Interaction of new kinase inhibitors cabozantinib and tofacitinib with human serum alpha-1 acid glycoprotein. A comprehensive spectroscopic and molecular Docking approach

Insight into intermolecular binding mechanism of apatinib mesylate and human alpha-1-acid glycoprotein: combined multi-spectroscopic approaches with in silico

Apatinib mesylate (APM), an oral tyrosine kinase inhibitor, has a good anti-tumor activity in the treatment of various cancers, particularly in advanced non-small cell lung cancer. In this study, the intermolecular binding mechanism between APM and human alpha-1-acid glycoprotein (HAG) was investigated by combining multi-spectroscopic approaches with in silico techniques. The findings revealed that APM gave rise to the fluorescence quenching of HAG by forming a ground-state complex between APM and HAG with a stoichiometric ratio of 1:1, and APM has a moderate affinity for HAG as the binding constant of APM and HAG of approximately 105 M-1, which was larger than the APM-HAG complex. The findings from thermodynamic parameter analysis indicated that the dominant driving forces for the formation of the APM-HAG complex were van der Waals forces, hydrogen bonding and hydrophobic interactions, which were also verified with site-probe studies and molecular docking. The findings from in silico study indicated that APM inserted into the opening of the hydrophobic cavity of HAG, leads to a slight conformational change in the HAG, which was verified by circular dichroism (CD) measurements, that was, the beta sheet level of HAG decreased. Additionally, the results of synchronous and 3D fluorescence spectroscopies confirmed the decline in hydrophobicity of the microenvironment around Trp and Tyr residues. Moreover, some common metal ions such as Cu2+, Mg2+, Fe3+, Ca2+, and Zn2+ could cause the alteration in the binding constant of APM with HAG, leading to the change in the efficacy of APM. It will be expected that these study findings are to provide useful information for further understanding pharmacokinetic and structural modifications of APM.Communicated by Ramaswamy H. Sarma.

Investigation on the binding behavior of human α1-acid glycoprotein with Janus Kinase inhibitor baricitinib: Multi-spectroscopic and molecular simulation methodologies

Baricitinib is a Janus Kinase (JAK) inhibitor that is primarily used to treat moderately to severely active rheumatoid arthritis in adults and has recently been reported for the treatment of patients with severe COVID-19. This paper describes the investigation of the binding behavior of baricitinib to human α1-acid glycoprotein (HAG) employing a variety of spectroscopic techniques, molecular docking and dynamics simulations. Baricitinib can quench the fluorescence from amino acids in HAG through a mix of dynamic and static quenching, according to steady-state fluorescence and UV spectra observations, but it is mainly static quenching at low concentration. The binding constant (K_b) of baricitinib to HAG at 298 K was at the level of 10⁴ M^-1, indicating a moderate affinity of baricitinib to HAG. Hydrogen bonding and hydrophobic interactions conducted the main effect, according to thermodynamic characteristics, competition studies between ANS and sucrose, and molecular dynamics simulations. For the change in HAG conformation, the results of multiple spectra showed that baricitinib was able to alter the secondary structure of HAG as well as increase the polarity of the microenvironment around the Trp amino acid. Furthermore, the binding behavior of baricitinib to HAG was investigated by molecular docking and molecular dynamics simulations, which validated experimental results. Also explored is the influence of K⁺, Co²⁺, Ni²⁺, Ca²⁺, Fe³⁺, Zn²⁺, Mg²⁺ and Cu²⁺plasma on binding affinity.

Elucidation of binding dynamics of tyrosine kinase inhibitor tepotinib, to human serum albumin, using spectroscopic and computational approach

Tepotinib (TPT), an anticancer drug, is a fibroblast growth factor receptor inhibitor approved by the FDA for the chemotherapy of urothelial carcinoma. The binding of anticancer medicines to HSA can affect their pharmacokinetics and pharmacodynamics. The absorption, fluorescence emission, circular dichroism, molecular docking, and simulation studies were used to evaluate the binding relationship between TPT and HSA. The absorption spectra exhibited a hyperchromic effect upon the interaction of TPT with HSA. The Stern-Volmer and binding constant of the HSA-TPT complex demonstrates that fluorescence quenching is triggered by a static rather than a dynamic process. Further, the displacement assays and molecular docking results revealed that TPT preferred binding to site III of HSA. Circular dichroism spectroscopy confirmed that TPT binding to HSA induces conformational changes and reduces α-helical content. The thermal CD spectra reveal that tepotinib enhances protein's stability in the temperature range of 20 to 90 °C. The findings of MDS studies provide further evidence for the stability of the HSA-TPT complex. Consequently, the findings of the present investigation provide a clear picture of the impacts of TPT on HSA interaction. These interactions are thought to make the microenvironment around HSA more hydrophobic than in its native state.

Exploring the binding effects and inhibiting mechanism of hyperoside to lipase using multi-spectroscopic approaches, isothermal titration calorimetry, inhibition kinetics and molecular dynamics

Hyperoside (HYP) is a flavonoid with various physiological activities. The present study examined the interaction mechanism between HYP and lipase using multi-spectrum and computer-aided techniques. Results demonstrated that the force type of HYP on lipase was mainly hydrogen bond, hydrophobic interaction force, and van der Waals force, and HYP had an excellent binding affinity with lipase at 1.576 × 10⁵ M^-1. HYP dose-dependently inhibited lipase in the inhibition experiment, and its IC₅₀ value was 1.92 × 10^-3 M. Moreover, the results suggested that HYP could inhibit the activity by binding to essential groups. Conformational studies indicated that the conformation and microenvironment of lipase were slightly changed after the addition of HYP. Computational simulations further confirmed the structural relationships of HYP to lipase. The interaction between HYP and lipase can provide ideas for the development of functional foods related to weight loss. The results of this study help comprehend the pathological significance of HYP in biological systems, as well as its mechanism.

Elucidation of the interaction mechanism of olmutinib with human α-1 acid glycoprotein: insights from spectroscopic and molecular modeling studies

Olmutinib, the third-generation tyrosine kinase inhibitor, is applied in treating non-small cell lung cancer (NSCLC). The aim of this study is to elucidate the interaction mechanism of olmutinib with human α-1 acid glycoprotein (HAG), an important carrier protein, by mean of multi-spectroscopic and molecular simulation techniques. Fluorescence spectral results confirmed that the fluorescence of this carrier protein can be quenched by olmutinib in the static quenching mode, and this anticancer drug possesses a moderate binding affinity on HAG. The evidence from thermodynamic analysis, replacement interaction with ANS and sucrose, and computational simulation results showed that hydrogen bonding, hydrophobic interactions, and van der Waals forces involved the olmutinib-HAG complexation process. The results from UV-vis, 3D fluorescence and synchronous fluorescence spectroscopy proved that binding anticancer drug olmutinib caused the alteration in the microenvironment around Trp residues. And, circular dichroism spectral results provided the support for the conformational alterations in the carrier protein. The data also proved that olmutinib preferably bound to the hydrophobic cavity of HAG and the binding distance between the two was 2.21 nm. In addition, it can be found that the presence of some metal ions such as Zn²⁺, Ca²⁺, Ni²⁺ and Cu²⁺ would exert a certain extent effect on the olmutinib-HAG complexation process.Communicated by Ramaswamy H. Sarma.

Comprehending binding features between ibrutinib and Human Alpha-1 acid glycoprotein: Combined experimental approaches and theoretical simulations

Human alpha-1 acidic glycoprotein (HAG) is one of the proteins widely present in the blood, and the level of HAG in patients with cancer and inflammation is significantly increased. As one of transport proteins in the blood, the ability of HAG to bind with a drug, especially alkaline drugs, affects significantly the drug content at the target site, which in turn affects the efficacy of the drug. In this study, the interaction mechanism between HAG and the first generation Bruton's tyrosine kinase (BTK) inhibitor namely ibrutinib was explored by a combination of multi-spectroscopic techniques and theoretical calculations. The findings revealed that the quenching and binding constants of the HAG-ibrutinib system both reduced as the temperature rose, demonstrating that ibrutinib quenched the intrinsic fluorescence of HAG in a static manner. It was confirmed that HAG and ibrutinib formed a 1:1 complex with moderate affinity due to the binding constant of around 10⁵ M^-1 and accompanied by Förster resonance energy transfer. It was verified by thermodynamic parameter analysis and competition assays as well as molecular simulation that the existence of hydrogen bonds, van der Waals forces, and hydrophobic forces in the complexation of HAG and ibrutinib.The findings from theoretical calculations including molecular docking and theoretical calculation simulation confirmed that ibrutinib bound to the barrel hydrophobic pocket of HAG with a binding energy of -41.9 kJ∙mol^-1, and the the binding constant of around 10⁵ M^-1 and the contribution of each residue in the complexation of ibrutinib and HAG. Additionally, it can be confirmed that metal ions affected the binding interaction of ibrutinib with HAG, among them, some promoted binding while others inhibited it.

The antioxidant activities, inhibitory effects, kinetics, and mechanisms of artocarpin and α-mangostin on α-glucosidase and α-amylase

This study investigated the antioxidant activities, enzyme inhibitory activities and the interaction mechanisms of artocarpin and α-mangostin on α-amylase and α-glucosidase. Results showed that artocarpin and α-mangostin had obvious antioxidant activities and inhibitory activities on α-glucosidase and α-amylase. The inhibitions of the two compounds on α-glucosidase were reversible and non-competitive according to the kinetics studies. Fluorescence intensity measurements indicated that the interaction mechanisms between the inhibitors and the two enzymes were static processes. Isothermal titration calorimetry (ITC) analysis showed that the bindings between the inhibitors and the enzymes complex were all spontaneous. The main driving forces between α-mangostin and artocarpin with α-glucosidase might be hydrogen bonds and electrostatic interactions, respectively. While the forces between the two inhibitors and α-amylase might be hydrophobic interactions. Furthermore, molecular docking results showed that artocarpin and α-mangostin could bind to the allosteric site of the two enzymes, except for artocarpin in the active site pocket of α-amylase. All the results indicated that artocarpin and α-mangostin might be promising candidates for hypoglycemic functional products.

Effect of pH on Diclofenac–Lysozyme Interaction: Structural and Functional Aspect

As a nonsteroidal antiinflammatory drug, diclofenac (DCF) is used in the treatment of a variety of human ailments. It has already been reported that the use of this class of drugs for a longer duration is associated with numerous side effects such as cardiovascular implications, reno-medullary complications, etc. In the present study, the effect of DCF on the structure, stability, and function of lysozyme was studied. The study was designed to examine the effect of DCF only at various pH values. Heat-induced denaturation of lysozyme was analyzed in the presence and absence of various molar concentrations of DCF at different pH values. The values of thermodynamic parameters, the midpoint of denaturation (T_m), enthalpy change at T_m (ΔH_m), constant pressure heat capacity change (ΔC_p), and Gibbs energy change at 25°C (ΔG_D^o), thus obtained under a given set of conditions (pH and molar concentration of DCF), demonstrated the following 1) DCF destabilized lysozyme with respect of T_m and ΔG_D^o at all the pH values, 2) the magnitude of protein destabilization is lesser at acidic pH than at physiological pH, 3) structural changes in lysozyme are less projecting at pH 2.0 than at pH 7.0, and 4) quenching is observed at both pH values. Furthermore, the process of protein destabilization in the presence of DCF is entropically driven.

Chebulinic and chebulagic acid binding with serum proteins: biophysical and molecular docking approach

Chebulinic acid (CHN) and chebulagic acid (CHG) have been known for centuries for their anti-cancer, anti-diabetes, HIV and anti-inflammatory properties. In this study, the interaction of these phytochemicals CHN/CHG, with the two major transport proteins for various drugs, human serum albumin (HSA) and α-1-acid glycoprotein (AGP), was unraveled by using several spectroscopic techniques and computational methods. The binding of CHN/CHG quenches the HSA/AGP fluorescence intensities, and also these phytochemicals are bound strongly to HSA/AGP proteins. An apparent decrease in fluorescence intensities of CHN/CHG-HSA and CHN/CHG-AGP complex showed the static mode of fluorescence quenching. Furthermore, the intrinsic fluorescence and using site-specific markers ibuprofen competing with these molecules, thereby replacing it in the binding site of subdomain IIIA. The computational methods substantiated the experimental findings, revealing that CHN interacted with Lys414A, Glu492A, Glu492A and Lys413A residues of subdomain IIIA of HSA and for CHG showed the interaction with Lys545A and Lys413A residues of subdomain IIIA of HSA. Fluorescence and surface plasmon resonance data unveiled a previously unreported binding event between CHN/CHG and HSA; the determined binding affinities of both compounds were slightly higher for HSA than AGP. A change in functionality of protein confirmed the esterase-like activity of HSA in the presence of CHG/CHN upon binding with CHG/CHN. Displacement and circular dichroism (CD) experiments analysis showed that the two CHN/CHG and binding specifically to IIIA subdomain on HSA results in the conformational changes in the HSA. Thus, CD revealed a few conformational changes in HSA due to CHN/CHG. The binding of these two phytochemicals to the plasma proteins would give a path to develop new inspired drug molecules for chronic diseases.Communicated by Ramaswamy H. Sarma.

On the binding reaction of loratadine with human serum acute phase protein alpha 1-acid glycoprotein

Loratadine is an important anti-allergic drug. It is a second generation antihistamine drug used to treat allergic rhinitis, hay fever and urticaria. Human serum alpha 1-acid glycoprotein (AG) is an important acute phase protein and its serum concentration is found to increase in inflammation and acute response.The binding interaction between loratadine and AG is studied using spectroscopy and molecular docking techniques. The results obtained from fluorescence quenching experiments demonstrated that the fluorescence intensity of AG is quenched by loratadine. Loratadine was found to bind AG with the binding constant of ≈10⁴ at 298 K. The Gibb's free energy change was found to be negative for the interaction of loratadine with AG indicating the binding process is spontaneous. Binding of loratadine with AG induced ordered structures in the protein. Hydrogen bonding and hydrophobic interactions were the main bonding forces between AG-loratadine as revealed by molecular docking results. This study suggests the importance of binding of anti-allergic drug to AG spatially in the diseases where the plasma concentration of AG increases many folds and interaction with this protein becomes significant. This study will help in design of drug dosage and adjustment accordingly to achieve optimal treatment outcome. Communicated by Ramaswamy H. Sarma.

Salmon sperm DNA binding study to cabozantinib, a tyrosine kinase inhibitor: Multi-spectroscopic and molecular docking approaches

In the current work, the binding interaction of cabozantinib with salmon sperm DNA (SS-DNA) was studied under simulated physiological conditions (pH 7.4) using fluorescence emission spectroscopy, UV-Vis absorption spectroscopy, viscosity measurement, ionic strength measurement, FT-IR spectroscopy, and molecular modeling methods. The obtained experimental data demonstrated an apparent binding interaction of cabozantinib with SS-DNA. The binding constant (K_b) of cabozantinib with SS-DNA evaluated from the Benesi-Hildebrand plot was equal to 5.79 × 10⁵ at 298 K. The entropy and enthalpy changes (∆S⁰ and ∆H⁰) in the binding interaction of SS-DNA with cabozantinib were 44.13 J mol^-1 K^-1 and -19.72 KJ mol^-1, respectively, demonstrating that the basic binding interaction forces are hydrophobic and hydrogen bonding interactions. Results from UV-Vis absorption spectroscopy, competitive binding interaction with rhodamine B or ethidium bromide, and viscosity measurements revealed that cabozantinib binds to SS-DNA via minor groove binding. The molecular docking results revealed that cabozantinib fits into the AT-rich region of the B-DNA minor groove and the binding site of cabozantinib was 4 base pairs long. Moreover, cabozantinib has eight active torsions, implying a high degree of flexibility in its structure, which played a significant role in the formation of a stable cabozantinib-DNA complex.

Revisiting Chiral Recognition Mechanism on Chicken Alpha 1-Acid Glycoprotein: Location of Chiral Binding Sites and Insight into Chiral Binding Mechanism

Chiral stationary phases based on chicken alpha 1-acid glycoprotein (cAGP) have been used for enantioseparations of various compounds. However, the chiral binding sites and mechanism have not been clarified yet. Based on chromatographic properties of native and W26-modified cAGP columns and docking simulations of studied compounds into the generated model structure of cAGP, the chiral binding sites were located on cAGP and the chiral binding mechanism was discussed. On cAGP, there existed a binding cavity lined with H25, W26, Y47, R128, T129, D161 and E168, which contribute electrostatic or hydrogen bonding interactions. Benzoin and chlorpheniramine enantiomers interacted with cAGP at almost the same sites a little away from W26, while propranolol enantiomers docked, slightly shifting toward H25 and W26. Furthermore, in addition to hydrophobic interactions, ionic interactions between amino groups of chlorpheniramine enantiomers and a carboxy group of D161 or E168 played an important role in the chiral recognition, while hydrophobic interactions and hydrogen bonding interactions worked for the chiral recognition of benzoin and propranolol enantiomers.

Structural changes in trypsin induced by the bile salts: An effect of amphiphile hydrophobicity

The present study reports the multi-technique results of the interaction of a series of bile salts, sodium cholate (NaC), sodium taurocholate (NaTC), sodium deoxycholate (NaDC), and sodium taurodeoxycholate (NaTDC) with trypsin under the experimental conditions of 25 °C and pH 7.0. The interactions between trypsin and the bile salts were characterized by the surface tension measurements and various spectroscopic techniques like UV-Visible absorption, steady-state fluorescence, and circular dichroism. The results of surface tension measurements reveal a strong interaction of trypsin (50 μM) with the increasing concentration of bile salts, being higher with the bile salt of greater hydrophobicity. The critical aggregation concentration of bile salts in the presence of trypsin (C₁) showed that the bile salts interact strongly with the trypsin in the order of NaTDC > NaDC > NaTC > NaC. UV-visible, steady-state fluorescence, and circular dichroism spectroscopic results confirmed significant unfolding of trypsin due to its interaction with the bile salts, the extent of which followed the same sequence as observed in the surface tension results. It could be concluded that the hydrophobic bile salts that show lower C₁ values and have less delocalized charge, are more effective in unfolding the trypsin. The study would help understand the hydrophobicity-driven unfolding of proteins aided by biological surfactants like bile salts and help devise efficient proteolytic enzyme-based detergent formulations and understand the role of such amphiphiles as antimicrobial agents.

Biophysical Insight into the Interaction of Human Lysozyme with Anticancer Drug Anastrozole: A Multitechnique Approach

In the present study, we employ fluorescence spectroscopy, dynamic light scattering, and molecular docking methods. Binding of anticancer drug anastrozole with human lysozyme (HL) is studied. Binding of anastrozole to HL is moderate but spontaneous. There is anastrozole persuaded hydrodynamic change in HL, leading to molecular compaction. Binding of anastrozole to HL also decreased in vitro lytic activity of HL. Molecular docking results suggest the electrostatic interactions and van der Waals forces played key role in binding interaction of anastrozole near the catalytic site. Binding interaction of anastrozole to proteins other than major transport proteins in blood can significantly affect pharmacokinetics of this molecule. Hence, rationalizing drug dosage is important. This study also points to unrelated effects that small molecules bring in the body that are considerable and need thorough investigation.

12-Deacetyl-12-epi-Scalaradial, a Scalarane Sesterterpenoid from a Marine Sponge Hippospongia sp., Induces HeLa Cells Apoptosis via MAPK/ERK Pathway and Modulates Nuclear Receptor Nur77

12-Deacetyl-12-epi-scalaradial, a scalarane sesterterpenoid from a marine sponge Hippospongia sp, has been reported to possess cytotoxic activity on HepG2, MCF-7, and HCT-116 cells. However, there is no research to indicate that 12-deacetyl-12-epi-scalaradial exhibited anticancer effect on cervical cancer HeLa cells. The aim of this study was to investigate the anticancer activity of 12-deacetyl-12-epi-scalaradial against HeLa cells and to explore the mechanism. The results from a methylthiazolyldiphenyl-tetrazolium (MTT) assay suggested that 12-deacetyl-12-epi-scalaradial suppressed the proliferation of HeLa cells and flow cytometry analysis showed 12-deacetyl-12-epi-scalaradial could induce the apoptosis of HeLa cells in dose- and time-dependent manner. Western blotting analysis demonstrated that 12-deacetyl-12-epi-scalaradial triggered apoptosis via mediating the extrinsic pathway and was found to suppress MAPK/ERK pathway which was associate with cancer cell death. Nur77, a critical number of orphan nuclear receptors, plays diverse roles in tumor development as a transcription factor and has been considered as a promising anticancer drug target. The dual-luciferase reporter assays suggested that 12-deacetyl-12-epi-scalaradial could selectively enhance the trans-activation activity of Nur77. Furthermore, Western blotting analysis and fluorescence quenching showed that 12-deacetyl-12-epi-scalaradial could induce the phosphorylation of Nur77 and interact with the ligand-binding domain (LBD) of Nur77. Our research confirmed 12-deacetyl-12-epi-scalaradial as a potential agent for cervical cancer therapy and provided a view that 12-deacetyl-12-epi-scalaradial may be a modulator of Nur77.

Biomolecular interactions and binding dynamics of tyrosine kinase inhibitor erdafitinib, with human serum albumin

Erdafitinib is an approved tyrosine kinase inhibitor that inhibits fibroblast growth factor receptor. It has been described as one of the potent anti-tumor drugs especially for the treatment of urothelial carcinoma. In this study, we have investigated the binding dynamics of erdafitinib with human serum albumin (HSA) using multiple spectroscopic techniques. The outcome of the results suggests the occurrence of static quenching during the interaction of HSA with erdafitinib which leads to the formation of non-fluorescent HSA-erdafitinib ground state complex. Formation of HSA-erdafitinib complex was also confirmed from the findings of absorption spectral analysis. The changes in microenvironment around hydrophobic domains (especially tryptophan and tyrosine) were deciphered from fluorescence spectroscopy which was further confirmed by synchronous spectral analysis. In order to gain insight into the binding site of erdafitinib in HSA, molecular docking combined with competitive displacement assay was performed. The modified form of Stern Volmer equation was used to estimate various binding parameters including number of binding sites. The findings are indicative of a single binding site (n = 1) with binding constant in the order of 10⁴. The negative values of thermodynamic parameters like ΔG, ΔH and ΔS were suggestive of the binding reaction being spontaneous and exothermic, while the hydrogen bonds and Van der Waals interactions being the major forces present between HSA and erdafitinib. Circular dichroism spectral analysis revealed the alterations in the conformation of HSA structure and reduction in its α-helical content.Communicated by Ramaswamy H. Sarma[Formula: see text].

Biophysical insight into the interaction of levocabastine with human serum albumin: spectroscopy and molecular docking approach

Interaction of levocabastine with human serum albumin (HSA) is investigated by applying fluorescence spectroscopy, circular dichroism spectroscopy and molecular docking methods. Levocabastine is an important drug in treatment of allergy and currently a target drug for drug repurposing to treat other diseases like vernal keratoconjuctivitis. Fluorescence quenching data revealed that levocabastine bind weakly to protein with binding constant in the order of 10³ M^-1. Förster resonance energy transfer results indicated the binding distance of 2.28 nm for levocabastine. Synchronous fluorescence result suggest slight blue shift for tryptophan upon levocabastine binding, binding of levocabastine impelled rise in α-helical structure in protein, while there are minimal changes in tertiary structure in protein. Moreover, docking results indicate levocabastine binds to pocket near to the drug site-I in HSA via hydrogen bonding and hydrophobic interactions. Understanding the interaction of levocabastine with HSA is significant for the advancement of therapeutic and diagnostic strategies for optimal treatment results.Communicated by Ramaswamy H. Sarma.

Toxicity of thimerosal in biological systems: Conformational changes in human hemoglobin, decrease of oxygen binding capacity, increase of protein glycation and amyloid's formation

Thimerosal (TH), an organomercurial compound, is used as a preservative in vaccines and cosmetics. Its interaction with human hemoglobin (Hb) was investigated under physiological conditions using biophysical and biological assays, aiming to evaluate hazardous effects. TH interacts spontaneously with Hb (stoichiometry 2:1, ligand-protein), preferably by electrostatic forces, with a binding constant of 1.41 × 10⁶ M^-1. Spectroscopic data allows to proposing that TH induces structural changes in Hg, through ethylmercury transfer to human Hb-Cys93 residues, forming thiosalicylic acid, which, in turn, interacts with the positive side of the amino acid in the Hb-HgEt adduct chain. As a consequence, inhibition of Hb-O₂ binding capacity up to 72% (human Hb), and 50% (human erythrocytes), was verified. Dose-dependent induction of TH forming advanced glycation end products (AGE) and protein aggregates (amyloids) was additionally observed. Finally, these results highlight the toxic potential of the use of TH in biological systems, with a consequent risk to human health.

Understanding the interaction between α-1-acid glycoprotein (AGP) and potential Cu/Zn metallo-drugs of benzimidazole derived organic motifs: A multi-spectroscopic and molecular docking study

Drug-binding and interactions with plasma proteins strongly affect their efficiency of delivery, hence considered as a key factor in determining the overall pharmacological action. Alpha-1-acid glycoprotein (AGP), a second most abundant plasma protein in blood circulation, has unique drug binding ability and involved in the transportation of various compounds. Here, we have investigated the mechanism of interaction between AGP and potential Cu/Zn metallo-drugs of benzimidazole derived organic motifs (CuL₂ and ZnL₂, where L is Schiff base ligand) by applying integrated spectroscopic, biophysical techniques and computational molecular docking analyses. We found that both the metallo-drugs (CuL₂ and ZnL₂) were bound at the central cavity of AGP interacting with the residues of lobe I, lobe II as well as lobe III. The binding of metallo-drugs to AGP occurs in 1:1 M ratios. Hydrogen bonding, electrostatic and hydrophobic interactions played a significant role in stabilizing the AGP-metallo-drug complexes. Binding affinities of both the metallo-drugs towards AGP at 298 K were of the order of 10⁴-10⁵ M^-1, corresponding to Gibbs free energy of stabilization of approximately -5.50 to -6.62 kcal mol^-1. Furthermore, the spectroscopic investigation by circular dichroism and synchronous fluorescence analyses suggest conformational changes in AGP upon the binding of metallic compounds.

Identification of Ellagitannins in the Unripe Fruit of Rubus Chingii Hu and Evaluation of its Potential Antidiabetic Activity

As a functional food, the unripe fruits of Rubus chingii Hu have been widely used in China for thousands of years. Twenty-five major ellagitannins (ETs) were identified from the unripe fruits, and a novel ellagitannin, chingiitannin A (1), together with four other known ETs (2-5) were isolated and identified by HPLC-QTOF-MS/MS and 2D-NMR. Chingiitannin A showed the highest α-glucosidase and α-amylase inhibitory activities (IC₅₀ 2.89 and 4.52 μM, respectively), which occurred in a reversible and noncompetitive manner. Static quenching was indicated in a fluorescence quenching assay. Molecular docking results revealed that chingiitannin A interacted with the enzymes mainly by hydrogen bonding and was bound in the allosteric site. Chingiitannin A was nontoxic, and it increased the glucose uptake in L6 myotubes. The results suggested that the unripe fruits of Rubus chingii Hu are rich sources of ETs, and chingiitannin A might be a good candidate for functional foods or antidiabetic drugs.

Cytotoxic Components from Hypericum elodeoides Targeting RXRα and Inducing HeLa Cell Apoptosis through Caspase-8 Activation and PARP Cleavage

To find small-molecule regulators of RXRα, a phytochemical study of Hypericum elodeoides was conducted. Fifteen compounds, including the new 1 and 6, were isolated from the whole plant of H. elodeoides. The absolute configuration of 1 was assigned by comparison of experimental and calculated ECD data. Compounds 1 and 6 exhibited concentration-dependent inhibitory effects on RXRα transcription and selectively inhibited the proliferation of HeLa cells. Western blot analysis suggested that 1 and 6 induced apoptosis of HeLa cells with time- and dose-dependent PARP cleavage. A caspase activation assay indicated that these two compounds triggered caspase-8 activation to induce apoptosis by the extrinsic pathway. Molecular docking results suggested that 1 and 6 interacted with the Arg319 moiety of RXRα-LBD. Ligands binding to RXRα have shown promise in the discovery of anticancer drugs. A fluorescence quenching assay indicated the binding of 1 and 6 to the RXRα with the binding constant ( K_D) fitted as 68.3 and 14.0 μM, respectively. A preliminary SAR study of the isolates was conducted to enhance the knowledge of the RXRα ligands. Thus, 1 and 6 might act as the small-molecule regulators of RXRα, which target RXRα and mediate HeLa cell apoptosis through the extrinsic pathways.

Effect of Salvia miltiorrhiza on acetylcholinesterase: Enzyme kinetics and interaction mechanism merging with molecular docking analysis

Acetylcholinesterase (AchE) serves as an important target for Alzheimer's disease. Salvia miltiorrhiza has been used to treat cardiovascular disease for hundreds of years. However, the interaction between S. miltiorrhiza and AchE is still inadequate. Herein, an integrated method including molecular docking and experimental studies was employed to investigate the interaction. Consequently, some components were screened as potent AchE inhibitors by in silico and in vitro. Among them, miltirone (MT) and salvianolic acid A (SAA) reversibly inhibited AchE in a mixed-competitive manner. Fluorescence data revealed that SAA and salvianolic acid C (SAC) strongly quenched the intrinsic fluorescence of AchE through a static quenching mechanism, and the binding was spontaneous and dominated by hydrophobic interaction inferred by the thermodynamic parameters. The synchronous and ANS-binding fluorescence spectra suggested that SAA and SAC could bind to the enzyme and induce its conformation changes of secondary structures, which was further confirmed by Fourier transform infrared spectra. Meanwhile, molecular docking presented the probable binding modes of inhibitors to AchE and highlighted the key role of hydrophobic interaction and hydrogen bonds for the stability of docking complex. These findings put more insights into understanding the interaction of S. miltiorrhiza chemicals and AchE, as well as Alzheimer's disease.

Different effects of Forsythia suspensa metabolites on bovine serum albumin (BSA)

Forsythia suspensa metabolites have many bioactivities, such as selective immuno suppression, antioxidation, anti-hepatic injury, etc. In the present study, the interactions of the three metabolites with BSA have been investigated in a buffer (pH 7.40) using multi-spectroscopic techniques in combination with molecular docking methods. Two isoformers, forsythoside A and forsythoside I can statically quench BSA intrinsic fluorescence by forming the complexes with BSA at stoichiometric ratio of 1:1 that is again proved by UV-visible absorption. During the binding, the proportion of α-helix in BSA increases, the microenvironment around Tryptophan 213 changes and FRET is one of the major factors to quench fluorescence. Forsythoside E forms BSA-forsythoside E complex (1:1) and thus enhances the intrinsic fluorescence of BSA. During the process, forsythoside E affects not only Tryptophan residues but also Tyrosine residues so that the conformation of BSA is consequently changed. All above binding processes are spontaneous mainly through hydrogen bonding and the hydrophobic force interaction, which is supported by docking analysis and thermodynamic parameters. In addition, three compounds do not induce BSA aggregation. These findings are beneficial to understand the detailed information of the interactions of Forsythia suspensa metabolites with BSA.

Spectroscopic techniques investigation on the interaction of glucoamylase with 1-deoxynojirimycin: Mechanistic and conformational study

1-Deoxynojirimycin (DNJ), a representative polyhydroxylated alkaloids, is widely used in the field of antidiabetic, antitumor, and anti-HIV. The present study tried to clarify the interaction mechanism of DNJ with glucoamylase by multi-spectroscopic techniques, dynamic light scattering in combination with molecular modeling strategies from biophysics point of view. Fluorescence and UV-vis data indicated that fluorescence quenching mechanism of glucoamylase and DNJ was a dynamic manner. The association constant, binding site and thermodynamic parameters were also obtained from fluorescence spectrum at different temperatures. Synchronous fluorescence, circular dichroism and dynamic light scattering methods demonstrated that their interaction induced microenvironment changes around tryptophan residue and protein conformational alteration. The main driving force was hydrophobic interaction and hydrogen bonding. In addition, molecular docking study indicated that 1-deoxynojirimycin could bind in the catalytic domain of glucoamylase and interact with amino acid residues Arg78, Asp79, Glu203 and Glu424 by forming hydrogen bonds. Molecular dynamics simulation demonstrated that profiles of atomic fluctuation remained the rigidity of ligand binding site. This study elucidated the detailed interaction mechanism of DNJ with glucoamylase, which will be helpful for pharmaceutical companies to design new α-glucosidase inhibitor drugs based on polyhydroxylated alkaloids compound like DNJ.

Identification of potential inhibitors of sortase A: Binding studies, in-silico docking and protein-protein interaction studies of sortase A from Enterococcus faecalis

Enterococcus faecalis (Ef) is a Gram positive multidrug resistant (MDR) bacterium contributing about 70% of total enterococcal infections. In Ef, a membrane anchored transpeptidase Sortase A plays a major role in biofilm formation. Therefore, it has been recognized as an ideal drug target against Ef. In this regard to identify the potential inhibitors of Ef Sortase A (EfSrtA_∆59), we have cloned, expressed and purified EfSrtA_∆59. We have also done the in-silico docking studies to identify lead molecules interacting with EfSrtA_∆59. Furthermore, the binding studies of these identified lead molecules were performed with EfSrtA_∆59 using fluorescence and CD spectroscopic studies. We also identified the interaction partner of EfSrtA_∆59 using STRING. Protein-protein docking studies were also performed. Docking experiment revealed that benzylpenicillin, cefotaxime, pantoprazole and valsartan were bound to same site on the protein with similar interactions. Binding studies using fluorescence spectroscopic studies confirmed the binding of all the ligands to EfSrtA_∆59, which was further validated by far and near-UV CD experiments. Thermo stability experiments validate the stability-activity trade-off hypothesis. Sequence based interaction studies identified that EfSrtA_∆59 interact with the Ef_1091, Ef_1093 and Ef_2658 proteins. Homology model of Ef_1091 and Ef_1093 was docked with modeled EfSrtA_∆59 and their interactions are also discussed.

Biophysical, docking, and cellular studies on the effects of cerium oxide nanoparticles on blood components: in vitro

Introduction

The application of nanoparticles (NPs) in medicine and biology has received great interest due to their novel features. However, their adverse effects on the biological system are not well understood.

Materials and methods

This study aims to evaluate the effect of cerium oxide nanoparticles (CNPs) on conformational changes of human hemoglobin (HHb) and lymphocytes by different spectroscopic (intrinsic and synchronous fluorescence spectroscopy and far and near circular dichroism [CD] spectroscopy), docking and cellular (MTT and flow cytometry) investigations.

Results and discussion

Transmission electron microscopy (TEM) showed that CNP diameter is ~30 nm. The infrared spectrum demonstrated a strong band around 783 cm⁻¹ corresponding to the CNP stretching bond. Fluorescence data revealed that the CNP is able to quench the intrinsic fluorescence of HHb through both dynamic and static quenching mechanisms. The binding constant (K_b), number of binding sites (n), and thermodynamic parameters over three different temperatures indicated that hydrophobic interactions might play a considerable role in the interaction of CNPs with HHb. Synchronous fluorescence spectroscopy indicated that microenvironmental changes around Trp and Tyr residues remain almost unchanged. CD studies displayed that the regular secondary structure of HHb had no significant changes; however, the quaternary structure of protein is subjected to marginal structural changes. Docking studies showed the larger CNP cluster is more oriented toward experimental data, compared with smaller counterparts. Cellular assays revealed that CNP, at high concentrations (>50 µg/mL), initiated an antiproliferative response through apoptosis induction on lymphocytes.

Conclusion

The findings may exhibit that, although CNPs did not significantly perturb the native conformation of HHb, they can stimulate some cellular adverse effects at high concentrations that may limit the medicinal and biological application of CNPs. In other words, CNP application in biological systems should be done at low concentrations.

Sugar osmolytes-induced stabilization of RNase A in macromolecular crowded cellular environment

Organisms synthesize sugar osmolytes during environmental stresses to protect proteins against denaturation. These studies were carried out in dilute buffer whereas intracellular milieu within cells has cytoplasmic concentration of macromolecules in the range of 80-400 mg ml^-1. Is the stabilizing effect of sugar osmolytes on the protein in dilute buffer different from that when protein is in cellular environment? To answer this question, we have measured and analysed the effect of sugar osmolytes on the structural and thermodynamic stability of ribonuclease A in the presence of dextran 70 at multiple concentrations of six sugars at different pH values. It was found that (i) each sugar osmolyte in the crowded environment provides stability to the protein in terms of T_m (midpoint of denaturation) and ∆G_D° (Gibbs energy change) and this stabilizing effect is under entropic control, (ii) the extent of osmolyte-induced stabilization of RNase A is pH dependent, and (iii) effect of sugars on the stability of protein in presence of the crowding agent remains unchanged. This study concludes that crowding does not affect the efficacy of osmolytes and vice versa; and emphasizes on understanding of internal architecture of the cellular environment with respect to molecular and macromolecular crowding.

Methylglyoxal induced glycation and aggregation of human serum albumin: Biochemical and biophysical approach

Serum protein glycation and formation of advanced glycation end products (AGEs) correlates with many diseases viz. diabetes signifying the importance of studying the glycation pattern of serum proteins. In our present study, methylglyoxal was investigated for its effect on the structure of human serum albumin (HSA); exploring the formation of AGEs and aggregates of HSA. The analytical tools employed includes intrinsic and extrinsic fluorescence, UV spectroscopy, far UV circular dichroism, Thioflavin T fluorescence, congo red binding, polyacrylamide gel electrophoresis (PAGE). UV and fluorescence spectroscopy revealed the structural transition of native HSA evident by new peaks and increased absorbance in UV spectra and quenched fluorescence in the presence of MG. Far UV CD spectroscopy revealed MG induced secondary structural alteration evident by reduced α-helical content. AGEs formation was confirmed by AGEs specific fluorescence. Increased ThT fluorescence and CR absorbance of 10mM MG incubated HSA suggests that glycated HSA results in the formation of aggregates of HSA. SEM and TEM were reported to have an insight of these aggregates. Molecular docking was also utilized to see site specific interaction of MG-HSA. This study is clinically significant as HSA is a clinically relevant protein which plays a crucial role in many diseases.

Biophysical and computational characterization of vandetanib-lysozyme interaction

Interaction of an anticancer drug, vandetanib (VDB) with a ligand transporter, lysozyme (LYZ) was explored using multispectroscopic techniques, such as fluorescence, absorption and circular dichroism along with computational analysis. Fluorescence data and absorption results confirmed VDB-LYZ complexation. VDB-induced quenching was characterized as static quenching based on inverse correlation of K_SV with temperature as well as k_q values. The complex was characterized by the weak binding constant (K_a=4.96-3.14×10³M^-1). Thermodynamic data (ΔS=+12.82Jmol^-1K^-1; ΔH=-16.73kJmol^-1) of VDB-LYZ interaction revealed participation of hydrophobic and van der Waals forces along with hydrogen bonds in VDB-LYZ complexation. Microenvironmental perturbations around tryptophan and tyrosine residues as well as secondary and tertiary structural alterations in LYZ upon addition of VDB were evident from the 3-D fluorescence, far- and near-UV CD spectral analyses, respectively. Interestingly, addition of VDB to LYZ significantly increased protein's thermostability. Molecular docking results suggested the location of VDB binding site near the LYZ active site while molecular dynamics simulation results suggested stability of VDB-LYZ complex. Presence of Mg²⁺, Ba²⁺ and Zn²⁺ was found to interfere with VDB-LYZ interaction.

The combinatorial effects of osmolytes and alcohols on the stability of pyrazinamidase: Methanol affects the enzyme stability through hydrophobic interactions and hydrogen bonds

Inside the cells, proteins are surrounded by mixtures of different osmolytes. However, our current understanding of the combinatorial effects of such mixtures on the stability of proteins remains elusive. In the present study, the stability and structure of recombinant pyrazinamidase (PZase) from Mycobacterium tuberculosis were analyzed in the presence of stabilizing osmolytes (sorbitol, sucrose and glycerol) and alcohols (methanol, ethanol, isopropanol and n-propanol). The far-UV and near-UV circular dichroism (CD), intrinsic fluorescence and thermostability results indicated that methanol, unexpectedly, has stronger effect on destabilization of the enzyme compared to ethanol which has larger log P. Interestingly, the relative half-life of PZase was longer in mixtures methanol with the osmolytes, sorbitol or sucrose (expectedly), or glycerol (unexpectedly), compared to other alcohols. Molecular dynamics simulation results showed that methanol increases the flexibility of region 5-40 and loop 51-71 in the PZase, which are potentially crucial for the stability and activity of the enzyme, respectively. Our results indicated that methanol can interact with PZase via hydrophobic interactions and hydrogen bonds, and therefore resulting in destabilization of the structure of the enzyme. In addition, glycerol probably increases the stability of the enzyme in methanol by disrupting the unfavorable hydrophobic interactions and hydrogen bonds.

Spectrofluorimetric and molecular docking studies on the interaction of cyanidin-3-O-glucoside with whey protein, β-lactoglobulin

The interaction of β-Lactoglobulin (β-Lg) with cyanidin-3-O-glucoside (C3G) was characterized using fluorescence, circular dichroism spectroscopy, and docking studies under physiological conditions. Fluorescence studies showed that β-Lg has a strong binding affinity for C3G via hydrophobic interaction with the binding constant, K_a, of 3.14×10⁴M^-1 at 298K. The secondary structure of β-Lg displayed an increase in the major structure of β-sheet upon binding with C3G, whereas a decrease in the minor structure of α-helix was also observed. In addition, evidenced by near UV-CD, the interaction also disrupted the environments of Trp residues. The molecular docking results illustrated that both hydrogen bonding and the hydrophobic interaction are involved as an acting force during the binding process. These results may contribute to a better understanding over the enhanced physicochemical proprieties of anthocyanins due to the complexation with milk proteins.