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Hua L, Wang D, Wang K, Wang Y, Gu J, Zhang Q, You Q, Wang L. Design of Tracers in Fluorescence Polarization Assay for Extensive Application in Small Molecule Drug Discovery. J Med Chem 2023; 66:10934-10958. [PMID: 37561645 DOI: 10.1021/acs.jmedchem.3c00881] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Development of fluorescence polarization (FP) assays, especially in a competitive manner, is a potent and mature tool for measuring the binding affinities of small molecules. This approach is suitable for high-throughput screening (HTS) for initial ligands and is also applicable for further study of the structure-activity relationships (SARs) of candidate compounds for drug discovery. Buffer and tracer, especially rational design of the tracer, play a vital role in an FP assay system. In this perspective, we provided different kinds of approaches for tracer design based on successful cases in recent years. We classified these tracers by different types of ligands in tracers, including peptide, nucleic acid, natural product, and small molecule. To make this technology accessible for more targets, we briefly described the basic theory and workflow, followed by highlighting the design and application of typical FP tracers from a perspective of medicinal chemistry.
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Affiliation(s)
- Liwen Hua
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Danni Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Keran Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yuxuan Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Jinying Gu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qiuyue Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Lei Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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2
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Tumor-targeted dual-starvation therapy based on redox-responsive micelle nanosystem with co-loaded LND and BPTES. Mater Today Bio 2022; 16:100449. [PMID: 36238964 PMCID: PMC9552111 DOI: 10.1016/j.mtbio.2022.100449] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/24/2022] [Accepted: 10/02/2022] [Indexed: 11/21/2022] Open
Abstract
The starvation therapy mediated by the lonidamine (LND) was limited by the low drug delivery efficiency, off-target effect and compensative glutamine metabolism. Herein, a hyaluronic acid (HA)-modified reduction-responsive micellar nanosystem co-loaded with glycolysis and glutamine metabolism inhibitor (LND and bis-2-(5-phenylacetmido-1,2,4-thiadiazol-2-yl)ethyl sulfide, BPTES) was constructed for tumor-targeted dual-starvation therapy. The in vitro and in vivo results collectively suggested that the fabricated nanosystem could effectively endocytosed by tumor cells via HA receptor-ligand recognition, and rapidly release starvation-inducers LND and BPTES in response to the GSH-rich intratumoral cytoplasm. Furthermore, the released LND and BPTES were capable of inducing glycolysis and glutamine metabolism suppression, and accompanied by significant mitochondrial damage, cell cycle arrest and tumor cells apoptosis, eventually devoting to the blockade of the energy and substance supply and tumor killing with high efficiency. In summary, HPPPH@L@B nanosystem significantly inhibited the compensatory glycolysis and glutamine metabolism via the dual-starvation therapy strategy, blocked the indispensable energy and substance supply of tumors, consequently leading to the desired tumor starvation and effective tumor killing with reliable biosafety.
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3
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Chan AM, Goodis CC, Pommier EG, Fletcher S. Recent applications of covalent chemistries in protein-protein interaction inhibitors. RSC Med Chem 2022; 13:921-928. [PMID: 36092144 PMCID: PMC9384789 DOI: 10.1039/d2md00112h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/30/2022] [Indexed: 10/17/2023] Open
Abstract
Protein-protein interactions (PPIs) are large, often featureless domains whose modulations by small-molecules are challenging. Whilst there are some notable successes, such as the BCL-2 inhibitor venetoclax, the requirement for larger ligands to achieve the desired level of potency and selectivity may result in poor "drug-like" properties. Covalent chemistry is presently enjoying a renaissance. In particular, targeted covalent inhibition (TCI), in which a weakly electrophilic "warhead" is installed onto a protein ligand scaffold, is a powerful strategy to develop potent inhibitors of PPIs that are smaller/more drug-like yet have enhanced affinities by virtue of the reinforcing effect on the existing non-covalent interactions by the resulting protein-ligand covalent bond. Furthermore, the covalent bond delivers sustained inhibition, which may translate into significantly reduced therapeutic dosing. Herein, we discuss recent applications of a spectrum of TCIs, as well as covalent screening strategies, in the discovery of more effective inhibitors of PPIs using the HDM2 and BCL-2 protein families as case studies.
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Affiliation(s)
- Alexandria M Chan
- University of Maryland School of Pharmacy, Department of Pharmaceutical Sciences 20 N. Pine St Baltimore MD 21201 USA
| | - Christopher C Goodis
- University of Maryland School of Pharmacy PharmD Program, 20 N. Pine St Baltimore MD 21201 USA
| | - Elie G Pommier
- University of Maryland School of Pharmacy PharmD Program, 20 N. Pine St Baltimore MD 21201 USA
| | - Steven Fletcher
- University of Maryland School of Pharmacy, Department of Pharmaceutical Sciences 20 N. Pine St Baltimore MD 21201 USA
- University of Maryland Greenebaum Cancer Center 20 S. Greene St Baltimore MD 21201 USA
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4
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Drennen B, Goodis CC, Bowen N, Yu W, Vickers G, Wilder PT, MacKerell AD, Fletcher S. Scaffold hopping from indoles to indazoles yields dual MCL-1/BCL-2 inhibitors from MCL-1 selective leads. RSC Med Chem 2022; 13:963-969. [PMID: 36092148 PMCID: PMC9384788 DOI: 10.1039/d2md00095d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/30/2022] [Indexed: 11/21/2022] Open
Abstract
Overexpression of the anti-apoptotic BCL-2 proteins is associated with the development and progression of a range of cancers. Venetoclax, an FDA-approved BCL-2 inhibitor, is fast becoming the standard-of-care for acute myeloid leukemia and chronic lymphocytic leukemia. However, the median survival offered by venetoclax is only 18 months (as part of a combination therapy regimen), and one of the primary culprits for this is the concomitant upregulation of sister anti-apoptotic proteins, in particular MCL-1 (and BCL-xL), which provides an escape route that manifests as venetoclax resistance. Since inhibition of BCL-xL leads to thrombocytopenia, we believe that a dual MCL-1/BCL-2 inhibitor may provide an enhanced therapeutic effect relative to a selective BCL-2 inhibitor. Beginning with a carboxylic acid-containing literature compound that is a potent inhibitor of MCL-1 and a moderate inhibitor of BCL-2, we herein describe our efforts to develop dual inhibitors of MCL-1 and BCL-2 by scaffold hopping from an indole core to an indazole framework. Subsequently, further elaboration of our novel N2-substituted, indazole-3-carboxylic acid lead into a family of indazole-3-acylsulfonamides resulted in improved inhibition of both MCL-1 and BCL-2, possibly through occupation of the p4 pocket, with minimal or no inhibition of BCL-xL.
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Affiliation(s)
- Brandon Drennen
- University of Maryland School of Pharmacy, Department of Pharmaceutical Sciences 20 N. Pine St. Baltimore MD 21201 USA
| | - Christopher C. Goodis
- University of Maryland School of Pharmacy, Department of Pharmaceutical Sciences20 N. Pine St.BaltimoreMD 21201USA
| | - Nathan Bowen
- Department of Chemistry, Cardiff UniversityCF10 3ATUK
| | - Wenbo Yu
- University of Maryland School of Pharmacy, Department of Pharmaceutical Sciences 20 N. Pine St. Baltimore MD 21201 USA
| | | | - Paul T. Wilder
- University of Maryland School of Medicine20 S. Greene St.BaltimoreMD 21201USA
| | - Alexander D. MacKerell
- University of Maryland School of Pharmacy, Department of Pharmaceutical Sciences20 N. Pine St.BaltimoreMD 21201USA,University of Maryland Greenebaum Cancer Center20 S. Greene St.BaltimoreMD 21201USA
| | - Steven Fletcher
- University of Maryland School of Pharmacy, Department of Pharmaceutical Sciences 20 N. Pine St. Baltimore MD 21201 USA .,University of Maryland Greenebaum Cancer Center 20 S. Greene St. Baltimore MD 21201 USA
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5
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Poustforoosh A, Faramarz S, Nematollahi MH, Hashemipour H, Negahdaripour M, Pardakhty A. In silico SELEX screening and statistical analysis of newly designed 5mer peptide-aptamers as Bcl-xl inhibitors using the Taguchi method. Comput Biol Med 2022; 146:105632. [PMID: 35617726 DOI: 10.1016/j.compbiomed.2022.105632] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 04/19/2022] [Accepted: 04/22/2022] [Indexed: 11/03/2022]
Abstract
Drug development for cancer treatment is a complex process that requires special efforts. Targeting crucial proteins is the most essential purpose of drug design in cancers. Bcl-xl is an anti-apoptotic protein that binds to pro-apoptotic proteins and interrupts their signals. Pro-apoptotic Bcl-xl effectors are short BH3 sequences that form an alpha helix and bind to anti-apoptotic proteins to inhibit their activity. Computational systematic evolution of ligands by exponential enrichment (SELEX) is an exclusive approach for developing peptide aptamers as potential effectors. Here, the amino acids with a high tendency for constructing an alpha-helical structure were selected. Due to the enormous number of pentapeptides, Taguchi method was used to study a selected number of peptides. The binding affinity of the peptides to Bcl-xl was assessed using molecular docking, and after analysis of the obtained results, a final set of optimized peptides was arranged and constructed. For a better comparison, three chemical compounds with approved anti-Bcl-xl activity were selected for comparison with the top-ranked 5mer peptides. The optimized peptides showed considerable binding affinity to Bcl-xl. The molecular dynamics (MD) simulation indicated that the designed peptide (PO5) could create considerable interactions with the BH3 domain of Bcl-xl. The MM/GBSA calculations revealed that these interactions were even stronger than those created by chemical compounds. In silico SELEX is a novel approach to design and evaluate peptide-aptamers. The experimental design improves the SELEX process considerably. Finally, PO5 could be considered a potential inhibitor of Bcl-xl and a potential candidate for cancer treatment.
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Affiliation(s)
- Alireza Poustforoosh
- Chemical Engineering Department, Faculty of Engineering, Shahid Bahonar University of Kerman, Kerman, Iran.
| | - Sanaz Faramarz
- Department of Clinical Biochemistry, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Hadi Nematollahi
- Physiology Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran; Department of Clinical Biochemistry, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Hassan Hashemipour
- Chemical Engineering Department, Faculty of Engineering, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran
| | - Manica Negahdaripour
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abbas Pardakhty
- Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
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6
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Smith NA, Wardak AZ, Cowan AD, Colman PM, Czabotar PE, Smith BJ. The Bak core dimer focuses triacylglycerides in the membrane. Biophys J 2022; 121:347-360. [PMID: 34973947 PMCID: PMC8822611 DOI: 10.1016/j.bpj.2021.12.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/15/2021] [Accepted: 12/28/2021] [Indexed: 02/03/2023] Open
Abstract
Apoptosis, the intrinsic programmed cell death process, is mediated by the Bcl-2 family members Bak and Bax. Activation via formation of symmetric core dimers and oligomerization on the mitochondrial outer membrane (MOM) leads to permeabilization and cell death. Although this process is linked to the MOM, the role of the membrane in facilitating such pores is poorly understood. We recently described Bak core domain dimers, revealing lipid binding sites and an initial role of lipids in oligomerization. Here we describe simulations that identified localized clustering and interaction of triacylglycerides (TAGs) with a minimized Bak dimer construct. Coalescence of TAGs occurred beneath this Bak dimer, mitigating dimer-induced local membrane thinning and curvature in representative coarse-grain MOM and model membrane systems. Furthermore, the effects observed as a result of coarse-grain TAG cluster formation was concentration dependent, scaling from low physiological MOM concentrations to those found in other organelles. We find that increasing the TAG concentration in liposomes mimicking the MOM decreased the ability of activated Bak to permeabilize these liposomes. These results suggest that the presence of TAGs within a Bak-lipid membrane preserves membrane integrity and is associated with reduced membrane stress, suggesting a possible role of TAGs in Bak-mediated apoptosis.
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Affiliation(s)
- Nicholas A. Smith
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Ahmad Z. Wardak
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Angus D. Cowan
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Peter M. Colman
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Peter E. Czabotar
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Brian J. Smith
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia,Corresponding author
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7
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Computational design of an apoptogenic protein that binds BCL-xL and MCL-1 simultaneously and potently. Comput Struct Biotechnol J 2022; 20:3019-3029. [PMID: 35782728 PMCID: PMC9218148 DOI: 10.1016/j.csbj.2022.06.021] [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] [Received: 04/21/2022] [Revised: 06/09/2022] [Accepted: 06/09/2022] [Indexed: 11/23/2022] Open
Abstract
One of the hallmarks of cancer cells is their ability to evade apoptosis, which confers survival advantages and resistance to anti-cancer drugs. Cancers often exhibit overexpression of anti-apoptotic BCL-2 proteins, the loss of which triggers apoptosis. In particular, the inhibition of both BCL-xL and MCL-1, but neither one individually, synergistically enhances apoptotic cell death. Here, we report computational design to produce a protein that inhibits both BCL-xL and MCL-1 simultaneously. To a reported artificial three-helix bundle whose second helix was designed to bind MCL-1, we added a fourth helix and designed it to bind BCL-xL. After structural validation of the design and further structure-based sequence design, we produced a dual-binding protein that interacts with both BCL-xL and MCL-1 with apparent dissociation constants of 820 pM and 196 pM, respectively. Expression of this dual binder in a subset of cancer cells induced apoptotic cell death at levels significantly higher than those induced by the pro-apoptotic BIM protein. With a genetic fusion of a mitochondria-targeting sequence or the BH3 sequence of BIM, the activity of the dual binder was enhanced even further. These data suggest that targeted delivery of this dual binder alone or as a part of a modular protein to cancers in the form of protein, mRNA, or DNA may be an effective way to induce cancer cell apoptosis.
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8
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Malignant pleural mesothelioma co-opts BCL-X L and autophagy to escape apoptosis. Cell Death Dis 2021; 12:406. [PMID: 33859162 PMCID: PMC8050302 DOI: 10.1038/s41419-021-03668-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 03/22/2021] [Accepted: 03/22/2021] [Indexed: 12/15/2022]
Abstract
Escape from programmed cell death is a hallmark of cancer. In this study, we investigated the anti-apoptotic mechanisms and explored the therapeutic potential of BCL-2 homology domain-3 (BH3) mimetics in malignant pleural mesothelioma (MPM), a lethal thoracic malignancy with an extreme dearth of treatment options. By implementing integrated analysis of functional genomic data of MPM cells and quantitative proteomics of patients’ tumors, we identified BCL-XL as an anti-apoptotic driver that is overexpressed and confers an oncogenic dependency in MPM. MPM cells harboring genetic alterations that inactivate the NF2/LATS1/2 signaling are associated with increased sensitivity to A-1155463, a BCL-XL-selective BH3 mimetic. Importantly, BCL-XL inhibition elicits protective autophagy, and concomitant blockade of BCL-XL and autophagic machinery with A-1155463 and hydroxychloroquine (HCQ), the US Food and Drug Administration (FDA)-approved autophagy inhibitor, synergistically enhances anti-MPM effects in vitro and in vivo. Together, our work delineates the molecular basis underlying resistance to apoptosis and uncovers an evasive mechanism that limits response to BH3 mimetics in MPM, suggesting a novel strategy to target this aggressive disease.
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9
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Arulananda S, Lee EF, Fairlie WD, John T. The role of BCL-2 family proteins and therapeutic potential of BH3-mimetics in malignant pleural mesothelioma. Expert Rev Anticancer Ther 2020; 21:413-424. [PMID: 33238762 DOI: 10.1080/14737140.2021.1856660] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction: With limited recent therapeutic changes, malignant pleural mesothelioma (MPM) is associated with poor survival and death within 12 months, making it one of the most lethal malignancies. Due to unregulated asbestos use in developing countries and home renovation exposures, cases of MPM are likely to present for decades. As MPM is largely driven by dysregulation of tumor suppressor genes, researchers have examined other mechanisms of subverting tumor proliferation and spread. Over-expression of pro-survival BCL-2 family proteins impairs cells from undergoing apoptosis, and BH3-mimetics targeting them are a novel treatment option across various cancers, though have not been widely investigated in MPM.Areas covered: This review provides an overview of MPM and its current treatment landscape. It summarizes the role of BCL-2 family proteins in tumorigenesis and the therapeutic potential of BH3-mimetics . Finally, it discusses the role of BCL-2 proteins in MPM and the pre-clinical rationale for investigating BH3-mimetics as a therapeutic strategy.Expert opinion: As a disease without readily actionable oncogene driver mutations and with modest benefit from immune checkpoint inhibition, novel therapeutic options are urgently needed for MPM. Hence, BH3-mimetics provide a promising treatment option, with evidence supporting dependence on pro-survival BCL-2 proteins for MPM cell survival.
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Affiliation(s)
- Surein Arulananda
- Department of Medical Oncology, Austin Health, Heidelberg, Australia.,Olivia Newton-John Cancer Research Institute, Heidelberg, Australia.,School of Cancer Medicine, La Trobe University, Heidelberg, Australia
| | - Erinna F Lee
- Olivia Newton-John Cancer Research Institute, Heidelberg, Australia.,School of Cancer Medicine, La Trobe University, Heidelberg, Australia.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Victoria, Australia
| | - W Douglas Fairlie
- Olivia Newton-John Cancer Research Institute, Heidelberg, Australia.,School of Cancer Medicine, La Trobe University, Heidelberg, Australia.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Victoria, Australia
| | - Thomas John
- Olivia Newton-John Cancer Research Institute, Heidelberg, Australia.,School of Cancer Medicine, La Trobe University, Heidelberg, Australia.,Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
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10
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Jo S, Xu A, Curtis JE, Somani S, MacKerell AD. Computational Characterization of Antibody-Excipient Interactions for Rational Excipient Selection Using the Site Identification by Ligand Competitive Saturation-Biologics Approach. Mol Pharm 2020; 17:4323-4333. [PMID: 32965126 DOI: 10.1021/acs.molpharmaceut.0c00775] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Protein therapeutics typically require a concentrated protein formulation, which can lead to self-association and/or high viscosity due to protein-protein interaction (PPI). Excipients are often added to improve stability, bioavailability, and manufacturability of the protein therapeutics, but the selection of excipients often relies on trial and error. Therefore, understanding the excipient-protein interaction and its effect on non-specific PPI is important for rational selection of formulation development. In this study, we validate a general workflow based on the site identification by ligand competitive saturation (SILCS) technology, termed SILCS-Biologics, that can be applied to protein therapeutics for rational excipient selection. The National Institute of Standards and Technology monoclonal antibody (NISTmAb) reference along with the CNTO607 mAb is used as model antibody proteins to examine PPIs, and NISTmAb was used to further examine excipient-protein interactions, in silico. Metrics from SILCS include the distribution and predicted affinity of excipients, buffer interactions with the NISTmAb Fab, and the relation of the interactions to predicted PPI. Comparison with a range of experimental data showed multiple SILCS metrics to be predictive. Specifically, the number of favorable sites to which an excipient binds and the number of sites to which an excipient binds that are involved in predicted PPIs correlate with the experimentally determined viscosity. In addition, a combination of the number of binding sites and the predicted binding affinity is indicated to be predictive of relative protein stability. Comparison of arginine, trehalose, and sucrose, all of which give the highest viscosity in combination with analysis of B22 and kD and the SILCS metrics, indicates that higher viscosities are associated with a low number of predicted binding sites, with lower binding affinity of arginine leading to its anomalously high impact on viscosity. The present study indicates the potential for the SILCS-Biologics approach to be of utility in the rational design of excipients during biologics formulation.
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Affiliation(s)
- Sunhwan Jo
- SilcsBio, LLC, 8 Market Place, Suite 300, Baltimore, Maryland 21202, United States
| | - Amy Xu
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, Maryland 20899, United States
| | - Joseph E Curtis
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, Maryland 20899, United States
| | - Sandeep Somani
- Discovery Sciences, Janssen Research and Development (Janssen R&D), Spring House, Pennsylvania 19477, United States
| | - Alexander D MacKerell
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201, United States
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11
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Somani S, Jo S, Thirumangalathu R, Rodrigues D, Tanenbaum LM, Amin K, MacKerell AD, Thakkar SV. Toward Biotherapeutics Formulation Composition Engineering using Site-Identification by Ligand Competitive Saturation (SILCS). J Pharm Sci 2020; 110:1103-1110. [PMID: 33137372 DOI: 10.1016/j.xphs.2020.10.051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 10/23/2022]
Abstract
Formulation of protein-based therapeutics employ advanced formulation and analytical technologies for screening various parameters such as buffer, pH, and excipients. At a molecular level, physico-chemical properties of a protein formulation depend on self-interaction between protein molecules, protein-solvent and protein-excipient interactions. This work describes a novel in silico approach, SILCS-Biologics, for structure-based modeling of protein formulations. SILCS Biologics is based on the Site-Identification by Ligand Competitive Saturation (SILCS) technology and enables modeling of interactions among different components of a formulation at an atomistic level while accounting for protein flexibility. It predicts potential hotspot regions on the protein surface for protein-protein and protein-excipient interactions. Here we apply SILCS-Biologics on a Fab domain of a monoclonal antibody (mAbN) to model Fab-Fab interactions and interactions with three amino acid excipients, namely, arginine HCl, proline and lysine HCl. Experiments on 100 mg/ml formulations of mAbN showed that arginine increased, lysine reduced, and proline did not impact viscosity. We use SILCS-Biologics modeling to explore a structure-based hypothesis for the viscosity modulating effect of these excipients. Current efforts are aimed at further validation of this novel computational framework and expanding the scope to model full mAb and other protein therapeutics.
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Affiliation(s)
- Sandeep Somani
- Discovery Sciences, Janssen Research and Development (Janssen R&D), Spring House, PA 19477, USA
| | | | - Renuka Thirumangalathu
- BioTherapeutics Drug Product Development (BioTD DPD), Janssen Research and Development (Janssen R&D), Malvern, PA 19355, USA
| | - Danika Rodrigues
- BioTherapeutics Drug Product Development (BioTD DPD), Janssen Research and Development (Janssen R&D), Malvern, PA 19355, USA
| | - Laura M Tanenbaum
- BioTherapeutics Drug Product Development (BioTD DPD), Janssen Research and Development (Janssen R&D), Malvern, PA 19355, USA
| | - Ketan Amin
- BioTherapeutics Drug Product Development (BioTD DPD), Janssen Research and Development (Janssen R&D), Malvern, PA 19355, USA
| | - Alexander D MacKerell
- SilcsBio LLC, Baltimore, MD 21202, USA; Computer-Aided Drug Design Center, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA.
| | - Santosh V Thakkar
- BioTherapeutics Drug Product Development (BioTD DPD), Janssen Research and Development (Janssen R&D), Malvern, PA 19355, USA; BioTherapeutics Cell and Developability Sciences (BioTD CDS), Janssen Research and Development (Janssen R&D), Spring House, PA 19477, USA.
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12
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Xu D, Yang H, Schmid RA, Peng RW. Therapeutic Landscape of Malignant Pleural Mesothelioma: Collateral Vulnerabilities and Evolutionary Dependencies in the Spotlight. Front Oncol 2020; 10:579464. [PMID: 33072611 PMCID: PMC7538645 DOI: 10.3389/fonc.2020.579464] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/02/2020] [Indexed: 12/21/2022] Open
Abstract
Malignant pleural mesothelioma (MPM) is the epitome of a recalcitrant cancer driven by pharmacologically intractable tumor suppressor proteins. A significant but largely unmet challenge in the field is the translation of genetic information on alterations in tumor suppressor genes (TSGs) into effective cancer-specific therapies. The notion that abnormal tumor genome subverts physiological cellular processes, which creates collateral vulnerabilities contextually related to specific genetic alterations, offers a promising strategy to target TSG-driven MPM. Moreover, emerging evidence has increasingly appreciated the therapeutic potential of genetic and pharmacological dependencies acquired en route to cancer development and drug resistance. Here, we review the most recent progress on vulnerabilities co-selected by functional loss of major TSGs and dependencies evolving out of cancer development and resistance to cisplatin based chemotherapy, the only first-line regimen approved by the US Food and Drug Administration (FDA). Finally, we highlight CRISPR-based functional genomics that has emerged as a powerful platform for cancer drug discovery in MPM. The repertoire of MPM-specific “Achilles heel” rises on the horizon, which holds the promise to elucidate therapeutic landscape and may promote precision oncology for MPM.
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Affiliation(s)
- Duo Xu
- Division of General Thoracic Surgery, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.,Department for BioMedical Research (DBMR), Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Haitang Yang
- Division of General Thoracic Surgery, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.,Department for BioMedical Research (DBMR), Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Ralph A Schmid
- Division of General Thoracic Surgery, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.,Department for BioMedical Research (DBMR), Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Ren-Wang Peng
- Division of General Thoracic Surgery, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.,Department for BioMedical Research (DBMR), Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
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13
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Verma P, Mittal P, Singh A, Singh IK. New Entrants into Clinical Trials for Targeted Therapy of Breast Cancer: An Insight. Anticancer Agents Med Chem 2020; 19:2156-2176. [PMID: 31656157 DOI: 10.2174/1871520619666191018172926] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 08/07/2019] [Accepted: 08/07/2019] [Indexed: 02/08/2023]
Abstract
Breast cancer is too complex with various different molecular alterations involved in its pathogenesis and progression. Over the decade, we have seen a surge in the development of drugs for bimolecular targets and for the signal transduction pathways involved in the treatment line of breast cancer. These drugs, either alone or in combination with conventional treatments like chemotherapy, hormone therapy and radiotherapy, will help oncologists to get a better insight and do the needful treatment. These novel therapies bring various challenges along with them, which include the dosage selection, patient selection, schedule of treatment and weighing of clinical benefits over side effects. In this review, we highlight the recently studied target molecules that have received indications in breast carcinoma, both in the localized and in an advanced state and about their inhibitors which are in clinical development which can give the immense potential to clinical care in the near future.
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Affiliation(s)
- Priyanka Verma
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India
| | - Pooja Mittal
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India
| | - Archana Singh
- Department of Botany, Hansraj College, University of Delhi, New Delhi, 110007, India.,Department of Molecular Ecology, Max-Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Indrakant K Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India.,Department of Molecular Ecology, Max-Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
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14
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Matos B, Howl J, Jerónimo C, Fardilha M. The disruption of protein-protein interactions as a therapeutic strategy for prostate cancer. Pharmacol Res 2020; 161:105145. [PMID: 32814172 DOI: 10.1016/j.phrs.2020.105145] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 08/11/2020] [Accepted: 08/11/2020] [Indexed: 12/14/2022]
Abstract
Prostate cancer (PCa) is one of the most common male-specific cancers worldwide, with high morbidity and mortality rates associated with advanced disease stages. The current treatment options of PCa are prostatectomy, hormonal therapy, chemotherapy or radiotherapy, the selection of which is usually dependent upon the stage of the disease. The development of PCa to a castration-resistant phenotype (CRPC) is associated with a more severe prognosis requiring the development of a new and effective therapy. Protein-protein interactions (PPIs) have been recognised as an emerging drug modality and targeting PPIs is a promising therapeutic approach for several diseases, including cancer. The efficacy of several compounds in which target PPIs and consequently impair disease progression were validated in phase I/II clinical trials for different types of cancer. In PCa, various small molecules and peptides proved successful in inhibiting important PPIs, mainly associated with the androgen receptor (AR), Bcl-2 family proteins, and kinases/phosphatases, thus impairing the growth of PCa cells in vitro. Moreover, a majority of these compounds require further validation in vivo and, preferably, in clinical trials. In addition, several other PPIs associated with PCa progression have been identified and now require experimental validation as potential therapeutic loci. In conclusion, we consider the disruption of PPIs to be a promising though challenging therapeutic strategy for PCa. Agents which modulate PPIs might be employed as a monotherapy or as an adjunct to classical chemotherapeutics to overcome drug resistance and improve efficacy. The discovery of new PPIs with important roles in disease progression, and of novel optimized strategies to target them are major challenges for the scientific and pharmacological communities.
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Affiliation(s)
- Bárbara Matos
- Laboratory of Signal Transduction, Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193, Aveiro, Portugal
| | - John Howl
- Molecular Pharmacology Group, Research Institute in Healthcare Science, University of Wolverhampton, Wolverhampton WV1 1LY, UK
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Institute of Oncology of Porto (IPO Porto), Research Center-LAB 3, F Bdg., 1st Floor, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar- University of Porto (ICBAS-UP), Porto, Portugal
| | - Margarida Fardilha
- Laboratory of Signal Transduction, Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193, Aveiro, Portugal.
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15
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Predicted Hotspot Residues Involved in Allosteric Signal Transmission in Pro-Apoptotic Peptide-Mcl1 Complexes. Biomolecules 2020; 10:biom10081114. [PMID: 32731448 PMCID: PMC7463671 DOI: 10.3390/biom10081114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/16/2020] [Accepted: 07/24/2020] [Indexed: 11/30/2022] Open
Abstract
Mcl1 is a primary member of the Bcl–2 family—anti–apoptotic proteins (AAP)—that is overexpressed in several cancer pathologies. The apoptotic regulation is mediated through the binding of pro-apoptotic peptides (PAPs) (e.g., Bak and Bid) at the canonical hydrophobic binding groove (CBG) of Mcl1. Although all PAPs form amphipathic α-helices, their amino acid sequences vary to different degree. This sequence variation exhibits a central role in the binding partner selectivity towards different AAPs. Thus, constructing a novel peptide or small organic molecule with the ability to mimic the natural regulatory process of PAP is essential to inhibit various AAPs. Previously reported experimental binding free energies (BFEs) were utilized in the current investigation aimed to understand the mechanistic basis of different PAPs targeted to mMcl1. Molecular dynamics (MD) simulations used to estimate BFEs between mMcl1—PAP complexes using Molecular Mechanics-Generalized Born Solvent Accessible (MMGBSA) approach with multiple parameters. Predicted BFE values showed an excellent agreement with the experiment (R2 = 0.92). The van–der Waals (ΔGvdw) and electrostatic (ΔGele) energy terms found to be the main energy components that drive heterodimerization of mMcl1—PAP complexes. Finally, the dynamic network analysis predicted the allosteric signal transmission pathway involves more favorable energy contributing residues. In total, the results obtained from the current investigation may provide valuable insights for the synthesis of a novel peptide or small organic inhibitor targeting Mcl1.
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16
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Saranya V, Mary PV, Vijayakumar S, Shankar R. The hazardous effects of the environmental toxic gases on amyloid beta-peptide aggregation: A theoretical perspective. Biophys Chem 2020; 263:106394. [PMID: 32480019 DOI: 10.1016/j.bpc.2020.106394] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/12/2020] [Accepted: 05/12/2020] [Indexed: 12/13/2022]
Abstract
Alzheimer's disease (AD) is one of the leading causes of dementia in elderly people. It has been well documented that the exposure to environmental toxins such as CO, CO2, SO2 and NO2 that are present in the air is considered as a hallmark for the progression of Alzheimer's disease. However, their actual mechanism by which environmental toxin triggers the aggregation of Aβ42 peptide at the molecular and atomic levels remain unknown. In this study, molecular dynamics simulation was carried out to study the aggregation mechanism of the Aβ42 peptide due to its interaction of toxic gas (CO, CO2, SO2 and NO2). During the 400 ns simulation, all the Aβ42 interacted toxic gas (CO, CO2, SO2, and NO2) complexes have smaller Root Mean Square Deviation values when compared to the Aβ42 peptide, which shows that the interaction of toxic gases (CO, CO2, SO2, and NO2) would increase the Aβ42 peptide structural stability. The radius of gyration analysis also supports that Aβ42 interacted CO2 and SO2 complexes have the minimum value in the range of 0.95 nm and 1.5 nm. It is accounted that the Aβ42 interacted CO2 and SO2 complexes have a greater compact structure in comparison to Aβ42 interacted CO and NO2 complexes. Furthermore, all the Aβ42 interacted toxic gas (CO, CO2, SO2, and NO2) complexes exhibited an enhanced secondary structural probability for coil and turn regions with a reduced α-helix probability, which indicates that the interaction of toxic gases may enhance the toxicity and aggregation of Aβ42.
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Affiliation(s)
- Vasudevan Saranya
- Molecular Simulation Laboratory, Department of Physics, Bharathiar University, Coimbatore 641 046, India
| | - Pitchumani Violet Mary
- Department of Physics, Sri Shakthi Institute of Engineering and Technology, Coimbatore 641 062, India
| | | | - Ramasamy Shankar
- Molecular Simulation Laboratory, Department of Physics, Bharathiar University, Coimbatore 641 046, India.
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17
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Jackson MR, Ashton M, Koessinger AL, Dick C, Verheij M, Chalmers AJ. Mesothelioma Cells Depend on the Antiapoptotic Protein Bcl-xL for Survival and Are Sensitized to Ionizing Radiation by BH3-Mimetics. Int J Radiat Oncol Biol Phys 2020; 106:867-877. [PMID: 31786278 DOI: 10.1016/j.ijrobp.2019.11.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/18/2019] [Accepted: 11/21/2019] [Indexed: 12/22/2022]
Abstract
PURPOSE The incidence of mesothelioma continues to rise and prognosis remains dismal owing to resistance to conventional therapies and few novel treatment options. Failure to activate apoptotic cell death is a resistance mechanism that may be overcome by inhibition of antiapoptotic Bcl-2 proteins using BH3-mimetic drugs. We investigated the role of antiapoptotic proteins in the radioresistance of mesothelioma, identifying clinically relevant targets for radiosensitization and evaluating the activity of BH3-mimetics alone and in combination with radiation therapy in preclinical models. METHODS, MATERIALS AND RESULTS Mesothelioma cell lines 211H, H2052, and H226 exposed to BH3-mimetics demonstrated Bcl-xL dependence that correlated with protein expression and was confirmed by genetic knockdown. The Bcl-xL inhibitor A1331852 exhibited cytotoxic (EC50, 0.13-1.42 μmol/L) and radiosensitizing activities (sensitizer enhancement ratios, 1.3-1.8). Cytotoxicity was associated with induction of mitochondrial outer membrane permeabilization and caspase-3/7 activation. Efficacy was maintained in a 3-dimensional model in which combination therapy completely eradicated mesothelioma spheroids. Clinical applicability was confirmed by immunohistochemical analysis of Bcl-2 proteins in patient samples and radiosensitizing activity of A1331852 in primary patient-derived mesothelioma cells. CONCLUSIONS Mesothelioma cells exhibit addiction to the antiapoptotic protein Bcl-xL, and their intrinsic radioresistance can be overcome by small molecule inhibition of this novel therapeutic target.
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Affiliation(s)
- Mark R Jackson
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Miranda Ashton
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom; Beatson West of Scotland Cancer Centre, Glasgow, United Kingdom
| | - Anna L Koessinger
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom; Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Craig Dick
- Beatson West of Scotland Cancer Centre, Glasgow, United Kingdom
| | - Marcel Verheij
- Department of Radiation Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Anthony J Chalmers
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom; Beatson West of Scotland Cancer Centre, Glasgow, United Kingdom.
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18
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Wang Z, Ji H. Targeting the Side-Chain Convergence of Hydrophobic α-Helical Hot Spots To Design Small-Molecule Mimetics: Key Binding Features for i, i + 3, and i + 7. J Med Chem 2019; 62:9906-9917. [PMID: 31593458 DOI: 10.1021/acs.jmedchem.9b01324] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The conformational convergence of hydrophobic α-helical hot spots was revealed by analyzing α-helix-mediated protein-protein interaction (PPI) complex structures. The pharmacophore models were derived for hydrophobic α-helical hot spots at positions i, i + 3, and i + 7. These provide the foundation for designing generalizable scaffolds that can directly mimic the binding mode of the side chains of α-helical hot spots, offering a new class of small-molecule α-helix mimetics. For the first time, the protocol was developed to identify the PPI targets that have similar binding pockets, allowing evaluation of inhibitor selectivities between α-helix-mediated PPIs. The mimicry efficiency of the previously designed scaffold 1 was disclosed. The close positioning of this small molecule to the additional α-helical hot spots suggests that the decoration of this series of generalizable scaffolds can conveniently reach the binding pockets of additional α-helical hot spots to produce potent small-molecule inhibitors for α-helix-mediated PPIs.
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Affiliation(s)
- Zhen Wang
- Drug Discovery Department , H. Lee Moffitt Cancer Center & Research Institute , 12902 Magnolia Drive , Tampa , Florida 33612-9497 , United States.,Departments of Chemistry and Oncologic Sciences , University of South Florida , Tampa , Florida 33620-9497 , United States
| | - Haitao Ji
- Drug Discovery Department , H. Lee Moffitt Cancer Center & Research Institute , 12902 Magnolia Drive , Tampa , Florida 33612-9497 , United States.,Departments of Chemistry and Oncologic Sciences , University of South Florida , Tampa , Florida 33620-9497 , United States
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19
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Wang T, Yang Z, Zhang Y, Zhang X, Wang L, Zhang S, Jia L. Caspase cleavage of Mcl-1 impairs its anti-apoptotic activity and proteasomal degradation in non-small lung cancer cells. Apoptosis 2019; 23:54-64. [PMID: 29256070 DOI: 10.1007/s10495-017-1436-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Global cleavage of cellular proteins by activated caspases is a hallmark of apoptosis, which causes biochemical collapse of the cell. Recent studies suggest that, rather than completely destroying a protein, caspase cleavage can confer novel characteristics or functions. In this respect, the post-caspase role of Bcl-2 family proteins remains uncharacterized. Here, we showed that Mcl-1, a pro-survival member of the Bcl-2 family, was cleaved by caspase-3 in non-small cell lung cancer (NSCLC) cells undergoing chemotherapeutic agent-triggered apoptosis. Caspase cleavage partially impaired the anti-apoptotic activity of Mcl-1 by reducing its mitochondrial localization and impeding its association with the permeability transition pore-forming protein Bak. However, the stability of cleaved Mcl-1 was markedly enhanced because it was more refractory to ubiquitination-dependent proteasomal degradation, thereby improving cell viability to a greater extent than full-length Mcl-1 when transiently expressed in NSCLC cells. These findings shed new light on the role of Mcl-1 in apoptosis and suggest potential novel targets for optimizing the tumoricidal capacity of chemotherapy.
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Affiliation(s)
- Ting Wang
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, China
| | - Zhiwei Yang
- Department of Applied Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Yimeng Zhang
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, China
| | - Xiang Zhang
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, China
| | - Lei Wang
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, China
| | - Shengli Zhang
- Department of Applied Physics, Xi'an Jiaotong University, Xi'an, 710049, China.
| | - Lintao Jia
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, China.
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20
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The chemical biology of apoptosis: Revisited after 17 years. Eur J Med Chem 2019; 177:63-75. [PMID: 31129454 DOI: 10.1016/j.ejmech.2019.05.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/30/2019] [Accepted: 05/06/2019] [Indexed: 12/13/2022]
Abstract
A balance of Bcl-2 family proteins dictates cell survival or death, as the interactions between these proteins regulate mitochondrial apoptotic signaling pathways. However, cancer cells frequently show upregulation of pro-survival Bcl-2 proteins and sequester activated pro-apoptotic BH3-only proteins driven by diverse cytotoxic stresses, resulting in tumor progression and chemoresistance. Synthetic molecules from either structure-based design or screening procedures to engage and inactivate pro-survival Bcl-2 proteins and restore apoptotic process represent a chemical biological means of selectively killing malignant cells. 17 years ago, one of us reviewed on the discovery of novel Bcl-2 targeted agents [1]. Here we revisit this area and examine the progress and current status of small molecule Bcl-2 inhibitor development, demonstrating the Bcl-2 family as a valid target for cancer therapy and providing successful examples for the discovery of inhibitors that target protein-protein interactions.
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21
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Investigating the Molecular Basis of N-Substituted 1-Hydroxy-4-Sulfamoyl-2-Naphthoate Compounds Binding to Mcl1. Processes (Basel) 2019. [DOI: 10.3390/pr7040224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Myeloid cell leukemia-1 (Mcl1) is an anti–apoptotic protein that has gained considerable attention due to its overexpression activity prevents cell death. Therefore, a potential inhibitor that specifically targets Mcl1 with higher binding affinity is necessary. Recently, a series of N-substituted 1-hydroxy-4-sulfamoyl-2-naphthoate compounds was reported that targets Mcl1, but its binding mechanism remains unexplored. Here, we attempted to explore the molecular mechanism of binding to Mcl1 using advanced computational approaches: pharmacophore-based 3D-QSAR, docking, and MD simulation. The selected pharmacophore—NNRRR—yielded a statistically significant 3D-QSAR model containing high confidence scores (R2 = 0.9209, Q2 = 0.8459, and RMSE = 0.3473). The contour maps—comprising hydrogen bond donor, hydrophobic, negative ionic and electron withdrawal effects—from our 3D-QSAR model identified the favorable regions crucial for maximum activity. Furthermore, the external validation of the selected model using enrichment and decoys analysis reveals a high predictive power. Also, the screening capacity of the selected model had scores of 0.94, 0.90, and 8.26 from ROC, AUC, and RIE analysis, respectively. The molecular docking of the highly active compound—C40; 4-(N-benzyl-N-(4-(4-chloro-3,5-dimethylphenoxy) phenyl) sulfamoyl)-1-hydroxy-2-naphthoate—predicted the low-energy conformational pose, and the MD simulation revealed crucial details responsible for the molecular mechanism of binding with Mcl1.
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22
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Peptidomimetics: A Synthetic Tool for Inhibiting Protein–Protein Interactions in Cancer. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09831-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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23
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Marimuthu P, Singaravelu K. Unraveling the molecular mechanism of benzothiophene and benzofuran scaffold-merged compounds binding to anti-apoptotic Myeloid cell leukemia 1. J Biomol Struct Dyn 2018; 37:1992-2003. [DOI: 10.1080/07391102.2018.1474805] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Parthiban Marimuthu
- Faculty of Science and Engineering, Structural Bioinformatics Laboratory, Biochemistry, Åbo Akademi University, Turku, Finland
| | - Kalaimathy Singaravelu
- Department of Information Technology, Turku Centre for Biotechnology, University of Turku, Turku, Finland
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24
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Lin J, Qi W, Chen K, Yan Y, Li X, Feng Z, Pan X. Downregulating STAT1/caspase‐3 signaling with fludarabine to alleviate progression in a rat model of steroid‐induced avascular necrosis of the femoral head. J Biochem Mol Toxicol 2018; 33:e22265. [PMID: 30506661 DOI: 10.1002/jbt.22265] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 10/03/2018] [Accepted: 10/24/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Jian Lin
- Department of OrthopaedicThe Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou China
- Key Laboratory of Orthopaedics of Zhejiang ProvinceWenzhou China
- The Second School of Medicine, Wenzhou Medical UniversityWenzhou China
| | - Weihui Qi
- Department of OrthopaedicThe Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou China
- Key Laboratory of Orthopaedics of Zhejiang ProvinceWenzhou China
- The Second School of Medicine, Wenzhou Medical UniversityWenzhou China
| | - Kai Chen
- Department of OrthopaedicThe Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou China
- Key Laboratory of Orthopaedics of Zhejiang ProvinceWenzhou China
- The Second School of Medicine, Wenzhou Medical UniversityWenzhou China
| | - Yingzhao Yan
- Department of OrthopaedicThe Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou China
- Key Laboratory of Orthopaedics of Zhejiang ProvinceWenzhou China
- The Second School of Medicine, Wenzhou Medical UniversityWenzhou China
| | - Xiaobin Li
- Department of OrthopaedicThe Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou China
- Key Laboratory of Orthopaedics of Zhejiang ProvinceWenzhou China
- The Second School of Medicine, Wenzhou Medical UniversityWenzhou China
| | - Zhenhua Feng
- Department of Orthopaedic SurgeryThe Second Affiliated Hospital of Jiaxing UniversityJiaxing China
| | - Xiaoyun Pan
- Department of OrthopaedicThe Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou China
- Key Laboratory of Orthopaedics of Zhejiang ProvinceWenzhou China
- The Second School of Medicine, Wenzhou Medical UniversityWenzhou China
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25
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HIV Protease-Generated Casp8p41, When Bound and Inactivated by Bcl2, Is Degraded by the Proteasome. J Virol 2018; 92:JVI.00037-18. [PMID: 29643240 PMCID: PMC6002723 DOI: 10.1128/jvi.00037-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 04/02/2018] [Indexed: 11/20/2022] Open
Abstract
HIV protease is known to cause cell death, which is dependent upon cleavage of procaspase 8. HIV protease cleavage of procaspase 8 generates Casp8p41, which directly binds Bak with nanomolar affinity, causing Bak activation and consequent cell death. Casp8p41 can also bind Bcl2 with nanomolar affinity, in which case cell death is averted. Central memory CD4 T cells express high levels of Bcl2, possibly explaining why those cells do not die when they reactivate HIV. Here, we determine that the Casp8p41-Bcl2 complex is polyubiquitinated and degraded by the proteasome. Ixazomib, a proteasome inhibitor in clinical use, blocks this pathway, increasing the abundance of Casp8p41 and causing more cells to die in a Casp8p41-dependent manner. IMPORTANCE The Casp8p41 pathway of cell death is unique to HIV-infected cells yet is blocked by Bcl2. Once bound by Bcl2, Casp8p41 is polyubiquitinated and degraded by the proteasome. Proteasome inhibition blocks degradation of Casp8p41, increasing Casp8p41 levels and causing more HIV-infected cells to die.
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26
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Perri M, Yap JL, Fletcher S, Cione E, Kane MA. Therapeutic potential of Bcl-x L/Mcl-1 synthetic inhibitor JY-1-106 and retinoids for human triple-negative breast cancer treatment. Oncol Lett 2018; 15:7231-7236. [PMID: 29849791 DOI: 10.3892/ol.2018.8258] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 12/14/2017] [Indexed: 02/01/2023] Open
Abstract
Overexpression of anti-apoptotic proteins belonging to the B cell lymphoma (Bcl)-2 family is observed in numerous cancer types and has been postulated to promote cancer cell survival and chemotherapy resistance. Bcl-extra large (xL)/myeloid cell leukemia sequence (Mcl)-1 was demonstrated to be expressed at relatively high levels in clinically aggressive basal-like cancers and inhibiting Bcl-xL overexpression could potentially provoke cell death. A molecule able to target Bcl-xL/Mcl-1, JY-1-106, is herein under investigation. It is also known that vitamin A-derived compounds exhibit antitumor activity in a variety of in vitro experimental models, promoting their effects via nuclear receptor isoforms including retinoic acid receptors (RARs). Pre-clinical observation highlighted that triple negative (estrogen receptor/progesterone receptor/human epidermal growth factor receptor)-breast cancer cells displayed resistance to retinoids due to the RARγ high expression profile. The present study used the triple-negative human breast cancer cell line, MDA-MB-231, to analyze the effects of the Bcl-xL/Mcl-1 synthetic inhibitor, JY-1-106, alone or in combination with retinoids on cell viability. The results revealed a synergistic effect in reducing cell viability primarily by using JY-1-106 with the selective RARγ antagonist SR11253, which induces massive autophagy and necrosis. Furthermore, the results highlighted that JY-1-106 alone is able to positively influence the gene expression profile of p53 and RARα, providing a therapeutic advantage in human triple-negative breast cancer treatment.
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Affiliation(s)
- Mariarita Perri
- Department of Pharmacy, Health and Nutritional Sciences, Ed. Polifunzionale, University of Calabria, I-87036, Arcavacata di Rende (Cs), Italy
| | - Jeremy L Yap
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA
| | - Steven Fletcher
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA
| | - Erika Cione
- Department of Pharmacy, Health and Nutritional Sciences, Ed. Polifunzionale, University of Calabria, I-87036, Arcavacata di Rende (Cs), Italy
| | - Maureen A Kane
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA
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27
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Meryet-Figuière M, Lecerf C, Varin E, Coll JL, Louis MH, Dutoit S, Giffard F, Blanc-Fournier C, Hedir S, Vigneron N, Brotin E, Pelletier L, Josserand V, Denoyelle C, Poulain L. Atelocollagen-mediated in vivo siRNA transfection in ovarian carcinoma is influenced by tumor site, siRNA target and administration route. Oncol Rep 2017; 38:1949-1958. [PMID: 28791387 PMCID: PMC5652939 DOI: 10.3892/or.2017.5882] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 06/12/2017] [Indexed: 12/16/2022] Open
Abstract
Ovarian cancer is the leading cause of death from gynecological malignancies worldwide, and innate or acquired chemoresistance of ovarian cancer cells is the major cause of therapeutic failure. It has been demonstrated that the concomitant inhibition of Bcl-xL and Mcl-1 anti-apoptotic activities is able to trigger apoptosis in chemoresistant ovarian cancer cells. In this context, siRNA-mediated Bcl‑xL and Mcl-1 inhibition constitutes an appealing strategy by which to eliminate chemoresistant cancer cells. However, the safest and most efficient way to vectorize siRNAs in vivo is still under debate. In the present study, using in vivo bioluminescence imaging, we evaluated the interest of atelocollagen to vectorize siRNAs by intraperitoneal (i.p.) or intravenous (i.v.) administration in 2 xenografted ovarian cancer models (peritoneal carcinomatosis and subcutaneous tumors in nude mice). Whereas i.p. administration of atelocollagen-vectorized siRNA in the peritoneal carcinomatosis model did not induce any gene downregulation, a 70% transient downregulation of luciferase expression was achieved after i.v. injection of atelocollagen-vectorized siRNA in the subcutaneous (s.c.) model. However, the use of siRNA targeting Bcl-xL or Mcl-1 did not induce target-specific downregulation in vivo in nude mice. Our results therefore show that atelocollagen complex formulation, the administration route, tumor site and the identity of the siRNA target influence the efficiency of atelocollagen‑mediated siRNA delivery.
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Affiliation(s)
- Matthieu Meryet-Figuière
- INSERM U1086 'ANTICIPE' Interdisciplinary Research Unit for Cancer Prevention and Treatment, Axe 2: 'Biology and Innovative Therapeutics for Locally Aggressive Cancers' (BioTICLA), Comprehensive Cancer Center François Baclesse, 14076 Caen Cedex 5, France
| | - Charlotte Lecerf
- INSERM U1086 'ANTICIPE' Interdisciplinary Research Unit for Cancer Prevention and Treatment, Axe 2: 'Biology and Innovative Therapeutics for Locally Aggressive Cancers' (BioTICLA), Comprehensive Cancer Center François Baclesse, 14076 Caen Cedex 5, France
| | - Emilie Varin
- INSERM U1086 'ANTICIPE' Interdisciplinary Research Unit for Cancer Prevention and Treatment, Axe 2: 'Biology and Innovative Therapeutics for Locally Aggressive Cancers' (BioTICLA), Comprehensive Cancer Center François Baclesse, 14076 Caen Cedex 5, France
| | - Jean-Luc Coll
- INSERM U1209, Institute of Advanced Biosciences, Institut pour l'Avancée des Biosciences, Centre de Recherche UGA, Site Santé, 38700 La Tronche, France
| | - Marie-Hélène Louis
- INSERM U1086 'ANTICIPE' Interdisciplinary Research Unit for Cancer Prevention and Treatment, Axe 2: 'Biology and Innovative Therapeutics for Locally Aggressive Cancers' (BioTICLA), Comprehensive Cancer Center François Baclesse, 14076 Caen Cedex 5, France
| | - Soizic Dutoit
- INSERM U1086 'ANTICIPE' Interdisciplinary Research Unit for Cancer Prevention and Treatment, Axe 2: 'Biology and Innovative Therapeutics for Locally Aggressive Cancers' (BioTICLA), Comprehensive Cancer Center François Baclesse, 14076 Caen Cedex 5, France
| | - Florence Giffard
- INSERM U1086 'ANTICIPE' Interdisciplinary Research Unit for Cancer Prevention and Treatment, Axe 2: 'Biology and Innovative Therapeutics for Locally Aggressive Cancers' (BioTICLA), Comprehensive Cancer Center François Baclesse, 14076 Caen Cedex 5, France
| | - Cécile Blanc-Fournier
- INSERM U1086 'ANTICIPE' Interdisciplinary Research Unit for Cancer Prevention and Treatment, Axe 2: 'Biology and Innovative Therapeutics for Locally Aggressive Cancers' (BioTICLA), Comprehensive Cancer Center François Baclesse, 14076 Caen Cedex 5, France
| | - Siham Hedir
- INSERM U1086 'ANTICIPE' Interdisciplinary Research Unit for Cancer Prevention and Treatment, Axe 2: 'Biology and Innovative Therapeutics for Locally Aggressive Cancers' (BioTICLA), Comprehensive Cancer Center François Baclesse, 14076 Caen Cedex 5, France
| | - Nicolas Vigneron
- INSERM U1086 'ANTICIPE' Interdisciplinary Research Unit for Cancer Prevention and Treatment, Axe 2: 'Biology and Innovative Therapeutics for Locally Aggressive Cancers' (BioTICLA), Comprehensive Cancer Center François Baclesse, 14076 Caen Cedex 5, France
| | - Emilie Brotin
- INSERM U1086 'ANTICIPE' Interdisciplinary Research Unit for Cancer Prevention and Treatment, Axe 2: 'Biology and Innovative Therapeutics for Locally Aggressive Cancers' (BioTICLA), Comprehensive Cancer Center François Baclesse, 14076 Caen Cedex 5, France
| | - Laurent Pelletier
- INSERM U836, Grenoble Institute of Neurosciences, Bâtiment Edmond J. Safra, Chemin Fortuné Ferrini, Site Santé, 38706 La Tronche Cedex, France
| | - Véronique Josserand
- INSERM U1209, Institute of Advanced Biosciences, Institut pour l'Avancée des Biosciences, Centre de Recherche UGA, Site Santé, 38700 La Tronche, France
| | - Christophe Denoyelle
- INSERM U1086 'ANTICIPE' Interdisciplinary Research Unit for Cancer Prevention and Treatment, Axe 2: 'Biology and Innovative Therapeutics for Locally Aggressive Cancers' (BioTICLA), Comprehensive Cancer Center François Baclesse, 14076 Caen Cedex 5, France
| | - Laurent Poulain
- INSERM U1086 'ANTICIPE' Interdisciplinary Research Unit for Cancer Prevention and Treatment, Axe 2: 'Biology and Innovative Therapeutics for Locally Aggressive Cancers' (BioTICLA), Comprehensive Cancer Center François Baclesse, 14076 Caen Cedex 5, France
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Raman EP, Lakkaraju SK, Denny RA, MacKerell AD. Estimation of relative free energies of binding using pre-computed ensembles based on the single-step free energy perturbation and the site-identification by Ligand competitive saturation approaches. J Comput Chem 2017; 38:1238-1251. [PMID: 27782307 PMCID: PMC5403604 DOI: 10.1002/jcc.24522] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 09/17/2016] [Accepted: 10/04/2016] [Indexed: 12/19/2022]
Abstract
Accurate and rapid estimation of relative binding affinities of ligand-protein complexes is a requirement of computational methods for their effective use in rational ligand design. Of the approaches commonly used, free energy perturbation (FEP) methods are considered one of the most accurate, although they require significant computational resources. Accordingly, it is desirable to have alternative methods of similar accuracy but greater computational efficiency to facilitate ligand design. In the present study relative free energies of binding are estimated for one or two non-hydrogen atom changes in compounds targeting the proteins ACK1 and p38 MAP kinase using three methods. The methods include standard FEP, single-step free energy perturbation (SSFEP) and the site-identification by ligand competitive saturation (SILCS) ligand grid free energy (LGFE) approach. Results show the SSFEP and SILCS LGFE methods to be competitive with or better than the FEP results for the studied systems, with SILCS LGFE giving the best agreement with experimental results. This is supported by additional comparisons with published FEP data on p38 MAP kinase inhibitors. While both the SSFEP and SILCS LGFE approaches require a significant upfront computational investment, they offer a 1000-fold computational savings over FEP for calculating the relative affinities of ligand modifications once those pre-computations are complete. An illustrative example of the potential application of these methods in the context of screening large numbers of transformations is presented. Thus, the SSFEP and SILCS LGFE approaches represent viable alternatives for actively driving ligand design during drug discovery and development. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- E. Prabhu Raman
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street HSF II, Baltimore MD 21201
| | - Sirish Kaushik Lakkaraju
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street HSF II, Baltimore MD 21201
| | - Rajiah Aldrin Denny
- Medicine Design, Worldwide Research & Development, Pfizer Inc, 610 Main Street, Cambridge, MA 02139, USA
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street HSF II, Baltimore MD 21201
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Verma S, Singh A, Kumari A, Tyagi C, Goyal S, Jamal S, Grover A. Natural polyphenolic inhibitors against the antiapoptotic BCL-2. J Recept Signal Transduct Res 2017; 37:391-400. [DOI: 10.1080/10799893.2017.1298129] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Sharad Verma
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Aditi Singh
- Department of Biotechnology, TERI University, Vasant Kunj, New Delhi, India
| | - Anchala Kumari
- Department of Biotechnology, TERI University, Vasant Kunj, New Delhi, India
| | - Chetna Tyagi
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Sukriti Goyal
- Department of Bioscience and Biotechnology, Banasthali University, Tonk, Rajasthan, India
| | - Salma Jamal
- Department of Bioscience and Biotechnology, Banasthali University, Tonk, Rajasthan, India
| | - Abhinav Grover
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
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Yap JL, Chen L, Lanning ME, Fletcher S. Expanding the Cancer Arsenal with Targeted Therapies: Disarmament of the Antiapoptotic Bcl-2 Proteins by Small Molecules. J Med Chem 2016; 60:821-838. [PMID: 27749061 DOI: 10.1021/acs.jmedchem.5b01888] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A hallmark of cancer is the evasion of apoptosis, which is often associated with the upregulation of the antiapoptotic members of the Bcl-2 family of proteins. The prosurvival function of the antiapoptotic Bcl-2 proteins is manifested by capturing and neutralizing the proapoptotic Bcl-2 proteins via their BH3 death domains. Accordingly, strategies to antagonize the antiapoptotic Bcl-2 proteins have largely focused on the development of low-molecular-weight, synthetic BH3 mimetics ("magic bullets") to disrupt the protein-protein interactions between anti- and proapoptotic Bcl-2 proteins. In this way, apoptosis has been reactivated in malignant cells. Moreover, several such Bcl-2 family inhibitors are presently being evaluated for a range of cancers in clinical trials and show great promise as new additions to the cancer armamentarium. Indeed, the selective Bcl-2 inhibitor venetoclax (Venclexta) recently received FDA approval for the treatment of a specific subset of patients with chronic lymphocytic leukemia. This review focuses on the major developments in the field of Bcl-2 inhibitors over the past decade, with particular emphasis on binding modes and, thus, the origins of selectivity for specific Bcl-2 family members.
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Affiliation(s)
- Jeremy L Yap
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy , 20 N. Pine Street, Baltimore, Maryland 21201, United States
| | - Lijia Chen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy , 20 N. Pine Street, Baltimore, Maryland 21201, United States
| | - Maryanna E Lanning
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy , 20 N. Pine Street, Baltimore, Maryland 21201, United States
| | - Steven Fletcher
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy , 20 N. Pine Street, Baltimore, Maryland 21201, United States.,University of Maryland Greenebaum Cancer Center , Baltimore, Maryland 21201, United States
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Abstract
INTRODUCTION The myeloid cell leukemia-1 (MCL-1) protein is one of the key anti-apoptotic members of the B-cell lymphoma-2 (BCL-2) protein family. Over-expression of MCL-1 has been closely related to tumor progression as well as to resistance, not only to traditional chemotherapies but also to targeted therapeutics including BCL-2 inhibitors such as ABT-263. Therefore, there has been extensive research and development in the last decade in both academic and industrial settings to address this unmet medical need. Areas covered: This review covers the research and patent literature of the past 10 years in the field of discovery and development of small-molecule inhibitors of the MCL-1 anti-apoptotic protein. Expert opinion: Small-molecule strategies to disrupt the protein-protein interactions between MCL-1 and its pro-apoptotic counterparts, such as BAK and BIM, have recently emerged. Several small-molecules based on different scaffolds describe promising in vitro data as MCL-1 selective inhibitors. While many lead compounds remain at the in vitro preclinical development stage, the two most recent patent applications describe promising in vivo data, and one small molecule inhibitor has recently entered into clinical development. It is such an exciting moment that the long awaited clinical studies will generate some insight into the therapeutic potential of this anti-cancer approach, and possibly facilitate the further development of other early stage inhibitors.
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Affiliation(s)
- Lijia Chen
- a Department of Pharmaceutical Sciences , University of Maryland School of Pharmacy , Baltimore , MD , USA
| | - Steven Fletcher
- a Department of Pharmaceutical Sciences , University of Maryland School of Pharmacy , Baltimore , MD , USA
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Hoda MA, Pirker C, Dong Y, Schelch K, Heffeter P, Kryeziu K, van Schoonhoven S, Klikovits T, Laszlo V, Rozsas A, Ozsvar J, Klepetko W, Döme B, Grusch M, Hegedüs B, Berger W. Trabectedin Is Active against Malignant Pleural Mesothelioma Cell and Xenograft Models and Synergizes with Chemotherapy and Bcl-2 Inhibition In Vitro. Mol Cancer Ther 2016; 15:2357-2369. [PMID: 27512118 DOI: 10.1158/1535-7163.mct-15-0846] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 07/26/2016] [Indexed: 11/16/2022]
Abstract
Malignant pleural mesothelioma (MPM) is characterized by widespread resistance to systemic therapy. Trabectedin is an antineoplastic agent targeting both the malignant cells and the tumor microenvironment that has been approved for the treatment of advanced soft tissue sarcoma and ovarian cancer. In this preclinical study, we evaluated the antineoplastic potential of trabectedin as a single agent and in drug combination approaches in human MPM. Therefore, we utilized an extended panel of MPM cell lines (n = 6) and primary cell cultures from surgical MPM specimens (n = 13), as well as nonmalignant pleural tissue samples (n = 2). Trabectedin exerted a dose-dependent cytotoxic effect in all MPM cell cultures in vitro when growing as adherent monolayers or nonadherent spheroids with IC50 values ≤ 2.6 nmol/L. Nonmalignant mesothelial cells were significantly less responsive. The strong antimesothelioma activity was based on cell-cycle perturbation and apoptosis induction. The activity of trabectedin against MPM cells was synergistically enhanced by coadministration of cisplatin, a drug routinely used for systemic MPM treatment. Comparison of gene expression signatures indicated an inverse correlation between trabectedin response and bcl-2 expression. Accordingly, bcl-2 inhibitors (Obatoclax, ABT-199) markedly synergized with trabectedin paralleled by deregulated expression of the bcl-2 family members bcl-2, bim, bax, Mcl-1, and bcl-xL as a consequence of trabectedin exposure. In addition, trabectedin exerted significant antitumor activity against an intraperitoneal MPM xenograft model. Together, these data suggest that trabectedin exerts strong activity in MPM and synergizes with chemotherapy and experimental bcl-2 inhibitors in vitro Thus, it represents a promising new therapeutic option for MPM. Mol Cancer Ther; 15(10); 2357-69. ©2016 AACR.
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Affiliation(s)
- Mir A Hoda
- Applied and Experimental Oncology, Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria. Translational Thoracic Oncology Laboratory, Division of Thoracic Surgery, Department of Surgery, Comprehensive Cancer Center, Medical University Vienna, Vienna, Austria
| | - Christine Pirker
- Applied and Experimental Oncology, Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Yawen Dong
- Translational Thoracic Oncology Laboratory, Division of Thoracic Surgery, Department of Surgery, Comprehensive Cancer Center, Medical University Vienna, Vienna, Austria
| | - Karin Schelch
- Applied and Experimental Oncology, Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria. Translational Thoracic Oncology Laboratory, Division of Thoracic Surgery, Department of Surgery, Comprehensive Cancer Center, Medical University Vienna, Vienna, Austria
| | - Petra Heffeter
- Applied and Experimental Oncology, Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Kushtrim Kryeziu
- Applied and Experimental Oncology, Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Sushilla van Schoonhoven
- Applied and Experimental Oncology, Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Thomas Klikovits
- Translational Thoracic Oncology Laboratory, Division of Thoracic Surgery, Department of Surgery, Comprehensive Cancer Center, Medical University Vienna, Vienna, Austria
| | - Viktoria Laszlo
- Translational Thoracic Oncology Laboratory, Division of Thoracic Surgery, Department of Surgery, Comprehensive Cancer Center, Medical University Vienna, Vienna, Austria
| | - Anita Rozsas
- Translational Thoracic Oncology Laboratory, Division of Thoracic Surgery, Department of Surgery, Comprehensive Cancer Center, Medical University Vienna, Vienna, Austria. National Koranyi Institute of Pulmonology, Budapest, Hungary
| | - Judit Ozsvar
- Translational Thoracic Oncology Laboratory, Division of Thoracic Surgery, Department of Surgery, Comprehensive Cancer Center, Medical University Vienna, Vienna, Austria
| | - Walter Klepetko
- Translational Thoracic Oncology Laboratory, Division of Thoracic Surgery, Department of Surgery, Comprehensive Cancer Center, Medical University Vienna, Vienna, Austria
| | - Balazs Döme
- Translational Thoracic Oncology Laboratory, Division of Thoracic Surgery, Department of Surgery, Comprehensive Cancer Center, Medical University Vienna, Vienna, Austria. National Koranyi Institute of Pulmonology, Budapest, Hungary. Department of Thoracic Surgery, National Institute of Oncology and Semmelweis University, Budapest, Hungary. Department of Biomedical Imaging and Image-guided Therapy, Division of Molecular and Gender Imaging, Medical University of Vienna, Vienna, Austria
| | - Michael Grusch
- Applied and Experimental Oncology, Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Balazs Hegedüs
- Translational Thoracic Oncology Laboratory, Division of Thoracic Surgery, Department of Surgery, Comprehensive Cancer Center, Medical University Vienna, Vienna, Austria. MTA-SE Molecular Oncology Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Walter Berger
- Applied and Experimental Oncology, Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.
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Luna-Vargas MPA, Chipuk JE. Physiological and Pharmacological Control of BAK, BAX, and Beyond. Trends Cell Biol 2016; 26:906-917. [PMID: 27498846 DOI: 10.1016/j.tcb.2016.07.002] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 07/13/2016] [Accepted: 07/14/2016] [Indexed: 01/01/2023]
Abstract
Cellular commitment to the mitochondrial pathway of apoptosis is accomplished when proapoptotic B cell chronic lymphocytic leukemia/lymphoma (BCL)-2 proteins compromise mitochondrial integrity through the process of mitochondrial outer membrane permeabilization (MOMP). For nearly three decades, intensive efforts focused on the identification and interactions of two key proapoptotic BCL-2 proteins: BCL-2 antagonist killer (BAK) and BCL-2-associated X (BAX). Indeed, we now have critical insights into which BCL-2 proteins interact with BAK/BAX to either preserve survival or initiate MOMP. In contrast, while mitochondria are targeted by BAK/BAX, a molecular understanding of how these organelles govern BAK/BAX function remains less clear. Here, we integrate recent mechanistic insights of proapoptotic BCL-2 protein function in the context of mitochondrial environment, and discuss current and potential pharmacological opportunities to control MOMP in disease.
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Affiliation(s)
- Mark P A Luna-Vargas
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jerry Edward Chipuk
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA; The Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA; Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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Cavalier MC, Melville Z, Aligholizadeh E, Raman EP, Yu W, Fang L, Alasady M, Pierce AD, Wilder PT, MacKerell AD, Weber DJ. Novel protein-inhibitor interactions in site 3 of Ca(2+)-bound S100B as discovered by X-ray crystallography. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:753-60. [PMID: 27303795 DOI: 10.1107/s2059798316005532] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/02/2016] [Indexed: 02/07/2023]
Abstract
Structure-based drug discovery is under way to identify and develop small-molecule S100B inhibitors (SBiXs). Such inhibitors have therapeutic potential for treating malignant melanoma, since high levels of S100B downregulate wild-type p53 tumor suppressor function in this cancer. Computational and X-ray crystallographic studies of two S100B-SBiX complexes are described, and both compounds (apomorphine hydrochloride and ethidium bromide) occupy an area of the S100B hydrophobic cleft which is termed site 3. These data also reveal novel protein-inhibitor interactions which can be used in future drug-design studies to improve SBiX affinity and specificity. Of particular interest, apomorphine hydrochloride showed S100B-dependent killing in melanoma cell assays, although the efficacy exceeds its affinity for S100B and implicates possible off-target contributions. Because there are no structural data available for compounds occupying site 3 alone, these studies contribute towards the structure-based approach to targeting S100B by including interactions with residues in site 3 of S100B.
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Affiliation(s)
- Michael C Cavalier
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics (CBT), University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Zephan Melville
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics (CBT), University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Ehson Aligholizadeh
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics (CBT), University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - E Prabhu Raman
- Computer Aided Drug Design Center, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA
| | - Wenbo Yu
- Computer Aided Drug Design Center, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA
| | - Lei Fang
- Computer Aided Drug Design Center, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA
| | - Milad Alasady
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics (CBT), University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Adam D Pierce
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics (CBT), University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Paul T Wilder
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics (CBT), University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Alexander D MacKerell
- Computer Aided Drug Design Center, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA
| | - David J Weber
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics (CBT), University of Maryland School of Medicine, Baltimore, MD 21201, USA
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Chura-Chambi RM, Arcuri HA, Lino F, Versati N, Palma MS, Favaro DC, Morganti L. Structural studies of the protein endostatin in fusion with BAX BH3 death domain, a hybrid that presents enhanced antitumoral activity. Biotechnol Appl Biochem 2016; 64:356-363. [PMID: 27144384 DOI: 10.1002/bab.1503] [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: 01/05/2016] [Accepted: 04/28/2016] [Indexed: 11/12/2022]
Abstract
Endostatin (ES) is an antiangiogenic protein that exhibits antitumor activity in animal models. However, the activity observed in animals was not observed in human clinical trials. ES-BAX is a fusion protein composed of two functional domains: ES, which presents specificity and is internalized by activated endothelial cells and the proapoptotic BH3 domain of the protein BAX, a peptide inductor of cellular death when internalized. We have previously shown (Chura-Chambi et al., Cell Death Dis, 5, e1371, 2014) that ES-BAX presents improved antitumor activity in relation to wild-type ES. Secondary and tertiary structures of ES-BAX are similar to ES, as indicated by homology-modeling studies and molecular dynamics simulations. Tryptophan intrinsic fluorescence and circular dichroism spectroscopy corroborate these data. 15 N HSQC NMR indicates that ES-BAX is structured, but some ES residues have suffered chemical shift perturbations, suggesting that the BH3 peptide interacts with some parts of the ES protein. ES and ES-BAX present similar stability to thermal denaturation. The production of stable hybrid proteins can be a new approach to the development of therapeutic agents presenting specificity for tumoral endothelium and improved antitumor effect.
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Affiliation(s)
- Rosa Maria Chura-Chambi
- Centro de Biotecnologia, Instituto de Pesquisas Energéticas e Nucleares, IPEN-CNEN/SP, São Paulo, Brazil
| | - Helen Andrade Arcuri
- Departamento de Imunologia Clínica e Alergia da Faculdade de Medicina da USP, São Paulo, Brazil
| | - Felipe Lino
- Centro de Biotecnologia, Instituto de Pesquisas Energéticas e Nucleares, IPEN-CNEN/SP, São Paulo, Brazil
| | - Natan Versati
- Centro de Biotecnologia, Instituto de Pesquisas Energéticas e Nucleares, IPEN-CNEN/SP, São Paulo, Brazil
| | - Mario Sergio Palma
- Centro de Estudos de Insetos Sociais, Instituto de Biociências de Rio Claro, UNESP, Rio Claro, São Paulo, Brazil
| | - Denize C Favaro
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ligia Morganti
- Centro de Biotecnologia, Instituto de Pesquisas Energéticas e Nucleares, IPEN-CNEN/SP, São Paulo, Brazil
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Besbes S, Mirshahi M, Pocard M, Billard C. New dimension in therapeutic targeting of BCL-2 family proteins. Oncotarget 2016; 6:12862-71. [PMID: 25970783 PMCID: PMC4536985 DOI: 10.18632/oncotarget.3868] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 04/01/2015] [Indexed: 01/22/2023] Open
Abstract
Proteins of the BCL-2 family control the mitochondrial pathway of apoptosis. Targeting these proteins proves to be an attractive strategy for anticancer therapy. The biological context is based on the fact that BH3-only members of the family are specific antagonists of prosurvival members. This prompted the identification of “BH3 mimetic” compounds. These small peptides or organic molecules indeed mimic the BH3 domain of BH3-only proteins: by selectively binding and antagonizing prosurvival proteins, they can induce apoptosis in malignant cells. Some small-molecule inhibitors of prosurvival proteins have already entered clinical trials in cancer patients and two of them have shown significant therapeutic effects. The latest developments in the field of targeting BCL-2 family proteins highlight several new antagonists of prosurvival proteins as well as direct activators of proapoptotic proteins. These compounds open up novel prospects for the development of BH3 mimetic anticancer drugs.
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Affiliation(s)
- Samaher Besbes
- INSERM U 965, Hôpital Lariboisière, Paris, France.,Université Paris Diderot, UMR S965, Paris, France
| | - Massoud Mirshahi
- INSERM U 965, Hôpital Lariboisière, Paris, France.,Université Paris Diderot, UMR S965, Paris, France
| | - Marc Pocard
- INSERM U 965, Hôpital Lariboisière, Paris, France.,Université Paris Diderot, UMR S965, Paris, France
| | - Christian Billard
- INSERM U 965, Hôpital Lariboisière, Paris, France.,Université Paris Diderot, UMR S965, Paris, France
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Lim Z, Duggan PJ, Wan SS, Lessene G, Meyer AG, Tuck KL. Exploiting the Biginelli reaction: nitrogen-rich pyrimidine-based tercyclic α-helix mimetics. Tetrahedron 2016. [DOI: 10.1016/j.tet.2015.12.044] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Drennen B, Scheenstra JA, Yap JL, Chen L, Lanning ME, Roth BM, Wilder PT, Fletcher S. Structural Re-engineering of the α-Helix Mimetic JY-1-106 into Small Molecules: Disruption of the Mcl-1-Bak-BH3 Protein-Protein Interaction with 2,6-Di-Substituted Nicotinates. ChemMedChem 2016; 11:827-33. [PMID: 26844930 DOI: 10.1002/cmdc.201500461] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 11/23/2015] [Indexed: 01/19/2023]
Abstract
The disruption of aberrant protein-protein interactions (PPIs) with synthetic agents remains a challenging goal in contemporary medicinal chemistry but some progress has been made. One such dysregulated PPI is that between the anti-apoptotic Bcl-2 proteins, including myeloid cell leukemia-1 (Mcl-1), and the α-helical Bcl-2 homology-3 (BH3) domains of its pro-apoptotic counterparts, such as Bak. Herein, we describe the discovery of small-molecule inhibitors of the Mcl-1 oncoprotein based on a novel chemotype. Particularly, re-engineering of our α-helix mimetic JY-1-106 into 2,6-di-substituted nicotinates afforded inhibitors of comparable potencies but with significantly decreased molecular weights. The most potent inhibitor 2-(benzyloxy)-6-(4-chloro-3,5-dimethylphenoxy)nicotinic acid (1 r: Ki =2.90 μm) likely binds in the p2 pocket of Mcl-1 and engages R263 in a salt bridge through its carboxylic acid, as supported by 2D (1) H-(15) N HSQC NMR data. Significantly, inhibitors were easily accessed in just four steps, which will facilitate future optimization efforts.
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Affiliation(s)
- Brandon Drennen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Jacob A Scheenstra
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Jeremy L Yap
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Lijia Chen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Maryanna E Lanning
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Braden M Roth
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Paul T Wilder
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,University of Maryland, Greenebaum Cancer Center, Baltimore, MD, 21201, USA
| | - Steven Fletcher
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA. .,University of Maryland, Greenebaum Cancer Center, Baltimore, MD, 21201, USA.
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Structure-based design of N-substituted 1-hydroxy-4-sulfamoyl-2-naphthoates as selective inhibitors of the Mcl-1 oncoprotein. Eur J Med Chem 2016; 113:273-92. [PMID: 26985630 DOI: 10.1016/j.ejmech.2016.02.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 02/02/2016] [Accepted: 02/03/2016] [Indexed: 12/21/2022]
Abstract
Structure-based drug design was utilized to develop novel, 1-hydroxy-2-naphthoate-based small-molecule inhibitors of Mcl-1. Ligand design was driven by exploiting a salt bridge with R263 and interactions with the p2 pocket of the protein. Significantly, target molecules were accessed in just two synthetic steps, suggesting further optimization will require minimal synthetic effort. Molecular modeling using the Site-Identification by Ligand Competitive Saturation (SILCS) approach was used to qualitatively direct ligand design as well as develop quantitative models for inhibitor binding affinity to Mcl-1 and the Bcl-2 relative Bcl-xL as well as for the specificity of binding to the two proteins. Results indicated hydrophobic interactions in the p2 pocket dominated affinity of the most favourable binding ligand (3bl: Ki = 31 nM). Compounds were up to 19-fold selective for Mcl-1 over Bcl-xL. Selectivity of the inhibitors was driven by interactions with the deeper p2 pocket in Mcl-1 versus Bcl-xL. The SILCS-based SAR of the present compounds represents the foundation for the development of Mcl-1 specific inhibitors with the potential to treat a wide range of solid tumours and hematological cancers, including acute myeloid leukemia.
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Li X, Zhang C, Zhang X, Wang S, Meng Q, Wu S, Yang H, Xia Y, Chen R. An acetyl-L-carnitine switch on mitochondrial dysfunction and rescue in the metabolomics study on aluminum oxide nanoparticles. Part Fibre Toxicol 2016; 13:4. [PMID: 26772537 PMCID: PMC4715336 DOI: 10.1186/s12989-016-0115-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 01/11/2016] [Indexed: 02/07/2023] Open
Abstract
Background Due to the wide application of engineered aluminum oxide nanoparticles and increased aluminum containing particulate matter suspending in air, exposure of human to nano-scale aluminum oxide nanoparticles (Al2O3 NPs) is becoming inevitable. Methods In the present study, RNA microarray coupled with metabolomics analysis were used to uncover mechanisms underlying cellular responses to Al2O3 NPs and imply the potential rescue. Results We found that Al2O3 NPs significantly triggered down-regulation of mitochondria-related genes located in complex I, IV and V, which were involved in oxidative phosphorylation and neural degeneration pathways, in human bronchial epithelial (HBE) cells. Subsequent cell- and animal- based assays confirmed that Al2O3 NPs caused mitochondria-dependent apoptosis and oxidative stress either in vitro or in vivo, which were consistent with the trends of gene regulation. To rescue the Al2O3 NPs induced mitochondria dysfunction, disruption of small molecular metabolites of HBE were profiled using metabolomics analysis, which facilitates identification of potential antagonizer or supplement against nanoparticle-involved damages. Supplementation of an antioxidant, acetyl-L-carnitine, completely or partially restored the Al2O3 NPs modulated gene expression levels in mitochondrial complex I, IV and V. It further reduced apoptosis and oxidative damages in both Al2O3 NPs treated HBE cells and animal lung tissues. Conclusion Thus, our results demonstrate the potential mechanism of respiratory system damages induced by Al2O3 NPs. Meanwhile, based on the metabolomics profiling, application of acetyl-L-carnitine is suggested to ameliorate mitochondria dysfunction associated with Al2O3 NPs. Electronic supplementary material The online version of this article (doi:10.1186/s12989-016-0115-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaobo Li
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Dingjiaqiao 87, Nanjing, 210009, China.
| | - Chengcheng Zhang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Dingjiaqiao 87, Nanjing, 210009, China.
| | - Xin Zhang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Dingjiaqiao 87, Nanjing, 210009, China.
| | - Shizhi Wang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Dingjiaqiao 87, Nanjing, 210009, China.
| | - Qingtao Meng
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Dingjiaqiao 87, Nanjing, 210009, China.
| | - Shenshen Wu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Dingjiaqiao 87, Nanjing, 210009, China.
| | - Hongbao Yang
- Center for Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing, 211198, China.
| | - Yankai Xia
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.
| | - Rui Chen
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Dingjiaqiao 87, Nanjing, 210009, China. .,State Key Laboratory of Bioelectronics, Southeast University, Nanjing, 210096, China.
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Lee JH, Oh M, Kim HS, Lee H, Im W, Lim HS. Converting One-Face α-Helix Mimetics into Amphiphilic α-Helix Mimetics as Potent Inhibitors of Protein-Protein Interactions. ACS COMBINATORIAL SCIENCE 2016; 18:36-42. [PMID: 26651509 DOI: 10.1021/acscombsci.5b00080] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Many biologically active α-helical peptides adopt amphiphilic helical structures that contain hydrophobic residues on one side and hydrophilic residues on the other side. Therefore, α-helix mimetics capable of mimicking such amphiphilic helical peptides should possess higher binding affinity and specificity to target proteins. Here we describe an efficient method for generating amphiphilic α-helix mimetics. One-face α-helix mimetics having hydrophobic side chains on one side was readily converted into amphiphilic α-helix mimetics by introducing appropriate charged residues on the opposite side. We also demonstrate that such two-face amphiphilic α-helix mimetics indeed show remarkably improved binding affinity to a target protein, compared to one-face hydrophobic α-helix mimetics. We believe that generating a large combinatorial library of these amphiphilic α-helix mimetics can be valuable for rapid discovery of highly potent and specific modulators of protein-protein interactions.
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Affiliation(s)
- Ji Hoon Lee
- New
Drug Development Center, Daegu Gyeongbuk Medical Innovation Foundation, Daegu 701-310, South Korea
| | - Misook Oh
- Department
of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 790-784, South Korea
- Department
of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Hyun Soo Kim
- Department
of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 790-784, South Korea
| | - Huisun Lee
- Department
of Molecular Biosciences and Centre for Computational Biology, The University of Kansas, Lawrence, Kansas 66047, United States
| | - Wonpil Im
- Department
of Molecular Biosciences and Centre for Computational Biology, The University of Kansas, Lawrence, Kansas 66047, United States
| | - Hyun-Suk Lim
- Department
of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 790-784, South Korea
- Department
of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
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Nhu D, Lessene G, Huang DCS, Burns CJ. Small molecules targeting Mcl-1: the search for a silver bullet in cancer therapy. MEDCHEMCOMM 2016. [DOI: 10.1039/c5md00582e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Progress towards the development of potent and selective inhibitors of the pro-survival protein Mcl-1 is reviewed.
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Affiliation(s)
- Duong Nhu
- The Walter and Eliza Hall Institute of Medical Research
- Australia
- Department of Medical Biology
- The University of Melbourne
- Australia
| | - Guillaume Lessene
- The Walter and Eliza Hall Institute of Medical Research
- Australia
- Department of Medical Biology
- The University of Melbourne
- Australia
| | - David C. S. Huang
- The Walter and Eliza Hall Institute of Medical Research
- Australia
- Department of Medical Biology
- The University of Melbourne
- Australia
| | - Christopher J. Burns
- The Walter and Eliza Hall Institute of Medical Research
- Australia
- Department of Medical Biology
- The University of Melbourne
- Australia
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43
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Chen L, Wilder PT, Drennen B, Tran J, Roth BM, Chesko K, Shapiro P, Fletcher S. Structure-based design of 3-carboxy-substituted 1,2,3,4-tetrahydroquinolines as inhibitors of myeloid cell leukemia-1 (Mcl-1). Org Biomol Chem 2016; 14:5505-10. [DOI: 10.1039/c5ob02063h] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A novel Mcl-1 inhibitor chemotype based on a tetrahydroquinoline carboxylic acid was developed utilizing structure-based design, which was subsequently validated by a fluorescence polarization competition assay and HSQC NMR analysis.
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Affiliation(s)
- L. Chen
- Department of Pharmaceutical Sciences
- University of Maryland School of Pharmacy
- Baltimore
- USA
| | - P. T. Wilder
- Department of Biochemistry and Molecular Biology
- University of Maryland School of Medicine
- Baltimore
- USA
- University of Maryland Greenebaum Cancer Center
| | - B. Drennen
- Department of Pharmaceutical Sciences
- University of Maryland School of Pharmacy
- Baltimore
- USA
| | - J. Tran
- PharmD Program
- University of Maryland School of Pharmacy
- Baltimore
- USA
| | - B. M. Roth
- Department of Biochemistry and Molecular Biology
- University of Maryland School of Medicine
- Baltimore
- USA
- University of Maryland Greenebaum Cancer Center
| | - K. Chesko
- Department of Pharmaceutical Sciences
- University of Maryland School of Pharmacy
- Baltimore
- USA
| | - P. Shapiro
- Department of Pharmaceutical Sciences
- University of Maryland School of Pharmacy
- Baltimore
- USA
- University of Maryland Greenebaum Cancer Center
| | - S. Fletcher
- Department of Pharmaceutical Sciences
- University of Maryland School of Pharmacy
- Baltimore
- USA
- University of Maryland Greenebaum Cancer Center
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Ludwig LM, Nassin ML, Hadji A, LaBelle JL. Killing Two Cells with One Stone: Pharmacologic BCL-2 Family Targeting for Cancer Cell Death and Immune Modulation. Front Pediatr 2016; 4:135. [PMID: 28066751 PMCID: PMC5174130 DOI: 10.3389/fped.2016.00135] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 11/30/2016] [Indexed: 12/31/2022] Open
Abstract
A crucial component of regulating organismal homeostasis is maintaining proper cell number and eliminating damaged or potentially malignant cells. Apoptosis, or programed cell death, is the mechanism responsible for this equilibrium. The intrinsic apoptotic pathway is also especially important in the development and maintenance of the immune system. Apoptosis is essential for proper positive and negative selection during B- and T-cell development and for efficient contraction of expanded lymphocytes following an immune response. Tight regulation of the apoptotic pathway is critical, as excessive cell death can lead to immunodeficiency while apoptotic resistance can lead to aberrant lymphoproliferation and autoimmune disease. Dysregulation of cell death is implicated in a wide range of hematological malignancies, and targeting various components of the apoptotic machinery in these cases is an attractive chemotherapeutic strategy. A wide array of compounds has been developed with the purpose of reactivating the intrinsic apoptotic pathway. These compounds, termed BH3 mimetics are garnering considerable attention as they gain greater clinical oncologic significance. As their use expands, it will be imperative to understand the effects these compounds have on immune homeostasis. Uncovering their potential immunomodulatory activity may allow for administration of BH3 mimetics for direct tumor cell killing as well as novel therapies for a wide range of immune-based directives. This review will summarize the major proteins involved in the intrinsic apoptotic pathway and define their roles in normal immune development and disease. Clinical and preclinical BH3 mimetics are described within the context of what is currently known about their ability to affect immune function. Prospects for future antitumor immune amplification and immune modulation are then proposed.
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Affiliation(s)
- Lindsey M Ludwig
- Section of Hematology, Oncology, Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Comer Children's Hospital, Chicago, IL, USA; Committee on Cancer Biology, University of Chicago, Chicago, IL, USA
| | - Michele L Nassin
- Section of Hematology, Oncology, Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Comer Children's Hospital , Chicago, IL , USA
| | - Abbas Hadji
- Section of Hematology, Oncology, Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Comer Children's Hospital , Chicago, IL , USA
| | - James L LaBelle
- Section of Hematology, Oncology, Stem Cell Transplantation, Department of Pediatrics, University of Chicago, Comer Children's Hospital, Chicago, IL, USA; Committee on Cancer Biology, University of Chicago, Chicago, IL, USA
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Drennen B, MacKerell AD, Fletcher S. Expedient access to pre-organized α-helix mimetics based on an isocinchomeronic acid core. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.10.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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46
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Wilson AJ. Helix mimetics: Recent developments. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 119:33-40. [DOI: 10.1016/j.pbiomolbio.2015.05.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Revised: 05/21/2015] [Accepted: 05/22/2015] [Indexed: 12/19/2022]
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47
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Besbes S, Mirshahi M, Pocard M, Billard C. Strategies targeting apoptosis proteins to improve therapy of chronic lymphocytic leukemia. Blood Rev 2015; 29:345-50. [DOI: 10.1016/j.blre.2015.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 03/02/2015] [Accepted: 03/26/2015] [Indexed: 12/21/2022]
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48
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Lanning ME, Fletcher S. Multi-Facial, Non-Peptidic α-Helix Mimetics. BIOLOGY 2015; 4:540-55. [PMID: 26404384 PMCID: PMC4588149 DOI: 10.3390/biology4030540] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 08/11/2015] [Accepted: 08/14/2015] [Indexed: 01/13/2023]
Abstract
α-Helices often recognize their target proteins at protein–protein interfaces through more than one recognition face. This review describes the state-of-the-art in the design of non-peptidic α-helix mimetics that reproduce functionality from multiple faces of an α-helix.
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Affiliation(s)
- Maryanna E Lanning
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N. Pine St., Baltimore, MD 21201, USA.
| | - Steven Fletcher
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N. Pine St., Baltimore, MD 21201, USA.
- University of Maryland Greenebaum Cancer Center, 22 S. Greene St., Baltimore, MD 21201, USA.
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Pelay-Gimeno M, Glas A, Koch O, Grossmann TN. Structure-Based Design of Inhibitors of Protein-Protein Interactions: Mimicking Peptide Binding Epitopes. Angew Chem Int Ed Engl 2015; 54:8896-927. [PMID: 26119925 PMCID: PMC4557054 DOI: 10.1002/anie.201412070] [Citation(s) in RCA: 496] [Impact Index Per Article: 55.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Indexed: 12/15/2022]
Abstract
Protein-protein interactions (PPIs) are involved at all levels of cellular organization, thus making the development of PPI inhibitors extremely valuable. The identification of selective inhibitors is challenging because of the shallow and extended nature of PPI interfaces. Inhibitors can be obtained by mimicking peptide binding epitopes in their bioactive conformation. For this purpose, several strategies have been evolved to enable a projection of side chain functionalities in analogy to peptide secondary structures, thereby yielding molecules that are generally referred to as peptidomimetics. Herein, we introduce a new classification of peptidomimetics (classes A-D) that enables a clear assignment of available approaches. Based on this classification, the Review summarizes strategies that have been applied for the structure-based design of PPI inhibitors through stabilizing or mimicking turns, β-sheets, and helices.
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Affiliation(s)
- Marta Pelay-Gimeno
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
| | - Adrian Glas
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
| | - Oliver Koch
- TU Dortmund University, Department of Chemistry and Chemical BiologyOtto-Hahn-Strasse 6, 44227 Dortmund (Germany)
| | - Tom N Grossmann
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
- TU Dortmund University, Department of Chemistry and Chemical BiologyOtto-Hahn-Strasse 6, 44227 Dortmund (Germany)
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50
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Lanning ME, Wilder PT, Bailey H, Drennen B, Cavalier M, Chen L, Yap JL, Raje M, Fletcher S. Towards more drug-like proteomimetics: two-faced, synthetic α-helix mimetics based on a purine scaffold. Org Biomol Chem 2015. [PMID: 26204921 DOI: 10.1039/c5ob00478k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Mimicry of two faces of an α-helix might yield more potent and more selective inhibitors of aberrant, helix-mediated protein-protein interactions (PPI). Herein, we demonstrate that a 2,6,9-tri-substituted purine is capable of disrupting the Mcl-1-Bak-BH3 PPI through effective mimicry of key residues on opposing faces of the Bak-BH3 α-helix.
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Affiliation(s)
- M E Lanning
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N. Pine St., Baltimore, MD 21201, USA.
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