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Article: An In Silico Functional Analysis of Non-Synonymous Single-Nucleotide Polymorphisms of Bovine

Ogun, Oluwamayowa Joshua / Soremekun, Opeyemi S / Thaller, Georg / Becker, Doreen

2023 Volume 12, Issue 4

Abstract: The sugar molecule N-glycolylneuraminic acid (Neu5Gc) is one of the most common sialic acids discovered in mammals. Cytidine monophospho-N-acetylneuraminic acid hydroxylase (CMAH) catalyses the conversion of N-acetylneuraminic acid (Neu5Ac) to Neu5Gc, ... ...

Abstract	The sugar molecule N-glycolylneuraminic acid (Neu5Gc) is one of the most common sialic acids discovered in mammals. Cytidine monophospho-N-acetylneuraminic acid hydroxylase (CMAH) catalyses the conversion of N-acetylneuraminic acid (Neu5Ac) to Neu5Gc, and it is encoded by the
Language	English
Publishing date	2023-04-13
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2695572-6
ISSN	2076-0817
ISSN	2076-0817
DOI	10.3390/pathogens12040591
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Article ; Online: Update and Potential Opportunities in CBP [Cyclic Adenosine Monophosphate (cAMP) Response Element-Binding Protein (CREB)-Binding Protein] Research Using Computational Techniques.

Akinsiku, Oluwayimika E / Soremekun, Opeyemi S / Soliman, Mahmoud E S

The protein journal

2021 Volume 40, Issue 1, Page(s) 19–27

Abstract: CBP [cyclic adenosine monophosphate (cAMP) response element-binding protein (CREB)-binding protein] is one of the most researched proteins for its therapeutic function. Several studies have identified its vast functions and interactions with other ... ...

Abstract	CBP [cyclic adenosine monophosphate (cAMP) response element-binding protein (CREB)-binding protein] is one of the most researched proteins for its therapeutic function. Several studies have identified its vast functions and interactions with other transcription factors to initiate cellular signals of survival. In cancer and other diseases such as Alzheimer's, Rubinstein-taybi syndrome, and inflammatory diseases, CBP has been implicated and hence an attractive target in drug design and development. In this review, we explore the various computational techniques that have been used in CBP research, furthermore we identified computational gaps that could be explored to facilitate the development of highly therapeutic CBP inhibitors.
MeSH term(s)	Alzheimer Disease/drug therapy ; Alzheimer Disease/genetics ; Alzheimer Disease/metabolism ; Alzheimer Disease/pathology ; Antineoplastic Agents/chemistry ; Antineoplastic Agents/therapeutic use ; Binding Sites ; CREB-Binding Protein/antagonists & inhibitors ; CREB-Binding Protein/chemistry ; CREB-Binding Protein/genetics ; CREB-Binding Protein/metabolism ; Cyclic AMP/chemistry ; Cyclic AMP/metabolism ; Enzyme Inhibitors/chemistry ; Enzyme Inhibitors/therapeutic use ; Humans ; Neoplasms/drug therapy ; Neoplasms/genetics ; Neoplasms/metabolism ; Neoplasms/pathology ; Neuroprotective Agents/chemistry ; Neuroprotective Agents/therapeutic use ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Interaction Mapping ; Protein Structure, Secondary ; Response Elements ; Rubinstein-Taybi Syndrome/drug therapy ; Rubinstein-Taybi Syndrome/genetics ; Rubinstein-Taybi Syndrome/metabolism ; Rubinstein-Taybi Syndrome/pathology
Chemical Substances	Antineoplastic Agents ; Enzyme Inhibitors ; Neuroprotective Agents ; Cyclic AMP (E0399OZS9N) ; CREB-Binding Protein (EC 2.3.1.48) ; CREBBP protein, human (EC 2.3.1.48)
Language	English
Publishing date	2021-01-04
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2143071-8
ISSN	1875-8355 ; 1572-3887
ISSN (online)	1875-8355
ISSN	1572-3887
DOI	10.1007/s10930-020-09951-8
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Article: Identification and classification of differentially expressed genes reveal potential molecular signature associated with SARS-CoV-2 infection in lung adenocarcinomal cells.

Soremekun, Opeyemi S / Omolabi, Kehinde F / Soliman, Mahmoud E S

Informatics in medicine unlocked

2020 Volume 20, Page(s) 100384

Abstract: Genomic techniques such as next-generation sequencing and microarrays have facilitated the identification and classification of molecular signatures inherent in cells upon viral infection, for possible therapeutic targets. Therefore, in this study, we ... ...

Abstract	Genomic techniques such as next-generation sequencing and microarrays have facilitated the identification and classification of molecular signatures inherent in cells upon viral infection, for possible therapeutic targets. Therefore, in this study, we performed a differential gene expression analysis, pathway enrichment analysis, and gene ontology on RNAseq data obtained from SARS-CoV-2 infected A549 cells. Differential expression analysis revealed that 753 genes were up-regulated while 746 down-regulated. SNORA81, OAS2, SYCP2, LOC100506985, and SNORD35B are the top 5 upregulated genes upon SARS-Cov-2 infection. Expectedly, these genes have been implicated in the immune response to viral assaults. In the Ontology of protein classification, a high percentage of the genes are classified as Gene-specific transcriptional regulator, metabolite interconversion enzyme, and Protein modifying enzymes. Twenty pathways with P-value lower than 0.05 were enriched in the up-regulated genes while 18 pathways are enriched in the down-regulated DEGs. The toll-like receptor signalling pathway is one of the major pathways enriched. This pathway plays an important role in the innate immune system by identifying the pathogen-associated molecular signature emanating from various microorganisms. Taken together, our results present a novel understanding of genes and corresponding pathways upon SARS-Cov-2 infection, and could facilitate the identification of novel therapeutic targets and biomarkers in the treatment of COVID-19.
Keywords	covid19
Language	English
Publishing date	2020-06-23
Publishing country	England
Document type	Journal Article
ISSN	2352-9148
ISSN	2352-9148
DOI	10.1016/j.imu.2020.100384
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Article ; Online: From a Computational Perspective: Elucidating the Neurotherapeutic and Inhibitory properties of LRRK2 Kinase Domain by a benzothiazole-based compound.

Subair, Temitayo I / Soremekun, Opeyemi S / Olotu, Fisayo A / Soliman, Mahmoud E S

Current pharmaceutical biotechnology

2022

Abstract: Background: Parkinson's disease (PD) is one of the most prominent neurodegenerative diseases hence the continual search for viable and effective treatment options. The pathogeny of PD is driven by many key proteins among which is the recently identified ...

Abstract	Background: Parkinson's disease (PD) is one of the most prominent neurodegenerative diseases hence the continual search for viable and effective treatment options. The pathogeny of PD is driven by many key proteins among which is the recently identified Leucine-rich repeated kinase 2 (LRRK2). Going forward, the onus lies on identifying small-molecule inhibitors that can halt its pathogenic involvement, and, importantly, possess the capacity to cross the blood-brain barrier (BBB). Although several compounds have been identified over the past decade for their potencies, a major limitation remains the inability of the majority to cross the blood-brain barrier (BBB). A novel series of benzothiazole-based compounds with varying LRRK2 inhibitory activities were recently synthesized, with one compound 14 (CPD14) that notably inhibited LRRK2 and promoted neuronal progenitor proliferation. Methods: Here, we implemented molecular modelling and computational simulation methods to characterize CPD14 inhibitory mechanisms and dynamics against LRRK2. More so, we employed pharmacokinetic parameters to evaluate the biological activity and CNS-suitability of CPD14. Results: Molecular dynamics evaluation revealed that CPD14 elicited disruptive effects on the secondary structure of LRRK2, including its catalytic kinase domain. Interaction analyses at the binding site further revealed crucial residues for the affinity binding and stability of CPD14, further supported by a highly favorable binding energy (ΔG). Pharmacokinetic predictions revealed the CNS-suitability of CPD14 based on its adherence to Lipinski's rule of 5 for neurogenic compounds. Also, CPD14 exhibited inhibitory tendencies against transcription proteins such as signal transducer and activation transcription (STAT) protein and STAT3; complementary mechanisms that could account for its in vitro potency. Conclusion: These findings, taken together, will aid the pharmacological and pharmacokinetic optimization of novel LRRK2 inhibitors for the treatment of PD.
Language	English
Publishing date	2022-05-23
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2132197-8
ISSN	1873-4316 ; 1389-2010
ISSN (online)	1873-4316
ISSN	1389-2010
DOI	10.2174/1389201023666220523153206
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Article ; Online: From genomic variation to protein aberration: Mutational analysis of single nucleotide polymorphism present in ULBP6 gene and implication in immune response.

Soremekun, Opeyemi S / Soliman, Mahmoud E S

Computers in biology and medicine

2019 Volume 111, Page(s) 103354

Abstract: Background: Genetic polymorphisms have been identified as one of the underlying factors in disease pathogenesis and drug resistance since they account for protein dysfunctionality, or in some cases, aberrancy. This explains the high degree of inactivity ...

Abstract	Background: Genetic polymorphisms have been identified as one of the underlying factors in disease pathogenesis and drug resistance since they account for protein dysfunctionality, or in some cases, aberrancy. This explains the high degree of inactivity that characterizes the polymorphic variants of ULBP6 binding protein, which in turn disrupts its primary interaction with human Natural Killer Group 2-member D (NKG2D) and accounts for an impediment to immuno-surveillance. The possible identification of deleterious non-synonymous Single Nucleotide Polymorphisms (nsSNPs) present in the ULBP6 gene is essential for the development of novel gene therapies to prevent the translation of dysfunctional protein variants. Methods/results: In this study, for the first time, we employed an SNP-informatics approach (SNPs retrieval, pathogenic/mutational analysis, phenotypic analysis, and structural analysis) and molecular dynamics techniques to identify and characterize undesirable SNPs coupled with their impact on ULBP6 structural activities relative to dysfunctionality. V52F was predictively pathogenic amongst SNPs studied. Conformational and dynamic studies revealed that in comparison to wildtype ULBP6 (ULBP6 Conclusion: This study provides a workable paradigm for investigating pathological nsSNPS using computational platforms which findings present ULBP6
MeSH term(s)	Computational Biology ; DNA Mutational Analysis ; Humans ; Membrane Proteins/chemistry ; Membrane Proteins/genetics ; Membrane Proteins/immunology ; Membrane Proteins/metabolism ; Molecular Dynamics Simulation ; Polymorphism, Single Nucleotide/genetics ; Polymorphism, Single Nucleotide/physiology ; Protein Interaction Maps
Chemical Substances	Membrane Proteins ; RAET1L protein, human
Language	English
Publishing date	2019-07-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2019.103354
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Article ; Online: Delving into the Characteristic Features of "Menace" Mycobacterium tuberculosis Homologs: A Structural Dynamics and Proteomics Perspectives.

Adewumi, Adeniyi T / Ramharack, Pritika / Soremekun, Opeyemi S / Soliman, Mahmoud E S

The protein journal

2020 Volume 39, Issue 2, Page(s) 118–132

Abstract: The global increase in the morbidity/mortality rate of Mycobacterial infections, predominantly renascent tuberculosis, leprosy, and Buruli ulcers have become worrisome over the years. More challenging is the incidence of resistance mediated by mutant ... ...

Abstract	The global increase in the morbidity/mortality rate of Mycobacterial infections, predominantly renascent tuberculosis, leprosy, and Buruli ulcers have become worrisome over the years. More challenging is the incidence of resistance mediated by mutant Mycobacterium strains against front-line antitubercular drugs. Homologous to all Mycobacteria species is the GlcNAc-6-phosphate deacetylase (NagA) which catalyzes essential amino sugars synthesis required for cell wall architecture, hence, metamorphosing into an important pharmacological target for curtailing virulence and drug-resistance. This study used integrated bioinformatics methods, MD simulations, and DynaMut and PolyPhen2 to; explore unique features, monitor dynamics, and analyze the functional impact of non-synonymous single-nucleotide polymorphisms of the six NagA of most ruinous Mycobacterium species; tuberculosis (Mtb), smegmatis (MS), marinum (MM), ulcerans, africanum, and microti respectively. This approach is essential for multi-targeting and could result in the identification of potential polypharmacological antitubercular compounds. Comparative sequential analyses revealed ≤ 50% of the overall structure, including the catalytic Asp267 and reactive Cys131, remained conserved. Interestingly, MS-NagA and MM-NagA possess unique hydrophobic isoleucine (Ile) residues at their active sites in contrast to leucine (Leu) found in other variants. More so, unique to the active sites of the NagA is a 'subunit loop' that covers the active site; probably crucial in binding (entry and exit) mechanisms of targeted NagA inhibitors. Relatively, nsSNP mutations exerted a destabilizing effect on the native NagA conformation. Structural and dynamical insights provided, basically pin-pointed the "Achilles' heel" explorable for the rational drug design of target-specific 'NagA' inhibitors potent against a wide range of mycobacterial diseases.
MeSH term(s)	Amidohydrolases/chemistry ; Amidohydrolases/genetics ; Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Catalytic Domain ; Computational Biology ; Models, Molecular ; Mycobacterium Infections, Nontuberculous/microbiology ; Mycobacterium tuberculosis/genetics ; Nontuberculous Mycobacteria/genetics ; Polymorphism, Single Nucleotide ; Protein Conformation
Chemical Substances	Bacterial Proteins ; Amidohydrolases (EC 3.5.-) ; N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25)
Language	English
Publishing date	2020-03-12
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2143071-8
ISSN	1875-8355 ; 1572-3887
ISSN (online)	1875-8355
ISSN	1572-3887
DOI	10.1007/s10930-020-09890-4
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Article: Exploring the effect of ritonavir and TMC-310911 on SARS-CoV-2 and SARS-CoV main proteases: potential from a molecular perspective.

Soremekun, Opeyemi S / Omolabi, Kehinde F / Adewumi, Adeniyi T / Soliman, Mahmoud Es

Future science OA

2020 Volume 7, Issue 1, Page(s) FSO640

Abstract: Aim: As coronavirus (CoV) disease 2019-associated pneumonia spreads globally, there has been an urgent need to combat the spread and develop vaccines.: Materials & methods: We used an integrated computational algorithm to explore the binding ... ...

Abstract	Aim: As coronavirus (CoV) disease 2019-associated pneumonia spreads globally, there has been an urgent need to combat the spread and develop vaccines. Materials & methods: We used an integrated computational algorithm to explore the binding mechanism of TMC-310911/ritonavir (RVT) with SARS-CoV-2 and SARS-CoV main proteases. Results: RVT and TMC-310911 had favorable interactions with the proteases, and these high interactions are facilitated by some significant residues such as Asn133, Gly195 and Gln192. Our study further implicated two important rings in the structure of RVT as a possible chemical culprit in its therapeutic activity. Conclusion: Although there are conflicting clinical results on the therapeutic potency of RVT in the treatment of coronavirus disease 2019, our findings provided molecular insight into the binding mechanism of TMC-310911 and RVT with SARS-CoV-2 and SARS-CoV main proteases.
Language	English
Publishing date	2020-11-09
Publishing country	England
Document type	Journal Article
ISSN	2056-5623
ISSN	2056-5623
DOI	10.2144/fsoa-2020-0079
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Article ; Online: Structural alterations in the catalytic core of hSIRT2 enzyme predict therapeutic benefits of

Akawa, Oluwole B / Subair, Temitayo I / Soremekun, Opeyemi S / Olotu, Fisayo A / Soliman, Mahmoud E S

RSC advances

2021 Volume 11, Issue 14, Page(s) 8003–8018

Abstract: Recent studies have shown that inhibition of the hSIRT2 enzyme provides favorable effects in neurodegenerative diseases such as Alzheimer's disease. Prenylated xanthone phytochemicals including α-mangostin, β-mangostin and γ-mangostin obtained ... ...

Abstract	Recent studies have shown that inhibition of the hSIRT2 enzyme provides favorable effects in neurodegenerative diseases such as Alzheimer's disease. Prenylated xanthone phytochemicals including α-mangostin, β-mangostin and γ-mangostin obtained from
Language	English
Publishing date	2021-02-18
Publishing country	England
Document type	Journal Article
ISSN	2046-2069
ISSN (online)	2046-2069
DOI	10.1039/d0ra10459k
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Article ; Online: East to West not North-West: Structure-Based Mechanistic Resolution of 8-Hydroxyl Replacement and Resulting Effects on the Activities of Imidazole-Based Heme Oxygenase-1 Inhibitors.

Okunlola, Felix O / Soremekun, Opeyemi S / Olotu, Fisayo A / Soliman, Mahmoud E S

The protein journal

2021 Volume 40, Issue 2, Page(s) 166–174

Abstract: Upregulation of Heme Oxygenase-1 (HO-1) has been widely implicated in cancer growth and chemoresistance. This explains the numerous drug discovery efforts aimed at mitigating its pro-carcinogenic roles till date. In a recent study, two selective azole- ... ...

Abstract	Upregulation of Heme Oxygenase-1 (HO-1) has been widely implicated in cancer growth and chemoresistance. This explains the numerous drug discovery efforts aimed at mitigating its pro-carcinogenic roles till date. In a recent study, two selective azole-based HO-1 inhibitors (Cpd1 and Cpd2) were synthesized, which exhibited differential inhibitory potencies of ~200μm. Interestingly, variations in the affinities of these compounds were determined by their positioning across specific regions of the HO-1 binding domain, pin-pointing a pharmacological interrelationship that remains unresolved. Therefore, in this study, using molecular dynamics simulations and binding free energy calculations, we investigate how dynamical orientations of these compounds influence their binding affinities at the active HO-1 domain. Findings revealed favorable binding for the bromobenzene and imidazole substituents of Cpd1 at the western and eastern regions of the HO-1 active domain. The constituent hydroxyl group was coordinated by residues Asp140 and Arg136 over the simulation period. On the contrary, stable binding of the bromobenzene and imidazole substituents were negated by the optimal orientations of the benzyl substituent, which extended into the northeastern region. These were supported by the displacement of Asp140 and Arg136, crucial for hydrogen bond formation in Cpd1. Also, we observed that Cpd2 exhibited high deviations indicative of an unstable binding relative to Cpd1. This further supports the presumption that Cpd2 was systematically oriented away from the active HO-1 region, a phenomenon that was due to the optimal motions of the benzyl group at the northeastern regions. The highlight of our findings is that the benzyl substituent in Cpd2 elicited negative effects on HO-1, vis a vis, instability, displacement of crucial residues, and low binding energy when compared to Cpd1. Findings pave the way for future drug discovery efforts related to HO-1 inhibition in cancer therapy.
MeSH term(s)	Antineoplastic Agents/chemistry ; Antineoplastic Agents/metabolism ; Drug Discovery ; Enzyme Inhibitors/chemistry ; Enzyme Inhibitors/metabolism ; Heme Oxygenase-1/chemistry ; Heme Oxygenase-1/metabolism ; Humans ; Imidazoles/chemistry ; Imidazoles/metabolism ; Molecular Dynamics Simulation ; Thermodynamics
Chemical Substances	Antineoplastic Agents ; Enzyme Inhibitors ; Imidazoles ; imidazole (7GBN705NH1) ; HMOX1 protein, human (EC 1.14.14.18) ; Heme Oxygenase-1 (EC 1.14.14.18)
Language	English
Publishing date	2021-03-01
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2143071-8
ISSN	1875-8355 ; 1572-3887
ISSN (online)	1875-8355
ISSN	1572-3887
DOI	10.1007/s10930-021-09969-6
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Article ; Online: Prospecting the therapeutic edge of a novel compound (B12) over berberine in the selective targeting of Retinoid X Receptor in colon cancer.

Subair, Temitayo I / Soremekun, Opeyemi S / Olotu, Fisayo A / Soliman, Mahmoud E S

Journal of molecular modeling

2021 Volume 27, Issue 8, Page(s) 231

Abstract: The Retinoid X Receptor (RXR) is an attractive target in the treatment of colon cancer. Different therapeutic binders with high potency have been used to specifically target RXR. Among these compounds is a novel analogue of berberine, B12. We provided ... ...

Abstract	The Retinoid X Receptor (RXR) is an attractive target in the treatment of colon cancer. Different therapeutic binders with high potency have been used to specifically target RXR. Among these compounds is a novel analogue of berberine, B12. We provided structural and molecular insights into the therapeutic activity properties of B12 relative to its parent compound, berberine, using force field estimations and thermodynamic calculations. Upon binding of B12 to RXR, the high instability elicited by RXR was markedly reduced; similar observation was seen in the berberine-bound RXR. However, our analysis revealed that B12 could have a more stabilizing effect on RXR when compared to berberine. Interestingly, the mechanistic behaviour of B12 in the active site of RXR opposed its impact on RXR protein. This disparity could be due to the bond formation and breaking elicited between B12/berberine and the active site residues. We observed that B12 and berberine could induce a disparate conformational change in regions Gly250-Asp258 located on the His-RXRα/LBD domain. Comparatively, the high agonistic and activation potential reported for B12 compared to berberine might be due to its superior binding affinity as evidenced in the thermodynamic estimations. The total affinity for B12 (-25.76 kcal/mol) was contributed by electrostatic interactions from Glu243 and Glu239. Also, Arg371, which plays a crucial role in the activity of RXR, formed a strong hydrogen bond with B12; however, a weak interaction was elicited between Arg371 and berberine. Taken together, our study has shown the RXRα activating potential of B12, and findings from this study could provide a framework in the future design of RXRα binders specifically tailored in the selective treatment of colon cancer.
MeSH term(s)	Berberine/analogs & derivatives ; Berberine/chemistry ; Berberine/therapeutic use ; Catalytic Domain/drug effects ; Colonic Neoplasms/drug therapy ; Colonic Neoplasms/genetics ; Humans ; Hydrogen Bonding/drug effects ; Molecular Targeted Therapy ; Protein Conformation/drug effects ; Retinoid X Receptors/antagonists & inhibitors ; Retinoid X Receptors/genetics ; Thermodynamics
Chemical Substances	Retinoid X Receptors ; Berberine (0I8Y3P32UF)
Language	English
Publishing date	2021-07-26
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1284729-X
ISSN	0948-5023 ; 1610-2940
ISSN (online)	0948-5023
ISSN	1610-2940
DOI	10.1007/s00894-021-04848-4
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