Mechanistic interaction studies of synthesized ZIF-8 nanoparticles with bovine serum albumin using spectroscopic and molecular docking approaches

Bovine serum albumin-coated ZIF-8 nanoparticles to enhance antitumor and antimetastatic activity of methotrexate: in vitro and in vivo study

In this study, a bovine serum albumin-decorated zeolitic imidazolate framework (ZIF-8@BSA) was used to enhance the anticancer and antimetastatic properties of methotrexate. SEM, DLS, FT-IR, and XRD confirmed the physicochemical suitability of the developed nanoparticles. According to the SEM analysis, the mean size of ZIF-8 nanoparticles was 68.5 ± 13.31 nm. The loading capacity and encapsulation efficiency of MTX@ZIF-8@BSA were 28.77 ± 2.54% and 96.3 ± 0.67%, respectively. According to the in vitro hemolysis test, MTX@ZIF-8@BSA showed excellent blood compatibility. MTX@ZIF-8@BSA exhibited pH sensitivity, releasing more MTX at pH 5.4 (1.73 times) than at pH 7.4. The IC50 value of MTX@ZIF-8@BSA on 4T1 cells was 32.7 ± 7.3 µg/mL after 48 h of treatment, outperforming compared to free MTX with an IC50 value of 53.3 ± 3.7 µg/mL. Treatment with MTX@ZIF-8@BSA resulted in superior tumor growth suppression in tumor-bearing mice than free MTX. Furthermore, based on histopathology tests, MTX@ZIF-8@BSA reduced the metastasis in lung and liver tissues. While there was not any noticeable toxicity in the vital organs of MTX@ZIF-8@BSA-receiving mice, free methotrexate resulted in severe toxicity in the kidneys and liver. According to the preliminary in vitro and in vivo findings, MTX@ZIF-8@BSA presents an attractive drug delivery system candidate for breast cancer due to its enhanced antitumor efficacy and lower toxicity.

Analytical Aspects of ANSA-BSA Association: A Thermodynamic and Conformational Approach

Many studies have demonstrated the manner in which ANS interacts with bovine serum albumin (BSA), although they are limited by the extremely low solubility of dye. The present study demonstrates the binding of ANSA dye with BSA, and since this dye can easily replace ANS, it not only simplifies research but also improves sensor accuracy for serum albumin. A combination of calorimetry and spectroscopy has been employed to establish the thermodynamic signatures associated with the interaction of ANSA with the protein and the consequent conformational changes in the latter. The results of differential scanning calorimetry reveal that when the concentration of ANSA in solution is increased, the thermal stability of the protein increases substantially. The fluorescence data demonstrated a decrease in the binding affinity of ANSA with the protein when pH increased but was unable to identify a change in the mode of interaction of the ligand. ITC has demonstrated that the mode of interaction between ANSA and the protein varies from a single set of binding sites at pH 5 and 7.4 to a sequential binding site at pH 10, emphasizing the potential relevance of protein conformational changes. TCSPC experiments suggested a dynamic type in the presence of ANSA. Molecular docking studies suggest that ANSA molecules are able to find ionic centers in the hydrophobic pockets of BSA. The findings further imply that given its ease of use in experiments, ANSA may be a useful probe for tracking the presence of serum albumin and partially folded protein states.

The Surface of Colloidal Metal-Organic Framework Nanoparticles Revealed by Vibrational Sum Frequency Scattering Spectroscopy

Solvation shells strongly influence the interfacial chemistry of colloidal systems, from the activity of proteins to the colloidal stability and catalysis of nanoparticles. Despite their fundamental and practical importance, solvation shells have remained largely undetected by spectroscopy. Furthermore, their ability to assemble at complex but realistic interfaces with heterogeneous and rough surfaces remains an open question. Here, we apply vibrational sum frequency scattering spectroscopy (VSFSS), an interface-specific technique, to colloidal nanocrystals with porous metal-organic frameworks (MOFs) as a case study. Due to the porous nature of the solvent-particle boundary, MOF particles challenge conventional models of colloidal and interfacial chemistry. Their multiweek colloidal stability in the absence of conventional surface ligands suggests that stability may arise in part from solvation forces. Spectra of colloidally stable Zn(2-methylimidazolate)2 (ZIF-8) in polar solvents indicate the presence of ordered solvation shells, solvent-metal binding, and spontaneous ordering of organic bridging linkers within the MOF. These findings help explain the unexpected colloidal stability of MOF colloids, while providing a roadmap for applying VSFSS to wide-ranging colloidal nanocrystals in general.

Design, Synthesis, Biological Evaluation and in Silico Studies of Curcumin Pyrrole Conjugates

Curcumin conjugated heterocyclic compounds are potent candidates with drug likeness against various bacterial pathogens. A set of curcumin-based pyrrole conjugates (CPs) were synthesized and characterized by FT-IR, 1H and 13C NMR and HR-MS techniques. The results of free radical scavenging activity of the synthesized CPs, evaluated by FRAP and CUPRAC assays, showed the potency of these compounds as effective antioxidants. CP3 exhibits the highest antioxidant activity amongst the CPs. The bactericidal efficacy of CPs was screened against ESKAP bacterial pathogens, and CPs were found to possess better antibacterial property than curcumin, specifically against staphylococcus aureus bacteria. In addition, serum albumin (BSA and HSA) binding interaction of these CPs were determined by UV-visible and fluorescence spectrophotometric techniques. In-silico molecular docking study was performed to determine the binding patterns of molecular targets against Staphylococcus aureus tyrosyl tRNA synthetase, and serum albumin proteins. The structure-activity relationship showed that the presence of multiple phenolic hydroxyl groups, and electron withdrawing groups on the structure of CP molecule, enhances its antioxidant and antibacterial activity, respectively.

Metal-Organic Framework Induced Stabilization of Proteins in Polymeric Nanoparticles

Developing protein confinement platforms is an attractive research area that not only promotes protein delivery but also can result in artificial environment mimicking of the cellular one, impacting both the controlled release of proteins and the fundamental protein biophysics. Polymeric nanoparticles (PNPs) are attractive platforms to confine proteins due to their superior biocompatibility, low cytotoxicity, and controllable release under external stimuli. However, loading proteins into PNPs can be challenging due to the potential protein structural perturbation upon contacting the interior of PNPs. In this work, we developed a novel approach to encapsulate proteins in PNPs with the assistance of the zeolitic imidazolate framework (ZIF). Here, ZIF offers an additional protection layer to the target protein by forming the protein@ZIF composite via aqueous-phase cocrystallization. We demonstrated our platform using a model protein, lysozyme, and a widely studied PNP composed of poly(ethylene glycol)-poly(lactic-co-glycolic acid) (PEG-PLGA). A comprehensive study via standard loading and release tests as well as various spectroscopic techniques was carried out on lysozyme loaded onto PEG-PLGA with and without ZIF protection. As compared with the direct protein encapsulation, an additional layer with ZIF prior to loading offered enhanced loading capacity, reduced leaching, especially in the initial stage, led to slower release kinetics, and reduced secondary structural perturbation. Meanwhile, the function, cytotoxicity, and cellular uptake of proteins encapsulated within the ZIF-bound systems are decent. Our results demonstrated the use of ZIF in assisting in protein encapsulation in PNPs and established the basis for developing more sophisticated protein encapsulation platforms using a combination of materials of diverse molecular architectures and disciplines. As such, we anticipate that the protein-encapsulated ZIF systems will serve as future polymer protein confinement and delivery platforms for both fundamental biophysics and biochemistry research and biomedical applications where protein delivery is needed to support therapeutics and/or nutrients.

Enhancing apoptosis-mediated anticancer activity of evodiamine through protein-based nanoparticles in breast cancer cells

In the cutting-edge era of developing precision therapeutics, nanoparticles have emerged as a potent drug delivery system. Altering the size of poorly water-soluble drugs to nanoscale could confer change in their physical properties, including enhanced water solubility and bioavailability. Evodiamine (EVO), a natural indolequinone alkaloid extract from Evodia rutaecarpa, has shown several important pharmacological applications, anti-cancer being one of them. Protein-based nano-drug delivery systems have gained the interest of researchers due to their better biocompatibility, biodegradability, non-immunogenicity and non-toxicity. In the present study, EVO encapsulated BSA nanoparticles (ENPs) were synthesized and characterized, which were nanoscale-sized (~ 150 nm), monodispersed, spherical shaped, and showed high entrapment efficiency (~ 86%) and controlled drug release. The in-vitro anti-cancer activity of ENPs on human breast cancer cells was dose- and time-dependent. The apoptotic molecular mechanism investigated using FACS, qRT-PCR, and western blotting analysis, revealed increased expression of p53 and Bax and decreased expression of Bcl-2. Biological studies demonstrated comparatively more efficient and targeted delivery of ENPs than pure EVO. The comprehensive physiochemical characterization and in-vitro validation collectively pinpoint ENPs as a promising avenue for harnessing the therapeutic potential of the natural anti-cancer compound EVO. The findings indicate improved cytotoxicity, positioning ENPs as a propitious strategy for advancing breast cancer treatment.

Molecular spectroscopic and docking analysis of the interaction of fluorescent thiadicarbocyanine dye with biomolecule bovine serum albumin

Binding studies of the water-soluble thiadicarbocyanine dye 3,3'-diethylthiadicarbocyanine acetate (DTC) with bovine serum albumin (BSA) were examined under physiological conditions using spectroscopic techniques like fluorescence, UV-Visible, circular dichroism (CD), FT-IR and molecular docking methods. Compiled experimental results envisage that DTC quench the fluorescence intensity of BSA. The increasing binding constants (K) were found to be in the order of 103 Mol-1 as a function of temperature, as calculated from the fluorescence quenching data. The quenching mechanism, thermodynamic parameters (ΔH0, ΔS0 and ΔG0) and the number of binding sites have been explored. CD values showed that the secondary structure of the BSA has been altered upon binding to DTC. Displacement experiments were carried out with different site probes to find out the binding site of DTC on BSA and it was found that binding interaction at site II of sub-domain IIIA. The interference of common metal ions on the interaction of DTC with BSA has also been studied. The experimental data exhibit that DTC interacts with BSA by hydrophobic forces. The experimental findings from BSA binding studies were validated by using in silico molecular docking technique. The results of the investigations were accurately supported by studies on molecular docking. The optimal shape of the molecular probe demonstrated the affinity as a free binding energy release of -7.37 Kcal/mol. The present research report endeavors to the approachable nature of water-soluble DTC dye and paves way for targeted biological interactions.Communicated by Ramaswamy H. Sarma.

Understanding and controlling the nucleation and growth of metal-organic frameworks

Metal-organic frameworks offer a diverse landscape of building blocks to design high performance materials for implications in almost every major industry. With this diversity stems complex crystallization mechanisms with various pathways and intermediates. Crystallization studies have been key to the advancement of countless biological and synthetic systems, with MOFs being no exception. This review provides an overview of the current theories and fundamental chemistry used to decipher MOF crystallization. We then discuss how intrinsic and extrinsic synthetic parameters can be used as tools to modulate the crystallization pathway to produce MOF crystals with finely tuned physical and chemical properties. Experimental and computational methods are provided to guide the probing of MOF crystal formation on the molecular and bulk scale. Lastly, we summarize the recent major advances in the field and our outlook on the exciting future of MOF crystallization.

Molecular Modeling Insights into Metal-Organic Frameworks (MOFs) as a Potential Matrix for Immobilization of Lipase: An In Silico Study

CRL is a highly versatile enzyme that finds extensive utility in numerous industries, which is attributed to its selectivity and catalytic efficiency, which have been impeded by the impracticality of its implementation, leading to a loss of native catalytic activity and non-reusability. Enzyme immobilization is a necessary step for enabling its reuse, and it provides methods for regulating the biocatalyst's functional efficacy in a synthetic setting. MOFs represent a novel category of porous materials possessing distinct superlative features that make MOFs an optimal host matrix for developing enzyme-MOF composites. In this study, we employed molecular modeling approaches, for instance, molecular docking and MD simulation, to explore the interactions between CRL and a specific MOF, ZIF-8. The present study involved conducting secondary structural analysis and homology modeling of CRL, followed by docking ZIF-8 with CRL. The results of the molecular docking analysis indicate that ZIF-8 was situated within the active site pocket of CRL, where it formed hydrogen bonds with Val-81, Phe-87, Ser-91, Asp-231, Thr-132, Lue-297, Phe-296, Phe-344, Thr-347, and Ser-450. The MD simulation analysis revealed that the CRL and ZIF-8 docked complex exhibited stability over the entire simulation period, and all interactions presented in the initial docked complex were maintained throughout the simulation. The findings derived from this investigation could promote comprehension of the molecular mechanisms underlying the interaction between CRL and ZIF-8 as well as the development of immobilized CRL for diverse industrial purposes.

Preservation of Proteins in Human Plasma through Metal-Organic Framework Encapsulation

Traditional cold chain systems of collection, transportation, and storage of biofluid specimens for eventual analysis pose a huge financial and environmental burden. These systems are impractical in pre-hospital and resource-limited settings, where refrigeration and electricity are not reliable or even available. Here, we develop an innovative technology using metal-organic frameworks (MOFs), a novel class of organic-inorganic hybrids with high thermal stability, as encapsulates for preserving the integrity of protein biomarkers in biofluids under ambient or non-refrigerated storage conditions. We encapsulate prostate-specific antigen (PSA) in whole patient plasma using hydrophilic zeolitic imidazolate framework-90 (ZIF-90) for preservation at 40 °C for 4 weeks and eventual on-demand reconstitution for antibody-based assays with recovery above 95% compared to storage at -20 °C. Without ZIF-90 encapsulation, only 10-30% of the PSA immunoactivity remained. Furthermore, we demonstrate encapsulation of multiple cancer biomarker proteins in whole patient plasma using ZIF-8 or ZIF-90 encapsulants for eventual on-demand reconstitution and analysis after 1 week at 40 °C. Overall, MOF encapsulation of patient biofluids is important as climate change may be affecting the stability and increase costs of maintaining biospecimen cold chain custody for the collection, transportation, and storage of biospecimens prior to analysis or for biobanking regardless of any countries' affluence.

pH-Responsible Doxorubicin-Loaded Fe3O4@CaCO3 Nanocomposites for Cancer Treatment

A magnetic nanocomposite (MNC) is an integrated nanoplatform that combines a set of functions of two types of materials. A successful combination can give rise to a completely new material with unique physical, chemical, and biological properties. The magnetic core of MNC provides the possibility of magnetic resonance or magnetic particle imaging, magnetic field-influenced targeted delivery, hyperthermia, and other outstanding applications. Recently, MNC gained attention for external magnetic field-guided specific delivery to cancer tissue. Further, drug loading enhancement, construction stability, and biocompatibility improvement may lead to high progress in the area. Herein, the novel method for nanoscale Fe3O4@CaCO3 composites synthesis was proposed. For the procedure, oleic acid-modified Fe3O4 nanoparticles were coated with porous CaCO3 using an ion coprecipitation technique. PEG-2000, Tween 20, and DMEM cell media was successfully used as a stabilization agent and template for Fe3O4@CaCO3 synthesis. Transmission electron microscopy (TEM), Fourier transform infrared (FTIR) spectroscopy, and dynamic light scattering (DLS) data were used for the Fe3O4@CaCO3 MNC’s characterization. To improve the nanocomposite properties, the concentration of the magnetic core was varied, yielding optimal size, polydispersity, and aggregation ability. The resulting Fe3O4@CaCO3 had a size of 135 nm with narrow size distributions, which is suitable for biomedical applications. The stability experiment in various pH, cell media, and fetal bovine serum was also evaluated. The material showed low cytotoxicity and high biocompatibility. An excellent anticancer drug doxorubicin (DOX) loading of up to 1900 µg/mg (DOX/MNC) was demonstrated. The Fe3O4@CaCO3/DOX displayed high stability at neutral pH and efficient acid-responsive drug release. The series of DOX-loaded Fe3O4@CaCO3 MNCs indicated effective inhibition of Hela and MCF-7 cell lines, and the IC 50 values were calculated. Moreover, 1.5 μg of the DOX-loaded Fe3O4@CaCO3 nanocomposite is sufficient to inhibit 50% of Hela cells, which shows a high prospect for cancer treatment. The stability experiments for DOX-loaded Fe3O4@CaCO3 in human serum albumin solution indicated the drug release due to the formation of a protein corona. The presented experiment showed the “pitfalls” of DOX-loaded nanocomposites and provided step-by-step guidance on efficient, smart, anticancer nanoconstruction fabrication. Thus, the Fe3O4@CaCO3 nanoplatform exhibits good performance in the cancer treatment area.

Biodegradable Microneedle Array-Mediated Transdermal Delivery of Dimethyloxalylglycine-Functionalized Zeolitic Imidazolate Framework-8 Nanoparticles for Bacteria-Infected Wound Treatment

Bacteria-infected skin wounds caused by external injuries remain a serious challenge to the whole society. Wound healing dressings, with excellent antibacterial activities and potent regeneration capability, are increasingly needed clinically. Here, we reported a novel functional microneedle (MN) array comprising methacrylated hyaluronic acid (MeHA) embedded with pH-responsive functionalized zeolitic imidazolate framework-8 (ZIF-8) nanoparticles to treat bacteria-infected cutaneous wounds. Antibacterial activity was introduced into Zn-ZIF-8 to achieve sterilization through releasing Zn ions, as well as increased angiogenesis by dimethyloxalylglycine (DMOG) molecules that were distributed within its framework. Furthermore, biodegradable MeHA was chosen as a substrate material carrier to fabricate DMOG@ZIF-8 MN arrays. By such design, DMOG@ZIF-8 MN arrays would not only exhibit excellent antibacterial activity against pathogenic bacteria but also enhance angiogenesis within wound bed by upregulating the expression of HIF-1α, leading to a significant therapeutic efficiency on bacteria-infected cutaneous wound healing. Based on these results, we conclude that this new treatment strategy can provide a promising alternative for accelerating infected wound healing via effective antibacterial activity and ameliorative angiogenesis.

DeepBLI: A Transferable Multichannel Model for Detecting β-Lactamase-Inhibitor Interaction

Pathogens producing β-lactamase pose a great challenge to antibiotic-resistant infection treatment; thus, it is urgent to discover novel β-lactamase inhibitors for drug development. Conventional high-throughput screening is very costly, and structure-based virtual screening is limited with mechanisms. In this study, we construct a novel multichannel deep neural network (DeepBLI) for β-lactamase inhibitor screening, pretrained with a label reversal KIBA data set and fine-tuned on β-lactamase-inhibitor pairs from BindingDB. First, the pairs of encoders (Conv and Att) fuse the information spatially and sequentially for both enzymes and inhibitors. Then, a co-attention module creates the connection between the inhibitor and enzyme embeddings. Finally, multichannel outputs fuse with an element-wise product and then are fed into 3-layer fully connected networks to predict interactions. Comparing the state-of-the-art methods, DeepBLI yields an AUROC of 0.9240 and an AUPRC of 0.9715, which indicates that it can identify new β-lactamase-inhibitor interactions. To demonstrate its prediction ability, an application of DeepBLI is described to screen potential inhibitor compounds for metallo-β-lactamase AIM-1 and repurpose rottlerin for four classes of β-lactamase targets, showing the possibility of being a broad-spectrum inhibitor. DeepBLI provides an effective way for antibacterial drug development, contributing to antibiotic-resistant therapeutics.