1
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Toy L, Huber ME, Lee M, Bartolomé AA, Ortiz Zacarías NV, Nasser S, Scholl S, Zlotos DP, Mandour YM, Heitman LH, Szpakowska M, Chevigné A, Schiedel M. Fluorophore-Labeled Pyrrolones Targeting the Intracellular Allosteric Binding Site of the Chemokine Receptor CCR1. ACS Pharmacol Transl Sci 2024; 7:2080-2092. [PMID: 39022357 PMCID: PMC11249626 DOI: 10.1021/acsptsci.4c00182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/18/2024] [Accepted: 06/10/2024] [Indexed: 07/20/2024]
Abstract
In this study, we describe the structure-based development of the first fluorescent ligands targeting the intracellular allosteric binding site (IABS) of the CC chemokine receptor type 1 (CCR1), a G protein-coupled receptor (GPCR) that has been pursued as a drug target in inflammation and immune diseases. Starting from previously reported intracellular allosteric modulators of CCR1, tetramethylrhodamine (TAMRA)-labeled ligands were designed, synthesized, and tested for their suitability as fluorescent tracers to probe binding to the IABS of CCR1. In the course of these studies, we developed LT166 (12) as a highly versatile fluorescent CCR1 ligand, enabling cell-free as well as cellular NanoBRET-based binding studies in a nonradioactive and high-throughput manner. Besides the detection of intracellular allosteric ligands by direct competition with 12, we were also able to monitor the binding of extracellular antagonists due to their positive cooperative binding with 12. Thereby, we provide a straightforward and nonradioactive method to easily distinguish between ligands binding to the IABS of CCR1 and extracellular negative modulators. Further, we applied 12 for the identification of novel chemotypes for intracellular CCR1 inhibition that feature high binding selectivity for CCR1 over CCR2. For one of the newly identified intracellular CCR1 ligands (i.e., 23), we were able to show CCR1 over CCR2 selectivity also on a functional level and demonstrated that this compound inhibits basal β-arrestin recruitment to CCR1, thereby acting as an inverse agonist. Thus, our fluorescent CCR1 ligand 12 represents a highly promising tool for future studies of CCR1-targeted pharmacology and drug discovery.
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Affiliation(s)
- Lara Toy
- Department
of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, Erlangen 91058, Germany
| | - Max E. Huber
- Department
of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, Erlangen 91058, Germany
| | - Minhee Lee
- Institute
of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Beethovenstraße 55, Braunschweig 38106, Germany
| | - Ana Alonso Bartolomé
- Immuno-Pharmacology
and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, Rue Henri Koch 29, Esch-sur-Alzette L-4354, Luxembourg
- Faculty
of Science, Technology and Medicine, University
of Luxembourg, 2 Avenue
de l’Université, Esch-sur-Alzette L-4365, Luxembourg
| | - Natalia V. Ortiz Zacarías
- Leiden
Academic Centre for Drug Research (LACDR), Division of Chemistry, Leiden University, Leiden 2333 CC, Netherlands
| | - Sherif Nasser
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, the German University in Cairo, New Cairo City 11835, Cairo, Egypt
| | - Stephan Scholl
- Institute
for Chemical and Thermal Process Engineering (ICTV), Technische Universität Braunschweig, Langer Kamp 7, Braunschweig 38106, Germany
| | - Darius P. Zlotos
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, the German University in Cairo, New Cairo City 11835, Cairo, Egypt
| | - Yasmine M. Mandour
- School
of Life and Medical Sciences, University
of Hertfordshire Hosted by Global Academic Foundation, New Administrative Capital, Cairo 11578, Egypt
| | - Laura H. Heitman
- Leiden
Academic Centre for Drug Research (LACDR), Division of Chemistry, Leiden University, Leiden 2333 CC, Netherlands
- Oncode
Institute, Leiden University, Leiden 2333 CC, Netherlands
| | - Martyna Szpakowska
- Immuno-Pharmacology
and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, Rue Henri Koch 29, Esch-sur-Alzette L-4354, Luxembourg
| | - Andy Chevigné
- Immuno-Pharmacology
and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, Rue Henri Koch 29, Esch-sur-Alzette L-4354, Luxembourg
| | - Matthias Schiedel
- Department
of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, Erlangen 91058, Germany
- Institute
of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Beethovenstraße 55, Braunschweig 38106, Germany
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Kayastha K, Zhou Y, Brünle S. Structural perspectives on chemokine receptors. Biochem Soc Trans 2024; 52:1011-1024. [PMID: 38856028 DOI: 10.1042/bst20230358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/02/2024] [Accepted: 05/07/2024] [Indexed: 06/11/2024]
Abstract
Chemokine receptors are integral to the immune system and prime targets in drug discovery that have undergone extensive structural elucidation in recent years. We outline a timeline of these structural achievements, discuss the intracellular negative allosteric modulation of chemokine receptors, analyze the mechanisms of orthosteric receptor activation, and report on the emerging concept of biased signaling. Additionally, we highlight differences of G-protein binding among chemokine receptors. Intracellular allosteric modulators in chemokine receptors interact with a conserved motif within transmembrane helix 7 and helix 8 and exhibit a two-fold inactivation mechanism that can be harnessed for drug-discovery efforts. Chemokine recognition is a multi-step process traditionally explained by a two-site model within chemokine recognition site 1 (CRS1) and CRS2. Recent structural studies have extended our understanding of this complex mechanism with the identification of CRS1.5 and CRS3. CRS3 is implicated in determining ligand specificity and surrounds the chemokine by almost 180°. Within CRS3 we identified the extracellular loop 2 residue 45.51 as a key interaction mediator for chemokine binding. Y2917.43 on the other hand was shown in CCR1 to be a key determinant of signaling bias which, along with specific chemokine-dependent phosphorylation ensembles at the G-protein coupled receptors (GPCR's) C-terminus, seems to play a pivotal role in determining the direction of signal bias in GPCRs.
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Affiliation(s)
- Kanwal Kayastha
- Leiden Institute of Chemistry, Faculty of Science, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Yangli Zhou
- Leiden Institute of Chemistry, Faculty of Science, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Steffen Brünle
- Leiden Institute of Chemistry, Faculty of Science, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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3
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Szwabowski GL, Griffing M, Mugabe EJ, O'Malley D, Baker LN, Baker DL, Parrill AL. G Protein-Coupled Receptor-Ligand Pose and Functional Class Prediction. Int J Mol Sci 2024; 25:6876. [PMID: 38999982 PMCID: PMC11241240 DOI: 10.3390/ijms25136876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/13/2024] [Accepted: 06/19/2024] [Indexed: 07/14/2024] Open
Abstract
G protein-coupled receptor (GPCR) transmembrane protein family members play essential roles in physiology. Numerous pharmaceuticals target GPCRs, and many drug discovery programs utilize virtual screening (VS) against GPCR targets. Improvements in the accuracy of predicting new molecules that bind to and either activate or inhibit GPCR function would accelerate such drug discovery programs. This work addresses two significant research questions. First, do ligand interaction fingerprints provide a substantial advantage over automated methods of binding site selection for classical docking? Second, can the functional status of prospective screening candidates be predicted from ligand interaction fingerprints using a random forest classifier? Ligand interaction fingerprints were found to offer modest advantages in sampling accurate poses, but no substantial advantage in the final set of top-ranked poses after scoring, and, thus, were not used in the generation of the ligand-receptor complexes used to train and test the random forest classifier. A binary classifier which treated agonists, antagonists, and inverse agonists as active and all other ligands as inactive proved highly effective in ligand function prediction in an external test set of GPR31 and TAAR2 candidate ligands with a hit rate of 82.6% actual actives within the set of predicted actives.
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Affiliation(s)
| | - Makenzie Griffing
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA
| | - Elijah J Mugabe
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA
| | - Daniel O'Malley
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA
| | - Lindsey N Baker
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA
| | - Daniel L Baker
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA
| | - Abby L Parrill
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA
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Kobayashi H, Suzuki H, Tanaka T, Kaneko MK, Kato Y. Epitope Mapping of an Anti-Mouse CCR8 Monoclonal Antibody C 8Mab-2 Using Flow Cytometry. Monoclon Antib Immunodiagn Immunother 2024. [PMID: 38836509 DOI: 10.1089/mab.2024.0002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024] Open
Abstract
The C-C motif chemokine receptor 8 (CCR8) is highly and selectively expressed in regulatory T (Treg) cells and is associated with tumor progression. The massive accumulation of Treg cells into tumors suppresses the effector function of CD8+ cells against tumor cells. Therefore, selective depletion of Treg cells using anti-CCR8 monoclonal antibodies (mAbs) reinvigorates antitumor immune responses and improves responses to cancer immunotherapy. Previously, we developed an anti-mouse CCR8 (mCCR8) mAb, C8Mab-2, using the Cell-Based Immunization and Screening method. In this study, the binding epitope of C8Mab-2 was investigated using flow cytometry. The mCCR8 extracellular domain-substituted mutant analysis showed that C8Mab-2 recognizes the N-terminal region (1-33 amino acids) of mCCR8. Next, 1×alanine (or glycine) scanning and 2×alanine (or glycine) scanning were conducted in the N-terminal region. The results revealed that the 17-DFFTAP-22 sequence is important for the recognition by C8Mab-2, and Thr20 is a central amino acid of the epitope. These results revealed the involvement of the N-terminus of mCCR8 in the recognition by C8Mab-2.
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Affiliation(s)
- Hiyori Kobayashi
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hiroyuki Suzuki
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tomohiro Tanaka
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Mika K Kaneko
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yukinari Kato
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Sendai, Japan
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Wang Y, Jin B, Wu X, Xing J, Zhang B, Chen X, Liu X, Wan X, Du S. Exploration of prognostic and treatment markers in hepatocellular carcinoma via GPCR-related genes analysis. Heliyon 2024; 10:e29659. [PMID: 38694033 PMCID: PMC11058304 DOI: 10.1016/j.heliyon.2024.e29659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 05/03/2024] Open
Abstract
Background G protein-coupled receptors (GPCRs), the biggest family of signaling receptors, account for 34 % of all the drug targets approved by the Food and Drug Administration (FDA). It has been gradually recognized that GPCRs are of significance for tumorigenesis, but in-depth studies are still required to explore specific mechanisms. In this study, the role of GPCRs in hepatocellular carcinoma (HCC) was elucidated, and GPCR-related genes were employed for building a risk-score model for the prognosis and treatment efficacy prediction of HCC patients. Methods Patients' data on HCC were sourced from the Liver Hepatocellular Carcinoma-Japan (LIRI-JP) and The Cancer Genome Atlas (TCGA) databases, while GPCR-related genes were obtained from the Molecular Signatures Database (MSigDB). Univariant and multivariant Cox regression analyses, as well as least absolute shrinkage and selection operator (LASSO) were performed with the aim of identifying differentially expressed GPCR-related genes and grouping patients. Differential expression and functional enrichment analyses were performed; protein-protein interaction (PPI) mechanisms were explored; hub genes and micro ribonucleic acid (miRNA)-target gene regulatory networks were constructed. The tumor immune dysfunction and exclusion (TIDE) algorithm was utilized to evaluate immune infiltration levels and genetic variations. Sensitivity to immunotherapy and common antitumor drugs was predicted via the database Genomics of Drug Sensitivity in Cancer (GDSC). Results A GPCR-related risk score containing eight GPCR-related genes (atypical chemokine receptor 3 (ACKR3), C-C chemokine receptor type 3 (CCR3), CCR7, frizzled homolog 5 (FZD5), metabotropic glutamate receptor 8 (GRM8), hydroxycarboxylic acid receptor 1 (HCAR1), 5-hydroxytryptamine receptor 5A (HTR5A) and nucleotide-binding oligomerization domain-like receptor family pyrin domain containing 6 (NLRP6)) was set up. In addition, patients were classified into groups with high and low risks. Patients in the high-risk group exhibited a worse prognosis but demonstrated a more favorable immunotherapy response rate compared with those in the low-risk group. Distinct sensitivity to chemotherapeutic drugs was observed. A clinical prediction model on the basis of GPCR-related risk scores was constructed. Areas under the curves (AUC) corresponding to one-, three- and five-year survival were 0.731, 0.765 and 0.731, respectively. Conclusions In this study, an efficient HCC prognostic prediction model was constructed by only GPCR-related genes, which are all potential targets for HCC treatment.
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Affiliation(s)
- Yuxin Wang
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Bao Jin
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Xiangan Wu
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Jiali Xing
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Baoluhe Zhang
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Xiaokun Chen
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Xiao Liu
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Xueshuai Wan
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Shunda Du
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
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6
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den Hollander LS, IJzerman AP, Heitman LH. Pharmacological characterization of allosteric modulators: A case for chemokine receptors. Med Res Rev 2024. [PMID: 38634664 DOI: 10.1002/med.22043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 04/03/2024] [Accepted: 04/08/2024] [Indexed: 04/19/2024]
Abstract
Chemokine receptors are relevant targets for a multitude of immunological diseases, but drug attrition for these receptors is remarkably high. While many drug discovery programs have been pursued, most prospective drugs failed in the follow-up studies due to clinical inefficacy, and hence there is a clear need for alternative approaches. Allosteric modulators of receptor function represent an excellent opportunity for novel drugs, as they modulate receptor activation in a controlled manner and display increased selectivity, and their pharmacological profile can be insurmountable. Here, we discuss allosteric ligands and their pharmacological characterization for modulation of chemokine receptors. Ligands are included if (1) they show clear signs of allosteric modulation in vitro and (2) display evidence of binding in a topologically distinct manner compared to endogenous chemokines. We discuss how allosteric ligands affect binding of orthosteric (endogenous) ligands in terms of affinity as well as binding kinetics in radioligand binding assays. Moreover, their effects on signaling events in functional assays and how their binding site can be elucidated are specified. We substantiate this with examples of published allosteric ligands targeting chemokine receptors and hypothetical graphs of pharmacological behavior. This review should serve as an effective starting point for setting up assays for characterizing allosteric ligands to develop safer and more efficacious drugs for chemokine receptors and, ultimately, other G protein-coupled receptors.
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Affiliation(s)
- Lisa S den Hollander
- Leiden Academic Centre for Drug Research, Division of Drug Discovery and Safety, Leiden, The Netherlands
| | - Adriaan P IJzerman
- Leiden Academic Centre for Drug Research, Division of Drug Discovery and Safety, Leiden, The Netherlands
| | - Laura H Heitman
- Leiden Academic Centre for Drug Research, Division of Drug Discovery and Safety, Leiden, The Netherlands
- Oncode Institute, Leiden, The Netherlands
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7
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Zhang M, Chen T, Lu X, Lan X, Chen Z, Lu S. G protein-coupled receptors (GPCRs): advances in structures, mechanisms, and drug discovery. Signal Transduct Target Ther 2024; 9:88. [PMID: 38594257 PMCID: PMC11004190 DOI: 10.1038/s41392-024-01803-6] [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: 08/15/2023] [Revised: 02/19/2024] [Accepted: 03/13/2024] [Indexed: 04/11/2024] Open
Abstract
G protein-coupled receptors (GPCRs), the largest family of human membrane proteins and an important class of drug targets, play a role in maintaining numerous physiological processes. Agonist or antagonist, orthosteric effects or allosteric effects, and biased signaling or balanced signaling, characterize the complexity of GPCR dynamic features. In this study, we first review the structural advancements, activation mechanisms, and functional diversity of GPCRs. We then focus on GPCR drug discovery by revealing the detailed drug-target interactions and the underlying mechanisms of orthosteric drugs approved by the US Food and Drug Administration in the past five years. Particularly, an up-to-date analysis is performed on available GPCR structures complexed with synthetic small-molecule allosteric modulators to elucidate key receptor-ligand interactions and allosteric mechanisms. Finally, we highlight how the widespread GPCR-druggable allosteric sites can guide structure- or mechanism-based drug design and propose prospects of designing bitopic ligands for the future therapeutic potential of targeting this receptor family.
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Affiliation(s)
- Mingyang Zhang
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ting Chen
- Department of Cardiology, Changzheng Hospital, Affiliated to Naval Medical University, Shanghai, 200003, China
| | - Xun Lu
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xiaobing Lan
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China
| | - Ziqiang Chen
- Department of Orthopedics, Changhai Hospital, Affiliated to Naval Medical University, Shanghai, 200433, China.
| | - Shaoyong Lu
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China.
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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8
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Ciechanowska A, Mika J. CC Chemokine Family Members' Modulation as a Novel Approach for Treating Central Nervous System and Peripheral Nervous System Injury-A Review of Clinical and Experimental Findings. Int J Mol Sci 2024; 25:3788. [PMID: 38612597 PMCID: PMC11011591 DOI: 10.3390/ijms25073788] [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: 02/05/2024] [Revised: 03/18/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Despite significant progress in modern medicine and pharmacology, damage to the nervous system with various etiologies still poses a challenge to doctors and scientists. Injuries lead to neuroimmunological changes in the central nervous system (CNS), which may result in both secondary damage and the development of tactile and thermal hypersensitivity. In our review, based on the analysis of many experimental and clinical studies, we indicate that the mechanisms occurring both at the level of the brain after direct damage and at the level of the spinal cord after peripheral nerve damage have a common immunological basis. This suggests that there are opportunities for similar pharmacological therapeutic interventions in the damage of various etiologies. Experimental data indicate that after CNS/PNS damage, the levels of 16 among the 28 CC-family chemokines, i.e., CCL1, CCL2, CCL3, CCL4, CCL5, CCL6, CCL7, CCL8, CCL9, CCL11, CCL12, CCL17, CCL19, CCL20, CCL21, and CCL22, increase in the brain and/or spinal cord and have strong proinflammatory and/or pronociceptive effects. According to the available literature data, further investigation is still needed for understanding the role of the remaining chemokines, especially six of them which were found in humans but not in mice/rats, i.e., CCL13, CCL14, CCL15, CCL16, CCL18, and CCL23. Over the past several years, the results of studies in which available pharmacological tools were used indicated that blocking individual receptors, e.g., CCR1 (J113863 and BX513), CCR2 (RS504393, CCX872, INCB3344, and AZ889), CCR3 (SB328437), CCR4 (C021 and AZD-2098), and CCR5 (maraviroc, AZD-5672, and TAK-220), has beneficial effects after damage to both the CNS and PNS. Recently, experimental data have proved that blockades exerted by double antagonists CCR1/3 (UCB 35625) and CCR2/5 (cenicriviroc) have very good anti-inflammatory and antinociceptive effects. In addition, both single (J113863, RS504393, SB328437, C021, and maraviroc) and dual (cenicriviroc) chemokine receptor antagonists enhanced the analgesic effect of opioid drugs. This review will display the evidence that a multidirectional strategy based on the modulation of neuronal-glial-immune interactions can significantly improve the health of patients after CNS and PNS damage by changing the activity of chemokines belonging to the CC family. Moreover, in the case of pain, the combined administration of such antagonists with opioid drugs could reduce therapeutic doses and minimize the risk of complications.
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Affiliation(s)
| | - Joanna Mika
- Department of Pain Pharmacology, Maj Institute of Pharmacology Polish Academy of Sciences, 12 Smetna Str., 31-343 Kraków, Poland;
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9
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Dawson JRD, Wadman GM, Zhang P, Tebben A, Carter PH, Gu S, Shroka T, Borrega-Roman L, Salanga CL, Handel TM, Kufareva I. Molecular determinants of antagonist interactions with chemokine receptors CCR2 and CCR5. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.15.567150. [PMID: 38014122 PMCID: PMC10680698 DOI: 10.1101/2023.11.15.567150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
By driving monocyte chemotaxis, the chemokine receptor CCR2 shapes inflammatory responses and the formation of tumor microenvironments. This makes it a promising target in inflammation and immuno-oncology; however, despite extensive efforts, there are no FDA-approved CCR2-targeting therapeutics. Cited challenges include the redundancy of the chemokine system, suboptimal properties of compound candidates, and species differences that confound the translation of results from animals to humans. Structure-based drug design can rationalize and accelerate the discovery and optimization of CCR2 antagonists to address these challenges. The prerequisites for such efforts include an atomic-level understanding of the molecular determinants of action of existing antagonists. In this study, using molecular docking and artificial-intelligence-powered compound library screening, we uncover the structural principles of small molecule antagonism and selectivity towards CCR2 and its sister receptor CCR5. CCR2 orthosteric inhibitors are shown to universally occupy an inactive-state-specific tunnel between receptor helices 1 and 7; we also discover an unexpected role for an extra-helical groove accessible through this tunnel, suggesting its potential as a new targetable interface for CCR2 and CCR5 modulation. By contrast, only shape complementarity and limited helix 8 hydrogen bonding govern the binding of various chemotypes of allosteric antagonists. CCR2 residues S1012.63 and V2446.36 are implicated as determinants of CCR2/CCR5 and human/mouse orthosteric and allosteric antagonist selectivity, respectively, and the role of S1012.63 is corroborated through experimental gain-of-function mutagenesis. We establish a critical role of induced fit in antagonist recognition, reveal strong chemotype selectivity of existing structures, and demonstrate the high predictive potential of a new deep-learning-based compound scoring function. Finally, this study expands the available CCR2 structural landscape with computationally generated chemotype-specific models well-suited for structure-based antagonist design.
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Affiliation(s)
- John R D Dawson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Grant M Wadman
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | | | | | - Percy H Carter
- Bristol Myers Squibb Company, Princeton, NJ, USA
- (current affiliation) Blueprint Medicines, Cambridge, MA, USA
| | - Siyi Gu
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- (current affiliation) Lycia Therapeutics, South San Francisco, CA
| | - Thomas Shroka
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- (current affiliation) Avidity Biosciences Inc., San Diego, CA
| | - Leire Borrega-Roman
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Catherina L Salanga
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Tracy M Handel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Irina Kufareva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
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10
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Jiang S, Lin X, Wu L, Wang L, Wu Y, Xu Z, Xu F. Unveiling the structural mechanisms of nonpeptide ligand recognition and activation in human chemokine receptor CCR8. SCIENCE ADVANCES 2024; 10:eadj7500. [PMID: 38306437 PMCID: PMC10836724 DOI: 10.1126/sciadv.adj7500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 01/03/2024] [Indexed: 02/04/2024]
Abstract
The human CC chemokine receptor 8 (CCR8) is an emerging therapeutic target for cancer immunotherapy and autoimmune diseases. Understanding the molecular recognition of CCR8, particularly with nonpeptide ligands, is valuable for drug development. Here, we report three cryo-electron microscopy structures of human CCR8 complexed with Gi trimers in the ligand-free state or activated by nonpeptide agonists LMD-009 and ZK 756326. A conserved Y1.39Y3.32E7.39 motif in the orthosteric binding pocket is shown to play a crucial role in the chemokine and nonpeptide ligand recognition. Structural and functional analyses indicate that the lack of conservation in Y1143.33 and Y1724.64 among the CC chemokine receptors could potentially contribute to the selectivity of the nonpeptide ligand binding to CCR8. These findings present the characterization of the molecular interaction between a nonpeptide agonist and a chemokine receptor, aiding the development of therapeutics targeting related diseases through a structure-based approach.
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Affiliation(s)
- Shan Jiang
- iHuman Institute, ShanghaiTech University, Pudong, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xi Lin
- iHuman Institute, ShanghaiTech University, Pudong, Shanghai 201210, China
| | - Lijie Wu
- iHuman Institute, ShanghaiTech University, Pudong, Shanghai 201210, China
| | - Ling Wang
- iHuman Institute, ShanghaiTech University, Pudong, Shanghai 201210, China
| | - Yiran Wu
- iHuman Institute, ShanghaiTech University, Pudong, Shanghai 201210, China
| | - Ziyi Xu
- iHuman Institute, ShanghaiTech University, Pudong, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Fei Xu
- iHuman Institute, ShanghaiTech University, Pudong, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Clinical Research Center, Shanghai 201210, China
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11
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Zhao H, Sun M, Zhang Y, Kong W, Fan L, Wang K, Xu Q, Chen B, Dong J, Shi Y, Wang Z, Wang S, Zhuang X, Li Q, Lin F, Yao X, Zhang W, Kong C, Zhang R, Feng D, Zhao X. Connecting the Dots: The Cerebral Lymphatic System as a Bridge Between the Central Nervous System and Peripheral System in Health and Disease. Aging Dis 2024; 15:115-152. [PMID: 37307828 PMCID: PMC10796102 DOI: 10.14336/ad.2023.0516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 05/16/2023] [Indexed: 06/14/2023] Open
Abstract
As a recently discovered waste removal system in the brain, cerebral lymphatic system is thought to play an important role in regulating the homeostasis of the central nervous system. Currently, more and more attention is being focused on the cerebral lymphatic system. Further understanding of the structural and functional characteristics of cerebral lymphatic system is essential to better understand the pathogenesis of diseases and to explore therapeutic approaches. In this review, we summarize the structural components and functional characteristics of cerebral lymphatic system. More importantly, it is closely associated with peripheral system diseases in the gastrointestinal tract, liver, and kidney. However, there is still a gap in the study of the cerebral lymphatic system. However, we believe that it is a critical mediator of the interactions between the central nervous system and the peripheral system.
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Affiliation(s)
- Hongxiang Zhao
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China.
- Shandong Provincial Medicine and Health Key Laboratory of Clinical Anesthesia, School of Anesthesiology, Weifang Medical University, Weifang, China.
| | - Meiyan Sun
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China.
- Shandong Provincial Medicine and Health Key Laboratory of Clinical Anesthesia, School of Anesthesiology, Weifang Medical University, Weifang, China.
| | - Yue Zhang
- Shandong Provincial Medicine and Health Key Laboratory of Clinical Anesthesia, School of Anesthesiology, Weifang Medical University, Weifang, China.
| | - Wenwen Kong
- Shandong Provincial Medicine and Health Key Laboratory of Clinical Anesthesia, School of Anesthesiology, Weifang Medical University, Weifang, China.
| | - Lulu Fan
- Shandong Provincial Medicine and Health Key Laboratory of Clinical Anesthesia, School of Anesthesiology, Weifang Medical University, Weifang, China.
| | - Kaifang Wang
- Shandong Provincial Medicine and Health Key Laboratory of Clinical Anesthesia, School of Anesthesiology, Weifang Medical University, Weifang, China.
| | - Qing Xu
- Department of Anesthesiology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Baiyan Chen
- Shandong Provincial Medicine and Health Key Laboratory of Clinical Anesthesia, School of Anesthesiology, Weifang Medical University, Weifang, China.
| | - Jianxin Dong
- Shandong Provincial Medicine and Health Key Laboratory of Clinical Anesthesia, School of Anesthesiology, Weifang Medical University, Weifang, China.
| | - Yanan Shi
- Shandong Provincial Medicine and Health Key Laboratory of Clinical Anesthesia, School of Anesthesiology, Weifang Medical University, Weifang, China.
| | - Zhengyan Wang
- Shandong Provincial Medicine and Health Key Laboratory of Clinical Anesthesia, School of Anesthesiology, Weifang Medical University, Weifang, China.
| | - ShiQi Wang
- Shandong Provincial Medicine and Health Key Laboratory of Clinical Anesthesia, School of Anesthesiology, Weifang Medical University, Weifang, China.
| | - Xiaoli Zhuang
- Department of Anesthesiology, Beijing Anzhen Hospital, Capital Medical University, Beijing, China.
| | - Qi Li
- Department of Anesthesiology, Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.
| | - Feihong Lin
- Department of Anesthesiology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China.
| | - Xinyu Yao
- Department of Anesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
| | - WenBo Zhang
- Department of Neurosurgery, The Children’s Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China.
| | - Chang Kong
- Department of Anesthesiology and Critical Care Medicine, Tianjin Nankai Hospital, Tianjin Medical University, Tianjin, China.
| | - Rui Zhang
- Department of Anesthesiology, Affiliated Hospital of Weifang Medical University, Weifang, China.
- Shandong Provincial Medicine and Health Key Laboratory of Clinical Anesthesia, School of Anesthesiology, Weifang Medical University, Weifang, China.
| | - Dayun Feng
- Department of neurosurgery, Tangdu hospital, Fourth Military Medical University, Xi'an, China.
| | - Xiaoyong Zhao
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China.
- Department of Anesthesiology, Affiliated Hospital of Weifang Medical University, Weifang, China.
- Shandong Provincial Medicine and Health Key Laboratory of Clinical Anesthesia, School of Anesthesiology, Weifang Medical University, Weifang, China.
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12
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Boon K, Vanalken N, Szpakowska M, Chevigné A, Schols D, Van Loy T. Systematic assessment of chemokine ligand bias at the human chemokine receptor CXCR2 indicates G protein bias over β-arrestin recruitment and receptor internalization. Cell Commun Signal 2024; 22:43. [PMID: 38233929 PMCID: PMC10795402 DOI: 10.1186/s12964-023-01460-2] [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: 11/10/2023] [Accepted: 12/26/2023] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND The human CXC chemokine receptor 2 (CXCR2) is a G protein-coupled receptor (GPCR) interacting with multiple chemokines (i.e., CXC chemokine ligands CXCL1-3 and CXCL5-8). It is involved in inflammatory diseases as well as cancer. Consequently, much effort is put into the identification of CXCR2 targeting drugs. Fundamental research regarding CXCR2 signaling is mainly focused on CXCL8 (IL-8), which is the first and best described high-affinity ligand for CXCR2. Much less is known about CXCR2 activation induced by other chemokines and it remains to be determined to what extent potential ligand bias exists within this signaling system. This insight might be important to unlock new opportunities in therapeutic targeting of CXCR2. METHODS Ligand binding was determined in a competition binding assay using labeled CXCL8. Activation of the ELR + chemokine-induced CXCR2 signaling pathways, including G protein activation, β-arrestin1/2 recruitment, and receptor internalization, were quantified using NanoBRET-based techniques. Ligand bias within and between these pathways was subsequently investigated by ligand bias calculations, with CXCL8 as the reference CXCR2 ligand. Statistical significance was tested through a one-way ANOVA followed by Dunnett's multiple comparisons test. RESULTS All chemokines (CXCL1-3 and CXCL5-8) were able to displace CXCL8 from CXCR2 with high affinity and activated the same panel of G protein subtypes (Gαi1, Gαi2, Gαi3, GαoA, GαoB, and Gα15) without any statistically significant ligand bias towards any one type of G protein. Compared to CXCL8, all other chemokines were less potent in β-arrestin1 and -2 recruitment and receptor internalization while equivalently activating G proteins, indicating a G protein activation bias for CXCL1,-2,-3,-5,-6 and CXCL7. Lastly, with CXCL8 used as reference ligand, CXCL2 and CXCL6 showed ligand bias towards β-arrestin1/2 recruitment compared to receptor internalization. CONCLUSION This study presents an in-depth analysis of signaling bias upon CXCR2 stimulation by its chemokine ligands. Using CXCL8 as a reference ligand for bias index calculations, no ligand bias was observed between chemokines with respect to activation of separate G proteins subtypes or recruitment of β-arrestin1/2 subtypes, respectively. However, compared to β-arrestin recruitment and receptor internalization, CXCL1-3 and CXCL5-7 were biased towards G protein activation when CXCL8 was used as reference ligand.
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Affiliation(s)
- Katrijn Boon
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, B-3000, Leuven, Belgium
| | - Nathan Vanalken
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, B-3000, Leuven, Belgium
| | - Martyna Szpakowska
- Department of Infection and Immunity, Immuno-Pharmacology and Interactomics, Luxembourg Institute of Health (LIH), Esch-Sur-Alzette, Luxembourg
| | - Andy Chevigné
- Department of Infection and Immunity, Immuno-Pharmacology and Interactomics, Luxembourg Institute of Health (LIH), Esch-Sur-Alzette, Luxembourg
| | - Dominique Schols
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, B-3000, Leuven, Belgium
| | - Tom Van Loy
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, KU Leuven, B-3000, Leuven, Belgium.
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13
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Zhao L, Qiu Z, Yang Z, Xu L, Pearce TM, Wu Q, Yang K, Li F, Saulnier O, Fei F, Yu H, Gimple RC, Varadharajan V, Liu J, Hendrikse LD, Fong V, Wang W, Zhang J, Lv D, Lee D, Lehrich BM, Jin C, Ouyang L, Dixit D, Wu H, Wang X, Sloan AE, Wang X, Huan T, Mark Brown J, Goldman SA, Taylor MD, Zhou S, Rich JN. Lymphatic endothelial-like cells promote glioblastoma stem cell growth through cytokine-driven cholesterol metabolism. NATURE CANCER 2024; 5:147-166. [PMID: 38172338 DOI: 10.1038/s43018-023-00658-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/26/2023] [Indexed: 01/05/2024]
Abstract
Glioblastoma is the most lethal primary brain tumor with glioblastoma stem cells (GSCs) atop a cellular hierarchy. GSCs often reside in a perivascular niche, where they receive maintenance cues from endothelial cells, but the role of heterogeneous endothelial cell populations remains unresolved. Here, we show that lymphatic endothelial-like cells (LECs), while previously unrecognized in brain parenchyma, are present in glioblastomas and promote growth of CCR7-positive GSCs through CCL21 secretion. Disruption of CCL21-CCR7 paracrine communication between LECs and GSCs inhibited GSC proliferation and growth. LEC-derived CCL21 induced KAT5-mediated acetylation of HMGCS1 on K273 in GSCs to enhance HMGCS1 protein stability. HMGCS1 promoted cholesterol synthesis in GSCs, favorable for tumor growth. Expression of the CCL21-CCR7 axis correlated with KAT5 expression and HMGCS1K273 acetylation in glioblastoma specimens, informing patient outcome. Collectively, glioblastomas contain previously unrecognized LECs that promote the molecular crosstalk between endothelial and tumor cells, offering potentially alternative therapeutic strategies.
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Affiliation(s)
- Linjie Zhao
- University of Pittsburgh Medical Center, Hillman Cancer Center, Pittsburgh, PA, USA
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Zhixin Qiu
- University of Pittsburgh Medical Center, Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Anesthesiology, Zhongshan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Zhengnan Yang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of the Ministry of Education, and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, and Collaborative Innovation Center, Chengdu, China
| | - Lian Xu
- Department of Pathology, West China Second Hospital, Sichuan University, Chengdu, China
| | - Thomas M Pearce
- Department of Pathology, Division of Neuropathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Qiulian Wu
- University of Pittsburgh Medical Center, Hillman Cancer Center, Pittsburgh, PA, USA
| | - Kailin Yang
- Department of Radiation Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH, USA
| | - FuLong Li
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Olivier Saulnier
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Fan Fei
- Department of Neurosurgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
| | - Huaxu Yu
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ryan C Gimple
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Venkateshwari Varadharajan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute Cleveland Clinic, Cleveland, OH, USA
- Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Juxiu Liu
- Division of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, China
| | - Liam D Hendrikse
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Vernon Fong
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Wei Wang
- Department of Gynecology, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
| | - Jiao Zhang
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Deguan Lv
- University of Pittsburgh Medical Center, Hillman Cancer Center, Pittsburgh, PA, USA
| | - Derrick Lee
- University of Pittsburgh Medical Center, Hillman Cancer Center, Pittsburgh, PA, USA
| | - Brandon M Lehrich
- University of Pittsburgh Medical Center, Hillman Cancer Center, Pittsburgh, PA, USA
| | - Chunyu Jin
- Howard Hughes Medical Institute, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Liang Ouyang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Deobrat Dixit
- Division of Regenerative Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Haoxing Wu
- Huaxi MR Research Center, Department of Radiology, Functional and Molecular Imaging Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Xiang Wang
- Division of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, China
| | - Andrew E Sloan
- Department of Neurosurgery, Case Western Reserve University, Cleveland, OH, USA
| | - Xiuxing Wang
- School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Tao Huan
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - J Mark Brown
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute Cleveland Clinic, Cleveland, OH, USA
- Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Steven A Goldman
- University of Rochester Medical Center, Rochester, NY, USA
- University of Copenhagen, Copenhagen, Denmark
| | - Michael D Taylor
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Neurosurgery, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Shengtao Zhou
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of the Ministry of Education, and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, and Collaborative Innovation Center, Chengdu, China.
| | - Jeremy N Rich
- University of Pittsburgh Medical Center, Hillman Cancer Center, Pittsburgh, PA, USA.
- Department of Neurology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
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14
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Zhang M, Lan X, Li X, Lu S. Pharmacologically targeting intracellular allosteric sites of GPCRs for drug discovery. Drug Discov Today 2023; 28:103803. [PMID: 37852356 DOI: 10.1016/j.drudis.2023.103803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/07/2023] [Accepted: 10/12/2023] [Indexed: 10/20/2023]
Abstract
G-protein-coupled receptors (GPCRs) are a family of cell surface proteins that can sense a variety of extracellular stimuli and mediate multiple signaling transduction pathways involved in human physiology. Recent advances in GPCR structural biology have revealed a relatively conserved intracellular allosteric site in multiple GPCRs, which can be utilized to modulate receptors from the inside. This novel intracellular site partially overlaps with the G-protein and β-arrestin coupling sites, providing a novel avenue for biological intervention. Here, we review evidence available for GPCR structures complexed with intracellular small-molecule allosteric modulators, elucidating drug-target interactions and allosteric mechanisms. Moreover, we highlight the potential of intracellular allosteric modulators in achieving biased signaling, which provides insights into biased allosteric mechanisms.
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Affiliation(s)
- Mingyang Zhang
- School of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region 750004, China; Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiaobing Lan
- School of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region 750004, China
| | - Xiaolong Li
- Department of Orthopedics, Changhai Hospital, The First Affiliated Hospital of Naval Medical University, Shanghai 200433, China.
| | - Shaoyong Lu
- School of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region 750004, China; Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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15
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Sun D, Sun Y, Janezic E, Zhou T, Johnson M, Azumaya C, Noreng S, Chiu C, Seki A, Arenzana TL, Nicoludis JM, Shi Y, Wang B, Ho H, Joshi P, Tam C, Payandeh J, Comps-Agrar L, Wang J, Rutz S, Koerber JT, Masureel M. Structural basis of antibody inhibition and chemokine activation of the human CC chemokine receptor 8. Nat Commun 2023; 14:7940. [PMID: 38040762 PMCID: PMC10692165 DOI: 10.1038/s41467-023-43601-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 11/14/2023] [Indexed: 12/03/2023] Open
Abstract
The C-C motif chemokine receptor 8 (CCR8) is a class A G-protein coupled receptor that has emerged as a promising therapeutic target in cancer. Targeting CCR8 with an antibody has appeared to be an attractive therapeutic approach, but the molecular basis for chemokine-mediated activation and antibody-mediated inhibition of CCR8 are not fully elucidated. Here, we obtain an antagonist antibody against human CCR8 and determine structures of CCR8 in complex with either the antibody or the endogenous agonist ligand CCL1. Our studies reveal characteristic antibody features allowing recognition of the CCR8 extracellular loops and CCL1-CCR8 interaction modes that are distinct from other chemokine receptor - ligand pairs. Informed by these structural insights, we demonstrate that CCL1 follows a two-step, two-site binding sequence to CCR8 and that antibody-mediated inhibition of CCL1 signaling can occur by preventing the second binding event. Together, our results provide a detailed structural and mechanistic framework of CCR8 activation and inhibition that expands our molecular understanding of chemokine - receptor interactions and offers insight into the development of therapeutic antibodies targeting chemokine GPCRs.
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Affiliation(s)
- Dawei Sun
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Yonglian Sun
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Eric Janezic
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Tricia Zhou
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Matthew Johnson
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Caleigh Azumaya
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Sigrid Noreng
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, 94080, USA
- Septerna Inc., South San Francisco, CA, 94080, USA
| | - Cecilia Chiu
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Akiko Seki
- Department of Cancer Immunology, Genentech Inc., South San Francisco, CA, 94080, USA
- Tune Therapeutics, Durham, NC, 27701, USA
| | - Teresita L Arenzana
- Department of Cancer Immunology, Genentech Inc., South San Francisco, CA, 94080, USA
- HIBio, South San Francisco, CA, 94080, USA
| | - John M Nicoludis
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Yongchang Shi
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Baomei Wang
- Department of Cancer Immunology, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Hoangdung Ho
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Prajakta Joshi
- Department of Biomolecular Resources, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Christine Tam
- Department of Biomolecular Resources, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Jian Payandeh
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, 94080, USA
- Exelixis Inc., Alameda, CA, 94502, USA
| | - Laëtitia Comps-Agrar
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Jianyong Wang
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Sascha Rutz
- Department of Cancer Immunology, Genentech Inc., South San Francisco, CA, 94080, USA.
| | - James T Koerber
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, 94080, USA.
| | - Matthieu Masureel
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, 94080, USA.
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16
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Luginina A, Maslov I, Khorn P, Volkov O, Khnykin A, Kuzmichev P, Shevtsov M, Belousov A, Kapranov I, Dashevskii D, Kornilov D, Bestsennaia E, Hofkens J, Hendrix J, Gensch T, Cherezov V, Ivanovich V, Mishin A, Borshchevskiy V. Functional GPCR Expression in Eukaryotic LEXSY System. J Mol Biol 2023; 435:168310. [PMID: 37806553 DOI: 10.1016/j.jmb.2023.168310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/10/2023]
Abstract
G protein-coupled receptors (GPCRs) form the largest superfamily of membrane proteins in the human genome, and represent one of the most important classes of drug targets. Their structural studies facilitate rational drug discovery. However, atomic structures of only about 20% of human GPCRs have been solved to date. Recombinant production of GPCRs for structural studies at a large scale is challenging due to their low expression levels and stability. Therefore, in this study, we explored the efficacy of the eukaryotic system LEXSY (Leishmania tarentolae) for GPCR production. We selected the human A2A adenosine receptor (A2AAR), as a model protein, expressed it in LEXSY, purified it, and compared with the same receptor produced in insect cells, which is the most popular expression system for structural studies of GPCRs. The A2AAR purified from both expression systems showed similar purity, stability, ligand-induced conformational changes and structural dynamics, with a remarkably higher protein yield in the case of LEXSY expression. Overall, our results suggest that LEXSY is a promising platform for large-scale production of GPCRs for structural studies.
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Affiliation(s)
- Aleksandra Luginina
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Ivan Maslov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia; Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre, Biomedical Research Institute, Agoralaan C (BIOMED), Hasselt University, Diepenbeek, Belgium; Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Polina Khorn
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | | | - Andrey Khnykin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Pavel Kuzmichev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Mikhail Shevtsov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Anatoliy Belousov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Ivan Kapranov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Dmitrii Dashevskii
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Daniil Kornilov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Ekaterina Bestsennaia
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Johan Hofkens
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium; Max Planck Institute for Polymer Research, Mainz, Germany
| | - Jelle Hendrix
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre, Biomedical Research Institute, Agoralaan C (BIOMED), Hasselt University, Diepenbeek, Belgium; Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Thomas Gensch
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Vadim Cherezov
- Bridge Institute, Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Valentin Ivanovich
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Alexey Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia; Joint Institute for Nuclear Research, Dubna, Russia.
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17
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Dragan P, Joshi K, Atzei A, Latek D. Keras/TensorFlow in Drug Design for Immunity Disorders. Int J Mol Sci 2023; 24:15009. [PMID: 37834457 PMCID: PMC10573944 DOI: 10.3390/ijms241915009] [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: 09/08/2023] [Revised: 09/21/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
Homeostasis of the host immune system is regulated by white blood cells with a variety of cell surface receptors for cytokines. Chemotactic cytokines (chemokines) activate their receptors to evoke the chemotaxis of immune cells in homeostatic migrations or inflammatory conditions towards inflamed tissue or pathogens. Dysregulation of the immune system leading to disorders such as allergies, autoimmune diseases, or cancer requires efficient, fast-acting drugs to minimize the long-term effects of chronic inflammation. Here, we performed structure-based virtual screening (SBVS) assisted by the Keras/TensorFlow neural network (NN) to find novel compound scaffolds acting on three chemokine receptors: CCR2, CCR3, and one CXC receptor, CXCR3. Keras/TensorFlow NN was used here not as a typically used binary classifier but as an efficient multi-class classifier that can discard not only inactive compounds but also low- or medium-activity compounds. Several compounds proposed by SBVS and NN were tested in 100 ns all-atom molecular dynamics simulations to confirm their binding affinity. To improve the basic binding affinity of the compounds, new chemical modifications were proposed. The modified compounds were compared with known antagonists of these three chemokine receptors. Known CXCR3 compounds were among the top predicted compounds; thus, the benefits of using Keras/TensorFlow in drug discovery have been shown in addition to structure-based approaches. Furthermore, we showed that Keras/TensorFlow NN can accurately predict the receptor subtype selectivity of compounds, for which SBVS often fails. We cross-tested chemokine receptor datasets retrieved from ChEMBL and curated datasets for cannabinoid receptors. The NN model trained on the cannabinoid receptor datasets retrieved from ChEMBL was the most accurate in the receptor subtype selectivity prediction. Among NN models trained on the chemokine receptor datasets, the CXCR3 model showed the highest accuracy in differentiating the receptor subtype for a given compound dataset.
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Affiliation(s)
- Paulina Dragan
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-903 Warsaw, Poland; (P.D.); (A.A.)
| | - Kavita Joshi
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-903 Warsaw, Poland; (P.D.); (A.A.)
| | - Alessandro Atzei
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-903 Warsaw, Poland; (P.D.); (A.A.)
- Department of Life and Environmental Science, Food Toxicology Unit, University of Cagliari, University Campus of Monserrato, SS 554, 09042 Cagliari, Italy
| | - Dorota Latek
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-903 Warsaw, Poland; (P.D.); (A.A.)
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18
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Casella B, Farmer JP, Nesheva DN, Williams HEL, Charlton SJ, Holliday ND, Laughton CA, Mistry SN. Design, Synthesis, and Application of Fluorescent Ligands Targeting the Intracellular Allosteric Binding Site of the CXC Chemokine Receptor 2. J Med Chem 2023; 66:12911-12930. [PMID: 37523859 PMCID: PMC10544029 DOI: 10.1021/acs.jmedchem.3c00849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Indexed: 08/02/2023]
Abstract
The inhibition of CXC chemokine receptor 2 (CXCR2), a key inflammatory mediator, is a potential strategy in the treatment of several pulmonary diseases and cancers. The complexity of endogenous chemokine interaction with the orthosteric binding site has led to the development of CXCR2 negative allosteric modulators (NAMs) targeting an intracellular pocket near the G protein binding site. Our understanding of NAM binding and mode of action has been limited by the availability of suitable tracer ligands for competition studies, allowing direct ligand binding measurements. Here, we report the rational design, synthesis, and pharmacological evaluation of a series of fluorescent NAMs, based on navarixin (2), which display high affinity and preferential binding for CXCR2 over CXCR1. We demonstrate their application in fluorescence imaging and NanoBRET binding assays, in whole cells or membranes, capable of kinetic and equilibrium analysis of NAM binding, providing a platform to screen for alternative chemophores targeting these receptors.
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Affiliation(s)
- Bianca
Maria Casella
- Division
of Biomolecular Sciences and Medicinal Chemistry, School of Pharmacy, University of Nottingham Biodiscovery Institute, Nottingham NG7 2RD, UK
| | - James P. Farmer
- Division
of Physiology, Pharmacology & Neuroscience, Medical School, School
of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
| | - Desislava N. Nesheva
- Division
of Physiology, Pharmacology & Neuroscience, Medical School, School
of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
| | - Huw E. L. Williams
- School
of Chemistry, University of Nottingham Biodiscovery
Institute, Nottingham NG7 2RD, UK
| | - Steven J. Charlton
- Division
of Physiology, Pharmacology & Neuroscience, Medical School, School
of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
- OMass
Therapeutics Ltd., Oxford OX4 2GX, UK
| | - Nicholas D. Holliday
- Division
of Physiology, Pharmacology & Neuroscience, Medical School, School
of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
- Excellerate
Bioscience Ltd., Biocity, University of
Nottingham, Nottingham NG1 1GF, UK
| | - Charles A. Laughton
- Division
of Biomolecular Sciences and Medicinal Chemistry, School of Pharmacy, University of Nottingham Biodiscovery Institute, Nottingham NG7 2RD, UK
| | - Shailesh N. Mistry
- Division
of Biomolecular Sciences and Medicinal Chemistry, School of Pharmacy, University of Nottingham Biodiscovery Institute, Nottingham NG7 2RD, UK
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19
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Huber ME, Wurnig S, Toy L, Weiler C, Merten N, Kostenis E, Hansen FK, Schiedel M. Fluorescent Ligands Enable Target Engagement Studies for the Intracellular Allosteric Binding Site of the Chemokine Receptor CXCR2. J Med Chem 2023. [PMID: 37463496 PMCID: PMC10388362 DOI: 10.1021/acs.jmedchem.3c00769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Herein, we report the structure-based development of fluorescent ligands targeting the intracellular allosteric binding site (IABS) of CXC chemokine receptor 2 (CXCR2), a G protein-coupled receptor (GPCR) that has been pursued as a drug target in oncology and inflammation. Starting from the cocrystallized intracellular CXCR2 antagonist 00767013 (1), tetramethylrhodamine (TAMRA)-labeled CXCR2 ligands were designed, synthesized, and tested for their suitability as fluorescent reporters to probe binding to the IABS of CXCR2. By means of these studies, we developed Mz438 (9a) as a high-affinity and selective fluorescent CXCR2 ligand, enabling cell-free as well as cellular NanoBRET-based binding studies in a nonisotopic and high-throughput manner. Further, we show that 9a can be used as a tool to visualize intracellular target engagement for CXCR2 via fluorescence microscopy. Thus, our small-molecule-based fluorescent CXCR2 ligand 9a represents a promising tool for future studies of CXCR2 pharmacology.
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Affiliation(s)
- Max E Huber
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany
| | - Silas Wurnig
- Department of Pharmaceutical & Cell Biological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Lara Toy
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany
| | - Corinna Weiler
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Nicole Merten
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Evi Kostenis
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Finn K Hansen
- Department of Pharmaceutical & Cell Biological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Matthias Schiedel
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany
- Institute of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Beethovenstraße 55, 38106 Braunschweig, Germany
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20
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Mastini C, Campisi M, Patrucco E, Mura G, Ferreira A, Costa C, Ambrogio C, Germena G, Martinengo C, Peola S, Mota I, Vissio E, Molinaro L, Arigoni M, Olivero M, Calogero R, Prokoph N, Tabbò F, Shoji B, Brugieres L, Geoerger B, Turner SD, Cuesta-Mateos C, D’Aliberti D, Mologni L, Piazza R, Gambacorti-Passerini C, Inghirami GG, Chiono V, Kamm RD, Hirsch E, Koch R, Weinstock DM, Aster JC, Voena C, Chiarle R. Targeting CCR7-PI3Kγ overcomes resistance to tyrosine kinase inhibitors in ALK-rearranged lymphoma. Sci Transl Med 2023; 15:eabo3826. [PMID: 37379367 PMCID: PMC10804420 DOI: 10.1126/scitranslmed.abo3826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 06/02/2023] [Indexed: 06/30/2023]
Abstract
Anaplastic lymphoma kinase (ALK) tyrosine kinase inhibitors (TKIs) show potent efficacy in several ALK-driven tumors, but the development of resistance limits their long-term clinical impact. Although resistance mechanisms have been studied extensively in ALK-driven non-small cell lung cancer, they are poorly understood in ALK-driven anaplastic large cell lymphoma (ALCL). Here, we identify a survival pathway supported by the tumor microenvironment that activates phosphatidylinositol 3-kinase γ (PI3K-γ) signaling through the C-C motif chemokine receptor 7 (CCR7). We found increased PI3K signaling in patients and ALCL cell lines resistant to ALK TKIs. PI3Kγ expression was predictive of a lack of response to ALK TKI in patients with ALCL. Expression of CCR7, PI3Kγ, and PI3Kδ were up-regulated during ALK or STAT3 inhibition or degradation and a constitutively active PI3Kγ isoform cooperated with oncogenic ALK to accelerate lymphomagenesis in mice. In a three-dimensional microfluidic chip, endothelial cells that produce the CCR7 ligands CCL19/CCL21 protected ALCL cells from apoptosis induced by crizotinib. The PI3Kγ/δ inhibitor duvelisib potentiated crizotinib activity against ALCL lines and patient-derived xenografts. Furthermore, genetic deletion of CCR7 blocked the central nervous system dissemination and perivascular growth of ALCL in mice treated with crizotinib. Thus, blockade of PI3Kγ or CCR7 signaling together with ALK TKI treatment reduces primary resistance and the survival of persister lymphoma cells in ALCL.
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Affiliation(s)
- Cristina Mastini
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino 10126, Italy
| | - Marco Campisi
- Dana Farber Cancer Institute, Boston, MA 02115, USA
- Department of Pathology, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Department of Mechanical and Aerospace Engineering, Politecnico of Torino, Torino 10129, Italy
| | - Enrico Patrucco
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino 10126, Italy
| | - Giulia Mura
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino 10126, Italy
| | - Antonio Ferreira
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston MA 02115, USA
| | - Carlotta Costa
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino 10126, Italy
| | - Chiara Ambrogio
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino 10126, Italy
| | - Giulia Germena
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino 10126, Italy
| | - Cinzia Martinengo
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino 10126, Italy
| | - Silvia Peola
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino 10126, Italy
| | - Ines Mota
- Department of Pathology, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Elena Vissio
- Department of Oncology, University of Torino, Orbassano, Torino 10043, Italy
| | - Luca Molinaro
- Department of Medical Science, University of Torino, Torino 10126, Italy
| | - Maddalena Arigoni
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino 10126, Italy
| | - Martina Olivero
- Department of Oncology, University of Torino, Orbassano, Torino 10043, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino 10060, Italy
| | - Raffaele Calogero
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino 10126, Italy
| | - Nina Prokoph
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK
| | - Fabrizio Tabbò
- Department of Pathology, Cornell University, New York NY 10121, USA
| | - Brent Shoji
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston MA 02115, USA
| | - Laurence Brugieres
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Center, Paris-Saclay University, Villejuif 94805, France
| | - Birgit Geoerger
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Center, Paris-Saclay University, Villejuif 94805, France
- Université Paris-Saclay, INSERM U1015, Villejuif 94805, France
| | - Suzanne D. Turner
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK
- Faculty of Medicine, Masaryk University, Brno 601 77, Czech Republic
| | - Carlos Cuesta-Mateos
- Department of Pre-Clinical Development, Catapult Therapeutics B.V., 8243 RC, Lelystad, Netherlands
| | - Deborah D’Aliberti
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza 20900, Italy
| | - Luca Mologni
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza 20900, Italy
| | - Rocco Piazza
- Department of Medicine and Surgery, University of Milan-Bicocca, Monza 20900, Italy
| | | | | | - Valeria Chiono
- Department of Mechanical and Aerospace Engineering, Politecnico of Torino, Torino 10129, Italy
| | - Roger D. Kamm
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Emilio Hirsch
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino 10126, Italy
| | - Raphael Koch
- Dana Farber Cancer Institute, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
- University Medical Center Göttingen, 37075 Göttingen, Germany
| | - David M. Weinstock
- Dana Farber Cancer Institute, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Jon C. Aster
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston MA 02115, USA
| | - Claudia Voena
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino 10126, Italy
| | - Roberto Chiarle
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino 10126, Italy
- Department of Pathology, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA
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21
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Amer M, Leka O, Jasko P, Frey D, Li X, Kammerer RA. A coiled-coil-based design strategy for the thermostabilization of G-protein-coupled receptors. Sci Rep 2023; 13:10159. [PMID: 37349348 PMCID: PMC10287670 DOI: 10.1038/s41598-023-36855-1] [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: 04/20/2022] [Accepted: 06/11/2023] [Indexed: 06/24/2023] Open
Abstract
Structure elucidation of inactive-state GPCRs still mostly relies on X-ray crystallography. The major goal of our work was to create a new GPCR tool that would provide receptor stability and additional soluble surface for crystallization. Towards this aim, we selected the two-stranded antiparallel coiled coil as a domain fold that satisfies both criteria. A selection of antiparallel coiled coils was used for structure-guided substitution of intracellular loop 3 of the β3 adrenergic receptor. Unexpectedly, only the two GPCR variants containing thermostable coiled coils were expressed. We showed that one GPCR chimera is stable upon purification in detergent, retains ligand-binding properties, and can be crystallized. However, the quality of the crystals was not suitable for structure determination. By using two other examples, 5HTR2C and α2BAR, we demonstrate that our approach is generally suitable for the stabilization of GPCRs. To provide additional surface for promoting crystal contacts, we replaced in a structure-based approach the loop connecting the antiparallel coiled coil by T4L. We found that the engineered GPCR is even more stable than the coiled-coil variant. Negative-staining TEM revealed a homogeneous distribution of particles, indicating that coiled-coil-T4L receptor variants might also be promising candidate proteins for structure elucidation by cryo-EM. Our approach should be of interest for applications that benefit from stable GPCRs.
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Affiliation(s)
- Marwa Amer
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, 5232, Villigen PSI, Switzerland
| | - Oneda Leka
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, 5232, Villigen PSI, Switzerland
| | - Piotr Jasko
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, 5232, Villigen PSI, Switzerland
| | - Daniel Frey
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, 5232, Villigen PSI, Switzerland
| | - Xiaodan Li
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, 5232, Villigen PSI, Switzerland
| | - Richard A Kammerer
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, 5232, Villigen PSI, Switzerland.
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22
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Kobayashi K, Kawakami K, Kusakizako T, Tomita A, Nishimura M, Sawada K, Okamoto HH, Hiratsuka S, Nakamura G, Kuwabara R, Noda H, Muramatsu H, Shimizu M, Taguchi T, Inoue A, Murata T, Nureki O. Class B1 GPCR activation by an intracellular agonist. Nature 2023; 618:1085-1093. [PMID: 37286611 PMCID: PMC10307627 DOI: 10.1038/s41586-023-06169-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 05/04/2023] [Indexed: 06/09/2023]
Abstract
G protein-coupled receptors (GPCRs) generally accommodate specific ligands in the orthosteric-binding pockets. Ligand binding triggers a receptor allosteric conformational change that leads to the activation of intracellular transducers, G proteins and β-arrestins. Because these signals often induce adverse effects, the selective activation mechanism for each transducer must be elucidated. Thus, many orthosteric-biased agonists have been developed, and intracellular-biased agonists have recently attracted broad interest. These agonists bind within the receptor intracellular cavity and preferentially tune the specific signalling pathway over other signalling pathways, without allosteric rearrangement of the receptor from the extracellular side1-3. However, only antagonist-bound structures are currently available1,4-6, and there is no evidence to support that biased agonist binding occurs within the intracellular cavity. This limits the comprehension of intracellular-biased agonism and potential drug development. Here we report the cryogenic electron microscopy structure of a complex of Gs and the human parathyroid hormone type 1 receptor (PTH1R) bound to a PTH1R agonist, PCO371. PCO371 binds within an intracellular pocket of PTH1R and directly interacts with Gs. The PCO371-binding mode rearranges the intracellular region towards the active conformation without extracellularly induced allosteric signal propagation. PCO371 stabilizes the significantly outward-bent conformation of transmembrane helix 6, which facilitates binding to G proteins rather than β-arrestins. Furthermore, PCO371 binds within the highly conserved intracellular pocket, activating 7 out of the 15 class B1 GPCRs. Our study identifies a new and conserved intracellular agonist-binding pocket and provides evidence of a biased signalling mechanism that targets the receptor-transducer interface.
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Affiliation(s)
- Kazuhiro Kobayashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Kouki Kawakami
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Tsukasa Kusakizako
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Atsuhiro Tomita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Preferred Networks, Tokyo, Japan
| | - Michihiro Nishimura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Kazuhiro Sawada
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki H Okamoto
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Suzune Hiratsuka
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Gaku Nakamura
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Riku Kuwabara
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Hiroshi Noda
- Research Division, Chugai Pharmaceutical, Shizuoka, Japan
| | | | - Masaru Shimizu
- Research Division, Chugai Pharmaceutical, Shizuoka, Japan
| | - Tomohiko Taguchi
- Laboratory of Organelle Pathophysiology, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan.
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba, Japan.
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
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23
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Künze G, Isermann B. Targeting biased signaling by PAR1: function and molecular mechanism of parmodulins. Blood 2023; 141:2675-2684. [PMID: 36952648 PMCID: PMC10646804 DOI: 10.1182/blood.2023019775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/01/2023] [Accepted: 03/21/2023] [Indexed: 03/25/2023] Open
Abstract
The G protein-coupled receptor (GPCR) protease-activated receptor 1 (PAR1) is a therapeutic target that was originally pursued with the aim of restricting platelet activation and the burden of cardiovascular diseases. In clinical studies, the use of orthosteric PAR1 inhibitors was associated with an increased risk of hemorrhage, including intracranial hemorrhage. Because (1) PAR1 is expressed by various cell types, including endothelial cells, (2) conveys in mice a physiological indispensable function for vascular development during embryogenesis, and (3) is subject to biased signaling dependent on the activating proteases, orthosteric PAR1 inhibition may be associated with unwanted side effects. Alternatively, the protease-activated protein C (aPC) and its variants can promote valuable anti-inflammatory signaling via PAR1. Most recently, small molecule allosteric modulators of PAR1 signaling, called parmodulins, have been developed. Parmodulins inhibit coagulation and platelet activation yet maintain cytoprotective effects typically provoked by PAR1 signaling upon the activation by aPC. In this study, we review the discovery of parmodulins and their preclinical data, summarize the current knowledge about their mode of action, and compare the structural interaction of parmodulin and PAR1 with that of other intracellularly binding allosteric GPCR modulators. Thus, we highlight the pharmaceutical potential and challenges associated with the future development of parmodulins.
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Affiliation(s)
- Georg Künze
- Institute for Drug Discovery, Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Berend Isermann
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostic, University Hospital, Leipzig, Germany
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24
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Liessmann F, Künze G, Meiler J. Improving the Modeling of Extracellular Ligand Binding Pockets in RosettaGPCR for Conformational Selection. Int J Mol Sci 2023; 24:7788. [PMID: 37175495 PMCID: PMC10178219 DOI: 10.3390/ijms24097788] [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: 04/03/2023] [Revised: 04/19/2023] [Accepted: 04/22/2023] [Indexed: 05/15/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are the largest class of drug targets and undergo substantial conformational changes in response to ligand binding. Despite recent progress in GPCR structure determination, static snapshots fail to reflect the conformational space of putative binding pocket geometries to which small molecule ligands can bind. In comparative modeling of GPCRs in the absence of a ligand, often a shrinking of the orthosteric binding pocket is observed. However, the exact prediction of the flexible orthosteric binding site is crucial for adequate structure-based drug discovery. In order to improve ligand docking and guide virtual screening experiments in computer-aided drug discovery, we developed RosettaGPCRPocketSize. The algorithm creates a conformational ensemble of biophysically realistic conformations of the GPCR binding pocket between the TM bundle, which is consistent with a knowledge base of expected pocket geometries. Specifically, tetrahedral volume restraints are defined based on information about critical residues in the orthosteric binding site and their experimentally observed range of Cα-Cα-distances. The output of RosettaGPCRPocketSize is an ensemble of binding pocket geometries that are filtered by energy to ensure biophysically probable arrangements, which can be used for docking simulations. In a benchmark set, pocket shrinkage observed in the default RosettaGPCR was reduced by up to 80% and the binding pocket volume range and geometric diversity were increased. Compared to models from four different GPCR homology model databases (RosettaGPCR, GPCR-Tasser, GPCR-SSFE, and GPCRdb), the here-created models showed more accurate volumes of the orthosteric pocket when evaluated with respect to the crystallographic reference structure. Furthermore, RosettaGPCRPocketSize was able to generate an improved realistic pocket distribution. However, while being superior to other homology models, the accuracy of generated model pockets was comparable to AlphaFold2 models. Furthermore, in a docking benchmark using small-molecule ligands with a higher molecular weight between 400 and 700 Da, a higher success rate in creating native-like binding poses was observed. In summary, RosettaGPCRPocketSize can generate GPCR models with realistic orthosteric pocket volumes, which are useful for structure-based drug discovery applications.
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Affiliation(s)
- Fabian Liessmann
- Institute for Drug Discovery, Medical Faculty, Leipzig University, 04103 Leipzig, Germany; (F.L.)
| | - Georg Künze
- Institute for Drug Discovery, Medical Faculty, Leipzig University, 04103 Leipzig, Germany; (F.L.)
| | - Jens Meiler
- Institute for Drug Discovery, Medical Faculty, Leipzig University, 04103 Leipzig, Germany; (F.L.)
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
- Center for Scalable Data Analytics and Artificial Intelligence, Leipzig University, 04105 Leipzig, Germany
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25
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Shpakov AO. Allosteric Regulation of G-Protein-Coupled Receptors: From Diversity of Molecular Mechanisms to Multiple Allosteric Sites and Their Ligands. Int J Mol Sci 2023; 24:6187. [PMID: 37047169 PMCID: PMC10094638 DOI: 10.3390/ijms24076187] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Allosteric regulation is critical for the functioning of G protein-coupled receptors (GPCRs) and their signaling pathways. Endogenous allosteric regulators of GPCRs are simple ions, various biomolecules, and protein components of GPCR signaling (G proteins and β-arrestins). The stability and functional activity of GPCR complexes is also due to multicenter allosteric interactions between protomers. The complexity of allosteric effects caused by numerous regulators differing in structure, availability, and mechanisms of action predetermines the multiplicity and different topology of allosteric sites in GPCRs. These sites can be localized in extracellular loops; inside the transmembrane tunnel and in its upper and lower vestibules; in cytoplasmic loops; and on the outer, membrane-contacting surface of the transmembrane domain. They are involved in the regulation of basal and orthosteric agonist-stimulated receptor activity, biased agonism, GPCR-complex formation, and endocytosis. They are targets for a large number of synthetic allosteric regulators and modulators, including those constructed using molecular docking. The review is devoted to the principles and mechanisms of GPCRs allosteric regulation, the multiplicity of allosteric sites and their topology, and the endogenous and synthetic allosteric regulators, including autoantibodies and pepducins. The allosteric regulation of chemokine receptors, proteinase-activated receptors, thyroid-stimulating and luteinizing hormone receptors, and beta-adrenergic receptors are described in more detail.
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Affiliation(s)
- Alexander O Shpakov
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, 194223 St. Petersburg, Russia
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Optimization of triazolo[4,5-d]pyrimidines towards human CC chemokine receptor 7 (CCR7) antagonists. Eur J Med Chem 2023; 251:115240. [PMID: 36924670 DOI: 10.1016/j.ejmech.2023.115240] [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: 12/14/2022] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 03/07/2023]
Abstract
CCR7 signaling directs the migration of both immune cells and cancer cells to the lymph nodes, is involved in numerous chronic inflammatory disorders and lymph node metastases. Despite the therapeutic promise of CCR7 antagonists, no potent and selective small molecule CCR7 antagonists have been reported to date. Since most human chemokine G protein-coupled receptors (GPCRs) share a conserved intracellular allosteric binding site, new CCR7 antagonist chemotypes may be identified by screening small molecules that are known to target this site in other chemokine GPCRs. In this work, our previously prepared series of 14 scaffold-modified analogues of a known thiazolo[4,5-d]pyrimidine CXCR2 antagonist were screened as potential CCR7 antagonists. This resulted in the discovery of a triazolo[4,5-d]pyrimidine analogue with an IC50 of 2.43 μM against CCR7 and 0.66 μM against CXCR2. Exploration of the structure-activity relationship (SAR) for the 3-, 5- and 7-position substituents of this triazolo[4,5-d]pyrimidine resulted in improved potency and selectivity, with an IC50 of 0.43 μM and 11.02 μM against CCR7 and CXCR2, respectively, for the most selective derivative. Molecular docking showed that the binding mode of these triazolo[4,5-d]pyrimidines in CCR7 and CXCR2 corresponds with those of previously co-crystallized ligands.
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Kawamura K, Lee C, Yoshikawa T, Hani AS, Usami Y, Toyosawa S, Tanaka S, Hiraoka SI. Prediction of cervical lymph node metastasis from immunostained specimens of tongue cancer using a multilayer perceptron neural network. Cancer Med 2023; 12:5312-5322. [PMID: 36307918 PMCID: PMC10028108 DOI: 10.1002/cam4.5343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 08/04/2022] [Accepted: 08/23/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Although cervical lymph node metastasis is an important prognostic factor for oral cancer, occult metastases remain undetected even by diagnostic imaging. We developed a learning model to predict lymph node metastasis in resected specimens of tongue cancer by classifying the level of immunohistochemical (IHC) staining for angiogenesis- and lymphangiogenesis-related proteins using a multilayer perceptron neural network (MNN). METHODS We obtained a dataset of 76 patients with squamous cell carcinoma of the tongue who had undergone primary tumor resection. All 76 specimens were IHC stained for the six types shown above (VEGF-C, VEGF-D, NRP1, NRP2, CCR7, and SEMA3E) and 456 slides were prepared. We scored the staining levels visually on all slides. We created virtual slides (4560 images) and the accuracy of the MNN model was verified by comparing it with a hue-saturation (HS) histogram, which quantifies the manually determined visual information. RESULTS The accuracy of the training model with the MNN was 98.6%, and when the training image was converted to grayscale, the accuracy decreased to 52.9%. This indicates that our MNN adequately evaluates the level of staining rather than the morphological features of the IHC images. Multivariate analysis revealed that CCR7 staining level and T classification were independent factors associated with the presence of cervical lymph node metastasis in both HS histograms and MNN. CONCLUSION These results suggest that IHC assessment using MNN may be useful for identifying lymph node metastasis in patients with tongue cancer.
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Affiliation(s)
- Kohei Kawamura
- 1st Department of Oral and Maxillofacial Surgery, Graduate School of Dentistry, Osaka University, Osaka, Japan
| | - Chonho Lee
- Cybermedia Center, Osaka University, Osaka, Japan
| | | | - Al-Shareef Hani
- Department of Oral & Maxillofacial Surgery, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Yu Usami
- Department of Oral Pathology, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Satoru Toyosawa
- Department of Oral Pathology, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Susumu Tanaka
- 1st Department of Oral and Maxillofacial Surgery, Graduate School of Dentistry, Osaka University, Osaka, Japan
| | - Shin-Ichiro Hiraoka
- 1st Department of Oral and Maxillofacial Surgery, Graduate School of Dentistry, Osaka University, Osaka, Japan
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28
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den Hollander LS, Béquignon OJM, Wang X, van Wezel K, Broekhuis J, Gorostiola González M, de Visser KE, IJzerman AP, van Westen GJP, Heitman LH. Impact of cancer-associated mutations in CC chemokine receptor 2 on receptor function and antagonism. Biochem Pharmacol 2023; 208:115399. [PMID: 36581051 DOI: 10.1016/j.bcp.2022.115399] [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: 10/14/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 12/27/2022]
Abstract
CC chemokine receptor 2 (CCR2), a G protein-coupled receptor, plays a role in many cancer-related processes such as metastasis formation and immunosuppression. Since ∼ 20 % of human cancers contain mutations in G protein-coupled receptors, ten cancer-associated CCR2 mutants obtained from the Genome Data Commons were investigated for their effect on receptor functionality and antagonist binding. Mutations were selected based on either their vicinity to CCR2's orthosteric or allosteric binding sites or their presence in conserved amino acid motifs. One of the mutant receptors, namely S101P2.63 with a mutation near the orthosteric binding site, did not express on the cell surface. All other studied mutants showed a decrease in or a lack of G protein activation in response to the main endogenous CCR2 ligand CCL2, but no change in potency was observed. Furthermore, INCB3344 and LUF7482 were chosen as representative orthosteric and allosteric antagonists, respectively. No change in potency was observed in a functional assay, but mutations located at F1163.28 impacted orthosteric antagonist binding significantly, while allosteric antagonist binding was abolished for L134Q3.46 and D137N3.49 mutants. As CC chemokine receptor 2 is an attractive drug target in cancer, the negative effect of these mutations on receptor functionality and drugability should be considered in the drug discovery process.
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Affiliation(s)
- L S den Hollander
- Leiden Academic Centre for Drug Research, Division of Drug Discovery and Safety, Leiden, The Netherlands
| | - O J M Béquignon
- Leiden Academic Centre for Drug Research, Division of Drug Discovery and Safety, Leiden, The Netherlands
| | - X Wang
- Leiden Academic Centre for Drug Research, Division of Drug Discovery and Safety, Leiden, The Netherlands
| | - K van Wezel
- Leiden Academic Centre for Drug Research, Division of Drug Discovery and Safety, Leiden, The Netherlands
| | - J Broekhuis
- Leiden Academic Centre for Drug Research, Division of Drug Discovery and Safety, Leiden, The Netherlands
| | - M Gorostiola González
- Leiden Academic Centre for Drug Research, Division of Drug Discovery and Safety, Leiden, The Netherlands; Oncode Institute, Leiden, The Netherlands
| | - K E de Visser
- Oncode Institute, Leiden, The Netherlands; Netherlands Cancer Institute, Division of Tumor Biology & Immunology, Amsterdam, The Netherlands; Leiden University, Department of Immunology, Medical Centre, Leiden, The Netherlands
| | - A P IJzerman
- Leiden Academic Centre for Drug Research, Division of Drug Discovery and Safety, Leiden, The Netherlands
| | - G J P van Westen
- Leiden Academic Centre for Drug Research, Division of Drug Discovery and Safety, Leiden, The Netherlands
| | - L H Heitman
- Leiden Academic Centre for Drug Research, Division of Drug Discovery and Safety, Leiden, The Netherlands; Oncode Institute, Leiden, The Netherlands.
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29
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Huber ME, Toy L, Schmidt MF, Weikert D, Schiedel M. Small Molecule Tools to Study Cellular Target Engagement for the Intracellular Allosteric Binding Site of GPCRs. Chemistry 2023; 29:e202202565. [PMID: 36193681 PMCID: PMC10100284 DOI: 10.1002/chem.202202565] [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: 08/17/2022] [Indexed: 11/11/2022]
Abstract
A conserved intracellular allosteric binding site (IABS) has recently been identified at several G protein-coupled receptors (GPCRs). Ligands targeting the IABS, so-called intracellular allosteric antagonists, are highly promising compounds for pharmaceutical intervention and currently evaluated in several clinical trials. Beside co-crystal structures that laid the foundation for the structure-based development of intracellular allosteric GPCR antagonists, small molecule tools that enable an unambiguous identification and characterization of intracellular allosteric GPCR ligands are of utmost importance for drug discovery campaigns in this field. Herein, we discuss recent approaches that leverage cellular target engagement studies for the IABS and thus play a critical role in the evaluation of IABS-targeted ligands as potential therapeutic agents.
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Affiliation(s)
- Max E Huber
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nikolaus-Fiebiger-Straße 10, 91058, Erlangen, Germany
| | - Lara Toy
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nikolaus-Fiebiger-Straße 10, 91058, Erlangen, Germany
| | - Maximilian F Schmidt
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nikolaus-Fiebiger-Straße 10, 91058, Erlangen, Germany
| | - Dorothee Weikert
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nikolaus-Fiebiger-Straße 10, 91058, Erlangen, Germany
| | - Matthias Schiedel
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nikolaus-Fiebiger-Straße 10, 91058, Erlangen, Germany
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30
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Li F, Li HM, Xiu RF, Zhang JK, Cui BD, Wan NW, Chen YZ, Han WY. Palladium-Catalyzed Domino Reaction for the Assembly of Norbornane-Containing Chromones with Dimethyl Squarate as the Solid C1 Source. Org Lett 2022; 24:9392-9397. [PMID: 36524990 DOI: 10.1021/acs.orglett.2c03713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Reported herein is a novel palladium-catalyzed [2 + 2 + 1] domino annulation of 3-iodochromones, bridged olefins, and dimethyl squarate allowing the construction of chromone-containing polycyclic compounds in good to high yields. Importantly, dimethyl squarate is first employed as the solid C1 source in organic synthesis. Gram-scale experiments, late-stage modification of natural products, as well as transformations of products show potential for further synthetic elaborations.
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Affiliation(s)
- Fei Li
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563006, PR China
| | - Hui-Min Li
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563006, PR China
| | - Ren-Feng Xiu
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563006, PR China
| | - Jin-Ke Zhang
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563006, PR China
| | - Bao-Dong Cui
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563006, PR China.,Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563006, PR China
| | - Nan-Wei Wan
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563006, PR China.,Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563006, PR China
| | - Yong-Zheng Chen
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563006, PR China.,Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563006, PR China
| | - Wen-Yong Han
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563006, PR China.,Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563006, PR China
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31
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Deng Y, Tan C, Huang S, Sun H, Li Z, Li J, Zhou Z, Sun M. Site-Specific Polyplex on CCR7 Down-Regulation and T Cell Elevation for Lymphatic Metastasis Blocking on Breast Cancer. Adv Healthc Mater 2022; 11:e2201166. [PMID: 36113849 DOI: 10.1002/adhm.202201166] [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: 05/16/2022] [Revised: 09/07/2022] [Indexed: 01/28/2023]
Abstract
Tumor metastasis contributes to high cancer mortality. Tumor cells in lymph nodes (LNs) are difficult to eliminate but underlie uncontrollable systemic metastasis. The CC chemokine receptor 7 (CCR7) is overexpressed in tumor cells and interacts with CC chemokine ligand 21 (CCL21) secreted from LNs, potentiating their lymphatic migration. Here, a site-specific polyplex is developed to block the CCR7-CCL21 signal and kill tumor cells toward LNs, greatly limiting their lymphatic infiltration. A CCR7-targeting small interfering RNA (siCCR7) is condensed by mPEG-poly-(lysine) with chlorin e6 (Ce6) modification (PPLC) to form PPLC/siCCR7. The knockdown of CCR7 by siCCR7 in tumor cells significantly reduced their response on CCL21 and LN tropism. Additionally, photodynamic therapy-mediated immune activation precisely targets and kills tumor cells released from the primary foci before they reaches the LNs, reducing the number of tumor cells entering the LNs. Consequently, the PPLC/siCCR7 polyplexes inhibited up to 92% of lung metastasis in 4T1 tumor bearing mice and reduced tumor cell migration to LNs by up to 80%. This site-specific strategy optimized anti-metastasis efficacy and promotes the clinical translational development of anti-metastatic therapy.
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Affiliation(s)
- Yueyang Deng
- NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing, 210009, China
| | - Caixia Tan
- NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing, 210009, China
| | - Shuguang Huang
- NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing, 210009, China
| | - Honghao Sun
- NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing, 210009, China
| | - Zhaoting Li
- NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing, 210009, China
| | - Jing Li
- NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing, 210009, China
| | - Zhanwei Zhou
- NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing, 210009, China
| | - Minjie Sun
- NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing, 210009, China
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Antibacterial Activity of Squaric Amide Derivative SA2 against Methicillin-Resistant Staphylococcus aureus. Antibiotics (Basel) 2022; 11:antibiotics11111497. [DOI: 10.3390/antibiotics11111497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 11/16/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA)-caused infection is difficult to treat because of its resistance to commonly used antibiotic, and poses a significant threat to public health. To develop new anti-bacterial agents to combat MRSA-induced infections, we synthesized novel squaric amide derivatives and evaluated their anti-bacterial activity by determining the minimum inhibitory concentration (MIC). Additionally, inhibitory activity of squaric amide 2 (SA2) was measured using the growth curve assay, time-kill assay, and an MRSA-induced skin infection animal model. A scanning electron microscope and transmission electron microscope were utilized to observe the effect of SA2 on the morphologies of MRSA. Transcriptome analysis and real-time PCR were used to test the possible anti-bacterial mechanism of SA2. The results showed that SA2 exerted bactericidal activity against a number of MRSA strains with an MIC at 4–8 µg/mL. It also inhibited the bacterial growth curve of MRSA strains in a dose-dependent manner, and reduced the colony formation unit in 4× MIC within 4–8 h. The infective lesion size and the bacterial number in the MRSA-induced infection tissue of mice were reduced significantly within 7 days after SA2 treatment. Moreover, SA2 disrupted the bacterial membrane and alanine dehydrogenase-dependent NAD+/NADH homeostasis. Our data indicates that SA2 is a possible lead compound for the development of new anti-bacterial agents against MRSA infection.
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Xu Z, Li S, Wan L, Hu J, Lu H, Zhang T. Role of low-intensity pulsed ultrasound in regulating macrophage polarization to accelerate tendon-bone interface repair. J Orthop Res 2022; 41:919-929. [PMID: 36203341 DOI: 10.1002/jor.25454] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 08/22/2022] [Accepted: 09/22/2022] [Indexed: 02/04/2023]
Abstract
Low-intensity pulsed ultrasound (LIPUS) has been proven to accelerate the healing of the tendon-bone interface (TBI), and macrophages are considered to play an important regulatory role. This study was designed to explore the polarization of macrophages during treatment of TBI injury with LIPUS. In a rat model of rotator cuff tear, LIPUS or mock sonication (controls) was administered from 1 week postoperatively. The supraspinatus-supraspinatus tendon-humerus complexes were harvested for further evaluation at different time points for measures such as new bone formation, TBI maturity, ultimate failure load and stiffness, and types of macrophages. In vitro, bone marrow-derived macrophages were cultured, and polarization was identified after stimulation with or without LIPUS (the LIPUS or control groups, respectively). Two weeks posttreatment, the LIPUS group showed higher bone volume/total volume ratios and better TBI maturity scores. Six weeks posttreatment, the failure load of the LIPUS group was significantly higher than that of the control group. LIPUS also accelerated initial inflammatory macrophage accumulation and facilitated anti-inflammatory macrophage polarization (M2) in the late period. In the in vitro macrophage polarization model, the LIPUS group showed a higher proportion of M2 macrophages and mRNA expression of anti-inflammatory genes than the control group, while there was no significant difference in the proinflammatory macrophages between the two groups. Our observations revealed that macrophage polarization may be a potential mechanism of LIPUS treatment for TBI repair.
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Affiliation(s)
- Zihan Xu
- Department of Sports Medicine, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Shengcan Li
- Department of Sports Medicine, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Liyang Wan
- Department of Sports Medicine, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Jianzhong Hu
- Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, China
| | - Hongbin Lu
- Department of Sports Medicine, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Tao Zhang
- Department of Sports Medicine, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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Ding T, Karlov DS, Pino-Angeles A, Tikhonova IG. Intermolecular Interactions in G Protein-Coupled Receptor Allosteric Sites at the Membrane Interface from Molecular Dynamics Simulations and Quantum Chemical Calculations. J Chem Inf Model 2022; 62:4736-4747. [PMID: 36178787 PMCID: PMC9554917 DOI: 10.1021/acs.jcim.2c00788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Allosteric modulators are called promising candidates in G protein-coupled receptor (GPCR) drug development by displaying subtype selectivity and more specific receptor modulation. Among the allosteric sites known to date, cavities at the receptor-lipid interface represent an uncharacteristic binding location that raises many questions about the ligand interactions and stability, the binding site structure, and how all of these are affected by lipid molecules. In this work, we analyze interactions in the allosteric sites of the PAR2, C5aR1, and GCGR receptors in three lipid compositions using molecular dynamics simulations. In addition, we performed quantum chemical calculations involving the symmetry-adapted perturbation theory (SAPT) and the natural population analysis to quantify the strength of intermolecular interactions. We show that besides classical hydrogen bonds, weak polar interactions such as O-HC, O-Br, and long-range electrostatics with the backbone amides contribute to the stability of allosteric modulators at the receptor-lipid interface. The allosteric cavities are detectable in various membrane compositions. The availability of polar atoms for interactions in such cavities can be assessed by water molecules from simulations. Although ligand-lipid interactions are weak, lipid tails play a role in ligand binding pose stability and the size of allosteric cavities. We discuss physicochemical aspects of ligand binding at the receptor-lipid interface and suggest a compound library enriched by weak donor groups for ligand search in such sites.
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Affiliation(s)
- Tianyi Ding
- School of Pharmacy, Medical Biology Centre, Queen's University Belfast, Belfast, Northern IrelandBT9 7BL, U.K
| | - Dmitry S Karlov
- School of Pharmacy, Medical Biology Centre, Queen's University Belfast, Belfast, Northern IrelandBT9 7BL, U.K
| | - Almudena Pino-Angeles
- School of Pharmacy, Medical Biology Centre, Queen's University Belfast, Belfast, Northern IrelandBT9 7BL, U.K
| | - Irina G Tikhonova
- School of Pharmacy, Medical Biology Centre, Queen's University Belfast, Belfast, Northern IrelandBT9 7BL, U.K
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35
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Bayrak A, Mohr F, Kolb K, Szpakowska M, Shevchenko E, Dicenta V, Rohlfing AK, Kudolo M, Pantsar T, Günther M, Kaczor AA, Poso A, Chevigné A, Pillaiyar T, Gawaz M, Laufer SA. Discovery and Development of First-in-Class ACKR3/CXCR7 Superagonists for Platelet Degranulation Modulation. J Med Chem 2022; 65:13365-13384. [PMID: 36150079 DOI: 10.1021/acs.jmedchem.2c01198] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The atypical chemokine receptor 3 (ACKR3), formerly known as CXC-chemokine receptor 7 (CXCR7), has been postulated to regulate platelet function and thrombus formation. Herein, we report the discovery and development of first-in-class ACKR3 agonists, which demonstrated superagonistic properties with Emax values of up to 160% compared to the endogenous reference ligand CXCL12 in a β-arrestin recruitment assay. Initial in silico screening using an ACKR3 homology model identified two hits, C10 (EC50 19.1 μM) and C11 (EC50 = 11.4 μM). Based on these hits, extensive structure-activity relationship studies were conducted by synthesis and testing of derivatives. It resulted in the identification of the novel thiadiazolopyrimidinone-based compounds 26 (LN5972, EC50 = 3.4 μM) and 27 (LN6023, EC50 = 3.5 μM). These compounds are selective for ACKR3 versus CXCR4 and show metabolic stability. In a platelet degranulation assay, these agonists effectively reduced P-selectin expression by up to 97%, suggesting potential candidates for the treatment of platelet-mediated thrombosis.
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Affiliation(s)
- Alp Bayrak
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Florian Mohr
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Kyra Kolb
- Department of Internal Medicine III, Cardiology and Angiology, University Hospital Tübingen, Otfried-Müller-Strasse 10, 72076 Tübingen, Germany
| | - Martyna Szpakowska
- Department of Infection and Immunity, Immuno-Pharmacology and Interactomics, Luxembourg Institute of Health (LIH), L-4354 Esch-sur-Alzette, Luxembourg
| | - Ekaterina Shevchenko
- Department of Internal Medicine VIII, Oncology and Pneumology, University Hospital Tübingen, Otfried-Müller-Strasse 14, 72076 Tübingen, Germany
| | - Valerie Dicenta
- Department of Internal Medicine III, Cardiology and Angiology, University Hospital Tübingen, Otfried-Müller-Strasse 10, 72076 Tübingen, Germany
| | - Anne-Katrin Rohlfing
- Department of Internal Medicine III, Cardiology and Angiology, University Hospital Tübingen, Otfried-Müller-Strasse 10, 72076 Tübingen, Germany
| | - Mark Kudolo
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Tatu Pantsar
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,School of Pharmacy, University of Eastern Finland, P.O. BOX 1627, 70211 Kuopio, Finland
| | - Marcel Günther
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Agnieszka A Kaczor
- School of Pharmacy, University of Eastern Finland, P.O. BOX 1627, 70211 Kuopio, Finland.,Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, 4A Chodzki St., PL-20093 Lublin, Poland
| | - Antti Poso
- School of Pharmacy, University of Eastern Finland, P.O. BOX 1627, 70211 Kuopio, Finland.,Department of Internal Medicine VIII, Oncology and Pneumology, University Hospital Tübingen, Otfried-Müller-Strasse 14, 72076 Tübingen, Germany
| | - Andy Chevigné
- Department of Infection and Immunity, Immuno-Pharmacology and Interactomics, Luxembourg Institute of Health (LIH), L-4354 Esch-sur-Alzette, Luxembourg
| | - Thanigaimalai Pillaiyar
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Meinrad Gawaz
- Department of Internal Medicine III, Cardiology and Angiology, University Hospital Tübingen, Otfried-Müller-Strasse 10, 72076 Tübingen, Germany
| | - Stefan A Laufer
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
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36
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Alrumaihi F. The Multi-Functional Roles of CCR7 in Human Immunology and as a Promising Therapeutic Target for Cancer Therapeutics. Front Mol Biosci 2022; 9:834149. [PMID: 35874608 PMCID: PMC9298655 DOI: 10.3389/fmolb.2022.834149] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
An important hallmark of the human immune system is to provide adaptive immunity against pathogens but tolerance toward self-antigens. The CC-chemokine receptor 7 (CCR7) provides a significant contribution in guiding cells to and within lymphoid organs and is important for acquiring immunity and tolerance. The CCR7 holds great importance in establishing thymic architecture and function and naïve and regulatory T-cell homing in the lymph nodes. Similarly, the receptor is a key regulator in cancer cell migration and the movement of dendritic cells. This makes the CCR7 an important receptor as a drug and prognostic marker. In this review, we discussed several biological roles of the CCR7 and its importance as a drug and prognostic marker.
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Affiliation(s)
- Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
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37
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Toy L, Huber ME, Schmidt MF, Weikert D, Schiedel M. Fluorescent Ligands Targeting the Intracellular Allosteric Binding Site of the Chemokine Receptor CCR2. ACS Chem Biol 2022; 17:2142-2152. [PMID: 35838163 DOI: 10.1021/acschembio.2c00263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Fluorescently labeled ligands are versatile molecular tools to study G protein-coupled receptors (GPCRs) and can be used for a range of different applications, including bioluminescence resonance energy transfer (BRET) assays. Here, we report the structure-based development of fluorescent ligands targeting the intracellular allosteric binding site (IABS) of the CC chemokine receptor 2 (CCR2), a class A GPCR that has been pursued as a drug target in oncology and inflammation. Starting from previously reported intracellular CCR2 antagonists, several tetramethylrhodamine (TAMRA)-labeled CCR2 ligands were designed, synthesized, and tested for their suitability as fluorescent reporters to probe binding to the IABS of CCR2. By means of these studies, we developed 14 as a fluorescent CCR2 ligand, enabling cell-free as well as cellular NanoBRET-based binding studies in a non-isotopic and high-throughput manner. Further, we show that 14 can be used as a tool for fragment-based screening approaches. Thus, our small-molecule-based fluorescent CCR2 ligand 14 represents a promising tool for future studies of CCR2 pharmacology.
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Affiliation(s)
- Lara Toy
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany
| | - Max E Huber
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany
| | - Maximilian F Schmidt
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany
| | - Dorothee Weikert
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany
| | - Matthias Schiedel
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany
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38
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Li H, Wu M, Zhao X. Role of chemokine systems in cancer and inflammatory diseases. MedComm (Beijing) 2022; 3:e147. [PMID: 35702353 PMCID: PMC9175564 DOI: 10.1002/mco2.147] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 12/12/2022] Open
Abstract
Chemokines are a large family of small secreted proteins that have fundamental roles in organ development, normal physiology, and immune responses upon binding to their corresponding receptors. The primary functions of chemokines are to coordinate and recruit immune cells to and from tissues and to participate in regulating interactions between immune cells. In addition to the generally recognized antimicrobial immunity, the chemokine/chemokine receptor axis also exerts a tumorigenic function in many different cancer models and is involved in the formation of immunosuppressive and protective tumor microenvironment (TME), making them potential prognostic markers for various hematologic and solid tumors. In fact, apart from its vital role in tumors, almost all inflammatory diseases involve chemokines and their receptors in one way or another. Modulating the expression of chemokines and/or their corresponding receptors on tumor cells or immune cells provides the basis for the exploitation of new drugs for clinical evaluation in the treatment of related diseases. Here, we summarize recent advances of chemokine systems in protumor and antitumor immune responses and discuss the prevailing understanding of how the chemokine system operates in inflammatory diseases. In this review, we also emphatically highlight the complexity of the chemokine system and explore its potential to guide the treatment of cancer and inflammatory diseases.
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Affiliation(s)
- Hongyi Li
- Department of Gynecology and Obstetrics, Development and Related Disease of Women and Children Key Laboratory of Sichuan Province, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of EducationWest China Second HospitalSichuan UniversityChengduChina
| | - Min Wu
- Department of Biomedical Sciences, School of Medicine and Health SciencesUniversity of North DakotaGrand ForksNorth DakotaUSA
| | - Xia Zhao
- Department of Gynecology and Obstetrics, Development and Related Disease of Women and Children Key Laboratory of Sichuan Province, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of EducationWest China Second HospitalSichuan UniversityChengduChina
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39
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Shifting CCR7 towards Its Monomeric Form Augments CCL19 Binding and Uptake. Cells 2022; 11:cells11091444. [PMID: 35563750 PMCID: PMC9101108 DOI: 10.3390/cells11091444] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/12/2022] [Accepted: 04/21/2022] [Indexed: 01/20/2023] Open
Abstract
The chemokine receptor CCR7, together with its ligands, is responsible for the migration and positioning of adaptive immune cells, and hence critical for launching adaptive immune responses. CCR7 is also induced on certain cancer cells and contributes to metastasis formation. Thus, CCR7 expression and signalling must be tightly regulated for proper function. CCR7, like many other members of the G-protein coupled receptor superfamily, can form homodimers and oligomers. Notably, danger signals associated with pathogen encounter promote oligomerisation of CCR7 and is considered as one layer of regulating its function. Here, we assessed the dimerisation of human CCR7 and several single point mutations using split-luciferase complementation assays. We demonstrate that dimerisation-defective CCR7 mutants can be transported to the cell surface and elicit normal chemokine-driven G-protein activation. By contrast, we discovered that CCR7 mutants whose expression are shifted towards monomers significantly augment their capacities to bind and internalise fluorescently labelled CCL19. Modeling of the receptor suggests that dimerisation-defective CCR7 mutants render the extracellular loops more flexible and less structured, such that the chemokine recognition site located in the binding pocket might become more accessible to its ligand. Overall, we provide new insights into how the dimerisation state of CCR7 affects CCL19 binding and receptor trafficking.
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40
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Proj M, De Jonghe S, Van Loy T, Jukič M, Meden A, Ciber L, Podlipnik Č, Grošelj U, Konc J, Schols D, Gobec S. A Set of Experimentally Validated Decoys for the Human CC Chemokine Receptor 7 (CCR7) Obtained by Virtual Screening. Front Pharmacol 2022; 13:855653. [PMID: 35370691 PMCID: PMC8972196 DOI: 10.3389/fphar.2022.855653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 02/28/2022] [Indexed: 11/21/2022] Open
Abstract
We present a state-of-the-art virtual screening workflow aiming at the identification of novel CC chemokine receptor 7 (CCR7) antagonists. Although CCR7 is associated with a variety of human diseases, such as immunological disorders, inflammatory diseases, and cancer, this target is underexplored in drug discovery and there are no potent and selective CCR7 small molecule antagonists available today. Therefore, computer-aided ligand-based, structure-based, and joint virtual screening campaigns were performed. Hits from these virtual screenings were tested in a CCL19-induced calcium signaling assay. After careful evaluation, none of the in silico hits were confirmed to have an antagonistic effect on CCR7. Hence, we report here a valuable set of 287 inactive compounds that can be used as experimentally validated decoys.
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Affiliation(s)
- Matic Proj
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Steven De Jonghe
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Tom Van Loy
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Marko Jukič
- Faculty of Chemistry and Chemical Engineering, Laboratory of Physical Chemistry and Chemical Thermodynamics, University of Maribor, Maribor, Slovenia.,Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Koper, Slovenia
| | - Anže Meden
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Luka Ciber
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Črtomir Podlipnik
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Uroš Grošelj
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Janez Konc
- National Institute of Chemistry, Ljubljana, Slovenia
| | - Dominique Schols
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Stanislav Gobec
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
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41
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Billen M, Schols D, Verwilst P. Targeting chemokine receptors from the inside-out: discovery and development of small-molecule intracellular antagonists. Chem Commun (Camb) 2022; 58:4132-4148. [PMID: 35274633 DOI: 10.1039/d1cc07080k] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ever since the first biologically active chemokines were discovered in the late 1980s, these messenger proteins and their receptors have been the target for a plethora of drug discovery efforts in the pharmaceutical industry, as well as in academia. Owing to the publication of several chemokine receptor X-ray crystal structures, a highly druggable, intracellular, allosteric binding site which partially overlaps with the G protein binding site was discovered. This intriguing, new approach for chemokine receptor antagonism has captured researchers around the world, pushing the exploration of this intracellular binding site and new antagonists thereof. In this review, we have highlighted the past two decades of research on small-molecule chemokine receptor antagonists that modulate receptor function at the intracellular binding site.
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Affiliation(s)
- Margaux Billen
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 - Box 1041, 3000 Leuven, Belgium.
| | - Dominique Schols
- KU Leuven, Rega Institute for Medical Research, Virology and Chemotherapy, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
| | - Peter Verwilst
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 - Box 1041, 3000 Leuven, Belgium.
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42
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Larsen O, van der Velden WJC, Mavri M, Schuermans S, Rummel PC, Karlshøj S, Gustavsson M, Proost P, Våbenø J, Rosenkilde MM. Identification of a conserved chemokine receptor motif that enables ligand discrimination. Sci Signal 2022; 15:eabg7042. [PMID: 35258997 DOI: 10.1126/scisignal.abg7042] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Extensive ligand-receptor promiscuity in the chemokine signaling system balances beneficial redundancy and specificity. However, this feature poses a major challenge to selectively modulate the system pharmacologically. Here, we identified a conserved cluster of three aromatic receptor residues that anchors the second extracellular loop (ECL2) to the top of receptor transmembrane helices (TM) 4 and 5 and enables recognition of both shared and specific characteristics of interacting chemokines. This cluster was essential for the activation of several chemokine receptors. Furthermore, characteristic motifs of the ß1 strand and 30s loop make the two main CC-chemokine subgroups-the macrophage inflammatory proteins (MIPs) and monocyte chemoattractant proteins (MCPs)-differentially dependent on this cluster in the promiscuous receptors CCR1, CCR2, and CCR5. The cluster additionally enabled CCR1 and CCR5 to discriminate between closely related MIPs based on the N terminus of the chemokine. G protein signaling and β-arrestin2 recruitment assays confirmed the importance of the conserved cluster in receptor discrimination of chemokine ligands. This extracellular site may facilitate the development of chemokine-related therapeutics.
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Affiliation(s)
- Olav Larsen
- Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.,Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | - Wijnand J C van der Velden
- Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Maša Mavri
- Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.,Institute of Preclinical Sciences, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia
| | - Sara Schuermans
- Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.,Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | - Pia C Rummel
- Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Stefanie Karlshøj
- Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Martin Gustavsson
- Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Paul Proost
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | - Jon Våbenø
- Helgeland Hospital Trust, Prestmarkveien 1, 8800 Sandnessjøen, Norway
| | - Mette M Rosenkilde
- Laboratory for Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
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43
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Hong W, Yang B, He Q, Wang J, Weng Q. New Insights of CCR7 Signaling in Dendritic Cell Migration and Inflammatory Diseases. Front Pharmacol 2022; 13:841687. [PMID: 35281921 PMCID: PMC8914285 DOI: 10.3389/fphar.2022.841687] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/07/2022] [Indexed: 12/14/2022] Open
Abstract
CCR7, collaborated with its ligands CCL19 and CCL21, controls extensive migratory events in the immune system. CCR7-bearing dendritic cells can swarm into T-cell zones in lymph nodes, initiating the antigen presentation and T-cell response. Abnormal expression of CCR7 in dendritic cells will cause a series of inflammatory diseases due to the chaotic dendritic cell trafficking. In this review, we take an in-depth look at the structural–functional domains of CCR7 and CCR7-bearing dendritic cell trajectory to lymph nodes. Then, we summarize the regulatory network of CCR7, including transcriptional regulation, translational and posttranslational regulation, internalization, desensitization, and recycling. Furthermore, the potential strategies of targeting the CCR7 network to regulate dendritic cell migration and to deal with inflammatory diseases are integrated, which not only emphasizes the possibility of CCR7 to be a potential target of immunotherapy but also has an implication on the homing of dendritic cells to benefit inflammatory diseases.
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Affiliation(s)
- Wenxiang Hong
- Center for Drug Safety Evaluation and Research, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Bo Yang
- Center for Drug Safety Evaluation and Research, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Qiaojun He
- Center for Drug Safety Evaluation and Research, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
- The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Jiajia Wang
- Center for Drug Safety Evaluation and Research, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
- *Correspondence: Qinjie Weng, ; Jiajia Wang,
| | - Qinjie Weng
- Center for Drug Safety Evaluation and Research, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
- The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- *Correspondence: Qinjie Weng, ; Jiajia Wang,
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44
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Huber ME, Toy L, Schmidt MF, Vogt H, Budzinski J, Wiefhoff MFJ, Merten N, Kostenis E, Weikert D, Schiedel M. Chemisch‐biologischer Werkzeugkasten für die intrazelluläre Bindungsstelle von CCR9: Fluoreszierende Liganden, neue Leitstrukturen und PROTACs. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202116782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Max E. Huber
- Department Chemie and Pharmazie Lehrstuhl für Pharmazeutische Chemie Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Nikolaus-Fiebiger-Straße 10 91058 Erlangen Deutschland
| | - Lara Toy
- Department Chemie and Pharmazie Lehrstuhl für Pharmazeutische Chemie Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Nikolaus-Fiebiger-Straße 10 91058 Erlangen Deutschland
| | - Maximilian F. Schmidt
- Department Chemie and Pharmazie Lehrstuhl für Pharmazeutische Chemie Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Nikolaus-Fiebiger-Straße 10 91058 Erlangen Deutschland
| | - Hannah Vogt
- Department Chemie and Pharmazie Lehrstuhl für Pharmazeutische Chemie Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Nikolaus-Fiebiger-Straße 10 91058 Erlangen Deutschland
| | - Julian Budzinski
- Department Chemie and Pharmazie Lehrstuhl für Pharmazeutische Chemie Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Nikolaus-Fiebiger-Straße 10 91058 Erlangen Deutschland
| | - Martin F. J. Wiefhoff
- Institut für Pharmazeutische Biologie Universität Bonn Nussallee 6 53115 Bonn Deutschland
| | - Nicole Merten
- Institut für Pharmazeutische Biologie Universität Bonn Nussallee 6 53115 Bonn Deutschland
| | - Evi Kostenis
- Institut für Pharmazeutische Biologie Universität Bonn Nussallee 6 53115 Bonn Deutschland
| | - Dorothee Weikert
- Department Chemie and Pharmazie Lehrstuhl für Pharmazeutische Chemie Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Nikolaus-Fiebiger-Straße 10 91058 Erlangen Deutschland
| | - Matthias Schiedel
- Department Chemie and Pharmazie Lehrstuhl für Pharmazeutische Chemie Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Nikolaus-Fiebiger-Straße 10 91058 Erlangen Deutschland
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45
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Allosteric modulation of dopamine D 2L receptor in complex with G i1 and G i2 proteins: the effect of subtle structural and stereochemical ligand modifications. Pharmacol Rep 2022; 74:406-424. [PMID: 35064921 PMCID: PMC8964653 DOI: 10.1007/s43440-021-00352-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/17/2021] [Accepted: 12/28/2021] [Indexed: 12/28/2022]
Abstract
Background Allosteric modulation of G protein-coupled receptors (GPCRs) is nowadays one of the hot topics in drug discovery. In particular, allosteric modulators of D2 receptor have been proposed as potential modern therapeutics to treat schizophrenia and Parkinson’s disease. Methods To address some subtle structural and stereochemical aspects of allosteric modulation of D2 receptor, we performed extensive in silico studies of both enantiomers of two compounds (compound 1 and compound 2), and one of them (compound 2) was synthesized as a racemate in-house and studied in vitro. Results Our molecular dynamics simulations confirmed literature reports that the R enantiomer of compound 1 is a positive allosteric modulator of the D2L receptor, while its S enantiomer is a negative allosteric modulator. Moreover, based on the principal component analysis (PCA), we hypothesized that both enantiomers of compound 2 behave as silent allosteric modulators, in line with our in vitro studies. PCA calculations suggest that the most pronounced modulator-induced receptor rearrangements occur at the transmembrane helix 7 (TM7). In particular, TM7 bending at the conserved P7.50 and G7.42 was observed. The latter resides next to the Y7.43, which is a significant part of the orthosteric binding site. Moreover, the W7.40 conformation seems to be affected by the presence of the positive allosteric modulator. Conclusions Our work reveals that allosteric modulation of the D2L receptor can be affected by subtle ligand modifications. A change in configuration of a chiral carbon and/or minor structural modulator modifications are solely responsible for the functional outcome of the allosteric modulator. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1007/s43440-021-00352-x.
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46
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Preparation of a stable CCL5·CCR5·Gi signaling complex for Cryo-EM analysis. Methods Cell Biol 2022; 169:115-141. [DOI: 10.1016/bs.mcb.2022.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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47
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Chen Y, Fleetwood O, Pérez-Conesa S, Delemotte L. Allosteric Effect of Nanobody Binding on Ligand-Specific Active States of the β2 Adrenergic Receptor. J Chem Inf Model 2021; 61:6024-6037. [PMID: 34780174 PMCID: PMC8715506 DOI: 10.1021/acs.jcim.1c00826] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Nanobody binding
stabilizes G-protein-coupled receptors (GPCR)
in a fully active state and modulates their affinity for bound ligands.
However, the atomic-level basis for this allosteric regulation remains
elusive. Here, we investigate the conformational changes induced by
the binding of a nanobody (Nb80) on the active-like β2 adrenergic
receptor (β2AR) via enhanced sampling molecular dynamics simulations.
Dimensionality reduction analysis shows that Nb80 stabilizes structural
features of the β2AR with an ∼14 Å outward movement
of transmembrane helix 6 and a close proximity of transmembrane (TM)
helices 5 and 7, and favors the fully active-like conformation of
the receptor, independent of ligand binding, in contrast to the conditions
under which no intracellular binding partner is bound, in which case
the receptor is only stabilized in an intermediate-active state. This
activation is supported by the residues located at hotspots located
on TMs 5, 6, and 7, as shown by supervised machine learning methods.
Besides, ligand-specific subtle differences in the conformations assumed
by intracellular loop 2 and extracellular loop 2 are captured from
the trajectories of various ligand-bound receptors in the presence
of Nb80. Dynamic network analysis further reveals that Nb80 binding
triggers tighter and stronger local communication networks between
the Nb80 and the ligand-binding sites, primarily involving residues
around ICL2 and the intracellular end of TM3, TM5, TM6, as well as
ECL2, ECL3, and the extracellular ends of TM6 and TM7. In particular,
we identify unique allosteric signal transmission mechanisms between
the Nb80-binding site and the extracellular domains in conformations
modulated by a full agonist, BI167107, and a G-protein-biased partial
agonist, salmeterol, involving mainly TM1 and TM2, and TM5, respectively.
Altogether, our results provide insights into the effect of intracellular
binding partners on the GPCR activation mechanism, which should be
taken into account in structure-based drug discovery.
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Affiliation(s)
- Yue Chen
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, SE-17121 Solna, Sweden
| | - Oliver Fleetwood
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, SE-17121 Solna, Sweden
| | - Sergio Pérez-Conesa
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, SE-17121 Solna, Sweden
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, SE-17121 Solna, Sweden
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48
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Huber ME, Toy L, Schmidt MF, Vogt H, Budzinski J, Wiefhoff MFJ, Merten N, Kostenis E, Weikert D, Schiedel M. A Chemical Biology Toolbox Targeting the Intracellular Binding Site of CCR9: Fluorescent Ligands, New Drug Leads and PROTACs. Angew Chem Int Ed Engl 2021; 61:e202116782. [PMID: 34936714 PMCID: PMC9306553 DOI: 10.1002/anie.202116782] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Indexed: 11/24/2022]
Abstract
A conserved intracellular allosteric binding site (IABS) has recently been identified at several G protein‐coupled receptors (GPCRs). Starting from vercirnon, an intracellular C−C chemokine receptor type 9 (CCR9) antagonist and previous phase III clinical candidate for the treatment of Crohn's disease, we developed a chemical biology toolbox targeting the IABS of CCR9. We first synthesized a fluorescent ligand enabling equilibrium and kinetic binding studies via NanoBRET as well as fluorescence microscopy. Applying this molecular tool in a membrane‐based setup and in living cells, we discovered a 4‐aminopyrimidine analogue as a new intracellular CCR9 antagonist with improved affinity. To chemically induce CCR9 degradation, we then developed the first PROTAC targeting the IABS of GPCRs. In a proof‐of‐principle study, we succeeded in showing that our CCR9‐PROTAC is able to reduce CCR9 levels, thereby offering an unprecedented approach to modulate GPCR activity.
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Affiliation(s)
- Max Erhard Huber
- Friedrich-Alexander-Universität Erlangen-Nürnberg: Friedrich-Alexander-Universitat Erlangen-Nurnberg, Department of Chemistry and Pharmacy, Nikolaus-Fiebiger-Straße 10, 91058, Erlangen, GERMANY
| | - Lara Toy
- Friedrich-Alexander-Universität Erlangen-Nürnberg: Friedrich-Alexander-Universitat Erlangen-Nurnberg, Department of Chemistry and Pharmacy, Nikolaus-Fiebiger-Straße 10, 91058, Erlangen, GERMANY
| | - Maximilian Franz Schmidt
- Friedrich-Alexander-Universität Erlangen-Nürnberg: Friedrich-Alexander-Universitat Erlangen-Nurnberg, Department of Chemistry and Pharmacy, Nikolaus-Fiebiger-Straße 10, 91058, Erlangen, GERMANY
| | - Hannah Vogt
- Friedrich-Alexander-Universität Erlangen-Nürnberg: Friedrich-Alexander-Universitat Erlangen-Nurnberg, Department of Chemistry and Pharmacy, Nikolaus-Fiebiger-Straße 10, 91058, Erlangen, GERMANY
| | - Julian Budzinski
- Friedrich-Alexander-Universität Erlangen-Nürnberg: Friedrich-Alexander-Universitat Erlangen-Nurnberg, Department of Chemistry and Pharmacy, Nikolaus-Fiebiger-Straße 10, 91058, Erlangen, GERMANY
| | - Martin Ferdinand Josef Wiefhoff
- University of Bonn: Rheinische Friedrich-Wilhelms-Universitat Bonn, Institute for Pharmaceutical Biology, Nussallee 6, 53115, Bonn, GERMANY
| | - Nicole Merten
- University of Bonn: Rheinische Friedrich-Wilhelms-Universitat Bonn, Institute for Pharmaceutical Biology, Nussallee 6, 53115, Bonn, GERMANY
| | - Evi Kostenis
- University of Bonn: Rheinische Friedrich-Wilhelms-Universitat Bonn, Institute of Pharmaceutical Biology, Nussallee 6, 53115, Bonn, GERMANY
| | - Dorothee Weikert
- Friedrich-Alexander-Universität Erlangen-Nürnberg: Friedrich-Alexander-Universitat Erlangen-Nurnberg, Department of Chemistry and Pharmacy, Nikolaus-Fiebiger-Straße 10, 91058, Erlangen, GERMANY
| | - Matthias Schiedel
- Friedrich-Alexander-Universität Erlangen-Nürnberg: Friedrich-Alexander-Universitat Erlangen-Nurnberg, Department of Chemistry and Pharmacy, Nikolaus-Fiebiger-Straße 10, Erlangen, 91058, Erlangen, GERMANY
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49
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Ciancetta A, Gill AK, Ding T, Karlov DS, Chalhoub G, McCormick PJ, Tikhonova IG. Probe Confined Dynamic Mapping for G Protein-Coupled Receptor Allosteric Site Prediction. ACS CENTRAL SCIENCE 2021; 7:1847-1862. [PMID: 34841058 PMCID: PMC8614102 DOI: 10.1021/acscentsci.1c00802] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Indexed: 05/06/2023]
Abstract
Targeting G protein-coupled receptors (GPCRs) through allosteric sites offers advantages over orthosteric sites in identifying drugs with increased selectivity and potentially reduced side effects. In this study, we developed a probe confined dynamic mapping protocol that allows the prediction of allosteric sites at both the GPCR extracellular and intracellular sides, as well as at the receptor-lipid interface. The applied harmonic wall potential enhanced sampling of probe molecules in a selected area of a GPCR while preventing membrane distortion in molecular dynamics simulations. The specific probes derived from GPCR allosteric ligand structures performed better in allosteric site mapping compared to commonly used cosolvents. The M2 muscarinic, β2 adrenergic, and P2Y1 purinergic receptors were selected for the protocol's retrospective validation. The protocol was next validated prospectively to locate the binding site of [5-fluoro-4-(hydroxymethyl)-2-methoxyphenyl]-(4-fluoro-1H-indol-1-yl)methanone at the D2 dopamine receptor, and subsequent mutagenesis confirmed the prediction. The protocol provides fast and efficient prediction of key amino acid residues surrounding allosteric sites in membrane proteins and facilitates the structure-based design of allosteric modulators.
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Affiliation(s)
- Antonella Ciancetta
- School
of Pharmacy, Medical Biology Centre, Queen’s
University Belfast, Belfast, Northern Ireland BT9 7BL, U.K.
| | - Amandeep Kaur Gill
- Centre
for Endocrinology, William Harvey Research Institute, Bart’s
and the London School of Medicine and Dentistry, Queen
Mary, University of London, London, EC1M 6BQ, U.K.
| | - Tianyi Ding
- School
of Pharmacy, Medical Biology Centre, Queen’s
University Belfast, Belfast, Northern Ireland BT9 7BL, U.K.
| | - Dmitry S. Karlov
- School
of Pharmacy, Medical Biology Centre, Queen’s
University Belfast, Belfast, Northern Ireland BT9 7BL, U.K.
| | - George Chalhoub
- Centre
for Endocrinology, William Harvey Research Institute, Bart’s
and the London School of Medicine and Dentistry, Queen
Mary, University of London, London, EC1M 6BQ, U.K.
| | - Peter J. McCormick
- Centre
for Endocrinology, William Harvey Research Institute, Bart’s
and the London School of Medicine and Dentistry, Queen
Mary, University of London, London, EC1M 6BQ, U.K.
| | - Irina G. Tikhonova
- School
of Pharmacy, Medical Biology Centre, Queen’s
University Belfast, Belfast, Northern Ireland BT9 7BL, U.K.
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50
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Alrumaihi F. A Comprehensive Computational Screening of Phytochemicals Derived from Saudi Medicinal Plants against Human CC Chemokine Receptor 7 to Identify Potential Anti-Cancer Therapeutics. Molecules 2021; 26:6354. [PMID: 34770763 PMCID: PMC8588288 DOI: 10.3390/molecules26216354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 01/03/2023] Open
Abstract
Homeostatic trafficking of immune cells by CC chemokine receptor 7 (CCR7) keeps immune responses and tolerance in a balance. The involvement of this protein in lymph node metastasis in cancer marks CCR7 as a penitential drug target. Using the crystal structure of CCR7, herein, a comprehensive virtual screening study is presented to filter novel strong CCR7 binding phytochemicals from Saudi medicinal plants that have a higher binding affinity for the intracellular allosteric binding pocket. By doing so, three small natural molecules named as Hit-1 (1,8,10-trihydroxy-3-methoxy-6-methylanthracen-9(4H)-one), Hit-2 (4-(3,4-dimethoxybenzyl)-3-(4-hydroxy-3-methoxybenzyl)dihydrofuran-2(3H)-one), and Hit-3 (10-methyl-12,13-dihydro-[1,2]dioxolo[3,4,5-de]furo[3,2-g]isochromeno[4,3-b]chromen-8-ol) are predicted showing strong binding potential for the CC chemokine receptor 7 allosteric pocket. During molecular dynamics simulations, the compounds were observed in the formation of several chemical bonding of short bond distances. Additionally, the molecules remained in strong contact with the active pocket residues and experienced small conformation changes that seemed to be mediated by the CCR7 loops to properly engage the ligands. Two types of binding energy methods (MM/GBPBSA and WaterSwap) were additionally applied to further validate docking and simulation findings. Both analyses complement the good affinity of compounds for CCR7, the electrostatic and van der Waals energies being the most dominant in intermolecular interactions. The active pocket residue's role in compounds binding was further evaluated via alanine scanning, which highlighted their importance in natural compounds binding. Additionally, the compounds fulfilled all drug-like rules: Lipinski, Ghose, Veber, Egan, and Muegge passed many safety parameters, making them excellent anti-cancer candidates for experimental testing.
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Affiliation(s)
- Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
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