Molecular dynamics study of carbon nanotube as a potential dual-functional inhibitor of HIV-1 integrase

Molecular dynamics simulation study on the binding mechanism between carbon nanotubes and RNA-dependent RNA polymerase

Carbon nanotubes (CNTs) have potential prospects in disease treatment, so it is of great significance to study CNTs as the possible inhibitors of RNA-dependent RNA polymerase (RdRp). Through the way of using the RdRp of SARS-COV-2 as a model, five armchair single-walled carbon nanotubes (SWCNTs) (namely Dn, which stands for CNTs (n, m = n), n = 3-7) and RdRp have been selected to study the interactions by means of molecular docking and molecular dynamics simulation. After five SWCNT-RdRp complex systems have been subjected to the molecular dynamics simulations of 100 ns, and Molecular Mechanics Poisson - Boltzmann Surface Area (MMPBSA) has been used to calculate the binding free energy, it is found that the binding free energy of the D6 system (-189.541 kJ/mol) is significantly higher than that of the other four systems, and most of the amino acids with strong positive effects on binding are usually basic amino acids. What's more, in the further investigation of the specific interaction mechanism between CNT (6,6) and RdRp, it is revealed that the three amino acid residues LYS545, ARG553 and ARG555 located in the nucleoside triphosphate (NTP) entry channel all have strong effects. In addition, it is also observed that when ARG555 has been inserted into SWCNT, a stable structure will be formed, which will break the original NTP entry channel structure and inhibit virus replication. Therefore, it can be concluded that certain specific types of SWCNT, such as CNT (6,6), could be potential small molecule inhibitors in the treatment of coronavirus.Communicated by Ramaswamy H. Sarma.

Coronavirus and Carbon Nanotubes: Seeking Immunological Relationships to Discover Immunotherapeutic Possibilities

Since December 2019, the world has faced an unprecedented pandemic crisis due to a new coronavirus disease, coronavirus disease-2019 (COVID-19), which has instigated intensive studies on prevention and treatment possibilities. Here, we investigate the relationships between the immune activation induced by three coronaviruses associated with recent outbreaks, with special attention to SARS-CoV-2, the causative agent of COVID-19, and the immune activation induced by carbon nanotubes (CNTs) to understand the points of convergence in immune induction and modulation. Evidence suggests that CNTs are among the most promising materials for use as immunotherapeutic agents. Therefore, this investigation explores new possibilities of effective immunotherapies for COVID-19. This study aimed to raise interest and knowledge about the use of CNTs as immunotherapeutic agents in coronavirus treatment. Thus, we summarize the most important immunological aspects of various coronavirus infections and describe key advances and challenges in using CNTs as immunotherapeutic agents against viral infections and the activation of the immune response induced by CNTs, which can shed light on the immunotherapeutic possibilities of CNTs.

Role of nanotechnology in facing SARS-CoV-2 pandemic: Solving crux of the matter with a hopeful arrow in the quiver

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a positive-sense single-stranded RNA virus species with a zoonotic origin and responsible for the coronavirus disease 2019(COVID-19). This novel virus has an extremely high infectious rate, which occurs through the contact of contaminated surfaces and also by cough, sneeze, hand-to-mouth-to-eye contact with an affected person. The progression of infection, which goes beyond complications of pneumonia to affecting other physiological functions which cause gastrointestinal, Renal, and neurological complication makes this a life threatening condition. Intense efforts are going across the scientific community in elucidating various aspects of this virus, such as understanding the pathophysiology of the disease, molecular biology, and cellular pathways of viral replication. We hope that nanotechnology and material science can provide a significant contribution to tackle this problem through both diagnostic and therapeutic strategies. But the area is still in the budding phase, which needs urgent and significant attention. This review provides a brief idea regarding the various nanotechnological approaches reported for managing COVID-19 infection. The nanomaterials recently said to have good antiviral activities like Carbon nanotubes (CNTs) and quantum dots (QDs) were also discussed since they are also in the emerging stage of attaining research interest regarding antiviral applications.

Advances in Antiviral Material Development

The rise in human pandemics demands prudent approaches in antiviral material development for disease prevention and treatment via effective protective equipment and therapeutic strategy. However, the current state of the antiviral materials research is predominantly aligned towards drug development and its related areas, catering to the field of pharmaceutical technology. This review distinguishes the research advances in terms of innovative materials exhibiting antiviral activities that take advantage of fast-developing nanotechnology and biopolymer technology. Essential concepts of antiviral principles and underlying mechanisms are illustrated, followed with detailed descriptions of novel antiviral materials including inorganic nanomaterials, organic nanomaterials and biopolymers. The biomedical applications of the antiviral materials are also elaborated based on the specific categorization. Challenges and future prospects are discussed to facilitate the research and development of protective solutions and curative treatments.

Harnessing nanostructured systems for improved treatment and prevention of HIV disease

Combination antiretroviral therapy effectively controls human immunodeficiency virus (HIV) viral replication, delaying the progression to acquired immune deficiency syndrome and improving and extending quality of life of patients. However, the inability of antiretroviral therapeutics to target latent virus and their poor penetration of viral reserve tissues result in the need for continued treatment for the life of the patient. Side effects from long-term antiretroviral use and the development of drug resistance due to patient noncompliance are also continuing problems. Nanostructured systems of antiretroviral therapeutics have the potential to improve targeted delivery to viral reservoirs, reduce drug toxicity, and increase dosing intervals, thereby improving treatment outcomes and enhancing patient adherence. Despite these advantages, very few nanostructured antiretroviral delivery systems have made it to clinical trials due to challenges in preclinical and clinical development. In this context, we review the current challenges in HIV disease management, and the recent progress in leveraging the unique performance of nanostructured systems in therapeutic delivery for improved treatment and prevention of this incurable human disease.

Extension of coarse-grained UNRES force field to treat carbon nanotubes

Carbon nanotubes (CNTs) have recently received considerable attention because of their possible applications in various branches of nanotechnology. For their cogent application, knowledge of their interactions with biological macromolecules, especially proteins, is essential and computer simulations are very useful for such studies. Classical all-atom force fields limit simulation time scale and size of the systems significantly. Therefore, in this work, we implemented CNTs into the coarse-grained UNited RESidue (UNRES) force field. A CNT is represented as a rigid infinite-length cylinder which interacts with a protein through the Kihara potential. Energy conservation in microcanonical coarse-grained molecular dynamics simulations and temperature conservation in canonical simulations with UNRES containing the CNT component have been verified. Subsequently, studies of three proteins, bovine serum albumin (BSA), soybean peroxidase (SBP), and α-chymotrypsin (CT), with and without CNTs, were performed to examine the influence of CNTs on the structure and dynamics of these proteins. It was found that nanotubes bind to these proteins and influence their structure. Our results show that the UNRES force field can be used for further studies of CNT-protein systems with 3-4 order of magnitude larger timescale than using regular all-atom force fields. Graphical abstract Bovine serum albumin (BSA), soybean peroxidase (SBP), and α-chymotrypsin (CT), with and without CNTsᅟ.

Molecular dynamics simulation strategies for designing carbon-nanotube-based targeted drug delivery

The carbon nanotube (CNT)-based target-specific delivery of drugs, or other molecular cargo, has emerged as one of the most promising biomedical applications of nanotechnology. To achieve efficient CNT-based drug delivery, the interactions between the drug, CNT and biomolecular target need to be properly optimized. Recent advances in the computer-aided molecular design tools, in particular molecular dynamics (MD) simulation studies, offer an appropriate low-cost approach for such optimization. This review highlights the various potential MD approaches for the simulation of CNT interactions with cell membranes while emphasizing various methods of cellular internalization and toxicities of CNTs to build new strategies for designing rational CNT-based targeted drug delivery to circumvent the limitations associated with the various clinically available nonspecific therapeutic agents.

Development of HIV-1 integrase inhibitors: recent molecular modeling perspectives

Of the three viral enzymes essential to HIV replication, HIV-1 integrase (IN) is gaining popularity as a target for the antiviral therapy of AIDS. Substantial work focusing on IN has been done over the past three decades, which has facilitated and led to the approval of three drugs. Here, we discuss in detail the development of IN inhibitors between January 2012 and May 2014, with a particular focus on molecular simulation. We highlight controversial aspects of computational drug design and refer to alternative practices where appropriate. The analysis of these computational approaches provides some useful clues to the possible future discovery of novel IN inhibitors.

Smart nanoparticles as targeting platforms for HIV infections

While Human Immunodeficiency Virus (HIV) infections are reducing in incidence with the advent of Highly Active Anti-retroviral Therapy (HAART), there remain a number of challenges including the existence of reservoirs, drug resistance and anatomical barriers to antiretroviral therapy. To overcome these, smart nanoparticles with stimuli responsive release are proposed for delivery of anti-retroviral agents. The paper highlights the strategic similarities between the design of smart antiretroviral nanocarriers and those optimized for cancer chemotherapy. This includes the development of nanoparticles capable of passive and active targeting as well as those that are responsive to various internal and external triggers. For antiretroviral therapy, the relevant triggers for stimuli responsive release of drugs include semen, enzymes, endosomal escape, temperature and magnetic field. Deriving from the experience of cancer chemotherapy, additional potential triggers are light and ultrasound which remain hitherto unexplored in HIV therapy. In addition, the roles of nanomicrobicides (nanogels) and virus mimetic nanoparticles are discussed from the point of view of prevention of HIV transmission. The challenges associated with translation of smart nanoparticles for HIV infections to realize the Millennium Development Goal of combating HIV infections are discussed.

Single-walled carbon nanotubes increase pandemic influenza A H1N1 virus infectivity of lung epithelial cells

Background

Airborne exposure to nanomaterials from unintended occupational or environmental exposures or as a consequence of product use may lead to adverse health effects. Numerous studies have focused on single-walled carbon nanotubes (SWCNTs) and their ability to cause pulmonary injury related to fibrosis, and cancer; however few studies have addressed their impact on infectious agents, particularly viruses that are known for causing severe disease. Here we have demonstrated the ability of pristine SWCNTs of diverse electronic structure to increase the susceptibility of small airway epithelial cells (SAEC) to pandemic influenza A H1N1 infection and discerned potential mechanisms of action driving this response.

Methods

Small airway epithelial cells (SAEC) were exposed to three types of SWCNTs with varying electronic structure (SG65, SG76, CG200) followed by infection with A/Mexico/4108/2009 (pH1N1). Cells were then assayed for viral infectivity by immunofluorescence and viral titers. We quantified mRNA and protein levels of targets involved in inflammation and anti-viral activity (INFβ1, IL-8, RANTES/CCL5, IFIT2, IFIT3, ST3GAL4, ST6GAL1, IL-10), localized sialic acid receptors, and assessed mitochondrial function. Hyperspectral imaging analysis was performed to map the SWCNTs and virus particles in fixed SAEC preparations. We additionally performed characterization analysis to monitor SWCNT aggregate size and structure under biological conditions using dynamic light scattering (DLS), static light scattering (SLS).

Results

Based on data from viral titer and immunofluorescence assays, we report that pre-treatment of SAEC with SWCNTs significantly enhances viral infectivity that is not dependent on SWCNT electronic structure and aggregate size within the range of 106 nm – 243 nm. We further provide evidence to support that this noted effect on infectivity is not likely due to direct interaction of the virus and nanoparticles, but rather a combination of suppression of pro-inflammatory (RANTES) and anti-viral (IFIT2, IFIT3) gene/protein expression, impaired mitochondrial function and modulation of viral receptors by SWCNTs.

Conclusions

Results of this work reveal the potential for SWCNTs to increase susceptibility to viral infections as a mechanism of adverse effect. These data highlight the importance of investigating the ability of carbon-nanomaterials to modulate the immune system, including impacts on anti-viral mechanisms in lung cells, thereby increasing susceptibility to infectious agents.

Electronic supplementary material

The online version of this article (doi:10.1186/s12989-014-0066-0) contains supplementary material, which is available to authorized users.