Controlled release of doxorubicin from the drug delivery formulation composed of single-walled carbon nanotubes and Congo red : a molecular dynamics study and dynamic light scattering analysis

The controlled delivery and release of drug molecules at specific targets increases the therapeutic efficacy of treatment. This paper presents a triple complex which is a new potential drug delivery system. Triple complex contains single-walled carbon nanotubes, Congo red, and doxorubicin. Nanotubes are built of a folded graphene layer providing a large surface for binding Congo red via “face-to-face” stacking which markedly increases the binding capacity of the carrier. Congo red is a compound that self-associates to form supramolecular ribbon-like structures, which are able to bind some drugs by intercalation. The nanotube–Congo red complex can bind the model drug doxorubicin. Thus, a new triple carrier system was obtained. The aim of this paper is to present studies on the controlled release of a model anticancer drug from a triple carrier system through pH changes. The specific aim of the study was to model the structure of the obtained experimental systems and to compare the changes in the average energy of interaction between its components induced by pH changes. The studies also aimed to compare the intensity of pH-dependent changes in hydrodynamic diameters of individual components of the triple carrier system. The effect of pH changes on the stability of the analyzed systems was examined using the molecular modeling method and dynamic light scattering. The decrease in pH influenced the structure and stability of the analyzed triple systems and ensured efficient drug release. The changes in hydrodynamic diameters of the obtained fractions were examined with the use of dynamic light scattering and were confirmed by computer simulation methods. The formulation presented in this paper shows potential for a therapeutic application owing to its high drug binding capacity and pH-dependent release. This ensures prolonged local action of the drug. The results reveal that the studied complex fulfills the basic requirements for its potential use as drug carrier, thus reducing side effects and enhancing pharmacological efficacy of drugs

Ionizable lipids penetrate phospholipid bilayers with high phase transition temperatures: perspectives from free energy calculations

The efficacies of modern gene-therapies strongly depend on their contents. At the same time the most potent formulations might not contain the best compounds. In this work we investigated the effect of phospholipids and their saturation on the binding ability of (6Z,9Z,28Z,31Z)-heptatriacont-6,9,28,31-tetraene-19-yl 4-(dimethylamino) butanoate (DLin-MC3-DMA) to model membranes at the neutral pH. We discovered that DLin-MC3-DMA has affinity to the most saturated monocomponent lipid bilayer 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and an aversion to the unsaturated one 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC). The preference to a certain membrane was also well-correlated to the phase transition temperatures of phospholipid bilayers, and to their structural and dynamical properties. Additionally, in the case of the presence of DLin-MC3-DMA in the membrane with DOPC the ionizable lipid penetrated it, which indicates possible synergistic effects. Comparisons with other ionizable lipids were performed using a model lipid bilayer of 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC). Particularly, the lipids heptadecan-9-yl 8-[2-hydroxyethyl-(6-oxo-6-undecoxyhexyl)amino]octanoate (SM-102) and [(4-hydroxybutyl) azanediyl] di(hexane-6,1-diyl) bis(2-hexyldecanoate) (ALC-0315) from modern mRNA-vaccines against COVID-19 were investigated and force fields parameters were derived for those new lipids. It was discovered that ALC-0315 binds strongest to the membrane, while DLin-MC3-DMA is not able to reside in the bilayer center. The ability to penetrate the membrane POPC by SM-102 and ALC-0315 can be related to their saturation, comparing to DLin-MC3-DMA

On the dynamics of two efficient malaria vectors of the Afrotropical region: Anopheles gambiae s.s. and Anopheles arabiensis

Weather and climate are only some of the factors influencing the dynamics of malaria. With the ongoing debate on the consequences of climate change, there is a need for models which are designed to address these questions. Historically, models have focused on the theoretical principles of eradication, with less emphasis on a changing environment. To estimate the potential impact of climate change on malaria, we need new models which consider a wider range of environmental variables. In this thesis, we point at some factors which are important to robustly project the influence of climate and weather on malaria. These factors are described using a mathematical model which focus on the weather sensitive parts of malaria transmission; the mosquitoes and the parasites. Mosquitoes transmitting malaria belong to the genus Anopheles. There are about 460 known anophelines, where 41 are considered to be dominant vectors of malaria. Each of these species have its own life history, and consequently weather and climate influence each species differently. In Africa, the public health impact of malaria is devastating, despite variable transmission. The most efficient mosquitoes are found in this continent: among them Anopehels gambiae sensu stricto and Anopheles arabiensis, which are considered to be of major importance. In this thesis (Paper I) we describe a dynamical model which include these two species. Based on a literature review, we formulate a model which allows weather to influence each of the two species according to their life history. They compete over puddles, important for reproduction; An. gambiae s.s. mainly feed on humans opposed to An. arabiensis which feed on cattle and humans; they are allowed to disperse, meaning new ares can be occupied by the species; and as they become older, the daily probability of survival changes. Many of these factors are not important in a short time perspective. But, since climate change is slow process compared to the life of a singe mosquito, there is a need for additional complexity to study how a slowly changing environment influence the population dynamics of these malaria vectors. To have confidence the model is realistic in the current climate we validated the model in paper II. To date, we constructed the most extensive database on the occurrence of the two mosquitoes. These data were used to validate the model described in paper I. We concluded the mosquito model produced comparable or better results than existing predictions of the two species under current climate. An. arabiensis feed on humans and cattle. Since the density and distribution of those are not static, but are changing over time, and the distribution of An. arabiensis is highly dependent on the density of cattle, there is a need to; 1. Document historical changes; 2. Understand how they are influenced by the environment. In paper III we reconstruct the cattle distribution and density in the 1960s, and show how climate variability influence the national cattle holdings. While climate variability has a minor influence in many countries, we also find variations in the climate can explain more than 40% of the national cattle holdings in some countries. The data developed in this paper can be used in the model described in paper I, as well as other studies where cattle is an important part of the system. It has been claimed the optimal temperature for malaria transmission is between 30 to 32°C, with the potential increasing linearly from 20 to 32°C. With this claim, any warming in sub-Saharan Africa would potentially cause more malaria. Using the model developed in paper I, we show malaria transmission is most effective around 25◦C, with a decline in efficiency over end below this temperature (Paper IV). This disputes the theory claimed in previous papers. Any projections relating temperature and malaria should be interpreted with care. The influence of climate change on malaria transmission is still uncertain. With this thesis, we have come a step further in understanding how the environment can alter malaria transmission. However, the future occurrence of malaria is dependent on many other factors, including malaria control measures, access to and usage of treatment, city planning, and immunity

Understanding fluorescent amyloid biomarkers by computational chemistry

Protein misfolding diseases, including neurodegenerative disorders like Alzheimer’s disease, are characterized by the involvement of amyloid aggregation, which emphasizes the need for molecular biomarkers for effective disease diagnosis. The thesis addresses two aspects of biomarker development: firstly, the computation of vibrationally resolved spectra of small fluorescent dyes to detect amyloid aggregation, and secondly, the binding and unbinding processes of a novel ligand to the target protein. In relation to the first aspect, a hybrid model for vibrational line shapes of optical spectra, called VCI-in-IMDHO, is introduced. This model enables the treatment of selected modes using highly accurate and anharmonic vibrational wave function methods while treating the remaining modes using the approximate IMDHO model. This model reduces the computational cost and allows for the calculation of emission line shapes of organic dyes with anharmonicity in both involved electronic states. The interaction between the dyes and their environment is also explored to predict the photophysical properties of the oxazine molecules in the condensed phase. The position and the choice of the solvent molecule have a significant impact on the spectra of the studied systems as they altered the spectral band shape. However, further studies are necessary to confirm the findings. In addition to neurodegenerative diseases, the systemic amyloidoses represent another group of disorders caused by misfolded or misassembled proteins. In the cardiac domain, the accumulation of amyloid fibrils formed by the transthyretin (TTR) protein leads to cardiac dysfunction and restrictive cardiomyopathy. The investigation of binding and unbinding pathways between the TTR protein and its ligands is crucial for gaining a comprehensive understanding and enabling early detection of systemic amyloidoses and related disorders. Hence, exploring the different binding modes and the dissociation pathways of TTR-ligand complex is the primary objective of the second aspect of this thesis. The experimental study provides evidence of binding and X-ray crystallographic structure data on TTR complex formation with the fluorescent salicylic acid-based pyrene amyloid ligand (Py1SA). However, the electron density from X-ray diffraction did not allow confident placement of Py1SA, possibly due to partial ligand occupancy. Molecular dynamics and umbrella sampling approaches were used to determine the preferred orientation of the Py1SA ligand in the binding pocket, with a distinct preference for the binding modes with the salicylic acid group pointing into the pocket.Deutsche Forschungs-gemeinschaft (DFG)/Emmy Noether/KO 5423/1- 1/E

Determining the Pace and Magnitude of Lake Level Changes in Southern Ethiopia Over the Last 20,000 Years Using Lake Balance Modeling and SEBAL

The Ethiopian rift is known for its diverse landscape, ranging from arid and semi-arid savannahs to high and humid mountainous regions. Lacustrine sediments and paleo-shorelines indicate water availability fluctuated dramatically from deep fresh water lakes, to shallow highly alkaline lakes, to completely desiccated lakes. To investigate the role lakes have played through time as readily available water sources to humans, an enhanced knowledge of the pace, character and magnitude of these changes is essential. Hydro-balance models are used to calculate paleo-precipitation rates and the potential pace of lake level changes. However, previous models did not consider changes in hydrological connectivity during humid periods in the rift system, which may have led to an overestimation of paleo-precipitation rates. Here we present a comprehensive hydro-balance modeling approach that simulates multiple rift lakes from the southern Ethiopian Rift (lakes Abaya, Chamo, and paleo-lake Chew Bahir) simultaneously, considering their temporal hydrological connectivity during high stands of the African Humid Period (AHP, ~15–5 ka). We further used the Surface Energy Balance Algorithm for Land (SEBAL) to calculate the evaporation of paleo-lake Chew Bahir's catchment. We also considered the possibility of an additional rainy season during the AHP as previously suggested by numerous studies. The results suggest that an increase in precipitation of 20–30% throughout the southern Ethiopian Rift is necessary to fill paleo-lake Chew Bahir to its overflow level. Furthermore, it was demonstrated that paleo-lake Chew Bahir was highly dependent on the water supply from the upper lakes Abaya and Chamo and dries out within ~40 years if the hydrological connection is cut off and the precipitation amount decreases to present day conditions. Several of such rapid lake level fluctuations, from a freshwater to a saline lake, might have occurred during the termination of the AHP, when humid conditions were less stable. Fast changes in fresh water availability requires high adaptability for humans living in the area and might have exerted severe environmental stress on humans in a sub-generational timescale

Structure and Thermodynamics of Polyglutamine Peptides and Amyloid Fibrils via Metadynamics and Molecular Dynamics Simulations

Aggregation of polyglutamine (polyQ)-rich polypeptides in neurons is a marker for nine neurodegenerative diseases. The molecular process responsible for the formation of polyQ fibrils is not well understood and represents a growing area of study. To enable development of treatments that could interfere with aggregation of polyQ peptides, it is crucial to understand the molecular mechanisms by which polyQ peptides aggregate into fibrils. Many experimental techniques have been employed to probe polyQ aggregation, however, observations from these studies have not lead to a unified understanding of the properties of these systems, instead yielding competing, fragmented theories of polyQ aggregation. This dissertation addresses these gaps in knowledge by shedding light on important steps of the aggregation process. The structural motif of polyQ fibrils is not agreed upon in the field, which is worrying, given that these structures are the endpoint of polyQ aggregation. Here, molecular dynamics (MD) simulations paired with UV resonance Raman (UVRR) experiments show that short polyQ peptides adopt extended antiparallel β-sheet fibrils, contrary to β-hairpin structures oft predicted in the polyQ field. The structure of monomeric polyQ peptides was then studied to gain insight into the beginnings of the aggregation mechanism. Metadynamics MD simulations were used to characterize the conformational energy landscape of polyQ peptides, and this data was compared to experimental UVRR results. We found short polyQ peptides can adopt PPII-rich and collapsed β-strand monomeric structures, which establishes that polyQ can form distinct conformational states as monomers. The effect of increased polyQ repeat length was also tested, and it was found that increased repeat length corresponds to lower energy barriers between monomeric conformational states, which may explain why longer polyQ repeats are quicker to aggregate. Hydrogen bonding strengths of polyQ monomers and fibrils were also investigated with MD and UVRR, showing that polyQ peptides favor intrapeptide hydrogen bonds over those between peptide and water. Overall, the work in this dissertation deepens the understanding of the polyQ aggregation mechanism by determining the structure and thermodynamics of monomeric and fibrillar states, as well as identifying polyQ peptide hydrogen bonding as one of the driving forces in these systems. This knowledge can aid the development of molecular mechanisms to interfere with the formation of toxic polyQ aggregates that trigger the onset of polyQ diseases