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Article: A comprehensive review of tumor proliferative and suppressive role of semaphorins and therapeutic approaches.

Ahammad, Ishtiaque

2020 Volume 12, Issue 5, Page(s) 1233–1247

Abstract: Semaphorins have been traditionally known as axon guidance proteins that negatively regulate axonal growth. However, in the past couple of decades, their versatile role in so many other biological processes has come to prominence as well. One such ... ...

Abstract	Semaphorins have been traditionally known as axon guidance proteins that negatively regulate axonal growth. However, in the past couple of decades, their versatile role in so many other biological processes has come to prominence as well. One such example is their role in cancer. In this review article, the focus was on the tumor proliferative and tumor suppressive role of all 20 semaphorin family members under the 7 semaphorin classes found in vertebrates and invertebrates as well as the ongoing and emerging therapeutic approaches to combat semaphorin-mediated cancers. Except sema6C, 19 of the 20 non-viral semaphorin family members have been discovered to be associated with cancer in one way or another. Eleven semaphorin family members have been discovered to be tumor proliferative and 8 to be tumor suppressive. Six therapeutic avenues and their safety profiles have been discussed which are currently at use or at the various stages of development. Finally, perspectives on which approach is the best for treating cancers associated with semaphorins have been given.
Language	English
Publishing date	2020-06-23
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	2486483-3
ISSN	1867-2469 ; 1867-2450
ISSN (online)	1867-2469
ISSN	1867-2450
DOI	10.1007/s12551-020-00709-1
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Article ; Online: A comprehensive in silico investigation into the nsSNPs of Drd2 gene predicts significant functional consequences in dopamine signaling and pharmacotherapy.

Lira, Samia Sultana / Ahammad, Ishtiaque

Scientific reports

2021 Volume 11, Issue 1, Page(s) 23212

Abstract: DRD2 is a neuronal cell surface protein involved in brain development and function. Variations in the Drd2 gene have clinical significance since DRD2 is a pharmacotherapeutic target for treating psychiatric disorders like ADHD and schizophrenia. Despite ... ...

Abstract	DRD2 is a neuronal cell surface protein involved in brain development and function. Variations in the Drd2 gene have clinical significance since DRD2 is a pharmacotherapeutic target for treating psychiatric disorders like ADHD and schizophrenia. Despite numerous studies on the disease association of single nucleotide polymorphisms (SNPs) in the intronic regions, investigation into the coding regions is surprisingly limited. In this study, we aimed at identifying potential functionally and pharmaco-therapeutically deleterious non-synonymous SNPs of Drd2. A wide array of bioinformatics tools was used to evaluate the impact of nsSNPs on protein structure and functionality. Out of 260 nsSNPs retrieved from the dbSNP database, initially 9 were predicted as deleterious by 15 tools. Upon further assessment of their domain association, conservation profile, homology models and inter-atomic interaction, the mutant F389V was considered as the most impactful. In-depth analysis of F389V through Molecular Docking and Dynamics Simulation revealed a decline in affinity for its native agonist dopamine and an increase in affinity for the antipsychotic drug risperidone. Remarkable alterations in binding interactions and stability of the protein-ligand complex in simulated physiological conditions were also noted. These findings will improve our understanding of the consequence of nsSNPs in disease-susceptibility and therapeutic efficacy.
MeSH term(s)	Binding Sites ; Dopamine/metabolism ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Polymorphism, Single Nucleotide ; Protein Conformation ; Receptors, Dopamine D2/chemistry ; Receptors, Dopamine D2/genetics ; Receptors, Dopamine D2/metabolism ; Signal Transduction
Chemical Substances	DRD2 protein, human ; Receptors, Dopamine D2 ; Dopamine (VTD58H1Z2X)
Language	English
Publishing date	2021-12-01
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-02715-z
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Article ; Online: A comprehensive in silico investigation into the nsSNPs of Drd2 gene predicts significant functional consequences in dopamine signaling and pharmacotherapy

Samia Sultana Lira / Ishtiaque Ahammad

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 16

Abstract: Abstract DRD2 is a neuronal cell surface protein involved in brain development and function. Variations in the Drd2 gene have clinical significance since DRD2 is a pharmacotherapeutic target for treating psychiatric disorders like ADHD and schizophrenia. ...

Abstract	Abstract DRD2 is a neuronal cell surface protein involved in brain development and function. Variations in the Drd2 gene have clinical significance since DRD2 is a pharmacotherapeutic target for treating psychiatric disorders like ADHD and schizophrenia. Despite numerous studies on the disease association of single nucleotide polymorphisms (SNPs) in the intronic regions, investigation into the coding regions is surprisingly limited. In this study, we aimed at identifying potential functionally and pharmaco-therapeutically deleterious non-synonymous SNPs of Drd2. A wide array of bioinformatics tools was used to evaluate the impact of nsSNPs on protein structure and functionality. Out of 260 nsSNPs retrieved from the dbSNP database, initially 9 were predicted as deleterious by 15 tools. Upon further assessment of their domain association, conservation profile, homology models and inter-atomic interaction, the mutant F389V was considered as the most impactful. In-depth analysis of F389V through Molecular Docking and Dynamics Simulation revealed a decline in affinity for its native agonist dopamine and an increase in affinity for the antipsychotic drug risperidone. Remarkable alterations in binding interactions and stability of the protein–ligand complex in simulated physiological conditions were also noted. These findings will improve our understanding of the consequence of nsSNPs in disease-susceptibility and therapeutic efficacy.
Keywords	Medicine ; R ; Science ; Q
Subject code	500
Language	English
Publishing date	2021-12-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
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Article ; Online: Designing a novel mRNA vaccine against SARS-CoV-2: An immunoinformatics approach.

Ahammad, Ishtiaque / Lira, Samia Sultana

International journal of biological macromolecules

2020 Volume 162, Page(s) 820–837

Abstract: SARS-CoV-2 is the deadly virus behind COVID-19, the disease that went on to ravage the world and caused the biggest pandemic 21st century has witnessed so far. On the face of ongoing death and destruction, the urgent need for the discovery of a vaccine ... ...

Abstract	SARS-CoV-2 is the deadly virus behind COVID-19, the disease that went on to ravage the world and caused the biggest pandemic 21st century has witnessed so far. On the face of ongoing death and destruction, the urgent need for the discovery of a vaccine against the virus is paramount. This study resorted to the emerging discipline of immunoinformatics in order to design a multi-epitope mRNA vaccine against the spike glycoprotein of SARS-CoV-2. Various immunoinformatics tools were utilized to predict T and B lymphocyte epitopes. The epitopes were channeled through a filtering pipeline comprised of antigenicity, toxicity, allergenicity, and cytokine inducibility evaluation with the goal of selecting epitopes capable of generating both T and B cell-mediated immune responses. Molecular docking simulation between the epitopes and their corresponding MHC molecules was carried out. 13 epitopes, a highly immunogenic adjuvant, elements for proper sub-cellular trafficking, a secretion booster, and appropriate linkers were combined for constructing the vaccine. The vaccine was found to be antigenic, almost neutral at physiological pH, non-toxic, non-allergenic, capable of generating a robust immune response and had a decent worldwide population coverage. Based on these parameters, this design can be considered a promising choice for a vaccine against SARS-CoV-2.
MeSH term(s)	Betacoronavirus/immunology ; COVID-19 ; COVID-19 Vaccines ; Coronavirus Infections/genetics ; Coronavirus Infections/immunology ; Coronavirus Infections/prevention & control ; Coronavirus Infections/virology ; Drug Design ; Epitopes, B-Lymphocyte/chemistry ; Epitopes, B-Lymphocyte/immunology ; Epitopes, T-Lymphocyte/chemistry ; Epitopes, T-Lymphocyte/immunology ; Humans ; Immunogenicity, Vaccine ; Molecular Docking Simulation ; Pandemics/prevention & control ; Pneumonia, Viral/immunology ; Pneumonia, Viral/prevention & control ; Pneumonia, Viral/virology ; RNA, Messenger/immunology ; SARS-CoV-2 ; Sequence Analysis, Protein ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/immunology ; Vaccines, Synthetic/chemistry ; Vaccines, Synthetic/genetics ; Vaccines, Synthetic/immunology ; Viral Vaccines/chemistry ; Viral Vaccines/genetics ; Viral Vaccines/immunology
Chemical Substances	COVID-19 Vaccines ; Epitopes, B-Lymphocyte ; Epitopes, T-Lymphocyte ; RNA, Messenger ; Spike Glycoprotein, Coronavirus ; Vaccines, Synthetic ; Viral Vaccines ; spike protein, SARS-CoV-2
Keywords	covid19
Language	English
Publishing date	2020-06-26
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2020.06.213
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Article ; Online: Designing a novel mRNA vaccine against SARS-CoV-2: An immunoinformatics approach

Ahammad, Ishtiaque / Lira, Samia Sultana

International Journal of Biological Macromolecules. 2020 Nov., v. 162 p.820-837

2020

Abstract	SARS-CoV-2 is the deadly virus behind COVID-19, the disease that went on to ravage the world and caused the biggest pandemic 21st century has witnessed so far. On the face of ongoing death and destruction, the urgent need for the discovery of a vaccine against the virus is paramount. This study resorted to the emerging discipline of immunoinformatics in order to design a multi-epitope mRNA vaccine against the spike glycoprotein of SARS-CoV-2. Various immunoinformatics tools were utilized to predict T and B lymphocyte epitopes. The epitopes were channeled through a filtering pipeline comprised of antigenicity, toxicity, allergenicity, and cytokine inducibility evaluation with the goal of selecting epitopes capable of generating both T and B cell-mediated immune responses. Molecular docking simulation between the epitopes and their corresponding MHC molecules was carried out. 13 epitopes, a highly immunogenic adjuvant, elements for proper sub-cellular trafficking, a secretion booster, and appropriate linkers were combined for constructing the vaccine. The vaccine was found to be antigenic, almost neutral at physiological pH, non-toxic, non-allergenic, capable of generating a robust immune response and had a decent worldwide population coverage. Based on these parameters, this design can be considered a promising choice for a vaccine against SARS-CoV-2.
Keywords	B-lymphocytes ; COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; adjuvants ; allergenicity ; cytokines ; death ; epitopes ; glycoproteins ; immune response ; immunoinformatics ; pH ; pandemic ; secretion ; toxicity ; vaccines ; viruses ; ACE2 ; AI ; ARCA ; ARDS ; COVID-19 ; CTL ; dsRNA ; GMP ; GM-CSF ; GRAVY ; HIV ; HSV ; HLA ; HPLC ; HTL ; ICTV ; IFN-γ ; Ig ; II ; IL-4 ; IL-10 ; LBL ; LNP ; MERS ; MERS-CoV ; MHC ; MITD ; NMR ; ORF ; PAMP ; pAPC ; pDNA ; PHEIC ; PSSM ; RBD ; RBM ; RTC ; SARS-CoV ; SARS CoV-2 ; TAP ; TCR ; TLR ; TMPRSS2 ; tPA ; UTR ; ViPR ; WHO ; SARS-CoV-2 ; mRNA vaccine
Language	English
Dates of publication	2020-11
Size	p. 820-837.
Publishing place	Elsevier B.V.
Document type	Article ; Online
Note	NAL-AP-2-clean
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2020.06.213
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Article ; Online: Designing a novel mRNA vaccine against SARS-CoV-2

Ahammad, Ishtiaque / Lira, Samia Sultana

International Journal of Biological Macromolecules

An immunoinformatics approach

2020 Volume 162, Page(s) 820–837

Keywords	Biochemistry ; Molecular Biology ; Structural Biology ; General Medicine ; covid19
Language	English
Publisher	Elsevier BV
Publishing country	us
Document type	Article ; Online
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2020.06.213
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Article ; Online: High risk genetic variants of human insulin receptor substrate 1(IRS1) infer structural instability and functional interference.

Bhattacharjee, Arittra / Pranto, S M Al Muied / Ahammad, Ishtiaque / Chowdhury, Zeshan Mahmud / Juliana, Farha Matin / Das, Keshob Chandra / Keya, Chaman Ara / Salimullah, Md

Journal of biomolecular structure & dynamics

2023 Volume 41, Issue 24, Page(s) 15150–15164

Abstract: Insulin receptor substrate 1(IRS1) is a signaling adapter protein encoded by ... ...

Abstract	Insulin receptor substrate 1(IRS1) is a signaling adapter protein encoded by the
MeSH term(s)	Humans ; Insulin Receptor Substrate Proteins/genetics ; Insulin Receptor Substrate Proteins/metabolism ; Diabetes Mellitus, Type 2/genetics ; Signal Transduction ; Extracellular Signal-Regulated MAP Kinases/metabolism ; Adaptor Proteins, Signal Transducing/metabolism
Chemical Substances	Insulin Receptor Substrate Proteins ; Extracellular Signal-Regulated MAP Kinases (EC 2.7.11.24) ; Adaptor Proteins, Signal Transducing ; IRS1 protein, human
Language	English
Publishing date	2023-03-12
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2187232
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Article: Identification of repurposable drug targets in

Chowdhury, Zeshan Mahmud / Jamal, Tabassum Binte / Ahammad, Ishtiaque / Bhattacharjee, Arittra / Lamisa, Anika Bushra / Jani, Jannatul Maoa / Israk, Md Fahim / Hossain, Mohammad Uzzal / Das, Keshob Chandra / Keya, Chaman Ara / Salimullah, Md

Heliyon

2023 Volume 9, Issue 11, Page(s) e21466

Abstract: Mycoplasma ... ...

Abstract	Mycoplasma pneumoniae
Language	English
Publishing date	2023-11-04
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2023.e21466
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Article ; Online: Gut microbiome composition reveals the distinctiveness between the Bengali people and the Indigenous ethnicities in Bangladesh.

Ahammad, Ishtiaque / Bhattacharjee, Arittra / Chowdhury, Zeshan Mahmud / Rahman, Anisur / Hossain, Mohammad Uzzal / Dewan, Gourab / Talukder, Shiny / Das, Keshob Chandra / Keya, Chaman Ara / Salimullah, Md

Communications biology

2024 Volume 7, Issue 1, Page(s) 500

Abstract: Ethnicity has a significant role in shaping the composition of the gut microbiome, which has implications in human physiology. This study intends to investigate the gut microbiome of Bengali people as well as several indigenous ethnicities (Chakma, Marma, ...

Abstract	Ethnicity has a significant role in shaping the composition of the gut microbiome, which has implications in human physiology. This study intends to investigate the gut microbiome of Bengali people as well as several indigenous ethnicities (Chakma, Marma, Khyang, and Tripura) residing in the Chittagong Hill Tracts areas of Bangladesh. Following fecal sample collection from each population, part of the bacterial 16 s rRNA gene was amplified and sequenced using Illumina NovaSeq platform. Our findings indicated that Bangladeshi gut microbiota have a distinct diversity profile when compared to other countries. We also found out that Bangladeshi indigenous communities had a higher Firmicutes to Bacteroidetes ratio than the Bengali population. The investigation revealed an unclassified bacterium that was differentially abundant in Bengali samples while the genus Alistipes was found to be prevalent in Chakma samples. Further research on these bacteria might help understand diseases associated with these populations. Also, the current small sample-sized pilot study hindered the comprehensive understanding of the gut microbial diversity of the Bangladeshi population and its potential health implications. However, our study will help establish a basic understanding of the gut microbiome of the Bangladeshi population.
MeSH term(s)	Adult ; Female ; Humans ; Male ; Bacteria/genetics ; Bacteria/classification ; Bangladesh ; Ethnicity ; Feces/microbiology ; Gastrointestinal Microbiome/genetics ; Indigenous Peoples ; RNA, Ribosomal, 16S/genetics ; South Asian People
Chemical Substances	RNA, Ribosomal, 16S
Language	English
Publishing date	2024-04-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-024-06191-9
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Article ; Online: Proteome-Based Investigation Identified Potential Drug Repurposable Small Molecules Against Monkeypox Disease.

Bhattacharjee, Arittra / Ahammad, Ishtiaque / Chowdhury, Zeshan Mahmud / Das, Keshob Chandra / Keya, Chaman Ara / Salimullah, Md

Molecular biotechnology

2022 Volume 66, Issue 4, Page(s) 626–640

Abstract: Monkeypox Virus (MPXV), the causative agent of Monkeypox (MPX) disease, is an emerging zoonotic pathogen spreading in different endemic and non-endemic nations and creating outbreaks. MPX treatment mainly includes Cidofovir and Tecovirimat but they have ... ...

Abstract	Monkeypox Virus (MPXV), the causative agent of Monkeypox (MPX) disease, is an emerging zoonotic pathogen spreading in different endemic and non-endemic nations and creating outbreaks. MPX treatment mainly includes Cidofovir and Tecovirimat but they have several side effects and solely depending on these drugs may promote the emergence of drug-resistant variants. Hence, new drugs are required to control the spread of the disease. In this study, we explored the MPXV proteome to suggest repurposable drugs. DrugBank screening revealed drugs such as Brinzolamide, Dorzolamide, Methazolamide, Zidovudine, Gemcitabine, Hydroxyurea, Fludarabine, and Tecovirimat as controls. Structural analogs of these compounds were extracted from ChEMBL Database. After Molecular docking and Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET)-based screening, we identified Zidovudine (binding affinity-5.9 kcal/mol) and a Harmala alkaloid (2S,4R)-4-(9H-Pyrido[3,4-b]indol-1-yl)-1,2,4-butanetriol (binding affinity - 6.6 kcal/mol) against L2R receptor (Thymidine Kinase). Moreover, Fludarabine (binding affinity - 6.4 kcal/mol) and 5'-Dehydroadenosine (binding affinity - 6.4 kcal/mol) can strongly interact with the I4L receptor (Ribonucleotide reductase large subunit R1). Molecular Dynamics (MD) simulations suggest all of these compounds can change the C-alpha backbone, residue mobility, compactness, and solvent accessible surface area of L2R and I4L. Our results strongly suggest that these drug repurposing small molecules are worth exploring in vivo and in vitro for clinical applications.
MeSH term(s)	Proteome ; Molecular Docking Simulation ; Antiviral Agents/pharmacology ; Antiviral Agents/chemistry ; Drug Repositioning ; Monkeypox virus/drug effects ; Monkeypox virus/chemistry ; Mpox (monkeypox)/drug therapy ; Mpox (monkeypox)/virology ; Humans ; Animals ; Small Molecule Libraries/pharmacology ; Small Molecule Libraries/chemistry ; Viral Proteins/chemistry ; Viral Proteins/metabolism
Chemical Substances	Proteome ; Antiviral Agents ; Small Molecule Libraries ; Viral Proteins
Language	English
Publishing date	2022-11-10
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1193057-3
ISSN	1559-0305 ; 1073-6085
ISSN (online)	1559-0305
ISSN	1073-6085
DOI	10.1007/s12033-022-00595-w
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