1
|
Shahabadi N, Ghaffari L, Mardani Z, Hadidi S. Analysis of the binding mechanism for a water-soluble Pd(II) complex containing β-amino alcohols with HSA applying experimental and computational methods. J Biomol Struct Dyn 2024; 42:3790-3801. [PMID: 37243704 DOI: 10.1080/07391102.2023.2216281] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 05/12/2023] [Indexed: 05/29/2023]
Abstract
In the study ahead, the binding interactions of the [Pd (HEAC) Cl2] complex with human serum albumin (HSA) protein have been assayed in vitro (pH= 7.40) utilizing computational and experimental procedures. The mentioned complex was synthesized as a water-soluble complex from {2-((2-((2-hydroxyethyl)amino)ethyl)amino) cyclohexanol} ligand = HEAC. The results of electronic absorption and circular dichroism investigations illustrated that the hydrophobicity of the Tryptophan microenvironment in HSA undergoes the changes by binding to the Pd(II) complex without substantial perturbations on the protein secondary structure. The fluorescence emission spectroscopy analysis revealed that with rising temperature, the quenching constant (Ksv) in the Stern-Volmer's relation decreases; so, it can be said that the interaction process is along with a static quenching mechanism. The values of 2.88 × 105 M-1, and 1.26 represent the binding constant (Kb) and the number of the binding sites (n), respectively. The Job graph showed the maximum point at χ = 0.5, which means organizing a new set with 1:1 stoichiometry. Thermodynamic profile (ΔH < 0, ΔS < 0, and ΔG < 0) has affirmed that van der Waals forces and hydrogen bonds have a basic function in the Pd(II) complex-albumin bindings. The ligand-competitive displacement studies utilizing warfarin and ibuprofen have represented that Pd(II) complex interacts with albumin by site II (subdomain IIIA). The computational molecular docking theory approved the results of the site-competitive tests; also, it indicated the existence of hydrogen bonds and van der Waals forces in Pd(II) complex-albumin interactions.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Nahid Shahabadi
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
| | - Lida Ghaffari
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
| | - Zahra Mardani
- Department of Inorganic Chemistry, Faculty of Chemistry, Urmia University, Urmia, Iran
| | - Saba Hadidi
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
| |
Collapse
|
2
|
Dong L, Zhang Y, Li Y, Liu Y, Chen Q, Liu L, Farag M, Liu L. The binding mechanism of oat phenolic acid to whey protein and its inhibition mechanism against AGEs as revealed using spectroscopy, chromatography and molecular docking. Food Funct 2023; 14:10221-10231. [PMID: 37916290 DOI: 10.1039/d3fo02474a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Heat sterilization of dairy products can promote the formation of advanced glycation end products (AGEs), protein oxidation products (POPs) and α-dicarbonyl compounds, which have a significant influence on health due to the close association of these products with diabetes complications. In this study, eight oat phenolic acids were first analyzed for their inhibitory effect against AGEs formation. Due to their strong inhibitory effects and structural differences, caffeic acid (CA) and gallic acid (GA) were further selected to assess their anti-glycosylation mechanisms using spectroscopy, chromatography and molecular docking. CA/GA reduced the production of total AGEs and POPs in various bovine milk simulation models and protected whey proteins from structural modifications, oxidation, and cross-linking. Comparative analyses showed a structure-effect relationship between CA/GA and AGEs inhibition. Oat phenolic acids against AGEs and POPs might be related to the unique bonding of key amino acid residues in whey proteins, the inhibitory role of early fructosamine and the trapping of reactive α-dicarbonyl groups to form adducts. In conclusion, oat phenolic acids might present a promising dietary strategy to alleviate AGEs production and glycation of proteins in dairy products upon storage.
Collapse
Affiliation(s)
- Lezhen Dong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Animal Protein Deep Processing Technology of Zhejiang, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, School of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, PR China
| | - Yunzhen Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Animal Protein Deep Processing Technology of Zhejiang, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, School of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, PR China
| | - Ying Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Animal Protein Deep Processing Technology of Zhejiang, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, School of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, PR China
| | - Yahui Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Animal Protein Deep Processing Technology of Zhejiang, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, School of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, PR China
| | - Qin Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Animal Protein Deep Processing Technology of Zhejiang, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, School of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, PR China
| | - Lingyi Liu
- Department of Food Science and Technology, University of Nebraska-Lincoln, 68588, NE, USA
| | - Mohamed Farag
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Lianliang Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Animal Protein Deep Processing Technology of Zhejiang, Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, School of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, PR China
| |
Collapse
|
3
|
Bhardwaj T, Ahmad I, Somvanshi P. Systematic analysis to identify novel disease indications and plausible potential chemical leads of glutamate ionotropic receptor NMDA type subunit 1, GRIN1. J Mol Recognit 2023; 36:e2997. [PMID: 36259267 DOI: 10.1002/jmr.2997] [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: 07/19/2022] [Revised: 09/19/2022] [Accepted: 10/07/2022] [Indexed: 12/15/2022]
Abstract
Schizophrenia is a mental illness affecting the normal lifestyle of adults and early adolescents incurring major symptoms as jumbled speech, involvement in everyday activities eventually got reduced, patients always struggle with attention and memory, reason being both the genetic and environmental factors responsible for altered brain chemistry and structure, resulting in schizophrenia and associated orphan diseases. The network biology describes the interactions among genes/proteins encoding molecular mechanisms of biological processes, development, and diseases. Besides, all the molecular networks, protein-protein Interaction Networks have been significant in distinguishing the pathogenesis of diseases and thereby drug discovery. The present meta-analysis prioritizes novel disease indications viz. rare and orphan diseases associated with target Glutamate Ionotropic Receptor NMDA Type Subunit 1, GRIN1 using text mining knowledge-based tools. Furthermore, ZINC database was virtually screened, and binding conformation of selected compounds was performed and resulted in the identification of Narciclasine (ZINC04097652) and Alvespimycin (ZINC73138787) as potential inhibitors. Furthermore, docked complexes were subjected to MD simulation studies which suggests that the identified leads could be a better potential drug to recuperate schizophrenia.
Collapse
Affiliation(s)
- Tulika Bhardwaj
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Irshad Ahmad
- Department of Medical Rehabilitation Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Pallavi Somvanshi
- School of Computational & Integrative Sciences (SC&IS), Jawaharlal Nehru University, New Delhi, India.,Special Centre of Systems Medicine (SCSM), Jawaharlal Nehru University, New Delhi, India
| |
Collapse
|
4
|
In Silico Comparative Exploration of Allergens of Periplaneta americana, Blattella germanica and Phoenix dactylifera for the Diagnosis of Patients Suffering from IgE-Mediated Allergic Respiratory Diseases. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248740. [PMID: 36557872 PMCID: PMC9785491 DOI: 10.3390/molecules27248740] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/03/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
The burden of allergic illnesses is continuously rising, and patient diagnosis is a significant problem because of how intricately hereditary and environmental variables interact. The past three to four decades have seen an outbreak of allergies in high-income countries. According to reports on the illness, asthma affects around 300 million individuals worldwide. Identifying clinically important allergens for the accurate classification of IgE-mediated allergy respiratory disease diagnosis would be beneficial for implementing standardized allergen-associated therapy. Therefore, the current study includes an in silico analysis to identify potential IgE-mediated allergens in date palms and cockroaches. Such an immunoinformatic approach aids the prioritization of allergens with probable involvement in IgE-mediated allergic respiratory diseases. Immunoglobulin E (IgE) was used for molecular dynamic simulations, antigen-antibody docking analyses, epitope identifications, and characterizations. The potential of these allergens (Per a7, Per a 1.0102, and Bla g 1.0101) in IgE-mediated allergic respiratory diseases was explored through the evaluation of physicochemical characteristics, interaction observations, docking, and molecular dynamics simulations for drug and vaccine development.
Collapse
|
5
|
Han X, Sun J, Niu T, Mao B, Gao S, Zhao P, Sun L. Molecular Insight into the Binding of Astilbin with Human Serum Albumin and Its Effect on Antioxidant Characteristics of Astilbin. Molecules 2022; 27:molecules27144487. [PMID: 35889360 PMCID: PMC9321622 DOI: 10.3390/molecules27144487] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/03/2022] [Accepted: 07/08/2022] [Indexed: 11/25/2022] Open
Abstract
Astilbin is a dihydroflavonol glycoside identified in many natural plants and functional food with promising biological activities which is used as an antioxidant in the pharmaceutical and food fields. This work investigated the interaction between astilbin and human serum albumin (HSA) and their effects on the antioxidant activity of astilbin by multi-spectroscopic and molecular modeling studies. The experimental results show that astilbin quenches the fluorescence emission of HSA through a static quenching mechanism. Astilbin and HSA prefer to bind at the Site Ⅰ position, which is mainly maintained by electrostatic force, hydrophobic and hydrogen bonding interactions. Multi-spectroscopic and MD results indicate that the secondary structure of HSA could be changed because of the interaction of astilbin with HSA. DPPH radical scavenging assay shows that the presence of HSA reduces the antioxidant capacity of astilbin. The explication of astilbin–HSA binding mechanism will provide insights into clinical use and resource development of astilbin in food and pharmaceutical industries.
Collapse
Affiliation(s)
- Xiangyu Han
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (X.H.); (J.S.); (T.N.); (B.M.)
| | - Jing Sun
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (X.H.); (J.S.); (T.N.); (B.M.)
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Tianmei Niu
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (X.H.); (J.S.); (T.N.); (B.M.)
| | - Beibei Mao
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (X.H.); (J.S.); (T.N.); (B.M.)
| | - Shijie Gao
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan 250355, China;
| | - Pan Zhao
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (X.H.); (J.S.); (T.N.); (B.M.)
- Correspondence: (P.Z.); (L.S.)
| | - Linlin Sun
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China; (X.H.); (J.S.); (T.N.); (B.M.)
- Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan 250355, China;
- Correspondence: (P.Z.); (L.S.)
| |
Collapse
|
6
|
Shahabadi N, Zendehcheshm S. Interaction of human hemoglobin (HHb) and cytochrome c (Cyt c) with biogenic chloroxine-conjugated silver nanoflowers: spectroscopic and molecular docking approaches. J Biomol Struct Dyn 2021; 40:8913-8924. [PMID: 33928842 DOI: 10.1080/07391102.2021.1919555] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this research, the biological activity of the antibacterial drug Chloroxine-conjugated biogenic AgNPs (COX-AgNPs) was investigated in simulated physiological conditions (pH = 7.40). Different spectroscopic methods such as UV-visible, fluorescence, and circular dichroism spectroscopic and docking simulation were employed to evaluate the structural changes in the most important blood proteins (human hemoglobin (HHb) and Cytochrome c (Cyt c)) in the presence of COX-AgNPs. The results showed that the COX-AgNPs can bind to HHb and Cyt c and the secondary structure of these proteins remains unchanged, which is crucial in providing insights into the side effects of newly synthesized drugs on their carriers.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Nahid Shahabadi
- Inorganic Chemistry Department, Faculty of Chemistry, Razi University, Kermanshah, Iran.,Medical Biology Research Center (MBRC), Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Saba Zendehcheshm
- Inorganic Chemistry Department, Faculty of Chemistry, Razi University, Kermanshah, Iran.,Medical Biology Research Center (MBRC), Kermanshah University of Medical Sciences, Kermanshah, Iran
| |
Collapse
|
7
|
Zhang S, Gan R, Zhao L, Sun Q, Xiang H, Xiang X, Zhao G, Li H. Unveiling the interaction mechanism of alogliptin benzoate with human serum albumin: Insights from spectroscopy, microcalorimetry, and molecular docking and molecular dynamics analyses. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 246:119040. [PMID: 33068900 DOI: 10.1016/j.saa.2020.119040] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 09/23/2020] [Accepted: 10/01/2020] [Indexed: 06/11/2023]
Abstract
The interaction between a DPP-4 inhibitor, alogliptin benzoate (AB), and human serum albumin (HSA) was systematically investigated via spectroscopy, microcalorimetry and molecular simulations. Steady-state fluorescence and time-resolved fluorescence spectrometry illustrated that the fluorescence quenching type of AB to HSA was static and caused by the formation of ground state AB-HSA complex. Isothermal titration calorimetry (ITC) combined with fluorescence spectra revealed that the affinity of AB to the subdomain IIA of HSA was moderate with a binding constant in the order of 104. Molecular docking analysis and thermodynamic parameters demonstrated that this combination was maintained by hydrogen bonding along with van der Waals force and hydrophobic force. Circular dichroism and three-dimensional (3D) fluorescence showed that AB increased the hydrophobicity of Trp residue and the α-helix content of HSA by 1.99%. Microdifferential scanning calorimetry revealed that the addition of AB enhanced the thermal stability of HSA. The action forces, binding stability, binding sites, and protein structure of the AB-HSA system were evaluated via molecular dynamics analysis in the simulated environment. On the basis of molecular docking, MD simulation constructed a more reliable 3D model of the AB-HSA complex in terms of spatial structure.
Collapse
Affiliation(s)
- Shuangshuang Zhang
- School of Chemical Engineering, Sichuan University, Chengdu 610065, Sichuan, China
| | - Ruixue Gan
- School of Chemical Engineering, Sichuan University, Chengdu 610065, Sichuan, China
| | - Ludan Zhao
- School of Chemical Engineering, Sichuan University, Chengdu 610065, Sichuan, China
| | - Qiaomei Sun
- School of Chemical Engineering, Sichuan University, Chengdu 610065, Sichuan, China.
| | - Hongzhao Xiang
- School of Chemical Engineering, Sichuan University, Chengdu 610065, Sichuan, China
| | - Xi Xiang
- School of Chemical Engineering, Sichuan University, Chengdu 610065, Sichuan, China
| | - Gang Zhao
- School of Chemical Engineering, Sichuan University, Chengdu 610065, Sichuan, China.
| | - Hui Li
- School of Chemical Engineering, Sichuan University, Chengdu 610065, Sichuan, China
| |
Collapse
|