1.In-silico discovery of the hapten-based interaction between idiosyncratic hepatotoxic ingredients of Polygonum multiflorum and HLA-B*35:01
Dake XIAO ; Xu ZHAO ; Xiaoyan ZHAN ; Zhuo SHI ; Zhaofang BAI ; Jiang ZHENG ; Xiaohe XIAO ; Jiabo WANG
Science of Traditional Chinese Medicine 2025;3(1):15-27
Background: The previous research has confirmed the existence of idiosyncratic drug-induced liver injury (IDILI) caused by Polygonum multiflorum (PM-IDILI), and demonstrated that PM-IDILI is an immune-mediated injury, with HLA-B*35:01 identified as a genetic susceptibility marker. Additionally, emodin-8-O-β-D-glucoside (EG) and 2, 3, 5, 4′-tetrahyd roxystilbene-2-O-β-D-glucoside have been proposed as potential contributory ingredients in the pathogenesis of PM-IDILI. However, the precise mechanisms through which these susceptible factors contribute to the development of PM-IDILI remain unclear. Objectives: This study aims to explore the molecular characteristics of HLA-B*35:01 that contribute to PM-DILI and to propose a mechanistic hypothesis based on our previous research on PM-induced protein adducts. Methods: Key differences between HLA-B*35:01 and general Chinese HLA-B alleles were identified by comparing protein sequences, peptide binding motifs, and protein structures. Molecular docking was employed to assess whether PM-induced haptenated peptides can be presented by HLA-B*35:01 and other related alleles. Additionally, a simplified dipeptide model was used to evaluate the binding affinity of HLA-B*35:01 to EG-haptenated peptides. Results: Our findings revealed significant differences in the residues of the B and F peptide binding pockets of HLA-B*35:01 compared to general Chinese HLA-B alleles. Further analysis suggested that the F pocket of HLA-B*35:01 was capable of binding EG-cysteine adducts and might be a key feature in the PM-IDILI pathogenesis. Peptide docking using DINC and molecular dynamics simulations indicated that HLA-B*35:01 could form stable complexes with EG-haptenated peptides. Molecular dynamics simulations also highlighted the critical roles of both the B and F pockets in peptide binding. Specifically, the F pocket binds the EG-modified residue in haptenated peptides, while the B pocket, despite lacking shared features among PM-IDILI patients, may indirectly influence the incidence of PM-IDILI by filtering haptenated peptides. The binding affinity of HLA-B*35:01 to EG-modified cysteine residues was experimentally validated through a dipeptide-based assay, confirming that HLA-B*35:01 could bind EG-haptenated peptides. Conclusions: This study identified the unique B and F binding pockets of HLA-B*35:01 as key factors in PM-IDILI pathogenesis and demonstrated that HLA-B*35:01 could bind EG-haptenated peptides. These findings suggest that PM-IDILI may be a hapten-based drug hypersensitivity reaction driven by EG, providing a theoretical framework for further research aimed at elucidating the molecular mechanisms underlying PM-IDILI.
2.In-silico discovery of the hapten-based interaction between idiosyncratic hepatotoxic ingredients of Polygonum multiflorum and HLA-B*35:01
Dake XIAO ; Xu ZHAO ; Xiaoyan ZHAN ; Zhuo SHI ; Zhaofang BAI ; Jiang ZHENG ; Xiaohe XIAO ; Jiabo WANG
Science of Traditional Chinese Medicine 2025;3(1):15-27
Background: The previous research has confirmed the existence of idiosyncratic drug-induced liver injury (IDILI) caused by Polygonum multiflorum (PM-IDILI), and demonstrated that PM-IDILI is an immune-mediated injury, with HLA-B*35:01 identified as a genetic susceptibility marker. Additionally, emodin-8-O-β-D-glucoside (EG) and 2, 3, 5, 4′-tetrahyd roxystilbene-2-O-β-D-glucoside have been proposed as potential contributory ingredients in the pathogenesis of PM-IDILI. However, the precise mechanisms through which these susceptible factors contribute to the development of PM-IDILI remain unclear. Objectives: This study aims to explore the molecular characteristics of HLA-B*35:01 that contribute to PM-DILI and to propose a mechanistic hypothesis based on our previous research on PM-induced protein adducts. Methods: Key differences between HLA-B*35:01 and general Chinese HLA-B alleles were identified by comparing protein sequences, peptide binding motifs, and protein structures. Molecular docking was employed to assess whether PM-induced haptenated peptides can be presented by HLA-B*35:01 and other related alleles. Additionally, a simplified dipeptide model was used to evaluate the binding affinity of HLA-B*35:01 to EG-haptenated peptides. Results: Our findings revealed significant differences in the residues of the B and F peptide binding pockets of HLA-B*35:01 compared to general Chinese HLA-B alleles. Further analysis suggested that the F pocket of HLA-B*35:01 was capable of binding EG-cysteine adducts and might be a key feature in the PM-IDILI pathogenesis. Peptide docking using DINC and molecular dynamics simulations indicated that HLA-B*35:01 could form stable complexes with EG-haptenated peptides. Molecular dynamics simulations also highlighted the critical roles of both the B and F pockets in peptide binding. Specifically, the F pocket binds the EG-modified residue in haptenated peptides, while the B pocket, despite lacking shared features among PM-IDILI patients, may indirectly influence the incidence of PM-IDILI by filtering haptenated peptides. The binding affinity of HLA-B*35:01 to EG-modified cysteine residues was experimentally validated through a dipeptide-based assay, confirming that HLA-B*35:01 could bind EG-haptenated peptides. Conclusions: This study identified the unique B and F binding pockets of HLA-B*35:01 as key factors in PM-IDILI pathogenesis and demonstrated that HLA-B*35:01 could bind EG-haptenated peptides. These findings suggest that PM-IDILI may be a hapten-based drug hypersensitivity reaction driven by EG, providing a theoretical framework for further research aimed at elucidating the molecular mechanisms underlying PM-IDILI.
3.In-silico discovery of the hapten-based interaction between idiosyncratic hepatotoxic ingredients of Polygonum multiflorum and HLA-B*35:01
Dake XIAO ; Xu ZHAO ; Xiaoyan ZHAN ; Zhuo SHI ; Zhaofang BAI ; Jiang ZHENG ; Xiaohe XIAO ; Jiabo WANG
Science of Traditional Chinese Medicine 2025;3(1):15-27
Background: The previous research has confirmed the existence of idiosyncratic drug-induced liver injury (IDILI) caused by Polygonum multiflorum (PM-IDILI), and demonstrated that PM-IDILI is an immune-mediated injury, with HLA-B*35:01 identified as a genetic susceptibility marker. Additionally, emodin-8-O-β-D-glucoside (EG) and 2, 3, 5, 4′-tetrahyd roxystilbene-2-O-β-D-glucoside have been proposed as potential contributory ingredients in the pathogenesis of PM-IDILI. However, the precise mechanisms through which these susceptible factors contribute to the development of PM-IDILI remain unclear. Objectives: This study aims to explore the molecular characteristics of HLA-B*35:01 that contribute to PM-DILI and to propose a mechanistic hypothesis based on our previous research on PM-induced protein adducts. Methods: Key differences between HLA-B*35:01 and general Chinese HLA-B alleles were identified by comparing protein sequences, peptide binding motifs, and protein structures. Molecular docking was employed to assess whether PM-induced haptenated peptides can be presented by HLA-B*35:01 and other related alleles. Additionally, a simplified dipeptide model was used to evaluate the binding affinity of HLA-B*35:01 to EG-haptenated peptides. Results: Our findings revealed significant differences in the residues of the B and F peptide binding pockets of HLA-B*35:01 compared to general Chinese HLA-B alleles. Further analysis suggested that the F pocket of HLA-B*35:01 was capable of binding EG-cysteine adducts and might be a key feature in the PM-IDILI pathogenesis. Peptide docking using DINC and molecular dynamics simulations indicated that HLA-B*35:01 could form stable complexes with EG-haptenated peptides. Molecular dynamics simulations also highlighted the critical roles of both the B and F pockets in peptide binding. Specifically, the F pocket binds the EG-modified residue in haptenated peptides, while the B pocket, despite lacking shared features among PM-IDILI patients, may indirectly influence the incidence of PM-IDILI by filtering haptenated peptides. The binding affinity of HLA-B*35:01 to EG-modified cysteine residues was experimentally validated through a dipeptide-based assay, confirming that HLA-B*35:01 could bind EG-haptenated peptides. Conclusions: This study identified the unique B and F binding pockets of HLA-B*35:01 as key factors in PM-IDILI pathogenesis and demonstrated that HLA-B*35:01 could bind EG-haptenated peptides. These findings suggest that PM-IDILI may be a hapten-based drug hypersensitivity reaction driven by EG, providing a theoretical framework for further research aimed at elucidating the molecular mechanisms underlying PM-IDILI.
4.Compare the calculation precision of collapsed cone convolution and pencil beam convolution algorithm in heterogeneous tissue
Yanqun ZHAO ; Pei WANG ; Jie LI ; Mingyong XIAO ; Jinyi LANG ; Dake WU
Chinese Journal of Radiation Oncology 2012;21(1):72-76
ObjectiveTo compare the calculation precision of the collapsed cone convolution (CCC) algorithm and pencil beam convolution (PBC) algorithm in TPS in heterogeneous tissue.Methods We made two virtual lung phantoms,one is single field phantom,In this case the photon beam incident into the phantom,the other is the two fields phantom and a cubic'tumor' was placed in the centre of the phantom.two opposite photon beams incident into the phantom.We calculated the dose of the'tumor' and the lung with the CCC and PBC algorithm.We compared the results in both case with if obtained from Monte Carlo (MC) method.ResultsIn the single field phantom,the photon beam incident from the high-density tissue to the low-density lung equivalent tissue,compared with the result of MC algorithm PBC algorithm overestimated the lung equivalent tissue dose (t =3.90,P =0.012) and the result of CCC algorithm is close to it ( t =2.25,P =0.087 ).In the two fields phantom,tumor boundary dose calculated by CCC algorithm and the MC algorithm are lower than that of the PBC algorithm (t =2.43,3.18,P =0.038,0.011 ),and the difference increase when the field size decrease, the beam energy increase and the density of the inhomogeneity decrease.ConclusionsWe had better use the CCC algorithm when calculating the dose of the tumor surrounded by low-density tissue or the tumor behind the low-density tissue,such as the lung cancer,esophageal cancer etc.
5.Impact of thermoplastic mask on X-ray surface dose calculated with Monte Carlo code
Yanqun ZHAO ; Jie LI ; Liping WU ; Pei WANG ; Jinyi LANG ; Dake WU ; Mingyong XIAO
Chinese Journal of Radiation Oncology 2010;19(4):336-339
Objective To calculate the effects of thermoplastic mask on X-ray surface dose.Methods The BEAMnrc Monte Carlo Code system, designed especially for computer simulation of radioactive sources, was performed to evaluate the effects of thermoplastic mask on X-ray surface dose.Thermoplastic mask came from our center with a material density of 1.12 g/cm2. The masks without holes,with holes size of 0. 1 cm× 0. 1 cm, and with holes size of 0. 1 cm × 0. 2 cm, and masks with different depth (0.12 cm and 0.24 cm) were evaluated separately. For those with holes, the material width between adjacent holes was 0. 1 cm. Virtual masks with a material density of 1.38 g/cm3 without holes with two different depths were also evaluated. Results Thermoplastic mask affected X-rays surface dose. When using a thermoplastic mask with the depth of 0. 24 cm without holes, the surface dose was 74. 9% and 57.0% for those with the density of 1.38 g/cm3 and 1.12 g/cm3 respectively. When focusing on the masks with the density of 1.12 g/cm3, the surface dose was 41.2% for those with 0.12 cm depth without holes;57.0% for those with 0. 24 cm depth without holes;44. 5% for those with 0. 24 cm depth with holes size of 0.1 cm ×0.2 cm;and 54.1% for those with 0.24 cm depths with holes size of 0.1 cm ×0.1 cm.Conclusions Using thermoplastic mask during the radiation increases patient surface dose. The severity is relative to the hole size and the depth of thermoplastic mask. The surface dose change should be considered in radiation planning to avoid severe skin reaction.

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