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Article ; Online: Advanced molecular mechanisms of modified DRV compounds in targeting HIV-1 protease mutations and interrupting monomer dimerization.

Tang, Bolin / Luo, Song / Wang, Qihang / Gao, Pengfei / Duan, Lili

Physical chemistry chemical physics : PCCP

2024 Volume 26, Issue 6, Page(s) 4989–5001

Abstract: HIV-1 protease (PR) plays a crucial role in the treatment of HIV as a key target. The global issue of emerging drug resistance is escalating, and PR mutations pose a substantial challenge to the effectiveness of inhibitors. HIV-1 PR is an ideal model for ...

Abstract	HIV-1 protease (PR) plays a crucial role in the treatment of HIV as a key target. The global issue of emerging drug resistance is escalating, and PR mutations pose a substantial challenge to the effectiveness of inhibitors. HIV-1 PR is an ideal model for studying drug resistance to inhibitors. The inhibitor, darunavir (DRV), exhibits a high genetic barrier to viral resistance, but with mutations of residues in the PR, there is also some resistance to DRV. Inhibitors can impede PR in two ways: one involves binding to the active site of the dimerization protease, and the other involves binding to the PR monomer, thereby preventing dimerization. In this study, we aimed to investigate the inhibitory effect of DRV with a modified inhibitor on PR, comparing the differences between wild-type and mutated PR, using molecular dynamics simulations. The inhibitory effect of the inhibitors on PR monomers was subsequently investigated. And molecular mechanics Poisson-Boltzmann surface area evaluated the binding free energy. The energy contribution of individual residues in the complex was accurately calculated by the alanine scanning binding interaction entropy method. The results showed that these inhibitors had strong inhibitory effects against PR mutations, with GRL-142 exhibiting potent inhibition of both the PR monomer and dimer. Improved inhibitors could strengthen hydrogen bonds and interactions with PR, thereby boosting inhibition efficacy. The binding of the inhibitor and mutation of the PR affected the distance between D25 and I50, preventing their dimerization and the development of drug resistance. This study could accelerate research targeting HIV-1 PR inhibitors and help to further facilitate drug design targeting both mechanisms.
MeSH term(s)	Darunavir ; HIV Protease Inhibitors/chemistry ; HIV Protease Inhibitors/pharmacology ; Dimerization ; HIV Protease/chemistry ; Molecular Dynamics Simulation ; Mutation
Chemical Substances	Darunavir (YO603Y8113) ; HIV Protease Inhibitors ; p16 protease, Human immunodeficiency virus 1 (EC 3.4.23.-) ; HIV Protease (EC 3.4.23.-)
Language	English
Publishing date	2024-02-07
Publishing country	England
Document type	Journal Article
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/d3cp05702j
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Article ; Online: Diagnostic value of combined FVC%/DLCO% and echocardiography in connective tissue disorder‑associated pulmonary hypertension.

Shi, Huimin / Gao, Pengfei / Liu, Huijin / Su, Jie / He, Xuegai

Medicine international

2024 Volume 4, Issue 1, Page(s) 8

Abstract: The main objective of the present study was to investigate whether forced vital capacity (FVC)%/diffusing capacity of the lungs for carbon monoxide (DLCO)% can be used to predict the presence of pulmonary hypertension (PH) in connective tissue disorders ( ...

Abstract	The main objective of the present study was to investigate whether forced vital capacity (FVC)%/diffusing capacity of the lungs for carbon monoxide (DLCO)% can be used to predict the presence of pulmonary hypertension (PH) in connective tissue disorders (CTDs). For this purpose, a total of 53 individuals who were diagnosed with CTDs and had undergone right heart catheterization between July, 2019 and July, 2022 were included in the present study. Based on the mean pulmonary artery pressure (mPAP) measured during right heart catheterization, the participants were divided into the PH and non-PH groups. The differences in demographic characteristics, including sex, age, body mass index, smoking index, FVC%/DLCO% and pulmonary artery systolic pressure (PASP) were determined by echocardiography; moreover, the 6-min walk distance, plasma brain natriuretic peptide (BNP) levels, white blood cell count, red blood cell distribution width, erythrocyte sedimentation rate and C-reactive protein levels were compared between the two groups to identify independent predictors of PH. The independent predictors were subsequently evaluated for their correlation with mPAP to assess their predictive value for PH. FVC%/DLCO%, echocardiographic PASP, and plasma BNP levels were identified as independent predictors of PH. FVC%/DLCO% and echocardiographic PASP exhibited a significant correlation with mPAP, while the correlation between plasma BNP and mPAP levels was not statistically significant. The area under the curve (AUC) value for FVC%/DLCO% alone in predicting PH was 0.791, with an optimal diagnostic threshold of 1.35, a sensitivity of 0.794 and a specificity of 0.789. The AUC for echocardiographic PASP alone in predicting PH was 0.783, with an optimal diagnostic threshold of 39.5 mmHg, a sensitivity of 0.794 and a specificity of 0.684. When combined, the AUC of the two factors in predicting PH was 0.872, with a sensitivity of 0.941 and a specificity of 0.684. Collectively, the data of the present study indicate that FVC%/DLCO% may be used as a predictive factor for CTD-PH, and its combined application with echocardiographic PASP measurement may provide additional evidence for the clinical diagnosis of CTD-PH.
Language	English
Publishing date	2024-01-05
Publishing country	England
Document type	Journal Article
ISSN	2754-1304
ISSN (online)	2754-1304
DOI	10.3892/mi.2024.132
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Article ; Online: Identifying potential ligand-receptor interactions based on gradient boosted neural network and interpretable boosting machine for intercellular communication analysis.

Peng, Lihong / Gao, Pengfei / Xiong, Wei / Li, Zejun / Chen, Xing

Computers in biology and medicine

2024 Volume 171, Page(s) 108110

Abstract: Cell-cell communication is essential to many key biological processes. Intercellular communication is generally mediated by ligand-receptor interactions (LRIs). Thus, building a comprehensive and high-quality LRI resource can significantly improve ... ...

Abstract	Cell-cell communication is essential to many key biological processes. Intercellular communication is generally mediated by ligand-receptor interactions (LRIs). Thus, building a comprehensive and high-quality LRI resource can significantly improve intercellular communication analysis. Meantime, due to lack of a "gold standard" dataset, it remains a challenge to evaluate LRI-mediated intercellular communication results. Here, we introduce CellGiQ, a high-confident LRI prediction framework for intercellular communication analysis. Highly confident LRIs are first inferred by LRI feature extraction with BioTriangle, LRI selection using LightGBM, and LRI classification based on ensemble of gradient boosted neural network and interpretable boosting machine. Subsequently, known and identified high-confident LRIs are filtered by combining single-cell RNA sequencing (scRNA-seq) data and further applied to intercellular communication inference through a quartile scoring strategy. To validation the predictions, CellGiQ exploited several evaluation strategies: using AUC and AUPR, it surpassed six competing LRI prediction models on four LRI datasets; through Venn diagrams and molecular docking, its predicted LRIs were validated by five other popular intercellular communication inference methods; based on the overlapping LRIs, it computed high Jaccard index with six other state-of-the-art intercellular communication prediction tools within human HNSCC tissues; by comparing with classical models and literature retrieve, its inferred HNSCC-related intercellular communication results was further validated. The novelty of this study is to identify high-confident LRIs based on machine learning as well as design several LRI validation ways, providing reference for computational LRI prediction. CellGiQ provides an open-source and useful tool to decompose LRI-mediated intercellular communication at single cell resolution. CellGiQ is freely available at https://github.com/plhhnu/CellGiQ.
MeSH term(s)	Humans ; Ligands ; Molecular Docking Simulation ; Squamous Cell Carcinoma of Head and Neck ; Neural Networks, Computer ; Head and Neck Neoplasms
Chemical Substances	Ligands
Language	English
Publishing date	2024-02-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2024.108110
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Article ; Online: Comparison of efficacy and safety of PD-1/PD-L1 combination therapy in first-line treatment of advanced NSCLC: an updated systematic review and network meta-analysis.

Yang, Yanqing / Chen, Wei / Dong, Lixian / Duan, Lian / Gao, Pengfei

Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico

2024

Abstract: Background: The use of immune checkpoint inhibitors has led to an increase in randomized controlled trials exploring various first-line combination treatment regimens. With the introduction of new PD-1/PD-L1 inhibitors, there are now more clinical ... ...

Abstract	Background: The use of immune checkpoint inhibitors has led to an increase in randomized controlled trials exploring various first-line combination treatment regimens. With the introduction of new PD-1/PD-L1 inhibitors, there are now more clinical options available. For the first time, the AK105 monoclonal antibody Penpulimab, developed in China, was included. The AK105-302 Phase III trial studied the efficacy and safety of Penpulimab combined with chemotherapy in patients with advanced or metastatic squamous NSCLC. To determine the optimal treatment options, we conducted an updated network meta-analysis to compare the effectiveness and safety of these regimens. Methods: The system retrieves data from Chinese and English electronic databases, Clinical Trials, and the gov Clinical Trial Registration website up to September 6, 2023. The study indirectly compared the efficacy and safety of PD-1/PD-L1 combination regimens, including overall survival (OS), progression-free survival (PFS), objective response rate (ORR), all-grade adverse events, and above-grade III adverse events. Subgroup analyses were conducted based on programmed death ligand 1 (PD-L1) level, histological type, ECOG score, sex, and smoking history. Results: Nineteen RCTS were included, with a total of ten thousand eight hundred patients. Penpulimab plus chemotherapy (Pen + CT) provided the best OS (HR = 0.55, 95% CI 0.38-0.81) for PD-L1 patients with non-selective advanced NSCLC. Except Nivolumab plus Ipilimumab (Niv + Ipi), other PD-1/PD-L1 combination therapies significantly extended PFS compared with CT, and Nivolumab plus Bevacizumab combined with chemotherapy (Niv + Bev + CT) (HR = 0.43, 95% CI 0.26-0.74) provided the best PFS benefit and was comparable to Pen + CT (HR = 1.0) for PFS prolongation. For ORR, except Niv + Ipi, all the other regimens significantly improved ORR compared with CT. In terms of safety, except Tor + CT, the incidence of any-grade AEs or grade ≥ 3 adverse events may be higher than those of chemotherapy. The subgroup analysis revealed that for patients with PD-L1 levels below 1%, treatment with Tor + CT resulted in the best progression-free survival (HR = 0.47, 95% CI 0.25-0.86). For patients with PD-L1 levels of 1% or higher, Sintilimab plus chemotherapy (Sin + CT) (HR = 0.56, 95% CI 0.31-0.99) and Camrelizumab plus chemotherapy (Cam + CT) (HR = 0.43, 95% CI 0.28-0.64) were associated with the best overall survival and progression-free survival, respectively. For patients with SqNSCLC, combined immunotherapy may provide greater survival benefits. For patients with Non-sqNSCLC, Niv + Bev + CT and Tor + CT were associated with optimal PFS and OS, respectively. Cam + CT provided the best PFS in male patients with a history of smoking and an ECOG score of 0. In both female and non-smoking patient subgroups, Pem + CT was associated with the best PFS and OS benefits. Conclusion: For patients with advanced non-selective PD-L1 NSCLC, two effective regimens are Pen + CT and Niv + Bev + CT, which rank first in OS and PFS among all patients. Cam + CT and Tor + CT have advantages for OS in patients with SqNSCLC and Non-sqNSCLC, respectively. Niv + Ipi + CT provided the best OS benefit for patients with an ECOG score of 0, while Pem + CT may be the most effective treatment for patients with an ECOG score of 1. Pem + CT has a better effect on female patients and non-smokers. Sin + CT was found to be the most effective treatment for male patients and the smoking subgroup, while Cam + CT was found to be the most effective for PFS. In addition, Tor + CT was associated with the best PFS for patients with negative PD-L1 expression. Pem + CT was found to significantly improve both PFS and OS compared to CT alone. For patients with positive PD-L1 expression, Sin + CT and Cam + CT were found to be optimal for OS and PFS, respectively. It is important to note that, with the exception of Tor + CT, the toxicity of the other combinations was higher than that of CT alone.
Language	English
Publishing date	2024-04-16
Publishing country	Italy
Document type	Journal Article
ZDB-ID	2397359-6
ISSN	1699-3055 ; 1699-048X
ISSN (online)	1699-3055
ISSN	1699-048X
DOI	10.1007/s12094-024-03442-3
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Article: The Buffering Role of Self-compassion in the Association Between Loneliness with Depressive Symptoms: A Cross-Sectional Survey Study Among Older Adults Living in Residential Care Homes During COVID-19.

Gao, Pengfei / Mosazadeh, Hasan / Nazari, Nabi

International journal of mental health and addiction

2023 , Page(s) 1–21

Abstract: The coronavirus disease 2019 (COVID-19) pandemic is an ongoing geriatric health emergency with a substantial increase in the prevalence of medical and mental health issues, particularly among older adults living in residential care homes. The knowledge ... ...

Abstract	The coronavirus disease 2019 (COVID-19) pandemic is an ongoing geriatric health emergency with a substantial increase in the prevalence of medical and mental health issues, particularly among older adults living in residential care homes. The knowledge of the risk and protective factors related to the psychological impact of the COVID-19 pandemic on older adults living in residential care homes is based on limited data. This study aimed to investigate whether loneliness mediates the effects of fear generated by a pandemic on depression. Additionally, we hypothesized that self-compassion moderates the effect of loneliness on depression. A sample comprised 323 older adults (females: Supplementary information: The online version contains supplementary material available at 10.1007/s11469-023-01014-0.
Language	English
Publishing date	2023-02-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	2235886-9
ISSN	1557-1882 ; 1557-1874
ISSN (online)	1557-1882
ISSN	1557-1874
DOI	10.1007/s11469-023-01014-0
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Article: Influence of the Hydrogen Doping Method on the Atomic Structure, Mechanical Properties and Relaxation Behaviors of Metallic Glasses.

Zhang, Jiacheng / Gao, Pengfei / Zhang, Weixu

Materials (Basel, Switzerland)

2023 Volume 16, Issue 4

Abstract: The interaction of metallic glasses (MGs) with hydrogen can trigger many interesting physical, chemical and mechanical phenomena. However, atomic-scale understanding is still lacking. In this work, molecular dynamics (MD) simulations are employed to ... ...

Abstract	The interaction of metallic glasses (MGs) with hydrogen can trigger many interesting physical, chemical and mechanical phenomena. However, atomic-scale understanding is still lacking. In this work, molecular dynamics (MD) simulations are employed to study the atomic structure, mechanical properties and relaxation behaviors of H-doped Ni50Al50 MGs doped by two methods. The properties of H-doped MGs are determined not only by the hydrogen content but also by the doping method. When H atoms are doped into the molten state of samples, H atoms can fully diffuse and interact with metallic atoms, resulting in loose local atomic structures, homogeneous deformation and enhanced β relaxation. In contrast, when H atoms are doped into as-cast MGs, the H content is crucial in affecting the atomic structure and mechanical properties. A small number of H atoms has little influence on the elastic matrix, while the percolation of shear transformation zones (STZs) is hindered by H atoms, resulting in the delay of shear band (SB) formation and an insignificant change in the strength. However, a large number of H atoms can make the elastic matrix loose, leading to the decrease in strength and the transition of the deformation mode from SB to homogeneous deformation. The H effects on the elastic matrix and flow units are also applied to the dynamic relaxation. The deformability of H-doped Ni50Al50 MGs is enhanced by both H-doping methods; however, our results reveal that the mechanisms are different.
Language	English
Publishing date	2023-02-20
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2487261-1
ISSN	1996-1944
ISSN	1996-1944
DOI	10.3390/ma16041731
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Article: Silencing circPalm2 inhibits sepsis-induced acute lung injury by sponging miR-376b-3p and targeting MAP3K1.

Gao, Pengfei / Duan, Wenying / Shi, Huiyan / Wang, Qingxiu

Toxicological research

2023 Volume 39, Issue 2, Page(s) 275–294

Abstract: The apoptosis and inflammation of pulmonary epithelial cells are important pathogenic factors of sepsis-induced acute lung injury (ALI). Upregulation of circPalm2 (circ_0001212) expression levels has been previously detected in the lung tissue of ALI ... ...

Abstract	The apoptosis and inflammation of pulmonary epithelial cells are important pathogenic factors of sepsis-induced acute lung injury (ALI). Upregulation of circPalm2 (circ_0001212) expression levels has been previously detected in the lung tissue of ALI rats. Herein, the biological significance and detailed mechanism of circPalm2 in ALI pathogenesis were investigated. In vivo models of sepsis-induced ALI were established by treating C57BL/6 mice with cecal ligation and puncture (CLP) surgery. Murine pulmonary epithelial cells (MLE-12 cells) were stimulated with lipopolysaccharide (LPS) to establish in vitro septic ALI models. MLE-12 cell viability and apoptosis were evaluated by CCK-8 assay and flow cytometry analysis, respectively. The pathological alterations of the lung tissue were analysed based on hematoxylin-eosin (H&E) staining. Cell apoptosis in the lung tissue samples was examined by TUNEL staining assay. LPS administration suppressed the viability and accelerated the inflammation and apoptotic behaviours of MLE-12 cells. CircPalm2 displayed high expression in LPS-stimulated MLE-12 cells and possessed circular characteristics. The silencing of circPalm2 impeded apoptosis and inflammation in LPS-stimulated MLE-12 cells. Mechanistically, circPalm2 bound with miR-376b-3p, which targeted MAP3K1. In rescue assays, MAP3K1 enhancement reversed the repressive effects of circPalm2 depletion on LPS-triggered inflammatory injury and MLE-12 cell apoptosis. Furthermore, the lung tissue collected from CLP model mice displayed low miR-376b-3p expression and high levels of circPalm2 and MAP3K1. CircPalm2 positively regulated MAP3K1 expression by downregulating miR-376b-3p in murine lung tissues. Importantly, circPalm2 knockdown attenuated CLP-induced inflammation, apoptosis, and pathological alterations in lung tissues collected from mice. Silenced circPalm2 inhibits LPS-induced pulmonary epithelial cell dysfunction and mitigates abnormalities in lung tissues collected from CLP-stimulated mice via the miR-376b-3p/MAP3K1 axis in septic ALI. Supplementary information: The online version contains supplementary material available at 10.1007/s43188-022-00169-7.
Language	English
Publishing date	2023-01-17
Publishing country	Singapore
Document type	Journal Article
ZDB-ID	2727978-9
ISSN	2234-2753 ; 1976-8257
ISSN (online)	2234-2753
ISSN	1976-8257
DOI	10.1007/s43188-022-00169-7
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Article ; Online: Research on the Forward Solving Method of Defect Leakage Signal Based on the Non-Uniform Magnetic Charge Model.

Gao, Pengfei / Geng, Hao / Yang, Lijian / Su, Yuming

Sensors (Basel, Switzerland)

2023 Volume 23, Issue 13

Abstract: Pipeline magnetic flux leakage inspection is widely used in the evaluation of material defect detection due to its advantages of having no coupling agent and easy implementation. The quantification of defect size is an important part of magnetic flux ... ...

Abstract	Pipeline magnetic flux leakage inspection is widely used in the evaluation of material defect detection due to its advantages of having no coupling agent and easy implementation. The quantification of defect size is an important part of magnetic flux leakage testing. Defects of different geometrical dimensions produce signal waveforms with different characteristics after excitation. The key to achieving defect quantification is an accurate description of the relationship between the magnetic leakage signal and the size. In this paper, a calculation model for solving the defect leakage field based on the non-uniform magnetic charge distribution of magnetic dipoles is developed. Based on the traditional uniformly distributed magnetic charge model, the magnetic charge density distribution model is improved. Considering the variation of magnetic charge density with different depth positions, the triaxial signal characteristics of the defect are obtained by vector synthesis calculation. Simultaneous design of excitation pulling experiment. The leakage field distribution of rectangular defects with different geometries is analyzed. The experimental results show that the change in defect size will have an impact on the area of the defect leakage field distribution, and the larger the length and wider the width of the defect, the more sensitive the impact on the leakage field distribution. The solution model is consistent with the experimentally obtained leakage signal distribution law, and the model is a practical guide by which to improve the quality of defect evaluation.
MeSH term(s)	Physical Phenomena ; Magnetic Phenomena
Language	English
Publishing date	2023-07-07
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2052857-7
ISSN	1424-8220 ; 1424-8220
ISSN (online)	1424-8220
ISSN	1424-8220
DOI	10.3390/s23136221
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Article ; Online: A survey of the post-traumatic stress disorder in medical staff during COVID-19.

Li, Shiyue / Wang, Tianhong / Gao, Pengfei / Ji, Yang

Asian journal of surgery

2023 Volume 46, Issue 8, Page(s) 3111–3112

MeSH term(s)	Humans ; COVID-19 ; Stress Disorders, Post-Traumatic/epidemiology ; Stress Disorders, Post-Traumatic/etiology ; Medical Staff ; SARS-CoV-2 ; Surveys and Questionnaires
Language	English
Publishing date	2023-02-27
Publishing country	Netherlands
Document type	Letter
ZDB-ID	1068461-x
ISSN	0219-3108 ; 1015-9584
ISSN (online)	0219-3108
ISSN	1015-9584
DOI	10.1016/j.asjsur.2023.02.072
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Article ; Online: The Role of Bone Morphogenetic Protein 4 in Lung Diseases.

Dong, Xiaoxiao / Mao, Yimin / Gao, Pengfei

Current molecular medicine

2023 Volume 23, Issue 4, Page(s) 324–331

Abstract: Bone morphogenetic protein 4 (BMP4) is a multifunctional secretory protein that belongs to the transforming growth factor β superfamily. BMPs transduce their signaling to the cytoplasm by binding to membrane receptors of the serine/threonine kinase ... ...

Abstract	Bone morphogenetic protein 4 (BMP4) is a multifunctional secretory protein that belongs to the transforming growth factor β superfamily. BMPs transduce their signaling to the cytoplasm by binding to membrane receptors of the serine/threonine kinase family, including BMP type I and type II receptors. BMP4 participates in various biological processes, such as embryonic development, epithelial-mesenchymal transition, and maintenance of tissue homeostasis. The interaction between BMP4 and the corresponding endogenous antagonists plays a key role in the precise regulation of BMP4 signaling. In this paper, we review the pathogenesis of BMP4-related lung diseases and the foundation on which BMP4 endogenous antagonists have been developed as potential targets.
MeSH term(s)	Female ; Humans ; Pregnancy ; Bone Morphogenetic Protein 4/antagonists & inhibitors ; Bone Morphogenetic Protein 4/genetics ; Bone Morphogenetic Protein 4/metabolism ; Cytoplasm/genetics ; Cytoplasm/metabolism ; Embryonic Development/genetics ; Embryonic Development/physiology ; Epithelial-Mesenchymal Transition/genetics ; Epithelial-Mesenchymal Transition/physiology ; Lung Diseases/drug therapy ; Lung Diseases/genetics ; Lung Diseases/metabolism ; Protein Serine-Threonine Kinases
Chemical Substances	BMP4 protein, human ; Bone Morphogenetic Protein 4 ; Protein Serine-Threonine Kinases (EC 2.7.11.1)
Language	English
Publishing date	2023-03-07
Publishing country	Netherlands
Document type	Review ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2064873-X
ISSN	1875-5666 ; 1566-5240
ISSN (online)	1875-5666
ISSN	1566-5240
DOI	10.2174/1566524022666220428110906
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