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Phosphorylated protein chip combined with artificial intelligence tools for precise drug screening

Journal of Biomedical Research 2024年第3期38卷 195-205页

作者： Katsuhisa Horimoto Yuki Suyama Tadamasa Sasaki Kazuhiko Fukui Lili Feng Meiling Sun Yamin Tang Yixuan Zhang Dongyin Chen Feng Han SOCIUM Inc. Tokyo 1350064Japan international Medical Center Saitama Medical UniversitySaitama 350-1298Japan Artificial Intelligence Research Center National Institute of Advanced Industrial Science and TechnologyTokyo 1350064Japan Department of Informatics and Data Science Sanyo-Onoda City UniversityYamaguchi 7560884Japan international Joint Laboratory for Drug Target of Critical Illnesses School of PharmacyNanjing Medical UniversityNanjingJiangsu 211166China Department of Physiology School of Basic Medical SciencesNanjing Medical UniversityNanjingJiangsu 211166China Gusu School Nanjing Medical UniversitySuzhouJiangsu 215001China National vaccine Innovation Platform Nanjing Medical UniversityNanjingJiangsu 211166China

We have developed a protein array system,named"Phospho-Totum",which reproduces the phosphorylation state of a sample on the *** protein array contains 1471 proteins from 273 known signaling *** to the activation degrees of tyrosine kinases in the sample,the corresponding groups of substrate proteins on the array are phosphorylated under the same *** addition to measuring the phosphorylation levels of the 1471 substrates,we have developed and performed the artificial intelligence-assisted tools to further characterize the phosphorylation state and estimate pathway activation,tyrosine kinase activation,and a list of kinase inhibitors that produce phosphorylation states similar to that of the *** Phospho-Totum system,which seamlessly links and interrogates the measurements and analyses,has the potential to not only elucidate pathophysiological mechanisms in diseases by reproducing the phosphorylation state of samples,but also be useful for drug discovery,particularly for screening targeted kinases for potential drug kinase inhibitors.

关键词： Phospho-Totum protein array signal transduction pathways artificial intelligence tools drug screening

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Crystal structures of RNA-dependent RNA polymerases from Jingmen tick virus and Alongshan virus

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hLife 2024年第1期2卷 18-31页

作者： Zhenyang Liu Qi Peng Pu Han Lu Kuai Jianxun Qi Yi Shi CAS Key Laboratory of Pathogen Microbiology and Immunology Institute of MicrobiologyChinese Academy of SciencesBeijingChina Beijing Life Science Academy BeijingChina international institute of vaccine Research and Innovation Savaid Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina Center for Influenza Research and Early-warning CAS-TWAS Center of Excellence for Emerging Infectious DiseaseChinese Academy of SciencesBeijingChina Research Unit of Adaptive Evolution and Control of Emerging Viruses Chinese Academy of Medical SciencesBeijingChina

Jingmenviruses are a group of flavi-like viruses with segmented genome and have been found in various types of hosts,including humans,cattle,monkeys,bats,rodents,sheep,ticks,mosquitoes and ***,including the Jingmen tick virus(JMTV)and Alongshan virus(ALSV),have been associated with febrile illness and flu-like symptoms in *** polymerase plays critical roles in genome replication and transcription and is an ideal target for antiviral ***,we determined the crystal structures of RNA-dependent RNA polymerase(RdRp)domains of JMTV and ALSV at 2.6Åand 3.2Åresolutions,*** overall structures of JMTV and ALSV RdRp domains are similar to those from the typical unsegmented viruses in Flaviviridae family,especially the Flavivirus *** and ALSV RdRps can be divided into three subdomains and the catalytical Motif A-G are conserved like the typical flaviviruses,whereas the zinc-binding pockets are absent from the JMTV and ALSV *** 50-ends of jingmenvirus genomes are varied in length and sequence,and a highly conserved 8-nucleotide element located on the tip of stem loop A was identified and shown to be required for binding with RdRp and performing de novo replication *** findings provide important structural insights into RdRp of segmented flavivirus and reveal the key region of virus genome responsible for replication initiation,which would promote molecular understanding of segmented flavivirus replication and the structure-based design of antiviral drugs against flaviviruses.

关键词： Jingmenviruses X-rays RNA-dependent RNA polymerase replication

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Estimating the instantaneous reproduction number(R_(t))by using particle filter

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Infectious Disease Modelling 2023年第4期8卷 1002-1014页

作者： Yong Sul Won Woo-Sik Son Sunhwa Choi Jong-Hoon Kim National institute for Mathematical Sciences DaejeonSouth Korea international vaccine institute SeoulSouth Korea

Background:Monitoring the transmission of coronavirus disease 2019(COVID-19)requires accurate estimation of the effective reproduction number(Rt).However,existing methods for calculating Rt may yield biased estimates if important real-world factors,such as delays in confirmation,pre-symptomatic transmissions,or imperfect data observation,are not ***:To include real-world factors,we expanded the susceptible-exposed-infectiousrecovered(SEIR)model by incorporating pre-symptomatic(P)and asymptomatic(A)states,creating the SEPIAR *** utilizing both stochastic and deterministic versions of the model,and incorporating predetermined time series of Rt,we generated simulated datasets that simulate real-world challenges in estimating *** then compared the performance of our proposed particle filtering method for estimating Rt with the existing EpiEstim approach based on renewal ***:The particle filtering method accurately estimated Rt even in the presence of data with delays,pre-symptomatic transmission,and imperfect *** evaluating via the root mean square error(RMSE)metric,the performance of the particle filtering method was better in general and was comparable to the EpiEstim approach if perfectly deconvolved infection time series were provided,and substantially better when Rt exhibited short-term fluctuations and the data was right ***:The SEPIAR model,in conjunction with the particle filtering method,offers a reliable tool for predicting the transmission trend of COVID-19 and assessing the impact of intervention *** approach enables enhanced monitoring of COVID-19 transmission and can inform public health policies aimed at controlling the spread of the disease.

关键词： Particle filter Sequential Monte Carlo Effective reproduction number COVID-19 Transmission model Compartment model

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Modularized viromimetic polymer nanoparticle vaccines(VPNVaxs) to elicit durable and effective humoral immune responses

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National Science Review 2024年第3期11卷 200-214页

作者： Zichao Huang Xinyu Zhuang Liping Liu Jiayu Zhao Sheng Ma Xinghui Si Zhenyi Zhu Fan Wu Ningyi Jin Mingyao Tian Wantong Song Xuesi Chen Key Laboratory of Polymer Ecomaterials Changchun Institute of Applied ChemistryChinese Academy of Sciences School of Applied Chemistry and Engineering University of Science and Technology of China Changchun Veterinary Research institute Chinese Academy of Agricultural Sciences Jilin Biomedical Polymers Engineering Laboratory State Key Laboratory of Polymer Physics and Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences

Virus-like particle(VLP) vaccines had shown great potential during the COVID-19 pandemic, and was thought to be the next generation of antiviral vaccine technology due to viromimetic structures. However,the time-consuming and complicated processes in establishing a current recombinant-protein–based VLP vaccine has limited its quick launch to the out-bursting pandemic. To simplify and optimize VLP vaccine design, we herein report a kind of viromimetic polymer nanoparticle vaccine(VPNVax), with subunit receptor-binding domain(RBD) proteins conjugated to the surface of polyethylene glycol-b-polylactic acid(PEG-b-PLA) nanoparticles for vaccination against SARS-CoV-2. The preparation of VPNVax based on synthetic polymer particle and chemical post-conjugation makes it possible to rapidly replace the antigens and construct matched vaccines at the emergence of different viruses. Using this modular preparation system, we identified that VPNVax with surface protein coverage of 20%–25% had the best immunostimulatory activity, which could keep high levels of specific antibody titers over 5 months and induce virus neutralizing activity when combined with an aluminum adjuvant. Moreover, the polymer nano-vectors could be armed with more immune-adjuvant functions by loading immunostimulant agents or chemical chirality design. This VPNVax platform provides a novel kind of rapidly producing and efficient vaccine against different variants of SARS-CoV-2 as well as other viral pandemics.

关键词： vaccine polymer nanomaterials SARS-CoV-2

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Adherence to Advisory Committee on Immunization Practices in diabetes mellitus patients in Saudi Arabia:A multicenter retrospective study

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World Journal of Diabetes 2024年第3期15卷 440-454页

作者： Saleh Fahad Alqifari Aya K Esmail Dalal M Alarifi Ghalya Y Alsuliman Maram M Alhati May R Mutlaq Mohammed Aldhaeefi Shaden A Alshuaibi Palanisamy Amirthalingam Abrar Abdallah Afaf S Wasel Heba R Hamad Shoroq Alamin Tasneem H Atia Tariq Alqahtani Department of Pharmacy Practice University of TabukTabuk 71491Saudi Arabia Department of Clinical Sciences Sulaiman Alrajhi UniversityQassim 52726Saudi Arabia Department of Family Medicine International Medical CenterJeddah 23214Saudi Arabia Clinical and Administrative Pharmacy Sciences College of PharmacyHoward UniversityWashingtonDC 20059United States Department of Pharmacology King Saud Bin Abdulaziz University for Health SciencesKing Abdullah International Medical Research CenterRiyadh 11481Saudi Arabia

BACKGROUND Patients with diabetes mellitus(DM)are predisposed to an increased risk of infection signifying the importance of vaccination to protect against its potentially severe *** Centers for Disease Control and Prevention/Advisory Committee on Immunization Practices(CDC/ACIP)issued immunization recommendations to protect this patient *** To assess the adherence of patients with DM to the CDC/ACIP immunization recommendations in Saudi Arabia and to identify the factors associated with the vaccine adherence *** An observational retrospective study conducted in 2023 was used to collect data on the vaccination records from 13 diabetes care centers in Saudi Arabia with 1000 eligible patients in phase I with data collected through chart review and 709 patients in phase II through online *** Among participants,10.01%(n=71)had never received any vaccine,while 85.89%(n=609)received at least one dose of the coronavirus disease 2019(COVID-19)vaccine,and 34.83%(n=247)had received the annual influenza *** 2.96%(n=21),2.11%(n=15),and 1.12%(n=8)received herpes zoster,tetanus,diphtheria,and pertussis(Tdap),and human papillomavirus(HPV)vaccines,*** patients with DM in Saudi Arabia,the rate of vaccination for annual influenza and COVID-19 vaccines was higher compared to other vaccinations such as herpes zoster,Tdap,pneumococcal,and *** such as vaccine recommendations provided by family physicians or specialists,site of care,income level,DM-related hospitalization history,residency site,hemoglobin A1c(HbA1c)level,and health sector type can significantly influence the vaccination rate in patients with *** non-vaccinated patients with DM,the most reported barriers were lack of knowledge and fear of side *** signifies the need for large-scale research in this area to identify additional factors that might facilitate adherence to CDC/ACIP vaccine recommendations in patients with *** In S

关键词： Diabetes mellitus vaccine recommendation COVID-19 vaccine Influenza vaccine Pneumococcal vaccine Immunization Retrospective study

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Impact of vaccination on the dynamics of COVID-19:A mathematical study using fractional derivatives

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international Journal of Biomathematics 2024年第2期17卷 201-232页

作者： Shraddha Ramdas Bandekar Mini Ghosh C.Rajivganthi Division of Mathematics School of Advanced Sciences Vellore Institute of TechnologyChennaiIndia

Arrival of a new disease marks a yearlong destruction of human lives and economy in general,and if the disease turns out to be a pandemic the loss is ***-19 is one such pandemic that has claimed millions of lives till *** is a suffering throughout the world due to various factors associated with the pandemic,be it loss of livelihoods because of sudden shutdown of companies and lockdown,or loss of lives due to lack of medical aid and inadequate vaccination *** this study,we develop a six-compartmental epidemiological model incorporating *** motivation behind the study is to analyze the significance of higher vaccination efficacy and higher rate of population getting vaccinated in controlling the rise in infectives and thereby the untimely demise of various *** work begins with an ordinary differential equation model followed by stability analysis of the same,after which a fractional-order derivative model of the same is formulated and the existence of uniformly stable solution for the system is *** addition to this,we present the stability of the equilibria in general for the fractional model *** sensitivity analysis of the basic reproduction number along with its correlation with various parameters is *** addition to this,sensitivity of certain state variables in the fractional model with respect to *** orders as well with respect to different infection rate is exhibited in this *** related to lockdown and usage of face shields are incorporated in the entire study,and importance of these is highlighted in the study as *** major takeaway from the study is that mere vaccination will not sufice in eradication of the *** vaccine efficacy plays a major role along with other intervention included in the *** numerical simulations are carried out in MATLAB software using ode45 and fdel2.

关键词： Caputo fractional derivative basic reproduction number stability analysis sensitivityanalysis vaccination

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Antibodies elicited by Newcastle disease virus-vectored H7N9 avian influenza vaccine are functional in activating the complement system

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Journal of Integrative Agriculture 2024年第6期23卷 2052-2064页

作者： Zenglei Hu Ya Huang Jiao Hu Xiaoquan Wang Shunlin Hu Xiufan Liu Joint international Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China Yangzhou UniversityYangzhou 225009China Animal Infectious Disease Laboratory School of Veterinary MedicineYangzhou UniversityYangzhou 225009China Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses Yangzhou UniversityYangzhou 225009China

H7N9 subtype avian influenza virus poses a great challenge for poultry *** disease virus(NDV)-vectored H7N9 avian influenza vaccines(NDV_(vec)H7N9)are effective in disease control because they are protective and allow mass *** note,these vaccines elicit undetectable H7N9-specific hemagglutination-inhibition(HI)but high IgG antibodies in ***,the molecular basis and protective mechanism underlying this particular antibody immunity remain ***,immunization with an NDV_(vec)H7N9 induced low anti-H7N9 HI and virus neutralization titers but high levels of hemagglutinin(HA)-binding IgG antibodies in *** residues(S150,G151 and S152)in HA of H7N9 virus were identified as the dominant epitopes recognized by the NDV_(vec)H7N9 immune *** transferred NDV_(vec)H7N9 immune serum conferred complete protection against H7N9 virus infection in *** NDV_(vec)H7N9 immune serum can mediate a potent lysis of HA-expressing and H7N9 virus-infected cells and significantly suppress H7N9 virus *** activities of the serum were significantly impaired after heat-inactivation or treatment with complement inhibitor,suggesting the engagement of the complement ***,mutations in the 150-SGS-152 sites in HA resulted in significant reductions in cell lysis and virus neutralization mediated by the NDV_(vec)H7N9 immune serum,indicating the requirement of antibody-antigen binding for complement ***,antibodies induced by the NDV_(vec)H7N9 can activate antibody-dependent complement-mediated lysis of H7N9 virus-infected cells and complement-mediated neutralization of H7N9 *** findings unveiled a novel role of the complement in protection conferred by the NDV_(vec)H7N9,highlighting a potential benefit of engaging the complement system in H7N9 vaccine design.

关键词： H7N9 subtype avian influenza virus NDV vector vaccine antibody immunity complement protection

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Advances in Zika virus vaccines and therapeutics:A systematic review

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Asian Pacific Journal of Tropical Medicine 2024年第3期17卷 97-109页

作者： Shiza Malik Khalid Muhammad Omar Ahsan Muhammad Tahir Khan Ranjit Sah Yasir Waheed Bridging Health Foundation Rawalpindi 46000Pakistan Department of Biology College of SciencesUAE University15551Al AinUnited Arab Emirates Department of Medicine Foundation University Medical CollegeFoundation University IslamabadIslamabad 44000Pakistan INTI international University Persiaran Perdana BBN Putra Nilai71800 NilaiNegeri SembilanMalaysia institute of Molecular Biology and Biotechnology the University of LahoreKM Defence RoadLahore 58810Pakistan Zhongjing Research and Industrialization institute of Chinese Medicine Zhongguancun Scientific ParkNanyang 473006China Department of Microbiology Tribhuvan University Teaching HospitalInstitute of MedicineKathmandu 44600Nepal Department of Microbiology Dr.D.Y.Patil Medical CollegeHospital and Research CentreDr.D.Y.Patil VidyapeethPune 411018MaharashtraIndia Department of Public Health Dentistry Dr.D.Y.Patil Dental College and HospitalDr.D.Y.Patil VidyapeethPune 411018MaharashtraIndia Gilbert and Rose-Marie Chagoury School of Medicine Lebanese American UniversityByblos 1401Lebanon

Zika virus(ZIKV)is the causative agent of a viral infection that causes neurological complications in newborns and adults *** wide transmission route and alarming spread rates are of great concern to the scientific *** trials have been conducted to develop treatment options for ZIKV *** review highlights the latest developments in the fields of vaccinology and pharmaceuticals developments for ZIKV infection.A systematic and comprehensive approach was used to gather relevant and up-to-date data so that inferences could be made about the gaps in therapeutic *** results indicate that several therapeutic interventions are being tested against ZIKV infection,such as DNA vaccines,subunit vaccines,live-attenuated vaccines,virus-vector-based vaccines,inactivated vaccines,virus-like particles,and mRNA-based *** addition,approved anti-ZIKV drugs that can reduce the global burden are *** many vaccine candidates for ZIKV are at different stages of development,none of them have received Food and Drug Authority approval for use up to *** issue of side effects associated with these drugs in vulnerable newborns and pregnant women is a major obstacle in the therapeutic pathway.

关键词： Zika virus Infection Therapeutics Antiviral agents vaccines Therapies Treatment Novel therapeutic Clinical management

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Mucosal vaccine development for respiratory viral infections

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hLife 2024年第2期2卷 50-63页

作者： Yifan Lin Zhenxiang Hu Yang-Xin Fu Hua Peng Department of Basic Medical Sciences School of MedicineTsinghua UniversityBeijingChina LivzonBio Inc. GuangdongChina Guangzhou Laboratory Guangzhou International Bio IslandGuangdongChina

Mucosal vaccines have risen to prominence in the corona virus disease 2019(COVID-19)pandemic due to their ability to elicit both local antibody and tissue-resident T cell responses,affording a dual-layered defense against infection and transmission at respiratory entry *** intramuscular vaccines predominantly focus on systemic immunity,mucosal vaccines offer a more nuanced,site-specific ***,the field faces a dearth of mucosal vaccine options for respiratory diseases,starkly contrasting to the extensive array of well-characterized injectable *** unique features of mucosal surfaces necessitate specialized adjuvants and delivery systems,adding complexity to adapting injectable vaccine technologies for mucosal ***,we review the recent insights into the specificities of respiratory mucosal immunology that provide a foundation for future innovations besides the emerging vaccine platforms,newly discovered adjuvants,and vaccine delivery systems,which may open promising avenues for developing mucosal vaccines targeting respiratory pathogens.

关键词： mucosal immunology respiratory viruses vaccine adjuvants

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The COVID-19 vaccines Evaluation Program:Implementation,Management,and Experiences,2021-2023

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China CDC weekly 2024年第26期6卷 642-648页

作者： Tingting Yan Hui Zheng Mingshuang Li Chao Ma Xuanyi Wang Xiaoqi Wang Zhenjun Li Yuansheng Chen Wenshang Hu Lance Rodewald Zhijie An Zundong Yin Zijian Feng National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases(NITFID).National Immunization Program Chinese Center for Disease Control and PreventionBeijingChina institutes of Biomedical Sciences Fudan UniversityShanghaiChina Office of international Cooperation Chinese Center for Disease Control and PreventionBeijingChina Office of Science and Technology Chinese Center for Disease Control and PreventionBeijingChina Office of Finance Chinese Center for Disease Control and PreventionBeijingChina Chinese Preventive Medicine Association BeijingChina

In 2021,China’s domestically produced coronavirus disease 2019(COVID-19)vaccines received approval from regulatory bodies and were administered *** to a low number of infections within China during that period,it became imperative to evaluate the vaccines’real-world effectiveness through international *** facilitate this,China CDC launched the COVID-19 vaccines Evaluation Program(COVEP).This program formed research collaboration agreements with health institutes across five World Health Organization regions,addressing key questions about vaccine performance through ten cooperative *** findings from COVEP projects reinforced confidence,both domestically and globally,in the effectiveness of the vaccines produced in ***,the outcomes observed internationally were frequently mirrored by later studies conducted within *** thus pioneered a novel approach for fostering cross-national research collaborations,addressing significant public health issues and exemplifying a framework for international *** approach is in line with the strategic objectives and other development efforts of China CDC’s national disease control and prevention initiatives.

关键词： approval COV prevention

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