ITQB: PM - MA Dissertations
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- An in-silico approach to target Coronviruses nsp14 and nsp15Publication . Queiróz, Fábio de Almeida; Soares, Cláudio"Nowadays, the absence of proper treatment for COVID-19 is still an issue to tackle since there are many of new cases and deaths occurring every day. Several ideas are being studied to compromise the virus’ replication cycle, like targeting the Spike protein that is the mediator of recognition between SARS-CoV-2 and human cells, or the RNA polymerase of the replication and transcription complex of the virus. There are, however, several other possible proteins to target, which are the main focus of this work. The non-structural proteins 14 and 15, also belonging to the replication and transcription complex of the virus, have important functions for the viral replication cycle since non-structural protein 14’s ExoN domain has an exoribonuclease activity and non-structural protein 15 an endoribonuclease activ- ity, both governing the viral proofreading mechanism. In this work, an in-silico approach is applied with the use of methodologies like Molecular Docking and Molecular Dynamics in an attempt to target and inhibit both of these proteins. (...)"
- Structural and dynamic properties of the Dengue fusion peptide in a membrane bilayer: A computational approachPublication . Valério, Mariana de Oliveira Farinha Fidalgo; Soares, Cláudio"Dengue virus is responsible for dengue fever, a mosquito-borne tropical disease that affects approximately 390 million people every year. Like all enveloped viruses, the dengue virus is encapsulated by a lipid membrane (envelope) and, in order to infect host cells, the virus must fuse its membrane with the host cell membrane.(...)"
- Validation and Optimization of a Structure-Based Enzyme Engineering PlatformPublication . João Pedro, Gorjão Araújo; Soares, Cláudio; Lousa, Diana"Organismsandenzymesarecurrentlyusedforcatalyzingtheproductionofvalue- added compounds,indiverseareaswitheconomicimpact.However,poorprotein expression, lowcatalyticlevels,lowconcentrationsofco-factorsorsubstrates,toxicity towardsthefinalproductandotherfactors,allcontributetothelowperformanceof microorganismsandenzymesintheseareas.Proteinengineeringisaneffectivestrategy forimprovingbiosyntheticpathwaysandovercomingtheseproblems,byre-designingan enzyme’scatalyticpropertiesinfavorofacertainreaction. Toaddressthisproblem,theProteinModelingLaboratoryofITQBNOVAdeveloped an automatedplatformforgenediscoveryandenzymeengineering,whichaimstoenhance or changetheenzymesthatcatalyzethelimitingstepsinpathwaysthatcanbeexploited fortheproductionofaddedvaluecompounds.Theobjectivesrangedfromincreasing an enzyme’sefficiencytoenablingittocatalyzeadifferenttransformationthantheone catalyzedbythewild-typesequence.(...)"
- Spike glycoprotein: molecular characterization and inactivation of a key player in SARS-CoV-2 infectionPublication . Buga, Carolina C.; Lousa, Diana Andreia Pereira; Veiga, Ana Salomé Rocha do Nascimento"The coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronaviruses 2 (SARS-CoV-2), emerged in late 2019 and quickly spread worldwide. So far, over 370 million infections and 5.6 million deaths were reported by the World Health Organization. Although a great effort has been made by the scientific community to study SARS-CoV-2, more research is needed to advance the knowledge on this virus. SARS-CoV-2 is an enveloped virus and its entry into host cells is mediated by a viral surface protein, the spike glycoprotein (S-protein). This protein is composed of two subunits (S1 and S2) that contain essential domains for the viral entry mechanism, namely the receptor-binding domain (RBD), known to bind to angiotensin-converting enzyme 2 (ACE2) present at the host cells surface, and the fusion peptide (FP), which promotes the fusion between the viral and host cell membranes. However, despite the relevance of the FP for viral entry, its location on the S-protein and amino acid sequence are still unclear.(...)"
- The impact of SARS-CoV-2 Omicron variant on the receptor binding domain conformational dynamics and interaction with human ACE2Publication . Teixeira, Rita I.; Lousa, Diana; Vicente, João"The COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to over 6.6 million deaths worldwide, as of 27 November 2022. The SARS-CoV-2 infection mechanism involves the viral binding to the angiotensin-converting enzyme 2 (ACE2) host receptor through the Spike (S) protein receptor-binding domain (RBD). Thus, understanding the molecular details of binding is of pharmaceutical interest. Nevertheless, the unbound RBD presents conformational changes in the “ridge” region that are hypothesized to also affect receptor recognition.(...)"