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Yu H, Xing Z, Jia K, Li S, Xu Y, Zhao P, Zhu X. Inquiry lipaseoring the mechanism of pancreatic lipase inhibition by isovitexin based on multispectral method and enzyme inhibition assay. LUMINESCENCE 2024; 39:e4765. [PMID: 38769927 DOI: 10.1002/bio.4765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/26/2024] [Accepted: 04/17/2024] [Indexed: 05/22/2024]
Abstract
Isovitexin is a main natural flavonoid component in various plants. Currently, the inhibitory effect of isovitexin on pancreatic lipase (PL) and its mechanism have not been elucidated yet. In the present study, we investigated the inhibitory effect of isovitexin on PL, as well as its interaction mechanism, using enzyme inhibition methods, spectroscopic analysis, and molecular simulations. Results showed that isovitexin possessed significant PL inhibitory activity, with IC50 values of 0.26 ± 0.02 mM. The interaction between isovitexin and PL was dominated by static quenching, and mainly through hydrogen bonding and hydrophobic interaction forces. Analysis of fluorescence spectroscopy confirmed that isovitexin binding altered the conformation of the PL. Circular dichroism (CD) spectrum indicated that isovitexin altered the secondary structure of PL by decreasing the α-helix content and increasing the β-fold content. Molecular simulations further characterize the conformational changes produced by the interaction between isovitexin with PL. The performed study may provide a new insight into the inhibitory mechanism of isovitexin as a novel PL inhibitor.
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Affiliation(s)
- Hui Yu
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Zhongfu Xing
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Kaijie Jia
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Sai Li
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yankun Xu
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Pan Zhao
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xiaojing Zhu
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
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Lu Y, Feng S, Zhao Y, Wang Y, Diao M, Liang Y, Zhang T. Comparison of interactions between alpha-lactalbumin and three protopanaxadiol ginsenosides: Impacts on the structure and antitumor properties. Food Chem 2024; 439:138046. [PMID: 38029562 DOI: 10.1016/j.foodchem.2023.138046] [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: 07/27/2023] [Revised: 11/16/2023] [Accepted: 11/18/2023] [Indexed: 12/01/2023]
Abstract
In this research, interactions between α-lactalbumin (ALA) and three protopanaxadiol ginsenosides [20(S)-Rg3, 20(S)-Rh2, and 20(S)-PPD] were compared to explore the effects of similar ligand on structure and cytotoxicity of ALA. Multi-spectroscopy revealed the binding between ALA and ginsenoside changed the conformation of ALA, which related to different structures and solubility of ligands. Scanning electron microscope illustrated that all ALA-ginsenoside complexes exhibited denser structures via hydrophobic interactions. Additionally, the cytotoxic experiments confirmed that the cytotoxicity of ginsenoside was enhanced after binding with ALA. Molecular docking showed all three ginsenosides were bound to the sulcus depression region of ALA via hydrogen bonding and hydrophobic interaction. Furthermore, molecular dynamics simulation elucidated the precise binding sites and pertinent system properties. Among all three composite systems, 20(S)-Rh2 had optimal binding affinity. These findings enhanced understanding of the synergistic utilization of ALA and ginsenosides as functional ingredients in food, medicine, and cosmetics.
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Affiliation(s)
- Yitong Lu
- College of Food Science and Engineering, Jilin University, Changchun 130062, China.
| | - Sitong Feng
- College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Yueying Zhao
- College of Food Science and Engineering, Jilin University, Changchun 130062, China.
| | - Yingyi Wang
- College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Mengxue Diao
- College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Yuan Liang
- College of Food Science and Engineering, Jilin University, Changchun 130062, China.
| | - Tiehua Zhang
- College of Food Science and Engineering, Jilin University, Changchun 130062, China.
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Yadollahi E, Shareghi B, Farhadian S, Hashemi Shahraki F. Conformational dynamics of trypsin in the presence of caffeic acid: a spectroscopic and computational investigation. J Biomol Struct Dyn 2024; 42:3108-3117. [PMID: 37278377 DOI: 10.1080/07391102.2023.2212077] [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: 10/19/2022] [Accepted: 05/01/2023] [Indexed: 06/07/2023]
Abstract
Caffeic acid is one of the widely distributed phenolic compounds in nature and can be found in planet products. On the other hand, trypsin is a vital digestive enzyme in the intestine that plays an essential role in the immune response, blood coagulation, apoptosis and protein maturation like protein digestion. Several studies have revealed the inhibitory effects of the phenolic compound on the digestive enzyme. The present study reports functional and conformational alteration of trypsin after caffeic acid addition using multiple experimental and computational techniques for the first time. The intrinsic fluorescence of trypsin is quenched in the presence of caffeic acid via a static mechanism. The percent of secondary structures (α-helix and β-sheet) of trypsin alter after caffeic acid addition. In the kinetic study, a reduction in the trypsin function is obtained with a lower Vmax and Kcat upon interaction with caffeic acid. The thermal study reveals an unstable structure of trypsin upon complex formation with this phenolic compound. Also, the binding sites and conformational changes of trypsin are elucidated through molecular docking and molecular dynamic simulation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Elham Yadollahi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, Iran
- Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Behzad Shareghi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, Iran
- Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, Iran
- Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Fatemeh Hashemi Shahraki
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, Iran
- Central Laboratory, Shahrekord University, Shahrekord, Iran
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Amir M, Aamir Qureshi M, Khan A, Nayeem SM, Ayoub Malik W, Javed S. Exploring the interaction of tepotinib with calf thymus DNA using molecular dynamics simulation and multispectroscopic techniques. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 308:123678. [PMID: 38039637 DOI: 10.1016/j.saa.2023.123678] [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: 08/03/2023] [Revised: 10/05/2023] [Accepted: 11/21/2023] [Indexed: 12/03/2023]
Abstract
In recent times, there has been a surge in the discovery of drugs that directly interact with DNA, influencing gene expression. As a result, understanding how biomolecules interact with DNA has become a major area of research. One such drug is Tepotinib (TPT), an FDA-approved anti-cancer medication known as a MET tyrosine kinase inhibitor, used in chemotherapy for metastatic non-small cell lung cancer (NSCLC) with MET exon 14 skipping alterations. In our study, we adopted both biophysical and in-silico methods to investigate the binding relationship of TPT and ctDNA. The absorption spectra of ctDNA exhibited a hypochromic effect when titrated with TPT and the binding constant of TPT-ctDNA complex was calculated, Ka = 9.91 × 104 M-1. By computing bimolecular enhancement constant (KB) and thermodynamic enhancement constant (KD) in fluorometric investigations, it was found that the fluorescence enhancement is a result of a static process involving the ctDNA-TPT complex formation in the ground state, as opposed to a dynamic process. The displacement assay results further supported this finding, showing that TPT exhibits a binding preference for minor groove of ct-DNA and was also demonstrated by KI quenching and CD spectroscopy. The molecular docking and molecular dynamic simulations validated TPT's groove binding nature and binding pattern with ctDNA, respectively. Thus, the results of our present investigation offer valuable insights into the interaction between TPT and ctDNA. It is evident that TPT, as an anti-cancer medication, binds to the minor groove of ctDNA.
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Affiliation(s)
- Mohd Amir
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India.
| | - Mohd Aamir Qureshi
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India.
| | - Ashma Khan
- Department of Chemistry, Faculty of Sciences, Aligarh Muslim University, Aligarh 202002, India.
| | - Shahid M Nayeem
- Department of Chemistry, Faculty of Sciences, Aligarh Muslim University, Aligarh 202002, India.
| | - Waseem Ayoub Malik
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India.
| | - Saleem Javed
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India.
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Farokhvand N, Shareghi B, Farhadian S. Evidence for paraquat-pepsin interaction: In vitro and silico study. CHEMOSPHERE 2024; 349:140714. [PMID: 38006922 DOI: 10.1016/j.chemosphere.2023.140714] [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: 04/19/2023] [Revised: 10/03/2023] [Accepted: 11/12/2023] [Indexed: 11/27/2023]
Abstract
The use of the herbicide paraquat (PQ) has raised concerns about potential environmental consequences due to its toxicity and persistence in the environment. Considering the affinity of dangerous compounds to biological molecules, it is necessary to know their binding properties. This article focuses on the behavior of the pepsin enzyme following its contact with paraquat poison, and the interaction between paraquat and pepsin has been investigated in laboratory conditions and simulated physiological conditions using multispectral techniques. Fluorescence experiments showed that PQ uses a static method to quench pepsin's intrinsic fluorescence. By causing structural damage to pepsin, PQ may be detrimental as it alters its conformational function based on FT-IR spectroscopy. The coupling reaction is a spontaneous process caused by hydrogen bonding and van der Waals forces according to the analysis of the thermodynamic parameters of each system at three different temperatures. The molecular structure of pepsin changes when it binds to PQ. Also, the results showed that PQ is a pepsin inhibitor that changes the function of the enzyme.
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Affiliation(s)
- Najimeh Farokhvand
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box.115, Iran
| | - Behzad Shareghi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box.115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
| | - Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box.115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
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Zhang Z, Li T, Zhang Y, Shao J, Ye C, Wang H, Zhu B, Zhang Y. Effect of polysaccharides on conformational changes and functional properties of protein-polyphenol binary complexes: A comparative study. Int J Biol Macromol 2023; 253:126890. [PMID: 37716302 DOI: 10.1016/j.ijbiomac.2023.126890] [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: 07/19/2023] [Revised: 09/05/2023] [Accepted: 09/11/2023] [Indexed: 09/18/2023]
Abstract
This study aimed to investigate the effect of different polysaccharides on the binding behavior and functional properties of soybean protein isolate (SPI)-quercetin (Que) complex. The binding behavior was assessed using multi-spectral technique with the Stern-Volmer equation, which confirmed the presence of static fluorescence quenching in Que and SPI. The addition of sodium alginate (SA) resulted in a reduction of the binding affinity between SPI and Que, while dextran (DX) exhibited some promoting effect. A slight blue shift was observed in amide I and amide II bands, indicating the presence of hydrophobic and electrostatic interactions. Circular dichroism spectra revealed the ordered structures transformed into a more disordered state when polysaccharides were added, leading to an increase in random coils (SA: 18.5 %, DX: 15.4 %). Docking and dynamic simulations demonstrated that SA displayed greater stability within the hydrophobic compartments of SPI than DX, increased rigidity and stability of the SPI structure in SPI-Que-SA complexes. Electrostatic forces played a significant role between SPI and SA, while van der Waals forces were the main driving forces in SPI-DX complexes. Overall, the introduction of SA led to a looser and stable structure of SPI-Que complexes, resulting in an improvement of their emulsifying, foaming, and antioxidant properties.
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Affiliation(s)
- Zifan Zhang
- College of Public Health and Health Sciences, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Taoran Li
- College of Public Health and Health Sciences, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yubo Zhang
- College of Public Health and Health Sciences, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Juanjuan Shao
- Department of Science and Technology, Hebei Agricultural University, Hebei 061100, China
| | - Chengxiang Ye
- College of Public Health and Health Sciences, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Hongwu Wang
- College of Public Health and Health Sciences, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Beibei Zhu
- College of Chinese Medicine Pharmaceutical Engineering, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China..
| | - Yating Zhang
- College of Public Health and Health Sciences, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
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Khan R, Naseem I. Antiglycation and antioxidant potential of coumaric acid isomers: a comparative in-vitro study. J Biomol Struct Dyn 2023:1-15. [PMID: 37850430 DOI: 10.1080/07391102.2023.2267699] [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: 03/16/2023] [Accepted: 09/04/2023] [Indexed: 10/19/2023]
Abstract
Advanced glycation end products (AGEs) are the product of non-enzymatic glycation of serum proteins. AGEs increase reactive oxygen species (ROS) formation, which leads to diabetic complications. Phytochemicals exhibit lesser side effects as compared to conventional therapy. In this study, three isomers of coumaric acid (ortho, meta, para) were used to deduce the better one in terms of reducing diabetic complications. For this purpose, human serum albumin (HSA) was incubated with glucose in the absence and presence of isomers for 28 days. To avoid any growth, NaN3 was added and temperature was kept constant throughout the incubation period. Studies like fluorescence, circular dichroism spectroscopy, fructosamine analysis, free lysine estimation, free thiol group estimation were done. To investigate the ROS production, fluorescence microscopy of isolated lymphocytes using DAPI and dichloro-dihydro-fluorescein diacetate were performed. Molecular docking and molecular dynamic simulations (root-mean-square deviation, root-mean-square fluctuations, radius of gyration and solvent-accessible surface area) of HSA and peroxisome proliferator activated receptor (PPAR) alpha and gamma were also done. It was observed that in glycated protein samples, the level of absorbance, fluorescence, fructosamine and carbonyl group increased along with the loss of secondary structure, free lysine and thiol group. These parameters were found gradually recovered in treated samples. ROS production and apoptosis were found to be reduced in lymphocytes treated with p-Coumaric acid (pCA)-treated protein samples as compared to lymphocyte treated with glycated protein. Computational modelling suggested a stable complex formation of HSA and PPARs with pCA. Results with pCA at 200 µM were consistently better than other two isomers. Our next step is to evaluate this study in rats.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rizwan Khan
- Department of Biochemistry, Life Sciences, Aligarh Muslim University, Aligarh, UP, India
| | - Imrana Naseem
- Department of Biochemistry, Life Sciences, Aligarh Muslim University, Aligarh, UP, India
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Kciuk M, Alam M, Ali N, Rashid S, Głowacka P, Sundaraj R, Celik I, Yahya EB, Dubey A, Zerroug E, Kontek R. Epigallocatechin-3-Gallate Therapeutic Potential in Cancer: Mechanism of Action and Clinical Implications. Molecules 2023; 28:5246. [PMID: 37446908 DOI: 10.3390/molecules28135246] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Cellular signaling pathways involved in the maintenance of the equilibrium between cell proliferation and apoptosis have emerged as rational targets that can be exploited in the prevention and treatment of cancer. Epigallocatechin-3-gallate (EGCG) is the most abundant phenolic compound found in green tea. It has been shown to regulate multiple crucial cellular signaling pathways, including those mediated by EGFR, JAK-STAT, MAPKs, NF-κB, PI3K-AKT-mTOR, and others. Deregulation of the abovementioned pathways is involved in the pathophysiology of cancer. It has been demonstrated that EGCG may exert anti-proliferative, anti-inflammatory, and apoptosis-inducing effects or induce epigenetic changes. Furthermore, preclinical and clinical studies suggest that EGCG may be used in the treatment of numerous disorders, including cancer. This review aims to summarize the existing knowledge regarding the biological properties of EGCG, especially in the context of cancer treatment and prophylaxis.
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Affiliation(s)
- Mateusz Kciuk
- Department of Molecular Biotechnology and Genetics, University of Lodz, Banacha Street 12/16, 90-237 Lodz, Poland
- Doctoral School of Exact and Natural Sciences, University of Lodz, Banacha Street 12/16, 90-237 Lodz, Poland
| | - Manzar Alam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Nemat Ali
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Summya Rashid
- Department of Pharmacology & Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, P.O. Box 173, Al-Kharj 11942, Saudi Arabia
| | - Pola Głowacka
- Department of Medical Biochemistry, Medical University of Lodz, Mazowiecka 6/8, 90-001 Lodz, Poland
- Doctoral School of Medical University of Lodz, Hallera 1 Square, 90-700 Lodz, Poland
| | - Rajamanikandan Sundaraj
- Department of Biochemistry, Centre for Drug Discovery, Karpagam Academy of Higher Education, Coimbatore 641021, India
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri 38280, Turkey
| | - Esam Bashir Yahya
- Bioprocess Technology Division, School of Industrial Technology, Universiti Sains Malaysia, Penang 11800, Malaysia
| | - Amit Dubey
- Computational Chemistry and Drug Discovery Division, Quanta Calculus, Greater Noida 201310, India
- Department of Pharmacology, Saveetha Institute of Medical and Technical Sciences, Saveetha Dental College and Hospital, Chennai 600077, India
| | - Enfale Zerroug
- LMCE Laboratory, Group of Computational and Pharmaceutical Chemistry, University of Biskra, Biskra 07000, Algeria
| | - Renata Kontek
- Department of Molecular Biotechnology and Genetics, University of Lodz, Banacha Street 12/16, 90-237 Lodz, Poland
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Hashemi-Shahraki F, Shareghi B, Farhadian S, Yadollahi E. A comprehensive insight into the effects of caffeic acid (CA) on pepsin: Multi-spectroscopy and MD simulations methods. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 289:122240. [PMID: 36527971 DOI: 10.1016/j.saa.2022.122240] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 12/08/2022] [Accepted: 12/10/2022] [Indexed: 06/17/2023]
Abstract
The interaction between caffeic acid (CA) and pepsin was investigated using multi-spectroscopy approaches and molecular dynamic simulations (MDS). The effects of CA on the structure, stability, and activity of pepsin were studied. Fluorescence emission spectra and UV-vis absorption peaks all represented the static quenching mechanism of pepsin by CA. Moreover, the fluorescence spectra displayed that the interaction of CA exposed the tryptophan chromophores of pepsin to a more hydrophilic micro-environment. Consistent with the simulation results, thermodynamic parameters revealed that CA was bound to pepsin with a high binding affinity. The Van der Waals force and Hydrogen bond interaction were the dominant driving forces during the binding process. The circular dichroism (CD) spectroscopy analysis showed that the CA binding to pepsin decreased the contents of α-Helix and Random Coil but increased the content of β-sheet in the pepsin structure. Accordingly, MD simulations confirmed all the experimental results. As a result, CA is considered an inhibitor with adverse effects on pepsin activity.
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Affiliation(s)
- Fatemeh Hashemi-Shahraki
- Department of Biology, Faculty of Science, Shahrekord University, P.O. Box.115, Shahrekord, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Behzad Shareghi
- Department of Biology, Faculty of Science, Shahrekord University, P.O. Box.115, Shahrekord, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
| | - Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, P.O. Box.115, Shahrekord, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
| | - Elham Yadollahi
- Department of Biology, Faculty of Science, Shahrekord University, P.O. Box.115, Shahrekord, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
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Leangnim N, Unban K, Thangsunan P, Tateing S, Khanongnuch C, Kanpiengjai A. Ultrasonic-assisted enzymatic improvement of polyphenol content, antioxidant potential, and in vitro inhibitory effect on digestive enzymes of Miang extracts. ULTRASONICS SONOCHEMISTRY 2023; 94:106351. [PMID: 36878085 PMCID: PMC9988395 DOI: 10.1016/j.ultsonch.2023.106351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/09/2023] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
The aims of this research were to optimize the ultrasonic-assisted enzymatic extraction of polyphenols under Miang and tannase treatment conditions for the improvement of antioxidant activity of Miang extracts via response surface methodology. Miang extracts treated with and without tannase were investigated for their inhibitory effects on digestive enzymes. The optimal conditions for ultrasonic-assisted enzymatic extraction of the highest total polyphenol (TP) (136.91 mg GAE/g dw) and total flavonoid (TF) (5.38 mg QE/g dw) contents were as follows: 1 U/g cellulase, 1 U/g xylanase, 1 U/g pectinase, temperature (74 °C), and time (45 min). The antioxidant activity of this extract was enhanced by the addition of tannase obtained from Sporidiobolus ruineniae A45.2 undergoing ultrasonic treatment and under optimal conditions (360 mU/g dw, 51 °C for 25 min). The ultrasonic-assisted enzymatic extraction selectively promoted the extraction of gallated catechins from Miang. Tannase treatment improved the ABTS and DPPH radical scavenging activities of untreated Miang extracts by 1.3 times. The treated Miang extracts possessed higher IC50 values for porcine pancreatic α-amylase inhibitory activity than those that were untreated. However, it expressed approximately 3 times lower IC50 values for porcine pancreatic lipase (PPL) inhibitory activity indicating a marked improvement in inhibitory activity. The molecular docking results support the contention that epigallocatechin, epicatechin, and catechin obtained via the biotransformation of the Miang extracts played a crucial role in the inhibitory activity of PPL. Overall, the tannase treated Miang extract could serve as a functional food and beneficial ingredient in medicinal products developed for obesity prevention.
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Affiliation(s)
- Nalapat Leangnim
- Program in Biotechnology, The Graduate School, Chiang Mai University, Chiang Mai 50200, Thailand; Division of Biochemistry and Biochemical Innovation, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Kridsada Unban
- Division of Food Science and Technology, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai 50100, Thailand; Research Center for Multidisciplinary Approaches to Miang, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Patcharapong Thangsunan
- Center of Excellence in Fish Infectious Diseases (CE FID), Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Suriya Tateing
- Department of Plant and Soil Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Chartchai Khanongnuch
- Research Center for Multidisciplinary Approaches to Miang, Chiang Mai University, Chiang Mai 50200, Thailand; Division of Biotechnology, Faculty of Agro-Industry, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Apinun Kanpiengjai
- Division of Biochemistry and Biochemical Innovation, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; Research Center for Multidisciplinary Approaches to Miang, Chiang Mai University, Chiang Mai 50200, Thailand; Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand.
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11
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Hussain I, Fatima S, Ahmed S, Tabish M. Biophysical and molecular modelling analysis of the binding of β-resorcylic acid with bovine serum albumin. Food Hydrocoll 2023. [DOI: 10.1016/j.foodhyd.2022.108175] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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12
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Yang K, Jin H, Gao X, Wang GC, Zhang GQ. Elucidating the molecular determinants in the process of gastrin C-terminal pentapeptide amide end activating cholecystokinin 2 receptor by Gaussian accelerated molecular dynamics simulations. Front Pharmacol 2023; 13:1054575. [PMID: 36756145 PMCID: PMC9899899 DOI: 10.3389/fphar.2022.1054575] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/02/2022] [Indexed: 01/24/2023] Open
Abstract
Gastrin plays important role in stimulating the initiation and development of many gastrointestinal diseases through interacting with the cholecystokinin 2 receptor (CCK2R). The smallest bioactive unit of gastrin activating CCK2R is the C-terminal tetrapeptide capped with an indispensable amide end. Understanding the mechanism of this smallest bioactive unit interacting with CCK2R on a molecular basis could provide significant insights for designing CCK2R antagonists, which can be used to treat gastrin-related diseases. To this end, we performed extensive Gaussian accelerated molecular dynamics simulations to investigate the interaction between gastrin C-terminal pentapeptide capped with/without amide end and CCK2R. The amide cap influences the binding modes of the pentapeptide with CCK2R by weakening the electrostatic attractions between the C-terminus of the pentapeptide and basic residues near the extracellular domain in CCK2R. The C-terminus with the amide cap penetrates into the transmembrane domain of CCK2R while floating at the extracellular domain without the amide cap. Different binding modes induced different conformational dynamics of CCK2R. Residue pairs in CCK2R had stronger correlated motions when binding with the amidated pentapeptide. Key residues and interactions important for CCK2R binding with the amidated pentagastrin were also identified. Our results provide molecular insights into the determinants of the bioactive unit of gastrin activating CCK2R, which would be of great help for the design of CCK2R antagonists.
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Affiliation(s)
- Kecheng Yang
- National Supercomputing Center in Zhengzhou, Zhengzhou University, Zhengzhou, China,*Correspondence: Kecheng Yang,
| | - Huiyuan Jin
- School of International Studies, Zhengzhou University, Zhengzhou, China
| | - Xu Gao
- National Supercomputing Center in Zhengzhou, Zhengzhou University, Zhengzhou, China
| | - Gang-Cheng Wang
- Department of General Surgery, Affiliated Cancer Hospitalof Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Guo-Qiang Zhang
- Department of General Surgery, Affiliated Cancer Hospitalof Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
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Martínez-Antequera FP, López-Ruiz R, Martos-Sitcha JA, Mancera JM, Moyano FJ. Assessing differences in the bioaccessibility of phenolics present in two wine by-products using an in-vitro model of fish digestion. Front Vet Sci 2023; 10:1151045. [PMID: 37205229 PMCID: PMC10186350 DOI: 10.3389/fvets.2023.1151045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/13/2023] [Indexed: 05/21/2023] Open
Abstract
Increasing attention is currently being paid to the protective role of polyphenols in health and oxidative status in fish. For this reason, the potential use of different natural sources of such compounds, like wine by products, is under study. One key step required to gain a better understanding on the biological roles of polyphenols for a given species is to assess the different factors affecting their digestive bioaccessibility, and a great number of such studies is based in the use of in vitro digestion models. In the present study the potential digestive bioavailability of the phenolic compounds present in wine bagasse and lees was evaluated for two fish species showing great differences in their digestive phisyiology: the omnivorous gilthead sea bream (Sparus aurata) and the herbivorous flathead grey mullet (Mugil cephalus). The study was developed using in vitro models adapted to simulate their digestion and a factorial experimental design that simultaneously evaluated the effects of the ingredient used as source of polyphenols, presence or absence of feed matrix, fish species and digestion time. The release of the phenolic compounds was evaluated using ultra-high performance liquid chromatography (UHPLC) coupled to high resolution mass spectrometry (HRMS) detection. Both the presence of feed matrix and the type of wine by-product showed a significant effect on the digestive release of both total and specific types of polyphenols while fish species showed to be significant only for some specific compounds, like eriodyctiol or syringic acid. The time of digestion was not identified as a statistically significant factor in the release of phenolic compounds due to the great variability in the patterns observed that were classified as early, sustained and late. The observed great variations in the patterns of release of different types of phenolic compounds with time suggest an important effect of gut transit rates on the net bioavailability of a given phenolic compound in the live fish. The present study is, to our knowledge, the first one on which an in vitro approach was applied to assess to what extent the possible complexation of wine polyphenols present in wine by-products with either digestive enzymes or components of the feed matrix could limit their bioaccessibility if included in diets of two different fish species.
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Affiliation(s)
- Francisca P. Martínez-Antequera
- Departamento de Biología y Geología, Facultad de Ciencias Experimentales, Universidad de Almería, Almería, Spain
- Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Instituto Universitario de Investigación Marina (INMAR), Campus de Excelencia Internacional del Mar (CEI·MAR), Cádiz, Spain
- *Correspondence: Francisca P. Martínez-Antequera,
| | - Rosalía López-Ruiz
- Research Group “Analytical Chemistry of Contaminants”, Department of Chemistry and Physics, Research Centre for Mediterranean Intensive Agrosystems and Agri-Food Biotechnology (CIAIMBITAL), Agrifood Campus of International Excellence, ceiA3, University of Almeria, Almeria, Spain
| | - Juan Antonio Martos-Sitcha
- Departamento de Biología y Geología, Facultad de Ciencias Experimentales, Universidad de Almería, Almería, Spain
| | - Juan Miguel Mancera
- Departamento de Biología y Geología, Facultad de Ciencias Experimentales, Universidad de Almería, Almería, Spain
| | - Francisco Javier Moyano
- Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Instituto Universitario de Investigación Marina (INMAR), Campus de Excelencia Internacional del Mar (CEI·MAR), Cádiz, Spain
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14
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Characterization of the binding behavior, structure and foaming properties of bovine α-lactalbumin combined with saponin by the multi-spectroscopic and silico approaches. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2021.107259] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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15
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Vidal-Limon A, Aguilar-Toalá JE, Liceaga AM. Integration of Molecular Docking Analysis and Molecular Dynamics Simulations for Studying Food Proteins and Bioactive Peptides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:934-943. [PMID: 34990125 DOI: 10.1021/acs.jafc.1c06110] [Citation(s) in RCA: 95] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In silico tools, such as molecular docking, are widely applied to study interactions and binding affinity of biological activity of proteins and peptides. However, restricted sampling of both ligand and receptor conformations and use of approximated scoring functions can produce results that do not correlate with actual experimental binding affinities. Molecular dynamics simulations (MDS) can provide valuable information in deciphering functional mechanisms of proteins/peptides and other biomolecules, overcoming the rigid sampling limitations in docking analysis. This review will discuss the information related to the traditional use of in silico models, such as molecular docking, and its application for studying food proteins and bioactive peptides, followed by an in-depth introduction to the theory of MDS and description of why these molecular simulation techniques are important in the theoretical prediction of structural and functional dynamics of food proteins and bioactive peptides. Applications, limitations, and future prospects of MDS will also be discussed.
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Affiliation(s)
- Abraham Vidal-Limon
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic, Instituto de Ecología A.C. (INECOL), Carretera Antigua a Coatepec 351, El Haya, Xalapa, Veracruz 91073, Mexico
| | - José E Aguilar-Toalá
- Departamento de Ciencias de la Alimentación, División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana Unidad Lerma, Avenida de las Garzas 10, Colonia El Panteón, Lerma de Villada, Estado de México 52005, Mexico
| | - Andrea M Liceaga
- Protein Chemistry and Bioactive Peptides Laboratory. Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, Indiana 47907, United States
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16
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S. A, V. S, R. S, V. S. Structural exploration of interactions of (+) catechin and (−) epicatechin with bovine serum albumin: Insights from molecular dynamics and spectroscopic methods. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118026] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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17
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Hussain I, Fatima S, Siddiqui S, Ahmed S, Tabish M. Exploring the binding mechanism of β-resorcylic acid with calf thymus DNA: Insights from multi-spectroscopic, thermodynamic and bioinformatics approaches. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 260:119952. [PMID: 34052761 DOI: 10.1016/j.saa.2021.119952] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 05/06/2021] [Accepted: 05/09/2021] [Indexed: 06/12/2023]
Abstract
β-resorcylic acid (BR) is a phytochemical which is widely used in the food industry as a flavouring agent and preservative. It has also been found to exhibit antibacterial action against several types of food-borne bacteria. DNA is the main molecular target for many small molecules of therapeutic importance. Hence, the interest is rapidly growing among the researchers to elucidate the interaction between small molecules and DNA. Thus, paving the way to design novel DNA-specific drugs. In this study, an attempt was made to examine the mechanism of binding of BR with calf thymus DNA (ctDNA) with the help of various experiments based on spectroscopy and in silico studies. The spectroscopic studies like UV absorption and fluorescence affirmed the complex formation between BR and ctDNA. The observed binding constant was in the order of 103 M-1 which is indicative of the groove binding mechanism. These findings were further verified by dye-displacement assay, potassium iodide quenching, urea denaturation assay, the study of the effect of ssDNA, circular dichroism and DNA thermal denaturing studies. Different temperature-based fluorescence and isothermal titration calorimetry (ITC) experiments were employed to evaluate thermodynamic parameters. The analysis of thermodynamic parameters supports the enthalpically driven, exothermic and spontaneous nature of the reaction between BR and ctDNA. The forces involved in the binding process were mainly found to be hydrogen bonding, van der Waals and hydrophobic interactions. The results obtained from the molecular docking and molecular dynamics (MD) simulation were consistent with the in vitro experiments, which support the groove binding mode of BR with ctDNA.
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Affiliation(s)
- Irfan Hussain
- Department of Biochemistry, Faculty of Life Sciences, A.M.U, Aligarh, U.P. 202002, India
| | - Sana Fatima
- Department of Biochemistry, Faculty of Life Sciences, A.M.U, Aligarh, U.P. 202002, India
| | - Sharmin Siddiqui
- Department of Biochemistry, Faculty of Life Sciences, A.M.U, Aligarh, U.P. 202002, India
| | - Shahbaz Ahmed
- Department of Biochemistry, Faculty of Life Sciences, A.M.U, Aligarh, U.P. 202002, India
| | - Mohammad Tabish
- Department of Biochemistry, Faculty of Life Sciences, A.M.U, Aligarh, U.P. 202002, India.
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18
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Wang H, Wang Y, Yuan Z, Wang Y, Li X, Song P, Lu F, Liu Y. Insight into the cross-linking preferences and characteristics of the transglutaminase from Bacillus subtilis by in vitro RNA display. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.112152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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19
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Qais FA, Khan MS, Ahmad I, Husain FM, Al-Kheraif AA, Arshad M, Alam P. Plumbagin inhibits quorum sensing-regulated virulence and biofilms of Gram-negative bacteria: in vitro and in silico investigations. BIOFOULING 2021; 37:724-739. [PMID: 34396840 DOI: 10.1080/08927014.2021.1955250] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 07/05/2021] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
The global rise in antimicrobial resistance and lack of discovery of new antimicrobials have created serious concerns. Targeting quorum sensing (QS) and biofilms of pathogenic bacteria is considered a promising approach in antimicrobial drug discovery. This study explored the inhibitory effect of plumbagin against biofilms and QS of Chromobacterium violaceum, Serratia marcescens and Pseudomonas aeruginosa. Violacein production in C. violaceum 12472 was reduced by >80%. The virulent traits of P. aeruginosa PAO1 such as pyocyanin, rhamnolipid and proteases were also inhibited at sub-minimum inhibitory concentrations. Moreover, the biofilms of the test bacteria were reduced by 56-70%. Plumbagin reduced the bacterial adherence and colonization on solid surface. Computational studies gave closer insights regarding the possible modes of action. Molecular dynamics simulations revealed that the protein complexes were quite stable under physiological conditions. This study provides both experimental and computational evidence regarding the efficacy of plumbagin against biofilms and the QS-controlled virulence factors of Gram-negative bacteria.
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Affiliation(s)
- Faizan Abul Qais
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Mohammad Shavez Khan
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Iqbal Ahmad
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Fohad Mabood Husain
- Department of Food Science and Nutrition, King Saud University, Riyadh, Saudi Arabia
| | - Abdulaziz Abdullah Al-Kheraif
- Dental Biomaterials Research Chair, Dental Health Department, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Arshad
- Dental Biomaterials Research Chair, Dental Health Department, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Pravej Alam
- Department of Biology, College of Science and Humanities, Prince Sattam bin Abdulaziz University, Al-kharj, Kingdom of Saudi Arabia
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Sabe VT, Ntombela T, Jhamba LA, Maguire GEM, Govender T, Naicker T, Kruger HG. Current trends in computer aided drug design and a highlight of drugs discovered via computational techniques: A review. Eur J Med Chem 2021; 224:113705. [PMID: 34303871 DOI: 10.1016/j.ejmech.2021.113705] [Citation(s) in RCA: 165] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/12/2021] [Accepted: 07/12/2021] [Indexed: 12/30/2022]
Abstract
Computer-aided drug design (CADD) is one of the pivotal approaches to contemporary pre-clinical drug discovery, and various computational techniques and software programs are typically used in combination, in a bid to achieve the desired outcome. Several approved drugs have been developed with the aid of CADD. On SciFinder®, we evaluated more than 600 publications through systematic searching and refining, using the terms, virtual screening; software methods; computational studies and publication year, in order to obtain data concerning particular aspects of CADD. The primary focus of this review was on the databases screened, virtual screening and/or molecular docking software program used. Furthermore, we evaluated the studies that subsequently performed molecular dynamics (MD) simulations and we reviewed the software programs applied, the application of density functional theory (DFT) calculations and experimental assays. To represent the latest trends, the most recent data obtained was between 2015 and 2020, consequently the most frequently employed techniques and software programs were recorded. Among these, the ZINC database was the most widely preferred with an average use of 31.2%. Structure-based virtual screening (SBVS) was the most prominently used type of virtual screening and it accounted for an average of 57.6%, with AutoDock being the preferred virtual screening/molecular docking program with 41.8% usage. Following the screening process, 38.5% of the studies performed MD simulations to complement the virtual screening and GROMACS with 39.3% usage, was the popular MD software program. Among the computational techniques, DFT was the least applied whereby it only accounts for 0.02% average use. An average of 36.5% of the studies included reports on experimental evaluations following virtual screening. Ultimately, since the inception and application of CADD in pre-clinical drug discovery, more than 70 approved drugs have been discovered, and this number is steadily increasing over time.
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Affiliation(s)
- Victor T Sabe
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa.
| | - Thandokuhle Ntombela
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa.
| | - Lindiwe A Jhamba
- HIV Pathogenesis Program, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Glenn E M Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa; School of Chemistry and Physics, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Thavendran Govender
- Faculty of Science and Agriculture, Department of Chemistry, University of Zululand, KwaDlangezwa, 3886, South Africa
| | - Tricia Naicker
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Hendrik G Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa.
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21
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Rath B, Abul Qais F, Patro R, Mohapatra S, Sharma T. Design, synthesis and molecular modeling studies of novel mesalamine linked coumarin for treatment of inflammatory bowel disease. Bioorg Med Chem Lett 2021; 41:128029. [PMID: 33839254 DOI: 10.1016/j.bmcl.2021.128029] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/01/2021] [Accepted: 04/05/2021] [Indexed: 02/07/2023]
Abstract
Inflammatory bowel diseases (IBD) are continuous idiopathic inflammation of GIT. Ulcerative colitis, inflammation of the colonic or rectal mucosa has no known medical cure and its treatment is aimed at reducing the signs and symptoms associated with the disorders, induction and maintenance of remission. In this study, we have reported the synthesis of mesalamine and coumarin linked together by a diazo group. The compound was characterized by various spectroscopic methods. Therapeutic potential of the synthesized compound was investigated through acetic acid induced ulcerative rat model. Pharmacokinetic properties were predicted for the compounds by ADMET related descriptors. Molecular docking studies were conducted with four proteins (COX-2, MMP-9, TNF-α and MPO) to examine the interaction of mesalamine (MS) and mesalamine coumarin derivative (MS-CU). Moreover, molecular dynamic simulations were carried out to study the dynamics and stability of the complexes in solvent system. The binding energy of MS-CU with MPO, COX-2, MMP-9 and TNF-α was found to be -9.5, -10.4, -9.2 and -8.4 kcal/mol respectively. MS-CU exhibited higher binding affinity towards all tested proteins than MS. Molecular dynamic simulation reveals that both MS and MS-CU formed a stable complex with all test proteins in aqueous system. Overall binding energy of MS-CU was more than MS showing stronger affinity towards the test portions. In conclusion, Mesalamine-coumarin derivative reduces colonic damage in acetic acid induced ulcerative colitis in rat model, and therefore may prove to be effective in the management of IBD.
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Affiliation(s)
- Biswabhusan Rath
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Siksha 'O'Anusandhan (Deemed to be University), Bhubaneswar 751003, Odisha, India
| | - Faizan Abul Qais
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, UP 202002, India
| | - Randeep Patro
- Department of Pharmacology, School of Pharmaceutical Sciences, Siksha 'O'Anusandhan (Deemed to be University), Bhubaneswar 751003, Odisha, India
| | - Sujata Mohapatra
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Siksha 'O'Anusandhan (Deemed to be University), Bhubaneswar 751003, Odisha, India.
| | - Tripti Sharma
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Siksha 'O'Anusandhan (Deemed to be University), Bhubaneswar 751003, Odisha, India.
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22
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Qureshi S, Khandelwal R, Madhavi M, Khurana N, Gupta N, Choudhary SK, Suresh RA, Hazarika L, Srija CD, Sharma K, Hindala MR, Hussain T, Nayarisseri A, Singh SK. A Multi-target Drug Designing for BTK, MMP9, Proteasome and TAK1 for the Clinical Treatment of Mantle Cell Lymphoma. Curr Top Med Chem 2021; 21:790-818. [PMID: 33463471 DOI: 10.2174/1568026621666210119112336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/18/2020] [Accepted: 12/24/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Mantle cell lymphoma (MCL) is a type of non-Hodgkin lymphoma characterized by the mutation and overexpression of the cyclin D1 protein by the reciprocal chromosomal translocation t(11;14)(q13:q32). AIM The present study aims to identify potential inhibition of MMP9, Proteasome, BTK, and TAK1 and determine the most suitable and effective protein target for the MCL. METHODOLOGY Nine known inhibitors for MMP9, 24 for proteasome, 15 for BTK and 14 for TAK1 were screened. SB-3CT (PubChem ID: 9883002), oprozomib (PubChem ID: 25067547), zanubrutinib (PubChem ID: 135565884) and TAK1 inhibitor (PubChem ID: 66760355) were recognized as drugs with high binding capacity with their respective protein receptors. 41, 72, 102 and 3 virtual screened compounds were obtained after the similarity search with compound (PubChem ID:102173753), PubChem compound SCHEMBL15569297 (PubChem ID:72374403), PubChem compound SCHEMBL17075298 (PubChem ID:136970120) and compound CID: 71814473 with best virtual screened compounds. RESULT MMP9 inhibitors show commendable affinity and good interaction profile of compound holding PubChem ID:102173753 over the most effective established inhibitor SB-3CT. The pharmacophore study of the best virtual screened compound reveals its high efficacy based on various interactions. The virtual screened compound's better affinity with the target MMP9 protein was deduced using toxicity and integration profile studies. CONCLUSION Based on the ADMET profile, the compound (PubChem ID: 102173753) could be a potent drug for MCL treatment. Similar to the established SB-3CT, the compound was non-toxic with LD50 values for both the compounds lying in the same range.
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Affiliation(s)
- Shahrukh Qureshi
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Ravina Khandelwal
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Maddala Madhavi
- Department of Zoology, Nizam College, Osmania University, Hyderabad - 500001, Telangana State, India
| | - Naveesha Khurana
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Neha Gupta
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Saurav K Choudhary
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Revathy A Suresh
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Lima Hazarika
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Chillamcherla D Srija
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Khushboo Sharma
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Mali R Hindala
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Tajamul Hussain
- Center of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Anuraj Nayarisseri
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Sanjeev K Singh
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 003, Tamil Nadu, India
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23
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Ravindran ASK, Venkatabalasubramanian S, Manickam R, Anusuyadevi M, K Swaminathan J. Plausible computational insights and new atomic-level perspective of epicathechin gallate from Crataegus oxycantha extract in preventing caspase 3 activation in conditions like post-myocardial infarction. J Biomol Struct Dyn 2020; 40:3400-3415. [PMID: 33200674 PMCID: PMC8692457 DOI: 10.1080/07391102.2020.1847196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Cardiovascular disease (CVD) is the leading cause of mortality among the human species, however the non-existence of successful therapies to curtail the effect of Myocardial Infarction (MI) is a disquieting reality. Even though successful herbal formulations using Crataegus oxycantha (COC) is available, however, it is not recognized as an alternative medicine due to the lack of explanation on the molecular mechanism of COC extract on CVD conditions. In vivo studies revealed that COC extract significantly prevented caspase activation in conditions like post-MI; however, the role of a specific secondary metabolite that could be involved in this action is under quest. The present study, therefore, aims at predicting the plausible mechanism of action of key secondary metabolite in COC extract on apoptotic executioner caspase - caspase 3 during MI through in silico tools. The protein-protein interaction network, QikProp, and molecular docking studies were performed to identify the lead compound that revealed Epicatechin Gallate (ECG) of COC as an effective inhibitor against candidate MI/apoptosis mediator - caspase 3. The docked complex was further taken for molecular dynamics simulation, which was achieved through Desmond. Molecular dynamics further confirmed the stability of the binding interactions between the docked complex. The overall in silico results proved that ECG could prevent the dissociation of cleaved caspases, which is essential for their activation. Computational observations were strongly supported by experimental evidence obtained from in vivo studies in the MI-model system. From the above observations, it was concluded that computational analysis was in good agreement with the experimental analysis on ECG's potential to prevent caspase 3 activation during MI. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Arul Salomee Kamalabai Ravindran
- Drug discovery and Molecular Cardiology lab, Department of Bioinformatics, School of Life sciences, Bharathidasan University, Tiruchirappalli, India
| | | | - Ranjani Manickam
- SRM-DBT Platform for Advanced Life Science Technologies, SRM Institute of Science and Technology, KTR Campus, Chennai, India
| | - Muthuswamy Anusuyadevi
- Molecular Gerontology Lab, Department of Biochemistry, School of Life sciences, Bharathidasan University, Tiruchirappalli, India
| | - Jayachandran K Swaminathan
- Drug discovery and Molecular Cardiology lab, Department of Bioinformatics, School of Life sciences, Bharathidasan University, Tiruchirappalli, India.,Center for Biomedical EPR Spectroscopy and Imaging, Davis Heart and Lung Research Institute, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
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24
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Kaempferol inhibits the activity of pancreatic lipase and its synergistic effect with orlistat. J Funct Foods 2020. [DOI: 10.1016/j.jff.2020.104041] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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25
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Luo M, Xiao J, Sun S, Cui F, Liu G, Li W, Li Y, Cao Y. Deciphering calcium-binding behaviors of casein phosphopeptides by experimental approaches and molecular simulation. Food Funct 2020; 11:5284-5292. [PMID: 32458848 DOI: 10.1039/d0fo00844c] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Casein phosphopeptides (CPPs) as premium additives in functional foods can facilitate the transport and adsorption of calcium. The atomic resolution decipherment of calcium-CPP binding behaviors is critical for understanding the calcium bioavailability enhancement potential of CPPs. In the present study, the experimental methods (UV-vis, FTIR and isothermal titration calorimetry) and molecular dynamics simulation were combined to reveal the calcium-binding behaviors of β-casein phosphopeptides (1-25) (P5) with the best capability in carrying calcium ions. We found that it could carry approximately six calcium ions, and the calcium-binding sites were primarily located at the carbonyl group of Glu-2 and the phosphate group of phosphorylated Ser-15, Ser-18, and Ser-19. An interesting finding was that calcium ions could be bound by three coordinated modes, including unidentate, bidentate and tridentate geometries, resulting in the strong binding abilities. The binding process of calcium ions to P5 was spontaneous with the binding free energies of -5.2 kcal mol-1. Hydrophobic interactions were considered to be the major driving force for the calcium ion binding. The present study provides novel molecular insights into the binding process between Ca2+ and calcium-binding peptides.
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Affiliation(s)
- Minna Luo
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, Engineering Research Center for Natural Actives, College of Food Science, South China Agricultural University, Guangzhou 510642, China. and Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, China
| | - Jie Xiao
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, Engineering Research Center for Natural Actives, College of Food Science, South China Agricultural University, Guangzhou 510642, China. and Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, China
| | - Shengwei Sun
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Fengchao Cui
- Key Laboratory of High-Performance Synthetic Rubber and its Composite Materials, Changchun institute of Applied Chemistry, Chinese Academy of Sciences Changchun, Chinese Academy of Sciences, Changchun 130022, China
| | - Guo Liu
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, Engineering Research Center for Natural Actives, College of Food Science, South China Agricultural University, Guangzhou 510642, China.
| | - Wei Li
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, Engineering Research Center for Natural Actives, College of Food Science, South China Agricultural University, Guangzhou 510642, China.
| | - Yunqi Li
- Key Laboratory of High-Performance Synthetic Rubber and its Composite Materials, Changchun institute of Applied Chemistry, Chinese Academy of Sciences Changchun, Chinese Academy of Sciences, Changchun 130022, China
| | - Yong Cao
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, Engineering Research Center for Natural Actives, College of Food Science, South China Agricultural University, Guangzhou 510642, China. and Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, China
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26
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Zhang M, Liu Y, Cui F, Rankl C, Qin J, Guan Y, Guo X, Zhang B, Tang J. Interaction of vascular endothelial growth factor and heparin quantified by single molecule force spectroscopy. NANOSCALE 2020; 12:11927-11935. [PMID: 32458960 DOI: 10.1039/d0nr01570a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Heparin, as an effective anticoagulant, has been increasingly used in clinical practice, but the binding characteristics and influence of exogenous heparin on heparin-affinity proteins in the body are still unclear. Vascular endothelial growth factor A (VEGF-A) is a kind of protein with heparin affinity involved in the pathogenesis and progression of many angiogenesis-dependent diseases including cancer. As an important step in the angiogenesis-related cascade, it is necessary to clarify the interaction between VEGF165 (the major form of VEGF-A) and heparin. In this work, we investigated this interaction based on single molecule force spectroscopy (SMFS) and molecular dynamics (MD) simulation. From the SMFS study, binding forces between VEGF165 and heparin at different loading rates were quantified under near-physiological conditions. Meanwhile, the kinetic and thermodynamic parameters of the VEGF165/heparin complex dissociation process were also obtained. Results of MD simulation visually displayed the most likely binding conformation of VEGF165/heparin* complex, indicating that hydrogen bonding and hydrophobic interaction play a positive role in the binding between the two molecules. This work provides a new insight into the binding between VEGF165 and heparin and offers a research framework to study the interaction between heparin and multiple heparin affinity proteins, which is helpful for guiding the safe application of heparin in the clinic.
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Affiliation(s)
- Miaomiao Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China. and University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Ying Liu
- College of Humanities & Information Changchun University of Technology, Changchun, 130122, P. R. China
| | - Fengchao Cui
- Key Laboratory of High-Performance Rubber and Its Composite Materials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
| | - Christian Rankl
- Research Center for Non Destructive Testing GmbH, Science Park 2/2. OG, Altenberger Straße 69, A-4040 Linz, Austria
| | - Juan Qin
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China. and University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Yanxue Guan
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China. and University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Xinyue Guo
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China. and University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Bailin Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China. and University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Jilin Tang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China. and University of Science and Technology of China, Hefei, 230026, P. R. China
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27
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Torkzadeh‐Mahani M, Zaboli M, Barani M, Torkzadeh‐Mahani M. A combined theoretical and experimental study to improve the thermal stability of recombinant D‐lactate dehydrogenase immobilized on a novel superparamagnetic Fe3O4NPs@metal–organic framework. Appl Organomet Chem 2020. [DOI: 10.1002/aoc.5581] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Mahdieh Torkzadeh‐Mahani
- Department of Biotechnology, Institute of Science and High Technology and Environmental SciencesGraduate University of Advanced Technology Kerman‐Iran Iran
| | - Maryam Zaboli
- Department of Chemistry, Faculty of ScienceUniversity of Birjand Birjand Iran
| | - Mahmood Barani
- Department of ChemistryShahid Bahonar University of Kerman Kerman Iran
| | - Masoud Torkzadeh‐Mahani
- Department of Biotechnology, Institute of Science and High Technology and Environmental SciencesGraduate University of Advanced Technology Kerman‐Iran Iran
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28
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Singh AN, Sharma N. Epigenetic Modulators as Potential Multi-targeted Drugs Against Hedgehog Pathway for Treatment of Cancer. Protein J 2020; 38:537-550. [PMID: 30993446 DOI: 10.1007/s10930-019-09832-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The Sonic hedgehog signalling is known to play a crucial role in regulating embryonic development, cancer stem cell maintenance and tissue patterning. Dysregulated hedgehog signalling has been reported to affect tumorigenesis and drug response in various human malignancies. Epigenetic therapy relying on DNA methyltransferase and Histone deacetylase inhibitors are being proposed as potential drug candidates considering their efficiency in preventing development of cancer progenitor cells, killing drug resistant cells and also dictating "on/off" switch of tumor suppressor genes and oncogenes. In this docking approach, epigenetic modulators were virtually screened for their efficiency in inhibiting key regulators of SHH pathway viz., sonic hedgehog, Smoothened and Gli using polypharmacological approach. The control drugs and epigenetic modulators were docked with PDB protein structures using AutoDock vina and further checked for their drug-likeness properties. Further molecular dynamics simulation using VMD and NAMD, and MMP/GBSA energy calculation were employed for verifying the stability and entropy of the ligand-receptor complex. EPZ-6438 and GSK 343 (EZH2 inhibitors), CHR 3996 and Mocetinostat (HDAC inhibitors), GSK 126 (HKMT inhibitor) and UNC 1215 (L3MBTL3 antagonist) exhibited multiple-targeted approach in modulating HH signalling. This is the first study to report these epigenetic drugs as potential multi-targeted hedgehog pathway inhibitors. Thus, epigenetic polypharmacology approach can be explored as a better alternative to challenges of acute long term toxicity and drug resistance occurring due to traditional single targeted chemotherapy in the future.
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Affiliation(s)
- Anshika N Singh
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Gram-Lavale, Taluka-Mulshi, Pune, 412115, India
| | - Neeti Sharma
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Gram-Lavale, Taluka-Mulshi, Pune, 412115, India.
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29
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Wang X, Leng X, Zhang G. The loosening effect of tea polyphenol on the structure of octenyl succinic anhydride modified waxy maize starch. Food Hydrocoll 2020. [DOI: 10.1016/j.foodhyd.2019.105367] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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30
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Tao X, Huang Y, Wang C, Chen F, Yang L, Ling L, Che Z, Chen X. Recent developments in molecular docking technology applied in food science: a review. Int J Food Sci Technol 2019. [DOI: 10.1111/ijfs.14325] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Xuan Tao
- School of Food and Bioengineering Xihua University Chengdu Sichuan 610039 China
| | - Yukun Huang
- School of Food and Bioengineering Xihua University Chengdu Sichuan 610039 China
- Key Laboratory of Food Non Thermal Processing Engineering Technology Research Center of Food Non Thermal Processing Yibin Xihua University Research Institute Yibin Sichuan 644404 China
| | - Chong Wang
- School of Food and Bioengineering Xihua University Chengdu Sichuan 610039 China
| | - Fang Chen
- School of Food and Bioengineering Xihua University Chengdu Sichuan 610039 China
| | - Lingling Yang
- School of Food and Bioengineering Xihua University Chengdu Sichuan 610039 China
| | - Li Ling
- School of Food and Bioengineering Xihua University Chengdu Sichuan 610039 China
- College of Pharmacy Chengdu University of Traditional Chinese Medicine Chengdu Sichuan 611137 China
| | - Zhenming Che
- School of Food and Bioengineering Xihua University Chengdu Sichuan 610039 China
| | - Xianggui Chen
- School of Food and Bioengineering Xihua University Chengdu Sichuan 610039 China
- Key Laboratory of Food Non Thermal Processing Engineering Technology Research Center of Food Non Thermal Processing Yibin Xihua University Research Institute Yibin Sichuan 644404 China
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31
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Poloni DM, Dangles O, Vinson JA. Binding of Plant Polyphenols to Serum Albumin and LDL: Healthy Implications for Heart Disease. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:9139-9147. [PMID: 30784273 DOI: 10.1021/acs.jafc.8b06674] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Cardiovascular disease (CVD) is the leading cause of death in industrialized nations. The initiating event in atherosclerosis, or hardening of the arteries, is oxidation of low density lipoprotein (LDL). Binding with serum albumin and LDL of 41 polyphenols (major antioxidants in plant foods) constituting four classes of flavonoids, three types of phenolic acids, and seven polyphenol conjugate metabolites was investigated indirectly by fluorescence quenching and directly by affinity separation/high-performance liquid chromatography (four of the polyphenols). Stern-Volmer plots yielded K values for the two proteins. Polyphenol binding was significantly stronger for albumin than with LDL. K values were highly correlated with the lipophilicity of the polyphenols. The number of polyphenol molecules determined by quenching was ∼1 for both proteins. Direct analysis under saturation conditions yielded from 2 to 13 molecules of polyphenols/LDL particle. Multiple substituent effects on binding were analyzed. Evidence was put forward that binding of polyphenols to these proteins is protective for CVD by multiple mechanisms.
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Affiliation(s)
- Dana M Poloni
- Department of Chemistry, Loyola Science Center , University of Scranton , 925 Ridge Row , Scranton , Pennsylvania 18510 , United States
| | - Olivier Dangles
- Avignon University, INRA, UMR408 SQPOV , 84000 Avignon , France
| | - Joe A Vinson
- Department of Chemistry, Loyola Science Center , University of Scranton , 925 Ridge Row , Scranton , Pennsylvania 18510 , United States
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32
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Meshram RJ, Bagul KT, Pawnikar SP, Barage SH, Kolte BS, Gacche RN. Known compounds and new lessons: structural and electronic basis of flavonoid-based bioactivities. J Biomol Struct Dyn 2019; 38:1168-1184. [DOI: 10.1080/07391102.2019.1597770] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Rohan J. Meshram
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Kamini T. Bagul
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Shristi P. Pawnikar
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Sagar H. Barage
- Amity Institute of Biotechnology, Amity University, Panvel, Maharashtra, India
| | - Baban S. Kolte
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, Maharashtra, India
- Department of Biotechnology, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Rajesh N. Gacche
- Department of Biotechnology, Savitribai Phule Pune University, Pune, Maharashtra, India
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33
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Patil KK, Meshram RJ, Barage SH, Gacche RN. Dietary flavonoids inhibit the glycation of lens proteins: implications in the management of diabetic cataract. 3 Biotech 2019; 9:47. [PMID: 30729071 DOI: 10.1007/s13205-019-1581-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 01/17/2019] [Indexed: 12/11/2022] Open
Abstract
The intervention of functional foods as complementary therapeutic approach for the amelioration of diabetes and sugar induced cataractogenesis is more appreciated over the present day chemotherapy agents owing to their nontoxic and increased bioavailability concerns. Dietary flavonoids, a class of bioactive phytochemicals is known to have wide range of biological activities against variety of human ailments. In the present study, we demonstrate anti-cataract effect of eight dietary flavonoids in sugar induced lens organ culture study. We present data on processes like inhibition of glycation-induced lens cloudiness, lens protein aggregation, glycation reaction and advanced glycation end products formation that can act as biochemical markers for this disease. The selected flavonoids were also tested for their aldose reductase (AR) inhibition (experimental and in silico). The molecular dynamics simulation results shed light on mechanistic details of flavonoid induced AR inhibition. The outcome of the present study clearly focuses the significance of kaempferol, taxifolin and quercetin as potential candidates for controlling diabetic cataract.
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Affiliation(s)
- Kapil K Patil
- 1School of Life Sciences, Swami Ramanand Teerth Marathwada University, Nanded, MS 431 606 India
| | - Rohan J Meshram
- 2Bioinformatics Centre, Savitribai Phule Pune University, Pune, MS 411007 India
| | - Sagar H Barage
- 2Bioinformatics Centre, Savitribai Phule Pune University, Pune, MS 411007 India
- 4Amity Institute of Biotechnology, Amity University, Panvel, MS India
| | - Rajesh N Gacche
- 1School of Life Sciences, Swami Ramanand Teerth Marathwada University, Nanded, MS 431 606 India
- 3Department of Biotechnology, Savitribai Phule Pune University, Pune, MS 411007 India
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34
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Siddiqui S, Ameen F, Jahan I, Nayeem SM, Tabish M. A comprehensive spectroscopic and computational investigation on the binding of the anti-asthmatic drug triamcinolone with serum albumin. NEW J CHEM 2019. [DOI: 10.1039/c8nj05486j] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Binding study of triamcinolone with BSA through in vitro and in silico approaches, helping in the development of drugs with better therapeutic efficacy.
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Affiliation(s)
- Sharmin Siddiqui
- Department of Biochemistry, Faculty of Life Sciences
- A.M. University
- Aligarh
- India
| | - Faisal Ameen
- Department of Biochemistry, Faculty of Life Sciences
- A.M. University
- Aligarh
- India
| | - Ishrat Jahan
- Department of Chemistry
- Faculty of Science
- A.M. University
- Aligarh
- India
| | - Shahid M. Nayeem
- Department of Chemistry
- Faculty of Science
- A.M. University
- Aligarh
- India
| | - Mohammad Tabish
- Department of Biochemistry, Faculty of Life Sciences
- A.M. University
- Aligarh
- India
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35
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Nakano S, Megro SI, Hase T, Suzuki T, Isemura M, Nakamura Y, Ito S. Computational Molecular Docking and X-ray Crystallographic Studies of Catechins in New Drug Design Strategies. Molecules 2018; 23:E2020. [PMID: 30104534 PMCID: PMC6222539 DOI: 10.3390/molecules23082020] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/09/2018] [Accepted: 08/11/2018] [Indexed: 12/16/2022] Open
Abstract
Epidemiological and laboratory studies have shown that green tea and green tea catechins exert beneficial effects on a variety of diseases, including cancer, metabolic syndrome, infectious diseases, and neurodegenerative diseases. In most cases, (-)-epigallocatechin gallate (EGCG) has been shown to play a central role in these effects by green tea. Catechins from other plant sources have also shown health benefits. Many studies have revealed that the binding of EGCG and other catechins to proteins is involved in its action mechanism. Computational docking analysis (CMDA) and X-ray crystallographic analysis (XCA) have provided detailed information on catechin-protein interactions. Several of these studies have revealed that the galloyl moiety anchors it to the cleft of proteins through interactions with its hydroxyl groups, explaining the higher activity of galloylated catechins such as EGCG and epicatechin gallate than non-galloylated catechins. In this paper, we review the results of CMDA and XCA of EGCG and other plant catechins to understand catechin-protein interactions with the expectation of developing new drugs with health-promoting properties.
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Affiliation(s)
- Shogo Nakano
- School of Food and Nutritional Sciences, Shizuoka University, Yada, Shizuoka 422-8526, Japan.
| | - Shin-Ichi Megro
- Biological Science Research, Kao Corporation, Ichikai-machi, Haga-gun, Tochigi 321-3497, Japan.
| | - Tadashi Hase
- Research and Development, Core Technology, Kao Corporation, Sumida, Tokyo 131-8501, Japan.
| | - Takuji Suzuki
- Faculty of Education, Art and Science, Yamagata University, Yamagata 990-8560, Japan.
| | - Mamoru Isemura
- School of Food and Nutritional Sciences, Shizuoka University, Yada, Shizuoka 422-8526, Japan.
| | - Yoriyuki Nakamura
- School of Food and Nutritional Sciences, Shizuoka University, Yada, Shizuoka 422-8526, Japan.
| | - Sohei Ito
- School of Food and Nutritional Sciences, Shizuoka University, Yada, Shizuoka 422-8526, Japan.
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36
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Patel P, Parmar K, Patel D, Kumar S, Trivedi M, Das M. Inhibition of amyloid fibril formation of lysozyme by ascorbic acid and a probable mechanism of action. Int J Biol Macromol 2018; 114:666-678. [DOI: 10.1016/j.ijbiomac.2018.03.152] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Revised: 03/23/2018] [Accepted: 03/25/2018] [Indexed: 12/20/2022]
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37
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Domínguez-Avila JA, Wall-Medrano A, Velderrain-Rodríguez GR, Chen CYO, Salazar-López NJ, Robles-Sánchez M, González-Aguilar GA. Gastrointestinal interactions, absorption, splanchnic metabolism and pharmacokinetics of orally ingested phenolic compounds. Food Funct 2018; 8:15-38. [PMID: 28074953 DOI: 10.1039/c6fo01475e] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The positive health effects of phenolic compounds (PCs) have been extensively reported in the literature. An understanding of their bioaccessibility and bioavailability is essential for the elucidation of their health benefits. Before reaching circulation and exerting bioactions in target tissues, numerous interactions take place before and during digestion with either the plant or host's macromolecules that directly impact the organism and modulate their own bioaccessibility and bioavailability. The present work is focused on the gastrointestinal (GI) interactions that are relevant to the absorption and metabolism of PCs and how these interactions impact their pharmacokinetic profiles. Non-digestible cell wall components (fiber) interact intimately with PCs and delay their absorption in the small intestine, instead carrying them to the large intestine. PCs not bound to fiber interact with digestible nutrients in the bolus where they interfere with the digestion and absorption of proteins, carbohydrates, lipids, cholesterol, bile salts and micronutrients through the inhibition of digestive enzymes and enterocyte transporters and the disruption of micelle formation. PCs internalized by enterocytes may reach circulation (through transcellular or paracellular transport), be effluxed back into the lumen (P-glycoprotein, P-gp) or be metabolized by phase I and phase II enzymes. Some PCs can inhibit P-gp or phase I/II enzymes, which can potentially lead to drug-nutrient interactions. The absorption and pharmacokinetic parameters are modified by all of the interactions within the digestive tract and by the presence of other PCs. Undesirable interactions have promoted the development of nanotechnological approaches to promote the bioaccessibility, bioavailability, and bioefficacy of PCs.
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Affiliation(s)
- J Abraham Domínguez-Avila
- Coordinación de Tecnología de Alimentos de Origen Vegetal, Centro de Investigación en Alimentación y Desarrollo, A.C. Carretera a la Victoria Km 0.6. C.P. 83304, Hermosillo, Sonora, Mexico.
| | - Abraham Wall-Medrano
- Departamento de Ciencias Químico-Biológicas, Instituto de Ciencias Biomédicas, Universidad Autónoma de Ciudad Juárez, Anillo Envolvente del Pronaf y Estocolmo s/n, CP 32310, Cd. Juárez, Chihuahua, Mexico.
| | - Gustavo R Velderrain-Rodríguez
- Coordinación de Tecnología de Alimentos de Origen Vegetal, Centro de Investigación en Alimentación y Desarrollo, A.C. Carretera a la Victoria Km 0.6. C.P. 83304, Hermosillo, Sonora, Mexico.
| | - C-Y Oliver Chen
- Antioxidants Research Laboratory, Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, 711 Washington Street, Boston, Massachusetts 02111, USA.
| | - Norma Julieta Salazar-López
- Departamento de Investigación y Posgrado en Alimentos, Universidad de Sonora, Blvd. Luis Encinas y Rosales S/N Col. Centro, C.P. 83000, Hermosillo, Sonora, Mexico.
| | - Maribel Robles-Sánchez
- Departamento de Investigación y Posgrado en Alimentos, Universidad de Sonora, Blvd. Luis Encinas y Rosales S/N Col. Centro, C.P. 83000, Hermosillo, Sonora, Mexico.
| | - Gustavo A González-Aguilar
- Coordinación de Tecnología de Alimentos de Origen Vegetal, Centro de Investigación en Alimentación y Desarrollo, A.C. Carretera a la Victoria Km 0.6. C.P. 83304, Hermosillo, Sonora, Mexico.
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In Vitro and In Silico Studies of the Molecular Interactions of Epigallocatechin-3- O-gallate (EGCG) with Proteins That Explain the Health Benefits of Green Tea. Molecules 2018; 23:molecules23061295. [PMID: 29843451 PMCID: PMC6099932 DOI: 10.3390/molecules23061295] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/18/2018] [Accepted: 05/25/2018] [Indexed: 01/08/2023] Open
Abstract
Green tea has been shown to have beneficial effects on many diseases such as cancer, obesity, inflammatory diseases, and neurodegenerative disorders. The major green tea component, epigallocatechin-3-O-gallate (EGCG), has been demonstrated to contribute to these effects through its anti-oxidative and pro-oxidative properties. Furthermore, several lines of evidence have indicated that the binding affinity of EGCG to specific proteins may explain its mechanism of action. This review article aims to reveal how EGCG-protein interactions can explain the mechanism by which green tea/EGCG can exhibit health beneficial effects. We conducted a literature search, using mainly the PubMed database. The results showed that several methods such as dot assays, affinity gel chromatography, surface plasmon resonance, computational docking analyses, and X-ray crystallography have been used for this purpose. These studies have provided evidence to show how EGCG can fit or occupy the position in or near functional sites and induce a conformational change, including a quaternary conformational change in some cases. Active site blocking, steric hindrance by binding of EGCG near an active site or induced conformational change appeared to cause inhibition of enzymatic activity and other biological activities of proteins, which are related to EGCG’s biological oligomer and formation of their toxic aggregates, leading to the prevention of neurodegenerative diseases and amyloidosis. In conclusion, these studies have provided useful information on the action of green tea/catechins and would lead to future studies that will provide further evidence for rational EGCG therapy and use EGCG as a lead compound for drug design.
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Zhang J, Zhang L, Xu Y, Jiang S, Shao Y. Deciphering the binding behavior of flavonoids to the cyclin dependent kinase 6/cyclin D complex. PLoS One 2018; 13:e0196651. [PMID: 29715320 PMCID: PMC5929560 DOI: 10.1371/journal.pone.0196651] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 04/17/2018] [Indexed: 12/17/2022] Open
Abstract
Flavonoids, a class of natural compounds with variable phenolic structures, have been found to possess anti-cancer activities by modulating different enzymes and receptors like CDK6. To understand the binding behavior of flavonoids that inhibit the active CDK6, molecular dynamics (MD) simulations were performed on six inhibitors, chrysin (M01), fisetin (M03), galangin (M04), genistein (M05), quercetin (M06) and kaempferol (M07), complexed with CDK6/cyclin D. For all six flavonoids, the 3'-OH and 4'-OH of B-ring were found to be favorable for hydrogen bond formation, but the 3-OH on the C-ring and 5-OH on the A-ring were unfavorable, which were confirmed by the MD simulation results of the test molecule, 3', 4', 7-trihydroxyflavone (M15). The binding efficiencies of flavonoids against the CDK6/cyclin D complex were mainly through the electrostatic (especially the H-bond force) and vdW interactions with residues ILE19, VAL27, ALA41, GLU61, PHE98, GLN103, ASP163 and LEU152. The order of binding affinities of these flavonoids toward the CDK6/cyclin D was M03 > M01 > M07 > M15 > M06 > M05 > M04. It is anticipated that the binding features of flavonoid inhibitors studied in the present work may provide valuable insights for the development of CDK6 inhibitors.
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Affiliation(s)
- Jingxiao Zhang
- College of Chemistry and Environmental Engineering, Hubei University for Nationalities, Enshi, Hubei, China
- College of Chemistry and Chemical Engineering, Luoyang Normal University, Luoyang, Henan, China
| | - Lilei Zhang
- College of Chemistry and Environmental Engineering, Hubei University for Nationalities, Enshi, Hubei, China
- College of Chemistry and Chemical Engineering, Luoyang Normal University, Luoyang, Henan, China
| | - Yangcheng Xu
- College of Chemistry and Environmental Engineering, Hubei University for Nationalities, Enshi, Hubei, China
| | - Shanshan Jiang
- College of Chemistry and Environmental Engineering, Hubei University for Nationalities, Enshi, Hubei, China
| | - Yueyue Shao
- College of Chemistry and Environmental Engineering, Hubei University for Nationalities, Enshi, Hubei, China
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Inhibition of insulin amyloid fibrillation by Morin hydrate. Int J Biol Macromol 2018; 108:225-239. [DOI: 10.1016/j.ijbiomac.2017.11.168] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/26/2017] [Accepted: 11/27/2017] [Indexed: 12/11/2022]
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Tang H, Cui F, Liu L, Li Y. Predictive models for tyrosinase inhibitors: Challenges from heterogeneous activity data determined by different experimental protocols. Comput Biol Chem 2018; 73:79-84. [PMID: 29471263 DOI: 10.1016/j.compbiolchem.2018.02.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 02/02/2018] [Accepted: 02/08/2018] [Indexed: 10/18/2022]
Abstract
Quantitative Structure-Activity Relationship (QSAR) models of tyrosinase inhibitors were built using Random Forest (RF) algorithm and evaluated by the out-of-bag estimation (R2OOB) and 10-fold cross validation (Q2CV). We found that the performances of QSAR models were closely correlated with the systematic errors of inhibitory activities of tyrosinase inhibitors arising from the different measuring protocols. By defining ERRsys, outliers with larger errors can be efficiently identified and removed from heterogeneous activity data. A reasonable QSAR model (R2OOB of 0.74 and Q2CV of 0.80) was obtained by the exclusion of 13 outliers with larger systematic errors. It is a clear example of the challenge for QSAR model that can overwhelm heterogeneous data from different experimental protocols.
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Affiliation(s)
- Haifeng Tang
- Key Laboratory of Synthetic Rubber, Changchun Institute of Applied Chemistry (CIAC), Chinese Academy of Sciences, Changchun 130022, PR China; School of Life Science, Jilin University, Changchun 130012, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Fengchao Cui
- Key Laboratory of Synthetic Rubber, Changchun Institute of Applied Chemistry (CIAC), Chinese Academy of Sciences, Changchun 130022, PR China.
| | - Lunyang Liu
- Key Laboratory of Synthetic Rubber, Changchun Institute of Applied Chemistry (CIAC), Chinese Academy of Sciences, Changchun 130022, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yunqi Li
- Key Laboratory of Synthetic Rubber, Changchun Institute of Applied Chemistry (CIAC), Chinese Academy of Sciences, Changchun 130022, PR China.
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42
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Tang H, Cui F, Li H, Huang Q, Li Y. Understanding the inhibitory mechanism of tea polyphenols against tyrosinase using fluorescence spectroscopy, cyclic voltammetry, oximetry, and molecular simulations. RSC Adv 2018; 8:8310-8318. [PMID: 35542029 PMCID: PMC9078569 DOI: 10.1039/c7ra12749a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 02/15/2018] [Indexed: 11/21/2022] Open
Abstract
Inhibiting the activity of tyrosinase is a very effective and safe way to prevent enzymatic browning in food and to resist pests in agriculture. Tea polyphenols (TPs), regarded as safe and non-toxic food additives, have been reported due to their potential inhibitory capability against tyrosinase, but their ambiguous inhibitory mechanisms have severely limited their application. In the present work, fluorescence spectroscopy, cyclic voltammetry (CV), oximetry and molecular simulation approaches were employed to shed light on the underlying inhibitory mechanisms of TPs with different structures including (+)-catechin, (−)-epicatechin gallate (ECG) and (−)-epigallocatechin gallate (EGCG) against tyrosinase. Fluorescence spectra show that the three TPs are capable of binding tyrosinase with a molar proportion of 1 : 1. The analysis of CV curves and oxygen utilization suggests that these three TPs can be oxidized by tyrosinase, revealing that these three TPs are suicide inhibitors of tyrosinase. Furthermore, ECG and catechin make tyrosinase irreversibly inactivated due to their catechol group (ring B) being catalyzed by tyrosinase through a cresolase-like pathway, while EGCG inhibits the activity of tyrosinase by competing with or delaying the oxidation of substrate. Molecular simulations further confirm that ring B of ECG and catechin makes a significant contribution to tyrosinase inhibitory activities, and has a direct interaction with the coupled binuclear copper ions in the optimal orientation required by the cresolase-like pathway. Revealing the inactivation mechanism of TPs on inhibiting the activity of tyrosinase.![]()
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Affiliation(s)
- Haifeng Tang
- Key Laboratory of Synthetic Rubber
- Changchun Institute of Applied Chemistry (CIAC)
- Chinese Academy of Sciences
- Changchun
- P. R. China
| | - Fengchao Cui
- Key Laboratory of Synthetic Rubber
- Changchun Institute of Applied Chemistry (CIAC)
- Chinese Academy of Sciences
- Changchun
- P. R. China
| | - Haijuan Li
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry (CIAC)
- Chinese Academy of Sciences
- Changchun
- P. R. China
| | - Qingrong Huang
- Department of Food Science
- Rutgers University
- New Brunswick
- USA
| | - Yunqi Li
- Key Laboratory of Synthetic Rubber
- Changchun Institute of Applied Chemistry (CIAC)
- Chinese Academy of Sciences
- Changchun
- P. R. China
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43
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Cirkovic Velickovic TD, Stanic-Vucinic DJ. The Role of Dietary Phenolic Compounds in Protein Digestion and Processing Technologies to Improve Their Antinutritive Properties. Compr Rev Food Sci Food Saf 2017; 17:82-103. [PMID: 33350063 DOI: 10.1111/1541-4337.12320] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 10/18/2017] [Accepted: 10/18/2017] [Indexed: 12/11/2022]
Abstract
Digestion is the key step for delivering nutrients and bioactive substances to the body. The way different food components interact with each other and with digestive enzymes can modify the digestion process and affect human health. Understanding how food components interact during digestion is essential for the rational design of functional food products. Plant polyphenols have gained much attention for the bioactive roles they play in the human body. However, their strong beneficial effects on human health have also been associated with a negative impact on the digestion process. Due to the generally low absorption of phenolic compounds after food intake, most of the consumed polyphenols remain in the gastrointestinal tract, where they then can exert inhibitory effects on enzymes involved in the degradation of saccharides, lipids, and proteins. While the inhibitory effects of phenolics on the digestion of energy-rich food components (saccharides and lipids) may be regarded as beneficial, primarily in weight-control diets, their inhibitory effects on the digestion of proteins are not desirable for the reason of reduced utilization of amino acids. The effect of polyphenols on protein digestion is reviewed in this article, with an emphasis on food processing methods to improve the antinutritive properties of polyphenols.
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Affiliation(s)
- Tanja D Cirkovic Velickovic
- the Ghent Univ. Global Campus, 119 Songdomunhwa-Ro, Yeonsu-Gu, Incheon 21985, Korea.,Faculty of Bioscience Engineering, Ghent Univ., Coupure Links 653, 9000 Ghent, Belgium.,Center of Excellence for Molecular Food Sciences, Faculty of Chemistry, Univ. of Belgrade, Studenstki trg 16, 11 000 Belgrade, Serbia
| | - Dragana J Stanic-Vucinic
- Center of Excellence for Molecular Food Sciences, Faculty of Chemistry, Univ. of Belgrade, Studenstki trg 16, 11 000 Belgrade, Serbia
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Patel P, Parmar K, Vyas VK, Patel D, Das M. Combined in silico approaches for the identification of novel inhibitors of human islet amyloid polypeptide (hIAPP) fibrillation. J Mol Graph Model 2017; 77:295-310. [PMID: 28917147 DOI: 10.1016/j.jmgm.2017.09.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 09/01/2017] [Accepted: 09/02/2017] [Indexed: 12/31/2022]
Abstract
Human islet amyloid polypeptide (hIAPP) is a natively unfolded polypeptide hormone of glucose metabolism, which is co-secreted with insulin by the β-cells of the pancreas. In patients with type 2 diabetes, IAPP forms amyloid fibrils because of diabetes-associated β-cells dysfunction and increasing fibrillation, in turn, lead to failure of secretory function of β-cells. This provides a target for the discovery of small organic molecules against protein aggregation diseases. However, the binding mechanism of these molecules with monomers, oligomers and fibrils to inhibit fibrillation is still an open question. In this work, ligand and structure-based in silico approaches were used to identify novel fibrillation inhibitors and/or fibril binding compounds. The best pharmacophore model was used as a 3D search query for virtual screening of a compound database to identify novel molecules having the potential to be therapeutic agents against protein aggregation diseases. Docking and molecular dynamics simulation studies were used to explore the interaction pattern and mechanism of the identified novel small molecules with predicted hIAPP structure, its aggregation prone conformation and fibril forming segments. We show that catechins with galloyl group and molecules having two to three planar apolar rings bind to hIAPP structures and fibril forming segments with greater affinity. The differences in binding affinities of different compounds against several fibril forming segments of the peptide suggest that a mixture of active compounds may be required for treatment of aggregation diseases.
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Affiliation(s)
- Palak Patel
- Institute of Science, Nirma University, Sarkhej-Gandhinagar Highway, Ahmedabad, Gujarat 382481, India
| | - Krupali Parmar
- Institute of Science, Nirma University, Sarkhej-Gandhinagar Highway, Ahmedabad, Gujarat 382481, India
| | - Vivek K Vyas
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Sarkhej-Gandhinagar Highway, Ahmedabad, Gujarat 382481, India
| | - Dhaval Patel
- Institute of Advanced Research, Koba Institutional Area, Gandhinagar, Gujarat 382007, India
| | - Mili Das
- Institute of Science, Nirma University, Sarkhej-Gandhinagar Highway, Ahmedabad, Gujarat 382481, India.
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45
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Pereira J, Lamzin VS. A distance geometry-based description and validation of protein main-chain conformation. IUCRJ 2017; 4:657-670. [PMID: 28989721 PMCID: PMC5619857 DOI: 10.1107/s2052252517008466] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/07/2017] [Indexed: 06/07/2023]
Abstract
Understanding the protein main-chain conformational space forms the basis for the modelling of protein structures and for the validation of models derived from structural biology techniques. Presented here is a novel idea for a three-dimensional distance geometry-based metric to account for the fine details of protein backbone conformations. The metrics are computed for dipeptide units, defined as blocks of Cαi-1-O i-1-Cαi -O i -Cαi+1 atoms, by obtaining the eigenvalues of their Euclidean distance matrices. These were computed for ∼1.3 million dipeptide units collected from nonredundant good-quality structures in the Protein Data Bank and subjected to principal component analysis. The resulting new Euclidean orthogonal three-dimensional space (DipSpace) allows a probabilistic description of protein backbone geometry. The three axes of the DipSpace describe the local extension of the dipeptide unit structure, its twist and its bend. By using a higher-dimensional metric, the method is efficient for the identification of Cα atoms in an unlikely or unusual geometrical environment, and its use for both local and overall validation of protein models is demonstrated. It is also shown, for the example of trypsin proteases, that the detection of unusual conformations that are conserved among the structures of this protein family may indicate geometrically strained residues of potentially functional importance.
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Affiliation(s)
- Joana Pereira
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Victor S. Lamzin
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
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46
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Hayashi N, Ujihara T. Conformations of Flavan-3-ols in Water: Analysis Using Density Functional Theory. JOURNAL OF NATURAL PRODUCTS 2017; 80:319-327. [PMID: 28124903 DOI: 10.1021/acs.jnatprod.6b00704] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
To elucidate the conformations and their relative stabilities of flavan-3-ols in water, the optimized structures and energies were calculated by density functional theory, in which M06-2X, ωB97X-D, B3LYP, and CAM-B3LYP were examined as exchange-correlation functionals. The results were evaluated by comparing calculated spin-spin coupling constants of vicinal protons with the corresponding values observed in experimental 1H NMR spectra in D2O. The M06-2X and ωB97X-D results showed good agreement with the experimental NMR data and revealed that the B-ring (pseudoequatorial)/3-O (pseudoaxial) conformers were more stable [5.4-8.7 kJ/mol (1.3-2.1 kcal/mol)] than the B-ring (pseudoaxial)/3-O (pseudoequatorial) conformers in the 2,3-cis-flavan-3-ols, while the B-ring (pseudoequatorial)/3-O (pseudoequatorial) conformers and the B-ring (pseudoaxial)/3-O (pseudoaxial) conformers had similar stabilities in the 2,3-trans-flavan-3-ols.
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Affiliation(s)
- Nobuyuki Hayashi
- Food Research Institute, National Agriculture and Food Research Organization (NARO) , 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Tomomi Ujihara
- Food Research Institute, National Agriculture and Food Research Organization (NARO) , 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
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47
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Shi C, Tang H, Xiao J, Cui F, Yang K, Li J, Zhao Q, Huang Q, Li Y. Small-Angle X-ray Scattering Study of Protein Complexes with Tea Polyphenols. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:656-665. [PMID: 28049293 DOI: 10.1021/acs.jafc.6b04630] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Exploration of the structure of protein complexes, especially the change in conformation and aggregation behavior of proteins upon ligand binding, is crucial to clarify their bioactivities at the molecular level. We applied solution small-angle X-ray scattering (SAXS) to study the complex structure of bovine serum albumin (BSA) and trypsin binding with tea polyphenols, that is, catechin and epigallocatechin gallate (EGCG). We found that tea polyphenols can steadily promote the aggregation of proteins and protein complexes through their bridging effect. The numbers of proteins in the complexes and in the aggregates of complexes are extracted from SAXS intensity profiles, and their dependences as a function of the molar ratio of polyphenol to protein are discussed. EGCG has stronger capability than catechin to promote complex formation and further aggregation, and the aggregates of complexes have a denser core with a relatively smooth surface. The aggregates induced by catechin are loosely packed with a rough surface. BSA shows higher stability than trypsin in the formation of complex with a well-folded conformation. The synergistic unfolding of trypsin results in larger aggregates in the mixtures with more tea polyphenols. The binding affinity and number of tea polyphenols bound to each protein are further determined using fluorescence spectroscopy. The structure of protein complexes explored in this work is referable in the preparation of protein complex-based particles and the understanding of polyphenol-induced formation and further aggregation of protein complexes.
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Affiliation(s)
- Ce Shi
- Key Laboratory of Synthetic Rubber & Laboratory of Advanced Power Sources, Changchun Institute of Applied Chemistry , Changchun 130022, People's Republic of China
| | - Haifeng Tang
- Key Laboratory of Synthetic Rubber & Laboratory of Advanced Power Sources, Changchun Institute of Applied Chemistry , Changchun 130022, People's Republic of China
- School of Life Science, Jilin University , Changchun 130012, People's Republic of China
| | - Jie Xiao
- Department of Food Science, Rutgers University , 65 Dudley Road, New Brunswick, New Jersey 08901, United States
| | - Fengchao Cui
- Key Laboratory of Synthetic Rubber & Laboratory of Advanced Power Sources, Changchun Institute of Applied Chemistry , Changchun 130022, People's Republic of China
| | - Kecheng Yang
- Key Laboratory of Synthetic Rubber & Laboratory of Advanced Power Sources, Changchun Institute of Applied Chemistry , Changchun 130022, People's Republic of China
| | - Ji Li
- Department of Food Science, Rutgers University , 65 Dudley Road, New Brunswick, New Jersey 08901, United States
| | - Qin Zhao
- Department of Food Science, Rutgers University , 65 Dudley Road, New Brunswick, New Jersey 08901, United States
| | - Qingrong Huang
- Department of Food Science, Rutgers University , 65 Dudley Road, New Brunswick, New Jersey 08901, United States
| | - Yunqi Li
- Key Laboratory of Synthetic Rubber & Laboratory of Advanced Power Sources, Changchun Institute of Applied Chemistry , Changchun 130022, People's Republic of China
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48
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Tavassoli Z, Taghdir M, Ranjbar B. Renin inhibition by soyasaponin I: a potent native anti-hypertensive compound. J Biomol Struct Dyn 2017; 36:166-176. [DOI: 10.1080/07391102.2016.1270855] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Zeinab Tavassoli
- Department of Biophysics, Tarbiat Modares University, Tehran, Iran
| | - Majid Taghdir
- Department of Biophysics, Tarbiat Modares University, Tehran, Iran
| | - Bijan Ranjbar
- Department of Biophysics, Tarbiat Modares University, Tehran, Iran
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Zhuang X, Zhao B, Liu S, Song F, Cui F, Liu Z, Li Y. Noncovalent Interactions between Superoxide Dismutase and Flavonoids Studied by Native Mass Spectrometry Combined with Molecular Simulations. Anal Chem 2016; 88:11720-11726. [PMID: 27760293 DOI: 10.1021/acs.analchem.6b03359] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Misfolding and aggregation of Cu, Zn superoxide dismutase (SOD1) is implicated in the etiology of amyotrophic lateral sclerosis (ALS). The use of small molecules may stabilize the spatial structure of SOD1 dimer, thus, preventing its dissociation and aggregation. In this study, "native" mass spectrometry (MS) was used to study the noncovalent interactions between SOD1 and flavonoid compounds. MS experiments were performed on a quadruple time-of-flight (Q-ToF) mass spectrometer with an electrospray ionization (ESI) source and T-wave ion mobility. ESI-MS was used to detect the SOD1-flavonoid complexes and compare their relative binding strengths. The complement of ion mobility separation allowed comparison in the binding affinities between flavonoid isomers and provided information on the conformational changes. Molecular docking together with molecular dynamics simulations and MM/PBSA methods were applied to gain insights into the binding modes and free energies of SOD1-flavonoid complexes at the molecule level. Among all the flavonoids investigated, flavonoid glycosides preferentially bind to SOD1 than their aglycone counterparts. Naringin, one of the compounds that has the strongest binding affinity to SOD1, was subjected to further characterization. Experiment results show that the binding of naringin can stabilize SOD1 dimer and inhibit the aggregation of SOD1. Molecular simulation results suggest that naringin could reduce the dissociation of SOD1 dimers through direct interaction with the dimer interface. This developed analytical strategy could also be applied to study the interactions between SOD1 and other drug-like molecules, which may have the effect to reduce the aggregation.
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Affiliation(s)
- Xiaoyu Zhuang
- University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Bing Zhao
- University of the Chinese Academy of Sciences, Beijing 100039, China
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50
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Cui F, Liu L, Tang H, Yang K, Li Y. Construction of explicit models to correlate the structure and the inhibitory activity of aldose reductase: Flavonoids and sulfonyl-pyridazinones as inhibitors. Chem Biol Drug Des 2016; 89:482-491. [PMID: 27637378 DOI: 10.1111/cbdd.12868] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 07/20/2016] [Accepted: 09/08/2016] [Indexed: 11/29/2022]
Abstract
The correlation between binding energies and bioactivities is the core of structure-based computer-aided drug design. However, many models to address this correlation are still strongly system-dependent at current stage. We constructed two explicit models to correlate the binding energies with the inhibitory activities of flavonoids and sulfonyl-pyridazinones as inhibitors of aldose reductase. The introduction of multiple complex states comprised of protein, coenzyme, substrate, and inhibitor can remarkably improve the correlation coefficients, compared with that using single complex state. Recombination of energy terms from complex structures and molecular descriptors of inhibitors can further improve the correlation. The explicit models provide correlation coefficients of 0.90 and 0.92 for flavonoids and sulfonyl-pyridazinones, respectively. These models also steadily present the contribution from each energy term and the favorite of protein-inhibitor complex states. Meanwhile, we also observed that some inhibitors can accommodate alternative sites out of the conserved binding pocket at the presence/absence of coenzyme and substrate. It is responsible for the remarkable change in the binding energies and thus significantly influences the correlation between the structures and the inhibitory activities. Overall, this work presents a rational way to construct reliable explicit models through the combination of multiple physically accessible complex states, even though each of them only bears marginal information related to their activities.
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Affiliation(s)
- Fengchao Cui
- Key Laboratory of Synthetic Rubber and Laboratory of Advanced Power Sources, Changchun Institute of Applied Chemistry (CIAC), Chinese Academy of Sciences, Changchun, China
| | - Lunyang Liu
- Key Laboratory of Synthetic Rubber and Laboratory of Advanced Power Sources, Changchun Institute of Applied Chemistry (CIAC), Chinese Academy of Sciences, Changchun, China
| | - Haifeng Tang
- Key Laboratory of Synthetic Rubber and Laboratory of Advanced Power Sources, Changchun Institute of Applied Chemistry (CIAC), Chinese Academy of Sciences, Changchun, China
| | - Kecheng Yang
- Key Laboratory of Synthetic Rubber and Laboratory of Advanced Power Sources, Changchun Institute of Applied Chemistry (CIAC), Chinese Academy of Sciences, Changchun, China
| | - Yunqi Li
- Key Laboratory of Synthetic Rubber and Laboratory of Advanced Power Sources, Changchun Institute of Applied Chemistry (CIAC), Chinese Academy of Sciences, Changchun, China
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