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Chauhan C, Singh P, Muthu SA, Parvez S, Selvapandiyan A, Ahmad B. Plumbagin accelerates serum albumin's amyloid aggregation kinetics and generates fibril polymorphism by inducing non-native β-sheet structures. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:141028. [PMID: 38849109 DOI: 10.1016/j.bbapap.2024.141028] [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: 03/08/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024]
Abstract
The ligand-induced conformational switch of proteins has great significance in understanding the biophysics and biochemistry of their self-assembly. In this work, we have investigated the ability of plumbagin (PL), a hydroxynaphthoquinone compound found in the root of the medicinal plant Plumbago zeylanica, to modulate aggregation precursor state, aggregation kinetics and generate distinct fibril of human serum albumin (HSA). PL was found to moderately bind (binding constant Ka ∼ 10-4 M-1)) to domain-II of HSA in the stoichiometric ratio of 1:1. We found that PL-HSA complex aggregation was accelerated as compared to that of HSA aggregation and it may be through an independent pathway. We also detected that fibril produced in the presence of PL is wider in diameter, contains a higher amount of β-sheet (∼18%) and disordered (∼46%) structures, and is less stable. We concluded that the acceleration of aggregation reaction and generation of fibril polymorphism was mainly because of the higher extent of unfolding and high content of non-native β-sheet structure in the aggregation precursor state of PL-HSA complex. This study offers opportunities to explore the ability of ligand binding to modulate aggregation reactions and generate polymorphic protein fibrils.
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Affiliation(s)
- Chanchal Chauhan
- Department of Medical Elementology and Toxicology, Jamia Hamdard, New Delhi 110062, India; Department of Molecular Medicine, Jamia Hamdard, New Delhi 10062, India
| | - Poonam Singh
- UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Vidyanagari Campus, Mumbai 400098, India
| | - Shivani A Muthu
- Department of Medical Elementology and Toxicology, Jamia Hamdard, New Delhi 110062, India; Department of Molecular Medicine, Jamia Hamdard, New Delhi 10062, India
| | - Suhel Parvez
- Department of Medical Elementology and Toxicology, Jamia Hamdard, New Delhi 110062, India
| | | | - Basir Ahmad
- Department of Medical Elementology and Toxicology, Jamia Hamdard, New Delhi 110062, India.
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2
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Maake R, Achilonu I. Expression, Purification and Biophysical Characterisation of Klebsiella Pneumoniae Protein Adenylyltransferase: A Systematic Integration of Empirical and Computational Modelling Approaches. Protein J 2024; 43:751-770. [PMID: 38981945 PMCID: PMC11345332 DOI: 10.1007/s10930-024-10210-3] [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] [Accepted: 05/25/2024] [Indexed: 07/11/2024]
Abstract
Infections that are acquired due to a prolonged hospital stay and manifest 2 days following the admission of a patient to a health-care institution can be classified as hospital-acquired infections. Klebsiella pneumoniae (K. pneumoniae) has become a critical pathogen, posing serious concern globally due to the rising incidences of hypervirulent and carbapenem-resistant strains. Glutaredoxin is a redox protein that protects cells from oxidative stress as it associates with glutathione to reduce mixed disulfides. Protein adenylyltransferase (PrAT) is a pseudokinase with a proposed mechanism of transferring an AMP group from ATP to glutaredoxin. Inducing oxidative stress to the bacterium by inhibiting the activity of PrAT is a promising approach to combating its contribution to hospital-acquired infections. Thus, this study aims to overexpress, purify, and analyse the effects of ATP and Mg2+ binding to Klebsiella pneumoniae PrAT (KpPrAT). The pET expression system and nickel affinity chromatography were effective in expressing and purifying KpPrAT. Far-UV CD spectroscopy demonstrates that the protein is predominantly α-helical, even in the presence of Mg2+. Extrinsic fluorescence spectroscopy with ANS indicates the presence of a hydrophobic pocket in the presence of ATP and Mg2+, while mant-ATP studies allude to the potential nucleotide binding ability of KpPrAT. The presence of Mg2+ increases the thermostability of the protein. Isothermal titration calorimetry provides insight into the binding affinity and thermodynamic parameters associated with the binding of ATP to KpPrAT, with or without Mg2+. Conclusively, the presence of Mg2+ induces a conformation in KpPrAT that favours nucleotide binding.
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Affiliation(s)
- Reabetswe Maake
- Protein Structure‑Function and Research Unit, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Braamfontein, Johannesburg, 2050, South Africa
| | - Ikechukwu Achilonu
- Protein Structure‑Function and Research Unit, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Braamfontein, Johannesburg, 2050, South Africa.
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3
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A H Kaeswurm J, Claasen B, S Mayer P, Buchweitz M. Multianalytical Approach to Understand Polyphenol-Mal d 1 Interactions to Predict Their Impact on the Allergenic Potential of Apples. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:16191-16203. [PMID: 38990326 PMCID: PMC11273618 DOI: 10.1021/acs.jafc.4c01555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/12/2024]
Abstract
Interactions between phenolic compounds and the allergen Mal d 1 are discussed to be the reason for better tolerance of apple cultivars, which are rich in polyphenols. Because Mal d 1 is susceptible to proteolytic digestion and allergenic symptoms are usually restricted to the mouth and throat area, the release of native Mal d 1 during the oral phase is of particular interest. Therefore, we studied the release of Mal d 1 under different in vitro oral digestion conditions and revealed that only 6-15% of the total Mal d 1 present in apples is released. To investigate proposed polyphenol-Mal d 1 interactions, various analytical methods, e.g., isothermal titration calorimetry, 1H-15N-HSQC NMR, and untargeted mass spectrometry, were applied. For monomeric polyphenols, only limited noncovalent interactions were observed, whereas oligomeric polyphenols and browning products caused aggregation. While covalent modifications were not detectable in apple samples, a Michael addition of epicatechin at cysteine 107 in r-Mal d 1.01 was observed.
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Affiliation(s)
- Julia. A H Kaeswurm
- Department
of Chemistry, University Hamburg, Institute
of Food Chemistry, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
- Department
of Food Chemistry, University Stuttgart,
Institute of Biochemistry and Technical Biochemistry, Allmandring 5b, 70569 Stuttgart, Germany
| | - Birgit Claasen
- University
Stuttgart, Institute of Organic Chemistry, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Pia. S Mayer
- Department
of Food Chemistry, University Stuttgart,
Institute of Biochemistry and Technical Biochemistry, Allmandring 5b, 70569 Stuttgart, Germany
| | - Maria Buchweitz
- Department
of Chemistry, University Hamburg, Institute
of Food Chemistry, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
- Department
of Food Chemistry, University Stuttgart,
Institute of Biochemistry and Technical Biochemistry, Allmandring 5b, 70569 Stuttgart, Germany
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4
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Zhao X, Yang C, Liu W, Lu K, Yin H. Inhibition of insulin fibrillation by carboxyphenylboronic acid-modified chitosan oligosaccharide based on electrostatic interactions and hydrophobic interactions. Biophys Chem 2024; 310:107236. [PMID: 38615538 DOI: 10.1016/j.bpc.2024.107236] [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: 02/04/2024] [Revised: 03/25/2024] [Accepted: 04/06/2024] [Indexed: 04/16/2024]
Abstract
A novel inhibitor, carboxyphenylboronic acid-modified chitosan oligosaccharide (COS-CPBA), was developed by coupling carboxyphenylboronic acid (CPBA) with chitosan oligosaccharide (COS) to inhibit insulin fibrillation. Extensive biophysical assays indicated that COS-CPBA could decelerate insulin aggregation, hinder the conformational transition from α-helix to β-sheet structure, change the morphology of insulin aggregates and alter fibrillation pathway. A mechanism for the inhibition of insulin fibrillation by COS-CPBA was proposed. It considers that insulin molecules bind to COS-CPBA via hydrophobic interactions, while the positively charged groups in COS-CPBA exert electrostatic repulsion on the bound insulin molecules. These two opposite forces cause the insulin molecules to display extended conformations and hinder the conformational transition of insulin from α-helix to β-sheet structure necessary for fibrillation, thus decelerating aggregation and altering the fibrillation pathway of insulin. The studies provide novel ideas for the development of more effective inhibitors of amyloid fibrillation.
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Affiliation(s)
- Xiangyuan Zhao
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300401, China
| | - Chunyan Yang
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300401, China; National-Local Joint Engineering Laboratory for Energy Conservation in Chemical Process Integration and Resources Utilization, Hebei University of Technology, Tianjin 300401, China.
| | - Wei Liu
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300401, China; Tianjin Key Laboratory of Chemical Process Safety, Hebei University of Technology, Tianjin 300401, China
| | - Ke Lu
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300401, China
| | - Hao Yin
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300401, China
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5
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Pratiwi NKC, Tayara H, Chong KT. An Ensemble Classifiers for Improved Prediction of Native-Non-Native Protein-Protein Interaction. Int J Mol Sci 2024; 25:5957. [PMID: 38892144 PMCID: PMC11172808 DOI: 10.3390/ijms25115957] [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: 04/22/2024] [Revised: 05/27/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
In this study, we present an innovative approach to improve the prediction of protein-protein interactions (PPIs) through the utilization of an ensemble classifier, specifically focusing on distinguishing between native and non-native interactions. Leveraging the strengths of various base models, including random forest, gradient boosting, extreme gradient boosting, and light gradient boosting, our ensemble classifier integrates these diverse predictions using a logistic regression meta-classifier. Our model was evaluated using a comprehensive dataset generated from molecular dynamics simulations. While the gains in AUC and other metrics might seem modest, they contribute to a model that is more robust, consistent, and adaptable. To assess the effectiveness of various approaches, we compared the performance of logistic regression to four baseline models. Our results indicate that logistic regression consistently underperforms across all evaluated metrics. This suggests that it may not be well-suited to capture the complex relationships within this dataset. Tree-based models, on the other hand, appear to be more effective for problems involving molecular dynamics simulations. Extreme gradient boosting (XGBoost) and light gradient boosting (LightGBM) are optimized for performance and speed, handling datasets effectively and incorporating regularizations to avoid over-fitting. Our findings indicate that the ensemble method enhances the predictive capability of PPIs, offering a promising tool for computational biology and drug discovery by accurately identifying potential interaction sites and facilitating the understanding of complex protein functions within biological systems.
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Affiliation(s)
- Nor Kumalasari Caecar Pratiwi
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, Republic of Korea;
- Department of Electrical Engineering, Telkom University, Bandung 40257, West Java, Indonesia
| | - Hilal Tayara
- School of International Engineering and Science, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Kil To Chong
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, Republic of Korea;
- Advances Electronics and Information Research Centre, Jeonbuk National University, Jeonju 54896, Republic of Korea
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6
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Güleç Ö, Türkeş C, Arslan M, Demir Y, Dincer B, Ece A, İrfan Küfrevioğlu Ö, Beydemir Ş. Novel spiroindoline derivatives targeting aldose reductase against diabetic complications: Bioactivity, cytotoxicity, and molecular modeling studies. Bioorg Chem 2024; 145:107221. [PMID: 38387398 DOI: 10.1016/j.bioorg.2024.107221] [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: 10/30/2023] [Revised: 02/01/2024] [Accepted: 02/16/2024] [Indexed: 02/24/2024]
Abstract
Despite significant developments in therapeutic strategies, Diabetes Mellitus remains an increasing concern, leading to various complications, e.g., cataracts, neuropathy, retinopathy, nephropathy, and several cardiovascular diseases. The polyol pathway, which involves Aldose reductase (AR) as a critical enzyme, has been focused on by many researchers as a target for intervention. On the other hand, spiroindoline-based compounds possess remarkable biological properties. This guided us to synthesize novel spiroindoline oxadiazolyl-based acetate derivatives and investigate their biological activities. The synthesized molecules' structures were confirmed herein, using IR, NMR (1H and 13C), and Mass spectroscopy. All compounds were potent inhibitors with KI constants spanning from 0.186 ± 0.020 μM to 0.662 ± 0.042 μM versus AR and appeared as better inhibitors than the clinically used drug, Epalrestat (EPR, KI: 0.841 ± 0.051 μM). Besides its remarkable inhibitory profile compared to EPR, compound 6k (KI: 0.186 ± 0.020 μM) was also determined to have an unusual pharmacokinetic profile. The results showed that 6k had less cytotoxic effect on normal mouse fibroblast (L929) cells (IC50 of 569.58 ± 0.80 μM) and reduced the viability of human breast adenocarcinoma (MCF-7) cells (IC50 of 110.87 ± 0.42 μM) more than the reference drug Doxorubicin (IC50s of 98.26 ± 0.45 μM and 158.49 ± 2.73 μM, respectively), thus exhibiting more potent anticancer activity. Moreover, molecular dynamic simulations for 200 ns were conducted to predict the docked complex's stability and reveal significant amino acid residues that 6k interacts with throughout the simulation.
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Affiliation(s)
- Özcan Güleç
- Department of Chemistry, Faculty of Arts and Sciences, Sakarya University, 54187 Sakarya, Turkey
| | - Cüneyt Türkeş
- Department of Biochemistry, Faculty of Pharmacy, Erzincan Binali Yıldırım University, 24002 Erzincan, Turkey.
| | - Mustafa Arslan
- Department of Chemistry, Faculty of Arts and Sciences, Sakarya University, 54187 Sakarya, Turkey.
| | - Yeliz Demir
- Department of Pharmacy Services, Nihat Delibalta Göle Vocational High School, Ardahan University, 75700 Ardahan, Turkey
| | - Busra Dincer
- Department of Pharmacology, Faculty of Pharmacy, Ondokuz Mayıs University, 55020 Samsun, Turkey
| | - Abdulilah Ece
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Biruni University, 34010 İstanbul, Turkey
| | | | - Şükrü Beydemir
- Department of Biochemistry, Faculty of Pharmacy, Anadolu University, 26470 Eskişehir, Turkey; Bilecik Şeyh Edebali University, 11230 Bilecik, Turkey
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7
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Onisuru O, Achilonu I. Describing the ligandin properties of Plasmodium falciparum and vivax glutathione transferase towards bromosulfophthalein from empirical and computational modelling viewpoints. J Biomol Struct Dyn 2024:1-16. [PMID: 38506165 DOI: 10.1080/07391102.2024.2329291] [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: 12/14/2023] [Accepted: 03/06/2024] [Indexed: 03/21/2024]
Abstract
Research has spotlighted glutathione transferase (GST) as a promising target for antimalarial drug development due to its pivotal role in cellular processes, including metabolizing toxins and managing oxidative stress. This interest arises from GST's potential to combat multidrug resistance in existing antimalarial drugs. Plasmodium falciparum GST (PfGST) and Plasmodium vivax GST (PvGST) are key targets; inhibiting them not only disrupt detoxification but also reduce their antioxidant capacity, a critical feature for potent antimalarials. Bromosulfophthalein (BSP), a clinical liver function dye, emerged as a potent cytosolic GST inhibitor. This study explored BSP's inhibitory properties on PfGST and PvGST, showcasing its binding capabilities through empirical and computational analyses. The study revealed BSP's ability to significantly inhibit GST activity, altering the proteins' structures and stability. Specifically, BSP binding induced spectral changes and impacted the proteins' thermal stability, reducing their melting temperatures. Computational simulations highlighted BSP's strong binding to PfGST and PvGST at their dimer interface, stabilized by various interactions, including hydrogen bonds and van der Waals forces. Notably, BSP's binding altered the proteins' compactness and conformational dynamics, suggesting a potential non-competitive, allosteric inhibition mechanism. This study provided novel insights into BSP's candidacy as an antimalarial drug by targeting PfGST and PvGST. Its ability to disrupt crucial functions of these enzymes' positions BSP as a promising candidate for further drug development in combating malariaCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Olalekan Onisuru
- Protein Structure-Function and Research Unit, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Braamfontein, Johannesburg, South Africa
| | - Ikechukwu Achilonu
- Protein Structure-Function and Research Unit, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Braamfontein, Johannesburg, South Africa
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8
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Lu X, Shi X, Fan J, Li M, Zhang Y, Lu S, Xu G, Chen Z. Mechanistic Elucidation of Activation/Deactivation Signal Transduction within Neurotensin Receptor 1 Triggered by 'Driver Chemical Groups' of Modulators: A Comparative Molecular Dynamics Simulation. Pharmaceutics 2023; 15:2000. [PMID: 37514186 PMCID: PMC10385606 DOI: 10.3390/pharmaceutics15072000] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/16/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Small-molecule modulators of neurotensin receptor 1 (NTSR1), a class A G-protein-coupled receptor (GPCR), has emerged as promising therapeutic agent for psychiatric disorders and cancer. Interestingly, a chemical group substitution in NTSR1 modulators can launch different types of downstream regulation, highlighting the significance of deciphering the internal fine-tuning mechanism. Here, we conducted a synergistic application of a Gaussian accelerated molecular dynamics simulation, a conventional molecular dynamics simulation, and Markov state models (MSM) to investigate the underlying mechanism of 'driver chemical groups' of modulators triggering inverse signaling. The results indicated that the flexibility of the leucine moiety in NTSR1 agonists contributes to the inward displacement of TM7 through a loosely coupled allosteric pathway, while the rigidity of the adamantane moiety in NTSR1 antagonists leads to unfavorable downward transduction of agonistic signaling. Furthermore, we found that R3226.54, Y3196.51, F3537.42, R1483.32, S3567.45, and S3577.46 may play a key role in inducing the activation of NTSR1. Together, our findings not only highlight the ingenious signal transduction within class A GPCRs but also lay a foundation for the development of targeted drugs harboring different regulatory functions of NTSR1.
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Affiliation(s)
- Xun Lu
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xinchao Shi
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jigang Fan
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Mingyu Li
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yuxiang Zhang
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Shaoyong Lu
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Guanghuan Xu
- Department of VIP Clinic, Changhai Hospital, Affiliated to Navy Medical University, Shanghai 200433, China
| | - Ziqiang Chen
- Department of Orthopedics, Changhai Hospital, Affiliated to Naval Medical University, Shanghai 200433, China
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9
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Monti A, Vitagliano L, Caporale A, Ruvo M, Doti N. Targeting Protein-Protein Interfaces with Peptides: The Contribution of Chemical Combinatorial Peptide Library Approaches. Int J Mol Sci 2023; 24:ijms24097842. [PMID: 37175549 PMCID: PMC10178479 DOI: 10.3390/ijms24097842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/22/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023] Open
Abstract
Protein-protein interfaces play fundamental roles in the molecular mechanisms underlying pathophysiological pathways and are important targets for the design of compounds of therapeutic interest. However, the identification of binding sites on protein surfaces and the development of modulators of protein-protein interactions still represent a major challenge due to their highly dynamic and extensive interfacial areas. Over the years, multiple strategies including structural, computational, and combinatorial approaches have been developed to characterize PPI and to date, several successful examples of small molecules, antibodies, peptides, and aptamers able to modulate these interfaces have been determined. Notably, peptides are a particularly useful tool for inhibiting PPIs due to their exquisite potency, specificity, and selectivity. Here, after an overview of PPIs and of the commonly used approaches to identify and characterize them, we describe and evaluate the impact of chemical peptide libraries in medicinal chemistry with a special focus on the results achieved through recent applications of this methodology. Finally, we also discuss the role that this methodology can have in the framework of the opportunities, and challenges that the application of new predictive approaches based on artificial intelligence is generating in structural biology.
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Affiliation(s)
- Alessandra Monti
- Institute of Biostructures and Bioimaging (IBB), National Research Council (CNR), 80131 Napoli, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging (IBB), National Research Council (CNR), 80131 Napoli, Italy
| | - Andrea Caporale
- Institute of Crystallography (IC), National Research Council (CNR), Strada Statale 14 km 163.5, Basovizza, 34149 Triese, Italy
| | - Menotti Ruvo
- Institute of Biostructures and Bioimaging (IBB), National Research Council (CNR), 80131 Napoli, Italy
| | - Nunzianna Doti
- Institute of Biostructures and Bioimaging (IBB), National Research Council (CNR), 80131 Napoli, Italy
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10
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Decoding the Conformational Selective Mechanism of FGFR Isoforms: A Comparative Molecular Dynamics Simulation. Molecules 2023; 28:molecules28062709. [PMID: 36985681 PMCID: PMC10052029 DOI: 10.3390/molecules28062709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/09/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023] Open
Abstract
Fibroblast growth factor receptors (FGFRs) play critical roles in the regulation of cell growth, differentiation, and proliferation. Specifically, FGFR2 gene amplification has been implicated in gastric and breast cancer. Pan-FGFR inhibitors often cause large toxic side effects, and the highly conserved ATP-binding pocket in the FGFR1/2/3 isoforms poses an immense challenge in designing selective FGFR2 inhibitors. Recently, an indazole-based inhibitor has been discovered that can selectively target FGFR2. However, the detailed mechanism involved in selective inhibition remains to be clarified. To this end, we performed extensive molecular dynamics simulations of the apo and inhibitor-bound systems along with multiple analyses, including Markov state models, principal component analysis, a cross-correlation matrix, binding free energy calculation, and community network analysis. Our results indicated that inhibitor binding induced the phosphate-binding loop (P-loop) of FGFR2 to switch from the open to the closed conformation. This effect enhanced extensive hydrophobic FGFR2-inhibitor contacts, contributing to inhibitor selectivity. Moreover, the key conformational intermediate states, dynamics, and driving forces of this transformation were uncovered. Overall, these findings not only provided a structural basis for understanding the closed P-loop conformation for therapeutic potential but also shed light on the design of selective inhibitors for treating specific types of cancer.
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11
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Solid state synthesis of bispyridyl-ferrocene conjugates with unusual site selective 1,4-Michael addition, as potential inhibitor and electrochemical probe for fibrillation in amyloidogenic protein. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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El Azab EF, Saleh AM, Yousif SO, Mazhari BBZ, Abu Alrub H, Elfaki EM, Hamza A, Abdulmalek S. New insights into geraniol's antihemolytic, anti-inflammatory, antioxidant, and anticoagulant potentials using a combined biological and in silico screening strategy. Inflammopharmacology 2022; 30:1811-1833. [PMID: 35932440 DOI: 10.1007/s10787-022-01039-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 07/15/2022] [Indexed: 11/05/2022]
Abstract
The study aims to assess the antihemolytic and antioxidant activities of geraniol versus 2, 2'-azobis, 2-amidinopropane dihydro-chloride- (AAPH-) induced oxidative damage and hemolysis to erythrocytes and its anti-inflammatory potential against lipopolysaccharide- (LPS-) induced inflammation in white blood cells (WBCs) with a focus on its integrated computational strategies against different targeted receptors participating in inflammation and coagulation. The rats' erythrocyte suspension was incubated with different geraniol concentrations. Molecular docking and simulation were used to explore the possible interaction patterns of geraniol against the potential targeted proteins for therapeutic screening. The results displayed that geraniol had a prolonged noteworthy effect on activated partial thromboplastin time and thromboplastin time. Geraniol displayed strong antioxidant effects via reduced malondialdehyde (MDA) formation and increased GSH level and SOD activity. We observed dose-dependent prevention of K+ ion leakage along with a remarkable decline of hemolysis in erythrocytes pretreated with geraniol. Geraniol 100 µg/mL and diclofenac 100 µM were nontoxic to WBCs. Geraniol significantly reduces the expression and release of cellular pro-inflammatory factors TNF-α, IL-1β, IL-8, and nitric oxide, accompanied by a significant upregulation of gene expression of anti-inflammatory cytokine IL-10 in LPS-induced WBCs compared to nontreated cells. It demonstrates a much stronger inhibition potential than diclofenac in terms of inflammation inhibition. When comparing molecular docking and simulation data, current work showed that geraniol has a good affinity toward apoptosis signal-regulating kinase 1 (ASK1) and human P2Y12 receptors and could be developed as an antioxidant, anti-inflammatory, and anticoagulant medication in the future. Consequently, geraniol is recommended to have a defensive influence against oxidative stress, and hemolysis also could be developed as a promising anti-inflammatory, antioxidant, and anticoagulant medication.
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Affiliation(s)
- Eman Fawzy El Azab
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences at Al-Qurayyat, Jouf University, Al-Qurayyat, 77454, Saudi Arabia. .,Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, 21511, Egypt.
| | - Abdulrahman M Saleh
- Pharmaceutical Medicinal Chemistry and Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, 11884, Egypt
| | - Sara Osman Yousif
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences at Al-Qurayyat, Jouf University, Al-Qurayyat, 77454, Saudi Arabia.,Department of Clinical Chemistry, Faculty of Medical Laboratory Sciences, Sudan University of Science and Technology, Khartoum, Sudan
| | - Bi Bi Zainab Mazhari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences at Al-Qurayyat, Jouf University, Al-Qurayyat, 77454, Saudi Arabia
| | - Heba Abu Alrub
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences at Al-Qurayyat, Jouf University, Al-Qurayyat, 77454, Saudi Arabia
| | - Elyasa Mustafa Elfaki
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences at Al-Qurayyat, Jouf University, Al-Qurayyat, 77454, Saudi Arabia
| | - Alneil Hamza
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences at Al-Qurayyat, Jouf University, Al-Qurayyat, 77454, Saudi Arabia
| | - Shaymaa Abdulmalek
- Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, 21511, Egypt
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Muneeswaran G, Lee JY. Histidine tautomerism dependent conformational transitions driven aggregation of profilin-1: Implications in amyotrophic lateral sclerosis. Int J Biol Macromol 2022; 214:241-251. [PMID: 35688275 DOI: 10.1016/j.ijbiomac.2022.06.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/17/2022] [Accepted: 06/01/2022] [Indexed: 11/26/2022]
Abstract
Aggregation of profilin-1 (PFN1) causes a fatal neurodegenerative disease, familial amyotrophic lateral sclerosis (fALS). Histidine (His) tautomerism has been linked to the formation of fibril aggregation causing neurodegenerative disease. Characterization of intermediate species that form during aggregation is crucial, however, this has proven very challenging for experimentalists due to their transient nature. Hence, molecular dynamics (MD) simulations have been performed on the His tautomeric isomers εε, εδ, δε, and δδ of PFN1 to explain the structural changes and to correlate them with its aggregation propensity. MD simulations show that His133 presumably plays a major role in the aggregation of PFN1 upon His tautomerism compared to His119. Further, the formation of a new 310-helix is observed in εε and δε but 310-helix is not observed in δδ and εδ isomers. In addition, our findings unveil that β-sheet dominating conformations are observed in His119(δ)-His133(δ) δδ isomer of PFN1 with significant antiparallel β-sheets between residues T15-G23, S29-A33, L63-L65, Q68-S76, F83-T89, T97-T105, and K107-K115, suggesting a novel aggregation mechanism possibly occur for the formation of PFN1 aggregates. Overall, these results propose that MD simulations of PFN1 His tautomers can provide a detailed microscopic understanding of the aggregation mechanisms which are hard to probe through experiments.
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Affiliation(s)
- Gurusamy Muneeswaran
- Department of Chemistry, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jin Yong Lee
- Department of Chemistry, Sungkyunkwan University, Suwon 16419, Republic of Korea.
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14
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Liu Y, Zhu J, Yu J, Chen X, Zhang S, Cai Y, Li L. Curcumin as a mild natural α‐glucosidase inhibitor: a study on its mechanism
in vitro. Int J Food Sci Technol 2022. [DOI: 10.1111/ijfs.15433] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Yujia Liu
- Key Laboratory of Healthy Food Development and Nutrition Regulation of China National Light Industry School of Chemical Engineering and Energy Technology Dongguan University of Technology Dongguan 523808 China
| | - Jie Zhu
- Key Laboratory of Healthy Food Development and Nutrition Regulation of China National Light Industry School of Chemical Engineering and Energy Technology Dongguan University of Technology Dongguan 523808 China
| | - Jiamei Yu
- Key Laboratory of Healthy Food Development and Nutrition Regulation of China National Light Industry School of Chemical Engineering and Energy Technology Dongguan University of Technology Dongguan 523808 China
| | - Xu Chen
- Key Laboratory of Healthy Food Development and Nutrition Regulation of China National Light Industry School of Chemical Engineering and Energy Technology Dongguan University of Technology Dongguan 523808 China
| | - Shuyan Zhang
- Key Laboratory of Healthy Food Development and Nutrition Regulation of China National Light Industry School of Chemical Engineering and Energy Technology Dongguan University of Technology Dongguan 523808 China
| | - Yanxue Cai
- Key Laboratory of Healthy Food Development and Nutrition Regulation of China National Light Industry School of Chemical Engineering and Energy Technology Dongguan University of Technology Dongguan 523808 China
| | - Lin Li
- Key Laboratory of Healthy Food Development and Nutrition Regulation of China National Light Industry School of Chemical Engineering and Energy Technology Dongguan University of Technology Dongguan 523808 China
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15
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Study on the characterization of polysaccharide from Tuber sinense and its desensitization effect to β-lactoglobulin in vivo. J Funct Foods 2022. [DOI: 10.1016/j.jff.2022.105028] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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16
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Han Q, Brown SJ, Drummond CJ, Greaves TL. Protein aggregation and crystallization with ionic liquids: Insights into the influence of solvent properties. J Colloid Interface Sci 2022; 608:1173-1190. [PMID: 34735853 DOI: 10.1016/j.jcis.2021.10.087] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/13/2021] [Accepted: 10/15/2021] [Indexed: 12/13/2022]
Abstract
Ionic liquids (ILs) have been used in solvents for proteins in many applications, including biotechnology, pharmaceutics, and medicine due to their tunable physicochemical and biological properties. Protein aggregation is often undesirable, and predominantly occurs during bioprocesses, while the aggregation process can be reversible or irreversible and the aggregates formed can be native/non-native and soluble/insoluble. Recent studies have clearly identified key properties of ILs and IL-water mixtures related to protein performance, suggesting the use of the tailorable properties of ILs to inhibit protein aggregation, to promote protein crystallization, and to control protein aggregation pathways. This review discusses the critical properties of IL and IL-water mixtures and presents the latest understanding of the protein aggregation pathways and the development of IL systems that affect or control the protein aggregation process. Through this feature article, we hope to inspire further advances in understanding and new approaches to controlling protein behavior to optimize bioprocesses.
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Affiliation(s)
- Qi Han
- School of Science, STEM College, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia
| | - Stuart J Brown
- School of Science, STEM College, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia
| | - Calum J Drummond
- School of Science, STEM College, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia
| | - Tamar L Greaves
- School of Science, STEM College, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia.
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17
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Shaikh SAM, Gawali SL, Jain VK, Priyadarsini KI. Unravelling the molecular interaction of diselenodipropionic acid (DSePA) with human serum albumin (HSA). NEW J CHEM 2022. [DOI: 10.1039/d2nj01443b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
DSePA, a pharmacologically efficient selenium compound shows strong binding with extracellular carrier protein, Human Serum Albumin.
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Affiliation(s)
- Shaukat Ali M. Shaikh
- School of Chemical Sciences, UM-DAE, Centre for Excellence in Basic Sciences, Mumbai University, (Kalina Campus), Santa Cruz (East), Mumbai 400098, India
| | - S. L. Gawali
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai-400076, India
| | - V. K. Jain
- School of Chemical Sciences, UM-DAE, Centre for Excellence in Basic Sciences, Mumbai University, (Kalina Campus), Santa Cruz (East), Mumbai 400098, India
| | - K. I. Priyadarsini
- School of Chemical Sciences, UM-DAE, Centre for Excellence in Basic Sciences, Mumbai University, (Kalina Campus), Santa Cruz (East), Mumbai 400098, India
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18
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Mittal C, Kumari A, De I, Singh M, Harsolia R, Yadav JK. Heat treatment of soluble proteins isolated from human cataract lens leads to the formation of non-fibrillar amyloid-like protein aggregates. Int J Biol Macromol 2021; 188:512-522. [PMID: 34333005 DOI: 10.1016/j.ijbiomac.2021.07.158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 11/29/2022]
Abstract
The loss of crystallins solubility with aging and the formation of amyloid-like aggregates is considered the hallmark characteristic of cataract pathology. The present study was carried out to assess the effect of temperature on the soluble lens protein and the formation of protein aggregates with typical amyloid characteristics. The soluble fraction of lens proteins was subjected for heat treatment in the range of 40-60 °C, and the nature of protein aggregates was assessed by using Congo red (CR), thioflavin T (ThT), and 8-anilinonaphthalene-1-sulfonic acid (ANS) binding assays, circular dichroism (CD), Fourier-transform infrared (FT-IR) spectroscopy, and transmission electron microscopy (TEM). The heat-treated protein samples displayed a substantial bathochromic shift (≈15 nm) in the CR's absorption maximum (λmax) and increased ThT and ANS binding. The heat treatment of lens soluble proteins results in the formation of nontoxic, β-sheet rich, non-fibrillar, protein aggregates similar to the structures evident in the insoluble fraction of proteins isolated from the cataractous lens. The data obtained from the present study suggest that the exposure of soluble lens proteins to elevated temperature leads to the formation of non-fibrillar aggregates, establishing the role of amyloid in the heat-induced augmentation of cataracts pathology.
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Affiliation(s)
- Chandrika Mittal
- Department of Biotechnology, Central University of Rajasthan, NH-8 Bandersindri, Kishangarh, Ajmer 305817, Rajasthan, India
| | - Ashwani Kumari
- Department of Biotechnology, Central University of Rajasthan, NH-8 Bandersindri, Kishangarh, Ajmer 305817, Rajasthan, India
| | - Indranil De
- Institute of Nano Science and Technology, Mohali 160062, Punjab, India
| | - Manish Singh
- Institute of Nano Science and Technology, Mohali 160062, Punjab, India
| | - Ramswaroop Harsolia
- Department of Ophthalmology, Jawaharlal Nehru Medical College and Hospital, Ajmer, Rajasthan, India
| | - Jay Kant Yadav
- Department of Biotechnology, Central University of Rajasthan, NH-8 Bandersindri, Kishangarh, Ajmer 305817, Rajasthan, India.
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19
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Prospecting the therapeutic edge of a novel compound (B12) over berberine in the selective targeting of Retinoid X Receptor in colon cancer. J Mol Model 2021; 27:231. [PMID: 34312718 DOI: 10.1007/s00894-021-04848-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 07/05/2021] [Indexed: 12/24/2022]
Abstract
The Retinoid X Receptor (RXR) is an attractive target in the treatment of colon cancer. Different therapeutic binders with high potency have been used to specifically target RXR. Among these compounds is a novel analogue of berberine, B12. We provided structural and molecular insights into the therapeutic activity properties of B12 relative to its parent compound, berberine, using force field estimations and thermodynamic calculations. Upon binding of B12 to RXR, the high instability elicited by RXR was markedly reduced; similar observation was seen in the berberine-bound RXR. However, our analysis revealed that B12 could have a more stabilizing effect on RXR when compared to berberine. Interestingly, the mechanistic behaviour of B12 in the active site of RXR opposed its impact on RXR protein. This disparity could be due to the bond formation and breaking elicited between B12/berberine and the active site residues. We observed that B12 and berberine could induce a disparate conformational change in regions Gly250-Asp258 located on the His-RXRα/LBD domain. Comparatively, the high agonistic and activation potential reported for B12 compared to berberine might be due to its superior binding affinity as evidenced in the thermodynamic estimations. The total affinity for B12 (-25.76 kcal/mol) was contributed by electrostatic interactions from Glu243 and Glu239. Also, Arg371, which plays a crucial role in the activity of RXR, formed a strong hydrogen bond with B12; however, a weak interaction was elicited between Arg371 and berberine. Taken together, our study has shown the RXRα activating potential of B12, and findings from this study could provide a framework in the future design of RXRα binders specifically tailored in the selective treatment of colon cancer.
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20
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Title of the manuscript: Mechanistic insights into chalcone butein-induced inhibition of α-synuclein fibrillation: Biophysical and insilico studies. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116105] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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21
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Modulation of α-synuclein fibrillation by plant metabolites, daidzein, fisetin and scopoletin under physiological conditions. Int J Biol Macromol 2021; 182:1278-1291. [PMID: 33991558 DOI: 10.1016/j.ijbiomac.2021.05.071] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/01/2021] [Accepted: 05/10/2021] [Indexed: 12/11/2022]
Abstract
The aggregation of α-synuclein is linked to neurological disorders, and of these, Parkinson's disease (PD) is among the most widely studied. In this background, we have investigated here the effects of three α, β-unsaturated carbonyl based plant metabolites, daidzein, fisetin and scopoletin on α-Syn aggregation. The ThT and light scattering kinetics studies establish that these compounds have ability to inhibit α-Syn fibrillation to different extents; this is confirmed by TEM studies. It is pertinent to note here that daidzein and scopoletin have been predicted to be able to cross the blood brain barrier. ANS binding assays demonstrate that the compounds interfere in the hydrophobic interactions. The tyrosine quenching, molecular docking and MD simulation studies showed that the compounds bind with α-Syn and provide structural rigidity which delays onset of structural transitions, which is confirmed by CD spectroscopy. The results obtained here throw light on the mechanisms underlying inhibition of α-Syn fibrillation by these compounds. Thus, the current work has significant therapeutic implications for identifying plant based potent therapeutic molecules for PD and other synucleinopathies, an area which needs extensive exploration.
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22
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Sepahvandi A, Ghaffari M, Bahmanpour AH, Moztarzadeh F, Zarrintaj P, Uludağ H, Mozafari M. COVID-19: insights into virus-receptor interactions. MOLECULAR BIOMEDICINE 2021; 2:10. [PMID: 34766003 PMCID: PMC8035060 DOI: 10.1186/s43556-021-00033-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 03/03/2021] [Indexed: 01/03/2023] Open
Abstract
The recent outbreak of Coronavirus Disease 2019 (COVID-19) calls for rapid mobilization of scientists to probe and explore solutions to this deadly disease. A limited understanding of the high transmissibility of SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) relative to other coronavirus strains guides a deeper investigation into the virus/receptor interactions. The cutting-edge studies in thermodynamic and kinetic properties of interactions such as protein-protein interplays have been reviewed in many modeling and analysis studies. Highlighting the thermodynamic assessments of biological interactions and emphasizing the boosted transmissibility of SARS-CoV-2 despite its high similarity in structure and sequence with other coronavirus strains is an important and highly valuable investigation that can lead scientists to discover analytical and fundamental approaches in studying virus's interactions. Accordingly, we have attempted to describe the crucial factors such as conformational changes and hydrophobicity particularities that influence on thermodynamic potentials in the SARS-COV-2 S-protein adsorption process. Discussing the thermodynamic potentials and the kinetics of the SARS-CoV-2 S-protein in its interaction with the ACE2 receptors of the host cell is a fundamental approach that would be extremely valuable in designing candidate pharmaceutical agents or exploring alternative treatments.
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Affiliation(s)
- Azadeh Sepahvandi
- Department of Mechanical Engineering College of Engineering and Computing, University of South Carolina, 301 Main St, Columbia, SC 29208 USA
| | - Maryam Ghaffari
- Biomaterial Group, Faculty of Biomedical Engineering (Center of Excellence), Amirkabir University of Technology, Tehran, Iran
| | - Amir Hossein Bahmanpour
- Biomaterial Group, Faculty of Biomedical Engineering (Center of Excellence), Amirkabir University of Technology, Tehran, Iran
| | - Fathollah Moztarzadeh
- Biomaterial Group, Faculty of Biomedical Engineering (Center of Excellence), Amirkabir University of Technology, Tehran, Iran
| | - Payam Zarrintaj
- School of Chemical Engineering, Oklahoma State University, 420 Engineering North, Stillwater, OK 74078 USA
| | - Hasan Uludağ
- Department of Chemical and Material Engineering, Faculty of Engineering, University of Alberta, Edmonton, AB T6G 2V4 Canada
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2E1 Canada
- Department of Biomedical Engineering, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2R3 Canada
| | - Masoud Mozafari
- Department of Tissue Engineering & Regenerative Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran
- Currently at: Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, ON Canada
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23
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Tian Y, Bao Q, Wang N, Wan N, Lv L, Hao H, He C, Ye H. Time-Resolved Acetaldehyde-Based Accessibility Profiling Maps Ligand-Target Interactions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:519-530. [PMID: 33382614 DOI: 10.1021/jasms.0c00382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Elucidating ligand-protein interactions is important in understanding the biochemical machinery for given proteins. Previously, formaldehyde (FH)-based labeling has been employed to obtain such structural knowledge, since reactive residues that participate in ligand-target interactions display reduced accessibility to FH-labeling reagents, and thus can be identified by quantitative proteomics. Although being rapid and efficient for probing proteinaceous lysine accessibility, here, we report an acetaldehyde (AcH)-labeling approach that complements with FH for probing ligand-target interactions. AcH labeling examines lysine accessibility at a more moderate reaction speed and hence delivers a cleaner reaction when compared to that of FH. The subsequent application of AcH to label RNase A without and with ligands has assisted to assign lysines involved in ligand-RNase A binding by detecting the time-dependent changes in accessibility profiles. We further employed multiple reaction monitoring (MRM) to quantify these ligand-binding-responsive sites when a variety of potential ligands were queried. We noted that the time-resolved abundance changes of these peptides can sensitively determine the ligand-binding sites and differentiate binding affinities among these ligands, which was confirmed by native mass spectrometry (MS) and molecular docking. Lastly, we demonstrated that the binding sites can be recognized by monitoring the chemical accessibility of these responsive peptides in cell lysates. Together, we believe that the proposed combined use of AcH-based lysine accessibility profiling, native MS, and MRM screening is a powerful toolbox in characterizing ligand-target interactions, mapping topography, and interrogating affinities and holds promise for future applications in a complex cellular environment.
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Affiliation(s)
- Yang Tian
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu 210009, China
| | - Qiuyu Bao
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu 210009, China
| | - Nian Wang
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu 210009, China
| | - Ning Wan
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu 210009, China
| | - Langlang Lv
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu 210009, China
| | - Haiping Hao
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu 210009, China
| | - Chaoyong He
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu 210009, China
| | - Hui Ye
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu 210009, China
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24
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Shiraishi N, Hirano Y. Combination of Copper Ions and Nucleotide Generates Aggregates from Prion Protein Fragments in the N-Terminal Domain. Protein Pept Lett 2021; 27:782-792. [PMID: 32096738 DOI: 10.2174/0929866527666200225124829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/13/2019] [Accepted: 12/17/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND It has been previously found that PrP23-98, which contains four highly conserved octarepeats (residues 60-91) and one partial repeat (residues 92-96), polymerizes into amyloid-like and proteinase K-resistant spherical aggregates in the presence of NADPH plus copper ions. OBJECTIVE We aimed to determine the requirements for the formation of these aggregates. METHODS In this study, we performed an aggregation experiment using N-acetylated and Camidated PrP fragments of the N-terminal domain, Octa1, Octa2, Octa3, Octa4, PrP84-114, and PrP76-114, in the presence of NADPH with copper ions, and focused on the effect of the number of copper-binding sites on aggregation. RESULTS Among these PrP fragments, Octa4, containing four copper-binding sites, was particularly effective in forming aggregates. We also tested the effect of other pyridine nucleotides and adenine nucleotides on the aggregation of Octa4. ATP was equally effective, but NADH, NADP, ADP, and AMP had no effect. CONCLUSION The phosphate group on the adenine-linked ribose moiety of adenine nucleotides and pyridine nucleotides is presumed to be essential for the observed effect on aggregation. Efficient aggregation requires the presence of the four octarepeats. These insights may be helpful in the eventual development of therapeutic agents against prion-related disorders.
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Affiliation(s)
- Noriyuki Shiraishi
- Department of Nutrition, Tokai Gakuen University, 2-901 Nakahira, Nagoya 468-8514, Japan
| | - Yoshiaki Hirano
- Department of Nutrition, Tokai Gakuen University, 2-901 Nakahira, Nagoya 468-8514, Japan
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Calderón-Garcidueñas L, González-Maciel A, Reynoso-Robles R, Hammond J, Kulesza R, Lachmann I, Torres-Jardón R, Mukherjee PS, Maher BA. Quadruple abnormal protein aggregates in brainstem pathology and exogenous metal-rich magnetic nanoparticles (and engineered Ti-rich nanorods). The substantia nigrae is a very early target in young urbanites and the gastrointestinal tract a key brainstem portal. ENVIRONMENTAL RESEARCH 2020; 191:110139. [PMID: 32888951 DOI: 10.1016/j.envres.2020.110139] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/21/2020] [Accepted: 08/22/2020] [Indexed: 06/11/2023]
Abstract
Fine particulate air pollution (PM2.5) exposures are linked with Alzheimer's and Parkinson's diseases (AD,PD). AD and PD neuropathological hallmarks are documented in children and young adults exposed lifelong to Metropolitan Mexico City air pollution; together with high frontal metal concentrations (especially iron)-rich nanoparticles (NP), matching air pollution combustion- and friction-derived particles. Here, we identify aberrant hyperphosphorylated tau, ɑ synuclein and TDP-43 in the brainstem of 186 Mexico City 27.29 ± 11.8y old residents. Critically, substantia nigrae (SN) pathology seen in mitochondria, endoplasmic reticulum and neuromelanin (NM) is co-associated with the abundant presence of exogenous, Fe-, Al- and Ti-rich NPs.The SN exhibits early and progressive neurovascular unit damage and mitochondria and NM are associated with metal-rich NPs including exogenous engineered Ti-rich nanorods, also identified in neuroenteric neurons. Such reactive, cytotoxic and magnetic NPs may act as catalysts for reactive oxygen species formation, altered cell signaling, and protein misfolding, aggregation and fibril formation. Hence, pervasive, airborne and environmental, metal-rich and magnetic nanoparticles may be a common denominator for quadruple misfolded protein neurodegenerative pathologies affecting urbanites from earliest childhood. The substantia nigrae is a very early target and the gastrointestinal tract (and the neuroenteric system) key brainstem portals. The ultimate neural damage and neuropathology (Alzheimer's, Parkinson's and TDP-43 pathology included) could depend on NP characteristics and the differential access and targets achieved via their portals of entry. Thus where you live, what air pollutants you are exposed to, what you are inhaling and swallowing from the air you breathe,what you eat, how you travel, and your occupational longlife history are key. Control of NP sources becomes critical.
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Affiliation(s)
| | | | | | - Jessica Hammond
- Centre for Environmental Magnetism and Paleomagnetism, Lancaster Environment Centre, University of Lancaster, Lancaster, LA1 4YQ, UK
| | - Randy Kulesza
- Auditory Research Center, Lake Erie College of Osteopathic Medicine, Erie, PA, USA
| | | | - Ricardo Torres-Jardón
- Centro de Ciencias de la Atmósfera, Universidad Nacional Autónoma de México, UNAM, Mexico City, 04510, Mexico
| | | | - Barbara A Maher
- Centre for Environmental Magnetism and Paleomagnetism, Lancaster Environment Centre, University of Lancaster, Lancaster, LA1 4YQ, UK
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Therapeutic Path to Double Knockout: Investigating the Selective Dual-Inhibitory Mechanisms of Adenosine Receptors A1 and A2 by a Novel Methoxy-Substituted Benzofuran Derivative in the Treatment of Parkinson's Disease. Cell Biochem Biophys 2020; 79:25-36. [PMID: 33222095 DOI: 10.1007/s12013-020-00957-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2020] [Indexed: 10/22/2022]
Abstract
The dual inhibition of adenosine receptors A1 (A1 AR) and A2 (A2A AR) has been considered as an efficient strategy in the treatment of Parkinson's disease (PD). This led to the recent development of a series of methoxy-substituted benzofuran derivatives among which compound 3j exhibited dual-inhibitory potencies in the micromolar range. Therefore, in this study, we seek to resolve the mechanisms by which this novel compound elicits its selective dual targeting against A1 AR and A2A AR. Unique to the binding of 3j in both proteins, from our findings, is the ring-ring interaction elicited by A1Phe275 (→ A2Phe170) with the benzofuran ring of the compound. As observed, this π-stacking interaction contributes notably to the stability of 3j at the active sites of A1 and A2A AR. Besides, conserved active site residues in the proteins such as A1Ala170 (→ A2Ala65), A1Ile173 (→ A2Ile68), A1Val191 (→ A2Val86), A1Leu192 (→ A2Leu87), A1Ala195 (→ A2Ala90), A1Met284 (→ A2Met179), A1Tyr375 (→ A2Tyr369), A1Ile378 (→ A2Ile372), and A1His382 (→ A2His376) were commonly involved with other ring substituents which further complement the dual binding and stability of 3j. This reflects a similar interaction mechanism that involved aromatic (π) interactions. Consequentially, vdW energies contributed immensely to the dual binding of the compound, which culminated in high ΔGbinds that were homogenous in both proteins. Furthermore, 3j commonly disrupted the stable and compact conformation of A1 and A2A AR, coupled with their active sites where Cα deviations were relatively high. Ligand mobility analysis also revealed that both compounds exhibited a similar motion pattern at the active site of the proteins relative to their optimal dual binding. We believe that findings from this study with significantly aid the structure-based design of highly selective dual-inhibitors of A1 and A2A AR.
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Zakariya SM, Furkan M, Zaman M, Chandel TI, Ali SM, Uversky VN, Khan RH. An in-vitro elucidation of inhibitory potential of carminic acid: Possible therapeutic approach for neurodegenerative diseases. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112692] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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28
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Ribeiro VS, Santana CA, Fassio AV, Cerqueira FR, da Silveira CH, Romanelli JPR, Patarroyo-Vargas A, Oliveira MGA, Gonçalves-Almeida V, Izidoro SC, de Melo-Minardi RC, Silveira SDA. visGReMLIN: graph mining-based detection and visualization of conserved motifs at 3D protein-ligand interface at the atomic level. BMC Bioinformatics 2020; 21:80. [PMID: 32164574 PMCID: PMC7068867 DOI: 10.1186/s12859-020-3347-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Background Interactions between proteins and non-proteic small molecule ligands play important roles in the biological processes of living systems. Thus, the development of computational methods to support our understanding of the ligand-receptor recognition process is of fundamental importance since these methods are a major step towards ligand prediction, target identification, lead discovery, and more. This article presents visGReMLIN, a web server that couples a graph mining-based strategy to detect motifs at the protein-ligand interface with an interactive platform to visually explore and interpret these motifs in the context of protein-ligand interfaces. Results To illustrate the potential of visGReMLIN, we conducted two cases in which our strategy was compared with previous experimentally and computationally determined results. visGReMLIN allowed us to detect patterns previously documented in the literature in a totally visual manner. In addition, we found some motifs that we believe are relevant to protein-ligand interactions in the analyzed datasets. Conclusions We aimed to build a visual analytics-oriented web server to detect and visualize common motifs at the protein-ligand interface. visGReMLIN motifs can support users in gaining insights on the key atoms/residues responsible for protein-ligand interactions in a dataset of complexes.
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Affiliation(s)
- Vagner S Ribeiro
- Department of Computer Science, Universidade Federal de Viçosa, Viçosa, 36570-900, Brazil
| | - Charles A Santana
- Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Alexandre V Fassio
- Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Fabio R Cerqueira
- Department of Production Engineering, Universidade Federal Fluminense, Petrópolis, 25650-050, Brazil
| | - Carlos H da Silveira
- Department of Computer Engineering, Advanced Campus at Itabira, Universidade Federal de Itajubá, Itabira, 35903-087, Brazil
| | - João P R Romanelli
- Department of Computer Engineering, Advanced Campus at Itabira, Universidade Federal de Itajubá, Itabira, 35903-087, Brazil
| | - Adriana Patarroyo-Vargas
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, 36570-900, Brazil
| | - Maria G A Oliveira
- Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, 36570-900, Brazil.,Instituto de Biotecnologia aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, 36570-900, Brazil
| | - Valdete Gonçalves-Almeida
- Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Sandro C Izidoro
- Department of Computer Engineering, Advanced Campus at Itabira, Universidade Federal de Itajubá, Itabira, 35903-087, Brazil
| | - Raquel C de Melo-Minardi
- Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Sabrina de A Silveira
- Department of Computer Science, Universidade Federal de Viçosa, Viçosa, 36570-900, Brazil. .,European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, CB10 1SD, UK.
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Carvalho Bertozo L, Fernandes AJFC, Yoguim MI, Bolean M, Ciancaglini P, Ximenes VF. Entropy‐driven binding of octyl gallate in albumin: Failure in the application of temperature effect to distinguish dynamic and static fluorescence quenching. J Mol Recognit 2020; 33:e2840. [DOI: 10.1002/jmr.2840] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/25/2020] [Accepted: 02/10/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Luiza Carvalho Bertozo
- Department of Chemistry, Faculty of SciencesUNESP—São Paulo State University São Paulo Brazil
| | - Ana J. F. C. Fernandes
- Department of Chemistry, Faculty of SciencesUNESP—São Paulo State University São Paulo Brazil
| | - Maurício I. Yoguim
- Department of Chemistry, Faculty of SciencesUNESP—São Paulo State University São Paulo Brazil
| | - Maytê Bolean
- Department of Chemistry, Faculty of Philosophy, Sciences and Letters at Ribeirão PretoUniversity of São Paulo Ribeirão Preto SP Brazil
| | - Pietro Ciancaglini
- Department of Chemistry, Faculty of Philosophy, Sciences and Letters at Ribeirão PretoUniversity of São Paulo Ribeirão Preto SP Brazil
| | - Valdecir F. Ximenes
- Department of Chemistry, Faculty of SciencesUNESP—São Paulo State University São Paulo Brazil
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Molecular insights into the inhibitory mechanism of bi-functional bis-tryptoline triazole against β-secretase (BACE1) enzyme. Amino Acids 2019; 51:1593-1607. [PMID: 31654211 DOI: 10.1007/s00726-019-02797-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 10/04/2019] [Indexed: 02/07/2023]
Abstract
The β-site amyloid precursor protein-cleaving enzyme 1 (β-secretase, BACE1) is involved in the formation of amyloid-β (Aβ) peptide that aggregates into soluble oligomers, amyloid fibrils, and plaques responsible for the neurodegeneration in Alzheimer disease (AD). BACE1 is one of the prime therapeutic targets for the design of inhibitors against AD as BACE1 participate in the rate-limiting step in Aβ production. Jiaranaikulwanitch et al. reported bis-tryptoline triazole (BTT) compound as a potent inhibitor against BACE1, Aβ aggregation as well as possessing metal chelation and antioxidant activity. However, the molecular mechanism of BACE1 inhibition by BTT remains unclear. Thus, molecular docking and molecular dynamics (MD) simulations were performed to elucidate the inhibitory mechanism of BTT against BACE1. MD simulations highlight that BTT interact with catalytic aspartic dyad residues (Asp32 and Asp228) and active pocket residues of BACE1. The hydrogen-bond interactions, hydrophobic contacts, and π-π stacking interactions of BTT with flap residues (Val67-Asp77) of BACE1 confine the movement of the flap and help to achieve closed (non-active) conformation. The PCA analysis highlights lower conformational fluctuations for BACE1-BTT complex, which suggests enhanced conformational stability in comparison to apo-BACE1. The results of the present study provide key insights into the underlying inhibitory mechanism of BTT against BACE1 and will be helpful for the rational design of novel inhibitors with enhanced potency against BACE1.
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Calderón-Garcidueñas L, Reynoso-Robles R, González-Maciel A. Combustion and friction-derived nanoparticles and industrial-sourced nanoparticles: The culprit of Alzheimer and Parkinson's diseases. ENVIRONMENTAL RESEARCH 2019; 176:108574. [PMID: 31299618 DOI: 10.1016/j.envres.2019.108574] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/11/2019] [Accepted: 07/02/2019] [Indexed: 05/20/2023]
Abstract
Redox-active, strongly magnetic, combustion and friction-derived nanoparticles (CFDNPs) are abundant in particulate matter air pollution. Urban children and young adults with Alzheimer disease Continuum have higher numbers of brain CFDNPs versus clean air controls. CFDNPs surface charge, dynamic magnetic susceptibility, iron content and redox activity contribute to ROS generation, neurovascular unit (NVU), mitochondria, and endoplasmic reticulum (ER) damage, and are catalysts for protein misfolding, aggregation and fibrillation. CFDNPs respond to external magnetic fields and are involved in cell damage by agglomeration/clustering, magnetic rotation and/or hyperthermia. This review focus in the interaction of CFDNPs, nanomedicine and industrial NPs with biological systems and the impact of portals of entry, particle sizes, surface charge, biomolecular corona, biodistribution, mitochondrial dysfunction, cellular toxicity, anterograde and retrograde axonal transport, brain dysfunction and pathology. NPs toxicity information come from researchers synthetizing particles and improving their performance for drug delivery, drug targeting, magnetic resonance imaging and heat mediators for cancer therapy. Critical information includes how these NPs overcome all barriers, the NPs protein corona changes as they cross the NVU and the complexity of NPs interaction with soluble proteins and key organelles. Oxidative, ER and mitochondrial stress, and a faulty complex protein quality control are at the core of Alzheimer and Parkinson's diseases and NPs mechanisms of action and toxicity are strong candidates for early development and progression of both fatal diseases. Nanoparticle exposure regardless of sources carries a high risk for the developing brain homeostasis and ought to be included in the AD and PD research framework.
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Affiliation(s)
- Lilian Calderón-Garcidueñas
- The University of Montana, Missoula, MT, 59812, USA; Universidad Del Valle de México, 04850, Mexico City, Mexico.
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Energetic parameters of β-casein/quercetin activated and thermodynamically stable complex formation accessed by Surface Plasmon Resonance. Colloids Surf B Biointerfaces 2019; 181:798-805. [DOI: 10.1016/j.colsurfb.2019.06.048] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/16/2019] [Accepted: 06/20/2019] [Indexed: 12/25/2022]
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Khalilzadeh B, Rashidi M, Soleimanian A, Tajalli H, Kanberoglu GS, Baradaran B, Rashidi MR. Development of a reliable microRNA based electrochemical genosensor for monitoring of miR-146a, as key regulatory agent of neurodegenerative disease. Int J Biol Macromol 2019; 134:695-703. [DOI: 10.1016/j.ijbiomac.2019.05.061] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 10/26/2022]
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Aricov L, Angelescu DG, Băran A, Leontieş AR, Popa VT, Precupaş A, Sandu R, Stîngă G, Anghel DF. Interaction of piroxicam with bovine serum albumin investigated by spectroscopic, calorimetric and computational molecular methods. J Biomol Struct Dyn 2019; 38:2659-2671. [PMID: 31315508 DOI: 10.1080/07391102.2019.1645733] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The binding of drugs to serum proteins is governed by weak non-covalent forces. In this study, the nature and magnitude of the interactions between piroxicam (PRX) and bovine serum albumin (BSA) was assessed using spectroscopic, calorimetric and computational molecular methods. The fluorescence data revealed an atypical behavior during PRX and BSA interaction. The quenching process of tryptophan (Trp) by PRX is a dual one (approximately equal static and dynamic quenched components). The FRET results indicate that a non-radiative transfer of energy occurred. The association constant and the number of binding sites indicate moderate PRX and BSA binding. The competitive binding study indicates that PRX is bound to site I from the hydrophobic pocket of subdomain IIA of BSA. The synchronous spectra showed that the microenvironment around the BSA fluorophores and protein conformation do not change considerably. The Trp lifetimes revealed that PRX mainly quenches the fluorescence of Trp-213 situated in the hydrophobic domain. The CD and DSC investigation show that addition of PRX stabilizes the protein structure. ITC results revealed that BSA-PRX binding involves a combination of electrostatic, hydrophobic and hydrogen interactions. The analysis of the computational data is consistent with the experimental results. This thorough investigation of the PRX-BSA binding may provide support for other studies concerning moderate affinity drugs with serum protein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ludmila Aricov
- "Ilie Murgulescu" Institute of Physical Chemistry of the Romanian Academy, Bucharest, Romania
| | - Daniel George Angelescu
- "Ilie Murgulescu" Institute of Physical Chemistry of the Romanian Academy, Bucharest, Romania
| | - Adriana Băran
- "Ilie Murgulescu" Institute of Physical Chemistry of the Romanian Academy, Bucharest, Romania
| | - Anca Ruxandra Leontieş
- "Ilie Murgulescu" Institute of Physical Chemistry of the Romanian Academy, Bucharest, Romania
| | - Vlad Tudor Popa
- "Ilie Murgulescu" Institute of Physical Chemistry of the Romanian Academy, Bucharest, Romania
| | - Aurica Precupaş
- "Ilie Murgulescu" Institute of Physical Chemistry of the Romanian Academy, Bucharest, Romania
| | - Romică Sandu
- "Ilie Murgulescu" Institute of Physical Chemistry of the Romanian Academy, Bucharest, Romania
| | - Gabriela Stîngă
- "Ilie Murgulescu" Institute of Physical Chemistry of the Romanian Academy, Bucharest, Romania
| | - Dan-Florin Anghel
- "Ilie Murgulescu" Institute of Physical Chemistry of the Romanian Academy, Bucharest, Romania
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A multiparametric analysis of the synergistic impact of anti-Parkinson's drugs on the fibrillation of human serum albumin. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:275-285. [DOI: 10.1016/j.bbapap.2018.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 09/25/2018] [Accepted: 10/08/2018] [Indexed: 01/26/2023]
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Insights into the Molecular Mechanisms of Protein-Ligand Interactions by Molecular Docking and Molecular Dynamics Simulation: A Case of Oligopeptide Binding Protein. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2018; 2018:3502514. [PMID: 30627209 PMCID: PMC6305025 DOI: 10.1155/2018/3502514] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 10/16/2018] [Indexed: 01/14/2023]
Abstract
Protein-ligand interactions are a necessary prerequisite for signal transduction, immunoreaction, and gene regulation. Protein-ligand interaction studies are important for understanding the mechanisms of biological regulation, and they provide a theoretical basis for the design and discovery of new drug targets. In this study, we analyzed the molecular interactions of protein-ligand which was docked by AutoDock 4.2 software. In AutoDock 4.2 software, we used a new search algorithm, hybrid algorithm of random drift particle swarm optimization and local search (LRDPSO), and the classical Lamarckian genetic algorithm (LGA) as energy optimization algorithms. The best conformations of each docking algorithm were subjected to molecular dynamic (MD) simulations to further analyze the molecular mechanisms of protein-ligand interactions. Here, we analyze the binding energy between protein receptors and ligands, the interactions of salt bridges and hydrogen bonds in the docking region, and the structural changes during complex unfolding. Our comparison of these complexes highlights differences in the protein-ligand interactions between the two docking methods. It also shows that salt bridge and hydrogen bond interactions play a crucial role in protein-ligand stability. The present work focuses on extracting the deterministic characteristics of docking interactions from their dynamic properties, which is important for understanding biological functions and determining which amino acid residues are crucial to docking interactions.
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Gelation of oil-in-water emulsions stabilized by heat-denatured and nanofibrillated whey proteins through ion bridging or citric acid-mediated cross-linking. Int J Biol Macromol 2018; 120:2247-2258. [DOI: 10.1016/j.ijbiomac.2018.08.085] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/30/2018] [Accepted: 08/15/2018] [Indexed: 01/09/2023]
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Najor M, Leverson BD, Goossens JL, Kothawala S, Olsen KW, Mota de Freitas D. Folding of G α Subunits: Implications for Disease States. ACS OMEGA 2018; 3:12320-12329. [PMID: 30411001 PMCID: PMC6210069 DOI: 10.1021/acsomega.8b01174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/18/2018] [Indexed: 06/08/2023]
Abstract
G-proteins play a central role in signal transduction by fluctuating between "on" and "off" phases that are determined by a conformational change. cAMP is a secondary messenger whose formation is inhibited or stimulated by activated Giα1 or Gsα subunit. We used tryptophan fluorescence, UV/vis spectrophotometry, and circular dichroism to probe distinct structural features within active and inactive conformations from wild-type and tryptophan mutants of Giα1 and Gsα. For all proteins studied, we found that the active conformations were more stable than the inactive conformations, and upon refolding from higher temperatures, activated wild-type subunits recovered significantly more native structure. We also observed that the wild-type subunits partially regained the ability to bind nucleotide. The increased compactness observed upon activation was consistent with the calculated decrease in solvent accessible surface area for wild-type Giα1. We found that as the temperature increased, Gα subunits, which are known to be rich in α-helices, converted to proteins with increased content of β-sheets and random coil. For active conformations from wild-type and tryptophan mutants of Giα1, melting temperatures indicated that denaturation starts around hydrophobic tryptophan microenvironments and then radiates toward tyrosine residues at the surface, followed by alteration of the secondary structure. For Gsα, however, disruption of secondary structure preceded unfolding around tyrosine residues. In the active conformations, a π-cation interaction between essential arginine and tryptophan residues, which was characterized by a fluorescence-measured red shift and modeled by molecular dynamics, was also shown to be a contributor to the stability of Gα subunits. The folding properties of Gα subunits reported here are discussed in the context of diseases associated to G-proteins.
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Coupling Multi Angle Light Scattering to Ion Exchange chromatography (IEX-MALS) for protein characterization. Sci Rep 2018; 8:6907. [PMID: 29720692 PMCID: PMC5931992 DOI: 10.1038/s41598-018-25246-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 04/16/2018] [Indexed: 12/21/2022] Open
Abstract
Multi-angle light scattering coupled with size exclusion chromatography (SEC-MALS) is a standard and common approach for characterizing protein mass, overall shape, aggregation, oligomerization, interactions and purity. The limited resolution of analytical SEC restricts in some instances the accurate analysis that can be accomplished by MALS. These include mixtures of protein populations with identical or very similar molecular masses, oligomers with poor separation and short peptides. Here we show that combining MALS with the higher resolution separation technique ion exchange (IEX-MALS) can allow precise analyses of samples that cannot be resolved by SEC-MALS. We conclude that IEX-MALS is a valuable and complementary method for protein characterization, especially for protein systems that could not be fully analyzed by SEC-MALS.
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Bryzgalov LO, Korbolina EE, Brusentsov II, Leberfarb EY, Bondar NP, Merkulova TI. Novel functional variants at the GWAS-implicated loci might confer risk to major depressive disorder, bipolar affective disorder and schizophrenia. BMC Neurosci 2018; 19:22. [PMID: 29745862 PMCID: PMC5998904 DOI: 10.1186/s12868-018-0414-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND A challenge of understanding the mechanisms underlying cognition including neurodevelopmental and neuropsychiatric disorders is mainly given by the potential severity of cognitive disorders for the quality of life and their prevalence. However, the field has been focused predominantly on protein coding variation until recently. Given the importance of tightly controlled gene expression for normal brain function, the goal of the study was to assess the functional variation including non-coding variation in human genome that is likely to play an important role in cognitive functions. To this end, we organized and utilized available genome-wide datasets from genomic, transcriptomic and association studies into a comprehensive data corpus. We focused on genomic regions that are enriched in regulatory activity-overlapping transcriptional factor binding regions and repurpose our data collection especially for identification of the regulatory SNPs (rSNPs) that showed associations both with allele-specific binding and allele-specific expression. We matched these rSNPs to the nearby and distant targeted genes and then selected the variants that could implicate the etiology of cognitive disorders according to Genome-Wide Association Studies (GWAS). Next, we use DeSeq 2.0 package to test the differences in the expression of the certain targeted genes between the controls and the patients that were diagnosed bipolar affective disorder and schizophrenia. Finally, we assess the potential biological role for identified drivers of cognition using DAVID and GeneMANIA. RESULTS As a result, we selected fourteen regulatory SNPs locating within the loci, implicated from GWAS for cognitive disorders with six of the variants unreported previously. Grouping of the targeted genes according to biological functions revealed the involvement of processes such as 'posttranscriptional regulation of gene expression', 'neuron differentiation', 'neuron projection development', 'regulation of cell cycle process' and 'protein catabolic processes'. We identified four rSNP-targeted genes that showed differential expression between patient and control groups depending on brain region: NRAS-in schizophrenia cohort, CDC25B, DDX21 and NUCKS1-in bipolar disorder cohort. CONCLUSIONS Overall, our findings are likely to provide the keys for unraveling the mechanisms that underlie cognitive functions including major depressive disorder, bipolar disorder and schizophrenia etiopathogenesis.
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Affiliation(s)
- Leonid O. Bryzgalov
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Science, 10 Lavrentyeva Prospekt, Novosibirsk, Russian Federation 630090
| | - Elena E. Korbolina
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Science, 10 Lavrentyeva Prospekt, Novosibirsk, Russian Federation 630090
- The Novosibirsk State University, 1 Pirogova st., Novosibirsk, Russian Federation 630090
| | - Ilja I. Brusentsov
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Science, 10 Lavrentyeva Prospekt, Novosibirsk, Russian Federation 630090
| | - Elena Y. Leberfarb
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Science, 10 Lavrentyeva Prospekt, Novosibirsk, Russian Federation 630090
| | - Natalia P. Bondar
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Science, 10 Lavrentyeva Prospekt, Novosibirsk, Russian Federation 630090
- The Novosibirsk State University, 1 Pirogova st., Novosibirsk, Russian Federation 630090
| | - Tatiana I. Merkulova
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Science, 10 Lavrentyeva Prospekt, Novosibirsk, Russian Federation 630090
- The Novosibirsk State University, 1 Pirogova st., Novosibirsk, Russian Federation 630090
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Goel R, Garg C, Gautam HK, Sharma AK, Kumar P, Gupta A. Fabrication of cationic nanostructures from short self-assembling amphiphilic mixed α/β-pentapeptide: Potential candidates for drug delivery, gene delivery, and antimicrobial applications. Int J Biol Macromol 2018; 111:880-893. [PMID: 29355630 DOI: 10.1016/j.ijbiomac.2018.01.079] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 01/11/2018] [Accepted: 01/12/2018] [Indexed: 12/18/2022]
Abstract
The present article describes designing and fabrication of nanostructures from a mixed α/β-pentapeptide, Lys-βAla-βAla-Lys-βAla, which majorly contains non-natural β-alanine residues in the backbone with two α-lysine residues at 1- and 4-positions. The amphiphilic pentapeptide showed the ability to self-assemble into cationic nanovesicles in an aqueous solution. The average size of peptide nanostructures was found to be ~270 nm with a very high cationic charge of ~+40 mV. TEM micrographs revealed the average size of the same nanostructures ~80 nm bearing vesicular morphology. CD and FTIR spectroscopic studies on self-assembled pentapeptide hinted at random coil conformation which was also correlated with conformational search program using Hyper Chem 8.0. The pentapeptide nanostructures were then tested for encapsulation of hydrophobic model drug moieties, L-Dopa, and curcumin. Transfection efficiency of the generated cationic nanostructures was evaluated on HEK293 cells and compared the results with those obtained in the presence of chloroquine. The cytotoxicity assay performed using MTT depicted ~75-80% cell viability. The obtained nanostructures also gave positive results against both Gram-negative and Gram-positive bacterial strains. Altogether the results advocate the promising potential of the pentapeptide foldamer, H-Lys-βAla-βAla-Lys-βAla-OEt, for drug and gene delivery applications along with the antimicrobial activity.
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Affiliation(s)
- Rahul Goel
- Department of Chemistry, Dyal Singh College, University of Delhi, Lodhi Road, New Delhi 110003, India
| | - Charu Garg
- Department of Chemistry, Dyal Singh College, University of Delhi, Lodhi Road, New Delhi 110003, India; Nucleic Acids Research Laboratory, CSIR-Institute of Genomics and Integrative Biology, Delhi University Campus, Mall Road, Delhi 110007, India
| | - Hemant Kumar Gautam
- Microbial Technology Laboratory, CSIR-Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi 110025, India
| | - Ashwani Kumar Sharma
- Nucleic Acids Research Laboratory, CSIR-Institute of Genomics and Integrative Biology, Delhi University Campus, Mall Road, Delhi 110007, India
| | - Pradeep Kumar
- Nucleic Acids Research Laboratory, CSIR-Institute of Genomics and Integrative Biology, Delhi University Campus, Mall Road, Delhi 110007, India
| | - Alka Gupta
- Department of Chemistry, Dyal Singh College, University of Delhi, Lodhi Road, New Delhi 110003, India.
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