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1.
PLoS One ; 18(1): e0279998, 2023.
Article in English | MEDLINE | ID: mdl-36608055

ABSTRACT

Infection with the SARS-CoV-2 virus results in manifestation of several clinical observations from asymptomatic to multi-organ failure. Biochemically, the serious effects are due to what is described as cytokine storm. The initial infection region for COVID-19 is the nasopharyngeal/oropharyngeal region which is the site where samples are taken to examine the presence of virus. We have now carried out detailed proteomic analysis of the nasopharyngeal/oropharyngeal swab samples collected from normal individuals and those tested positive for SARS-CoV-2, in India, during the early days of the pandemic in 2020, by RTPCR, involving high throughput quantitative proteomics analysis. Several proteins like annexins, cytokines and histones were found differentially regulated in the host human cells following SARS-CoV-2 infection. Genes for these proteins were also observed to be differentially regulated when their expression was analyzed. Majority of the cytokine proteins were found to be up regulated in the infected individuals. Cell to Cell signaling interaction, Immune cell trafficking and inflammatory response pathways were found associated with the differentially regulated proteins based on network pathway analysis.


Subject(s)
COVID-19 , Cytokines , Humans , SARS-CoV-2 , Proteomics , Histones
2.
Acta Virol ; 66(3): 249-253, 2022.
Article in English | MEDLINE | ID: mdl-36029089

ABSTRACT

Defensins, crucial components of the innate immune system, play a vital role against infection as part of frontline immunity. Association of SARS-CoV-2 infection with defensins has not been investigated. In this study, we have investigated the expression of defensin genes in the buccal cavity from patients with COVID-19 infection along with negative control samples. Nasopharyngeal/oropharyngeal swab samples collected for screening SARS-CoV-2 infection in early 2020 from Hyderabad, India, were analyzed for the expression of major defensin genes by the quantitative real-time reverse transcription polymerase chain reaction, qRT-PCR. Forty SARS-CoV-2 infected positive and 40 negative swab samples were selected for this study. Based on the qRT-PCR analysis involving gene specific primers for defensin genes, 9 defensin genes were found to be expressed in the nasopharyngeal/oropharyngeal cavity. Four defensin genes were found to be significantly down regulated in SARS-CoV-2 infected patients in comparison with the control samples based on differential expression analysis. The significantly down regulated genes were defensin beta 4A/B, 106B, 107B, and 103A. Down regulation of human beta defensin 2, 3, 6 and 7 suggests that antiviral innate immune response provided by defensins may be compromised in SARS-CoV-2 infection resulting in progression of the disease. Correction of the down regulation process through appropriate defensin peptide-based therapy could be an attractive method of treatment. Keywords: host defense; defensins; COVID-19; gene regulation; SARS-CoV-2.


Subject(s)
COVID-19 , beta-Defensins , Antiviral Agents , COVID-19/genetics , Down-Regulation , Humans , SARS-CoV-2/genetics , beta-Defensins/genetics
4.
J Pept Sci ; 28(11): e3427, 2022 Nov.
Article in English | MEDLINE | ID: mdl-35595709

ABSTRACT

Peptides designed with residues that have a high propensity to occur in ß-turns form ß-hairpin structures in apolar as well as in polar organic solvents such as dimethyl sulfoxide (DMSO). Due to limited solubility, their conformations have not been investigated experimentally in water. We have examined the conformations of four of such designed peptides that fold into well-defined ß-hairpin structures facilitated by ß-turns, in the crystalline state and in solution, by molecular dynamics simulations (MDS). The peptides folded into ß-hairpin structures in water, starting from the fully extended conformation. However, in DMSO, neither folding nor unfolding was observed during MDS, when the starting structures were unfolded and folded, respectively. The lack of folding in DMSO was investigated by constructing folding free energy landscapes by umbrella sampling. The folding free energy landscape is smooth in water, whereas in DMSO, folded and unfolded structures are separated by high-energy barriers. The folding free energy is less in DMSO compared with water due to a more stable unfolded structure in DMSO compared with water, which in turn is due to stabilisation of the unfolded state by hydrophobic interactions in DMSO. This finding will be helpful to researchers to accurately model and/or design small peptide structures in water and organic solvents.


Subject(s)
Dimethyl Sulfoxide , Protein Folding , Amino Acid Sequence , Hydrophobic and Hydrophilic Interactions , Peptides/chemistry , Solvents/chemistry , Water/chemistry
5.
Sci Rep ; 12(1): 3446, 2022 03 02.
Article in English | MEDLINE | ID: mdl-35236909

ABSTRACT

The COVID19 pandemic has led to multipronged approaches for treatment of the disease. Since de novo discovery of drugs is time consuming, repurposing of molecules is now considered as one of the alternative strategies to treat COVID19. Antibacterial peptides are being recognized as attractive candidates for repurposing to treat viral infections. In this study, we describe the anti-SARS-CoV-2 activity of the well-studied antibacterial peptides gramicidin S and melittin obtained from Bacillus brevis and bee venom respectively. The EC50 values for gramicidin S and melittin were 1.571 µg and 0.656 µg respectively based on in vitro antiviral assay. Significant decrease in the viral load as compared to the untreated group with no/very less cytotoxicity was observed. Both the peptides treated to the SARS-CoV-2 infected Vero cells showed viral clearance from 12 h onwards with a maximal viral clearance after 24 h post infection. Proteomics analysis indicated that more than 250 proteins were differentially regulated in the gramicidin S and melittin treated SARS-CoV-2 infected Vero cells against control SARS-CoV-2 infected Vero cells after 24 and 48 h post infection. The identified proteins were found to be associated in the metabolic and mRNA processing of the Vero cells post-treatment and infection. Both these peptides could be attractive candidates for repurposing to treat SARS-CoV-2 infection.


Subject(s)
Antiviral Agents/therapeutic use , COVID-19 Drug Treatment , Gramicidin/therapeutic use , Melitten/therapeutic use , SARS-CoV-2/isolation & purification , Animals , COVID-19/metabolism , COVID-19/virology , Chlorocebus aethiops , Humans , Proteomics , Vero Cells
6.
J Biomol Tech ; 32(1): 30-35, 2021 04.
Article in English | MEDLINE | ID: mdl-33953644

ABSTRACT

Sequence determination of peptides is a crucial step in mass spectrometry-based proteomics. Peptide sequences are determined either by database search or by de novo sequencing using tandem mass spectrometry. Determination of all the theoretical expected peptide fragments and eliminating false discoveries remains a challenge in proteomics. Developing standards for evaluating the performance of mass spectrometers and algorithms used for identification of proteins is important for proteomics studies. The current study is focused on these aspects by using synthetic peptides. A total of 599 peptides were designed from in silico tryptic digest with 1 or 2 missed cleavages from 199 human proteins, and synthetic peptides corresponding to these sequences were obtained. The peptides were mixed together, and analysis was carried out using liquid chromatography-electrospray ionization tandem mass spectrometry on a Q-Exactive HF mass spectrometer. The peptides and proteins were identified with SEQUEST program. The analysis was carried out using the proteomics workflows. A total of 573 peptides representing 196 proteins could be identified, and a spectral library was created for these peptides. Analysis parameters such as "no enzyme selection" gave the maximum number of detected peptides as compared with trypsin in the selection. False discoveries could be identified. This study highlights the limitations of peptide detection and the need for developing powerful algorithms along with tools to evaluate mass spectrometers and algorithms. It also shows the limitations of peptide detection even with high-end mass spectrometers. The mass spectral data are available in ProteomeXchange with accession no. PXD017992.


Subject(s)
Peptides , Proteomics , Algorithms , Chromatography, Liquid , Humans , Proteins , Tandem Mass Spectrometry
7.
J Biomol Tech ; 2020 Nov 20.
Article in English | MEDLINE | ID: mdl-33304200

ABSTRACT

Sequence determination of peptides is a crucial step in mass spectrometry-based proteomics. Peptide sequences are determined either by database search or by de novo sequencing using tandem mass spectrometry. Determination of all the theoretical expected peptide fragments and eliminating false discoveries remains a challenge in proteomics. Developing standards for evaluating the performance of mass spectrometers and algorithms used for identification of proteins is important for proteomics studies. The current study is focused on these aspects by using synthetic peptides. A total of 599 peptides were designed from in silico tryptic digest with 1 or 2 missed cleavages from 199 human proteins, and synthetic peptides corresponding to these sequences were obtained. The peptides were mixed together, and analysis was carried out using liquid chromatography-electrospray ionization tandem mass spectrometry on a Q-Exactive HF mass spectrometer. The peptides and proteins were identified with SEQUEST program. The analysis was carried out using the proteomics workflows. A total of 573 peptides representing 196 proteins could be identified, and a spectral library was created for these peptides. Analysis parameters such as "no enzyme selection" gave the maximum number of detected peptides as compared with trypsin in the selection. False discoveries could be identified. This study highlights the limitations of peptide detection and the need for developing powerful algorithms along with tools to evaluate mass spectrometers and algorithms. It also shows the limitations of peptide detection even with high-end mass spectrometers. The mass spectral data are available in ProteomeXchange with accession no. PXD017992.

8.
ACS Omega ; 5(12): 6366-6375, 2020 Mar 31.
Article in English | MEDLINE | ID: mdl-32258871

ABSTRACT

Human-ß-defensins (HBD1-3) are antibacterial peptides containing three disulphide bonds. In the present study, the effect of Escherichia coli lipopolysaccharide (LPS) on the antibacterial activities of HBD2-3, C-terminal analogues having a single disulphide bond, Phd1-3, and their corresponding myristoylated analogues MPhd1-3 were investigated. The effect of LPS on the activities of linear amphipathic peptides melittin, LL37 and non-ribosomally synthesized peptides, polymyxin B, alamethicin, gramicidin A, and gramicidin S was also examined. The antibacterial activity of HBD 2-3, Phd1-3, and MPhd1-3 in the presence of LPS against E. coli and Staphylococcus aureus was inhibited. While LPS inhibited the antibacterial activity of LL37, the inhibition of melittin activity was partial. The hemolytic activity exhibited by MPhd1, MPhd3, melittin, and LL37 was inhibited in the presence of LPS. HBD2-3, Phd1-3, and MPhd1-3 also showed endotoxin neutralizing activity. The antibacterial and hemolytic activities of polymyxin B, alamethicin, gramicidin A, and gramicidin S were not inhibited in the presence of LPS. Fluorescence assays employing dansyl cadaverine showed that HBD2-3 and defensin analogues bind to LPS more strongly as compared to alamethicin, gramicidin A, and gramicidin S. Electron microscopy images indicated that peptides disintegrate the structure of LPS. The inhibition of the antibacterial activity of native defensins and analogues in the presence of LPS indicates that the initial interaction with the bacterial surface is similar. The native defensin sequence or structure is also not essential, although cationic charges are necessary for binding to LPS. Hydrophobic interaction is the main driving force for association of non-ribosomally synthesized polymyxin B, alamethicin, gramicidin A, and gramicidin S with LPS. It is likely that these peptides rapidly insert into membranes and do not interact with the bacterial cell surface, whereas cationic peptides such as ß-defensin and their analogues, melittin and LL37, first interact with the bacterial cell surface and then the membrane. Our results suggest that evaluating interaction of antibacterial and hemolytic peptides with LPS is a compelling way of elucidating the mechanism of bacterial killing or hemolysis.

9.
J Phys Chem B ; 124(3): 577-588, 2020 01 23.
Article in English | MEDLINE | ID: mdl-31880938

ABSTRACT

Peptide-based gels are emerging as an interesting class of biocompatible soft materials. 9-Fluorenylmethoxycarbonyl-protected amino acids and short peptides have gained considerable attention as promising gelators. Peptide amphiphiles, wherein an alkyl chain is appended to a polar peptidic moiety, are another important class of peptide-based gelators. Here, we report the alcohol/water bigels formed by the rather simple fatty acylated dipeptides wherein the peptidic moiety is made up of hydrophobic amino acids, viz., Val, Ile, and Leu. Lauroyl, myristoyl, and palmitoyl were investigated as the N-terminal fatty acyl groups. None of the lauroylated peptides caused gelation of methanol/water and ethanol/water mixtures up to 2 wt % peptide concentration. Eight out of the 27 peptides resulted in distinct bigels. The gels are composed of fibrous aggregates as characterized by electron microscopy. Infrared spectroscopy suggests the ß-sheet conformation of the peptidic region in the gels. Using the Ma-IV ethanol/water bigel as the representative gel, entrapment and steady release of the anticancer drug docetaxel are demonstrated. Such bigels from rather simple amphipathic peptides that are easily synthesized and purified through solvent extraction could be attractive gelator candidates with potential application in drug delivery.


Subject(s)
Dipeptides/chemistry , Ethanol/chemistry , Gels/chemical synthesis , Lipopeptides/chemistry , Methanol/chemistry , Water/chemistry , Docetaxel/chemistry , Drug Delivery Systems , Drug Liberation , Rhodamines/chemistry
10.
Soft Matter ; 15(24): 4827-4835, 2019 Jun 19.
Article in English | MEDLINE | ID: mdl-31180412

ABSTRACT

Self-assembling peptides constitute an important class of functional biomaterials. A number of short amyloidogenic stretches have been identified from amyloid proteins. Such peptides, as such or through subtle modifications, can turn out to be promising candidates for functional biomaterials. End-capped Aß16-22, the well-studied amyloidogenic stretch from ß-amyloid, is reported to be non-hydrogelating up to 20 mM concentration. Here we investigated the hydrogelation propensity of Aß16-22 repeats connected through ß-turn-supporting motifs. The peptide repeats connected through Asn-Gly, Aib-DPro, and DPro-Gly formed transparent hydrogels at concentrations ≥2 mM. The repeats of the aromatic analog Aß16-22(F20Y) also resulted in similar hydrogels. Like other peptide-based gels reported earlier, these gels could trap the anticancer drug doxorubicin and displayed steady release in water. In addition, the gels supported the growth of mammalian cell lines, HEK-293 and RIN-5F. These data show that turn-inducing motifs can have marked effects on the hydrogelating propensity of self-assembling peptides.


Subject(s)
Amyloid beta-Peptides/chemistry , Doxorubicin/pharmacokinetics , Drug Carriers/pharmacokinetics , Hydrogels/chemistry , Peptide Fragments/chemistry , Amino Acid Motifs , Animals , Cell Culture Techniques/instrumentation , Cell Culture Techniques/methods , Circular Dichroism , Drug Carriers/chemistry , HEK293 Cells , Humans , Insulin/genetics , Microscopy, Atomic Force , Pancreas/cytology , Rats , Repetitive Sequences, Amino Acid , Spectroscopy, Fourier Transform Infrared
11.
Chem Biol Drug Des ; 92(2): 1504-1513, 2018 08.
Article in English | MEDLINE | ID: mdl-29682907

ABSTRACT

Analogs of the cationic C-terminal segments of human-ß-defensins HBD1-3, Phd1-3 with a single disulfide bond, exhibited comparable antimicrobial activity that was salt sensitive. They did not show hemolytic activity. In this study, N-terminal myristoylation was carried out on Phd1-3 to examine whether increasing hydrophobicity would result in improved antibacterial activity. The antibacterial activity of the oxidized myristoylated peptides MPhd1-3 and their reduced forms MPhd1r-3r was determined. These peptides showed enhanced antibacterial activity as compared to Phd1-3, on mid-log phase and stationary phase of Staphylococcus aureus and Escherichia coli, except MPhd1r-3r that were inactive on stationary-phase E. coli. In the presence of 150 mm NaCl, MPhd1-3 showed activity against S. aureus. MPhd1and two exhibited activity against E. coli but MPhd3 was inactive. Zeta potential measurements indicated that MPhd1-3 were more effective in surface charge neutralization of bacteria as compared to Phd1-3. MPhd1-3 exhibited hemolytic activity to varying extents with MPhd1 being most hemolytic. The data indicate that myristoylation enhances antibacterial activity and modulates hemolytic activity to different extents. Apart from hydrophobicity, distribution of cationic residues in MPhd1-3 plays important roles for these activities.


Subject(s)
Anti-Bacterial Agents/chemistry , Antimicrobial Cationic Peptides/chemistry , beta-Defensins/metabolism , Amino Acid Sequence , Animals , Anti-Bacterial Agents/metabolism , Anti-Bacterial Agents/pharmacology , Antimicrobial Cationic Peptides/metabolism , Antimicrobial Cationic Peptides/pharmacology , Escherichia coli/drug effects , Hemolysis/drug effects , Humans , Hydrophobic and Hydrophilic Interactions , Microbial Sensitivity Tests , Permeability/drug effects , Rats , Staphylococcus aureus/drug effects , Unilamellar Liposomes/chemistry , Unilamellar Liposomes/metabolism
13.
Biopolymers ; 108(6)2017 Nov.
Article in English | MEDLINE | ID: mdl-28589640

ABSTRACT

Short peptides composed of phenylalanine and sequences derived from amyloidogenic peptides have the ability to self-assemble to form nanostructures including hydrogels. The self-assembly of peptides composed of only hydrophobic amino acids and aliphatic protecting groups have not been investigated in detail. We have examined various aspects of nanostructures formed by N-terminal t-butyloxycarbonyl-protected aliphatic dipeptide methyl esters dissolved in various solvents. Scanning electron microscopic images indicate that depending on the sequence, position of the amino acid and solvent of dissolution, the peptides self-assemble into superstructures such as nanotubes and needles particularly from aqueous mixtures of organic solvents. Crystallization was not required for self-assembly into nanostructures. Circular dichroism and attenuated total internal reflection fourier transform infrared spectroscopy studies indicate that the peptides adopt ß-conformation in the superstructures both in solution and solid state. The nanostructures composed of entirely aliphatic moieties have the ability to bind to aromatic dyes such as Rhodamine 6G, Nile red and Congo red. They also bind to Thioflavin T although the structures do not resemble amyloid fibrils. The powder X-ray diffraction patterns suggest distinctive packing of the monomers. These structures are stabilized by intermolecular hydrogen bonds and hydrophobic interactions resulting in superstructures containing long distance order and were devoid of hemolytic activity.


Subject(s)
Alcohols/chemistry , Dipeptides/chemistry , Isoleucine/chemistry , Leucine/chemistry , Valine/chemistry , Water/chemistry , Circular Dichroism , Congo Red/chemistry , Dipeptides/metabolism , Dipeptides/pharmacology , Erythrocytes/cytology , Erythrocytes/drug effects , Erythrocytes/metabolism , Esters/chemistry , Hemolysis/drug effects , Humans , Hydrogen Bonding , Hydrophobic and Hydrophilic Interactions , Microscopy, Electron, Scanning , Nanostructures/chemistry , Spectroscopy, Fourier Transform Infrared , X-Ray Diffraction
14.
PLoS One ; 12(4): e0175858, 2017.
Article in English | MEDLINE | ID: mdl-28423004

ABSTRACT

Human α and ß-defensins are cationic antimicrobial peptides characterized by three disulfide bonds with a triple stranded ß-sheet motif. It is presumed that interaction with the bacterial cell surface and membrane permeabilization by defensins is an important step in the killing process. In this study, we have compared interactions of three human α-defensins HNP3, HNP4, HD5 and human ß-defensins HBD1-4 that are active against Escherichia coli, with its cell surface and inner membrane as well as negatively charged model membranes. We have also included the inactive α-defensin HD6 in the study. Among the α-defensins, HNP4, HD5 and HD6 were more effective in increasing the zeta potential as compared to HNP3. Among the ß-defensins, HBD1 was the least effective in increasing the zeta potential. The zeta potential modulation data indicate variations in the surface charge neutralizing ability of α- and ß-defensins. Comparison of E. coli inner membrane and model membrane permeabilizing abilities indicated that HD5, HD6 and HBD1 do not permeabilize membranes. Although HBD4 does not permeabilize model membranes, considerable damage to the inner membrane of E. coli is observed. Our data indicate that mammalian defensins do not kill E. coli by a simple mechanism involving membrane permeabilization though their antibacterial potencies are very similar.


Subject(s)
Cell Membrane/drug effects , Escherichia coli/drug effects , alpha-Defensins/pharmacology , beta-Defensins/pharmacology , Amino Acid Sequence , Anti-Bacterial Agents/chemistry , Anti-Bacterial Agents/pharmacology , Cell Membrane/chemistry , Cell Membrane/ultrastructure , Cell Membrane Permeability , Escherichia coli/chemistry , Escherichia coli/ultrastructure , Fluorescent Dyes/chemistry , Humans , Membranes, Artificial , Microbial Sensitivity Tests , Microscopy, Fluorescence , Organic Chemicals/chemistry , Static Electricity , Structure-Activity Relationship , Time-Lapse Imaging , alpha-Defensins/chemistry , beta-Defensins/chemistry
15.
Curr Protein Pept Sci ; 18(9): 920-938, 2017.
Article in English | MEDLINE | ID: mdl-27455966

ABSTRACT

BACKGROUND: Amyloid fibrils, which are implicated in several diseases, are highly ordered structures formed by aggregation of proteins. Intriguingly, several short peptides, some of which are unrelated to the disease-causing proteins, also aggregate to form amyloid fibrils in vitro. The aggregation behavior of these short peptides can be modulated so that they form nanostructures that are not in any way related to amyloid fibrils. These observations have led to extensive research aimed at getting insights into how peptides aggregate to form amyloids as well as non-amyloidogenic structures. METHODS: This review examines the aggregation behavior of peptides that form highly polymorphic structures including fibrils, nanotubes, nanospheres and hydrogels. The review also describes how short peptides composed of only two and three hydrophobic and aromatic amino acids can selfassemble to form nanotubes and nanospheres. RESULTS: Peptides with widely varying amino acid composition and lengths aggregate to form indistinguishable fibrils and nanostructures. The potential application of these aggregated structures in the design of novel biomaterials is reviewed and highlighted. CONCLUSION: It is evident that highly polymorphic aggregated structures of peptides can be obtained by varying conditions such as solvent of dissolution, temperatures, pH and even surfaces of deposition.


Subject(s)
Nanostructures/chemistry , Peptides/chemistry , Amino Acid Sequence , Amino Acids/chemistry , Amyloid/chemistry , Humans , Hydrophobic and Hydrophilic Interactions , Protein Aggregates , Protein Conformation
16.
Biopolymers ; 104(6): 790-803, 2015 Nov.
Article in English | MEDLINE | ID: mdl-26473431

ABSTRACT

Amyloid deposits have been found to be abundant in patients with Alzheimer's disease due to fibril formation by the Aß peptides. Peptide Aß16-22, comprising of the seven-residue segment KLVFFAE, spanning residues 16-22 of the full length Aß42 peptide, aggregates to form fibrils or other nanostructures in isolation, depending on the conditions of dissolution and incubation. In this study, we have examined the self-assembly of PAß, a tandem repeat peptide of the Aß16-22 sequence, joined by a ß-turn-inducing sequence Asn-Gly. To study the effect of various solvents on the self-association, hexafluoroisopropanol (HFIP), trifluoroethanol (TFE) and methanol were used. The peptide was also incubated in fibril-promoting conditions of 20% fluorinated alcohol-water mixtures which form dynamical solvent clusters, as well as in 20% MeOH-water mixture which does not form solvent clusters. Secondary structural studies suggest the presence of ß-structures. Electron microscopic images indicate that fibril formation occurs in a time-dependent manner, under different conditions of solvent composition. Thioflavin-T fluorescence studies confirm the presence of amyloid fibrils in the aggregates. Although the insertion of the Asn-Gly sequence has not facilitated the formation of an ideal Type I' rigid turn, the intramolecular interactions aid the formation of a flexible ß-turn conformation, with twisted ß-sheets. Interactions between the intermolecular ß-sheets result in the formation of amyloid fibrils. Organic solvents appear to play an important role in modulating self-assembly of peptide PAß during fibril formation. Studies on ß-hairpin engineered amyloidogenic peptides could lead to knowledge about suitable conditions for generating a diverse range of polymorphic structures.


Subject(s)
Amyloid beta-Peptides/chemistry , Dipeptides/chemistry , Peptide Fragments/chemistry , Circular Dichroism , Fluorescence , Microscopy, Electron, Transmission , Protein Structure, Secondary , Solvents/chemistry , Spectroscopy, Fourier Transform Infrared
17.
J Pept Sci ; 21(11): 811-8, 2015 Nov.
Article in English | MEDLINE | ID: mdl-26400692

ABSTRACT

Human α-defensin 6 (HD6), unlike other mammalian defensins, does not exhibit bactericidal activity, particularly against aerobic bacteria. Monomeric HD6 has a tertiary structure similar to other α-defensins in the crystalline state. However, the physico-chemical reasons behind the lack of antibacterial activity of HD6 are yet to be established unequivocally. In this study, we have investigated the antimicrobial activity of HD6 analogs. A linear analog of HD6, in which the distribution of arginine residues was similar to active α-defensins, shows broad-spectrum antimicrobial activity, indicating that atypical distribution of arginine residues contributes to the inactivity of HD6. Peptides spanning the N-terminal cationic segment were active against a wide range of organisms. Antimicrobial potency of these shorter analogs was further enhanced when myristic acid was conjugated at the N-terminus. Cytoplasmic localization of the analogs without fatty acylation was observed to be necessary for bacterial killing, while they exhibited fungicidal activity by permeabilizing Candida albicans membranes. Myristoylated analogs and the linear full-length arginine analog exhibited activity by permeabilizing bacterial and fungal membranes. Our study provides insights into the lack of bactericidal activity of HD6 against aerobic bacteria.


Subject(s)
Anti-Infective Agents/pharmacology , Drug Design , Peptides/pharmacology , alpha-Defensins/pharmacology , Amino Acid Sequence , Amino Acid Substitution , Anti-Infective Agents/chemical synthesis , Anti-Infective Agents/chemistry , Antifungal Agents/chemical synthesis , Antifungal Agents/chemistry , Antifungal Agents/pharmacology , Candida albicans/cytology , Candida albicans/drug effects , Candida albicans/growth & development , Candida albicans/ultrastructure , Cell Membrane Permeability/drug effects , Chemical Phenomena , Circular Dichroism , Cystine/chemistry , Gram-Negative Bacteria/cytology , Gram-Negative Bacteria/drug effects , Gram-Negative Bacteria/growth & development , Gram-Negative Bacteria/ultrastructure , Humans , Lipoylation , Membrane Potentials/drug effects , Microbial Sensitivity Tests , Microscopy, Confocal , Microscopy, Electron, Transmission , Myristic Acid/chemistry , Peptides/chemical synthesis , Peptides/chemistry , Protein Structure, Tertiary , Staphylococcus aureus/cytology , Staphylococcus aureus/drug effects , Staphylococcus aureus/growth & development , Staphylococcus aureus/ultrastructure , alpha-Defensins/chemistry
18.
PLoS One ; 10(8): e0136567, 2015.
Article in English | MEDLINE | ID: mdl-26308214

ABSTRACT

Fluorinated alcohols such as hexafluoroisopropanol (HFIP) and trifluoroethanol (TFE) have the ability to promote α-helix and ß-hairpin structure in proteins and peptides. HFIP has been used extensively to dissolve various amyloidogenic proteins and peptides including Aß, in order to ensure their monomeric status. In this paper, we have investigated the self-assembly of Aß40, Aß42, and Aß43 in aqueous mixtures of fluorinated alcohols from freshly dissolved stock solutions in HFIP. We have observed that formation of fibrillar and non-fibrillar structures are dependent on the solvent composition. Peptides form fibrils with ease when reconstituted in deionized water from freshly dissolved HFIP stocks. In aqueous mixtures of fluorinated alcohols, either predominant fibrillar structures or clustered aggregates were observed. Aqueous mixtures of 20% HFIP are more favourable for Aß fibril formation as compared to 20% TFE. When Aß40, Aß42, and Aß43 stocks in HFIP are diluted in 50% aqueous mixtures in phosphate buffer or deionized water followed by slow evaporation of HFIP, Aß peptides form fibrils in phosphate buffer and deionized water. The clustered structures could be off-pathway aggregates. Aß40, Aß42, and Aß43 showed significant α-helical content in freshly dissolved HFIP stocks. The α-helical conformational intermediate in Aß40, Aß42, and Aß43 could favour the formation of both fibrillar and non-fibrillar aggregates depending on solvent conditions and rate of α-helical to ß-sheet transition.


Subject(s)
Amyloid beta-Peptides/chemistry , Peptide Fragments/chemistry , Propanols/chemistry , Trifluoroethanol/chemistry , Circular Dichroism , Halogenation , Humans , Microscopy, Electron, Transmission , Protein Conformation , Solvents , Spectrometry, Fluorescence , Spectroscopy, Fourier Transform Infrared
19.
Peptides ; 71: 128-40, 2015 Sep.
Article in English | MEDLINE | ID: mdl-26206286

ABSTRACT

Human α-defensin 5 (HD5) exhibits broad spectrum antimicrobial activity and plays an important role in mucosal immunity of the small intestine. Although there have been several studies, the structural requirements for activity and mechanism of bacterial killing is yet to be established unequivocally. In this study, we have investigated the antimicrobial activity of HD5 and linear analogs. Cysteine deletions attenuated the antibacterial activity considerably. Candidacidal activity was affected to a lesser extent. Fatty acid conjugated linear analogs showed antimicrobial activity comparable activity to HD5. Effective surface charge neutralization of bacteria was observed for HD5 as compared to the non-fatty acylated linear analogs. Our results show that HD5 and non-fatty acylated linear analogs enter the bacterial cytoplasm without causing damage to the bacterial inner membrane. Although fatty acylated peptides exhibited antimicrobial activity comparable to HD5, their mechanism of action involved permeabilization of the Escherichia coli inner membrane. HD5 and analogs had the ability to bind plasmid DNA. HD5 had greater binding affinity to plasmid DNA as compared to the analogs. The three dimensional structure of HD5 favors greater interaction with the bacterial cell surface and also with DNA. Antibacterial activity of HD5 involves entry into bacterial cytoplasm and binding to DNA which would result in shut down of the bacterial metabolism leading to cell death. We show how a moderately active linear peptide derived from the α-defensin HD5 can be engineered to enhance antimicrobial activity almost comparable to the native peptide.


Subject(s)
Anti-Infective Agents/chemistry , Anti-Infective Agents/pharmacology , Escherichia coli/growth & development , alpha-Defensins/chemistry , alpha-Defensins/pharmacology , Acylation , Humans , Protein Structure, Secondary
20.
J Pept Sci ; 21(6): 501-11, 2015 Jun.
Article in English | MEDLINE | ID: mdl-25810238

ABSTRACT

Human ß-defensins (HBDs) are cationic antimicrobial peptides constrained by three disulfide bridges. They have diverse range of functions in the innate immune response. It is of interest to investigate whether linear analogs of defensins can be generated, which possess antimicrobial activity. In this study, we have designed linear peptides with potent antimicrobial activity from an inactive peptide spanning the N-terminus of HBD4. Our results show that l-arginine to d-arginine substitution imparts considerable antimicrobial activity against both bacteria and Candida albicans. Increase in hydrophobicity by fatty acylation of the peptides with myristic acid further enhances their potency. In the presence of high concentrations of salt, antimicrobial activity of the myristoylated peptide with l-arginine is attenuated relatively to a lesser extent as compared with the linear active peptide with d-arginine. Substitution of cysteine with the hydrophobic helix-promoting amino acid α-aminoisobutyric acid favors candidacidal activity but not antibacterial activity. The mechanism of killing by d-arginine substituted unacylated analog involves transient interaction with the bacterial membrane followed by translocation into the cytoplasm without membrane permeabilization. Accumulation of peptides in the cytoplasm can affect various cellular processes that lead to cell death. However, the peptide causes membrane permeabilization in case of C. albicans. Myristoylation results in greater interaction of the peptide chain with the microbial cell surface and causes membrane permeabilization. Results described in the study demonstrate that it is possible to generate highly active linear analogs of defensins by selective introduction of d-amino acids and fatty acids, which could be attractive candidates for development as therapeutic agents.


Subject(s)
Anti-Infective Agents/pharmacology , Biomedical Engineering , Gram-Negative Bacteria/drug effects , Peptides/pharmacology , beta-Defensins/chemistry , Aminoisobutyric Acids/chemistry , Aminoisobutyric Acids/metabolism , Anti-Infective Agents/chemistry , Arginine/chemistry , Arginine/metabolism , Candida albicans/drug effects , Humans , Myristic Acid/chemistry , Myristic Acid/metabolism , Peptides/chemistry
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