A potential anticancer dihydropyrimidine derivative and its protein binding mechanism by multispectroscopic, molecular docking and molecular dynamic simulation along with its in-silico toxicity and metabolic profile

Impacts of monosaccharide composition on immunomodulation by cello-pentaose, manno-pentaose, and xylo-pentaose: Unraveling the underlying molecular mechanisms

Different types of functional oligosaccharides exhibit varying degrees of immune-enhancing effects, which might be attributable to differences in their glycosyl structures. The differences in the immunomodulatory action of three functional oligosaccharides with distinct glycosyl compositions: cello-oligosaccharides (COS), manno-oligosaccharides (MOS), and xylo-oligosaccharides (XOS), were investigated in mouse-derived macrophage RAW264.7. Moreover, the immune enhancement mechanism of oligosaccharides with diverse glycosyl compositions was investigated from a molecular interaction perspective. The TLR4-dependent immunoregulatory effect of functional oligosaccharides was shown by measuring the levels of tumor necrosis factor (TNF)-α and interleukin (IL)-6 in RAW264.7 cells treated with different functional oligosaccharides, both with and without Resatorvid [TAK-242] (a Toll-like receptor 4 [TLR4] inhibitor). Western blot analysis showed that binding of the three oligosaccharides to TLR4 activated the downstream signaling pathway and consequently enhanced the immune response. The fluorescence spectra and molecular docking results revealed that the main mechanisms by which these oligosaccharides attach to the TLR4 active pocket are hydrogen bonds and van der Waals forces. Functional oligosaccharides were ranked according to their affinity for TLR4, as follows: MOS > COS > XOS, indicating that oligosaccharides or polysaccharides containing mannose units may confer significant advantages for immune enhancement.

Molecular insight on the binding of halogenated organic phosphate esters to human serum albumin and its effect on cytotoxicity of halogenated organic phosphate esters

Halogenated Organic Phosphate Esters (OPEs) are commonly found in plasticizers and flame retardants. However, they are one kind of persistent contaminants that can pose a significant threat to human health and ecosystem as new environmental estrogen. In this study, two representative halogenated OPEs, tris(1,3-dichloro-2-propyl) phosphate (TDCP) and tris(2,3-dibromopropyl) phosphate (TDBP), were selected as experimental subjects to investigate their interaction with human serum albumin (HSA). Despite having similar structures, the two ligands exhibited contrasting effects on enzyme activity of HSA, TDCP inhibiting enzyme activity and TDBP activating it. Furthermore, both TDCP and TDBP could bind to HSA at site I, interacted with Arg222 and other residues, and made the conformation of HSA unfolded. Thermodynamic parameters indicated the main driving forces between TDBP and HSA were hydrogen bonding and van der Waals forces, while TDCP was mainly hydrophobic force. Molecular simulations found that more hydrogen bonds of HSA-TDBP formed during the binding process, and the larger charge area of TDBP than TDCP could partially account for the differences observed in their binding abilities to HSA. Notably, the cytotoxicity of TDBP/TDCP was inversely proportional to their binding ability to HSA, implying a new method for determining the cytotoxicity of halogenated OPEs in vitro.

Biophysical insights on the interaction of anticoagulant drug dicoumarol with calf thymus-DNA: deciphering the binding mode and binding force with thermodynamics

The biological activity of drugs is exhibited due to their interactions with bio-receptors. Dicoumarol (DIC) is a natural hydroxycoumarin and a well-known anticoagulant. DNA is the genetic material and one of the targets of numerous drugs. The interaction of DIC with calf-thymus DNA (ct-DNA) has been studied using different biophysical techniques and docking studies. The binding constant in the order of 103 to 104 M-1 was observed from spectroscopic studies. Thermodynamic studies at 4 different temperatures revealed the spontaneity of the interaction with the entropy-driven process. Marker displacement studies with competitive markers of intercalators (ethidium bromide) and groove binders (Hoechst 33258) confirmed the groove-binding nature of DIC in DNA. The groove-binding mode of DIC was complemented by different studies like viscosity measurements, DNA melting, and the effect of KI on the binding. A minor perturbation in the DNA viscosity and no significant change in the DNA melting temperature (Tm) after binding with DIC further confirms the groove binding mode. The effect of KI on the DIC and DIC-DNA system suggested the absence of DIC intercalation. The absence of significant electrostatic force was revealed from the ionic-strength effect study. Binding-induced conformational variation in ct-DNA was absent in circular dichroism studies. Molecular docking studies suggested the position of DIC within the minor groove of ct-DNA, covering three base pairs long. The outcome of this report may help in understanding the pharmacodynamics and pharmacokinetics of dicoumarol analogs and related molecules.Communicated by Ramaswamy H. Sarma.

Exploring the role of microbial proteins in controlling environmental pollutants based on molecular simulation

Molecular simulation has been widely used to study microbial proteins' structural composition and dynamic properties, such as volatility, flexibility, and stability at the microscopic scale. Herein, this review describes the key elements of molecular docking and molecular dynamics (MD) simulations in molecular simulation; reviews the techniques combined with molecular simulation, such as crystallography, spectroscopy, molecular biology, and machine learning, to validate simulation results and bridge information gaps in the structure, microenvironmental changes, expression mechanisms, and intensity quantification; illustrates the application of molecular simulation, in characterizing the molecular mechanisms of interaction of microbial proteins with four different types of contaminants, namely heavy metals (HMs), pesticides, dyes and emerging contaminants (ECs). Finally, the review outlines the important role of molecular simulations in the study of microbial proteins for controlling environmental contamination and provides ideas for the application of molecular simulation in screening microbial proteins and incorporating targeted mutagenesis to obtain more effective contaminant control proteins.

Identification of 1,3,4-oxadiazoles as tubulin-targeted anticancer agents: a combined field-based 3D-QSAR, pharmacophore model-based virtual screening, molecular docking, molecular dynamics simulation, and density functional theory calculation approach

Cancer is one of the most prominent causes of death worldwide and tubulin is a crucial protein of cytoskeleton that maintains essential cellular functions including cell division as well as cell signalling, that makes an attractive drug target for cancer drug development. 1,3,4-oxadiazoles disrupt microtubule causing G2-M phase cell cycle arrest and provide anti-proliferative effect. In this study, field-based 3D-QSAR models were developed using 62 bioactive anti-tubulin 1,3,4-oxadiazoles. The best model characterized by PLS factor 7 was rigorously validated using various statistical parameters. Generated 3D-QSAR model having high degree of confidence showed favourable and unfavourable contours around 1,3,4-oxadiazole core that assisted in defining proper spatial positioning of desired functional groups for better bioactivity. A five featured pharmacophore model (AAHHR_1) was developed using same ligand library and validated through enrichment analysis (BEDROC160.9 value = 0.59, Average EF 1% = 27.05, and AUC = 0.74). Total 30,212 derivatives of 1,3,4-oxadiazole obtained from PubChem database was prefiltered through validated pharmacophore model and docked in XP mode on binding cavity of tubulin protein (PDB code: 1SA0) which led into the identification of 11 HITs having docking scores between -7.530 and -9.719 kcal/mol while the reference compound Colchicine exerted docking score of -7.046 kcal/mol. Following the analysis of MM-GBSA and ADME studies, HIT1 and HIT4 emerged as the two promising hits. To verify their thermodynamic stability at the target site, molecular dynamic simulations were carried out. Both HITs were further subjected to DFT analysis to determine their HOMO-LUMO energy gap for ensuring their biological feasibility. Finally, molecular docking based structural exploration for 1,3,4-oxadiazoles to set up a lead of Formula I for further advancements of tubulin polymerization inhibitors as anti-cancer agents.Communicated by Ramaswamy H. Sarma.

A 3D copper (II) coordination polymer based on sulfanilic acid ligand (CP 1) for efficient biomolecular interaction with bovine serum albumin: spectroscopic, molecular modelling and DFT analysis

Several biochemical reactions occur during the interaction of metal complexes and proteins due to conformational modifications in the structure of the protein, which provide fundamental knowledge of the effect, mechanism, and transport of many drugs throughout the body. Here, we report the synthesis, identification, and impact of the 3-dimensional Copper(II)sulfanilic acid coordination polymer (CP 1) on interactions with bovine serum albumin (BSA). The CP 1 was synthesized via a simple hot stirring method, and the single crystal XRD confirms the effective bonding interactions between metal and organic ligand, forming a crystalline polymeric chain and the topological study shows the sql type of underlying net topology. Powder XRD, Fourier transform infrared spectroscopy, and thermogravimetric analysis were also performed. Moreover, DFT/B3LYP calculations provide chemical precision for the resulting complex. Further, the changes that occur in the secondary structure of protein when CP 1 binds with BSA as well as its binding capacity were investigated via circular dichroism analysis and spectroscopic methods such as UV-absorption spectroscopy and fluorescence spectroscopy, respectively. The CP 1/BSA complex melting point was also measured, and its temperature-dependent heat denaturation was studied along with molecular docking.Communicated by Ramaswamy H. Sarma.

Molecular Recognition Study toward the Mitochondrial Electron Transport Chain Inhibitor Mubritinib and Human Serum Albumin

The ability to bind plasma proteins helps in comprehending relevant aspects related to the pharmacological properties of many drugs. Despite the vital role of the drug mubritinib (MUB) in the prophylaxis of various diseases, its interaction with carrier proteins still needs to be clarified. The present work focuses on the interaction between MUB and Human serum albumin (HSA), investigated by employing multispectroscopic, biochemical, and molecular docking approaches. The results reveal that MUB has quenched HSA intrinsic fluorescence (following a static mechanism) by attaching very close (r = 6.76 Å) and with moderate affinity (Kb ≈ 104 M-1) to the protein site I (mainly by H-bonds, hydrophobic and Van der Waals forces). On one side, the HSA-MUB interaction has been accompanied by a slight disturbance in the HSA chemical environment (around the Trp residue) and protein secondary structure modifications. On another side, MUB competitively inhibits HSA esterase-like activity, which is very similar to other Tyrosine kinase inhibitors, and evidence that protein functional alterations have been triggered by MUB interaction. In summary, all of the presented observations can shed light on diverse pharmacological factors associated with drug administration.

Toxicity Study and Binding Analysis of Newly Synthesized Antifungal N-(4-aryl/cyclohexyl)-2-(pyridine-4-yl carbonyl) hydrazinecarbothioamide Derivative with Bovine Serum Albumin

The presence of the p-aryl/cyclohexyl ring in the N-(4-aryl/cyclohexyl)-2-(pyridine-4-yl carbonyl) hydrazine carbothioamide derivative (2C) is reported to enhance the antifungal properties when compared to those of itraconazole. Serum albumins present in plasma bind and transport ligands, including pharmaceuticals. This study explored 2C interactions with BSA using spectroscopic methods such as fluorescence and UV-visible spectroscopy. In order to acquire a deeper comprehension of how BSA interacts with binding pockets, a molecular docking study was carried out. The fluorescence of BSA was quenched by 2C via a static quenching mechanism since a decrease in quenching constants was observed from 1.27 × 10⁵ to 1.14 × 10⁵. Thermodynamic parameters indicated hydrogen and van der Waals forces responsible for the BSA-2C complex formation with binding constants ranging between 2.91 × 10⁵ and 1.29 × 10⁵, which suggest a strong binding interaction. Site marker studies displayed that 2C binds to BSA's subdomains IIA and IIIA. Molecular docking studies were conducted to further comprehend the molecular mechanism of the BSA-2C interaction. The toxicity of 2C was predicted by Derek Nexus software. Human and mammalian carcinogenicity and skin sensitivity predictions were associated with a reasoning level of equivocal, inferring 2C to be a potential drug candidate.

Effects of combined binding of chlorogenic acid/caffeic acid and gallic acid to trypsin on their synergistic antioxidant activity, enzyme activity and stability

The combined application of multiple natural polyphenols in functional foods may provide better health benefits. The binding of polyphenols with different structures to proteins will affect their respective functions. Spectroscopy and molecular docking were used to investigate the competitive binding of chlorogenic acid (CGA)/caffeic acid (CA) and gallic acid (GA) to trypsin. The effects of different molecular structures and the order of adding the three phenolic acids on the binding were assessed. The stability of trypsin and its docked complexes with CGA/CA/GA was evaluated by molecular dynamics simulation. The effects of the binding process on the activity and thermal stability of trypsin, as well as on the antioxidant activity and stability of CGA/CA/GA were explored. The competitive binding of CGA/CA and GA to trypsin affected their synergistic antioxidant effects. The results may provide a reference for the combined application of CGA/CA and GA in food and pharmaceutical fields.

Insights into the Effects and Mechanism of Andrographolide-Mediated Recovery of Susceptibility of Methicillin-Resistant Staphylococcus aureus to β-Lactam Antibiotics

The frequent resistance associated with β-lactam antibiotics and the high frequency of mutations in β-lactamases constitute a major clinical challenge that can no longer be ignored. Andrographolide (AP), a natural active compound, has been shown to restore susceptibility to β-lactam antibiotics. Fluorescence quenching and molecular simulation showed that AP quenched the intrinsic fluorescence of β-lactamase BlaZ and stably bound to the residues in the catalytic cavity of BlaZ. Of note, AP was found to reduce the stability of the cell wall (CW) in methicillin-resistant Staphylococcus aureus (MRSA), and in combination with penicillin G (PEN), it significantly induced CW roughness and dispersion and even caused its disintegration, while the same concentration of PEN did not. In addition, transcriptome sequencing revealed that AP induced a significant stress response and increased peptidoglycan (PG) synthesis but disrupted its cross-linking, and it repressed the expression of critical genes such as mecA, blaZ, and sarA. We also validated these findings by quantitative reverse transcription-PCR (qRT-PCR). Association analysis using the GEO database showed that the alterations caused by AP were similar to those caused by mutations in the sarA gene. In summary, AP was able to restore the susceptibility of MRSA to β-lactam antibiotics, mainly by inhibiting the β-lactamase BlaZ, by downregulating the expression of critical resistance genes such as mecA and blaZ, and by disrupting CW homeostasis. In addition, restoration of susceptibility to antibiotics could be achieved by inhibiting the global regulator SarA, providing an effective solution to alleviate the problem of bacterial resistance. IMPORTANCE Increasingly, alternatives to antibiotics are being used to mitigate the rapid onset and development of bacterial resistance, and the combination of natural compounds with traditional antibiotics has become an effective therapeutic strategy. Therefore, we attempted to discover more mechanisms to restore susceptibility and effective dosing strategies. Andrographolide (AP), as a natural active ingredient, can mediate recovery of susceptibility of MRSA to β-lactam antibiotics. AP bound stably to the β-lactamase BlaZ and impaired its hydrolytic activity. Notably, AP was able to downregulate the expression of critical resistance genes such as mecA, blaZ, and sarA. Meanwhile, it disrupted the CW cross-linking and homeostasis, while the same concentration of penicillin could not. The multiple inhibitory effect of AP resensitizes intrinsically resistant bacteria to β-lactam antibiotics, effectively prolonging the use cycle of these antibiotics and providing an effective solution to reduce the dosage of antibiotics and providing a theoretical reference for the prevention and control of MRSA.

Insights into the interaction of azinphos-methyl with bovine serum albumin: experimental and molecular docking studies

In the present study, combining spectroscopic and molecular modeling techniques has been used to analyze azinphos-methyl binding properties, as an organophosphorus pesticide, to bovine serum albumin. The quenching interaction of azinphos-methyl with bovine serum albumin was investigated in an appropriate physiological state (pH = 7.4). Fluorescence spectroscopy, UV-visible spectroscopy, circular dichroism (CD) and Fourier transform infrared spectroscopy (FTIR). Findings showed differences in the secondary protein structure microenvironment following interaction with azinphos-methyl. The results from spectroscopic experiments suggest that azinphos-methyl binds to bovine serum albumin residues with a binding constant in the range of 0.099 × 10⁵-0.209 × 10⁵ M^-1 in one binding site (Tyr 160). The experimental results are supported by computational techniques such as docking using a bovine serum albumin crystal model. The results show that azinphos-methyl is linked to the site I of bovine serum albumin (in subdomain IB), and the result was in accordance with the experimental result. Based on the negative ΔG°, ΔH° and ΔS° values, the binding between azinphos-methyl and bovine serum albumin was spontaneous, and docking studies confirmed hydrogen bonding and van der Waals forces between them.Communicated by Ramaswamy H. Sarma.

1,2,4‐Triazole and benzimidazole fused dihydropyrimidine derivatives: Design, green synthesis, antibacterial, antitubercular, and antimalarial activities

This study reports the design and synthesis of novel 1,2,4-triazolo/benzimidazolo-pyrimidine linked 1-benzyl-4-[(p-tolyloxy)methyl]-1,2,3-triazole derivatives as potent antimicrobial agents according to their in vitro antibacterial, antifungal, antitubercular as well as antimalarial activities. An efficient, ecologically benign, and facile multicomponent synthesis was employed to synthesize these derivatives. The synthesis is accelerated with the mild and eco-friendly organocatalyst tetrabutylammonium bromide, providing a yield of 82%-96% within the short reaction time of 0.5-1.5 h. Compared with the MIC values of ciprofloxacin and ampicillin on the respective strains, compound d2 showed better activity against Escherichia coli and Streptococcus pyogenes and compound d8 showed better MIC against Staphylococcus aureus. Additionally, compounds d3, d4, and d5 showed potent MIC values against Pseudomonas aeruginosa. All triazolo-pyrimidine derivatives d1-d8 showed potent inhibitory action against Gram-positive strains. Compound e3 showed good potency against Mycobacterium tuberculosis H37Rv. The IC₅₀ values of d3 and e2 indicated better activity against Plasmodium falciparum. Collectively, these derivatives depict potent multifaceted activity and provide promising access for further antimicrobial and antimalarial investigations.

Interaction mechanism of benzophenone-type UV filters on bovine serum albumin: Insights from structure-affinity relationship

Benzophenone (BP)-type UV filters can cause structural changes of carrier protein in plasma. The binding process of five BP-type UV filters with bovine serum albumin (BSA) was investigated by multiple characterization methods, along with their structure-affinity relationship involving the structure of the five BP-type UV filters and their binding affinity for BSA. The BP-type UV filters investigated bound to BSA spontaneously, and altered conformation of BSA. The binding constants and number of binding sites between BP-type UV filters and BSA were 10³-10⁶ M^-1 and 0.82-1.26, respectively. These BP-type UV filters and BSA interacted with the same binding forces and went through the similar binding process, suggesting that the benzophenone skeleton structure was primarily responsible for the BP-type UV filters and BSA binding, and changes in the structure of the BSA. The BP-type UV filters with hydroxyl substituent (BP-1 and BP-9) and non-polar molecules (BP-6) had a high affinity for binding BSA and had a greater impact on BSA conformation.

Potential toxic effects of sulfonamides antibiotics: Molecular modeling, multiple-spectroscopy techniques and density functional theory calculations

Sulfonamide antibiotics (SAs) are widely used in medicine, animal husbandry and aquaculture, and excessive intake of SAs may pose potential toxicity to organisms. The toxicological mechanisms of two classical SAs, sulfamerazine (SMR) and sulfamethoxazole (SMT), were investigated by molecular docking, DFT and multi-spectroscopic techniques using HSA and BSA as model proteins. The quenching of HSA/BSA endogenous fluorescence by SMR was higher than that by SMT due to the stronger binding effect of the pyrimidine ring on HSA/BSA compared to the oxazole ring, and that result was consistent with that predicted by DFT calculations. Thermodynamic parameters show that the binding of SAs to HSA/BSA is an exothermic process that proceeds spontaneously (ΔG < 0). Marker competition experiments illustrate that the binding site of SMR/SMT on serum albumin is located in subdomain IIIA. The combination of SAs and HSA/BSA is mainly realized by hydrogen bond and hydrophobic interaction, and the concept is also supported by molecular modeling. The reduced α-helix content of HSA/BSA induced by SMR/SMT indicates a greater stretching of the protein α-helix structure of the SMR/SMT-HSA/BSA. The results could provide useful toxicological information on the hazards of SAs in response to growing concern that SAs may pose a toxic threat to organisms.

Imperative persistent interaction analysis of anticancer noscapine-ionic liquid with calf thymus DNA

In this study, we have shown the interaction between opium poppy alkaloid noscapine-based ionic liquid [Pip-Nos]OTf and ct-DNA using UV-visible absorption spectroscopy, fluorescence spectroscopy, CD, and computational studies. The absorption spectra showed a hypochromic shift with no shift in the absorption maxima suggesting groove or electrostatic binding. Fluorescence spectra showed an enhancement in fluorescence emission suggesting that the probable mode of binding should be groove binding. Ethidium bromide (EB) competitive and Ionic strength study showed the absence of intercalative and electrostatic modes of interaction. Further, CD analysis of ct-DNA suggested a groove binding mode of interaction of [Pip-Nos]OTf with ct-DNA. [Pip-Nos]OTf displayed a strong binding with the target ct-DNA with a molecular docking score of -41.47 kJ/mol with all 3D coordinates and full conformation. Also, molecular binding contact analyses depicted the stable binding of drug and ct-DNA with potential hydrogen bonds and hydrophobic interactions. The structural superimposition dynamics analysis showed the stable binding of [Pip-Nos]OTf with the ct-DNA model through RMSD statistics. Moreover, the ligand interaction calculations revealed the involvement of large binding energy along with a high static number of molecular forces including the hydrogen bonds and hydrophobic interactions in their complexation. These significant results report the potency of [Pip-Nos]OTf and its important futuristic role in cancer therapeutics.

Deciphering the nature of binding of dexlansoprazole with DNA: Biophysical and docking approaches

Drugs, in general, exhibit their pharmacological activity in binding with intracellular targets. Numerous anticancer and antibacterial drugs target DNA as one of their primary intracellular targets. Dexlansoprazole (DLP) is a heterocyclic compound containing benzimidazole moiety and a proton pump inhibitor used to treat gastroesophageal reflux disease. The interaction of dexlansoprazole with calf thymus DNA (ct-DNA) has been studied using biophysical methods. The UV-Visible studies revealed a binding constant of 2.15 ± 0.3 × 104 M^-1 which is close to the value of 2.44 ± 0.3 × 10⁴ M^-1 obtained from the fluorescence studies. Competitive displacement studies using the fluorescence spectroscopic method with ethidium bromide and Hoechst as DNA markers suggested the groove binding mode of DLP in ct-DNA. The groove binding mode of DLP in ct-DNA was complemented by the results of viscosity and DNA melting studies. Further studies on the effect of ionic strength and potassium iodide on DLP binding with ct-DNA supported the observed binding mode. Circular dichroism studies reflected no significant conformational variation in ct-DNA after the interaction. The binding mode obtained from the experimental studies was corroborated by the molecular docking studies that showed the position of DLP in the minor groove of ct-DNA along with the receptor interface restudies involved in the interaction.

Inhibitory effect of flavonoid glycosides on digestive enzymes: In silico, in vitro, and in vivo studies

Flavonoid glycosides (FGs) appear to be good candidates for controlling blood glucose levels, so regular consumption of vegetables/fruits rich in FGs may prevent the consequences of type 2 diabetes (DM). Inhibition of digestive enzymes using natural FGs is a suitable dietary tool to regulate the hydrolysis of polysaccharides and overcome hyperglycemia. The aim of the current research is to find FGs that can effectively inhibit the digestive enzymes α-glucosidase (α-Gl) and α-amylase (α-Am). Accordingly, twenty-three FGs were selected and filtered through docking-based virtual screening. Based on the molecular docking and molecular dynamics (MD) simulation, among the 23 selected FGs, nicotiflorin and swertisin significantly inhibited α-Gl and α-Am, respectively. In vitro analysis revealed the inhibitory capacity of nicotiflorin on α-Gl was equal to IC50 at 0.148 mg/ml and the inhibitory activity of swertisin on α-Am was equal to IC50 at 1.894 mg/ml. It was found that nicotiflorin and swertisin act much like as a competitive inhibitor on α-Gl and α-Am, respectively. Furthermore, the fluorescence intensity of both enzymes decreased after interaction with two FGs. FT-IR and scanning electron microscopy (SEM) measurements suggested that the interactions could alter the conformation and microenvironment of the enzymes. Moreover, in vivo evaluation showed that the administration of nicotiflorin and swertisin can alleviate the blood glucose level of rats compared to the starch group (p < 0.05). The findings highlight that nicotiflorin and swertisin can be considered as possible inhibitors in treating diabetes mellitus via digestive enzymes inhibition.

An insight into the interaction between Indisulam and human serum albumin: Spectroscopic method, computer simulation and in vitro cytotoxicity assay

Indisulam (IDM) is a sulfanilamide anticancer agent and has been identified as a molecular glue recently. It shows potential for novel therapies development and brings more hope for curing human diseases. The affinity between molecular glues and plasma protein makes it significant to understand the characteristics of such substances. Therefore, the interaction between IDM and human serum albumin (HSA) was explored through solvent experiments, computer simulation experiments, enzyme kinetics experiments, and cell viability assay. The results revealed that IDM and HSA spontaneously formed stable binary complex with the binding constant of the order 10⁵ M^-1. IDM inserted in the site I of HSA, resulting the change in HSA secondary structure. And π electrons in IDM's benzene rings, as well as van der Waals forces and the H-bond, all helped to stabilize the HSA-IDM complex. The results of molecular dynamic simulation (MD) corresponded with the results from solvent experiment well. For instance, there were approximately 1-5 H-bonds between IDM and HSA. Lys199 and Arg218 were crucial energy contributors in the binding process. The esterase-like activity experiment confirmed that IDM inhibited the catalytic activity of HSA. In addition, cell experiment revealed that serum albumin can significantly reduce the cytotoxicity of IDM towards human embryonic kidney 293T (HEK293T) cells.

Association Mechanism and Conformational Changes in Trypsin on Its Interaction with Atrazine: A Multi- Spectroscopic and Biochemical Study with Computational Approach

Atrazine (ATR) is a herbicide globally used to eliminate undesired weeds. Herbicide usage leads to various adverse effects on human health and the environment. The primary source of herbicides in humans is the food laced with the herbicides. The ATR binding to trypsin (TYP) was investigated in this study to explore its binding potential and toxicity. In vitro interaction of ATR with TYP was studied using multi-spectroscopic methods, molecular docking, and enzyme kinetics to explore the mechanism of binding for the TYP-ATR system. The TYP-ATR complex revealed binding constants (10³ M^-1), suggesting a moderate binding. The free energy for the TYP-ATR complexes was negative, suggesting a spontaneous interaction. Thermodynamic parameters enthalpy (ΔH) and entropy (ΔS) obtained positive values for the TYP-ATR system suggesting hydrophobic interactions in the binding process. Micro-environmental and conformational changes in TYP molecules were induced on interaction with ATR. Reduced catalytic activity of TYP was observed after interaction with ATR owing to the changes in the secondary structure of the TYP.

A Comprehensive Investigation of Interactions between Antipsychotic Drug Quetiapine and Human Serum Albumin Using Multi-Spectroscopic, Biochemical, and Molecular Modeling Approaches

Quetiapine (QTP) is a short-acting atypical antipsychotic drug that treats schizophrenia or manic episodes of bipolar disorder. Human serum albumin (HSA) is an essential transport protein that transports hormones and various other ligands to their intended site of action. The interactions of QTP with HSA and their binding mechanism in the HSA-QTP system was studied using spectroscopic and molecular docking techniques. The UV-Vis absorption study shows hyperchromicity in the spectra of HSA on the addition of QTP, suggesting the complex formation and interactions between QTP and HSA. The results of intrinsic fluorescence indicate that QTP quenched the fluorescence of HSA and confirmed the complex formation between HSA and QTP, and this quenching mechanism was a static one. Thermodynamic analysis of the HSA-QTP system confirms the involvement of hydrophobic forces, and this complex formation is spontaneous. The competitive displacement and molecular docking experiments demonstrated that QTP is preferentially bound to HSA subdomain IB. Furthermore, the CD experiment results showed conformational changes in the HSA-QTP system. Besides this, the addition of QTP does not affect the esterase-like activity of HSA. This study will help further understand the credible mechanism of transport and delivery of QTP via HSA and design new QTP-based derivatives with greater efficacy.

Biochemical characterization, cytotoxic, antimutagenic, anticancer and molecular docking studies on Tecomella undulata

In this study bioassay-guided screening of Tecomella undulate was performed for its cytotoxic, antimutagenic and anticancer potential. The ariel parts were extracted on a polarity basis (methanol, dichloromethane and hexane). The in vivo toxicity was assessed on Caenorhabditis elegans, and its locomotion was affected by Tecomella undulata hexane (TUAH) the most. Ames test for antimutagenicity showed Tecomella undulata methanol (TUAM) exhibited against mutagen 2AA showed inhibition of 71.03% and 26.32% 2AA in TA98 while in in vitro MTT assay on carcinoma cell lines TUAM showed 68.1% cytotoxicity. Moreover, In resazurin assay on fibroblast cells African green monkey kidney VERO and on the panel of carcinoma cell lines, the most effective extract was TUAM on liver HepG-2 with CC50 value 117.37 ± 4.73 µg/ml followed by on lungs A549 with 142.01 ± 5.3. Furthermore, for the bioassay-guided screening, the selectivity index was calculated for TUAM CC50 ratio on HepG-2 and VERO which showed a decent 2.77 score. After column chromatography, the fraction TU-63 should remarkable cytotoxic effect in dose-response manner assay as (Hep-G2) CC50 value 11. 67 ± 1.37 µg/ml followed by (A549) CC50 value 17.23 ± 0.58 µg/ml. For qualitative analysis of anticancer potential LC-ESI-MS/MS the potential phytochemicals were identified. In silico molecular modelling against selected carcinogenic proteins. The results suggest Tecomella undulate the substantial anticancer potential which supports potential natural anticancer therapeutic drug candidate development for combating cancer.

Influence of Rutin, Sinapic Acid, and Naringenin on Binding of Tyrosine Kinase Inhibitor Erlotinib to Bovine Serum Albumin Using Analytical Techniques Along with Computational Approach

Flavonoid-containing food supplements are widely used as antioxidants, and the continuous use of these supplements with other drugs can lead to clinically significant interactions between these and other drugs. The medications in systemic circulation are mainly transported by serum albumin, a major transport protein. This study evaluated the interactions of rutin (RUT), naringenin (NAR), and sinapic acid (SIN) with the most abundant transport protein, bovine serum albumin (BSA), and the anticancer drug, the tyrosine kinase inhibitor Erlotinib (ETB), using various analytical methods. Interaction between multiple types of ligands with the transport proteins and competition between themselves can lead to the bound ETB’s displacement from the BSA-binding site, leading to elevated ETB concentrations in the systemic circulation. These elevated drug fractions can lead to adverse events and lower tolerance, and increased resistance to the therapeutic regimen of ETB. The experimental and computational methods, including molecular-docking studies, were used to understand the molecular interactions. The results suggested that the complexes formed were utterly different in the binary and the ternary system. Furthermore, comparing the ternary systems amongst themselves, the spectra differed from each other. They thus inferred that complexes formed between BSA-ETB in the presence of each RUT, NAR, and SIN separately were also different, with the highest value of the reduction in the binding energy in RUT, followed by SIN and then NAR. Thus, we conclude that a competitive binding between the ETB and these flavonoids might influence the ETB pharmacokinetics in cancer patients by increasing ETB tolerance or resistance.

Mode of interaction of altretamine with calf thymus DNA: biophysical insights

Insights into drug-DNA interactions have importance in medicinal chemistry as it has a major role in the evolution of new therapeutic drugs. Therefore, binding studies of small molecules with DNA are of significant interest. Spectroscopy, coupled with measurements of viscosity and molecular docking studies were employed to obtain mechanistic insights into the binding of altretamine with calf thymus DNA (CT-DNA). The UV-visible spectroscopic measurements study confirmed altretamine-CT-DNA complex formation with affinity constant ([15.68 ± 0.04] × 10³ M^-1), a value associated with groove binding phenomenon. The associated thermodynamic signatures suggest enthalpically driven interactions. The values of standard molar free energy change (ΔGmo) -(23.93 ± 0.23) kJ mol^-1, enthalpy change (ΔvHHmo) -(50.84 ± 0.19) kJ mol^-1 and entropy change (ΔSmo) -(90.29 ± 0.12) JK^-1 mol^-1 indicate the binding is thermodynamically favorable and an important role of the hydrogen bonds and Van der Waals interactions in the binding of altretamine with CT-DNA. Circular dichroism spectroscopy indicated insignificant conformational changes in the DNA backbone upon interaction with altretamine suggesting no distortion and/or unstacking of the base pairs in the DNA helix. UV-melting study suggested that the thermal stability of the DNA backbone is not affected by the binding of the drug. Competitive displacement assays with ethidium bromide, Hoechst-33258 and DAPI established the binding of altretamine with CT-DNA in the minor groove. The mode of binding was further confirmed by viscosity and molecular docking studies. Molecular docking further ascertained binding of altretamine in the minor groove of the CT-DNA, preferably with the A-T rich sequences.

Malachite Green, the hazardous materials that can bind to Apo-transferrin and change the iron transfer

Different groups of synthetic dyes might lead to environmental pollution. The binding affinity among hazardous materials with biomolecules necessitates a detailed understanding of their binding properties. Malachite Green might induce a change in the iron transfer by Apo-transferrin. Spectroscopic studies showed malachite green oxalate (MGO) could form the apo-transferrin-MGO complex and change the Accessible Surface Area (ASA) of the key amino acids for iron transfer. According to the ASA results the accessible surface area of Tyrosine, Aspartate, and Histidine of apo-transferrin significantly were changed, which can be considered as a convincing reason for changing the iron transfer. Moreover, based on the fluorescence data MGO could quench the fluorescence intensity of apo-transferrin in a static quenching mechanism. The experimental and Molecular Dynamic simulation results represented that the binding process led to micro environmental changes, around tryptophan residues and altered the tertiary structure of apo-transferrin. The Circular Dichroism (CD) spectra result represented a decrease in the amount of the α-Helix, as well as, increase in the β-sheet volumes of the apo-transferrin structure. Moreover, FTIR spectroscopy results showed a hypochromic shift in the peaks of amide I and II. Molecular docking and MD simulation confirmed all the computational findings.

In silico and multi-spectroscopic analyses on the interaction of 5-amino-8-hydroxyquinoline and bovine serum albumin as a potential anticancer agent

5-Amino-8-hydroxyquinoline (5A8HQ), an amino derivative of 8-hydroxyquinoline, has become a potential anticancer candidate because of its promising proteasome inhibitory activity to overcome and yet synergize bortezomib for fighting cancers. Therefore, in this study, its physicochemical properties and interaction activities with serum protein have extensively been elucidated by both in vitro and in silico approaches to fulfill the pharmacokinetic and pharmacodynamic gaps. 5A8HQ exhibited the drug-likeness properties, where oral administration seems to be a route of choice owing to its high-water solubility and intestinal absorptivity. Multi-spectroscopic investigations suggested that 5A8HQ tended to associate with bovine serum albumin (BSA), a representative of serum protein, via the ground-state complexation. It apparently bound in a protein cleft between subdomains IIA and IIIA of BSA as suggested by the molecular docking and molecular dynamics simulations. The binding was mainly driven by hydrogen bonding and electrostatic interactions with a moderate binding constant at 10⁴ M⁻¹, conforming with the predicted free fraction in serum at 0.484. Therefore, 5A8HQ seems to display a good bioavailability in plasma to reach target sites and exerts its potent pharmacological activity. Likewise, serum albumin is a good candidate to be reservoir and transporter of 5A8HQ in the circulatory system.

Interaction between phloretin and insulin: a spectroscopic study

Diabetes is among the top ten deadly diseases in the world. It occurs either when the pancreas does not produce enough insulin (INS) or when the body cannot effectively use the insulin it produces. Phloretin (PHL) has a biological effect that can treat diabetes. A spectroscopic study was carried out to explore the interaction between phloretin and insulin. UV/Vis spectroscopy, fluorescence spectroscopy, and circular dichroism spectropolarimeter were used in the study. UV/Vis spectra showed that the interaction between PHL and INS produced strong absorption at a wavelength of 282 nm. The fluorescence analysis results showed that the excitation and emission occurred at 280-nm and 305-nm wavelengths, respectively. Temperature changes did not affect INS emissions. However, the interaction of PHL–INS caused a redshift at 305 to 317 nm. Temperature affected the binding constant (Ka) and the binding site (n). Ka decreased with increasing temperature and increased the binding site. The thermodynamic parameters such as enthalpy (ΔH0) and entropy (ΔS0) each had a value of − 16,514 kJ/mol and 22.65 J/mol·K. PHL and INS interaction formed hydrogen bonds and hydrophobic interaction. The free energy (ΔG0) recorded was negative. PHL and INS interactions took place spontaneously. The quenching effect was dynamic and static. KD values were greater than KS. The higher the temperature, the less was KD and KS. The appearance of two negative signals on circular dichroism (CD) spectropolarimeter implies that phloretin could induce regional configuration changes in insulin. The addition of PHL has revealed that the proportion of α-helix in the insulin stabilizes its structure. Phloretin’s stabilization and enhancement of the α-helix structural configuration in insulin indicate that phloretin can improve insulin resistance.

Solid-phase microextraction for assessment of plasma protein binding, a complement to rapid equilibrium dialysis

Aim: Determination of plasma protein binding (PPB) is considered vital for better understanding of pharmacokinetic and pharmacodynamic activities of drugs due to the role of free concentration in pharmacological response. Methodology & results: Solid-phase microextraction (SPME) was investigated for measurement of PPB from biological matrices and compared with a gold standard approach (rapid equilibrium dialysis [RED]). Discussion & conclusion: SPME-derived values of PPB correlated well with literature values, and those determined by RED. Respectively, average protein binding across three concentrations by RED and SPME was 33.1 and 31.7% for metoprolol, 89.0 and 86.6% for propranolol and 99.2 and 99.0% for diclofenac. This study generates some evidence for SPME as an alternative platform for the determination of PPB.