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1.
J Biol Chem ; 299(7): 104914, 2023 07.
Article in English | MEDLINE | ID: mdl-37315787

ABSTRACT

The epidermal growth factor receptor (EGFR) is a receptor tyrosine kinase (RTK) commonly targeted for inhibition by anticancer therapeutics. Current therapeutics target EGFR's kinase domain or extracellular region. However, these types of inhibitors are not specific for tumors over healthy tissue and therefore cause undesirable side effects. Our lab has recently developed a new strategy to regulate RTK activity by designing a peptide that specifically binds to the transmembrane (TM) region of the RTK to allosterically modify kinase activity. These peptides are acidity-responsive, allowing them to preferentially target acidic environments like tumors. We have applied this strategy to EGFR and created the PET1 peptide. We observed that PET1 behaves as a pH-responsive peptide that modulates the configuration of the EGFR TM through a direct interaction. Our data indicated that PET1 inhibits EGFR-mediated cell migration. Finally, we investigated the mechanism of inhibition through molecular dynamics simulations, which showed that PET1 sits between the two EGFR TM helices; this molecular mechanism was additionally supported by AlphaFold-Multimer predictions. We propose that the PET1-induced disruption of native TM interactions disturbs the conformation of the kinase domain in such a way that it inhibits EGFR's ability to send migratory cell signals. This study is a proof-of-concept that acidity-responsive membrane peptide ligands can be generally applied to RTKs. In addition, PET1 constitutes a viable approach to therapeutically target the TM of EGFR.


Subject(s)
Allosteric Regulation , Cell Membrane , ErbB Receptors , Peptides , Humans , Epidermal Growth Factor/metabolism , ErbB Receptors/antagonists & inhibitors , ErbB Receptors/chemistry , ErbB Receptors/metabolism , Neoplasms/drug therapy , Neoplasms/metabolism , Neoplasms/pathology , Phosphorylation/drug effects , Protein Structure, Secondary/drug effects , Receptor Protein-Tyrosine Kinases/metabolism , Allosteric Regulation/drug effects , Cell Membrane/chemistry , Cell Membrane/metabolism , Hydrogen-Ion Concentration , Peptides/pharmacology , Cell Movement/drug effects , Protein Domains/drug effects , Antineoplastic Agents/pharmacology
2.
Int J Mol Sci ; 23(3)2022 Jan 18.
Article in English | MEDLINE | ID: mdl-35162961

ABSTRACT

Spike protein of SARS-CoV-2 contains a single-span transmembrane (TM) domain and plays roles in receptor binding, viral attachment and viral entry to the host cells. The TM domain of spike protein is critical for viral infectivity. Herein, the TM domain of spike protein of SARS-CoV-2 was reconstituted in detergent micelles and subjected to structural analysis using solution NMR spectroscopy. The results demonstrate that the TM domain of the protein forms a helical structure in detergent micelles. An unstructured linker is identified between the TM helix and heptapeptide repeat 2 region. The linker is due to the proline residue at position 1213. Side chains of the three tryptophan residues preceding to and within the TM helix important for the function of S-protein might adopt multiple conformations which may be critical for their function. The side chain of W1212 was shown to be exposed to solvent and the side chains of residues W1214 and W1217 are buried in micelles. Relaxation study shows that the TM helix is rigid in solution while several residues have exchanges. The secondary structure and dynamics of the TM domain in this study provide insights into the function of the TM domain of spike protein.


Subject(s)
Detergents/pharmacology , Spike Glycoprotein, Coronavirus/chemistry , Amino Acid Sequence , COVID-19/virology , Cell Membrane/metabolism , Cross-Linking Reagents/pharmacology , Detergents/chemistry , Humans , Magnetic Resonance Spectroscopy , Micelles , Models, Molecular , Nuclear Magnetic Resonance, Biomolecular , Protein Domains/drug effects , Protein Structure, Secondary/drug effects , SARS-CoV-2/chemistry , SARS-CoV-2/metabolism , Spike Glycoprotein, Coronavirus/drug effects , Spike Glycoprotein, Coronavirus/metabolism
3.
FEBS J ; 289(3): 832-853, 2022 02.
Article in English | MEDLINE | ID: mdl-34555271

ABSTRACT

Mycobacterium leprae, the causative organism of leprosy, harbors many antigenic proteins, and one such protein is the 18-kDa antigen. This protein belongs to the small heat shock protein family and is commonly known as HSP18. Its chaperone function plays an important role in the growth and survival of M. leprae inside infected hosts. HSP18/18-kDa antigen is often used as a diagnostic marker for determining the efficacy of multidrug therapy (MDT) in leprosy. However, whether MDT drugs (dapsone, clofazimine, and rifampicin) do interact with HSP18 and how these interactions affect its structure and chaperone function is still unclear. Here, we report evidence of HSP18-dapsone/clofazimine/rifampicin interaction and its impact on the structure and chaperone function of HSP18. These three drugs interact efficiently with HSP18 (having submicromolar binding affinity) with 1 : 1 stoichiometry. Binding of these MDT drugs to the 'α-crystallin domain' of HSP18 alters its secondary structure and tryptophan micro-environment. Furthermore, surface hydrophobicity, oligomeric size, and thermostability of the protein are reduced upon interaction with these three drugs. Eventually, all these structural alterations synergistically decrease the chaperone function of HSP18. Interestingly, the effect of rifampicin on the structure, stability, and chaperone function of this mycobacterial small heat shock protein is more pronounced than the other two MDT drugs. This reduction in the chaperone function of HSP18 may additionally abate M. leprae survivability during multidrug treatment. Altogether, this study provides a possible foundation for rational designing and development of suitable HSP18 inhibitors in the context of effective treatment of leprosy.


Subject(s)
Antigens, Bacterial/genetics , Bacterial Proteins/genetics , Heat-Shock Proteins/genetics , Leprosy/drug therapy , Mycobacterium leprae/genetics , Antigens, Bacterial/immunology , Bacterial Proteins/ultrastructure , Clofazimine/pharmacology , Dapsone/pharmacology , Heat-Shock Proteins/ultrastructure , Host-Pathogen Interactions/genetics , Humans , Hydrophobic and Hydrophilic Interactions/drug effects , Leprostatic Agents/chemistry , Leprostatic Agents/pharmacology , Leprosy/genetics , Leprosy/immunology , Leprosy/microbiology , Molecular Chaperones/chemistry , Molecular Chaperones/genetics , Mycobacterium leprae/pathogenicity , Protein Binding/drug effects , Protein Structure, Secondary/drug effects , Rifampin/pharmacology
4.
Int J Mol Sci ; 22(22)2021 Nov 19.
Article in English | MEDLINE | ID: mdl-34830391

ABSTRACT

Parkinson's disease (PD) is the second most common neurodegenerative disorder. An important hallmark of PD involves the pathological aggregation of proteins in structures known as Lewy bodies. The major component of these proteinaceous inclusions is alpha (α)-synuclein. In different conditions, α-synuclein can assume conformations rich in either α-helix or ß-sheets. The mechanisms of α-synuclein misfolding, aggregation, and fibrillation remain unknown, but it is thought that ß-sheet conformation of α-synuclein is responsible for its associated toxic mechanisms. To gain fundamental insights into the process of α-synuclein misfolding and aggregation, the secondary structure of this protein in the presence of charged and non-charged surfactant solutions was characterized. The selected surfactants were (anionic) sodium dodecyl sulphate (SDS), (cationic) cetyltrimethylammonium chloride (CTAC), and (uncharged) octyl ß-D-glucopyranoside (OG). The effect of surfactants in α-synuclein misfolding was assessed by ultra-structural analyses, in vitro aggregation assays, and secondary structure analyses. The α-synuclein aggregation in the presence of negatively charged SDS suggests that SDS-monomer complexes stimulate the aggregation process. A reduction in the electrostatic repulsion between N- and C-terminal and in the hydrophobic interactions between the NAC (non-amyloid beta component) region and the C-terminal seems to be important to undergo aggregation. Fourier transform infrared spectroscopy (FTIR) measurements show that ß-sheet structures comprise the assembly of the fibrils.


Subject(s)
Neurodegenerative Diseases/drug therapy , Parkinson Disease/drug therapy , Protein Aggregation, Pathological/drug therapy , alpha-Synuclein/genetics , Amyloid/antagonists & inhibitors , Amyloid/genetics , Cetrimonium/pharmacology , Circular Dichroism , Galactosides/pharmacology , Humans , Lewy Bodies/drug effects , Lewy Bodies/ultrastructure , Neurodegenerative Diseases/pathology , Parkinson Disease/genetics , Parkinson Disease/pathology , Protein Aggregation, Pathological/genetics , Protein Aggregation, Pathological/pathology , Protein Conformation , Protein Conformation, beta-Strand/genetics , Protein Folding/drug effects , Protein Structure, Secondary/drug effects , Sodium Dodecyl Sulfate/pharmacology , Spectroscopy, Fourier Transform Infrared , alpha-Synuclein/antagonists & inhibitors
5.
Arch Biochem Biophys ; 713: 109062, 2021 11 30.
Article in English | MEDLINE | ID: mdl-34688606

ABSTRACT

Bacterial biofilms are an alternative lifestyle in which communities of bacteria are embedded in an extracellular matrix manly composed by polysaccharides, nucleic acids and proteins, being the hallmark of bacterial survival in a variety of ecological niches. Amyloid fibrils are one of the proteinaceous components of such extracellular crowded environments. FapC is the main component of the functional amyloid recently discovered in Pseudomonas species, including the opportunistic pathogen P. aeruginosa, which is a major cause of nosocomial infections and contamination of medical devices. Considering that several functional roles have been attributed to this bacterial amyloid, FapC emerged as a novel target to control Pseudomonas biofilm formation and to design new treatments against chronic infections. In this study, we used complementary biophysical techniques to evaluate conformational signatures of FapC amyloids formed in the presence of alginate, the major exopolysaccharide associated with the mucoid phenotype of P. aeruginosa strains isolated from cystic fibrosis patients. We found that the this naturally occurring macromolecular crowder leads to morphological similar yet polymorphic FapC fibrils, highlighting the importance of considering the complexity of the extracellular matrix in order to improve our understanding of microbial functional amyloids.


Subject(s)
Alginates/pharmacology , Amyloidogenic Proteins/metabolism , Bacterial Proteins/metabolism , Biofilms/drug effects , Protein Multimerization/drug effects , Protein Structure, Secondary/drug effects , Pseudomonas aeruginosa/drug effects , Pseudomonas aeruginosa/physiology
6.
Sci Rep ; 11(1): 18851, 2021 09 22.
Article in English | MEDLINE | ID: mdl-34552128

ABSTRACT

In this pandemic SARS-CoV-2 crisis, any attempt to contain and eliminate the virus will also stop its spread and consequently decrease the risk of severe illness and death. While ozone treatment has been suggested as an effective disinfection process, no precise mechanism of action has been previously reported. This study aimed to further investigate the effect of ozone treatment on SARS-CoV-2. Therefore, virus collected from nasopharyngeal and oropharyngeal swab and sputum samples from symptomatic patients was exposed to ozone for different exposure times. The virus morphology and structure were monitored and analyzed through Atomic Force Microscopy (AFM), Transmission Electron Microscopy (TEM), Atomic Absorption Spectroscopy (AAS), and ATR-FTIR. The obtained results showed that ozone treatment not only unsettles the virus morphology but also alters the virus proteins' structure and conformation through amino acid disturbance and Zn ion release from the virus non-structural proteins. These results could provide a clearer pathway for virus elimination and therapeutics preparation.


Subject(s)
COVID-19 Drug Treatment , Ozone/pharmacology , SARS-CoV-2/chemistry , SARS-CoV-2/drug effects , Coronavirus Papain-Like Proteases/chemistry , Coronavirus Papain-Like Proteases/metabolism , Coronavirus RNA-Dependent RNA Polymerase/chemistry , Coronavirus RNA-Dependent RNA Polymerase/metabolism , Humans , Microscopy, Electron, Transmission , Protein Structure, Secondary/drug effects , Protein Structure, Tertiary/drug effects , SARS-CoV-2/ultrastructure , Time Factors , Viral Envelope/chemistry , Viral Envelope/drug effects , Viral Regulatory and Accessory Proteins/chemistry , Viral Regulatory and Accessory Proteins/metabolism , Zinc/chemistry , Zinc/metabolism
7.
Food Chem Toxicol ; 155: 112396, 2021 Sep.
Article in English | MEDLINE | ID: mdl-34245828

ABSTRACT

Calothrixin A (CLA), as a carbazole-1,4-quinone alkaloid with unique indolo [3,2-j] phenanthridine framework, is a natural metabolite from the Calothrix cyanobacteria. Since the interaction to the functional serum albumins may play an important role in estimating its potential physiological or toxicological effects in vivo, we here explored the binding information of CLA with human serum albumin (HSA) by multi-spectroscopic experiments and computational approaches. The molecular docking results showed that there was one binding site of CLA to the site I (subdomain IIA) of HSA, causing the spontaneous formation of the ground state complex of CLA-HSA through the integration of hydrogen bond, hydrophobic interaction, and electrostatic interaction. Moreover, CLA could effectively trigger the change of HSA's secondary structure because of an obvious decrease of α-helical content in HSA. Taking into consideration of the crucial role of HSA to transport extraneous functional small molecules in vivo, this study may provide a worthy theoretical basis to evaluate the in vivo toxicity of CLA, aiming to reduce/avoid the potential toxic side effects of CLA in the next hit-to-lead campaign.


Subject(s)
Indole Alkaloids/metabolism , Indole Alkaloids/toxicity , Serum Albumin, Human/metabolism , Humans , Hydrogen Bonding , Hydrophobic and Hydrophilic Interactions , Molecular Docking Simulation , Molecular Dynamics Simulation , Protein Binding , Protein Structure, Secondary/drug effects , Serum Albumin, Human/chemistry , Spectrometry, Fluorescence , Static Electricity , Thermodynamics
8.
Int J Biol Macromol ; 183: 1939-1947, 2021 Jul 31.
Article in English | MEDLINE | ID: mdl-34097957

ABSTRACT

Protein aggregation, such as amyloid fibril formation, is molecular hallmark of many neurodegenerative disorders including Alzheimer's, Parkinson's, and Prion disease. Indole alkaloids are well-known as the compounds having the ability to inhibit protein fibrillation. In this study, we experimentally and computationally have investigated the anti-amyloid property of a derivative of a synthesized tetracyclic indole alkaloid (TCIA), possessing capable functional groups. The fibrillation reaction of Hen White Egg Lysozyme (HEWL) was performed in absence and presence of the indole alkaloid. For quantitative analysis, we used Thioflovin T binding assay which showed ~50% reduction in fibril formation in the presence of 20 µM TCIA. Using TEM imaging, we observed a significant morphological change in our model protein in the presence of TCIA. In addition, we exploited FT-IR assay by which Amide I peak's shifting toward lower wavenumber was clearly observed. Using Molecular Docking, the interaction of the inhibitor (TCIA) with the protein's amyloidogenic region was modeled. Also, different biophysical parameters were calculated by Molecular Dynamics (MD) simulation. Various biochemical assays, conformational change, and hydrophobicity exposure of the protein during amyloid formation indicated that the compound assists HEWL to keep its native structure via destabilizing ß-sheet structure.


Subject(s)
Benzothiazoles/chemistry , Indole Alkaloids/pharmacology , Muramidase/chemistry , Animals , Chickens , Enzyme Stability/drug effects , Hydrophobic and Hydrophilic Interactions , Indole Alkaloids/chemistry , Molecular Docking Simulation , Molecular Dynamics Simulation , Muramidase/drug effects , Protein Aggregates/drug effects , Protein Structure, Secondary/drug effects , Spectroscopy, Fourier Transform Infrared
9.
Carbohydr Polym ; 263: 117888, 2021 Jul 01.
Article in English | MEDLINE | ID: mdl-33858564

ABSTRACT

The molecular structure of sulfonated chitosan is similar to heparin, and it has been proved to have some heparin functions. Studies have shown that heparin and bone morphogenetic protein-2 (BMP-2) have synergistic effects, but heparin has limitations in clinical application. In this paper, the synergistic effect of 2-N,6-O-sulfonated chitosan (26SCS) and BMP-2 was studied. The preparation of 26SCS was explored and 26SCS was co-cultured with bone marrow mesenchymal stem cells (BMSCs) to study the effects of 26SCS on the proliferation, adhesion behavior and osteogenic differentiation of BMSCs. The synergistic mechanism of 26SCS and BMP-2 was explored by circular dichroism and isothermal calorimetric titration. The results showed that 26SCS affected the secondary structure of BMP-2 protein, mainly caused the significant change of antiparallel conformation in ß-fold, and then improved the biological activity of BMP-2 and showed a dose-dependent manner. 26SCS was expected to be a synergistic factor of BMP-2.


Subject(s)
Bone Morphogenetic Protein 2/chemistry , Bone Morphogenetic Protein 2/metabolism , Chitosan/chemistry , Chitosan/pharmacology , Alkaline Phosphatase/metabolism , Animals , Calcification, Physiologic/drug effects , Cell Adhesion/drug effects , Cell Differentiation/drug effects , Cell Proliferation/drug effects , Cells, Cultured , Heparin/chemistry , Heparin/pharmacology , Mesenchymal Stem Cells/drug effects , Osteogenesis/drug effects , Protein Structure, Secondary/drug effects , Rabbits , Sulfur/chemistry
10.
Mol Cell Neurosci ; 112: 103612, 2021 04.
Article in English | MEDLINE | ID: mdl-33722677

ABSTRACT

The multifactorial neurological condition called Alzheimer's disease (AD) primarily affects elderly individuals. Despite the calamitous consequences of AD, curative strategies for a regimen to apply remain inadequate as several factors contribute to AD etiology. Drug repurposing is an advance strategy prior to drug discovery as various effective drugs perform through alteration of multiple targets, and the present "poly-pharmacology" can be a curative approach to complex disorders. AD's multifactorial behavior actively encourages the hypothesis for a drug design approach focused on drug repurposing. In this study, we discovered that an antifungal drug, Caspofungin (CAS) is a potent Aß aggregation inhibitor that displays significantly reduced toxicity associated with AD. Drug reprofiling and REMD simulations demonstrated that CAS interacts with the ß-sheet section, known as Aß amyloid fibrils hotspot. CAS leads to destabilization of ß-sheet and, conclusively, in its devaluation. Later, in vitro experiments were acquired in which the fibrillar volume was reduced for CAS-treated Aß peptide. For the first time ever, this study has determined an antifungal agent as the Aß amyloid aggregation's potent inhibitor. Several efficient sequence-reliant potent inhibitors can be developed in future against the amyloid aggregation for different amyloid peptide by the processing and conformational optimization of CAS.


Subject(s)
Amyloid beta-Peptides/drug effects , Antifungal Agents/pharmacology , Caspofungin/pharmacology , Protein Aggregation, Pathological/prevention & control , Alzheimer Disease/drug therapy , Amino Acid Sequence , Animals , Antifungal Agents/therapeutic use , Caspofungin/therapeutic use , Drug Repositioning , Humans , Hydrogen Bonding , Hydrophobic and Hydrophilic Interactions , Ligands , Models, Molecular , Molecular Docking Simulation , Molecular Dynamics Simulation , Protein Aggregation, Pathological/drug therapy , Protein Conformation , Protein Structure, Secondary/drug effects
11.
Int J Biol Macromol ; 174: 309-318, 2021 Mar 31.
Article in English | MEDLINE | ID: mdl-33524481

ABSTRACT

Human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) is the key enzyme for the virus gene replication and the most important target for antiviral therapy. Toxicity, drug resistance and side effects have led to search for new antiviral agents. Farnesiferol C (FC) is a well-known biologically active sesquiterpene coumarin derivative from genus Ferula. The current study was designed to examine the impacts of FC on the structure and function of HIV-1 RT, using some theoretical and experimental methods. FC inhibited HIV-1RT activity via mixed inhibition mechanism (IC50 = 30 µM). Spectroscopic data showed some conformational changes in the secondary as well as tertiary structure of HIV-1RT following the interaction with FC. Results showed that FC could quench the intrinsic fluorescence emission of HIV-1RT through static quenching mechanism. Thermodynamic parameters revealed that hydrogen bondings and van der Waals forces are the major forces in the binding reaction and the low equilibrium constants (KD) value obtained from surface plasmon resonance data, confirmed the high affinity of FC for HIV-1RT. Molecular docking studies indicated that FC interacts with enzyme through hydrophobic pocket. Taken together, the outcomes of this research revealed that, sesquiterpene coumarines can be used to design natural remedies as anti-HIV agents.


Subject(s)
Coumarins/pharmacology , Ferula/chemistry , HIV Reverse Transcriptase/metabolism , HIV-1/enzymology , Reverse Transcriptase Inhibitors/pharmacology , Coumarins/chemistry , HIV Reverse Transcriptase/chemistry , HIV-1/drug effects , Hydrogen Bonding , Models, Molecular , Molecular Docking Simulation , Molecular Structure , Phytochemicals/chemistry , Phytochemicals/pharmacology , Protein Structure, Secondary/drug effects , Protein Structure, Tertiary/drug effects , Reverse Transcriptase Inhibitors/chemistry , Surface Plasmon Resonance
12.
Int J Biol Macromol ; 174: 207-215, 2021 Mar 31.
Article in English | MEDLINE | ID: mdl-33482212

ABSTRACT

Phenoloxidase (PO) is a typical metal enzyme, which requires metal ions as prosthetic groups to enable the full exertion of its activity. To study how metal ions affected the activity and structure of PO enzymes, while providing reference materials for in-depth investigations, we examined the effects of different metal ions (Cu2+, Zn2+, Mg2+, Ca2+, and Ba2+) on their activities. Furthermore, Cu2+ and Mg2+ were selected for further investigation through UV spectra, intrinsic fluorescence spectroscopy, AFM, and FTIR. It was revealed that Cu2+ had a more obvious effect on PO compared to Mg2+. The PO could be activated when the concentrations of Cu2+ and Mg2+ were lower than 10-3 and 10-2 mol/L, respectively, and maximum PO activities (182.14% and 141.02%) were observed at 10-4 mol/L concentrations of Cu2+ and Mg2+. When the concentrations of Cu2+ and Mg2+ were higher than 10-2 and 10-1 mol/L, the activities PO were inhibited. The results of the UV-vis and fluorescence spectra revealed that Cu2+ shaped the tertiary structure of PO, whereas the effect of Mg2+ was slight. The AFM results demonstrated that high concentrations of Cu2+ and Mg2+ resulted in PO aggregation. FTIR analysis indicated that the total content of PO α-helices and ß-sheets decreased with higher concentrations of Cu2+ and Mg2+.


Subject(s)
Copper/pharmacology , Magnesium/pharmacology , Monophenol Monooxygenase/chemistry , Monophenol Monooxygenase/metabolism , Penaeidae/enzymology , Animals , Arthropod Proteins/chemistry , Arthropod Proteins/metabolism , Dose-Response Relationship, Drug , Enzyme Activation/drug effects , Fluorescence Resonance Energy Transfer , Microscopy, Atomic Force , Protein Structure, Secondary/drug effects , Protein Structure, Tertiary/drug effects , Spectrometry, Fluorescence
13.
Arch Biochem Biophys ; 699: 108764, 2021 03 15.
Article in English | MEDLINE | ID: mdl-33460582

ABSTRACT

The interaction of a dirhamnolipid biosurfactant secreted by Pseudomonas aeruginosa with calcium ATPase from sarcoplasmic reticulum (SR) was studied by means of different approaches, such as enzyme activity, fluorescence spectroscopy, Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), and molecular docking simulations. The ATP hydrolysis activity was fully inhibited by incubation with dirhamnolipid (diRL) up to 0.1 mM concentration, corresponding to a surfactant concentration below membrane solubilization threshold. Surfactant-protein interaction induced conformational changes in the protein observed by an increase in the accessibility of tryptophan residues to the aqueous phase and by changes in the secondary structure of the protein as seen by fluorescence and FTIR spectroscopy. As a consequence, the protein become more unstable and denatured at lower temperatures, as seen by enzyme activity and DSC studies. Finally, these results were explained at molecular level throughout molecular docking simulations. It is concluded that there is a specific dirhamnolipid-protein interaction not related to the surface activity of the surfactant but to the particular physicochemical properties of the biosurfactant molecule.


Subject(s)
Glycolipids/metabolism , Sarcoplasmic Reticulum Calcium-Transporting ATPases/metabolism , Surface-Active Agents/metabolism , Animals , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/metabolism , Glycolipids/chemistry , Molecular Docking Simulation , Protein Binding , Protein Structure, Secondary/drug effects , Pseudomonas aeruginosa/chemistry , Rabbits , Sarcoplasmic Reticulum Calcium-Transporting ATPases/antagonists & inhibitors , Sarcoplasmic Reticulum Calcium-Transporting ATPases/chemistry , Surface-Active Agents/chemistry
14.
J Appl Microbiol ; 130(3): 736-744, 2021 Mar.
Article in English | MEDLINE | ID: mdl-32750224

ABSTRACT

AIMS: Streptococcus suis is a highly zoonotic pathogen that is a serious threat to human health and the development of the pig industry worldwide. The virulence factors produced during S. suis infection play an important role, and the pore-forming activity of suilysin is considered an important virulence-related factor, especially in meningitis. Treatment of S. suis infection with traditional antibiotics is becoming increasingly challenging due to bacterial resistance. The purpose of this study is to verify the role of cryptotanshinone in the process of S. suis infection and provide a new drug precursor for the treatment of S. suis infection. METHODS AND RESULTS: In this study, we used circular dichroism spectroscopy to demonstrate that cryptotanshinone alters the secondary structure of suilysin. The results of the antibacterial activity and haemolysis assays showed cryptotanshinone could inhibit the pore-forming activity of suilysin without affecting bacterial growth or its expression. We also showed that cryptotanshinone reduces bacterial damage and penetration in vitro, reduce the S. suis-induced inflammatory response and provide protection against bacterial infections in vivo and in vitro. CONCLUSIONS: Cryptotanshinone is a potential compound precursor for treating S. suis infection. SIGNIFICANCE AND IMPACT OF THE STUDY: Cryptotanshinone may be a promising leading compound for S. suis infection and related diseases.


Subject(s)
Anti-Bacterial Agents/pharmacology , Hemolysin Proteins/antagonists & inhibitors , Phenanthrenes/pharmacology , Streptococcal Infections/drug therapy , Streptococcus suis/drug effects , Animals , Anti-Bacterial Agents/therapeutic use , Hemolysin Proteins/chemistry , Hemolysis/drug effects , Humans , Inflammation/drug therapy , Mice , Phenanthrenes/therapeutic use , Protein Structure, Secondary/drug effects , Streptococcus suis/pathogenicity , Virulence/drug effects , Virulence Factors/metabolism
15.
Biochem Soc Trans ; 49(1): 237-251, 2021 02 26.
Article in English | MEDLINE | ID: mdl-33367512

ABSTRACT

The RAS-regulated RAF-MEK1/2-ERK1/2 pathway promotes cell proliferation and survival and RAS and BRAF proteins are commonly mutated in cancer. This has fuelled the development of small molecule kinase inhibitors including ATP-competitive RAF inhibitors. Type I and type I½ ATP-competitive RAF inhibitors are effective in BRAFV600E/K-mutant cancer cells. However, in RAS-mutant cells these compounds instead promote RAS-dependent dimerisation and paradoxical activation of wild-type RAF proteins. RAF dimerisation is mediated by two key regions within each RAF protein; the RKTR motif of the αC-helix and the NtA-region of the dimer partner. Dimer formation requires the adoption of a closed, active kinase conformation which can be induced by RAS-dependent activation of RAF or by the binding of type I and I½ RAF inhibitors. Binding of type I or I½ RAF inhibitors to one dimer partner reduces the binding affinity of the other, thereby leaving a single dimer partner uninhibited and able to activate MEK. To overcome this paradox two classes of drug are currently under development; type II pan-RAF inhibitors that induce RAF dimer formation but bind both dimer partners thus allowing effective inhibition of both wild-type RAF dimer partners and monomeric active class I mutant RAF, and the recently developed "paradox breakers" which interrupt BRAF dimerisation through disruption of the αC-helix. Here we review the regulation of RAF proteins, including RAF dimers, and the progress towards effective targeting of the wild-type RAF proteins.


Subject(s)
Protein Kinase Inhibitors/pharmacology , raf Kinases/antagonists & inhibitors , Animals , Antineoplastic Agents/pharmacology , Humans , MAP Kinase Signaling System/drug effects , Protein Multimerization/drug effects , Protein Multimerization/physiology , Protein Structure, Secondary/drug effects , Proto-Oncogene Proteins B-raf/antagonists & inhibitors , Proto-Oncogene Proteins B-raf/physiology , raf Kinases/chemistry , raf Kinases/metabolism
16.
Int J Biol Macromol ; 170: 33-41, 2021 Feb 15.
Article in English | MEDLINE | ID: mdl-33352157

ABSTRACT

Fast green FCF (FGF) is often used in foods, pharmaceuticals, and cosmetics. However, little is known about the interactions of FGF with amyloid-ß protein (Aß) associated with Alzheimer's disease. In this study, the inhibitory effects of FGF on Aß fibrillogenesis, the disruption of preformed Aß fibrils, the reduction of Aß-induced cytotoxicity, and the attenuation of Aß-induced learning and memory impairments in mice were investigated. FGF significantly inhibited Aß fibrillogenesis and disintegrated the mature fibrils as evidenced by thioflavin T fluorescence and atomic force microscopy studies. Co-incubation of Aß with FGF greatly reduced Aß-induced cytotoxicity in vitro. Moreover, FGF showed a protective effect against cognitive impairment in Aß-treated mice. Molecular dynamics simulations further showed that FGF could synergistically interact with the Aß17-42 pentamer via electrostatic interactions, hydrogen bonds and π-π interactions, which reduced the ß-sheet content, and disordered random coils and bend structures of the Aß17-42 pentamer. This study offers a comprehensive understanding of the inhibitory effects of FGF against Aß neurotoxicity, which is critical for the search of effective food additives that can combat amyloid-associated disease.


Subject(s)
Amyloid beta-Peptides/drug effects , Amyloid/antagonists & inhibitors , Cognitive Dysfunction/prevention & control , Food Additives/therapeutic use , Lissamine Green Dyes/therapeutic use , Neuroprotective Agents/therapeutic use , Protein Aggregation, Pathological/prevention & control , Alzheimer Disease/metabolism , Alzheimer Disease/prevention & control , Amyloid/drug effects , Amyloid/toxicity , Amyloid/ultrastructure , Amyloid beta-Peptides/chemistry , Animals , Cognitive Dysfunction/etiology , Cognitive Dysfunction/metabolism , Exploratory Behavior/drug effects , Food Additives/pharmacology , Humans , Hydrogen Bonding , Lissamine Green Dyes/pharmacology , Mice , Microscopy, Atomic Force , Models, Molecular , Molecular Dynamics Simulation , Morris Water Maze Test/drug effects , Neuroprotective Agents/pharmacology , Peptide Fragments/chemistry , Peptide Fragments/drug effects , Protein Aggregation, Pathological/drug therapy , Protein Structure, Secondary/drug effects , Random Allocation , Static Electricity
17.
Biochem Biophys Res Commun ; 534: 950-956, 2021 01 01.
Article in English | MEDLINE | ID: mdl-33143872

ABSTRACT

Peptide sequence modulates amyloid fibril formation and triggers Alzheimer's disease. The N-terminal region of amyloid peptide is disordered and lack any specific secondary structure. An ionic interaction of Aß1-11 with factor XII is critical for the activation of the contact system in Alzheimer's disease. In this study, we report the self-assembly of fluctuating N-terminal Aß1-11 into nanotubes using atomic force micrography, transmission electron microscopy, circular dichroism studies and molecular modeling studies. The effect of four polyphenols: baicalein, rutin, vanillin and cyanidin-3-O-glucoside (C3G) was also explored on the amyloid fibril inhibitor perspective using amyloid specific dye Thioflavin T (ThT). AFM micrographs suggested the self-assembly of Aß1-11 into nanotubes after three weeks of incubation. Microwave treatment results in the conformational variation of disordered structure to ß-sheet rich amyloid fibrils. The presence of salts (sodium and potassium chloride) induces the structural transformation of Aß1-11 to super-helix. Fluorescence spectroscopy studies using ThT suggested differential inhibition of amyloid fibrils formation in the presence of polyphenols. Molecular modeling studies suggested that binding of polyphenols to Aß1-11 through hydrophobic interaction (Phe4 and Tyr 10) and hydrogen bonding (Glu3 and Arg5) play a substantial role in stabilizing Aß1-11-polyphenols complex. In the presence of polyphenols, Aß1-11 transforms to hybrid nanostructures thus hindering amyloid fibril formation. These results provide structural insights and importance of the N-terminal residues in the Aß1-42 self-assembly mechanism.


Subject(s)
Alzheimer Disease/metabolism , Amyloid beta-Peptides/metabolism , Peptide Fragments/metabolism , Alzheimer Disease/drug therapy , Amyloid beta-Peptides/analysis , Amyloid beta-Peptides/antagonists & inhibitors , Amyloid beta-Peptides/ultrastructure , Humans , Models, Molecular , Peptide Fragments/analysis , Peptide Fragments/antagonists & inhibitors , Peptide Fragments/ultrastructure , Polyphenols/pharmacology , Protein Structure, Secondary/drug effects
18.
J Mol Recognit ; 34(2): e2874, 2021 02.
Article in English | MEDLINE | ID: mdl-32893930

ABSTRACT

Due to the rapid development of industrial society, air pollution is becoming a serious problem which has being a huge threat to human health. Ultrafine particles (UFPs), one of the major air pollutants, are often the culprits of human diseases. At present, most of the toxicological studies of UFPs focus on their biological effects on lung cells and tissues, but there are less researches taking aim at the negative effects on functional proteins within the body. Therefore, we experimentally explored the effects of ultrafine carbon black (UFCB) on the structure and function of trypsin. After a short-term exposure to UFCB, the trypsin aromatic amino acid microenvironment, protein backbone and secondary structure were changed significantly, and the enzyme activity showed a trend that rose at first, then dropped. In addition, UFCB interacts with trypsin in the form of a complex. These studies demonstrated the negative effects of UFCB on trypsin, evidencing potential effects on animals and humans.


Subject(s)
Particulate Matter/toxicity , Soot/toxicity , Trypsin/chemistry , Trypsin/metabolism , Animals , Cattle , Circular Dichroism , Gene Expression Regulation/drug effects , Models, Molecular , Particle Size , Protein Structure, Secondary/drug effects , Spectrum Analysis , Trypsin/drug effects
19.
Chem Biol Interact ; 332: 109309, 2020 Dec 01.
Article in English | MEDLINE | ID: mdl-33181114

ABSTRACT

In the present situation, COVID-19 has become the global health concern due to its high contagious nature. It initially appeared in December 2019 in Wuhan, China and now affected more than 190 countries. As of now preventive measures are the sole solution to stop this disease for further transmission from person to person transmissions as there is no effective treatment or vaccine available to date. Research and development of new molecule is a laborious process; therefore, drug repurposing can be an alternative solution that involves the identification of potential compounds from the already available data. Alkaloids are potential source of therapeutic agents which might be able to treat novel COVID-19. Therefore, in the present study, twenty potential alkaloid molecules that possess antiviral activity against different viral diseases have taken into consideration and scrutinized using Lipinski's rule. Then out of twenty compounds seventeen were further selected for docking study. Docking study was performed using Autodock software and the best four molecule which provides maximum negative binding energy was selected for further analysis. Two alkaloids namely thalimonine and sophaline D showed potential activity to inhibit the Mpro but to confirm the claim further in-vitro studies are required.


Subject(s)
Alkaloids/metabolism , Antiviral Agents/metabolism , Coronavirus 3C Proteases/antagonists & inhibitors , Cysteine Proteinase Inhibitors/metabolism , SARS-CoV-2/enzymology , Alkaloids/chemistry , Antiviral Agents/chemistry , Catalytic Domain , Coronavirus 3C Proteases/chemistry , Coronavirus 3C Proteases/metabolism , Cysteine Proteinase Inhibitors/chemistry , Ligands , Molecular Docking Simulation , Molecular Dynamics Simulation , Protein Binding , Protein Structure, Secondary/drug effects
20.
Neurochem Int ; 140: 104806, 2020 11.
Article in English | MEDLINE | ID: mdl-32758584

ABSTRACT

Human cystatin C (CysC) is an amyloid forming protein involved in the hereditary cerebral amyloid angiopathy (HCCAA) that affects arteries in the brain and the peripheral nervous system. In this study we measured the influence of several substances on human CysC aggregation and amyloid fibril formation, induced at pH 4 in vitro. The effect of three polyphenols: resveratrol, quercetin and curcumin and of two antioxidants: vitamin C (VitC) and N-acetyl-L-cysteine (NAC) was explored as well as the effect of sulphoraphane (SF) and α-lipoic acid (AL). The formation of amyloid fibrils was followed by Thioflavin T (ThT) fluorescence and by transmission electron microscopy (TEM). Effects on the length of the lag phase were revealed by following the increase of ThT fluorescence intensity with time. The amount and morphology of fibrils in comparison to prefibrillar aggregates and globular oligomers were evaluated by TEM at the plateau stage of the reaction. Thermal stabilization of the CysC monomer by the small compounds was measured by differential scanning fluorimetry (DSF). NAC, VitC and SF exhibited the largest inhibitory effect on amyloid fibril growth. The effects of polyphenols were not significant, apart from resveratrol, which partly inhibited the amyloid fibril growth.


Subject(s)
Amyloid/chemistry , Antioxidants/pharmacology , Cystatin C/chemistry , Polyphenols/pharmacology , Recombinant Proteins/chemistry , Circular Dichroism/methods , Dose-Response Relationship, Drug , Humans , Protein Structure, Secondary/drug effects
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