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Deng J, Yang Z, Wang H, Ojima I, Samaras D, Wang F. A systematic study of key elements underlying molecular property prediction. Nat Commun 2023; 14:6395. [PMID: 37833262 PMCID: PMC10575948 DOI: 10.1038/s41467-023-41948-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 09/18/2023] [Indexed: 10/15/2023] Open
Abstract
Artificial intelligence (AI) has been widely applied in drug discovery with a major task as molecular property prediction. Despite booming techniques in molecular representation learning, key elements underlying molecular property prediction remain largely unexplored, which impedes further advancements in this field. Herein, we conduct an extensive evaluation of representative models using various representations on the MoleculeNet datasets, a suite of opioids-related datasets and two additional activity datasets from the literature. To investigate the predictive power in low-data and high-data space, a series of descriptors datasets of varying sizes are also assembled to evaluate the models. In total, we have trained 62,820 models, including 50,220 models on fixed representations, 4200 models on SMILES sequences and 8400 models on molecular graphs. Based on extensive experimentation and rigorous comparison, we show that representation learning models exhibit limited performance in molecular property prediction in most datasets. Besides, multiple key elements underlying molecular property prediction can affect the evaluation results. Furthermore, we show that activity cliffs can significantly impact model prediction. Finally, we explore into potential causes why representation learning models can fail and show that dataset size is essential for representation learning models to excel.
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Affiliation(s)
- Jianyuan Deng
- Stony Brook University, Department of Biomedical Informatics, Stony Brook, NY, 11794, USA
| | - Zhibo Yang
- Stony Brook University, Department of Computer Science, Stony Brook, NY, 11794, USA
| | - Hehe Wang
- Stony Brook University, Department of Chemistry, Stony Brook, NY, 11794, USA
| | - Iwao Ojima
- Stony Brook University, Department of Chemistry, Stony Brook, NY, 11794, USA
| | - Dimitris Samaras
- Stony Brook University, Department of Computer Science, Stony Brook, NY, 11794, USA
| | - Fusheng Wang
- Stony Brook University, Department of Biomedical Informatics, Stony Brook, NY, 11794, USA.
- Stony Brook University, Department of Computer Science, Stony Brook, NY, 11794, USA.
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Braden K, Campolo M, Li Y, Chen Z, Doyle TM, Giancotti LA, Esposito E, Zhang J, Cuzzocrea S, Arnatt CK, Salvemini D. Activation of GPR183 by 7 α,25-Dihydroxycholesterol Induces Behavioral Hypersensitivity through Mitogen-Activated Protein Kinase and Nuclear Factor- κB. J Pharmacol Exp Ther 2022; 383:172-181. [PMID: 36116795 PMCID: PMC9553113 DOI: 10.1124/jpet.122.001283] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 08/17/2022] [Indexed: 01/07/2023] Open
Abstract
Emerging evidence implicates the G-protein coupled receptor (GPCR) GPR183 in the development of neuropathic pain. Further investigation of the signaling pathways downstream of GPR183 is needed to support the development of GPR183 antagonists as analgesics. In rodents, intrathecal injection of its ligand, 7α,25-dihydroxycholesterol (7α,25-OHC), causes time-dependent development of mechano-and cold- allodynia (behavioral hypersensitivity). These effects are blocked by the selective small molecule GPR183 antagonist, SAE-14. However, the molecular mechanisms engaged downstream of GPR183 in the spinal cord are not known. Here, we show that 7α,25-OHC-induced behavioral hypersensitivity is Gα i dependent, but not β-arrestin 2-dependent. Non-biased transcriptomic analyses of dorsal-horn spinal cord (DH-SC) tissues harvested at the time of peak hypersensitivity implicate potential contributions of mitogen-activated protein kinase (MAPK) and nuclear factor κB (NF-κB). In support, we found that the development of 7α,25-OHC/GPR183-induced mechano-allodynia was associated with significant activation of MAPKs (extracellular signal-regulated kinase [ERK], p38) and redox-sensitive transcription factors (NF-κB) and increased formation of inflammatory and neuroexcitatory cytokines. SAE-14 blocked these effects and behavioral hypersensitivity. Our findings provide novel mechanistic insight into how GPR183 signaling in the spinal cord produces hypersensitivity through MAPK and NF-κB activation. SIGNIFICANCE STATEMENT: Using a multi-disciplinary approach, we have characterized the molecular mechanisms underpinning 7α,25-OHC/GPR183-induced hypersensitivity in mice. Intrathecal injections of the GPR183 agonist 7α,25-OHC induce behavioral hypersensitivity, and these effects are blocked by the selective GPR183 antagonist SAE-14. We found that 7α,25-OHC-induced allodynia is dependent on MAPK and NF-κB signaling pathways and results in an increase in pro-inflammatory cytokine expression. This study provides a first insight into how GPR183 signaling in the spinal cord is pronociceptive.
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Affiliation(s)
- Kathryn Braden
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (K.B., Y.L., Z.C., T.M.D., L.A.G., J.Z., C.K.A., D.S.); Henry and Amelia Nasrallah Center for Neuroscience, Saint Louis University, Saint Louis, Missouri (K.B., Y.L., Z.C., T.M.D., L.A.G., J.Z., C.K.A.,D.S.); Department of Clinical and Experimental Medicine and Pharmacology, University of Messina, Messina, Italy (M.C., E.E., S.C.); and Department of Chemistry, Saint Louis University, Saint Louis, Missouri (C.K.A.)
| | - Michela Campolo
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (K.B., Y.L., Z.C., T.M.D., L.A.G., J.Z., C.K.A., D.S.); Henry and Amelia Nasrallah Center for Neuroscience, Saint Louis University, Saint Louis, Missouri (K.B., Y.L., Z.C., T.M.D., L.A.G., J.Z., C.K.A.,D.S.); Department of Clinical and Experimental Medicine and Pharmacology, University of Messina, Messina, Italy (M.C., E.E., S.C.); and Department of Chemistry, Saint Louis University, Saint Louis, Missouri (C.K.A.)
| | - Ying Li
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (K.B., Y.L., Z.C., T.M.D., L.A.G., J.Z., C.K.A., D.S.); Henry and Amelia Nasrallah Center for Neuroscience, Saint Louis University, Saint Louis, Missouri (K.B., Y.L., Z.C., T.M.D., L.A.G., J.Z., C.K.A.,D.S.); Department of Clinical and Experimental Medicine and Pharmacology, University of Messina, Messina, Italy (M.C., E.E., S.C.); and Department of Chemistry, Saint Louis University, Saint Louis, Missouri (C.K.A.)
| | - Zhoumou Chen
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (K.B., Y.L., Z.C., T.M.D., L.A.G., J.Z., C.K.A., D.S.); Henry and Amelia Nasrallah Center for Neuroscience, Saint Louis University, Saint Louis, Missouri (K.B., Y.L., Z.C., T.M.D., L.A.G., J.Z., C.K.A.,D.S.); Department of Clinical and Experimental Medicine and Pharmacology, University of Messina, Messina, Italy (M.C., E.E., S.C.); and Department of Chemistry, Saint Louis University, Saint Louis, Missouri (C.K.A.)
| | - Timothy M Doyle
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (K.B., Y.L., Z.C., T.M.D., L.A.G., J.Z., C.K.A., D.S.); Henry and Amelia Nasrallah Center for Neuroscience, Saint Louis University, Saint Louis, Missouri (K.B., Y.L., Z.C., T.M.D., L.A.G., J.Z., C.K.A.,D.S.); Department of Clinical and Experimental Medicine and Pharmacology, University of Messina, Messina, Italy (M.C., E.E., S.C.); and Department of Chemistry, Saint Louis University, Saint Louis, Missouri (C.K.A.)
| | - Luigino Antonio Giancotti
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (K.B., Y.L., Z.C., T.M.D., L.A.G., J.Z., C.K.A., D.S.); Henry and Amelia Nasrallah Center for Neuroscience, Saint Louis University, Saint Louis, Missouri (K.B., Y.L., Z.C., T.M.D., L.A.G., J.Z., C.K.A.,D.S.); Department of Clinical and Experimental Medicine and Pharmacology, University of Messina, Messina, Italy (M.C., E.E., S.C.); and Department of Chemistry, Saint Louis University, Saint Louis, Missouri (C.K.A.)
| | - Emanuela Esposito
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (K.B., Y.L., Z.C., T.M.D., L.A.G., J.Z., C.K.A., D.S.); Henry and Amelia Nasrallah Center for Neuroscience, Saint Louis University, Saint Louis, Missouri (K.B., Y.L., Z.C., T.M.D., L.A.G., J.Z., C.K.A.,D.S.); Department of Clinical and Experimental Medicine and Pharmacology, University of Messina, Messina, Italy (M.C., E.E., S.C.); and Department of Chemistry, Saint Louis University, Saint Louis, Missouri (C.K.A.)
| | - Jinsong Zhang
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (K.B., Y.L., Z.C., T.M.D., L.A.G., J.Z., C.K.A., D.S.); Henry and Amelia Nasrallah Center for Neuroscience, Saint Louis University, Saint Louis, Missouri (K.B., Y.L., Z.C., T.M.D., L.A.G., J.Z., C.K.A.,D.S.); Department of Clinical and Experimental Medicine and Pharmacology, University of Messina, Messina, Italy (M.C., E.E., S.C.); and Department of Chemistry, Saint Louis University, Saint Louis, Missouri (C.K.A.)
| | - Salvatore Cuzzocrea
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (K.B., Y.L., Z.C., T.M.D., L.A.G., J.Z., C.K.A., D.S.); Henry and Amelia Nasrallah Center for Neuroscience, Saint Louis University, Saint Louis, Missouri (K.B., Y.L., Z.C., T.M.D., L.A.G., J.Z., C.K.A.,D.S.); Department of Clinical and Experimental Medicine and Pharmacology, University of Messina, Messina, Italy (M.C., E.E., S.C.); and Department of Chemistry, Saint Louis University, Saint Louis, Missouri (C.K.A.)
| | - Christopher Kent Arnatt
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (K.B., Y.L., Z.C., T.M.D., L.A.G., J.Z., C.K.A., D.S.); Henry and Amelia Nasrallah Center for Neuroscience, Saint Louis University, Saint Louis, Missouri (K.B., Y.L., Z.C., T.M.D., L.A.G., J.Z., C.K.A.,D.S.); Department of Clinical and Experimental Medicine and Pharmacology, University of Messina, Messina, Italy (M.C., E.E., S.C.); and Department of Chemistry, Saint Louis University, Saint Louis, Missouri (C.K.A.)
| | - Daniela Salvemini
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, Missouri (K.B., Y.L., Z.C., T.M.D., L.A.G., J.Z., C.K.A., D.S.); Henry and Amelia Nasrallah Center for Neuroscience, Saint Louis University, Saint Louis, Missouri (K.B., Y.L., Z.C., T.M.D., L.A.G., J.Z., C.K.A.,D.S.); Department of Clinical and Experimental Medicine and Pharmacology, University of Messina, Messina, Italy (M.C., E.E., S.C.); and Department of Chemistry, Saint Louis University, Saint Louis, Missouri (C.K.A.)
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