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Alghamdi S, Baeissa HM, Azhar Kamal M, Rafeeq MM, Al Zahrani A, Maslum AA, Hakeem IJ, Alazragi RS, Alam Q. Unveiling the multitargeted potency of Sodium Danshensu against cervical cancer: a multitargeted docking-based, structural fingerprinting and molecular dynamics simulation study. J Biomol Struct Dyn 2023:1-13. [PMID: 37599470 DOI: 10.1080/07391102.2023.2248260] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/30/2023] [Indexed: 08/22/2023]
Abstract
Cervical Cancer (CC) is one of the most common types of cancer in women worldwide, with a significant number of deaths reported yearly. Despite the various treatment options available, the high mortality rate associated with CC highlights the need to develop new and effective therapeutic agents. In this study, we have screened the complete prepared FDA library against the Mitotic kinesin-like protein 1, Cyclin B1, DNA polymerase, and MCM10-ID using three glide-based molecular docking algorithms: HTVS, SP and XP to produce a robust calculation. All four proteins are crucial proteins that actively participate in CC development, and inhibiting them together can be a game-changer step for multitargeted drug designing. Our multitargeted screening identified Sodium (Na) Danshensu, a natural FDA-approved phenolic compound of caffeic acid derivatives isolated from Salvia miltiorrhiza. The docking score ranges from -5.892 to -13.103 Kcal/mol, and the screening study was evaluated with the pharmacokinetics and interaction fingerprinting to identify the pattern of interactions that revealed that the compound has bound to the best site it can be fitted to where maximum bonds were created to make the complex stable. The molecular dynamics simulations for 100 ns were then extended to validate the stability of the protein-ligand complexes. The results provide insight into the repurposing, and Na-danshensu exhibited strong binding affinity and stable complex formation with the target proteins, indicating its potential as a multitargeted drug against CC.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Saad Alghamdi
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Kingdom of Saudi Arabia
| | - Hanadi M Baeissa
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Kingdom of Saudi Arabia
| | - Mohammad Azhar Kamal
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Kingdom of Saudi Arabia
| | - Misbahuddin M Rafeeq
- Department of Pharmacology, Faculty of Medicine, Rabigh, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Abdullah Al Zahrani
- Central Military Laboratory and Blood Bank Department - Microbiology Division, Prince Sultan Military Medical City, Riyadh, Kingdom of Saudi Arabia
| | - Ali Ahmed Maslum
- Central Military Laboratory and Blood Bank Department - Microbiology Division, Prince Sultan Military Medical City, Riyadh, Kingdom of Saudi Arabia
| | - Israa J Hakeem
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Kingdom of Saudi Arabia
| | - Reem S Alazragi
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Kingdom of Saudi Arabia
| | - Qamre Alam
- Department of Molecular Genomics and Precision Medicine, ExpressMed Laboratories, Zinj, Kingdom of Bahrain
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Hakeem IJ. Molecular docking analysis of acetylcholinesterase inhibitors for Alzheimer's disease management. Bioinformation 2023; 19:565-570. [PMID: 37886145 PMCID: PMC10599677 DOI: 10.6026/97320630019565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 05/31/2023] [Accepted: 05/31/2023] [Indexed: 10/28/2023] Open
Abstract
Alzheimer's disease (AD) is a neurological disease that is related to aging and is the leading cause of dementia globally. AD has a significant influence on cognitive functions, particularly memory, resulting in a variety of functional deficits. Given the increasing prevalence of AD, there is an urgent need for the development of effective therapeutic therapies. In a quest to uncover a holistic remedy for AD, a total of 41 bioactive compounds derived from three distinct medicinal plant sources were screened to evaluate their potential to inhibit the active sites of acetylcholinesterase (AChE). The insilico screening protocol included 24 licorice-derived compounds, 5 ginkgo biloba-derived compounds, and 11 ginseng-derived compounds. Two compounds (Ginkgolide A and Licorice glycoside D2) were observed to display greater binding energy (BE) relative to the control by interacting with crucial residues in the active site of AChE. Ginkgolide A and Licorice glycoside D2 exhibited BEs of -11.3 and -11.2 kcal/mol, respectively, whereas the control, Donepezil, demonstrated a BE of -10.8 kcal/mol. Further, these compounds exhibit favorable drug-likeness properties. This study suggests that further experimental investigations can be conducted on Ginkgolide A and Licorice glycoside D2 to explore their potential therapeutic applications for AD.
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Affiliation(s)
- Israa J Hakeem
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
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Ashy RA, Jalal RS, Sonbol HS, Alqahtani MD, Sefrji FO, Alshareef SA, Alshehrei FM, Abuauf HW, Baz L, Tashkandi MA, Hakeem IJ, Refai MY, Abulfaraj AA. Functional annotation of rhizospheric phageome of the wild plant species Moringa oleifera. Front Microbiol 2023; 14:1166148. [PMID: 37260683 PMCID: PMC10227523 DOI: 10.3389/fmicb.2023.1166148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/10/2023] [Indexed: 06/02/2023] Open
Abstract
Introduction The study aims to describe phageome of soil rhizosphere of M.oleifera in terms of the genes encoding CAZymes and other KEGG enzymes. Methods Genes of the rhizospheric virome of the wild plant species Moringa oleifera were investigated for their ability to encode useful CAZymes and other KEGG (Kyoto Encyclopedia of Genes and Genomes) enzymes and to resist antibiotic resistance genes (ARGs) in the soil. Results Abundance of these genes was higher in the rhizospheric microbiome than in the bulk soil. Detected viral families include the plant viral family Potyviridae as well as the tailed bacteriophages of class Caudoviricetes that are mainly associated with bacterial genera Pseudomonas, Streptomyces and Mycobacterium. Viral CAZymes in this soil mainly belong to glycoside hydrolase (GH) families GH43 and GH23. Some of these CAZymes participate in a KEGG pathway with actions included debranching and degradation of hemicellulose. Other actions include biosynthesizing biopolymer of the bacterial cell wall and the layered cell wall structure of peptidoglycan. Other CAZymes promote plant physiological activities such as cell-cell recognition, embryogenesis and programmed cell death (PCD). Enzymes of other pathways help reduce the level of soil H2O2 and participate in the biosynthesis of glycine, malate, isoprenoids, as well as isoprene that protects plant from heat stress. Other enzymes act in promoting both the permeability of bacterial peroxisome membrane and carbon fixation in plants. Some enzymes participate in a balanced supply of dNTPs, successful DNA replication and mismatch repair during bacterial cell division. They also catalyze the release of signal peptides from bacterial membrane prolipoproteins. Phages with the most highly abundant antibiotic resistance genes (ARGs) transduce species of bacterial genera Pseudomonas, Streptomyces, and Mycobacterium. Abundant mechanisms of antibiotic resistance in the rhizosphere include "antibiotic efflux pump" for ARGs soxR, OleC, and MuxB, "antibiotic target alteration" for parY mutant, and "antibiotic inactivation" for arr-1. Discussion These ARGs can act synergistically to inhibit several antibiotics including tetracycline, penam, cephalosporin, rifamycins, aminocoumarin, and oleandomycin. The study highlighted the issue of horizontal transfer of ARGs to clinical isolates and human gut microbiome.
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Affiliation(s)
- Ruba A. Ashy
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Rewaa S. Jalal
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Hana S. Sonbol
- Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Mashael D. Alqahtani
- Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Fatmah O. Sefrji
- Department of Biology, College of Science, Taibah University, Al-Madinah Al-Munawwarah, Saudi Arabia
| | - Sahar A. Alshareef
- Department of Biology, College of Science and Arts at Khulis, University of Jeddah, Jeddah, Saudi Arabia
| | - Fatimah M. Alshehrei
- Department of Biology, Jumum College University, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Haneen W. Abuauf
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Lina Baz
- Department of Biochemistry, Faculty of Science, King AbdulAziz University, Jeddah, Saudi Arabia
| | - Manal A. Tashkandi
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Israa J. Hakeem
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Mohammed Y. Refai
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Aala A. Abulfaraj
- Biological Sciences Department, College of Science & Arts, King AbdulAziz University, Rabigh, Saudi Arabia
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J. Hakeem I, Alsharif FH, Aljadani M, Fahad Alabbas I, Faqihi MS, Aloufi AH, Almutairi WA, Akber AH, Alam Q. Molecular docking analysis of KRAS inhibitors for cancer management. Bioinformation 2023; 19:411-416. [PMID: 37822837 PMCID: PMC10563554 DOI: 10.6026/97320630019411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 04/30/2023] [Accepted: 04/30/2023] [Indexed: 10/13/2023] Open
Abstract
The majority of human tumors are characterized by abnormal signaling caused by oncogenic RAS proteins. KRAS is a member of the RAS family and is currently one of the most thoroughly researched targets for cancer treatment due to its prevalence in a variety of deadly malignancies. Targeting the KRAS protein, which plays a crucial role in regulating cell growth, differentiation, and apoptosis, shows great potential as a strategy for fighting cancer. Herein, in silico screening of 530 natural compounds against KRAS protein was performed. The top-scoring hits, namely ZINC32502206, ZINC98363763, ZINC85645815, and ZINC98364259 displayed a robust affinity towards KRAS as evidenced by their respective binding affinity values of -10.50, -10.01, -9.80, and -9.70 kcal/mol, respectively which were notably higher than that of the control compound AMG 510 (-9.10 kcal/mol). Through virtual screening and visual inspection, it was observed that these hits effectively interacted with the essential residues located within the active site of KRAS. Based on the findings of this study, it can be inferred that these compounds may have the potential to be employed in the treatment of cancer by targeting KRAS.
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Affiliation(s)
- Israa J. Hakeem
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Fatmah Hazza Alsharif
- Department of Medical Surgical Nursing Oncology and Palliative Care Nursing, Faculty of Nursing, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Majidah Aljadani
- Department of Chemistry, College of Sciences and Arts, King Abdulaziz University, Rabigh, Saudi Arabia
| | - Ibrahim Fahad Alabbas
- Central Military Laboratory and Blood Bank Department - Virology Division, Prince Sultan Military Medical City, Riyadh 12233, Saudi Arabia
| | - Mohammed Saud Faqihi
- Central Military Laboratory and Blood Bank Department - Microbiology Division, Prince Sultan Military Medical City, Riyadh 12233, Saudi Arabia
| | - Ahmed Hamdan Aloufi
- Department of Pathology and Laboratory Medicine, Imam Abdulrahman bin Faisal Hospital Ministry of National Guard Health Affairs, P.O. Box 34232 Dhahran, Saudi Arabia
| | - Wael Abdullah Almutairi
- Department of Respiratory Services, Ministry of National Guard Hospital and Health Affairs (MNGHA) P.O. box 22490, kingdom of Saudi Arabia
| | - Asif Hussain Akber
- Central Military Laboratory and Blood Bank Department - Virology Division, Prince Sultan Military Medical City, Riyadh 12233, Saudi Arabia
| | - Qamre Alam
- Molecular Genomics and Precision Medicine Department, ExpressMed laboratories, Block, 359, Zinj, Kingdom of Bahrain
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Kamal MA, M Baeissa H, J. Hakeem I, S Alazragi R, S.Hazzazi M, Bakhsh T, Aslam A, Refaat B, B. Khidir E, Juma Alkhenaizi K, Alam Q. Insights from the molecular docking analysis of EGFR antagonists. Bioinformation 2023; 19:260-265. [PMID: 37808374 PMCID: PMC10557452 DOI: 10.6026/97320630019260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/31/2023] [Accepted: 03/31/2023] [Indexed: 10/10/2023] Open
Abstract
Overexpression of the epidermal growth factor receptor (EGFR) has been shown to be a critical factor in tumor development and cancer progression. Although established EGFR inhibitors have been effective in the treatment of cancer, they are associated with several side effects. As a result, there is an urgent need to develop novel EGFR inhibitors that can effectively target the receptor while causing no adverse side effects. Here, the bioactive compounds of Glycyrrhiza glabra and established EGFR inhibitors have been screened against the EGFR catalytic site. The compounds LTS0058805, LTS0114552, LTS0128805, LTS0174203, LTS0007447, and LTS0164690 exhibited binding energies to the EGFR that were comparable to those of established EGFR inhibitors. Further, these hit compounds were observed to interact with critical residues of the EGFR, suggesting their potential as inhibitors of the receptor. In addition, these hits possess good drug-like properties and merit further exploration for their potential application in cancer management.
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Affiliation(s)
- Mohammad Azhar Kamal
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkharj 11942, Saudi Arabia
| | - Hanadi M Baeissa
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Israa J. Hakeem
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Reem S Alazragi
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Mohannad S.Hazzazi
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 22254, Saudi Arabia
- Hematology Research Unit, King Fahad Medical Research Center, King Abdulaziz University, Jeddah 22254, Saudi Arabia
| | - Tahani Bakhsh
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia, P.O. Box 80327, Jeddah 21589
| | - Akhmed Aslam
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Bassem Refaat
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Elshiekh B. Khidir
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Kadhem Juma Alkhenaizi
- Molecular Genomics and Precision Medicine, ExpressMed Laboratories, Block, 359, Zinj,Kingdom of Bahrain
| | - Qamre Alam
- Molecular Genomics and Precision Medicine, ExpressMed Laboratories, Block, 359, Zinj,Kingdom of Bahrain
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Muhammad N, Usmani D, Tarique M, Naz H, Ashraf M, Raliya R, Tabrez S, Zughaibi TA, Alsaieedi A, Hakeem IJ, Suhail M. The Role of Natural Products and Their Multitargeted Approach to Treat Solid Cancer. Cells 2022; 11:cells11142209. [PMID: 35883653 PMCID: PMC9318484 DOI: 10.3390/cells11142209] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/08/2022] [Accepted: 07/13/2022] [Indexed: 02/07/2023] Open
Abstract
Natural products play a critical role in the discovery and development of numerous drugs for the treatment of various types of cancer. These phytochemicals have demonstrated anti-carcinogenic properties by interfering with the initiation, development, and progression of cancer through altering various mechanisms such as cellular proliferation, differentiation, apoptosis, angiogenesis, and metastasis. Treating multifactorial diseases, such as cancer with agents targeting a single target, might lead to limited success and, in many cases, unsatisfactory outcomes. Various epidemiological studies have shown that the steady consumption of fruits and vegetables is intensely associated with a reduced risk of cancer. Since ancient period, plants, herbs, and other natural products have been used as healing agents. Likewise, most of the medicinal ingredients accessible today are originated from the natural resources. Regardless of achievements, developing bioactive compounds and drugs from natural products has remained challenging, in part because of the problem associated with large-scale sequestration and mechanistic understanding. With significant progress in the landscape of cancer therapy and the rising use of cutting-edge technologies, we may have come to a crossroads to review approaches to identify the potential natural products and investigate their therapeutic efficacy. In the present review, we summarize the recent developments in natural products-based cancer research and its application in generating novel systemic strategies with a focus on underlying molecular mechanisms in solid cancer.
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Affiliation(s)
- Naoshad Muhammad
- Department of Radiation Oncology, School of Medicine, Washington University, Saint Louis, MO 63130, USA;
| | | | - Mohammad Tarique
- Department of Child Health, University of Missouri, Columbia, MO 65211, USA;
| | - Huma Naz
- Department of Internal Medicine, University of Missouri, Columbia, MO 65211, USA;
| | - Mohammad Ashraf
- Department of Chemistry, Bundelkhand University Jhansi, Jhansi 284128, Uttar Pradesh, India;
| | - Ramesh Raliya
- IFFCO Nano Biotechnology Research Center, Kalol 382423, Gujarat, India;
| | - Shams Tabrez
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (S.T.); (T.A.Z.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Torki A. Zughaibi
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (S.T.); (T.A.Z.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Ahdab Alsaieedi
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Israa J. Hakeem
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah 21959, Saudi Arabia;
| | - Mohd Suhail
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (S.T.); (T.A.Z.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Correspondence:
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A. Aldlgan A, J. Hakeem I, N. Alandes M, M. Alfahmi M. Alcohol and Substance Abuse in Riyadh, Saudi Arabia: A Hospital -based Survey. Arab J Forensic Sci Forensic Med 2019. [DOI: 10.26735/16586794.2019.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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