A proteomic perspective and involvement of cytokines in SARS-CoV-2 infection.

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.

Down regulation of defensin genes during SARS-CoV-2 infection.

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.

In silico folding of hydrophobic peptides that form β-hairpin structures in solution.

Peptides designed with residues that have a high propensity to occur in β-turns form β-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 β-hairpin structures facilitated by β-turns, in the crystalline state and in solution, by molecular dynamics simulations (MDS).

Gramicidin S and melittin: potential anti-viral therapeutic peptides to treat SARS-CoV-2 infection.

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.

Mass Spectral Analysis of Synthetic Peptides: Implications in Proteomics.

Sequence determination of peptides is a crucial step in mass spectrometry-based proteomics. Peptide sequences are determined either by database search or by sequencing using tandem mass spectrometry. Determination of all the theoretical expected peptide fragments and eliminating false discoveries remains a challenge in proteomics.

Lipopolysaccharide Modulates Biological Activities of Human-β-Defensin Analogues but Not Non-Ribosomally Synthesized Peptides.

Human-β-defensins (HBD1-3) are antibacterial peptides containing three disulphide bonds. In the present study, the effect of 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.

Water-Alcohol Bigels from Fatty Acylated Dipeptides.

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.

Limpid hydrogels from β-turn motif-connected tandem repeats of Aβ.

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.

Effects of increasing hydrophobicity by N-terminal myristoylation on the antibacterial and hemolytic activities of the C-terminal cationic segments of human-β-defensins 1-3.

Analogs of the cationic C-terminal segments of human-β-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.

Self-assembly of t-butyloxycarbonyl protected dipeptide methyl esters composed of leucine, isoleucine, and valine into highly organized structures from alcohol and aqueous alcohol mixtures.

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.

Variations in the interaction of human defensins with Escherichia coli: Possible implications in bacterial killing.

Human α and β-defensins are cationic antimicrobial peptides characterized by three disulfide bonds with a triple stranded β-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 β-defensins HBD1-4 that are active against Escherichia coli, with its cell surface and inner membrane as well as negatively charged model membranes.

Formation of Nanostructures by Peptides.

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.

Self-assembly of a peptide with a tandem repeat of the Aβ16-22 sequence linked by a β turn-promoting dipeptide sequence.

Amyloid deposits have been found to be abundant in patients with Alzheimer's disease due to fibril formation by the Aβ peptides. Peptide Aβ16-22, comprising of the seven-residue segment KLVFFAE, spanning residues 16-22 of the full length Aβ42 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 PAβ, a tandem repeat peptide of the Aβ16-22 sequence, joined by a β-turn-inducing sequence Asn-Gly.

Antimicrobial activity of human α-defensin 6 analogs: insights into the physico-chemical reasons behind weak bactericidal activity of HD6 in vitro.

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.

Self-Assembly of Aβ40, Aβ42 and Aβ43 Peptides in Aqueous Mixtures of Fluorinated Alcohols.

Fluorinated alcohols such as hexafluoroisopropanol (HFIP) and trifluoroethanol (TFE) have the ability to promote α-helix and β-hairpin structure in proteins and peptides. HFIP has been used extensively to dissolve various amyloidogenic proteins and peptides including Aβ, in order to ensure their monomeric status. In this paper, we have investigated the self-assembly of Aβ40, Aβ42, and Aβ43 in aqueous mixtures of fluorinated alcohols from freshly dissolved stock solutions in HFIP.

Antimicrobial activity of human α-defensin 5 and its linear analogs: N-terminal fatty acylation results in enhanced antimicrobial activity of the linear analogs.

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.

Probing the role of aromatic residues in the self-assembly of Aβ(16-22) in fluorinated alcohols and their aqueous mixtures.

The Aβ(16-22) sequence KLVFFAE spans the hydrophobic core of the Aβ peptide and plays an important role in its self-assembly. Apart from forming amyloid fibrils, Aβ(16-22) can self-associate into highly ordered nanotubes and ribbon-like structures depending on the composition of solvent used for dissolution. The Aβ(16-22) sequence which has FF at the 19th and 20th positions would be a good model to investigate peptide self-assembly in the context of aromatic interactions.

Engineering of a linear inactive analog of human β-defensin 4 to generate peptides with potent antimicrobial activity.

Human β-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.

N-Terminal fatty acylation of peptides spanning the cationic C-terminal segment of bovine β-defensin-2 results in salt-resistant antibacterial activity.

Peptides spanning the C-terminal segment of bovine-β-defensin-2 (BNBD-2) rich in cationic amino acids, show antimicrobial activity. However, they exhibit considerably reduced activity at physiological concentration of NaCl. In the present study, we have investigated whether N-terminal acylation (acetylation and palmitoylation) of these peptides would result in improved antimicrobial activity.

Human β-defensin 4 with non-native disulfide bridges exhibit antimicrobial activity.

Human defensins play multiple roles in innate immunity including direct antimicrobial killing and immunomodulatory activity. They have three disulfide bridges which contribute to the stability of three anti-parallel β-strands. The exact role of disulfide bridges and canonical β-structure in the antimicrobial action is not yet fully understood.

A hybrid cationic peptide composed of human β-defensin-1 and humanized θ-defensin sequences exhibits salt-resistant antimicrobial activity.

We have designed a hybrid peptide by combining sequences of human β-defensin-1 (HBD-1) and θ-defensin, in an attempt to generate a molecule that combines the diversity in structure and biological activity of two different peptides to yield a promising therapeutic candidate. HBD-1 was chosen as it is a natural defensin of humans that is constitutively expressed, but its antibacterial activity is considerably impaired by elevated ionic strength. θ-Defensins are expressed in human bone marrow as a pseudogene and are homologous to rhesus monkey circular minidefensins.

Peptide self-assembly: from toxins to amyloid fibrils and nanotubes.

The process of self-assembly is universal and lies at the heart of biological structures and function. Peptide aggregation, while considered a nuisance in peptide chemistry, soon gained interest with the discovery of pore-forming peptide toxins and had been an area of intense research during last century and even to date. This has also resulted in the increasing use of the more respectable term peptide self-assembly.

Covalently attached fatty acyl chains alter the aggregation behavior of an amyloidogenic peptide derived from human β(2)-microglobulin.

Aggregation of a polypeptide chain into highly ordered amyloid aggregates is a complex process. Various factors, both extrinsic and intrinsic to the polypeptide chain, have been shown to perturb this process, leading to a drastic change in the amyloidogenic behavior, which is reflected in the polymorphism of amyloid aggregates at various levels of self-assembly. In this paper, we have investigated the ability of covalently linked long-chain fatty acids in modulating the self-assembly of an aromatic amino acid-rich highly amyloidogenic sequence derived from the amino acid region 59-71 of human β2-microglobulin by thioflavin T (ThT) fluorescence microscopy, circular dichroism, and fluorescence spectroscopy.