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Benns HJ, Storch M, Falco JA, Fisher FR, Tamaki F, Alves E, Wincott CJ, Milne R, Wiedemar N, Craven G, Baragaña B, Wyllie S, Baum J, Baldwin GS, Weerapana E, Tate EW, Child MA. CRISPR-based oligo recombineering prioritizes apicomplexan cysteines for drug discovery. Nat Microbiol 2022; 7:1891-1905. [PMID: 36266336 PMCID: PMC9613468 DOI: 10.1038/s41564-022-01249-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 09/09/2022] [Indexed: 11/30/2022]
Abstract
Nucleophilic amino acids are important in covalent drug development yet underutilized as anti-microbial targets. Chemoproteomic technologies have been developed to mine chemically accessible residues via their intrinsic reactivity towards electrophilic probes but cannot discern which chemically reactive sites contribute to protein function and should therefore be prioritized for drug discovery. To address this, we have developed a CRISPR-based oligo recombineering (CORe) platform to support the rapid identification, functional prioritization and rational targeting of chemically reactive sites in haploid systems. Our approach couples protein sequence and function with biological fitness of live cells. Here we profile the electrophile sensitivity of proteinogenic cysteines in the eukaryotic pathogen Toxoplasma gondii and prioritize functional sites using CORe. Electrophile-sensitive cysteines decorating the ribosome were found to be critical for parasite growth, with target-based screening identifying a parasite-selective anti-malarial lead molecule and validating the apicomplexan translation machinery as a target for ongoing covalent ligand development.
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Affiliation(s)
- H J Benns
- Department of Life Sciences, Imperial College London, London, UK
- Department of Chemistry, Imperial College London, London, UK
| | - M Storch
- London Biofoundry, Imperial College Translation & Innovation Hub, London, UK
| | - J A Falco
- Department of Chemistry, Boston College, Boston, MA, USA
| | - F R Fisher
- Department of Life Sciences, Imperial College London, London, UK
| | - F Tamaki
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, UK
| | - E Alves
- Department of Life Sciences, Imperial College London, London, UK
| | - C J Wincott
- Department of Life Sciences, Imperial College London, London, UK
| | - R Milne
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, UK
| | - N Wiedemar
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, UK
| | - G Craven
- Department of Chemistry, Imperial College London, London, UK
| | - B Baragaña
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, UK
| | - S Wyllie
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, UK
| | - J Baum
- Department of Life Sciences, Imperial College London, London, UK
- School of Biomedical Sciences, UNSW, Sydney, NSW, Australia
| | - G S Baldwin
- Department of Life Sciences, Imperial College London, London, UK
| | - E Weerapana
- Department of Chemistry, Boston College, Boston, MA, USA
| | - E W Tate
- Department of Chemistry, Imperial College London, London, UK.
| | - M A Child
- Department of Life Sciences, Imperial College London, London, UK.
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Palafox MF, Desai HS, Arboleda VA, Backus KM. From chemoproteomic-detected amino acids to genomic coordinates: insights into precise multi-omic data integration. Mol Syst Biol 2021; 17:e9840. [PMID: 33599394 PMCID: PMC7890448 DOI: 10.15252/msb.20209840] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 12/31/2022] Open
Abstract
The integration of proteomic, transcriptomic, and genetic variant annotation data will improve our understanding of genotype-phenotype associations. Due, in part, to challenges associated with accurate inter-database mapping, such multi-omic studies have not extended to chemoproteomics, a method that measures the intrinsic reactivity and potential "druggability" of nucleophilic amino acid side chains. Here, we evaluated mapping approaches to match chemoproteomic-detected cysteine and lysine residues with their genetic coordinates. Our analysis revealed that database update cycles and reliance on stable identifiers can lead to pervasive misidentification of labeled residues. Enabled by this examination of mapping strategies, we then integrated our chemoproteomics data with computational methods for predicting genetic variant pathogenicity, which revealed that codons of highly reactive cysteines are enriched for genetic variants that are predicted to be more deleterious and allowed us to identify and functionally characterize a new damaging residue in the cysteine protease caspase-8. Our study provides a roadmap for more precise inter-database mapping and points to untapped opportunities to improve the predictive power of pathogenicity scores and to advance prioritization of putative druggable sites.
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Affiliation(s)
- Maria F Palafox
- Department of Human GeneticsDavid Geffen School of MedicineUCLALos AngelesCAUSA
- Department of Biological ChemistryDavid Geffen School of MedicineUCLALos AngelesCAUSA
- Department of Pathology and Laboratory MedicineDavid Geffen School of MedicineUCLALos AngelesCAUSA
| | - Heta S Desai
- Department of Biological ChemistryDavid Geffen School of MedicineUCLALos AngelesCAUSA
- Molecular Biology InstituteUCLALos AngelesCAUSA
| | - Valerie A Arboleda
- Department of Human GeneticsDavid Geffen School of MedicineUCLALos AngelesCAUSA
- Department of Pathology and Laboratory MedicineDavid Geffen School of MedicineUCLALos AngelesCAUSA
- Molecular Biology InstituteUCLALos AngelesCAUSA
- Jonsson Comprehensive Cancer CenterUCLALos AngelesCAUSA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell ResearchUCLALos AngelesCAUSA
| | - Keriann M Backus
- Department of Biological ChemistryDavid Geffen School of MedicineUCLALos AngelesCAUSA
- Molecular Biology InstituteUCLALos AngelesCAUSA
- Jonsson Comprehensive Cancer CenterUCLALos AngelesCAUSA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell ResearchUCLALos AngelesCAUSA
- Department of Chemistry and BiochemistryCollege of Arts and SciencesUCLALos AngelesCAUSA
- DOE Institute for Genomics and ProteomicsUCLALos AngelesCAUSA
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