| 1. |
- Caldeweyher, Eike, et al.
(författare)
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Hybrid Machine Learning Approach to Predict the Site Selectivity of Iridium-Catalyzed Arene Borylation
- 2023
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 145:31, s. 17367-17376
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Tidskriftsartikel (refereegranskat)abstract
- The borylation of aryl and heteroaryl C–H bonds is valuable for the site-selective functionalization of C–H bonds in complex molecules. Iridium catalysts ligated by bipyridine ligands catalyze the borylation of the C–H bond that is most acidic and least sterically hindered in an arene, but predicting the site of borylation in molecules containing multiple arenes is difficult. To address this challenge, we report a hybrid computational model that predicts the Site of Borylation (SoBo) in complex molecules. The SoBo model combines density functional theory, semiempirical quantum mechanics, cheminformatics, linear regression, and machine learning to predict site selectivity and to extrapolate these predictions to new chemical space. Experimental validation of SoBo showed that the model predicts the major site of borylation of pharmaceutical intermediates with higher accuracy than prior machine-learning models or human experts, demonstrating that SoBo will be useful to guide experiments for the borylation of specific C(sp2)–H bonds during pharmaceutical development.
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| 2. |
- Andappan, Murugaiah M. S., et al.
(författare)
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From the First Selective Non-Peptide AT(2) Receptor Agonist to Structurally Related Antagonists
- 2012
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Ingår i: Journal of Medicinal Chemistry. - : American Chemical Society (ACS). - 0022-2623 .- 1520-4804. ; 55:5, s. 2265-2278
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Tidskriftsartikel (refereegranskat)abstract
- A para substitution pattern of the phenyl ring is a characteristic feature of the first reported selective AT(2) receptor agonist M024/C21 (1) and all the nonpeptidic AT(2) receptor agonists described so far. Two series of compounds structurally related to 1 but with a meta substitution pattern have now been synthesized and biologically evaluated for their affinity to the AT(1) and AT(2) receptors. A high AT(2)/AT(1) receptor selectivity was obtained with all 41 compounds synthesized, and the majority exhibited K-i ranging from 2 to 100 nM. Five compounds were evaluated for their functional activity at the AT(2) receptor, applying a neurite outgrowth assay in NG108-15 cells.. Notably, four of the five compounds, with representatives from both series, acted as potent AT(2) receptor antagonists. These compounds were found to be considerably more effective than PD 123,319, the standard AT(2) receptor antagonist used in most laboratories. No AT(2) receptor antagonists were previously reported among the derivatives with a para substitution pattern. Hence, by a minor modification of the agonist 1 it could be transformed into the antagonist, compound 38. These compounds should serve as valuable tools in the assessment of the role of the AT(2) receptor in more complex physiological models.
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| 3. |
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| 4. |
- Belfrage, Anna Karin, 1977-, et al.
(författare)
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Efficient and Selective Palladium-Catalysed C-3 Urea Couplings to 3,5-Dichloro-2(1H)-pyrazinones
- 2015
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Ingår i: European Journal of Organic Chemistry. - : Wiley. - 1434-193X .- 1099-0690. ; :5, s. 978-986
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Tidskriftsartikel (refereegranskat)abstract
- The development of a robust palladium-catalysed urea N-arylation protocol to install various ureas at the 3-position of the 2(1H)-pyrazinone scaffold is described. The method involves Pd(OAc)2 in combination with bidentate ligands, xantphos [4,5-bis(diphenylphosphino)-9,9-dimethylxanthene] in particular, and resulted in good to excellent coupling yields of aliphatic, aromatic, and sterically hindered ureas. Furthermore, the C-3 chlorine was shown to be selectively displaced in the presence of aryl halide ureas, and this finding was supported by density functional theory (DFT) calculations. This allows further diversification of the scaffold for the production of compound libraries. Overall, the protocol facilitates further exploitation of pyrazinones as beta-sheet-inducing scaffolds in the development of sophisticated peptidomimetics/protease inhibitors. This is exemplified here by the synthesis of a new pyrazinone-based hepatitis C virus (HCV) NS3 protease inhibitor.
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| 5. |
- Borhade, Sanjay R, et al.
(författare)
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Inhibition of Insulin-Regulated Aminopeptidase (IRAP) by Arylsulfonamides
- 2014
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Ingår i: ChemistryOpen. - : Wiley. - 2191-1363. ; 3:6, s. 256-263
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Tidskriftsartikel (refereegranskat)abstract
- The inhibition of insulin-regulated aminopeptidase (IRAP, EC 3.4.11.3) by angiotenesin IV is known to improve memory and learning in rats. Screening 10 500 low-molecular-weight compounds in an enzyme inhibition assay with IRAP from Chinese Hamster Ovary (CHO) cells provided an arylsulfonamide (N-(3-(1H-tetrazol-5-yl)phenyl)-4-bromo-5-chlorothiophene-2-sulfonamide), comprising a tetrazole in the meta position of the aromatic ring, as a hit. Analogues of this hit were synthesized, and their inhibitory capacities were determined. A small structure-activity relationship study revealed that the sulfonamide function and the tetrazole ring are crucial for IRAP inhibition. The inhibitors exhibited a moderate inhibitory potency with an IC50=1.1±0.5 μm for the best inhibitor in the series. Further optimization of this new class of IRAP inhibitors is required to make them attractive as research tools and as potential cognitive enhancers.
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| 6. |
- Bradshaw, Clare, et al.
(författare)
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Physical Disturbance by Bottom Trawling Suspends Particulate Matter and Alters Biogeochemical Processes on and Near the Seafloor
- 2021
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Ingår i: Frontiers in Marine Science. - : Frontiers Media SA. - 2296-7745. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Bottom trawling is known to affect benthic faunal communities but its effects on sediment suspension and seabed biogeochemistry are less well described. In addition, few studies have been carried out in the Baltic Sea, despite decades of trawling in this unique brackish environment and the frequent occurrence of trawling in areas where hypoxia and low and variable salinity already act as ecosystem stressors. We measured the physical and biogeochemical impacts of an otter trawl on a muddy Baltic seabed. Multibeam bathymetry revealed a 36 m-wide trawl track, comprising parallel furrows and sediment piles caused by the trawl doors and shallower grooves from the groundgear, that displaced 1,000 m3 (500 t) sediment and suspended 9.5 t sediment per km of track. The trawl doors had less effect than the rest of the gear in terms of total sediment mass but per m2 the doors had 5× the displacement and 2× the suspension effect, due to their greater penetration and hydrodynamic drag. The suspended sediment spread >1 km away over the following 3–4 days, creating a 5–10 m thick layer of turbid bottom water. Turbidity reached 4.3 NTU (7 mgDW L–1), 550 m from the track, 20 h post-trawling. Particulate Al, Ti, Fe, P, and Mn were correlated with the spatio-temporal pattern of suspension. There was a pulse of dissolved N, P, and Mn to a height of 10 m above the seabed within a few hundred meters of the track, 2 h post-trawling. Dissolved methane concentrations were elevated in the water for at least 20 h. Sediment biogeochemistry in the door track was still perturbed after 48 h, with a decreased oxygen penetration depth and nutrient and oxygen fluxes across the sediment-water interface. These results clearly show the physical effects of bottom trawling, both on seabed topography (on the scale of km and years) and on sediment and particle suspension (on the scale of km and days-weeks). Alterations to biogeochemical processes suggest that, where bottom trawling is frequent, sediment biogeochemistry may not have time to recover between disturbance events and elevated turbidity may persist, even outside the trawled area.
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| 7. |
- Byrne, Liam, et al.
(författare)
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Enantioselective Synthesis of Atropisomeric Biaryls using Biaryl 2,5-Diphenylphospholanes as Ligands for Palladium-Catalysed Suzuki-Miyaura Reactions
- 2021
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Ingår i: Advanced Synthesis and Catalysis. - : John Wiley & Sons. - 1615-4150 .- 1615-4169. ; 363:1, s. 259-267
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Tidskriftsartikel (refereegranskat)abstract
- Here we describe the development of biaryl 2,5-diphenylphospholanes as a new class of C-2-symmetric, monodentate ligands for asymmetric Suzuki-Miyaura (ASM) reactions. Screening of a series of exemplary phospholanes led to the identification of two ligands that were used to prepare a range of atropisomeric biaryl and heterobiaryl products with good to excellent levels of enantioselectivity (up to 97:3 e.r.) under mild conditions. DFT studies suggest that the formation of a constraining ligand pocket and coordination of one of the biaryl methoxy groups in the optimised ligands to the metal centre is crucial for restricting conformational freedom in the bond-forming step.
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| 8. |
- Claerhout, Stijn, et al.
(författare)
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Synthesis of functionalized furopyrazines as restricted dipeptidomimetics
- 2012
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Ingår i: Tetrahedron. - : Elsevier BV. - 0040-4020 .- 1464-5416. ; 68:14, s. 3019-3029
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Tidskriftsartikel (refereegranskat)abstract
- Herein, an efficient synthetic approach to a furopyrazine scaffold with four points of diversity, starting from 2(1H)-pyrazinones, with dipeptomimetic properties, is presented. R-groups corresponding to amino acid side chains were introduced during the 2(1H)-pyrazinone and subsequent furopyrazine formation. The furopyrazine scaffold was further functionalized with an amino- and a carboxy-terminus resulting in a conformationally restricted dipeptidomimetic scaffold. The carboxy-terminus was introduced via a chemoselective vinylation of the 7-position followed by oxidative cleavage, while the amino-terminus was obtained via Buchwald-Hartwig amidation of the 2-position of the scaffold. The versatility of the synthetic method was demonstrated by the synthesis of a small library of diversely substituted furopyrazines having various amino acid side chains on the four points of diversity. Evaluation with an X-ray structure of the scaffold and computational analysis supports the exploitation of the furopyrazine scaffold as a restricted dipeptide mimic, which can mimic the two central residues of a beta-turn.
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| 9. |
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| 10. |
- Danielsson, Christian, et al.
(författare)
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Polytherapy with hERG-blocking antiepileptic drugs : Increased risk for embryonic cardiac arrhythmia and teratogenicity
- 2007
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Ingår i: Birth defects research. Clinical and molecular teratology. - : Wiley. - 1542-0752 .- 1542-0760. ; 79:8, s. 595-603
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The antiepileptic drugs (AEDs) phenytoin, phenobarbital, dimethadione, and carbamazepine cause a similar pattern of malformations in humans, with an increased risk after polytherapy. The teratogenicity has been linked to cardiac rhythm disturbances and hypoxic damage as a consequence of their common potential to inhibit a specific potassium ion current (IKr). The IKr is of major importance for embryonic cardiac repolarization and rhythm regulation. This study investigated whether these AEDs cause irregular rhythm and if various combinations of AEDs result in higher arrhythmia risk than exposure to a single AED. METHODS: The effects on heart rhythm of a single AED (monotherapy), and of various combinations (polytherapy) of AEDs, in gestational day 10 C57BL mouse embryos in culture were analyzed and graphically illustrated during a 25 s recording with a digitalization technique. RESULTS: All of the studied AEDs caused increased intervals between heartbeats (resulting in bradycardia) and large variations in the interval between heartbeats (resulting in irregular rhythm) in a concentration-dependent manner in cultured mouse embryos. Dimethadione caused irregular rhythm at concentrations within and phenytoin slightly above the therapeutic ranges. Polytherapy resulted in more substantial prolongation of the mean interval between heartbeats (>60 ms) than monotherapy at clinically relevant concentrations. CONCLUSIONS: The results suggest that polytherapy more than monotherapy causes substantial prolongation of the cardiac repolarization, a marker associated with high risk of developing irregular rhythm during longer exposure periods (days to months). This supports the idea that the increased risk for malformations following polytherapy is linked to an increased risk for cardiac rhythm disturbances.
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| 11. |
- Ekblom Bak, Elin, 1981-, et al.
(författare)
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Accelerometer derived physical activity patterns in 27.890 middle‐aged adults : The SCAPIS cohort study
- 2022
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Ingår i: Scandinavian Journal of Medicine and Science in Sports. - : John Wiley & Sons. - 0905-7188 .- 1600-0838. ; 32:5, s. 866-880
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Tidskriftsartikel (refereegranskat)abstract
- The present study aims to describe accelerometer-assessed physical activity (PA) patterns and fulfillment of PA recommendations in a large sample of middle-aged men and women, and to study differences between subgroups of socio-demographic, socio-economic, and lifestyle-related variables. A total of 27 890 (92.5% of total participants, 52% women, aged 50–64 years) middle-aged men and women with at least four days of valid hip-worn accelerometer data (Actigraph GT3X+, wGT3X+ and wGT3X-BT) from the Swedish CArdioPulmonary bioImage Study, SCAPIS, were included. In total, 54.5% of daily wear time was spent sedentary, 39.1% in low, 5.4% in moderate, and only 0.1% in vigorous PA. Male sex, higher education, low financial strain, born in Sweden, and sedentary/light working situation were related to higher sedentary time, but also higher levels of vigorous PA. High BMI and having multiple chronic diseases associated strongly with higher sedentary time and less time in all three PA intensities. All-year physically active commuters had an overall more active PA pattern. The proportion fulfilling current PA recommendations varied substantially (1.4% to 92.2%) depending on data handling procedures and definition used. Twenty-eight percent was defined as having an “at-risk” behavior, which included both high sedentary time and low vigorous PA. In this large population-based sample, a majority of time was spent sedentary and only a fraction in vigorous PA, with clinically important variations between subgroups. This study provides important reference material and emphasizes the importance of a comprehensive assessment of all aspects of the individual PA pattern in future research and clinical practice.
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| 12. |
- Erdélyi, Máté, et al.
(författare)
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Chemistry and folding of photomodulable peptides : stilbene and thioaurone-type candidates for conformational switches
- 2008
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Ingår i: Organic and biomolecular chemistry. - : Royal Society of Chemistry (RSC). - 1477-0520 .- 1477-0539. ; 6:23, s. 4356-4373
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Tidskriftsartikel (refereegranskat)abstract
- Optimized synthetic strategies for the preparation of photoswitchable molecular scaffolds based on stilbene or on thioaurone chromophores and their conformationally directing properties, as studied by computations and by NMR spectroscopy, are addressed. For the stilbene peptidomimetics 1, 2 and 3, the length of connecting linkers between the chromophore and the peptide strands was varied, resulting in photochromic dipeptidomimetics with various flexibility. Building blocks of higher rigidity, based on para-substituted thioaurone ( 4 and 6) and meta-substituted thioaurone chromophores ( 5 and 7) are shown to have a stronger conformationally directing effect. Design, synthesis, theoretical and experimental conformational analyses are presented.
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| 13. |
- Erdelyi, Mate, 1975, et al.
(författare)
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Chemistry and Folding of Photomodulable Peptides - Stilbene and Thioaurone-type Conformational Switches
- 2008
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Ingår i: Organic & Biomolecular Chemistry. - 1477-0520. ; 6:23, s. 5346-4373
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Tidskriftsartikel (refereegranskat)abstract
- Optimized synthetic strategies for the preparation of photoswitchable molecular scaffolds based on stilbene or on thioaurone chromophores and their conformationally directing properties, as studied by computations and by NMR spectroscopy, are addressed. For the stilbene peptidomimetics 1, 2 and 3, the length of connecting linkers between the chromophore and the peptide strands was varied, resulting in photochromic dipeptidomimetics with various flexibility. Building blocks of higher rigidity, based on para-substituted thioaurone (4 and 6) and meta-substituted thioaurone chromophores (5 and 7) are shown to have a stronger conformationally directing effect. Design, synthesis, theoretical and experimental conformational analyses are presented.
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| 14. |
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| 15. |
- Eriksson, Jonas, et al.
(författare)
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Synthesis and preclinical evaluation of the CRTH2 antagonist [11C]MK-7246 as a novel PET tracer and potential surrogate marker for pancreatic beta-cell mass
- 2019
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Ingår i: Nuclear Medicine and Biology. - : Elsevier BV. - 0969-8051 .- 1872-9614. ; 71, s. 1-10
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Tidskriftsartikel (refereegranskat)abstract
- Introduction: MK-7246 is a potent and selective antagonist for chemoattractant receptor-homologous molecule expressed on Th2 cells (CRTH2). Within the pancreas CRTH2 is selectively expressed in pancreatic β-cells where it is believed to play a role in insulin release. Reduction in β-cell mass and insufficient insulin secretion in response to elevated blood glucose levels is a hallmark for type 1 and type 2 diabetes. Reported here is the synthesis of [11C]MK-7246 and initial preclinical evaluation towards CRTH2 imaging. The aim is to develop a method to quantify β-cell mass with PET and facilitate non-invasive studies of disease progression in individuals with type 2 diabetes.Methods: The precursor N-desmethyl-O-methyl MK-7246 was synthesized in seven steps and subjected to methylation with [11C]methyl iodide followed by hydrolysis to obtain [11C]MK-7246 labelled in the N-methyl position. Preclinical evaluation included in vitro radiography and immune-staining performed in human pancreatic biopsies. Biodistribution studies were performed in rat by PET-MRI and in pig by PET-CT imaging. The specific tracer uptake was examined in pig by scanning before and after administration of MK-7246 (1 mg/kg). Predicted dosimetry of [11C]MK-7246 in human males was estimated based on the biodistribution in rat.Results: [11C]MK-7246 was obtained with activities sufficient for the current investigations (270±120 MBq) and a radiochemical purity of 93±2%. The tracer displayed focal binding in areas with insulin positive islet of Langerhans in human pancreas sections. Baseline uptake in pig was significantly reduced in CRTH2-rich areas after administration of MK-7246; pancreas (66% reduction) and spleen (88% reduction). [11C]MK-7246 exhibited a safe human predicted dosimetry profile as extrapolated from the rat biodistribution data.Conclusions: Initial preclinical in vitro and in vivo evaluation of [11C]MK-7246 show binding and biodistribution properties suitable for PET imaging of CRTH2. Further studies are warranted to assess its potential in β-cell mass imaging and CRTH2 drug development.
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| 16. |
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| 17. |
- Fransson, Rebecca, 1980-, et al.
(författare)
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Constrained H-Phe-Phe-NH2 Analogues With High Affinity to the Substance P 1-7 Binding Site and With Improved Metabolic Stability and Cell Permeability
- 2013
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Ingår i: Journal of Medicinal Chemistry. - : American Chemical Society (ACS). - 0022-2623 .- 1520-4804. ; 56:12, s. 4953-4965
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Tidskriftsartikel (refereegranskat)abstract
- We recently reported the discovery of H-Phe-Phe-NH2 as a small and high affinity ligand for the substance P 1-7 (SP1-7, H-Arg-Pro-Lys-Pro-Gln-Gln-Phe-OH) specific binding site and its intriguing ability to reduce neuropathic pain. With the overall aim to develop stable and orally bioavailable SP1-7 mimetics, the dipeptide was chosen as a lead compound. Herein the structure-activity relationship (SAR) of a set of modified H-Phe-Phe-NH2 analogues is presented together with their potential active uptake by PEPT1 transporter, intestinal permeability, and metabolic stability. Local constraints via peptide backbone methylation or preparation of cyclized analogues based on pyrrolidine were evaluated and were shown to significantly improve the in vitro pharmacokinetic properties. The SAR was rationalized by deriving a plausible binding pose for the high affinity ligands. Rigidification using a 3-phenylpyrrolidine moiety in the C-terminal of H-Phe-Phe-NH2 resulted in high affinity and improved intrinsic clearance and intestinal epithelial permeability.
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| 18. |
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| 19. |
- Fransson, Rebecca, et al.
(författare)
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Discovery of Dipeptides with High Affinity to the Specific Binding Site for Substance P1-7
- 2010
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Ingår i: Journal of Medicinal Chemistry. - : American Chemical Society (ACS). - 0022-2623 .- 1520-4804. ; 53:6, s. 2383-2389
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Tidskriftsartikel (refereegranskat)abstract
- Substance P 1-7 (SP1-7, H-Arg-Pro-Lys-Pro-Gln-Gln-Phe-OH) is the major bioactive metabolite of substance P. The interest in this heptapeptide originates from the observation that it modulates, and in certain cases opposes the effects of the parent peptide. e.g., the nociceptive effect. The p-opioid receptor agonist endomorphin-2 (EM-2, H-Tyr-Pro-Phe-Phe-NH2) has been found to also interact with the specific binding site of SP1-7 with only a 10-fold lower affinity compared to the native peptide. Considering the smaller size of EM-2 compared to the target heptapeptide, it was selected as a lead compound in the development of low-molecular-weight ligands to the SP1-7 binding site. An alanine scan and truncation study led to the unexpected discovery of the dipeptide H-Phe-Phe-NH2 (K-i = 1.5 nM), having equal affinity as the endogenous heptapeptide SP1-7. Moreover, the studies show that the C-terminal phenylalanine amide is crucial for the affinity of the dipeptide.
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| 20. |
- Georgsson, Jennie, et al.
(författare)
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Angiotensin II Pseudopeptides Containing 1,3,5-Trisubstituted Benzene Scaffolds with High AT2 Receptor Affinity
- 2005
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Ingår i: Journal of Medicinal Chemistry. - : American Chemical Society (ACS). - 0022-2623 .- 1520-4804. ; 48:21, s. 6620-6631
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Tidskriftsartikel (refereegranskat)abstract
- Two 1,3,5-trisubstituted aromatic scaffolds intended to serve as γ-turn mimetics have been synthesized and incorporated in five pseudopeptide analogues of angiotensin II (Asp-Arg-Val-Tyr-Ile-His-Pro-Phe), replacing Val-Tyr-Ile, Val-Tyr, or Tyr-Ile. All the tested compounds exhibited nanomolar affinity for the AT2 receptor with the best compound (3) having a Ki of 1.85 nM. Four pseudopeptides were AT2 selective, while one (5) also exhibited good affinity for the AT1 receptor (Ki = 30.3 nM). This pseudopeptide exerted full agonistic activity in an AT2 receptor induced neurite outgrowth assay but displayed no agonistic effect in an AT1 receptor functional assay. Molecular modeling, using the program DISCOtech, showed that the high-affinity ligands could interact similarly with the AT2 receptor as other ligands with high affinity for this receptor. A tentative agonist model is proposed for AT2 receptor activation by angiotensin II analogues. We conclude that the 1,3,5-trisubstituted benzene rings can be conveniently prepared and are suitable as γ-turn mimics.
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| 21. |
- Georgsson, Jennie, et al.
(författare)
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Synthesis of a new class of druglike angiotensin II C-terminal mimics with affinity for the AT2 receptor
- 2007
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Ingår i: Journal of Medicinal Chemistry. - : American Chemical Society (ACS). - 0022-2623 .- 1520-4804. ; 50:7, s. 1711-1715
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Tidskriftsartikel (refereegranskat)abstract
- Four tripeptides corresponding to the C-terminal region of angiotensin II were synthesized. One of these peptides (Ac-His-Pro-Ile) showed moderate binding affinity for the AT2 receptor. Two aromatic histidine-related scaffolds were synthesized and introduced in the tripeptides to give eight new peptidomimetic structures. Three of the new peptide-derived druglike molecules exhibited selective, nanomolar affinity for the AT2 receptor. These ligands may become lead compounds in the future development of novel classes of selective AT2 receptor agonists.
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| 22. |
- Hansson, Magnus L., et al.
(författare)
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Artificial spider silk supports and guides neurite extension in vitro
- 2021
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Ingår i: The FASEB Journal. - : John Wiley & Sons. - 0892-6638 .- 1530-6860. ; 35:11
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Tidskriftsartikel (refereegranskat)abstract
- Surgical intervention with the use of autografts is considered the gold standard to treat peripheral nerve injuries. However, a biomaterial that supports and guides nerve growth would be an attractive alternative to overcome problems with limited availability, morbidity at the site of harvest, and nerve mismatches related to autografts. Native spider silk is a promising material for construction of nerve guidance conduit (NGC), as it enables regeneration of cm-long nerve injuries in sheep, but regulatory requirements for medical devices demand synthetic materials. Here, we use a recombinant spider silk protein (NT2RepCT) and a functionalized variant carrying a peptide derived from vitronectin (VN-NT2RepCT) as substrates for nerve growth support and neurite extension, using a dorsal root ganglion cell line, ND7/23. Two-dimensional coatings were benchmarked against poly-d-lysine and recombinant laminins. Both spider silk coatings performed as the control substrates with regards to proliferation, survival, and neurite growth. Furthermore, NT2RepCT and VN-NT2RepCT spun into continuous fibers in a biomimetic spinning set-up support cell survival, neurite growth, and guidance to an even larger extent than native spider silk. Thus, artificial spider silk is a promising biomaterial for development of NGCs.
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| 23. |
- Henriksson, Tommy, 1978-
(författare)
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CONTRIBUTION TO QUANTITATIVE MICROWAVE IMAGING TECHNIQUES FOR BIOMEDICAL APPLICATIONS
- 2009
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This dissertation presents a contribution to quantitative microwave imaging for breast tumor detection. The study made in the frame of a joint supervision Ph.D. thesis between University Paris-SUD 11 (France) and Mälardalen University (Sweden), has been conducted through two experimental microwave imaging setups, the existing 2.45 GHz planar camera (France) and the multi-frequency flexible robotic system, (Sweden), under development. In this context a 2D scalar flexible numerical tool based on a Newton-Kantorovich (NK) scheme, has been developed. Quantitative microwave imaging is a three dimensional vectorial nonlinear inverse scattering problem, where the complex permittivity of an object is reconstructed from the measured scattered field, produced by the object. The NK scheme is used in order to deal with the nonlinearity and the ill-posed nature of this problem. A TM polarization and a two dimensional medium configuration have been considered in order to avoid its vectorial aspect. The solution is found iteratively by minimizing the square norm of the error with respect to the scattered field data. Consequently, the convergence of such iterative process requires, at least two conditions. First, an efficient calibration of the experimental system has to be associated to the minimization of model errors. Second, the mean square difference of the scattered field introduced by the presence of the tumor has to be large enough, according to the sensitivity of the imaging system. The existing planar camera associated to a flexible 2D scalar NK code, are considered as an experimental platform for quantitative breast imaging. A preliminary numerical study shows that the multi-view planar system is quite efficient for realistic breast tumor phantoms, according to its characteristics (frequency, planar geometry and water as a coupling medium), as long as realistic noisy data are considered. Furthermore, a multi-incidence planar system, more appropriate in term of antenna-array arrangement, is proposed and its concept is numerically validated. On the other hand, an experimental work which includes a new fluid-mixture for the realization of a narrow band cylindrical breast phantom, a deep investigation in the calibration process and model error minimization, is presented. This conducts to the first quantitative reconstruction of a realistic breast phantom by using multi-view data from the planar camera. Next, both the qualitative and quantitative reconstruction of 3D inclusions into the cylindrical breast phantom, by using data from all the retina, are shown and discussed. Finally, the extended work towards the flexible robotic system is presented.
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| 24. |
- Jorner, Kjell, et al.
(författare)
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Organic reactivity from mechanism to machine learning
- 2021
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Ingår i: Nature Reviews Chemistry. - : Springer Nature. - 2397-3358. ; 5:4, s. 240-255
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Forskningsöversikt (refereegranskat)abstract
- As more data are introduced in the building of models of chemical reactivity, the mechanistic component can be reduced until 'big data' applications are reached. These methods no longer depend on underlying mechanistic hypotheses, potentially learning them implicitly through extensive data training. Reactivity models often focus on reaction barribers, but can also be trained to directly predict lab-relevant properties, such as yields or conditions. Calculations with a quantum-mechanical component are still preferred for quantitative predictions of reactivity. Although big data applications tend to be more qualitative, they have the advantage to be broadly applied to different kinds of reactions. There is a continuum of methods in between these extremes, such as methods that use quantum-derived data or descriptors in machine learning models. Here, we present an overview of the recent machine learning applications in the field of chemical reactivity from a mechanistic perspective. Starting with a summary of how reactivity questions are addressed by quantum-mechanical methods, we discuss methods that augment or replace quantum-based modelling with faster alternatives relying on machine learning.
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| 25. |
- Lindh, Martin, et al.
(författare)
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Toward a Benchmarking Data Set Able to Evaluate Ligand- and Structure-based Virtual Screening Using Public HTS Data
- 2015
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Ingår i: Journal of Chemical Information and Modeling. - : American Chemical Society (ACS). - 1549-9596 .- 1549-960X. ; 55:2, s. 343-353
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Tidskriftsartikel (refereegranskat)abstract
- Virtual screening has the potential to accelerate and reduce costs of probe development and drug discovery. To develop and benchmark virtual screening methods, validation data sets are commonly used. Over the years, such data sets have been constructed to overcome the problems of analogue bias and artificial enrichment. With the rapid growth of public domain databases containing high-throughput screening data, such as the PubChem BioAssay database, there is an increased possibility to use such data for validation. In this study, we identify PubChem data sets suitable for validation of both structure- and ligand-based virtual screening methods. To achieve this, high-throughput screening data for which a crystal structure of the bioassay target was available in the PDB were identified. Thereafter, the data sets were inspected to identify structures and data suitable for use in validation studies. In this work, we present seven data sets (MMP13, DUSP3, PTPN22, EPHX2, CTDSP1, MAPK10, and CDK5) compiled using this method. In the seven data sets, the number of active compounds varies between 19 and 369 and the number of inactive compounds between 59 405 and 337 634. This gives a higher ratio of the number of inactive to active compounds than what is found in most benchmark data sets. We have also evaluated the screening performance using docking and 3D shape similarity with default settings. To characterize the data sets, we used physicochemical similarity and 2D fingerprint searches. We envision that these data sets can be a useful complement to current data sets used for method evaluation.
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| 26. |
- Lindman, Jens, 1990-
(författare)
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Palladium(0)-Catalyzed Spirocyclization and Carbonylation Reactions : Ligands Targeting the Angiotensin II Type 2 Receptor
- 2023
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Palladium(0)-catalyzed chemistry represents one of the most important methods for the construction of carbon-carbon bonds, which are ubiquitous in organic compounds. The first part of this thesis describes the palladium(0)-catalyzed diastereoselective Mizoroki-Heck reaction of Vince lactam-derived precursors for the formation of spiroindolines (paper I) and spirooxindoles, which are scaffolds present in several natural products with interesting biological activity. The scope of the spiroindoline synthesis was investigated by varying the substitution on the cyclopentenyl-tethered aniline spirocyclization precursor. The mechanistic reasons behind the high diastereoselectivity of the spirocyclization reaction was also investigated through density functional theory (DFT) calculations. Functionalization of the N-terminal amino acid of therapeutic peptides is a strategy that has been employed for the improvement of metabolic stability. In paper II, a palladium(0)-catalyzed carbonylation method employing ex situ carbon monoxide generation from Mo(CO)6 in a two-chamber system is used for the N-capping of amino acids using various aryl bromides and triflates. The second part of the thesis describes the synthesis and biological evaluation of angiotensin II type 2 receptor (AT2R) ligands. The AT2R is a G-protein coupled receptor belonging to the renin-angiotensin-aldosterone system (RAAS), which is most commonly associated with the hypertensive disorder caused by an exaggerated activation of the angiotensin II type 1 receptor (AT1R). However, activation of AT2R exerts different and sometimes completely opposing effects to AT1R and has been implicated in processes related to neuropathic pain, where the AT2R antagonist EMA401 has been in clinical trials for this indication. In papers III and IV, the AT2R antagonist C38 developed in our laboratory, is used as a model compound for the synthesis of analogs with the aim of expanding our knowledge regarding the structure-activity relationship of the C38 scaffold. Three general strategies were used; functionalization of the C38 phenyl ring, replacement of the benzyl imidazole of C38 with bicyclic amides and extension of the linker between the phenyl ring and imidazole by the inclusion of a carbonyl. Through these approaches, compounds with improved affinity towards AT2R and increased metabolic stability were identified, which might serve as tools for the continued study of the AT2R.
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| 27. |
- Moldanova, Jana, et al.
(författare)
-
Sammanställning av flygets klimatpåverkan och möjlighet till minskning av dessa - alternativa flygrutter för minskade höghöjdseffekter och biobränslen
- 2018
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Idag står den globala flygtrafiken för ca 2-3% av det fossila CO2-utsläppet härlett från mänskliga aktiviteter. Flygtrafikens bidrag till global uppvärmningen i form av strålningsdrivning är dock 4.9% om man tar hänsyn till effekt från kortlivade klimatföroreningar (short-lived climate pollutants, SLCP) relaterade till flyget, även kallade höghöjdseffekter. Dessa innefattar utsläpp av vattenånga, sot och andra partiklar, bildning av kondensstrimmor och flyginducerade cirrusmoln samt utsläpp av NOX som leder till förändringar av halter av ozon och metan i atmosfären. Det relativa bidraget av SLCP från flyget varierar kraftigt beroende på vilket mått man använder, med GWP20 (Global Warming Potential på en tidshorisont 20 år) ligger total effekt av flygemissionerna relativt till CO2 inom intervallet 2.1-4.8, för GWP100 ligger samma proportion mellan 1.3 och 2.0, använder man Global TemperaturPotential GTP ligger proportionen mellan 1.0 och 1.1 för GTP100. Klimatpåverkan av SLCP är starkt beroende av atmosfäriska förhållanden där utsläppen sker. Persistenta kondensstrimmor bildas och värmer upp klimatet när flygplan rör sig i områden som har luftfuktighet övermättad mot is och som är molnfri. Även utsläpp av NOx kan ge olika effekter beroende på förhållandena vid utsläpp. Flera studier har utvärderat möjligheterna att optimera flygrutter med hänsyn till både CO2 utsläpp och effekter från SLCP genom att justera var/när största delen av utsläppen sker. Man har visat att trots en högre bränsleförbrukning vid alternativa flygrutter kunde man uppnå en minskad klimatpåverkan med mått GWP100. Klimatmålet med max. 2° temperaturhöjning kräver mer än en halvering av utsläppen av växthusgaser till år 2050 vilket kräver en bred övergång till alternativa bränslen fria från fossilt kol. För flyget finns ett flertal alternativa jetbränslen (AJF) med lägre halter fossilt kol i sin well-to-wake cykel (WTWk). WTWk minskningen varierar kraftigt med processen som bränslet framställts genom samt vilket råmaterial som använts. Det finns flera negativa effekter kring ändrad markanvändning som är en mycket viktigt hållbarhetsaspekt. Det alternativ som ger störst WTWk minskning är att producera AJF från restprodukter som avfallsolja och skogsrester. För vissa alternativ, som sojabönor och palmolja, ligger WTWk högre hos AJF än hos de konventionella jetbränslena. Dessutom kopplas AJF-produktionen till en konflikt mellan matproduktion och bränsleproduktion, potentiellt minskad biodiversitet, vattenkonsumtion samt föroreningar som uppstår vid produktion vilka inte går att ignorera ur ett hållbarhetsperspektiv.
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| 28. |
- Olanders, Gustav, 1991-
(författare)
-
Computational Modeling of Macrocycles and Structure-Based Design of Novel Antibacterial Compounds
- 2021
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The integration of computational methods into the drug discovery process provides valuable tools to help advance new and improved drugs into the clinic. As medicinal chemists explore novel targets and new areas of chemical space, our computational toolkit must also evolve.Macrocycles are high-value scaffolds in medicinal chemistry due to their attractive physiochemical properties and intricate interactions with biomolecules. However, given the significant challenges associated with their synthesis, improved computational tools are required to both understand macrocycle conformation and binding preferences and to also efficiently guide medicinal chemistry efforts. Therefore, this thesis focuses on the evaluation, optimization and application of computational methods for macrocycle drug discovery.Our initial work, Paper I, investigated both rigid and flexible macrocycle docking techniques. This showed that rigid docking of conformational ensembles generated using a range of sampling methods could result in significant differences in docking accuracy. Furthermore, we showed that either rigid docking of MD/LLMOD generated conformers or flexible docking could be applied.In Paper II, we conducted further investigations of macrocycle conformational sampling by comparing more general sampling methods to those specialized towards macrocyclic scaffolds. The study showed that the general conformational sampling methods perform well compared with the more specialized methods. Our work also shows that the general methods can themselves be modified for improved macrocycle sampling.Building on these findings, Paper III compares the conformational preferences of linear ligands and their closely related macrocyclic analogs. Interestingly, our analysis showed that for many of the macrocyclic ensembles they were not significantly more focused towards the bioactive conformation than their linear analogs.In Paper IV, our computational toolkit was used to design novel antibacterial macrocycles targeting signal peptidase I. Here we developed macrocyclic compounds with nanomolar inhibitory activity against signal peptidase I, which also showed antibacterial activity.
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| 29. |
- Olanders, Gustav, et al.
(författare)
-
Computational studies of molecular pre-organization through macrocyclization : Conformational distribution analysis of closely related non-macrocyclic and macrocyclic analogs
- 2021
-
Ingår i: Bioorganic & Medicinal Chemistry. - : Elsevier. - 0968-0896 .- 1464-3391. ; 49
-
Tidskriftsartikel (refereegranskat)abstract
- Macrocycles form an important compound class in medicinal chemistry due to their interesting structural and biological properties. To help design macrocycles, it is important to understand how the conformational preferences are affected upon macrocyclization of a lead compound. To address this, we collected a unique data set of protein-ligand complexes containing "non-macrocyclic" ("linear") ligands matched with macrocyclic analogs binding to the same protein in a similar pose. Out of the 39 co-crystallized ligands considered, 10 were linear and 29 were macrocyclic. To enable a more general analysis, 128 additional ligands from the publications associated with these protein data bank entries were added to the data set. Using in total 167 collected ligands, we investigated if the conformers in the macrocyclic conformational ensembles were more similar to the bioactive conformation in comparison to the conformers of their linear counterparts. Unexpectedly, in most cases the macrocycle conformational ensemble distributions were not very different from those of the linear compounds. Thus, care should be taken when designing macrocycles with the aim to focus their conformational preference towards the bioactive conformation. We also set out to investigate potential conformational flexibility differences between the two compound classes, computational energy window settings and evaluate a literature metric for approximating the conformational focusing on the bioactive conformation.
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| 30. |
- Rosenström, Ulrika, et al.
(författare)
-
A Selective AT2 Receptor Ligand with a γ-Turn-Like Mimetic replacing the Amino Acid Residues 4-5 of Angiotensin II
- 2004
-
Ingår i: Journal of Medicinal Chemistry. - : American Chemical Society (ACS). - 0022-2623 .- 1520-4804. ; 47:4, s. 859-870
-
Tidskriftsartikel (refereegranskat)abstract
- Three angiotensin II (Ang II) analogues encompassing a benzodiazepine-based γ-turn-like scaffold have been synthesized. Evaluation of the compounds in a radioligand binding assay showed that they had no affinity to the rat liver AT1 receptor. However, one of the compounds displayed considerable affinity to the pig uterus AT2 receptor (Ki = 3.0 nM) while the other two lacked affinity to this receptor. It was hypothesized that the reason for the inactivity of one of these analogues to the AT2 receptor was that the guanidino group of the Arg2 residue and/or the N-terminal end of the pseudopeptide could not interact optimally with the receptor. To investigate this hypothesis, a conformational analysis was performed and a comparison was carried out with the monocyclic methylenedithioether analogue cyclo(S−CH2−S)[Cys3,5]Ang II which is known to bind with high affinity to the AT2 receptor (Ki = 0.62 nM). This comparison showed that, in the compounds with high AT2 receptor affinity, the guanidino group of the Arg2 residue and the N-terminal end could access common regions of space that were not accessible to the inactive compound. To examine the importance of the guanidino group for binding, the Arg side chain was removed by substituting Arg2 for Ala2 in the analogue having the high affinity. This analogue lacked affinity to AT2 receptors, which supports the role of the guanidino group in receptor binding.
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| 31. |
- Rosenström, Ulrika, et al.
(författare)
-
Design, synthesis, and incorporation of a beta-turn mimetic in angiotensin II forming novel pseudopeptides with affinity for AT(1) and AT(2) receptors
- 2006
-
Ingår i: Journal of Medicinal Chemistry. - : American Chemical Society (ACS). - 0022-2623 .- 1520-4804. ; 49:20, s. 6133-6137
-
Tidskriftsartikel (refereegranskat)abstract
- A benzodiazepine-based beta-turn mimetic has been designed, synthesized, and incorporated into angiotensin II. Comparison of the mimetic with beta-turns in crystallized proteins showed that it most closely resembles a type II beta-turn. The compounds exhibited high to moderate binding affinity for the AT(2) receptor, and one also displayed high affinity for the AT(1) receptor. Molecular modeling showed that the high-affinity compounds could be incorporated into a previously derived model of AT(2) receptor ligands.
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| 32. |
- Rosenström, Ulrika, et al.
(författare)
-
New selective AT2 receptor ligands encompassing a γ-turn mimetic replacing the amino acid residues 4-5 of angiotensin II act as agonists
- 2005
-
Ingår i: Journal of Medicinal Chemistry. - : American Chemical Society (ACS). - 0022-2623 .- 1520-4804. ; 48:12, s. 4009-4024
-
Tidskriftsartikel (refereegranskat)abstract
- New benzodiazepine-based γ-turn mimetics with one or two amino acid side chains were synthesized. The γ-turn mimetics were incorporated into angiotensin II (Ang II) replacing the Val3-Tyr4-Ile5 or Tyr4-Ile5 peptide segments. All of the resulting pseudopeptides displayed high AT2/AT1 receptor selectivity and exhibited AT2 receptor affinity in the low nanomolar range. Molecular modeling was used to investigate whether the compounds binding to the AT2 receptor could position important structural elements in common areas. A previously described benzodiazepine-based γ-turn mimetic with high affinity for the AT2 receptor was also included in the modeling. It was found that the molecules, although being structurally quite different, could adopt the same binding mode/interaction pattern in agreement with the model hypothesis. The pseudopeptides selected for agonist studies were shown to act as AT2 receptor agonists being able to induce outgrowth of neurite cells, stimulate p42/p44mapk, and suppress proliferation of PC12 cells.
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| 33. |
- Rosenström, Ulrika, et al.
(författare)
-
Synthesis and AT2 receptor-binding properties of angiotensin II analogues
- 2004
-
Ingår i: Journal of Peptide Research. - : Wiley. - 1397-002X .- 1399-3011. ; 64:5, s. 194-201
-
Tidskriftsartikel (refereegranskat)abstract
- The present study investigates the importance of the amino acid side chains in the octapeptide angiotensin II (Ang II) for binding to the AT2 receptor. A Gly scan was performed where each amino acid in Ang II was substituted one-by-one with glycine. The resulting set of peptides was tested for affinity to the AT2 receptor (porcine myometrial membranes). For a comparison, the peptides were also tested for affinity to the AT1 receptor (rat liver membranes). Only the substitution of Arg2 reduced affinity to the AT2 receptor considerably (92-fold when compared with Ang II). For the other Gly-substituted analogues the affinity to the AT2 receptor was only moderately affected. To further investigate the role of the Arg2 side chain for receptor binding, we synthesized some N-terminally modified Ang II analogues. According to these studies a positive charge in the N-terminal end of angiotensin III [Ang II (2–8)] is not required for high AT2 receptor affinity but seems to be more important in Ang II. With respect to the AT1 receptor, [Gly2]Ang II and [Gly8]Ang II lacked binding affinity (Ki > 10 μm). Replacement of the Val3 or Ile5 residues with Gly produced only a slight decrease in affinity. Interestingly, substitution of Tyr4 or His6, which are known to be very important for AT1 receptor binding, resulted in only 48 and 14 times reduction in affinity, respectively.
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| 34. |
- Rydfjord, Jonas, et al.
(författare)
-
Decarboxylative Palladium(II)-Catalyzed Synthesis of Aryl Amidines from Aryl Carboxylic Acids : Development and Mechanistic Investigation
- 2013
-
Ingår i: Chemistry - A European Journal. - : Wiley. - 0947-6539 .- 1521-3765. ; 19:41, s. 13803-13810
-
Tidskriftsartikel (refereegranskat)abstract
- A fast and convenient synthesis of aryl amidines starting from carboxylic acids and cyanamides is reported. The reaction was achieved by palladium(II)-catalysis in a one-step microwave protocol using [Pd(O2CCF3)(2)], 6-methyl-2,2-bipyridyl and trifluoroacetic acid (TFA) in N-methylpyrrolidinone (NMP), providing the corresponding aryl amidines in moderate to excellent yields. The protocol is very robust with regards to the cyanamide coupling partner but requires electron-rich ortho-substituted aryl carboxylic acids. Mechanistic insight was provided by a DFT investigation and direct ESI-MS studies of the reaction. The results of the DFT study correlated well with the experimental findings and, together with the ESI-MS study, support the suggested mechanism. Furthermore, a scale-out (scale-up) was performed with a non-resonant microwave continuous-flow system, achieving a maximum throughput of 11mmolh(-1) by using a glass reactor with an inner diameter of 3mm at a flow rate of 1mLmin(-1).
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| 35. |
- Sawant, Rajiv T., et al.
(författare)
-
Microwave-Assisted Branching Cascades : A Route to Diverse 3,4-Dihydroquinazolinone-Embedded Polyheterocyclic Scaffolds
- 2016
-
Ingår i: Organic Letters. - : American Chemical Society (ACS). - 1523-7060 .- 1523-7052. ; 18:20, s. 5392-5395
-
Tidskriftsartikel (refereegranskat)abstract
- A novel metal-free microwave-assisted branching cascades strategy for the efficient synthesis of 3,4-dihydro-quinazolinone-embedded polyheterocyclic scaffolds is reported. Starting from in situ generated key N-acyliminium ion precursors, 12 distinct and skeletally diverse polycyclic frameworks were accessed in a single step/pot via adjustment of the nucleophile(s) and reaction conditions. Postcascade functionalization of these compounds was also demonstrated, proving the utility of this method in accessing structurally diverse chemical entities.
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| 36. |
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| 37. |
- Skillinghaug, Bobo, et al.
(författare)
-
Palladium(II)-Catalyzed Desulfitative Synthesis of Aryl Ketones from Sodium Arylsulfinates and Nitriles : Scope, Limitations, and Mechanistic Studies
- 2014
-
Ingår i: Journal of Organic Chemistry. - : American Chemical Society (ACS). - 0022-3263 .- 1520-6904. ; 79:24, s. 12018-12032
-
Tidskriftsartikel (refereegranskat)abstract
- A fast and efficient protocol for the palladium(II)-catalyzed production of aryl ketones from sodium arylsulfinates and various organic nitriles under controlled microwave irradiation has been developed. The wide scope of the reaction has been demonstrated by combining 14 sodium arylsulfinates and 21 nitriles to give 55 examples of aryl ketones. One additional example illustrated that, through the choice of the nitrile reactant, benzofurans are also accessible. The reaction mechanism was investigated by electrospray ionization mass spectrometry and DFT calculations. The desulfitative synthesis of aryl ketones from nitriles was also compared to the corresponding transformation starting from benzoic acids. Comparison of the energy profiles indicates that the free energy requirement for decarboxylation of 2,6-dimethoxybenzoic acid and especially benzoic acid is higher than the corresponding desulfitative process for generating the key aryl palladium intermediate. The palladium(II) intermediates detected by ESI-MS and the DFT calculations provide a detailed understanding of the catalytic cycle.
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| 38. |
- Skogh, Anna, et al.
(författare)
-
Aminocarbonylation of 4-Iodo-1H-imidazoles with an Amino Acid Amide Nucleophile : Synthesis of Constrained H-Phe-Phe-NH2 Analogues
- 2013
-
Ingår i: Journal of Organic Chemistry. - : American Chemical Society (ACS). - 0022-3263 .- 1520-6904. ; 78:23, s. 12251-12256
-
Tidskriftsartikel (refereegranskat)abstract
- A simple and an expedient process to prepare 5-aryl-1benzyl-1H-imidazole-4-carboxamides by the aminocarbonylation of 5aryl-4-iodo-1H-imidazoles using ex situ generation of CO from Mo(CO)(6) with an amino acid amide nucleophile is reported. Furthermore, a microwave-assisted protocol for the direct C-5 arylation of 1-benzyl-1H-imidazole and a regioselective C-4 iodination method to acquire starting material for our aminocarbonylation are presented. The method can be used to prepare imidazole based peptidomimetics, herein exemplified by the synthesis of constrained H-Phe-Phe-NH2 analogues.
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| 39. |
- Skogh, Anna, et al.
(författare)
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An imidazole based H-Phe-Phe-NH2 peptidomimetic with anti-allodynic effect in spared nerve injury mice
- 2018
-
Ingår i: Bioorganic & Medicinal Chemistry Letters. - : Elsevier BV. - 0960-894X .- 1464-3405. ; 28:14, s. 2446-2450
-
Tidskriftsartikel (refereegranskat)abstract
- The dipeptide amide H-Phe-Phe-NH2 (1) that previously was identified as a ligand for the substance P 1-7 (SP1-7) binding site exerts intriguing results in animal models of neuropathic pain after central but not after peripheral administration. The dipeptide 1 is derived from stepwise modifications of the anti-nociceptive heptapeptide SP1-7 and the tetrapeptide endomorphin-2 that is also binding to the SP1-7 site. We herein report a strong anti-allodynic effect of a new H-Phe-Phe-NH2 peptidomimetic (4) comprising an imidazole ring as a bioisosteric element, in the spare nerve injury (SNI) mice model after peripheral administration. Peptidomimetic 4 was stable in plasma, displayed a fair membrane permeability and a favorable neurotoxic profile. Moreover, the effective dose (ED50) of 4 was superior as compared to gabapentin and morphine that are used in clinic.
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| 40. |
- Skogh, Anna, 1986-
(författare)
-
Development of Substance P 1–7 Related Peptides and Peptidomimetics : Targeting Neuropathic Pain
- 2018
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The neuropeptide substance P 1–7 (SP1–7, H-Arg1-Pro2-Lys3-Pro4-Gln5-Gln6-Phe7-OH) and its amidated analogue SP1–7 amide, have displayed intriguing effects in experimental models for neuropathic pain acting on a specific, yet unknown SP1–7 target. The aim of this thesis was to design and synthesise SP1–7 related peptides and peptidomimetics, to be used as research tools to study the SP1–7 system, and to serve as drug leads in the neuropathic pain area.The in vivo structure activity relationship (SAR) of the SP1–7 amide was elucidated using Ala-substituted, N-terminally truncated and N-methylated variants. By evaluation of the anti-allodynic effect in spared nerve injury (SNI) mice and the pharmacokinetic properties it is suggested that Phe7 acts as a message residue and Arg1 as an address residue, both important for the overall anti-allodynic activity. In contrast, Lys3 could be substituted by alanine, and the Pro2-Lys3 and Pro4-Gln5 bond could be N-methylated with retained anti-allodynic effect. The Pro2-Lys3 bond was found most sensitive towards proteolysis and indeed, N-methylation of this bond delivered peptides completely inert in plasma. Conversely, prolonged plasma stability did not improve the overall in vivo activity for these peptides. Instead, the SP1–7 amide remained the most potent peptide in vivo, despite fast degradation in plasma. Besides peptide synthesis, the synthetic work included development of a Pd-catalysed aminocarbonylation protocol using an amino acid nucleophile, which was used for the synthesis of an imidazole-based peptidomimetic. This peptidomimetic was equipotent to the SP1–7 amide, and more potent than the drug gabapentin, in regard to its anti-allodynic effect in SNI mice, and it is a promising drug lead for further development. The Pd-catalysed aminocarbonylation protocol was refined further, in regards to reaction scope and requirements for solid-phase peptide synthesis and has proven useful for N-capping, isotopic labelling, and intramolecular cyclisation of peptides.In summary, the work presented herein resulted in an in vivo SAR for SP1–7 related peptides, a novel small molecule SP1–7 peptidomimetic, and methods expanding the toolbox for synthesising modified peptides and peptidomimetics – a field in drug discovery that presently gaining increasing attention.
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| 41. |
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| 42. |
- Sköld, Christian, 1976-
(författare)
-
Computational Modeling of the AT2 Receptor and AT2 Receptor Ligands : Investigating Ligand Binding, Structure–Activity Relationships, and Receptor-Bound Models
- 2007
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Rational conversion of biologically active peptides to nonpeptide compounds with retained activity is an appealing approach in drug development. One important objective of the work presented in this thesis was to use computational modeling to aid in such a conversion of the peptide angiotensin II (Ang II, Asp-Arg-Val-Tyr-Ile-His-Pro-Phe). An equally important objective was to gain an understanding of the requirements for ligand binding to the Ang II receptors, with a focus on interactions with the AT2 receptor. The bioactive conformation of a peptide can provide important guidance in peptidomimetic design. By designing and introducing well-defined secondary structure mimetics into Ang II the bioactive conformation can be addressed. In this work, both γ- and β-turn mimetic scaffolds have been designed and characterized for incorporation into Ang II. Using conformational analysis and the pharmacophore recognition method DISCO, a model was derived of the binding mode of the pseudopeptide Ang II analogues. This model indicated that the positioning of the Arg side chain was important for AT2 receptor binding, which was also supported when the structure–activity relationship of Ang II was investigated by performing a glycine scan. To further examine ligand binding, a 3D model of the AT2 receptor was constructed employing homology modeling. Using this receptor model in a docking study of the ligands, binding modes were identified that were in agreement with data from point-mutation studies of the AT2 receptor. By investigating truncated Ang II analogues, small pseudopeptides were developed that were structurally similar to nonpeptide AT2 receptor ligands. For further guidance in ligand design of nonpeptide compounds, three-dimensional quantitative structure–activity relationship models for AT1 and AT2 receptor affinity as well as selectivity were derived.
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| 43. |
- Sköld, Christian, et al.
(författare)
-
Development of CoMFA models of affinity and selectivity to angiotensin II type-1 and type-2 receptors
- 2007
-
Ingår i: Journal of Molecular Graphics and Modelling. - : Elsevier BV. - 1093-3263 .- 1873-4243. ; 26:1, s. 145-153
-
Tidskriftsartikel (refereegranskat)abstract
- The renin-angiotensin system (RAS) is of major importance in cardiovascular and renal regulation and has been an attractive target in drug discovery for a long time. The main receptors involved in the RAS are the Angiotensin type-1 (AT1) and type-2 (AT2) receptors, which are both activated by the endogenous octapeptide angiotensin II (AngII). This study describes the development of 3D-QSAR models for AT1 and AT2 receptor affinity and AT1/AT2 receptor selectivity using CoMFA. A data set of 244 compounds, based on the triazolinone and quinazolinone structural classes was compiled from the literature. Before CoMFA could be performed, an alignment rule for the two structural classes was defined using the pharmacophore-searching program DISCOtech. Models were validated using a test set obtained by dividing the data set into a training set and test set using hierarchical clustering, based on the CoMFA fields, AT1-, AT2-receptor affinities, and AT1/AT2 selectivity values. Predictive models with good statistics could be developed both for AT1 and AT2 receptor affinity as well as selectivity towards these receptors.
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| 44. |
- Sköld, Christian, et al.
(författare)
-
Modeling binding modes of angiotensin II and pseudopeptide analogues to the AT2 receptor
- 2008
-
Ingår i: Journal of Molecular Graphics and Modelling. - : Elsevier BV. - 1093-3263 .- 1873-4243. ; 26:6, s. 991-1003
-
Tidskriftsartikel (refereegranskat)abstract
- The 3D model of the AT(2) receptor has been built employing homology to the transmembrane domain of rhodopsin and a novel build-up procedure for restoring the extracellular loops. By docking a model peptide of angiotensin II in the AT(2) receptor model two plausible binding modes were identified. These binding modes were in agreement with most of the suggested ligand-receptor contact points reported in the literature. Eight active and one inactive pseuclopeptide angiotensin II analogue were also docked in the receptor and four of the active pseudopeptides were found to mimic the binding mode of angiotensin II. An alternative binding mode for the other four active pseudopeptides was found.
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| 45. |
- Sköld, Christian, et al.
(författare)
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Transmetallation Versus β-Hydride Elimination : The Role of 1,4 Benzoquinone in Chelation-Controlled Arylation Reactions with Arylboronic Acids
- 2012
-
Ingår i: Chemistry - A European Journal. - : Wiley-VCH Verlagsgesellschaft. - 0947-6539 .- 1521-3765. ; 18:15, s. 4714-4722
-
Tidskriftsartikel (refereegranskat)abstract
- The formation of an atypical, saturated, diarylated, Heck/Suzuki, domino product produced under oxidative Heck reaction conditions, employing arylboronic acids and a chelating vinyl ether, has been investigated by DFT calculations. The calculations highlight the crucial role of 1,4-benzoquinone (BQ) in the reaction. In addition to its role as an oxidant of palladium, which is necessary to complete the catalytic cycle, this electron-deficient alkene opens up a low-energy reaction pathway from the post-insertion sigma-alkyl complex. The association of BQ lowers the free-energy barrier for transmetallation of the s-alkyl complex to create a pathway that is energetically lower than the oxidative Heck reaction pathway. Furthermore, the calculations showed that the reaction is made viable by BQ-mediated reductive elimination and leads to the saturated diarylated product.
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| 46. |
- Svensson, Fredrik, 1987-
(författare)
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Computational Methods in Medicinal Chemistry : Mechanistic Investigations and Virtual Screening Development
- 2015
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Computational methods have become an integral part of drug development and can help bring new and better drugs to the market faster. The process of predicting the biological activity of large compound collections is known as virtual screening, and has been instrumental in the development of several drugs today in the market. Computational methods can also be used to elucidate the energies associated with chemical reactivity and predict how to improve a synthetic protocol. These two applications of computational medicinal chemistry is the focus of this thesis.In the first part of this work, quantum mechanics has been used to probe the energy surface of palladium(II)-catalyzed decarboxylative reactions in order to gain a better understating of these systems (paper I-III). These studies have mapped the reaction pathways and been able to make accurate predictions that were verified experimentally.The other focus of this work has been to develop virtual screening methodology. Our first study in the area (paper IV) investigated if the results from several virtual screening methods could be combined using data fusion techniques in order to get a more consistent result and better performance. The study showed that the results obtained from data fusion were more consistent than the results from any single method. The data fusion methods also for several target had a better performance than any of the included single methods.Next, we developed a dataset suitable for evaluating the performance of virtual screening methods when applied to large compound collection as a replacement or complement for high throughput screening (paper V). This is the first benchmark dataset of its kind.Finally, a method for using computationally derived reaction coordinates as basis for virtual screening was developed. The aim was to find inhibitors that resemble key steps in the mechanism (paper VI). This initial proof of concept study managed to locate several known and one previously not reported reaction mimetics against insulin regulated amino peptidase.
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| 47. |
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| 48. |
- Svensson, Fredrik, et al.
(författare)
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Theoretical and Experimental Investigation of Palladium(II)-Catalyzed Decarboxylative Addition of Arenecarboxylic Acid to Nitrile
- 2013
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Ingår i: Organometallics. - : American Chemical Society (ACS). - 0276-7333 .- 1520-6041. ; 32:2, s. 490-497
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Tidskriftsartikel (refereegranskat)abstract
- The reaction mechanism of palladium(II)-catalyzed decarboxylative addition of 2,6-dimethoxybenzoic acid to acetonitrile was investigated by means of density functional theory (DFT) calculations. Calculations of the free energy profile for decarboxylation and carbopalladation indicated carbopalladation as the rate-determining step of the reaction. Investigation of the free energy profile for a series of experimentally evaluated nitrogen-based bidentate palladium ligands revealed that higher energy is required for decarboxylation and carbopalladation employing the experimentally least efficient ligand. The DFT investigation also showed that the relative free energies of the transition states were lowered in polar solvent, and preparative experiments confirmed that a nonoptimal ligand could be greatly improved by addition of water to the reaction system.
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| 49. |
- Svensson, Fredrik, et al.
(författare)
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Virtual Screening Data Fusion Using Both Structure- and Ligand-Based Methods
- 2012
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Ingår i: Journal of Chemical Information and Modeling. - : American Chemical Society (ACS). - 1549-9596 .- 1549-960X. ; 52:1, s. 225-232
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Tidskriftsartikel (refereegranskat)abstract
- Virtual screening is widely applied in drug discovery, and significant effort has been put into improving current methods. In this study, we have evaluated the performance of compound ranking in virtual screening using five different data fusion algorithms on a total of 16 data sets. The data were generated by docking, pharmacophore search, shape similarity, and electrostatic similarity, spanning both structure- and ligand-based methods. The algorithms used for data fusion were sum rank, rank vote, sum score, Pareto ranking, and parallel selection. None of the fusion methods require any prior knowledge or input other than the results from the single methods and, thus, are readily applicable. The results show that compound ranking using data fusion improves the performance and consistency of virtual screening compared to the single methods alone. The best performing data fusion algorithm was parallel selection, but both rank voting and Pareto ranking also have good performance.
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| 50. |
- Svensson, Fredrik, et al.
(författare)
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Virtual Screening for Transition State Analogue Inhibitors of IRAP Based on Quantum Mechanically Derived Reaction Coordinates
- 2015
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Ingår i: Journal of Chemical Information and Modeling. - : American Chemical Society (ACS). - 1549-960X .- 1549-9596. ; 55:9, s. 1984-1993
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Tidskriftsartikel (refereegranskat)abstract
- Transition state- and high energy intermediate mimetics have the potential to be very potent enzyme inhibitors. In this study a model of peptide hydrolysis in the active site of insulin-regulated aminopeptidase (IRAP) was developed using density functional theory calculations and the cluster approach. The 3D structure models of the reaction coordinates were used for virtual screening to obtain new chemical starting points for IRAP inhibitors. This mechanism-based virtual screening process managed to identify several known peptidase inhibitors from a library of over five million compounds and biological testing identified one compound not previously reported as an IRAP inhibitor. This novel methodology for virtual screening is a promising approach to identify new inhibitors mimicking key transition states or intermediates of an enzymatic reaction.
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