Inspiratsioon kunstis ja meditsiinis

Eesti Arst 2012; 91(3):16

Structure-based Druggability Predictions of RNA Binding Sites and Design of RNA Ligands

Den post-antibotiske æraen truer og for å møte denne krisen trengs det tilgang til nye klasser av antibiotika. Ribvoswitcher er cis-genregulerende foldete strukturer av ikke-kodende RNA, som handler gjennom konformasjonsendringer indusert av binding til mindre molekyler. Siden disse riboswitchene har blitt identifisert som nøkkelkomponenter i bakteriell biologi, og er essensielt utelukket i mammalske celler, er de lovende mål for nye klasser av antibiotika I denne oppgaven har vi utforsket riboswitcher som lovende legemiddelmål. Et legemiddelmål må være relevant for en gitt sykdom og må også kunne være regularbar gjennom enten biologiske molekyler eller mindre molekyler. I det siste tilfellet, må legemiddemålet kunne binde seg til små legemiddelaktige molekyler med høy affinitet, og slik binding blir referert som "druggable" (norsk: dopbar). Tidligere i Brenk-gruppen har en prediktor (DrugPred) blitt utviklet for å identifisere slike bindingsseter i proteiner. Som et av målene i denne avhandlingen, har denne prediktoren blitt utvidet til å være kompatibel med bindigsseter i RNA. Grunnet mangelen på validerte dopbare RNA bindingsseter, er den nye prediktoren, DrugPred_RNA, trent på protein bindingsseter med deskriptorer som gjelder for bindingsseter både i RNA og proteinstrukturer. Denne versjonen kunne både predikere med høy treffsikkehet og presisjon, og hadde resultater sammenlignbare med den siste versjonen av DrugPred. Etter at den nye prediktoren ble brukt på en større samling av ligand-inneholdende RNA krystallstrukturer funnet i Protein Data Bank, evaluerte vi resultatene fra DrugPred_RNA og fant at de dopbare RNA bindingssetene var riktig klassifisert av programvaren. Prediksjonene fra DrugPred_RNA var også funnet til å være høyt robuste og gjennom det hele ble bindingsseter som var lignende i konformasjon og bindingssetekomposisjon gitt like prediksjoner. Det ble også funnet at konformasjonsendringer kunne gi alvorlige utslag på utfallet av prediksjonen. Blant de funne dopbare RNA-bindingssetene, var mange riboswitcher funnet, noe som understreker denne klassen av makromolekyler som potensielle mål for nye antibiotika. Mange av de dopbare strukturene var også funnet til å være ribosomale bindingsseter, som kan være med på å dirigere utviklingen av nye antibiotika. Alt i alt, ble DrugPred_RNA funnet til å være et nyttig verktøy for prediksjonen av dopbare RNA bindingsseter. Blant riboswitchene som ble funnet til å være dopbare bar FMN riboswitchen. Denne riboswitchen regulerer uttrykking av gener involvert i biosyntese av riboflavin og binder til flavin mononukleotid (FMN). FMN riboswitchen hører til en av de mest studerte kalssene av riboswitcher og flere potente bindere har blitt identifisert. Det har også blitt vist at disse binderne greier å inhibere bakterievekst, og dette tatt i betraktning sammen med høy tilstedeværelse i menneskelige patogener, som inkluderer varianter beslektet med nosokomiale infeksjoner, gjør det til et av de mest relevante målene å forfølge. Gjennom strukturell bioinformatikk, har vi designet stoffer in silico, og predikert deres bindingsmoduser. Drivkreftene til designen av disse kandidatene var å skape syntetisk tilgjengelige molekyler som ivaretar nøkkelinteraksjoner observert eller postulert mellom bindingssetet i FMN riboswitchen og FMN, ribocil (et stoff oppdaget av Merck) samt RSL-0035 (et stoff opdaget i tidligere arbeid i Brenklaben), mens samtidig utforske nye interaksjoner.The threat of the post-antibiotic era is looming and addressing this crisis requires access to new classes of antibiotics. Riboswitches are cis-gene regulating folded structures of non-coding RNA, which act through conformational changes induced after binding to small molecules. As riboswitches have been identified as a key component in bacterial biology and are essentially absent in mammalian cells, they constitute promising targets for novel classes of antibiotics Herein, we have explored the possibility of addressing riboswitches as potential drug targets. A drug target needs to be relevant for a given disease and needs to be mofiable by either biological molecules or small molecules. In the latter case, the drug target needs to be able to bind small drug-like molecules with high affinity. Such binding sites are referred to as “druggable”. Previously in the Brenk group, a predictor (DrugPred) was developed to identify such binding sites in proteins. As part of this thesis, this predictor has been extended to be compatible with RNA binding sites. Due to the paucity of validated druggable RNA binding sites, the predictor, DrugPred_RNA, was trained on protein binding sites with descriptors that are applicable for both protein and RNA binding sites. It was found that this version was able to make predictions with high accuracy and precision, which were comparable to the last iteration of DrugPred. After applying this predictor on a large swathe of ligand-containing RNA crystal structures deposited in the Protein Data Bank, we have evaluated the predictions of DrugPred_RNA and found that known druggable RNA binding sites were classified correctly. The predictions of DrugPred_RNA were also found to be highly robust, and overall, binding sites which were found to be both similar in conformation and binding site composition were given the same prediction. However, it was also found that conformational changes could severely affect the outcomes. Further amon the RNA binding sites predicted to be druggable, many riboswitches were found, underlining this class of macromolecules as a potential target for new antibiotics. Many of the druggable structures were also ribosomal binding sites, which could also guide the development of new antibiotics. Overall, DrugPred_RNA was found to be a useful tool for the prediction of druggable RNA binding sites Among the riboswitches which were found to be druggable was the FMN riboswitch. This riboswitch regulates the expression of genes involved in biosynthesis of riboflavin and binds to flavin mononucleotide (FMN). The FMN riboswitch belongs to one of the most studied classes of riboswitches, and several potent binders have been identified. It has also been shown that these binders are able to inhibit growth of bacteria, and this, combined with its prevalence in human pathogens, including strains associated with nosocomial infections, makes it one of the most relevant targets to pursue. Using structural bioinformatics, we have designed compounds in silico and predicted their binding modes. The driving forces of the design of these candidates were to create synthetically feasible compounds which retain what we believe are key interactions observed or postulated between the FMN riboswitch binding site and FMN, ribocil A (a compound discovered by Merck) as well as for RSL-0035 (a compound discovered in previous work within the Brenk lab), while simultaneously exploring new interactions.Doktorgradsavhandlin

Püsiv vegetatiivne seisund

Püsiva vegetatiivse seisundi (persistent vegetative state, PVS) problemaatika on haiglale ja omastele eetiliselt raskem ning oma kulukuselt suurem kui ajusurma oma. Selle patofüsioloogia ei ole ka nii selgepiiriline. Näib, et PVS-sündroomis on kesksed kahjustused talamuses kui kognitiivse teabe vahendajas. Nüüdisaegsete diagnostiliste vahendite seas on positron-emissioon-tomograafia (PET) kõige tundlikum nende patoloogiliste muutuste suhtes, mis on eriomased PVSile. Eesti Arst 2003; 82 (1): 45–5

DrugPred_RNA—A Tool for Structure-Based Druggability Predictions for RNA Binding Sites

RNA is an emerging target for drug discovery. However, like for proteins, not all RNA binding sites are equally suited to be addressed with conventional drug-like ligands. To this end, we have developed the structure-based druggability predictor DrugPred_RNA to identify druggable RNA binding sites. Due to the paucity of annotated RNA binding sites, the predictor was trained on protein pockets, albeit using only descriptors that can be calculated for both RNA and protein binding sites. DrugPred_RNA performed well in discriminating druggable from less druggable binding sites for the protein set and delivered predictions for selected RNA binding sites that agreed with manual assignment. In addition, most drug-like ligands contained in an RNA test set were found in pockets predicted to be druggable, further adding confidence to the performance of DrugPred_RNA. The method is robust against conformational and sequence changes in the binding sites and can contribute to direct drug discovery efforts for RNA targets.publishedVersio

Safety and Clinical Efficacy of Mesenchymal Stem Cell Treatment in Traumatic Spinal Cord Injury, Multiple Sclerosis and Ischemic Stroke – A Systematic Review and Meta-Analysis

Background: Mesenchymal stem cells (MSCs) is an attractive candidate in regenerative research and clinical trials have assessed their therapeutic potential in different neurological conditions with disparate etiologies. In this systematic review, we aimed to assess safety and clinical effect of MSC treatment in traumatic spinal cord injury (TSCI), multiple sclerosis (MS) and ischemic stroke (IS). Methods: A systematic search was performed 2021-12-10 in MEDLINE, EMBASE, Web of Science and Cochrane where clinical studies assessing MSC treatment in TSCI, MS or IS were included. Studies without control group were excluded for efficacy analysis, but included in the safety analysis. For efficacy, AIS score, EDSS score and mRS were used as clinical endpoints and assessed in a meta-analysis using the random effects model. Findings: Of 5,548 identified records, 54 studies were included. Twenty-six studies assessed MSC treatment in TSCI, 14 in MS and nine in IS, of which seven, seven and five studies were controlled, respectively. There were seven serious adverse events (SAEs), of which four were related to the surgical procedure and included one death due to complications following the implantation of MSCs. Three SAEs were considered directly related to the MSC treatment and all these had a transient course. In TSCI, a meta-analysis showed no difference in conversion from AIS A to C and a trend toward more patients treated with MSCs improving from AIS A to B as compared to controls (p = 0.05). A subgroup analysis performed per protocol, showed more MSC treated patients improving from AIS A to C in studies including patients within 8 weeks after injury (p = 0.04). In MS and IS, there were no significant differences in clinical outcomes between MSC treated patients and controls as measured by EDSS and mRS, respectively. Interpretation: MSC-treatment is safe in patients with TSCI, MS and IS, although surgical implantation of MSC led to one fatal outcome in TSCI. There was no clear clinical benefit of MSC treatment, but this is not necessarily a proof of inefficacy due to the low number of controlled studies. Future studies assessing efficacy of MSC treatment should aim to do this in randomized, controlled studies.publishedVersio

Genetic epidemiology of amyotrophic lateral sclerosis in Norway - a 2-year population based study

Background: Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease that affects motor neurons. In Europe, disease-causing genetic variants have been identified in 40-70% of familial ALS patients and approximately in 5% of sporadic ALS patients. In Norway, the contribution of genetic variants to ALS has not yet been studied. In light of the potential development of personalized medicine, knowledge of genetic causes of ALS in a population is becoming increasingly important. The present study provides clinical and genetic data on familial and sporadic ALS patients in a Norwegian population-based cohort. Methods: Blood samples and clinical information from ALS patients were obtained at all 17 neurological departments throughout Norway during a 2-year period. Genetic analysis of the samples involved expansion analysis of C9orf72 and exome sequencing targeting 30 known ALS-linked genes. The variants were classified using genotype-phenotype correlations and bioinformatics tools. Results: A total of 279 ALS patients were included in the study. Of these, 11.5% had one or several family members affected with ALS, whereas 88.5% had no known family history of ALS. A genetic cause of ALS was identified in 31 individuals (11.1%), among which 18 (58.1%) were familial and 13 (41.9%) were sporadic. The most common genetic cause was the C9orf72 expansion (6.8%), which was identified in 8 familial and 11 sporadic ALS patients. Pathogenic or likely pathogenic variants of SOD1 and TBK1 were identified in 10 familial and 2 sporadic cases. C9orf72 expansions dominated in patients from the Northern and Central regions, whereas SOD1 variants dominated in patients from the South-Eastern region. Conclusion: In the present study, we identified several pathogenic gene variants in both familial and sporadic ALS patients. Restricting genetic analysis to only familial cases would miss more than 40 percent of those with a disease-causing genetic variant, indicating the need for genetic analysis in sporadic cases as well.publishedVersio

Exercise therapy and cognitive behavioural therapy to improve fatigue, daily activity performance and quality of life in Postpoliomyelitis Syndrome: the protocol of the FACTS-2-PPS trial

Contains fulltext : 88661.pdf (publisher's version ) (Open Access)BACKGROUND: Postpoliomyelitis Syndrome (PPS) is a complex of late onset neuromuscular symptoms with new or increased muscle weakness and muscle fatigability as key symptoms. Main clinical complaints are severe fatigue, deterioration in functional abilities and health related quality of life. Rehabilitation management is the mainstay of treatment. Two different therapeutic interventions may be prescribed (1) exercise therapy or (2) cognitive behavioural therapy (CBT). However, the evidence on the effectiveness of both interventions is limited. The primary aim of the FACTS-2-PPS trial is to study the efficacy of exercise therapy and CBT for reducing fatigue and improving activities and quality of life in patients with PPS. Additionally, the working mechanisms, patients' and therapists' expectations of and experiences with both interventions and cost-effectiveness will be evaluated. METHODS/DESIGN: A multi-centre, single-blinded, randomized controlled trial will be conducted. A sample of 81 severely fatigued patients with PPS will be recruited from 3 different university hospitals and their affiliate rehabilitation centres. Patients will be randomized to one of three groups i.e. (1) exercise therapy + usual care, (2) CBT + usual care, (3) usual care. At baseline, immediately post-intervention and at 3- and 6-months follow-up, fatigue, activities, quality of life and secondary outcomes will be assessed. Costs will be based on a cost questionnaire, and statistical analyses on GEE (generalized estimated equations). Analysis will also consider mechanisms of change during therapy. A responsive evaluation will be conducted to monitor the implementation process and to investigate the perspectives of patients and therapists on both interventions. DISCUSSION: A major strength of the FACTS-2-PPS study is the use of a mixed methods design in which a responsive and economic evaluation runs parallel to the trial. The results of this study will generate new evidence for the rehabilitation treatment of persons with PPS. TRIAL REGISTRATION: Dutch Trial Register NTR1371

Whole organisms or pure compounds? entourage effect versus drug specificity

As the therapeutic use of sacred plants and fungi becomes increasingly accepted by Western medicine, a tug of war has been taking place between those who advocate the traditional consumption of whole organisms and those who defend exclusively the utilization of purified compounds. The attempt to reduce organisms to single active principles is challenged by the sheer complexity of traditional medicine. Ayahuasca, for example, is a concoction of at least two plant species containing multiple psychoactive substances with complex interactions. Similarly, cannabis contains dozens of psychoactive substances whose specific combinations in different strains correspond to different types of therapeutic and cognitive effects. The “entourage effect” refers to the synergistic effects of the multiple compounds present in whole organisms, which may potentiate clinical efficacy while attenuating side effects. In opposition to this view, mainstream pharmacology is adamant about the need to use purified substances, presumably more specific and safe. In this chapter, I will review the evidence on both sides to discuss the scientific, economic, and political implications of this controversy. The evidence indicates that it is time to embrace the therapeutic complexity of psychedelics.2019-07-3