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Mitchell SM, Heise RM, Murray ME, Lambo DJ, Daso RE, Banerjee IA. An investigation of binding interactions of tumor-targeted peptide conjugated polyphenols with the kinase domain of ephrin B4 and B2 receptors. Mol Divers 2024; 28:817-849. [PMID: 36847923 PMCID: PMC9969393 DOI: 10.1007/s11030-023-10621-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 02/02/2023] [Indexed: 03/01/2023]
Abstract
Recent studies have shown that Ephrin receptors may be upregulated in several types of cancers including breast, ovarian and endometrial cancers, making them a target for drug design. In this work, we have utilized a target-hopping approach to design new natural product-peptide conjugates and examined their interactions with the kinase-binding domain of EphB4 and EphB2 receptors. The peptide sequences were generated through point mutations of the known EphB4 antagonist peptide TNYLFSPNGPIA. Their anticancer properties and secondary structures were analyzed computationally. Conjugates of most optimum of peptides were then designed by binding the N-terminal of the peptides with the free carboxyl group of the polyphenols sinapate, gallate and coumarate, which are known for their inherent anticancer properties. To investigate if these conjugates have a potential to bind to the kinase domain, we carried out docking studies and MMGBSA free energy calculations of the trajectories based on the molecular dynamics simulations, with both the apo and the ATP bound kinase domains of both receptors. In most cases binding interactions occurred within the catalytic loop region, while in some cases the conjugates were found to spread out across the N-lobe and the DFG motif region. The conjugates were further tested for prediction of pharmacokinetic properties using ADME studies. Our results indicated that the conjugates were lipophilic and MDCK permeable with no CYP interactions. These findings provide an insight into the molecular interactions of these peptides and conjugates with the kinase domain of the EphB4 and EphB2 receptor. As a proof of concept, we synthesized and carried out SPR analysis with two of the conjugates (gallate-TNYLFSPNGPIA and sinapate-TNYLFSPNGPIA). Results indicated that the conjugates showed higher binding with the EphB4 receptor and minimal binding to EphB2 receptor. Sinapate-TNYLFSPNGPIA showed inhibitory activity against EphB4. These studies reveal that some of the conjugates may be developed for further investigation into in vitro and in vivo studies and potential development as therapeutics.
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Affiliation(s)
- Saige M Mitchell
- Department of Chemistry, Fordham University, 441 E. Fordham Rd, Bronx, NY, 10458, USA
| | - Ryan M Heise
- Department of Chemistry, Fordham University, 441 E. Fordham Rd, Bronx, NY, 10458, USA
| | - Molly E Murray
- Department of Chemistry, Fordham University, 441 E. Fordham Rd, Bronx, NY, 10458, USA
| | - Dominic J Lambo
- Department of Chemistry, Fordham University, 441 E. Fordham Rd, Bronx, NY, 10458, USA
| | - Rachel E Daso
- Department of Chemistry, Fordham University, 441 E. Fordham Rd, Bronx, NY, 10458, USA
| | - Ipsita A Banerjee
- Department of Chemistry, Fordham University, 441 E. Fordham Rd, Bronx, NY, 10458, USA.
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Yssartier T, Liu L, Pardoue S, Le Questel JY, Guérard F, Montavon G, Galland N. In vivo stability of 211At-radiopharmaceuticals: on the impact of halogen bond formation. RSC Med Chem 2024; 15:223-233. [PMID: 38283213 PMCID: PMC10809332 DOI: 10.1039/d3md00579h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/22/2023] [Indexed: 01/30/2024] Open
Abstract
211At, when coupled to a targeting agent, is one of the most promising radionuclides for therapeutic applications. The main labelling approach consists in the formation of astatoaryl compounds, which often show a lack of in vivo stability. The hypothesis that halogen bond (XB) interactions with protein functional groups initiate a deastatination mechanism is investigated through radiochemical experiments and DFT modelling. Several descriptors agree on the known mechanism of iodoaryl substrates dehalogenation by iodothyronine deiodinases, supporting the higher in vivo dehalogenation of N-succinimidyl 3-[211At]astatobenzoate (SAB) conjugates in comparison with their iodinated counterparts. The guanidinium group in 3-[211At]astato-4-guanidinomethylbenzoate (SAGMB) prevents the formation of At-mediated XBs with the selenocysteine active site in iodothyronine deiodinases. The initial step of At-aryl bond dissociation is inhibited, elucidating the better in vivo stability of SAGMB conjugates compared with those of SAB. The impact of astatine's ability to form XB interactions on radiopharmaceutical degradation may not be limited to the case of aryl radiolabeling.
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Affiliation(s)
- Thibault Yssartier
- CNRS, CEISAM UMR 6230, Nantes Université F-44000 Nantes France
- CNRS, SUBATECH UMR 6457, IMT Atlantique F-44307 Nantes France
| | - Lu Liu
- CNRS, IPHC UMR 7178, Université de Strasbourg F-67037 Strasbourg France
| | - Sylvain Pardoue
- CNRS, SUBATECH UMR 6457, IMT Atlantique F-44307 Nantes France
| | | | - François Guérard
- Inserm UMR 1307, CNRS UMR 6075, CRCI2NA, Nantes Université, Université d'Angers F-44000 Nantes France
| | - Gilles Montavon
- CNRS, SUBATECH UMR 6457, IMT Atlantique F-44307 Nantes France
| | - Nicolas Galland
- CNRS, CEISAM UMR 6230, Nantes Université F-44000 Nantes France
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3
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Abstract
Evidence implicating Eph receptor tyrosine kinases and their ephrin ligands (that together make up the 'Eph system') in cancer development and progression has been accumulating since the discovery of the first Eph receptor approximately 35 years ago. Advances in the past decade and a half have considerably increased the understanding of Eph receptor-ephrin signalling mechanisms in cancer and have uncovered intriguing new roles in cancer progression and drug resistance. This Review focuses mainly on these more recent developments. I provide an update on the different mechanisms of Eph receptor-ephrin-mediated cell-cell communication and cell autonomous signalling, as well as on the interplay of the Eph system with other signalling systems. I further discuss recent advances in elucidating how the Eph system controls tumour expansion, invasiveness and metastasis, supports cancer stem cells, and drives therapy resistance. In addition to functioning within cancer cells, the Eph system also mediates the reciprocal communication between cancer cells and cells of the tumour microenvironment. The involvement of the Eph system in tumour angiogenesis is well established, but recent findings also demonstrate roles in immune cells, cancer-associated fibroblasts and the extracellular matrix. Lastly, I discuss strategies under evaluation for therapeutic targeting of Eph receptors-ephrins in cancer and conclude with an outlook on promising future research directions.
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Affiliation(s)
- Elena B Pasquale
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
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Ullah A, Razzaq A, Zhou C, Ullah N, Shehzadi S, Aziz T, Alfaifi MY, Elbehairi SEI, Iqbal H. Biological Significance of EphB4 Expression in Cancer. Curr Protein Pept Sci 2024; 25:244-255. [PMID: 37909437 DOI: 10.2174/0113892037269589231017055642] [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: 06/28/2023] [Revised: 09/03/2023] [Accepted: 09/15/2023] [Indexed: 11/03/2023]
Abstract
Eph receptors and their Eph receptor-interacting (ephrin) ligands comprise a vital cell communication system with several functions. In cancer cells, there was evidence of bilateral Eph receptor signaling with both tumor-suppressing and tumor-promoting actions. As a member of the Eph receptor family, EphB4 has been linked to tumor angiogenesis, growth, and metastasis, which makes it a viable and desirable target for drug development in therapeutic applications. Many investigations have been conducted over the last decade to elucidate the structure and function of EphB4 in association with its ligand ephrinB2 for its involvement in tumorigenesis. Although several EphB4-targeting drugs have been investigated, and some selective inhibitors have been evaluated in clinical trials. This article addresses the structure and function of the EphB4 receptor, analyses its possibility as an anticancer therapeutic target, and summarises knowledge of EphB4 kinase inhibitors. To summarise, EphB4 is a difficult but potential treatment option for cancers.
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Affiliation(s)
- Asmat Ullah
- Clinical Research Institute, Zhejiang Provincial People's Hospital, Hangzhou, 310014, Zhejiang, China
| | - Anam Razzaq
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China
| | - Chuanzan Zhou
- Clinical Research Institute, Zhejiang Provincial People's Hospital, Hangzhou, 310014, Zhejiang, China
| | - Najeeb Ullah
- Department of Biomedical Engineering, Louisiana Tech University, Ruston, LA, 818 Nelson Ave, 71272, USA
| | - Somia Shehzadi
- University Institute of Medical Laboratory Technology, The University of Lahore, Lahore 54000, Pakistan
| | - Tariq Aziz
- Westlake University, School of Engineering, Hangzhou, Zhejiang Province, 310024, China
| | - Mohammad Y Alfaifi
- Department of Biology, Faculty of Science, King Khalid University, Abha 9004, Saudi Arabia
| | | | - Haroon Iqbal
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences Hangzhou, Zhejiang, 310022, China
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5
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Targeting receptor tyrosine kinases in ovarian cancer: Genomic dysregulation, clinical evaluation of inhibitors, and potential for combinatorial therapies. Mol Ther Oncolytics 2023; 28:293-306. [PMID: 36911068 PMCID: PMC9999170 DOI: 10.1016/j.omto.2023.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023] Open
Abstract
Epithelial ovarian cancer (EOC) remains one of the leading causes of cancer-related deaths among women worldwide. Receptor tyrosine kinases (RTKs) have long been sought as therapeutic targets for EOC, as they are frequently hyperactivated in primary tumors and drive disease relapse, progression, and metastasis. More recently, these oncogenic drivers have been implicated in EOC response to poly(ADP-ribose) polymerase (PARP) inhibitors and epigenome-interfering agents. This evidence revives RTKs as promising targets for therapeutic intervention of EOC. This review summarizes recent studies on the role of RTKs in EOC malignancy and the use of their inhibitors for clinical treatment. Our focus is on the ERBB family, c-Met, and VEGFR, as they are linked to drug resistance and targetable using commercially available drugs. The importance of these RTKs and their inhibitors is highlighted by their impact on signal transduction and intratumoral heterogeneity in EOC and successful use as maintenance therapy in the clinic through suppression of the VEGF/VEGFR axis. Finally, the therapeutic potential of RTK inhibitors is discussed in the context of combinatorial targeting via co-inhibiting proliferative and anti-apoptotic pathways, epigenomic/transcriptional programs, and harnessing the efficacy of PARP inhibitors and programmed cell death 1/ligand 1 immune checkpoint therapies.
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Podkościelna B, Klimek K, Karczmarzyk Z, Wysocki W, Brodacka M, Serafin K, Kozyra P, Kowalczuk D, Ginalska G, Pitucha M. Polymer microspheres modified with pyrazole derivatives as potential agents in anticancer therapy – preliminary studies. Bioorg Chem 2022; 123:105765. [DOI: 10.1016/j.bioorg.2022.105765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/28/2022] [Accepted: 03/24/2022] [Indexed: 11/28/2022]
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Protein-Protein Interaction Inhibitors Targeting the Eph-Ephrin System with a Focus on Amino Acid Conjugates of Bile Acids. Pharmaceuticals (Basel) 2022; 15:ph15020137. [PMID: 35215250 PMCID: PMC8880657 DOI: 10.3390/ph15020137] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 02/05/2023] Open
Abstract
The role of the Eph-ephrin system in the etiology of pathological conditions has been consolidated throughout the years. In this context, approaches directed against this signaling system, intended to modulate its activity, can be strategic therapeutic opportunities. Currently, the most promising class of compounds able to interfere with the Eph receptor-ephrin protein interaction is composed of synthetic derivatives of bile acids. In the present review, we summarize the progresses achieved, in terms of chemical expansions and structure-activity relationships, both in the steroidal core and the terminal carboxylic acid group, along with the pharmacological characterization for the most promising Eph-ephrin antagonists in in vivo settings.
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Yi C, Zhang X, Li H, Chen G, Zeng B, Li Y, Wang C, He Y, Chen X, Huang Z, Yu D. EPHB4 Regulates the Proliferation and Metastasis of Oral Squamous Cell Carcinoma through the HMGB1/NF-κB Signalling Pathway. J Cancer 2021; 12:5999-6011. [PMID: 34539874 PMCID: PMC8425198 DOI: 10.7150/jca.59331] [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: 02/11/2021] [Accepted: 08/08/2021] [Indexed: 11/05/2022] Open
Abstract
Background: Malignant proliferation and cervical lymphatic metastasis restrict the prognosis of oral squamous cell carcinoma (OSCC). Erythropoietin-producing human hepatocellular B4 (EPHB4) regulates a series of tumour functions involving tumourigenesis, cancer cell attachment and metastasis. However, the mechanism of EphB4 regulating the malignant progression of OSCC has not been fully elucidated. Methods: EPHB4 expression was analysed in 65 OSCC samples and adjacent noncancerous tissues through immunohistochemistry (IHC). siRNA and overexpression plasmids were transfected into OSCC cells to modify EPHB4 expression, and then, regulatory functions were explored in vitro and in vivo. Co-immunoprecipitation (Co-IP) and mass spectrometry were applied to detect proteins interacting with EPHB4. Subsequently, protein stability assays and NF-κB pathway inhibition assays were used to verify the regulation of EPHB4, high-mobility group box 1 (HMGB1) and nuclear factor-κB (NF-κB) activation. Results: EPHB4 was found to be highly expressed in OSCC tissues, which was related to tumour stage and lymphatic metastasis and resulted in a poor prognosis. Cellular experiments and mouse tongue xenograft models further confirmed that high EPHB4 expression promoted the proliferation and metastasis of OSCC tumours. Mechanistically, co-IP and mass spectrometry studies indicated that EPHB4 could bind to HMGB1 and maintain HMGB1 stability. Downregulation of HMGB1 inhibited the proliferation and metastasis of OSCC cells and inhibited NF-κB phosphorylation activation but did not affect EPHB4 expression. Conclusion: This study revealed the mechanism by which EPHB4 promotes the proliferation and metastasis of OSCC by activating the HMGB1-mediated NF-κB signalling pathway, which can be exploited as a novel marker or therapeutic target to control metastasis and improve the survival rate of OSCC.
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Affiliation(s)
- Chen Yi
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University. Guangzhou, Guangdong, China, 510055
- Guangdong Provincial Key Laboratory of Stomatology. Guangzhou, Guangdong, China, 510055
| | - Xiliu Zhang
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University. Guangzhou, Guangdong, China, 510055
- Guangdong Provincial Key Laboratory of Stomatology. Guangzhou, Guangdong, China, 510055
| | - Hongyu Li
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University. Guangzhou, Guangdong, China, 510055
- Guangdong Provincial Key Laboratory of Stomatology. Guangzhou, Guangdong, China, 510055
| | - Guanhui Chen
- Department of Stomatology, the Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen. Guangdong, China, 518107
| | - Binghui Zeng
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University. Guangzhou, Guangdong, China, 510055
- Guangdong Provincial Key Laboratory of Stomatology. Guangzhou, Guangdong, China, 510055
| | - Yiming Li
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University. Guangzhou, Guangdong, China, 510055
- Guangdong Provincial Key Laboratory of Stomatology. Guangzhou, Guangdong, China, 510055
| | - Chao Wang
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University. Guangzhou, Guangdong, China, 510055
- Guangdong Provincial Key Laboratory of Stomatology. Guangzhou, Guangdong, China, 510055
| | - Yi He
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University. Guangzhou, Guangdong, China, 510055
- Guangdong Provincial Key Laboratory of Stomatology. Guangzhou, Guangdong, China, 510055
| | - Xun Chen
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University. Guangzhou, Guangdong, China, 510055
- Guangdong Provincial Key Laboratory of Stomatology. Guangzhou, Guangdong, China, 510055
| | - Zixian Huang
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China, 510120
| | - Dongsheng Yu
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University. Guangzhou, Guangdong, China, 510055
- Guangdong Provincial Key Laboratory of Stomatology. Guangzhou, Guangdong, China, 510055
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9
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Baudet S, Bécret J, Nicol X. Approaches to Manipulate Ephrin-A:EphA Forward Signaling Pathway. Pharmaceuticals (Basel) 2020; 13:ph13070140. [PMID: 32629797 PMCID: PMC7407804 DOI: 10.3390/ph13070140] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/19/2020] [Accepted: 06/28/2020] [Indexed: 02/07/2023] Open
Abstract
Erythropoietin-producing hepatocellular carcinoma A (EphA) receptors and their ephrin-A ligands are key players of developmental events shaping the mature organism. Their expression is mostly restricted to stem cell niches in adults but is reactivated in pathological conditions including lesions in the heart, lung, or nervous system. They are also often misregulated in tumors. A wide range of molecular tools enabling the manipulation of the ephrin-A:EphA system are available, ranging from small molecules to peptides and genetically-encoded strategies. Their mechanism is either direct, targeting EphA receptors, or indirect through the modification of intracellular downstream pathways. Approaches enabling manipulation of ephrin-A:EphA forward signaling for the dissection of its signaling cascade, the investigation of its physiological roles or the development of therapeutic strategies are summarized here.
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Unzue A, Jessen-Trefzer C, Spiliotopoulos D, Gaudio E, Tarantelli C, Dong J, Zhao H, Pachmayr J, Zahler S, Bernasconi E, Sartori G, Cascione L, Bertoni F, Śledź P, Caflisch A, Nevado C. Understanding the mechanism of action of pyrrolo[3,2- b]quinoxaline-derivatives as kinase inhibitors. RSC Med Chem 2020; 11:665-675. [PMID: 33479666 PMCID: PMC7557569 DOI: 10.1039/d0md00049c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/16/2020] [Indexed: 12/02/2022] Open
Abstract
Two novel quinoxaline-based EphA3 tyrosine kinase inhibitors have been designed and characterized in vivo in a relevant lymphoma model, showing high efficacy in the control of tumor size.
The X-ray structure of the catalytic domain of the EphA3 tyrosine kinase in complex with a previously reported type II inhibitor was used to design two novel quinoxaline derivatives, inspired by kinase inhibitors that have reached clinical development. These two new compounds were characterized by an array of cell-based assays and gene expression profiling experiments. A global chemical proteomics approach was used to generate the drug-protein interaction profile, which suggested suitable therapeutic indications. Both inhibitors, studied in the context of angiogenesis and in vivo in a relevant lymphoma model, showed high efficacy in the control of tumor size.
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Affiliation(s)
- Andrea Unzue
- Department of Chemistry , University of Zurich , Winterthurerstrasse 190 , CH-8057 , Zürich , Switzerland . ; ; Tel: (+41) 446353945
| | - Claudia Jessen-Trefzer
- Department of Chemistry , University of Zurich , Winterthurerstrasse 190 , CH-8057 , Zürich , Switzerland . ; ; Tel: (+41) 446353945
| | - Dimitrios Spiliotopoulos
- Department of Biochemistry , University of Zurich , Winterthurerstrasse 190 , CH-8057 , Zürich , Switzerland
| | - Eugenio Gaudio
- Institute of Oncology Research , Faculty of Biomedical Sciences , USI , Bellinzona , Switzerland
| | - Chiara Tarantelli
- Institute of Oncology Research , Faculty of Biomedical Sciences , USI , Bellinzona , Switzerland
| | - Jing Dong
- Department of Biochemistry , University of Zurich , Winterthurerstrasse 190 , CH-8057 , Zürich , Switzerland
| | - Hongtao Zhao
- Department of Biochemistry , University of Zurich , Winterthurerstrasse 190 , CH-8057 , Zürich , Switzerland
| | - Johanna Pachmayr
- Department of Pharmacy , University of Munich , Butenandstrasse 5-13 , 81377 Munich , Germany
| | - Stefan Zahler
- Department of Pharmacy , University of Munich , Butenandstrasse 5-13 , 81377 Munich , Germany
| | - Elena Bernasconi
- Institute of Oncology Research , Faculty of Biomedical Sciences , USI , Bellinzona , Switzerland
| | - Giulio Sartori
- Institute of Oncology Research , Faculty of Biomedical Sciences , USI , Bellinzona , Switzerland
| | - Luciano Cascione
- Institute of Oncology Research , Faculty of Biomedical Sciences , USI , Bellinzona , Switzerland.,SIB Swiss Institute of Bioinformatics , Lausanne , Switzerland
| | - Francesco Bertoni
- Institute of Oncology Research , Faculty of Biomedical Sciences , USI , Bellinzona , Switzerland.,Oncology Institute of Southern Switzerland (IOSI) , Bellinzona , Switzerland
| | - Paweł Śledź
- Department of Biochemistry , University of Zurich , Winterthurerstrasse 190 , CH-8057 , Zürich , Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry , University of Zurich , Winterthurerstrasse 190 , CH-8057 , Zürich , Switzerland
| | - Cristina Nevado
- Department of Chemistry , University of Zurich , Winterthurerstrasse 190 , CH-8057 , Zürich , Switzerland . ; ; Tel: (+41) 446353945
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11
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Incerti M, Russo S, Corrado M, Giorgio C, Ballabeni V, Chiodelli P, Rusnati M, Scalvini L, Callegari D, Castelli R, Vacondio F, Ferlenghi F, Tognolini M, Lodola A. Optimization of EphA2 antagonists based on a lithocholic acid core led to the identification of UniPR505, a new 3α-carbamoyloxy derivative with antiangiogenetic properties. Eur J Med Chem 2020; 189:112083. [PMID: 32000051 DOI: 10.1016/j.ejmech.2020.112083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 01/16/2020] [Accepted: 01/19/2020] [Indexed: 11/24/2022]
Abstract
The EphA2 receptor has been validated in animal models as new target for treating tumors depending on angiogenesis and vasculogenic mimicry. In the present work, we extended our current knowledge on structure-activity relationship (SAR) data of two related classes of antagonists of the EphA2 receptor, namely 5β-cholan-24-oic acids and 5β-cholan-24-oyl l-β-homotryptophan conjugates, with the aim to develop new antiangiogenic compounds able to efficiently prevent the formation of blood vessels. As a result of our exploration, we identified UniPR505, N-[3α-(Ethylcarbamoyl)oxy-5β-cholan-24-oyl]-l-β-homo-tryptophan (compound 14), as a submicromolar antagonist of the EphA2 receptor capable to block EphA2 phosphorylation and to inhibit neovascularization in a chorioallantoic membrane (CAM) assay.
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Affiliation(s)
- Matteo Incerti
- Department of Food and Drug, University of Parma, 43124, Parma, Italy
| | - Simonetta Russo
- Department of Food and Drug, University of Parma, 43124, Parma, Italy
| | - Miriam Corrado
- Department of Food and Drug, University of Parma, 43124, Parma, Italy
| | - Carmine Giorgio
- Department of Food and Drug, University of Parma, 43124, Parma, Italy
| | - Vigilio Ballabeni
- Department of Food and Drug, University of Parma, 43124, Parma, Italy
| | - Paola Chiodelli
- Department of Molecular and Translational Medicine, University of Brescia, 25123, Brescia, Italy
| | - Marco Rusnati
- Department of Molecular and Translational Medicine, University of Brescia, 25123, Brescia, Italy
| | - Laura Scalvini
- Department of Food and Drug, University of Parma, 43124, Parma, Italy
| | | | - Riccardo Castelli
- Department of Food and Drug, University of Parma, 43124, Parma, Italy
| | - Federica Vacondio
- Department of Food and Drug, University of Parma, 43124, Parma, Italy
| | | | | | - Alessio Lodola
- Department of Food and Drug, University of Parma, 43124, Parma, Italy.
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12
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Rezaei Z, Mahdi Didehvar M, Mahdavi M, Azizian H, Hamedifar H, Mohammed EHM, Ostad S, Amini M. Anticancer properties of N-alkyl-2, 4-diphenylimidazo [1, 2-a] quinoxalin-1-amine derivatives; kinase inhibitors. Bioorg Chem 2019; 90:103055. [PMID: 31220669 DOI: 10.1016/j.bioorg.2019.103055] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 03/27/2019] [Accepted: 06/06/2019] [Indexed: 12/24/2022]
Abstract
Structure activity correlation revealed that the quinoxaline ring is a satisfactory backbone for anticancer activity and a specific functional group at position 1 and 2 can improve the activity. In this basis, besides quinoxaline, imidazoles as potential anticancer agents were used as a supplementary agents for cancer treatment. In this paper, a new series of N-alkyl-2, 4-diphenylimidazo [1, 2-a] quinoxalin-1-amine derivatives were synthesized in a simple and efficient step. The products are fully characterized by 1H NMR, 13C NMR, FT-IR, HRMS, and CHN elemental analysis. Several starting materials with different functionalities have been used for the synthesis of the final products with high isolated yields. The biological activities of the synthesized compounds were evaluated in kinase inhibition and cytotoxic activity in several cancerous cell lines. All compounds (6) were evaluated for inhibition of the cell proliferation using 4 cancerous cell lines. Five of the more active compounds were studied for determination of IC50%. Compounds 6(32-34) showed good activity on some of cancerous cell lines. The results showed that compound 6-32 has the highest biological activity (IC50% 9.77 for K562 cell line). An IC50% value of 15.84 µM was observed for 6-34. Furthermore 6-34 exhibited inhibition of ABL1 and c-Src kinases with an IC50% value of 5.25 µM and 3.94 µM respectively. Docking simulation was performed to position active synthesized compounds 6-32, 6-33, and 6-34 over the ABL1 active site in two different wild-type (DFG-in and DFG-out motif conformer) and T315I mutant to determine the probable binding orientation, conformation and mode of interaction. According to docking study, the docked location in wild type forms is similar and can be found near the P-loop region while in the case of T315I mutant form, the compounds have a distinct docked location which is close to the αC helix and activation loop. Also, it concluded the role of R1 substituent on phenyl ring produced higher interaction energy. Additionally, the detailed inter-molecular energy and types of non-bonding interaction of these compounds over the wild-type and mutant form of ABL1.
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Affiliation(s)
- Zahra Rezaei
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, 14176 Tehran, Iran
| | - Mir Mahdi Didehvar
- School of Chemistry, University College of Science, University of Tehran, PO Box 14155-6455, Tehran, Iran
| | - Mohammad Mahdavi
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Homa Azizian
- Department of Medicinal Chemistry, School of Pharmacy-International Campus, Iran University of Medical Sciences, Tehran, Iran
| | - Haleh Hamedifar
- CinnaGen Medical Biotechnology Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Eman H M Mohammed
- Department of Chemistry, Faculty of Sciences, Menoufia University, Shebin EI-Koam, Egypt
| | - Sayednaser Ostad
- Department of Toxicology & Pharmacology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohsen Amini
- Department of Medicinal Chemistry, Faculty of Pharmacy and Drug Design and Development Research Center, The Institute of Pharmaceutical Sciences (TIPS), Tehran, Iran.
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13
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Saha N, Robev D, Mason EO, Himanen JP, Nikolov DB. Therapeutic potential of targeting the Eph/ephrin signaling complex. Int J Biochem Cell Biol 2018; 105:123-133. [PMID: 30343150 DOI: 10.1016/j.biocel.2018.10.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/09/2018] [Accepted: 10/16/2018] [Indexed: 12/27/2022]
Abstract
The Eph-ephrin signaling pathway mediates developmental processes and the proper functioning of the adult human body. This distinctive bidirectional signaling pathway includes a canonical downstream signal cascade inside the Eph-bearing cells, as well as a reverse signaling in the ephrin-bearing cells. The signaling is terminated by ADAM metalloproteinase cleavage, internalization, and degradation of the Eph/ephrin complexes. Consequently, the Eph-ephrin-ADAM signaling cascade has emerged as a key target with immense therapeutic potential particularly in the context of cancer. An interesting twist was brought forth by the emergence of ephrins as the entry receptors for the pathological Henipaviruses, which has spurred new studies to target the viral entry. The availability of high-resolution structures of the multi-modular Eph receptors in complexes with ephrins and other binding partners, such as peptides, small molecule inhibitors and antibodies, offers a wealth of information for the structure-guided development of therapeutic intervention. Furthermore, genomic data mining of Eph mutants involved in cancer provides information for targeted drug development. In this review we summarize the distinct avenues for targeting the Eph-ephrin signaling pathway, including its termination by ADAM proteinases. We highlight the latest developments in Eph-related pharmacology in the context of Eph-ephrin-ADAM-based antibodies and small molecules. Finally, the future prospects of genomics- and proteomics-based medicine are discussed.
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Affiliation(s)
- Nayanendu Saha
- Sloan-Kettering Institute for Cancer Research, Structural Biology Program, 1275 York Avenue, New York, NY 10065, United States
| | - Dorothea Robev
- Sloan-Kettering Institute for Cancer Research, Structural Biology Program, 1275 York Avenue, New York, NY 10065, United States
| | - Emilia O Mason
- Sloan-Kettering Institute for Cancer Research, Structural Biology Program, 1275 York Avenue, New York, NY 10065, United States
| | - Juha P Himanen
- Sloan-Kettering Institute for Cancer Research, Structural Biology Program, 1275 York Avenue, New York, NY 10065, United States.
| | - Dimitar B Nikolov
- Sloan-Kettering Institute for Cancer Research, Structural Biology Program, 1275 York Avenue, New York, NY 10065, United States
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14
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Marchand JR, Caflisch A. In silico fragment-based drug design with SEED. Eur J Med Chem 2018; 156:907-917. [PMID: 30064119 DOI: 10.1016/j.ejmech.2018.07.042] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/11/2018] [Accepted: 07/15/2018] [Indexed: 12/13/2022]
Abstract
We report on two fragment-based drug design protocols, SEED2XR and ALTA, which start by high-throughput docking. SEED2XR is a two-stage protocol for fragment-based drug design. The first stage is in silico and consists of the automatic docking of 103-104 fragments using SEED, which requires about 1 s per fragment. SEED is a docking software developed specifically for fragment docking and binding energy evaluation by a force field with implicit solvent. In the second stage of SEED2XR, the 10-102 fragments with the most favorable predicted binding energies are validated by protein X-ray crystallography. The recent applications of SEED2XR to bromodomains demonstrate that the whole SEED2XR protocol can be carried out in about a week of working time, with hit rates ranging from 10% to 40%. Information on fragment-target interactions generated by the SEED2XR protocol or directly from SEED docking has been used for the discovery of hundreds of hits. ALTA is a computational protocol for screening which identifies candidate ligands that preserve the interactions between the optimal SEED fragments and the protein target. Medicinal chemistry optimization of ligands predicted by ALTA has resulted in pre-clinical candidates for protein kinases and bromodomains. The high-throughput, very low cost, sustainability, and high hit rate of the SEED-based protocols, unreachable by purely experimental techniques, make them perfectly suitable for both academic and industrial drug discovery research.
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Affiliation(s)
- Jean-Rémy Marchand
- Department of Biochemistry, University of Zürich, CH-8057, Zürich, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich, CH-8057, Zürich, Switzerland.
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15
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One-pot synthesis of biologically active 1,2,3-trisubstituted pyrrolo[2,3-b]quinoxalines through a palladium-catalyzed reaction with internal alkyne moieties. Mol Divers 2018; 22:879-891. [PMID: 29909566 DOI: 10.1007/s11030-018-9838-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 05/29/2018] [Indexed: 10/14/2022]
Abstract
Synthesis of 2,3-disubstituted 1-alkylpyrrolo[2,3-b]quinoxalines was accomplished through the reaction of 3-chloroquinoxalin-2-amines with internal alkynes in the presence of Pd(OAc)[Formula: see text], NaOAc, and KOtBu in DMSO. This method afforded desired pyrrolo[2,3-b]quinoxalines in 65-92% reaction yields. The minimum inhibition concentration and minimum bactericidal concentration determinations against Micrococcus luteus and Pseudomonas aeruginosa revealed that some of the synthesized compounds showed the same values compared to tetracycline. These compounds could be used in the future research for the development of new antibiotics.
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16
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Shan Y, Wang B, Zhang J. New strategies in achieving antiangiogenic effect: Multiplex inhibitors suppressing compensatory activations of RTKs. Med Res Rev 2018; 38:1674-1705. [DOI: 10.1002/med.21517] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/19/2018] [Accepted: 05/19/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Yuanyuan Shan
- Department of Pharmacy; The First Affiliated Hospital of Xi'an Jiaotong University; Xi'an China
| | - Binghe Wang
- Department of Chemistry; Center for Diagnostics and Therapeutics; Georgia State University; Atlanta GA USA
| | - Jie Zhang
- School of Pharmacy, Health Science Center; Xi'an Jiaotong University; Xi'an China
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17
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Salgia R, Kulkarni P, Gill PS. EphB4: A promising target for upper aerodigestive malignancies. Biochim Biophys Acta Rev Cancer 2018; 1869:128-137. [PMID: 29369779 PMCID: PMC5955724 DOI: 10.1016/j.bbcan.2018.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/11/2018] [Accepted: 01/11/2018] [Indexed: 12/14/2022]
Abstract
The erythropoietin-producing hepatocellular carcinoma (Eph) receptors are the largest family of receptor tyrosine kinases (RTKs) that include two major subclasses, EphA and EphB. They form an important cell communication system with critical and diverse roles in a variety of biological processes during embryonic development. However, dysregulation of the Eph/ephrin interactions is implicated in cancer contributing to tumour growth, metastasis, and angiogenesis. Here, we focus on EphB4 and review recent developments in elucidating its role in upper aerodigestive malignancies to include lung cancer, head and neck cancer, and mesothelioma. In particular, we summarize information regarding EphB4 structure/function and role in disease pathobiology. We also review the data supporting EphB4 as a potential pharmacological and immunotherapy target and finally, progress in the development of new therapeutic strategies including small molecule inhibitors of its activity is discussed. The emerging picture suggests that EphB4 is a valuable and attractive therapeutic target for upper aerodigestive malignancies.
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MESH Headings
- Animals
- Antineoplastic Agents/therapeutic use
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Squamous Cell/drug therapy
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/metabolism
- Carcinoma, Squamous Cell/pathology
- Gene Expression Regulation, Neoplastic
- Head and Neck Neoplasms/drug therapy
- Head and Neck Neoplasms/genetics
- Head and Neck Neoplasms/metabolism
- Head and Neck Neoplasms/pathology
- Humans
- Lung Neoplasms/drug therapy
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Lung Neoplasms/pathology
- Mesothelioma/drug therapy
- Mesothelioma/genetics
- Mesothelioma/metabolism
- Mesothelioma/pathology
- Mesothelioma, Malignant
- Molecular Targeted Therapy
- Receptor, EphB4/antagonists & inhibitors
- Receptor, EphB4/genetics
- Receptor, EphB4/metabolism
- Signal Transduction
- Squamous Cell Carcinoma of Head and Neck
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Affiliation(s)
- Ravi Salgia
- Department of Medical Oncology & Therapeutics Research, City of Hope National Medical Center, 1500 East Duarte Road, Duarte, CA, United States.
| | - Prakash Kulkarni
- Department of Medical Oncology & Therapeutics Research, City of Hope National Medical Center, 1500 East Duarte Road, Duarte, CA, United States
| | - Prakash S Gill
- Department of Medicine, Division of Medical Oncology, University of Southern California, Los Angeles, CA, United States
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18
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The Long Noncoding RNA HOTAIR in Breast Cancer: Does Autophagy Play a Role? Int J Mol Sci 2017; 18:ijms18112317. [PMID: 29469819 PMCID: PMC5713286 DOI: 10.3390/ijms18112317] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 10/27/2017] [Accepted: 10/31/2017] [Indexed: 01/17/2023] Open
Abstract
HOTAIR (HOX transcript antisense RNA) plays a critical role in chromatin dynamics through the interaction with histone modifiers resulting in transcriptional gene silencing. The promoter of the HOTAIR gene contains multiple estrogen response elements (EREs) and is transcriptionally activated by estradiol in estrogen receptor-positive breast cancer cells. HOTAIR competes with BRCA1, a critical protein in breast cancer and is a critical regulator of genes involved in epithelial-to-mesenchymal transition. It mediates an oncogenic action of c-Myc, essential for breast carcinogenesis. The carcinogenic action of HOTAIR was confirmed in breast cancer stem-like cells, in which it was essential for self-renewal and proliferation. Several miRNAs regulate the expression of HOTAIR and HOTAIR interacts with many miRNAs to support cancer transformation. Many studies point at miR-34a as a major component of HOTAIR–miRNAs–cancer cross-talk. The most important role of HOTAIR can be attributed to cancer progression as its overexpression stimulates invasion and metastasis. HOTAIR can regulate autophagy, important for breast cancer cells survival, through the interaction with miRNAs specific for autophagy genes and directly with these genes. The role of HOTAIR-mediated autophagy in breast cancer progression can be underlined by its interaction with matrix metalloproteinases, essential for cancer invasion, and β-catenin can be important for this interaction. Therefore, there are several mechanisms of the interplay between HOTAIR and autophagy important for breast cancer, but further studies are needed to determine more details of this interplay.
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19
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Chen Y, Zhang H, Zhang Y. Targeting receptor tyrosine kinase EphB4 in cancer therapy. Semin Cancer Biol 2017; 56:37-46. [PMID: 28993206 DOI: 10.1016/j.semcancer.2017.10.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 09/13/2017] [Accepted: 10/04/2017] [Indexed: 12/12/2022]
Abstract
Eph receptors and their Eph receptor-interacting (ephrin) ligands together form an important cell communication system with diverse roles. Experimental evidence demonstrated Eph receptor bidirectional signaling with both tumor-suppressing and tumor-promoting activities in cancer cells. The tyrosine kinase EphB4, a member of the Eph receptor family, has been associated with tumor angiogenesis, growth and metastasis, thus making it a valuable and attractive target for drug design for therapeutic applications. In the past decade, many studies have focused on elucidating the structure and function of EphB4 in complex with its ligand ephrinB2 for their role in carcinogenesis. Meanwhile, an array of compounds targeting EphB4 have been studied and several selective inhibitors have been tested in clinical studies. This review discusses the structure and function of the EphB4 receptor, analyzes its potential as a target for anticancer therapy, and summarizes the information about inhibitors of EphB4 kinase activity. Conclusively, EphB4 is a challenging but promising therapeutic target in cancer.
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Affiliation(s)
- Yinnan Chen
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Hongmei Zhang
- Department of Endocrinology, Xinhua Hospital affiliated to Shanghai Jiaotong University School of Medicine, 1665 Kongjiang Road, Shanghai 200092, PR China.
| | - Yanmin Zhang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76, Yanta West Street, #54, Xi'an, Shaanxi Province 710061, PR China.
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20
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Marchand JR, Dalle Vedove A, Lolli G, Caflisch A. Discovery of Inhibitors of Four Bromodomains by Fragment-Anchored Ligand Docking. J Chem Inf Model 2017; 57:2584-2597. [PMID: 28862840 DOI: 10.1021/acs.jcim.7b00336] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The high-throughput docking protocol called ALTA-VS (anchor-based library tailoring approach for virtual screening) was developed in 2005 for the efficient in silico screening of large libraries of compounds by preselection of only those molecules that have optimal fragments (anchors) for the protein target. Here we present an updated version of ALTA-VS with a broader range of potential applications. The evaluation of binding energy makes use of a classical force field with implicit solvent in the continuum dielectric approximation. In about 2 days per protein target on a 96-core compute cluster (equipped with Xeon E3-1280 quad core processors at 2.5 GHz), the screening of a library of nearly 77 000 diverse molecules with the updated ALTA-VS protocol has resulted in the identification of 19, 3, 3, and 2 μM inhibitors of the human bromodomains ATAD2, BAZ2B, BRD4(1), and CREBBP, respectively. The success ratio (i.e., number of actives in a competition binding assay in vitro divided by the number of compounds tested) ranges from 8% to 13% in dose-response measurements. The poses predicted by fragment-based docking for the three ligands of the BAZ2B bromodomain were confirmed by protein X-ray crystallography.
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Affiliation(s)
- Jean-Rémy Marchand
- Department of Biochemistry, University of Zürich , CH-8057, Zürich, Switzerland
| | | | - Graziano Lolli
- Centre for Integrative Biology, University of Trento , I-38123, Povo, Italy
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich , CH-8057, Zürich, Switzerland
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21
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Targeting Eph/ephrin system in cancer therapy. Eur J Med Chem 2017; 142:152-162. [PMID: 28780190 DOI: 10.1016/j.ejmech.2017.07.029] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/12/2017] [Accepted: 07/16/2017] [Indexed: 12/19/2022]
Abstract
It is well established that the Eph/ephrin system plays a central role in the embryonic development, with minor implications in the physiology of the adult. However, it is overexpressed and deregulated in a variety of tumors, with a primary involvement in tumorigenesis, tumor angiogenesis, metastasis development, and cancer stem cell regeneration. Targeting the Eph/ephrin system with biologicals, including antibodies and recombinant proteins, reduces tumor growth in animal models of hematological malignancies, breast, prostate, colon, head and neck cancers and glioblastoma. Currently, some of these biopharmaceutical agents are under investigations in phase I or phase II clinical trials. Peptides and small molecules targeting protein-protein-interaction (PPI) are in the late preclinical phase where they are showing promising activity in models of glioblastoma, ovarian and lung cancer. The present review summarizes the most critical findings proposing the Eph/ephrin signaling system as a new target in molecularly targeted oncology.
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22
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Incerti M, Russo S, Callegari D, Pala D, Giorgio C, Zanotti I, Barocelli E, Vicini P, Vacondio F, Rivara S, Castelli R, Tognolini M, Lodola A. Metadynamics for Perspective Drug Design: Computationally Driven Synthesis of New Protein-Protein Interaction Inhibitors Targeting the EphA2 Receptor. J Med Chem 2017; 60:787-796. [PMID: 28005388 DOI: 10.1021/acs.jmedchem.6b01642] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Metadynamics (META-D) is emerging as a powerful method for the computation of the multidimensional free-energy surface (FES) describing the protein-ligand binding process. Herein, the FES of unbinding of the antagonist N-(3α-hydroxy-5β-cholan-24-oyl)-l-β-homotryptophan (UniPR129) from its EphA2 receptor was reconstructed by META-D simulations. The characterization of the free-energy minima identified on this FES proposes a binding mode fully consistent with previously reported and new structure-activity relationship data. To validate this binding mode, new N-(3α-hydroxy-5β-cholan-24-oyl)-l-β-homotryptophan derivatives were designed, synthesized, and tested for their ability to displace ephrin-A1 from the EphA2 receptor. Among them, two antagonists, namely compounds 21 and 22, displayed high affinity versus the EphA2 receptor and resulted endowed with better physicochemical and pharmacokinetic properties than the parent compound. These findings highlight the importance of free-energy calculations in drug design, confirming that META-D simulations can be used to successfully design novel bioactive compounds.
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Affiliation(s)
- Matteo Incerti
- Dipartimento di Farmacia, Università degli Studi di Parma , Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Simonetta Russo
- Dipartimento di Farmacia, Università degli Studi di Parma , Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Donatella Callegari
- Dipartimento di Farmacia, Università degli Studi di Parma , Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Daniele Pala
- Dipartimento di Farmacia, Università degli Studi di Parma , Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Carmine Giorgio
- Dipartimento di Farmacia, Università degli Studi di Parma , Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Ilaria Zanotti
- Dipartimento di Farmacia, Università degli Studi di Parma , Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Elisabetta Barocelli
- Dipartimento di Farmacia, Università degli Studi di Parma , Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Paola Vicini
- Dipartimento di Farmacia, Università degli Studi di Parma , Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Federica Vacondio
- Dipartimento di Farmacia, Università degli Studi di Parma , Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Silvia Rivara
- Dipartimento di Farmacia, Università degli Studi di Parma , Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Riccardo Castelli
- Dipartimento di Farmacia, Università degli Studi di Parma , Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Massimiliano Tognolini
- Dipartimento di Farmacia, Università degli Studi di Parma , Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Alessio Lodola
- Dipartimento di Farmacia, Università degli Studi di Parma , Parco Area delle Scienze 27/A, 43124 Parma, Italy.,Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University , Newcastle upon Tyne NE1 8ST, United Kingdom
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23
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Unzue A, Zhao H, Lolli G, Dong J, Zhu J, Zechner M, Dolbois A, Caflisch A, Nevado C. The “Gatekeeper” Residue Influences the Mode of Binding of Acetyl Indoles to Bromodomains. J Med Chem 2016; 59:3087-97. [DOI: 10.1021/acs.jmedchem.5b01757] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Andrea Unzue
- Department of Chemistry and ‡Department of
Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Hongtao Zhao
- Department of Chemistry and ‡Department of
Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Graziano Lolli
- Department of Chemistry and ‡Department of
Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Jing Dong
- Department of Chemistry and ‡Department of
Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Jian Zhu
- Department of Chemistry and ‡Department of
Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Melanie Zechner
- Department of Chemistry and ‡Department of
Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Aymeric Dolbois
- Department of Chemistry and ‡Department of
Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Amedeo Caflisch
- Department of Chemistry and ‡Department of
Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Cristina Nevado
- Department of Chemistry and ‡Department of
Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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