1
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Biondi B, Formaggio F, Toniolo C, Peggion C, Crisma M. Isolated α-turns in peptides: a selected literature survey. J Pept Sci 2023:e3476. [PMID: 36603599 DOI: 10.1002/psc.3476] [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: 10/28/2022] [Revised: 12/21/2022] [Accepted: 12/26/2022] [Indexed: 01/07/2023]
Abstract
The results of classifying into various types the 68 examples of isolated α-turns in the X-ray diffraction crystal structures of peptides documented in the literature are presented and discussed in this review article. α-Turns characterized by the trans disposition of all ω torsion angles are common for the backbone linear peptides investigated. In contrast, the cis arrangement of the N-terminal (ωi + 1 ) torsion angle, among those generated by the three residues internal to the α-turn, is a peculiar feature of 65% of the cyclic peptides. Among linear and cyclic peptides featuring the all-trans disposition of the ω torsion angles, only one third of the α-turns display φ,ψ values not too far from those characterizing regular α-helices. In general, our findings, taken together, suggest that a significant conformational diversity is compatible with the formation of an intramolecularly H-bonded C13 -member pseudocycle (α-turn) in linear and cyclic peptides.
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Affiliation(s)
- Barbara Biondi
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy
| | - Fernando Formaggio
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy.,Department of Chemical Sciences, University of Padova, Padua, Italy
| | - Claudio Toniolo
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy.,Department of Chemical Sciences, University of Padova, Padua, Italy
| | - Cristina Peggion
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy.,Department of Chemical Sciences, University of Padova, Padua, Italy
| | - Marco Crisma
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy
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2
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Lal J, Prajapati G, Meena R, Kant R, Sankar Ampapathi R, Reddy DN. Influence of Proline Chirality on Neighbouring Azaproline Residue Stereodynamic Nitrogen Preorganization. Chem Asian J 2023; 18:e202201023. [PMID: 36349404 DOI: 10.1002/asia.202201023] [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: 10/06/2022] [Revised: 11/04/2022] [Indexed: 11/10/2022]
Abstract
We report herein the first systematic crystal structural investigation of azaproline incorporated in homo- and heterochiral diprolyl peptides. The X-ray crystallography data of peptides 1-5 illustrates that stereodynamic nitrogen in azaproline adopted the stereochemistry of neighbouring proline residue without depending on its position in the peptide sequence. Natural bond orbital analysis of crystal structures indicates OazPro -C'Pro of peptides 4 and 5 participating in n→π* interaction with stabilization energy about 1.21-1.33 kcal/mol. Density functional theory calculations suggested that the endo-proline ring puckering favoured over exo-conformation by 6.72-7.64 kcal/mol. NBO and DFT data reveals that the n→π* interactions and proline ring puckering stabilize azaproline chirality with the neighbouring proline stereochemistry. The CD, solvent titration, variable-temperature and 2D NMR experimental results further supported the crystal structures conformation.
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Affiliation(s)
- Jhajan Lal
- Division of Medicinal and Process Chemistry, CSIR-CDRI, Lucknow, 226031, India) .,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, UP-201002, India
| | - Gurudayal Prajapati
- Division of Sophisticated Analytical Instrument Facility and Research, CSIR-CDRI, Lucknow, 226031, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, UP-201002, India
| | - Rachana Meena
- Division of Medicinal and Process Chemistry, CSIR-CDRI, Lucknow, 226031, India) .,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, UP-201002, India
| | - Ruchir Kant
- Biochemistry and Structural Biology Division, CSIR-CDRI, Lucknow, 226031, India
| | - Ravi Sankar Ampapathi
- Division of Sophisticated Analytical Instrument Facility and Research, CSIR-CDRI, Lucknow, 226031, India.,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, UP-201002, India
| | - Damodara N Reddy
- Division of Medicinal and Process Chemistry, CSIR-CDRI, Lucknow, 226031, India) .,Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, UP-201002, India
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3
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Nuskol M, Šutalo P, Đaković M, Kovačević M, Kodrin I, Čakić Semenčić M. Testing the Potential of the Ferrocene Chromophore as a Circular Dichroism Probe for the Assignment of the Screw-Sense Preference of Tripeptides. Organometallics 2021. [DOI: 10.1021/acs.organomet.1c00138] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Marko Nuskol
- Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Petar Šutalo
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Marijana Đaković
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Monika Kovačević
- Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Ivan Kodrin
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Mojca Čakić Semenčić
- Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
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4
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Parajuli P, Sable R, Shrestha L, Dahal A, Gauthier T, Taneja V, Jois S. Modulation of co-stimulatory signal from CD2-CD58 proteins by a grafted peptide. Chem Biol Drug Des 2021; 97:607-627. [PMID: 32946175 PMCID: PMC8717467 DOI: 10.1111/cbdd.13797] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 06/23/2020] [Accepted: 09/09/2020] [Indexed: 12/12/2022]
Abstract
Peptides were designed to inhibit the protein-protein interaction of CD2 and CD58 to modulate the immune response. This work involved the design and synthesis of eight different peptides by replacing each amino acid residue in peptide 6 with alanine as well as grafting the peptide to the sunflower trypsin-inhibitor framework. From the alanine scanning studies, mutation at position 2 of the peptide was shown to result in increased potency to inhibit cell adhesion interactions. The most potent peptide from the alanine scanning was further studied for its detailed three-dimensional structure and binding to CD58 protein using surface plasmon resonance and flow cytometry. This peptide was used to graft to the sunflower trypsin inhibitor to improve the stability of the peptide. The grafted peptide, SFTI-a1, was further studied for its potency as well as its thermal, chemical, and enzymatic stability. The grafted peptide exhibited improved activity compared to our previously grafted peptide and was stable against thermal and enzymatic degradation.
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Affiliation(s)
- Pravin Parajuli
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana at Monroe, Monroe LA 71201 USA
| | - Rushikesh Sable
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana at Monroe, Monroe LA 71201 USA
| | - Leeza Shrestha
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana at Monroe, Monroe LA 71201 USA
| | - Achyut Dahal
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana at Monroe, Monroe LA 71201 USA
| | - Ted Gauthier
- Biotechnology Laboratory, LSU AgCenter, Louisiana State University, Baton Rouge, LA 70803 USA
| | - Veena Taneja
- Department of Immunology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Seetharama Jois
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana at Monroe, Monroe LA 71201 USA
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5
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Pal S, Banerjee S, Prabhakaran EN. Helix-Coil Transition at a Glycine Following a Nascent α-Helix: A Synergetic Guidance Mechanism for Helix Growth. J Phys Chem A 2020; 124:7478-7490. [PMID: 32877193 DOI: 10.1021/acs.jpca.0c05489] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A detailed understanding of forces guiding the rapid folding of a polypeptide from an apparently random coil state to an ordered α-helical structure following the rate-limiting preorganization of the initial three residue backbones into helical conformation is imperative to comprehending and regulating protein folding and for the rational design of biological mimetics. However, several details of this process are still unknown. First, although the helix-coil transition was proposed to originate at the residue level (J. Chem. Phys. 1959, 31, 526-535; J. Chem. Phys. 1961, 34, 1963-1974), all helix-folding studies have only established it between time-averaged bulk states of a long-lived helix and several transiently populated random coils, along the whole helix model sequence. Second, the predominant thermodynamic forces driving either this two-state transition or the faster helix growth following helix nucleation are still unclear. Third, the conformational space of the random coil state is not well-defined unlike its corresponding α-helix. Here we investigate the restrictions placed on the conformational space of a Gly residue backbone, as a result of it immediately succeeding a nascent α-helical turn. Analyses of the temperature-dependent 1D-, 2D-NMR, FT-IR, and CD spectra and GROMACS MD simulation trajectory of a Gly residue backbone following a model α-helical turn, which is artificially rigidified by a covalent hydrogen bond surrogate, reveal that: (i) the α-helical turn guides the ϕ torsion of the Gly exclusively into either a predominantly populated entropically favored α-helical (α-ϕ) state or a scarcely populated random coil (RC-ϕ) state; (ii) the α-ϕ state of Gly in turn favors the stability of the preceding α-helical turn, while the RC-ϕ state disrupts it, revealing an entropy-driven synergetic guidance for helix growth in the residue following helix nucleation. The applicability of a current synergetic guidance mechanism to explain rapid helix growth in folded and unfolded states of proteins and helical peptides is discussed.
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Affiliation(s)
- Sunit Pal
- Department of Chemistry, Indian Institute of Science, Bangalore, Karnataka-560012, India
| | - Shreya Banerjee
- Department of Chemistry, Indian Institute of Science, Bangalore, Karnataka-560012, India
| | - Erode N Prabhakaran
- Department of Chemistry, Indian Institute of Science, Bangalore, Karnataka-560012, India
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6
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Yarava JR, Nishiyama Y, Raghothama S, Ramanathan KV. Conformational investigation of peptides using solid-state NMR spectroscopy-A study of polymorphism of β-turn peptides containing diprolines. Chem Biol Drug Des 2019; 95:394-407. [PMID: 31755652 DOI: 10.1111/cbdd.13649] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/02/2019] [Accepted: 11/16/2019] [Indexed: 11/26/2022]
Abstract
The construction of complex protein folds relies on the precise conversion of a linear polypeptide chain into a compact 3-dimensional structure. In this context, study of isolated secondary structural modules containing short stretches of amino acids assumes significance. Additionally, peptides, both natural and synthetic, play a major role as potential drugs. With a view to understand the local conformations adopted by peptides in the solid state, we propose a multinuclear NMR approach utilizing spectra of nuclei in their natural isotopic abundance. Various solid-state NMR experiments have been utilized for assignment of the spectra. Additionally, the gauge-including projector augmented-wave (GIPAW) calculations were used to confirm the assignments. Particularly, the utility of the double-quantum-single-quantum correlation experiments is highlighted for the purpose of assignment and for inferring the conformation across the peptide bond. The methodology is illustrated for the case of designed peptides containing diproline residues occurring at the β-turns for identifying their cis-trans conformational polymorphism. The proposed method promises to be of use in the study of conformations of small- to medium-sized peptides such as antimicrobial peptides and in the study of polymorphism leading to applications in drug development protocols.
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Affiliation(s)
- Jayasubba Reddy Yarava
- NMR Research Centre, Indian Institute of Science, Bangalore, India.,Department of Physics, Indian Institute of Science, Bangalore, India
| | - Yusuke Nishiyama
- JEOL RESONANCE Inc., Musashino, Akishima, Japan.,RIKEN-JEOL Collaboration Center, Tsurumi, Yokohama, Japan
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7
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Yamada Y, Patel NL, Kalen JD, Schneider JP. Design of a Peptide-Based Electronegative Hydrogel for the Direct Encapsulation, 3D Culturing, in Vivo Syringe-Based Delivery, and Long-Term Tissue Engraftment of Cells. ACS APPLIED MATERIALS & INTERFACES 2019; 11:34688-34697. [PMID: 31448901 PMCID: PMC8274941 DOI: 10.1021/acsami.9b12152] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Soft materials that facilitate the three-dimensional (3D) encapsulation, proliferation, and facile local delivery of cells to targeted tissues will aid cell-based therapies, especially those that depend on the local engraftment of implanted cells. Herein, we develop a negatively charged fibrillar hydrogel based on the de novo-designed self-assembling peptide AcVES3-RGDV. Cells are easily encapsulated during the triggered self-assembly of the peptide leading to gel formation. Self-assembly is induced by adjusting the ionic strength and/or temperature of the solution, while avoiding large changes in pH. The AcVES3-RGDV gel allows cell-material attachment enabling both two-dimensional and 3D cell culture of adherent cells. Gel-cell constructs display shear-thin/recovery rheological properties enabling their syringe-based delivery. In vivo cellular fluorescence as well as tissue resection experiments show that the gel supports the long-term engraftment of cells delivered subcutaneously into mice.
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Affiliation(s)
- Y. Yamada
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute-Frederick, National Institutes of Health, Frederick, Maryland 21702, United States
| | - N. L. Patel
- Small Animal Imaging Program, Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Incorporation, Frederick, Maryland 21702, United States
| | - J. D. Kalen
- Small Animal Imaging Program, Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Incorporation, Frederick, Maryland 21702, United States
| | - J. P. Schneider
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute-Frederick, National Institutes of Health, Frederick, Maryland 21702, United States
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8
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Mir FM, Crisma M, Toniolo C, Lubell WD. Isolated α-turn and incipient γ-helix. Chem Sci 2019; 10:6908-6914. [PMID: 31391913 PMCID: PMC6640192 DOI: 10.1039/c9sc01683j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 06/07/2019] [Indexed: 12/17/2022] Open
Abstract
The unique abilities of homo-oligo-adamantyl peptides to adopt α- and γ-turn conformations are demonstrated by X-ray diffraction, and NMR and FT-IR absorption spectroscopies. Assembled by an Ugi multiple component reaction strategy, N α-formyl-adamantyl tripeptide iso-propyl and tert-butyl amides are respectively found to adopt an isolated α-turn and an incipient γ-helix conformation by X-ray diffraction crystallography. The shortest example of a single α-turn with ideal geometry is observed in the crystalline state. In solution both peptides predominantly assume γ-helical structures.
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Affiliation(s)
- Fatemeh M Mir
- Département de Chimie , Université de Montréal , C. P. 6128, Succursale Centre-Ville , Montréal , Québec , Canada H3C 3J7 .
| | - Marco Crisma
- Department of Chemistry , University of Padova and Institute of Biomolecular Chemistry , Padova Unit , CNR , 35131 Padova , Italy
| | - Claudio Toniolo
- Department of Chemistry , University of Padova and Institute of Biomolecular Chemistry , Padova Unit , CNR , 35131 Padova , Italy
| | - William D Lubell
- Département de Chimie , Université de Montréal , C. P. 6128, Succursale Centre-Ville , Montréal , Québec , Canada H3C 3J7 .
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9
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Yuan F, Tian Y, Qin W, Li J, Yang D, Zhao B, Yin F, Li Z. Evaluation of topologically distinct constrained antimicrobial peptides with broad-spectrum antimicrobial activity. Org Biomol Chem 2019; 16:5764-5770. [PMID: 30004546 DOI: 10.1039/c8ob00483h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Antimicrobial peptides (AMPs) are short cationic peptides with a high affinity for membranes and emerged as a promising therapeutic approach with potential for treating infectious diseases. Chemical stabilization of short peptides proved to be a successful approach for enhancing their bio-physical properties. Herein, we designed and synthesized a panel of conformationally constrained antimicrobial peptides with either α-helical or β-hairpin conformation using templating strategies. These synthetic short constrained peptides possess different topological distributions of hydrophobic and hydrophilic residues and displayed distinct antimicrobial activity. Notably, the conformationally constrained α-helical peptides displayed a faster internalization into the bacteria cells compared to their β-hairpin analogues. These synthetic short constrained peptides showed killing effects on a broad spectrum of microorganisms mainly through pore formation and membrane damage which provided a potentially promising skeleton for the next generation of stabilized antimicrobial peptides.
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Affiliation(s)
- Fang Yuan
- Institute of Scientific and Technical Information of China, Beijing, 100038, China
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10
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Vardhishna MV, Srinivasulu G, Harikrishna A, Thakur SS, Chatterjee B. Simultaneous Occurrence of Nanospheres and Nanofibers Self-Assembled from Achiral Tripeptides. ChemistryOpen 2019; 8:266-270. [PMID: 30868048 PMCID: PMC6398100 DOI: 10.1002/open.201800258] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 11/28/2018] [Indexed: 11/24/2022] Open
Abstract
The achiral tripeptide Boc‐Aib‐MABA‐Aib‐OMe has the ability to co‐exist as nanospheres and as a network of nanofibers in methanol. Furthermore, AFM and TEM images show the presence of bulges in the network of nanofibers. Interestingly, the formation of nanofibers is seen to emerge from the outer boundary of the spherical structures. Some of the nanofibers curl up at the tip and later result in the formation of hollow nanospheres with thick boundaries. The presence of β‐turn‐like structures with hydrogen bonding is observed using FT‐IR studies. The presence of hydrogen bonding is also demonstrated by using NMR studies.
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Affiliation(s)
- Malapaka Venkata Vardhishna
- National Institute of Pharmaceutical Education and Research (NIPER) NIPER-Hyderabad Dept. of Pharmaceuticals, Ministry of Chemicals and Fertilizers, Govt. of India Balanagar Hyderabad - 500 037, Telangana India
| | - Gannoju Srinivasulu
- National Institute of Pharmaceutical Education and Research (NIPER) NIPER-Hyderabad Dept. of Pharmaceuticals, Ministry of Chemicals and Fertilizers, Govt. of India Balanagar Hyderabad - 500 037, Telangana India
| | - Adicherl Harikrishna
- Proteomics and Cell Signaling, Lab E409 Centre for Cellular and Molecular Biology Uppal Road Hyderabad - 500007 India
| | - Suman Siddharth Thakur
- Proteomics and Cell Signaling, Lab E409 Centre for Cellular and Molecular Biology Uppal Road Hyderabad - 500007 India
| | - Bhaswati Chatterjee
- National Institute of Pharmaceutical Education and Research (NIPER) NIPER-Hyderabad Dept. of Pharmaceuticals, Ministry of Chemicals and Fertilizers, Govt. of India Balanagar Hyderabad - 500 037, Telangana India
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11
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Yang D, Qin W, Shi X, Zhu B, Xie M, Zhao H, Teng B, Wu Y, Zhao R, Yin F, Ren P, Liu L, Li Z. Stabilized β-Hairpin Peptide Inhibits Insulin Degrading Enzyme. J Med Chem 2018; 61:8174-8185. [DOI: 10.1021/acs.jmedchem.8b00418] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Dan Yang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology & Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, Guangdong, China
- Department of Science & Technology of Shandong Province, Jinan 250101, Shandong, China
| | - Weirong Qin
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology & Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, Guangdong, China
| | - Xiaodong Shi
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology & Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, Guangdong, China
| | - Bili Zhu
- School of Medicine, Shenzhen University, Shenzhen 518055, Guangdong, China
| | - Mingsheng Xie
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology & Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, Guangdong, China
| | - Hui Zhao
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology & Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, Guangdong, China
| | - Bin Teng
- Center for Translational Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, Guangdong, China
- Shenzhen College of Advanced Technology, University of Chinese Academy of Sciences, Shenzhen 518055, Guangdong, China
| | - Yujie Wu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology & Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, Guangdong, China
| | - Rongtong Zhao
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology & Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, Guangdong, China
| | - Feng Yin
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology & Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, Guangdong, China
| | - Peigen Ren
- Center for Translational Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, Guangdong, China
- Shenzhen College of Advanced Technology, University of Chinese Academy of Sciences, Shenzhen 518055, Guangdong, China
| | - Lizhong Liu
- School of Medicine, Shenzhen University, Shenzhen 518055, Guangdong, China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology & Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, Guangdong, China
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12
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Pallerla S, Naik H, Singh S, Gauthier T, Sable R, Jois SD. Design of cyclic and d-amino acids containing peptidomimetics for inhibition of protein-protein interactions of HER2-HER3. J Pept Sci 2018; 24. [PMID: 29436155 DOI: 10.1002/psc.3066] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 01/02/2018] [Accepted: 01/09/2018] [Indexed: 01/10/2023]
Abstract
HER2 receptors are surface proteins belonging to the epidermal growth factor family of receptors. Their numbers are elevated in breast, lung, and ovarian cancers. HER2-positive cancers are aggressive, have higher mortality rate, and have a poor prognosis. We have designed peptidomimetics that bind to HER2 and block the HER2-mediated dimerization of epidermal growth factor family of receptors. Among these, a symmetrical cyclic peptidomimetic (compound 18) exhibited antiproliferative activity in HER2-overexpressing lung cancer cell lines with IC50 values in the nanomolar concentration range. To improve the stability of the peptidomimetic, d-amino acids were introduced into the peptidomimetic, and several analogs of compound 18 were designed. Among the analogs of compound 18, compound 32, a cyclic, d-amino acid-containing peptidomimetic, was found to have an IC50 value in the nanomolar range in HER2-overexpressing cancer cell lines. The antiproliferative activity of compound 32 was also measured by using a 3D cell culture model that mimics the in vivo conditions. The binding of compound 32 to the HER2 protein was studied by surface plasmon resonance. In vitro stability studies indicated that compound 32 was stable in serum for 48 hours and intact peptide was detectable in vivo for 12 hours. Results from our studies indicated that 1 of the d-amino acid analogs of 18, compound 32, binds to the HER2 extracellular domain, inhibiting the phosphorylation of kinase of HER2.
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Affiliation(s)
- Sandeep Pallerla
- Department of Basic Pharmaceutical Sciences, School of Pharmacy, University of Louisiana at Monroe, Monroe, LA, 71201, USA
| | - Himgauri Naik
- Department of Basic Pharmaceutical Sciences, School of Pharmacy, University of Louisiana at Monroe, Monroe, LA, 71201, USA
| | - Sitanshu Singh
- Department of Basic Pharmaceutical Sciences, School of Pharmacy, University of Louisiana at Monroe, Monroe, LA, 71201, USA
| | - Ted Gauthier
- Biotechnology Laboratory, LSU AgCenter, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Rushikesh Sable
- Department of Basic Pharmaceutical Sciences, School of Pharmacy, University of Louisiana at Monroe, Monroe, LA, 71201, USA
| | - Seetharama D Jois
- Department of Basic Pharmaceutical Sciences, School of Pharmacy, University of Louisiana at Monroe, Monroe, LA, 71201, USA
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13
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Rigling C, Kisunzu JK, Duschmalé J, Häussinger D, Wiesner M, Ebert MO, Wennemers H. Conformational Properties of a Peptidic Catalyst: Insights from NMR Spectroscopic Studies. J Am Chem Soc 2018; 140:10829-10838. [PMID: 30106584 DOI: 10.1021/jacs.8b05459] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Peptides have become valuable as catalysts for a variety of different reactions, but little is known about the conformational properties of peptidic catalysts. We investigated the conformation of the peptide H-dPro-Pro-Glu-NH2, a highly reactive and stereoselective catalyst for conjugate addition reactions, and the corresponding enamine intermediate in solution by NMR spectroscopy and computational methods. The combination of nuclear Overhauser effects (NOEs), residual dipolar couplings (RDCs), J-couplings, and temperature coefficients revealed that the tripeptide adopts a single predominant conformation in its ground state. The structure is a type I β-turn, which gains stabilization from three hydrogen bonds that are cooperatively formed between all functional groups (secondary amine, carboxylic acid, amides) within the tripeptide. In contrast, the conformation of the enamine intermediate is significantly more flexible. The conformational ensemble of the enamine is still dominated by the β-turn, but the backbone and the side chain of the glutamic acid residue are more dynamic. The key to the switch between rigidity and flexibility of the peptidic catalyst is the CO2H group in the side chain of the glutamic acid residue, which acts as a lid that can open and close. As a result, the peptidic catalyst is able to adapt to the structural requirements of the intermediates and transition states of the catalytic cycle. These insights might explain the robustness and high reactivity of the peptidic catalyst, which exceeds that of other secondary amine-based organocatalysts. The data suggest that a balance between rigidity and flexibility, which is reminiscent of the dynamic nature of enzymes, is beneficial for peptidic catalysts and other synthetic catalysts.
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Affiliation(s)
- Carla Rigling
- Laboratorium für Organische Chemie , ETH Zürich , D-CHAB, Vladimir-Prelog-Weg 3 , 8093 Zürich , Switzerland
| | - Jessica K Kisunzu
- Laboratorium für Organische Chemie , ETH Zürich , D-CHAB, Vladimir-Prelog-Weg 3 , 8093 Zürich , Switzerland
| | - Jörg Duschmalé
- Laboratorium für Organische Chemie , ETH Zürich , D-CHAB, Vladimir-Prelog-Weg 3 , 8093 Zürich , Switzerland.,Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland
| | - Daniel Häussinger
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland
| | - Markus Wiesner
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland
| | - Marc-Olivier Ebert
- Laboratorium für Organische Chemie , ETH Zürich , D-CHAB, Vladimir-Prelog-Weg 3 , 8093 Zürich , Switzerland
| | - Helma Wennemers
- Laboratorium für Organische Chemie , ETH Zürich , D-CHAB, Vladimir-Prelog-Weg 3 , 8093 Zürich , Switzerland
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14
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Northfield SE, Wielens J, Headey SJ, Williams-Noonan BJ, Mulcair M, Scanlon MJ, Parker MW, Thompson PE, Chalmers DK. Cyclic Hexapeptide Mimics of the LEDGF Integrase Recognition Loop in Complex with HIV-1 Integrase. ChemMedChem 2018; 13:1555-1565. [PMID: 29862651 DOI: 10.1002/cmdc.201800129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/21/2018] [Indexed: 12/18/2022]
Abstract
The p75 splice variant of lens epithelium-derived growth factor (LEDGF) is a 75 kDa protein, which is recruited by the human immunodeficiency virus (HIV) to tether the pre-integration complex to the host chromatin and promote integration of proviral DNA into the host genome. We designed a series of small cyclic peptides that are structural mimics of the LEDGF binding domain, which interact with integrase as potential binding inhibitors. Herein we present the X-ray crystal structures, NMR studies, SPR analysis, and conformational studies of four cyclic peptides bound to the HIV-1 integrase core domain. Although the X-ray studies show that the peptides closely mimic the LEDGF binding loop, the measured affinities of the peptides are in the low millimolar range. Computational analysis using conformational searching and free energy calculations suggest that the low affinity of the peptides is due to mismatch between the low-energy solution and bound conformations.
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Affiliation(s)
- Susan E Northfield
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Jerome Wielens
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria, 3052, Australia.,ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, 41 Victoria Parade, Fitzroy, Victoria, 3065, Australia
| | - Stephen J Headey
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Billy J Williams-Noonan
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Mark Mulcair
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Martin J Scanlon
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Michael W Parker
- ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, 41 Victoria Parade, Fitzroy, Victoria, 3065, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria, 3010, Australia
| | - Philip E Thompson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - David K Chalmers
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, 381 Royal Parade, Parkville, Victoria, 3052, Australia
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15
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Chilukuri H, Kulkarni MJ, Fernandes M. Revisiting amino acids and peptides as anti-glycation agents. MEDCHEMCOMM 2018; 9:614-624. [PMID: 30108952 PMCID: PMC6071831 DOI: 10.1039/c7md00514h] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 02/09/2018] [Indexed: 12/15/2022]
Abstract
The importance of controlling or preventing protein glycation cannot be overstated and is of prime importance in the treatment of diabetes and associated complications including Alzheimer's disease, cataracts, atherosclerosis, kidney aliments among others. In this respect, simple molecules such as amino acids and peptides hold much promise both in terms of ease and scale-up of synthesis as well as in relation to negligible/low associated toxicity. In view of this, a comprehensive account of literature reports is presented, that documents the anti-glycation activity of natural and non-natural amino acids and peptides. This review also discusses the chemical reactions involved in glycation and the formation of advanced glycation end-products (AGEs) and possible/probable intervention sites and mechanism of action of the reported amino acids/peptides. This aspect of amino acids/peptides adds to their growing importance in medicinal and therapeutic applications.
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Affiliation(s)
- H Chilukuri
- Organic Chemistry Division , CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road , Pune 411008 , India . ;
- Academy of Scientific and Innovative Research (AcSIR) , CSIR-NCL Campus , Pune -411008 , India
| | - M J Kulkarni
- Academy of Scientific and Innovative Research (AcSIR) , CSIR-NCL Campus , Pune -411008 , India
- Proteomics Facility , Division of Biochemical Sciences , CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road , Pune 411008 , India
| | - M Fernandes
- Organic Chemistry Division , CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road , Pune 411008 , India . ;
- Academy of Scientific and Innovative Research (AcSIR) , CSIR-NCL Campus , Pune -411008 , India
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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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Kanthala SP, Liu YY, Singh S, Sable R, Pallerla S, Jois SD. A peptidomimetic with a chiral switch is an inhibitor of epidermal growth factor receptor heterodimerization. Oncotarget 2017; 8:74244-74262. [PMID: 29088782 PMCID: PMC5650337 DOI: 10.18632/oncotarget.19013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 06/16/2017] [Indexed: 12/15/2022] Open
Abstract
Among different types of EGFR dimers, EGFR-HER2 and HER2-HER3 are well known in different types of cancers. Targeting dimerization of EGFR will have a significant impact on cancer therapies. A symmetric peptidomimetic was designed to inhibit the protein-protein interaction of EGFR. The peptidomimetic (Cyclo(1,10)PpR (R) Anapa-FDDF-(R)-Anapa)R, compound 18) was shown to exhibit antiproliferative activity with an IC50 of 194 nM in HER2-expressing breast cancer cell lines and 18 nM in lung cancer cell lines. The peptidomimetic has a Pro-Pro sequence in the structure to stabilize the β-turn and a β-amino acid, amino napthyl propionic acid. To investigate the effect of the chirality of β-amino acid on the structure of the peptide and its antiproliferative activity, diastereoisomers of compound 18 were designed and synthesized. Structure-activity relationships of these compounds indicated that there is a chiral switch at β-amino acid in the designed compound. The peptidomimetic with R configuration at β-amino acid and with a L-Pro-D-Pro sequence was the most active compound (18). Using enzyme complement fragmentation assay and proximity ligation assay, we show that compound 18 inhibits HER2:HER3 and EGFR:HER2 dimerization. Surface plasmon resonance studies suggested that compound 18 binds to the HER2 extracellular domain and in particular to domain IV. The anticancer activity of compound 18 was evaluated using a xenograft model of breast cancer in mice; compound 18 suppressed the tumor growth in mice compared to control. Compound 18 was also shown to have a synergistic effect with erlotinib on EGFR mutated lung cancer cell lines.
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Affiliation(s)
- Shanthi P Kanthala
- Basic Pharmaceutical Sciences, School of Pharmacy, University of Louisiana at Monroe, Monroe LA 71201, USA
| | - Yong-Yu Liu
- Basic Pharmaceutical Sciences, School of Pharmacy, University of Louisiana at Monroe, Monroe LA 71201, USA
| | - Sitanshu Singh
- Basic Pharmaceutical Sciences, School of Pharmacy, University of Louisiana at Monroe, Monroe LA 71201, USA
| | - Rushikesh Sable
- Basic Pharmaceutical Sciences, School of Pharmacy, University of Louisiana at Monroe, Monroe LA 71201, USA
| | - Sandeep Pallerla
- Basic Pharmaceutical Sciences, School of Pharmacy, University of Louisiana at Monroe, Monroe LA 71201, USA
| | - Seetharama D Jois
- Basic Pharmaceutical Sciences, School of Pharmacy, University of Louisiana at Monroe, Monroe LA 71201, USA
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18
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Critical role of select peptides in the loop region of G-rich PNA in the preferred G-quadruplex topology and stability. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.01.055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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19
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Grünenfelder CE, Kisunzu JK, Trapp N, Kastl R, Wennemers H. Crystal structures of peptidic catalysts of the H-d
Pro-Pro-Xaa type. Biopolymers 2017; 108. [DOI: 10.1002/bip.22912] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 06/27/2016] [Accepted: 07/04/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Claudio E. Grünenfelder
- Laboratory of Organic Chemistry, D-CHAB, ETH Zürich; Vladimir-Prelog-Weg 3 CH-8093 Zürich Switzerland
| | - Jessica K. Kisunzu
- Laboratory of Organic Chemistry, D-CHAB, ETH Zürich; Vladimir-Prelog-Weg 3 CH-8093 Zürich Switzerland
| | - Nils Trapp
- Laboratory of Organic Chemistry, D-CHAB, ETH Zürich; Vladimir-Prelog-Weg 3 CH-8093 Zürich Switzerland
| | - Robert Kastl
- Laboratory of Organic Chemistry, D-CHAB, ETH Zürich; Vladimir-Prelog-Weg 3 CH-8093 Zürich Switzerland
| | - Helma Wennemers
- Laboratory of Organic Chemistry, D-CHAB, ETH Zürich; Vladimir-Prelog-Weg 3 CH-8093 Zürich Switzerland
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20
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Das S, Pal U, Chatterjee M, Pramanik SK, Banerji B, Maiti NC. Envisaging Structural Insight of a Terminally Protected Proline Dipeptide by Raman Spectroscopy and Density Functional Theory Analyses. J Phys Chem A 2016; 120:9829-9840. [PMID: 27973793 DOI: 10.1021/acs.jpca.6b10017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Supriya Das
- Structural Biology & Bio-informatics Division and ‡Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology; 4, Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Uttam Pal
- Structural Biology & Bio-informatics Division and ‡Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology; 4, Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Moumita Chatterjee
- Structural Biology & Bio-informatics Division and ‡Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology; 4, Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Sumit Kumar Pramanik
- Structural Biology & Bio-informatics Division and ‡Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology; 4, Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Biswadip Banerji
- Structural Biology & Bio-informatics Division and ‡Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology; 4, Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Nakul C. Maiti
- Structural Biology & Bio-informatics Division and ‡Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology; 4, Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
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21
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Wani NA, Gupta VK, Singh UP, Aravinda S, Rai R. Folded Structure Stabilized by C 7, C 10and C 12Hydrogen Bonds in αγ Hybrid Peptides. ChemistrySelect 2016. [DOI: 10.1002/slct.201600389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Naiem Ahmad Wani
- Medicinal Chemistry Division; Indian Institute of Integrative Medicine; Canal Road, Jammu- 180001 India
| | - Vivek Kumar Gupta
- X-ray Crystallography Laboratory; Post-Graduate Department of Physics and Electronics; University of Jammu; Jammu Tawi 180 006 India
| | - Umesh Prasad Singh
- CSIR-Indian Institute of Chemical Biology; 4, Raja, S.C. Mullick Road Kolkata- 700032 India
| | - Subrayashastry Aravinda
- Medicinal Chemistry Division; Indian Institute of Integrative Medicine; Canal Road, Jammu- 180001 India
| | - Rajkishor Rai
- Medicinal Chemistry Division; Indian Institute of Integrative Medicine; Canal Road, Jammu- 180001 India
- Academy of Scientific and Innovative Research; New Delhi India
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22
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Yang B, Li X, Zhang C, Yan S, Wei W, Wang X, Deng X, Qian H, Lin H, Huang W. Design, synthesis and biological evaluation of novel peptide MC2 analogues from Momordica charantia as potential anti-diabetic agents. Org Biomol Chem 2016; 13:4551-61. [PMID: 25778708 DOI: 10.1039/c5ob00333d] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Three series of Momordica charantia (MC)2 analogues were designed, synthesized and evaluated for their anti-hyperglycaemic effects. Alanine scanning focusing on the peptide MC2 indicated the importance of the residues proline (Pro)(3), serine (Ser)(6), isoleucine (Ile)(7) and Ser(10) for anti-hyperglycaemic effects. Among the first series of MC2 analogues, peptide I-4 exhibited a better anti-hyperglycaemic effect and was chosen for further modification. A further two series of conformationally constrained analogues were designed by scanning the residues Pro(3), Ser(6), Ile(7), and Ser(10) with an i - (i + 2) lactam bridge consisting of a glutamic acid-Xaa-lysine (Glu-Xaa-Lys) scaffold and a diproline fragment. By screening in normal mice and mice with diabetes mellitus, peptides II-1, II-2 and III-3 showed a significant improvement in anti-hyperglycaemic and anti-oxidative activities compared with I-4. These data suggest that II-1, II-2 and III-3 could be candidates for future treatment of diabetes mellitus.
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Affiliation(s)
- Baowei Yang
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, Jiangsu 210009, China.
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23
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Ingole TS, Vijayadas KN, Chaitanya KN, Kotmale AS, Gawade RL, Gonnade RG, Rajamohanan PR, Sanjayan GJ. Disruption of Native β-Turns: Consequence of Folding Competition between Native and Orthanilic Acid Proline-BasedPseudoβ-Turn. European J Org Chem 2016. [DOI: 10.1002/ejoc.201501558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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24
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Goyal B, Kumar A, Srivastava KR, Durani S. Computational scrutiny of the effect of N-terminal proline and residue stereochemistry in the nucleation of α-helix fold. RSC Adv 2016. [DOI: 10.1039/c6ra10934a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
N-Terminal l- to d-residue mutation nucleate helical fold in Ac–DAla–LAla3–NHMe (Ib, m2), Ac–DPro–LAla3–NHMe (IIb, m1), and Ac–DPro–LPro–LAla2–NHMe (IIIb, m2) peptides.
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Affiliation(s)
- Bhupesh Goyal
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - Anil Kumar
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | | | - Susheel Durani
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
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25
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Pelay-Gimeno M, Glas A, Koch O, Grossmann TN. Structure-Based Design of Inhibitors of Protein-Protein Interactions: Mimicking Peptide Binding Epitopes. Angew Chem Int Ed Engl 2015; 54:8896-927. [PMID: 26119925 PMCID: PMC4557054 DOI: 10.1002/anie.201412070] [Citation(s) in RCA: 496] [Impact Index Per Article: 55.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Indexed: 12/15/2022]
Abstract
Protein-protein interactions (PPIs) are involved at all levels of cellular organization, thus making the development of PPI inhibitors extremely valuable. The identification of selective inhibitors is challenging because of the shallow and extended nature of PPI interfaces. Inhibitors can be obtained by mimicking peptide binding epitopes in their bioactive conformation. For this purpose, several strategies have been evolved to enable a projection of side chain functionalities in analogy to peptide secondary structures, thereby yielding molecules that are generally referred to as peptidomimetics. Herein, we introduce a new classification of peptidomimetics (classes A-D) that enables a clear assignment of available approaches. Based on this classification, the Review summarizes strategies that have been applied for the structure-based design of PPI inhibitors through stabilizing or mimicking turns, β-sheets, and helices.
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Affiliation(s)
- Marta Pelay-Gimeno
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
| | - Adrian Glas
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
| | - Oliver Koch
- TU Dortmund University, Department of Chemistry and Chemical BiologyOtto-Hahn-Strasse 6, 44227 Dortmund (Germany)
| | - Tom N Grossmann
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
- TU Dortmund University, Department of Chemistry and Chemical BiologyOtto-Hahn-Strasse 6, 44227 Dortmund (Germany)
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26
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Pelay-Gimeno M, Glas A, Koch O, Grossmann TN. Strukturbasierte Entwicklung von Protein-Protein-Interaktionsinhibitoren: Stabilisierung und Nachahmung von Peptidliganden. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201412070] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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27
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Pichumani K, George G, Hebbar S, Chatterjee B, Raghothama S. Effects of hydrogen bonding on amide-proton chemical shift anisotropy in a proline-containing model peptide. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.03.048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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28
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Yang B, Zhang C, Li X, Yan S, Wei W, Wang X, Deng X, Huang W, Qian H. Design, Synthesis, and Biological Evaluation of Novel Peptide Gly3-MC62 Analogues as Potential Antidiabetic Agents. Chem Biol Drug Des 2015; 86:979-89. [DOI: 10.1111/cbdd.12564] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 03/23/2015] [Accepted: 03/28/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Baowei Yang
- Center of Drug Discovery, State Key Laboratory of Natural Medicines; China Pharmaceutical University; 24 Tongjiaxiang Nanjing Jiangsu 210009 China
- Medical and Health Management Department; Jiangsu Food & Pharmaceutical Science College; 4 Meicheng Road, Higher Education Area Huaian Jiangsu 223003 China
| | - Chenyu Zhang
- Center of Drug Discovery, State Key Laboratory of Natural Medicines; China Pharmaceutical University; 24 Tongjiaxiang Nanjing Jiangsu 210009 China
| | - Xue Li
- Center of Drug Discovery, State Key Laboratory of Natural Medicines; China Pharmaceutical University; 24 Tongjiaxiang Nanjing Jiangsu 210009 China
| | - Sijia Yan
- Center of Drug Discovery, State Key Laboratory of Natural Medicines; China Pharmaceutical University; 24 Tongjiaxiang Nanjing Jiangsu 210009 China
| | - Wei Wei
- Center of Drug Discovery, State Key Laboratory of Natural Medicines; China Pharmaceutical University; 24 Tongjiaxiang Nanjing Jiangsu 210009 China
| | - Xuekun Wang
- Center of Drug Discovery, State Key Laboratory of Natural Medicines; China Pharmaceutical University; 24 Tongjiaxiang Nanjing Jiangsu 210009 China
| | - Xin Deng
- Center of Drug Discovery, State Key Laboratory of Natural Medicines; China Pharmaceutical University; 24 Tongjiaxiang Nanjing Jiangsu 210009 China
| | - Wenlong Huang
- Center of Drug Discovery, State Key Laboratory of Natural Medicines; China Pharmaceutical University; 24 Tongjiaxiang Nanjing Jiangsu 210009 China
| | - Hai Qian
- Center of Drug Discovery, State Key Laboratory of Natural Medicines; China Pharmaceutical University; 24 Tongjiaxiang Nanjing Jiangsu 210009 China
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29
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Verlinden S, Geudens N, Martins JC, Tourwé D, Ballet S, Verniest G. Oxidative α,ω-diyne coupling as an approach towards novel peptidic macrocycles. Org Biomol Chem 2015; 13:9398-404. [DOI: 10.1039/c5ob01153a] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The Glaser–Hay diyne coupling proved to be an efficient cyclisation approach towards diyne containing peptidic macrocycles.
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Affiliation(s)
- S. Verlinden
- Research Group of Organic Chemistry
- Department of Chemistry and Department of Bio-engineering Sciences
- Faculty of Science and Bio-engineering Sciences
- Vrije Universiteit Brussel
- B-1050 Brussels
| | - N. Geudens
- NMR and Structure Analysis Unit
- Department of Organic and Macromolecular Chemistry
- Ghent University
- 9000 Ghent
- Belgium
| | - J. C. Martins
- NMR and Structure Analysis Unit
- Department of Organic and Macromolecular Chemistry
- Ghent University
- 9000 Ghent
- Belgium
| | - D. Tourwé
- Research Group of Organic Chemistry
- Department of Chemistry and Department of Bio-engineering Sciences
- Faculty of Science and Bio-engineering Sciences
- Vrije Universiteit Brussel
- B-1050 Brussels
| | - S. Ballet
- Research Group of Organic Chemistry
- Department of Chemistry and Department of Bio-engineering Sciences
- Faculty of Science and Bio-engineering Sciences
- Vrije Universiteit Brussel
- B-1050 Brussels
| | - G. Verniest
- Research Group of Organic Chemistry
- Department of Chemistry and Department of Bio-engineering Sciences
- Faculty of Science and Bio-engineering Sciences
- Vrije Universiteit Brussel
- B-1050 Brussels
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30
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Nair RV, Baravkar SB, Ingole TS, Sanjayan GJ. Synthetic turn mimetics and hairpin nucleators: Quo Vadimus? Chem Commun (Camb) 2014; 50:13874-84. [PMID: 25051222 DOI: 10.1039/c4cc03114h] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Structural mimicry of peptides has witnessed perceptible progress in the last three decades. Reverse turn and β-hairpin units are the smallest secondary structural motifs that are some of the most scrutinized functional cores of peptides and proteins. The practice of mimicking, without altering the function of the bioactive core, ranges from conformational locking of the basic skeleton to total replacement of structural architecture using synthetic analogues. Development of heterogeneous backbones--using unnatural residues in place of natural ones--has broadened further opportunities for efficient structural rigidification. This feature article endeavours to trail the path of progress achieved hitherto and envisage the possibilities that lie ahead in the development of synthetic turn mimetics and hairpin nucleators.
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Affiliation(s)
- Roshna V Nair
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India.
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31
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Basu S, Kandiyal PS, Neelamraju VSK, Singh H, Ampapathi RS, Chakraborty TK. Peptidomimetics with tunable tertiary amide bond containing substituted β-proline and β-homoproline. Tetrahedron 2014. [DOI: 10.1016/j.tet.2013.12.078] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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32
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Proline-glutamate chimera’s side chain conformation directs the type of β-hairpin structure. Amino Acids 2013; 46:177-86. [DOI: 10.1007/s00726-013-1610-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 10/19/2013] [Indexed: 01/02/2023]
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33
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Saha I, Shamala N. Investigating proline puckering states in diproline segments in proteins. Biopolymers 2013; 99:605-10. [DOI: 10.1002/bip.22224] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 02/13/2013] [Accepted: 02/15/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Indranil Saha
- Department of Physics; Indian Institute of Science; Bangalore; 560012; Karnataka; India
| | - Narayanaswamy Shamala
- Department of Physics; Indian Institute of Science; Bangalore; 560012; Karnataka; India
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Thorat VH, Ingole TS, Vijayadas KN, Nair RV, Kale SS, Ramesh VVE, Davis HC, Prabhakaran P, Gonnade RG, Gawade RL, Puranik VG, Rajamohanan PR, Sanjayan GJ. The Ant-Pro Reverse-Turn Motif. Structural Features and Conformational Characteristics. European J Org Chem 2013. [DOI: 10.1002/ejoc.201201739] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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35
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Reddy DN, George G, Prabhakaran EN. Crystal-Structure Analysis of cis-X-Pro-Containing Peptidomimetics: Understanding the Steric Interactions at cisX-Pro Amide Bonds. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201209517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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36
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Ramesh VVE, Kale SS, Kotmale AS, Gawade RL, Puranik VG, Rajamohanan PR, Sanjayan GJ. Carboxamide versus Sulfonamide in Peptide Backbone Folding: A Case Study with a Hetero Foldamer. Org Lett 2013; 15:1504-7. [DOI: 10.1021/ol4002762] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Veera V. E. Ramesh
- Division of Organic Chemistry, Central NMR Facility, and Center for Materials Characterization, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India
| | - Sangram S. Kale
- Division of Organic Chemistry, Central NMR Facility, and Center for Materials Characterization, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India
| | - Amol S. Kotmale
- Division of Organic Chemistry, Central NMR Facility, and Center for Materials Characterization, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India
| | - Rupesh L. Gawade
- Division of Organic Chemistry, Central NMR Facility, and Center for Materials Characterization, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India
| | - Vedavati G. Puranik
- Division of Organic Chemistry, Central NMR Facility, and Center for Materials Characterization, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India
| | - P. R. Rajamohanan
- Division of Organic Chemistry, Central NMR Facility, and Center for Materials Characterization, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India
| | - Gangadhar J. Sanjayan
- Division of Organic Chemistry, Central NMR Facility, and Center for Materials Characterization, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India
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37
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Reddy DN, George G, Prabhakaran EN. Crystal-structure analysis of cis-X-Pro-containing peptidomimetics: understanding the steric interactions at cis X-Pro amide bonds. Angew Chem Int Ed Engl 2013; 52:3935-9. [PMID: 23450815 DOI: 10.1002/anie.201209517] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 01/18/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Damodara N Reddy
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, Karnataka, 560012, India
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38
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Jacques A, Mettra B, Lebrun V, Latour JM, Sénèque O. On the design of zinc-finger models with cyclic peptides bearing a linear tail. Chemistry 2013; 19:3921-31. [PMID: 23436718 DOI: 10.1002/chem.201204167] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Indexed: 11/07/2022]
Abstract
Cyclic peptides with a linear tail (CPLT) have been successfully used to model two zinc fingers (ZFs) adopting the treble-clef- and loosened zinc-ribbon folds. In this article, we examine the factors that may influence the design of such ZF models: mutations in the sequence, size of the cycle, and size of the tail. For this purpose, several peptides derived from the CPLT-based models of the treble-clef- and loosened zinc-ribbon ZF were synthesized and studied. CPLT-based models appear to be robust toward mutations, accommodate various cycle sizes, and are sensible to the size of the linking region of the tail located between the cycle and the coordinating amino acids. Based on these criteria, we describe the design of a new CPLT-based model for the zinc-ribbon ZFs, LZR , and compare it to a linear analogue, LZR(lin) . The model complex Zn⋅LZR is able to fold correctly around the metal ion contrary to Zn⋅LZR(lin) , suggesting that CPLT-based models are more likely to yield structurally meaningful models of ZF sites than linear peptide models. Finally, we draw some rules that could allow the design of new CPLT-based metallopeptides with a controlled fold.
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Affiliation(s)
- Aurélie Jacques
- Laboratoire de Chimie et Biologie des Métaux, Equipe de Physicochimie des Métaux en Biologie, UMR 5249 CNRS/CEA-DSV-iRTSV/, Université Joseph Fourier, 17 rue des Martyrs, Grenoble 38054, France
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3-Substituted prolines: from synthesis to structural applications, from peptides to foldamers. Molecules 2013; 18:2307-27. [PMID: 23429346 PMCID: PMC6270394 DOI: 10.3390/molecules18022307] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 02/05/2013] [Accepted: 02/06/2013] [Indexed: 12/17/2022] Open
Abstract
Among the twenty natural proteinogenic amino acids, proline is unique as its secondary amine forms a tertiary amide when incorporated into biopolymers, thus preventing hydrogen bond formation. Despite the lack of hydrogen bonds and thanks to conformational restriction of flexibility linked to the pyrrolidine ring, proline is able to stabilize peptide secondary structures such as β-turns or polyproline helices. These unique conformational properties have aroused a great interest in the development of proline analogues. Among them, proline chimeras are tools combining the proline restriction of flexibility together with the information brought by natural amino acids side chains. This review will focus on the chemical syntheses of 3-substituted proline chimeras of potential use for peptide syntheses and as potential use as tools for SAR studies of biologically active peptides and the development of secondary structure mimetics. Their influence on peptide structure will be briefly described.
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Airaghi F, Fiorati A, Lesma G, Musolino M, Sacchetti A, Silvani A. The diketopiperazine-fused tetrahydro-β-carboline scaffold as a model peptidomimetic with an unusual α-turn secondary structure. Beilstein J Org Chem 2013; 9:147-54. [PMID: 23399789 PMCID: PMC3566863 DOI: 10.3762/bjoc.9.17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 12/20/2012] [Indexed: 12/30/2022] Open
Abstract
Aiming at restricting the conformational freedom of tryptophan-containing peptide ligands, we designed a THBC (tetrahydro-β-carboline)-DKP (diketopiperazine)-based peptidomimetic scaffold capable of arranging in an unusual α-turn conformation. The synthesis is based on a diastereoselective Pictet–Spengler condensation to give the THBC core, followed by an intramolecular lactamization to complete the tetracyclic THBC-DKP fused ring system. The presence of conformers bearing the intramolecular thirteen-membered hydrogen bond that characterizes the α-turn structure is confirmed by 1H NMR conformational studies. To the best of our knowledge, this scaffold represents one of the rare examples of a designed constrained α-turn mimic.
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Affiliation(s)
- Francesco Airaghi
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
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41
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Ramesh VVE, Vijayadas KN, Dhokale S, Gonnade RG, Rajamohanan PR, Sanjayan GJ. Switching the H-bonding network of a foldamer by modulating the backbone chirality and constitutional ratio of amino acids. Org Biomol Chem 2013; 11:7072-5. [DOI: 10.1039/c3ob41369a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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42
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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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43
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Chung MK, Lee SJ, Waters ML, Gagné MR. Self-Assembled Multi-Component Catenanes: The Effect of Multivalency and Cooperativity on Structure and Stability. J Am Chem Soc 2012; 134:11430-43. [DOI: 10.1021/ja302347q] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mee-Kyung Chung
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel
Hill, North Carolina 27599-3290, United States
| | - Stephen J. Lee
- U.S. Army Research Office, P.O. Box 12211, Research Triangle Park, North
Carolina 27709, United States
| | - Marcey L. Waters
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel
Hill, North Carolina 27599-3290, United States
| | - Michel R. Gagné
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel
Hill, North Carolina 27599-3290, United States
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44
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Ganguly HK, Majumder B, Chattopadhyay S, Chakrabarti P, Basu G. Direct Evidence for CH···π Interaction Mediated Stabilization of Pro-cisPro Bond in Peptides with Pro-Pro-Aromatic motifs. J Am Chem Soc 2012; 134:4661-9. [DOI: 10.1021/ja209334v] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Himal K. Ganguly
- Department
of Biophysics and ‡Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, India
| | - Barun Majumder
- Department
of Biophysics and ‡Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, India
| | - Sarbani Chattopadhyay
- Department
of Biophysics and ‡Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, India
| | - Pinak Chakrabarti
- Department
of Biophysics and ‡Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, India
| | - Gautam Basu
- Department
of Biophysics and ‡Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, India
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45
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Kale SS, Kotmale AS, Dutta AK, Pal S, Rajamohanan PR, Sanjayan GJ. Conformational modulation of Ant–Pro oligomers using chirality alteration of proline residues. Org Biomol Chem 2012; 10:8426-33. [DOI: 10.1039/c2ob26132d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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46
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Saha I, Shamala N. Investigating diproline segments in proteins: occurrences, conformation and classification. Biopolymers 2011; 97:54-64. [PMID: 21898361 DOI: 10.1002/bip.21703] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Revised: 07/18/2011] [Accepted: 07/18/2011] [Indexed: 11/06/2022]
Abstract
The covalent linkage between the side-chain and the backbone nitrogen atom of proline leads to the formation of the five-membered pyrrolidine ring and hence restriction of the backbone torsional angle ϕ to values of -60 °± 30° for the L-proline. Diproline segments constitute a chain fragment with considerably reduced conformational choices. In the current study, the conformational states for the diproline segment (( L) Pro-( L) Pro) found in proteins has been investigated with an emphasis on the cis and trans states for the Pro-Pro peptide bond. The occurrence of diproline segments in turns and other secondary structures has been studied and compared to that of Xaa-Pro-Yaa segments in proteins which gives us a better understanding on the restriction imposed on other residues by the diproline segment and the single proline residue. The study indicates that P(II) -P(II) and P(II) -α are the most favorable conformational states for the diproline segment. The analysis on Xaa-Pro-Yaa sequences reveals that the Xaa-Pro peptide bond exists preferably as the trans conformer rather than the cis conformer. The present study may lead to a better understanding of the behavior of proline occurring in diproline segments which can facilitate various designed diproline-based synthetic templates for biological and structural studies.
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Affiliation(s)
- Indranil Saha
- Department of Physics, Indian Institute of Science, Bangalore, India.
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47
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Reddy DN, Thirupathi R, Prabhakaran EN. Accessing the disallowed conformations of peptides employing amide-to-imidate modification. Chem Commun (Camb) 2011; 47:9417-9. [PMID: 21773612 DOI: 10.1039/c1cc13515e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Selective modification of the C-terminal amide in peptides to dihydrooxazine (a novel stable imidate isostere) by intramolecular nucleophilic cyclo-O-alkylation of the corresponding N-(3-bromopropyl)amides results in constraining of the C-terminal residue in natively disallowed conformations both in crystals and in solution.
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Affiliation(s)
- Damodara N Reddy
- Department of Organic Chemistry, Indian Institute of Science, CV Raman Avenue, Bangalore, India 560012
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48
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Guitot K, Larregola M, Pradhan TK, Vasse JL, Lavielle S, Bertus P, Szymoniak J, Lequin O, Karoyan P. The Combination of Prolinoamino Acids and Cyclopropylamino Acids Leads to Fully Functionalized, Stable β-Turns in Water. Chembiochem 2011; 12:1039-42. [DOI: 10.1002/cbic.201000707] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Indexed: 12/17/2022]
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49
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Rajagopal A, Aravinda S, Raghothama S, Shamala N, Balaram P. Chain length effects on helix-hairpin distribution in short peptides with Aib-DAla and Aib-Aib Segments. Biopolymers 2011; 96:744-56. [DOI: 10.1002/bip.21613] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Revised: 02/14/2011] [Accepted: 02/18/2011] [Indexed: 11/11/2022]
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50
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