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1.
J Chem Inf Model ; 64(16): 6557-6569, 2024 Aug 26.
Artigo em Inglês | MEDLINE | ID: mdl-39150323

RESUMO

Fungal infections with high mortality rates represent an increasing health risk. The Neosartorya (Aspergillus) fischeri antifungal protein 2 (NFAP2) is a small, cysteine-rich, cationic protein exhibiting potent anti-Candida activity. As the underlying mechanism, pore formation has been demonstrated; however, molecular level details on its membrane disruption action are lacking. Herein, we addressed the lipid binding of NFAP2 using a combined computational and experimental approach to simple lipid compositions with various surface charge properties. Simulation results revealed binding preferences for negatively charged model membranes, where selectivity is mediated by anionic lipid components enriched at the protein binding site but also assisted by zwitterionic lipid species. Several potential binding routes initiated by various anchoring contacts were observed, which resulted in one main binding mode and a few variants, with NFAP2 residing on the membrane surface. Region 10NCPNNCKHKKG20 of the flexible N-terminal part of the protein showed potency to insert into the lipid bilayer, where the disulfide bond-stabilized short motif 11CPNNC15 could play a key role. In addition, several areas, including the beginning of the N-terminal (residues 1-8), played roles in facilitating initial membrane contacts. Besides, individual roles of residues such as Lys24, Lys32, Lys34, and Trp42 were also revealed by the simulations. Combined data demonstrated that the solution conformation was not perturbed markedly upon membrane interaction, and the folded part of the protein also contributed to stabilizing the bound state. Data also highlighted that the binding of NFAP2 to lipid vesicles is sensitively affected by environmental factors such as ionic strength. Electrostatic interactions driven by anionic lipids were found pivotal, explaining the reduced membrane activity observed under high salt conditions. Experimental data supported the lipid-selective binding mechanisms and pointed to salt-dependent effects, particularly to protein-assisted vesicle aggregation at low ionic strength. Our findings can contribute to the development of NFAP2-based anti-Candida agents and studies aiming at future medical use of peptide-based natural antifungal compounds.


Assuntos
Antifúngicos , Proteínas Fúngicas , Antifúngicos/farmacologia , Antifúngicos/química , Antifúngicos/metabolismo , Proteínas Fúngicas/química , Proteínas Fúngicas/metabolismo , Sítios de Ligação , Ligação Proteica , Simulação de Dinâmica Molecular , Sequência de Aminoácidos , Bicamadas Lipídicas/metabolismo , Bicamadas Lipídicas/química , Modelos Moleculares
2.
J Chem Inf Model ; 63(12): 3799-3813, 2023 06 26.
Artigo em Inglês | MEDLINE | ID: mdl-37278479

RESUMO

Computer-assisted study and design of non-natural peptidomimetics is increasingly important in the development of novel constructs with widespread applicability. Among these methods, molecular dynamics can accurately describe monomeric as well as oligomeric states of these compounds. We studied seven different sequences composed of cyclic and acyclic ß-amino acids, the closest homologues of natural peptides, and compared the performance on them of three force field families in which specific modifications were made to improve reproduction of ß-peptide structures. Altogether 17 systems were simulated, each for 500 ns, testing multiple starting conformations and in three cases also oligomer formation and stability from eight ß-peptide monomers. The results indicated that our recently developed CHARMM force field extension, based on torsional energy path matching of the ß-peptide backbone against quantum-chemical calculations, performs best overall, reproducing the experimental structures accurately in all monomeric simulations and correctly describing all the oligomeric examples. The Amber and GROMOS force fields could only treat some of the seven peptides (four in each case) without further parametrization. Amber was able to reproduce the experimental secondary structure of those ß-peptides which contained cyclic ß-amino acids, while the GROMOS force field had the lowest performance in this sense. From the latter two, Amber was able to hold together already formed associates in the prepared state but was not able to yield spontaneous oligomer formation in the simulations.


Assuntos
Âmbar , Simulação de Dinâmica Molecular , Humanos , Peptídeos/química , Estrutura Secundária de Proteína , Aminoácidos
3.
J Chem Inf Model ; 63(21): 6877-6889, 2023 11 13.
Artigo em Inglês | MEDLINE | ID: mdl-37905818

RESUMO

Antimicrobial cationic peptides (AMPs) are excellent candidates for use as therapeutic antimicrobial agents. Among them, short peptides possessing sequences of 9-11 amino acids have some advantages over long-sequence peptides. However, one of the main limitations of short peptides is that their mechanism of action at the molecular level is not well-known. In this article, we report a model based on multiscale molecular dynamics simulations of short peptides interacting with vesicles containing palmitoyl-oleoyl-phosphatidylglycerol (POPG)/palmitoyl-oleoyl-phosphatidylethanolamine (POPE). Simulations using this approach have allowed us to understand the different behaviors of peptides with antimicrobial activity with respect to those that do not produce this effect. We found remarkable agreement with a series of experimental results directly supporting our model. Moreover, these results allow us to understand the mechanism of action at the molecular level of these short peptides. Our simulations suggest that mechanical inhomogeneities appear in the membrane, promoting membrane rupture when a threshold concentration of peptides adsorbed on the membrane is achieved. These results explain the high structural demand for these peptides to maintain a delicate balance between the affinity for the bilayer surface, a low peptide-peptide repulsion (in order to reach the threshold concentration), and an acceptable tendency to penetrate into the bilayer. This mechanism is different from those proposed for peptides with long amino acid sequences. Such information is very useful from the medicinal chemistry point of view for the design of new small antimicrobial peptides.


Assuntos
Anti-Infecciosos , Peptídeos Catiônicos Antimicrobianos , Peptídeos Catiônicos Antimicrobianos/farmacologia , Peptídeos Catiônicos Antimicrobianos/química , Anti-Infecciosos/farmacologia , Anti-Infecciosos/química , Sequência de Aminoácidos , Simulação de Dinâmica Molecular , Bicamadas Lipídicas/química
4.
Cell Mol Life Sci ; 79(9): 471, 2022 Aug 06.
Artigo em Inglês | MEDLINE | ID: mdl-35932293

RESUMO

In synapses that show signs of local apoptosis and mitochondrial stress and undergo neuro-immunological synapse pruning, an increase in the levels of the presynaptic protein, neuronal-specific septin-3 can be observed. Septin-3 is a member of the septin GTPase family with the ability to form multimers and contribute to the cytoskeleton. However, the function of septin-3 remains elusive. Here, we provide evidence that septin-3 is capable of binding the most-studied autophagy protein Atg8 homolog microtubule-associated protein 1 light chain 3B (LC3B), besides another homolog, GABA receptor-associated protein-like 2 (GABARAPL2). Moreover, we demonstrate that colocalization of septin-3 and LC3B increases upon chemical autophagy induction in primary neuronal cells. Septin-3 is accumulated in primary neurons upon autophagy enhancement or blockade, similar to autophagy proteins. Using electron microscopy, we also show that septin-3 localizes to LC3B positive membranes and can be found at mitochondria. However, colocalization results of septin-3 and the early mitophagy marker PTEN-induced kinase 1 (PINK1) do not support that binding of septin-3 to mitochondria is mitophagy related. We conclude that septin-3 correlates with synaptic/neuronal autophagy, binds Atg8 and localizes to autophagic membranes that can be enhanced with chemical autophagy induction. Based on our results, elevated septin-3 levels might indicate enhanced or impeded autophagy in neurons.


Assuntos
Autofagossomos , Septinas , Autofagossomos/metabolismo , Autofagia , Proteínas Associadas aos Microtúbulos/metabolismo , Mitofagia , Neurônios/metabolismo , Septinas/metabolismo
5.
Nucleic Acids Res ; 49(D1): D1102-D1112, 2021 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-33125057

RESUMO

Peptide-drug conjugates are organic molecules composed of (i) a small drug molecule, (ii) a peptide and (iii) a linker. The drug molecule is mandatory for the biological action, however, its efficacy can be enhanced by targeted delivery, which often also reduces unwanted side effects. For site-specificity the peptide part is mainly responsible. The linker attaches chemically the drug to the peptide, but it could also be biodegradable which ensures controlled liberation of the small drug. Despite the importance of the field, there is no public comprehensive database on these species. Herein we describe ConjuPepBD, a freely available, fully annotated and manually curated database of peptide drug conjugates. ConjuPepDB contains basic information about the entries, e.g. CAS number. Furthermore, it also implies their biomedical application and the type of chemical conjugation employed. It covers more than 1600 conjugates from ∼230 publications. The web-interface is user-friendly, intuitive, and useable on several devices, e.g. phones, tablets, PCs. The webpage allows the user to search for content using numerous criteria, chemical structure and a help page is also provided. Besides giving quick insight for newcomers, ConjuPepDB is hoped to be also helpful for researchers from various related fields. The database is accessible at: https://conjupepdb.ttk.hu/.


Assuntos
Bases de Dados Factuais , Preparações de Ação Retardada/química , Drogas em Investigação/química , Peptídeos/química , Medicamentos sob Prescrição/química , Anti-Infecciosos/química , Anti-Infecciosos/classificação , Anti-Infecciosos/uso terapêutico , Anti-Inflamatórios/química , Anti-Inflamatórios/classificação , Anti-Inflamatórios/uso terapêutico , Antineoplásicos/química , Antineoplásicos/classificação , Antineoplásicos/uso terapêutico , Preparações de Ação Retardada/classificação , Preparações de Ação Retardada/uso terapêutico , Drogas em Investigação/classificação , Drogas em Investigação/uso terapêutico , Humanos , Internet , Fármacos Neuroprotetores/química , Fármacos Neuroprotetores/classificação , Fármacos Neuroprotetores/uso terapêutico , Peptídeos/uso terapêutico , Medicamentos sob Prescrição/classificação , Medicamentos sob Prescrição/uso terapêutico , Software
6.
Proc Natl Acad Sci U S A ; 117(47): 29677-29683, 2020 11 24.
Artigo em Inglês | MEDLINE | ID: mdl-33168711

RESUMO

Yeast prions provide self-templating protein-based mechanisms of inheritance whose conformational changes lead to the acquisition of diverse new phenotypes. The best studied of these is the prion domain (NM) of Sup35, which forms an amyloid that can adopt several distinct conformations (strains) that confer distinct phenotypes when introduced into cells that do not carry the prion. Classic dyes, such as thioflavin T and Congo red, exhibit large increases in fluorescence when bound to amyloids, but these dyes are not sensitive to local structural differences that distinguish amyloid strains. Here we describe the use of Michler's hydrol blue (MHB) to investigate fibrils formed by the weak and strong prion fibrils of Sup35NM and find that MHB differentiates between these two polymorphs. Quantum mechanical time-dependent density functional theory (TDDFT) calculations indicate that the fluorescence properties of amyloid-bound MHB can be correlated to the change of binding site polarity and that a tyrosine to phenylalanine substitution at a binding site could be detected. Through the use of site-specific mutants, we demonstrate that MHB is a site-specific environmentally sensitive probe that can provide structural details about amyloid fibrils and their polymorphs.


Assuntos
Compostos de Anilina/química , Compostos Benzidrílicos/química , Príons/química , Amiloide/química , Sítios de Ligação , Vermelho Congo/química , Fluorescência , Proteínas Fúngicas/química , Fatores de Terminação de Peptídeos/química , Domínios Proteicos , Leveduras/química
7.
Q Rev Biophys ; 53: e5, 2020 03 02.
Artigo em Inglês | MEDLINE | ID: mdl-32115014

RESUMO

Here it is demonstrated how some anionic food additives commonly used in our diet, such as tartrazine (TZ), bind to DHVAR4, an antimicrobial peptide (AMP) derived from oral host defense peptides, resulting in significantly fostered toxic activity against both Gram-positive and Gram-negative bacteria, but not against mammalian cells. Biophysical studies on the DHVAR4-TZ interaction indicate that initially large, positively charged aggregates are formed, but in the presence of lipid bilayers, they rather associate with the membrane surface. In contrast to synergistic effects observed for mixed antibacterial compounds, this is a principally different mechanism, where TZ directly acts on the membrane-associated AMP promoting its biologically active helical conformation. Model vesicle studies show that compared to dye-free DHVAR4, peptide-TZ complexes are more prone to form H-bonds with the phosphate ester moiety of the bilayer head-group region resulting in more controlled bilayer fusion mechanism and concerted severe cell damage. AMPs are considered as promising compounds to combat formidable antibiotic-resistant bacterial infections; however, we know very little on their in vivo actions, especially on how they interact with other chemical agents. The current example illustrates how food dyes can modulate AMP activity, which is hoped to inspire improved therapies against microbial infections in the alimentary tract. Results also imply that the structure and function of natural AMPs could be manipulated by small compounds, which may also offer a new strategic concept for the future design of peptide-based antimicrobials.


Assuntos
Antibacterianos/química , Membrana Celular/metabolismo , Corantes de Alimentos/química , Histatinas/química , Peptídeos/química , Animais , Transporte Biológico/efeitos dos fármacos , Dicroísmo Circular , Escherichia coli/efeitos dos fármacos , Escherichia coli/metabolismo , Citometria de Fluxo , Células HeLa , Humanos , Bicamadas Lipídicas/química , Testes de Sensibilidade Microbiana , Microscopia de Fluorescência , Monócitos/efeitos dos fármacos , Fosfatos/química , Espectrofotometria , Espectroscopia de Infravermelho com Transformada de Fourier , Streptococcus pneumoniae/efeitos dos fármacos
8.
Nucleic Acids Res ; 48(D1): D1122-D1128, 2020 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-31686102

RESUMO

Foldamers are non-natural oligomers that mimic the structural behaviour of natural peptides, proteins and nucleotides by folding into a well-defined 3D conformation in solution. Since their first description about two decades ago, numerous studies have been undertaken dealing with the design, synthesis, characterization and application of foldamers. They have huge application potential as antimicrobial, anticancer and anti-HIV agents and in materials science. Despite their importance, there is no publicly available web resource providing comprehensive information on these compounds. Here we describe FoldamerDB, an open-source, fully annotated and manually curated database of peptidic foldamers. FoldamerDB holds the information about the sequence, structure and biological activities of the foldamer entries. It contains the information on over 1319 species and 1018 activities, collected from more than 160 research papers. The web-interface is designed to be clutter-free, user-friendly and it is compatible with devices of different screen sizes. The interface allows the user to search the database, browse and filter the foldamers using multiple criteria. It also offers a detailed help page to assist new users. FoldamerDB is hoped to bridge the gap in the freely available web-based resources on foldamers and will be of interest to diverse groups of scientists from chemists to biologists. The database can be accessed at http://foldamerdb.ttk.hu/.


Assuntos
Biologia Computacional/métodos , Bases de Dados de Proteínas , Peptídeos , Proteômica/métodos , Software , Peptídeos/química , Interface Usuário-Computador , Navegador
9.
Int J Mol Sci ; 22(16)2021 Aug 10.
Artigo em Inglês | MEDLINE | ID: mdl-34445303

RESUMO

Macromolecular associates, such as membraneless organelles or lipid-protein assemblies, provide a hydrophobic environment, i.e., a liquid protein phase (LP), where folding preferences can be drastically altered. LP as well as the associated phase change from water (W) is an intriguing phenomenon related to numerous biological processes and also possesses potential in nanotechnological applications. However, the energetic effects of a hydrophobic yet water-containing environment on protein folding are poorly understood. Here, we focus on small ß-sheets, the key motifs of proteins, undergoing structural changes in liquid-liquid phase separation (LLPS) and also model the mechanism of energy-coupled unfolding, e.g., in proteases, during W → LP transition. Due to the importance of the accurate description for hydrogen bonding patterns, the employed models were studied by using quantum mechanical calculations. The results demonstrate that unfolding is energetically less favored in LP by ~0.3-0.5 kcal·mol-1 per residue in which the difference further increased by the presence of explicit structural water molecules, where the folded state was preferred by ~1.2-2.3 kcal·mol-1 per residue relative to that in W. Energetics at the LP/W interfaces was also addressed by theoretical isodesmic reactions. While the models predict folded state preference in LP, the unfolding from LP to W renders the process highly favorable since the unfolded end state has >1 kcal·mol-1 per residue excess stabilization.


Assuntos
Transição de Fase/efeitos dos fármacos , Conformação Proteica em Folha beta/efeitos dos fármacos , Água/farmacologia , Motivos de Aminoácidos/efeitos dos fármacos , Fracionamento Químico/métodos , Simulação por Computador , Interações Hidrofóbicas e Hidrofílicas/efeitos dos fármacos , Cinética , Substâncias Macromoleculares/química , Modelos Moleculares , Conformação Proteica/efeitos dos fármacos , Dobramento de Proteína/efeitos dos fármacos , Estabilidade Proteica/efeitos dos fármacos , Teoria Quântica , Viscosidade , Água/química
10.
Int J Mol Sci ; 22(16)2021 Aug 10.
Artigo em Inglês | MEDLINE | ID: mdl-34445319

RESUMO

Anticancer peptides (ACPs) could potentially offer many advantages over other cancer therapies. ACPs often target cell membranes, where their surface mechanism is coupled to a conformational change into helical structures. However, details on their binding are still unclear, which would be crucial to reach progress in connecting structural aspects to ACP action and to therapeutic developments. Here we investigated natural helical ACPs, Lasioglossin LL-III, Macropin 1, Temporin-La, FK-16, and LL-37, on model liposomes, and also on extracellular vesicles (EVs), with an outer leaflet composition similar to cancer cells. The combined simulations and experiments identified three distinct binding modes to the membranes. Firstly, a highly helical structure, lying mainly on the membrane surface; secondly, a similar, yet only partially helical structure with disordered regions; and thirdly, a helical monomeric form with a non-inserted perpendicular orientation relative to the membrane surface. The latter allows large swings of the helix while the N-terminal is anchored to the headgroup region. These results indicate that subtle differences in sequence and charge can result in altered binding modes. The first two modes could be part of the well-known carpet model mechanism, whereas the newly identified third mode could be an intermediate state, existing prior to membrane insertion.


Assuntos
Peptídeos Catiônicos Antimicrobianos/química , Antineoplásicos/química , Venenos de Abelha/química , Membrana Celular/metabolismo , Motivos de Aminoácidos , Peptídeos Catiônicos Antimicrobianos/metabolismo , Antineoplásicos/metabolismo , Venenos de Abelha/metabolismo , Vesículas Extracelulares/metabolismo , Humanos , Ligação Proteica , Domínios Proteicos , Catelicidinas
11.
Biochem Biophys Res Commun ; 526(3): 780-785, 2020 06 04.
Artigo em Inglês | MEDLINE | ID: mdl-32265033

RESUMO

A growing number of evidence shows that human-associated microbiota is an important contributor in health and disease. However, much of the complexity of host-microbiota interaction remains to be elucidated both at cellular and molecular levels. Siderophores are chemically diverse, ferric-specific chelators synthesized and secreted by microbes to secure their iron acquisition. The host defense peptide LL-37 is ubiquitously produced at epithelial surfaces modulating microbial communities and suppressing pathogenic strains. The present work demonstrates that LL-37 binds tightly siderocalin-resistant stealth siderophores which are important contributors to the virulence of several pathogens. As indicated by circular dichroism spectroscopic experiments, addition of aerobactin and rhizoferrin increases the membrane active α-helical conformation of the partially folded peptide. The cationic nature of LL-37 (+6 net charge at pH 7.4) and the multiple carboxylate groups present in siderophores refer to the dominant contribution of electrostatic interactions in the stabilization of peptide-chelator adducts. It is proposed that aside siderocalin proteins, LL-37 may be a complementary, less specific component of the siderophore scavenging repertoire of the innate immune system.


Assuntos
Peptídeos Catiônicos Antimicrobianos/farmacologia , Compostos Férricos/farmacologia , Ácidos Hidroxâmicos/farmacologia , Lipocalina-2/metabolismo , Sideróforos/metabolismo , Transporte Biológico , Quelantes/química , Humanos , Microbiota/efeitos dos fármacos , Modelos Moleculares , Ligação Proteica , Conformação Proteica , Eletricidade Estática , Virulência , Catelicidinas
12.
Langmuir ; 36(6): 1615-1622, 2020 02 18.
Artigo em Inglês | MEDLINE | ID: mdl-31967838

RESUMO

Body fluids flow all over the body and affect the biological processes at biointerfaces. To simulate such a case, sum frequency generation (SFG) vibrational spectroscopy and a self-designed microfluidic chip were combined together to investigate the interaction between a pH-responsive polymeric drug, poly(α-propylacrylic acid) (PPAAc), and the model cell membranes in different liquid environments. By examining the SFG spectra under the static and flowing conditions, the drug-membrane interaction was revealed comprehensively. The interfacial water layer was screened as the key factor affecting the drug-membrane interaction. The interfacial water layer can prevent the side propyl groups on PPAAc from inserting into the model cell membrane but would be disrupted by numerous ions in buffer solutions. Without flowing, at pH 6.6, the interaction between PPAAc and the model cell membrane was strongest; with flowing, at pH 5.8, the interaction was strongest. Flowing was proven to substantially affect the interaction between PPAAc and the model cell membranes, suggesting that the fluid environment was of key significance for biointerfaces. This work demonstrated that, by combining SFG and microfluidics, new information about the molecular-level interaction between macromolecules and the model cell membranes can be acquired, which cannot be obtained by collecting the normal static SFG spectra.

13.
Org Biomol Chem ; 18(10): 1957-1967, 2020 03 14.
Artigo em Inglês | MEDLINE | ID: mdl-32101244

RESUMO

1,4- and 1,5-Disubstituted triazole amino acid monomers have gained increasing interest among peptidic foldamers, as they are easily prepared via Cu- and Ru-catalyzed click reactions, with the potential for side chain variation. While the latter is key to their applicability, the synthesis and structural properties of the chiral mono- or disubstituted triazole amino acids have only been partially addressed. We here present the synthesis of all eight possible chiral derivatives of a triazole monomer prepared via a ruthenium-catalyzed azide alkyne cycloaddition (RuAAC). To evaluate the conformational properties of the individual building units, a systematic quantum chemical study was performed on all monomers, indicating their capacity to form several low energy conformers. This feature may be used to effect structural diversity when the monomers are inserted into various peptide sequences. We envisage that these results will facilitate new applications for these artificial oligomeric compounds in diverse areas, ranging from pharmaceutics to biotechnology.


Assuntos
Peptidomiméticos/síntese química , Triazóis/síntese química , Alcinos/química , Azidas/química , Química Click , Reação de Cicloadição , Modelos Moleculares , Polimerização , Polímeros/síntese química , Teoria Quântica , Estereoisomerismo , Termodinâmica
14.
Q Rev Biophys ; 50: e11, 2017 01.
Artigo em Inglês | MEDLINE | ID: mdl-29233223

RESUMO

We have discovered a well-defined extended conformation of double-stranded DNA, which we call Σ-DNA, using laser-tweezers force-spectroscopy experiments. At a transition force corresponding to free energy change ΔG = 1·57 ± 0·12 kcal (mol base pair)-1 60 or 122 base-pair long synthetic GC-rich sequences, when pulled by the 3'-3' strands, undergo a sharp transition to the 1·52 ± 0·04 times longer Σ-DNA. Intriguingly, the same degree of extension is also found in DNA complexes with recombinase proteins, such as bacterial RecA and eukaryotic Rad51. Despite vital importance to all biological organisms for survival, genome maintenance and evolution, the recombination reaction is not yet understood at atomic level. We here propose that the structural distortion represented by Σ-DNA, which is thus physically inherent to the nucleic acid, is related to how recombination proteins mediate recognition of sequence homology and execute strand exchange. Our hypothesis is that a homogeneously stretched DNA undergoes a 'disproportionation' into an inhomogeneous Σ-form consisting of triplets of locally B-like perpendicularly stacked bases. This structure may ensure improved fidelity of base-pair recognition and promote rejection in case of mismatch during homologous recombination reaction. Because a triplet is the length of a gene codon, we speculate that the structural physics of nucleic acids may have biased the evolution of recombinase proteins to exploit triplet base stacks and also the genetic code.


Assuntos
DNA/química , Fenômenos Mecânicos , Conformação de Ácido Nucleico , Fenômenos Biomecânicos , Modelos Moleculares
15.
Chembiochem ; 20(12): 1578-1590, 2019 06 14.
Artigo em Inglês | MEDLINE | ID: mdl-30720915

RESUMO

Antimicrobial peptides (AMPs) kill bacteria by targeting their membranes through various mechanisms involving peptide assembly, often coupled with disorder-to-order structural transition. However, for several AMPs, similar conformational changes in cases in which small organic compounds of both endogenous and exogenous origin have induced folded peptide conformations have recently been reported. Thus, the function of AMPs and of natural host defence peptides can be significantly affected by the local complex molecular environment in vivo; nonetheless, this area is hardly explored. To address the relevance of such interactions with regard to structure and function, we have tested the effects of the therapeutic drug suramin on the membrane activity and antibacterial efficiency of CM15, a potent hybrid AMP. The results provided insight into a dynamic system in which peptide interaction with lipid bilayers is interfered with by the competitive binding of CM15 to suramin, resulting in an equilibrium dependent on peptide-to-drug ratio and vesicle surface charge. In vitro bacterial tests showed that when CM15⋅suramin complex formation dominates over membrane binding, antimicrobial activity is abolished. On the basis of this case study, it is proposed that small-molecule secondary structure regulators can modify AMP function and that this should be considered and could potentially be exploited in future development of AMP-based antimicrobial agents.


Assuntos
Anti-Infecciosos , Peptídeos Catiônicos Antimicrobianos , Suramina , Anti-Infecciosos/química , Anti-Infecciosos/farmacologia , Peptídeos Catiônicos Antimicrobianos/química , Peptídeos Catiônicos Antimicrobianos/farmacologia , Células Cultivadas , Dicroísmo Circular/métodos , Escherichia coli , Humanos , Bicamadas Lipídicas/química , Estrutura Secundária de Proteína , Suramina/química , Suramina/farmacologia
16.
Langmuir ; 35(39): 12831-12838, 2019 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-31475518

RESUMO

The interfacial hydrolysis of phospholipids catalyzed by phospholipase A1 (PLA1) was studied via sum frequency generation (SFG) vibrational spectroscopy and fluorescence microscopy. Both monolayer and bilayer setups were used to confirm the hydrolysis mechanism. During the hydrolysis, lysophospholipids, one of the hydrolysis products, were desorbed from the interface into the solution, while the other products, fatty acids, self-organized and accumulated with PLA1 at the interface to form the PLA1-induced regions, which can serve as nonspecific binding domains for proteins and thus lead to human vascular diseases. This experimental study provides the essential information on revealing the interfacial biochemical process related to the metabolism of the lipids, which is one of the basic building blocks for cells.


Assuntos
Biocatálise , Microscopia de Fluorescência , Fosfolipases A1/metabolismo , Fosfolipídeos/metabolismo , Hidrólise , Bicamadas Lipídicas/química , Bicamadas Lipídicas/metabolismo , Modelos Moleculares , Fosfolipases A1/química , Conformação Proteica , Espectrometria de Fluorescência
17.
Phys Chem Chem Phys ; 21(20): 10644-10659, 2019 May 28.
Artigo em Inglês | MEDLINE | ID: mdl-31080973

RESUMO

Dynamic increase of resistant bacterial infectious diseases continuously requires development of novel compounds against them. The molecular level understanding of the mechanism and interactions of natural host-defense peptides or antimicrobial peptides (AMPs) is an important step towards rational design and development of compounds inspired by their function. A particular set of these peptides have disordered structure, the ordering of which may modify their antimicrobial properties. Recent experiments demonstrate that such conformational transitions of AMPs could be mediated by the presence of small organic compounds, such as approved drug molecules. However, the molecular mechanisms underlying these structural changes are unclear. In this study, we apply molecular docking and molecular dynamics-based approaches to rigorously analyze the interactions between the drug suramin and the AMP CM15, a synthetic unstructured hybrid peptide. We characterize the energetic properties of putative CM15-suramin complexes revealing particular impacts of CM15 residues as well as the parts of suramin on these interactions. We find that α-helical content of the peptide is increased in the presence of suramin, which is in agreement with the experimental data. Kinetics analysis from canonical molecular dynamics and metadynamics simulations suggest that the effect of suramin does not promote the formation of α-helix but rather results from its ability to stabilize the α-helical population in the conformational pool of the peptide. Potentially, understanding the physico-chemical basis underlying the interactions between drug molecules and disordered AMPs will prove useful in strategies for antimicrobial compound development. Further on, the given computational protocol for the analysis of such flexible systems provide a basis for future theoretical investigation of similar biomolecular complexes.


Assuntos
Peptídeos Catiônicos Antimicrobianos/química , Simulação por Computador , Modelos Químicos , Suramina/química , Anti-Infecciosos/química , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular
18.
Chembiochem ; 19(6): 545-551, 2018 03 16.
Artigo em Inglês | MEDLINE | ID: mdl-29237098

RESUMO

Extracellular vesicles (EVs) are currently in scientific focus, as they have great potential to revolutionize the diagnosis and therapy of various diseases. However, numerous aspects of these species are still poorly understood, and thus, additional insight into their molecular-level properties, membrane-protein interactions, and membrane rigidity is still needed. We here demonstrate the use of red-blood-cell-derived EVs (REVs) that polarized light spectroscopy techniques, linear and circular dichroism, can provide molecular-level structural information on these systems. Flow-linear dichroism (flow-LD) measurements show that EVs can be oriented by shear force and indicate that hemoglobin molecules are associated to the lipid bilayer in freshly released REVs. During storage, this interaction ceases; this is coupled to major protein conformational changes relative to the initial state. Further on, the degree of orientation gives insight into vesicle rigidity, which decreases in time parallel to changes in protein conformation. Overall, we propose that both linear dichroism and circular dichroism spectroscopy can provide simple, rapid, yet efficient ways to track changes in the membrane-protein interactions of EV components at the molecular level, which may also give insight into processes occurring during vesiculation.


Assuntos
Vesículas Extracelulares/metabolismo , Luz , Fosfatidilcolinas/metabolismo , Dicroísmo Circular , Eritrócitos/química , Eritrócitos/metabolismo , Vesículas Extracelulares/química , Humanos , Lipossomos/química , Lipossomos/metabolismo , Substâncias Macromoleculares/química , Substâncias Macromoleculares/metabolismo , Microscopia de Polarização , Fosfatidilcolinas/química
19.
Chem Rev ; 116(23): 14726-14768, 2016 Dec 14.
Artigo em Inglês | MEDLINE | ID: mdl-27960271

RESUMO

The ruthenium-catalyzed azide alkyne cycloaddition (RuAAC) affords 1,5-disubstituted 1,2,3-triazoles in one step and complements the more established copper-catalyzed reaction providing the 1,4-isomer. The RuAAC reaction has quickly found its way into the organic chemistry toolbox and found applications in many different areas, such as medicinal chemistry, polymer synthesis, organocatalysis, supramolecular chemistry, and the construction of electronic devices. This Review discusses the mechanism, scope, and applications of the RuAAC reaction, covering the literature from the last 10 years.

20.
Chirality ; 30(2): 195-205, 2018 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-29110341

RESUMO

The interaction of protoporphyrin compounds of human origin with the major bee venom component melittin (26 a.a., Z +6) and its hybrid derivative (CM15, 15 a.a., Z +6) were studied by a combination of various spectroscopic methods. Throughout a two-state, concentration-dependent process, hemin and its metabolites (biliverdin, bilirubin, bilirubin ditaurate) increase the parallel ß-sheet content of the natively unfolded melittin, suggesting the oligomerization of the peptide chains. In contrast, α-helix promoting effect was observed with the also disordered but more cationic CM15. According to fluorescence quenching experiments, the sole Trp residue of melittin is the key player during the binding, in the vicinity of which the first pigment molecule is accommodated presumably making indole-porphyrin π-π stacking interaction. As circular dichroism titration data suggest, cooperative association of additional ligands subsequently occurs, resulting in multimeric complexes with an apparent dissociation constant ranged from 20 to 65 µM. Spectroscopic measurements conducted with the bilirubin catabolite urobilin and stercobilin refer to the requirement of intact dipyrrinone moieties for inducing secondary structure transformations. The binding topography of porphyrin rings on a model parallel ß-sheet motif was evaluated by absorption spectroscopy and computational modeling showing a slipped-cofacial binding mode responsible for the red shift and hypochromism of the Soret band. Our results may aid to recognize porphyrin-responsive binding motifs of biologically relevant, intrinsically disordered peptides and proteins, where transient conformations play a vital role in their functions.


Assuntos
Anti-Infecciosos/química , Pigmentos Biliares/farmacologia , Hemina/farmacologia , Proteínas Intrinsicamente Desordenadas/química , Peptídeos Catiônicos Antimicrobianos/química , Meliteno/química , Estrutura Secundária de Proteína/efeitos dos fármacos
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