Amino Acid Residues Research Articles

A conserved oomycete effector RxLR23 triggers plant defense responses by targeting ERD15La to release NbNAC68

Oomycete pathogens deliver many effectors to enhance virulence or suppress plant immunity. Plant immune networks are interconnected, in which a few effectors can trigger a strong defense response when recognized by immunity-related proteins. How effectors activate plant defense response remains poorly understood. Here we report Phytophthora capsici effector RxLR23KM can induce plant cell death and plant immunity. RxLR23KM specifically binds to ERD15La, a regulator of abscisic acid and salicylic acid pathway, and the binding intensity depends on the amino acid residues (K93 and M320). NbNAC68, a downstream protein of ERD15La, can stimulate plant immunity that is compromised after binding with ERD15La. Silencing of NbNAC68 substantially prevents the activation of plant defense response. RxLR23KM binds to ERD15La, releasing NbNAC68 to activate plant immunity. These findings highlight a strategy of plant defense response that ERD15La as a central regulator coordinates RxLR23KM to regulate NbNAC68-triggered plant immunity.

Removal of Residual DNA and Host Cell Proteins for the Purification of Recombinant Staphylokinase Expressed in Escherichia coli

Removal of Residual DNA and Host Cell Proteins for the Purification of Recombinant Staphylokinase Expressed in <i>Escherichia coli</i>

Ubiquitin-derived artificial binding proteins targeting oncofetal fibronectin reveal scaffold plasticity by β-strand slippage

Affilin proteins, artificial binding proteins based on the ubiquitin scaffold, have been generated by directed protein evolution to yield de-novo variants that bind the extra-domain B (EDB) of oncofetal fibronectin, an established marker of tumor neovasculature. The crystal structures of two EDB-specific Affilin variants reveal a striking structural plasticity of the ubiquitin scaffold, characterised by β-strand slippage, leading to different negative register shifts of the β5 strands. This process recruits amino acid residues from β5 towards the N-terminus to an adjacent loop region and subsequent residues into β5, respectively, remodeling the binding interface and leading to target specificity and affinity. Protein backbone alterations resulting from β-strand register shifts, as seen in the ubiquitin fold, can pose additional challenges to protein engineering as structural evidence of these events is still limited and they are difficult to predict. However, they can surface under the selection pressure of directed evolution and suggest that backbone plasticity allowing β-strand slippages can increase structural diversity, enhancing the evolutionary potential of a protein scaffold.

The Ile35 Residue of the ALS-Associated Mutant SOD1 Plays a Crucial Role in the Intracellular Aggregation of the Molecule.

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with an unknown pathogenesis. It has been reported that mutations in the gene for Cu/Zn superoxide dismutase (SOD1) cause familial ALS. Mutant SOD1 undergoes aggregation and forms amyloid more easily, and SOD1-immunopositive inclusions have been observed in the spinal cords of ALS patients. Because of this, SOD1 aggregation is thought to be related to the pathogenesis of ALS. Some core regions of amyloid have been identified, but the issue of whether these regions form aggregates in living cells remains unclear, and the mechanism responsible for intracellular SOD1 aggregation also remains unclear. The findings reported in this study indicate that the aggregation of the ALS-linked mutant SOD1-EGFP was significantly enhanced when the BioID2 gene was fused to the N-terminus of the mutant SOD1-EGFP plasmid for cellular expression. Expression of a series of BioID2-(C-terminal deletion peptides of SOD1)-EGFP permitted us to identify 1-35 as a minimal N-terminal sequence and Ile35 as an essential amino acid residue that contributes to the intracellular aggregation of SOD1. The findings also showed that an additional substitution of Ile35 with Ser into the ALS mutant SOD1 resulted in the significant suppression of aggregate formation. The fact that no Ile35 mutations have been reported to date in ALS patients indicates that all ALS mutant SOD1s contain Ile35. Taken together, we propose that Ile35 plays a pivotal role in the aggregation of the ALS-linked SOD1 and that this study will contribute to our understanding of the mechanism responsible for SOD1 aggregation.

In silico designing of multi-epitope vaccine against canine parvovirus using reverse vaccinology.

Canine parvovirus (CPV-2) is a highly contagious virus affecting dogs worldwide, posing a significant threat. The VP2 protein stands out as the predominant and highly immunogenic structural component of CPV-2. Soon after its emergence, CPV-2 was replaced by variants known as CPV-2a, 2b and 2c, marked by changes in amino acid residue 426 of VP2. Additional amino acid alterations have been identified within VP2, with certain modifications serving as signatures of emerging variants. In Brazil, CPV-2 outbreaks persist with diverse VP2 profiles. Vaccination is the main preventive measure against the virus. However, the emergence of substitutions presents challenges to conventional vaccine methods. Commercial vaccines are formulated with strains that usually do not match those currently circulating in the field. To address this, the study aimed to investigate CPV-2 variants in Brazil, predict epitopes, and design an in silico vaccine tailored to local variants employing reverse vaccinology. The methodology involved data collection, genetic sequence analysis, and amino acid comparison between field strains and vaccines, followed by the prediction of B and T cell epitope regions. The predicted epitopes were evaluated for antigenicity, allergenicity and toxicity. The final vaccine construct consisted of selected epitopes linked to an adjuvant and optimized for expression in Escherichia coli. Structural predictions confirmed the stability and antigenicity of the vaccine, while molecular docking demonstrated interaction with the canine toll-like receptor 4. Molecular dynamics simulations indicated a stable complex formation. In silico immune simulations demonstrated a progressive immune response post-vaccination, including increased antibody production and T-helper cell activity. The multi-epitope vaccine design targeted prevalent CPV-2 variants in Brazil and potentially other regions globally. However, experimental validation is essential to confirm our in silico findings.

Synthesis and Antifungal ActivitiesofGlucosamineAromatic Derivativesagainst Four Phytopathogenic Fungi of Crops.

A series of diversified glucosamine derivatives(3a-3y)was synthesized and theirantifungal activitywas examined against four kinds of phytopathogens, Fusarium graminearum(F. graminearum), Fusarium moniliforme(F. moniliforme), Curvularia. lunata(C. lunata), and Rhizoctonia solani (R. solani)which cause seriously economic losses worldwide by affecting crops. The compound 3oshowedremarkable antifungal activity against F. graminearumwith EC50values of 3.96 μg/mL, compared to the standard drug triadimefon (10.1μg/mL).3D-QSAR model with the statistically recommended values (r2= 0.915, q2=0.872)show that positive charge group and bulky groupin the benzyl ring were favorable for the antifungal activity. Enzyme activityassays confirmed that 3ohasamoderate inhibition oftrehalasewith inhibition rate of 51.4%at 5 μg/mL, which is comparable to those of commercial inhibitors validamycin Awith inhibition rate of 83.3%.Molecular docking analysis revealed that 3oalso had a hydrogen bond interaction with key amino acid residue compared to validoxylamine.

Design of Hepatitis C Protease Inhibitors Based on Knottin Fold

AbstractKnottins are very stable peptides (also called miniproteins) containing approximately 30 amino acid residues. Their structures are stabilized by three disulfide bonds forming a characteristic ‘pseudo‐knotted’ structure. This research was devoted to the design of potential inhibitors of human hepatitis C (HCV) NS3 protease by means of knottin fold using loop grafting, amino acid residues replacements and L/D amino acid epimerization. The initial structure used for design was a trypsin inhibitor from Momordica cochinchinensis seeds, MCOTI‐II. Modifications of the knottin template for optimization of the NS3 protease‐peptide interaction included deletion of several residues from the N‐terminus, replacement of residues in‐ and outside the inhibitor loop and replacement of certain L‐amino acids by their D‐stereoisomers. Stability of modified knottins and their complexes with HCV protease were evaluated by molecular dynamics simulation. Binding energy values for protein‐knottin complexes were calculated by MM‐GBSA method. The designed modified knottin characterized by the highest stability of the complex with HCV NS3 protease, was proposed for further experimental testing.

The inhibitory activity of Flos Sophorae Immaturus extract and its major flavonoid components on pancreatic lipase

Inhibition of pancreatic lipase (PL) is a strategy to prevent obesity. The inhibitory effects of Flos Sophorae Immaturus (FSI) extract and its main flavonoid components, rutin and quercetin, on PL were investigated. The contents of rutin and quercetin in FSI extract were 44.10 ± 1.33 % and 6.07 ± 1.62 %, respectively. The IC50 values of FSI extract, rutin and quercetin on PL were 322, 258 and 71 μg/mL, respectively. Rutin and quercetin inhibited PL in a reversible and noncompetitive manner. The combination of rutin and quercetin exhibited synergistic inhibitory effects at low concentration. The binding of rutin/quercetin with PL caused the fluorescence quenching of protein. Fluorescence titration showed the binding affinity of quercetin with PL protein was stronger than that of rutin. Circular dichroism analysis showed the binding changed the secondary structure of PL with an increase in random coil and a decrease in α-Helix and β-Sheet. Molecular docking revealed that rutin and quercetin could interact with the amino acid residues around the catalytic site through multiple secondary interactions. In vivo studies showed that FSI extract can reduce fat absorption and promote fecal fat excretion through inhibition of PL activity, and the effects were mainly due to rutin and quercetin.

HLA Mismatches Identified by a Novel Algorithm Predict Risk of Antibody-mediated Rejection From De Novo Donor-specific Antibodies.

The development of de novo donor-specific antibodies (dnDSA) and antibody-mediated rejection (AMR) remains a barrier to long-term graft and patient survival. Most dnDSA are directed against mismatched donor HLA-DQ antigens. Here, we describe a novel algorithm, which we have termed categorical amino acid mismatched epitope, to evaluate HLA-DQ mismatches. In this algorithm, amino acid residues of HLA-DQ protein were categorized into 4 groups based on their chemical characteristics. The likelihood of categorically mismatched peptides presented by the recipient's HLA-DRB1 was expressed as a normalized value, %Rank score. Categorical HLA-DQ mismatches were analyzed in 386 heart transplant recipients who were mismatched with their donors at the HLA-DQB1 locus. We found that the presence of DQB1 mismatches with %Rank score ≤1 was associated with the development of dnDSA (P = 0.002). Furthermore, dnDSA increased the risk of AMR only in recipients who had DQ mismatches with %Rank score ≤1 (hazard ratio = 5.8), but the freedom from AMR was comparable between recipients with dnDSA and those without dnDSA if %Rank scores of DQ mismatching were >1. These results suggest that HLA-DQ mismatches evaluated by the categorical amino acid mismatched epitope algorithm can stratify the risk of development of dnDSA and AMR in heart transplant recipients.

Antiplasmodial potential of isolated xanthones from Mesua ferrea Linn. roots: an in vitro and in silico molecular docking and pharmacokinetics study

BackgroundMalaria is a major global health concern, particularly in tropical and subtropical countries. With growing resistance to first-line treatment with artemisinin, there is an urgent need to discover novel antimalarial drugs. Mesua ferrea Linn., a plant used in traditional medicine for various purposes, has previously been investigated by our research group for its cytotoxic properties. The objective of this study was to explore the compounds isolated from M. ferrea with regards to their potential antiplasmodial activity, their interaction with Plasmodium falciparum lactate dehydrogenase (PfLDH), a crucial enzyme for parasite survival, and their pharmacokinetic and toxicity profiles.MethodsThe isolated compounds were assessed for in vitro antiplasmodial activity against a multidrug-resistant strain of P. falciparum K1 using a parasite lactate dehydrogenase (pLDH) assay. In vitro cytotoxicity against Vero cells was determined using the MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay. The interactions between the isolated compounds and the target enzyme PfLDH were investigated using molecular docking. Additionally, pharmacokinetic and toxicity properties were estimated using online web tools SwissADME and ProTox-II, respectively.ResultsAmong the seven compounds isolated from M. ferrea roots, rheediachromenoxanthone (5), which belongs to the pyranoxanthone class, demonstrated good in vitro antiplasmodial activity, with the IC50 being 19.93 µM. Additionally, there was no toxicity towards Vero cells (CC50 = 112.34 µM) and a selectivity index (SI) of 5.64. Molecular docking analysis revealed that compound (5) exhibited a strong binding affinity of − 8.6 kcal/mol towards PfLDH and was stabilized by forming hydrogen bonds with key amino acid residues, including ASP53, TYR85, and GLU122. Pharmacokinetic predictions indicated that compound (5) possessed favorable drug-like properties and desired pharmacokinetic characteristics. These include high absorption in the gastrointestinal tract, classification as a non-substrate of permeability glycoprotein (P-gp), non-inhibition of CYP2C19, ease of synthesis, a high predicted LD50 value of 4,000 mg/kg, and importantly, non-hepatotoxic, non-carcinogenic, and non-cytotoxic effects.ConclusionsThis study demonstrated that compounds isolated from M. ferrea exhibit activity against P. falciparum. Rheediachromenoxanthone has significant potential as a scaffold for the development of potent antimalarial drugs.

Female-Biased Odorant Receptor MmedOR48 in the Parasitoid Microplitis mediator Broadly Tunes to Plant Volatiles.

Odorant receptors (ORs) play a crucial role in insect chemoreception. Here, a female-biased odorant receptor MmedOR48 in parasitoid Microplitis mediator was fully functionally characterized. The qPCR analysis suggested that the expression level of MmedOR48 increased significantly after adult emergence and was expressed much more in the antennae. Moreover, an in situ hybridization assay showed MmedOR48 was extensively located in the olfactory sensory neurons. In two-electrode voltage clamp recordings, recombinant MmedOR48 was broadly tuned to 23 kinds of volatiles, among which five plant aldehyde volatiles excited the strongest current recording values. Subsequent molecular docking analysis coupled with site-directed mutagenesis demonstrated that key amino acid residues Thr142, Gln80, Gln282, and Thr312 together formed the binding site in the active pocket for the typical aldehyde ligands. Furthermore, ligands of MmedOR48 could stimulate electrophysiological activities in female adults of the M. mediator. The main aldehyde ligand, nonanal, aroused significant behavioral preference of M. mediator in females than in males. These findings suggest that MmedOR48 may be involved in the recognition of plant volatiles in M. mediator, which provides valuable insight into understanding the olfactory mechanisms of parasitoids.

In vitro antioxidant activity, QSAR, in silico toxicity prediction, molecular docking studies, and molecular dynamics of a series of N-ferrocenylmethylanilines as potent antioxidant agents

The superoxide anion radical scavenging activities of a series of twenty-eight ferrocenylmethylaniline derivatives were measured in an in vitro study followed by in silico studies which included quantitative structure-activity relationship (QSAR), toxicity prediction, molecular docking studies, and molecular dynamics simulations. Multilinear regression analysis was employed to establish a quantitative correlation between the scavenging activity of superoxide anion radicals and various structural properties. The QSAR model obtained underwent validation, demonstrating statistical significance with a squared fitting correlation coefficient (R2) of 0.934, an adjusted squared correlation coefficient (R2 adj) value of 0.849, and a cross-validation coefficient (Q2) value of 0.873. Additionally, the calculated Fisher ratio (F) value of 36.525 indicates the model's strong predictability. Toxicity perdition studies demonstrated that among the five most potent compounds, FMA27 and FMA12 were predicted to be non-toxic. The molecular Docking study revealed that compound FMA23 exhibited the least activity against the glutathione reductase enzyme, with the highest inhibitory concentration recorded at 4.16 × 10–6 M and the lowest docking scores observed at −7.34 kcal.mol-1. Interactions between the compound and the amino acid residues of glutathione reductase were primarily hydrophobic and π-cation in nature. Analysis of root mean square deviation (RMSD), radius of gyration (Rg), and root mean square fluctuation (RMSF), from molecular dynamics study, revealed stable fluctuations in protein backbone conformations, consistent compactness of the complex, and minimal fluctuations in most protein residues, respectively.

Evaluation of the potential food allergy risks of human lactoferrin expressed in Komagataella phaffii.

Prior to the introduction of novel food ingredients into the food supply, safety risk assessments are required, and numerous prediction models have been developed and validated to evaluate safety. The allergenic risk potential of Helaina recombinant human lactoferrin (rhLF, Effera™), produced in Komagataella phaffii (K. phaffii) was assessed by literature search, bioinformatics sequence comparisons to known allergens, glycan allergenicity assessment, and a simulated pepsin digestion model. The literature search identified no allergenic risk for Helaina rhLF, K. phaffii, or its glycans. Bioinformatics search strategies showed no significant risk for cross-reactivity or allergenicity between rhLF or the 36 residual host proteins and known human allergens. Helaina rhLF was also rapidly digested in simulated gastric fluid and its digestibility profile was comparable to human milk lactoferrin (hmLF), further demonstrating a low allergenic risk and similarity to the hmLF protein. Collectively, these results demonstrate a low allergenic risk potential of Helaina rhLF and do not indicate the need for further clinical testing or serum IgE binding to evaluate Helaina rhLF for risk of food allergy prior to introduction into the food supply.

Enhancing the rigidity of the catalytic pocket entrance to improve catalytic efficiency and thermal stability of alginate Lyase from Pseudoalteromonas

Alginate lyase plays a critical role in the production of alginate oligosaccharides (AOS), necessitating efficient activity and a certain level of thermal stability for industrial AOS production. In this study, through sequence alignment and structural analysis, a non-catalytic amino acid residue, Ala195, located at the entrance of the catalytic pocket was identified. This residue is crucial for the catalytic efficiency and thermal stability of Alg2944, a member of the polysaccharide lyase family 18. The specific activities of A195F, A195I, and A195L were enhanced by 1.84-, 1.39-, and 1.98-fold, respectively, while the thermal stability of mutants A195L and A195I showed significant improvements at 35 °C and 40 °C compared to the wild-type (WT) enzyme. Furthermore, molecular docking, structural analysis, and molecular dynamics (MD) simulations revealed that the enhanced specific activity and thermal stability of the A195L mutant can be attributed to the creation of a hydrophobic pocket, increased rigidity in the loop region, and a notably lower binding free energy of the A195L mutant (-45.96 ± 7.69 kcal/mol) compared to the WT (-38.40 ± 4.25 kcal/mol). These findings underscore the essential role of rigidity and hydrophobicity at the entrance of the catalytic pocket in ensuring both catalytic efficiency and thermal stability of alginate lyase.

6-Phosphogluconate dehydrogenase 2 bridges the OPP and shikimate pathways to enhance aromatic amino acid production in plants.

The oxidative pentose phosphate (OPP) pathway provides metabolic intermediates for the shikimate pathway and directs carbon flow to the biosynthesis of aromatic amino acids (AAAs), which serve as basic protein building blocks and precursors of numerous metabolites essential for plant growth. However, genetic evidence linking the two pathways is largely unclear. In this study, we identified 6-phosphogluconate dehydrogenase 2 (PGD2), the rate-limiting enzyme of the cytosolic OPP pathway, through suppressor screening of arogenate dehydrogenase 2 (adh2) in Arabidopsis. Our data indicated that a single amino acid substitution at position 63 (glutamic acid to lysine) of PGD2 enhanced its enzyme activity by facilitating the dissociation of products from the active site of PGD2, thus increasing the accumulation of AAAs and partially restoring the defective phenotype of adh2. Phylogenetic analysis indicated that the point mutation occurred in a well-conserved amino acid residue. Plants with different amino acids at this conserved site of PGDs confer diverse catalytic activities, thus exhibiting distinct AAAs producing capability. These findings uncover the genetic link between the OPP pathway and AAAs biosynthesis through PGD2. The gain-of-function point mutation of PGD2 identified here could be considered as a potential engineering target to alter the metabolic flux for the production of AAAs and downstream compounds.

Effect of the killing method and developmental stage on cricket (Acheta domesticus) composition and chitin recovery

Abstract After receiving a positive safety assessment as a novel food by the European Food Safety Authority, Acheta domesticus (house cricket) was extensively studied due to its recognised high nutritional value. However, the nutritional quality of crickets depends on several factors related to the insect itself (e.g. metamorphic stage, gender, habitat, and diet) or processing (e.g. killing methods). These variables also influence the isolation of the insect’s main components: proteins, lipids, and chitin. Notably, chitin purification is particularly challenging in insects. This study aimed to evaluate the influence of two killing methods (blanching and freezing) and five developmental stages (hatching, three nymphs, and adult) on the nutritional composition of crickets. The impact of these factors was also assessed in terms of chitin purification. Different macronutrients were found to be maximised at different developmental stages, suggesting that the stage can be selected based on the target nutritional value. Chitin with a higher purity was obtained from 28-day crickets because of the lowest percentage of protein bound to chitin. In the chitin samples of the crickets in the middle stages killed by blanching, the proteins bound to chitin were lower than in the freezing one, possibly due to lower activation of the melanisation and sclerotization pathways. In addition, these residual proteins had a defined amino acid composition, suggesting the presence of cuticular proteins capable of binding chitin.

Enterovirus 3A protein disrupts endoplasmic reticulum homeostasis through interaction with GBF1.

Enteroviruses are single-stranded, positive-sense RNA viruses causing endoplasmic reticulum (ER) stress to induce or modulate downstream signaling pathways known as the unfolded protein responses (UPR). However, viral and host factors involved in the UPR related to viral pathogenesis remain unclear. In the present study, we aimed to identify the major regulator of enterovirus-induced UPR and elucidate the underlying molecular mechanisms. We showed that host Golgi-specific brefeldin A-resistant guanine nucleotide exchange factor 1 (GBF1), which supports enteroviruses replication, was a major regulator of the UPR caused by infection with enteroviruses. In addition, we found that severe UPR was induced by the expression of 3A proteins encoded in human pathogenic enteroviruses, such as enterovirus A71, coxsackievirus B3, poliovirus, and enterovirus D68. The N-terminal-conserved residues of 3A protein interact with the GBF1 and induce UPR through inhibition of ADP-ribosylation factor 1 (ARF1) activation via GBF1 sequestration. Remodeling and expansion of ER and accumulation of ER-resident proteins were observed in cells infected with enteroviruses. Finally, 3A induced apoptosis in cells infected with enteroviruses via activation of the protein kinase RNA-like endoplasmic reticulum kinase (PERK)/C/EBP homologous protein (CHOP) pathway of UPR. Pharmaceutical inhibition of PERK suppressed the cell death caused by infection with enteroviruses, suggesting the UPR pathway is a therapeutic target for treating diseases caused by infection with enteroviruses.IMPORTANCEInfection caused by several plus-stranded RNA viruses leads to dysregulated ER homeostasis in the host cells. The mechanisms underlying the disruption and impairment of ER homeostasis and its significance in pathogenesis upon enteroviral infection remain unclear. Our findings suggested that the 3A protein encoded in human pathogenic enteroviruses disrupts ER homeostasis by interacting with GBF1, a major regulator of UPR. Enterovirus-mediated infections drive ER into pathogenic conditions, where ER-resident proteins are accumulated. Furthermore, in such scenarios, the PERK/CHOP signaling pathway induced by an unresolved imbalance of ER homeostasis essentially drives apoptosis. Therefore, elucidating the mechanisms underlying the virus-induced disruption of ER homeostasis might be a potential target to mitigate the pathogenesis of enteroviruses.

Regulation of NS5B Polymerase Activity of Hepatitis C Virus by Target Specific Phytotherapeutics: An In-Silico Molecular Dynamics Approach.

Chronic hepatitis caused by the hepatitis C virus (HCV) is closely linked with the advancement of liver disease. The research hypothesis suggests that the NS5B enzyme (non-structural 5B protein) of HCV plays a pivotal role in facilitating viral replication within host cells. Hence, the objective of the present investigation is to identify the binding interactions between the structurally diverse phytotherapeutics and those of the catalytic residue of the target NS5B polymerase protein. Results of our docking simulations reveal that compounds such as arjunolic acid, sesamin, arjungenin, astragalin, piperic acid, piperidine, piperine, acalyphin, adhatodine, amyrin, anisotine, apigenin, cuminaldehyde, and curcumin exhibit a maximum of three interactions with the catalytic residues (Asp 220, Asp 318, and Asp 319) present on the Hepatitis C virus NS5B polymerase of HCV. Molecular dynamic simulation, particularly focusing on the best binding lead compound, arjunolic acid (-8.78 kcal/mol), was further extensively analyzed using RMSD, RMSF, Rg, and SASA techniques. The results of the MD simulation confirm that the NS5B-arjunolic acid complex becomes increasingly stable from 20 to 100 ns. The orientation of both arjunolic acid and sofosbuvir triphosphate (standard) within the active site was investigated through DCCM, PCA, and FEL analysis, indicating highly stable interactions of the lead arjunolic acid with the catalytic region of the NS5B enzyme. The findings of our current investigation suggest that bioactive therapeutics like arjunolic acid could serve as promising candidates for limiting the NS5B polymerase activity of the hepatitis C virus, offering hope for the future of HCV treatment.

Inhibition of human epidermal growth factor receptor-2 protein by some alkaloid inhibitors

BackgroundHuman Epidermal Growth Factor Receptor-2 (HER2), a transmembrane tyrosine kinase receptor, has been associated with several types of cancer, including breast, lung, ovarian, etc. Therefore, this receptor is targeted by a variety of therapeutic approaches for cancer treatments. The alkaloid and lead compounds are among the selective and potent HER2 inhibitors that have been reported so far. MethodsThe present work involves molecular docking, molecular dynamics (MD) simulations, and density functional theory (DFT) calculations on alkaloid and lead compounds as HER2 inhibitors. Significant findingsThe docking results expressed that the alkaloids mainly interacted with Cys805, Val734, and Ala751 residues of HER2 protein. The MD simulation outcomes represented that all the complexes have adequate dynamic stability and flexibility based on the root mean square deviation, root mean square fluctuation, and radius of gyration. Furthermore, it is found that the strongest HER2 − ligand interaction belongs to the nocamycin I (NOI, ΔGbind = -12.84 kcal mol−1) molecule. The DFT calculations showed that electron density and the second − order perturbation stabilization energy values for HER2 − NOI interactions are higher than the other complexes. The molecular docking, MD simulation, and DFT calculation results are all in agreement and complementary. It is expected that the results obtained here can present very helpful information for the design of efficacious inhibitors for the treatment of HER2 − related cancer disease.

Reactivity of a Morita-Baylis-Hillman adduct derivative bearing a triphenylamine moiety with lysine models.

The reactivity of Morita-Baylis-Hillman Adduct (MBHA) derivative 7 was studied with different primary amine derivatives such as n-butylamine, Na-acetyl-L-lysine methyl ester, and a poly-(L-lysine) derivative as lysine models to obtain information about the possible reactions in complex protein environments. MBHA derivative 7 reacted with n-butylamine or Na-acetyl-L-lysine methyl ester producing monoadducts 9a or 9c, which showed bright emission features in the green region at 526-535 nm with photoluminescence quantum yield values in solutions of 73% and 51%, respectively. Based on these results, MBHA derivative 7 can be considered an interesting new fluorogenic probe potentially useful in the labelling of basic amino acid residues. Furthermore, similar to other MBHA derivatives, compound 7 showed the tendency to produce diadducts especially in polar solvents system where specific interactions between the extended aromatic moieties may play a major role.