Computer-aided evolution and experimental validation of a novel L-asparaginase from Bacillus sp. SD3 toward enhanced thermal stability.

L-asparaginase, a key biocatalyst for therapeutic and industrial applications, is often limited by poor thermal stability. A novel L-asparaginase gene from Bacillus sp. SD3 was identified, cloned, expressed, and characterized.

Thymol inhibits ergosterol biosynthesis in Nakaseomyces glabratus, but differently from azole antifungals.

Introduction: Nakaseomyces glabratus is considered a high priority of attention according to WHO, and also is an important yeast species due to its high rate of intrinsic/acquired resistance against fluconazole. This study aimed at the possible mechanisms of action of thymol, as the promising new antifungal agent, in N. glabratus.

Repurposing naproxen as a potential nucleocapsid antagonist of beta-coronaviruses: targeting a conserved protein in the search for a broad-spectrum treatment option.

Ongoing mutations in the coronavirus family, especially beta-coronaviruses, raise new concerns about the possibility of new unexpected outbreaks. Therefore, it is crucial to explore new alternative treatments to reduce the impact of potential future strains until new vaccines can be developed. A promising approach to combat the virus is to target its conserved parts such as the nucleocapsid, especially repurposing of existing drugs.

Designing novel peptides for detecting the Omicron variant, specifying SARS-CoV-2, and simultaneously screening coronavirus infections.

In this study a candidate diagnostic peptide-based tool was designed in four stages including diagnosis of coronavirus diseases, simultaneously identifying of COVID-19 and SARS from other members of this family, specific identification of SARS-CoV2, and diagnosis of COVID-19 Omicron. Designed candidate peptides consist of four immunodominant peptides from the proteins of the SARS-CoV-2 spike (S) and membrane (M). The tertiary structure of each peptide was predicted.

Design and assessment of novel synthetic peptides to inhibit quorum sensing-dependent biofilm formation in .

is one of the most common biofilm-producing bacteria, often leading to long-term and chronic infections. The LasR regulator protein acts as the central regulator of the quorum sensing (QS) system and coordinates the expression of some virulence and biofilm genes. In this study, novel peptides (WSF, FASK, YDVD) were designed for binding to the domain of the transcriptional activator of the LasR protein and interfere with LasR in the QS system of .

Enhancing thermostabilization of a newly discovered α-amylase from Bacillus cereus GL96 by combining computer-aided directed evolution and site-directed mutagenesis.

This study has described the characterization of a new a-amylase from the recently isolated Bacillus cereus GL96. Subsequently, an in-silico approach was taken into account to redesign the enzyme to meet higher thermal stability. Finally, the engineered enzyme was constructed experimentally using side-directed mutagenesis (SDM) and characterized accordingly.

Prediction and interpretation of rare missense variant in OTOG associated with hearing loss.

OTOG encodes for otogelin, a component of the tectorial membrane. This gene is associated with nonprogressive mild-to-moderate hearing loss. However, no studies have yet identified the association between OTOG variation and severe-to-profound hearing loss.

Multi-stage screening to predict the specific anticancer activity of Ni(II) mixed-ligand complex on gastric cancer cells; biological activity, FTIR spectrum, DNA binding behavior and simulation studies.

The anticancer activity of a transition metal complex with [Ni(L)L]HO (where L and L were acetylacetonato (acac) and 2-aminopyridine (2-ampy), respectively) was evaluated in MKN45 cell line. Methyl thiazolyl tetrazolium (MTT) assay was performed to assess the antitumor capacity of the Ni(II) complex against gastric cancer cell line MKN45. The complexexhibited high in vitro antitumor activity against MKN45 cells with ICvalues of 1.

Identification of new potential cyclooxygenase-2 inhibitors: insight from high throughput virtual screening of 18 million compounds combined with molecular dynamic simulation and quantum mechanics.

The cyclooxygenase isoenzymes (COX-1 and COX-2) have a critical role in inflammation, fever, and pain. In contrary to COX-1, COX-2 is specifically expressed in inflamed tissues. Because of the subtle difference between both enzyme active sites, targeting COX-2 represents an efficient strategy for the development of novel inhibitors against inflammation with fewer side effects.

In-vitro and in-silico investigation of protective mechanisms of crocin against E46K α-synuclein amyloid formation.

α-Synuclein is a presynaptic neuronal protein that is abundant in the human brain and is linked genetically and neuropathologically to Parkinson's disease (PD). The E46K mutation of the α-synuclein gene has been linked to autosomal dominant early-onset of PD. Crocin is a carotenoid chemical compound of saffron that has been shown antioxidant and neural protective activity.

Novel Point Mutations in and Genes Associated with Itraconazole and Posaconazole Resistance in Isolates.

is a common environmental species known to cause occupational allergic disease in grain handlers. We have recently observed azole-resistant isolates of this fungus as a cause of onychomycosis. To further characterize the cause of resistance, the genes encoding 14 α-sterol demethylase enzyme ( and ) were characterized and analyzed in 9 ITC-susceptible isolates and 6 isolates with high minimum inhibitory concentrations (MICs) of clinical (nail and sputum) and environmental strains.

Identification of new promising plant-based lead compounds for inhibition of prokaryotic replicative DNA polymerases: combination of and studies.

Emerging widespread bacterial resistance to current antibiotics with traditional targets is one of the major global concerns. Therefore, so many investigations are exploring the potential of other druggable macromolecules of bacteria such as replication machinery components that are not addressed by previous antibiotics. DNA polymerase is the major part of this machine.

Molecular Modeling and Structural Stability of Wild-Type and Mutant CYP51 from Leishmania major: In Vitro and In Silico Analysis of a Laboratory Strain.

Cutaneous leishmaniasis is a neglected tropical disease and a major public health in the most countries. is the most common cause of cutaneous leishmaniasis. In the parasites, sterol 14α-demethylase (CYP51), which is involved in the biosynthesis of sterols, has been identified as an attractive target for development of new therapeutic agents.

A thermostable alkaliphilic protein-disulfide isomerase from Bacillus subtilis DR8806: cloning, expression, biochemical characterization and molecular dynamics simulation.

Disulfide bonds are among the most important factors related to correct folding of the proteins. Protein disulfide isomerase (PDI) is the enzyme responsible for the correct formation and isomerization of these bonds. It is rarely studied so far and none of them showed industrial properties.

The potential inhibitory effect of β-casein on the aggregation and deposition of Aβ fibrils in Alzheimer's disease: insight from in-vitro and in-silico studies.

Aβ and Aβ have been shown to be the main components of the amyloid plaques found in the extracellular environment of neurons in Alzheimer's disease. β-Casein, a milk protein, has been shown to display a remarkable chaperone ability in preventing the aggregation of proteins. In this study, the ability of β-casein to suppress the amyloid fibril formation of Aβ has been examined through in vitro studies and molecular docking simulation.

Functional and Key Gene Expression Analyses of Chicken Monocyte-derived Dendritic Cells with Recombinant Interleukin 4.

The central role of dendritic cells (DCs) as bridging innate and adaptive immunity leads to the expanding use of these cells in the poultry vaccine studies. The most effective way to produce enough DCs is monocyte transformation by combined induction of interleukin-4 (IL-4) and granulocyte-macrophage colony-stimulating factor (GM-CSF). In this study full length of chicken IL-4 (cIL-4) cDNA was cloned, characterized and expressed in Escherichia coli.

In vitro responses of chicken macrophage-like monocytes following exposure to pathogenic and non-pathogenic E. coli ghosts loaded with a rational design of conserved genetic materials of influenza and Newcastle disease viruses.

Avian influenza virus (AIV) and Newcastle disease virus (NDV) are two important viral diseases in the poultry industry. Therefore, new disease-fighting strategies, especially effective genetic vaccination, are in high demand. Bacterial Ghost (BG) is a promising platform for delivering genetic materials to macrophages, cells that are among the first to encounter these viruses.

An ice nucleation protein from Fusarium acuminatum: cloning, expression, biochemical characterization and computational modeling.

Ice nucleation proteins (INP) are a major cause of frost damage in plants and crops. Here, an INP gene from Fusarium acuminatum was optimized, synthesized, expressed in E.coli and subsequently purified and characterized.

An extremely thermotolerant, alkaliphilic subtilisin-like protease from hyperthermophilic Bacillus sp. MLA64.

The current work is a report on a new extremely thermostable protease from newly isolated hyperthermophilic Bacillus sp. MLA64. The protease was purified with a 16.

A novel thermostable, acidophilic alpha-amylase from a new thermophilic "Bacillus sp. Ferdowsicous" isolated from Ferdows hot mineral spring in Iran: Purification and biochemical characterization.

This paper describes the purification and characterization of a novel acidophile alpha-amylase from newly isolated Bacillus sp. Ferdowsicous. The enzyme displayed a molecular weight of 53 kDa and it was stable over a range of pH from 3.