1.Study on mechanism of naringin in alleviating cerebral ischemia/reperfusion injury based on DRP1/LRRK2/MCU axis.
Kai-Mei TAN ; Hong-Yu ZENG ; Feng QIU ; Yun XIANG ; Zi-Yang ZHOU ; Da-Hua WU ; Chang LEI ; Hong-Qing ZHAO ; Yu-Hong WANG ; Xiu-Li ZHANG
China Journal of Chinese Materia Medica 2025;50(9):2484-2494
This study aims to investigate the molecular mechanism by which naringin alleviates cerebral ischemia/reperfusion(CI/R) injury through DRP1/LRRK2/MCU signaling axis. A total of 60 SD rats were randomly divided into the sham group, the model group, the sodium Danshensu group, and low-, medium-, and high-dose(50, 100, and 200 mg·kg~(-1)) naringin groups, with 10 rats in each group. Except for the sham group, a transient middle cerebral artery occlusion/reperfusion(tMCAO/R) model was established in SD rats using the suture method. Longa 5-point scale was used to assess neurological deficits. 2,3,5-Triphenyl tetrazolium chloride(TTC) staining was used to detect the volume percentage of cerebral infarction in rats. Hematoxylin-eosin(HE) staining and Nissl staining were employed to assess neuronal structural alterations and the number of Nissl bodies in cortex, respectively. Western blot was used to determine the protein expression levels of B-cell lymphoma-2 gene(Bcl-2), Bcl-2-associated X protein(Bax), cleaved cysteine-aspartate protease-3(cleaved caspase-3), mitochondrial calcium uniporter(MCU), microtubule-associated protein 1 light chain 3(LC3), and P62. Mitochondrial structure and autophagy in cortical neurons were observed by transmission electron microscopy. Immunofluorescence assay was used to quantify the fluorescence intensities of MCU and mitochondrial calcium ion, as well as the co-localization of dynamin-related protein 1(DRP1) with leucine-rich repeat kinase 2(LRRK2) and translocase of outer mitochondrial membrane 20(TOMM20) with LC3 in cortical mitochondria. The results showed that compared with the model group, naringin significantly decreased the volume percentage of cerebral infarction and neurological deficit score in tMCAO/R rats, alleviated the structural damage and Nissl body loss of cortical neurons in tMCAO/R rats, inhibited autophagosomes in cortical neurons, and increased the average diameter of cortical mitochondria. The Western blot results showed that compared to the sham group, the model group exhibited increased levels of cleaved caspase-3, Bax, MCU, and the LC3Ⅱ/LC3Ⅰ ratio in the cortex and reduced protein levels of Bcl-2 and P62. However, naringin down-regulated the protein expression of cleaved caspase-3, Bax, MCU and the ratio of LC3Ⅱ/LC3Ⅰ ratio and up-regulated the expression of Bcl-2 and P62 proteins in cortical area. In addition, immunofluorescence analysis showed that compared with the model group, naringin and positive drug treatments significantly decreased the fluorescence intensities of MCU and mitochondrial calcium ion. Meanwhile, the co-localization of DRP1 with LRRK2 and TOMM20 with LC3 in cortical mitochondria was also decreased significantly after the intervention. These findings suggest that naringin can alleviate cortical neuronal damage in tMCAO/R rats by inhibiting DRP1/LRRK2/MCU-mediated mitochondrial fragmentation and the resultant excessive mitophagy.
Animals
;
Rats, Sprague-Dawley
;
Reperfusion Injury/genetics*
;
Flavanones/administration & dosage*
;
Rats
;
Dynamins/genetics*
;
Male
;
Brain Ischemia/genetics*
;
Protein Serine-Threonine Kinases/genetics*
;
Signal Transduction/drug effects*
;
Humans
;
Drugs, Chinese Herbal/administration & dosage*
2.Effects of combined use of active ingredients in Buyang Huanwu Decoction on oxygen-glucose deprivation/reglucose-reoxygenation-induced inflammation and oxidative stress of BV2 cells.
Tian-Qing XIA ; Ying CHEN ; Jian-Lin HUA ; Qin SU ; Cun-Yan DAN ; Meng-Wei RONG ; Shi-Ning GE ; Hong GUO ; Bao-Guo XIAO ; Jie-Zhong YU ; Cun-Gen MA ; Li-Juan SONG
China Journal of Chinese Materia Medica 2025;50(14):3835-3846
This study aims to explore the effects and action mechanisms of the active ingredients in Buyang Huanwu Decoction(BYHWD), namely tetramethylpyrazine(TMP) and hydroxy-safflor yellow A(HSYA), on oxygen-glucose deprivation/reglucose-reoxygenation(OGD/R)-induced inflammation and oxidative stress of microglia(MG). Network pharmacology was used to screen the effective monomer ingredients of BYHWD and determine the safe concentration range for each component. Inflammation and oxidative stress models were established to further screen the best ingredient combination and optimal concentration ratio with the most effective anti-inflammatory and antioxidant effects. OGD/R BV2 cell models were constructed, and BV2 cells in the logarithmic growth phase were divided into a normal group, a model group, an HSYA group, a TMP group, and an HSYA + TMP group. Enzyme-linked immunosorbent assay(ELISA) was used to detect the levels of inflammatory cytokines such as interleukin-1β(IL-1β), tumor necrosis factor-α(TNF-α), and interleukin-6(IL-6). Oxidative stress markers, including superoxide dismutase(SOD), nitric oxide(NO), and malondialdehyde(MDA), were also measured. Western blot was used to analyze the protein expression of both inflammation-related pathway [Toll-like receptor 4(TLR4)/nuclear factor-kappa B(NF-κB)] and oxidative stress-related pathway [nuclear factor erythroid 2-related factor 2(Nrf2)/heme oxygenase-1(HO-1)]. Immunofluorescence was used to assess the expression of proteins such as inducible nitric oxide synthase(iNOS) and arginase-1(Arg-1). The most effective ingredients for anti-inflammatory and antioxidant effects in BYHWD were TMP and HSYA. Compared to the normal group, the model group showed significantly increased levels of IL-1β, TNF-α, IL-6, NO, and MDA, along with significantly higher protein expression of NF-κB, TLR4, Nrf2, and HO-1 and significantly lower SOD levels. The differences between the two groups were statistically significant. Compared to the model group, both the HSYA group and the TMP group showed significantly reduced levels of IL-1β, TNF-α, IL-6, NO, and MDA, lower expression of NF-κB and TLR4 proteins, higher levels of SOD, and significantly increased protein expression of Nrf2 and HO-1. Additionally, the expression of the M1-type MG marker iNOS was significantly reduced, while the expression of the M2-type MG marker Arg-1 was significantly increased. The results of the HSYA group and the TMP group had statistically significant differences from those of the model group. Compared to the HSYA group and the TMP group, the HSYA + TMP group showed further significant reductions in IL-1β, TNF-α, IL-6, NO, and MDA levels, along with significant reductions in NF-κB and TLR4 protein expression, an increase in SOD levels, and elevated Nrf2 and HO-1 protein expression. Additionally, the expression of the M1-type MG marker iNOS was reduced, while the M2-type MG marker Arg-1 expression increased significantly in the HSYA + TMP group compared to the TMP or HSYA group. The differences in the results were statistically significant between the HSYA + TMP group and the TMP or HSYA group. The findings indicated that the combined use of HSYA and TMP, the active ingredients of BYHWD, can effectively inhibit OGD/R-induced inflammation and oxidative stress of MG, showing superior effects compared to the individual use of either component.
Oxidative Stress/drug effects*
;
Drugs, Chinese Herbal/pharmacology*
;
Animals
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Mice
;
Glucose/metabolism*
;
Cell Line
;
Inflammation/genetics*
;
Oxygen/metabolism*
;
Pyrazines/pharmacology*
;
Microglia/metabolism*
;
NF-E2-Related Factor 2/immunology*
;
NF-kappa B/immunology*
;
Toll-Like Receptor 4/immunology*
;
Anti-Inflammatory Agents/pharmacology*
;
Humans
4.Umbrella review of robotic-assisted total knee arthroplasty versus conventional total knee arthroplasty:surgical outcomes.
Xue-Qing TIAN ; Hong JI ; Yu-Hua XIANG ; Guo-An JIA
China Journal of Orthopaedics and Traumatology 2025;38(10):1037-1046
OBJECTIVE:
To systematically evaluate and re-evaluate the surgical outcomes of robotic-assisted total knee arthroplasty(RA-TKA) compared with to conventional total knee arthroplasty(C-TKA).
METHODS:
Ten databases, including PubMed, EmBase, Web of Science, Cochrane Library, CINAHL, JBI, CNKI, Wanfang, VIP, CBM, were comprehensively searched from inception to September 2024. Eligible studies included systematic reviews and meta-analysis comparing the surgical outcomes of RA-TKA and C-TKA. Two independen researchers performed data extraction and quality assessment. Methodological quality was evaluated using the AMSTAR tool, while the certainty of evidence was graded using GRADE system. The degree of overlap among primary studies included in the systematic reviews/meta-analyses was investigated using the corrected covered area (CCA).
RESULTS:
A total of 15 systematic reviews/Meta-analyses were included, 5 were rateak as high quality, 1 as moderate quality, and 9 as low quality. A total of 53 pieces of evidence were identified, 11 pieces of evidence were of high quality, 19 were of moderate quality, 16 were of low quality, and 7 were of very low quality. Ten studies assessed the Knee Society score(KSS) and performed a meta-analysis. Among these, seven studies reported that there was no statistically significant difference in postoperative KSS scores between the two surgical methods. Nine studies evaluated the Hospital for Special Surgery(HSS) score, with seven indicating no statistically significant difference in HSS scores following surgery. Twelve studies examined the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) score postoperatively, and five found no significant difference between the two surgical approaches. Five studies compared the hip-knee-ankle (HKA) angle deviation between the two groups, all of which demonstrated that the HKA angle deviation in RA-TKA was significantly lower than in C-TKA. Eight studies reported on the range of motion (ROM) of the knee joint after surgery, with six showing no statistically significant difference between the two methods. Finally, nine studies compared the duration of the surgical procedures, all of which concluded that RA-TKA required a longer operative time than C-TKA.
CONCLUSION
With regard to functional outcomes, no statistically significant difference was observed between RA-TKA and C-TKA. Nevertheless, RA-TKA demonstrates advantages in terms of surgical accuracy, precision, and alignment correction.
Humans
;
Arthroplasty, Replacement, Knee/methods*
;
Robotic Surgical Procedures/methods*
;
Treatment Outcome
;
Meta-Analysis as Topic
;
Systematic Reviews as Topic
5.Clinical characteristics and survival analysis of pediatric Hodgkin lymphoma: a multicenter study.
Ying LIN ; Li-Li PAN ; Shao-Hua LE ; Jian LI ; Bi-Yun GUO ; Yu ZHU ; Kai-Zhi WENG ; Jin-Hong LUO ; Gao-Yuan SUN ; Yong-Zhi ZHENG
Chinese Journal of Contemporary Pediatrics 2025;27(6):668-674
OBJECTIVES:
To investigate the clinicopathological characteristics and prognostic factors of pediatric Hodgkin lymphoma (HL).
METHODS:
A retrospective analysis was conducted on the clinical data of children with newly diagnosed HL from January 2011 to December 2023 at four hospitals: Fujian Medical University Union Hospital, Fujian Medical University Zhangzhou Hospital, First Affiliated Hospital of Xiamen University, and Fujian Children's Hospital. Patients were categorized into low-risk (R1), intermediate-risk (R2), and high-risk (R3) groups based on HL staging and pre-treatment risk factors. The patients received ABVD regimen or Chinese Pediatric HL-2013 regimen chemotherapy. Early treatment response and long-term efficacy were assessed, and prognostic factors were analyzed using the Cox proportional hazards regression model.
RESULTS:
The overall complete response (CR) rates after 2 and 4 cycles of chemotherapy were 42% and 68%, respectively. Compared with the ABVD regimen group, patients treated with the HL-2013 regimen in the R1 group showed significantly higher CR rates after both 2 and 4 cycles (P<0.05). However, no statistically significant differences in CR rates were observed between the two regimens in the R2 and R3 groups (P>0.05). The 5-year event-free survival (EFS) rate, overall survival rate, and freedom from treatment failure rate were 83%±4%, 97%±2%, and 88%±4%, respectively. Cox analysis indicated that the presence of a large tumor mass at diagnosis and failure to achieve CR after 4 cycles of chemotherapy were independent risk factors for lower EFS rates (P<0.05).
CONCLUSIONS
Pediatric HL generally has a favorable prognosis. The presence of a large tumor mass at diagnosis and failure to achieve CR after 4 cycles of chemotherapy indicate poor prognosis.
Humans
;
Hodgkin Disease/pathology*
;
Male
;
Child
;
Female
;
Adolescent
;
Retrospective Studies
;
Child, Preschool
;
Antineoplastic Combined Chemotherapy Protocols/therapeutic use*
;
Prognosis
;
Proportional Hazards Models
;
Survival Analysis
;
Infant
6.Granulomatous primary central nervous system vasculitis in a child.
Ya-Nan ZHANG ; Chang-Hong DING ; Shu-Hong REN ; Wei-Hua ZHANG ; Fang LIU ; Nan ZHANG ; Yu-Juan ZHANG
Chinese Journal of Contemporary Pediatrics 2025;27(9):1140-1142
A 14-year-old boy was admitted to the hospital due to a single episode of afebrile seizure and four hours of impaired consciousness. Three months prior to admission, he had a history of bilateral uveitis. Cerebrospinal fluid analysis revealed a mild elevation in white blood cell count. Cranial magnetic resonance imaging and contrast-enhanced scans showed multiple abnormal signals in both cerebral hemispheres, with punctate and nodular enhancement. Susceptibility-weighted imaging revealed multiple punctate hemorrhages within lesions in the bilateral frontal and left parietal lobes, suggestive of vasculitis. Brain biopsy demonstrated inflammatory granulomatous lesions. No secondary causes were identified, and the final diagnosis was granulomatous primary central nervous system vasculitis. The patient's condition improved after treatment with methylprednisolone sodium succinate and mycophenolate mofetil. This report describes a rare case of granulomatous central nervous system vasculitis in a child and provides valuable insights for the diagnosis and treatment of this disease.
Humans
;
Male
;
Vasculitis, Central Nervous System/diagnosis*
;
Adolescent
;
Magnetic Resonance Imaging
;
Granuloma/diagnosis*
7.Electroacupuncture Promotes Gastric Motility by Suppressing Pyroptosis via NLRP3/Caspase-1/GSDMD Signaling Pathway in Diabetic Gastroparesis Rats.
Hao HUANG ; Yan PENG ; Le XIAO ; Jing WANG ; Yu-Hong XIN ; Tian-Hua ZHANG ; Xiao-Yu LI ; Xing WEI
Chinese journal of integrative medicine 2025;31(5):448-457
OBJECTIVE:
To investigate the mechanism of electroacupuncture (EA) in treating diabetic gastroparesis (DGP) by inhibiting the activation of Nod-like receptor family pyrin domain-containing protein 3 (NLRP3) inflammasome and pyroptosis mediated via NLRP3/cysteinyl aspartate specific proteinase-1 (caspase-1)/gasdermin D (GSDMD) signaling pathway.
METHODS:
Forty Sprague-Dawley rats were randomly divided into 4 groups including the control, DGP model, EA, and MCC950 groups. The DGP model was established by a one-time high-dose intraperitoneal injection of 2% streptozotocin and a high-glucose and high-fat diet for 8 weeks. EA intervention was conducted at Zusanli (ST 36), Liangmen (ST 21) and Sanyinjiao (SP 6) with sparse-dense wave for 15 min, and was administered for 3 courses of 5 days. After intervention, the blood glucose, urine glucose, gastric emptying, and intestinal propulsive rate were observed. Besides, HE staining was used to observe histopathological changes in gastric antrum tissues, and TUNEL staining was utilized to detect DNA damage. Protein expression levels of NLRP3, apoptosis-associated speck-like protein containing CARD (ASC), pro-caspase-1, caspase-1 and GSDMD were measured by Western blot. Immunofluorescence staining was employed to assess the activity of GSDMD-N. Lactate dehydrogenase (LDH) levels were detected by using a biochemical kit.
RESULTS:
DGP rats showed persistent hyperglycemia and a significant decrease in gastrointestinal motility (P<0.05 or P<0.01), accompanied by pathological damage in their gastric antrum tissues. Cellular DNA was obviously damaged, and the expressions of NLRP3, ASC, pro-caspase-1, caspase-1 and GSDMD proteins were significantly elevated, along with enhanced fluorescence signals of GSDMD-N and increased LDH release (P<0.01). EA mitigated hyperglycemia, improved gastrointestinal motility in DGP rats and alleviated their pathological injury (P<0.05). Furthermore, EA reduced cellular DNA damage, lowered the protein levels of NLRP3, ASC, pro-caspase-1, caspase-1 and GSDMD, suppressed GSDMD-N activity, and decreased LDH release (P<0.05 or P<0.01), demonstrating effects comparable to MCC950.
CONCLUSION
EA promotes gastrointestinal motility and repairs the pathological damage in DGP rats, and its mechanism may be related to the inhibition of NLRP3 inflammasome and pyroptosis mediated by NLRP3/caspase-1/GSDMD pathway.
Animals
;
Electroacupuncture
;
NLR Family, Pyrin Domain-Containing 3 Protein/metabolism*
;
Pyroptosis
;
Rats, Sprague-Dawley
;
Caspase 1/metabolism*
;
Gastroparesis/physiopathology*
;
Signal Transduction
;
Male
;
Diabetes Mellitus, Experimental/physiopathology*
;
Phosphate-Binding Proteins/metabolism*
;
Gastrointestinal Motility
;
Rats
;
Intracellular Signaling Peptides and Proteins/metabolism*
;
Diabetes Complications/physiopathology*
;
Gasdermins
8.Plastrum Testudinis Stimulates Bone Formation through Wnt/β-catenin Signaling Pathway Regulated by miR-214.
Qing LIN ; Bi-Yi ZHAO ; Xiao-Yun LI ; Wei-Peng SUN ; Hong-Hao HUANG ; Yu-Mei YANG ; Hao-Yu WANG ; Xiao-Feng ZHU ; Li YANG ; Rong-Hua ZHANG
Chinese journal of integrative medicine 2025;31(8):707-716
OBJECTIVE:
To investigate the Wnt signaling pathway and miRNAs mechanism of extracts of Plastrum Testudinis (PT) in the treatment of osteoporosis (OP).
METHODS:
Thirty female Sprague Dawley rats were randomly divided into 5 groups by random number table method, including sham group, ovariectomized group (OVX), ovariectomized groups treated with high-, medium-, and low-dose PT (160, 80, 40 mg/kg per day, respectively), with 6 rats in each group. Except for the sham group, the other rats underwent bilateral ovariectomy to simulate OP and received PT by oral gavage for 10 consecutive weeks. After treatment, bone mineral density was measured by dual-energy X-ray absorptiometry; bone microstructure was analyzed by micro-computed tomography and hematoxylin and eosin staining; and the expressions of osteogenic differentiation-related factors were detected by immunochemistry, Western blot, and quantitative polymerase chain reaction. In addition, Dickkopf-1 (Dkk-1) was used to inhibit the Wnt signaling pathway in bone marrow mesenchymal stem cells (BMSCs) and miRNA overexpression was used to evaluate the effect of miR-214 on the osteogenic differentiation of BMSCs. Subsequently, PT extract was used to rescue the effects of Dkk-1 and miR-214, and its impacts on the osteogenic differentiation-related factors of BMSCs were evaluated.
RESULTS:
PT-M and PT-L significantly reduced the weight gain in OVX rats (P<0.05). PT also regulated the bone mass and bone microarchitecture of the femur in OVX rats, and increased the expressions of bone formation-related factors including alkaline phosphatase, bone morphogenetic protein type 2, collagen type I alpha 1, and runt-related transcription factor 2 when compared with the OVX group (P<0.05 or P<0.01). Meanwhile, different doses of PT significantly rescued the inhibition of Wnt signaling pathway-related factors in OVX rats, and increased the mRNA or protein expressions of Wnt3a, β-catenin, glycogen synthase kinase-3β, and low-density lipoprotein receptor-related protein 5 (P<0.05 or P<0.01). PT stimulated the osteogenic differentiation of BMSCs inhibited by Dkk-1 and activated the Wnt signaling pathway. In addition, the expression of miR-214 was decreased in OVX rats (P<0.01), and it was negatively correlated with the osteogenic differentiation of BMSCs (P<0.01). MiR-214 mimic inhibited Wnt signaling pathway in BMSCs (P<0.05 or P<0.01). Conversely, PT effectively counteracted the effect of miR-214 mimic, thereby activating the Wnt signaling pathway and stimulating osteogenic differentiation in BMSCs (P<0.05 or P<0.01).
CONCLUSION
PT stimulates bone formation in OVX rats through β-catenin-mediated Wnt signaling pathway, which may be related to inhibiting miR-214 in BMSCs.
Animals
;
MicroRNAs/genetics*
;
Female
;
Rats, Sprague-Dawley
;
Wnt Signaling Pathway/genetics*
;
Osteogenesis/genetics*
;
Mesenchymal Stem Cells/cytology*
;
Cell Differentiation/drug effects*
;
Bone Density/drug effects*
;
Ovariectomy
;
Osteoporosis/drug therapy*
;
beta Catenin/metabolism*
;
Rats
;
Intercellular Signaling Peptides and Proteins/metabolism*
;
Drugs, Chinese Herbal/pharmacology*
9.Effect of Acupuncture on Clinical Symptoms of Patients with Intractable Facial Paralysis: A Multicentre, Randomized, Controlled Trial.
Hong-Yu XIE ; Ze-Hua WANG ; Wen-Jing KAN ; Ai-Hong YUAN ; Jun YANG ; Min YE ; Jie SHI ; Zhen LIU ; Hong-Mei TONG ; Bi-Xiang CHA ; Bo LI ; Xu-Wen YUAN ; Chao ZHOU ; Xiao-Jun LIU
Chinese journal of integrative medicine 2025;31(9):773-781
OBJECTIVE:
To evaluate the clinical effect and safety of acupuncture manipulation on treatment of intractable facial paralysis (IFP), and verify the practicality and precision of the Anzhong Facial Paralysis Precision Scale (Eyelid Closure Grading Scale, AFPPS-ECGS).
METHODS:
A multicentre, single-blind, randomized controlled trial was conducted from October 2022 to June 2024. Eighty-nine IFP participants were randomly assigned to an ordinary acupuncture group (OAG, 45 cases) and a characteristic acupuncture group (CAG, 44 cases) using a random number table method. The main acupoints selected included Yangbai (GB 14), Quanliao (SI 18), Yingxiang (LI 20), Shuigou (GV 26), Dicang (ST 4), Chengjiang (CV 24), Taiyang (EX-HN 5), Jiache (ST 6), Fengchi (GB 20), and Hegu (LI 4). The OAG patients received ordinary acupuncture manipulation, while the CAG received characteristic acupuncture manipulation. Both groups received acupuncture treatment 3 times a week, with 10 times per course, lasting for 10 weeks. Facial recovery was assessed at baseline and after the 1st, 2nd and 3rd treatment course by AFPPS-ECGS and the House-Brackmann (H-B) Grading Scale. Infrared thermography technology was used to observe the temperature difference between healthy and affected sides in various facial regions. Adverse events and laboratory test abnormalities were recorded. The correlation between the scores of the two scales was analyzed using Pearson correlation coefficient.
RESULTS:
After the 2nd treatment course, the two groups showed statistically significant differences in AFPPS-ECGS scores (P<0.05), with even greater significance after the 3rd course (P<0.01). Similarly, H-B Grading Scale scores demonstrated significant differences between groups following the 3rd treatment course (P<0.05). Regarding temperature measurements, significant differences in temperatures of frontal and ocular areas were observed after the 2nd course (P<0.05), becoming more pronounced after the 3rd course (P<0.01). Additionally, mouth corner temperature differences reached statistical significance by the 3rd course (P<0.05). No safety-related incidents were observed during the study. Correlation analysis revealed that the AFPPS-ECGS and the H-B Grading Scale were strongly correlated (r=0.86, 0.91, 0.93, and 0.91 at baseline, and after 1st, 2nd, and 3rd treatment course, respectively, all P<0.01).
CONCLUSIONS
Acupuncture is an effective treatment for IFP, and the characteristic acupuncture manipulation enhances the therapeutic effect. The use of the AFPPS-ECGS can more accurately reflect the recovery status of patients with IFP. (Trial registration No. ChiCTR2200065442).
Humans
;
Acupuncture Therapy/methods*
;
Facial Paralysis/therapy*
;
Female
;
Male
;
Middle Aged
;
Adult
;
Treatment Outcome
;
Acupuncture Points
;
Aged
10.VenusMutHub: A systematic evaluation of protein mutation effect predictors on small-scale experimental data.
Liang ZHANG ; Hua PANG ; Chenghao ZHANG ; Song LI ; Yang TAN ; Fan JIANG ; Mingchen LI ; Yuanxi YU ; Ziyi ZHOU ; Banghao WU ; Bingxin ZHOU ; Hao LIU ; Pan TAN ; Liang HONG
Acta Pharmaceutica Sinica B 2025;15(5):2454-2467
In protein engineering, while computational models are increasingly used to predict mutation effects, their evaluations primarily rely on high-throughput deep mutational scanning (DMS) experiments that use surrogate readouts, which may not adequately capture the complex biochemical properties of interest. Many proteins and their functions cannot be assessed through high-throughput methods due to technical limitations or the nature of the desired properties, and this is particularly true for the real industrial application scenario. Therefore, the desired testing datasets, will be small-size (∼10-100) experimental data for each protein, and involve as many proteins as possible and as many properties as possible, which is, however, lacking. Here, we present VenusMutHub, a comprehensive benchmark study using 905 small-scale experimental datasets curated from published literature and public databases, spanning 527 proteins across diverse functional properties including stability, activity, binding affinity, and selectivity. These datasets feature direct biochemical measurements rather than surrogate readouts, providing a more rigorous assessment of model performance in predicting mutations that affect specific molecular functions. We evaluate 23 computational models across various methodological paradigms, such as sequence-based, structure-informed and evolutionary approaches. This benchmark provides practical guidance for selecting appropriate prediction methods in protein engineering applications where accurate prediction of specific functional properties is crucial.

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