Decoding the conformational binding of drug mixtures on ovalbumin: An integrated multimodal network.

This research addresses the crucial necessity for a deeper understanding of the binding interactions between surfactants and proteins, with a specific focus on ovalbumin. Considering ovalbumin's role in diverse biochemical processes, it remains a subject of significant interest for drug discovery and design. To fill existing knowledge gaps, we investigated the binding interaction between dicloxacillin and cetyltrimethylammonium bromide (CTAB) on ovalbumin, employing a comprehensive approach that combines computational modeling with experimental validations. Using the ezPocket tool, the computational phase predicted ten relevant binding sites on ovalbumin's surface. The isobologram combination index (CI) heatmap strongly suggested a complex interplay of antagonistic and synergistic effects. Besides, a conformational drug-drug interaction network was proposed to explore the stability of the surfactant mixture within specific binding sites of ovalbumin, revealing a dynamic landscape of suggested antagonist effects. Experimental validations through UV-vis, Fluorescence, and circular dichroism (CD) spectroscopy further corroborated the computational findings, confirming the formation of stable complexes. Finally, this study not only advances our comprehension of ovalbumin's interactions with surfactants but also offers a multidimensional perspective and an advanced methodological framework for efficient therapeutic strategies, opening new avenues for future applications in drug development and applied biochemistry.

Trends in Nanoparticles for Leishmania Treatment: A Bibliometric and Network Analysis.

Leishmaniasis is a neglected tropical illness with a wide variety of clinical signs ranging from visceral to cutaneous symptoms, resulting in millions of new cases and thousands of fatalities reported annually. This article provides a bibliometric analysis of the main authors' contributions, institutions, and nations in terms of productivity, citations, and bibliographic linkages to the application of nanoparticles (NPs) for the treatment of leishmania. The study is based on a sample of 524 Scopus documents from 1991 to 2022. Utilising the Bibliometrix R-Tool version 4.0 and VOSviewer software, version 1.6.17 the analysis was developed. We identified crucial subjects associated with the application of NPs in the field of antileishmanial development (NPs and drug formulation for leishmaniasis treatment, animal models, and experiments). We selected research topics that were out of date and oversaturated. Simultaneously, we proposed developing subjects based on multiple analyses of the corpus of published scientific literature (title, abstract, and keywords). Finally, the technique used contributed to the development of a broader and more specific "big picture" of nanomedicine research in antileishmanial studies for future projects.

Killing Bacteria by Faradaic Processes through Nano-Hydroxyapatite/MoOx Platforms.

Following the secular idea of ″restitutio ad integrum″, regeneration is the pursued option to restore bones lost after a disease; accordingly, complementing antibiotic and regeneration capacity to bone grafts represents a great scientific success. This study is a framework proposal for understanding the antimicrobial effect of biocompatible nano-hydroxyapatite/MoOx (nano-HA/MoOx) platforms on the basis of their electroactive behavior. Through cyclic voltammetry and chronoamperometry measurements, the electron transference capacity of nano-HA and nano-HA/MoOx electrodes was determined in the presence of pathogenic organisms: Pseudomonas aeruginosa and Staphylococcus aureus. Faradaic processes were confirmed and related to the switch of MoO42-/PO43- groups in the original hexagonal nano-HA crystal lattice and to the extent of OH vacancies that act as electron acceptors. Microscopic analysis of bacteria's ultrastructure showed a disruptive effect on the cytoplasmic membrane upon direct contact with the materials, which is not evident in the presence of eukaryotic cells. Experiments support the existence of a type of extracellular electron transfer (EET) process that alters the function of the bacterial cytoplasmic membrane, accelerating their death. Our findings provide strong quantitative support for a drug-independent biocidal physical approach based on EET processes between microorganisms and phosphate ceramics that can be used to combat local orthopedic infections associated with implants.

Microfluidic Fabrication of Gadolinium-Doped Hydroxyapatite for Theragnostic Applications.

Among the several possible uses of nanoparticulated systems in biomedicine, their potential as theragnostic agents has received significant interest in recent times. In this work, we have taken advantage of the medical applications of Gadolinium as a contrast agent with the versatility and huge array of possibilities that microfluidics can help to create doped Hydroxyapatite nanoparticles with magnetic properties in an efficient and functional way. First, with the help of Computational Fluid Dynamics (CFD), we performed a complete and precise study of all the elements and phases of our device to guarantee that our microfluidic system worked in the laminar regime and was not affected by the presence of nanoparticles through the flow requisite that is essential to guarantee homogeneous diffusion between the elements or phases in play. Then the obtained biomaterials were physiochemically characterized by means of XRD, FE-SEM, EDX, confocal Raman microscopy, and FT-IR, confirming the successful incorporation of the lanthanide element Gadolinium in part of the Ca (II) binding sites. Finally, the magnetic characterization confirmed the paramagnetic behaviour of the nanoparticles, demonstrating that, with a simple and automatized system, it is possible to obtain advanced nanomaterials that can offer a promising and innovative solution in theragnostic applications.

Research on the Mechanism of Multi-Domain Coupling Centrifugal Electrostatic Blowing Flying Deposition.

The centrifugal electrostatic blowing process proposed in this paper solves the difficult continuous and stable deposition problem in the traditional centrifugal electrostatic spinning process. By establishing a flight deposition model of the centrifugal electrostatic spraying process, CFD is used to simulate and analyze the electrohydrodynamic effect of centrifugal jets, and the driving mechanism is explored. Subsequently, MATLAB is used to obtain the optimal solution conditions, and finally, the establishment of a two-dimensional flight trajectory model is completed and experimentally verified. In addition, the deposition model of the jet is established to clarify the flight trajectory under the multi-field coupling, the stable draft area of the jet is found according to this, and the optimal drafting station is clarified. This research provides new ideas and references for the exploration of the deposition mechanism of the centrifugal electrostatic blowing and electrostatic spinning process.

Role of nanostructured materials in hard tissue engineering.

The rise in the use of biomaterials in bone regeneration in the last decade has exponentially multiplied the number of publications, methods, and approaches to improve and optimize their functionalities and applications. In particular, biomimetic strategies based on the self-assembly of molecules to design, create and characterize nanostructured materials have played a very relevant role. We address this idea on four different but related points: self-setting bone cements based on calcium phosphate, as stable tissue support and regeneration induction; metallic prosthesis coatings for cell adhesion optimization and prevention of inflammatory response exacerbation; bio-adhesive hybrid materials as multiple drug delivery localized platforms and finally bio-inks. The effect of the physical, chemical, and biological properties of the newest biomedical devices on their bone tissue regenerative capacity are summarized, described, and analyzed in detail. The roles of experimental conditions, characterization methods and synthesis routes are emphasized. Finally, the future opportunities and challenges of nanostructured biomaterials with their advantages and shortcomings are proposed in order to forecast the future directions of this field of research.

NIR-Reflective and Hydrophobic Bio-Inspired Nano-Holed Configurations on Titanium Alloy.

Near-infrared (NIR) radiation plays an important role in guided external stimulus therapies; its application in bone-related treatments is becoming more and more frequent. Therefore, metallic biomaterials that exhibit properties activated by NIR are promising for further orthopedic procedures. In this work, we present an adapted electroforming approach to attain a biomorphic nano-holed TiO2 coating on Ti6Al4V alloy. Through a precise control of the anodization conditions, structures revealed the formation of localized nano-pores arranged in a periodic assembly. This specific organization provoked higher stability against thermal oxidation and precise hydrophobic wettability behavior according to Cassie-Baxter's model; both characteristics are a prerequisite to ensure a favorable biological response in an implantable structure for guided bone regeneration. In addition, the periodically arranged sub-wavelength-sized unit cell on the metallic-dielectric structure exhibits a peculiar optical response, which results in higher NIR reflectivity. Accordingly, we have proved that this effect enhances the efficiency of the scattering processes and provokes a significant improvement of light confinement producing a spontaneous NIR fluorescence emission. The combination of the already favorable mechanical and biocompatibility properties of Ti6Al4V, along with suitable thermal stability, wetting, and electro-optical behavior, opens a promising path toward strategic bone therapeutic procedures.

Modeling and experimental validation of covalent immobilization of Trametes maxima laccase on glyoxyl and MANA-Sepharose CL 4B supports, for the use in bioconversion of residual colorants.

Our novel strategy for the rational design of immobilized derivatives (RDID) is directed to predict the behavior of the protein immobilized derivative before its synthesis, by the usage of mathematic algorithms and bioinformatics tools. However, this approach needs to be validated for each target enzyme. The objective of this work was to validate the RDID strategy for covalent immobilization of the enzyme laccase from Trametes maxima MUCL 44155 on glyoxyl- and monoaminoethyl-N-aminoethyl (MANA)-Sepharose CL 4B supports. Protein surface clusters, more probable configurations of the protein-supports systems at immobilization pHs, immobilized enzyme activity, and protein load were predicted by RDID1.0 software. Afterward, immobilization was performed and predictions were experimentally confirmed. As a result, the laccase-MANA-Sepharose CL 4B immobilized derivative is better than laccase-glyoxyl-Sepharose CL 4B in predicted immobilized derivative activity (63.6% vs. 29.5%). Activity prediction was confirmed by an experimentally expressed enzymatic activity of 68%, using 2,6-dimethoxyphenol as substrate. Experimental maximum protein load matches the estimated value (11.2 ± 1.3 vs. 12.1 protein mg/support mL). The laccase-MANA-Sepharose CL 4B biocatalyst has a high specificity for the acid blue 62 colorant. The results obtained in this work suggest the possibility of using this biocatalyst for wastewater treatment.

Study of the interaction of folic acid-modified gold nanorods and fibrinogen through microfluidics: implications for protein adsorption, incorporation and viability of cancer cells.

Gold nanoparticles (GNPs) are an attractive nanomaterial for potential applications in therapy and diagnostics due to their capability to direct toward specific sites in the organism. However, when exposed to plasma, GNPs can interact with different biomolecules that form a dynamic nano-bio interface called a "protein corona" (PC). Remarkably, the PC could affect multiple biological processes, such as cell targeting and uptake, cytotoxicity, and nanoparticle (NP) clearance. The interaction of nanomaterials with plasmatic proteins has been widely studied under bulk conditions, however, under dynamic conditions, it has just recently been explored. Thus, to mimic a dynamic natural environment found in arteries and veins, microfluidic devices were used. In this work, gold nanorods (GNRs) were synthesized and conjugated with polyethylene glycol (PEG) to reduce their interaction with plasma proteins and increase their biocompatibility. Then, GNRs were functionalized with folic acid, a targeting ligand typically used to recognize tumor cells. The resulting nanosystem was exposed to fibrinogen (FB) to study the development and biological impact of PC formation through two strategies: bulk and laminar flow conditions. The obtained nanosystems were characterized by absorption spectrophotometry, DLS, laser Doppler microelectrophoresis, neutron activation analysis, circular dichroism spectroscopy and TEM. Finally, cell viability and cellular uptake assays were performed to study the influence of the PC on the cell viability and delivery of nanosystems.

Unraveling the Compositional and Molecular Features Involved in Lysozyme-Benzothiazole Derivative Interactions.

In this work we present a computational analysis together with experimental studies, focusing on the interaction between a benzothiazole (BTS) and lysozyme. Results obtained from isothermal titration calorimetry, UV-vis, and fluorescence were contrasted and complemented with molecular docking and machine learning techniques. The free energy values obtained both experimentally and theoretically showed excellent similarity. Calorimetry, UV-vis, and 3D/2D-lig-plot analysis revealed that the most relevant interactions between BTS and lysozyme are based on a predominance of aromatic, hydrophobic Van der Waals interactions, mainly aromatic edge-to-face (T-shaped) π-π stacking interactions between the benzene ring belonging to the 2-(methylthio)-benzothiazole moiety of BTS and the aromatic amino acid residue TRP108 of the lysozyme receptor. Next, conventional hydrogen bonding interactions contribute to the stability of the BTS-lysozyme coupling complex. In addition, mechanistic approaches performed using elastic network models revealed that the BTS ligand theoretically induces propagation of allosteric signals, suggesting non-physiological conformational flexing in large blocks of lysozyme affecting α-helices. Likewise, the BTS ligand interacts directly with allosteric residues, inducing perturbations in the conformational dynamics expressed as a moderate conformational softening in the α-helices H1, H2, and their corresponding ß-loop in the lysozyme receptor, in contrast to the unbound state of lysozyme.

Advanced Materials Based on Nanosized Hydroxyapatite.

The development of new materials based on hydroxyapatite has undergone a great evolution in recent decades due to technological advances and development of computational techniques. The focus of this review is the various attempts to improve new hydroxyapatite-based materials. First, we comment on the most used processing routes, highlighting their advantages and disadvantages. We will now focus on other routes, less common due to their specificity and/or recent development. We also include a block dedicated to the impact of computational techniques in the development of these new systems, including: QSAR, DFT, Finite Elements of Machine Learning. In the following part we focus on the most innovative applications of these materials, ranging from medicine to new disciplines such as catalysis, environment, filtration, or energy. The review concludes with an outlook for possible new research directions.

Corrigendum to: Computational Modeling of Environmental Co-exposure on Oil-Derived Hydrocarbon Overload by Using Substrate-Specific Transport Protein (TodX) with Graphene Nanostructures.

Due to an oversight of the publisher, Page no 2310 was missing in the published paper and page no 2311 repeated twice in the article entitled "Computational Modeling of Environmental Co-exposure on Oil-Derived Hydrocarbon Overload by Using Substrate-Specific Transport Protein (TodX) with Graphene Nanostructures, 2020, 20(25), 2308-2325 [1]. The page no 2310 is added in the article and the repetition of page no 2311 is corrected. The original article can be found online at https://doi.org/10.2174/1568026620666200820145412.

New Mechanistic Insights on Carbon Nanotubes' Nanotoxicity Using Isolated Submitochondrial Particles, Molecular Docking, and Nano-QSTR Approaches.

Single-walled carbon nanotubes can induce mitochondrial F0F1-ATPase nanotoxicity through inhibition. To completely characterize the mechanistic effect triggering the toxicity, we have developed a new approach based on the combination of experimental and computational study, since the use of only one or few techniques may not fully describe the phenomena. To this end, the in vitro inhibition responses in submitochondrial particles (SMP) was combined with docking, elastic network models, fractal surface analysis, and Nano-QSTR models. In vitro studies suggest that inhibition responses in SMP of F0F1-ATPase enzyme were strongly dependent on the concentration assay (from 3 to 5 µg/mL) for both pristine and COOH single-walled carbon nanotubes types (SWCNT). Besides, both SWCNTs show an interaction inhibition pattern mimicking the oligomycin A (the specific mitochondria F0F1-ATPase inhibitor blocking the c-ring F0 subunit). Performed docking studies denote the best crystallography binding pose obtained for the docking complexes based on the free energy of binding (FEB) fit well with the in vitro evidence from the thermodynamics point of view, following an affinity order such as: FEB (oligomycin A/F0-ATPase complex) = -9.8 kcal/mol > FEB (SWCNT-COOH/F0-ATPase complex) = -6.8 kcal/mol ~ FEB (SWCNT-pristine complex) = -5.9 kcal/mol, with predominance of van der Waals hydrophobic nano-interactions with key F0-ATPase binding site residues (Phe 55 and Phe 64). Elastic network models and fractal surface analysis were performed to study conformational perturbations induced by SWCNT. Our results suggest that interaction may be triggering abnormal allosteric responses and signals propagation in the inter-residue network, which could affect the substrate recognition ligand geometrical specificity of the F0F1-ATPase enzyme in order (SWCNT-pristine > SWCNT-COOH). In addition, Nano-QSTR models have been developed to predict toxicity induced by both SWCNTs, using results of in vitro and docking studies. Results show that this method may be used for the fast prediction of the nanotoxicity induced by SWCNT, avoiding time- and money-consuming techniques. Overall, the obtained results may open new avenues toward to the better understanding and prediction of new nanotoxicity mechanisms, rational drug design-based nanotechnology, and potential biomedical application in precision nanomedicine.

Targeting Beta-Blocker Drug-Drug Interactions with Fibrinogen Blood Plasma Protein: A Computational and Experimental Study.

In this work, one of the most prevalent polypharmacology drug-drug interaction events that occurs between two widely used beta-blocker drugs-i.e., acebutolol and propranolol-with the most abundant blood plasma fibrinogen protein was evaluated. Towards that end, molecular docking and Density Functional Theory (DFT) calculations were used as complementary tools. A fibrinogen crystallographic validation for the three best ranked binding-sites shows 100% of conformationally favored residues with total absence of restricted flexibility. From those three sites, results on both the binding-site druggability and ligand transport analysis-based free energy trajectories pointed out the most preferred biophysical environment site for drug-drug interactions. Furthermore, the total affinity for the stabilization of the drug-drug complexes was mostly influenced by steric energy contributions, based mainly on multiple hydrophobic contacts with critical residues (THR22: P and SER50: Q) in such best-ranked site. Additionally, the DFT calculations revealed that the beta-blocker drug-drug complexes have a spontaneous thermodynamic stabilization following the same affinity order obtained in the docking simulations, without covalent-bond formation between both interacting beta-blockers in the best-ranked site. Lastly, experimental ultrasound density and velocity measurements were performed and allowed us to validate and corroborate the computational obtained results.

Computational Modeling of Environmental Co-exposure on Oil-Derived Hydrocarbon Overload by Using Substrate-Specific Transport Protein (TodX) with Graphene Nanostructures.

BACKGROUND: Bioremediation is a biotechnology field that uses living organisms to remove contaminants from soil and water; therefore, they could be used to treat oil spills from the environment. METHODS: Herein, we present a new mechanistic approach combining Molecular Docking Simulation and Density Functional Theory to modeling the bioremediation-based nanointeractions of a heterogeneous mixture of oil-derived hydrocarbons by using pristine and oxidized graphene nanostructures and the substrate-specific transport protein (TodX) from Pseudomonas putida. RESULTS: The theoretical evidences pointing that the binding interactions are mainly based on noncovalent bonds characteristic of physical adsorption mechanism mimicking the "Trojan-horse effect". CONCLUSION: These results open new horizons to improve bioremediation strategies in over-saturation conditions against oil-spills and expanding the use of nanotechnologies in the context of environmental modeling health and safety.

Soft Actuated Hybrid Hydrogel with Bioinspired Complexity to Control Mechanical Flexure Behavior for Tissue Engineering.

Hydrogels exhibit excellent properties that enable them as nanostructured scaffolds for soft tissue engineering. However, single-component hydrogels have significant limitations due to the low versatility of the single component. To achieve this goal, we have designed and characterized different multi-component hydrogels composed of gelatin, alginate, hydroxyapatite, and a protein (BSA and fibrinogen). First, we describe the surface morphology of the samples and the main characteristics of the physiological interplay by using fourier transform infrared (FT-IR), and confocal Raman microscopy. Then, their degradation and swelling were studied and mechanical properties were determined by rheology measurements. Experimental data were carefully collected and quantitatively analyzed by developing specific approaches and different theoretical models to determining the most important parameters. Finally, we determine how the nanoscale of the system influences its macroscopic properties and characterize the extent to which degree each component maintains its own functionality, demonstrating that with the optimal components, in the right proportion, multifunctional hydrogels can be developed.

Mapping the underlying mechanisms of fibrinogen benzothiazole drug interactions using computational and experimental approaches.

Three-dimensional conformational crystallographic binding-modes are of paramount importance to understand the docking mechanism of protein-ligand interactions and to identify potential "leading drugs" conformers towards rational drugs-design. Herein, we present an integrated computational-experimental study tackling the problem of multiple binding modes among the ligand 3-(2-Benzothiazolylthio)-propane sulfonic acid (BTS) and the fibrinogen receptor (E-region). Based on molecular docking simulations, we found that the free energy of binding values for nine of different BTS-docking complexes (i.e., BTS-pose_1-9) were very close. We have also identified a docking-mechanism of BTS-interaction mainly based on non-covalent hydrophobic interactions with H-bond contacts stabilizing the fibrinogen-BTS docking complexes. Interestingly, the different BTS-poses_1-9 were found to be able to block the fibrinogen binding site (E-region) by inducing local perturbations in effector and allosteric residues, reducing the degree of collectivity in its flexibility normal modes. As such, we theoretically suggest that the BTS-binding modes can significantly affect the physiological condition of the unoccupied fibrinogen protein structure by bringing global and local perturbations in the frequency domain spectra. The proposed theoretical mechanisms, the interactions involved and the conformational changes suggested, were further corroborated by different experimental techniques such as isothermal titration calorimetry (ITC), zeta potential, UV-vis, fluorescence and small angle X-ray scattering (SAXS). The combined results shall open new avenues towards the application of complex supra-molecular information in rational drugs-design.

Self-fluorescent antibiotic MoOx-hydroxyapatite: a nano-theranostic platform for bone infection therapies.

Nowadays, the repair of large-size bone defects represents a huge medical challenge. A line of attack is the construction of advanced biomaterials having multifunctional properties. In this work, we show the creation of biocompatible MoOx-hydroxyapatite nanoparticles (nano-HA/MoOx) that simultaneously exhibit self-activated fluorescence and antibiotic skills. Along this text, we demonstrate that the insertion of molybdenum, an essential trace element, into the non-stoichiometric calcium deficient hydroxyapatite lattice generates intrinsic electronic point defects that exacerbate its epifluorescence blue emission and provokes new red emissions, preserving, always, its bioactivity. Furthermore, these point defects, acting as electron acceptors, stimulate the materials' biological redox status and promote the death of pathogen microorganisms after their direct contact. A putative mechanism, by which bacteria lose electrons from their metabolic circuit that alter the function of their cytoplasmic membrane and potentially die, agrees with our results. Our findings highlight the importance of tuning the electronic communications between biomaterial interfaces and biological units, and support the use of self-fluorescent MoOx-hydroxyapatite nanoparticles as fundamental building blocks for new real-time imaging platforms against bone infection.

Structural and energetic evolution of fibrinogen toward to the betablocker interactions.

We present a computational analysis coupled with experimental studies, focusing on the binding-interaction between beta-adrenoreceptor blocking agents (acebutolol and propranolol) with fibrinogen protein (E-region). Herein, computational modeling on structural validation and flexibility properties of fibrinogen E-region showed that the E-region interacting residues, which form the funnel-shaped hydrophobic cavity for ligand-binding, can be efficiently modeled. The obtained free energy of binding (FEB) values for the docking complexes, namely acebutolol/fibrinogen E-region and propranolol/fibrinogen E-region, were very close and amounted to - 6.9 kcal/mol and - 6.8 kcal/mol, respectively. They were supported by a high binding-accuracy (R.M.S.D < 2 Å) for the best crystallographic binding-poses in both cases. In this regard, we identify a docking-mechanism of interaction for the propranolol and acebutolol mainly based on non-covalent hydrophobic contacts with the fibrinogen E-region binding-site. Besides, the beta-adrenoreceptor blocking agents are able to induce local perturbations affecting particularly the fibrinogen E-region allosteric residues linked to significant changes in the inter-residue communication and flexibility properties of residue network. In this sense, we show that the key biophysical parameters like frequency and collectivity degree may be compromised in different ways by the interaction with acebutolol and propranolol. Isothermal titration calorimetry, zeta potential and small angle X-ray scattering (SAXS) measurements were performed to complete and corroborate computational analysis. The combined experimental results point out that acebutolol acts to a lesser extent to fibrinogen structure than propranolol.

Noble microfluidic system for bioceramic nanoparticles engineering.

Bioceramic nanoparticles have many potential applications within the biomedical device industry. However, these applications demand a precise control of their sizes, shapes and morphology which play a main role in most properties. In this work, we report a new route for the synthesis of hydroxyapatite nanoparticles using a microfluidic device. The process is carried out by continuous laminar flow through the device. The obtained nanoparticles have showed same properties (composition, length, orientation, roughness) than those produced by conventional methods, however, our device can afford to fine tune the structure via simple engineering, i.e., produce nanoparticles of different size only by varying the flow velocity. In addition to the efficiency and novelty of this system, the optimization of personnel costs makes it very profitable economically.