Characterization of dye-decolorizing peroxidase from Bacillus subtilis

Molecular basis of H2O2/O2.-/.OH discrimination during electrochemical activation of DyP peroxidases: The critical role of the distal residues

Here, we show that the replacement of the distal residues Asp and/or Arg of the DyP peroxidases from Bacillus subtilis and Pseudomonas putida results in functional enzymes, albeit with spectroscopically perturbed active sites. All the enzymes can be activated either by the addition of exogenous H2O2 or by in situ electrochemical generation of the reactive oxygen species (ROS) •OH, O2•- and H2O2. The latter method leads to broader and upshifted pH-activity profiles. Both WT enzymes exhibit a differential predominance of ROS involved in their electrochemical activation, which follows the order •OH > O2•- > H2O2 for BsDyP and O2•- > H2O2 > •OH for PpDyP. This ROS selectivity is preserved in mutants with unperturbed sites but is blurred out for distorted sites. The underlying molecular basis of the selectivity mechanisms is analysed through molecular dynamics simulations, which reveal distorted hydrogen bonding networks and higher throughput of the access tunnels in the variants exhibiting no selectivity. The electrochemical activation method provides superior performance for protein variants with a high prevalence of the alternative •OH and O2•- species. These results constitute a promising advance towards engineering DyPs for electrocatalytic applications.

Robust peroxidase from Bacillus mojavensis TH309: Immobilization on walnut shell hydrochar and evaluation of its potential in dye decolorization

Peroxidases have received considerable attention as a cost-effective and environmentally friendly catalyst for bioremediation. Their rapid activity loss under harsh environmental conditions and inability to be used repetitively limit their exploitation in real-world wastewater treatment. First, a peroxidase was produced extracellularly by Bacillus mojavensis TH309 and purified 8.12-fold with a final yield of 47.10 % using Sephadex G-100 superfine resin. The pure peroxidase (BmPer) possessed a relatively low molecular weight of ∼21 kDa and was active against L-DOPA on acrylamide gel after electrophoresis. BmPer was immobilized by adsorption functionalized walnut shell hydrochar (WsH) with 61.99 ± 1.34 % efficiency and 37.07 ± 4.16 % activity loss. BmPer and its immobilized form (WsH-BmPer) exhibited maximum activity at 50 °C and pH 9. WsH-BmPer exhibited 3.23-, 2.37-, 1.65-, and 2.25-fold longer half-life than BmPer at 50, 60, 70, and 80 °C, respectively. Immobilization significantly enhanced the stability of the enzyme under acidic conditions. BmPer and WsH-BmPer showed maximal activity in the presence of 1 % salt and retained more than 85 % of their activity even after pre-incubation with 2.5 M salt for 60 min at 50 °C. Their catalytic efficiency was significantly stimulated by pre-incubation with Triton X-100 (1 mM), Tween20 (1 mM), and Mg2+ (1 and 10 mM). Immobilization strongly reduced the loss of activity caused by inhibitors including Ba2+, Hg2+, and Cu2+. Moreover, both forms of the enzyme were compatible with solvents. The Michaelis constant (Km) values of BmPer and WsH-BmPer were 0.88 and 2.66 mM for 2,4 DCP, respectively. WsH-BmPer peroxidase maintained about 82 % and 85 % of its activity when stored at 4 °C for 30 days and reused for up to 10 cycles, respectively. Furthermore, it decolorized Cibacron red (CR), Poly R-478 (PR), Remazol Brilliant Blue R (RBBR), and Methyl red (MR) dyes by 60.13 %, 91.34 %, 86.41 %, and 50.51 % within 60 min, respectively.

Deciphering the ecological impact of azo dye pollution through microbial community analysis in water-sediment microcosms

The uncontrolled release of untreated dyeing wastewater into aquatic ecosystems poses global environmental risks. It alters native microbial communities and associated ecological processes, often going unnoticed. Therefore, the influence of acid orange 7 dye (AO7) contamination on the natural microbial community was investigated using a water-sediment microcosm. Compared to sterile microcosms, complete dye decolourization in natural microcosms showed microbial communities' significance in combating xenobiotic contamination. Proteobacteria dominated the water community, whereas Firmicutes dominated the sediment. AO7 exposure induced notable shifts in the structural composition of the bacterial community in both water and sediment. Niveispirillum exhibited a marked decrease, and Pseudomonas demonstrated a notable increase. The - 9.0 log2FC in Niveispirillum, a nitrogen-fixing bacterium, from 24.4% in the control to 0.1% post-treatment, may disrupt nutrient balance, plant growth, and ecosystem productivity. Conversely, elevated levels of Pseudomonas sp. resulting from azo dye exposure demonstrate its ability to tolerate and bioremediate organic pollutants, highlighting its resilience. Functional profiling via KEGG pathway analysis revealed differential expression patterns under AO7 stress. Specifically, valine, leucine, and isoleucine degradation pathways in water decreased by 52.2%, and cysteine and methionine metabolism ceased expression entirely, indicating reduced protein metabolism and nutrient bioavailability under dye exposure. Furthermore, in sediment, glutathione metabolism ceased, indicating increased oxidative stress following AO7 infusion. However, C5-branched dibasic acid metabolism and limonene and pinene degradation were uniquely expressed in sediment. Decreased methane metabolism exacerbates the effects of global warming on aquatic ecosystems. Further, ceased-butanoate metabolic pathways reflect the textile dye wastewater-induced adverse impact on ecological processes, such as organic matter decomposition, energy flow, nutrient cycling, and community dynamics that help maintain self-purification and ecological balance in river ecosystems. These findings underscore the critical need for more comprehensive environmental monitoring and management strategies to mitigate ecological risks posed by textile dyes in aquatic ecosystems, which remain unnoticed.

Metagenomic-based discovery and comparison of the lignin degrading potential of microbiomes in aquatic and terrestrial ecosystems via the LCdb database

Lignin, as an abundant organic carbon, plays a vital role in the global carbon cycle. However, our understanding of the global lignin-degrading microbiome remains elusive. The greatest barrier has been absence of a comprehensive and accurate functional gene database. Here, we first developed a curated functional gene database (LCdb) for metagenomic profiling of lignin degrading microbial consortia. Via the LCdb, we draw a clear picture describing the global biogeography of communities with lignin-degrading potential. They exhibit clear niche differentiation at the levels of taxonomy and functional traits. The terrestrial microbiomes showed the highest diversity, yet the lowest correlations. In particular, there were few correlations between genes involved in aerobic and anaerobic degradation pathways, showing a clear functional redundancy property. In contrast, enhanced correlations, especially closer inter-connections between anaerobic and aerobic groups, were observed in aquatic consortia in response to the lower diversity. Specifically, dypB and dypA, are widespread on Earth, indicating their essential roles in lignin depolymerization. Estuarine and marine consortia featured the laccase and mnsod genes, respectively. Notably, the roles of archaea in lignin degradation were revealed in marine ecosystems. Environmental factors strongly influenced functional traits, but weakly shaped taxonomic groups. Null mode analysis further verified that composition of functional traits was deterministic, while taxonomic composition was highly stochastic, demonstrating that the environment selects functional genes rather than taxonomic groups. Our study not only develops a useful tool to study lignin degrading microbial communities via metagenome sequencing but also advances our understanding of ecological traits of these global microbiomes.

Anti-quorum Sensing and Anti-biofilm Effect of Nocardiopsis synnemataformans RMN 4 (MN061002) Compound 2,6-Di-tert-butyl, 1,4-Benzoquinone Against Biofilm-Producing Bacteria

In this study, the anti-biofilm compound of 2,6-Di-tert-butyl, 1,4-benzoquinone was purified from Nocardiopsis synnemataformans (N. synnemataformans) RMN 4 (MN061002). To confirm the compound, various spectroscopy analyses were done including ultraviolet (UV) spectrometer, Fourier transform infrared spectroscopy (FTIR), analytical high-performance liquid chromatography (HPLC), preparative HPLC, gas chromatography-mass spectroscopy (GC-MS), liquid chromatography-mass spectroscopy (LC-MS), and 2D nuclear magnetic resonance (NMR). Furthermore, the purified compound was shown 94% inhibition against biofilm-producing Proteus mirabilis (P. mirabilis) (MN396686) at 70 µg/mL concentrations. Furthermore, the metabolic activity, exopolysaccharide damage, and hydrophobicity degradation results of identified compound exhibited excellent inhibition at 100 µg/mL concentration. Furthermore, the confocal laser scanning electron microscope (CLSM) and scanning electron microscope (SEM) results were shown with intracellular damages and architectural changes in bacteria. Consecutively, the in vivo toxicity effect of the compound against Artemia franciscana (A. franciscana) was shown to have a low mortality rate at 100 µg/mL. Finally, the molecular docking interaction between the quorum sensing (QS) genes and identified compound clearly suggested that the identified compound 2,6-Di-tert-butyl, 1,4-benzoquinone has anti-quorum sensing and anti-biofilm activities against P. mirabilis (MN396686).

Characterization of Amycolatopsis 75iv2 dye-decolorizing peroxidase on O-glycosides

Dye-decolorizing peroxidases are heme peroxidases with a broad range of substrate specificity. Their physiological function is still largely unknown, but a role in the depolymerization of plant cell wall polymers has been widely proposed. Here, a new expression system for bacterial dye-decolorizing peroxidases as well as the activity with previously unexplored plant molecules are reported. The dye-decolorizing peroxidase from Amycolatopsis 75iv2 (DyP2) was heterologously produced in the Gram-positive bacterium Streptomyces lividans TK24 in both intracellular and extracellular forms without external heme supplementation. The enzyme was tested on a series of O-glycosides, which are plant secondary metabolites with a phenyl glycosidic linkage. O-glycosides are of great interest, both for studying the compounds themselves and as potential models for studying specific lignin-carbohydrate complexes. The primary DyP reaction products of salicin, arbutin, fraxin, naringin, rutin, and gossypin were oxidatively coupled oligomers. A cleavage of the glycone moiety upon radical polymerization was observed when using arbutin, fraxin, rutin, and gossypin as substrates. The amount of released glucose from arbutin and fraxin reached 23% and 3% of the total substrate, respectively. The proposed mechanism suggests a destabilization of the ether linkage due to the localization of the radical in the para position. In addition, DyP2 was tested on complex lignocellulosic materials such as wheat straw, spruce, willow, and purified water-soluble lignin fractions, but no remarkable changes in the carbohydrate profile were observed, despite obvious oxidative activity. The exact action of DyP2 on such lignin-carbohydrate complexes therefore remains elusive.

IMPORTANCE

Peroxidases require correct incorporation of the heme cofactor for activity. Heterologous overproduction of peroxidases often results in an inactive enzyme due to insufficient heme synthesis by the host organism. Therefore, peroxidases are incubated with excess heme during or after purification to reconstitute activity. S. lividans as a production host can produce fully active peroxidases both intracellularly and extracellularly without the need for heme supplementation. This reduces the number of downstream processing steps and is beneficial for more sustainable production of industrially relevant enzymes. Moreover, this research has extended the scope of dye-decolorizing peroxidase applications by studying naturally relevant plant secondary metabolites and analyzing the formed products. A previously overlooked artifact of radical polymerization leading to the release of the glycosyl moiety was revealed, shedding light on the mechanism of DyP peroxidases. The key aspect is the continuous addition, rather than the more common approach of a single addition, of the cosubstrate, hydrogen peroxide. This continuous addition allows the peroxidase to complete a high number of turnovers without self-oxidation.

Engineering A-type Dye-Decolorizing Peroxidases by Modification of a Conserved Glutamate Residue

Dye-decolorizing peroxidases (DyPs) are recently identified microbial enzymes that have been used in several Biotechnology applications from wastewater treatment to lignin valorization. However, their properties and mechanism of action still have many open questions. Their heme-containing active site is buried by three conserved flexible loops with a putative role in modulating substrate access and enzyme catalysis. Here, we investigated the role of a conserved glutamate residue in stabilizing interactions in loop 2 of A-type DyPs. First, we did site saturation mutagenesis of this residue, replacing it with all possible amino acids in bacterial DyPs from Bacillus subtilis (BsDyP) and from Kitasatospora aureofaciens (KaDyP1), the latter being characterized here for the first time. We screened the resulting libraries of variants for activity towards ABTS and identified variants with increased catalytic efficiency. The selected variants were purified and characterized for activity and stability. We furthermore used Molecular Dynamics simulations to rationalize the increased catalytic efficiency and found that the main reason is the electron channeling becoming easier from surface-exposed tryptophans. Based on our findings, we also propose that this glutamate could work as a pH switch in the wild-type enzyme, preventing intracellular damage.

Iso-mukaadial acetate and ursolic acid acetate bind to Plasmodium Falciparum heat shock protein 70: towards targeting parasite protein folding pathway

Plasmodium falciparum is the most lethal malaria parasite. P. falciparum Hsp70 (PfHsp70) is an essential molecular chaperone (facilitates protein folding) and is deemed a prospective antimalarial drug target. The present study investigates the binding capabilities of select plant derivatives, iso-mukaadial acetate (IMA) and ursolic acid acetate (UAA), against P. falciparum using an in silico docking approach. The interaction between the ligands and PfHsp70 was evaluated using plasmon resonance (SPR) analysis. Molecular docking, binding free energy analysis and molecular dynamics simulations were conducted towards understanding the mechanisms by which the compounds bind to PfHsp70. The molecular docking results revealed ligand flexibilities, conformations and positions of key amino acid residues and protein-ligand interactions as crucial factors accounting for selective inhibition of Hsp70. The simulation results also suggest protein-ligand van der Waals forces as the driving force guiding the interaction of these compounds with PfHsp70. Of the two compounds, UAA and IMA bound to PfHsp70 within the micromolar range based on surface plasmon resonance (SPR) based binding assay. Our findings pave way for future rational design of new selective compounds targeting PfHsp70.

Biodegradation of malachite green by Pleurotus eryngii: a study on decolorization, mechanism, toxicity, and enzyme

The purpose of this study was to investigate the biodegradation of malachite green (MG) by Pleurotus eryngii via decolorization. This study also explored the possible mechanisms and toxicity. The results indicated that this fungus exhibited strong decolorizing potential. MG degradation based on UPLC-TOF-Triple-MS analysis revealed the formation of intermediates such as 4-(dimethylamino)benzophenone, 4-(methylamino)benzophenone, and 4-(dimethylamino)phenol. Furthermore, a significant reduction in the toxicity of the degradation products was observed using the zebrafish animal model. A newly discovered dye-decolorizing peroxidase (DyP-PE) from P. eryngii was amplified, cloned, and expressed. The purified 56.4 kDa DyP-PE strongly decolorized MG, suggesting potentially application in the bioremediation of MG pollution. Thus, the DyP-PE derived from P. eryngii may contribute to the degradation of MG.

pH-dependent and whole-cell catalytic decolorization of dyes using recombinant dye-decolorizing peroxidase from Rhodococcus jostii

Dyes in wastewater have adverse effects on the environment and human health. Dye-decolorizing peroxidase (DyP) is a promising biocatalyst to dyes degradation, but the decolorization rates varied greatly which influencing factors and mechanisms remain to be fully disclosed. To explore an effective decolorizing approach, we have studied a DyP from Rhodococcus jostii (RhDyPB) which was overexpressed in Escherichia coli to decolorize four kinds of dyes, Reactive blue 19, Eosin Y, Indigo carmine, and Malachite green. We found the decolorization rates of the dyes by purified RhDyPB were all pH-dependent and the highest one was 94.4% of Malachite green at pH 6.0. ESI-MS analysis of intermediates in the decolorization process of Reactive blue 19 proved the degradation was due to peroxidase catalysis. Molecular docking predicated the interaction of RhDyPB with dyes, and a radical transfer reaction. In addition, we performed decolorization of dyes with whole E. coli cell with and without expressing RhDyPB. It was found that decolorization of dyes by E. coli cell was due to both cell absorption and degradation, and RhDyPB expression improved the degradation rates towards Reactive blue 19, Indigo carmine and Malachite green. The effective decolorization of Malachite green and the successful application of whole DyP-overexpressed cells in dye decolorization is conducive to the bioremediation of dye-containing wastewaters by DyPs.

Dye-Decolorizing Peroxidase of Streptomyces coelicolor (ScDyPB) Exists as a Dynamic Mixture of Kinetically Different Oligomers

Dye-decolorizing peroxidases (DyPs) are heme-dependent enzymes that catalyze the oxidation of various substrates including environmental pollutants such as azo dyes and also lignin. DyPs often display complex non-Michaelis-Menten kinetics with substrate inhibition or positive cooperativity. Here, we performed in-depth kinetic characterization of the DyP of the bacterium Streptomyces coelicolor (ScDyPB). The activity of ScDyPB was found to be dependent on its concentration in the working stock used to initiate the reactions as well as on the pH of the working stock. Furthermore, the above-listed conditions had different effects on the oxidation of 2,2'-azino-di(3-ethyl-benzothiazoline-6-sulfonic acid) (ABTS) and methylhydroquinone, suggesting that different mechanisms are used in the oxidation of these substrates. The kinetics of the oxidation of ABTS were best described by the model whereby ScDyPB exists as a mixture of two kinetically different enzyme forms. Both forms obey the ping-pong kinetic mechanism, but one form is substrate-inhibited by the ABTS, whereas the other is not. Gel filtration chromatography and dynamic light scattering analyses revealed that ScDyPB exists as a complex mixture of molecules with different sizes. We propose that ScDyPB populations with low and high degrees of oligomerization have different kinetic properties. Such enzyme oligomerization-dependent modulation of the kinetic properties adds further dimension to the complexity of the kinetics of DyPs but also suggests novel possibilities for the regulation of their catalytic activity.

Induction of apoptotic cell death of cholangiocarcinoma cells by tiliacorinine from Tiliacora triandra: A mechanistic insight

BACKGROUND

Cholangiocarcinoma (CCA) exhibits poor response to the present chemotherapeutic agents and frequently develops drug resistance. Finding novel anticancer drugs might enhance patient outcomes. Tiliacorinine, a bisbenzylisoquinoline alkaloid from the Thai medicinal plant Tiliacora triandra, effectively induced apoptosis of human CCA cell lines and inhibited tumor growth in mice. Here, we elucidate further the molecular mechanisms underlining the cytotoxicity of tiliacorinine and its implication in overcoming gemcitabine-resistance of CCA cells.

METHODS

Cytotoxicity of tiliacorinine against CCA cell lines was assessed using MTT assay. The molecular signaling was determined using Western blot analysis. Molecular docking simulations were applied to predict the binding affinity and orientation of tiliacorinine to the possible binding site(s) of the target proteins.

RESULTS

Tiliacorinine induced apoptotic cell death of CCA cells in a dose- and time-dependent manner. Tiliacorinine significantly suppressed the expression of anti-apoptotic proteins, Bcl-xL and XIAP; activated apoptotic machinery proteins, caspase-3, caspase-9, and PARP; and decreased the levels of pAkt and pSTAT3. EGF/EGFR activation model and molecular docking simulations revealed EGFR, Akt, and STAT3 as potent targets of tiliacorinine. Molecular docking simulations indicated a strong binding affinity of tiliacorinine to the ATP-binding pockets of EGFR, PI3K, Akt, JAK2, and SH2 domain of STAT3. Tiliacorinine could synergize with gemcitabine and restore the cytotoxicity of gemcitabine against gemcitabine-resistant CCA cells.

CONCLUSION

Tiliacorinine effectively induced apoptosis via binding and blocking the actions of EGFR, Akt, and STAT3.

GENERAL SIGNIFICANCE

Tiliacorinine is a novel multi-kinase inhibitor and possibly a potent anti-cancer agent, in cancers with high activation of EGFR.

Potential inhibitors of FemC to combat Staphylococcus aureus: virtual screening, molecular docking, dynamics simulation, and MM-PBSA analysis

FemC is a methicillin resistance factor involved in the alterations of peptidoglycan and glutamine synthesis in Staphylococcus aureus. To identify the potent antibacterial agents, antibacterial molecules were screened against the predicted and validated FemC model. Based on docking scores, presence of essential interactions with active site residues of FemC, pharmacokinetic, and ADMET properties, six candidates were shortlisted and subjected to molecular dynamics to evaluate the stability of FemC-ligand complexes. Further, per residue decomposition analysis and Molecular Mechanics/Poisson-Boltzmann Surface Area (MMPBSA) analysis confirmed that S15, M16, S17, R31, R43, Q47, K48 and R49 of FemC played a vital role in the formation of lower energy stable FemC-inhibitor(s) complexes. Therefore, in the present study, the reported six molecules (Z317461228, Z92241701, Z30923155, Z30202349, Z2609517102 and Z92470167) may pave the path to design the scaffold of novel potent antimicrobials against S. aureus.Communicated by Ramaswamy H. Sarma.

Promising antibacterials for LLM of Staphylococcus aureus using virtual screening, molecular docking, dynamics, and MMPBSA

In S. aureus, lipophilic membrane (LLM) protein is a methicillin resistance factor and is an essential role in peptidoglycan metabolism. The virtual screening of antibacterial molecules against the model of LLM was performed to identify the potent antibacterial molecules. Molecular docking results of pharmacokinetic filtered molecules illustrated that five molecules had higher binding affinities than tunicamycin (TUM) and were stabled via non-covalent interactions (hydrogen bond and hydrophobic interactions) at the active site of LLM. Further, molecular dynamics results revealed that binding of identified antibacterial molecules with LLM resulted in stable LLM-inhibitor(s) complexes. Molecular Mechanics/Position-Boltzmann Surface Area (MMPBSA) analysis showed that LLM-inhibitor(s) complexes had high binding affinities in the range of -213.49 ± 2.24 to -227.42 ± 3.05 kJ/mol. The amino acid residues decomposition analysis confirmed that identified antibacterial molecules bound at the active site (Asn148, Leu149, Asp151, Asp208, His269, His271, and His272) of LLM. Noticeably, the current study found five antibacterial molecules (BDE 27575101, BDE 33638168, BDE 33672484, LAS 51502073, and BDE 25098678) were highly potent than TUM and even than earlier reported molecules. Therefore, here reported antibacterial molecules may be used directly or developed to inhibit LLM of S. aureus.Communicated by Ramaswamy H. Sarma.

Identification and evaluation of potential inhibitor molecules against TcyA from Candidatus Liberibacter asiaticus

Of the two putative amino acid binding periplasmic receptors of ABC transporter family in Candidatus Liberibacter asiaticus (CLas), cystine binding receptor (CLasTcyA) has been shown to mainly express in phloem of citrus plant and is a target for inhibitor development. The crystal structure of CLasTcyA in complex with substrates has been reported earlier. The present work reports the identification and evaluation of potential candidates for their inhibitory potential against CLasTcyA. Among many compounds, selected through virtual screening, and MD simulation, pimozide, clidinium, sulfasalazine and folic acid showed significantly higher affinities and stability in complex with CLasTcyA. The SPR studies with CLasTcyA revealed significantly higher binding affinities for pimozide and clidinium (Kd, 2.73 nM and 70 nM, respectively) as compared to cystine (Kd, 1.26 µM). The higher binding affinities could be attributed to significantly increased number of interactions in the binding pocket as evident from the crystal structures of CLasTcyA in complex with pimozide and clidinium as compared to cystine. The CLasTcyA possess relatively large binding pocket where bulkier inhibitors fit quite well. In planta studies, carried out to assess the effect of inhibitors on HLB infected Mosambi plants, showed significant reduction in CLas titre in plants treated with inhibitors as compared to control plants. The results showed that pimozide exhibited higher efficiency as compared to clidinium in reducing CLas titre in treated plants. Our results showed that the inhibitor development against critical proteins like CLasTcyA can be an important strategy in management of HLB.

Protein structural insights into a rare PCSK9 gain-of-function variant (R496W) causing familial hypercholesterolemia in a Saudi family: whole exome sequencing and computational analysis

Familial hypercholesterolemia (FH) is a globally underdiagnosed genetic condition associated with premature cardiovascular death. The genetic etiology data on Arab FH patients is scarce. Therefore, this study aimed to identify the genetic basis of FH in a Saudi family using whole exome sequencing (WES) and multidimensional bioinformatic analysis. Our WES findings revealed a rare heterozygous gain-of-function variant (R496W) in the exon 9 of the PCSK9 gene as a causal factor for FH in this family. This variant was absent in healthy relatives of the proband and 200 healthy normolipidemic controls from Saudi Arabia. Furthermore, this variant has not been previously reported in various regional and global population genomic variant databases. Interestingly, this variant is classified as "likely pathogenic" (PP5) based on the variant interpretation guidelines of the American College of Medical Genetics (ACMG). Computational functional characterization suggested that this variant could destabilize the native PCSK9 protein and alter its secondary and tertiary structural features. In addition, this variant was predicted to negatively influence its ligand-binding ability with LDLR and Alirocumab antibody molecules. This rare PCSK9 (R496W) variant is likely to expand our understanding of the genetic basis of FH in Saudi Arabia. This study also provides computational structural insights into the genotype-protein phenotype relationship of PCSK9 pathogenic variants and contributes to the development of personalized medicine for FH patients in the future.

Electrochemical Actuation of a DyP Peroxidase: A Facile Method for Drastic Improvement of the Catalytic Performance

Dye decolorizing peroxidases (DyP) have attracted interest for applications such as dye-containing wastewater remediation and biomass processing. So far, efforts to improve operational pH ranges, activities, and stabilities have focused on site-directed mutagenesis and directed evolution strategies. Here, we show that the performance of the DyP from Bacillus subtilis can be drastically boosted without the need for complex molecular biology procedures by simply activating the enzyme electrochemically in the absence of externally added H2O2. Under these conditions, the enzyme shows specific activities toward a variety of chemically different substrates that are significantly higher than in its canonical operation. Moreover, it presents much broader pH activity profiles with the maxima shifted toward neutral to alkaline. We also show that the enzyme can be successfully immobilized on biocompatible electrodes. When actuated electrochemically, the enzymatic electrodes have two orders of magnitude higher turnover numbers than with the standard H2O2-dependent operation and preserve about 30% of the initial electrocatalytic activity after 5 days of operation-storage cycles.

HR-LCMS and evaluation of anti-diabetic activity of Hemidesmus indicus (anantmool): Kinetic study, and molecular modelling approach

This study delved into the exploration of novel antidiabetic medications acquired from natural resources, utilizing the Ayurvedic Rasayana herb Hemidesmus indicus through cutting-edge chemoprofiling and molecular modelling techniques. The methanolic extract of Hemidesmus indicus root exhibited the highest extractive yield (24.70 ± 0.08 %) and contained substantial levels of total phenolic and flavonoid content as 154.15 ± 1.24 mg Gallic Acid Equivalent/g extract and 70.61 ± 0.35 Quercetin Equivalent/g extract respectively. Invitro study revealed the potent inhibitory potential of methanolic extract of the herb against essential carbohydrate hydrolytic enzymes α-amylase (IC₅₀ = 4.19 ± 0.04 mg/ml) and α-glucosidase (IC₅₀ = 5.78 ± 0.10 mg/ml). Further, the enzyme kinetic study demonstrated the competitive mode of inhibition of both enzymes. HR-LCMS analysis identified the major phytoconstituents present in the extracts, including Solanocapsine, Cyclovirobuxine C, Lucidine B, Zygadenine, Aspidospermidine, silychristin, 3beta-3-Hydroxy-18-lupen-21-one, Manglupenone, and 19-Noretiocholanolone. Molecular docking, molecular dynamic simulation, and MM/GBSA analysis have proved stable, rigid, compact, and folded form of complexes during the entire 100 ns simulation, illustrating Zygadenine, Solanocapsine, and Cyclovirobuxine C as the superior inhibitors of α-A protein, while Zygadenine, Plumieride, and Phlegmarine exhibited greater inhibitory behaviour towards α-G protein than the FDA-approved drug acarbose. Collectively, our findings indicate that the Hemidesmus indicus could be a promising source of α-A and α-G inhibitors, potentially serving as a lead in order to develop medications for type-2 diabetes.

Structural insights, biocatalytic characteristics, and application prospects of lignin-modifying enzymes for sustainable biotechnology-A review

Lignin modifying enzymes (LMEs) have gained widespread recognition in depolymerization of lignin polymers by oxidative cleavage. LMEs are a robust class of biocatalysts that include lignin peroxidase (LiP), manganese peroxidase (MnP), versatile peroxidase (VP), laccase (LAC), and dye-decolorizing peroxidase (DyP). Members of the LMEs family act on phenolic, non-phenolic substrates and have been widely researched for valorization of lignin, oxidative cleavage of xenobiotics and phenolics. LMEs implementation in the biotechnological and industrial sectors has sparked significant attention, although its potential future applications remain underexploited. To understand the mechanism of LMEs in sustainable pollution mitigation, several studies have been undertaken to assess the feasibility of LMEs in correlating to diverse pollutants for binding and intermolecular interactions at the molecular level. However, further investigation is required to fully comprehend the underlying mechanism. In this review we presented the key structural and functional features of LMEs, including the computational aspects, as well as the advanced applications in biotechnology and industrial research. Furthermore, concluding remarks and a look ahead, the use of LMEs coupled with computational frameworks, built upon artificial intelligence (AI) and machine learning (ML), has been emphasized as a recent milestone in environmental research.

Field measures of strengthen plant-microbial remediation of PAHs-FQs compound pollution

In this study, five PAHs (benzo [b] fluoranthene (BbF), phenanthrene (Phe), fluoranthene (Flu), fluorene (Fl), benzo [A] pyrene (Bap)), and five FQs (ofloxacin (OFL), enrofloxacin (ENR), ciprofloxacin (CIP), norfloxacin (NOR), lomefloxacin (LOM)) were selected as ligands; peroxidase (1NML) was selected as receptor degrading protein. In the plant-microbial degradation, the factors with significant inhibitory effects are NOR, Bap, CIP, ENR, OFL, Flu, LOM, Phe, Fl, and BbF by the fractional factorial design experiment and molecular docking-assisted molecular dynamics methods. Using Taguchi experiment and molecular dynamics simulation methods, the main external field measures were designed and screened to effectively promote the degradation of PAHs-FQs under the combined pollution scenarios of Bap-CIP and BbF-NOR, respectively. The peroxidase mutation design plans with enhanced substrate affinity were then designed and screened using the DS software by predicting the virtual key amino acid of peroxidase. The novel biodegradable enzymes 2YCD-1, 2YCD-4, 2YCD-5, 2YCD-7, and 2YCD-9 had better structures and showed excellent degradability for PAHs and FQs. This study explored the degradation rules of the composite pollutants in the coexistence systems of multiple PAHs and FQs, providing the best external field measures for the control and treatment of the combined pollution effects of different PAHs and FQs. Overall, the current study has important practical significance for promoting the plant-microbial joint remediation of PAHs-FQs pollution and for reducing the combined pollution of PAHs and FQs in farmland systems.

Structural insights at acidic pH of dye-decolorizing peroxidase from Bacillus subtilis

Dye-decolorizing peroxidases (DyPs), a type of heme-containing oxidoreductase enzymes, catalyze the peroxide-dependent oxidation of various industrial dyes as well as lignin and lignin model compounds. In our previous work, we have recently reported the crystal structures of class A-type DyP from Bacillus subtilis at pH 7.0 (BsDyP7), exposing the location of three binding sites for small substrates and high redox-potential substrates. The biochemical studies revealed the optimum acidic pH for enzyme activity. In the present study, the crystal structure of BsDyP at acidic pH (BsDyP4) reveals two-monomer units stabilized by intermolecular salt bridges and a hydrogen bond network in a homo-dimeric unit. Based on the monomeric structural comparison of BsDyP4 and BsDyP7, minor differences were observed in the loop regions, that is, LI (Ala64-Gln71), LII (Glu96-Lys108), LIII (Pro117-Leu124), and LIV (Leu295-Asp303). Despite these differences, BsDyP4 adopts similar heme architecture as well as three substrate-binding sites to BsDyP7. In BsDyP4, a shift in Asp187, heme pocket residue discloses the plausible reason for optimal acidic pH for BsDyP activity. This study provides insight into the structural changes in BsDyP at acidic pH, where BsDyP is biologically active.

A bacterial cold-active dye-decolorizing peroxidase from an Antarctic Pseudomonas strain

DyP (dye-decolorizing peroxidase) enzymes are hemeproteins that catalyze the H₂O₂-dependent oxidation of various molecules and also carry out lignin degradation, albeit with low activity. We identified a dyp gene in the genome of an Antarctic cold-tolerant microbe (Pseudomonas sp. AU10) that codes for a class B DyP. The recombinant protein (rDyP-AU10) was produced using Escherichia coli as a host and purified. We found that rDyP-AU10 is mainly produced as a dimer and has characteristics that resemble psychrophilic enzymes, such as high activity at low temperatures (20 °C) when using 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid (ABTS) and H₂O₂ as substrates, thermo-instability, low content of arginine, and a catalytic pocket surface larger than the DyPs from some mesophilic and thermophilic microbes. We also report the steady-state kinetic parameters of rDyP-AU10 for ABTS, hydroquinone, and ascorbate. Stopped-flow kinetics revealed that Compound I is formed with a rate constant of (2.07 ± 0.09) × 10⁶ M^-1 s^-1 at pH 5 and that this is the predominant species during turnover. The enzyme decolors dyes and modifies kraft lignin, suggesting that this enzyme may have potential use in bioremediation and in the cellulose and biofuel industries. KEY POINTS: • An Antarctic Pseudomonas strain produces a dye-decolorizing peroxidase. • The recombinant enzyme (rDyP-AU10) was produced in E. coli and purified. • rDyP-AU10 showed high activity at low temperatures. • rDyP-AU10 is potentially useful for biotechnological applications.

Computational investigation of potent inhibitors against YsxC: structure-based pharmacophore modeling, molecular docking, molecular dynamics, and binding free energy

In S. aureus, ribosome biogenesis GTP-binding (YsxC), a GTPase interacts with 50S subunit and 30S subunit of ribosome, and β' subunit of RNA polymerase and played an important role in protein synthesis. For the identification of potent lead molecules, we have conducted pharmacophore modeling by consideration of pharmacophore features of GTP among YsxC-GTP complex. Virtual screening and molecular docking results displayed that five pharmacokinetic and ADMET filtered molecules-ZINC000006424138, ZINC000095502032, ZINC000225415132, ZINC000095475800, and ZINC000012990761-had higher binding affinities than GTP with YsxC. All the identified molecules shared similar pharmacophore features of GTP and were stabilized via hydrogen bonds and hydrophobic interactions with YsxC. Molecular dynamics analysis revealed that YsxC-inhibitor(s) complexes were lesser dynamics and higher stable than YsxC-GTP complex. Molecular Mechanics/Poisson-Boltzmann Surface Area (MMPBSA) results confirmed that identified molecules bound at the active site (Arg33, Ser34, Asn35, Val36, Lys38, Ser39, Thr40, Thr54, Ser55, Pro58, Lys60, Thr61, Thr144, Lys145, Ser178, and Ile179) of YsxC and formed the lower energy (-190.32 ± 3.46 to -217.03 ± 2.55 kJ/mol) complexes than YsxC-GTP (-157.16 ± 2.89 kJ/mol) complex. The identified molecules in this study can be further tested and utilized to design novel antimicrobial agents for S. aureus.Communicated by Ramaswamy H. Sarma.

Potential diagnostic markers and therapeutic targets for rheumatoid arthritis with comorbid depression based on bioinformatics analysis

Background

Rheumatoid arthritis (RA) and depression are prevalent diseases that have a negative impact on the quality of life and place a significant economic burden on society. There is increasing evidence that the two diseases are closely related, which could make the disease outcomes worse. In this study, we aimed to identify diagnostic markers and analyzed the therapeutic potential of key genes.

Methods

We assessed the differentially expressed genes (DEGs) specific for RA and Major depressive disorder (MDD) and used weighted gene co-expression network analysis (WGCNA) to identify co-expressed gene modules by obtaining the Gene expression profile data from Gene Expression Omnibus (GEO) database. By using the STRING database, a protein-protein interaction (PPI) network constructed and identified key genes. We also employed two types of machine learning techniques to derive diagnostic markers, which were assessed for their association with immune cells and potential therapeutic effects. Molecular docking and in vitro experiments were used to validate these analytical results.

Results

In total, 48 DEGs were identified in RA with comorbid MDD. The PPI network was combined with WGCNA to identify 26 key genes of RA with comorbid MDD. Machine learning-based methods indicated that RA combined with MDD is likely related to six diagnostic markers: AURKA, BTN3A2, CXCL10, ERAP2, MARCO, and PLA2G7. CXCL10 and MARCO are closely associated with diverse immune cells in RA. However, apart from PLA2G7, the expression levels of the other five genes were associated with the composition of the majority of immune cells in MDD. Molecular docking and in vitro studies have revealed that Aucubin (AU) exerts the therapeutic effect through the downregulation of CXCL10 and BTN3A2 gene expression in PC12 cells.

Conclusion

Our study indicates that six diagnostic markers were the basis of the comorbidity mechanism of RA and MDD and may also be potential therapeutic targets. Further mechanistic studies of the pathogenesis and treatment of RA and MDD may be able to identify new targets using these shared pathways.

Structural screening into the recognition of a potent inhibitor against non-structural protein 16: a molecular simulation to inhibit SARS-CoV-2 infection

COVID-19 infection is caused by endemic crown infection (SARS-CoV-2) and is associated with lung damage and severe immune response. Non-Structural Proteins are the central components of coronaviral transcription and replication machinery in SARS-CoV-2 and also stimulate mRNA cap methylation to avoid the immune response. Non-Structural Protein 16 (NSP16) is one of the primary targets for the drug discovery of coronaviruses. Discovering an effective inhibitor against the NSP16 in comparison with Sinefungin was the main purpose of this investigation. Binding free-energy calculations, computational methods of molecular dynamics, docking, and virtual screening were utilized in this study. The ZINC and PubChem databases were applied to screen some chemical compounds regarding Sinefungin as a control inhibitor. Based on structural similarity to Sinefungin, 355 structures were obtained from the mentioned databases. Subsequently, this set of compounds were monitored by AutoDock Vina software, and ultimately the potent inhibitor (PUBCHEM512713) was chosen. At the next stage, molecular dynamics were carried out by GROMACS software to evaluate the potential elected compounds in a simulated environment and in a timescale of 100 nanoseconds. MM-PBSA investigation exhibited that the value of binding free energy for PUBCHEM512713 (-30.829 kJ.mol^-1) is more potent than Sinefungin (-11.941 kJ.mol^-1). Furthermore, the results of ADME analysis illustrated that the pharmacokinetics, drug-likeness, and lipophilicity parameters of PUBCHEM512713 are admissible for human utilization. Finally, our data suggested that PUBCHEM512713 is an effective drug candidate for inhibiting the NSP16 and is suitable for in vitro and in vivo studies.Communicated by Ramaswamy H. Sarma.

Molecular modeling and dynamics simulation of alcohol dehydrogenase enzyme from high efficacy cellulosic ethanol-producing yeast mutant strain Pichia kudriavzevii BGY1-γm

One of the major constraints limiting the use of abundantly available lignocellulosic biomass as potential feedstock for alcohol industry is the lack of C₆/C₅ co-sugar fermenting yeast. The present study explores a mutant yeast Pichia kudriavzevii BGY1-γm as a potential strain for bioconversion of glucose/xylose sugars of green biomass into ethanol under batch fermentation. The mutant strain having higher alcohol dehydrogenase activity (11.31%) showed significantly higher ethanol concentration during co-fermentation of glucose/xylose sugars (14.2%) as compared to the native strain. Based on 99% sequence similarity of ADH encoding gene from the mutant with the gene sequences from other yeast strains, the ADH enzyme was identified as ADH-1 type. The study reveals first three-dimensional model of ADH-1 utilizing glucose/xylose sugars from P. kudriavzevii BGY1-γm (PkADH mutant). The refined and validated model of PkADH mutant was used for molecular docking against the substrate (acetaldehyde) and product (ethanol). Molecular docking results showed that substrate and product exhibited a binding affinity of -4.55 and -4.5 kcal/mol with PkADH mutant. Acetaldehyde and ethanol interacted at the active site of PkADH mutant via hydrogen bonds (Ser42, His69 and Asp163) and hydrophobic interactions (Cys40, Ser42, His69, Cys95, Trp123 and Asp163) to form the stable protein-ligand complex. Molecular dynamics analysis revealed that PkADH-mutant acetaldehyde and PkADH-mutant ethanol complexes were more stable than PkADH mutant. MMPBSA binding energy confirmed that binding of substrate and product results in the formation of a lower energy stable protein-ligand complex.Communicated by Ramaswamy H. Sarma.

Identification of potential inhibitors for LLM of Staphylococcus aureus: structure-based pharmacophore modeling, molecular dynamics, and binding free energy studies

Staphylococcus aureus causes various life-threatening diseases in humans and developed resistance to several antibiotics. Lipophilic membrane (LLM) protein regulates bacterial lysis rate and methicillin resistance level in S. aureus. To identify potential lead molecules, we performed a structure-based pharmacophore modeling by consideration of pharmacophore properties from LLM-tunicamycin complex. Further, virtual screening of ZINC database against the LLM was conducted and compounds were assessed for Lipinski and ADMET properties. Based on pharmacokinetic, and molecular docking, five potential inhibitors (ZINC000072380005, ZINC000257219974, ZINC000176045471, ZINC000035296288, and ZINC000008789934) were identified. Molecular dynamics simulation (MDS) of these five molecules was performed to evaluate the dynamics and stability of protein after binding of the ligands. Several MDS analysis like RMSD, RMSF, Rg, SASA, and PCA confirm that identified compounds exhibit higher binding affinity as compared to tunicamycin for LLM. The binding free energy analysis reveals that five compounds exhibit higher binding energy in the range of -218.76 to -159.52 kJ/mol, which is higher as compared to tunicamycin (-116.13 kJ/mol). Individual residue decomposition analysis concludes that Asn148, Asp151, Asp208, His271, and His272 of LLM play a significant role in the formation of lower energy LLM-inhibitor(s) complexes. These predicted molecules displayed pharmacological and structural properties and may be further used to develop novel antimicrobial compounds against S. aureus.Communicated by Ramaswamy H. Sarma.

Discovery of the key active compounds in Citri Reticulatae Pericarpium (Citrus reticulata "Chachi") and their therapeutic potential for the treatment of COVID-19 based on comparative metabolomics and network pharmacology

Edible herbal medicines contain macro- and micronutrients and active metabolites that can take part in biochemical processes to help achieve or maintain a state of well-being. Citri Reticulatae Pericarpium (CRP) is an edible and medicinal herb used as a component of the traditional Chinese medicine (TCM) approach to treating COVID-19 in China. However, the material basis and related mechanistic research regarding this herb for the treatment of COVID-19 are still unclear. First, a wide-targeted UPLC-ESI-MS/MS-based comparative metabolomics analysis was conducted to screen for the active metabolites of CRP. Second, network pharmacology was used to uncover the initial linkages among these metabolites, their possible targets, and COVID-19. Each metabolite was then further studied via molecular docking with the identified potential SARS-CoV-2 targets 3CL hydrolase, host cell target angiotensin-converting enzyme II, spike protein, and RNA-dependent RNA polymerase. Finally, the most potential small molecule compound was verified by in vitro and in vivo experiments, and the mechanism of its treatment of COVID-19 was further explored. In total, 399 metabolites were identified and nine upregulated differential metabolites were screened out as potential key active metabolites, among which isorhamnetin have anti-inflammatory activity in vitro validation assays. In addition, the molecular docking results also showed that isorhamnetin had a good binding ability with the key targets of COVID-19. Furthermore, in vivo results showed that isorhamnetin could significantly reduced the lung pathological injury and inflammatory injury by regulating ATK1, EGFR, MAPK8, and MAPK14 to involve in TNF signaling pathway, PI3K-Akt signalling pathway, and T cell receptor signaling pathway. Our results indicated that isorhamnetin, as screened from CRP, may have great potential for use in the treatment of patients with COVID-19. This study has also demonstrated that comparative metabolomics combined with network pharmacology strategy could be used as an effective approach for discovering potential compounds in herbal medicines that are effective against COVID-19.

Drug-Repurposing Approach To Combat Staphylococcus aureus: Biomolecular and Binding Interaction Study

Staphylococcus aureus is considered as one of the most widespread bacterial pathogens and continues to be a prevalent cause of mortality and morbidity across the globe. FmtA is a key factor linked with methicillin resistance in S. aureus. Consequently, new antibacterial compounds are crucial to combat S. aureus resistance. Here, we present the virtual screening of a set of compounds against the available crystal structure of FmtA. The findings indicate that gemifloxacin, paromomycin, streptomycin, and tobramycin were the top-ranked potential drug molecules based on the binding affinity. Furthermore, these drug molecules were analyzed with molecular dynamics simulations, which showed that the identified molecules formed highly stable FmtA-inhibitor(s) complexes. Molecular mechanics Poisson-Boltzmann surface area and quantum mechanics/molecular mechanics calculations suggested that the active site residues (Ser127, Lys130, Tyr211, and Asp213) of FmtA are crucial for the interaction with the inhibitor(s) to form stable protein-inhibitor(s) complexes. Moreover, fluorescence- and isothermal calorimetry-based binding studies showed that all the molecules possess dissociation constant values in the micromolar scale, revealing a strong binding affinity with FmtA^Δ80, leading to stable protein-drug(s) complexes. The findings of this study present potential beginning points for the rational development of advanced, safe, and efficacious antibacterial agents targeting FmtA.

In-silico functional and structural annotation of hypothetical protein from Klebsiella pneumonia: A potential drug target

Klebsiella pneumonia is known to cause several nosocomial infections in immunocompromised patients. It has developed resistance against a broad range of presently available antibiotics, resulting in high mortality rates in patients and declared an urgent threat. Therefore, exploration of possible novel drug targets against this opportunistic bacteria needs to be undertaken. In the present study, we performed an extensive in-silico analysis for functional and structural annotation and characterized HP CP995_08280 from K. pneumonia as a drug target and aimed to identify potent drug candidates. The functional and structural studies using several bioinformatics tools and databases predicted that HP CP995_08280 is a cytosolic protein that belongs to the β-lactamase family and shares structural similarity with FmtA protein from Staphylococcus aureus (PDB ID: 5ZH8). The structure of HP CP995_08280 was successfully modeled followed by structure-based virtual screening, docking, molecular dynamics, and Molecular mechanic/Poisson-Boltzmann surface area (MMPBSA) were performed to identify the potential compounds. We have found five potent antibacterial molecules, namely BDD 24083171, BDD 24085737, BDE 25098678, BDE 33638819, and BDE 33672484, which exhibited high binding affinity (>-7.5 kcal/mol) and were stabilized by hydrogen bonding and hydrophobic interactions with active site residues (Ser42, Lys45, Tyr126, and Asp128) of protein. Molecular dynamics and MMPBSA revealed that HP CP995_08280 - ligand(s) complexes were less dynamic and more stable than native HP CP995_08280. Hence, the present study may serve as a potential lead for developing inhibitors against drug-resistant Klebsiella pneumonia.

Potential and mechanism for bioremediation of papermaking black liquor by a psychrotrophic lignin-degrading bacterium, Arthrobacter sp. C2

To meet the challenge of bioremediation of black liquor in pulp and paper mills at low temperatures, a psychrotrophic lignin-degrading bacterium was employed in black liquor treatment for the first time. In this study, Arthrobacter sp. C2 exhibited excellent cold adaptability and lignin degradation ability, with a lignin degradation rate of 65.5% and a mineralization rate of 43.9% for 3 g/L lignin at 15 °C. Bioinformatics analysis and multiple experiments confirmed that cold shock protein 1 (Csp1) was the dominant cold regulator of strain C2, and dye-decolorizing peroxidase (DyP) played a crucial role in lignin degradation. Moreover, structural equation modeling (SEM), mRNA monitoring, and phenotypic variation analysis demonstrated that Csp1 not only mediated cold adaptation but also modulated DyP activity by controlling dyp gene expression, thus driving lignin depolymerization for strain C2 at low temperatures. Furthermore, 96.4% of color, 64.2% of chemical oxygen demand (COD), and 100% of nitrate nitrogen (NO₃^--N) were removed from papermaking black liquor by strain C2 within 15 days at 15 °C. This study provides insights into the association between the cold regulator and catalytic enzyme of psychrotrophic bacteria and offers a feasible alternative strategy for the bioremediation of papermaking black liquor in cold regions.

Bacterial Peroxidase on Electrochemically Reduced Graphene Oxide for Highly Sensitive H2 O2 Detection

Peroxidase enzymes enable the construction of electrochemical sensors for highly sensitive and selective quantitative detection of various molecules, pathogens and diseases. Herein, we describe the immobilization of a peroxidase from Bacillus s. (BsDyP) on electrochemically reduced graphene oxide (ERGO) deposited on indium tin oxide (ITO) and polyethylene terephthalate (PET) layers. XRD, SEM, AFM, FT-IR and Raman characterization of the sensor confirmed its structural integrity and a higher enzyme surface occupancy. The BsDyP-ERGO/ITO/PET electrode performed better than other horseradish peroxidase-based electrodes, as evinced by an improved electrochemical response in the nanomolar range (linearity 0.05-280 μM of H2 O2 , LOD 32 nM). The bioelectrode was mechanically robust, active in the 3.5-6 pH range and exhibited no loss of activity upon storage for 8 weeks at 4 °C.

Identification of a novel immune-inflammatory signature of COVID-19 infections, and evaluation of pharmacokinetics and therapeutic potential of RXn-02, a novel small-molecule derivative of quinolone

Coronavirus disease 2019 (COVID-19) is a global pandemic and respiratory infection that has enormous damage to human lives and economies. It is caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), a non-pair-stranded positive-sense RNA virus. With increasing global threats and few therapeutic options, the discovery of new potential drug targets and the development of new therapy candidates against COVID-19 are urgently needed. Based on these premises, we conducted an analysis of transcriptomic datasets from SARS-CoV-2-infected patients and identified several SARS-CoV-2 infection signatures, among which TNFRSF5/PTPRC/IDO1/MKI67 appeared to be the most pertinent signature. Subsequent integrated bioinformatics analysis identified the signature as an important immunomodulatory and inflammatory signature of SARS-CoV-2 infection. It was suggested that this gene signature mediates the interplay of immune and immunosuppressive cells leading to infiltration-exclusion of effector memory T cells in the lungs, which is of translation relevance for developing novel SARS-CoV-2 drug and vaccine candidates. Consequently, we designed and synthesized a novel small-molecule quinoline derivative (RXn-02) and evaluated its pharmacokinetics in rats, revealing a peak plasma concentration (Cmax) and time to Cmax (Tmax) of 1.756 μg/mL and 0.6 h, respectively. Values of the area under the curve (AUC) (0–24 h) and AUC (0 h∼∞) were 18.90 and 71.20 μg h/mL, respectively. Drug absorption from the various regional segments revealed that the duodenum (49.84%), jejunum (47.885%), cecum (1.82%), and ileum (0.32%) were prime sites of RXn-02 absorption. No absorption was detected from the stomach, and the least was from the colon (0.19%). Interestingly, RXn-02 exhibited in vitro antiproliferative activities against hub gene hyper-expressing cell lines; A549 (IC₅₀ = 48.1 μM), K-562 (IC₅₀ = 100 μM), and MCF7 (IC₅₀ = 0.047 μM) and against five cell lines originating from human lungs (IC₅₀ range of 33.2–69.5 μM). In addition, RXn-02 exhibited high binding efficacies for targeting the TNFRSF5/PTPRC/IDO1/MK signature with binding affinities (ΔG) of −6.6, −6.0, −9.9, −6.9 kcal/mol respectively. In conclusion, our study identified a novel signature of SARS-CoV-2 pathogenesis. RXn-02 is a drug-like candidate with good in vivo pharmacokinetics and hence possesses great translational relevance worthy of further preclinical and clinical investigations for treating SARS-CoV-2 infections.

Promising antivirals for PLpro of SARS-CoV-2 using virtual screening, molecular docking, dynamics, and MMPBSA

The recent pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (COVID-19) is a viral respiratory disease that has been spread all over the globe. Therefore, it is an urgent requirement to identify and develop drugs for this contagious infection. The papain-like protease (PLpro) of SARS-CoV-2 performs critical functions in virus replication and immune evasion, making it an enticing therapeutic target. SARS-CoV-2 and SARS-CoV PLpro proteases have significant similarities, and an inhibitor discovered for SARS-CoV PLpro is an exciting first step toward therapeutic development. Here, a set of antiviral molecules were screened at the catalytic and S-binding allosteric sites of papain-like protease (PLpro). Molecular docking results suggested that five molecules (44560613, 136277567, S5652, SC75741, and S3833) had good binding affinities at both sites of PLpro. Molecular dynamics analysis like root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), and hydrogen bond results showed that identified molecules with PLpro tend to form stable PLpro-inhibitor(s) complexes. Molecular Mechanics/Position-Boltzmann Surface Area (MMPBSA) analysis confirmed that antiviral molecules bound PLpro complex had lower energy (-184.72 ± 7.81 to -215.67 ± 6.73 kJ/mol) complexes. Noticeably, computational approaches revealed promising antivirals candidates for PLpro, which may be further tested by biochemical and cell-based assays to assess their potential for SARS-CoV-2.Communicated by Ramaswamy H. Sarma.

Microbial approaches for sustainable remediation of dye-contaminated wastewater: a review

The coloured effluents produced from different industries, such as textile, plastics, printing, cosmetics, leather and paper, are extremely toxic and a tremendous threat to the aquatic organisms and human beings. The removal of coloured dye pollutants from the aqueous environment is a great challenge and a pressing task. The growing demand for low-cost and efficient treatment approaches has given rise to alternative and eco-friendly methods, such as biodegradation and microbial remediation. This work summarizes the overview and current research on the remediation of dye pollutants from the aqueous environment by microbial bio-sorbents, such as bacteria, fungi, algae, and yeast. In addition, dye degradation capabilities of microbial enzymes have been highlighted and discussed. Further, the influence of various experimental parameters, such as temperature, pH, and concentrations of nutrients, and dye, has been summarized. The proposed mechanism for dye removal by microorganisms is also discussed. The object of this review is to provide a state-of-the-art of microbial remediation technologies in eliminating dye pollutants from water resources.

Structure of dye-decolorizing peroxidase from Bacillus subtilis in complex with veratryl alcohol

Dye-decolorizing peroxidases (DyPs) are heme-containing peroxidases, which have promising application in biodegradation of phenolic lignin compounds and in detoxification of dyes. In this study, the crystal structure of BsDyP- veratryl alcohol (VA) complex delves deep into the binding of small substrate molecules within the DyP heme cavity. The biochemical analysis shows that BsDyP oxidizes the VA with a turnover number of 0.065 s^-1, followed by the oxidation of 2,6-dimethoxyphenol (DMP) and guaiacol with a comparable turnover number (k_cat) of 0.07 s^-1 and 0.07 s^-1, respectively. Moreover, biophysical and computational studies reveal the comparable binding affinity of substrates to BsDyP and produce lower-energy stable BsDyP-ligand(s) complexes. All together with our previous findings, we are providing a complete structural description of substrate-binding sites in DyP. The structural insight of BsDyP helps to modulate its engineering to enhance the activity towards the oxidation of a wide range of substrates.

Direct Electrochemical Generation of Catalytically Competent Oxyferryl Species of Classes I and P Dye Decolorizing Peroxidases

This work introduces a novel way to obtain catalytically competent oxyferryl species for two different dye-decolorizing peroxidases (DyPs) in the absence of H2O2 or any other peroxide by simply applying a reductive electrochemical potential under aerobic conditions. UV-vis and resonance Raman spectroscopies show that this method yields long-lived compounds II and I for the DyPs from Bacillus subtilis (BsDyP; Class I) and Pseudomonas putida (PpDyP; Class P), respectively. Both electrochemically generated high valent intermediates are able to oxidize ABTS at both acidic and alkaline pH. Interestingly, the electrocatalytic efficiencies obtained at pH 7.6 are very similar to the values recorded for regular catalytic ABTS/H2O2 assays at the optimal pH of the enzymes, ca. 3.7. These findings pave the way for the design of DyP-based electrocatalytic reactors operable in an extended pH range without the need of harmful reagents such as H2O2.

Loops around the Heme Pocket Have a Critical Role in the Function and Stability of BsDyP from Bacillus subtilis

Bacillus subtilis BsDyP belongs to class I of the dye-decolorizing peroxidase (DyP) family of enzymes and is an interesting biocatalyst due to its high redox potential, broad substrate spectrum and thermostability. This work reports the optimization of BsDyP using directed evolution for improved oxidation of 2,6-dimethoxyphenol, a model lignin-derived phenolic. After three rounds of evolution, one variant was identified displaying 7-fold higher catalytic rates and higher production yields as compared to the wild-type enzyme. The analysis of X-ray structures of the wild type and the evolved variant showed that the heme pocket is delimited by three long conserved loop regions and a small α helix where, incidentally, the mutations were inserted in the course of evolution. One loop in the proximal side of the heme pocket becomes more flexible in the evolved variant and the size of the active site cavity is increased, as well as the width of its mouth, resulting in an enhanced exposure of the heme to solvent. These conformational changes have a positive functional role in facilitating electron transfer from the substrate to the enzyme. However, they concomitantly resulted in decreasing the enzyme’s overall stability by 2 kcal mol⁻¹, indicating a trade-off between functionality and stability. Furthermore, the evolved variant exhibited slightly reduced thermal stability compared to the wild type. The obtained data indicate that understanding the role of loops close to the heme pocket in the catalysis and stability of DyPs is critical for the development of new and more powerful biocatalysts: loops can be modulated for tuning important DyP properties such as activity, specificity and stability.

Aspartate or arginine? Validated redox state X-ray structures elucidate mechanistic subtleties of FeIV = O formation in bacterial dye-decolorizing peroxidases

Structure determination of proteins and enzymes by X-ray crystallography remains the most widely used approach to complement functional and mechanistic studies. Capturing the structures of intact redox states in metalloenzymes is critical for assigning the chemistry carried out by the metal in the catalytic cycle. Unfortunately, X-rays interact with protein crystals to generate solvated photoelectrons that can reduce redox active metals and hence change the coordination geometry and the coupled protein structure. Approaches to mitigate such site-specific radiation damage continue to be developed, but nevertheless application of such approaches to metalloenzymes in combination with mechanistic studies are often overlooked. In this review, we summarize our recent structural and kinetic studies on a set of three heme peroxidases found in the bacterium Streptomyces lividans that each belong to the dye decolourizing peroxidase (DyP) superfamily. Kinetically, each of these DyPs has a distinct reactivity with hydrogen peroxide. Through a combination of low dose synchrotron X-ray crystallography and zero dose serial femtosecond X-ray crystallography using an X-ray free electron laser (XFEL), high-resolution structures with unambiguous redox state assignment of the ferric and ferryl (Fe^IV = O) heme species have been obtained. Experiments using stopped-flow kinetics, solvent-isotope exchange and site-directed mutagenesis with this set of redox state validated DyP structures have provided the first comprehensive kinetic and structural framework for how DyPs can modulate their distal heme pocket Asp/Arg dyad to use either the Asp or the Arg to facilitate proton transfer and rate enhancement of peroxide heterolysis.

In-silico evidences on filarial cystatin as a putative ligand of human TLR4

Cystatin is a small molecular weight immunomodulatory protein of filarial parasite that plays a pivotal role in downregulating the host immune response to prolong the survival of the parasite inside the host body. Hitherto, this protein is familiar as an inhibitor of human proteases. However, growing evidences on the role of cystatin in regulating inflammatory homeostasis prompted us to investigate the molecular reasons behind the explicit anti-inflammatory trait of this protein. We have explored molecular docking and molecular dynamics simulation approaches to explore the interaction of cystatin of Wuchereria bancrofti (causative parasite of human filariasis) with human Toll-like receptors (TLRs). TLRs are the most crucial component of frontline host defence against pathogenic infections including filarial infection. Our in-silico data clearly revealed that cystatin strongly interacts with the extracellular domain of TLR4 (binding energy=-93.5 ± 10 kJ/mol) and this biophysical interaction is mediated by hydrogen bonding and hydrophobic interaction. Molecular dynamics simulation analysis revealed excellent stability of the cystatin-TLR4 complex. Taken together, our data indicated that cystatin appears to be a ligand of TLR4 and we hypothesize that cystatin-TLR4 interaction most likely to play a key role in activating the alternative activation pathways to establish an anti-inflammatory milieu. Thus, the study provokes the development of chemotherapeutics and/or vaccines for targeting the cystatin-TLR4 interaction to disrupt the pathological attributes of human lymphatic filariasis. Our findings are expected to provide a novel dimension to the existing knowledge on filarial immunopathogenesis and it will encourage the scientific communities for experimental validation of the present investigation. Communicated by Ramaswamy H. Sarma.

In-silico screening and identification of potential inhibitors against 2Cys peroxiredoxin of Candidatus Liberibacter asiaticus

Huanglongbing (HLB) is a worldwide citrus plant disease-related to non-culturable and fastidious α-proteobacteria Candidatus Liberibacter asiaticus (CLas). In CLas, Peroxiredoxin (Prx) plays a major role in the reduction of the level of reactive species such as reactive oxygen species (ROS), free radicals and peroxides, etc. Here, we have used structure-based drug designing approach was used to screen and identify the potent molecules against 2Cys Prx. The virtual screening of fragments library was performed against the three-dimensional validated model of Prx. To evaluate the binding affinity, the top four molecules (N-Boc-2-amino isobutyric acid (B2AI), BOC-L-Valine (BLV), 1-(boc-amino) cyclobutane carboxylic acid (1BAC), and N-Benzoyl-DL-alanine (BDLA)) were docked at the active site of Prx. The molecular docking results revealed that all the identified molecules had a higher binding affinity than Tert butyl hydroperoxide (TBHP), a substrate of Prx. Molecular dynamics analysis such as RMSD, Rg, SASA, hydrogen bonds, and PCA results indicated that Prx-inhibitor(s) complexes had lesser fluctuations and were more stable and compact than Prx-TBHP complex. MMPBSA results confirmed that the identified compounds could bind at the active site of Prx to form a lower energy Prx-inhibitor(s) complex than Prx-TBHP complex. The identified potent molecules may pave the path for the development of antimicrobial agents against CLA.Communicated by Ramaswamy H. Sarma.

Efficient biodegradation of malachite green by an artificial enzyme designed in myoglobin

Synthetic dyes such as malachite green (MG) have a wide range of applications. Meanwhile, they bring great challenges for environmental security and cause potential damages to human health. Compared with traditional approaches, enzymatic catalysis is an emerging technique for wastewater treatment. As alternatives to natural enzymes, artificial enzymes have received much attention for potential applications. In previous studies, we have rationally designed artificial enzymes based on myoglobin (Mb), such as by introducing a distal histidine (F43H mutation) and creating a channel to the heme pocket (H64A mutation). We herein show that the artificial enzyme of F43H/H64A Mb can be successfully applied for efficient biodegradation of MG under weak acid conditions. The degradation efficiency is much higher than those of natural enzymes, such as dye-decolorizing peroxidase and laccase (13-18-fold). The interaction of MG and F43H/H64A Mb was investigated by using both experimental and molecular docking studies, and the biodegradation products of MG were also revealed by UPLC-ESI-MS analysis. Based on these results, we proposed a plausible biodegradation mechanism of MG. With the high-yield of overexpression in E. coli cells, this study suggests that the artificial enzyme has potential applications in the biodegradation of MG in fisheries and textile industries.

Designing a natural inhibitor against human kynurenine aminotransferase type II and a comparison with PF-04859989: a computational effort against schizophrenia

The Kynurenine aminotransferase II (KATII) enzyme has an essential role in L-kynurenine transmission to kynurenic acid (KYNA). High concentration of kynurenic acid associates with schizophrenia and some neurocognitive disorders. Decreasing KYNA production via inhibiting KATII would be an effective method for treating and understanding the related central nervous system (CNS) diseases. This study aimed to discover a potent inhibitor against human KATII (hKATII) in comparison with PF-04859989. We utilized the computational methods of molecular dynamics, virtual screening, docking, and binding free-energy calculations. Initially, the 58722 compounds from three drug libraries, including IBS library, DrugBank library, and Analyticon library, were obtained. At the next stage, these sets of compounds were screened by AutoDock Vina software, and a potent inhibitor (ZINC35466084) was selected. Following the screening, molecular dynamics simulations for both ZINC35466084 and PF-04859989 were performed by GROMACS software. MM-PBSA analysis showed that the amount of binding free energy for ZINC35466084 (-61.26 KJ mol^-1) is more potent than PF-04859989 (-43.14 KJ mol^-1). Furthermore, the ADME analysis results revealed that the pharmacokinetic parameters of ZINC35466084 are acceptable for human use. Eventually, our data demonstrated that ZINC35466084 is suitable for hKATII inhibition, and it is an appropriate candidate for further studies in the laboratory. Communicated by Ramaswamy H. Sarma.