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Szustak M, Korkus E, Madaj R, Chworos A, Dąbrowski G, Czaplicki S, Tabandeh E, Maciejewska G, Koziołkiewicz M, Konopka I, Gliszczyńska A, Gendaszewska-Darmach E. Lysophosphatidylcholines Enriched with cis and trans Palmitoleic Acid Regulate Insulin Secretion via GPR119 Receptor. ACS Med Chem Lett 2024; 15:197-204. [PMID: 38352825 PMCID: PMC10860191 DOI: 10.1021/acsmedchemlett.3c00263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 12/17/2023] [Accepted: 12/21/2023] [Indexed: 02/16/2024] Open
Abstract
Among lipids, lysophosphatidylcholines (LPCs) with various fatty acyl chains have been identified as potential agonists of G protein-coupled receptors (GPCRs). Recently, targeting GPCRs has been switched to diabetes and obesity. Concomitantly, our last findings indicate the insulin secretagogue properties of cis and trans palmitoleic acid (16:1, n-7) resulting from GPCR activation, however, associated with different signaling pathways. We here report the synthesis of LPCs bearing two geometrical isomers of palmitoleic acids and investigation of their impact on human pancreatic β cells viability, insulin secretion, and activation of four GPCRs previously demonstrated to be targeted by free fatty acids and LPCs. Moreover, molecular modeling was exploited to investigate the probable binding sites of tested ligands and calculate their affinity toward GPR40, GPR55, GPR119, and GPR120 receptors.
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Affiliation(s)
- Marcin Szustak
- Faculty
of Biotechnology and Food Sciences, Institute of Molecular and Industrial
Biotechnology, Lodz University of Technology, Stefanowskiego 2/22, 90-537 Lodz, Poland
| | - Eliza Korkus
- Faculty
of Biotechnology and Food Sciences, Institute of Molecular and Industrial
Biotechnology, Lodz University of Technology, Stefanowskiego 2/22, 90-537 Lodz, Poland
| | - Rafal Madaj
- Division
of Bioorganic Chemistry Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza, 112, 90-363 Lodz, Poland
- Institute
of Evolutionary Biology, Faculty of Biology, Biological and Chemical
Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Arkadiusz Chworos
- Division
of Bioorganic Chemistry Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza, 112, 90-363 Lodz, Poland
| | - Grzegorz Dąbrowski
- Faculty
of Food Sciences, Chair of Plant Food Chemistry and Processing, University of Warmia and Mazury in Olsztyn, Pl. Cieszyński 1, 10-957 Olsztyn, Poland
| | - Sylwester Czaplicki
- Faculty
of Food Sciences, Chair of Plant Food Chemistry and Processing, University of Warmia and Mazury in Olsztyn, Pl. Cieszyński 1, 10-957 Olsztyn, Poland
| | - Erfan Tabandeh
- Faculty
of Biotechnology and Food Sciences, Institute of Molecular and Industrial
Biotechnology, Lodz University of Technology, Stefanowskiego 2/22, 90-537 Lodz, Poland
| | - Gabriela Maciejewska
- Central
Laboatory of the Instrumental Analysis, Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, Wroclaw 50-370, Poland
| | - Maria Koziołkiewicz
- Faculty
of Biotechnology and Food Sciences, Institute of Molecular and Industrial
Biotechnology, Lodz University of Technology, Stefanowskiego 2/22, 90-537 Lodz, Poland
| | - Iwona Konopka
- Faculty
of Food Sciences, Chair of Plant Food Chemistry and Processing, University of Warmia and Mazury in Olsztyn, Pl. Cieszyński 1, 10-957 Olsztyn, Poland
| | - Anna Gliszczyńska
- Department
of Food Chemistry and Biocatalysis, Wroclaw
University of Environmental and Life Sciences, Norwida 25, 50-375 Wrocław, Poland
| | - Edyta Gendaszewska-Darmach
- Faculty
of Biotechnology and Food Sciences, Institute of Molecular and Industrial
Biotechnology, Lodz University of Technology, Stefanowskiego 2/22, 90-537 Lodz, Poland
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Kang-Pettinger T, Walker K, Brown R, Cowan R, Wright H, Baravalle R, Waters LC, Muskett FW, Bowler MW, Sawmynaden K, Coombs PJ, Carr MD, Hall G. Identification, binding, and structural characterization of single domain anti-PD-L1 antibodies inhibitory of immune regulatory proteins PD-1 and CD80. J Biol Chem 2022; 299:102769. [PMID: 36470427 PMCID: PMC9811221 DOI: 10.1016/j.jbc.2022.102769] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/23/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Programmed death-ligand 1 (PD-L1) is a key immune regulatory protein that interacts with programmed cell death protein 1 (PD-1), leading to T-cell suppression. Whilst this interaction is key in self-tolerance, cancer cells evade the immune system by overexpressing PD-L1. Inhibition of the PD-1/PD-L1 pathway with standard monoclonal antibodies has proven a highly effective cancer treatment; however, single domain antibodies (VHH) may offer numerous potential benefits. Here, we report the identification and characterization of a diverse panel of 16 novel VHHs specific to PD-L1. The panel of VHHs demonstrate affinities of 0.7 nM to 5.1 μM and were able to completely inhibit PD-1 binding to PD-L1. The binding site for each VHH on PD-L1 was determined using NMR chemical shift perturbation mapping and revealed a common binding surface encompassing the PD-1-binding site. Additionally, we solved crystal structures of two representative VHHs in complex with PD-L1, which revealed unique binding modes. Similar NMR experiments were used to identify the binding site of CD80 on PD-L1, which is another immune response regulatory element and interacts with PD-L1 localized on the same cell surface. CD80 and PD-1 were revealed to share a highly overlapping binding site on PD-L1, with the panel of VHHs identified expected to inhibit CD80 binding. Comparison of the CD80 and PD-1 binding sites on PD-L1 enabled the identification of a potential antibody binding region able to confer specificity for the inhibition of PD-1 binding only, which may offer therapeutic benefits to counteract cancer cell evasion of the immune system.
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Affiliation(s)
- Tara Kang-Pettinger
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, UK
| | - Kayleigh Walker
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, UK
| | - Richard Brown
- LifeArc, Centre for Therapeutics Discovery, Open Innovation Campus, Stevenage, UK
| | - Richard Cowan
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, UK
| | - Helena Wright
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, UK
| | - Roberta Baravalle
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, UK
| | - Lorna C. Waters
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, UK
| | - Frederick W. Muskett
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, UK
| | | | - Kovilen Sawmynaden
- LifeArc, Centre for Therapeutics Discovery, Open Innovation Campus, Stevenage, UK
| | - Peter J. Coombs
- LifeArc, Centre for Therapeutics Discovery, Open Innovation Campus, Stevenage, UK
| | - Mark D. Carr
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, UK,For correspondence: Gareth Hall; Mark D. Carr
| | - Gareth Hall
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, UK,For correspondence: Gareth Hall; Mark D. Carr
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3
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Shams R, Ito Y, Miyatake H. Development of an RHEB-Targeting Peptide To Inhibit mTORC1 Kinase Activity. ACS OMEGA 2022; 7:23479-23486. [PMID: 35847293 PMCID: PMC9280966 DOI: 10.1021/acsomega.2c01865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In cancer, the mechanistic/mammalian target of rapamycin complex-1 (mTORC1) is hyperactivated to promote survival under adverse conditions. The kinase activity of mTORC1 is activated by small-GTPase RHEB-GTP. Therefore, a new modality to inhibit mTORC1 activity has emerged, through intercepting RHEB. However, due to the relatively large contact area involved in the interaction between RHEB and mTORC1, facilitating this inhibition through small molecules has been challenging. Here, we report the development of a peptide that can inhibit the RHEB-mTORC1 interaction. The peptide, P1_WT, was designed based on the α-helix (aa 101-115) of the N-heat domain of mTOR to interact with switch II of RHEB. P1_WT bound to RHEB (K D = 0.14 μM) and inhibited RHEB-mTORN-heat interaction (IC50 = 0.33 μM) in vitro. Consequently, P1_WT inhibited mTORC1 activity at a sub-micromolar level (IC50 ∼ 0.3 μM). P1_WT was predicted to be cell-permeable due to the rich content of arginine (23%), enhancing the intracellular translocation. These results show that P1_WT is a potential compound to further develop inhibitors for mTORC1 by intercepting RHEB from mTORC1.
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Affiliation(s)
- Raef Shams
- Emergent
Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, Wako, Saitama 351-0198, Japan
- Department
of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama City, Saitama 338-8570, Japan
| | - Yoshihiro Ito
- Emergent
Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, Wako, Saitama 351-0198, Japan
- Nano
Medical Engineering Laboratory, RIKEN Cluster
for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Hideyuki Miyatake
- Department
of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama City, Saitama 338-8570, Japan
- Nano
Medical Engineering Laboratory, RIKEN Cluster
for Pioneering Research, Wako, Saitama 351-0198, Japan
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Ma C, Qiao S, Liu Z, Shan L, Liang C, Fan M, Sun F. A Novel Type of PD-L1 Inhibitor rU1 snRNPA From Human-Derived Protein Scaffolds Library. Front Oncol 2021; 11:781046. [PMID: 34912719 PMCID: PMC8666589 DOI: 10.3389/fonc.2021.781046] [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: 09/22/2021] [Accepted: 11/05/2021] [Indexed: 11/13/2022] Open
Abstract
Three marketed anti-PD-L1 antibodies almost have severe immune-mediated side effects. The therapeutic effects of anti-PD-L1 chemical inhibitors are not satisfied in the clinical trials. Here we constructed human-derived protein scaffolds library and screened scaffolds with a shape complementary to the PD-1 binding domain of PD-L1. The RNA binding domain of U1 snRNPA was selected as one of potential binders because it had the most favorable binding energies with PD-L1 and conformed to pre-established biological criteria for the screening of candidates. The recombinant U1 snRNPA (rU1 snRNPA) in Escherichia coli exhibits anti-cancer activity in melanoma and breast cancer by reactivating tumor-suppressed T cells in vitro and anti-melanoma activity in vivo. Considering hydrophobic and electrostatic interactions, three residues were mutated on the interface of U1 snRNPA and PD-L1 complex, and the ranked variants by PatchDock and A32D showed an increased active phenotype. The screening of human-derived protein scaffolds may become the potential development of therapeutic agents.
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Affiliation(s)
- Chuang Ma
- School of Pharmaceutical Sciences, Jilin University, Changchun, China
| | - Sennan Qiao
- School of Pharmaceutical Sciences, Jilin University, Changchun, China
| | - Zhiyi Liu
- Institute of Frontier Medical Science, Jilin University, Changchun, China
| | - Liang Shan
- School of Pharmaceutical Sciences, Jilin University, Changchun, China
| | - Chongyang Liang
- Institute of Frontier Medical Science, Jilin University, Changchun, China
| | - Meiling Fan
- Jilin Academy of Chinese Medicine Sciences, Changchun, China
| | - Fei Sun
- School of Pharmaceutical Sciences, Jilin University, Changchun, China
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Shams R, Ito Y, Miyatake H. Evaluation of the Binding Kinetics of RHEB with mTORC1 by In-Cell and In Vitro Assays. Int J Mol Sci 2021; 22:ijms22168766. [PMID: 34445471 PMCID: PMC8395731 DOI: 10.3390/ijms22168766] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/04/2021] [Accepted: 08/13/2021] [Indexed: 11/16/2022] Open
Abstract
The mammalian/mechanistic target of rapamycin complex 1 (mTORC1) is activated by the small G-protein, Ras homolog enriched in brain (RHEB–GTPase). On lysosome, RHEB activates mTORC1 by binding the domains of N-heat, M-heat, and the focal adhesion targeting (FAT) domain, which allosterically regulates ATP binding in the active site for further phosphorylation. The crucial role of RHEB in regulating growth and survival through mTORC1 makes it a targetable site for anti-cancer therapeutics. However, the binding kinetics of RHEB to mTORC1 is still unknown at the molecular level. Therefore, we studied the kinetics by in vitro and in-cell protein–protein interaction (PPI) assays. To this end, we used the split-luciferase system (NanoBiT®) for in-cell studies and prepared proteins for the in vitro measurements. Consequently, we demonstrated that RHEB binds to the whole mTOR both in the presence or absence of GTPγS, with five-fold weaker affinity in the presence of GTPγS. In addition, RHEB bound to the truncated mTOR fragments of N-heat domain (∆N, aa 60–167) or M-heat domain (∆M, aa 967–1023) with the same affinity in the absence of GTP. The reconstructed binding site of RHEB, ∆N-FAT-M, however, bound to RHEB with the same affinity as ∆N-M, indicating that the FAT domain (∆FAT, aa 1240–1360) is dispensable for RHEB binding. Furthermore, RHEB bound to the truncated kinase domain (∆ATP, aa 2148–2300) with higher affinity than to ∆N-FAT-M. In conclusion, RHEB engages two different binding sites of mTOR, ∆N-FAT-M and ∆ATP, with higher affinity for ∆ATP, which likely regulates the kinase activity of mTOR through multiple different biding modes.
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Affiliation(s)
- Raef Shams
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, RIKEN, Wako 351-0198, Saitama, Japan; (R.S.); (Y.I.)
- Department of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama City 338-8570, Saitama, Japan
| | - Yoshihiro Ito
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, RIKEN, Wako 351-0198, Saitama, Japan; (R.S.); (Y.I.)
- Nano Medical Engineering Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Wako 351-0198, Saitama, Japan
| | - Hideyuki Miyatake
- Department of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama City 338-8570, Saitama, Japan
- Nano Medical Engineering Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Wako 351-0198, Saitama, Japan
- Correspondence: ; Tel.: +81-48-467-4979
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6
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Shams R, Matsukawa A, Ochi Y, Ito Y, Miyatake H. In Silico and In Cell Hybrid Selection of Nonrapalog Ligands to Allosterically Inhibit the Kinase Activity of mTORC1. J Med Chem 2021; 65:1329-1341. [PMID: 34191518 DOI: 10.1021/acs.jmedchem.1c00536] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cancer-specific metabolic alterations hyperactivate the kinase activity of the mammalian/mechanistic target of rapamycin (mTOR) for overcoming stressful environments. Rapalogs, which allosterically inhibit mTOR complex 1 (mTORC1), have been approved as anticancer agents. However, the immunosuppressive side effect of these compounds results in the promotion of tumor metastasis, thereby limiting their therapeutic efficacy. We first report a nonrapalog inhibitor, WRX606, identified by a hybrid strategy of in silico and in cell selections. Our studies showed that WRX606 formed a ternary complex with FK506-binding protein-12 (FKBP12) and FKBP-rapamycin-binding (FRB) domain of mTOR, resulting in the allosteric inhibition of mTORC1. WRX606 inhibited the phosphorylation of not only the ribosomal protein S6 kinase 1 (S6K1) but also eIF4E-binding protein-1 (4E-BP1). Hence, WRX606 efficiently suppressed tumor growth in mice without promotion of metastasis. These results suggest that WRX606 is a potent lead compound for developing anticancer drugs discovered by in silico and in cell methods.
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Affiliation(s)
- Raef Shams
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, RIKEN, Wako, Saitama 351-0198, Japan.,Department of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama City, Saitama 338-8570, Japan
| | - Akihiro Matsukawa
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, 2-5-1, Shikata, Kita-ku, 700-8558 Okayama, Japan
| | - Yukari Ochi
- Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, 2-5-1, Shikata, Kita-ku, 700-8558 Okayama, Japan
| | - Yoshihiro Ito
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, RIKEN, Wako, Saitama 351-0198, Japan.,Nano Medical Engineering Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Wako, Saitama 351-0198, Japan
| | - Hideyuki Miyatake
- Department of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama City, Saitama 338-8570, Japan.,Nano Medical Engineering Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Wako, Saitama 351-0198, Japan
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