Unraveling Hydrogen Adsorption on Transition Metal-Doped [Mo3S13]2- Clusters: Insights from Density Functional Theory Calculations.

Molecular and dissociative hydrogen adsorption of transition metal (TM)-doped [Mo3S13]2- atomic clusters were investigated using density functional theory calculations. The introduced TM dopants form stable bonds with S atoms, preserving the geometric structure. The S-TM-S bridging bond emerges as the most stable configuration. The preferred adsorption sites were found to be influenced by various factors, such as the relative electronegativity, coordination number, and charge of the TM atom. Notably, the presence of these TM atoms remarkably improved the hydrogen adsorption activity. The dissociation of a single hydrogen molecule on TM[Mo3S13]2- clusters (TM = Sc, Cr, Mn, Fe, Co, and Ni) is thermodynamically and kinetically favorable compared to their bare counterparts. The extent of favorability monotonically depends on the TM impurity, with a maximum activation barrier energy ranging from 0.62 to 1.58 eV, lower than that of the bare cluster (1.69 eV). Findings provide insights for experimental research on hydrogen adsorption using TM-doped molybdenum sulfide nanoclusters, with potential applications in the field of hydrogen energy.

Preimplantation Genetic Diagnosis of Androgen Resistance Syndrome Caused by Mutation on the AR Gene in Vietnam.

Background: Androgen resistance syndrome or androgen insensitivity syndrome (AIS - Androgen Insensitivity Syndrome, OMIM 300068) is an X-linked recessive genetic syndrome causing disorders of sexual development in males. This disease is caused by mutations in the AR gene located on the X chromosome, which encodes the protein that structures the androgen receptor, with the role of receiving androgens. Mutation of the AR gene causes complete or partial loss of androgen receptor function, thereby androgen not being obtained and exerting its effect on target organs, resulting in abnormalities of the male reproductive system due to this organ system, differentiating towards feminization under the influence of estrogen. Disease prevention can be achieved by using pre-implantation genetic diagnosis, which enables couples carrying the mutation to have healthy offspring. Aim: To carry out preimplantation genetic diagnosis of androgen resistance syndrome. Methods: Sanger sequencing was used to detect the mutation in the blood samples of the couple, their son, and 01 embryo that were biopsied on the fifth day based on the findings of next-generation sequencing (NGS) of the affected son. We combined Sanger sequencing and linkage analysis using short tandem repeats (STR) to provide diagnostic results. Results: We performed preimplantation genetic diagnosis for AIS on an embryo from a couple who had previously had an affected son. Consequently, one healthy embryo was diagnosed without the variant NM_000044: c.796del (p.Asp266IlefsTer30). Conclusion: We report on a novel variant (NM_000044: c.796del (p.Asp266IlefsTer30)) in the AR gene discovered in Vietnam. The developed protocol was helpful for the preimplantation genetic diagnosis process to help families with the monogenic disease of AIS but wish to have healthy children.

Different Impacts of Traffic-Related Air Pollution on Early-Onset and Late-Onset Asthma.

Background: Early-onset asthma (EOA) and late-onset asthma (LOA) are two distinct phenotypes. Air pollution has been associated with an increase in poorer asthma outcomes. The objective of this study was to examine the effects of traffic-related air pollution (TRAP) on asthma outcomes in EOA and LOA patients. Methods: A cross-sectional study was conducted on 675 asthma patients (LOA: 415) recruited from a major medical center in Taiwan. The land-use regression (LUR) model was used to estimate the level of exposure to PM10, PM2.5, NO2, and O3 on an individual level. We investigated the association between TRAP and asthma outcomes in EOA and LOA patients, stratified by allergic sensitization status, using a regression approach. Results: An increase in PM10 was associated with younger age of onset, increased asthma duration, and decreased lung function in EOA patients (p<0.05). An increase in PM10 was associated with older age of onset, and decreased asthma duration, eosinophil count, and Asthma Control Test (ACT) score in LOA patients. An increase in PM2.5 was associated with younger age of onset, increased asthma duration, decreased eosinophil count, and lung function in EOA patients (p<0.05). An increase in PM2.5 was associated with decreased lung function and ACT score in LOA patients. An increase in NO2 was associated with increased eosinophil count and decreased lung function in EOA patients (p<0.05). An increase in O3 was associated with decreased lung function in LOA patients (p<0.05). In addition, associations of TRAP with age of onset and eosinophil counts were mainly observed in both EOA and LOA patients with allergic sensitization, and an association with ACT was mainly observed in LOA patients without allergic sensitization. Conclusion: The impact of TRAP on age of onset, eosinophil count, and lung function in EOA patients, and ACT in LOA patients, was affected by the status of allergic sensitization.

Natural compounds inhibit Monkeypox virus methyltransferase VP39 in silico studies.

VP39, an essential 2'-O-RNA methyltransferase enzyme discovered in Monkeypox virus (MPXV), plays a vital role in viral RNA replication and transcription. Inhibition of the enzyme may prevent viral replication. In this context, using a combination of molecular docking and molecular dynamics (MDs) simulations, the inhibitory ability of NCI Diversity Set VII natural compounds to VP39 protein was investigated. It should be noted that the computed binding free energy of ligand via molecular docking and linear interaction energy (LIE) approaches are in good agreement with the corresponding experiments with coefficients of R=0.72 and 0.75, respectively. NSC 319990, NSC 196515 and NSC 376254 compounds were demonstrated that can inhibit MPVX methyltransferase VP39 protein with the similar affinity compared to available inhibitor sinefungin. Moreover, nine residues involving Gln39, Gly68, Gly72, Asp95, Arg97, Val116, Asp138, Arg140 and Asn156 may be argued that they play an important role in binding process of inhibitors to VP39.Communicated by Ramaswamy H. Sarma.

Direct Tumor Irradiation Potentiates Adoptive NK Cell Targeting Against Parental and Stemlike Cancer in Human Liver Cancer Models.

PURPOSE: Radiation therapy (RT) has been shown to effectively induce the expression of intercellular adhesion molecule-1 (ICAM-1), which is recognized by lymphocyte function-associated antigen 1 (LFA-1) expressed on natural killer (NK) cells. However, the potential synergistic antitumor immune response of tumor irradiation and administered NK cells has not been explored in intractable human liver cancers. Furthermore, NK cell targeting against both parental and cancer stemness has never been investigated. METHODS AND MATERIALS: Highly activated ex vivo NK cells were administered into the human liver tumor-bearing mice. Tumor direct RT was optimized according to tumor bearing site. HepG2 and Hep3B ICAM-1 knockout cells were generated using CRISPR/CAS9. Stemness tumor spheres were generated. NK cell cytolysis against parental and tumor sphere was evaluated using flow cytometry and real-time cytotoxicity assay. RESULTS: A combination of adoptive NK cell therapy with RT significantly improved therapeutic efficacy over monotherapies against subcutaneous, orthotopic, and metastatic human liver tumor models. Direct tumor irradiation potentiated NK cell recognition and conjugation against liver cancer through the LFA-1/ICAM-1 axis. Suppression of immune synapse formation on NK cells using high-affinity LFA-1 inhibitors or ICAM-1 knockout liver cancer induced "outside-in" signal blocking in NK cells, resulting in failure to eliminate liver tumor despite the combination therapy. NK cells effectively recognized and targeted triple-high epithelial cell adhesion molecule+CD133+CD24+ liver cancer expressing upregulated ICAM-1 in the irradiated tumor microenvironment, which led to prevention of the initiation of metastasis, improving survival in a metastatic model. In addition, the LFA-1/ICAM-1 axis interruption between NK cells and stemness liver tumor spheres significantly diminished NK cell cytolysis. Consistent with our preclinical data, the LFA-1/ICAM-1 axis correlated with survival outcomes in patients with metastatic cancer from the The Cancer Genome Atlas databases. CONCLUSIONS: NK cells in combination with tumor irradiation can provide synergistic therapeutic effects for NK cell recognition and elimination against both parental and stemlike liver cancer through LFA-1/ICAM-1.

Intensified NK cell therapy in combination with low-dose chemoradiotherapy against human colorectal cancer.

The therapeutic potential of adoptive natural Killer (NK) cells immunotherapy in combination with chemoradiotherapy, the main treatment modality for colorectal cancer (CRC), has not yet been explored. Here, we aimed to investigate the efficacy of NK cells to potentiate primary tumor control and improve survival outcomes, especially in combination with low-dose chemoradiotherapy. Ex vivo activated NK cells (> 90% purity) from healthy donors were obtained. NK cells were administered intravenously to the CRC-bearing mice and intensified in vivo in combination with low-dose 5-fluorouracil (0.5 mg/kg or 1 mg/Kg) and irradiated tumors with low doses (2 Gy or 4 Gy). Real-time NK cell cytotoxicity demonstrated a synergistic killing effect of a combination of low-dose chemoradiotherapy, mainly through NKp30 and NKG2D, showing a decrease in NK cell degranulation after blocking NKG2D and NKp30. In vivo tumor characteristics after combination treatment showed decreased CD112, CD155, MICA, and MICB expression. Under the combination strategy, 70% of the mice had free lung metastasis and 90% without secondary gross tumors, indicating suppressed distant metastasis to lung and axillary regions. This combination therapy resulted in significantly synergistic antitumor activity against primary solid tumors compared to chemoradiotherapy only. Furthermore, the intensified NK cell administration showed significantly better primary tumor control and survival outcomes than the non-intensified NK cell administration in a human colorectal HT-29 model treated with low-dose chemoradiotherapy. Optimized NK cell therapy combined with low-dose chemoradiotherapy can provide effective therapeutic potential for intractable cold human colorectal cancer.

Escalating Catalytic Activity for Hydrogen Evolution Reaction on MoSe2@Graphene Functionalization.

Developing highly efficient and durable hydrogen evolution reaction (HER) electrocatalysts is crucial for addressing the energy and environmental challenges. Among the 2D-layered chalcogenides, MoSe2 possesses superior features for HER catalysis. The van der Waals attractions and high surface energy, however, stack the MoSe2 layers, resulting in a loss of edge active catalytic sites. In addition, MoSe2 suffers from low intrinsic conductivity and weak electrical contact with active sites. To overcome the issues, this work presents a novel approach, wherein the in situ incorporated diethylene glycol solvent into the interlayers of MoSe2 during synthesis when treated thermally in an inert atmosphere at 600 °C transformed into graphene (Gr). This widened the interlayer spacing of MoSe2, thereby exposing more HER active edge sites with high conductivity offered by the incorporated Gr. The resulting MoSe2-Gr composite exhibited a significantly enhanced HER catalytic activity compared to the pristine MoSe2 in an acidic medium and demonstrated a superior HER catalytic activity compared to the state-of-the-art Pt/C catalyst, particularly at a high current density beyond ca. 55 mA cm-2. Additionally, the MoSe2-Gr catalyst demonstrated long-term electrochemical stability during HER. This work, thus, presents a facile and novel approach for obtaining an efficient MoSe2 electrocatalyst applicable in green hydrogen production.

Upgrading nirmatrelvir to inhibit SARS-CoV-2 Mpro via DeepFrag and free energy calculations.

The first oral drug for the treatment of COVID-19, Paxlovid, has been authorized; however, nirmatrelvir, a major component of the drug, is reported to be associated with some side effects. Moreover, the appearance of many novel variants raises concerns about drug resistance, and designing new potent inhibitors to prevent viral replication is thus urgent. In this context, using a hybrid approach combining machine learning (ML) and free energy simulations, 6 compounds obtained by modifying nirmatrelvir were proposed to bind strongly to SARS-CoV-2 Mpro. The structural modification of nirmatrelvir significantly enhances the electrostatic interaction free energy between the protein and ligand and slightly decreases the vdW term. However, the vdW term is the most important factor in controlling the ligand-binding affinity. In addition, the modified nirmatrelvir might be less toxic to the human body than the original inhibitor.

Higher Particulate Matter Deposition in Alveolar Region Could Accelerate Body Fat Accumulation in Obstructive Sleep Apnea.

We conducted a cross-sectional study to investigate associations of particulate matter (PM) of less than 2.5 µm in aerodynamic diameter (PM2.5) and PM deposition with nocturnal changes in body composition in obstructive sleep apnea (OSA) patients. A bioelectric impedance analysis was used to measure the pre- and postsleep body composition of 185 OSA patients. Annual exposure to PM2.5 was estimated by the hybrid kriging/land-use regression model. A multiple-path particle dosimetry model was employed to estimate PM deposition in lung regions. We observed that an increase in the interquartile range (IQR) (1 µg/m3) of PM2.5 was associated with a 20.1% increase in right arm fat percentage and a 0.012 kg increase in right arm fat mass in OSA (p < 0.05). We observed that a 1 µg/m3 increase in PM deposition in lung regions (i.e., total lung region, head and nasal region, tracheobronchial region, and alveolar region) was associated with increases in changes of fat percentage and fat mass of the right arm (ß coefficient) (p < 0.05). The ß coefficients decreased as follows: alveolar region > head and nasal region > tracheobronchial region > total lung region (p < 0.05). Our findings demonstrated that an increase in PM deposition in lung regions, especially in the alveolar region, could be associated with nocturnal changes in the fat percentage and fat mass of the right arm. PM deposition in the alveolar region could accelerate the body fat accumulation in OSA.

Associations of overnight changes in body composition with positional obstructive sleep apnea.

PURPOSE: Body composition is considered to be associated with obstructive sleep apnea (OSA) severity. This cross-sectional study aimed to examine associations of overnight body composition changes with positional OSA. METHODS: The body composition of patients diagnosed with non-positional and positional OSA was measured before and after overnight polysomnography. Odds ratios (ORs) of outcome variables between the case (positional OSA) and reference (non-positional OSA) groups were examined for associations with sleep-related parameters and with changes in body composition by a logistic regression analysis. RESULTS: Among 1584 patients with OSA, we used 1056 patients with non-positional OSA as the reference group. We found that a 1-unit increase in overnight changes of total fat percentage and total fat mass were associated with 1.076-fold increased OR (95% confidence interval (CI): 1.014, 1.142) and 1.096-fold increased OR (95% CI: 1.010, 1.189) of positional OSA, respectively (all p < 0.05). Additionally, a 1-unit increase in overnight changes of lower limb fat percentage and upper limb fat mass were associated with 1.043-fold increased OR (95% CI: 1.004, 1.084) and 2.638-fold increased OR (95% CI: 1.313, 5.302) of positional OSA, respectively (all p < 0.05). We observed that a 1-unit increase in overnight changes of trunk fat percentage and trunk fat mass were associated with 1.056-fold increased OR (95% CI: 1.008, 1.106) and 1.150-fold increased OR (95% CI: 1.016, 1.301) of positional OSA, respectively (all p < 0.05). CONCLUSION: Our findings indicated that nocturnal changes in the body's composition, especially total fat mass, total fat percentage, lower limb fat percentage, upper limb fat mass, trunk fat percentage, and trunk fat mass, may be associated with increased odds ratio of positional OSA compared with non-positional OSA.

Correction: Characterizing the ligand-binding affinity toward SARS-CoV-2 Mpro via physics- and knowledge-based approaches.

Correction for 'Characterizing the ligand-binding affinity toward SARS-CoV-2 Mpro via physics- and knowledge-based approaches' by Son Tung Ngo et al., Phys. Chem. Chem. Phys., 2022, https://doi.org/10.1039/d2cp04476e.

Correction: Rapid prediction of possible inhibitors for SARS-CoV-2 main protease using docking and FPL simulations.

[This corrects the article DOI: 10.1039/D0RA06212J.].

Characterizing the ligand-binding affinity toward SARS-CoV-2 Mpro via physics- and knowledge-based approaches.

Computational approaches, including physics- and knowledge-based methods, have commonly been used to determine the ligand-binding affinity toward SARS-CoV-2 main protease (Mpro or 3CLpro). Strong binding ligands can thus be suggested as potential inhibitors for blocking the biological activity of the protease. In this context, this paper aims to provide a short review of computational approaches that have recently been applied in the search for inhibitor candidates of Mpro. In particular, molecular docking and molecular dynamics (MD) simulations are usually combined to predict the binding affinity of thousands of compounds. Quantitative structure-activity relationship (QSAR) is the least computationally demanding and therefore can be used for large chemical collections of ligands. However, its accuracy may not be high. Moreover, the quantum mechanics/molecular mechanics (QM/MM) method is most commonly used for covalently binding inhibitors, which also play an important role in inhibiting the activity of SARS-CoV-2. Furthermore, machine learning (ML) models can significantly increase the searching space of ligands with high accuracy for binding affinity prediction. Physical insights into the binding process can then be confirmed via physics-based calculations. Integration of ML models into computational chemistry provides many more benefits and can lead to new therapies sooner.

Density Functional Study of Size-Dependent Hydrogen Adsorption on Ag n Cr (n = 1-12) Clusters.

Increasing interest has been paid for hydrogen adsorption on atomically controlled nanoalloys due to their potential applications in catalytic processes and energy storage. In this work, we investigate the interaction of H2 with small-sized Ag n Cr (n = 1-12) using density functional theory calculations. It is found that the cluster structures are preserved during the adsorption of H2 either molecularly or dissociatively. Ag3Cr-H2, Ag6Cr-H2, and Ag9Cr-H2 clusters are identified to be relatively more stable from computed binding energies and second-order energy difference. The dissociation of adsorbed H2 on Ag2Cr, Ag3Cr, Ag6Cr, and Ag7Cr clusters is favored both thermodynamically and kinetically. The dissociative adsorption is unlikely to occur because of a considerable energy barrier before reaching the final state for Ag4Cr or due to energetic preferences for n = 1, 5, and 8-12 species. Comprehensive analysis shows that the geometric structure of clusters, the relative electronegativity, and the coordination number of the Cr impurity play a decisive role in determining the preferred adsorption configuration.

Dioctyl Phthalate-Modified Graphene Nanoplatelets: An Effective Additive for Enhanced Mechanical Properties of Natural Rubber.

Graphene has been extensively considered an ideal additive to improve the mechanical properties of many composite materials, including rubbers, because of its novel strength, high surface area, and remarkable thermal and electron conductivity. However, the pristine graphene shows low dispersibility in the rubber matrix resulting in only slightly enhanced mechanical properties of the rubber composite. In this work, graphene nanoplatelets (GNPs) were modified with dioctyl phthalate (DOP) to improve the dispersibility of the graphene in the natural rubber (NR). The distribution of the DOP-modified GNPs in the NR matrix was investigated using scanning electron microscopy, X-ray diffraction, and Raman spectroscopy. The effect of the modified GNPs' contents on the mechanical properties of the GNPs/NR composite was studied in detail. The results showed that the abrasion resistance of the graphene-reinforced rubber composite significantly improved by 10 times compared to that of the rubber without graphene (from 0.3 to 0.03 g/cycle without and with addition of the 0.3 phr modified GNPs). The addition of the modified GNPs also improved the shear and tensile strength of the rubber composite. The tensile strength and shear strength of the NR/GNPs composite with a GNPs loading of 0.3 phr were determined to be 23.63 MPa and 42.69 N/mm, respectively. Even the presence of the graphene reduced the other mechanical properties such as Shore hardness, elongation at break, and residual elongation; however, these reductions were negligible, which still makes the modified GNPs significant as an effective additive for the natural rubber in applications requiring high abrasion resistance.

Randomized multicenter phase II trial of prophylactic irradiation of para-aortic lymph nodes in advanced cervical cancer according to tumor hypoxia: Korean Radiation Oncology Group (KROG 07-01) study.

We conducted a prospective phase II study on whether extended-field irradiation (EFI) confers survival benefits depending on hypoxic markers in locally advanced uterine cervical cancer (LAUCC). RNA-seq was performed to identify immune and hypoxic gene signatures. A total of 288 patients were randomized to either EFI or pelvic radiotherapy (PRT). All patients completed chemoradiotherapy. Overall, significantly higher 5-year para-aortic recurrence free survival (PARFS) rate occurred in EFI (97.6%) than in PRT group (87.2%), with marginal tendency to improve disease-free survival (DFS; 78% vs 70%, P = .066). Subgroup analyses were performed based on carbonic anhydrase 9 (CA9)-only positive, CA9/hypoxia-inducible factor (HIF) double positive and CA9 negative. In the CA9-only positive, EFI successfully increased 5-year PARFS (100% vs 76.4%, P = .010), resulting in significantly improved long-term DFS (85.7% vs 54.7%, P = .023) compared to the PRT, while there was no such benefit of EFI in the CA9/HIFs double positive. RNA-seq analysis identified distinct immunehigh subgroup with negative correlation with hypoxia gene signatures (R = -.37, P < .01), which showed a higher 5-year DFS than the immunelow (P = .032). Hypoxia-related genes were upregulated in the CA9/HIFs double positive compared to CA9 negative (P < .05). Only 17.4% of patients in CA9-negative group showed immunelow signatures, while 40.0% of patients in the double-positive group exhibited immunelow signatures. In conclusion, EFI improved PARFS significantly in all patients, but therapeutic efficacy of EFI in terms of improved DFS was solely observed in CA9-only positive LAUCC, and not in CA9/HIFs double-positive subgroup. RNA-seq analysis suggested that hypoxia-induced immunosuppression may be related to treatment resistance in LAUCC.

Systematic synthesis of different-sized AgInS2/GaSxnanocrystals for emitting the strong and narrow excitonic luminescence.

This paper presents for the first time the systematic synthesis of AgInS2(AIS) nanocrystals (NCs) with different sizes of 2.6-6.8 nm just by controlling only the reaction temperature. The synthesis of AIS core NCs was carried out in 2 steps: (i) synthesis of Ag2S NCs and then (ii) partial exchange of Ag+with In3+in the template Ag2S NCs. For step (i), Ag2S NCs of different sizes were synthesized by reaction of the Ag and S precursors at different temperatures of 30 °C to 130 °C, for the same reaction time of 30 min. For step (ii), AIS NCs were created by the exchange of Ag+with In3+at 120 °C for 60 min. Finally, GaSxwas shelled on AIS core NCs to produce the AgInS2/GaSxcore/shell structures. The synthesized AIS/GaSxNCs demonstrate the clear excitonic absorptions and strong, narrow excitonic luminescence peaking at 530-606 nm depending on the size of AIS core NCs.

A computationally affordable approach for accurate prediction of the binding affinity of JAK2 inhibitors.

Janus kinase 2 (JAK2) inhibitors are potential anticancer drugs in the treatment of lymphoma, leukemia, thrombocytosis and particularly myeloproliferative diseases. However, the resemblance among JAK family members has challenged the identification of highly selective inhibitors for JAK2 to reduce undesired side effects. As a result, a robust search for promising JAK2 inhibitors using a computational approach that can effectively nominate new potential candidates to be further analyzed through laborious experimental operations has become necessary. In this study, the binding affinities of JAK2 inhibitors were rapidly and precisely estimated using the fast pulling of ligand (FPL) simulations combined with a modified linear interaction energy (LIE) method. The approach correlates with the experimental binding affinities of JAK2 inhibitors with a correlation coefficient of R = 0.82 and a root-mean-square error of 0.67 kcal•mol-1. The data reveal that the FPL/LIE method is highly approximate in anticipating the relative binding free energies of known JAK2 inhibitors with an affordable consumption of computational resources, and thus, it is very promising to be applied in in silico screening for new potential JAK2 inhibitors from a large number of molecules available.

First-row transition metal doped germanium clusters Ge16M: some remarkable superhalogens.

A theoretical study of geometric and electronic structures, stability and magnetic properties of both neutral and anionic Ge16M0/- clusters with M being a first-row 3d transition metal atom, is performed using quantum chemical approaches. Both the isoelectronic Ge16Sc- anion and neutral Ge16Ti that have a perfect Frank-Kasper tetrahedral T d shape and an electron shell filled with 68 valence electrons, emerge as magic clusters with an enhanced thermodynamic stability. The latter can be rationalized by the simple Jellium model. Geometric distortions from the Frank-Kasper tetrahedron of Ge16M having more or less than 68 valence electrons can be understood by a Jahn-Teller effect. Remarkably, DFT calculations reveal that both neutral Ge16Sc and Ge16Cu can be considered as superhalogens as their electron affinities (≥3.6 eV) exceed the value of the halogen atoms and even that of icosahedral Al13. A detailed view of the magnetic behavior of Ge16M0/- clusters shows that the magnetic moments of the atomic metals remain large even when they are quenched upon doping. When M goes from Sc to Zn, the total spin magnetic moment of Ge16M0/- increases steadily and reaches the maximum value of 3 µ B with M = Mn before decreasing towards the end of the first-row 3d block metals. Furthermore, the IR spectra of some tetrahedral Ge16M are also predicted.

Insights into the binding and covalent inhibition mechanism of PF-07321332 to SARS-CoV-2 Mpro.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been causing the COVID-19 pandemic, resulting in several million deaths being reported. Numerous investigations have been carried out to discover a compound that can inhibit the biological activity of the SARS-CoV-2 main protease, which is an enzyme related to the viral replication. Among these, PF-07321332 (Nirmatrelvir) is currently under clinical trials for COVID-19 therapy. Therefore, in this work, atomistic and electronic simulations were performed to unravel the binding and covalent inhibition mechanism of the compound to Mpro. Initially, 5 µs of steered-molecular dynamics simulations were carried out to evaluate the ligand-binding process to SARS-CoV-2 Mpro. The successfully generated bound state between the two molecules showed the important role of the PF-07321332 pyrrolidinyl group and the residues Glu166 and Gln189 in the ligand-binding process. Moreover, from the MD-refined structure, quantum mechanics/molecular mechanics (QM/MM) calculations were carried out to unravel the reaction mechanism for the formation of the thioimidate product from SARS-CoV-2 Mpro and the PF-07321332 inhibitor. We found that the catalytic triad Cys145-His41-Asp187 of SARS-CoV-2 Mpro plays an important role in the activation of the PF-07321332 covalent inhibitor, which renders the deprotonation of Cys145 and, thus, facilitates further reaction. Our results are definitely beneficial for a better understanding of the inhibition mechanism and designing new effective inhibitors for SARS-CoV-2 Mpro.