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Hsieh KL, Plascencia-Villa G, Lin KH, Perry G, Jiang X, Kim Y. Synthesize heterogeneous biological knowledge via representation learning for Alzheimer's disease drug repurposing. iScience 2023; 26:105678. [PMID: 36594024 PMCID: PMC9804117 DOI: 10.1016/j.isci.2022.105678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 11/04/2022] [Accepted: 11/23/2022] [Indexed: 11/27/2022] Open
Abstract
Developing drugs for treating Alzheimer's disease has been extremely challenging and costly due to limited knowledge of underlying mechanisms and therapeutic targets. To address the challenge in AD drug development, we developed a multi-task deep learning pipeline that learns biological interactions and AD risk genes, then utilizes multi-level evidence on drug efficacy to identify repurposable drug candidates. Using the embedding derived from the model, we ranked drug candidates based on evidence from post-treatment transcriptomic patterns, efficacy in preclinical models, population-based treatment effects, and clinical trials. We mechanistically validated the top-ranked candidates in neuronal cells, identifying drug combinations with efficacy in reducing oxidative stress and safety in maintaining neuronal viability and morphology. Our neuronal response experiments confirmed several biologically efficacious drug combinations. This pipeline showed that harmonizing heterogeneous and complementary data/knowledge, including human interactome, transcriptome patterns, experimental efficacy, and real-world patient data shed light on the drug development of complex diseases.
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Affiliation(s)
- Kang-Lin Hsieh
- Center for Secure Artificial Intelligence for Healthcare, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - German Plascencia-Villa
- Department of Neuroscience, Developmental and Regenerative Biology, University of Texas at San Antonio, San Antonio, TX 78729, USA
| | - Ko-Hong Lin
- Center for Secure Artificial Intelligence for Healthcare, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - George Perry
- Department of Neuroscience, Developmental and Regenerative Biology, University of Texas at San Antonio, San Antonio, TX 78729, USA
| | - Xiaoqian Jiang
- Center for Secure Artificial Intelligence for Healthcare, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Yejin Kim
- Center for Secure Artificial Intelligence for Healthcare, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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Plascencia-Villa G, Perry G. P4-513: ACTIVATION OF FERROPTOSIS, AN IRON-DEPENDENT FORM OF NON-APOPTOTIC DEATH IN NEURONS. Alzheimers Dement 2019. [DOI: 10.1016/j.jalz.2019.08.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
| | - George Perry
- The University of Texas at San Antonio; San Antonio TX USA
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López-Lozano X, Plascencia-Villa G, Calero G, Whetten RL, Weissker HC. Is the largest aqueous gold cluster a superatom complex? Electronic structure & optical response of the structurally determined Au 146(p-MBA) 57. Nanoscale 2017; 9:18629-18634. [PMID: 29182699 DOI: 10.1039/c7nr04764a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The new water-soluble gold cluster Au146(p-MBA)57, the structure of which has been recently determined at sub-atomic resolution by Vergara et al., is the largest aqueous gold cluster ever structurally determined and likewise the smallest cluster with a stacking fault. The core presents a twinned truncated octahedron, while additional peripheral gold atoms follow a C2 rotational symmetry. According to the usual counting rules of the superatom complex (SAC) model, the compound attains a number of 92 SAC electrons if the overall net charge is 3- (three additional electrons). As this is the number of electrons required for a major shell closing, the question arises of whether Au146(p-MBA)57 should be regarded as a superatom complex. Starting from the experimental coordinates we have analyzed the structure using density-functional theory. The optimized (relaxed) structure retains all the connectivity of the experimental coordinates, while removing much of its irregularities in interatomic distances, thereby enhancing the C2-symmetry feature. On analyzing the angular-momentum-projected states, we show that, despite a small gap, the electronic structure does not exhibit SAC model character. In addition, optical absorption spectra are found to be relatively smooth compared to the example of the Au144(SR)60 cluster. The Au146(SR)57 does not derive its stability from SAC character; it cannot be considered as a superatom complex.
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Affiliation(s)
- Xóchitl López-Lozano
- Department of Physics & Astronomy, The University of Texas at San Antonio, One UTSA circle, 78249-0697 San Antonio, TX, USA.
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Vergara S, Lukes DA, Martynowycz MW, Santiago U, Plascencia-Villa G, Weiss SC, de la Cruz MJ, Black DM, Alvarez MM, Lopez-Lozano X, Barnes CO, Lin G, Weissker HC, Whetten RL, Gonen T, Jose-Yacaman M, Calero G. MicroED Structure of Au 146(p-MBA) 57 at Subatomic Resolution Reveals a Twinned FCC Cluster. J Phys Chem Lett 2017; 8:5523-5530. [PMID: 29072840 PMCID: PMC5769702 DOI: 10.1021/acs.jpclett.7b02621] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Solving the atomic structure of metallic clusters is fundamental to understanding their optical, electronic, and chemical properties. Herein we present the structure of the largest aqueous gold cluster, Au146(p-MBA)57 (p-MBA: para-mercaptobenzoic acid), solved by electron micro-diffraction (MicroED) to subatomic resolution (0.85 Å) and by X-ray diffraction at atomic resolution (1.3 Å). The 146 gold atoms may be decomposed into two constituent sets consisting of 119 core and 27 peripheral atoms. The core atoms are organized in a twinned FCC structure, whereas the surface gold atoms follow a C2 rotational symmetry about an axis bisecting the twinning plane. The protective layer of 57 p-MBAs fully encloses the cluster and comprises bridging, monomeric, and dimeric staple motifs. Au146(p-MBA)57 is the largest cluster observed exhibiting a bulk-like FCC structure as well as the smallest gold particle exhibiting a stacking fault.
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Affiliation(s)
- Sandra Vergara
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Dylan A. Lukes
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Ulises Santiago
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX, USA
| | - German Plascencia-Villa
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Simon C. Weiss
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - David M. Black
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Marcos M. Alvarez
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Xochitl Lopez-Lozano
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX, USA
| | | | - Guowu Lin
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Robert L. Whetten
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Tamir Gonen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Howard Hughes Medical Institute, Departments of Biological Chemistry and Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Miguel Jose-Yacaman
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA, USA
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