Molecular Dynamics Simulations to Study Drug Delivery Systems

Molecular dynamics simulation is a very powerful tool to understand biomolecular processes. In this chapter, we go over different applications of this methodology to drug delivery systems (DDS) carried out in the group. DDS—a formulation or a device that enables the introduction of a therapeutic substance in the body and improves its efficacy and safety by controlling the rate, time, and place of release of drugs—are an important component of drug development and therapeutics. Biocompatible nanoparticles are materials in the nanoscale that emerged as important players, improving efficacy of approved drugs, for example. The molecular understanding of the encapsulation process could be very helpful to guide the nanocarrier for a specific system. Here we discuss different applications of drug delivery carriers, such as liposomes, polymeric micelles, and polymersomes using atomistic and coarse grain (CG) molecular dynamics simulations

Differential Stability of Aurein 1.2 Pores in Model Membranes of Two Probiotic Strains

Aurein 1.2 is an antimicrobial peptide from the skin secretion of an Australian frog. In the previous experimental work, we reported a differential action of aurein 1.2 on two probiotic strains Lactobacillus delbrueckii subsp. bulgaricus (CIDCA 331) and Lactobacillus delbrueckii subsp. lactis (CIDCA 133). The differences found were attributed to the bilayer compositions. Cell cultures and CIDCA 331-derived liposomes showed higher susceptibility than the ones derived from the CIDCA 133 strain, leading to content leakage and structural disruption. Here, we used molecular dynamics simulations to explore these systems at the atomistic level. We hypothesize that if the antimicrobial peptides organized themselves to form a pore, it will be more stable in membranes that emulate the CIDCA 331 strain than in those of the CIDCA 133 strain. To test this hypothesis, we simulated preassembled aurein 1.2 pores embedded into bilayer models that emulate the two probiotic strains. It was found that the general behavior of the systems depends on the composition of the membrane rather than the preassemble system characteristics. Overall, it was observed that aurein 1.2 pores are more stable in the CIDCA 331 model membranes. This fact coincides with the high susceptibility of this strain against antimicrobial peptide. In contrast, in the case of the CIDCA 133 model membranes, peptides migrate to the water-lipid interphase, the pore shrinks, and the transport of water through the pore is reduced. The tendency of glycolipids to make hydrogen bonds with peptides destabilizes the pore structures. This feature is observed to a lesser extent in CIDCA 331 due to the presence of anionic lipids. Glycolipid transverse diffusion (flip-flop) between monolayers occurs in the pore surface region in all the cases considered. These findings expand our understanding of the antimicrobial peptide resistance properties of probiotic strains.Fil: Balatti, Galo Ezequiel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Física de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Física de Buenos Aires; ArgentinaFil: Domene, Carmen. University of Bath; Reino UnidoFil: Martini, María Florencia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Química y Metabolismo del Fármaco. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Química y Metabolismo del Fármaco; ArgentinaFil: Pickholz, Mónica Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Física de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Física de Buenos Aires; Argentin

A global review on short peptides: frontiers and perspectives

Peptides are fragments of proteins that carry out biological functions. They act as signaling entities via all domains of life and interfere with protein-protein interactions, which are indispensable in bio-processes. Short peptides include fundamental molecular information for a prelude to the symphony of life. They have aroused considerable interest due to their unique features and great promise in innovative bio-therapies. This work focusing on the current state-of-the-art short peptide-based therapeutical developments is the first global review written by researchers from all continents, as a celebration of 100 years of peptide therapeutics since the commencement of insulin therapy in the 1920s. Peptide “drugs” initially played only the role of hormone analogs to balance disorders. Nowadays, they achieve numerous biomedical tasks, can cross membranes, or reach intracellular targets. The role of peptides in bio-processes can hardly be mimicked by other chemical substances. The article is divided into independent sections, which are related to either the progress in short peptide-based theranostics or the problems posing challenge to bio-medicine. In particular, the SWOT analysis of short peptides, their relevance in therapies of diverse diseases, improvements in (bio)synthesis platforms, advanced nano-supramolecular technologies, aptamers, altered peptide ligands and in silico methodologies to overcome peptide limitations, modern smart bio-functional materials, vaccines, and drug/gene-targeted delivery systems are discussed

Macromoléculas conjugadas : um estudo teórico de propriedades de interesse para o desenvolvimento de novos materiais

Orientador: Maria Cristina dos SantosTese (doutorado) - Universidade Estadual de Campinas, Instituto de Fisica "Gleb Wataghin"Resumo: Neste trabalho de tese investigamos teoricamente três sistemas conjugados diferentes. O primeiro destes problemas consistiu no estudo de uma molécula orgânica de tipo "push-pull", Q3CnQ, que apresentaria propriedades retificadoras. Esta molécula possi duas estruturas de ressonância principais, uma neutra e a outra de carga separada (switteriônica). Estudamos o mecanismo de transferência de carga intramolecular que leva ao comportamento retificador do sistema, e as conformações adotadas pela molécula em diferentes ambientes químicos mediante métodos semi-empíricos baseados na teoria Hartree-Fock (AM1,AM1/campo elétrico, AM1/CI, AM1/solvente). No segundo problema estudamos as interações entre pares de oligômeros de tiofeno em funcão da carga e do aumento do tamanho da cadeia mediante cálculos ab initio baseados na teoria Hartree-Fock, avaliando os efeitos de correção eletrônica. Investigamos os principais mecanismos responsáveis pela coesão entre as moléculas para arranjos paralelos e antiparalelos de bitiofenos, tetiofenos e quatertiofenos. Para meléculas neutras só são observados estados ligados se a correlação eletrônica é explicitamente considerada, resultado em energias de ligação na faixa de 0.32 a 0.70 eV. Pares formados por dois radicais cátions foram reportados na literatura em condições de baixas temperaturas e altas concentrações e foram denominados dímeros p . As entalpias de dimerização calculadas neste trabalho são da ordem de grandeza das experimentais e seguem a mesma têndencia com o aumento do tamanho da cadeia. Os dímeros formados por um dicátion e uma molécula neutra possuem uma energia de ligação da ordem de 1 e V. Estes dímeros não foram reportados na literatura. A partir dos resultados deste trabalho pode-se pensar que este fato se deve a que estes dímeros são instaveis com respeito a pares formados por dois radicais cátion. Os espectros de absorção dos pares foram simulados e comparados com dados da literatura. No último trabalho estudamos a estrutura eletrônica de diferentes aglomerados formados por carbono e nitrogênio utilizando o Hamiltoniano Efeitvo de Valência (VEH). Estudamos aglomerados de grafite com átomos de nitrogênio substituidos aleatoriamente para diferentes concentrações [N]/[C] ( previamente otimizados mediante métodos semi-empíricos). Obtivemos ainda as estrutura eletrônica de aglomerados representativos das fases a e b cristalinas preditas para C3N4. Os calculos foram comparados com resultados experimentais e identificados os diferentes picos observados. Discutimos o ambiente quimico do carbono em função da concentração relativa [N]/[C]Abstract: In this work we have investigated theoretically three different conjugated systems. Firstly, we have studied an organic push-pull type molecule, Q3CNQ, which presents rectifying properties. This molecule has two main resonance structures, one neutral and the other with separated charges (zwitterionic). We have studied the intramolecula5r charge transfer, which leads to the rectifying behavior of the system, as well as the conformations adopted by the molecule in different chemical environments. The calculations were carried out using semi-empirical methods based on the Hartree-Fock theory (AM1,AM1/eletric field, AM1/CI, AM1/solvent). The second problem concerns the study of the interaction between oligothiophene pairs as a function of both the net charge of the molecules and the number of thiophene rings. We employed ab initio methods based on the Hartree-Fock t heory, and correlations effects were evaluated by th second order Moller-Plesset perturbation theory. We have investigated the mechanisms responsible for the cohesion between the molecules for both parallel and anti-parallel arrangements of bithiophenes, terthiophenes and quaterthiophenes. For neutral molecules we have found bound states only if the electronic correlation is explicity considered, leading to binding energies in the range 0.32-0.70 eV. Pairs formed by two cation radicals were reported in the literature for low temperature and high concentration conditions, and have been called the p- dimers. The dimenrization enthalpies calculated in this work are of the same order of maqnitude of the experimental ones, and follow the same trend with increasing chain lenth. the dimers formed by a dication and a neutral molecule present a binding energy of the order of 1 e V. These dimmers were not yet reported in the literature. A reason for this could be that these dimmers ara unstable with respect to the pairs formed by two cation radicals. The absorption spectra of the pairs were simulated through the semi-empirical ZINDO/CI technique and compared with experimental data from the literature. Finally, in the last part of this work we have studied the electronic structure of different clusters formed by carbon and nitrogen, using the Valence Effective Hamiltonian (VEH) pseudo-potencial technique. We have studies graphite clusters with randomly substituted nitrogen atoms, for different [N]/[C] concentrations (previously optimised by means of semi-empirical methods), as well as clusters that are representative of the predicted crystalline structures a and b - C3N4. The calculations were compared with the experimental UPS and XPS spectra. The identification of the serveral features present in the experimental density-of-states and nitrogen core-level spectra was done. We have discussed the carbion chemical environments as function of the relative concentrations [N]/[C]DoutoradoFísicaDoutor em Ciência

Preferential location of prilocaine and etidocaine in phospholipid bilayers: A molecular dynamics study

In this work, we report a 20-ns constant pressure molecular dynamics simulation of the uncharged form of two amino-amide local anesthetics (LA). etidocaine and prilocaine, present at 1:3 LA:lipid, molar ratio inside the membrane, in the hydrated liquid crystal bilayer phase of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC). Both LAs induced lateral expansion and a concomitant contraction in the bilayer thickness. A decrease in the acyl chain segment order parameter, -S(CD), compared to neat bilayers, was also observed. Besides, both LA molecules got preferentially located in the hydrophobic acyl chains region, with a maximum probability at similar to 12 and similar to 10 angstrom from the center of the bilayer for prilocaine and etidocaine, respectively. (C) 2009 Elsevier B.V. All rights reserved.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP

Distribution of neutral prilocaine in a phospholipid bilayer: Insights from molecular dynamics simulations

In this work, we report a 20-ns constant pressure molecular dynamics simulation of prilocaine (PLC), in amine-amide local anesthetic, in a hydrated liquid crystal bilayer of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine. The partition of PLC induces the lateral expansion of the bilayer and a concomitant contraction in its thickness. PLC molecules are preferentially found in the hydrophobic acyl chains region, with a maximum probability at similar to 12 angstrom from the center of the bilayer (between the C(4) and C(5) methylene groups). A decrease in the acyl chain segmental order parameter, vertical bar S-CD vertical bar, compared to neat bilayers, is found, in good agreement with experimental H-2-NMR studies. The decrease in vertical bar S-CD vertical bar induced by PLC is attributed to a larger accessible volume per lipid in the acyl chain region. (C) 2008 Wiley Periodicals, Inc

Combining nuclear magnetic resonance with molecular dynamics simulations to address sumatriptan interaction with model membranes

The goal of this work is to obtain a complete map on the interactions between sumatriptan, an amphiphilic ionizable anti-migraine drug, with lipid bilayers. To this end, we combined two physico-chemical techniques-nuclear magnetic resonance and molecular dynamics simulations - to obtain a detailed picture at different pH values. Both approaches were used considering the strength and constraints of each one. NMR experiments were performed at pH 7.4 where at least 95% of the drug molecules are in their protonated state. From NMR, sumatriptan shows partition on the interfacial region of model membranes (near the head groups and intercalating between adjacent lipids), inducing changes in chemical environment and affecting lipid dynamics of liposomes, in a dose dependent manner. Due to the experimental instability of lipid bilayers at high pH, we took advantage of the molecular dynamics power to emulate different pH values, to simulate sumatriptan in bilayers including at fully uncharged state. Simulations show that the neutral species have preferential orientation within the bilayer interface while the distribution of protonated drugs is independent on the initial conditions. In summary, several properties depicted the interfacial partition of the anti-migraine drug at the water-lipid interface at different conditions. Both techniques were found complementary to shed light on the structural and dynamics of sumatriptan-lipid bilayer interactions225CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQ1420869/2016-6The authors would like to acknowledge IQUIMEFA (CONICET-UBA) for NMR facility; LF for performing, processing and interpretation of NMR experiments; LAFEDAR for the donation of Sumatriptan Succinate; CONICET and Conselho Nacional Pesquisa (CNPq/Brazil, #1420869/2016-6) for the financial suppor

Non-inclusion complexes between riboflavin and cyclodextrins

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Objectives To investigate the molecular interaction between beta-cyclodextrin (beta CD) or hydroxypropyl-beta-cyclodextrin (HP beta CD) and riboflavin (RF), and to test the anticancer potential of these formulations. Methods The physicochemical characterization of the association between RF and CDs was performed by UV-vis absorption, fluorescence, differential scanning calorimetry and NMR techniques. Molecular dynamics simulation was used to shed light on the mechanism of interaction of RF and CDs. Additionally, in-vitro cell culture tests were performed to evaluate the cytotoxicity of the RFCD complexes against prostate cancer cells. Key findings Neither beta CD nor HP beta CD led to substantial changes in the physicochemical properties of RF (with the exception of solubility). Additionally, rotating frame Overhauser effect spectroscopy experiments detected no spatial correlations between hydrogens from the internal cavity of CDs and RF, while molecular dynamics simulations revealed out-of-ring RFCD interactions. Notwithstanding, both RF beta CD and RFHP beta CD complexes were cytotoxic to PC3 prostate cancer cells. Conclusions The interaction between RF and either beta CD or HP beta CD, at low concentrations, seems to be made through hydrogen bonding between the flavonoid and the external rim of both CDs. Regardless of the mechanism of complexation, our findings indicate that RFCD complexes significantly increase RF solubility and potentiate its antitumour effect.646832842Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)National Science Research Council (CONICET, Argentina)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq