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Shree M, Vaishnav J, Gurudayal, Ampapathi RS. In-silico assessment of novel peptidomimetics inhibitor targeting STAT3 and STAT4 N-terminal domain dimerization: A comprehensive study using molecular docking, molecular dynamics simulation, and binding free energy analysis. Biochem Biophys Res Commun 2024; 733:150584. [PMID: 39208642 DOI: 10.1016/j.bbrc.2024.150584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 08/04/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024]
Abstract
Dysregulation in Janus kinase-Signal Transducer and Activation of Transcription (JAK-STAT) pathway is closely linked to various cancer types. The N-terminal domain (NTD) of STAT proteins, upon dimerization, assumes a multifaceted role with remarkable adaptability in mediating interactions between proteins. Consequently, the strategic targeting of the N-terminal domain of STATs has emerged as a promising tactic for disrupting dimerization and impeding the translocation of STAT proteins. In this study, we have deployed an integrated in-silico methodology to rationally design Peptidomimetic foldamers as inhibitors of the N-terminal domains of STAT3 and STAT4, with the objective of disrupting protein dimerization. Consequently, we have judiciously designed a series of peptidomimetics that encompass β3-amino acids, bearing side chains that mimic the residues within interface II of the dimeric structures of the NTDs. Employing molecular docking techniques; we have assessed the binding affinity of these designed peptidomimetics toward both the NTDs. Furthermore, we have conducted an evaluation of the stability and conformational alterations within the docked complexes over an extensive Molecular Dynamics, subsequently computing the binding free energy utilizing MM/PBSA calculations. Our findings unequivocally demonstrate that the peptidomimetic foldamers we have devised (Peptide-A, Peptide-B, and Peptide-C) exhibit a propensity to bind to and impede the dimerization process of the NTDs of both STAT3 and STAT4. These outcomes serve to underscore the potential of these meticulously designed peptidomimetics as potential candidates meriting further exploration in the realm of cancer prevention and management.
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Affiliation(s)
- Megha Shree
- Sophisticated Analytical Instrumentation Facility & Research (SAIF-R), CSIR-Central Drug Research Institute (CDRI), Lucknow, 226031, India; Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India
| | - Jayanti Vaishnav
- Sophisticated Analytical Instrumentation Facility & Research (SAIF-R), CSIR-Central Drug Research Institute (CDRI), Lucknow, 226031, India
| | - Gurudayal
- Sophisticated Analytical Instrumentation Facility & Research (SAIF-R), CSIR-Central Drug Research Institute (CDRI), Lucknow, 226031, India
| | - Ravi Sankar Ampapathi
- Sophisticated Analytical Instrumentation Facility & Research (SAIF-R), CSIR-Central Drug Research Institute (CDRI), Lucknow, 226031, India; Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India.
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2
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Alamdari-Palangi V, Jaberi KR, Shahverdi M, Naeimzadeh Y, Tajbakhsh A, Khajeh S, Razban V, Fallahi J. Recent advances and applications of peptide-agent conjugates for targeting tumor cells. J Cancer Res Clin Oncol 2023; 149:15249-15273. [PMID: 37581648 DOI: 10.1007/s00432-023-05144-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/08/2023] [Indexed: 08/16/2023]
Abstract
BACKGROUND Cancer, being a complex disease, presents a major challenge for the scientific and medical communities. Peptide therapeutics have played a significant role in different medical practices, including cancer treatment. METHOD This review provides an overview of the current situation and potential development prospects of anticancer peptides (ACPs), with a particular focus on peptide vaccines and peptide-drug conjugates for cancer treatment. RESULTS ACPs can be used directly as cytotoxic agents (molecularly targeted peptides) or can act as carriers (guiding missile) of chemotherapeutic agents and radionuclides by specifically targeting cancer cells. More than 60 natural and synthetic cationic peptides are approved in the USA and other major markets for the treatment of cancer and other diseases. Compared to traditional cancer treatments, peptides exhibit anticancer activity with high specificity and the ability to rapidly kill target cancer cells. ACP's target and kill cancer cells via different mechanisms, including membrane disruption, pore formation, induction of apoptosis, necrosis, autophagy, and regulation of the immune system. Modified peptides have been developed as carriers for drugs, vaccines, and peptide-drug conjugates, which have been evaluated in various phases of clinical trials for the treatment of different types of solid and leukemia cancer. CONCLUSIONS This review highlights the potential of ACPs as a promising therapeutic option for cancer treatment, particularly through the use of peptide vaccines and peptide-drug conjugates. Despite the limitations of peptides, such as poor metabolic stability and low bioavailability, modified peptides show promise in addressing these challenges. Various mechanism of action of anticancer peptides. Modes of action against cancer cells including: inducing apoptosis by cytochrome c release, direct cell membrane lysis (necrosis), inhibiting angiogenesis, inducing autophagy-mediated cell death and immune cell regulation.
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Affiliation(s)
- Vahab Alamdari-Palangi
- Department of Molecular Medicine, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, 7133654361, Iran
| | - Khojaste Rahimi Jaberi
- Department of Neuroscience, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mahshid Shahverdi
- Medical Biotechnology Research Center, Arak University of Medical Sciences, Arak, Iran
| | - Yasaman Naeimzadeh
- Department of Molecular Medicine, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, 7133654361, Iran
| | - Amir Tajbakhsh
- Department of Molecular Medicine, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, 7133654361, Iran
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sahar Khajeh
- Bone and Joint Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Vahid Razban
- Department of Molecular Medicine, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, 7133654361, Iran.
| | - Jafar Fallahi
- Department of Molecular Medicine, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, 7133654361, Iran.
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3
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Reza D, Balo R, Otero JM, Fletcher AM, García-Fandino R, Sánchez-Pedregal VM, Davies SG, Estévez RJ, Estévez JC. β-Peptides incorporating polyhydroxylated cyclohexane β-amino acid: synthesis and conformational study. Org Biomol Chem 2023; 21:8535-8547. [PMID: 37840474 DOI: 10.1039/d3ob00906h] [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: 10/17/2023]
Abstract
We describe the synthesis of trihydroxylated cyclohexane β-amino acids from (-)-shikimic acid, in their cis and trans configuration, and the incorporation of the trans isomer into a trans-2-aminocyclohexanecarboxylic acid peptide chain. Subsequently, the hydroxyl groups were partially or totally deprotected. The structural study of the new peptides by FTIR, CD, solution NMR and DFT calculations revealed that they all fold into a 14-helix secondary structure, similarly to the homooligomer of trans-2-aminocyclohexanecarboxylic acid. This means that the high degree of substitution of the cyclohexane ring of the new residue is compatible with the adoption of a stable helical secondary structure and opens opportunities for the design of more elaborate peptidic foldamers with oriented polar substituents at selected positions of the cycloalkane residues.
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Affiliation(s)
- David Reza
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica. Universidade de Santiago de Compostela, c/Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain.
| | - Rosalino Balo
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica. Universidade de Santiago de Compostela, c/Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain.
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - José M Otero
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica. Universidade de Santiago de Compostela, c/Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain.
| | - Ai M Fletcher
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Rebeca García-Fandino
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica. Universidade de Santiago de Compostela, c/Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain.
- Departamento de Química Orgánica, Universidade de Santiago de Compostela, Avda. das Ciencias s/n, 15782 Santiago de Compostela, Spain
| | - Víctor M Sánchez-Pedregal
- Departamento de Química Orgánica, Universidade de Santiago de Compostela, Avda. das Ciencias s/n, 15782 Santiago de Compostela, Spain
| | - Stephen G Davies
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Ramón J Estévez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica. Universidade de Santiago de Compostela, c/Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain.
- Departamento de Química Orgánica, Universidade de Santiago de Compostela, Avda. das Ciencias s/n, 15782 Santiago de Compostela, Spain
| | - Juan C Estévez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica. Universidade de Santiago de Compostela, c/Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain.
- Departamento de Química Orgánica, Universidade de Santiago de Compostela, Avda. das Ciencias s/n, 15782 Santiago de Compostela, Spain
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4
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Shah SKH, Modi U, Patel K, James A, N S, De S, Vasita R, Prabhakaran P. Site-selective post-modification of short α/γ hybrid foldamers: a powerful approach for molecular diversification towards biomedical applications. Biomater Sci 2023; 11:6210-6222. [PMID: 37526301 DOI: 10.1039/d3bm00766a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
The extensive research work in the exhilarating area of foldamers (artificial oligomers possessing well-defined conformation in solution) has shown them to be promising candidates in biomedical research and materials science. The post-modification approach is successful in peptides, proteins, and polymers to modulate their functions. To the best of our knowledge, site-selective post-modification of a foldamer affording molecules with different pendant functional groups within a molecular scaffold has not yet been reported. We demonstrate for the first time that late-stage site-selective functionalization of short hybrid oligomers is an efficient approach to afford molecules with diverse functional groups. In this article, we report the design and synthesis of hybrid peptides with repeating units of leucine (Leu) and 5-amino salicylic acid (ASA), regioselective post-modification, conformational analyses (based on solution-state NMR, circular dichroism and computational studies) and morphological studies of the peptide nanostructures. As a proof-of-concept, we demonstrate the applications of differently modified peptides as drug delivery agents, imaging probes, and anticancer agents. The novel feature of the work is that the difference in reactivity of two phenolic OH groups in short biomimetic peptides was utilized to achieve site-selective post-modification. It is challenging to apply the same approach to short α-peptides having a poor folding tendency, and their post-functionalization may considerably affect their conformation.
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Affiliation(s)
| | - Unnati Modi
- School of Life Sciences, Central University of Gujarat, Gandhinagar 382030, India
| | - Karma Patel
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar 382030, India.
| | - Anjima James
- Department of Applied Chemistry, Cochin University of Science and Technology, Kochi 682022, India
| | - Sreerag N
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar 382030, India.
| | - Susmita De
- Department of Chemistry, University of Calicut, Calicut 673635, India
| | - Rajesh Vasita
- School of Life Sciences, Central University of Gujarat, Gandhinagar 382030, India
| | - Panchami Prabhakaran
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar 382030, India.
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5
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Khalily MP, Soydan M. Peptide-based diagnostic and therapeutic agents: Where we are and where we are heading? Chem Biol Drug Des 2023; 101:772-793. [PMID: 36366980 DOI: 10.1111/cbdd.14180] [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: 07/26/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022]
Abstract
Peptides are increasingly present in all branches of medicine as innovative drugs, imaging agents, theragnostic, and constituent moieties of other sophisticated drugs such as peptide-drug conjugates. Due to new developments in chemical synthesis strategies, computational biology, recombinant technology, and chemical biology, peptide drug development has made a great progress in the last decade. Numerous natural peptides and peptide mimics have been obtained and studied, covering multiple therapeutic areas. Even though peptides have been investigated across the wide therapeutic spectrum, oncology, metabolism, and endocrinology are the most frequent medical indications of them. This review summarizes the current use of and the emerging new opportunities of peptides for diagnosis and treatment of various diseases.
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Affiliation(s)
- Melek P Khalily
- Department of Basic Science and Health, Cannabis Research Institute, Yozgat Bozok University, Yozgat, Turkey
| | - Medine Soydan
- Department of Chemistry, Faculty of Arts and Science, Middle East Technical University, Ankara, Turkey
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6
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Monroe MK, Wang H, Anderson CF, Jia H, Flexner C, Cui H. Leveraging the therapeutic, biological, and self-assembling potential of peptides for the treatment of viral infections. J Control Release 2022; 348:1028-1049. [PMID: 35752254 PMCID: PMC11022941 DOI: 10.1016/j.jconrel.2022.06.037] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/06/2022] [Accepted: 06/20/2022] [Indexed: 12/12/2022]
Abstract
Peptides and peptide-based materials have an increasing role in the treatment of viral infections through their use as active pharmaceutical ingredients, targeting moieties, excipients, carriers, or structural components in drug delivery systems. The discovery of peptide-based therapeutic compounds, coupled with the development of new stabilization and formulation strategies, has led to a resurgence of antiviral peptide therapeutics over the past two decades. The ability of peptides to bind cell receptors and to facilitate membrane penetration and subsequent intracellular trafficking enables their use in various antiviral systems for improved targeting efficiency and treatment efficacy. Importantly, the self-assembly of peptides into well-defined nanostructures provides a vast library of discrete constructs and supramolecular biomaterials for systemic and local delivery of antiviral agents. We review here the recent progress in exploiting the therapeutic, biological, and self-assembling potential of peptides, peptide conjugates, and their supramolecular assemblies in treating human viral infections, with an emphasis on the treatment strategies for Human Immunodeficiency Virus (HIV).
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Affiliation(s)
- Maya K Monroe
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, 3400 N Charles Street, Baltimore, MD 21218, United States of America; Institute for NanoBioTechnology, The Johns Hopkins University, 3400 N Charles Street, Baltimore, MD 21218, United States of America
| | - Han Wang
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, 3400 N Charles Street, Baltimore, MD 21218, United States of America; Institute for NanoBioTechnology, The Johns Hopkins University, 3400 N Charles Street, Baltimore, MD 21218, United States of America
| | - Caleb F Anderson
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, 3400 N Charles Street, Baltimore, MD 21218, United States of America; Institute for NanoBioTechnology, The Johns Hopkins University, 3400 N Charles Street, Baltimore, MD 21218, United States of America
| | - Hongpeng Jia
- Department of Surgery, The Johns Hopkins University School of Medicine, United States of America
| | - Charles Flexner
- Divisions of Clinical Pharmacology and Infectious Diseases, The Johns Hopkins University School of Medicine and Bloomberg School of Public Health, Baltimore, MD 21205, United States of America.
| | - Honggang Cui
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, 3400 N Charles Street, Baltimore, MD 21218, United States of America; Institute for NanoBioTechnology, The Johns Hopkins University, 3400 N Charles Street, Baltimore, MD 21218, United States of America; Deptartment of Oncology and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States of America; Center for Nanomedicine, The Wilmer Eye Institute, The Johns Hopkins University School of Medicine, 400 North Broadway, Baltimore, MD 21231, United States of America.
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7
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Iwanov I, Rossi A, Montesi M, Doytchinova I, Sargsyan A, Momekov G, Panseri S, Naydenova E. Peptide-based targeted cancer therapeutics: design, synthesis and biological evaluation. Eur J Pharm Sci 2022; 176:106249. [PMID: 35779821 DOI: 10.1016/j.ejps.2022.106249] [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: 04/12/2022] [Revised: 06/17/2022] [Accepted: 06/28/2022] [Indexed: 11/29/2022]
Abstract
Cancer is the leading cause for human mortality together with cardiovascular diseases. Abl (Abelson) tyrosine kinases play a fundamental role in transducing various signals that control proliferation, survival, migration and invasion in several cancers such as Chronic Myeloid Leukemia (CML), breast cancer and brain cancer. For these reasons Abl tyrosine kinases are considered important biological targets in drug discovery. In this study a series of lysine-based oligopeptides with expected Abl inhibitory activity were designed resembling the binding of FDA-approved drugs (i.e. of Imatinib and Nilotinib), synthesized, purified by High Performance Liquid Chromatography (HPLC), analyzed by mass spectrometry (MS) and biologically tested in vitro in CML (AR-230 and K-562), breast cancers (MDA-MB 231 and MDA-MB 468) and glioblastoma cell lines (U87 and U118). The solid-phase peptide synthesis (SPPS) by Fmoc (9-fluorenylmethoxycarbonyl) chemistry was used to synthesize target compounds. AutoDock Vina was applied for simulation binding to Abl. The biological activities were measured evaluating cytotoxic effect, induction of apoptosis and inhibition of cancer cells migration. The new peptides exhibited different concentration-dependent antiproliferative effect against the tumor cell lines after 72 h treatment. The most promising results were obtained with the U87 glioblastoma cell line where a significant reduction of the migration ability was detected with one compound (H-Lys1-Lys2-Lys3-NH2).
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Affiliation(s)
- Iwan Iwanov
- University of Chemical Technology and Metallurgy, 8 Blvd. Kliment Ohridski, 1756, Sofia, Bulgaria
| | - Arianna Rossi
- Institute of Science and Technology for Ceramics, National Research Council of Italy, via Granarolo 64, Faenza (RA), Italy; University of Messina, Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Piazza Pugliatti 1, Messina (ME), Italy
| | - Monica Montesi
- Institute of Science and Technology for Ceramics, National Research Council of Italy, via Granarolo 64, Faenza (RA), Italy
| | | | - Armen Sargsyan
- Scientific and Production Center "Armbiotechnology" NAS RA, 14 Gyurjyan str., Yerevan, 0056, Armenia
| | - Georgi Momekov
- Medical University of Sofia, 2 Dunav st., Sofia, 1000, Bulgaria
| | - Silvia Panseri
- Institute of Science and Technology for Ceramics, National Research Council of Italy, via Granarolo 64, Faenza (RA), Italy.
| | - Emilia Naydenova
- University of Chemical Technology and Metallurgy, 8 Blvd. Kliment Ohridski, 1756, Sofia, Bulgaria.
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8
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Helical Foldamers and Stapled Peptides as New Modalities in Drug Discovery: Modulators of Protein-Protein Interactions. Processes (Basel) 2022. [DOI: 10.3390/pr10050924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A “foldamer” is an artificial oligomeric molecule with a regular secondary or tertiary structure consisting of various building blocks. A “stapled peptide” is a peptide with stabilized secondary structures, in particular, helical structures by intramolecular covalent side-chain cross-linking. Helical foldamers and stapled peptides are potential drug candidates that can target protein-protein interactions because they enable multipoint molecular recognition, which is difficult to achieve with low-molecular-weight compounds. This mini-review describes a variety of peptide-based foldamers and stapled peptides with a view to their applications in drug discovery, including our recent progress.
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9
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Hecht SM. Expansion of the Genetic Code Through the Use of Modified Bacterial Ribosomes. J Mol Biol 2022; 434:167211. [PMID: 34419431 PMCID: PMC9990327 DOI: 10.1016/j.jmb.2021.167211] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 11/29/2022]
Abstract
Biological protein synthesis is mediated by the ribosome, and employs ~20 proteinogenic amino acids as building blocks. Through the use of misacylated tRNAs, presently accessible by any of several strategies, it is now possible to employ in vitro and in vivo protein biosynthesis to elaborate proteins containing a much larger variety of amino acid building blocks. However, the incorporation of this broader variety of amino acids is limited to those species utilized by the ribosome. As a consequence, virtually all of the substrates utilized over time have been L-α-amino acids. In recent years, a variety of structural and biochemical studies have provided important insights into those regions of the 23S ribosomal RNA that are involved in peptide bond formation. Subsequent experiments, involving the randomization of key regions of 23S rRNA required for peptide bond formation, have afforded libraries of E. coli harboring plasmids with the rrnB gene modified in the key regions. Selections based on the use of modified puromycin derivatives with altered amino acids then identified clones uniquely sensitive to individual puromycin derivatives. These clones often recognized misacylated tRNAs containing altered amino acids similar to those in the modified puromycins, and incorporated the amino acid analogues into proteins. In this fashion, it has been possible to realize the synthesis of proteins containing D-amino acids, β-amino acids, phosphorylated amino acids, as well as long chain and cyclic amino acids in which the nucleophilic amino group is not in the α-position. Of special interest have been dipeptides and dipeptidomimetics of diverse utility.
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Affiliation(s)
- Sidney M Hecht
- Center for BioEnergetics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA.
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10
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Misra R, Rudnick-Glick S, Adler-Abramovich L. From Folding to Assembly: Functional Supramolecular Architectures of Peptides Comprised of Non-Canonical Amino Acids. Macromol Biosci 2021; 21:e2100090. [PMID: 34142442 DOI: 10.1002/mabi.202100090] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/06/2021] [Indexed: 12/27/2022]
Abstract
The engineering of biological molecules is the fundamental concept behind the design of complex materials with desirable functions. Over the last few decades, peptides and proteins have emerged as useful building blocks for well-defined nanostructures with controlled size and dimensions. Short peptides in particular have received much attention due to their inherent biocompatibility, lower synthetic cost, and ease of tunability. In addition to the diverse self-assembling properties of short peptides comprising coded amino acids and their emerging applications in nanotechnology, there is now growing interest in the properties of peptides composed of non-canonical amino acids. Such non-natural oligomers have been shown in recent years to form well-defined secondary structures similar to natural proteins, with the ability to self-assemble to generate a wide variety of nanostructures with excellent biostability. This review describes recent events in the development of supramolecular assemblies of peptides composed completely of non-coded amino acids and their hybrid analogues. Special attention is paid to understanding the supramolecular assemblies at the atomic level and to considering their potential applications in nanotechnology.
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Affiliation(s)
- Rajkumar Misra
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine and the Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Safra Rudnick-Glick
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine and the Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Lihi Adler-Abramovich
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine and the Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, 69978, Israel
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11
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Abstract
N,N'-linked oligoureas are a class of enantiopure, sequence-defined peptidomimetic oligomers without amino acids that form well-defined and predictable helical structures akin to the peptide α-helix. Oligourea-based foldamers combine a number of features-such as synthetic accessibility, sequence modularity, and folding fidelity-that bode well for their use in a range of applications from medicinal chemistry to catalysis. Moreover, it was recently recognized that this synthetic helical backbone can be combined with regular peptides to generate helically folded peptide-oligourea hybrids that display additional features in terms of helix mimicry and protein-surface recognition properties. Here we provide detailed protocols for the preparation of requested monomers and for the synthesis and purification of homo-oligoureas and peptide-oligourea hybrids.
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12
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Milbeo P, Martinez J, Amblard M, Calmès M, Legrand B. 1-Aminobicyclo[2.2.2]octane-2-carboxylic Acid and Derivatives As Chiral Constrained Bridged Scaffolds for Foldamers and Chiral Catalysts. Acc Chem Res 2021; 54:685-696. [PMID: 33464823 DOI: 10.1021/acs.accounts.0c00680] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The improvement of molecular diversity is one of the major concerns of chemists since the continuous development of original synthetic molecules provides unique scaffolds usable in organic and bioorganic chemistry. The challenge is to develop versatile platforms with highly controlled chemical three-dimensional space thanks to controlled chirality and conformational restraints. In this respect, cyclic β-amino acids are of great interest with applications in various fields of chemistry. In addition to their intrinsic biological properties, they are important precursors for the synthesis of new generations of bioactive compounds such as antibiotics, enzyme inhibitors, and antitumor agents. They have also been involved in asymmetric synthesis as efficient organo-catalysts in their free form and as derivatives. Finally, constrained cyclic β-amino acids have been incorporated into oligomers to successfully stabilize original structures in foldamer science with recent successes in health, material science, and catalysis. Over the last ∼10 years, we focused on bicyclic β-amino acids possessing a bicyclo[2.2.2]octane structure. This latter is a structural key element in numerous families of biologically active natural and synthetic products and is an interesting template for asymmetric synthesis. Nonetheless, reported studies on bicyclic carbo-bridged compounds are rather limited compared to those on bicyclic-fused and heterobridged derivatives. In this Account, we particularly focused on the synthesis and applications of the 1-aminobicyclo[2.2.2]octane-2-carboxylic acid, named, ABOC, and its derivatives. This highly constrained bicyclic β-amino acid, with a sterically hindered bridgehead primary amine and an endocyclic chiral center, displays drastically reduced conformational freedom. In addition, its high bulkiness strongly impacts the spatial orientation of the appended functionalities and the conformation of adjacent building blocks. Thus, we have first expanded a fundamental synthetic work by a wide ranging study in the field of foldamers, in the design of various stable peptide/peptidomimetic helical structures incorporating the ABOC residue (11/9-, 18/16-, 12/14/14-, and 12/10-helices). In addition, such bicyclic residue was fully compatible with and stabilized the canonical oligourea helix, whereas very few cyclic β-amino acids have been incorporated into oligoureas. In addition, we have pursued with the synthesis of some ABOC derivatives, in particular the 1,2-diaminobicyclo[2.2.2]octane chiral diamine, named DABO, and its investigation in chiral catalytic systems. Covalent organo-catalysis of the aldol reaction using ABOC-containing tripeptide catalysts provided a range of aldol products with high enantioselectivity. Moreover, the double reductive condensation of DABO with various aldehydes allowed the building of new chiral ligands that proved their efficiency in the copper-catalyzed asymmetric Henry reaction.
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Affiliation(s)
- Pierre Milbeo
- Institut des Biomolécules Max Mousseron, IBMM, University of Montpellier, ENSCM, CNRS, Montpellier, France
| | - Jean Martinez
- Institut des Biomolécules Max Mousseron, IBMM, University of Montpellier, ENSCM, CNRS, Montpellier, France
| | - Muriel Amblard
- Institut des Biomolécules Max Mousseron, IBMM, University of Montpellier, ENSCM, CNRS, Montpellier, France
| | - Monique Calmès
- Institut des Biomolécules Max Mousseron, IBMM, University of Montpellier, ENSCM, CNRS, Montpellier, France
| | - Baptiste Legrand
- Institut des Biomolécules Max Mousseron, IBMM, University of Montpellier, ENSCM, CNRS, Montpellier, France
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13
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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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14
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Covalent peptides and proteins for therapeutics. Bioorg Med Chem 2021; 29:115896. [DOI: 10.1016/j.bmc.2020.115896] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/19/2020] [Accepted: 11/21/2020] [Indexed: 12/11/2022]
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15
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Boto A, González CC, Hernández D, Romero-Estudillo I, Saavedra CJ. Site-selective modification of peptide backbones. Org Chem Front 2021. [DOI: 10.1039/d1qo00892g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Exciting developments in the site-selective modification of peptide backbones are allowing an outstanding fine-tuning of peptide conformation, folding ability, and physico-chemical and biological properties.
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Affiliation(s)
- Alicia Boto
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206-La Laguna, Tenerife, Spain
| | - Concepción C. González
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206-La Laguna, Tenerife, Spain
| | - Dácil Hernández
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206-La Laguna, Tenerife, Spain
| | - Iván Romero-Estudillo
- Centro de Investigaciones Químicas-IICBA, Universidad Autónoma del Estado de Morelos. Av. Universidad 1001, Cuernavaca, Morelos 62209, Mexico
- Catedrático CONACYT-CIQ-UAEM, Mexico
| | - Carlos J. Saavedra
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206-La Laguna, Tenerife, Spain
- Programa Agustín de Betancourt, Universidad de la Laguna, 38200 Tenerife, Spain
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16
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Zwillinger M, Reddy PS, Wicher B, Mandal PK, Csékei M, Fischer L, Kotschy A, Huc I. Aromatic Foldamer Helices as α-Helix Extended Surface Mimetics. Chemistry 2020; 26:17366-17370. [PMID: 32910480 PMCID: PMC7839445 DOI: 10.1002/chem.202004064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Indexed: 12/15/2022]
Abstract
Helically folded aromatic oligoamide foldamers have a size and geometrical parameters very distinct from those of α-helices and are not obvious candidates for α-helix mimicry. Nevertheless, they offer multiple sites for attaching side chains. It was found that some arrays of side chains at the surface of an aromatic helix make it possible to mimic extended α-helical surfaces. Synthetic methods were developed to produce quinoline monomers suitably functionalized for solid phase synthesis. A dodecamer was prepared. Its crystal structure validated the initial design and showed helix bundling involving the α-helix-like interface. These results open up new uses of aromatic helices to recognize protein surfaces and to program helix bundling in water.
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Affiliation(s)
- Márton Zwillinger
- Servier Research Institute of Medicinal ChemistryZáhony utca 7.Budapest1031Hungary
- Hevesy György PhD School of ChemistryEötvös Loránd UniversityBudapestHungary
| | - Post Sai Reddy
- CNRS, Bordeaux Institut National PolytechniqueCBMN (UMR 5248)IECBUniversité de Bordeaux2 rue Robert Escarpit33600PessacFrance
- Department of Pharmacy and Center for Integrated Protein ScienceLudwig-Maximilians-UniversitätButenandtstr. 5–1381377MünchenGermany
| | - Barbara Wicher
- Department of Chemical Technology of DrugsPoznan University of Medical SciencesGrunwaldzka 660780PoznanPoland
| | - Pradeep K. Mandal
- Department of Pharmacy and Center for Integrated Protein ScienceLudwig-Maximilians-UniversitätButenandtstr. 5–1381377MünchenGermany
| | - Márton Csékei
- Servier Research Institute of Medicinal ChemistryZáhony utca 7.Budapest1031Hungary
| | - Lucile Fischer
- CNRS, Bordeaux Institut National PolytechniqueCBMN (UMR 5248)IECBUniversité de Bordeaux2 rue Robert Escarpit33600PessacFrance
| | - András Kotschy
- Servier Research Institute of Medicinal ChemistryZáhony utca 7.Budapest1031Hungary
| | - Ivan Huc
- Department of Pharmacy and Center for Integrated Protein ScienceLudwig-Maximilians-UniversitätButenandtstr. 5–1381377MünchenGermany
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17
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Mehrotra N, Kharbanda S, Singh H. Peptide-based combination nanoformulations for cancer therapy. Nanomedicine (Lond) 2020; 15:2201-2217. [PMID: 32914691 DOI: 10.2217/nnm-2020-0220] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Research in cancer therapy is moving towards the use of biomolecules in combination with conventional approaches for improved disease outcome. Among the biomolecules explored, peptides are strong contenders due to their small size, high specificity, low systemic toxicity and wide inter/intracellular targets. The use of nanoformulations for such combination approaches can lead to further improvement in efficacy by reducing off-target cytotoxicity, increasing circulation time, tumor penetration and accumulation. This review focuses on nanodelivery systems for peptide-based combinations with chemo, immuno, radiation and hormone therapy. It gives an overview of the latest therapeutic research being conducted using combination nanoformulations with anticancer peptides, cell penetrating/tumor targeting peptides, peptide nanocarriers, peptidomimetics, peptide-based hormones and peptide vaccines. The challenges hindering clinical translation are also discussed.
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Affiliation(s)
- Neha Mehrotra
- Centre for Biomedical Engineering, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Surender Kharbanda
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Harpal Singh
- Centre for Biomedical Engineering, Indian Institute of Technology Delhi, New Delhi, 110016, India
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18
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Mantsyzov AB, Sokolov MN, Ivantcova PM, Bräse S, Polshakov VI, Kudryavtsev KV. Interplay of Pyrrolidine Units with Homo/Hetero Chirality and CF 3-Aryl Substituents on Secondary Structures of β-Proline Tripeptides in Solution. J Org Chem 2020; 85:8865-8871. [PMID: 32526142 DOI: 10.1021/acs.joc.0c00598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
All possible variants of β-proline functionalized tripeptides consisting of homo/hetero chiral monomeric all-cis 5-arylpyrrolidine-2,4-dicarboxylate units were synthesized for the first time by a nonpeptidic coupling method based on 1,3-dipolar cycloaddition chemistry of azomethine ylides. Secondary structures of β-proline tripeptides in solution were determined using the NMR spectroscopy data. o-(Trifluoromethyl)phenyl substituent contributes to stereoselectivity of 1,3-dipolar cycloaddition and structural features of β-proline tripeptides. A β-proline CF3-tripeptide with alternating absolute chirality between adjacent pyrrolidine units mimics natural PPII helix secondary structure.
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Affiliation(s)
- Alexey B Mantsyzov
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Lomonosovsky Ave 31/5, Moscow, 119992, Russian Federation
| | - Mikhail N Sokolov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russian Federation
| | - Polina M Ivantcova
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russian Federation
| | - Stefan Bräse
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, Karlsruhe, 76131, Germany.,Institute of Biological and Chemical Systems - Functional Molecular Systems, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen, D-76344, Germany
| | - Vladimir I Polshakov
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Lomonosovsky Ave 31/5, Moscow, 119992, Russian Federation
| | - Konstantin V Kudryavtsev
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russian Federation.,Pirogov Russian National Research Medical University, Ostrovityanova Street 1, 117997, Moscow, Russian Federation
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19
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Frenkel-Pinter M, Samanta M, Ashkenasy G, Leman LJ. Prebiotic Peptides: Molecular Hubs in the Origin of Life. Chem Rev 2020; 120:4707-4765. [PMID: 32101414 DOI: 10.1021/acs.chemrev.9b00664] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.
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Affiliation(s)
- Moran Frenkel-Pinter
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Mousumi Samanta
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Gonen Ashkenasy
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Luke J Leman
- NSF/NASA Center for Chemical Evolution, https://centerforchemicalevolution.com/.,Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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20
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Wacha A, Beke‐Somfai T, Nagy T. Improved Modeling of Peptidic Foldamers Using a Quantum Chemical Parametrization Based on Torsional Minimum Energy Path Matching. Chempluschem 2019; 84:927-941. [PMID: 31423411 PMCID: PMC6686720 DOI: 10.1002/cplu.201900180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 06/12/2019] [Indexed: 11/11/2022]
Abstract
The increasing interest in novel foldamer constructs demands an accurate computational treatment on an extensive timescale. However, it is still a challenge to derive a force field (FF) that can reproduce the experimentally known fold while also allowing the spontaneous exploration of other structures. Here, aiming at a realistic reproduction of backbone torsional barriers, the relevant proper dihedrals of acyclic β2-, β3- and β2,3-amino acids were added to the CHARMM FF and optimized using a novel, self-consistent iterative procedure based on quantum chemical relaxed scans. The new FF was validated by molecular dynamics simulations on three acyclic peptides. While they resided most of the time in their preferred fold (>80 % in helices and >50 % in hairpin), they also visited other conformations. Owing to the CHARMM36m-consistent parametrization, the proposed extension is suitable for exploring new foldamer structures and assemblies, and their interactions with diverse biomolecules.
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Affiliation(s)
- András Wacha
- Institute of Materials and Environmental Chemistry Research Centre for Natural SciencesHungarian Academy of SciencesH-1117Budapest, Magyar tudósok körútja 2Hungary
| | - Tamás Beke‐Somfai
- Institute of Materials and Environmental Chemistry Research Centre for Natural SciencesHungarian Academy of SciencesH-1117Budapest, Magyar tudósok körútja 2Hungary
| | - Tibor Nagy
- Institute of Materials and Environmental Chemistry Research Centre for Natural SciencesHungarian Academy of SciencesH-1117Budapest, Magyar tudósok körútja 2Hungary
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21
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Guarracino DA, Riordan JA, Barreto GM, Oldfield AL, Kouba CM, Agrinsoni D. Macrocyclic Control in Helix Mimetics. Chem Rev 2019; 119:9915-9949. [DOI: 10.1021/acs.chemrev.8b00623] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Danielle A. Guarracino
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
| | - Jacob A. Riordan
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
| | - Gianna M. Barreto
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
| | - Alexis L. Oldfield
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
| | - Christopher M. Kouba
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
| | - Desiree Agrinsoni
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
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22
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Dedkova LM, Hecht SM. Expanding the Scope of Protein Synthesis Using Modified Ribosomes. J Am Chem Soc 2019; 141:6430-6447. [PMID: 30901982 DOI: 10.1021/jacs.9b02109] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The ribosome produces all of the proteins and many of the peptides present in cells. As a macromolecular complex composed of both RNAs and proteins, it employs a constituent RNA to catalyze the formation of peptide bonds rapidly and with high fidelity. Thus, the ribosome can be argued to represent the key link between the RNA World, in which RNAs were the primary catalysts, and present biological systems in which protein catalysts predominate. In spite of the well-known phylogenetic conservation of rRNAs through evolutionary history, rRNAs can be altered readily when placed under suitable pressure, e.g. in the presence of antibiotics which bind to functionally critical regions of rRNAs. While the structures of rRNAs have been altered intentionally for decades to enable the study of their role(s) in the mechanism of peptide bond formation, it is remarkable that the purposeful alteration of rRNA structure to enable the elaboration of proteins and peptides containing noncanonical amino acids has occurred only recently. In this Perspective, we summarize the history of rRNA modifications, and demonstrate how the intentional modification of 23S rRNA in regions critical for peptide bond formation now enables the direct ribosomal incorporation of d-amino acids, β-amino acids, dipeptides and dipeptidomimetic analogues of the normal proteinogenic l-α-amino acids. While proteins containing metabolically important functional groups such as carbohydrates and phosphate groups are normally elaborated by the post-translational modification of nascent polypeptides, the use of modified ribosomes to produce such polymers directly is also discussed. Finally, we describe the elaboration of such modified proteins both in vitro and in bacterial cells, and suggest how such novel biomaterials may be exploited in future studies.
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Affiliation(s)
- Larisa M Dedkova
- Biodesign Center for BioEnergetics and School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics and School of Molecular Sciences , Arizona State University , Tempe , Arizona 85287 , United States
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23
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Olajos G, Hetényi A, Wéber E, Szögi T, Fülöp L, Martinek TA. Peripheral cyclic β-amino acids balance the stability and edge-protection of β-sandwiches. Org Biomol Chem 2019; 16:5492-5499. [PMID: 30024580 DOI: 10.1039/c8ob01322e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Engineering water-soluble stand-alone β-sandwich mimetics is a current challenge because of the difficulties associated with tailoring long-range interactions. In this work, single cis-(1R,2S)-2-aminocyclohexanecarboxylic acid mutations were introduced into the edge strands of the eight-stranded β-sandwich mimetic structures from the betabellin family. Temperature-dependent NMR and CD measurements, together with thermodynamic analyses, demonstrated that the modified peripheral strands exhibited an irregular and partially disordered structure but were able to exert sufficient shielding on the hydrophobic core to retain the predominantly β-sandwich structure. Although the frustrated interactions decreased the free energy of unfolding, the temperature of the maximum stabilities increased to or remained at physiologically relevant temperatures. We found that the irregular peripheral strands were able to prevent edge-to-edge association and fibril formation in the aggregation-prone model. These findings establish a β-sandwich stabilization and aggregation inhibition approach, which does not interfere with the pillars of the peptide bond or change the net charge of the peptide.
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Affiliation(s)
- Gábor Olajos
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research Group, University of Szeged, Somogyi u. 4., H-6720 Szeged, Hungary. and MTA-SZTE Biomimetic Systems Research Group, University of Szeged, Dóm ter 8., H-6720 Szeged, Hungary
| | - Anasztázia Hetényi
- Department of Medical Chemistry, University of Szeged, Dóm ter 8., H-6720 Szeged, Hungary
| | - Edit Wéber
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research Group, University of Szeged, Somogyi u. 4., H-6720 Szeged, Hungary.
| | - Titanilla Szögi
- Department of Medical Chemistry, University of Szeged, Dóm ter 8., H-6720 Szeged, Hungary
| | - Lívia Fülöp
- Department of Medical Chemistry, University of Szeged, Dóm ter 8., H-6720 Szeged, Hungary
| | - Tamás A Martinek
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research Group, University of Szeged, Somogyi u. 4., H-6720 Szeged, Hungary. and MTA-SZTE Biomimetic Systems Research Group, University of Szeged, Dóm ter 8., H-6720 Szeged, Hungary
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24
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Peptidomimetics: A Synthetic Tool for Inhibiting Protein–Protein Interactions in Cancer. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09831-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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25
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Zacharie B, Abbott SD, Baigent CB, Doyle C, Yalagala RS. An Efficient Two-Step Preparation of α-, β-, γ- or δ-Amino Acids from 2-Pyrazinones, 2-Hydroxypyrimidines or 2-Pyridones Respectively. European J Org Chem 2018. [DOI: 10.1002/ejoc.201801134] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Boulos Zacharie
- Prometic Biosciences Inc.; 500 boul. Cartier Ouest, Bureau 150 H7V 5B7 Laval Québec Canada
| | - Shaun D. Abbott
- Prometic Biosciences Inc.; 500 boul. Cartier Ouest, Bureau 150 H7V 5B7 Laval Québec Canada
| | - Christopher B. Baigent
- Prometic Biosciences Inc.; 500 boul. Cartier Ouest, Bureau 150 H7V 5B7 Laval Québec Canada
| | - Christopher Doyle
- Prometic Biosciences Inc.; 500 boul. Cartier Ouest, Bureau 150 H7V 5B7 Laval Québec Canada
| | - Ravi Shekar Yalagala
- Prometic Biosciences Inc.; 500 boul. Cartier Ouest, Bureau 150 H7V 5B7 Laval Québec Canada
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26
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Enhancing Aromatic Foldamer Helix Dynamics to Probe Interactions with Protein Surfaces. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800855] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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27
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Sussman F, Sánchez-Pedregal VM, Estévez JC, Balo R, Jiménez-Barbero J, Ardá A, Gimeno A, Royo M, Villaverde MC, Estévez RJ. Environmental Effects Determine the Structure of Potential β-Amino Acid Based Foldamers. Chemistry 2018; 24:10625-10629. [DOI: 10.1002/chem.201801953] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 05/24/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Fredy Sussman
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS); Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Víctor M. Sánchez-Pedregal
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS); Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Juan C. Estévez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS); Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Rosalino Balo
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS); Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Jesús Jiménez-Barbero
- Molecular Recognition & Host-Pathogen Interactions Unit; CIC bioGUNE; Bizkaia Technology Park, Building 801A 48170 Derio Spain
- Ikerbasque; Basque Foundation for Science; Maria Diaz de Haro 13 48009 Bilbao Spain
- Department of Organic Chemistry II, Faculty of Science & Technology; University of the Basque Country; 48940 Leioa Spain
| | - Ana Ardá
- Molecular Recognition & Host-Pathogen Interactions Unit; CIC bioGUNE; Bizkaia Technology Park, Building 801A 48170 Derio Spain
| | - Ana Gimeno
- Molecular Recognition & Host-Pathogen Interactions Unit; CIC bioGUNE; Bizkaia Technology Park, Building 801A 48170 Derio Spain
| | - Miriam Royo
- Combinatorial Chemistry Unit; Barcelona Science Park; Baldiri Reixac 10 08028 Barcelona Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN); Barcelona Science Park; Baldiri Reixac 10 08028 Barcelona Spain
| | - M. Carmen Villaverde
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS); Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Ramón J. Estévez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS); Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
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28
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Guarracino DA, Gentile K, Grossman A, Li E, Refai N, Mohnot J, King D. Salt-bridging effects on short amphiphilic helical structure and introducing sequence-based short beta-turn motifs. J Biomol Struct Dyn 2018; 36:475-485. [PMID: 28278764 DOI: 10.1080/07391102.2017.1286265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Determining the minimal sequence necessary to induce protein folding is beneficial in understanding the role of protein-protein interactions in biological systems, as their three-dimensional structures often dictate their activity. Proteins are generally comprised of discrete secondary structures, from α-helices to β-turns and larger β-sheets, each of which is influenced by its primary structure. Manipulating the sequence of short, moderately helical peptides can help elucidate the influences on folding. We created two new scaffolds based on a modestly helical eight-residue peptide, PT3, we previously published. Using circular dichroism (CD) spectroscopy and changing the possible salt-bridging residues to new combinations of Lys, Arg, Glu, and Asp, we found that our most helical improvements came from the Arg-Glu combination, whereas the Lys-Asp was not significantly different from the Lys-Glu of the parent scaffold, PT3. The marked 310-helical contributions in PT3 were lessened in the Arg-Glu-containing peptide with the beginning of cooperative unfolding seen through a thermal denaturation. However, a unique and unexpected signature was seen for the denaturation of the Lys-Asp peptide which could help elucidate the stages of folding between the 310 and α-helix. In addition, we developed a short six-residue peptide with β-turn/sheet CD signature, again to help study minimal sequences needed for folding. Overall, the results indicate that improvements made to short peptide scaffolds by fine-tuning the salt-bridging residues can enhance scaffold structure. Likewise, with the results from the new, short β-turn motif, these can help impact future peptidomimetic designs in creating biologically useful, short, structured β-sheet-forming peptides.
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Affiliation(s)
- Danielle A Guarracino
- a Department of Chemistry , The College of New Jersey , 2000 Pennington Road, Ewing , NJ , USA
| | - Kayla Gentile
- a Department of Chemistry , The College of New Jersey , 2000 Pennington Road, Ewing , NJ , USA
| | - Alec Grossman
- a Department of Chemistry , The College of New Jersey , 2000 Pennington Road, Ewing , NJ , USA
| | - Evan Li
- a Department of Chemistry , The College of New Jersey , 2000 Pennington Road, Ewing , NJ , USA
| | - Nader Refai
- a Department of Chemistry , The College of New Jersey , 2000 Pennington Road, Ewing , NJ , USA
| | - Joy Mohnot
- a Department of Chemistry , The College of New Jersey , 2000 Pennington Road, Ewing , NJ , USA
| | - Daniel King
- a Department of Chemistry , The College of New Jersey , 2000 Pennington Road, Ewing , NJ , USA
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29
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Zeng X, Wu P, Yao C, Liang J, Zhang S, Yin H. Small Molecule and Peptide Recognition of Protein Transmembrane Domains. Biochemistry 2017; 56:2076-2085. [DOI: 10.1021/acs.biochem.6b00909] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Xianfeng Zeng
- Center
of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100082, China
| | - Peiyao Wu
- Center
of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100082, China
| | - Chengbo Yao
- Center
of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100082, China
| | - Jiaqi Liang
- Center
of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100082, China
| | - Shuting Zhang
- Center
of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100082, China
- School
of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, China
| | - Hang Yin
- Center
of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100082, China
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30
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Teveroni E, Lucà R, Pellegrino M, Ciolli G, Pontecorvi A, Moretti F. Peptides and peptidomimetics in the p53/MDM2/MDM4 circuitry - a patent review. Expert Opin Ther Pat 2016; 26:1417-1429. [DOI: 10.1080/13543776.2017.1233179] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Emanuela Teveroni
- Institute of Cell Biology and Neurobiology, CNR, Roma, Italy
- Institute of Medical Pathology, Catholic University of Roma, Roma, Italy
| | - Rossella Lucà
- Institute of Cell Biology and Neurobiology, CNR, Roma, Italy
| | | | - Germana Ciolli
- Institute of Cell Biology and Neurobiology, CNR, Roma, Italy
- Institute of Medical Pathology, Catholic University of Roma, Roma, Italy
| | - Alfredo Pontecorvi
- Institute of Medical Pathology, Catholic University of Roma, Roma, Italy
| | - Fabiola Moretti
- Institute of Cell Biology and Neurobiology, CNR, Roma, Italy
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31
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Stone TA, Deber CM. Therapeutic design of peptide modulators of protein-protein interactions in membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1859:577-585. [PMID: 27580024 DOI: 10.1016/j.bbamem.2016.08.013] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 08/22/2016] [Accepted: 08/24/2016] [Indexed: 12/12/2022]
Abstract
Membrane proteins play the central roles in a variety of cellular processes, ranging from nutrient uptake and signalling, to cell-cell communication. Their biological functions are directly related to how they fold and assemble; defects often lead to disease. Protein-protein interactions (PPIs) within the membrane are therefore of great interest as therapeutic targets. Here we review the progress in the application of membrane-insertable peptides for the disruption or stabilization of membrane-based PPIs. We describe the design and preparation of transmembrane peptide mimics; and of several categories of peptidomimetics used for study, including d-enantiomers, non-natural amino acids, peptoids, and β-peptides. Further aspects of the review describe modifications to membrane-insertable peptides, including lipidation and cyclization via hydrocarbon stapling. These approaches provide a pathway toward the development of metabolically stable, non-toxic, and efficacious peptide modulators of membrane-based PPIs. This article is part of a Special Issue entitled: Lipid order/lipid defects and lipid-control of protein activity edited by Dirk Schneider.
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Affiliation(s)
- Tracy A Stone
- Division of Molecular Structure & Function, Research Institute, Hospital for Sick Children, Toronto M5G 0A4, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto M5S 1A8, Ontario, Canada
| | - Charles M Deber
- Division of Molecular Structure & Function, Research Institute, Hospital for Sick Children, Toronto M5G 0A4, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto M5S 1A8, Ontario, Canada.
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32
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Hu K, Geng H, Zhang Q, Liu Q, Xie M, Sun C, Li W, Lin H, Jiang F, Wang T, Wu YD, Li Z. An In-tether Chiral Center Modulates the Helicity, Cell Permeability, and Target Binding Affinity of a Peptide. Angew Chem Int Ed Engl 2016; 55:8013-7. [PMID: 27167181 DOI: 10.1002/anie.201602806] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Indexed: 11/11/2022]
Abstract
The addition of a precisely positioned chiral center in the tether of a constrained peptide is reported, yielding two separable peptide diastereomers with significantly different helicity, as supported by circular dichroism (CD) and NMR spectroscopy. Single crystal X-ray diffraction analysis suggests that the absolute configuration of the in-tether chiral center in helical form is R, which is in agreement with theoretical simulations. The relationship between the secondary structure of the short peptides and their biochemical/biophysical properties remains elusive, largely because of the lack of proper controls. The present strategy provides the only method for investigating the influence of solely conformational differences upon the biochemical/biophysical properties of peptides. The significant differences in permeability and target binding affinity between the peptide diastereomers demonstrate the importance of helical conformation.
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Affiliation(s)
- Kuan Hu
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Hao Geng
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Qingzhou Zhang
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Qisong Liu
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Mingsheng Xie
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Chengjie Sun
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Wenjun Li
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Huacan Lin
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Fan Jiang
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Tao Wang
- Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Yun-Dong Wu
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
| | - Zigang Li
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
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33
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Hu K, Geng H, Zhang Q, Liu Q, Xie M, Sun C, Li W, Lin H, Jiang F, Wang T, Wu YD, Li Z. An In-tether Chiral Center Modulates the Helicity, Cell Permeability, and Target Binding Affinity of a Peptide. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602806] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kuan Hu
- School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Hao Geng
- School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Qingzhou Zhang
- School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Qisong Liu
- School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Mingsheng Xie
- School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Chengjie Sun
- School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Wenjun Li
- School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Huacan Lin
- School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Fan Jiang
- School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Tao Wang
- Department of Biology; Southern University of Science and Technology; Shenzhen 518055 China
| | - Yun-Dong Wu
- School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Zigang Li
- School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
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34
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Abstract
The majority of therapeutics target membrane proteins, accessible on the surface of cells, to alter cellular signaling. Cells use membrane proteins to transduce signals into cells, transport ions and molecules, bind cells to a surface or substrate, and catalyze reactions. Newly devised technologies allow us to drug conventionally "undruggable" regions of membrane proteins, enabling modulation of protein-protein, protein-lipid, and protein-nucleic acid interactions. In this review, we survey the state of the art of high-throughput screening and rational design in drug discovery, and we evaluate the advances in biological understanding and technological capacity that will drive pharmacotherapy forward against unorthodox membrane protein targets.
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Affiliation(s)
- Hang Yin
- Department of Chemistry and Biochemistry.,BioFrontiers Institute, and.,Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100082, China
| | - Aaron D Flynn
- BioFrontiers Institute, and.,Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309; ,
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35
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Archer RM, Hutchby M, Winn CL, Fossey JS, Bull SD. A chiral ligand mediated aza-conjugate addition strategy for the enantioselective synthesis of β-amino esters that contain hydrogenolytically sensitive functionality. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.08.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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36
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A novel microtubule de-stabilizing complementarity-determining region C36L1 peptide displays antitumor activity against melanoma in vitro and in vivo. Sci Rep 2015; 5:14310. [PMID: 26391685 PMCID: PMC4585759 DOI: 10.1038/srep14310] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 08/24/2015] [Indexed: 12/22/2022] Open
Abstract
Short peptide sequences from complementarity-determining regions (CDRs) of different immunoglobulins may exert anti-infective, immunomodulatory and antitumor activities regardless of the specificity of the original monoclonal antibody (mAb). In this sense, they resemble early molecules of innate immunity. C36L1 was identified as a bioactive light-chain CDR1 peptide by screening 19 conserved CDR sequences targeting murine B16F10-Nex2 melanoma. The 17-amino acid peptide is readily taken up by melanoma cells and acts on microtubules causing depolymerization, stress of the endoplasmic reticulum and intrinsic apoptosis. At low concentrations, C36L1 inhibited migration, invasion and proliferation of B16F10-Nex2 cells with cell cycle arrest at G2/M phase, by regulating the PI3K/Akt signaling axis involving Rho-GTPase and PTEN mediation. Peritumor injection of the peptide delayed growth of subcutaneously grafted melanoma cells. Intraperitoneal administration of C36L1 induced a significant immune-response dependent anti-tumor protection in a syngeneic metastatic melanoma model. Dendritic cells stimulated ex-vivo by the peptide and transferred to animals challenged with tumor cells were equally effective. The C36 VL CDR1 peptide is a promising microtubule-interacting drug that induces tumor cell death by apoptosis and inhibits metastases of highly aggressive melanoma cells.
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37
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Pelay-Gimeno M, Glas A, Koch O, Grossmann TN. Structure-Based Design of Inhibitors of Protein-Protein Interactions: Mimicking Peptide Binding Epitopes. Angew Chem Int Ed Engl 2015; 54:8896-927. [PMID: 26119925 PMCID: PMC4557054 DOI: 10.1002/anie.201412070] [Citation(s) in RCA: 496] [Impact Index Per Article: 55.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Indexed: 12/15/2022]
Abstract
Protein-protein interactions (PPIs) are involved at all levels of cellular organization, thus making the development of PPI inhibitors extremely valuable. The identification of selective inhibitors is challenging because of the shallow and extended nature of PPI interfaces. Inhibitors can be obtained by mimicking peptide binding epitopes in their bioactive conformation. For this purpose, several strategies have been evolved to enable a projection of side chain functionalities in analogy to peptide secondary structures, thereby yielding molecules that are generally referred to as peptidomimetics. Herein, we introduce a new classification of peptidomimetics (classes A-D) that enables a clear assignment of available approaches. Based on this classification, the Review summarizes strategies that have been applied for the structure-based design of PPI inhibitors through stabilizing or mimicking turns, β-sheets, and helices.
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Affiliation(s)
- Marta Pelay-Gimeno
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
| | - Adrian Glas
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
| | - Oliver Koch
- TU Dortmund University, Department of Chemistry and Chemical BiologyOtto-Hahn-Strasse 6, 44227 Dortmund (Germany)
| | - Tom N Grossmann
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
- TU Dortmund University, Department of Chemistry and Chemical BiologyOtto-Hahn-Strasse 6, 44227 Dortmund (Germany)
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38
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Pelay-Gimeno M, Glas A, Koch O, Grossmann TN. Strukturbasierte Entwicklung von Protein-Protein-Interaktionsinhibitoren: Stabilisierung und Nachahmung von Peptidliganden. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201412070] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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39
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Maini R, Chowdhury SR, Dedkova LM, Roy B, Daskalova SM, Paul R, Chen S, Hecht SM. Protein Synthesis with Ribosomes Selected for the Incorporation of β-Amino Acids. Biochemistry 2015; 54:3694-706. [PMID: 25982410 PMCID: PMC4472090 DOI: 10.1021/acs.biochem.5b00389] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 05/16/2015] [Indexed: 02/04/2023]
Abstract
In an earlier study, β³-puromycin was used for the selection of modified ribosomes, which were utilized for the incorporation of five different β-amino acids into Escherichia coli dihydrofolate reductase (DHFR). The selected ribosomes were able to incorporate structurally disparate β-amino acids into DHFR, in spite of the use of a single puromycin for the selection of the individual clones. In this study, we examine the extent to which the structure of the β³-puromycin employed for ribosome selection influences the regio- and stereochemical preferences of the modified ribosomes during protein synthesis; the mechanistic probe was a single suppressor tRNA(CUA) activated with each of four methyl-β-alanine isomers (1-4). The modified ribosomes were found to incorporate each of the four isomeric methyl-β-alanines into DHFR but exhibited a preference for incorporation of 3(S)-methyl-β-alanine (β-mAla; 4), i.e., the isomer having the same regio- and stereochemistry as the O-methylated β-tyrosine moiety of β³-puromycin. Also conducted were a selection of clones that are responsive to β²-puromycin and a demonstration of reversal of the regio- and stereochemical preferences of these clones during protein synthesis. These results were incorporated into a structural model of the modified regions of 23S rRNA, which included in silico prediction of a H-bonding network. Finally, it was demonstrated that incorporation of 3(S)-methyl-β-alanine (β-mAla; 4) into a short α-helical region of the nucleic acid binding domain of hnRNP LL significantly stabilized the helix without affecting its DNA binding properties.
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MESH Headings
- Alanine/analogs & derivatives
- Alanine/chemistry
- Alanine/metabolism
- Escherichia coli/enzymology
- Escherichia coli/metabolism
- Escherichia coli Proteins/biosynthesis
- Escherichia coli Proteins/chemistry
- Heterogeneous-Nuclear Ribonucleoprotein L/biosynthesis
- Heterogeneous-Nuclear Ribonucleoprotein L/chemistry
- Heterogeneous-Nuclear Ribonucleoprotein L/genetics
- Humans
- Hydrogen Bonding
- Models, Molecular
- Molecular Dynamics Simulation
- Mutant Proteins/biosynthesis
- Mutant Proteins/chemistry
- Mutant Proteins/genetics
- Nucleotide Motifs
- Peptidyl Transferases/genetics
- Peptidyl Transferases/metabolism
- Protein Conformation
- Protein Stability
- Puromycin/analogs & derivatives
- Puromycin/chemistry
- Puromycin/metabolism
- RNA, Bacterial/chemistry
- RNA, Bacterial/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/metabolism
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/metabolism
- Recombinant Proteins/biosynthesis
- Recombinant Proteins/chemistry
- Ribosomes/metabolism
- Stereoisomerism
- Substrate Specificity
- Tetrahydrofolate Dehydrogenase/biosynthesis
- Tetrahydrofolate Dehydrogenase/chemistry
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Affiliation(s)
- Rumit Maini
- Center for BioEnergetics,
Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Sandipan Roy Chowdhury
- Center for BioEnergetics,
Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Larisa M. Dedkova
- Center for BioEnergetics,
Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Basab Roy
- Center for BioEnergetics,
Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Sasha M. Daskalova
- Center for BioEnergetics,
Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Rakesh Paul
- Center for BioEnergetics,
Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Shengxi Chen
- Center for BioEnergetics,
Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Sidney M. Hecht
- Center for BioEnergetics,
Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
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40
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Pawar NJ, Diederichsen U, Dhavale DD. Multivalent presentation of carbohydrates by 314-helical peptide templates: synthesis, conformational analysis using CD spectroscopy and saccharide recognition. Org Biomol Chem 2015; 13:11278-85. [DOI: 10.1039/c5ob01673h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A tetrameric glycoconjugate template, SSFT 1, was coupled with a variety of six aminooxy sugars to achieve multivalent glycoconjugates 2–7.
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Affiliation(s)
- Nitin J. Pawar
- Department of Chemistry
- Garware Research Centre
- Savitribai Phule Pune University (Formerly University of Pune)
- Pune - 411 007
- India
| | - Ulf Diederichsen
- Institute of Organic and Biomolecular Chemistry
- Georg-August University Göttingen
- D-37077 Göttingen
- Germany
| | - Dilip. D. Dhavale
- Department of Chemistry
- Garware Research Centre
- Savitribai Phule Pune University (Formerly University of Pune)
- Pune - 411 007
- India
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41
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Miller J, Melicher MS, Schepartz A. Positive allostery in metal ion binding by a cooperatively folded β-peptide bundle. J Am Chem Soc 2014; 136:14726-9. [PMID: 25290247 PMCID: PMC4210112 DOI: 10.1021/ja508872q] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Indexed: 01/19/2023]
Abstract
Metal ion binding is exploited by proteins in nature to catalyze reactions, bind molecules, and favor discrete structures, but it has not been demonstrated in β-peptides or their assemblies. Here we report the design, synthesis, and characterization of a β-peptide bundle that uniquely binds two Cd(II) ions in a distinct bicoordinate array. The two Cd(II) ions bind with positive allosteric cooperativity and increase the thermodynamic stability of the bundle by more than 50 °C. This system provides a unique, synthetic context to explore allosteric regulation and should pave the way to sophisticated molecular assemblies with catalytic and substrate-sensing functions that have historically not been available to de novo designed synthetic proteomimetics in water.
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Affiliation(s)
- Jonathan
P. Miller
- Department
of Chemistry and Department of Molecular, Cellular and Developmental
Biology, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Michael S. Melicher
- Department
of Chemistry and Department of Molecular, Cellular and Developmental
Biology, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Alanna Schepartz
- Department
of Chemistry and Department of Molecular, Cellular and Developmental
Biology, Yale University, New Haven, Connecticut 06520-8107, United States
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42
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Mayer C, Müller MM, Gellman SH, Hilvert D. Building Proficient Enzymes with Foldamer Prostheses. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201400945] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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43
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Mayer C, Müller MM, Gellman SH, Hilvert D. Building proficient enzymes with foldamer prostheses. Angew Chem Int Ed Engl 2014; 53:6978-81. [PMID: 24828837 DOI: 10.1002/anie.201400945] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Indexed: 01/28/2023]
Abstract
Foldamers are non-natural oligomers that adopt stable conformations reminiscent of those found in proteins. To evaluate the potential of foldameric subunits for catalysis, semisynthetic enzymes containing foldamer fragments constructed from α- and β-amino acid residues were designed and characterized. Systematic variation of the α→β substitution pattern and types of β-residue afforded highly proficient hybrid catalysts, thus demonstrating the feasibility of expanding the enzyme-engineering toolkit with non-natural backbones.
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Affiliation(s)
- Clemens Mayer
- Laboratory of Organic Chemistry, ETH Zürich, Hönggerberg HCI F339, 8093 Zürich (Switzerland)
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44
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Wang PSP, Nguyen JB, Schepartz A. Design and high-resolution structure of a β³-peptide bundle catalyst. J Am Chem Soc 2014; 136:6810-3. [PMID: 24802883 DOI: 10.1021/ja5013849] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Despite the widespread exploration of α-peptides as catalysts, there are few examples of β-peptides that alter the course of a chemical transformation. Our previous work demonstrated that a special class of β(3)-peptides spontaneously self-assembles in water into discrete protein-like bundles possessing unique quaternary structures and exceptional thermodynamic stability. Here we describe a series of β(3)-peptide bundles capable of both substrate binding and chemical catalysis--ester hydrolysis. A combination of kinetic and high-resolution structural analysis suggests an active site triad composed of residues from at least two strands of the octameric bundle structure.
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Affiliation(s)
- Pam S P Wang
- Department of Chemistry and ‡Department of Molecular, Cellular and Developmental Biology, Yale University , New Haven, Connecticut 06520-8107, United States
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45
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Pawar NJ, Sidhu NS, Sheldrick GM, Dhavale DD, Diederichsen U. Molecular architecture with carbohydrate functionalized β-peptides adopting 314-helical conformation. Beilstein J Org Chem 2014; 10:948-55. [PMID: 24991244 PMCID: PMC4077383 DOI: 10.3762/bjoc.10.93] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Accepted: 03/31/2014] [Indexed: 12/14/2022] Open
Abstract
Carbohydrate recognition is essential in cellular interactions and biological processes. It is characterized by structural diversity, multivalency and cooperative effects. To evaluate carbohydrate interaction and recognition, the structurally defined attachment of sugar units to a rigid template is highly desired. β-Peptide helices offer conformationally stable templates for the linear presentation of sugar units in defined distances. The synthesis and β-peptide incorporation of sugar-β-amino acids are described providing the saccharide units as amino acid side chain. The respective sugar-β-amino acids are accessible by Michael addition of ammonia to sugar units derivatized as α,β-unsaturated esters. Three sugar units were incorporated in β-peptide oligomers varying the sugar (glucose, galactose, xylose) and sugar protecting groups. The influence of sugar units and the configuration of sugar-β-amino acids on β-peptide secondary structure were investigated by CD spectroscopy.
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Affiliation(s)
- Nitin J Pawar
- Institute for Organic and Biomolecular Chemistry, Georg-August University Göttingen, Tammannstrasse 2, D-37077 Göttingen, Germany
- Department of Chemistry, Garware Research Centre, University of Pune, Pune 411 007, India
| | - Navdeep S Sidhu
- Institute for Inorganic Chemistry, Georg-August University Göttingen, Tammannstraße 4, D-37077 Göttingen, Germany
| | - George M Sheldrick
- Institute for Inorganic Chemistry, Georg-August University Göttingen, Tammannstraße 4, D-37077 Göttingen, Germany
| | - Dilip D Dhavale
- Department of Chemistry, Garware Research Centre, University of Pune, Pune 411 007, India
| | - Ulf Diederichsen
- Institute for Organic and Biomolecular Chemistry, Georg-August University Göttingen, Tammannstrasse 2, D-37077 Göttingen, Germany
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46
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Milroy LG, Grossmann TN, Hennig S, Brunsveld L, Ottmann C. Modulators of Protein–Protein Interactions. Chem Rev 2014; 114:4695-748. [DOI: 10.1021/cr400698c] [Citation(s) in RCA: 352] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Lech-Gustav Milroy
- Laboratory
of Chemical Biology and Institute of Complex Molecular Systems, Department
of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech
2, 5612 AZ Eindhoven, The Netherlands
| | - Tom N. Grossmann
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn Straße 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Sven Hennig
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn Straße 15, 44227 Dortmund, Germany
| | - Luc Brunsveld
- Laboratory
of Chemical Biology and Institute of Complex Molecular Systems, Department
of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech
2, 5612 AZ Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory
of Chemical Biology and Institute of Complex Molecular Systems, Department
of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech
2, 5612 AZ Eindhoven, The Netherlands
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47
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Guarracino DA, Alabanza AM, Robertson CT, Sanghvi SS. The role of primary sequence in helical control compared across shortα- andβ3-peptides. J Biomol Struct Dyn 2014; 33:597-605. [DOI: 10.1080/07391102.2014.897260] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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48
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Nanaware PP, Ramteke MP, Somavarapu AK, Venkatraman P. Discovery of multiple interacting partners of gankyrin, a proteasomal chaperone and an oncoprotein--evidence for a common hot spot site at the interface and its functional relevance. Proteins 2014; 82:1283-300. [PMID: 24338975 DOI: 10.1002/prot.24494] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 11/20/2013] [Accepted: 12/09/2013] [Indexed: 12/27/2022]
Abstract
Gankyrin, a non-ATPase component of the proteasome and a chaperone of proteasome assembly, is also an oncoprotein. Gankyrin regulates a variety of oncogenic signaling pathways in cancer cells and accelerates degradation of tumor suppressor proteins p53 and Rb. Therefore gankyrin may be a unique hub integrating signaling networks with the degradation pathway. To identify new interactions that may be crucial in consolidating its role as an oncogenic hub, crystal structure of gankyrin-proteasome ATPase complex was used to predict novel interacting partners. EEVD, a four amino acid linear sequence seems a hot spot site at this interface. By searching for EEVD in exposed regions of human proteins in PDB database, we predicted 34 novel interactions. Eight proteins were tested and seven of them were found to interact with gankyrin. Affinity of four interactions is high enough for endogenous detection. Others require gankyrin overexpression in HEK 293 cells or occur endogenously in breast cancer cell line- MDA-MB-435, reflecting lower affinity or presence of a deregulated network. Mutagenesis and peptide inhibition confirm that EEVD is the common hot spot site at these interfaces and therefore a potential polypharmacological drug target. In MDA-MB-231 cells in which the endogenous CLIC1 is silenced, trans-expression of Wt protein (CLIC1_EEVD) and not the hot spot site mutant (CLIC1_AAVA) resulted in significant rescue of the migratory potential. Our approach can be extended to identify novel functionally relevant protein-protein interactions, in expansion of oncogenic networks and in identifying potential therapeutic targets.
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Affiliation(s)
- Padma P Nanaware
- Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India
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49
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Lim Z, Duggan PJ, Meyer AG, Tuck KL. An iterative in silico and modular synthetic approach to aqueous soluble tercyclic α-helix mimetics. Org Biomol Chem 2014; 12:4432-44. [DOI: 10.1039/c4ob00647j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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50
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Avan I, Hall CD, Katritzky AR. Peptidomimetics via modifications of amino acids and peptide bonds. Chem Soc Rev 2014; 43:3575-94. [DOI: 10.1039/c3cs60384a] [Citation(s) in RCA: 183] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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