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Yang H, Li S, Li W, Yang Y, Zhang Y, Zhang S, Hao Y, Cao W, Xu F, Wang H, Du G, Wang J. Actinomycin D synergizes with Doxorubicin in triple-negative breast cancer by inducing P53-dependent cell apoptosis. Carcinogenesis 2024; 45:262-273. [PMID: 37997385 DOI: 10.1093/carcin/bgad086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/18/2023] [Accepted: 11/19/2023] [Indexed: 11/25/2023] Open
Abstract
OBJECTIVES There are three major subtypes of breast cancer, ER+, HER2+ and triple-negative breast cancer (TNBC), namely ER-, PR-, HER2-. TNBC is the most aggressive breast cancer with poor prognosis and no target drug up to now. Actinomycin D (ActD) is a bioactive metabolite of marine bacteria that has been reported to have antitumor activity. The aim of study is to investigate whether ActD has a synergetic effect on TNBC with Doxorubicin (Dox), the major chemotherapeutic drug for TNBC, and explore the underlying mechanism. METHODS TNBC cell lines HCC1937, MDA-MB-436 and nude mice were used in the study. Drug synergy determination, LDH assay, MMP assay, Hoechst 33342 staining, Flow cytometry, Flexible docking and CESTA assay were carried out. The expression of proteins associated with apoptosis was checked by Western blot and siRNA experiments were performed to investigate the role of P53 and PUMA induced by drugs. RESULTS There was much higher apoptosis rate of cells in the ActD + Dox group than that in ActD group or Dox group. Expression of MDM2 and BCL-2 was reduced while expression of P53, PUMA and BAX were increased in the groups treated with ActD + Dox or Dox compared to the control group. Furthermore, P53 siRNA or PUMA siRNA tremendously abrogated the cell apoptosis in the groups treated by ActD, Dox and ActD + Dox. Flexible docking and CESTA showed that ActD can bind MDM2. CONCLUSIONS ActD had a synergetic effect on TNBC with Dox via P53-dependent apoptosis and it may be a new choice for treatment of TNBC.
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Affiliation(s)
- Hong Yang
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing, China
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Sha Li
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing, China
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Wan Li
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing, China
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yihui Yang
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing, China
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yizhi Zhang
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing, China
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Sen Zhang
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing, China
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yue Hao
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing, China
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Wanxin Cao
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing, China
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Fang Xu
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing, China
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Hongquan Wang
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, 300060, Tianjin, China
| | - Guanhua Du
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing, China
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Jinhua Wang
- The State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing, China
- Key Laboratory of Drug Target Research and Drug Screen, Institute of Materia Medica, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
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2
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Cheng J, Zhou J, Kong L, Wang H, Zhang Y, Wang X, Liu G, Chu Q. Stabilized cyclic peptides as modulators of protein-protein interactions: promising strategies and biological evaluation. RSC Med Chem 2023; 14:2496-2508. [PMID: 38107173 PMCID: PMC10718590 DOI: 10.1039/d3md00487b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 10/04/2023] [Indexed: 12/19/2023] Open
Abstract
Protein-protein interactions (PPIs) control many essential biological pathways which are often misregulated in disease. As such, selective PPI modulators are desirable to unravel complex functions of PPIs and thus expand the repertoire of therapeutic targets. However, the large size and relative flatness of PPI interfaces make them challenging molecular targets for conventional drug modalities, rendering most PPIs "undruggable". Therefore, there is a growing need to discover innovative molecules that are able to modulate crucial PPIs. Peptides are ideal candidates to deliver such therapeutics attributed to their ability to closely mimic structural features of protein interfaces. However, their inherently poor proteolysis resistance and cell permeability inevitably hamper their biomedical applications. The introduction of a constraint (i.e., peptide cyclization) to stabilize peptides' secondary structure is a promising strategy to address this problem as witnessed by the rapid development of cyclic peptide drugs in the past two decades. Here, we comprehensively review the recent progress on stabilized cyclic peptides in targeting challenging PPIs. Technological advancements and emerging chemical approaches for stabilizing active peptide conformations are categorized in terms of α-helix stapling, β-hairpin mimetics and macrocyclization. To discover potent and selective ligands, cyclic peptide library technologies were updated based on genetic, biochemical or synthetic methodologies. Moreover, several advances to improve the permeability and oral bioavailability of biologically active cyclic peptides enable the de novo development of cyclic peptide ligands with pharmacological properties. In summary, the development of cyclic peptide-based PPI modulators carries tremendous promise for the next generation of therapeutic agents to target historically "intractable" PPI systems.
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Affiliation(s)
- Jiongjia Cheng
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University 3601 Hongjing Avenue Nanjing 211171 China
| | - Junlong Zhou
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University 639 Longmian Avenue Nanjing 211198 China
| | - Lingyan Kong
- College of Food Science and Engineering, Nanjing University of Finance and Economics Nanjing 210023 China
| | - Haiying Wang
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University 3601 Hongjing Avenue Nanjing 211171 China
| | - Yuchi Zhang
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University 3601 Hongjing Avenue Nanjing 211171 China
| | - Xiaofeng Wang
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University 3601 Hongjing Avenue Nanjing 211171 China
| | - Guangxiang Liu
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University 3601 Hongjing Avenue Nanjing 211171 China
| | - Qian Chu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University 639 Longmian Avenue Nanjing 211198 China
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University Nanjing 210009 China
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3
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Targeted Degradation of Androgen Receptor by VNPP433-3β in Castration-Resistant Prostate Cancer Cells Implicates Interaction with E3 Ligase MDM2 Resulting in Ubiquitin-Proteasomal Degradation. Cancers (Basel) 2023; 15:cancers15041198. [PMID: 36831540 PMCID: PMC9954018 DOI: 10.3390/cancers15041198] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/08/2023] [Accepted: 02/13/2023] [Indexed: 02/16/2023] Open
Abstract
Targeted protein degradation is a fast-evolving therapeutic strategy to target even the traditionally undruggable target proteins. Contrary to the traditional small-molecule inhibitors of enzyme or receptor antagonists that bind the active site pockets in the target protein, molecular glue degraders facilitate interaction of target proteins with E3 ubiquitin ligases by stabilizing the ternary complex and induce physical proximity, thereby triggering ubiquitination and subsequent proteasomal degradation. AR plays a key role in all stages of prostate cancer. It is activated by the binding of androgenic hormones and transcriptionally regulates multiple genes including the ones that regulate cell cycle. Using HiBiT CRISPR cell line, biochemical methods, and RNA sequencing, we report the potential role of VNPP433-3β, the next generation galeterone analog as molecular glue that brings together AR, the key driver of prostate cancer and MDM2, an E3 ubiquitin ligase leading to ubiquitination and subsequent degradation of f-AR and AR-V7 in prostate cancer cells.
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4
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Ochoa R, Cossio P, Fox T. Protocol for iterative optimization of modified peptides bound to protein targets. J Comput Aided Mol Des 2022; 36:825-835. [PMID: 36258137 PMCID: PMC9640467 DOI: 10.1007/s10822-022-00482-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/03/2022] [Indexed: 12/02/2022]
Abstract
Peptides are commonly used as therapeutic agents. However, they suffer from easy degradation and instability. Replacing natural by non-natural amino acids can avoid these problems, and potentially improve the affinity towards the target protein. Here, we present a computational pipeline to optimize peptides based on adding non-natural amino acids while improving their binding affinity. The workflow is an iterative computational evolution algorithm, inspired by the PARCE protocol, that performs single-point mutations on the peptide sequence using modules from the Rosetta framework. The modifications can be guided based on the structural properties or previous knowledge of the biological system. At each mutation step, the affinity to the protein is estimated by sampling the complex conformations and applying a consensus metric using various open protein-ligand scoring functions. The mutations are accepted based on the score differences, allowing for an iterative optimization of the initial peptide. The sampling/scoring scheme was benchmarked with a set of protein-peptide complexes where experimental affinity values have been reported. In addition, a basic application using a known protein-peptide complex is also provided. The structure- and dynamic-based approach allows users to optimize bound peptides, with the option to personalize the code for further applications. The protocol, called mPARCE, is available at: https://github.com/rochoa85/mPARCE/.
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Affiliation(s)
- Rodrigo Ochoa
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia, Medellín, 050010, Colombia. .,Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co KG, 88397, Biberach/Riss, Germany.
| | - Pilar Cossio
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia, Medellín, 050010, Colombia.,Center for Computational Mathematics, Flatiron Institute, New York, 10010, USA.,Center for Computational Biology, Flatiron Institute, New York, 10010, USA
| | - Thomas Fox
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co KG, 88397, Biberach/Riss, Germany
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5
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Martínez FA, Adler NS, Cavasotto CN, Aucar GA. Solvent effects on the NMR shieldings of stacked DNA base pairs. Phys Chem Chem Phys 2022; 24:18150-18160. [PMID: 35861154 DOI: 10.1039/d2cp00398h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Stacking effects are among the most important effects in DNA. We have recently studied their influence in fragments of DNA through the analysis of NMR magnetic shieldings, firstly in vacuo. As a continuation of this line of research we show here the influence of solvent effects on the shieldings through the application of both explicit and implicit models. We found that the explicit solvent model is more appropriate for consideration due to the results matching better in general with experiments, as well as providing clear knowledge of the electronic origin of the value of the shieldings. Our study is grounded on a recently developed theoretical model of our own, by which we are able to learn about the magnetic effects of given fragments of DNA molecules on selected base pairs. We use the shieldings of the atoms of a central base pair (guanine-cytosine) of a selected fragment of DNA molecules as descriptors of physical effects, like π-stacking and solvent effects. They can be taken separately and altogether. The effect of π-stacking is introduced through the addition of some pairs above and below of the central base pair, and now, the solvent effect is considered including a network of water molecules that consist of two solvation layers, which were fixed in the calculations performed in all fragments. We show that the solvent effects enhance the stacking effects on the magnetic shieldings of atoms that belong to the external N-H bonds. The net effect is of deshielding on both atoms. There is also a deshielding effect on the carbon atoms that belong to CO bonds, for which the oxygen atom has an explicit hydrogen bond (HB) with a solvent water molecule. Solvent effects are found to be no higher than a few percent of the total value of the shieldings (between 1% and 5%) for most atoms, although there are few for which such an effect can be higher. There is one nitrogen atom, the acceptor of the HB between guanine and cytosine, that is more highly shielded (around 15 ppm or 10%) when the explicit solvent is considered. In a similar manner, the most external nitrogen atom of cytosine and the hydrogen atom that is bonded to it are highly deshielded (around 10 ppm for nitrogen and around 3 ppm for hydrogen).
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Affiliation(s)
- Fernando A Martínez
- Institute of Modelling and Innovation on Technology (IMIT), CONICET-UNNE, Avda Libertad 5460, W3404AAS Corrientes, Argentina.,Chemistry Department, Natural and Exact Science Faculty, Northeastern University of Argentina, Avda Libertad 5460, W3404AAS Corrientes, Argentina
| | - Natalia S Adler
- Computational Drug Design and Biomedical Informatics Laboratory, Instituto de Investigaciones en Medicina Translacional (IIMT), CONICET-Universidad Austral, Pilar, Buenos Aires, Argentina.,Centro de Investigaciones en BioNanociencias (CIBION), CONICET, Buenos Aires, Argentina
| | - Claudio N Cavasotto
- Computational Drug Design and Biomedical Informatics Laboratory, Instituto de Investigaciones en Medicina Translacional (IIMT), CONICET-Universidad Austral, Pilar, Buenos Aires, Argentina.,Facultad de Ciencias Biomédicas and Facultad de Ingeniería, Universidad Austral, Pilar, Buenos Aires, Argentina.,Austral Institute for Applied Artificial Intelligence, Universidad Austral, Pilar, Buenos Aires, Argentina
| | - Gustavo A Aucar
- Institute of Modelling and Innovation on Technology (IMIT), CONICET-UNNE, Avda Libertad 5460, W3404AAS Corrientes, Argentina.,Physics Department, Natural and Exact Science Faculty, Northeastern University of Argentina, Avda Libertad 5460, W3404AAS Corrientes, Argentina.
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6
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Li X, Gohain N, Chen S, Li Y, Zhao X, Li B, Tolbert WD, He W, Pazgier M, Hu H, Lu W. Design of ultrahigh-affinity and dual-specificity peptide antagonists of MDM2 and MDMX for P53 activation and tumor suppression. Acta Pharm Sin B 2021; 11:2655-2669. [PMID: 34589387 PMCID: PMC8463443 DOI: 10.1016/j.apsb.2021.06.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/28/2021] [Accepted: 06/03/2021] [Indexed: 12/13/2022] Open
Abstract
Peptide inhibition of the interactions of the tumor suppressor protein P53 with its negative regulators MDM2 and MDMX activates P53 in vitro and in vivo, representing a viable therapeutic strategy for cancer treatment. Using phage display techniques, we previously identified a potent peptide activator of P53, termed PMI (TSFAEYWNLLSP), with binding affinities for both MDM2 and MDMX in the low nanomolar concentration range. Here we report an ultrahigh affinity, dual-specificity peptide antagonist of MDM2 and MDMX obtained through systematic mutational analysis and additivity-based molecular design. Functional assays of over 100 peptide analogs of PMI using surface plasmon resonance and fluorescence polarization techniques yielded a dodecameric peptide termed PMI-M3 (LTFLEYWAQLMQ) that bound to MDM2 and MDMX with Kd values in the low picomolar concentration range as verified by isothermal titration calorimetry. Co-crystal structures of MDM2 and of MDMX in complex with PMI-M3 were solved at 1.65 and 3.0 Å resolution, respectively. Similar to PMI, PMI-M3 occupied the P53-binding pocket of MDM2/MDMX, which was dominated energetically by intermolecular interactions involving Phe3, Tyr6, Trp7, and Leu10. Notable differences in binding between PMI-M3 and PMI were observed at other positions such as Leu4 and Met11 with MDM2, and Leu1 and Met11 with MDMX, collectively contributing to a significantly enhanced binding affinity of PMI-M3 for both proteins. By adding lysine residues to both ends of PMI and PMI-M3 to improve their cellular uptake, we obtained modified peptides termed PMI-2K (KTSFAEYWNLLSPK) and M3-2K (KLTFLEYWAQLMQK). Compared with PMI-2K, M3-2K exhibited significantly improved antitumor activities in vitro and in vivo in a P53-dependent manner. This super-strong peptide inhibitor of the P53-MDM2/MDMX interactions may become, in its own right, a powerful lead compound for anticancer drug development, and can aid molecular design of other classes of P53 activators as well for anticancer therapy.
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Affiliation(s)
- Xiang Li
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
- Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Neelakshi Gohain
- Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Si Chen
- School of Medicine, Shanghai University, Shanghai 200444, China
| | - Yinghua Li
- Institute of Translational Medicine, Shanghai University, Shanghai 200444, China
| | - Xiaoyuan Zhao
- Institute of Translational Medicine, Shanghai University, Shanghai 200444, China
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Bo Li
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - William D. Tolbert
- Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Wangxiao He
- Department of Talent Highland, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Marzena Pazgier
- Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Corresponding authors. Tel./fax: +86 21 54237607 (Wuyuan Lu), +86 21 66131281 (Honggang Hu), +1 301 295 3291 (Marzena Pazgier).
| | - Honggang Hu
- Institute of Translational Medicine, Shanghai University, Shanghai 200444, China
- Corresponding authors. Tel./fax: +86 21 54237607 (Wuyuan Lu), +86 21 66131281 (Honggang Hu), +1 301 295 3291 (Marzena Pazgier).
| | - Wuyuan Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS) of School of Basic Medical Sciences and Shanghai Institute of Infectious Disease and Biosecurity of School of Public Health, Fudan University, Shanghai 200032, China
- Corresponding authors. Tel./fax: +86 21 54237607 (Wuyuan Lu), +86 21 66131281 (Honggang Hu), +1 301 295 3291 (Marzena Pazgier).
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7
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Messelberger J, Pinter P, Heinemann FW, Munz D. A lead(II) toluene complex. MENDELEEV COMMUNICATIONS 2021. [DOI: 10.1016/j.mencom.2021.07.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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8
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Ge Y, Zhang S, Erdelyi M, Voelz VA. Solution-State Preorganization of Cyclic β-Hairpin Ligands Determines Binding Mechanism and Affinities for MDM2. J Chem Inf Model 2021; 61:2353-2367. [PMID: 33905247 PMCID: PMC9960209 DOI: 10.1021/acs.jcim.1c00029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Understanding mechanisms of protein folding and binding is crucial to designing their molecular function. Molecular dynamics (MD) simulations and Markov state model (MSM) approaches provide a powerful way to understand complex conformational change that occurs over long time scales. Such dynamics are important for the design of therapeutic peptidomimetic ligands, whose affinity and binding mechanism are dictated by a combination of folding and binding. To examine the role of preorganization in peptide binding to protein targets, we performed massively parallel explicit-solvent MD simulations of cyclic β-hairpin ligands designed to mimic the p53 transactivation domain and competitively bind mouse double minute 2 homologue (MDM2). Disrupting the MDM2-p53 interaction is a therapeutic strategy to prevent degradation of the p53 tumor suppressor in cancer cells. MSM analysis of over 3 ms of aggregate trajectory data enabled us to build a detailed mechanistic model of coupled folding and binding of four cyclic peptides which we compare to experimental binding affinities and rates. The results show a striking relationship between the relative preorganization of each ligand in solution and its affinity for MDM2. Specifically, changes in peptide conformational populations predicted by the MSMs suggest that entropy loss upon binding is the main factor influencing affinity. The MSMs also enable detailed examination of non-native interactions which lead to misfolded states and comparison of structural ensembles with experimental NMR measurements. In contrast to an MSM study of p53 transactivation domain (TAD) binding to MDM2, MSMs of cyclic β-hairpin binding show a conformational selection mechanism. Finally, we make progress toward predicting accurate off rates of cyclic peptides using multiensemble Markov models (MEMMs) constructed from unbiased and biased simulated trajectories.
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Affiliation(s)
- Yunui Ge
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
| | - Si Zhang
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
| | - Mate Erdelyi
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Vincent A. Voelz
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
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9
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Miles JA, Hobor F, Trinh CH, Taylor J, Tiede C, Rowell PR, Jackson BR, Nadat FA, Ramsahye P, Kyle HF, Wicky BIM, Clarke J, Tomlinson DC, Wilson AJ, Edwards TA. Selective Affimers Recognise the BCL-2 Family Proteins BCL-x L and MCL-1 through Noncanonical Structural Motifs*. Chembiochem 2021; 22:232-240. [PMID: 32961017 PMCID: PMC7821230 DOI: 10.1002/cbic.202000585] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/17/2020] [Indexed: 12/26/2022]
Abstract
The BCL-2 family is a challenging group of proteins to target selectively due to sequence and structural homologies across the family. Selective ligands for the BCL-2 family regulators of apoptosis are useful as probes to understand cell biology and apoptotic signalling pathways, and as starting points for inhibitor design. We have used phage display to isolate Affimer reagents (non-antibody-binding proteins based on a conserved scaffold) to identify ligands for MCL-1, BCL-xL , BCL-2, BAK and BAX, then used multiple biophysical characterisation methods to probe the interactions. We established that purified Affimers elicit selective recognition of their target BCL-2 protein. For anti-apoptotic targets BCL-xL and MCL-1, competitive inhibition of their canonical protein-protein interactions is demonstrated. Co-crystal structures reveal an unprecedented mode of molecular recognition; where a BH3 helix is normally bound, flexible loops from the Affimer dock into the BH3 binding cleft. Moreover, the Affimers induce a change in the target proteins towards a desirable drug-bound-like conformation. These proof-of-concept studies indicate that Affimers could be used as alternative templates to inspire the design of selective BCL-2 family modulators and more generally other protein-protein interaction inhibitors.
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Affiliation(s)
- Jennifer A. Miles
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Fruzsina Hobor
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Chi H. Trinh
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - James Taylor
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Christian Tiede
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Philip R. Rowell
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Brian R. Jackson
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Protein Production FacilityUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Fatima A. Nadat
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Protein Production FacilityUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Pallavi Ramsahye
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Hannah F. Kyle
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Basile I. M. Wicky
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Jane Clarke
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Darren C. Tomlinson
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Andrew J. Wilson
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Thomas A. Edwards
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre For Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
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10
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Abdildinova A, Gong YD. Traceless solid-phase synthesis and β-turn propensity of 1,3-thiazole-based peptidomimetics. RSC Adv 2020; 11:1050-1056. [PMID: 35423674 PMCID: PMC8693395 DOI: 10.1039/d0ra10127c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 12/18/2020] [Indexed: 12/15/2022] Open
Abstract
The design and solid-phase synthesis of 1,3-thiazole-based peptidomimetic molecules is described. The solid-phase synthesis was based on the utilization of a traceless linker strategy. The synthesis starts from the conversion of chloromethyl polystyrene resin to the resin with a sulfur linker unit. The key intermediate 4-amino-thiazole-5-carboxylic acid resin is prepared in three steps from Merrifield resin. The amide coupling proceeded at the C4 and C5 positions via an Fmoc solid-phase peptide synthesis strategy. After cleavage, the final compounds were obtained in moderate yields (average 9%, 11-step overall yields) with high purities (≥87%). Geometric measurements of Cα distances and dihedral angles along with an rmsd of 0.5434 for attachment with Cα of the β-turn template suggest type IV β-turn structural motifs. Additionally, the physicochemical properties of the molecules have been evaluated.
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Affiliation(s)
- Aizhan Abdildinova
- Innovative Drug Library Research Center, Department of Chemistry, College of Science, Dongguk University 30, Pildong-ro 1-gil, Jung-gu Seoul 04620 Korea
| | - Young-Dae Gong
- Innovative Drug Library Research Center, Department of Chemistry, College of Science, Dongguk University 30, Pildong-ro 1-gil, Jung-gu Seoul 04620 Korea
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11
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Nakadai M, Tomida S. Diameter Is a Key 3D Characteristic for Assessments of Efficient Inhibitors of Protein-Protein Interactions. J Chem Inf Model 2020; 60:4785-4790. [PMID: 32808775 DOI: 10.1021/acs.jcim.0c00607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Three-dimensional (3D) molecular descriptors, including physicochemical and shape properties, for protein-protein interaction (PPI) interface inhibitors have become a topic of discussion. However, the relationships between such properties and binding free energy have not been adequately investigated. In this study, we focused on identifying key 3D molecular descriptors related to the binding free energy and/or the ligand efficiency (LE) of PPI interface inhibitors. A positive correlation was found between the binding free energy and the diameter (D) of cylindrical 3D molecules, in addition to a correlation between LE and D/heavy atom count (HAC). In addition, we showed a correlation between LE and D/HAC for macrocyclic compounds, suggesting that the present findings could be applied during assessments of the potential of macrocyclic PPI interface inhibitors in drug discovery processes.
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Affiliation(s)
- Masakazu Nakadai
- Genome Pharmaceutical Institute Company, Ltd., 1-27-8-1207 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shuta Tomida
- Center for Comprehensive Genomic Medicine, Okayama University Hospital, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan
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12
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Anananuchatkul T, Tsutsumi H, Miki T, Mihara H. hDM2 protein-binding peptides screened from stapled α-helical peptide phage display libraries with different types of staple linkers. Bioorg Med Chem Lett 2020; 30:127605. [PMID: 33038548 DOI: 10.1016/j.bmcl.2020.127605] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/29/2020] [Accepted: 10/03/2020] [Indexed: 11/18/2022]
Abstract
Chemically modified peptide ligands were identified from α-helix peptide phage libraries with different types of staple linkers. The hDM2-protein was used as a representative target of protein-protein interactions to screen ligands for p53 binding sites in hDM2. Two types of staple linkers were used for the chemical modification of the peptide phage display libraries before affinity selection. The identified stapled peptides could bind to hDM2 competitively with the p53 peptide. The stapled peptide phage libraries developed in this study will improve the discovery of protein-protein interaction inhibitors through the synergistic effect of peptide units and staple linkers.
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Affiliation(s)
- Teerapat Anananuchatkul
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Hiroshi Tsutsumi
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Takayuki Miki
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Hisakazu Mihara
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.
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13
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Hetherington K, Hegedus Z, Edwards TA, Sessions RB, Nelson A, Wilson AJ. Stapled Peptides as HIF-1α/p300 Inhibitors: Helicity Enhancement in the Bound State Increases Inhibitory Potency. Chemistry 2020; 26:7638-7646. [PMID: 32307728 PMCID: PMC7318359 DOI: 10.1002/chem.202000417] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/13/2020] [Indexed: 12/17/2022]
Abstract
Protein-protein interactions (PPIs) control virtually all cellular processes and have thus emerged as potential targets for development of molecular therapeutics. Peptide-based inhibitors of PPIs are attractive given that they offer recognition potency and selectivity features that are ideal for function, yet, they do not predominantly populate the bioactive conformation, frequently suffer from poor cellular uptake and are easily degraded, for example, by proteases. The constraint of peptides in a bioactive conformation has emerged as a promising strategy to mitigate against these liabilities. In this work, using peptides derived from hypoxia-inducible factor 1 (HIF-1α) together with dibromomaleimide stapling, we identify constrained peptide inhibitors of the HIF-1α/p300 interaction that are more potent than their unconstrained sequences. Contrary to expectation, the increased potency does not correlate with an increased population of an α-helical conformation in the unbound state as demonstrated by experimental circular dichroism analysis. Rather, the ability of the peptide to adopt a bioactive α-helical conformation in the p300 bound state is better supported in the constrained variant as demonstrated by molecular dynamics simulations and circular dichroism difference spectra.
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Affiliation(s)
- Kristina Hetherington
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Zsofia Hegedus
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Thomas A. Edwards
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- School of Molecular and Cellular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Richard B. Sessions
- School of BiochemistryUniversity of BristolMedical Sciences Building, University WalkBristolBS8 1TDUK
- BrisSynBioUniversity of Bristol, Life Sciences BuildingTyndall AvenueBristolBS8 1TQUK
| | - Adam Nelson
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Andrew J. Wilson
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
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14
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Ninković D, Blagojević Filipović JP, Hall MB, Brothers EN, Zarić SD. What Is Special about Aromatic-Aromatic Interactions? Significant Attraction at Large Horizontal Displacement. ACS CENTRAL SCIENCE 2020; 6:420-425. [PMID: 32232142 PMCID: PMC7099588 DOI: 10.1021/acscentsci.0c00005] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Indexed: 05/22/2023]
Abstract
High-level ab initio calculations show that the most stable stacking for benzene-cyclohexane is 17% stronger than that for benzene-benzene. However, as these systems are displaced horizontally the benzene-benzene attraction retains its strength. At a displacement of 5.0 Å, the benzene-benzene attraction is still ∼70% of its maximum strength, while benzene-cyclohexane attraction has fallen to ∼40% of its maximum strength. Alternatively, the radius of attraction (>2.0 kcal/mol) for benzene-benzene is 250% larger than that for benzene-cyclohexane. Thus, at relatively large distances aromatic rings can recognize each other, a phenomenon that helps explain their importance in protein folding and supramolecular structures.
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Affiliation(s)
- Dragan
B. Ninković
- Innovation
Center of the Faculty of Chemistry in Belgrade, Studentski trg 12-16, Belgrade 11001, Serbia
| | | | - Michael B. Hall
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843-3255, United States
- E-mail:
| | - Edward N. Brothers
- Department
of Chemistry, Texas A&M University at
Qatar, P.O. Box 23874, Doha, Qatar
| | - Snežana D. Zarić
- Faculty
of Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade 11000, Serbia
- Department
of Chemistry, Texas A&M University at
Qatar, P.O. Box 23874, Doha, Qatar
- E-mail:
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15
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Ricardo MG, Ali AM, Plewka J, Surmiak E, Labuzek B, Neochoritis CG, Atmaj J, Skalniak L, Zhang R, Holak TA, Groves M, Rivera DG, Dömling A. Multicomponent Peptide Stapling as a Diversity‐Driven Tool for the Development of Inhibitors of Protein–Protein Interactions. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916257] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Manuel G. Ricardo
- Faculty of Chemistry, Center for Natural Product ResearchUniversity of Havana Cuba
| | - Ameena M. Ali
- Department of PharmacyDrug Design group, University of Groningen The Netherlands
| | - Jacek Plewka
- Faculty of ChemistryJagiellonian University Krakow Poland
| | - Ewa Surmiak
- Faculty of ChemistryJagiellonian University Krakow Poland
| | - Beata Labuzek
- Faculty of ChemistryJagiellonian University Krakow Poland
| | - Constantinos G. Neochoritis
- Department of PharmacyDrug Design group, University of Groningen The Netherlands
- Department of ChemistryUniversity of Crete Greece
| | - Jack Atmaj
- Department of PharmacyDrug Design group, University of Groningen The Netherlands
- Faculty of ChemistryJagiellonian University Krakow Poland
| | | | - Ran Zhang
- Department of PharmacyDrug Design group, University of Groningen The Netherlands
| | - Tad A. Holak
- Faculty of ChemistryJagiellonian University Krakow Poland
| | - Matthew Groves
- Department of PharmacyDrug Design group, University of Groningen The Netherlands
| | - Daniel G. Rivera
- Faculty of Chemistry, Center for Natural Product ResearchUniversity of Havana Cuba
| | - Alexander Dömling
- Department of PharmacyDrug Design group, University of Groningen The Netherlands
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16
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Ricardo MG, Ali AM, Plewka J, Surmiak E, Labuzek B, Neochoritis CG, Atmaj J, Skalniak L, Zhang R, Holak TA, Groves M, Rivera DG, Dömling A. Multicomponent Peptide Stapling as a Diversity-Driven Tool for the Development of Inhibitors of Protein-Protein Interactions. Angew Chem Int Ed Engl 2020; 59:5235-5241. [PMID: 31944488 DOI: 10.1002/anie.201916257] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Indexed: 12/12/2022]
Abstract
Stapled peptides are chemical entities in-between biologics and small molecules, which have proven to be the solution to high affinity protein-protein interaction antagonism, while keeping control over pharmacological performance such as stability and membrane penetration. We demonstrate that the multicomponent reaction-based stapling is an effective strategy for the development of α-helical peptides with highly potent dual antagonistic action of MDM2 and MDMX binding p53. Such a potent inhibitory activity of p53-MDM2/X interactions was assessed by fluorescence polarization, microscale thermophoresis, and 2D NMR, while several cocrystal structures with MDM2 were obtained. This MCR stapling protocol proved efficient and versatile in terms of diversity generation at the staple, as evidenced by the incorporation of both exo- and endo-cyclic hydrophobic moieties at the side chain cross-linkers. The interaction of the Ugi-staple fragments with the target protein was demonstrated by crystallography.
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Affiliation(s)
- Manuel G Ricardo
- Faculty of Chemistry, Center for Natural Product Research, University of Havana, Cuba
| | - Ameena M Ali
- Department of Pharmacy, Drug Design group, University of, Groningen, The Netherlands
| | - Jacek Plewka
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Ewa Surmiak
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Beata Labuzek
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Constantinos G Neochoritis
- Department of Pharmacy, Drug Design group, University of, Groningen, The Netherlands.,Department of Chemistry, University of, Crete, Greece
| | - Jack Atmaj
- Department of Pharmacy, Drug Design group, University of, Groningen, The Netherlands.,Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Lukasz Skalniak
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Ran Zhang
- Department of Pharmacy, Drug Design group, University of, Groningen, The Netherlands
| | - Tad A Holak
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
| | - Matthew Groves
- Department of Pharmacy, Drug Design group, University of, Groningen, The Netherlands
| | - Daniel G Rivera
- Faculty of Chemistry, Center for Natural Product Research, University of Havana, Cuba
| | - Alexander Dömling
- Department of Pharmacy, Drug Design group, University of, Groningen, The Netherlands
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17
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Diller DJ, Swanson J, Bayden AS, Brown CJ, Thean D, Lane DP, Partridge AW, Sawyer TK, Audie J. Rigorous Computational and Experimental Investigations on MDM2/MDMX-Targeted Linear and Macrocyclic Peptides. Molecules 2019; 24:E4586. [PMID: 31847417 PMCID: PMC6943714 DOI: 10.3390/molecules24244586] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 12/11/2019] [Accepted: 12/12/2019] [Indexed: 12/25/2022] Open
Abstract
There is interest in peptide drug design, especially for targeting intracellular protein-protein interactions. Therefore, the experimental validation of a computational platform for enabling peptide drug design is of interest. Here, we describe our peptide drug design platform (CMDInventus) and demonstrate its use in modeling and predicting the structural and binding aspects of diverse peptides that interact with oncology targets MDM2/MDMX in comparison to both retrospective (pre-prediction) and prospective (post-prediction) data. In the retrospective study, CMDInventus modules (CMDpeptide, CMDboltzmann, CMDescore and CMDyscore) were used to accurately reproduce structural and binding data across multiple MDM2/MDMX data sets. In the prospective study, CMDescore, CMDyscore and CMDboltzmann were used to accurately predict binding affinities for an Ala-scan of the stapled α-helical peptide ATSP-7041. Remarkably, CMDboltzmann was used to accurately predict the results of a novel D-amino acid scan of ATSP-7041. Our investigations rigorously validate CMDInventus and support its utility for enabling peptide drug design.
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Affiliation(s)
- David J. Diller
- CMDBioscience, 5 Park Avenue, New Haven, CT 06511, USA; (D.J.D.); (J.S.); (A.S.B.)
- Venenum BioDesign, LLC, 8 Black Forest Road, Hamilton, NJ 08691, USA
| | - Jon Swanson
- CMDBioscience, 5 Park Avenue, New Haven, CT 06511, USA; (D.J.D.); (J.S.); (A.S.B.)
- ChemModeling, LLC, Suite 101, 500 Huber Park Ct, Weldon Spring, MO 63304, USA
| | - Alexander S. Bayden
- CMDBioscience, 5 Park Avenue, New Haven, CT 06511, USA; (D.J.D.); (J.S.); (A.S.B.)
- Kleo Pharmaceuticals, 25 Science Park, Ste 235, New Haven, CT 06511, USA
| | - Chris J. Brown
- A*STAR, p53 Laboratory, Singapore 138648, Singapore; (C.J.B.); (D.T.); (D.P.L.)
| | - Dawn Thean
- A*STAR, p53 Laboratory, Singapore 138648, Singapore; (C.J.B.); (D.T.); (D.P.L.)
| | - David P. Lane
- A*STAR, p53 Laboratory, Singapore 138648, Singapore; (C.J.B.); (D.T.); (D.P.L.)
| | - Anthony W. Partridge
- MSD International GmbH, Singapore 138665, Singapore;
- Merck Research Laboratories, 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Tomi K. Sawyer
- Merck Research Laboratories, 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Joseph Audie
- CMDBioscience, 5 Park Avenue, New Haven, CT 06511, USA; (D.J.D.); (J.S.); (A.S.B.)
- College of Arts and Sciences, Department of Chemistry, Sacred Heart University, 5151 Park Avenue, Fairfield, CT 06825, USA
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18
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Headen TF. Temperature dependent structural changes in liquid benzene studied using neutron diffraction. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1631496] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Thomas F. Headen
- ISIS Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Didcot, Oxon, UK
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19
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Sadeghi I, Asatekin A. Membranes with Functionalized Nanopores for Aromaticity-Based Separation of Small Molecules. ACS APPLIED MATERIALS & INTERFACES 2019; 11:12854-12862. [PMID: 30844237 DOI: 10.1021/acsami.9b00090] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Membranes that can separate molecules of similar size based on chemical features could transform chemical manufacturing. We demonstrate membranes with functional, 1-3 nm pores prepared using a simple and scalable approach: coating a porous support with random copolymer micelles in alcohol, followed by precipitation in water and functionalization of pore surfaces. This approach was used to prepare membranes that can separate two hormones of similar size and charge, differentiated by aromaticity, mediated through π-π interactions between the aromatic solute and pore walls functionalized with phenol groups. The aromatic molecule permeates more slowly in single-solute experiments. In competitive diffusion experiments, however, it permeates 7.1 times faster than its nonaromatic analogue. This approach can be used to manufacture membranes for complex separations based on various intermolecular interactions.
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Affiliation(s)
- Ilin Sadeghi
- Chemical and Biological Engineering Department , Tufts University , Medford , Massachusetts 02155 , United States
| | - Ayse Asatekin
- Chemical and Biological Engineering Department , Tufts University , Medford , Massachusetts 02155 , United States
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20
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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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21
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Reichart F, Maltsev OV, Kapp TG, Räder AFB, Weinmüller M, Marelli UK, Notni J, Wurzer A, Beck R, Wester HJ, Steiger K, Di Maro S, Di Leva FS, Marinelli L, Nieberler M, Reuning U, Schwaiger M, Kessler H. Selective Targeting of Integrin αvβ8 by a Highly Active Cyclic Peptide. J Med Chem 2019; 62:2024-2037. [DOI: 10.1021/acs.jmedchem.8b01588] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Florian Reichart
- Institute for Advanced Study and Center of Integrated Protein Science (CIPSM), Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Oleg V. Maltsev
- Institute for Advanced Study and Center of Integrated Protein Science (CIPSM), Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Tobias G. Kapp
- Institute for Advanced Study and Center of Integrated Protein Science (CIPSM), Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Andreas F. B. Räder
- Institute for Advanced Study and Center of Integrated Protein Science (CIPSM), Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Michael Weinmüller
- Institute for Advanced Study and Center of Integrated Protein Science (CIPSM), Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Udaya Kiran Marelli
- Central NMR Facility and Division of Organic Chemistry, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, 411008 Pune, India
| | - Johannes Notni
- Lehrstuhl für Pharmazeutische Radiochemie, Technische Universität München, Walther-Meißner Straße 3, 85748 Garching, Germany
| | - Alexander Wurzer
- Lehrstuhl für Pharmazeutische Radiochemie, Technische Universität München, Walther-Meißner Straße 3, 85748 Garching, Germany
| | - Roswitha Beck
- Lehrstuhl für Pharmazeutische Radiochemie, Technische Universität München, Walther-Meißner Straße 3, 85748 Garching, Germany
| | - Hans-Jürgen Wester
- Lehrstuhl für Pharmazeutische Radiochemie, Technische Universität München, Walther-Meißner Straße 3, 85748 Garching, Germany
| | - Katja Steiger
- Department of Pathology, Technische Universität München, Trogerstraße 18, 81675 München, Germany
| | - Salvatore Di Maro
- DiSTABiF, Università degli Studi della Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Francesco Saverio Di Leva
- Dipartimento di Farmacia, Università degli Studi di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Luciana Marinelli
- Dipartimento di Farmacia, Università degli Studi di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Markus Nieberler
- Department of Oral and Maxillofacial Surgery, University Hospital Rechts der Isar, Technische Universität München, Ismaninger Straße 22, 81679 München, Germany
| | | | | | - Horst Kessler
- Institute for Advanced Study and Center of Integrated Protein Science (CIPSM), Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
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22
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Toxin Neutralization Using Alternative Binding Proteins. Toxins (Basel) 2019; 11:toxins11010053. [PMID: 30658491 PMCID: PMC6356946 DOI: 10.3390/toxins11010053] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 01/07/2019] [Accepted: 01/12/2019] [Indexed: 12/20/2022] Open
Abstract
Animal toxins present a major threat to human health worldwide, predominantly through snakebite envenomings, which are responsible for over 100,000 deaths each year. To date, the only available treatment against snakebite envenoming is plasma-derived antivenom. However, despite being key to limiting morbidity and mortality among snakebite victims, current antivenoms suffer from several drawbacks, such as immunogenicity and high cost of production. Consequently, avenues for improving envenoming therapy, such as the discovery of toxin-sequestering monoclonal antibodies against medically important target toxins through phage display selection, are being explored. However, alternative binding protein scaffolds that exhibit certain advantages compared to the well-known immunoglobulin G scaffold, including high stability under harsh conditions and low cost of production, may pose as possible low-cost alternatives to antibody-based therapeutics. There is now a plethora of alternative binding protein scaffolds, ranging from antibody derivatives (e.g., nanobodies), through rationally designed derivatives of other human proteins (e.g., DARPins), to derivatives of non-human proteins (e.g., affibodies), all exhibiting different biochemical and pharmacokinetic profiles. Undeniably, the high level of engineerability and potentially low cost of production, associated with many alternative protein scaffolds, present an exciting possibility for the future of snakebite therapeutics and merit thorough investigation. In this review, a comprehensive overview of the different types of binding protein scaffolds is provided together with a discussion on their relevance as potential modalities for use as next-generation antivenoms.
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23
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Danelius E, Pettersson M, Bred M, Min J, Waddell MB, Guy RK, Grøtli M, Erdelyi M. Flexibility is important for inhibition of the MDM2/p53 protein-protein interaction by cyclic β-hairpins. Org Biomol Chem 2018; 14:10386-10393. [PMID: 27731454 DOI: 10.1039/c6ob01510g] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein-protein interactions that have large, flat and featureless binding sites are difficult drug targets. In the development of their modulators conventional drug discovery strategies are often unsuccessful. Gaining a detailed understanding of the binding mode of protein-protein interaction inhibitors is therefore of vast importance for their future pharmaceutical use. The MDM2/p53 protein pair is a highly promising target for cancer treatment. Disruption of the protein complex using p53 α-helix mimetics has been shown to be a successful strategy to control p53 activity. To gain further insight into the binding of inhibitors to MDM2, the flexibility of four cyclic β-hairpins that act as α-helical mimetics and potential MDM2/p53 interaction inhibitors was investigated in relation to their inhibitory activity. MDM2-binding of the mimetics was determined using fluorescence polarization and surface plasmon resonance assays, whereas their conformation and dynamics in solution was described by the combined experimental and computational NAMFIS analysis. Molecular flexibility was shown to be important for the activity of the cyclic β-hairpin based MDM2 inhibitors.
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Affiliation(s)
- Emma Danelius
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-41296 Gothenburg, Sweden.
| | - Mariell Pettersson
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-41296 Gothenburg, Sweden.
| | - Matilda Bred
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-41296 Gothenburg, Sweden.
| | - Jaeki Min
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - M Brett Waddell
- Molecular Interaction Analysis Shared Resource, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - R Kiplin Guy
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-41296 Gothenburg, Sweden.
| | - Mate Erdelyi
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-41296 Gothenburg, Sweden. and Swedish NMR Centre, Medicinaregatan 5, SE-41390 Gothenburg, Sweden
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24
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Alihodžić S, Bukvić M, Elenkov IJ, Hutinec A, Koštrun S, Pešić D, Saxty G, Tomašković L, Žiher D. Current Trends in Macrocyclic Drug Discovery and beyond -Ro5. PROGRESS IN MEDICINAL CHEMISTRY 2018; 57:113-233. [DOI: 10.1016/bs.pmch.2018.01.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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25
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Diana D, Di Salvo C, Celentano V, De Rosa L, Romanelli A, Fattorusso R, D'Andrea LD. Conformational stabilization of a β-hairpin through a triazole–tryptophan interaction. Org Biomol Chem 2018; 16:787-795. [DOI: 10.1039/c7ob02815f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Triazole and indole rings stabilize a β-hairpin conformation through an aromatic–aromatic interaction.
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Affiliation(s)
| | | | | | - Lucia De Rosa
- Istituto di Biostrutture e Bioimmagini
- CNR
- Napoli
- Italy
| | | | - Roberto Fattorusso
- Dipartimento di Scienze e Tecnologie Ambientali
- Biologiche e Farmaceutiche
- Università della Campania “L. Vanvitelli”
- Caserta
- Italy
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26
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Headen TF, Cullen PL, Patel R, Taylor A, Skipper NT. The structures of liquid pyridine and naphthalene: the effects of heteroatoms and core size on aromatic interactions. Phys Chem Chem Phys 2018; 20:2704-2715. [DOI: 10.1039/c7cp06689a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Spatial and orientational structures of liquid naphthalene and pyridine revealed using neutron scattering combined with empirical potential structure refinement.
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Affiliation(s)
- T. F. Headen
- ISIS Neutron Facility, STFC Rutherford Appleton Laboratory, Harwell Campus
- Didcot
- UK
| | - P. L. Cullen
- University College London, Dept. Physics and Astronomy
- London
- UK
| | - R. Patel
- University College London, Dept. Physics and Astronomy
- London
- UK
| | - A. Taylor
- University College London, Dept. Physics and Astronomy
- London
- UK
| | - N. T. Skipper
- University College London, Dept. Physics and Astronomy
- London
- UK
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27
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Chee SMQ, Wongsantichon J, Siau J, Thean D, Ferrer F, Robinson RC, Lane DP, Brown CJ, Ghadessy FJ. Structure-activity studies of Mdm2/Mdm4-binding stapled peptides comprising non-natural amino acids. PLoS One 2017; 12:e0189379. [PMID: 29228061 PMCID: PMC5724825 DOI: 10.1371/journal.pone.0189379] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 11/24/2017] [Indexed: 11/24/2022] Open
Abstract
As primary p53 antagonists, Mdm2 and the closely related Mdm4 are relevant cancer therapeutic targets. We have previously described a series of cell-permeable stapled peptides that bind to Mdm2 with high affinity, resulting in activation of the p53 tumour suppressor. Within this series, highest affinity was obtained by modification of an obligate tryptophan residue to the non-natural L-6-chlorotryptophan. To understand the structural basis for improved affinity we have solved the crystal structure of this stapled peptide (M011) bound to Mdm2 (residues 6–125) at 1.66 Å resolution. Surprisingly, near identity to the structure of a related peptide (M06) without the 6-chloro modification is observed. Further analysis of linear and stapled peptides comprising 6-Me-tryptophan provides mechanistic insight into dual Mdm2/Mdm4 antagonism and confirms L98 of Mdm4 as a mutable steric gate. The results also highlight a possible role of the flexible hinge region in determining Mdm2/Mdm4 plasticity.
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Affiliation(s)
- Sharon Min Qi Chee
- p53Lab, Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | | | - Jiawei Siau
- p53Lab, Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | - Dawn Thean
- p53Lab, Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | - Fernando Ferrer
- p53Lab, Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | - Robert C. Robinson
- Institute of Molecular and Cellular Biology, A*STAR, Singapore, Singapore
| | - David P. Lane
- p53Lab, Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | - Christopher J. Brown
- p53Lab, Agency for Science Technology and Research (A*STAR), Singapore, Singapore
- * E-mail: (CJB); (FJG)
| | - Farid J. Ghadessy
- p53Lab, Agency for Science Technology and Research (A*STAR), Singapore, Singapore
- * E-mail: (CJB); (FJG)
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28
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Nishihara T, Kitada H, Fujiwara D, Fujii I. Macrocyclization and labeling of helix-loop-helix peptide with intramolecular bis-thioether linkage. Biopolymers 2017; 106:415-21. [PMID: 26917088 DOI: 10.1002/bip.22826] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 01/27/2016] [Accepted: 02/13/2016] [Indexed: 11/07/2022]
Abstract
Conformationally constrained peptides have been developed as an inhibitor for protein-protein interactions (PPIs), and we have de novo designed cyclized helix-loop-helix (cHLH) peptide with a disulfide bond consisting of 40 amino acids to generate molecular-targeting peptides. However, synthesis of long peptides has sometimes resulted in low yield according to the respective amino acid sequences. Here we developed a method for efficient synthesis and labeling for cHLH peptides. First, we synthesized two peptide fragments and connected them by the copper-mediated alkyne and azide cycloaddition (CuAAC) reaction. Cyclization was performed by bis-thioether linkage using 1,3-dibromomethyl-5-propargyloxybenzene, and subsequently, the cHLH peptide was labeled with an azide-labeled probe. Finally, we designed and synthesized a peptide inhibitor for the p53-HDM2 interaction using a structure-guided design and successfully labeled it with a fluorescent probe or a functional peptide, respectively, by click chemistry. This macrocyclization and labeling method for cHLH peptide would facilitate the discovery of de novo bioactive ligands and therapeutic leads. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 415-421, 2016.
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Affiliation(s)
- Toshio Nishihara
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Hidekazu Kitada
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Daisuke Fujiwara
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
| | - Ikuo Fujii
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan
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29
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30
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Fujiwara D, Kitada H, Oguri M, Nishihara T, Michigami M, Shiraishi K, Yuba E, Nakase I, Im H, Cho S, Joung JY, Kodama S, Kono K, Ham S, Fujii I. A Cyclized Helix-Loop-Helix Peptide as a Molecular Scaffold for the Design of Inhibitors of Intracellular Protein-Protein Interactions by Epitope and Arginine Grafting. Angew Chem Int Ed Engl 2016; 55:10612-5. [DOI: 10.1002/anie.201603230] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 06/07/2016] [Indexed: 01/08/2023]
Affiliation(s)
- Daisuke Fujiwara
- Department of Biological Science; Graduate School of Science; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Hidekazu Kitada
- Department of Biological Science; Graduate School of Science; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Masahiro Oguri
- Department of Biological Science; Graduate School of Science; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Toshio Nishihara
- Department of Biological Science; Graduate School of Science; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Masataka Michigami
- Department of Biological Science; Graduate School of Science; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Kazunori Shiraishi
- Department of Biological Science; Graduate School of Science; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Eiji Yuba
- Department of Applied Chemistry; Graduate School of Engineering; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Ikuhiko Nakase
- N2RC; Osaka Prefecture University; 1-2, Gakuen-cho, Naka-ku Osaka 599-8570 Japan
| | - Haeri Im
- Department of Chemistry; Sookmyung Women's University; Hyochangwongil 52, Yongsanku Seoul 140-742 Korea
| | - Sunhee Cho
- Department of Chemistry; Sookmyung Women's University; Hyochangwongil 52, Yongsanku Seoul 140-742 Korea
| | - Jong Young Joung
- Department of Chemistry; Sookmyung Women's University; Hyochangwongil 52, Yongsanku Seoul 140-742 Korea
| | - Seiji Kodama
- Department of Biological Science; Graduate School of Science; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Kenji Kono
- Department of Applied Chemistry; Graduate School of Engineering; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Sihyun Ham
- Department of Chemistry; Sookmyung Women's University; Hyochangwongil 52, Yongsanku Seoul 140-742 Korea
| | - Ikuo Fujii
- Department of Biological Science; Graduate School of Science; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
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31
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Fujiwara D, Kitada H, Oguri M, Nishihara T, Michigami M, Shiraishi K, Yuba E, Nakase I, Im H, Cho S, Joung JY, Kodama S, Kono K, Ham S, Fujii I. A Cyclized Helix-Loop-Helix Peptide as a Molecular Scaffold for the Design of Inhibitors of Intracellular Protein-Protein Interactions by Epitope and Arginine Grafting. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603230] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Daisuke Fujiwara
- Department of Biological Science; Graduate School of Science; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Hidekazu Kitada
- Department of Biological Science; Graduate School of Science; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Masahiro Oguri
- Department of Biological Science; Graduate School of Science; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Toshio Nishihara
- Department of Biological Science; Graduate School of Science; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Masataka Michigami
- Department of Biological Science; Graduate School of Science; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Kazunori Shiraishi
- Department of Biological Science; Graduate School of Science; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Eiji Yuba
- Department of Applied Chemistry; Graduate School of Engineering; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Ikuhiko Nakase
- N2RC; Osaka Prefecture University; 1-2, Gakuen-cho, Naka-ku Osaka 599-8570 Japan
| | - Haeri Im
- Department of Chemistry; Sookmyung Women's University; Hyochangwongil 52, Yongsanku Seoul 140-742 Korea
| | - Sunhee Cho
- Department of Chemistry; Sookmyung Women's University; Hyochangwongil 52, Yongsanku Seoul 140-742 Korea
| | - Jong Young Joung
- Department of Chemistry; Sookmyung Women's University; Hyochangwongil 52, Yongsanku Seoul 140-742 Korea
| | - Seiji Kodama
- Department of Biological Science; Graduate School of Science; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Kenji Kono
- Department of Applied Chemistry; Graduate School of Engineering; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
| | - Sihyun Ham
- Department of Chemistry; Sookmyung Women's University; Hyochangwongil 52, Yongsanku Seoul 140-742 Korea
| | - Ikuo Fujii
- Department of Biological Science; Graduate School of Science; Osaka Prefecture University; 1-1, Gakuen-cho, Naka-ku Osaka 599-8531 Japan
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32
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Litvinov IA, Voronina YK, Galyametdinova IV, Shashin MS, Semenov VE, Reznik VS. Molecular and crystal structure of 1-(2-hydroxyethyl)-1,2-dihydro-3,4,6-trimethyl-2-oxopyrimidinium iodide: the N-alkylation product of xymedone. J STRUCT CHEM+ 2016. [DOI: 10.1134/s0022476616030185] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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33
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Azzarito V, Rowell P, Barnard A, Edwards TA, Macdonald A, Warriner SL, Wilson AJ. Probing Protein Surfaces: QSAR Analysis with Helix Mimetics. Chembiochem 2016; 17:768-73. [PMID: 26690307 PMCID: PMC6591138 DOI: 10.1002/cbic.201500504] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Indexed: 12/17/2022]
Abstract
α-Helix-mediated protein-protein interactions (PPIs) are important targets for small-molecule inhibition; however, generic approaches to inhibitor design are in their infancy and would benefit from QSAR analyses to rationalise the noncovalent basis of molecular recognition by designed ligands. Using a helix mimetic based on an oligoamide scaffold, we have exploited the power of a modular synthesis to access compounds that can readily be used to understand the noncovalent determinants of hDM2 recognition by this series of cell-active p53/hDM2 inhibitors.
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Affiliation(s)
- Valeria Azzarito
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Philip Rowell
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
- School of Molecular and Cellular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Anna Barnard
- Department of Chemistry, Imperial College London, London, London, SW7 2AZ, UK
- Institue of Chemical Biology, Imperial College London, London, SW7 2AZ, UK
| | - Thomas A Edwards
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
- School of Molecular and Cellular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Andrew Macdonald
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
- School of Molecular and Cellular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Stuart L Warriner
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
| | - Andrew J Wilson
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
- Astbury Centre For Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
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34
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Orts J, Wälti MA, Marsh M, Vera L, Gossert AD, Güntert P, Riek R. NMR-Based Determination of the 3D Structure of the Ligand-Protein Interaction Site without Protein Resonance Assignment. J Am Chem Soc 2016; 138:4393-400. [PMID: 26943491 DOI: 10.1021/jacs.5b12391] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular replacement in X-ray crystallography is the prime method for establishing structure-activity relationships of pharmaceutically relevant molecules. Such an approach is not available for NMR. Here, we establish a comparable method, called NMR molecular replacement (NMR(2)). The method requires experimentally measured ligand intramolecular NOEs and ligand-protein intermolecular NOEs as well as a previously known receptor structure or model. Our findings demonstrate that NMR(2) may open a new avenue for the fast and robust determination of the interaction site of ligand-protein complexes at atomic resolution.
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Affiliation(s)
- Julien Orts
- ETH Zürich , Laboratory of Physical Chemistry, HCI F217, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Marielle Aulikki Wälti
- ETH Zürich , Laboratory of Physical Chemistry, HCI F217, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - May Marsh
- Swiss Light Source, Paul Scherrer Institute , CH-5232 Villigen, Switzerland
| | - Laura Vera
- Swiss Light Source, Paul Scherrer Institute , CH-5232 Villigen, Switzerland
| | - Alvar D Gossert
- Novartis Institutes for BioMedical Research, Novartis AG , CH-4002 Basel, Switzerland
| | - Peter Güntert
- ETH Zürich , Laboratory of Physical Chemistry, HCI F217, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland.,Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute of Advanced Studies, Goethe University Frankfurt am Main , Frankfurt am Main 60323, Germany
| | - Roland Riek
- ETH Zürich , Laboratory of Physical Chemistry, HCI F217, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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35
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Peptide-based inhibitors of protein–protein interactions. Bioorg Med Chem Lett 2016; 26:707-713. [DOI: 10.1016/j.bmcl.2015.12.084] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Revised: 12/22/2015] [Accepted: 12/23/2015] [Indexed: 12/22/2022]
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36
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Bandyopadhyay A, Misra R, Gopi HN. Structural features and molecular aggregations of designed triple-stranded β-sheets in single crystals. Chem Commun (Camb) 2016; 52:4938-41. [DOI: 10.1039/c6cc00127k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Design, synthesis, single-crystal conformations and molecular aggregations of hybrid triple-stranded β-sheets, and their structural analogy with protein structures are reported.
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Affiliation(s)
- Anupam Bandyopadhyay
- Department of Chemistry
- Indian Institute of Science Education and Research-Pune
- Pune
- India
| | - Rajkumar Misra
- Department of Chemistry
- Indian Institute of Science Education and Research-Pune
- Pune
- India
| | - Hosahudya N. Gopi
- Department of Chemistry
- Indian Institute of Science Education and Research-Pune
- Pune
- India
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37
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Maltsev OV, Marelli UK, Kapp TG, Di Leva FS, Di Maro S, Nieberler M, Reuning U, Schwaiger M, Novellino E, Marinelli L, Kessler H. Stable Peptides Instead of Stapled Peptides: Highly Potent αvβ6-Selective Integrin Ligands. Angew Chem Int Ed Engl 2015; 55:1535-9. [PMID: 26663660 DOI: 10.1002/anie.201508709] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 10/26/2015] [Indexed: 12/15/2022]
Abstract
The αvβ6 integrin binds the RGD-containing peptide of the foot and mouth disease virus with high selectivity. In this study, the long binding helix of this ligand was downsized to an enzymatically stable cyclic peptide endowed with sub-nanomolar binding affinity toward the αvβ6 receptor and remarkable selectivity against other integrins. Computational studies were performed to disclose the molecular bases underlying the high binding affinity and receptor subtype selectivity of this peptide. Finally, the utility of the ligand for use in biomedical studies was also demonstrated here.
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Affiliation(s)
- Oleg V Maltsev
- Institute for Advanced Study and Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Udaya Kiran Marelli
- Institute for Advanced Study and Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Tobias G Kapp
- Institute for Advanced Study and Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Francesco Saverio Di Leva
- Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131, Napoli, Italy
| | - Salvatore Di Maro
- DiSTABiF, Secondo Università di Napoli, Via Vivaldi 43, 81100, Caserta, Italy
| | - Markus Nieberler
- Department of Oral and Maxillofacial Surgery, University Hospital rechts der Isar, Technische Universität München, Ismaninger Strasse 22, 81675, München, Germany
| | - Ute Reuning
- Klinische Forschergruppe der Frauenklinik, University Hospital rechts der Isar, Technische Universität München, Ismaninger Strasse 22, 81675, München, Germany
| | - Markus Schwaiger
- Department of Nuclear Medicine, University Hospital rechts der Isar, Technische Universität München, Ismaninger Strasse 22, 81675, München, Germany
| | - Ettore Novellino
- Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131, Napoli, Italy
| | - Luciana Marinelli
- Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131, Napoli, Italy
| | - Horst Kessler
- Institute for Advanced Study and Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany.
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38
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Maltsev OV, Marelli UK, Kapp TG, Di Leva FS, Di Maro S, Nieberler M, Reuning U, Schwaiger M, Novellino E, Marinelli L, Kessler H. Stabile Peptide statt “gestapelte Peptide”: hochaffine αvβ6-selektive Integrinliganden. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201508709] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Oleg V. Maltsev
- Institute for Advanced Study and Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Udaya Kiran Marelli
- Institute for Advanced Study and Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Tobias G. Kapp
- Institute for Advanced Study and Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Francesco Saverio Di Leva
- Dipartimento di Farmacia; Università di Napoli Federico II; Via D. Montesano 49 80131 Napoli Italien
| | - Salvatore Di Maro
- DiSTABiF; Secondo Università di Napoli; Via Vivaldi 43 81100 Caserta Italien
| | - Markus Nieberler
- Department of Oral and Maxillofacial Surgery; University Hospital rechts der Isar, Technische Universität München; Ismaninger Straße 22 81675 München Deutschland
| | - Ute Reuning
- Klinische Forschergruppe der Frauenklinik; University Hospital rechts der Isar, Technische Universität München; Ismaninger Straße 22 81675 München Deutschland
| | - Markus Schwaiger
- Department of Nuclear Medicine; University Hospital rechts der Isar, Technische Universität München; Ismaninger Straße 22 81675 München Deutschland
| | - Ettore Novellino
- Dipartimento di Farmacia; Università di Napoli Federico II; Via D. Montesano 49 80131 Napoli Italien
| | - Luciana Marinelli
- Dipartimento di Farmacia; Università di Napoli Federico II; Via D. Montesano 49 80131 Napoli Italien
| | - Horst Kessler
- Institute for Advanced Study and Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
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39
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Computational identification of novel piperidine derivatives as potential HDM2 inhibitors designed by fragment-based QSAR, molecular docking and molecular dynamics simulations. Struct Chem 2015. [DOI: 10.1007/s11224-015-0697-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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40
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Lp...π Interactions involving π-systems with different degrees of electron density delocalization: uracil and isocyanurate. Russ Chem Bull 2015. [DOI: 10.1007/s11172-015-1199-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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41
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Frost JR, Jacob NT, Papa LJ, Owens AE, Fasan R. Ribosomal Synthesis of Macrocyclic Peptides in Vitro and in Vivo Mediated by Genetically Encoded Aminothiol Unnatural Amino Acids. ACS Chem Biol 2015; 10:1805-16. [PMID: 25933125 DOI: 10.1021/acschembio.5b00119] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A versatile method for orchestrating the formation of side chain-to-tail cyclic peptides from ribosomally derived polypeptide precursors is reported. Upon ribosomal incorporation into intein-containing precursor proteins, designer unnatural amino acids bearing side chain 1,3- or 1,2-aminothiol functionalities are able to promote the cyclization of a downstream target peptide sequence via a C-terminal ligation/ring contraction mechanism. Using this approach, peptide macrocycles of variable size and composition could be generated in a pH-triggered manner in vitro or directly in living bacterial cells. This methodology furnishes a new platform for the creation and screening of genetically encoded libraries of conformationally constrained peptides. This strategy was applied to identify and isolate a low-micromolar streptavidin binder (KD = 1.1 μM) from a library of cyclic peptides produced in Escherichia coli, thereby illustrating its potential toward aiding the discovery of functional peptide macrocycles.
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Affiliation(s)
- John R. Frost
- Department of Chemistry, University of Rochester, Hutchinson Hall, Rochester, New York 14627, United States
| | - Nicholas T. Jacob
- Department of Chemistry, University of Rochester, Hutchinson Hall, Rochester, New York 14627, United States
| | - Louis J. Papa
- Department of Chemistry, University of Rochester, Hutchinson Hall, Rochester, New York 14627, United States
| | - Andrew E. Owens
- Department of Chemistry, University of Rochester, Hutchinson Hall, Rochester, New York 14627, United States
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, Hutchinson Hall, Rochester, New York 14627, United States
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Bionda N, Fasan R. Ribosomal Synthesis of Natural-Product-Like Bicyclic Peptides in Escherichia coli. Chembiochem 2015; 16:2011-6. [PMID: 26179106 DOI: 10.1002/cbic.201500179] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Indexed: 12/28/2022]
Abstract
Methods to access natural-product-like macrocyclic peptides can disclose new opportunities for the exploration of this important structural class for chemical biology and drug discovery applications. Here, the scope and mechanism of a novel strategy for directing the biosynthesis of thioether-bridged bicyclic peptides in bacterial cells was investigated. This method entails split intein-catalyzed head-to-tail cyclization of a ribosomally produced precursor peptide, combined with inter-side-chain crosslinking through a genetically encoded cysteine-reactive amino acid. This strategy could be successfully applied to achieve formation of structurally diverse bicyclic peptides with high efficiency and selectivity in Escherichia coli. Insights into the sequence of reactions underlying the peptide bicyclization process were gained from time-course experiments. Finally, the potential utility of this methodology toward the discovery of macrocyclic peptides with enhanced functional properties was demonstrated through the isolation of a bicyclic peptide with sub-micromolar affinity for streptavidin.
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Affiliation(s)
- Nina Bionda
- Department of Chemistry, University of Rochester, RC Box 270216, Rochester, NY, 14627, USA
| | - Rudi Fasan
- Department of Chemistry, University of Rochester, RC Box 270216, Rochester, NY, 14627, 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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Pelay-Gimeno M, Glas A, Koch O, Grossmann TN. Strukturbasierte Entwicklung von Protein-Protein-Interaktionsinhibitoren: Stabilisierung und Nachahmung von Peptidliganden. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201412070] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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45
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Azzarito V, Miles JA, Fisher J, Edwards TA, Warriner SL, Wilson AJ. Stereocontrolled protein surface recognition using chiral oligoamide proteomimetic foldamers. Chem Sci 2015; 6:2434-2443. [PMID: 29308155 PMCID: PMC5646261 DOI: 10.1039/c4sc03559c] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 01/29/2015] [Indexed: 12/26/2022] Open
Abstract
An oligoamide helix mimicking foldamer with well-defined conformation is shown to recognize its target protein hDM2 in a manner that depends upon the composition, spatial projection and stereochemistry of functional groups appended to the scaffold.
The development of foldamers capable of selective molecular recognition of solvent exposed protein surfaces represents an outstanding challenge in supramolecular chemical biology. Here we introduce an oligoamide foldamer with well-defined conformation that bears all the hallmarks of an information rich oligomer. Specifically, the foldamer recognizes its target protein hDM2 leading to inhibition of its protein–protein interaction with p53 in a manner that depends upon the composition, spatial projection and stereochemistry of functional groups appended to the scaffold. Most significantly, selective inhibition of p53/hDM2 can be achieved against four other targets and the selectivity for p53/hDM2 inhibition versus Mcl-1/NOXA-B inhibition is critically dependent upon the stereochemistry of the helix mimetic.
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Affiliation(s)
- Valeria Azzarito
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK . .,Astbury Centre for Structural and Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
| | - Jennifer A Miles
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK . .,Astbury Centre for Structural and Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
| | - Julie Fisher
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK .
| | - Thomas A Edwards
- Astbury Centre for Structural and Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK.,School of Molecular and Cellular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
| | - Stuart L Warriner
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK . .,Astbury Centre for Structural and Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
| | - Andrew J Wilson
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK . .,Astbury Centre for Structural and Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
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Mondal C, Halder AK, Adhikari N, Saha A, Saha KD, Gayen S, Jha T. Comparative validated molecular modeling of p53-HDM2 inhibitors as antiproliferative agents. Eur J Med Chem 2015; 90:860-75. [DOI: 10.1016/j.ejmech.2014.12.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Revised: 12/02/2014] [Accepted: 12/06/2014] [Indexed: 01/28/2023]
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Thansandote P, Harris RM, Dexter HL, Simpson GL, Pal S, Upton RJ, Valko K. Improving the passive permeability of macrocyclic peptides: Balancing permeability with other physicochemical properties. Bioorg Med Chem 2015; 23:322-7. [DOI: 10.1016/j.bmc.2014.11.034] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 11/17/2014] [Accepted: 11/21/2014] [Indexed: 12/29/2022]
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Ermert P, Moehle K, Obrecht D. Macrocyclic Inhibitors of GPCR's, Integrins and Protein–Protein Interactions. MACROCYCLES IN DRUG DISCOVERY 2014. [DOI: 10.1039/9781782623113-00283] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
This chapter summarizes some highlights of macrocyclic drug discovery in the area of GPCRs, integrins, and protein–protein interactions spanning roughly the last 30 years. Several examples demonstrate that incorporation of pharmacophores derived from natural peptide ligands into the context of a constrained macrocycle (“lock of the bioactive conformation”) has proven a powerful approach for the discovery of potent and selective macrocyclic drugs. In addition, it will be shown that macrocycles, due to their semi-rigid nature, can exhibit unique properties that can be beneficially exploited by medicinal chemists. Macrocycles can adapt their conformation during binding to a flexible protein target surface (“induced fit”), and due to their size, can interact with larger protein interfaces (“hot spots”). Also, macrocycles can display favorable ADME properties well beyond the rule of 5 in particular exhibiting favorable cell penetrating properties and oral bioavailability.
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Affiliation(s)
- Philipp Ermert
- Polyphor Ltd Hegenheimermattweg 125 CH-4123 Allschwil Switzerland
| | - Kerstin Moehle
- University of Zurich Winterthurerstrasse 190 CH-8057 Zurich Switzerland
| | - Daniel Obrecht
- Polyphor Ltd Hegenheimermattweg 125 CH-4123 Allschwil Switzerland
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Hill TA, Shepherd NE, Diness F, Fairlie DP. Constraining cyclic peptides to mimic protein structure motifs. Angew Chem Int Ed Engl 2014; 53:13020-41. [PMID: 25287434 DOI: 10.1002/anie.201401058] [Citation(s) in RCA: 306] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 04/02/2013] [Indexed: 12/18/2022]
Abstract
Many proteins exert their biological activities through small exposed surface regions called epitopes that are folded peptides of well-defined three-dimensional structures. Short synthetic peptide sequences corresponding to these bioactive protein surfaces do not form thermodynamically stable protein-like structures in water. However, short peptides can be induced to fold into protein-like bioactive conformations (strands, helices, turns) by cyclization, in conjunction with the use of other molecular constraints, that helps to fine-tune three-dimensional structure. Such constrained cyclic peptides can have protein-like biological activities and potencies, enabling their uses as biological probes and leads to therapeutics, diagnostics and vaccines. This Review highlights examples of cyclic peptides that mimic three-dimensional structures of strand, turn or helical segments of peptides and proteins, and identifies some additional restraints incorporated into natural product cyclic peptides and synthetic macrocyclic peptidomimetics that refine peptide structure and confer biological properties.
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Affiliation(s)
- Timothy A Hill
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072 (Australia)
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Hill TA, Shepherd NE, Diness F, Fairlie DP. Fixierung cyclischer Peptide: Mimetika von Proteinstrukturmotiven. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201401058] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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