Hydrophobic Amino Acid Residues Research Articles

Molecular modeling, synthesis and biological evaluation of caffeic acid based Dihydrofolate reductase inhibitors

Dihydrofolate reductase (DHFR) is an enzyme that plays a crucial role in folate metabolism, which is essential for cell growth and division. DHFR has been identified as a molecular target for numerous diseases due to its significance in various biological processes. DHFR inhibitors can disrupt folate metabolism by inhibiting DHFR, leading to the inhibition of cell growth. So, a series of caffeic acid derivatives were designed, synthesized, characterized and evaluated for their in vitro ability to inhibit DHFR, as well as their antimicrobial and anticancer properties. Among all synthesized compounds, compound CE11 exhibited the highest DHFR inhibitory activity, with an IC50 value of 0.048 µM, which is approximately four times more potent than methotrexate. Compound CE11 exhibited similar docking performance to methotrexate, binding to the same site and engaging key residues such as Glh30, Phe31, Phe34, and Ser59. It also fit snugly in the hydrophobic pocket of modeled protein. Moreover, substantial hydrophobic interactions were noted between the ligand and the hydrophobic amino acid residues of DHFR. This effectively secured the derivative within the restricted substrate cavity. Furthermore, compound CE11 demonstrated a significant anticancer activity against MCF-7 breast cancer cell line, with an IC50 value of 5.37 ± 0.16 µM. Compounds CE3 and CE15 displayed better antibacterial activity compared to trimethoprim and comparable to ampicillin against the gram-positive bacteria S. aureus. Moreover, compounds CE3 and CE15 have shown better antibacterial activity than standard trimethoprim, ampicillin and tetracycline against the gram-negative bacteria, particularly P. aeruginosa and E. coli. Molecular docking analysis of CE3 revealed that it firmly entrapped into the active site of enzyme through hydrophobic interaction with hydrophobic residues. Additionally, it forms hydrogen bonds with important amino acid residues Ala7, Asn18, and Thr121 with excellent docking score and binding energy (-9.9, -71.77 kcal/mol). These interactions might be contributed to the significant DHFR inhibition and antimicrobial activity. The generated model holds potential value in facilitating the development of a novel category of DHFR inhibitors as anticancer and antimicrobial agents.

Debittering and antioxidant improvement of soy protein hydrolysates using curcumin as hydrophobic core.

Protein hydrolysates possess various bioactive functions (e.g. antioxidant), but their bitter taste is unacceptable to most consumers. In the present study, a novel approach for debittering was introduced, which involved the utilization of a hydrophobic compound, curcumin (Cur). Soy protein hydrolysates (SPH), prepared through alcalase hydrolysis, served as the research model for this investigation. It was found that bitter intensity of SPH was dominated by the hydrophobic amino acid residues, and the addition of Cur could remarkably reduce bitterness. The debittering mechanism is attributed to the direct binding of Cur to the exposed hydrophobic amino acid residues of SPH via hydrophobic interaction, thereby shielding the hydrophobic bitter groups and hindering their interaction with the bitter taste receptors. Moreover, this debittering strategy leads to the generation of stable nanoparticles with a Cur-core/SPH-shell architecture, which can significantly improve the antioxidant capacity of SPH compared to those using biomacromolecules for encapsulation. Using curcumin as a hydrophobic core is a facile and feasible strategy with bifunction of debittering as well as improving bioactive effect of SPH, which may extend its application in foods. © 2024 Society of Chemical Industry.

Effect of ultrasonic treatment on the structure and emulsification properties of soybean isolate protein-hyaluronic acid complexes and the stability of their loaded astaxanthin emulsions

The purpose of this work was to prepare an astaxanthin emulsion stabilized by a soybean isolate protein (SPI)-hyaluronic acid (HA) complex and to investigate its protective effect on astaxanthin. In order to examine the impact of various ultrasonic energies (0 W–300 W) on the structural characteristics of the complex and the stability of the emulsion, the SPI-HA complex was created via ultrasonography. The findings demonstrated that ultrasonication may had an impact on the hydrophobic, electrostatic, and hydrogen bonding interactions between SPI and HA, which caused the protein structure to unfold and reveal the interior hydrophobic amino acid residues. Moreover, ultrasonication enhanced the emulsification qualities of SPI-HA complexes by lowering their average particle size. The rheological findings demonstrated that the emulsion's viscosity and energy storage modulus (G′) were considerably decreased by the ultrasonic treatment. The appearance of the emulsions and optical microscopy results further indicated that the emulsions prepared from SPI-HA had superior storage stability, pH stability, and light stability compared to pure SPI. SPI-HA exhibited superior emulsion stability and lower particle size at 150 W ultrasonic power. The AST incorporated in the emulsion was also well protected. The emulsion effectively slows down the degradation of AST. The findings of this study may help create more robust and natural emulsion delivery systems that guarantee the continuous or regulated release of lipophilic bioactive compounds.

Biological evaluation of sophoridine by interaction with plasma transport protein and protective effects in cardiomyocytes

Numerous studies have demonstrated the protective benefits of sophoridine, a bioactive alkaloid, on cell damage. However, its primary biological properties such as interaction with plasma protein, which serves as the primary drug carrier, and its cardioprotective properties are still unknown. In the present study, we aimed to analyze the binding characteristics of sophoridine with alpha-2-macroglobulin (α2M) by spectroscopic and theoretical studies. Then, the cardioprotective effects of sophoridine on myocardial ischemia/reperfusion (MI/R) injury in vitro were investigated using H9c2 cardiomyocytes. The results reveal that one molecule of sophoridine favorably binds to one molecule of α2M dominantly through interaction with hydrophobic amino acid residues (VAL758, PHE735, PHE735, and TRP739). Also, sophoridine leads to partial changes in the structure of this carrier protein in the vicinity of TRP739 residue. Cellular assays exhibit that sophoridine recovered cell viability, membrane leakage, and apoptosis induced by MI/R injury. It was detected that sophoridine could mitigate the oxidative stress and intrinsic apoptosis pathway through regulation of Bax, Bcl-2, and caspase. ELISA analysis also exhibits that sophoridine upregulates phosphorylation of Akt and PI3K in H9c2 cells. Our findings suggest that sophoridine could show favorable plasma protein interaction and promising cardioprotection against MI/R injury mediated by the upregulation of PI3K/AKT signaling pathway.

Molecular architecture of chitin and chitosan-dominated cell walls in zygomycetous fungal pathogens by solid-state NMR

Zygomycetous fungal infections pose an emerging medical threat among individuals with compromised immunity and metabolic abnormalities. Our pathophysiological understanding of these infections, particularly the role of fungal cell walls in growth and immune response, remains limited. Here we conducted multidimensional solid-state NMR analysis to examine cell walls in five Mucorales species, including key mucormycosis causative agents like Rhizopus and Mucor species. We show that the rigid core of the cell wall primarily comprises highly polymorphic chitin and chitosan, with minimal quantities of β-glucans linked to a specific chitin subtype. Chitosan emerges as a pivotal molecule preserving hydration and dynamics. Some proteins are entrapped within this semi-crystalline chitin/chitosan layer, stabilized by the sidechains of hydrophobic amino acid residues, and situated distantly from β-glucans. The mobile domain contains galactan- and mannan-based polysaccharides, along with polymeric α-fucoses. Treatment with the chitin synthase inhibitor nikkomycin removes the β-glucan-chitin/chitosan complex, leaving the other chitin and chitosan allomorphs untouched while simultaneously thickening and rigidifying the cell wall. These findings shed light on the organization of Mucorales cell walls and emphasize the necessity for a deeper understanding of the diverse families of chitin synthases and deacetylases as potential targets for novel antifungal therapies.

Intracellular bactericidal activity and action mechanism of MDP1 antimicrobial peptide against VRSA and MRSA in human endothelial cells.

Staphylococcus aureus is a prominent cause of postoperative infections, often persisting within host cells, leading to chronic infections. Conventional antibiotics struggle to eliminate intracellular S. aureus due to poor cell penetration. Antimicrobial peptides are a new hope for tackling intracellular bacteria. Accordingly, this study examines the antimicrobial peptide MDP1, derived from melittin, for its efficacy against intracellular S. aureus. In this study, the physiochemical properties (Prediction of three-dimensional structure, circular dichroism and helical wheel projection analysis) were investigated. Extracellular antibacterial activity and cytotoxicity of MDP1 were also assessed. The mechanism of interaction of MDP1 with S. aureus was evaluated by molecular dynamic simulation, atomic force and confocal microscopy. Bacterial internalization into an endothelial cell model was confirmed through culture and transmission electron microscopy. The effect of the peptide on intracellular bacteria was investigated by culture and epi-fluorescence microscopy. 3D structural prediction proved the conformation of MDP1 as an α-helix peptide. Helical-wheel projection analysis indicated the proper orientation of hydrophobic amino acid residues for membrane interaction. CD spectroscopy of MDP1 showed that MDP1 in SDS 10 and 30 mM adopted 87 and 91% helical conformation. Atomic force and confocal microscopy assessments as well as molecular dynamics studies revealed the peptide-bacterial membrane interaction. MDP1, at the concentration of 0.32 μg mL-1, demonstrated a fold reduction of 21.7 ± 1.8, 1.7 ± 0.2, and 7.3 ± 0.8 in intracellular bacterial load for ATCC, VRSA, and MRSA, respectively. Molecular dynamics results demonstrate a preferential interaction of MDP1 with POPG/POPE membranes, primarily driven by electrostatic forces and hydrogen bonding. In POPC systems, two out of four MDP1 interacted effectively, while all four MDP1 engaged with POPG/POPE membranes. Gathering all data together, MDP1 is efficacious in the reduction of intracellular VRSA and MRSA proved by culture and epi-fluorescent microscopy although further studies should be performed to increase the intracellular activity of MDP1.

Optimizing gelation properties of mixed meat myofibrillar proteins: investigating the effects of different proportions of beef, pork and chicken on physicochemical, structural and gelation properties.

The gelation properties of myofibrillar protein (MP) directly affect the texture, taste and water-holding capacity (WHC) of meat products. To enhance the gelation properties of single-species meat MP, the present study investigated the influence of different proportions of beef, pork and chicken MP on the physicochemical properties, structure and gelation properties of the MP. The results revealed that, when the proportion reached 5:2:3, the particle size decreases, leading to the maximum decomposition and unfolding of MPs, which exposes a greater number of hydrophobic amino acid residues. These changes promote interactions between protein molecules, especially the unfolding of α-helices and the formation of β-sheets during the heating process, which provides favorable conditions for the formation of protein gels and improves the gel strength and WHC of MP gels. Additionally, scanning electron microscopy revealed that the mixed MP gels are more compact and have more uniform gel networks and pores compared to single-species MP gels. Based on these results, the synergistic effect is induced by the interactions between proteins from different. This research provides a method for the subsequent development of new meat products and improvement of meat product quality, and also lays a theoretical foundation for composite research of proteins from different sources. © 2024 Society of Chemical Industry.

Enhancing the Intrinsic Antiplasmodial Activity and Improving the Stability and Selectivity of a Tunable Peptide Scaffold Derived from Human Platelet Factor 4.

The control of malaria, a disease caused by Plasmodium parasites that kills over half a million people every year, is threatened by the continual emergence and spread of drug resistance. Therefore, new molecules with different mechanisms of action are needed in the antimalarial drug development pipeline. Peptides developed from host defense molecules are gaining traction as anti-infectives due to theood of inducing drug resistance. Human platelet factor 4 (PF4) has intrinsic activity against P. falciparum, and a macrocyclic helix-loop-helix peptide derived from its active domain recapitulates this activity. In this study, we used a stepwise approach to optimize first-generation PF4-derived internalization peptides (PDIPs) by producing analogues with substitutions to charged and hydrophobic amino acid residues or with modifications to terminal residues including backbone cyclization. We evaluated the in vitro activity of PDIP analogues against P. falciparum compared to their overall helical structure, resistance to breakdown by serum proteases, selective binding to negatively charged membranes, and hemolytic activity. Next, we combined antiplasmodial potency-enhancing substitutions that retained favorable membrane and cell-selective properties onto the most stable scaffold to produce a backbone cyclic PDIP analogue with four-fold improved activity against P. falciparum compared to first-generation peptides. These studies demonstrate the ability to modify PDIP to select for and combine desirable properties and further validate the suitability of this unique peptide scaffold for developing a new molecule class that is distinct from existing antimalarial drugs.

Investigation of Antioxidant Mechanisms of Novel Peptides Derived from Asian Swamp Eel Hydrolysate in Chemical Systems and AAPH-Induced Human Erythrocytes.

Sixteen novel antioxidant peptides from Asian swamp eel (ASE) were identified in previous studies. However, their chemical and cellular antioxidant mechanisms remain unclear. Molecular docking of these peptides with ABTS and DPPH radicals revealed the critical role of hydrogen bonding and Pi-Pi stacking hydrophobic interactions between hydrophobic amino acid residues and free radicals. Residues, such as tryptophan, proline, leucine, and valine, played significant roles in these interactions. All these peptides exhibited notable erythrocyte morphoprotective effects in a model of AAPH-induced oxidative damage of human erythrocytes. Erythrocyte hemolysis was reduced primarily through the modulation of both non-enzymatic (GSH/GSSG) and enzymatic antioxidant systems (SOD, CAT, and GSH-Px) by these peptides. A decrease in levels of MDA, LDH release, and hemoglobin oxidation was observed. Among the peptides, VLYPW demonstrated superior chemical and cellular antioxidant activities, which may be attributed to its higher levels of tyrosine and tryptophan, as well as to its increased hydrophobic amino acid content.

Promotion and modulation of amyloid fibrillation of bovine beta-lactoglobulin by hydroxychalcones

Hydroxychalcones are naturally occurring compounds having biological relevance. This work demonstrates the synthesis of some chalcones having hydrophobic and polar groups and the investigation of their effect on the stability of a model protein beta-lactoglobulin (β-lg). An easy and simple method (Simon-Smith) was utilized to synthesize the four chalcone compounds. The binding of the chalcone molecules to the protein destabilized the protein structure and subsequently exposed the hydrophobic cores resulting in the aggregation of β-lg under thermal conditions. Using multiple spectroscopic methods (UV-Vis, fluorescence, FT-IR), imaging techniques like TEM, and theoretical tools were used to monitor the formation of protein aggregation and to understand the underlying mechanism. Exposures of hydrophobic amino acid residues in the aqueous medium by binding of the chalcones are responsible for protein aggregation through protein-protein interactions. It is sensitive to the polarity of the hydroxychalcones. In this process, polar group-containing hydroxychalcones are less effective, and unsubstituted hydroxychalcones are most efficient in promoting the amyloid fibrillation of β-lg.

Effects and improvement mechanisms of ultrasonic pretreatment on the quality of fermented skim milk

Fermented skim milk is an ideal food for consumers such as diabetic and obese patients, but its low-fat content affects its texture and viscosity. In this study, we developed an effective pretreatment method for fermented skim milk using low-frequency ultrasound (US), and investigated the molecular mechanism of the corresponding quality improvement. The skim milk samples were treated by optimal ultrasonication conditions (336 W power for 7 min at 3 °C), which improved the viscosity, water-holding capacity, sensory attributes, texture, and microstructure of fermented skim milk (P < 0.05). Further mechanistic analyses revealed that the US treatment enhanced the exposure of fluorescent amino acids within proteins, facilitating the cross-linking between casein and whey. The increased surface hydrophobicity of fermented milk indicates that the US treatment led to the exposure of hydrophobic amino acid residues inside proteins, contributing to the formation of a denser gel network; the average particle size of milk protein was reduced from 24.85 to 18.06 µm, which also contributed to the development of a softer curd texture. This work is the first attempt to explain the effect of a low-frequency ultrasound treatment on the quality of fermented skim milk and discuss the molecular mechanism of its improvement.

Binding and Stabilization of a Semiquinone Radical by an Artificial Metalloenzyme Containing a Binuclear Copper (II) Cofactor.

A binuclear Cu(II) cofactor was covalently bound to a lauric acid anchor. The resulting conjugate was characterized then combined with beta-lactoglobulin (βLG) to generate a new biohybrid following the so-called "Trojan horse" strategy. This biohybrid was examined for its effectiveness in the oxidation of a catechol derivative to the corresponding quinone. The resulting biohybrid did not exhibit the sought after catecholase activity, likely due to its ability to bind and stabilize the semiquinone radical intermediate DTB-SQ. This semi-quinone radical was stabilized only in the presence of the protein and was characterized using optical and magnetic spectroscopic techniques, demonstrating stability for over 16 hours. Molecular docking studies revealed that this stabilization could occur owing to interactions of the semi-quinone with hydrophobic amino acid residues of βLG.

Prediction of Pesticide Interactions with Proteins Involved in Human Reproduction by Using a Virtual Screening Approach: A Case Study of Famoxadone Binding CRBP-III and Izumo.

In recent years, the awareness that pesticides can have other effects apart from generic toxicity is growing. In particular, several pieces of evidence highlight their influence on human fertility. In this study, we investigated, by a virtual screening approach, the binding between pesticides and proteins present in human gametes or associated with reproduction, in order to identify new interactions that could affect human fertility. To this aim, we prepared ligand (pesticides) and receptor (proteins) 3D structure datasets from online structural databases (such as PubChem and RCSB), and performed a virtual screening analysis using Autodock Vina. In the comparison of the predicted interactions, we found that famoxadone was predicted to bind Cellular Retinol Binding Protein-III in the retinol-binding site with a better minimum energy value of -10.4 Kcal/mol and an RMSD of 3.77 with respect to retinol (-7.1 Kcal/mol). In addition to a similar network of interactions, famoxadone binding is more stabilized by additional hydrophobic patches including L20, V29, A33, F57, L117, and L118 amino acid residues and hydrogen bonds with Y19 and K40. These results support a possible competitive effect of famoxadone on retinol binding with impacts on the ability of developing the cardiac tissue, in accordance with the literature data on zebrafish embryos. Moreover, famoxadone binds, with a minimum energy value between -8.3 and -8.0 Kcal/mol, to the IZUMO Sperm-Egg Fusion Protein, interacting with a network of polar and hydrophobic amino acid residues in the cavity between the 4HB and Ig-like domains. This binding is more stabilized by a predicted hydrogen bond with the N185 residue of the protein. A hindrance in this position can probably affect the conformational change for JUNO binding, avoiding the gamete membrane fusion to form the zygote. This work opens new interesting perspectives of study on the effects of pesticides on fertility, extending the knowledge to other typologies of interaction which can affect different steps of the reproductive process.

Identification and Free Radical Scavenging Activity of Oligopeptides from Mixed-Distillate Fermented Baijiu Grains and Soy Sauce Residue.

This study aimed to explore the potential antioxidant activity and mechanism of oligopeptides from sauce-aroma Baijiu. The oligopeptides of Val-Leu-Pro-Phe (VLPF), Pro-Leu-Phe (PLF), Val-Gly-Phe-Cys (VGFC), Leu-Tyr-Pro (LYP), Leu-Pro-Phe (LPF), and Phe-Thr-Phe (FTF) were identified by liquid chromatography-mass spectrometry (LC-MS) from the mixed-distillate of Baijiu fermented grains and soy sauce residue (MDFS). The antioxidant mechanism of these oligopeptides on scavenging DPPH•, ABTS•+, and hydroxide radicals was investigated, respectively. Among them, VGFC had the strongest potential antioxidant activity, which was responsible for its hydrogen bonds with these radicals with high affinity. The binding energies between VGFC and these radicals were -1.26 kcal/mol, -1.33 kcal/mol, and -1.93 kcal/mol, respectively. Additionally, free radicals prefer to bind the oligopeptide composed of hydrophobic amino acid residues such as Leu, Val, Phe, and Pro, thus being scavenged for exerting antioxidant activity. It provided a new idea for the development and utilization of bioactive oligopeptides in sauce-aroma Baijiu.

Crystal structure of a newly identified M61 family aminopeptidase with broad substrate specificity that is solely responsible for recycling acidic amino acids.

Aminopeptidases with varied substrate specificities are involved in different crucial physiological processes of cellular homeostasis. They also have wide applications in food and pharma industries. Within the bacterial cell, broad specificity aminopeptidases primarily participate in the recycling of amino acids by degrading oligopeptides generated via primary proteolysis mediated by cellular ATP-dependent proteases. However, in bacteria, a truly broad specificity enzyme, which can cleave off acidic, basic, Gly and hydrophobic amino acid residues, is extremely rare. Here, we report structure-function of a putative glycyl aminopeptidase (M61xc) from Xanthomonas campestris pv campestris (Xcc) belonging to the M61 peptidase family. The enzyme exhibits broad specificity and cleaves Ala, Leu, Asp, Glu, Met, Ser, Phe, Tyr, Gly, Arg, and Lys at the N terminus, optimally of peptides with a length of 3-7 amino acids. Further, we report the high-resolution crystal structure of M61xc in the apo form (2.1 Å) and bestatin-bound form (1.95 Å), detailing its catalytic and substrate preference mechanisms. Comparative analysis of enzyme activity in crude cell extracts from both wild-type and m61xc-knockout mutant strains of Xcc has elucidated the unique intracellular role of M61xc. This study suggests that M61xc is the exclusive enzyme in these bacteria that is responsible for liberating Asp/Glu residues from the N-termini of peptides. Also, in view of its broad specificity and peptide degradation ability, it could be considered equivalent to M1 or other oligomeric peptidases from families like M17, M18, M42 or S9, who have an important auxiliary role in post-proteasomal protein degradation in prokaryotes.

Unlocking the Therapeutic Potential of a Manila Clam-Derived Antioxidant Peptide: Insights into Mechanisms of Action and Cytoprotective Effects against Oxidative Stress.

Reactive oxygen species (ROS) are implicated in various pathological conditions due to their ability to induce oxidative damage to cellular components. In this study, we investigated the antioxidant properties of a peptide isolated from the hydrolysate of Manila clam (Ruditapes philippinarum) muscle. Purification steps yielded RPTE2-2-4, exhibiting potent scavenging activities against DPPH•, HO•, and O2•-, akin to Vitamin C. Structural analysis showed that the isolated peptide, LFKKNLLTL, exhibited characteristics associated with antioxidant activity, including a short peptide length and the presence of aromatic and hydrophobic amino acid residues. Moreover, our study demonstrated the cytoprotective effects of the peptide against H2O2-induced oxidative stress in HepG2 cells. Pretreatment with the peptide resulted in a dose-dependent reduction in intracellular ROS levels and elevation of glutathione (GSH) levels, indicating its ability to modulate cellular defense mechanisms against oxidative damage. Furthermore, the peptide stimulated the expression of the cytoprotective enzyme heme oxygenase-1 (HO-1), further reinforcing its antioxidant properties. Overall, our findings highlight the potential of the Manila clam-derived peptide as a natural antioxidant agent with therapeutic implications for oxidative stress-related diseases. Further investigation into its mechanisms of action and in vivo efficacy is warranted to validate its therapeutic potential.

Sodium Alginate–Soy Protein Isolate–Chitosan–Capsaicin–Nanosilver Multifunctional Antibacterial Composite Gel

We constructed a sodium alginate/soy protein isolate/chitosan gel system and incorporated silver nanoparticles reduced by capsaicin into the system, forming a sodium alginate–soy protein isolate–chitosan–capsaicin–silver nanoparticle composite gel (SA/SPI/CTS/CAP/Ag). In tests, the SA/SPI/CTS/CAP/Ag gel exhibited excellent antimicrobial properties. Using the agar diffusion method, the inhibition zone diameter for Staphylococcus aureus was determined to be 29.5 mm. Soy protein isolate (SPI), containing a large number of hydrophobic amino acid residues, effectively enhanced the moisture retention capability of the gel and improved its stability to a certain extent at an appropriate addition concentration. In a milk preservation experiment, the SA/SPI/CTS/CAP/Ag gel significantly extended the shelf-life of the milk. In dye adsorption experiments, the adsorption curve of the SA/SPI/CTS/CAP/Ag gel well fitted a pseudo-second-order kinetic model. It showed a degree of adsorption capacity for methylene blue, malachite green, methyl orange, and Congo red, with the most significant adsorption effect for malachite green being 42.48 mg/g. Considering its outstanding antimicrobial performance, preservation ability, and adsorption capacity, the SA/SPI/CTS/CAP/Ag gel holds significant potential in wastewater treatment and as an antimicrobial gel in the exploration of food preservation.

Risk mitigation strategy and mechanism analysis of neonicotinoid pesticides on earthworms

Neonicotinoid insecticides (NNIs) are a new class of widely used insecticides with certain risks to non-target organisms, like earthworms. The gray correlation method was used to calculate the comprehensive risk effect value of acute toxicity (LC50) and bioaccumulation (logKow) of NNIs on earthworms. A comprehensive effects three-dimensional quantitative structure–activity relationship (3D-QSAR) model was constructed, using NNIs molecular structures and the comprehensive effect value as the independent and dependent variables, respectively. One of the representatives guadipyr (GUA) was selected as the template molecule for the molecular design and modification. A total of 63 NNIs alternatives were designed with a reduced comprehensive value higher than 10%, and as high as 42%. After screening, 15 NNIs alternatives were screened with decreased acute toxicity to earthworms, bioaccumulation effects and improved functional property. The calculated primary acute risk quotient of earthworms shows that the designed NNIs alternatives have lower earthworm risks (reduction of 70.48–99.99%). Results also found that the electronic, geometric and topological parameters of NNIs are the key descriptors that affect NNIs alternatives' toxicity. The number of hydrophobic interaction amino acid residues in NNIs molecules also contributes to the acute toxicity and the bioaccumulation of NNIs alternatives on earthworms. This study aims to design and screen functionally improved and environmentally friendly NNIs alternatives that have low risk to earthworms and provide theoretical methods and new ideas for the risk control and development of pesticides represented by NNIs.

Reduced Macrophage Uptake of Nanoparticles through Surface Modification of Polypeptides with Valine Residues†

Comprehensive SummaryThe structural and surface properties of nanomedicines play an important role in determining their biological fate. Surface chemistry of nanomedicines is one of the key parameters, where researchers used various strategies such as PEGylation to avoid the undesired clearance of nanoparticles (NPs) for enhanced targeting effect. Nevertheless, the fine‐tuning of surface chemistry through polymer functionalization remains largely unexplored. In this concise report, we find that the incorporation of only 10 mol% valine residues into the surface‐anchored poly(L‐glutamic acid) significantly lowered the macrophage uptake of NPs. The introduction of other hydrophobic amino acid residues, however, increased the NPs internalization instead. The chirality and the side‐chain structure of valine played an important role in the unexpected uptake behavior. We believe this work highlights the impact of slight changes of the surface‐anchored polymer structure on the behavior of NPs, drawing people's attention to the careful design of surface chemistry to optimize the nanomedicine design.

Molecular Characterization of Alpha-Amylase of Aspergillus flavus and Aspergillus oryzae: An In Silico Study

Alpha amylases (EC 3.2.1.1.) hydrolyze polysaccharides like starch and glycogen to create oligosaccharides of different sizes by random cleavage of internal 1, 4-glucosidic linkages. These enzymes are produced by many different bacteria and fungi. In this investigation, α-amylase from Aspergillus flavus and Aspergillus oryzae was taken into consideration. Amino acid sequences and protein structure were retrieved from databases. Sequences of Aspergillus oryzae possess a high number of charged residues whereas Aspergillus flavus have a higher abundance of uncharged polar and hydrophobic amino acid residues. 3 common superfamilies were observed between both species. The alignment of sequences showed their similar conservative nature. Non-covalent intra-protein interactions like the salt bridge, aromatic-aromatic interactions, aromatic-sulfur interactions and cation-pi interactions helped to increase the stability of α-amylase of Aspergillus oryzae. The tunnels and cavities also help to increase the functionality and catalytic activity of α-amylase. This study will also be helpful for protein engineering.