1
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Nazarian-Firouzabadi F, Torres MDT, de la Fuente-Nunez C. Recombinant production of antimicrobial peptides in plants. Biotechnol Adv 2024; 71:108296. [PMID: 38042311 PMCID: PMC11537283 DOI: 10.1016/j.biotechadv.2023.108296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/10/2023] [Accepted: 11/26/2023] [Indexed: 12/04/2023]
Abstract
Classical plant breeding methods are limited in their ability to confer disease resistance on plants. However, in recent years, advancements in molecular breeding and biotechnological have provided new approaches to overcome these limitations and protect plants from disease. Antimicrobial peptides (AMPs) constitute promising agents that may be able to protect against infectious agents. Recently, peptides have been recombinantly produced in plants at scale and low cost. Because AMPs are less likely than conventional antimicrobials to elicit resistance of pathogenic bacteria, they open up exciting new avenues for agricultural applications. Here, we review recent advances in the design and production of bioactive recombinant AMPs that can effectively protect crop plants from diseases.
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Affiliation(s)
- Farhad Nazarian-Firouzabadi
- Production Engineering and Plant Genetics Department, Faculty of Agriculture, Lorestan University, P.O. Box, 465, Khorramabad, Iran.
| | - Marcelo Der Torossian Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America; Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, United States of America; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America; Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, United States of America; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, United States of America.
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2
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Wang Y, Sun Y, Zeng X, Zhuang R, Huang J, Zhang X, Guo Z, Li Y. 68Ga-Labeled TMTP1 Modified with d-Amino Acid for Positron Emission Tomography Diagnosis of Highly Metastatic Hepatocellular Carcinoma. J Med Chem 2024; 67:2165-2175. [PMID: 38270637 DOI: 10.1021/acs.jmedchem.3c02090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
TMTP1 (NVVRQ) has been proven to selectively target various highly metastatic tumor cells. Nonetheless, existing TMTP1 probes encounter challenges such as rapid blood clearance, limited tumor uptake, and inadequate suitability for therapeutic interventions. To overcome these constraints, we designed and synthesized eight peptide probes, employing innovative chemical modification strategies involving d-amino acid modification and retro-inverso isomerization. Notably, [68Ga]TV2 exhibited particularly impressive performance, displaying an 88.88, 76.90, and 90.32% improvement in uptake at 15, 30, and 60 min, respectively, while maintaining a high target-to-nontarget ratio. Further research has demonstrated that [68Ga]TV2 also exhibits remarkable diagnostic potential for detecting in situ microtumors in the liver. The results suggest that through the implementation of innovative chemical modification strategies, we successfully developed a peptide precursor, NOTA-G-NVvRQ, with specific affinity for highly metastatic tumors, enhanced in vivo pharmacokinetic profile, and heightened stability in vivo, rendering it well suited for prospective investigations in combination therapy studies.
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Affiliation(s)
- Yanjie Wang
- State Key Laboratory of Vaccines for Infectious Diseases, Center for Molecular Imaging and Translational Medicine, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Yuan Sun
- State Key Laboratory of Vaccines for Infectious Diseases, Center for Molecular Imaging and Translational Medicine, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Xueyuan Zeng
- State Key Laboratory of Vaccines for Infectious Diseases, Center for Molecular Imaging and Translational Medicine, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Rongqiang Zhuang
- State Key Laboratory of Vaccines for Infectious Diseases, Center for Molecular Imaging and Translational Medicine, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Jinxiong Huang
- Department of Nuclear Medicine, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361003, China
| | - Xianzhong Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, Center for Molecular Imaging and Translational Medicine, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361102, China
- Theranostics and Translational Research Center, Institute of Clinical Medicine, Department of Nuclear Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Zhide Guo
- State Key Laboratory of Vaccines for Infectious Diseases, Center for Molecular Imaging and Translational Medicine, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Yesen Li
- Department of Nuclear Medicine, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361003, China
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3
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Quagliata M, Papini AM, Rovero P. Chemically modified antiviral peptides against SARS-CoV-2. J Pept Sci 2024; 30:e3541. [PMID: 37699615 DOI: 10.1002/psc.3541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/31/2023] [Accepted: 08/22/2023] [Indexed: 09/14/2023]
Abstract
To date, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) COVID-19 pandemic continues to be a potentially lethal disease. Although both vaccines and specific antiviral drugs have been approved, the search for more specific therapeutic approaches is still ongoing. The infection mechanism of SARS-CoV-2 consists of several stages, and each one can be selectively blocked to disrupt viral infection. Peptides are a promising class of antiviral compounds, which may be suitably modified to be more stable, more effective, and more selective towards a specific viral replication step. The latter two goals might be obtained by increasing the specificity and/or the affinity of the interaction with a specific target and often imply the stabilization of the secondary structure of the active peptide. This review is focused on modified antiviral peptides against SARS-CoV-2 acting at different stages of virus replication, including ACE2-RBD interaction, membrane fusion mechanism, and the proteolytic cleavage by different viral proteases. Therefore, the landscape presented herein provides a useful springboard for the design of new and powerful antiviral therapeutics.
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Affiliation(s)
- Michael Quagliata
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Anna Maria Papini
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Paolo Rovero
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of NeuroFarBa, University of Florence, Sesto Fiorentino, Italy
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4
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Marciano Y, Nayeem N, Dave D, Ulijn RV, Contel M. N-Acetylation of Biodegradable Supramolecular Peptide Nanofilaments Selectively Enhances Their Proteolytic Stability for Targeted Delivery of Gold-Based Anticancer Agents. ACS Biomater Sci Eng 2023; 9:3379-3389. [PMID: 37192486 PMCID: PMC10699682 DOI: 10.1021/acsbiomaterials.3c00312] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Peptide materials are promising for various biomedical applications; however, a significant concern is their lack of stability and rapid degradation in vivo due to non-specific proteolysis. For materials specifically designed to respond to disease-specific proteases, it would be desirable to retain high susceptibility to target proteases while minimizing the impact of non-specific proteolysis. We describe N-terminal acetylation as a simple synthetic modification of amphiphilic self-assembling peptides that contain an MMP-9-cleavable segment and form soluble, nanoscale filaments. We found that the N-terminus capping of these peptides did not significantly impact their self-assembly behavior, critical aggregation concentration, or ability to encapsulate hydrophobic payloads. By contrast, their proteolytic stability in human plasma (especially for anionic peptide sequences) was considerably increased while susceptibility to hydrolysis by MMP-9 was retained when compared to non-acetylated peptides, especially during the first 12 h. We note, however, that due to the longer time scale required for in vitro studies (72 h), non-specific proteolysis of both anionic acetylated peptides leads to similar activity in vitro despite differing MMP-9 kinetics during the early stages. Overall, the enhanced stability against non-specific proteases, combined with the ability of these nanofilaments to enhance the effectiveness of gold-based drugs toward cancerous cells compared to healthy cells, brings these acetylated peptide filaments a step closer toward clinical translation.
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Affiliation(s)
- Yaron Marciano
- Department of Chemistry, Brooklyn College, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- Advanced Science Research Center at The Graduate Center of the City University of New York, 85 Saint Nicholas Terrace, New York, NY 10031, USA
- PhD Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Nazia Nayeem
- Department of Chemistry, Brooklyn College, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- PhD Program Biology, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Dhwanit Dave
- Advanced Science Research Center at The Graduate Center of the City University of New York, 85 Saint Nicholas Terrace, New York, NY 10031, USA
- PhD Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
- Department of Chemistry, Hunter College, City University of New York, 695 Park Avenue, New York, NY 10065, USA
| | - Rein V. Ulijn
- Advanced Science Research Center at The Graduate Center of the City University of New York, 85 Saint Nicholas Terrace, New York, NY 10031, USA
- PhD Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
- PhD Program in Biochemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
- Department of Chemistry, Hunter College, City University of New York, 695 Park Avenue, New York, NY 10065, USA
| | - Maria Contel
- Department of Chemistry, Brooklyn College, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- PhD Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
- PhD Program in Biochemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
- PhD Program Biology, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
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5
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Todaro B, Ottalagana E, Luin S, Santi M. Targeting Peptides: The New Generation of Targeted Drug Delivery Systems. Pharmaceutics 2023; 15:1648. [PMID: 37376097 DOI: 10.3390/pharmaceutics15061648] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/22/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Peptides can act as targeting molecules, analogously to oligonucleotide aptamers and antibodies. They are particularly efficient in terms of production and stability in physiological environments; in recent years, they have been increasingly studied as targeting agents for several diseases, from tumors to central nervous system disorders, also thanks to the ability of some of them to cross the blood-brain barrier. In this review, we will describe the techniques employed for their experimental and in silico design, as well as their possible applications. We will also discuss advancements in their formulation and chemical modifications that make them even more stable and effective. Finally, we will discuss how their use could effectively help to overcome various physiological problems and improve existing treatments.
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Affiliation(s)
- Biagio Todaro
- NEST Laboratory, Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Elisa Ottalagana
- NEST Laboratory, Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
- Fondazione Pisana per la Scienza, Via Ferruccio Giovannini 13, San Giuliano Terme, 56017 Pisa, Italy
| | - Stefano Luin
- NEST Laboratory, Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
- NEST, Istituto Nanoscienze-CNR and Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Melissa Santi
- NEST, Istituto Nanoscienze-CNR and Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
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6
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Deciphering the conformational landscape of few selected aromatic noncoded amino acids (NCAAs) for applications in rational design of peptide therapeutics. Amino Acids 2022; 54:1183-1202. [PMID: 35723743 PMCID: PMC9207436 DOI: 10.1007/s00726-022-03175-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 05/23/2022] [Indexed: 11/01/2022]
Abstract
Amino acids are the essential building blocks of both synthetic and natural peptides, which are crucial for biological functions and also important as biological probes for mapping the complex protein-protein interactions (PPIs) in both prokaryotic and eukaryotic systems. Mapping the PPIs through the chemical biology approach provides pharmacologically relevant peptides, which can have agonistic or antagonistic effects on the targeted biological systems. It is evidenced that ≥ 60 peptide-based drugs have been approved by the US-FDA so far, and the number will improve further in the foreseeable future, as ≥ 140 peptides are currently in clinical trials. However, natural peptides often require fine-tuning of their pharmacological properties by strategically replacing the αL-amino acids of the peptides with non-coded amino acids (NCAA), for which codons are absent in the genetic code for biosynthesis of proteins, prior to their applications as therapeutics. Considering the diverse repertoire of the NCAAs, the conformational space of many NCAAs is yet to be explored systematically in the context of the rational design of therapeutic peptides. The current study deciphers the conformational landscape of a few such Cα-substituted aromatic NCAAs (Ing: 2-indanyl-L-Glycine; Bpa: 4-benzoyl-L-phenylalanine; Aic: 2-aminoindane-2-carboxylic acid) both in the context of tripeptides and model synthetic peptide sequences, using alanine (Ala) and proline (Pro) as the reference. The combined data obtained from the computational and biophysical studies indicate the general success of this approach, which can be exploited further to rationally design optimized peptide sequences of unusual architecture with potent antimicrobial, antiviral, gluco-regulatory, immunomodulatory, and anti-inflammatory activities.
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7
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Baeriswyl S, Personne H, Di Bonaventura I, Köhler T, van Delden C, Stocker A, Javor S, Reymond JL. A mixed chirality α-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography. RSC Chem Biol 2021; 2:1608-1617. [PMID: 34977576 PMCID: PMC8637766 DOI: 10.1039/d1cb00124h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/20/2021] [Indexed: 01/01/2023] Open
Abstract
The peptide α-helix is right-handed when containing amino acids with l-chirality, and left-handed with d-chirality, however mixed chirality peptides generally do not form α-helices unless a helix inducer such as the non-natural residue amino-isobutyric acid is used. Herein we report the first X-ray crystal structures of mixed chirality α-helices in short peptides comprising only natural residues as the example of a stapled bicyclic and a linear membrane disruptive amphiphilic antimicrobial peptide (AMP) containing seven l- and four d-residues, as complexes of fucosylated analogs with the bacterial lectin LecB. The mixed chirality α-helices are superimposable onto the homochiral α-helices and form under similar conditions as shown by CD spectra and MD simulations but non-hemolytic and resistant to proteolysis. The observation of a mixed chirality α-helix with only natural residues in the protein environment of LecB suggests a vast unexplored territory of α-helical mixed chirality sequences and their possible use for optimizing bioactive α-helical peptides. We report the first X-ray crystal structures of mixed chirality α-helices comprising only natural residues as the example of bicyclic and linear membrane disruptive amphiphilic antimicrobial peptides containing seven l- and four d-residues.![]()
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Affiliation(s)
- Stéphane Baeriswyl
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Hippolyte Personne
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Ivan Di Bonaventura
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Thilo Köhler
- Department of Microbiology and Molecular Medicine, University of Geneva, Service of Infectious Diseases, University Hospital of Geneva Geneva Switzerland
| | - Christian van Delden
- Department of Microbiology and Molecular Medicine, University of Geneva, Service of Infectious Diseases, University Hospital of Geneva Geneva Switzerland
| | - Achim Stocker
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Sacha Javor
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern Freiestrasse 3 3012 Bern Switzerland
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8
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Wang ZY, Zhang NN, Li JC, Lu J, Zhao L, Fang XD, Liu K. Serum albumin guided plasmonic nanoassemblies with opposite chiralities. SOFT MATTER 2021; 17:6298-6304. [PMID: 34160542 DOI: 10.1039/d1sm00784j] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Chiral assemblies by combining natural biomolecules with plasmonic nanostructures hold great promise for plasmonic enhanced sensing, imaging, and catalytic applications. Herein, we demonstrate that human serum albumin (HSA) and porcine serum albumin (PSA) can guide the chiral assembly of gold nanorods (GNRs) with left-handed chiroptical responses opposite to those by a series of other homologous animal serum albumins (SAs) due to the difference of their surface charge distributions. Under physiological pH conditions, the assembly of HSA or PSA with GNRs yielded left-handed twisted aggregates, while bovine serum albumin (BSA), sheep serum albumin, and equine serum albumin behaved on the contrary. The driving force for the chiral assembly is mainly attributed to electrostatic interaction. The opposite chiroptical signals acquired are correlated with the chiral surface charge distributions of the tertiary structures of SAs. Moreover, the chirality of the assembly induced by both HSA and BSA can be enhanced or reversed by adjusting the pH values. This work provides new insights into the modulation of protein-induced chiral assemblies and promotes their applications.
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Affiliation(s)
- Zhao-Yi Wang
- China-Japan Union Hospital of Jilin University, Changchun, 130033, P. R. China.
| | - Ning-Ning Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, P. R. China.
| | - Jin-Cheng Li
- China-Japan Union Hospital of Jilin University, Changchun, 130033, P. R. China.
| | - Jun Lu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, P. R. China. and Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Li Zhao
- College of Life Science, Jilin University, Changchun, 130012, P. R. China
| | - Xue-Dong Fang
- China-Japan Union Hospital of Jilin University, Changchun, 130033, P. R. China.
| | - Kun Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, P. R. China.
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9
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Siriwardena T, Gan BH, Köhler T, van Delden C, Javor S, Reymond JL. Stereorandomization as a Method to Probe Peptide Bioactivity. ACS CENTRAL SCIENCE 2021; 7:126-134. [PMID: 33532575 PMCID: PMC7845017 DOI: 10.1021/acscentsci.0c01135] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Indexed: 06/01/2023]
Abstract
Solid-phase peptide synthesis (SPPS) is usually performed with optically pure building blocks to prepare peptides as single enantiomers. Herein we report that SPPS using racemic amino acids provides stereorandomized (sr) peptides, containing up to billions of different stereoisomers, as well-defined single HPLC peaks, single mass products with high yield, which can be used to investigate peptide bioactivity. To exemplify our method, we show that stereorandomization abolishes the membrane-disruptive effect of α-helical amphiphilic antimicrobial peptides but preserves their antibiofilm effect, implying different mechanisms involving folded versus disordered conformations. For antimicrobial peptide dendrimers by contrast, stereorandomization preserves antibacterial, membrane-disruptive, and antibiofilm effects but reduces hemolysis and cytotoxicity, thereby increasing their therapeutic index. Finally, we identify partially stereorandomized analogues of the last resort cyclic peptide antibiotic polymyxin B with preserved antibacterial activity but lacking membrane-disruptive and lipopolysaccharide-neutralizing activity, pointing to the existence of additional targets.
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Affiliation(s)
- Thissa
N. Siriwardena
- Department
of Chemistry and Biochemistry, University
of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Bee-Ha Gan
- Department
of Chemistry and Biochemistry, University
of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Thilo Köhler
- Department
of Microbiology and Molecular Medicine, University of Geneva, Service
of Infectious Diseases, University Hospital
of Geneva, 1211 Geneva, Switzerland
| | - Christian van Delden
- Department
of Microbiology and Molecular Medicine, University of Geneva, Service
of Infectious Diseases, University Hospital
of Geneva, 1211 Geneva, Switzerland
| | - Sacha Javor
- Department
of Chemistry and Biochemistry, University
of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Jean-Louis Reymond
- Department
of Chemistry and Biochemistry, University
of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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10
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Hazam PK, Phukan C, Akhil R, Singh A, Ramakrishnan V. Antimicrobial effects of syndiotactic polypeptides. Sci Rep 2021; 11:1823. [PMID: 33469079 PMCID: PMC7815786 DOI: 10.1038/s41598-021-81394-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 12/21/2020] [Indexed: 12/03/2022] Open
Abstract
We present design and antibacterial studies of stereochemically diversified antimicrobial peptides against multidrug-resistant bacterial pathogens. Syndiotactic polypeptides are polymers of alternating L and D amino acids with LDLD or DLDL backbone stereochemical sequence, which can form stable gramicidin like helical conformations. We designed, synthesized and characterized eight model molecular systems with varied electrostatic fingerprints, modulated through calibrated sequence positioning. Six out of eight model systems showed very impressive antimicrobial activity against three difficult to treat bacterial species, Gentamicin resistant MRSA, E. coli and Mycobacterium. More importantly, the designed LDLD peptides were equally potent in serum, an important drawback of poly L peptide sequences due to enzyme mediated degradation and ion sensitivity. Further, we tested the activity of the designed peptides against drug-resistant clinical isolates of Staphylococcus aureus and Escherichia coli. Molecular dynamics simulation studies suggest formation of an assembly of individual peptides, preceding the membrane interaction and deformation. The activity estimates are comparable with the available peptide based antimicrobials, and are also highly specific and less toxic as per standard estimates. Incorporation of D amino-acids can significantly expand the peptide design space, which can in turn manifest in future biomaterial designs, especially antimicrobials.
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Affiliation(s)
- Prakash Kishore Hazam
- Molecular Informatics and Design Laboratory, Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.,Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research Guwahati, Guwahati, Assam, 781125, India
| | - Chimanjita Phukan
- Guwahati Medical College Hospital, Bhangagarh, Guwahati, Assam, 781032, India
| | - R Akhil
- Molecular Informatics and Design Laboratory, Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Anjali Singh
- Molecular Informatics and Design Laboratory, Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Vibin Ramakrishnan
- Molecular Informatics and Design Laboratory, Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
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11
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Mirror-image antiparallel β-sheets organize water molecules into superstructures of opposite chirality. Proc Natl Acad Sci U S A 2020; 117:32902-32909. [PMID: 33318168 DOI: 10.1073/pnas.2015567117] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Biomolecular hydration is fundamental to biological functions. Using phase-resolved chiral sum-frequency generation spectroscopy (SFG), we probe molecular architectures and interactions of water molecules around a self-assembling antiparallel β-sheet protein. We find that the phase of the chiroptical response from the O-H stretching vibrational modes of water flips with the absolute chirality of the (l-) or (d-) antiparallel β-sheet. Therefore, we can conclude that the (d-) antiparallel β-sheet organizes water solvent into a chiral supermolecular structure with opposite handedness relative to that of the (l-) antiparallel β-sheet. We use molecular dynamics to characterize the chiral water superstructure at atomic resolution. The results show that the macroscopic chirality of antiparallel β-sheets breaks the symmetry of assemblies of surrounding water molecules. We also calculate the chiral SFG response of water surrounding (l-) and (d-) LK7β to confirm the presence of chiral water structures. Our results offer a different perspective as well as introduce experimental and computational methodologies for elucidating hydration of biomacromolecules. The findings imply potentially important but largely unexplored roles of water solvent in chiral selectivity of biomolecular interactions and the molecular origins of homochirality in the biological world.
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12
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Prakash V, Ranbhor R, Ramakrishnan V. De Novo Designed Heterochiral Blue Fluorescent Protein. ACS OMEGA 2020; 5:26382-26388. [PMID: 33110966 PMCID: PMC7581079 DOI: 10.1021/acsomega.0c02574] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 09/24/2020] [Indexed: 05/08/2023]
Abstract
Diversification of chain stereochemistry offers a tremendous increase in protein design space. We have designed a minimal fluorescent protein, pregnant with β-(1-azulenyl)-l-alanine in the hydrophobic core of a heterotactic protein scaffold, employing automated design tools such as automated repetitive simulated annealing molecular dynamics and IDeAS. The de novo designed heterochiral protein can be selectively excited at 342 nm, quite distant from the intrinsic fluorophore, and emits in the blue region. The structure and stability of the designed proteins were evaluated by established spectroscopic and calorimetric methods.
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Affiliation(s)
- Vivek Prakash
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Guwahati, Guwahati 781039, India
| | - Ranjit Ranbhor
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Bombay, Mumbai 400076, India
| | - Vibin Ramakrishnan
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Guwahati, Guwahati 781039, India
- . Phone: +91-361-258-2227
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13
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Evans BJ, King AT, Katsifis A, Matesic L, Jamie JF. Methods to Enhance the Metabolic Stability of Peptide-Based PET Radiopharmaceuticals. Molecules 2020; 25:molecules25102314. [PMID: 32423178 PMCID: PMC7287708 DOI: 10.3390/molecules25102314] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/11/2020] [Accepted: 05/13/2020] [Indexed: 12/28/2022] Open
Abstract
The high affinity and specificity of peptides towards biological targets, in addition to their favorable pharmacological properties, has encouraged the development of many peptide-based pharmaceuticals, including peptide-based positron emission tomography (PET) radiopharmaceuticals. However, the poor in vivo stability of unmodified peptides against proteolysis is a major challenge that must be overcome, as it can result in an impractically short in vivo biological half-life and a subsequently poor bioavailability when used in imaging and therapeutic applications. Consequently, many biologically and pharmacologically interesting peptide-based drugs may never see application. A potential way to overcome this is using peptide analogues designed to mimic the pharmacophore of a native peptide while also containing unnatural modifications that act to maintain or improve the pharmacological properties. This review explores strategies that have been developed to increase the metabolic stability of peptide-based pharmaceuticals. It includes modifications of the C- and/or N-termini, introduction of d- or other unnatural amino acids, backbone modification, PEGylation and alkyl chain incorporation, cyclization and peptide bond substitution, and where those strategies have been, or could be, applied to PET peptide-based radiopharmaceuticals.
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Affiliation(s)
- Brendan J. Evans
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; (B.J.E.); (A.T.K.)
| | - Andrew T. King
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; (B.J.E.); (A.T.K.)
| | - Andrew Katsifis
- Department of Molecular Imaging, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia;
| | - Lidia Matesic
- Australian Nuclear Science and Technology Organisation (ANSTO), Lucas Heights, NSW 2234, Australia;
| | - Joanne F. Jamie
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; (B.J.E.); (A.T.K.)
- Correspondence: ; Tel.: +61-2-9850-8283
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14
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More SH, Ganesh KN. Spiegelmeric 4
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‐hydroxy/amino‐L/D‐prolyl collagen peptides: conformation and morphology of self‐assembled structures. Pept Sci (Hoboken) 2019. [DOI: 10.1002/pep2.24140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Shahaji H More
- Chemistry DepartmentIndian Institute of Science Education and Research Pune Pune India
| | - Krishna N Ganesh
- Chemistry DepartmentIndian Institute of Science Education and Research Pune Pune India
- Department of ChemistryIndian Institute of Science Education and Research Tirupati Tirupati Andhra Pradesh India
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15
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Oda A, Nakayoshi T, Kato K, Fukuyoshi S, Kurimoto E. Three dimensional structures of putative, primitive proteins to investigate the origin of homochirality. Sci Rep 2019; 9:11594. [PMID: 31406272 PMCID: PMC6690948 DOI: 10.1038/s41598-019-48134-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/30/2019] [Indexed: 12/19/2022] Open
Abstract
Primitive proteins are likely to have been constructed from non-enzymatically generated amino acids, due to the weak enzymatic activities of primitive biomolecules such as ribozymes. On the other hand, almost all present proteins are constructed only from L-amino acids. Therefore, there must have been a mechanism early in the origins of life that selected for one of the optical isomers of amino acids. In this study, we used molecular dynamics simulations to predict the three-dimensional structures of the putative primitive proteins constructed only from glycine, alanine, aspartic acid, and valine ([GADV]-peptides). The [GADV]-peptides were generated computationally at random from L-amino acids (L-[GADV]-peptides) and from both L- and D-amino acids (DL-[GADV]-peptides). The results indicate that the tendency of secondary structure formation for L-[GADV]-peptides was larger than that for DL-[GADV]-peptides, and L-[GADV]-peptides were more rigid than DL-[GADV]-peptides. These results suggest that the proteins with rigid structure motifs were more prone to have been generated in a primordial soup that included only L-amino acids than a the soup including racemic amino acids. The tendency of the rigid structure motif formation may have played a role in selecting for the homochirality that dominates life on Earth today.
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Affiliation(s)
- Akifumi Oda
- Meijo University, Faculty of Pharmacy, Nagoya, 468-8503, Japan. .,Osaka University, Institute for Protein Research, Suita, 565-0871, Japan. .,Kanazawa University, Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa, 920-1192, Japan.
| | - Tomoki Nakayoshi
- Meijo University, Faculty of Pharmacy, Nagoya, 468-8503, Japan.,Kanazawa University, Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa, 920-1192, Japan
| | - Koichi Kato
- Meijo University, Faculty of Pharmacy, Nagoya, 468-8503, Japan.,Kinjo Gakuin University, Faculty of Pharmacy, Nagoya, 463-8521, Japan
| | - Shuichi Fukuyoshi
- Kanazawa University, Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa, 920-1192, Japan
| | - Eiji Kurimoto
- Meijo University, Faculty of Pharmacy, Nagoya, 468-8503, Japan
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16
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Perets EA, Videla PE, Yan ECY, Batista VS. Chiral Inversion of Amino Acids in Antiparallel β-Sheets at Interfaces Probed by Vibrational Sum Frequency Generation Spectroscopy. J Phys Chem B 2019; 123:5769-5781. [PMID: 31194546 PMCID: PMC9059514 DOI: 10.1021/acs.jpcb.9b04029] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A parallel study of protein variants with all (l-), all (d-), or mixed (l-)/(d-) amino acids can be used to assess how backbone architecture versus side chain identity determines protein structure. Here, we investigate the secondary structure and side chain orientation dynamics of the antiparallel β-sheet peptide LK7β (Ac-Leu-Lys-Leu-Lys-Leu-Lys-Leu-NH2) composed of all (l-), all (d-), or alternating (l-Leu)/(d-Lys) amino acids. Using interface-selective vibrational sum frequency generation spectroscopy (VSFG), we observe that the alternating (l-)/(d-) peptide lacks a resonant C-H stretching mode compared to the (l-) and (d-) variants and does not form antiparallel β-sheets. We rationalize our observations on the basis of density functional theory calculations and molecular dynamics (MD) simulations of LK7β at the air-water interface. Irrespective of the handedness of the amino acids, leucine side chains prefer to orient toward the hydrophobic air phase while lysine side chains prefer the hydrophilic water phase. These preferences dictate the backbone configuration of LK7β and thereby the folding of the peptide. Our MD simulations show that the preferred side chain orientations can force the backbone of a single strand of (l-) LK7β at the air-water interface to adopt β-sheet Ramachandran angles. However, denaturation of the β-sheets at pH = 2 results in a negligible chiral VSFG amide I response. The combined computational and experimental results lend critical support to the theory that a chiral VSFG response requires macroscopic chirality, such as in β-sheets. Our results can guide expectations about the VSFG optical responses of proteins and should improve understanding of how amino acid chirality modulates the structure and function of natural and de novo proteins at biological interfaces.
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Affiliation(s)
- Ethan A. Perets
- Department of Chemistry, Yale University, 225 Prospect St., New Haven, CT 06520
| | - Pablo E. Videla
- Department of Chemistry, Yale University, 225 Prospect St., New Haven, CT 06520
- Energy Sciences Institute, Yale University, 810 West Campus Drive, West Haven, CT 06516
| | - Elsa C. Y. Yan
- Department of Chemistry, Yale University, 225 Prospect St., New Haven, CT 06520
| | - Victor S. Batista
- Department of Chemistry, Yale University, 225 Prospect St., New Haven, CT 06520
- Energy Sciences Institute, Yale University, 810 West Campus Drive, West Haven, CT 06516
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17
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Hazam PK, Akhil R, Jerath G, Saikia J, Ramakrishnan V. Topological effects on the designability and bactericidal potency of antimicrobial peptides. Biophys Chem 2019; 248:1-8. [DOI: 10.1016/j.bpc.2019.02.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 02/22/2019] [Accepted: 02/22/2019] [Indexed: 12/21/2022]
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18
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Zerze GH, Stillinger FH, Debenedetti PG. Effect of heterochiral inversions on the structure of a β-hairpin peptide. Proteins 2019; 87:569-578. [PMID: 30811673 DOI: 10.1002/prot.25680] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 02/24/2019] [Indexed: 01/25/2023]
Abstract
We study computationally a family of β-hairpin peptides with systematically introduced chiral inversions, in explicit water, and we investigate the extent to which the backbone structure is able to fold in the presence of heterochiral perturbations. In contrast to the recently investigated case of a helical peptide, we do not find a monotonic change in secondary structure content as a function of the number of L- to D-inversions. The effects of L- to D-inversions are instead found to be highly position-specific. Additionally, in contrast to the helical peptide, some inversions increase the stability of the folded peptide: in such cases, we compute an increase in β-sheet content in the aqueous solution equilibrium ensemble. However, the tertiary structures of the stable (folded) configurations for peptides for which inversions cause an increase in β-sheet content show differences from one another, as well as from the native fold of the nonchirally perturbed β-hairpin. Our results suggest that although some chiral perturbations can increase folding stability, chirally perturbed proteins may still underperform functionally, given the relationship between structure and function.
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Affiliation(s)
- Gül H Zerze
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey
| | | | - Pablo G Debenedetti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey
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19
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Yue P, Peng S, Parkin S, Li T, Yu F, Long S. Peptidomimicry with C 2
-Symmetric Oligourea Derivatives of 1,2-Diaminocyclohexane and 1,2-Diphenyl-1,2-diaminoethane: Chirality and Chain Length-Dependent Conformation. ChemistrySelect 2018. [DOI: 10.1002/slct.201801900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Pengyun Yue
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology; School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, 206 1 Rd Optics Valley, East Lake New Technology Development District, Wuhan, Hubei; 430205 China
| | - Siqing Peng
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology; School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, 206 1 Rd Optics Valley, East Lake New Technology Development District, Wuhan, Hubei; 430205 China
| | - Sean Parkin
- Department of Chemistry; University of Kentucky, Lexington, Kentucky; 40506 USA
| | - Tonglei Li
- Department of Industrial and Physical Pharmacy; Purdue University, West Lafayette; Indiana 47907 U.S.A
| | - Faquan Yu
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology; School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, 206 1 Rd Optics Valley, East Lake New Technology Development District, Wuhan, Hubei; 430205 China
| | - Sihui Long
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology; School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, 206 1 Rd Optics Valley, East Lake New Technology Development District, Wuhan, Hubei; 430205 China
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20
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Hazam PK, Goyal R, Ramakrishnan V. Peptide based antimicrobials: Design strategies and therapeutic potential. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 142:10-22. [PMID: 30125585 DOI: 10.1016/j.pbiomolbio.2018.08.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 08/13/2018] [Accepted: 08/14/2018] [Indexed: 12/24/2022]
Abstract
Therapeutic activity of antibiotics is noteworthy, as they are used in the treatment of microbial infections. Regardless of their utility, there has been a steep decrease in the number of drug candidates due to antibiotic resistance, an inevitable consequence of noncompliance with the full therapeutic regimen. A variety of resistant species like MDR (Multi-Drug Resistant), XDR (Extensively Drug-Resistant) and PDR (Pan Drug-Resistant) species have evolved, but discovery pipeline has already shown signs of getting dried up. Therefore, the need for newer antibiotics is of utmost priority to combat the microbial infections of future times. Peptides have some interesting features like minimal side effect, high tolerability and selectivity towards specific targets, which would help them successfully comply with the stringent safety standards set for clinical trials. In this review, we attempt to present the state of the art in the discovery of peptide-based antimicrobials from a design perspective.
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Affiliation(s)
- Prakash Kishore Hazam
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati, 781039, India
| | - Ruchika Goyal
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati, 781039, India
| | - Vibin Ramakrishnan
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati, 781039, India.
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21
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Ranbhor R, Kumar A, Tendulkar A, Patel K, Ramakrishnan V, Durani S. IDeAS: automated design tool for hetero-chiral protein folds. Phys Biol 2018; 15:066005. [PMID: 29923499 DOI: 10.1088/1478-3975/aacdc3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Incorporating D amino acids in the protein design alphabet can in principle multiply the design space by many orders of magnitude. All native proteins are polymers composed of L chiral amino acids. Practically limitless in diversity over amino acid sequences, protein structure is limited in folds and thus shapes, principally due to the poly L stereochemistry of their backbone. To diversify shapes, we introduced both L- and D α-amino acids as design alphabets to explore the possibility of generating novel folds, varied in chemical as well as stereo-chemical sequence. Now, to have stereochemically-defined proteins tuned chemically, we present the Inverse Design and Automation Software, IDeAS. Retro-fitting side chains on a backbone with L and D stereochemistry, the software demonstrate functional fits over stereo-chemically diverse folds in a range of applications of interest in protein design.
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Affiliation(s)
- Ranjit Ranbhor
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
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22
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Hiraoka S. Unresolved Issues that Remain in Molecular Self-Assembly. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2018. [DOI: 10.1246/bcsj.20180008] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Shuichi Hiraoka
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
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23
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Setiawan D, Brender J, Zhang Y. Recent advances in automated protein design and its future challenges. Expert Opin Drug Discov 2018; 13:587-604. [PMID: 29695210 DOI: 10.1080/17460441.2018.1465922] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Protein function is determined by protein structure which is in turn determined by the corresponding protein sequence. If the rules that cause a protein to adopt a particular structure are understood, it should be possible to refine or even redefine the function of a protein by working backwards from the desired structure to the sequence. Automated protein design attempts to calculate the effects of mutations computationally with the goal of more radical or complex transformations than are accessible by experimental techniques. Areas covered: The authors give a brief overview of the recent methodological advances in computer-aided protein design, showing how methodological choices affect final design and how automated protein design can be used to address problems considered beyond traditional protein engineering, including the creation of novel protein scaffolds for drug development. Also, the authors address specifically the future challenges in the development of automated protein design. Expert opinion: Automated protein design holds potential as a protein engineering technique, particularly in cases where screening by combinatorial mutagenesis is problematic. Considering solubility and immunogenicity issues, automated protein design is initially more likely to make an impact as a research tool for exploring basic biology in drug discovery than in the design of protein biologics.
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Affiliation(s)
- Dani Setiawan
- a Department of Computational Medicine and Bioinformatics , University of Michigan , Ann Arbor , MI , USA
| | - Jeffrey Brender
- b Radiation Biology Branch , Center for Cancer Research, National Cancer Institute - NIH , Bethesda , MD , USA
| | - Yang Zhang
- a Department of Computational Medicine and Bioinformatics , University of Michigan , Ann Arbor , MI , USA.,c Department of Biological Chemistry , University of Michigan , Ann Arbor , MI , USA
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24
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Chiral self-sorting process in the self-assembly of homochiral coordination cages from axially chiral ligands. Commun Chem 2018. [DOI: 10.1038/s42004-018-0020-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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25
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Bactericidal Potency and Extended Serum Life of Stereo-Chemically Engineered Peptides Against Mycobacterium. Int J Pept Res Ther 2018. [DOI: 10.1007/s10989-018-9690-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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26
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Ranbhor R, Kumar A, Patel K, Ramakrishnan V, Durani S. Automated design evolution of stereochemically randomized protein foldamers. Phys Biol 2018; 15:036001. [PMID: 29393061 DOI: 10.1088/1478-3975/aaac9a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Diversification of chain stereochemistry opens up the possibilities of an 'in principle' increase in the design space of proteins. This huge increase in the sequence and consequent structural variation is aimed at the generation of smart materials. To diversify protein structure stereochemically, we introduced L- and D-α-amino acids as the design alphabet. With a sequence design algorithm, we explored the usage of specific variables such as chirality and the sequence of this alphabet in independent steps. With molecular dynamics, we folded stereochemically diverse homopolypeptides and evaluated their 'fitness' for possible design as protein-like foldamers. We propose a fitness function to prune the most optimal fold among 1000 structures simulated with an automated repetitive simulated annealing molecular dynamics (AR-SAMD) approach. The highly scored poly-leucine fold with sequence lengths of 24 and 30 amino acids were later sequence-optimized using a Dead End Elimination cum Monte Carlo based optimization tool. This paper demonstrates a novel approach for the de novo design of protein-like foldamers.
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Affiliation(s)
- Ranjit Ranbhor
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India. Joint first authors
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27
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Chaume G, Simon J, Lensen N, Pytkowicz J, Brigaud T, Miclet E. Homochiral versus Heterochiral Trifluoromethylated Pseudoproline Containing Dipeptides: A Powerful Tool to Switch the Prolyl-Amide Bond Conformation. J Org Chem 2017; 82:13602-13608. [DOI: 10.1021/acs.joc.7b01944] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Grégory Chaume
- Laboratoire de Chimie Biologique (LCB), Université de Cergy-Pontoise, EA 4505, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France
- Sorbonne Universités, UPMC Univ. Paris 06, École normale supérieure, PSL Research University, CNRS, Laboratoire des Biomolécules (LBM), 4 place Jussieu, 75005 Paris, France
| | - Julien Simon
- Laboratoire de Chimie Biologique (LCB), Université de Cergy-Pontoise, EA 4505, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France
| | - Nathalie Lensen
- Laboratoire de Chimie Biologique (LCB), Université de Cergy-Pontoise, EA 4505, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France
| | - Julien Pytkowicz
- Laboratoire de Chimie Biologique (LCB), Université de Cergy-Pontoise, EA 4505, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France
| | - Thierry Brigaud
- Laboratoire de Chimie Biologique (LCB), Université de Cergy-Pontoise, EA 4505, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France
| | - Emeric Miclet
- Sorbonne Universités, UPMC Univ. Paris 06, École normale supérieure, PSL Research University, CNRS, Laboratoire des Biomolécules (LBM), 4 place Jussieu, 75005 Paris, France
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29
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Ruckthong L, Peacock AFA, Pascoe CE, Hemmingsen L, Stuckey JA, Pecoraro VL. d-Cysteine Ligands Control Metal Geometries within De Novo Designed Three-Stranded Coiled Coils. Chemistry 2017; 23:8232-8243. [PMID: 28384393 DOI: 10.1002/chem.201700660] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Indexed: 12/31/2022]
Abstract
Although metal ion binding to naturally occurring l-amino acid proteins is well documented, understanding the impact of the opposite chirality (d-)amino acids on the structure and stereochemistry of metals is in its infancy. We examine the effect of a d-configuration cysteine within a designed l-amino acid three-stranded coiled coil in order to enforce a precise coordination number on a metal center. The d chirality does not alter the native fold, but the side-chain re-orientation modifies the sterics of the metal binding pocket. l-Cys side chains within the coiled-coil structure have previously been shown to rotate substantially from their preferred positions in the apo structure to create a binding site for a tetra-coordinate metal ion. However, here we show by X-ray crystallography that d-Cys side chains are preorganized within a suitable geometry to bind such a ligand. This is confirmed by comparison of the structure of ZnII Cl(CSL16D C)32- to the published structure of ZnII (H2 O)(GRAND-CSL12AL16L C)3- . Moreover, spectroscopic analysis indicates that the CdII geometry observed by using l-Cys ligands (a mixture of three- and four-coordinate CdII ) is altered to a single four-coordinate species when d-Cys is present. This work opens a new avenue for the control of the metal site environment in man-made proteins, by simply altering the binding ligand with its mirror-imaged d configuration. Thus, the use of non-coded amino acids in the coordination sphere of a metal promises to be a powerful tool for controlling the properties of future metalloproteins.
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Affiliation(s)
- Leela Ruckthong
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Present address: Department Chemistry, Faculty of Science, King Mongkut's University of Technology Thonburi (KMUTT), Bang Mod, ThungKhru, Bangkok, 10140, Thailand
| | - Anna F A Peacock
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Present address: School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Cherilyn E Pascoe
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Lars Hemmingsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, København Ø, Denmark
| | - Jeanne A Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Vincent L Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
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30
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Hazam PK, Jerath G, Kumar A, Chaudhary N, Ramakrishnan V. Effect of tacticity-derived topological constraints in bactericidal peptides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1388-1395. [PMID: 28479275 DOI: 10.1016/j.bbamem.2017.05.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 04/16/2017] [Accepted: 05/03/2017] [Indexed: 12/25/2022]
Abstract
Topology is a key element in structure-activity relationship estimation while designing physiologically-active molecular constructs. Peptides may be a preferred choice for therapeutics, principally due to their biocompatibility, low toxicity and predictable metabolism. Peptide design only guarantees functional group constitution by opting specific amino acid sequence, and not their spatial orientation to bind and incite physiological response on chosen targets. This is principally because peptide conformation is subject to external flux, due to the isotactic stereochemistry of the peptide chain. Stereochemical engineering of the peptide main chain offers the possibility of multiplying the structural space of a typical sequence to many orders of magnitude, and limiting the otherwise fluxional non-specific functional group dispensation in space by offering greater conformational rigidity. We put to test, this conceptual possibility already established in theoretical models, by designing amphipathic peptide systems and experimenting with them on Gram-positive, Gram-negative and antibiotic-resistant bacteria. The unusual conformational rigidity and stability of syndiotactic peptides enable them to retain the designed electrostatic environment, while they encounter the membrane surface. All the six designed systems exhibited bactericidal activity, pointing to the utility and specificity of stereo-engineered peptide systems for therapeutic applications. Overall, we hope that this work provides important insights and useful directives in designing novel peptide systems with antimicrobial activity, by expanding the design space, incorporating D-amino acid as an additional design variable.
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Affiliation(s)
- Prakash Kishore Hazam
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, India
| | - Gaurav Jerath
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, India
| | - Anil Kumar
- Biological and Organic Chemistry, University of Toronto, Ontario M5S 3H6, Canada
| | - Nitin Chaudhary
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, India
| | - Vibin Ramakrishnan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, India.
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31
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Goyal B, Srivastava KR, Durani S. N-terminal diproline and charge group effects on the stabilization of helical conformation in alanine-based short peptides: CD studies with water and methanol as solvent. J Pept Sci 2017; 23:431-437. [PMID: 28425159 DOI: 10.1002/psc.3005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 03/17/2017] [Accepted: 03/20/2017] [Indexed: 12/25/2022]
Abstract
Protein folding problem remains a formidable challenge as main chain, side chain and solvent interactions remain entangled and have been difficult to resolve. Alanine-based short peptides are promising models to dissect protein folding initiation and propagation structurally as well as energetically. The effect of N-terminal diproline and charged side chains is assessed on the stabilization of helical conformation in alanine-based short peptides using circular dichroism (CD) with water and methanol as solvent. A1 (Ac-Pro-Pro-Ala-Lys-Ala-Lys-Ala-Lys-Ala-NH2 ) is designed to assess the effect of N-terminal homochiral diproline and lysine side chains to induce helical conformation. A2 (Ac-Pro-Pro-Glu-Glu-Ala-Ala-Lys-Lys-Ala-NH2 ) and A3 (Ac-dPro-Pro-Glu-Glu-Ala-Ala-Lys-Lys-Ala-NH2 ) with N-terminal homochiral and heterochiral diproline, respectively, are designed to assess the effect of Glu...Lys (i, i + 4) salt bridge interactions on the stabilization of helical conformation. The CD spectra of A1, A2 and A3 in water manifest different amplitudes of the observed polyproline II (PPII) signals, which indicate different conformational distributions of the polypeptide structure. The strong effect of solvent substitution from water to methanol is observed for the peptides, and CD spectra in methanol evidence A2 and A3 as helical folds. Temperature-dependent CD spectra of A1 and A2 in water depict an isodichroic point reflecting coexistence of two conformations, PPII and β-strand conformation, which is consistent with the previous studies. The results illuminate the effect of N-terminal diproline and charged side chains in dictating the preferences for extended-β, semi-extended PPII and helical conformation in alanine-based short peptides. The results of the present study will enhance our understanding on stabilization of helical conformation in short peptides and hence aid in the design of novel peptides with helical structures. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Bhupesh Goyal
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.,Department of Chemistry, School of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, 140406, Punjab, India
| | - Kinshuk Raj Srivastava
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.,Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48105, USA
| | - Susheel Durani
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
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Jędrzejewska H, Szumna A. Making a Right or Left Choice: Chiral Self-Sorting as a Tool for the Formation of Discrete Complex Structures. Chem Rev 2017; 117:4863-4899. [PMID: 28277655 DOI: 10.1021/acs.chemrev.6b00745] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
This review discusses chiral self-sorting-the process of choosing an interaction partner with a given chirality from a complex mixture of many possible racemic partners. Chiral self-sorting (also known as chiral self-recognition or chiral self-discrimination) is fundamental for creating functional structures in nature and in the world of chemistry because interactions between molecules of the same or the opposite chirality are characterized by different interaction energies and intrinsically different resulting structures. However, due to the similarity between recognition sites of enantiomers and common conformational lability, high fidelity homochiral or heterochiral self-sorting poses a substantial challenge. Chiral self-sorting occurs among natural and synthetic molecules that leads to the amplification of discrete species. The review covers a variety of complex self-assembled structures ranging from aggregates made of natural and racemic peptides and DNA, through artificial functional receptors, macrocyles, and cages to catalytically active metal complexes and helix mimics. The examples involve a plethora of reversible interactions: electrostatic interactions, π-π stacking, hydrogen bonds, coordination bonds, and dynamic covalent bonds. A generalized view of the examples collected from different fields allows us to suggest suitable geometric models that enable a rationalization of the observed experimental preferences and establishment of the rules that can facilitate further design.
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Affiliation(s)
- Hanna Jędrzejewska
- Institute of Organic Chemistry, Polish Academy of Sciences , Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Agnieszka Szumna
- Institute of Organic Chemistry, Polish Academy of Sciences , Kasprzaka 44/52, 01-224 Warsaw, Poland
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Abstract
Bio-inspired synthetic backbones leading to foldamers can provide effective biopolymer mimics with new and improved properties in a physiological environment, and in turn could serve as useful tools to study biology and lead to practical applications in the areas of diagnostics or therapeutics. Remarkable progress has been accomplished over the past 20 years with the discovery of many potent bioactive foldamers originating from diverse backbones and targeting a whole spectrum of bio(macro)molecules such as membranes, protein surfaces, and nucleic acids. These current achievements, future opportunities, and key challenges that remain are discussed in this article.
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Goyal B, Srivastava KR, Durani S. Examination of the Effect of N-terminal Diproline and Charged Side Chains on the Stabilization of Helical Conformation in Alanine-based Short Peptides: A Molecular Dynamics Study. ChemistrySelect 2016. [DOI: 10.1002/slct.201601381] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Bhupesh Goyal
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai-400076 India
- Department of Chemistry; School of Basic and Applied Sciences; Sri Guru Granth Sahib World University, Fatehgarh; Sahib-140406, Punjab India
| | - Kinshuk Raj Srivastava
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai-400076 India
- Life Sciences Institute; University of Michigan; Ann Arbor, MI USA 48105
| | - Susheel Durani
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai-400076 India
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Probing the stereospecificity of tyrosyl- and glutaminyl-tRNA synthetase with molecular dynamics. J Mol Graph Model 2016; 71:192-199. [PMID: 27939931 DOI: 10.1016/j.jmgm.2016.11.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 11/08/2016] [Accepted: 11/11/2016] [Indexed: 12/28/2022]
Abstract
The stereospecificity of aminoacyl-tRNA synthetases helps exclude d-amino acids from protein synthesis and could perhaps be engineered to allow controlled d-amino acylation of tRNA. We use molecular dynamics simulations to probe the stereospecificity of the class I tyrosyl- and glutaminyl-tRNA synthetases (TyrRS, GlnRS), including wildtype enzymes and three point mutants suggested by three different protein design methods. l/d binding free energy differences are obtained by alchemically and reversibly transforming the ligand from L to D in simulations of the protein-ligand complex. The D81Q mutation in Escherichia coli TyrRS is homologous to the D81R mutant shown earlier to have inverted stereospecificity. D81Q is predicted to lead to a rotated ligand backbone and an increased, not a decreased l-Tyr preference. The E36Q mutation in Methanococcus jannaschii TyrRS has a predicted l/d binding free energy difference ΔΔG of just 0.5±0.9kcal/mol, compared to 3.1±0.8kcal/mol for the wildtype enzyme (favoring l-Tyr). The ligand ammonium position is preserved in the d-Tyr complex, while the carboxylate is shifted. Wildtype GlnRS has a similar preference for l-glutaminyl adenylate; the R260Q mutant has an increased preference, even though Arg260 makes a large contribution to the wildtype ΔΔG value.
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Vasudev PG, Aravinda S, Shamala N. Crystal structure of a tripeptide containing aminocyclododecane carboxylic acid: a supramolecular twisted parallel β-sheet in crystals. J Pept Sci 2016; 22:166-73. [PMID: 26856690 DOI: 10.1002/psc.2854] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 12/03/2015] [Accepted: 12/17/2015] [Indexed: 12/25/2022]
Abstract
The crystal structure of a tripeptide Boc-Leu-Val-Ac12 c-OMe (1) is determined, which incorporates a bulky 1-aminocyclododecane-1-carboxylic acid (Ac12 c) side chain. The peptide adopts a semi-extended backbone conformation for Leu and Val residues, while the backbone torsion angles of the C(α,α) -dialkylated residue Ac12 c are in the helical region of the Ramachandran map. The molecular packing of 1 revealed a unique supramolecular twisted parallel β-sheet coiling into a helical architecture in crystals, with the bulky hydrophobic Ac12 c side chains projecting outward the helical column. This arrangement resembles the packing of peptide helices in crystal structures. Although short oligopeptides often assemble as parallel or anti-parallel β-sheet in crystals, twisted or helical β-sheet formation has been observed in a few examples of dipeptide crystal structures. Peptide 1 presents the first example of a tripeptide showing twisted β-sheet assembly in crystals.
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Affiliation(s)
- Prema G Vasudev
- Department of Physics, Indian Institute of Science, Bangalore, 560012, India
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Goyal B, Kumar A, Srivastava KR, Durani S. Scrutiny of chain-length and N-terminal effects in α-helix folding: a molecular dynamics study on polyalanine peptides. J Biomol Struct Dyn 2016; 35:1923-1935. [DOI: 10.1080/07391102.2016.1199972] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Bhupesh Goyal
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
- Department of Chemistry, School of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
| | - Anil Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | - Kinshuk Raj Srivastava
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824, USA
| | - Susheel Durani
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
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Goyal B, Srivastava KR, Patel K, Durani S. Modulation of β-Hairpin Peptide Self-Assembly: A Twenty-Residue Poly-lβ-Hairpin Modified Rationally as a Mixed-l,dHydrolase. ChemistrySelect 2016. [DOI: 10.1002/slct.201600078] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Bhupesh Goyal
- Department of Chemistry; Indian Institute of Technology Bombay; Powai Mumbai- 400076 India
- Department of Chemistry; School of Basic and Applied Sciences; Sri Guru Granth Sahib World University; Fatehgarh Sahib- 140406 Punjab India
| | - Kinshuk Raj Srivastava
- Department of Chemistry; Indian Institute of Technology Bombay; Powai Mumbai- 400076 India
- Department of Physics and Astronomy; Michigan State University; East Lansing USA
| | - Kirti Patel
- Department of Chemistry; Indian Institute of Technology Bombay; Powai Mumbai- 400076 India
- Department of Chemistry; N. B. Mehta Science College, Bordi, Dahanu; Dist. Thane Maharashtra India
| | - Susheel Durani
- Department of Chemistry; Indian Institute of Technology Bombay; Powai Mumbai- 400076 India
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De Marco R, Mazzotti G, Dattoli SD, Baiula M, Spampinato S, Greco A, Gentilucci L. 5-aminomethyloxazolidine-2,4-dione hybrid α/β-dipeptide scaffolds as inductors of constrained conformations: Applications to the synthesis of integrin antagonists. Biopolymers 2016. [PMID: 26211418 DOI: 10.1002/bip.22704] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Peptidomimetics represent an attractive starting point for drug discovery programs; in particular, peptidomimetics that result from the incorporation of a heterocycle may take advantage of increased enzymatic stability and higher ability to reproduce the bioactive conformations of the parent peptides, resulting in enhanced therapeutic potential. Herein, we present mimetics of the α4β1 integrin antagonist BIO1211 (MPUPA-Leu-Asp-Val-Pro-OH), containing a aminomethyloxazolidine-2,4-dione scaffold (Amo). Interestingly, the retro-sequences PhCOAsp(OH)-Amo-APUMP including either (S)- or (R)-configured Amo displayed significant ability to inhibit the adhesion of α4β1 integrin expressing cells, and remarkable stability in mouse serum. Possibly, the conformational bias exerted by the Amo scaffold determined the affinity for the receptors. These peptidomimetics could be of interest for the development of small-molecule agents effective against inflammatory processes and correlated autoimmune diseases.
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Affiliation(s)
- Rossella De Marco
- Department of Chemistry "G. Ciamician", University of Bologna, via Selmi 2, Bologna, 40126, Italy
| | - Giacomo Mazzotti
- Department of Chemistry "G. Ciamician", University of Bologna, via Selmi 2, Bologna, 40126, Italy
| | - Samantha D Dattoli
- Department of Pharmacy and BioTechnology, University of Bologna, via Irnerio 48, Bologna, 40126, Italy
| | - Monica Baiula
- Department of Pharmacy and BioTechnology, University of Bologna, via Irnerio 48, Bologna, 40126, Italy
| | - Santi Spampinato
- Department of Pharmacy and BioTechnology, University of Bologna, via Irnerio 48, Bologna, 40126, Italy
| | - Arianna Greco
- Department of Chemistry "G. Ciamician", University of Bologna, via Selmi 2, Bologna, 40126, Italy
| | - Luca Gentilucci
- Department of Chemistry "G. Ciamician", University of Bologna, via Selmi 2, Bologna, 40126, Italy
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Simonson T, Ye-Lehmann S, Palmai Z, Amara N, Wydau-Dematteis S, Bigan E, Druart K, Moch C, Plateau P. Redesigning the stereospecificity of tyrosyl-tRNA synthetase. Proteins 2016; 84:240-53. [PMID: 26676967 DOI: 10.1002/prot.24972] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 09/30/2015] [Accepted: 11/26/2015] [Indexed: 12/14/2022]
Abstract
D-Amino acids are largely excluded from protein synthesis, yet they are of great interest in biotechnology. Unnatural amino acids have been introduced into proteins using engineered aminoacyl-tRNA synthetases (aaRSs), and this strategy might be applicable to D-amino acids. Several aaRSs can aminoacylate their tRNA with a D-amino acid; of these, tyrosyl-tRNA synthetase (TyrRS) has the weakest stereospecificity. We use computational protein design to suggest active site mutations in Escherichia coli TyrRS that could increase its D-Tyr binding further, relative to L-Tyr. The mutations selected all modify one or more sidechain charges in the Tyr binding pocket. We test their effect by probing the aminoacyl-adenylation reaction through pyrophosphate exchange experiments. We also perform extensive alchemical free energy simulations to obtain L-Tyr/D-Tyr binding free energy differences. Agreement with experiment is good, validating the structural models and detailed thermodynamic predictions the simulations provide. The TyrRS stereospecificity proves hard to engineer through charge-altering mutations in the first and second coordination shells of the Tyr ammonium group. Of six mutants tested, two are active towards D-Tyr; one of these has an inverted stereospecificity, with a large preference for D-Tyr. However, its activity is low. Evidently, the TyrRS stereospecificity is robust towards charge rearrangements near the ligand. Future design may have to consider more distant and/or electrically neutral target mutations, and possibly design for binding of the transition state, whose structure however can only be modeled.
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Affiliation(s)
- Thomas Simonson
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | | | - Zoltan Palmai
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | - Najette Amara
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | - Sandra Wydau-Dematteis
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | - Erwan Bigan
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | - Karen Druart
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | - Clara Moch
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
| | - Pierre Plateau
- Department of Biology, Laboratoire De Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, 91128, France
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41
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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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42
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Goyal B, Srivastava KR, Kumar A, Patwari GN, Durani S. Probing the role of electrostatics of polypeptide main-chain in protein folding by perturbing N-terminal residue stereochemistry: DFT study with oligoalanine models. RSC Adv 2016. [DOI: 10.1039/c6ra22870d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Energetics of folding (ΔHE→F, in kcal mol−1) from the extended (E) structure to the folded (F) structure for Ia and Ib critically depend on the geometrical relationship between the backbone peptide units of the polypeptide structure.
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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
| | - G. Naresh Patwari
- 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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43
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Ghosh P, Pednekar D, Durani S. Biomimetic design: a programmed tetradecapeptide folds and auto-dimerizes as a stereochemically articulated receptor protein. RSC Adv 2016. [DOI: 10.1039/c5ra17350g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Treating protein-structure evolution as a hierarchy of selections, a fourteen residue polypeptide was made as a C2 symmetric receptor structure in mimicry of HIV protease. This shows the value of a biomimetic algorithm and of stereochemistry as a variable in protein design.
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Affiliation(s)
- Punam Ghosh
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - Deepa Pednekar
- 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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44
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Gupta P, Durani S. Algorithm to design inhibitors using stereochemically mixed l,d polypeptides: Validation against HIV protease. Int J Biol Macromol 2015; 81:410-7. [PMID: 26279121 DOI: 10.1016/j.ijbiomac.2015.08.029] [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: 02/18/2015] [Revised: 08/11/2015] [Accepted: 08/11/2015] [Indexed: 10/23/2022]
Abstract
Polypeptides have potential to be designed as drugs or inhibitors against the desired targets. In polypeptides, every chiral α-amino acid has enantiomeric structural possibility to become l or d amino acids and can be used as design monomer. Among the various possibilities, use of stereochemistry as a design tool has potential to determine both functional specificity and metabolic stability of the designed polypeptides. The polypeptides with mixed l,d amino acids are a class of peptidomimitics, an attractive drug like molecules and also less susceptible to proteolytic activities. Therefore in this study, a three step algorithm is proposed to design the polypeptides against desired drug targets. For this, all possible configurational isomers of mixed l,d polyleucine (Ac-Leu8-NHMe) structure were randomly modeled with simulated annealing molecular dynamics and the resultant library of discrete folds were scored against HIV protease as a model target. The best scored folds of mixed l,d structures were inverse optimized for sequences in situ and the resultant sequences as inhibitors were validated for conformational integrity using molecular dynamics. This study presents and validates an algorithm to design polypeptides of mixed l,d structures as drugs/inhibitors by inverse fitting them as molecular ligands against desired target.
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Affiliation(s)
- Pooja Gupta
- 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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45
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Jadhav KB, Lichtenecker RJ, Bullach A, Mandal B, Arndt HD. Dynamic Combinatorial Enrichment of PolyconformationalD-/L-Peptide Dimers. Chemistry 2015; 21:5898-908. [DOI: 10.1002/chem.201405413] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Indexed: 01/19/2023]
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46
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Goyal B, Patel K, Srivastava KR, Durani S. De novo design of stereochemically-bent sixteen-residue β-hairpin as a hydrolase mimic. RSC Adv 2015. [DOI: 10.1039/c5ra19015k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Stepwise design of sixteen-residue β-hairpin as a hydrolase mimic involving fold design by stereochemical mutation followed by inverse-design of sequence.
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Affiliation(s)
- Bhupesh Goyal
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai–400076
- India
| | - Kirti Patel
- 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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47
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Nair RV, Kotmale AS, Dhokale SA, Gawade RL, Puranik VG, Rajamohanan PR, Sanjayan GJ. Formation of a pseudo-β-hairpin motif utilizing the Ant–Pro reverse turn: consequences of stereochemical reordering. Org Biomol Chem 2014; 12:774-82. [DOI: 10.1039/c3ob42016g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, we report a special case of pseudo-β-hairpin formation by tetrapeptide sequences featuring a two-residue Ant–Pro dipeptide motif (Ant = anthranilic acid and Pro = proline) at the loop region.
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Affiliation(s)
- Roshna V. Nair
- Division of Organic Synthesis
- National Chemical Laboratory
- Pune 411 008, India
| | - Amol S. Kotmale
- Central Material Characterization Division
- National Chemical Laboratory
- Pune 411 008, India
| | - Snehal A. Dhokale
- Central Material Characterization Division
- National Chemical Laboratory
- Pune 411 008, India
| | - Rupesh L. Gawade
- Central NMR Facility
- National Chemical Laboratory
- Pune 411 008, India
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48
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Demizu Y, Misawa T, Kurihara M. Development of Stabilized Short Helical Peptides and Their Functionalization. J SYN ORG CHEM JPN 2014. [DOI: 10.5059/yukigoseikyokaishi.72.1336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yosuke Demizu
- Division of Organic Chemistry, National Institute of Health Sciences
| | | | - Masaaki Kurihara
- Division of Organic Chemistry, National Institute of Health Sciences
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49
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Lichtenecker RJ, Ellinger B, Han HM, Jadhav KB, Baumann S, Makarewicz O, Grabenbauer M, Arndt HD. Iterative antimicrobial candidate selection from informed d-/l-Peptide dimer libraries. Chembiochem 2013; 14:2492-9. [PMID: 24151156 DOI: 10.1002/cbic.201300243] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Indexed: 11/11/2022]
Abstract
Growing resistance to antibiotics, as well as newly emerging pathogens, stimulate the investigation of antimicrobial peptides (AMPs) as therapeutic agents. Here, we report a new library design concept based on a stochastic distribution of natural AMP amino acid sequences onto half-length synthetic peptides. For these compounds, a non-natural motif of alternating D- and L-backbone stereochemistry of the peptide chain predisposed for β-helix formation was explored. Synthetic D-/L-peptides with permuted half-length sequences were delineated from a full-length starter sequence and covalently recombined to create two-dimensional compound arrays for antibacterial screening. Using the natural AMP magainin as a seed sequence, we identified and iteratively optimized hit compounds showing high antimicrobial activity against Gram-positive and Gram-negative bacteria with low hemolytic activity. Cryo-electron microscopy characterized the membrane-associated mechanism of action of the new D-/L-peptide antibiotics.
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Affiliation(s)
- Roman J Lichtenecker
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund (Germany); Current address: Institute of Organic Chemistry, University of Vienna, Währingerstrasse 38, 1090 Wien (Austria)
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Hayward S, Leader DP, Al-Shubailly F, Milner-White EJ. Rings and ribbons in protein structures: Characterization using helical parameters and Ramachandran plots for repeating dipeptides. Proteins 2013; 82:230-9. [DOI: 10.1002/prot.24357] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 06/10/2013] [Accepted: 06/10/2013] [Indexed: 12/30/2022]
Affiliation(s)
- Steven Hayward
- School of Computing Sciences; University of East Anglia; Norwich NR4 7TJ United Kingdom
| | - David P. Leader
- College of Medical, Veterinary and Life Sciences; University of Glasgow; Glasgow G12 8QQ United Kingdom
| | - Fawzia Al-Shubailly
- College of Medical, Veterinary and Life Sciences; University of Glasgow; Glasgow G12 8QQ United Kingdom
| | - E. James Milner-White
- College of Medical, Veterinary and Life Sciences; University of Glasgow; Glasgow G12 8QQ United Kingdom
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