LIVIVO - Search results -

Search results

Result 1 - 10 of total 13

Search options

Article ; Online: In silico analysis of SARS-CoV-2 spike protein N501Y and N501T mutation effects on human ACE2 binding.

Çubuk, Hasan / Özbi L, Mehmet

Journal of molecular graphics & modelling

2022 Volume 116, Page(s) 108260

Abstract: The SARS-CoV-2 is an RNA-based virus and the most vital step of its survival is the attachment to hACE2 through its spike protein. Although SARS-CoV-2 has the ability to maintain high accurate replication and it can be accepted as a low mutation risked ... ...

Abstract	The SARS-CoV-2 is an RNA-based virus and the most vital step of its survival is the attachment to hACE2 through its spike protein. Although SARS-CoV-2 has the ability to maintain high accurate replication and it can be accepted as a low mutation risked virus, it already showed more than nine thousand mutations in spike protein, of which 44 mutations are located within a 3.2 Å interacting distance from the hACE2 receptor. Mutations on spike protein, N501Y and N501T raised serious concerns for higher transmissibility and resistance towards current vaccines. In the current study, the mutational outcomes of N501Y and N501T on the hACE2-SARS CoV-2 spike protein complexation were analyzed by employing all-atom classic molecular dynamics (MD) simulations. These simulations revealed that both N501Y and N501T mutations increased the binding strength of spike protein to the host hACE2, predicted by binding free energy analysis via MM/GBSA rescoring scheme. This study highlights the importance of energy-based analysis for identifying mutational outcomes and will shed light on handling long-term and effective treatment strategies including repurposing anti-viral drugs, anti-SARS-CoV-2 antibodies, vaccines, and antisense based-therapies.
MeSH term(s)	Angiotensin-Converting Enzyme 2/genetics ; COVID-19 ; Humans ; Mutation ; Peptidyl-Dipeptidase A/chemistry ; Protein Binding ; Receptors, Virus/chemistry ; SARS-CoV-2/genetics ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/metabolism
Chemical Substances	Receptors, Virus ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Peptidyl-Dipeptidase A (EC 3.4.15.1) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Language	English
Publishing date	2022-07-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	1396450-1
ISSN	1873-4243 ; 1093-3263
ISSN (online)	1873-4243
ISSN	1093-3263
DOI	10.1016/j.jmgm.2022.108260
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 3491: 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)

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.

Details ▾
- See ZB MED holdings
- Order with fees

Article: Comparison of clinically approved molecules on SARS-CoV-2 drug target proteins: a molecular docking study.

Çubuk, Hasan / Özbİl, Mehmet

Turkish journal of chemistry

2021 Volume 45, Issue 1, Page(s) 35–41

Abstract: The new type of coronavirus, SARS-CoV-2 has affected more than 22.6 million people worldwide. Since the first day the virus was spotted in Wuhan, China, numerous drug design studies have been conducted all over the globe. Most of these studies target the ...

Abstract	The new type of coronavirus, SARS-CoV-2 has affected more than 22.6 million people worldwide. Since the first day the virus was spotted in Wuhan, China, numerous drug design studies have been conducted all over the globe. Most of these studies target the receptor-binding domain of spike protein of SARS-CoV-2, which is known to bind to the human ACE2 receptor and SARS-CoV-2 main protease, vital for the virus' replication. However, there might be a third target, human furin protease, which cleaves the virus' S1-S2 domains playing an active role in its entry into the host cell. In this study, we docked five clinically used drug molecules, favipiravir, hydroxychloroquine, remdesivir, lopinavir, and ritonavir onto three target proteins, the receptor-binding domain of SARS-CoV-2 spike protein, SARS-CoV-2 main protease, and human furin protease. Results of molecular docking simulations revealed that human furin protease might be targeted by COVID-19. Remdesivir, a nucleic acid derivative, strongly bound to the active site of this protease, suggesting that this molecule can be used as a template for designing novel furin protease inhibitors to fight against the disease. Protein-drug interactions revealed in this study at the molecular level, can pave the way for better drug design for each specific target.
Language	English
Publishing date	2021-02-17
Publishing country	Turkey
Document type	Journal Article
ZDB-ID	2046471-X
ISSN	1303-6130 ; 1300-0527
ISSN (online)	1303-6130
ISSN	1300-0527
DOI	10.3906/kim-2008-35
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Book ; Online: A Promising Strategy Against SARS-CoV-2 Infected Patients

Hasan Cubuk

Antisense Therapy

2020

Abstract: As of July 25-2020, 643,412 people in more than 215 countries have been victims of the new type of coronavirus, SARS-CoV-2. Thereby, there is a huge effort to develop a strategy to treat, and or prevent people from SARS-CoV-2 infection. Those efforts ... ...

Abstract	As of July 25-2020, 643,412 people in more than 215 countries have been victims of the new type of coronavirus, SARS-CoV-2. Thereby, there is a huge effort to develop a strategy to treat, and or prevent people from SARS-CoV-2 infection. Those efforts could be mainly categorized as drug repurposing, anti-SARS-CoV-2 antibodies from people who recovered, and vaccines. However, there is currently no specific treatment available against SARS-CoV-2 infected patients. That`s why many new approaches and ideas are still studied every day for the treatment of SARS-CoV-2 infected patients. Antisense therapy is one of these promising approaches to target SARS-CoV-2 genomic RNA specifically and inhibit its activity upon incorrect viral RNA processing. In this study, antisense oligonucleotide (ASO) candidates targeting SARS-CoV-2 genomic RNA were designed. High-scored ASOs with a high potential to inhibit SARS-CoV-2 replication and transcription by inducing cleavage of the viral genomic were determined among ASO candidates. For the future, those promising ASOs can be synthesized followed by required modifications and test on SARS-CoV-2 infected Vero cells to screen their efficacy for the treatment of SARS-CoV-2 infected patients.
Keywords	Biochemistry ; Bioinformatics and Computational Biology ; Chemical Biology ; Drug Discovery and Drug Delivery Systems ; antisense oligonucleotides (ASOs) ; antisense RNA therapy ; drug development ; SARS-CoV-2 ; In silico study ; covid19
Subject code	616
Publishing date	2020-09-14T10:05:23Z
Document type	Book ; 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: A Review of Functional Characterization of Single Amino Acid Change Mutations in HNF Transcription Factors in MODY Pathogenesis.

Çubuk, Hasan / Yalçın Çapan, Özlem

The protein journal

2021 Volume 40, Issue 3, Page(s) 348–360

Abstract: Mutations in HNF transcription factor genes cause the most common subtypes of maturity-onset of diabetes of youth (MODY), a monogenic form of diabetes mellitus. Mutations in the HNF1-α, HNF4-α, and HNF1-β genes are primarily considered as the cause of ... ...

Abstract	Mutations in HNF transcription factor genes cause the most common subtypes of maturity-onset of diabetes of youth (MODY), a monogenic form of diabetes mellitus. Mutations in the HNF1-α, HNF4-α, and HNF1-β genes are primarily considered as the cause of MODY3, MODY1, and MODY5 subtypes, respectively. Although patients with different subtypes display similar symptoms, they may develop distinct diabetes-related complications and require different treatments depending on the type of the mutation. Genetic analysis of MODY patients revealed more than 400 missense/nonsense mutations in HNF1-α, HNF4-α, and HNF1-β genes, however only a small portion of them are functionally characterized. Evaluation of nonsense mutations are more direct as they lead to premature stop codons and mostly in mRNA decay or nonfunctional truncated proteins. However, interpretation of the single amino acid change (missense) mutation is not such definite, as effect of the variant may vary depending on the location and also the substituted amino acid. Mutations with benign effect on the protein function may not be the pathologic variant and further genetic testing may be required. Here, we discuss the functional characterization analysis of single amino acid change mutations identified in HNF1-α, HNF4-α, and HNF1-β genes and evaluate their roles in MODY pathogenesis. This review will contribute to comprehend HNF nuclear family-related molecular mechanisms and to develop more accurate diagnosis and treatment based on correct evaluation of pathologic effects of the variants.
MeSH term(s)	Amino Acid Substitution ; Diabetes Mellitus, Type 2/genetics ; Diabetes Mellitus, Type 2/metabolism ; Hepatocyte Nuclear Factor 1-alpha/genetics ; Hepatocyte Nuclear Factor 1-alpha/metabolism ; Hepatocyte Nuclear Factor 1-beta/genetics ; Hepatocyte Nuclear Factor 1-beta/metabolism ; Hepatocyte Nuclear Factor 4/genetics ; Hepatocyte Nuclear Factor 4/metabolism ; Humans ; Mutation, Missense ; RNA Stability
Chemical Substances	HNF1A protein, human ; HNF1B protein, human ; HNF4A protein, human ; Hepatocyte Nuclear Factor 1-alpha ; Hepatocyte Nuclear Factor 4 ; Hepatocyte Nuclear Factor 1-beta (138674-15-4)
Language	English
Publishing date	2021-05-05
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	2143071-8
ISSN	1875-8355 ; 1572-3887
ISSN (online)	1875-8355
ISSN	1572-3887
DOI	10.1007/s10930-021-09991-8
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Book ; Online: A Promising Strategy Against SARS-CoV-2 Infected Patients

Cubuk, Hasan

Antisense Therapy

2020

Abstract: ... As of July 25-2020, 643,412 people in more than 215 countries have been victims of the new type of coronavirus, SARS-CoV-2. Thereby, there is a huge effort to develop a strategy to treat, and or prevent people from SARS-CoV-2 infection. Those ... ...

Abstract	As of July 25-2020, 643,412 people in more than 215 countries have been victims of the new type of coronavirus, SARS-CoV-2. Thereby, there is a huge effort to develop a strategy to treat, and or prevent people from SARS-CoV-2 infection. Those efforts could be mainly categorized as drug repurposing, anti-SARS-CoV-2 antibodies from people who recovered, and vaccines. However, there is currently no specific treatment available against SARS-CoV-2 infected patients. That`s why many new approaches and ideas are still studied every day for the treatment of SARS-CoV-2 infected patients. Antisense therapy is one of these promising approaches to target SARS-CoV-2 genomic RNA specifically and inhibit its activity upon incorrect viral RNA processing. In this study, antisense oligonucleotide (ASO) candidates targeting SARS-CoV-2 genomic RNA were designed. High-scored ASOs with a high potential to inhibit SARS-CoV-2 replication and transcription by inducing cleavage of the viral genomic were determined among ASO candidates. For the future, those promising ASOs can be synthesized followed by required modifications and test on SARS-CoV-2 infected Vero cells to screen their efficacy for the treatment of SARS-CoV-2 infected patients.
Keywords	covid19
Publisher	American Chemical Society (ACS)
Publishing country	us
Document type	Book ; Online
DOI	10.26434/chemrxiv.12948746
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.

Book ; Online: A Promising Strategy Against SARS-CoV-2 Infected Patients

Cubuk, Hasan

Antisense Therapy

2020

Abstract	As of July 25-2020, 643,412 people in more than 215 countries have been victims of the new type of coronavirus, SARS-CoV-2. Thereby, there is a huge effort to develop a strategy to treat, and or prevent people from SARS-CoV-2 infection. Those efforts could be mainly categorized as drug repurposing, anti-SARS-CoV-2 antibodies from people who recovered, and vaccines. However, there is currently no specific treatment available against SARS-CoV-2 infected patients. That`s why many new approaches and ideas are still studied every day for the treatment of SARS-CoV-2 infected patients. Antisense therapy is one of these promising approaches to target SARS-CoV-2 genomic RNA specifically and inhibit its activity upon incorrect viral RNA processing. In this study, antisense oligonucleotide (ASO) candidates targeting SARS-CoV-2 genomic RNA were designed. High-scored ASOs with a high potential to inhibit SARS-CoV-2 replication and transcription by inducing cleavage of the viral genomic were determined among ASO candidates. For the future, those promising ASOs can be synthesized followed by required modifications and test on SARS-CoV-2 infected Vero cells to screen their efficacy for the treatment of SARS-CoV-2 infected patients.
Keywords	covid19
Publisher	American Chemical Society (ACS)
Publishing country	us
Document type	Book ; Online
DOI	10.26434/chemrxiv.12948746.v1
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: Computational analysis of functional monomers used in molecular imprinting for promising COVID-19 detection.

Cubuk, Hasan / Ozbil, Mehmet / Cakir Hatir, Pinar

Computational & theoretical chemistry

2021 Volume 1199, Page(s) 113215

Abstract: Today, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has recently caused a severe outbreak worldwide. There are still several challenges in COVID-19 diagnoses, such as limited reagents, equipment, and long turnaround times. In this ... ...

Abstract	Today, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has recently caused a severe outbreak worldwide. There are still several challenges in COVID-19 diagnoses, such as limited reagents, equipment, and long turnaround times. In this research, we propose to design molecularly imprinted polymers as a novel approach for the rapid and accurate detection of SARS-CoV-2. For this purpose, we investigated molecular interactions between the target spike protein, receptor-binding domain of the virus, and the common functional monomers used in molecular imprinting by a plethora of computational analyses; sequence analysis, molecular docking, and molecular dynamics (MD) simulations. Our results demonstrated that AMPS and IA monomers gave promising results on the SARS-CoV-2 specific TEIYQAGST sequence for further analysis. Therefore, we propose an epitope approach-based synthesis route for specific recognition of SARS-CoV-2 by using AMPS and IA as functional monomers and the peptide fragment of the TEIYQAGST sequence as a template molecule.
Language	English
Publishing date	2021-03-16
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2587365-9
ISSN	2210-271X
ISSN	2210-271X
DOI	10.1016/j.comptc.2021.113215
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Book ; Online: Comparison of Clinically Approved Molecules on SARS-CoV-2 Drug Target Proteins

Hasan Cubuk / Mehmet Ozbil

A Molecular Docking Study

2020

Abstract: The new type of coronavirus, SARS-CoV-2 has affected more than 6.3 million people worldwide. Since the first day the virus has been spotted in Wuhan, China, there are numerous drug design studies conducted all over the globe. Most of these studies target ...

Abstract	The new type of coronavirus, SARS-CoV-2 has affected more than 6.3 million people worldwide. Since the first day the virus has been spotted in Wuhan, China, there are numerous drug design studies conducted all over the globe. Most of these studies target the receptor-binding domain of spike protein of SASR-CoV-2, which is known to bind human ACE2 receptor and SARS-CoV-2 main protease, vital for the virus’ replication. However, there might be a third target, human furin protease, which cleaves the virus’ S1-S2 domains taking active role in its entry into the host cell. In this study we docked five clinically used drug molecules, favipiravir, hydroxychloroquine, remdesivir, lopinavir, and ritonavir onto three target proteins, receptor binding domain of SARS-CoV-2 spike protein, SARS-CoV-2 main protease, and human furin protease. Results of molecular docking simulations revealed that human furin protease might be targeted against COVID-19. Remdesivir, a nucleic acid derivative, strongly bound to the active site of this protease, suggesting this molecule can be used as a template for designing novel furin protease inhibitorsto fight with the disease. Protein-drug interactions revealed at the molecular level in this study can pave the way for better drug design for each specific target.
Keywords	Bioinformatics and Computational Biology ; Chemical Biology ; Computational Chemistry and Modeling ; Theory - Computational ; Chemoinformatics - Computational Chemistry ; SARS-CoV-2 ; COVID-19 ; Human Furin Protease ; Ritonavir ; Molecular Docking ; covid19
Publishing date	2020-04-13T07:47:08Z
Document type	Book ; 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.

Book ; Online: Comparison of Clinically Approved Molecules on SARS-CoV-2 Drug Target Proteins

Cubuk, Hasan / Ozbil, Mehmet

A Molecular Docking Study

2020

Abstract: ... There are numerous drug design studies conducted all over the globe. Most of these studies target the receptor-binding domain of spike protein of SASR-CoV-2, which is known to bind human ACE2 receptor and SARS-CoV-2 main protease, vital for the virus’ ...

Abstract	There are numerous drug design studies conducted all over the globe. Most of these studies target the receptor-binding domain of spike protein of SASR-CoV-2, which is known to bind human ACE2 receptor and SARS-CoV-2 main protease, vital for the virus’ replication. However, there might be a third target, human furin protease, which cleaves the virus’ S1-S2 domains taking active role in its entry into the host cell. In this study we docked five clinically used drug molecules, favipiravir, hydroxychloroquine, remdesivir, lopinavir, and ritonavir onto three target proteins, receptor binding domain of SARS-CoV-2 spike protein, SARS-CoV-2 main protease, and human furin protease. Computational results clearly showed that all ligands provided higher binding affinities towards furin protease, except hydroxychloroquine and ritonavir yielding the highest binding affinity. This proves that furin protease might be targeted for drug design studies and must be further explored in vitro and in vivo.
Keywords	covid19
Publisher	American Chemical Society (ACS)
Publishing country	us
Document type	Book ; Online
DOI	10.26434/chemrxiv.12090828.v1
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.

Book ; Online: Comparison of Clinically Approved Molecules on SARS-CoV-2 Drug Target Proteins

Cubuk, Hasan / Ozbil, Mehmet

A Molecular Docking Study

2020

Abstract: ... The new type of coronavirus, SARS-CoV-2 has affected more than 6.3 million people worldwide. Since the first day the virus has been spotted in Wuhan, China, there are numerous drug design studies conducted all over the globe. Most of these studies ... ...

Abstract	The new type of coronavirus, SARS-CoV-2 has affected more than 6.3 million people worldwide. Since the first day the virus has been spotted in Wuhan, China, there are numerous drug design studies conducted all over the globe. Most of these studies target the receptor-binding domain of spike protein of SASR-CoV-2, which is known to bind human ACE2 receptor and SARS-CoV-2 main protease, vital for the virus’ replication. However, there might be a third target, human furin protease, which cleaves the virus’ S1-S2 domains taking active role in its entry into the host cell. In this study we docked five clinically used drug molecules, favipiravir, hydroxychloroquine, remdesivir, lopinavir, and ritonavir onto three target proteins, receptor binding domain of SARS-CoV-2 spike protein, SARS-CoV-2 main protease, and human furin protease. Results of molecular docking simulations revealed that human furin protease might be targeted against COVID-19. Remdesivir, a nucleic acid derivative, strongly bound to the active site of this protease, suggesting this molecule can be used as a template for designing novel furin protease inhibitorsto fight with the disease. Protein-drug interactions revealed at the molecular level in this study can pave the way for better drug design for each specific target.
Keywords	covid19
Publisher	American Chemical Society (ACS)
Publishing country	us
Document type	Book ; Online
DOI	10.26434/chemrxiv.12090828.v2
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.

To top

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

Full text online

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

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

Full text online

More links

Kategorien

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