1
|
Varnava KG, Edwards PJB, Cameron AJ, Harjes E, Sarojini V. Cyclic peptides bearing the d-Phe-2-Abz turn motif: Structural characterization and antimicrobial potential. J Pept Sci 2020; 27:e3291. [PMID: 33283398 DOI: 10.1002/psc.3291] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/07/2020] [Accepted: 10/14/2020] [Indexed: 11/10/2022]
Abstract
The effect on secondary structure and antimicrobial activity of introducing different cyclic constraints in linear β-hairpin antimicrobial peptides has been investigated with the intention of generating cyclic β sheets as promising antimicrobials with improved therapeutic potential. The linear peptides were cyclized head to tail either directly or after the addition of either a second turn motif or a disulfide bridge. The propensity of these peptides to adopt a cyclic β-sheet structure has been correlated to their antibacterial activity. All cyclic peptides showed enhanced activity, compared with their linear counterparts against methicillin-resistant Staphylococcus aureus. Scanning electron microscopy and transmission electron microscopy studies showed that this family kills bacteria through membrane lysis. The peptide that showed the best efficacy against all strains (exhibiting nanomolar activity), while retaining low haemolysis, bears two symmetrical, homochiral d-phe-2-Abz-d-ala turns and adopted a flexible structure. Its twin peptide that bears heterochiral turns (one with d-ala and one with L-Ala) showed reduced antibacterial activity and higher percentage of haemolysis. Circular dichroism and nuclear magnetic resonance spectroscopy indicate that heterochirality in the two turns leads to oligomerization of the peptide at higher concentrations, stabilizing the β-sheet secondary structure. More rigid secondary structure is associated with lower activity against bacteria and loss of selectivity.
Collapse
Affiliation(s)
- Kyriakos G Varnava
- School of Chemical Sciences, The University of Auckland, Auckland, 1142, New Zealand
| | - Patrick J B Edwards
- School of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand.,Maurice Wilkins Centre for Molecular BioDiscovery, Auckland, 1142, New Zealand
| | - Alan J Cameron
- School of Chemical Sciences, The University of Auckland, Auckland, 1142, New Zealand.,Maurice Wilkins Centre for Molecular BioDiscovery, Auckland, 1142, New Zealand
| | - Elena Harjes
- School of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand.,Maurice Wilkins Centre for Molecular BioDiscovery, Auckland, 1142, New Zealand
| | - Vijayalekshmi Sarojini
- School of Chemical Sciences, The University of Auckland, Auckland, 1142, New Zealand.,The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, 6140, New Zealand
| |
Collapse
|
2
|
Arrata I, Grison CM, Coubrough HM, Prabhakaran P, Little MA, Tomlinson DC, Webb ME, Wilson AJ. Control of conformation in α-helix mimicking aromatic oligoamide foldamers through interactions between adjacent side-chains. Org Biomol Chem 2019; 17:3861-3867. [PMID: 30938392 DOI: 10.1039/c9ob00123a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The design, synthesis and structural characterization of non-natural oligomers that adopt well-defined conformations, so called foldamers, is a key objective in developing biomimetic 3D functional architectures. For the aromatic oligoamide foldamer family, use of interactions between side-chains to control conformation is underexplored. The current manuscript addresses this objective through the design, synthesis and conformational analyses of model dimers derived from 3-O-alkylated para-aminobenzoic acid monomers. The O-alkyl groups on these foldamers are capable of adopting syn- or anti-conformers through rotation around the Ar-CO/NH axes. In the syn-conformation this allows the foldamer to act as a topographical mimic of the α-helix whereby the O-alkyl groups mimic the spatial orientation of the i and i + 4 side-chains from the α-helix. Using molecular modelling and 2D NMR analyses, this work illustrates that covalent links and hydrogen-bonding interactions between side-chains can bias the conformation in favour of the α-helix mimicking syn-conformer, offering insight that may be more widely applied to control secondary structure in foldamers.
Collapse
Affiliation(s)
- Irene Arrata
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.
| | | | | | | | | | | | | | | |
Collapse
|
3
|
Crisma M, Formaggio F, Alemán C, Torras J, Ramakrishnan C, Kalmankar N, Balaram P, Toniolo C. The fully‐extended conformation in peptides and proteins. Pept Sci (Hoboken) 2018. [DOI: 10.1002/bip.23100] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Marco Crisma
- Institute of Biomolecular Chemistry, Padova Unit, CNRPadova35131 Italy
| | - Fernando Formaggio
- Institute of Biomolecular Chemistry, Padova Unit, CNRPadova35131 Italy
- Department of ChemistryUniversity of PadovaPadova35131 Italy
| | - Carlos Alemán
- Departament d'Enginyeria QuímicaEEBE, Universitat Politècnica de CatalunyaBarcelona08019 Spain
- Barcelona Research Center in Multiscale Science and EngineeringUniversitat Politècnica de CatalunyaBarcelona08019 Spain
| | - Joan Torras
- Departament d'Enginyeria QuímicaEEBE, Universitat Politècnica de CatalunyaBarcelona08019 Spain
- Barcelona Research Center in Multiscale Science and EngineeringUniversitat Politècnica de CatalunyaBarcelona08019 Spain
| | | | - Neha Kalmankar
- National Centre for Biological Sciences (TIFR), GKVK CampusBangalore560065 India
| | | | - Claudio Toniolo
- Institute of Biomolecular Chemistry, Padova Unit, CNRPadova35131 Italy
- Department of ChemistryUniversity of PadovaPadova35131 Italy
| |
Collapse
|
4
|
Cameron AJ, Squire CJ, Edwards PJB, Harjes E, Sarojini V. Crystal and NMR Structures of a Peptidomimetic β-Turn That Provides Facile Synthesis of 13-Membered Cyclic Tetrapeptides. Chem Asian J 2017; 12:3195-3202. [PMID: 29098772 DOI: 10.1002/asia.201701422] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 10/30/2017] [Indexed: 12/31/2022]
Abstract
Herein we report the unique conformations adopted by linear and cyclic tetrapeptides (CTPs) containing 2-aminobenzoic acid (2-Abz) in solution and as single crystals. The crystal structure of the linear tetrapeptide H2 N-d-Leu-d-Phe-2-Abz-d-Ala-COOH (1) reveals a novel planar peptidomimetic β-turn stabilized by three hydrogen bonds and is in agreement with its NMR structure in solution. While CTPs are often synthetically inaccessible or cyclize in poor yield, both 1 and its N-Me-d-Phe analogue (2) adopt pseudo-cyclic frameworks enabling near quantitative conversion to the corresponding CTPs 3 and 4. The crystal structure of the N-methylated peptide (4) is the first reported for a CTP containing 2-Abz and reveals a distinctly planar 13-membered ring, which is also evident in solution. The N-methylation of d-Phe results in a peptide bond inversion compared to the conformation of 3 in solution.
Collapse
Affiliation(s)
- Alan J Cameron
- School of Chemical Sciences, The University of Auckland, Auckland, 1142, New Zealand
| | - Christopher J Squire
- School of Biological Sciences, The University of Auckland, Auckland, 1142, New Zealand
| | - Patrick J B Edwards
- Institute of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Elena Harjes
- Institute of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
| | | |
Collapse
|
5
|
Konda M, Bhowmik S, Mobin SM, Biswas S, Das AK. Modulating Hydrogen Bonded Self-assembled Patterns and Morphological Features by a Change in Side Chain of Third Amino Acid of Synthetic γ- Amino Acid Based Tripeptides. ChemistrySelect 2016. [DOI: 10.1002/slct.201600557] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Maruthi Konda
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 453552 India
| | - Soumitra Bhowmik
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 453552 India
| | - Shaikh M. Mobin
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 453552 India
| | - Sagar Biswas
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 453552 India
| | - Apurba K. Das
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 453552 India
| |
Collapse
|
6
|
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]
|
7
|
Konda M, Kauffmann B, Rasale DB, Das AK. Structural and morphological diversity of self-assembled synthetic γ-amino acid containing peptides. Org Biomol Chem 2016; 14:4089-102. [DOI: 10.1039/c6ob00380j] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We report the synthesis of constrained amino acid building block gabapentin (Gpn) based hybrid peptides and their structural and morphological diversity in different conditions.
Collapse
Affiliation(s)
- Maruthi Konda
- Department of Chemistry
- Indian Institute of Technology Indore
- Indore 452020
- India
| | - Brice Kauffmann
- Université de Bordeaux
- UMS3033
- Institut Européen de Chimie et Biologie (IECB)
- 33600 Pessac
- France
| | | | - Apurba K. Das
- Department of Chemistry
- Indian Institute of Technology Indore
- Indore 452020
- India
| |
Collapse
|
8
|
Vijayadas KN, Kotmale AS, Thorat SH, Gonnade RG, Nair RV, Rajamohanan PR, Sanjayan GJ. Reversal of H-bonding direction by N-sulfonation in a synthetic reverse-turn peptide motif. Org Biomol Chem 2015; 13:3064-9. [PMID: 25624112 DOI: 10.1039/c4ob02438a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This communication depicts an intriguing example of hydrogen-bonding reversal upon introduction of a sulfonamide linkage at the N-terminus of a synthetic reverse-turn peptide motif. The ready availability of two sulfonyl oxygen atoms, as hydrogen-bonding acceptors, combined with the inherent twisted conformation of sulfonamides are seen to act as switches that engage/disengage the hydrogen-bond at the sticky ends/termini.
Collapse
Affiliation(s)
- Kuruppanthara N Vijayadas
- Division of Organic Chemistry, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India.
| | | | | | | | | | | | | |
Collapse
|
9
|
Azzarito V, Miles JA, Fisher J, Edwards TA, Warriner SL, Wilson AJ. Stereocontrolled protein surface recognition using chiral oligoamide proteomimetic foldamers. Chem Sci 2015; 6:2434-2443. [PMID: 29308155 PMCID: PMC5646261 DOI: 10.1039/c4sc03559c] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 01/29/2015] [Indexed: 12/26/2022] Open
Abstract
An oligoamide helix mimicking foldamer with well-defined conformation is shown to recognize its target protein hDM2 in a manner that depends upon the composition, spatial projection and stereochemistry of functional groups appended to the scaffold.
The development of foldamers capable of selective molecular recognition of solvent exposed protein surfaces represents an outstanding challenge in supramolecular chemical biology. Here we introduce an oligoamide foldamer with well-defined conformation that bears all the hallmarks of an information rich oligomer. Specifically, the foldamer recognizes its target protein hDM2 leading to inhibition of its protein–protein interaction with p53 in a manner that depends upon the composition, spatial projection and stereochemistry of functional groups appended to the scaffold. Most significantly, selective inhibition of p53/hDM2 can be achieved against four other targets and the selectivity for p53/hDM2 inhibition versus Mcl-1/NOXA-B inhibition is critically dependent upon the stereochemistry of the helix mimetic.
Collapse
Affiliation(s)
- Valeria Azzarito
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK . .,Astbury Centre for Structural and Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
| | - Jennifer A Miles
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK . .,Astbury Centre for Structural and Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
| | - Julie Fisher
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK .
| | - Thomas A Edwards
- Astbury Centre for Structural and Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK.,School of Molecular and Cellular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
| | - Stuart L Warriner
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK . .,Astbury Centre for Structural and Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
| | - Andrew J Wilson
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK . .,Astbury Centre for Structural and Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
| |
Collapse
|
10
|
Nair RV, Vijayadas KN, Roy A, Sanjayan GJ. Heterogeneous Foldamers from Aliphatic-Aromatic Amino Acid Building Blocks: Current Trends and Future Prospects. European J Org Chem 2014. [DOI: 10.1002/ejoc.201402877] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
11
|
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.
Collapse
Affiliation(s)
- Roshna V Nair
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India.
| | | | | | | |
Collapse
|