1
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Kavčič L, Ilc G, Wang B, Vlahoviček-Kahlina K, Jerić I, Plavec J. α-Hydrazino Acid Insertion Governs Peptide Organization in Solution by Local Structure Ordering. ACS OMEGA 2024; 9:22175-22185. [PMID: 38799301 PMCID: PMC11112695 DOI: 10.1021/acsomega.4c00804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/18/2024] [Accepted: 04/29/2024] [Indexed: 05/29/2024]
Abstract
In this work, we have applied the concept of α-hydrazino acid insertion in a peptide sequence as a means of structurally organizing a potential protein-protein interactions (PPI) inhibitor. Hydrazino peptides characterized by the incorporation of an α-hydrazino acid at specific positions introduce an additional nitrogen atom into their backbone. This modification leads to a change in the electrostatic properties of the peptide and induces the restructuring of its hydrogen bonding network, resulting in conformational changes toward more stable structural motifs. Despite the successful use of synthetic hydrazino oligomers in binding to nucleic acids, the structural changes due to the incorporation of α-hydrazino acid into short natural peptides in solution are still poorly understood. Based on NMR data, we report structural models of p53-derived hydrazino peptides with elements of localized peptide structuring in the form of an α-, β-, or γ-turn as a result of hydrazino modification in the peptide backbone. The modifications could potentially lead to the preorganization of a helical secondary peptide structure in a solution that is favorable for binding to a biological receptor. Spectroscopically, we observed that the ensemble averaged rapidly interconverting conformations, including isomerization of the E-Z hydrazide bond. This further increases the adaptability by expanding the conformational space of hydrazine peptides as potential protein-protein interaction antagonists.
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Affiliation(s)
- Luka Kavčič
- Slovenian
NMR Centre, National Institute of Chemistry, Ljubljana 1000, Slovenia
| | - Gregor Ilc
- Slovenian
NMR Centre, National Institute of Chemistry, Ljubljana 1000, Slovenia
- EN-FIST
Centre of Excellence, Ljubljana 1000, Slovenia
| | - Baifan Wang
- Slovenian
NMR Centre, National Institute of Chemistry, Ljubljana 1000, Slovenia
| | | | - Ivanka Jerić
- Division
of Organic Chemistry and Biochemistry, Rudjer
Bošković Institute, Zagreb 10000, Croatia
| | - Janez Plavec
- Slovenian
NMR Centre, National Institute of Chemistry, Ljubljana 1000, Slovenia
- EN-FIST
Centre of Excellence, Ljubljana 1000, Slovenia
- Faculty
of Chemistry and Chemical Technology, University
of Ljubljana, Ljubljana 1000, Slovenia
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2
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Kumari S, Ali A, Kumar M. Nucleotide-induced ClpC oligomerization and its non-preferential association with ClpP isoforms of pathogenic Leptospira. Int J Biol Macromol 2024; 266:131371. [PMID: 38580013 DOI: 10.1016/j.ijbiomac.2024.131371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/15/2024] [Accepted: 04/02/2024] [Indexed: 04/07/2024]
Abstract
Bacterial caseinolytic protease-chaperone complexes participate in the elimination of misfolded and aggregated protein substrates. The spirochete Leptospira interrogans possess a set of Clp-chaperones (ClpX, ClpA, and ClpC), which may associate functionally with two different isoforms of LinClpP (ClpP1 and ClpP2). The L. interrogans ClpC (LinClpC) belongs to class-I chaperone with two active ATPase domains separated by a middle domain. Using the size exclusion chromatography, ANS dye binding, and dynamic light scattering analysis, the LinClpC is suggested to undergo nucleotide-induced oligomerization. LinClpC associates with either pure LinClpP1 or LinClpP2 isoforms non-preferentially and with equal affinity. Regardless, pure LinClpP isoforms cannot constitute an active protease complex with LinClpC. Interestingly, the heterocomplex LinClpP1P2 in association with LinClpC forms a functional proteolytic machinery and degrade β-casein or FITC-casein in an energy-independent manner. Adding either ATP or ATPγS further fosters the LinClpCP1P2 complex protease activity by nurturing the functional oligomerization of LinClpC. The antibiotic, acyldepsipeptides (ADEP1) display a higher activatory role on LinClpP1P2 protease activity than LinClpC. Altogether, this work illustrates an in-depth study of hetero-tetradecamer LinClpP1P2 association with its cognate ATPase and unveils a new insight into the structural reorganization of LinClpP1P2 in the presence of chaperone, LinClpC to gain protease activity.
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Affiliation(s)
- Surbhi Kumari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Arfan Ali
- Department of Veterinary Microbiology, College of Veterinary Science, Assam Agricultural University, Khanapara, Assam 781022, India
| | - Manish Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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3
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Fujimura A, Ishida H, Nozaki T, Terada S, Azumaya Y, Ishiguro T, Kamimura YR, Kujirai T, Kurumizaka H, Kono H, Yamatsugu K, Kawashima SA, Kanai M. Designer Adaptor Proteins for Functional Conversion of Peptides to Small-Molecule Ligands toward In-Cell Catalytic Protein Modification. ACS CENTRAL SCIENCE 2023; 9:2115-2128. [PMID: 38033808 PMCID: PMC10683481 DOI: 10.1021/acscentsci.3c00930] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/19/2023] [Accepted: 10/12/2023] [Indexed: 12/02/2023]
Abstract
Peptides are privileged ligands for diverse biomacromolecules, including proteins; however, their utility is often limited due to low membrane permeability and in-cell instability. Here, we report peptide ligand-inserted eDHFR (PLIED) fusion protein as a universal adaptor for targeting proteins of interest (POI) with cell-permeable and stable synthetic functional small molecules (SFSM). PLIED binds to POI through the peptide moiety, properly orienting its eDHFR moiety, which then recruits trimethoprim (TMP)-conjugated SFSM to POI. Using a lysine-acylating BAHA catalyst as SFSM, we demonstrate that POI (MDM2 and chromatin histone) are post-translationally and synthetically acetylated at specific lysine residues. The residue-selectivity is predictable in an atomic resolution from molecular dynamics simulations of the POI/PLIED/TMP-BAHA (MTX was used as a TMP model) ternary complex. This designer adaptor approach universally enables functional conversion of impermeable peptide ligands to permeable small-molecule ligands, thus expanding the in-cell toolbox of chemical biology.
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Affiliation(s)
- Akiko Fujimura
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, Tokyo 113-0033, Japan
| | - Hisashi Ishida
- Institute
for Quantum Life Science, National Institutes
for Quantum Science and Technology, Chiba 263-8555, Japan
| | - Tamiko Nozaki
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, Tokyo 113-0033, Japan
| | - Shuhei Terada
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, Tokyo 113-0033, Japan
| | - Yuto Azumaya
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, Tokyo 113-0033, Japan
| | - Tadashi Ishiguro
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, Tokyo 113-0033, Japan
| | - Yugo R. Kamimura
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, Tokyo 113-0033, Japan
| | - Tomoya Kujirai
- Institute
for Quantitative Biosciences, The University
of Tokyo, Tokyo 113-0032, Japan
| | - Hitoshi Kurumizaka
- Institute
for Quantitative Biosciences, The University
of Tokyo, Tokyo 113-0032, Japan
| | - Hidetoshi Kono
- Institute
for Quantum Life Science, National Institutes
for Quantum Science and Technology, Chiba 263-8555, Japan
| | - Kenzo Yamatsugu
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, Tokyo 113-0033, Japan
| | - Shigehiro A. Kawashima
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, Tokyo 113-0033, Japan
| | - Motomu Kanai
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, Tokyo 113-0033, Japan
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4
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Eslami SM, Rahman IR, van der Donk WA. Expression of Lanthipeptides in Human Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.19.563208. [PMID: 37961259 PMCID: PMC10634679 DOI: 10.1101/2023.10.19.563208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Cyclic peptides represent a burgeoning area of interest in therapeutic and biotechnological research. In opposition to their linear counterparts, cyclic peptides, such as certain ribosomally synthesized and post-translationally modified peptides (RiPPs), are more conformationally constrained and less susceptible to proteolytic degradation. The lanthipeptide RiPP cytolysin L forms a covalently enforced helical structure that may be used to disrupt helical interactions at protein-protein interfaces. Herein, an expression system is reported to produce lanthipeptides and structurally diverse cytolysin L derivatives in mammalian cells. Successful targeting of lanthipeptides to the nucleus is demonstrated. In vivo expression and targeting of such peptides in mammalian cells may allow for screening of lanthipeptide inhibitors of native protein-protein interactions.
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Affiliation(s)
- Sara M. Eslami
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Imran R. Rahman
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Wilfred A. van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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5
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Ma K, Wang Z, Ju X, Huang J, He R. Rapeseed peptide inhibits HepG2 cell proliferation by regulating the mitochondrial and P53 signaling pathways. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:1474-1483. [PMID: 36168817 DOI: 10.1002/jsfa.12243] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 05/12/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Rapeseed peptide, extracted from rapeseed protein, is known to have a variety of biological activities. In this study, the anti-proliferation effect and molecular mechanism of rapeseed peptide on HepG2 cells were investigated. RESULTS In vitro anticancer experiments showed that the rapeseed peptide NDGNQPL could inhibit HepG2 cell proliferation in a concentration-dependent manner [half maximal inhibitory concentration (IC50 ), 1.56 mmol L-1 ). HepG2 cells were induced by NDGNQPL at a 0.5 mmol L-1 concentration and exhibited a 28.39 ± 0.80% apoptosis rate and a cell cycle arrest in the G0/G1 phase. Meanwhile, rapeseed peptide induced a decrease in mitochondrial membrane potential, an increase in reactive oxygen species (ROS) release, and changes in the nuclear morphology of HepG2 cells, indicating that rapeseed peptide could induce cell apoptosis through the mitochondrial pathway. In addition, rapeseed peptide activated the proliferation-related P53 signaling pathway, in which the expression levels of P53, P21, and cleaved-caspase3 were up-regulated, while the expression levels of murine double minute 2 (MDM2) were down-regulated. In molecular docking simulations, NDGNQPL exhibited a good affinity for the MDM2 molecule, which supported the notion that the rapeseed peptide is able to inhibit MDM2, a negative regulator of P53. CONCLUSION The current results indicate that the rapeseed-derived NDGNQPL peptide has the potential to inhibit the proliferation of HepG2 cells and promote human health. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Keer Ma
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing, China
| | - Zhigao Wang
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing, China
| | - Xingrong Ju
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing, China
| | - Jiankang Huang
- Thyroid and Breast Surgery, Second People's Hospital of Anhui Province, Hefei, China
| | - Rong He
- College of Food Science and Engineering, Nanjing University of Finance and Economics/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing, China
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6
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Xue S, Wang L, Cai J. Sulfono-γ-AApeptides as Protein Helical Domain Mimetics to Manipulate the Angiogenesis. Chembiochem 2022; 23:e202200298. [PMID: 36006398 PMCID: PMC9741949 DOI: 10.1002/cbic.202200298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/23/2022] [Indexed: 02/03/2023]
Abstract
Sulfono-γ-AApeptides recently developed in our group have been proven to be a new class of unnatural foldamer with well-defined helical structure and have been demonstrated to mimic protein helical domains and disrupt biomedically relevant protein-protein interactions (PPIs). Based on our design concept in a recent report, we discovered two similar sulfono-γ-AApeptides V2 and V3 which were designed to mimic the VEGF N-terminal helix α1 known to directly interact with VEGFRs. Interestingly, V2 was shown to possess the pro-angiogenic effect, whereas V3 was proved to be a potent inhibitor for angiogenesis. We speculate that the distinct angiogenesis signaling was due to the selective binding of the two molecules to VEGFR1 and VEGFR2, respectively. Together with their remarkable resistance to proteolytic degradation, relatively small sizes, and amenability to modification with diverse functional groups, V2 and V3 could serve as lead molecules for the development of potential therapeutic agents and molecular probes. These findings highlight sulfono-γ-AApeptides as an alternative paradigm to mimic the α-helical domain to modulate a wide variety of PPIs in the future.
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Affiliation(s)
- Songyi Xue
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL, USA
| | - Lei Wang
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL, USA
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL, USA
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7
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Somsen BA, Craenmehr FWB, Liu WHW, Koops AA, Pennings MAM, Visser EJ, Ottmann C, Cossar PJ, Brunsveld L. Functional mapping of the 14-3-3 hub protein as a guide to design 14-3-3 molecular glues. Chem Sci 2022; 13:13122-13131. [PMID: 36425501 PMCID: PMC9667936 DOI: 10.1039/d2sc04662h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 10/24/2022] [Indexed: 12/03/2022] Open
Abstract
Molecular glues represent an evolution in drug discovery, however, targeted stabilization of protein complexes remains challenging, owing to a paucity of drug design rules. The functional mapping of hotspots has been critical to protein-protein interaction (PPI) inhibitor research, however, the orthogonal approach to stabilize PPIs has not exploited this information. Utilizing the hub protein 14-3-3 as a case study we demonstrate that functional mapping of hotspots provides a triage map for 14-3-3 molecular glue development. Truncation and mutation studies allowed deconvoluting the energetic contributions of sidechain and backbone interactions of a 14-3-3-binding non-natural peptide. Three central 14-3-3 hotspots were identified and their thermodynamic characteristics profiled. In addition to the phospho-binding pocket; (i) Asn226, (ii) Lys122 and (iii) the hydrophobic patch formed by Leu218, Ile219 and Leu222 were critical for protein complex formation. Exploiting this hotspot information allowed a peptide-based molecular glue that elicits high cooperativity (α = 36) and selectively stabilizes the 14-3-3/ChREBP PPI to be uniquely developed.
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Affiliation(s)
- Bente A Somsen
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology P.O. Box 513 Eindhoven 5600 MB The Netherlands
| | - Fenna W B Craenmehr
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology P.O. Box 513 Eindhoven 5600 MB The Netherlands
| | - Wei-Hong W Liu
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology P.O. Box 513 Eindhoven 5600 MB The Netherlands
| | - Auke A Koops
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology P.O. Box 513 Eindhoven 5600 MB The Netherlands
| | - Marloes A M Pennings
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology P.O. Box 513 Eindhoven 5600 MB The Netherlands
| | - Emira J Visser
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology P.O. Box 513 Eindhoven 5600 MB The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology P.O. Box 513 Eindhoven 5600 MB The Netherlands
| | - Peter J Cossar
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology P.O. Box 513 Eindhoven 5600 MB The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology P.O. Box 513 Eindhoven 5600 MB The Netherlands
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8
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Molecular Dynamics and TD‐DFT Study of the Ternary Complexes of Cucurbit[8]uril with Aromatic Amino Acids and Auxiliary Ligands. ChemistrySelect 2022. [DOI: 10.1002/slct.202201988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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9
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Chatterjee C, Singh SK. Peptide and protein chemistry approaches to study the tumor suppressor protein p53. Org Biomol Chem 2022; 20:5500-5509. [PMID: 35786742 PMCID: PMC10112546 DOI: 10.1039/d2ob00902a] [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
The tumor suppressor and master gene regulator protein p53 has been the subject of intense investigation for several decades due to its mutation in about half of all human cancers. However, mechanistic studies of p53 in cells are complicated by its many dynamic binding partners and heterogeneous post-translational modifications. The design of therapeutics that rescue p53 functions in cells requires a mechanistic understanding of its protein-protein interactions in specific protein complexes and identifying changes in p53 activity by diverse post-translational modifications. This review highlights the important roles that peptide and protein chemistry have played in biophysical and biochemical studies aimed at elucidating p53 regulation by several key binding partners. The design of various peptide inhibitors that rescue p53 function in cells and new opportunities in targeting p53-protein interactions are discussed. In addition, the review highlights the importance of a protein semisynthesis approach to comprehend the role of site-specific PTMs in p53 regulation.
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Affiliation(s)
- Champak Chatterjee
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA.
| | - Sumeet K Singh
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA.
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10
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Cheng X, Chen R, Zhou T, Zhang B, Li Z, Gao M, Huang Y, Liu H, Su Z. Leveraging the multivalent p53 peptide-MdmX interaction to guide the improvement of small molecule inhibitors. Nat Commun 2022; 13:1087. [PMID: 35228542 PMCID: PMC8885691 DOI: 10.1038/s41467-022-28721-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 01/27/2022] [Indexed: 12/21/2022] Open
Abstract
Overexpressed Mdm2 and its 7homolog MdmX impair p53 activity in many cancers. Small molecules mimicking a p53 peptide can effectively inhibit Mdm2 but not MdmX. Here, we show a strategy for improving lead compounds for Mdm2 and MdmX inhibition based on the multivalency of the p53 peptide. Crystal structures of MdmX complexed with nutlin-3a, a strong Mdm2 inhibitor but a weak one for MdmX, reveal that nutlin-3a fits into the ligand binding pocket of MdmX mimicking the p53 peptide. However, due to distinct flexibility around the MdmX ligand binding pocket, the structures are missing many important intermolecular interactions that exist in the MdmX/p53 peptide and Mdm2/nultin-3a complexes. By targeting these flexible regions, we identify allosteric and additive fragments that enhance the binding affinity of nutlin-3a for MdmX, leading to potent Mdm2/MdmX inhibitors with anticancer activity. Our work provides a practical approach to drug design for signal transduction therapy. Peptide fragments derived from the interfaces of protein-protein interactions (PPIs) provide useful templates for designing small molecule PPI inhibitors. Here, the authors utilize the multivalency of an MdmX-binding p53 peptide to develop a weak inhibitor of MdmX into potent Mdm2/MdmX inhibitors.
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11
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Santini BL, Zacharias M. Rapid Rational Design of Cyclic Peptides Mimicking Protein-Protein Interfaces. Methods Mol Biol 2022; 2405:231-244. [PMID: 35298817 DOI: 10.1007/978-1-0716-1855-4_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The cPEPmatch approach is a rapid computational methodology for the rational design of cyclic peptides to target desired regions of protein-protein interfaces. The method selects cyclic peptides that structurally match backbone structures of short segments at a protein-protein interface. In a second step, the cyclic peptides act as templates for designed binders by adapting the amino acid side chains to the side chains found in the target complex. A link to access the different tools that comprise the cPEPmatch method and a detailed step-by-step guide is provided. We outline the protocol by following the application to a trypsin protease in complex with the bovine inhibitor protein (BPTI). An extension of our original approach is also presented, where we give a detailed description of the usage of the cPEPmatch methodology focusing on identifying hot regions of protein-protein interfaces prior to the matching. This extension allows one to reduce the amount of evaluated putative cyclic peptides and to specifically design only those that compete with the strongest protein-protein binding regions. It is illustrated by an application to an MHC class I protein complex.
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Affiliation(s)
- Brianda L Santini
- Center for Functional Protein Assemblies, Physics Department T38, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, Garching, Germany
| | - Martin Zacharias
- Center for Functional Protein Assemblies, Physics Department T38, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, Garching, Germany.
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12
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Understanding the Role of Flavonoid Based Small Molecules in Modulating the Oncogenic Protein-Protein Interactions: A Quest for Therapeutic Arsenal. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Bodoor K, El-Barghouthi MI, Assaf KI, Al Hourani BJ, Rawashdeh AMM, Abuhasan OM, Alhamad DF, Abdel-Halim HM. A molecular dynamics study of the complexation of tryptophan, phenylalanine and tyrosine amino acids with cucurbit[7]uril. J INCL PHENOM MACRO 2021. [DOI: 10.1007/s10847-021-01113-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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14
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A Rational Design of α-Helix-Shaped Peptides Employing the Hydrogen-Bond Surrogate Approach: A Modulation Strategy for Ras-RasGRF1 Interaction in Neuropsychiatric Disorders. Pharmaceuticals (Basel) 2021; 14:ph14111099. [PMID: 34832880 PMCID: PMC8623491 DOI: 10.3390/ph14111099] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 01/09/2023] Open
Abstract
In the last two decades, abnormal Ras (rat sarcoma protein)-ERK (extracellular signal-regulated kinase) signalling in the brain has been involved in a variety of neuropsychiatric disorders, including drug addiction, certain forms of intellectual disability, and autism spectrum disorder. Modulation of membrane-receptor-mediated Ras activation has been proposed as a potential target mechanism to attenuate ERK signalling in the brain. Previously, we showed that a cell penetrating peptide, RB3, was able to inhibit downstream signalling by preventing RasGRF1 (Ras guanine nucleotide-releasing factor 1), a neuronal specific GDP/GTP exchange factor, to bind Ras proteins, both in brain slices and in vivo, with an IC50 value in the micromolar range. The aim of this work was to mutate and improve this peptide through computer-aided techniques to increase its inhibitory activity against RasGRF1. The designed peptides were built based on the RB3 peptide structure corresponding to the α-helix of RasGRF1 responsible for Ras binding. For this purpose, the hydrogen-bond surrogate (HBS) approach was exploited to maintain the helical conformation of the designed peptides. Finally, residue scanning, MD simulations, and MM-GBSA calculations were used to identify 18 most promising α-helix-shaped peptides that will be assayed to check their potential activity against Ras-RasGRF1 and prevent downstream molecular events implicated in brain disorders.
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15
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Shi Y, Sang P, Lu J, Higbee P, Chen L, Yang L, Odom T, Daughdrill G, Chen J, Cai J. Rational Design of Right-Handed Heterogeneous Peptidomimetics as Inhibitors of Protein-Protein Interactions. J Med Chem 2020; 63:13187-13196. [PMID: 33140956 DOI: 10.1021/acs.jmedchem.0c01638] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Peptidomimetics have gained great attention for their function as protein-protein interaction (PPI) inhibitors. Herein, we report the design and investigation of a series of right-handed helical heterogeneous 1:1 α/Sulfono-γ-AA peptides as unprecedented inhibitors for p53-MDM2 and p53-MDMX. The most potent helical heterogeneous 1:1 α/Sulfono-γ-AA peptides were shown to bind tightly to MDM2 and MDMX, with Kd of 19.3 and 66.8 nM, respectively. Circular dichroism spectra, 2D-NMR spectroscopy, and the computational simulations suggested that these helical sulfono-γ-AA peptides could mimic the critical side chains of p53 and disrupt p53/MDM2 PPI effectively. It was noted that these 1:1 α/Sulfono-γ-AA peptides were completely resistant to proteolytic degradation, boosting their potential for biomedical applications. Furthermore, effective cellular activity is achieved by the stapled 1:1 α/Sulfono-γ-AA peptides, evidenced by significantly enhanced p53 transcriptional activity and much more induced level of MDM2 and p21. The 1:1 α/Sulfono-γ-AA peptides could be an alternative strategy to antagonize a myriad of PPIs.
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Affiliation(s)
- Yan Shi
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa, Florida 33620, United States
| | - Peng Sang
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa, Florida 33620, United States
| | - Junhao Lu
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Pirada Higbee
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 E. Fowler Ave., Tampa, Florida 33620, United States
| | - Lihong Chen
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Leixiang Yang
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Timothy Odom
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa, Florida 33620, United States
| | - Gary Daughdrill
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 E. Fowler Ave., Tampa, Florida 33620, United States
| | - Jiandong Chen
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa, Florida 33620, United States
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16
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Sang P, Shi Y, Huang B, Xue S, Odom T, Cai J. Sulfono-γ-AApeptides as Helical Mimetics: Crystal Structures and Applications. Acc Chem Res 2020; 53:2425-2442. [PMID: 32940995 DOI: 10.1021/acs.accounts.0c00482] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Foldamers have defined and predictable structures, improved resistance to proteolytic degradation, enhanced chemical diversity, and are versatile in their mimicry of biological molecules, making them promising candidates in biomedical and material applications. However, as natural macromolecules exhibit endless folding structures and functions, the exploration of the applications of foldamers remains crucial. As such, it is imperative to continue to discover unnatural foldameric architectures with new frameworks and molecular scaffolds. To this end, we recently developed a new class of peptidomimetics termed ″γ-AApeptides", oligomers of γ-substituted-N-acylated-N-aminoethyl amino acids, which are inspired by the chiral peptide nucleic acid backbone. To date γ-AApeptides have been shown to be resistant to proteolytic degradation and possess limitless potential to introduce chemically diverse functional groups, demonstrating promise in biomedical and material sciences. However, the structures of γ-AApeptides were initially unknown, rendering their rational design for the mimicry of a protein helical domain impossible in the beginning, which limited their potential development. To our delight, in the past few years, we have obtained a series of crystal structures of helical sulfono-γ-AApeptides, a subclass of γ-AApeptides. The single-crystal X-ray crystallography indicates that sulfono-γ-AApeptides fold into unprecedented and well-defined helices with unique helical parameters. On the basis of the well-established size, shape, and folding conformation, the design of sulfono-γ-AApeptide-based foldamers opens a new avenue for the development of alternative unnatural peptidomimetics for their potential applications in chemistry, biology, medicine, materials science, and so on.In this Account, we will outline our journey on sulfono-γ-AApeptides and their application as helical mimetics. We will first briefly introduce the design and synthetic strategy of sulfono-γ-AApeptides and then describe the crystal structures of helical sulfono-γ-AApeptides, including left-handed homogeneous sulfono-γ-AApeptides, right-handed 1:1 α/sulfono-γ-AA peptide hybrids, and right-handed 2:1 α/sulfono-γ-AA peptide hybrids. After that, we will illustrate the potential of helical sulfono-γ-AApeptides for biological applications such as the disruption of medicinally relevant protein-protein interactions (PPIs) of BCL9-β-catenin and p53-MDM2/MDMX as well as the mimicry of glucagon-like peptide 1 (GLP-1). In addition, we also exemplify their potential application in material science. We expect that this Account will shed light on the structure-based design and function of helical sulfono-γ-AApeptides, which can provide a new and alternative way to explore and generate novel foldamers with distinctive structural and functional properties.
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Affiliation(s)
- Peng Sang
- Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Yan Shi
- Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Bo Huang
- Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Songyi Xue
- Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Timothy Odom
- Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
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17
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Itaconic acid derivatives: structure, function, biosynthesis, and perspectives. Appl Microbiol Biotechnol 2020; 104:9041-9051. [PMID: 32945901 DOI: 10.1007/s00253-020-10908-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 08/21/2020] [Accepted: 09/13/2020] [Indexed: 12/15/2022]
Abstract
Itaconic acid possessing a vinylidene group, which is mainly produced by fungi, is used as a biobased platform chemical and shows distinctive bioactivities. On the other hand, some fungi and lichens produce itaconic acid derivatives possessing itaconic acid skeleton, and the number of the derivatives is currently more than seventy. Based on the molecular structures, they can be categorized into two groups, alkylitaconic acids and α-methylene-γ-butyrolactones. Interestingly, some itaconic acid derivatives show versatile functions such as antimicrobial, anti-inflammatory, antitumor, and plant growth-regulating activities. The vinylidene group of itaconic acid derivatives likely participates in these functions. It is suggested that α-methylene-γ-butyrolactones are biosynthesized from alkylitaconic acids which are first biosynthesized from acyl-CoA and oxaloacetic acid. Some modifying enzymes such as hydroxylase and dehydratase are likely involved in the further modification after biosynthesis of their precursors. This contributes to the diversity of itaconic acid derivatives. In this review, we summarize their structures, functions, and biosynthetic pathways together with a discussion of a strategy for the industrial use. KEY POINTS: • Itaconic acid derivatives can be categorized into alkylitaconic acids and α-methylene-γ-butyrolactones. • The vinylidene group of itaconic acid derivatives likely participates in their versatile function. • It is suggested that α-methylene-γ-butyrolactones are biosynthesized from alkylitaconic acids which are first synthesized from acyl-CoA and oxaloacetic acid.
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18
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Sang P, Shi Y, Higbee P, Wang M, Abdulkadir S, Lu J, Daughdrill G, Chen J, Cai J. Rational Design and Synthesis of Right-Handed d-Sulfono-γ-AApeptide Helical Foldamers as Potent Inhibitors of Protein-Protein Interactions. J Org Chem 2020; 85:10552-10560. [PMID: 32700908 DOI: 10.1021/acs.joc.0c00996] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Novel unprecedented helical foldamers have been effectively designed and synthesized. The homogeneous right-handed d-sulfono-γ-AApeptides represent a new generation of unnatural helical peptidomimetics, which have similar folding conformation to α-peptides, making them an ideal molecular scaffold to design α-helical mimetics. As demonstrated with p53-MDM2 PPI as a model application, the right-handed d-sulfono-γ-AApeptides reveal much-enhanced binding affinity compared to the p53 peptide. The design of d-sulfono-γ-AApeptides may provide a new and alternative strategy to modulate protein-protein interactions.
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Affiliation(s)
- Peng Sang
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa, Florida 33620, United States
| | - Yan Shi
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa, Florida 33620, United States
| | - Pirada Higbee
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, Florida 33620, United States
| | - Minghui Wang
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa, Florida 33620, United States
| | - Sami Abdulkadir
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa, Florida 33620, United States
| | - Junhao Lu
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Gary Daughdrill
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, Florida 33620, United States
| | - Jiandong Chen
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa, Florida 33620, United States
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19
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He W, Yan J, Li Y, Yan S, Wang S, Hou P, Lu W. Resurrecting a p53 peptide activator - An enabling nanoengineering strategy for peptide therapeutics. J Control Release 2020; 325:293-303. [PMID: 32653500 DOI: 10.1016/j.jconrel.2020.06.041] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 06/18/2020] [Accepted: 06/22/2020] [Indexed: 01/10/2023]
Abstract
Many high-affinity peptide antagonists of MDM2 and MDMX have been reported as activators of the tumor suppressor protein p53 with therapeutic potential. Unfortunately, peptide activators of p53 generally suffer poor proteolytic stability and low membrane permeability, posing a major pharmacological challenge to anticancer peptide drug development. We previously obtained several potent dodecameric peptide antagonists of MDM2 and MDMX termed PMIs, one of which, TSFAEYWALLSP, bound to MDM2 and MDMX at respective affinities of 0.49 and 2.4 nM. Here we report the development of gold nanoparticles (Np) as a membrane-traversing delivery vehicle to carry PMI for anticancer therapy. Np-PMI was substantially more active in vitro than Nutlin-3 in killing tumor cells bearing wild-type p53, and effectively inhibited tumor growth in metastasis in a mouse homograft mode of melanoma and a patient-derived xenograft model of colon cancer with a favorable safety profile. This clinically viable drug delivery strategy can be applied not only to peptide activators of p53 for cancer therapy, but also to peptide therapeutics in general aimed at targeting intracellular protein-protein interactions for disease intervention.
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Affiliation(s)
- Wangxiao He
- Institute of Human Virology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Department of Talent Highland, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Jin Yan
- National & Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710014, China.
| | - Yujun Li
- National & Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710014, China; Key Laboratory for Tumor Precision Medicine of Shaanxi Province, Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Siqi Yan
- Department of Talent Highland, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Simeng Wang
- Key Laboratory for Tumor Precision Medicine of Shaanxi Province, Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Peng Hou
- Key Laboratory for Tumor Precision Medicine of Shaanxi Province, Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China.
| | - Wuyuan Lu
- Institute of Human Virology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
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20
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Zhong M, Lynch A, Muellers SN, Jehle S, Luo L, Hall DR, Iwase R, Carolan JP, Egbert M, Wakefield A, Streu K, Harvey CM, Ortet PC, Kozakov D, Vajda S, Allen KN, Whitty A. Interaction Energetics and Druggability of the Protein-Protein Interaction between Kelch-like ECH-Associated Protein 1 (KEAP1) and Nuclear Factor Erythroid 2 Like 2 (Nrf2). Biochemistry 2020; 59:563-581. [PMID: 31851823 PMCID: PMC8177486 DOI: 10.1021/acs.biochem.9b00943] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Development of small molecule inhibitors of protein-protein interactions (PPIs) is hampered by our poor understanding of the druggability of PPI target sites. Here, we describe the combined application of alanine-scanning mutagenesis, fragment screening, and FTMap computational hot spot mapping to evaluate the energetics and druggability of the highly charged PPI interface between Kelch-like ECH-associated protein 1 (KEAP1) and nuclear factor erythroid 2 like 2 (Nrf2), an important drug target. FTMap identifies four binding energy hot spots at the active site. Only two of these are exploited by Nrf2, which alanine scanning of both proteins shows to bind primarily through E79 and E82 interacting with KEAP1 residues S363, R380, R415, R483, and S508. We identify fragment hits and obtain X-ray complex structures for three fragments via crystal soaking using a new crystal form of KEAP1. Combining these results provides a comprehensive and quantitative picture of the origins of binding energy at the interface. Our findings additionally reveal non-native interactions that might be exploited in the design of uncharged synthetic ligands to occupy the same site on KEAP1 that has evolved to bind the highly charged DEETGE binding loop of Nrf2. These include π-stacking with KEAP1 Y525 and interactions at an FTMap-identified hot spot deep in the binding site. Finally, we discuss how the complementary information provided by alanine-scanning mutagenesis, fragment screening, and computational hot spot mapping can be integrated to more comprehensively evaluate PPI druggability.
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Affiliation(s)
| | | | | | | | | | - David R Hall
- Acpharis, Inc. , 160 North Mill Street , Holliston , Massachusetts 01746 , United States
| | | | | | | | | | | | | | | | - Dima Kozakov
- Department of Applied Mathematics , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Sandor Vajda
- Biomolecular Engineering Research Center , Boston University , Boston , Massachusetts 02215 , United States
| | - Karen N Allen
- Biomolecular Engineering Research Center , Boston University , Boston , Massachusetts 02215 , United States
| | - Adrian Whitty
- Biomolecular Engineering Research Center , Boston University , Boston , Massachusetts 02215 , United States
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21
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Sang P, Shi Y, Lu J, Chen L, Yang L, Borcherds W, Abdulkadir S, Li Q, Daughdrill G, Chen J, Cai J. α-Helix-Mimicking Sulfono-γ-AApeptide Inhibitors for p53-MDM2/MDMX Protein-Protein Interactions. J Med Chem 2020; 63:975-986. [PMID: 31971801 PMCID: PMC7025332 DOI: 10.1021/acs.jmedchem.9b00993] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The use of peptidomimetic scaffolds is a promising strategy for the inhibition of protein-protein interactions (PPIs). Herein, we demonstrate that sulfono-γ-AApeptides can be rationally designed to mimic the p53 α-helix and inhibit p53-MDM2 PPIs. The best inhibitor, with Kd and IC50 values of 26 nM and 0.891 μM toward MDM2, respectively, is among the most potent unnatural peptidomimetic inhibitors disrupting the p53-MDM2/MDMX interaction. Using fluorescence polarization assays, circular dichroism, nuclear magnetic resonance spectroscopy, and computational simulations, we demonstrate that sulfono-γ-AApeptides adopt helical structures resembling p53 and competitively inhibit the p53-MDM2 interaction by binding to the hydrophobic cleft of MDM2. Intriguingly, the stapled sulfono-γ-AApeptides showed promising cellular activity by enhancing p53 transcriptional activity and inducing expression of MDM2 and p21. Moreover, sulfono-γ-AApeptides exhibited remarkable resistance to proteolysis, augmenting their biological potential. Our results suggest that sulfono-γ-AApeptides are a new class of unnatural helical foldamers that disrupt PPIs.
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Affiliation(s)
- Peng Sang
- Department of Chemistry , University of South Florida , 4202 E. Fowler Avenue , Tampa , Florida 33620 , United States
| | - Yan Shi
- Department of Chemistry , University of South Florida , 4202 E. Fowler Avenue , Tampa , Florida 33620 , United States
| | - Junhao Lu
- Department of Molecular Oncology , H. Lee Moffitt Cancer Center and Research Institute , 12902 Magnolia Drive , Tampa , Florida 33612 , United States
| | - Lihong Chen
- Department of Molecular Oncology , H. Lee Moffitt Cancer Center and Research Institute , 12902 Magnolia Drive , Tampa , Florida 33612 , United States
| | - Leixiang Yang
- Department of Molecular Oncology , H. Lee Moffitt Cancer Center and Research Institute , 12902 Magnolia Drive , Tampa , Florida 33612 , United States
| | - Wade Borcherds
- Department of Cell Biology, Microbiology and Molecular Biology , University of South Florida , Tampa , Florida 33620 , United States
| | - Sami Abdulkadir
- Department of Chemistry , University of South Florida , 4202 E. Fowler Avenue , Tampa , Florida 33620 , United States
| | - Qi Li
- Department of Medical Oncology , Shuguang Hospital, Shanghai University of Traditional Chinese Medicine , Shanghai 201203 , China
| | - Gary Daughdrill
- Department of Cell Biology, Microbiology and Molecular Biology , University of South Florida , Tampa , Florida 33620 , United States
| | - Jiandong Chen
- Department of Molecular Oncology , H. Lee Moffitt Cancer Center and Research Institute , 12902 Magnolia Drive , Tampa , Florida 33612 , United States
| | - Jianfeng Cai
- Department of Chemistry , University of South Florida , 4202 E. Fowler Avenue , Tampa , Florida 33620 , United States
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22
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Miller JJ, Gaiddon C, Storr T. A balancing act: using small molecules for therapeutic intervention of the p53 pathway in cancer. Chem Soc Rev 2020; 49:6995-7014. [DOI: 10.1039/d0cs00163e] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Small molecules targeting various aspects of the p53 protein pathway have shown significant promise in the treatment of a number of cancer types.
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Affiliation(s)
| | - Christian Gaiddon
- Inserm UMR_S 1113
- Université de Strasbourg
- Molecular Mechanisms of Stress Response and Pathologies
- ITI InnoVec
- Strasbourg
| | - Tim Storr
- Department of Chemistry
- Simon Fraser University
- Burnaby
- Canada
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23
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Fundamental physical and chemical concepts behind “drug-likeness” and “natural product-likeness”. PHYSICAL SCIENCES REVIEWS 2019. [DOI: 10.1515/psr-2018-0101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The discovery of a drug is known to be quite cumbersome, both in terms of the microscopic fundamental research behind it and the industrial scale manufacturing process. A major concern in drug discovery is the acceleration of the process and cost reduction. The fact that clinical trials cannot be accelerated, therefore, emphasizes the need to accelerate the strategies for identifying lead compounds at an early stage. We, herein, focus on the definition of what would be regarded as a “drug-like” molecule and a “lead-like” one. In particular, “drug-likeness” is referred to as resemblance to existing drugs, whereas “lead-likeness” is characterized by the similarity with structural and physicochemical properties of a “lead”compound, i.e. a reference compound or a starting point for further drug development. It is now well known that a huge proportion of the drug discovery is inspired or derived from natural products (NPs), which have larger complexity as well as size when compared with synthetic compounds. Therefore, similar definitions of “drug-likeness” and “lead-likeness” cannot be applied for the NP-likeness. Rather, there is the dire need to define and explain NP-likeness in regard to chemical structure. An attempt has been made here to give an overview of the general concepts associated with NP discovery, and to provide the foundational basis for defining a molecule as a “drug”, a “lead” or a “natural compound.”
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24
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Shi S, Sui K, Liu W, Lei Y, Zhang S, Zhang Q. Revealing binding selectivity of ligands toward murine double minute 2 and murine double minute X based on molecular dynamics simulations and binding free energy calculations. J Biomol Struct Dyn 2019; 38:5081-5094. [PMID: 31755361 DOI: 10.1080/07391102.2019.1695671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
It is well known that the interactions of p53 with murine double minute 2 and murine double minute X, namely MDM2 and MDMX, have been significant targets of efficient anti-cancer drug design. In this study, molecular dynamics (MD) simulations, principal component (PC) analysis and binding free energy calculations are combined to recognize binding selectivity of three ligands to MDM2 and MDMX. The binding free energies were estimated by using molecular mechanics generalized Born surface area (MM-GBSA) method and the obtained results display that the increase in the binding enthalpy of three ligands to MDM2 relative to MDMX mainly drives the binding selectivity of them toward MDM2 and MDMX. The information obtained from PC analysis shows that the associations of ligands exert important impacts on internal dynamics of MDM2 and MDMX. Meanwhile, the calculations of residue-based free energy decomposition not only identify the hot interaction spots of ligands with MDM2 and MDMX, but also show the residues (L54, M53), (Y67, Y66), (V93, V92), (H96, P95), (I99, I98) and (Y100, Y99) in (MDM2, MDMX) are responsible for most contributions to the binding selectivity of three ligands toward MDM2 and MDMX. It is believed that this work can provide useful information for design of highly selective and dual inhibitors targeting MDM2 and MDMX.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shuhua Shi
- School of Science, Shandong Jianzhu University, Jinan, China
| | - Kai Sui
- School of Science, Shandong Jianzhu University, Jinan, China
| | - Weizhe Liu
- School of Science, Shandong Jianzhu University, Jinan, China
| | - Yanzi Lei
- School of Science, Shandong Jianzhu University, Jinan, China
| | - Shaolong Zhang
- College of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Qinggang Zhang
- College of Physics and Electronics, Shandong Normal University, Jinan, China
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25
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Nimmagadda A, Shi Y, Cai J. γ-AApeptides as a New Strategy for Therapeutic Development. Curr Med Chem 2019; 26:2313-2329. [PMID: 29110596 DOI: 10.2174/0929867324666171107095913] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 11/11/2016] [Accepted: 01/16/2017] [Indexed: 12/30/2022]
Abstract
A new class of peptidomimetics termed as "γ-AApeptides" was recently developed by our group. Similar to other peptidomimetics, γ-AApeptides are resistant to proteolytic degradation, and possess limitless potential to introduce chemically diverse functional groups. γ-AApeptides have shown great promise in biomedical applications. In this article, we will review a few examples of γ-AApeptides with biological potential. Certain γ-AApeptides can permeate cell membranes and therefore they can be used as potential drug carrier. γ-AApeptides can also bind to HIV RNA with high specificity and affinity, suggesting their potential application as anti-HIV agents. Moreover, they can mimic host-defense peptides and display potent and broad-spectrum activity towards a range of drug-resistant bacterial pathogens. They are also potential anti-cancer agents. For instance, they have shown great promise in targeted imaging of tumor in mouse model, and they are also capable of disrupting p53/DNA interactions, and thus antagonize STAT3 signaling pathway. Recently, from combinatorial screening, γ-AApeptides are identified to inhibit Aβ peptide aggregation, and thus they can be developed into potential anti- Alzheimer's disease agent.
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Affiliation(s)
- Alekhya Nimmagadda
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620, United States
| | - Yan Shi
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620, United States
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620, United States
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26
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Ganeshpurkar A, Swetha R, Kumar D, Gangaram GP, Singh R, Gutti G, Jana S, Kumar D, Kumar A, Singh SK. Protein-Protein Interactions and Aggregation Inhibitors in Alzheimer's Disease. Curr Top Med Chem 2019; 19:501-533. [PMID: 30836921 DOI: 10.2174/1568026619666190304153353] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 10/31/2018] [Accepted: 11/20/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND Alzheimer's Disease (AD), a multifaceted disorder, involves complex pathophysiology and plethora of protein-protein interactions. Thus such interactions can be exploited to develop anti-AD drugs. OBJECTIVE The interaction of dynamin-related protein 1, cellular prion protein, phosphoprotein phosphatase 2A and Mint 2 with amyloid β, etc., studied recently, may have critical role in progression of the disease. Our objective has been to review such studies and their implications in design and development of drugs against the Alzheimer's disease. METHODS Such studies have been reviewed and critically assessed. RESULTS Review has led to show how such studies are useful to develop anti-AD drugs. CONCLUSION There are several PPIs which are current topics of research including Drp1, Aβ interactions with various targets including PrPC, Fyn kinase, NMDAR and mGluR5 and interaction of Mint2 with PDZ domain, etc., and thus have potential role in neurodegeneration and AD. Finally, the multi-targeted approach in AD may be fruitful and opens a new vista for identification and targeting of PPIs in various cellular pathways to find a cure for the disease.
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Affiliation(s)
- Ankit Ganeshpurkar
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Rayala Swetha
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Devendra Kumar
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Gore P Gangaram
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Ravi Singh
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Gopichand Gutti
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Srabanti Jana
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Dileep Kumar
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Ashok Kumar
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Sushil K Singh
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
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27
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Yuen TY, Brown CJ, Xue Y, Tan YS, Ferrer Gago FJ, Lee XE, Neo JY, Thean D, Kaan HYK, Partridge AW, Verma CS, Lane DP, Johannes CW. Stereoisomerism of stapled peptide inhibitors of the p53-Mdm2 interaction: an assessment of synthetic strategies and activity profiles. Chem Sci 2019; 10:6457-6466. [PMID: 31316744 PMCID: PMC6610352 DOI: 10.1039/c9sc01456j] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 05/19/2019] [Indexed: 12/26/2022] Open
Abstract
Staple composition can influence target binding and bioactivity of peptides. We present strategies to modulate E/Z ratios and access saturated analogues.
All-hydrocarbon, i, i+7 stapled peptide inhibitors of the p53-Mdm2 interaction have emerged as promising new leads for cancer therapy. Typical chemical synthesis via olefin metathesis results in the formation of both E- and Z-isomers, an observation that is rarely disclosed but may be of importance in targeting PPI. In this study, we evaluated the effect of staple geometry on the biological activity of five p53-reactivating peptides. We also present strategies for the modulation of the E/Z ratio and attainment of the hydrogenated adduct through repurposing of the metathesis catalyst.
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Affiliation(s)
- Tsz Ying Yuen
- Institute of Chemical and Engineering Sciences , Agency for Science , Technology and Research , 8 Biomedical Grove, Neuros, #07-01 , Singapore 138665 .
| | - Christopher J Brown
- P53 Laboratory , Agency for Science , Technology and Research , 8A Biomedical Grove, #06-06, Immunos , Singapore 138648
| | - Yuezhen Xue
- P53 Laboratory , Agency for Science , Technology and Research , 8A Biomedical Grove, #06-06, Immunos , Singapore 138648
| | - Yaw Sing Tan
- Bioinformatics Institute , Agency for Science , Technology and Research , 30 Biopolis Street, #07-01, Matrix , Singapore 138671
| | - Fernando J Ferrer Gago
- P53 Laboratory , Agency for Science , Technology and Research , 8A Biomedical Grove, #06-06, Immunos , Singapore 138648
| | - Xue Er Lee
- P53 Laboratory , Agency for Science , Technology and Research , 8A Biomedical Grove, #06-06, Immunos , Singapore 138648
| | - Jin Yong Neo
- Institute of Chemical and Engineering Sciences , Agency for Science , Technology and Research , 8 Biomedical Grove, Neuros, #07-01 , Singapore 138665 .
| | - Dawn Thean
- P53 Laboratory , Agency for Science , Technology and Research , 8A Biomedical Grove, #06-06, Immunos , Singapore 138648
| | - Hung Yi Kristal Kaan
- MSD Translational Medicine Research Centre , 8 Biomedical Grove #04-01, Neuros , Singapore 138665
| | - Anthony W Partridge
- MSD Translational Medicine Research Centre , 8 Biomedical Grove #04-01, Neuros , Singapore 138665
| | - Chandra S Verma
- Bioinformatics Institute , Agency for Science , Technology and Research , 30 Biopolis Street, #07-01, Matrix , Singapore 138671
| | - David P Lane
- P53 Laboratory , Agency for Science , Technology and Research , 8A Biomedical Grove, #06-06, Immunos , Singapore 138648
| | - Charles W Johannes
- Institute of Chemical and Engineering Sciences , Agency for Science , Technology and Research , 8 Biomedical Grove, Neuros, #07-01 , Singapore 138665 .
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Coufalova D, Remnant L, Hernychova L, Muller P, Healy A, Kannan S, Westwood N, Verma CS, Vojtesek B, Hupp TR, Houston DR. An inter-subunit protein-peptide interface that stabilizes the specific activity and oligomerization of the AAA+ chaperone Reptin. J Proteomics 2019; 199:89-101. [PMID: 30862565 DOI: 10.1016/j.jprot.2019.02.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/16/2019] [Accepted: 02/23/2019] [Indexed: 12/26/2022]
Abstract
Reptin is a member of the AAA+ superfamily whose members can exist in equilibrium between monomeric apo forms and ligand bound hexamers. Inter-subunit protein-protein interfaces that stabilize Reptin in its oligomeric state are not well-defined. A self-peptide binding assay identified a protein-peptide interface mapping to an inter-subunit "rim" of the hexamer bridged by Tyrosine-340. A Y340A mutation reduced ADP-dependent oligomer formation using a gel filtration assay, suggesting that Y340 forms a dominant oligomer stabilizing side chain. The monomeric ReptinY340A mutant protein exhibited increased activity to its partner protein AGR2 in an ELISA assay, further suggesting that hexamer formation can preclude certain protein interactions. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) demonstrated that the Y340A mutation attenuated deuterium suppression of Reptin in this motif in the presence of ligand. By contrast, the tyrosine motif of Reptin interacts with a shallower pocket in the hetero-oligomeric structure containing Pontin and HDX-MS revealed no obvious role of the Y340 side chain in stabilizing the Reptin-Pontin oligomer. Molecular dynamic simulations (MDS) rationalized how the Y340A mutation impacts upon a normally stabilizing inter-subunit amino acid contact. MDS also revealed how the D299N mutation can, by contrast, remove oligomer de-stabilizing contacts. These data suggest that the Reptin interactome can be regulated by a ligand dependent equilibrium between monomeric and hexameric forms through a hydrophobic inter-subunit protein-protein interaction motif bridged by Tyrosine-340. SIGNIFICANCE: Discovering dynamic protein-protein interactions is a fundamental aim of research in the life sciences. An emerging view of protein-protein interactions in higher eukaryotes is that they are driven by small linear polypeptide sequences; the linear motif. We report on the use of linear-peptide motif screens to discover a relatively high affinity peptide-protein interaction for the AAA+ and pro-oncogenic protein Reptin. This peptide interaction site was shown to form a 'hot-spot' protein-protein interaction site, and validated to be important for ligand-induced oligomerization of the Reptin protein. These biochemical data provide a foundation to understand how single point mutations in Reptin can impact on its oligomerization and protein-protein interaction landscape.
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Affiliation(s)
- Dominika Coufalova
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Lucy Remnant
- University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, Scotland EH4 2XR, United Kingdom
| | - Lenka Hernychova
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Petr Muller
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Alan Healy
- St Andrews University, St Andrews, Scotland, United Kingdom
| | - Srinivasaraghavan Kannan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix 07-01 138671, Singapore
| | | | - Chandra S Verma
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix 07-01 138671, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore; Department of Biological Sciences, National University of Singapore, 14, Science Drive 4, 117543, Singapore
| | - Borek Vojtesek
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Ted R Hupp
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic; University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, Scotland EH4 2XR, United Kingdom; University of Gdansk, International Centre for Cancer Vaccine Science, ul. Wita Stwosza 63, 80-308 Gdansk, Poland.
| | - Douglas R Houston
- University of Edinburgh, Institute of Quantitative Biology, Biochemistry and Biotechnology, Edinburgh, Scotland EH9 3BF, United Kingdom
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29
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Diharce J, Cueto M, Beltramo M, Aucagne V, Bonnet P. In Silico Peptide Ligation: Iterative Residue Docking and Linking as a New Approach to Predict Protein-Peptide Interactions. Molecules 2019; 24:E1351. [PMID: 30959812 PMCID: PMC6480567 DOI: 10.3390/molecules24071351] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 04/02/2019] [Accepted: 04/03/2019] [Indexed: 11/16/2022] Open
Abstract
Peptide⁻protein interactions are corner-stones of living functions involved in essential mechanisms, such as cell signaling. Given the difficulty of obtaining direct experimental structural biology data, prediction of those interactions is of crucial interest for the rational development of new drugs, notably to fight diseases, such as cancer or Alzheimer's disease. Because of the high flexibility of natural unconstrained linear peptides, prediction of their binding mode in a protein cavity remains challenging. Several theoretical approaches have been developed in the last decade to address this issue. Nevertheless, improvements are needed, such as the conformation prediction of peptide side-chains, which are dependent on peptide length and flexibility. Here, we present a novel in silico method, Iterative Residue Docking and Linking (IRDL), to efficiently predict peptide⁻protein interactions. In order to reduce the conformational space, this innovative method splits peptides into several short segments. Then, it uses the performance of intramolecular covalent docking to rebuild, sequentially, the complete peptide in the active site of its protein target. Once the peptide is constructed, a rescoring step is applied in order to correctly rank all IRDL solutions. Applied on a set of 11 crystallized peptide⁻protein complexes, the IRDL method shows promising results, since it is able to retrieve experimental binding conformations with a Root Mean Square Deviation (RMSD) below 2 Å in the top five ranked solutions. For some complexes, IRDL method outperforms two other docking protocols evaluated in this study. Hence, IRDL is a new tool that could be used in drug design projects to predict peptide⁻protein interactions.
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Affiliation(s)
- Julien Diharce
- Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d'Orléans 7311, Université d'Orléans BP 6759, 45067, Orléans CEDEX 2, France.
| | - Mickaël Cueto
- Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d'Orléans 7311, Université d'Orléans BP 6759, 45067, Orléans CEDEX 2, France.
| | - Massimiliano Beltramo
- UMR Physiologie de la Reproduction et des Comportements (INRA, UMR85; CNRS, UMR7247; Universitéde Tours; IFCE), F-37380 Nouzilly, France.
| | - Vincent Aucagne
- Centre de Biophysique Moléculaire (CNRS UPR4301), Rue Charles Sadron, F-45071 Orléans cedex 2, France.
| | - Pascal Bonnet
- Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d'Orléans 7311, Université d'Orléans BP 6759, 45067, Orléans CEDEX 2, France.
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30
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A simple fluorescent assay for the discovery of protein-protein interaction inhibitors. Anal Biochem 2019; 569:46-52. [PMID: 30707898 DOI: 10.1016/j.ab.2019.01.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 12/14/2022]
Abstract
Due to the therapeutic potential of targeting protein-protein interactions (PPIs) there is a need for easily executed assays to perform high throughput screening (HTS) of inhibitors. We have developed and optimized an innovative and robust fluorescence-based assay for detecting PPI inhibitors, called FluorIA (Fluorescence-based protein-protein Interaction Assay). Targeting the PPI of RAD52 with replication protein A (RPA) was used as an example, and the FluorIA protocol design, optimization and successful application to HTS of large chemical libraries are described. Here enhanced green fluorescent protein (EGFP)-tagged RAD52 detected the PPI using full-length RPA heterotrimer coated, black microtiter plates and loss in fluorescence intensity identified small molecule inhibitors (SMIs) that displaced the EGFP-tagged RAD52. The FluorIA design and protocol can be adapted and applied to detect PPIs for other protein systems. This should push forward efforts to develop targeted therapeutics against protein complexes in pathological processes.
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31
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Karekar VV, Bhoge BA, Saraogi I. An expeditious synthetic route to proteomimetic foldamers. NEW J CHEM 2019. [DOI: 10.1039/c8nj04758h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a method for rapid generation of an α-helix proteomimetic library via the late stage modification of a protected oligobenzamide intermediate.
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Affiliation(s)
- Vaibhav V. Karekar
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal
- India
| | - Bapurao A. Bhoge
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal
- India
| | - Ishu Saraogi
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal
- India
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal
- India
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32
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Huang D, Qi Y, Song J, Zhang JZH. Calculation of hot spots for protein–protein interaction in p53/PMI‐MDM2/MDMX complexes. J Comput Chem 2018; 40:1045-1056. [DOI: 10.1002/jcc.25592] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/04/2018] [Accepted: 08/23/2018] [Indexed: 12/24/2022]
Affiliation(s)
- Dading Huang
- School of Physics and Material Science, Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular EngineeringEast China Normal University Shanghai 200062 China
| | - Yifei Qi
- School of Physics and Material Science, Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular EngineeringEast China Normal University Shanghai 200062 China
- NYU‐ECNU Center for Computational Chemistry at NYU Shanghai Shanghai 200062 China
| | - Jianing Song
- NYU‐ECNU Center for Computational Chemistry at NYU Shanghai Shanghai 200062 China
| | - John Z. H. Zhang
- School of Physics and Material Science, Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular EngineeringEast China Normal University Shanghai 200062 China
- NYU‐ECNU Center for Computational Chemistry at NYU Shanghai Shanghai 200062 China
- Department of ChemistryNew York University New York New York, 10003
- Collaborative Innovation Center of Extreme OpticsShanxi University Taiyuan Shanxi, 030006 China
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33
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Li X, Liu C, Chen S, Hu H, Su J, Zou Y. d-Amino acid mutation of PMI as potent dual peptide inhibitors of p53-MDM2/MDMX interactions. Bioorg Med Chem Lett 2017; 27:4678-4681. [PMID: 28916339 DOI: 10.1016/j.bmcl.2017.09.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 09/04/2017] [Accepted: 09/05/2017] [Indexed: 12/26/2022]
Abstract
According to the previously reported potent dual l-peptide PMI of p53-MDM2/MDMX interactions, a series of d-amino acid mutational PMI analogues, PMI-1-4, with enhanced proteolytic resistence and in vitro tumor cell inhibitory activities were reported, of which Liposome-PMI-1 showed a stronger inhibitory activity against the U87 cell lines than Nutlin-3. This d-amino acid mutation strategy may give a hand for enhancing the potential of peptide drugs.
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Affiliation(s)
- Xiang Li
- Department of Organic Chemistry, College of Pharmacy, Second Military Medical University, Shanghai 200433, People's Republic of China; Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, United States
| | - Chao Liu
- Department of Organic Chemistry, College of Pharmacy, Second Military Medical University, Shanghai 200433, People's Republic of China
| | - Si Chen
- Department of Organic Chemistry, College of Pharmacy, Second Military Medical University, Shanghai 200433, People's Republic of China
| | - Honggang Hu
- Department of Organic Chemistry, College of Pharmacy, Second Military Medical University, Shanghai 200433, People's Republic of China
| | - Jiacan Su
- Changhai Hospital, Second Military Medical University, Shanghai 200433, People's Republic of China.
| | - Yan Zou
- Department of Organic Chemistry, College of Pharmacy, Second Military Medical University, Shanghai 200433, People's Republic of China.
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34
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Kulp JL, Cloudsdale IS, Kulp JL, Guarnieri F. Hot-spot identification on a broad class of proteins and RNA suggest unifying principles of molecular recognition. PLoS One 2017; 12:e0183327. [PMID: 28837642 PMCID: PMC5570288 DOI: 10.1371/journal.pone.0183327] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 08/02/2017] [Indexed: 01/03/2023] Open
Abstract
Chemically diverse fragments tend to collectively bind at localized sites on proteins, which is a cornerstone of fragment-based techniques. A central question is how general are these strategies for predicting a wide variety of molecular interactions such as small molecule-protein, protein-protein and protein-nucleic acid for both experimental and computational methods. To address this issue, we recently proposed three governing principles, (1) accurate prediction of fragment-macromolecule binding free energy, (2) accurate prediction of water-macromolecule binding free energy, and (3) locating sites on a macromolecule that have high affinity for a diversity of fragments and low affinity for water. To test the generality of these concepts we used the computational technique of Simulated Annealing of Chemical Potential to design one small fragment to break the RecA-RecA protein-protein interaction and three fragments that inhibit peptide-deformylase via water-mediated multi-body interactions. Experiments confirm the predictions that 6-hydroxydopamine potently inhibits RecA and that PDF inhibition quantitatively tracks the water-mediated binding predictions. Additionally, the principles correctly predict the essential bound waters in HIV Protease, the surprisingly extensive binding site of elastase, the pinpoint location of electron transfer in dihydrofolate reductase, the HIV TAT-TAR protein-RNA interactions, and the MDM2-MDM4 differential binding to p53. The experimental confirmations of highly non-obvious predictions combined with the precise characterization of a broad range of known phenomena lend strong support to the generality of fragment-based methods for characterizing molecular recognition.
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Affiliation(s)
- John L. Kulp
- Conifer Point Pharmaceuticals, Doylestown, Pennsylvania, United States of America
- Department of Chemistry, Baruch S. Blumberg Institute, Doylestown, Pennsylvania, United States of America
| | - Ian S. Cloudsdale
- Conifer Point Pharmaceuticals, Doylestown, Pennsylvania, United States of America
| | - John L. Kulp
- Conifer Point Pharmaceuticals, Doylestown, Pennsylvania, United States of America
| | - Frank Guarnieri
- PAKA Pulmonary Pharmaceuticals, Acton, Massachusetts, United States of America
- * E-mail:
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35
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Low dose arsenite confers resistance to UV induced apoptosis via p53-MDM2 pathway in ketatinocytes. Oncogenesis 2017; 6:e370. [PMID: 28785074 PMCID: PMC5608918 DOI: 10.1038/oncsis.2017.67] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 06/17/2017] [Accepted: 06/26/2017] [Indexed: 12/17/2022] Open
Abstract
Chronic arsenite and ultraviolet (UV) exposure are associated with skin tumor. To investigate the details by low concentrations of arsenite and UV induced carcinogenesis in skin, hTERT-immortalized human keratinocytes were used as a cellular model with exposure to low concentrations of sodium arsenite and UV. The effect of NaAsO2 on UV treatment-induced apoptosis was measured by flow cytometry and Hoechst staining. We found that the cell apoptosis induced by UV exposure was significantly attenuated after exposure to low-dose arsenite, and knockdown of p53 could block UV-induced apoptosis indicating that this phenomenon depended on p53. Interestingly, the expression of murine double minute 2 (MDM2), including its protein and transcriptional levels, was remarkably high after exposure to low-dose arsenite. Moreover, low-dose arsenite treatment dramatically decreased the MDM2 gene promoter activity, suggesting that this effect has been mediated through transcription. In addition, treatment of PD98059 reversed low-dose arsenite-induced MDM2 expression, and the inhibition of ERK2 expression could significantly block MDM2 expression as a consequence, and p53 expression automatically was increased. To validate the role of p53 in exposure to low-dose arsenite, the expression of p53 was examined by immunohistochemistry in the skin of Sprague−Dawley rats model by chronic arsenite exposure for 6 months and in patients with arsenic keratosis, and the results showed that the expression of p53 was decreased in those samples. Taken together, our results demonstrated that low-dose arsenite-induced resistance to apoptosis through p53 mediated by MDM2 in keratinocytes.
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36
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Lee K, Lanier ML, Kwak JH, Kim H, Hong J. Advances in the synthesis of glycosidic macrolides: clavosolides A-D and cyanolide A. Nat Prod Rep 2017; 33:1393-1424. [PMID: 27714078 DOI: 10.1039/c6np00073h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: 2005 to 2016Clavosolides A-D and cyanolide A are glycosidic macrolides and represent a new family of marine natural products. They possess a number of unusual structural features and have attracted considerable interest from the synthetic community. This review presents a comprehensive survey of all aspects of the clavosolides A-D and cyanolide A. Specific topics include isolation, structure determination, biological activity, and synthetic approaches.
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Affiliation(s)
- Kiyoun Lee
- Department of Chemistry, The Catholic University of Korea, Bucheon 14662, Republic of Korea.
| | - Megan L Lanier
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA.
| | - Jae-Hwan Kwak
- College of Pharmacy, Kyungsung University, Busan 48434, Republic of Korea.
| | - Hyoungsu Kim
- College of Pharmacy and Institute of Pharmaceutical Science and Technology, Ajou University, Suwon 16499, Republic of Korea.
| | - Jiyong Hong
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA.
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37
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Jana T, Ghosh A, Das Mandal S, Banerjee R, Saha S. PPIMpred: a web server for high-throughput screening of small molecules targeting protein-protein interaction. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160501. [PMID: 28484602 PMCID: PMC5414239 DOI: 10.1098/rsos.160501] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 03/20/2017] [Indexed: 05/31/2023]
Abstract
PPIMpred is a web server that allows high-throughput screening of small molecules for targeting specific protein-protein interactions, namely Mdm2/P53, Bcl2/Bak and c-Myc/Max. Three different kernels of support vector machine (SVM), namely, linear, polynomial and radial basis function (RBF), and two other machine learning techniques including Naive Bayes and Random Forest were used to train the models. A fivefold cross-validation technique was used to measure the performance of these classifiers. The RBF kernel of SVM outperformed and/or was comparable with all other methods with accuracy values of 83%, 79% and 90% for Mdm2/P53, Bcl2/Bak and c-Myc/Max, respectively. About 80% of the predicted SVM scores of training/testing datasets from Mdm2/P53 and Bcl2/Bak have significant IC50 values and docking scores. The proposed models achieved an accuracy of 66-90% with blind sets. The three mentioned (Mdm2/P53, Bcl2/Bak and c-Myc/Max) proposed models were screened in a large dataset of 265 242 small chemicals from National Cancer Institute open database. To further realize the robustness of this approach, hits with high and random SVM scores were used for molecular docking in AutoDock Vina wherein the molecules with high and random predicted SVM scores yielded moderately significant docking scores (p-values < 0.1). In addition to the above-mentioned classification scheme, this web server also allows users to get the structural and chemical similarities with known chemical modulators or drug-like molecules based on Tanimoto coefficient similarity search algorithm. PPIMpred is freely available at http://bicresources.jcbose.ac.in/ssaha4/PPIMpred/.
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Affiliation(s)
- Tanmoy Jana
- Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Road, Scheme-VII (M), Kolkata, West Bengal, India
| | - Abhirupa Ghosh
- Department of Bioinformatics, Bose Institute, P 1/12, C.I.T. Road, Scheme-VII (M), Kolkata, West Bengal, India
| | - Sukhen Das Mandal
- Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Road, Scheme-VII (M), Kolkata, West Bengal, India
| | - Raja Banerjee
- Department of Bioinformatics, Bose Institute, P 1/12, C.I.T. Road, Scheme-VII (M), Kolkata, West Bengal, India
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, West Bengal, India
| | - Sudipto Saha
- Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Road, Scheme-VII (M), Kolkata, West Bengal, India
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38
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Arachchige D, Margaret Harris M, Coon Z, Carlsen J, Holub JM. Role of single disulfide linkages in the folding and activity of scyllatoxin-based BH3 domain mimetics. J Pept Sci 2017; 23:367-373. [PMID: 28326661 DOI: 10.1002/psc.2999] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/06/2017] [Accepted: 03/07/2017] [Indexed: 12/18/2022]
Abstract
Anti-apoptotic Bcl-2 proteins are implicated in pathogenic cell survival and have attracted considerable interest as therapeutic targets. We recently developed a class of synthetic peptide based on scyllatoxin (ScTx) designed to mimic the helical BH3 interaction domain of the pro-apoptotic Bcl-2 protein Bax. In this communication, the contribution of single disulfides in the folding and function of ScTx-Bax peptides was investigated. We synthesized five ScTx-Bax variants, each presenting a different combination of native disulfide linkage and evaluated their ability to directly bind Bcl-2 in vitro. It was determined that the position of the disulfide linkage had significant implications on the structure and function of ScTx-Bax peptides. This study underscores the importance of structural dynamics in BH3:Bcl-2 interactions and further validates ScTx-based ligands as potential modulators of anti-apoptotic Bcl-2 function. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Danushka Arachchige
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
| | - M Margaret Harris
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
| | - Zachary Coon
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
| | - Jacob Carlsen
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
| | - Justin M Holub
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA.,Edison Biotechnology Institute, Ohio University, Athens, OH, 45701, USA.,Molecular and Cellular Biology Program, Ohio University, Athens, OH, 45701, USA
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39
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Bolarinwa O, Nimmagadda A, Su M, Cai J. Structure and Function of AApeptides. Biochemistry 2017; 56:445-457. [PMID: 28029249 DOI: 10.1021/acs.biochem.6b01132] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The intrinsic drawbacks encountered in bioactive peptides in chemical biology and biomedical sciences have diverted research efforts to the development of sequence-specific peptidomimetics that are capable of mimicking the structure and function of peptides and proteins. Modifications in the backbone and/or the side chain of peptides have been explored to develop biomimetic molecular probes or drug leads for biologically important targets. To expand the family of oligomeric peptidomimetics to facilitate their further application, we recently developed a new class of peptidomimetics, AApeptides based on a chiral peptide nucleic acid backbone. AApeptides are resistant to proteolytic degradation and amenable to enormous chemical diversification. Moreover, they could mimic the primary structure of peptides and also fold into discrete secondary structure such as helices and turn-like structures. Furthermore, they have started to show promise in applications in material and biomedical sciences. Herein, we highlight the structural design and some function of AApeptides and present our perspective on their future development.
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Affiliation(s)
- Olapeju Bolarinwa
- Department of Chemistry, University of South Florida , 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Alekhya Nimmagadda
- Department of Chemistry, University of South Florida , 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Ma Su
- Department of Chemistry, University of South Florida , 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida , 4202 East Fowler Avenue, Tampa, Florida 33620, United States
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40
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Abstract
Bio-inspired synthetic backbones leading to foldamers can provide effective biopolymer mimics with new and improved properties in a physiological environment, and in turn could serve as useful tools to study biology and lead to practical applications in the areas of diagnostics or therapeutics. Remarkable progress has been accomplished over the past 20 years with the discovery of many potent bioactive foldamers originating from diverse backbones and targeting a whole spectrum of bio(macro)molecules such as membranes, protein surfaces, and nucleic acids. These current achievements, future opportunities, and key challenges that remain are discussed in this article.
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41
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Corbi-Verge C, Garton M, Nim S, Kim PM. Strategies to Develop Inhibitors of Motif-Mediated Protein-Protein Interactions as Drug Leads. Annu Rev Pharmacol Toxicol 2016; 57:39-60. [PMID: 27618737 DOI: 10.1146/annurev-pharmtox-010716-104805] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Protein-protein interactions are fundamental for virtually all functions of the cell. A large fraction of these interactions involve short peptide motifs, and there has been increased interest in targeting them using peptide-based therapeutics. Peptides benefit from being specific, relatively safe, and easy to produce. They are also easy to modify using chemical synthesis and molecular biology techniques. However, significant challenges remain regarding the use of peptides as therapeutic agents. Identification of peptide motifs is difficult, and peptides typically display low cell permeability and sensitivity to enzymatic degradation. In this review, we outline the principal high-throughput methodologies for motif discovery and describe current methods for overcoming pharmacokinetic and bioavailability limitations.
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Affiliation(s)
- Carles Corbi-Verge
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada; , , ,
| | - Michael Garton
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada; , , ,
| | - Satra Nim
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada; , , ,
| | - Philip M Kim
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada; , , , .,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3E1, Canada
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42
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Denèfle T, Boullet H, Herbi L, Newton C, Martinez-Torres AC, Guez A, Pramil E, Quiney C, Pourcelot M, Levasseur MD, Lardé E, Moumné R, Ogi FX, Grondin P, Merle-Beral H, Lequin O, Susin SA, Karoyan P. Thrombospondin-1 Mimetic Agonist Peptides Induce Selective Death in Tumor Cells: Design, Synthesis, and Structure-Activity Relationship Studies. J Med Chem 2016; 59:8412-21. [PMID: 27526615 DOI: 10.1021/acs.jmedchem.6b00781] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Thrombospondin-1 (TSP-1) is a glycoprotein considered as a key actor within the tumor microenvironment. Its binding to CD47, a cell surface receptor, triggers programmed cell death. Previous studies allowed the identification of 4N1K decapeptide derived from the TSP-1/CD47 binding epitope. Here, we demonstrate that this peptide is able to induce selective apoptosis of various cancer cell lines while sparing normal cells. A structure-activity relationship study led to the design of the first serum stable TSP-1 mimetic agonist peptide able to trigger selective programmed cell death (PCD) of at least lung, breast, and colorectal cancer cells. Altogether, these results will be of valuable interest for further investigation in the design of potent CD47 agonist peptides, opening new perspectives for the development of original anticancer therapies.
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Affiliation(s)
- Thomas Denèfle
- Sorbonne Universités, UPMC Université Paris 06, Ecole Normale Supérieure, CNRS, Laboratoire des Biomolécules, 75005 Paris, France.,Département de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Université Paris 06, CNRS, Laboratoire des Biomolécules, 75005 Paris, France.,UPMC Université Paris 06, Laboratoire des BioMolécules, Site GSK, 25-27 Avenue du Québec, 91140 Les Ulis, France
| | - Héloise Boullet
- Sorbonne Universités, UPMC Université Paris 06, Ecole Normale Supérieure, CNRS, Laboratoire des Biomolécules, 75005 Paris, France.,Département de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Université Paris 06, CNRS, Laboratoire des Biomolécules, 75005 Paris, France
| | - Linda Herbi
- Cell Death and Drug Resistance in Lymphoproliferative Disorders Team, Centre de Recherche des Cordeliers, INSERM UMRS, 1138, Paris, France.,Sorbonne Universités, UPMC Université Paris 06, UMRS 1138, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, UMRS 1138, Paris, France
| | - Clara Newton
- Sorbonne Universités, UPMC Université Paris 06, Ecole Normale Supérieure, CNRS, Laboratoire des Biomolécules, 75005 Paris, France.,Département de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Université Paris 06, CNRS, Laboratoire des Biomolécules, 75005 Paris, France.,UPMC Université Paris 06, Laboratoire des BioMolécules, Site GSK, 25-27 Avenue du Québec, 91140 Les Ulis, France
| | - Ana-Carolina Martinez-Torres
- Cell Death and Drug Resistance in Lymphoproliferative Disorders Team, Centre de Recherche des Cordeliers, INSERM UMRS, 1138, Paris, France.,Sorbonne Universités, UPMC Université Paris 06, UMRS 1138, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, UMRS 1138, Paris, France
| | - Alexandre Guez
- Sorbonne Universités, UPMC Université Paris 06, Ecole Normale Supérieure, CNRS, Laboratoire des Biomolécules, 75005 Paris, France.,Département de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Université Paris 06, CNRS, Laboratoire des Biomolécules, 75005 Paris, France
| | - Elodie Pramil
- Sorbonne Universités, UPMC Université Paris 06, Ecole Normale Supérieure, CNRS, Laboratoire des Biomolécules, 75005 Paris, France.,Département de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Université Paris 06, CNRS, Laboratoire des Biomolécules, 75005 Paris, France.,Cell Death and Drug Resistance in Lymphoproliferative Disorders Team, Centre de Recherche des Cordeliers, INSERM UMRS, 1138, Paris, France.,Sorbonne Universités, UPMC Université Paris 06, UMRS 1138, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, UMRS 1138, Paris, France
| | - Claire Quiney
- Cell Death and Drug Resistance in Lymphoproliferative Disorders Team, Centre de Recherche des Cordeliers, INSERM UMRS, 1138, Paris, France.,Sorbonne Universités, UPMC Université Paris 06, UMRS 1138, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, UMRS 1138, Paris, France
| | - Marilyne Pourcelot
- Sorbonne Universités, UPMC Université Paris 06, Ecole Normale Supérieure, CNRS, Laboratoire des Biomolécules, 75005 Paris, France.,Département de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Université Paris 06, CNRS, Laboratoire des Biomolécules, 75005 Paris, France.,UPMC Université Paris 06, Laboratoire des BioMolécules, Site GSK, 25-27 Avenue du Québec, 91140 Les Ulis, France
| | - Mikail D Levasseur
- Sorbonne Universités, UPMC Université Paris 06, Ecole Normale Supérieure, CNRS, Laboratoire des Biomolécules, 75005 Paris, France.,Département de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Université Paris 06, CNRS, Laboratoire des Biomolécules, 75005 Paris, France.,UPMC Université Paris 06, Laboratoire des BioMolécules, Site GSK, 25-27 Avenue du Québec, 91140 Les Ulis, France
| | - Eva Lardé
- Sorbonne Universités, UPMC Université Paris 06, Ecole Normale Supérieure, CNRS, Laboratoire des Biomolécules, 75005 Paris, France.,Département de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Université Paris 06, CNRS, Laboratoire des Biomolécules, 75005 Paris, France.,UPMC Université Paris 06, Laboratoire des BioMolécules, Site GSK, 25-27 Avenue du Québec, 91140 Les Ulis, France
| | - Roba Moumné
- Sorbonne Universités, UPMC Université Paris 06, Ecole Normale Supérieure, CNRS, Laboratoire des Biomolécules, 75005 Paris, France.,Département de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Université Paris 06, CNRS, Laboratoire des Biomolécules, 75005 Paris, France
| | | | | | - Hélène Merle-Beral
- Cell Death and Drug Resistance in Lymphoproliferative Disorders Team, Centre de Recherche des Cordeliers, INSERM UMRS, 1138, Paris, France.,Sorbonne Universités, UPMC Université Paris 06, UMRS 1138, Paris, France.,AP-HP, GH Pitié-Salpêtrière, Service d'Hématologie Biologique, 75013 Paris, France
| | - Olivier Lequin
- Sorbonne Universités, UPMC Université Paris 06, Ecole Normale Supérieure, CNRS, Laboratoire des Biomolécules, 75005 Paris, France.,Département de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Université Paris 06, CNRS, Laboratoire des Biomolécules, 75005 Paris, France
| | - Santos A Susin
- Cell Death and Drug Resistance in Lymphoproliferative Disorders Team, Centre de Recherche des Cordeliers, INSERM UMRS, 1138, Paris, France.,Sorbonne Universités, UPMC Université Paris 06, UMRS 1138, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, UMRS 1138, Paris, France
| | - Philippe Karoyan
- Sorbonne Universités, UPMC Université Paris 06, Ecole Normale Supérieure, CNRS, Laboratoire des Biomolécules, 75005 Paris, France.,Département de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Université Paris 06, CNRS, Laboratoire des Biomolécules, 75005 Paris, France.,UPMC Université Paris 06, Laboratoire des BioMolécules, Site GSK, 25-27 Avenue du Québec, 91140 Les Ulis, France
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43
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Sarkar D, Patra P, Ghosh A, Saha S. Computational Framework for Prediction of Peptide Sequences That May Mediate Multiple Protein Interactions in Cancer-Associated Hub Proteins. PLoS One 2016; 11:e0155911. [PMID: 27218803 PMCID: PMC4878775 DOI: 10.1371/journal.pone.0155911] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 05/08/2016] [Indexed: 01/26/2023] Open
Abstract
A considerable proportion of protein-protein interactions (PPIs) in the cell are estimated to be mediated by very short peptide segments that approximately conform to specific sequence patterns known as linear motifs (LMs), often present in the disordered regions in the eukaryotic proteins. These peptides have been found to interact with low affinity and are able bind to multiple interactors, thus playing an important role in the PPI networks involving date hubs. In this work, PPI data and de novo motif identification based method (MEME) were used to identify such peptides in three cancer-associated hub proteins—MYC, APC and MDM2. The peptides corresponding to the significant LMs identified for each hub protein were aligned, the overlapping regions across these peptides being termed as overlapping linear peptides (OLPs). These OLPs were thus predicted to be responsible for multiple PPIs of the corresponding hub proteins and a scoring system was developed to rank them. We predicted six OLPs in MYC and five OLPs in MDM2 that scored higher than OLP predictions from randomly generated protein sets. Two OLP sequences from the C-terminal of MYC were predicted to bind with FBXW7, component of an E3 ubiquitin-protein ligase complex involved in proteasomal degradation of MYC. Similarly, we identified peptides in the C-terminal of MDM2 interacting with FKBP3, which has a specific role in auto-ubiquitinylation of MDM2. The peptide sequences predicted in MYC and MDM2 look promising for designing orthosteric inhibitors against possible disease-associated PPIs. Since these OLPs can interact with other proteins as well, these inhibitors should be specific to the targeted interactor to prevent undesired side-effects. This computational framework has been designed to predict and rank the peptide regions that may mediate multiple PPIs and can be applied to other disease-associated date hub proteins for prediction of novel therapeutic targets of small molecule PPI modulators.
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Affiliation(s)
| | - Piya Patra
- Maulana Abdul Kalam Azad University of Technology, Kolkata, India
| | - Abhirupa Ghosh
- Maulana Abdul Kalam Azad University of Technology, Kolkata, India
| | - Sudipto Saha
- Bioinformatics Centre, Bose Institute, Kolkata, India
- * E-mail: ;
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44
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Suć J, Tumir LM, Glavaš-Obrovac L, Jukić M, Piantanida I, Jerić I. The impact of α-hydrazino acids embedded in short fluorescent peptides on peptide interactions with DNA and RNA. Org Biomol Chem 2016; 14:4865-74. [PMID: 27161341 DOI: 10.1039/c6ob00425c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of novel hydrazino-based peptidomimetics and analogues comprising N-terminal lysine and C-terminal phenanthridinyl-l-alanine were prepared. The presented results demonstrate the up to now unknown possibility to finely modulate peptide interactions with DNA/RNA by α-hydrazino group insertion and how the different positioning of two α-hydrazino groups in peptides controls binding to various double stranded and single stranded DNA and RNA. All peptidomimetics bind with 1-10 micromolar affinity to ds-DNA/RNA, whereby the binding mode is a combination of electrostatic interactions and hydrophobic interactions within DNA/RNA grooves. Insertion of the α-hydrazino group into the peptide systematically decreased its fluorimetric response to DNA/RNA binding in the order: mono-hydrazino < alternating-hydrazino < sequential-hydrazino group. Binding studies of ss-polynucleotides suggest intercalation of phenanthridine between polynucleotide bases, whereby affinity and fluorimetric response decrease with the number of α-hydrazino groups in the peptide sequence. Particularly interesting was the interaction of two sequential α-hydrazino acids-peptidomimetic with poly rG, characterised by a specific strong increase of CD bands, while all other peptide/ssRNA combinations gave only a CD-band decrease. All mentioned interactions could also be reversibly controlled by adjusting the pH, due to the protonation of the fluorophore.
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Affiliation(s)
- Josipa Suć
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia.
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45
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Shi Y, Teng P, Sang P, She F, Wei L, Cai J. γ-AApeptides: Design, Structure, and Applications. Acc Chem Res 2016; 49:428-41. [PMID: 26900964 DOI: 10.1021/acs.accounts.5b00492] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The development of sequence-specific peptidomimetics has led to a variety of fascinating discoveries in chemical biology. Many peptidomimetics can mimic primary, secondary, and even tertiary structure of peptides and proteins, and because of their unnatural backbones, they also possess significantly enhanced resistance to enzymatic hydrolysis, improved bioavailability, and chemodiversity. It is known that peptide nucleic acids (PNAs) are peptidic sequences developed for the mimicry of nucleic acids; however, their unique backbone as the molecular scaffold of peptidomimetics to mimic structure and function of bioactive peptides has not been investigated systematically. As such, we recently developed a new class of peptidomimetics, "γ-AApeptides", based on the chiral γ-PNA backbone. They are termed γ-AApeptides because they are the oligomers of γ-substituted-N-acylated-N-aminoethyl amino acids. Similar to other classes of peptidomimetics, γ-AApeptides are also resistant to proteolytic degradation and possess the potential to enhance chemodiversity. Moreover, in our scientific journey on the exploration of this class of peptidomimetics, we have discovered some intriguing structures and functions of γ-AApeptides. In this Account, we summarize the current development and application of γ-AApeptides with biological potential. Briefly, both linear and cyclic (either through head-to-tail or head-to-side-chain cyclization) γ-AApeptides with diverse functional groups can be synthesized easily on the solid phase using the synthetic protocol we developed. γ-AApeptides could mimic the primary structure of peptides, as they project the same number of side chains as peptides of the same lengths. For instance, they could mimic the Tat peptide to permeate cell membranes and bind to HIV RNA with high specificity and affinity. Certain γ-AApeptides show similar activity to the RGD peptide and target integrin specifically on the cell surface. γ-AApeptides with function akin to fMLF peptides are also identified. More importantly, we found that γ-AApeptides can fold into discrete secondary structures, such as helical and β-turn-like structures. Therefore, they could be rationally designed for a range of biological applications. For instance, γ-AApeptides can mimic host-defense peptides and display potent and broad-spectrum activity toward a panel of drug-resistant bacterial pathogens. Meanwhile, because of their stability against proteolysis and their chemodiversity, γ-AApeptides are also amenable for combinatorial screening. We demonstrate that, through combinatorial selection, certain γ-AApeptides are identified to inhibit Aβ40 peptide aggregation, suggesting their potential use as a molecular probe to intervene in Alzheimer's disease. In addition, a few γ-AApeptides identified from the γ-AApeptide library have been shown to bind to the DNA-binding domain of STAT3 and antagonize STAT3/DNA interactions. Our studies suggest that, with further studies and exploration on both structures and functions, γ-AApeptides may emerge to be a new class of peptidomimetics that play an important role in chemical biology and biomedical sciences.
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Affiliation(s)
- Yan Shi
- Department of Chemistry, University of South Florida, 4202
East Fowler Ave, Tampa, Florida 33620, United States
| | - Peng Teng
- Department of Chemistry, University of South Florida, 4202
East Fowler Ave, Tampa, Florida 33620, United States
| | - Peng Sang
- Department of Chemistry, University of South Florida, 4202
East Fowler Ave, Tampa, Florida 33620, United States
| | - Fengyu She
- Department of Chemistry, University of South Florida, 4202
East Fowler Ave, Tampa, Florida 33620, United States
| | - Lulu Wei
- Department of Chemistry, University of South Florida, 4202
East Fowler Ave, Tampa, Florida 33620, United States
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, 4202
East Fowler Ave, Tampa, Florida 33620, United States
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46
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Corbi-Verge C, Kim PM. Motif mediated protein-protein interactions as drug targets. Cell Commun Signal 2016; 14:8. [PMID: 26936767 PMCID: PMC4776425 DOI: 10.1186/s12964-016-0131-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 02/25/2016] [Indexed: 12/17/2022] Open
Abstract
Protein-protein interactions (PPI) are involved in virtually every cellular process and thus represent an attractive target for therapeutic interventions. A significant number of protein interactions are frequently formed between globular domains and short linear peptide motifs (DMI). Targeting these DMIs has proven challenging and classical approaches to inhibiting such interactions with small molecules have had limited success. However, recent new approaches have led to the discovery of potent inhibitors, some of them, such as Obatoclax, ABT-199, AEG-40826 and SAH-p53-8 are likely to become approved drugs. These novel inhibitors belong to a wide range of different molecule classes, ranging from small molecules to peptidomimetics and biologicals. This article reviews the main reasons for limited success in targeting PPIs, discusses how successful approaches overcome these obstacles to discovery promising inhibitors for human protein double minute 2 (HDM2), B-cell lymphoma 2 (Bcl-2), X-linked inhibitor of apoptosis protein (XIAP), and provides a summary of the promising approaches currently in development that indicate the future potential of PPI inhibitors in drug discovery.
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Affiliation(s)
- Carles Corbi-Verge
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada.
| | - Philip M Kim
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 3E1, Canada.
- Department of Computer Science, University of Toronto, Toronto, ON, M5S 3E1, Canada.
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47
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Shi S, Zhang S, Zhang Q. Probing Difference in Binding Modes of Inhibitors to MDMX by Molecular Dynamics Simulations and Different Free Energy Methods. PLoS One 2015; 10:e0141409. [PMID: 26513747 PMCID: PMC4625964 DOI: 10.1371/journal.pone.0141409] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 10/08/2015] [Indexed: 01/20/2023] Open
Abstract
The p53-MDMX interaction has attracted extensive attention of anti-cancer drug development in recent years. This current work adopted molecular dynamics (MD) simulations and cross-correlation analysis to investigate conformation changes of MDMX caused by inhibitor bindings. The obtained information indicates that the binding cleft of MDMX undergoes a large conformational change and the dynamic behavior of residues obviously change by the presence of different structural inhibitors. Two different methods of binding free energy predictions were employed to carry out a comparable insight into binding mechanisms of four inhibitors PMI, pDI, WK23 and WW8 to MDMX. The data show that the main factor controlling the inhibitor bindings to MDMX arises from van der Waals interactions. The binding free energies were further divided into contribution of each residue and the derived information gives a conclusion that the hydrophobic interactions, such as CH-CH, CH-π and π-π interactions, are responsible for the inhibitor associations with MDMX.
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Affiliation(s)
- Shuhua Shi
- School of Science, Shandong Jianzhu University, Jinan, China
- * E-mail: ;
| | - Shaolong Zhang
- College of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Qinggang Zhang
- College of Physics and Electronics, Shandong Normal University, Jinan, China
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48
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Abstract
A powerful early approach to evaluating the druggability of proteins involved determining the hit rate in NMR-based screening of a library of small compounds. Here, we show that a computational analog of this method, based on mapping proteins using small molecules as probes, can reliably reproduce druggability results from NMR-based screening and can provide a more meaningful assessment in cases where the two approaches disagree. We apply the method to a large set of proteins. The results show that, because the method is based on the biophysics of binding rather than on empirical parametrization, meaningful information can be gained about classes of proteins and classes of compounds beyond those resembling validated targets and conventionally druglike ligands. In particular, the method identifies targets that, while not druggable by druglike compounds, may become druggable using compound classes such as macrocycles or other large molecules beyond the rule-of-five limit.
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Affiliation(s)
- Dima Kozakov
- Department of Applied Mathematics & Statistics, Stony Brook University , Stony Brook, New York 11794, United States
| | - David R Hall
- Acpharis Inc. , Holliston, Massachusetts 01746, United States
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49
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Surfing the Protein-Protein Interaction Surface Using Docking Methods: Application to the Design of PPI Inhibitors. Molecules 2015; 20:11569-603. [PMID: 26111183 PMCID: PMC6272567 DOI: 10.3390/molecules200611569] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 06/02/2015] [Accepted: 06/15/2015] [Indexed: 02/06/2023] Open
Abstract
Blocking protein-protein interactions (PPI) using small molecules or peptides modulates biochemical pathways and has therapeutic significance. PPI inhibition for designing drug-like molecules is a new area that has been explored extensively during the last decade. Considering the number of available PPI inhibitor databases and the limited number of 3D structures available for proteins, docking and scoring methods play a major role in designing PPI inhibitors as well as stabilizers. Docking methods are used in the design of PPI inhibitors at several stages of finding a lead compound, including modeling the protein complex, screening for hot spots on the protein-protein interaction interface and screening small molecules or peptides that bind to the PPI interface. There are three major challenges to the use of docking on the relatively flat surfaces of PPI. In this review we will provide some examples of the use of docking in PPI inhibitor design as well as its limitations. The combination of experimental and docking methods with improved scoring function has thus far resulted in few success stories of PPI inhibitors for therapeutic purposes. Docking algorithms used for PPI are in the early stages, however, and as more data are available docking will become a highly promising area in the design of PPI inhibitors or stabilizers.
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50
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Interactions of HIV-1 proteins as targets for developing anti-HIV-1 peptides. Future Med Chem 2015; 7:1055-77. [DOI: 10.4155/fmc.15.46] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Protein–protein interactions (PPI) are essential in every step of the HIV replication cycle. Mapping the interactions between viral and host proteins is a fundamental target for the design and development of new therapeutics. In this review, we focus on rational development of anti-HIV-1 peptides based on mapping viral–host and viral–viral protein interactions all across the HIV-1 replication cycle. We also discuss the mechanism of action, specificity and stability of these peptides, which are designed to inhibit PPI. Some of these peptides are excellent tools to study the mechanisms of PPI in HIV-1 replication cycle and for the development of anti-HIV-1 drug leads that modulate PPI.
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