Carrera Ingeniería Bioquímica
Permanent URI for this collectionhttp://repositorio.uta.edu.ec/handle/123456789/809
Browse
24 results
Search Results
Item Identificación de posibles dianas terapéuticas para la Enfermedad de Parkinson mediante la aplicación de métodos in silico(Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Ingeniería Bioquímica, 2024-02) Chimbo Gavilanes, Klever Javier; Galarza Galarza, Cristian FernandoIn the exploration of possible therapeutic targets to treat Parkinson's disease through computational chemistry, drug design using docking tools is employed. This process is based on the analysis of genes such as LRRK2, where the main objective is to identify the most optimal binding sites in terms of energetic stability, considering them as possible ideal locations for protein action. In this context, virtual screening makes it possible to verify whether the complexes formed between the protein and the ligand represent a potential avenue for the investigation of a disease-specific drug. The analysis of several disease databases, such as MalaCards, Harmonizome, KEGG, OMIM, Unitpro, Disgenet, GeneReviews and Orphanet, has allowed the identification of key genes in Parkinson's disease. These genes are of great importance since, among numerous candidates, those with similarities in molecular processes and common dysfunctions were selected. The grouping and categorization of these genes facilitated the creation of a biological network of interactions using Cytoscape, accompanied by a bibliographic investigation of the metabolic pathways and the relationships between them, thanks to this approach, mutations in the LRRK2 gene were identified to then search for possible druggable sites in this molecule, with the aim of forming protein-ligand complexes. Thus, existing drugs or ligands can be analyzed by screening and evaluation of toxicological properties. In this bioinformatics study of therapeutic targets, I point out that the main ligand Losulazine presents a higher affinity of pharmacological interaction with the LRRK2 gene.Item Análisis In Silico de toxinas animales con potenciales aplicaciones biotecnológicas(Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Ingeniería Bioquímica, 2023-03) Álvarez Robles, María Belén; García Solís, Mario DanielCurrently available drugs have increased life expectancy; resulting in population aging with a greater number of geriatric patients who increase the culture of prescription and self-medication originating resistant viruses and bacteria. In addition, the development of new diseases, such as the recent Covid-19 pandemic, a product of the irresponsible interaction of humans with the environment, causes millions of deaths, especially in the poorest countries without access to palliative medicines. This reality reflects a paradox that brings the health system closer to the brink of collapse. To face the crisis, alternative uses for known drugs are sought or the development of new, more effective and specific drugs for each medical condition. Omissive research has developed new drugs taking advantage of the great potential of peptides with biotechnological activity isolated from toxic biological secretions produced by certain poisonous animals. In this study, the UNIPROT and RCSB PDB databases were used to group peptides with sequence and structural homology with three different biological activities: anticancer, antiepileptic, and antinociceptive. From nucleotide sequencing, a three-dimensional base structure was obtained, with PyMOL, which confers the biological activity for each group. In addition to a phylogenetic analysis with MEGA that shows the evolutionary roots of the groups. The results are expected to encourage future research that uses the base structures of these peptides isolated from animal toxins as a template and takes advantage of their biological activity for the synthesis of new therapeutic drugs.Item Búsqueda de posibles dianas terapéuticas para el cáncer papilar de tiroides (PTC)(Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Ingeniería Bioquímica, 2022-09) Lagua Mainato, Christian Orley; Galarza Galarza, Cristian FernandoIn the search for possible therapeutic targets through computational chemistry for papillary thyroid cancer (PTC), the design of drugs with docking tools is based on the analysis of the BRAF gene, where the best binding sites are mainly identified. Regarding energy stability, therefore, the virtual screening allowed to verify the drugability of said complexes that were created between protein and ligand, this represents a potential avenue of research for the development of an optimal and specific drug for said disease. The analysis within the databases of diseases such as MalaCards, Harmonizome, KEGG, OMIM, Unitpro, Disgenet, GeneReviews and Orphanet allowed to know the main genes that lead the carcinogenesis process in PTC, certain genes presented common dysfunctions so that it was possible to group and categorize them to then create a biological network of interaction with the help of Cytoscape and subsequently the metabolic pathways of these genes and the relationship between them were investigated bibliographically. In this way, the mutations that this target gene presents and the alterations in its metabolic pathway were identified. Finally, the mutations that the BRAF gene suffers were found to subsequently identify possible drugable sites that can create protein-ligand complexes, so that the existing drugs currently they were analyzed by screening and subsequent analysis of toxicological properties. Therefore, this bioinformatic study allowed to determine that the ligands Entrectinib, Bms-833923, Afacifenacin, Floxacrine, Olaparib, Nolpitantium, Aleplasinin present pharmacological potential for the BRAF gene.Item Análisis in silico de las rutas metabólicas necesarias para la síntesis de celulosa bacteriana en Komagataeibacter xylinus a partir de lactosa(Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Ingeniería Bioquímica, 2022-09) Zapata Berrones, Karina Elizabeth; García Solís, Mario DanielBacterial Cellulose symbolizes a multifaceted resource of exceptional capabilities and fascinatingproperties. Currently, the demand for this exopolysaccharide has progressively increasing, in function of the optimization of processes and the implementation of agro-industrial waste as alternative carbon sources. In such a context, the archetype productor (K. xylinus) represents one of the most valuable organisms in the biotechnological field, a scenario that has made it possible to demonstrate its enormous power to synthesize BC from a wide range of substrates. However, some authors have elucidated its inability to metabolize lactose, caused by the lack of genes responsible for the transport and catabolism of this substrate. Here, DSM 2004 and the analogous strain E25 (identified by phylogenetic analysis), were studied with the aim of identifying missing genes and minimal genetic equipment. A critical analysis of metabolic pathways in BAL and BAA was carried out to list the transporter and the enzymes involved in the process of interest. In this, the summarized proteins were evaluated according to kinetic parameters, where the best results report access code and both peptide and nucleotide sequence of the gene that encodes them. In this, the genes of Escherichia coli K-12 (Lactose permease), Alicyclobacillus acidocaldarius ATCC 27009 (β – galactosidase), Bifidobacterium longum subsp. Infantis ATCC 15697 (galactokinase), and Escherichia coli XL1-Blue (galactose-1-P-uridyltransferase) were selected. Finally, the modeling of the new biosynthetic route presented two related modules: i) Transport and hydrolysis of Lactose and ii) Biosynthesis of CB, after the total replacement of glucose by whey lactose.Item Análisis comparativo de secuencias de genoma completo de Salmonella entérica serovar Infantis de origen humano y animal(Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Ingeniería Bioquímica, 2022-03) Sánchez Guerrero, Alex Xavier; Calero Cáceres, William RicardoAdvances in the development of molecular and bioinformatics tools now allow for a faster and more efficient epidemiological investigation of infectious diseases. Whole genome sequencing represents one of the most revolutionary methodologies in the study of pathogens and is becoming a tool commonly used by several health control agencies (CDC, EFSA), as well as by academia. Salmonella enterica constitutes one of the main pathogens causing diseases around the world, thus, among its different non-typhoidal serovars, Infantis constitutes one of the most relevant from the epidemiological point of view, due to the evolution of virulence mechanisms, dissemination and antimicrobial resistance. Therefore, in the present study, a comparative analysis of whole genome sequences of S. infantis from different origins was performed. Five complete genome sequences of human origin belonging to the ST32 type, the detection of 3 pathogenicity islands, the presence of IncFIB type plasmids, genotypic profiles of antibiotic resistance and a phylogenetic analysis between isolates of Ecuadorian origin and representative isolates from different parts of the world were characterized. The phylogenetic distances evidenced close relationships between Ecuadorian isolates with countries of the South American Pacific profile and the United States, which could be a shared common ancestor. Finally, with respect to resistance genes, Ecuadorian isolates show resistance mechanisms for fosfomycins, aminoglycosides, tetracyclines and the presence of the clinically relevant beta-lactamase blaCTX-M-65.Item Diseño y validación in silico de primers para la construcción de las variantes mutantes S121E, S121D, D186H y R280A de la enzima PETasa de Ideonella sakaiensis mediante tres diferentes métodos de mutagénesis dirigida al sitio(Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Ingeniería Bioquímica, 2022-03) Herrera Aldaz, Bryan Alexander; Cerda Mejía, Liliana AlexandraThe PETase enzyme from Ideonella sakaiensis (IsPETase) can be used to degrade PET, however, although it has been reported to date to have the highest enzymatic activity under normal conditions of all PET degrading enzymes, its low thermal stability limits its analysis and application. Therefore, by targeted mutagenesis, specific mutations can be introduced into the DNA to significantly increase its enzymatic activity. The purpose of this study was the design and in silico validation of primers for the construction of S121E, S121D, D186H and R280A mutant variants of IsPETase using three site-directed mutagenesis techniques: QuikChange, Q5 Site-Directed Mutagenesis and Phusion Site-Directed Mutagenesis. For the design of the primers, the parameters contained in the design guidelines for targeted mutagenesis methods were considered. The results showed that the 24 primers obtained meet the general criteria such as length, melting temperature, percentage of GC content and the position of the mutation in the primer. For the validation of the proposed primers, hairpin, autodimer and heterodimer analysis was performed with bioinformatics tools, the calculated values are within acceptable ranges. Finally, the specificity of the primers design was carried out by means of alignments, whose results indicate a high specificity for their respective targets. Likewise, an in silico PCR assay confirmed the specificity of the primers, which represent the expected amplification product, thus demonstrating the correct selection of the designed primers and the execution of the mutagenic PCR process.Item Estudios bioinformáticos para la identificación de posibles dianas terapéuticas en la enfermedad de la Diabetes Mellitus tipo 2 (T2DM)(Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Ingeniería Bioquímica, 2022-03) Guevara Proaño, Luis David; Galarza Galarza, Cristian FernandoThe search for therapeutic targets for the disease type 2 diabetes mellitus is based on computer-aided drug development through molecular concentration analysis and virtual screening in disease databases. The identification of the study gene requires analysis in different databases such as MalaCards, OMIM, Harmonizome and KEGG to validate the information on the genes involved in the disease. Thus, the genes with the greatest connections are chosen and grouped according to their genetic dysfunction to create biological networks and validated in the DrugBank database. Subsequently, an analysis of the metabolic pathway taken from KEGG that connect the target genes that maintain the identified mutation is performed and the three-dimensional structures are used to evaluate the domains plus drugs. Molecular coupling and screening simulations are then carried out, considering the compounds with the highest affinity for IRS-1, and finally the toxicity of the drugs is analyzed. QSAR models show that Zosuquidar, Rimacalib, Uk432097, Mosapramine, Devazepide and Setipiprant are the safest ligand compounds in toxicity analyses. The present study is based on the identification of the genes most associated with T2DM and the search for possible therapeutic targets through bioinformatics applied to computer-assisted drug design. The results obtained can be used for subsequent research studies to increase the therapeutic spectrum for T2DM or other metabolic degenerations.Item Diseño y validación in silico de primers para la amplificación del Gen GSTM(Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Ingeniería Bioquímica, 2022-03) Guevara Guevara, Kevin Joel; Galarza Galarza, Cristian FernandoLung cancer is a disease that affects a large part of the population, there are several reasons why it develops, one of them involves the GSTM1 gene, for this reason the possible relationship with cancer was consulted through the databases Malacards and Harmonizome, using the NM_000561.4 sequence for primer design. The region taken for the design of the primers comprised between exon 5 and exon 7, since in this there is a SNP related to lung cancer, a substitution of a C for a G in position 534, resulting in the GSTM1 A and GSTM1 B alleles containing a lysine and an asparagine respectively at position 172, a third GSTM1 0 allele called the null allele generated by a homozygous deletion, which leads to susceptibility to lung cancer. Hence the importance of design for both diagnostic and research use. The design was carried out in the Primer-Blast and Primer3Plus programs with default parameters and another design modifying them, mainly the concentrations of divalent cations and dNTPs, the rest of the configurations were modified according to the purpose of the primers. Once the set of primers was obtained, compatibility was analyzed using the MultiPLX 2.1 program and the melting curves were obtained using the uMELT software. Finally, the in silico validation was carried out with the Oligoanalyzer and Beacon designer free edition programs.Item Análisis estructural de la enzima PETasa de Ideonella sakaiensis y enzimas homólogas(Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Ingeniería Bioquímica, 2022-03) Aguirre Muñoz, Adriana Alexandra; García Solís, Mario DanielPolyethylene terephthalate (PET), a low-cost thermoplastic produced industrially from fossil raw materials, is massively used in industry, and has become a high-impact pollutant. Among the latest discoveries related to the enzymatic treatment of PET is PETase from I. sakaiensis (IsPETase), which is a hydrolase capable of degrading PET. The present work was elaborated to establish possible mutations and modifications that improve the catalytic activity and enzymatic stability of IsPETase, for which a structural analysis of the same was carried out. Using the UNIPROT and PDBeFOLD databases, the enzymes that share a high degree of homology with IsPETase were identified. From these results, an analysis was carried out based on their percentage of sequence identity and secondary structure identity (SEQ and SSE respectively), E-value, Score, RMSD, and Q. The enzymes of greatest interest were selected for this analysis, the main ones being PbLipaseT, RgPETase, BbHydrolase, and SvCUT190, establishing that the N212S mutation can be used to improve the enzymatic activity and stability, in addition, possible substitutions to be studied were described to evaluate the effect that these would cause in the enzyme (S188E, S188A, and S114H). In the analysis of mutant variants, the presence of different amino acids in each case was identified; therefore, different possible substitutions to be made in the IsPETase enzyme were proposed, among the most relevant ones are W159F and S238T.Item Análisis bioinformático de péptidos con actividad antimicrobiana(2022-03) Acosta Bustos, Daniela Estefanía; García Solís, Mario DanielThis project was made with the purpose of studying the great antimicrobial potential of different proteins like response to developing of resistance of pathogenic microorganisms to conventional antimicrobial compounds. To reach this goal, a total of 126 peptides was collected and analyzed from the PDB and UniProt. The analyzed proteins belong to various species and have been into 12 groups such as cecropins, magainins, bombinins, dermaseptins, cathelicidins, brevinins, esculentins, ranalexins, defensins, drosocins, PR- 39 and gaeugerins. Multiple sequence alignment showed that peptides have highly conserved regions, which generate folding patterns responsible for their activity. When ordering the 126 antimicrobial peptides into 4 groups according to their secondary structure, a high conservation was identified between peptides of different classes and origin, this explains the similarities that these peptides present when interacting with the phospholipid bilayer of microorganisms, proving that the most used mechanisms of action is the “barrel stave” mode, the amphipathicity of these molecules allows the hydrophobic end to interact with the lipid core of the membrane, while the hydrophilic end is directed inwards, producing an aqueous pore. Finally, a phylogenetic tree was constructed by the maximum likelihood method for each class of antimicrobial peptides. From this analysis it was concluded that although the analyzed sequences belong to different species, these are related because they maintain the same evolutionary line and mechanism of action. In summary, this study offers a starting pint for the identification of peptides of interest through the use of open databases, which potentially antimicrobial activity.
- «
- 1 (current)
- 2
- 3
- »