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Priyanka, Sharma S, Joshi H, Kumar C, Waseem R, Sharma M. Mycobacterium tuberculosis protein PPE15 (Rv1039c) possesses eukaryote-like SH3 domain that interferes with NADPH Oxidase assembly and Reactive Oxygen Species production. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119702. [PMID: 38408543 DOI: 10.1016/j.bbamcr.2024.119702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 02/28/2024]
Abstract
Inhibition of Reactive Oxygen Species (ROS) is one of the strategies that Mycobacterium tuberculosis (Mtb) employs as its defence mechanism. In this study, the role of PPE15 (Rv1039c), a late-stage protein, has been investigated in modulating the cellular ROS. We discovered PPE15 to be a secretory protein that downregulates ROS generation in THP1 macrophages. Our in-silico analysis revealed the presence of a eukaryote-like SH3 (SH3e) domain in PPE15. The predicted SH3e-domain of PPE15 was found to interact with cytosolic components of NADPH Oxidase (NOX), p67phox and p47phox through molecular docking. In-vitro experiments using THP1 macrophages showed a diminished NADP/NADPH ratio, indicating reduced NOX activity. We also observed increased levels of p67phox and p47phox in the cytoplasmic fraction of PPE15 treated macrophages as compared to the plasma membrane fraction. To understand the role of the SH3e-domain in ROS modulation, this domain was deleted from the full-length PPE15 (PPE15-/-SH3). We observed an increase in cellular ROS and NADP/NADPH ratio in response to PPE15-/-SH3 protein. The interaction of PPE15-/-SH3 with p67phox or p47phox was also reduced in the cytoplasm, indicating migration of NOX subunits to the plasma membrane. Additionally, M. smegmatis expressing PPE15 was observed to be resistant to oxidative stress with significant intracellular survival in THP1 macrophages as compared to M. smegmatis expressing PPE15-/-SH3. These observations suggest that the SH3e-domain of PPE15 interferes with ROS generation by sequestering NOX components that inhibit NOX assembly at the cell membrane. Therefore, PPE15 acts like a molecular mimic of SH3-domain carrying eukaryotic proteins that can be employed by Mtb at late stages of infection for its survival. These findings give us new insights about the pathogen evading strategy of Mtb which may help in improving the therapeutics for TB treatment.
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Affiliation(s)
- Priyanka
- DSKC BioDiscovery Laboratory and Department of Zoology, Miranda House, University of Delhi, Delhi, India.
| | - Sadhna Sharma
- DSKC BioDiscovery Laboratory and Department of Zoology, Miranda House, University of Delhi, Delhi, India.
| | - Hemant Joshi
- School of Biotechnology, Jawaharlal Nehru University, Delhi, India
| | - Chanchal Kumar
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Rashid Waseem
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Monika Sharma
- DSKC BioDiscovery Laboratory and Department of Zoology, Miranda House, University of Delhi, Delhi, India.
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Shamsi A, Shahwan M, Das Gupta D, Abdullah KM, Khan MS. Implication of Caffeic Acid for the Prevention and Treatment of Alzheimer's Disease: Understanding the Binding with Human Transferrin Using In Silico and In Vitro Approaches. Mol Neurobiol 2024; 61:2176-2185. [PMID: 37864768 DOI: 10.1007/s12035-023-03696-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/04/2023] [Indexed: 10/23/2023]
Abstract
In present times, a switch from chemical molecules towards natural products is taking place, and the latter is being increasingly explored in the management of diseases due to their broad range of therapeutic potential. Consumption of coffee is thought to reduce Alzheimer's disease (AD); however, the mechanism is still unexplored. Primarily, it is thought that components of coffee are the key players in making it a neuroprotectant. Caffeic acid (CA) is found in high quantities in coffee; thus, it is being increasingly explored to decipher its neuroprotection by various mechanisms. Iron is a toxic element in a free form capable of causing oxidative damage and ultimately contributing to the pathogenesis of AD. Thus, maintaining the proper iron levels is vital and human transferrin (Htf), a glycoprotein, is a key player in this aspect. In this work, we explored the binding mechanism of CA with Htf at the atomistic level, employing molecular docking and extensive molecular dynamics simulation (MD) approaches coupled with spectroscopic techniques in a bid to decipher the mode of interaction of CA with Htf. Molecular docking results demonstrated a strong binding affinity between CA and Htf. Furthermore, MD study highlighted the Htf-CA complex's stability and the ligand's minimal impact on Htf's overall structure. In silico approaches were further backed up by experimental approaches. Strong binding of CA with Htf was ascertained by UV-visible and fluorescence spectroscopy observations. Together, the study provides a comprehensive understanding of the Htf-CA interaction, adding to the knowledge of the use of CA in the treatment of AD, thereby adding another feather to its already known neuroprotective role.
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Affiliation(s)
- Anas Shamsi
- Center for Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates.
| | - Moyad Shahwan
- Center for Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
- Department of Clinical Sciences, College of Pharmacy and Health Sciences, Ajman University, Ajman, United Arab Emirates
| | - Debarati Das Gupta
- College of Pharmacy, University of Michigan, 2428 Church Street, Ann Arbor, MI, 48109, USA
| | - K M Abdullah
- Department of Chemistry and Biochemistry, School of Sciences, Jain University, Bengaluru, India
| | - Mohd Shahnawaz Khan
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
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Yousuf M, Khan S, Hussain A, Alajmi MF, Shamsi A, Haque QMR, Islam A, Hassan MI. Exploring therapeutic potential of Rutin by investigating its cyclin-dependent kinase 6 inhibitory activity and binding affinity. Int J Biol Macromol 2024; 264:130624. [PMID: 38453105 DOI: 10.1016/j.ijbiomac.2024.130624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/20/2024] [Accepted: 03/03/2024] [Indexed: 03/09/2024]
Abstract
Cyclin-dependent kinase 6 (CDK6) participates in numerous signalling pathways and regulates various physiological processes. Due to its unique structural features and promising therapeutic potential, CDK6 has emerged as a drug target for designing and developing small-molecule inhibitors for anti-cancer therapeutics and other CDK6-associated diseases. The current study evaluates binding affinity and the inhibitory potential of rutin for CDK6 to develop a proof of concept for rutin as a potent CDK6 inhibitor. Molecular docking and 200 ns all-atom simulations reveal that rutin binds to the active site pocket of CDK6, forming interactions with key residues of the binding pocket. In addition, the CDK6-rutin complex remains stable throughout the simulation trajectory. A high binding constant (Ka = 7.6 × 105M-1) indicates that rutin has a strong affinity for CDK6. Isothermal titration calorimetry has further validated a strong binding of rutin with CDK6 and its spontaneous nature. The kinase activity of CDK6 is significantly inhibited by rutin with an IC50 value of 3.10 μM. Our findings highlight the significant role of rutin in developing potential therapeutic molecules to manage cancer and CDK6-associated diseases via therapeutic targeting of CDK6.
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Affiliation(s)
- Mohd Yousuf
- Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Shama Khan
- South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Science, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohamed F Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Anas Shamsi
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman 346, United Arab Emirates
| | | | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India.
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Khan T, Waseem R, Shahid M, Ansari J, Ahanger IA, Hassan I, Islam A. Recent advancement in therapeutic strategies for Alzheimer's disease: Insights from clinical trials. Ageing Res Rev 2023; 92:102113. [PMID: 37918760 DOI: 10.1016/j.arr.2023.102113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/16/2023] [Accepted: 10/27/2023] [Indexed: 11/04/2023]
Abstract
Alzheimer's disease (AD) is the most prevalent form of dementia, characterized by the presence of plaques of amyloid beta and Tau proteins. There is currently no permanent cure for AD; the only medications approved by the FDA for mild to moderate AD are cholinesterase inhibitors, NMDA receptor antagonists, and immunotherapies against core pathophysiology, that provide temporary relief only. Researchers worldwide have made significant attempts to find new targets and develop innovative therapeutic molecules to treat AD. The FDA-approved drugs are palliative and couldn't restore the damaged neuron cells of AD. Stem cells have self-differentiation properties, making them prospective therapeutics to treat AD. The promising results in pre-clinical studies of stem cell therapy for AD seek attention worldwide. Various stem cells, mainly mesenchymal stem cells, are currently in different phases of clinical trials and need more advancements to take this therapy to the translational level. Here, we review research from the past decade that has identified several hypotheses related to AD pathology. Moreover, this article also focuses on the recent advancement in therapeutic strategies for AD treatment including immunotherapy and stem cell therapy detailing the clinical trials that are currently undergoing development.
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Affiliation(s)
- Tanzeel Khan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Rashid Waseem
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Mohammad Shahid
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Jaoud Ansari
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Ishfaq Ahmad Ahanger
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; Department of Clinical Biochemistry, University of Kashmir,190006, India
| | - Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
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Al-Wahaibi LH, Rehman MT, Al-Saleem MSM, Basudan OA, El-Gamal AA, Abdelkader MSA, AlAjmi MF, Abdel-Mageed WM. Virtual screening and molecular dynamics simulation study of abyssomicins as potential inhibitors of COVID-19 virus main protease and spike protein. J Biomol Struct Dyn 2023; 41:8961-8977. [PMID: 36300522 DOI: 10.1080/07391102.2022.2139295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 10/18/2022] [Indexed: 10/31/2022]
Abstract
The lack of any effective cure for the infectious COVID-19 disease has created a sense of urgency and motivated the search for effective antiviral drugs. Abyssomicins are actinomyces-derived spirotetronates polyketides antibiotics known for their promising antibacterial, antitumor, and antiviral activities. In this study, computational approaches were used to investigate the binding mechanism and the inhibitory ability of 38 abyssomicins against the main protease (Mpro) and the spike protein receptor-binding domain (RBD) of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The results identified abyssomicins C, J, W, atrop-O-benzyl abyssomicin C, and atrop-O-benzyl desmethyl abyssomicin C as the most potential inhibitors of Mpro and RBD with binding energy ranges between -8.1 and -9.9 kcal mol-1; and between -6.9 and -8.2 kcal mol-1, respectively. Further analyses of physicochemical properties and drug-likeness suggested that all selected active abyssomicins, with the exception of abyssomicin J, obeyed Lipinski's rule of five. The stability of protein-ligand complexes was confirmed by performing molecular dynamics simulation for 100 ns and evaluating parameters such as such as root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), total number of contacts, and secondary structure. Prime/MM-GBSA (Molecular Mechanics-General Born Surface Area) and principal component analysis (PCA) analyses also confirmed the stable nature of protein-ligand complexes. Overall, the results showed that the studied abyssomicins have significant interactions with the selected protein targets; therefore, they were deemed viable candidates for further in vitro and in vivo evaluation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Lamya H Al-Wahaibi
- Department of Chemistry, Science College, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Muneera S M Al-Saleem
- Department of Chemistry, Science College, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Omer A Basudan
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ali A El-Gamal
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
- Pharmacognosy Department, Faculty of Pharmacy, Mansoura University, El Mansoura, Egypt
| | | | - Mohamed F AlAjmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Wael M Abdel-Mageed
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
- Pharmacognosy Department, Faculty of Pharmacy, Assiut University, Assiut, Egypt
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Almalki SG, Alqurashi YE, Alturaiki W, Almawash S, Khan A, Ahmad P, Iqbal D. Antioxidant, LC-MS Analysis, and Cholinesterase Inhibitory Potentials of Phoenix dactylifera Cultivar Khudari: An In Vitro Enzyme Kinetics and In Silico Study. Biomolecules 2023; 13:1474. [PMID: 37892156 PMCID: PMC10605097 DOI: 10.3390/biom13101474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
We evaluated the therapeutic potentials of Khudari fruit pulp, a functional food and cultivar of Phoenix dactylifera, against neurological disorders. Our results demonstrate a good amount of phytochemicals (total phenolic content: 17.77 ± 8.21 µg GA/mg extract) with a high antioxidant potential of aqueous extract (DPPH assay IC50 = 235.84 ± 11.65 µg/mL) and FRAP value: 331.81 ± 4.56 µmol. Furthermore, the aqueous extract showed the marked inhibition of cell-free acetylcholinesterase (electric eel) with an IC50 value of 48.25 ± 2.04 µg/mL, and an enzyme inhibition kinetics study revealed that it exhibits mixed inhibition. Thereafter, we listed the 18 best-matched phytochemical compounds present in aqueous extract through LC/MS analysis. The computational study revealed that five out of eighteen predicted compounds can cross the BBB and exert considerable aqueous solubility. where 2-{5-[(1E)-3-methylbuta-1,3-dien-1-yl]-1H-indol-3-yl}ethanol (MDIE) indicates an acceptable LD50. value. A molecular docking study exhibited that the compounds occupied the key residues of acetylcholinesterase with ΔG range between -6.91 and -9.49 kcal/mol, where MDIE has ∆G: -8.67 kcal/mol, which was better than that of tacrine, ∆G: -8.25 kcal/mol. Molecular dynamics analyses of 100 ns supported the stability of the protein-ligand complexes analyzed through RMSD, RMSF, Rg, and SASA parameters. TRP_84 and GLY_442 are the most critical hydrophobic contacts for the complex, although GLU_199 is important for H-bonds. Prime/MM-GBSA showed that the protein-ligand complex formed a stable confirmation. These findings suggest that the aqueous extract of Khudari fruit pulp has significant antioxidant and acetylcholinesterase inhibition potentials, and its compound, MDIE, forms stably with confirmation with the target protein, though this fruit of Khudari dates can be a better functional food for the treatment of Alzheimer's disease. Further investigations are needed to fully understand the therapeutic role of this plant-based compound via in vivo study.
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Affiliation(s)
- Sami G. Almalki
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi Arabia;
| | - Yaser E. Alqurashi
- Department of Biology, College of Science Al-Zulfi, Majmaah University, Al-Majmaah 11952, Saudi Arabia;
| | - Wael Alturaiki
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11952, Saudi Arabia;
| | - Saud Almawash
- Department of Pharmaceutical Sciences, College of Pharmacy, Shaqra University, Shaqra 11961, Saudi Arabia;
| | - Amir Khan
- Oral Medicine and Allied Dental Sciences Department, Faculty of Dentistry, Taif University, Taif 11099, Saudi Arabia;
| | - Parvej Ahmad
- IIRC-5 Clinical Biochemistry and Natural Product Research Laboratory, Integral University, Lucknow 226026, India;
| | - Danish Iqbal
- Department of Health Information Management, College of Applied Medical Sciences, Buraydah Private Colleges, Buraydah 51418, Saudi Arabia
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Eslami Moghadam M, Tavakoli Hafshajani K, Sohrabi N, Rezaeisadat M, Oftadeh M. Platinum (II) complex of isopentyl glycine ligand: DNA binding, molecular dynamic, and anticancer activity against breast cancer. J Biomol Struct Dyn 2023:1-13. [PMID: 37578043 DOI: 10.1080/07391102.2023.2246564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/29/2023] [Indexed: 08/15/2023]
Abstract
In this paper, we performed thorough experimental and theoretical calculations to examine the interaction between Pt derivative, as an anticancer, and ct-DNA. The mode of DNA binding with [Pt(NH3)2(Isopentylgly)]NO3, where Isopentylgly is Isopentyl glycine, was evaluated by various spectroscopic methods, docking, and molecular dynamics simulation studies. UV-Vis and fluorescence spectroscopic titration results and CD spectra of DNA-drug showed this interaction is via groove binding. Also, thermal stability studies or DNA melting temperature changes (ΔTm), as well as the quenching emissions monitoring proved it. Also, the thermodynamic parameter and binding constant displayed that complex-DNA formation is a spontaneous process, and H-binding and also groove binding were found to be the main forces. Theoretical studies stated [Pt(NH3)2(Isopentylgly)]NO3-DNA formation occurs on C-G center on DNA, along with rising DNA-compound stability. IC50 value against the human breast cell line probably is due to the Isopentyl glycine ligand in the structure of the Pt compound, and it was obtained more than cisplatin and less than carboplatin against the MCF7 cell.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Nasrin Sohrabi
- Department of Chemistry, Payame Noor University (PNU), Tehran, Iran
| | | | - Mohsen Oftadeh
- Department of Chemistry, Payame Noor University (PNU), Tehran, Iran
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Waseem R, Khan T, Shamsi A, Shahid M, Kazim SN, Hassan MI, Islam A. Inhibitory potential of N-acetylaspartate against protein glycation, AGEs formation and aggregation: Implication of brain osmolyte in glycation-related complications. Int J Biol Macromol 2023:125405. [PMID: 37336383 DOI: 10.1016/j.ijbiomac.2023.125405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 06/11/2023] [Accepted: 06/13/2023] [Indexed: 06/21/2023]
Abstract
Protein glycation and aggregation have a pivotal role in many diseases including diabetes and neurodegenerative disorders. N-acetyl aspartate (NAA), an osmolyte derived from L-aspartic acid, is one of the most abundant metabolites in the mammalian brain. Although NAA is supposed to be a substitute for a neuronal marker, its function is not fully elucidated. Herein, we have investigated the effect of NAA on glycation, AGEs formation and aggregation of irisin. AGE-specific fluorescence showed the strong inhibition of AGEs formation in the presence of NAA, demonstrating its anti-glycating property. The aggregates present in MG-modified irisin were also reduced by NAA, which was confirmed by Thioflavin T fluorescence and fluorescence microscopy. Further, for the explanation of the strong anti-glycating potential of NAA, the interaction between irisin and NAA was also examined. Interaction studies involving steady-state fluorescence and molecular docking demonstrated that hydrogen bonding and salt bridges by NAA stabilize the irisin. It was found that glycation-prone residues i.e., lysine and arginine are specifically involved in the interaction which might prevent them from getting modified during the process of glycation. This study for the first time reported the antiglycating potential of NAA which can be implicated in the therapeutic management of various glycation-related complications.
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Affiliation(s)
- Rashid Waseem
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Tanzeel Khan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Anas Shamsi
- Centre of Medical and Bio-allied Health Sciences Research, Ajman University, United Arab Emirates
| | - Mohammad Shahid
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Syed Naqui Kazim
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.
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Tavakoli Hafshajani K, Sohrabi N, Eslami Moghadam M, Oftadeh M. Spectroscopy and molecular dynamic study of the interaction of calf thymus DNA by anticancer Pt complex with butyl glycine ligand. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 299:122826. [PMID: 37216815 DOI: 10.1016/j.saa.2023.122826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 04/29/2023] [Accepted: 05/04/2023] [Indexed: 05/24/2023]
Abstract
Despite the past few decades since the discovery of anticancer drugs, there is still no definitive treatment for its treatment. Cisplatin is a chemotherapy medication used to treat some cancers. In this research, the DNA binding affinity of Pt complex with butyl glycine ligand was studied by various spectroscopy methods and simulation studies. Fluorescence and UV-Vis spectroscopic data showed groove binding in ct-DNA-[Pt(NH3)2(butylgly)]NO3 complex formation by the spontaneous process. The results were also confirmed by small changes in CD spectra and thermal study (Tm), as well as the quenching emission of [Pt(NH3)2(butylgly)]NO3 complex on DNA. Finally, thermodynamic and binding parameters displayed that hydrophobic forces are the main forces. Based on docking simulation, [Pt(NH3)2(butylgly)]NO3 could bind to DNA and via minor groove binding on C-G center on DNA, formed a stable DNA complex.
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Affiliation(s)
| | - Nasrin Sohrabi
- Department of Chemistry, Payame Noor University (PNU), P.O.Box 19395-4697, Tehran, Iran.
| | | | - Mohsen Oftadeh
- Department of Chemistry, Payame Noor University (PNU), P.O.Box 19395-4697, Tehran, Iran
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Li X, Han L, Song Z, Xu R, Wang L. Comparative study on the interaction between transferrin and flavonols: Experimental and computational modeling approaches. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 288:122128. [PMID: 36455462 DOI: 10.1016/j.saa.2022.122128] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/27/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Transferrin is the indispensable component in the body fluids and has been explored as a potential drug carrier for target drugs to cancer cells. Flavonols are widely distributed in plants and shown a wide range of biological activities. In the present study, the interaction between flavonols (including galangin, kaempferol, quercetin, and myricetin) and transferrin under physiological conditions was investigated by using experimental as well as computational approaches. Fluorescence data reveal that the fluorescence quenching mechanism of transferrin by flavonols is static quenching. Transferrin has moderate affinity with flavonols, and the binding constants (Ka) are 103-104 L/mol. In addition, there are two different binding sites for the interaction between kaempferol and transferrin. Thermodynamic parameter analysis shows that the interaction of flavonols and transferrin is synergistically driven by enthalpy and entropy. Hydrophobic interaction, electrostatic force and hydrogen bonds are the main force types. Synchronous fluorescence spectroscopy shows that flavonols decrease the hydrophobicity of the microenvironment around tryptophan (Trp) and have no effect on the microenvironment around tyrosine (Tyr). UV-vis and CD spectra show that the interaction between transferrin and flavonols leads to the loosening and unfolding of transferrin backbone. The increase of β-sheet is accompanied by the decrease of α-helix and β-turn. The specific binding sites of flavonols to transferrin are confirmed by molecular docking. Molecular dynamic simulation suggests that the transferrin-flavonols docked complex is stable throughout the simulation trajectory.
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Affiliation(s)
- Xiangrong Li
- Department of Medical Chemistry, Key Laboratory of Medical Molecular Probes, School of Basic Medicine, Xinxiang Medical University, Xinxiang, Henan 453003, PR China.
| | - Linyu Han
- Grade 2020, Clinical Medicine, School of Basic Medicine, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
| | - Zhizhi Song
- Grade 2020, Clinical Medicine, School of Basic Medicine, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
| | - Ruonan Xu
- Department of Medical Chemistry, Key Laboratory of Medical Molecular Probes, School of Basic Medicine, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
| | - Lixia Wang
- College of Science, Henan Agricultural University, Zhengzhou, Henan 450002, PR China
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A review on cyclin-dependent kinase 5: An emerging drug target for neurodegenerative diseases. Int J Biol Macromol 2023; 230:123259. [PMID: 36641018 DOI: 10.1016/j.ijbiomac.2023.123259] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/05/2023] [Accepted: 01/10/2023] [Indexed: 01/13/2023]
Abstract
Cyclin-dependent kinase 5 (CDK5) is the serine/threonine-directed kinase mainly found in the brain and plays a significant role in developing the central nervous system. Recent evidence suggests that CDK5 is activated by specific cyclins regulating its expression and activity. P35 and p39 activate CDK5, and their proteolytic degradation produces p25 and p29, which are stable products involved in the hyperphosphorylation of tau protein, a significant hallmark of various neurological diseases. Numerous high-affinity inhibitors of CDK5 have been designed, and some are marketed drugs. Roscovitine, like other drugs, is being used to minimize neurological symptoms. Here, we performed an extensive literature analysis to highlight the role of CDK5 in neurons, synaptic plasticity, DNA damage repair, cell cycle, etc. We have investigated the structural features of CDK5, and their binding mode with the designed inhibitors is discussed in detail to develop attractive strategies in the therapeutic targeting of CDK5 for neurodegenerative diseases. This review provides deeper mechanistic insights into the therapeutic potential of CDK5 inhibitors and their implications in the clinical management of neurodegenerative diseases.
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Alzheimer's Disease-Biochemical and Psychological Background for Diagnosis and Treatment. Int J Mol Sci 2023; 24:ijms24021059. [PMID: 36674580 PMCID: PMC9866942 DOI: 10.3390/ijms24021059] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 12/29/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023] Open
Abstract
There is a paucity of empirical research on the use of non-pharmacological interventions to both treat and curb the spread of Alzheimer's disease (AD) across the globe. This paper examines the biochemical and clinical outlook and the social implications of the condition in relation to psychological aspects that may indicate a direction for further interventions. There is a scarcity of research on the effectiveness of using various psychological aspects of AD, a disease characterized by a process of transition from health and independence to a dependent state with a progressive loss of memory and functional skills. The paper investigates the biochemical and psychological aspects of AD and their significance for improving quality of life for patients with this disease. Psychological interventions based on, among other factors, biochemical studies, are conducted to improve the emotional wellbeing of AD patients and may assist in slowing down the progression of the disease. To date, however, no effective methods of AD treatment have been established.
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13
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AlAjmi MF, Rehman MT, Hussain A. Celecoxib, Glipizide, Lapatinib, and Sitagliptin as potential suspects of aggravating SARS-CoV-2 (COVID-19) infection: a computational approach. J Biomol Struct Dyn 2022; 40:13747-13758. [PMID: 34709124 PMCID: PMC8567293 DOI: 10.1080/07391102.2021.1994013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
COVID-19 caused by SARS-CoV-2 has emerged as a potential threat to human life, especially to people suffering from chronic diseases. In this study, we investigated the ability of selected FDA-approved drugs to inhibit TACE (tumor necrosis factor α converting enzyme), which is responsible for the shedding of membrane-bound ACE2 (angiotensin-converting enzyme2) receptors into soluble ACE2. The inhibition of TACE would lead to an increased population of membrane-bound ACE2, which would facilitate ACE2-Spike protein interaction and viral entry. A total of 50 drugs prescribed in treating various chronic diseases in Saudi Arabia were screened by performing molecular docking using AutoDock4.2. Based on docking energy (≤ -9.00 kcal mol-1), four drugs (Celecoxib, Glipizide, Lapatinib, and Sitagliptin) were identified as potential inhibitors of TACE, with binding affinities up to 106-107 M-1. Analysis of the molecular docking suggests that these drugs were bound to TACE's catalytic domain and interact with the key residues such as His405, Glu406, and His415, which are involved in active site Zn2+ ion chelation. Molecular dynamics simulation was performed to confirm the stability of TACE-drugs complexes. RMSD (root mean square deviation), RMSF (root mean square fluctuation), Rg (radius of gyration), and SASA (solvent accessible surface area) were within the acceptable limits. Free energy calculations using Prime-MM/GBSA suggest that Celecoxib formed the most stable complex with TACE, followed by Glipizide, Sitagliptin, and Lapatinib. The finding of this study suggests a mechanism for drugs to aggravate SARS-CoV-2 infection and hence high mortality in patients suffering from chronic diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohamed F. AlAjmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia,CONTACT Md Tabish Rehman Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh11451, Saudi Arabia
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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14
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He F, Wang J, Yuan D, Liu Y, Liu R, Zong W. Ferric ions release from iron-binding protein: Interaction between acrylamide and human serum transferrin and the underlying mechanisms of their binding. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 847:157583. [PMID: 35882343 DOI: 10.1016/j.scitotenv.2022.157583] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/17/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
Acrylamide (ACR) is a surprisingly common chemical due to its widespread use in industry and various other applications. However, its toxicity is a matter of grave concern for public health. Even worse, ACR is frequently detected in numerous fried or baked carbohydrate-rich foods due to the Maillard browning reaction. Herein, this study intends to delineate the underlying molecular mechanisms of Fe ions released from iron-binding protein transferrin (TF) after acrylamide binding by combining multiple methods, including multiple complementary spectroscopic techniques (UV-Vis, fluorescence, and circular dichroism spectroscopy), isothermal titration calorimetry, ICP-MS measurements, and modeling simulations. Results indicated that free Fe was released from TF only under high-dose ACR exposure (>100 μM). Acrylamide binding induced the loosening and unfolding of the backbone and polypeptide chain and destroyed the secondary structure of TF, thereby leading to protein misfolding and denaturation of TF and forming a larger size of TF agglomerates. Of which, H-binding and van der Waals force are the primary driving force during the binding interaction between ACR and TF. Further modeling simulations illustrated that ACR prefers to bind to the hinge region connecting the C-lobe and N-lobe, after that it attaches to the Fe binding sites of this protein, which is the cause of free Fe release from TF. Moreover, ACR interacted with the critical fluorophore residues (Tyr, Trp, and Phe) in the binding pocket, which might explain such a phenomenon of fluorescence sensitization. The two binding sites (Site 2 and Site 3) located around the Fe (III) ions with low-energy conformations are more suitable for ACR binding. Collectively, our study demonstrated that the loss of iron in TF caused by acrylamide-induced structural and conformational changes of transferrin.
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Affiliation(s)
- Falin He
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China
| | - Jinhu Wang
- College of Chemistry, Chemical Engineering and Material Science, Zaozhuang University, Zaozhuang, Shandong 277160, PR China
| | - Dong Yuan
- Department of Chemistry and Chemical Engineering, Qilu Normal University, Jinan 250013, PR China.
| | - Yang Liu
- Department of Chemistry and Chemical Engineering, Qilu Normal University, Jinan 250013, PR China
| | - Rutao Liu
- School of Environmental Science and Engineering, Shandong University, China-America CRC for Environment & Health, 72# Jimo Binhai Road, Qingdao, Shandong 266237, PR China.
| | - Wansong Zong
- College of Geography and Environment, Shandong Normal University, 88# East Wenhua Road, Jinan, Shandong 250014, PR China
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15
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Targeting inhibition of microtubule affinity regulating kinase 4 by Harmaline: Strategy to combat Alzheimer's disease. Int J Biol Macromol 2022; 224:188-195. [DOI: 10.1016/j.ijbiomac.2022.10.115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/03/2022] [Accepted: 10/13/2022] [Indexed: 11/05/2022]
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16
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Identification of a Potential Inhibitor (MCULE-8777613195-0-12) of New Delhi Metallo-β-Lactamase-1 (NDM-1) Using In Silico and In Vitro Approaches. Molecules 2022; 27:molecules27185930. [PMID: 36144666 PMCID: PMC9504514 DOI: 10.3390/molecules27185930] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/04/2022] [Accepted: 08/08/2022] [Indexed: 11/17/2022] Open
Abstract
New Delhi metallo-β-lactamase-1 (NDM-1), expressed in different Gram-negative bacteria, is a versatile enzyme capable of hydrolyzing β-lactam rings containing antibiotics such as penicillins, cephalosporins, and even carbapenems. Multidrug resistance in bacteria mediated by NDM-1 is an emerging threat to the public health, with an enormous economic burden. There is a scarcity in the availability of specific NDM-1 inhibitors, and also a lag in the development of new inhibitors in pharmaceutical industries. In order to identify novel inhibitors of NDM-1, we screened a library of more than 20 million compounds, available at the MCULE purchasable database. Virtual screening led to the identification of six potential inhibitors, namely, MCULE-1996250788-0-2, MCULE-8777613195-0-12, MCULE-2896881895-0-14, MCULE-5843881524-0-3, MCULE-4937132985-0-1, and MCULE-7157846117-0-1. Furthermore, analyses by molecular docking and ADME properties showed that MCULE-8777613195-0-12 was the most suitable inhibitor against NDM-1. An analysis of the binding pose revealed that MCULE-8777613195-0-12 formed four hydrogen bonds with the catalytic residues of NDM-1 (His120, His122, His189, and Cys208) and interacted with other key residues. Molecular dynamics simulation and principal component analysis confirmed the stability of the NDM-1 and MCULE-8777613195-0-12 complex. The in vitro enzyme kinetics showed that the catalytic efficiency (i.e., kcat/Km) of NDM-1 on various antibiotics decreased significantly in the presence of MCULE-8777613195-0-12, due to poor catalytic proficiency (kcat) and affinity (Km). The IC50 value of MCULE-8777613195-0-12 (54.2 µM) was comparable to that of a known inhibitor, i.e., D-captopril (10.3 µM). In sum, MCULE-8777613195-0-12 may serve as a scaffold to further design/develop more potent inhibitors of NDM-1 and other β-lactamases.
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17
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Blagov AV, Grechko AV, Nikiforov NG, Borisov EE, Sadykhov NK, Orekhov AN. Role of Impaired Mitochondrial Dynamics Processes in the Pathogenesis of Alzheimer’s Disease. Int J Mol Sci 2022; 23:ijms23136954. [PMID: 35805958 PMCID: PMC9266759 DOI: 10.3390/ijms23136954] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/17/2022] [Accepted: 06/21/2022] [Indexed: 02/06/2023] Open
Abstract
Mitochondrial dysfunction is now recognized as a contributing factor to neurodegenerative diseases, including Alzheimer’s disease (AD). Mitochondria are signaling organelles with a variety of functions ranging from energy production to the regulation of cellular metabolism, energy homeostasis, and response to stress. The successful functioning of these complex processes is critically dependent on the accuracy of mitochondrial dynamics, which includes the ability of mitochondria to change shape and position in the cell, which is necessary to maintain proper function and quality control, especially in polarized cells such as neurons. There has been much evidence to suggest that the disruption of mitochondrial dynamics may play a critical role in the pathogenesis of AD. This review highlights aspects of altered mitochondrial dynamics in AD that may contribute to the etiology of this debilitating condition. We also discuss therapeutic strategies to improve mitochondrial dynamics and function that may provide an alternative treatment approach.
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Affiliation(s)
- Alexander V. Blagov
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Russian Academy of Medical Sciences, 8 Baltiiskaya Street, 125315 Moscow, Russia; (N.G.N.); (N.K.S.)
- Correspondence: (A.V.B.); (A.N.O.)
| | - Andrey V. Grechko
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, 14-3 Solyanka Street, 109240 Moscow, Russia;
| | - Nikita G. Nikiforov
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Russian Academy of Medical Sciences, 8 Baltiiskaya Street, 125315 Moscow, Russia; (N.G.N.); (N.K.S.)
| | - Evgeny E. Borisov
- Petrovsky National Research Centre of Surgery, AP Avtsyn Institute of Human Morphology, 117418 Moscow, Russia;
| | - Nikolay K. Sadykhov
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Russian Academy of Medical Sciences, 8 Baltiiskaya Street, 125315 Moscow, Russia; (N.G.N.); (N.K.S.)
| | - Alexander N. Orekhov
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Russian Academy of Medical Sciences, 8 Baltiiskaya Street, 125315 Moscow, Russia; (N.G.N.); (N.K.S.)
- Correspondence: (A.V.B.); (A.N.O.)
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18
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Binding Studies of Caffeic and p-Coumaric Acid with α-Amylase: Multispectroscopic and Computational Approaches Deciphering the Effect on Advanced Glycation End Products (AGEs). Molecules 2022; 27:molecules27133992. [PMID: 35807235 PMCID: PMC9267998 DOI: 10.3390/molecules27133992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 12/04/2022] Open
Abstract
Alpha-amylase (α-amylase) is a key player in the management of diabetes and its related complications. This study was intended to have an insight into the binding of caffeic acid and coumaric acid with α-amylase and analyze the effect of these compounds on the formation of advanced glycation end-products (AGEs). Fluorescence quenching studies suggested that both the compounds showed an appreciable binding affinity towards α-amylase. The evaluation of thermodynamic parameters (ΔH and ΔS) suggested that the α-amylase-caffeic/coumaric acid complex formation is driven by van der Waals force and hydrogen bonding, and thus complexation process is seemingly specific. Moreover, glycation and oxidation studies were also performed to explore the multitarget to manage diabetes complications. Caffeic and coumaric acid both inhibited fructosamine content and AGE fluorescence, suggesting their role in the inhibition of early and advanced glycation end-products (AGEs). However, the glycation inhibitory potential of caffeic acid was more in comparison to p-coumaric acid. This high antiglycative potential can be attributed to its additional –OH group and high antioxidant activity. There was a significant recovery of 84.5% in free thiol groups in the presence of caffeic acid, while coumaric attenuated the slow recovery of 29.4% of thiol groups. In vitro studies were further entrenched by in silico studies. Molecular docking studies revealed that caffeic acid formed six hydrogen bonds (Trp 59, Gln 63, Arg 195, Arg 195, Asp 197 and Asp 197) while coumaric acid formed four H-bonds with Trp 59, Gln 63, Arg 195 and Asp 300. Our studies highlighted the role of hydrogen bonding, and the ligands such as caffeic or coumaric acid could be exploited to design antidiabetic drugs.
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19
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Xue B, DasGupta D, Alam M, Khan MS, Wang S, Shamsi A, Islam A, Hassan MI. Investigating binding mechanism of thymoquinone to human transferrin, targeting Alzheimer's disease therapy. J Cell Biochem 2022; 123:1381-1393. [PMID: 35722728 DOI: 10.1002/jcb.30299] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/20/2022] [Accepted: 06/09/2022] [Indexed: 11/09/2022]
Abstract
Iron deposition in the central nervous system (CNS) is one of the causes of neurodegenerative diseases. Human transferrin (hTf) acts as an iron carrier present in the blood plasma, preventing it from contributing to redox reactions. Plant compounds and their derivatives are frequently being used in preventing or delaying Alzheimer's disease (AD). Thymoquinone (TQ), a natural product has gained popularity because of its broad therapeutic applications. TQ is one of the significant phytoconstituent of Nigella sativa. The binding of TQ to hTf was determined by spectroscopic methods and isothermal titration calorimetry. We have observed that TQ strongly binds to hTf with a binding constant (K) of 0.22 × 106 M-1 and forming a stable complex. In addition, isothermal titration calorimetry revealed the spontaneous binding of TQ with hTf. Molecular docking analysis showed key residues of the hTf that were involved in the binding to TQ. We further performed a 250 ns molecular dynamics simulation which deciphered the dynamics and stability of the hTf-TQ complex. Structure analysis suggested that the binding of TQ doesn't cause any significant alterations in the hTf structure during the course of simulation and a stable complex is formed. Altogether, we have elucidated the mechanism of binding of TQ with hTf, which can be further implicated in the development of a novel strategy for AD therapy.
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Affiliation(s)
- Bin Xue
- School of Engineering, Guangzhou College of Technology and Business, Guangzhou, China
| | - Debarati DasGupta
- College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Manzar Alam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Mohd Shahnawaz Khan
- Department of Biochemistry, College of Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Shuo Wang
- School of Engineering, Guangzhou College of Technology and Business, Guangzhou, China
| | - Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India.,Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, UAE, Ajman
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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20
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Waseem R, Shamsi A, Khan T, Hassan MI, Kazim SN, Shahid M, Islam A. Unraveling the Binding Mechanism of Alzheimer's Drugs with Irisin: Spectroscopic, Calorimetric, and Computational Approaches. Int J Mol Sci 2022; 23:ijms23115965. [PMID: 35682643 PMCID: PMC9180407 DOI: 10.3390/ijms23115965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/13/2022] [Accepted: 05/23/2022] [Indexed: 12/19/2022] Open
Abstract
The prevalence of Alzheimer’s disease (AD) has been a major health concern for a long time. Despite recent progress, there is still a strong need to develop effective disease-modifying therapies. Several drugs have already been approved to retard the progression of AD-related symptoms; however, there is a need to develop an effective carrier system for the delivery of drugs to combat such diseases. In recent years, various biological macromolecules, including proteins, have been used as carriers for drug delivery. Irisin is a beneficial hormone in such diseases, including AD and related pathologies. Herein, the interaction mechanism of irisin with AD drugs such as memantine, galantamine, and fluoxetine is investigated. Fluorescence studies revealed that the above drugs bind to irisin with significant affinity, with fluoxetine having the highest binding affinity. Isothermal titration calorimetry (ITC) complemented the spontaneous binding of these drugs with irisin, delineating various associated thermodynamic and binding parameters. Molecular docking further validated the fluorescence and ITC results and unfolded the mechanism that hydrogen bonding governs the binding of fluoxetine to irisin with a significant binding score, i.e., −6.3 kcal/mol. We believe that these findings provide a promising solution to fight against AD as well as a platform for further research to utilize irisin in the drug-delivery system for an effective therapeutic strategy.
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Affiliation(s)
- Rashid Waseem
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India; (R.W.); (A.S.); (T.K.); (M.I.H.); (S.N.K.)
| | - Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India; (R.W.); (A.S.); (T.K.); (M.I.H.); (S.N.K.)
| | - Tanzeel Khan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India; (R.W.); (A.S.); (T.K.); (M.I.H.); (S.N.K.)
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India; (R.W.); (A.S.); (T.K.); (M.I.H.); (S.N.K.)
| | - Syed Naqui Kazim
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India; (R.W.); (A.S.); (T.K.); (M.I.H.); (S.N.K.)
| | - Mohammad Shahid
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia;
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India; (R.W.); (A.S.); (T.K.); (M.I.H.); (S.N.K.)
- Correspondence:
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21
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Michailidis M, Tata DA, Moraitou D, Kavvadas D, Karachrysafi S, Papamitsou T, Vareltzis P, Papaliagkas V. Antidiabetic Drugs in the Treatment of Alzheimer's Disease. Int J Mol Sci 2022; 23:4641. [PMID: 35563031 PMCID: PMC9102472 DOI: 10.3390/ijms23094641] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 02/04/2023] Open
Abstract
The public health burden of type 2 diabetes mellitus and Alzheimer's disease is steadily increasing worldwide, especially in the population of older adults. Epidemiological and clinical studies suggest a possible shared pathophysiology between the two diseases and an increased risk of AD in patients with type 2 diabetes mellitus. Therefore, in recent years, there has been a substantial interest in identifying the mechanisms of action of antidiabetic drugs and their potential use in Alzheimer's disease. Human studies in patients with mild cognitive impairment and Alzheimer's disease have shown that administration of some antidiabetic medications, such as intranasal insulin, metformin, incretins, and thiazolidinediones, can improve cognition and memory. This review aims to examine the latest evidence on antidiabetic medications as a potential candidate for the treatment of Alzheimer's disease.
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Affiliation(s)
- Michalis Michailidis
- Laboratory of Psychology, School of Psychology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Despina A. Tata
- Laboratory of Cognitive Neuroscience, School of Psychology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (D.A.T.); (D.M.)
| | - Despina Moraitou
- Laboratory of Cognitive Neuroscience, School of Psychology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (D.A.T.); (D.M.)
| | - Dimitrios Kavvadas
- Histology and Embryology Department, Faculty of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (D.K.); (S.K.); (T.P.)
| | - Sofia Karachrysafi
- Histology and Embryology Department, Faculty of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (D.K.); (S.K.); (T.P.)
| | - Theodora Papamitsou
- Histology and Embryology Department, Faculty of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (D.K.); (S.K.); (T.P.)
| | - Patroklos Vareltzis
- Department of Chemical Engineering, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Vasileios Papaliagkas
- Department of Biomedical Sciences, School of Health Sciences, International Hellenic University, 57400 Thessaloniki, Greece
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22
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Khan MS, Shahwan M, Shamsi A, Alhumaydhi FA, Alsagaby SA, Al Abdulmonem W, Abdullaev B, Yadav DK. Elucidating the Interactions of Fluoxetine with Human Transferrin Employing Spectroscopic, Calorimetric, and In Silico Approaches: Implications of a Potent Alzheimer's Drug. ACS OMEGA 2022; 7:9015-9023. [PMID: 35309456 PMCID: PMC8928501 DOI: 10.1021/acsomega.2c00182] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/21/2022] [Indexed: 06/12/2023]
Abstract
Neurodegenerative complexities, such as dementia, Alzheimer's disease (AD), and so forth, have been a crucial health concern for ages. Transferrin (Tf) is a chief target to explore in AD management. Fluoxetine (FXT) presents itself as a potent anti-AD drug-like compound and has been explored against several diseases based on the drug repurposing readings. The present study delineates the binding of FXT to Tf employing structure-based docking, molecular dynamics (MD) simulations, and principal component analysis (PCA). Docking results showed the binding of FXT with Tf with an appreciable binding affinity, making various close interactions. MD simulation of FXT with Tf for 100 ns suggested their stable binding without any significant structural alteration. Furthermore, fluorescence-based binding revealed a significant interaction between FXT and Tf. FXT binds to Tf with a binding constant of 5.5 × 105 M-1. Isothermal titration calorimetry (ITC) advocated the binding of FXT to Tf as spontaneous in nature, affirming earlier observations. This work indicated plausible interactions between FXT and Tf, which are worth considering for further studies in the clinical management of neurological disorders, including AD.
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Affiliation(s)
- Mohd Shahnawaz Khan
- Department
of Biochemistry, College of Sciences, King
Saud University, Riyadh 11451, Saudi Arabia
| | - Moyad Shahwan
- College
of Pharmacy & Health Sciences, Ajman
University, Ajman 346, United Arab Emirates
- Centre
of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman 346, United Arab Emirates
| | - Anas Shamsi
- Centre
of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman 346, United Arab Emirates
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Fahad A. Alhumaydhi
- Department
of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Suliman A. Alsagaby
- Department
of Medical Laboratories Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah 11932, Saudi Arabia
| | - Waleed Al Abdulmonem
- Department
of Pathology, College of Medicine, Qassim
University, Buraydah 51452, Saudi Arabia
| | | | - Dharmendra Kumar Yadav
- College
of Pharmacy, Gachon University of Medicine
and Science, Hambakmoeiro, Yeonsu-gu, Incheon City 21924, South Korea
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23
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Risedronate and Methotrexate Are High-Affinity Inhibitors of New Delhi Metallo-β-Lactamase-1 (NDM-1): A Drug Repurposing Approach. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27041283. [PMID: 35209073 PMCID: PMC8878330 DOI: 10.3390/molecules27041283] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/01/2022] [Accepted: 02/08/2022] [Indexed: 01/01/2023]
Abstract
Bacteria expressing New Delhi metallo-β-lactamase-1 (NDM-1) can hydrolyze β-lactam antibiotics (penicillins, cephalosporins, and carbapenems) and, thus, mediate multidrug resistance. The worldwide dissemination of NDM-1 poses a serious threat to public health, imposing a huge economic burden in the development of new antibiotics. Thus, there is an urgent need for the identification of novel NDM-1 inhibitors from a pool of already-known drug molecules. Here, we screened a library of FDA-approved drugs to identify novel non-β-lactam ring-containing inhibitors of NDM-1 by applying computational as well as in vitro experimental approaches. Different steps of high-throughput virtual screening, molecular docking, molecular dynamics simulation, and enzyme kinetics were performed to identify risedronate and methotrexate as the inhibitors with the most potential. The molecular mechanics/generalized Born surface area (MM/GBSA) and molecular dynamics (MD) simulations showed that both of the compounds (risedronate and methotrexate) formed a stable complex with NDM-1. Furthermore, analyses of the binding pose revealed that risedronate formed two hydrogen bonds and three electrostatic interactions with the catalytic residues of NDM-1. Similarly, methotrexate formed four hydrogen bonds and one electrostatic interaction with NDM-1’s active site residues. The docking scores of risedronate and methotrexate for NDM-1 were –10.543 kcal mol−1 and −10.189 kcal mol−1, respectively. Steady-state enzyme kinetics in the presence of risedronate and methotrexate showed a decreased catalytic efficiency (i.e., kcat/Km) of NDM-1 on various antibiotics, owing to poor catalytic proficiency and affinity. The results were further validated by determining the MICs of imipenem and meropenem in the presence of risedronate and methotrexate. The IC50 values of the identified inhibitors were in the micromolar range. The findings of this study should be helpful in further characterizing the potential of risedronate and methotrexate to treat bacterial infections.
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Li S, Li N, Wang Y, Wang Q, Li R, Zhang M, Panichayupakaranant P, Gao Y, Chen H. Structural, functional and proteomic differences of proteins extracted from white garlic and Laba garlic. Food Res Int 2022; 155:111047. [PMID: 35400432 DOI: 10.1016/j.foodres.2022.111047] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 02/16/2022] [Accepted: 02/18/2022] [Indexed: 02/05/2023]
Affiliation(s)
- Shuqin Li
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, PR China
| | - Nannan Li
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, PR China
| | - Yajie Wang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, PR China
| | - Qirou Wang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, PR China
| | - Ruilin Li
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, PR China
| | - Min Zhang
- Tianjin Agricultural University, Tianjin 300384, PR China; State Key Laboratory of Nutrition and Safety, Tianjin University of Science & Technology, Tianjin 300457, PR China
| | - Pharkphoom Panichayupakaranant
- Phytomedicine and Pharmaceutical Biotechnology Excellence Center, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Hat-Yai, Songkhla 90112, Thailand
| | - Yan Gao
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, PR China
| | - Haixia Chen
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, PR China.
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Exploring the Binding Pattern of Geraniol with Acetylcholinesterase through In Silico Docking, Molecular Dynamics Simulation, and In Vitro Enzyme Inhibition Kinetics Studies. Cells 2021; 10:cells10123533. [PMID: 34944045 PMCID: PMC8700130 DOI: 10.3390/cells10123533] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/25/2021] [Accepted: 12/10/2021] [Indexed: 01/01/2023] Open
Abstract
Acetylcholinesterase (AChE) inhibition is a key element in enhancing cholinergic transmission and subsequently relieving major symptoms of several neurological and neuromuscular disorders. Here, the inhibitory potential of geraniol and its mechanism of inhibition against AChE were elucidated in vitro and validated via an in silico study. Our in vitro enzyme inhibition kinetics results show that at increasing concentrations of geraniol and substrate, Vmax did not change significantly, but Km increased, which indicates that geraniol is a competitive inhibitor against AChE with an IC50 value 98.06 ± 3.92 µM. All the parameters of the ADME study revealed that geraniol is an acceptable drug candidate. A docking study showed that the binding energy of geraniol (−5.6 kcal mol−1) was lower than that of acetylcholine (−4.1 kcal mol−1) with AChE, which exhibited around a 12.58-fold higher binding affinity of geraniol. Furthermore, molecular dynamics simulation revealed that the RMSD of AChE alone or in complex with geraniol fluctuated within acceptable limits throughout the simulation. The mean RMSF value of the complex ensures that the overall conformation of the protein remains conserved. The average values of Rg, MolSA, SASA, and PSA of the complex were 3.16 Å, 204.78, 9.13, and 51.58 Å2, respectively. We found that the total SSE of AChE in the complex was 38.84% (α-helix: 26.57% and β-sheets: 12.27%) and remained consistent throughout the simulation. These findings suggest that geraniol remained inside the binding cavity of AChE in a stable conformation. Further in vivo investigation is required to fully characterize the pharmacokinetic properties, optimization of dose administration, and efficacy of this plant-based natural compound.
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Campos-Escamilla C, Siliqi D, Gonzalez-Ramirez LA, Lopez-Sanchez C, Gavira JA, Moreno A. X-ray Characterization of Conformational Changes of Human Apo- and Holo-Transferrin. Int J Mol Sci 2021; 22:13392. [PMID: 34948188 PMCID: PMC8705962 DOI: 10.3390/ijms222413392] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 11/29/2021] [Accepted: 12/07/2021] [Indexed: 11/16/2022] Open
Abstract
Human serum transferrin (Tf) is a bilobed glycoprotein whose function is to transport iron through receptor-mediated endocytosis. The mechanism for iron release is pH-dependent and involves conformational changes in the protein, thus making it an attractive system for possible biomedical applications. In this contribution, two powerful X-ray techniques, namely Macromolecular X-ray Crystallography (MX) and Small Angle X-ray Scattering (SAXS), were used to study the conformational changes of iron-free (apo) and iron-loaded (holo) transferrin in crystal and solution states, respectively, at three different pH values of physiological relevance. A crystallographic model of glycosylated apo-Tf was obtained at 3.0 Å resolution, which did not resolve further despite many efforts to improve crystal quality. In the solution, apo-Tf remained mostly globular in all the pH conditions tested; however, the co-existence of closed, partially open, and open conformations was observed for holo-Tf, which showed a more elongated and flexible shape overall.
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Affiliation(s)
- Camila Campos-Escamilla
- Instituto de Química, Universidad Nacional Autónoma de Mexico, Av. Universidad 3000, Ciudad Universitaria, Ciudad de Mexico 04510, Mexico;
| | - Dritan Siliqi
- Istitituto di Cristallografia (IC), National Research Council (CNR), Via Amendola 122/O, 70126 Bari, Italy
| | - Luis A. Gonzalez-Ramirez
- Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la Tierra, C.S.I.C. University of Granada, Avenida de las Palmeras No. 4, 18100 Armilla, Granada, Spain; (L.A.G.-R.); (C.L.-S.); (J.A.G.)
| | - Carmen Lopez-Sanchez
- Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la Tierra, C.S.I.C. University of Granada, Avenida de las Palmeras No. 4, 18100 Armilla, Granada, Spain; (L.A.G.-R.); (C.L.-S.); (J.A.G.)
| | - Jose Antonio Gavira
- Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la Tierra, C.S.I.C. University of Granada, Avenida de las Palmeras No. 4, 18100 Armilla, Granada, Spain; (L.A.G.-R.); (C.L.-S.); (J.A.G.)
| | - Abel Moreno
- Instituto de Química, Universidad Nacional Autónoma de Mexico, Av. Universidad 3000, Ciudad Universitaria, Ciudad de Mexico 04510, Mexico;
- Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la Tierra, C.S.I.C. University of Granada, Avenida de las Palmeras No. 4, 18100 Armilla, Granada, Spain; (L.A.G.-R.); (C.L.-S.); (J.A.G.)
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Khan MS, Rehman MT, Ismael MA, AlAjmi MF, Alruwaished GI, Alokail MS, Khan MR. Bioflavonoid (Hesperidin) Restrains Protein Oxidation and Advanced Glycation End Product Formation by Targeting AGEs and Glycolytic Enzymes. Cell Biochem Biophys 2021; 79:833-844. [PMID: 34110566 DOI: 10.1007/s12013-021-00997-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 05/12/2021] [Indexed: 10/21/2022]
Abstract
Alpha-amylase (α-amylase) not long ago has acquire recognition as a possible drug target for the management of diabetes. Here, we have investigated the binding and enzyme activity of α-amylase by hesperidin; a naturally occurring flavanone having wide therapeutic potential. Hesperidin exerted an inhibitory influence on α-amylase activity with an IC50 value of 16.6 µM. Hesperidin shows a significant binding toward α-amylase with a binding constant (Ka) of the order of 104 M-1. The evaluation of thermodynamic parameters (∆H and ∆S) suggested that van der Waals force and hydrogen bonding drive seemingly specific hesperidin-α-amylase complex formation. Glycation and oxidation studies were performed using human serum albumin (HSA) as ideal protein. Hesperidin inhibited fructosamine content ≈40% at 50 µM and inhibited advanced glycation end products (AGEs) formation by 71.2% at the same concentration. Moreover, significant recovery was evident in free -SH groups and carbonyl content of HSA. Additionally, molecular docking also entrenched in vitro observations and provided an insight into the important residues (Trp58, Gln63, His101, Glu233, Asp300, and His305) at the heart of hesperidin-α-amylase interaction. This study delineates mechanistic insight of hesperidin-α-amylase interaction and provides a platform for use of hesperidin to treat AGEs directed diseases.
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Affiliation(s)
- Mohd Shahnawaz Khan
- Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia.
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed A Ismael
- Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed F AlAjmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ghaida I Alruwaished
- Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
- Cosmetic Department, National Drug and Cosmetic Control Laboratory, Saudi Food and Drug Authority (SFDA), Riyadh, 11561, Saudi Arabia
| | - Majed S Alokail
- Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Rashid Khan
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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Jamshidnejad-Tosaramandani T, Kashanian S, Babaei M, Al-Sabri MH, Schiöth HB. The Potential Effect of Insulin on AChE and Its Interactions with Rivastigmine In Vitro. Pharmaceuticals (Basel) 2021; 14:ph14111136. [PMID: 34832918 PMCID: PMC8617642 DOI: 10.3390/ph14111136] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/03/2021] [Accepted: 11/05/2021] [Indexed: 12/14/2022] Open
Abstract
There is no definite cure for Alzheimer’s disease (AD) due to its multifactorial origin. Drugs that inhibit acetylcholinesterase (AChE), such as rivastigmine, are promising symptomatic treatments for AD. Emerging evidence suggests that insulin therapy can hinder several aspects of AD pathology. Insulin has been shown to modify the activity of AChE, but it is still unknown how insulin and AChE interact. Combination therapy, which targets several features of the disease based on existing medications, can provide a worthy therapy option for AD management. However, to date, no studies have examined the potential interaction of insulin with AChE and/or rivastigmine in vitro. In the present study, we employed the Response Surface Methodology (RSM) as an in vitro assessment to investigate the effect of insulin on both AChE activity and rivastigmine inhibitory action using a common spectrophotometric assay for cholinesterase activity, Ellman’s method. Our results showed that insulin, even at high concentrations, has an insignificant effect on both the activity of AChE and rivastigmine’s inhibitory action. The variance of our data is near zero, which means that the dispersion is negligible. However, to improve our understanding of the possible interaction of insulin and rivastigmine, or its target AChE, more in silico modelling and in vivo studies are needed.
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Affiliation(s)
- Tahereh Jamshidnejad-Tosaramandani
- Nanobiotechnology Department, Faculty of Innovative Science and Technology, Razi University, Kermanshah 6714414971, Iran;
- Department of Biology, Faculty of Science, Razi University, Kermanshah 6714414971, Iran;
- Department of Neuroscience, Functional Pharmacology, University of Uppsala, BMC, Husargatan 3, Box 593, 751 24 Uppsala, Sweden; (M.H.A.-S.); (H.B.S.)
| | - Soheila Kashanian
- Nanobiotechnology Department, Faculty of Innovative Science and Technology, Razi University, Kermanshah 6714414971, Iran;
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Science, Kermanshah 6734667149, Iran
- Faculty of Chemistry, Sensor and Biosensor Research Center (SBRC), Razi University, Kermanshah 6714414971, Iran
- Correspondence: ; Tel./Fax: +98-833-4274559
| | - Mahsa Babaei
- Department of Biology, Faculty of Science, Razi University, Kermanshah 6714414971, Iran;
| | - Mohamed H. Al-Sabri
- Department of Neuroscience, Functional Pharmacology, University of Uppsala, BMC, Husargatan 3, Box 593, 751 24 Uppsala, Sweden; (M.H.A.-S.); (H.B.S.)
| | - Helgi B. Schiöth
- Department of Neuroscience, Functional Pharmacology, University of Uppsala, BMC, Husargatan 3, Box 593, 751 24 Uppsala, Sweden; (M.H.A.-S.); (H.B.S.)
- Institute for Translational Medicine and Biotechnology, I.M. Sechenov First Moscow State Medical University, Trubetskay Str. 8, bldg 2, 119991 Moscow, Russia
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Evaluation of interactions between food colorant, tartrazine, and Apo-transferrin using spectroscopic analysis and docking simulation. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116715] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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High-Throughput Screening and Molecular Dynamics Simulation of Natural Product-like Compounds against Alzheimer's Disease through Multitarget Approach. Pharmaceuticals (Basel) 2021; 14:ph14090937. [PMID: 34577637 PMCID: PMC8466787 DOI: 10.3390/ph14090937] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 01/20/2023] Open
Abstract
Alzheimer’s disease (AD) is a progressive neurological disorder that affects 50 million people. Despite this, only two classes of medication have been approved by the FDA. Therefore, we have planned to develop therapeutics by multitarget approach. We have explored the library of 2029 natural product-like compounds for their multi-targeting potential against AD by inhibiting AChE, BChE (cholinergic pathway) MAO-A, and MOA-B (oxidative stress pathway) through in silico high-throughput screening and molecular dynamics simulation. Based on the binding energy of these target enzymes, approximately 189 compounds exhibited a score of less than −10 kcal/mol against all targets. However, none of the control inhibitors exhibited a binding affinity of less than −10 kcal/mol. Among these, the top 10 hits of compounds against all four targets were selected for ADME-T analysis. As a result, only F0850-4777 exhibited an acceptable range of physicochemical properties, drug-likeness, pharmacokinetics, and suitability for BBB permeation with high GI-A and non-toxic effects. The molecular dynamics study confirmed that F0850-4777 remained inside the binding cavity of targets in a stable conformation throughout the simulation and Prime-MM/GBSA study revealed that van der Waals’ energy (ΔGvdW) and non-polar solvation or lipophilic energy (ΔGSol_Lipo) contribute favorably towards the formation of a stable protein–ligand complex. Thus, F0850-4777 could be a potential candidate against multiple targets of two pathophysiological pathways of AD and opens the doors for further confirmation through in vitro and in vivo systems.
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Jabir NR, Rehman MT, Tabrez S, Alserihi RF, AlAjmi MF, Khan MS, Husain FM, Ahmed BA. Identification of Butyrylcholinesterase and Monoamine Oxidase B Targeted Ligands and their Putative Application in Alzheimer's Treatment: A Computational Strategy. Curr Pharm Des 2021; 27:2425-2434. [PMID: 33634754 DOI: 10.2174/1381612827666210226123240] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 02/19/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND With the burgeoning worldwide aging population, the incidence of Alzheimer's disease (AD) and its associated disorders is continuously rising. To appraise other relevant drug targets that could lead to potent enzyme targeting, 13 previously predicted ligands (shown favorable binding with AChE (acetylcholinesterase) and GSK-3 (glycogen synthase kinase) were screened for targeting 3 different enzymes, namely butyrylcholinesterase (BChE), monoamine oxidase A (MAO-A), and monoamine oxidase B (MAO-B) to possibly meet the unmet medical need of better AD treatment. MATERIALS AND METHODS The study utilized in silico screening of 13 ligands against BChE, MAO-A and MAOB using PyRx-Python prescription 0.8. The visualization of the active interaction of studied compounds with targeted proteins was performed by Discovery Studio 2020 (BIOVIA). RESULTS The computational screening of studied ligands revealed the docking energies in the range of -2.4 to -11.3 kcal/mol for all the studied enzymes. Among the 13 ligands, 8 ligands (55E, 6Z2, 6Z5, BRW, F1B, GVP, IQ6, and X37) showed the binding energies of ≤ -8.0 kcal/mol towards BChE, MAO-A and MAO-B. The ligand 6Z5 was found to be the most potent inhibitor of BChE and MAO-B, with a binding energy of -9.7 and -10.4 kcal mol, respectively. Molecular dynamics simulation of BChE-6Z5 and MAO-B-6Z5 complex confirmed the formation of a stable complex. CONCLUSION Our computational screening, molecular docking, and molecular dynamics simulation studies revealed that the above-mentioned enzymes targeted ligands might expedite the future design of potent anti-AD drugs generated on this chemical scaffold.
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Affiliation(s)
- Nasimudeen R Jabir
- Department of Biochemistry, Centre for Research and Development, PRIST University, Vallam, Thanjavur, Tamil Nadu, India
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Shams Tabrez
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Raed F Alserihi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohamed F AlAjmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohd Shahnawaz Khan
- Protein Research Chair, Department of Biochemistry, College of Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Fohad Mabood Husain
- Department of Food Science and Nutrition, Faculty of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Bakrudeen Ali Ahmed
- Department of Biochemistry, Centre for Research and Development, PRIST University, Vallam, Thanjavur, Tamil Nadu, India
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Khan MS, Khan RA, Rehman MT, Ismael MA, Husain FM, AlAjmi MF, Alokail MS, Altwaijry N, Alsalme AM. Elucidation of molecular interactions of theaflavin monogallate with camel milk lactoferrin: detailed spectroscopic and dynamic simulation studies. RSC Adv 2021; 11:26710-26720. [PMID: 35479994 PMCID: PMC9037349 DOI: 10.1039/d1ra03256a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/15/2021] [Indexed: 12/23/2022] Open
Abstract
Lactoferrin is a heme-binding multifunctional glycoprotein known for iron transportation in the blood and also contributes to innate immunity. In this study, the interaction of theaflavin monogallate, a polyphenolic component of black tea, with camel milk lactoferrin was studied using various biophysical and computational techniques. Fluorescence quenching at different temperatures suggests that theaflavin monogallate interacted with lactoferrin by forming a non-fluorescent complex, i.e., static quenching. Theaflavin monogallate shows a significant affinity towards lactoferrin with a binding constant of ∼104–105 M−1 at different temperatures. ANS binding shows that the binding of polyphenol resulted in the burial of hydrophobic domains of lactoferrin. Moreover, thermodynamic parameters (ΔH, ΔS and ΔG) suggested that the interaction between protein and polyphenol was entropically favored and spontaneous. Circular dichroism confirmed there was no alteration in the secondary structure of lactoferrin. The energy transfer efficiency (FRET) from lactoferrin to theaflavin was found to be approximately 50%, with a distance between protein and polyphenol of 2.44 nm. Molecular docking shows that the binding energy of lactoferrin–theaflavin monogallate interaction was −9.7 kcal mol−1. Theaflavin monogallate was bound at the central cavity of lactoferrin and formed hydrogen bonds with Gln89, Tyr192, Lys301, Ser303, Gln87, and Val250 of lactoferrin. Other residues, such as Tyr82, Tyr92, and Tyr192, were involved in hydrophobic interactions. The calculation of various molecular dynamics simulations parameters indicated the formation of a stable complex between protein and polyphenol. This study delineates the binding mechanism of polyphenol with milk protein and could be helpful in milk formulations and play a key role in the food industry. Lactoferrin is a heme-binding multifunctional glycoprotein known for iron transportation in the blood and also contributes to innate immunity.![]()
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Affiliation(s)
- Mohd Shahnawaz Khan
- Protein Research Chair, Department of Biochemistry, College of Science, King Saud University Riyadh 11451 Saudi Arabia
| | - Rais Ahmad Khan
- Department of Chemistry, College of Science, King Saud University Riyadh Saudi Arabia
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University Riyadh Saudi Arabia
| | - Mohamed A Ismael
- Protein Research Chair, Department of Biochemistry, College of Science, King Saud University Riyadh 11451 Saudi Arabia
| | - Fohad Mabood Husain
- Department of Food Science and Nutrition, College of Food and Agriculture Science, King Saud University Riyadh Saudi Arabia
| | - Mohamed F AlAjmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University Riyadh Saudi Arabia
| | - Majed S Alokail
- Protein Research Chair, Department of Biochemistry, College of Science, King Saud University Riyadh 11451 Saudi Arabia
| | - Nojood Altwaijry
- Protein Research Chair, Department of Biochemistry, College of Science, King Saud University Riyadh 11451 Saudi Arabia
| | - Ali M Alsalme
- Department of Chemistry, College of Science, King Saud University Riyadh Saudi Arabia
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Anwar S, Khan S, Shamsi A, Anjum F, Shafie A, Islam A, Ahmad F, Hassan MI. Structure-based investigation of MARK4 inhibitory potential of Naringenin for therapeutic management of cancer and neurodegenerative diseases. J Cell Biochem 2021; 122:1445-1459. [PMID: 34121218 DOI: 10.1002/jcb.30022] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/25/2021] [Accepted: 05/31/2021] [Indexed: 12/20/2022]
Abstract
MAP/microtubule affinity-regulating kinase 4 (MARK4) is a member of serine/threonine kinase family and considered an attractive drug target for many diseases. Screening of Indian Medicinal Plants, Phytochemistry, and Therapeutics (IMPPAT) using virtual high-throughput screening coupled with enzyme assay suggested that Naringenin (NAG) could be a potent inhibitor of MARK4. Structure-based molecular docking analysis showed that NAG binds to the critical residues found in the active site pocket of MARK4. Furthermore, molecular dynamics (MD) simulation studies for 100 ns have delineated the binding mechanism of NAG to MARK4. Results of MD simulation suggested that binding of NAG further stabilizes the structure of MARK4 by forming a stable complex. In addition, no significant conformational change in the MARK4 structure was observed. Fluorescence binding and isothermal titration calorimetric measurements revealed an excellent binding affinity of NAG to MARK4 with a binding constant (K) = 0.13 × 106 M-1 obtained from fluorescence binding studies. Further, enzyme inhibition studies showed that NAG has an admirable IC50 value of 4.11 µM for MARK4. Together, these findings suggest that NAG could be an effective MARK4 inhibitor that can potentially be used to treat cancer and neurodegenerative diseases.
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Affiliation(s)
- Saleha Anwar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Shama Khan
- Drug Discovery and Development Centre (H3D), University of Cape Town, Rondebosch, South Africa
| | - Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Farah Anjum
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Alaa Shafie
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
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Alazoumi KKM, Ahmed A, Alamery SF, Shamsi A, Ahmad B, Islam A, Farooqi H. Effect of Antioxidants on Heavy Metals Induced Conformational Alteration of Cytochrome C and Myoglobin. Protein Pept Lett 2021; 28:31-42. [PMID: 32520671 DOI: 10.2174/0929866527666200610134442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/13/2020] [Accepted: 03/15/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND The exposure to heavy metals due to unrestrained industrialization, pollution and non-degradability imposes a significant risk to human health. Proteins are prime targets of heavy metal stress, however, the underlying mechanisms and its impact on heme proteins is still not entirely clear. OBJECTIVE To analyze the deleterious effect of heavy metals such as cadmium, chromium and mercury on conformation of two proteins namely, cytochrome c and myoglobin. The protective effect of glycine and ascorbic acid (animal origin), gallic acid and sesamol (plant origin) on heavy metal exposure was studied. METHODS Far- and near-UV Circular Dichroism (CD) measurements monitored the changes in secondary and tertiary structure. Absorption Soret spectroscopy study revealed changes in heme-protein interaction. Peroxidase activity has been assayed to measure the absorption of tetraguaiacol. The interaction of heme proteins with different heavy metals was done using docking study. RESULTS Far- and near-UV CD measurements reveal that heavy metals disrupt the secondary and tertiary structure of heme proteins. Antioxidants counteract the deleterious effect of heavy metals. Absorption spectroscopy revealed changes in the Soret region of these heme proteins. Changes in peroxidase activity was observed on addition of heavy metals and antioxidants. Molecular docking validated interaction of the heavy metals with proteins with a significant binding affinity (-2.3 kcal/- mol). CONCLUSION Heavy metals interfered and disrupted both the heme proteins and mercury showed the maximum deleterious effect, further, chromium showed detrimental effect at very small concentration. The antioxidants from animal origin exhibited better protective response than those from plant source.
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Affiliation(s)
| | - Anwar Ahmed
- Center of Excellence in Biotechnology Research, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Salman Freeh Alamery
- Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi-110025, India
| | - Basir Ahmad
- Institute of Molecular Medicine, Jamia Hamdard, New Delhi-110062, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi-110025, India
| | - Humaira Farooqi
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi-110062, India
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Waseem R, Shamsi A, Mohammad T, Alhumaydhi FA, Kazim SN, Hassan MI, Ahmad F, Islam A. Multispectroscopic and Molecular Docking Insight into Elucidating the Interaction of Irisin with Rivastigmine Tartrate: A Combinational Therapy Approach to Fight Alzheimer's Disease. ACS OMEGA 2021; 6:7910-7921. [PMID: 33778302 PMCID: PMC7992156 DOI: 10.1021/acsomega.1c00517] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
This study was aimed to study the interaction between purified irisin and rivastigmine tartrate (RT), a cholinesterase inhibitor used in Alzheimer's therapy. Irisin mainly promotes brown fat-like features in white adipose tissues; however, it has some important role in the nervous system also, i.e., capable of opposing synapse and memory failure in Alzheimer's disease (AD). The recombinant protein was purified by Ni-NTA chromatography and characterized using spectroscopic and in silico techniques. Further, the mechanism of interaction between irisin and RT was investigated using various biophysical techniques. Fluorescence quenching studies suggested that there exists a moderate binding between irisin and RT with a binding constant (K) of 104 M-1 and the irisin-RT complex is guided by a combination of both static and dynamic modes of quenching. Thermodynamic parameters suggested the reaction to be driven by hydrogen bonding, making it specific. FTIR and CD spectroscopy suggested no secondary structural alterations in irisin in the presence of RT. Molecular docking investigation provided an insight into the important residues that play a key role in irisin-RT interactions. This study delineates an important finding in AD therapy and can provide a platform further to explore the potential of irisin in AD treatment.
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Affiliation(s)
- Rashid Waseem
- Center
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Anas Shamsi
- Center
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Taj Mohammad
- Center
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Fahad A. Alhumaydhi
- Department
of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 52571, Saudi Arabia
| | - Syed Naqui Kazim
- Center
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Md. Imtaiyaz Hassan
- Center
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Faizan Ahmad
- Center
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Asimul Islam
- Center
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
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The role of transferrins and iron-related proteins in brain iron transport: applications to neurological diseases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 123:133-162. [PMID: 33485481 DOI: 10.1016/bs.apcsb.2020.09.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Iron transport in the central nervous system (CNS) is a highly regulated process in which several important proteins participate to ensure this important metal reaches its sites of action. However, iron accumulation has been shown to be a common factor in different neurological disorders such as Alzheimer's disease, Parkinson's disease, Huntington's disease, Multiple Sclerosis, and Sanfilippo syndrome. This review is divided into four parts. The first part describes brain iron transport in homeostasis, mentioning the main proteins involved, whereas the second part contrasts the consequences of iron dysregulation, elaborating on its role in the aforementioned neurodegenerative diseases. The third part details the functions of the main proteins involved in brain iron homeostasis and their role in neurodegeneration. In the fourth part, in order to highlight the importance of transport proteins, the focus is set on human serum transferrin, the main iron transport protein. This final part describes perspectives about the mechanisms and chemical properties of human transferrin for the development of potential targeted drug delivery systems across the blood-brain barrier (BBB) or enhancers for the treatment of neurological diseases.
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Shamsi A, Anwar S, Shahbaaz M, Mohammad T, Alajmi MF, Hussain A, Hassan I, Ahmad F, Islam A. Evaluation of Binding of Rosmarinic Acid with Human Transferrin and Its Impact on the Protein Structure: Targeting Polyphenolic Acid-Induced Protection of Neurodegenerative Disorders. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:1245875. [PMID: 33204390 PMCID: PMC7661129 DOI: 10.1155/2020/1245875] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 07/30/2020] [Indexed: 12/15/2022]
Abstract
Rosmarinic acid (RA) is a natural compound that is gaining wide popularity owing to its broad-spectrum biological activities. RA is known for its wide range of medicinal properties and therapeutic applications in a vast range of neurodegenerative disorders thus making it a vital natural compound. Human transferrin (hTf) is a clinically significant protein that plays a pivotal role in maintaining iron homeostasis. The importance of studies pertaining to hTf is attributable to the pivotal role of iron deposition in CNS in neurodegenerative disorders. The study was intended to have an insight into the interaction between RA and hTf employing multispectroscopic approach, molecular docking, and molecular dynamic simulation studies. Fluorescence quenching studies revealed that RA shows an excellent binding affinity to hTf with a binding constant (K) of 107 M-1 and is guided by static mode of quenching. Isothermal titration calorimetry (ITC) further validated the spontaneous nature of binding. The estimation of enthalpy change (∆H) and entropy change (∆S) suggested that the RA-hTf complex formation is driven by hydrogen bonding, thereby making this process seemingly specific. Further, Fourier transform infrared (FTIR) and circular dichroism (CD) spectra suggested that RA induces conformational and structural changes in hTf. Additionally, molecular dynamics (MD) studies were carried out to investigate the stability of the hTf and hTf-RA system and suggested that binding of RA induces structural alteration in hTf with free hTf being more stable. This study provides a rationale to use RA in drug development against neurodegenerative disorders by designing novel functional foods containing RA.
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Affiliation(s)
- Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, New Delhi, India
| | - Saleha Anwar
- Centre for Interdisciplinary Research in Basic Sciences, New Delhi, India
| | - Mohd Shahbaaz
- South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa
- Laboratory of Computational Modeling of Drugs, South Ural State University, 76 Lenin Prospekt, Chelyabinsk, 454080, Russia
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, New Delhi, India
| | - Mohamed F. Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, New Delhi, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, New Delhi, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, New Delhi, India
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Shamsi A, Ahmed A, Khan MS, Husain FM, Bano B. Rosmarinic acid restrains protein glycation and aggregation in human serum albumin: Multi spectroscopic and microscopic insight - Possible Therapeutics Targeting Diseases. Int J Biol Macromol 2020; 161:187-193. [PMID: 32526295 DOI: 10.1016/j.ijbiomac.2020.06.048] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/19/2020] [Accepted: 06/05/2020] [Indexed: 12/30/2022]
Abstract
Protein aggregation and glycation are directly associated with many pathological conditions including several neurodegenerative disorders. This study investigates the potential of naturally occurring plant product, Rosmarinic acid (RA), to inhibit the glycation and aggregation process. In this study, we report that varying concentrations of methylglyoxal (MG) induce advanced glycation end products (AGEs) and aggregates formation in HSA in vitro on day 6 and day 8, respectively. AGEs specific fluorescence confirmed the formation of AGEs in HSA in the presence of MG and further characterized the inhibitory potential of RA. It was found that the presence of RA prevented AGEs formation in vitro. Further, aggregates of HSA were characterized employing multi spectroscopic and microscopic techniques and RA was found to inhibit this process. This study proposes that RA could be a potential natural molecule to treat disorders where AGEs and aggregates of proteins play a pivotal role.
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Affiliation(s)
- Anas Shamsi
- Department of Biochemistry, Aligarh Muslim University, Aligarh, India
| | - Azaj Ahmed
- Department of Biochemistry, Aligarh Muslim University, Aligarh, India
| | - Mohd Shahnawaz Khan
- Department of Biochemistry, College of Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Fohad Mabood Husain
- Department of Food Science and Nutrition, Faculty of Food and Agricultural Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Bilqees Bano
- Department of Biochemistry, Aligarh Muslim University, Aligarh, India.
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Raina N, Singh AK, Hassan MI, Ahmad F, Islam A. Concentration dependent effect of ethylene glycol on the structure and stability of holo α-lactalbumin: Characterization of intermediate state amidst soft interactions. Int J Biol Macromol 2020; 164:2151-2161. [PMID: 32735932 DOI: 10.1016/j.ijbiomac.2020.07.224] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 12/16/2022]
Abstract
The interior of the cell is crowded with different kinds of biological molecules with varying sizes, shapes and compositions which may affect physiological processes especially protein folding, protein conformation and protein stability. To understand the consequences of such a crowded environment, pH-induced unfolding of holo alpha-lactalbumin (holo α-LA) was studied in the presence of ethylene glycol (EG). The effect of EG on the folding and stability of holo α-LA in aqueous solution was investigated using several spectroscopic techniques. The results indicate that stabilization/destabilization of holo α-LA by EG is concentration- and pH-dependent. Low concentration of EG stabilizes the protein at pH near its pI. From the results of far-UV CD, UV-visible and ANS fluorescence, intermediate state (MG state) was characterized in the presence of high concentration of ethylene glycol. The results invoke a new mechanism for the formation of MG state identical to active component of BAMLET. MG state of holo α-LA has a direct implication to cancer therapy. MG state of α-LA in complex with specific type of lipid is a novel class of protein-based anti-cancer complexes that incorporate oleic acid and deliver it to the cancer cells.
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Affiliation(s)
- Neha Raina
- Department of Biotechnology, Sharda University, Greater Noida, Uttar Pradesh 201310, India; Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Amit Kumar Singh
- Department of Biotechnology, Sharda University, Greater Noida, Uttar Pradesh 201310, India.
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India.
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Wani TA, Alsaif N, Bakheit AH, Zargar S, Al-Mehizia AA, Khan AA. Interaction of an abiraterone with calf thymus DNA: Investigation with spectroscopic technique and modelling studies. Bioorg Chem 2020; 100:103957. [DOI: 10.1016/j.bioorg.2020.103957] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/15/2020] [Accepted: 05/18/2020] [Indexed: 01/11/2023]
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Anwar S, Shamsi A, Kar RK, Queen A, Islam A, Ahmad F, Hassan MI. Structural and biochemical investigation of MARK4 inhibitory potential of cholic acid: Towards therapeutic implications in neurodegenerative diseases. Int J Biol Macromol 2020; 161:596-604. [PMID: 32535203 DOI: 10.1016/j.ijbiomac.2020.06.078] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 02/06/2023]
Abstract
Microtubule affinity regulating kinase (MARK4) is considered as a potential drug target for diabetes, cancer, and neurodegenerative diseases. Since the role of MARK4 in the phosphorylation of tau protein and subsequently Alzheimer's disease has been established, therefore, we have investigated the binding affinity and MARK4 inhibitory potential of cholic acid (CHA) using both computational and spectroscopic methods. Molecular docking suggested a strong binding of CHA to the functionally important residues of MARK4. We further performed 500 ns molecular dynamics simulation which suggested the MARK4-CHA system was quite stable throughout the simulation trajectory. CHA potential binds to the MARK4 with a binding constant (K) of 107 M-1 at 288 K. Further, MARK4 activity was inhibited by CHA with an IC50 = 5.5 μM. Further insights into the thermodynamic parameters suggested that MARK4-CHA complex formation is driven by both electrostatic and van der Waals interactions. Overall study provides a rationale to use CHA in the drug development via MARK4 inhibition, towards possible therapeutic implications in neurodegenerative diseases.
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Affiliation(s)
- Saleha Anwar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Rajiv K Kar
- Fritz Haber Center for Molecular Dynamic Research, Hebrew University of Jerusalem, Israel
| | - Aarfa Queen
- Department of Chemistry, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India..
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Yousuf M, Shamsi A, Khan P, Shahbaaz M, AlAjmi MF, Hussain A, Hassan GM, Islam A, Rizwanul Haque QM, Hassan MI. Ellagic Acid Controls Cell Proliferation and Induces Apoptosis in Breast Cancer Cells via Inhibition of Cyclin-Dependent Kinase 6. Int J Mol Sci 2020; 21:E3526. [PMID: 32429317 PMCID: PMC7278979 DOI: 10.3390/ijms21103526] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/24/2020] [Accepted: 04/24/2020] [Indexed: 02/06/2023] Open
Abstract
Cyclin-Dependent Kinase 6 (CDK6) plays an important role in cancer progression, and thus, it is considered as an attractive drug target in anticancer therapeutics. This study presents an evaluation of dietary phytochemicals, capsaicin, tocopherol, rosmarinic acid, ursolic acid, ellagic acid (EA), limonene, caffeic acid, and ferulic acid for their potential to inhibit the activity of CDK6. Molecular docking and fluorescence binding studies revealed appreciable binding affinities of these compounds to the CDK6. Among them, EA shows the highest binding affinity for CDK6, and thus a molecular dynamics simulation study of 200 ns was performed to get deeper insights into the binding mechanism and stability of the CDK6-EA complex. Fluorescence binding studies revealed that EA binds to the CDK6 with a binding constant of K = 107 M-1 and subsequently inhibits its enzyme activity with an IC50 value of 3.053 µM. Analysis of thermodynamic parameters of CDK6-EA complex formation suggested a hydrophobic interaction driven process. The treatment of EA decreases the colonization of cancer cells and induces apoptosis. Moreover, the expression of CDK6 has been downregulated in EA-treated human breast cancer cell lines. In conclusion, this study establishes EA as a potent CDK6 inhibitor that can be further evaluated in CDK6 directed anticancer therapies.
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Affiliation(s)
- Mohd Yousuf
- Microbiology Research Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (M.Y.); (Q.M.R.H.)
| | - Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (A.S.); (P.K.); (A.I.)
| | - Parvez Khan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (A.S.); (P.K.); (A.I.)
| | - Mohd Shahbaaz
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa;
- Laboratory of Computational Modeling of Drugs, South Ural State University, 76 Lenin Prospekt, 454080 Chelyabinsk, Russia
| | - Mohamed F. AlAjmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (M.F.A.); (A.H.)
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (M.F.A.); (A.H.)
| | - Gulam Mustafa Hassan
- Department of Biochemistry, College of Medicine, Prince Sattam Bin Abdulaziz University, P.O. Box 173, Al-Kharj 11942, Saudi Arabia;
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (A.S.); (P.K.); (A.I.)
| | - Qazi Mohd Rizwanul Haque
- Microbiology Research Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (M.Y.); (Q.M.R.H.)
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (A.S.); (P.K.); (A.I.)
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Anwar S, Mohammad T, Shamsi A, Queen A, Parveen S, Luqman S, Hasan GM, Alamry KA, Azum N, Asiri AM, Hassan MI. Discovery of Hordenine as a Potential Inhibitor of Pyruvate Dehydrogenase Kinase 3: Implication in Lung Cancer Therapy. Biomedicines 2020; 8:E119. [PMID: 32422877 PMCID: PMC7277448 DOI: 10.3390/biomedicines8050119] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/09/2020] [Accepted: 05/11/2020] [Indexed: 11/16/2022] Open
Abstract
Design and development of potential pyruvate dehydrogenase kinase 3 (PDK3) inhibitors have gained attention because of their possible therapeutic uses in lung cancer therapy. In the present study, the binding affinity of naturally occurring alkaloids, hordenine, vincamine, tryptamine, cinchonine, and colcemid was measured with PDK3. The molecular docking and fluorescence binding studies suggested that all these compounds show a considerable binding affinity for PDK3. Among them, the affinity of hordenine to the PDK3 was excellent (K = 106 M-1) which was further complemented by isothermal titration calorimetric measurements. Hordenine binds in the active site pocket of PDK3 and forms a significant number of non-covalent interactions with functionally important residues. All-atom molecular dynamics (MD) simulation study suggested that the PDK3-hordenine complex is stabilized throughout the trajectory of 100ns and leads to fewer conformational changes. The enzyme inhibition studies showed that hordenine inhibits the activity of PDK3 with an IC50 value of 5.4 µM. Furthermore, hordenine showed a cytotoxic effect on human lung cancer cells (A549 and H1299) with an admirable IC50 value. However, it did not inhibit the growth of HEK293 cells up to 200 µM, indicating its non-toxicity to non-cancerous cell lines. In summary, our findings provide the basis for the therapeutic implication of hordenine and its derivatives in lung cancer and PDK3-related diseases after required in vivo validation.
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Affiliation(s)
- Saleha Anwar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (S.A.); (T.M.); (A.S.)
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (S.A.); (T.M.); (A.S.)
| | - Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (S.A.); (T.M.); (A.S.)
| | - Aarfa Queen
- Department of Chemistry, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India;
| | - Shahnaz Parveen
- Molecular Bioprospection Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India; (S.P.); (S.L.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Suaib Luqman
- Molecular Bioprospection Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India; (S.P.); (S.L.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Gulam Mustafa Hasan
- Department of Biochemistry, College of Medicine, Prince Sattam Bin Abdulaziz University, P.O. Box 173, Al-Kharj 11942, Saudi Arabia;
| | - Khalid A. Alamry
- Chemistry Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; (K.A.A.); (N.A.); (A.M.A.)
| | - Naved Azum
- Chemistry Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; (K.A.A.); (N.A.); (A.M.A.)
| | - Abdullah M. Asiri
- Chemistry Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; (K.A.A.); (N.A.); (A.M.A.)
- Center of Excellence for Advanced Materials Research (CEAMR), King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India; (S.A.); (T.M.); (A.S.)
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Mohammad T, Arif K, Alajmi MF, Hussain A, Islam A, Rehman MT, Hassan I. Identification of high-affinity inhibitors of pyruvate dehydrogenase kinase-3: towards therapeutic management of cancer. J Biomol Struct Dyn 2020; 39:586-594. [DOI: 10.1080/07391102.2020.1711810] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Kaynat Arif
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Mohamed F. Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Md. Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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