A couple of antitumor Pd(II) complexes make DNA-refolding and HSA-unfolding: Experimental and docking studies

GSH-responsive and folate receptor-targeted pyridine bisfolate-encapsulated chitosan nanoparticles for enhanced intracellular drug delivery in MCF-7 cells

Folic acid receptor-targeted drug delivery system is a promising candidate for tumor-targeted delivery because its elevated expression specifically on tumor cells enables the selective delivery of cytotoxic cargo to cancerous tissue, thereby minimizing toxic side effects and increasing the therapeutic index. Pyridine bisfolate-chitosan (PyBFA@CS NPs) and folate-chitosan nanocomposite (FA@CS NPs) were synthesized with suitable particle size (256.0 ± 15.0 and 161.0 ± 5.0 nm), high stability (ζ = -27.0 ± 0.1 and -30.0 ± 0.2 mV), respectively, and satisfactory biocompatibility to target cells expressing folate receptors and try to answer the question: Is the metal center always important for activity? Since almost all pharmaceuticals work by binding to specific proteins or DNA, the in vitro binding of human serum albumin (HSA) to PyBFA@CS NPs and FA@CS NPs has been investigated and compared with PyBFA. Strong affinity to HSA is shown by quenching and binding constants in the range of 105 and 104 M-1, respectively with PyBFA@CS NPs showing the strongest. The compounds-HSA kinetic stability, affinity, and association constants were investigated using a stopped-flow method. The findings showed that all formulations bind by a static quenching mechanism that consists of two reversible steps: rapid second-order binding and a more slowly first-order isomerization reaction. The overall coordination affinity of HSA to PyBFA@CS NPs (6.6 × 106 M-1), PyBFA (4.4 × 106 M-1), and FA@CS NPs (1.3 × 106 M-1) was measured and The relative reactivity is roughly (PyBFA@CS NPs)/(PyBFA)/(FA@CS NPs) = 5/3/1. Additionally, in vitro cytotoxicity revealed that, consistent with the binding constants and coordination affinity, active-targeting formulations greatly inhibited FR-positive MCF-7 cells in compared to FRs-negative A549 cells in the following trend: PyBFA@CS NPs > PyBFA > FA@CS NPs. Furthermore, in vitro drug release of PyBFA@CS NPs was found to be stable in PBS at pH 7.4, however, the in pH 5.4 and in pH 5.4 containing 10 mM glutathione (GSH) (mimicking the tumor microenvironment) reached 43 % and 73 %, respectively indicating that the PyBFA@CS NPs system is sensitive to GSH. Folate-modified nanoparticles, PyBFA@CS NPs, are a promising therapeutic for MCF-7 therapy because they not only showed a greater affinity for HSA, but also showed higher cleavage efficiency toward the minor groove of pBR322 DNA via the hydrolytic way, as well as effective antibacterial activity that avoids the usage of extra antibiotics.‬‬‬‬‬‬‬‬‬‬‬‬ ‬‬‬‬‬‬‬‬‬‬‬‬‬‬.

Computational and experimental examinations of new antitumor palladium(II) complex: CT-DNA-/BSA-binding, in-silico prediction, DFT perspective, docking, molecular dynamics simulation and ONIOM

Since the design of metal complexes with better biological activities is important, herein a new palladium(II) complex bearing en and acac (en and acac stand for ethylenediamine and acetylacetonato, respectively) as its ligands, [Pd(en)(acac)]NO3 complex, was synthesized and fully characterized. Quantum chemical computations of the palladium(II) complex were done via DFT/B3LYP method. Cytotoxicity activity of the new compound on leukemia cell line (K562) was assessed via MTT method. The findings indicated that the metal complex has remarkable cytotoxic effect than cisplatin. OSIRIS DataWarrior software was employed to calculate in-silico physicochemical and toxicity parameters of the synthesized complex which rendered significant results. To comprehend the interaction type of new metal compound with macromolecules, the in depth investigation of interaction of mentioned complex with CT-DNA and BSA was accomplished by fluorescence, UV-Visible absorption spectroscopy, viscosity measurement, gel electrophoresis, FRET analysis and circular dichroism (CD) spectroscopy. On the other hand, computational molecular docking was carried out and the obtained data demonstrated that H-bond and van der Waals forces are the dominant forces for the binding of the compound to the mentioned biomolecules. Molecular dynamics simulation was also done and confirmed the stability of best docked pose of palladium(II) complex inside DNA or BSA over the time and in presence of water solvent. Also, Our own N-layered Integrated molecular Orbital and molecular Mechanics (ONIOM) methodology based on the hybridization of quantum mechanics and molecular mechanics (QM/MM) methodology was accomplished to inquire about binding of Pd(II) complex with DNA or BSA.HIGHLIGHTSNew biologically active Pd(II) complex was synthesized and characterized.The in silico studies of the designed complex and its ligands were accomplished by OSIRIS DataWarrior softwareInteraction with CT-DNA and BSA was assessed by various spectroscopic methods.Molecular docking simulation supported the interaction with both macromolecules.Based on ONIOM analysis, the structures of the complex and biomolecules are altered after binding. Communicated by Ramaswamy H. Sarma.

Thermodynamic and functional changes of alpha-chymotrypsin after interaction with gallic acid

In the present study, the interaction mechanism between gallic acid (GA) and α-Chymotrypsin (α-CT) was investigated by employing a series ofspectroscopic methods, computational docking and molecular dynamic (MD) simulation. Fluorescence spectra analysis indicated the formation of a stable complex between GA and α-CT, where the quenching of the fluorescence emission was predominantly characterized by a static mechanism. TheCA obtained binding constants for the α-CT-GA complex were in the order of 103 M-1, indicating the moderate binding affinity of GA for α-CT. The corresponding CD findings showed that the interaction between GA and α-CT resulted in an alteration of the protein's secondary structure. The findings of the enzyme activity investigation clearly showed that the presence of GA led to a notable decline in the enzymatic activity of α-CT, highlighting GA's function as an effective inhibitor for α-CT. The molecular docking simulations revealed the optimal binding site for the GA molecule within the α-CT structure and MD simulations confirmed the stability of the α-CT-GA complex. This research expands our comprehension regarding the behavior of enzymes in the presence of small-molecule ligands and opens avenues for food safety.

Analysis of the binding mechanism for a water-soluble Pd(II) complex containing β-amino alcohols with HSA applying experimental and computational methods

In the study ahead, the binding interactions of the [Pd (HEAC) Cl2] complex with human serum albumin (HSA) protein have been assayed in vitro (pH= 7.40) utilizing computational and experimental procedures. The mentioned complex was synthesized as a water-soluble complex from {2-((2-((2-hydroxyethyl)amino)ethyl)amino) cyclohexanol} ligand = HEAC. The results of electronic absorption and circular dichroism investigations illustrated that the hydrophobicity of the Tryptophan microenvironment in HSA undergoes the changes by binding to the Pd(II) complex without substantial perturbations on the protein secondary structure. The fluorescence emission spectroscopy analysis revealed that with rising temperature, the quenching constant (Ksv) in the Stern-Volmer's relation decreases; so, it can be said that the interaction process is along with a static quenching mechanism. The values of 2.88 × 105 M-1, and 1.26 represent the binding constant (Kb) and the number of the binding sites (n), respectively. The Job graph showed the maximum point at χ = 0.5, which means organizing a new set with 1:1 stoichiometry. Thermodynamic profile (ΔH < 0, ΔS < 0, and ΔG < 0) has affirmed that van der Waals forces and hydrogen bonds have a basic function in the Pd(II) complex-albumin bindings. The ligand-competitive displacement studies utilizing warfarin and ibuprofen have represented that Pd(II) complex interacts with albumin by site II (subdomain IIIA). The computational molecular docking theory approved the results of the site-competitive tests; also, it indicated the existence of hydrogen bonds and van der Waals forces in Pd(II) complex-albumin interactions.Communicated by Ramaswamy H. Sarma.

In-silico and in-detail experimental interaction studies of new antitumor Zn(II) complex with CT-DNA and serum albumin

In this study, a novel Zn(II) complex with the formula [Zn(pyrr-ac)2] (pyrr-ac: pyrrolidineacetate) was synthesized and characterized through molar conductivity, elemental analysis, 1H Nuclear Magnetic Resonance (1H NMR), UV-Visible spectroscopy, and Fourier transform infrared (FT-IR) methods. B3LYP level of DFT method along with aug-cc-pVTZ-PP/6-311G(d,p) basis set was utilized to perform the geometry optimization and HOMO-LUMO analysis. In addition, MEP, NLO and NBO computations were also performed at the same level of theory. In vitro antitumor activity of the mentioned complex on leukemia cell line, K562, was investigated using the MTT assay which surprisingly revealed the effective antitumor activity of the studied zinc complex. Interaction of this compound with biological macromolecules viz., CT-DNA and BSA was studied via different spectroscopic methods. The results of fluorescence experiment displayed that the metal complex binds to both macromolecules through hydrogen bond (H-bond) and van der Waals (vdW) forces. UV-Vis tests indicated a decline in the absorption spectra of CT-DNA/BSA in the presence of the compound. The interaction was further corroborated for CT-DNA via gel electrophoresis, CD spectroscopy and viscosity experiments and for BSA using CD spectroscopy. Furthermore, molecular docking simulation was done to evaluate the nature of interaction between the aforementioned zinc complex and CT-DNA/BSA. These results were in agreement with experimental findings and demonstrated that the main interaction is hydrogen bonding. The above type of investigations may provide a pathway through which zinc complexes join the anticancer category.[Figure: see text]The in-silico and in-vitro results confirm that the newly made [Zn(pyrr-ac)2] complex interacts with CT-DNA than BSA.Communicated by Ramaswamy H. Sarma.

Affinity binding of COVID-19 drug candidates (chloroquine/hydroxychloroquine) and serum albumin: Based on photochemistry and molecular docking

Chloroquine (CQ) and hydroxychloroquine (HCQ) show good efficacy in the treatment of SARS-CoV-2 in the early stage, while they are no longer recommended due to their side effects. As an important drug delivery carrier, serum albumin (SA) is closely related to the efficacy of drugs. Here, the affinity behaviour of chloroquine and hydroxychloroquine with two SA were investigated through the multispectral method of biochemistry and computer simulation. The results showed that the intrinsic emission of both SA was quenched by CQ and HCQ in a spontaneous exothermic entropy reduction static process, which relied mainly on hydrogen bonding and van der Waals forces. The lower binding constants suggested weak binding between the two drugs and SA, which might lead to differences in efficacy and possibly even to varying side effects. Binding site recognition demonstrated that CQ preferred to bind to the two sites of both SA, while HCQ tended to bind to site I of SA. The results of conformational studies demonstrated that CQ and HCQ could affect the structure of both SA by slightly increasing the α-helix content of SA. Finally, we combine the results from experimental start with molecular simulations to suggest drug modifications to guide the design of drugs. This work has important implications for guiding drug design improvements to select CQ derivatives with fewer side effects for the treatment of COVID-19.

Cytotoxic effects of Pd(II) complexes on cancer and normal cells: Their DNA & BSA adduct formation and theoretical approaches

Herein, we report the synthesis and characterisation of a series of Pd(II) complexes: Pd(TEEDA)Cl₂, C-1; [Pd(TEEDA)(OH₂)₂](NO₃)₂, C-2; [Pd(TEEDA)(l-cys)](NO₃)₂, C-3; [Pd(TEEDA)(NALC)], C-4; [Pd(TEEDA)(Meth)](NO₃)₂, C-5; and [Pd(TEEDA)(GSH)], C-6 (where TEEDA = N,N,N'-Triethylenediamine, l-cys = l-cysteine, NALC = N-acetyl-l-cysteine, Meth = dl-methionine and GSH = glutathione). UV-Vis spectroscopic characterisation was supported by TD-DFT theoretical simulation using Gaussian09 software. Different reactivity parameters were calculated from the energy difference between HOMO and LUMO of the complexes by DFT. The bonding mode of the labile ligands was confirmed by NBO analysis. Interaction of the complexes with DNA has been observed by gel electrophoresis experiment. DNA binding nature as well as binding constants of the complexes were measured with UV-Vis and fluorescence spectroscopic method. The binding nature of the complexes with DNA was confirmed by viscometric titration. Interaction of the complexes with BSA was investigated by UV-Vis and fluorescence titration method. Cytotoxic activity of the Pd(II) complexes was evaluated on A549 (lung carcinoma epithelial cells), HCT116(Colorectal Carcinoma) and HEK293 (Human embryonic kidney cells) cell lines. The ROS generation in the presence of the complexes was tested both on cancer cell lines A549 and HCT116 as well as human normal cell HEK293.

The Mechanism of Dynamic Interaction between Doxorubicin and Calf Thymus DNA at the Single-Molecule Level Based on Confocal Raman Spectroscopy

It is of great fundamental significance and practical application to understand the binding sites and dynamic process of the interaction between doxorubicin (DOX) and DNA molecules. Based on the Confocal Raman spectroscopy, the interaction between DOX and calf thymus DNA has been systemically investigated, and some meaningful findings have been found. DOX molecules can not only interact with all four bases of DNA molecules, i.e., adenine, thymine, cytosine, guanine, and phosphate, but also affect the DNA conformation. Meanwhile, the binding site of DOX and its derivatives such as daunorubicin and epirubicin is certain. Furthermore, the interaction between DOX and DNA molecules is a dynamic process since the intensities of each characteristic peaks of the base, e.g., adenine, cytosine, and phosphate, are all regularly changed with the interaction time. Finally, a dynamic mechanism model of the interaction between DOX and DNA molecules is proposed; that is, there are two kinds of interaction between DOX and DNA molecules: DOX-DNA acts to form a complex, and DOX-DOX acts to form a multimer. The two effects are competitive, as the former compresses DNA molecules, and the latter decompresses these DNA molecules. This work is helpful for accurately understanding and developing new drugs and pathways to improve and treat DOX-induced cytotoxicity and cardiotoxicity.