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Ye L, Ajuyo NMC, Wu Z, Yuan N, Xiao Z, Gu W, Zhao J, Pei Y, Min Y, Wang D. Molecular Integrative Study on Inhibitory Effects of Pentapeptides on Polymerization and Cell Toxicity of Amyloid-β Peptide (1-42). Curr Issues Mol Biol 2024; 46:10160-10179. [PMID: 39329958 PMCID: PMC11431437 DOI: 10.3390/cimb46090606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Revised: 09/07/2024] [Accepted: 09/11/2024] [Indexed: 09/28/2024] Open
Abstract
Alzheimer's Disease (AD) is a multifaceted neurodegenerative disease predominantly defined by the extracellular accumulation of amyloid-β (Aβ) peptide. In light of this, in the past decade, several clinical approaches have been used aiming at developing peptides for therapeutic use in AD. The use of cationic arginine-rich peptides (CARPs) in targeting protein aggregations has been on the rise. Also, the process of peptide development employing computational approaches has attracted a lot of attention recently. Using a structure database containing pentapeptides made from 20 L-α amino acids, we employed molecular docking to sort pentapeptides that can bind to Aβ42, then performed molecular dynamics (MD) analyses, including analysis of the binding stability, interaction energy, and binding free energy to screen ligands. Transmission electron microscopy (TEM), circular dichroism (CD), thioflavin T (ThT) fluorescence detection of Aβ42 polymerization, MTT (3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide) assay, and the flow cytometry of reactive oxygen species (ROS) were carried out to evaluate the influence of pentapeptides on the aggregation and cell toxicity of Aβ42. Two pentapeptides (TRRRR and ARRGR) were found to have strong effects on inhibiting the aggregation of Aβ42 and reducing the toxicity of Aβ42 secreted by SH-SY5Y cells, including cell death, reactive oxygen species (ROS) production, and apoptosis.
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Affiliation(s)
- Lianmeng Ye
- Key Laboratory of Tropical Biological Resources of the Ministry of Education of China, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, One Health Cooperative Innovation Center, Hainan University, Haikou 570228, China
- Department of Biotechnology, School of Life and Health Sciences, Hainan University, Haikou 570228, China
| | - Nuela Manka'a Che Ajuyo
- Key Laboratory of Tropical Biological Resources of the Ministry of Education of China, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, One Health Cooperative Innovation Center, Hainan University, Haikou 570228, China
| | - Zhongyun Wu
- Key Laboratory of Tropical Biological Resources of the Ministry of Education of China, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, One Health Cooperative Innovation Center, Hainan University, Haikou 570228, China
- Department of Biotechnology, School of Life and Health Sciences, Hainan University, Haikou 570228, China
| | - Nan Yuan
- Key Laboratory of Tropical Biological Resources of the Ministry of Education of China, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, One Health Cooperative Innovation Center, Hainan University, Haikou 570228, China
- Department of Biotechnology, School of Life and Health Sciences, Hainan University, Haikou 570228, China
| | - Zhengpan Xiao
- Key Laboratory of Tropical Biological Resources of the Ministry of Education of China, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, One Health Cooperative Innovation Center, Hainan University, Haikou 570228, China
- Department of Biotechnology, School of Life and Health Sciences, Hainan University, Haikou 570228, China
| | - Wenyu Gu
- Key Laboratory of Tropical Biological Resources of the Ministry of Education of China, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, One Health Cooperative Innovation Center, Hainan University, Haikou 570228, China
- Department of Biotechnology, School of Life and Health Sciences, Hainan University, Haikou 570228, China
| | - Jiazheng Zhao
- Key Laboratory of Tropical Biological Resources of the Ministry of Education of China, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, One Health Cooperative Innovation Center, Hainan University, Haikou 570228, China
- Department of Biotechnology, School of Life and Health Sciences, Hainan University, Haikou 570228, China
| | - Yechun Pei
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, One Health Cooperative Innovation Center, Hainan University, Haikou 570228, China
- Department of Biotechnology, School of Life and Health Sciences, Hainan University, Haikou 570228, China
| | - Yi Min
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, One Health Cooperative Innovation Center, Hainan University, Haikou 570228, China
- Department of Biotechnology, School of Life and Health Sciences, Hainan University, Haikou 570228, China
| | - Dayong Wang
- Key Laboratory of Tropical Biological Resources of the Ministry of Education of China, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, One Health Cooperative Innovation Center, Hainan University, Haikou 570228, China
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Roytrakul S, Jaresitthikunchai J, Phaonakrop N, Charoenlappanit S, Thaisakun S, Kumsri N, Arpornsuwan T. Secretomic changes of amyloid beta peptides on Alzheimer's disease related proteins in differentiated human SH-SY5Y neuroblastoma cells. PeerJ 2024; 12:e17732. [PMID: 39035166 PMCID: PMC11260076 DOI: 10.7717/peerj.17732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/21/2024] [Indexed: 07/23/2024] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease that causes physical damage to neuronal connections, leading to brain atrophy. This disruption of synaptic connections results in mild to severe cognitive impairments. Unfortunately, no effective treatment is currently known to prevent or reverse the symptoms of AD. The aim of this study was to investigate the effects of three synthetic peptides, i.e., KLVFF, RGKLVFFGR and RIIGL, on an AD in vitro model represented by differentiated SH-SY5Y neuroblastoma cells exposed to retinoic acid (RA) and brain-derived neurotrophic factor (BDNF). The results demonstrated that RIIGL peptide had the least significant cytotoxic activity to normal SH-SY5Y while exerting high cytotoxicity against the differentiated cells. The mechanism of RIIGL peptide in the differentiated SH-SY5Y was investigated based on changes in secretory proteins compared to another two peptides. A total of 380 proteins were identified, and five of them were significantly detected after treatment with RIIGL peptide. These secretory proteins were found to be related to microtubule-associated protein tau (MAPT) and amyloid-beta precursor protein (APP). RIIGL peptide acts on differentiated SH-SY5Y by regulating amyloid-beta formation, neuron apoptotic process, ceramide catabolic process, and oxidative phosphorylation and thus has the potentials to treat AD.
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Affiliation(s)
- Sittiruk Roytrakul
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand
| | - Janthima Jaresitthikunchai
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand
| | - Narumon Phaonakrop
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand
| | - Sawanya Charoenlappanit
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand
| | - Siriwan Thaisakun
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand
| | - Nitithorn Kumsri
- Undergraduate Student of Department of Medical Technology, Faculty of Allied Health Sciences, Thammasat University, Pathumtani, Thailand
| | - Teerakul Arpornsuwan
- Medical Technology Research and Service Unit, Health Care Service Center, Faculty of Allied Health Sciences, Thammasat University, Pathumthani, Thailand
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3
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Malhis M, Funke SA. Mirror-Image Phage Display for the Selection of D-Amino Acid Peptide Ligands as Potential Therapeutics. Curr Protoc 2024; 4:e957. [PMID: 38372457 DOI: 10.1002/cpz1.957] [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] [Indexed: 02/20/2024]
Abstract
In neurodegenerative diseases like Alzheimer's disease (AD), endogenous proteins or peptides aggregate with themselves. These proteins may lose their function or aggregates and/or oligomers can obtain toxicity, causing injury or death to cells. Aggregation of two major proteins characterizes AD. Amyloid-β peptide (Aβ) is deposited in amyloid plaques within the extracellular space of the brain and Tau in so-called neurofibrillary tangles in neurons. Finding peptide ligands to halt protein aggregation is a promising therapeutical approach. Using mirror-image phage display with a commercially available, randomized 12-mer peptide library, we have selected D-amino acid peptides, which bind to the Tau protein and modulate its aggregation in vitro. Peptides can bind specifically and selectively to a target molecule, but natural L-amino acid peptides may have crucial disadvantages for in vivo applications, as they are sensitive to protease degradation and may elicit immune responses. One strategy to circumvent these disadvantages is the use of non-naturally occurring D-amino acid peptides as they exhibit increased protease resistance and generally do not activate the immune system. To perform mirror-image phage display, the target protein needs to be synthesized as D-amino acid version. If the target protein sequence is too long to be synthesized properly, smaller peptides derived from the full length protein can be used for the selection process. This also offers the possibility to influence the binding region of the selected D-peptides in the full-length target protein. Here we provide the protocols for mirror-image phage display selection on the PHF6* peptide of Tau, based on the commercially available Ph.D.™-12 Phage Display Peptide Library Kit, leading to D-peptides that also bind the full length Tau protein (Tau441), next to PHF6*. In addition, we provide protocols and data for the first characterization of those D-peptides that inhibit Tau aggregation in vitro. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Mirror image phage display selection against D-PHF6* fibrils Support Protocol 1: Single phage ELISA Basic Protocol 2: Sequencing and D-peptide generation Basic Protocol 3: Thioflavin-T (ThT) test to control inhibition of Tau aggregation Support Protocol 2: Purification of full-length Tau protein Basic Protocol 4: ELISA to demonstrate the binding of the generated D-peptides to PHF6* and full-length Tau fibrils.
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Affiliation(s)
- Marwa Malhis
- Institut für Bioanalytik, Hochschule für Angewandte Wissenschaften, Coburg, Germany
| | - Susanne Aileen Funke
- Institut für Bioanalytik, Hochschule für Angewandte Wissenschaften, Coburg, Germany
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Yuan N, Ye L, Sun Y, Wu H, Xiao Z, Fu W, Chen Z, Pei Y, Min Y, Wang D. Molecular Integrative Analysis of the Inhibitory Effects of Dipeptides on Amyloid β Peptide 1-42 Polymerization. Int J Mol Sci 2023; 24:7673. [PMID: 37108834 PMCID: PMC10141046 DOI: 10.3390/ijms24087673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/02/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
The major pathological feature of Alzheimer's disease (AD) is the aggregation of amyloid β peptide (Aβ) in the brain. Inhibition of Aβ42 aggregation may prevent the advancement of AD. This study employed molecular dynamics, molecular docking, electron microscopy, circular dichroism, staining of aggregated Aβ with ThT, cell viability, and flow cytometry for the detection of reactive oxygen species (ROS) and apoptosis. Aβ42 polymerizes into fibrils due to hydrophobic interactions to minimize free energy, adopting a β-strand structure and forming three hydrophobic areas. Eight dipeptides were screened by molecular docking from a structural database of 20 L-α-amino acids, and the docking was validated by molecular dynamics (MD) analysis of binding stability and interaction potential energy. Among the dipeptides, arginine dipeptide (RR) inhibited Aβ42 aggregation the most. The ThT assay and EM revealed that RR reduced Aβ42 aggregation, whereas the circular dichroism spectroscopy analysis showed a 62.8% decrease in β-sheet conformation and a 39.3% increase in random coiling of Aβ42 in the presence of RR. RR also significantly reduced the toxicity of Aβ42 secreted by SH-SY5Y cells, including cell death, ROS production, and apoptosis. The formation of three hydrophobic regions and polymerization of Aβ42 reduced the Gibbs free energy, and RR was the most effective dipeptide at interfering with polymerization.
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Affiliation(s)
- Nan Yuan
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Lianmeng Ye
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Yan Sun
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Hao Wu
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Zhengpan Xiao
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Wanmeng Fu
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Zuqian Chen
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Yechun Pei
- One Health Cooperative Innovation Center, Hainan University, Haikou 570228, China
- Department of Biosciences, School of Life Sciences, Hainan University, Haikou 570228, China
| | - Yi Min
- Department of Biosciences, School of Life Sciences, Hainan University, Haikou 570228, China
| | - Dayong Wang
- Laboratory of Biopharmaceuticals and Molecular Pharmacology, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
- One Health Cooperative Innovation Center, Hainan University, Haikou 570228, China
- Key Laboratory of Tropical Biological Resources of the Ministry of China, Hainan University, Haikou 570228, China
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Aillaud I, Funke SA. Tau Aggregation Inhibiting Peptides as Potential Therapeutics for Alzheimer Disease. Cell Mol Neurobiol 2023; 43:951-961. [PMID: 35596819 PMCID: PMC10006036 DOI: 10.1007/s10571-022-01230-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/05/2022] [Indexed: 11/30/2022]
Abstract
Alzheimer disease (AD) is the most common progressive neurodegenerative disorder. AD causes enormous personal and economic burden to society as currently only limited palliative therapeutic options are available. The pathological hallmarks of the disease are extracellular plaques, composed of fibrillar amyloid-β (Aβ), and neurofibrillary tangles inside neurons, composed of Tau protein. Until recently, the search for AD therapeutics was focussed more on the Aβ peptide and its pathology, but the results were unsatisfying. As an alternative, Tau might be a promising therapeutic target as its pathology is closely correlated to clinical symptoms. In addition, pathological Tau aggregation occurs in a large group of diseases, called Tauopathies, and in most of them Aβ aggregation does not play a role in disease pathogenesis. The formation of Tau aggregates is triggered by two hexapeptide motifs within Tau; PHF6* and PHF6. Both fragments are interesting targets for the development of Tau aggregation inhibitors (TAI). Peptides represent a unique class of pharmaceutical compounds and are reasonable alternatives to chemical substances or antibodies. They are attributed with high biological activity, valuable specificity and low toxicity, and often are developed as drug candidates to interrupt protein-protein interactions. The preparation of peptides is simple, controllable and the peptides can be easily modified. However, their application may also have disadvantages. Currently, a few peptide compounds acting as TAI are described in the literature, most of them developed by structure-based design or phage display. Here, we review the current state of research in this promising field of AD therapy development.
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Affiliation(s)
- Isabelle Aillaud
- Institute of Bioanalysis, Coburg University of Applied Sciences, Coburg, Germany
| | - Susanne Aileen Funke
- Institute of Bioanalysis, Coburg University of Applied Sciences, Coburg, Germany.
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Mlakar L, Garrett SM, Watanabe T, Sanderson M, Nishimoto T, Heywood J, Helke KL, Pilewski JM, Herzog EL, Feghali-Bostwick C. Ameliorating Fibrosis in Murine and Human Tissues with END55, an Endostatin-Derived Fusion Protein Made in Plants. Biomedicines 2022; 10:2861. [PMID: 36359382 PMCID: PMC9687961 DOI: 10.3390/biomedicines10112861] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/12/2022] [Accepted: 11/04/2022] [Indexed: 11/12/2022] Open
Abstract
Organ fibrosis, particularly of the lungs, causes significant morbidity and mortality. Effective treatments are needed to reduce the health burden. A fragment of the carboxyl-terminal end of collagen XVIII/endostatin reduces skin and lung fibrosis. This fragment was modified to facilitate its production in plants, which resulted in the recombinant fusion protein, END55. We found that expression of END55 had significant anti-fibrotic effects on the treatment and prevention of skin and lung fibrosis in a bleomycin mouse model. We validated these effects in a second mouse model of pulmonary fibrosis involving inducible, lung-targeted expression of transforming growth factor β1. END55 also exerted anti-fibrotic effects in human lung and skin tissues maintained in organ culture in which fibrosis was experimentally induced. The anti-fibrotic effect of END55 was mediated by a decrease in the expression of extracellular matrix genes and an increase in the levels of matrix-degrading enzymes. Finally, END55 reduced fibrosis in the lungs of patients with systemic sclerosis (SSc) and idiopathic pulmonary fibrosis (IPF) who underwent lung transplantation due to the severity of their lung disease, displaying efficacy in human tissues directly relevant to human disease. These findings demonstrate that END55 is an effective anti-fibrotic therapy in different organs.
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Affiliation(s)
- Logan Mlakar
- Division of Rheumatology, Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Sara M. Garrett
- Division of Rheumatology, Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Tomoya Watanabe
- Division of Rheumatology, Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Matthew Sanderson
- Division of Rheumatology, Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Tetsuya Nishimoto
- Division of Rheumatology, Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Jonathan Heywood
- Division of Rheumatology, Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Kristi L. Helke
- Department of Comparative Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Joseph M. Pilewski
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Erica L. Herzog
- Yale ILD Center of Excellence, Department of Medicine, Yale School of Medicine, New Haven, CT 06519, USA
| | - Carol Feghali-Bostwick
- Division of Rheumatology, Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
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7
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Tang Y, Zhang D, Liu Y, Zhang Y, Zhou Y, Chang Y, Zheng B, Xu A, Zheng J. A new strategy to reconcile amyloid cross-seeding and amyloid prevention in a binary system of α-synuclein fragmental peptide and hIAPP. Protein Sci 2022; 31:485-497. [PMID: 34850985 PMCID: PMC8820123 DOI: 10.1002/pro.4247] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/19/2021] [Accepted: 11/19/2021] [Indexed: 02/03/2023]
Abstract
Amyloid cross-seeding and amyloid inhibition are two different research subjects being studied separately for different pathological purposes, in which amyloid cross-seeding targets to study the co-aggregation of different amyloid proteins and potential molecular links between different neurodegenerative diseases, while amyloid inhibition aims to design different molecules for preventing amyloid aggregation. While both amyloid cross-seeding and amyloid inhibition are critical for better understanding the pathological causes of different neurodegenerative diseases including Parkinson disease (PD) and Type 2 diabetes (T2D), less efforts have been made to reconcile the two phenomena. Herein, we proposed a new preventive strategy to demonstrate (a) the cross-seeding of octapeptide TKEQVTNV from α-synuclein (associated with PD) with hIAPP (associated with T2D) and (b) the cross-seeding-promoted hIAPP fibrillization and cross-seeding-reduced hIAPP toxicity. Collective results confirmed that TKEQVTNV can indeed cross-seed with hIAPP monomers and oligomers, not protofibrils, to form β-structure-rich fibrils and to accelerate hIAPP fibrillization. Moreover, such cross-seeding-induced promotion effect by TKEQVTNV also rescued the pancreatic cells from hIAPP-induced cytotoxicity by increasing cell viability and reducing cell apoptosis simultaneously. This work provides a new angle to discover amyloid fragments and use them as amyloid modulators (inhibitors or promotors) to interfere with amyloid aggregation of other amyloid proteins, as well as sequence/structure basis to explore the amyloid cross-seeding between different amyloid proteins that may help explain a potential molecular talk between different neurodegenerative diseases.
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Affiliation(s)
- Yijing Tang
- Department of Chemical, Biomolecular, and Corrosion EngineeringThe University of AkronAkronOhioUSA
| | - Dong Zhang
- Department of Chemical, Biomolecular, and Corrosion EngineeringThe University of AkronAkronOhioUSA
| | - Yonglan Liu
- Department of Chemical, Biomolecular, and Corrosion EngineeringThe University of AkronAkronOhioUSA
| | - Yanxian Zhang
- Department of Chemical, Biomolecular, and Corrosion EngineeringThe University of AkronAkronOhioUSA
| | - Yifan Zhou
- Department of Polymer ScienceThe University of AkronAkronOhioUSA
| | - Yung Chang
- R&D Center for Membrane Technology, Department of Chemical EngineeringChung Yuan Christian UniversityTaoyuanTaiwan
| | | | | | - Jie Zheng
- Department of Chemical, Biomolecular, and Corrosion EngineeringThe University of AkronAkronOhioUSA
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Kalmankar NV, Hari H, Sowdhamini R, Venkatesan R. Disulfide-Rich Cyclic Peptides from Clitoria ternatea Protect against β-Amyloid Toxicity and Oxidative Stress in Transgenic Caenorhabditis elegans. J Med Chem 2021; 64:7422-7433. [PMID: 34048659 DOI: 10.1021/acs.jmedchem.1c00033] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Neurotoxic aggregation of β-amyloid (Aβ) peptides is a hallmark of Alzheimer's disease and increased reactive oxygen species (ROS) is an associated process. In the present study, we report the neuroprotective effects of disulfide-rich, circular peptides from Clitoria ternatea (C. ternatea) (butterfly pea) on Aβ-induced toxicity in transgenic Caenorhabditis elegans. Cyclotides (∼30 amino acids long) are a special class of cyclic cysteine knot peptides. We show that cyclotide-rich fractions from different plant tissues delay Aβ-induced paralysis in the transgenic CL4176 strain expressing the human muscle-specific Aβ1-42 gene. They also improved Aβ-induced chemotaxis defects in CL2355 strain expressing Aβ1-42 in the neuronal cells. ROS assay suggests that this protection is likely mediated by the inhibition of Aβ oligomerization. Furthermore, Aβ deposits were reduced in the CL2006 strain treated with the fractions. The study shows that cyclotides from C. ternatea could be a source of a novel pharmacophore scaffold against neurodegenerative diseases.
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Affiliation(s)
- Neha V Kalmankar
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, Bangalore, Karnataka 560065, India.,The University of Trans-Disciplinary Health Sciences and Technology (TDU), #74/2, Jarakabande Kaval, Post Attur, via Yelahanka, Bangalore, Karnataka 560064, India
| | - Hrudya Hari
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, Bangalore, Karnataka 560065, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, Bangalore, Karnataka 560065, India
| | - Radhika Venkatesan
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, Bangalore, Karnataka 560065, India.,Department of Biological Sciences, Indian Institute of Science Education and Research, Mohanpur, West Bengal 741246, India
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9
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Forner M, Defaus S, Andreu D. Peptide-Based Multiepitopic Vaccine Platforms via Click Reactions. J Org Chem 2019; 85:1626-1634. [PMID: 31782300 DOI: 10.1021/acs.joc.9b02798] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Multimeric antigen display and high overall valency are increasingly regarded as strategic goals for potent and broadly efficacious synthetic vaccines with potential market prospects. Herein, a modular and versatile approach to multifunctional peptide-based vaccine platforms at multimilligram scale in reasonable yields is reported. Preparation of chemoselectively modified peptide building blocks of medium-to-large size, conjugation of these subunits, and final assembly were achieved by a combination of Michael-type thiol-ene addition and copper(I)-mediated alkyne-azide cycloaddition. The size and structural complexity of the building blocks required exploration of a further level of orthogonality, namely furan/maleimide Diels-Alder chemistry. After process optimization, a finely tuned, stepwise click approach has emerged as a workable, on-demand strategy to create macromolecular therapeutic vaccine assemblies.
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Affiliation(s)
- Mar Forner
- Department of Experimental and Health Science , Pompeu Fabra University , Barcelona Biomedical Research Park, 08003 Barcelona , Spain
| | - Sira Defaus
- Department of Experimental and Health Science , Pompeu Fabra University , Barcelona Biomedical Research Park, 08003 Barcelona , Spain
| | - David Andreu
- Department of Experimental and Health Science , Pompeu Fabra University , Barcelona Biomedical Research Park, 08003 Barcelona , Spain
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Jokar S, Khazaei S, Behnammanesh H, Shamloo A, Erfani M, Beiki D, Bavi O. Recent advances in the design and applications of amyloid-β peptide aggregation inhibitors for Alzheimer's disease therapy. Biophys Rev 2019; 11:10.1007/s12551-019-00606-2. [PMID: 31713720 DOI: 10.1007/s12551-019-00606-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 10/31/2019] [Indexed: 01/05/2023] Open
Abstract
Alzheimer's disease (AD) is an irreversible neurological disorder that progresses gradually and can cause severe cognitive and behavioral impairments. This disease is currently considered a social and economic incurable issue due to its complicated and multifactorial characteristics. Despite decades of extensive research, we still lack definitive AD diagnostic and effective therapeutic tools. Consequently, one of the most challenging subjects in modern medicine is the need for the development of new strategies for the treatment of AD. A large body of evidence indicates that amyloid-β (Aβ) peptide fibrillation plays a key role in the onset and progression of AD. Recent studies have reported that amyloid hypothesis-based treatments can be developed as a new approach to overcome the limitations and challenges associated with conventional AD therapeutics. In this review, we will provide a comprehensive view of the challenges in AD therapy and pathophysiology. We also discuss currently known compounds that can inhibit amyloid-β (Aβ) aggregation and their potential role in advancing current AD treatments. We have specifically focused on Aβ aggregation inhibitors including metal chelators, nanostructures, organic molecules, peptides (or peptide mimics), and antibodies. To date, these molecules have been the subject of numerous in vitro and in vivo assays as well as molecular dynamics simulations to explore their mechanism of action and the fundamental structural groups involved in Aβ aggregation. Ultimately, the aim of these studies (and current review) is to achieve a rational design for effective therapeutic agents for AD treatment and diagnostics.
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Affiliation(s)
- Safura Jokar
- Department of Nuclear Pharmacy, Faculty of Pharmacy, Tehran University of Medical Sciences, P.O. BOX: 14155-6559, Tehran, Iran
| | - Saeedeh Khazaei
- Department of Pharmaceutical Biomaterials , Faculty of Pharmacy, Tehran University of Medical Sciences, P.O. BOX: 14155-6559, Tehran, Iran
| | - Hossein Behnammanesh
- Department of Nuclear Pharmacy, Faculty of Pharmacy, Tehran University of Medical Sciences, P.O. BOX: 14155-6559, Tehran, Iran
| | - Amir Shamloo
- Department of Mechanical Engineering, Sharif University of Technology, P.O. Box: 11365-11155, Tehran, Iran
| | - Mostafa Erfani
- Radiation Application Research School, Nuclear Science and Technology Research Institute (NSTRI), P.O. Box: 14155-1339, Tehran, Iran
| | - Davood Beiki
- Research Center for Nuclear Medicine, Tehran University of Medical Sciences, P.O. BOX: 14155-6559, Tehran, Iran
| | - Omid Bavi
- Department of Mechanical and Aerospace Engineering, Shiraz University of Technology, P.O. Box: 71555-313, Shiraz, Iran.
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11
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Pan H, Xie Y, Lu W, Chen Y, Lu Z, Zhen J, Wang W, Shang A. Engineering an enhanced thrombin-based GLP-1 analog with long-lasting glucose-lowering and efficient weight reduction. RSC Adv 2019; 9:30707-30714. [PMID: 35529389 PMCID: PMC9072222 DOI: 10.1039/c9ra06771j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 09/20/2019] [Indexed: 11/21/2022] Open
Abstract
Peptides are considered as potent therapeutic drugs primarily due to the exquisite potency and selectivity to targets. However, the development and clinical application of peptide drugs were severely limited by the poor in vivo lifespans. Here, we designed an improved small albumin-binding polypeptide that can associate with human serum albumin (HSA) and liberate the bioactive peptide. Using glucagon-like peptide-1 (GLP-1) as a model, two new long-lasting GLP-1 analogs (termed XTS1 and XTS2) containing an albumin-binding domain, a protease-cleavable linker and a mutated GLP-1(A8Aib) were designed to demonstrate the sustained release of GLP-1 due to the plasma thrombin (TBN) digestion. Two XTS peptides were prepared of high purity (>99%) and accurate molecular weight determined by reversed high-performance liquid chromatography and mass spectrometry, respectively. In vitro measurements of surface plasmon resonance indicated that XTS1 associate with serum albumins of all species with higher affinity compared with XTS2. Metabolic stability of XTS1 in vitro in human plasma was also better than that of XTS2. Protease cleavage assay results of XTS peptides demonstrated the controlled-release of transient GLP-1 from the XTS1 and XTS2 mixture after thrombin-catalyzed hydrolysis. Then the intraperitoneal glucose tolerance test (IPGTT) showed that the glucose-lowering efficacies of XTS1 were in a dosage-dependent manner within the range of 0.1–0.9 mg kg−1. In addition, XTS1 showed similar hypoglycemic intensity and significantly longer action duration compared to Liraglutide in both multiple IPGTTs and hypoglycemic duration test. Apparently extended plasma half-lives of ∼2.3 and ∼3.5 days were observed after a single subcutaneous administration of XTS1 (0.9 mg kg−1) in rats and cynomolgus monkeys, respectively. Furthermore, twice-weekly subcutaneously dosed XTS1 in db/db mice achieved long-term beneficial effects on body weight, hemoglobin A1C (HbA1C) lowering and the function of pancreatic beta cells. These studies support that XTS1 exerts potential as a therapeutic drug for the treatment of T2DM. Peptides are considered as potent therapeutic drugs primarily due to the exquisite potency and selectivity to targets.![]()
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Affiliation(s)
- Hongchao Pan
- Department of Laboratory Medicine, Shanghai Simple Gene Medical Laboratory Shanghai 200025 P.R. China
| | - Yini Xie
- Department of Laboratory Medicine, The People's Hospital of Jiedong Jieyang 515500 P. R. China
| | - Wenying Lu
- Department of Experimental Medicine Center, The Sixth People's Hospital of Yancheng City Yancheng 224001 P. R. China
| | - Yin Chen
- Key Laboratory of Biological Medicine, Department of Life Science and Technology, Jinan University 51000 P. R. China
| | - Zhao Lu
- Key Laboratory of Drug Discovery for Metabolic Disease, China Pharmaceutical University Nanjing 210000 P. R. China
| | - Jun Zhen
- Key Laboratory of Drug Discovery for Metabolic Disease, China Pharmaceutical University Nanjing 210000 P. R. China
| | - Weiwei Wang
- Department of Experimental Medicine Center, The Sixth People's Hospital of Yancheng City Yancheng 224001 P. R. China
| | - Anquan Shang
- Department of Laboratory Medicine, Tongji Hospital of Tongji University Shanghai 200065 P. R. China
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12
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Peptide based therapeutics and their use for the treatment of neurodegenerative and other diseases. Biomed Pharmacother 2018; 103:574-581. [PMID: 29677544 DOI: 10.1016/j.biopha.2018.04.025] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 03/21/2018] [Accepted: 04/03/2018] [Indexed: 12/16/2022] Open
Abstract
Bioactive peptides are actively involved in different biological functions and importantly contribute to human health, and the use of peptides as therapeutics has a long successful history in disease management. A number of peptides have wide-ranging therapeutic effects, such as antioxidant, antimicrobial, and antithrombotic effects. Neurodegenerative diseases are typically caused by abnormal aggregations of proteins or peptides, and the depositions of these aggregates in or on neurons, disrupt signaling and eventually kill neurons. During recent years, research on short peptides has advanced tremendously. This review offers a brief introduction to peptide based therapeutics and their application in disease management and provides an overview of peptide vaccines, and toxicity related issues. In addition, the importance of peptides in the management of different neurodegenerative diseases and their therapeutic applications is discussed. The present review provides an understanding of peptides and their applications for the management of different diseases, but with focus on neurodegenerative diseases. The role of peptides as anti-cancer, antimicrobial and antidiabetic agents has also been discussed.
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13
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Zhu Z, Shaginian A, Grady LC, O’Keeffe T, Shi XE, Davie CP, Simpson GL, Messer JA, Evindar G, Bream RN, Thansandote PP, Prentice NR, Mason AM, Pal S. Design and Application of a DNA-Encoded Macrocyclic Peptide Library. ACS Chem Biol 2018; 13:53-59. [PMID: 29185700 DOI: 10.1021/acschembio.7b00852] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A DNA-encoded macrocyclic peptide library was designed and synthesized with 2.4 × 1012 members composed of 4-20 natural and non-natural amino acids. Affinity-based selection was performed against two therapeutic targets, VHL and RSV N protein. On the basis of selection data, some peptides were selected for resynthesis without a DNA tag, and their activity was confirmed.
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Affiliation(s)
- Zhengrong Zhu
- GlaxoSmithKline, 200 Cambridge Park Dr., Cambridge, Massachusetts 02140, United States
| | - Alex Shaginian
- GlaxoSmithKline, 200 Cambridge Park Dr., Cambridge, Massachusetts 02140, United States
| | - LaShadric C. Grady
- GlaxoSmithKline, 200 Cambridge Park Dr., Cambridge, Massachusetts 02140, United States
| | - Thomas O’Keeffe
- GlaxoSmithKline, 200 Cambridge Park Dr., Cambridge, Massachusetts 02140, United States
| | - Xiangguo E. Shi
- GlaxoSmithKline, 200 Cambridge Park Dr., Cambridge, Massachusetts 02140, United States
| | - Christopher P. Davie
- GlaxoSmithKline, 200 Cambridge Park Dr., Cambridge, Massachusetts 02140, United States
| | - Graham L. Simpson
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, United Kingdom
| | - Jeffrey A. Messer
- GlaxoSmithKline, 200 Cambridge Park Dr., Cambridge, Massachusetts 02140, United States
| | - Ghotas Evindar
- GlaxoSmithKline, 200 Cambridge Park Dr., Cambridge, Massachusetts 02140, United States
| | - Robert N. Bream
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, United Kingdom
| | | | - Naomi R. Prentice
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, United Kingdom
| | - Andrew M. Mason
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, United Kingdom
| | - Sandeep Pal
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, United Kingdom
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14
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Rezaeian N, Shirvanizadeh N, Mohammadi S, Nikkhah M, Arab SS. The inhibitory effects of biomimetically designed peptides on α-synuclein aggregation. Arch Biochem Biophys 2017; 634:96-106. [PMID: 28965745 DOI: 10.1016/j.abb.2017.09.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/05/2017] [Accepted: 09/20/2017] [Indexed: 01/10/2023]
Abstract
Parkinson's disease is characterized by accumulation of inclusion bodies in dopaminergic neurons, where insoluble and fibrillar α-synuclein makes up the major component of these inclusion bodies. So far, several strategies have been applied in order to suppress α-synuclein aggregation and toxicity in Parkinson's disease. In the present study, a new database has been established by segmentation of all the proteins deposited in protein Data Bank. The database data base was searched for the sequences which adopt β structure and are identical or very similar to the regions of α-synuclein which are involved in aggregation. The adjacent β strands of the found sequences were chosen as the peptide inhibitors of α-synuclein aggregation. Two of the predicted peptides, namely KISVRV and GQTYVLPG, were experimentally proved to be efficient in suppressing aggregation of α-synuclein in vitro. Moreover, KISVRV exhibited the ability to disrupt oligomers of α-syn which are assumed to be the pathogenic species in Parkinson's disease.
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Affiliation(s)
- Niloofar Rezaeian
- Department of Biology, Faculty of Basic Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Niloofar Shirvanizadeh
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Soheila Mohammadi
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Maryam Nikkhah
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Seyed Shahriar Arab
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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15
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Dammers C, Yolcu D, Kukuk L, Willbold D, Pickhardt M, Mandelkow E, Horn AHC, Sticht H, Malhis MN, Will N, Schuster J, Funke SA. Selection and Characterization of Tau Binding ᴅ-Enantiomeric Peptides with Potential for Therapy of Alzheimer Disease. PLoS One 2016; 11:e0167432. [PMID: 28006031 PMCID: PMC5179029 DOI: 10.1371/journal.pone.0167432] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 11/14/2016] [Indexed: 11/19/2022] Open
Abstract
A variety of neurodegenerative disorders, including Alzheimer disease (AD), are associated with neurofibrillary tangles composed of the tau protein, as well as toxic tau oligomers. Inhibitors of pathological tau aggregation, interrupting tau self-assembly, might be useful for the development of therapeutics. Employing mirror image phage display with a large peptide library (over 109 different peptides), we have identified tau fibril binding peptides consisting of d-enantiomeric amino acids. d-enantiomeric peptides are extremely protease stable and not or less immunogenic than l-peptides, and the suitability of d-peptides for in vivo applications have already been demonstrated. Phage display selections were performed using fibrils of the d-enantiomeric hexapeptide VQIVYK, representing residues 306 to 311 of the tau protein, as a target. VQIVYK has been demonstrated to be important for fibril formation of the full lengths protein and forms fibrils by itself. Here, we report on d-enantiomeric peptides, which bind to VQIVYK, tau isoforms like tau3RD (K19) as well as to full lengths tau fibrils, and modulate the aggregation of the respective tau form. The peptides are able to penetrate cells and might be interesting for therapeutic and diagnostic applications in AD research.
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Affiliation(s)
- Christina Dammers
- Institute of Complex Systems (ICS-6), Forschungszentrum Jülich, Jülich, Germany
| | - Deniz Yolcu
- Institute of Complex Systems (ICS-6), Forschungszentrum Jülich, Jülich, Germany
| | - Laura Kukuk
- Institute of Complex Systems (ICS-6), Forschungszentrum Jülich, Jülich, Germany
| | - Dieter Willbold
- Institute of Complex Systems (ICS-6), Forschungszentrum Jülich, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Marcus Pickhardt
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
- CAESAR Research Center, Bonn, Germany
| | - Eckhard Mandelkow
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
- CAESAR Research Center, Bonn, Germany
- Max Planck Institute for Metabolism Research, Köln, Germany
| | - Anselm H C Horn
- Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Heinrich Sticht
- Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | | | - Nadja Will
- Bioanalytik, Hochschule für angewandte Wissenschaften, Coburg, Germany
| | - Judith Schuster
- Bioanalytik, Hochschule für angewandte Wissenschaften, Coburg, Germany
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16
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The molecular basis for the prolonged blood circulation of lipidated incretin peptides: Peptide oligomerization or binding to serum albumin? J Control Release 2016; 241:25-33. [DOI: 10.1016/j.jconrel.2016.08.035] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 07/30/2016] [Accepted: 08/26/2016] [Indexed: 12/25/2022]
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17
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Mukherjee RP, Beitle R, Jayanthi S, Kumar T, McNabb DS. Production of an anti-Candidapeptide via fed batch and ion exchange chromatography. Biotechnol Prog 2016; 32:865-71. [DOI: 10.1002/btpr.2296] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 04/22/2016] [Indexed: 11/09/2022]
Affiliation(s)
| | - Robert Beitle
- Ralph E. Martin Dept. of Chemical Engineering; University of Arkansas; Fayetteville AR
| | - Srinivas Jayanthi
- Dept. of Chemistry and Biochemistry; University of Arkansas; Fayetteville AR
| | - T.K.S. Kumar
- Dept. of Chemistry and Biochemistry; University of Arkansas; Fayetteville AR
| | - David S. McNabb
- Dept. of Biological Sciences; University of Arkansas; Fayetteville AR
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18
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Dengl S, Hoffmann E, Grote M, Wagner C, Mundigl O, Georges G, Thorey I, Stubenrauch KG, Bujotzek A, Josel HP, Dziadek S, Benz J, Brinkmann U. Hapten-directed spontaneous disulfide shuffling: a universal technology for site-directed covalent coupling of payloads to antibodies. FASEB J 2015; 29:1763-79. [PMID: 25670234 PMCID: PMC4415024 DOI: 10.1096/fj.14-263665] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 12/15/2014] [Indexed: 01/14/2023]
Abstract
Humanized hapten-binding IgGs were designed with an accessible cysteine close to their binding pockets, for specific covalent payload attachment. Individual analyses of known structures of digoxigenin (Dig)- and fluorescein (Fluo) binding antibodies and a new structure of a biotin (Biot)-binder, revealed a “universal” coupling position (52+2) in proximity to binding pockets but without contributing to hapten interactions. Payloads that carry a free thiol are positioned on the antibody and covalently linked to it via disulfides. Covalent coupling is achieved and driven toward complete (95–100%) payload occupancy by spontaneous redox shuffling between antibody and payload. Attachment at the universal position works with different haptens, antibodies, and payloads. Examples are the haptens Fluo, Dig, and Biot combined with various fluorescent or peptidic payloads. Disulfide-bonded covalent antibody-payload complexes do not dissociate in vitro and in vivo. Coupling requires the designed cysteine and matching payload thiol because payload or antibody without the Cys/thiol are not linked (<5% nonspecific coupling). Hapten-mediated positioning is necessary as hapten-thiol-payload is only coupled to antibodies that bind matching haptens. Covalent complexes are more stable in vivo than noncovalent counterparts because digoxigeninylated or biotinylated fluorescent payloads without disulfide-linkage are cleared more rapidly in mice (approximately 50% reduced 48 hour serum levels) compared with their covalently linked counterparts. The coupling technology is applicable to many haptens and hapten binding antibodies (confirmed by automated analyses of the structures of 140 additional hapten binding antibodies) and can be applied to modulate the pharmacokinetics of small compounds or peptides. It is also suitable to link payloads in a reduction-releasable manner to tumor- or tissue-targeting delivery vehicles.—Dengl, S., Hoffmann, E., Grote, M., Wagner, C., Mundigl, O., Georges, G., Thorey, I., Stubenrauch, K.-G., Bujotzek, A., Josel, H.-P., Dziadek, S., Benz, J., Brinkmann, U. Hapten-directed spontaneous disulfide shuffling: a universal technology for site-directed covalent coupling of payloads to antibodies.
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Affiliation(s)
- Stefan Dengl
- *Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Penzberg, Penzberg, Germany; Roche Diagnostics GmbH, Penzberg, Germany; and Roche Discovery Technologies, Roche Innovation Center Basel, Basel, Switzerland
| | - Eike Hoffmann
- *Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Penzberg, Penzberg, Germany; Roche Diagnostics GmbH, Penzberg, Germany; and Roche Discovery Technologies, Roche Innovation Center Basel, Basel, Switzerland
| | - Michael Grote
- *Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Penzberg, Penzberg, Germany; Roche Diagnostics GmbH, Penzberg, Germany; and Roche Discovery Technologies, Roche Innovation Center Basel, Basel, Switzerland
| | - Cornelia Wagner
- *Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Penzberg, Penzberg, Germany; Roche Diagnostics GmbH, Penzberg, Germany; and Roche Discovery Technologies, Roche Innovation Center Basel, Basel, Switzerland
| | - Olaf Mundigl
- *Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Penzberg, Penzberg, Germany; Roche Diagnostics GmbH, Penzberg, Germany; and Roche Discovery Technologies, Roche Innovation Center Basel, Basel, Switzerland
| | - Guy Georges
- *Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Penzberg, Penzberg, Germany; Roche Diagnostics GmbH, Penzberg, Germany; and Roche Discovery Technologies, Roche Innovation Center Basel, Basel, Switzerland
| | - Irmgard Thorey
- *Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Penzberg, Penzberg, Germany; Roche Diagnostics GmbH, Penzberg, Germany; and Roche Discovery Technologies, Roche Innovation Center Basel, Basel, Switzerland
| | - Kay-Gunnar Stubenrauch
- *Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Penzberg, Penzberg, Germany; Roche Diagnostics GmbH, Penzberg, Germany; and Roche Discovery Technologies, Roche Innovation Center Basel, Basel, Switzerland
| | - Alexander Bujotzek
- *Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Penzberg, Penzberg, Germany; Roche Diagnostics GmbH, Penzberg, Germany; and Roche Discovery Technologies, Roche Innovation Center Basel, Basel, Switzerland
| | - Hans-Peter Josel
- *Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Penzberg, Penzberg, Germany; Roche Diagnostics GmbH, Penzberg, Germany; and Roche Discovery Technologies, Roche Innovation Center Basel, Basel, Switzerland
| | - Sebastian Dziadek
- *Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Penzberg, Penzberg, Germany; Roche Diagnostics GmbH, Penzberg, Germany; and Roche Discovery Technologies, Roche Innovation Center Basel, Basel, Switzerland
| | - Joerg Benz
- *Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Penzberg, Penzberg, Germany; Roche Diagnostics GmbH, Penzberg, Germany; and Roche Discovery Technologies, Roche Innovation Center Basel, Basel, Switzerland
| | - Ulrich Brinkmann
- *Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Penzberg, Penzberg, Germany; Roche Diagnostics GmbH, Penzberg, Germany; and Roche Discovery Technologies, Roche Innovation Center Basel, Basel, Switzerland
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19
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Hill TA, Lohman RJ, Hoang HN, Nielsen DS, Scully CCG, Kok WM, Liu L, Lucke AJ, Stoermer MJ, Schroeder CI, Chaousis S, Colless B, Bernhardt PV, Edmonds DJ, Griffith DA, Rotter CJ, Ruggeri RB, Price DA, Liras S, Craik DJ, Fairlie DP. Cyclic Penta- and Hexaleucine Peptides without N-Methylation Are Orally Absorbed. ACS Med Chem Lett 2014; 5:1148-51. [PMID: 25313329 DOI: 10.1021/ml5002823] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 08/04/2014] [Indexed: 02/08/2023] Open
Abstract
Development of peptide-based drugs has been severely limited by lack of oral bioavailability with less than a handful of peptides being truly orally bioavailable, mainly cyclic peptides with N-methyl amino acids and few hydrogen bond donors. Here we report that cyclic penta- and hexa-leucine peptides, with no N-methylation and five or six amide NH protons, exhibit some degree of oral bioavailability (4-17%) approaching that of the heavily N-methylated drug cyclosporine (22%) under the same conditions. These simple cyclic peptides demonstrate that oral bioavailability is achievable for peptides that fall outside of rule-of-five guidelines without the need for N-methylation or modified amino acids.
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Affiliation(s)
- Timothy A. Hill
- Division
of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Rink-Jan Lohman
- Division
of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Huy N. Hoang
- Division
of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Daniel S. Nielsen
- Division
of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Conor C. G. Scully
- Division
of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - W. Mei Kok
- Division
of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ligong Liu
- Division
of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Andrew J. Lucke
- Division
of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Martin J. Stoermer
- Division
of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Christina I. Schroeder
- Division
of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Stephanie Chaousis
- Division
of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Barbara Colless
- Division
of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Paul V. Bernhardt
- School
of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane 4072, Australia
| | - David J. Edmonds
- World
Wide Medicinal Chemistry, CVMED, Pfizer, Cambridge, Massachusetts 02140, United States
| | - David A. Griffith
- World
Wide Medicinal Chemistry, CVMED, Pfizer, Cambridge, Massachusetts 02140, United States
| | - Charles J. Rotter
- Pfizer Pharmacokinetics, Dynamics, and Metabolism, Groton, Connecticut 06340, United States
| | - Roger B. Ruggeri
- World
Wide Medicinal Chemistry, CVMED, Pfizer, Cambridge, Massachusetts 02140, United States
| | - David A. Price
- World
Wide Medicinal Chemistry, CVMED, Pfizer, Cambridge, Massachusetts 02140, United States
| | - Spiros Liras
- World
Wide Medicinal Chemistry, CVMED, Pfizer, Cambridge, Massachusetts 02140, United States
| | - David J. Craik
- Division
of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David P. Fairlie
- Division
of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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20
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Hoffmann E, Konkar A, Dziadek S, Josel HP, Conde-Knape K, Kropp H, Kling L, Stubenrauch K, Thorey I, Dengl S, Brinkmann U. PK modulation of haptenylated peptides via non-covalent antibody complexation. J Control Release 2013; 171:48-56. [PMID: 23800420 DOI: 10.1016/j.jconrel.2013.06.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 06/11/2013] [Accepted: 06/15/2013] [Indexed: 11/15/2022]
Abstract
We applied noncovalent complexes of digoxigenin (Dig) binding antibodies with digoxigeninylated peptide derivatives to modulate their pharmacokinetic properties. A peptide derivative which activates the Y2R receptor was selectively mono-digoxigeninylated by reacting a NHS-Dig derivative with an ε-amino group of lysine 2. This position tolerates modifications without destroying receptor binding and functionality of the peptide. Dig-peptide derivatives can be loaded onto Dig-binding IgGs in a simple and robust reaction, thereby generating peptide-IgG complexes in a defined two to one molar ratio. This indicates that each antibody arm becomes occupied by one haptenylated peptide. In vitro receptor binding and signaling assays showed that Dig-peptides as well as the peptide-antibody complexes retain better potency than the corresponding pegylated peptides. In vivo analyses revealed prolonged serum half-life of antibody-complexed peptides compared to unmodified peptides. Thus, complexes are of sufficient stability for PK modulation. We observed more prolonged weight reduction in a murine diet-induced obesity (DIO) model with antibody-complexed peptides compared to unmodified peptides. We conclude that antibody-hapten complexation can be applied to modulate the PK of haptenylated peptides and in consequence improve the therapeutic efficacy of therapeutic peptides.
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Affiliation(s)
- Eike Hoffmann
- Roche Pharma Research & Early Development pRED, Large Molecule Research, Nonnenwald 2, D-82372 Penzberg, Germany.
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21
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Abstract
The suite of currently used drugs can be divided into two categories - traditional 'small molecule' drugs with typical molecular weights of <500 Da but with oral bioavailability, and much larger 'biologics' typically >5000 Da that are not orally bioavailable and need to be delivered via injection. Due to their small size, conventional small molecule drugs may suffer from reduced target selectivity that often ultimately manifests in human side-effects, whereas protein therapeutics tend to be exquisitely specific for their targets due to many more interactions with them, but this comes at a cost of low bioavailability, poor membrane permeability, and metabolic instability. The time has now come to reinvestigate new drug leads that fit between these two molecular weight extremes, with the goal of combining advantages of small molecules (cost, conformational restriction, membrane permeability, metabolic stability, oral bioavailability) with those of proteins (natural components, target specificity, high potency). This article uses selected examples of peptides to highlight the importance of peptide drugs, some potential new opportunities for their exploitation, and some difficult challenges ahead in this field.
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Affiliation(s)
- David J Craik
- Division of Chemistry & Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld 4072, Australia.
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22
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Ambaye ND, Gunzburg MJ, Lim RCC, Price JT, Wilce MCJ, Wilce JA. The discovery of phenylbenzamide derivatives as Grb7-based antitumor agents. ChemMedChem 2012; 8:280-8. [PMID: 23355456 DOI: 10.1002/cmdc.201200400] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Revised: 11/20/2012] [Indexed: 11/06/2022]
Abstract
Grb7 is a non-catalytic protein, the overexpression of which has been associated with the proliferative and migratory potentials of cancer cells. Virtual screening strategies involving a shape-based similarity search, molecular docking, and 2D-similarity searches complemented by experimental binding studies (Thermofluor and isothermal titration calorimetry) resulted in the identification of nine novel phenylbenzamide-based antagonists of the Grb7 SH2 domain. Moderate binding affinities were observed, ranging from K(d)=32.3 μM for lead phenylbenzamide NSC 104999 (1) to K(d)=1.1 μM for a structurally related compound, NSC 57148 (2). Deconvolution of the affinity data into its components revealed differences in lead binding, from being entropy based (lead 1) to enthalpically driven (NSC 100874 (3), NSC 55158 (4), and compound 2). Finally, the lead compound 1 was found to decrease the growth of MDA-MB-468 breast cancer cells, with an IC(50) value of 39.9 μM. It is expected that these structures will serve as novel leads in the development of Grb7-based anticancer therapeutics.
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Affiliation(s)
- Nigus D Ambaye
- Biochemistry and Molecular Biology, Monash University, Wellington Road, VIC 3800, Australia
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Funke SA, Willbold D. Peptides for therapy and diagnosis of Alzheimer's disease. Curr Pharm Des 2012; 18:755-67. [PMID: 22236121 PMCID: PMC3426787 DOI: 10.2174/138161212799277752] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2011] [Accepted: 12/09/2011] [Indexed: 12/21/2022]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder with devastating effects. The greatest risk factor to develop AD is age. Today, only symptomatic therapies are available. Additionally, AD can be diagnosed with certainty only post mortem, whereas the diagnosis "probable AD" can be established earliest when severe clinical symptoms appear. Specific neuropathological changes like neurofibrillary tangles and amyloid plaques define AD. Amyloid plaques are mainly composed of the amyloid-βpeptide (Aβ). Several lines of evidence suggest that the progressive concentration and subsequent aggregation and accumulation of Aβ play a fundamental role in the disease progress. Therefore, substances which bind to Aβ and influence aggregation thereof are of great interest. An enormous number of organic substances for therapeutic purposes are described. This review focuses on peptides developed for diagnosis and therapy of AD and discusses the pre- and disadvantages of peptide drugs.
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Affiliation(s)
| | - Dieter Willbold
- Forschungszentrum Jülich, ICS-6, 52425 Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
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24
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Abstract
The development of peptides with therapeutic activities can be based on naturally occurring peptides or alternatively on de novo design. The discovery of natural peptides is often a matter of serendipity. In part, this is because natural peptides are typically proteolytically cleaved out from precursor proteins, a feature that averts the direct benefits of the genomic revolution. The first part of this review describes attempts to create a more systematic identification of natural peptides relying on a two step process. In the initial step, an in silico peptidome is predicted through the use of machine learning. Then, various computational biology tools are tailored to focus on peptides predicted to have the desired biological activity; for example, activating a GPCR or modulating the cellular arm of the immune system. The second part of the review is devoted to de novo peptide design and focuses on arguably the simplest scenario in which the designed peptide corresponds to a contiguous protein subsequence. Amongst these peptides, those corresponding to helical segments are prominent, mainly due to their relative ability to fold independently. Inspired by the clinical success of viral entry inhibitors, which are peptides corresponding to helical segments in viral envelope proteins, a computational tool for the identification of intramolecular helix-helix interactions was developed. Using this approach, peptides having anti-cancer, anti-angiogenic, and anti-inflammatory activities have been recently rationally designed and biologically characterized.
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Affiliation(s)
- Yossef Kliger
- Compugen LTD, 72 Pinchas Rosen, Tel Aviv 69512, Israel.
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25
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Velásquez JE, van der Donk W. Genome mining for ribosomally synthesized natural products. Curr Opin Chem Biol 2011; 15:11-21. [PMID: 21095156 PMCID: PMC3090663 DOI: 10.1016/j.cbpa.2010.10.027] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Revised: 10/20/2010] [Accepted: 10/25/2010] [Indexed: 11/20/2022]
Abstract
In recent years, the number of known peptide natural products that are synthesized via the ribosomal pathway has rapidly grown. Taking advantage of sequence homology among genes encoding precursor peptides or biosynthetic proteins, in silico mining of genomes combined with molecular biology approaches has guided the discovery of a large number of new ribosomal natural products, including lantipeptides, cyanobactins, linear thiazole/oxazole-containing peptides, microviridins, lasso peptides, amatoxins, cyclotides, and conopeptides. In this review, we describe the strategies used for the identification of these ribosomally synthesized and posttranslationally modified peptides (RiPPs) and the structures of newly identified compounds. The increasing number of chemical entities and their remarkable structural and functional diversity may lead to novel pharmaceutical applications.
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Affiliation(s)
- Juan E. Velásquez
- Department of Chemistry, University of Illinois at Urbana-Champaign; Urbana, Illinois, 61801; USA
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign; Urbana, Illinois, 61801; USA
| | - Wilfred van der Donk
- Department of Chemistry, University of Illinois at Urbana-Champaign; Urbana, Illinois, 61801; USA
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign; Urbana, Illinois, 61801; USA
- Howard Hughes Medical Institute; University of Illinois at Urbana-Champaign; Urbana, Illinois, 61801; USA
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Ambaye ND, Gunzburg MJ, Lim RCC, Price JT, Wilce MCJ, Wilce JA. Benzopyrazine derivatives: A novel class of growth factor receptor bound protein 7 antagonists. Bioorg Med Chem 2010; 19:693-701. [PMID: 21134757 DOI: 10.1016/j.bmc.2010.10.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 10/08/2010] [Accepted: 10/12/2010] [Indexed: 11/15/2022]
Abstract
Growth factor receptor bound protein 7 (Grb7) is an adapter protein that functions as a downstream effector of growth factor mediated signal transduction. Over-expression of Grb7 has been implicated in a variety of cancers such as breast, blood, pancreatic, esophageal, and gastric carcinomas. Inhibition of Grb7 has been shown to reduce the migratory and proliferative potential of these cancers, making it an attractive therapeutic target. Starting with a known peptide antagonist, the present work reports the application of a succession of computational ligand design tools comprising a ligand shape based similarity search, molecular docking and a 2D-similarity search to identify small molecular antagonists of the Grb7-SH2 domain from the NCI chemical database. Binding to the Grb7-SH2 domain was then experimentally tested using melting point shift assays and isothermal titration calorimetry. Overall, a total of 11 benzopyrazine based small molecular antagonists were identified with affinity for the Grb7-SH2 domain. Representative compounds tested using ITC were revealed to possess moderate binding affinity in the low micromolar range. Finally, the lead compound (NSC642056) was found to reduce the growth of a Grb7-expressing breast cancer cell line with an IC(50) of 86μM. It is expected that the identified antagonists will be useful additions to further explore the function of Grb7 and for the development of inhibitors with therapeutic potential.
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Affiliation(s)
- Nigus D Ambaye
- Department of Biochemistry and Molecular Biology, Monash University, Wellington Road, Victoria 3800, Australia
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Ovadia O, Greenberg S, Laufer B, Gilon C, Hoffman A, Kessler H. Improvement of drug-like properties of peptides: the somatostatin paradigm. Expert Opin Drug Discov 2010; 5:655-71. [DOI: 10.1517/17460441.2010.493935] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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