Browsing by Subject "INHIBITORS"

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  • Cruz, Cristina D; Wrigstedt, Pauli; Moslova, Karina; Iashin, Vladimir; Mäkkylä, Heidi; Ghemtio, Leo; Heikkinen, Sami; Tammela, Päivi; Perea-Buceta, Jesus Enrique (2021)
    N-aryl-oxazolidinones is a prominent family of antimicrobials used for treating infections caused by clinically prevalent Gram-positive bacteria. Recently, boron-containing compounds have displayed intriguing potential in the antibiotic discovery setting. Herein, we report the unprecedented introduction of a boron-containing moiety such as an aryl boronic acid in the external region of the oxazolidinone structure via a chemoselective acyl coupling reaction. As a result, we accessed a series of analogues with a distal aryl boronic pharmacophore on the oxazolidinone scaffold. We identified that a peripheric linear conformation coupled with freedom of rotation and no further substitution on the external aryl boronic ring, an amido linkage with hydrogen bonding character, in addition to a para-relative disposition between boronic group and linker, are the optimal combination of structural features in this series for antimicrobial activity. In comparison to linezolid, the analogue comprising all those features, compound 20b, displayed levels of antimicrobial activity augmented by an eight-fold to a thirty-two-fold against a panel of Gram-positive strains, and a near one hundred-fold against Escherichia coli JW5503, a Gram-negative mutant strain with a defective efflux capability.
  • Heinjoki, Marjo; Karjalainen, Merja; Saltevo, Juha; Tiihonen, Miia; Haanpaa, Maija; Kautiainen, Hannu; Mäntyselkä, Pekka (2020)
    Background Due to these changes in kidney function, aging kidneys are more prone to drug-induced impairments in renal properties. Diabetes has been associated with the declined kidney function and an elevated risk of renal failure. The aim of this study is to compare kidney function and potentially nephrotoxic drug use among home-dwelling older persons with or without diabetes. Methods A total of 259 persons with and 259 persons without diabetes and aged >= 65 years were randomly selected to participate in a health examination with complete data gathered from 363 individuals (187 with diabetes and 176 without diabetes). The estimated glomerular filtration rate (eGFR) was calculated using CKD-EPI equation. Each participant was categorized based on the nephrotoxic profile of their medications. Results There were no differences in mean eGFR values (77.5 +/- 18.8 vs. 80.5 +/- 14.8 ml/min/1.73m(2), p = 0.089) or in the proportion of participants with eGFR <60 ml/min/1.73m(2) among persons with diabetes (16% vs. 10%, p = 0.070), compared to persons without diabetes. Potentially nephrotoxic drug use was similar between the groups. The mean number of potentially nephrotoxic drugs was 1.06 +/- 0.88 in those with and 0.97 +/- 1.05 in those without diabetes (p = 0.39). Conclusions The kidney function of older persons with diabetes does not differ from that of older persons without diabetes and furthermore potentially nephrotoxic drug use seem to play only a minor role in the decline in kidney function among home-dwelling persons in the Inner-Savo district.
  • Ilina, Polina; Ma, Xiaochu; Sintim, Herman O.; Tammela, Päivi Sirpa Marjaana (2018)
    The continuing emergence and spread of antibiotic-resistant bacteria is worrisome and new strategies to curb bacterial infections are being sought. The interference of bacterial quorum sensing (QS) signaling has been suggested as a prospective antivirulence strategy. The AI-2 QS system is present in multiple bacterial species and has been shown to be correlated with pathogenicity. To facilitate the discovery of novel compounds interfering with AI-2 QS, we established a high-throughput setup of whole-cell bioreporter assay, which can be performed in either 96- or 384-well format. Agonistic or antagonistic activities of the test compounds against Escherichia coli LsrB-type AI-2 QS system are monitored by measuring the level of beta-galactosidase expression. A control strain expressing beta-galactosidase in quorum sensing-independent manner is included into the assay for false-positive detection.
  • Majumder, Muntasir M.; Leppä, Aino-Maija; Hellesøy, Monica; Dowling, Paul; Malyutina, Alina; Kopperud, Reidun; Bazou, Despina; Andersson, Emma; Parsons, Alun; Tang, Jing; Kallioniemi, Olli; Mustjoki, Satu; O´Gorman, Peter; Wennerberg, Krister; Porkka, Kimmo; Gjertsen, Bjørn T.; Heckman, Caroline A. (2020)
    Innate drug sensitivity in healthy cells aids identification of lineage specific anti-cancer therapies and reveals off-target effects. To characterize the diversity in drug responses in the major hematopoietic cell types, we simultaneously assessed their sensitivity to 71 small molecules utilizing a multi-parametric flow cytometry assay and mapped their proteomic and basal signaling profiles. Unsupervised hierarchical clustering identified distinct drug responses in healthy cell subsets based on their cellular lineage. Compared to other cell types, CD19+/B and CD56+/NK cells were more sensitive to dexamethasone, venetoclax and midostaurin, while monocytes were more sensitive to trametinib. Venetoclax exhibited dose dependent cell selectivity that inversely correlated to STAT3 phosphorylation. Lineage specific effect of midostaurin was similarly detected in CD19+/B cells from healthy, acute myeloid leukemia and chronic lymphocytic leukemia samples. Comparison of drug responses in healthy and neoplastic cells showed that healthy cell responses are predictive of the corresponding malignant cell response. Taken together, understanding drug sensitivity in the healthy cell-of-origin provides opportunities to obtain a new level of therapy precision and avoid off-target toxicity.
  • Ianevski, Aleksandr; Zusinaite, Eva; Kuivanen, Suvi; Strand, Mårten; Lysvand, Hilde; Teppor, Mona; Kakkola, Laura; Paavilainen, Henrik; Laajala, Mira; Kallio-Kokko, Hannimari; Valkonen, Miia; Kantele, Anu; Telling, Kaidi; Lutsar, Irja; Letjuka, Pille; Metelitsa, Natalja; Oksenych, Valentyn; Bjørås, Magnar; Nordbø, Svein Arne; Dumpis, Uga; Vitkauskiene, Astra; Öhrmalm, Christina; Bondeson, Kåre; Bergqvist, Anders; Aittokallio, Tero; Cox, Rebecca J.; Evander, Magnus; Hukkanen, Veijo; Marjomaki, Varpu; Julkunen, Ilkka; Vapalahti, Olli; Tenson, Tanel; Merits, Andres; Kainov, Denis (2018)
    Abstract According to the WHO, there is an urgent need for better control of viral diseases. Re-positioning existing safe-in-human antiviral agents from one viral disease to another could play a pivotal role in this process. Here, we reviewed all approved, investigational and experimental antiviral agents, which are safe in man, and identified 59 compounds that target at least three viral diseases. We tested 55 of these compounds against eight different RNA and DNA viruses. We found novel activities for dalbavancin against echovirus 1, ezetimibe against human immunodeficiency virus 1 and Zika virus, as well as azacitidine, cyclosporine, minocycline, oritavancin and ritonavir against Rift valley fever virus. Thus, the spectrum of antiviral activities of existing antiviral agents could be expanded towards other viral diseases.
  • Elmadani, Manar; Khan, Suleiman; Tenhunen, Olli; Magga, Johanna; Aittokallio, Tero; Wennerberg, Krister; Kerkelä, Risto (2019)
    Background-Small molecule kinase inhibitors (KIs) are a class of agents currently used for treatment of various cancers. Unfortunately, treatment of cancer patients with some of the KIs is associated with cardiotoxicity, and there is an unmet need for methods to predict their cardiotoxicity. Here, we utilized a novel computational method to identify protein kinases crucial for cardiomyocyte viability. Methods and Results-One hundred forty KIs were screened for their toxicity in cultured neonatal cardiomyocytes. The kinase targets of KIs were determined based on integrated data from binding assays. The key kinases mediating the toxicity of KIs to cardiomyocytes were identified by using a novel machine learning method for target deconvolution that combines the information from the toxicity screen and from the kinase profiling assays. The top kinases identified by the model were phosphoinositide 3-kinase catalytic subunit alpha, mammalian target of rapamycin, and insulin-like growth factor 1 receptor. Knockdown of the individual kinases in cardiomyocytes confirmed their role in regulating cardiomyocyte viability. Conclusions-Combining the data from analysis of KI toxicity on cardiomyocytes and KI target profiling provides a novel method to predict cardiomyocyte toxicity of KIs.
  • Mannisto, Jere K.; Sahari, Aleksi; Lagerblom, Kalle; Niemi, Teemu; Nieger, Martin; Sztanó, Gábor; Repo, Timo (2019)
    2-Oxazolidinones are saturated heterocyclic compounds, which are highly attractive targets in modern drug design. Herein, we describe a new, single-step approach to 3,4-disubstituted 2-oxazolidinones by aza-Michael addition using CO2 as a carbonyl source and 1,1,3,3-tetramethylguanidine (TMG) as a catalyst. The modular reaction, which occurs between a gamma-brominated Michael acceptor, CO2 and an arylamine, aliphatic amine or phenylhydrazine, is performed under mild conditions. The regiospecific reaction displays good yields (av. 75 %) and excellent functional-group compatibility. In addition, late-stage functionalization of drug and drug-like molecules is demonstrated. The experimental results suggest a mechanism consisting of several elementary steps: TMG-assisted carboxylation of aniline; generation of an O-alkyl carbamate; and the final ring-forming step through an intramolecular aza-Michael addition.
  • Santio, Niina M.; Eerola, Sini K.; Paatero, Ilkka; Yli-Kauhaluoma, Jari; Anizon, Fabrice; Moreau, Pascale; Tuomela, Johanna; Härkönen, Pirkko; Koskinen, Päivi J. (2015)
    Background and methods Pim family proteins are oncogenic kinases implicated in several types of cancer and involved in regulation of cell proliferation, survival as well as motility. Here we have investigated the ability of Pim kinases to promote metastatic growth of prostate cancer cells in two xenograft models for human prostate cancer. We have also evaluated the efficacy of Pim-selective inhibitors to antagonize these effects. Results We show here that tumorigenic growth of both subcutaneously and orthotopically inoculated prostate cancer xenografts is enhanced by stable overexpression of either Pim-1 or Pim-3. Moreover, Pim-overexpressing orthotopic prostate tumors are highly invasive and able to migrate not only to the nearby prostate-draining lymph nodes, but also into the lungs to form metastases. When the xenografted mice are daily treated with the Pim-selective inhibitor DHPCC-9, both the volumes as well as the metastatic capacity of the tumors are drastically decreased. Interestingly, the Pim-promoted metastatic growth of the orthotopic xenografts is associated with enhanced angiogenesis and lymphangiogenesis. Furthermore, forced Pim expression also increases phosphorylation of the CXCR4 chemokine receptor, which may enable the tumor cells to migrate towards tissues such as the lungs that express the CXCL12 chemokine ligand. Conclusions Our results indicate that Pim overexpression enhances the invasive properties of prostate cancer cells in vivo. These effects can be reduced by the Pim-selective inhibitor DHPCC-9, which can reach tumor tissues without serious side effects. Thus, Pim-targeting therapies with DHPCC-9-like compounds may help to prevent progression of local prostate carcinomas to fatally metastatic malignancies.
  • Bromann, Paul Andrew; Korkaya, Hasan; Webb, Craig P.; Miller, Jeremy; Calvin, Tammy L.; Courtneidge, Sara A. (2005)
    The Src family of protein-tyrosine kinases (SFKs) participates in a variety of signal transduction pathways, including promotion of cell growth, prevention of apoptosis, and regulation of cell interactions and motility. In particular, SFKs are required for the mitogenic response to platelet-derived growth factor (PDGF). However, it is not clear whether there is a discrete SFK-specific pathway leading to enhanced gene expression or whether SFKs act to generally enhance PDGF-stimulated gene expression. To examine this, we treated quiescent NIH3T3 cells with PDGF in the presence or absence of small molecule inhibitors of SFKs, phosphatidylinositol 3-kinase (PI3K), and MEK1/2. Global patterns of gene expression were analyzed by using Affymetrix Gene-Chip arrays, and data were validated by using reverse transcription-PCR and ribonuclease protection assay. We identified a discrete set of immediate early genes induced by PDGF and inhibited in the presence of the SFK-selective inhibitor SU6656. A subset of these SFK-dependent genes was induced by PDGF even in the presence of the MEK1/2 inhibitor U0126 or the PI3K inhibitor LY294002. By using ribonuclease protection assays and nuclear run-off assays, we further determined that PDGF did not stimulate the rate of transcription of these SFK-dependent immediate early genes but rather promoted mRNA stabilization. Our data suggest that PDGF regulates gene expression through an SFK-specific pathway that is distinct from the Ras-MAPK and PI3K pathways, and that SFKs signal gene expression by enhancing mRNA stability.
  • Wolthers, Katja C.; Susi, Petri; Jochmans, Dirk; Koskinen, Janne; Landt, Olfert; Sanchez, Neus; Palm, Kaia; Neyts, Johan; Butcher, Sarah J. (2019)
    Several research groups in Europe are active on different aspects of human picornavirus research. The AIROPico (Academia-Industry R&D Opportunities for Picornaviruses) consortium combined the disciplines of pathogenesis, diagnostics and therapy development in order to fill the gaps in our understanding of how picornaviruses cause human disease and how to combat them. AIROPico was the first EU consortium dedicated to human picornavirus research and development, and has largely accelerated and improved R&D on picornavirus biology, diagnostics and therapy. In this article, we present the progress on pathogenesis, diagnostics and treatment strategy developments for human picornaviruses resulting from the structured, translational research approach of the AIROPico consortium. We here summarize new insights in protection against infection by maternal or cross-protective antibodies, the visualisation of interactions between virus and neutralizing antibodies by cryoEM structural imaging, and the outcomes from a picornavirus-infected human 3D organoid. Progress in molecular detection and a fast typing assay for rhinovirus species are presented, as well as the identification of new compounds potentially interesting as therapeutic compounds.
  • Qiu, Tianyi; Xiao, Han; Zhang, Qingchen; Qiu, Jingxuan; Yang, Yiyan; Wu, Dingfeng; Cao, Zhiwei; Zhu, Ruixin (2015)
    Despite the high specificity between antigen and antibody binding, similar epitopes can be recognized or cross-neutralized by paratopes of antibody with different binding affinities. How to accurately characterize this slight variation which may or may not change the antigen-antibody binding affinity is a key issue in this area. In this report, by combining cylinder model with shell structure model, a new fingerprint was introduced to describe both the structural and physical-chemical features of the antigen and antibody protein. Furthermore, beside the description of individual protein, the specific epitope-paratope interaction fingerprint (EPIF) was developed to reflect the bond and the environment of the antigen-antibody interface. Finally, Proteochemometric Modeling of the antigen-antibody interaction was established and evaluated on 429 antigen-antibody complexes. By using only protein descriptors, our model achieved the best performance (R-2 = 0: 91; Q(test)(2) = 0: 68) among peers. Further, together with EPIF as a new cross-term, our model (R-2 = 0: 92; Q(2) test = 0: 74) can significantly outperform peers with multiplication of ligand and protein descriptors as a cross-term (R2
  • Aly, Ashraf A.; Hassan, Alaa A.; AbdAl-Latif, El-Shimaa S. M.; Ibrahim, Mahmoud A. A.; Bräse, Stefan; Nieger, Martin (2018)
    Reaction of hydrazinecarbothioamides with 2-bromoacetophenones furnished the formation of thiazole-, bis-thiazole-, pyrazole- and 1,3,4-thiadiazole- derivatives in good yields. The mechanism was discussed. The structures of products were proved by MS, IR, NMR, elemental analyses and X-ray structure analyses. [GRAPHICS] .
  • Hassan, Alaa A.; Mohamed, Nasr K.; El-Shaieb, Kamal M. A.; Tawfeek, Hendawy N.; Bräse, Stefan; Nieger, Martin (2016)
    2-{Amino-[5-amino-2-(substituted diazenyl) thiazol-4-yl] methylene} malononitriles were synthesized from the reaction of 2-substituted hydrazinecarbothioamides with tetracyanoethylene (TCNE) to give tetracyanoethane adduct, followed by heterocyclization afforded the target compounds. The structure of (E)-2-{amino-[5-amino-2-(phenyldiazenyl) thiazol-4-yl] methylene} malononitrile was supported by single crystal X-ray crystallography.
  • Hertel, Christina; Fishman, Dmytro; Lorenc, Anna; Ranki, Annamari; Krohn, Kai; Peterson, Pärt; Kisand, Kai; Hayday, Adrian (2019)
    In 2016, we reported four substantial observations of APECED/APS1 patients, who are deficient in AIRE, a major regulator of central T cell tolerance (Meyer et al., 2016). Two of those observations have been challenged. Specifically, 'private' autoantibody reactivities shared by only a few patients but collectively targeting >1000 autoantigens have been attributed to false positives (Landegren, 2019). While acknowledging this risk, our study-design included follow-up validation, permitting us to adopt statistical approaches to also limit false negatives. Importantly, many such private specificities have now been validated by multiple, independent means including the autoantibodies ' molecular cloning and expression. Second, a significant correlation of antibody-mediated IFN a neutralization with an absence of disease in patients highly disposed to Type I diabetes has been challenged because of a claimed failure to replicate our findings (Landegren, 2019). However, flaws in design and implementation invalidate this challenge. Thus, our results present robust, insightful, independently validated depictions of APECED/APS1, that have spawned productive follow-up studies.
  • Rathnayake, Nilminie; Gustafsson, Anders; Norhammar, Anna; Kjellstrom, Barbro; Klinge, Bjorn; Ryden, Lars; Tervahartiala, Taina; Sorsa, Timo; PAROKRANK Steering Grp (2015)
    Background and Objective Matrix metalloproteinase (MMP) -8, -9 and myeloperoxidase (MPO) are inflammatory mediators. The potential associations between MMP-8, -9, MPO and their abilities to reflect cardiovascular risk remains to be evaluated in saliva. The objective of this study was to investigate the levels and associations of salivary MMP-8, -9, MPO and tissue inhibitors of metalloproteinase (TIMP)-1 in myocardial infarction (MI) patients and controls with or without periodontitis. Materials and Methods 200 patients with a first MI admitted to coronary care units in Sweden from May 2010 to December 2011 and 200 controls matched for age, gender, residential area and without previous MI were included. Dental examination and saliva sample collection was performed 6-10 weeks after the MI in patients and at baseline in controls. The biomarkers MMP -8, -9, MPO and TIMP-1 were analyzed by time-resolved immunofluorescence assay (IFMA), Western blot and Enzyme-Linked ImmunoSorbent Assay (ELISA). Results After compensation for gingivitis, gingival pockets and smoking, the mean salivary levels of MMP-8 (543 vs 440 ng/mL, p = 0.003) and MPO (1899 vs 1637 ng/mL, p = 0.02) were higher in non-MI subjects compared to MI patients. MMP-8, -9 and MPO correlated positively with clinical signs of gingival/periodontal inflammation while TIMP-1 correlated mainly negatively with these signs. The levels of latent and active forms of MMP-8 did not differ between the MI and non-MI groups. Additionally, MMP-8, MPO levels and MMP-8/TIMP-1 ratio were significantly higher in men compared to women with MI. Conclusions This study shows that salivary levels of the analyzed biomarkers are associated with periodontal status. However, these biomarkers could not differentiate between patients with or without a MI. These findings illustrate the importance to consider the influence of oral conditions when analyzing levels of inflammatory salivary biomarkers.
  • Helin-Salmivaara, Arja; Korhonen, Maarit J.; Lehenkari, Petri; Junnila, Seppo Y. T.; Neuvonen, Pertti J.; Ruokoniemi, Päivi; Huupponen, Risto (2012)
  • Sheetz, Joshua B.; Mathea, Sebastian; Karvonen, Hanna; Malhotra, Ketan; Chatterjee, Deep; Niininen, Wilhelmiina; Perttilä, Robert; Preuss, Franziska; Suresh, Krishna; Stayrook, Steven E.; Tsutsui, Yuko; Radhakrishnan, Ravi; Ungureanu, Daniela; Knapp, Stefan; Lemmon, Mark A. (2020)
    Despite their apparent lack of catalytic activity, pseudokinases are essential signaling molecules. Here, we describe the structural and dynamic properties of pseudokinase domains from the Wnt-binding receptor tyrosine kinases (PTK7, ROR1, ROR2, and RYK), which play important roles in development. We determined structures of all pseudokinase domains in this family and found that they share a conserved inactive conformation in their activation loop that resembles the autoinhibited insulin receptor kinase (IRK). They also have inaccessible ATP-binding pockets, occluded by aromatic residues that mimic a cofactor-bound state. Structural comparisons revealed significant domain plasticity and alternative interactions that substitute for absent conserved motifs. The pseudokinases also showed dynamic properties that were strikingly similar to those of IRK. Despite the inaccessible ATP site, screening identified ATP-competitive type-II inhibitors for ROR1. Our results set the stage for an emerging therapeutic modality of "conformational disruptors" to inhibit or modulate non-catalytic functions of pseudokinases deregulated in disease.
  • Keurulainen, Leena; Heiskari, Mikko; Nenonen, Satu; Nasereddin, Abedelmajeed; Kopelyanskiy, Dmitry; Leino, Teppo O.; Yli-Kauhaluoma, Jari; Jaffe, Charles L.; Kiuru, Paula (2015)
    A facile synthesis route to carboxyimidamide-substituted benzoxadiazoles and related derivatives was developed. A total of 25 derivatives were synthesized. They were evaluated for antileishmanial activity by inhibition of Leishmania donovani axenic amastigote growth using a fluorescent viability microplate assay. The most promising derivative (14) demonstrated an antileishmanial EC50 of 4.0 mu M, and it also showed activity in infected macrophages (EC50 5.92 mu M) without signs of cytotoxicity.
  • Grosjean, Sylvain; Hodapp, Patrick; Hassan, Zahid; Woell, Christof; Nieger, Martin; Bräse, Stefan (2019)
    Modular synthesis of structurally diverse functionalized azobiphenyls and azoterphenyls for the realization of optically switchable materials has been described. The corresponding synthesis of azobiphenyls and azoterphenyls by stepwise Mills/Suzuki-Miyaura cross-coupling reaction, proceeds with high yields and provides facile access to a library of functionalized building blocks. The synthetic methods described herein allow combining several distinct functional groups within a single unit, each intended for a specific task, such as 1) the -N=N- azobenzene core as a photoswitchable moiety, 2) aryls and heteroaryls, functionalized with carboxylic acids or pyridine at its peripheries, as coordinating moieties and 3) varying substitution, size and length of the backbone for adaptability to specific applications. These specifically designed azobiphenyls and azoterphenyls provide modular bricks, potentially useful for the assembly of a variety of polymers, molecular containers and coordination networks, offering a high degree of molecular functionality. Once integrated into materials, the azobenzene system, as a side group on the organic linker backbone, can be exploited for remotely controlling the structural, mechanical or physical properties, thus being applicable for a broad variety of 'smart' applications.
  • Aly, Ashraf A.; Hassan, Alaa A.; Mohamed, Nasr K.; Abd El-Haleem, Lamiaa E.; Bräse, Stefan; Polamo, Mika; Nieger, Martin; Brown, Alan B. (2019)
    Herein, we report the synthesis of 5,12-dihydropyrazino[2,3-c:5,6-c ' ]difuro[2,3-c:4,5-c ']-diquinoline-6,14(5H,12H)diones, 2-(4-hydroxy-2-oxo-1,2-dihydroquinolin-3-yl)-1,4-diphenyl- butane-1,4-diones and 4-(benzo-[d]oxazol-2-yl)-3-hydroxy-1H-[4,5]oxazolo[3,2-a]pyridine-1-one. The new candidates were synthesized and identified by different spectroscopic techniques, and X-ray crystallography.