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Improved prediction and characterization of blood-brain barrier penetrating peptides using estimated propensity scores of dipeptides. J Comput Aided Mol Des 2022; 36:781-796. [DOI: 10.1007/s10822-022-00476-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/15/2022] [Indexed: 11/27/2022]
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B3Pred: A Random-Forest-Based Method for Predicting and Designing Blood-Brain Barrier Penetrating Peptides. Pharmaceutics 2021; 13:pharmaceutics13081237. [PMID: 34452198 PMCID: PMC8399279 DOI: 10.3390/pharmaceutics13081237] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/07/2021] [Accepted: 07/14/2021] [Indexed: 12/14/2022] Open
Abstract
The blood–brain barrier is a major obstacle in treating brain-related disorders, as it does not allow the delivery of drugs into the brain. We developed a method for predicting blood–brain barrier penetrating peptides to facilitate drug delivery into the brain. These blood–brain barrier penetrating peptides (B3PPs) can act as therapeutics, as well as drug delivery agents. We trained, tested, and evaluated our models on blood–brain barrier peptides obtained from the B3Pdb database. First, we computed a wide range of peptide features. Then, we selected relevant peptide features. Finally, we developed numerous machine-learning-based models for predicting blood–brain barrier peptides using the selected features. The random-forest-based model performed the best with respect to the top 80 selected features and achieved a maximal 85.08% accuracy with an AUROC of 0.93. We also developed a webserver, B3pred, that implements our best models. It has three major modules that allow users to predict/design B3PPs and scan B3PPs in a protein sequence.
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Dhir N, Medhi B, Prakash A, Goyal MK, Modi M, Mohindra S. Pre-clinical to Clinical Translational Failures and Current Status of Clinical Trials in Stroke Therapy: A Brief Review. Curr Neuropharmacol 2020; 18:596-612. [PMID: 31934841 PMCID: PMC7457423 DOI: 10.2174/1570159x18666200114160844] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/31/2019] [Accepted: 12/28/2019] [Indexed: 12/16/2022] Open
Abstract
In stroke (cerebral ischemia), despite continuous efforts both at the experimental and clinical level, the only approved pharmacological treatment has been restricted to tissue plasminogen activator (tPA). Stroke is the leading cause of functional disability and mortality throughout worldwide. Its pathophysiology starts with energy pump failure, followed by complex signaling cascade that ultimately ends in neuronal cell death. Ischemic cascade involves excessive glutamate release followed by raised intracellular sodium and calcium influx along with free radicals' generation, activation of inflammatory cytokines, NO synthases, lipases, endonucleases and other apoptotic pathways leading to cell edema and death. At the pre-clinical stage, several agents have been tried and proven as an effective neuroprotectant in animal models of ischemia. However, these agents failed to show convincing results in terms of efficacy and safety when the trials were conducted in humans following stroke. This article highlights the various agents which have been tried in the past but failed to translate into stroke therapy along with key points that are responsible for the lagging of experimental success to translational failure in stroke treatment.
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Affiliation(s)
| | - Bikash Medhi
- Address correspondence to this author at the Department of Pharmacology, Research Block B, 4th Floor, Room no 4043, Postgraduate Institute of Medical Education & Research (PGIMER), Chandigarh, 160012, India; E-mail:
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Meloni BP, Milani D, Edwards AB, Anderton RS, O'Hare Doig RL, Fitzgerald M, Palmer TN, Knuckey NW. Neuroprotective peptides fused to arginine-rich cell penetrating peptides: Neuroprotective mechanism likely mediated by peptide endocytic properties. Pharmacol Ther 2015; 153:36-54. [PMID: 26048328 DOI: 10.1016/j.pharmthera.2015.06.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/29/2015] [Indexed: 12/22/2022]
Abstract
Several recent studies have demonstrated that TAT and other arginine-rich cell penetrating peptides (CPPs) have intrinsic neuroprotective properties in their own right. Examples, we have demonstrated that in addition to TAT, poly-arginine peptides (R8 to R18; containing 8-18 arginine residues) as well as some other arginine-rich peptides are neuroprotective in vitro (in neurons exposed to glutamic acid excitotoxicity and oxygen glucose deprivation) and in the case of R9 in vivo (after permanent middle cerebral artery occlusion in the rat). Based on several lines of evidence, we propose that this neuroprotection is related to the peptide's endocytosis-inducing properties, with peptide charge and arginine residues being critical factors. Specifically, we propose that during peptide endocytosis neuronal cell surface structures such as ion channels and transporters are internalised, thereby reducing calcium influx associated with excitotoxicity and other receptor-mediated neurodamaging signalling pathways. We also hypothesise that a peptide cargo can act synergistically with TAT and other arginine-rich CPPs due to potentiation of the CPPs endocytic traits rather than by the cargo-peptide acting directly on its supposedly intended intracellular target. In this review, we systematically consider a number of studies that have used CPPs to deliver neuroprotective peptides to the central nervous system (CNS) following stroke and other neurological disorders. Consequently, we critically review evidence that supports our hypothesis that neuroprotection is mediated by carrier peptide endocytosis. In conclusion, we believe that there are strong grounds to regard arginine-rich peptides as a new class of neuroprotective molecules for the treatment of a range of neurological disorders.
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Affiliation(s)
- Bruno P Meloni
- Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, Australia; Department of Neurosurgery, Sir Charles Gairdner Hospital, QEII Medical Centre, Nedlands, Western Australia, Australia; Western Australian Neuroscience Research Institute, Nedlands, Australia.
| | - Diego Milani
- Western Australian Neuroscience Research Institute, Nedlands, Australia; School of Heath Sciences, The University Notre Dame, Fremantle, Western Australia, Australia
| | - Adam B Edwards
- Western Australian Neuroscience Research Institute, Nedlands, Australia; School of Heath Sciences, The University Notre Dame, Fremantle, Western Australia, Australia
| | - Ryan S Anderton
- Western Australian Neuroscience Research Institute, Nedlands, Australia; School of Heath Sciences, The University Notre Dame, Fremantle, Western Australia, Australia
| | - Ryan L O'Hare Doig
- Experimental and Regenerative Neurosciences, Western Australia, Australia; School of Anatomy, Physiology and Human Biology, The University of Western Australia, Nedlands, Australia; School of Animal Biology, The University of Western Australia, Nedlands, Australia
| | - Melinda Fitzgerald
- Experimental and Regenerative Neurosciences, Western Australia, Australia; School of Anatomy, Physiology and Human Biology, The University of Western Australia, Nedlands, Australia; School of Animal Biology, The University of Western Australia, Nedlands, Australia
| | - T Norman Palmer
- Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, Australia; Western Australian Neuroscience Research Institute, Nedlands, Australia
| | - Neville W Knuckey
- Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Nedlands, Australia; Department of Neurosurgery, Sir Charles Gairdner Hospital, QEII Medical Centre, Nedlands, Western Australia, Australia; Western Australian Neuroscience Research Institute, Nedlands, Australia
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Elshan NGRD, Jayasundera T, Weber CS, Lynch RM, Mash EA. Development of a time-resolved fluorescence probe for evaluation of competitive binding to the cholecystokinin 2 receptor. Bioorg Med Chem 2015; 23:1841-8. [PMID: 25769518 PMCID: PMC4380538 DOI: 10.1016/j.bmc.2015.02.028] [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: 01/09/2015] [Revised: 02/06/2015] [Accepted: 02/16/2015] [Indexed: 10/23/2022]
Abstract
The synthesis, characterization, and use of Eu-DTPA-PEGO-Trp-Nle-Asp-Phe-NH2 (Eu-DTPA-PEGO-CCK4), a luminescent probe targeted to cholecystokinin 2 receptor (CCK2R, aka CCKBR), are described. The probe was prepared by solid phase synthesis. A Kd value of 17±2nM was determined by means of saturation binding assays using HEK-293 cells that overexpress CCK2R. The probe was then used in competitive binding assays against Ac-CCK4 and three new trivalent CCK4 compounds. Repeatable and reproducible binding assay results were obtained. Given its ease of synthesis, purification, receptor binding properties, and utility in competitive binding assays, Eu-DTPA-PEGO-CCK4 could become a standard tool for high-throughput screening of compounds in development targeted to cholecystokinin receptors.
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Affiliation(s)
- N G R Dayan Elshan
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721-0041, USA
| | | | - Craig S Weber
- Department of Physiology, University of Arizona, Tucson, AZ 85724-5051, USA
| | - Ronald M Lynch
- Department of Physiology, University of Arizona, Tucson, AZ 85724-5051, USA; The Bio5 Institute, University of Arizona, Tucson, AZ 85721-0240, USA
| | - Eugene A Mash
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721-0041, USA.
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Identification and characterization of a novel cell-penetrating peptide of 30Kc19 protein derived from Bombyx mori. Process Biochem 2014. [DOI: 10.1016/j.procbio.2014.05.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Wängler C, Chowdhury S, Höfner G, Djurova P, Purisima EO, Bartenstein P, Wängler B, Fricker G, Wanner KT, Schirrmacher R. Shuttle-cargo fusion molecules of transport peptides and the hD2/3 receptor antagonist fallypride: a feasible approach to preserve ligand-receptor binding? J Med Chem 2014; 57:4368-81. [PMID: 24779610 DOI: 10.1021/jm5004123] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
To determine if the conjugation of a small receptor ligand to a peptidic carrier to potentially facilitate transport across the blood-brain barrier (BBB) by "molecular Trojan horse" transcytosis is feasible, we synthesized several transport peptide-fallypride fusion molecules as model systems and determined their binding affinities to the hD2 receptor. Although they were affected by conjugation, the binding affinities were found to be still in the nanomolar range (between 1.5 and 64.2 nM). In addition, homology modeling of the receptor and docking studies for the most potent compounds were performed, elucidating the binding modes of the fusion molecules and the structure elements contributing to the observed high receptor binding. Furthermore, no interaction between the hybrid compounds and P-gp, the main excretory transporter of the BBB, was found. From these results, it can be inferred that the approach to deliver small neuroreceptor ligands across the BBB by transport peptide carriers is feasible.
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Affiliation(s)
- Carmen Wängler
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University , Montreal H3A 2B4, Canada
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The neuroprotective efficacy of cell-penetrating peptides TAT, penetratin, Arg-9, and Pep-1 in glutamic acid, kainic acid, and in vitro ischemia injury models using primary cortical neuronal cultures. Cell Mol Neurobiol 2013; 34:173-81. [PMID: 24213248 DOI: 10.1007/s10571-013-9999-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Accepted: 10/17/2013] [Indexed: 02/04/2023]
Abstract
Cell-penetrating peptides (CPPs) are small peptides (typically 5-25 amino acids), which are used to facilitate the delivery of normally non-permeable cargos such as other peptides, proteins, nucleic acids, or drugs into cells. However, several recent studies have demonstrated that the TAT CPP has neuroprotective properties. Therefore, in this study, we assessed the TAT and three other CPPs (penetratin, Arg-9, Pep-1) for their neuroprotective properties in cortical neuronal cultures following exposure to glutamic acid, kainic acid, or in vitro ischemia (oxygen-glucose deprivation). Arg-9, penetratin, and TAT-D displayed consistent and high level neuroprotective activity in both the glutamic acid (IC50: 0.78, 3.4, 13.9 μM) and kainic acid (IC50: 0.81, 2.0, 6.2 μM) injury models, while Pep-1 was ineffective. The TAT-D isoform displayed similar efficacy to the TAT-L isoform in the glutamic acid model. Interestingly, Arg-9 was the only CPP that displayed efficacy when washed-out prior to glutamic acid exposure. Neuroprotection following in vitro ischemia was more variable with all peptides providing some level of neuroprotection (IC50; Arg-9: 6.0 μM, TAT-D: 7.1 μM, penetratin/Pep-1: >10 μM). The positive control peptides JNKI-1D-TAT (JNK inhibitory peptide) and/or PYC36L-TAT (AP-1 inhibitory peptide) were neuroprotective in all models. Finally, in a post-glutamic acid treatment experiment, Arg-9 was highly effective when added immediately after, and mildly effective when added 15 min post-insult, while the JNKI-1D-TAT control peptide was ineffective when added post-insult. These findings demonstrate that different CPPs have the ability to inhibit neurodamaging events/pathways associated with excitotoxic and ischemic injuries. More importantly, they highlight the need to interpret neuroprotection studies when using CPPs as delivery agents with caution. On a positive note, the cytoprotective properties of CPPs suggests they are ideal carrier molecules to deliver neuroprotective drugs to the CNS following injury and/or potential neuroprotectants in their own right.
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Halder SK, Matsunaga H, Yamaguchi H, Ueda H. Novel neuroprotective action of prothymosin alpha-derived peptide against retinal and brain ischemic damages. J Neurochem 2013; 125:713-23. [DOI: 10.1111/jnc.12132] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 12/03/2012] [Accepted: 12/04/2012] [Indexed: 12/21/2022]
Affiliation(s)
- Sebok Kumar Halder
- Department of Molecular Pharmacology and Neuroscience; Nagasaki University Graduate School of Biomedical Sciences; Nagasaki Japan
| | - Hayato Matsunaga
- Department of Molecular Pharmacology and Neuroscience; Nagasaki University Graduate School of Biomedical Sciences; Nagasaki Japan
| | - Haruka Yamaguchi
- Department of Molecular Pharmacology and Neuroscience; Nagasaki University Graduate School of Biomedical Sciences; Nagasaki Japan
| | - Hiroshi Ueda
- Department of Molecular Pharmacology and Neuroscience; Nagasaki University Graduate School of Biomedical Sciences; Nagasaki Japan
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