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  1. Article ; Online: Insight into the Conformational Transitions of Serine Acetyl Transferase Isoforms in

    Idrees, Danish / Naqvi, Ahmad Abu Turab / Hassan, Md Imtaiyaz / Ahmad, Faizan / Gourinath, Samudrala

    ACS omega

    2022  Volume 7, Issue 28, Page(s) 24626–24637

    Abstract: Serine acetyl transferase (SAT) is one of the crucial enzymes in the cysteine biosynthetic pathway and an essential enzyme for the survival ... ...

    Abstract Serine acetyl transferase (SAT) is one of the crucial enzymes in the cysteine biosynthetic pathway and an essential enzyme for the survival of
    Language English
    Publishing date 2022-07-07
    Publishing country United States
    Document type Journal Article
    ISSN 2470-1343
    ISSN (online) 2470-1343
    DOI 10.1021/acsomega.2c02467
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Pan-cancer analysis of Chromobox (CBX) genes for prognostic significance and cancer classification.

    Naqvi, Ahmad Abu Turab / Rizvi, Syed Afzal Murtaza / Hassan, Md Imtaiyaz

    Biochimica et biophysica acta. Molecular basis of disease

    2022  Volume 1869, Issue 1, Page(s) 166561

    Abstract: Polycomb group of proteins play a significant role in chromatin remodelling essential for epigenetic regulation of transcription. Chromobox (CBX) gene family is an important part of canonical polycomb repressive complex 1 (PRC1), belonging to the ... ...

    Abstract Polycomb group of proteins play a significant role in chromatin remodelling essential for epigenetic regulation of transcription. Chromobox (CBX) gene family is an important part of canonical polycomb repressive complex 1 (PRC1), belonging to the polycomb group involved in chromatin remodelling. Aberrations in CBX expression are linked to various cancers. To assess their biomarker significance, we performed a pan-cancer analysis of CBX mRNA levels in 18 cancer types. We also performed cancer classification using CBX genes as distinctive features for machine learning model development. Logistic regression (L.R.), support vector machine (SVM), random forest (R.F.), decision tree (D.T.), and XGBoost (XGB) algorithms for model training and classification. The expression of CBX genes was significantly changed in four cancer types, i.e., cholangiocarcinoma (CHOL), colon adenocarcinoma (COAD), lung adenocarcinoma (LUAD), and lung squamous cell carcinoma (LUSC). The fold change (FC) values suggest that CBX2 was significantly upregulated in CHOL (FC = 1.639), COAD (FC = 1.734), and LUSC (FC = 1.506). On the other hand, CBX7 was found downregulated in COAD (FC = -1.209), LUAD (FC = -1.190), and LUSC (FC = -1.214). The performance of machine learning models for classification was excellent. L.R., R.F., SVM, and XGB obtained a prediction accuracy of 100 % for most cancers. However, D.T. performed comparatively poorly in prediction accuracy. The results suggest that CBX expression is significantly altered in all the cancers studied; therefore, they might be treated as potential biomarkers for therapeutic intervention of these cancers.
    MeSH term(s) Humans ; Adenocarcinoma/genetics ; Epigenesis, Genetic ; Polycomb Repressive Complex 1/genetics ; Polycomb-Group Proteins/genetics ; Prognosis ; Carcinoma/genetics
    Chemical Substances CBX7 protein, human ; Polycomb Repressive Complex 1 (EC 2.3.2.27) ; Polycomb-Group Proteins
    Language English
    Publishing date 2022-09-29
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 60-7
    ISSN 1879-260X ; 1879-2596 ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
    ISSN (online) 1879-260X ; 1879-2596 ; 1872-8006 ; 1879-2642 ; 1879-2618 ; 1879-2650
    ISSN 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
    DOI 10.1016/j.bbadis.2022.166561
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Uc I Zs.247: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  3. Article ; Online: Measuring Structural Changes in Cytochrome

    Parray, Zahoor Ahmad / Naqvi, Ahmad Abu Turab / Ahanger, Ishfaq Ahmad / Shahid, Mohammad / Ahmad, Faizan / Hassan, Md Imtaiyaz / Islam, Asimul

    Polymers

    2022  Volume 14, Issue 22

    Abstract: It is known from in vitro studies that macromolecular crowding in the cell effects protein structure, stability and function; but predictive studies are relatively unexplored. There are few reports where the effect of various crowder mixtures has been ... ...

    Abstract It is known from in vitro studies that macromolecular crowding in the cell effects protein structure, stability and function; but predictive studies are relatively unexplored. There are few reports where the effect of various crowder mixtures has been exploited to discern their combined effect on the structural stability of proteins. These studies are more significant because their effect can mimicked with in vivo conditions, where the environment is heterogeneous. Effects of two crowders, polyethylene glycol (PEG 400 Da), and its monomer ethylene glycol (EG) alone and in mixture on the structural stability of cytochrome
    Language English
    Publishing date 2022-11-09
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2527146-5
    ISSN 2073-4360 ; 2073-4360
    ISSN (online) 2073-4360
    ISSN 2073-4360
    DOI 10.3390/polym14224808
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Targeting Tau Hyperphosphorylation

    Turab Naqvi, Ahmad Abu / Hasan, Gulam Mustafa / Hassan, Md Imtaiyaz

    Current topics in medicinal chemistry

    2020  Volume 20, Issue 12, Page(s) 1059–1073

    Abstract: Microtubule-associated protein tau is involved in the tubulin binding leading to microtubule stabilization in neuronal cells which is essential for stabilization of neuron cytoskeleton. The regulation of tau activity is accommodated by several kinases ... ...

    Abstract Microtubule-associated protein tau is involved in the tubulin binding leading to microtubule stabilization in neuronal cells which is essential for stabilization of neuron cytoskeleton. The regulation of tau activity is accommodated by several kinases which phosphorylate tau protein on specific sites. In pathological conditions, abnormal activity of tau kinases such as glycogen synthase kinase-3 β (GSK3β), cyclin-dependent kinase 5 (CDK5), c-Jun N-terminal kinases (JNKs), extracellular signal-regulated kinase 1 and 2 (ERK1/2) and microtubule affinity regulating kinase (MARK) lead to tau hyperphosphorylation. Hyperphosphorylation of tau protein leads to aggregation of tau into paired helical filaments like structures which are major constituents of neurofibrillary tangles, a hallmark of Alzheimer's disease. In this review, we discuss various tau protein kinases and their association with tau hyperphosphorylation. We also discuss various strategies and the advancements made in the area of Alzheimer's disease drug development by designing effective and specific inhibitors for such kinases using traditional in vitro/in vivo methods and state of the art in silico techniques.
    MeSH term(s) Alzheimer Disease/drug therapy ; Alzheimer Disease/metabolism ; Animals ; Drug Development ; Humans ; Phosphorylation/drug effects ; Protein Kinase Inhibitors/chemical synthesis ; Protein Kinase Inhibitors/chemistry ; Protein Kinase Inhibitors/pharmacology ; Protein Kinases/metabolism ; tau Proteins/antagonists & inhibitors ; tau Proteins/metabolism
    Chemical Substances Protein Kinase Inhibitors ; tau Proteins ; Protein Kinases (EC 2.7.-)
    Language English
    Publishing date 2020-01-12
    Publishing country United Arab Emirates
    Document type Journal Article ; Review
    ZDB-ID 2064823-6
    ISSN 1873-4294 ; 1568-0266
    ISSN (online) 1873-4294
    ISSN 1568-0266
    DOI 10.2174/1568026620666200106125910
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5572: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  5. Article ; Online: Correction: Identification of Functional Candidates amongst Hypothetical Proteins of Treponema pallidum ssp. pallidum.

    Naqvi, Ahmad Abu Turab / Shahbaaz, Mohd / Ahmad, Faizan / Hassan, Md Imtaiyaz

    PloS one

    2018  Volume 13, Issue 5, Page(s) e0197452

    Abstract: This corrects the article DOI: 10.1371/journal.pone.0124177.]. ...

    Abstract [This corrects the article DOI: 10.1371/journal.pone.0124177.].
    Language English
    Publishing date 2018-05-14
    Publishing country United States
    Document type Journal Article ; Published Erratum
    ISSN 1932-6203
    ISSN (online) 1932-6203
    DOI 10.1371/journal.pone.0197452
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Role of sulfur in combating arsenic stress through upregulation of important proteins, and in-silico analysis to study the interaction between phosphate transporter (PHO1), arsenic and phosphate in spinach.

    Amna, Syeda / Qamar, Sadia / Turab Naqvi, Ahmad Abu / Al-Huqail, Asma A / Qureshi, M Irfan

    Plant physiology and biochemistry : PPB

    2020  Volume 157, Page(s) 348–358

    Abstract: An adequate amount of Sulfur (S) is essential for proper plant growth and defence against abiotic stresses including metals and metalloids. Arsenic (As) contamination is increasing in agricultural soils rapidly due to anthropogenic activities. Sulfur ... ...

    Abstract An adequate amount of Sulfur (S) is essential for proper plant growth and defence against abiotic stresses including metals and metalloids. Arsenic (As) contamination is increasing in agricultural soils rapidly due to anthropogenic activities. Sulfur deficiency and arsenic stress could be more harmful than these individual stresses alone. To understand the impact of S-deficiency and arsenic (31 ppm Na
    MeSH term(s) Arsenic/toxicity ; Molecular Docking Simulation ; Phosphate Transport Proteins/metabolism ; Phosphates/metabolism ; Plant Proteins/metabolism ; Proteomics ; Spinacia oleracea/drug effects ; Spinacia oleracea/metabolism ; Stress, Physiological ; Sulfur/metabolism ; Tandem Mass Spectrometry ; Up-Regulation
    Chemical Substances Phosphate Transport Proteins ; Phosphates ; Plant Proteins ; Sulfur (70FD1KFU70) ; Arsenic (N712M78A8G)
    Language English
    Publishing date 2020-11-05
    Publishing country France
    Document type Journal Article
    ZDB-ID 742978-2
    ISSN 1873-2690 ; 0981-9428
    ISSN (online) 1873-2690
    ISSN 0981-9428
    DOI 10.1016/j.plaphy.2020.11.002
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Bonn / Germany

    Z 2696: Show issues
    Z 2005/727: Show issues

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  7. Article: Sequence Analysis of Hypothetical Proteins from

    Naqvi, Ahmad Abu Turab / Anjum, Farah / Khan, Faez Iqbal / Islam, Asimul / Ahmad, Faizan / Hassan, Md Imtaiyaz

    Genomics & informatics

    2016  Volume 14, Issue 3, Page(s) 125–135

    Abstract: Helicobacter ... ...

    Abstract Helicobacter pylori
    Language English
    Publishing date 2016-09-30
    Publishing country Korea (South)
    Document type Journal Article
    ZDB-ID 2802682-2
    ISSN 2234-0742 ; 1598-866X
    ISSN (online) 2234-0742
    ISSN 1598-866X
    DOI 10.5808/GI.2016.14.3.125
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  8. Article ; Online: Investigating host-virus interaction mechanism and phylogenetic analysis of viral proteins involved in the pathogenesis.

    Ahmad Abu Turab Naqvi / Farah Anjum / Alaa Shafie / Sufian Badar / Abdelbaset Mohamed Elasbali / Dharmendra Kumar Yadav / Md Imtaiyaz Hassan

    PLoS ONE, Vol 16, Iss 12, p e

    2021  Volume 0261497

    Abstract: Since the emergence of yellow fever in the Americas and the devastating 1918 influenza pandemic, biologists and clinicians have been drawn to human infecting viruses to understand their mechanisms of infection better and develop effective therapeutics ... ...

    Abstract Since the emergence of yellow fever in the Americas and the devastating 1918 influenza pandemic, biologists and clinicians have been drawn to human infecting viruses to understand their mechanisms of infection better and develop effective therapeutics against them. However, the complex molecular and cellular processes that these viruses use to infect and multiply in human cells have been a source of great concern for the scientific community since the discovery of the first human infecting virus. Viral disease outbreaks, such as the recent COVID-19 pandemic caused by a novel coronavirus, have claimed millions of lives and caused significant economic damage worldwide. In this study, we investigated the mechanisms of host-virus interaction and the molecular machinery involved in the pathogenesis of some common human viruses. We also performed a phylogenetic analysis of viral proteins involved in host-virus interaction to understand the changes in the sequence organization of these proteins during evolution for various strains of viruses to gain insights into the viral origin's evolutionary perspectives.
    Keywords Medicine ; R ; Science ; Q
    Subject code 572
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Correction

    Ahmad Abu Turab Naqvi / Mohd Shahbaaz / Faizan Ahmad / Md Imtaiyaz Hassan

    PLoS ONE, Vol 13, Iss 5, p e

    Identification of Functional Candidates amongst Hypothetical Proteins of Treponema pallidum ssp. pallidum.

    2018  Volume 0197452

    Abstract: This corrects the article DOI:10.1371/journal.pone.0124177.]. ...

    Abstract [This corrects the article DOI:10.1371/journal.pone.0124177.].
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2018-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Investigating host-virus interaction mechanism and phylogenetic analysis of viral proteins involved in the pathogenesis.

    Naqvi, Ahmad Abu Turab / Anjum, Farah / Shafie, Alaa / Badar, Sufian / Elasbali, Abdelbaset Mohamed / Yadav, Dharmendra Kumar / Hassan, Md Imtaiyaz

    PloS one

    2021  Volume 16, Issue 12, Page(s) e0261497

    Abstract: Since the emergence of yellow fever in the Americas and the devastating 1918 influenza pandemic, biologists and clinicians have been drawn to human infecting viruses to understand their mechanisms of infection better and develop effective therapeutics ... ...

    Abstract Since the emergence of yellow fever in the Americas and the devastating 1918 influenza pandemic, biologists and clinicians have been drawn to human infecting viruses to understand their mechanisms of infection better and develop effective therapeutics against them. However, the complex molecular and cellular processes that these viruses use to infect and multiply in human cells have been a source of great concern for the scientific community since the discovery of the first human infecting virus. Viral disease outbreaks, such as the recent COVID-19 pandemic caused by a novel coronavirus, have claimed millions of lives and caused significant economic damage worldwide. In this study, we investigated the mechanisms of host-virus interaction and the molecular machinery involved in the pathogenesis of some common human viruses. We also performed a phylogenetic analysis of viral proteins involved in host-virus interaction to understand the changes in the sequence organization of these proteins during evolution for various strains of viruses to gain insights into the viral origin's evolutionary perspectives.
    MeSH term(s) HIV Envelope Protein gp160/genetics ; Host-Pathogen Interactions ; Humans ; Phylogeny ; Viral Proteins/genetics ; Virus Diseases/virology
    Chemical Substances HIV Envelope Protein gp160 ; Viral Proteins
    Language English
    Publishing date 2021-12-16
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0261497
    Database MEDical Literature Analysis and Retrieval System OnLINE

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