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Structural basis of SARS-CoV-2 3CL^pro and anti-COVID-19 drug discovery from medicinal plants

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Journal of Pharmaceutical Analysis 2020年第4期10卷 313-319页

作者： muhammad tahir ul qamar Safar MAlqahtani Mubarak AAlamri Ling-Ling Chen College of Life Science and Technology Guangxi UniversityNanning530004PR China Hubei Key Laboratory of Agricultural Bioinformatics College of InformaticsHuazhong Agricultural UniversityWuhan430070PR China Department of Pharmaceutical Chemistry College of PharmacyPrince Sattam Bin Abdulaziz University11323AlkarjSaudi Arabia

The recent pandemic of coronavirus disease 2019(COVID-19)caused by SARS-CoV-2 has raised global health *** viral 3-chymotrypsin-like cysteine protease(3CL^pro)enzyme controls coronavirus replication and is essential for its life cycle.3CL^pro is a proven drug discovery target in the case of severe acute respiratory syndrome coronavirus(SARS-CoV)and Middle East respiratory syndrome coronavirus(MERS-CoV).Recent studies revealed that the genome sequence of SARS-CoV-2 is very similar to that of ***,herein,we analysed the 3CL^pro sequence,constructed its 3D homology model,and screened it against a medicinal plant library containing 32,297 potential anti-viral phytochemicals/traditional Chinese medicinal *** analyses revealed that the top nine hits might serve as potential anti-SARS-CoV-2 lead molecules for further optimisation and drug development process to combat COVID-19.

关键词： Coronavirus SARS-CoV-2 COVID-19 Natural products Protein homology modelling Molecular docking Molecular dynamics simulation

Discovery of human coronaviruses pan-papain-like protease inhibitors using computational approaches

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Journal of Pharmaceutical Analysis 2020年第6期10卷 546-559页

作者： Mubarak A.Alamri muhammad tahir ul qamar muhammad Usman Mirza Safar M.Alqahtani Matheus Froeyen Ling-Ling Chen Department of Pharmaceutical Chemistry College of PharmacyPrince Sattam Bin Abdulaziz UniversityAlkarjSaudi Arabia College of Life Science and Technology Guangxi UniversityNanningChina Department of Pharmaceutical and Pharmacological Sciences Rega Institute for Medical ResearchMedicinal ChemistryUniversity of LeuvenB-3000LeuvenBelgium Hubei Key Laboratory of Agricultural Bioinformatics College of InformaticsHuazhong Agricultural UniversityWuhan430070China

The papain-like protease(PLpro)is vital for the replication of coronaviruses(Co Vs),as well as for escaping innate-immune responses of the ***,it has emerged as an attractive antiviral *** this study,computational approaches were employed,mainly the structure-based virtual screening coupled with all-atom molecular dynamics(MD)simulations to computationally identify specific inhibitors of severe acute respiratory syndrome coronavirus 2(SARS-Co V-2)PLpro,which can be further developed as potential pan-PLprobased broad-spectrum antiviral *** sequence,structure,and functional conserveness of most deadly human Co Vs PLprowere explored,and it was revealed that functionally important catalytic triad residues are well conserved among SARS-Co V,SARS-Co V-2,and middle east respiratory syndrome coronavirus(MERS-Co V).The subsequent screening of a focused protease inhibitors database composed of^7,000 compounds resulted in the identification of three candidate compounds,ADM13083841,LMG15521745,and *** three compounds established conserved interactions which were further explored through MD simulations,free energy calculations,and residual energy contribution estimated by MM-PB(GB)SA *** these compounds showed stable conformation and interacted well with the active residues of SARS-Co V-2 PLpro,and showed consistent interaction profile with SARS-Co V PLproand MERS-Co V PLproas ***,the reported SARS-Co V-2 PLprospecific compounds could serve as seeds for developing potent pan-PLprobased broad-spectrum antiviral drugs against deadly human ***,the presented information related to binding site residual energy contribution could lead to further optimization of these compounds.

关键词： COVID-19 MERS-CoV Molecular dynamic simulation Pan-inhibitors Papain-like protease SARS-CoV SARS-CoV-2 Virtual screening

Ribosome profiling reveals the translational landscape and allele-specific translational efficiency in rice

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Plant Communications 2023年第2期4卷 119-135页

作者： Xi-Tong Zhu Run Zhou Jian Che Yu-Yu Zheng muhammad tahir ul qamar Jia-Wu Feng Jianwei Zhang Junxiang Gao Ling-Ling Chen National Key Laboratory of Crop Genetic Improvement College of InformaticsHuazhong Agricultural UniversityWuhan 430070China State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources College of Life Science and TechnologyGuangxi UniversityNanning 530004China

Translational regulation is a critical step in the process of gene expression and governs the synthesis of proteins from *** studies have revealed translational regulation in plants in response to various environmental ***,there have been no studies documenting the comprehensive landscape of translational regulation and allele-specific translational efficiency in multiple plant tissues,especially those of rice,a main staple crop that feeds nearly half of the world’s *** we used RNA sequencing and ribosome profiling data to analyze the transcriptome and translatome of an elite hybrid rice,Shanyou 63(SY63),and its parental varieties Zhenshan 97 and Minghui *** results revealed that gene expression patterns varied more among tissues than among varieties at the transcriptional and translational *** identified 3392 upstream open reading frames(uORFs),and the uORF-containing genes were enriched in transcription *** 668 of 13492 long non-coding RNAs could be translated into ***,we discovered numerous genes with allele-specific translational efficiency in SY63 and demonstrated that some cis-regulatory elements may contribute to allelic divergence in translational ***,these findings may improve our understanding of translational regulation in rice and provide information for molecular breeding research.

关键词： Ribo-seq translational landscape uORFs lncRNAs allele-specific translational efficiency rice Oryza sativa

Citrus Pan-Genome to Breeding Database(CPBD):A comprehensive genome database for citrus breeding

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Molecular Plant 2022年第10期15卷 1503-1505页

作者： Hanmingzi Liu Xia Wang Shengjun Liu Yue Huang Yi-Xiong Guo Wen-Zhao Xie Hao Liu muhammad tahir ul qamar Qiang Xu Ling-Ling Chen College of Informatics Huazhong Agricultural UniversityWuhan 430070China Key Laboratory of Horticultural Plant Biology of Ministry of Education Huazhong Agricultural UniversityWuhan 430070China State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources College of Life Science and TechnologyGuangxi UniversityNanning 530004China Hubei Hongshan Laboratory Wuhan 430070China

Dear Editor,The genus Citrus comprises more than 30 species worldwide(Swingle,1943).However,citrus genetics and traditional breeding are hindered due to asexual reproduction,long generation time,and empirical utilization of the *** whole-genome information of different citrus species accelerates the genetic studies and improves the breeding efficiency by high-density markers.

关键词： breeding citrus Citrus

Direct RNA sequencing in plants:Practical applications and future perspectives

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Plant Communications 2024年第11期5卷 54-71页

作者： Xi-Tong Zhu Pablo Sanz-Jimenez Xiao-Tong Ning muhammad tahir ul qamar Ling-Ling Chen State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources College of Life Science and TechnologyGuangxi UniversityNanning 530004China National Key Laboratory of Crop Genetic Improvement College of InformaticsHuazhong Agricultural UniversityWuhan 430070China Integrative Omics and Molecular Modeling Laboratory Department of Bioinformatics and BiotechnologyGovernment College University Faisalabad(GCUF)Faisalabad 38000Pakistan These authors contributed equally to this article

The transcriptome serves as a bridge that links genomic variation to phenotypic diversity.A vast number of studies using next-generation RNA sequencing(RNA-seq)over the last 2 decades have emphasized the essential roles of the plant transcriptome in response to developmental and environmental conditions,providing numerous insights into the dynamic changes,evolutionary traces,and elaborate regulation of the plant *** substantial improvement in accuracy and throughput,direct RNA sequencing(DRS)has emerged as a new and powerful sequencing platform for precise detection of native and full-length transcripts,overcoming many limitations such as read length and PCR bias that are inherent to short-read ***,we review recent advances in dissecting the complexity and diversity of plant transcriptomes using DRS as the main technological approach,covering many aspects of RNA metabolism,including novel isoforms,poly(A)tails,and RNA modification,and we propose a comprehensive workflow for processing of plant DRS *** challenges to the application of DRS in plants,such as the need for machine learning tools tailored to plant transcriptomes,remain to be overcome,and together we outline future biological questions that can be addressed by DRS,such as allele-specific RNA *** technology provides convenient support on which the connection of distinct RNA features is tightly built,sustainably refining our understanding of the biological functions of the plant transcriptome.

关键词： direct RNA sequencing novel isoforms fusion transcripts poly(A)tail RNA modifications

Reverse vaccinology assisted designing of multiepitope-based subunit vaccine against SARS-CoV-2

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Infectious Diseases of Poverty 2020年第5期9卷 117-117页

作者： muhammad tahir ul qamar Farah Shahid Sadia Aslam Usman Ali Ashfaq Sidra Aslam Israr Fatima muhammad Mazhar Fareed Ali Zohaib Ling-Ling Chen College of Life Science and Technology Guangxi UniversityNanningP.R.China Department of Bioinformatics and Biotechnology Government College University Faisalabad(GCUF)FaisalabadPakistan 不详

Background:Coronavirus disease 2019(COVID-19)linked with severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)cause severe illness and life-threatening pneumonia in *** current COVID-19 pandemic demands an effective vaccine to acquire protection against the ***,the present study was aimed to design a multiepitope-based subunit vaccine(MESV)against ***:Structural proteins(Surface glycoprotein,Envelope protein,and Membrane glycoprotein)of SARS-CoV-2 are responsible for its prime *** of proteins were downloaded from GenBank and several immunoinformatics coupled with computational approaches were employed to forecast B-and T-cell epitopes from the SARS-CoV-2 highly antigenic structural proteins to design an effective ***:Predicted epitopes suggested high antigenicity,conserveness,substantial interactions with the human leukocyte antigen(HLA)binding alleles,and collective global population coverage of 88.40%.Taken together,276 amino acids long MESV was designed by connecting 3 cytotoxic T lymphocytes(CTL),6 helper T lymphocyte(HTL)and 4 B-cell epitopes with suitable adjuvant and *** MESV construct was non-allergenic,stable,and highly *** docking showed a stable and high binding affinity of MESV with human pathogenic toll-like receptors-3(TLR3).Furthermore,in silico immune simulation revealed significant immunogenic response of ***,MEV codons were optimized for its in silico cloning into the Escherichia coli K-12 system,to ensure its increased ***:The MESV developed in this study is capable of generating immune response against ***,if designed MESV further investigated experimentally,it would be an effective vaccine candidate against SARS-CoV-2 to control and prevent COVID-19.

关键词： SARS-CoV-2 COVID-19 Structural protein Epitope Vaccine Multiepitope-based subunit vaccine Immunoinformatics

Drought Stress Impairs Grain Yield and Quality of Rice Genotypes by Impaired Photosynthetic Attributes and K Nutrition

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Rice science 2020年第1期27卷 5-9页

作者： muhammad Zahid MUMTAZ muhammad SAQIB Ghulam ABBAS Javaid AKHTAR Zia ul-qamar Institute of Soil and Environmental Sciences University of Agriculture Institute of Molecular Biology and Biotechnology The University of Lahore Department of Environmental Sciences COMSATS University Plant Breeding and Genetics Division Nuclear Institute for Agriculture and Biology

Drought is one of the most prevalent abiotic stresses that adversely affect rice productivity(Petrozza et al, 2014). Rice is very sensitive to drought stress and drought can cause 50% reduction in rice production globally(Yang et al, 2008). To meet the food needs for global population, 63% more agricultural production will be required by the year 2050 than.

关键词： drought Yield globally

Schamel equation in an inhomogeneous magnetized sheared flow plasma with q-nonextensive trapped electrons

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Chinese Physics B 2018年第2期27卷 428-434页

作者： Shaukat Ali Shan qamar-ul-Haque Theoretical Physics Division (TPD) PINSTECH

An investigation is carried out for understanding the properties of ion–acoustic（IA） solitary waves in an inhomogeneous magnetized electron-ion plasma with field-aligned sheared flow under the impact of q-nonextensive trapped electrons. The Schamel equation and its stationary solution in the form of solitary waves are obtained for this inhomogeneous plasma. It is shown that the amplitude of IA solitary waves increases with higher trapping efficiency（β）, while the width remains almost the same. Further, it is found that the amplitude of the solitary waves decreases with enhanced normalized drift speed, shear flow parameter and the population of the energetic particles. The size of the nonlinear solitary structures is calculated to be a few hundred meters and it is pointed out that the present results are useful to understand the solar wind plasma.

关键词： sheared flow plasma density inhomogeniety electron trapping

Re-analysis of temperature dependent neutron capture rates and stellarβ-decay rates of^(95-98)Mo

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Chinese Physics C 2024年第9期48卷 142-149页

作者： Abdul Kabir Jameel-Un Nabi muhammad tahir Abdul Muneem Zain ul Abideen Space and Astrophysics Research lab National Centre of GIS and Space ApplicationsDepartment of Space ScienceInstitute of Space TechnologyIslamabad 44000Pakistan University of Wah Quaid AvenueWah Cantt 47040PunjabPakistan Faculty of Engineering Sciences GIK Institute of Engineering Sciences and TechnologyTopi 23640Khyber PakhtunkhwaPakistan

The neutron capture rates and temperature dependent stellar beta decay rates of Mo isotopes are investigated within the framework of the statistical code TALYS v1.96 and the proton neutron quasi particle random phase approximation(pn-QRPA)*** Maxwellian average cross-section(MACS)and neutron capture rates for the^(95-98)Mo(n,γ)^(96-99)Mo radiative capture process are analyzed within the framework of the statistical code TALYS v1.96 based on the phenomenological nuclear level density model and gamma strength *** present model-based computations for the MACS are comparable to the existing measured *** sensitivity of stellar weak interaction rates to various densities and temperatures is investigated within the framework of the pn-QRPA *** attention is paid to the impact of thermally filled excited states in the decaying nuclei(^(95-98)Mo)on electron emission and positron capture ***,we compare the neutron capture rates and stellar beta decay *** is found that neutron capture rates are higher than stellar beta decay rates at both lower and higher temperatures.

关键词： cross-section TALYS nuclear level density decay rates capture rates