Synthesis, characterization and interaction studies of 1,3,4-oxadiazole derivatives of fatty acid with human serum albumin (HSA): A combined multi-spectroscopic and molecular docking study

A Novel Protocol for the Synthesis of 1,2,4-Oxadiazoles Active against Trypanosomatids and Drug-Resistant Leukemia Cell Lines

Cancer and parasitic diseases, such as leishmaniasis and Chagas disease, share similarities that allow the co-development of new antiproliferative agents as a strategy to quickly track the discovery of new drugs. This strategy is especially interesting regarding tropical neglected diseases, for which chemotherapeutic alternatives are extremely outdated. We designed a series of (E)-3-aryl-5-(2-aryl-vinyl)-1,2,4-oxadiazoles based on the reported antiparasitic and anticancer activities of structurally related compounds. The synthesis of such compounds led to the development of a new, fast, and efficient strategy for the construction of a 1,2,4-oxadiazole ring on a silica-supported system under microwave irradiation. One hit compound (23) was identified during the in vitro evaluation against drug-sensitive and drug-resistant chronic myeloid leukemia cell lines (EC₅₀ values ranging from 5.5 to 13.2 µM), Trypanosoma cruzi amastigotes (EC₅₀ = 2.9 µM) and Leishmania amazonensis promastigotes (EC₅₀ = 12.2 µM) and amastigotes (EC₅₀ = 13.5 µM). In silico studies indicate a correlation between the in vitro activity and the interaction with tubulin at the colchicine binding site. Furthermore, ADMET in silico predictions indicate that the compounds possess a high druggability potential due to their physicochemical, pharmacokinetic, and toxicity profiles, and for hit 23, it was identified by multiple spectroscopic approaches that this compound binds with human serum albumin (HSA) via a spontaneous ground-state association with a moderate affinity driven by entropically and enthalpically energies into subdomain IIA (site I) without significantly perturbing the secondary content of the protein.

Study of modeling and optimization for predicting the acute toxicity of carbamate pesticides using the binding information with carrier protein

To predict drug acute toxicity using the binding information with human serum albumin, our research group established a new method (Carrier protein binding information-toxicity relationship, CPBITR). Unfortunately, the previous model had too few data sets which may affect the accuracy and credibility of the model. In this paper, therefore, we measured the binding modes of three carbamate pesticides, Bendiocarb, Butocarboxim and Dioxacarb with human serum albumin (HSA) to supplement the previously modeled training set. Multispectral methods and molecular docking were used to study their binding modes. We built and optimized the previous models with the combined information of three different toxicity pesticides and HSA in order to find better prediction method. The results showed that Back-propagation Artificial Neural Network model has the best fitting effect among these models. In conclusion, the proposed model effectively improves the accuracy and credibility of the existing model. It results in significant predict drug acute toxicity using the binding information with carrier protein and contribute to drug development and research.

Effect of ascorbic acid on tyrosinase and its anti-browning activity in fresh-cut Fuji apple

Tyrosinase (polyphenol oxidase) is the key enzyme of enzymatic browning in fruits and vegetables. In this research, the impact of ascorbic acid on tyrosinase and its anti-browning effect on fresh-cut Fuji apple were investigated. Ascorbic acid had a dual effect on tyrosinase with a half inhibitory concentration (IC₅₀ ) of 13.40 ± 0.05 µM. Fluorescence assay demonstrated that ascorbic acid interacted with tyrosinase in a dynamic contaction caused by Förster's resonance energy transfer (FRET) and induced a conformational change of the enzyme. Thermodynamic analysis, copper interaction, and molecular docking further confirmed that ascorbic acid could chelate the copper ions located in active center and interact with amino acid residues of tyrosinase via hydrophobic interaction. In addition, ascorbic acid prevented the browning of fresh-cut apples by increasing APX activity and inhibiting PPO and POD activities which reduce the oxidation of total phenolics and flavonoids. PRACTICAL APPLICATIONS: The present study demonstrated that ascorbic acid had a strong inhibitory activity against tyrosinase (IC₅₀ = 13.40 ± 0.05 µM) and anti-browning activity against fresh-cut Fuji apple. It could delay the browning degree of apple juice, increase APX activity, inhibit PPO and POD activities, and reduce the oxidation of total phenolics and flavonoids. These findings provided a basis for the feasible application of ascorbic acid on the preservation of fruits.

Yb/Chitosan Catalyzed Synthesis of Highly Substituted Piperidine Derivatives for Potential Nuclease Activity and DNA Binding Study

BACKGROUND

Herein, a new chitosan-supported ytterbium nano-catalyst has been prepared and used in a mild, efficient, and expeditious method for the synthesis of substituted piperidine derivatives via threecomponent condensation of substituted anilines, formaldehyde and different cyclic/acyclic active methylene compounds at room temperature.

METHODS

The catalyst was characterized by FTIR, XRD, SEM, EDX, TEM, ICP-AES and the stability of the catalyst was evaluated by TG analysis. The synthesized compound 3,3,11,11-Tetramethyl-15-(phenyl)-15- azadispiro[5.1.5.3]hexadecane-1,5,9,13-tetrone (3a) was explored for pBR322 DNA cleavage activity and genotoxicity. Further, the interaction of 3a with CT-DNA was investigated through UV-vis, fluorescence and viscosity.

RESULTS

The preparation of Yb/chitosan nano-catalyst was verified and the catalyst was found effective towards substituted piperidine formations with the catalyst reusability. Compound 3a was successfully tested for DNA cleavage activity. In addition, fluorescence results revealed that compound 3a interacted with DNA with a binding affinity of 4.84 x 10⁴ M^-1.

CONCLUSION

Our findings suggest that compounds bearing spiro-piperidine scaffold, synthesized using reusable nano-catalyst, could be effective biological agents.

Structural and Photodynamic Studies on Nitrosylruthenium-Complexed Serum Albumin as a Delivery System for Controlled Nitric Oxide Release

How to deliver nitric oxide (NO) to a physiological target and control its release quantitatively is a key issue for biomedical applications. Here, a water-soluble nitrosylruthenium complex, [(CH₃)₄N][RuCl₃(5cqn)(NO)] (H5cqn = 5-chloro-8-quinoline), was synthesized, and its structure was confirmed with ¹H NMR and X-ray crystal diffraction. Photoinduced NO release was investigated with time-resolved Fourier transform infrared and electron paramagnetic resonance (EPR) spectroscopies. The binding constant of the [RuCl₃(5cqn)(NO)]^- complex with human serum albumin (HSA) was determined by fluorescence spectroscopy, and the binding mode was identified by X-ray crystallography of the HSA and Ru-NO complex adduct. The crystal structure reveals that two molecules of the Ru-NO complex are located in the subdomain IB, which is one of the major drug binding regions of HSA. The chemical structures of the Ru complexes were [RuCl₃(5cqn)(NO)]^- and [RuCl₃(Glycerin)NO]^-, in which the electron densities for all ligands to Ru are unambiguously identified. EPR spin-trapping data showed that photoirradiation triggered NO radical generation from the HSA complex adduct. Moreover, the near-infrared image of exogenous NO from the nitrosylruthenium complex in living cells was observed using a NO-selective fluorescent probe. This study provides a strategy to design an appropriate delivery system to transport NO and metallodrugs in vivo for potential applications.

In silico prediction, molecular docking and binding studies of acetaminophen and dexamethasone to Enterococcus faecalis diaminopimelate epimerase

Enterococcus faecalis (E. faecalis) is a Gram-positive coccoid, non-sporulating, facultative anaerobic, multidrug resistance bacterium responsible for almost 65% to 80% of all enterococcal nosocomial infections. It usually causes infective endocarditis, urinary tract and surgical wound infections. The increase in E. faecalis resistance to conventionally available antibiotic has rekindled intense interest in developing useful antibacterial drugs. In E. faecalis, diaminopimelate epimerase (DapF) is involved in the lysine biosynthetic pathway. The product of this pathway is precursors of peptidoglycan synthesis, which is a component of bacterial cell wall. Also, because mammals lack this enzyme, consequently E. faecalis diaminopimelate epimerase (EfDapF) represents a potential target for developing novel class of antibiotics. In this regard, we have successfully cloned, overexpressed the gene encoding DapF in BL-21(DE3) and purified with Ni-NTA Agarose resin. In addition to this, binding studies were performed using fluorescence spectroscopy in order to confirm the bindings of the identified lead compounds (acetaminophen and dexamethasone) with EfDapF. Docking studies revealed that acetaminophen found to make hydrogen bonds with Asn72 and Asn13 while dexamethasone interacted by forming hydrogen bonds with Asn205 and Glu223. Thus, biochemical studies indicated acetaminophen and dexamethasone, as potential inhibitors of EfDapF and eventually can reduce the catalytic activity of EfDapF.

Synthesis, spectroscopic characterization and DNA/HSA binding studies of (phenyl/naphthyl)ethenyl-substituted 1,3,4-oxadiazolyl-1,2,4-oxadiazoles

Novel 1,3,4-oxadiazolyl-1,2,4-oxadiazole derivatives with promising photophysical and DNA/HSA-binding properties are reported.

Synthesis and Biological Evaluation of 1,3,4-Oxadiazole Fused Resveratrol Derivatives as Anticancer Agents

A novel target compounds (9a-j) were design and synthesized and characterized by 1H & 13C NMR, ESI-MS spectral analysis. Further, these were tested for their anticancer activity against three human cancer cell lines such as MCF-7, MDA MB-231 (breast), A549 (Lung) and adriamycin was used as positive control. Among ten compounds, two compounds like 9b and 9j were showed a significant anticancer activity compared to control drug.

Spectroscopy and molecular docking approach for investigation on the binding of nocodazole to human serum albumin

The interaction between nocodazole (Nz) and human serum albumin (HSA) under controlled physiological condition (pH 7.4) is examined using absorption, emission, fluorescence lifetime (FLT) and circular dichroism (CD) spectroscopic techniques. The binding constant (order of 10⁵ M^-1) from UV-vis and fluorescence spectroscopy reveals a strong interaction between Nz and HSA. Fluorescence quenching study shows that Nz binds with HSA through static quenching process. It is induced by formation of Nz-HSA complex because the Stern-Volmer quenching constant is inversely correlated with the temperature which is further verified by time-resolved fluorescence spectroscopy. The thermodynamic parameters at different temperatures indicate that the binding process is spontaneous where hydrogen bonding interactions and Van der Waals forces play major roles during the interaction between Nz and HSA. By means of spectroscopy and molecular modeling, we have discovered and interpreted the alteration of the secondary structure of HSA by Nz complexation. Synchronous, three-dimensional fluorescence and CD spectroscopic results reveal that the addition of Nz to HSA affects changes in the micro-environment and conformation of HSA. According to Förster Resonance Energy Transfer (FRET), the binding distance (r) between Nz and residue of HSA is <8 nm with excellent energy efficiency. The docking study suggests that nocodazole binds at Domain IIA in the hydrophobic pocket of human serum albumin.

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.

Interaction mechanism between α-glucosidase and A-type trimer procyanidin revealed by integrated spectroscopic analysis techniques

α-Glucosidase is an important enzyme in human intestine, and inhibition of its activity can lower blood sugar levels to effectively prevent hyperglycaemia induced tissue damage. Here, we investigated the inhibitory activities of procyanidins with different structures on α-glucosidase and the underlying mechanism. The results showed that the IC₅₀ of catechin and compounds 2-7 on α-glucosidase was lower than that of acarbose. A-type procyanidins might have better inhibitory activity than B-type procyanidins. In addition, there was no positive correlation between the polymerization degree of A-type procyanidin oligomer and its inhibitory effect on α-glucosidase. Compound 7 (A-type trimer) with the best inhibitory effect reversibly inhibited the activity of α-glucosidase in a mixed-type manner. Fluorescence data confirmed that the intrinsic fluorescence of α-glucosidase was quenched by compound 7 through static-dynamic quenching. The calculated thermodynamic parameters indicated that their binding was spontaneous and driven by hydrophobic interaction, which was also confirmed by the UV spectrum experiment. Besides, circular dichroism analysis displayed that their binding resulted in conformational changes of α-glucosidase characterized by a decrease in α-helix and an increase in β-sheet. The results demonstrate the ability of procyanidins to intervene in the progression of type 2 diabetes by inhibiting α-glucosidase.

Explication of bovine serum albumin binding with naphthyl hydroxamic acids using a multispectroscopic and molecular docking approach along with its antioxidant activity

In the present investigation, the protein-binding properties of naphthyl-based hydroxamic acids (HAs), N-1-naphthyllaurohydroxamic acid (1) and N-1-naphthyl-p-methylbenzohydroxamic acid (2) were studied using bovine serum albumin (BSA) and UV-visible spectroscopy, fluorescence spectroscopy, diffuse reflectance spectroscopy-Fourier transform infrared (DRS-FTIR), circular dichroism (CD), and cyclic voltammetry along with computational approaches, i.e. molecular docking. Alteration in the antioxidant activities of compound 1 and compound 2 during interaction with BSA was also studied. From the fluorescence studies, thermodynamic parameters such as Gibb's free energy (ΔG), entropy change (ΔS) and enthalpy change (ΔH) were calculated at five different temperatures (viz., 298, 303, 308, 313 or 318 K) for the HAs-BSA interaction. The results suggested that the binding process was enthalpy driven with dominating hydrogen bonds and van der Waals' interactions for both compounds. Warfarin (WF) and ibuprofen (IB) were used for competitive site-specific marker binding interaction and revealed that compound 1 and compound 2 were located in subdomain IIA (Sudlow's site I) on the BSA molecule. Conclusions based on above-applied techniques signify that various non-covalent forces were involved during the HAs-BSA interaction. Therefore the resulted HAs-BSA interaction manifested its effect in transportation, distribution and metabolism for the drug in the blood circulation system, therefore establishing HAs as a drug-like molecule.

Characterization of the interaction between recombinant porcine aminopeptidase N and spike glycoprotein of porcine epidemic diarrhea virus

Porcine epidemic diarrhea (PED) has caused huge economic losses to the global pork industry. Infection by its causative agent PED virus (PEDV), an Alpha-coronavirus, was previously proven to be mediated by its spike (S) glycoprotein and a cellular receptor porcine aminopeptidase N (pAPN). Interestingly, some recent studies have indicated that pAPN is not a functional receptor for PEDV. To date, there is a lack of a direct evidence for the interaction between pAPN and PEDV S protein in vitro. Here, we prepared pAPN ectodomain and the truncated variants of PEDV S protein in Drosophila S2 cells. These recombinant proteins were homogeneous after purification by metal-affinity and size-exclusion chromatography. We then assayed the purified target proteins through immunogenicity tests, PEDV binding interference assays, circular dichroism (CD) measurements, pAPN activity assay and structural determination, demonstrating that they were biologically functional. Finally, we characterized their interactions by gel filtration chromatography, native-polyacrylamide gel electrophoresis (PAGE) and surface plasmon resonance (SPR) analyses. The results showed that their affinities were too low to form complexes, which suggest that pAPN may be controversial as the genuine receptor for PEDV. Therefore, further research needs to be carried out to elucidate the interaction between PEDV and its genuine receptor.

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.

Inhibitory kinetics and mechanism of rifampicin on α-glucosidase: Insights from spectroscopic and molecular docking analyses

α-Glucosidase is a critical enzyme associated with diabetes mellitus, and the inhibitors of the enzyme play important roles in the treatment of the disease. In this study, the inhibitory effect and mechanism of rifampicin on α-glucosidase were investigated by multispectroscopic methods along with molecular docking technique. The results showed that rifampicin inhibited α-glucosidase activity prominently (IC₅₀ = 135 ± 1.2 μM) in a reversible and competitive-type manner. The fluorescence intensity of α-glucosidase was quenched by rifampicin through forming rifampicin-α-glucosidase complex in a static procedure. And the formation of the rifampicin-α-glucosidase complex was driven spontaneously by hydrophobic forces and hydrogen bonds. The results obtained from molecular docking further indicated that hydrophobic forces were formed between rifampicin and amino acid residues Phe 173, Pro151, and hydrogen bonds were generated by the interactions of rifampicin with residues Ser 180, Asn 414, Gly160, and Gly161 of α-glucosidase. Moreover, it was found that the binding of rifampicin to α-glucosidase could alter the conformation of the enzyme to make it steady, and the binding distance was estimated to be 1.02 nm. Therefore, this study confirmed a novel α-glucosidase inhibitor and possibly contributed to the improvement of newfangled anti-diabetic agent.

Binding behavior of trelagliptin and human serum albumin: Molecular docking, dynamical simulation, and multi-spectroscopy

This study aims to investigate the interaction mechanism of a hypoglycemic agent, trelagliptin (TLP), and human serum albumin (HSA) through computer simulation and assisted spectroscopy methods. Computer simulation including molecular docking and molecular dynamics analysis was conducted under physiological conditions. Molecular docking results indicate that TLP bound to HSA at site I, and the binding behavior was mainly governed by hydrophobic force. Competitive experiments further verified the theoretical conclusion from molecular docking. Molecular dynamics simulation revealed that TLP indeed stably bound to site I of HSA in the hydrophobic subdomain IIA. Moreover, TLP presented a certain effect on the structural compactness of HSA. In molecular dynamics simulation, hydrogen bonds appeared, which suggested the reliability and stability of the combination. The binding energy of the stable phase is around -250 kJ/mol. Fluorescence quenching studies and time-resolved fluorescence analysis indicated that the evident fluorescence quenching phenomenon of HSA could be due to TLP binding initiated by static quenching mechanism. The binding constants (K_a) of the complex were found to be around 10⁴ via fluorescence data, and the calculated thermodynamic parameters indicated that hydrophobic force played major role in the binding of TLP to HSA. Synchronous fluorescence and three-dimensional fluorescence results demonstrated that TLP slightly disturbed the microenvironment of amino residues. Circular dichroism spectra showed that TLP affected the secondary structure of HSA. The theoretical and experimental results showed excellent agreement.

Interaction between Saikosaponin D, Paeoniflorin, and Human Serum Albumin

Saikosaponin D (SSD) and paeoniflorin (PF) are the major active constituents of Bupleuri Radix and Paeonia lactiflora Pall, respectively, and have been widely used in China to treat liver and other diseases for many centuries. We explored the binding of SSD/PF to human serum albumin (HSA) by using fluorospectrophotometry, circular dichroism (CD) and molecular docking. Both SSD and PF produced a conformational change in HSA. Fluorescence quenching was accompanied by a blue shift in the fluorescence spectra. Co-binding of PF and SSD also induced quenching and a conformational change in HSA. The Stern-Volmer equation showed that quenching was dominated by static quenching. The binding constant for ternary interaction was below that for binary interaction. Site-competitive experiments demonstrated that SSD/PF bound to site I (subdomain IIA) and site II (subdomain IIIA) in HSA. Analysis of thermodynamic parameters indicated that hydrogen bonding and van der Waals forces were mostly responsible for the binary association. Also, there was energy transfer upon binary interaction. Molecular docking supported the experimental findings in conformation, binding sites and binding forces.