LIVIVO - Search results -

Search results

Result 1 - 10 of total 70

Search options

Article ; Online: Targeting Essential Hypothetical Proteins of

Rahman, Atikur / Sarker, Md Takim / Islam, Md Ashiqul / Hossain, Mohammad Uzzal / Hasan, Mahmudul / Susmi, Tasmina Ferdous

BioMed research international

2023 Volume 2023, Page(s) 1787485

Abstract: As an omnipresent opportunistic bacterium, ...

Abstract	As an omnipresent opportunistic bacterium,
MeSH term(s)	Humans ; Pseudomonas aeruginosa ; Virulence Factors/genetics ; Virulence Factors/metabolism ; Proteome/metabolism ; Computational Biology ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism
Chemical Substances	Virulence Factors ; Proteome ; Bacterial Proteins
Language	English
Publishing date	2023-04-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	2698540-8
ISSN	2314-6141 ; 2314-6133
ISSN (online)	2314-6141
ISSN	2314-6133
DOI	10.1155/2023/1787485
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

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
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Subtractive genomics study of Xanthomonas oryzae pv. Oryzae reveals repurposable drug candidate for the treatment of bacterial leaf blight in rice.

Ahammad, Ishtiaque / Jamal, Tabassum Binte / Lamisa, Anika Bushra / Bhattacharjee, Arittra / Zinan, Nayeematul / Hasan Chowdhury, Md Zahid / Naimul Islam, Shah Mohammad / Faruque, Kazi Md Omar / Mahmud Chowdhury, Zeshan / Uzzal Hossain, Mohammad / Chandra Das, Keshob / Ara Keya, Chaman / Salimullah, Md

Journal, genetic engineering & biotechnology

2024 Volume 22, Issue 1, Page(s) 100353

Abstract: Background: Xanthomonas oryzae pv. oryzae is a plant pathogen responsible for causing one of the most severe bacterial diseases in rice, known as bacterial leaf blight that poses a major threat to global rice production. Even though several experimental ...

Abstract	Background: Xanthomonas oryzae pv. oryzae is a plant pathogen responsible for causing one of the most severe bacterial diseases in rice, known as bacterial leaf blight that poses a major threat to global rice production. Even though several experimental compounds and chemical agents have been tested against X. oryzae pv. oryzae, still no approved drug is available. In this study, a subtractive genomic approach was used to identify potential therapeutic targets and repurposible drug candidates that could control of bacterial leaf blight in rice plants. Results: The entire proteome of the pathogen underwent an extensive filtering process which involved removal of the paralogous proteins, rice homologs, non-essential proteins. Out of the 4382 proteins present in Xoo proteome, five hub proteins such as dnaA, dnaN, recJ, ruvA, and recR were identified for the druggability analysis. This analysis led to the identification of dnaN-encoded Beta sliding clamp protein as a potential therapeutic target and one experimental drug named [(5R)-5-(2,3-dibromo-5-ethoxy-4hydroxybenzyl)-4-oxo-2-thioxo-1,3-thiazolidin-3-yl]acetic acid that can be repurposed against it. Molecular docking and 100 ns long molecular dynamics simulation suggested that the drug can form stable complexes with the target protein over time. Conclusion: Findings from our study indicated that the proposed drug showed potential effectiveness against bacterial leaf blight in rice caused by X. oryzae pv. oryzae. It is essential to keep in consideration that the procedure for developing novel drugs can be challenging and complicated. Even the most promising results from in silico studies should be validated through further in vitro and in vivo investigation before approval.
Language	English
Publishing date	2024-01-23
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2637420-1
ISSN	2090-5920 ; 1687-157X ; 2090-5920
ISSN (online)	2090-5920
ISSN	1687-157X ; 2090-5920
DOI	10.1016/j.jgeb.2024.100353
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

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)	Bangladesh ; Humans ; Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Ethnicity ; Bacteria/genetics ; Bacteria/classification ; Female ; Adult ; Male ; Indigenous Peoples ; 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
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: High-Risk Polymorphisms Associated with the Molecular Function of Human HMGCR Gene Infer the Inhibition of Cholesterol Biosynthesis

Keshob Chandra Das / Mohammad Uzzal Hossain / Md Moniruzzaman / Md Salimullah / Sharif Akhteruzzaman

BioMed Research International, Vol

2022 Volume 2022

Abstract: HMG-CoA reductase or HMGCR (3-hydroxy-3-methylglutaryl-CoA reductase) is a rate-limiting enzyme involved in cholesterol biosynthesis. HMGCR plays an important role in the possible occurrence of hypercholesterolemia leading to atherosclerosis and coronary ...

Abstract	HMG-CoA reductase or HMGCR (3-hydroxy-3-methylglutaryl-CoA reductase) is a rate-limiting enzyme involved in cholesterol biosynthesis. HMGCR plays an important role in the possible occurrence of hypercholesterolemia leading to atherosclerosis and coronary heart disease. This enzyme is a major target for cholesterol-lowering drugs such as “statin” which blocks the synthesis of mevalonate, a precursor for cholesterol biosynthesis. This study is aimed at characterizing deleterious mutations and classifying functional single nucleotide polymorphisms (SNPs) of the HMGCR gene through analysis of functional and structural evaluation, domain association, solvent accessibility, and energy minimization studies. The functional and characterization tools such as SIFT, PolyPhen, SNPs and GO, Panther, I-Mutant, and Pfam along with programming were employed to explore all the available SNPs in the HMGCR gene in the database. Among 6815 SNP entries from different databases, approximately 388 SNPs were found to be missense. Analysis showed that seven missense SNPs are more likely to have deleterious effects. A tertiary model of the mutant protein was constructed to determine the functional and structural effects of the HMGCR mutation. In addition, the location of the mutations suggests that they may have deleterious effects because most of the mutations are residing in the functional domain of the protein. The findings from the analysis predicted that rs147043821 and rs193026499 missense SNPs could cause significant structural and functional instability in the mutated proteins of the HMGCR gene. The findings of the current study will likely be useful in future efforts to uncover the mechanism and cause of hypercholesterolemia. In addition, the identified SNPs of HMGCR gene could set up a strong foundation for further therapeutic discovery.
Keywords	Medicine ; R
Subject code	572
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Hindawi Limited
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Mpropred

Nadim Ferdous / Mahjerin Nasrin Reza / Mohammad Uzzal Hossain / Shahin Mahmud / Suhami Napis / Kamal Chowdhury / A K M Mohiuddin

PLoS ONE, Vol 18, Iss 6, p e

A machine learning (ML) driven Web-App for bioactivity prediction of SARS-CoV-2 main protease (Mpro) antagonists.

2023 Volume 0287179

Abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic emerged in 2019 and still requiring treatments with fast clinical translatability. Frequent occurrence of mutations in spike glycoprotein of SARS-CoV-2 led the consideration of an ... ...

Abstract	The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic emerged in 2019 and still requiring treatments with fast clinical translatability. Frequent occurrence of mutations in spike glycoprotein of SARS-CoV-2 led the consideration of an alternative therapeutic target to combat the ongoing pandemic. The main protease (Mpro) is such an attractive drug target due to its importance in maturating several polyproteins during the replication process. In the present study, we used a classification structure-activity relationship (CSAR) model to find substructures that leads to to anti-Mpro activities among 758 non-redundant compounds. A set of 12 fingerprints were used to describe Mpro inhibitors, and the random forest approach was used to build prediction models from 100 distinct data splits. The data set's modelability (MODI index) was found to be robust, with a value of 0.79 above the 0.65 threshold. The accuracy (89%), sensitivity (89%), specificity (73%), and Matthews correlation coefficient (79%) used to calculate the prediction performance, was also found to be statistically robust. An extensive analysis of the top significant descriptors unveiled the significance of methyl side chains, aromatic ring and halogen groups for Mpro inhibition. Finally, the predictive model is made publicly accessible as a web-app named Mpropred in order to allow users to predict the bioactivity of compounds against SARS-CoV-2 Mpro. Later, CMNPD, a marine compound database was screened by our app to predict bioactivity of all the compounds and results revealed significant correlation with their binding affinity to Mpro. Molecular dynamics (MD) simulation and molecular mechanics/Poisson Boltzmann surface area (MM/PBSA) analysis showed improved properties of the complexes. Thus, the knowledge and web-app shown herein can be used to develop more effective and specific inhibitors against the SARS-CoV-2 Mpro. The web-app can be accessed from https://share.streamlit.io/nadimfrds/mpropred/Mpropred_app.py.
Keywords	Medicine ; R ; Science ; Q
Subject code	540
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Gene silencing of Helicobacter pylori through newly designed siRNA convenes the treatment of gastric cancer.

Reza, Mahjerin Nasrin / Mahmud, Shahin / Ferdous, Nadim / Ahammad, Ishtiaque / Hossain, Mohammad Uzzal / Al Amin, Md / Mohiuddin, A K M

Cancer medicine

2023 Volume 12, Issue 24, Page(s) 22407–22419

Abstract: Background: Helicobacter pylori is a gastric pathogen that is responsible for causing chronic inflammation and increasing the risk of gastric cancer development. It is capable of persisting for decades in the harsh gastric environment because of the ... ...

Abstract	Background: Helicobacter pylori is a gastric pathogen that is responsible for causing chronic inflammation and increasing the risk of gastric cancer development. It is capable of persisting for decades in the harsh gastric environment because of the inability of the host to eradicate the infection. Several treatment strategies have been developed against this bacterium using different antibiotics. But the effectiveness of treating H. pylori has significantly decreased due to widespread antibiotic resistance, including an increased risk of gastric cancer. The small interfering RNAs (siRNA), which is capable of sequence-specific gene-silencing can be used as a new therapeutic approach for the treatment of a variety of such malignancies. In the current study, we rationally designed two siRNA molecules to silence the cytotoxin-associated gene A (CagA) and vacuolating cytotoxin A (VacA) genes of H. pylori for their significant involvement in developing cancer. Methods: We selected a common region of all the available transcripts from different countries of CagA and VacA to design the siRNA molecules. The final siRNA candidate was selected based on the results from machine learning algorithms, off-target similarity, and various thermodynamic properties. Result: Further, we utilized molecular docking and all atom molecular dynamics (MD) simulations to assess the binding interactions of the designed siRNAs with the major components of the RNA-induced silencing complex (RISC) and results revealed the ability of the designed siRNAs to interact with the proteins of RISC complex in comparable to those of the experimentally reported siRNAs. Conclusion: These designed siRNAs should effectively silence the CagA and VacA genes of H. pylori during siRNA mediated treatment in gastric cancer.
MeSH term(s)	Humans ; Antigens, Bacterial/genetics ; Bacterial Proteins/genetics ; Helicobacter pylori/genetics ; RNA, Small Interfering/genetics ; RNA, Small Interfering/therapeutic use ; RNA, Small Interfering/metabolism ; Stomach Neoplasms/genetics ; Stomach Neoplasms/therapy ; Stomach Neoplasms/microbiology ; Molecular Docking Simulation ; Cytotoxins/metabolism ; Helicobacter Infections/genetics ; Helicobacter Infections/microbiology
Chemical Substances	Antigens, Bacterial ; Bacterial Proteins ; RNA, Small Interfering ; Cytotoxins
Language	English
Publishing date	2023-12-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	2659751-2
ISSN	2045-7634 ; 2045-7634
ISSN (online)	2045-7634
ISSN	2045-7634
DOI	10.1002/cam4.6772
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Mpropred: A machine learning (ML) driven Web-App for bioactivity prediction of SARS-CoV-2 main protease (Mpro) antagonists.

Ferdous, Nadim / Reza, Mahjerin Nasrin / Hossain, Mohammad Uzzal / Mahmud, Shahin / Napis, Suhami / Chowdhury, Kamal / Mohiuddin, A K M

PloS one

2023 Volume 18, Issue 6, Page(s) e0287179

Abstract	The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic emerged in 2019 and still requiring treatments with fast clinical translatability. Frequent occurrence of mutations in spike glycoprotein of SARS-CoV-2 led the consideration of an alternative therapeutic target to combat the ongoing pandemic. The main protease (Mpro) is such an attractive drug target due to its importance in maturating several polyproteins during the replication process. In the present study, we used a classification structure-activity relationship (CSAR) model to find substructures that leads to to anti-Mpro activities among 758 non-redundant compounds. A set of 12 fingerprints were used to describe Mpro inhibitors, and the random forest approach was used to build prediction models from 100 distinct data splits. The data set's modelability (MODI index) was found to be robust, with a value of 0.79 above the 0.65 threshold. The accuracy (89%), sensitivity (89%), specificity (73%), and Matthews correlation coefficient (79%) used to calculate the prediction performance, was also found to be statistically robust. An extensive analysis of the top significant descriptors unveiled the significance of methyl side chains, aromatic ring and halogen groups for Mpro inhibition. Finally, the predictive model is made publicly accessible as a web-app named Mpropred in order to allow users to predict the bioactivity of compounds against SARS-CoV-2 Mpro. Later, CMNPD, a marine compound database was screened by our app to predict bioactivity of all the compounds and results revealed significant correlation with their binding affinity to Mpro. Molecular dynamics (MD) simulation and molecular mechanics/Poisson Boltzmann surface area (MM/PBSA) analysis showed improved properties of the complexes. Thus, the knowledge and web-app shown herein can be used to develop more effective and specific inhibitors against the SARS-CoV-2 Mpro. The web-app can be accessed from https://share.streamlit.io/nadimfrds/mpropred/Mpropred_app.py.
MeSH term(s)	Humans ; COVID-19 ; Mobile Applications ; SARS-CoV-2 ; Machine Learning ; Protease Inhibitors/pharmacology ; Molecular Docking Simulation
Chemical Substances	3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Protease Inhibitors
Language	English
Publishing date	2023-06-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0287179
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: High-Risk Polymorphisms Associated with the Molecular Function of Human HMGCR Gene Infer the Inhibition of Cholesterol Biosynthesis.

Das, Keshob Chandra / Hossain, Mohammad Uzzal / Moniruzzaman, Md / Salimullah, Md / Akhteruzzaman, Sharif

BioMed research international

2022 Volume 2022, Page(s) 4558867

Abstract	HMG-CoA reductase or HMGCR (3-hydroxy-3-methylglutaryl-CoA reductase) is a rate-limiting enzyme involved in cholesterol biosynthesis. HMGCR plays an important role in the possible occurrence of hypercholesterolemia leading to atherosclerosis and coronary heart disease. This enzyme is a major target for cholesterol-lowering drugs such as "statin" which blocks the synthesis of mevalonate, a precursor for cholesterol biosynthesis. This study is aimed at characterizing deleterious mutations and classifying functional single nucleotide polymorphisms (SNPs) of the HMGCR gene through analysis of functional and structural evaluation, domain association, solvent accessibility, and energy minimization studies. The functional and characterization tools such as SIFT, PolyPhen, SNPs and GO, Panther, I-Mutant, and Pfam along with programming were employed to explore all the available SNPs in the HMGCR gene in the database. Among 6815 SNP entries from different databases, approximately 388 SNPs were found to be missense. Analysis showed that seven missense SNPs are more likely to have deleterious effects. A tertiary model of the mutant protein was constructed to determine the functional and structural effects of the HMGCR mutation. In addition, the location of the mutations suggests that they may have deleterious effects because most of the mutations are residing in the functional domain of the protein. The findings from the analysis predicted that rs147043821 and rs193026499 missense SNPs could cause significant structural and functional instability in the mutated proteins of the HMGCR gene. The findings of the current study will likely be useful in future efforts to uncover the mechanism and cause of hypercholesterolemia. In addition, the identified SNPs of HMGCR gene could set up a strong foundation for further therapeutic discovery.
MeSH term(s)	Cholesterol/metabolism ; Humans ; Hydroxymethylglutaryl CoA Reductases/genetics ; Hydroxymethylglutaryl-CoA Reductase Inhibitors/pharmacology ; Hydroxymethylglutaryl-CoA Reductase Inhibitors/therapeutic use ; Hypercholesterolemia/drug therapy ; Hypercholesterolemia/genetics ; Mevalonic Acid/metabolism ; Polymorphism, Single Nucleotide/genetics
Chemical Substances	Hydroxymethylglutaryl-CoA Reductase Inhibitors ; Cholesterol (97C5T2UQ7J) ; HMGCR protein, human (EC 1.1.1.-) ; Hydroxymethylglutaryl CoA Reductases (EC 1.1.1.-) ; Mevalonic Acid (S5UOB36OCZ)
Language	English
Publishing date	2022-06-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	2698540-8
ISSN	2314-6141 ; 2314-6133
ISSN (online)	2314-6141
ISSN	2314-6133
DOI	10.1155/2022/4558867
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: Hypothetical protein predicted to be tumor suppressor: a protein functional analysis.

Kader, Md Abdul / Ahammed, Akash / Khan, Md Sharif / Ashik, Sheikh Abdullah Al / Islam, Md Shariful / Hossain, Mohammad Uzzal

Genomics & informatics

2022 Volume 20, Issue 1, Page(s) e6

Abstract: Litorilituus sediminis is a Gram-negative, aerobic, novel bacterium under the family of Colwelliaceae, has a stunning hypothetical protein containing domain called von Hippel-Lindau that has significant tumor suppressor activity. Therefore, this study ... ...

Abstract	Litorilituus sediminis is a Gram-negative, aerobic, novel bacterium under the family of Colwelliaceae, has a stunning hypothetical protein containing domain called von Hippel-Lindau that has significant tumor suppressor activity. Therefore, this study was designed to elucidate the structure and function of the biologically important hypothetical protein EMK97_00595 (QBG34344.1) using several bioinformatics tools. The functional annotation exposed that the hypothetical protein is an extracellular secretory soluble signal peptide and contains the von Hippel-Lindau (VHL; VHL beta) domain that has a significant role in tumor suppression. This domain is conserved throughout evolution, as its homologs are available in various types of the organism like mammals, insects, and nematode. The gene product of VHL has a critical regulatory activity in the ubiquitous oxygen-sensing pathway. This domain has a significant role in inhibiting cell proliferation, angiogenesis progression, kidney cancer, breast cancer, and colon cancer. At last, the current study depicts that the annotated hypothetical protein is linked with tumor suppressor activity which might be of great interest to future research in the higher organism.
Language	English
Publishing date	2022-03-31
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.21073
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

To top

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito