How do probiotics alleviate constipation? A narrative review of mechanisms.

Constipation is a common gastrointestinal condition, which may occur at any age and affects countless people. The search for new treatments for constipation is ongoing as current drug treatments fail to provide fully satisfactory results. In recent years, probiotics have attracted much attention because of their demonstrated therapeutic efficacy and fewer side effects than pharmaceutical products. Many studies attempted to answer the question of how probiotics can alleviate constipation. It has been shown that different probiotic strains can alleviate constipation by different mechanisms. The mechanisms on probiotics in relieving constipation were associated with various aspects, including regulation of the gut microbiota composition, the level of short-chain fatty acids, aquaporin expression levels, neurotransmitters and hormone levels, inflammation, the intestinal environmental metabolic status, neurotrophic factor levels and the body's antioxidant levels. This paper summarizes the perception of the mechanisms on probiotics in relieving constipation and provides some suggestions on new research directions.

Attenuation of inflammatory bowel disease by oral administration of mucoadhesive polydopamine-coated yeast ß-glucan via ROS scavenging and gut microbiota regulation.

Treatment for inflammatory bowel disease (IBD) is challenging since current anti-inflammatory and immunosuppressive therapies do not address the underlying causes of the illness, which include increased levels of reactive oxygen species (ROS) and dysbiosis of the gut commensal microbiota. Additionally, these treatments often have systemic off-target effects and adverse side effects. In this study, we have developed a prebiotic yeast ß-glucan nanocomplex coated with bio-adhesive polydopamine (YBNs@PDA) to effectively prolong their retention time in the gastrointestinal (GI) tract. The oral administration of YBNs@PDA restored the epithelium barriers, reduced ROS levels, and minimized systemic drug exposure while improved therapeutic efficacy in an acute colitis mouse model. Furthermore, 16S ribosomal RNA genes sequencing demonstrated a higher richness and diversity in gut microflora composition following the treatments. In particular, YBNs@PDA markedly augmented the abundance of Lachnospiraceae NK4A136 and Bifidobacterium, both of which are probiotics with crucial roles in relieving colitis via retaining gut homeostasis. Cumulatively, these results demonstrate that the potential of YBNs@PDA as a novel drug-free, ROS-scavenging and gut microbiota regulation nanoplatform for the treatment of GI disorders.

Correction: An activator of G protein-coupled receptor and MEK1/2-ERK1/2 signaling inhibits HIV-1 replication by altering viral RNA processing.

[This corrects the article DOI: 10.1371/journal.ppat.1008307.].

Predictive evolutionary modelling for influenza virus by site-based dynamics of mutations.

Influenza virus continuously evolves to escape human adaptive immunity and generates seasonal epidemics. Therefore, influenza vaccine strains need to be updated annually for the upcoming flu season to ensure vaccine effectiveness. We develop a computational approach, beth-1, to forecast virus evolution and select representative virus for influenza vaccine. The method involves modelling site-wise mutation fitness. Informed by virus genome and population sero-positivity, we calibrate transition time of mutations and project the fitness landscape to future time, based on which beth-1 selects the optimal vaccine strain. In season-to-season prediction in historical data for the influenza A pH1N1 and H3N2 viruses, beth-1 demonstrates superior genetic matching compared to existing approaches. In prospective validations, the model shows superior or non-inferior genetic matching and neutralization against circulating virus in mice immunization experiments compared to the current vaccine. The method offers a promising and ready-to-use tool to facilitate vaccine strain selection for the influenza virus through capturing heterogeneous evolutionary dynamics over genome space-time and linking molecular variants to population immune response.

How probiotics, prebiotics, synbiotics, and postbiotics prevent dental caries: an oral microbiota perspective.

Dental caries, a highly prevalent oral disease, impacts a significant portion of the global population. Conventional approaches that indiscriminately eradicate microbes disrupt the natural equilibrium of the oral microbiota. In contrast, biointervention strategies aim to restore this balance by introducing beneficial microorganisms or inhibiting cariogenic ones. Over the past three decades, microbial preparations have garnered considerable attention in dental research for the prevention and treatment of dental caries. However, unlike related pathologies in the gastrointestinal, vaginal, and respiratory tracts, dental caries occurs on hard tissues such as tooth enamel and is closely associated with localized acid overproduction facilitated by cariogenic biofilms. Therefore, it is insufficient to rely solely on previous mechanisms to delineate the role of microbial preparations in the oral cavity. A more comprehensive perspective should involve considering the concepts of cariogenic biofilms. This review elucidates the latest research progress, mechanisms of action, challenges, and future research directions regarding probiotics, prebiotics, synbiotics, and postbiotics for the prevention and treatment of dental caries, taking into account the unique pathogenic mechanisms of dental caries. With an enhanced understanding of oral microbiota, personalized microbial therapy will emerge as a critical future research trend.

Effects of Oat ß-Glucan and Inulin on Alleviation of Nonalcoholic Steatohepatitis Aggravated by Circadian Disruption in C57BL/6J Mice.

This was the first study that examined the effects of oat ß-glucan and inulin on diet-induced nonalcoholic steatohepatitis (NASH) in circadian-disrupted (CD)-male C57BL/6J mice. CD intensified NASH, significantly increasing alanine aminotransferase and upregulating hepatic tumor necrosis factor α (TNFα) and transforming growth factor ß 1 (TGFß1). However, these observations were significantly alleviated by oat ß-glucan and inulin treatments. Compared to CD NASH mice, oat ß-glucan significantly decreased the liver index, aspartate aminotransferase (AST), and insulin. In prebiotic-treated and CD NASH mice, significant negative correlations were found between enrichment of Muribaculaceae bacterium Isolate-036 (Harlan), Muribaculaceae bacterium Isolate-001 (NCI), and Bacteroides ovatus after oat ß-glucan supplementation with TNFα and TGFß1 levels; and enrichment of Muribaculaceae bacterium Isolate-110 (HZI) after inulin supplementation with AST level. In conclusion, oat ß-glucan and inulin exhibited similar antiliver injury, anti-inflammatory, and antifibrotic activities but had no effect on cecal short-chain fatty acids and gut microbiota diversity in CD NASH mice.

A jingmenvirus RNA-dependent RNA polymerase structurally resembles the flavivirus counterpart but with different features at the initiation phase.

Jingmenviruses are a category of emerging segmented viruses that have garnered global attention in recent years, and are close relatives of the flaviviruses in the Flaviviridae family. One of their genome segments encodes NSP1 homologous to flavivirus NS5. NSP1 comprises both the methyltransferase (MTase) and RNA-dependent RNA polymerase (RdRP) modules playing essential roles in viral genome replication and capping. Here we solved a 1.8-Å resolution crystal structure of the NSP1 RdRP module from Jingmen tick virus (JMTV), the type species of jingmenviruses. The structure highly resembles flavivirus NS5 RdRP despite a sequence identity less than 30%. NSP1 RdRP enzymatic properties were dissected in a comparative setting with several representative Flaviviridae RdRPs included. Our data indicate that JMTV NSP1 produces characteristic 3-mer abortive products similar to the hepatitis C virus RdRP, and exhibits the highest preference of terminal initiation and shorter-primer usage. Unlike flavivirus NS5, JMTV RdRP may require the MTase for optimal transition from initiation to elongation, as an MTase-less NSP1 construct produced more 4-5-mer intermediate products than the full-length protein. Taken together, this work consolidates the evolutionary relationship between the jingmenvirus group and the Flaviviridae family, providing a basis to the further understanding of their viral replication/transcription process.

1,10-phenanthroline inhibits sumoylation and reveals that yeast SUMO modifications are highly transient.

The steady-state levels of protein sumoylation depend on relative rates of conjugation and desumoylation. Whether SUMO modifications are generally long-lasting or short-lived is unknown. Here we show that treating budding yeast cultures with 1,10-phenanthroline abolishes most SUMO conjugations within one minute, without impacting ubiquitination, an analogous post-translational modification. 1,10-phenanthroline inhibits the formation of the E1~SUMO thioester intermediate, demonstrating that it targets the first step in the sumoylation pathway. SUMO conjugations are retained after treatment with 1,10-phenanthroline in yeast that express a defective form of the desumoylase Ulp1, indicating that Ulp1 is responsible for eliminating existing SUMO modifications almost instantly when de novo sumoylation is inhibited. This reveals that SUMO modifications are normally extremely transient because of continuous desumoylation by Ulp1. Supporting our findings, we demonstrate that sumoylation of two specific targets, Sko1 and Tfg1, virtually disappears within one minute of impairing de novo sumoylation. Altogether, we have identified an extremely rapid and potent inhibitor of sumoylation, and our work reveals that SUMO modifications are remarkably short-lived.

Exopolysaccharides produced by Antrodia cinnamomea using microparticle-enhanced cultivation: Optimization, primary structure and antibacterial property.

Microparticle-enhanced cultivation was used to enhance the production of exopolysaccharides (EPSs) from Antrodia cinnamomea. The structure and antibacterial activity of two EPSs produced by A. cinnamomea treated with Al2O3 [EPS-Al (crude) and EPS-Al-p (purified)] and without Al2O3 [EPS-C (crude) and EPS-C-p (purified)] were compared. It was observed that the addition of 4 g/L Al2O3 at 0 h resulted in the highest EPS yield of 1.46 g/L, possible attributed to the enhanced permeability of the cell membrane. The structural analysis revealed that EPS-C-p and EPS-Al-p had different structures. EPS-C-p was hyperbranched and spherical with a Mw of 10.8 kDa, while EPS-Al-p was irregular and linear with a Mw of 12.5 kDa. The proportion of Man in EPS-Al-p decreased, while those of Gal and Glc increased when compared to EPS-C-p. The total molar ratios of 6-Glcp and 4-Glcp in EPS-Al-p are 1.45 times that of EPS-C-p. Moreover, EPSs could alter bacterial cell morphology, causing intracellular substance leakage and growth inhibition, with EPS-Al having a stronger antibacterial activity than EPS-C. In conclusion, A. cinnamomea treated with Al2O3 could produce more EPSs, changing monosaccharide composition and glycosidic linkage profile, which could exert stronger antibacterial activity than that produced by untreated A. cinnamomea.

Lesson learned from COVID-19 pandemic for the future of food industry.

With WHO announcing COVID-19 no longer as a public health emergency of international concern (PHEIC) on May 5, 2023, coupled with the fact that the majority of the countries of the world have dropped strict city lockdown or border closure, this perhaps signals the end of the COVID-19 crisis caused by the SARS-CoV-2 virus. However, the COVID-19 pandemic has resulted in far-reaching effects affecting nearly every aspect of our lives and society. Notably, the food industry including agriculture, food manufacturers, food logistics, distributors and retailers have all felt the profound impact and had experienced significant stress during the pandemic. Therefore, it is essential to retrospect the lessons that can be learned from this pandemic for the food industry. This short review aims to address the food safety issues related to the COVID-19 pandemic by focusing on its foodborne transmission potential, innovations of virus detection strategies suitable for food industry; development of phathogenicaidal methods and devices to inactivate SARS-CoV-2 virus (particularly in industrial scale); and the set-up of related food regulations and guidelines as preventive and control measures for preventing the spread of SARS-CoV-2 virus through the food supply chain during the pandemic. This article may provide useful references for the food industry to minimize the food safety impact of COVID-19 (as well as other respiratory virus) and allows them to better prepare for similar future challenges.

In Vitro Fermentation Characteristics of Fungal Polysaccharides Derived from Wolfiporia cocos and Their Effect on Human Fecal Microbiota.

Gut microbiota has been described as a new 'organ' that interferes with host physiology by its metabolites produced from the utilization and biotransformation of undigested food components. Fu Ling (FL), the sclerotia of fungi Wolfiporia cocos, contains ß-glucan, which is a known natural polysaccharide with strong medicinal efficacy. This study endeavors to evaluate the fermentability of FL and polysaccharides extracted from its sclerotia. An in vitro fermentation of structurally characterized FL and its ß-glucan by human fecal microbiota was conducted. Total bacterial count, pH change, short-chain fatty acid profile and microbiota profile were assessed post-fermentation. FL containing over 70% of ß-(1 → 3) and (1 → 6)-glucans with a low degree of branching of 0.24 could enhance acetic acid (a major microbial metabolite) production. Both FL and its extracted ß-glucan had similar modulation on microbial composition. They enriched Phascolarctobacterium faecium, Bacteroides dorei and Parabacteroides distasonis, all of which are shown to possess anti-inflammatory effects. FL polysaccharide can be utilized as a natural whole food for its potential health benefits to human gut bacteria.

SARS-CoV-2 RNA-Dependent RNA Polymerase Follows Asynchronous Translocation Pathway for Viral Transcription and Replication.

Translocation is one essential step for the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) to exert viral replication and transcription. Although cryo-EM structures of SARS-CoV-2 RdRp are available, the molecular mechanisms of dynamic translocation remain elusive. Herein, we constructed a Markov state model based on extensive molecular dynamics simulations to elucidate the translocation dynamics of the SARS-CoV-2 RdRp. We identified two intermediates that pinpoint the rate-limiting step of translocation and characterize the asynchronous movement of the template-primer duplex. The 3'-terminal nucleotide in the primer strand lags behind due to the uneven distribution of protein-RNA interactions, while the translocation of the template strand is delayed by the hurdle residue K500. Even so, the two strands share the same "ratchet" to stabilize the polymerase in the post-translocation state, suggesting a Brownian-ratchet model. Overall, our study provides intriguing insights into SARS-CoV-2 replication and transcription, which would open a new avenue for drug discoveries.

A Web-Based Patient Empowerment to Medication Adherence Program for Patients With Rheumatoid Arthritis: Feasibility Randomized Controlled Trial.

BACKGROUND: Living with a chronic illness such as rheumatoid arthritis (RA) requires medications and therapies, as well as long-term follow-up with multidisciplinary clinical teams. Patient involvement in the shared decision-making process on medication regimens is an important element in promoting medication adherence. Literature review and needs assessment showed the viability of technology-based interventions to equip patients with knowledge about chronic illness and competencies to improve their adherence to medications. Thus, a web-based intervention was developed to empower patients living with RA to adhere to their disease-modifying antirheumatic drugs (DMARDs) medication regimen. OBJECTIVE: This study aims to discuss the intervention mapping process in the design of a web-based intervention that supports patient empowerment to medication adherence and to evaluate its feasibility among patients living with RA. METHODS: The theory-based Patient Empowerment to Medication Adherence Programme (PE2MAP) for patients with RA was built upon the Zimmerman Psychological Empowerment framework, a web-based program launched through the Udemy website. PE2MAP was developed using a 6-step intervention mapping process: (1) needs assessment, (2) program objectives, (3) conceptual framework to guide the intervention, (4) program plan, (5) adoption, and (6) evaluation involving multidisciplinary health care professionals (HCPs) and a multimedia team. PE2MAP is designed as a 4-week web-based intervention program with a complementary RA handbook. A feasibility randomized controlled trial was completed on 30 participants from the intervention group who are actively taking DMARD medication for RA to test the acceptability and feasibility of the PE2MAP. RESULTS: The mean age and disease duration of the 30 participants were 52.63 and 8.50 years, respectively. The feasibility data showed 87% (n=26) completed the 4-week web-based PE2MAP intervention, 57% (n=17) completed all 100% of the contents, and 27% (n=8) completed 96% to 74% of the contents, indicating the overall feasibility of the intervention. As a whole, 96% (n=24) of the participants found the information on managing the side effects of medications, keeping fit, managing flare-ups, and monitoring joint swelling/pain/stiffness as the most useful contents of the intervention. In addition, 88% (n=23) and 92% (n=24) agreed that the intervention improved their adherence to medications and management of their side effects, including confidence in communicating with their health care team, respectively. The dos and do nots of traditional Chinese medicine were found by 96% (n=25) to be useful. Goal setting was rated as the least useful skill by 6 (23.1%) of the participants. CONCLUSIONS: The web-based PE2MAP intervention was found to be acceptable, feasible, and effective as a web-based tool to empower patients with RA to manage and adhere to their DMARD medications. Further well-designed randomized controlled trials are warranted to explore the effectiveness of this intervention in the management of patients with RA.

Effects of Synbiotic Supplementation on Metabolic Syndrome Traits and Gut Microbial Profile among Overweight and Obese Hong Kong Chinese Individuals: A Randomized Trial.

In view of the limited evidence showing anti-obesity effects of synbiotics via modulation of the gut microbiota in humans, a randomized clinical trial was performed. Assessment of the metabolic syndrome traits and profiling of the fecal gut microbiota using 16S rRNA gene sequencing in overweight and obese Hong Kong Chinese individuals before and after dietary intervention with an 8-week increased consumption of fruits and vegetables and/or synbiotic supplementation was conducted. The selected synbiotic contained two probiotics (Lactobacillus acidophilus NCFM and Bifidobacterium lactis HN019) and a prebiotic (polydextrose). Fifty-five overweight or obese individuals were randomized and divided into a synbiotic group (SG; n = 19), a dietary intervention group (DG; n = 18), and a group receiving combined interventions (DSG; n = 18). DSG showed the greatest weight loss effects and number of significant differences in clinical parameters compared to its baseline values-notably, decreases in fasting glucose, insulin, HOMA-IR, and triglycerides and an increase in HDL-cholesterol. DSG lowered Megamonas abundance, which was positively associated with BMI, body fat mass, and trunk fat mass. The results suggested that increasing dietary fiber consumption from fruits and vegetables combined with synbiotic supplementation is more effective than either approach alone in tackling obesity.

Utilization of Food-Derived ß-Glucans to Prevent and Treat Non-Alcoholic Fatty Liver Disease (NAFLD).

Non-alcoholic fatty liver disease (NAFLD) has become the most common chronic liver disease nowadays. Currently, there is no officially approved drug to treat NAFLD. In view of the increasing global prevalence of NAFLD and an absence of treatments, the development of effective treatments is of utmost importance. ß-glucan, a natural bioactive polysaccharide, has demonstrated hepatoprotective effects in NAFLD prevention and treatment. This review solely focuses on gathering the published preclinical animal studies that demonstrated the anti-liver injury, anti-steatotic, anti-inflammatory, anti-fibrotic, and antioxidant activities of ß-glucan. The impact of ß-glucan on gut microbiota and its metabolites including short-chain fatty acids and bile acids as the underlying mechanism for its bioactive beneficial effect on NAFLD is also explored. Given the limited knowledge of ß-glucan on anti-fibrotic activity, bile acid metabolism, and gut microbiota function, additional relevant research is highly encouraged to lay a solid foundation for the use of food-derived ß-glucan as a functional food for NAFLD. It is envisaged that further investigation of food-derived ß-glucan in human clinical studies should be carried out for its wider utilization.

Prevalence and factors associated with flares following COVID-19 mRNA vaccination in patients with rheumatoid arthritis, psoriatic arthritis and spondyloarthritis: a national cohort study.

OBJECTIVE: To determine prevalence and factors associated with flares post Coronavirus disease 2019 (COVID-19) mRNA vaccination in patients with rheumatoid arthritis (RA), psoriatic arthritis (PsA) and spondyloarthritis (SpA). METHODS: A retrospective multi-centre study was conducted (January 2021 to February 2022). Data were collected during index visit, defined as first post-vaccine visit in which the patient had a physician-defined flare, or if at least 3 months had elapsed since first vaccine dose, whichever came first. Factors associated with flares were identified using mixed effects Cox regression and expressed as hazard ratio (HR) and 95% confidence interval (CI). RESULTS: Total of 2377 patients were included (1563 RA, 415 PsA and 399 SpA). Among patients with RA, PsA and SpA, 21.3%, 24.1% and 21.8% experienced a flare respectively. Of those who experienced a flare, only 10.2%, 11.0% and 14.9% were severe in patients with RA, PsA and SpA respectively. Patients with low or moderate/high disease were more likely to flare compared to those in remission in patients with RA only (HR: 1.68, 95% CI 1.22-2.31; HR: 2.28, 95% CI 1.50-3.48, respectively). Receiving the Moderna vaccine was associated with a higher HR of flare compared to the Pfizer vaccine in patients with PsA only (HR: 2.21, 95% CI 1.20-4.08). Patients who had two vaccine doses were found to be less likely to flare (HR: 0.08, 95% CI 0.06-0.10). HRs of flares were not significantly different among RA, PsA and SpA. CONCLUSION: About one-fifth of patients experienced a disease flare post COVID-19 mRNA vaccination, but most flares were non-severe. Patients with active disease prior to vaccination should be monitored closely for disease flares, especially in patients with RA.

Enhanced In Vitro Anti-Photoaging Effect of Degraded Seaweed Polysaccharides by UV/H2O2 Treatment.

The high molecular weight and poor solubility of seaweed polysaccharides have limited their function and application. In this study, ultraviolet/hydrogen peroxide (UV/H2O2) treatment was used to prepare low-molecular-weight seaweed polysaccharides from Sargassum fusiforme. The effects of UV/H2O2 treatment on the physicochemical properties and anti-photoaging activity of S. fusiforme polysaccharides were studied. UV/H2O2 treatment effectively degraded polysaccharides from S. fusiforme (DSFPs), reducing their molecular weight from 271 kDa to 26 kDa after 2 h treatment. The treatment did not affect the functional groups in DSFPs but changed their molar percentage of monosaccharide composition and morphology. The effects of the treatment on the anti-photoaging function of S. fusiforme polysaccharides were investigated using human epidermal HaCaT cells in vitro. DFSPs significantly improved the cell viability and hydroxyproline secretion of UVB-irradiated HaCaT cells. In particular, DSFP-45 obtained from UV/H2O2 treatment for 45 min showed the best anti-photoaging effect. Moreover, DSFP-45 significantly increased the content and expression of collagen I and decreased those of pro-inflammatory cytokines, including interleukin-1ß, interleukin-6, and tumor necrosis factor-α. Thus, UV/H2O2 treatment could effectively improve the anti-photoaging activity of S. fusiforme polysaccharides. These results provide some insights for developing novel and efficient anti-photoaging drugs or functional foods from seaweed polysaccharides.

Rapid microfluidics prototyping through variotherm desktop injection molding for multiplex diagnostics.

In this work, we demonstrate an inexpensive method of prototyping microfluidics using a desktop injection molding machine. A centrifugal microfluidic device with a novel central filling mechanism was developed to demonstrate the technique. We overcame the limitations of desktop machines in replicating microfluidic features by variotherm heating and cooling the mold between 50 °C and 110 °C within two minutes. Variotherm heating enabled good replication of microfeatures, with a coefficient of variation averaging only 3.6% attained for the measured widths of 100 µm wide molded channels. Using this methodology, we produced functional polystyrene centrifugal microfluidic chips, capable of aliquoting fluids into 5.0 µL reaction chambers with 97.5% accuracy. We performed allele-specific loop-mediated isothermal amplification (AS-LAMP) reactions for genotyping CYP2C19 alleles on these chips. Readouts were generated using optical pH sensors integrated onto chips, by drop-casting sensor precursor solutions into reaction chambers before final chip assembly. Positive reactions could be discerned by decreases in pH sensor fluorescence, thresholded against negative control reactions lacking the primers for nucleic acid amplification and with time-to-results averaging 38 minutes. Variotherm desktop injection molding can enable researchers to prototype microfluidic devices more cost-effectively, in an iterative fashion, due to reduced costs of smaller, in-house molds. Designs prototyped this way can be directly translated to mass production, enhancing their commercialization potential and positive impacts.

A Tetrazine-Caged Carbon-Dipyrromethene as a Bioorthogonally Activatable Fluorescent Probe.

A water-soluble 1,2,4,5-tetrazine-substituted carbon-dipyrromethene (C-DIPY) was synthesized from the previously reported carbonyl pyrrole dimer through a two-step procedure. Owing to the presence of a tetrazine moiety, the fluorescence emission of this compound was largely quenched in phosphate-buffered saline at pH 7.4. Upon addition of a bicyclo[6.1.0]non-4-yne (BCN) derivative, the tetrazine-based quenching component of the compound was disrupted through the inverse electron-demand Diels-Alder reaction to restore the fluorescence in up to 6.6-fold. This bioorthogonal activation was also demonstrated using U-87 MG human glioblastoma cells, in which the fluorescence intensity of this C-DIPY could be enhanced by 8.7-fold upon post-incubation with the BCN derivative. The results showed that this tetrazine-caged C-DIPY can serve as a bioorthogonally activatable fluorescent probe for bioimaging. The compound, however, was found to reside preferentially in the lysosomes instead of the mitochondria of the cells as predicted based on its cationic character, which could be attributed to its energy-dependent endocytic cellular uptake pathway, for which lysosomes are the end station.

Predicting the antigenic evolution of SARS-COV-2 with deep learning.

The relentless evolution of SARS-CoV-2 poses a significant threat to public health, as it adapts to immune pressure from vaccines and natural infections. Gaining insights into potential antigenic changes is critical but challenging due to the vast sequence space. Here, we introduce the Machine Learning-guided Antigenic Evolution Prediction (MLAEP), which combines structure modeling, multi-task learning, and genetic algorithms to predict the viral fitness landscape and explore antigenic evolution via in silico directed evolution. By analyzing existing SARS-CoV-2 variants, MLAEP accurately infers variant order along antigenic evolutionary trajectories, correlating with corresponding sampling time. Our approach identified novel mutations in immunocompromised COVID-19 patients and emerging variants like XBB1.5. Additionally, MLAEP predictions were validated through in vitro neutralizing antibody binding assays, demonstrating that the predicted variants exhibited enhanced immune evasion. By profiling existing variants and predicting potential antigenic changes, MLAEP aids in vaccine development and enhances preparedness against future SARS-CoV-2 variants.