1
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King HR, Bycroft M, Nguyen TB, Kelly G, Vinogradov AA, Rowling PJE, Stott K, Ascher DB, Suga H, Itzhaki LS, Artavanis-Tsakonas K. Targeting the Plasmodium falciparum UCHL3 ubiquitin hydrolase using chemically constrained peptides. Proc Natl Acad Sci U S A 2024; 121:e2322923121. [PMID: 38739798 PMCID: PMC11126973 DOI: 10.1073/pnas.2322923121] [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: 01/11/2024] [Accepted: 03/18/2024] [Indexed: 05/16/2024] Open
Abstract
The ubiquitin-proteasome system is essential to all eukaryotes and has been shown to be critical to parasite survival as well, including Plasmodium falciparum, the causative agent of the deadliest form of malarial disease. Despite the central role of the ubiquitin-proteasome pathway to parasite viability across its entire life-cycle, specific inhibitors targeting the individual enzymes mediating ubiquitin attachment and removal do not currently exist. The ability to disrupt P. falciparum growth at multiple developmental stages is particularly attractive as this could potentially prevent both disease pathology, caused by asexually dividing parasites, as well as transmission which is mediated by sexually differentiated parasites. The deubiquitinating enzyme PfUCHL3 is an essential protein, transcribed across both human and mosquito developmental stages. PfUCHL3 is considered hard to drug by conventional methods given the high level of homology of its active site to human UCHL3 as well as to other UCH domain enzymes. Here, we apply the RaPID mRNA display technology and identify constrained peptides capable of binding to PfUCHL3 with nanomolar affinities. The two lead peptides were found to selectively inhibit the deubiquitinase activity of PfUCHL3 versus HsUCHL3. NMR spectroscopy revealed that the peptides do not act by binding to the active site but instead block binding of the ubiquitin substrate. We demonstrate that this approach can be used to target essential protein-protein interactions within the Plasmodium ubiquitin pathway, enabling the application of chemically constrained peptides as a novel class of antimalarial therapeutics.
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Affiliation(s)
- Harry R. King
- Department of Pathology, University of Cambridge, CambridgeCB2 1QP, United Kingdom
- Department of Pharmacology, University of Cambridge, CambridgeCB2 1PD, United Kingdom
| | - Mark Bycroft
- Department of Pharmacology, University of Cambridge, CambridgeCB2 1PD, United Kingdom
| | - Thanh-Binh Nguyen
- School of Chemistry and Molecular Biosciences, University of Queensland, BrisbaneQLD 4067, Australia
| | - Geoff Kelly
- NMR Centre, Francis Crick Institute, LondonNW1 1AT, United Kingdom
| | - Alexander A. Vinogradov
- Department of Chemistry, Graduate School of Science, University of Tokyo, Tokyo113-0033, Japan
| | - Pamela J. E. Rowling
- Department of Pharmacology, University of Cambridge, CambridgeCB2 1PD, United Kingdom
| | - Katherine Stott
- Department of Biochemistry, University of Cambridge, CambridgeCB2 1GA, United Kingdom
| | - David B. Ascher
- School of Chemistry and Molecular Biosciences, University of Queensland, BrisbaneQLD 4067, Australia
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, University of Tokyo, Tokyo113-0033, Japan
| | - Laura S. Itzhaki
- Department of Pharmacology, University of Cambridge, CambridgeCB2 1PD, United Kingdom
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2
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Kröner L, Lötters S, Hopp MT. Insights into caudate amphibian skin secretions with a focus on the chemistry and bioactivity of derived peptides. Biol Chem 2024; 0:hsz-2024-0035. [PMID: 38766708 DOI: 10.1515/hsz-2024-0035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/06/2024] [Indexed: 05/22/2024]
Abstract
Amphibians are well-known for their ability to produce and secrete a mixture of bioactive substances in specialized skin glands for the purpose of antibiotic self-protection and defense against predators. Some of these secretions contain various small molecules, such as the highly toxic batrachotoxin, tetrodotoxin, and samandarine. For some time, the presence of peptides in amphibian skin secretions has attracted researchers, consisting of a diverse collection of - to the current state of knowledge - three to 104 amino acid long sequences. From these more than 2000 peptides many are known to exert antimicrobial effects. In addition, there are some reports on amphibian skin peptides that can promote wound healing, regulate immunoreactions, and may serve as antiparasitic and antioxidative substances. So far, the focus has mainly been on skin peptides from frogs and toads (Anura), eclipsing the research on skin peptides of the ca. 700 salamanders and newts (Caudata). Just recently, several novel observations dealing with caudate peptides and their structure-function relationships were reported. This review focuses on the chemistry and bioactivity of caudate amphibian skin peptides and their potential as novel agents for clinical applications.
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Affiliation(s)
- Lorena Kröner
- Department of Chemistry, Institute for Integrated Natural Sciences, 38899 University of Koblenz , D-56070 Koblenz, Germany
| | - Stefan Lötters
- Department of Biogeography, University of Trier, D-54286 Trier, Germany
| | - Marie-T Hopp
- Department of Chemistry, Institute for Integrated Natural Sciences, 38899 University of Koblenz , D-56070 Koblenz, Germany
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3
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He RN, Zhang MJ, Dai B, Kong XD. Selection of Peptide-Bismuth Bicycles Using Phage Display. ACS Chem Biol 2024; 19:1040-1044. [PMID: 38620022 DOI: 10.1021/acschembio.4c00099] [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: 04/17/2024]
Abstract
Cysteine conjugation is widely used to constrain phage displayed peptides for the selection of cyclic peptides against specific targets. In this study, the nontoxic Bi3+ ion was used as a cysteine conjugation reagent to cross-link peptide libraries without compromising phage infectivity. We constructed a randomized 3-cysteine peptide library and cyclized it with Bi3+, followed by a selection against the maltose-binding protein as a model target. Next-generation sequencing of selection samples revealed the enrichment of peptides containing clear consensus sequences. Chemically synthesized linear and Bi3+ cyclized peptides were used for affinity validation. The cyclized peptide showed a hundred-fold better affinity (0.31 ± 0.04 μM) than the linear form (39 ± 6 μM). Overall, our study proved the feasibility of developing Bi3+ constrained bicyclic peptides against a specific target using phage display, which would potentially accelerate the development of new peptide-bismuth bicycles for therapeutic or diagnostic applications.
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Affiliation(s)
- Ruo-Nan He
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, 429 Zhangheng Road, Shanghai 201203, China
| | - Meng-Jie Zhang
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, 429 Zhangheng Road, Shanghai 201203, China
| | - Bin Dai
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xu-Dong Kong
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, 429 Zhangheng Road, Shanghai 201203, China
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4
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Saunders GJ, Spring SA, Jayawant E, Wilkening I, Roesner S, Clarkson GJ, Dixon AM, Notman R, Shipman M. Synthesis and Functionalization of Azetidine-Containing Small Macrocyclic Peptides. Chemistry 2024; 30:e202400308. [PMID: 38488326 DOI: 10.1002/chem.202400308] [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: 02/25/2024] [Indexed: 04/11/2024]
Abstract
Cyclic peptides are increasingly important structures in drugs but their development can be impeded by difficulties associated with their synthesis. Here, we introduce the 3-aminoazetidine (3-AAz) subunit as a new turn-inducing element for the efficient synthesis of small head-to-tail cyclic peptides. Greatly improved cyclizations of tetra-, penta- and hexapeptides (28 examples) under standard reaction conditions are achieved by introduction of this element within the linear peptide precursor. Post-cyclization deprotection of the amino acid side chains with strong acid is realized without degradation of the strained four-membered azetidine. A special feature of this chemistry is that further late-stage modification of the resultant macrocyclic peptides can be achieved via the 3-AAz unit. This is done by: (i) chemoselective deprotection and substitution at the azetidine nitrogen, or by (ii) a click-based approach employing a 2-propynyl carbamate on the azetidine nitrogen. In this way, a range of dye and biotin tagged macrocycles are readily produced. Structural insights gained by XRD analysis of a cyclic tetrapeptide indicate that the azetidine ring encourages access to the less stable, all-trans conformation. Moreover, introduction of a 3-AAz into a representative cyclohexapeptide improves stability towards proteases compared to the homodetic macrocycle.
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Affiliation(s)
- George J Saunders
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Sam A Spring
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Eleanor Jayawant
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Ina Wilkening
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Stefan Roesner
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Guy J Clarkson
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Ann M Dixon
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Rebecca Notman
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
| | - Michael Shipman
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, U.K
- The Palatine Centre, Stockton Road, Durham, DH1 3LE, U.K
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5
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Pirhaghi M, Mamashli F, Moosavi-Movahedi F, Arghavani P, Amiri A, Davaeil B, Mohammad-Zaheri M, Mousavi-Jarrahi Z, Sharma D, Langel Ü, Otzen DE, Saboury AA. Cell-Penetrating Peptides: Promising Therapeutics and Drug-Delivery Systems for Neurodegenerative Diseases. Mol Pharm 2024; 21:2097-2117. [PMID: 38440998 DOI: 10.1021/acs.molpharmaceut.3c01167] [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: 03/06/2024]
Abstract
Currently, one of the most significant and rapidly growing unmet medical challenges is the treatment of neurodegenerative diseases such as Alzheimer's disease (AD) and Parkinson's disease (PD). This challenge encompasses the imperative development of efficacious therapeutic agents and overcoming the intricacies of the blood-brain barrier for successful drug delivery. Here we focus on the delivery aspect with particular emphasis on cell-penetrating peptides (CPPs), widely used in basic and translational research as they enhance drug delivery to challenging targets such as tissue and cellular compartments and thus increase therapeutic efficacy. The combination of CPPs with nanomaterials such as nanoparticles (NPs) improves the performance, accuracy, and stability of drug delivery and enables higher drug loads. Our review presents and discusses research that utilizes CPPs, either alone or in conjugation with NPs, to mitigate the pathogenic effects of neurodegenerative diseases with particular reference to AD and PD.
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Affiliation(s)
- Mitra Pirhaghi
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 6673145137, Iran
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614335, Iran
| | - Fatemeh Mamashli
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614335, Iran
| | | | - Payam Arghavani
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614335, Iran
| | - Ahmad Amiri
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614335, Iran
| | - Bagher Davaeil
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614335, Iran
| | - Mahya Mohammad-Zaheri
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614335, Iran
| | - Zahra Mousavi-Jarrahi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614335, Iran
| | - Deepak Sharma
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh 160036, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh 201002, India
| | - Ülo Langel
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
| | - Daniel Erik Otzen
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, 8000 Aarhus C 1592-224, Denmark
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614335, Iran
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6
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Sharma A, Singh LR. An insight into the pharmacology of cysteine/methionine containing peptide drugs. Eur J Med Chem 2024; 271:116456. [PMID: 38691890 DOI: 10.1016/j.ejmech.2024.116456] [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: 01/16/2024] [Revised: 04/13/2024] [Accepted: 04/16/2024] [Indexed: 05/03/2024]
Abstract
Since last century, peptides have emerged as potential drugs with >90 FDA approvals for various targets with several in the pipeline. Sulphur, in peptides is present either as thiol (-SH) from Cys or thioether from Met. In this review, all the peptides approved by FDA since 2000 containing sulphur have been included. Among them ∼50 % contains disulphide bridges. This clearly demonstrates the significance of disulphide bonds in peptide drugs. This can be achieved synthetically by using orthogonal protecting groups (PGs) for -SH. These PGs are compatible with Solid Phase Peptide Synthesis (SPPS), which is still the method of choice for peptide synthesis. The orthogonal PGs used for Cys thiol side chain protecting for disulphide bond formation have been included which are currently in use both by academia and industry from small scale to large scale synthesis. In addition, the details of the FDA approved drugs containing Cys and Met (or both) have also been discussed.
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Affiliation(s)
- Anamika Sharma
- Department of Natural Products and Medicinal Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500007, India; Chemical Science Division, Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - L Ravithej Singh
- Chemical Science Division, Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; Fluoro-Agrochemicals Division, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India.
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7
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Villequey C, Zurmühl SS, Cramer CN, Bhusan B, Andersen B, Ren Q, Liu H, Qu X, Yang Y, Pan J, Chen Q, Münzel M. An efficient mRNA display protocol yields potent bicyclic peptide inhibitors for FGFR3c: outperforming linear and monocyclic formats in affinity and stability. Chem Sci 2024; 15:6122-6129. [PMID: 38665530 PMCID: PMC11040643 DOI: 10.1039/d3sc04763f] [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: 09/08/2023] [Accepted: 03/15/2024] [Indexed: 04/28/2024] Open
Abstract
Macrocyclization has positioned itself as a powerful method for engineering potent peptide drug candidates. Introducing one or multiple cyclizations is a common strategy to improve properties such as affinity, bioavailability and proteolytic stability. Consequently, methodologies to create large libraries of polycyclic peptides by phage or mRNA display have emerged, allowing the rapid identification of binders to virtually any target. Yet, within those libraries, the performance of linear vs. mono- or bicyclic peptides has rarely been studied. Indeed, a key parameter to perform such a comparison is to use a display protocol and cyclization chemistry that enables the formation of all 3 formats in equal quality and diversity. Here, we developed a simple, efficient and fast mRNA display protocol which meets these criteria and can be used to generate highly diverse libraries of thioether cyclized polycyclic peptides. As a proof of concept, we selected peptides against fibroblast growth factor receptor 3c (FGFR3c) and compared the different formats regarding affinity, specificity, and human plasma stability. The peptides with the best KD's and stability were identified among bicyclic peptide hits, further strengthening the body of evidence pointing at the superiority of this class of molecules and providing functional and selective inhibitors of FGFR3c.
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Affiliation(s)
- Camille Villequey
- Global Research Technologies, Novo Nordisk A/S Novo Nordisk Park 2760 Måløv Denmark
| | - Silvana S Zurmühl
- Global Research Technologies, Novo Nordisk A/S Novo Nordisk Park 2760 Måløv Denmark
| | - Christian N Cramer
- Global Research Technologies, Novo Nordisk A/S Novo Nordisk Park 2760 Måløv Denmark
| | - Bhaskar Bhusan
- Department of Chemistry, Oxford University, Chemistry Research Laboratory 12 Mansfield Road Oxford UK
| | - Birgitte Andersen
- Global Drug Discovery, Novo Nordisk A/S Novo Nordisk Park 2760 Måløv Denmark
| | - Qianshen Ren
- Novo Nordisk Research Center China, Novo Nordisk A/S Shengmingyuan West Ring Rd, Changping District Beijing China
| | - Haimo Liu
- Novo Nordisk Research Center China, Novo Nordisk A/S Shengmingyuan West Ring Rd, Changping District Beijing China
| | - Xinping Qu
- Novo Nordisk Research Center China, Novo Nordisk A/S Shengmingyuan West Ring Rd, Changping District Beijing China
| | - Yang Yang
- Novo Nordisk Research Center China, Novo Nordisk A/S Shengmingyuan West Ring Rd, Changping District Beijing China
| | - Jia Pan
- Novo Nordisk Research Center China, Novo Nordisk A/S Shengmingyuan West Ring Rd, Changping District Beijing China
| | - Qiujia Chen
- Novo Nordisk Research Center China, Novo Nordisk A/S Shengmingyuan West Ring Rd, Changping District Beijing China
| | - Martin Münzel
- Global Research Technologies, Novo Nordisk A/S Novo Nordisk Park 2760 Måløv Denmark
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8
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Frazee N, Billlings KR, Mertz B. Gaussian accelerated molecular dynamics simulations facilitate prediction of the permeability of cyclic peptides. PLoS One 2024; 19:e0300688. [PMID: 38652734 PMCID: PMC11037548 DOI: 10.1371/journal.pone.0300688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 03/02/2024] [Indexed: 04/25/2024] Open
Abstract
Despite their widespread use as therapeutics, clinical development of small molecule drugs remains challenging. Among the many parameters that undergo optimization during the drug development process, increasing passive cell permeability (i.e., log(P)) can have some of the largest impact on potency. Cyclic peptides (CPs) have emerged as a viable alternative to small molecules, as they retain many of the advantages of small molecules (oral availability, target specificity) while being highly effective at traversing the plasma membrane. However, the relationship between the dominant conformations that typify CPs in an aqueous versus a membrane environment and cell permeability remain poorly characterized. In this study, we have used Gaussian accelerated molecular dynamics (GaMD) simulations to characterize the effect of solvent on the free energy landscape of lariat peptides, a subset of CPs that have recently shown potential for drug development (Kelly et al., JACS 2021). Differences in the free energy of lariat peptides as a function of solvent can be used to predict permeability of these molecules, and our results show that permeability is most greatly influenced by N-methylation and exposure to solvent. Our approach lays the groundwork for using GaMD as a way to virtually screen large libraries of CPs and drive forward development of CP-based therapeutics.
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Affiliation(s)
- Nicolas Frazee
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, United States of America
| | - Kyle R. Billlings
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, United States of America
| | - Blake Mertz
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, United States of America
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9
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Belenichev I, Popazova O, Bukhtiyarova N, Savchenko D, Oksenych V, Kamyshnyi O. Modulating Nitric Oxide: Implications for Cytotoxicity and Cytoprotection. Antioxidants (Basel) 2024; 13:504. [PMID: 38790609 PMCID: PMC11118938 DOI: 10.3390/antiox13050504] [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: 03/26/2024] [Revised: 04/19/2024] [Accepted: 04/20/2024] [Indexed: 05/26/2024] Open
Abstract
Despite the significant progress in the fields of biology, physiology, molecular medicine, and pharmacology; the designation of the properties of nitrogen monoxide in the regulation of life-supporting functions of the organism; and numerous works devoted to this molecule, there are still many open questions in this field. It is widely accepted that nitric oxide (•NO) is a unique molecule that, despite its extremely simple structure, has a wide range of functions in the body, including the cardiovascular system, the central nervous system (CNS), reproduction, the endocrine system, respiration, digestion, etc. Here, we systematize the properties of •NO, contributing in conditions of physiological norms, as well as in various pathological processes, to the mechanisms of cytoprotection and cytodestruction. Current experimental and clinical studies are contradictory in describing the role of •NO in the pathogenesis of many diseases of the cardiovascular system and CNS. We describe the mechanisms of cytoprotective action of •NO associated with the regulation of the expression of antiapoptotic and chaperone proteins and the regulation of mitochondrial function. The most prominent mechanisms of cytodestruction-the initiation of nitrosative and oxidative stresses, the production of reactive oxygen and nitrogen species, and participation in apoptosis and mitosis. The role of •NO in the formation of endothelial and mitochondrial dysfunction is also considered. Moreover, we focus on the various ways of pharmacological modulation in the nitroxidergic system that allow for a decrease in the cytodestructive mechanisms of •NO and increase cytoprotective ones.
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Affiliation(s)
- Igor Belenichev
- Department of Pharmacology and Medical Formulation with Course of Normal Physiology, Zaporizhzhia State Medical and Pharmaceutical University, 69000 Zaporizhzhia, Ukraine
| | - Olena Popazova
- Department of Histology, Cytology and Embryology, Zaporizhzhia State Medical and Pharmaceutical University, 69000 Zaporizhzhia, Ukraine
| | - Nina Bukhtiyarova
- Department of Clinical Laboratory Diagnostics, Zaporizhzhia State Medical and Pharmaceutical University, 69000 Zaporizhzhia, Ukraine
| | - Dmytro Savchenko
- Department of Pharmacy and Industrial Drug Technology, Bogomolets National Medical University, 01601 Kyiv, Ukraine
| | - Valentyn Oksenych
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway
| | - Oleksandr Kamyshnyi
- Department of Microbiology, Virology and Immunology, I. Horbachevsky Ternopil State Medical University, 46001 Ternopil, Ukraine;
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10
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Giancola JB, Grimm JB, Jun JV, Petri YD, Lavis LD, Raines RT. Evaluation of the Cytosolic Uptake of HaloTag Using a pH-Sensitive Dye. ACS Chem Biol 2024; 19:908-915. [PMID: 38525961 DOI: 10.1021/acschembio.3c00713] [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: 03/26/2024]
Abstract
The efficient cytosolic delivery of proteins is critical for advancing novel therapeutic strategies. Current delivery methods are severely limited by endosomal entrapment, and detection methods lack sophistication in tracking the fate of delivered protein cargo. HaloTag, a commonly used protein in chemical biology and a challenging delivery target, is an exceptional model system for understanding and exploiting cellular delivery. Here, we employed a combinatorial strategy to direct HaloTag to the cytosol. We established the use of Virginia Orange, a pH-sensitive fluorophore, and Janelia Fluor 585, a similar but pH-agnostic fluorophore, in a fluorogenic assay to ascertain protein localization within human cells. Using this assay, we investigated HaloTag delivery upon modification with cell-penetrating peptides, carboxyl group esterification, and cotreatment with an endosomolytic agent. We found efficacious cytosolic entry with two distinct delivery methods. This study expands the toolkit for detecting the cytosolic access of proteins and highlights that multiple intracellular delivery strategies can be used synergistically to effect cytosolic access. Moreover, HaloTag is poised to serve as a platform for the delivery of varied cargo into human cells.
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Affiliation(s)
- JoLynn B Giancola
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jonathan B Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
| | - Joomyung V Jun
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Yana D Petri
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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11
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Fukunaga I, Matsukiyo Y, Kaitoh K, Yamanishi Y. Automatic generation of functional peptides with desired bioactivity and membrane permeability using Bayesian optimization. Mol Inform 2024; 43:e202300148. [PMID: 38182544 DOI: 10.1002/minf.202300148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 02/03/2024] [Accepted: 02/03/2024] [Indexed: 01/07/2024]
Abstract
Peptides are potentially useful modalities of drugs; however, cell membrane permeability is an obstacle in peptide drug discovery. The identification of bioactive peptides for a therapeutic target is also challenging because of the huge amino acid sequence patterns of peptides. In this study, we propose a novel computational method, PEptide generation system using Neural network Trained on Amino acid sequence data and Gaussian process-based optimizatiON (PENTAGON), to automatically generate new peptides with desired bioactivity and cell membrane permeability. In the algorithm, we mapped peptide amino acid sequences onto the latent space constructed using a variational autoencoder and searched for peptides with desired bioactivity and cell membrane permeability using Bayesian optimization. We used our proposed method to generate peptides with cell membrane permeability and bioactivity for each of the nine therapeutic targets, such as the estrogen receptor (ER). Our proposed method outperformed a previously developed peptide generator in terms of similarity to known active peptide sequences and the length of generated peptide sequences.
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Affiliation(s)
- Itsuki Fukunaga
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
| | - Yuki Matsukiyo
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
| | - Kazuma Kaitoh
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
- Department of Complex Systems Science, Graduate School of Informatics, Nagoya University, Chikusa, Nagoya, Aichi, 464-8601, Japan
| | - Yoshihiro Yamanishi
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
- Department of Complex Systems Science, Graduate School of Informatics, Nagoya University, Chikusa, Nagoya, Aichi, 464-8601, Japan
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12
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Pelton JM, Hochuli JE, Sadecki PW, Katoh T, Suga H, Hicks LM, Muratov EN, Tropsha A, Bowers AA. Cheminformatics-Guided Cell-Free Exploration of Peptide Natural Products. J Am Chem Soc 2024; 146:8016-8030. [PMID: 38470819 DOI: 10.1021/jacs.3c11306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
There have been significant advances in the flexibility and power of in vitro cell-free translation systems. The increasing ability to incorporate noncanonical amino acids and complement translation with recombinant enzymes has enabled cell-free production of peptide-based natural products (NPs) and NP-like molecules. We anticipate that many more such compounds and analogs might be accessed in this way. To assess the peptide NP space that is directly accessible to current cell-free technologies, we developed a peptide parsing algorithm that breaks down peptide NPs into building blocks based on ribosomal translation logic. Using the resultant data set, we broadly analyze the biophysical properties of these privileged compounds and perform a retrobiosynthetic analysis to predict which peptide NPs could be directly synthesized in augmented cell-free translation reactions. We then tested these predictions by preparing a library of highly modified peptide NPs. Two macrocyclases, PatG and PCY1, were used to effect the head-to-tail macrocyclization of candidate NPs. This retrobiosynthetic analysis identified a collection of high-priority building blocks that are enriched throughout peptide NPs, yet they had not previously been tested in cell-free translation. To expand the cell-free toolbox into this space, we established, optimized, and characterized the flexizyme-enabled ribosomal incorporation of piperazic acids. Overall, these results demonstrate the feasibility of cell-free translation for peptide NP total synthesis while expanding the limits of the technology. This work provides a novel computational tool for exploration of peptide NP chemical space, that could be expanded in the future to allow design of ribosomal biosynthetic pathways for NPs and NP-like molecules.
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Affiliation(s)
- Jarrett M Pelton
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Joshua E Hochuli
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Patric W Sadecki
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Eugene N Muratov
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Alexander Tropsha
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Albert A Bowers
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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13
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Zhang C, Liu F, Zhang Y, Song C. Macrocycles and macrocyclization in anticancer drug discovery: Important pieces of the puzzle. Eur J Med Chem 2024; 268:116234. [PMID: 38401189 DOI: 10.1016/j.ejmech.2024.116234] [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: 11/17/2023] [Revised: 02/10/2024] [Accepted: 02/11/2024] [Indexed: 02/26/2024]
Abstract
Increasing disease-related proteins have been identified as novel therapeutic targets. Macrocycles are emerging as potential solutions, bridging the gap between conventional small molecules and biomacromolecules in drug discovery. Inspired by successful macrocyclic drugs of natural origins, macrocycles are attracting more attention for enhanced binding affinity and target selectivity. Due to the conformation constraint and structure preorganization, macrocycles can reach bioactive conformations more easily than parent acyclic compounds. Also, rational macrocyclization combined with sequent structural modification will help improve oral bioavailability and combat drug resistance. This review introduces various strategies to enhance membrane permeability in macrocyclization and subsequent modification, such as N-methylation, intramolecular hydrogen bonding modulation, isomerization, and reversible bicyclization. Several case studies highlight macrocyclic inhibitors targeting kinases, HDAC, and protein-protein interactions. Finally, some macrocyclic agents targeting tumor microenvironments are illustrated.
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Affiliation(s)
- Chao Zhang
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China
| | - Fenfen Liu
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
| | - Chun Song
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
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14
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Ly HM, Desgagné M, Nguyen DT, Comeau C, Froehlich U, Marsault É, Boudreault PL. Insights on Structure-Passive Permeability Relationship in Pyrrole and Furan-Containing Macrocycles. J Med Chem 2024; 67:3711-3726. [PMID: 38417040 PMCID: PMC10946398 DOI: 10.1021/acs.jmedchem.3c02162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/19/2023] [Accepted: 01/11/2024] [Indexed: 03/01/2024]
Abstract
Macrocycles have recognized therapeutic potential, but their limited cellular permeability can hinder their development as oral drugs. To better understand the structure-permeability relationship of heterocycle-containing, semipeptidic macrocycles, a library was synthesized. These compounds were created by developing two novel reactions described herein: the reduction of activated oximes by LiBH4 and the aqueous reductive mono-N-alkylation of aldehydes using catalytic SmI2 and stoichiometric Zn. The permeability of the macrocycles was evaluated through a parallel artificial membrane permeability assay (PAMPA), and the results indicated that macrocycles with a furan incorporated into the structure have better passive permeability than those with a pyrrole moiety. Compounds bearing a 2,5-disubstituted pyrrole (endo orientation) were shown to be implicated in intramolecular H-bonds, enhancing their permeability. This study highlighted the impact of heterocycles moieties in semipeptides, creating highly permeable macrocycles, thus showing promising avenues for passive diffusion of drugs beyond the rule-of-five chemical space.
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Affiliation(s)
- Huy M Ly
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001 12e ave Nord, Sherbrooke, QC J1H5N4, Canada
| | - Michael Desgagné
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001 12e ave Nord, Sherbrooke, QC J1H5N4, Canada
| | - Duc Tai Nguyen
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001 12e ave Nord, Sherbrooke, QC J1H5N4, Canada
| | - Christian Comeau
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001 12e ave Nord, Sherbrooke, QC J1H5N4, Canada
| | - Ulrike Froehlich
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001 12e ave Nord, Sherbrooke, QC J1H5N4, Canada
| | - Éric Marsault
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001 12e ave Nord, Sherbrooke, QC J1H5N4, Canada
| | - Pierre-Luc Boudreault
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001 12e ave Nord, Sherbrooke, QC J1H5N4, Canada
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15
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Ghaemi B, Tanwar S, Singh A, Arifin DR, McMahon MT, Barman I, Bulte JWM. Cell-Penetrating and Enzyme-Responsive Peptides for Targeted Cancer Therapy: Role of Arginine Residue Length on Cell Penetration and In Vivo Systemic Toxicity. ACS APPLIED MATERIALS & INTERFACES 2024; 16:11159-11171. [PMID: 38385360 DOI: 10.1021/acsami.3c14908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
For the improved delivery of cancer therapeutics and imaging agents, the conjugation of cell-penetrating peptides (CPPs) increases the cellular uptake and water solubility of agents. Among the various CPPs, arginine-rich peptides have been the most widely used. Combining CPPs with enzyme-responsive peptides presents an innovative strategy to target specific intracellular enzymes in cancer cells and when combined with the appropriate click chemistry can enhance theranostic drug delivery through the formation of intracellular self-assembled nanostructures. However, one drawback of CPPs is their high positive charge which can cause nonspecific binding, leading to off-target accumulation and potential toxicity. Hence, balancing cell-specific penetration, toxicity, and biocompatibility is essential for future clinical efficacy. We synthesized six cancer-specific, legumain-responsive RnAANCK peptides containing one to six arginine residues, with legumain being an asparaginyl endopeptidase that is overexpressed in aggressive prostate tumors. When conjugated to Alexa Fluor 488, R1-R6AANCK peptides exhibited a concentration- and time-dependent cell penetration in prostate cancer cells, which was higher for peptides with higher R values, reaching a plateau after approximately 120 min. Highly aggressive DU145 prostate tumor cells, but not less aggressive LNCaP cells, self-assembled nanoparticles in the cytosol after the cleavage of the legumain-specific peptide. The in vivo biocompatibility was assessed in mice after the intravenous injection of R1-R6AANCK peptides, with concentrations ranging from 0.0125 to 0.4 mmol/kg. The higher arginine content in R4-6 peptides showed blood and urine indicators for the impairment of bone marrow, liver, and kidney function in a dose-dependent manner, with instant hemolysis and morbidity in extreme cases. These findings underscore the importance of designing peptides with the optimal arginine residue length for a proper balance of cell-specific penetration, toxicity, and in vivo biocompatibility.
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Affiliation(s)
- Behnaz Ghaemi
- Russell H. Morgan Department of Radiology and Radiological Science, Division of MR Research, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Cellular Imaging Section and Vascular Biology Program, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Swati Tanwar
- Department of Mechanical Engineering, The Johns Hopkins University Whiting School of Engineering, Baltimore, Maryland 21218, United States
| | - Aruna Singh
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Inc., Baltimore, Maryland 21205, United States
| | - Dian R Arifin
- Russell H. Morgan Department of Radiology and Radiological Science, Division of MR Research, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Cellular Imaging Section and Vascular Biology Program, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Michael T McMahon
- Russell H. Morgan Department of Radiology and Radiological Science, Division of MR Research, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Inc., Baltimore, Maryland 21205, United States
| | - Ishan Barman
- Russell H. Morgan Department of Radiology and Radiological Science, Division of MR Research, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Department of Mechanical Engineering, The Johns Hopkins University Whiting School of Engineering, Baltimore, Maryland 21218, United States
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Jeff W M Bulte
- Russell H. Morgan Department of Radiology and Radiological Science, Division of MR Research, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Cellular Imaging Section and Vascular Biology Program, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Inc., Baltimore, Maryland 21205, United States
- Department of Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University Whiting School of Engineering, Baltimore, Maryland 21218, United States
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16
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Voss S, Adair LD, Achazi K, Kim H, Bergemann S, Bartenschlager R, New EJ, Rademann J, Nitsche C. Cell-Penetrating Peptide-Bismuth Bicycles. Angew Chem Int Ed Engl 2024; 63:e202318615. [PMID: 38126926 DOI: 10.1002/anie.202318615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 12/23/2023]
Abstract
Cell-penetrating peptides (CPPs) play a significant role in the delivery of cargos into human cells. We report the first CPPs based on peptide-bismuth bicycles, which can be readily obtained from commercially available peptide precursors, making them accessible for a wide range of applications. These CPPs enter human cells as demonstrated by live-cell confocal microscopy using fluorescently labelled peptides. We report efficient sequences that demonstrate increased cellular uptake compared to conventional CPPs like the TAT peptide (derived from the transactivating transcriptional activator of human immunodeficiency virus 1) or octaarginine (R8 ), despite requiring only three positive charges. Bicyclization triggered by the presence of bismuth(III) increases cellular uptake by more than one order of magnitude. Through the analysis of cell lysates using inductive coupled plasma mass spectrometry (ICP-MS), we have introduced an alternative approach to examine the cellular uptake of CPPs. This has allowed us to confirm the presence of bismuth in cells after exposure to our CPPs. Mechanistic studies indicated an energy-dependent endocytic cellular uptake sensitive to inhibition by rottlerin, most likely involving macropinocytosis.
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Affiliation(s)
- Saan Voss
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- Department of Biology, Chemistry and Pharmacy, Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Liam D Adair
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Katharina Achazi
- Institut für Chemie und Biochemie, Freie Universität Berlin, Altensteinstraße 23a, 14195, Berlin, Germany
| | - Heeyoung Kim
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Diseases Research (CIID), 69120, Heidelberg, Germany
- German Center for Infection Research, Heidelberg partner site, 69120, Heidelberg, Germany
| | - Silke Bergemann
- Department of Biology, Chemistry and Pharmacy, Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Ralf Bartenschlager
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Diseases Research (CIID), 69120, Heidelberg, Germany
- German Center for Infection Research, Heidelberg partner site, 69120, Heidelberg, Germany
| | - Elizabeth J New
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jörg Rademann
- Department of Biology, Chemistry and Pharmacy, Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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17
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Tang A, Yokota T. Duchenne muscular dystrophy: promising early-stage clinical trials to watch. Expert Opin Investig Drugs 2024; 33:201-217. [PMID: 38291016 DOI: 10.1080/13543784.2024.2313105] [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: 09/23/2023] [Accepted: 01/28/2024] [Indexed: 02/01/2024]
Abstract
INTRODUCTION Current therapies are unable to cure Duchenne muscular dystrophy (DMD), a severe and common form of muscular dystrophy, and instead aim to delay disease progression. Several treatments currently in phase I trials could increase the number of therapeutic options available to patients. AREAS COVERED This review aims to provide an overview of current treatments undergoing or having recently undergone early-stage trials. Several exon-skipping and gene therapy approaches are currently being investigated at the clinical stage to address an unmet need for DMD treatments. This article also covers Phase I trials from the last 5 years that involve inhibitors, small molecules, a purified synthetic flavanol, a cell-based therapy, and repurposed cardiac or tumor medications. EXPERT OPINION With antisense oligonucleotide (AON) treatments making up the majority of conditionally approved DMD therapies, most of the clinical trials occurring within the last 5 years have also evaluated exon-skipping AONs. The approval of Elevidys, a micro-dystrophin therapy, is reflected in a recent trend toward gene transfer therapies in phase I DMD clinical trials, but their safety and efficacy are being established in this phase of development. Other Phase I clinical-stage approaches are diverse, but have a range in efficacy, safety, and endpoint measures.
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Affiliation(s)
- Annie Tang
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
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18
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Geers DWT, Gavriel K, Neumann K. Rapid, traceless and facile peptide cyclization enabled by tetrazine-thiol exchange. J Pept Sci 2024; 30:e3548. [PMID: 37779097 DOI: 10.1002/psc.3548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/25/2023] [Accepted: 09/14/2023] [Indexed: 10/03/2023]
Abstract
Cyclic peptides offer many advantages compared to their linear counterparts, including prolonged stability within the biological environment and enhanced binding affinity. Typically, peptides are cyclized by forming an amide bond, either on-resin or in solution, through extensive use of orthogonal protecting groups or chemoselective ligation strategies, respectively. Here, we show that the chemoselective tetrazine-thiol exchange is a powerful tool for rapid in situ cyclization of peptides without the need for additional activation reagents or extensive protecting group reshuffling. The reaction between N-terminal sulfide-bearing unsymmetric tetrazines and internal cysteines occurs spontaneously within a mildly acidic environment (pH 6.5) and is of traceless nature. The rapidly available unsymmetric sulfide tetrazine building blocks can be incorporated on resin using standard solid-phase peptide synthesis protocols and are orthogonal to trifluoroacetic acid cleavage conditions. The cyclized peptides display high stability, even when incubated with a large excess of free thiols. Due to its traceless and mild nature, we expect that the tetrazine-thiol exchange will be of high value for the in situ formation of cyclic peptide libraries, thus being applicable in drug discovery and development.
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Affiliation(s)
- Daniëlle W T Geers
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Katerina Gavriel
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Kevin Neumann
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
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19
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Ferrie RP, Fuselier T, Wimley WC. Cytosolic Delivery of Bioactive Cyclic Peptide Cargo by Spontaneous Membrane Translocating Peptides. ACS OMEGA 2024; 9:8179-8187. [PMID: 38405535 PMCID: PMC10882622 DOI: 10.1021/acsomega.3c08701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/23/2023] [Accepted: 01/18/2024] [Indexed: 02/27/2024]
Abstract
Cyclic peptides that inhibit protein-protein interactions have significant advantages over linear peptides and small molecules for modulating cellular signaling networks in cancer and other diseases. However, the permeability barrier of the plasma membrane remains a formidable obstacle to the development of cyclic peptides into applicable drugs. Here, we test the ability of a family of synthetically evolved spontaneous membrane translocating peptides (SMTPs) to deliver phalloidin, a representative bioactive cyclic peptide, to the cytosol of human cells in culture. Phalloidin does not enter cells spontaneously, but if delivered to the cytosol, it inhibits actin depolymerization. We thus use a wound-healing cell mobility assay to assess the biological activity of phalloidin conjugated to three SMTPs that we previously discovered. All three SMTPs can deliver phalloidin to the cell cytosol, and one does so at concentrations as low as 3 μM. Delivery occurs despite the fact that the SMTPs were originally selected based on membrane translocation with no cargo other than a small fluorescent dye. These results show that SMTPs are viable delivery vehicles for cyclic peptides, although their efficiency is moderate. Further, these results suggest that one additional generation of synthetic molecular evolution could be used to optimize SMTPs for the efficient delivery of any bioactive cyclic peptide into cells.
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Affiliation(s)
- Ryan P. Ferrie
- Department of Biochemistry
and Molecular Biology, Tulane University
School of Medicine, New Orleans, Louisiana 70112, United States
| | - Taylor Fuselier
- Department of Biochemistry
and Molecular Biology, Tulane University
School of Medicine, New Orleans, Louisiana 70112, United States
| | - William C. Wimley
- Department of Biochemistry
and Molecular Biology, Tulane University
School of Medicine, New Orleans, Louisiana 70112, United States
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20
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Preto AJ, Caniceiro AB, Duarte F, Fernandes H, Ferreira L, Mourão J, Moreira IS. POSEIDON: Peptidic Objects SEquence-based Interaction with cellular DOmaiNs: a new database and predictor. J Cheminform 2024; 16:18. [PMID: 38365724 PMCID: PMC10874016 DOI: 10.1186/s13321-024-00810-7] [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: 10/17/2023] [Accepted: 02/07/2024] [Indexed: 02/18/2024] Open
Abstract
Cell-penetrating peptides (CPPs) are short chains of amino acids that have shown remarkable potential to cross the cell membrane and deliver coupled therapeutic cargoes into cells. Designing and testing different CPPs to target specific cells or tissues is crucial to ensure high delivery efficiency and reduced toxicity. However, in vivo/in vitro testing of various CPPs can be both time-consuming and costly, which has led to interest in computational methodologies, such as Machine Learning (ML) approaches, as faster and cheaper methods for CPP design and uptake prediction. However, most ML models developed to date focus on classification rather than regression techniques, because of the lack of informative quantitative uptake values. To address these challenges, we developed POSEIDON, an open-access and up-to-date curated database that provides experimental quantitative uptake values for over 2,300 entries and physicochemical properties of 1,315 peptides. POSEIDON also offers physicochemical properties, such as cell line, cargo, and sequence, among others. By leveraging this database along with cell line genomic features, we processed a dataset of over 1,200 entries to develop an ML regression CPP uptake predictor. Our results demonstrated that POSEIDON accurately predicted peptide cell line uptake, achieving a Pearson correlation of 0.87, Spearman correlation of 0.88, and r2 score of 0.76, on an independent test set. With its comprehensive and novel dataset, along with its potent predictive capabilities, the POSEIDON database and its associated ML predictor signify a significant leap forward in CPP research and development. The POSEIDON database and ML Predictor are available for free and with a user-friendly interface at https://moreiralab.com/resources/poseidon/ , making them valuable resources for advancing research on CPP-related topics. Scientific Contribution Statement: Our research addresses the critical need for more efficient and cost-effective methodologies in Cell-Penetrating Peptide (CPP) research. We introduced POSEIDON, a comprehensive and freely accessible database that delivers quantitative uptake values for over 2,300 entries, along with detailed physicochemical profiles for 1,315 peptides. Recognizing the limitations of current Machine Learning (ML) models for CPP design, our work leveraged the rich dataset provided by POSEIDON to develop a highly accurate ML regression model for predicting CPP uptake.
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Affiliation(s)
- António J Preto
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal
- PhD Programme in Experimental Biology and Biomedicine, Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Casa Costa Alemão, 3030-789, Coimbra, Portugal
| | - Ana B Caniceiro
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal
- Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
| | - Francisco Duarte
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal
| | - Hugo Fernandes
- CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
- FMUC - Faculty of Medicine, University of Coimbra, Coimbra, Portugal
- MIA - Multidisciplinary Institute of Ageing, University of Coimbra, Coimbra, Portugal
| | - Lino Ferreira
- CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
- FMUC - Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Joana Mourão
- CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Irina S Moreira
- Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal.
- CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.
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21
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Quagliata M, Papini AM, Rovero P. Chemically modified antiviral peptides against SARS-CoV-2. J Pept Sci 2024; 30:e3541. [PMID: 37699615 DOI: 10.1002/psc.3541] [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: 07/03/2023] [Revised: 07/31/2023] [Accepted: 08/22/2023] [Indexed: 09/14/2023]
Abstract
To date, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) COVID-19 pandemic continues to be a potentially lethal disease. Although both vaccines and specific antiviral drugs have been approved, the search for more specific therapeutic approaches is still ongoing. The infection mechanism of SARS-CoV-2 consists of several stages, and each one can be selectively blocked to disrupt viral infection. Peptides are a promising class of antiviral compounds, which may be suitably modified to be more stable, more effective, and more selective towards a specific viral replication step. The latter two goals might be obtained by increasing the specificity and/or the affinity of the interaction with a specific target and often imply the stabilization of the secondary structure of the active peptide. This review is focused on modified antiviral peptides against SARS-CoV-2 acting at different stages of virus replication, including ACE2-RBD interaction, membrane fusion mechanism, and the proteolytic cleavage by different viral proteases. Therefore, the landscape presented herein provides a useful springboard for the design of new and powerful antiviral therapeutics.
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Affiliation(s)
- Michael Quagliata
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Anna Maria Papini
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Paolo Rovero
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of NeuroFarBa, University of Florence, Sesto Fiorentino, Italy
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22
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Shi K, Xiong Y, Wang Y, Deng Y, Wang W, Jing B, Gao X. PractiCPP: a deep learning approach tailored for extremely imbalanced datasets in cell-penetrating peptide prediction. Bioinformatics 2024; 40:btae058. [PMID: 38305405 DOI: 10.1093/bioinformatics/btae058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 02/03/2024] Open
Abstract
MOTIVATION Effective drug delivery systems are paramount in enhancing pharmaceutical outcomes, particularly through the use of cell-penetrating peptides (CPPs). These peptides are gaining prominence due to their ability to penetrate eukaryotic cells efficiently without inflicting significant damage to the cellular membrane, thereby ensuring optimal drug delivery. However, the identification and characterization of CPPs remain a challenge due to the laborious and time-consuming nature of conventional methods, despite advances in proteomics. Current computational models, however, are predominantly tailored for balanced datasets, an approach that falls short in real-world applications characterized by a scarcity of known positive CPP instances. RESULTS To navigate this shortfall, we introduce PractiCPP, a novel deep-learning framework tailored for CPP prediction in highly imbalanced data scenarios. Uniquely designed with the integration of hard negative sampling and a sophisticated feature extraction and prediction module, PractiCPP facilitates an intricate understanding and learning from imbalanced data. Our extensive computational validations highlight PractiCPP's exceptional ability to outperform existing state-of-the-art methods, demonstrating remarkable accuracy, even in datasets with an extreme positive-to-negative ratio of 1:1000. Furthermore, through methodical embedding visualizations, we have established that models trained on balanced datasets are not conducive to practical, large-scale CPP identification, as they do not accurately reflect real-world complexities. In summary, PractiCPP potentially offers new perspectives in CPP prediction methodologies. Its design and validation, informed by real-world dataset constraints, suggest its utility as a valuable tool in supporting the acceleration of drug delivery advancements. AVAILABILITY AND IMPLEMENTATION The source code of PractiCPP is available on Figshare at https://doi.org/10.6084/m9.figshare.25053878.v1.
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Affiliation(s)
- Kexin Shi
- Syneron Technology, Guangzhou 510000, China
- Individualized Interdisciplinary Program (Data Science and Analytics), The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | | | - Yu Wang
- Syneron Technology, Guangzhou 510000, China
| | - Yifan Deng
- Syneron Technology, Guangzhou 510000, China
| | - Wenjia Wang
- Data Science and Analytics Thrust, The Hong Kong University of Science and Technology (Guangzhou), Nansha, Guangzhou, 511400, Guangdong, China
| | - Bingyi Jing
- Department of Statistics and Data Science, Southern University of Science and Technology, Shenzhen 518000, China
| | - Xin Gao
- Syneron Technology, Guangzhou 510000, China
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
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23
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Wan C, Zhang Y, Wang J, Xing Y, Yang D, Luo Q, Liu J, Ye Y, Liu Z, Yin F, Wang R, Li Z. Traceless Peptide and Protein Modification via Rational Tuning of Pyridiniums. J Am Chem Soc 2024; 146:2624-2633. [PMID: 38239111 DOI: 10.1021/jacs.3c11864] [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: 02/01/2024]
Abstract
Herein, we report a versatile reaction platform for tracelessly cleavable cysteine-selective peptide/protein modification. This platform offers highly tunable and predictable conjugation and cleavage by rationally estimating the electron effect on the nucleophilic halopyridiniums. Cleavable peptide stapling, antibody conjugation, enzyme masking/de-masking, and proteome labeling were achieved based on this facile pyridinium-thiol-exchange protocol.
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Affiliation(s)
- Chuan Wan
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen 518118, China
| | - Yichi Zhang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Jinpeng Wang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Yun Xing
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, China
| | - Dongyan Yang
- College of Chemistry and Chemical Engineering, Zhongkai University of Agriculture and Engineering, Guangzhou 510230, China
| | - Qinhong Luo
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Jianbo Liu
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, China
| | - Yuxin Ye
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, China
| | - Zhihong Liu
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, China
| | - Feng Yin
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, China
| | - Rui Wang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, China
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24
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Chan A, Tsourkas A. Intracellular Protein Delivery: Approaches, Challenges, and Clinical Applications. BME FRONTIERS 2024; 5:0035. [PMID: 38282957 PMCID: PMC10809898 DOI: 10.34133/bmef.0035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 12/14/2023] [Indexed: 01/30/2024] Open
Abstract
Protein biologics are powerful therapeutic agents with diverse inhibitory and enzymatic functions. However, their clinical use has been limited to extracellular applications due to their inability to cross plasma membranes. Overcoming this physiological barrier would unlock the potential of protein drugs for the treatment of many intractable diseases. In this review, we highlight progress made toward achieving cytosolic delivery of recombinant proteins. We start by first considering intracellular protein delivery as a drug modality compared to existing Food and Drug Administration-approved drug modalities. Then, we summarize strategies that have been reported to achieve protein internalization. These techniques can be broadly classified into 3 categories: physical methods, direct protein engineering, and nanocarrier-mediated delivery. Finally, we highlight existing challenges for cytosolic protein delivery and offer an outlook for future advances.
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Affiliation(s)
| | - Andrew Tsourkas
- Department of Bioengineering,
University of Pennsylvania, Philadelphia, PA, USA
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25
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Dibdiakova J, Matic J, Wubshet SG, Uhl W, Manamperuma LD, Rusten B, Vik EA. Membrane Separation of Chicken Byproduct Hydrolysate for Up-Concentration of Bioactive Peptides. MEMBRANES 2024; 14:28. [PMID: 38392655 PMCID: PMC10889955 DOI: 10.3390/membranes14020028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/19/2024] [Accepted: 01/21/2024] [Indexed: 02/24/2024]
Abstract
Membrane processes, such as microfiltration, ultrafiltration, and nanofiltration, are increasingly used for various applications in both upstream and downstream processing. Membrane-based processes play a critical role in the field of separation/purification of biotechnological products, including protein production/purification. The possibility of using membranes to separate peptides from a chicken byproduct hydrolysate and the effect of the performed downstream processing on the DPP-IV dipeptidyl peptidase IV (DPP-IV) inhibitory activity of mechanical deboning chicken residue (MDCR) has been investigated. The chicken byproduct hydrolysate was prepared by enzymatic hydrolysis followed by microfiltration (MF), ultrafiltration (UF), nanofiltration (NF), and reverse osmosis (RO) separation. Comparing all separation treatments, hydrolysates processed only by MF and UF show the best DPP-IV inhibition (59.5-60.0% at 1 mg/mL and 34.2-40.7% at 0.5 mg/mL). These samples show dose-responsive behavior. Bioactivity was correlated with molecular weight distribution profiles and average molecular weights. The nanofiltration process notably decrease the inhibitory activity, and these permeates show low DPP-IV inhibition (9.5-21.8% at 1 mg/mL and 3.6-12.1% at 0.5 mg/mL). The size-exclusion chromatography-organic carbon detection-organic nitrogen detection (LC-OCD-OND) analysis confirms that NF and RO would retain the bioactive peptides in the concentrate in comparison to MF and UF. Bioactivity was correlated with molecular weight distribution profiles and average molecular weights. Permeates after ultrafiltration show an IC50 value of 0.75 mg/mL, comparable to other potent DPP-IV inhibitors derived from various food sources, and significantly more potent compared to the microfiltration sample, which shows an IC50 value of 1.04 mg/mL. The average molecular weight of the permeates calculated from the SEC chromatograms was 883 g/mol for UF and 1437 g/mol for MF. Of the four membranes studied, the UF membrane shows the best separation properties with respect to maximizing the yield and up-concentration of the bioactive peptides. Overall, UF was demonstrated to be a feasible technology for the removal of the undesired high-molecular-weight substances and up-concentration of small-molecular-weight bioactive peptides from chicken byproduct hydrolysate. These peptides might exhibit biological activity and could offer several health benefits. There is a high potential for the use of bioactive peptides, and more research in this field can lead to promising results that have significant effects in the food and medical industries.
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Affiliation(s)
| | | | | | - Wolfgang Uhl
- Aquateam COWI AS, Karvesvingen 2, 0579 Oslo, Norway
| | | | - Bjørn Rusten
- Aquateam COWI AS, Karvesvingen 2, 0579 Oslo, Norway
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26
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Aiello F, Caputo P, Oliviero Rossi C, Restuccia D, Spizzirri UG. Formulation of Antioxidant Gummies Based on Gelatin Enriched with Citrus Fruit Peels Extract. Foods 2024; 13:320. [PMID: 38275689 PMCID: PMC10815181 DOI: 10.3390/foods13020320] [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: 12/23/2023] [Revised: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
In this work, the peels of red and blonde oranges as well as lemons were efficiently (5.75-9.65% yield) extracted by hydroalcoholic solution with ultrasound assistance and employed as active molecule sources in the preparation of functional gummies. Antioxidant performances of the hydroalcoholic extracts were characterized by colorimetric assays, whereas LC-HRMS analyses identified the main bioactive compounds (phenolic acids and flavonoids). The highest scavenging activity was recorded for lemon extract in an aqueous environment (IC50 = 0.081 mg mL-1). An ecofriendly grafting procedure was performed to anchor polyphenols to gelatin chains, providing macromolecular systems characterized by thermal analysis and antioxidant properties. Scavenger abilities (IC50 = 0.201-0.454 mg mL-1) allowed the employment of the conjugates as functional ingredients in the preparation of gummies with remarkable antioxidant and rheological properties over time (14 days). These findings confirmed the possible employment of highly polluting wastes as valuable sources of bioactive compounds for functional gummies preparation.
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Affiliation(s)
- Francesca Aiello
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy; (F.A.); (D.R.)
| | - Paolino Caputo
- Department of Chemistry and Chemical Technologies & UdR INSTM, University of Calabria, 87036 Rende, Italy; (P.C.); (C.O.R.)
| | - Cesare Oliviero Rossi
- Department of Chemistry and Chemical Technologies & UdR INSTM, University of Calabria, 87036 Rende, Italy; (P.C.); (C.O.R.)
| | - Donatella Restuccia
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy; (F.A.); (D.R.)
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27
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Hade MD, Suire CN, Suo Z. Significant Enhancement of Fibroblast Migration, Invasion, and Proliferation by Exosomes Loaded with Human Fibroblast Growth Factor 1. ACS APPLIED MATERIALS & INTERFACES 2024; 16:1969-1984. [PMID: 38181175 DOI: 10.1021/acsami.3c10350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2024]
Abstract
Exosomes possess several inherent properties that make them ideal for biomedical applications, including robust stability, biocompatibility, minimal immunogenicity, and the ability to cross biological barriers. These natural nanoparticles have recently been developed as drug delivery vesicles. To do so, therapeutic molecules must be efficiently loaded into exosomes first. Very recently, we developed a cell-penetrating peptide (CPP)-based platform for loading of nucleic acids and small molecules into exosomes by taking advantage of the membrane-penetration power of CPPs. Here, we extended this simple but effective platform by loading a protein cargo into exosomes isolated from either mesenchymal stem cells from three different sources or two different cancer cell lines. The protein cargo is a fusion protein YARA-FGF1-GFP through the covalent conjugation of a model CPP called YARA to human fibroblast growth factor 1 (FGF1) and green fluorescence protein (GFP). Loading of YARA-FGF1-GFP into exosomes was time-dependent and reached a maximum of about 1600 YARA-FGF1-GFP molecules in each exosome after 16 h. The ladened exosomes were effectively internalized by mammalian cells, and subsequently, the loaded protein cargo YARA-FGF1-GFP was delivered intracellularly. In comparison to YARA, YARA-FGF1-GFP, the unloaded exosomes, and the exosomes loaded with YARA, the exosomes loaded with YARA-FGF1-GFP substantially promoted the migration, proliferation, and invasion capabilities of mouse and human fibroblasts, which are important factors for wound repair. The work extended our CPP-based exosomal cargo loading platform and established a foundation for developing novel wound-healing therapies using exosomes loaded with FGF1 and other growth factors.
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Affiliation(s)
- Mangesh D Hade
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306, United States
| | - Caitlin N Suire
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306, United States
| | - Zucai Suo
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida 32306, United States
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28
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de Raffele D, Ilie IM. Unlocking novel therapies: cyclic peptide design for amyloidogenic targets through synergies of experiments, simulations, and machine learning. Chem Commun (Camb) 2024; 60:632-645. [PMID: 38131333 DOI: 10.1039/d3cc04630c] [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: 12/23/2023]
Abstract
Existing therapies for neurodegenerative diseases like Parkinson's and Alzheimer's address only their symptoms and do not prevent disease onset. Common therapeutic agents, such as small molecules and antibodies struggle with insufficient selectivity, stability and bioavailability, leading to poor performance in clinical trials. Peptide-based therapeutics are emerging as promising candidates, with successful applications for cardiovascular diseases and cancers due to their high bioavailability, good efficacy and specificity. In particular, cyclic peptides have a long in vivo stability, while maintaining a robust antibody-like binding affinity. However, the de novo design of cyclic peptides is challenging due to the lack of long-lived druggable pockets of the target polypeptide, absence of exhaustive conformational distributions of the target and/or the binder, unknown binding site, methodological limitations, associated constraints (failed trials, time, money) and the vast combinatorial sequence space. Hence, efficient alignment and cooperation between disciplines, and synergies between experiments and simulations complemented by popular techniques like machine-learning can significantly speed up the therapeutic cyclic-peptide development for neurodegenerative diseases. We review the latest advancements in cyclic peptide design against amyloidogenic targets from a computational perspective in light of recent advancements and potential of machine learning to optimize the design process. We discuss the difficulties encountered when designing novel peptide-based inhibitors and we propose new strategies incorporating experiments, simulations and machine learning to design cyclic peptides to inhibit the toxic propagation of amyloidogenic polypeptides. Importantly, these strategies extend beyond the mere design of cyclic peptides and serve as template for the de novo generation of (bio)materials with programmable properties.
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Affiliation(s)
- Daria de Raffele
- University of Amsterdam, van 't Hoff Institute for Molecular Sciences, Science Park 904, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands.
- Amsterdam Center for Multiscale Modeling (ACMM), University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
| | - Ioana M Ilie
- University of Amsterdam, van 't Hoff Institute for Molecular Sciences, Science Park 904, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands.
- Amsterdam Center for Multiscale Modeling (ACMM), University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
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29
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Abstract
Cyclic peptides are fascinating molecules abundantly found in nature and exploited as molecular format for drug development as well as other applications, ranging from research tools to food additives. Advances in peptide technologies made over many years through improved methods for synthesis and drug development have resulted in a steady stream of new drugs, with an average of around one cyclic peptide drug approved per year. Powerful technologies for screening random peptide libraries, and de novo generating ligands, have enabled the development of cyclic peptide drugs independent of naturally derived molecules and now offer virtually unlimited development opportunities. In this review, we feature therapeutically relevant cyclic peptides derived from nature and discuss the unique properties of cyclic peptides, the enormous technological advances in peptide ligand development in recent years, and current challenges and opportunities for developing cyclic peptides that address unmet medical needs.
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Affiliation(s)
- Xinjian Ji
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Alexander L Nielsen
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
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30
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Jin X, Wu H, Yu J, Cao Y, Zhang L, Zhang Z, Lv H. Glutamate affects self-assembly, protein corona, and anti-4 T1 tumor effects of melittin/vitamin E-succinic acid-(glutamate)n nanoparticles. J Control Release 2024; 365:802-817. [PMID: 38092255 DOI: 10.1016/j.jconrel.2023.12.013] [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: 08/21/2023] [Revised: 12/02/2023] [Accepted: 12/08/2023] [Indexed: 12/18/2023]
Abstract
Melittin (M) has attracted increasing attention for its significant antitumor effects and various immunomodulatory effects. However, various obstacles such as the short plasma half-life and adverse reactions restrict its application. This study aimed to systematically investigate the self-assembly mechanism, components of the protein corona, targeting behavior, and anti-4 T1 tumor effect of vitamin E-succinic acid-(glutamate)n /melittin nanoparticles with varying amounts of glutamic acid. Here, we present a new vitamin E-succinic acid-(glutamate)5 (E5), vitamin E-succinic acid-(glutamate)10 (E10) or vitamin E-succinic acid-(glutamate)15 (E15), and their co-assembly system with positively charged melittin in water. The molecular dynamics simulations demonstrated that the electrostatic energy and van der Waals force in the system decreased significantly with the increase in the amount of glutamic acid. The melittin and E15 system exhibited the optimal stability for nanoparticle self-assembly. When nanoparticles derived from different self-assembly systems were co-incubated with plasma from patients with breast cancer, the protein corona showed heterogeneity. In vivo imaging demonstrated that an increase in the number of glutamic acid residues enhanced circulation duration and tumor-targeting effects. Both in vitro and in vivo antitumor evaluation indicated a significant increase in the antitumor effect with the addition of glutamic acid. According to our research findings, the number of glutamic acid residues plays a crucial role in the targeted delivery of melittin for immunomodulation and inhibition of 4 T1 breast cancer. Due to the self-assembly capabilities of vitamin E-succinic acid-(glutamate)n in water, these nanoparticles carry significant potential for delivering cationic peptides such as melittin.
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Affiliation(s)
- Xin Jin
- Department of Pharmaceutics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, China; Department of Pharmaceutics, The Affiliated Suqian First People's Hospital of Nanjing Medical University, Suqian, Jiangsu, China
| | - Hangyi Wu
- Department of Pharmaceutics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Jie Yu
- Department of Pharmaceutics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Yanni Cao
- Department of Pharmaceutics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Lanyi Zhang
- Department of Pharmaceutics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Zhenhai Zhang
- Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing, Jiangsu, China.
| | - Huixia Lv
- Department of Pharmaceutics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, China.
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31
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Jiang X, Gao L, Li Z, Shen Y, Lin ZH. Development and Challenges of Cyclic Peptides for Immunomodulation. Curr Protein Pept Sci 2024; 25:353-375. [PMID: 37990433 DOI: 10.2174/0113892037272528231030074158] [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: 07/16/2023] [Revised: 09/12/2023] [Accepted: 09/15/2023] [Indexed: 11/23/2023]
Abstract
Cyclic peptides are polypeptide chains formed by cyclic sequences of amide bonds between protein-derived or non-protein-derived amino acids. Compared to linear peptides, cyclic peptides offer several unique advantages, such as increased stability, stronger affinity, improved selectivity, and reduced toxicity. Cyclic peptide has been proved to have a promising application prospect in the medical field. In addition, this paper mainly describes that cyclic peptides play an important role in anti-cancer, anti-inflammatory, anti-virus, treatment of multiple sclerosis and membranous nephropathy through immunomodulation. In order to know more useful information about cyclic peptides in clinical research and drug application, this paper also summarizes cyclic peptides currently in the clinical trial stage and cyclic peptide drugs approved for marketing in the recent five years. Cyclic peptides have many advantages and great potential in treating various diseases, but there are still many challenges to be solved in the development process of cyclic peptides.
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Affiliation(s)
- Xianqiong Jiang
- School of Pharmacy and Bioengineering, Chongqing University of Technology, 405400 Chongqing, China
| | - Li Gao
- School of Pharmacy and Bioengineering, Chongqing University of Technology, 405400 Chongqing, China
| | - Zhilong Li
- School of Pharmacy and Bioengineering, Chongqing University of Technology, 405400 Chongqing, China
| | - Yan Shen
- School of Pharmacy and Bioengineering, Chongqing University of Technology, 405400 Chongqing, China
- Chongqing Key Laboratory of Medicinal Chemistry & Molecular Pharmacology, Chongqing University of Technology, Chongqing 400054, China
- Chongqing Key Laboratory of Target Based Drug Screening and Activity Evaluation, Chongqing University of Technology, Chongqing 400054, China
| | - Zhi-Hua Lin
- School of Pharmacy and Bioengineering, Chongqing University of Technology, 405400 Chongqing, China
- Chongqing College of Traditional Chinese Medicine, 402760
- Chongqing Key Laboratory of Medicinal Chemistry & Molecular Pharmacology, Chongqing University of Technology, Chongqing 400054, China
- Chongqing Key Laboratory of Target Based Drug Screening and Activity Evaluation, Chongqing University of Technology, Chongqing 400054, China
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32
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Kotadiya DD, Patel P, Patel HD. Cell-Penetrating Peptides: A Powerful Tool for Targeted Drug Delivery. Curr Drug Deliv 2024; 21:368-388. [PMID: 37026498 DOI: 10.2174/1567201820666230407092924] [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: 09/27/2022] [Revised: 01/19/2023] [Accepted: 01/30/2023] [Indexed: 04/08/2023]
Abstract
The cellular membrane hinders the effective delivery of therapeutics to targeted sites. Cellpenetrating peptide (CPP) is one of the best options for rapidly internalizing across the cellular membrane. CPPs have recently attracted lots of attention because of their excellent transduction efficiency and low cytotoxicity. The CPP-cargo complex is an effective and efficient method of delivering several chemotherapeutic agents used to treat various diseases. Additionally, CPP has become another strategy to overcome some of the current therapeutic agents' limitations. However, no CPP complex is approved by the US FDA because of its limitations and issues. In this review, we mainly discuss the cellpenetrating peptide as the delivery vehicle, the cellular uptake mechanism of CPPs, their design, and some strategies to synthesize the CPP complex via some linkers such as disulfide bond, oxime, etc. Here, we also discuss the recent status of CPPs in the market.
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Affiliation(s)
- Dushyant D Kotadiya
- Department of Chemistry, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Piyushkumar Patel
- Department of Chemistry, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Hitesh D Patel
- Department of Chemistry, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
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33
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Tang TM, Mason JM. Intracellular Application of an Asparaginyl Endopeptidase for Producing Recombinant Head-to-Tail Cyclic Proteins. JACS AU 2023; 3:3290-3296. [PMID: 38155637 PMCID: PMC10751764 DOI: 10.1021/jacsau.3c00591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 12/30/2023]
Abstract
Peptide backbone cyclization is commonly observed in nature and is increasingly applied to proteins and peptides to improve thermal and chemical stability and resistance to proteolytic enzymes and enhance biological activity. However, chemical synthesis of head-to-tail cyclic peptides and proteins is challenging, is often low yielding, and employs toxic and unsustainable reagents. Plant derived asparaginyl endopeptidases such as OaAEP1 have been employed to catalyze the head-to-tail cyclization of peptides in vitro, offering a safer and more sustainable alternative to chemical methods. However, while asparaginyl endopeptidases have been used in vitro and in native and transgenic plant species, they have never been used to generate recombinant cyclic proteins in live recombinant organisms outside of plants. Using dihydrofolate reductase as a proof of concept, we show that a truncated OaAEP1 variant C247A is functional in the Escherichia coli physiological environment and can therefore be coexpressed with a substrate protein to enable concomitant in situ cyclization. The bacterial system is ideal for cyclic protein production owing to the fast growth rate, durability, ease of use, and low cost. This streamlines cyclic protein production via a biocatalytic process with fast kinetics and minimal ligation scarring, while negating the need to purify the enzyme, substrate, and reaction mixtures individually. The resulting cyclic protein was characterized in vitro, demonstrating enhanced thermal stability compared to the corresponding linear protein without impacting enzyme activity. We anticipate this convenient method for generating cyclic peptides will have broad utility in a range of biochemical and chemical applications.
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Affiliation(s)
- T. M.
Simon Tang
- Department
of Life Sciences, University of Bath, Claverton Down, Bath, North Somerset BA2
7AY, U.K.
| | - Jody M. Mason
- Department
of Life Sciences, University of Bath, Claverton Down, Bath, North Somerset BA2
7AY, U.K.
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34
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Rüdisser SH, Matabaro E, Sonderegger L, Güntert P, Künzler M, Gossert AD. Conformations of Macrocyclic Peptides Sampled by Nuclear Magnetic Resonance: Models for Cell-Permeability. J Am Chem Soc 2023; 145:27601-27615. [PMID: 38062770 PMCID: PMC10739998 DOI: 10.1021/jacs.3c09367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/21/2023]
Abstract
The biological activities and pharmacological properties of peptides and peptide mimetics are determined by their conformational states. Therefore, a detailed understanding of the conformational landscape is crucial for rational drug design. Nuclear magnetic resonance (NMR) is the only method for structure determination in solution. However, it remains challenging to determine the structures of peptides using NMR because of very weak nuclear Overhauser effects (NOEs), the semiquantitative nature of the rotating frame Overhauser effect (ROE), and the low number of NOEs/ROEs in N-methylated peptides. In this study, we introduce a new approach to investigating the structures of modified macrocyclic peptides. We utilize exact NOEs (eNOEs) in viscous solvent mixtures to replicate various cellular environments. eNOEs provide detailed structural information for highly dynamic modified peptides. Structures of high precision were obtained for cyclosporin A, with a backbone atom rmsd of 0.10 Å. Distinct conformational states in different environments were identified for omphalotin A (OmphA), a fungal nematotoxic and multiple backbone N-methylated macrocyclic peptides. A model for cell-permeation is presented for OmphA, based on its structures in polar, apolar, and mixed polarity solvents. During the transition from a polar to an apolar environment, OmphA undergoes a rearrangement of its H-bonding network, accompanied by a cis to trans isomerization of the ω torsion angle within a type VIa β-turn. We hypothesize that the kinetics of these conformational transitions play a crucial role in determining the membrane-permeation capabilities of OmphA.
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Affiliation(s)
| | | | | | - Peter Güntert
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Zürich 8093, Switzerland
- Institute
of Biophysical Chemistry, Goethe University, Frankfurt am Main 60438, Germany
- Department
of Chemistry, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Markus Künzler
- Department
of Biology, ETH Zürich, Zürich 8093, Switzerland
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35
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Neto V, Victor BL, Galamba N. Cyclic Peptides as Aggregation Inhibitors for Sickle Cell Disease. J Med Chem 2023; 66:16062-16074. [PMID: 37988411 DOI: 10.1021/acs.jmedchem.3c01484] [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: 11/23/2023]
Abstract
Sickle cell disease is a missense genetic disorder characterized by the aggregation of deoxy-HbS into helical fibers that distort erythrocytes into a sickle-like shape. Herein, we investigate, through molecular dynamics, the effect of nine 5-mer cyclic peptides (CPs), tailor-designed to block key lateral contacts of the fibers. Our results show that the CPs bind orthogonally to the main HbS pocket involved in the latter contacts, with some revealing exceedingly long residence times. These CPs display moderate to high specificity, exhibiting molecular recognition events even at a HbS/CP (1:1) ratio. A much lower HbS-CP binding free energy, longer residence times, and higher specificity are also found relative to a previously reported CP with modest in vitro antisickling activity. These results indicate that some of these CPs have the potential to reduce the concentration of aggregation-competent deoxy-HbS, precluding or delaying the formation of lateral contact at the homogeneous nucleation stage.
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Affiliation(s)
- Vasco Neto
- Biosystems and Integrative Sciences Institute, Faculdade de Ciências da Universidade de Lisboa, Edifício C8, Campo Grande 1749-016, Lisboa, Portugal
| | - Bruno Lourenço Victor
- Biosystems and Integrative Sciences Institute, Faculdade de Ciências da Universidade de Lisboa, Edifício C8, Campo Grande 1749-016, Lisboa, Portugal
| | - Nuno Galamba
- Biosystems and Integrative Sciences Institute, Faculdade de Ciências da Universidade de Lisboa, Edifício C8, Campo Grande 1749-016, Lisboa, Portugal
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36
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Peker T, Zagiel B, Rocard L, Bich C, Sachon E, Moumné R. Analytical Tools for Dynamic Combinatorial Libraries of Cyclic Peptides. Chembiochem 2023; 24:e202300688. [PMID: 37815502 DOI: 10.1002/cbic.202300688] [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: 10/08/2023] [Accepted: 10/10/2023] [Indexed: 10/11/2023]
Abstract
Target-directed dynamic combinatorial chemistry is a very attractive strategy for the discovery of bioactive peptides. However, its application has not yet been demonstrated, presumably due to analytical challenges that arise from the diversity of a peptide library with combinatorial side-chains. We previously reported an efficient method to generate, under biocompatible conditions, large dynamic libraries of cyclic peptides grafted with amino acid's side-chains, by thiol-to-thioester exchanges. In this work, we present analytical tools to easily characterize such libraries by HPLC and mass spectrometry, and in particular to simplify the isomers' distinction requiring sequencing by MS/MS fragmentations. After structural optimization, the cyclic scaffold exhibits a UV-tag, absorbing at 415 nm, and an ornithine residue which favors the regioselective ring-opening and simultaneous MS/MS fragmentation, in the gas-phase.
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Affiliation(s)
- Taleen Peker
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France
| | - Benjamin Zagiel
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France
| | - Lou Rocard
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France
| | - Claudia Bich
- UMR 5247-CNRS-UM-ENSCM, Institut des Biomolécules Max Mousseron (IBMM), Université de Montpellier, Montpellier, France
| | - Emmanuelle Sachon
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France
- MS3U Platform, Fédération de Chimie Moléculaire de Paris Centre - FR2769, Sorbonne Université, 4 Place Jussieu, 75005, Paris, France
| | - Roba Moumné
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France
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37
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Cheng J, Zhou J, Kong L, Wang H, Zhang Y, Wang X, Liu G, Chu Q. Stabilized cyclic peptides as modulators of protein-protein interactions: promising strategies and biological evaluation. RSC Med Chem 2023; 14:2496-2508. [PMID: 38107173 PMCID: PMC10718590 DOI: 10.1039/d3md00487b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 10/04/2023] [Indexed: 12/19/2023] Open
Abstract
Protein-protein interactions (PPIs) control many essential biological pathways which are often misregulated in disease. As such, selective PPI modulators are desirable to unravel complex functions of PPIs and thus expand the repertoire of therapeutic targets. However, the large size and relative flatness of PPI interfaces make them challenging molecular targets for conventional drug modalities, rendering most PPIs "undruggable". Therefore, there is a growing need to discover innovative molecules that are able to modulate crucial PPIs. Peptides are ideal candidates to deliver such therapeutics attributed to their ability to closely mimic structural features of protein interfaces. However, their inherently poor proteolysis resistance and cell permeability inevitably hamper their biomedical applications. The introduction of a constraint (i.e., peptide cyclization) to stabilize peptides' secondary structure is a promising strategy to address this problem as witnessed by the rapid development of cyclic peptide drugs in the past two decades. Here, we comprehensively review the recent progress on stabilized cyclic peptides in targeting challenging PPIs. Technological advancements and emerging chemical approaches for stabilizing active peptide conformations are categorized in terms of α-helix stapling, β-hairpin mimetics and macrocyclization. To discover potent and selective ligands, cyclic peptide library technologies were updated based on genetic, biochemical or synthetic methodologies. Moreover, several advances to improve the permeability and oral bioavailability of biologically active cyclic peptides enable the de novo development of cyclic peptide ligands with pharmacological properties. In summary, the development of cyclic peptide-based PPI modulators carries tremendous promise for the next generation of therapeutic agents to target historically "intractable" PPI systems.
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Affiliation(s)
- Jiongjia Cheng
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University 3601 Hongjing Avenue Nanjing 211171 China
| | - Junlong Zhou
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University 639 Longmian Avenue Nanjing 211198 China
| | - Lingyan Kong
- College of Food Science and Engineering, Nanjing University of Finance and Economics Nanjing 210023 China
| | - Haiying Wang
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University 3601 Hongjing Avenue Nanjing 211171 China
| | - Yuchi Zhang
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University 3601 Hongjing Avenue Nanjing 211171 China
| | - Xiaofeng Wang
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University 3601 Hongjing Avenue Nanjing 211171 China
| | - Guangxiang Liu
- Key Laboratory of Advanced Functional Materials of Nanjing, School of Environmental Science, Nanjing Xiaozhuang University 3601 Hongjing Avenue Nanjing 211171 China
| | - Qian Chu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University 639 Longmian Avenue Nanjing 211198 China
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University Nanjing 210009 China
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38
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Li X, Wang N, Liu Y, Li W, Bai X, Liu P, He CY. Backbone N-methylation of peptides: Advances in synthesis and applications in pharmaceutical drug development. Bioorg Chem 2023; 141:106892. [PMID: 37776681 DOI: 10.1016/j.bioorg.2023.106892] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 09/16/2023] [Accepted: 09/25/2023] [Indexed: 10/02/2023]
Abstract
Peptide-based drugs have garnered considerable attention in recent years owing to their increasingly crucial role in the treatment of diverse diseases. However, the limited pharmacokinetic properties of peptides have hindered their full potential. One prominent strategy for enhancing the druggability of peptides is N-methylation, which involves the addition of a methyl group to the nitrogen atom of the peptide backbone. This modification significantly improves the stability, bioavailability, receptor binding affinity and selectivity of peptide drug candidates. In this review, we provide a comprehensive overview of the advancements in synthetic methods for N-methylated peptide synthesis, as well as the associated limitations. Moreover, we explore the versatile effects of N-methylation on various aspects of peptide properties. Furthermore, we emphasize the efforts dedicated to N-methylated peptide pharmaceuticals that have successfully obtained marketing approval.
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Affiliation(s)
- Xuefei Li
- Key Laboratory of Basic Pharmacology of Ministry of Education, Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China; Central Research Institute, United-Imaging Healthcare Group Co., Ltd, Shanghai, China
| | - Ningchao Wang
- Central Research Institute, United-Imaging Healthcare Group Co., Ltd, Shanghai, China
| | - Yuhang Liu
- Central Research Institute, United-Imaging Healthcare Group Co., Ltd, Shanghai, China
| | - Weipiao Li
- Key Laboratory of Basic Pharmacology of Ministry of Education, Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Xinyu Bai
- Key Laboratory of Basic Pharmacology of Ministry of Education, Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Ping Liu
- Key Laboratory of Basic Pharmacology of Ministry of Education, Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Chun-Yang He
- Key Laboratory of Basic Pharmacology of Ministry of Education, Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China.
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39
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Alvero-Gonzalez LM, Aurora Perini D, Queralt-Martín M, Perálvarez-Marín A, Viñas C, Alcaraz A. Probing electrophysiological activity of amphiphilic Dynorphin A in planar neutral membranes reveals both ion channel-like activity and neuropeptide translocation. Bioelectrochemistry 2023; 154:108527. [PMID: 37531663 DOI: 10.1016/j.bioelechem.2023.108527] [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: 05/26/2023] [Revised: 07/10/2023] [Accepted: 07/26/2023] [Indexed: 08/04/2023]
Abstract
Dynorphin A (DynA) is an endogenous neuropeptide that besides acting as a ligand of the κ-opioid receptor, presents some non-opioid pathophysiological properties associated to its ability to induce cell permeability similarly to cell-penetrating peptides (CPPs). Here, we use electrophysiology experiments to show that amphiphilic DynA generates aqueous pores in neutral membranes similar to those reported previously in charged membranes, but we also find other events thermodynamically incompatible with voltage-driven ion channel activity (i.e. non-zero currents with no applied voltage in symmetric salt conditions, reversal potentials that exceed the theoretical limit for a given salt concentration gradient). By comparison with current traces generated by other amphiphilic molecule known to spontaneously cross membranes, we hypothesize that DynA could directly translocate across neutral bilayers, a feature never observed in charged membranes following the same electrophysiological protocol. Our findings suggest that DynA interaction with the cellular membrane is modulated by the lipid charge distribution, enabling either passive ionic transport via membrane remodeling and pore formation or by peptide direct internalization independent of cellular transduction pathways.
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Affiliation(s)
- Laidy M Alvero-Gonzalez
- Laboratory of Molecular Biophysics, Department of Physics, University Jaume I, 12071 Castellón, Spain
| | - D Aurora Perini
- Laboratory of Molecular Biophysics, Department of Physics, University Jaume I, 12071 Castellón, Spain
| | - María Queralt-Martín
- Laboratory of Molecular Biophysics, Department of Physics, University Jaume I, 12071 Castellón, Spain
| | - Alex Perálvarez-Marín
- Biophysics Unit, Department of Biochemistry and Molecular Biology, School of Medicine, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; Institute of Neuroscience, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.
| | - Clara Viñas
- Institut de Ciència de Materials de Barcelona, ICMAB-CSIC, Campus Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Antonio Alcaraz
- Laboratory of Molecular Biophysics, Department of Physics, University Jaume I, 12071 Castellón, Spain.
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40
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Lee Y, Kim KM, Nguyen DL, Jannah F, Seong HJ, Kim JM, Kim YP. Cyclized proteins with tags as permeable and stable cargos for delivery into cells and liposomes. Int J Biol Macromol 2023; 252:126520. [PMID: 37625744 DOI: 10.1016/j.ijbiomac.2023.126520] [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: 07/04/2023] [Revised: 08/18/2023] [Accepted: 08/23/2023] [Indexed: 08/27/2023]
Abstract
Despite the therapeutic potential of recombinant proteins, their cell permeabilities and stabilities remain significant challenges. Here we demonstrate that cyclized recombinant proteins can be used as universal cargos for permeable and stable delivery into cells and polydiacetylene liposomes. Utilizing a split intein-mediated process, cyclized model fluorescent proteins containing short tetraarginine (R4) and hexahistidine (H6) tags were generated without compromising their native protein functions. Strikingly, as compared to linear R4/H6-tagged proteins, the cyclized counterparts have substantially increased permeabilities in both cancer cells and synthetic liposomes, as well as higher resistances to enzymatic degradation in cancer cells. These properties are likely a consequence of structural constraints imposed on the proteins in the presence of short functional peptides. Additionally, photodynamic therapy by cyclized photoprotein-loaded liposomes in cancer cells was significantly improved in comparison to that by their non-cyclized counterparts. These findings suggest that our strategy will be universally applicable to intercellular delivery of proteins and therapeutics.
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Affiliation(s)
- Yeonju Lee
- Department of Life Science, Hanyang University, Seoul 04763, Republic of Korea
| | - Kyung-Min Kim
- Department of Life Science, Hanyang University, Seoul 04763, Republic of Korea
| | - Duc Long Nguyen
- Department of Life Science, Hanyang University, Seoul 04763, Republic of Korea; Research Institute for Convergence of Basic Science, Hanyang University, Seoul 04763, Republic of Korea
| | - Fadilatul Jannah
- Department of Chemical Engineering, Hanyang University, Seoul 04763, Republic of Korea
| | - Hyun-Jung Seong
- Department of Life Science, Hanyang University, Seoul 04763, Republic of Korea
| | - Jong-Man Kim
- Department of Chemical Engineering, Hanyang University, Seoul 04763, Republic of Korea; Institute of Nano Science and Technology, Hanyang University, Seoul 04763, Republic of Korea.
| | - Young-Pil Kim
- Department of Life Science, Hanyang University, Seoul 04763, Republic of Korea; Research Institute for Convergence of Basic Science, Hanyang University, Seoul 04763, Republic of Korea; Institute of Nano Science and Technology, Hanyang University, Seoul 04763, Republic of Korea; Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea; Department of HY-KIST Bio-Convergence, Hanyang University, Seoul 04763, Republic of Korea; Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul 04763, Republic of Korea.
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41
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Jelinska C, Kannan S, Frosi Y, Ramlan SR, Winnerdy F, Lakshminarayanan R, Johannes CW, Brown CJ, Phan AT, Rhodes D, Verma CS. Stitched peptides as potential cell permeable inhibitors of oncogenic DAXX protein. RSC Chem Biol 2023; 4:1096-1110. [PMID: 38033728 PMCID: PMC10685803 DOI: 10.1039/d3cb00149k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 09/25/2023] [Indexed: 12/02/2023] Open
Abstract
DAXX (Death Domain Associated Protein 6) is frequently upregulated in various common cancers, and its suppression has been linked to reduced tumor progression. Consequently, DAXX has gained significant interest as a therapeutic target in such cancers. DAXX is known to function in several critical biological pathways including chromatin remodelling, transcription regulation, and DNA repair. Leveraging structural information, we have designed and developed a novel set of stapled/stitched peptides that specifically target a surface on the N-terminal helical bundle domain of DAXX. This surface serves as the anchor point for binding to multiple interaction partners, such as Rassf1C, p53, Mdm2, and ATRX, as well as for the auto-regulation of the DAXX N-terminal SUMO interaction motif (SIM). Our experiments demonstrate that these peptides effectively bind to and inhibit DAXX with a higher affinity than the known interaction partners. Furthermore, these peptides release the auto-inhibited SIM, enabling it to interact with SUMO-1. Importantly, we have developed stitched peptides that can enter cells, maintaining their intracellular concentrations at nanomolar levels even after 24 hours, without causing any membrane perturbation. Collectively, our findings suggest that these stitched peptides not only serve as valuable tools for probing the molecular interactions of DAXX but also hold potential as precursors to the development of therapeutic interventions.
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Affiliation(s)
- Clare Jelinska
- NTU Institute of Structural Biology, Experimental Medicine Building Level 06-01, 59 Nanyang Drive 636921 Singapore
- NTU School of Biological Sciences, 60 Nanyang Drive 637551 Singapore
- NTU Lee Kong Chian School of Medicine, Experimental Medicine Building, 59 Nanyang Drive 636921 Singapore
| | | | - Yuri Frosi
- DITL, Institute of Cellular and Molecular Biology (A*STAR), 8a Biomedical Grove 138648 Singapore
| | - Siti Radhiah Ramlan
- DITL, Institute of Cellular and Molecular Biology (A*STAR), 8a Biomedical Grove 138648 Singapore
| | - Fernaldo Winnerdy
- NTU Institute of Structural Biology, Experimental Medicine Building Level 06-01, 59 Nanyang Drive 636921 Singapore
| | - Rajamani Lakshminarayanan
- Ocular Infections and Anti-Microbials Research Group, Singapore Eye Research Institute, The Academia, 20 College Road Singapore 169856 Singapore
- Department of Pharmacy, National University of Singapore Singapore 117543 Singapore
- Academic Clinical Program in Ophthalmology and Visual Sciences Academic Clinical Program, Duke-NUS Medical School 169857 Singapore
| | - Charles W Johannes
- DITL, Institute of Cellular and Molecular Biology (A*STAR), 8a Biomedical Grove 138648 Singapore
| | - Christopher J Brown
- DITL, Institute of Cellular and Molecular Biology (A*STAR), 8a Biomedical Grove 138648 Singapore
| | - Anh-Tuan Phan
- NTU Institute of Structural Biology, Experimental Medicine Building Level 06-01, 59 Nanyang Drive 636921 Singapore
- NTU School of Physical and Mathematical Sciences. 21 Nanyang link 637371 Singapore
| | - Daniela Rhodes
- NTU Institute of Structural Biology, Experimental Medicine Building Level 06-01, 59 Nanyang Drive 636921 Singapore
- NTU School of Biological Sciences, 60 Nanyang Drive 637551 Singapore
- NTU Lee Kong Chian School of Medicine, Experimental Medicine Building, 59 Nanyang Drive 636921 Singapore
| | - Chandra S Verma
- NTU School of Biological Sciences, 60 Nanyang Drive 637551 Singapore
- Bioinformatics institute (A*STAR), 30 Biopolis Street, Matrix Level 07-01 138671 Singapore
- Department of Biological Sciences, National University of Singapore Block S3 #05-01 16 Science Drive 4 117558 Singapore
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42
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Vandborg BC, Horsfall AJ, Pederick JL, Abell AD, Bruning JB. Towards a High-Affinity Peptidomimetic Targeting Proliferating Cell Nuclear Antigen from Aspergillus fumigatus. J Fungi (Basel) 2023; 9:1098. [PMID: 37998903 PMCID: PMC10672205 DOI: 10.3390/jof9111098] [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: 10/11/2023] [Revised: 11/04/2023] [Accepted: 11/07/2023] [Indexed: 11/25/2023] Open
Abstract
Invasive fungal infections (IFIs) are prevalent in immunocompromised patients. Due to alarming levels of increasing resistance in clinical settings, new drugs targeting the major fungal pathogen Aspergillus fumigatus are required. Attractive drug targets are those involved in essential processes like DNA replication, such as proliferating cell nuclear antigens (PCNAs). PCNA has been previously studied in cancer research and presents a viable target for antifungals. Human PCNA interacts with the p21 protein, outcompeting binding proteins to halt DNA replication. The affinity of p21 for hPCNA has been shown to outcompete other associating proteins, presenting an attractive scaffold for peptidomimetic design. p21 has no A. fumigatus homolog to our knowledge, yet our group has previously demonstrated that human p21 can interact with A. fumigatus PCNA (afumPCNA). This suggests that a p21-based inhibitor could be designed to outcompete the native binding partners of afumPCNA to inhibit fungal growth. Here, we present an investigation of extensive structure-activity relationships between designed p21-based peptides and afumPCNA and the first crystal structure of a p21 peptide bound to afumPCNA, demonstrating that the A. fumigatus replication model uses a PIP-box sequence as the method for binding to afumPCNA. These results inform the new optimized secondary structure design of a potential peptidomimetic inhibitor of afumPCNA.
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Affiliation(s)
- Bethiney C. Vandborg
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide 5005, Australia; (B.C.V.); (J.L.P.); (A.D.A.)
- School of Biological Sciences, The University of Adelaide, Adelaide 5005, Australia
| | - Aimee J. Horsfall
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide 5005, Australia; (B.C.V.); (J.L.P.); (A.D.A.)
- ARC Centre of Excellence for Nanoscale BioPhotonics, The University of Adelaide, Adelaide 5005, Australia
| | - Jordan L. Pederick
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide 5005, Australia; (B.C.V.); (J.L.P.); (A.D.A.)
- School of Biological Sciences, The University of Adelaide, Adelaide 5005, Australia
| | - Andrew D. Abell
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide 5005, Australia; (B.C.V.); (J.L.P.); (A.D.A.)
- ARC Centre of Excellence for Nanoscale BioPhotonics, The University of Adelaide, Adelaide 5005, Australia
| | - John B. Bruning
- Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide 5005, Australia; (B.C.V.); (J.L.P.); (A.D.A.)
- School of Biological Sciences, The University of Adelaide, Adelaide 5005, Australia
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43
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Chen B, Li Y, Bai H, Ji Y, Cong W, Hu H, He S. Unleashing the potential of natural biological peptide Macropin: Hydrocarbon stapling for effective breast cancer treatment. Bioorg Chem 2023; 140:106770. [PMID: 37604094 DOI: 10.1016/j.bioorg.2023.106770] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 08/02/2023] [Accepted: 08/06/2023] [Indexed: 08/23/2023]
Abstract
The identification of novel candidate molecules with the potential to revolutionize the treatment of breast cancer holds profound clinical significance. Macropin (Mac)-1, derived from the venom of wild bees, emerges as an auspicious therapeutic agent for combating breast cancers. Nevertheless, linear peptides have long grappled with the challenges of traversing cell membranes and succumbing to protease hydrolysis. To address this challenge, the present study employed hydrocarbon stapling modification to synthesize a range of stapled Mac-1 peptides, which were comprehensively evaluated for their chemical and biological properties. Significantly, Mac-1-sp4 exhibited a remarkable set of improvements, including enhanced helicity, proteolytic stability, cell membrane permeability, induction of cell apoptosis, in vivo antitumor activity, and inhibition of tubulin polymerization. This study explores the significant impact of the hydrocarbon stapling technique on the secondary structure, hydrolase stability, and biological activity of Mac-1, shedding light on its potential as a revolutionary and potent anti-breast cancer therapy. The findings establish a strong basis for the development of innovative and highly effective anti-tumor treatments.
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Affiliation(s)
- Baobao Chen
- Institute of Translational Medicine, Shanghai University, 200444, China
| | - Yinghua Li
- Institute of Translational Medicine, Shanghai University, 200444, China
| | - Haohao Bai
- Institute of Translational Medicine, Shanghai University, 200444, China
| | - Yajing Ji
- Institute of Translational Medicine, Shanghai University, 200444, China
| | - Wei Cong
- School of Medicine, Shanghai University, 200444, China.
| | - Honggang Hu
- School of Medicine, Shanghai University, 200444, China
| | - Shipeng He
- Institute of Translational Medicine, Shanghai University, 200444, China.
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44
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Shao H, Adebomi V, Bruce A, Raj M, Houk KN. Intramolecular Hydrogen Bonding Enables a Zwitterionic Mechanism for Macrocyclic Peptide Formation: Computational Mechanistic Studies of CyClick Chemistry. Angew Chem Int Ed Engl 2023; 62:e202307210. [PMID: 37475575 PMCID: PMC10592271 DOI: 10.1002/anie.202307210] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 07/22/2023]
Abstract
Macrocyclic peptides have become increasingly important in the pharmaceutical industry. We present a detailed computational investigation of the reaction mechanism of the recently developed "CyClick" chemistry to selectively form imidazolidinone cyclic peptides from linear peptide aldehydes, without using catalysts or directing groups (Angew. Chem. Int. Ed. 2019, 58, 19073-19080). We conducted computational mechanistic to investigate the effects of intramolecular hydrogen bonds (IMHBs) in promoting a kinetically facile zwitterionic mechanism in "CyClick" of pentapeptide aldehyde AFGPA. Our DFT calculations highlighted the importance of IMHB in pre-organization of the resting state, stabilization of the zwitterion intermediate, and the control of the product stereoselectivity. Furthermore, we have also identified that the low ring strain energy promotes the "CyClick" of hexapeptide aldehyde AAGPFA to form a thermodynamically more stable 15+5 imidazolidinone cyclic peptide product. In contrast, large ring strain energy suppresses "CyClick" reactivity of tetra peptide aldehyde AFPA from forming the 9+5 imidazolidinone cyclic peptide product.
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Affiliation(s)
- Huiling Shao
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Victor Adebomi
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Angele Bruce
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Monika Raj
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Kendall N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
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Dognini P, Chaudhry T, Scagnetti G, Assante M, Hanson GSM, Ross K, Giuntini F, Coxon CR. 5,10,15,20-Tetrakis(pentafluorophenyl)porphyrin as a Functional Platform for Peptide Stapling and Multicyclisation. Chemistry 2023; 29:e202301410. [PMID: 37402229 PMCID: PMC10946732 DOI: 10.1002/chem.202301410] [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: 05/03/2023] [Revised: 06/22/2023] [Accepted: 07/04/2023] [Indexed: 07/06/2023]
Abstract
Polyfluorinated aromatic reagents readily react with thiolates via nucleophilic aromatic substitution (SN Ar) and provide excellent scaffolds for peptide cyclisation. Here we report a robust and versatile platform for peptide stapling and multicyclisation templated by 5,10,15,20-tetrakis(pentafluorophenyl)porphyrin, opening the door to the next generation of functional scaffolds for 3D peptide architectures. We demonstrate that stapling and multicyclisation occurs with a range of non-protected peptides under peptide-compatible conditions, exhibiting chemoselectivity and wide-applicability. Peptides containing two cysteine residues are readily stapled, and the remaining perfluoroaryl groups permit the introduction of a second peptide in a modular fashion to access bicyclic peptides. Similarly, peptides with more than two cysteine residues can afford multicyclic products containing up to three peptide 'loops'. Finally, we demonstrate that a porphyrin-templated stapled peptide containing the Skin Penetrating and Cell Entering (SPACE) peptide affords a skin cell penetrating conjugate with intrinsic fluorescence.
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Affiliation(s)
- Paolo Dognini
- School of Pharmacy and Biomolecular SciencesLiverpool John Moores UniversityByrom Street CampusL3 3AFLiverpoolUK
| | - Talhat Chaudhry
- School of Pharmacy and Biomolecular SciencesLiverpool John Moores UniversityByrom Street CampusL3 3AFLiverpoolUK
| | - Giulia Scagnetti
- School of Pharmacy and Biomolecular SciencesLiverpool John Moores UniversityByrom Street CampusL3 3AFLiverpoolUK
| | - Michele Assante
- School of Pharmacy and Biomolecular SciencesLiverpool John Moores UniversityByrom Street CampusL3 3AFLiverpoolUK
| | - George S. M. Hanson
- EaStCHEMSchool of ChemistryThe University of EdinburghJoseph Black Building, David Brewster RoadEH9 3FJEdinburghUK
| | - Kehinde Ross
- School of Pharmacy and Biomolecular SciencesLiverpool John Moores UniversityByrom Street CampusL3 3AFLiverpoolUK
| | - Francesca Giuntini
- School of Pharmacy and Biomolecular SciencesLiverpool John Moores UniversityByrom Street CampusL3 3AFLiverpoolUK
| | - Christopher R. Coxon
- EaStCHEMSchool of ChemistryThe University of EdinburghJoseph Black Building, David Brewster RoadEH9 3FJEdinburghUK
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Shi YY, Dong DR, Fan G, Dai MY, Liu M. A cyclic peptide-based PROTAC induces intracellular degradation of palmitoyltransferase and potently decreases PD-L1 expression in human cervical cancer cells. Front Immunol 2023; 14:1237964. [PMID: 37849747 PMCID: PMC10577221 DOI: 10.3389/fimmu.2023.1237964] [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: 06/10/2023] [Accepted: 09/18/2023] [Indexed: 10/19/2023] Open
Abstract
Introduction Our previous research has found that degradation of palmitoyltransferase in tumor cells using a linear peptide PROTAC leads to a significant decrease in PD-L1 expression in tumors. However, this degradation is not a sustained and efficient process. Therefore, we designed a cyclic peptide PROTAC to achieve this efficient anti-PD-L1 effect. Methods We designed and synthesized an improvement in linear peptide PROTAC targeting palmitoyltransferase DHHC3, and used disulfide bonds to stabilize the continuous N- and C-termini of the peptides to maintain their structure. Cellular and molecular biology techniques were used to test the effect of this cyclic peptide on PD-L1. Results In human cervical cancer cells, our cyclic peptide PROTAC can significantly downregulate palmitoyl transferase DHHC3 and PD-L1 expressions. This targeted degradation effect is enhanced with increasing doses and treatment duration, with a DC50 value much lower than that of linear peptides. Additionally, flow cytometry analysis of fluorescence intensity shows an increase in the amount of cyclic peptide entering the cell membrane with prolonged treatment time and higher concentrations. The Cellular Thermal Shift Assay (CETSA) method used in this study indicates effective binding between our novel cyclic peptide and DHHC3 protein, leading to a change in the thermal stability of the latter. The degradation of PD-L1 can be effectively blocked by the proteasome inhibitor MG132. Results from clone formation experiments illustrate that our cyclic peptide can enhance the proliferative inhibition effect of cisplatin on the C33A cell line. Furthermore, in the T cell-C33A co-culture system, cyclic peptides target the degradation of PD-L1, thereby blocking the interaction between PD-L1 and PD-1, and promoting the secretion of IFN-γ and TNF-α in the co-culture system supernatant. Conclusion Our results demonstrate that a disulfide-bridged cyclic peptide PROTAC targeting palmitoyltransferase can provide a stable and improved anti-PD-L1 activity in human tumor cells.
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Affiliation(s)
- Yu-Ying Shi
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Di-Rong Dong
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Gang Fan
- Department of Urology, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
| | - Meng-Yuan Dai
- Department of Gynecological Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Miao Liu
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
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Lozada C, Gonzalez S, Agniel R, Hindie M, Manciocchi L, Mazzanti L, Ha-Duong T, Santoro F, Carotenuto A, Ballet S, Lubin-Germain N. Introduction of constrained Trp analogs in RW9 modulates structure and partition in membrane models. Bioorg Chem 2023; 139:106731. [PMID: 37480815 DOI: 10.1016/j.bioorg.2023.106731] [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: 05/04/2023] [Revised: 06/28/2023] [Accepted: 07/10/2023] [Indexed: 07/24/2023]
Abstract
Over the past decades, many cell-penetrating peptides (CPP) have been studied for their capacity to cross cellular membranes, mostly in order to improve cellular uptake of therapeutic agents. Even though hydrophobic and anionic CPPs have been described, many of them are polycationic, due to the presence of several arginine (Arg) residues. Noteworthy, however, the presence of aromatic amino acids such as tryptophan (Trp) within CPPs seems to play an important role to reach high membranotropic activity. RW9 (RRWWRRWRR) is a designed CPP derived from the polyarginine R9 presenting both features. In general, when interacting with membranes, CPPs adopt an optimal conformation for membrane interactions - an amphipathic helical secondary structure in the case of RW9. Herein, we assumed that the incorporation of a locally constrained amino acid in the peptide sequence could improve the membranotropic activity of RW9, by facilitating its structuration upon contact with a membrane, while leaving a certain plasticity. Therefore, two cyclized Trp derivatives (Tcc and Aia) were synthesized to be incorporated in RW9 as surrogates of Trp residues. Thus, a series of peptides containing these building blocks has been synthesized by varying the type, position, and number of modifications. The membranotropic activity of the RW9 analogs was studied by spectrofluorescence titration of the peptides in presence of liposomes (DMPG), allowing to calculate partition coefficients (Kp). Our results indicate that the partitioning of the modified peptides depends on the type, the number and the position of the modification, with the best sequence being [Aia4]RW9. Interestingly, both NMR analysis and molecular dynamic (MD) simulations indicate that this analog presents an extended conformation similar to the native RW9, but with a much-reduced structural flexibility. Finally, cell internalization properties were also confirmed by confocal microscopy.
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Affiliation(s)
- Camille Lozada
- CNRS, BioCIS, CY Cergy-Paris Université, 95000 Neuville sur Oise, France; CNRS, BioCIS, Université Paris-Saclay, 92290 Châtenay-Malabry, France; Research Group of Organic Chemistry, Vrije Universiteit Brussel, Brussels, Belgium
| | - Simon Gonzalez
- CNRS, BioCIS, CY Cergy-Paris Université, 95000 Neuville sur Oise, France; CNRS, BioCIS, Université Paris-Saclay, 92290 Châtenay-Malabry, France
| | - Rémy Agniel
- ERRMECe, Institut des Matériaux I-MAT (FD4122), CY Cergy Paris Université, 95000 Neuville sur Oise, France
| | - Mathilde Hindie
- ERRMECe, Institut des Matériaux I-MAT (FD4122), CY Cergy Paris Université, 95000 Neuville sur Oise, France
| | - Luca Manciocchi
- CNRS, BioCIS, Université Paris-Saclay, 92290 Châtenay-Malabry, France
| | - Liuba Mazzanti
- CNRS, BioCIS, Université Paris-Saclay, 92290 Châtenay-Malabry, France
| | - Tap Ha-Duong
- CNRS, BioCIS, Université Paris-Saclay, 92290 Châtenay-Malabry, France
| | - Federica Santoro
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
| | - Alfonso Carotenuto
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
| | - Steven Ballet
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Brussels, Belgium.
| | - Nadège Lubin-Germain
- CNRS, BioCIS, CY Cergy-Paris Université, 95000 Neuville sur Oise, France; CNRS, BioCIS, Université Paris-Saclay, 92290 Châtenay-Malabry, France.
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Ghosh P, Raj N, Verma H, Patel M, Chakraborti S, Khatri B, Doreswamy CM, Anandakumar SR, Seekallu S, Dinesh MB, Jadhav G, Yadav PN, Chatterjee J. An amide to thioamide substitution improves the permeability and bioavailability of macrocyclic peptides. Nat Commun 2023; 14:6050. [PMID: 37770425 PMCID: PMC10539501 DOI: 10.1038/s41467-023-41748-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 09/06/2023] [Indexed: 09/30/2023] Open
Abstract
Solvent shielding of the amide hydrogen bond donor (NH groups) through chemical modification or conformational control has been successfully utilized to impart membrane permeability to macrocyclic peptides. We demonstrate that passive membrane permeability can also be conferred by masking the amide hydrogen bond acceptor (>C = O) through a thioamide substitution (>C = S). The membrane permeability is a consequence of the lower desolvation penalty of the macrocycle resulting from a concerted effect of conformational restriction, local desolvation of the thioamide bond, and solvent shielding of the amide NH groups. The enhanced permeability and metabolic stability on thioamidation improve the bioavailability of a macrocyclic peptide composed of hydrophobic amino acids when administered through the oral route in rats. Thioamidation of a bioactive macrocyclic peptide composed of polar amino acids results in analogs with longer duration of action in rats when delivered subcutaneously. These results highlight the potential of O to S substitution as a stable backbone modification in improving the pharmacological properties of peptide macrocycles.
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Affiliation(s)
- Pritha Ghosh
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Nishant Raj
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Hitesh Verma
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Monika Patel
- Neuroscience & Ageing Biology, CSIR-CDRI, Lucknow, 226031, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sohini Chakraborti
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Bhavesh Khatri
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Chandrashekar M Doreswamy
- Department of Pre-clinical Research, Anthem Biosciences Pvt. Ltd., Bangalore, 560099, Karnataka, India
| | - S R Anandakumar
- Department of Pre-clinical Research, Anthem Biosciences Pvt. Ltd., Bangalore, 560099, Karnataka, India
| | - Srinivas Seekallu
- Department of Pre-clinical Research, Anthem Biosciences Pvt. Ltd., Bangalore, 560099, Karnataka, India
| | - M B Dinesh
- Central Animal Facility, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Gajanan Jadhav
- Eurofins Advinus Biopharma Services India Pvt. Ltd., Bangalore, 560058, Karnataka, India
| | - Prem Narayan Yadav
- Neuroscience & Ageing Biology, CSIR-CDRI, Lucknow, 226031, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Jayanta Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India.
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Zhou Q, Xiang J, Qiu N, Wang Y, Piao Y, Shao S, Tang J, Zhou Z, Shen Y. Tumor Abnormality-Oriented Nanomedicine Design. Chem Rev 2023; 123:10920-10989. [PMID: 37713432 DOI: 10.1021/acs.chemrev.3c00062] [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: 09/17/2023]
Abstract
Anticancer nanomedicines have been proven effective in mitigating the side effects of chemotherapeutic drugs. However, challenges remain in augmenting their therapeutic efficacy. Nanomedicines responsive to the pathological abnormalities in the tumor microenvironment (TME) are expected to overcome the biological limitations of conventional nanomedicines, enhance the therapeutic efficacies, and further reduce the side effects. This Review aims to quantitate the various pathological abnormalities in the TME, which may serve as unique endogenous stimuli for the design of stimuli-responsive nanomedicines, and to provide a broad and objective perspective on the current understanding of stimuli-responsive nanomedicines for cancer treatment. We dissect the typical transport process and barriers of cancer drug delivery, highlight the key design principles of stimuli-responsive nanomedicines designed to tackle the series of barriers in the typical drug delivery process, and discuss the "all-into-one" and "one-for-all" strategies for integrating the needed properties for nanomedicines. Ultimately, we provide insight into the challenges and future perspectives toward the clinical translation of stimuli-responsive nanomedicines.
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Affiliation(s)
- Quan Zhou
- Zhejiang Key Laboratory of Smart Biomaterials and Center for Bionanoengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
- Department of Cell Biology, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Jiajia Xiang
- Zhejiang Key Laboratory of Smart Biomaterials and Center for Bionanoengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
- Department of Cell Biology, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Nasha Qiu
- Zhejiang Key Laboratory of Smart Biomaterials and Center for Bionanoengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
| | - Yechun Wang
- Department of Cell Biology, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Ying Piao
- Zhejiang Key Laboratory of Smart Biomaterials and Center for Bionanoengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
| | - Shiqun Shao
- Zhejiang Key Laboratory of Smart Biomaterials and Center for Bionanoengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
| | - Jianbin Tang
- Zhejiang Key Laboratory of Smart Biomaterials and Center for Bionanoengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
| | - Zhuxian Zhou
- Zhejiang Key Laboratory of Smart Biomaterials and Center for Bionanoengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
| | - Youqing Shen
- Zhejiang Key Laboratory of Smart Biomaterials and Center for Bionanoengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, China
- State Key Laboratory of Chemical Engineering, Zhejiang University, Hangzhou 310058, China
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50
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Pragti, Kundu BK, Singh S, Carlton Ranjith WA, Sarkar S, Sonawane A, Mukhopadhyay S. Chitosan-Biotin-Conjugated pH-Responsive Ru(II) Glucose Nanogel: A Dual Pathway of Targeting Cancer Cells and Self-Drug Delivery. ACS APPLIED MATERIALS & INTERFACES 2023; 15:43345-43358. [PMID: 37658475 DOI: 10.1021/acsami.3c07157] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/03/2023]
Abstract
The current study paves the way for improved chemotherapy by creating pH-responsive nanogels (NGs) (GC1 and GC2) loaded with synthetic ruthenium(II) arene complexes to increase biological potency. NGs are fabricated by the conjugation of chitosan (CTS)-biotin biopolymers that selectively target the cancer cells as CTS has the pH-responsive property, which helps in releasing the drug in cancer cells having pH ∼ 5.5, and biotin provides the way to target the cancer cells selectively due to the overexpression of integrin. The synthesized compounds and NGs were thoroughly characterized using various spectroscopic and analytical techniques such as NMR, electrospray ionization-mass spectrometry, Fourier transform infrared, UV-vis, scanning electron microscopy, transmission electron microscopy, X-ray photoelectron spectroscopy, rheology, Brunauer-Emmett-Teller, and others. NGs displayed exceptional increased efficacy toward cancerous cells with IC50 values ranging from 7.50 to 18.86 μM via induced apoptosis in three human cancer cell lines. Apart from its potency, NGs were found to be highly selective toward cancer cells. Moreover, based on the results of immunoblot analysis, it was observed that the synthesized compounds exhibit a significant increase in the expression of cleaved caspase-3 and a decrease in the expression of the antiapoptotic protein BCL-XL. Interestingly, the complexes were discovered to have the additional capability of catalyzing the conversion of NADH to NAD+, leading to the generation of radical oxygen species within the cells. Additionally, it was discovered that NG-induced apoptosis depends on ROS production and DNA binding. A narrower range of LD50 values (1185.93 and 823.03 μM) was seen after administering NGs to zebrafish embryos in vivo. The results support the use of drug-loaded NGs as potential chemotherapeutic and chemopreventive agents for human cancer cells.
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Affiliation(s)
- Pragti
- Department of Chemistry, School of Basic Sciences, Indian Institute of Technology Indore, Simrol, Khandwa Road, Indore 453552, India
| | - Bidyut Kumar Kundu
- Department of Chemistry, School of Basic Sciences, Indian Institute of Technology Indore, Simrol, Khandwa Road, Indore 453552, India
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Satyam Singh
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore 453 552, Madhya Pradesh, India
| | - Wilson Alphonse Carlton Ranjith
- Molecular and Nanomedicine Research Unit, Centre for Nanoscience and Nanotechnology (CNSNT), Sathyabama Institute of Science and Technology, Jeppiaar Nagar, Chennai 600119, Tamil Nadu, India
| | - Sayantan Sarkar
- Department of Chemistry, School of Basic Sciences, Indian Institute of Technology Indore, Simrol, Khandwa Road, Indore 453552, India
| | - Avinash Sonawane
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore 453 552, Madhya Pradesh, India
| | - Suman Mukhopadhyay
- Department of Chemistry, School of Basic Sciences, Indian Institute of Technology Indore, Simrol, Khandwa Road, Indore 453552, India
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