Chemically Modified Carbon Nanohorns as Nanovectors of the Cisplatin Drug: A Molecular Dynamics Study

Fluorescent Nanocarbons: From Synthesis and Structure to Cancer Imaging and Therapy

Nanocarbons are emerging at the forefront of nanoscience, with diverse carbon nanoforms emerging over the past two decades. Early cancer diagnosis and therapy, driven by advanced chemistry techniques, play a pivotal role in mitigating mortality rates associated with cancer. Nanocarbons, with an attractive combination of well-defined architectures, biocompatibility, and nanoscale dimension, offer an incredibly versatile platform for cancer imaging and therapy. This paper aims to review the underlying principles regarding the controllable synthesis, fluorescence origins, cellular toxicity, and surface functionalization routes of several classes of nanocarbons: carbon nanodots, nanodiamonds, carbon nanoonions, and carbon nanohorns. This review also highlights recent breakthroughs regarding the green synthesis of different nanocarbons from renewable sources. It also presents a comprehensive and unified overview of the latest cancer-related applications of nanocarbons and how they can be designed to interface with biological systems and work as cancer diagnostics and therapeutic tools. The commercial status for large-scale manufacturing of nanocarbons is also presented. Finally, it proposes future research opportunities aimed at engendering modifiable and high-performance nanocarbons for emerging applications across medical industries. This work is envisioned as a cornerstone to guide interdisciplinary teams in crafting fluorescent nanocarbons with tailored attributes that can revolutionize cancer diagnostics and therapy.

Metal-Organic Frameworks for Cisplatin Delivery to Cancer Cells: A Molecular Dynamics Simulation

Metal-organic frameworks (MOFs) are utilized as nanocarriers to enhance the efficiency of chemotherapy drugs, including cisplatin, which exhibit limitations such as side effects and resistance mechanisms. To evaluate the role of MOFs, we employed a molecular dynamics simulation, which, unlike other experiments, is cost-effective, less dangerous, and provides accurate results. Furthermore, we conducted molecular docking simulations to understand the interaction between cisplatin and MOF, as well as their internal interactions and how they bind to each other. Cisplatin and MOF molecules were parametrized using the Avogadro software and x2top command in GROMACS 5.1.2 and optimized by CP2K software; the Charmm-GUI site parametrized the cell cancer membrane. Three molecular dynamics simulations were conducted in four stages at various pHs, followed by simulated umbrella sampling. The simulations analyzed the pH responsiveness, total energy, Gibbs free energy, gyration radius, radial distribution function (RDF), solvent accessible surface area, and nanoparticles' toxicity. Results demonstrated that a neutral pH level (7.4) has greater adsorption and interaction compared to acidic pH values (6.4 and 5.4) because it displays the highest total energy (-17.1 kJ/mol), the highest RDF value (6.66), and the shortest distance (0.51 nm). Furthermore, the combination of cisplatin and MOFs displayed increased penetration compared to that of their individual forms. This study highlights the suitability of MOFs as nanocarriers and identifies the optimal pH values for desirable outcomes. Thus, it provides future studies with appropriate data to conduct their experiments in assessing MOFs.

Molecular docking, simulations of animal peptides against the envelope protein of Dengue virus

Peptides are biologically active, small molecules with high specificity in its mode of action that can be effective at nanomolar concentrations. Peptide-based antiviral medicines have already been licensed and used to treat human immunodeficiency virus (HIV), influenza virus and hepatitis C virus. So far, no peptide drug has been approved for antiviral treatment against Dengue virus, and many are under clinical trials. Therefore, developing a reasonable peptide against the Dengue virus Envelope protein structure will be a successful strategy for treating Dengue. Hence, we investigated protein-protein docking interactions between 215 peptides retrieved from the AVP database against the envelope protein using Cluspro and HADDOCK followed by the evaluation of their allegenicity, toxicity and physicochemical characteristics investigation. Further validation of the protein-peptide complexes was performed with Molecular dynamics simulations and Molecular Mechanics Poisson-Boltzmann surface area (MMPBSA) analysis on the hit inhibitors. This study revealed that Indolicidin (-75.026 ± 1.54 KJ/mol) and Human Neutrophil peptide-1 (-71.6551 ± 2.112 KJ/mol) shows higher negative ΔG binding implicating their relative stabilization in the protein-peptide interactions during 100 ns of dynamic simulations. Also, both the peptides exhibited desirable physicochemical properties and were nonallergenic. Hence, we further aim to test these peptides by in vitro and in vivo studies to confirm their efficacy against Dengue virus.Communicated by Ramaswamy H. Sarma.

Unveiling the Releasing Processes of Pt(II)-Based Anticancer Drugs from Oxidized Carbon Nanohorn: An In Silico Study

About half of all cancer chemotherapies currently applied involve medication with the three worldwide approved Pt(II)-based drugs, cisplatin (cddp), carboplatin (cpx), and oxaliplatin (oxa), due to their notable antitumor activity for several cancers. However, this wide application is accompanied by severe side effects, such as nephrotoxicity, myelosuppression, and neurotoxicity, as a result of their low bioavailability and selectivity for cancer cells. To mitigate these drawbacks, the use of chemically functionalized carbon nanohorns (CNH) as nanocarriers represents a potential formulation since CNH has been noted for their biodegradability, biocompatibility, low toxicity, and cavities dimensionally compatible with small drugs. This work reports energetic and dynamic analyses of complexes formed by oxidized CNH (CNHox) and the cddp, cpx, and oxa drugs. Using unbiased molecular dynamics (MD) simulations, we show that the encapsulated formulations (cddp@CNHox, cpx@CNHox, and oxa@CNHox) were more stable by ∼11.0 kcal mol-1 than the adsorbed ones (cddp > CNHox, cpx > CNHox, and oxa > CNHox). This high stability, mainly governed by van der Waals interactions, was responsible for the drug confinement during the entire simulation time (200 ns). The biased MD simulations of the inclusion complexes confirmed the nonspontaneity of the drug release since the potentials of mean force (PMF) indicated the endergonic character of this process. Additionally, the releasing energy profiles pointed out that the free energy barrier (ΔΔG≠) for the escape from CNHox cavity follows the order oxa > cpx ∼ cddp, with the value for the oxa complex (21-26 kcal mol-1) found to be about 36 and 30% larger than those for cpx and cddp, respectively. While the approximate residence time (tres) of the oxa drug inside the CNHox cavity was 5.45 × 108 s, the same measure for the cddp and cpx drugs was 5.3 × 105 and 1.60 × 103 s. Simulations also revealed that the escape of oxa with the oxalate group facing the nanowindow was the most unfavorable process, giving tres = 1.09 × 109 s. Besides reinforcing and extending the nanovectorization of cddp, cpx, and oxa in CNHox for cancer chemotherapies, all features considered may provide interpretations for experimental data and encourage new investigations aiming to propose less aggressive treatments for oncological diseases.

Carbon nanohorns as nanocontainers for cisplatin: insight into their interaction with the plasma membranes of normal and breast cancer cells

Cisplatin (cddp)-based chemotherapy is one of the most effective therapeutic alternatives for breast cancer treatment, the most common form of cancer, despite the severe side effects related to the high toxicity and low selectivity of cddp. To circumvent these drawbacks, the encapsulation of cddp into oxidized carbon nanohorns (CNHoxs) has been shown as a promising formulation with biocompatibility and low toxicity. However, there is still a lack of studies regarding the behavior of this cddp@CNHox nanovector on the cell membranes. This study presents an in silico description of the interactions between cddp@CNHox and membrane models of cancer (C_memb) and normal (N_memb) cells referring to a typical human breast. The results revealed the interaction mechanism of the inclusion complex 3cddp@CNHox (three cddp molecules are included in the CNHox cavity) with these biomembranes, which is a multistep process including approach, landing, insertion, and penetration. The 3cddp@CNHox stability was monitored over time, and demonstrated the trapping of cddp molecules inside the CNHox cavity over all simulations. The van der Waals contribution played a primary role (∼74%) for the complex stability. Moreover, the binding free energy calculations indicated that the interaction of the 3cddp@CNHox complex with the C_memb model was slightly more favorable, on average, than with the N_memb model. Analysis of the hydrogen bonds (HBs) formed over simulations of 800 ns explains the selectivity for the C_memb model, since the total number of HBs established between the inclusion complex and the C_memb model was about three times greater than that with the N_memb model. By reinforcing the potentiality of oxidized CNHox as a nanovector of cddp, the results presented in this study may assist and drive new experimental studies with this nanomaterial, focusing on the development of less aggressive formulations for breast cancer treatment.

A DFT investigation of lithium adsorption on graphenes as a potential anode material in lithium-ion batteries

We present a detailed study of the Li⁺ ion adsorption on two different hydrogenated carbon nanostructures, namely as pristine graphene (PG) and topologic Stone-Wales defective graphene (SWG) using the density functional theory (DFT). The studies are focused to analyze the structure-stability relationship with the estimated electronic and electrical properties for lithium-ion batteries (LIB) formed with an anode based on the Li/Li⁺#PG and Li/Li⁺#SWG systems. In addition, the electronic effects induced due to Li⁺ adsorption and the presence of SW defect on the graphene models were analyzed by the frontier molecular orbitals, ChelpG charges, Raman and UV-Vis spectra. It was verified that Li⁺ is more stably adsorbed on the edges on both graphene structures through an electrostatic interaction between cation and more negatively charged edges of nanostructures. TD-DFT calculations showed that the metallic nature of isolated graphene is disturbed after the adsorption of Li⁺, and this was demonstrated from the calculated HOMO-LUMO gap. The same Li⁺-Graphene geometries were optimized by introducing neutral charge in order to enable the calculation of ionization potentials. I was also found that such systems potentially contributed to the modeling of graphene-based anodes with reasonable electrical voltage responses estimated for a LIB. The simulation of Raman and UV-Vis spectra revealed significant variations in intensity and shifts the typical bands of graphene due to the presence of the Li⁺ ion that can contribute to point out new experiments to the spectroscopic characterization of these systems. Our results suggest that these carbon nanostructures are potential candidates for efficient applications in electrochemical systems, mainly dealing with LIB.

1H and 195Pt NMR prediction for inclusion compounds formed by cisplatin and oxidized carbon nanostructures

Prediction of NMR chemical shifts can assist experimentalists in the characterization of drug delivery systems based on carbon nanocomposites. Chemical shifts are strongly correlated to the nucleus position and its chemical neighborhood. Therefore, to predict structures and NMR properties of complex chemical models, choosing a more consistent theoretical level capable of providing more realistic results and moderate computational demand is a major challenge. In this work, we predicted the NMR spectra of inclusion compounds formed by cisplatin (cDDP) and an oxidized carbon nanotube (CNTox) and nanocone (CNCox) considered by specialists as potential drug delivery systems. The ¹⁹⁵Pt NMR chemical shifts calculated at the DFT level with the new relativistic NMR-DKH basis set were −2314 ppm and −2192 ppm for cDDP@CNTox and cDDP@CNCox complexes, respectively, which are both high-field shifted relative to the free cDDP (−2110 ppm). ¹H NMR chemical shifts are also sensitive to the inclusion process. The H (NH₃) signals are found on average at +4.3 (cDDP), −5.1 (cDDP@CNTox) and +6.6 ppm (cDDP@CNCox). Interestingly, despite the similar inclusion modes in CNTox and CNCox cavities, the ¹H NMR shifts were in opposite directions. A possible reason might be the higher stability of cDDP@CNTox (ΔE_F = −19.9 kcal mol⁻¹) than that of cDDP@CNCox (ΔE_F = −5.7 kcal mol⁻¹), which suggests a short guest–host contact in the former and consequently, a more efficient shielding of hydrogen atoms due to the electron-rich carbon structure. These results may be helpful as comparison data in the NMR spectra assignment in solution and the inclusion compounds' structural elucidation.

¹⁹⁵Pt NMR chemical shifts of the cisplatin molecule in the inclusion complex formed by oxidized carbon nanotubes.

Carbon Nanohorns as Effective Nanotherapeutics in Cancer Therapy

Different carbon nanostructures have been explored as functional materials for the development of effective nanomaterials in cancer treatment applications. This review mainly aims to discuss the features, either strength or weakness, of carbon nanohorn (CNH), carbon conical horn-shaped nanostructures of sp2 carbon atoms. The interest for these materials arises from their ability to couple the clinically relevant properties of carbon nanomaterials as drug carriers with the negligible toxicity described in vivo. Here, we offer a comprehensive overview of the recent advances in the use of CNH in cancer treatments, underlining the benefits of each functionalization route and approach, as well as the biological performances of either loaded and unloaded materials, while discussing the importance of delivery devices.

Application of a quantum genetic algorithm and QTAIM analysis in the study of structural and electronic properties of neutral bimetallic clusters NaxLiy (4 ≤ x + y ≤ 10)

Alloy clusters of Na_xLi_y (4 ≤ x + y ≤ 10) are studied by exploring the potential energy surface in the ab initio MP2 level with the support of a quantum genetic algorithm (QGA). In some cases, the structures have been also refined with DFT and coupled-cluster methods. The general trends of sodium-lithium structures are in line with previous studies. The ionization potentials and polarizabilities to all structures were calculated with MP2 method and the average error between these two properties compared with experimental data was 6% and 13%, respectively. The topological analysis based on quantum theory of atoms in molecules (QTAIM) showed that by increasing the cluster size of the diatomic system there was a decrease of atomic interaction energies. The degree of degeneracy from D3BIA aromaticity index and the analysis of the atomic charges showed the influence (by charge transfer) of the chemical element in lower quantity in the cluster with respect to the other atoms. Our achievements of comparing our theoretical results with available experimental data have demonstrated that our approach can also predict satisfactorily quantum atomic and alloy clusters properties, at least, for low nuclearities.