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Ebola virus disease: Recent advances in diagnostics and therapeutics

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Asian Pacific Journal of Tropical Medicine 2019年第9期12卷 385-395页

作者： Supriya Jagga Ashish Ranjan Sharma CHIRANJIB CHAKRABORTY Sang-Soo Lee Institute for Skeletal Aging&Orthopedic Surgery Chuncheon Sacred Heart HospitalHallym UniversityChuncheon 24252 Republie of Korea Department of Biotechnology School of Life Science and BiotechnologyAdamas UniversityBarasat Barackpore RdKlltaWest Bengal 700126 lndia

Ebola virus disease(EVD)is associated with haemorrhagic fever in humans and nonhuman primates,with a high rate of fatality(up to 90%).Some outbreaks in human history have proven the lethality of EVD.The recent epidemic of 2014 and 2015 in West Africa was the deadliest of all time(11 284 deaths).To understand the transmission dynamics,we have reviewed the epidemiology of EVD to date.The absence of any licensed vaccines or approved drugs against Ebola virus(EBOV)further highlights the severity and crisis level of EVD.Some organizations(public and private)are making considerable efforts to develop novel therapeutic approaches or vaccines to contain the outbreak of EBOV shortly.Here,we summarized the various potential drugs and vaccines(undergoing multiple phases of clinical trials)that have arisen as an alternative against EBOV,and we highlighted the numerous issues and limitations hindering this process.Alternatively,an increasing focus on strengthening the medical and civic health structure could provide speedy benefits in containing the spread of EVD,as well as offer a resilient foundation for the deployment of novel drugs and vaccines to the affected countries,once such drugs and vaccines become available.

关键词： Ebola virus Vaccines Therapeutics Ebola outbreaks Diagnostics Epidemiology Haemorrhagic fever

PPARγLBD and its ligand specificity reveal a selection of potential partial agonist:Molecular dynamics based T2D drug discovery initiative

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BIOCELL 2021年第4期45卷 953-961页

作者： BIDYUT MALLICK ASHISH RANJAN SHARMA MANOJIT BHATTACHARYA SANG-SOO LEE CHIRANJIB CHAKRABORTY Department of Applied Science Galgotias College of Engineering and TechnologyKnowledge Park-IIGreater Noida201306India Institute for Skeletal Aging&Orthopedic Surgery Hallym University-Chuncheon Sacred Heart HospitalChuncheon-si24252Korea Department of Zoology Fakir Mohan UniversityVyasa ViharBalasore756020India Department of Biotechnology School of Life Science and BiotechnologyAdamas UniversityKolkata700126India

PPARγis a peroxisome proliferator-activated receptor(PPAR)family protein and is a target for type 2 diabetes(T2D).In this paper,we have performed a molecular docking analysis between ligand molecules(CID9816265,CID11608015,CID20251380,CID20251343,CID20556263,CID624491,CID42609928,and CID86287562)and PPARγto determine the ligand specificity.It also helps to understand the ligand-binding domain(LBD)activity of PPARγduring the binding of the ligand.Further,a molecular dynamics simulation study was performed to determine the ligand biding stability in the PPARγLBD.Its ligand specificity informed us about the potentiality of selecting a partial agonist.The study also shows the binding conformation of Ceramicine B having hydrogen bonding affinity with a tricyclic polar head and stabilized theβ-sheet region.On the other hand,the tricyclic polar head of nimbolide also formed hydrogen bonding(Ser342),but it shows a lesser degree of stabilization in theβ-sheet region.It shows the binding conformation of partial agonist(PPARγ)in the Pocket-II of PPARγLBD,which has a significant role in stabilizing theβ-sheet region.It might help to regulate ERK/Cdk5 mediated phosphorylation of Ser245.The study helps us understand the valid pose of a set of ligands confirmation and target protein conformation using docking and molecular dynamics study.This in silico study will also help to initiate a drug discovery process of T2D.

关键词： PPARγ Partial agonist Molecular simulation T2D Drug discovery

Altered gut microbiota patterns in COVID-19:Markers for inflammation and disease severity

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World Journal of Gastroenterology 2022年第25期28卷 2802-2822页

作者： CHIRANJIB CHAKRABORTY Ashish Ranjan Sharma Manojit Bhattacharya Kuldeep Dhama Sang-Soo Lee School of Life Science and Biotechnology Adamas UniversityKolkata 700126India Institute for Skeletal Aging&Orthopaedic Surgery Hallym UniversityChuncheon-si 24252South Korea Department of Zoology Fakir Mohan UniversityBalasore 756020India Division of Pathology Indian Council of Agricultural Research(ICAR)-Indian Veterinary Research Institute(IVRI)Bareilly 243122Uttar PradeshIndia Institute for Skeletal Aging&Orthopedic Surgery Hallym UniversityChuncheon-si 24252South Korea

The severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)infection leads to a severe respiratory illness and alters the gut microbiota,which dynamically interacts with the human immune system.Microbiota alterations include decreased levels of beneficial bacteria and augmentation of opportunistic pathogens.Here,we describe critical factors affecting the microbiota in coronavirus disease 2019(COVID-19)patients.These include,such as gut microbiota imbalance and gastrointestinal symptoms,the pattern of altered gut microbiota composition in COVID-19 patients,and crosstalk between the microbiome and the gut-lung axis/gut-brain-lung axis.Moreover,we have illustrated the hypoxia state in COVID-19 associated gut microbiota alteration.The role of ACE2 in the digestive system,and control of its expression using the gut microbiota is discussed,highlighting the interactions between the lungs,the gut,and the brain during COVID-19 infection.Similarly,we address the gut microbiota in elderly or co-morbid patients as well as gut microbiota dysbiosis of in severe COVID-19.Several clinical trials to understand the role of probiotics in COVID-19 patients are listed in this review.Augmented inflammation is one of the major driving forces for COVID-19 symptoms and gut microbiome disruption and is associated with disease severity.However,understanding the role of the gut microbiota in immune modulation during SARS-CoV-2 infection may help improve therapeutic strategies for COVID-19 treatment.

关键词： COVID-19 Inflammation Gut microbiota Therapeutic

The bacteriophage mu lysis system–A new mechanism of host lysis?

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BIOCELL 2021年第5期45卷 1175-1186页

作者： SAIKAT SAMANTA ASHISH RANJAN SHARMA ABINIT SAHA MANOJ KUMAR SINGH ARPITA DAS MANOJIT BHATTACHARYA RUDRA PRASAD SAHA SANG-SOO LEE CHIRANJIB CHAKRABORTY Department of Biotechnology School of Life Science&BiotechnologyAdamas UniversityKolkata700126India Institute for Skeletal Aging&Orthopedic Surgery Hallym University-Chuncheon Sacred Heart HospitalChuncheon-si24252Korea Department of Zoology Fakir Mohan UniversityBalasore56020India

Bacteriophages are viruses that infect bacteria and can choose any one of the two alternative pathways for infection,i.e.,lysis or lysogeny.Phage lysis is one of the conventional biological processes required to spread infection from one bacterium to another.Our analysis suggests that in the paradigm bacteriophage Mu,six proteins might be involved in host cell lysis.Mu has a broad host range,and Mu-like phages were found in both Gram-negative and Gram-positive bacteria.An analysis of the genomes of Mu and Mu-like phages could be useful in elucidating the lysis mechanism in this group of phages.A detailed review of the various mechanisms of phage lysis and different proteins associated with the process will help researchers understand the phage biology and their life cycle in different bacteria.The recent increase in the number of multidrug-resistant(MDR)strains of bacteria and the usual long-term nature of new drug development has encouraged scientists to look for alternative strategies like phage therapy and the discovery of new lysis mechanisms.Understanding the lysis mechanism in the Mu-like phages could be exploited to develop alternative therapeutics to kill drug-resistant pathogenic bacteria.In this review article,we have analyzed the phage Mu-mediated host lysis system,which is unknown till now,and our analysis indicates a possibility of the existence of a new lysis mechanism operating in Mu.

关键词： Bacteriophage Mu Host cell lysis Endolysin Holin Spanin

Virtual screening of the inhibitors targeting at the viral protein 40 of Ebola virus

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Infectious Diseases of Poverty 2016年第1期5卷 97-106页

作者： V.Karthick N.Nagasundaram C.George Priya Doss CHIRANJIB CHAKRABORTY R.Siva Aiping Lu Ge Zhang Hailong Zhu School of Chinese Medicine Hong Kong Baptist UniversityKowloon TongHong Kong Department of Integrative Biology School of Biosciences and TechnologyVIT UniversityVelloreTamil NaduIndia Department of Bioinformatics School of Computer and Information SciencesGalgotias UniversityNoidaIndia Department of Biotechnology School of Biosciences and TechnologyVIT UniversityVelloreTamil NaduIndia

Background:The Ebola virus is highly pathogenic and destructive to humans and other primates.The Ebola virus encodes viral protein 40(VP40),which is highly expressed and regulates the assembly and release of viral particles in the host cell.Because VP40 plays a prominent role in the life cycle of the Ebola virus,it is considered as a key target for antiviral treatment.However,there is currently no FDA-approved drug for treating Ebola virus infection,resulting in an urgent need to develop effective antiviral inhibitors that display good safety profiles in a short duration.Methods:This study aimed to screen the effective lead candidate against Ebola infection.First,the lead molecules were filtered based on the docking score.Second,Lipinski rule of five and the other drug likeliness properties are predicted to assess the safety profile of the lead candidates.Finally,molecular dynamics simulations was performed to validate the lead compound.Results:Our results revealed that emodin-8-beta-D-glucoside from the Traditional Chinese Medicine Database(TCMD)represents an active lead candidate that targets the Ebola virus by inhibiting the activity of VP40,and displays good pharmacokinetic properties.Conclusion:This report will considerably assist in the development of the competitive and robust antiviral agents against Ebola infection.

关键词： Ebola VP40 Traditional Chinese Medicine Database Molecular docking Molecular dynamics

Zika:How safe is India?

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Infectious Diseases of Poverty 2017年第1期6卷 335-338页

作者： C.George Priya Doss R.Siva B.Prabhu Christopher CHIRANJIB CHAKRABORTY Hailong Zhu School of Biosciences and Technology VIT UniversityVelloreTamil Nadu 632014India VIT-BS VIT UniversityVelloreTamil Nadu 632014India Department of Bioinformatics School of Computer and Information SciencesGalgotias UniversityGreater NoidaUttar Pradesh 201310India Integrated Bioinformedicine and Translational Science School of Chinese MedicineHong Kong Baptist University7 Baptist University RoadHong KongChina

Zika virus,which originated from a forest in Uganda,has affected countries in Africa,Latin America and Asia.Most people infected with Zika are asymptomatic and present with clinical manifestations ranging from mild fever to severe neurological disorders.Recent outbreaks in Southeast Asian countries,Centers for Disease Control and Prevention has warned pregnant woman to avoid nonessential traveling to 11 Asian countries.Reports about the sexual transmission route of Zika have pushed the World Health Organization to declare it a‘public health emergency’.Having this current warning status,it has become mandatory to consider where second highly populated country India stands in terms of spreading awareness and taking precautionary measures against the Zika virus infection.Therefore,this paper aims to highlight the importance of Zika in Indian population by considering several indicators such as the population size and ratio,rates of mortality,closely related diseases,government initiatives,and other micro-level factors which are prone to Zika effects.

关键词： Zika virus Preventive measures India

GIScience research challenges for realizing discrete global grid systems as a Digital Earth

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Big Earth Data 2022年第3期6卷 358-379页

作者： Majid Hojati Colin Robertson Steven Roberts chiranjib Chaudhuri Department of Geography and Environmental Studies Wilfrid Laurier UniversityWaterlooONCanada Coldwater Laboratory University of SaskatchewanCanmoreABCanada

Increasing data resources are available for documenting and detecting changes in environmental,ecological,and socioeconomic processes.Currently,data are distributed across a wide variety of sources(e.***.data silos)and published in a variety of formats,scales,and semantic representations.A key issue,therefore,in building systems that can realize a vision of earth system monitoring remains data integration.Discrete global grid systems(DGGSs)have emerged as a key technology that can provide a common multi-resolution spatial fabric in support of Digital Earth monitoring.However,DGGSs remain in their infancy with many technical,conceptual,and operational challenges.With renewed interest in DGGS brought on by a recently proposed standard,the demands of big data,and growing needs for monitoring environmental changes across a variety of scales,we seek to highlight current challenges that we see as central to moving the field(s)and technologies of DGGS forward.For each of the identified challenges,we illustrate the issue and provide a potential solution using a reference DGGS implementation.Through articulation of these challenges,we hope to identify a clear research agenda,expand the DGGS research footprint,and provide some ideas for moving forward towards a scaleable Digital Earth vision.Addressing such challenges helps the GIScience research community to achieve the real benefits of DGGS and provides DGGS an opportunity to play a role in the next generation of GIS.

关键词： DGGS discrete global grid systems GIScience Digital Earth

马来西亚一所私立大学使用视觉显示装置的学生非斜视双眼视觉异常

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国际眼科杂志 2020年第6期20卷 940-945页

作者： chiranjib Majumder Toh Ching Ling UCSI大学视光学院马来西亚吉隆坡56000

目的:评估马来西亚一所私立大学使用视觉显示装置(VDU)的学生非斜视双眼视觉异常(NSBVA)情况。方法:对2019-01/2019-05期间每天使用3h及以上VDU的大学生进行横断面研究。使用一种简便的样本收集方法,所有受试者均通过初级视力检查且满... 详细信息

目的:评估马来西亚一所私立大学使用视觉显示装置(VDU)的学生非斜视双眼视觉异常(NSBVA)情况。方法:对2019-01/2019-05期间每天使用3h及以上VDU的大学生进行横断面研究。使用一种简便的样本收集方法,所有受试者均通过初级视力检查且满足入选标准,对符合入选标准的学生进一步进行NSBVA评估。采用描述性分析排除NSBVA的百分比,采用Chi-square独立性检验,观察NSBVA与年龄、性别、VDU使用时间的相关性。结果:研究共纳入140名学生,其中女88名(62.9%),男52名(37.1%)。受试者平均年龄为22.54±1.48a,平均VDU使用时间为5.76±2.49h。使用VDU学生的NSBVA百分比为40%。在VDU使用者中,调节异常和倾斜异常的发生率分别为17.86%和22.14%。性别与NSBVA之间存在适度关联(P=0.010)。但是,年龄(P=0.334)和VDU使用时间(P=0.835)与NSBVA无显著相关。结论:马来西亚一所私立大学的学生中,有40%的人使用VDU。在所有NSBVA中,VDU用户调节异常(15%)和会聚功能异常(10%)更为常见。

关键词：非斜视双眼视觉异常视觉显示装置调节性异常聚散度异常大学生

Effect of undercut on the lower bound stability of vertical rock escarpment using finite element and power cone programming

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Frontiers of Structural and Civil Engineering 2022年第8期16卷 1040-1055页

作者： Shuvankar DAS Debarghya chakraborty Department of Civil Engineering Indian Institute of Technology KharagpurWest Bengal 721302India

In the present study,the stability of a vertical rock escarpment is determined by considering the influence of undercut.Lower bound finite element limit analysis in association with Power Cone Programming(PCP)is applied to incorporate the failure of rock mass with the help of the Generalized Hoek-Brown yield criterion.The change in stability due to the presence of undercut is expressed in terms of a non-dimensional stability number(σci/γH).The variations of the magnitude ofσci/γH are presented as design charts by considering the different magnitudes of undercut offset(H/vu and wu/vu)from the vertical edge and different magnitudes of Hoek-Brown rock mass strength parameters(Geological Strength Index(GSI),rock parameter(mi),Disturbance factor(D)).The obtained results indicate that undercut can cause a severe stability problem in rock mass having poor strength.With the help of regression analysis of the computed results,a simplified design equation is proposed for obtainingσci/γH.By performing sensitivity analysis for an undisturbed vertical rock escarpment,we have found that the undercut height ratio(H/vu)is the most sensitive parameter followed by GSI,undercut shape ratio(wu/vu),and mi.The developed design equation as well as design charts can be useful for practicing engineers to determine the stability of the vertical rock escarpment in the presence of undercut.Failure patterns are also presented to understand type of failure and extent of plastic state during collapse.

关键词： undercut vertical escarpment stability Hoek-Brown yield criterion PCP