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Xu X, Xie M, Luo S, Jia X. Revisiting Protein-Copolymer Binding Mechanisms: Insights beyond the "Lock-and-Key" Model. J Phys Chem Lett 2024; 15:773-781. [PMID: 38227953 DOI: 10.1021/acs.jpclett.3c03200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
The "lock-and-key" model that emphasizes the concept of chemical-structural complementary is the key mechanism for explaining the selectivity between small ligands and a larger adsorbent molecule. In this work, concerning the copolymer chain using only the combination of N-isopropylacrylamide (NIPAm) and hydrophobic N-tert-butylacrylamide (TBAm) monomers and by large-scale atomistic molecular dynamics simulations, our results show that the flexible copolymer chain may exhibit strong binding affinity for the biomarker protein epithelial cell adhesion molecule, in the absence of hydrophobic matching and strong structural complementarity. This surprising binding behavior, which cannot be anticipated by the "lock-and-key" model, can be attributed to the preferential interactions established by the copolymer with the protein's hydrophilic exterior. We observe that increasing the fraction of incorporated TBAm monomers leads to a prevalence of interactions with asparagine and glutamine amino acids due to the emerging hydrogen bonding with both NIPAm and TBAm monomers. Our findings suggest the appearance of highly specific and high-affinity binding sites on the protein created by engineering the copolymer composition, which motivates the applications of copolymers as protein affinity reagents.
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Affiliation(s)
- Xiao Xu
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, 200 Xiao Ling Wei, Nanjing 210094, P. R. China
- State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
| | - Menghan Xie
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, 200 Xiao Ling Wei, Nanjing 210094, P. R. China
| | - Shejia Luo
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, 200 Xiao Ling Wei, Nanjing 210094, P. R. China
| | - Xu Jia
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, 200 Xiao Ling Wei, Nanjing 210094, P. R. China
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Wang X, Ni D, Liu Y, Lu S. Rational Design of Peptide-Based Inhibitors Disrupting Protein-Protein Interactions. Front Chem 2021; 9:682675. [PMID: 34017824 PMCID: PMC8128998 DOI: 10.3389/fchem.2021.682675] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 04/09/2021] [Indexed: 12/12/2022] Open
Abstract
Protein-protein interactions (PPIs) are well-established as a class of promising drug targets for their implications in a wide range of biological processes. However, drug development toward PPIs is inevitably hampered by their flat and wide interfaces, which generally lack suitable pockets for ligand binding, rendering most PPI systems "undruggable." Here, we summarized drug design strategies for developing peptide-based PPI inhibitors. Importantly, several quintessential examples toward well-established PPI targets such as Bcl-2 family members, p53-MDM2, as well as APC-Asef are presented to illustrate the detailed schemes for peptide-based PPI inhibitor development and optimizations. This review supplies a comprehensive overview of recent progresses in drug discovery targeting PPIs through peptides or peptidomimetics, and will shed light on future therapeutic agent development toward the historically "intractable" PPI systems.
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Affiliation(s)
- Xuefei Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Duan Ni
- The Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Yaqin Liu
- Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Shaoyong Lu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
- Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
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Valdés-Tresanco ME, Valdés-Tresanco MS, Valiente PA, Cocho G, Mansilla R, Nieto-Villar JM. Protein surface roughness accounts for binding free energy of Plasmepsin II-ligand complexes. J Mol Recognit 2017; 31. [PMID: 28895236 DOI: 10.1002/jmr.2661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 08/10/2017] [Accepted: 08/11/2017] [Indexed: 11/10/2022]
Abstract
The calculation of absolute binding affinities for protein-inhibitor complexes remains as one of the main challenges in computational structure-based ligand design. The present work explored the calculations of surface fractal dimension (as a measure of surface roughness) and the relationship with experimental binding free energies of Plasmepsin II complexes. Plasmepsin II is an attractive target for novel therapeutic compounds to treat malaria. However, the structural flexibility of this enzyme is a drawback when searching for specific inhibitors. Concerning that, we performed separate explicitly solvated molecular dynamics simulations using the available high-resolution crystal structures of different Plasmepsin II complexes. Molecular dynamics simulations allowed a better approximation to systems dynamics and, therefore, a more reliable estimation of surface roughness. This constitutes a novel approximation in order to obtain more realistic values of fractal dimension, because previous works considered only x-ray structures. Binding site fractal dimension was calculated considering the ensemble of structures generated at different simulation times. A linear relationship between binding site fractal dimension and experimental binding free energies of the complexes was observed within 20 ns. Previous studies of the subject did not uncover this relationship. Regression model, coined FD model, was built to estimate binding free energies from binding site fractal dimension values. Leave-one-out cross-validation showed that our model reproduced accurately the absolute binding free energies for our training set (R2 = 0.76; <|error|> =0.55 kcal/mol; SDerror = 0.19 kcal/mol). The fact that such a simple model may be applied raises some questions that are addressed in the article.
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Affiliation(s)
- Mario E Valdés-Tresanco
- Computational Biology and Biomolecular Dynamics Laboratory, Center for Proteins Studies, Faculty of Biology, University of Havana, Havana, Cuba
| | | | - Pedro A Valiente
- Computational Biology and Biomolecular Dynamics Laboratory, Center for Proteins Studies, Faculty of Biology, University of Havana, Havana, Cuba
| | - Germinal Cocho
- C3 Complex Systems Institute and UNAM Physics Institute, Mexico
| | - Ricardo Mansilla
- Center for Interdisciplinary Investigations of Humanities and Sciences, UNAM, Mexico
| | - J M Nieto-Villar
- Department of Chemical-Physics, Faculty of Chemistry and H. Poincare Group of Complex Systems, Faculty of Physics, University of Havana, Havana, Cuba
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Wang X, Reynolds AR, Elshahawi SI, Shaaban KA, Ponomareva LV, Saunders MA, Elgumati IS, Zhang Y, Copley GC, Hower JC, Sunkara M, Morris AJ, Kharel MK, Van Lanen SG, Prendergast MA, Thorson JS. Terfestatins B and C, New p-Terphenyl Glycosides Produced by Streptomyces sp. RM-5-8. Org Lett 2015; 17:2796-9. [PMID: 25961722 PMCID: PMC4472964 DOI: 10.1021/acs.orglett.5b01203] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Terfestatins B (1) and C (2), new p-terphenyls bearing a novel unsaturated hexuronic acid (4-deoxy-α-L-threo-hex-4-enopyranuronate), a unique β-D-glycosyl ester of 5-isoprenylindole-3-carboxylate (3) and the same rare sugar, and two new hygromycin precursors, were characterized as metabolites of the coal mine fire isolate Streptomyces sp. RM-5-8. EtOH damage neuroprotection assays using rat hippocampal-derived primary cell cultures with 1, 2, 3 and echoside B (a terfestatin C-3'-β-D-glucuronide from Streptomyces sp. RM-5-8) revealed 1 as potently neuroprotective, highlighting a new potential application of the terfestatin scaffold.
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Affiliation(s)
- Xiachang Wang
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Anna R. Reynolds
- Department of Psychology and Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Sherif I. Elshahawi
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Khaled A. Shaaban
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Larissa V. Ponomareva
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Meredith A. Saunders
- Department of Psychology and Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Ibrahim S. Elgumati
- Department of Psychology and Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Yinan Zhang
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Gregory C. Copley
- Center for Applied Energy Research, University of Kentucky, Lexington, Kentucky 40511, United States
| | - James C. Hower
- Center for Applied Energy Research, University of Kentucky, Lexington, Kentucky 40511, United States
| | - Manjula Sunkara
- Division of Cardiovascular Medicine, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Andrew J. Morris
- Division of Cardiovascular Medicine, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Madan K. Kharel
- School of Pharmacy, University of Maryland Eastern Shore, Princess Anne, Maryland 21853, United States
| | - Steven G. Van Lanen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Mark A. Prendergast
- Department of Psychology and Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Jon S. Thorson
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
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Sperandio O, Villoutreix BO, Morelli X, Roche P. [Chemical libraries dedicated to protein-protein interactions]. Med Sci (Paris) 2015; 31:312-9. [PMID: 25855285 DOI: 10.1051/medsci/20153103017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The identification of complete networks of protein-protein interactions (PPI) within a cell has contributed to major breakthroughs in understanding biological pathways, host-pathogen interactions and cancer development. As a consequence, PPI have emerged as a new class of promising therapeutic targets. However, they are still considered as a challenging class of targets for drug discovery programs. Recent successes have allowed the characterization of structural and physicochemical properties of protein-protein interfaces leading to a better understanding of how they can be disrupted with small molecule compounds. In addition, characterization of the profiles of PPI inhibitors has allowed the development of PPI-focused libraries. In this review, we present the current efforts at developing chemical libraries dedicated to these innovative targets.
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Affiliation(s)
- Olivier Sperandio
- Molécules thérapeutiques in silico (MTi), université Paris Diderot, Inserm UMR-S973, 35, rue Hélène Brion, 75205 Paris Cedex 13, France
| | - Bruno O Villoutreix
- Molécules thérapeutiques in silico (MTi), université Paris Diderot, Inserm UMR-S973, 35, rue Hélène Brion, 75205 Paris Cedex 13, France
| | - Xavier Morelli
- Centre de recherche en cancérologie de Marseille (CRCM), CNRS UMR7258 ; Inserm U1068 ; institut Paoli-Calmettes ; université d'Aix-Marseille UM105, 27, boulevard Lei Roure,13009, Marseille, France
| | - Philippe Roche
- Centre de recherche en cancérologie de Marseille (CRCM), CNRS UMR7258 ; Inserm U1068 ; institut Paoli-Calmettes ; université d'Aix-Marseille UM105, 27, boulevard Lei Roure,13009, Marseille, France
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Focused chemical libraries--design and enrichment: an example of protein-protein interaction chemical space. Future Med Chem 2014; 6:1291-307. [PMID: 24773599 DOI: 10.4155/fmc.14.57] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
One of the many obstacles in the development of new drugs lies in the limited number of therapeutic targets and in the quality of screening collections of compounds. In this review, we present general strategies for building target-focused chemical libraries with a particular emphasis on protein-protein interactions (PPIs). We describe the chemical spaces spanned by nine commercially available PPI-focused libraries and compare them to our 2P2I3D academic library, dedicated to orthosteric PPI modulators. We show that although PPI-focused libraries have been designed using different strategies, they share common subspaces. PPI inhibitors are larger and more hydrophobic than standard drugs; however, an effort has been made to improve the drug-likeness of focused chemical libraries dedicated to this challenging class of targets.
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