1
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Kim DH, Kang SM. Stapled Peptides: An Innovative and Ultimate Future Drug Offering a Highly Powerful and Potent Therapeutic Alternative. Biomimetics (Basel) 2024; 9:537. [PMID: 39329559 PMCID: PMC11430733 DOI: 10.3390/biomimetics9090537] [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: 07/23/2024] [Revised: 08/28/2024] [Accepted: 08/30/2024] [Indexed: 09/28/2024] Open
Abstract
Peptide-based therapeutics have traditionally faced challenges, including instability in the bloodstream and limited cell membrane permeability. However, recent advancements in α-helix stapled peptide modification techniques have rekindled interest in their efficacy. Notably, these developments ensure a highly effective method for improving peptide stability and enhancing cell membrane penetration. Particularly in the realm of antimicrobial peptides (AMPs), the application of stapled peptide techniques has significantly increased peptide stability and has been successfully applied to many peptides. Furthermore, constraining the secondary structure of peptides has also been proven to enhance their biological activity. In this review, the entire process through which hydrocarbon-stapled antimicrobial peptides attain improved drug-like properties is examined. First, the essential secondary structural elements required for their activity as drugs are validated, specific residues are identified using alanine scanning, and stapling techniques are strategically incorporated at precise locations. Additionally, the mechanisms by which these structure-based stapled peptides function as AMPs are explored, providing a comprehensive and engaging discussion.
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Affiliation(s)
- Do-Hee Kim
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Sung-Min Kang
- College of Pharmacy, Duksung Women's University, Seoul 01369, Republic of Korea
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2
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Lewis K, Lee RE, Brötz-Oesterhelt H, Hiller S, Rodnina MV, Schneider T, Weingarth M, Wohlgemuth I. Sophisticated natural products as antibiotics. Nature 2024; 632:39-49. [PMID: 39085542 DOI: 10.1038/s41586-024-07530-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/07/2024] [Indexed: 08/02/2024]
Abstract
In this Review, we explore natural product antibiotics that do more than simply inhibit an active site of an essential enzyme. We review these compounds to provide inspiration for the design of much-needed new antibacterial agents, and examine the complex mechanisms that have evolved to effectively target bacteria, including covalent binders, inhibitors of resistance, compounds that utilize self-promoted entry, those that evade resistance, prodrugs, target corrupters, inhibitors of 'undruggable' targets, compounds that form supramolecular complexes, and selective membrane-acting agents. These are exemplified by β-lactams that bind covalently to inhibit transpeptidases and β-lactamases, siderophore chimeras that hijack import mechanisms to smuggle antibiotics into the cell, compounds that are activated by bacterial enzymes to produce reactive molecules, and antibiotics such as aminoglycosides that corrupt, rather than merely inhibit, their targets. Some of these mechanisms are highly sophisticated, such as the preformed β-strands of darobactins that target the undruggable β-barrel chaperone BamA, or teixobactin, which binds to a precursor of peptidoglycan and then forms a supramolecular structure that damages the membrane, impeding the emergence of resistance. Many of the compounds exhibit more than one notable feature, such as resistance evasion and target corruption. Understanding the surprising complexity of the best antimicrobial compounds provides a roadmap for developing novel compounds to address the antimicrobial resistance crisis by mining for new natural products and inspiring us to design similarly sophisticated antibiotics.
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Affiliation(s)
- Kim Lewis
- Antimicrobial Discovery Center, Northeastern University, Boston, MA, USA.
| | - Richard E Lee
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, Memphis, TN, USA.
| | - Heike Brötz-Oesterhelt
- Interfaculty Institute of Microbiology and Infection Medicine, Tubingen, Germany
- Controlling Microbes to Fight Infection-Cluster of Excellence, Tubingen, Germany
| | | | - Marina V Rodnina
- Max Planck Institute for Multidisciplinary Sciences, Goettingen, Germany
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology, University of Bonn, University Hospital Bonn, Bonn, Germany
- German Center for Infection Research (DZIF), Partner Site Cologne-Bonn, Bonn, Germany
| | - Markus Weingarth
- Chemistry Department, Utrecht University, Utrecht, the Netherlands
| | - Ingo Wohlgemuth
- Max Planck Institute for Multidisciplinary Sciences, Goettingen, Germany
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3
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Yuan W, Zhang R, Lyu H, Xiao S, Guo D, Zhang Q, Ali DW, Michalak M, Chen XZ, Zhou C, Tang J. Dysregulation of tRNA methylation in cancer: Mechanisms and targeting therapeutic strategies. Cell Death Discov 2024; 10:327. [PMID: 39019857 PMCID: PMC11254935 DOI: 10.1038/s41420-024-02097-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 07/04/2024] [Accepted: 07/09/2024] [Indexed: 07/19/2024] Open
Abstract
tRNA is the RNA type that undergoes the most modifications among known RNA, and in recent years, tRNA methylation has emerged as a crucial process in regulating gene translation. Dysregulation of tRNA abundance occurs in cancer cells, along with increased expression and activity of tRNA methyltransferases to raise the level of tRNA modification and stability. This leads to hijacking of translation and synthesis of multiple proteins associated with tumor proliferation, metastasis, invasion, autophagy, chemotherapy resistance, and metabolic reprogramming. In this review, we provide an overview of current research on tRNA methylation in cancer to clarify its involvement in human malignancies and establish a theoretical framework for future therapeutic interventions targeting tRNA methylation processes.
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Affiliation(s)
- Wenbin Yuan
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China
| | - Rui Zhang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China
| | - Hao Lyu
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China
| | - Shuai Xiao
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China
| | - Dong Guo
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China
| | - Qi Zhang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China
| | - Declan William Ali
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Marek Michalak
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Xing-Zhen Chen
- Membrane Protein Disease Research Group, Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Cefan Zhou
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China.
| | - Jingfeng Tang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China.
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4
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Lima MP, Hornsby BD, Lim CS, Cheatham TE. Molecular Modeling of Single- and Double-Hydrocarbon-Stapled Coiled-Coil Inhibitors against Bcr-Abl: Toward a Treatment Strategy for CML. J Phys Chem B 2024; 128:6476-6491. [PMID: 38951498 PMCID: PMC11247501 DOI: 10.1021/acs.jpcb.4c02699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 07/03/2024]
Abstract
The chimeric oncoprotein Bcr-Abl is the causative agent of virtually all chronic myeloid leukemias and a subset of acute lymphoblastic leukemias. As a result of the so-called Philadelphia chromosome translocation t(9;22), Bcr-Abl manifests as a constitutively active tyrosine kinase, which promotes leukemogenesis by activation of cell cycle signaling pathways. Constitutive and oncogenic activation is mediated by an N-terminal coiled-coil oligomerization domain in Bcr (Bcr-CC), presenting a therapeutic target for inhibition of Bcr-Abl activity toward the treatment of Bcr-Abl+ leukemias. Previously, we demonstrated that a rationally designed Bcr-CC mutant, CCmut3, exerts a dominant negative effect upon Bcr-Abl activity by preferential oligomerization with Bcr-CC. Moreover, we have shown that conjugation to a leukemia-specific cell-penetrating peptide (CPP-CCmut3) improves intracellular delivery and activity. However, our full-length CPP-CCmut3 construct (81 aa) is encumbered by an intrinsically high degree of conformational variability and susceptibility to proteolytic degradation relative to traditional small-molecule therapeutics. Here, we iterate a new generation of CCmut3 inhibitors against Bcr-CC-mediated Bcr-Abl assembly designed to address these constraints through incorporation of all-hydrocarbon staples spanning i and i + 7 positions in α-helix 2 (CPP-CCmut3-st). We utilize computational modeling and biomolecular simulation to evaluate single- and double-stapled CCmut3 candidates in silico for dynamics and binding energetics. We further model a truncated system characterized by the deletion of α-helix 1 and the flexible loop linker, which are known to impart high conformational variability. To study the impact of the N-terminal cyclic CPP toward model stability and inhibitor activity, we also model the full-length and truncated systems devoid of the CPP, with a cyclized CPP, and with an open-configuration CPP, for a total of six systems that comprise our library. From this library, we present lead-stapled peptide candidates to be synthesized and evaluated experimentally as our next iteration of inhibitors against Bcr-Abl.
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MESH Headings
- Fusion Proteins, bcr-abl/antagonists & inhibitors
- Fusion Proteins, bcr-abl/metabolism
- Fusion Proteins, bcr-abl/chemistry
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Humans
- Protein Kinase Inhibitors/chemistry
- Protein Kinase Inhibitors/pharmacology
- Protein Kinase Inhibitors/metabolism
- Models, Molecular
- Molecular Dynamics Simulation
- Antineoplastic Agents/chemistry
- Antineoplastic Agents/pharmacology
- Cell-Penetrating Peptides/chemistry
- Cell-Penetrating Peptides/pharmacology
- Cell-Penetrating Peptides/metabolism
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Affiliation(s)
- Maria
Carolina P. Lima
- Department
of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Braxten D. Hornsby
- Department
of Molecular Pharmaceutics, University of
Utah, Salt Lake City, Utah 84112, United States
| | - Carol S. Lim
- Department
of Molecular Pharmaceutics, University of
Utah, Salt Lake City, Utah 84112, United States
| | - Thomas E. Cheatham
- Department
of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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5
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Li Y, Wu M, Fu Y, Xue J, Yuan F, Qu T, Rissanou AN, Wang Y, Li X, Hu H. Therapeutic stapled peptides: Efficacy and molecular targets. Pharmacol Res 2024; 203:107137. [PMID: 38522761 DOI: 10.1016/j.phrs.2024.107137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 03/26/2024]
Abstract
Peptide stapling, by employing a stable, preformed alpha-helical conformation, results in the production of peptides with improved membrane permeability and enhanced proteolytic stability, compared to the original peptides, and provides an effective solution to accelerate the rapid development of peptide drugs. Various reviews present peptide stapling chemistries, anchoring residues and one- or two-component cyclization, however, therapeutic stapled peptides have not been systematically summarized, especially focusing on various disease-related targets. This review highlights the latest advances in therapeutic peptide drug development facilitated by the application of stapling technology, including different stapling techniques, synthetic accessibility, applicability to biological targets, potential for solving biological problems, as well as the current status of development. Stapled peptides as therapeutic drug candidates have been classified and analysed mainly by receptor- and ligand-based stapled peptide design against various diseases, including cancer, infectious diseases, inflammation, and diabetes. This review is expected to provide a comprehensive reference for the rational design of stapled peptides for different diseases and targets to facilitate the development of therapeutic peptides with enhanced pharmacokinetic and biological properties.
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Affiliation(s)
- Yulei Li
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China.
| | - Minghao Wu
- School of Medicine, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Yinxue Fu
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China
| | - Jingwen Xue
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China
| | - Fei Yuan
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China
| | - Tianci Qu
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China
| | - Anastassia N Rissanou
- Theoretical & Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, Athens 11635, Greece
| | - Yilin Wang
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, 131 Dong'an Road, Shanghai 200032, China
| | - Xiang Li
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, China.
| | - Honggang Hu
- School of Medicine, Shanghai University, 99 Shangda Road, Shanghai 200444, China.
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6
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Zhang J, Dong S. In-Bridge Stereochemistry: A Determinant of Stapled Peptide Conformation and Activity. Chembiochem 2024; 25:e202300747. [PMID: 38191871 DOI: 10.1002/cbic.202300747] [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: 11/01/2023] [Revised: 11/30/2023] [Indexed: 01/10/2024]
Abstract
Peptide side chain stapling has been proven to be an effective strategy for fine-tuning peptide properties. This innovative approach leads to the creation of stapled peptides characterized by stabilized α-helical conformations, enhanced protein-binding affinity, improved cell permeability, superior enzymatic stability, and numerous other advantages. Extensive research has explored the impact of various stapling bridges on the properties of these peptides, with limited investigation into the influence of bridge chirality, until very recently. In this concise review, we provide a brief overview of the current state of knowledge regarding the stereochemistry within the bridges of stapled peptides, offering insights into the potential applications of chiral bridges in the design and development of stapled peptides.
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Affiliation(s)
- Jingyi Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, and School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Suwei Dong
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, and School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
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7
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Faraji N, Daly NL, Arab SS, Khosroushahi AY. In silico design of potential Mcl-1 peptide-based inhibitors. J Mol Model 2024; 30:108. [PMID: 38499818 DOI: 10.1007/s00894-024-05901-8] [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: 12/09/2023] [Accepted: 03/10/2024] [Indexed: 03/20/2024]
Abstract
CONTEXT BIM (Bcl-2 interacting mediator of apoptosis)-derived peptides that specifically target over-expressed Mcl-1 (myeloid cell leukemia-1) protein and induce apoptosis are potentially anti-cancer agents. Since the helicity of BIM-derived peptides has a crucial role in their functionality, a range of strategies have been used to increase the helicity including the introduction of unnatural residues and stapling methods that have some drawbacks such as the accumulation in the liver. To avoid these drawbacks, this study aimed to design a more helical peptide by utilizing bioinformatics algorithms and molecular dynamics simulations without exploiting unnatural residues and stapling methods. MM-PBSA results showed that the mutations of A4fE and A2eE in analogue 5 demonstrate a preference towards binding with Mcl-1. As evidenced by Circular dichroism results, the helicity increases from 18 to 34%, these findings could enhance the potential of analogue 5 as an anti-cancer agent targeting Mcl-1. The applied strategies in this research could shed light on the in silico peptide design. Moreover, analogue 5 as a drug candidate can be evaluated in vitro and in vivo studies. METHODS The sequence of the lead peptide was determined using the ApInAPDB database and PRALINE program. Contact finder and PDBsum web server softwares were used to determine the contact involved amino acids in complex with Mcl-1. All identified salt bridge contributing residues were unaltered to preserve the binding affinity. After proposing novel analogues, their secondary structures were predicted by Cham finder web server software and GOR, Neural Network, and Chou-Fasman algorithms. Finally, molecular dynamics simulations run for 100 ns were done using the GROMACS, version 5.0.7, with the CHARMM36 force field. MM-PBSA was used to assess binding affinity specificity in targeting Mcl-1 and Bcl-xL (B-cell lymphoma extra-large).
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Affiliation(s)
- Naser Faraji
- Department of Medical Nanotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Daneshgah Street, Tabriz, Iran
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Norelle L Daly
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, 4870, Australia
| | - Seyed Shahriar Arab
- Department of Biophysics, Faculty of Biological Sciences, School of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Ahmad Yari Khosroushahi
- Department of Medical Nanotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Daneshgah Street, Tabriz, Iran.
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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8
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Ma B, Liu D, Zheng M, Wang Z, Zhang D, Jian Y, Ma J, Fan Y, Chen Y, Gao Y, Liu J, Li X, Li L. Development of a Double-Stapled Peptide Stabilizing Both α-Helix and β-Sheet Structures for Degrading Transcription Factor AR-V7. JACS AU 2024; 4:816-827. [PMID: 38425893 PMCID: PMC10900202 DOI: 10.1021/jacsau.3c00795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/08/2024] [Accepted: 01/08/2024] [Indexed: 03/02/2024]
Abstract
Peptide drugs offer distinct advantages in therapeutics; however, their limited stability and membrane penetration abilities hinder their widespread application. One strategy to overcome these challenges is the hydrocarbon peptide stapling technique, which addresses issues such as poor conformational stability, weak proteolytic resistance, and limited membrane permeability. Nonetheless, while peptide stapling has successfully stabilized α-helical peptides, it has shown limited applicability for most β-sheet peptide motifs. In this study, we present the design of a novel double-stapled peptide capable of simultaneously stabilizing both α-helix and β-sheet structures. Our designed double-stapled peptide, named DSARTC, specifically targets the androgen receptor (AR) DNA binding domain and MDM2 as E3 ligase. Serving as a peptide-based PROTAC (proteolysis-targeting chimera), DSARTC exhibits the ability to degrade both the full-length AR and AR-V7. Molecular dynamics simulations and circular dichroism analysis validate the successful constraint of both secondary structures, demonstrating that DSARTC is a "first-in-class" heterogeneous-conformational double-stapled peptide drug candidate. Compared to its linear counterpart, DSARTC displays enhanced stability and an improved cell penetration ability. In an enzalutamide-resistant prostate cancer animal model, DSARTC effectively inhibits tumor growth and reduces the levels of both AR and AR-V7 proteins. These results highlight the potential of DSARTC as a more potent and specific peptide PROTAC for AR-V7. Furthermore, our findings provide a promising strategy for expanding the design of staple peptide-based PROTAC drugs, targeting a wide range of "undruggable" transcription factors.
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Affiliation(s)
- Bohan Ma
- Department
of Urology, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an 710049, China
| | - Donghua Liu
- Department
of Urology, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an 710049, China
| | - Mengjun Zheng
- School
of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
| | - Zhe Wang
- Institute
of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Dize Zhang
- Department
of Urology, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an 710049, China
| | - Yanlin Jian
- Department
of Urology, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an 710049, China
| | - Jian Ma
- Department
of Urology, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an 710049, China
| | - Yizeng Fan
- Department
of Urology, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an 710049, China
| | - Yule Chen
- Department
of Urology, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an 710049, China
| | - Yang Gao
- Department
of Urology, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an 710049, China
| | - Jing Liu
- Department
of Urology, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an 710049, China
| | - Xiang Li
- School
of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
| | - Lei Li
- Department
of Urology, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an 710049, China
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9
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Paquette AR, Boddy CN. Double Stranded DNA Binding Stapled Peptides: An Emerging Tool for Transcriptional Regulation. Chembiochem 2023; 24:e202300594. [PMID: 37750576 DOI: 10.1002/cbic.202300594] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 09/27/2023]
Abstract
Stapled peptides have rapidly established themselves as a powerful technique to mimic α-helical interactions with a short peptide sequence. There are many examples of stapled peptides that successfully disrupt α-helix-mediated protein-protein interactions, with an example currently in clinical trials. DNA-protein interactions are also often mediated by α-helices and are involved in all transcriptional regulation processes. Unlike DNA-binding small molecules, which typically lack DNA sequence selectivity, DNA-binding proteins bind with high affinity and high selectivity. These are ideal candidates for the design DNA-binding stapled peptides. Despite the parallel to protein-protein interaction disrupting stapled peptides and the need for sequence specific DNA binders, there are very few DNA-binding stapled peptides. In this review we examine all the known DNA-binding stapled peptides. Their design concepts are compared to stapled peptides that disrupt protein-protein interactions and based on the few examples in the literature, DNA-binding stapled peptide trends are discussed.
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Affiliation(s)
- André R Paquette
- Department of Chemistry and Biomolecular Sciences, The University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Christopher N Boddy
- Department of Chemistry and Biomolecular Sciences, The University of Ottawa, Ottawa, ON, K1N 6N5, Canada
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10
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Mi T, Siriwibool S, Burgess K. Streamlined Protein-Protein Interface Loop Mimicry. Angew Chem Int Ed Engl 2023; 62:e202307092. [PMID: 37849440 DOI: 10.1002/anie.202307092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 10/12/2023] [Accepted: 10/17/2023] [Indexed: 10/19/2023]
Abstract
Cyclic peptides comprising endocyclic organic fragments, "cyclo-organopeptides", can be probes for perturbing protein-protein interactions (PPIs). Finding loop mimics is difficult because of high conformational variability amongst targets. Backbone Matching (BM), introduced here, helps solve this problem in the illustrative cases by facilitating efficient evaluation of virtual cyclo-organopeptide core-structure libraries. Thus, 86 rigid organic fragments were selected to build a library of 602 cyclo-organopeptides comprising Ala and organic parts: "cyclo-{-(Ala)n -organo-}". The central hypothesis is "hit" library members have accessible low energy conformers corresponding to backbone structures of target protein loops, while library members which cannot attain this conformation are probably unworthy of further evaluation. BM thereby prioritizes candidate loop mimics, so that less than 10 cyclo-organopeptides are needed to be prepared to find leads for two illustrative PPIs: iNOS ⋅ SPSB2, and uPA ⋅ uPAR.
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Affiliation(s)
- Tianxiong Mi
- Department of Chemistry, Texas A & M University, 77842, College Station, TX, USA
| | - Siriwalee Siriwibool
- School of Chemistry, Institute of Science, Suranaree University of Technology, 30000, Nakhon Ratchasima, Thailand
| | - Kevin Burgess
- Department of Chemistry, Texas A & M University, 77842, College Station, TX, USA
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11
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Lima MCP, Hornsby BD, Lim CS, Cheatham TE. Computational Modeling of Stapled Coiled-Coil Inhibitors Against Bcr-Abl: Toward a Treatment Strategy for CML. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.15.566894. [PMID: 38014060 PMCID: PMC10680756 DOI: 10.1101/2023.11.15.566894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The chimeric oncoprotein Bcr-Abl is the causative agent of virtually all chronic myeloid leukemias (CML) and a subset of acute lymphoblastic leukemias (ALL). As a result of the so-called Philadelphia Chromosome translocation t(9;22), Bcr-Abl manifests as a constitutively active tyrosine kinase which promotes leukemogenesis by activation of cell cycle signaling pathways. Constitutive and oncogenic activation is mediated by an N-terminal coiled-coil oligomerization domain in Bcr (Bcr-CC), presenting a therapeutic target for inhibition of Bcr-Abl activity toward the treatment of Bcr-Abl+ leukemias. Previously, we demonstrated that a rationally designed Bcr-CC mutant, CCmut3, exerts a dominant negative effect upon Bcr-Abl activity by preferential oligomerization with Bcr-CC. Moreover, we have shown conjugation to a leukemia-specific cell-penetrating peptide (CPP-CCmut3) improves intracellular delivery and activity. However, our full-length CPP-CCmut3 construct (81 aa) is encumbered by an intrinsically high degree of conformational variability and susceptibility to proteolytic degradation, relative to traditional small molecule therapeutics. Here, we iterate a new generation of our inhibitor against Bcr-CC mediated Bcr-Abl assembly that is designed to address these constraints through incorporation of all-hydrocarbon staples spanning i, i + 7 positions in helix α2 (CPP-CCmut3-st). We utilize computational modeling and biomolecular simulation to design and characterize single and double staple candidates in silico, evaluating binding energetics and building upon our seminal work modeling single hydrocarbon staples when applied to a truncated Bcr-CC sequence. This strategy enables us to efficiently build, characterize, and screen lead single/double stapled CPP-CCmut3-st candidates for experimental studies and validation in vitro and in vivo. In addition to full-length CPP-CCmut, we model a truncated system characterized by deletion of helix α1 and the flexible-loop linker, which are known to impart high conformational variability. To study the impact of the N-terminal cyclic CPP toward model stability and inhibitor activity, we also model the full-length and truncated systems without CPP, with cyclized CPP, and with linear CPP, for a total of six systems which comprise our library. From this library, we present lead stapled peptide candidates to be synthesized and evaluated experimentally as our next-generation inhibitors against Bcr-Abl.
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Affiliation(s)
- Maria Carolina P. Lima
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Braxten D. Hornsby
- Department of Molecular Pharmaceutics, University of Utah, Salt Lake City, Utah 84112, United States
| | - Carol S. Lim
- Department of Molecular Pharmaceutics, University of Utah, Salt Lake City, Utah 84112, United States
| | - Thomas E. Cheatham
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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12
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Thakkar R, Agarwal DK, Ranaweera CB, Ishiguro S, Conda-Sheridan M, Gaudreault NN, Richt JA, Tamura M, Comer J. De novo design of a stapled peptide targeting SARS-CoV-2 spike protein receptor-binding domain. RSC Med Chem 2023; 14:1722-1733. [PMID: 37731704 PMCID: PMC10507807 DOI: 10.1039/d3md00222e] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 07/12/2023] [Indexed: 09/22/2023] Open
Abstract
Although effective vaccines have been developed against SARS-CoV-2, many regions in the world still have low rates of vaccination and new variants with mutations in the viral spike protein have reduced the effectiveness of most available vaccines and treatments. There is an urgent need for a drug to cure this disease and prevent infection. The SARS-CoV-2 virus enters the host cell through protein-protein interaction between the virus's spike protein and the host's angiotensin converting enzyme (ACE2). Using protein design software and molecular dynamics simulations, we have designed a 17-residue peptide (pep39), that binds to the spike protein receptor-binding domain (RBD) and blocks interaction of spike protein with ACE2. We have confirmed the binding activity of the designed peptide for the original spike protein and the delta variant spike protein using micro-cantilever and bio-layer interferometry (BLI) based methods. We also confirmed that pep39 strongly inhibits SARS-CoV-2 virus replication in Vero E6 cells. Taken together these data suggest that a newly designed spike protein RBD blocking peptide pep39 has a potential as a SARS-CoV-2 virus inhibitor.
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Affiliation(s)
- Ravindra Thakkar
- Department of Anatomy & Physiology, Kansas State University College of Veterinary Medicine Manhattan Kansas USA
| | - Dilip K Agarwal
- Department of Material Science and Engineering and NUANCE Center, Northwestern University Evanston Illinois USA
| | - Chathuranga B Ranaweera
- Department of Medical Laboratory Sciences, General Sir John Kotelawala Defense University Colombo Sri Lanka
| | - Susumu Ishiguro
- Department of Anatomy & Physiology, Kansas State University College of Veterinary Medicine Manhattan Kansas USA
| | - Martin Conda-Sheridan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center Omaha Nebraska USA
| | - Natasha N Gaudreault
- Department of Diagnostic Medicine & Pathobiology, Kansas State University College of Veterinary Medicine Manhattan Kansas USA
| | - Juergen A Richt
- Department of Diagnostic Medicine & Pathobiology, Kansas State University College of Veterinary Medicine Manhattan Kansas USA
| | - Masaaki Tamura
- Department of Anatomy & Physiology, Kansas State University College of Veterinary Medicine Manhattan Kansas USA
| | - Jeffrey Comer
- Department of Anatomy & Physiology, Kansas State University College of Veterinary Medicine Manhattan Kansas USA
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13
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Lourenço ALP, Rios TB, da Silva ÁP, Franco OL, Ramada MHS. Peptide Stapling Applied to Antimicrobial Peptides. Antibiotics (Basel) 2023; 12:1400. [PMID: 37760697 PMCID: PMC10525709 DOI: 10.3390/antibiotics12091400] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
Antimicrobial peptides (AMPs) are considered a promising therapeutic approach against multi-drug resistant microorganisms. Besides their advantages, there are limitations to be overcome so that these molecules can become market competitive. One of the biggest limitations is proteolytic susceptibility, which could be overcome by structural modifications such as cyclization, especially for helix-constraining strategies. Over the years, many helix stabilization techniques have arisen, such as lactam-bridging, triazole-based, N-alkylation and all-hydrocarbon stapling. All-hydrocarbon stapling takes advantage of modified amino acid residues and olefinic cross-linking to constrain peptide helices. Despite being a well-established strategy and presenting efficient stability results, there are different limitations especially related to toxicity. In this review, recent studies on stapled AMPs for antimicrobial usage are explored with the aim of understanding the future of these molecules as putative antimicrobial agents.
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Affiliation(s)
- Ana Laura Pereira Lourenço
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília 71966-700, Brazil
| | - Thuanny Borba Rios
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília 71966-700, Brazil
- S-Inova Biotech, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande 79117-900, Brazil
| | - Állan Pires da Silva
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília 71966-700, Brazil
| | - Octávio Luiz Franco
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília 71966-700, Brazil
- S-Inova Biotech, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande 79117-900, Brazil
| | - Marcelo Henrique Soller Ramada
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília 71966-700, Brazil
- Programa de Pós-Graduação em Gerontologia, Universidade Católica de Brasília, Brasília 71966-700, Brazil
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14
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Rashno Z, Rismani E, Ghasemi JB, Mansouri M, Shabani M, Afgar A, Dabiri S, Rezaei Makhouri F, Hatami A, Harandi MF. Design of ion channel blocking, toxin-like Kunitz inhibitor peptides from the tapeworm, Echinococcus granulosus, with potential anti-cancer activity. Sci Rep 2023; 13:11465. [PMID: 37454225 PMCID: PMC10349847 DOI: 10.1038/s41598-023-38159-w] [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: 12/23/2022] [Accepted: 07/04/2023] [Indexed: 07/18/2023] Open
Abstract
Over-expression of K+ channels has been reported in human cancers and is associated with the poor prognosis of several malignancies. EAG1, a particular potassium ion channel, is widely expressed in the brain but poorly expressed in other normal tissues. Kunitz proteins are dominant in metazoan including the dog tapeworm, Echinococcus granulosus. Using computational analyses on one A-type potassium channel, EAG1, and in vitro cellular methods, including major cancer cell biomarkers expression, immunocytochemistry and whole-cell patch clamp, we demonstrated the anti-tumor activity of three synthetic small peptides derived from E. granulosus Kunitz4 protease inhibitors. Experiments showed induced significant apoptosis and inhibition of proliferation in both cancer cell lines via disruption in cell-cycle transition from the G0/G1 to S phase. Western blotting showed that the levels of cell cycle-related proteins including P27 and P53 were altered upon kunitz4-a and kunitz4-c treatment. Patch clamp analysis demonstrated a significant increase in spontaneous firing frequency in Purkinje neurons, and exposure to kunitz4-c was associated with an increase in the number of rebound action potentials after hyperpolarized current. This noteworthy component in nature could act as an ion channel blocker and is a potential candidate for cancer chemotherapy based on potassium channel blockage.
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Affiliation(s)
- Zahra Rashno
- Research Center for Hydatid Disease in Iran, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, 7616914115, Iran
| | - Elham Rismani
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Jahan B Ghasemi
- Faculty of Chemistry, School of Sciences, University of Tehran, Tehran, Iran
| | - Mehdi Mansouri
- Department of Agricultural Biotechnology, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Mohammad Shabani
- Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Ali Afgar
- Research Center for Hydatid Disease in Iran, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, 7616914115, Iran
| | - Shahriar Dabiri
- Pathology and Stem Cell Research Center, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | | | - Abbas Hatami
- Pathology and Stem Cell Research Center, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Majid Fasihi Harandi
- Research Center for Hydatid Disease in Iran, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, 7616914115, Iran.
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15
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Jones M, Grosche P, Floersheimer A, André J, Gattlen R, Oser D, Tinchant J, Wille R, Chie-Leon B, Gerspacher M, Ertl P, Ostermann N, Altmann E, Manchado E, Vorherr T, Chène P. Design and Biochemical Characterization of Peptidic Inhibitors of the Myb/p300 Interaction. Biochemistry 2023; 62:1321-1329. [PMID: 36883372 DOI: 10.1021/acs.biochem.2c00690] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
The Myb transcription factor is involved in the proliferation of hematopoietic cells, and deregulation of its expression can lead to cancers such as leukemia. Myb interacts with various proteins, including the histone acetyltransferases p300 and CBP. Myb binds to a small domain of p300, the KIX domain (p300KIX), and inhibiting this interaction is a potential new drug discovery strategy in oncology. The available structures show that Myb binds to a very shallow pocket of the KIX domain, indicating that it might be challenging to identify inhibitors of this interaction. Here, we report the design of Myb-derived peptides which interact with p300KIX. We show that by mutating only two Myb residues that bind in or near a hotspot at the surface of p300KIX, it is possible to obtain single-digit nanomolar peptidic inhibitors of the Myb/p300KIX interaction that bind 400-fold tighter to p300KIX than wildtype Myb. These findings suggest that it might also be possible to design potent low molecular-weight compounds to disrupt the Myb/p300KIX interaction.
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Affiliation(s)
- Matthew Jones
- Disease Area Oncology, Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | - Philipp Grosche
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | - Andreas Floersheimer
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | - Jérome André
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | - Raphael Gattlen
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | - Dieter Oser
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | - Juliette Tinchant
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | - Roman Wille
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | - Barbara Chie-Leon
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Emeryville, California 94608, United States
| | - Marc Gerspacher
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | - Peter Ertl
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | - Nils Ostermann
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Emeryville, California 94608, United States
| | - Eva Altmann
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | - Eusebio Manchado
- Disease Area Oncology, Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | - Thomas Vorherr
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
| | - Patrick Chène
- Disease Area Oncology, Novartis Institutes for Biomedical Research, Basel CH-4002, Switzerland
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16
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Rehman AU, Khurshid B, Ali Y, Rasheed S, Wadood A, Ng HL, Chen HF, Wei Z, Luo R, Zhang J. Computational approaches for the design of modulators targeting protein-protein interactions. Expert Opin Drug Discov 2023; 18:315-333. [PMID: 36715303 PMCID: PMC10149343 DOI: 10.1080/17460441.2023.2171396] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 01/18/2023] [Indexed: 01/31/2023]
Abstract
BACKGROUND Protein-protein interactions (PPIs) are intriguing targets for designing novel small-molecule inhibitors. The role of PPIs in various infectious and neurodegenerative disorders makes them potential therapeutic targets . Despite being portrayed as undruggable targets, due to their flat surfaces, disorderedness, and lack of grooves. Recent progresses in computational biology have led researchers to reconsider PPIs in drug discovery. AREAS COVERED In this review, we introduce in-silico methods used to identify PPI interfaces and present an in-depth overview of various computational methodologies that are successfully applied to annotate the PPIs. We also discuss several successful case studies that use computational tools to understand PPIs modulation and their key roles in various physiological processes. EXPERT OPINION Computational methods face challenges due to the inherent flexibility of proteins, which makes them expensive, and result in the use of rigid models. This problem becomes more significant in PPIs due to their flexible and flat interfaces. Computational methods like molecular dynamics (MD) simulation and machine learning can integrate the chemical structure data into biochemical and can be used for target identification and modulation. These computational methodologies have been crucial in understanding the structure of PPIs, designing PPI modulators, discovering new drug targets, and predicting treatment outcomes.
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Affiliation(s)
- Ashfaq Ur Rehman
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, Graduate Program in Chemical and Materials Physics, University of California Irvine, Irvine, California, USA
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai, Zhejiang, China
| | - Beenish Khurshid
- Department of Biochemistry, Abdul Wali Khan University Mardan, Pakistan
| | - Yasir Ali
- National Center for Bioinformatics, Quaid-e-Azam University, Islamabad, Pakistan
| | - Salman Rasheed
- National Center for Bioinformatics, Quaid-e-Azam University, Islamabad, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Pakistan
| | - Ho-Leung Ng
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, USA
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, Zhejiang, China
| | - Zhiqiang Wei
- Medicinal Chemistry and Bioinformatics Center, Ocean University of China, Qingdao, Shandong, China
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, Graduate Program in Chemical and Materials Physics, University of California Irvine, Irvine, California, USA
| | - Jian Zhang
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai, Zhejiang, China
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
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17
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You Y, Liu H, Zhu Y, Zheng H. Rational design of stapled antimicrobial peptides. Amino Acids 2023; 55:421-442. [PMID: 36781451 DOI: 10.1007/s00726-023-03245-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 01/30/2023] [Indexed: 02/15/2023]
Abstract
The global increase in antimicrobial drug resistance has dramatically reduced the effectiveness of traditional antibiotics. Structurally diverse antibiotics are urgently needed to combat multiple-resistant bacterial infections. As part of innate immunity, antimicrobial peptides have been recognized as the most promising candidates because they comprise diverse sequences and mechanisms of action and have a relatively low induction rate of resistance. However, because of their low chemical stability, susceptibility to proteases, and high hemolytic effect, their usage is subject to many restrictions. Chemical modifications such as D-amino acid substitution, cyclization, and unnatural amino acid modification have been used to improve the stability of antimicrobial peptides for decades. Among them, a side-chain covalent bridge modification, the so-called stapled peptide, has attracted much attention. The stapled side-chain bridge stabilizes the secondary structure, induces protease resistance, and increases cell penetration and biological activity. Recent progress in computer-aided drug design and artificial intelligence methods has also been used in the design of stapled antimicrobial peptides and has led to the successful discovery of many prospective peptides. This article reviews the possible structure-activity relationships of stapled antimicrobial peptides, the physicochemical properties that influence their activity (such as net charge, hydrophobicity, helicity, and dipole moment), and computer-aided methods of stapled peptide design. Antimicrobial peptides under clinical trial: Pexiganan (NCT01594762, 2012-05-07). Omiganan (NCT02576847, 2015-10-13).
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Affiliation(s)
- YuHao You
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, People's Republic of China
| | - HongYu Liu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, People's Republic of China
| | - YouZhuo Zhu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, People's Republic of China
| | - Heng Zheng
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, People's Republic of China.
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18
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Banerjee A, Gosavi S. Potential Self-Peptide Inhibitors of the SARS-CoV-2 Main Protease. J Phys Chem B 2023; 127:855-865. [PMID: 36689738 PMCID: PMC9883841 DOI: 10.1021/acs.jpcb.2c05917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/23/2022] [Indexed: 01/24/2023]
Abstract
The SARS-CoV-2 main protease (Mpro) plays an essential role in viral replication, cleaving viral polyproteins into functional proteins. This makes Mpro an important drug target. Mpro consists of an N-terminal catalytic domain and a C-terminal α-helical domain (MproC). Previous studies have shown that peptides derived from a given protein sequence (self-peptides) can affect the folding and, in turn, the function of that protein. Since the SARS-CoV-1 MproC is known to stabilize its Mpro and regulate its function, we hypothesized that SARS-CoV-2 MproC-derived self-peptides may modulate the folding and the function of SARS-CoV-2 Mpro. To test this, we studied the folding of MproC in the presence of various self-peptides using coarse-grained structure-based models and molecular dynamics simulations. In these simulations of MproC and one self-peptide, we found that two self-peptides, the α1-helix and the loop between α4 and α5 (loop4), could replace the equivalent native sequences in the MproC structure. Replacement of either sequence in full-length Mpro should, in principle, be able to perturb Mpro function albeit through different mechanisms. Some general principles for the rational design of self-peptide inhibitors emerge: The simulations show that prefolded self-peptides are more likely to replace native sequences than those which do not possess structure. Additionally, the α1-helix self-peptide is kinetically stable and once inserted rarely exchanges with the native α1-helix, while the loop4 self-peptide is easily replaced by the native loop4, making it less useful for modulating function. In summary, a prefolded α1-derived peptide should be able to inhibit SARS-CoV-2 Mpro function.
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Affiliation(s)
- Arkadeep Banerjee
- Simons Centre for the Study
of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Shachi Gosavi
- Simons Centre for the Study
of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
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19
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AmyP53 Prevents the Formation of Neurotoxic β-Amyloid Oligomers through an Unprecedent Mechanism of Interaction with Gangliosides: Insights for Alzheimer's Disease Therapy. Int J Mol Sci 2023; 24:ijms24021760. [PMID: 36675271 PMCID: PMC9864847 DOI: 10.3390/ijms24021760] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 01/19/2023] Open
Abstract
A broad range of data identify Ca2+-permeable amyloid pores as the most neurotoxic species of Alzheimer's β-amyloid peptide (Aβ1-42). Following the failures of clinical trials targeting amyloid plaques by immunotherapy, a consensus is gradually emerging to change the paradigm, the strategy, and the target to cure Alzheimer's disease. In this context, the therapeutic peptide AmyP53 was designed to prevent amyloid pore formation driven by lipid raft microdomains of the plasma membrane. Here, we show that AmyP53 outcompetes Aβ1-42 binding to lipid rafts through a unique mode of interaction with gangliosides. Using a combination of cellular, physicochemical, and in silico approaches, we unraveled the mechanism of action of AmyP53 at the atomic, molecular, and cellular levels. Molecular dynamics simulations (MDS) indicated that AmyP53 rapidly adapts its conformation to gangliosides for an optimal interaction at the periphery of a lipid raft, where amyloid pore formation occurs. Hence, we define it as an adaptive peptide. Our results describe for the first time the kinetics of AmyP53 interaction with lipid raft gangliosides at the atomic level. Physicochemical studies and in silico simulations indicated that Aβ1-42 cannot interact with lipid rafts in presence of AmyP53. These data demonstrated that AmyP53 prevents amyloid pore formation and cellular Ca2+ entry by competitive inhibition of Aβ1-42 binding to lipid raft gangliosides. The molecular details of AmyP53 action revealed an unprecedent mechanism of interaction with lipid rafts, offering innovative therapeutic opportunities for lipid raft and ganglioside-associated diseases, including Alzheimer's, Parkinson's, and related proteinopathies.
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20
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Abstract
Mutations in the TP53 tumour suppressor gene are very frequent in cancer, and attempts to restore the functionality of p53 in tumours as a therapeutic strategy began decades ago. However, very few of these drug development programmes have reached late-stage clinical trials, and no p53-based therapeutics have been approved in the USA or Europe so far. This is probably because, as a nuclear transcription factor, p53 does not possess typical drug target features and has therefore long been considered undruggable. Nevertheless, several promising approaches towards p53-based therapy have emerged in recent years, including improved versions of earlier strategies and novel approaches to make undruggable targets druggable. Small molecules that can either protect p53 from its negative regulators or restore the functionality of mutant p53 proteins are gaining interest, and drugs tailored to specific types of p53 mutants are emerging. In parallel, there is renewed interest in gene therapy strategies and p53-based immunotherapy approaches. However, major concerns still remain to be addressed. This Review re-evaluates the efforts made towards targeting p53-dysfunctional cancers, and discusses the challenges encountered during clinical development.
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Affiliation(s)
- Ori Hassin
- grid.13992.300000 0004 0604 7563Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Moshe Oren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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21
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Mittal N, Sharma G, Katare OP, Bhadada SK. A Narrative Review on Non-Invasive Drug Delivery of Teriparatide: A Ray of Hope. Crit Rev Ther Drug Carrier Syst 2023; 40:117-140. [PMID: 37585311 DOI: 10.1615/critrevtherdrugcarriersyst.2023045480] [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: 08/18/2023]
Abstract
In the field of pharmaceutical biotechnology and formulation development, various protein and peptide-based drugs have been used for therapeutic and clinical implications. These are mainly given via parenteral routes like intravenous, subcutaneous or intramuscular delivery. Teriparatide, also known as PTH 1-34, is a U.S. Food & Drug Administartion-approved anabolic drug to treat osteoporosis is currently available in market only as subcutaneous injection. The quest for elimination of needle in case of given peptidal delivery to replace it with alternative routes like nasal, buccal, transdermal and pulmonary pathways has driven meticulous drug research. The pharmaceutical scientists are working on innovation and approaches involving new materials and methods to develop the formulations for protein and peptides by noninvasive routes. Lately, various approaches have been carried out which involve many strategies and technologies to deliver teriparatide via alternative routes. But, physicochemical instability, proteolytic degradation, low bioavailability, etc. are some obstacles to develop suitable delivery system for teriparatide. This review intends to gather the overall developments in delivery systems specific to teriparatide which meant for better convenience and avoids vulnerability of multiple subcutaneous injections. In addition, the article emphasizes on the successes to develop noninvasive technologies and devices, and new milestones for teriparatide delivery.
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Affiliation(s)
- Neeraj Mittal
- Department of Endocrinology, Postgraduate Institute of Medical Education & Research, Chandigarh 160012, India; Chitkara College of Pharmacy, Chitkara University, Punjab 140401, India
| | - Gajanand Sharma
- University Institute of Pharmaceutical Sciences, UGC-Centre of Advanced Studies, Panjab University, Chandigarh 160014, India
| | - Om Parkash Katare
- University Institute of Pharmaceutical Sciences, UGC Centre of Advanced Studies, Panjab University, Chandigarh 160014, India
| | - Sanjay Kumar Bhadada
- Department of Endocrinology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India
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22
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Ullrich S, George J, Coram AE, Morewood R, Nitsche C. Biocompatible and Selective Generation of Bicyclic Peptides. Angew Chem Int Ed Engl 2022; 61:e202208400. [PMID: 35852030 DOI: 10.1002/anie.202208400] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Indexed: 01/07/2023]
Abstract
Bicyclic peptides possess superior properties for drug discovery; however, their chemical synthesis is not straightforward and often neither biocompatible nor fully orthogonal to all canonical amino acids. The selective reaction between 1,2-aminothiols and 2,6-dicyanopyridine allows direct access to complex bicyclic peptides in high yield. The process can be fully automated using standard solid-phase peptide synthesis. Bicyclization occurs in water at physiological pH within minutes and without the need for a catalyst. The use of various linkers allows tailored bicyclic peptides with qualities such as plasma stability, conformational preorganization, and high target affinity. We demonstrate this for a bicyclic inhibitor of the Zika virus protease NS2B-NS3 as well as for bicyclic versions of the α-helical antimicrobial peptide aurein 1.2.
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Affiliation(s)
- Sven Ullrich
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Josemon George
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Alexandra E Coram
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Richard Morewood
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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23
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Valer L, Rossetto D, Parkkila T, Sebastianelli L, Guella G, Hendricks AL, Cowan JA, Sang L, Mansy SS. Histidine Ligated Iron-Sulfur Peptides. Chembiochem 2022; 23:e202200202. [PMID: 35674331 PMCID: PMC9400863 DOI: 10.1002/cbic.202200202] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/08/2022] [Indexed: 11/17/2022]
Abstract
Iron-sulfur clusters are thought to be ancient cofactors that could have played a role in early protometabolic systems. Thus far, redox active, prebiotically plausible iron-sulfur clusters have always contained cysteine ligands to the cluster. However, extant iron-sulfur proteins can be found to exploit other modes of binding, including ligation by histidine residues, as seen with [2Fe-2S] Rieske and MitoNEET proteins. Here, we investigated the ability of cysteine- and histidine-containing peptides to coordinate a mononuclear Fe2+ center and a [2Fe-2S] cluster and compare their properties with purified iron-sulfur proteins. The iron-sulfur peptides were characterized by UV-vis, circular dichroism, and paramagnetic NMR spectroscopies and cyclic voltammetry. Small (≤6 amino acids) peptides can coordinate [2Fe-2S] clusters through a combination of cysteine and histidine residues with similar reduction potentials as their corresponding proteins. Such complexes may have been important for early cell-like systems.
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Affiliation(s)
- Luca Valer
- D-CIBIOUniversity of Trentovia Sommarive 938123Trento 28123Italy
- Department of ChemistryUniversity of Alberta11227 Saskatchewan DriveEdmontonT6G 2G2AlbertaCanada
| | - Daniele Rossetto
- D-CIBIOUniversity of Trentovia Sommarive 938123Trento 28123Italy
- Department of ChemistryUniversity of Alberta11227 Saskatchewan DriveEdmontonT6G 2G2AlbertaCanada
| | - Taylor Parkkila
- Department of ChemistryUniversity of Alberta11227 Saskatchewan DriveEdmontonT6G 2G2AlbertaCanada
| | - Lorenzo Sebastianelli
- Department of ChemistryUniversity of Alberta11227 Saskatchewan DriveEdmontonT6G 2G2AlbertaCanada
| | - Graziano Guella
- Department of PhysicsUniversity of TrentoVia Sommarive 14Trento38123Italy
| | - Amber L. Hendricks
- Department of Chemistry and BiochemistryThe Ohio State University100 West 18th AveColumbusOH 43210USA
| | - James A. Cowan
- Department of Chemistry and BiochemistryThe Ohio State University100 West 18th AveColumbusOH 43210USA
| | - Lingzi Sang
- Department of ChemistryUniversity of Alberta11227 Saskatchewan DriveEdmontonT6G 2G2AlbertaCanada
| | - Sheref S. Mansy
- D-CIBIOUniversity of Trentovia Sommarive 938123Trento 28123Italy
- Department of ChemistryUniversity of Alberta11227 Saskatchewan DriveEdmontonT6G 2G2AlbertaCanada
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24
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Ullrich S, George J, Coram A, Morewood R, Nitsche C. Biocompatible and Selective Generation of Bicyclic Peptides. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202208400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sven Ullrich
- Australian National University Research School of Chemistry AUSTRALIA
| | - Josemon George
- Australian National University Research School of Chemistry AUSTRALIA
| | - Alexandra Coram
- Australian National University Research School of Chemistry AUSTRALIA
| | - Richard Morewood
- Australian National University Research School of Chemistry AUSTRALIA
| | - Christoph Nitsche
- Australian National University Research School of Chemistry Sullivans Creek Road ACT 2601 Canberra AUSTRALIA
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25
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Anada C, Ikeda K, Nakao H, Nakano M. Improvement of Thermal Stability of Amphipathic Peptide-Phospholipid Nanodiscs via Lateral Association of α-Helices by Disulfide Cross-Linking. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:6977-6983. [PMID: 35613431 DOI: 10.1021/acs.langmuir.2c00533] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Amphipathic α-helical peptides have been reported to form discoidal particles or nanodiscs with phospholipids, in which a lipid bilayer patch is encircled by peptides. Peptide-based nanodiscs have broad applicability because of their ease of preparation, size flexibility, and structural plasticity. We previously revealed that the nanodiscs formed by apolipoprotein-A-I-derived peptide 18A showed temperature-dependent structural destabilization above the gel-to-liquid-crystalline phase transition temperature of the lipid bilayer. It has been suggested that this destabilization is due to the migration of peptides bound to the edge of the discs to the bilayer surface. In this study, we designed a peptide that could stabilize nanodisc structures against the phase transition of lipid bilayers by disulfide cross-linking of peptides. An 18A-dimer cross-linked by a proline residue, 37pA (Ac-18A-P-18A-CONH2), also showed thermal destabilization of nanodiscs like 18A. However, cross-linking the sides of the two α-helices of the cysteine-substituted analogue 37pA-C2 with disulfide bonds led to the formation of nanodiscs that were more stable to temperature changes. This stabilizing effect was mainly due to the formation of a cyclic 37pA-C2 monomer by intramolecular disulfide cross-linking. These results suggest that the lateral association of two α-helices, which is the basis of the double-belt structure, is an important factor for the implementation of stable nanodiscs. The results of this study will help in development of more stable nanoparticles with membrane proteins in the future.
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Affiliation(s)
- Chiharu Anada
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan
| | - Keisuke Ikeda
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan
| | - Hiroyuki Nakao
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan
| | - Minoru Nakano
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan
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26
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Lackner RM, O’Connell W, Zhang H, Chenoweth DM. A general strategy for the design and evaluation of heterobifunctional tools: applications to protein localization and phase separation. Chembiochem 2022; 23:e202200209. [DOI: 10.1002/cbic.202200209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/18/2022] [Indexed: 11/12/2022]
Affiliation(s)
| | - Will O’Connell
- Carnegie Mellon University Biological Sciences UNITED STATES
| | - Huaiying Zhang
- Carnegie Mellon University Biological Sciences UNITED STATES
| | - David M. Chenoweth
- University of Pennsylvania Chemistry 231 South 34th Street 19104-6323 Philadelphia UNITED STATES
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27
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Choudhury AR, Maity A, Chakraborty S, Chakrabarti R. Computational design of stapled peptide inhibitor against
SARS‐CoV
‐2 receptor binding domain. Pept Sci (Hoboken) 2022; 114:e24267. [PMID: 35574509 PMCID: PMC9088457 DOI: 10.1002/pep2.24267] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 03/18/2022] [Accepted: 03/28/2022] [Indexed: 12/25/2022]
Abstract
Since its first detection in 2019, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2) has been the cause of millions of deaths worldwide. Despite the development and administration of different vaccines, the situation is still worrisome as the virus is constantly mutating to produce newer variants some of which are highly infectious. This raises an urgent requirement to understand the infection mechanism and thereby design therapeutic‐based treatment for COVID‐19. The gateway of the virus to the host cell is mediated by the binding of the receptor binding domain (RBD) of the virus spike protein to the angiotensin‐converting enzyme 2 (ACE2) of the human cell. Therefore, the RBD of SARS‐CoV‐2 can be used as a target to design therapeutics. The α1 helix of ACE2, which forms direct contact with the RBD surface, has been used as a template in the current study to design stapled peptide therapeutics. Using computer simulation, the mechanism and thermodynamics of the binding of six stapled peptides with RBD have been estimated. Among these, the one with two lactam stapling agents has shown binding affinity, sufficient to overcome RBD‐ACE2 binding. Analyses of the mechanistic detail reveal that a reorganization of amino acids at the RBD‐ACE2 interface produces favorable enthalpy of binding whereas conformational restriction of the free peptide reduces the loss in entropy to result higher binding affinity. The understanding of the relation of the nature of the stapling agent with their binding affinity opens up the avenue to explore stapled peptides as therapeutic against SARS‐CoV‐2.
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Affiliation(s)
- Asha Rani Choudhury
- Department of Chemistry Indian Institute of Technology Bombay, Powai Mumbai India
| | - Atanu Maity
- Department of Chemistry Indian Institute of Technology Bombay, Powai Mumbai India
| | | | - Rajarshi Chakrabarti
- Department of Chemistry Indian Institute of Technology Bombay, Powai Mumbai India
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28
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Chen H, Zhou J, Chen H, Liang J, Xie C, Gu X, Wang R, Mao Z, Zhang Y, Li Q, Zuo G, Miao D, Jin J. Bmi-1-RING1B prevents GATA4-dependent senescence-associated pathological cardiac hypertrophy by promoting autophagic degradation of GATA4. Clin Transl Med 2022; 12:e574. [PMID: 35390228 PMCID: PMC8989148 DOI: 10.1002/ctm2.574] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 01/05/2023] Open
Abstract
AIMS Senescence-associated pathological cardiac hypertrophy (SA-PCH) is associated with upregulation of foetal genes, fibrosis, senescence-associated secretory phenotype (SASP), cardiac dysfunction and increased morbidity and mortality. Therefore, we conducted experiments to investigate whether GATA4 accumulation induces SA-PCH, and whether Bmi-1-RING1B promotes GATA4 ubiquitination and its selective autophagic degradation to prevent SA-PCH. METHODS AND RESULTS Bmi-1-deficient (Bmi-1-/- ), transgenic Bmi-1 overexpressing (Bmi-1Tg ) and wild-type (WT) mice were infused with angiotensin II (Ang II) to stimulate the development of SA-PCH. Through bioinformatics analysis with RNA sequencing data from cardiac tissues, we found that Bmi-1-RING1B and autophagy are negatively related to SA-PCH. Bmi-1 deficiency promoted GATA4-dependent SA-PCH by increasing GATA4 protein and hypertrophy-related molecules transcribed by GATA4 such as ANP and BNP. Bmi-1 deficiency stimulated NF-κB-p65-dependent SASP, leading to cardiac dysfunction, cardiomyocyte hypertrophy and senescence. Bmi-1 overexpression repressed GATA4-dependent SA-PCH. GATA4 degraded by Bmi-1 was mainly dependent on autophagy rather than proteasome. In human myocardium, p16 positively correlated with ANP and GATA4 and negatively correlated with LC3B, Bmi-1 and RING1B; GATA4 positively correlated with p62 and negatively correlated with Bmi-1 and LC3B. With increased p16 protein levels, ANP-, BNP- and GATA4-positive cells or areas increased; however, LC3B-positive cells or areas decreased in human myocardium. GATA4 is ubiquitinated after combining with Bmi-1-RING1B, which is then recognised by p62, is translocated to autophagosomes to form autophagolysosomes and degraded. Downregulated GATA4 ameliorated SA-PCH and cardiac dysfunction by reducing GATA4-dependent hypertrophy and SASP-related molecules. Bmi-1 combined with RING1B (residues 1-179) and C-terminus of GATA4 (residues 206-443 including zinc finger domains) through residues 1-95, including a RING-HC-finger. RING1B combined with C-terminus of GATA4 through the C-terminus (residues 180-336). Adeno-associated viral vector serotype 9 (AAV9)-cytomegalovirus (CMV)-Bmi-1-RING1B treatment significantly attenuated GATA4-dependent SA-PCH through promoting GATA4 autophagic degradation. CONCLUSIONS Bmi-1-RING1B maintained cardiac function and prevented SA-PCH by promoting selective autophagy for degrading GATA4. TRANSLATIONAL PERSPECTIVE AAV9-CMV-Bmi-1-RING1B could be used for translational gene therapy to ubiquitinate GATA4 and prevent GATA4-dependent SA-PCH. Also, the combined domains between Bmi-1-RING1B and GATA4 in aging cardiomyocytes could be therapeutic targets for identifying stapled peptides in clinical applications to promote the combination of Bmi-1-RING1B with GATA4 and the ubiquitination of GATA4 to prevent SA-PCH and heart failure. We found that degradation of cardiac GATA4 by Bmi-1 was mainly dependent on autophagy rather than proteasome, and autophagy agonists metformin and rapamycin could ameliorate the SA-PCH, suggesting that activation of autophagy with metformin or rapamycin could also be a promising method to prevent SA-PCH.
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Affiliation(s)
- Haiyun Chen
- The Research Center for AgingAffiliated Friendship Plastic Surgery Hospital of Nanjing Medical UniversityNanjingJiangsu210029China
| | - Jiawen Zhou
- Department of Human AnatomyResearch Centre for Bone and Stem CellsKey Laboratory for Aging & DiseaseThe State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingJiangsu211166China
| | - Hongjie Chen
- Department of Human AnatomyResearch Centre for Bone and Stem CellsKey Laboratory for Aging & DiseaseThe State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingJiangsu211166China
| | - Jialong Liang
- Department of Human AnatomyResearch Centre for Bone and Stem CellsKey Laboratory for Aging & DiseaseThe State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingJiangsu211166China
| | - Chunfeng Xie
- Department of Nutrition and Food SafetySchool of Public HealthNanjing Medical UniversityNanjingJiangsu211166China
| | - Xin Gu
- Department of Human AnatomyResearch Centre for Bone and Stem CellsKey Laboratory for Aging & DiseaseThe State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingJiangsu211166China
| | - Rong Wang
- Department of Human AnatomyResearch Centre for Bone and Stem CellsKey Laboratory for Aging & DiseaseThe State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingJiangsu211166China
| | - Zhiyuan Mao
- Department of Human AnatomyResearch Centre for Bone and Stem CellsKey Laboratory for Aging & DiseaseThe State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingJiangsu211166China
| | - Yongjie Zhang
- Department of Human AnatomyResearch Centre for Bone and Stem CellsKey Laboratory for Aging & DiseaseThe State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingJiangsu211166China
| | - Qing Li
- Department of Science and TechnologyJiangsu Jiankang Vocational CollegeNanjingJiangsu210029China
| | - Guoping Zuo
- Department of Human AnatomyResearch Centre for Bone and Stem CellsKey Laboratory for Aging & DiseaseThe State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingJiangsu211166China
| | - Dengshun Miao
- Department of Human AnatomyResearch Centre for Bone and Stem CellsKey Laboratory for Aging & DiseaseThe State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingJiangsu211166China
- The Research Center for AgingAffiliated Friendship Plastic Surgery Hospital of Nanjing Medical UniversityNanjingJiangsu210029China
| | - Jianliang Jin
- Department of Human AnatomyResearch Centre for Bone and Stem CellsKey Laboratory for Aging & DiseaseThe State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingJiangsu211166China
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29
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Lubos M, Mrázková L, Gwozdiaková P, Pícha J, Buděšínský M, Jiráček J, Kaminský J, Žáková L. Functional stapled fragments of human preptin of minimised length. Org Biomol Chem 2022; 20:2446-2454. [PMID: 35253830 DOI: 10.1039/d1ob02193a] [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
Preptin is a 34-amino-acid-long peptide derived from the E-domain of a precursor of insulin-like growth factor 2 (pro-IGF2) with bone-anabolic and insulin secretion amplifying properties. Here, we describe the synthesis, structures, and biological activities of six shortened analogues of human preptin. Eight- and nine-amino-acid-long peptide amides corresponding to the C-terminal part of human preptin were stabilised by two types of staples to induce a higher proportion of helicity in their secondary structure. We monitored the secondary structure of the stapled peptides using circular dichroism. The biological effect of the structural changes was determined afterwards by the ability of peptides to stimulate the release of intracellular calcium ions. We confirmed the previous observation that the stabilisation of the disordered conformation of human preptin has a deleterious effect on biological potency. However, surprisingly, one of our preptin analogues, a nonapeptide stabilised by olefin metathesis between positions 3 and 7 of the amino acid chain, had a similar ability to stimulate calcium ions' release to the full-length human preptin. Our findings could open up new ways to design new preptin analogues, which may have potential as drugs for the treatment of diabetes and osteoporosis.
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Affiliation(s)
- Marta Lubos
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 166 10 Prague, Czech Republic.
| | - Lucie Mrázková
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 166 10 Prague, Czech Republic.
| | - Petra Gwozdiaková
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 166 10 Prague, Czech Republic.
| | - Jan Pícha
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 166 10 Prague, Czech Republic.
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 166 10 Prague, Czech Republic.
| | - Jiří Jiráček
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 166 10 Prague, Czech Republic.
| | - Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 166 10 Prague, Czech Republic.
| | - Lenka Žáková
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo nám. 2, 166 10 Prague, Czech Republic.
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30
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Delaunay M, Ha-Duong T. Computational Tools and Strategies to Develop Peptide-Based Inhibitors of Protein-Protein Interactions. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2405:205-230. [PMID: 35298816 DOI: 10.1007/978-1-0716-1855-4_11] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein-protein interactions play crucial and subtle roles in many biological processes and modifications of their fine mechanisms generally result in severe diseases. Peptide derivatives are very promising therapeutic agents for modulating protein-protein associations with sizes and specificities between those of small compounds and antibodies. For the same reasons, rational design of peptide-based inhibitors naturally borrows and combines computational methods from both protein-ligand and protein-protein research fields. In this chapter, we aim to provide an overview of computational tools and approaches used for identifying and optimizing peptides that target protein-protein interfaces with high affinity and specificity. We hope that this review will help to implement appropriate in silico strategies for peptide-based drug design that builds on available information for the systems of interest.
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Affiliation(s)
| | - Tâp Ha-Duong
- Université Paris-Saclay, CNRS, BioCIS, Châtenay-Malabry, France.
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31
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PTHG2 Reduces Bone Loss in Ovariectomized Mice by Directing Bone Marrow Mesenchymal Stem Cell Fate. Stem Cells Int 2022; 2021:8546739. [PMID: 34976071 PMCID: PMC8720025 DOI: 10.1155/2021/8546739] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/21/2021] [Accepted: 10/23/2021] [Indexed: 12/15/2022] Open
Abstract
Teriparatide, also known as 1-34 parathyroid hormone (PTH (1-34)), is commonly used for the treatment of osteoporosis in postmenopausal women. But its therapeutic application is restricted by poor metabolic stability, low bioavailability, and rapid clearance. Herein, PTHG2, a glycosylated teriparatide derivative, is designed and synthesized to improve PTH stability and exert more potent antiosteoporosis effect. Surface plasmon resonance (SPR) analysis shows that PTHG2 combines to PTH 1 receptor. Additional acetylglucosamine covalent bonding in the first serine at the N terminal of PTH (1-34) improves stability and increases protein hydrolysis resistance. Intermittent administration of PTHG2 preserves bone quality in ovariectomy- (OVX-) induced osteoporosis mice model, along with increased osteoblastic differentiation and bone formation, and reduced marrow adipogenesis. In vitro, PTHG2 inhibits adipogenic differentiation and promotes osteoblastic differentiation of bone marrow mesenchymal stem cells (BMSCs). For molecular mechanism, PTHG2 directs BMSCs fate through stimulating the cAMP-PKA signaling pathway. Blocking PKA abrogates the pro-osteogenic effect of PTHG2. In conclusion, our study reveals that PTHG2 can accelerate osteogenic differentiation of BMSCs and inhibit adipogenic differentiation of BMSCs and show a better protective effect than PTH (1-34) in the treatment of osteoporosis.
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32
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Ding Y, Li Z, Jaklenec A, Hu Q. Vaccine delivery systems toward lymph nodes. Adv Drug Deliv Rev 2021; 179:113914. [PMID: 34363861 PMCID: PMC9418125 DOI: 10.1016/j.addr.2021.113914] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/05/2021] [Accepted: 07/31/2021] [Indexed: 12/15/2022]
Abstract
Strategies of improving vaccine targeting ability toward lymph nodes have been attracting considerable interest in recent years, though there are remaining delivery barriers based on the inherent properties of lymphatic systems and limited administration routes of vaccination. Recently, emerging vaccine delivery systems using various materials as carriers are widely developed to achieve efficient lymph node targeting and improve vaccine-triggered adaptive immune response. In this review, to further optimize the vaccine targeting ability for future research, the design principles of lymph node targeting vaccine delivery based on the anatomy of lymph nodes and vaccine administration routes are first summarized. Then different designs of lymph node targeting vaccine delivery systems, including vaccine delivery systems in clinical applications, are carefully surveyed. Also, the challenges and opportunities of current delivery systems for vaccines are concluded in the end.
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Affiliation(s)
- Yingyue Ding
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, United States,Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, United States
| | - Zhaoting Li
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, United States,Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, United States
| | - Ana Jaklenec
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, United States
| | - Quanyin Hu
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, United States; Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, United States.
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33
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Liu J, Wang P, Zeng W, Lu Q, Zhu Q. Late-stage construction of stapled peptides through Fujiwara-Moritani reaction between tryptophan and olefins. Chem Commun (Camb) 2021; 57:11661-11664. [PMID: 34671802 DOI: 10.1039/d1cc04202e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Herein, the first example of a palladium-catalyzed Fujiwara-Moritani reaction for olefination of tryptophan (Trp) residues, free from directing groups, was presented. The developed reaction proceeds efficiently for peptide modification, ligation and peptide stapling.
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Affiliation(s)
- Jiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Peng Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Wei Zeng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Qi Lu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Qing Zhu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
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34
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Romagnoli A, Di Marino D. The Use of Peptides in the Treatment of Fragile X Syndrome: Challenges and Opportunities. Front Psychiatry 2021; 12:754485. [PMID: 34803767 PMCID: PMC8599826 DOI: 10.3389/fpsyt.2021.754485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/11/2021] [Indexed: 01/17/2023] Open
Abstract
Fragile X Syndrome (FXS) is the most frequent cause of inherited intellectual disabilities and autism spectrum disorders, characterized by cognitive deficits and autistic behaviors. The silencing of the Fmr1 gene and consequent lack of FMRP protein, is the major contribution to FXS pathophysiology. FMRP is an RNA binding protein involved in the maturation and plasticity of synapses and its absence culminates in a range of morphological, synaptic and behavioral phenotypes. Currently, there are no approved medications for the treatment of FXS, with the approaches under study being fairly specific and unsatisfying in human trials. Here we propose peptides/peptidomimetics as candidates in the pharmacotherapy of FXS; in the last years this class of molecules has catalyzed the attention of pharmaceutical research, being highly selective and well-tolerated. Thanks to their ability to target protein-protein interactions (PPIs), they are already being tested for a wide range of diseases, including cancer, diabetes, inflammation, Alzheimer's disease, but this approach has never been applied to FXS. As FXS is at the forefront of efforts to develop new drugs and approaches, we discuss opportunities, challenges and potential issues of peptides/peptidomimetics in FXS drug design and development.
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Affiliation(s)
| | - Daniele Di Marino
- Department of Life and Environmental Sciences, New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Ancona, Italy
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35
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Li C, Zhao N, An L, Dai Z, Chen X, Yang F, You Q, Di B, Hu C, Xu L. Apoptosis-inducing activity of synthetic hydrocarbon-stapled peptides in H358 cancer cells expressing KRAS G12C. Acta Pharm Sin B 2021; 11:2670-2684. [PMID: 34589388 PMCID: PMC8463269 DOI: 10.1016/j.apsb.2021.06.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/16/2021] [Accepted: 06/16/2021] [Indexed: 11/25/2022] Open
Abstract
Lung cancers are the leading cause of cancer deaths worldwide and pose a grave threat to human life and health. Non-small cell lung cancer (NSCLC) is the most frequent malignancy occupying 80% of all lung cancer subtypes. Except for other mutations (e.g., KRASG12V/D) that are also vital for the occurrence, KRASG12C gene mutation is a significant driving force of NSCLC, with a prevalence of approximately 14% of all NSCLC patients. However, there are only a few therapeutic drugs targeting KRASG12C mutations currently. Here, we synthesized hydrocarbon-stapled peptide 3 that was much shorter and more stable with modest KRASG12C binding affinity and the same anti-tumor effect based on the α-helical peptide mimic SAH-SOS1A. The stapled peptide 3 effectively induced G2/M arrest and apoptosis, inhibiting cell growth in KRAS-mutated lung cancer cells via disrupting the KRAS-mediated RAF/MEK/ERK signaling, which was verified from the perspective of genomics and proteomics. Peptide 3 also exhibited strong anti-trypsin and anti-chymotrypsin abilities, as well as good plasma stability and human liver microsomal metabolic stability. Overall, peptide 3 retains the equivalent anti-tumor activity of SAH-SOS1A but with improved stability and affinity, superior to SAH-SOS1A. Our work offers a structural optimization approach of KRASG12C peptide inhibitors for cancer therapy.
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36
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Unarta IC, Xu J, Shang Y, Cheung CHP, Zhu R, Chen X, Cao S, Cheung PPH, Bierer D, Zhang M, Huang X, Li X. Entropy of stapled peptide inhibitors in free state is the major contributor to the improvement of binding affinity with the GK domain. RSC Chem Biol 2021; 2:1274-1284. [PMID: 34458841 PMCID: PMC8341669 DOI: 10.1039/d1cb00087j] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/24/2021] [Indexed: 01/03/2023] Open
Abstract
Stapled peptides are promising protein–protein interaction (PPI) inhibitors that can increase the binding potency. Different from small-molecule inhibitors in which the binding mainly depends on energetic interactions with their protein targets, the binding of stapled peptides has long been suggested to be benefited from entropy. However, it remains challenging to reveal the molecular features that lead to this entropy gain, which could originate from the stabilization of the stapled peptide in solution or from the increased flexibility of the complex upon binding. This hinders the rational design of stapled peptides as PPI inhibitors. Using the guanylate kinase (GK) domain of the postsynaptic density protein 95 (PSD-95) as the target, we quantified the enthalpic and entropic contributions by combining isothermal titration calorimetry (ITC), X-ray crystallography, and free energy calculations based on all-atom molecular dynamics (MD) simulations. We successfully designed a stapled peptide inhibitor (staple 1) of the PSD-95 GK domain that led to a 25-fold increase in the binding affinity (from tens of μMs to 1.36 μM) with high cell permeability. We showed that entropy indeed greatly enhanced the binding affinity and the entropy gain was mainly due to the constrained-helix structure of the stapled peptide in solution (free state). Based on staple 1, we further designed two other stapled peptides (staple 2 and 3), which exerted even larger entropy gains compared to staple 1 because of their more flexible bound complexes (bound state). However, for staple 2 and 3, the overall binding affinities were not improved, as the loose binding in their bound states led to an enthalpic loss that largely compensated the excess entropy gain. Our work suggests that increasing the stability of the stapled peptide in free solution is an effective strategy for the rational design of stapled peptides as PPI inhibitors. The significant improvement in the binding affinity of the stapled peptide to the PSD-95 GK domain is mostly contributed by the reduction in the entropy penalty of the stapled peptide due to the restriction in the α-helical structure by stapling in the free state.![]()
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Affiliation(s)
- Ilona Christy Unarta
- Bioengineering Graduate Program, Department of Biological and Chemical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay Kowloon Hong Kong .,Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
| | - Jianchao Xu
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Hong Kong
| | - Yuan Shang
- Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong .,Division of Life Science, The Hong Kong University of Science and Technology Kowloon Hong Kong
| | - Carina Hey Pui Cheung
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Hong Kong
| | - Ruichi Zhu
- Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong .,Division of Life Science, The Hong Kong University of Science and Technology Kowloon Hong Kong
| | - Xudong Chen
- Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong .,Division of Life Science, The Hong Kong University of Science and Technology Kowloon Hong Kong
| | - Siqin Cao
- Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong .,Department of Chemistry, The Hong Kong University of Science and Technology Kowloon Hong Kong
| | - Peter Pak-Hang Cheung
- Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong .,Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Hong Kong
| | - Donald Bierer
- Department of Medicinal Chemistry, Bayer AG Aprather Weg 18A 42096 Wuppertal Germany
| | - Mingjie Zhang
- Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong .,Division of Life Science, The Hong Kong University of Science and Technology Kowloon Hong Kong
| | - Xuhui Huang
- Bioengineering Graduate Program, Department of Biological and Chemical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay Kowloon Hong Kong .,Centre of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong .,Department of Chemistry, The Hong Kong University of Science and Technology Kowloon Hong Kong.,Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park Hong Kong
| | - Xuechen Li
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Hong Kong
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37
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Preleukemic and leukemic evolution at the stem cell level. Blood 2021; 137:1013-1018. [PMID: 33275656 DOI: 10.1182/blood.2019004397] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 12/01/2020] [Indexed: 02/07/2023] Open
Abstract
Hematological malignancies are an aggregate of diverse populations of cells that arise following a complex process of clonal evolution and selection. Recent approaches have facilitated the study of clonal populations and their evolution over time across multiple phenotypic cell populations. In this review, we present current concepts on the role of clonal evolution in leukemic initiation, disease progression, and relapse. We highlight recent advances and unanswered questions about the contribution of the hematopoietic stem cell population to these processes.
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38
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Holdbrook DA, Marzinek JK, Boncel S, Boags A, Tan YS, Huber RG, Verma CS, Bond PJ. The nanotube express: Delivering a stapled peptide to the cell surface. J Colloid Interface Sci 2021; 604:670-679. [PMID: 34280765 DOI: 10.1016/j.jcis.2021.07.023] [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: 02/11/2021] [Revised: 06/23/2021] [Accepted: 07/04/2021] [Indexed: 10/20/2022]
Abstract
HYPOTHESIS Carbon nanotubes (CNTs) represent a novel platform for cellular delivery of therapeutic peptides. Chemically-functionalized CNTs may enhance peptide uptake by improving their membrane targeting properties. EXPERIMENTS Using coarse-grained (CG) molecular dynamics (MD) simulations, we investigate membrane interactions of a peptide conjugated to pristine and chemically-modified CNTs. As proof of principle, we focus on their interactions with PM2, an amphipathic stapled peptide that inhibits the E3 ubiquitin ligase HDM2 from negatively regulating the p53 tumor suppressor. CNT interaction with both simple planar lipid bilayers as well as spherical lipid vesicles was studied, the latter as a surrogate for curved cellular membranes. FINDINGS Membrane permeation was rapid and spontaneous for both pristine and oxidized CNTs when unconjugated. This was slowed upon addition of a noncovalently attached peptide surface "sheath", which may be an effective way to slow CNT entry and avert membrane rupture. The CNT conjugates were observed to "desheath" their peptide layer at the bilayer interface upon insertion, leaving their cargo behind in the outer leaflet. This suggests that a synergy may exist to optimize CNT safety whilst enhancing the delivery efficiency of "hitchhiking" therapeutic molecules.
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Affiliation(s)
- Daniel A Holdbrook
- Bioinformatics Institute (A*STAR), 30 Biopolis Str., #07-01 Matrix, 38671 Singapore, Singapore
| | - Jan K Marzinek
- Bioinformatics Institute (A*STAR), 30 Biopolis Str., #07-01 Matrix, 38671 Singapore, Singapore
| | - Slawomir Boncel
- Silesian University of Technology, Faculty of Chemistry, Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Krzywoustego 4, 44-100 Gliwice, Poland.
| | - Alister Boags
- Bioinformatics Institute (A*STAR), 30 Biopolis Str., #07-01 Matrix, 38671 Singapore, Singapore
| | - Yaw Sing Tan
- Bioinformatics Institute (A*STAR), 30 Biopolis Str., #07-01 Matrix, 38671 Singapore, Singapore
| | - Roland G Huber
- Bioinformatics Institute (A*STAR), 30 Biopolis Str., #07-01 Matrix, 38671 Singapore, Singapore
| | - Chandra S Verma
- Bioinformatics Institute (A*STAR), 30 Biopolis Str., #07-01 Matrix, 38671 Singapore, Singapore; National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, 117543 Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore, Singapore.
| | - Peter J Bond
- Bioinformatics Institute (A*STAR), 30 Biopolis Str., #07-01 Matrix, 38671 Singapore, Singapore; National University of Singapore, Department of Biological Sciences, 14 Science Drive 4, 117543 Singapore, Singapore.
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39
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Vu QN, Young R, Sudhakar HK, Gao T, Huang T, Tan YS, Lau YH. Cyclisation strategies for stabilising peptides with irregular conformations. RSC Med Chem 2021; 12:887-901. [PMID: 34263169 PMCID: PMC8230030 DOI: 10.1039/d1md00098e] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 04/12/2021] [Indexed: 11/21/2022] Open
Abstract
Cyclisation is a common synthetic strategy for enhancing the therapeutic potential of peptide-based molecules. While there are extensive studies on peptide cyclisation for reinforcing regular secondary structures such as α-helices and β-sheets, there are remarkably few reports of cyclising peptides which adopt irregular conformations in their bioactive target-bound state. In this review, we highlight examples where cyclisation techniques have been successful in stabilising irregular conformations, then discuss how the design of cyclic constraints for irregularly structured peptides can be informed by existing β-strand stabilisation approaches, new computational design techniques, and structural principles extracted from cyclic peptide library screening hits. Through this analysis, we demonstrate how existing peptide cyclisation techniques can be adapted to address the synthetic design challenge of stabilising irregularly structured binding motifs.
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Affiliation(s)
- Quynh Ngoc Vu
- School of Chemistry, Eastern Ave, The University of Sydney NSW 2006 Australia
| | - Reginald Young
- School of Chemistry, Eastern Ave, The University of Sydney NSW 2006 Australia
| | | | - Tianyi Gao
- School of Chemistry, Eastern Ave, The University of Sydney NSW 2006 Australia
| | - Tiancheng Huang
- School of Chemistry, Eastern Ave, The University of Sydney NSW 2006 Australia
| | - Yaw Sing Tan
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR) 30 Biopolis Street, #07-01, Matrix Singapore 138671 Singapore
| | - Yu Heng Lau
- School of Chemistry, Eastern Ave, The University of Sydney NSW 2006 Australia
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40
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Perez JJ, Perez RA, Perez A. Computational Modeling as a Tool to Investigate PPI: From Drug Design to Tissue Engineering. Front Mol Biosci 2021; 8:681617. [PMID: 34095231 PMCID: PMC8173110 DOI: 10.3389/fmolb.2021.681617] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/05/2021] [Indexed: 12/13/2022] Open
Abstract
Protein-protein interactions (PPIs) mediate a large number of important regulatory pathways. Their modulation represents an important strategy for discovering novel therapeutic agents. However, the features of PPI binding surfaces make the use of structure-based drug discovery methods very challenging. Among the diverse approaches used in the literature to tackle the problem, linear peptides have demonstrated to be a suitable methodology to discover PPI disruptors. Unfortunately, the poor pharmacokinetic properties of linear peptides prevent their direct use as drugs. However, they can be used as models to design enzyme resistant analogs including, cyclic peptides, peptide surrogates or peptidomimetics. Small molecules have a narrower set of targets they can bind to, but the screening technology based on virtual docking is robust and well tested, adding to the computational tools used to disrupt PPI. We review computational approaches used to understand and modulate PPI and highlight applications in a few case studies involved in physiological processes such as cell growth, apoptosis and intercellular communication.
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Affiliation(s)
- Juan J Perez
- Department of Chemical Engineering, Universitat Politecnica de Catalunya, Barcelona, Spain
| | - Roman A Perez
- Bioengineering Institute of Technology, Universitat Internacional de Catalunya, Sant Cugat, Spain
| | - Alberto Perez
- The Quantum Theory Project, Department of Chemistry, University of Florida, Gainesville, FL, United States
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41
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Liu J, Wang P, Yan Z, Yan J, Kenry, Zhu Q. Recent Advances in Late-Stage Construction of Stapled Peptides via C-H Activation. Chembiochem 2021; 22:2762-2771. [PMID: 33949069 DOI: 10.1002/cbic.202100044] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/29/2021] [Indexed: 01/09/2023]
Abstract
Stapled peptides have been widely applied in many fields, including pharmaceutical chemistry, diagnostic reagents, and materials science. However, most traditional stapled peptide preparation methods rely on prefunctionalizations, which limit the diversity of stapled peptides. Recently, the emergence of late-stage transition metal-catalyzed C-H activation in amino acids and peptides has attracted wide interest due to its robustness and applicability for peptide stapling. In this review, we summarize the methods for late-stage construction of stapled peptides via transition metal-catalyzed C-H activation.
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Affiliation(s)
- Jiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, P. R. China
| | - Peng Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, P. R. China
| | - Zhengqing Yan
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, P. R. China
| | - Jiahui Yan
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, P. R. China
| | - Kenry
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA.,Department of Imaging, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Qing Zhu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, P. R. China
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42
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Cheung CHP, Xu J, Lee CL, Zhang Y, Wei R, Bierer D, Huang X, Li X. Construction of diverse peptide structural architectures via chemoselective peptide ligation. Chem Sci 2021; 12:7091-7097. [PMID: 34123337 PMCID: PMC8153220 DOI: 10.1039/d1sc01174j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/13/2021] [Indexed: 12/22/2022] Open
Abstract
Herein, we report the development of a facile synthetic strategy for constructing diverse peptide structural architectures via chemoselective peptide ligation. The key advancement involved is to utilize the benzofuran moiety as the peptide salicylaldehyde ester surrogate, and Dap-Ser/Lys-Ser dipeptide as the hydroxyl amino functionality, which could be successfully introduced at the side chain of peptides enabling peptide ligation. With this method, the side chain-to-side chain cyclic peptide, branched/bridged peptides, tailed cyclic peptides and multi-cyclic peptides have been designed and successfully synthesized with native peptidic linkages at the ligation sites. This strategy has provided an alternative strategic opportunity for synthetic peptide development. It also serves as an inspiration for the structural design of PPI inhibitors with new modalities.
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Affiliation(s)
- Carina Hey Pui Cheung
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Hong Kong
| | - Jianchao Xu
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Hong Kong
| | - Chi Lung Lee
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Hong Kong
| | - Yanfeng Zhang
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Hong Kong
| | - Ruohan Wei
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Hong Kong
| | - Donald Bierer
- Department of Medicinal Chemistry, Bayer AG Aprather Weg 18A 42096 Wuppertal Germany
| | - Xuhui Huang
- Department of Biological and Chemical Engineering, The Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
| | - Xuechen Li
- Department of Chemistry, State Key Lab of Synthetic Chemistry, The University of Hong Kong Hong Kong
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43
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Maity A, Choudhury AR, Chakrabarti R. Effect of Stapling on the Thermodynamics of mdm2-p53 Binding. J Chem Inf Model 2021; 61:1989-2000. [PMID: 33830760 DOI: 10.1021/acs.jcim.1c00219] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Protein-protein interaction (PPI) is one of the key regulatory features driving biomolecular processes and hence is targeted for designing therapeutics against diseases. Small peptides are a new and emerging class of therapeutics owing to their high specificity and low toxicity. For achieving efficient targeting of the PPI, amino acid side chains are often stapled together, resulting in the rigidification of these peptides. Exploring the scope of these peptides demands a comprehensive understanding of their working principle. In this work, two stapled p53 peptides have been considered to delineate their binding mechanism with mdm2 using computational approaches. The addition of stapling agent protects the secondary structure of the peptides even in the case of thermal and chemical denaturation. Although the introduction of a stapling agent increases the hydrophobicity of the peptide, the enthalpic stabilization decreases. This is overcome by the lowering of the entropic penalty, and the overall binding affinity improves. The mechanistic insights into the benefit of peptide stapling can be adopted for further improvement of peptide therapeutics.
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Affiliation(s)
- Atanu Maity
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Asha Rani Choudhury
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Rajarshi Chakrabarti
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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44
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González-Muñiz R, Bonache MÁ, Pérez de Vega MJ. Modulating Protein-Protein Interactions by Cyclic and Macrocyclic Peptides. Prominent Strategies and Examples. Molecules 2021; 26:445. [PMID: 33467010 PMCID: PMC7830901 DOI: 10.3390/molecules26020445] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 12/11/2022] Open
Abstract
Cyclic and macrocyclic peptides constitute advanced molecules for modulating protein-protein interactions (PPIs). Although still peptide derivatives, they are metabolically more stable than linear counterparts, and should have a lower degree of flexibility, with more defined secondary structure conformations that can be adapted to imitate protein interfaces. In this review, we analyze recent progress on the main methods to access cyclic/macrocyclic peptide derivatives, with emphasis in a few selected examples designed to interfere within PPIs. These types of peptides can be from natural origin, or prepared by biochemical or synthetic methodologies, and their design could be aided by computational approaches. Some advances to facilitate the permeability of these quite big molecules by conjugation with cell penetrating peptides, and the incorporation of β-amino acid and peptoid structures to improve metabolic stability, are also commented. It is predicted that this field of research could have an important future mission, running in parallel to the discovery of new, relevant PPIs involved in pathological processes.
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Affiliation(s)
- Rosario González-Muñiz
- Instituto de Química Médica (IQM-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain; (M.Á.B.); (M.J.P.d.V.)
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45
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Oral peptide delivery: challenges and the way ahead. Drug Discov Today 2021; 26:931-950. [PMID: 33444788 DOI: 10.1016/j.drudis.2021.01.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 10/16/2020] [Accepted: 01/06/2021] [Indexed: 12/14/2022]
Abstract
Peptides and proteins have emerged as potential therapeutic agents and, in the search for the best treatment regimen, the oral route has been extensively evaluated because of its non-invasive and safe nature. The physicochemical properties of peptides and proteins along with the hurdles in the gastrointestinal tract (GIT), such as degrading enzymes and permeation barriers, are challenges to their delivery. To address these challenges, several conventional and novel approaches, such as nanocarriers, site-specific and stimuli specific delivery, are being used. In this review, we discuss the challenges to the oral delivery of peptides and the approaches used to tackle these challenges.
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46
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He PY, Chen H, Hu HG, Hu JJ, Lim YJ, Li YM. Late-stage peptide and protein modifications through phospha-Michael addition reaction. Chem Commun (Camb) 2020; 56:12632-12635. [PMID: 32960198 DOI: 10.1039/d0cc04969g] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We developed a late-stage modification strategy by a phospha-Michael addition reaction between various functional phosphines and unprotected dehydroalanine (Dha) peptides and proteins under mild conditions. This strategy was applied to generate a staple peptide to enhance its cell membrane penetrability, and it was also able to regulate α-synuclein aggregation properties and morphological characteristics with the addition of different charges.
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Affiliation(s)
- Pei-Yang He
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China.
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47
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Structure dictates the mechanism of ligand recognition in the histidine and maltose binding proteins. Curr Res Struct Biol 2020; 2:180-190. [PMID: 34235478 PMCID: PMC8244415 DOI: 10.1016/j.crstbi.2020.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/26/2020] [Accepted: 08/06/2020] [Indexed: 12/21/2022] Open
Abstract
Two mechanisms, induced fit (IF) and conformational selection (CS), have been proposed to explain ligand recognition coupled conformational changes. The histidine binding protein (HisJ) adopts the CS mechanism, in which a pre-equilibrium is established between the open and the closed states with the ligand binding to the closed state. Despite being structurally similar to HisJ, the maltose binding protein (MBP) adopts the IF mechanism, in which the ligand binds the open state and induces a transition to the closed state. To understand the molecular determinants of this difference, we performed molecular dynamics (MD) simulations of coarse-grained dual structure based models. We find that intra-protein contacts unique to the closed state are sufficient to promote the conformational transition in HisJ, indicating a CS-like mechanism. In contrast, additional ligand-mimicking contacts are required to “induce” the conformational transition in MBP suggesting an IF-like mechanism. In agreement with experiments, destabilizing modifications to two structural features, the spine helix (SH) and the balancing interface (BI), present in MBP but absent in HisJ, reduce the need for ligand-mimicking contacts indicating that SH and BI act as structural restraints that keep MBP in the open state. We introduce an SH like element into HisJ and observe that this can impede the conformational transition increasing the importance of ligand-mimicking contacts. Similarly, simultaneous mutations to BI and SH in MBP reduce the barrier to conformational transitions significantly and promote a CS-like mechanism. Together, our results show that structural restraints present in the protein structure can determine the mechanism of conformational transitions and even simple models that correctly capture such structural features can predict their positions. MD simulations of such models can thus be used, in conjunction with mutational experiments, to regulate protein ligand interactions, and modulate ligand binding affinities. MBP operates by induced fit, HisJ by the conformational selection mechanism. Dual structure based models (dSBMs) encode two structures of a protein. MD simulations of dSBMs can identify the mechanism of conformational transitions. Locks, absent in HisJ, hold MBP open with ligand contacts required for closing. Binding mechanisms can be modified by altering such structural locks.
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Key Words
- BI, Balancing interface
- CS, conformational selection
- CTD, C-terminal domain
- Conformational selection
- Dual structure based models
- FEP, free energy profile
- HisJ, histidine binding protein
- IF, induced fit
- Induced fit
- MBP, maltose binding protein
- MD simulations
- MD, molecular dynamics
- NTD, N-terminal domain
- PBP, periplasmic binding protein
- Periplasmic binding proteins
- SH, spine helix
- Structural restraints
- WT, wild-type
- dSBM, dual structure-based model
- sSBM, single structure-based model
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48
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Li X, Chen S, Zhang WD, Hu HG. Stapled Helical Peptides Bearing Different Anchoring Residues. Chem Rev 2020; 120:10079-10144. [DOI: 10.1021/acs.chemrev.0c00532] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Xiang Li
- School of Pharmacy, Second Military Medical University, Shanghai, China
- Insititute of Translational Medicine, Shanghai University, Shanghai, China
| | - Si Chen
- School of Medicine, Shanghai University, Shanghai, China
| | - Wei-Dong Zhang
- School of Pharmacy, Second Military Medical University, Shanghai, China
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hong-Gang Hu
- Insititute of Translational Medicine, Shanghai University, Shanghai, China
- Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
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49
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Tan YS, Mhoumadi Y, Verma CS. Roles of computational modelling in understanding p53 structure, biology, and its therapeutic targeting. J Mol Cell Biol 2020; 11:306-316. [PMID: 30726928 PMCID: PMC6487789 DOI: 10.1093/jmcb/mjz009] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/14/2018] [Accepted: 01/31/2019] [Indexed: 12/21/2022] Open
Abstract
The transcription factor p53 plays pivotal roles in numerous biological processes, including the suppression of tumours. The rich availability of biophysical data aimed at understanding its structure–function relationships since the 1990s has enabled the application of a variety of computational modelling techniques towards the establishment of mechanistic models. Together they have provided deep insights into the structure, mechanics, energetics, and dynamics of p53. In parallel, the observation that mutations in p53 or changes in its associated pathways characterize several human cancers has resulted in a race to develop therapeutic modulators of p53, some of which have entered clinical trials. This review describes how computational modelling has played key roles in understanding structural-dynamic aspects of p53, formulating hypotheses about domains that are beyond current experimental investigations, and the development of therapeutic molecules that target the p53 pathway.
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Affiliation(s)
- Yaw Sing Tan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore
| | - Yasmina Mhoumadi
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore
| | - Chandra S Verma
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore
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Wang N, Li J, Song H, Liu C, Hu H, Liao H, Cong W. Synthesis and anti-osteoporosis activity of novel Teriparatide glycosylation derivatives. RSC Adv 2020; 10:25730-25735. [PMID: 35518599 PMCID: PMC9055339 DOI: 10.1039/d0ra05136e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/01/2020] [Indexed: 12/13/2022] Open
Abstract
Osteoporosis is a metabolic bone disease that is characterized by low bone mass and micro-architectural deterioration of bones. The mechanism underlying this disease implicates an imbalance between bone resorption and bone remodeling. In 2002, the US Food and Drug Administration (FDA) approved Teriparatide for the treatment of osteoporosis, and so far, this compound is the only permitted osteoanabolic. However, as a structurally flexible linear peptide, this drug may be further optimized. In this study, we develop a series of novel N-acetyl glucosamine glycosylation derivatives of Teriparatide and examine their characteristics. Of the analyzed compounds, PTHG-9 exhibits enhanced helicity, greater protease stability, and increased osteoblast differentiation promoting ability compared with the original Teriparatide. Accordingly, PTHG-9 is suggested as a therapeutic candidate for postmenopausal osteoporosis (PMOP) and other related diseases. The successful development of an enhanced osteoporosis drug proves that the method proposed herein can be used to effectively enhance the chemical and biological properties of linear peptides with various biological functions.
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Affiliation(s)
- Nan Wang
- Institute of Translational Medicine, Shanghai University Shanghai China
| | - Jingyang Li
- Department of Pediatric Respiratory Medicine, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Hui Song
- Institute of Translational Medicine, Shanghai University Shanghai China
| | - Chao Liu
- Institute of Translational Medicine, Shanghai University Shanghai China
| | - Honggang Hu
- Institute of Translational Medicine, Shanghai University Shanghai China
| | - Hongli Liao
- School of Pharmacy, Chengdu Medical College Chengdu China
| | - Wei Cong
- Institute of Translational Medicine, Shanghai University Shanghai China
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