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Lam UTF, Nguyen TTT, Raechell R, Yang J, Singer H, Chen ES. A Normalization Protocol Reduces Edge Effect in High-Throughput Analyses of Hydroxyurea Hypersensitivity in Fission Yeast. Biomedicines 2023; 11:2829. [PMID: 37893202 PMCID: PMC10604075 DOI: 10.3390/biomedicines11102829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/05/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Edge effect denotes better growth of microbial organisms situated at the edge of the solid agar media. Although the precise reason underlying edge effect is unresolved, it is generally attributed to greater nutrient availability with less competing neighbors at the edge. Nonetheless, edge effect constitutes an unavoidable confounding factor that results in misinterpretation of cell fitness, especially in high-throughput screening experiments widely employed for genome-wide investigation using microbial gene knockout or mutant libraries. Here, we visualize edge effect in high-throughput high-density pinning arrays and report a normalization approach based on colony growth rate to quantify drug (hydroxyurea)-hypersensitivity in fission yeast strains. This normalization procedure improved the accuracy of fitness measurement by compensating cell growth rate discrepancy at different locations on the plate and reducing false-positive and -negative frequencies. Our work thus provides a simple and coding-free solution for a struggling problem in robotics-based high-throughput screening experiments.
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Affiliation(s)
- Ulysses Tsz-Fung Lam
- Department of Biochemistry, National University of Singapore, Singapore 117596, Singapore; (U.T.-F.L.); (T.T.T.N.); (R.R.)
| | - Thi Thuy Trang Nguyen
- Department of Biochemistry, National University of Singapore, Singapore 117596, Singapore; (U.T.-F.L.); (T.T.T.N.); (R.R.)
| | - Raechell Raechell
- Department of Biochemistry, National University of Singapore, Singapore 117596, Singapore; (U.T.-F.L.); (T.T.T.N.); (R.R.)
| | - Jay Yang
- Singer Instruments, Roadwater, Watchet TA23 0RE, UK; (J.Y.); (H.S.)
| | - Harry Singer
- Singer Instruments, Roadwater, Watchet TA23 0RE, UK; (J.Y.); (H.S.)
| | - Ee Sin Chen
- Department of Biochemistry, National University of Singapore, Singapore 117596, Singapore; (U.T.-F.L.); (T.T.T.N.); (R.R.)
- NUS Center for Cancer Research, National University of Singapore, Singapore 117599, Singapore
- NUS Synthetic Biology for Clinical & Technological Innovation (SynCTI), Life Science Institute, National University of Singapore, Singapore 117456, Singapore
- National University Health System (NUHS), Singapore 119228, Singapore
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Maksimov AY, Balandina SY, Topanov PA, Mashevskaya IV, Chaudhary S. Organic Antifungal Drugs and Targets of Their Action. Curr Top Med Chem 2021; 21:705-736. [PMID: 33423647 DOI: 10.2174/1568026621666210108122622] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/20/2020] [Accepted: 09/03/2020] [Indexed: 11/22/2022]
Abstract
In recent decades, there has been a significant increase in the number of fungal diseases. This is due to a wide spectrum of action, immunosuppressants and other group drugs. In terms of frequency, rapid spread and globality, fungal infections are approaching acute respiratory infections. Antimycotics are medicinal substances endorsed with fungicidal or fungistatic properties. For the treatment of fungal diseases, several groups of compounds are used that differ in their origin (natural or synthetic), molecular targets and mechanism of action, antifungal effect (fungicidal or fungistatic), indications for use (local or systemic infections), and methods of administration (parenteral, oral, outdoor). Several efforts have been made by various medicinal chemists around the world for the development of antifungal drugs with high efficacy with the least toxicity and maximum selectivity in the area of antifungal chemotherapy. The pharmacokinetic properties of the new antimycotics are also important: the ability to penetrate biological barriers, be absorbed and distributed in tissues and organs, get accumulated in tissues affected by micromycetes, undergo drug metabolism in the intestinal microflora and human organs, and in the kinetics of excretion from the body. There are several ways to search for new effective antimycotics: - Obtaining new derivatives of the already used classes of antimycotics with improved activity properties. - Screening of new chemical classes of synthetic antimycotic compounds. - Screening of natural compounds. - Identification of new unique molecular targets in the fungal cell. - Development of new compositions and dosage forms with effective delivery vehicles. The methods of informatics, bioinformatics, genomics and proteomics were extensively investigated for the development of new antimycotics. These techniques were employed in finding and identification of new molecular proteins in a fungal cell; in the determination of the selectivity of drugprotein interactions, evaluation of drug-drug interactions and synergism of drugs; determination of the structure-activity relationship (SAR) studies; determination of the molecular design of the most active, selective and safer drugs for the humans, animals and plants. In medical applications, the methods of information analysis and pharmacogenomics allow taking into account the individual phenotype of the patient, the level of expression of the targets of antifungal drugs when choosing antifungal agents and their dosage. This review article incorporates some of the most significant studies covering the basic structures and approaches for the synthesis of antifungal drugs and the directions for their further development.
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Affiliation(s)
- Alexander Yu Maksimov
- Department of Pharmacy and Pharmacology, Faculty of Chemistry, Perm State University, Perm 614990, Russian Federation
| | - Svetlana Yu Balandina
- Department of Pharmacy and Pharmacology, Faculty of Chemistry, Perm State University, Perm 614990, Russian Federation
| | - Pavel A Topanov
- Department of Pharmacy and Pharmacology, Faculty of Chemistry, Perm State University, Perm 614990, Russian Federation
| | - Irina V Mashevskaya
- Department of Pharmacy and Pharmacology, Faculty of Chemistry, Perm State University, Perm 614990, Russian Federation
| | - Sandeep Chaudhary
- Laboratory of Organic and Medicinal Chemistry (OMC lab), Department of Chemistry, Malaviya National Institute of Technology Jaipur, Jawaharlal Nehru Marg, Jaipur 302017, India
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Hagihara K, Kanda Y, Ishida K, Satoh R, Takasaki T, Maeda T, Sugiura R. Chemical genetic analysis of FTY720- and Ca 2+ -sensitive mutants reveals a functional connection between FTY720 and membrane trafficking. Genes Cells 2020; 25:637-645. [PMID: 32682352 DOI: 10.1111/gtc.12800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/25/2020] [Accepted: 07/05/2020] [Indexed: 11/27/2022]
Abstract
FTY720, a sphingosine-1-phosphate (S1P) analog, is used as an immune modulator to treat multiple sclerosis. Accumulating evidence has suggested the mode of action of FTY720 independent of an S1P modulator. In fission yeast, FTY720 induces an increase in intracellular Ca2+ and ROS levels. We have previously identified 49 genes of which deletion causes FTY720 sensitivity. Here, we characterized the FTY720-sensitive mutants in terms of their relevance to the Ca2+ homeostasis and identified the 16 FTY720- and Ca2+ -sensitive mutants (fcs mutants). Most of the FTY720-sensitive mutants showed elevated Ca2+ levels and exhibited Ca2+ dysregulation by FTY720 treatment. One of the functional categories among the genes whose deletion renders cells susceptible to FTY720 and Ca2+ include the Golgi/endosomal membrane trafficking. Notably, FTY720, but not phosphorylated FTY720 incapable of inducing Ca2+ increase, inhibited the secretion of acid phosphatase in the wild-type cells. Importantly, secretory defects of the Golgi/endosomal trafficking mutants, Vps45, or Ryh1 deletion, were further exacerbated by FTY720. Our fcs mutant screen also identified the adenylyl cyclase-associated protein Cap1 and a Rictor homolog Ste20, whose deletion markedly exacerbated FTY720-sensitive secretory impairment. Collectively, our data may suggest a synergistic impact of FTY720 combined with secretion perturbation on proliferation and Ca2+ homeostasis.
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Affiliation(s)
- Kanako Hagihara
- Laboratory of Molecular Pharmacogenomics, Department of Pharmaceutical Sciences, Faculty of Pharmacy, Kindai University, Higashi-Osaka City, Japan.,Laboratory of Hygienic Science, Department of Pharmacy, School of Pharmacy, Hyogo University of Health Sciences, Kobe, Japan
| | - Yuki Kanda
- Laboratory of Molecular Pharmacogenomics, Department of Pharmaceutical Sciences, Faculty of Pharmacy, Kindai University, Higashi-Osaka City, Japan
| | - Kouki Ishida
- Laboratory of Molecular Pharmacogenomics, Department of Pharmaceutical Sciences, Faculty of Pharmacy, Kindai University, Higashi-Osaka City, Japan
| | - Ryosuke Satoh
- Laboratory of Molecular Pharmacogenomics, Department of Pharmaceutical Sciences, Faculty of Pharmacy, Kindai University, Higashi-Osaka City, Japan
| | - Teruaki Takasaki
- Laboratory of Molecular Pharmacogenomics, Department of Pharmaceutical Sciences, Faculty of Pharmacy, Kindai University, Higashi-Osaka City, Japan
| | - Takuya Maeda
- Laboratory of Hygienic Science, Department of Pharmacy, School of Pharmacy, Hyogo University of Health Sciences, Kobe, Japan
| | - Reiko Sugiura
- Laboratory of Molecular Pharmacogenomics, Department of Pharmaceutical Sciences, Faculty of Pharmacy, Kindai University, Higashi-Osaka City, Japan
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Novel Molecular Targets Participating in Myocardial Ischemia-Reperfusion Injury and Cardioprotection. Cardiol Res Pract 2019; 2019:6935147. [PMID: 31275641 PMCID: PMC6558612 DOI: 10.1155/2019/6935147] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 03/28/2019] [Indexed: 12/11/2022] Open
Abstract
Worldwide morbidity and mortality from acute myocardial infarction (AMI) and related heart failure remain high. While effective early reperfusion of the criminal coronary artery after a confirmed AMI is the typical treatment at present, collateral myocardial ischemia-reperfusion injury (MIRI) and pertinent cardioprotection are still challenging to address and have inadequately understood mechanisms. Therefore, unveiling the related novel molecular targets and networks participating in triggering and resisting the pathobiology of MIRI is a promising and valuable frontier. The present study specifically focuses on the recent MIRI advances that are supported by sophisticated bio-methodology in order to bring the poorly understood interrelationship among pro- and anti-MIRI participant molecules up to date, as well as to identify findings that may facilitate the further investigation of novel targets.
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Hofer S, Kainz K, Zimmermann A, Bauer MA, Pendl T, Poglitsch M, Madeo F, Carmona-Gutierrez D. Studying Huntington's Disease in Yeast: From Mechanisms to Pharmacological Approaches. Front Mol Neurosci 2018; 11:318. [PMID: 30233317 PMCID: PMC6131589 DOI: 10.3389/fnmol.2018.00318] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 08/16/2018] [Indexed: 12/22/2022] Open
Abstract
Huntington's disease (HD) is a neurodegenerative disorder that leads to progressive neuronal loss, provoking impaired motor control, cognitive decline, and dementia. So far, HD remains incurable, and available drugs are effective only for symptomatic management. HD is caused by a mutant form of the huntingtin protein, which harbors an elongated polyglutamine domain and is highly prone to aggregation. However, many aspects underlying the cytotoxicity of mutant huntingtin (mHTT) remain elusive, hindering the efficient development of applicable interventions to counteract HD. An important strategy to obtain molecular insights into human disorders in general is the use of eukaryotic model organisms, which are easy to genetically manipulate and display a high degree of conservation regarding disease-relevant cellular processes. The budding yeast Saccharomyces cerevisiae has a long-standing and successful history in modeling a plethora of human maladies and has recently emerged as an effective tool to study neurodegenerative disorders, including HD. Here, we summarize some of the most important contributions of yeast to HD research, specifically concerning the elucidation of mechanistic features of mHTT cytotoxicity and the potential of yeast as a platform to screen for pharmacological agents against HD.
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Affiliation(s)
- Sebastian Hofer
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Katharina Kainz
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Andreas Zimmermann
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Maria A. Bauer
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Tobias Pendl
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Michael Poglitsch
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Frank Madeo
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
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Zimmermann A, Hofer S, Pendl T, Kainz K, Madeo F, Carmona-Gutierrez D. Yeast as a tool to identify anti-aging compounds. FEMS Yeast Res 2018; 18:4919731. [PMID: 29905792 PMCID: PMC6001894 DOI: 10.1093/femsyr/foy020] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 02/27/2018] [Indexed: 12/23/2022] Open
Abstract
In the search for interventions against aging and age-related diseases, biological screening platforms are indispensable tools to identify anti-aging compounds among large substance libraries. The budding yeast, Saccharomyces cerevisiae, has emerged as a powerful chemical and genetic screening platform, as it combines a rapid workflow with experimental amenability and the availability of a wide range of genetic mutant libraries. Given the amount of conserved genes and aging mechanisms between yeast and human, testing candidate anti-aging substances in yeast gene-deletion or overexpression collections, or de novo derived mutants, has proven highly successful in finding potential molecular targets. Yeast-based studies, for example, have led to the discovery of the polyphenol resveratrol and the natural polyamine spermidine as potential anti-aging agents. Here, we present strategies for pharmacological anti-aging screens in yeast, discuss common pitfalls and summarize studies that have used yeast for drug discovery and target identification.
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Affiliation(s)
- Andreas Zimmermann
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
| | - Sebastian Hofer
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
| | - Tobias Pendl
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
| | - Katharina Kainz
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
| | - Frank Madeo
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, 8010, Austria
- BioTechMed Graz, Graz, 8010, Austria
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More than Just an Immunosuppressant: The Emerging Role of FTY720 as a Novel Inducer of ROS and Apoptosis. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:4397159. [PMID: 29785244 PMCID: PMC5896217 DOI: 10.1155/2018/4397159] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 02/28/2018] [Indexed: 02/03/2023]
Abstract
Fingolimod hydrochloride (FTY720) is a first-in-class of sphingosine-1-phosphate (S1P) receptor modulator approved to treat multiple sclerosis by its phosphorylated form (FTY720-P). Recently, a novel role of FTY720 as a potential anticancer drug has emerged. One of the anticancer mechanisms of FTY720 involves the induction of reactive oxygen species (ROS) and subsequent apoptosis, which is largely independent of its property as an S1P modulator. ROS have been considered as a double-edged sword in tumor initiation/progression. Intriguingly, prooxidant therapies have attracted much attention due to its efficacy in cancer treatment. These strategies include diverse chemotherapeutic agents and molecular targeted drugs such as sulfasalazine which inhibits the CD44v-xCT (cystine transporter) axis. In this review, we introduce our recent discoveries using a chemical genomics approach to uncover a signaling network relevant to FTY720-mediated ROS signaling and apoptosis, thereby proposing new potential targets for combination therapy as a means to enhance the antitumor efficacy of FTY720 as a ROS generator. We extend our knowledge by summarizing various measures targeting the vulnerability of cancer cells' defense mechanisms against oxidative stress. Future directions that may lead to the best use of FTY720 and ROS-targeted strategies as a promising cancer treatment are also discussed.
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Amino Acid Metabolism and Transport Mechanisms as Potential Antifungal Targets. Int J Mol Sci 2018; 19:ijms19030909. [PMID: 29562716 PMCID: PMC5877770 DOI: 10.3390/ijms19030909] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 03/13/2018] [Accepted: 03/15/2018] [Indexed: 01/15/2023] Open
Abstract
Discovering new drugs for treatment of invasive fungal infections is an enduring challenge. There are only three major classes of antifungal agents, and no new class has been introduced into clinical practice in more than a decade. However, recent advances in our understanding of the fungal life cycle, functional genomics, proteomics, and gene mapping have enabled the identification of new drug targets to treat these potentially deadly infections. In this paper, we examine amino acid transport mechanisms and metabolism as potential drug targets to treat invasive fungal infections, including pathogenic yeasts, such as species of Candida and Cryptococcus, as well as molds, such as Aspergillus fumigatus. We also explore the mechanisms by which amino acids may be exploited to identify novel drug targets and review potential hurdles to bringing this approach into clinical practice.
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