Investigation of the Effect of Temperature on the Structure of SARS-CoV-2 Spike Protein by Molecular Dynamics Simulations

AlphaFold2 Reveals Structural Patterns of Seasonal Haplotype Diversification in SARS-CoV-2 Spike Protein Variants

The slow experimental acquisition of high-quality atomic structures of the rapidly changing proteins of the COVID-19 virus challenges vaccine and therapeutic drug development efforts. Fortunately, deep learning tools such as AlphaFold2 can quickly generate reliable models of atomic structure at experimental resolution. Current modeling studies have focused solely on definitions of mutant constellations of Variants of Concern (VOCs), leaving out the impact of haplotypes on protein structure. Here, we conduct a thorough comparative structural analysis of S-proteins belonging to major VOCs and corresponding latitude-delimited haplotypes that affect viral seasonal behavior. Our approach identified molecular regions of importance as well as patterns of structural recruitment. The S1 subunit hosted the majority of structural changes, especially those involving the N-terminal domain (NTD) and the receptor-binding domain (RBD). In particular, structural changes in the NTD were much greater than just translations in three-dimensional space, altering the sub-structures to greater extents. We also revealed a notable pattern of structural recruitment with the early VOCs Alpha and Delta behaving antagonistically by suppressing regions of structural change introduced by their corresponding haplotypes, and the current VOC Omicron behaving synergistically by amplifying or collecting structural change. Remarkably, haplotypes altering the galectin-like structure of the NTD were major contributors to seasonal behavior, supporting its putative environmental-sensing role. Our results provide an extensive view of the evolutionary landscape of the S-protein across the COVID-19 pandemic. This view will help predict important regions of structural change in future variants and haplotypes for more efficient vaccine and drug development.

Comparative Study of the Mutations Observed in the SARS-CoV-2 RBD Variants of Concern and Their Impact on the Interaction with the ACE2 Protein

SARS-CoV-2 strains have made an appearance across the globe, causing over 757 million cases and over 6.85 million deaths at the time of writing. The emergence of these variants shows the amplitude of genetic variation to which the wild-type strains have been subjected. The rise of the different SARS-CoV-2 variants resulting from such genetic modification has significantly affected COVD-19's major impact on proliferation, virulence, and clinics. With the emergence of the variants of concern, the spike protein has been identified as a possible therapeutic target due to its critical role in binding to human cells and pathogenesis. These mutations could be linked to functional heterogeneity and use a different infection strategy. For example, the Omicron variant's multiple mutations should be carefully examined, as they represent one of the most widely spread strains and hint to us that there may be more genetic changes in the virus. As a result, we applied a common protocol where we reconstructed SARS-CoV-2 variants of concern and performed molecular dynamics simulations to study the stability of the ACE2-RBD complex in each variant. We also carried out free energy calculations to compare the binding and biophysical properties of the different SARS-CoV-2 variants when they interact with ACE2. Therefore, we were able to obtain consistent results and uncover new crucial residues that were essential for preserving a balance between maintaining a high affinity for ACE2 and the capacity to evade RBD-targeted antibodies. Our detailed structural analysis showed that SARS-CoV-2 variants of concern show a higher affinity for ACE2 compared to the Wuhan strain. Additionally, residues K417N and E484K/A might play a crucial role in antibody evasion, whereas Q498R and N501Y are specifically mutated to strengthen RBD affinity to ACE2 and, thereby, increase the viral effect of the COVID-19 virus.

Conformational characterization of the mammalian-expressed SARS-CoV-2 recombinant receptor binding domain, a COVID-19 vaccine

The COVID-19 pandemic has caused a large number of diseases worldwide. There are few vaccines to constrain this disease and the value of them is high. In this sense, the antigens of the vaccine platform Soberana, the receptor binding domain from SARS-CoV-2 Spike protein, both the monomeric (mRBD) and dimeric (dRBD) forms, have been developed. This study encompassed several analyses by different techniques like circular dichroism (CD), fluorescence spectroscopy (FS) and Gel Filtration- High Performance Liquid ChLC of mRBD and dRBD. Monomer and dimer exhibited similar far-UV CD spectral characteristics with 54% of β-sheet content. Similar conformational features according to near-UV CD and FS studies were observed in both RBD. Stress stability studies by far-UV CD, FS, biological activity and GF-HPLC at 37 °C showed that mRBD is very stable. On the other hand, dRBD fluorescent emission showed a shift towards higher wavelengths as the incubation time increases, suggesting exposition of tryptophan residues, unlike what happens with mRBD. Biological activity outcome confirms these results. GF-HPLC profiles showed that in mRBD, the product of molecular stress are dimers and does not increase over time. However, dRBD showed dimer fragmentation as the main degradation species. This study reveals the usefulness of CD techniques for the analysis of degradation of RBD molecules as well as showed the difference in stability of both RBD molecules. Besides, our work provides useful insights into the production of a key protein used in diagnosis and therapeutics to fight COVID-19 pandemia.

Seasonal effects decouple SARS-CoV-2 haplotypes worldwide

Background: Variants of concern (VOCs) have been replacing each other during the still rampant COVID-19 pandemic. As a result, SARS-CoV-2 populations have evolved increasingly intricate constellations of mutations that often enhance transmissibility, disease severity, and other epidemiological characteristics. The origin and evolution of these constellations remain puzzling. Methods: Here we study the evolution of VOCs at the proteome level by analyzing about 12 million genomic sequences retrieved from GISAID on July 23, 2022. A total 183,276 mutations were identified and filtered with a relevancy heuristic. The prevalence of haplotypes and free-standing mutations was then tracked monthly in various latitude corridors of the world. Results: A chronology of 22 haplotypes defined three phases driven by protein flexibility-rigidity, environmental sensing, and immune escape. A network of haplotypes illustrated the recruitment and coalescence of mutations into major VOC constellations and seasonal effects of decoupling and loss. Protein interaction networks mediated by haplotypes predicted communications impacting the structure and function of proteins, showing the increasingly central role of molecular interactions involving the spike (S), nucleocapsid (N), and membrane (M) proteins. Haplotype markers either affected fusogenic regions while spreading along the sequence of the S-protein or clustered around binding domains. Modeling of protein structure with AlphaFold2 showed that VOC Omicron and one of its haplotypes were major contributors to the distortion of the M-protein endodomain, which behaves as a receptor of other structural proteins during virion assembly. Remarkably, VOC constellations acted cooperatively to balance the more extreme effects of individual haplotypes. Conclusions: Our study uncovers seasonal patterns of emergence and diversification occurring amid a highly dynamic evolutionary landscape of bursts and waves. The mapping of genetically-linked mutations to structures that sense environmental change with powerful ab initio modeling tools demonstrates the potential of deep-learning for COVID-19 predictive intelligence and therapeutic intervention.

Adsorption and Inactivation of SARS-CoV-2 on the Surface of Anatase TiO2(101)

We investigated the adsorption of severe acute respiratory syndrome corona virus 2 (SARS-CoV-2), the virus responsible for the current pandemic, on the surface of the model catalyst TiO₂(101) using atomic force microscopy, transmission electron microscopy, fluorescence microscopy, and X-ray photoelectron spectroscopy, accompanied by density functional theory calculations. Three different methods were employed to inactivate the virus after it was loaded on the surface of TiO₂(101): (i) ethanol, (ii) thermal, and (iii) UV treatments. Microscopic studies demonstrate that the denatured spike proteins and other proteins in the virus structure readsorb on the surface of TiO₂ under thermal and UV treatments. The interaction of the virus with the surface of TiO₂ was different for the thermally and UV treated samples compared to the sample inactivated via ethanol treatment. AFM and TEM results on the UV-treated sample suggested that the adsorbed viral particles undergo damage and photocatalytic oxidation at the surface of TiO₂(101) which can affect the structural proteins of SARS-CoV-2 and denature the spike proteins in 30 min. The role of Pd nanoparticles (NPs) was investigated in the interaction between SARS-CoV-2 and TiO₂(101). The presence of Pd NPs enhanced the adsorption of the virus due to the possible interaction of the spike protein with the NPs. This study is the first investigation of the interaction of SARS-CoV-2 with the surface of single crystalline TiO₂(101) as a potential candidate for virus deactivation applications. Clarification of the interaction of the virus with the surface of semiconductor oxides will aid in obtaining a deeper understanding of the chemical processes involved in photoinactivation of microorganisms, which is important for the design of effective photocatalysts for air purification and self-cleaning materials.

Cold-adapted SARS-CoV-2 variants with different temperature sensitivity exhibit an attenuated phenotype and confer protective immunity

As novel SARS-CoV-2 Variants of Concern emerge, the efficacy of existing vaccines against COVID-19 is declining. A possible solution to this problem lies in the development of a live attenuated vaccine potentially able of providing cross-protective activity against a wide range of SARS-CoV-2 antigenic variants. Cold-adapted (ca) SARS-CoV-2 variants, Dubrovka-ca-B4 (D-B4) and Dubrovka-ca-D2 (D-D2), were obtained after long-term passaging of the Dubrovka (D) strain in Vero cells at reduced temperatures. Virulence, immunogenicity, and protective activity of SARS-CoV-2 variants were evaluated in experiments on intranasal infection of Syrian golden hamsters (Mesocricetus auratus). In animal model infecting with ca variants, the absence of body weight loss, the significantly lower viral titer and viral RNA concentration in animal tissues, the less pronounced inflammatory lesions in animal lungs as compared with the D strain indicated the reduced virulence of the virus variant. Single intranasal immunization with D-B4 and D-D2 variants induced the production of neutralizing antibodies in hamsters and protected them from infection with the D strain and the development of severe pneumonia. It was shown that for ca SARS-CoV-2 variants, the temperature-sensitive (ts) phenotype was not obligate for virulence reduction. Indeed, the D-B4 variant, which did not possess the ts phenotype but had lost the ability to infect human lung cells Calu-3, exhibited reduced virulence in hamsters. Consequently, the potential phenotypic markers of attenuation of ca SARS-CoV-2 variants are the ca phenotype, the ts phenotype, and the change in species specificity of the virus. This study demonstrates the great potential of SARS-CoV-2 cold adaptation as a strategy to develop a live attenuated COVID-19 vaccine.

Computational Exploration of Anti-cancer Potential of Flavonoids against Cyclin-Dependent Kinase 8: An In Silico Molecular Docking and Dynamic Approach

Over the centuries, cancer has been considered one of the significant health threats. It holds the position in the list of deadliest diseases over the globe. In women, breast cancer is the most common among many cancers and is the second most common cancer all over the world, while lung cancer is the first. Cyclin-dependent kinase 8 (CDK8) has been identified as a critical oncogenic driver that is found in breast cancer and associated with tumor progression. Flavonoids were virtually screened against CDK8 using molecular docking, drug-likeness, ADMET prediction, and a molecular dynamics (MD) simulation approach to determine the potential flavonoid structure against CDK8. The results indicated that ZINC000005854718 showed the highest negative binding affinity of -10.7 kcal/mol with the targeted protein and passed all the drug-likeness parameters. Performed molecular dynamics simulation showed that docked complex systems have good conformational stability over 100 ns in different temperatures (298, 300, 305, 310, and 320 K). The comparison between calculated binding free energy via MM/PB(GB)SA methods and binding affinity calculated via molecular docking suggested tight binding of ZINC000005854718 with targeted protein. The results concluded that ZINC000005854718 has drug-like properties with tight and stable binding with the targeted protein.

Computational Approaches to Designing Antiviral Drugs against COVID-19: A Comprehensive Review

The global impact of the COVID-19 pandemic caused by SARS-CoV-2 necessitates innovative strategies for the rapid development of effective treatments. Computational methodologies, such as molecular modelling, molecular dynamics simulations, and artificial intelligence, have emerged as indispensable tools in the drug discovery process. This review aimed to provide a comprehensive overview of these computational approaches and their application in the design of antiviral agents for COVID-19. Starting with an examination of ligand-based and structure-based drug discovery, the review has delved into the intricate ways through which molecular modelling can accelerate the identification of potential therapies. Additionally, the investigation extends to phytochemicals sourced from nature, which have shown promise as potential antiviral agents. Noteworthy compounds, including gallic acid, naringin, hesperidin, Tinospora cordifolia, curcumin, nimbin, azadironic acid, nimbionone, nimbionol, and nimocinol, have exhibited high affinity for COVID-19 Mpro and favourable binding energy profiles compared to current drugs. Although these compounds hold potential, their further validation through in vitro and in vivo experimentation is imperative. Throughout this exploration, the review has emphasized the pivotal role of computational biologists, bioinformaticians, and biotechnologists in driving rapid advancements in clinical research and therapeutic development. By combining state-of-the-art computational techniques with insights from structural and molecular biology, the search for potent antiviral agents has been accelerated. The collaboration between these disciplines holds immense promise in addressing the transmissibility and virulence of SARS-CoV-2.

Survival of human coronavirus 229E at different temperatures on various food-contact surfaces and food and under simulated digestive conditions

The COVID-19 pandemic caused by SARS-CoV-2 has had a major impact on human health and the global economy. Various transmission possibilities of SARS-CoV-2 have been proposed, such as the surface of food in the cold chain and food packaging, as well as the fecal-oral route, although person-to-person contact via droplets and aerosols has been confirmed as the main route of transmission. This study evaluated the survivability of HCoV-229E, a SARS-CoV-2 surrogate, in suspension, on food-contact surfaces and on food at various temperatures, and in simulated digestive fluids by TCID₅₀ assay. In suspension, HCoV-229E survived after 5 days at 20 °C with a 3.69 log reduction, after 28 days at 4 °C with a 3.07 log reduction, and after 12 weeks at -20 °C with a 1.18 log reduction. On food-contact surfaces, HCoV-229E was not detected on day 3 on stainless steel (SS), plastic (LDPE), and silicone rubber (SR) at 20 °C with a 3.28, 3.24 and 3.28 log reduction, respectively, and survived after 28 days on SS and LDPE at 4 °C with a 3.13 and 2.88 log reduction, respectively, and survived after 12 weeks on SS, LDPE, and SR at -20 °C with a 1.92, 1.32 and 1.99 log reduction, respectively. On food, HCoV-229E was not detected on day 3 on lettuce and day 4 on chicken breast and salmon at 20 °C with a 3.61, 3.26 and 3.08 log reduction, respectively, and on day 14 on lettuce and day 21 on chicken breast and salmon at 4 °C with a 3.88, 3.44 and 3.56 log reduction, respectively. The virus remained viable for 12 weeks in all foods at -20 °C with 2-2.47 log reduction. In addition, in simulated digestive fluid experiments, HCoV-229E was relatively resistant in simulated salivary fluid (SSF; pH 7, 5), fed state simulated gastric fluid (FeSSGF; pH 3, 5, 7), and fasted state simulated intestinal fluid (FaSSIF; pH 7). However, the virus was less tolerant in fasted state simulated gastric fluid (FaSSGF; pH 1.6) and fed state simulated intestinal fluid (FeSSIF; pH 5). Therefore, this study suggested that HCoV-229E remained infectious on various food-contact surfaces and foods; in particular, it survived longer at lower temperatures and survived depending on the pH of the simulated digestive fluid.

Homology Modeling and Molecular Dynamics-Driven Search for Natural Inhibitors That Universally Target Receptor-Binding Domain of Spike Glycoprotein in SARS-CoV-2 Variants

The rapid spread of SARS-CoV-2 required immediate actions to control the transmission of the virus and minimize its impact on humanity. An extensive mutation rate of this viral genome contributes to the virus' ability to quickly adapt to environmental changes, impacts transmissibility and antigenicity, and may facilitate immune escape. Therefore, it is of great interest for researchers working in vaccine development and drug design to consider the impact of mutations on virus-drug interactions. Here, we propose a multitarget drug discovery pipeline for identifying potential drug candidates which can efficiently inhibit the Receptor Binding Domain (RBD) of spike glycoproteins from different variants of SARS-CoV-2. Eight homology models of RBDs for selected variants were created and validated using reference crystal structures. We then investigated interactions between host receptor ACE2 and RBDs from nine variants of SARS-CoV-2. It led us to conclude that efficient multi-variant targeting drugs should be capable of blocking residues Q(R)493 and N487 in RBDs. Using methods of molecular docking, molecular mechanics, and molecular dynamics, we identified three lead compounds (hesperidin, narirutin, and neohesperidin) suitable for multitarget SARS-CoV-2 inhibition. These compounds are flavanone glycosides found in citrus fruits - an active ingredient of Traditional Chinese Medicines. The developed pipeline can be further used to (1) model mutants for which crystal structures are not yet available and (2) scan a more extensive library of compounds against other mutated viral proteins.

Prerequisite for COVID-19 Prediction: A Review on Factors Affecting the Infection Rate

Since the year 2020, coronavirus disease 2019 (COVID-19) has emerged as the dominant topic of discussion in the public and research domains. Intensive research has been carried out on several aspects of COVID-19, including vaccines, its transmission mechanism, detection of COVID-19 infection, and its infection rate and factors. The awareness of the public related to the COVID-19 infection factors enables the public to adhere to the standard operating procedures, while a full elucidation on the correlation of different factors to the infection rate facilitates effective measures to minimize the risk of COVID-19 infection by policy makers and enforcers. Hence, this paper aims to provide a comprehensive and analytical review of different factors affecting the COVID-19 infection rate. Furthermore, this review analyses factors which directly and indirectly affect the COVID-19 infection risk, such as physical distance, ventilation, face masks, meteorological factor, socioeconomic factor, vaccination, host factor, SARS-CoV-2 variants, and the availability of COVID-19 testing. Critical analysis was performed for the different factors by providing quantitative and qualitative studies. Lastly, the challenges of correlating each infection risk factor to the predicted risk of COVID-19 infection are discussed, and recommendations for further research works and interventions are outlined.

Understanding the role of water on temperature-dependent structural modifications of SARS CoV-2 main protease binding sites

Thermally stable and labile proteases are found in microorganisms. Protease mediates the cleavage of polyproteins in the virus replication and transcription process. 6 µs MD simulations were performed for monomer/dimer SARS CoV-2 main protease system in both SPC/E and mTIP3P water model to analyse the temperature-dependent behaviour of the protein. It is found that maximum conformational changes are observed at 348 K which is near the melting temperature. Network distribution of evolved conformations shows an increase in the number of communities with the rise in the temperature. The global conformation of the protein was found to be intact whereas a local conformational space evolved due to thermal fluctuations. The global conformational change in the free energy ΔΔG value for the monomer and the dimer between 278 K and 383 K is found to be 2.51 and 2.10 kJ/mol respectively. A detailed analysis was carried out on the effect of water on the temperature-dependent structural modifications of four binding pockets of SARS CoV-2 main protease namely, catalytic dyad, substrate-binding site, dimerization site and allosteric site. It is found that the water structure around the binding sites is altered with temperature. The water around the dimer sites is more ordered than the monomer sites regardless of the rise in temperature due to structural rigidity. The energy expense of binding the small molecules at substrate binding is less compared to the allosteric site. The water-water hydrogen bond lifetime is found to be more near the cavity of His41. Also, it is observed that mTIP3P water molecules have a similar effect to that of SPC/E water molecules on the main protease.

Modeling of the thermal properties of SARS-CoV-2 S-protein

We calculate the thermal and conformational states of the spike glycoprotein (S-protein) of SARS-CoV-2 at seven temperatures ranging from 3°C to 95°C by all-atom molecular dynamics (MD) µs-scale simulations with the objectives to understand the structural variations on the temperatures and to determine the potential phase transition while trying to correlate such findings of the S-protein with the observed properties of the SARS-CoV2. Our simulations revealed the following thermal properties of the S-protein: 1) It is structurally stable at 3°C, agreeing with observations that the virus stays active for more than two weeks in the cold supply chain; 2) Its structure varies more significantly at temperature values of 60°C–80°C; 3) The sharpest structural variations occur near 60°C, signaling a plausible critical temperature nearby; 4) The maximum deviation of the receptor-binding domain at 37°C, corroborating the anecdotal observations that the virus is most infective at 37°C; 5) The in silico data agree with reported experiments of the SARS-CoV-2 survival times from weeks to seconds by our clustering approach analysis. Our MD simulations at µs scales demonstrated the S-protein’s thermodynamics of the critical states at around 60°C, and the stable and denatured states for temperatures below and above this value, respectively.

Effect of heat inactivation and bulk lysis on real-time reverse transcription PCR detection of the SARS-COV-2: an experimental study

Objective

This study aimed to investigate the effect of heat inactivation and chemical bulklysis on SARS-CoV-2 detection.

Results

About 6.2% (5/80) of samples were changed to negative results in heat inactivation at 60 °C and about 8.7% (7/80) of samples were changed to negative in heat inactivation at 100 °C. The Ct values of heat-inactivated samples (at 60 °C, at 100 °C, and bulk lysis) were significantly different from the temperature at 56 °C. The effect of heat on Ct value should be considered when interpreting diagnostic PCR results from clinical samples which could have an initial low virus concentration. The efficacy of heat-inactivation varies greatly depending on temperature and duration. Local validation of heat-inactivation and its effects is therefore essential for molecular testing.

Unfolding of the SARS-CoV-2 spike protein through infrared and ultraviolet-C radiation based disinfection

The spreading of coronavirus from contacting surfaces and aerosols created a pandemic around the world. To prevent the transmission of SARS-CoV-2 virus and other contagious microbes, disinfection of contacting surfaces is necessary. In this study, a disinfection box equipped with infrared (IR) radiation heating and ultraviolet-C (UV-C) radiation is designed and tested for its disinfection ability against pathogenic bacteria and SARS-CoV-2 spike protein. The killing of a Gram-positive, namely, S. aureus and a Gram-negative namely, S. typhi bacteria was studied followed by the inactivation of the spike protein. The experimental parameters were optimized using a statistical tool. For the broad-spectrum antibacterial activity, the optimum condition was holding at 65.61 °C for 13.54 min. The killing of the bacterial pathogen occurred via rupturing the cell walls as depicted by electron microscopy. Further, the unfolding of SARS-CoV-2 spike protein and RNase was studied under IR and UV-C irradiations at the aforesaid optimized condition. The unfolding of both the proteins was confirmed by changes in the secondary structure, particularly an increase in β-sheets and a decrease in α-helixes. Remarkably, the higher penetration depth of IR waves up to subcutaneous tissue resulted in lower optimum disinfection temperature, <70 °C in vogue. Thus, the combined UV-C and IR radiation is effective in killing the pathogenic bacteria and denaturing the glycoproteins.

Risk of air and surface contamination of SARS-CoV-2 in isolation wards and its relationship with patient and environmental characteristics

Air and surface contamination of the SARS-CoV-2 have been reported by multiple studies. However, the evidence is limited for the change of environmental contamination of this virus in the surrounding of patients with COVID-19 at different time points during the course of disease and under different conditions of the patients. Therefore, this study aims to understand the risk factors associated with the appearance of SARS-CoV-2 through the period when the patients were staying in the isolation wards. In this study, COVID-19 patients admitted to the isolation wards were followed up for up to 10 days for daily collection of air and surface samples in their surroundings. The positivity rate of the environmental samples at different locations was plotted, and multiple multi-level mixed-effect logistic regressions were used to examine the association between the positivity of environmental samples and their daily health conditions and environmental factors. It found 6.6 % of surface samples (133/2031 samples) and 2.1 % of air samples (22/1075 samples) were positive, and the positivity rate reached to peak during 2-3 days after admission to the ward. The virus was more likely to present at bedrail, patients' personal items and medical equipment, while less likely to be detected in the air outside the range of 2 m from the patients. It also revealed that higher positivity rate is associated with lower environmental temperature, fever and cough at the day of sampling, lower Ct values of latest test for respiratory tract samples, and pre-existing respiratory or cardiovascular conditions. The finding can be used to guide the hospital infection control strategies by identifying high-risk areas and patients. Extra personal hygiene precautions and equipment for continuously environmental disinfection can be used for these high-risk areas and patients to reduce the risk of hospital infection.

Molecular dynamics simulations explore effects of electric field orientations on spike proteins of SARS-CoV-2 virions

Emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its current worldwide spread have caused a pandemic of acute respiratory disease COVID-19. The virus can result in mild to severe, and even to fatal respiratory illness in humans, threatening human health and public safety. The spike (S) protein on the surface of viral membrane is responsible for viral entry into host cells. The discovery of methods to inactivate the entry of SARS-CoV-2 through disruption of the S protein binding to its cognate receptor on the host cell is an active research area. To explore other prevention strategies against the quick spread of the virus and its mutants, non-equilibrium molecular dynamics simulations have been employed to explore the possibility of manipulating the structure–activity of the SARS-CoV-2 spike glycoprotein by applying electric fields (EFs) in both the protein axial directions and in the direction perpendicular to the protein axis. We have found out the application of EFs perpendicular to the protein axis is most effective in denaturing the HR2 domain which plays critical role in viral-host membrane fusion. This finding suggests that varying irradiation angles may be an important consideration in developing EF based non-invasive technologies to inactivate the virus.

How Does Temperature Affect the Dynamics of SARS-CoV-2 M Proteins? Insights from Molecular Dynamics Simulations

Enveloped viruses, in general, have several transmembrane proteins and glycoproteins, which assist the virus in entry and attachment onto the host cells. These proteins also play a significant role in determining the shape and size of the newly formed virus particles. The lipid membrane and the embedded proteins affect each other in non-trivial ways during the course of the viral life cycle. Unraveling the nature of the protein-protein and protein-lipid interactions, under various environmental and physiological conditions, could therefore prove to be crucial in development of therapeutics. Here, we study the M protein of SARS-CoV-2 to understand the effect of temperature on the properties of the protein-membrane system. The membrane-embedded dimeric M proteins were studied using atomistic and coarse-grained molecular dynamics simulations at temperatures ranging between 10 and 50 °C. While temperature-induced fluctuations are expected to be monotonic, we observe a steady rise in the protein dynamics up to 40 °C, beyond which it surprisingly reverts back to the low-temperature behavior. Detailed investigation reveals disordering of the membrane lipids in the presence of the protein, which induces additional curvature around the transmembrane region. Coarse-grained simulations indicate temperature-dependent aggregation of M protein dimers. Our study clearly indicates that the dynamics of membrane lipids and integral M protein of SARS-CoV-2 enables it to better associate and aggregate only at a certain temperature range (i.e., ~ 30-40 °C). This can have important implications in the protein aggregation and subsequent viral budding/fission processes.

Fever as an evolutionary agent to select immune complexes interfaces

We herein analyzed all available protein–protein interfaces of the immune complexes from the Protein Data Bank whose antigens belong to pathogens or cancers that are modulated by fever in mammalian hosts. We also included, for comparison, protein interfaces from immune complexes that are not significantly modulated by the fever response. We highlight the distribution of amino acids at these viral, bacterial, protozoan and cancer epitopes, and at their corresponding paratopes that belong strictly to monoclonal antibodies. We identify the “hotspots”, i.e. residues that are highly connected at such interfaces, and assess the structural, kinetic and thermodynamic parameters responsible for complex formation. We argue for an evolutionary pressure for the types of residues at these protein interfaces that may explain the role of fever as a selective force for optimizing antibody binding to antigens.

Peptide-based simple detection of SARS-CoV-2 with electrochemical readout

Coronavirus disease 2019 (COVID-19) caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is considered one of the worst pandemic outbreaks worldwide. This ongoing pandemic urgently requires rapid, accurate, and specific testing devices to detect the virus. We report a simple electrochemical biosensor based on a highly specific synthetic peptide to detect SARS-CoV-2 Spike protein. Unlike other reported electrochemical biosensors involving nanomaterials or complex approaches, our electrochemical platform uses screen-printed gold electrodes functionalized with the thiolated peptide, whose interaction with the Spike protein is directly followed by Electrochemical Impedance Spectroscopy. The electrochemical platform was Spike protein concentration-dependent, with high sensitivity and reproducibility and a limit of detection of 18.2 ng/mL when tested in Spike protein commercial solutions and 0.01 copies/mL in lysed SARS-CoV-2 particles. The label-free biosensor successfully detected the Spike protein in samples from infected patients straightforwardly in only 15 min. The simplicity of the proposed format combined with an on-demand designed peptide opens the path for detecting other pathogen-related antigens.

Molecular Dynamics Studies on the Structural Stability Prediction of SARS-CoV-2 Variants Including Multiple Mutants

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused the Coronavirus Disease (COVID-19) pandemic worldwide. The spike protein in SARS-CoV-2 fuses with and invades cells in the host respiratory system by binding to angiotensin-converting enzyme 2 (ACE2). The spike protein, however, undergoes continuous mutation from a D614G single mutant to an omicron variant, including multiple mutants. In this study, variants, including multiple mutants (double, triple mutants, B.1.620, delta, alpha, delta_E484Q, mu, and omicron) were investigated in patients. The 3D structure of the full-length spike protein was used in conformational analysis depending on the SARS-CoV-2 variants. The structural stability of the variant types was analyzed based on the distance between the receptor-binding domain (RBD) of each chain in the spike protein and the binding free energy between the spike protein and bound ACE2 in the one-, two-, and three-open-complex forms using molecular dynamics (MD) simulation. Omicron variants, the most prevalent in the recent history of the global pandemic, which consist of 32 mutations, showed higher stability in all open-complex forms compared with that of the wild type and other variants. We suggest that the conformational stability of the spike protein is the one of the important determinants for the differences in viral infectivity among variants, including multiple mutants.

Pharmaceutical Prospects of Curcuminoids for the Remedy of COVID-19: Truth or Myth

Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is a positive-strand RNA virus, and has rapidly spread worldwide as a pandemic. The vaccines, repurposed drugs, and specific treatments have led to a surge of novel therapies and guidelines nowadays; however, the epidemic of COVID-19 is not yet fully combated and is still in a vital crisis. In repositioning drugs, natural products are gaining attention because of the large therapeutic window and potent antiviral, immunomodulatory, anti-inflammatory, and antioxidant properties. Of note, the predominant curcumoid extracted from turmeric (Curcuma longa L.) including phenolic curcumin influences multiple signaling pathways and has demonstrated to possess anti-inflammatory, antioxidant, antimicrobial, hypoglycemic, wound healing, chemopreventive, chemosensitizing, and radiosensitizing spectrums. In this review, all pieces of current information related to curcumin-used for the treatment and prevention of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection through in vitro, in vivo, and in silico studies, clinical trials, and new formulation designs are retrieved to re-evaluate the applications based on the pharmaceutical efficacy of clinical therapy and to provide deep insights into knowledge and strategy about the curcumin's role as an immune booster, inflammatory modulator, and therapeutic agent against COVID-19. Moreover, this study will also afford a favorable application or approach with evidence based on the drug discovery and development, pharmacology, functional foods, and nutraceuticals for effectively fighting the COVID-19 pandemic.

Molecular dynamics simulation and docking analysis of NF-κB protein binding with sulindac acid

It is of interest to document the Molecular Dynamics Simulation and docking analysis of NF-κB target with sulindac sodium in combating COVID-19 for further consideration. Sulindac is a nonsteroidal anti-inflammatory drug (NSAID) of the arylalkanoic acid class that is marketed by Merck under the brand name Clinoril. We show the binding features of sulindac sodium with NF-κB that can be useful in drug repurposing in COVID-19 therapy.

Intra-protein interactions of SARS-CoV-2 and SARS: a bioinformatic analysis for plausible explanation regarding stability, divergency, and severity

The current nightmare for the whole world is COVID-19. The occurrence of concentrated pneumonia cases in Wuhan city, Hubei province of China, was first reported on December 30, 2019. SARS-CoV first disclosed in 2002 but had not outspread worldwide. After 18 years, in 2020, it reemerged and outspread worldwide as SARS-CoV-2 (COVID-19), as the most dangerous virus-creating disease in the world. Is it possible to create a favorable evolution within the short time (18 years)? If possible, then what are those properties or factors that are changed in SARS-CoV-2 to make it undefeated? What are the fundamental differences between SARS-CoV-2 and SARS? The study is one of the initiatives to find out all those queries. Here, four types of protein sequences from SARS-CoV-2 and SARS were retrieved from the database to study their physicochemical and structural properties. Results showed that charged residues are playing a pivotal role in SARS-CoV-2 evolution and contribute to the helix stabilization. The formation of the cyclic salt bridge and other intra-protein interactions specially network aromatic-aromatic interaction also play the crucial role in SAS-CoV-2. This comparative study will help to understand the evolution from SARS to SARS-CoV-2 and helpful in protein engineering.

Determination of the denaturation temperature of the Spike protein S1 of SARS-CoV-2 (2019 nCoV) by Raman spectroscopy

In the present work the temperature response of the constitutive S1 segment of the SARS-CoV-2 Spike Glycoprotein (GPS) has been studied. The intensity of the Raman bands remained almost constant before reaching a temperature of 133 °C. At this temperature a significant reduction of peak intensities was observed. Above 144 °C the spectra ceased to show any recognizable feature as that of the GPS S1, indicating that it had transformed after the denaturation process that it was subjected. The GPS S1 change is irreversible. Hence, Raman Spectroscopy (RS) provides a precision method to determine the denaturation temperature (T_D) of dry powder GPS S1. The ability of RS was calibrated through the reproduction of T_D of other well studied proteins as well as those of the decomposition temperature of some amino acids (AA). Through this study we established a T_D of 139 ± 3 °C for powder GPS S1 of SARS-CoV-2.

SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessibility

Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has killed over 6 million people and is having a devastating social and economic impact around the world. The rise of new variants of concern (VOCs) represents a difficult challenge due to the loss of vaccine and natural immunity, as well as increased transmissibility. All VOCs contain mutations in the spike glycoprotein, which mediates fusion between the viral and host cell membranes. The spike glycoprotein binds to angiotensin-converting enzyme 2 (ACE2) via its receptor binding domain (RBD) initiating the infection process. Attempting to understand the effect of RBD mutations in VOCs, a lot of attention has been given to the RBD-ACE2 interaction. However, this type of analysis ignores more indirect effects, such as the conformational dynamics of the RBD itself. Observing that some mutations occur in residues that are not in direct contact with ACE2, we hypothesized that they could affect the RBD conformational dynamics. To test this, we performed long atomistic (AA) molecular dynamics (MD) simulations to investigate the structural dynamics of wt RBD, and that of four VOCs (Alpha, Beta, Delta, and Omicron). Our results show that the wt RBD presents two distinct conformations: an "open" conformation where it is free to bind ACE2; and a "closed" conformation, where the RBM ridge blocks the binding surface. The Alpha and Beta variants shift the open/closed equilibrium towards the open conformation by roughly 20%, likely increasing ACE2 binding affinity. Simulations of the Delta and Omicron variants showed extreme results, with the closed conformation being rarely observed. The Delta variant also differed substantially from the other variants, alternating between the open conformation and an alternative "reversed" one, with a significantly changed orientation of the RBM ridge. This alternate conformation could provide a fitness advantage due to increased availability for ACE2 binding, and by aiding antibody escape through epitope occlusion. These results support the hypothesis that VOCs, and particularly the Omicron and Delta variants, impact RBD conformational dynamics in a direction that promotes efficient binding to ACE2 and, in the case of Delta, may assist antibody escape.

Roles of the polybasic furin cleavage site of spike protein in SARS-CoV-2 replication, pathogenesis, and host immune responses and vaccination

The polybasic furin cleavage site insertion with four amino acid motifs (PRRA) in spike protein's S1/S2 junction site is important in determining viral infectivity, transmission, and host range. However, there is no review so far explaining the effect of the furin cleavage site of the spike protein on SARS-CoV-2 replication and pathogenesis in the host and immune responses and vaccination. Therefore, here we specifically focused on genomic evolution and properties of the cleavage site of spike protein in the context of SARS-CoV-2 followed by its effect on viral entry, replication, and pathogenesis. We also explored whether the spike protein furin cleavage site affected the host immune responses and SARS-CoV-2 vaccination. This review will help to provide novel insights into the effects of polybasic furin cleavage site on the current COVID-19 pandemic.

An impedimetric approach for COVID-19 detection

In this study, an electrochemical approach for the determination of coronavirus disease (COVID-19) was developed. The biosensor system relied on the spike protein (S-protein) based infection mechanism of the virus and included separate interactions of receptors like angiotensin-converting enzyme 2 (ACE2) and CD147. After the optimization of experimental parameters, the analytical characteristics of both receptors ACE2 and CD147 were investigated. For ACE2 receptor, the linear detection ranges of the S-protein were found in the range of 700 ng mL^-1 to 1500 ng mL^-1 and from 1500 ng mL^-1 to 7000 ng mL^-1 with a limit of detection (LOD) value of 299.30 ng mL^-1. Meanwhile, for CD147 receptor the linear range was in the range of 500 ng mL^-1 to 5000 ng mL^-1 with a LOD value of 38.99 ng mL^-1. After the examination of analytical characteristics, the developed electrochemical approach was applied for severe acute respiratory syndrome coronavirus 2 samples and the obtained results were validated with real time polymerase chain reaction method.

Denaturation of the SARS-CoV-2 spike protein under non-thermal microwave radiation

SARS-CoV-2, the virus that causes COVID-19, is still a widespread threat to society. The spike protein of this virus facilitates viral entry into the host cell. Here, the denaturation of the S1 subunit of this spike protein by 2.45 GHz electromagnetic radiation was studied quantitatively. The study only pertains to the pure electromagnetic effects by eliminating the bulk heating effect of the microwave radiation in an innovative setup that is capable of controlling the temperature of the sample at any desired intensity of the electromagnetic field. This study was performed at the internal human body temperature, 37 °C, for a relatively short amount of time under a high-power electromagnetic field. The results showed that irradiating the protein with a 700 W, 2.45 GHz electromagnetic field for 2 min can denature the protein to around 95%. In comparison, this is comparable to thermal denaturation at 75 °C for 40 min. Electromagnetic denaturation of the proteins of the virus may open doors to potential therapeutic or sanitation applications.

Structural behavior of monomer of SARS-CoV-2 spike protein during initial stage of adsorption on graphene

Spike glycoprotein of the SARS-CoV-2 virus and its structure play a crucial role in the infections of cells containing angiotensin-converting enzyme 2 (ACE2) as well as in the interactions of this virus with surfaces. Protection against viruses and often even their deactivation is one of the great varieties of graphene applications. The structural changes of the non-glycosylated monomer of the spike glycoprotein trimer (denoted as S-protein in this work) triggered by its adsorption onto graphene at the initial stage are investigated by means of atomistic molecular dynamics simulations. The adsorption of the S-protein happens readily during the first 10 ns. The shape of the S-protein becomes more prolate during the adsorption, but this trend, albeit less pronounced, is observed also for the freely relaxing S-protein in water. The receptor-binding domain (RBD) of the free and adsorbed S-protein manifests itself as the most rigid fragment of the whole S-protein. The adsorption even enhances the rigidity of the whole S-protein as well as its subunits. Only one residue of the RBD involved in the specific interactions with ACE2 during the cell infection is involved in the direct contact of the adsorbed S-protein with the graphene. The new intramolecular hydrogen bonds formed during the S-protein adsorption replace the S-protein-water hydrogen bonds; this trend, although less apparent, is observed also during the relaxation of the free S-protein in water. In the initial phase, the secondary structure of the RBD fragment specifically interacting with ACE2 receptor is not affected during the S-protein adsorption onto the graphene.

Millisecond dynamic of SARS-CoV-2 spike and its interaction with ACE2 receptor and small extracellular vesicles

SARS-CoV-2 spike protein (S) binds to human angiotensin-converting enzyme 2 (hACE2), allowing virus to dock on cell membrane follow by viral entry. Here, we use high-speed atomic force microscopy (HS-AFM) for real-time visualization of S, and its interaction with hACE2 and small extracellular vesicles (sEVs). Results show conformational heterogeneity of S, flexibility of S stalk and receptor-binding domain (RBD), and pH/temperature-induced conformational change of S. S in an S-ACE2 complex appears as an all-RBD up conformation. The complex acquires a distinct topology upon acidification. S and S2 subunit demonstrate different membrane docking mechanisms on sEVs. S-hACE2 interaction facilitates S to dock on sEVs, implying the feasibility of ACE2-expressing sEVs for viral neutralization. In contrary, S2 subunit docks on lipid layer and enters sEV using its fusion peptide, mimicking the viral entry scenario. Altogether, our study provides a platform that is suitable for real-time visualization of various entry inhibitors, neutralizing antibodies, and sEV-based decoy in blocking viral entry. Teaser: Comprehensive observation of SARS-CoV-2 spike and its interaction with receptor ACE2 and sEV-based decoy in real time using HS-AFM.

The seasonal behaviour of COVID-19 and its galectin-like culprit of the viral spike

Seasonal behaviour is an attribute of many viral diseases. Like other 'winter' RNA viruses, infections caused by the causative agent of COVID-19, SARS-CoV-2, appear to exhibit significant seasonal changes. Here we discuss the seasonal behaviour of COVID-19, emerging viral phenotypes, viral evolution, and how the mutational landscape of the virus affects the seasonal attributes of the disease. We propose that the multiple seasonal drivers behind infectious disease spread (and the spread of COVID-19 specifically) are in 'trade-off' relationships and can be better described within a framework of a 'triangle of viral persistence' modulated by the environment, physiology, and behaviour. This 'trade-off' exists as one trait cannot increase without a decrease in another. We also propose that molecular components of the virus can act as sensors of environment and physiology, and could represent molecular culprits of seasonality. We searched for flexible protein structures capable of being modulated by the environment and identified a galectin-like fold within the N-terminal domain of the spike protein of SARS-CoV-2 as a potential candidate. Tracking the prevalence of mutations in this structure resulted in the identification of a hemisphere-dependent seasonal pattern driven by mutational bursts. We propose that the galectin-like structure is a frequent target of mutations because it helps the virus evade or modulate the physiological responses of the host to further its spread and survival. The flexible regions of the N-terminal domain should now become a focus for mitigation through vaccines and therapeutics and for prediction and informed public health decision making.

Epidemiological Analysis of SARS-CoV-2 Transmission Dynamics in the State of Odisha, India: A Yearlong Exploratory Data Analysis

COVID-19 remains a matter of global public health concern. Previous research suggested the association between local environmental factors and viral transmission. We present a multivariate observational analysis of SARS-CoV-2 transmission in the state of Odisha, India, hinting at a seasonal activity. We aim to investigate the demographic characteristics of COVID-19 in the Indian state of Odisha for two specific timelines in 2020 and 2021. For a comparative outlook, we chose similar datasets from the state of New York, USA. Further, we present a critical analysis pertaining to the effects of environmental factors and the emergence of variants on SARS-CoV-2 transmission and persistence. We assessed the datasets for confirmed cases, death, age, and gender for 29 February 2020 to 31 May 2020, and 1 March 2021 to 31 May 2021. We determined the case fatalities, crude death rates, sex ratio, and incidence rates for both states along with monthly average temperature analysis. A yearlong epi-curve analysis was conducted to depict the coronavirus infection spread pattern in the respective states. The Indian state of Odisha reported a massive 436,455 confirmed cases and 875 deaths during the 2021 timeline as compared to a mere 2223 cases and 7 deaths during the 2020 timeline. We further discuss the demographic and temperature association of SARS-CoV-2 transmission during early 2020 and additionally comment on the variant-associated massive rise in cases during 2021. Along with the rapid rise of variants, the high population density and population behavior seem to be leading causes for the 2021 pandemic, whereas factors such as age group, gender, and average local temperature were prominent during the 2020 spread. A seasonal occurrence of SARS-CoV-2 transmission is also observed from the yearlong epidemiological plot. The recent second wave of COVID-19 is a lesson that emphasizes the significance of continuous epidemiological surveillance to predict the relative risk of viral transmission for a specific region.

COVID-19 and environmental concerns: A rapid review

COVID-19 has slowed global economic growth and consequently impacted the environment as well. Parallelly, the environment also influences the transmission of this novel coronavirus through various factors. Every nation deals with varied population density and size; air quality and pollutants; the nature of land and water, which significantly impact the transmission of coronavirus. The WHO (Ziaeepour et al., 2008) [1] has recommended rapid reviews to provide timely evidence to the policymakers to respond to the emergency. The present study follows a rapid review along with a brief bibliometric analysis of 328 research papers, which synthesizes the evidence regarding the environmental concerns of COVID-19. The novel contribution of this rapid review is threefold. One, we take stock of the diverse findings as regards the transmission of the novel coronavirus in different types of environments for providing conclusive directions to the ongoing debate regarding the transmission of the virus. Two, our findings provide topical insights as well as methodological guidance for future researchers in the field. Three, we inform the policymakers on the efficacy of environmental measures for controlling the spread of COVID-19.

Carbon Nanotube Mask Filters and Their Hydrophobic Barrier and Hyperthermic Antiviral Effects on SARS-CoV-2

Carbon nanotube face mask filters have strong and uniform hydrophobicity, high durability, and high thermal conductivity and exhibit excellent barrier and antiviral effects against SARS-CoV-2. The nanocarbon filter functions as a superior barrier compared to those in conventional masks owing to the stronger, more uniform, and more durable hydrophobic nature of the carbon nanotubes. A tightly knit carbon nanotube network has a pore size smaller than that of the average coronavirus; nevertheless, the breathability is equal to that of the conventional polypropylene filter. The exceptional thermal conductivity of carbon nanotubes transpires hyperthermic antiviral effects, which offers stronger protection against the virus, as well as reusability. The facile processability, low cost, and light weight of the aerosol-synthesized carbon nanotube filter warrants its viability, reinforcing the fight against the COVID-19 pandemic.

Accelerating COVID-19 Research Using Molecular Dynamics Simulation

The COVID-19 pandemic has emerged as a global medico-socio-economic disaster. Given the lack of effective therapeutics against SARS-CoV-2, scientists are racing to disseminate suggestions for rapidly deployable therapeutic options, including drug repurposing and repositioning strategies. Molecular dynamics (MD) simulations have provided the opportunity to make rational scientific breakthroughs in a time of crisis. Advancements in these technologies in recent years have become an indispensable tool for scientists studying protein structure, function, dynamics, interactions, and drug discovery. Integrating the structural data obtained from high-resolution methods with MD simulations has helped in comprehending the process of infection and pathogenesis, as well as the SARS-CoV-2 maturation in host cells, in a short duration of time. It has also guided us to identify and prioritize drug targets and new chemical entities, and to repurpose drugs. Here, we discuss how MD simulation has been explored by the scientific community to accelerate and guide translational research on SARS-CoV-2 in the past year. We have also considered future research directions for researchers, where MD simulations can help fill the existing gaps in COVID-19 research.

Molecular Dynamics Studies on the Structural Characteristics for the Stability Prediction of SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) affects the COVID-19 pandemic in the world. The spike protein of the various proteins encoded in SARS-CoV-2 binds to human ACE2, fuses, and enters human cells in the respiratory system. Spike protein, however, is highly variable, and many variants were identified continuously. In this study, Korean mutants for spike protein (D614G and D614A-C terminal domain, L455F and F456L-RBD, and Q787H-S2 domain) were investigated in patients. Because RBD in spike protein is related to direct interaction with ACE2, almost all researches were focused on the RBD region or ACE2-free whole domain region. The 3D structure for spike protein complexed with ACE2 was recently released. The stability analysis through RBD distance among each spike protein chain and the binding free energy calculation between spike protein and ACE2 were performed using MD simulation depending on mutant types in 1-, 2-, and 3-open-complex forms. D614G mutant of CT2 domain, showing to be the most prevalent in the global pandemic, showed higher stability in all open-complex forms than the wild type and other mutants. We hope this study will provide an insight into the importance of conformational fluctuation in the whole domain, although RBD is involved in the direct interaction with ACE2.

S494 O-glycosylation site on the SARS-CoV-2 RBD affects the virus affinity to ACE2 and its infectivity; a molecular dynamics study

SARS-CoV-2 is a strain of Coronavirus family that caused the ongoing pandemic of COVID-19. Several studies showed that the glycosylation of virus spike (S) protein and the Angiotensin-Converting Enzyme 2 (ACE2) receptor on the host cell is critical for the virus infectivity. Molecular Dynamics (MD) simulations were used to explore the role of a novel mutated O-glycosylation site (D494S) on the Receptor Binding Domain (RBD) of S protein. This site was suggested as a key mediator of virus-host interaction. By exploring the dynamics of three O-glycosylated models and the control systems of unglcosylated S4944 and S494D complexes, it was shown that the decoration of S494 with elongated O-glycans results in stabilized interactions on the direct RBD-ACE2. Calculation of the distances between RBD and two major H1, H2 helices of ACE2 and the interacting pairs of amino acids in the interface showed that the elongated O-glycan maintains these interactions by forming several polar contacts with the neighbouring residues while it would not interfere in the direct binding interface. Relative binding free energy of RBD-ACE2 is also more favorable in the O-glycosylated models with longer glycans. The increase of RBD binding affinity to ACE2 depends on the size of attached O-glycan. By increasing the size of O-glycan, the RBD-ACE2 binding affinity will increase. Hence, this crucial factor must be taken into account for any further inhibitory approaches towards RBD-ACE2 interaction.

Low-cost biosensor for rapid detection of SARS-CoV-2 at the point of care

SARS-CoV-2, the virus that causes COVID-19, has killed over 3 million people worldwide. Despite the urgency of the current pandemic, most available diagnostic methods for COVID-19 use RT-PCR to detect nucleic acid sequences specific to SARS-CoV-2. These tests are limited by their requirement of a large laboratory space, high reagent costs, multistep sample preparation, and the potential for cross-contamination. Moreover, results usually take hours to days to become available. Therefore, fast, reliable, inexpensive, and scalable point-of-care diagnostics are urgently needed. Here, we describe RAPID 1.0, a simple, handheld, and highly sensitive miniaturized biosensor modified with human receptor angiotensin-converting enzyme-2. RAPID 1.0 can detect SARS-CoV-2 using 10 μL of sample within 4 min through its increased resistance to charge transfer of a redox probe measured by electrochemical impedance spectroscopy. The sensitivity and specificity of RAPID for nasopharyngeal/oropharyngeal swab and saliva samples are 85.3% and 100% and 100% and 86.5%, respectively.

Novel insights of waterborne human rotavirus A in Riyadh (Saudi Arabia) involving G2 predominance and emergence of a thermotolerant sequence

The routine evaluation of water environments is necessary to manage enteric virus-mediated fecal contamination and the possible emergence of novel variants. Here, we detected human rotavirus A (HRVA) circulating in two wastewater treatment plants, two lakes, irrigation water and a wastewater landfill located in Riyadh. VP7-derived surface protein sequences were assessed by phylogenetic analyses and inspection of thermotolerance-mediated secondary structure and seasonal variation. HRVA was most prevalent at An-Nazim wastewater landfill (AN-WWLF; 63.89%). Phylogenetic analyzes revealed the predominance of HRVA G2 lineage for the first time in Saudi Arabia. Moreover, a single HRVA sequence (2B64I-ANLF3/2018) was recovered at 45 °C from AN-WWLF; secondary structure prediction indicated that this sequence was thermotolerant with a high hydrophobicity, an absence of Ramachandran outliers, and a higher content of proline patches on the protein surface. Varied relationships were significantly observed between sampling areas influenced by temperature ranges (p < 0.05). HRVA prevalence was influenced by seasonal variations, favoring moderate temperatures in late autumn and early winter in all locations. However, a significant temperature impact was detected in Wadi-Hanifah Lake (p = 0.01). Our study extends the knowledge of currently circulating HRVA genotypes, and indicates the probable emergence of thermotolerant strains and seasonally mediated HRVA prevalence.

A potential peptide inhibitor of SARS-CoV-2 S and human ACE2 complex

The disease COVID-19 has caused heavy socio-economic burden and there is immediate need to control it. The disease is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. The viral entry into human cell depends on the attachment of spike (S) protein via its receptor binding domain (RBD) to human cell receptor angiotensin-converting enzyme 2 (hACE2). Thus, blocking the virus attachment to hACE2 could serve as potential therapeutics for viral infection. We have designed a peptide inhibitor (ΔABP-α2) targeting the RBD of S protein using in-silico approach. Docking studies and computed affinities suggested that peptide inhibitor binds at the RBD with ∼95-fold higher affinity than hACE2. Molecular dynamics (MD) simulation confirms the stable binding of inhibitor to hACE2. Immunoinformatics studies suggest non-immunogenic and non-toxic nature of peptide. Thus, the proposed peptide could serve as potential blocker for viral attachment.

Communicated by Ramaswamy H. Sarma

Supervised machine learning approach to molecular dynamics forecast of SARS-CoV-2 spike glycoproteins at varying temperatures

Abstract

Molecular dynamics (MD) simulations are a widely used technique in modeling complex nanoscale interactions of atoms and molecules. These simulations can provide detailed insight into how molecules behave under certain environmental conditions. This work explores a machine learning (ML) solution to predicting long-term properties of SARS-CoV-2 spike glycoproteins (S-protein) through the analysis of its nanosecond backbone RMSD (root-mean-square deviation) MD simulation data at varying temperatures. The simulation data were denoised with fast Fourier transforms. The performance of the models was measured by evaluating their mean squared error (MSE) accuracy scores in recurrent forecasts for long-term predictions. The models evaluated include k-nearest neighbors (kNN) regression models, as well as GRU (gated recurrent unit) neural networks and LSTM (long short-term memory) autoencoder models. Results demonstrated that the kNN model achieved the greatest accuracy in forecasts with MSE scores over around 0.01 nm less than those of the GRU model and the LSTM autoencoder. Furthermore, it demonstrated that the kNN model accuracy increases with data size but can still forecast relatively well when trained on small amounts of data, having achieved MSE scores of around 0.02 nm when trained on 10,000 ns of simulation data. This study provides valuable information on the feasibility of accelerating the MD simulation process through training and predicting supervised ML models, which is particularly applicable in time-sensitive studies.

Graphic abstract

SARS-CoV-2 spike glycoprotein molecular dynamics simulation. Extraction and denoising of backbone RMSD data. Evaluation of k-nearest neighbors regression, GRU neural network, and LSTM autoencoder models in recurrent forecasting for long-term property predictions.

Does Temperature Affect COVID-19 Transmission?

This study utilizes the non-linear least squares method to estimate the impact of temperature on COVID-19 cases per million in forty-three countries, divided into three groups as follows: the first group is composed of thirteen countries that announced the first COVID-19 cases in January 2020, while the second and third groups contain thirteen and seventeen countries, respectively, that witnessed the pandemic for the first time in February and March of the same year. This relationship was measured after four time periods from the date of reporting the first case until April 1, April 15, May 15, and July 8, 2020. The results show an inverse relationship between COVID-19 cases per million and the temperature in the studies of the four-time periods for the three-country groups. These results were only significant statistically (p < 0.1) after 110.8, 164.8 days on average from the beginning of the pandemic in the case of "January" countries.