51
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Song G, Lee EM, Pan J, Xu M, Rho HS, Cheng Y, Whitt N, Yang S, Kouznetsova J, Klumpp-Thomas C, Michael SG, Moore C, Yoon KJ, Christian KM, Simeonov A, Huang W, Xia M, Huang R, Lal-Nag M, Tang H, Zheng W, Qian J, Song H, Ming GL, Zhu H. Corrigendum to "An Integrated Systems Biology Approach Identifies the Proteasome as A Critical Host Machinery for ZIKV and DENV Replication" [Genomics Proteomics Bioinformatics19 (1) (2021) 108-122]. Genomics Proteomics Bioinformatics 2022; 20:808-809. [PMID: 36669818 PMCID: PMC9880883 DOI: 10.1016/j.gpb.2022.12.009] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Guang Song
- Department of Pharmacology & Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Emily M. Lee
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Jianbo Pan
- Department of Ophthalmology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Miao Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA,Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Hee-Sool Rho
- Department of Pharmacology & Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Yichen Cheng
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Nadia Whitt
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shu Yang
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jennifer Kouznetsova
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Carleen Klumpp-Thomas
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Samuel G. Michael
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cedric Moore
- Department of Pharmacology & Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Ki-Jun Yoon
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA,Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kimberly M. Christian
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wenwei Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Madhu Lal-Nag
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA,Corresponding authors.
| | - Hengli Tang
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA,Corresponding authors.
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA,Corresponding authors.
| | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA,Corresponding authors.
| | - Hongjun Song
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA,Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Department of Cell and Developmental Biology, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Institute for Regenerative Medicine, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,The Epigenetics Institute, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Corresponding authors.
| | - Guo-li Ming
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA,Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Department of Cell and Developmental Biology, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Institute for Regenerative Medicine, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Corresponding authors.
| | - Heng Zhu
- Department of Pharmacology & Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA,Corresponding authors.
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Sakamuru S, Huang R, Xia M. Use of Tox21 Screening Data to Evaluate the COVID-19 Drug Candidates for Their Potential Toxic Effects and Related Pathways. Front Pharmacol 2022; 13:935399. [PMID: 35910344 PMCID: PMC9333127 DOI: 10.3389/fphar.2022.935399] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/16/2022] [Indexed: 12/15/2022] Open
Abstract
Currently, various potential therapeutic agents for coronavirus disease-2019 (COVID-19), a global pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), are being investigated worldwide mainly through the drug repurposing approach. Several anti-viral, anti-bacterial, anti-malarial, and anti-inflammatory drugs were employed in randomized trials and observational studies for developing new therapeutics for COVID-19. Although an increasing number of repurposed drugs have shown anti-SARS-CoV-2 activities in vitro, so far only remdesivir has been approved by the US FDA to treat COVID-19, and several other drugs approved for Emergency Use Authorization, including sotrovimab, tocilizumab, baricitinib, paxlovid, molnupiravir, and other potential strategies to develop safe and effective therapeutics for SARS-CoV-2 infection are still underway. Many drugs employed as anti-viral may exert unwanted side effects (i.e., toxicity) via unknown mechanisms. To quickly assess these drugs for their potential toxicological effects and mechanisms, we used the Tox21 in vitro assay datasets generated from screening ∼10,000 compounds consisting of approved drugs and environmental chemicals against multiple cellular targets and pathways. Here we summarize the toxicological profiles of small molecule drugs that are currently under clinical trials for the treatment of COVID-19 based on their in vitro activities against various targets and cellular signaling pathways.
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Kabir M, Padilha EC, Shah P, Huang R, Sakamuru S, Gonzalez E, Ye L, Hu X, Henderson MJ, Xia M, Xu X. Identification of Selective CYP3A7 and CYP3A4 Substrates and Inhibitors Using a High-Throughput Screening Platform. Front Pharmacol 2022; 13:899536. [PMID: 35847040 PMCID: PMC9283723 DOI: 10.3389/fphar.2022.899536] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/27/2022] [Indexed: 11/26/2022] Open
Abstract
Cytochrome P450 (CYP) 3A7 is one of the major xenobiotic metabolizing enzymes in human embryonic, fetal, and newborn liver. CYP3A7 expression has also been observed in a subset of the adult population, including pregnant women, as well as in various cancer patients. The characterization of CYP3A7 is not as extensive as other CYPs, and health authorities have yet to provide guidance towards DDI assessment. To identify potential CYP3A7-specific molecules, we used a P450-Glo CYP3A7 enzyme assay to screen a library of ∼5,000 compounds, including FDA-approved drugs and drug-like molecules, and compared these screening data with that from a P450-Glo CYP3A4 assay. Additionally, a subset of 1,000 randomly selected compounds were tested in a metabolic stability assay. By combining the data from the qHTS P450-Glo and metabolic stability assays, we identified several chemical features important for CYP3A7 selectivity. Halometasone was chosen for further evaluation as a potential CYP3A7-selective inhibitor using molecular docking. From the metabolic stability assay, we identified twenty-two CYP3A7-selective substrates over CYP3A4 in supersome setting. Our data shows that CYP3A7 has ligand promiscuity, much like CYP3A4. Furthermore, we have established a large, high-quality dataset that can be used in predictive modeling for future drug metabolism and interaction studies.
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Affiliation(s)
- Md Kabir
- Division of Pre-Clinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
- Department of Pharmacology, The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Elias C. Padilha
- Division of Pre-Clinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
| | - Pranav Shah
- Division of Pre-Clinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
| | - Ruili Huang
- Division of Pre-Clinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
| | - Srilatha Sakamuru
- Division of Pre-Clinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
| | - Eric Gonzalez
- Division of Pre-Clinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
- Novartis Institutes for BioMedical Research, Cambridge, MA, United States
| | - Lin Ye
- Division of Pre-Clinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
| | - Xin Hu
- Division of Pre-Clinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
| | - Mark J. Henderson
- Division of Pre-Clinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
| | - Menghang Xia
- Division of Pre-Clinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
- *Correspondence: Menghang Xia, ; Xin Xu,
| | - Xin Xu
- Division of Pre-Clinical Innovation, National Center for Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
- *Correspondence: Menghang Xia, ; Xin Xu,
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Stern S, Liang D, Li L, Kurian R, Lynch C, Sakamuru S, Heyward S, Zhang J, Kareem KA, Chun YW, Huang R, Xia M, Hong CC, Xue F, Wang H. Targeting CAR and Nrf2 improves cyclophosphamide bioactivation while reducing doxorubicin-induced cardiotoxicity in triple-negative breast cancer treatment. JCI Insight 2022; 7:e153868. [PMID: 35579950 PMCID: PMC9309041 DOI: 10.1172/jci.insight.153868] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 05/10/2022] [Indexed: 11/17/2022] Open
Abstract
Cyclophosphamide (CPA) and doxorubicin (DOX) are key components of chemotherapy for triple-negative breast cancer (TNBC), although suboptimal outcomes are commonly associated with drug resistance and/or intolerable side effects. Through an approach combining high-throughput screening and chemical modification, we developed CN06 as a dual activator of the constitutive androstane receptor (CAR) and nuclear factor erythroid 2-related factor 2 (Nrf2). CN06 enhances CAR-induced bioactivation of CPA (a prodrug) by provoking hepatic expression of CYP2B6, while repressing DOX-induced cytotoxicity in cardiomyocytes in vitro via stimulating Nrf2-antioxidant signaling. Utilizing a multicellular coculture model incorporating human primary hepatocytes, TNBC cells, and cardiomyocytes, we show that CN06 increased CPA/DOX-mediated TNBC cell death via CAR-dependent CYP2B6 induction and subsequent conversion of CPA to its active metabolite 4-hydroxy-CPA, while protecting against DOX-induced cardiotoxicity by selectively activating Nrf2-antioxidant signaling in cardiomyocytes but not in TNBC cells. Furthermore, CN06 preserves the viability and function of human iPSC-derived cardiomyocytes by modulating antioxidant defenses, decreasing apoptosis, and enhancing the kinetics of contraction and relaxation. Collectively, our findings identify CAR and Nrf2 as potentially novel combined therapeutic targets whereby CN06 holds the potential to improve the efficacy/toxicity ratio of CPA/DOX-containing chemotherapy.
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Affiliation(s)
- Sydney Stern
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland, USA
| | - Dongdong Liang
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland, USA
| | - Linhao Li
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland, USA
| | - Ritika Kurian
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland, USA
| | - Caitlin Lynch
- National Center for Advancing Translational Science (NCATS), NIH, Rockville, Maryland, USA
| | - Srilatha Sakamuru
- National Center for Advancing Translational Science (NCATS), NIH, Rockville, Maryland, USA
| | - Scott Heyward
- Bioreclamation In Vitro Technologies, Halethorpe, Maryland, USA
| | - Junran Zhang
- Department of Radiation Oncology, The Ohio State University James Comprehensive Cancer Center and College of Medicine, Columbus, Ohio, USA
| | - Kafayat Ajoke Kareem
- Division of Cardiovascular Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Young Wook Chun
- Division of Cardiovascular Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Ruili Huang
- National Center for Advancing Translational Science (NCATS), NIH, Rockville, Maryland, USA
| | - Menghang Xia
- National Center for Advancing Translational Science (NCATS), NIH, Rockville, Maryland, USA
| | - Charles C. Hong
- Division of Cardiovascular Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Fengtian Xue
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland, USA
| | - Hongbing Wang
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland, USA
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55
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Dong YC, Huang R, Zhao CY, Li XY. [Effects and mechanism of negative pressure microenvironment on the neogenesis of human umbilical vein endothelial cells]. Zhonghua Shao Shang Yu Chuang Mian Xiu Fu Za Zhi 2022; 38:520-531. [PMID: 35764577 DOI: 10.3760/cma.j.cn501225-20220119-00009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Objective: To investigate the effects and mechanism of negative pressure microenvironment on the neogenesis of human umbilical vein endothelial cells (HUVECs). Methods: The experimental research methods were adopted. The third to the fifth passage of HUVECs in the logarithmic growth stage were used for the subsequent experiments. Three batches of cells were taken, with each batch of cells being divided into normal control group and negative pressure treatment alone group (both routinely cultured for 24 h), and 17-allylamino-17-demethoxy-geldanamycin (17-AAG) alone group and 17-AAG+negative pressure treatment group (both cultured with 17-AAG for 24 h). In addition, the intermittent negative pressure suction, with the negative pressure value of -5.33 kPa (suction for 30 s, pause for 10 s) was continuously applied for 8 h on cells in the two negative pressure treatment groups using an automatic three-dimensional cell gradient negative pressure loading device designed and developed by ourselves. After the treatment of the first batch of cells, the cell proliferation level was detected by cell counting kit 8 method at 0 (immediately), 24, 48, and 72 h of culture, with the number of samples being 6. After the treatment of the second batch of cells, the scratch experiment was performed. At 12 h after scratching, the cell migration was observed under an inverted phase contrast microscope and the cell migration rate was calculated, with the number of samples being 3. After the treatment of the third batch of cells, the tubule formation experiment was conducted. After 6 h of culture, the tubulogenesis was observed under an inverted phase contrast microscope and the total tubule length and the number of branch nodes of cells were calculated, with the number of samples being 3. The cells were taken and divided into normal control group, negative pressure treatment alone group, and 17-AAG+negative pressure treatment group. The cells were treated the same as in the previous corresponding group. After the treatment, Western blotting was used to detect the protein expressions of heat shock protein 90 (HSP90), caveolin 1, endothelial nitric oxide synthase (eNOS), and eNOS phosphorylation site 1177 in the cells, and the eNOS phosphorylation site 1177/eNOS ratio was calculated, with the number of samples being 3; co-immunoprecipitation (co-precipitating HSP90 and caveolin 1, caveolin 1 and eNOS) and Western blotting were used to detect the protein expressions of caveolin 1 and eNOS in the cells, with the number of samples being 3; the protein co-localization of HSP90 and caveolin 1 and that of caveolin 1 and eNOS in the cells was assessed by immunofluorescence double staining. The molecular docking prediction of caveolin 1 and eNOS was processed by HADDOCK 2.4 protein-protein docking program. Data were statistically analyzed with analysis of variance for factorial design, one-way analysis of variance, and least significant difference method. Results: Compared with that in normal control group, the cell proliferation level in 17-AAG alone group was significantly decreased at culture hour of 24, 48, and 72 after the treatment (P<0.01), while the cell proliferation level in negative pressure treatment alone group was significantly increased at culture hour of 24, 48, and 72 after the treatment (P<0.01). Compared with that in 17-AAG alone group, the cell proliferation level in 17-AAG+negative pressure treatment group was significantly increased at culture hour of 48 and 72 after the treatment (P<0.05 or P<0.01). Compared with that in negative pressure treatment alone group, the cell proliferation level in 17-AAG+negative pressure treatment group was significantly decreased at culture hour of 24, 48, and 72 after the treatment (P<0.01). At 12 h after scratching, compared with (39.9±2.7)% in normal control group, the cell migration rate in 17-AAG alone group was significantly decreased ((10.7±2.7)%, P<0.01), while the cell migration rate in negative pressure treatment alone group was significantly increased ((61.9±2.4)%, P<0.01). Compared with those in 17-AAG alone group, the cell migration rate in 17-AAG+negative pressure treatment group was significantly increased ((37.7±3.7)%, P<0.01). Compared with that in negative pressure treatment alone group, the cell migration rate in 17-AAG+negative pressure treatment group was significantly decreased (P<0.01). At culture hour of 6 after the treatment, compared with those in normal control group, the total length of the tube formed by the cells in 17-AAG alone group was significantly shortened (P<0.05) and the number of branch nodes was significantly reduced (P<0.05), while the total length of the tube formed by the cells in negative pressure treatment alone group was significantly prolonged (P<0.01) and the number of branch nodes was dramatically increased (P<0.01). Compared with that in 17-AAG alone group, the number of branch nodes of the tube formed by the cells was significantly increased in 17-AAG+negative pressure treatment group (P<0.05). Compared with those in negative pressure treatment alone group, the total length of the tube formed by the cells in 17-AAG+negative pressure treatment group was significantly shortened (P<0.01) and the number of branch nodes was significantly reduced (P<0.01). Western blotting detection showed that after treatment, the overall comparison of eNOS and caveolin 1 protein expressions among the three groups of cells showed no statistically significant differences (P>0.05). The expression of HSP90 protein and the eNOS phosphorylation site 1177/eNOS ratio in the cells of negative pressure treatment alone group were significantly increased (P<0.01) compared with those in normal control group. Compared with those in negative pressure treatment alone group, the HSP90 protein expression and the eNOS phosphorylation site 1177/eNOS ratio in the cells of 17-AAG+negative pressure treatment group were significantly decreased (P<0.01). Co-immunoprecipitation and Western blotting detection after the treatment showed that compared with those in normal control group, the expression of caveolin 1 protein in the cells of negative pressure treatment alone group was significantly increased (P<0.01), while the protein expression of eNOS was significantly decreased (P<0.05). Compared with those in negative pressure treatment alone group, the expression of caveolin 1 protein in the cells of 17-AAG+negative pressure treatment group was significantly decreased (P<0.01), while the protein expression of eNOS was significantly increased (P<0.01). After the treatment, compared with those in normal control group, the co-localization of HSP90 and caveolin 1 protein in the cells of negative pressure treatment alone group was significantly increased, while the co-localization of caveolin 1 and eNOS protein was significantly decreased. Compared with those in negative pressure treatment alone group, the co-localization of HSP90 and caveolin 1 protein in the cells of 17-AAG+negative pressure treatment group was significantly decreased, while the co-localization of caveolin 1 and eNOS protein was significantly increased. Molecular docking prediction suggested that caveolin 1 interacted strongly with eNOS and inhibited the 1177 site phosphorylation of eNOS. Conclusions: The negative pressure microenvironment may inhibit the binding of caveolin 1 to eNOS by promoting the binding of HSP90 to caveolin 1 in HUVECs, so as to relieve the inhibition of 1177 site phosphorylation of eNOS by caveolin 1, thereby promoting the proliferation, migration, and tubulogenesis of HUVECs, and ultimately promoting the neogenesis of HUVECs.
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Affiliation(s)
- Y C Dong
- Department of Burns and Plastic Surgery, the Second Affiliated Hospital of Air Force Medical University, Xi'an 710038, China
| | - R Huang
- Department of Burns and Plastic Surgery, the Second Affiliated Hospital of Air Force Medical University, Xi'an 710038, China
| | - C Y Zhao
- Department of Burns and Plastic Surgery, the Second Affiliated Hospital of Air Force Medical University, Xi'an 710038, China
| | - X Y Li
- Department of Burns and Plastic Surgery, the Second Affiliated Hospital of Air Force Medical University, Xi'an 710038, China
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Wang Y, Michael S, Yang SM, Huang R, Cruz-Gutierrez K, Zhang Y, Zhao J, Xia M, Shinn P, Sun H. Retro Drug Design: From Target Properties to Molecular Structures. J Chem Inf Model 2022; 62:2659-2669. [PMID: 35653613 PMCID: PMC9198977 DOI: 10.1021/acs.jcim.2c00123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
![]()
To
deliver more therapeutics to more patients more quickly and
economically is the ultimate goal of pharmaceutical researchers. The
advent and rapid development of artificial intelligence (AI), in combination
with other powerful computational methods in drug discovery, makes
this goal more practical than ever before. Here, we describe a new
strategy, retro drug design, or RDD, to create novel small-molecule
drugs from scratch to meet multiple predefined requirements, including
biological activity against a drug target and optimal range of physicochemical
and ADMET properties. The molecular structure was represented by an
atom typing based molecular descriptor system, optATP, which was further
transformed to the space of loading vectors from principal component
analysis. Traditional predictive models were trained over experimental
data for the target properties using optATP and shallow machine learning
methods. The Monte Carlo sampling algorithm was then utilized to find
the solutions in the space of loading vectors that have the target
properties. Finally, a deep learning model was employed to decode
molecular structures from the solutions. To test the feasibility of
the algorithm, we challenged RDD to generate novel kinase inhibitors
from random numbers with five different ADMET properties optimized
at the same time. The best Tanimoto similarity score between the generated
valid structures and the available 4,314 kinase inhibitors was <
0.50, indicating a high extent of novelty of the generated compounds.
From the 3,040 structures that met all six target properties, 20 were
selected for synthesis and experimental measurement of inhibition
activity over 97 representative kinases and the ADMET properties.
Fifteen and eight compounds were determined to be hits or strong hits,
respectively. Five of the six strong kinase inhibitors have excellent
experimental ADMET properties. The results presented in this paper
illustrate that RDD has the potential to significantly improve the
current drug discovery process.
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Affiliation(s)
- Yuhong Wang
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Sam Michael
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Shyh-Ming Yang
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Ruili Huang
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Kennie Cruz-Gutierrez
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Yaqing Zhang
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Jinghua Zhao
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Menghang Xia
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Paul Shinn
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Hongmao Sun
- National Center for Advancing Translational Sciences (NCATS), 9800 Medical Center Drive, Rockville, Maryland 20850, United States
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Tran T, Huang R, Shen C. P-98 Diabetes promotes the progression of pancreatic ductal adenocarcinoma via the interaction between transforming acinar cells and cancer cells through AKT/CEBPβ/LCN2 pathway. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.04.188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Huang R, Wen Q, Wang X, Yan H, Ma Y, Wang M, Han X, Gao L, Gao L, Zhang C, Zhang X. S133: OFF-THE-SHELF CD33 CAR-NK CELL THERAPY FOR RELAPSE/REFRACTORY AML: FIRST-IN-HUMAN, PHASE I TRIAL. Hemasphere 2022. [DOI: 10.1097/01.hs9.0000843424.14245.d9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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59
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Ooka M, Zhao J, Shah P, Travers J, Klumpp-Thomas C, Xu X, Huang R, Ferguson S, Witt KL, Smith-Roe SL, Simeonov A, Xia M. Identification of environmental chemicals that activate p53 signaling after in vitro metabolic activation. Arch Toxicol 2022; 96:1975-1987. [PMID: 35435491 PMCID: PMC9151520 DOI: 10.1007/s00204-022-03291-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 03/24/2022] [Indexed: 12/11/2022]
Abstract
Currently, approximately 80,000 chemicals are used in commerce. Most have little-to-no toxicity information. The U.S. Toxicology in the 21st Century (Tox21) program has conducted a battery of in vitro assays using a quantitative high-throughput screening (qHTS) platform to gain toxicity information on environmental chemicals. Due to technical challenges, standard methods for providing xenobiotic metabolism could not be applied to qHTS assays. To address this limitation, we screened the Tox21 10,000-compound (10K) library, with concentrations ranging from 2.8 nM to 92 µM, using a p53 beta-lactamase reporter gene assay (p53-bla) alone or with rat liver microsomes (RLM) or human liver microsomes (HLM) supplemented with NADPH, to identify compounds that induce p53 signaling after biotransformation. Two hundred and seventy-eight compounds were identified as active under any of these three conditions. Of these 278 compounds, 73 gave more potent responses in the p53-bla assay with RLM, and 2 were more potent in the p53-bla assay with HLM compared with the responses they generated in the p53-bla assay without microsomes. To confirm the role of metabolism in the differential responses, we re-tested these 75 compounds in the absence of NADPH or with heat-attenuated microsomes. Forty-four compounds treated with RLM, but none with HLM, became less potent under these conditions, confirming the role of RLM in metabolic activation. Further evidence of biotransformation was obtained by measuring the half-life of the parent compounds in the presence of microsomes. Together, the data support the use of RLM in qHTS for identifying chemicals requiring biotransformation to induce biological responses.
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Affiliation(s)
- Masato Ooka
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Jinghua Zhao
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Pranav Shah
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Jameson Travers
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Carleen Klumpp-Thomas
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Xin Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Stephen Ferguson
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Kristine L Witt
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Stephanie L Smith-Roe
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA.
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Ngan DK, Xu T, Xia M, Zheng W, Huang R. Repurposing drugs as COVID-19 therapies: a toxicity evaluation. Drug Discov Today 2022; 27:1983-1993. [PMID: 35395401 PMCID: PMC8983078 DOI: 10.1016/j.drudis.2022.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 02/17/2022] [Accepted: 04/01/2022] [Indexed: 12/24/2022]
Abstract
Drug repurposing is an appealing method to address the Coronavirus 2019 (COVID-19) pandemic because of the low cost and efficiency. We analyzed our in-house database of approved drug screens and compared their activity profiles with results from a severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) cytopathic effect (CPE) assay. The activity profiles of the human ether-à-go-go-related gene (hERG), phospholipidosis (PLD), and many cytotoxicity screens were found significantly correlated with anti-SARS-CoV-2 activity. hERG inhibition is a nonspecific off-target effect that has contributed to promiscuous drug interactions, whereas drug-induced PLD is an undesirable effect linked to hERG blockers. Thus, this study identifies preferred drug candidates as well as chemical structures that should be avoided because of their potential to induce toxicity. Lastly, we highlight the hERG liability of anti-SARS-CoV-2 drugs currently enrolled in clinical trials.
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Affiliation(s)
- Deborah K Ngan
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Tuan Xu
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Menghang Xia
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Wei Zheng
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Ruili Huang
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA.
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Mizrahi I, Shah P, Nagamine T, Huang R, Lum C, Khan Z, Lee D, Shimabuku L, Shiraishi K, Brodsky M. Ethnicities of Patients Presenting with Methamphetamine Associated Cardiomyopathy at a Tertiary Hospital System in Hawaii. J Heart Lung Transplant 2022. [DOI: 10.1016/j.healun.2022.01.793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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62
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Mizrahi I, Lum C, Khan Z, Shah P, Huang R, Nagamine T, Shimabuku L, Lee D, Shiraishi K, Brodsky M. Characteristics of Methamphetamine Associated Cardiomyopathy at a Tertiary Clinical Center in Hawaii. J Heart Lung Transplant 2022. [DOI: 10.1016/j.healun.2022.01.1125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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63
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Mizrahi I, Shah P, Lum C, Khan Z, Huang R, Nagamine T, Lee D, Shimabuku L, Shiraishi K, Brodsky M. Contemporary Evaluation of Gender, Race, and Socioeconomics with Outcomes in Heart Failure. J Heart Lung Transplant 2022. [DOI: 10.1016/j.healun.2022.01.1681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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64
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Zhu Y, He X, Huang R, Wang W, Yu Y, Zhou T. Screening Bacillus subtilis for Effective L-theanine Production from Tea Plant Rhizosphere Soil. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s000368382202017x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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65
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Xu T, Xu M, Zhu W, Chen CZ, Zhang Q, Zheng W, Huang R. Efficient Identification of Anti-SARS-CoV-2 Compounds Using Chemical Structure- and Biological Activity-Based Modeling. J Med Chem 2022; 65:4590-4599. [PMID: 35275639 PMCID: PMC8936051 DOI: 10.1021/acs.jmedchem.1c01372] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Indexed: 12/12/2022]
Abstract
Identification of anti-SARS-CoV-2 compounds through traditional high-throughput screening (HTS) assays is limited by high costs and low hit rates. To address these challenges, we developed machine learning models to identify compounds acting via inhibition of the entry of SARS-CoV-2 into human host cells or the SARS-CoV-2 3-chymotrypsin-like (3CL) protease. The optimal classification models achieved good performance with area under the receiver operating characteristic curve (AUC-ROC) values of >0.78. Experimental validation showed that the best performing models increased the assay hit rate by 2.1-fold for viral entry inhibitors and 10.4-fold for 3CL protease inhibitors compared to those of the original drug repurposing screens. Twenty-two compounds showed potent (<5 μM) antiviral activities in a SARS-CoV-2 live virus assay. In conclusion, machine learning models can be developed and used as a complementary approach to HTS to expand compound screening capacities and improve the speed and efficiency of anti-SARS-CoV-2 drug discovery.
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Affiliation(s)
- Tuan Xu
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Miao Xu
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Wei Zhu
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Catherine Z Chen
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Qi Zhang
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Wei Zheng
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Ruili Huang
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
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Abstract
The U.S. Tox21 program has developed in vitro assays to test large collections of environmental chemicals in a quantitative high-throughput screening (qHTS) format, using triplicate 15-dose titrations to generate over 100 million data points to date. Counterscreens are also employed to minimize interferences from non-target-specific assay artifacts, such as compound autofluorescence and cytotoxicity. New data analysis approaches are needed to integrate these data and characterize the activities observed from these assays. Here, we describe a complete analysis pipeline that evaluates these qHTS data for technical quality in terms of signal reproducibility. We integrate signals from repeated assay runs, primary readouts and counterscreens to produce a final call on on-target compound activity.
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Affiliation(s)
- Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA.
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67
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Korunes KL, Liu J, Huang R, Xia M, Houck KA, Corton JC. A gene expression biomarker for predictive toxicology to identify chemical modulators of NF-κB. PLoS One 2022; 17:e0261854. [PMID: 35108274 PMCID: PMC8809623 DOI: 10.1371/journal.pone.0261854] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 12/12/2021] [Indexed: 11/29/2022] Open
Abstract
The nuclear factor-kappa B (NF-κB) is a transcription factor with important roles in inflammation, immune response, and oncogenesis. Dysregulation of NF-κB signaling is associated with inflammation and certain cancers. We developed a gene expression biomarker predictive of NF-κB modulation and used the biomarker to screen a large compendia of gene expression data. The biomarker consists of 108 genes responsive to tumor necrosis factor α in the absence but not the presence of IκB, an inhibitor of NF-κB. Using a set of 450 profiles from cells treated with immunomodulatory factors with known NF-κB activity, the balanced accuracy for prediction of NF-κB activation was > 90%. The biomarker was used to screen a microarray compendium consisting of 12,061 microarray comparisons from human cells exposed to 2,672 individual chemicals to identify chemicals that could cause toxic effects through NF-κB. There were 215 and 49 chemicals that were identified as putative or known NF-κB activators or suppressors, respectively. NF-κB activators were also identified using two high-throughput screening assays; 165 out of the ~3,800 chemicals (ToxCast assay) and 55 out of ~7,500 unique compounds (Tox21 assay) were identified as potential activators. A set of 32 chemicals not previously associated with NF-κB activation and which partially overlapped between the different screens were selected for validation in wild-type and NFKB1-null HeLa cells. Using RT-qPCR and targeted RNA-Seq, 31 of the 32 chemicals were confirmed to be NF-κB activators. These results comprehensively identify a set of chemicals that could cause toxic effects through NF-κB.
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Affiliation(s)
- Katharine L. Korunes
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Research Triangle Park, North Carolina, United States of America
- Biology Department, Duke University, Durham, North Carolina, United States of America
| | - Jie Liu
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Research Triangle Park, North Carolina, United States of America
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Keith A. Houck
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Research Triangle Park, North Carolina, United States of America
| | - J. Christopher Corton
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Research Triangle Park, North Carolina, United States of America
- * E-mail:
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68
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Yu L, Huang R, Okuagu C, Bardawil E, Balls-Berry J, Ross W. National trends in the surgical management of uterine leiomyoma. Am J Obstet Gynecol 2022. [DOI: 10.1016/j.ajog.2021.12.097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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69
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Smith MK, Chow J, Huang R, Omar M, Ebadi M, Wong P, Huard G, Yoshida EM, Peretz D, Brahmania M, Montano-Loza AJ, Bhanji R. A224 COVID-19 INFECTION IN LIVER TRANSPLANT RECIPIENTS: CLINICAL FEATURES, HOSPITALIZATION, AND MORTALITY FROM A CANADIAN MULTICENTRE COHORT. J Can Assoc Gastroenterol 2022. [PMCID: PMC8859339 DOI: 10.1093/jcag/gwab049.223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
The COVID-19 pandemic has brought significant challenges to clinicians caring for liver transplant (LT) recipients. Researchers have sought to better understand the risk and clinical outcomes of LT recipients infected with COVID-19 globally, however, there is a paucity of data from within Canada.
Aims
Our multi-center study aims to examine the characteristics and clinical outcomes of LT patients with COVID-19 in Canada.
Methods
We identified a retrospective cohort of adult LT recipients with RT-PCR confirmed COVID-19 from 7 Canadian tertiary care centers between March 2020 and June 2021. Demographic and clinical data were compiled by clinicians within those centers. We identified liver enzyme profile at the time of COVID-19 infection, immunosuppression type and post-infection adjustments, rate of hospitalization, ICU admission, mechanical ventilation, and death.
Results
A total of 49 patients with a history of LT and COVID-19 infection were identified. Twenty nine patients (59%) were male, the median time from LT was 66 months (1, 128) and the median age at COVID-19 infection was 59 years (52, 65). At COVID-19 diagnosis, the median ALT was 37 U/L (21, 41), AST U/L was 34 (20, 37), ALP U/L was 156 (88, 156), Total Bilirubin was 11 umol/L (7, 14), and INR was 1.1 (1.0, 1.1). The majority of patients (92%) were on tacrolimus monotherapy or a combination of tacrolimus and mycophenolate mofetil (MMF); median tacrolimus level at COVID-19 diagnosis was 5.3 ug/L (4.0, 8.1). Immunosuppression was modified in 8 (16%) patients post-infection; either the tacrolimus dose was reduced or MMF was held. One patient developed acute cellular rejection which recovered after re-initiation of the prior regimen. Eighteen patients (37%) required hospitalization, 6 (12%) were treated with dexamethasone, and 3 (6%) required ICU admission and mechanical ventilation. Four patients (8%) died due to complications of COVID-19. On univariate analysis, neither age, sex, co-morbidities nor duration post-transplant were associated with risk of hospitalization.
Conclusions
In our national retrospective study, approximately 40% of patients required hospitalization with a mortality rate of < 10%. Previous studies have shown proximity to LT as an independent factor for mortality with COVID-19; the median time from LT for our patients was 5 years, which may explain the lower mortality rate. Of note, the median tacrolimus levels were much lower in comparison to the target of 8–10 ug/L used in the first year post-transplant. As the landscape of COVID-19 changes with vaccination, evolving treatments, and increasing rates of variant transmission, additional studies are required to continue identifying trends in clinical outcomes.
Funding Agencies
None
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Affiliation(s)
- M K Smith
- University of Alberta Faculty of Medicine & Dentistry, Edmonton, AB, Canada
| | - J Chow
- University of Alberta Faculty of Medicine & Dentistry, Edmonton, AB, Canada
| | - R Huang
- Division of Gastroenterology & Liver Unit, University of Alberta, Edmonton, AB, Canada
| | - M Omar
- The University of British Columbia Faculty of Medicine, Vancouver, BC, Canada
| | - M Ebadi
- University of Alberta Faculty of Medicine & Dentistry, Edmonton, AB, Canada
| | - P Wong
- Gastroenterology, McGill University, Brossard, QC, Canada
| | - G Huard
- Liver diseases, Centre Hospitalier de l’Université de Montréal, Montreal, QC, Canada
| | - E M Yoshida
- Division of Gastroenterology, University of British Columbia, Vancouver, BC, Canada
| | - D Peretz
- University of Manitoba, Winnipeg, MB, Canada
| | | | - A J Montano-Loza
- Division of Gastroenterology & Liver Unit, University of Alberta, Edmonton, AB, Canada
| | - R Bhanji
- Division of Gastroenterology & Liver Unit, University of Alberta, Edmonton, AB, Canada
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70
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Li W, Huang X, Yu W, Xu Y, Huang R, Park J, Moshaverinia A, Arora P, Chen C. Activation of Functional Somatic Stem Cells Promotes Endogenous Tissue Regeneration. J Dent Res 2022; 101:802-811. [PMID: 35114850 DOI: 10.1177/00220345211070222] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Periodontal ligament derived stem cells (PDLSCs) are capable of differentiating into multiple cell types and inducing a promising immunomodulation for tissue regeneration and disease treatment. However, it is still challenging to develop a practical approach to activate endogenous stem cells for tissue self-healing and regeneration. In this study, transcriptome analysis reveals that resveratrol promotes PDLSC stemness through activation of stem cell, osteoprogenitor, and chondroprogenitor markers. Self-renewal and multipotent differentiation abilities are also improved in resveratrol-treated PDLSCs. In addition, immunomodulation of PDLSCs is dramatically increased after resveratrol treatment. Mechanistically, we show that resveratrol activates ERK/WNT crosstalk through elevation of olfactory and growth factor signaling pathways to upregulate the expression levels of RUNX2 and FASL for osteogenesis and immunomodulation, respectively. By using a periodontitis animal model, administration of resveratrol partially rescues bone loss through activation of endogenous somatic stem cells and inhibition of inflammatory T-cell infiltration. Taken together, our findings identify a novel pharmacological approach to achieve autotherapies for endogenous tissue regeneration.
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Affiliation(s)
- W Li
- Department of Oral and Maxillofacial Surgery and Pharmacology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA.,The Affiliated Hospital of Stomatology, School of Stomatology, Zhejiang University School of Medicine, and Key Laboratory of Oral Biomedical Research of Zhejiang Province, Hangzhou, Zhejiang, China
| | - X Huang
- Department of Oral and Maxillofacial Surgery and Pharmacology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - W Yu
- Department of Oral and Maxillofacial Surgery and Pharmacology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Orthodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Y Xu
- Department of Oral and Maxillofacial Surgery and Pharmacology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - R Huang
- Department of Oral and Maxillofacial Surgery and Pharmacology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - J Park
- Department of Oral and Maxillofacial Surgery and Pharmacology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Orthodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - A Moshaverinia
- Weintraub Center for Reconstructive Biotechnology, Division of Advanced Prosthodontics, School of Dentistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - P Arora
- Early-Research Oral Care, Colgate-Palmolive Company, Piscataway, NJ, USA
| | - C Chen
- Department of Oral and Maxillofacial Surgery and Pharmacology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Center of Innovation and Precision Dentistry, School of Dental Medicine, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
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Tamalunas A, Wendt A, Huang R, Wang R, Liu Y, Rutz B, Ciotkowska A, Stief C, Hennenberg M. YM254890 inhibits prostate smooth muscle contraction by fully disrupting intracellular post-receptor signaling. Eur Urol 2022. [DOI: 10.1016/s0302-2838(22)00683-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Huang R, Tamalunas A, Waidelich R, Strittmatter F, Stief C, Hennenberg M. Inhibition of smooth muscle contraction in isolated human detrusor tissues by mirabegron requires concentrations out of therapeutic range, and is limited to neurogenic contractions. Eur Urol 2022. [DOI: 10.1016/s0302-2838(22)00521-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Wu G, Zou X, Wu Y, Zhang Z, Yuan Y, Zhang G, Xiao R, Wang X, Xu H, Liu F, Liao Y, Xia W, Huang R. Clinical study of urethroplasty combined free grafting of internal preputial lamina with onlay local pedicled flap. Eur Urol 2022. [DOI: 10.1016/s0302-2838(22)00862-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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74
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Liu Y, Huang R, Li B, Wang R, Tamalunas A, Waidelich R, Strittmatter F, Stief C, Hennenberg M. WNK463 and HTH01-015 simultaneously inhibit neurogenic and α1-blocker-resistant, non-adrenergic contractions of human prostate tissues, and growth-related functions of prostate stromal cells. Eur Urol 2022. [DOI: 10.1016/s0302-2838(22)00681-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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75
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Krishna S, Borrel A, Huang R, Zhao J, Xia M, Kleinstreuer N. High-Throughput Chemical Screening and Structure-Based Models to Predict hERG Inhibition. Biology (Basel) 2022; 11:biology11020209. [PMID: 35205076 PMCID: PMC8869358 DOI: 10.3390/biology11020209] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/18/2022] [Accepted: 01/21/2022] [Indexed: 12/23/2022]
Abstract
Simple Summary Cardiovascular disease is the leading cause of death for people of most ethnicities in the United States. The human ether-a-go-go-related gene (hERG) potassium channel plays a pivotal role in cardiac rhythm regulation, and cardiotoxicity associated with hERG inhibition by drug molecules and environmental chemicals is a major public health concern. An evaluation of the effect of environmental chemicals on hERG channel function can help inform the potential public health risks of these compounds. To assess the cardiotoxic effect of diverse drugs and environmental compounds, the Tox21 federal research program has screened a collection of 9667 chemicals for inhibitory activity against the hERG channel. A set of molecular descriptors covering physicochemical and structural properties of chemicals, self-organizing maps, and hierarchical clustering were applied to characterize the chemicals inhibiting hERG. Machine learning approaches were applied to build robust statistical models that can predict the probability of any new chemical to cause cardiotoxicity via this mechanism. Abstract Chemical inhibition of the human ether-a -go-go-related gene (hERG) potassium channel leads to a prolonged QT interval that can contribute to severe cardiotoxicity. The adverse effects of hERG inhibition are one of the principal causes of drug attrition in clinical and pre-clinical development. Preliminary studies have demonstrated that a wide range of environmental chemicals and toxicants may also inhibit the hERG channel and contribute to the pathophysiology of cardiovascular (CV) diseases. As part of the US federal Tox21 program, the National Center for Advancing Translational Science (NCATS) applied a quantitative high throughput screening (qHTS) approach to screen the Tox21 library of 10,000 compounds (~7871 unique chemicals) at 14 concentrations in triplicate to identify chemicals perturbing hERG activity in the U2OS cell line thallium flux assay platform. The qHTS cell-based thallium influx assay provided a robust and reliable dataset to evaluate the ability of thousands of drugs and environmental chemicals to inhibit hERG channel protein, and the use of chemical structure-based clustering and chemotype enrichment analysis facilitated the identification of molecular features that are likely responsible for the observed hERG activity. We employed several machine-learning approaches to develop QSAR prediction models for the assessment of hERG liabilities for drug-like and environmental chemicals. The training set was compiled by integrating hERG bioactivity data from the ChEMBL database with the Tox21 qHTS thallium flux assay data. The best results were obtained with the random forest method (~92.6% balanced accuracy). The data and scripts used to generate hERG prediction models are provided in an open-access format as key in vitro and in silico tools that can be applied in a translational toxicology pipeline for drug development and environmental chemical screening.
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Affiliation(s)
- Shagun Krishna
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences (NIEHS), Research Triangle, NC 27560, USA;
| | | | - Ruili Huang
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Bethesda, MD 20892-4874, USA; (R.H.); (J.Z.); (M.X.)
| | - Jinghua Zhao
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Bethesda, MD 20892-4874, USA; (R.H.); (J.Z.); (M.X.)
| | - Menghang Xia
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Bethesda, MD 20892-4874, USA; (R.H.); (J.Z.); (M.X.)
| | - Nicole Kleinstreuer
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences (NIEHS), Research Triangle, NC 27560, USA;
- Correspondence: ; Tel.: +1-984-287-3150
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Li S, Li AJ, Travers J, Xu T, Sakamuru S, Klumpp-Thomas C, Huang R, Xia M. Identification of Compounds for Butyrylcholinesterase Inhibition. SLAS Discov 2021; 26:1355-1364. [PMID: 34269114 PMCID: PMC8637366 DOI: 10.1177/24725552211030897] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/30/2021] [Accepted: 06/10/2021] [Indexed: 11/24/2022]
Abstract
Butyrylcholinesterase (BChE) is a nonspecific cholinesterase enzyme that hydrolyzes choline-based esters. BChE plays a critical role in maintaining normal cholinergic function like acetylcholinesterase (AChE) through hydrolyzing acetylcholine (ACh). Selective BChE inhibition has been regarded as a viable therapeutic approach in Alzheimer's disease. As of now, a limited number of selective BChE inhibitors are available. To identify BChE inhibitors rapidly and efficiently, we have screened 8998 compounds from several annotated libraries against an enzyme-based BChE inhibition assay in a quantitative high-throughput screening (qHTS) format. From the primary screening, we identified a group of 125 compounds that were further confirmed to inhibit BChE activity, including previously reported BChE inhibitors (e.g., bambuterol and rivastigmine) and potential novel BChE inhibitors (e.g., pancuronium bromide and NNC 756), representing diverse structural classes. These BChE inhibitors were also tested for their selectivity by comparing their IC50 values in BChE and AChE inhibition assays. The binding modes of these compounds were further studied using molecular docking analyses to identify the differences between the interactions of these BChE inhibitors within the active sites of AChE and BChE. Our qHTS approach allowed us to establish a robust and reliable process to screen large compound collections for potential BChE inhibitors.
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Affiliation(s)
- Shuaizhang Li
- Division for Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Andrew J. Li
- Division for Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Jameson Travers
- Division for Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Tuan Xu
- Division for Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Srilatha Sakamuru
- Division for Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Carleen Klumpp-Thomas
- Division for Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Ruili Huang
- Division for Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Menghang Xia
- Division for Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
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Li J, Zhang Y, Sun J, Chen L, Gou W, Chen C, Zhou Y, Li Z, Chan DW, Huang R, Pei H, Zheng W, Li Y, Xia M, Zhu W. Discovery and characterization of potent And-1 inhibitors for cancer treatment. Clin Transl Med 2021; 11:e627. [PMID: 34923765 PMCID: PMC8684776 DOI: 10.1002/ctm2.627] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 10/01/2021] [Accepted: 10/08/2021] [Indexed: 12/19/2022] Open
Abstract
Acidic nucleoplasmic DNA-binding protein 1 (And-1), an important factor for deoxyribonucleic acid (DNA) replication and repair, is overexpressed in many types of cancer but not in normal tissues. Although multiple independent studies have elucidated And-1 as a promising target gene for cancer therapy, an And-1 inhibitor has yet to be identified. Using an And-1 luciferase reporter assay to screen the Library of Pharmacologically Active Compounds (LOPAC) in a high throughput screening (HTS) platform, and then further screen the compound analog collection, we identified two potent And-1 inhibitors, bazedoxifene acetate (BZA) and an uncharacterized compound [(E)-5-(3,4-dichlorostyryl)benzo[c][1,2]oxaborol-1(3H)-ol] (CH3), which specifically inhibit And-1 by promoting its degradation. Specifically, through direct interaction with And-1 WD40 domain, CH3 interrupts the polymerization of And-1. Depolymerization of And-1 promotes its interaction with E3 ligase Cullin 4B (CUL4B), resulting in its ubiquitination and subsequent degradation. Furthermore, CH3 suppresses the growth of a broad range of cancers. Moreover, And-1 inhibitors re-sensitize platinum-resistant ovarian cancer cells to platinum drugs in vitro and in vivo. Since BZA is an FDA approved drug, we expect a clinical trial of BZA-mediated cancer therapy in the near future. Taken together, our findings suggest that targeting And-1 by its inhibitors is a potential broad-spectrum anti-cancer chemotherapy regimen.
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Affiliation(s)
- Jing Li
- Department of Biochemistry and Molecular MedicineThe George Washington University School of Medicine and Health SciencesWashingtonDistrict of ColumbiaUSA
- GW Cancer CenterThe George Washington UniversityWashingtonDistrict of ColumbiaUSA
| | - Yi Zhang
- Department of Biochemistry and Molecular MedicineThe George Washington University School of Medicine and Health SciencesWashingtonDistrict of ColumbiaUSA
- GW Cancer CenterThe George Washington UniversityWashingtonDistrict of ColumbiaUSA
| | - Jing Sun
- Department of Biochemistry and Molecular MedicineThe George Washington University School of Medicine and Health SciencesWashingtonDistrict of ColumbiaUSA
- GW Cancer CenterThe George Washington UniversityWashingtonDistrict of ColumbiaUSA
| | - Leyuan Chen
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation MedicinePeking Union Medical College & Chinese Academy of Medical SciencesTianjinChina
| | - Wenfeng Gou
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation MedicinePeking Union Medical College & Chinese Academy of Medical SciencesTianjinChina
| | - Chi‐Wei Chen
- Department of Biochemistry and Molecular MedicineThe George Washington University School of Medicine and Health SciencesWashingtonDistrict of ColumbiaUSA
- GW Cancer CenterThe George Washington UniversityWashingtonDistrict of ColumbiaUSA
| | - Yuan Zhou
- Department of Biochemistry and Molecular MedicineThe George Washington University School of Medicine and Health SciencesWashingtonDistrict of ColumbiaUSA
- GW Cancer CenterThe George Washington UniversityWashingtonDistrict of ColumbiaUSA
| | - Zhuqing Li
- Department of Biochemistry and Molecular MedicineThe George Washington University School of Medicine and Health SciencesWashingtonDistrict of ColumbiaUSA
- GW Cancer CenterThe George Washington UniversityWashingtonDistrict of ColumbiaUSA
| | - David W. Chan
- Department of Obstetrics and Gynecology, LKS Faculty of MedicineThe University of Hong KongHong, China
| | - Ruili Huang
- Division of Preclinical Innovation, National Center for Advancing Translational SciencesNational Institutes of HealthBethesdaMarylandUSA
| | - Huadong Pei
- Department of Biochemistry and Molecular MedicineThe George Washington University School of Medicine and Health SciencesWashingtonDistrict of ColumbiaUSA
- GW Cancer CenterThe George Washington UniversityWashingtonDistrict of ColumbiaUSA
| | - Wei Zheng
- Division of Preclinical Innovation, National Center for Advancing Translational SciencesNational Institutes of HealthBethesdaMarylandUSA
| | - Yiliang Li
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation MedicinePeking Union Medical College & Chinese Academy of Medical SciencesTianjinChina
| | - Menghang Xia
- Division of Preclinical Innovation, National Center for Advancing Translational SciencesNational Institutes of HealthBethesdaMarylandUSA
| | - Wenge Zhu
- Department of Biochemistry and Molecular MedicineThe George Washington University School of Medicine and Health SciencesWashingtonDistrict of ColumbiaUSA
- GW Cancer CenterThe George Washington UniversityWashingtonDistrict of ColumbiaUSA
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Huang R, Yue J. Predictive Value of Absolute Lymphocyte Count and Systemic Immune-Inflammation Index in Advanced Hepatocellular Carcinoma Patients Treated With Anti–PD-1 Therapy. Int J Radiat Oncol Biol Phys 2021. [DOI: 10.1016/j.ijrobp.2021.07.374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Lee JK, Flowers A, Williams J, Li S, Yi X, Huang R. Immunoglobulin D Multiple Myeloma with a “Hidden” Lambda Light Chain. Am J Clin Pathol 2021. [DOI: 10.1093/ajcp/aqab191.061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Introduction/Objective
In rare cases, the conventional immunofixation gel electrophoresis technique fails to detect the light chain of an M-protein. We report a case of immunoglobulin (Ig) D multiple myeloma with a hidden lambda (λ) light chain.
Methods/Case Report
Capillary electrophoresis (CE) (Sebia CAPILLARYS 2) was used to detect and quantify M- proteins in serum specimens. Immunosubtraction (IS) on the CAPILLARYS 2 systems was used to identify the classes of M-proteins. Conventional gel immunofixation electrophoresis (IFE) was performed, using monospecific antisera for IgD, IgE, kappa (κ) or λ in the Sebia HYDRASYS system, and IgG, IgA, IgM, κ or λ in the Helena SPIFE3000 system. Beta-mercaptoethanol (BME) with Fluidil were used as reduction agents.
Results (if a Case Study enter NA)
Results of serum CE showed two abnormal peaks in beta 2 and gamma regions, suspected to be positive for M-proteins. IS results showed subtraction for λ light chain only in both peaks, suggesting two monoclonal λ light chains. In contrary, no monoclonal λ light chain was detected in gamma region by IFE (Sebia). Epitope masking in the folded monoclonal protein was suspected to cause the “hidden λ light chain” and was further investigated by two laboratory approaches. IFE performed on the Helena SPIFE3000 system found two λ bands in beta 2 and gamma regions, which was consistent with the results from IS. The treatment of BME with Fluidil helped unmasking the hidden epitope and revealed the λ band in gamma region on IFE (Sebia).
Conclusion
The medical laboratories should be aware of the described scenario. The failure to detect light chains of certain intact M-proteins is most likely due to the structurally inaccessibility of light chains. It is recommended that treatment with reduction agents or use of an alternative methodology or IS might be helpful for investigating suspected heavy chain only cases, due to the limitation of conventional methodology.
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Affiliation(s)
- J K Lee
- Pathology, The Ohio State University, Columbus, Ohio, UNITED STATES
| | - A Flowers
- Pathology, The Ohio State University, Columbus, Ohio, UNITED STATES
| | - J Williams
- Pathology, The Ohio State University, Columbus, Ohio, UNITED STATES
| | - S Li
- Pathology, The Ohio State University, Columbus, Ohio, UNITED STATES
| | - X Yi
- Pathology and Genomic Medicine, Houston Methodist Hospital and Research Institute, Houston, Texas, UNITED STATES
| | - R Huang
- Pathology and Immunology, Baylor College of Medicine, Houston, Texas, UNITED STATES
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Xu T, Zheng W, Huang R. High-throughput screening assays for SARS-CoV-2 drug development: Current status and future directions. Drug Discov Today 2021; 26:2439-2444. [PMID: 34048893 PMCID: PMC8146264 DOI: 10.1016/j.drudis.2021.05.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/16/2021] [Accepted: 05/19/2021] [Indexed: 02/08/2023]
Abstract
In response to the ongoing coronavirus disease 2019 (COVID-19) pandemic, a panel of assays has been developed and applied to screen collections of approved and investigational drugs for anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) activity in a quantitative high-throughput screening (qHTS) format. In this review, we applied data-driven approaches to evaluate the ability of each assay to identify potential anti-SARS-CoV-2 leads. Multitarget assays were found to show advantages in terms of accuracy and efficiency over single-target assays, whereas target-specific assays were more suitable for investigating compound mechanisms of action. Moreover, strict filtering with counter screens might be more detrimental than beneficial in identifying true positives. Thus, developing novel HTS assays acting simultaneously against multiple targets in the SARS-CoV-2 life cycle will benefit anti-COVID-19 drug discovery.
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Wang J, Lu S, Wang Z, Hu C, Sun Y, Yang K, Chen M, Zhao J, Liang L, Huo Y, Zhang Y, Huang R, Wu X, Ma X, Leaw S, Bai F, Shen Z. FP04.02 RATIONALE-307: Updated Biomarker Analysis of Phase 3 Study of Tislelizumab Plus Chemo vs Chemo Alone For 1L Advanced Sq-NSCLC. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.08.216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Ma J, Huang R, Ma XL, Li X, Zhang TS, Ruan B. [Identification and genetic analysis of new mutations in EYA1 gene of BOS syndrome]. Zhonghua Er Bi Yan Hou Tou Jing Wai Ke Za Zhi 2021; 56:966-971. [PMID: 34666446 DOI: 10.3760/cma.j.cn115330-20210126-00040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To analyze the clinical manifestations of a patient with branchiootic syndrome(BOS) and her families and to carry out genetic testing in order to specify the biological pathogenesis. Methods: Clinical data of the patient and her families were collected. Genomic DNA in the peripheral blood of the proband and her family members was extracted. All exons of 406 deafness-related susceptible genes as well as their flanking regions were sequenced by high-throughput sequencing, and the mutation sites of the proband and her parents were validated by Sanger sequencing. Results: There were nine members in three generations, of whom four presented with hearing loss, preauricular fistula and branchial fistula which met the diagnostic criteria of BOS. Proband and her mother presented with auricle malformation and inner ear malformation. And no one had abnormalities in the kidneys of all the patients. Pedigree analysis revealed that the mode of inheritance in the family was consistent with the autosomal dominant pattern. Mutational analysis showed that all the affected patients detected a heterozygous frameshift variation c.1255delT in the EYA1 gene, which had not been reported. Genotype and phenotype were co-isolated in this family. Such a frameshift variation produced a premature termination codon, thereby causing premature termination of translation (p.C419VFS*12). ACMG identified that the mutation was pathogenic. This mutation was novel and not detected in controls. A heterozygous missense variation mutation c.403G>A(p.G135S) in EYA1 gene was also detected in three members of this family. ACMG identified that the mutation clinical significance was uncertain. However, two of whom were normal, which seemed the disease was not caused by this mutation in this family. Conclusions: A novel frameshift mutation in EYA1(c.1255delT) is the main molecular etiology of BOS in the Chinese family. This study expands the mutational spectrum of EYA1 gene. The clinical manifestations are heterogeneous among patients in this family. The diagnosis of BOS should combine gene tests with clinical phenotypes analysis.
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Affiliation(s)
- J Ma
- Department of Otorhinolaryngology Head and Neck Surgery, Kunming Children's Hospital, Kunming Key Laboratory for Prevention and Control of Congenital Birth Defects of Children, Yunnan Key Laboratory of Children's Major Disease Research, Kunming 650228, China
| | - R Huang
- Department of Otorhinolaryngology Head and Neck Surgery, Kunming Children's Hospital, Kunming Key Laboratory for Prevention and Control of Congenital Birth Defects of Children, Yunnan Key Laboratory of Children's Major Disease Research, Kunming 650228, China
| | - X L Ma
- Department of Otorhinolaryngology Head and Neck Surgery, Kunming Children's Hospital, Kunming Key Laboratory for Prevention and Control of Congenital Birth Defects of Children, Yunnan Key Laboratory of Children's Major Disease Research, Kunming 650228, China
| | - X Li
- Department of Otorhinolaryngology Head and Neck Surgery, Kunming Children's Hospital, Kunming Key Laboratory for Prevention and Control of Congenital Birth Defects of Children, Yunnan Key Laboratory of Children's Major Disease Research, Kunming 650228, China
| | - T S Zhang
- Department of Otorhinolaryngology Head and Neck Surgery, Kunming Children's Hospital, Kunming Key Laboratory for Prevention and Control of Congenital Birth Defects of Children, Yunnan Key Laboratory of Children's Major Disease Research, Kunming 650228, China
| | - B Ruan
- Department of Otorhinolaryngology, the First Hospital of Kunming Medical University, Kunming 650032, China
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Gonzalez E, Jain S, Shah P, Torimoto-Katori N, Zakharov A, Nguyễn ÐT, Sakamuru S, Huang R, Xia M, Obach RS, Hop CECA, Simeonov A, Xu X. Development of Robust Quantitative Structure-Activity Relationship Models for CYP2C9, CYP2D6, and CYP3A4 Catalysis and Inhibition. Drug Metab Dispos 2021; 49:822-832. [PMID: 34183376 PMCID: PMC11022912 DOI: 10.1124/dmd.120.000320] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 06/17/2021] [Indexed: 11/22/2022] Open
Abstract
Cytochrome P450 enzymes are responsible for the metabolism of >75% of marketed drugs, making it essential to identify the contributions of individual cytochromes P450 to the total clearance of a new candidate drug. Overreliance on one cytochrome P450 for clearance levies a high risk of drug-drug interactions; and considering that several human cytochrome P450 enzymes are polymorphic, it can also lead to highly variable pharmacokinetics in the clinic. Thus, it would be advantageous to understand the likelihood of new chemical entities to interact with the major cytochrome P450 enzymes at an early stage in the drug discovery process. Typical screening assays using human liver microsomes do not provide sufficient information to distinguish the specific cytochromes P450 responsible for clearance. In this regard, we experimentally assessed the metabolic stability of ∼5000 compounds for the three most prominent xenobiotic metabolizing human cytochromes P450, i.e., CYP2C9, CYP2D6, and CYP3A4, and used the data sets to develop quantitative structure-activity relationship models for the prediction of high-clearance substrates for these enzymes. Screening library included the NCATS Pharmaceutical Collection, comprising clinically approved low-molecular-weight compounds, and an annotated library consisting of drug-like compounds. To identify inhibitors, the library was screened against a luminescence-based cytochrome P450 inhibition assay; and through crossreferencing hits from the two assays, we were able to distinguish substrates and inhibitors of these enzymes. The best substrate and inhibitor models (balanced accuracies ∼0.7), as well as the data used to develop these models, have been made publicly available (https://opendata.ncats.nih.gov/adme) to advance drug discovery across all research groups. SIGNIFICANCE STATEMENT: In drug discovery and development, drug candidates with indiscriminate cytochrome P450 metabolic profiles are considered advantageous, since they provide less risk of potential issues with cytochrome P450 polymorphisms and drug-drug interactions. This study developed robust substrate and inhibitor quantitative structure-activity relationship models for the three major xenobiotic metabolizing cytochromes P450, i.e., CYP2C9, CYP2D6, and CYP3A4. The use of these models early in drug discovery will enable project teams to strategize or pivot when necessary, thereby accelerating drug discovery research.
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Affiliation(s)
- Eric Gonzalez
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Rockville, Maryland (E.G., S.J., P.S., N.T.-K., A.Z., D.-T.N., S.S., R.H., M.X. A.S., X.X.); Discovery Technology Laboratories, Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Yokohama-shi, Japan (N.T.-K.); Pfizer Inc. Department of Pharmacokinetics, Dynamics and Metabolism, Pfizer, Groton, Connecticut (R.S.O.); and Genentech Inc. Department of Drug Metabolism and Pharmacokinetics, Genentech Inc., San Francisco, California (C.E.C.A.H.)
| | - Sankalp Jain
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Rockville, Maryland (E.G., S.J., P.S., N.T.-K., A.Z., D.-T.N., S.S., R.H., M.X. A.S., X.X.); Discovery Technology Laboratories, Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Yokohama-shi, Japan (N.T.-K.); Pfizer Inc. Department of Pharmacokinetics, Dynamics and Metabolism, Pfizer, Groton, Connecticut (R.S.O.); and Genentech Inc. Department of Drug Metabolism and Pharmacokinetics, Genentech Inc., San Francisco, California (C.E.C.A.H.)
| | - Pranav Shah
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Rockville, Maryland (E.G., S.J., P.S., N.T.-K., A.Z., D.-T.N., S.S., R.H., M.X. A.S., X.X.); Discovery Technology Laboratories, Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Yokohama-shi, Japan (N.T.-K.); Pfizer Inc. Department of Pharmacokinetics, Dynamics and Metabolism, Pfizer, Groton, Connecticut (R.S.O.); and Genentech Inc. Department of Drug Metabolism and Pharmacokinetics, Genentech Inc., San Francisco, California (C.E.C.A.H.)
| | - Nao Torimoto-Katori
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Rockville, Maryland (E.G., S.J., P.S., N.T.-K., A.Z., D.-T.N., S.S., R.H., M.X. A.S., X.X.); Discovery Technology Laboratories, Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Yokohama-shi, Japan (N.T.-K.); Pfizer Inc. Department of Pharmacokinetics, Dynamics and Metabolism, Pfizer, Groton, Connecticut (R.S.O.); and Genentech Inc. Department of Drug Metabolism and Pharmacokinetics, Genentech Inc., San Francisco, California (C.E.C.A.H.)
| | - Alexey Zakharov
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Rockville, Maryland (E.G., S.J., P.S., N.T.-K., A.Z., D.-T.N., S.S., R.H., M.X. A.S., X.X.); Discovery Technology Laboratories, Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Yokohama-shi, Japan (N.T.-K.); Pfizer Inc. Department of Pharmacokinetics, Dynamics and Metabolism, Pfizer, Groton, Connecticut (R.S.O.); and Genentech Inc. Department of Drug Metabolism and Pharmacokinetics, Genentech Inc., San Francisco, California (C.E.C.A.H.)
| | - Ðắc-Trung Nguyễn
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Rockville, Maryland (E.G., S.J., P.S., N.T.-K., A.Z., D.-T.N., S.S., R.H., M.X. A.S., X.X.); Discovery Technology Laboratories, Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Yokohama-shi, Japan (N.T.-K.); Pfizer Inc. Department of Pharmacokinetics, Dynamics and Metabolism, Pfizer, Groton, Connecticut (R.S.O.); and Genentech Inc. Department of Drug Metabolism and Pharmacokinetics, Genentech Inc., San Francisco, California (C.E.C.A.H.)
| | - Srilatha Sakamuru
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Rockville, Maryland (E.G., S.J., P.S., N.T.-K., A.Z., D.-T.N., S.S., R.H., M.X. A.S., X.X.); Discovery Technology Laboratories, Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Yokohama-shi, Japan (N.T.-K.); Pfizer Inc. Department of Pharmacokinetics, Dynamics and Metabolism, Pfizer, Groton, Connecticut (R.S.O.); and Genentech Inc. Department of Drug Metabolism and Pharmacokinetics, Genentech Inc., San Francisco, California (C.E.C.A.H.)
| | - Ruili Huang
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Rockville, Maryland (E.G., S.J., P.S., N.T.-K., A.Z., D.-T.N., S.S., R.H., M.X. A.S., X.X.); Discovery Technology Laboratories, Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Yokohama-shi, Japan (N.T.-K.); Pfizer Inc. Department of Pharmacokinetics, Dynamics and Metabolism, Pfizer, Groton, Connecticut (R.S.O.); and Genentech Inc. Department of Drug Metabolism and Pharmacokinetics, Genentech Inc., San Francisco, California (C.E.C.A.H.)
| | - Menghang Xia
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Rockville, Maryland (E.G., S.J., P.S., N.T.-K., A.Z., D.-T.N., S.S., R.H., M.X. A.S., X.X.); Discovery Technology Laboratories, Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Yokohama-shi, Japan (N.T.-K.); Pfizer Inc. Department of Pharmacokinetics, Dynamics and Metabolism, Pfizer, Groton, Connecticut (R.S.O.); and Genentech Inc. Department of Drug Metabolism and Pharmacokinetics, Genentech Inc., San Francisco, California (C.E.C.A.H.)
| | - R Scott Obach
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Rockville, Maryland (E.G., S.J., P.S., N.T.-K., A.Z., D.-T.N., S.S., R.H., M.X. A.S., X.X.); Discovery Technology Laboratories, Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Yokohama-shi, Japan (N.T.-K.); Pfizer Inc. Department of Pharmacokinetics, Dynamics and Metabolism, Pfizer, Groton, Connecticut (R.S.O.); and Genentech Inc. Department of Drug Metabolism and Pharmacokinetics, Genentech Inc., San Francisco, California (C.E.C.A.H.)
| | - Cornelis E C A Hop
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Rockville, Maryland (E.G., S.J., P.S., N.T.-K., A.Z., D.-T.N., S.S., R.H., M.X. A.S., X.X.); Discovery Technology Laboratories, Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Yokohama-shi, Japan (N.T.-K.); Pfizer Inc. Department of Pharmacokinetics, Dynamics and Metabolism, Pfizer, Groton, Connecticut (R.S.O.); and Genentech Inc. Department of Drug Metabolism and Pharmacokinetics, Genentech Inc., San Francisco, California (C.E.C.A.H.)
| | - Anton Simeonov
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Rockville, Maryland (E.G., S.J., P.S., N.T.-K., A.Z., D.-T.N., S.S., R.H., M.X. A.S., X.X.); Discovery Technology Laboratories, Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Yokohama-shi, Japan (N.T.-K.); Pfizer Inc. Department of Pharmacokinetics, Dynamics and Metabolism, Pfizer, Groton, Connecticut (R.S.O.); and Genentech Inc. Department of Drug Metabolism and Pharmacokinetics, Genentech Inc., San Francisco, California (C.E.C.A.H.)
| | - Xin Xu
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Rockville, Maryland (E.G., S.J., P.S., N.T.-K., A.Z., D.-T.N., S.S., R.H., M.X. A.S., X.X.); Discovery Technology Laboratories, Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Yokohama-shi, Japan (N.T.-K.); Pfizer Inc. Department of Pharmacokinetics, Dynamics and Metabolism, Pfizer, Groton, Connecticut (R.S.O.); and Genentech Inc. Department of Drug Metabolism and Pharmacokinetics, Genentech Inc., San Francisco, California (C.E.C.A.H.)
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Wei Y, Zhong Y, Wang Y, Huang R. Association between periodontal disease and prostate cancer: a systematic review and meta-analysis. Med Oral Patol Oral Cir Bucal 2021; 26:e459-e465. [PMID: 33247563 PMCID: PMC8254894 DOI: 10.4317/medoral.24308] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 11/16/2020] [Indexed: 02/05/2023] Open
Abstract
Background Periodontal disease is a chronic infectious disease caused by bacterial infection which may lead to various systematic diseases. Recently, increasing studies have explored the correlation of periodontal disease with the risk of prostate cancer. However, the findings were inconsistent. Hence, this study aims to investigate the association between periodontal disease and the risk of prostate cancer by a meta-analysis.
Material and Methods PubMed, EMBASE, and Cochrane were searched for publications up to July 17, 2020. Cohort and case-control studies evaluating the risk of prostate cancer in patients with periodontal disease were included. A fixed or random-effect model was used to calculate the summary relative risk (RR) along with 95% confidence interval (CI). All analyses were conducted using Stata 12.0 software.
Results Seven studies were included in the final analysis. The pooled estimates showed that periodontal disease was significantly associated with the risk of prostate cancer (RR = 1.17; 95% CI = 1.07-1.27; P = 0.001). Findings of sensitivity analyses proved that the overall results were robust.
Conclusions Periodontal disease may be considered as a potential risk factor for prostate cancer. Although it’s a possibility, males should be more aware of their oral health and implement effective measures to prevent and treat periodontal disease. Key words:Periodontal disease, periodontitis, prostate cancer, meta-analysis
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Affiliation(s)
- Y Wei
- State Key Laboratory of Oral Diseases National Clinical Research Center for Oral Diseases Dept. of Pediatric Dentistry, West China Hospital of Stomatology Sichuan University, Chengdu, P. R. China
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Liu Z, Roberts RA, Lal-Nag M, Chen X, Huang R, Tong W. AI-based language models powering drug discovery and development. Drug Discov Today 2021; 26:2593-2607. [PMID: 34216835 PMCID: PMC8604259 DOI: 10.1016/j.drudis.2021.06.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 04/28/2021] [Accepted: 06/25/2021] [Indexed: 02/08/2023]
Abstract
The discovery and development of new medicines is expensive, time-consuming, and often inefficient, with many failures along the way. Powered by artificial intelligence (AI), language models (LMs) have changed the landscape of natural language processing (NLP), offering possibilities to transform treatment development more effectively. Here, we summarize advances in AI-powered LMs and their potential to aid drug discovery and development. We highlight opportunities for AI-powered LMs in target identification, clinical design, regulatory decision-making, and pharmacovigilance. We specifically emphasize the potential role of AI-powered LMs for developing new treatments for Coronavirus 2019 (COVID-19) strategies, including drug repurposing, which can be extrapolated to other infectious diseases that have the potential to cause pandemics. Finally, we set out the remaining challenges and propose possible solutions for improvement.
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Affiliation(s)
- Zhichao Liu
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA.
| | - Ruth A Roberts
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA; ApconiX, BioHub at Alderley Park, Alderley Edge SK10 4TG, UK; University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Madhu Lal-Nag
- Office of Translational Sciences, Center for Drug Evaluation and Research, US FDA, Silver Spring, MD 20993, USA
| | - Xi Chen
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
| | - Weida Tong
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA.
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Burns AP, Zhang YQ, Xu T, Wei Z, Yao Q, Fang Y, Cebotaru V, Xia M, Hall MD, Huang R, Simeonov A, LeClair CA, Tao D. A Universal and High-Throughput Proteomics Sample Preparation Platform. Anal Chem 2021; 93:8423-8431. [PMID: 34110797 PMCID: PMC9876622 DOI: 10.1021/acs.analchem.1c00265] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Major advances have been made to improve the sensitivity of mass analyzers, spectral quality, and speed of data processing enabling more comprehensive proteome discovery and quantitation. While focus has recently begun shifting toward robust proteomics sample preparation efforts, a high-throughput proteomics sample preparation is still lacking. We report the development of a highly automated universal 384-well plate sample preparation platform with high reproducibility and adaptability for extraction of proteins from cells within a culture plate. Digestion efficiency was excellent in comparison to a commercial digest peptide standard with minimal sample loss while improving sample preparation throughput by 20- to 40-fold (the entire process from plated cells to clean peptides is complete in ∼300 min). Analysis of six human cell types, including two primary cell samples, identified and quantified ∼4,000 proteins for each sample in a single high-performance liquid chromatography (HPLC)-tandem mass spectrometry injection with only 100-10K cells, thus demonstrating universality of the platform. The selected protein was further quantified using a developed HPLC-multiple reaction monitoring method for HeLa digests with two heavy labeled internal standard peptides spiked in. Excellent linearity was achieved across different cell numbers indicating a potential for target protein quantitation in clinical research.
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Affiliation(s)
- Andrew P. Burns
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Ya-Qin Zhang
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Tuan Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Zhengxi Wei
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Qin Yao
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | - Yuhong Fang
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Valeriu Cebotaru
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Matthew D. Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Christopher A. LeClair
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States.,Corresponding authors: Dr. Christopher A. LeClair, and Dr. Dingyin Tao,
| | - Dingyin Tao
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States.,Corresponding authors: Dr. Christopher A. LeClair, and Dr. Dingyin Tao,
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Lin ZX, Zhang YH, Huang R, Li XY. [Effects and mechanisms of polycaprolactone-cellulose acetate nanofiber scaffold loaded with rat epidermal stem cells on wound healing of full-thickness skin defects in rats]. Zhonghua Shao Shang Za Zhi 2021; 37:460-468. [PMID: 33894697 DOI: 10.3760/cma.j.cn501120-20210104-00005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To explore the effects and mechanisms of polycaprolactone-cellulose acetate (PCL-CA) nanofiber scaffold loaded with rat epidermal stem cells (ESCs) on wound healing of full-thickness skin defects in rats. Methods: The experiment research method was applied. The primary ESCs were isolated from 1-3 d old Sprague-Dawley (SD) rats (undefined gender) by rapid adherent method and cultured by rapid adherent method. ESCs of the first passage were used for the subsequent experiments after the positive expressions of integrin β1 and cytokeratin 19 (CK19) in primary cells were identified respectively by flow cytometey and immunofluorescence method. PCL-CA nanofiber scaffolds with polycaprolactone and cellulose acetate as components were prepared by electrospinning technique. The topological structure of the nanofiber scaffolds was determined and the diameter of 25 fibers was measured by scanning electron microscope. The constructed PCL-CA nanofiber scaffolds were used as the culture substrate for ESCs, which were cultured in keratinocytes (KCs) medium to construct ESCs-nanofiber scaffold complex (hereinafter referred to as ESCs scaffold). After 3 days of culture, the morphology of ESCs in the scaffold and their relationship was observed by scanning electron microscopy. The ESCs in ESCs scaffold were set as PCL-CA nanofiber scaffold group, and the ESCs cultured with KCs medium in culture dishes coated with type Ⅳ collagen were set as type Ⅳ collagen group. Western blotting was used to detect the protein expression level of CK19 in ESCs in the two groups after 3 days of culture (n=3). The protein expressions of CK19 and proliferating nuclear antigen (PCNA) in ESCs in the two groups were detected by immunofluorescence method after 7 days of culture. A circular full-thickness skin wound of about 2 cm in diameter was prepared on both left and right sides of the back of 15 male SD rats aged 6-8 weeks. The rats were then equally divided into blank control group without implantation, scaffold alone group implanted with PCL-CA nanofiber scaffold, and ESCs scaffold group implanted with ESCs scaffold which were constructed after 3 days of culture according to the random number table. The percentage of wound areas on post injury day (PID) 3, 7, 14, and 21 was calculated (n=5). The new skin tissue at the wound edge was collected on PID 21, the wound healing quality was evaluated by Masson staining, and the protein expression levels of Notch1, Jagged1, and Hes1, which are key proteins of Notch signaling pathway, were detected by Western blotting (n=3). Data were statistically analyzed with one-way analysis of variance, one-way analysis of variance, analysis of variance for repeated measurement, independent sample t test, and Bonferroni correction. Results: The constructed PCL-CA nanofiber scaffolds had a porous, mesh-like, and multilayered three-dimensional structure, in which the surface of the fibers was smooth and non-porous, and the fiber diameter was (383±24) nm. The ESCs in ESCs scaffold showed intact cellular structures and were tightly attached to the scaffold after 3 days of culture. The cells were interconnected and fully extended on the surface of the scaffold to form a membrane. After 3 days of culture, the protein expression level of CK19 of ESCs in PCL-CA nanofiber scaffold group was significantly higher than that in type Ⅳ collagen group (t=24.56, P<0.01). After 7 days of culture, compared with those in type Ⅳ collagen group, there was no significant change in the proportion of PCNA positive cells of ESCs in PCL-CA nanofiber scaffold group, while the proportion of CK19 positive cells was higher. On PID 3, 7, 14, and 21, the percentages of wound areas of rats in ESCs scaffold group were (78.0±1.8)%, (40.9±2.0)%, (17.9±1.1)%, and (5.0±1.0)%, respectively, which were significantly lower than (84.2±1.9)%, (45.4±2.6)%, (21.8±1.7)%, and (10.1±1.1)% in blank control group (t=5.42, 3.09, 4.33, 7.58, P<0.05 or P<0.01) and (82.7±1.2)%, (44.8±2.0)%, (22.4±2.4)%, and (10.3±2.4)% in scaffold alone group (t=4.98, 3.11, 3.84, 4.57, P<0.05 or P<0.01), while the percentages of wound areas of rats between blank control group and scaffold alone group were similar (t=1.47, 0.39, 0.47, 0.22, P>0.05). On PID 21, the layer of new skin at the wound edge of rats in each group was intact; compared with that in blank control group or scaffold alone group, the new skin tissue at the wound edge of rats in ESCs scaffold group had more orderly collagen arrangement; the scaffolds in the new skin at the wound edge of rats were completely degraded in ESCs scaffold group and scaffold alone group. On PID 21, the protein expression levels of Notch1, Jagged1, and Hes1 in the new skin tissue at the wound edge of rats in scaffold alone group were similar to those in blank control group (t=1.70, 1.94, 0.18, P>0.05), while the protein expression levels of Notch1, Jagged1, and Hes1 in the new skin tissue at the wound edge of rats in ESCs scaffold group were significantly higher than those in scaffold alone group (t=13.31, 22.07, 20.71, P<0.01). Conclusions: PCL-CA nanofiber scaffolds can inhibit the differentiation of ESCs of rats without affecting their proliferation in vitro. ESCs scaffolds constructed through using PCL-CA nanofiber scaffolds as the carrier to culture ESCs of rats can significantly promote the wound healing of full-thickness skin defects in rats, and the mechanism may be related to the activation of Notch signaling pathway.
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Affiliation(s)
- Z X Lin
- Department of Burns and Plastic Surgery, the Second Affiliated Hospital of Air Force Medical University, Xi'an 710038, China
| | - Y H Zhang
- Department of Burns and Plastic Surgery, the Second Affiliated Hospital of Air Force Medical University, Xi'an 710038, China
| | - R Huang
- Department of Burns and Plastic Surgery, the Second Affiliated Hospital of Air Force Medical University, Xi'an 710038, China
| | - X Y Li
- Department of Burns and Plastic Surgery, the Second Affiliated Hospital of Air Force Medical University, Xi'an 710038, China
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Xu T, Cui Z, Wang J, Feng Y, Xie R, Li D, Peng J, Huang R, Li T. [Aryl hydrocarbon receptor modulates airway inflammation in mice with cockroach allergen-induced asthma by regulating Th17/Treg differentiation]. Nan Fang Yi Ke Da Xue Xue Bao 2021; 41:716-721. [PMID: 34134959 DOI: 10.12122/j.issn.1673-4254.2021.05.12] [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] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To investigate whether aryl hydrocarbon receptor (AhR) modulates cockroach allergen (CRE)-induced asthma by regulating Th17/Treg differentiation. OBJECTIVE Mouse models of CRE-induced asthma established by sensitizing and challenging the mice with CRE were randomized into asthma model group, AhR agonist group treated with TCDD (10 μg/ kg), and AhR antagonist group treated with TCDD and CH223191 (10 mg/kg) (n=5), with 5 mice without CRE challenge as the control group. The expressions of AhR, Cyp1a1 and Cyp1b1 mRNA in the lung tissues of the mice were detected using RT-PCR, and pulmonary inflammation was evaluated with immumohistochemical staining. The expressions of inflammatory cytokines in the lungs were detected using ELISA, and the expression of Treg in the lung tissues and pulmonary lymph nodes was analyzed with flow cytometry. OBJECTIVE Both TCDD and CH223191 were capable of modulating pulmonary expressions of AhR and its downstream genes Cyp1a1 and Cyp1b1 in asthmatic mice (P < 0.002). TCDD treatment significantly decreased inflammatory cells and mucus production in the lungs of asthmatic mice, and BALFs from TCDD-treated mice with CRE challenge contained lowered levels of the proinflammatory factors including IL-4, IL-13 and IL-17A (P < 0.001) but increased anti-inflammatory factors including IL-10, IL-22 and TGF-β1 (P < 0.001). All these changes were significantly reversed by treatment with CH223191 to the levels comparable with those in the asthma model group (P>0.05). More importantly, TCDD treatment significantly increased the number of Tregs cells and FOXP3 expression and lowered RORγt mRNA expression in the lungs and pulmonary lymph nodes in asthmatic mice (P < 0.001); inhibition of AhR with CH223191, as compared with TCDD, significantly decreased the expression of CD4+CD25+Foxp3+Treg cells in the lungs and pulmonary lymph nodes and the expression of FOXP3 mRNA in lymphocytes and increased RORγt mRNA expression (P < 0.001) to the levels comparable with those in asthma model group (P>0.05). OBJECTIVE AhR activation modulates airway inflammation in mice with CRE-induced asthma by modulating the differentiation of Th17/Treg.
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Affiliation(s)
- T Xu
- Sleep Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Z Cui
- Department of Orthopedics and Traumatology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - J Wang
- Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510260, China
| | - Y Feng
- Sleep Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - R Xie
- Sleep Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - D Li
- Sleep Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - J Peng
- Sleep Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - R Huang
- Sleep Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - T Li
- Sleep Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
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Necchi A, Grivas P, Spiess P, Jacob J, Schrock A, Madison R, Pavlick D, Sokol E, Danziger N, Ramkissoon S, Severson E, Huang R, Lin D, Mata D, Decker B, Gjoerup O, Mcgregor K, Venstrom J, Alexander B, Ross J, Bratslavsky G. Methylthioadenosine Phosphorylase (MTAP) deletion is more common in Sarcomatoid (srcRCC) than in clear cell Renal Cell Carcinoma (ccRCC). Eur Urol 2021. [DOI: 10.1016/s0302-2838(21)01008-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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90
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Necchi A, Spiess P, Mata D, Bratslavsky G, Jacob J, Gjoerup O, Martini A, Danziger N, Lin D, Decker B, Sokol E, Huang R, Ross J. Clinically advanced pelvic Squamous Cell Carcinomas (pSCC) in men and women: A Comprehensive Genomic Profiling (CGP) study. Eur Urol 2021. [DOI: 10.1016/s0302-2838(21)01054-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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91
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Sakamuru S, Zhao J, Xia M, Hong H, Simeonov A, Vaisman I, Huang R. Predictive Models to Identify Small Molecule Activators and Inhibitors of Opioid Receptors. J Chem Inf Model 2021; 61:2675-2685. [PMID: 34047186 DOI: 10.1021/acs.jcim.1c00439] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Opioid receptors (OPRs) are the main targets for the treatment of pain and related disorders. The opiate compounds that activate these receptors are effective analgesics but their use leads to adverse effects, and they often are highly addictive drugs of abuse. There is an urgent need for alternative chemicals that are analgesics and to reduce/avoid the unwanted effects in order to relieve the public health crisis of opioid addiction. Here, we aim to develop computational models to predict the OPR activity of small molecule compounds based on chemical structures and apply these models to identify novel OPR active compounds. We used four different machine learning algorithms to build models based on quantitative high throughput screening (qHTS) data sets of three OPRs in both agonist and antagonist modes. The best performing models were applied to virtually screen a large collection of compounds. The model predicted active compounds were experimentally validated using the same qHTS assays that generated the training data. Random forest was the best classifier with the highest performance metrics, and the mu OPR (OPRM)-agonist model achieved the best performance measured by AUC-ROC (0.88) and MCC (0.7) values. The model predicted actives resulted in hit rates ranging from 2.3% (delta OPR-agonist) to 15.8% (OPRM-agonist) after experimental confirmation. Compared to the original assay hit rate, all models enriched the hit rate by ≥2-fold. Our approach produced robust OPR prediction models that can be applied to prioritize compounds from large libraries for further experimental validation. The models identified several novel potent compounds as activators/inhibitors of OPRs that were confirmed experimentally. The potent hits were further investigated using molecular docking to find the interactions of the novel ligands in the active site of the corresponding OPR.
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Affiliation(s)
- Srilatha Sakamuru
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States.,Bioinformatics and Computational Biology, School of Systems Biology, College of Science, George Mason University, Manassas, Virginia 20110, United States
| | - Jinghua Zhao
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Menghang Xia
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA), Jefferson, Arkansas 72079, United States
| | - Anton Simeonov
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
| | - Iosif Vaisman
- Bioinformatics and Computational Biology, School of Systems Biology, College of Science, George Mason University, Manassas, Virginia 20110, United States
| | - Ruili Huang
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, United States
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Vejzagić N, Prodjinotho UF, El-Khafif N, Huang R, Simeonov A, Spangenberg T, Prazeres da Costa C. Identification of hit compounds with anti-schistosomal activity on in vitro generated juvenile worms in cell-free medium. PLoS Negl Trop Dis 2021; 15:e0009432. [PMID: 34033658 PMCID: PMC8191877 DOI: 10.1371/journal.pntd.0009432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 06/10/2021] [Accepted: 05/01/2021] [Indexed: 11/30/2022] Open
Abstract
Background Anthelminthic treatment options against schistosomiasis are limited. The current treatment relies almost exclusively on a single drug, praziquantel (PZQ). As a consequence, the development of resistance to PZQ and limited activity of PZQ against earlier development stages are respectively a risk and a limitation to achieving the goals of the new WHO roadmap towards elimination. For the discovery of new chemical starting points, the in vitro drug screening on Schistosoma mansoni (S. mansoni) against newly transformed schistosomula (NTS) is still the most predominant approach. The use of only NTS in the initial screening limits sensitivity to potential new compounds which are predominantly active in later developmental stages. Using our recently described highly standardized, straightforward and reliable culture method that generates high rates of juvenile worms, we aimed to repurpose a subset of the National Center for Advancing Translational Sciences (NCATS) Pharmaceutical Collection (340 compounds) to identify new hits with an in vitro worm culture assay. Methodology/Principal findings Cercariae were mechanically transformed into skin-stage (SkS) schistosomula and continuously cultured for 3–6 weeks to the liver stage (LiS). A commercial source of serum was identified, and decrease of NTS/well along with optimal drug testing conditions was established to test compounds on early and late LiS worms. The library was screened in 96-well format assays using praziquantel (PZQ) as a positive control. Primary screening allowed a 5.9% hit rate and generated two confirmed hits on adult worms; a prophylactic antianginal agent and an antihistaminic drug. Conclusion With this standardized and reliable in vitro assay, important S. mansoni developmental stages up to LiS worms can be generated and cultured over an extended period. When exposed to a subset of the NCATS Pharmaceutical Collection, 3 compounds yielded a defined anti-schistosomal phenotype on juvenile worms. Translation of activity on perfused adult S. mansoni worms was achieved only for perhexiline (a prophylactic antianginal agent) and astemizole (an antihistaminic drug). Schistosomiasis continues to be a major public health problem, mainly in developing countries. Although there have been some advances in finding new drugs, praziquantel is still the drug of choice. Certainly, one of the most important advances in the search for new treatments was the ability to in vitro transform cercariae and to grow schistosomula in culture. To reduce animal use in future drug discovery efforts (3Rs), we optimized a previously established reliable and robust in vitro cell-free culture system for the generation of liver-stage worms that we applied to the screening of a compound library stemming from the National Center for Advancing Translational Sciences (NCATS) Pharmaceutical Collection.
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Affiliation(s)
- Nermina Vejzagić
- Institute for Microbiology, Immunology and Hygiene, Technische Universität München, Munich, Germany
- Center for Global Health, TUM School of Medicine, Technische Universität München, Munich, Germany
| | - Ulrich Fabien Prodjinotho
- Institute for Microbiology, Immunology and Hygiene, Technische Universität München, Munich, Germany
- Center for Global Health, TUM School of Medicine, Technische Universität München, Munich, Germany
| | - Nagwa El-Khafif
- Theodor Bilharz Research Institute, Mahad Al Abhas Al Bahari, Warraq Al Arab, El Warraq, Giza Governorate, Egypt
| | - Ruili Huang
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Anton Simeonov
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Thomas Spangenberg
- Global Health Institute of Merck, Ares Trading S.A. (a subsidiary of Merck KGaA Darmstadt Germany), Eysins, Switzerland
| | - Clarissa Prazeres da Costa
- Institute for Microbiology, Immunology and Hygiene, Technische Universität München, Munich, Germany
- Center for Global Health, TUM School of Medicine, Technische Universität München, Munich, Germany
- * E-mail:
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Guo JW, Huang R, Xiao Y. [Facial identification in the diagnosis of obstructive sleep apnea]. Zhonghua Jie He He Hu Xi Za Zhi 2021; 44:496-499. [PMID: 34865372 DOI: 10.3760/cma.j.cn112147-20200628-00755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
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Wang Y, Michael S, Huang R, Zhao J, Recabo K, Bougie D, Shu Q, Shinn P, Sun H. Retro Drug Design: From Target Properties to Molecular Structures. bioRxiv 2021. [PMID: 34013260 PMCID: PMC8132216 DOI: 10.1101/2021.05.11.442656] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
To generate drug molecules of desired properties with computational methods is the holy grail in pharmaceutical research. Here we describe an AI strategy, retro drug design, or RDD, to generate novel small molecule drugs from scratch to meet predefined requirements, including but not limited to biological activity against a drug target, and optimal range of physicochemical and ADMET properties. Traditional predictive models were first trained over experimental data for the target properties, using an atom typing based molecular descriptor system, ATP. Monte Carlo sampling algorithm was then utilized to find the solutions in the ATP space defined by the target properties, and the deep learning model of Seq2Seq was employed to decode molecular structures from the solutions. To test feasibility of the algorithm, we challenged RDD to generate novel drugs that can activate μ opioid receptor (MOR) and penetrate blood brain barrier (BBB). Starting from vectors of random numbers, RDD generated 180,000 chemical structures, of which 78% were chemically valid. About 42,000 (31%) of the valid structures fell into the property space defined by MOR activity and BBB permeability. Out of the 42,000 structures, only 267 chemicals were commercially available, indicating a high extent of novelty of the AI-generated compounds. We purchased and assayed 96 compounds, and 25 of which were found to be MOR agonists. These compounds also have excellent BBB scores. The results presented in this paper illustrate that RDD has potential to revolutionize the current drug discovery process and create novel structures with multiple desired properties, including biological functions and ADMET properties. Availability of an AI-enabled fast track in drug discovery is essential to cope with emergent public health threat, such as pandemic of COVID-19.
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Armengaud E, Augier C, Barabash AS, Bellini F, Benato G, Benoît A, Beretta M, Bergé L, Billard J, Borovlev YA, Bourgeois C, Brudanin VB, Camus P, Cardani L, Casali N, Cazes A, Chapellier M, Charlieux F, Chiesa D, de Combarieu M, Dafinei I, Danevich FA, De Jesus M, Dixon T, Dumoulin L, Eitel K, Ferri F, Fujikawa BK, Gascon J, Gironi L, Giuliani A, Grigorieva VD, Gros M, Guerard E, Helis DL, Huang HZ, Huang R, Johnston J, Juillard A, Khalife H, Kleifges M, Kobychev VV, Kolomensky YG, Konovalov SI, Leder A, Loaiza P, Ma L, Makarov EP, de Marcillac P, Mariam R, Marini L, Marnieros S, Misiak D, Navick XF, Nones C, Norman EB, Novati V, Olivieri E, Ouellet JL, Pagnanini L, Pari P, Pattavina L, Paul B, Pavan M, Peng H, Pessina G, Pirro S, Poda DV, Polischuk OG, Pozzi S, Previtali E, Redon T, Rojas A, Rozov S, Rusconi C, Sanglard V, Scarpaci JA, Schäffner K, Schmidt B, Shen Y, Shlegel VN, Siebenborn B, Singh V, Tomei C, Tretyak VI, Umatov VI, Vagneron L, Velázquez M, Welliver B, Winslow L, Xue M, Yakushev E, Zarytskyy M, Zolotarova AS. New Limit for Neutrinoless Double-Beta Decay of ^{100}Mo from the CUPID-Mo Experiment. Phys Rev Lett 2021; 126:181802. [PMID: 34018798 DOI: 10.1103/physrevlett.126.181802] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 02/02/2021] [Accepted: 04/05/2021] [Indexed: 06/12/2023]
Abstract
The CUPID-Mo experiment at the Laboratoire Souterrain de Modane (France) is a demonstrator for CUPID, the next-generation ton-scale bolometric 0νββ experiment. It consists of a 4.2 kg array of 20 enriched Li_{2}^{100}MoO_{4} scintillating bolometers to search for the lepton-number-violating process of 0νββ decay in ^{100}Mo. With more than one year of operation (^{100}Mo exposure of 1.17 kg×yr for physics data), no event in the region of interest and, hence, no evidence for 0νββ is observed. We report a new limit on the half-life of 0νββ decay in ^{100}Mo of T_{1/2}>1.5×10^{24} yr at 90% C.I. The limit corresponds to an effective Majorana neutrino mass ⟨m_{ββ}⟩<(0.31-0.54) eV, dependent on the nuclear matrix element in the light Majorana neutrino exchange interpretation.
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Affiliation(s)
- E Armengaud
- IRFU, CEA, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - C Augier
- Univ Lyon, Université Lyon 1, CNRS/IN2P3, IP2I-Lyon, F-69622 Villeurbanne, France
| | - A S Barabash
- National Research Centre Kurchatov Institute, Institute of Theoretical and Experimental Physics, 117218 Moscow, Russia
| | - F Bellini
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale Aldo Moro 2, I-00185 Rome, Italy
- INFN, Sezione di Roma, Piazzale Aldo Moro 2, I-00185 Rome, Italy
| | - G Benato
- INFN, Laboratori Nazionali del Gran Sasso, I-67100 Assergi (AQ), Italy
| | - A Benoît
- CNRS-Néel, 38042 Grenoble Cedex 9, France
| | - M Beretta
- University of California, Berkeley, California 94720, USA
| | - L Bergé
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - J Billard
- Univ Lyon, Université Lyon 1, CNRS/IN2P3, IP2I-Lyon, F-69622 Villeurbanne, France
| | - Yu A Borovlev
- Nikolaev Institute of Inorganic Chemistry, 630090 Novosibirsk, Russia
| | - Ch Bourgeois
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - V B Brudanin
- Laboratory of Nuclear Problems, JINR, 141980 Dubna, Moscow region, Russia
| | - P Camus
- CNRS-Néel, 38042 Grenoble Cedex 9, France
| | - L Cardani
- INFN, Sezione di Roma, Piazzale Aldo Moro 2, I-00185 Rome, Italy
| | - N Casali
- INFN, Sezione di Roma, Piazzale Aldo Moro 2, I-00185 Rome, Italy
| | - A Cazes
- Univ Lyon, Université Lyon 1, CNRS/IN2P3, IP2I-Lyon, F-69622 Villeurbanne, France
| | - M Chapellier
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - F Charlieux
- Univ Lyon, Université Lyon 1, CNRS/IN2P3, IP2I-Lyon, F-69622 Villeurbanne, France
| | - D Chiesa
- Dipartimento di Fisica, Università di Milano-Bicocca, I-20126 Milano, Italy
- INFN, Sezione di Milano-Bicocca, I-20126 Milano, Italy
| | - M de Combarieu
- IRAMIS, CEA, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - I Dafinei
- INFN, Sezione di Roma, Piazzale Aldo Moro 2, I-00185 Rome, Italy
| | - F A Danevich
- Institute for Nuclear Research of NASU, 03028 Kyiv, Ukraine
| | - M De Jesus
- Univ Lyon, Université Lyon 1, CNRS/IN2P3, IP2I-Lyon, F-69622 Villeurbanne, France
| | - T Dixon
- University of California, Berkeley, California 94720, USA
| | - L Dumoulin
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - K Eitel
- Karlsruhe Institute of Technology, Institute for Astroparticle Physics, 76021 Karlsruhe, Germany
| | - F Ferri
- IRFU, CEA, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - B K Fujikawa
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - J Gascon
- Univ Lyon, Université Lyon 1, CNRS/IN2P3, IP2I-Lyon, F-69622 Villeurbanne, France
| | - L Gironi
- Dipartimento di Fisica, Università di Milano-Bicocca, I-20126 Milano, Italy
- INFN, Sezione di Milano-Bicocca, I-20126 Milano, Italy
| | - A Giuliani
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - V D Grigorieva
- Nikolaev Institute of Inorganic Chemistry, 630090 Novosibirsk, Russia
| | - M Gros
- IRFU, CEA, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - E Guerard
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - D L Helis
- IRFU, CEA, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - H Z Huang
- Key Laboratory of Nuclear Physics and Ion-beam Application (MOE), Fudan University, Shanghai 200433, People's Republic of China
| | - R Huang
- University of California, Berkeley, California 94720, USA
| | - J Johnston
- Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - A Juillard
- Univ Lyon, Université Lyon 1, CNRS/IN2P3, IP2I-Lyon, F-69622 Villeurbanne, France
| | - H Khalife
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - M Kleifges
- Karlsruhe Institute of Technology, Institute for Data Processing and Electronics, 76021 Karlsruhe, Germany
| | - V V Kobychev
- Institute for Nuclear Research of NASU, 03028 Kyiv, Ukraine
| | - Yu G Kolomensky
- University of California, Berkeley, California 94720, USA
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - S I Konovalov
- National Research Centre Kurchatov Institute, Institute of Theoretical and Experimental Physics, 117218 Moscow, Russia
| | - A Leder
- Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - P Loaiza
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - L Ma
- Key Laboratory of Nuclear Physics and Ion-beam Application (MOE), Fudan University, Shanghai 200433, People's Republic of China
| | - E P Makarov
- Nikolaev Institute of Inorganic Chemistry, 630090 Novosibirsk, Russia
| | - P de Marcillac
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - R Mariam
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - L Marini
- INFN, Laboratori Nazionali del Gran Sasso, I-67100 Assergi (AQ), Italy
- University of California, Berkeley, California 94720, USA
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - S Marnieros
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - D Misiak
- Univ Lyon, Université Lyon 1, CNRS/IN2P3, IP2I-Lyon, F-69622 Villeurbanne, France
| | - X-F Navick
- IRFU, CEA, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - C Nones
- IRFU, CEA, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - E B Norman
- University of California, Berkeley, California 94720, USA
| | - V Novati
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - E Olivieri
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - J L Ouellet
- Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - L Pagnanini
- INFN, Laboratori Nazionali del Gran Sasso, I-67100 Assergi (AQ), Italy
- INFN, Gran Sasso Science Institute, I-67100 L'Aquila, Italy
| | - P Pari
- IRAMIS, CEA, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - L Pattavina
- INFN, Laboratori Nazionali del Gran Sasso, I-67100 Assergi (AQ), Italy
- Physik Department, Technische Universität München, Garching D-85748, Germany
| | - B Paul
- IRFU, CEA, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - M Pavan
- Dipartimento di Fisica, Università di Milano-Bicocca, I-20126 Milano, Italy
- INFN, Sezione di Milano-Bicocca, I-20126 Milano, Italy
| | - H Peng
- Department of Modern Physics, University of Science and Technology of China, Hefei 230027, People's Republic of China
| | - G Pessina
- INFN, Sezione di Milano-Bicocca, I-20126 Milano, Italy
| | - S Pirro
- INFN, Laboratori Nazionali del Gran Sasso, I-67100 Assergi (AQ), Italy
| | - D V Poda
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - O G Polischuk
- Institute for Nuclear Research of NASU, 03028 Kyiv, Ukraine
| | - S Pozzi
- INFN, Sezione di Milano-Bicocca, I-20126 Milano, Italy
| | - E Previtali
- Dipartimento di Fisica, Università di Milano-Bicocca, I-20126 Milano, Italy
- INFN, Sezione di Milano-Bicocca, I-20126 Milano, Italy
| | - Th Redon
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - A Rojas
- LSM, Laboratoire Souterrain de Modane, 73500 Modane, France
| | - S Rozov
- Laboratory of Nuclear Problems, JINR, 141980 Dubna, Moscow region, Russia
| | - C Rusconi
- Department of Physics and Astronomy, University of South Carolina, Columbia, South Carolina 29208, USA
| | - V Sanglard
- Univ Lyon, Université Lyon 1, CNRS/IN2P3, IP2I-Lyon, F-69622 Villeurbanne, France
| | - J A Scarpaci
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
| | - K Schäffner
- INFN, Laboratori Nazionali del Gran Sasso, I-67100 Assergi (AQ), Italy
| | - B Schmidt
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Y Shen
- Key Laboratory of Nuclear Physics and Ion-beam Application (MOE), Fudan University, Shanghai 200433, People's Republic of China
| | - V N Shlegel
- Nikolaev Institute of Inorganic Chemistry, 630090 Novosibirsk, Russia
| | - B Siebenborn
- Karlsruhe Institute of Technology, Institute for Astroparticle Physics, 76021 Karlsruhe, Germany
| | - V Singh
- University of California, Berkeley, California 94720, USA
| | - C Tomei
- INFN, Sezione di Roma, Piazzale Aldo Moro 2, I-00185 Rome, Italy
| | - V I Tretyak
- Institute for Nuclear Research of NASU, 03028 Kyiv, Ukraine
| | - V I Umatov
- National Research Centre Kurchatov Institute, Institute of Theoretical and Experimental Physics, 117218 Moscow, Russia
| | - L Vagneron
- Univ Lyon, Université Lyon 1, CNRS/IN2P3, IP2I-Lyon, F-69622 Villeurbanne, France
| | - M Velázquez
- Université Grenoble Alpes, CNRS, Grenoble INP, SIMAP, 38402 Saint Martin d'Héres, France
| | - B Welliver
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - L Winslow
- Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - M Xue
- Department of Modern Physics, University of Science and Technology of China, Hefei 230027, People's Republic of China
| | - E Yakushev
- Laboratory of Nuclear Problems, JINR, 141980 Dubna, Moscow region, Russia
| | - M Zarytskyy
- Institute for Nuclear Research of NASU, 03028 Kyiv, Ukraine
| | - A S Zolotarova
- Université Paris-Saclay, CNRS/IN2P3, IJCLab, 91405 Orsay, France
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96
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Liu Z, Chen X, Roberts R, Huang R, Mikailov M, Tong W. Unraveling Gene Fusions for Drug Repositioning in High-Risk Neuroblastoma. Front Pharmacol 2021; 12:608778. [PMID: 33967751 PMCID: PMC8105087 DOI: 10.3389/fphar.2021.608778] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 03/23/2021] [Indexed: 11/13/2022] Open
Abstract
High-risk neuroblastoma (NB) remains a significant therapeutic challenge facing current pediatric oncology patients. Structural variants such as gene fusions have shown an initial promise in enhancing mechanistic understanding of NB and improving survival rates. In this study, we performed a comprehensive in silico investigation on the translational ability of gene fusions for patient stratification and treatment development for high-risk NB patients. Specifically, three state-of-the-art gene fusion detection algorithms, including ChimeraScan, SOAPfuse, and TopHat-Fusion, were employed to identify the fusion transcripts in a RNA-seq data set of 498 neuroblastoma patients. Then, the 176 high-risk patients were further stratified into four different subgroups based on gene fusion profiles. Furthermore, Kaplan-Meier survival analysis was performed, and differentially expressed genes (DEGs) for the redefined high-risk group were extracted and functionally analyzed. Finally, repositioning candidates were enriched in each patient subgroup with drug transcriptomic profiles from the LINCS L1000 Connectivity Map. We found the number of identified gene fusions was increased from clinical the low-risk stage to the high-risk stage. Although the technical concordance of fusion detection algorithms was suboptimal, they have a similar biological relevance concerning perturbed pathways and regulated DEGs. The gene fusion profiles could be utilized to redefine high-risk patient subgroups with significant onset age of NB, which yielded the improved survival curves (Log-rank p value ≤ 0.05). Out of 48 enriched repositioning candidates, 45 (93.8%) have antitumor potency, and 24 (50%) were confirmed with either on-going clinical trials or literature reports. The gene fusion profiles have a discrimination power for redefining patient subgroups in high-risk NB and facilitate precision medicine-based drug repositioning implementation.
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Affiliation(s)
- Zhichao Liu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, United States
| | - Xi Chen
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, United States
| | - Ruth Roberts
- ApconiX, BioHub at Alderley Park, Alderley Edge, United Kingdom.,University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Mike Mikailov
- Office of Science and Engineering Labs, Center for Devices and Radiological Health, US Food and Drug Administration, Silver Spring, MD, United States
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, United States
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97
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Ni J, Fu C, Huang R, Li Z, Li S, Cao P, Zhong K, Ge M, Gao Y. Metabolic syndrome cannot mask the changes of faecal microbiota compositions caused by primary hepatocellular carcinoma. Lett Appl Microbiol 2021; 73:73-80. [PMID: 33768575 DOI: 10.1111/lam.13477] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/16/2021] [Accepted: 03/22/2021] [Indexed: 12/19/2022]
Abstract
Both hepatocellular carcinoma (HCC) and metabolic syndrome are closely associated with the composition of the gut microbiota (GM). Although it has been proposed that elements of the GM can be used as biomarkers for the early diagnosis of HCC, whether metabolic syndrome results in a misrepresentation of the results of the early diagnosis of HCC using GM remains unclear. We compared the differences in the faecal microbiota of 10 patients with primary HCC, six patients with type 2 diabetes mellitus (T2DM), seven patients with arterial hypertension, six patients with both HCC and T2DM, and 10 patients with both HCC and arterial hypertension, as well as 10 healthy subjects, using high-throughput sequencing of 16S rRNA gene amplicons. Our results revealed a significant difference in the GM between subjects with and without HCC. The 49 bacterial genera out of the 494 detected genera were significantly different between the groups. These results show that changes in the GM can be used to distinguish between subjects with and without HCC, and can resist interference of T2DM and arterial hypertension with the GM. The results of the present study provide an important basis for the clinical auxiliary diagnosis of HCC by detecting the GM.
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Affiliation(s)
- J Ni
- Research and Development Center, Guangdong Meilikang Bio-Sciences Ltd., Dongguan, China.,Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center of Artificial Organ and Tissue Engineering, Zhujiang Hospital of Southern Medical University, Guangzhou, China.,Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, Guangdong Medical University, Dongguan, China
| | - C Fu
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center of Artificial Organ and Tissue Engineering, Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - R Huang
- Department of Neonatal Surgery, Guangdong Women and Children Hospital, Guangzhou, China
| | - Z Li
- Research and Development Center, Guangdong Meilikang Bio-Sciences Ltd., Dongguan, China
| | - S Li
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center of Artificial Organ and Tissue Engineering, Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - P Cao
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center of Artificial Organ and Tissue Engineering, Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - K Zhong
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center of Artificial Organ and Tissue Engineering, Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - M Ge
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center of Artificial Organ and Tissue Engineering, Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - Y Gao
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center of Artificial Organ and Tissue Engineering, Zhujiang Hospital of Southern Medical University, Guangzhou, China.,State Key Laboratory of Organ Failure Research, Southern Medical University, Guangzhou, China
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98
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Li S, Zhao J, Huang R, Travers J, Klumpp-Thomas C, Yu W, MacKerell AD, Sakamuru S, Ooka M, Xue F, Sipes NS, Hsieh JH, Ryan K, Simeonov A, Santillo MF, Xia M. Profiling the Tox21 Chemical Collection for Acetylcholinesterase Inhibition. Environ Health Perspect 2021; 129:47008. [PMID: 33844597 PMCID: PMC8041433 DOI: 10.1289/ehp6993] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/01/2021] [Accepted: 03/09/2021] [Indexed: 05/26/2023]
Abstract
BACKGROUND Inhibition of acetylcholinesterase (AChE), a biomarker of organophosphorous and carbamate exposure in environmental and occupational human health, has been commonly used to identify potential safety liabilities. So far, many environmental chemicals, including drug candidates, food additives, and industrial chemicals, have not been thoroughly evaluated for their inhibitory effects on AChE activity. AChE inhibitors can have therapeutic applications (e.g., tacrine and donepezil) or neurotoxic consequences (e.g., insecticides and nerve agents). OBJECTIVES The objective of the current study was to identify environmental chemicals that inhibit AChE activity using in vitro and in silico models. METHODS To identify AChE inhibitors rapidly and efficiently, we have screened the Toxicology in the 21st Century (Tox21) 10K compound library in a quantitative high-throughput screening (qHTS) platform by using the homogenous cell-based AChE inhibition assay and enzyme-based AChE inhibition assays (with or without microsomes). AChE inhibitors identified from the primary screening were further tested in monolayer or spheroid formed by SH-SY5Y and neural stem cell models. The inhibition and binding modes of these identified compounds were studied with time-dependent enzyme-based AChE inhibition assay and molecular docking, respectively. RESULTS A group of known AChE inhibitors, such as donepezil, ambenonium dichloride, and tacrine hydrochloride, as well as many previously unreported AChE inhibitors, such as chelerythrine chloride and cilostazol, were identified in this study. Many of these compounds, such as pyrazophos, phosalone, and triazophos, needed metabolic activation. This study identified both reversible (e.g., donepezil and tacrine) and irreversible inhibitors (e.g., chlorpyrifos and bromophos-ethyl). Molecular docking analyses were performed to explain the relative inhibitory potency of selected compounds. CONCLUSIONS Our tiered qHTS approach allowed us to generate a robust and reliable data set to evaluate large sets of environmental compounds for their AChE inhibitory activity. https://doi.org/10.1289/EHP6993.
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Affiliation(s)
- Shuaizhang Li
- Division for Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Jinghua Zhao
- Division for Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Ruili Huang
- Division for Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Jameson Travers
- Division for Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Carleen Klumpp-Thomas
- Division for Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Wenbo Yu
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland, USA
| | | | - Srilatha Sakamuru
- Division for Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Masato Ooka
- Division for Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Fengtian Xue
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland, USA
| | - Nisha S. Sipes
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Jui-Hua Hsieh
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Kristen Ryan
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Anton Simeonov
- Division for Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Michael F. Santillo
- Division of Toxicology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Menghang Xia
- Division for Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
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99
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Zhu H, Chen CZ, Sakamuru S, Zhao J, Ngan DK, Simeonov A, Hall MD, Xia M, Zheng W, Huang R. Mining of high throughput screening database reveals AP-1 and autophagy pathways as potential targets for COVID-19 therapeutics. Sci Rep 2021; 11:6725. [PMID: 33762619 PMCID: PMC7990955 DOI: 10.1038/s41598-021-86110-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 03/10/2021] [Indexed: 02/07/2023] Open
Abstract
The recent global pandemic of the Coronavirus disease 2019 (COVID-19) caused by the new coronavirus SARS-CoV-2 presents an urgent need for the development of new therapeutic candidates. Many efforts have been devoted to screening existing drug libraries with the hope to repurpose approved drugs as potential treatments for COVID-19. However, the antiviral mechanisms of action of the drugs found active in these phenotypic screens remain largely unknown. In an effort to deconvolute the viral targets in pursuit of more effective anti-COVID-19 drug development, we mined our in-house database of approved drug screens against 994 assays and compared their activity profiles with the drug activity profile in a cytopathic effect (CPE) assay of SARS-CoV-2. We found that the autophagy and AP-1 signaling pathway activity profiles are significantly correlated with the anti-SARS-CoV-2 activity profile. In addition, a class of neurology/psychiatry drugs was found to be significantly enriched with anti-SARS-CoV-2 activity. Taken together, these results provide new insights into SARS-CoV-2 infection and potential targets for COVID-19 therapeutics, which can be further validated by in vivo animal studies and human clinical trials.
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Affiliation(s)
- Hu Zhu
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), DPI/NCATS, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Catherine Z Chen
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), DPI/NCATS, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Srilatha Sakamuru
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), DPI/NCATS, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Jinghua Zhao
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), DPI/NCATS, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Deborah K Ngan
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), DPI/NCATS, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Anton Simeonov
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), DPI/NCATS, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Mathew D Hall
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), DPI/NCATS, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Menghang Xia
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), DPI/NCATS, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Wei Zheng
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), DPI/NCATS, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Ruili Huang
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), DPI/NCATS, 9800 Medical Center Drive, Rockville, MD, 20850, USA.
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Shamim K, Xu M, Hu X, Lee EM, Lu X, Huang R, Shah P, Xu X, Chen CZ, Shen M, Guo H, Chen L, Itkin Z, Eastman RT, Shinn P, Klumpp-Thomas C, Michael S, Simeonov A, Lo DC, Ming GL, Song H, Tang H, Zheng W, Huang W. Application of niclosamide and analogs as small molecule inhibitors of Zika virus and SARS-CoV-2 infection. Bioorg Med Chem Lett 2021; 40:127906. [PMID: 33689873 PMCID: PMC7936759 DOI: 10.1016/j.bmcl.2021.127906] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/15/2021] [Accepted: 02/21/2021] [Indexed: 12/12/2022]
Abstract
Zika virus has emerged as a potential threat to human health globally. A previous drug repurposing screen identified the approved anthelminthic drug niclosamide as a small molecule inhibitor of Zika virus infection. However, as antihelminthic drugs are generally designed to have low absorption when dosed orally, the very limited bioavailability of niclosamide will likely hinder its potential direct repurposing as an antiviral medication. Here, we conducted SAR studies focusing on the anilide and salicylic acid regions of niclosamide to improve physicochemical properties such as microsomal metabolic stability, permeability and solubility. We found that the 5-bromo substitution in the salicylic acid region retains potency while providing better drug-like properties. Other modifications in the anilide region with 2′-OMe and 2′-H substitutions were also advantageous. We found that the 4′-NO2 substituent can be replaced with a 4′-CN or 4′-CF3 substituents. Together, these modifications provide a basis for optimizing the structure of niclosamide to improve systemic exposure for application of niclosamide analogs as drug lead candidates for treating Zika and other viral infections. Indeed, key analogs were also able to rescue cells from the cytopathic effect of SARS-CoV-2 infection, indicating relevance for therapeutic strategies targeting the COVID-19 pandemic.
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Affiliation(s)
- Khalida Shamim
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA.
| | - Miao Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Xin Hu
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Emily M Lee
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA; Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Xiao Lu
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Pranav Shah
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Xin Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Catherine Z Chen
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Min Shen
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Hui Guo
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Lu Chen
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Zina Itkin
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Richard T Eastman
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Paul Shinn
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Carleen Klumpp-Thomas
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Sam Michael
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Donald C Lo
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hengli Tang
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA
| | - Wenwei Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Bethesda, MD 20892-3370, USA.
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