Computation of the Binding Energies between Human ACE2 and Spike RBDs of the Original Strain, Delta and Omicron Variants of the SARS-CoV-2: A DFT Simulation Approach

Interface-Engineered 2D Heterojunction with Photoelectric Dual Gain: Mxene@MOF-Enhanced SPR Spectroscopy for Direct Sensing of Exosomes

MXene is widely used in the construction of optoelectronic interfaces due to its excellent properties. However, the hydrophilicity and metastable surface of MXene lead to its oxidation behavior, resulting in the degradation of its various properties, which seriously limits its practical application. In this work, a 2D metal-organic framework (2D MOF) with matching 2D morphology, excellent stability performance, and outstanding optoelectronic performance is grown in situ on the MXene surface through heterojunction engineering to suppress the direct contact between reactive molecules and the inner layer material without affecting the original advantages of MXene. The photoelectric dual gain MXene@MOF heterojunction is confirmed. As a photoelectric material, its properties are highly suitable for the demand of interface sensitization layer materials of surface plasmon resonance (SPR). Therefore, using SPR as a platform for the application of this interface material, the performance of MXene@MOF and its potential mechanism to enhance SPR are analyzed in depth using experiments combined with simulation calculations (FDTD/DFT). Finally, the MXene@MOF/peptides-SPR sensor is constructed for rapid and sensitive detection of the cancer marker exosomes to explore its potential in practical applications. This work offers a forward-looking strategy for the design of interface materials with excellent photoelectric performance.

2D MOF-enhanced SPR detector based on tunable supramolecular probes for direct and sensitive detection of DOX in serum

Therapeutic drug monitoring of doxorubicin (DOX) is important to study pharmacokinetics in patients undergoing chemotherapy for reduction of side effects and improve patient survival by rationally controlling the dose of DOX. A fast and ultra-sensitive surface plasmon resonance (SPR) detector without sample pre-handling was developed for DOX monitoring. First, the two-dimensional metal-organic framework was modified on the Au film to enhance SPR, and then, the supramolecular probes with tunable cavity structure were self-assembled at the sensing interface for direct detection of DOX through specific host-guest interactions with a low detection limit of 60.24 pM. The precise monitoring of DOX in serum proved the possibility of clinical application with recoveries in the range 102.86-109.47%. The mechanisms of host-guest interactions between supramolecular and small-molecule drugs were explored in depth through first-principles calculations combined with SPR experiments. The study paves the way for designing facile and sensitive detectors and provides theoretical support and a new methodology for the specific detection of small molecules through calixarene cavity modulation.

Interaction of SARS-CoV-2 with host cells and antibodies: experiment and simulation

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the devastating global COVID-19 pandemic announced by WHO in March 2020. Through unprecedented scientific effort, several vaccines, drugs and antibodies have been developed, saving millions of lives, but the fight against COVID-19 continues as immune escape variants of concern such as Delta and Omicron emerge. To develop more effective treatments and to elucidate the side effects caused by vaccines and therapeutic agents, a deeper understanding of the molecular interactions of SARS-CoV-2 with them and human cells is required. With special interest in computational approaches, we will focus on the structure of SARS-CoV-2 and the interaction of its spike protein with human angiotensin-converting enzyme-2 (ACE2) as a prime entry point of the virus into host cells. In addition, other possible viral receptors will be considered. The fusion of viral and human membranes and the interaction of the spike protein with antibodies and nanobodies will be discussed, as well as the effect of SARS-CoV-2 on protein synthesis in host cells.

Correlating the differences in the receptor binding domain of SARS-CoV-2 spike variants on their interactions with human ACE2 receptor

Spike glycoprotein of SARS-CoV-2 variants plays a critical role in infection and transmission through its interaction with human angiotensin converting enzyme 2 (hACE2) receptors. Prior findings using molecular docking and biomolecular studies reported varied findings on the difference in the interactions among the spike variants with the hACE2 receptors. Hence, it is a prerequisite to understand these interactions in a more precise manner. To this end, firstly, we performed ELISA with trimeric spike glycoproteins of SARS-CoV-2 variants including Wuhan Hu-1(Wild), Delta, C.1.2 and Omicron. Further, to study the interactions in a more specific manner by mimicking the natural infection, we developed hACE2 receptors expressing HEK-293T cell line, evaluated their binding efficiencies and competitive binding of spike variants with D614G spike pseudotyped virus. In line with the existing findings, we observed that Omicron had higher binding efficiency compared to Delta in both ELISA and Cellular models. Intriguingly, we found that cellular models could differentiate the subtle differences between the closely related C.1.2 and Delta in their binding to hACE2 receptors. Our study using the cellular model provides a precise method to evaluate the binding interactions between spike sub-lineages to hACE2 receptors.

2D MOF-enhanced SPR sensing platform: Facile and ultrasensitive detection of Sulfamethazine via supramolecular probe

Sulfamethazine (SMZ) is widely present in the environment and can cause severe allergic reactions and cancer in humans. Accurate and facile monitoring of SMZ is crucial for maintaining environmental safety, ecological balance, and human health. In this work, a real-time and label-free surface plasmon resonance (SPR) sensor was devised using a two-dimensional metal-organic framework with superior photoelectric performance as an SPR sensitizer. The supramolecular probe was incorporated at the sensing interface, allowing for the specific capture of SMZ from other analogous antibiotics through host-guest recognition. The intrinsic mechanism of the specific interaction of the supramolecular probe-SMZ was elucidated through the SPR selectivity test in combination with analysis by density functional theory, including p-π conjugation, size effect, electrostatic interaction, π-π stacking, and hydrophobic interaction. This method facilitates a facile and ultrasensitive detection of SMZ with a limit of detection of 75.54 pM. The accurate detection of SMZ in six environmental samples demonstrates the potential practical application of the sensor. Leveraging the specific recognition of supramolecular probes, this direct and simple approach offers a novel pathway for the development of novel SPR biosensors with outstanding sensitivity.

The impact of mutation sets in receptor-binding domain of SARS-CoV-2 variants on the stability of RBD–ACE2 complex

Aim: Bioinformatic analysis of mutation sets in receptor-binding domain (RBD) of currently and previously circulating SARS-CoV-2 variants of concern (VOCs) and interest (VOIs) to assess their ability to bind the ACE2 receptor. Methods: In silico sequence and structure-oriented approaches were used to evaluate the impact of single and multiple mutations. Results: Mutations detected in VOCs and VOIs led to the reduction of binding free energy of the RBD–ACE2 complex, forming additional chemical bonds with ACE2, and to an increase of RBD–ACE2 complex stability. Conclusion: Mutation sets characteristic of SARS-CoV-2 variants have complex effects on the ACE2 receptor-binding affinity associated with amino acid interactions at mutation sites, as well as on the acquisition of other viral adaptive advantages.