SARS-CoV-2 Unrevealed: Ultrastructural and Nanomechanical Analysis

Nanotechnology meets medicine: applications of atomic force microscopy in disease

Atomic force microscopy (AFM) is a scanning imaging technique able to work at the nanoscale. It uses a cantilever with a tip to move across samples' surface and a laser to measure the cantilever bending, enabling the assessment of interaction forces between tip and sample and creating a three-dimensional visual representation of its surface. AFM has been gaining notoriety in the biomedical field due to its high-resolution images, as well as due to its ability to measure the inter- and intramolecular interaction forces involved in the pathophysiology of many diseases. Here, we highlight some of the current applications of AFM in the biomedical field. First, a brief overview of the AFM technique is presented. This theoretical framework is then used to link AFM to its novel translational applications, handling broad clinical questions in different areas, such as infectious diseases, cardiovascular diseases, cancer, and neurodegenerative diseases. Morphological and nanomechanical characteristics such as cell height, volume, stiffness, and adhesion forces may serve as novel parameters used to tailor patient care through nanodiagnostics, individualized risk stratification, and therapeutic monitoring. Despite an increasing development of AFM biomedical research with patient cells, showing its unique capabilities in terms of resolution, speed, and accuracy, there is a notable need for applied AFM research in clinical settings. More translational research with AFM may provide new grounds for the valuable collaboration between biomedical researchers and healthcare professionals.

Unraveling the Nanomechanical and Vibrational Properties of the Mayaro Virus

Mayaro virus (MAYV) is an emerging mosquito-borne viral pathogen whose infection results in arthritogenic disease. Despite ongoing research efforts, MAYV biology is largely unknown. Physical virology can assess MAYV nanoparticle metastability, assembly/disassembly, and polymorphism, allowing us to understand virion architecture and dynamics. Here, we employ atomic force microscopy (AFM) and surface enhancement Raman spectroscopy (SERS) to assess MAYV nanomechanical properties, including maps of adhesion force and Young's modulus on individual viral particles. We established topographic maps of MAYV in two and three dimensions, revealing the three-dimensional arrangement and distribution of charges on viral spikes at the virus surface. Furthermore, the organization of the densely packaged RNA, which affords the viral particle exceptional mechanical resistance compared to chikungunya (CHIKV), was observed using MAYV adsorption patterns. The vibrational signature of MAYV particles differs from CHIKV, with more intense protein modes matching the distribution of E1/E2 dimers and the nucleocapsid, which are well structured and suggestive of mechanical strength.

Diabetes and Cognitive Decline: An Innovative Approach to Analyzing the Biophysical and Vibrational Properties of the Hippocampus

Diabetes Mellitus (DM) is a disease characterized by high blood glucose levels, known as hyperglycemia. Diabetes represents a risk factor for the development of neurodegenerative diseases, such as Alzheimer's Disease (AD), one of the most prevalent neurodegenerative diseases worldwide, which leads to progressive mental, behavioral, and functional decline, affecting many brain structures, especially the hippocampus. Here, we aim to characterize the ultrastructural, nanomechanical, and vibrational changes in hyperglycemic hippocampal tissue using atomic force microscopy (AFM) and Raman spectroscopy. DM was induced in rats by streptozotocin injection (type 1) or dietary intervention (type 2). Cryosections of the hippocampus were prepared and analyzed on an MM8 AFM (Bruker) in Peak Force Quantitative Nanomechanics mode, performing 25 μm2 scans in 9 regions of 3 samples from each group. Ultrastructural and nanomechanical data such as surface roughness, area, volume, Young's modulus, and adhesion were evaluated. The hippocampal samples were also analyzed on a T64000 Spectrometer (Horiba), using a laser λ = 632.8 nm, and for each sample, four spectra were obtained in different regions. AFM analyses show changes on the ultrastructural scale since diabetic animals had hippocampal tissue with greater roughness and volume. Meanwhile, diabetic tissues had decreased adhesion and Young's modulus compared to control tissues. These were corroboratedby Raman data that shows changes in the molecular composition of diabetic tissues. The individual spectra show that the most significant changes are in the amide, cholesterol, and lipid bands. Overall, the data presented here show that hyperglycemia induces biophysical alterations in the hippocampal tissue of diabetic rats, providing novel biophysical and vibrational cues on the relationship between hyperglycemia and dementia.

Insights on the Mechanical Properties of SARS-CoV-2 Particles and the Effects of the Photosensitizer Hypericin

SARS-CoV-2 is a highly pathogenic virus responsible for the COVID-19 disease. It belongs to the Coronaviridae family, characterized by a phospholipid envelope, which is crucial for viral entry and replication in host cells. Hypericin, a lipophilic, naturally occurring photosensitizer, was reported to effectively inactivate enveloped viruses, including SARS-CoV-2, upon light irradiation. In addition to its photodynamic activity, Hyp was found to exert an antiviral action also in the dark. This study explores the mechanical properties of heat-inactivated SARS-CoV-2 viral particles using Atomic Force Microscopy (AFM). Results reveal a flexible structure under external stress, potentially contributing to the virus pathogenicity. Although the fixation protocol causes damage to some particles, correlation with fluorescence demonstrates colocalization of partially degraded virions with their genome. The impact of hypericin on the mechanical properties of the virus was assessed and found particularly relevant in dark conditions. These preliminary results suggest that hypericin can affect the mechanical properties of the viral envelope, an effect that warrants further investigation in the context of antiviral therapies.

Physical virology: how physics is enabling a better understanding of recent viral invaders

The world is frequently afflicted by several viral outbreaks that bring diseases and health crises. It is vital to comprehend how viral assemblies' fundamental components work to counteract them. Determining the ultrastructure and nanomechanical characteristics of viruses from a physical standpoint helps categorize their mechanical characteristics, offers insight into new treatment options, and/or shows weak spots that can clarify methods for medication targeting. This study compiles the findings from studies on the ultrastructure and nanomechanical behavior of SARS-CoV-2, ZIKV (Zika virus), and CHIKV (Chikungunya virus) viral particles. With results that uncovered aspects of the organization and the spatial distribution of the proteins on the surface of the viral particle as well as the deformation response of the particles when applied a recurring loading force, this review aims to provide further discussion on the mechanical properties of viral particles at the nanoscale, offering new prospects that could be employed for designing strategies for the prevention and treatment of viral diseases.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12551-023-01075-4.

Nanomechanical and Vibrational Signature of Chikungunya Viral Particles

Chikungunya virus (CHIKV) belongs to the genus Alphaviridae, with a single-stranded positive-sense RNA genome of 11.8 kbp encoding a polyprotein that generates both non-structural proteins and structural proteins. The virus is transmitted by the Aedes aegypti and A. albopictus mosquitoes, depending on the location. CHIKV infection leads to dengue-like musculoskeletal symptoms and has been responsible for several outbreaks worldwide since its discovery in 1952. Patients often experience fever, headache, muscle pain, joint swelling, and skin rashes. However, the ultrastructural and mechanical properties of CHIKV have not been fully characterized. Thus, this study aims to apply a physical approach to investigate CHIKV's ultrastructural morphology and mechanical properties, using atomic force microscopy and Raman spectroscopy as the main tools. Using nanomechanical assays of AFM and a gold nanoparticles substrate for Raman signal enhancement, we explored the conformational plasticity, morphology, vibrational signature, and nanomechanical properties of the chikungunya virus, providing new information on its ultrastructure at the nanoscale and offering a novel understanding of the virus' behavior upon mechanical disruptions besides its molecular composition.

Optimized production and fluorescent labeling of SARS-CoV-2 virus-like particles

SARS-CoV-2 is an RNA enveloped virus responsible for the COVID-19 pandemic that conducted in 6 million deaths worldwide so far. SARS-CoV-2 particles are mainly composed of the 4 main structural proteins M, N, E and S to form 100 nm diameter viral particles. Based on productive assays, we propose an optimal transfected plasmid ratio mimicking the viral RNA ratio in infected cells. This allows SARS-CoV-2 Virus-Like Particle (VLPs) formation composed of the viral structural proteins M, N, E and mature S. Furthermore, fluorescent or photoconvertible VLPs were generated by adding a fluorescent protein tag on N or M mixing with unlabeled viral proteins and characterized by western blots, atomic force microscopy coupled to fluorescence and immuno-spotting. Thanks to live fluorescence and super-resolution microscopies, we quantified VLPs size and concentration. SARS-CoV-2 VLPs present a diameter of 110 and 140 nm respectively for MNE-VLPs and MNES-VLPs with a concentration of 10e12 VLP/ml. In this condition, we were able to establish the incorporation of the Spike in the fluorescent VLPs. Finally, the Spike functionality was assessed by monitoring fluorescent MNES-VLPs docking and internalization in human pulmonary cells expressing or not the receptor hACE2. Results show a preferential maturation of S on N(GFP) labeled VLPs and an hACE2-dependent VLP internalization and a potential fusion in host cells. This work provides new insights on the use of non-fluorescent and fluorescent VLPs to study and visualize the SARS-CoV-2 viral life cycle in a safe environment (BSL-2 instead of BSL-3). Moreover, optimized SARS-CoV-2 VLP production can be further adapted to vaccine design strategies.

Zika Virus (ZIKV): A New Perspective on the Nanomechanical and Structural Properties

Zika virus (ZIKV) is an arthropod-borne virus (arbovirus) from Flavivirus. In 2015, Brazil and other Latin American countries experienced an outbreak of ZIKV infections associated with severe neurological disorders such as Guillain–Barre syndrome (GBS), encephalopathy, and encephalitis. Here, a complete mechanical and structural analysis of the ZIKV has been performed using Atomic Force Microscopy (AFM). AFM analysis corroborated the virus mean size (~50 nm) and icosahedral geometry and revealed high mechanical resistance of both: the viral surface particle (~200 kPa) and its internal content (~800 kPa). The analysis demonstrated the detailed organization of the nucleocapsid structure (such as RNA strips). An interesting finding was the discovery that ZIKV has no surface self-assembling property. These results can contribute to the development of future treatment candidates and circumscribe the magnitude of viral transmission.

Layer-by-Layer Investigation of Ultrastructures and Biomechanics of Human Cornea

The cornea is an avascular, innervated, and transparent tissue composed of five layers: the epithelium, Bowman’s layer, stroma, Descemet’s membrane, and endothelium. It is located in the outermost fraction of the eyeball and is responsible for the refraction of two-thirds of light and protection from external mechanical damage. Although several studies have been done on the cornea on the macroscopic scale, there is a lack of studies on the micro-nanoscopic scale, especially an analysis evaluating the cornea layer by layer. In this study, atomic force microscopy (AFM) was employed to assess four layers that form the cornea, analyzing: adhesion, stiffness, and roughness. The results showed microvilli in the epithelial and endothelial layers, pores in the basement membrane, and collagen fibers in the Stroma. These data increase the knowledge about the human cornea layers’ ultrastructures and adds new information about its biophysical properties.

Polymeric nanoparticles and nanomicelles of hydroxychloroquine co-loaded with azithromycin potentiate anti-SARS-CoV-2 effect

The outbreak of coronavirus (COVID-19) has put the world in an unprecedented scenario. To reestablish the world routine as promote the effective treatment of this disease, the world is looking for new (and old) drug that can efficiently kill the virus. In this study, we have developed two nanosystems: polymeric nanoparticles and nanomicelles-based on hydroxychloroquine and azithromycin. The nanosystem was fully characterized by AFM and DLS techniques. Also, the nanosystems were radiolabeled with 99mTc and pulmonary applied (installation) in vivo to evaluate the biological behavior. The toxicity of both nanosystem were evaluated in primary cells (FGH). Finally, both nanosystems were evaluated in vitro against the SARS-CoV-2. The results demonstrated that the methodology used to produce the nanomicelles and the nanoparticle was efficient, the characterization showed a nanoparticle with a spherical shape and a medium size of 390 nm and a nanomicelle also with a spherical shape and a medium size of 602 nm. The nanomicelles were more efficient (~ 70%) against SARS-CoV-2 than the nanoparticles. The radiolabeling process with 99mTc was efficient (> 95%) in both nanosystems and the pulmonary application demonstrated to be a viable route for both nanosystems with a local retention time of approximately, 24 h. None of the nanosystems showed cytotoxic effect on FGH cells, even in high doses, corroborating the safety of both nanosystems. Thus, claiming the benefits of the nanotechnology, especially with regard the reduced adverse we believe that the use of nanosystems for COVID-19 treatment can be an optimized choice.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s40097-022-00476-3.