1
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Pandey V, Adhikrao PA, Motiram GM, Yadav N, Jagtap U, Kumar G, Paul A. Biaryl carboxamide-based peptidomimetics analogs as potential pancreatic lipase inhibitors for treating obesity. Arch Pharm (Weinheim) 2024; 357:e2300503. [PMID: 38251950 DOI: 10.1002/ardp.202300503] [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: 09/13/2023] [Revised: 12/30/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024]
Abstract
A series of 1,1'-biphenyl-3-carboxamide and furan-phenyl-carboxamide analogs were synthesized using an optimized scheme and confirmed by 1H and 13C nuclear magnetic resonance and high-resolution mass spectrometry techniques. The synthesized peptidomimetics analogs were screened in vitro to understand the inhibitory potential of pancreatic lipase (PL). Analogs were assessed for the PL inhibitory activity based on interactions, geometric complementarity, and docking score. Among the synthesized analogs, 9, 29, and 24 were found to have the most potent PL inhibitory activity with IC50 values of 3.87, 4.95, and 5.34 µM, respectively, compared to that of the standard drug, that is, orlistat, which inhibits PL with an IC50 value of 0.99 µM. The most potent analog, 9, exhibited a competitive-type inhibition with an inhibition constant (Ki) of 2.72 µM. In silico molecular docking of analog 9 with the PL (PDB ID:1LPB) showed a docking score of -11.00 kcal/mol. Analog 9 formed crucial hydrogen bond interaction with Ser152, His263, π-cation interaction with Asp79, Arg256, and π-π stacking with Phe77, Tyr114 at the protein's active site. The molecular dynamic simulation confirmed that analog 9 forms stable interactions with PL at the end of 200 ns with root mean square deviation values of 2.5 and 6 Å. No toxicity was observed for analog 9 (concentration range of 1-20 µM) when tested by MTT assay in RAW 264.7 cells.
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Affiliation(s)
- Vikash Pandey
- Department of Natural Products, Chemical Sciences, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Patil A Adhikrao
- Department of Natural Products, Chemical Sciences, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Gudle M Motiram
- Department of Natural Products, Chemical Sciences, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Nisha Yadav
- Laboratory of Natural Product Chemistry, Department of Pharmacy, Birla Institute of Technology and Science, Pilani (Pilani Campus), Pilani, Rajasthan, India
| | - Utkarsh Jagtap
- Laboratory of Natural Product Chemistry, Department of Pharmacy, Birla Institute of Technology and Science, Pilani (Pilani Campus), Pilani, Rajasthan, India
| | - Gautam Kumar
- Department of Natural Products, Chemical Sciences, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Atish Paul
- Laboratory of Natural Product Chemistry, Department of Pharmacy, Birla Institute of Technology and Science, Pilani (Pilani Campus), Pilani, Rajasthan, India
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2
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S100 Proteins as Novel Therapeutic Targets in Psoriasis and Other Autoimmune Diseases. Molecules 2022; 27:molecules27196640. [PMID: 36235175 PMCID: PMC9572071 DOI: 10.3390/molecules27196640] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/29/2022] [Accepted: 10/01/2022] [Indexed: 01/07/2023] Open
Abstract
Psoriasis is one of the most common inflammatory skin diseases affecting about 1-3% of the population. One of the characteristic abnormalities in psoriasis is the excessive production of antimicrobial peptides and proteins, which play an essential role in the pathogenesis of the disease. Antimicrobial peptides and proteins can be expressed differently in normal and diseased skin, reflecting their usefulness as diagnostic biomarkers. Moreover, due to their very important functions in innate immunity, members of host defense peptides and proteins are currently considered to be promising new therapeutic targets for many inflammatory diseases. Koebnerisin (S100A15) belongs to an S100 family of antimicrobial proteins, which constitute the multigenetic group of calcium-binding proteins involved in ion-dependent cellular functions and regulation of immune mechanisms. S100A15 was first discovered to be overexpressed in 'koebnerized' psoriatic skin, indicating its involvement in the disease phenotype and the same promising potential as a new therapeutic target. This review describes the involvement of antimicrobial peptides and proteins in inflammatory diseases' development and therapy. The discussion focuses on S100 proteins, especially koebnerisin, which may be involved in the underlying mechanism of the Köebner phenomenon in psoriasis, as well as other immune-mediated inflammatory diseases described in the last decade.
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3
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α/Sulfono-γ-AA peptide hybrids agonist of GLP-1R with prolonged action both in vitro and in vivo. Acta Pharm Sin B 2022; 13:1648-1659. [PMID: 37139407 PMCID: PMC10149899 DOI: 10.1016/j.apsb.2022.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/22/2022] [Accepted: 10/14/2022] [Indexed: 11/01/2022] Open
Abstract
Peptides are increasingly important resources for biological and therapeutic development, however, their intrinsic susceptibility to proteolytic degradation represents a big hurdle. As a natural agonist for GLP-1R, glucagon-like peptide 1 (GLP-1) is of significant clinical interest for the treatment of type-2 diabetes mellitus, but its in vivo instability and short half-life have largely prevented its therapeutic application. Here, we describe the rational design of a series of α/sulfono-γ-AA peptide hybrid analogues of GLP-1 as the GLP-1R agonists. Certain GLP-1 hybrid analogues exhibited enhanced stability (t 1/2 > 14 days) compared to t 1/2 (<1 day) of GLP-1 in the blood plasma and in vivo. These newly developed peptide hybrids may be viable alternative of semaglutide for type-2 diabetes treatment. Additionally, our findings suggest that sulfono-γ-AA residues could be adopted to substitute canonical amino acids residues to improve the pharmacological activity of peptide-based drugs.
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4
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Dahal A, Sonju JJ, Kousoulas KG, Jois SD. Peptides and peptidomimetics as therapeutic agents for Covid-19. Pept Sci (Hoboken) 2022; 114:e24245. [PMID: 34901700 PMCID: PMC8646791 DOI: 10.1002/pep2.24245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 12/27/2022]
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Covid-19 pandemic has caused high morbidity and mortality rates worldwide. Virus entry into cells can be blocked using several strategies, including inhibition of protein-protein interactions (PPIs) between the viral spike glycoprotein and cellular receptors, as well as blocking of spike protein conformational changes that are required for cleavage/activation and fusogenicity. The spike-mediated viral attachment and entry into cells via fusion of the viral envelope with cellular membranes involve PPIs mediated by short peptide fragments exhibiting particular secondary structures. Thus, peptides that can inhibit these PPIs may be used as potential antiviral agents preventing virus entry and spread. This review is focused on peptides and peptidomimetics as PPI modulators and protease inhibitors against SARS-CoV-2.
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Affiliation(s)
- Achyut Dahal
- School of Basic Pharmaceutical and Toxicological Sciences, College of PharmacyUniversity of Louisiana at MonroeMonroeLouisianaUSA
| | - Jafrin Jobayer Sonju
- School of Basic Pharmaceutical and Toxicological Sciences, College of PharmacyUniversity of Louisiana at MonroeMonroeLouisianaUSA
| | - Konstantin G. Kousoulas
- Department of Pathobiological Sciences, School of Veterinary MedicineLouisiana State UniversityBaton RougeLouisianaUSA
| | - Seetharama D. Jois
- School of Basic Pharmaceutical and Toxicological Sciences, College of PharmacyUniversity of Louisiana at MonroeMonroeLouisianaUSA
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5
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Discovery of α-helix-mimicking sulfono-γ-AApeptides as p53-MDM2 inhibitors. Future Med Chem 2021; 13:1021-1023. [PMID: 33906432 DOI: 10.4155/fmc-2021-0044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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6
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Li Z, Fu X, Huang S, Sun J, Li Z. Oligo(β-peptoid)s with Backbone Chirality from Aspartic Acid Derivatives: Synthesis and Property Investigation. ACS OMEGA 2020; 5:33125-33132. [PMID: 33403274 PMCID: PMC7774267 DOI: 10.1021/acsomega.0c04726] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 12/04/2020] [Indexed: 06/12/2023]
Abstract
Poly(β-peptoid)s (N-substituted poly-β-alanines) are an intriguing class of pseudopeptidic materials for biomedical applications, but the polymers prepared by solution polymerization have restricted diversity and functionality due to synthetic difficulty. Synthesis of structurally diverse poly(β-peptoid)s is highly desirable yet challenging. Herein, we report a new approach to synthesize skeletal chiral β-peptoid polymers from readily available aspartic acid derivatives. Two types of N-substituted β3-homoalanine monomers, i.e., N-(methyl propionate)-Asp-OMe ( N MeP-Asp-OMe) and N-(tert-butyl propionate)-Asp-OMe ( N tBuP-Asp-OMe), were synthesized in high yield via an aza-Michael addition reaction between l-aspartic acid-1-methyl ester (l-Asp-OMe) and acrylate species. Both N-substituted β3-homoalanines can be readily converted into polymerizable N-substituted β3-homoalanine N-carboxyanhydrides (β-NNCAs). Subsequent ring-opening polymerization (ROP) of these β-NNCA monomers provides access to oligo(β-peptoid)s and mPEG-poly(β-peptoid) diblocks with backbone chirality. Their conformations were preliminarily studied by circular dichroism (CD) spectra and Fourier transform infrared spectroscopy (FT-IR). The synthetic strategy would significantly facilitate the development of novel poly(β-peptoid)s with well-defined and diverse structures.
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Affiliation(s)
- Zheng Li
- Key
Laboratory of Biobased Polymer Materials, Shandong Provincial Education
Department, College of Polymer Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Xiaohui Fu
- Key
Laboratory of Biobased Polymer Materials, Shandong Provincial Education
Department, College of Polymer Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Saixi Huang
- Key
Laboratory of Biobased Polymer Materials, Shandong Provincial Education
Department, College of Polymer Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Jing Sun
- Key
Laboratory of Biobased Polymer Materials, Shandong Provincial Education
Department, College of Polymer Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Zhibo Li
- Key
Laboratory of Biobased Polymer Materials, Shandong Provincial Education
Department, College of Polymer Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
- College
of Chemical Engineering, Qingdao University
of Science and Technology, Qingdao 266042, China
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7
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Shi Y, Sang P, Lu J, Higbee P, Chen L, Yang L, Odom T, Daughdrill G, Chen J, Cai J. Rational Design of Right-Handed Heterogeneous Peptidomimetics as Inhibitors of Protein-Protein Interactions. J Med Chem 2020; 63:13187-13196. [PMID: 33140956 DOI: 10.1021/acs.jmedchem.0c01638] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Peptidomimetics have gained great attention for their function as protein-protein interaction (PPI) inhibitors. Herein, we report the design and investigation of a series of right-handed helical heterogeneous 1:1 α/Sulfono-γ-AA peptides as unprecedented inhibitors for p53-MDM2 and p53-MDMX. The most potent helical heterogeneous 1:1 α/Sulfono-γ-AA peptides were shown to bind tightly to MDM2 and MDMX, with Kd of 19.3 and 66.8 nM, respectively. Circular dichroism spectra, 2D-NMR spectroscopy, and the computational simulations suggested that these helical sulfono-γ-AA peptides could mimic the critical side chains of p53 and disrupt p53/MDM2 PPI effectively. It was noted that these 1:1 α/Sulfono-γ-AA peptides were completely resistant to proteolytic degradation, boosting their potential for biomedical applications. Furthermore, effective cellular activity is achieved by the stapled 1:1 α/Sulfono-γ-AA peptides, evidenced by significantly enhanced p53 transcriptional activity and much more induced level of MDM2 and p21. The 1:1 α/Sulfono-γ-AA peptides could be an alternative strategy to antagonize a myriad of PPIs.
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Affiliation(s)
- Yan Shi
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa, Florida 33620, United States
| | - Peng Sang
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa, Florida 33620, United States
| | - Junhao Lu
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Pirada Higbee
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 E. Fowler Ave., Tampa, Florida 33620, United States
| | - Lihong Chen
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Leixiang Yang
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Timothy Odom
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa, Florida 33620, United States
| | - Gary Daughdrill
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 E. Fowler Ave., Tampa, Florida 33620, United States
| | - Jiandong Chen
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa, Florida 33620, United States
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8
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Shi Y, Sang P, Yin G, Gao R, Liang X, Brzozowski R, Odom T, Eswara P, Zheng Y, Li X, Cai J. Aggregation-Induced Emissive and Circularly Polarized Homogeneous Sulfono-γ-AApeptide Foldamers. ADVANCED OPTICAL MATERIALS 2020; 8:1902122. [PMID: 33072491 PMCID: PMC7567131 DOI: 10.1002/adom.201902122] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/22/2020] [Indexed: 05/13/2023]
Abstract
Through our continuous effort in developing a new class of foldamers, we have both designed and synthesized homogenous sulfono-γ-AApeptides using tetraphenylethylene (TPE) moieties attached to the backbone as luminogenic sidechains. Based on previous crystal structures, we have found that these foldamers adopted a left-handed 414-helix. Due to the constraint of the helical scaffold, the rotation of the TPE moieties were restricted, leading to fluorescent emissive properties with high quantum yields not only at the aggregate state but also in solution. Investigation of the relationship between the structure and fluorescence behavior reveals that emission was induced by the combined effect of the aggregation-induced emission (AIE) and the rotated restriction from the backbone. Furthermore, as the packing mode of the luminogens could be precisely adjusted by the helical backbone, these foldamers were found to be circularly polarizable with relatively large luminescence dissymmetry factor (g lum). Interestingly, possessing cationic amphipathic structures similar to that of host-defense peptides (HDPs), these sulfono-γ-AApeptides were able to inhibit the growth of Gram-positive bacteria methicillin-resistant S. aureus (MRSA) through membrane interactions.
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Affiliation(s)
- Yan Shi
- Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Peng Sang
- Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Guangqiang Yin
- Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Ruixuan Gao
- Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Xiao Liang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Robert Brzozowski
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Timothy Odom
- Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Prahathees Eswara
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Youxuan Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing, China
| | - Xiaopeng Li
- Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
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9
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Highly efficient and enantioselective syntheses of (2S,3R)-3-alkyl- and alkenylglutamates from Fmoc-protected Garner's aldehyde. Amino Acids 2020; 52:987-998. [PMID: 32621203 DOI: 10.1007/s00726-020-02868-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 06/25/2020] [Indexed: 02/06/2023]
Abstract
A 6-step enantioselective synthesis of (2S,3R)-3-alkyl/alkenylglutamates, including the biologically significant amino acid, (2S,3R)-3-methylglutamate, protected for Fmoc SPPS, is reported. Overall yields range from 52-65%. Key to the success of these syntheses was the development of a high-yielding 2-step synthesis of Fmoc Garner's aldehyde followed by a Horner-Wadsworth-Emmons reaction to give the corresponding Fmoc Garner's enoate in a 94% yield. The diastereoselective 1,4-addition of lithium dialkylcuprates to the Fmoc Garner's enoate was explored. Significant decomposition occurred when using lithium diethylcuprate and conditions previously reported for the 1,4-addition of lithium dialkylcuprates to Boc or Cbz-protected Garner's enoate. An optimization study of this reaction resulted in a robust set of conditions that addressed the shortcomings of previously reported conditions. Under these conditions, highly diastereoselective (> 20:1 in most cases) 1,4-addition reactions of lithium dialkyl/dialkenylcuprates to the Fmoc Garner's enoate were achieved in 76-99% yield. The resulting 1,4-addition products were easily converted into the Fmoc-(2S,3R)-3-alkyl/alkenylglutamates in two steps.
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10
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Nimmagadda A, Shi Y, Cai J. γ-AApeptides as a New Strategy for Therapeutic Development. Curr Med Chem 2019; 26:2313-2329. [PMID: 29110596 DOI: 10.2174/0929867324666171107095913] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 11/11/2016] [Accepted: 01/16/2017] [Indexed: 12/30/2022]
Abstract
A new class of peptidomimetics termed as "γ-AApeptides" was recently developed by our group. Similar to other peptidomimetics, γ-AApeptides are resistant to proteolytic degradation, and possess limitless potential to introduce chemically diverse functional groups. γ-AApeptides have shown great promise in biomedical applications. In this article, we will review a few examples of γ-AApeptides with biological potential. Certain γ-AApeptides can permeate cell membranes and therefore they can be used as potential drug carrier. γ-AApeptides can also bind to HIV RNA with high specificity and affinity, suggesting their potential application as anti-HIV agents. Moreover, they can mimic host-defense peptides and display potent and broad-spectrum activity towards a range of drug-resistant bacterial pathogens. They are also potential anti-cancer agents. For instance, they have shown great promise in targeted imaging of tumor in mouse model, and they are also capable of disrupting p53/DNA interactions, and thus antagonize STAT3 signaling pathway. Recently, from combinatorial screening, γ-AApeptides are identified to inhibit Aβ peptide aggregation, and thus they can be developed into potential anti- Alzheimer's disease agent.
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Affiliation(s)
- Alekhya Nimmagadda
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620, United States
| | - Yan Shi
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620, United States
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620, United States
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11
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Lafuente M, Alfonso I, Solà J. Structurally Selective Assembly of a Specific Macrobicycle from a Dynamic Library of Pseudopeptidic Disulfides. CHEMSYSTEMSCHEM 2019. [DOI: 10.1002/syst.201900002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- María Lafuente
- Department of Biological ChemistryInstitute for Advanced Chemistry of Catalonia c/ Jordi Girona 18–26 Barcelona 08034 Spain
| | - Ignacio Alfonso
- Department of Biological ChemistryInstitute for Advanced Chemistry of Catalonia c/ Jordi Girona 18–26 Barcelona 08034 Spain
| | - Jordi Solà
- Department of Biological ChemistryInstitute for Advanced Chemistry of Catalonia c/ Jordi Girona 18–26 Barcelona 08034 Spain
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12
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Gorla L, Martí-Centelles V, Altava B, Burguete MI, Luis SV. The role of the side chain in the conformational and self-assembly patterns of C2-symmetric Val and Phe pseudopeptidic derivatives. CrystEngComm 2019. [DOI: 10.1039/c8ce02088d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Side chain as the main conformational and self-assembly structural factor for C2-pseudopeptides.
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Affiliation(s)
- Lingaraju Gorla
- Departamento de Química Inorgánica y Orgánica
- Universitat Jaume I
- Castellón
- Spain
| | | | - Belén Altava
- Departamento de Química Inorgánica y Orgánica
- Universitat Jaume I
- Castellón
- Spain
| | - M. Isabel Burguete
- Departamento de Química Inorgánica y Orgánica
- Universitat Jaume I
- Castellón
- Spain
| | - Santiago V. Luis
- Departamento de Química Inorgánica y Orgánica
- Universitat Jaume I
- Castellón
- Spain
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13
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Costa F, Teixeira C, Gomes P, Martins MCL. Clinical Application of AMPs. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1117:281-298. [PMID: 30980363 DOI: 10.1007/978-981-13-3588-4_15] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Antimicrobial peptides (AMPs) have been described as one of the most promising compounds able to address one of the main health threats of the twenty-first century that is the continuous rise of multidrug-resistant microorganisms. However, despite the clear advantages of AMPs as a new class of antimicrobials, such as broad spectrum of activity, high selectivity, low toxicity and low propensity to induce resistance, only a small fraction of AMPs reported thus far have been able to successfully complete all phases of clinical trials and become accessible to patients. This is mainly related to the low bioavailability and still somewhat expensive production of AMP along with regulatory obstacles. This chapter offers an overview of selected AMPs that are currently in the market or under clinical trials. Strategies for assisting AMP industrial translation and major regulatory difficulties associated with AMP approval for clinical evaluation will be also discussed.
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Affiliation(s)
- Fabíola Costa
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,INEB, Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal
| | - Cátia Teixeira
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Paula Gomes
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - M Cristina L Martins
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal. .,INEB, Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal. .,Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal.
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14
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Collaborative routes to clarifying the murky waters of aqueous supramolecular chemistry. Nat Chem 2017; 10:8-16. [DOI: 10.1038/nchem.2894] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 10/20/2017] [Indexed: 12/19/2022]
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15
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Shi Y, Challa S, Sang P, She F, Li C, Gray GM, Nimmagadda A, Teng P, Odom T, Wang Y, van der Vaart A, Li Q, Cai J. One-Bead-Two-Compound Thioether Bridged Macrocyclic γ-AApeptide Screening Library against EphA2. J Med Chem 2017; 60:9290-9298. [PMID: 29111705 DOI: 10.1021/acs.jmedchem.7b01280] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Identification of molecular ligands that recognize peptides or proteins is significant but poses a fundamental challenge in chemical biology and biomedical sciences. Development of cyclic peptidomimetic library is scarce, and thus discovery of cyclic peptidomimetic ligands for protein targets is rare. Herein we report the unprecedented one-bead-two-compound (OBTC) combinatorial library based on a novel class of the macrocyclic peptidomimetics γ-AApeptides. In the library, we utilized the coding peptide tags synthesized with Dde-protected α-amino acids, which were orthogonal to solid phase synthesis of γ-AApeptides. Employing the thioether linkage, the desired macrocyclic γ-AApeptides were found to be effective for ligand identification. Screening the library against the receptor tyrosine kinase EphA2 led to the discovery of one lead compound that tightly bound to EphA2 (Kd = 81 nM) and potently antagonized EphA2-mediated signaling. This new approach of macrocyclic peptidomimetic library may lead to a novel platform for biomacromolecular surface recognition and function modulation.
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Affiliation(s)
- Yan Shi
- Department of Chemistry, University of South Florida , 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Sridevi Challa
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute , 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Peng Sang
- Department of Chemistry, University of South Florida , 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Fengyu She
- Department of Chemistry, University of South Florida , 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Chunpu Li
- Department of Medical Oncology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Geoffrey M Gray
- Department of Chemistry, University of South Florida , 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Alekhya Nimmagadda
- Department of Chemistry, University of South Florida , 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Peng Teng
- Department of Chemistry, University of South Florida , 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Timothy Odom
- Department of Chemistry, University of South Florida , 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Yan Wang
- Department of Medical Oncology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Arjan van der Vaart
- Department of Chemistry, University of South Florida , 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Qi Li
- Department of Medical Oncology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida , 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
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16
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Kovačević M, Kodrin I, Roca S, Molčanov K, Shen Y, Adhikari B, Kraatz H, Barišić L. Helically Chiral Peptides That Contain Ferrocene‐1,1′‐diamine Scaffolds as a Turn Inducer. Chemistry 2017; 23:10372-10395. [DOI: 10.1002/chem.201701602] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Indexed: 01/08/2023]
Affiliation(s)
- Monika Kovačević
- Department of Chemistry and BiochemistryFaculty of Food Technology and BiotechnologyUniversity of Zagreb Pierottijeva 6 Zagreb Croatia
| | - Ivan Kodrin
- Department of ChemistryFaculty of ScienceUniversity of Zagreb Horvatovac 102a Zagreb Croatia
| | - Sunčica Roca
- NMR CentreRuđer Bošković Institute Bijenička cesta 54 Zagreb Croatia
| | - Krešimir Molčanov
- Division of Physical ChemistryRuđer Bošković Institute Bijenička cesta 54 Zagreb Croatia
| | - Yuning Shen
- Department of Physical and Environmental SciencesUniversity of Toronto 1265 Military Trail Toronto M1C 1 A4 Canada
| | - Bimalendu Adhikari
- Department of Chemical SciencesIndian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, S. A. S. Nagar, Manauli PO Punjab 140306 India
| | - Heinz‐Bernhard Kraatz
- Department of Physical and Environmental SciencesUniversity of Toronto 1265 Military Trail Toronto M1C 1 A4 Canada
- Department of ChemistryUniversity of Toronto 80 St. George Street Toronto Ontario M5S 3H6 Canada
| | - Lidija Barišić
- Department of Chemistry and BiochemistryFaculty of Food Technology and BiotechnologyUniversity of Zagreb Pierottijeva 6 Zagreb Croatia
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17
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Baravkar SB, Kotmale AS, Shaikh SR, Gonnade RG, Sanjayan GJ. Structural Insights into the Hydrogen-Bonding and Folding Pattern in Ant-Ant-Pro-Gly Tetrapeptides. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Sachin B. Baravkar
- Division of Organic Chemistry; CSIR-National Chemical Laboratory (CSIR-NCL); Dr. Homi Bhabha Road 411008 Pune India
| | - Amol S. Kotmale
- Central NMR facility; CSIR-National Chemical Laboratory (CSIR-NCL); Dr. Homi Bhabha Road 411008 Pune India
| | - Samir R. Shaikh
- Center for Materials Characterization; CSIR-National Chemical Laboratory (CSIR-NCL); Dr. Homi Bhabha Road 411008 Pune India
| | - Rajesh G. Gonnade
- Center for Materials Characterization; CSIR-National Chemical Laboratory (CSIR-NCL); Dr. Homi Bhabha Road 411008 Pune India
| | - Gangadhar J. Sanjayan
- Division of Organic Chemistry; CSIR-National Chemical Laboratory (CSIR-NCL); Dr. Homi Bhabha Road 411008 Pune India
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18
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Madica K, Nadimpally KC, Sanjayan GJ. Novel silaproline (Sip)-incorporated close structural mimics of potent antidepressant peptide drug rapastinel (GLYX-13). Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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19
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Khadka NK, Teng P, Cai J, Pan J. Modulation of lipid membrane structural and mechanical properties by a peptidomimetic derived from reduced amide scaffold. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:734-744. [PMID: 28132901 DOI: 10.1016/j.bbamem.2017.01.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 01/22/2017] [Accepted: 01/25/2017] [Indexed: 10/20/2022]
Abstract
Understanding how antimicrobial peptidomimetics interact with lipid membranes is important in battling multidrug resistant bacterial pathogens. We study the effects of a recently reported peptidomimetic on lipid bilayer structural and mechanical properties. The compound referred to as E107-3 is synthesized based on the acylated reduced amide scaffold and has been shown to exhibit good antimicrobial potency. Our vesicle leakage assay indicates that the compound increases lipid bilayer permeability. We use micropipette aspiration to explore the kinetic response of giant unilamellar vesicles (GUVs). Exposure to the compound causes the GUV protrusion length LP to spontaneously increase and then decrease, followed by GUV rupture. Solution atomic force microscopy (AFM) is used to visualize lipid bilayer structural modulation within a nanoscopic regime. Unlike melittin, which produces pore-like structures, the peptidomimetic compound is found to induce nanoscopic heterogeneous structures. Finally, we use AFM-based force spectroscopy to study the impact of the compound on lipid bilayer mechanical properties. We find that incremental addition of the compound to planar lipid bilayers results in a moderate decrease of the bilayer puncture force FP and a 39% decrease of the bilayer area compressibility modulus KA. To explain our experimental data, we propose a membrane interaction model encompassing disruption of lipid chain packing and extraction of lipid molecules. The later action mode is supported by our observation of a double-bilayer structure in the presence of fusogenic calcium ions.
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Affiliation(s)
- Nawal K Khadka
- Department of Physics, University of South Florida, Tampa, FL 33620, United States
| | - Peng Teng
- Department of Chemistry, University of South Florida, Tampa, FL 33620, United States
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, Tampa, FL 33620, United States
| | - Jianjun Pan
- Department of Physics, University of South Florida, Tampa, FL 33620, United States.
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20
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Atcher J, Solà J, Alfonso I. Pseudopeptidic compounds for the generation of dynamic combinatorial libraries of chemically diverse macrocycles in aqueous media. Org Biomol Chem 2017; 15:213-219. [DOI: 10.1039/c6ob02441f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The combination of pseudopeptidic dithiol building blocks leads to the generation of highly diverse dynamic libraries of macrocycles in aqueous media.
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Affiliation(s)
- Joan Atcher
- Department of Biological Chemistry and Molecular Modelling
- IQAC-CSIC
- Barcelona
- Spain
| | - Jordi Solà
- Department of Biological Chemistry and Molecular Modelling
- IQAC-CSIC
- Barcelona
- Spain
| | - Ignacio Alfonso
- Department of Biological Chemistry and Molecular Modelling
- IQAC-CSIC
- Barcelona
- Spain
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21
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Gorla L, Martí-Centelles V, Freimuth L, Altava B, Burguete MI, Luis SV. Cu(2+), Zn(2+), and Ni(2+) Complexes of C2-Symmetric Pseudopeptides with an Aromatic Central Spacer. Inorg Chem 2016; 55:7617-29. [PMID: 27438410 DOI: 10.1021/acs.inorgchem.6b01066] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Two new tetradentate C2-symmetric pseudopeptidic ligands derived from Val and Phe containing two amino and two amido groups and a central o-substituted aromatic spacer have been prepared. Their complexes with Cu(2+), Zn(2+), and Ni(2+) have been studied by potentiometry, UV-vis spectrophotometry, FT-IR, and ESI-MS. The presence of the aromatic spacer provides Cu(2+) complexes with stability constants several orders of magnitude higher than those observed for related ligands containing aliphatic central spacers. Besides, the formation of [MH-2L] complex species is favored. Crystal structures for the corresponding Cu(2+) and Ni(2+) have been obtained, revealing the metal atom in an essentially square-planar geometry, although, in several instances, the oxygen atom of an amide carbonyl of a second complex species can act as a fifth coordination site. In the case of Zn(2+), the only crystal structure obtained displays a square-pyramidal arrangement of the metal center. Finally, preliminary experiments show the catalytic activity of some of these complexes, in particular, Zn(2+) complexes, for epoxide ring-opening with using aniline as the nucleophile in a ligand accelerated process.
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Affiliation(s)
- Lingaraju Gorla
- Departamento de Química Inorgánica y Orgánica, Universitat Jaume I , Av. de Vicent Sos Baynat, s/n, 12071, Castellón, Spain
| | - Vicente Martí-Centelles
- Departamento de Química Inorgánica y Orgánica, Universitat Jaume I , Av. de Vicent Sos Baynat, s/n, 12071, Castellón, Spain
| | - Lena Freimuth
- Departamento de Química Inorgánica y Orgánica, Universitat Jaume I , Av. de Vicent Sos Baynat, s/n, 12071, Castellón, Spain
| | - Belén Altava
- Departamento de Química Inorgánica y Orgánica, Universitat Jaume I , Av. de Vicent Sos Baynat, s/n, 12071, Castellón, Spain
| | - M Isabel Burguete
- Departamento de Química Inorgánica y Orgánica, Universitat Jaume I , Av. de Vicent Sos Baynat, s/n, 12071, Castellón, Spain
| | - Santiago V Luis
- Departamento de Química Inorgánica y Orgánica, Universitat Jaume I , Av. de Vicent Sos Baynat, s/n, 12071, Castellón, Spain
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22
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Lee KJ, Lee WS, Yun H, Hyun YJ, Seo CD, Lee CW, Lim HS. Oligomers of N-Substituted β(2)-Homoalanines: Peptoids with Backbone Chirality. Org Lett 2016; 18:3678-81. [PMID: 27404658 DOI: 10.1021/acs.orglett.6b01726] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A new class of peptoid-based peptidomimetics composed of oligomers of N-substituted β(2)-homoalanines is reported. Design, solid-phase synthesis, and preliminary circular dichroism studies of oligomers of N-alkylated β(2)-homoalanines consisting of up to 8-mers are described.
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Affiliation(s)
- Kang Ju Lee
- Departments of Chemistry and Advanced Material Science, Pohang University of Science and Technology (POSTECH) , Pohang 37673, South Korea
| | - Woo Sirl Lee
- Departments of Chemistry and Advanced Material Science, Pohang University of Science and Technology (POSTECH) , Pohang 37673, South Korea
| | - Hyosuk Yun
- Department of Chemistry, Chonnam National University , Gwangju 61186, South Korea
| | - Yu-Jung Hyun
- Departments of Chemistry and Advanced Material Science, Pohang University of Science and Technology (POSTECH) , Pohang 37673, South Korea
| | - Chang Deok Seo
- Departments of Chemistry and Advanced Material Science, Pohang University of Science and Technology (POSTECH) , Pohang 37673, South Korea
| | - Chul Won Lee
- Department of Chemistry, Chonnam National University , Gwangju 61186, South Korea
| | - Hyun-Suk Lim
- Departments of Chemistry and Advanced Material Science, Pohang University of Science and Technology (POSTECH) , Pohang 37673, South Korea.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine , Indianapolis, Indiana 46202, United States
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23
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Shi Y, Teng P, Sang P, She F, Wei L, Cai J. γ-AApeptides: Design, Structure, and Applications. Acc Chem Res 2016; 49:428-41. [PMID: 26900964 DOI: 10.1021/acs.accounts.5b00492] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The development of sequence-specific peptidomimetics has led to a variety of fascinating discoveries in chemical biology. Many peptidomimetics can mimic primary, secondary, and even tertiary structure of peptides and proteins, and because of their unnatural backbones, they also possess significantly enhanced resistance to enzymatic hydrolysis, improved bioavailability, and chemodiversity. It is known that peptide nucleic acids (PNAs) are peptidic sequences developed for the mimicry of nucleic acids; however, their unique backbone as the molecular scaffold of peptidomimetics to mimic structure and function of bioactive peptides has not been investigated systematically. As such, we recently developed a new class of peptidomimetics, "γ-AApeptides", based on the chiral γ-PNA backbone. They are termed γ-AApeptides because they are the oligomers of γ-substituted-N-acylated-N-aminoethyl amino acids. Similar to other classes of peptidomimetics, γ-AApeptides are also resistant to proteolytic degradation and possess the potential to enhance chemodiversity. Moreover, in our scientific journey on the exploration of this class of peptidomimetics, we have discovered some intriguing structures and functions of γ-AApeptides. In this Account, we summarize the current development and application of γ-AApeptides with biological potential. Briefly, both linear and cyclic (either through head-to-tail or head-to-side-chain cyclization) γ-AApeptides with diverse functional groups can be synthesized easily on the solid phase using the synthetic protocol we developed. γ-AApeptides could mimic the primary structure of peptides, as they project the same number of side chains as peptides of the same lengths. For instance, they could mimic the Tat peptide to permeate cell membranes and bind to HIV RNA with high specificity and affinity. Certain γ-AApeptides show similar activity to the RGD peptide and target integrin specifically on the cell surface. γ-AApeptides with function akin to fMLF peptides are also identified. More importantly, we found that γ-AApeptides can fold into discrete secondary structures, such as helical and β-turn-like structures. Therefore, they could be rationally designed for a range of biological applications. For instance, γ-AApeptides can mimic host-defense peptides and display potent and broad-spectrum activity toward a panel of drug-resistant bacterial pathogens. Meanwhile, because of their stability against proteolysis and their chemodiversity, γ-AApeptides are also amenable for combinatorial screening. We demonstrate that, through combinatorial selection, certain γ-AApeptides are identified to inhibit Aβ40 peptide aggregation, suggesting their potential use as a molecular probe to intervene in Alzheimer's disease. In addition, a few γ-AApeptides identified from the γ-AApeptide library have been shown to bind to the DNA-binding domain of STAT3 and antagonize STAT3/DNA interactions. Our studies suggest that, with further studies and exploration on both structures and functions, γ-AApeptides may emerge to be a new class of peptidomimetics that play an important role in chemical biology and biomedical sciences.
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Affiliation(s)
- Yan Shi
- Department of Chemistry, University of South Florida, 4202
East Fowler Ave, Tampa, Florida 33620, United States
| | - Peng Teng
- Department of Chemistry, University of South Florida, 4202
East Fowler Ave, Tampa, Florida 33620, United States
| | - Peng Sang
- Department of Chemistry, University of South Florida, 4202
East Fowler Ave, Tampa, Florida 33620, United States
| | - Fengyu She
- Department of Chemistry, University of South Florida, 4202
East Fowler Ave, Tampa, Florida 33620, United States
| | - Lulu Wei
- Department of Chemistry, University of South Florida, 4202
East Fowler Ave, Tampa, Florida 33620, United States
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, 4202
East Fowler Ave, Tampa, Florida 33620, United States
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24
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Alfonso I. From simplicity to complex systems with bioinspired pseudopeptides. Chem Commun (Camb) 2016; 52:239-50. [DOI: 10.1039/c5cc07596c] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
This feature article highlights some of the recent advances in creating complexity from simple pseudopeptidic molecules. The bioinspired approaches discussed here allowed an increase in the structural, chemical and interactional complexity (see figure).
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Affiliation(s)
- Ignacio Alfonso
- Department of Biological Chemistry and Molecular Modelling
- Institute of Advanced Chemistry of Catalonia
- IQAC-CSIC
- Jordi Girona
- 18-26
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25
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Highly stable atropisomers by electrophilic amination of a chiral γ-lactam within the synthesis of an elusive conformationally restricted analogue of α-methylhomoserine. Amino Acids 2015; 48:461-78. [DOI: 10.1007/s00726-015-2100-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 09/11/2015] [Indexed: 02/01/2023]
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26
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Romero-Estudillo I, Boto A. Domino Process Achieves Site-Selective Peptide Modification with High Optical Purity. Applications to Chain Diversification and Peptide Ligation. J Org Chem 2015; 80:9379-91. [DOI: 10.1021/acs.joc.5b00932] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Ivan Romero-Estudillo
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206-La Laguna, Tenerife, Spain
| | - Alicia Boto
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206-La Laguna, Tenerife, Spain
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27
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Wu H, Qiao Q, Teng P, Hu Y, Antoniadis D, Zuo X, Cai J. New Class of Heterogeneous Helical Peptidomimetics. Org Lett 2015; 17:3524-7. [PMID: 26153619 DOI: 10.1021/acs.orglett.5b01608] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new class of unnatural heterogeneous foldamers is reported to contain alternative α-amino acid and sulfono-γ-AA amino acid residues in a 1:1 repeat pattern. Two-dimensional NMR data show that two 1:1 α/sulfono-γ-AA peptides with diverse side chains form analogous right-handed helical structures in solution. The effects of sequence length, side chain, N-capping, and temperature on folding propensity were further investigated using circular dichroism and small-angle X-ray scattering.
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Affiliation(s)
- Haifan Wu
- †Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Qiao Qiao
- †Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Peng Teng
- †Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Yaogang Hu
- †Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Dimitrios Antoniadis
- †Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Xiaobing Zuo
- ‡X-ray Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Jianfeng Cai
- †Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
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28
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Wu H, She F, Gao W, Prince A, Li Y, Wei L, Mercer A, Wojtas L, Ma S, Cai J. The synthesis of head-to-tail cyclic sulfono-γ-AApeptides. Org Biomol Chem 2015; 13:672-6. [DOI: 10.1039/c4ob02232g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Head-to-tail cyclic sulfono-γ-AApeptides.
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Affiliation(s)
- Haifan Wu
- Department of Chemistry
- University of South Florida
- Tampa
- USA
| | - Fengyu She
- Department of Chemistry
- University of South Florida
- Tampa
- USA
| | - Wenyang Gao
- Department of Chemistry
- University of South Florida
- Tampa
- USA
| | - Austin Prince
- Department of Chemistry
- University of South Florida
- Tampa
- USA
| | - Yaqiong Li
- Department of Chemistry
- University of South Florida
- Tampa
- USA
| | - Lulu Wei
- Department of Chemistry
- University of South Florida
- Tampa
- USA
| | - Allison Mercer
- Department of Chemistry
- University of South Florida
- Tampa
- USA
| | - Lukasz Wojtas
- Department of Chemistry
- University of South Florida
- Tampa
- USA
| | - Shengqian Ma
- Department of Chemistry
- University of South Florida
- Tampa
- USA
| | - Jianfeng Cai
- Department of Chemistry
- University of South Florida
- Tampa
- USA
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29
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Wadhavane PD, Gorla L, Ferrer A, Altava B, Burguete MI, Izquierdo MÁ, Luis SV. Coordination behaviour of new open chain and macrocyclic peptidomimetic compounds with copper(ii). RSC Adv 2015. [DOI: 10.1039/c5ra15852d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Two valine-derived bis(amino amides) ligands have been prepared and fully characterized.
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Affiliation(s)
- Prashant D. Wadhavane
- Departament of Inorganic and Organic Chemistry
- Universitat Jaume I
- Campus del Riu Sec
- Castellón
- Spain
| | - Lingaraju Gorla
- Departament of Inorganic and Organic Chemistry
- Universitat Jaume I
- Campus del Riu Sec
- Castellón
- Spain
| | - Armando Ferrer
- Departament of Inorganic and Organic Chemistry
- Universitat Jaume I
- Campus del Riu Sec
- Castellón
- Spain
| | - Belén Altava
- Departament of Inorganic and Organic Chemistry
- Universitat Jaume I
- Campus del Riu Sec
- Castellón
- Spain
| | - M. Isabel Burguete
- Departament of Inorganic and Organic Chemistry
- Universitat Jaume I
- Campus del Riu Sec
- Castellón
- Spain
| | - M. Ángeles Izquierdo
- Departament of Inorganic and Organic Chemistry
- Universitat Jaume I
- Campus del Riu Sec
- Castellón
- Spain
| | - Santiago V. Luis
- Departament of Inorganic and Organic Chemistry
- Universitat Jaume I
- Campus del Riu Sec
- Castellón
- Spain
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30
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Wu H, Qiao Q, Hu Y, Teng P, Gao W, Zuo X, Wojtas L, Larsen RW, Ma S, Cai J. Sulfono-γ-AApeptides as a new class of nonnatural helical foldamer. Chemistry 2014; 21:2501-7. [PMID: 25504756 DOI: 10.1002/chem.201406112] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Indexed: 11/06/2022]
Abstract
Foldamers offer an attractive opportunity for the design of novel molecules that mimic the structures and functions of proteins and enzymes including biocatalysis and biomolecular recognition. Herein we report a new class of nonnatural helical sulfono-γ-AApeptide foldamers of varying lengths. The crystal structure of the sulfono-γ-AApeptide monomer S6 illustrates the intrinsic folding propensity of sulfono-γ-AApeptides, which likely originates from the bulkiness of tertiary sulfonamide moiety. The two-dimensional solution NMR spectroscopy data for the longest sequence S1 demonstrates a 10/16 right-handed helical structure. Optical analysis using circular dichroism further supports well- defined helical conformation of sulfono-γ-AApeptides in solution containing as few as five building blocks. Future development of sulfono-γ-AApeptides may lead to new foldamers with discrete functions, enabling expanded application in chemical biology and biomedical sciences.
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Affiliation(s)
- Haifan Wu
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620 (USA)
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31
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Ilisz I, Gecse Z, Pataj Z, Fülöp F, Tóth G, Lindner W, Péter A. Direct high-performance liquid chromatographic enantioseparation of secondary amino acids on Cinchona alkaloid-based chiral zwitterionic stationary phases. Unusual temperature behavior. J Chromatogr A 2014; 1363:169-77. [DOI: 10.1016/j.chroma.2014.06.087] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 06/04/2014] [Accepted: 06/25/2014] [Indexed: 11/17/2022]
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32
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33
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Ortega PGR, Montejo M, González JJL. Study of the chelating properties of Ge(OH)2 functionality as metal binding group for Zn2+ cation in simplified protease-like environments: a DFT analysis. J Mol Model 2014; 20:2430. [PMID: 25142338 DOI: 10.1007/s00894-014-2430-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 08/07/2014] [Indexed: 10/24/2022]
Abstract
The development of protease's inhibitors is an active field of research in the pharmaceutical industry. As concerns the design of new inhibitors, the theoretical study of the binding patterns and energies of known metal binding groups (MBGs) toward Zn(2+) using quantum-chemical calculations may offer a better understanding of their interaction models and may be useful for the improvement and design of novel ZBGs. Here the properties of gem-Ge(OH)(2)-based compounds as ZBG were assessed theoretically using DFT calculations. [Zn(Imdz)(2) R - OH(2)](2+) complexes (Imdz =imidazole rings; R = imidazole ring, acetic acid molecule or acetate anion) were used to partially reproduce the coordination sphere in metalloproteases (ACE, amgiotensin converting enzyme, and TLN, thermolysine) being inhibited by related compounds (i.e., silanediols). The MBG- Zn(2+) interaction was analyzed through the energy of the reaction: [Zn(Imdz)(2) R - OH(2)](2+) + L → [Zn(Imdz)(2) R - L](2+) + H(2)O using DFT (M06L/cc-pVDZ) in gas-phase and in solution (IEF-PCM). Although the functional used (M06L) has proven its efficiency to study systems containing transition metal governed by non-covalent interactions, dispersion effects were implemented by the correction of the computed energies using the DFT-D3 program. Accounting for dispersion effects produced a systematic increase of c.a. 13 kJ mol(-1) on the energies, whereas the effect of solvent goes in the opposite direction (i.e., BE under the IEF-PCM model are on average 125 kJ mol(-1) lower). The Ge(OH)(2) - Zn(2+) interaction seems to be similar (or even stronger) than the Si(OH)(2) -Zn(2+). Their better performance as ZBG is explained by the combined NBO-AIM analysis. The results of this work may encourage the preparation, isolation, and experimental assay of the chelating properties of these compounds, which may propose a new family of protease's inhibitors.
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Affiliation(s)
- Pilar Gema Rodríguez Ortega
- Physical and Analytical Chemistry Department, University of Jaén, Campus "Las Lagunillas", Ed. B3, Jaén, 23071, Spain
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Abstract
For years researchers have tried to understand the molecular behavior of complex biomolecules through the development of small molecules that can partially mimic their function. Now researchers are implementing the reverse approach: using the structural and mechanistic knowledge obtained from those complex systems to design small molecules with defined properties and for specific applications. One successful strategy for constructing bioinspired, minimalistic molecules is to combine natural building blocks that provide functional elements with abiotic fragments that serve as structural scaffolds. Therefore pseudopeptidic compounds, most of them based on C2 symmetric structures, represent a unique opportunity to explore and evaluate this approach. Some of these molecules are as simple as two amino acids connected by a diamino spacer. The results in this Account show how bioinspired minimalistic pseudopeptides can form ordered structures, participate in the recognition and transcription of information events in molecular devices, and catalyze reactions. This strategy allows researchers to design and prepare a variety of open-chain and macrocyclic compounds leading to systems that can self-aggregate to form hierarchically ordered micro- and nanostructures. In addition, small changes in the molecule or external stimuli can regulate the self-aggregation pattern. In the same way, researchers can also tune the molecular movements of simple pseudopeptides through environmental factors, providing a means to control new molecular devices. In addition, some of the prepared model compounds have shown interesting properties in molecular recognition and even as sensors for several targets of interest. Finally we have observed remarkable catalytic activities from these types of molecules, although those results are still far from the efficiency shown by natural peptides. This family of pseudopeptidic compounds offers the opportunity for the more elaborate design of relatively simple abiotic but bioinspired systems that display specific properties. In addition, the results can provide additional information that will increase the molecular understanding of the basic principles that underlie the extraordinary behavior of natural systems.
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Affiliation(s)
- Santiago V. Luis
- Department of Inorganic and Organic Chemistry, ESTCE, University Jaume I, Castellón. Spain
| | - I. Alfonso
- Department of Biological Chemistry and Molecular Modeling, IQAC−CSIC, Barcelona, Spain
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35
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Rapid Access to Multiple Classes of Peptidomimetics from Common γ-AApeptide Building Blocks. European J Org Chem 2014. [DOI: 10.1002/ejoc.201301841] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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36
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Rabong C, Schuster C, Liptaj T, Prónayová N, Delchev VB, Jordis U, Phopase J. NXO beta structure mimicry: an ultrashort turn/hairpin mimic that folds in water. RSC Adv 2014. [DOI: 10.1039/c4ra01210k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
An NXO building block derived tetrapeptide mimic emulates a natural proline-glycine β-turn/hairpin in polar media, including water at room temperature.
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Affiliation(s)
- Constantin Rabong
- Institute of Applied Synthetic Chemistry
- Vienna University of Technology
- A-1060 Vienna, Austria
| | - Christoph Schuster
- Department of Environmental Geosciences
- University of Vienna
- A-1090 Vienna, Austria
| | - Tibor Liptaj
- Department of NMR and Mass Spectrometry
- Institute of Analytical Chemistry
- Faculty of Chemical and Food Technology
- Slovak University of Technology
- 81237 Bratislava, Slovak Republic
| | - Nadežda Prónayová
- Department of NMR and Mass Spectrometry
- Institute of Analytical Chemistry
- Faculty of Chemical and Food Technology
- Slovak University of Technology
- 81237 Bratislava, Slovak Republic
| | - Vassil B. Delchev
- Department of Physical Chemistry
- University of Plovdiv
- 4000 Plovdiv, Bulgaria
| | - Ulrich Jordis
- Institute of Applied Synthetic Chemistry
- Vienna University of Technology
- A-1060 Vienna, Austria
| | - Jaywant Phopase
- Integrative Regenerative Medicine Centre (IGEN) & Department of Physics
- Chemistry and Biology (IFM)
- 58183 Linköping, Sweden
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Rajasekhar K, Narayanaswamy N, Mishra P, Suresh SN, Manjithaya R, Govindaraju T. Synthesis of Hybrid Cyclic Peptoids and Identification of Autophagy Enhancer. Chempluschem 2013; 79:25-30. [DOI: 10.1002/cplu.201300343] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Indexed: 01/02/2023]
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38
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Synthesis of divalent glycoamino acids with bis-triazole linkage. Carbohydr Res 2013; 381:51-8. [DOI: 10.1016/j.carres.2013.08.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 08/08/2013] [Accepted: 08/09/2013] [Indexed: 11/20/2022]
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39
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Insertion of beta-alanine in model peptides for copper binding to His96 and His111 of the human prion protein. J Inorg Biochem 2013; 126:104-10. [DOI: 10.1016/j.jinorgbio.2013.05.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 05/29/2013] [Accepted: 05/29/2013] [Indexed: 12/30/2022]
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40
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Del Borgo MP, Mechler AI, Traore D, Forsyth C, Wilce JA, Wilce MCJ, Aguilar MI, Perlmutter P. Supramolecular Self-Assembly ofN-Acetyl-Capped β-Peptides Leads to Nano- to Macroscale Fiber Formation. Angew Chem Int Ed Engl 2013; 52:8266-70. [DOI: 10.1002/anie.201303175] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Indexed: 12/26/2022]
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41
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Del Borgo MP, Mechler AI, Traore D, Forsyth C, Wilce JA, Wilce MCJ, Aguilar MI, Perlmutter P. Supramolecular Self-Assembly ofN-Acetyl-Capped β-Peptides Leads to Nano- to Macroscale Fiber Formation. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201303175] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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42
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Abstract
Antimicrobial peptides (AMPs) hold promise to circumvent the emergence of drug resistance occurring in the treatment of bacteria using many conventional antibiotics. Antimicrobial peptidomimetics, which mimic bactericidal mechanisms of AMPs, may overcome the disadvantages of AMPs and become the new generation of antibiotic therapeutics. In this review, some recent examples in the development of antimicrobial peptidomimetics are highlighted. The potential of antimicrobial agents has been demonstrated for therapeutic uses. Meanwhile, perspectives on their further development and applications are also presented.
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43
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Laursen JS, Engel-Andreasen J, Fristrup P, Harris P, Olsen CA. Cis-trans amide bond rotamers in β-peptoids and peptoids: evaluation of stereoelectronic effects in backbone and side chains. J Am Chem Soc 2013; 135:2835-44. [PMID: 23343406 DOI: 10.1021/ja312532x] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Non-natural peptide analogs have significant potential for the development of new materials and pharmacologically active ligands. One such architecture, the β-peptoids (N-alkyl-β-alanines), has found use in a variety of biologically active compounds but has been sparsely studied with respect to folding propensity. Thus, we here report an investigation of the effect of structural variations on the cis-trans amide bond rotamer equilibria in a selection of monomer model systems. In addition to various side chain effects, which correlated well with previous studies of α-peptoids, we present the synthesis and investigation of cis-trans isomerism in the first examples of peptoids and β-peptoids containing thioamide bonds as well as trifluoroacetylated peptoids and β-peptoids. These systems revealed an increase in the preference for cis-amides as compared to their parent compounds and thus provide novel strategies for affecting the folding of peptoid constructs. By using NMR spectroscopy, X-ray crystallographic analysis, and density functional theory calculations, we present evidence for the presence of thioamide-aromatic interactions through C(sp(2))-H···S(amide) hydrogen bonding, which stabilize certain peptoid conformations.
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Affiliation(s)
- Jonas S Laursen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800, Kongens Lyngby, Denmark
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44
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Abstract
The creation and development of nonnatural peptidomimetics has become an area of increasing significance in bioorganic and chemical biology. A wide range of new peptide mimics with novel structures and functions are urgently needed to be explored in order to identify potential drug candidates and targeted probes, and to study protein functions. AApeptides are a new class of peptide mimics based on chiral PNA backbone. They are resistant to proteolytic degradation and have limitless potential for diversification. They have been found to have a wide variety of biological applications including cellular translocation, disruption of protein-protein interactions, formation of nanostructures, antimicrobial activity, etc. The synthesis of AApeptides is modular and straightforward. In this chapter, methods for the synthesis of AApeptides (including different subclasses) are described.
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Affiliation(s)
- Youhong Niu
- Department of Chemistry, University of South Florida, Tampa, FL, USA
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45
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Vijayadas KN, Nair RV, Gawade RL, Kotmale AS, Prabhakaran P, Gonnade RG, Puranik VG, Rajamohanan PR, Sanjayan GJ. Ester vs. amide on folding: a case study with a 2-residue synthetic peptide. Org Biomol Chem 2013; 11:8348-56. [DOI: 10.1039/c3ob41967c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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46
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Wu H, Amin MN, Niu Y, Qiao Q, Harfouch N, Nimer A, Cai J. Solid-phase synthesis of γ-AApeptides using a submonomeric approach. Org Lett 2012; 14:3446-9. [PMID: 22731678 DOI: 10.1021/ol301406a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The solid-phase synthesis of γ-AApeptides using a novel submonomeric approach that utilizes an allyl protection is reported. The strategy successfully circumvents the necessity of preparing γ-AApeptide building blocks in order to prepare γ-AApeptide sequences. This method will maximize the potential of developing chemically diverse γ-AApeptide libraries and thereby facilitate the biological applications of γ-AApeptides in the future.
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Affiliation(s)
- Haifan Wu
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, USA
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47
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Pellegrino S, Contini A, Clerici F, Gori A, Nava D, Gelmi ML. 1H-Azepine-4-amino-4-carboxylic acid: a new α,α-disubstituted ornithine analogue capable of inducing helix conformations in short Ala-Aib pentapeptides. Chemistry 2012; 18:8705-15. [PMID: 22689465 DOI: 10.1002/chem.201104023] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 03/30/2012] [Indexed: 11/08/2022]
Abstract
A very efficient synthesis of orthogonally protected 1H-azepine-4-amino-4-carboxylic acid, abbreviated as Azn, a conformationally restricted analogue of ornithine, was realized. It was obtained on a gram scale in good overall yield in five steps, three of which did not require isolation of the intermediates, starting from the readily available 1-amino-4-oxo-cyclohexane-4-carboxylic acid. Both enantiomers were used for the preparation of pentapeptide models containing Ala, Aib, and Azn. Conformational studies using both spectroscopic techniques (NMR, CD) and molecular dynamics on model 5-mer peptides showed that the (R)-Azn isomer possesses a marked helicogenic effect.
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Affiliation(s)
- Sara Pellegrino
- DISMAB, Sezione di Chimica Organica A. Marchesini, Facoltà di Farmacia, Università degli Studi Milano, Via Venezian 21, 20133 Milano, Italy.
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48
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Seebach D, Lukaszuk A, Patora-Komisarska K, Podwysocka D, Gardiner J, Ebert MO, Reubi JC, Cescato R, Waser B, Gmeiner P, Hübner H, Rougeot C. On the Terminal Homologation of Physiologically Active Peptides as a Means of Increasing Stability in Human Serum - Neurotensin, Opiorphin, B27-KK10 Epitope, NPY. Chem Biodivers 2011; 8:711-39. [DOI: 10.1002/cbdv.201100093] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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49
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Soengas RG, Estévez AM, Estévez JC, Estévez RJ. An overview on the synthesis of furanoid and pyranoid sugar α- and β-amino acids and related aminocycloalkanecarboxylic acids from carbohydrates. CR CHIM 2011. [DOI: 10.1016/j.crci.2010.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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50
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Rodriguez A, Mokoema P, Corcho F, Bisetty K, Perez JJ. Computational study of the free energy landscape of the miniprotein CLN025 in explicit and implicit solvent. J Phys Chem B 2011; 115:1440-9. [PMID: 21254763 DOI: 10.1021/jp106475c] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The prediction capabilities of atomistic simulations of peptides are hampered by different difficulties, including the reliability of force fields, the treatment of the solvent or the adequate sampling of the conformational space. In this work, we have studied the conformational profile of the 10 residue miniprotein CLN025 known to exhibit a β-hairpin in its native state to understand the limitations of implicit methods to describe solvent effects and how these may be compensated by using different force fields. For this purpose, we carried out a thorough sampling of the conformational space of CLN025 in explicit solvent using the replica exchange molecular dynamics method as a sampling technique and compared the results with simulations of the system modeled using the analytical linearized Poisson-Boltzmann (ALPB) method with three different AMBER force fields: parm94, parm96, and parm99SB. The results show the peptide to exhibit a funnel-like free energy landscape with two minima in explicit solvent. In contrast, the higher minimum nearly disappears from the energy surface when the system is studied with an implicit representation of the solvent. Moreover, the different force fields used in combination with the ALPB method do not describe the system in the same manner. The results of this work suggest that the balance between intra- and intermolecular interactions is the cause of the differences between implicit and explicit solvent simulations in this system, stressing the role of the environment to define properly the conformational profile of a peptide in solution.
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Affiliation(s)
- Alex Rodriguez
- Department d'Enginyeria Quimica (UPC) ETS d'Enginyers Industrials, Av. Diagonal, 647, 08028 Barcelona, Spain
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