| 1. |
- Alterman, Mathias, et al.
(författare)
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P1/P1' modified HIV protease inhibitors as tools in two new sensitive surface plasmon resonance biosensor screening assays
- 2001
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Ingår i: European Journal of Pharmaceutical Sciences. - : Elsevier. - 0928-0987 .- 1879-0720. ; 13:2, s. 203-212
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Tidskriftsartikel (refereegranskat)abstract
- The commonly used HIV-1 protease assays rely on measurements of the effect of inhibitions on the hydrolysis rate of synthetic peptides. Recently an assay based on surface plasmon resonance (SPR) was introduced. We have taken advantage of the fact that the SPR signal is proportional to the mass of the analyte interacting with the immobilised molecule and developed two new improved efficient competition assay methods. Thus, high molecular weight binders were used as amplifiers of the surface plasmon resonance signal. Linkers were attached by a Heck reaction to the para-positions of the P1/P1′ benzyloxy groups of a linear C2-symmetric C-terminal duplicated inhibitor to enable (a) biotin labelling or (b) direct immobilisation of the inhibitor to the biosensor surface matrix. The interaction properties of a series of 17 structurally diverse inhibitors was assessed and compared to previously reported data. The most sensitive assay was obtained by immobilising the enzyme and amplifying the signal with an antibody, giving a detection range between 0.1 nM and 10 μM. Immobilisation of the inhibitor resulted in a stable and durable surface but a narrower detection range (1–100 nM). The two competition assays are anticipated to be very suitable for fast screening of potential HIV inhibitors.
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| 5. |
- Elinder, Malin, 1977-, et al.
(författare)
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Screening for NNRTIs with Slow Dissociation and High Affinity for a Panel of HIV-1 RT Variants
- 2009
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Ingår i: Journal of Biomolecular Screening. - : SAGE. - 1087-0571 .- 1552-454X. ; 14:4, s. 395-403
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Tidskriftsartikel (refereegranskat)abstract
- A lead optimization library consisting of 800 HIV-1 nonnucleoside reverse transcriptase inhibitors (NNRTIs) was screened in parallel against 4 clinically relevant variants of HIV-1 RT (Wt, L100I, Y181C, and K103N) using a surface plasmon resonance-based biosensor. the aim was to identify inhibitors suitable in specific topical microbicides efficient for preventing the transmission of a range of clinically significant strains of HIV-1. the authors hypothesized that such compounds should have high affinity and slow dissociation rates for multiple variants of the target. to efficiently analyze the large amount of real-time data (sensorgrams) that were generated in the screening, they initially used signals from 3 selected time points to identify compounds with high affinity and slow dissociation for the complete panel of enzyme variants. hits were confirmed by visually inspecting the complete sensorgrams. two structurally unrelated compounds fulfilled the hit criteria, but only 1 compound was found to (a) compete with a known NNRTI for binding to the NNRTI site, (b) inhibit HIV-1 RT activity, and (c) inhibit HIV-1 replication in cell culture, for all 4 enzyme variants. this novel screening methodology offers high-resolution real-time kinetic data for multiple targets in parallel. it is expected to have broad applicability for the discovery of compounds with defined kinetic profiles, crucial for optimal therapeutic effects.
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| 6. |
- Hämäläinen, Markku D., et al.
(författare)
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Characterization of a set of HIV-1 protease inhibitors using binding kinetics data from a biosensor-based screen
- 2000
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Ingår i: Journal of Biomolecular Screening. - : Elsevier BV. - 1087-0571 .- 1552-454X. ; 5:5, s. 353-359
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Tidskriftsartikel (refereegranskat)abstract
- The interaction between 290 structurally diverse human immunodeficiency virus type 1 (HIV-1) protease inhibitors and the immobilized enzyme was analyzed with an optical biosensor, Although only a single concentration of inhibitor was used, information about the kinetics of the interaction could be obtained by extracting binding signals at discrete time points. The statistical correlation between the biosensor binding data, inhibition of enzyme activity (K-i), and viral replication (EC50) revealed that the association and dissociation rates for the interaction could be resolved and that they were characteristic for the compounds. The most potent inhibitors, with respect to K-i and EC50 values, including the clinically used drugs, all exhibited fast association and slow dissociation rates. Selective or partially selective binders for HIV-1 protease could be distinguished from compounds that showed a general protein-binding tendency by using three reference target proteins. This biosensor-based direct binding assay revealed a capacity to efficiently provide high-resolution information on the interaction kinetics and specificity of the interaction of a set of compounds with several targets simultaneously.
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| 7. |
- Lim, Elaine T, et al.
(författare)
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Distribution and Medical Impact of Loss-of-Function Variants in the Finnish Founder Population.
- 2014
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Ingår i: PLoS Genetics. - : Public Library of Science (PLoS). - 1553-7404. ; 10:7
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Tidskriftsartikel (refereegranskat)abstract
- Exome sequencing studies in complex diseases are challenged by the allelic heterogeneity, large number and modest effect sizes of associated variants on disease risk and the presence of large numbers of neutral variants, even in phenotypically relevant genes. Isolated populations with recent bottlenecks offer advantages for studying rare variants in complex diseases as they have deleterious variants that are present at higher frequencies as well as a substantial reduction in rare neutral variation. To explore the potential of the Finnish founder population for studying low-frequency (0.5-5%) variants in complex diseases, we compared exome sequence data on 3,000 Finns to the same number of non-Finnish Europeans and discovered that, despite having fewer variable sites overall, the average Finn has more low-frequency loss-of-function variants and complete gene knockouts. We then used several well-characterized Finnish population cohorts to study the phenotypic effects of 83 enriched loss-of-function variants across 60 phenotypes in 36,262 Finns. Using a deep set of quantitative traits collected on these cohorts, we show 5 associations (p<5×10-8) including splice variants in LPA that lowered plasma lipoprotein(a) levels (P = 1.5×10-117). Through accessing the national medical records of these participants, we evaluate the LPA finding via Mendelian randomization and confirm that these splice variants confer protection from cardiovascular disease (OR = 0.84, P = 3×10-4), demonstrating for the first time the correlation between very low levels of LPA in humans with potential therapeutic implications for cardiovascular diseases. More generally, this study articulates substantial advantages for studying the role of rare variation in complex phenotypes in founder populations like the Finns and by combining a unique population genetic history with data from large population cohorts and centralized research access to National Health Registers.
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| 12. |
- Markgren, Per-Olof, et al.
(författare)
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Screening of compounds interacting with HIV-1 proteinase using optical biosensor technology
- 1998
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Ingår i: Analytical Biochemistry. - : Elsevier BV. - 0003-2697 .- 1096-0309. ; 265:2, s. 340-350
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Tidskriftsartikel (refereegranskat)abstract
- A high-resolution optical biosensor assay for screening of low-molecular-weight compounds, using an immobilized protein target, has been developed. HIV-1 proteinase was immobilized on the sensor surface by direct amine coupling and a variety of inhibitors and noninteracting reference drugs were applied to the sensor surface in a continuous how of buffer. The procedure did not require intrinsic reporter groups, substrates, inhibitors, or other ligands for detection. By using a reference protein, the signal could be corrected for the relatively large background signal caused by differences in dimethyl sulfoxide concentration between running and sample buffers. Substances binding with high affinity (K-i in nM range) required efficient regeneration of the sensor surface and washing of the injection system between sample cycles to get consistent results. Analysis was simplified by using report points, extracted during both association and dissociation phases, and a simple graphical display of data. The optimized assay could correctly distinguish HIV-1 inhibitors from other compounds in a randomized series, indicate differences in their interaction kinetics, and reveal artifacts due to nonspecific signals, incomplete regeneration, or carryover. The method is expected to be generally applicable to secondary screening of low-molecular-weight compound libraries with proteins as targets.
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| 15. |
- Nordström, Helena, et al.
(författare)
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Identification of MMP-12 Inhibitors by Using Biosensor-Based Screening of a Fragment Library
- 2008
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Ingår i: Journal of Medicinal Chemistry. - : American Chemical Society (ACS). - 0022-2623 .- 1520-4804. ; 51:12, s. 3449-3459
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Tidskriftsartikel (refereegranskat)abstract
- Small inhibitors of matrix metalloproteinase 12 (MMP-12) have been identified with a biosensor-based screening strategy and a specifically designed fragment library. The interaction between fragments and three variants of the target and a reference protein with an active-site zinc ion was measured continuously by surface plasmon resonance. The developed experimental design overcame the inherent instability of MMP-12 and allowed the identification of fragments that interacted specifically with the active-site of MMP-12 but not with the reference protein. The interaction with MMP-12 for selected compounds were analyzed for concentration dependence and saturability. Compounds interacting distinctly with the target were further evaluated by an activity-based assay, verifying MMP-12 inhibition. Two effective inhibitors were identified, and the compound with highest affinity was confirmed to be a competitive inhibitor with an IC50 of 290 nM and a ligand efficiency of 0.7 kcal/mol heavy atom. This procedure integrates selectivity and binding site identification into the screening procedure and does not require structure determination.
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| 17. |
- Shuman, Cynthia F., et al.
(författare)
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Kinetic and thermodynamic characterization of HIV-1 protease inhibitors
- 2004
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Ingår i: Journal of Molecular Recognition. - 0952-3499 .- 1099-1352. ; 17:2, s. 106-19
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Tidskriftsartikel (refereegranskat)abstract
- Interaction kinetic and thermodynamic analyses provide information beyond that obtained in general inhibition studies, and may contribute to the design of improved inhibitors and increased understanding of molecular interactions. Thus, a biosensor-based method was used to characterize the interactions between HIV-1 protease and seven inhibitors, revealing distinguishing kinetic and thermodynamic characteristics for the inhibitors. Lopinavir had fast association and the highest affinity of the tested compounds, and the interaction kinetics were less temperature-dependent as compared with the other inhibitors. Amprenavir, indinavir and ritonavir showed non-linear temperature dependencies of the kinetics. The free energy, enthalpy and entropy (DeltaG, DeltaH, DeltaS) were determined, and the energetics of complex association (DeltaG(on), DeltaH(on), DeltaS(on)) and dissociation (DeltaG(off), DeltaH(off), DeltaS(off)) were resolved. In general, the energetics for the studied inhibitors was in the same range, with the negative free energy change (DeltaG < 0) due primarily to increased entropy (DeltaS > 0). Thus, the driving force of the interaction was increased degrees of freedom in the system (entropy) rather than the formation of bonds between the enzyme and inhibitor (enthalpy). Although the DeltaG(on) and DeltaG(off) were in the same range for all inhibitors, the enthalpy and entropy terms contributed differently to association and dissociation, distinguishing these phases energetically. Dissociation was accompanied by positive enthalpy (DeltaH(off) > 0) and negative entropy (DeltaS(off) < 0) changes, whereas association for all inhibitors except lopinavir had positive entropy changes (DeltaS(on) > 0), demonstrating unique energetic characteristics for lopinavir. This study indicates that this type of data will be useful for the characterization of target-ligand interactions and the development of new inhibitors of HIV-1 protease
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| 19. |
- Wallden, Mats, et al.
(författare)
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Evaluation of 6 years of eHealth data in the alcohol use disorder field indicates improved efficacy of care
- 2024
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Ingår i: Frontiers in Digital Health. - : Frontiers Media S.A.. - 2673-253X. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundPredictive eHealth tools will change the field of medicine, however long-term data is scarce. Here, we report findings on data collected over 6 years with an AI-based eHealth system for supporting the treatment of alcohol use disorder.MethodsSince the deployment of Previct Alcohol, structured data has been archived in a data warehouse, currently comprising 505,641 patient days. The frequencies of relapse and caregiver-patient messaging over time was studied. The effects of both introducing an AI-driven relapse prediction tool and the COVID-19 pandemic were analyzed.ResultsThe relapse frequency per patient day among Previct Alcohol users was 0.28 in 2016, 0.22 in 2020 and 0.25 in 2022 with no drastic change during COVID-19. When a relapse was predicted, the actual occurrence of relapse in the days immediately after was found to be above average. Additionally, there was a noticeable increase in caregiver interactions following these predictions. When caregivers were not informed of these predictions, the risk of relapse was found to be higher compared to when the prediction tool was actively being used. The prediction tool decreased the relapse risk by 9% for relapses that were of short duration and by 18% for relapses that lasted more than 3 days.ConclusionsThe eHealth system Previct Alcohol allows for high resolution measurements, enabling precise identifications of relapse patterns and follow up on individual and population-based alcohol use disorder treatment. eHealth relapse prediction aids the caregiver to act timely, which reduces, delays, and shortens relapses.
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| 21. |
- Zetterström, Andreas, et al.
(författare)
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Maximum Time Between Tests : A Digital Biomarker to Detect Therapy Compliance and Assess Schedule Quality in Measurement-Based eHealth Systems for Alcohol Use Disorder
- 2019
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Ingår i: Alcohol and Alcoholism. - : OXFORD UNIV PRESS. - 0735-0414 .- 1464-3502. ; 54:1, s. 70-72
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Tidskriftsartikel (refereegranskat)abstract
- Aim: To evaluate, in a breathalyzer-based eHealth system, whether the time-based digital biomarker maximum time between tests' (MTBT) brings valuable information on alcohol consumption patterns as confirmed by correlation with blood phosphatidyl ethanol (PEth), serum carbohydrate deficient transferrin (CDT) and timeline follow-back data.Method: Data on 54 patients in follow-up for treatment of alcohol use disorder were analysed.Results: The model of weekly averages of 24-log transformed MTBT adequately described timeline follow-back data (P < 0.0001, R = 0.27-0.38, n = 650). Significant correlations were noted between MTBT and PEth (P < 0.0001, R = 0.41, n = 148) and between MTBT and CDT (P < 0.0079, R = 0.22, n = 120).Conclusions: The time-based digital biomarker maximum time between tests' described here has the potential to become a generally useful metric for all scheduled measurement-based eHealth systems to monitor test behaviour and compliance, factors important for dosing' of eHealth systems and for early prediction and interventions of lapse/relapse.
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| 22. |
- Zetterström, Andreas, et al.
(författare)
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Processing incomplete questionnaire data into continuous digital biomarkers for addiction monitoring
- 2022
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 17:7
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: eHealth systems allow efficient daily smartphone-based collection of self-reported data on mood, wellbeing, routines, and motivation; however, missing data is frequent. Within addictive disorders, missing data may reflect lack of motivation to stay sober. We hypothesize that qualitative questionnaire data contains valuable information, which after proper handling of missing data becomes more useful for practitioners.Methods: Anonymized data from daily questionnaires containing 11 questions was collected with an eHealth system for 751 patients with alcohol use disorder (AUD). Two digital continuous biomarkers were composed from 9 wellbeing questions (WeBe-i) and from two questions representing motivation/self-confidence to remain sober (MotSC-i). To investigate possible loss of information in the process of composing the digital biomarkers, performance of neural networks to predict exacerbation events (relapse) in alcohol use disorder was compared.Results: Long short-term memory (LSTM) neural networks predicted a coming exacerbation event 1-3 days (AUC 0.68-0.70) and 5-7 days (AUC 0.65-0.68) in advance on unseen patients. The predictive capability of digital biomarkers and raw questionnaire data was equal, indicating no loss of information. The transformation into digital biomarkers enable a continuous graphical display of each patient's clinical course and a combined interpretation of qualitative and quantitative aspects of recovery on a time scale.Conclusion: By transforming questionnaire data with large proportion of missing data into continuous digital biomarkers, the information captured by questionnaires can be more easily used in clinical practice. Information, assessed by the capability to predict exacerbation events of AUD, is preserved when processing raw questionnaire data into digital biomarkers.
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| 23. |
- Zetterström, Andreas, et al.
(författare)
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The Clinical Course of Alcohol Use Disorder Depicted by Digital Biomarkers
- 2021
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Ingår i: Frontiers in Digital Health. - : Frontiers Media S.A.. - 2673-253X. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- Aims: This study introduces new digital biomarkers to be used as precise, objective tools to measure and describe the clinical course of patients with alcohol use disorder (AUD).Methods: An algorithm is outlined for the calculation of a new digital biomarker, the recovery and exacerbation index (REI), which describes the current trend in a patient's clinical course of AUD. A threshold applied to the REI identifies the starting point and the length of an exacerbation event (EE). The disease patterns and periodicity are described by the number, length, and distance between EEs. The algorithms were tested on data from patients from previous clinical trials (n = 51) and clinical practice (n = 1,717).Results: Our study indicates that the digital biomarker-based description of the clinical course of AUD might be superior to the traditional self-reported relapse/remission concept and conventional biomarkers due to higher data quality (alcohol measured) and time resolution. We found that EEs and the REI introduce distinct tools to identify qualitative and quantitative differences in drinking patterns (drinks per drinking day, phosphatidyl ethanol levels, weekday and holiday patterns) and effect of treatment time.Conclusions: This study indicates that the disease state-level, trend and periodicity-can be mathematically described and visualized with digital biomarkers, thereby improving knowledge about the clinical course of AUD and enabling clinical decision-making and adaptive care. The algorithms provide a basis for machine-learning-driven research that might also be applied for other disorders where daily data are available from digital health systems.
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