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Sheet T, Banerjee R. Design of a Peptide-Based Model Leads for Scavenging Anions. ACS OMEGA 2020; 5:9759-9767. [PMID: 32391463 PMCID: PMC7203709 DOI: 10.1021/acsomega.9b04180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 04/03/2020] [Indexed: 06/11/2023]
Abstract
Among several peptide-based anion recognition motifs, the "CαNN" motif containing C-1 α, N0, and N+1 of three consecutive residues is unique in its mode of interaction. Having a spatial geometry of βαα or βαβ, this motif occurs in the N terminus of a helix and often found at the functional interface of a protein, mediating crucial biological significance upon interaction with anion(s). The interaction of anion(s) with chimeric peptide sequences containing the naturally occurring "CαNN" motif (CPS224Ac, CPS226, and CPS228) reported in our previous attempts strongly confirms that the information regarding the interaction is embedded within the local sequences of the motif segment. At these prevailing circumstances, an effort has been pursued to design novel scaffolds based on the "CαNN" motif for achieving better recognition of anion(s). Exploring the existing data set of the "CαNN" motif available in the FSSP database, four novel peptide-based scaffolds have been designed (DS1, DS2, DS3, and DS4), and preliminary screenings have been performed using computational approaches. Our initial work suggests that two (DS1 and DS3) out of the four scaffolds are potential candidates for better anion recognition. By employing biophysical characterization using both qualitative and quantitative measures, in this present study, we report the interaction of sulfate and phosphate ions with these two designed scaffolds, in which there is much better recognition of anions by these scaffolds than the natural sequences, justifying their logical engineering. Our observation strongly suggests that these designed scaffolds are better potential candidates than those of the naturally occurring "CαNN" motif in terms of anion recognition and could be utilized for the scavenging of anion(s) for different purposes.
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Affiliation(s)
- Tridip Sheet
- Department
of Bioinformatics, Maulana Abul Kalam Azad
University of Technology, West Bengal (Formerly Known as West Bengal
University of Technology), BF-142, Sector-1, Salt Lake, Kolkata 700064, India
| | - Raja Banerjee
- Department
of Bioinformatics, Maulana Abul Kalam Azad
University of Technology, West Bengal (Formerly Known as West Bengal
University of Technology), BF-142, Sector-1, Salt Lake, Kolkata 700064, India
- Department
of Biotechnology, Maulana Abul Kalam Azad
University of Technology, West Bengal (Formerly Known as West Bengal
University of Technology), BF-142, Sector-1, Salt Lake, Kolkata 700064, India
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Sahu S, Sheet T, Banerjee R. Interaction landscape of a 'C αNN' motif with arsenate and arsenite: a potential peptide-based scavenger of arsenic. RSC Adv 2019; 9:1062-1074. [PMID: 35517606 PMCID: PMC9059529 DOI: 10.1039/c8ra08225a] [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: 10/04/2018] [Accepted: 12/08/2018] [Indexed: 12/01/2022] Open
Abstract
Arsenic (As) is a toxic metalloid that has drawn immense attention from the scientific community recently due to its fatal effects through its unwanted occurrence in ground water around the globe. The presence of an excess amount of water soluble arsenate and/or arsenite salt (permissible limit 10 μg L-1 as recommended by the WHO) in water has been correlated with several human diseases. Although arsenate (HAsO4 2-) is a molecular analogue of phosphate (HPO4 2-), phosphate is indispensable for life, while arsenic and its salts are toxic. Therefore, it is worthwhile to focus on the removal of arsenic from water. Towards this end, the design of peptide-based scaffolds for the recognition of arsenate and arsenite would add a new dimension. Utilizing the stereochemical similarity between arsenate (HAsO4 2-) and phosphate (HPO4 2-), we successfully investigated the recognition of arsenate and arsenite with a naturally occurring novel phosphate binding 'CαNN' motif and its related designed analogues. Using computational as well as biophysical approaches, for the first time, we report here that a designed peptide-based scaffold based on the 'CαNN' motif can recognize anions of arsenic in a thermodynamically favorable manner in a context-free system. This peptide-based arsenic binding agent has the potential for future development as a scavenger of arsenic anions to obtain arsenic free water.
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Affiliation(s)
- Subhankar Sahu
- Department of Biotechnology and Head Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly Known as West Bengal University of Technology) BF-142, Salt Lake Kolkata 700064 West Bengal India
| | - Tridip Sheet
- Department of Biotechnology and Head Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly Known as West Bengal University of Technology) BF-142, Salt Lake Kolkata 700064 West Bengal India
| | - Raja Banerjee
- Department of Biotechnology and Head Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly Known as West Bengal University of Technology) BF-142, Salt Lake Kolkata 700064 West Bengal India
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Patra P, Ghosh M, Banerjee R, Chakrabarti J. Quantum chemical studies on anion specificity of C αNN motif in functional proteins. J Comput Aided Mol Des 2018; 32:929-936. [PMID: 30182143 DOI: 10.1007/s10822-018-0157-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 08/29/2018] [Indexed: 10/28/2022]
Abstract
Anion binding CαNN motif is found in functionally important regions of protein structures. This motif based only on backbone atoms from three adjacent residues, recognizes free sulphate or phosphate ion as well as phosphate groups in nucleotides and in a variety of cofactors. The mode of anion recognition and microscopic picture of binding interaction remains unclear. Here we perform self-consistent quantum chemical calculations considering sulphate and phosphate bound CαNN motif fragments from crystal structures of functional proteins in order to figure out microscopic basis of anion recognition. Our calculations indicate that stability and preference of the anion in the motif depends on the sequence of the motif. The stabilization energy is larger in case of polar residue containing motif fragment. Nitrogen atom of the polar residue of motif mainly participates in the coordination at the lowest energy levels. Anion replacement decreases stabilization energy along with coordination between motif atoms and oxygen atoms of anion shifted to higher energies, suggesting preference of the motif residues to specific anion. Our analysis may be helpful to understand microscopic basis of interaction between proteins and ionic species.
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Affiliation(s)
- Piya Patra
- Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly known as WBUT), BF-142, Sector-I, Salt Lake, Kolkata, 700064, India.
| | - Mahua Ghosh
- Department of Chemical, Biological and Macro-Molecular Sciences, S.N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata, 700106, India
| | - Raja Banerjee
- Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly known as WBUT), BF-142, Sector-I, Salt Lake, Kolkata, 700064, India
| | - Jaydeb Chakrabarti
- Department of Chemical, Biological and Macro-Molecular Sciences, S.N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata, 700106, India. .,The Thematic Unit of Excellence on Computational Materials Science, S.N. Bose National Centre for Basic Sciences, Sector-III, Block JD, Salt Lake, Kolkata, 700106, India.
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Patra P, Ghosh M, Banerjee R, Chakrabarti J. Anion induced conformational preference of C α NN motif residues in functional proteins. Proteins 2017; 85:2179-2190. [PMID: 28905427 DOI: 10.1002/prot.25382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/16/2017] [Accepted: 09/10/2017] [Indexed: 11/12/2022]
Abstract
Among different ligand binding motifs, anion binding Cα NN motif consisting of peptide backbone atoms of three consecutive residues are observed to be important for recognition of free anions, like sulphate or biphosphate and participate in different key functions. Here we study the interaction of sulphate and biphosphate with Cα NN motif present in different proteins. Instead of total protein, a peptide fragment has been studied keeping Cα NN motif flanked in between other residues. We use classical force field based molecular dynamics simulations to understand the stability of this motif. Our data indicate fluctuations in conformational preferences of the motif residues in absence of the anion. The anion gives stability to one of these conformations. However, the anion induced conformational preferences are highly sequence dependent and specific to the type of anion. In particular, the polar residues are more favourable compared to the other residues for recognising the anion.
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Affiliation(s)
- Piya Patra
- Maulana Abul Kalam Azad University of Technology, West Bengal, (Formerly known as WBUT), BF-142, Sector-I, Saltlake, Kolkata, 700 064, India
| | - Mahua Ghosh
- Department of Chemical, Biological and Macro-Molecular Sciences, S.N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata, 700106, India
| | - Raja Banerjee
- Maulana Abul Kalam Azad University of Technology, West Bengal, (Formerly known as WBUT), BF-142, Sector-I, Saltlake, Kolkata, 700 064, India
| | - Jaydeb Chakrabarti
- Department of Chemical, Biological and Macro-Molecular Sciences, S.N. Bose National Centre for Basic Sciences, Sector III, Block JD, Salt Lake, Kolkata, 700106, India.,The Thematic Unit of Excellence on Computational Materials Science, S. N. Bose National Centre for Basic Sciences, Sector-III, Block JD, Salt Lake, Kolkata, 700106, India
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5
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Sheet T, Ghosh S, Pal D, Banerjee R. Computational design of model scaffold for anion recognition based on the 'C α NN' motif. Biopolymers 2017; 108. [PMID: 27428807 DOI: 10.1002/bip.22921] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 07/05/2016] [Accepted: 07/14/2016] [Indexed: 11/06/2022]
Abstract
The 'novel phosphate binding 'Cα NN' motif', consisting of three consecutive amino acid residues, usually occurs in the protein loop regions preceding a helix. Recent computational and complementary biophysical experiments on a series of chimeric peptides containing the naturally occurring 'Cα NN' motif at the N-terminus of a designed helix establishes that the motif segment recognizes the anion (sulfate and phosphate ions) through local interaction along with extension of the helical conformation which is thermodynamically favored even in a context-free, nonproteinaceous isolated system. However, the strength of the interaction depends on the amino acid sequence/conformation of the motif. Such a locally-mediated recognition of anions validates its intrinsic affinity towards anions and confirms that the affinity for recognition of anions is embedded within the 'local sequence' of the motif. Based on the knowledge gathered on the sequence/structural aspects of the naturally occurring 'Cα NN' segment, which provides the guideline for rationally engineering model scaffolds, we have modeled a series of templates and investigated their interactions with anions using computational approach. Two of these designed scaffolds show more efficient anion recognition than those of the naturally occurring 'Cα NN' motif which have been studied. This may provide an avenue in designing better anion receptors suitable for various biochemical applications.
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Affiliation(s)
- Tridip Sheet
- Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly Known as West Bengal University of Technology), BF-142, Sector-1, Salt Lake, Kolkata, 700064, India
| | - Suvankar Ghosh
- Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly Known as West Bengal University of Technology), BF-142, Sector-1, Salt Lake, Kolkata, 700064, India
| | - Debnath Pal
- Indian Institute of Science, Bangalore, 560012, India
| | - Raja Banerjee
- Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly Known as West Bengal University of Technology), BF-142, Sector-1, Salt Lake, Kolkata, 700064, India
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Mishra NM, Briers Y, Lamberigts C, Steenackers H, Robijns S, Landuyt B, Vanderleyden J, Schoofs L, Lavigne R, Luyten W, Van der Eycken EV. Evaluation of the antibacterial and antibiofilm activities of novel CRAMP-vancomycin conjugates with diverse linkers. Org Biomol Chem 2016; 13:7477-86. [PMID: 26068402 DOI: 10.1039/c5ob00830a] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We report the design, synthesis and antibacterial activity analysis of conjugates of vancomycin and cathelicidin-related antimicrobial peptides (CRAMP). Vancomycin inhibits the nascent peptidoglycan synthesis and is highly active against Gram-positive bacteria, whereas Gram-negative bacteria are generally insensitive due to a protective outer membrane. CRAMP is known to translocate across the Gram-negative outer membrane by a self-promoted uptake mechanism. Vancomycin-CRAMP conjugates were synthesized using click chemistry with diverse hydrophilic and hydrophobic linkers, with CRAMP functioning as a carrier peptide for the transfer of vancomycin through the outer membrane. Small hydrophobic linkers with an aromatic group result in the most active conjugates against planktonic Gram-negative bacteria, while maintaining the high activity of vancomycin against Gram-positive bacteria. These conjugates thus show a broad-spectrum activity, which is absent in CRAMP or vancomycin alone, and which is strongly improved compared to an equimolar mixture of CRAMP and vancomycin. In addition, these conjugates also show a strong inhibitory activity against S. Typhimurium biofilm formation.
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Affiliation(s)
- Nigam M Mishra
- Laboratory for Organic & Microwave-Assisted Chemistry (LOMAC), Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium.
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Langton MJ, Serpell CJ, Beer PD. Anion Recognition in Water: Recent Advances from a Supramolecular and Macromolecular Perspective. Angew Chem Int Ed Engl 2016; 55:1974-87. [PMID: 26612067 PMCID: PMC4755225 DOI: 10.1002/anie.201506589] [Citation(s) in RCA: 315] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Indexed: 12/22/2022]
Abstract
The recognition of anions in water remains a key challenge in modern supramolecular chemistry, and is essential if proposed applications in biological, medical, and environmental arenas that typically require aqueous conditions are to be achieved. However, synthetic anion receptors that operate in water have, in general, been the exception rather than the norm to date. Nevertheless, a significant step change towards routinely conducting anion recognition in water has been achieved in the past few years, and this Review highlights these approaches, with particular focus on controlling and using the hydrophobic effect, as well as more exotic interactions such as C-H hydrogen bonding and halogen bonding. We also look beyond the field of small-molecule recognition into the macromolecular domain, covering recent advances in anion recognition based on biomolecules, polymers, and nanoparticles.
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Affiliation(s)
- Matthew J Langton
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Christopher J Serpell
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.
- School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH, UK.
| | - Paul D Beer
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.
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Abstract
The ‘CαNN’ motif has an intrinsic affinity for the anions and can recognize anion through local interactions along with augmentation of the helical conformation at the motif segment.
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Affiliation(s)
- Tridip Sheet
- Maulana Abul Kalam Azad University of Technology (Formerly Known as West Bengal University of Technology)
- Kolkata – 700064
- India
| | - Raja Banerjee
- Maulana Abul Kalam Azad University of Technology (Formerly Known as West Bengal University of Technology)
- Kolkata – 700064
- India
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Langton MJ, Serpell CJ, Beer PD. Anionenerkennung in Wasser: aktuelle Fortschritte aus supramolekularer und makromolarer Sicht. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506589] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Matthew J. Langton
- Chemistry Research Laboratory; Department of Chemistry; University of Oxford; Mansfield Road Oxford OX1 3TA Vereinigtes Königreich
| | - Christopher J. Serpell
- Chemistry Research Laboratory; Department of Chemistry; University of Oxford; Mansfield Road Oxford OX1 3TA Vereinigtes Königreich
- School of Physical Sciences, Ingram Building; University of Kent; Canterbury Kent CT2 7NH Vereinigtes Königreich
| | - Paul D. Beer
- Chemistry Research Laboratory; Department of Chemistry; University of Oxford; Mansfield Road Oxford OX1 3TA Vereinigtes Königreich
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Sheet T, Supakar S, Banerjee R. Conformational preference of 'CαNN' short peptide motif towards recognition of anions. PLoS One 2013; 8:e57366. [PMID: 23516403 PMCID: PMC3596363 DOI: 10.1371/journal.pone.0057366] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 01/21/2013] [Indexed: 11/18/2022] Open
Abstract
Among several ‘anion binding motifs’, the recently described ‘CαNN’ motif occurring in the loop regions preceding a helix, is conserved through evolution both in sequence and its conformation. To establish the significance of the conserved sequence and their intrinsic affinity for anions, a series of peptides containing the naturally occurring ‘CαNN’ motif at the N-terminus of a designed helix, have been modeled and studied in a context free system using computational techniques. Appearance of a single interacting site with negative binding free-energy for both the sulfate and phosphate ions, as evidenced in docking experiments, establishes that the ‘CαNN’ segment has an intrinsic affinity for anions. Molecular Dynamics (MD) simulation studies reveal that interaction with anion triggers a conformational switch from non-helical to helical state at the ‘CαNN’ segment, which extends the length of the anchoring-helix by one turn at the N-terminus. Computational experiments substantiate the significance of sequence/structural context and justify the conserved nature of the ‘CαNN’ sequence for anion recognition through “local” interaction.
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Affiliation(s)
- Tridip Sheet
- Department of Bioinformatics, West Bengal University of Technology, Salt Lake, Kolkata, India
| | - Subhrangshu Supakar
- Department of Bioinformatics, West Bengal University of Technology, Salt Lake, Kolkata, India
| | - Raja Banerjee
- Department of Bioinformatics, West Bengal University of Technology, Salt Lake, Kolkata, India
- * E-mail:
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Pernot M, Vanderesse R, Frochot C, Guillemin F, Barberi-Heyob M. Stability of peptides and therapeutic success in cancer. Expert Opin Drug Metab Toxicol 2011; 7:793-802. [PMID: 21457110 DOI: 10.1517/17425255.2011.574126] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Although naturally occurring peptides have been widely used as drugs, their rapid in vivo degradation by proteolysis and their interactions at multiple receptors are part of the reason for the limitation of their clinical applications. AREAS COVERED This paper reviews peptide-metabolizing enzymes in the brain and intestinal brush-border membranes, and discusses potential strategies to improve biological activity, specificity and stability of peptides. The reader will gain, via some examples, an appreciation of the challenges involved in identifying peptides stability to improve their biological properties such as selectivity. EXPERT OPINION Due to the metabolic process, it is crucial to follow the biodistribution of a peptide drug and/or a peptidic moiety in order to improve its biological properties such as selectivity. To these purposes, pseudopeptides and peptidomimetics preserving the biological properties of native peptides have been developed to increase their resistance to degradation and elimination, bioavailability and selectivity to become good drug candidates.
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Affiliation(s)
- Marlène Pernot
- Centre de Recherche en Automatique de Nancy, Centre Alexis Vautrin, Nancy-University, Avenue de Bourgogne, Brabois, F 54511 Vandœuvre-lès-Nancy, France
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