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Gaikani HK, Stolar M, Kriti D, Nislow C, Giaever G. From beer to breadboards: yeast as a force for biological innovation. Genome Biol 2024; 25:10. [PMID: 38178179 PMCID: PMC10768129 DOI: 10.1186/s13059-023-03156-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 12/21/2023] [Indexed: 01/06/2024] Open
Abstract
The history of yeast Saccharomyces cerevisiae, aka brewer's or baker's yeast, is intertwined with our own. Initially domesticated 8,000 years ago to provide sustenance to our ancestors, for the past 150 years, yeast has served as a model research subject and a platform for technology. In this review, we highlight many ways in which yeast has served to catalyze the fields of functional genomics, genome editing, gene-environment interaction investigation, proteomics, and bioinformatics-emphasizing how yeast has served as a catalyst for innovation. Several possible futures for this model organism in synthetic biology, drug personalization, and multi-omics research are also presented.
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Affiliation(s)
- Hamid Kian Gaikani
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - Monika Stolar
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Divya Kriti
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Corey Nislow
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada.
| | - Guri Giaever
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
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Theerawatanasirikul S, Kuo CJ, Phecharat N, Chootip J, Lekcharoensuk C, Lekcharoensuk P. Structural-based virtual screening and in vitro assays for small molecules inhibiting the feline coronavirus 3CL protease as a surrogate platform for coronaviruses. Antiviral Res 2020; 182:104927. [PMID: 32910955 PMCID: PMC7476565 DOI: 10.1016/j.antiviral.2020.104927] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/30/2020] [Accepted: 09/01/2020] [Indexed: 02/07/2023]
Abstract
Feline infectious peritonitis (FIP) which is caused by feline infectious peritonitis virus (FIPV), a variant of feline coronavirus (FCoV), is a member of family Coronaviridae, together with severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and SARS-CoV-2. So far, neither effective vaccines nor approved antiviral therapeutics are currently available for the treatment of FIPV infection. Both human and animal CoVs shares similar functional proteins, particularly the 3CL protease (3CLpro), which plays the pivotal role on viral replication. We investigated the potential drug-liked compounds and their inhibitory interaction on the 3CLpro active sites of CoVs by the structural-bases virtual screening. Fluorescence resonance energy transfer (FRET) assay revealed that three out of twenty-eight compounds could hamper FIPV 3CLpro activities with IC50 of 3.57 ± 0.36 μM to 25.90 ± 1.40 μM, and Ki values of 2.04 ± 0.08 to 15.21 ± 1.76 μM, respectively. Evaluation of antiviral activity using cell-based assay showed that NSC629301 and NSC71097 could strongly inhibit the cytopathic effect and also reduced replication of FIPV in CRFK cells in all examined conditions with the low range of EC50 (6.11 ± 1.90 to 7.75 ± 0.48 μM and 1.99 ± 0.30 to 4.03 ± 0.60 μM, respectively), less than those of ribavirin and lopinavir. Analysis of FIPV 3CLpro-ligand interaction demonstrated that the selected compounds reacted to the crucial residues (His41 and Cys144) of catalytic dyad. Our investigations provide a fundamental knowledge for the further development of antiviral agents and increase the number of anti-CoV agent pools for feline coronavirus and other related CoVs. Virtual screening and molecular docking revealed three lead compounds bound to FIPV 3CLpro active site. The 3D structures of 3CLpro of coronaviruses including SARS-CoV-2 are highly conserved. These compounds showed inhibitory effects on the proteases of FIPV, PEDV, SARS-CoV and SARS-CoV-2. Their antiviral activities are better than Ribavirin and Lopinavir while comparable to GC376.
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Affiliation(s)
- Sirin Theerawatanasirikul
- Department of Anatomy, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, 10900, Thailand
| | - Chih Jung Kuo
- Department of Veterinary Medicine, National Chung Hsing University, Taichung, 40227, Taiwan.
| | - Nanthawan Phecharat
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, 10900, Thailand
| | - Jullada Chootip
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, 10900, Thailand
| | - Chalermpol Lekcharoensuk
- Department of Companion Animals Clinical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, 10900, Thailand
| | - Porntippa Lekcharoensuk
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, 10900, Thailand; Center of Advanced Studies in Agriculture and Food, KU Institute, Thailand.
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Thomas FM, Goode KM, Rajwa B, Bieberich AA, Avramova LV, Hazbun TR, Davisson VJ. A Chemogenomic Screening Platform Used to Identify Chemotypes Perturbing HSP90 Pathways. SLAS DISCOVERY 2017; 22:706-719. [PMID: 28346089 DOI: 10.1177/2472555216687525] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Compounds that modulate the heat shock protein (HSP) network have potential in a broad range of research applications and diseases. A yeast-based liquid culture assay that measured time-dependent turbidity enabled the high-throughput screening of different Saccharomyces cerevisae strains to identify HSP modulators with unique molecular mechanisms. A focused set of four strains, with differing sensitivities to Hsp90 inhibitors, was used to screen a compound library of 3680 compounds. Computed turbidity curve functions were used to classify strain responses and sensitivity to chemical effects across the compound library. Filtering based on single-strain selectivity identified nine compounds as potential heat shock modulators, including the known Hsp90 inhibitor macbecin. Haploid yeast deletion strains (360), mined from previous Hsp90 inhibitor yeast screens and heat shock protein interaction data, were screened for differential sensitivities to known N-terminal ATP site-directed Hsp90 inhibitors to reveal functional distinctions. Strains demonstrating differential sensitivity (13) to Hsp90 inhibitors were used to prioritize primary screen hit compounds, with NSC145366 emerging as the lead hit. Our follow-up biochemical and functional studies show that NSC145366 directly interacts and inhibits the C-terminus of Hsp90, validating the platform as a powerful approach for early-stage identification of bioactive modulators of heat shock-dependent pathways.
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Affiliation(s)
- Fiona M Thomas
- 1 Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN, USA
| | - Kourtney M Goode
- 1 Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN, USA
| | - Bartek Rajwa
- 2 Bindley Bioscience Center, Purdue Discovery Park, Purdue University, West Lafayette, IN, USA
| | - Andrew A Bieberich
- 1 Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN, USA
| | - Larisa V Avramova
- 2 Bindley Bioscience Center, Purdue Discovery Park, Purdue University, West Lafayette, IN, USA
| | - Tony R Hazbun
- 1 Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN, USA.,3 Purdue University Center for Cancer Research, West Lafayette, IN, USA
| | - V Jo Davisson
- 1 Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN, USA.,3 Purdue University Center for Cancer Research, West Lafayette, IN, USA
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Abstract
Despite a billion years of divergent evolution, the baker’s yeast Saccharomyces cerevisiae has long proven to be an invaluable model organism for studying human biology. Given its tractability and ease of genetic manipulation, along with extensive genetic conservation with humans, it is perhaps no surprise that researchers have been able to expand its utility by expressing human proteins in yeast, or by humanizing specific yeast amino acids, proteins or even entire pathways. These methods are increasingly being scaled in throughput, further enabling the detailed investigation of human biology and disease-specific variations of human genes in a simplified model organism.
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Heiskanen MA, Aittokallio T. Predicting drug-target interactions through integrative analysis of chemogenetic assays in yeast. MOLECULAR BIOSYSTEMS 2013; 9:768-79. [PMID: 23420501 DOI: 10.1039/c3mb25591c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Chemical-genomic and genetic interaction profiling approaches are widely used to study mechanisms of drug action and resistance. However, there exist a number of scoring algorithms customized to different experimental assays, the relative performance of which remains poorly understood, especially with respect to different types of chemogenetic assays. Using yeast Saccharomyces cerevisiae as a test bed, we carried out a systematic evaluation among the main drug target analysis approaches in terms of predicting global drug-target interaction networks. We found drastic differences in their performance across different chemical-genomic assay types, such as those based on heterozygous and homozygous diploid or haploid deletion mutant libraries. Moreover, a relatively small overlap in the predicted targets was observed between those approaches that use either chemical-genomic screening alone or combined with genetic interaction profiling. A rank-based integration of the complementary scoring approaches led to improved overall performance, demonstrating that genetic interaction profiling provides added information on drug target prediction. Optimal performance was achieved when focusing specifically on the negative tail of the genetic interactions, suggesting that combining synthetic lethal interactions with chemical-genetic interactions provides highest information on drug-target interactions. A network view of rapamycin-interacting genes, pathways and complexes was used as an example to demonstrate the benefits of such integrated and optimized analysis of chemogenetic assays in yeast.
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Affiliation(s)
- Marja A Heiskanen
- Biomathematics Research Group, Department of Mathematics, University of Turku, FI-20014, Finland
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