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Article ; Online: Delineation of the CENP-LN sub-complex dissociation mechanism upon multisite phosphorylation during mitosis.

Durojaye, Olanrewaju Ayodeji

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–19

Abstract: Phosphorylation is the most prevalent form of regulation in cells, organizing virtually all cellular functions, including survival, motility, differentiation, proliferation, and metabolism. This regulatory function has been largely conserved from the ... ...

Abstract	Phosphorylation is the most prevalent form of regulation in cells, organizing virtually all cellular functions, including survival, motility, differentiation, proliferation, and metabolism. This regulatory function has been largely conserved from the primitive single-cell to the more complex multicellular organisms. More than a third of proteins in eukaryotes are phosphorylated, and essentially every class of protein undergoes regulation by phosphorylation. A decline in the cellular level of CENP-L and CENP-N (components of the constitutive centromere associated network) has earlier been reported and linked to cyclin-dependent kinase (CDK) phosphorylation upon transition into mitosis. Given the importance of posttranslational modifications in cell cycle regulation, mechanistic comprehension of the impact of phosphorylation on both proteins (CENP-L and CENP-N) is of high significance. Through the application of diverse computational analytical techniques, including atomistic molecular dynamics simulations, the mechanism of kinetochore mis-localization and dissociation of the CENP-LN sub-complex in mitosis was delineated. We showed that the phosphorylation of both components of the sub-complex induces global conformational destabilizing effects on the proteins, combined with changes in the electrostatic potential and increase in steric clashes around the protein-protein interaction interface. This, consistent with earlier experimental reports, suggest that the multisite phosphorylation of the CENP-LN sub-complex plays a crucial role in the regulation of cell division.Communicated by Ramaswamy H. Sarma.
Language	English
Publishing date	2023-08-22
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2249101
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Article: Intracellular proteome compartmentalization: a biotin ligase-based proximity labeling approach.

Durojaye, Olanrewaju Ayodeji

Cell & bioscience

2021 Volume 11, Issue 1, Page(s) 165

Abstract: Specialized biological processes occur in different regions and organelles of the cell. Additionally, the function of proteins correlate greatly with their interactions and subcellular localization. Understanding the mechanism underlying the specialized ... ...

Abstract	Specialized biological processes occur in different regions and organelles of the cell. Additionally, the function of proteins correlate greatly with their interactions and subcellular localization. Understanding the mechanism underlying the specialized functions of cellular structures therefore requires a detailed identification of proteins within spatially defined domains of the cell. Furthermore, the identification of interacting proteins is also crucial for the elucidation of the underlying mechanism of complex cellular processes. Mass spectrometry methods have been utilized systematically for the characterization of the proteome of isolated organelles and protein interactors purified through affinity pull-down or following crosslinking. However, the available methods of purification have limited these approaches, as it is difficult to derive intact organelles of high purity in many circumstances. Furthermore, contamination that leads to the identification of false positive is widespread even when purification is possible. Here, we present a highlight of the BioID proximity labeling approach which has been used to effectively characterize the proteomic composition of several cellular compartments. In addition, an observed limitation of this method based on proteomic spatiotemporal dynamics, was also discussed.
Language	English
Publishing date	2021-08-23
Publishing country	England
Document type	Journal Article
ZDB-ID	2593367-X
ISSN	2045-3701
ISSN	2045-3701
DOI	10.1186/s13578-021-00666-6
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Article ; Online: MasitinibL shows promise as a drug-like analog of masitinib that elicits comparable SARS-Cov-2 3CLpro inhibition with low kinase preference.

Durojaye, Olanrewaju Ayodeji / Okoro, Nkwachukwu Oziamara / Odiba, Arome Solomon / Nwanguma, Bennett Chima

Scientific reports

2023 Volume 13, Issue 1, Page(s) 6972

Abstract: SARS-CoV-2 infection has led to several million deaths worldwide and ravaged the economies of many countries. Hence, developing therapeutics against SARS-CoV-2 remains a core priority in the fight against COVID-19. Most of the drugs that have received ... ...

Abstract	SARS-CoV-2 infection has led to several million deaths worldwide and ravaged the economies of many countries. Hence, developing therapeutics against SARS-CoV-2 remains a core priority in the fight against COVID-19. Most of the drugs that have received emergency use authorization for treating SARS-CoV-2 infection exhibit a number of limitations, including side effects and questionable efficacy. This challenge is further compounded by reinfection after vaccination and the high likelihood of mutations, as well as the emergence of viral escape mutants that render SARS-CoV-2 spike glycoprotein-targeting vaccines ineffective. Employing de novo drug synthesis or repurposing to discover broad-spectrum antivirals that target highly conserved pathways within the viral machinery is a focus of current research. In a recent drug repurposing study, masitinib, a clinically safe drug against the human coronavirus OC43 (HCoV-OC43), was identified as an antiviral agent with effective inhibitory activity against the SARS-CoV-2 3CLpro. Masitinib is currently under clinical trial in combination with isoquercetin in hospitalized patients (NCT04622865). Nevertheless, masitinib has kinase-related side effects; hence, the development of masitinib analogs with lower anti-tyrosine kinase activity becomes necessary. In this study, in an attempt to address this limitation, we executed a comprehensive virtual workflow in silico to discover drug-like compounds matching selected pharmacophore features in the SARS-CoV-2 3CLpro-bound state of masitinib. We identified a novel lead compound, "masitinibL", a drug-like analog of masitinib that demonstrated strong inhibitory properties against the SARS-CoV-2 3CLpro. In addition, masitinibL further displayed low selectivity for tyrosine kinases, which strongly suggests that masitinibL is a highly promising therapeutic that is preferable to masitinib.
MeSH term(s)	Humans ; Antiviral Agents/pharmacology ; Antiviral Agents/metabolism ; COVID-19 ; SARS-CoV-2/metabolism ; Thiazoles
Chemical Substances	Antiviral Agents ; masitinib (M59NC4E26P) ; Thiazoles ; 3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-)
Language	English
Publishing date	2023-04-28
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/s41598-023-33024-2
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Article: CHAPERON

Yekeen, Abeeb Abiodun / Durojaye, Olanrewaju Ayodeji / Idris, Mukhtar Oluwaseun / Muritala, Hamdalat Folake / Arise, Rotimi Olusanya

Computational and structural biotechnology journal

2023 Volume 21, Page(s) 4849–4858

Abstract: Molecular dynamics (MD) simulation is a powerful computational tool used in biomolecular studies to investigate the dynamics, energetics, and interactions of a wide range of biological systems at the atomic level. GROMACS is a widely used free and open- ... ...

Abstract	Molecular dynamics (MD) simulation is a powerful computational tool used in biomolecular studies to investigate the dynamics, energetics, and interactions of a wide range of biological systems at the atomic level. GROMACS is a widely used free and open-source biomolecular MD simulation software recognized for its efficiency, accuracy, and extensive range of simulation options. However, the complexity of setting up, running, and analyzing MD simulations for diverse systems often poses a significant challenge, requiring considerable time, effort, and expertise. Here, we introduce CHAPERON
Language	English
Publishing date	2023-09-28
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2694435-2
ISSN	2001-0370
ISSN	2001-0370
DOI	10.1016/j.csbj.2023.09.024
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Article ; Online: Characterization of the SARS-CoV-2 coronavirus X4-like accessory protein.

Durojaye, Olanrewaju Ayodeji / Okoro, Nkwachukwu Oziamara / Odiba, Arome Solomon

The Egyptian journal of medical human genetics

2021 Volume 22, Issue 1, Page(s) 48

Abstract: Background: The novel coronavirus SARS-CoV-2 is currently a global threat to health and economies. Therapeutics and vaccines are in rapid development; however, none of these therapeutics are considered as absolute cure, and the potential to mutate makes ...

Abstract	Background: The novel coronavirus SARS-CoV-2 is currently a global threat to health and economies. Therapeutics and vaccines are in rapid development; however, none of these therapeutics are considered as absolute cure, and the potential to mutate makes it necessary to find therapeutics that target a highly conserved regions of the viral structure. Results: In this study, we characterized an essential but poorly understood coronavirus accessory X4 protein, a core and stable component of the SARS-CoV family. Sequence analysis shows a conserved ~ 90% identity between the SARS-CoV-2 and previously characterized X4 protein in the database. QMEAN Conclusions: The protein data obtained from this study provides robust information for further in vitro and in vivo experiment, targeted at devising therapeutics against the virus. Phylogenetic analysis further supports previous evidence that the SARS-CoV-2 is positioned with the SL-CoVZC45, BtRs-BetaCoV/YN2018B and the RS4231 Bat SARS-like corona viruses.
Language	English
Publishing date	2021-05-08
Publishing country	Egypt
Document type	Journal Article
ZDB-ID	2515357-2
ISSN	2090-2441 ; 2090-2441
ISSN (online)	2090-2441
ISSN	2090-2441
DOI	10.1186/s43042-021-00160-1
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Article ; Online: Investigation of the MDM2-binding potential of de novo designed peptides using enhanced sampling simulations.

Durojaye, Olanrewaju Ayodeji / Yekeen, Abeeb Abiodun / Idris, Mukhtar Oluwaseun / Okoro, Nkwachukwu Oziamara / Odiba, Arome Solomon / Nwanguma, Bennett Chima

International journal of biological macromolecules

2024 , Page(s) 131840

Abstract: The tumor suppressor p53 plays a crucial role in cellular responses to various stresses, regulating key processes such as apoptosis, senescence, and DNA repair. Dysfunctional p53, prevalent in approximately 50 % of human cancers, contributes to tumor ... ...

Abstract	The tumor suppressor p53 plays a crucial role in cellular responses to various stresses, regulating key processes such as apoptosis, senescence, and DNA repair. Dysfunctional p53, prevalent in approximately 50 % of human cancers, contributes to tumor development and resistance to treatment. This study employed deep learning-based protein design and structure prediction methods to identify novel high-affinity peptide binders (Pep1 and Pep2) targeting MDM2, with the aim of disrupting its interaction with p53. Extensive all-atom molecular dynamics simulations highlighted the stability of the designed peptide in complex with the target, supported by several structural analyses, including RMSD, RMSF, Rg, SASA, PCA, and free energy landscapes. Using the steered molecular dynamics and umbrella sampling simulations, we elucidate the dissociation dynamics of p53, Pep1, and Pep2 from MDM2. Notable differences in interaction profiles were observed, emphasizing the distinct dissociation patterns of each peptide. In conclusion, the results of our umbrella sampling simulations suggest Pep1 as a higher-affinity MDM2 binder compared to p53 and Pep2, positioning it as a potential inhibitor of the MDM2-p53 interaction. Using state-of-the-art protein design tools and advanced MD simulations, this study provides a comprehensive framework for rational in silico design of peptide binders with therapeutic implications in disrupting MDM2-p53 interactions for anticancer interventions.
Language	English
Publishing date	2024-04-26
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.2024.131840
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Article ; Online: Gene therapy in PIDs, hemoglobin, ocular, neurodegenerative, and hemophilia B disorders.

Odiba, Arome Solomon / Okoro, Nkwachukwu Oziamara / Durojaye, Olanrewaju Ayodeji / Wu, Yanjun

Open life sciences

2021 Volume 16, Issue 1, Page(s) 431–441

Abstract: A new approach is adopted to treat primary immunodeficiency disorders, such as the severe combined immunodeficiency (SCID; e.g., adenosine deaminase SCID [ADA-SCID] and IL-2 receptor X-linked severe combined immunodeficiency [SCID-X1]). The success, ... ...

Abstract	A new approach is adopted to treat primary immunodeficiency disorders, such as the severe combined immunodeficiency (SCID; e.g., adenosine deaminase SCID [ADA-SCID] and IL-2 receptor X-linked severe combined immunodeficiency [SCID-X1]). The success, along with the feasibility of gene therapy, is undeniable when considering the benefits recorded for patients with different classes of diseases or disorders needing treatment, including SCID-X1 and ADA-SCID, within the last two decades. β-Thalassemia and sickle cell anemia are two prominent monogenic blood hemoglobin disorders for which a solution has been sought using gene therapy. For instance, transduced autologous CD34+ HSCs via a self-inactivating (SIN)-Lentivirus (LV) coding for a functional copy of the β-globin gene has become a feasible procedure. adeno-associated virus (AAV) vectors have found application in ocular gene transfer in retinal disease gene therapy (e.g., Leber's congenital amaurosis type 2), where no prior treatment existed. In neurodegenerative disorders, successes are now reported for cases involving metachromatic leukodystrophy causing severe cognitive and motor damage. Gene therapy for hemophilia also remains a viable option because of the amount of cell types that are capable of synthesizing biologically active FVIII and FIX following gene transfer using AAV vectors
Language	English
Publishing date	2021-05-03
Publishing country	Poland
Document type	Journal Article ; Review
ZDB-ID	2817958-4
ISSN	2391-5412 ; 2391-5412
ISSN (online)	2391-5412
ISSN	2391-5412
DOI	10.1515/biol-2021-0033
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Article: A New Variant of Mutational and Polymorphic Signatures in the

Odiba, Arome Solomon / Durojaye, Olanrewaju Ayodeji / Ezeonu, Ifeoma Maureen / Mgbeahuruike, Anthony Christian / Nwanguma, Bennett Chima

Infection and drug resistance

2022 Volume 15, Page(s) 3111–3133

Abstract: Background: Resistance to antifungal drugs for treating : Materials and methods: Classical methods were employed to characterize clinical isolates sampled from women and dogs of reproductive age. For fluconazole efficacy studies, CLSI guidelines on ... ...

Abstract	Background: Resistance to antifungal drugs for treating Materials and methods: Classical methods were employed to characterize clinical isolates sampled from women and dogs of reproductive age. For fluconazole efficacy studies, CLSI guidelines on drug susceptibility testing were used. To understand the susceptibility pattern, various molecular and structural analytic approaches, including sequencing, in silico site-directed mutagenesis, and protein-ligand profiling, were applied to the Results: The following Conclusion: Taken together, our results showed new mutations in the heme-binding pocket of caCYP51 that explain the resistance to fluconazole exhibited by the
Language	English
Publishing date	2022-06-17
Publishing country	New Zealand
Document type	Journal Article
ZDB-ID	2494856-1
ISSN	1178-6973
ISSN	1178-6973
DOI	10.2147/IDR.S360973
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Article ; Online: Oral cavity infection by the SARS-CoV-2: emphasizing the essence of masking and peptide therapeutics.

Ibiang, Glory Omini / Malachi, Joseph / Ibiang, Mercy Omini / Chukwudi, Daniel Kenechi / Durojaye, Olanrewaju Ayodeji

The Egyptian journal of medical human genetics

2022 Volume 23, Issue 1, Page(s) 1

Abstract: The SARS-CoV-2 has infected many people globally with the ravaging COVID-19; a disease, which has become challenging for every aspect of modern healthcare. The saliva and oral mucosa are sites of high risk for increased viral loads, and aside from the ... ...

Abstract	The SARS-CoV-2 has infected many people globally with the ravaging COVID-19; a disease, which has become challenging for every aspect of modern healthcare. The saliva and oral mucosa are sites of high risk for increased viral loads, and aside from the usual epithelial functions like lining and protection, the oral mucosa is also specialized for crucial functions, such as secretion, mastication, sensory perception, and taste perception. The human ACE2 receptor has been extensively studied for its essential role in the regulation of blood pressure homeostasis. However, scRNA-Seq studies have revealed high expression levels of the protein in keratinized epithelial surfaces of the oral cavity. The SARS-CoV-2 have access to the host's body by binding to the ACE2 receptor, leading to the cleavage and major conformational changes in the viral spike glycoprotein for the release of its nucleocapsid into the cellular cytoplasm. This proteolytic cleavage is carried out by the TMPRSS2 and cathepsin L. In this study, we harnessed the information from the binding interface of TMPRSS2 and PAI-1 (a protease inhibitor known to inhibit the TMPRSS2 and several other proteases) to design a potential therapeutic peptide for the inhibition of the TMPRSS2, while also emphasizing the need for preventive masking. Supplementary information: The online version contains supplementary material available at 10.1186/s43042-022-00213-z.
Language	English
Publishing date	2022-01-10
Publishing country	Egypt
Document type	Journal Article
ZDB-ID	2515357-2
ISSN	2090-2441 ; 2090-2441
ISSN (online)	2090-2441
ISSN	2090-2441
DOI	10.1186/s43042-022-00213-z
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Article ; Online: Gene therapy in PIDs, hemoglobin, ocular, neurodegenerative, and hemophilia B disorders

Odiba Arome Solomon / Okoro Nkwachukwu Oziamara / Durojaye Olanrewaju Ayodeji / Wu Yanjun

Open Life Sciences, Vol 16, Iss 1, Pp 431-

2021 Volume 441

Abstract	A new approach is adopted to treat primary immunodeficiency disorders, such as the severe combined immunodeficiency (SCID; e.g., adenosine deaminase SCID [ADA-SCID] and IL-2 receptor X-linked severe combined immunodeficiency [SCID-X1]). The success, along with the feasibility of gene therapy, is undeniable when considering the benefits recorded for patients with different classes of diseases or disorders needing treatment, including SCID-X1 and ADA-SCID, within the last two decades. β-Thalassemia and sickle cell anemia are two prominent monogenic blood hemoglobin disorders for which a solution has been sought using gene therapy. For instance, transduced autologous CD34+ HSCs via a self-inactivating (SIN)-Lentivirus (LV) coding for a functional copy of the β-globin gene has become a feasible procedure. adeno-associated virus (AAV) vectors have found application in ocular gene transfer in retinal disease gene therapy (e.g., Leber’s congenital amaurosis type 2), where no prior treatment existed. In neurodegenerative disorders, successes are now reported for cases involving metachromatic leukodystrophy causing severe cognitive and motor damage. Gene therapy for hemophilia also remains a viable option because of the amount of cell types that are capable of synthesizing biologically active FVIII and FIX following gene transfer using AAV vectors in vivo to correct hemophilia B (FIX deficiency), and it is considered an ideal target, as proven in preclinical studies. Recently, the clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 gene-editing tool has taken a center stage in gene therapy research and is reported to be efficient and highly precise. The application of gene therapy to these areas has pushed forward the therapeutic clinical application.
Keywords	clinical trials ; gene therapy ; hemoglobin ; hemophilia b ; neurodegenerative ; ocular ; Biology (General) ; QH301-705.5
Subject code	610
Language	English
Publishing date	2021-05-01T00:00:00Z
Publisher	De Gruyter
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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