1
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Ramirez-Cando LJ, Rodríguez-Cazar LG, Acosta-Tobar LA, Ballaz SJ. Molecular docking analysis of chlorpyrifos at the human α7-nAChR and its potential relationship with neurocytoxicity in SH-SY5Y cells. J Environ Sci Health B 2024; 59:277-284. [PMID: 38600794 DOI: 10.1080/03601234.2024.2340929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 04/03/2024] [Indexed: 04/12/2024]
Abstract
The organophosphate insecticide chlorpyrifos (CPF), an acetylcholinesterase inhibitor, has raised serious concerns about human safety. Apart from inducing synaptic acetylcholine accumulation, CPF could also act at nicotinic acetylcholine receptors, like the α7-isoform (α7-nAChR), which could potentially be harmful to developing brains. Our aims were to use molecular docking to assess the binding interactions between CPF and α7-nAChR through, to test the neurocytotoxic and oxidative effects of very low concentrations of CPF on SH-SY5Y cells, and to hypothesize about the potential mediation of α7-nAChR. Docking analysis showed a significant binding affinity of CPH for the E fragment of the α7-nAChR (ΔGibbs: -5.63 to -6.85 Kcal/mol). According to the MTT- and Trypan Blue-based viability assays, commercial CPF showed concentration- and time-dependent neurotoxic effects at a concentration range (2.5-20 µM), ten-folds lower than those reported to have crucial effects for sheer CPF. A rise of the production of radical oxygen species (ROS) was seen at even lower concentrations (1-2.5 µM) of CPF after 24h. Notably, our docking analysis supports the antagonistic actions of CPF on α7-nAChR that were recently published. In conclusion, while α7-nAChR is responsible for neuronal survival and neurodevelopmental processes, its activity may also mediate the neurotoxicity of CPF.
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Affiliation(s)
- Lenin J Ramirez-Cando
- School of Biological Sciences & Engineering, Universidad Yachay Tech, Urcuquí, Ecuador
| | | | - Luis A Acosta-Tobar
- School of Biological Sciences & Engineering, Universidad Yachay Tech, Urcuquí, Ecuador
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2
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Arumugam M, Shanmugavel B, Sellppan M, Pavadai P. In silico evaluation of some commercially available terpenoids as spike glycoprotein of SARS-CoV-2 - inhibitors using molecular dynamic approach. J Biomol Struct Dyn 2024; 42:1072-1078. [PMID: 37139540 DOI: 10.1080/07391102.2023.2201848] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 03/28/2023] [Indexed: 05/05/2023]
Abstract
Coronavirus, an extremely contagious infections disease had a harmful effect on the world's population. It is a family of enveloped, single-stranded, positive-strand RNA viruses of Nidovirales order belongs to coroviridae family. At present, worldwide several lakhs of deaths and several billions of infections have been reported. Hence, the focus of the present study was to assess the SARS-CoV-2 enzyme inhibitory potential of certain commercially available terpenoids using Lamarckian genetic algorithm as a working principle and molecular dynamic studies was also performed. AutoDock 4.2 software was used to perform the computational docking calculations of terpenoids against SARS-CoV-2 enzyme. The terpenoids such as, Andrographolide, Betulonic acid, Erythrodiol, Friedelin, Mimuscopic acid, Moronic acid, and Retinol were selected based on the drug likeness properties. Remdesivir a well-known anti-viral drug was selected as the standard drug. Molecular dynamic simulation studies were carried using Desmond module of Schrodinger Suite. In the current study we observed that, Friedelin was exhibited excellent SARS-CoV-2 enzyme inhibitory potential than the standard drug and other selected terpenoids. Friedelin and the standard Remdesivir was undergone the molecular dynamic studies and Friedelin showed a good number of hydrogen bonds over the simulation time of 100 ns. Based on the in silico computational evaluation, it can be concluded that Friedelin could be worthwhile terpenoid against SARS-CoV-2 spike protein. A further study on Friedelin is required to develop a potential chemical entity against the management of COVID disease.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Madeswaran Arumugam
- Department of Pharmacology, Karpagam College of Pharmacy, Affiliated to The Tamil Nadu Dr. M.G.R. Medical University, Coimbatore, Tamil Nadu, India
| | - Brahmasundari Shanmugavel
- Department of Pharmacology, Sri Ramakrishna Institute of Paramedical Sciences, Affiliated to The Tamil Nadu Dr. M.G.R. Medical University, Coimbatore, Tamil Nadu, India
| | - Mohan Sellppan
- Karpagam College of Pharmacy, Affiliated to The Tamil Nadu Dr. M.G.R. Medical University, Coimbatore, Tamil Nadu, India
| | - Parasuraman Pavadai
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bengaluru, Karnataka, India
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Gligorijević N, Jovanović Z, Cvijetić I, Šunderić M, Veličković L, Katrlík J, Holazová A, Nikolić M, Minić S. Investigation of the Potential of Selected Food-Derived Antioxidants to Bind and Stabilise the Bioactive Blue Protein C-Phycocyanin from Cyanobacteria Spirulina. Int J Mol Sci 2023; 25:229. [PMID: 38203400 PMCID: PMC10779248 DOI: 10.3390/ijms25010229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Blue C-phycocyanin (C-PC), the major Spirulina protein with innumerable health-promoting benefits, is an attractive colourant and food supplement. A crucial obstacle to its more extensive use is its relatively low stability. This study aimed to screen various food-derived ligands for their ability to bind and stabilise C-PC, utilising spectroscopic techniques and molecular docking. Among twelve examined ligands, the protein fluorescence quenching revealed that only quercetin, coenzyme Q10 and resveratrol had a moderate affinity to C-PC (Ka of 2.2 to 3.7 × 105 M-1). Docking revealed these three ligands bind more strongly to the C-PC hexamer than the trimer, with the binding sites located at the interface of two (αβ)3 trimers. UV/VIS absorption spectroscopy demonstrated the changes in the C-PC absorption spectra in a complex with quercetin and resveratrol compared to the spectra of free protein and ligands. Selected ligands did not affect the secondary structure content, but they induced changes in the tertiary protein structure in the CD study. A fluorescence-based thermal stability assay demonstrated quercetin and coenzyme Q10 increased the C-PC melting point by nearly 5 °C. Our study identified food-derived ligands that interact with C-PC and improve its thermal stability, indicating their potential as stabilising agents for C-PC in the food industry.
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Affiliation(s)
- Nikola Gligorijević
- University of Belgrade, Institute of Chemistry, Technology and Metallurgy, Department of Chemistry, National Institute of the Republic of Serbia, Studentski trg 12–16, 11000 Belgrade, Serbia;
| | - Zorana Jovanović
- University of Belgrade-Faculty of Chemistry, Center of Excellence for Molecular Food Sciences & Department of Biochemistry, Studentski trg 12–16, 11000 Belgrade, Serbia; (Z.J.); (L.V.)
| | - Ilija Cvijetić
- University of Belgrade-Faculty of Chemistry, Department of Analytical Chemistry, Studentski trg 12–16, 11000 Belgrade, Serbia;
| | - Miloš Šunderić
- University of Belgrade-Institute for the Application of Nuclear Energy (INEP), Banatska 31b, 11000 Belgrade, Serbia;
| | - Luka Veličković
- University of Belgrade-Faculty of Chemistry, Center of Excellence for Molecular Food Sciences & Department of Biochemistry, Studentski trg 12–16, 11000 Belgrade, Serbia; (Z.J.); (L.V.)
| | - Jaroslav Katrlík
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 5807/9, 84538 Bratislava, Slovakia; (J.K.); (A.H.)
| | - Alena Holazová
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 5807/9, 84538 Bratislava, Slovakia; (J.K.); (A.H.)
| | - Milan Nikolić
- University of Belgrade-Faculty of Chemistry, Center of Excellence for Molecular Food Sciences & Department of Biochemistry, Studentski trg 12–16, 11000 Belgrade, Serbia; (Z.J.); (L.V.)
| | - Simeon Minić
- University of Belgrade-Faculty of Chemistry, Center of Excellence for Molecular Food Sciences & Department of Biochemistry, Studentski trg 12–16, 11000 Belgrade, Serbia; (Z.J.); (L.V.)
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Chen X, Zhang W, Quek SY, Zhao L. Flavor-food ingredient interactions in fortified or reformulated novel food: Binding behaviors, manipulation strategies, sensory impacts, and future trends in delicious and healthy food design. Compr Rev Food Sci Food Saf 2023; 22:4004-4029. [PMID: 37350045 DOI: 10.1111/1541-4337.13195] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/02/2023] [Accepted: 05/27/2023] [Indexed: 06/24/2023]
Abstract
With consumers gaining prominent awareness of health and well-being, a diverse range of fortified or reformulated novel food is developed to achieve personalized or tailored nutrition using protein, carbohydrates, or fat as building blocks. Flavor property is a critical factor in the acceptability and marketability of fortified or reformulated food. Major food ingredients are able to interact with flavor compounds, leading to a significant change in flavor release from the food matrix and, ultimately, altering flavor perception. Although many efforts have been made to elucidate how food matrix components change flavor binding capacities, the influences on flavor perception and their implications for the innovation of fortified or reformulated novel food have not been systematically summarized up to now. Thus, this review provides detailed knowledge about the binding behaviors of flavors to major food ingredients, as well as their influences on flavor retention, release, and perception. Practical approaches for manipulating these interactions and the resulting flavor quality are also reviewed, from the scope of their intrinsic and extrinsic influencing factors with technologies available, which is helpful for future food innovation. Evaluation of food-ingredient interactions using real food matrices while considering multisensory flavor perception is also prospected, to well motivate food industries to investigate new strategies for tasteful and healthy food design in response to consumers' unwillingness to compromise on flavor for health.
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Affiliation(s)
- Xiao Chen
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, P. R. China
- School of Chemical Sciences, The University of Auckland, Auckland, New Zealand
| | - Wangang Zhang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, P. R. China
| | - Siew Young Quek
- School of Chemical Sciences, The University of Auckland, Auckland, New Zealand
- Riddet Institute, Centre of Research Excellence in Food Research, Palmerston North, New Zealand
| | - Liyan Zhao
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, P. R. China
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Mittal A, Singh A, Zhang B, Zhao Q, Benjakul S. Inhibition Mechanism of Chitooligosaccharide-Polyphenol Conjugates toward Polyphenoloxidase from Shrimp Cephalothorax. Molecules 2023; 28:5560. [PMID: 37513432 PMCID: PMC10385636 DOI: 10.3390/molecules28145560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
Crustaceans are perishable with a short shelf-life. They are prone to deterioration after capture, particularly during handling, processing, and storage due to melanosis caused by polyphenoloxidase (PPO). Therefore, inhibitory effects of chitooligosaccharide (CHOS) in comparison with CHOS-catechin (CHOS-CAT), CHOS-epigallocatechin gallate (CHOS-EGCG), and CHOS-gallic acid (CHOS-GAL) conjugates on Pacific white shrimp cephalothorax PPO were studied. IC50 of CHOS-CAT (0.32 mg/mL) toward PPO was less than those of all conjugates tested (p < 0.05). CHOS-CAT exhibited the mixed-type inhibition. Kic (0.58 mg/mL) and Kiu (0.02 mg/mL) of CHOS-CAT were lower than those of other conjugates (p < 0.05). CHOS-CAT showed static fluorescence-quenching, suggesting a change in micro-environment around the active site of PPO. Moreover, CHOS-CAT was linked with various amino acid residues, including Tyr208 or Tyr209 of proPPO via van der Waals, hydrophobic interaction, and hydrogen bonding as elucidated by the molecular docking of proPPO. Although CHOS-CAT had the highest PPO inhibitory activity, it showed a lower binding energy (-8.5 kcal/mol) than other samples, except for CHOS-EGCG (-10.2 kcal/mol). Therefore, CHOS-CAT could act as an anti-melanosis agent in shrimp and other crustaceans to prevent undesirable discoloration associated with quality losses.
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Affiliation(s)
- Ajay Mittal
- International Center of Excellence in Seafood Science and Innovation, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai 90110, Thailand
| | - Avtar Singh
- International Center of Excellence in Seafood Science and Innovation, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai 90110, Thailand
| | - Bin Zhang
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, College of Food Science and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China
| | - Qiancheng Zhao
- School of Food Science and Engineering, Dalian Ocean University, Dalian 116023, China
| | - Soottawat Benjakul
- International Center of Excellence in Seafood Science and Innovation, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai 90110, Thailand
- Department of Food and Nutrition, Kyung Hee University, Seoul 02447, Republic of Korea
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6
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Xiong Y, Gu C, Yu J, Copeland L, Wang S. Inhibition of In Vitro Amylolysis of Wheat Starch by Gluten Peptides. J Agric Food Chem 2023; 71:7514-7520. [PMID: 37143352 DOI: 10.1021/acs.jafc.3c01434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The effect of gluten peptides (GPs) isolated from a gluten proteolysate on in vitro amylolysis of gelatinized wheat starch was investigated. GPs in a pepsin hydrolysate were fractionated into fractions with molecular weights (MWs) of 500-3000, 3500-7000, 10-17, and 35-48 kDa. The fractions containing peptides with MW > 10 kDa had a strong inhibitory effect on enzyme activity and amylolysis of starch, whereas GPs with MW <10 kDa had no inhibitory effect. Binding constants estimated by surface plasmon resonance showed that peptides in the fractions with MW > 10 kDa bound more strongly to α-amylase, in contrast to peptides of MW <10 kDa. Significant correlations were observed between digestion parameters and equilibrium binding affinity. We conclude that peptides with MW >10 kDa in a pepsin digest of gluten have a strong inhibitory effect on in vitro enzymatic hydrolysis of starch due to their strong binding affinity to α-amylase.
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Affiliation(s)
- Yanmin Xiong
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin 300457, China
- School of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Chunkai Gu
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin 300457, China
- School of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Jinglin Yu
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Les Copeland
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Shujun Wang
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin 300457, China
- School of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin 300457, China
- Food Laboratory of Zhongyuan, Tianjin University of Science & Technology, Tianjin 300457, China
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Almazar CA, Mendoza MV, Rivera WL. In Silico Approaches for the Identification of Aptamer Binding Interactions to Leptospira spp. Cell Surface Proteins. Trop Med Infect Dis 2023; 8. [PMID: 36828542 DOI: 10.3390/tropicalmed8020125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Aptamers are nucleic acids that can bind with high affinity and specificity to a range of target molecules. However, their functionality relies on their secondary and tertiary structures such that the combination of nucleotides determines their three-dimensional conformation. In this study, the binding mechanisms of candidate aptamers and their interactions with selected target proteins found in the cell surface of Leptospira were predicted to select high-affinity aptamers. Four aptamers were evaluated through molecular modeling and docking using available software and web-based tools, following the workflow previously designed for in silico evaluation of DNA aptamers. The most predominant and highly conserved surface-exposed proteins among pathogenic Leptospira species were used as aptamer targets. The highest number of interactions was seen in aptamers AP5 and AP1. Hydrogen bonds, along with a few hydrophobic interactions, occur in most aptamer-protein complexes. Further analysis revealed serine, threonine, glutamine, and lysine as main protein residues. H-bond interactions occur mostly with polar amino acids, as reflected in the predicted interaction profiles of aptamer-protein complexes. In silico strategies allowed the identification of key residues crucial in aptamer-target interaction during aptamer screening. Such information can be used in aptamer modification for improved binding affinity and accuracy for diagnostics application.
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8
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Rombel‐Bryzek A, Miller A, Witkowska D. Thermodynamic analysis of the interactions between human ACE2 and spike RBD of Betacoronaviruses (SARS-CoV-1 and SARS-CoV-2). FEBS Open Bio 2022; 13:174-184. [PMID: 36416453 PMCID: PMC9808565 DOI: 10.1002/2211-5463.13525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 11/11/2022] [Accepted: 11/22/2022] [Indexed: 11/24/2022] Open
Abstract
There are many scientific reports on the interaction of the SARS-CoV-2 virus S protein (and its RBD) with the human ACE2 receptor protein. However, there are no reliable data on how this interaction differs from the interaction of the receptor binding domain of SARS-CoV-1 with ACE2, in terms of binding strength and changes in reaction enthalpy and entropy. Our studies have revealed these differences and the impact of zinc ions on this interaction. Intriguingly, the binding affinity of both RBDs (of SARS-CoV-1 and of SARS-CoV-2) to the ACE2 receptor protein is almost identical; however, there are some differences in the entropic and enthalpic contributions to these interactions.
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9
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Gopi P, Gurnani M, Singh S, Sharma P, Pandya P. Structural aspects of SARS-CoV-2 mutations: Implications to plausible infectivity with ACE-2 using computational modeling approach. J Biomol Struct Dyn 2022:1-16. [PMID: 35938696 DOI: 10.1080/07391102.2022.2108901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Some of the SARS-CoV-2 variants are said to be more infectious than the previous others and are causing panic around the globe. Cases related to Delta plus (δ+) and omicron (ο) variants are on the rise worldwide. This sudden surge warrants an investigation into the reasons for its binding with ACE-2. The present study attempts to find out the structural basis of binding interactions of SARS-CoV-2 mutants based on computational modeling and comparative analysis. In silico strategies including protein-protein docking, mutation analysis, molecular dynamics, and binding energy calculations were used to study the binding of the 'receptor binding domain' (RBD) of the seven 'variants of concern' which include Alpha (α), Beta (β), Gamma (γ), Kappa (κ), Delta (δ), Delta plus (δ+) and omicron (ο) with ACE-2 (human angiotensin-converting enzyme-2) and with antibodies. Among all the variants dealt with in this study, Delta plus and omicron were found to be binding more strongly to ACE-2 than others due to inherent mutations and the consequent change in the hydrophilic and hydrophobic environment of the binding site. Furthermore, molecular dynamic (MD) simulations and subsequent MM/PBSA calculations provided useful structural insights into key residues participating in the interaction. Infectivity of a virus could be dependent on the interplay of evading antibodies and simultaneously attaching strongly with the host receptor. A cross-correlation between mutant spike proteins' binding with ACE-2 and antibodies provides a holistic assessment of the binding nature of these mutants vis-à-vis native virus and offers opportunities for designing potential therapeutics against these new mutants.
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Affiliation(s)
- Priyanka Gopi
- Amity Institute of Forensic Sciences, Amity University, Noida, Uttar Pradesh, India
| | - Manisha Gurnani
- Amity Institute of Environmental Science, Amity University, Noida, Uttar Pradesh, India
| | - Shweta Singh
- Amity Institute of Forensic Sciences, Amity University, Noida, Uttar Pradesh, India
| | - Palak Sharma
- Amity Institute of Forensic Sciences, Amity University, Noida, Uttar Pradesh, India
| | - Prateek Pandya
- Amity Institute of Forensic Sciences, Amity University, Noida, Uttar Pradesh, India
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10
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Ginnard SM, Winkler AE, Mellado Fritz C, Bluhm T, Kemmer R, Gilliam M, Butkevich N, Abdrabbo S, Bricker K, Feiler J, Miller I, Zoerman J, El-Mohri Z, Khuansanguan P, Basch M, Petzold T, Kostoff M, Konopka S, Kociba B, Gillis T, Heyl DL, Trievel RC, Albaugh BN. Molecular investigation of the tandem Tudor domain and plant homeodomain histone binding domains of the epigenetic regulator UHRF2. Proteins 2021; 90:835-847. [PMID: 34766381 DOI: 10.1002/prot.26278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/25/2021] [Accepted: 11/07/2021] [Indexed: 11/12/2022]
Abstract
Ubiquitin-like containing PHD and ring finger (UHRF)1 and UHRF2 are multidomain epigenetic proteins that play a critical role in bridging crosstalk between histone modifications and DNA methylation. Both proteins contain two histone reader domains, called tandem Tudor domain (TTD) and plant homeodomain (PHD), which read the modification status on histone H3 to regulate DNA methylation and gene expression. To shed light on the mechanism of histone binding by UHRF2, we have undergone a detailed molecular investigation with the TTD, PHD and TTD-PHD domains and compared the binding activity to its UHRF1 counterpart. We found that unlike UHRF1 where the PHD is the primary binding contributor, the TTD of UHRF2 has modestly higher affinity toward the H3 tail, while the PHD has a weaker binding interaction. We also demonstrated that like UHRF1, the aromatic amino acids within the TTD are important for binding to H3K9me3 and a conserved aspartic acid within the PHD forms an ionic interaction with R2 of H3. However, while the aromatic amino acids in the TTD of UHRF1 contribute to selectivity, the analogous residues in UHRF2 contribute to both selectivity and affinity. We also discovered that the PHD of UHRF2 contains a distinct asparagine in the H3R2 binding pocket that lowers the binding affinity of the PHD by reducing a potential electrostatic interaction with the H3 tail. Furthermore, we demonstrate the PHD and TTD of UHRF2 cooperate to interact with the H3 tail and that dual domain engagement with the H3 tail relies on specific amino acids. Lastly, our data indicate that the unique stretch region in the TTD of UHRF2 can decrease the melting temperature of the TTD-PHD and represents a disordered region. Thus, these subtle but important mechanistic differences are potential avenues for selectively targeting the histone binding interactions of UHRF1 and UHRF2 with small molecules.
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Affiliation(s)
- Shane M Ginnard
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Alyssa E Winkler
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | | | - Tatum Bluhm
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Ray Kemmer
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Marisa Gilliam
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Nick Butkevich
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Sara Abdrabbo
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Kaitlyn Bricker
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Justin Feiler
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Isaak Miller
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Jenna Zoerman
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Zeineb El-Mohri
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Panida Khuansanguan
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Madyson Basch
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Timothy Petzold
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Matthew Kostoff
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Sean Konopka
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Brendon Kociba
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Thomas Gillis
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Deborah L Heyl
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
| | - Raymond C Trievel
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Brittany N Albaugh
- Department of Chemistry, Eastern Michigan University, Ypsilanti, Michigan, USA
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Migliore R, D’Antona N, Sgarlata C, Consoli GML. Co-Loading of Temozolomide and Curcumin into a Calix[4]arene-Based Nanocontainer for Potential Combined Chemotherapy: Binding Features, Enhanced Drug Solubility and Stability in Aqueous Medium. Nanomaterials (Basel) 2021; 11:2930. [PMID: 34835694 PMCID: PMC8623626 DOI: 10.3390/nano11112930] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/28/2021] [Accepted: 10/28/2021] [Indexed: 11/16/2022]
Abstract
The co-delivery of anticancer drugs into tumor cells by a nanocarrier may provide a new paradigm in chemotherapy. Temozolomide and curcumin are anticancer drugs with a synergistic effect in the treatment of multiform glioblastoma. In this study, the entrapment and co-entrapment of temozolomide and curcumin in a p-sulfonato-calix[4]arene nanoparticle was investigated by NMR spectroscopy, UV-vis spectrophotometry, isothermal titration calorimetry, and dynamic light scattering. Critical micellar concentration, nanoparticle size, zeta potential, drug loading percentage, and thermodynamic parameters were all consistent with a drug delivery system. Our data showed that temozolomide is hosted in the cavity of the calix[4]arene building blocks while curcumin is entrapped within the nanoparticle. Isothermal titration calorimetry evidenced that drug complexation and entrapment are entropy driven processes. The loading in the calixarene-based nanocontainer enhanced the solubility and half-life of both drugs, whose medicinal efficacy is affected by low solubility and rapid degradation. The calixarene-based nanocontainer appears to be a promising new candidate for nanocarrier-based drug combination therapy for glioblastoma.
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Affiliation(s)
- Rossella Migliore
- Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche, Via Paolo Gaifami 18, 95126 Catania, Italy; (R.M.); (N.D.)
| | - Nicola D’Antona
- Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche, Via Paolo Gaifami 18, 95126 Catania, Italy; (R.M.); (N.D.)
| | - Carmelo Sgarlata
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Grazia M. L. Consoli
- Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche, Via Paolo Gaifami 18, 95126 Catania, Italy; (R.M.); (N.D.)
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Li W, Song Y, Sun W, Yang X, Liu X, Sun L. Both Acidic pH Value and Binding Interactions of Tartaric Acid With α-Glucosidase Cause the Enzyme Inhibition: The Mechanism in α-Glucosidase Inhibition of Four Caffeic and Tartaric Acid Derivates. Front Nutr 2021; 8:766756. [PMID: 34692755 PMCID: PMC8529059 DOI: 10.3389/fnut.2021.766756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 09/10/2021] [Indexed: 01/02/2023] Open
Abstract
The inhibition mechanism of four caffeic and tartaric acid derivates, including caffeic acid (CA), tartaric acid (TA), caftaric acid (CFA) and chicoric acid (CHA) against α-glucosidase was characterized by substrate depletion, fluorescence quenching, isothermal titration calorimetry (ITC) and molecular docking. TA and CA were found with the highest and no inhibition effect respectively, and caffeoyl substitution at 2 and/or 3-OH of TA significantly decreased its inhibition. The enzyme inhibition effects of organic acids were not in an inhibitor concentration-dependent mode, and there was a rush increase in inhibition at a respective acidic pH value, especially for CFA and CHA, suggesting the important role of acidic pH in the enzyme inhibition for both compounds. Besides, CA, CFA and CHA were shown with strong quenching effects on α-glucosidase fluorescence because of π-conjugations between aromatic ring of caffeoyl moiety and that of enzyme fluorescent residues. However, no fluorescence quenching effect was observed for TA due to lack of aromatic ring. Additionally, a direct binding interaction behavior was observed for TA with α-glucosidase according to the fitted independent binding model in ITC, but not for CFA and CHA. Therefore, both acidic pH and binding interactions of TA with α-glucosidase resulted in the enzyme inhibition.
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Affiliation(s)
- Wenyue Li
- College of Food Science and Engineering, Northwest A&F University, Xianyang, China
| | - Yi Song
- College of Food Science and Engineering, Northwest A&F University, Xianyang, China
| | - Wanshu Sun
- College of Food Science and Engineering, Northwest A&F University, Xianyang, China
| | - Xi Yang
- College of Food Science and Engineering, Northwest A&F University, Xianyang, China
| | - Xuebo Liu
- College of Food Science and Engineering, Northwest A&F University, Xianyang, China
| | - Lijun Sun
- College of Food Science and Engineering, Northwest A&F University, Xianyang, China
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13
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Wang Y, Li S, Bai F, Cao J, Sun L. The Physical Adsorption of Gelatinized Starch with Tannic Acid Decreases the Inhibitory Activity of the Polyphenol against α-Amylase. Foods 2021; 10:foods10061233. [PMID: 34071531 PMCID: PMC8226663 DOI: 10.3390/foods10061233] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/27/2021] [Accepted: 05/27/2021] [Indexed: 02/01/2023] Open
Abstract
The effects of mixing orders of tannic acid (TA), starch, and α-amylase on the enzyme inhibition of TA were studied, including mixing TA with α-amylase before starch addition (order 1), mixing TA with pre-gelatinized starch before α-amylase addition (order 2) and co-gelatinizing TA with starch before α-amylase addition (order 3). It was found that the enzyme inhibition was always highest for order 1 because TA could bind with the enzyme active site thoroughly before digestion occurred. Both order 2 and 3 reduced α-amylase inhibition through decreasing binding of TA with the enzyme, which resulted from the non-covalent physical adsorption of TA with gelatinized starch. Interestingly, at low TA concentration, α-amylase inhibition for order 2 was higher than order 3, while at high TA concentration, the inhibition was shown with the opposite trend, which arose from the difference in the adsorption property between the pre-gelatinized and co-gelatinized starch at the corresponding TA concentrations. Moreover, both the crystalline structures and apparent morphology of starch were not significantly altered by TA addition for order 2 and 3. Conclusively, although a polyphenol has an acceptable inhibitory activity in vitro, the actual effect may not reach the expected one when taking processing procedures into account.
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Affiliation(s)
| | | | | | | | - Lijun Sun
- Correspondence: ; Tel.: +86-136-0929-2796
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14
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Kock FVC, Costa AR, de Oliveira KM, Batista AA, Ferreira AG, Venâncio T. A Supramolecular Interaction of a Ruthenium Complex With Calf-Thymus DNA: A Ligand Binding Approach by NMR Spectroscopy. Front Chem 2019; 7:762. [PMID: 31781544 PMCID: PMC6857657 DOI: 10.3389/fchem.2019.00762] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/23/2019] [Indexed: 12/29/2022] Open
Abstract
Lawsone itself exhibits interesting biological activities, and its complexation with a metal center can improve the potency. In this context a cytotoxic Ru-complex, [Ru(law)(dppb)(bipy)] (law = lawsone, dppb = 1,4-bis(diphenylphosphino)butane and bipy = 2,2'-bipyridine), named as CBLAU, was prepared as reported. In this work, NMR binding-target studies were performed to bring to light the most accessible interaction sites of this Ru-complex toward Calf-Thymus DNA (CT-DNA, used as a model), in a similar approach used for other metallic complexes with anti-cancer activity, such as cisplatin and carboplatin. Advanced and robust NMR binding-target studies, among them Saturation Transfer Difference (STD)-NMR and longitudinal relaxometry (T1), were explored. The 1H and 31P -NMR data indicate that the structure of Ru-complex remains preserved in the presence of CT-DNA, and some linewidth broadening is also observed for all the signals, pointing out some interaction. Looking at the binding efficiency, the T1 values are highly influenced by the formation of the CBLAU-DNA adduct, decreasing from 11.4 s (without DNA) to 1.4 s (with DNA), where the difference is bigger for the lawsone protons. Besides, the STD-NMR titration experiments revealed a stronger interaction (KD = 5.9 mM) for CBLAU-DNA in comparison to non-complexed lawsone-DNA (KD = 34.0 mM). The epitope map, obtained by STD-NMR, shows that aromatic protons from the complexed lawsone exhibits higher saturation transfer, in comparison to other Ru-ligands (DPPB and bipy), suggesting the supramolecular contact with CT-DNA takes place by the lawsone face of the Ru-complex, possibly by a spatial π-π stacking involving π-bonds on nucleic acids segments of the DNA chain and the naphthoquinone group.
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Affiliation(s)
| | - Analu Rocha Costa
- Laboratory of Structure and Reactivity of Inorganic Compounds, Department of Chemistry, Federal University of São Carlos, São Carlos, Brazil
| | - Katia Mara de Oliveira
- Laboratory of Structure and Reactivity of Inorganic Compounds, Department of Chemistry, Federal University of São Carlos, São Carlos, Brazil
| | - Alzir Azevedo Batista
- Laboratory of Structure and Reactivity of Inorganic Compounds, Department of Chemistry, Federal University of São Carlos, São Carlos, Brazil
| | - Antônio Gilberto Ferreira
- Laboratory of Nuclear Magnetic Resonance, Department of Chemistry, Federal University of São Carlos, São Carlos, Brazil
| | - Tiago Venâncio
- Laboratory of Nuclear Magnetic Resonance, Department of Chemistry, Federal University of São Carlos, São Carlos, Brazil
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15
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Rakesh KP, Darshini N, Manukumar HM, Vivek HK, Eissa MYH, Prasanna DS, Mallesha N. Xanthone Conjugated Amino Acids as Potential Anticancer and DNA Binding Agents: Molecular Docking, Cytotoxicity and SAR Studies. Anticancer Agents Med Chem 2019; 18:2169-2177. [PMID: 30179146 DOI: 10.2174/1871520618666180903105256] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 08/28/2018] [Accepted: 08/29/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Amino acids conjugated with heterocyclic molecules are well known for their effective bioactive properties. In search of effective anticancer agents, a series of xanthone linked amino acids 2-23 were synthesized and tested for in vitro anticancer activity. METHODS In vitro anticancer activity of the synthesized xanthone linked amino acids 2-23 are tested against three different cancer cell lines MCF-7, MDA-MB-435 and A549 by MTT assay and validated by DNA binding and molecular docking approaches. Doxorubicin and ethidium bromide used as standard and positive control respectively. RESULTS Compounds 7, 8 and 9 exhibited potent anticancer activity against tested cancer cell lines and DNA binding study using methyl green. In the molecular docking study, binding interactions of the most active compounds 7, 8 and 9 were confirmed to molecular surface of DNA. CONCLUSION Structure-Activity Relationship (SAR) showed that the aromatic and hydrophobic amino acids (phenylalanine, tyrosine, and tryptophan) favoured the DNA binding studies and anticancer activity whereas, aliphatic amino acids showed least anticancer activity.
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Affiliation(s)
- Kadallipura P Rakesh
- Department of Pharmaceutical Engineering, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 205 Luoshi Road, Wuhan, 430070, China.,SRI RAM CHEM, R & D Centre, Plot No. 31, JCK Industrial Park, Belagola Industrial Area, Mysore 570016, Karnataka, India
| | - Nanjudappa Darshini
- SRI RAM CHEM, R & D Centre, Plot No. 31, JCK Industrial Park, Belagola Industrial Area, Mysore 570016, Karnataka, India
| | | | - Hamse K Vivek
- Analytical Research and Development, Syngene International Ltd, Biocon Park, Bommasandra Industrial Estate, Bangaluru-560099, Karnataka, India
| | - Mohammed Y H Eissa
- Department of Biochemistry, Faculty of Applied Science College, University of Hajjah, Hajjah, Yemen
| | - Doddakunche S Prasanna
- Department of Nanotechnology, Visvesvaraya Technological University, Bengaluru Region, Muddenahalli, Chikkaballapur - 562 101, India
| | - Ningegowda Mallesha
- Department of Pharmaceutical Engineering, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 205 Luoshi Road, Wuhan, 430070, China
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16
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Mota É, Sousa F, Queiroz JA, Cruz C. Quantitative analysis of the interaction between l-methionine derivative and oligonucleotides. J Biochem 2014; 157:261-70. [PMID: 25425656 DOI: 10.1093/jb/mvu073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This study explores the use of l-methionine derivative as a potential affinity ligand for nucleic acids purification. The l-methionine derivative is synthesized by activation of the carboxylic acid group with 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide/N-hydroxysuccinimide follow by immobilization on amine sensor surface, previously activated and treated with ethylenediamine. Their affinity towards oligonucleotides has been determined by surface plasmon resonance biosensor. The highest affinity is found for cytosine and thymine, followed by adenine, whereas the lowest affinity is found for guanine. For hetero-oligonucleotides the affinity order is CCCTTT > CCCAAA ≈ AAATTT > GGGTTT, showing that nucleotides with cytosine have the highest affinity, and the presence of guanine reduces the affinity, corroborating with the results obtained with homo-oligonucleotides.
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Affiliation(s)
- Élia Mota
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - Fani Sousa
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - João A Queiroz
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - Carla Cruz
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
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Shi N, Ugaz VM. An entropic force microscope enables nano-scale conformational probing of biomolecules. Small 2014; 10:2553-2557. [PMID: 24648409 DOI: 10.1002/smll.201303046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 01/21/2014] [Indexed: 06/03/2023]
Affiliation(s)
- Nan Shi
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, 3122 TAMU, College Station, Texas, 77843, USA
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18
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Medina JR, Blackledge CW, Heerding DA, Campobasso N, Ward P, Briand J, Wright L, Axten JM. Aminoindazole PDK1 Inhibitors: A Case Study in Fragment-Based Drug Discovery. ACS Med Chem Lett 2010; 1:439-42. [PMID: 24900229 DOI: 10.1021/ml100136n] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Accepted: 07/12/2010] [Indexed: 11/29/2022] Open
Abstract
Fragment screening of phosphoinositide-dependent kinase-1 (PDK1) in a biochemical kinase assay afforded hits that were characterized and prioritized based on ligand efficiency and binding interactions with PDK1 as determined by NMR. Subsequent crystallography and follow-up screening led to the discovery of aminoindazole 19, a potent leadlike PDK1 inhibitor with high ligand efficiency. Well-defined structure-activity relationships and protein crystallography provide a basis for further elaboration and optimization of 19 as a PDK1 inhibitor.
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Affiliation(s)
- Jesús R. Medina
- Oncology Research, Signal Transduction DPU Medicinal Chemistry
| | | | | | - Nino Campobasso
- Molecular Discovery Research, Computational and Structural Chemistry
| | - Paris Ward
- Molecular Discovery Research, Computational and Structural Chemistry
| | | | - Lois Wright
- Molecular Discovery Research, Screening and Compound Profiling, GlaxoSmithKline, Research Triangle Park, North Carolina 27709
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