Study on the interaction of the epilepsy drug, zonisamide with human serum albumin (HSA) by spectroscopic and molecular docking techniques

Study on the toxicity prediction model ofacetolactate synthase inhibitor herbicides based on human serum albumin and superoxide dismutase binding information

Toxicity significantly influences the successful development of drugs. Based on the toxicity prediction method (carrier protein binding information-toxicity relationship) previously established by the our group, this paper introduces information on the interaction between pesticides and environmental markers (SOD) into the model for the first time, so that the toxicity prediction model can not only predict the toxicity of pesticides to humans and animals, but also predict the toxicity of pesticides to the environment. Firstly, the interaction of acetolactate synthase inhibitor herbicides (ALS inhibitor herbicides) with human serum albumin (HSA) and superoxide dismutase (SOD) was investigated systematically from theory combined with experiments by spectroscopy methods and molecular docking, and important fluorescence parameters were obtained. Then, the fluorescence parameters, pesticides acute toxicity LD50 and structural splitting information were used to construct predictive modeling of ALS inhibitor herbicides based on the carrier protein binding information (R2 = 0.977) and the predictive modeling of drug acute toxicity based on carrier protein binding information and conformational relationship (R2 = 0.991), which had effectively predicted pesticides toxicity in humans and animals. To predict potential environmental toxicity, the predictive modeling of drug acute toxicity based on superoxide dismutase binding information was established (R2 = 0.883) by ALS inhibitor herbicides-SOD binding information, which has a good predictive ability in the potential toxicity of pesticides to the environment. This study lays the foundation for developing low toxicity pesticides.

Molecular interaction of antiviral drug penciclovir with DNA and HSA insights from experimental and docking studies

One approach to accelerate the availability of new cancer drugs is to test drugs approved for other conditions as anticancer agents. During recent decades, penciclovir (PNV) has been frequently utilized as a potent antiviral drug, in particular against infections caused by herpes viruses. Many antivirals interact with DNA and change their expression level, so determining the binding mode is of great importance. In our laboratory, we have focused our attention to design improved drugs that target cellular DNA, to understand the mechanism of action at the molecular level, and also to investigate the effect of antiviral drugs as anticancer agents. The results of ct-DNA-PNV interactions at physiological pH using fluorescence spectroscopy, UV-visible absorption spectroscopy, and molecular modeling reveal this drug binds well to ct-DNA through groove binding. The circular dichroism measurements displayed that PNV caused a slight change in the DNA structure which affirmed that the binding of PNV with the DNA occurs through the groove mode. Besides, multi-spectroscopic and molecular docking were used to evaluate how PNV interacts with human serum albumin under physiological conditions. The findings of fluorescence quenching suggested that static quenching was involved in the spontaneous development of HSA-PNV complex through hydrophobic force. The docking simulation results validated the findings of spectroscopic techniques.Communicated by Ramaswamy H. Sarma.

Probing the Interaction between Isoflucypram Fungicides and Human Serum Albumin: Multiple Spectroscopic and Molecular Modeling Investigations

To better understand the potential toxicity risks of isoflucypram in humans, The interaction between isoflucypram and HSA (human serum albumin) was studied through molecular docking, molecular dynamics simulations, ultraviolet-visible absorption, fluorescence, synchronous fluorescence, three-dimensional fluorescence, Fourier transform infrared spectroscopies, and circular dichroism spectroscopies. The interaction details were studied using the molecular docking method and molecular dynamics simulation method. The results revealed that the effect of isoflucypram on human serum albumin was mixed (static and dynamic) quenching. Additionally, we were able to obtain important information on the number of binding sites, binding constants, and binding distance. The interaction between isoflucypram and human serum albumin occurred mainly through hydrogen bonds and van der Waals forces. Spectroscopic results showed that isoflucypram caused conformational changes in HSA (human serum albumin), in which the α-helix was transformed into a β-turn, β-sheet, and random coil, causing the HSA structure to loosen. By providing new insights into the mechanism of binding between isoflucypram and human serum albumin, our study has important implications for assessing the potential toxicity risks associated with isoflucypram exposure.

Protein sustained release from isobutyramide-grafted stellate mesoporous silica nanoparticles

Proteins are great therapeutic candidates as endogenous biomolecules providing a wide range of applications. However, their delivery suffers from some limitations and specifically designed delivery systems having an efficient protein anchoring and delivery strategy are still needed. In this work, we propose to combine large pore stellate mesoporous silica (STMS) with isobutyramide (IBAM), as a “glue” molecule which has been shown promising for immobilization of various biomacromolecules at silica surface. We address here for the first time the ability of such IBAM-modified NPs to sustainably deliver proteins over a prolonged time. In this work, a quantitative loading study of proteins (serum albumin (HSA), peroxidase (HRP), immunoglobulin (IgG) and polylysine (PLL)) on STMS@IBAM is first presented using three complementary detection techniques to ensure precision and avoid protein quantification issues. The results demonstrated a high loading capacity for HSA and HRP (≥ ca. 350 μg.mg⁻¹) but a moderate one for IgG and PLL. After evaluating the physicochemical properties of the loaded particles and their stability over scaling-up and washings, the ability of STMS@IBAM to release proteins over prolonged time was evaluated in equilibrium (static) and flow mimicking (dynamic) conditions and at different temperatures (25, 37, 45 °C). Results show not only the potential of such “glue” functionalized STMS to release proteins in a sustained way, but also the retention of the biological activity of immobilized and released HRP, used as an enzyme model. Finally, an AFM-force spectroscopy study was conducted to decipher the interactions between IBAM and proteins, showing the involvement of different interactions in the adsorption and release processes.

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Isobutyramide bound stellate mesoporous silica allow the immobilization of various proteins.

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Protein release was achieved from the nanoparticles in a sustained way in buffer.

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Peroxidase activity was retained whether in immobilized or released conditions.

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Choice of protein detection techniques was shown to be crucial.

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AFM-spectroscopy was used to investigate IBAM-protein intermolecular bonding.

Broad-Spectrum Inhibitors against Class A, B, and C Type β-Lactamases to Block the Hydrolysis against Antibiotics: Kinetics and Structural Characterization

The emergence of antibiotic resistance has led to a global crisis for the physician to handle infection control issues. All antibiotics, including colistin, have lost efficiency against emerging drug-resistant bacterial strains due to the production of metallo-β-lactamases (MBLs) and serine-β-lactamases (SBLs). Therefore, it is of the utmost importance to design inhibitors against these enzymes to block the hydrolytic action against antibiotics being used. Although various novel β-lactamase inhibitors are being authorized or are under clinical studies, the coverage of their activity spectrum does not include MDR organisms expressing multiple classes of β-lactamases at a single time. This study reports three novel broad-spectrum inhibitors effective against both SBLs and MBLs. Virtual screening, molecular docking, molecular dynamics simulations, and an in silico pharmacokinetic study were performed to identify the lead molecules with broad-spectrum ability to inhibit the hydrolysis of β-lactam. The selected compounds were further assessed by in vitro cell assays (MIC, 50% inhibitory concentration [IC₅₀], kinetics, and fluorescence against class A, B, and C type β-lactamases) to confirm their efficacies. A 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay was performed to check the toxicity of screened lead molecules. All three selected inhibitors were found to reduce MIC and showed good affinity against all the SBLs and MBLs produced by class A, B, and C type β-lactamases. These nontoxic novel non-β-lactam broad-spectrum inhibitors bind to the active site residues of selected β-lactamases, which are crucial for β-lactam antibiotic hydrolysis. These inhibitors may be proposed as a future drug candidate in combination with antibiotics as a single formulation to control infection caused by resistant strains. Hence, this study plays a significant role in the cure of infections caused by antibiotic-resistant bacteria.

IMPORTANCE Several inhibitors for usage in conjunction with antibiotics have been developed. However, to date, there is no commercially available broad-spectrum β-lactamase inhibitor that targets both MBLs and SBLs. Here, we showed three novel broad-spectrum inhibitors with promising results through computational techniques and in vitro studies. These inhibitors are effective against both SBLs and MBLs and hence could be used as future drug candidates to treat infections caused by multidrug-resistant bacteria producing both types of enzymes (SBLs and MBLs).

Chemically synthesised flavone and coumarin based isoxazole derivatives as broad spectrum inhibitors of serine β-lactamases and metallo-β-lactamases: a computational, biophysical and biochemical study

The β-lactam antibiotics are the most effective medicines for treating bacterial infections. Resistance to them, particularly through the production of β-lactamases, which can hydrolyse all kinds of β-lactams, poses a threat to their continued use. The synthesised flavone and coumarin based isoxazole derivatives have the potential to be used as broad-spectrum inhibitors of the mechanistically different serine-(SBL) and metallo-β-lactamases (MBL). The synthesised compounds were discovered as potent β-lactamase inhibitors using molecular docking and in silico pharmacokinetic analysis. We studied the binding of chemically synthesised inhibitors to clinically significant β-lactamases of class A, B, and C using biophysical and biochemical approaches, and computational analyses. These molecules follow Lipinski's rule of five and have acceptable solubility, permeability, and oral bioavailability. These molecules were found to be non-toxic and non-carcinogenic. MIC results suggest that these molecules restore the antibiotic efficacy against class A, B, and C β-lactamases. Kinetics data showed that these molecules reduce the catalytic efficiency of clinically relevant class A, B, and C β-lactamases. Fluorescence study showed significant interaction between these flavone-/coumarin-based isoxazole derivatives and class A/B/ C β-lactamases. This study showed promising effect of these new generation compounds as broad spectrum β-lactamase inhibitors of both SBLs and MBLs.Communicated by Ramaswamy H. Sarma.

Insight into the binding characteristics of rutin and alcohol dehydrogenase: Based on the biochemical method, spectroscopic experimental and molecular model

Alcohol dehydrogenase (ADH) is a crucial enzyme in the alcohol metabolism pathway. Its activity is associated with the development of alcohol-relative diseases. Rutin is a kind of widely distributed dietary flavonoids, which have the ability to resist alcohol-induced liver injury. Here, the role of rutin on alcohol metabolism was investigated via the methods of biochemistry, spectroscopy and computer simulation. The experiment results demonstrated that rutin entered into the position of coenzyme (NAD) on ADH and formed a binary complex, which of process activated the catalyze activity of ADH in a concentration dependent manner. The combination of rutin on ADH induced microenvironmental variations as well as secondary structural change of ADH, where the level of α-helix reduced yet β-sheet raised. The values of ∆H and ∆S suggested that H-bonds and van der Waals force occupied vital roles in the stabilization of ADH-rutin complex. Furthermore, molecular docking results further confirmed that the H-bonds between the hydroxyl groups on the benzene rings of rutin and surrounding amino acid were beneficial to maintain the stability of complex. Particularly, the van der Waals force and π-alkyl between rutin and Val residues may be the main reason for activation of ADH activity.

Interactions between Human Serum Albumin and Sulfadimethoxine Determined Using Spectroscopy and Molecular Docking

Sulfonamides are widely used antibiotics in agricultural production. However, the potential threat of these drugs to human health has increased global concern. Human serum albumin (HSA) is the main reservoir and transporter of exogenous small molecules in humans. In this study, the interaction between sulfadimethoxine (SMT) and human serum albumin (HSA) was studied using spectroscopy and computer simulation. Our results showed that the hydrogen bonding and van der Waals forces drove SMT to enter the binding site I of HSA spontaneously and resulted in the fluorescence quenching of HSA. The stability of the HSA–SMT complex decreased with an increase in temperature. The binding of SMT to HSA induced alterations in the secondary structure of HSA, where the content of α-helix decreased from 61.0% of the free state to 59.0% of the compound state. The π–π, π–σ, and π–alkyl interactions between HSA and SMT were found to play important roles in maintaining the stability of the complex.

A new method for predicting the acute toxicity of carbamate pesticides based on the perspective of binding information with carrier protein

Toxicity is one of the most important factors limiting the success of new drug development. In this paper, we built a fast and convenient new method (Carrier protein binding information-toxicity relationship, CPBITR) for predicting drug acute toxicity based on the perspective of binding information with carrier protein. First, we studied the binding information between carbamate pesticides and human serum albumin (HSA) through various spectroscopic methods and molecular docking. Then a total of 16 models were established to clarify the relationship between binding information with HSA and drug toxicity. The results showed that the binding information was related to toxicity. Finally we obtained the effective toxicity prediction model for carbamate pesticides. And the "Platform for Predicting Drug Toxicity Based on the Information of Binding with Carrier Protein" was established with the Back-propagation neural network model. We proposed and proved that it was feasible to predict drug toxicity from this new perspective: binding with carrier protein. According to this new perspective, toxicity prediction model of other drugs can also be established. This new method has the advantages of convenience and fast, and can be used to screen out low-toxic drugs quickly in the early stage. It is helpful for drug research and development.

Metallodrug-protein interaction probed by synchrotron terahertz and neutron scattering spectroscopy

This experimental work applied coherent synchrotron-radiation terahertz spectroscopy and inelastic neutron scattering to address two processes directly associated with the mode of action of metal-based anticancer agents that can severely undermine chemotherapeutic treatment: drug binding to human serum albumin, occurring during intravenous drug transport, and intracellular coordination to thiol-containing biomolecules (such as metallothioneins) associated with acquired drug resistance. Cisplatin and two dinuclear platinum (Pt)- and palladium (Pd)-polyamine agents developed by this research group, which have yielded promising results toward some types of human cancers, were investigated. Complementary synchrotron-radiation-terahertz and inelastic neutron scattering data revealed protein metalation, through S- and N-donor ligands from cysteine, methionine, and histidine residues. A clear impact of the Pt and Pd agents was evidenced, drug binding to albumin and metallothionein having been responsible for significant changes in the overall protein conformation, as well as for an increased flexibility and possible aggregation.

Investigations of the molecular mechanism of diltiazem binding to human serum albumin in the presence of metal ions, glucose and urea

The molecular mechanism and thermodynamic properties of the interaction between diltiazem (DTZ) and human serum albumin (HSA), has been studied in vitro using spectroscopic techniques (UV-Vis, fluorescence, FTIR), and molecular docking methods. The effect of acidic and basic pH, glucose, urea, and metal ions on the DTZ-HSA binding has been investigated as well. According to the results, there is a 1:1 interaction between DTZ and HSA, while the quenching mechanism is static up to 313 K. The apparent binding constant was 2.09 × 10⁶ M^-1 that indicates a strong binding between DTZ and HSA. DTZ binding was increased in acidic pH while its binding was slowly decreased in the presence of glucose, urea, and metal ions. Thermodynamic studies showed that DTZ binds to HSA via an exothermic and spontaneous reaction via hydrogen bonding and electrostatic interactions. The conformational alteration of HSA is obvious according to the FTIR study. The site marker competitive study confirmed the binding of DTZ to the warfarin binding site. Molecular docking studies showed that DTZ binds to subdomain IB (-9.22 kcal mol^-1) and subdomain IIIA (-9.03 kcal mol^-1) with a higher tendency. Also, the results showed that the oxygen and nitrogen atoms of hydroxyl and amino functional groups of DTZ facilitate hydrogen bond formation. HighlightsStrong binding of diltiazem to HSA was studied and confirmed by fluorescence quenching titrations.Diltiazem binding to HSA reduces in the presence of metal ions, glucose, urea and alkaline pH.Diltiazem binding to HSA is exothermic and spontaneous.

Investigation of the binding properties between levamlodipine and HSA based on MCR-ALS and computer modeling

Levamlodipine (LEE) is a drug commonly used for antihypertensive treatment in clinical therapy. The overlapping fluorescence spectra of LEE and human serum albumin (HSA) cause some trouble in analysis of interactions between them by using the classic fluorescence method. Here, the multivariate curve resolution-alternating least squares (MCR-ALS) approach was used to overcome this disadvantage. Meanwhile, the binding properties of LEE-HSA complex were then explored through computer modeling. The MCR-ALS results suggested that LEE-HSA complex was present in the mixture solution of LEE and HSA. This conclusion was then confirmed by the Stern-Volmer equation and time-resolved fluorescence experiment. The binding constant (K_a) was 2.139 × 10⁴ L·mol^-1 at 298 K. LEE was located close to the Trp-214 residue of HSA, with van der Waals forces and hydrogen bonding as main driving forces for this interaction. LEE can alter the conformation of HSA, in which the content of α-helix reduced from 57.2% to 52.3%. The Pi-Alkyl interactions contributed to maintaining the stability of the LEE-HSA complex. The results of molecular dynamics simulations showed that LEE-HSA complex was formed within 5 ns, and the particle size (R_g) of HSA was altered by the binding reaction. This study would promote better understanding of the transportation and distribution mechanisms of LEE in the human body.

Ex vivo binding studies of the anti-cancer drug noscapine with human hemoglobin: a spectroscopic and molecular docking study

Noscapine binds human hemoglobin spontaneously forming a stable complex that affects noscapine's ADMET profile, bioavailability and toxicity.

Assessment of binding interaction dihydromyricetin and myricetin with bovine lactoferrin and effects on antioxidant activity

The binding interactions of bovine lactoferrin (BLF) with two flavonoids dihydromyricetin (DMY) and myricetin (MY) were investigated by the multi-spectroscopic, microscale thermophoresis (MST) techniques, molecular docking, and then their antioxidant activities were studied by detection of free radical scavenging activity against DPPH. Results of UV-vis and fluorescence spectroscopies showed that DMY/MY and BLF formed the ground state complex through the static quenching mechanism. Moreover, MY with more planar stereochemical structure had higher affinity for BLF than DMY with twisted stereochemical structure, according to the binding constant (K_b), free energy change (ΔG°), dissociation constant (K_d) and donor-acceptor distance (r). Thermodynamic parameters revealed that hydrogen bond and van der Waals force were major forces in the formation of BLF-DMY complex, while hydrophobic interactions played major roles in the formation of BLF-DMY complex. The circular dichroism (CD) study indicated that MY induced more conformational change in BLF than DMY. Furthermore, molecular modeling provided insights into the difference of binding interactions between BLF and two flavonoids. Finally, the radical scavenging activity assays indicated the presence of BLF delayed the decrease in antioxidant capacities of two flavonoids. These results were helpful to understand the binding mechanism and biological effects of non-covalent BLF-flavonoid interaction.

Investigation of the Interaction between N-Acetyl-l-Cysteine and Ovalbumin by Spectroscopic Studies, Molecular Docking Simulation, and Real-Time Quartz Crystal Microbalance with Dissipation

This study investigated the interaction between N-acetyl-l-cysteine (NAC) and ovalbumin (OVA) using multispectroscopic technology, molecular docking, and quartz crystal microbalance with dissipation (QCM-D). Fluorescence intensity and UV absorption of OVA were decreased substantially upon the addition of NAC. The calculated K_q values were obtained at 298, 304, and 310 K for 13.48, 15.59, and 17.50 (× 10¹² L mol^-1), respectively, suggesting that the static quenching was dominated. Thermodynamic parameters such as ΔH (-150.58 kJ mol^-1), ΔS (-433.51 J mol^-1 K^-1), and ΔG values (-21.39 kJ mol^-1), combined with molecular docking and QCM-D data, showed that the interaction was spontaneous and van der Waals and hydrogen bonding were identified as the main driving forces. FTIR and CD results showed that the α-helix content of OVA increased from 2.8 to 22.9%, and the β-sheet decreased from 0.2 to 21.9% in the presence of 5 and 10 μM NAC, respectively, compared to the pure OVA, respectively.

Binding interaction of potent HIV-1 NNRTIs, amino-oxy-diarylquinoline with the transport protein using spectroscopic and molecular docking

In the present investigation, the intermolecular interaction of 4-(4'-cyanophenoxy)-2-(4''-cyanophenyl)-aminoquinoline (1), a potent non-nucleoside HIV-1 reverse transcriptase inhibitors, with the transport proteins, namely bovine serum albumin (BSA) and human serum albumin (HSA), has been investigated under physiological conditions employing UV-Vis, fluorescence spectrophotometry, competitive binding experiments and molecular docking methods. The results indicated that binding of (1) to the transport proteins caused fluorescence quenching though a static quenching mechanism. The number of binding site (n) and the apparent binding constant (K_b) between (1) and the transport proteins were determined to be about 1 and 10⁴-10⁵ L·mol^-1 (at three different temperatures; 298, 308, 318 K), respectively. The interaction of (1) upon binding to the transport proteins was spontaneous. The enthalpic change (ΔH°) and the entropic change (ΔS°) were calculated to be -56.50 kJ·mol^-1, -72.31 J·mol^-1 K^-1 for (1)/BSA, respectively and computed to be -49.35 kJ·mol^-1, -58.64 J·mol^-1 K^-1, respectively for (1)/HSA, respectively. The results implied that the process of interaction force of (1) with the transport protein were Vander Waals force and/or hydrogen bonding interactions. The site maker competitive experiments revealed that the binding site of (1) with the transport proteins were mainly located within site I (sub-domain IIA) in both proteins. Additionally, the molecular docking experiment supported the above results which confirmed the binding interaction between (1) and the transport proteins. This study will come up with basic data for explicating the binding mechanisms of (1) with the transport protein and can be great significance in the opening to clarify the transport process of (1) in vivo.

Understanding effect of interaction of nanoparticles and antibiotics on bacteria survival under aquatic conditions: Knowns and unknowns

The review provides a comprehensive overview of the available state-of-the-art of nanoparticles (NPs) and antibiotics (ABs) occurrence and their fate in the natural aquatic settings by addressing different research questions and the challenges faced while addressing those questions. Firstly, understand the interaction of NPs and ABs with themselves in addition to other matrix components (presence of natural organic matter, bacteria, biofilms, other anthropogenic pollutants and metals from natural sources). Secondly, summarize the bactericidal activity of NP and AB due to reactive oxygen species (ROS) production. The complete information was gathered from database and analysed as per the conjectured questions under laboratory versus environmental-relevant conditions (1. Fate of NPs and ABs, and 2. Will the presence of NPs and ABs alone and their mixtures influence the ROS concentration and antibacterial activity), and proposed six reactions to describe the fate of NP and AB in natural aquatic settings. However, laboratory-based studies revealed that NP and AB fate largely depend on the ionic strength, organic matter content and pH of the matrix whereas field based information is missing about this. The former was performed at sterile conditions using sophisticated instruments and standard protocol as compared to latter and can't be replicated under natural aquatic settings due to lack of: (i) accurate environmental concentration of NPs and ABs, (ii) knowledge of bacterial type and their concentration, (iii) optimized protocol and tracking systems. The author's recommendation is to verify the proposed reactions experimentally by using the frequently found pairs of NPs and ABs in the natural aquatic settings. Further, ranked them on their decreasing order of toxicity and informed regulatory bodies for further action. Overall research is needed in the suggested directions to reduce uncertainty behind the impacts of NPs and ABs on the aquatic settings and their role in bactericidal activity.

Z-Acrylonitrile Derivatives: Improved Synthesis, X-ray Structure, and Interaction with Human Serum Albumin

AIMS AND OBJECTIVE

In the synthesis of heterocyclic compounds, acrylonitrile derivatives are the most important and appropriate precursors. These compounds are the most important intermediates and subunits for the enhancement of molecules having pharmaceutical or biological interests. Nitrogen-containing compounds have received extensive consideration in the literature over the years.

MATERIALS AND METHODS

A facile, economic and efficient method has been developed for the synthesis of acrylonitrile derivatives using p-nitrophenylacetonitrile and aromatic/heterocyclic aldehydes in the presence of zinc chloride at room temperature. Spectroscopic data were obtained using the following instruments: Fourier transform infrared spectra (KBr discs, 4000-400 cm-1) by Shimadzu IR-408 Perkin-Elmer 1800 instrument; 1H NMR and 13C NMR spectra by Bruker Avance-II 400 MHz using DMSO-d6 as a solvent containing TMS as the internal standard.

RESULTS

To continue our ongoing studies to synthesize heterocyclic and pharmaceutical compounds by mild, facile and efficient protocols, herein we wish to report our experimental results on the synthesis of acrylonitrile derivatives, using various aromatic/heterocyclic aldehydes and p-nitrophenylacetonitrile in the presence of zinc chloride in ethanolic media at room temperature. Some of the new compounds were tested for their human serum albumin activity (HSA) while a study of interaction with HSA protein was performed for compounds 3a and 3b. The results show that compound 3b binds tightly to HSA as compared to compound 3a.

CONCLUSION

It can be concluded that acrylonitrile derivatives can be synthesized by an efficient method via the reaction of p-nitrophenylacetonitrile with aromatic/heterocyclic aldehydes by the use of zinc chloride as an effective solid catalyst. The remarkable features of this procedure include excellent yields (90-95%), short reaction period (30 min.), moderate reaction environment, easy workup procedure and managing of the catalyst. This method may find a wide significance in organic synthesis for the synthesis of the Z-acrylonitrile.

Probing the interaction of a coumarin-di(2-picolyl)amine hybrid drug-like molecular entity with human serum albumin: Multiple spectroscopic and molecular modeling techniques

HSA is an important plasma protein responsible for transport of drug molecules. Coumarin derivatives play critical role as anticancer, antidiabetic and antiparkinson agents. In our lab we have synthesized coumarin-based pharmacophore, di(2-picolyl)amine-3(bromoacetyl) coumarin (ligand-L) endowed with anticancer activity. Anticancer agents binding mode of HSA provides valuable pharmacological information and is a structural guidance in synthesizing new drugs with greater efficacy. Thus, binding mechanism of ligand-L with HSA was explored using spectroscopic and molecular docking techniques. UV-Vis spectroscopy demonstrates hyperchromism in the absorbance spectra of HSA on addition of ligand-L suggesting interaction of ligand-L with HSA. Fluorescence spectroscopy indicates quenching in the fluorescence of HSA in the presence of ligand-L confirming the complex formation and this binding follows static mechanism. Steady state fluorescence spectroscopy revealed high binding affinity between ligand-L and HSA with a 1:1 stoichiometry. Thermodynamic parameters obtained by ITC suggest that the interaction between ligand-L and HSA is mainly driven by van der Waals forces and hydrogen bonds, and the negative value of ΔG is an indication of spontaneous binding process. Competitive binding and molecular docking experiments showed that the binding site of ligand-L mainly resides in sub-domain IIA of HSA. CD experiments revealed no significant conformational changes in the secondary structure of HSA on binding of ligand-L. We also found that esterase-like activity of HSA was not affected by ligand-L. In conclusion, this study demonstrates binding mechanism of ligand-L with HSA, and the binding did not induce conformational changes in HSA. This study is likely to provide better understanding of transport and delivery of ligand-L via HSA. Overall, it will provide insights into pharmacokinetic properties of ligand-L and designing new ligand-L based derivatives with greater efficacy.

A critical view on the analysis of fluorescence quenching data for determining ligand-protein binding affinity

The past decade has seen an increase in the number of research papers on ligand binding to proteins based on fluorescence spectroscopy. In most cases, determination of the binding affinity is made by analyzing the quenching of protein fluorescence induced by the ligand. However, many such articles, even those published in reputed journals, suffer from several mistakes with regard to analysis of fluorescence quenching data. Using the binding of phenylbutazone to human serum albumin as a model, we consider some of these mistakes and show how they affect the values of the association constant. In particular, the failure to correct for the inner filter effect and the use of unsuitable equations are discussed. Ligand binding data presented in these articles should be treated with caution, especially in the absence of data from complementary techniques.

Binding properties of sodium glucose co-transporter-2 inhibitor empagliflozin to human serum albumin: spectroscopic methods and computer simulations

Empagliflozin is an oral sodium glucose co-transporter-2 inhibitor for type 2 diabetes mellitus. The interaction between empagliflozin and human serum albumin (HSA) was investigated experimentally and theoretically. Fluorescence quenching and time-resolved fluorescence spectroscopy indicated that the quenching mechanism of empagliflozin and HSA was dynamic and that the effective binding constant at body temperature was 3.495 × 10³ M^-1. Thermodynamic parameters showed that hydrophobic forces were the major binding force in the interaction between empagliflozin and HSA. Circular dichroism, Fourier transform infrared, and 3 D fluorescence spectroscopy revealed that empagliflozin showed a slight change in secondary structure without changing the basic carbon framework of HSA. Site marker displacement experiments revealed that empagliflozin bound to site I of HSA, which was supported by molecular docking. Molecular dynamic simulations indicated that empagliflozin could bind to HSA stably. This study provided insights into the binding mechanism between empagliflozin and HSA.Communicated by Ramaswamy H. Sarma.

Multi-Spectroscopic Characterization of Human Serum Albumin Binding with Cyclobenzaprine Hydrochloride: Insights from Biophysical and In Silico Approaches

Cyclobenzaprine hydrochloride (CBH) is a well-known muscle relaxant that is widely used to relieve muscle spasms and other pain associated with acute musculoskeletal conditions. In this study, we elucidated the binding characteristics of this muscle relaxant to human serum albumin (HSA). From a pharmaceutical and biochemical viewpoint, insight into the structure, functions, dynamics, and features of HSA-CBH complex holds great importance. The binding of CBH with this major circulatory transport protein was studied using a combination of biophysical approaches such as UV-VIS absorption, fluorescence quenching, and circular dichroism (CD) spectroscopy. Various in silico techniques, molecular docking and molecular dynamics, were also used to gain deeper insight into the binding. A reduction in the fluorescence intensities of HSA-CBH complex with a constant increase in temperature, revealed the static mode of protein fluorescence quenching upon CBH addition, which confirmed the formation of the HSA-CBH ground state complex. The alteration in the UV-VIS and far-UV CD spectrum indicated changes in both secondary and tertiary structures of HSA upon binding of CBH, further proving CBH binding to HSA. The analysis of thermodynamic parameters ∆H° and ∆S° showed that binding of CBH to HSA was dominated by intermolecular hydrophobic forces. The results of the molecular docking and molecular dynamics simulation studies also confirmed the stability of the complex and supported the experimental results.

In vitro cytotoxicity and DNA/HSA interaction study of triamterene using molecular modelling and multi-spectroscopic methods

The anticancer activity of triamterene on HCT116 and CT26 colon cancer cells lines was investigated. Furthermore, the mechanism of interaction between triamterene and calf thymus DNA (ct-DNA) and also human serum albumin (HSA) was conducted using spectroscopic and molecular docking techniques. In vitro cytotoxicity of triamterene against HCT116 and CT26 cells showed promising anticancer effects with IC50 values of 31.30 and 24.45 μM, respectively. Competitive studies of the triamterene with NR (neutral red) and MB (methylene blue) as intercalator probes showed that triamterene can be replaced by these probes. The viscosity data also confirmed that triamterene binds to calf-thymus DNA through intercalation binding mode. Binding properties of triamterene with HSA in the presence of warfarin and ibuprofen showed that triamterene competes with warfarin for the site I of human serum albumin (HSA). In addition, the binding modes of triamterene with DNA and HSA were verified by molecular docking technique. Abbreviations ct-DNA calf thymus DNA CV cyclic voltammetry DNA deoxyribonucleic acid DPV differential pulse voltammetry FBS fetal bovine serum HSA human serum albumin NR neutral red MB methylene blue MTT 3-(4,5-dimethylthiazol-2yl)-2,5-diphenyltetrazoliumbromide Communicated by Ramaswamy H. Sarma.

Mechanistic investigation on binding interaction of konjac glucomannan with Zanthoxylum armatum DC. seed glutelin in solution

Interaction between konjac glucomannan (KGM) and Zanthoxylum armatum DC. seed glutelin (ZSG) was believed to influence the conformational and physicochemical properties of ZSG and impact the texture and shelf-life of food. We investigated changes in fluorescence, ultraviolet-visible (UV-Vis) and fourier transform infrared (FTIR) spectroscopies to explore the interaction of ZSG and KGM. The Stern-Volmer quenching constant (K_SV) at three temperatures was evaluated in order to determine the quenching mechanism. The results showed that KGM quenches the fluorescence intensity of ZSG through a static quenching process. Thermodynamic parameters at different temperatures demonstrated that the interaction between ZSG and KGM was mainly favored by van der Waals forces and hydrogen bonding forces, and the binding process was spontaneous and exothermic. The fluorescence spectroscopy, UV-Vis absorption spectroscopy and FTIR spectroscopy data revealed the conformational changes of ZSG upon its interaction with KGM. According to the obtained results, the ZSG-KGM complex was formed.

Molecular design and synthesis of new dithiocarbazate complexes; crystal structure, bioactivities and nano studies

The syntheses of a new set of metal complexes MoO₂L′(CH₃OH), VOL′(CH₃O)(CH₃OH), , , SnL′Cl₂ and SnL′I₂ with a new ligand (L = (2,2′(disulfanediylbis((ethylthio)methylene)bis(hydrazin-2-yl-1-ylidene)bis(methanylylidene)) diphenol; L′ = S-ethyl-3-(2-hydroxyphenyl)methylenedithiocarbazate are described along with characterization by elemental analysis, mass spectrometry, spectroscopic (IR, ¹H- and ¹³C-NMR) and TGA techniques. The crystal structures of compounds were determined by single crystal X-ray diffraction analysis and compared to powder X-ray diffraction (PXRD) patterns of the nano complexes obtained using ultrasonic methods. The PXRD results indicate that the compounds synthesized by ultrasonic methods have high crystallinity. The compounds were evaluated in an in vitro cytotoxicity study with two human cancer cell lines. The results of this study revealed that all complexes exhibit good cytotoxic activity when compared to the clinical drug, cisplatin. Interaction of the samples with human serum albumin (HSA) was investigated using fluorescence spectrophotometric methods and the Stern–Volmer quenching constant (K_SV) and free energy changes (ΔG) were calculated at 298 K. The fluorescence quenching method is used to determine the number of binding sites (n) and association constants (K_a) at the same temperatures.

New metal complexes are synthesized and characterized by elemental analysis, mass spectrometry, spectroscopic, TGA and X-ray techniques. The compounds were evaluated in an in vitro cytotoxicity. Interaction of the samples with HSA was investigated.

Exploration of interaction of canthaxanthin with human serum albumin by spectroscopic and molecular simulation methods

The interaction between the food colorant canthaxanthin (CA) and human serum albumin (HSA) in aqueous solution was explored by using fluorescence spectroscopy, three-dimensional fluorescence spectra, synchronous fluorescence spectra, UV-vis absorbance spectroscopy, circular dichroism (CD) spectra and molecular docking methods. The thermodynamic parameters calculated from fluorescence spectra data showed that CA could result in the HSA fluorescence quenching. From the K_SV change with the temperature dependence, it was concluded that HSA fluorescence quenching triggered by CA is the static quenching and the number of binding sites is one. Furthermore, the secondary structure of HSA was changed with the addition of CA based on the results of synchronous fluorescence, three-dimensional fluorescence and CD spectra. Hydrogen bonds and van der Waals forces played key roles in the binding process of CA with HSA, which can be obtained from negative standard enthalpy (ΔH) and negative standard entropy (ΔS). Furthermore, the conclusions were certified by molecular docking studies and the binding mode was further analyzed with Discovery Studio. These conclusions can highlight the potential of the interaction mechanism of food additives and HSA.

Study on the interaction of paeoniflorin with human serum albumin (HSA) by spectroscopic and molecular docking techniques

The interaction of paeoniflorin with human serum albumin (HSA) was investigated using fluorescence, UV–vis absorption, circular dichroism (CD) spectra and molecular docking techniques under simulative physiological conditions. The results clarified that the fluorescence quenching of HSA by paeoniflorin was a static quenching process and energy transfer as a result of a newly formed complex (1:1). Paeoniflorin spontaneously bound to HSA in site I (subdomain IIA), which was primarily driven by hydrophobic forces and hydrogen bonds (ΔH° = − 9.98 kJ mol⁻¹, ΔS° = 28.18 J mol⁻¹ K⁻¹). The binding constant was calculated to be 1.909 × 10³ L mol⁻¹ at 288 K and it decreased with the increase of the temperature. The binding distance was estimated to be 1.74 nm at 288 K, showing the occurrence of fluorescence energy transfer. The results of CD and three-dimensional fluorescence spectra showed that paeoniflorin induced the conformational changes of HSA. Meanwhile, the study of molecular docking also indicated that paeoniflorin could bind to the site I of HSA mainly by hydrophobic and hydrogen bond interactions.

Potential inhibitors designed against NDM-1 type metallo-β-lactamases: an attempt to enhance efficacies of antibiotics against multi-drug-resistant bacteria

NDM-1 and its variants are the most prevalent types of metallo-β-lactamases, hydrolyze almost all antibiotics of β-lactam group leading to multiple-drug resistance in bacteria. No inhibitor has yet been obtained for NDM-1 or other class of metallo-β-lactamases. Therefore, strategies to identify novel anti-β-lactamase agents with specific mechanisms of action are the need of an hour. In this study, we have reported the discovery of novel non-β-lactam inhibitors against NDM-1 by multi-step virtual screening approach. The potential for virtually screened drugs was estimated through in vitro cell assays. Five chemical compounds were finally purchased and evaluated experimentally for their efficacies to inhibit NDM-1 producing bacterial cells, in vitro. The dissociation constants (Kd), association constant (Ka), stoichiometry (n) and binding energies (ΔG) of compounds with the respective targets were determined using isothermal titration calorimetry (ITC). Molecular dynamic simulation carried out for 25 ns revealed that these complexes were stable throughout the simulation with relative RMSD in acceptable range. Moreover, Microbiological and kinetic studies further confirmed high efficacies of these inhibitors by reducing the minimum inhibitory concentration (MIC) and catalysis of antibiotics by β-lactamases in the presence of inhibitors. Therefore, we conclude that these potential inhibitors may be used as lead molecules for future drug candidates.

Molecular interaction of 2,4-diacetylphloroglucinol (DAPG) with human serum albumin (HSA): The spectroscopic, calorimetric and computational investigation

Drug molecule interaction with human serum albumin (HSA) affects the distribution and elimination of the drug. The compound, 2,4-diacetylphloroglucinol (DAPG) has been known for its antimicrobial, antiviral, antihelminthic and anticancer properties. However, its interaction with HSA is not yet reported. In this study, the interaction between HSA and DAPG was investigated through steady-state fluorescence, time-resolved fluorescence (TRF), circular dichroism (CD), Fourier transform infrared (FT-IR) spectroscopy, isothermal titration calorimetry (ITC), molecular docking and molecular dynamics simulation (MDS). Fluorescence spectroscopy results showed the strong quenching of intrinsic fluorescence of HSA due to interaction with DAPG, through dynamic quenching mechanism. The compound bound to HSA with reversible and moderate affinity which explained its easy diffusion from circulatory system to target tissue. The thermodynamic parameters from fluorescence spectroscopic data clearly revealed the contribution of hydrophobic forces but, the role of hydrogen bonds was not negligible according to the ITC studies. The interaction was exothermic and spontaneous in nature. Binding with DAPG reduced the helical content of protein suggesting the unfolding of HSA. Site marker fluorescence experiments revealed the change in binding constant of DAPG in the presence of site I (warfarin) but not site II marker (ibuprofen) which confirmed that the DAPG bound to site I. ITC experiments also supported this as site I marker could not bind to HSA-DAPG complex while site II marker was accommodated in the complex. In silico studies further showed the lowest binding affinity and more stability of DAPG in site I than in site II. Thus the data presented in this study confirms the binding of DAPG to the site I of HSA which may help in further understanding of pharmacokinetic properties of DAPG.

Designing of inhibitors against CTX-M-15 type β-lactamase: potential drug candidate against β-lactamases-producing multi-drug-resistant bacteria

CTX-M-15 are the most prevalent types of β-lactamases that hydrolyze almost all antibiotics of β-lactam group lead to multiple-antibiotic resistance in bacteria. Three β-lactam inhibitors are available for use in combination with different antibiotics of cephalosporine group against the CTX-M-15-producing strains. Therefore, strategies to identify novel anti β-lactamase agents with specific mechanisms of action are the need of an hour. In this study, we screened three novel non-β-lactam inhibitors against CTX-M-15 by multi-step virtual screening approach. The potential for virtually screened drugs was estimated through in vitro cell assays. Hence, we proposed a study to understand the binding mode of CTX-M-15 with inhibitors using bioinformatics and experimental approach. We calculated the dissociation constants (K_d), association constant (K_a), stoichiometry (n) and binding energies (ΔG) of compounds with the respective targets. Molecular dynamic simulation carried out for 25 ns, revealed that these complexes were found stable throughout the simulation with relative RMSD in acceptable range. Moreover, microbiological and kinetic studies further confirmed high efficacies of these inhibitors by reducing the minimum inhibitory concentration (MIC) and catalysis of antibiotics by β-lactamases in the presence of inhibitors. Therefore, we conclude that these potential inhibitors may be used as a lead molecule for future drug candidates against β-lactamases-producing bacteria.

Probing the binding reaction of cytarabine to human serum albumin using multispectroscopic techniques with the aid of molecular docking

Cytarabine is a kind of chemotherapy medication. In the present study, the molecular interaction between cytarabine and human serum albumin (HSA) was investigated via fluorescence, UV-vis absorption, circular dichroism (CD) spectroscopy and molecular docking method under simulative physiological conditions. It was found that cytarabine could effectively quench the intrinsic fluorescence of HSA through a static quenching process. The apparent binding constants between drug and HSA at 288, 293 and 298K were estimated to be in the order of 10³L·mol^-1. The thermodynamic parameters ΔH°, ΔG°and ΔS° were calculated, in which the negative ΔG°suggested that the binding of cytarabine to HSA was spontaneous, moreover the negative ΔS°and negative ΔH°revealed that van der Waals force and hydrogen bonds were the major forces to stabilize the protein-cytarabine (1:1) complex. The competitive binding experiments showed that the primary binding site of cytarabine was located in the site I (subdomain IIA) of HSA. In addition, the binding distance was calculated to be 3.4nm according to the Förster no-radiation energy transfer theory. The analysis of CD and three-dimensional (3D) fluorescence spectra demonstrated that the binding of drug to HSA induced some conformational changes in HSA. The molecular docking study also led to the same conclusion obtained from the spectral results.

Investigating the affinity of BDE154 and 3OH-BDE154 with HSA: Experimental and simulation validation

The physicochemical properties of polybrominated diphenyl ethers are important for modeling their transport, but these data are often missing. Here, satisfactory bioactivity results were obtained using human serum albumin as the carrier, 2,2',4,4',5,6'-hexabromodiphenyl ether (BDE154) and 3-hydroxy-2,2',4,4', 5,6'-hexabromodiphenyl ether (3OH-BDE154) as the ligands, using UV-visible absorbance, fluorescence, circular dichroism, molecular docking, and molecular dynamics methods. The interactions between human serum albumin and BDE154 or 3OH-BDE154 were verified, consistent with the static quenching procedure. At pH 7.4, the binding constants of the complexes for site I were relatively comparable and increased in the order BDE154<3OH-BDE154. Then, the secondary structure and kinetic parameters of albumin were analyzed using the circular dichroism spectra and GROMACS software. The data obtained from these simulations indicate that hydrophobic attraction might be the key factor for the stability of complexes. The docking experiments provided further insight into the hydrophobic pocket and showed that 3OH-BDE154 has a stronger binding affinity to human serum albumin than BDE154. The experimental spectral data were obtained and compared with the simulation results, showing good agreement. A detailed analysis of PBDEs-HSA interactions would provide valuable information to better understand the interaction on this class of compounds.

Antileukemic activity of an arsenomolybdate in the human HL-60 and U937 leukemia cells

The antileukemic activity, mechanisms and serum albumin interactions of an arsenomolybdate, K₂Na[AsMo₆O₂₁(O₂CCH₂NH₃)₃]·6H₂O (1), was evaluated in the human leukemia HL-60 and U937 cells. The results indicated that 1 could inhibit the proliferation of both leukemia cell lines in a dose-dependent manner with the 50% lethal concentration (IC₅₀) value of 8.61μM for HL-60 and 14.50μM for U937 at 24h, compare to the positive controls, all-trans retinoic acid (ATRA) with IC₅₀ value of 20.76μM and 14.85μM,and As₂O₃ with IC₅₀ value of 6.40μM and 8.75μM at 24h, respectively (P<0.05). Furthermore, the anti-leukemia activity of compound 1 might be medicated by arresting the leukemic cells in the G₁ phase and inducing apoptosis via caspase-3 and bcl-2 regulatory proteins. Spectroscopic techniques results showed that the fluorescence of human serum albumin was quenched by compound 1, and the quenching mechanism was mainly static quenching. Compound 1 might be a potential medicinal candidate against acute promyelocytic leukemia.