Exploring the site-selective binding of jatrorrhizine to human serum albumin: spectroscopic and molecular modeling approaches

Profiling the interaction of a novel toxic pyruvate dehydrogenase kinase inhibitor with human serum albumin

To discover novel pyruvate dehydrogenase kinase (PDK) inhibitors, a new compound 2,2-dichloro-1-(4-((4-isopropylphenyl)amino)-3-nitrophenyl)ethan-1-one, namely XB-1 was identified, which inhibited PDK activity with a half maximal inhibitory concentration (IC₅₀) value of 337.0 nM, and reduced A549 cell proliferation with a half maximal effective concentration (EC₅₀) value of 330.0 nM. However, the compound appears to exhibit a negligible selectivity between cancer cell and normal one, indicating a potential toxicity existed for the compound. Herein, the interaction of the toxic XB-1 to human serum albumin (HSA) was firstly explored by spectroscopic approaches with the aim to reduce/avoid the toxicity of PDK inhibitors in the next hit-to-lead campaign. In detail, it was found that the XB-1 could effectively bind to HSA mainly via hydrogen bond interaction in PBS buffer (pH = 7.4, 10.0 mM), resulting in the formation of HSA-XB-1 complex. The negative value of ΔG showed that the binding of XB-1 to HSA is a spontaneous process. The result from site-selective binding assay suggested that the XB-1 bound to the site I of HSA by competing with warfarin, which was perfect in agreement with the molecular docking method. The results of this paper may offer a valuable theoretical basis to study the toxicity of biofunctional molecules and may offer thoughts about how to avoid/reduce toxicity for a small molecule.

Jatrorrhizine: a review of its pharmacological effects

OBJECTIVES

Jatrorrhizine is an isoquinoline alkaloid found in medicinal plants. It is the main bioactive compound of the Chinese herbs, Coptis chinensis, Rhizoma coptidis, and Phellodendron chinense Schneid, plants that are predominantly used in traditional Chinese medicine (TCM) for the treatment of metabolic disorders, gastritis, stomachache among a host of others. This manuscript aims to provide a comprehensive review of the pharmacological effects of jatrorrhizine, proffer suggestions on research areas that need redress and potentially serve as a reference for future studies.

KEY FINDINGS

Published scientific literature was therefore retrieved from all credible sources including Pubmed, Elsevier, Research Gate, Web of Science, Google Scholar, Science Direct, Europe PMC and Wiley Online library using key words such as 'jatrorrhizine', 'botanical sources', 'pharmacology', 'toxicology', 'pharmacokinetics' or their combinations. A cursory examination of relevant scientific literature using the aforementioned key words produced more than 400 publications.

CONCLUSIONS

Using an inclusion/exclusion criteria the subject matter of this review was adequately addressed. It is our hope that this review will provide a good platform for further research on fully harnessing the potential of this bioactive compound.

Ethnobotany and the Role of Plant Natural Products in Antibiotic Drug Discovery

The crisis of antibiotic resistance necessitates creative and innovative approaches, from chemical identification and analysis to the assessment of bioactivity. Plant natural products (NPs) represent a promising source of antibacterial lead compounds that could help fill the drug discovery pipeline in response to the growing antibiotic resistance crisis. The major strength of plant NPs lies in their rich and unique chemodiversity, their worldwide distribution and ease of access, their various antibacterial modes of action, and the proven clinical effectiveness of plant extracts from which they are isolated. While many studies have tried to summarize NPs with antibacterial activities, a comprehensive review with rigorous selection criteria has never been performed. In this work, the literature from 2012 to 2019 was systematically reviewed to highlight plant-derived compounds with antibacterial activity by focusing on their growth inhibitory activity. A total of 459 compounds are included in this Review, of which 50.8% are phenolic derivatives, 26.6% are terpenoids, 5.7% are alkaloids, and 17% are classified as other metabolites. A selection of 183 compounds is further discussed regarding their antibacterial activity, biosynthesis, structure-activity relationship, mechanism of action, and potential as antibiotics. Emerging trends in the field of antibacterial drug discovery from plants are also discussed. This Review brings to the forefront key findings on the antibacterial potential of plant NPs for consideration in future antibiotic discovery and development efforts.

The interaction mechanism between fludarabine and human serum albumin researched by comprehensive spectroscopic methods and molecular docking technique

Fludarabine (Flu) is widely used to treat B-cell chronic lymphocytic leukemia. HSA is of the essence to human, especially in blood circulation system. The interaction mechanism between Flu and HSA was studied by comprehensive spectroscopic methods and molecular docking technique. UV-vis and FL spectrum results indicated that Flu bond with HSA, and there was a new complex produced at the binding site I in subdomain IIA. Association constants at 298 K were 1.637 × 10⁴ M^-1 and 1.552 × 10⁴ M^-1 at 310 K, respectively. The negative enthalpy (ΔH) and positive entropy (ΔS) values for the interaction revealed that the binding behavior was driven by hydrophobic forces and hydrogen bonds. The results obtained from UV, RLS spectra, 3D fluorescence and CD spectrum illustrated that Flu could change the secondary structure of HSA. According to molecule docking result, the binding energy of interaction is -11.15 kcal/mol.

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.

Mechanism and inhibition kinetics of peptide P13 as thrombin inhibitor

Excessive coagulation can easily lead to arterial and venous thrombosis, which is the main reason for the evolution of myocardial infarction and cerebrovascular accidents. As a key coagulation factor for the coagulation pathway, thrombin has become a remarkable target for the control of thrombosis. The synthesized peptide P13 with amino acid sequence of N-RGDAGFAGDDAPR was expected to be an inhibitor with higher antithrombotic activity. The results showed that the IC₅₀ (50% inhibition of thrombin activity) of the peptide P13 was determined by colorimetric method to be 115 µM. And enzyme kinetic experiments showed that P13 was a competitive inhibitor of thrombin with K_i = 106 µM. Fluorescence spectra and three-dimensional fluorescence showed that P13 could alter the secondary structure of thrombin and the microenvironment of certain chromogenic amino acids. P13 can spontaneously bind with thrombin exosite 1 in the form of 1:1 mainly through hydrogen bonding and van der Waals force. And the optimal docking mode of P13 and thrombin was revealed by molecular docking with "-CDOCKER_Energy" of 178.679 kcal mol^-1. This study revealed P13 may become a potential anticoagulant drug widely used after further studies in preclinical and clinical trials.

Comparative studies on the interaction between biogenic polyamines and bovine intestinal alkaline phosphatases: spectroscopic and theoretical approaches

In this work, the effect of two organic polyamines (spermine and spermidine) on the fluorescence intensity and activity of bovine intestinal alkaline phosphatase (BIALP) are investigated. The interaction of BIALP with spermine and spermidine was studied in a diethanolamine buffer with 0.5 mM magnesium chloride (pH 9.8) and at two temperatures by using the fluorescence quenching method. Furthermore, the activity of enzyme was studied using UV-Vis spectrophotometry in a diethanolamine buffer with 0.5 mM magnesium chloride, at 37 °C, in the absence and presence of different concentrations of each polyamine (0-5 mM). It was demonstrated that both polyamines quenched the intrinsic fluorescence of BIALP by the static quenching process. Based on these results, the values of the binding site for both polyamines were close to each other and decreased by increasing the temperature. The calculated thermodynamic parameters (ΔH° < 0 and ΔS° < 0) also showed that the acting forces in the formation of the complex between BIALP and polyamines were hydrogen bonds and van der Waals forces with an overall favorable Gibbs free energy change (∆G° < 0). In addition, kinetic studies revealed that these polyamines enhanced the enzyme activity of BIALP in a concentration-dependent manner. This result also indicated that spermine had more of an effect on BIALP activity in the same condition. Also, molecular docking as well as thermodynamic parameters showed that hydrogen bonds and van der Waals forces played an important role in the stabilization of BIALP-polyamine complexes.

Synthesis of a novel p-hydroxycinnamic amide with anticancer capability and its interaction with human serum albumin

In the present study, a novel p-hydroxycinnamic amide (E)-3-(4-hydroxyphenyl)-N-(4-(N-(5-meth oxypyrimidin-2-yl)-sulfamoyl)phenyl)acrylamide (HMSP) was synthesized and confirmed. In vitro cytotoxic assays indicated that HMSP was able to inhibit the proliferation of various cancer cell lines. The interaction between HMSP and human serum albumin (HSA) was examined by fluorescence, UV-Vis and circular dichroism (CD) spectra, in addition to molecular simulation. The fluorescence and UV-Vis spectra data indicated that the binding of HMSP with HSA was a static process. According to the fluorescence quenching calculation, the corresponding thermodynamic parameters, bimolecular quenching rate constant and apparent quenching constants were calculated. Van der Walls forces and hydrogen bonds were vital in the binding of HMSP on HSA. The distances between HSA and its derivatives were obtained. Furthermore, competitive experiments and molecular modeling results suggested that the binding of the compound on HSA mainly occurred in site I (sub-domain IIA). Changes in HSA conformation were observed from synchronous fluorescence and CD spectra, which were further investigated by molecular dynamic simulations.

Interaction studies of copper complex containing food additive carmoisine dye with human serum albumin (HSA): Spectroscopic investigations

In this study, the interaction between human serum albumin (HSA) and a copper complex of carmoisine dye; [Cu(carmoisine)₂ (H₂ O)₂ ], was studied in vitro using multi-spectroscopic methods. It was found that the intrinsic fluorescence of HSA was quenched by the addition of the [Cu(carmoisine)₂ (H₂ O)₂ ] complex and the quenching mechanism was considered as static quenching by formation of a [Cu(carmoisine)₂ (H₂ O)₂ ]-HSA complex. The binding constant was about 10⁴  M^-1 at room temperature. The values of the calculated thermodynamic parameters (ΔH < 0 and ΔS > 0) suggested that both hydrogen bonds and the hydrophobic interactions were involved in the binding process. The site marker competitive experiments revealed that the binding of [Cu(carmoisine)₂ (H₂ O)₂ ] to HSA primarily occurred in subdomain IIIA (site II) of HSA. The results of circular dichroism (CD) and UV-vis spectroscopy showed that the micro-environment of amino acid residues and the conformation of HSA were changed after addition of the [Cu(carmoisine)₂ (H₂ O)₂ ] complex. Finally, the binding of the [Cu(carmoisine)₂ (H₂ O)₂ ] complex to HSA was modelled by a molecular docking method. Excellent agreement was obtained between the experimental and theoretical results with respect to the binding forces and binding constant.

Binding properties of drospirenone with human serum albumin and lysozyme in vitro

The interaction of drospirenone (DP) with human serum albumin (HSA)/lysozyme (LYZ) was investigated using different optical techniques and molecular models. Results from the emission and time resolved fluorescence studies revealed that HSA/LYZ emission quenching with DP was initiated by static quenching mechanism. The LYZ-DP system was more easily influenced by temperature than the HSA-DP system. Displacement experiments demonstrated that the DP binding site was mainly located in site 1 of HSA. Based on the docking methods, DP was mainly bound in the active site hinge region where Trp-62 and Trp-63 are located. Conformation study showed that DP had different effects on the local conformation of HSA and LYZ molecules.

Modeling techniques and fluorescence imaging investigation of the interactions of an anthraquinone derivative with HSA and ctDNA

A new anthraquinone derivative (AORha) was synthesized. Its interactions with human serum albumin (HSA) and calf thymus DNA (ctDNA) were investigated by fluorescence spectroscopy, UV-visible absorption spectroscopy and molecular modeling. Cell viability assay and cell imaging experiment were performed using cervical cancer cells (HepG2 cells). The fluorescence results revealed that the quenching mechanism was static quenching. At different temperatures (290, 300, 310 K), the binding constants (K) and the number of binding sites (n) were determined, respectively. The positive ΔH and ΔS values showed that the binding of AORha with HSA was hydrophobic force, which was identical with the molecular docking result. Studying the fluorescence spectra, UV spectra and molecular modeling also verified that the binding mode of AORha and ctDNA might be intercalative. When HepG2 cells were treated with AORha, the fluorescence became brighter and turned green, which could be used for bioimaging.

Design, synthesis, characterization, cytotoxicity, molecular docking and analysis of binding interactions of novel acetylacetonatopalladium(ii) alanine and valine complexes with CT-DNA and BSA

The neutral, water soluble palladium(ii) amino acid complexes, interact with CT-DNA (groove binding) and BSA (H-binding in main pocket). Molecular docking supports the interactions.

Natural isoquinoline alkaloids: binding aspects to functional proteins, serum albumins, hemoglobin, and lysozyme

The putative anticancer alkaloids berberine, palmatine, jatrorrhizine, and sanguinarine are known to bind to nucleic acids. To develop them as potential drugs for therapeutic use, their binding affinity to functional proteins and mode of transport in the circulatory system need to be clearly understood. Towards this, many studies on their binding aspects to proteins have been reported and a considerable amount of data, mostly of biophysical nature, exists in the literature. The importance of these natural isoquinoline alkaloids and the recent literature on their interaction phenomena with functional proteins, serum albumins, hemoglobin, and lysozyme are presented in this review.

Evaluation of the interaction between naringenin and human serum albumin: Insights from fluorescence spectroscopy, electrochemical measurement and molecular docking

Naringenin (Nar) is a flavanone compound found in grapefruits that is endowed with diverse pharmacological and biological activities. Here, the interaction between Nar and human serum albumin (HSA) was investigated via various methods, including fluorescence spectroscopy, electrochemical methods and molecular docking. The Stern-Volmer quenching constants inversely correlated with temperature, demonstrating that the fluorescence quenching about HSA-Nar system is initiated by the formation of a compound, which has confirmed by electrochemical measurements. Three-dimensional fluorescence demonstrated that Nar induces the slight unfolding of the polypeptides of HSA. The calculated thermodynamic parameters suggesting that the binding of Nar to HSA is spontaneous, and the mainly force is electrostatic interactions. In addition, site marker competitive experiments indicated that Nar binds to HSA both on site I (subdomain IIA) and site II (subdomain IIIA), with higher affinity to the latter one, consistence with molecular docking. Furthermore, the fluorescence resonance energy transfer (FRET) experiment showed the binding distance (r) is 2.65 nm. And the effects of metal ions on the HSA-Nar system are also discussed.

Binding properties of palmatine to DNA: spectroscopic and molecular modeling investigations

Palmatine, an isoquinoline alkaloid, is an important medicinal herbal extract with diverse pharmacological and biological properties. In this work, spectroscopic and molecular modeling approaches were employed to reveal the interaction between palmatine and DNA isolated from herring sperm. The absorption spectra and iodide quenching results indicated that groove binding was the main binding mode of palmatine to DNA. Fluorescence studies indicated that the binding constant (K) of palmatine and DNA was ~ 10(4)L·mol(-1). The associated thermodynamic parameters, ΔG, ΔH, and ΔS, indicated that hydrogen bonds and van der Waals forces played major roles in the interaction. The effects of chemical denaturant, thermal denaturation and pH on the interaction were investigated and provided further support for the groove binding mode. In addition to experimental approaches, molecular modeling was conducted to verify binding pattern of palmatine-DNA.

Development of morin-conjugated Au nanoparticles: exploring the interaction efficiency with BSA using spectroscopic methods

In order to enhance its interaction efficiency with biomacromolecules for the usage as a therapeutic agent, we have conjugated morin, an antioxidant activity and anti-tumor drug, with citrate-coated Au nanoparticles (M-C-AuNPs). M-C-AuNPs were prepared by reducing chloroauric acid using trisodium citrate in the boiling condition, and the resulted M-C-AuNPs were characterized by UV-vis absorption spectroscopy, Transmission Electron Microscopy (TEM), X-ray diffraction (XRD) and FTIR analysis. In this article, UV-vis absorption spectroscopy in combination with fluorescence spectroscopy, and circular dichroism (CD) spectroscopy were employed to investigate the interactions between M-C-AuNPs and bovine serum albumin (BSA), C-AuNPs and BSA in a phosphate buffer at pH 7.4. By comparing the quenching constant KSV, effective quenching constant Ka, binding constant Kb and the number of binding sites n, it is clearly suggested that M-C-AuNPs could enhance the binding force of morin with BSA, which would pave the way for the design of nanotherapeutic agents with improved functionality.

A Refined Model of the HCV NS5A protein bound to daclatasvir explains drug-resistant mutations and activity against divergent genotypes

Many direct-acting antiviral agents (DAAs) that selectively block hepatitis C virus (HCV) replication are currently under development. Among these agents is Daclatasvir, a first-in-class inhibitor targeting the NS5A viral protein. Although Daclatasvir is the most potent HCV antiviral molecule yet developed, its binding location and mode of binding remain unknown. The drug exhibits a low barrier to resistance mutations, particularly in genotype 1 viruses, but its efficacy against other genotypes is unclear. Using state-of-the-art modeling techniques combined with the massive computational power of Blue Gene/Q, we identified the atomic interactions of Daclatasvir within NS5A for different HCV genotypes and for several reported resistant mutations. The proposed model is the first to reveal the detailed binding mode of Daclatasvir. It also provides a tool to facilitate design of second generation drugs, which may confer less resistance and/or broader activity against HCV.