1.Mechanism study of SIRT3 alleviating oxidative-stress injury in renal tubular cells by promoting mitochondrial biogenesis via regulating mitochondrial redox balance
Yaojun LIU ; Jun ZHOU ; Jing LIU ; Yunfei SHAN ; Huhai ZHANG ; Pan XIE ; Liying ZOU ; Lingyu RAN ; Huanping LONG ; Lunli XIANG ; Hong HUANG ; Hongwen ZHAO
Organ Transplantation 2026;17(1):86-94
Objective To elucidate the molecular mechanism of sirtuin-3 (SIRT3) in regulating mitochondrial biogenesis in human renal tubular epithelial cells. Methods Cells were stimulated with different concentrations of H2O2 and divided into four groups: control (NC), 50 μmol/L H2O2, 110 μmol/L H2O2 and 150 μmol/L H2O2. SIRT3 protein expression was then measured. SIRT3 was knocked down with siRNA, and cells were further assigned to five groups: control (NC), negative-control siRNA (NCsi), SIRT3-siRNA (siSIRT3), NCsi+H2O2, and siSIRT3+H2O2. After 24 h, cellular adenosine triphosphate (ATP) and mitochondrial superoxide anion (O2•−) levels were determined, together with mitochondrial expression of SIRT3, peroxisome proliferator-activated receptor γ coactivator-1α (PGC-1α), nuclear respiratory factor 1 (NRF1), mitochondrial transcription factor A (TFAM), superoxide dismutase 2 (SOD2), acetylated-SOD2 and adenosine monophosphate activated protein kinase α1 (AMPKα1). Results The 110 and 150 μmol/L H2O2 decreased SIRT3 protein (both P<0.05). ATP and mitochondrial O2•− did not differ between NC and NCsi groups (both P>0.05). Compared to the NCsi group, the siSIRT3 group exhibited elevated O2•− level, decreased SIRT3 protein and increased expression levels of SOD2 and acetylated SOD2 protein (all P<0.05). Compared to the NCsi group, the NCsi+H2O2 group exhibited decreased cellular ATP levels, elevated mitochondrial O2•− levels, and reduced protein expression levels of SIRT3, SOD2, TFAM, AMPKα1, PGC-1α and NRF1 (all P<0.05). Compared with the siSIRT3 group, the siSIRT3+H2O2 group showed a decrease in cellular ATP levels, an increase in mitochondrial O2•− levels, a decrease in SIRT3, SOD2, TFAM, AMPKα1, PGC-1α and NRF1 protein expression levels and a decrease in acetylated SOD2 protein expression levels (all P<0.05). Compared with the NCsi+H2O2 group, the siSIRT3+H2O2 group showed a decrease in cellular ATP levels, an increase in mitochondrial O2•− levels, a decrease in SIRT3, AMPKα1, PGC-1α and NRF1, TFAM protein expression levels, and an increase in SOD2 and acetylated SOD2 protein expression levels (all P<0.05). Conclusions SIRT3 promotes mitochondrial biogenesis in tubular epithelial cells via the AMPK/PGC-1α/NRF1/TFAM axis, representing a key mechanism through which SIRT3 ameliorates oxidative stress-induced mitochondrial dysfunction.
2.MCC950 Targeted Inhibition of TXNIP-NLRP3 Axis-mediated Podocyte Pyroptosis in Diabetic Nephropathy
Hong ZHENG ; Zhong-Cheng MO ; Hang LIU ; Xi-Zhang PAN ; Bing WEI
Progress in Biochemistry and Biophysics 2026;53(2):418-430
Diabetic Nephropathy (DN) is the leading cause of end-stage renal disease (ESRD) globally, representing a major global health burden with limited disease-modifying therapies. Podocyte injury serves as the core pathological hallmark of DN, and conventional treatments targeting metabolic disorders or hemodynamic abnormalities fail to reverse the progressive decline of renal function. Accumulating evidence over the past decade has established that high glucose-induced podocyte pyroptosis—a pro-inflammatory form of programmed cell death—is a key driving force in DN progression. Its core molecular mechanism hinges on the activation of the TXNIP-NLRP3 inflammasome axis. Under sustained hyperglycemic conditions, excessive reactive oxygen species (ROS) are generated via pathways including the polyol pathway, advanced glycation end products (AGEs) accumulation, and mitochondrial dysfunction. Concurrently, methylglyoxal (a glucose metabolite) mediates post-translational modification of thioredoxin-interacting protein (TXNIP). These events collectively trigger the dissociation of TXNIP from thioredoxin (TRX), a redox-regulating protein. The free TXNIP then translocates to the mitochondria, where it binds to The NACHT, LRR, and PYD domain-containing protein 3 (NLRP3) and promotes inflammasome assembly. This assembly activates cysteine-aspartic acid protease 1 (caspase-1), which cleaves Gasdermin D (GSDMD) to generate its N-terminal fragment (GSDMD-NT). GSDMD-NT oligomerizes to form membrane pores, leading to podocyte swelling, rupture, and the release of pro-inflammatory cytokines interleukin-1β (IL-1β) and interleukin-18 (IL-18). These cytokines amplify local inflammatory responses, induce mesangial cell proliferation, and accelerate extracellular matrix deposition, ultimately exacerbating glomerulosclerosis. MCC950, a highly selective NLRP3 inhibitor, exerts its therapeutic effects through a multi-layered mechanism: it binds to the NACHT domain (NAIP, CIITA, HET-E and TP1 domain) of NLRP3 with nanomolar affinity, forming hydrogen bonds with key residues (Lys-42 and Asp-166) within the ATP-hydrolysis pocket to block ATP hydrolysis, thereby locking NLRP3 in an inactive conformational state. Additionally, MCC950 interferes with the protein-protein interaction between TXNIP and NLRP3 and regulates mitochondrial homeostasis to reduce ROS production. Preclinical studies have demonstrated that MCC950 dose-dependently reduces proteinuria, restores the expression of podocyte-specific markers (nephrin and Wilms tumor 1 protein, WT1), and alleviates podocyte foot process fusion and glomerulosclerosis in both streptozotocin (STZ)-induced type 1 diabetic models (characterized by absolute insulin deficiency) and db/db type 2 diabetic models (driven by insulin resistance). However, discrepancies in therapeutic outcomes exist across different models—some studies report exacerbated renal inflammation and fibrosis in STZ-induced models—which may stem from differences in disease pathogenesis, intervention timing (early vs. mid-stage disease), and dosing duration. Despite its promising preclinical efficacy, MCC950 faces significant translational challenges, including low oral bioavailability, insufficient podocyte targeting, potential hepatotoxicity, and drug-drug interactions with statins (commonly prescribed to diabetic patients for cardiovascular risk management). Furthermore, off-target effects such as the inhibition of carbonic anhydrase 2 have been identified, raising concerns about its safety profile. Nevertheless, its unique mechanism of action—directly blocking podocyte pyroptosis by targeting the TXNIP-NLRP3 axis—endows it with substantial translational value. In the future, strategies to overcome these barriers are expected to advance its clinical application: targeted delivery via nanocarriers (e.g., PLGA-PEG nanoparticles or nephrin antibody-conjugated systems) to enhance renal accumulation and podocyte specificity; precise patient stratification based on biomarkers such as serum IL-18 and renal TXNIP/NLRP3 expression to identify “inflammatory-phenotype” DN patients most likely to benefit; and combination therapy with sodium-glucose cotransporter 2 (SGLT2) inhibitors—whose metabolic benefits synergize with MCC950’s anti-inflammatory effects. These approaches hold great potential to break through clinical translation bottlenecks, offering a novel, precise anti-inflammatory treatment option for DN and addressing an unmet clinical need for therapies targeting the inflammatory underpinnings of the disease.
3.MCC950 Targeted Inhibition of TXNIP-NLRP3 Axis-mediated Podocyte Pyroptosis in Diabetic Nephropathy
Hong ZHENG ; Zhong-Cheng MO ; Hang LIU ; Xi-Zhang PAN ; Bing WEI
Progress in Biochemistry and Biophysics 2026;53(2):418-430
Diabetic Nephropathy (DN) is the leading cause of end-stage renal disease (ESRD) globally, representing a major global health burden with limited disease-modifying therapies. Podocyte injury serves as the core pathological hallmark of DN, and conventional treatments targeting metabolic disorders or hemodynamic abnormalities fail to reverse the progressive decline of renal function. Accumulating evidence over the past decade has established that high glucose-induced podocyte pyroptosis—a pro-inflammatory form of programmed cell death—is a key driving force in DN progression. Its core molecular mechanism hinges on the activation of the TXNIP-NLRP3 inflammasome axis. Under sustained hyperglycemic conditions, excessive reactive oxygen species (ROS) are generated via pathways including the polyol pathway, advanced glycation end products (AGEs) accumulation, and mitochondrial dysfunction. Concurrently, methylglyoxal (a glucose metabolite) mediates post-translational modification of thioredoxin-interacting protein (TXNIP). These events collectively trigger the dissociation of TXNIP from thioredoxin (TRX), a redox-regulating protein. The free TXNIP then translocates to the mitochondria, where it binds to The NACHT, LRR, and PYD domain-containing protein 3 (NLRP3) and promotes inflammasome assembly. This assembly activates cysteine-aspartic acid protease 1 (caspase-1), which cleaves Gasdermin D (GSDMD) to generate its N-terminal fragment (GSDMD-NT). GSDMD-NT oligomerizes to form membrane pores, leading to podocyte swelling, rupture, and the release of pro-inflammatory cytokines interleukin-1β (IL-1β) and interleukin-18 (IL-18). These cytokines amplify local inflammatory responses, induce mesangial cell proliferation, and accelerate extracellular matrix deposition, ultimately exacerbating glomerulosclerosis. MCC950, a highly selective NLRP3 inhibitor, exerts its therapeutic effects through a multi-layered mechanism: it binds to the NACHT domain (NAIP, CIITA, HET-E and TP1 domain) of NLRP3 with nanomolar affinity, forming hydrogen bonds with key residues (Lys-42 and Asp-166) within the ATP-hydrolysis pocket to block ATP hydrolysis, thereby locking NLRP3 in an inactive conformational state. Additionally, MCC950 interferes with the protein-protein interaction between TXNIP and NLRP3 and regulates mitochondrial homeostasis to reduce ROS production. Preclinical studies have demonstrated that MCC950 dose-dependently reduces proteinuria, restores the expression of podocyte-specific markers (nephrin and Wilms tumor 1 protein, WT1), and alleviates podocyte foot process fusion and glomerulosclerosis in both streptozotocin (STZ)-induced type 1 diabetic models (characterized by absolute insulin deficiency) and db/db type 2 diabetic models (driven by insulin resistance). However, discrepancies in therapeutic outcomes exist across different models—some studies report exacerbated renal inflammation and fibrosis in STZ-induced models—which may stem from differences in disease pathogenesis, intervention timing (early vs. mid-stage disease), and dosing duration. Despite its promising preclinical efficacy, MCC950 faces significant translational challenges, including low oral bioavailability, insufficient podocyte targeting, potential hepatotoxicity, and drug-drug interactions with statins (commonly prescribed to diabetic patients for cardiovascular risk management). Furthermore, off-target effects such as the inhibition of carbonic anhydrase 2 have been identified, raising concerns about its safety profile. Nevertheless, its unique mechanism of action—directly blocking podocyte pyroptosis by targeting the TXNIP-NLRP3 axis—endows it with substantial translational value. In the future, strategies to overcome these barriers are expected to advance its clinical application: targeted delivery via nanocarriers (e.g., PLGA-PEG nanoparticles or nephrin antibody-conjugated systems) to enhance renal accumulation and podocyte specificity; precise patient stratification based on biomarkers such as serum IL-18 and renal TXNIP/NLRP3 expression to identify “inflammatory-phenotype” DN patients most likely to benefit; and combination therapy with sodium-glucose cotransporter 2 (SGLT2) inhibitors—whose metabolic benefits synergize with MCC950’s anti-inflammatory effects. These approaches hold great potential to break through clinical translation bottlenecks, offering a novel, precise anti-inflammatory treatment option for DN and addressing an unmet clinical need for therapies targeting the inflammatory underpinnings of the disease.
4.Mechanisms of Yishen Juanbi Pills-containing Bone Marrow Fluid in Improving Kidney-deficiency Rheumatoid Arthritis by Regulating CD4+ T Lymphocyte Differentiation via SDF-1/CXCR4 Signaling Pathway
Jinlin TONG ; Yuyao WANG ; Hong LIU ; Jinghua PAN ; Danping FAN ; Hongyan ZHAO
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(4):90-99
ObjectiveTo investigate the effects of Yishen Juanbi pills (YSJB)-containing bone marrow fluid on the migration and differentiation phenotypes of CD4⁺T lymphocytes based on the stromal cell-derived factor-1/chemokine receptor 4 (SDF-1/CXCR4) signaling pathway. MethodsPrimary CD4⁺T lymphocytes were isolated from mice using magnetic bead separation and identified for purity by flow cytometry. A CD4⁺T lymphocyte culture system was then established to observe the effects of SDF-1 on CD4⁺T-cell migration and differentiation. On this basis, the experimental groups included the Sham group, the ovariectomy (OVX) group, the Sham+collagen-induced arthritis (CIA) group, the OVX+CIA group, the Sham+CIA+YSJB group (2.16 g·kg-1), the OVX+CIA+YSJB group (2.16 g·kg-1), and the OVX+CIA+methotrexate (MTX) group (1.5 mg·kg-1). Bone marrow fluid from each group was prepared according to previous methods and added to the CD4⁺ T-cell culture system at 5% (v/v). Transwell assays were used to examine CD4⁺T-cell migration in each group. Real-time PCR was used to measure the mRNA expression levels of interleukin (IL)-17, tumor necrosis factor-α (TNF-α), retinoic-acid-related orphan receptor γt (RORγt), IL-10, transforming growth factor-β (TGF-β), forkhead box P3 (FoxP3), CXCR4, phosphoinositide 3-kinase (PI3K), and protein kinase B (Akt). Western blot was used to detect the expression of helper T (Th)17/regulatory T (Treg) cell signature factors (RORγt, FoxP3), CXCR4, PI3K, phosphorylated (p)-PI3K, Akt, and p-Akt. In a separate set of experiments, cells were divided into the Sham group, OVX+CIA group, OVX+CIA+CXCR4 antagonist AMD3100 group, and OVX+CIA+YSJB+AMD3100 group to observe changes in the above indicators following AMD3100 intervention. ResultsCompared with the Sham group, the number of migrated cells in the lower chamber was significantly increased in the Sham+CIA and OVX+CIA groups (P<0.05, P<0.01). The mRNA expression of RORγt, IL-17, TNF-α, CXCR4, PI3K, and Akt was significantly upregulated, whereas FoxP3, IL-10, and TGF-β mRNA expression was significantly decreased (P<0.05, P<0.01). Protein expression of RORγt, CXCR4, p-PI3K/PI3K, and p-Akt/Akt was significantly increased, while FoxP3 protein expression was markedly decreased (P<0.05, P<0.01). Compared with the OVX+CIA group, the OVX+CIA+YSJB group and OVX+CIA+MTX group showed significantly reduced migration (P<0.05), mRNA expression of RORγt, IL-17, TNF-α, CXCR4, PI3K, and Akt was also significantly decreased, while FoxP3, IL-10, and TGF-β mRNA expression was significantly increased (P<0.05, P<0.01). RORγt protein expression was significantly downregulated, and FoxP3 protein expression markedly upregulated (P<0.05). In the OVX+CIA+YSJB group, CXCR4, p-PI3K/PI3K, and p-Akt/Akt protein expression was significantly decreased (P<0.05). Compared with the OVX+CIA group, RORγt, CXCR4, PI3K, and Akt mRNA expression in CD4⁺T cells was significantly decreased in the OVX+CIA+AMD3100 group and the OVX+CIA+YSJB+AMD3100 group, while FoxP3 mRNA and protein expression was significantly upregulated (P<0.05, P<0.01). RORγt, CXCR4, p-PI3K/PI3K, and p-Akt/Akt protein expression was also markedly decreased (P<0.05, P<0.01). Compared with the OVX+CIA+AMD3100 group, the OVX+CIA+YSJB+AMD3100 group showed significantly decreased RORγt and Akt mRNA expression (P<0.05) and significantly lower p-Akt/Akt protein expression (P<0.05). ConclusionYSJB-containing bone marrow fluid suppresses CD4⁺T-cell migration and regulates Th17/Treg balance by downregulating Th17-associated signature factors and upregulating Treg-associated signature factors through inhibition of the SDF-1/CXCR4 signaling pathway and PI3K/Akt signaling pathway. The SDF-1/CXCR4 signaling pathway is one of the targets through which YSJB inhibits CD4⁺T-cell differentiation.
5.Research progress on cell membrane biomimetic nanoparticles for delivery of antitumor natural products
Luhua MENG ; Hong PAN ; Shuhuan LIU ; Mengmeng SHEN
China Pharmacy 2026;37(4):547-552
Natural products have shown great potential in the research and development of antitumor drugs. However, their clinical application is severely limited by inherent drawbacks such as poor water solubility, low stability, and low bioavailability. Cell membrane biomimetic nanoparticles, as a novel drug delivery system, have provided new strategies to overcome this bottleneck. This review systematically summarizes the preparation methods (e.g., membrane extrusion, ultrasonic fusion, and microfluidic electroporation) and characterization techniques (e.g., particle size, Zeta potential, and membrane surface protein detection) of cell membrane biomimetic nanoparticles, with a focus on the application of these derived from various sources in delivering antitumor natural products. Cell membrane biomimetic nanoparticles are endowed with unique biological functions, including low immunogenicity conferred by stem cell membranes, prolonged systemic circulation enabled by red blood cell membranes, and homologous targeting facilitated by tumor cell membranes. Despite these advancements, the technology still faces challenges such as difficulties in large-scale production, high costs, and limited characterization methods. Future research needs to further optimize the relevant processes to promote the clinical translation of cell membrane-biomimetic nanoparticles, thereby offering an efficient and safe novel delivery approach for antitumor therapy using natural products.
6.A clinical study on the effectiveness of feedforward control mode on improving occupational burnout among operating room nurses
Ru GU ; Liyan ZHAO ; Qianru WANG ; Hong ZHANG ; Dan LEI ; Yang YAO ; Pan LIU ; Jinzhu SUN ; Na LI
Chinese Medical Ethics 2025;38(10):1373-1378
ObjectiveTo explore the effectiveness of feedforward control mode on improving occupational burnout among operating room nurses through theoretical research and clinical practice, with a view to promoting their physical and mental health and enhancing the quality of surgical nursing. MethodsA total of 440 operating room nurses from different regions, scales, and nursing experiences in Shaanxi Province from November 2023 to December 2023 were randomly divided into an experimental group and a control group, with 220 nurses in each group. While the control group received routine intervention measures, the experimental group introduced a feedforward control mode based on the control group, with “emotional exhaustion,” “depersonalization,”and“personal achievement” as observation indicators. ResultsThe incidence of occupational burnout in the experimental group was 11.4%, while that in the control group was 20.0%. The experimental group showed a significantly lower incidence than the control group (P=0.013). ConclusionThe feedforward control mode can significantly alleviate nurses’ sense of job burnout, promote the improvement of surgical nursing quality, as well as continuously improve the scientific rigor, advancement, and humanistic nature of nursing services, which is conducive to building a harmonious and efficient nursing team. The spirit of teamwork, reflected in mutual support, mutual trust, and joint efforts for surgical success and patient health, has become an important component of nurses’ professional ethics.
7.Advancements and applications in radiopharmaceutical therapy.
Shiya WANG ; Mingyi CAO ; Yifei CHEN ; Jingjing LIN ; Jiahao LI ; Xinyu WU ; Zhiyue DAI ; Yuhan PAN ; Xiao LIU ; Xian LIU ; Liang-Ting LIN ; Jianbing WU ; Ji LIU ; Qifeng ZHONG ; Zhenwei YUAN
Chinese Journal of Natural Medicines (English Ed.) 2025;23(6):641-657
Radiopharmaceuticals operate by combining radionuclides with carriers. The radiation energy emitted by radionuclides is utilized to selectively irradiate diseased tissues while minimizing damage to healthy tissues. In comparison to external beam radiation therapy, radionuclide drugs demonstrate research potential due to their biological targeting capabilities and reduced normal tissue toxicity. This article reviews the applications and research progress of radiopharmaceuticals in cancer treatment. Several key radionuclides are examined, including 223Ra, 90Y, Lutetium-177 (177Lu), 212Pb, and Actinium-225 (225Ac). It also explores the current development trends of radiopharmaceuticals, encompassing the introduction of novel radionuclides, advancements in imaging technologies, integrated diagnosis and treatment approaches, and equipment-medication combinations. We review the progress in the development of new treatments, such as neutron capture therapy, proton therapy, and heavy ion therapy. Furthermore, we examine the challenges and breakthroughs associated with the clinical translation of radiopharmaceuticals and provide recommendations for the research and development of novel radionuclide drugs.
Humans
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Radiopharmaceuticals/therapeutic use*
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Neoplasms/radiotherapy*
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Radioisotopes/therapeutic use*
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Animals
8.Expert consensus on clinical randomized controlled trial design and evaluation methods for bone grafting or substitute materials in alveolar bone defects.
Xiaoyu LIAO ; Yang XUE ; Xueni ZHENG ; Enbo WANG ; Jian PAN ; Duohong ZOU ; Jihong ZHAO ; Bing HAN ; Changkui LIU ; Hong HUA ; Xinhua LIANG ; Shuhuan SHANG ; Wenmei WANG ; Shuibing LIU ; Hu WANG ; Pei WANG ; Bin FENG ; Jia JU ; Linlin ZHANG ; Kaijin HU
West China Journal of Stomatology 2025;43(5):613-619
Bone grafting is a primary method for treating bone defects. Among various graft materials, xenogeneic bone substitutes are widely used in clinical practice due to their abundant sources, convenient processing and storage, and avoidance of secondary surgeries. With the advancement of domestic production and the limitations of imported products, an increasing number of bone filling or grafting substitute materials isentering clinical trials. Relevant experts have drafted this consensus to enhance the management of medical device clinical trials, protect the rights of participants, and ensure the scientific and effective execution of trials. It summarizes clinical experience in aspects, such as design principles, participant inclusion/exclusion criteria, observation periods, efficacy evaluation metrics, safety assessment indicators, and quality control, to provide guidance for professionals in the field.
Humans
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Bone Substitutes/therapeutic use*
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Randomized Controlled Trials as Topic/methods*
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Consensus
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Bone Transplantation
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Research Design
9.Anti-SARS-CoV-2 prodrug ATV006 has broad-spectrum antiviral activity against human and animal coronaviruses.
Tiefeng XU ; Kun LI ; Siyao HUANG ; Konstantin I IVANOV ; Sidi YANG ; Yanxi JI ; Hanwei ZHANG ; Wenbin WU ; Ye HE ; Qiang ZENG ; Feng CONG ; Qifan ZHOU ; Yingjun LI ; Jian PAN ; Jincun ZHAO ; Chunmei LI ; Xumu ZHANG ; Liu CAO ; Deyin GUO
Acta Pharmaceutica Sinica B 2025;15(5):2498-2510
Coronavirus-related diseases pose a significant challenge to the global health system. Given the diversity of coronaviruses and the unpredictable nature of disease outbreaks, the traditional "one bug, one drug" paradigm struggles to address the growing number of emerging crises. Therefore, there is an urgent need for therapeutic agents with broad-spectrum anti-coronavirus activity. Here, we provide evidence that ATV006, an anti-SARS-CoV-2 nucleoside analog targeting RNA-dependent RNA polymerase (RdRp), has broad antiviral activity against human and animal coronaviruses. Using mouse hepatitis virus (MHV) and human coronavirus NL63 (HCoV-NL63) as a model, we show that ATV006 has potent prophylactic and therapeutic activity against murine coronavirus infection in vivo. Remarkably, ATV006 successfully inhibits viral replication in mice even when administered 96 h after infection. Due to its oral bioavailability and potency against multiple coronaviruses, ATV006 has the potential to become a useful antiviral agent against SARS-CoV-2 and other circulating and emerging coronaviruses in humans and animals.
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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