Metallofullerenol Gd@C₈₂(OH)₂₂ distracts the proline-rich-motif from putative binding on the SH3 domain

Molecular Dynamic Simulations for Biopolymers with Biomedical Applications

Computational modeling (CM) is a versatile scientific methodology used to examine the properties and behavior of complex systems, such as polymeric materials for biomedical bioengineering. CM has emerged as a primary tool for predicting, setting up, and interpreting experimental results. Integrating in silico and in vitro experiments accelerates scientific advancements, yielding quicker results at a reduced cost. While CM is a mature discipline, its use in biomedical engineering for biopolymer materials has only recently gained prominence. In biopolymer biomedical engineering, CM focuses on three key research areas: (A) Computer-aided design (CAD/CAM) utilizes specialized software to design and model biopolymers for various biomedical applications. This technology allows researchers to create precise three-dimensional models of biopolymers, taking into account their chemical, structural, and functional properties. These models can be used to enhance the structure of biopolymers and improve their effectiveness in specific medical applications. (B) Finite element analysis, a computational technique used to analyze and solve problems in engineering and physics. This approach divides the physical domain into small finite elements with simple geometric shapes. This computational technique enables the study and understanding of the mechanical and structural behavior of biopolymers in biomedical environments. (C) Molecular dynamics (MD) simulations involve using advanced computational techniques to study the behavior of biopolymers at the molecular and atomic levels. These simulations are fundamental for better understanding biological processes at the molecular level. Studying the wide-ranging uses of MD simulations in biopolymers involves examining the structural, functional, and evolutionary aspects of biomolecular systems over time. MD simulations solve Newton's equations of motion for all-atom systems, producing spatial trajectories for each atom. This provides valuable insights into properties such as water absorption on biopolymer surfaces and interactions with solid surfaces, which are crucial for assessing biomaterials. This review provides a comprehensive overview of the various applications of MD simulations in biopolymers. Additionally, it highlights the flexibility, robustness, and synergistic relationship between in silico and experimental techniques.

Metallofullerenols in biomedical applications

Metallofullerenols (MFs) are functionalized endohedral fullerenes connecting at least three levels of organization of matter: atomic, molecular, and supramolecular, resulting in their unique activity at the nanoscale. Biomedical applications of MFs started from gadolinium-containing contrasting agents, but today their potential medical applications go far beyond diagnostics and magnetic resonance imaging. In many cases, preclinical studies have shown a great therapeutic value of MFs, and here we provide an overview of interactions of MFs with high-energy radiation and with reactive oxygen species generated during radiation as a ground for potential applications in modern therapy of cancer patients. We also present the current knowledge on interactions of MFs with proteins and with other components of cells and tissues. Due to their antioxidant properties, as well as their ability to regulate the expression of genes involved in apoptosis, angiogenesis, and stimulation of the immune response, MFs can contribute to inhibition of tumor growth and protection of normal cells. MFs with enclosed gadolinium act as inhibitors of tumor growth in targeted therapy along with imaging techniques, but we hope that the data gathered in this review will help to accelerate further progress in the implementation of MFs, also the ones containing rare earth metals other than gadolinium, in a broad range of bioapplications covering not only diagnostics and bioimaging but also radiation therapy and cancer treatment by not-cytotoxic agents.

The Molecular Mechanism of Human Voltage-Dependent Anion Channel 1 Blockade by the Metallofullerenol Gd@C82(OH)22: An In Silico Study

The endohedral metallofullerenol Gd@C₈₂(OH)₂₂ has been identified as a possible antineoplastic agent that can inhibit both the growth and metastasis of cancer cells. Despite these potentially important effects, our understanding of the interactions between Gd@C₈₂(OH)₂₂ and biomacromolecules remains incomplete. Here, we study the interaction between Gd@C₈₂(OH)₂₂ and the human voltage-dependent anion channel 1 (hVDAC1), the most abundant porin embedded in the mitochondrial outer membrane (MOM), and a potential druggable target for novel anticancer therapeutics. Using in silico approaches, we observe that Gd@C₈₂(OH)₂₂ molecules can permeate and form stable interactions with the pore of hVDAC1. Further, this penetration can occur from either side of the MOM to elicit blockage of the pore. The binding between Gd@C₈₂(OH)₂₂ and hVDAC1 is largely driven by long-range electrostatic interactions. Analysis of the binding free energies indicates that it is thermodynamically more favorable for Gd@C₈₂(OH)₂₂ to bind to the hVDAC1 pore when it enters the channel from inside the membrane rather than from the cytoplasmic side of the protein. Multiple factors contribute to the preferential penetration, including the surface electrostatic landscape of hVDAC1 and the unique physicochemical properties of Gd@C₈₂(OH)₂₂. Our findings provide insights into the potential molecular interactions of macromolecular biological systems with the Gd@C₈₂(OH)₂₂ nanodrug.

Self-assembly of ultra-small-sized carbon nanoparticles in lipid membrane disrupts its integrity

Although nanomaterials are widely studied in biomedical applications, the major concern of nanotoxicity still exists. Therefore, numerous studies have been conducted on the interactions of various biomolecules with various types of nanomaterials, including carbon nanotubes, graphene, fullerene etc. However, the size effect of nanomaterials is poorly documented, especially ultra-small particles. Here, the interactions of the smallest carbon nanoparticle (NP), C₂₈, with the cell membrane were studied using molecular dynamics (MD) simulations. The results show that similar to fullerene C₆₀, the C₂₈ NPs can self-assemble into stable clusters in water. Inside the membrane, the C₂₈ NPs are more prone to aggregate to form clusters than C₆₀ NPs. The reason for C₂₈ aggregation is characterized by the potential of mean force (PMF) and can be explained by the polarized nature of C₂₈ NPs while the acyl chains of lipids are nonpolar. At the C₂₈ cluster regions, the thickness of the membrane is significantly reduced by the C₂₈ aggregation. Accordingly, the membrane loses its structural integrity, and translocation of water molecules through it was observed. Thus, these results predict a stronger cytotoxicity to cells than C₆₀ NPs. The present findings might shed light on the understanding of the cytotoxicity of NPs with different sizes and would be helpful for the potential biomedical applications of carbon NPs, especially as antibacterial agents.

Tungsten Oxide Nanodots Exhibit Mild Interactions with WW and SH3 Modular Protein Domains

Tungsten oxide nanodot (WO_3-x ) is an active photothermal nanomaterial that has recently been discovered as a promising candidate for tumor theranostics and treatments. However, its potential cytotoxicity remains elusive and needs to be evaluated to assess its biosafety risks. Herein, we investigate the interactions between WO_3-x and two ubiquitous protein domains involved in protein-protein interactions, namely, WW and SH3 domains, using atomistic molecular dynamics simulations. Our results show that WO_3-x interacts only weakly with the key residues at the putative proline-rich motif (PRM) ligand-binding site of both domains. More importantly, our free energy landscape calculations reveal that the binding strength between WO_3-x and WW/SH3 is weaker than that of the native PRM ligand with WW/SH3, implying that WO_3-x has a limited inhibitory effect over PRM on both the WW and SH3 domains. These findings suggest that the cytotoxic effects of WO_3-x on the key modular protein domains could be very mild, which provides new insights for the future potential biomedical applications of this nanomaterial.

A Novel Drug Design Strategy: An Inspiration from Encaging Tumor by Metallofullerenol Gd@C82(OH)22

Cancer remains a major threat to human health worldwide. Cytotoxicity has imposed restrictions on the conventional cytotoxic drug-based chemotherapy. The rapidly-developing nanomedicine has shown great promise in revolutionizing chemotherapy with improved efficiency and reduced toxicity. Gd@C₈₂(OH)₂₂, a novel endohedral metallofullerenol, was first reported by our research group to suppress tumor growth and metastasis efficiently without obvious toxicity. Gd@C₈₂(OH)₂₂ imprisons tumors by facilitating the formation of surrounding fibrous layers which is different from chemotherapeutics that poison tumor cells. In this review, the authors first reported the antineoplastic activity of metallofullerenol Gd@C₈₂(OH)₂₂ followed by further discussions on its new anti-cancer molecular mechanism—tumor encaging. On this basis, the unparalleled advantages of nanomedicine in the future drug design are discussed. The unique interaction modes of Gd@C₈₂(OH)₂₂ with specific targeted biomolecules may shed light on a new avenue for drug design. Depending on the surface characteristics of target biomolecules, nanomedicine, just like a transformable and dynamic key, can self-assemble into suitable shapes to match several locks for the thermodynamic stability, suggesting the target-tailoring ability of nanomedicine.

Concentration-dependent binding of CdSe quantum dots on the SH3 domain

Quantum dots (QDs) are being used increasingly in applications for solar panels, consumer electronics, and biomedical imaging. For biomedical applications, QDs are typically coated with a biocompatible molecule for the system of interest. Experiments have indicated a QD dose-dependent and surface coating-dependent toxicity, with a portion of the toxicity being ascribed to interference with biomolecules. In this work, the interaction of trioctylphosphine oxide (TOPO) coated (CdSe)₁₃ QDs with the SRC homology 3 domain (SH3) protein domain are explored using molecular dynamics simulations. The results of this research agree well with experiments that show that at the lowest concentration, the QDs have little affinity for the native proline-rich motif (PRM) binding site of SH3. At higher concentrations, the QDs aggregate and increasingly prefer the PRM binding site, indicating that the normal SH3 function is impeded. This binding dependence is attributed to changes in the local density of the surface coated TOPO molecules upon aggregation. These results present possible interesting QD toxicity patterns and reveal the interdependence between dose and surface coating effects in QD toxicity.

Molecular mechanism of Gd@C82(OH)22 increasing collagen expression: Implication for encaging tumor

Gadolinium-containing fullerenol Gd@C₈₂(OH)₂₂ has demonstrated low-toxicity and highly therapeutic efficacy in inhibiting tumor growth and metastasis through new strategy of encaging cancer, however, little is known about the mechanisms how this nanoparticle regulates fibroblast cells to prison (instead of poison) cancer cells. Here, we report that Gd@C₈₂(OH)₂₂ promote the binding activity of tumor necrosis factor (TNFα) to tumor necrosis factor receptors 2 (TNFR2), activate TNFR2/p38 MAPK signaling pathway to increase cellular collagen expression in fibrosarcoma cells and human primary lung cancer associated fibroblasts isolated from patients. We also employ molecular dynamics simulations to study the atomic-scale mechanisms that dictate how Gd@C₈₂(OH)₂₂ mediates interactions between TNFα and TNFRs. Our data suggest that Gd@C₈₂(OH)₂₂ might enhance the association between TNFα and TNFR2 through a "bridge-like" mode of interaction; by contrast, the fullerenol appears to inhibit TNFα-TNFR1 association by binding to two of the receptor's cysteine-rich domains. In concert, our results uncover a sequential, systemic process by which Gd@C₈₂(OH)₂₂ acts to prison tumor cells, providing new insights into principles of designs of cancer therapeutics.

Metallofullerenol Inhibits Cellular Iron Uptake by Inducing Transferrin Tetramerization

Herein, A549 tumor cell proliferation was confirmed to be positively dependent on the concentration of Fe³⁺ or transferrin (Tf). Gd@C₈₂ (OH)₂₂ or C₆₀ (OH)₂₂ effectively inhibited the iron uptake and the subsequent proliferation of A549 cells. The conformational changes of Tf mixed with FeCl₃ , GdCl₃ , C₆₀ (OH)₂₂ or Gd@C₈₂ (OH)₂₂ were obtained by SAXS. The results demonstrate that Tf homodimers can be decomposed into monomers in the presence of FeCl₃ , GdCl₃ or C₆₀ (OH)₂₂ , but associated into tetramers in the presence of Gd@C₈₂ (OH)₂₂ . The larger change of SAXS shapes between Tf+C₆₀ (OH)₂₂ and Tf+FeCl₃ implies that C₆₀ (OH)₂₂ is bound to Tf, blocking the iron-binding site. The larger deviation of the SAXS shape from a possible crystal structure of Tf tetramer implies that Gd@C₈₂ (OH)₂₂ is bound to the Tf tetramer, thus disturbing iron transport. This study well explains the inhibition mechanism of Gd@C₈₂ (OH)₂₂ and C₆₀ (OH)₂₂ on the iron uptake and the proliferation of A549 tumor cells and highlights the specific interactions of a nanomedicine with the target biomolecules in cancer therapy.

Surface Curvature Relation to Protein Adsorption for Carbon-based Nanomaterials

The adsorption of proteins onto carbon-based nanomaterials (CBNs) is dictated by hydrophobic and π-π interactions between aliphatic and aromatic residues and the conjugated CBN surface. Accordingly, protein adsorption is highly sensitive to topological constraints imposed by CBN surface structure; in particular, adsorption capacity is thought to increase as the incident surface curvature decreases. In this work, we couple Molecular Dynamics (MD) simulations with fluorescence spectroscopy experiments to characterize this curvature dependence in detail for the model protein bovine serum albumin (BSA). By studying BSA adsorption onto carbon nanotubes of increasing radius (featuring descending local curvatures) and a flat graphene sheet, we confirm that adsorption capacity is indeed enhanced on flatter surfaces. Naïve fluorescence experiments featuring multi-walled carbon nanotubes (MWCNTs), however, conform to an opposing trend. To reconcile these observations, we conduct additional MD simulations with MWCNTs that match those prepared in experiments; such simulations indicate that increased mass to surface area ratios in multi-walled systems explain the observed discrepancies. In reduction, our work substantiates the inverse relationship between protein adsorption capacity and surface curvature and further demonstrates the need for subtle consideration in experimental and simulation design.

A strong charge-transfer effect in surface-enhanced Raman scattering induced by valence electrons of actinide elements

The 6d electrons of Ac atom involved in excited transitions induce a strong CT-SERS enhancement which can be tuned by changing the conformation of pyridine-Ac@Au₇ complexes.

Structural and electronic properties of uranium-encapsulated Au₁₄ cage

The structural properties of the uranium-encapsulated nano-cage U@Au₁₄ are predicted using density functional theory. The presence of the uranium atom makes the Au₁₄ structure more stable than the empty Au₁₄-cage, with a triplet ground electronic state for U@Au₁₄. Analysis of the electronic structure shows that the two frontier single-occupied molecular orbital electrons of U@Au₁₄ mainly originate from the 5f shell of the U atom after charge transfer. Meanwhile, the bonding orbitals and charge population indicate that the designed U@Au₁₄ nano-cage structure is stabilized by ionocovalent interactions. The current findings provide theoretical basis for future syntheses and further study of actinide doped gold nanoclusters, which might subsequently facilitate applications of such structure in radio-labeling, nanodrug carrier and other biomedical applications.

Cytotoxicity of graphene: recent advances and future perspective

Graphene, a unique two-dimensional single-atom-thin nanomaterial with exceptional structural, mechanical, and electronic properties, has spurred an enormous interest in many fields, including biomedical applications, which at the same time ignites a growing concern on its biosafety and potential cytotoxicity to human and animal cells. In this review, we present a summary of some very recent studies on this important subject with both experimental and theoretical approaches. The molecular interactions of graphene with proteins, DNAs, and cell membranes (both bacteria and mammalian cells) are discussed in detail. Severe distortions in structures and functions of these biomacromolecules by graphene are identified and characterized. For example, the graphene is shown to disrupt bacteria cell membranes by insertion/cutting as well as destructive extraction of lipid molecules directly. More interestingly, this cytotoxicity has been shown to have implications in de novo design of nanomedicine, such as graphene-based band-aid, a potential 'green' antibiotics due to its strong physical-based (instead of chemical-based) antibacterial capability. These studies have provided a better understanding of graphene nanotoxicity at both cellular and molecular levels, and also suggested therapeutic potential by using graphene's cytotoxicity against bacteria cells.

Dual inhibitory pathways of metallofullerenol Gd@C₈₂(OH)₂₂ on matrix metalloproteinase-2: molecular insight into drug-like nanomedicine

Cancer metastasis is an important criterion to evaluate tumor malignancy. Matrix metalloproteinases (MMPs) play a crucial role in cancer proliferation and migration by virtue of their proteolytic functions in angiogenesis and extracelluar matrix (ECM) degradation, making them potential targets of anti-metastaic therapeutics. Recently we showed with both in vivo and in vitro experiments that metallofullerenol Gd@C₈₂(OH)₂₂ can effectively inhibit MMP-2 and MMP-9 with high antitumoral efficacy. Furthermore, our in silico study revealed that Gd@C₈₂(OH)₂₂ could indirectly inhibit the proteolysis of MMP-9 via allosteric modulation exclusively at the ligand specificity S1′ loop. Here, we expand our study toward another gelatinase, MMP-2, using molecular dynamics simulations. Despite the high structural similarity with 64.3% sequence identity, their responses to Gd@C₈₂(OH)₂₂ were quite different. Toward MMP-2, Gd@C₈₂(OH)₂₂ could block either the Zn²⁺-catalylitic site directly or the S1′ loop indirectly. Surface electrostatics uniquely determines the initial adsorption of Gd@C₈₂(OH)₂₂ on MMP-2, and then its further location of the most favorable binding site(s). These findings not only illustrated how the inhibitory mechanism of Gd@C₈₂(OH)₂₂ is distinguished between the two gelatinase MMPs with atomic details, but also shed light on the de novo design of anti-metastatic nanotherapeutics with enhanced target specificity.

Molecular modeling in structural nano-toxicology: interactions of nano-particles with nano-machinery of cells

Over the past two decades, nanotechnology has emerged as a key player in various disciplines of science and technology. Some of the most exciting applications are in the field of biomedicine - for theranostics (for combined diagnostic and therapeutic purposes) as well as for exploration of biological systems. A detailed understanding of the molecular interactions between nanoparticles and biological nano-machinery - macromolecules, membranes, and intracellular organelles - is crucial for obtaining adequate information on mechanisms of action of nanomaterials as well as a perspective on the long term effects of these materials and their possible toxicological outcomes. This review focuses on the use of structure-based computational molecular modeling as a tool to understand and to predict the interactions between nanomaterials and nano-biosystems. We review major approaches and provide examples of computational analysis of the structural principles behind such interactions. A rationale on how nanoparticles of different sizes, shape, structure and chemical properties can affect the organization and functions of nano-machinery of cells is also presented.