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Artikel ; Online: An immunoinformatics and structural vaccinology approach to design a novel and potent multi-epitope base vaccine targeting Zika virus.

Hakami, Mohammed Ageeli

BMC chemistry

2024 Band 18, Heft 1, Seite(n) 31

Abstract: Zika virus is an infectious virus, that belongs to Flaviviridae family, which is transferred to humans through mosquito vectors and severely threatens human health; but, apart from available resources, no effective and secure vaccine is present against ... ...

Abstract	Zika virus is an infectious virus, that belongs to Flaviviridae family, which is transferred to humans through mosquito vectors and severely threatens human health; but, apart from available resources, no effective and secure vaccine is present against Zika virus, to prevent such infections. In current study, we employed structural vaccinology approach to design an epitope-based vaccine against Zika virus, which is biocompatible, and secure and might trigger an adaptive and innate immune response by using computational approaches. We first retrieved the protein sequence from National Center for Biotechnology Information (NCBI) database and carried out for BLAST P. After BLAST P, predicted protein sequences were shortlisted and checked for allergic features and antigenic properties. Final sequence of Zika virus, with accession number (APO40588.1) was selected based on high antigenic score and non-allergenicity. Final protein sequence used various computational approaches including antigenicity testing, toxicity evaluation, allergenicity, and conservancy assessment to identify superior B-cell and T-cell epitopes. Two B-cell epitopes, five MHC-six MHC-II epitopes and I were used to construct an immunogenic multi-epitope-based vaccine by using suitable linkers. A 50S ribosomal protein was added at N terminal to improve the immunogenicity of vaccine. In molecular docking, strong interactions were presented between constructed vaccine and Toll-like receptor 9 (- 1100.6 kcal/mol), suggesting their possible relevance in the immunological response to vaccine. The molecular dynamics simulations ensure the dynamic and structural stability of constructed vaccine. The results of C-immune simulation revealed that constructed vaccine activate B and T lymphocytes which induce high level of antibodies and cytokines to combat Zika infection. The constructed vaccine is an effective biomarker with non-sensitization, nontoxicity; nonallergic, good immunogenicity, and antigenicity, however, experimental assays are required to verify the results of present study.
Sprache	Englisch
Erscheinungsdatum	2024-02-13
Erscheinungsland	Switzerland
Dokumenttyp	Journal Article
ISSN	2661-801X
ISSN (online)	2661-801X
DOI	10.1186/s13065-024-01132-3
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Mitoxantrone 2HCl's adroit activity against cervical cancer replication and maintenance proteins: a multitargeted approach.

Hakami, Mohammed Ageeli / Hazazi, Ali / Alsulami, Mishal Olayan / Alsaiari, Ahad Amer

Journal of biomolecular structure & dynamics

2024 , Seite(n) 1–14

Abstract: Cervical cancer poses a significant global health challenge, ranking as the fourth most common cancer among women worldwide and resulting in approximately 300,000 deaths yearly, predominantly caused by high-risk human papillomavirus strains (HPV), mainly ...

Abstract	Cervical cancer poses a significant global health challenge, ranking as the fourth most common cancer among women worldwide and resulting in approximately 300,000 deaths yearly, predominantly caused by high-risk human papillomavirus strains (HPV), mainly types 16 and 18. The scenario poses the urgent need of the hour to develop effective treatment strategies that can address the complexity of cervical cancer and multitargeted inhibitor designing that holds promise as it can simultaneously target multiple proteins and pathways involved in its progression and have the potential to enhance treatment efficacy, reduce the likelihood of drug resistance. In this study, we have performed multitargeted molecular docking of FDA-approved drugs against cervical cancer replication and maintenance proteins- Xenopus kinesin-like protein-2 (3KND), cell division cycle protein-20 (4N14), MCM2-histone complex (4UUZ) and MCM6 Minichromosome maintenance (2KLQ) with HTVS, SP and XP algorithms and have obtained the docking and MM\GBSA score ranging from -8.492 to -5.189 Kcal/mol and -58.16 to -39.07 Kcal/mol. Further, the molecular interaction fingerprints identified ALA, THR, SER, ASN, LEU, and ILE were among the most interacted residues, leaning towards hydrophobic and polar amino acids. The pharmacokinetics and DFT of the compound have shown promising results. The complexes were simulated for 100 ns to study the stability by computing the deviation, fluctuations, and intermolecular interactions formed during the simulation. This study produced promising results, satisfying the criteria that Mitoxantrone 2HCl can be a multitargeted inhibitor against cervical cancer proteins-however, experimental validation is a must before human use.Communicated by Ramaswamy H. Sarma.
Sprache	Englisch
Erscheinungsdatum	2024-03-22
Erscheinungsland	England
Dokumenttyp	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2024.2329796
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Structure-based investigation of pyruvate dehydrogenase kinase-3 inhibitory potential of thymoquinone, targeting lung cancer therapy.

Alotaibi, Bader S / Hakami, Mohammed Ageeli / Anwar, Saleha / Mawkili, Wedad / Albaqami, Amirah / Hassan, Md Imtaiyaz

International journal of biological macromolecules

2024 Band 265, Heft Pt 2, Seite(n) 131064

Abstract: Protein kinases are an attractive therapeutic target for cardiovascular, cancer and neurodegenerative diseases. Cancer cells demand energy generation through aerobic glycolysis, surpassing "oxidative phosphorylation" (OXPHOS) in mitochondria. The ... ...

Abstract	Protein kinases are an attractive therapeutic target for cardiovascular, cancer and neurodegenerative diseases. Cancer cells demand energy generation through aerobic glycolysis, surpassing "oxidative phosphorylation" (OXPHOS) in mitochondria. The pyruvate dehydrogenase kinases (PDKs) have many regulatory roles in energy generation balance by controlling the pyruvate dehydrogenase complex. Overexpression of PDKs is associated with the overall survival of cancer. PDK3, an isoform of PDK is highly expressed in various cancer types, is targeted for inhibition in this study. PDK3 has been shown to binds strongly with a natural compound, thymoquinone (TQ), which is known to exhibit anti-cancer potential. Detailed interaction between the PDK3 and TQ was carried out using spectroscopic and docking methods. The overall changes in the protein's structures after TQ binding were estimated by UV-Vis spectroscopy, circular dichroism and fluorescence binding studies. The kinase activity assay was also carried out to see the kinase inhibitory potential of TQ. The enzyme inhibition assay suggested an excellent inhibitory potential of TQ towards PDK3 (IC
Mesh-Begriff(e)	Humans ; Pyruvate Dehydrogenase Acetyl-Transferring Kinase/chemistry ; Protein Serine-Threonine Kinases ; Lung Neoplasms/drug therapy ; Oxidative Phosphorylation ; Benzoquinones
Chemische Substanzen	Pyruvate Dehydrogenase Acetyl-Transferring Kinase ; Protein Serine-Threonine Kinases (EC 2.7.11.1) ; thymoquinone (O60IE26NUF) ; Benzoquinones
Sprache	Englisch
Erscheinungsdatum	2024-03-20
Erscheinungsland	Netherlands
Dokumenttyp	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2024.131064
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Delineated 3-1-BenCarMethInYlPro-Phosphonic Acid's Adroit Activity against Lung Cancer through Multitargeted Docking, MM\GBSA, QM-DFT and Multiscale Simulations.

Hakami, Mohammed Ageeli / Hazazi, Ali / Albloui, Fawaz / Gharib, Amal F / Alsaeedi, Fouzeyyah Ali / Abdulaziz, Osama / Alhazmi, Abdulfattah Y / Alsaiari, Ahad Amer

International journal of molecular sciences

2024 Band 25, Heft 1

Abstract: Lung cancer is a pervasive and challenging disease with limited treatment options, with global health challenges often present with complex molecular profiles necessitating the exploration of innovative therapeutic strategies. Single-target drugs have ... ...

Abstract	Lung cancer is a pervasive and challenging disease with limited treatment options, with global health challenges often present with complex molecular profiles necessitating the exploration of innovative therapeutic strategies. Single-target drugs have shown limited success due to the heterogeneity of this disease. Multitargeted drug designing is imperative to combat this complexity by simultaneously targeting multiple target proteins and pathways, which can enhance treatment efficacy and overcome resistance by addressing the dynamic nature of the disease and stopping tumour growth and spread. In this study, we performed the molecular docking studies of Drug Bank compounds with a multitargeted approach against crucial proteins of lung cancer such as heat shock protein 5 (BIP/GRP78) ATPase, myosin 9B RhoGAP, EYA2 phosphatase inhibitor, RSK4 N-terminal kinase, and collapsin response mediator protein-1 (CRMP-1) using HTVS, SP with XP algorithms, and poses were filtered using MM\GBSA which identified [3-(1-Benzyl-3-Carbamoylmethyl-2-Methyl-1h-Indol-5-Yloxy)-Propyl-]-Phosphonic Acid (3-1-BenCarMethIn YlPro-Phosphonic Acid) (DB02504) as multitargeted drug candidate with docking and MM\GBSA score ranges from -5.83 to -10.66 and -7.56 to -50.14 Kcal/mol, respectively. Further, the pharmacokinetic and QM-based DFT studies have shown complete acceptance results, and interaction fingerprinting reveals that ILE, GLY, VAL, TYR, LEU, and GLN were among the most interacting residues. The 100 ns MD simulation in the SPC water model with NPT ensemble showed stable performance with deviation and fluctuations <2 Å with huge interactions, making it a promising multitargeted drug candidate; however, experimental studies are needed before use.
Mesh-Begriff(e)	Humans ; Lung Neoplasms/drug therapy ; Molecular Docking Simulation ; Adenosine Triphosphatases ; Algorithms ; Endoplasmic Reticulum Chaperone BiP ; Phosphorous Acids
Chemische Substanzen	phosphonic acid (13598-36-2) ; Adenosine Triphosphatases (EC 3.6.1.-) ; Endoplasmic Reticulum Chaperone BiP ; Phosphorous Acids
Sprache	Englisch
Erscheinungsdatum	2024-01-02
Erscheinungsland	Switzerland
Dokumenttyp	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms25010592
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Sakuranetin ameliorates streptozotocin-induced diabetes in rodents by inhibiting caspase-3 activity, modulating hematological parameters, and suppressing inflammatory cytokines: a molecular docking and dynamics study.

Almasoudi, Hassan H / Nahari, Mohammed H / Binshaya, Abdulkarim S / Hakami, Mohammed Ageeli / Alhazmi, Abdulfattah Y / Al Shmrany, Humood / Alqasem, Abdullah / Khan, Farhan R

Journal of biomolecular structure & dynamics

2024 , Seite(n) 1–18

Abstract: Diabetes affects people of all ages, regardless of gender and background. To date, there is no evidence for the effect of sakuranetin against the streptozotocin (STZ)-induced diabetes paradigm. The research was directed to evaluate the antidiabetic ... ...

Abstract	Diabetes affects people of all ages, regardless of gender and background. To date, there is no evidence for the effect of sakuranetin against the streptozotocin (STZ)-induced diabetes paradigm. The research was directed to evaluate the antidiabetic activity of sakuranetin in the STZ model invoking the diabetes-induced disease paradigm. STZ (I.P. 60 mg/kg) is directed to induce type 2 diabetes in experimental rats. Recent research pursued to regulate the anti-diabetic ability of sakuranetin at both 10 and 20 mg/kg in STZ-induced rats. Furthermore, molecular docking research was implemented to evaluate sakuranetin requisite attraction to inflammatory indicators. Various anti-diabetic [(glucose, hemoglobin A1c (HbA1c), and insulin)], lipid profile [triglycerides (TG), total cholesterol (TC), and high-density lipoproteins (HDL)], hematological parameters [Hemoglobin (HGB), packed cell volume (PCV), red blood cells (RBC), mean corpuscular volume (MCV), platelet (PLT), and white blood cells (WBC), pro-inflammatory cytokines [tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), and interleukin-6 (IL-6)], antioxidant level [catalase (CAT), superoxide dismutase (SOD), glutathione (GSH)], lipid oxidation, and caspase-3 were evaluated. Furthermore, molecular docking and dynamics were performed for TNF-α (2AZ5), IL-6 (1ALU), IL-1β (6Y8M), Caspase-3 (1NME) and serum insulin (4IBM) target ligands. Sakuranetin treatment at both doses restored the biochemical parameters i.e. blood glucose, insulin, HbA1c, lipid profile, hematological parameters, pro-inflammatory markers, antioxidant levels, lipid oxidation, and caspase-3 in the context of diabetic rats. It also showed favorable binding affinity on inflammatory markers. Sakuranetin binds to proteins 2AZ5, 1ALU, 6Y8M, 1NME, and 4IBM at -7.489, -6.381, -6.742, -7.202, and -8.166 Kcal/mol, respectively. All of the findings from the molecular dynamics simulations points toward a considerable change in the conformational dynamics of protein upon binding with sakuranetin. The potential use of sakuranetin as an alternative diabetes medication will aid future research as a potent anti-diabetic agent.Communicated by Ramaswamy H. Sarma.
Sprache	Englisch
Erscheinungsdatum	2024-03-09
Erscheinungsland	England
Dokumenttyp	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2024.2325659
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Identification of potential

Alotaibi, Bader S / Hakami, Mohammed Ageeli / Jawaid, Talha / Alshammari, Nawaf / Binsuwaidan, Reem / Adnan, Mohd

Journal of biomolecular structure & dynamics

2023 , Seite(n) 1–12

Abstract: The alarming rise in the rate of antibiotic resistance is a matter of significant concern. DNA gyrase B (GyrB), a critical bacterial enzyme involved in DNA replication, transcription, and recombination, has emerged as a promising target for antibacterial ...

Abstract	The alarming rise in the rate of antibiotic resistance is a matter of significant concern. DNA gyrase B (GyrB), a critical bacterial enzyme involved in DNA replication, transcription, and recombination, has emerged as a promising target for antibacterial agents. Inhibition of GyrB disrupts bacterial DNA replication, leading to cell death, making it an attractive candidate for antibiotic development. Although several classes of antibiotics targeting GyrB are currently in clinical use, the emergence of antibiotic resistance necessitates the exploration of novel inhibitors. In this study, we aimed to identify potential
Sprache	Englisch
Erscheinungsdatum	2023-08-22
Erscheinungsland	England
Dokumenttyp	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2249117
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel: New drug target identification in

Alotaibi, Bader S / Ajmal, Amar / Hakami, Mohammed Ageeli / Mahmood, Arif / Wadood, Abdul / Hu, Junjian

Heliyon

2023 Band 9, Heft 7, Seite(n) e17650

Abstract: ... Vibrio ... ...

Abstract	Vibrio vulnificus
Sprache	Englisch
Erscheinungsdatum	2023-06-26
Erscheinungsland	England
Dokumenttyp	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2023.e17650
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Delineating Pixantrone Maleate's adroit activity against cervical cancer proteins through multitargeted docking-based MM\GBSA, QM-DFT and MD simulation.

Almasoudi, Hassan Hussain / Nahari, Mohammed H / Alhazmi, Abdulfattah Yahya M / Almasabi, Saleh Hussain A / Al-Mansour, Fares Saeed H / Hakami, Mohammed Ageeli

PloS one

2023 Band 18, Heft 12, Seite(n) e0295714

Abstract: Cervical cancer poses a substantial worldwide health challenge, especially in low- and middle-income nations, caused by high-risk types of human papillomavirus. It accounted for a significant percentage of cancer-related deaths among women, particularly ... ...

Abstract	Cervical cancer poses a substantial worldwide health challenge, especially in low- and middle-income nations, caused by high-risk types of human papillomavirus. It accounted for a significant percentage of cancer-related deaths among women, particularly in areas with limited healthcare resources, necessitating innovative therapeutic approaches, and single-targeted studies have produced significant results, with a considerable chance of developing resistance. Therefore, the multitargeted studies can work as a beacon of hope. This study is focused on performing the multitargeted molecular docking of FDA-approved drugs with the three crucial proteins TBK1, DNA polymerase epsilon, and integrin α-V β-8 of cervical cancer. The docking studies using multisampling algorithms HTVS, SP, and XP reveal Pixantrone Maleate (DB06193) as a multitargeted inhibitor with docking scores of -8.147, -8.206 and -7.31 Kcal/mol and pose filtration with MM\GBSA computations with scores -40.55, -33.67, and -37.64 Kcal/mol. We also have performed QM-based DFT and pharmacokinetics studies of the compound and compared it with the standard values, which results in the compound being entirely suitable against cervical cancer proteins. The interaction fingerprints have revealed that PHE, VAL, SER and ALA are the residues among most interactions. We also explore the stability of the multitargeted potential of Pixantrone Maleate through 100ns MD simulations and investigate the RMSD, RMSF and intermolecular interactions between all three proteins-ligand complexes. All computational studies favour Pixantrone Maleate as a multitargeted inhibitor of the TBK1, DNA polymerase epsilon, and integrin α-V β-8 and can be validated experimentally before use.
Mesh-Begriff(e)	Female ; Humans ; Molecular Docking Simulation ; Protein Binding ; Molecular Dynamics Simulation ; Uterine Cervical Neoplasms/drug therapy ; DNA Polymerase II ; Integrins ; Maleates
Chemische Substanzen	pixantrone (F5SXN2KNMR) ; DNA Polymerase II (EC 2.7.7.7) ; Integrins ; Maleates
Sprache	Englisch
Erscheinungsdatum	2023-12-15
Erscheinungsland	United States
Dokumenttyp	Journal Article
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0295714
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel ; Online: Simultaneous Detection of Influenza A/B, Respiratory Syncytial Virus, and SARS-CoV-2 in Nasopharyngeal Swabs by One-Tube Multiplex Reverse Transcription Polymerase Chain Reaction.

Alotaibi, Bader S / Tantry, Bilal Ahmad / Bandy, Altaf / Ahmad, Reyaz / Khursheed, Syed Quibtiya / Ahmad, Arshid / Hakami, Mohammed Ageeli / Shah, Naveed Nazir

Tropical medicine and infectious disease

2023 Band 8, Heft 6

Abstract: The treatment and outcome of respiratory virus infections differ. SARS-CoV-2, as well as other respiratory viruses such as influenza virus (A and B) and respiratory syncytial virus (RSV), require simultaneous, cost-effective, and rapid differential ... ...

Abstract	The treatment and outcome of respiratory virus infections differ. SARS-CoV-2, as well as other respiratory viruses such as influenza virus (A and B) and respiratory syncytial virus (RSV), require simultaneous, cost-effective, and rapid differential detection. We used a gold standard five-target single-step RT-PCR to detect influenza viruses, RSV, and SARS-CoV-2, and this method can be extended to detect influenza virus subtypes. As a result, this five-target single-step RT-PCR method is ideal for differentiating respiratory viruses. The 5' nuclease activity of Taq DNA polymerase is used in the real-time reverse transcription PCR assay. The Taq man fast viral 1-step enzyme is a 4× Master mix and five-target primer probe mix that detects influenza A, influenza B, SARS-CoV-2 ORF1ab, respiratory syncytial viruses A/B and actin. When compared with TaqMan
Sprache	Englisch
Erscheinungsdatum	2023-06-19
Erscheinungsland	Switzerland
Dokumenttyp	Journal Article
ISSN	2414-6366
ISSN (online)	2414-6366
DOI	10.3390/tropicalmed8060326
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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Artikel: In Silico Exploration and Experimental Validation of

Hakami, Mohammed Ageeli / Malak, Nosheen / Khan, Afshan / Ullah, Hidayat / Cossío-Bayúgar, Raquel / Nasreen, Nasreen / Niaz, Sadaf / Khan, Adil / Chen, Chien-Chin

Life (Basel, Switzerland)

2023 Band 13, Heft 10

Abstract: Sarcoptes ... ...

Abstract	Sarcoptes scabiei
Sprache	Englisch
Erscheinungsdatum	2023-10-11
Erscheinungsland	Switzerland
Dokumenttyp	Journal Article
ZDB-ID	2662250-6
ISSN	2075-1729
ISSN	2075-1729
DOI	10.3390/life13102040
Datenquelle	MEDical Literature Analysis and Retrieval System OnLINE

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