. [PMID: 34534383 DOI: 10.1111/gcb.15890] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/30/2021] [Accepted: 09/04/2021] [Indexed: 06/13/2023]
Abstract
Many regions across the globe are shifting to more arid climates. For shallow lakes, decreasing rainfall volume and timing, changing regional wind patterns and increased evaporation rates alter water regimes so that dry periods occur more frequently and for longer. Drier conditions may affect fauna directly and indirectly through altered physicochemical conditions in lakes. Although many studies have predicted negative effects of such changes on aquatic biodiversity, empirical studies demonstrating these effects are rare. Global warming has caused severe climatic drying in southwestern Australia since the 1970s, so we aimed to determine whether lakes in this region showed impacts on lake hydroperiod, water quality, and α, β and γ diversity of lake invertebrates from 1998 to 2011. Seventeen lakes across a range of salinities were sampled biennially in spring in the Wheatbelt and Great Southern regions of Western Australia. Multivariate analyses were used to identify changes in α, β and γ diversity and examine patterns in physicochemical data. Salinity and average rainfall partially explained patterns in invertebrate richness and assemblage composition. Climatic drying was associated with significant declines in lake depth, increased frequency of dry periods, and reduced α and γ diversity (γ declined from ~300 to ~100 taxa from 1998 to 2011 in the 17 wetlands). In contrast, β diversity remained consistently high, because each lake retained a distinct fauna. Mean α diversity per-lake declined both in lakes that dried and lakes that did not dry out, but lakes which retained a greater proportion of their maximum depth retained more α diversity. Accumulated losses in α diversity caused the decline in γ diversity likely through shrinking habitat area, fewer stepping stones for dispersal and loss of specific habitat types. Biodiversity loss is thus likely from lakes in drying regions globally. Management actions will need to sustain water depth in lakes to prevent biodiversity loss.
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Affiliation(s)
- S T Atkinson
- Harry Butler Institute & Environmental & Conservation Sciences, Murdoch University, Murdoch, Western Australia, Australia
| | - D Cale
- Department of Biodiversity, Conservation and Attractions, Bentley, Western Australia, Australia
| | - A Pinder
- Department of Biodiversity, Conservation and Attractions, Bentley, Western Australia, Australia
| | - J M Chambers
- Harry Butler Institute & Environmental & Conservation Sciences, Murdoch University, Murdoch, Western Australia, Australia
| | - S A Halse
- Department of Biodiversity, Conservation and Attractions, Bentley, Western Australia, Australia
- Bennelongia Environmental Consultants, Jolimont, Western Australia, Australia
| | - Belinda J Robson
- Harry Butler Institute & Environmental & Conservation Sciences, Murdoch University, Murdoch, Western Australia, Australia
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Sohl CD, Matteo DA, Wells G, Luna L, Upadhye V, Quichocho G, Chambers JM, Miller W, Scott D, Schiffer JM. The Catalytic Features of IDH1 Mutations Can Drive Neomorphic Activity, Phenotype Severity, and Inhibitor Binding. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.01939] [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: 11/11/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | - David Scott
- Sanford Burnham Prebys Medical Discovery Institute
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Chambers JM, Miller W, Quichocho G, Upadhye V, Matteo DA, Bobkov AA, Sohl CD, Schiffer JM. Water Networks and Correlated Motions in Mutant Isocitrate Dehydrogenase 1 (IDH1) Are Critical for Allosteric Inhibitor Binding and Activity. Biochemistry 2020; 59:479-490. [PMID: 31869219 DOI: 10.1021/acs.biochem.9b01023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Point mutations in human isocitrate dehydrogenase 1 (IDH1) can drive malignancies, including lower-grade gliomas and secondary glioblastomas, chondrosarcomas, and acute myeloid leukemias. These mutations, which usually affect residue R132, ablate the normal activity of catalyzing the NADP+-dependent oxidation of isocitrate to α-ketoglutarate (αKG) while also acquiring a neomorphic activity of reducing αKG to d-2-hydroxyglutarate (D2HG). Mutant IDH1 can be selectively therapeutically targeted due to structural differences that occur in the wild type (WT) versus mutant form of the enzyme, though the full mechanisms of this selectivity are still under investigation. Here we probe the mechanistic features of the neomorphic activity and selective small molecule inhibition through a new lens, employing WaterMap and molecular dynamics simulations. These tools identified a high-energy path of water molecules connecting the inhibitor binding site with the αKG and NADP+ binding sites in mutant IDH1. This water path aligns spatially with the α10 helix from WT IDH1 crystal structures. Mutating residues at the termini of this water path specifically disrupted inhibitor binding and/or D2HG production, revealing additional key residues to consider in optimizing druglike molecules against mutant IDH1. Taken together, our findings from molecular simulations and mutant enzyme kinetic assays provide insight into how disrupting water paths through enzyme active sites can impact not only inhibitor potency but also substrate recognition and activity.
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Affiliation(s)
- Jennifer M Chambers
- Schrödinger , 120 West 45th Street , New York , New York 10036 , United States
| | - Wade Miller
- Schrödinger , 222 Third Street, Suite 2230 , Cambridge , Massachusetts 02142 , United States
| | - Giovanni Quichocho
- Department of Chemistry and Biochemistry , San Diego State University , San Diego , California 92182 , United States
| | - Viraj Upadhye
- Department of Chemistry and Biochemistry , San Diego State University , San Diego , California 92182 , United States
| | - Diego Avellaneda Matteo
- Department of Chemistry and Biochemistry , San Diego State University , San Diego , California 92182 , United States
| | - Andrey A Bobkov
- Sanford Burnham Prebys Medical Discovery Institute , La Jolla , California 92037 , United States
| | - Christal D Sohl
- Department of Chemistry and Biochemistry , San Diego State University , San Diego , California 92182 , United States
| | - Jamie M Schiffer
- Janssen Research and Development , 3210 Merryfield Row , San Diego , California 92121 , United States
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Feng H, Zhang Y, Bos PH, Chambers JM, Dupont MM, Stockwell BR. K-Ras G12D Has a Potential Allosteric Small Molecule Binding Site. Biochemistry 2019; 58:2542-2554. [PMID: 31042025 DOI: 10.1021/acs.biochem.8b01300] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
KRAS is the most commonly mutated oncogene in human cancer, with particularly high mutation frequencies in pancreatic cancers, colorectal cancers, and lung cancers [Ostrem, J. M., and Shokat, K. M. (2016) Nat. Rev. Drug Discovery 15, 771-785]. The high prevalence of KRAS mutations and its essential role in many cancers make it a potentially attractive drug target; however, it has been difficult to create small molecule inhibitors of mutant K-Ras proteins. Here, we identified a putative small molecule binding site on K-RasG12D using computational analyses of the protein structure and then used a combination of computational and biochemical approaches to discover small molecules that may bind to this pocket, which we have termed the P110 site, due to its adjacency to proline 110. We confirmed that one compound, named K-Ras allosteric ligand KAL-21404358, bound to K-RasG12D, as measured by microscale thermophoresis, a thermal shift assay, and nuclear magnetic resonance spectroscopy. KAL-21404358 did not bind to four mutants in the P110 site, supporting our hypothesis that KAL-21404358 binds to the P110 site of K-RasG12D. This compound impaired the interaction of K-RasG12D with B-Raf and disrupted the RAF-MEK-ERK and PI3K-AKT signaling pathways. We synthesized additional compounds, based on the KAL-21404358 scaffold with more potent binding and greater aqueous solubility. In summary, these findings suggest that the P110 site is a potential site for binding of small molecule allosteric inhibitors of K-RasG12D.
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Welsch ME, Kaplan A, Chambers JM, Stokes ME, Bos PH, Zask A, Zhang Y, Sanchez-Martin M, Badgley MA, Huang CS, Tran TH, Akkiraju H, Brown LM, Nandakumar R, Cremers S, Yang WS, Tong L, Olive KP, Ferrando A, Stockwell BR. Multivalent Small-Molecule Pan-RAS Inhibitors. Cell 2017; 168:878-889.e29. [PMID: 28235199 DOI: 10.1016/j.cell.2017.02.006] [Citation(s) in RCA: 182] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 10/23/2016] [Accepted: 02/01/2017] [Indexed: 12/30/2022]
Abstract
Design of small molecules that disrupt protein-protein interactions, including the interaction of RAS proteins and their effectors, may provide chemical probes and therapeutic agents. We describe here the synthesis and testing of potential small-molecule pan-RAS ligands, which were designed to interact with adjacent sites on the surface of oncogenic KRAS. One compound, termed 3144, was found to bind to RAS proteins using microscale thermophoresis, nuclear magnetic resonance spectroscopy, and isothermal titration calorimetry and to exhibit lethality in cells partially dependent on expression of RAS proteins. This compound was metabolically stable in liver microsomes and displayed anti-tumor activity in xenograft mouse cancer models. These findings suggest that pan-RAS inhibition may be an effective therapeutic strategy for some cancers and that structure-based design of small molecules targeting multiple adjacent sites to create multivalent inhibitors may be effective for some proteins.
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Affiliation(s)
- Matthew E Welsch
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Anna Kaplan
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Jennifer M Chambers
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Michael E Stokes
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Pieter H Bos
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Arie Zask
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Yan Zhang
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Marta Sanchez-Martin
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY 10032, USA
| | - Michael A Badgley
- Department of Pathology, Columbia University Medical Center, New York, NY 10032, USA; Division of Digestive and Liver Diseases in the Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Christine S Huang
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Timothy H Tran
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Hemanth Akkiraju
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Quantitative Proteomics and Metabolomics Center, Columbia University, New York, NY 10027, USA
| | - Lewis M Brown
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Quantitative Proteomics and Metabolomics Center, Columbia University, New York, NY 10027, USA
| | - Renu Nandakumar
- Irving Institute for Clinical and Translational Research, Columbia University Medical Center, New York, NY 10032, USA
| | - Serge Cremers
- Department of Pathology, Columbia University Medical Center, New York, NY 10032, USA; Irving Institute for Clinical and Translational Research, Columbia University Medical Center, New York, NY 10032, USA
| | - Wan Seok Yang
- Department of Biological Sciences, St. John's University, Queens, NY 11439, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Kenneth P Olive
- Department of Pathology, Columbia University Medical Center, New York, NY 10032, USA; Division of Digestive and Liver Diseases in the Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Adolfo Ferrando
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY 10032, USA; Department of Pathology, Columbia University Medical Center, New York, NY 10032, USA; Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
| | - Brent R Stockwell
- Department of Chemistry, Columbia University, New York, NY 10027, USA; Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
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Saunders EC, de Souza DP, Chambers JM, Ng M, Pyke J, McConville MJ. Use of (13)C stable isotope labelling for pathway and metabolic flux analysis in Leishmania parasites. Methods Mol Biol 2015; 1201:281-296. [PMID: 25388122 DOI: 10.1007/978-1-4939-1438-8_18] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
This protocol describes the combined use of metabolite profiling and stable isotope labelling to define pathways of central carbon metabolism in the protozoa parasite, Leishmania mexicana. Parasite stages are cultivated in standard or completely defined media and then rapidly transferred to chemically equivalent media containing a single (13)C-labelled nutrient. The incorporation of label can be followed over time or after establishment of isotopic equilibrium by harvesting parasites with rapid metabolic quenching. (13)C enrichment of multiple intracellular polar and apolar (lipidic) metabolites can be quantified using gas chromatography-mass spectrometry (GC-MS), while the uptake and secretion of (13)C-labelled metabolites can be measured by (13)C-NMR. Analysis of the mass isotopomer distribution of key metabolites provides information on pathway structure, while analysis of labelling kinetics can be used to infer metabolic fluxes. This protocol is exemplified using L. mexicana labelled with (13)C-U-glucose. The method can be used to measure perturbations in parasite metabolism induced by drug inhibition or genetic manipulation of enzyme levels and is broadly applicable to any cultured parasite stages.
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Affiliation(s)
- Eleanor C Saunders
- Department of Biochemistry and Molecular Biology, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, 30 Flemington Rd, Parkville, VIC, 3010, Australia
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Hawkins BC, Lindqvist LM, Nhu D, Sharp PP, Segal D, Powell AK, Campbell M, Ryan E, Chambers JM, White JM, Rizzacasa MA, Lessene G, Huang DCS, Burns CJ. Simplified silvestrol analogues with potent cytotoxic activity. ChemMedChem 2014; 9:1556-66. [PMID: 24677741 DOI: 10.1002/cmdc.201400024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Indexed: 01/11/2023]
Abstract
The complex natural products silvestrol (1) and episilvestrol (2) are inhibitors of translation initiation through binding to the DEAD-box helicase eukaryotic initiation factor 4A (eIF4A). Both compounds are potently cytotoxic to cancer cells in vitro, and 1 has demonstrated efficacy in vivo in several xenograft cancer models. Here we show that 2 has limited plasma membrane permeability and is metabolized in liver microsomes in a manner consistent with that reported for 1. In addition, we have prepared a series of analogues of these compounds where the complex pseudo-sugar at C6 has been replaced with chemically simpler moieties to improve drug-likeness. Selected compounds from this work possess excellent activity in biochemical and cellular translation assays with potent activity against leukemia cell lines.
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Affiliation(s)
- Bill C Hawkins
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052 (Australia); Department of Medical Biology, The University of Melbourne, VIC 3010 (Australia)
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MacRae JI, Dixon MW, Dearnley MK, Chua HH, Chambers JM, Kenny S, Bottova I, Tilley L, McConville MJ. Mitochondrial metabolism of sexual and asexual blood stages of the malaria parasite Plasmodium falciparum. BMC Biol 2013; 11:67. [PMID: 23763941 PMCID: PMC3704724 DOI: 10.1186/1741-7007-11-67] [Citation(s) in RCA: 183] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 06/10/2013] [Indexed: 12/22/2022] Open
Abstract
Background The carbon metabolism of the blood stages of Plasmodium falciparum, comprising rapidly dividing asexual stages and non-dividing gametocytes, is thought to be highly streamlined, with glycolysis providing most of the cellular ATP. However, these parasitic stages express all the enzymes needed for a canonical mitochondrial tricarboxylic acid (TCA) cycle, and it was recently proposed that they may catabolize glutamine via an atypical branched TCA cycle. Whether these stages catabolize glucose in the TCA cycle and what is the functional significance of mitochondrial metabolism remains unresolved. Results We reassessed the central carbon metabolism of P. falciparum asexual and sexual blood stages, by metabolically labeling each stage with 13C-glucose and 13C-glutamine, and analyzing isotopic enrichment in key pathways using mass spectrometry. In contrast to previous findings, we found that carbon skeletons derived from both glucose and glutamine are catabolized in a canonical oxidative TCA cycle in both the asexual and sexual blood stages. Flux of glucose carbon skeletons into the TCA cycle is low in the asexual blood stages, with glutamine providing most of the carbon skeletons, but increases dramatically in the gametocyte stages. Increased glucose catabolism in the gametocyte TCA cycle was associated with increased glucose uptake, suggesting that the energy requirements of this stage are high. Significantly, whereas chemical inhibition of the TCA cycle had little effect on the growth or viability of asexual stages, inhibition of the gametocyte TCA cycle led to arrested development and death. Conclusions Our metabolomics approach has allowed us to revise current models of P. falciparum carbon metabolism. In particular, we found that both asexual and sexual blood stages utilize a conventional TCA cycle to catabolize glucose and glutamine. Gametocyte differentiation is associated with a programmed remodeling of central carbon metabolism that may be required for parasite survival either before or after uptake by the mosquito vector. The increased sensitivity of gametocyte stages to TCA-cycle inhibitors provides a potential target for transmission-blocking drugs.
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Affiliation(s)
- James I MacRae
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, Parkville, VIC 3010, Australia
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Chambers JM, Lindqvist LM, Webb A, Huang DCS, Savage GP, Rizzacasa MA. Synthesis of biotinylated episilvestrol: highly selective targeting of the translation factors eIF4AI/II. Org Lett 2013; 15:1406-9. [PMID: 23461621 DOI: 10.1021/ol400401d] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Silvestrol (1) and episilvestrol (2) are protein synthesis inhibitors, and the former has shown efficacy in multiple mouse models of cancer; however, the selectivity of these potent cytotoxic natural products has not been described. Herein, it is demonstrated that eukaryotic initiation factors eIF4AI/II were the only proteins detected to bind silvestrol (1) and biotinylated episilvestrol (9) by affinity purification. Our study demonstrates the remarkable selectivity of these promising chemotherapeutics.
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Affiliation(s)
- Jennifer M Chambers
- School of Chemistry, The Bio21 Institute, The University of Melbourne, Melbourne, Victoria 3010, Australia
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Lindqvist LM, Vikström I, Chambers JM, McArthur K, Ann Anderson M, Henley KJ, Happo L, Cluse L, Johnstone RW, Roberts AW, Kile BT, Croker BA, Burns CJ, Rizzacasa MA, Strasser A, Huang DCS. Translation inhibitors induce cell death by multiple mechanisms and Mcl-1 reduction is only a minor contributor. Cell Death Dis 2012; 3:e409. [PMID: 23059828 PMCID: PMC3481137 DOI: 10.1038/cddis.2012.149] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
There is significant interest in treating cancers by blocking protein synthesis, to which hematological malignancies seem particularly sensitive. The translation elongation inhibitor homoharringtonine (Omacetaxine mepesuccinate) is undergoing clinical trials for chronic myeloid leukemia, whereas the translation initiation inhibitor silvestrol has shown promise in mouse models of cancer. Precisely how these compounds induce cell death is unclear, but reduction in Mcl-1, a labile pro-survival Bcl-2 family member, has been proposed to constitute the critical event. Moreover, the contribution of translation inhibitors to neutropenia and lymphopenia has not been precisely defined. Herein, we demonstrate that primary B cells and neutrophils are highly sensitive to translation inhibitors, which trigger the Bax/Bak-mediated apoptotic pathway. However, contrary to expectations, reduction of Mcl-1 did not significantly enhance cytotoxicity of these compounds, suggesting that it does not have a principal role and cautions that strong correlations do not always signify causality. On the other hand, the killing of T lymphocytes was less dependent on Bax and Bak, indicating that translation inhibitors can also induce cell death via alternative mechanisms. Indeed, loss of clonogenic survival proved to be independent of the Bax/Bak-mediated apoptosis altogether. Our findings warn of potential toxicity as these translation inhibitors are cytotoxic to many differentiated non-cycling cells.
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Affiliation(s)
- L M Lindqvist
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
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Chambers JM, Huang DCS, Lindqvist LM, Savage GP, White JM, Rizzacasa MA. Total synthesis of 2''',5'''-diepisilvestrol and its C1''' epimer: key structure activity relationships at C1''' and C2'''. J Nat Prod 2012; 75:1500-1504. [PMID: 22817615 DOI: 10.1021/np300376f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The first total synthesis of the low-abundance natural product 2''',5'''-diepisilvestrol (4) is described. The key step involved a Mitsunobu coupling between cyclopenta[b]benzofuran phenol 7 and dioxane lactol 6. Deprotection then gave a 1:2.6 ratio of natural product 2''',5'''-diepisilvestrol (4) and its C1 epimer 1''',2''',5'''-triepisilvestrol (15) in 50% overall yield. An in vitro protein translation inhibition assay showed that 2''',5'''-diepisilvestrol (4) was considerably less active than episilvestrol (2), while the unnatural isomer 1''',2''',5'''-triepisilvestrol (15) was essentially inactive, showing that the configuration at C1''' and C2''' has a large effect on the biological activity.
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Affiliation(s)
- Jennifer M Chambers
- School of Chemistry, The Bio21 Institute, The University of Melbourne, Victoria 3010, Australia
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Saunders EC, Ng WW, Chambers JM, Ng M, Naderer T, Krömer JO, Likic VA, McConville MJ. Isotopomer profiling of Leishmania mexicana promastigotes reveals important roles for succinate fermentation and aspartate uptake in tricarboxylic acid cycle (TCA) anaplerosis, glutamate synthesis, and growth. J Biol Chem 2011; 286:27706-17. [PMID: 21636575 DOI: 10.1074/jbc.m110.213553] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Leishmania parasites proliferate within nutritionally complex niches in their sandfly vector and mammalian hosts. However, the extent to which these parasites utilize different carbon sources remains poorly defined. In this study, we have followed the incorporation of various (13)C-labeled carbon sources into the intracellular and secreted metabolites of Leishmania mexicana promastigotes using gas chromatography-mass spectrometry and (13)C NMR. [U-(13)C]Glucose was rapidly incorporated into intermediates in glycolysis, the pentose phosphate pathway, and the cytoplasmic carbohydrate reserve material, mannogen. Enzymes involved in the upper glycolytic pathway are sequestered within glycosomes, and the ATP and NAD(+) consumed by these reactions were primarily regenerated by the fermentation of phosphoenolpyruvate to succinate (glycosomal succinate fermentation). The initiating enzyme in this pathway, phosphoenolpyruvate carboxykinase, was exclusively localized to the glycosome. Although some of the glycosomal succinate was secreted, most of the C4 dicarboxylic acids generated during succinate fermentation were further catabolized in the TCA cycle. A high rate of TCA cycle anaplerosis was further suggested by measurement of [U-(13)C]aspartate and [U-(13)C]alanine uptake and catabolism. TCA cycle anaplerosis is apparently needed to sustain glutamate production under standard culture conditions. Specifically, inhibition of mitochondrial aconitase with sodium fluoroacetate resulted in the rapid depletion of intracellular glutamate pools and growth arrest. Addition of high concentrations of exogenous glutamate alleviated this growth arrest. These findings suggest that glycosomal and mitochondrial metabolism in Leishmania promastigotes is tightly coupled and that, in contrast to the situation in some other trypanosomatid parasites, the TCA cycle has crucial anabolic functions.
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Affiliation(s)
- Eleanor C Saunders
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
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Chambers JM, Hill PA, Aaron JA, Han Z, Christianson DW, Kuzma NN, Dmochowski IJ. Cryptophane xenon-129 nuclear magnetic resonance biosensors targeting human carbonic anhydrase. J Am Chem Soc 2009; 131:563-9. [PMID: 19140795 PMCID: PMC2629400 DOI: 10.1021/ja806092w] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
(129)Xe NMR biosensors are promising agents for early disease detection, especially when their interactions with target biomolecules can perturb (129)Xe chemical shifts well beyond the typical field inhomogeneity of clinical MRI. We introduce human carbonic anhydrase (CA) as a single-binding-site enzyme for studying xenon biosensor-protein interactions. A xenon-binding cryptophane was substituted with linkers of varying lengths to p-benzenesulfonamide to yield nondiastereomeric biosensors with a single (129)Xe NMR resonance. X-ray crystallography confirmed binding of the eight-bond-linked biosensor containing a single xenon atom in the CAII active site. Biosensor dissociation constants (K(d) = 20-110 nM) were determined by isothermal titration calorimetry (ITC) for isozymes CA I and II. The biosensor-CA complexes yielded "bound" hyperpolarized (129)Xe NMR resonances of narrow line width that were shifted by 3.0-7.5 ppm downfield, signifying much larger shifts than seen previously. Moreover, isozyme-specific chemical shifts clearly differentiated CA I and II, despite their similar structures. Thus, xenon biosensors may provide a powerful strategy for diagnosing human diseases characterized by the upregulation of specific CA isozymes and other protein biomarkers.
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Affiliation(s)
- Jennifer M. Chambers
- Contribution from the Department of Chemistry, University of Pennsylvania, Department of Biomedical Engineering, University of Rochester
| | - P. Aru Hill
- Contribution from the Department of Chemistry, University of Pennsylvania, Department of Biomedical Engineering, University of Rochester
| | - Julie A. Aaron
- Contribution from the Department of Chemistry, University of Pennsylvania, Department of Biomedical Engineering, University of Rochester
| | - Zhaohui Han
- Contribution from the Department of Chemistry, University of Pennsylvania, Department of Biomedical Engineering, University of Rochester
| | - David W. Christianson
- Contribution from the Department of Chemistry, University of Pennsylvania, Department of Biomedical Engineering, University of Rochester
| | - Nicholas N. Kuzma
- Contribution from the Department of Chemistry, University of Pennsylvania, Department of Biomedical Engineering, University of Rochester
| | - Ivan J. Dmochowski
- Contribution from the Department of Chemistry, University of Pennsylvania, Department of Biomedical Engineering, University of Rochester
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Aaron JA, Chambers JM, Jude KM, Di Costanzo L, Dmochowski IJ, Christianson DW. Structure of a 129Xe-cryptophane biosensor complexed with human carbonic anhydrase II. J Am Chem Soc 2008; 130:6942-3. [PMID: 18461940 PMCID: PMC2408383 DOI: 10.1021/ja802214x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cryptophanes represent an exciting class of xenon-encapsulating molecules that can be exploited as probes for nuclear magnetic resonance imaging. The 1.70 A resolution crystal structure of a cryptophane-derivatized benezenesulfonamide complexed with human carbonic anhydrase II shows how an encapsulated xenon atom can be directed to a specific biological target. The crystal structure confirms binding measurements indicating that the cryptophane cage does not strongly interact with the surface of the protein, which may enhance the sensitivity of 129Xe NMR spectroscopic measurements in solution.
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Affiliation(s)
- Julie A Aaron
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA
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Katz HR, Vivier E, Castells MC, McCormick MJ, Chambers JM, Austen KF. Mouse mast cell gp49B1 contains two immunoreceptor tyrosine-based inhibition motifs and suppresses mast cell activation when coligated with the high-affinity Fc receptor for IgE. Proc Natl Acad Sci U S A 1996; 93:10809-14. [PMID: 8855262 PMCID: PMC38237 DOI: 10.1073/pnas.93.20.10809] [Citation(s) in RCA: 114] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Mouse mast cells express gp49B1, a cell-surface member of the Ig superfamily encoded by the gp49B gene. We now report that by ALIGN comparison of the amino acid sequence of gp49B1 with numerous receptors of the Ig superfamily, a newly recognized family has been established that includes gp49B1, the human myeloid cell Fc receptor for IgA, the bovine myeloid cell Fc receptor for IgG2, and the human killer cell inhibitory receptors expressed on natural killer cells and T lymphocyte subsets. Furthermore, the cytoplasmic domain of gp49B1 contains two immunoreceptor tyrosine-based inhibition motifs that are also present in killer cell inhibitory receptors; these motifs downregulate natural killer cell and T-cell activation signals that lead to cytotoxic activity. As assessed by flow cytometry with transfectants that express either gp49B1 or gp49A, which are 89% identical in the amino acid sequences of their extracellular domains, mAb B23.1 was shown to recognize only gp49B1. Coligation of mAb B23.1 bound to gp49B1 and IgE fixed to the high-affinity Fc receptor for IgE on the surface of mouse bone marrow-derived mast cells inhibited exocytosis in a dose-related manner, as defined by the release of the secretory granule constituent beta-hexosaminidase, as well as the generation of the membrane-derived lipid mediator, leukotriene C4. Thus, gp49B1 is an immunoreceptor tyrosine-based inhibition motif-containing integral cell-surface protein that downregulates the high-affinity Fc receptor for IgE-mediated release of proinflammatory mediators from mast cells. Our findings establish a novel counterregulatory transmembrane pathway by which mast cell activation can be inhibited.
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Affiliation(s)
- H R Katz
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
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Abstract
Intestinal digestive and absorptive function and the gross and histologic appearance of the gastrointestinal tract were evaluated in Basenji dogs with chronic diarrhea, asymptomatic Basenji dogs, and healthy control dogs. Gastric rugal hypertrophy, lymphocytic gastritis, and gastric mucosal atrophy occurred in asymptomatic and affected Basenji dogs. All affected dogs had moderate or severe intestinal lesions characterized by villous clubbing and fusion, increased tortuosity of intestinal crypts, and diffuse infiltration of mononuclear inflammatory cells. Intestinal lesions in asymptomatic Basenji dogs invariably were less severe than those in affected dogs, but the small intestinal lamina propria of asymptomatic Basenji dogs consistently contained greater numbers of mononuclear inflammatory cells than did that of control dogs. The proportion of cells containing each immunoglobulin isotype (IgG, IgM, IgA) was similar among affected Basenji dogs, asymptomatic Basenji dogs, and control dogs. As compared to healthy beagle controls, intestinal function was abnormal in both affected and asymptomatic Basenji dogs evaluated by combined N-benzoyl-L-tyrosyl-p-aminobenzoic acid and d-xylose test, but malabsorption and maldigestion were most pronounced in affected Basenji dogs.
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Affiliation(s)
- N J MacLachlan
- Department of Microbiology, School of Veterinary Medicine, North Carolina State University, Raleigh
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Hardie EM, Chambers JM, Mahaffey MB. Segmental hemiatrophy in a dog. J Am Vet Med Assoc 1985; 186:1315-7. [PMID: 4019294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Congenital asymmetric development, resulting in a small right thoracic limb, was diagnosed in a dog. The limb was anatomically normal. The lesion closely resembled hemiatrophy. Congenital asymmetric development should be considered in the differential diagnosis of limb length discrepancies. Treatment is required only in cases of extreme discrepancy between the normal and affected limb.
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Chambers JM. Nursing care study: chronic granulocytic leukaemia in blast transformation. Nurs Times 1979; 75:400-3. [PMID: 284321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Chambers JM. Communicating a product complaint. J Pract Nurs 1978; 28:27. [PMID: 246473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Chambers JM. How to market your idea. J Pract Nurs 1978; 28:27. [PMID: 244526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Chambers JM. On methods of asymptotic approximation for multivariate distributions. Biometrika 1967; 54:367-83. [PMID: 6064000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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