Delicate Balance of Non-Covalent Forces Govern the Biocompatibility of Graphitic Carbon Nitride towards Genetic Materials

Screening 2D Materials for Their Nanotoxicity toward Nucleic Acids and Proteins: An In Silico Outlook

Since the discovery of graphene, two-dimensional (2D) materials have been anticipated to demonstrate enormous potential in bionanomedicine. Unfortunately, the majority of 2D materials induce nanotoxicity via disruption of the structure of biomolecules. Consequently, there has been an urge to synthesize and identify biocompatible 2D materials. Before the cytotoxicity of 2D nanomaterials is experimentally tested, computational studies can rapidly screen them. Additionally, computational analyses can provide invaluable insights into molecular-level interactions. Recently, various "in silico" techniques have identified these interactions and helped to develop a comprehensive understanding of nanotoxicity of 2D materials. In this article, we discuss the key recent advances in the application of computational methods for the screening of 2D materials for their nanotoxicity toward two important categories of abundant biomolecules, namely, nucleic acids and proteins. We believe the present article would help to develop newer computational protocols for the identification of novel biocompatible materials, thereby paving the way for next-generation biomedical and therapeutic applications based on 2D materials.

Computational Assessment of the Biocompatibility of Two-Dimensional g-C3N3 Toward Lipid Membranes

One of the most recent additions to the family of two-dimensional (2D) materials, graphitic C3N3 (g-C3N3), has been considered a viable contender for biomedical applications, although its potential toxicity remains elusive. We perform all-atom molecular dynamics simulations to decipher the interactions between model lipid membranes and g-C3N3 as a first step toward exploring the cytotoxicity induced at the nanoscale. We show that g-C3N3 can easily insert into the cellular membranes following a multistage mechanism consisting of simultaneous desolvation of the 2D material along with enrichment of nanomaterial-lipid interactions. Free energy calculations indicate that g-C3N3 is more stable in a membrane-bound state compared to an aqueous solution; however, the insertion of the material does not disturb the structural integrity of lipid membranes. After being inserted into a membrane, g-C3N3 is unlikely to be released into the cellular environment and is incapable of extracting lipid molecules from the membrane. The nature of interaction between the 2D material and membranes is found to be independent of the nanomaterial size. Also, the performance of g-C3N3 toward biomolecular delivery is shown to be significantly improved compared to the state-of-the-art 2D materials graphene and hexagonal boron nitride (h-BN). It is revealed that, the affinity of g-C3N3 toward lipid membranes is weaker compared to the nanotoxic graphene and h-BN, while being marginally higher than h2D-C2N, which in turn, increases the biocompatibility of the material, thereby brightening its future as a noncytotoxic material for forthcoming biomedical applications.

B, P, and S heteroatom doped, bio- and hemo-compatible 2D graphitic-carbon nitride (g-C3N4) with antioxidant, light-induced antibacterial, and bioimaging endeavors

The synthesis of two-dimensional (2D) graphiticg-C3N4and heteroatom-doped graphitic H@g-C3N4(H: B, P, or S) particles were successfully done using melamine as source compounds and boric acid, phosphorous red, and sulfur as doping agents. The band gap values of 2Dg-C3N4, B50@g-C3N4, P50@g-C3N4, and S50@g-C3N4structures were determined as 2.90, 3.03, 2.89, and 2.93 eV, respectively. The fluorescent emission wavelengths of 2Dg-C3N4, B50@g-C3N4, P50@g-C3N4, and S50@g-C3N4structures were observed at 442, 430, 441, and 442 nm, respectively upon excitation atλEx= 325 nm. There is also one additional new emission wavelength was found at 345 nm for B50@g-C3N4structure. The blood compatibility test results ofg-C3N4, B50@g-C3N4, P50@g-C3N4, and S50@g-C3N4structures revealed that all materials are blood compatible with <2% hemolysis and >90% blood clotting indices at 100μg ml-1concentration. The cell toxicity of the prepared 2D graphitic structures were also tested on L929 fibroblast cells, and even the heteroatom doped hasg-C3N4structures induce no cytotoxicity was observed with >91% cell viability even at 250μg ml-1particle concentration with the exception of P50@g-C3N4which as >75 viability. Moreover, for 2Dg-C3N4, B50@g-C3N4, and S50@g-C3N4constructs, even at 500μg ml-1concentration, >90% cell viabilities was monitored. As a diagnostic material, B50@g-C3N4was found to have significantly high penetration and distribution abilities into L929 fibroblast cells granting a great potential in fluorescence imaging and bioimaging applications. Furthermore, the elemental doping with B, P, and S ofg-C3N4were found to significantly increase the photodynamic antibacterial activity e.g. more than half of bacterial elimination by heteroatom-doped forms ofg-C3N4under UVA treatment was achieved.

Dissociation of the Watson-Crick base pairs in vacuum and in aqueous solution: a first-principles molecular dynamics study

The damage of the DNA structure can affect the correct functioning of the cellular processes. This work investigates the required forces to dissociate the Watson-Crick (WC) base pairs AT into A and T, and GC into G and C. The WC base pairs are immersed in water under realistic conditions of temperature, volume, and density that reproduce the main characteristics of a biological system. The simulations are based on first-principles molecular dynamics combined with steering atomic forces. In addition to the force intensities, the charge transfers between the nucleic acid bases, energy variations, and temperature fluctuations in the cleavage moments are reported. With the purpose of evaluating the effects of the aqueous medium, simulations of the WC base pairs in vacuum are included. The results considering the solvated medium are consistent with the experimental measurements, and show the importance of the aqueous solution to regulate the structural modifications of the nucleic acid bases. The investigation contributes with a novel molecular model in molecular simulations, and to better understand the biological processes where the DNA compounds play an active role in life forms.Communicated by Ramaswamy H. Sarma.

Two dimensional materials are non-nanotoxic and biocompatible towards cyclotides: evidence from classical molecular dynamics simulations

Cyclotides are backbone-cyclized peptides of plant origin enriched with disulfide bonds, having exceptional stability towards thermal denaturation and proteolytic degradation. They have a plethora of activities like antibacterial, antifungal, anti-tumor and anti-HIV properties predominantly owing to their selective interaction with certain phospholipids, thereby leading to the disruption of cellular membranes. On the other hand, low-dimensional materials like graphene and hexagonal boron nitride (h-BN) are also known to show membrane-proliferating activities through lipid extraction. A plausible and more effective antibacterial, anti-tumor and antifungal agent would be a composite of these 2D materials and cyclotides, provided the structures of the peptides remain unperturbed upon adsorption and interaction. In this study, classical molecular dynamics simulations are performed to understand the nature of adsorption of cyclotides belonging to different families on graphene and h-BN and analyze the resulting structural changes. It is revealed that, due to their exceptional structural stability, cyclotides maintain their structural integrity upon adsorption on the 2D materials. In addition, the aggregated states of the cyclotides, which are ubiquitous in plant organs, are also not disrupted upon adsorption. Extensive free energy calculations show that the adsorption strength of the cyclotides is moderate in comparison to those of other similar-sized biomolecules, and the larger the size of the aggregates, the weaker the binding of individual peptides with the 2D materials, thereby leading to their lower release times from the materials. It is predicted that graphene and h-BN may safely be used for the preparation of composites with cyclotides, which in turn may be envisaged to be probable candidates for manufacturing next-generation bionano agents for agricultural, antibacterial and therapeutic applications.

Thiazole Containing PNA Mimic Regulates c-MYC Gene Expression through DNA G-Quadruplex

Peptide nucleic acids (PNAs), besides hybridizing to complementary DNA and RNAs, bind and stabilize DNA secondary structures. Herein, we illustrate the design and synthesis of PNA-like scaffolds by incorporating five-membered thiazole rings as modified bases instead of nucleobases and their subsequent effects on gene regulation by biophysical and in vitro assays. A thiazole-modified PNA trimer selectively recognizes c-MYC G-quadruplex (G4) DNA over other G4s and duplex DNA. It displays a high stabilization potential for the c-MYC G4 DNA and shows remarkable fluorescence enhancement with the c-MYC G4. It is flexible enough to bind at 5' and 3' ends as well as in the groove region of c-MYC G4. Furthermore, the PNA trimer easily permeates the cellular membrane and suppresses c-MYC mRNA expression in HeLa cells by targeting the promoter G4. This study illuminates modified PNAs as flexible molecular tools for selective targeting of noncanonical nucleic acids and modulating gene function.

Substituent effect of benzyl moiety in nitroquinoxaline small molecules upon DNA binding: Cumulative destacking of DNA nucleobases leading to histone eviction

Cooperative disruption of Watson-Crick hydrogen bonds, as well as base-destacking, is shown to be triggered by a quinoxaline-based small molecule consisting of an N,N-dimethylaminopropyl tether, and a para-substituted benzyl moiety. This events lead to superstructure formation and DNA condensation as evident from biophysical experiments and classical molecular dynamics simulations. The DNA superstructure formation by mono-quinoxaline derivatives is highly entropically favored and predominantly driven by hydrophobic interactions. Furthermore, oversupercoiling of DNA and base-destacking cumulatively induces histone eviction from in-vitro assembled nucleosomes at lower micromolar concentrations implicating biological relevance. The DNA structural modulation and histone eviction capacity of the benzyl para-substituents are in the order: -I > -CF₃> -Br > -Me > -OMe > -OH, which is largely guided by the polarity of benzyl para-substituent and the resulting molecular topology. The most hydrophobic derivative 3c with para-iodo benzyl moiety causes maximal disruption of base pairing and generation of superstructures. Both these events gradually diminish as the polarity of the benzyl para-substituent increases. On the other hand, quinoxaline derivatives having heterocyclic ring instead of benzyl ring, or in the absence of N,N-dimethylamino head-group, is incapable of inducing any DNA structural change and histone eviction. Further, the quinoxaline compounds displayed potent anticancer activities against different cancer cell lines which directly correlates with the hydrophobic effects of the benzyl para-substituents. Overall, the present study provides new insights into the mechanistic approach of DNA structural modulation driven histone eviction guided by the hydrophobicity of synthesized compounds leading to cellular cytotoxicity towards cancer cells.

Molecular Mechanism for the Self-Supported Synthesis of Graphitic Carbon Nitride from Urea Pyrolysis

Quantum chemical calculations combined with kinetic Monte Carlo simulations are performed to decipher the kinetics for the one-pot synthesis of two-dimensional graphitic carbon nitride (g-C₃N₄) from urea pyrolysis. Two mechanisms are considered, one involving ammelide as the intermediate compound and the other considering cyanuric acid. Different grid growing patterns are investigated, and the size, shape, and density of the grids as well as the number and position of the defects are evaluated. We find that the mechanistic pathway involving ammelide is preferred. Larger g-C₃N₄ grids with lower density are achieved when the rate constant for melon growing is inversely proportional to the number of local reaction sites, while nearly filled smaller grids are obtained in the opposite scenario. Larger defects appear at the grid periphery while smaller holes appear throughout the grid. The synthesis of extended g-C₃N₄ structures is favored if the g-C₃N₄ growing propensity is directly proportional to the number of reaction sites.

Disentangling the liquid phase exfoliation of two-dimensional materials: an "in silico" perspective

Liquid Phase Exfoliation (LPE) is one of the most successful synthetic roots for the preparation of two-dimensional (2D) materials from their bulk counterparts. In recent years, significant progress has been accomplished for the development and modification of LPE techniques. However, precise identification of the hierarchical steps of the molecular mechanism of LPE remains to some extent elusive. Additionally, the a priori choice of suitable solvents for successful exfoliation and dispersion of various layered materials poses a challenge for both academia and industry. Computational methods, particularly Molecular Dynamics (MD) simulations with classical force-fields have contributed a great deal towards the understanding of the underlying mechanism of LPE, providing remarkable insights into the molecular-level details of the solvent-material interactions at the nanoscale and predicting "good" and "bad" solvents for exfoliation as well as stabilization of the dispersed state. With an intention to build up a unified understanding, in this perspective article, we summarize the recent advancements of molecular simulation techniques employed to decipher the mechanism of LPE, pointing out the key features of molecular interactions and identifying several thermodynamic parameters governing the phenomena. In addition, we outline the necessary characteristics of solvent molecules, essential for their use as "good" solvents towards LPE. Also, we highlight the limitations of simulation methods for the modelling of LPE. We believe that this article will be beneficial for the selection of solvents for the synthesis of novel 2D materials via LPE and will also provide a comprehensive view to computational material scientists towards the development of novel simulation protocols for investigating and analysing such complex molecular events.