1
|
Tong L, Chen Z, Li Y, Wang X, Yang C, Li Y, Zhu Y, Lu Y, Liu Q, Xu N, Shao S, Wu L, Zhang P, Wu G, Wu X, Chen X, Fang J, Jia R, Xu T, Li B, Zheng L, Liu J, Tong X. Transketolase promotes MAFLD by limiting inosine-induced mitochondrial activity. Cell Metab 2024; 36:1013-1029.e5. [PMID: 38547864 DOI: 10.1016/j.cmet.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 01/10/2024] [Accepted: 03/06/2024] [Indexed: 05/12/2024]
Abstract
Metabolic dysfunction-associated fatty liver disease (MAFLD) has a global prevalence of about 25% and no approved therapy. Using metabolomic and proteomic analyses, we identified high expression of hepatic transketolase (TKT), a metabolic enzyme of the pentose phosphate pathway, in human and mouse MAFLD. Hyperinsulinemia promoted TKT expression through the insulin receptor-CCAAT/enhancer-binding protein alpha axis. Utilizing liver-specific TKT overexpression and knockout mouse models, we demonstrated that TKT was sufficient and required for MAFLD progression. Further metabolic flux analysis revealed that Tkt deletion increased hepatic inosine levels to activate the protein kinase A-cAMP response element binding protein cascade, promote phosphatidylcholine synthesis, and improve mitochondrial function. Moreover, insulin induced hepatic TKT to limit inosine-dependent mitochondrial activity. Importantly, N-acetylgalactosamine (GalNAc)-siRNA conjugates targeting hepatic TKT showed promising therapeutic effects on mouse MAFLD. Our study uncovers how hyperinsulinemia regulates TKT-orchestrated inosine metabolism and mitochondrial function and provides a novel therapeutic strategy for MAFLD prevention and treatment.
Collapse
Affiliation(s)
- Lingfeng Tong
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Zhangbing Chen
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yangyang Li
- Unit of Immune and Metabolic Regulation, School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
| | - Xinxia Wang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Changjie Yang
- Department of Liver Surgery, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yakui Li
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yemin Zhu
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ying Lu
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Qi Liu
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Nannan Xu
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Sijia Shao
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lifang Wu
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ping Zhang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Guangyu Wu
- Department of Radiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Xiaoyu Wu
- Key Laboratory of Pediatric Hematology and Oncology, Ministry of Health, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Xiaosong Chen
- Department of Liver Surgery, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Junwei Fang
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, National Clinical Research Center for Eye Diseases, Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai 200032, China
| | - Renbing Jia
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Tianle Xu
- Center for Brain Science of Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200062, China; Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Bin Li
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Liang Zheng
- Key Laboratory of Pediatric Hematology and Oncology, Ministry of Health, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Junling Liu
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Shanghai Synvida Biotechnology Co., Ltd, Shanghai, China.
| | - Xuemei Tong
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| |
Collapse
|
2
|
Krug A, Tosolini M, Madji Hounoum B, Fournié JJ, Geiger R, Pecoraro M, Emond P, Gaulard P, Lemonnier F, Ricci JE, Verhoeyen E. Inhibition of choline metabolism in an angioimmunoblastic T-cell lymphoma preclinical model reveals a new metabolic vulnerability as possible target for treatment. J Exp Clin Cancer Res 2024; 43:43. [PMID: 38321568 PMCID: PMC10845598 DOI: 10.1186/s13046-024-02952-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 01/10/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND Angioimmunoblastic T-cell lymphoma (AITL) is a malignancy with very poor survival outcome, in urgent need of more specific therapeutic strategies. The drivers of malignancy in this disease are CD4+ follicular helper T cells (Tfh). The metabolism of these malignant Tfh cells was not yet elucidated. Therefore, we decided to identify their metabolic requirements with the objective to propose a novel therapeutic option. METHODS To reveal the prominent metabolic pathways used by the AITL lymphoma cells, we relied on metabolomic and proteomic analysis of murine AITL (mAITL) T cells isolated from our established mAITL model. We confirmed these results using AITL patient and healthy T cell expression data. RESULTS Strikingly, the mAITL Tfh cells were highly dependent on the second branch of the Kennedy pathway, the choline lipid pathway, responsible for the production of the major membrane constituent phosphatidylcholine. Moreover, gene expression data from Tfh cells isolated from AITL patient tumors, confirmed the upregulation of the choline lipid pathway. Several enzymes involved in this pathway such as choline kinase, catalyzing the first step in the phosphatidylcholine pathway, are upregulated in multiple tumors other than AITL. Here we showed that treatment of our mAITL preclinical mouse model with a fatty acid oxydation inhibitor, significantly increased their survival and even reverted the exhausted CD8 T cells in the tumor into potent cytotoxic anti-tumor cells. Specific inhibition of Chokα confirmed the importance of the phosphatidylcholine production pathway in neoplastic CD4 + T cells, nearly eradicating mAITL Tfh cells from the tumors. Finally, the same inhibitor induced in human AITL lymphoma biopsies cell death of the majority of the hAITL PD-1high neoplastic cells. CONCLUSION Our results suggest that interfering with choline metabolism in AITL reveals a specific metabolic vulnerability and might represent a new therapeutic strategy for these patients.
Collapse
Affiliation(s)
- Adrien Krug
- Université Côte d'Azur, INSERM, C3M, 06204, Nice, France
- Equipe Labellisée Ligue Contre Le Cancer, 06204, Nice, France
| | - Marie Tosolini
- Centre de Recherches en Cancérologie de Toulouse, CRCT, Université de Toulouse, CNRS, Université Toulouse III-Paul Sabatier, Inserm, Toulouse, France
| | - Blandine Madji Hounoum
- Université Côte d'Azur, INSERM, C3M, 06204, Nice, France
- Equipe Labellisée Ligue Contre Le Cancer, 06204, Nice, France
| | - Jean-Jacques Fournié
- Centre de Recherches en Cancérologie de Toulouse, CRCT, Université de Toulouse, CNRS, Université Toulouse III-Paul Sabatier, Inserm, Toulouse, France
- Labex TOUCAN, Toulouse, France
| | - Roger Geiger
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana, Bellinzona, Switzerland
- Institute of Oncology Research (IOR), Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Matteo Pecoraro
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana, Bellinzona, Switzerland
| | - Patrick Emond
- UMR iBrain, Université de Tours, Inserm, Tours, France
| | - Philippe Gaulard
- Université Paris-Est Créteil, Institut Mondor de Recherche Biomedicale, Creteil, INSERMU955, France
- AP-HP, Groupe Hospitalo-Universitaire Chenevier Mondor, Département de Pathologie, 94010, Créteil, France
| | - François Lemonnier
- Université Paris-Est Créteil, Institut Mondor de Recherche Biomedicale, Creteil, INSERMU955, France
- AP-HP, Groupe Hospitalo-Universitaire Chenevier Mondor, Service Unité Hémopathies Lymphoides, 94010, Créteil, France
| | - Jean-Ehrland Ricci
- Université Côte d'Azur, INSERM, C3M, 06204, Nice, France
- Equipe Labellisée Ligue Contre Le Cancer, 06204, Nice, France
| | - Els Verhoeyen
- Université Côte d'Azur, INSERM, C3M, 06204, Nice, France.
- Equipe Labellisée Ligue Contre Le Cancer, 06204, Nice, France.
- CIRI, Université de Lyon, INSERM U1111, ENS de Lyon, University Lyon1, CNRS, UMR5308, Lyon, 69007, France.
| |
Collapse
|
3
|
Ueno H, Sano M, Hara M, Noji H. Digital Cascade Assays for ADP- or ATP-Producing Enzymes Using a Femtoliter Reactor Array Device. ACS Sens 2023; 8:3400-3407. [PMID: 37590841 PMCID: PMC10521141 DOI: 10.1021/acssensors.3c00587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 07/31/2023] [Indexed: 08/19/2023]
Abstract
Digital enzyme assays are emerging biosensing methods for highly sensitive quantitative analysis of biomolecules with single-molecule detection sensitivity. However, current digital enzyme assays require a fluorogenic substrate for detection, which limits the applicability of this method to certain enzymes. ATPases and kinases are representative enzymes for which fluorogenic substrates are not available; however, these enzymes form large domains and play a central role in biology. In this study, we implemented a fluorogenic cascade reaction in a femtoliter reactor array device to develop a digital bioassay platform for ATPases and kinases. The digital cascade assay enabled quantitative measurement of the single-molecule activity of F1-ATPase, the catalytic portion of ATP synthase. We also demonstrated a digital assay for human choline kinase α. Furthermore, we developed a digital cascade assay for ATP-synthesizing enzymes and demonstrated a digital assay for pyruvate kinase. These results show the high versatility of this assay platform. Thus, the digital cascade assay has great potential for the highly sensitive detection and accurate characterization of various ADP- and ATP-producing enzymes, such as kinases, which may serve as disease biomarkers.
Collapse
Affiliation(s)
| | - Mio Sano
- Department of Applied Chemistry,
Graduate School of Engineering, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Digital Bioanalysis Laboratory, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Mayu Hara
- Department of Applied Chemistry,
Graduate School of Engineering, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Digital Bioanalysis Laboratory, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | | |
Collapse
|
4
|
Wang X, Zhang J, Zheng K, Du Q, Wang G, Huang J, Zhou Y, Li Y, Jin H, He J. Discovering metabolic vulnerability using spatially resolved metabolomics for antitumor small molecule-drug conjugates development as a precise cancer therapy strategy. J Pharm Anal 2023; 13:776-787. [PMID: 37577390 PMCID: PMC10422108 DOI: 10.1016/j.jpha.2023.02.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 02/19/2023] [Accepted: 02/23/2023] [Indexed: 03/04/2023] Open
Abstract
Against tumor-dependent metabolic vulnerability is an attractive strategy for tumor-targeted therapy. However, metabolic inhibitors are limited by the drug resistance of cancerous cells due to their metabolic plasticity and heterogeneity. Herein, choline metabolism was discovered by spatially resolved metabolomics analysis as metabolic vulnerability which is highly active in different cancer types, and a choline-modified strategy for small molecule-drug conjugates (SMDCs) design was developed to fool tumor cells into indiscriminately taking in choline-modified chemotherapy drugs for targeted cancer therapy, instead of directly inhibiting choline metabolism. As a proof-of-concept, choline-modified SMDCs were designed, screened, and investigated for their druggability in vitro and in vivo. This strategy improved tumor targeting, preserved tumor inhibition and reduced toxicity of paclitaxel, through targeted drug delivery to tumor by highly expressed choline transporters, and site-specific release by carboxylesterase. This study expands the strategy of targeting metabolic vulnerability and provides new ideas of developing SMDCs for precise cancer therapy.
Collapse
Affiliation(s)
- Xiangyi Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
- NMPA Key Laboratory of Safety Research and Evaluation of Innovative Drug, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Jin Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
- NMPA Key Laboratory of Safety Research and Evaluation of Innovative Drug, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Kailu Zheng
- Beijing Key Laboratory of New Drug Mechanisms and Pharmacological Evaluation Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Qianqian Du
- Beijing Key Laboratory of New Drug Mechanisms and Pharmacological Evaluation Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Guocai Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
- NMPA Key Laboratory of Safety Research and Evaluation of Innovative Drug, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Jianpeng Huang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
- NMPA Key Laboratory of Safety Research and Evaluation of Innovative Drug, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Yanhe Zhou
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
- NMPA Key Laboratory of Safety Research and Evaluation of Innovative Drug, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Yan Li
- Beijing Key Laboratory of New Drug Mechanisms and Pharmacological Evaluation Study, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Hongtao Jin
- NMPA Key Laboratory of Safety Research and Evaluation of Innovative Drug, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
- New Drug Safety Evaluation Center, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Jiuming He
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
- NMPA Key Laboratory of Safety Research and Evaluation of Innovative Drug, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| |
Collapse
|
5
|
Luque-Navarro PM, Carrasco-Jiménez MP, Goracci L, Paredes JM, Espinar-Barranco L, Valverde-Pozo J, Torretta A, Parisini E, Mariotto E, Marchioro C, Laso A, Marco C, Viola G, Lanari D, López Cara LC. New bioisosteric sulphur-containing choline kinase inhibitors with a tracked mode of action. Eur J Med Chem 2023; 246:115003. [PMID: 36493617 DOI: 10.1016/j.ejmech.2022.115003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Since the identification of human choline kinase as a protein target against cancer progression, many compounds have been designed to inhibit its function and reduce the biosynthesis of phosphatidylcholine. Herein, we propose a series of bioisosteric inhibitors that are based on the introduction of sulphur and feature improved activity and lipophilic/hydrophilic balance. The evaluation of the inhibitory and of the antiproliferative properties of the PL (dithioethane) and FP (disulphide) libraries led to the identification of PL 48, PL 55 and PL 69 as the most active compounds of the series. Docking analysis using FLAP suggests that for hits to leads, binding mostly involves an interaction with the Mg2+ cofactor, or its destabilization. The most active compounds of the two series are capable of inducing apoptosis following the mitochondrial pathway and to significantly reduce the expression of anti-apoptotic proteins such as the Mcl-1. The fluorescence properties of the compounds of the PL library allowed the tracking of their mode of action, while PAINS (Pan Assays Interference Structures) filtration databases suggest the lack of any unspecific biological response.
Collapse
Affiliation(s)
- Pilar M Luque-Navarro
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, University of Granada, Campus of Cartuja s/n, Granada, 18071, Spain; Department of Pharmaceutical Sciences, University of Perugia, Perugia, 06123 Italy
| | - M Paz Carrasco-Jiménez
- Department of Biochemistry and Molecular Biology I, University of Granada, Campus of Fuentenueva s/n, Granada, 18071, Spain.
| | - Laura Goracci
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, 06123, Italy
| | - Jose M Paredes
- Department of Physical-Chemistry, Faculty of Pharmacy, University of Granada, Campus of Cartuja s/n, Granada, 18071, Spain
| | - Laura Espinar-Barranco
- Department of Physical-Chemistry, Faculty of Pharmacy, University of Granada, Campus of Cartuja s/n, Granada, 18071, Spain
| | - Javier Valverde-Pozo
- Department of Physical-Chemistry, Faculty of Pharmacy, University of Granada, Campus of Cartuja s/n, Granada, 18071, Spain
| | - Archimede Torretta
- Center for Nano Science and Technology @PoliMi, Istituto Italiano di Tecnologia, Via Pascoli 70/3, Milano, 20133, Italy
| | - Emilio Parisini
- Center for Nano Science and Technology @PoliMi, Istituto Italiano di Tecnologia, Via Pascoli 70/3, Milano, 20133, Italy; Department of Biotechnology, Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV, 1006, Latvia; Department of Chemistry "G. Ciamician", University of Bologna, Via Selmi 2, Bologna, 40126, Italy
| | - Elena Mariotto
- Department of Woman's and Child's Health, Laboratory of Oncohematology, University of Padova, Padova, 35128, Italy
| | - Chiara Marchioro
- Department of Woman's and Child's Health, Laboratory of Oncohematology, University of Padova, Padova, 35128, Italy
| | - Alejandro Laso
- Department of Biochemistry and Molecular Biology I, University of Granada, Campus of Fuentenueva s/n, Granada, 18071, Spain
| | - Carmen Marco
- Department of Biochemistry and Molecular Biology I, University of Granada, Campus of Fuentenueva s/n, Granada, 18071, Spain
| | - Giampietro Viola
- Department of Woman's and Child's Health, Laboratory of Oncohematology, University of Padova, Padova, 35128, Italy; Istituto di Ricerca Pediatrica (IRP) Fondazione Città della Speranza, Corso Stati Uniti 4, Padova, 35128, Italy.
| | - Daniela Lanari
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, 06123 Italy.
| | - Luisa Carlota López Cara
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, University of Granada, Campus of Cartuja s/n, Granada, 18071, Spain.
| |
Collapse
|
6
|
Zou Y, Huang L, Sun S, Yue F, Li Z, Ma Y, Ma H. Choline Kinase Alpha Promoted Glioma Development by Activating PI3K/AKT Signaling Pathway. Cancer Biother Radiopharm 2021. [PMID: 34788108 DOI: 10.1089/cbr.2021.0294] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Objective: The most commonly reported primary brain tumor in adults is glioma. Choline kinase alpha (CHKA) has been proved to play important roles in glioma. However, the mechanism of CHKA involved remains unclear. Therefore, this study aims to explore the mechanism of CHKA in glioma development. Methods: Immunohistochemistry, qRT-PCR, and Western blot were used to detect the expression of CHKA. Flow cytometry, Cell Counting Kit-8 (CCK-8), transwell, and wound healing assays were performed to evaluate cell apoptosis, proliferation, invasion, and migration, respectively. RNA sequencing was used to explore the differentially expressed genes affected by CHKA. The enrichment analysis of gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) helped to detect the signaling pathways CHKA affected. Tumor-bearing mice were established and evaluated by TUNEL assay, Ki-67 immunohistochemistry. and hematoxylin and eosin staining. Results: CHKA increased in glioma tissues and promoted cell proliferation, invasion, and migration, while inhibiting the glioma cell apoptosis. It was also showed that CHKA promoted glioma development in vivo. GO and KEGG analysis indicated that PI3K/AKT was significantly enriched in CHKA knockdown U251 cells. And CHKA promoted glioma development by activating PI3K/AKT signaling pathway. Conclusions: The authors demonstrated that CHKA was significantly elevated in glioma tissues. Mechanism analysis indicated that CHKA could promote glioma development by activating PI3K/AKT signaling pathway, suggesting that CHKA is promising to be a biomarker and therapeutic strategy for prognostic prediction of patients with glioma.
Collapse
Affiliation(s)
- Yourui Zou
- Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Ling Huang
- School of Clinical Medicine, Ningxia Medical University, Yinchuan, China
| | - Shengyu Sun
- Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Fangqian Yue
- School of Clinical Medicine, Ningxia Medical University, Yinchuan, China
| | - Zhuoqi Li
- School of Clinical Medicine, Ningxia Medical University, Yinchuan, China
| | - Yue Ma
- School of Clinical Medicine, Ningxia Medical University, Yinchuan, China
| | - Hui Ma
- Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, China
| |
Collapse
|
7
|
Quartieri F, Nesi M, Avanzi NR, Borghi D, Casale E, Corti E, Cucchi U, Donati D, Fasolini M, Felder ER, Galvani A, Giorgini ML, Lomolino A, Menichincheri M, Orrenius C, Perrera C, Re Depaolini S, Riccardi-Sirtori F, Salsi E, Isacchi A, Gnocchi P. Identification of unprecedented ATP-competitive choline kinase inhibitors. Bioorg Med Chem Lett 2021; 51:128310. [PMID: 34416377 DOI: 10.1016/j.bmcl.2021.128310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/22/2021] [Accepted: 08/03/2021] [Indexed: 10/20/2022]
Abstract
In this article we describe the identification of unprecedented ATP-competitive ChoKα inhibitors starting from initial hit NMS-P830 that binds to ChoKα in an ATP concentration-dependent manner. This result is confirmed by the co-crystal structure of NMS-P830 in complex with Δ75-ChoKα. NMS-P830 is able to inhibit ChoKα in cells resulting in the reduction of intracellular phosphocholine formation. A structure-based medicinal chemistry program resulted in the identification of selective compounds that have good biochemical activity, solubility and metabolic stability and are suitable for further optimization. The ChoKα inhibitors disclosed in this article demonstrate for the first time the possibility to inhibit ChoKα with ATP-competitive compounds.
Collapse
Affiliation(s)
- Francesca Quartieri
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy.
| | - Marcella Nesi
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy
| | - Nilla R Avanzi
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy
| | - Daniela Borghi
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy
| | - Elena Casale
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy
| | - Emiliana Corti
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy
| | - Ulisse Cucchi
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy
| | - Daniele Donati
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy
| | - Marina Fasolini
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy
| | - Eduard R Felder
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy
| | - Arturo Galvani
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy
| | - Maria L Giorgini
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy
| | - Antonio Lomolino
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy
| | | | - Christian Orrenius
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy
| | - Claudia Perrera
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy
| | | | | | - Enea Salsi
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy
| | - Antonella Isacchi
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy
| | - Paola Gnocchi
- Nerviano Medical Sciences Srl, Viale Pasteur 10, 20014 Nerviano (MI), Italy
| |
Collapse
|
8
|
Nussinov R, Zhang M, Maloney R, Tsai CJ, Yavuz BR, Tuncbag N, Jang H. Mechanism of activation and the rewired network: New drug design concepts. Med Res Rev 2021; 42:770-799. [PMID: 34693559 PMCID: PMC8837674 DOI: 10.1002/med.21863] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/06/2021] [Accepted: 10/07/2021] [Indexed: 12/13/2022]
Abstract
Precision oncology benefits from effective early phase drug discovery decisions. Recently, drugging inactive protein conformations has shown impressive successes, raising the cardinal questions of which targets can profit and what are the principles of the active/inactive protein pharmacology. Cancer driver mutations have been established to mimic the protein activation mechanism. We suggest that the decision whether to target an inactive (or active) conformation should largely rest on the protein mechanism of activation. We next discuss the recent identification of double (multiple) same-allele driver mutations and their impact on cell proliferation and suggest that like single driver mutations, double drivers also mimic the mechanism of activation. We further suggest that the structural perturbations of double (multiple) in cis mutations may reveal new surfaces/pockets for drug design. Finally, we underscore the preeminent role of the cellular network which is deregulated in cancer. Our structure-based review and outlook updates the traditional Mechanism of Action, informs decisions, and calls attention to the intrinsic activation mechanism of the target protein and the rewired tumor-specific network, ushering innovative considerations in precision medicine.
Collapse
Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA.,Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Mingzhen Zhang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA
| | - Ryan Maloney
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA
| | - Bengi Ruken Yavuz
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Nurcan Tuncbag
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey.,Department of Chemical and Biological Engineering, College of Engineering, Koc University, Istanbul, Turkey.,Koc University Research Center for Translational Medicine, School of Medicine, Koc University, Istanbul, Turkey
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA
| |
Collapse
|
9
|
Schiaffino-Ortega S, Mariotto E, Luque-Navarro PM, Kimatrai-Salvador M, Rios-Marco P, Hurtado-Guerrero R, Marco C, Carrasco-Jimenez MP, Viola G, López-Cara LC. Anticancer and Structure Activity Relationship of Non-Symmetrical Choline Kinase Inhibitors. Pharmaceutics 2021; 13:pharmaceutics13091360. [PMID: 34575436 PMCID: PMC8464809 DOI: 10.3390/pharmaceutics13091360] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 11/21/2022] Open
Abstract
Choline kinase inhibitors are an outstanding class of cytotoxic compounds useful for the treatment of different forms of cancer since aberrant choline metabolism is a feature of neoplastic cells. Here, we present the most in-depth structure-activity relationship studies of an interesting series of non-symmetric choline kinase inhibitors previously reported by our group: 3a–h and 4a–h. They are characterized by cationic heads of 3-aminophenol bound to 4-(dimethylamino)- or 4-(pyrrolidin-1-yl)pyridinium through several linkers. These derivatives were evaluated both for their inhibitory activity on the enzyme and their antiproliferative activity in a panel of six human tumor cell lines. The compounds with the N-atom connected to the linker (4a–h) show the best inhibitory results, in the manner of results supported by docking studies. On the contrary, the best antiproliferative compounds were those with the O-atom bounded to the linker (3a–h). On the other hand, as was predictable in both families, the inhibitory effect on the enzyme is better the shorter the length of the linker. However, in tumor cells, lipophilicity and choline uptake inhibition could play a decisive role. Interestingly, compounds 3c and 4f, selected for both their ability to inhibit the enzyme and good antiproliferative activity, are endowed with low toxicity in non-tumoral cells (e.g., human peripheral lymphocytes) concerning cancer cells. These compounds were also able to induce apoptosis in Jurkat leukemic cells without causing significant variations of the cell cycle. It is worth mentioning that these derivatives, besides their inhibitory effect on choline kinase, displayed a modest ability to inhibit choline uptake thus suggesting that this mechanism may also contribute to the observed cytotoxicity.
Collapse
Affiliation(s)
- Santiago Schiaffino-Ortega
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain; (S.S.-O.); (P.M.L.-N.); (M.K.-S.)
| | - Elena Mariotto
- Laboratory of Oncohematology, Department of Woman’s and Child’s Health, University of Padova, 35128 Padova, Italy;
| | - Pilar María Luque-Navarro
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain; (S.S.-O.); (P.M.L.-N.); (M.K.-S.)
| | - María Kimatrai-Salvador
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain; (S.S.-O.); (P.M.L.-N.); (M.K.-S.)
| | - Pablo Rios-Marco
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, 18071 Granada, Spain; (P.R.-M.); (C.M.)
| | - Ramon Hurtado-Guerrero
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, University of Zaragoza, 50018 Zaragoza, Spain;
| | - Carmen Marco
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, 18071 Granada, Spain; (P.R.-M.); (C.M.)
| | - María Paz Carrasco-Jimenez
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, 18071 Granada, Spain; (P.R.-M.); (C.M.)
- Correspondence: (M.P.C.-J.); (G.V.); (L.C.L.-C.); Tel.: +34-958-243-248 (M.P.C.-J.); +34-958-243-849 (L.C.L.-C.)
| | - Giampietro Viola
- Laboratory of Oncohematology, Department of Woman’s and Child’s Health, University of Padova, 35128 Padova, Italy;
- Correspondence: (M.P.C.-J.); (G.V.); (L.C.L.-C.); Tel.: +34-958-243-248 (M.P.C.-J.); +34-958-243-849 (L.C.L.-C.)
| | - Luisa Carlota López-Cara
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain; (S.S.-O.); (P.M.L.-N.); (M.K.-S.)
- Correspondence: (M.P.C.-J.); (G.V.); (L.C.L.-C.); Tel.: +34-958-243-248 (M.P.C.-J.); +34-958-243-849 (L.C.L.-C.)
| |
Collapse
|
10
|
Wang N, Brickute D, Braga M, Barnes C, Lu H, Allott L, Aboagye EO. Novel Non-Congeneric Derivatives of the Choline Kinase Alpha Inhibitor ICL-CCIC-0019. Pharmaceutics 2021; 13:1078. [PMID: 34371769 PMCID: PMC8309005 DOI: 10.3390/pharmaceutics13071078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/06/2021] [Accepted: 07/09/2021] [Indexed: 01/07/2023] Open
Abstract
Choline kinase alpha (CHKA) is a promising target for the development of cancer therapeutics. We have previously reported ICL-CCIC-0019, a potent CHKA inhibitor with high cellular activity but with some unfavorable pharmacological properties. In this work, we present an active analogue of ICL-CCIC-0019 bearing a piperazine handle (CK146) to facilitate further structural elaboration of the pharmacophore and thus improve the biological profile. Two different strategies were evaluated in this study: (1) a prodrug approach whereby selective CHKA inhibition could be achieved through modulating the activity of CK146, via the incorporation of an ε-(Ac) Lys motif, cleavable by elevated levels of histone deacetylase (HDAC) and cathepsin L (CTSL) in tumour cells; (2) a prostate-specific membrane antigen (PSMA) receptor targeted delivery strategy. Prodrug (CK145) and PSMA-targeted (CK147) derivatives were successfully synthesized and evaluated in vitro. While the exploitation of CK146 in those two strategies did not deliver the expected results, important and informative structure-activity relationships were observed and have been reported.
Collapse
Affiliation(s)
- Ning Wang
- Comprehensive Cancer Imaging Centre, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London W12 0NN, UK; (N.W.); (D.B.); (M.B.); (C.B.); (H.L.)
| | - Diana Brickute
- Comprehensive Cancer Imaging Centre, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London W12 0NN, UK; (N.W.); (D.B.); (M.B.); (C.B.); (H.L.)
| | - Marta Braga
- Comprehensive Cancer Imaging Centre, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London W12 0NN, UK; (N.W.); (D.B.); (M.B.); (C.B.); (H.L.)
| | - Chris Barnes
- Comprehensive Cancer Imaging Centre, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London W12 0NN, UK; (N.W.); (D.B.); (M.B.); (C.B.); (H.L.)
| | - Haonan Lu
- Comprehensive Cancer Imaging Centre, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London W12 0NN, UK; (N.W.); (D.B.); (M.B.); (C.B.); (H.L.)
| | - Louis Allott
- Comprehensive Cancer Imaging Centre, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London W12 0NN, UK; (N.W.); (D.B.); (M.B.); (C.B.); (H.L.)
- Positron Emission Tomography Research Centre, Faculty of Health Sciences, University of Hull, Kingston upon Hull HU6 7RX, UK
| | - Eric O. Aboagye
- Comprehensive Cancer Imaging Centre, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London W12 0NN, UK; (N.W.); (D.B.); (M.B.); (C.B.); (H.L.)
| |
Collapse
|
11
|
ChoK-Full of Potential: Choline Kinase in B Cell and T Cell Malignancies. Pharmaceutics 2021; 13:pharmaceutics13060911. [PMID: 34202989 PMCID: PMC8234087 DOI: 10.3390/pharmaceutics13060911] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/09/2021] [Accepted: 06/17/2021] [Indexed: 12/20/2022] Open
Abstract
Aberrant choline metabolism, characterized by an increase in total choline-containing compounds, phosphocholine and phosphatidylcholine (PC), is a metabolic hallmark of carcinogenesis and tumor progression. This aberration arises from alterations in metabolic enzymes that control PC biosynthesis and catabolism. Among these enzymes, choline kinase α (CHKα) exhibits the most frequent alterations and is commonly overexpressed in human cancers. CHKα catalyzes the phosphorylation of choline to generate phosphocholine, the first step in de novo PC biosynthesis. CHKα overexpression is associated with the malignant phenotype, metastatic capability and drug resistance in human cancers, and thus has been recognized as a robust biomarker and therapeutic target of cancer. Of clinical importance, increased choline metabolism and CHKα activity can be detected by non-invasive magnetic resonance spectroscopy (MRS) or positron emission tomography/computed tomography (PET/CT) imaging with radiolabeled choline analogs for diagnosis and treatment monitoring of cancer patients. Both choline-based MRS and PET/CT imaging have also been clinically applied for lymphoid malignancies, including non-Hodgkin lymphoma, multiple myeloma and central nervous system lymphoma. However, information on how choline kinase is dysregulated in lymphoid malignancies is very limited and has just begun to be unraveled. In this review, we provide an overview of the current understanding of choline kinase in B cell and T cell malignancies with the goal of promoting future investigation in this area.
Collapse
|
12
|
Lacal JC, Zimmerman T, Campos JM. Choline Kinase: An Unexpected Journey for a Precision Medicine Strategy in Human Diseases. Pharmaceutics 2021; 13:788. [PMID: 34070409 PMCID: PMC8226952 DOI: 10.3390/pharmaceutics13060788] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/13/2021] [Accepted: 05/19/2021] [Indexed: 12/17/2022] Open
Abstract
Choline kinase (ChoK) is a cytosolic enzyme that catalyzes the phosphorylation of choline to form phosphorylcholine (PCho) in the presence of ATP and magnesium. ChoK is required for the synthesis of key membrane phospholipids and is involved in malignant transformation in a large variety of human tumours. Active compounds against ChoK have been identified and proposed as antitumor agents. The ChoK inhibitory and antiproliferative activities of symmetrical bispyridinium and bisquinolinium compounds have been defined using quantitative structure-activity relationships (QSARs) and structural parameters. The design strategy followed in the development of the most active molecules is presented. The selective anticancer activity of these structures is also described. One promising anticancer compound has even entered clinical trials. Recently, ChoKα inhibitors have also been proposed as a novel therapeutic approach against parasites, rheumatoid arthritis, inflammatory processes, and pathogenic bacteria. The evidence for ChoKα as a novel drug target for approaches in precision medicine is discussed.
Collapse
Affiliation(s)
- Juan Carlos Lacal
- Instituto de Investigaciones Biomédicas, CSIC, 28029 Madrid, Spain
- Instituto de Investigación Sanitaria Hospital La Paz, IDIPAZ, 28046 Madrid, Spain
| | - Tahl Zimmerman
- Food Microbiology and Biotechnology Laboratory, Department of Family and Consumer Sciences, College of Agriculture and Environmental Sciences, North Carolina University, 1601 East Market Street, Greensboro, NC 27411, USA;
| | - Joaquín M. Campos
- Departamento de Química Farmacéutica y Orgánica, Facultad de Farmacia, c/Campus de Cartuja, s/n, Universidad de Granada, 18071 Granada, Spain
- Instituto Biosanitario de Granada (ibs. GRANADA), SAS-Universidad de Granada, 18071 Granada, Spain
| |
Collapse
|
13
|
Boz E, Stein M. Accurate Receptor-Ligand Binding Free Energies from Fast QM Conformational Chemical Space Sampling. Int J Mol Sci 2021; 22:3078. [PMID: 33802920 PMCID: PMC8002627 DOI: 10.3390/ijms22063078] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/13/2021] [Accepted: 03/15/2021] [Indexed: 12/22/2022] Open
Abstract
Small molecule receptor-binding is dominated by weak, non-covalent interactions such as van-der-Waals hydrogen bonding or electrostatics. Calculating these non-covalent ligand-receptor interactions is a challenge to computational means in terms of accuracy and efficacy since the ligand may bind in a number of thermally accessible conformations. The conformational rotamer ensemble sampling tool (CREST) uses an iterative scheme to efficiently sample the conformational space and calculates energies using the semi-empirical 'Geometry, Frequency, Noncovalent, eXtended Tight Binding' (GFN2-xTB) method. This combined approach is applied to blind predictions of the modes and free energies of binding for a set of 10 drug molecule ligands to the cucurbit[n]urils CB[8] receptor from the recent 'Statistical Assessment of the Modeling of Proteins and Ligands' (SAMPL) challenge including morphine, hydromorphine, cocaine, fentanyl, and ketamine. For each system, the conformational space was sufficiently sampled for the free ligand and the ligand-receptor complexes using the quantum chemical Hamiltonian. A multitude of structures makes up the final conformer-rotamer ensemble, for which then free energies of binding are calculated. For those large and complex molecules, the results are in good agreement with experimental values with a mean error of 3 kcal/mol. The GFN2-xTB energies of binding are validated by advanced density functional theory calculations and found to be in good agreement. The efficacy of the automated QM sampling workflow allows the extension towards other complex molecular interaction scenarios.
Collapse
Affiliation(s)
| | - Matthias Stein
- Max Planck Institute for Dynamics of Complex Technical Systems, Molecular Simulations and Design Group, 39106 Magdeburg, Germany;
| |
Collapse
|