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Thorman AW, Reigle J, Chutipongtanate S, Yang J, Shamsaei B, Pilarczyk M, Fazel-Najafabadi M, Adamczak R, Kouril M, Bhatnagar S, Hummel S, Niu W, Morrow AL, Czyzyk-Krzeska MF, McCullumsmith R, Seibel W, Nassar N, Zheng Y, Hildeman DA, Medvedovic M, Herr AB, Meller J. Accelerating drug discovery and repurposing by combining transcriptional signature connectivity with docking. SCIENCE ADVANCES 2024; 10:eadj3010. [PMID: 39213358 PMCID: PMC11364105 DOI: 10.1126/sciadv.adj3010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 07/26/2024] [Indexed: 09/04/2024]
Abstract
We present an in silico approach for drug discovery, dubbed connectivity enhanced structure activity relationship (ceSAR). Building on the landmark LINCS library of transcriptional signatures of drug-like molecules and gene knockdowns, ceSAR combines cheminformatic techniques with signature concordance analysis to connect small molecules and their targets and further assess their biophysical compatibility using molecular docking. Candidate compounds are first ranked in a target structure-independent manner, using chemical similarity to LINCS analogs that exhibit transcriptomic concordance with a target gene knockdown. Top candidates are subsequently rescored using docking simulations and machine learning-based consensus of the two approaches. Using extensive benchmarking, we show that ceSAR greatly reduces false-positive rates, while cutting run times by multiple orders of magnitude and further democratizing drug discovery pipelines. We further demonstrate the utility of ceSAR by identifying and experimentally validating inhibitors of BCL2A1, an important antiapoptotic target in melanoma and preterm birth-associated inflammation.
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Affiliation(s)
- Alexander W. Thorman
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - James Reigle
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
- Department of Biostatistics, Health Informatics and Data Sciences, University of Cincinnati, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Somchai Chutipongtanate
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Juechen Yang
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
- Department of Biostatistics, Health Informatics and Data Sciences, University of Cincinnati, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Behrouz Shamsaei
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Marcin Pilarczyk
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Mehdi Fazel-Najafabadi
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Rafal Adamczak
- Department of Informatics, Faculty of Physics, Astronomy an Informatics, Nicolaus Copernicus University, Toruń, Poland
| | - Michal Kouril
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Surbhi Bhatnagar
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Computer Science, University of Cincinnati, Cincinnati, OH, USA
| | - Sarah Hummel
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Wen Niu
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Ardythe L. Morrow
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Maria F. Czyzyk-Krzeska
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Department of Veterans Affairs, Cincinnati Veteran Affairs Medical Center, Cincinnati, OH, USA
| | | | - William Seibel
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Nicolas Nassar
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Yi Zheng
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - David A. Hildeman
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Mario Medvedovic
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
- Department of Biostatistics, Health Informatics and Data Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Andrew B. Herr
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Division of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Jarek Meller
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
- Department of Biostatistics, Health Informatics and Data Sciences, University of Cincinnati, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Informatics, Faculty of Physics, Astronomy an Informatics, Nicolaus Copernicus University, Toruń, Poland
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Department of Computer Science, University of Cincinnati, Cincinnati, OH, USA
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Salame N, Fooks K, El-Hachem N, Bikorimana JP, Mercier FE, Rafei M. Recent Advances in Cancer Drug Discovery Through the Use of Phenotypic Reporter Systems, Connectivity Mapping, and Pooled CRISPR Screening. Front Pharmacol 2022; 13:852143. [PMID: 35795568 PMCID: PMC9250974 DOI: 10.3389/fphar.2022.852143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
Multi-omic approaches offer an unprecedented overview of the development, plasticity, and resistance of cancer. However, the translation from anti-cancer compounds identified in vitro to clinically active drugs have a notoriously low success rate. Here, we review how technical advances in cell culture, robotics, computational biology, and development of reporter systems have transformed drug discovery, enabling screening approaches tailored to clinically relevant functional readouts (e.g., bypassing drug resistance). Illustrating with selected examples of “success stories,” we describe the process of phenotype-based high-throughput drug screening to target malignant cells or the immune system. Second, we describe computational approaches that link transcriptomic profiling of cancers with existing pharmaceutical compounds to accelerate drug repurposing. Finally, we review how CRISPR-based screening can be applied for the discovery of mechanisms of drug resistance and sensitization. Overall, we explore how the complementary strengths of each of these approaches allow them to transform the paradigm of pre-clinical drug development.
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Affiliation(s)
- Natasha Salame
- Department of Biomedical Sciences, Université de Montréal, Montreal, QC, Canada
| | - Katharine Fooks
- Lady Davis Institute for Medical Research, Montreal, QC, Canada
- Department of Medicine, McGill University, Montreal, QC, Canada
| | - Nehme El-Hachem
- Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC, Canada
| | - Jean-Pierre Bikorimana
- Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montreal, QC, Canada
| | - François E. Mercier
- Lady Davis Institute for Medical Research, Montreal, QC, Canada
- Department of Medicine, McGill University, Montreal, QC, Canada
- *Correspondence: François E. Mercier, ; Moutih Rafei,
| | - Moutih Rafei
- Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC, Canada
- Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montreal, QC, Canada
- Molecular Biology Program, Université de Montréal, Montreal, QC, Canada
- *Correspondence: François E. Mercier, ; Moutih Rafei,
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Thu KL, Soria-Bretones I, Mak TW, Cescon DW. Targeting the cell cycle in breast cancer: towards the next phase. Cell Cycle 2018; 17:1871-1885. [PMID: 30078354 DOI: 10.1080/15384101.2018.1502567] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Deregulation of the cell cycle is a hallmark of cancer that enables limitless cell division. To support this malignant phenotype, cells acquire molecular alterations that abrogate or bypass control mechanisms in signaling pathways and cellular checkpoints that normally function to prevent genomic instability and uncontrolled cell proliferation. Consequently, therapeutic targeting of the cell cycle has long been viewed as a promising anti-cancer strategy. Until recently, attempts to target the cell cycle for cancer therapy using selective inhibitors have proven unsuccessful due to intolerable toxicities and a lack of target specificity. However, improvements in our understanding of malignant cell-specific vulnerabilities has revealed a therapeutic window for preferential targeting of the cell cycle in cancer cells, and has led to the development of agents now in the clinic. In this review, we discuss the latest generation of cell cycle targeting anti-cancer agents for breast cancer, including approved CDK4/6 inhibitors, and investigational TTK and PLK4 inhibitors that are currently in clinical trials. In recognition of the emerging population of ER+ breast cancers with acquired resistance to CDK4/6 inhibitors we suggest new therapeutic avenues to treat these patients. We also offer our perspective on the direction of future research to address the problem of drug resistance, and discuss the mechanistic insights required for the successful implementation of these strategies.
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Affiliation(s)
- K L Thu
- a Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre , University Health Network , Toronto , Canada
| | - I Soria-Bretones
- a Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre , University Health Network , Toronto , Canada
| | - T W Mak
- a Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre , University Health Network , Toronto , Canada.,b Department of Medical Biophysics , University Health Network , Toronto , Canada
| | - D W Cescon
- a Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre , University Health Network , Toronto , Canada.,c Department of Medicine , University of Toronto , Toronto , Canada
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Zhao C, Gammie SC. The circadian gene Nr1d1 in the mouse nucleus accumbens modulates sociability and anxiety-related behaviour. Eur J Neurosci 2018; 48:1924-1943. [PMID: 30028550 DOI: 10.1111/ejn.14066] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 06/11/2018] [Accepted: 07/14/2018] [Indexed: 12/17/2022]
Abstract
Nuclear receptor subfamily 1, group D, member 1 (Nr1d1) (also known as Rev-erb alpha) has been linked to circadian rhythm regulation, mood-related behaviour and disorders associated with social deficits. Recent work from our laboratory found striking decreases in Nr1d1 in the nucleus accumbens (NAc) in the maternal condition and indirect evidence that Nr1d1 was interacting with numerous addiction and reward-related genes to modulate social reward. In this study, we applied our insights from the maternal state to nonparental adult mice to determine whether decreases in Nr1d1 expression in the NAc via adeno-associated viral (AAV) vectors and short hairpin RNA (shRNA)-mediated gene knockdown were sufficient to modulate social behaviours and mood-related behaviours. Knockdown of Nr1d1 in the NAc enhanced sociability and reduced anxiety, but did not affect depressive-like traits in female mice. In male mice, Nr1d1 knockdown had no significant behavioural effects. Microarray analysis of Nr1d1 knockdown in females identified changes in circadian rhythm and histone deacetylase genes and suggested possible drugs, including histone deacetylase inhibitors, that could mimic actions of Nr1d1 knockdown. Quantitative real-time PCR (qPCR) analysis confirmed expression upregulation of gene period circadian clock 1 (Per1) and period circadian clock 2 (Per2) with Nr1d1 knockdown. The evidence for roles for opioid-related genes opioid receptor, delta 1 (Oprd1) and preproenkephalin (Penk) was also found. Together, these results suggest that Nr1d1 in the NAc modulates sociability and anxiety-related behaviour in a sex-specific manner, and circadian, histone deacetylase and opioid-related genes may be involved in the expression of these behavioural phenotypes.
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Affiliation(s)
- Changjiu Zhao
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin
| | - Stephen C Gammie
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin.,Neuroscience Training Program, University of Wisconsin-Madison, Madison, Wisconsin
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