The synthesis and properties of Ca3 Sc2 Si3 O12 :Ce3+ (CSSG) phosphor are utilized for the development of human-centric lighting light-emitting diodes (HCL-LEDs).

In this study, cerium ion (Ce3+ )-doped calcium scandium silicate garnet (Ca3 Sc2 Si3 O12 , abbreviated CSSG) phosphors were successfully synthesized using the sol-gel method. The crystal phase, morphology, and photoluminescence properties of the synthesized phosphors were thoroughly investigated. Under excitation by a blue light-emitting diode (LED) chip (450 nm), the CSSG phosphor displayed a wide emission spectrum spanning from green to yellow. Remarkably, the material exhibited exceptional thermal stability, with an emissivity ratio at 150°C to that at 25°C reaching approximately 85%. Additionally, the material showcased impressive optical performance when tested with a blue LED chip, including a color rendering index (CRI) exceeding 90, an R9 value surpassing 50, and a biological impact ratio (M/P) above 0.6. These noteworthy findings underscore the potential applications of CSSG as a white light-converting phosphor, particularly in the realm of human-centered lighting.

Enhancing Si3N4 Selectivity over SiO2 in Low-RF Power NF3-O2 Reactive Ion Etching: The Effect of NO Surface Reaction.

Highly selective etching of silicon nitride (Si3N4) and silicon dioxide (SiO2) has received considerable attention from the semiconductor community owing to its precise patterning and cost efficiency. We investigated the etching selectivity of Si3N4 and SiO2 in an NF3/O2 radio-frequency glow discharge. The etch rate linearly depended on the source and bias powers, whereas the etch selectivity was affected by the power and ratio of the gas mixture. We found that the selectivity can be controlled by lowering the power with a suitable gas ratio, which affects the surface reaction during the etching process. X-ray photoelectron spectroscopy of the Si3N4 and QMS measurements support the effect of surface reaction on the selectivity change by surface oxidation and nitrogen reduction with the increasing flow of O2. We suggest that the creation of SiOxNy bonds on the surface by NO oxidation is the key mechanism to change the etch selectivity of Si3N4 over SiO2.

Monkeypox Virus Infection in 2 Female Travelers Returning to Vietnam from Dubai, United Arab Emirates, 2022.

Mpox was diagnosed in 2 women returning to Vietnam from the United Arab Emirates. The monkeypox viruses belonged to an emerging sublineage, A.2.1, distinct from B.1, which is responsible for the ongoing multicountry outbreak. Women could contribute to mpox transmission, and enhanced genomic surveillance is needed to clarify pathogen evolution.

Spatiotemporal Evolution of SARS-CoV-2 Alpha and Delta Variants during Large Nationwide Outbreak of COVID-19, Vietnam, 2021.

We analyzed 1,303 SARS-CoV-2 whole-genome sequences from Vietnam, and found the Alpha and Delta variants were responsible for a large nationwide outbreak of COVID-19 in 2021. The Delta variant was confined to the AY.57 lineage and caused >1.7 million infections and >32,000 deaths. Viral transmission was strongly affected by nonpharmaceutical interventions.

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.

Association between serum interleukin-17 levels and ectopic bone formation in OPLL patients with DISH.

OBJECTIVE: To investigate the relationship between the severity and morphology of heterotopic ossification in the spinal ligaments including sacroiliac (SI) joints, and serum interleukin-17 (IL-17) levels in patients with ossification of the posterior longitudinal ligament (OPLL) with or without diffuse idiopathic skeletal hyperostosis (DISH), as well as a non-OPLL group. METHODS: A total of 103 patients with OPLL (DISH (-), n = 50; DISH (+), n = 53) and 53 age- and gender-matched controls were included. The serum levels of IL-17 were analyzed, and the severity of ectopic ossification and the morphology of ectopic bone formation were evaluated. The SI joint morphological variations were categorized into four types. RESULTS: No significant differences were found in serum IL-17 levels between the OPLL and control groups. However, the DISH (+) group showed higher IL-17 levels than the DISH (-) group, especially in female patients (p = 0.003). Additionally, IL-17 levels were positively correlated with the number of Flat vertebral units, meaning one of the characteristics of DISH ossification type (R2 = 0.199, p = 0.012). IL-17 levels in type 4 were significantly higher in the DISH (+) group than in the DISH (-) group. CONCLUSIONS: The morphological characteristics of paravertebral bone formation in the entire spine, including the SI joint, are likely associated with serum IL-17 levels in OPLL. These findings provide pathological and serological evidence of local inflammation contributing to paravertebral ossification of OPLL patients.

Anti-malarial activity of the alkaloid, heptaphylline, and the furanocoumarin, imperatorin, from Clausena anisata against human Plasmodium falciparum malaria parasites: ex vivo trophozoitocidal, schizonticidal and gametocytocidal approach.

BACKGROUND: The erythrocytic stage of the life cycle of the malaria parasite, Plasmodium falciparum, consists of trophozoite, schizont and gametocyte stages in humans. Various anti-malarial agents target different stages of the parasite to produce treatment outcomes. This study reports on the stage-specific anti-malarial activity of heptaphylline and imperatorin against human P. falciparum in addition to their cytotoxicity and selectivity indices (SI). METHODS: The compounds were isolated from Clausena anisata using column chromatography and their structures elucidated using NMR spectroscopy. The anti-malarial activity was determined by measuring the trophozoitocidal, schizonticidal and gametocytocidal activities of the compounds using the SYBR green assay. Cytotoxicity was evaluated using the tetrazolium-based colorimetric assay. RESULTS: Heptaphylline and imperatorin produced trophozoitocidal, schizonticidal and gametocytocidal activities with IC50s of 1.57 (0.2317)-26.92 (0.3144) µM with those of artesunate (the standard drug) being 0.00024 (0.0036)-0.0070 (0.0013) µM. In the cytotoxicity assay, the compounds produced CC50S greater than 350 µM and SI of 13.76-235.90. Also, the trophozoitocidal and schizonticidal activities of the compounds were more pronounced than their gametocytocidal activity. Imperatorin was 42.04% more trophozoitocidal than hepthaphyline. However, hepthaphyline has more schizonticidal and gametocytocidal properties than imperatorin. CONCLUSION: Heptaphylline and imperatorin are promising anti-malarial agents, since they possess potent anti-malarial activity with weak cytotoxicity on RBCs. However, imperatorin is a better anti-malarial prophylactic agent whereas heptaphylline is a better malaria treatment agent.

Shared and unique antibody and B cell profiles in HIV-positive and HIV-negative individuals with cryptococcal meningoencephalitis.

Host non-T cell markers to aid in the diagnosis of cryptococcal meningoencephalitis (CM) have not been identified. In this case-control study, we characterized antibody and B cell profiles in HIV-negative and HIV-positive Vietnamese individuals of the Kinh ethnicity recently diagnosed with CM and controls. The study included 60 HIV-negative with no known immunocompromising condition and 60 HIV-positive individuals, with 30 CM cases and 30 controls in each group. Participants were matched by age, sex, HIV serostatus, and CD4 count in the HIV-positive group. Plasma immunoglobulin (Ig) levels, including IgG1, IgG2, IgM, and IgA, Cryptococcus spp. glucuronoxylomannan (GXM)- and laminarin (branched ${\rm{\beta }}$-[1-3]-glucan)-binding IgG, IgM, IgA levels, and peripheral blood B cell subsets were measured. Logistic regression, principal component, and mediation analyses were conducted to assess associations between antibody, B cell levels, and CM. The results showed that GXM-IgG levels were higher and IgG1 and IgG2 were lower in CM cases than controls, regardless of HIV status. In HIV-negative individuals, IgG2 mediated an inverse association between CD19+CD27+CD43+CD5- (B-1b-like) cells and CM. In HIV-positive individuals, lower levels of IgA, laminarin-IgA, and CD19+CD27+IgM+IgD- (IgM+ memory B) cells were each associated with CM. The shared and distinct antibody and B cell profiles identified in HIV-negative and HIV-positive CM cases may inform the identification of non-T-cell markers of CM risk or unsuspected disease, particularly in HIV-negative individuals.

Unlike cryptococcal meningitis (CM) in HIV-positive individuals, there are no known biomarkers of risk in HIV-negative individuals and the diagnosis is often not suspected and delayed. This study identified non-T cells, including antibody and B cell CM-associated profiles that may guide cryptococcal antigen testing in HIV-negative individuals.

Synthesis of solar-driven Cu-doped graphitic carbon nitride photocatalyst for enhanced removal of caffeine in wastewater.

Caffeine (CaF), a widely consumed compound, has been associated with various harmful effects on human health, including metabolic, cardiovascular disease, and reproductive disorders. Moreover, it poses a signifincant threat to organisms and aquatic ecosystems, leading to water pollution concerns. Therefore, the removal of CaF from wastewater is crucial for mitigating water pollution and minimizing its detrimental impacts on both humans and the environment. In this study, a solar-driven Cu-doped graphitic carbon nitride (Cu/CN) photocatalyst was synthesized and evaluated for its effectiveness in oxidizing CaF in wastewater. The Cu/CN photocatalyst, with a low band gap energy of 2.58eV, exhibited superior performance in degrading CaF compared to pure graphitic carbon nitride (CN). Under solar light irradiation, CuCN achieved a remarkable CaF degradation efficiency of 98.7% CaF, surpassing CN's efficiency of 74.5% by 24.2%. The synthesized Cu/CN photocatalyst demonstrated excellent removal capability, achieving a removal rate of over 88% for CaF in wastewater. Moreover, the reusability test showed that Cu/CN could be successfully reused up to five cycles maintaining a high removal efficiency of 74% for CaF in the fifth cycle. Additionally, the study elucidated the oxidation mechanism of CaF using solar-driven Cu/CN photocatalyst and highlighted the environmental implications of the process.

Facile preparation of porphyrin@g-C3N4/Ag nanocomposite for improved photocatalytic degradation of organic dyes in aqueous solution.

In the quest of improving the photocatalytic efficiency of photocatalysts, the combination of two and more semiconductors recently has garnered significant attention among scientists in the field. The doping of conductive metals is also an effective pathway to improve photocatalytic performance by avoiding electron/hole pair recombination and enhancing photon energy absorption. This work presented a design and fabrication of porphyrin@g-C3N4/Ag nanocomposite using acid-base neutralization-induced self-assembly approach from monomeric porphyrin and g-C3N4/Ag material. g-C3N4/Ag material was synthesized by a green reductant of Cleistocalyx operculatus leaf extract. Electron scanning microscopy (SEM), X-ray diffraction (XRD), FT-IR spectroscopy, and UV-vis spectrometer were utilized to analyse the properties of the prepared materials. The prepared porphyrin@g-C3N4/Ag nanocomposite showed well integration of porphyrin nanostructures on the g-C3N4/Ag's surface, in which porphyrin nanofiber was of the diameter in nanoscales and the length of several micrometers, and Ag NPs had an average particle size of less than 20 nm. The photocatalytic behavior of the resultant nanocomposite was tested for the degradation of Rhodamine B dye, which exhibited a remarkable RhB photodegrading percentage. The possible mechanism for photocatalysis of the porphyrin@g-C3N4/Ag nanocomposite toward Rhodamine B dye was also proposed and discussed.

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.

Development of taste-masking microcapsules containing azithromycin by fluid bed coating for powder for suspension and in vivo evaluation.

This research aims to develop bitter taste-masking microcapsules containing azithromycin (AZI) by a simpler and familiar method, fluid-bed coating technology, in comparison with Zithromax®. Cores of microcapsules, AZI microparticles, were prepared by fluid-bed granulation, then taste-masking polymer was covered on by fluid-bed coating technique. Eudragit L100, Eudragit RL100, and ethyl cellulose in single and combined with Eudragit L100 and Eudragit E100 were used as taste-masking polymers. The obtained microcapsules were characterised by taste-masking ability, in vitro release, SEM, coating thickness, and coating efficiency. Combination of ethyl cellulose and Eudragit E100 (3:1) in coating thickness of 45.13 ± 2.12% w/w prevents AZI release from microcapsules below bitter taste threshold (1.78 ± 1.17 µg/ml). Bioavailability of powders containing AZI microcapsules and pH modulators (50 mg Na3PO4 and 35 mg Mg(OH)2) was not significantly different from the reference product (Zithromax®, Pfizer, New York, NY) in the rabbit model (p > 0.05). These results support the possibility of developing a generic product containing AZI.

Microorganisms for Ginsenosides Biosynthesis: Recent Progress, Challenges, and Perspectives.

Ginsenosides are major bioactive compounds present in the Panax species. Ginsenosides exhibit various pharmaceutical properties, including anticancer, anti-inflammatory, antimetastatic, hypertension, and neurodegenerative disorder activities. Although several commercial products have been presented on the market, most of the current chemical processes have an unfriendly environment and a high cost of downstream processing. Compared to plant extraction, microbial production exhibits high efficiency, high selectivity, and saves time for the manufacturing of industrial products. To reach the full potential of the pharmaceutical resource of ginsenoside, a suitable microorganism has been developed as a novel approach. In this review, cell biological mechanisms in anticancer activities and the present state of research on the production of ginsenosides are summarized. Microbial hosts, including native endophytes and engineered microbes, have been used as novel and promising approaches. Furthermore, the present challenges and perspectives of using microbial hosts to produce ginsenosides have been discussed.

Triterpenoid esters from Capparis erythrocarpos (Isert), Capparaceae, root bark ameliorates CFA-induced arthritis.

The root bark of Capparis erythrocarpos (CERB) is employed to treat rheumatoid arthritis (RA) in Africa, particularly in Ghana. However, there was no isolation and characterization of the bioactive constituents responsible for the pharmacological actions of this plant. The aim of this study is to isolate, characterize and evaluate the anti-arthritic activity of the constituents of CERB. CERB was soxhleted and partitioned into various fractions. The constituents were isolated using column chromatography and characterized by 1D and 2D NMR spectroscopy. The precise carboxylic acid residues of the esters were determined using saponification, derivatization and GC-MS analysis. Anti-arthritic activity was evaluated in the CFA-induced arthritic model. Two triterpenoid esters namely, sitosterol 3-hexadecanoate or sitosterol 3-palmatate (1) and sitosterol 3-tetradecanoate or sitosterol 3-myristate (2) in addition to beta sitosterol (3) were isolated and characterized. Compounds 1 and 2 administered at 3 µmol/kg (p.o.) produced anti-inflammatory activity (P < 0.0001) of 31.02 and 39.14% respectively, in addition to arthritic score index (P < 0.0001) of 1.600 ± 0.2449 and 1.400 ± 0.2449 against CFA-induced arthritis which are equivalent to those of the standard drug, diclofenac sodium (DS), 3 µmol/kg (p.o.), (30.79% anti-inflammatory activity and 1.800 ± 0.3742 arthritic score index). The compounds produced similar anti-inflammatory effects as DS. Also, radiographical and histopathological studies showed that, the compounds and DS protected against bone destruction, inflammatory cells invasion into interstitial spaces and synovial liner hyperplasia of the joints. This is the first study to report the characterization of the constituents of C. erythrocarpos in addition to anti-arthritic activity of sitosterol 3-palmatate and sitosterol 3-myristate. These results provide the missing link between the chemistry and the pharmacological activities of C. erythrocarpos. The isolates also offer a different class of molecule which could provide alternative treatment for RA.

Field transcriptome analysis reveals a molecular mechanism for cassava-flowering in a mountainous environment in Southeast Asia.

KEY MESSAGE: The field survey in this article showed in 'KU50', a popular variety and late-branching type of cassava in Southeast Asia, that flowering rarely occurs in normal-field conditions in Southeast Asia but is strongly induced in the dry season in the mountainous region. Flowering time is correlated with the expression patterns of MeFT1 and homologs of Arabidopsis GI, PHYA, and NF-Ys. Cassava (Manihot esculenta Crantz) is a tropical crop that is propagated vegetatively rather than sexually by seed. Flowering rarely occurs in the erect-type variety grown in Southeast Asia, but it is known that cassava produces flowers every year in mountainous regions. Data pertaining to the effect of environmental factors on flowering time and gene expression in cassava, however, is limited. The aim of the present study was to determine the kinds of environmental conditions that regulate flowering time in cassava and the underlying molecular mechanisms. The flowering status of KU50, a popular variety in Southeast Asia and late-branching type of cassava, was monitored in six fields in Vietnam and Cambodia. At non-flowering and flowering field locations in North Vietnam, the two FLOWERING LOCUS T (FT)-like genes, MeFT1 and MeFT2, were characterized by qPCR, and the pattern of expression of flowering-related genes and genes responsive to environmental signals were analyzed by using RNA sequencing data from time-series samples. Results indicate that cassava flowering was induced in the dry season in the mountain region, and that flowering time was correlated with the expression of MeFT1, and homologs of Arabidopsis GI, PHYA, and NF-Ys. Based upon these data, we hypothesize that floral induction in cassava is triggered by some conditions present in the mountain regions during the dry season.

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.

Improving ligand-ranking of AutoDock Vina by changing the empirical parameters.

AutoDock Vina (Vina) achieved a very high docking-success rate, p^ , but give a rather low correlation coefficient, R , for binding affinity with respect to experiments. This low correlation can be an obstacle for ranking of ligand-binding affinity, which is the main objective of docking simulations. In this context, we evaluated the dependence of Vina R coefficient upon its empirical parameters. R is affected more by changing the gauss2 and rotation than other terms. The docking-success rate p^ is sensitive to the alterations of the gauss1, gauss2, repulsion, and hydrogen bond parameters. Based on our benchmarks, the parameter set1 has been suggested to be the most optimal. The testing study over 800 complexes indicated that the modified Vina provided higher correlation with experiment Rset1=0.556±0.025 compared with RDefault=0.493±0.028 obtained by the original Vina and RVina1.2=0.503±0.029 by Vina version 1.2. Besides, the modified Vina can be also applied more widely, giving R≥0.500 for 32/48 targets, compared with the default package, giving R≥0.500 for 31/48 targets. In addition, validation calculations for 1036 complexes obtained from version 2019 of PDBbind refined structures showed that the set1 of parameters gave higher correlation coefficient ( Rset1=0.617±0.017 ) than the default package ( RDefault=0.543±0.020 ) and Vina version 1.2 ( RVina1.2=0.540±0.020 ). The version of Vina with set1 of parameters can be downloaded at https://github.com/sontungngo/mvina. The outcomes would enhance the ranking of ligand-binding affinity using Autodock Vina.

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.

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.

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.