Advances in the discovery of activin receptor-like kinase 5 (ALK5) inhibitors

Activin receptor‑like kinase-5 (ALK5) is an outstanding member of the transforming growth factor-β (TGF-β) family. (TGF-β) signaling pathway integrates pleiotropic proteins that regulate various cellular processes such as growth, proliferation, and differentiation. Dysregulation within the signaling pathway can cause variety of diseases, such as fibrosis, cardiovascular disease, and especially cancer, rendering ALK5 a potential drug target. Hence, various small molecules have been designed and synthesized as potent ALK5 inhibitors. In this review, we shed light on the current ATP-competitive inhibitors of ALK5 through diverse heterocyclic based scaffolds that are in clinical or pre-clinical phases of development. Moreover, we focused on the binding interactions of the compounds to the ATP binding site and the structure-activity relationship (SAR) of each scaffold, revealing new scopes for designing novel candidates with enhanced selectivity and metabolic profiles.

Metal-free production of natural blue colorants through anthocyanin-protein interactions

INTRODUCTION

The scarcity of naturally available sources for blue colorants has driven reliance on synthetic alternatives. Nevertheless, growing health concerns have prompted the development of naturally derived blue colorants, which remains challenging with limited success thus far. Anthocyanins (ACNs) are known for providing blue colors in plants, and metal complexation with acylated ACNs remains the primary strategy to generate stable blue hues. However, this approach can be costly and raise concerns regarding potential metal consumption risks.

OBJECTIVES

Our study aims to introduce a metal-free approach to achieve blue coloration in commonly distributed non-acylated 3-glucoside ACNs by exploring their interactions with proteins and unveiling the underlying mechanisms.

METHODS

Using human serum albumin (HSA) as a model protein, we investigated the structural influences of ACNs on their blue color generation using visible absorption spectroscopy, fluorescence quenching, and molecular simulations. Additionally, we examined the bluing effects of six proteins derived from milk and egg and identified the remarkable roles of bovine serum albumin (BSA) and lysozyme (LYS).

RESULTS

Our findings highlighted the importance of two or more hydroxyl or methoxyl substituents in the B-ring of ACNs for generating blue colors. Cyanidin-, delphinidin- and petunidin-3-glucoside, featuring two neighboring hydroxyl groups in the B-ring, exhibited blue coloration when interacting with HSA or LYS, driven primarily by favorable enthalpy changes. In contrast, malvidin-3-glucoside, with two methoxyl substituents, achieved blue coloration through interactions with HSA or BSA, where entropy change played significant roles.

CONCLUSION

Our work, for the first time, demonstrates the remarkable capability of widely distributed 3-glucoside ACNs to generate diverse blue shades through interactions with certain proteins. This offers a promising and straightforward strategy for the production of ACN-based blue colorants, stimulating further research in this field.

Molecular Modeling Techniques and In-Silico Drug Discovery

Molecular modeling is the technique to determine the overall structure of an unknown molecule, be it a small one or a macromolecule. The technique encompasses the method of screening ligand libraries for the development of new candidate drug molecules. All these aspects have become an essential topic of research. This field is truly interdisciplinary and finds its applications in almost all fields of life science research. In this chapter, an overview of the protocol associated with molecular modeling techniques will be discussed.

Mechanistic insights into pyridine exposure induced toxicity in model Eisenia fetida species: Evidence from whole-animal, cellular, and molecular-based perspectives

Pyridine and its derivatives are widely used in many applications and inevitably cause extreme scenarios of serious soil contamination, which pose a threat to soil organisms. Still, the eco-toxicological effects and underlying mechanisms of pyridine-caused toxicity toward soil fauna have not been well established. Thus, earthworms (Eisenia fetida), coelomocytes, and oxidative stress-related proteins were selected as targeted receptors to probe the ecotoxicity mechanism of extreme pyridine soil exposure targeted to earthworms by using a combination of in vivo animal experiments, cell-based in vitro tests, in vitro functional and conformational analyses, and in silico analyses. The results showed that pyridine caused severe toxicity to E. fetida at extreme environmental concentrations. Exposure of pyridine induced excessive ROS formation in earthworms, causing oxidative stress and various deleterious effects, including lipid damage, DNA injury, histopathological change, and decreased defense capacity. Also, pyridine destroyed the cell membrane of earthworm coelomic cells and triggered a significant cytotoxicity. Importantly, the intracellular ROS (e.g., O₂^-, H₂O₂, and OH·^-) was release-activated, which eventually inducing oxidative stress effects (lipid peroxidation, inhibited defense capacity, and genotoxicity) through the ROS-mediated mitochondrial pathway. Moreover, the antioxidant defence mechanisms in coelomocytes responded quickly to reduce ROS-mediated oxidative injury. It was conformed that the abnormal expression of targeted genes associated with oxidative stress in coelomic cells was activated after pyridine exposure. Particularly, we found that the normal conformation (particle sizes, intrinsic fluorescence, and polypeptide backbone structure) of CAT/SOD was destroyed by the direct binding of pyridine. Furthermore, pyridine bound easily to the active center of CAT, but preferentially to the junction cavity of two subunits of SOD, which is considered to be a reason for impaired protein function in cells and in vitro. Based on these evidences, the ecotoxicity mechanisms of pyridine toward soil fauna are elucidated based on multi-level evaluation.

Soluble dietary fibres decrease α-glucosidase inhibition of epigallocatechin gallate through affecting polyphenol-enzyme binding interactions

The effects of soluble dietary fibres (SDFs) on α-glucosidase inhibition of EGCG were studied. Three arabinoxylans and polygalacturonic acid (PGA) significantly decreased inhibitory activity of EGCG against α-glucosidase, while two β-glucans hardly affected the inhibition. Although arabinoxylans and PGA weakened the competitive inhibition character of EGCG, they maintained the fluorescence quenching effect of EGCG. Then, arabinoxylans and PGA significantly decreased the particle size and turbidity of EGCG-enzyme complex. These results suggest that there formed SDFs-EGCG-enzyme ternary complexes. The stronger decreasing-effects of arabinoxylans and PGA on α-glucosidase inhibition of EGCG than β-glucans resulted from the stronger non-covalent interactions of arabinoxylans and PGA with EGCG. This is considered to arise from the short-branches of arabinoxylans that provided more opportunity for capturing EGCG, and from the strong polarity of PGA carboxyl that promoted hydrogen bondings with EGCG. Conclusively, SDFs should be considered as an impact factor when evaluating α-glucosidase inhibition of dietary polyphenols.

Genetic variations of Plasmodium falciparum circumsporozoite protein and the impact on interactions with human immunoproteins and malaria vaccine efficacy

In October 2021, the world's first malaria vaccine RTS,S was endorsed by WHO for broad use in children, despite its low efficacy. This study examined polyclonal infections and the associations of parasite genetic variations with binding affinity to human leukocyte antigen (HLA). Multiplicity of infection was determined by amplicon deep sequencing of PfMSP1. Genetic variations in PfCSP were examined across 88 samples from Ghana and analyzed together with 1655 PfCSP sequences from other African and non-African isolates. Binding interactions of PfCSP peptide variants and HLA were predicted using NetChop and HADDOCK. High polyclonality was detected among infections, with each infection harboring multiple non-3D7 PfCSP variants. Twenty-seven PfCSP haplotypes were detected in the Ghanaian samples, and they broadly represented PfCSP diversity across Africa. The number of genetic differences between 3D7 and non-3D7 PfCSP variants does not influence binding to HLA. However, CSP peptide length after proteolytic degradation significantly affects its molecular weight and binding affinity to HLA. Despite the high diversity of HLA, the majority of the HLAI and II alleles interacted/bound with all Ghana CSP peptides. Multiple non-3D7 strains among P. falciparum infections could impact the effectiveness of RTS,S. Longer peptides of the Th2R/Th3R CSP regions should be considered in future versions of RTS,S.

Computational Modeling on Binding Interactions of Cyclodextrin s with the Human Multidrug Resistance P-glycoprotein Toward Efficient Drug-delivery System Applications

BACKGROUND

Herein, molecular docking approaches and DFT ab initio simulations were combined for the first time, to study the key interactions of cyclodextrins (CDs: α-CD, β-CD, and γ-CD) family with potential pharmacological relevance and the multidrug resistance P-gp protein toward efficient drug-delivery applications. The treatment of neurological disorders and cancer therapy where the multiple drug-resistance phenomenon mediated by the P-gp protein constitutes the fundamental cause of unsuccessful therapies.

OBJECTIVES

To understand more about the CD docking mechanism and the P-gp.

METHODS

In order to achieve the main goal, the computational docking process was used. The observed docking-mechanism of the CDs on the P-gp was fundamentally based on hybrid backbone/side-chain hydrophobic interactions,and also hybrid electrostatic/side-chain interactions of the CD-ligands' OHmotifs with acceptor and donor characteristics, which might theoretically cause local perturbations in the TMD/P-gp inter-residues network, influencing ligand extrusion through the blood-brain barrier. P-gp residues were conformationally favored. Despite the structural differences, all the cyclodextrins exhibit very close Gibbs free binding energy values (or affinity) by the P-gp binding site (transmembrane domains - TMDs).

RESULT

The obtained theoretical docking-mechanism of the CDs on the P-gp was fundamentally based on hybrid backbone/side-chain hydrophobic interactions, and also hybrid electrostatic/side-chain interactions of the OH-motifs of the CD-ligands with acceptor and donor properties which theoretically could induce allosteric local-perturbations in the TMDs-inter-residues network of P-gp modulating to the CD-ligand extrusion from the blood-brain-barrier (or cancer cells).

CONCLUSION

Finally, these theoretical results open new horizons for evaluating new nanotherapeutic drugs with potential pharmacological relevance for efficient drug-delivery applications and precision nanomedicine.

Inconsistency between polyphenol-enzyme binding interactions and enzyme inhibition: Galloyl moiety decreases amyloglucosidase inhibition of catechins

Inhibiting carbohydrate-hydrolyzing enzymes has been considered as an effective approach for controlling starch digestion and postprandial blood glucose level. α-Amylase and amyloglucosidase (AMG) are commonly applied in analysis of starch digestion behaviour. Catechins have been shown with the inhibiting effects on α-amylase. However, the inhibitory activity of catechins against AMG needs to be further studied. Therefore, AMG inhibition of 8 catechins and the mechanisms were studied in this work through substrate depletion, inhibition kinetics, molecular docking, fluorescence quenching, differential scanning calorimetry, and isothermal titration calorimetry. The inhibitory activity of catechins with galloyl moiety (CGMs) was found to be lower than the corresponding catechins without the moiety (Cs). All catechins were anti-competitive inhibitors, indicating that they tended to bind with AMG-starch complex in the digestion system, rather than with AMG directly. Interestingly, CGMs had higher quenching effects on AMG fluorescence than Cs, due to the additional π-stacking between aromatic rings of GM and AMG fluorophores. Also, CGMs had a higher binding affinity to AMG, due to the tendency of GM to AMG active site, although the affinity was much weaker than that of starch to AMG. Besides, catechins did not affect AMG thermostability. Therefore, there was an inconsistency between catechins-AMG binding interactions and the enzyme inhibition because the predominant sites for catechins binding were the non-active sites on AMG-starch complex, rather than the enzyme active ones. Conclusively, inhibition mode should also be considered when evaluating the inhibitory activity of a polyphenol based on the polyphenol-enzyme binding affinity.

Comparison of the binding interactions of 4-hydroxyphenylpyruvate dioxygenase inhibitor herbicides with humic acid: Insights from multispectroscopic techniques, DFT and 2D-COS-FTIR

4-Hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor is one of the important herbicides to solve the problem of weed control. With the widespread and continued use of HPPD inhibitor (HPPDi) herbicides, it may inevitably put pressure on the environment. Humic acid (HA) can effectively interact with pesticides through sorption or covalent bond formation and promote the degradation of pesticides, which can reduce the risk of pesticides in the environment. In the present study, the interactions of four HPPDi herbicides (sulcotrione, tembotrione, topramezone and mesotrione) with HA were reported and comparative assessment of the binding using multispectral technology, density functional theory (DFT) calculation and two-dimensional correlation spectroscopy (2D-COS). Time-resolved measurements and the Stern-Volmer constant at different temperature verified that HPPDi can bind with HA through the static quenching mechanism. From the thermodynamic parameters, the interaction force between HA and sulcotrione, tembotrione, topramezone and mesotrione was provided by electrostatic force. DFT, binding constant and three-dimensional (3D) fluorescence peak variation all indicated that the order of the binding ability of the four HPPDi and HA was mesotrione > tembotrione > sulcotrione > topramezone. According to dynamic light scattering (DLS), pH 7 is most conducive to the formation of HA-HPPDi complexes. Fourier transform infrared spectroscopy (FTIR) and 2D-COS showed that HA combined with HPPDi through aromatic C-H, CO and C-X, and the first binding group to HA was almost all CO. Sulcotrione, tembotrione, topramezone and mesotrione quench the endogenous fluorescence of HA by a static quenching mechanism and bind to HA through electrostatic interaction to form a complex. These results provide important insights into the combination of environmental pollutants with HA.

Binding of methylmercury to humic acids (HA): Influence of solar radiation and sulfide addition reaction of HA

Methylmercury (MeHg) is a neurotoxin that bioaccumulates in organisms and it forms strong complexes with reduced sulfur-containing ligands in dissolved organic matter (DOM). In the present study, the influences of solar radiation and sulfide addition reaction of humic acids (HA) on MeHg binding to HA were investigated using synchronous fluorescence and FT-IR two-dimensional correlation spectroscopic (2DCOS) analysis. Results showed that the complexation of fluorescent fractions of HA and sulfur-reacted HA (S-HA) with MeHg was not significantly affected by photoreaction treatments and the affinity of fluorescent fractions followed the order of protein-like fractions > humic-like fractions > fulvic-like fractions for both HA and S-HA. FT-IR 2DCOS analysis showed that the affinity of various binding sites in DOM for MeHg changed under different photoreaction treatments. Under dark treatment, small molecular compounds with low humification degree such as aromatic amino acids may be the site with the strongest binding ability to MeHg in HA, whereas aliphatic amino acids and sulfur-containing groups from sulfide addition reactions play a role in complexing of S-HA and MeHg. Under BS treatment (irradiation of DOM before MeHg binding), aliphatic compounds in HA preferentially bind to MeHg and aliphatic amino acids are the components with the strongest complexing ability; but for S-HA binding to MeHg, unsaturated functional groups and aromatic groups are more sensitive (alkenes > alkanes, phenols > alcohols). Under AS treatment (irradiation of DOM after MeHg binding), unsaturated bonds and aromatic compounds in HA preferentially bind to MeHg and aromatic amino acids show the strongest complexing ability; but for S-HA binding to MeHg, aliphatic groups show the strongest complexing ability (alkanes, alkenes > aromatics). These findings help us to better understand the complexation mechanisms between MeHg and DOM.

Enzymic catalyzing affinity to substrate affects inhibitor-enzyme binding interactions: Inhibition behaviors of EGCG against starch digestion by individual and co-existing α-amylase and amyloglucosidase

The inhibition of (-)-epigallocatechin-gallate (EGCG) against starch digestion by α-amylase (AA), amyloglucosidase (AMG) and co-existing enzymes (AA/AMG) were comparatively studied. EGCG inhibited AA only at slowly-digestible-starch (SDS) phase. This resulted from high catalytic efficiency of AA for rapidly-digestible-starch (RDS), counteracting the inhibition at this phase. EGCG inhibited AMG and AA/AMG during whole process. At RDS phase, the catalytic velocity of AMG was always higher than AA/AMG because of an antagonistic effect of two enzymes. However, at SDS phase with EGCG, the catalytic velocity of AA/AMG was higher than AMG. This is because binding of EGCG with both enzymes caused more unbound AMG that generated more glucose in co-existing AA/AMG than AMG. Although EGCG-AA binding affinity was higher than EGCG-AMG, competitive inhibition of EGCG against AA was weaker than AMG, indicating relatively higher binding/catalyzing affinity of AA to starch significantly weakened EGCG-AA binding due to competitive relationship between starch and EGCG.

Caffeoyl substitution decreased the binding and inhibitory activity of quinic acid against α-amylase: The reason why chlorogenic acid is a relatively weak enzyme inhibitor

α-Amylase inhibition of chlorogenic acid (CHA) and its component moieties including quinic acid (QA) and caffeic acid (CA) were characterized by IC₅₀, inhibition kinetics, fluorescence quenching, isothermal titration calorimetry, differential scanning calorimetry and molecular docking. QA was found with the highest inhibitory activity in a competitive-mode, and caffeoyl substitution significantly decreased its inhibition but maintained inhibition type. Interestingly, QA hardly quenched α-amylase fluorescence, while CA quenched that significantly without inhibitory activity. This resulted from lack of aromatic ring in QA that can form π-conjugation with α-amylase fluorescent residues. Besides, the binding constant of QA with α-amylase was higher than CHA. Additionally, QA and CA decreased but CHA remained α-amylase thermal stability, indicating that change in α-amylase spatial structure was related with enzyme residue sites involved in interactions with inhibitors, instead of with inhibition effect. Conclusively, caffeoyl substitution decreased α-amylase inhibition of QA through reducing its binding affinity to the enzyme.

Mechanistic insights into primary biotransformation of diethyl phthalate in earthworm and significant SOD inhibitory effect of esterolytic products

Phthalic acid esters (PAEs) are used as plasticizer or modifier in artificially-manufactured products. Though the rapid biotransformation of phthalates in microbes and plants have been well documented, it is less studied yet in terrestrial animals, e.g. earthworm. In this study, the major biotransformation of diethyl phthalate (DEP) in Eisenia fetida was illustrated using in vitro incubation of earthworm crude enzymes. DEP could be substantially biotransformed into phthalate monoester (MEP) and a small amount of phthalic acid (PA) through esterolysis, which was verified to be driven by endogenous carboxylesterase. Despite the inferior contribution, the oxidation of DEP might also occur under the initiated electron transfer by NADPH coenzyme. The dominant metabolite MEP showed a higher inhibition of superoxide dismutase (SOD) activity than DEP with EC₅₀ of 0.0082 ± 0.0016 mmol/L, so the higher ecological risks of MEP would be marked. The inhibition effect of PA was validated to be even stronger than MEP though it was slightly generated. The direct binding interaction with SOD was proved to be an important molecular event for regulation of SOD activity. Besides the static quenching mechanism, the caused conformational changes including despiralization of α-helix and spatial reorientation of tryptophan were spectrally believed to affect binding and underlie inhibition efficiency of SOD activity.

Molecular dynamics simulations, docking and MMGBSA studies of newly designed peptide-conjugated glucosyloxy stilbene derivatives with tumor cell receptors

In this work, for the first time, we designed derivatives of beta-D-glucosyloxy-3-hydroxy-trans-stiblene-2-carboxylic acid (GHS), by conjugating GHS with tumor targeting peptides RPARPAR and GGKRPAR to target over-expressed receptors in tumor cells. The sequences RPARPAR and GGKRPAR are known to target the neuropilin1 (NRP1) receptor due to the C-terminal Arg domain; however, their effectiveness has never been examined with other commonly over-expressed receptors in tumor cells, particularly of chronic lymphocytic leukemia that include integrin α1β1 and CD22. By conjugating these peptides with GHS, which is known for its inherent anti-cancer properties, the goal is to further enhance tumor cell targeting by developing compounds that can target multiple receptors. The physicochemical properties of the conjugates and individual peptides were analyzed using Turbomole and COSMOthermX20 in order to determine their hydrogen bond accepting and donating capabilities. The web server POCASA was used in order to determine the surface cavities and binding pockets of the three receptors. To explore the binding affinities, we conducted molecular docking studies with the peptides and the conjugates with each of the receptors. After molecular docking, the complexes were analyzed using Protein-Ligand Interaction Profiler to determine the types of interactions involved. Molecular dynamics simulation studies were conducted to explore the stability of the receptor-ligand complexes. Our results indicated that in most cases the conjugates showed higher binding and stability with the receptors. Additionally, highly stable complexes of conjugates were obtained with CD22, NRP1 and in most cases with the integrin α1β1 receptor as well. The binding energies were calculated for each of the receptor ligand complexes through trajectory analysis using MMGBSA studies. SwissADME studies revealed that the compounds showed low GI absorption and were not found to be CYP inhibitors and had bioavailability score that would allow them to be considered as potential drug candidates. Overall, our results for the first time show that the designed conjugates can target multiple over-expressed receptors in tumor cells and may be potentially developed as future therapeutics for targeting tumor cells.

Study on active response of superoxide dismutase and relevant binding interaction with bioaccumulated phthalates and key metabolites in Eisenia fetida

Phthalic acid esters (PAEs) are a group of widespread persistent organic pollutants in the environment. Though the harmful effect of PAEs including activity inhibition of superoxide dismutase (SOD) to arouse oxidative stress were well documented, the deep insights into mechanisms that are relevant with SOD activity are still lacking. By 7d-cultivation of Eisenia fetida in artificially-polluted soil, the different active responses of SOD in earthworm were shown to PAE congeners. Despite the less bioaccumulation and bioavailability, the di-butyl phthalate (DBP) etc. structurally coupled with longer ester-chains appeared more effective to trigger the up-regulation and then the slight decline of SOD activity. Given the remarkable biotransformation especially for short-chain PAEs, the SOD activity response in earthworm should be regarded as joint effect with their metabolites, e.g. monophthalates (MAEs) and phthalic acid (PA). The in vitro SOD activity was shown with the obvious inhibition of 21.31% by DBP, 88.93% by MBP, and 58.57% by PA respectively when the concentrations were elevated up to 0.03 mM. The SOD activity inhibition confirmed the molecular binding with pollutants as an essential event besides the biological regulation for activity. The binding interaction was thermodynamically exothermic, spontaneous and strengthened primarily by Van der Waals force and hydrogen bonds, and was spectrally diagnosed with the conformational changes including diminution of α-helix content and spatial reorientation of fluorophore tryptophan. As coherently illustrated with the larger fluorescence quenching constants (3.65*10⁴-4.47*10⁴/mol) than DBP, the metabolites should be the priority concern due to stronger activity inhibition and toxicological risks.

Interactions between the antibiotic tetracycline and humic acid: Examination of the binding sites, and effects of complexation on the oxidation of tetracycline

The binding between dissolved organic matter (DOM) and micro-pollutants (MPs) results in significant impacts on their migration, transformation and degradation. However, the role of the DOM/MP binding on their oxidative transformation remains poorly studied. The binding of MPs by DOM, in combination with DOM's roles as a photosensitizer and/or a competitor for free radicals, needs to be considered in the context of understanding the DOM's impacts on the oxidative degradation of MPs. This study aims to explore this aspect of DOM/MP interactions based on the quantitation of humic acid (HA) and tetracycline (TET) complexation and its role in TET removal. This study also compared the degradation of free TET versus that bound in HA-TET complexes in different oxidation processes. Fourier transform infrared (FTIR) data show that the carboxyl and phenolic hydroxyl groups in HA are the main binding sites of TET, while nuclear magnetic resonance (NMR) analysis shows the binding of TET engages its -N(CH₃)₂ groups, and two-dimensional correlation spectroscopy (2D-COS) data show that the carboxyl groups in DOM are sensitive than phenolic groups in the binding of TET. The difference between the degradation rates (Δk_obs) of the free and bound TET decreased with the increase of ionic strength using sodium nitrate, but increased with the introduction of Ca²⁺ and Mg²⁺ due to the formation of TET-Ca²⁺/Mg²⁺ complexes. Quenching experiments showed that the free radicals (•OH and •SO₄^-), PMS oxidant and UV light were the main contributors to the TET degradation in UV/PS, UV/PMS and UV/H₂O₂ processes, respectively. In-situ fluorescence time scanning and differential absorbance spectra showed that free TET was preferentially oxidized over the bound TET in all the tested treatments except UV/PS. These results provide new insights into the role of DOM/MP complexation in the degradation of MPs in natural and engineered systems.

Essential moieties of myricetins, quercetins and catechins for binding and inhibitory activity against α-Glucosidase

α-Glucosidase inhibition of 11 flavonoids, including myricetins, quercetins and catechins were studied through initial reaction velocity, IC₅₀ value, inhibition kinetics, fluorescence quenching and molecular docking. It was found that C4 = O, C2 = C3, 3-OH and 5'-OH were essential moieties for α-glucosidase inhibition of myricetin that was shown with the highest inhibitory activity. The trans-conformational catechins was shown with stronger inhibition effects than the cis-conformational ones. Further, gallocatechin was an uncompetitive inhibitor, while myricetin, myricetrin, quercetin and catechin were competitive ones. 3-OH and 5'-OH promoted myricetin to bind with the enzyme active site through hydrogen bondings. The presence of C4 = O and C2 = C3 increased electron delocalization in ring A-C for myricetin and quercetin, and this enhanced stability of π-conjugations with aromatic residues of amino acids. However, 5'-OH decreased the quenching effects because it limited π-conjugations of ring B with key fluorescent residues. Notably, for same flavonoid sort, the constants that indicate binding affinity of flavonoids to α-glucosidase, including reciprocal of competitive inhibition constant, fluorescence quenching constant and binding energy followed same order as the inhibitory activity, indicating that α-glucosidase inhibition of the flavonoids resulted from binding interactions between them, and that the methods above can be combined reasonably to characterize flavonoid-enzyme binding interactions.

In vivo and in vitro studies on inactivation of selenium containing protein- glutathione peroxidase 3 in mice nephrocytes caused by lead

Glutathione peroxidases (Gpxs) play vital roles in elimination of hydroperoxide and other reactive oxygen species through catalyzing reduced glutathione to protect from oxidative stress caused by heavy metals such as lead. Among the family of Gpxs, Gpx3 is the only extracellular enzyme synthesized in the kidney and actively secreted into the plasma. This study investigated mechanisms of lead-induced GPx3 inactivation both at the animal and molecular levels. Six-week-old mice were randomly divided into 4 groups, and exposed to different lead concentrations (0, 1, 2 and 4 g/L) in their drinking water for 4 weeks. Contents of GPx3 in blood serum were tested by enzyme-linked immunosorbent assay (ELISA) and the mRNA levels of Gpx3 in mice nephrocytes were determined by quantitative real-time PCR (qPCR), both of which showed significantly inhibited at higher lead concentrations accompanied by the decreased Gpx3 activities and the elevated levels of malondialdehyde (MDA) in nephrocytes, which indicated that lead could induce strongly oxidative stress through affecting Gpx3 function. So we further investigated molecular mechanisms of GPx3 inactivation caused by lead with multiple spectroscopic techniques, isothermal titration calorimetry (ITC) and molecular docking studies in vitro. Results showed that lead statically quenched GPx3 fluorescence by tightly binding to the structural domain of GPx3 in a 3:1 ratio with high binding affinity (K = 3.1(±0.087) × 10⁷ mol^-1). Further investigation of the conformation of GPx3 by UV-visible spectroscopy and circular dichroism (CD) spectroscopy indicated that lead changed the secondary structure of GPx3 by loosening the GPx3 skeleton and decreasing the hydrophobicity around tryptophan residues. This work proved in vivo and in vitro experiments that lead could induce oxidative stress in mice nephrocytes by interacting with GPx3.

Characterization of heparin and severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) spike glycoprotein binding interactions

Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) has resulted in a pandemic and continues to spread around the globe at an unprecedented rate. To date, no effective therapeutic is available to fight its associated disease, COVID-19. Our discovery of a novel insertion of glycosaminoglycan (GAG)-binding motif at S1/S2 proteolytic cleavage site (681-686 (PRRARS)) and two other GAG-binding-like motifs within SARS-CoV-2 spike glycoprotein (SGP) led us to hypothesize that host cell surface GAGs may interact SARS-CoV-2 SGPs to facilitate host cell entry. Using a surface plasmon resonance direct binding assay, we found that both monomeric and trimeric SARS-CoV-2 SGP bind more tightly to immobilized heparin (K_D = 40 pM and 73 pM, respectively) than the SARS-CoV and MERS-CoV SGPs (500 nM and 1 nM, respectively). In competitive binding studies, the IC₅₀ of heparin, tri-sulfated non-anticoagulant heparan sulfate, and non-anticoagulant low molecular weight heparin against SARS-CoV-2 SGP binding to immobilized heparin were 0.056 μM, 0.12 μM, and 26.4 μM, respectively. Finally, unbiased computational ligand docking indicates that heparan sulfate interacts with the GAG-binding motif at the S1/S2 site on each monomer interface in the trimeric SARS-CoV-2 SGP, and at another site (453-459 (YRLFRKS)) when the receptor-binding domain is in an open conformation. The current study serves a foundation to further investigate biological roles of GAGs in SARS-CoV-2 pathogenesis. Furthermore, our findings may provide additional basis for further heparin-based interventions for COVID-19 patients exhibiting thrombotic complications.

H-bond interactions between arsenite and deoxynucleotides at different pH values: A combined computational and experimental study

Deoxynucleotides can be good monomers for arsenite ion-imprinted polymers (IIPs) due to the successful obtainment of aptamers which can specifically recognize arsenite. However, the recognition and interaction mechanism between arsenite and deoxynucleotides is still not clear. In this work, the binding interactions between arsenite and deoxynucleotides (dAMP, dTMP, dGMP, dCMP) as pH changing from 1 to 14 were investigated using density functional theory calculations as well as spectroscopy analysis. dGMP was calculated to have the largest affinity towards arsenite. H₃AsO₃⁰-dGMP⁰ binding at phosphate group, H₃AsO₃⁰-dAMP^2-, H₃AsO₃⁰-dCMP⁰ and H₃AsO₃⁰-dTMP^2- binding around nucleobase were found to be the most stable complexes. This suggests the optimal pH ranges for binding interactions of dAMP, dCMP, dGMP and dTMP towards arsenite might be 6.10-9.23, 1.00-4.50, 1.00-2.40 and 6.40-9.23, respectively, which agree with UV/VIS experimental results. Reduced Density Gradient method indicated that the binding interactions of arsenite with deoxynucleotides are mainly attributed to hydrogen bonds (H-bond). The strengths of these H-bonds are affected by pH. FT-IR and NMR spectroscopy analysis also provided essential H-bonding information, giving direct evidence to support the computational conclusions.

Effect of sodium deoxycholate sulfate on outer membrane permeability and neutralization of bacterial lipopolysaccharides by polymyxin B formulations

We demonstrated binding interactions of polymyxin B (PMB), PMB formulations in the mole ratios of 1:2 and 1:3 of PMB:sodium deoxycholate sulfate (SDCS) and a commercial PMB formulation (CPMB) with lipopolysaccharides (LPS). The 1:2 PMB formulation (78.5-135.2 nM) exhibited a lower number of binding sites to the tested LPS compared to CPMB (112.6-140.9 nM) whereas 1:3 PMB formulation exhibited a higher number of binding sites (143.9-340.2 nM). Similarly, in the presence of LPS, the 1:2 PMB formulation (163.8-221.4 nm) exhibited smaller particle sizes compared to PMB, CPMB and 1:3 PMB formulation (248.8-603.5 nm). Molecular docking simulation suggested that the fatty acyl tails of LPS wrap together to produce a pseudo-globular structure of PMB-LPS complex, and among those 1:2 PMB formulation formed a more stable structure. The primary forces behind this complex are hydrogen bonds and salt bridges among the LPS, PMB, and SDCS. This study revealed that the PMB, CPMB, and PMB formulations inserted into the LPS micelles to disrupt the LPS membrane, whereas the SDCS may induce aggregation. The 1:2 PMB formulation also had higher bacterial uptake than other PMB formulations. The 1:2 PMB formulation neutralized the LPS micelles and was effective against Escherichia coli and Pseudomonas aeruginosa.

Aging of microplastics affects their surface properties, thermal decomposition, additives leaching and interactions in simulated fluids

Most microplastics (MPs) have undergone extensive aging in the environment. Aged MPs exhibit different physical and chemical properties from unaged ones. Here, we studied the effects of accelerated aging on the characteristics and pyrolysis of commercial pigmented MPs, as well as pigments leaching and their interactions in simulated gastric and intestinal fluids of mammals. We report that the carbonyl index, surface area, and color change of MPs increased after aging treatment. Cracks and fragmentation of MPs facilitated the accessibility of light and oxygen to internal layer and therefore accelerated the aging process. TGA/GC-MS analysis showed that the high temperature resistance of MPs decreased after aging. Thermal decomposition of pigments and polyethylene occurred in temperature ranges of 340-406 °C and 406-550 °C, respectively. Mono (di)-alkenes and saturated alkanes were the thermal decomposition products of polyethylene. Aging of MPs also caused an increased release of pigments and prolonged aging time led to more release in simulated fluids. Pigments would result in fluorescence quenching of the enzymes through binding interactions once they were released from MPs into simulated fluids. Charge neutralization and polymer bridging accounted for the formation of pigment-enzyme complexes and flocs. These novel findings will allow us to better assess how aging process affects the characteristics, leaching, and toxicity of MPs.

Robust therapeutic potential of carbazole-triazine hybrids as a new class of urease inhibitors: A distinctive combination of nitrogen-containing heterocycles

The inhibition of urease enzyme is very important as it plays a key role in the treatment of several urinary and gastrointestinal tract infections. This enzyme provides a suitable environment for Helicobacter pylori at the low pH of the stomach, a causative agent of gastric and peptic ulcer that may lead to cancer. In agriculture, the high urease content causes environmental and economic problems. In this pursuit, given the well-established importance of integrated pharmacophores in medicinal chemistry and to explore new inhibitors of urease featuring two distinct heterocyclic functionalities, we herein report a facile synthesis of carbazole-triazine hybrids (3a-j). These new propeller-shaped chemical scaffolds were evaluated for their urease inhibitory potential in order to identify suitable leads. The initial structure-activity survey work guided through in vitro bioactivity results recognized 3e and 3f as new starting point hits incorporating bulky iodo (3e) and strong electron-withdrawing nitro (3f) groups at the para-position of aryl amine component. The potent compounds (3e &3f) exhibited the highest activity with IC₅₀ values of 5.6 and 6.7 µM, respectively. In the molecular docking analysis, these compounds depicted excellent binding interactions with the active site residues. The key interactions observed include hydrogen bonding, π-π interactions, π-cation and nickel atom coordination to the triazine nitrogen of both inhibitors.

Binding interactions of bacterial lipopolysaccharides to polymyxin B in an amphiphilic carrier 'sodium deoxycholate sulfate'

This work presents the outcomes of a comparative study of molecular interactions of polymyxin B (PMB) and F12 and F13 formulations in the mole ratios of 1:2 and 1:3 of PMB:sodium deoxycholate sulfate (SDCS), respectively, and a commercial PMB formulation (CPMB) with lipopolysaccharides (LPS). Several spectroscopic and interfacial studies were performed to obtain LPS-peptide interactions at a molecular level. The fluorescence titrimetry method revealed that the F12 formulation (325 nM) exhibited a lower number of binding sites to the LPS compared to CPMB and F13 as well as PMB alone (537 nM). Similarly, in the presence of LPS, the F12 formulation (88 nm) exhibited smaller particle sizes in the dynamic light scattering study compared to PMB (116 nm), CPMB, and the F13 formulation. An interfacial study and circular dichroism spectroscopy revealed PMB and CPMB insertion into the LPS micelles to destabilize and disrupt the LPS membrane, whereas the F12 and F13 formulations may induce pseudo-aggregation. The NMR and IR studies showed that the presence of SDCS, the hydrophobicity of PMB increased by hydrogen bonding and electrostatic interactions and formed stabilized PMB-SDCS micelles. The PMB-SDCS formulation is likely to release PMB for easy penetration into the lipid membrane and cause disruption of the complex LPS micelles. Furthermore, the PMB-SDCS formulations neutralized and detoxified the LPS micelles with minimal toxicity to normal kidney tubular cells as well as an immortalised kidney cell line. The antimicrobial properties of PMBloaded SDCS nanomicelles were effective against a resistant strain of Pseudomonas aeruginosa.

Dietary polyphenols modulate starch digestion and glycaemic level: a review

Polyphenols, as one group of secondary metabolite, are widely distributed in plants and have been reported to show various bioactivities in recent year. Starch digestion not only is related with food industrial applications such as brewing but also plays an important role in postprandial blood glucose level, and therefore insulin resistance. Many studies have shown that dietary phenolic extracts and pure polyphenols can retard starch digestion in vitro, and the retarding effect depends on the phenolic composition and molecular structure. Besides, dietary polyphenols have also been reported to alleviate elevation of blood glucose level after meal, indicating the inhibition of starch digestion in vivo. This review aims to analyze how dietary polyphenols affect starch digestion both in vitro and in vivo. We can conclude that the retarded starch digestion in vitro by polyphenols results from inhibition of key digestive enzymes, including α-amylase and α-glucosidase, as well as from interactions between polyphenols and starch. The alleviation of postprandial hyperglycemia by polyphenols might be caused by both the inhibited starch digestion in vivo and the influenced glucose transport. Therefore, phenolic extracts or pure polyphenols may be alternatives for preventing and treating type II diabetes disease.

Mechanism of binding interactions between young apple polyphenols and porcine pancreatic α-amylase

The binding interactions between young apple polyphenols and porcine pancreatic α-amylase were investigated through isothermal titration calorimetry (ITC), differential scanning calorimetry (DSC) and molecular docking. The results obtained were compared with those obtained through inhibition kinetics and fluorescence quenching. It was found that binding of tannic acid, chlorogenic acid, caffeic acid and epicatechin with α-amylase is an exothermal process, with the binding constants in the order of tannic acid > chlorogenic acid > caffeic acid > epicatechin. This is consistent with the orders of reciprocal of competitive inhibition constant and fluorescence quenching constant. The binding energy obtained through molecular docking showed the same order, except for epicatechin. These results are consistent with the inhibition of α-amylase being caused by the binding of the polyphenols with the enzyme. In addition, from the fluorescence quenching and DSC data, total polyphenols, tannic acid, chlorogenic acid and caffeic acid were found to partially unfold the enzyme structure.

Thermophoresis for characterizing biomolecular interaction

The study of biomolecular interactions is crucial to get more insight into the biological system. The interactions of protein-protein, protein-nucleic acids, protein-sugars, nucleic acid-nucleic acids and protein-small molecules are supporting therapeutics and technological developments. Recently, the development in a large number of analytical techniques for characterizing biomolecular interactions reflect the promising research investments in this field. In this review, microscale thermophoresis technology (MST) is presented as an analytical technique for characterizing biomolecular interactions. Recent years have seen much progress and several applications established. MST is a powerful technique in quantitation of binding events based on the movement of molecules in microscopic temperature gradient. Simplicity, free solutions analysis, low sample volume, short analysis time, and immobilization free are the MST advantages over other competitive techniques. A wide range of studies in biomolecular interactions have been successfully carried out using MST, which tend to the versatility of the technique to use in screening binding events in order to save time, cost and obtained high data quality.

Molecular insight into the activity of LasR protein from Pseudomonas aeruginosa in the regulation of virulence gene expression by this organism

Pseudomonas aeruginosa is an opportunistic human pathogen. This organism attacks human patients suffering from diseases like AIDS, cancer, cystic fibrosis, etc. One of the important virulent factors produced by this organism is Hydrogen Cyanide. This is expressed from the genes encoded by the hcnABC operon. The expressions of the genes encoded by hcnABC operon are mediated mainly by the interactions of LasR protein with the corresponding promoter region of the hcnABC operon. The LasR protein acts as a dimer and binds to the promoter DNA with the help of an autoinducer ligand. However, till date the detailed molecular mechanism of how the LasR protein interacts with the promoter DNA is not clearly known. Therefore, in this work, an attempt has been made to analyze the mode of interactions of the LasR protein with the promoter DNA region of the hcnABC operon. We analyzed the three dimensional structure of the LasR protein from Pseudomonas aeruginosa and docked the protein with the autoinducer ligand. We then docked the ligand-bound-LasR-protein as well the LasR-protein-without-the-autoinducer-ligand on to the promoter DNA region of hcnABC operon. We analyzed the details of the interaction profiles of LasR protein with the autoinducer ligand. We also deciphered the details of the LasR promoter-DNA interactions. We compared the modes of DNA bindings by the LasR protein in presence and absence of the autoinducer ligand and tried to analyze the molecular details of the binding of LasR protein with the promoter DNA region of hcnABC operon during hcnABC gene expression. This study may therefore pave the pathway for future experiments to determine the relative effects of the amino acid residues of LasR protein in DNA binding during the transcription of hcnABC operon.

Molecular docking study of P4-Benzoxaborolesubstituted ligands as inhibitors of HCV NS3/4A protease

NS3/4A protease is an important emerging target for the cure of hepatitis C. There are many inhibitors of HCV NS3/4A protease that are passing through the clinical improvement indicating momentous reduction in the viral infection rate of patients. In this study molecular docking via MOE-Dock program was used to evaluate binding interactions of ligands with HCV NS3/4A protease. The docking and experimental results were found in good correlation. The best conformations of ligands were analyzed for binding interactions with the residues of binding cavity of NS3/4A protease. The valuable binding interactions and docking scores were observed for compounds 01, 05, 06, 07, 08 and 09.