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In Silico Screening of Potential Spike Glycoprotein Inhibitors of SARS-CoV-2 with Drug Repurposing Strategy

Chinese Journal of Integrative Medicine 2020年第9期26卷 663-669页

作者： WEI Tian-zi WANG Hao WU Xue-qing LU Yi GUAN Sheng-hui DONG Feng-quan DONG Chen-le ZHU Gu-li BAO Yu-zhou ZHANG Jian WANG Guan-yu LI Hai-ying Department of Biology Southern University of Science and TechnologyShenzhen(518055)GuangdongChina School of Medicine Southern University of Science and TechnologyShenzhen(518055)GuangdongChina School of Biomedical Sciences Li Ka Shing Faculty of Medicinethe University of Hong KongHong Kong SARChina Department of Obstetrics and Gynecology Shenzhen University General HospitalShenzhen(518055)GuangdongChina Clinical Medical Academy Shenzhen UniversityShenzhen(518055)GuangdongChina Department of Cardiology Shenzhen University General HospitalShenzhen(518055)GuangdongChina Department of Obstetrics and Gynecology the First Affiliated Hospital of Wenzhou Medical UniversityWenzhou(325000)ZhejiangChina Guangdong Provincial Key Laboratory of Computational Science and Material Design Shenzhen(518055)GuangdongChina Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research Shenzhen(518055)GuangdongChina

Objective:To select potential molecules that can target viral spike proteins,which may potentially interrupt the interaction between the human angiotension-converting enzyme 2(ACE2)receptor and viral spike protein by virtual ***:The three-dimensional(3D)-coordinate file of the receptor-binding domain(RBD)-ACE2 complex for searching a suitable docking pocket was firstly downloaded and ***,approximately 15,000 molecular candidates were prepared,including US Food and Drug Administration(FDA)-approved drngs from DrugBank and natural compounds from Traditional Chinese Medicine Systems Pharmacology(TCMSP),for the docking ***,virtual screening was performed and the binding energy in Autodock Vina was ***,the top 20 molecules with high binding energy and their Chinese medicine(CM)herb sources were listed in this ***:It was found that digitoxin,a cardiac glycoside in DrugBank and bisindigotin in TCMSP had the highest docking ***,two of the CM herbs containing the natural compounds that had relatively high binding scores,Forsyfh/ae frucft/s and/saf/d/s racWx,are components of Lianhua Qingwen(莲花清痕),a CM formula reportedly exerting activity against severe acute respiratory syndrome(SARS)-***,raltegravir,an HIV integrase inhibitor,was found to have a relatively high binding ***:A class of compounds,which are from FDA-approved drugs and CM natural compounds,that had high binding energy with RBD of the viral spike *** work provides potential candidates for other researchers to identify inhibitors to prevent SARS-CoV-2 infection,and highlights the importance of CM and integrative application of CM and Western medicine on treating COVID-19.

关键词： COVID-19 SARS-CoV-2 drug repurposing virtual screening Chinese medicine

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Performance evaluation of high-order reconstruction for discrete unified gas-kinetics scheme in tracking fluid interfaces

arXiv

引用

arXiv 2020年

作者： Yang, Zeren Zhong, Chengwen Zhuo, Congshan National Key Laboratory of Science Technology on Aerodynamic Design Research Northwestern Polytechnical University Xi’an Shaanxi710072 China

MSC Codes 82B40, 35Q20, 76M12, *** a noticeable increase in research centered on modeling micro fluid interfaces in the framework of mesoscopic methods, we conduct an exhaustive study of discrete unified gas-kinetics scheme (DUGKS) in handling complicated interface deformations. High-order isotropic finite-difference schemes are first utilized in DUGKS to improve its capability in tracking interfaces. The performance of third-stage third-order DUGKS where source term is incorporated has also been assessed for the first time and a series of numerical tests have been conducted to investigate their capability. The comparative analysis have revealed the reason why the performance of lattice Boltzmann method is superior to that of discrete velocity method and DUGKS in general condition from an informed perspective. The mechanism behind the performance distinction between the central scheme and upwind scheme utilized in meso-flux construction in DUGKS have also been clarified. Numerical results have shown that the employment of high-order schemes in DUGKS does have an effect on the reduction of numerical dissipation, but the overall accuracy of this method is limited by the precision of prediction of source terms on mesh interface. The capability of third-stage third-order DUGKS is severely inhibited by its intrinsic limitation of the ratio of time step to particle collision time. Among the various kinds of DUGKS employed with different reconstruction methods, the most promising scheme is the one with third-order isotropic reconstruction and upwind-based meso-flux evaluation, which is able to ensure an unique balance between efficiency and accuracy. Copyright © 2020, The Authors. All rights reserved.

关键词： Finite difference method

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Effect of clamping failure on flow induced vibration and fretting wear of fuel rods

Effect of clamping failure on flow induced vibration and fre...

引用

ASME 2018 Pressure Vessels and Piping Conference, PVP 2018

作者： Huan-Huan, Qi Zhi-Peng, Feng Fu-Rui, Xiong Nai-Bin, Jiang Qian, Huang Xuan, Huang Science and Technology on Reactor System Design Technology Laboratory Nuclear Power Institute of China Chengdu China

ISBN: (纸本)9780791851654

Fuel rods are subjected to both axial and lateral flow in the reactor core. In this study, we present a study on the flow induced vibration (FIV) and fretting wear of fuel rod with failed clamping at grids. First, according to the flow distribution around a type of pressurized water reactor (PWR) fuel rod, the power spectral density (PSD) is obtained to characterize the turbulence excitation. Next, by combining the correlation PSD test parameters, the mean square value of the vibration displacement of each rod mode is found, and then the wear depth of dimple position is calculated based on the ARCHARD wear formula. The clamping of fuel rod at various grids may fail due to inaccurate manufacturing, fuel transportation and in-core irradiation. The absence of clamping force would significantly influence the rod mode and thereby changes its FIV responses. Simulation results show that the failure of the leaf spring has negligible effect on the rod natural frequency whereas the dimple failure near the location with larger FIV amplitude has a much significant effect. The lateral flow velocities at the inlet and outlet of the core are larger. For the fully clamped fuel rod, the response amplitude of turbulent excitation at the bottom and top of the fuel rod is larger. This is even more obvious with a failed dimple at these locations. Comparatively, the effect of dimple support failure in the middle is less influential. The influence of dimple support failure over the rod wear depth depicts basically the same trend as on the maximum FIV amplitude. In addition to the FIV amplitude, wear depth is also related to rod natural frequency. By examining the multiplication of amplitude and frequency at the top and bottom grid, we found that the dimple failure has greater impact at the top grid. Copyright © 2018 ASME.

关键词： Natural frequencies

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Inverse-electron-demand Diels–Alder approach to densely substituted bicyclo[3.2.2]nonanes: Discovery of an autophagy regulator

引用

Chinese Chemical Letters 2025年

作者： Jiulong Li Pengxin Ren Lin Wang Yuting Zhang Peng Yang Weiwei He Ang Li College of Chemistry & Henan Institute of Advanced Technology Zhengzhou University Zhengzhou 450001 China State Key Laboratory of Chemical Biology Shanghai Institute of Organic Chemistry University of Chinese Academy of Sciences Chinese Academy of Sciences Shanghai 200032 China Shanghai Key Laboratory of New Drug Design School of Pharmacy East China University of Science and Technology Shanghai 200237 China

Natural products bearing a bicyclo[3.2.2]nonane motif pose a considerable challenge to chemical synthesis. We developed a europium-promoted inverse-electron-demand Diels–Alder reaction of benzo[2,3]tropone derivatives with electron-rich olefins, which offers an expeditious approach to densely substituted bicyclo[3.2.2]nonanes. This method enabled the concise synthesis of a tetracyclic amine, subsequently identified as a downstream suppressor of autophagy.

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design of a Multi-Valent SARS-CoV-2 Peptide Vaccine for Broad Immune Protection via Deep Learning

引用

Engineering 2025年

作者： Ziyan Feng Xuelian Pang Qian Xu Zijie Gu Shiliang Li Lili Zhu Honglin Li Shanghai Key Laboratory of New Drug Design School of Pharmacy East China University of Science and Technology Shanghai 200237 China Innovation Center for AI and Drug Discovery School of Pharmacy East China Normal University Shanghai 200062 China Lingang Laboratory Shanghai 200031 China

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants capable of evading both convalescent and vaccine-triggered antibody responses has underscored the pivotal role of T-cell immunity in antiviral defense. Here, we develop the ConFormer network for epitope prediction, which couples convolutional neural network (CNN) local features with Transformer global representations to enhance binding prediction performance, and employ a deep learning algorithm and bioinformatics workflows to identify conserved T-cell epitopes within the SARS-CoV-2 proteome. Five epitopes are identified as potential inducers of T-cell immune responses. Notably, the multi-valent vaccine composed of these five peptides significantly activates cluster of differentiation (CD)8 + and CD4 + T cells both in vitro and in vivo . The serum of mice immunized with this vaccine is able to neutralize the five major SARS-CoV-2 variants of concern. This study provides a candidate peptide vaccine with the potential to trigger antiviral T-cell responses, thereby offering the prospect of immune protection against SARS-CoV-2 variants.

关键词： SARS-CoV-2 Artificial intelligence ConFormer Multi-epitope vaccine T-cell immunity

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Dual Representation Learning for One-Step Clustering of Multi-View Data

arXiv

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arXiv 2022年

作者： Zhang, Wei Deng, Zhaohong Choi, Kup-Sze Wang, Jun Wang, Shitong The School of Artificial Intelligence and Computer Science Jiangnan University Jiangsu Key Laboratory of Media Design and Software Technology Wuxi214122 China The School of Artificial Intelligence and Computer Science Jiangnan University Wuxi214122 China ZJLab Shanghai200433 China The Centre for Smart Health The Hong Kong Polytechnic University Hong Kong The Key laboratory of Specialty Fiber Optics and Optical Access Networks Joint International Research Laboratory of Specialty Fiber Optics and Advanced Communication Shanghai Institute for Advanced Communication and Data Science School of Communication and Information Engineering Shanghai University Shanghai200444 China

Multi-view data are commonly encountered in data mining applications. Effective extraction of information from multi-view data requires specific design of clustering methods to cater for data with multiple views, which is non-trivial and challenging. In this paper, we propose a novel one-step multi-view clustering method by exploiting the dual representation of both the common and specific information of different views. The motivation originates from the rationale that multi-view data contain not only the consistent knowledge between views but also the unique knowledge of each view. Meanwhile, to make the representation learning more specific to the clustering task, a one-step learning framework is proposed to integrate representation learning and clustering partition as a whole. With this framework, the representation learning and clustering partition mutually benefit each other, which effectively improves the clustering performance. Results from extensive experiments conducted on benchmark multi-view datasets clearly demonstrate the superiority of the proposed method. Copyright © 2022, The Authors. All rights reserved.

关键词： Cluster analysis

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Hydrodynamic design and verification of water-jet mixed-flow pump bases on controllable velocity moment method 29th

Hydrodynamic design and verification of water-jet mixed-flow...

引用

29th International Ocean and Polar Engineering Conference, ISOPE 2019

作者： Chen, Gang Yu, Bin Fan, Sheming Cai, Youlin Science and Technology on Water-jet Propulsion Laboratory Shanghai China Marine Design and Research Institute of China Shanghai China

ISBN: (纸本)9781880653852

The water-jet mixed-flow model pump is designed by applying controllable velocity moment design theory aiming at the demand of water-jet technique for high performance vessels. The model is machined and experimented after being predicted by CFD. Experimental result shows that the working point of the model pump is consistent with the design parameter, the hydrodynamic performance predicted by CFD accords with experiment and the hydrodynamic performance arrives at international advance level. The 3D hydrodynamic design and the performance predicted by CFD are successful. High performance water-jet units can be developed based on the model pump research in this paper. © 2019 by the International Society of Offshore and Polar Engineers (ISOPE).

关键词： Computational fluid dynamics

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A high order kinetic flow solver based on flux reconstruction framework

arXiv

引用

arXiv 2020年

作者： Li, Ji Zhong, Chengwen Liu, Sha National Key Laboratory of Science and Technology on Aerodynamic Design and Research Northwestern Polytechnical University Xi’an Shaanxi710072 China

The goal of this paper is to develop a high order numerical method based on Kinetic Inviscid Flux (KIF) method and Flux Reconstruction (FR) framework. The KIF aims to find a balance between the excellent merits of Gas-Kinetic Scheme (GKS) and the lower computational costs. The idea of KIF can be viewed as an inviscid-viscous splitting version of the gas-kinetic scheme, and Shu and Ohwada have made the fundamental contribution. The combination of Totally Thermalized Transport (TTT) scheme and Kinetic Flux Vector Splitting (KFVS) method are achieved in KIF. Using a coefficient which is related to time step δt and averaged collision time τ, KIF can adjust the weights of TTT and KFVS flux in the simulation adaptively. By doing the inviscid-viscous splitting, KIF is very suitable and easy to integrate into the existing framework. The well understood FR framework is used widely for the advantages of robustness, economical costs and compactness. The combination of KIF and FR is originated by three motivations. The first purpose is to develop a high order method based on the gas kinetic theory. The second reason is to keep the advantages of GKS. The last aim is that the designed method should be more efficient. In present work, we use the KIF method to replace the Riemann flux solver applied in the interfaces of elements. The common solution at the interface is computed according to the gas kinetic theory, which makes the combination of KIF and FR scheme more reasonable and available. The accuracy and performance of present method are validated by several numerical cases. The Taylor-Green vortex problem has been used to verify its potential to simulate turbulent *** Codes 82B40, 76M12, 35Q20. Copyright © 2020, The Authors. All rights reserved.

关键词： Kinetics

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Climate-Informed Clustering Based Nonstationary Regional Extreme Flood Events Spatio-Temporal Evolution Using Hierarchical Bayesian Modeling

SSRN

引用

SSRN 2024年

作者： Zeng, Hang Zhou, Yang Liu, Pei Li, Xin Huang, Jiaqi Zhou, Hui Yu, Weihou School of Hydraulic and Environmental Engineering Changsha University of Science & Technology Changsha410114 China Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province Changsha410114 China Key Laboratory of Water-Sediment Sciences and Water Disaster Prevention of Hunan Province Changsha410114 China Power China Zhongnan Engineering Corporation Limited Changsha410014 China College of Hydrology and Water Resources Hohai University Nanjing210098 China Yueyang Institute of Water Resources and Hydropower Survey Planning and Design Corporation Limited Yueyang414000 China Hydrology and Water Resources Survey Center of Hunan Province Changsha410008 China

Study region: Xiangjiang River basin, is at the middle and lower Yangtze *** focus: Increasing evidence shows that large-scale climate indices are being linked to the spatio-temporal evolution of extreme flood events in many regions. It is widely recognized that identifying the response of flood risks to climate factors is investigated by nonstationary local hydrological frequency analysis (NLFFA). However, high uncertainty by utilizing NLFFA usually cannot achieve the accuracy for engineering design, creating need for nonstationary regional flood frequency analysis (NRFFA) for reducing uncertainty. This study presents a NRFFA for extreme flood risk under changing environment that is conditioned on the large-scale climate index. The nonstationary regional analysis is developed in a hierarchical Bayesian framework to support partial and full pooling, which can enhance climate-based regionalization skill as well as retain site-specific characteristics. Simultaneously, the modeling structure is designed to consider the spatial dependence across the *** hydrological insights for the region: Regional models for whole basin and climatically homogeneous sub-region respectively, and local models are compared: the regional models exhibit a great benefit with the estimates uncertainty reduction and allows a better quantification of large-scale climate effect on flood extremes. Moreover, the regional partial pooling model for homogeneous sub-region indicate that the regional model can be further improved by considering a prior pooling stations formed by similar significant climate response. © 2024, The Authors. All rights reserved.

关键词： Floods

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Symmetry-enforced nodal chain phonons

arXiv

引用

arXiv 2021年

作者： Zhu, Jiaojiao Wu, Weikang Zhao, Jianzhou Chen, Hao Zhang, Lifa Yang, Shengyuan A. Research Laboratory for Quantum Materials Singapore University of Technology and Design Singapore487372 Singapore Division of Physics and Applied Physics School of Physical and Mathematical Sciences Nanyang Technological University Singapore637371 Singapore Co-Innovation Center for New Energetic Materials Southwest University of Science and Technology Mianyang621010 China School of Physics and Technology Nanjing Normal University Nanjing210023 China

Topological phonons in crystalline materials have been attracting great interest. However, most cases studied so far are direct generalizations of the topological states from electronic systems. Here, we reveal a novel class of topological phonons-the symmetry-enforced nodal-chain phonons, which manifest features unique for phononic systems. We show that with D2d little co-group at a non-time-reversal-invariant-momentum point, the phononic nodal chain is guaranteed to exist owing to the vector basis symmetry of phonons, which is a unique character distinct from electronic and other systems. Combined with the spinless character, this makes the proposed nodal-chain phonons enforced by symmorphic crystal symmetries. We further screen all 230 space groups, and find five candidate groups. Interestingly, the nodal chains in these five groups exhibit two different patterns: for tetragonal systems, they are one-dimensional along the fourfold axis;for cubic systems, they form a three-dimensional network structure. Based on first-principles calculations, we identify K2O as a realistic material hosting almost ideal nodal-chain phonons. We show that the effect of LO-TO splitting, another unique feature for phonons, helps to expose the nodal-chain phonons in K2O in a large energy window. In addition, all the five candidate groups have spacetime inversion symmetry, so the nodal chains also feature a quantized π Berry phase. This leads to drumhead surface phonon modes that must exist on multiple surfaces of a sample. © 2021, CC BY.

关键词： Phonons

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