1
|
Ma W, Hu N, Xu W, Zhao L, Tian C, Kamei KI. Ferroptosis inducers: A new frontier in cancer therapy. Bioorg Chem 2024; 146:107331. [PMID: 38579614 DOI: 10.1016/j.bioorg.2024.107331] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/31/2024] [Accepted: 04/02/2024] [Indexed: 04/07/2024]
Abstract
Ferroptosis represents a non-apoptotic form of programmed cell death characterized by iron-dependent lipid peroxidation. This cell death modality not only facilitates the direct elimination of cancer cells, but also enhances their susceptibility to other pharmacological anti-cancer agents. The burgeoning interest in ferroptosis has been driven by a growing body of evidence that underscores the efficiency and minimal toxicity of ferroptosis inducers. Traditional inducers, such as erastin and RSL3 have shown substantial promise in clinical applications due to their potent therapeutic effects. Their significant potential of these inducers has spurred the development of a variety of small molecule ferroptosis inducers. These novel inducers boast an enhanced structural variety, improved metabolic stability, the capability to initiate ferroptosis without triggering apoptosis, making them well-suited for in vivo use. Despite these advancements, challenges still remain, particularly concerning the drug delivery, tumor specificity, and circulation duration of these small molecules in vivo. Addressing these challenges, contemporary research has pivoted towards innovative delivery systems tailored for ferroptosis inducers to facilitate precise, targeted, and synegestic therapeutic delivery. This review scrutinizes the latest progress in small molecule ferroptosis inducers and nano drug delivery systems geared towards ferroptosis sensitization. Furthermore, it delineated the prospective therapeutic advantages and the existing hurdles in the development of ferroptosis inducers for malignant tumor treatment.
Collapse
Affiliation(s)
- Wenjing Ma
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Naiyuan Hu
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Wenqian Xu
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Linxi Zhao
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Chutong Tian
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China; Key Laboratory of Advanced Drug Delivery Systems of Zhejiang Province, Hangzhou 310058, China; Joint International Research Laboratory of Intelligent Drug Delivery Systems, Ministry of Education, Shenyang 110016, China.
| | - Ken-Ichiro Kamei
- Department of Pharmaceutics, Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China; Joint International Research Laboratory of Intelligent Drug Delivery Systems, Ministry of Education, Shenyang 110016, China; Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501, Japan; Program of Biology, Division of Science, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates; Program of Bioengineering, Division of Engineering, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates; Department of Biomedical Engineering, Tandon School of Engineering, New York University, MetroTech, Brooklyn, NY 11201, United States.
| |
Collapse
|
2
|
Li Y, Li B, Wang Q, Zhang X, Zhang Q, Zhou X, Shi R, Wu Y, Zhai W, Chen Z, Zhou X, Zhao W. Dual targeting of TIGIT and PD-1 with a novel small molecule for cancer immunotherapy. Biochem Pharmacol 2024; 223:116162. [PMID: 38527557 DOI: 10.1016/j.bcp.2024.116162] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 03/13/2024] [Accepted: 03/21/2024] [Indexed: 03/27/2024]
Abstract
Immune checkpoint inhibitors have unveiled promising clinical prospects in cancer treatment. Nonetheless, their effectiveness remains restricted, marked by consistently low response rates and affecting only a subset of patients. The co-blockade of TIGIT with PD-1 has exhibited substantial anti-tumor effects. Notably, there is a dearth of reports on small-molecule inhibitors concurrently targeting both TIGIT and PD-1. In this study, we employed Microscale Thermophoresis (MST) to screen our laboratory's existing repository of small molecules. Our findings illuminated Gln(TrT) 's affinity for both TIGIT and PD-1, affirming its potential to effectively inhibit TIGIT/PVR and PD-1/PD-L1 pathways. In vitro co-culture experiments substantiated Gln(TrT)'s proficiency in restoring Jurkat T-cell functionality by blocking both TIGIT/PVR and PD-1/PD-L1 interactions. In the MC38 murine tumor model, Gln(TrT) emerges as a pivotal modulator, promoting the intratumoral infiltration and functional competence of CD8+ T cells. Furthermore, whether used as a monotherapy or in conjunction with radiotherapy, Gln(TrT) substantially impedes MC38 tumor progression, significantly extending the survival of murine subjects.
Collapse
Affiliation(s)
- Yang Li
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Beibei Li
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Qingchao Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xiangrui Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Qiongqiong Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xiuman Zhou
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Ranran Shi
- Department of Basic Medical Sciences, Luohe Medical College, Luohe 462000, China
| | - Yahong Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; International Joint Laboratory for Protein and Peptide Drugs of Henan Province, Zhengzhou University, Zhengzhou 450001, China
| | - Wenjie Zhai
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; International Joint Laboratory for Protein and Peptide Drugs of Henan Province, Zhengzhou University, Zhengzhou 450001, China
| | - Zhenzhen Chen
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xiaowen Zhou
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China.
| | - Wenshan Zhao
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China.
| |
Collapse
|
3
|
Thomas C, Byer-Alcorace A, Wang T. Human Serum Albumin Immobilized On Magnetizable Beads: A Rapid Method for Compound HSA Binding Study. J Pharm Sci 2024; 113:1359-1367. [PMID: 38325737 DOI: 10.1016/j.xphs.2024.01.018] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/09/2024]
Abstract
Immobilized human serum albumin (HSA) was developed by coupling His-tagged HSA onto Ni2+-coupled magnetizable beads (HSA-beads), allowing the HSA to be easily removed from incubation components. The HSA-beads system provides a rapid and convenient method to study HSA compound binding. In this study, the HSA-beads system was characterized and evaluated as a tool for assessing compound HSA binding properties. The free fraction (fu) values of test compounds measured using HSA-beads were comparable to those determined by equilibrium dialysis (ED), which is commonly used to evaluate albumin binding in vitro. The equilibrium dissociation constant (Kd) values determined for a series of compounds using the HSA-beads method demonstrated good correlation with literature data. This good correlation also suggests that the binding of His-HSA to the beads does not impact the conformations of the two compound binding sites of HSA, as the range of compounds tested encompassed binding to both sites. Furthermore, the Kd values of representative compounds itraconazole and BIRT2584 that were difficult to assess using ED, due to significant cellulose membrane adsorption, were successfully determined. The HSA-beads provide several advantages over ED, such as simple preparation, short assay incubation duration, and the ability to quantify both free and HSA-bound species of the test compound, facilitated by the simple separation of HSA-beads from the solution phase using a magnetic field. These properties render the HSA-beads method suitable for high-throughput studies on compound HSA binding.
Collapse
Affiliation(s)
- Cody Thomas
- Department of Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Rd., Ridgefield, CT 06877, USA
| | - Alexander Byer-Alcorace
- Department of Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Rd., Ridgefield, CT 06877, USA
| | - Ting Wang
- Department of Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Rd., Ridgefield, CT 06877, USA.
| |
Collapse
|
4
|
Zhao T, Duan S, Li J, Zheng H, Liu C, Zhang H, Luo H, Xu Y. Mapping of repeat-associated non-AUG (RAN) translation knowledge: A bibliometric analysis. Heliyon 2024; 10:e29141. [PMID: 38628764 PMCID: PMC11019168 DOI: 10.1016/j.heliyon.2024.e29141] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/08/2024] [Accepted: 04/01/2024] [Indexed: 04/19/2024] Open
Abstract
Over 50 genetic human disorders are attributed to the irregular expansion of microsatellites. These expanded microsatellite sequences can experience bidirectional transcription, leading to new reading frames. Beyond the standard AUG initiation or adjacent start codons, they are translated into proteins characterized by disease-causing amino acid repeats through repeat-associated non-AUG translation. Despite its significance, there's a discernible gap in comprehensive and objective articles on RAN translation. This study endeavors to evaluate and delineate the contemporary landscape and progress of RAN translation research via a bibliometric analysis. We sourced literature on RAN translation from the Web of Science Core Collection. Utilizing two bibliometric analysis tools, CiteSpace and VOSviewer, we gauged individual impacts and interactions by examining annual publications, journals, co-cited journals, countries/regions, institutions, authors, and co-cited authors. Following this, we assessed the co-occurrence and bursts of keywords and co-cited references to pinpoint research hotspots and trending in RAN translation. Between 2011 and 2022, 1317 authors across 359 institutions from 34 countries/regions contributed to 250 publications on RAN translation, spread across 118 academic journals. This article presents a systematic, objective, and comprehensive analysis of the current literature on RAN translation. Our findings emphasize that mechanisms related to C9orf72 ALS/FTD are pivotal topics in the realm of RAN translation, with cellular stress and the utilization of small molecule marking the trending research areas.
Collapse
Affiliation(s)
- Taiqi Zhao
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, China
| | - Suying Duan
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, China
| | - Jiaqi Li
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, China
| | - Honglin Zheng
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, China
- The Academy of Medical Sciences of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, China
| | - Chenyang Liu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, China
| | - Hang Zhang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, China
| | - Haiyang Luo
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, Henan, China
| | - Yuming Xu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, Henan, China
| |
Collapse
|
5
|
Zhang J, Yu Q, Chen W. Advancements in Small Molecule Fluorescent Probes for Superoxide Anion Detection: A Review. J Fluoresc 2024:10.1007/s10895-024-03727-4. [PMID: 38656646 DOI: 10.1007/s10895-024-03727-4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 04/11/2024] [Indexed: 04/26/2024]
Abstract
Superoxide anion (O2•-), a significant reactive oxygen species (ROS) within biological systems, plays a widespread role in cellular function regulation and is closely linked to the onset and progression of numerous diseases. To unveil the pathological implications of O2•- in these diseases, the development of effective monitoring techniques within biological systems is imperative. Small molecule fluorescent probes have garnered considerable attention due to their advantages: simplicity in operation, heightened sensitivity, exceptional selectivity, and direct applicability in monitoring living cells, tissues, and animals. In the past few years, few reports have focused on small molecule fluorescence probes for the detection of O2•-. In this small review, we systematically summarize the design and application of O2•- responsive small molecule fluorescent probes. In addition, we present the limitations of the current detection of O2•- and suggest the construction of new fluorescent imaging probes to indicate O2•- in living cells and in vivo.
Collapse
Affiliation(s)
- Jiao Zhang
- School of Pharmacy and Bioengineering, Chongqing University of Technology, No. 69, Hongguang Avenue, Banan District, Chongqing, 400054, China
| | - Qinghua Yu
- Department of Pharmacy, Chongqing University Cancer Hospital, NO.181 Hanyu Road, Shapingba District, Chongqing, 400030, P. R. China
| | - Wanyi Chen
- Department of Pharmacy, Chongqing University Cancer Hospital, NO.181 Hanyu Road, Shapingba District, Chongqing, 400030, P. R. China.
| |
Collapse
|
6
|
Yang J, Yu YC, Wang ZX, Li QQ, Ding N, Leng XJ, Cai J, Zhang MY, Wang JJ, Zhou Y, Wei TH, Xue X, Dai WC, Sun SL, Yang Y, Li NG, Shi ZH. Research strategies of small molecules as chemotherapeutics to overcome multiple myeloma resistance. Eur J Med Chem 2024; 271:116435. [PMID: 38648728 DOI: 10.1016/j.ejmech.2024.116435] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/08/2024] [Accepted: 04/17/2024] [Indexed: 04/25/2024]
Abstract
Multiple myeloma (MM), a cancer of plasma cells, is the second most common hematological malignancy which is characterized by aberrant plasma cells infiltration in the bone marrow and complex heterogeneous cytogenetic abnormalities. Over the past two decades, novel treatment strategies such as proteasome inhibitors, immunomodulators, and monoclonal antibodies have significantly improved the relative survival rate of MM patients. However, the development of drug resistance results in the majority of MM patients suffering from relapse, limited treatment options and uncontrolled disease progression after relapse. There are urgent needs to develop and explore novel MM treatment strategies to overcome drug resistance and improve efficacy. Here, we review the recent small molecule therapeutic strategies for MM, and introduce potential new targets and corresponding modulators in detail. In addition, this paper also summarizes the progress of multi-target inhibitor therapy and protein degradation technology in the treatment of MM.
Collapse
Affiliation(s)
- Jin Yang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Yan-Cheng Yu
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Zi-Xuan Wang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Qing-Qing Li
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Ning Ding
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Xue-Jiao Leng
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Jiao Cai
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Meng-Yuan Zhang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Jing-Jing Wang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Yun Zhou
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Tian-Hua Wei
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Xin Xue
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Wei-Chen Dai
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China
| | - Shan-Liang Sun
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China.
| | - Ye Yang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China.
| | - Nian-Guang Li
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, Jiangsu, 210023, China.
| | - Zhi-Hao Shi
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu, 211198, China.
| |
Collapse
|
7
|
Coulson RL, Frattini V, Moyer CE, Hodges J, Walter P, Mourrain P, Zuo Y, Wang GX. Translational modulator ISRIB alleviates synaptic and behavioral phenotypes in Fragile X syndrome. iScience 2024; 27:109259. [PMID: 38510125 PMCID: PMC10951902 DOI: 10.1016/j.isci.2024.109259] [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: 02/01/2022] [Revised: 07/31/2023] [Accepted: 02/13/2024] [Indexed: 03/22/2024] Open
Abstract
Fragile X syndrome (FXS) is caused by the loss of fragile X messenger ribonucleoprotein (FMRP), a translational regulator that binds the transcripts of proteins involved in synaptic function and plasticity. Dysregulated protein synthesis is a central effect of FMRP loss, however, direct translational modulation has not been leveraged in the treatment of FXS. Thus, we examined the effect of the translational modulator integrated stress response inhibitor (ISRIB) in treating synaptic and behavioral symptoms of FXS. We show that FMRP loss dysregulates synaptic protein abundance, stabilizing dendritic spines through increased PSD-95 levels while preventing spine maturation through reduced glutamate receptor accumulation, thus leading to the formation of dense, immature dendritic spines, characteristic of FXS patients and Fmr1 knockout (KO) mice. ISRIB rescues these deficits and improves social recognition in Fmr1 KO mice. These findings highlight the therapeutic potential of targeting core translational mechanisms in FXS and neurodevelopmental disorders more broadly.
Collapse
Affiliation(s)
- Rochelle L. Coulson
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Valentina Frattini
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Caitlin E. Moyer
- National Institute on Drug Abuse, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jennifer Hodges
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Peter Walter
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA 94143, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Philippe Mourrain
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
- INSERM 1024, Ecole Normale Supérieure, Paris, France
| | - Yi Zuo
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Gordon X. Wang
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
- Wu Tsai Neuroscience Institute, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
8
|
Vik D, Pii D, Mudaliar C, Nørregaard-Madsen M, Kontijevskis A. Performance and robustness of small molecule retention time prediction with molecular graph neural networks in industrial drug discovery campaigns. Sci Rep 2024; 14:8733. [PMID: 38627535 PMCID: PMC11021461 DOI: 10.1038/s41598-024-59620-4] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 04/12/2024] [Indexed: 04/19/2024] Open
Abstract
This study explores how machine-learning can be used to predict chromatographic retention times (RT) for the analysis of small molecules, with the objective of identifying a machine-learning framework with the robustness required to support a chemical synthesis production platform. We used internally generated data from high-throughput parallel synthesis in context of pharmaceutical drug discovery projects. We tested machine-learning models from the following frameworks: XGBoost, ChemProp, and DeepChem, using a dataset of 7552 small molecules. Our findings show that two specific models, AttentiveFP and ChemProp, performed better than XGBoost and a regular neural network in predicting RT accurately. We also assessed how well these models performed over time and found that molecular graph neural networks consistently gave accurate predictions for new chemical series. In addition, when we applied ChemProp on the publicly available METLIN SMRT dataset, it performed impressively with an average error of 38.70 s. These results highlight the efficacy of molecular graph neural networks, especially ChemProp, in diverse RT prediction scenarios, thereby enhancing the efficiency of chromatographic analysis.
Collapse
Affiliation(s)
- Daniel Vik
- Amgen Research Copenhagen, Amgen Inc., 2100, Copenhagen, Denmark.
| | - David Pii
- Amgen Research Copenhagen, Amgen Inc., 2100, Copenhagen, Denmark
| | - Chirag Mudaliar
- Amgen Research Copenhagen, Amgen Inc., 2100, Copenhagen, Denmark
| | | | | |
Collapse
|
9
|
Chen H, Fang G, Ren Y, Zou W, Ying K, Yang Z, Chen Q. Super-resolution imaging for in situ monitoring sub-cellular micro-dynamics of small molecule drug. Acta Pharm Sin B 2024; 14:1864-1877. [PMID: 38572114 PMCID: PMC10985125 DOI: 10.1016/j.apsb.2023.11.022] [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: 07/21/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 04/05/2024] Open
Abstract
Small molecule drugs play a pivotal role in the arsenal of anticancer pharmacological agents. Nonetheless, their small size poses a challenge when directly visualizing their localization, distribution, mechanism of action (MOA), and target engagement at the subcellular level in real time. We propose a strategy for developing triple-functioning drug beacons that seamlessly integrate therapeutically relevant bioactivity, precise subcellular localization, and direct visualization capabilities within a single molecular entity. As a proof of concept, we have meticulously designed and constructed a boronic acid fluorescence drug beacon using coumarin-hemicyanine (CHB). Our CHB design includes three pivotal features: a boronic acid moiety that binds both adenosine triphosphate (ATP) and adenosine diphosphate (ADP), thus depleting their levels and disrupting the energy supply within mitochondria; a positively charged component that targets the drug beacon to mitochondria; and a sizeable conjugated luminophore that emits fluorescence, facilitating the application of structured illumination microscopy (SIM). Our study indicates the exceptional responsiveness of our proof-of-concept drug beacon to ADP and ATP, its efficacy in inhibiting tumor growth, and its ability to facilitate the tracking of ADP and ATP distribution around the mitochondrial cristae. Furthermore, our investigation reveals that the micro-dynamics of CHB induce mitochondrial dysfunction by causing damage to the mitochondrial cristae and mitochondrial DNA. Altogether, our findings highlight the potential of SIM in conjunction with visual drug design as a potent tool for monitoring the in situ MOA of small molecule anticancer compounds. This approach represents a crucial advancement in addressing a current challenge within the field of small molecule drug discovery and validation.
Collapse
Affiliation(s)
- Huimin Chen
- School of Pharmaceutical Sciences & Institute of Materia Medica, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250062, China
| | - Guiqian Fang
- School of Pharmaceutical Sciences & Institute of Materia Medica, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250062, China
| | - Youxiao Ren
- School of Pharmaceutical Sciences & Institute of Materia Medica, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250062, China
| | - Weiwei Zou
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Kang Ying
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Qixin Chen
- School of Pharmaceutical Sciences & Institute of Materia Medica, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250062, China
| |
Collapse
|
10
|
Pan Y, Fu Q, Li Y, Yang J, Cheng K. Discovery of an ellipticine derivative as TLR3 inhibitor against influenza A virus and SARS-CoV-2. Bioorg Med Chem Lett 2024; 101:129672. [PMID: 38387691 DOI: 10.1016/j.bmcl.2024.129672] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 02/24/2024]
Abstract
Influenza and COVID-19 continue to pose global threats to public health. Classic antiviral drugs have certain limitations, coupled with frequent viral mutations leading to many drugs being ineffective, the development of new antiviral drugs is urgent. Meanwhile, the invasion of influenza virus can cause an immune response, and an excessive immune response can generate a large number of inflammatory storms, leading to tissue damage. Toll-like receptor 3 (TLR3) recognizes virus dsRNA to ignite the innate immune response, and inhibit TLR3 can block the excess immune response and protect the host tissues. Taking TLR3 as the target, SMU-CX1 was obtained as the specific TLR3 inhibitor by high-throughput screening of 15,700 compounds with IC50 value of 0.11 µM. Its anti-influenza A virus activity with IC50 ranged from 0.14 to 0.33 µM against multiple subtypes of influenza A virus and also showed promising anti-SARS-CoV-2 activity with IC50 at 0.43 µM. Primary antiviral mechanism study indicated that SMU-CX1 significantly inhibited PB2 and NP protein of viruses, it can also inhibit inflammatory factors in host cells including IFN-β, IP-10 and CCL-5. In conclusion, this study demonstrates the potential of SMU-CX1 in inhibiting IAV and SARS-CoV-2 activity, thereby offering a novel approach for designing antiviral drugs against highly pathogenic viruses.
Collapse
Affiliation(s)
- Yue Pan
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism and Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Qiuyue Fu
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism and Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yinyan Li
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism and Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jie Yang
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism and Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Kui Cheng
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism and Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China.
| |
Collapse
|
11
|
Hu X, Li E, Zhou Y, You Q, Jiang Z. Casitas b cell lymphoma‑B (Cbl-b): A new therapeutic avenue for small-molecule immunotherapy. Bioorg Med Chem 2024; 102:117677. [PMID: 38457911 DOI: 10.1016/j.bmc.2024.117677] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/25/2024] [Accepted: 03/04/2024] [Indexed: 03/10/2024]
Abstract
Immunotherapy has revolutionized the area of cancer treatment. Although most immunotherapies now are antibodies targeting membrane checkpoint molecules, there is an increasing demand for small-molecule drugs that address intracellular pathways. The E3 ubiquitin ligase Casitas B cell lymphoma‑b (Cbl-b) has been regarded as a promising intracellular immunotherapy target. Cbl-b regulates the downstream proteins of multiple membrane receptors and co-receptors, restricting the activation of the innate and adaptive immune system. Recently, Cbl-b inhibitors have been reported with promising effects on immune surveillance activation and anti-tumor efficacy. Several molecules have entered phase Ⅰ clinical trials. In this review, the biological rationale of Cbl-b as a promising target for cancer immunotherapy and the latest research progress of Cbl-b are summarized, with special emphasis on the allosteric small-molecule inhibitors of Cbl-b.
Collapse
Affiliation(s)
- Xiuqi Hu
- State Key Laboratory of Natural Medicines, and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Erdong Li
- State Key Laboratory of Natural Medicines, and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yangguo Zhou
- State Key Laboratory of Natural Medicines, and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qidong You
- State Key Laboratory of Natural Medicines, and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
| | - Zhengyu Jiang
- State Key Laboratory of Natural Medicines, and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
| |
Collapse
|
12
|
Feigl B, Lewis SJG, Rawashdeh O. Targeting sleep and the circadian system as a novel treatment strategy for Parkinson's disease. J Neurol 2024; 271:1483-1491. [PMID: 37943299 PMCID: PMC10896880 DOI: 10.1007/s00415-023-12073-7] [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: 09/13/2023] [Revised: 10/12/2023] [Accepted: 10/18/2023] [Indexed: 11/10/2023]
Abstract
There is a growing appreciation of the wide range of sleep-wake disturbances that occur frequently in Parkinson's disease. These are known to be associated with a range of motor and non-motor symptoms and significantly impact not only on the quality of life of the patient, but also on their bed partner. The underlying causes for fragmented sleep and daytime somnolence are no doubt multifactorial but there is clear evidence for circadian disruption in Parkinson's disease. This appears to be occurring not only as a result of the neuropathological changes that occur across a distributed neural network, but even down to the cellular level. Such observations indicate that circadian changes may in fact be a driver of neurodegeneration, as well as a cause for some of the sleep-wake symptoms observed in Parkinson's disease. Thus, efforts are now required to evaluate approaches including the prescription of precision medicine to modulate photoreceptor activation ratios that reflect daylight inputs to the circadian pacemaker, the use of small molecules to target clock genes, the manipulation of orexin pathways that could help restore the circadian system, to offer novel symptomatic and novel disease modifying strategies.
Collapse
Affiliation(s)
- Beatrix Feigl
- Centre for Vision and Eye Research, Queensland University of Technology (QUT), Brisbane, QLD, 4059, Australia
- School of Biomedical Sciences, Queensland University of Technology (QUT), Brisbane, QLD, 4059, Australia
- Queensland Eye Institute, South Brisbane, QLD, 4101, Australia
| | - Simon J G Lewis
- Parkinson's Disease Research Clinic, Brain and Mind Centre, School of Medical Sciences, University of Sydney, Camperdown, NSW, 2006, Australia.
| | - Oliver Rawashdeh
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, QLD, 4072, Australia
| |
Collapse
|
13
|
Sirisereephap K, Tamura H, Lim JH, Surboyo MDC, Isono T, Hiyoshi T, Rosenkranz AL, Sato-Yamada Y, Domon H, Ikeda A, Hirose T, Sunazuka T, Yoshiba N, Okada H, Terao Y, Maeda T, Tabeta K, Chavakis T, Hajishengallis G, Maekawa T. A novel macrolide-Del-1 axis to regenerate bone in old age. iScience 2024; 27:108798. [PMID: 38261928 PMCID: PMC10797555 DOI: 10.1016/j.isci.2024.108798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/24/2023] [Accepted: 01/02/2024] [Indexed: 01/25/2024] Open
Abstract
Aging is associated with increased susceptibility to chronic inflammatory bone loss disorders, such as periodontitis, in large part due to the impaired regenerative potential of aging tissues. DEL-1 exerts osteogenic activity and promotes bone regeneration. However, DEL-1 expression declines with age. Here we show that systemically administered macrolide antibiotics and a non-antibiotic erythromycin derivative, EM-523, restore DEL-1 expression in 18-month-old ("aged") mice while promoting regeneration of bone lost due to naturally occurring age-related periodontitis. These compounds failed to induce bone regeneration in age-matched DEL-1-deficient mice. Consequently, these drugs promoted DEL-1-dependent functions, including alkaline phosphatase activity and osteogenic gene expression in the periodontal tissue while inhibiting osteoclastogenesis, leading to net bone growth. Macrolide-treated aged mice exhibited increased skeletal bone mass, suggesting that this treatment may be pertinent to systemic bone loss disorders. In conclusion, we identified a macrolide-DEL-1 axis that can regenerate bone lost due to aging-related disease.
Collapse
Affiliation(s)
- Kridtapat Sirisereephap
- Division of Periodontology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8514, Japan
- Center for Advanced Oral Science, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8514, Japan
- Faculty of Dentistry, Chulalongkorn University, Bangkok 10330, Thailand
| | - Hikaru Tamura
- Center for Advanced Oral Science, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8514, Japan
| | - Jong-Hyung Lim
- Department of Basic and Translational Sciences, Laboratory of Innate Immunity and Inflammation, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Meircurius Dwi Condro Surboyo
- Center for Advanced Oral Science, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8514, Japan
- Faculty of Dentistry, Universitas Airlangga, Surabaya 60132, Indonesia
| | - Toshihito Isono
- Division of Microbiology and Infectious Diseases, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8514, Japan
| | - Takumi Hiyoshi
- Center for Advanced Oral Science, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8514, Japan
| | - Andrea L. Rosenkranz
- Center for Advanced Oral Science, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8514, Japan
| | - Yurie Sato-Yamada
- Center for Advanced Oral Science, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8514, Japan
| | - Hisanori Domon
- Division of Microbiology and Infectious Diseases, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8514, Japan
| | - Akari Ikeda
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Tomoyasu Hirose
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Toshiaki Sunazuka
- Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
- Graduate School of Infection Control Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Nagako Yoshiba
- Division of Cariology, Operative Dentistry and Endodontics, Department of Oral Health Science, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8514, Japan
| | - Hiroyuki Okada
- Laboratory of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Yutaka Terao
- Division of Microbiology and Infectious Diseases, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8514, Japan
| | - Takeyasu Maeda
- Center for Advanced Oral Science, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8514, Japan
| | - Koichi Tabeta
- Division of Periodontology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8514, Japan
| | - Triantafyllos Chavakis
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - George Hajishengallis
- Department of Basic and Translational Sciences, Laboratory of Innate Immunity and Inflammation, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Tomoki Maekawa
- Center for Advanced Oral Science, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8514, Japan
| |
Collapse
|
14
|
Péter B, Szekacs I, Horvath R. Label-free biomolecular and cellular methods in small molecule epigallocatechin-gallate research. Heliyon 2024; 10:e25603. [PMID: 38371993 PMCID: PMC10873674 DOI: 10.1016/j.heliyon.2024.e25603] [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: 11/05/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/20/2024] Open
Abstract
Small molecule natural compounds are gaining popularity in biomedicine due to their easy access to wide structural diversity and their proven health benefits in several case studies. Affinity measurements of small molecules below 100 Da molecular weight in a label-free and automatized manner using small amounts of samples have now become a possibility and reviewed in the present work. We also highlight novel label-free setups with excellent time resolution, which is important for kinetic measurements of biomolecules and living cells. We summarize how molecular-scale affinity data can be obtained from the in-depth analysis of cellular kinetic signals. Unlike traditional measurements, label-free biosensors have made such measurements possible, even without the isolation of specific cellular receptors of interest. Throughout this review, we consider epigallocatechin gallate (EGCG) as an exemplary compound. EGCG, a catechin found in green tea, is a well-established anti-inflammatory and anti-cancer agent. It has undergone extensive examination in numerous studies, which typically rely on fluorescent-based methods to explore its effects on both healthy and tumor cells. The summarized research topics range from molecular interactions with proteins and biological films to the kinetics of cellular adhesion and movement on novel biomimetic interfaces in the presence of EGCG. While the direct impact of small molecules on living cells and biomolecules is relatively well investigated in the literature using traditional biological measurements, this review also highlights the indirect influence of these molecules on the cells by modifying their nano-environment. Moreover, we underscore the significance of novel high-throughput label-free techniques in small molecular measurements, facilitating the investigation of both molecular-scale interactions and cellular processes in one single experiment. This advancement opens the door to exploring more complex multicomponent models that were previously beyond the reach of traditional assays.
Collapse
Affiliation(s)
- Beatrix Péter
- Nanobiosensorics Laboratory, Institute of Technical Physics and Materials Science, HUN-REN Centre for Energy Research, Konkoly-Thege M. út 29-33., 1121 Budapest, Hungary
| | - Inna Szekacs
- Nanobiosensorics Laboratory, Institute of Technical Physics and Materials Science, HUN-REN Centre for Energy Research, Konkoly-Thege M. út 29-33., 1121 Budapest, Hungary
| | - Robert Horvath
- Nanobiosensorics Laboratory, Institute of Technical Physics and Materials Science, HUN-REN Centre for Energy Research, Konkoly-Thege M. út 29-33., 1121 Budapest, Hungary
| |
Collapse
|
15
|
Jha S, Kim JH, Kim M, Nguyen AH, Ali KH, Gupta SK, Park SY, Ha E, Seo YH. Design, synthesis, and biological evaluation of HDAC6 inhibitors targeting L1 loop and serine 531 residue. Eur J Med Chem 2024; 265:116057. [PMID: 38142511 DOI: 10.1016/j.ejmech.2023.116057] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 12/26/2023]
Abstract
Histone deacetylases (HDACs) are a group of enzymes that remove acetyl groups from histones, leading to the silencing of genes. Targeting specific isoforms of HDACs has emerged as a promising approach for cancer therapy, as it can overcome drawbacks associated with pan-HDAC inhibitors. HDAC6 is a unique HDAC isoform that deacetylates non-histone proteins and is primarily located in the cytoplasm. It also has two catalytic domains and a zinc-finger ubiquitin binding domain (Zf-UBD) unlike other HDACs. HDAC6 plays a critical role in various cellular processes, including cell motility, protein degradation, cell proliferation, and transcription. Hence, the deregulation of HDAC6 is associated with various malignancies. In this study, we report the design and synthesis of a series of HDAC6 inhibitors. We evaluated the synthesized compounds by HDAC enzyme assay and identified that compound 8g exhibited an IC50 value of 21 nM and 40-fold selective activity towards HDAC6. We also assessed the effect of compound 8g on various cell lines and determined its ability to increase protein acetylation levels by Western blotting. Furthermore, the increased acetylation of α-tubulin resulted in microtubule polymerization and changes in cell morphology. Our molecular docking study supported these findings by demonstrating that compound 8g binds well to the catalytic pocket via L1 loop of HDAC6 enzyme. Altogether, compound 8g represents a preferential HDAC6 inhibitor that could serve as a lead for the development of more potent and specific inhibitors.
Collapse
Affiliation(s)
- Sonam Jha
- College of Pharmacy, Keimyung University, Daegu, 704-701, South Korea
| | - Ji Hyun Kim
- College of Pharmacy, Keimyung University, Daegu, 704-701, South Korea
| | - Mikyung Kim
- Department of Biochemistry, School of Medicine, Keimyung University, Daegu, 704-701, South Korea
| | - Ai-Han Nguyen
- College of Pharmacy, Keimyung University, Daegu, 704-701, South Korea
| | - Khan Hashim Ali
- College of Pharmacy, Keimyung University, Daegu, 704-701, South Korea
| | - Sunil K Gupta
- College of Pharmacy, Keimyung University, Daegu, 704-701, South Korea
| | - Sun You Park
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (KMEDIhub), 41061, South Korea
| | - Eunyoung Ha
- Department of Biochemistry, School of Medicine, Keimyung University, Daegu, 704-701, South Korea.
| | - Young Ho Seo
- College of Pharmacy, Keimyung University, Daegu, 704-701, South Korea.
| |
Collapse
|
16
|
Xie T, Huang Q, Huang Q, Huang Y, Liu S, Zeng H, Liu J. Dysregulated lncRNAs regulate human umbilical cord mesenchymal stem cell differentiation into insulin-producing cells by forming a regulatory network with mRNAs. Stem Cell Res Ther 2024; 15:22. [PMID: 38273351 PMCID: PMC10809572 DOI: 10.1186/s13287-023-03572-5] [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: 11/18/2021] [Accepted: 11/16/2023] [Indexed: 01/27/2024] Open
Abstract
OBJECTIVE In recent years, cell therapy has emerged as a new research direction in the treatment of diabetes. However, the underlying molecular mechanisms of mesenchymal stem cell (MSC) differentiation necessary to form such treatment have not been clarified. METHODS In this study, human umbilical cord mesenchymal stem cells (HUC-MSCs) isolated from newborns were progressively induced into insulin-producing cells (IPCs) using small molecules. HUC-MSC (S0) and four induced stage (S1-S4) samples were prepared. We then performed transcriptome sequencing experiments to obtain the dynamic expression profiles of both mRNAs and long noncoding RNAs (lncRNAs). RESULTS We found that the number of differentially expressed lncRNAs and mRNAs trended downwards during differentiation. Gene Ontology (GO) analysis showed that the target genes of differentially expressed lncRNAs were associated with translation, cell adhesion, and cell connection. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the NF-KB signalling pathway, MAPK signalling pathway, HIPPO signalling pathway, PI3K-Akt signalling pathway, and p53 signalling pathway were enriched in these differentially expressed lncRNA-targeting genes. We also found that the coexpression of the lncRNA CTBP1-AS2 with PROX1 and the lncRNAs AC009014.3 and GS1-72M22.1 with JARID2 mRNA was related to the development of pancreatic beta cells. Moreover, the coexpression of the lncRNAs: XLOC_ 050969, LINC00883, XLOC_050981, XLOC_050925, MAP3K14- AS1, RP11-148K1.12, and CTD2020K17.3 with p53, regulated insulin secretion by pancreatic beta cells. CONCLUSION In this study, HUC-MSCs combined with small molecule compounds were successfully induced into IPCs. Differentially expressed lncRNAs may regulate the insulin secretion of pancreatic beta cells by regulating multiple signalling pathways. The lncRNAs AC009014.3, Gs1-72m21.1, and CTBP1-AS2 may be involved in the development of pancreatic beta cells, and the lncRNAs: XLOC_050969, LINC00883, XLOC_050981, XLOC_050925, MAP3K14-AS1, RP11-148K1.12, and CTD2020K17.3 may be involved in regulating the insulin secretion of pancreatic beta cells, thus providing a lncRNA catalogue for future research regarding the mechanism of the transdifferentiation of HUC-MSCs into IPCs. It also provides a new theoretical basis for the transplantation of insulin-producing cells into diabetic patients in the future.
Collapse
Affiliation(s)
- Tianqin Xie
- Department of Endocrinology Medicine, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang of Jiangxi, 330006, China
| | - Qiming Huang
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translation Medicine, Nanchang University, Nanchang of Jiangxi, China
| | - Qiulan Huang
- Department of Endocrinology Medicine, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang of Jiangxi, 330006, China
| | - Yanting Huang
- Department of Endocrinology Medicine, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang of Jiangxi, 330006, China
| | - Shuang Liu
- Department of Endocrinology Medicine, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang of Jiangxi, 330006, China
| | - Haixia Zeng
- Department of Endocrinology Medicine, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang of Jiangxi, 330006, China
| | - Jianping Liu
- Department of Endocrinology Medicine, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang of Jiangxi, 330006, China.
| |
Collapse
|
17
|
Shao Z, Xie J, Jiang J, Shen R, Gui Z, Li H, Wang X, Li W, Guo S, Liu Y, Zheng G. Research on topological effect of natural small molecule and high-performance antibacterial air filtration application by electrospinning. Sci Total Environ 2024; 909:168654. [PMID: 37979876 DOI: 10.1016/j.scitotenv.2023.168654] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/04/2023] [Accepted: 11/15/2023] [Indexed: 11/20/2023]
Abstract
The application of natural small molecule (NSM) in electrospun fibers is the key to achieving powerful functionality and sustainable development. However, the lack of understanding regarding the mechanism for loading NSM hinders the advancement of high-performance functional fibers. This work clarified the loading mechanism of NSM in polymer solution by comparing the different behaviors of curcumin (Cur), phloretin (PL), and tea polyphenols (TP) blended ethyl cellulose (EC) solutions. We found that TP may lead to the folding of polymer chains due to its strongest hydrogen bond, which in turn promoted the dispersion of TP along the polymer chain. Therefore, TP could achieve good electrospinnability at the highest loading capacity (16 times the Cur and 4 times the PL). Finally, chitosan was introduced into EC/TP to prepare tree-like nanofibers, achieving high-performance antibacterial air filtration. The filtration efficiency for 0.3 μm NaCl particles, pressure drop, and quality factor were 99.991 %, 85.5 Pa, and 0.1089 Pa-1, respectively. The bacteriostatic rates against Escherichia coli and Staphylococcus aureus were all 99.99 %. This work will promote the application of NSM and the developments of multifunctional electrospun fibers and high-performance air filters.
Collapse
Affiliation(s)
- Zungui Shao
- Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361102, China; Shenzhen Research Institute of Xiamen University, Shenzhen 518000, China
| | - Junjie Xie
- Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361102, China; Shenzhen Research Institute of Xiamen University, Shenzhen 518000, China
| | - Jiaxin Jiang
- School of Mechanical and Automotive Engineering, Xiamen University of Technology, Xiamen 361024, China
| | - Ruimin Shen
- Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361102, China; Shenzhen Research Institute of Xiamen University, Shenzhen 518000, China
| | - Zeqian Gui
- Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361102, China; Shenzhen Research Institute of Xiamen University, Shenzhen 518000, China
| | - Haonan Li
- Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361102, China; Shenzhen Research Institute of Xiamen University, Shenzhen 518000, China
| | - Xiang Wang
- School of Mechanical and Automotive Engineering, Xiamen University of Technology, Xiamen 361024, China
| | - Wenwang Li
- School of Mechanical and Automotive Engineering, Xiamen University of Technology, Xiamen 361024, China
| | - Shumin Guo
- School of Mathematical Sciences, Xiamen University, Xiamen 361102, China
| | - Yifang Liu
- Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361102, China; Shenzhen Research Institute of Xiamen University, Shenzhen 518000, China
| | - Gaofeng Zheng
- Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361102, China; Shenzhen Research Institute of Xiamen University, Shenzhen 518000, China.
| |
Collapse
|
18
|
Yenurkar D, Ruocco M, Pragya P, Liang L, Mukherjee S. Small molecule conjugation reduces macrophage uptake and increases in vivo blood circulation of polystyrene nanoparticles. Biomed Mater 2024. [PMID: 38215477 DOI: 10.1088/1748-605x/ad1df8] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2024]
Abstract
Nanomedicine often failed clinically to show therapeutic efficacy due to reduced particle circulation and enhanced capture by the reticuloendothelial system (RES), including the liver. Developing novel immunomodulatory surface coating can prevent macrophage capture and increase the particle circulation of the nanomedicine, resulting in higher therapeutic efficiency. Herein, we demonstrate the development of immunomodulatory small molecule (RZA15) with triazole functionality using copper-catalyzed click chemistry to conjugate onto spherical polystyrene nanoparticles using amide coupling reactions, achieving higher blood circulation and lesser macrophage uptake of the nanoconjugates. In this work, we evaluated the effectiveness of RZA15 coating for the enhanced circulation of polystyrene nanoparticles of 100 nm size, which is commonly utilized for various drug delivery applications, and compared with poly(ethylene)glycol (PEG) coatings. Several polystyrene nanoconjugate formulations were analyzed in vitro in normal and macrophage cells for cell viability and cellular uptake studies. In vitro studies demonstrated lesser macrophage uptake of the nanoconjugates following RZA15 coating. Finally, in vivo, blood-circulation, pharmacokinetics, and biodistribution studies were performed in the C57BL/6J mouse model that endorsed the substantial role of RZA15 in preventing liver and spleen capture and results in extended circulation. Coating immunomodulatory small molecules to nanoparticles can severely enhance the potential therapeutic effects of nanomedicine at lower doses.
Collapse
Affiliation(s)
- Devyani Yenurkar
- Biomedical Engineering, Indian Institute of Technology BHU Varanasi, School of Biomedical Engineering, Indian Institute of Technology (BHU), Varanasi 221005, UP, India, Varanasi, 221005, INDIA
| | - Maria Ruocco
- Department of Bioengineering, Rice University, Department of Bioengineering, Rice University, Houston, TX 77030, USA, Houston, 77005-1892, UNITED STATES
| | - Pragya Pragya
- Indian Institute of Technology BHU Varanasi, School of Biomedical Engineering, Indian Institute of Technology (BHU), Varanasi 221005, UP, India, Varanasi, Uttar Pradesh, 221005, INDIA
| | - Lily Liang
- Johns Hopkins University, Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA, Baltimore, Maryland, 21218-2625, UNITED STATES
| | - Sudip Mukherjee
- Department of Biomedical Engineering, Indian Institute of Technology BHU Varanasi, School of Biomedical Engineering, Indian Institute of Technology (BHU), Varanasi 221005, UP, India, Varanasi, Uttar Pradesh, 221005, INDIA
| |
Collapse
|
19
|
Guan YJ, Yu CQ, Li LP, You ZH, Wei MM, Wang XF, Yang C, Guo LX. MHESMMR: a multilevel model for predicting the regulation of miRNAs expression by small molecules. BMC Bioinformatics 2024; 25:6. [PMID: 38166644 PMCID: PMC10763044 DOI: 10.1186/s12859-023-05629-x] [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: 09/07/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024] Open
Abstract
According to the expression of miRNA in pathological processes, miRNAs can be divided into oncogenes or tumor suppressors. Prediction of the regulation relations between miRNAs and small molecules (SMs) becomes a vital goal for miRNA-target therapy. But traditional biological approaches are laborious and expensive. Thus, there is an urgent need to develop a computational model. In this study, we proposed a computational model to predict whether the regulatory relationship between miRNAs and SMs is up-regulated or down-regulated. Specifically, we first use the Large-scale Information Network Embedding (LINE) algorithm to construct the node features from the self-similarity networks, then use the General Attributed Multiplex Heterogeneous Network Embedding (GATNE) algorithm to extract the topological information from the attribute network, and finally utilize the Light Gradient Boosting Machine (LightGBM) algorithm to predict the regulatory relationship between miRNAs and SMs. In the fivefold cross-validation experiment, the average accuracies of the proposed model on the SM2miR dataset reached 79.59% and 80.37% for up-regulation pairs and down-regulation pairs, respectively. In addition, we compared our model with another published model. Moreover, in the case study for 5-FU, 7 of 10 candidate miRNAs are confirmed by related literature. Therefore, we believe that our model can promote the research of miRNA-targeted therapy.
Collapse
Affiliation(s)
- Yong-Jian Guan
- School of Information Engineering, Xijing University, Xi'an, China
| | - Chang-Qing Yu
- School of Information Engineering, Xijing University, Xi'an, China.
| | - Li-Ping Li
- College of Grassland and Environment Sciences, Xinjiang Agricultural University, Urumqi, China.
- College of Agriculture and Forestry, Longdong University, Qingyang, China.
| | - Zhu-Hong You
- School of Computer Science, North-Western Polytechnical University, Xi'an, China
| | - Meng-Meng Wei
- School of Information Engineering, Xijing University, Xi'an, China
| | - Xin-Fei Wang
- School of Information Engineering, Xijing University, Xi'an, China
| | - Chen Yang
- School of Information Engineering, Xijing University, Xi'an, China
| | - Lu-Xiang Guo
- School of Information Engineering, Xijing University, Xi'an, China
| |
Collapse
|
20
|
Biswas P, More SS. Using Small Molecules for Targeting Heavy Metals in Neurotoxicity and Neuroinflammation. Methods Mol Biol 2024; 2761:135-148. [PMID: 38427235 DOI: 10.1007/978-1-0716-3662-6_11] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Pharmaceutical drugs, natural toxins, industrial chemicals, and various environmental toxins negatively impact the nervous system. A significant cause of many neurodegenerative diseases is neurotoxicity. Although trace amounts of heavy metals are required for the proper functioning of several metabolic pathways, their dysregulation can cause many cellular and molecular alterations, which can enhance the risks associated with several neurodegenerative diseases. For example, high levels of heavy metals like manganese (Mn) affect the central nervous system with implications in both higher-order cognitive and motor functions. In addition, the buildup of amyloid aggregates and metal ions in the brain of patients with Alzheimer's disease is associated with disease pathogenesis. Small molecules capable of targeting neuroinflammation and neuroprotection pathways would be valuable to elucidate the pathological pathways associated with metal toxicity in neurogenerative disease. This chapter will summarize the necessary steps involved in (1) culturing of cell lines and maintenance of animal models, (2) design and preparation of samples of small molecules and treatment methodologies, (3) RNA and protein isolation and preparation of tissue and cell culture samples for quantitative studies, and (4) quantitative estimation of cellular products.
Collapse
Affiliation(s)
- Pronama Biswas
- School of Basic and Applied Sciences, Dayananda Sagar University, Bangalore, Karnataka, India
| | - Sunil S More
- School of Basic and Applied Sciences, Dayananda Sagar University, Bangalore, Karnataka, India
| |
Collapse
|
21
|
Addis P, Bali U, Baron F, Campbell A, Harborne S, Jagger L, Milne G, Pearce M, Rosethorne EM, Satchell R, Swift D, Young B, Unitt JF. Key aspects of modern GPCR drug discovery. SLAS Discov 2024; 29:1-22. [PMID: 37625784 DOI: 10.1016/j.slasd.2023.08.007] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/07/2023] [Accepted: 08/22/2023] [Indexed: 08/27/2023]
Abstract
G-protein-coupled receptors (GPCRs) are the largest and most versatile cell surface receptor family with a broad repertoire of ligands and functions. We've learned an enormous amount about discovering drugs of this receptor class since the first GPCR was cloned and expressed in 1986, such that it's now well-recognized that GPCRs are the most successful target class for approved drugs. Here we take the reader through a GPCR drug discovery journey from target to the clinic, highlighting the key learnings, best practices, challenges, trends and insights on discovering drugs that ultimately modulate GPCR function therapeutically in patients. The future of GPCR drug discovery is inspiring, with more desirable drug mechanisms and new technologies enabling the delivery of better and more successful drugs.
Collapse
Affiliation(s)
- Phil Addis
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Utsav Bali
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Frank Baron
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Adrian Campbell
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Steven Harborne
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Liz Jagger
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Gavin Milne
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Martin Pearce
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Elizabeth M Rosethorne
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Rupert Satchell
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Denise Swift
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Barbara Young
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - John F Unitt
- Bioscience, Medicinal Chemistry, Pharmacology and Protein Science Departments, Sygnature Discovery Ltd, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK.
| |
Collapse
|
22
|
Gao J, Pei H, Lv F, Niu X, You Y, He L, Hu S, Shah KM, Liu M, Chen Y, Du B, Xiong H, Luo J. JD-312 - A novel small molecule that facilitates cartilage repair and alleviates osteoarthritis progression. J Orthop Translat 2024; 44:60-71. [PMID: 38269355 PMCID: PMC10805627 DOI: 10.1016/j.jot.2023.11.007] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/12/2023] [Accepted: 11/21/2023] [Indexed: 01/26/2024] Open
Abstract
Background The chondrogenic differentiation of mesenchymal stem cells (MSCs) to enhance cartilage repair and regeneration is a promising strategy to alleviate osteoarthritis (OA) progression. Method The potency of JD-312 in inducing chondrogenic differentiation of MSCs was assessed and verified. The efficacy of JD-312-treated MSCs was evaluated using a Sprague-Dawley rat DMM model. Additionally, the capacity of JD-312 to successfully recruit bone marrow-derived mesenchymal stem cells (BMSCs) for the treatment of OA in vitro was confirmed via intra-articular injection. The repair status of the articular cartilage was analyzed in vivo through histological examination. Result In this study, we identify JD-312 as a novel non-toxic small molecule that can promote chondrogenic differentiation in human umbilical cord-derived MSCs (hUCMSCs) and human bone marrow MSCS (hBMSCs) in vitro. We also show that transient differentiation of MSCs with JD-312 prior to in vivo administration remarkably improves the regeneration of cartilage and promotes Col2a1 and Acan expression in rat models of DMM, in comparison to kartogenin (KGN) pre-treatment or MSCs alone. Furthermore, direct intra-articular injection of JD-312 in murine model of OA showed reduced loss of articular cartilage and improved pain parameters. Lastly, we identified that the effects of JD-312 are at least in part mediated via upregulation of genes associated with the focal adhesion, PI3K-Akt signaling and the ECM-receptor interaction pathways, and specifically cartilage oligomeric matrix protein (COMP) may play a vital role. Conclusion Our study demonstrated that JD-312 showed encouraging repair effects for OA in vivo. The translational potential of this article Together, our findings demonstrate that JD-312 is a promising new therapeutic molecule for cartilage regeneration with clinical potential.
Collapse
Affiliation(s)
- Jingduo Gao
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, PR China
| | - Haixiang Pei
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, PR China
- Institute for Advanced Study, Shenzhen University and Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, PR China
| | - Fang Lv
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, PR China
| | - Xin Niu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, PR China
| | - Yu You
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, PR China
| | - Liang He
- Yangzhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), Tongji University School of Medicine, Shanghai, PR China
| | - Shijia Hu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, PR China
| | - Karan M. Shah
- Department of Oncology and Metabolism, The Medical School, The University of Sheffield, Sheffield, United Kingdom
| | - Mingyao Liu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, PR China
| | - Yihua Chen
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, PR China
| | - Bing Du
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, PR China
| | - Hai Xiong
- Institute for Advanced Study, Shenzhen University and Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, PR China
| | - Jian Luo
- Yangzhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center), Tongji University School of Medicine, Shanghai, PR China
| |
Collapse
|
23
|
Zhang S, Feng R, Wu H, Guo J, Zhou Y, Lai X, Sun Y, Shen Y, Liu B, Yang X, Wang B. Development of an ultrasensitive sandwich immunoassay for detecting small molecule semicarbazide. Food Chem 2023; 429:136835. [PMID: 37463535 DOI: 10.1016/j.foodchem.2023.136835] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/07/2023] [Accepted: 07/05/2023] [Indexed: 07/20/2023]
Abstract
Ultrasensitive sandwich immunoassays for detecting the small molecule semicarbazide (SEM) were developed based on derivatization. Several SEM derivatizing agents were synthesized by linking o-nitrobenzaldehyde (NBA) and biotin with dihydroxyalkanes (different lengths), which were then used to evaluate the distance effect of two epitopes. Sandwich ELISA for SEM derivatives was developed using an anti-SEM-NBA antibody and horseradish peroxidase-labeled avidin or anti-biotin antibody as a secondary conjugate. The advantageous distances of the two epitopes under the double-antibody sandwich and antibody-avidin sandwich modes were ≥12 and ≥13 Å, respectively. Under the distances, the sensitivities of the sandwich ELISA were no lower than those of competitive ELISA. The obtained optimal EC50 values were 11.2 pg/mL (double-antibody sandwich with the epitope distance ≥16 Å) and 7.3 pg/mL (antibody-avidin sandwich with the epitope distance ≥17 Å). Compared with competitive ELISA, the developed method achieved a 30-fold improvement in sensitivity, with simpler aquatic product pretreatment.
Collapse
Affiliation(s)
- Shiwei Zhang
- Shenzhen Academy of Metrology and Quality Inspection, Shenzhen, PR China
| | - Ronghu Feng
- Shenzhen Academy of Metrology and Quality Inspection, Shenzhen, PR China
| | - Huiling Wu
- Shenzhen Academy of Metrology and Quality Inspection, Shenzhen, PR China
| | - Jiping Guo
- Shenzhen Academy of Metrology and Quality Inspection, Shenzhen, PR China
| | - Yingchun Zhou
- Shenzhen Academy of Metrology and Quality Inspection, Shenzhen, PR China
| | - Xintian Lai
- Shenzhen Academy of Metrology and Quality Inspection, Shenzhen, PR China
| | - Yanyan Sun
- Department of Anesthesiology, Shenzhen University General Hospital, Shenzhen University, Shenzhen, PR China.
| | - Yudong Shen
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou, PR China.
| | - Bing Liu
- College of Material Science and Engineering, Guangdong Research Center for Interfacial Engineering of Functional Materials, State Key Laboratory of Fine Chemicals, Shenzhen University, Shenzhen, PR China
| | - Xingxing Yang
- Shenzhen Bioeasy Biotechnology Co., Ltd., Shenzhen, PR China
| | - Bingzhi Wang
- Shenzhen Bioeasy Biotechnology Co., Ltd., Shenzhen, PR China
| |
Collapse
|
24
|
Sperling AL, Eves-van den Akker S. Whole mount multiplexed visualization of DNA, mRNA, and protein in plant-parasitic nematodes. Plant Methods 2023; 19:139. [PMID: 38049899 PMCID: PMC10696717 DOI: 10.1186/s13007-023-01112-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/16/2023] [Indexed: 12/06/2023]
Abstract
BACKGROUND Plant-parasitic nematodes compromise the agriculture of a wide variety of the most common crops worldwide. Obtaining information on the fundamental biology of these organisms and how they infect the plant has been restricted by the ability to visualize intact nematodes using small molecule stains, antibodies, or in situ hybridization. Consequently, there is limited information available about the internal composition of the nematodes or the biology of the effector molecules they use to reprogram their host plant. RESULTS We present the Sperling prep - a whole mount method for nematode preparation that enables staining with small molecules, antibodies, or in situ hybridization chain reaction. This method does not require specialized apparatus and utilizes typical laboratory equipment and materials. By dissociating the strong cuticle and interior muscle layers, we enabled entry of the small molecule stains into the tissue. After permeabilization, small molecule stains can be used to visualize the nuclei with the DNA stain DAPI and the internal structures of the digestive tract and longitudinal musculature with the filamentous actin stain phalloidin. The permeabilization even allows entry of larger antibodies, albeit with lower efficiency. Finally, this method works exceptionally well with in situ HCR. Using this method, we have visualized effector transcripts specific to the dorsal gland and the subventral grand of the sugar beet cyst nematode, Heterodera schachtii, multiplexed in the same nematode. CONCLUSION We were able to visualize the internal structures of the nematode as well as key effector transcripts that are used during plant infection and parasitism. Therefore, this method provides an important toolkit for studying the biology of plant-parasitic nematodes.
Collapse
Affiliation(s)
- Alexis L Sperling
- Department of Plant Sciences, Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, Cambridge, UK
| | - Sebastian Eves-van den Akker
- Department of Plant Sciences, Crop Science Centre, University of Cambridge, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, Cambridge, UK.
| |
Collapse
|
25
|
Babazadeh A, Rayner SL, Lee A, Chung RS. TDP-43 as a therapeutic target in neurodegenerative diseases: Focusing on motor neuron disease and frontotemporal dementia. Ageing Res Rev 2023; 92:102085. [PMID: 37813308 DOI: 10.1016/j.arr.2023.102085] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/11/2023]
Abstract
A common feature of adult-onset neurodegenerative diseases is the presence of characteristic pathological accumulations of specific proteins. These pathological protein depositions can vary in their protein composition, cell-type distribution, and intracellular (or extracellular) location. For example, abnormal cytoplasmic protein deposits which consist of the TDP-43 protein are found within motor neurons in patients with amyotrophic lateral sclerosis (ALS, a common form of motor neuron disease) and frontotemporal dementia (FTD). The presence of these insoluble intracellular TDP-43 inclusions suggests that restoring TDP-43 homeostasis represents a potential therapeutical strategy, which has been demonstrated in alleviating neurodegenerative symptoms in cell and animal models of ALS/FTD. We have reviewed the mechanisms that lead to disrupted TDP-43 homeostasis and discussed how small molecule-based therapies could be applied in modulating these mechanisms. This review covers recent advancements and challenges in small molecule-based therapies that could be used to clear pathological forms of TDP-43 through various protein homeostasis mechanisms and advance the way towards finding effective therapeutical drug discoveries for neurodegenerative diseases characterized by TDP-43 proteinopathies, especially ALS and FTD. We also consider the wider insight of these therapeutic strategies for other neurodegenerative diseases.
Collapse
Affiliation(s)
- Afshin Babazadeh
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Stephanie L Rayner
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Albert Lee
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Roger S Chung
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| |
Collapse
|
26
|
Surme S, Ergun C, Gul S, Akyel YK, Gul ZM, Ozcan O, Ipek OS, Akarlar BA, Ozlu N, Taskin AC, Turkay M, Gören AC, Baris I, Ozturk N, Guzel M, Aydin C, Okyar A, Kavakli IH. TW68, cryptochromes stabilizer, regulates fasting blood glucose levels in diabetic ob/ob and high fat-diet-induced obese mice. Biochem Pharmacol 2023; 218:115896. [PMID: 37898388 DOI: 10.1016/j.bcp.2023.115896] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 10/30/2023]
Abstract
Cryptochromes (CRYs), transcriptional repressors of the circadian clock in mammals, inhibit cAMP production when glucagon activates G-protein coupled receptors. Therefore, molecules that modulate CRYs have the potential to regulate gluconeogenesis. In this study, we discovered a new molecule called TW68 that interacts with the primary pockets of mammalian CRY1/2, leading to reduced ubiquitination levels and increased stability. In cell-based circadian rhythm assays using U2OS Bmal1-dLuc cells, TW68 extended the period length of the circadian rhythm. Additionally, TW68 decreased the transcriptional levels of two genes, Phosphoenolpyruvate carboxykinase 1 (PCK1) and Glucose-6-phosphatase (G6PC), which play crucial roles in glucose biosynthesis during glucagon-induced gluconeogenesis in HepG2 cells. Oral administration of TW68 in mice showed good tolerance, a good pharmacokinetic profile, and remarkable bioavailability. Finally, when administered to fasting diabetic animals from ob/ob and HFD-fed obese mice, TW68 reduced blood glucose levels by enhancing CRY stabilization and subsequently decreasing the transcriptional levels of Pck1 and G6pc. These findings collectively demonstrate the antidiabetic efficacy of TW68 in vivo, suggesting its therapeutic potential for controlling fasting glucose levels in the treatment of type 2 diabetes mellitus.
Collapse
Affiliation(s)
- Saliha Surme
- Department of Molecular Biology and Genetics, Koc University, Rumelifeneri Yolu, Istanbul, Türkiye
| | - Cagla Ergun
- Department of Chemical and Biological Engineering, Koc University, Rumelifeneri Yolu, Istanbul, Türkiye
| | - Seref Gul
- Istanbul University, Department of Biology, Biotechnology Division, TR-34116 Beyazit-İstanbul, Türkiye; Current address: Bezmialem Vakif University, Institute of Life Sciences and Biotechnology, Beykoz, Istanbul, Türkiye
| | - Yasemin Kubra Akyel
- Istanbul Medipol University, School of Medicine, Department of Medical Pharmacology, İstanbul, Türkiye; Istanbul University, Faculty of Pharmacy Department of Pharmacology, TR-34116 Beyazit-İstanbul, Türkiye
| | - Zeynep Melis Gul
- Department of Molecular Biology and Genetics, Koc University, Rumelifeneri Yolu, Istanbul, Türkiye
| | - Onur Ozcan
- Department of Molecular Biology and Genetics, Koc University, Rumelifeneri Yolu, Istanbul, Türkiye
| | - Ozgecan Savlug Ipek
- Istanbul Medipol University, Regenerative and Restorative Medicine Research Center (REMER), Kavacik Campus, Kavacik-Beykoz/İstanbul 34810, Türkiye
| | - Busra Aytul Akarlar
- Department of Molecular Biology and Genetics, Koc University, Rumelifeneri Yolu, Istanbul, Türkiye
| | - Nurhan Ozlu
- Department of Molecular Biology and Genetics, Koc University, Rumelifeneri Yolu, Istanbul, Türkiye
| | - Ali Cihan Taskin
- Department of Laboratory Animal Science, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Türkiye
| | - Metin Turkay
- Department of Industrial Engineering, Koc University, Rumelifeneri Yolu, İstanbul, Türkiye
| | - Ahmet Ceyhan Gören
- Gebze Technical University, Department of Chemistry, Gebze, Kocaeli, Türkiye
| | - Ibrahim Baris
- Department of Molecular Biology and Genetics, Koc University, Rumelifeneri Yolu, Istanbul, Türkiye
| | - Nuri Ozturk
- Gebze Technical University, Department of Molecular Biology and Genetics, Gebze, Kocaeli, Türkiye
| | - Mustafa Guzel
- Istanbul Medipol University, Regenerative and Restorative Medicine Research Center (REMER), Kavacik Campus, Kavacik-Beykoz/İstanbul 34810, Türkiye
| | - Cihan Aydin
- Department of Molecular Biology and Genetics, Istanbul Medeniyet University, Istanbul, Türkiye
| | - Alper Okyar
- Istanbul University, Faculty of Pharmacy Department of Pharmacology, TR-34116 Beyazit-İstanbul, Türkiye
| | - Ibrahim Halil Kavakli
- Department of Molecular Biology and Genetics, Koc University, Rumelifeneri Yolu, Istanbul, Türkiye; Department of Chemical and Biological Engineering, Koc University, Rumelifeneri Yolu, Istanbul, Türkiye.
| |
Collapse
|
27
|
Haga CL, Yang XD, Gheit IS, Phinney DG. Graph neural networks for the identification of novel inhibitors of a small RNA. SLAS Discov 2023; 28:402-409. [PMID: 37839522 DOI: 10.1016/j.slasd.2023.10.002] [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] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 09/16/2023] [Accepted: 10/11/2023] [Indexed: 10/17/2023]
Abstract
MicroRNAs (miRNAs) play a crucial role in post-transcriptional gene regulation and have been implicated in various diseases, including cancers and lung disease. In recent years, Graph Neural Networks (GNNs) have emerged as powerful tools for analyzing graph-structured data, making them well-suited for the analysis of molecular structures. In this work, we explore the application of GNNs in ligand-based drug screening for small molecules targeting miR-21. By representing a known dataset of small molecules targeting miR-21 as graphs, GNNs can learn complex relationships between their structures and activities, enabling the prediction of potential miRNA-targeting small molecules by capturing the structural features and similarity between known miRNA-targeting compounds. The use of GNNs in miRNA-targeting drug screening holds promise for the discovery of novel therapeutic agents and provides a computational framework for efficient screening of large chemical libraries.
Collapse
Affiliation(s)
- Christopher L Haga
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, 33458, USA.
| | - Xue D Yang
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, 33458, USA
| | - Ibrahim S Gheit
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, 33458, USA
| | - Donald G Phinney
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, 33458, USA
| |
Collapse
|
28
|
Pal C. Redox modulating small molecules having antimalarial efficacy. Biochem Pharmacol 2023; 218:115927. [PMID: 37992998 DOI: 10.1016/j.bcp.2023.115927] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/24/2023]
Abstract
The search for effective antimalarial agents remains a critical priority because malaria is widely spread and drug-resistant strains are becoming more prevalent. In this review, a variety of small molecules capable of modulating redox processes were showcased for their potential as antimalarial agents. The compounds were designed to target the redox balance of Plasmodium parasites, which has a pivotal function in their ability to survive and multiply within the host organism. A thorough screening method was utilized to assess the effectiveness of these compounds against both drug-sensitive and drug-resistant strains of Plasmodium falciparum, the malaria-causing parasite. The results revealed that several of the tested compounds exhibited significant effectiveness against malaria, displaying IC50 values at a low micromolar range. Furthermore, these compounds displayed promising selectivity for the parasite, as they exhibited low cytotoxicity towards mammalian cells. Thorough mechanistic studies were undertaken to clarify how the active compounds exert their mode of action. The findings revealed that these compounds disrupted the parasites' redox balance, causing oxidative stress and interfering with essential cellular functions. Additionally, the compounds showed synergistic effects when combined with existing antimalarial drugs, suggesting their potential for combination therapies to combat drug resistance. Overall, this study highlights the potential of redox-modulating small molecules as effective antimalarial agents. The identified compounds demonstrate promising antimalarial activity, and their mechanism of action offers insights into targeting the redox balance of Plasmodium parasites. Further optimization and preclinical studies are warranted to determine their efficacy, safety, and potential for clinical development as novel antimalarial therapeutics.
Collapse
Affiliation(s)
- Chinmay Pal
- Department of Chemistry, Gobardanga Hindu College, North 24 Parganas, West Bengal 743273, India.
| |
Collapse
|
29
|
Zelesky T, Baertschi SW, Foti C, Allain LR, Hostyn S, Franca JR, Li Y, Marden S, Mohan S, Ultramari M, Huang Z, Adams N, Campbell JM, Jansen PJ, Kotoni D, Laue C. Pharmaceutical Forced Degradation (Stress Testing) Endpoints: A Scientific Rationale and Industry Perspective. J Pharm Sci 2023; 112:2948-2964. [PMID: 37690775 DOI: 10.1016/j.xphs.2023.09.003] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/01/2023] [Accepted: 09/01/2023] [Indexed: 09/12/2023]
Abstract
Forced degradation (i.e., stress testing) of small molecule drug substances and products is a critical part of the drug development process, providing insight into the intrinsic stability of a drug that is foundational to the development and validation of stability-indicating analytical methods. There is a lack of clarity in the scientific literature and regulatory guidance as to what constitutes an "appropriate" endpoint to a set of stress experiments. That is, there is no clear agreement regarding how to determine if a sample has been sufficiently stressed. Notably, it is unclear what represents a suitable justification for declaring a drug substance (DS) or drug product (DP) "stable" to a specific forced degradation condition. To address these concerns and to ensure all pharmaceutically-relevant, potential degradation pathways have been suitably evaluated, we introduce a two-endpoint classification designation supported by experimental data. These two endpoints are 1) a % total degradation target outcome (e.g., for "reactive" drugs) or, 2) a specified amount of stress, even in the absence of any degradation (e.g., for "stable" drugs). These recommended endpoints are based on a review of the scientific literature, regulatory guidance, and a forced degradation data set from ten global pharmaceutical companies. The experimental data set, derived from the Campbell et al. (2022) benchmarking study,1 provides justification for the recommendations. Herein we provide a single source reference for small molecule DS and DP forced degradation stress conditions and endpoint best practices to support regulatory submissions (e.g., marketing applications). Application of these forced degradation conditions and endpoints, as part of a well-designed, comprehensive and a sufficiently rigorous study plan that includes both the DS and DP, provides comprehensive coverage of pharmaceutically-relevant degradation and avoids unreasonably extreme stress conditions and drastic endpoint recommendations sometimes found in the literature.
Collapse
Affiliation(s)
- Todd Zelesky
- Analytical Research & Development, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA.
| | | | - Chris Foti
- Analytical Development and Operations, Gilead Sciences Inc., Foster City, California, USA.
| | | | - Steven Hostyn
- Predictive Analytics & Stability Sciences CoE, Janssen Pharmaceutica, Johnson & Johnson, Beerse, Belgium
| | | | - Yi Li
- Analytical Development and Operations, Gilead Sciences Inc., Foster City, California, USA
| | - Stacey Marden
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Boston, MA, USA
| | - Shikhar Mohan
- Analytical Development and Operations, Gilead Sciences Inc., Foster City, California, USA
| | - Mariah Ultramari
- Spektra Soluções Científico-Regulatórias Ltda, São Paulo, Brazil
| | - Zongyun Huang
- Bristol-Myers Squibb Company, 1 Squibb Drive, New Brunswick, NJ 08901, USA
| | - Neal Adams
- Pfizer, Scientific and Laboratory Services - Analytical Sciences, Pfizer Inc., 7000 Portage Road, Kalamazoo, MI 49001, USA
| | - John M Campbell
- Analytical Development, GSK, Upper Providence, PA 19426, USA
| | - Patrick J Jansen
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - Dorina Kotoni
- Chemical & Analytical Development, Novartis Pharma AG, Basel, Switzerland
| | - Christian Laue
- Chemical & Pharmaceutical Development, Merck Healthcare KGaA, Darmstadt, Germany
| |
Collapse
|
30
|
Zhu D, Xu X, Zou P, Liu Y, Wang H, Han G, Lu C, Xie M. Synthesis and preliminary biological evaluation of a novel 99mTc-labeled small molecule for PD-L1 imaging. Bioorg Med Chem Lett 2023; 96:129496. [PMID: 37797805 DOI: 10.1016/j.bmcl.2023.129496] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/26/2023] [Accepted: 10/02/2023] [Indexed: 10/07/2023]
Abstract
In recent years, PD-1/PD-L1 checkpoint blockade immunotherapy with remarkable efficacy has set off a heat wave. The expression level of PD-L1, which plays a predictive role in anti-PD-1/PD-L1 therapy, could be quantified by noninvasive imaging with radiotracers. Herein, we introduced the synthesis and preliminary biological evaluation of a novel 99mTc-labeled small molecule radiotracer [99mTc]G3C-CBM for PD-L1 imaging. [99mTc]G3C-CBM was achieved with high radiochemical purity (>96 %) and remained good stability in PBS and FBS. In competitive combination experiment, [99mTc]G3C-CBM was displaced by increasing concentrations of unlabeled G3C-CBM, resulting in an IC50 value of 41.25±2.23 nM for G3C-CBM. The uptake of [99mTc]G3C-CBM in A375-hPD-L1 cells (17.51±2.08 %) was approximately 6.47 folds of that in A375 cells (2.71±0.36 %) after co-incubation for 2 h. The biodistribution results showed that the radioactivity uptake in A375-hPD-L1 tumor reached the maximum (0.35±0.01 %ID/g) at 2 h post injection, and the optimum tumor/muscle ratio of 2.94±0.29 occurred at the same time. In addition, [99mTc]G3C-CBM was quickly cleared from the blood with a clearance half-life of just 119.25 min. These results indicate that [99mTc]G3C-CBM is a potential SPECT PD-L1 imaging agent and is worthy of further study.
Collapse
Affiliation(s)
- Dandan Zhu
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China; NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Xiang Xu
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China; NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Pei Zou
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Yaling Liu
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Hongyong Wang
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Guoqing Han
- NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China
| | - Chunxiong Lu
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China; NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China.
| | - Minhao Xie
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China; NHC Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, China.
| |
Collapse
|
31
|
He K, Lin H, Zhang S, Ou Y, Lu J, Chen W, Zhou Y, Li Y, Lin Y, Su J, Xing Y, Chen H, Chen J. BNTA attenuates temporomandibular joint osteoarthritis progression by directly targeting ALDH3A1: An in vivo and in vitro study. Int Immunopharmacol 2023; 124:110963. [PMID: 37741125 DOI: 10.1016/j.intimp.2023.110963] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 09/15/2023] [Accepted: 09/16/2023] [Indexed: 09/25/2023]
Abstract
BNTA is known to have a therapeutic effect on knee osteoarthritis and inflammatory osteoclastogenesis. However, the protective effect of BNTA regarding temporomandibular mandibular joint osteoarthritis (TMJOA) and its underlying mechanism and physiological target remains unclear. In the present study, BNTA ameliorated cartilage degradation and inflammation responses in monosodium iodoacetate (MIA)-induced TMJOA in vivo. In IL-1β-induced condylar chondrocytes, BNTA prevents oxidative stress, inflammatory responses and increasing synthesis of cartilage extracellular matrix through activating nuclear factor-E2-related factor 2 (NRF2) signaling. Suppression of NRF2 signaling abolishes the protective effect of BNTA in TMJOA. Notably, BNTA may bind directly to ALDH3A1 and act as a stabilizer, as evidenced by drug affinity responsive target stability assay (DARTS), cellular thermal shift assay (CETSA) and molecular docking results. Further investigation of the underlying molecular and cellular mechanism infers a positive correlation of ALDH3A1 regulating NRF2 signaling. In conclusion, BNTA may attenuate TMJOA progression via the ALDH3A1/NRF2 axis, inferring that BNTA is a therapeutic target for treating temporomandibular mandibular joint osteoarthritis.
Collapse
Affiliation(s)
- Kaixun He
- Fujian Key Laboratory of Oral Diseases & Fujian Provincial Engineering Research Center of Oral Biomaterial & Stomatological Key Lab of Fujian College and University, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, Fujian 350002, PR China; Institute of Stomatology & Research Center of Dental and Craniofacial Implants, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, Fujian 350002, PR China
| | - Hanyu Lin
- Fujian Key Laboratory of Oral Diseases & Fujian Provincial Engineering Research Center of Oral Biomaterial & Stomatological Key Lab of Fujian College and University, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, Fujian 350002, PR China; Institute of Stomatology & Research Center of Dental and Craniofacial Implants, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, Fujian 350002, PR China
| | - Sihui Zhang
- Fujian Key Laboratory of Oral Diseases & Fujian Provincial Engineering Research Center of Oral Biomaterial & Stomatological Key Lab of Fujian College and University, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, Fujian 350002, PR China; Institute of Stomatology & Research Center of Dental and Craniofacial Implants, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, Fujian 350002, PR China
| | - Yanjing Ou
- Fujian Key Laboratory of Oral Diseases & Fujian Provincial Engineering Research Center of Oral Biomaterial & Stomatological Key Lab of Fujian College and University, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, Fujian 350002, PR China; Institute of Stomatology & Research Center of Dental and Craniofacial Implants, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, Fujian 350002, PR China
| | - Jie Lu
- Fujian Key Laboratory of Oral Diseases & Fujian Provincial Engineering Research Center of Oral Biomaterial & Stomatological Key Lab of Fujian College and University, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, Fujian 350002, PR China
| | - Wenqian Chen
- Fujian Key Laboratory of Oral Diseases & Fujian Provincial Engineering Research Center of Oral Biomaterial & Stomatological Key Lab of Fujian College and University, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, Fujian 350002, PR China
| | - Yuwei Zhou
- Fujian Key Laboratory of Oral Diseases & Fujian Provincial Engineering Research Center of Oral Biomaterial & Stomatological Key Lab of Fujian College and University, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, Fujian 350002, PR China
| | - Yang Li
- Fujian Key Laboratory of Oral Diseases & Fujian Provincial Engineering Research Center of Oral Biomaterial & Stomatological Key Lab of Fujian College and University, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, Fujian 350002, PR China
| | - Yanjun Lin
- Fujian Key Laboratory of Oral Diseases & Fujian Provincial Engineering Research Center of Oral Biomaterial & Stomatological Key Lab of Fujian College and University, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, Fujian 350002, PR China; Institute of Stomatology & Research Center of Dental and Craniofacial Implants, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, Fujian 350002, PR China
| | - Jingjing Su
- Fujian Key Laboratory of Oral Diseases & Fujian Provincial Engineering Research Center of Oral Biomaterial & Stomatological Key Lab of Fujian College and University, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, Fujian 350002, PR China
| | - Yifeng Xing
- Fujian Key Laboratory of Oral Diseases & Fujian Provincial Engineering Research Center of Oral Biomaterial & Stomatological Key Lab of Fujian College and University, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, Fujian 350002, PR China
| | - Huachen Chen
- Fujian Key Laboratory of Oral Diseases & Fujian Provincial Engineering Research Center of Oral Biomaterial & Stomatological Key Lab of Fujian College and University, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, Fujian 350002, PR China
| | - Jiang Chen
- Fujian Key Laboratory of Oral Diseases & Fujian Provincial Engineering Research Center of Oral Biomaterial & Stomatological Key Lab of Fujian College and University, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, Fujian 350002, PR China; Institute of Stomatology & Research Center of Dental and Craniofacial Implants, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, Fujian 350002, PR China.
| |
Collapse
|
32
|
Tabana Y, Babu D, Fahlman R, Siraki AG, Barakat K. Target identification of small molecules: an overview of the current applications in drug discovery. BMC Biotechnol 2023; 23:44. [PMID: 37817108 PMCID: PMC10566111 DOI: 10.1186/s12896-023-00815-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 04/20/2023] [Accepted: 09/22/2023] [Indexed: 10/12/2023] Open
Abstract
Target identification is an essential part of the drug discovery and development process, and its efficacy plays a crucial role in the success of any given therapy. Although protein target identification research can be challenging, two main approaches can help researchers make significant discoveries: affinity-based pull-down and label-free methods. Affinity-based pull-down methods use small molecules conjugated with tags to selectively isolate target proteins, while label-free methods utilize small molecules in their natural state to identify targets. Target identification strategy selection is essential to the success of any drug discovery process and must be carefully considered when determining how to best pursue a specific project. This paper provides an overview of the current target identification approaches in drug discovery related to experimental biological assays, focusing primarily on affinity-based pull-down and label-free approaches, and discusses their main limitations and advantages.
Collapse
Affiliation(s)
- Yasser Tabana
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Dinesh Babu
- Li Ka Shing Applied Virology Institute, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Richard Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Arno G Siraki
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - Khaled Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada.
| |
Collapse
|
33
|
Bennett JB, Wu SL, Chennuri PR, Myles KM, Ndeffo-Mbah ML. Expansions to the MGDrivE suite for simulating the efficacy of novel gene-drive constructs in the control of mosquito-borne diseases. BMC Res Notes 2023; 16:258. [PMID: 37798614 PMCID: PMC10557238 DOI: 10.1186/s13104-023-06533-6] [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: 05/30/2023] [Accepted: 09/25/2023] [Indexed: 10/07/2023] Open
Abstract
OBJECTIVE The MGDrivE (MGDrivE 1 and MGDrivE 2) modeling framework provides a flexible and expansive environment for testing the efficacy of novel gene-drive constructs for the control of mosquito-borne diseases. However, the existing model framework did not previously support several features necessary to simulate some types of intervention strategies. Namely, current MGDrivE versions do not permit modeling of small molecule inducible systems for controlling gene expression in gene drive designs or the inheritance patterns of self-eliminating gene drive mechanisms. RESULTS Here, we demonstrate a new MGDrivE 2 module that permits the simulation of gene drive strategies incorporating small molecule-inducible systems and self-eliminating gene drive mechanisms. Additionally, we also implemented novel sparsity-aware sampling algorithms for improved computational efficiency in MGDrivE 2 and supplied an analysis and plotting function applicable to the outputs of MGDrivE 1 and MGDrivE 2.
Collapse
Affiliation(s)
| | - Sean L Wu
- Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA, 98121, USA
| | - Pratima R Chennuri
- Department of Entomology, Texas A & M University, College Station, TX, 77843, USA
- Future Fields, Edmonton, AB, T5H 0L5, Canada
| | - Kevin M Myles
- Department of Entomology, Texas A & M University, College Station, TX, 77843, USA
| | - Martial L Ndeffo-Mbah
- Department of Integrative Biosciences, Texas A&M University, College Station, TX, 77843, USA.
| |
Collapse
|
34
|
Rajagopal L, Mahjour S, Huang M, Ryan CA, Elzokaky A, Csakai AJ, Orr MJ, Scheidt K, Meltzer HY. NU-1223, a simplified analog of alstonine, with 5-HT 2cR agonist-like activity, rescues memory deficit and positive and negative symptoms in subchronic phencyclidine mouse model of schizophrenia. Behav Brain Res 2023; 454:114614. [PMID: 37572758 DOI: 10.1016/j.bbr.2023.114614] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 08/14/2023]
Abstract
The serotonin (5-HT)2 C receptor(R) is a widely distributed G-protein-coupled receptor, expressed abundantly in the central nervous system. Alstonine is a natural product that has significant properties of atypical antipsychotic drugs (AAPDs), in part attributed to 5-HT2 CR agonism. Based on alstonine, we developed NU-1223, a simplified β carboline analog of alstonine, which shows efficacies comparable to alstonine and to other 5-HT2 CR agonists, Ro-60-0175 and lorcaserin. The 5-HT2 CR antagonism of some APDs, including olanzapine, contributes to weight gain, a major side effect which limits its tolerability, while the 5-HT2 CR agonists and/or modulators, may minimize weight gain. We used the well-established rodent subchronic phencyclidine (PCP) model to test the efficacy of NU-1223 on episodic memory, using novel object recognition (NOR) task, positive (locomotor activity), and negative symptoms (social interaction) of schizophrenia (SCH). We found that NU-1223 produced both transient and prolonged rescue of the subchronic PCP-induced deficits in NOR and SI. Further, NU-1223, but not Ro-60-0175, blocked PCP and amphetamine (AMPH)-induced increase in LMA in subchronic PCP mice. These transient efficacies in LMA were blocked by the 5-HT2 CR antagonist, SB242084. Sub-chronic NU-1223 treatment rescued NOR and SI deficits in subchronic PCP mice for at least 39 days after 3 days injection. Chronic treatment with NU-1223, ip, twice a day for 21 days, did not increase average body weight vs olanzapine. These findings clearly indicate NU-1223 as a class of small molecules with a possible 5-HT2 CR-agonist-like mechanism of action, attributing to its efficacy. Additional in-depth receptor mechanistic studies are warranted, as this small molecule, both transiently and chronically rescued PCP-induced deficits. Furthermore, NU-1223 did not induce weight gain post long-term administrations vs AAPDs such as olanzapine, making NU-1223 a putative therapeutic compound for SCH.
Collapse
Affiliation(s)
- Lakshmi Rajagopal
- Department of Psychiatry and Behavioral Sciences, Northwestern Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Sanaz Mahjour
- Department of Psychiatry and Behavioral Sciences, Northwestern Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Mei Huang
- Department of Psychiatry and Behavioral Sciences, Northwestern Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Chelsea A Ryan
- Department of Psychiatry and Behavioral Sciences, Northwestern Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ahmad Elzokaky
- Department of Psychiatry and Behavioral Sciences, Northwestern Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Adam J Csakai
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Meghan J Orr
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Karl Scheidt
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA; Department of Pharmacology, Northwestern Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Herbert Y Meltzer
- Department of Psychiatry and Behavioral Sciences, Northwestern Feinberg School of Medicine, Chicago, IL 60611, USA.
| |
Collapse
|
35
|
Qu J, Song Z, Cheng X, Jiang Z, Zhou J. Neighborhood-based inference and restricted Boltzmann machine for small molecule-miRNA associations prediction. PeerJ 2023; 11:e15889. [PMID: 37641598 PMCID: PMC10460564 DOI: 10.7717/peerj.15889] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/21/2023] [Indexed: 08/31/2023] Open
Abstract
Background A growing number of experiments have shown that microRNAs (miRNAs) can be used as target of small molecules (SMs) to regulate gene expression for treating diseases. Therefore, identifying SM-related miRNAs is helpful for the treatment of diseases in the domain of medical investigation. Methods This article presents a new computational model, called NIRBMSMMA (neighborhood-based inference (NI) and restricted Boltzmann machine (RBM)), which we developed to identify potential small molecule-miRNA associations (NIRBMSMMA). First, grounded on known SM-miRNAs associations, SM similarity and miRNA similarity, NI was used to predict score of an unknown SM-miRNA pair by reckoning the sum of known associations between neighbors of the SM (miRNA) and the miRNA (SM). Second, utilizing a two-layered generative stochastic artificial neural network, RBM was used to predict SM-miRNA association by learning potential probability distribution from known SM-miRNA associations. At last, an ensemble learning model was conducted to combine NI and RBM for identifying potential SM-miRNA associations. Results Furthermore, we conducted global leave one out cross validation (LOOCV), miRNA-fixed LOOCV, SM-fixed LOOCV and five-fold cross validation to assess performance of NIRBMSMMA based on three datasets. Results showed that NIRBMSMMA obtained areas under the curve (AUC) of 0.9912, 0.9875, 0.8376 and 0.9898 ± 0.0009 under global LOOCV, miRNA-fixed LOOCV, SM-fixed LOOCV and five-fold cross validation based on dataset 1, respectively. For dataset 2, the AUCs are 0.8645, 0.8720, 0.7066 and 0.8547 ± 0.0046 in turn. For dataset 3, the AUCs are 0.9884, 0.9802, 0.8239 and 0.9870 ± 0.0015 in turn. Also, we conducted case studies to further assess the predictive performance of NIRBMSMMA. These results illustrated the proposed model is a useful tool in predicting potential SM-miRNA associations.
Collapse
Affiliation(s)
- Jia Qu
- School of Computer Science and Artificial Intelligence, Changzhou University, Changzhou, Jiangsu, China
| | - Zihao Song
- School of Computer Science and Artificial Intelligence, Changzhou University, Changzhou, Jiangsu, China
| | - Xiaolong Cheng
- School of Computer Science and Artificial Intelligence, Changzhou University, Changzhou, Jiangsu, China
| | - Zhibin Jiang
- Department of Computer Science and Engineering, Shaoxing University, Shaoxing, Zhejiang, China
| | - Jie Zhou
- Department of Computer Science and Engineering, Shaoxing University, Shaoxing, Zhejiang, China
| |
Collapse
|
36
|
Maruri-Lopez I, Chodasiewicz M. Involvement of small molecules and metabolites in regulation of biomolecular condensate properties. Curr Opin Plant Biol 2023; 74:102385. [PMID: 37348448 DOI: 10.1016/j.pbi.2023.102385] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 05/01/2023] [Accepted: 05/05/2023] [Indexed: 06/24/2023]
Abstract
Biomolecular condensate (BMCs) formation facilitates the grouping of molecules, including proteins, nucleic acids, and small molecules, creating specific microenvironments with particular functions. They are often assembled through liquid-liquid phase separation (LLPS), a phenomenon that arises when specific proteins, nucleic acids, and small molecules demix from the aqueous environment into another phase with different physiochemical properties. BMCs assemble and disassemble in response to external and internal stimuli such as temperature, molecule concentration, ionic strength, pH, and cellular redox state. Likewise, the nature of the regulatory stimuli may affect the lifespan, morphology, and content of BMCs. In humans, compelling evidence points to the critical role of BMCs in diseases. By contrast, the link between BMC formation, stress resistance, and cell survival has not been revealed in plants. Recent studies have pointed out the nascent roles of small molecules in the assembly and dynamics of BMCs; however, this is still an emerging field of study. This review briefly highlights the most significant efforts to identify the molecular mechanisms between small molecules and BMC formation and regulation in plants and other organisms. We then discuss (i) how small molecules exert control over the BMC assembly and dynamics in plants and (ii) how small molecules can influence the formation and material properties of plant BMCs. Finally, we propose novel alternatives that might help to understand the relationship between chemicals and condensation dynamics and their possible application to plant biotechnology.
Collapse
Affiliation(s)
- Israel Maruri-Lopez
- Biological and Environmental Science and Engineering Division, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Monika Chodasiewicz
- Biological and Environmental Science and Engineering Division, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
| |
Collapse
|
37
|
Kiperman T, Li W, Xiong X, Li H, Horne D, Ma K. Targeted screening and identification of chlorhexidine as a pro-myogenic circadian clock activator. Stem Cell Res Ther 2023; 14:190. [PMID: 37525228 PMCID: PMC10391781 DOI: 10.1186/s13287-023-03424-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 07/21/2023] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND The circadian clock is an evolutionarily conserved mechanism that exerts pervasive temporal control in stem cell behavior. This time-keeping machinery is required for orchestrating myogenic progenitor properties in regenerative myogenesis that ameliorates muscular dystrophy. Here we report a screening platform to discover circadian clock modulators that promote myogenesis and identify chlorhexidine (CHX) as a clock-activating molecule with pro-myogenic activities. METHODS A high-throughput molecular docking pipeline was applied to identify compounds with a structural fit for a hydrophobic pocket within the key circadian transcription factor protein, Circadian Locomotor Output Cycles Kaput (CLOCK). These identified molecules were further screened for clock-modulatory activities and functional validations for pro-myogenic properties. RESULTS CHX was identified as a clock activator that promotes distinct aspects of myogenesis. CHX activated circadian clock that reduced cycling period length and augmented amplitude. This action was mediated by the targeted CLOCK structure via augmented interaction with heterodimer partner Bmal1, leading to enhanced CLOCK/Bmal1-controlled transcription with upregulation of core clock genes. Consistent with its clock-activating function, CHX displayed robust effects on stimulating myogenic differentiation in a clock-dependent manner. In addition, CHX augmented the proliferative and migratory activities of myoblasts. CONCLUSION Our findings demonstrate the feasibility of a screening platform to discover clock modulators with myogenic regulatory activities. Discovery of CHX as a pro-myogenic molecule could be applicable to promote regenerative capacities in ameliorating dystrophic or degenerative muscle diseases.
Collapse
Affiliation(s)
- Tali Kiperman
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Weini Li
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Xuekai Xiong
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Hongzhi Li
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - David Horne
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Ke Ma
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA.
| |
Collapse
|
38
|
Chen Y, Du J, Zheng L, Wang Z, Zhang Z, Wu Z, Zhu X, Xiong JW. Chemical screening links disulfiram with cardiac protection after ischemic injury. Cell Regen 2023; 12:25. [PMID: 37466803 DOI: 10.1186/s13619-023-00170-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/03/2023] [Indexed: 07/20/2023]
Abstract
Ischemia-reperfusion injury occurs after reperfusion treatment for patients suffering myocardial infarction, however the underlying mechanisms are incompletely understood and effective pharmacological interventions are limited. Here, we report the identification and characterization of the FDA-approved drug disulfiram (DSF) as a cardioprotective compound. By applying high-throughput chemical screening, we found that DSF decreased H2O2-induced cardiomyocyte death by inhibiting Gasdermin D, but not ALDH1, in cardiomyocytes. Oral gavage of DSF decreased myocardial infarct size and improved heart function after myocardial ischemia-reperfusion injury in rats. Therefore, this work reveals DSF as a potential therapeutic compound for the treatment of ischemic heart disease.
Collapse
Affiliation(s)
- Yuanyuan Chen
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100871, China
| | - Jianyong Du
- School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao, 266071, China
| | - Lixia Zheng
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100871, China
| | - Zihao Wang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100871, China
| | - Zongwang Zhang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100871, China
| | - Zhengyuan Wu
- PKU-Nanjing Institute of Translational Medicine, Nanjing, 211800, China
| | - Xiaojun Zhu
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100871, China
| | - Jing-Wei Xiong
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, 100871, China.
- PKU-Nanjing Institute of Translational Medicine, Nanjing, 211800, China.
| |
Collapse
|
39
|
Lu W, Tian Y, Teng W, Qiu X, Li M. Plasmonic colorimetric immunosensor based on Poly-HRP and AuNS etching for tri-modal readout of small molecule. Talanta 2023; 265:124883. [PMID: 37393715 DOI: 10.1016/j.talanta.2023.124883] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/14/2023] [Accepted: 06/25/2023] [Indexed: 07/04/2023]
Abstract
It was urgent to improve the intuitive, portable, sensitive and multi-modal detection method for small molecules. In this study, a tri-modal readout of plasmonic colorimetric immunosensor (PCIS) for small molecule (zearalenone, ZEN, as an example) had been established based on the Poly-HRP amplification and gold nanostars (AuNS) etching. The immobilized Poly-HRP from the competitive immunoassay was used to catalyze iodide (I-) into iodine (I2), which could prevent the AuNS etching by I-. With the increasing of ZEN, the AuNS etching was enhanced, and the localized surface plasmon resonance (LSPR) peak of AuNS showed stronger blue shift, which resulted in the color changing from deep blue (no-etching) to blue violet (half-etching) and finally to shiny red (all-etching). The results of PCIS could be selectively obtained by the tri-modal readout: (1) naked eye (LOD of 0.10 ng/mL), (2) smartphone (LOD of 0.07 ng/mL) and (3) UV-spectrum (LOD of 0.04 ng/mL). The proposed PCIS had performed well in the sensitivity, specificity, accuracy and reliability. In addition, the harmless reagents were used in the overall process to further guarantee the environmental friendliness. Therefore, the PCIS might provide a novel and green avenue for the tri-modal readout of ZEN via the intuitive naked eye, portable smartphone and accurate UV-spectrum, which hold great potential for small molecule monitoring.
Collapse
Affiliation(s)
- Wenying Lu
- Institute of Environmental Health and Ecological Security, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Ye Tian
- Institute of Environmental Health and Ecological Security, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Weipeng Teng
- Institute of Environmental Health and Ecological Security, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Xuchun Qiu
- Institute of Environmental Health and Ecological Security, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Ming Li
- Institute of Environmental Health and Ecological Security, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, PR China.
| |
Collapse
|
40
|
Xu LC, Ochetto A, Chen C, Sun D, Allcock HR, Siedlecki CA. Surfaces modified with small molecules that interfere with nucleotide signaling reduce Staphylococcus epidermidis biofilm and increase the efficacy of ciprofloxacin. Colloids Surf B Biointerfaces 2023; 227:113345. [PMID: 37196462 DOI: 10.1016/j.colsurfb.2023.113345] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 03/30/2023] [Accepted: 05/11/2023] [Indexed: 05/19/2023]
Abstract
Staphylococcus epidermidis are common bacteria associated with biofilm related infections on implanted medical devices. Antibiotics are often used in combating such infections, but they may lose their efficacy in the presence of biofilms. Bacterial intracellular nucleotide second messenger signaling plays an important role in biofilm formation, and interference with the nucleotide signaling pathways provides a possible way to control biofilm formation and to increase biofilm susceptibility to antibiotic therapy. This study synthesized small molecule derivates of 4-arylazo-3,5-diamino-1 H-pyrazole (named as SP02 and SP03) and found these molecules inhibited S. epidermidis biofilm formation and induced biofilm dispersal. Analysis of bacterial nucleotide signaling molecules showed that both SP02 and SP03 significantly reduced cyclic dimeric adenosine monophosphate (c-di-AMP) levels in S. epidermidis at doses as low as 25 µM while having significant effects on multiple nucleotides signaling including cyclic dimeric guanosine monophosphate (c-di-GMP), c-di-AMP, and cyclic adenosine monophosphate (cAMP) at high doses (100 µM or greater). We then tethered these small molecules to polyurethane (PU) biomaterial surfaces and investigated biofilm formation on the modified surfaces. Results showed that the modified surfaces significantly inhibited biofilm formation during 24 h and 7-day incubations. The antibiotic ciprofloxacin was used to treat these biofilms and the efficacy of the antibiotic (2 µg/mL) was found to increase from 94.8% on unmodified PU surfaces to > 99.9% on both SP02 and SP03 modified surfaces (>3 log units). Results demonstrated the feasibility of tethering small molecules that interfere with nucleotide signaling onto polymeric biomaterial surfaces and in a way that interrupts biofilm formation and increases antibiotic efficacy for S. epidermidis infections.
Collapse
Affiliation(s)
- Li-Chong Xu
- Department of Surgery, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
| | - Alyssa Ochetto
- Department of Biological and Biomedical Sciences, Rowan University, Glassboro, NJ 08028, USA
| | - Chen Chen
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Dongxiao Sun
- Department of Pharmacology, Mass Spectrometry Core Facilities (RRID: SCR_017831), The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Harry R Allcock
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Christopher A Siedlecki
- Department of Surgery, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA; Department of Biomedical Engineering, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| |
Collapse
|
41
|
Zhou Z, Zhang Y, Ji H, Jin Y, Chen S, Duan P, Liu Y. Enantioselective Effect of Chiral Small Molecules in SARS-CoV-2 Vaccine-Induced Immune Response. Angew Chem Int Ed Engl 2023:e202301085. [PMID: 37163203 DOI: 10.1002/anie.202301085] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/29/2023] [Accepted: 05/09/2023] [Indexed: 05/11/2023]
Abstract
Although numerous chiral small molecules have been discovered and synthesized, the investigation on their enantioselective immunological effects remains limited. In this study, we designed and synthesized a pair of small molecule enantiomers (R/S-ResP) by covalently bonding two immunostimulators (resiquimod/Res) onto a planar chiral framework (paracyclophane/P). Notably, we found that S-ResP exhibits a 4.05-fold higher affinity for toll-like receptor 7 (TLR7) than R-ResP, thereby more effectively enhancing the functions of dendritic cells and macrophages in cytokine secretion and antigen internalization. Furthermore, we observed that S-ResP significantly enhances RBD antigen-induced cross-neutralization against various SARS-CoV-2 strains compared to R-ResP. These findings demonstrate the enantioselective effects of small molecules on regulating vaccine-induced immune responses and emphasize the significance of chirality in designing small molecular adjuvants.
Collapse
Affiliation(s)
- Zhengmiao Zhou
- Chinese Academy of Medical Sciences & Peking Union Medical College Institute of Medical Biology, Institute of Medical Biology, 650000, Kunming, CHINA
| | - Yufang Zhang
- Chinese Academy of Medical Sciences & Peking Union Medical College Institute of Medical Biology, Institute of Medical Biology, 650000, Kunming, CHINA
| | - Honghan Ji
- National Center for Nanoscience and Technology, CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, 100190, Beijing, CHINA
| | - Yu Jin
- Chinese Academy of Medical Sciences & Peking Union Medical College Institute of Medical Biology, Institute of Medical Biology, 650000, Kunming, CHINA
| | - Sisi Chen
- Chinese Academy of Medical Sciences & Peking Union Medical College Institute of Medical Biology, Institute of Medical Biology, 650000, Kunming, CHINA
| | - Pengfei Duan
- National Center for Nanoscience and Technology, Key Laboratory of Nanosystem and Hierarchical Fabrication, No.11 ZhongGuanCunBeiYiTiao, 100190, Beijing, CHINA
| | - Ye Liu
- Chinese Academy of Medical Sciences & Peking Union Medical College Institute of Medical Biology, Institute of Medical Biology, 650000, Kunming, CHINA
| |
Collapse
|
42
|
Mi D, Li Y, Gu H, Li Y, Chen Y. Current advances of small molecule E3 ligands for proteolysis-targeting chimeras design. Eur J Med Chem 2023; 256:115444. [PMID: 37178483 DOI: 10.1016/j.ejmech.2023.115444] [Citation(s) in RCA: 5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/30/2023] [Accepted: 05/01/2023] [Indexed: 05/15/2023]
Abstract
Proteolysis-targeting chimeras (PROTACs) as an emerging drug discovery modality has been extensively concerned in recent years. Over 20 years development, accumulated studies have demonstrated that PROTACs show unique advantages over traditional therapy in operable target scope, efficacy, and overcoming drug resistance. However, only limited E3 ligases, the essential elements of PROTACs, have been harnessed for PROTACs design. The optimization of novel ligands for well-established E3 ligases and the employment of additional E3 ligases remain urgent challenges for investigators. Here, we systematically summarize the current status of E3 ligases and corresponding ligands for PROTACs design with a focus on their discovery history, design principles, application benefits, and potential defects. Meanwhile, the prospects and future directions for this field are briefly discussed.
Collapse
Affiliation(s)
- Dazhao Mi
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yuzhan Li
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Haijun Gu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yan Li
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yihua Chen
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
| |
Collapse
|
43
|
Wu M, Wu A, Zhang X, Li Y, Li B, Jin S, Dong Q, Niu X, Zhang L, Zhou X, Du J, Wu Y, Zhai W, Zhou X, Qiu L, Gao Y, Zhao W. Identification of a novel small-molecule inhibitor targeting TIM-3 for cancer immunotherapy. Biochem Pharmacol 2023; 212:115583. [PMID: 37148978 DOI: 10.1016/j.bcp.2023.115583] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/27/2023] [Accepted: 04/27/2023] [Indexed: 05/08/2023]
Abstract
PD-1/PD-L1 blockade has achieved substantial clinical results in cancer treatment. However, the expression of other immune checkpoints leads to resistance and hinders the efficacy of PD-1/PD-L1 blockade. T cell immunoglobulin and mucin domain 3 (TIM-3), a non-redundant immune checkpoint, synergizes with PD-1 to mediate T cell dysfunction in tumor microenvironment. Development of small molecules targeting TIM-3 is a promising strategy for cancer immunotherapy. Here, to identify small molecule inhibitors targeting TIM-3, the docking pocket in TIM-3 was analyzed by Molecular Operating Environment (MOE) and the Chemdiv compound database was screened. The small molecule SMI402 could bind to TIM-3 with high affinity and prevent the ligation of PtdSer, HMGB1, and CEACAM1. SMI402 reinvigorated T cell function in vitro. In the MC38-bearing mouse model, SMI402 inhibited tumor growth by increasing CD8+ T and natural killing (NK) cells infiltration at the tumor site, as well as restoring the function of CD8+ T and NK cells. In conclusions, the small molecule SMI402 shows promise as a leading compound which targets TIM-3 for cancer immunotherapy.
Collapse
Affiliation(s)
- Menghan Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Aijun Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xiangrui Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yang Li
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Beibei Li
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Shengzhe Jin
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Qingyu Dong
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xiaoshuang Niu
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - Lihan Zhang
- The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou 450008, China
| | - Xiaowen Zhou
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Jiangfeng Du
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yahong Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; Henan Key Laboratory of Bioactive Macromolecules, Zhengzhou University, Zhengzhou 450001, China
| | - Wenjie Zhai
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; International Joint Laboratory for Protein and Peptide Drugs of Henan Province, Zhengzhou University, Zhengzhou 450001, China
| | - Xiuman Zhou
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - Lu Qiu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - Yanfeng Gao
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China.
| | - Wenshan Zhao
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China.
| |
Collapse
|
44
|
Kanagaki S, Tsutsui Y, Kobayashi N, Komine T, Ito M, Akasaka Y, Nagasawa M, Ide T, Omae N, Nakao K, Rembutsu M, Iwago M, Yonezawa A, Hosokawa Y, Hosooka T, Ogawa W, Murakami K. Activation of AMP-activated protein kinase (AMPK) through inhibiting interaction with prohibitins. iScience 2023; 26:106293. [PMID: 36950117 PMCID: PMC10025096 DOI: 10.1016/j.isci.2023.106293] [Citation(s) in RCA: 1] [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] [Received: 07/07/2022] [Revised: 09/16/2022] [Accepted: 02/16/2023] [Indexed: 03/08/2023] Open
Abstract
5'-Adenosine monophosphate-activated protein kinase (AMPK) is a potential therapeutic target for various medical conditions. We here identify a small-molecule compound (RX-375) that activates AMPK and inhibits fatty acid synthesis in cultured human hepatocytes. RX-375 does not bind to AMPK but interacts with prohibitins (PHB1 and PHB2), which were found to form a complex with AMPK. RX-375 induced dissociation of this complex, and PHBs knockdown resulted in AMPK activation, in the cultured cells. Administration of RX-375 to obese mice activated AMPK and ameliorated steatosis in the liver. High-throughput screening based on disruption of the AMPK-PHB interaction identified a second small-molecule compound that activates AMPK, confirming the importance of this interaction in the regulation of AMPK. Our results thus indicate that PHBs are previously unrecognized negative regulators of AMPK, and that compounds that prevent the AMPK-PHB interaction constitute a class of AMPK activator.
Collapse
Affiliation(s)
- Shuhei Kanagaki
- Watarase Research Center, Kyorin Pharmaceutical Co. Ltd., Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Yusuke Tsutsui
- Watarase Research Center, Kyorin Pharmaceutical Co. Ltd., Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Naoki Kobayashi
- Watarase Research Center, Kyorin Pharmaceutical Co. Ltd., Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Takashi Komine
- Watarase Research Center, Kyorin Pharmaceutical Co. Ltd., Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Minoru Ito
- Watarase Research Center, Kyorin Pharmaceutical Co. Ltd., Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Yunike Akasaka
- Watarase Research Center, Kyorin Pharmaceutical Co. Ltd., Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Michiaki Nagasawa
- Watarase Research Center, Kyorin Pharmaceutical Co. Ltd., Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Tomohiro Ide
- Watarase Research Center, Kyorin Pharmaceutical Co. Ltd., Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Naoki Omae
- Watarase Research Center, Kyorin Pharmaceutical Co. Ltd., Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Kazuhisa Nakao
- Watarase Research Center, Kyorin Pharmaceutical Co. Ltd., Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Makoto Rembutsu
- Watarase Research Center, Kyorin Pharmaceutical Co. Ltd., Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Maki Iwago
- Watarase Research Center, Kyorin Pharmaceutical Co. Ltd., Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Aki Yonezawa
- Watarase Research Center, Kyorin Pharmaceutical Co. Ltd., Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Yusei Hosokawa
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
| | - Tetsuya Hosooka
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
| | - Wataru Ogawa
- Division of Diabetes and Endocrinology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
| | - Koji Murakami
- Watarase Research Center, Kyorin Pharmaceutical Co. Ltd., Shimotsuga-gun, Tochigi 329-0114, Japan
- Corresponding author
| |
Collapse
|
45
|
Lien ST, Lin TE, Hsieh JH, Sung TY, Chen JH, Hsu KC. Establishment of extensive artificial intelligence models for kinase inhibitor prediction: Identification of novel PDGFRB inhibitors. Comput Biol Med 2023; 156:106722. [PMID: 36878123 DOI: 10.1016/j.compbiomed.2023.106722] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/16/2023] [Accepted: 02/26/2023] [Indexed: 03/06/2023]
Abstract
Identifying hit compounds is an important step in drug development. Unfortunately, this process continues to be a challenging task. Several machine learning models have been generated to aid in simplifying and improving the prediction of candidate compounds. Models tuned for predicting kinase inhibitors have been established. However, an effective model can be limited by the size of the chosen training dataset. In this study, we tested several machine learning models to predict potential kinase inhibitors. A dataset was curated from a number of publicly available repositories. This resulted in a comprehensive dataset covering more than half of the human kinome. More than 2,000 kinase models were established using different model approaches. The performances of the models were compared, and the Keras-MLP model was determined to be the best performing model. The model was then used to screen a chemical library for potential inhibitors targeting platelet-derived growth factor receptor-β (PDGFRB). Several PDGFRB candidates were selected, and in vitro assays confirmed four compounds with PDGFRB inhibitory activity and IC50 values in the nanomolar range. These results show the effectiveness of machine learning models trained on the reported dataset. This report would aid in the establishment of machine learning models as well as in the discovery of novel kinase inhibitors.
Collapse
Affiliation(s)
- Ssu-Ting Lien
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Tony Eight Lin
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan; Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Jui-Hua Hsieh
- Division of Translational Toxicology, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, USA
| | - Tzu-Ying Sung
- Biomedical Translation Research Center, Academia Sinica, Taipei, Taiwan
| | - Jun-Hong Chen
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Kai-Cheng Hsu
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan; Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan; Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan; Cancer Center, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan; TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, Taiwan; TMU Research Center of Drug Discovery, Taipei Medical University, Taipei, Taiwan.
| |
Collapse
|
46
|
Liang Y, Zheng Y, Yang J, Ke J, Cheng K. Design, synthesis and bioactivity evaluation of a series of quinazolinone derivatives as potent PI3Kγ antagonist. Bioorg Med Chem 2023; 84:117261. [PMID: 37011446 DOI: 10.1016/j.bmc.2023.117261] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 03/17/2023] [Accepted: 03/24/2023] [Indexed: 04/05/2023]
Abstract
Targeting PI3Kγ would be a useful strategy for treating inflammatory and cancer diseases. However, the development of selective inhibitors of PI3Kγ is very challenging due to the high structural and sequence homology with other PI3K isoforms. A series of quinazolinone derivatives were designed, synthesized and biologically evaluated as PI3Kγ-selective inhibitors. Among all the 28 compounds, compound 9b was found to be the most potent selective inhibitor with IC50 values of 13.11 nM against PI3Kγ kinase. Additionally, compound 9b could generate toxicity on leukemia cells in a panel of 12 different of cancer cell lines with the IC50 value of 2.41 ± 0.11 μM on Jurkat cell. Preliminary mechanism studies indicated that compound 9b through inhibit the activity of PI3K-AKT in human and murine leukemia cells, and activated phosphorylated p38 and phosphorylated ERK presented potent antiproliferative activity, which provided a potent small molecule for further cancer therapy.
Collapse
Affiliation(s)
- Yuqing Liang
- Guangdong Provincial Key Laboratory of New Drug Screening and Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yanjun Zheng
- Guangdong Provincial Key Laboratory of New Drug Screening and Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Junjie Yang
- Guangdong Provincial Key Laboratory of New Drug Screening and Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jiahua Ke
- Guangdong Provincial Key Laboratory of New Drug Screening and Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Kui Cheng
- Guangdong Provincial Key Laboratory of New Drug Screening and Guangzhou Key Laboratory of Drug Research for Emerging Virus Prevention and Treatment, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China.
| |
Collapse
|
47
|
Duque MAL, Vallavoju N, Woo CM. Chemical tools for the opioids. Mol Cell Neurosci 2023; 125:103845. [PMID: 36948231 DOI: 10.1016/j.mcn.2023.103845] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/09/2023] [Accepted: 03/15/2023] [Indexed: 03/24/2023] Open
Abstract
The opioids are potent and widely used pain management medicines despite also possessing severe liabilities that have fueled the opioid crisis. The pharmacological properties of the opioids primarily derive from agonism or antagonism of the opioid receptors, but additional effects may arise from specific compounds, opioid receptors, or independent targets. The study of the opioids, their receptors, and the development of remediation strategies has benefitted from derivatization of the opioids as chemical tools. While these studies have primarily focused on the opioids in the context of the opioid receptors, these chemical tools may also play a role in delineating mechanisms that are independent of the opioid receptors. In this review, we describe recent advances in the development and applications of opioid derivatives as chemical tools and highlight opportunities for the future.
Collapse
Affiliation(s)
- Mark Anthony Leon Duque
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, MA 02138, United States of America
| | - Nandini Vallavoju
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, MA 02138, United States of America
| | - Christina M Woo
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, MA 02138, United States of America.
| |
Collapse
|
48
|
Cho O, Lee JW, Kim HS, Jeong YJ, Heo TH. Chelerythrine, a novel small molecule targeting IL-2, inhibits melanoma progression by blocking the interaction between IL-2 and its receptor. Life Sci 2023; 320:121559. [PMID: 36893941 DOI: 10.1016/j.lfs.2023.121559] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/20/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023]
Abstract
AIMS In this study, we investigated the inhibition of IL-2 activity and anticancer efficacy of chelerythrine (CHE), a natural small molecule that targets IL-2 and inhibits CD25 binding, and elucidated the mechanism underlying the action of CHE on immune cells. MAIN METHODS CHE was discovered by competitive binding ELISA and SPR analysis. The effect of CHE on IL-2 activity was evaluated in CTLL-2, HEK-Blue reporter and immune cells, and in ex vivo generation of regulatory T cells (Treg cells). The antitumor activity of CHE was evaluated in B16F10 tumor-bearing C57BL/6 or BALB/c nude mice. KEY FINDINGS We identified that CHE, which acts as an IL-2 inhibitor, selectively inhibits the interaction between IL-2 and IL-2Rα and directly binds to IL-2. CHE inhibited the proliferation and signaling of CTLL-2 cells and suppressed IL-2 activity in HEK-Blue reporter and immune cells. CHE prevented the conversion of naive CD4+ T cells into CD4+CD25+Foxp3+ Treg cells in response to IL-2. CHE reduced tumor growth in C57BL/6 mice but not in T-cell-deficient mice, upregulated the expression of IFN-γ and cytotoxic molecules, and limited Foxp3 expression. Furthermore, the combination of CHE and a PD-1 inhibitor synergistically increased antitumor activity in melanoma-bearing mice and almost completely regressed the implanted tumors. SIGNIFICANCE We found that CHE, which targets IL-2 and inhibits its binding to CD25, exhibits T cell-mediated antitumor activity and that combination therapy with CHE and PD-1 inhibitor induced synergistic antitumor effects, suggesting that CHE may be a promising anticancer agent for melanoma monotherapy and combination therapy.
Collapse
|
49
|
Issmail L, Ramsbeck D, Jäger C, Henning T, Kleinschmidt M, Buchholz M, Grunwald T. Identification and evaluation of a novel tribenzamide derivative as an inhibitor targeting the entry of the respiratory syncytial virus. Antiviral Res 2023; 211:105547. [PMID: 36682463 DOI: 10.1016/j.antiviral.2023.105547] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/06/2023] [Accepted: 01/18/2023] [Indexed: 01/21/2023]
Abstract
Human respiratory syncytial virus (RSV) is the leading cause of severe lower respiratory tract infections in infants, the elderly, and the immunocompromised, yet no licensed vaccine and only limited therapeutic options for prevention and treatment are available, which poses a global health challenge and emphasizes the urgent medical need for novel antiviral agents. In the current study, a novel potent small molecule inhibitor of RSV was identified by performing a screening and structure optimization campaign, wherein a naturally occurring dicaffeoylquinic acid (DCQA) compound served as a chemical starting point. The reported benzamide derivative inhibitor, designated as 2f, was selected for its improved stability and potent antiviral activity from a series of investigated structurally related compounds. 2f was well tolerated by cells and able to inhibit RSV infection with a half maximal inhibitory concentration (IC50) of 35 nM and a favorable selectivity index (SI) of 3742. Although the exact molecular target for 2f is not known, in vitro mechanism of action investigations revealed that the compound inhibits the early stage of infection by interacting with RSV virion and interferes primarily with the attachment and potentially with the virus-cell fusion step. Moreover, intranasal administration of 2f to mice simultaneously or prior to intranasal infection with RSV significantly decreased viral load in the lungs, pointing to the in vivo potential of the compound. Our results suggest that 2f is a viable candidate for further preclinical development and evaluation as an antiviral agent against RSV infections.
Collapse
Affiliation(s)
- Leila Issmail
- Department of Vaccines and Infection Models, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Daniel Ramsbeck
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology IZI-MWT, Halle, Saale, Germany
| | - Christian Jäger
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology IZI-MWT, Halle, Saale, Germany
| | - Tanja Henning
- Department of Vaccines and Infection Models, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Martin Kleinschmidt
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology IZI-MWT, Halle, Saale, Germany
| | - Mirko Buchholz
- Department of Drug Design and Target Validation, Fraunhofer Institute for Cell Therapy and Immunology IZI-MWT, Halle, Saale, Germany
| | - Thomas Grunwald
- Department of Vaccines and Infection Models, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany.
| |
Collapse
|
50
|
Ma H, Mu X, Tang Y, Li C, Wang Y, Lu Y, Zhou X, Li Z. Programmable multistage small-molecule nano-photosensitizer for multimodal imaging-guided photothermal therapy. Acta Biomater 2023; 157:408-416. [PMID: 36549634 DOI: 10.1016/j.actbio.2022.12.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
Abstract
Photothermal therapy has become a promising approach as precision medicine to allow spatial control of therapeutic effect only in the site of interest. However, the full potential of PTT has not been realized due to the lack of simple photosensitizers (PSs) that can overcome multistage biological barriers and improve theranostic efficiency. Here, we develop a small molecule-based PS to enhance tumor-specific PTT by programming multistage transport and activation properties in molecular architecture. This PS can self-assemble into stable nanoparticles that accumulate passively in tumor, and then actively internalize through ligand-mediated endocytosis. Subsequently, the programmable degradable linkers are selectively cleaved, enabling size shrinkage for better tumor penetration, binding albumin to enhance the near-infrared fluorescence for low-background imaging, and activating photothermal conversion for tumor suppression. The self-delivery process can be programmed, representing the first multistage small-molecule nano-photosensitizer that overcomes multiple biological barriers and improves the PTT index of tumor. STATEMENT OF SIGNIFICANCE: Photothermal therapy has become a promising approach as precision medicine, but has not been realized due to the lack of simple photosensitizers that can overcome multistage biological barriers and improve theranostic efficiency. In this contribution, we solve this dilemma by developing a small molecule-based photosensitizer by programming multistage transport and activation properties in molecular architecture, which could self-assemble into stable nanoparticles that accumulate passively in tumor, and actively internalized through ligand-mediated endocytosis. Subsequently, the programmable activation by ROS triggered size reduction for tumor penetration and minimized the phototoxicity to normal tissue. The activatable fluorescence and photothermal properties made the photosensitizer intrinsically suitable for multimodal imaging-guided PTT, providing a promising supramolecular nanomedicine towards tumor precise diagnosis and therapy.
Collapse
Affiliation(s)
- Huihui Ma
- Key Lab of Biobased Polymer Materials of Shandong Provincial Education Department, College of Polymer Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Xueluer Mu
- Key Lab of Biobased Polymer Materials of Shandong Provincial Education Department, College of Polymer Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Ying Tang
- Key Lab of Biobased Polymer Materials of Shandong Provincial Education Department, College of Polymer Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Chunfeng Li
- Key Lab of Biobased Polymer Materials of Shandong Provincial Education Department, College of Polymer Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Yukun Wang
- Key Lab of Biobased Polymer Materials of Shandong Provincial Education Department, College of Polymer Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Yingxi Lu
- College of Material Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Xianfeng Zhou
- Key Lab of Biobased Polymer Materials of Shandong Provincial Education Department, College of Polymer Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China.
| | - Zhibo Li
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China.
| |
Collapse
|