Works presented

Summary
Over the last decades, graphene has drawn remarkable attention from the scientific community due to its impressive combination of physical properties. In this field, nanographenes are presented as privileged molecular materials to fine-tune these properties through well-controlled bottom-up synthesis. Here, we demonstrate the preparation of two new strained triyne structures, which can evolve through transannular hexadehydro-Diels-Alder reactions to obtain polycyclic arynes. These arynes can afford structurally interesting helicenes by [4+2] cycloaddition with furan followed by deoxygenation.

Direction
PEÑA GIL, DIEGO (Tutorships)

Court
PEREZ MEIRAS, MARIA DOLORES (Chairman)
INSUA LOPEZ, IGNACIO (Secretary)
GIMENEZ LOPEZ, MARIA DEL CARMEN (Member)

Summary
The development of non-natural, synthetic reactions that interact with the metabolism of living systems is an emerging field at the interface of chemical and biological synthesis. These reactions would give access to new sustainable synthetic routes for molecules of interest, and have potential applications in biomedicine and biology. In this Master dissertation, we demonstrate that the redox metabolism of live bacteria can be harnessed to promote non-natural bond-forming radical reactions. We show that the electrogenic bacterium Shewanella oneidensis MR-1 and the model bacterium Escherichia coli DH5-alpha can reduce aryl diazonium salts to promote the Meerwein arylation of naphthoquinones using electron transfer and radical chain mechanisms. We have also tested our methodology for the bacteria-promoted synthesis of benzothiophenes, opening the door to structures of biomedical interest.

Direction
Mascareñas Cid, Jose Luis (Tutorships)
TOMAS GAMASA, MARIA (Co-tutorships)

Court
PEREZ MEIRAS, MARIA DOLORES (Chairman)
INSUA LOPEZ, IGNACIO (Secretary)
GIMENEZ LOPEZ, MARIA DEL CARMEN (Member)

Summary
Understanding the mechanisms behind cancer progression and proliferation has posed a significant challenge for researchers worldwide. Gaining insight into the origins and functioning of cancer cells could provide a valuable approach for targeting cancer without harming healthy cells. Recent advancements in cancer treatments, such as targeted therapy and immunotherapy, are moving in this direction. This study specifically examines the alteration of the lipid composition of cell membranes as a key differentiating factor between healthy and cancerous cells. In healthy mammalian cells, the outer monolayer of the membrane is zwitterionic, predominantly composed of phosphatidylcholine (PC), sphingomyelin (SM), and cholesterol. In contrast, cancer cells exhibit anionic membranes, primarily composed of phosphatidylserine (PS). Antimicrobial peptides (AMPs), such as melittin (MLT) and LL-37, have demonstrated selective targeting of anionic membranes, effectively mimicking immune system functions. However, the uncontrolled proliferation of cancer cells suggests that there may be factors disrupting the lipid-peptide interaction. This study investigates the potential role of lysophosphatidic acid (LPA), a signalling molecule within the human innate immune system, as a competitor for peptide-lipid binding on the membranes of cancer cells. By disrupting the interaction between lipids and peptides, LPA may prevent the effective destruction of cancer cells, allowing for their continued proliferation.

Direction
GARCIA FANDIÑO, REBECA (Tutorships)
Granja Guillán, Juan Ramón (Co-tutorships)

Court
PEREZ MEIRAS, MARIA DOLORES (Chairman)
INSUA LOPEZ, IGNACIO (Secretary)
GIMENEZ LOPEZ, MARIA DEL CARMEN (Member)

Summary
Therapeutic DNA targets have been known for a long time and pharmacological agents targeting them, such as cisplatin, are powerful weapons for fighting cancer. In addition to B-DNA, non-canonical DNA structures, such as three-way DNA junctions (3WJs), have recently emerged as new promising targets that may enable the development and design of new chemotherapeutic agents with better therapeutic properties. Three-way DNA junctions are symmetric assemblies formed by three intertwined duplex DNA segments; these structures can arise through the defective replication of repetitive DNA sequences called microsatellites. Therefore, 3WJ binding agents could find application as selective drugs that target microsatellite instability/mismatch repair (MMR) deficient phenotypes, such as in colorectal carcinomas. Modeling, synthesizing, and characterizing new therapeutic molecules, as well as measuring their DNA binding properties through their dissociation constants (KD) are the first steps in the path to generate new compounds, until reaching viable and effective treatments. Here, I will describe rationally designed short helical peptides that selectively bind to the central cavity of 3WJs, I will explore the structural determinants of the binding and further optimize the structure via exploring other secondary structures, such as 310 helix.

Direction
VAZQUEZ SENTIS, MARCO EUGENIO (Tutorships)

Court
PEREZ MEIRAS, MARIA DOLORES (Chairman)
INSUA LOPEZ, IGNACIO (Secretary)
GIMENEZ LOPEZ, MARIA DEL CARMEN (Member)

Summary
Dodecahedral boron clusters have proven to be versatile molecules with applications in catalysis, nuclear waste treatment, material science, and cancer therapy. Recent studies have revealed that these clusters can also act as membrane carriers, due to their superchaotropic properties. This novel approach addresses some of the limitations that the traditional amphiphilic carriers exhibit such as aggregation, nonspecific binding, endocytic entrapment, and membrane-lytic propensity. Thus, to continue exploring this approach, we modified the dodecaborate cluster [B12H12]2- to allow covalent attachment of a cargo. For this purpose, we explored three synthetic routes to functionalize the dodecaborate cluster with an alkyne moiety. Once we selected the most efficient approach to bind the alkyne moiety, we covalently attached 5-Carboxytetramethylrhodamine azide via Cu-catalyzed Azide-Alkyne cycloaddition reaction. This study demonstrates the viability of functionalizing boron clusters with bioactive cargos like fluorescent dyes.

Direction
MONTENEGRO GARCIA, JAVIER (Tutorships)
QUEME PEÑA, MAYRA MARITZA (Co-tutorships)

Court
PEREZ MEIRAS, MARIA DOLORES (Chairman)
INSUA LOPEZ, IGNACIO (Secretary)
GIMENEZ LOPEZ, MARIA DEL CARMEN (Member)

Summary
The cytoskeleton is one of the most important cellular structures for its functions of transport, motility and internal organisation. Thus, to understand more about this complex structure the development of simple encapsulation systems seems to be crucial. With that purpose, this project studies a model based on the biocatalytic fibrillation of the novel peptide amphiphile PC10T6 in totally aqueous membrane-less droplets obtained by liquid-liquid phase separation (LLPS). This project was realized at CiQUS during the 2024/2025 academic year from September to January, both included. First, the molecular design and the fibrillation capacity of the peptide are discussed by a combination in situ of the PC10 fragment (synthesised and optimised) and the aldehyde T6, whose production is carried out by the enzyme ADH and the coenzyme NAD+. After that, the fibrillation experiments are shown and results demonstrates that the pH plays a key role in controlling the aggregation/dispersion process as well as the formation of fibers, which was faster than expected. Finally, kinetic experiments were carried out to monitor the formation of T6 observing the reduction of the coenzyme NAD+ to NADH by UV-VIS. Results reveal that the rate of the aldehyde formation supports the fibrillation velocity obtained, showing the importance of the kinetic control of the system for a gradual production of the fibers. In conclusion, this project demonstrates the importance of understanding all aspects of a system such as pH or kinetics and how small changes in these can lead to different results like aggregation, dispersion or fibrillation. Herein it is shown the first very promising progress to a new model of encapsulation in aqueous medium using a peptide with high fibrillation capacity. This study provides deep insight into the molecular foundations of cellular cytoskeleton, setting the basis to a further understand of the evolution and the formation of this complex structure.

Direction
MONTENEGRO GARCIA, JAVIER (Tutorships)
INSUA LOPEZ, IGNACIO (Co-tutorships)

Court
PEREZ MEIRAS, MARIA DOLORES (Chairman)
INSUA LOPEZ, IGNACIO (Secretary)
GIMENEZ LOPEZ, MARIA DEL CARMEN (Member)

Summary
Lanthanide metal-organic frameworks (Ln-MOFs) have been the focus of numerous studies in recent years due to their remarkable characteristics, including Lewis’s acid sites, luminescence, magnetism, intrinsic porosity, and low toxicity. Moreover, Ln-MOFs are recognized as promising candidates for cancer therapy through stimuli-responsive degradation (SRD). Currently, several research efforts focus on synthesizing functionalized MOFs containing imine bonds to release encapsulated drugs upon reaching tumor tissues via SRD. However, these imine-functionalized MOFs still have limitations, as they hydrolyze in acidic environments. Thus, in my introductory research project, we studied the effect of different modulators such as acetic acid (AA) and triethylamine (TEA) based on the synthesis of novel imine-based lanthanide MOFs without post-synthetic modifications, particularly diimine Tb-MOF, in an economical manner. Firstly, we observed that attempts to synthesize the intended MOF via a direct solvothermal method using LBNT2 (linker bionanotools-2) formed through the reaction of aminoisophthalic acid (AIA) and terephthalaldehyde (TA), or a one-pot synthesis using the precursors' AIA, TA, and terbium ions in the presence of 2-fluorobenzoic acid (2-FBA) and AA, were unsuccessful. This failure was attributed to the cleavage of imine bonds under acetic conditions. To address this issue, we conducted the synthesis again without AA. Analysis of the resulting samples using Scanning Electron Microscopy (SEM) and Powder X-ray Diffraction (PXRD) confirmed the stability of the imine bonds under these modified conditions. Finally, we attempted to substitute AA with TEA. However, this approach still requires further optimization for successful MOF formation. Therefore, in this TFM, in our attempts to synthesize a novel imine-based lanthanide MOF (diimine Ln-MOFs), we first varied the molar amount of TEA in a direct synthesis using the diimine ligand LBNT2 and lanthanide precursors. Despite these efforts, we were unable to obtain the desired diimine Ln-MOF. Next, we focused on adjusting the molar amount of 2-FBA in both the direct synthesis using LBNT2 and the one-pot synthesis using the LBNT-2´s precursors, AIA and TA. By reducing the acidity and characterizing the samples using PXRD, we determined that an optimal molar amount of 2-FBA for synthesizing the diimine Ln-MOF via the one-pot synthesis approach is 3 mmol. Subsequently, we aimed to optimize additional parameters, including the volume of the solvent dimethylformamide (DMF), the pressure within the autoclave, and the choice of lanthanide precursors. The aim was to produce single crystals of the diimine Ln-MOF to enable the determination of its physicochemical and structural properties. However, this goal remains elusive, likely due to the shape of the crystals obtained, and efforts to achieve it are still ongoing.

Direction
DEL PINO GONZALEZ DE LA HIGUERA, PABLO ALFONSO (Tutorships)

Court
PEREZ MEIRAS, MARIA DOLORES (Chairman)
INSUA LOPEZ, IGNACIO (Secretary)
GIMENEZ LOPEZ, MARIA DEL CARMEN (Member)