Comprehensive Data-Driven Assessment of Non-Kinase Targets of Inhibitors of the Human Kinome.

Protein kinases (PKs) are involved in many intracellular signal transduction pathways through phosphorylation cascades and have become intensely investigated pharmaceutical targets over the past two decades. Inhibition of PKs using small-molecular inhibitors is a premier strategy for the treatment of diseases in different therapeutic areas that are caused by uncontrolled PK-mediated phosphorylation and aberrant signaling. Most PK inhibitors (PKIs) are directed against the ATP cofactor binding site that is largely conserved across the human kinome comprising 518 wild-type PKs (and many mutant forms). Hence, these PKIs often have varying degrees of multi-PK activity (promiscuity) that is also influenced by factors such as single-site mutations in the cofactor binding region, compound binding kinetics, and residence times. The promiscuity of PKIs is often-but not always-critically important for therapeutic efficacy through polypharmacology. Various in vitro and in vivo studies have also indicated that PKIs have the potential of interacting with additional targets other than PKs, and different secondary cellular targets of individual PKIs have been identified on a case-by-case basis. Given the strong interest in PKs as drug targets, a wealth of PKIs from medicinal chemistry and their activity data from many assays and biological screens have become publicly available over the years. On the basis of these data, for the first time, we conducted a systematic search for non-PK targets of PKIs across the human kinome. Starting from a pool of more than 155,000 curated human PKIs, our large-scale analysis confirmed secondary targets from diverse protein classes for 447 PKIs on the basis of high-confidence activity data. These PKIs were active against 390 human PKs, covering all kinase groups of the kinome and 210 non-PK targets, which included other popular pharmaceutical targets as well as currently unclassified proteins. The target distribution and promiscuity of the 447 PKIs were determined, and different interaction profiles with PK and non-PK targets were identified. As a part of our study, the collection of PKIs with activity against non-PK targets and the associated information are made freely available.

Assessment of Kinome-Wide Activity Remodeling upon Picornavirus Infection.

Picornaviridae represent a large family of single-stranded positive RNA viruses of which different members can infect both humans and animals. These include the enteroviruses (e.g., poliovirus, coxsackievirus, and rhinoviruses) as well as the cardioviruses (e.g., encephalomyocarditis virus). Picornaviruses have evolved to interact with, use, and/or evade cellular host systems to create the optimal environment for replication and spreading. It is known that viruses modify kinase activity during infection, but a proteome-wide overview of the (de)regulation of cellular kinases during picornavirus infection is lacking. To study the kinase activity landscape during picornavirus infection, we here applied dedicated targeted mass spectrometry-based assays covering ∼40% of the human kinome. Our data show that upon infection, kinases of the MAPK pathways become activated (e.g., ERK1/2, RSK1/2, JNK1/2/3, and p38), while kinases involved in regulating the cell cycle (e.g., CDK1/2, GWL, and DYRK3) become inactivated. Additionally, we observed the activation of CHK2, an important kinase involved in the DNA damage response. Using pharmacological kinase inhibitors, we demonstrate that several of these activated kinases are essential for the replication of encephalomyocarditis virus. Altogether, the data provide a quantitative understanding of the regulation of kinome activity induced by picornavirus infection, providing a resource important for developing novel antiviral therapeutic interventions.

The cost of the circadian desynchrony on the Leydig cell function.

The increased frequency of different lifestyles that disrupts circadian rhythms, together with a trend in the accretion of male idiopathic infertility, imposes the necessity to understand the contribution of circadian rhythms disruption to fertility regulation. In this study, the effects of circadian desynchrony (CD) on the steroidogenic capacity of adult Leydig cells were studied. Adult rats were housed under a disturbing light regime (2 days of constant light, 2 days of continual dark, and 3 days of 12:12 h light:dark schedule) designed to mimic shiftwork in humans. CD was characterized by changed and decreased rhythmic locomotor activity and reduced blood testosterone. In the Leydig cells changed transcription of the clock genes (Bmal1, Clock, Cry1 and Reverba/b increased while Per1/2 reversed phase) was detected. This was followed by reduced transcription of genes (Star, Cyp11a1, and Hsd3b1/2) primarily involved in mitosteroidogenesis. In parallel, mitochondrial membrane potential (Δψi) and ATP production declined losing their characteristic oscillatory pattern. Also, the main markers of mitochondrial biogenesis (Ppargc1a, Nrf1, Tfam, Cytc), fusion (Mfn2), and mitophagy (Pink1 and Tfeb) were disturbed. Collectively, CD targets mitochondria in Leydig cells by reducing mitosteroidogenesis, mitoenergetics, and disturbing mitochondrial dynamics. These changes contribute to testosterone decline compromising androgen-dependent functions, including reproduction.

Gain-of-function mutations in ALPK1 cause an NF-κB-mediated autoinflammatory disease: functional assessment, clinical phenotyping and disease course of patients with ROSAH syndrome.

OBJECTIVES: To test the hypothesis that ROSAH (retinal dystrophy, optic nerve oedema, splenomegaly, anhidrosis and headache) syndrome, caused by dominant mutation in ALPK1, is an autoinflammatory disease. METHODS: This cohort study systematically evaluated 27 patients with ROSAH syndrome for inflammatory features and investigated the effect of ALPK1 mutations on immune signalling. Clinical, immunologic and radiographical examinations were performed, and 10 patients were empirically initiated on anticytokine therapy and monitored. Exome sequencing was used to identify a new pathogenic variant. Cytokine profiling, transcriptomics, immunoblotting and knock-in mice were used to assess the impact of ALPK1 mutations on protein function and immune signalling. RESULTS: The majority of the cohort carried the p.Thr237Met mutation but we also identified a new ROSAH-associated mutation, p.Tyr254Cys.Nearly all patients exhibited at least one feature consistent with inflammation including recurrent fever, headaches with meningeal enhancement and premature basal ganglia/brainstem mineralisation on MRI, deforming arthritis and AA amyloidosis. However, there was significant phenotypic variation, even within families and some adults lacked functional visual deficits. While anti-TNF and anti-IL-1 therapies suppressed systemic inflammation and improved quality of life, anti-IL-6 (tocilizumab) was the only anticytokine therapy that improved intraocular inflammation (two of two patients).Patients' primary samples and in vitro assays with mutated ALPK1 constructs showed immune activation with increased NF-κB signalling, STAT1 phosphorylation and interferon gene expression signature. Knock-in mice with the Alpk1 T237M mutation exhibited subclinical inflammation.Clinical features not conventionally attributed to inflammation were also common in the cohort and included short dental roots, enamel defects and decreased salivary flow. CONCLUSION: ROSAH syndrome is an autoinflammatory disease caused by gain-of-function mutations in ALPK1 and some features of disease are amenable to immunomodulatory therapy.

[Prevalence of Adverse Effects of Tyrosine Kinase Inhibitors Used in Management of Chronic Myeloid Leukemia at Sidi Bel-Abbès University Hospital Center]. / Prévalence des Effets Indésirables des Inhibiteurs de Tyrosine Kinase Utilisés dans le Traitement de la Leucémie Myéloïde Chronique au CHU de Sidi Bel-Abbès.

INTRODUCTION: Chronic myeloid leukemia (CML) is a malignant hemopathy within the framework of chronic myeloproliferative syndromes, predominant on the granular line. Her drug treatment is based on tyrosine kinase inhibitors (TKIs) which inhibit the abnormal BCR-ABL protein kinase that causes CML and thus block the signals that cause cancer cells to multiply abnormally. However, other proteins are also inhibited, so they can cause a wide range of adverse effects (AEs). The objective of this study was to study the prevalence of AEs of TKIs used in the therapeutic management of CML by the hematology department of University Hospital Center (UHC) of Sidi Bel-Abbes in Algeria and that of the ITK discontinuation following an AE. MATERIALS AND METHODS: It was a retrospective descriptive study carried out over a period of four months, from April 01st, 2021 to July 31st, 2021, on CML patients treated with TKI in the hematology department of Sidi Bel-Abbes HUC in Algeria. The primary outcome measure was the prevalence of AEs associated with the use of normal dosages or overdose of the following TKIs: Imatinib, Dasatinib and Nilotinib. Data were collected from patient charts, filled by doctors of hematology department, using questionnaire, and analyzed by Statistical Package for the Social Sciences software, version 20. RESULTS: A total of 40 patients were included, including 22 women, mean age 51.55±11.66years (23-78). Twenty-six patients reported at least one AE. Among the 106 AEs declared, 69 AEs (65.09 %) declared with Imatinib, 26 AEs (24.53 %) with Dasatinib and 11 AEs (10.38 %) with Nilotinib. A predominance of musculoskeletal effects 43 (40.56 %), followed by general disorders 18 (17 %), myelosuppression 14 (13.20 %) and digestive system 12 (11.32 %). AEs were responsible for permanent discontinuation of ITK in three cases (11.54 %), including two cases (07.70 %) on Imatinib because of neutropenia and one case (03.84 %) onDasatinibsuffering from pleural effusion. AEs could be controlled in 13 (50 %) of cases, including 9 (34.62%) by temporary discontinuation and 4 (15.38 %) by reducing the dosage, allowing improvement of symptoms and continuation or reintroduction of treatment. CONCLUSION: The prevalence of AEs was high in the studied population, their occurrence was inevitable, good management of AEs from the start of treatment is necessary to avoid switching to another TKI, especially in good responders. It is recommended to establish a low-sodium diet beforehand for all TKIs and a low-carbohydrate diet, especially for Nilotinib, and not to rush to stop the TKI because most often, EIs regress over time in order to allow good therapeutic adherence and obtain better results.

Monitoramento do horizonte tecnológico: Medicamentos em desenvolvimento para tratamento do câncer de mama triplo negativo localmente avançado irressecável ou metastático / Monitoring the technological horizon: Drugs in development for the treatment of unresectable or metastatic locally advanced triple negative breast cancer

A DOENÇA: O câncer de mama triplo negativo (CMTN) é definido pela ausência da expressão dos receptores de estrogênio (RE), receptores de progesterona (RP) e receptores do fator de crescimento epidermal humano (HER2 ­ human epidermal growth factor receptor 2), que são marcadores presentes na maioria dos tipos de câncer de mama e utilizados para a definição do tratamento. Em média, entre os casos de câncer de mama, 15 a 20% são definidos como CMTN e mais de 30% desses casos progridem para doença metastática. Diferente dos outros tipos de câncer de mama, sua frequência é maior entre mulheres jovens abaixo de 50 anos, com maior prevalência entre aquelas com 35 anos. Os pacientes com CMTN apresentam geralmente tumores em graus mais avançados e desfechos clínicos ruins em termos de sobrevida global e sobrevida livre de doença. As curvas de sobrevida no CMTN, diferentes de outros subtipos de câncer de mama, são caracterizadas por um aumento na recidiva e uma diminuição na sobrevida durante os primeiros três a cinco anos após o diagnóstico. Apesar de avanços substanciais nos resultados clínicos de novos tratamentos para o câncer de mama nos últimos anos, o subtipo de CMTN permanece uma área com necessidade clínica ainda não atendida. Como não apresentam expressão de RE, RP e HER2, os tratamentos com hormonioterapia e terapia anti-HER2 não estão indicados para esses pacientes, sendo adotada a estratégia de quimioterapia, além da cirurgia e radioterapia, conforme preconizado nas Diretrizes Diagnósticas e Terapêuticas do Carcinoma de Mama. TRATAMENTO DISPONÍVEL: As Diretrizes Diagnósticas e Terapêuticas do Carcinoma de Mama de 2019 não fazem recomendação específica para o tratamento dos pacientes com CMTN. Entretanto, entre os medicamentos utilizados para o tratamento dos tipos de câncer de mama é relatado que a associação do bevacizumabe ao paclitaxel nos pacientes com CMTN proporciona um aumento na taxa de resposta e na sobrevida livre de progressão de doença sem alterar a sobrevida mediana global. De acordo com as Diretrizes de Tratamentos Oncológicos recomendados pela Sociedade Brasileira de Oncologia Clínica (SBOC) de 2021 para o câncer de mama metastático, os pacientes com CMTN devem ser tratados com quimioterapia. O regime deve ser individualizado com base no tamanho, localização e características do tumor; e sintomas e preferências do paciente. Além disso, devem ser considerados a resposta e o intervalo sem progressão com os tratamentos anteriores. Os taxanos e antracíclicos são os medicamentos do tratamento padrão tanto em (neo) adjuvância como na primeira linha de doença metastática. A doxorrubicina e a epirrubicina são os antracíclicos mais comumente usados no tratamento do câncer de mama. A escolha entre os taxanos é determinada pelo tratamento prévio, podendo-se escolher entre o paclitaxel e o docetaxel, de acordo com o perfil de toxicidade e preferência do paciente. No caso de pacientes refratários a antracíclicos e taxanos, existe uma série de opções de tratamentos quimioterápicos, que podem ser utilizados em monoterapia e associados. Os principais medicamentos utilizados em monoterapia são: capecitabina, eribulina, vinorelbine e gemcitabina. As terapias com medicamentos associados mais comumente utilizados são paclitaxel com gencitabina, docetaxel com capecitabina e combinações com platinas6 . Além desses, a adição de bevacizumabe à quimioterapia, em primeira ou segunda linha, resultou em aumento modesto de resposta objetiva e sobrevida livre de progressão, sem aumento de sobrevida global. ESTRATÉGIA DE BUSCA: Os medicamentos em fase de pesquisa clínica para câncer de mama triplo negativo foram identificados, inicialmente, na base de pesquisa clínica Clinicatrials.gov em 19 de abril de 2021, com filtros para estudo de intervenção, em fase 3 de ensaio clínico e em andamento. Foram excluídos da análise os estudos cuja situação estava desatualizada a mais de um ano na base e os estudos cujo objetivo da tecnologia era atuar como adjuvante ou neoadjuvante. Além disso, foram consultados as bases eletrônicas MEDLINE (via PubMed) e EMBASE (via Periódicos Capes) em 19 de abril de 2021; e Cortellis15, da Clarivate Analytics, em 28 de abril de 2021, utilizando o termo "advanced triple negative breast cancer" e seus sinônimos, com filtro para tecnologias em desenvolvimento na fase 3 de ensaio clínico. TECNOLOGIAS EM DESENVOLVIMENTO: Foram identificados 55 ensaios clínicos de fase 3, com 10 tecnologias em desenvolvimento para a indicação estudada e que foram elegíveis para compor este informe20: sacituzumabe govitecan, olaparibe, carelizumabe, pembrolizumabe, toripalimabe, TQB2450, alpelisibe, capivasertibe, ipatasertibe, e bicalutamida. O quadro 1 apresenta essas tecnologias consideradas com informações sobre sua classe terapêutica e situação regulatória nas agências sanitárias FDA, EMA, Health Canada e Anvisa. Algumas tecnologias estão em estágios iniciais do ensaio clínico de fase 3 sem resultados parciais publicados, entretanto, suas características serão descritas nesta seção. São eles: carelizumabe, toripalimabe, TQB2450, alpelisibe, capivasertibe e bicalutamida. CONSIDERAÇÕES FINAIS: O câncer de mama triplo negativo localmente avançado irressecável ou metastático é uma doença heterogênea com um prognóstico ruim e atualmente com poucas opções de tratamento em uso. A aprovação do medicamento atezolizumabe no Brasil, para uso em combinação com nab-paclitaxel trouxe um avanço para o tratamento alvo-direcionado para essa população. Este informe apresentou o panorama das tecnologias mais promissoras em fase de desenvolvimento clínico para a doença. Algumas em vias de administração com maior comodidade posológica, como a via oral (olaparibe, alpelisibe, capivasertibe, ipatasertibe e bicalutamida). A identificação dessas tecnologias neste informe projeta uma expectativa sobre diferentes vias moleculares de combate a doença que podem impactar no prognóstico dos pacientes com câncer de mama triplo negativo localmente avançado irressecável ou metastático. Algumas dessas tecnologias estão em fases finais de pesquisa clínica com resultados publicados e já são autorizadas ou iniciaram seus pedidos nas agências sanitárias internacionais. Entre elas destacam-se o sacituzumabe govitecan e o pembrolizumabe, ambas com autorização de comercialização recente pela agência sanitária dos EUA para a indicação de CMTN. Mesmo sendo essa autorização em um contexto de aprovação acelerada, que necessita de acompanhamento dos resultados dos estudos em andamento, existe um avanço para o tratamento da doença que hoje ainda é considerada com uma necessidade não atendida. O sacituzumabe govitecan obteve bons resultados para os desfechos de sobrevida livre de progressão, sobrevida global e taxa de resposta objetiva. Os resultados com pembrolizumabe, apesar de não indicarem uma diferença grande em relação ao comparador nos desfechos de sobrevida livre de progressão, se mostraram consistentes ao longo do tempo e foram maiores conforme o aumento da expressão de PD-1, indicando que pode existir uma relação direta com esse marcador. As tecnologias em desenvolvimento identificadas estão direcionadas a alvos moleculares específicos do desenvolvimento da doença, de modo que a definição dos subtipos moleculares é essencial para o planejamento das estratégias de tratamento, que cada vez mais serão baseadas em medicina personalizada, como por exemplo, a quantificação da expressão do PD-1 como biomarcador preditivo de benefício para a escolha dos pacientes que devem fazer imunoterapia. Espera-se que a conclusão dos estudos em andamento possa trazer resultados clínicos robustos que possam aumentar as opções terapêuticas do tratamento e assim representar um melhor prognóstico da doença.

Functional assessment of the V390F mutation in the CCTδ subunit of chaperonin containing tailless complex polypeptide 1.

The chaperonin containing tailless complex polypeptide 1 (CCT) is a multi-subunit molecular chaperone. It is found in the cytoplasm of all eukaryotic cells, where the oligomeric form plays an essential role in the folding of predominantly the cytoskeletal proteins actin and tubulin. Both the CCT oligomer and monomeric subunits also display functions that extend beyond folding, which are often associated with microtubules and actin filaments. Here, we assess the functional significance of the CCTδ V390F mutation, reported in several cancer cell lines. Upon transfection into B16F1 mouse melanoma cells, GFP-CCTδV390F incorporates into the CCT oligomer more readily than GFP-CCTδ. Furthermore, unlike GFP-CCTδ, GFP-CCTδV390F does not interact with the dynactin complex component, p150Glued. As CCTδ has previously been implicated in altered migration in wound healing assays, we assessed the behaviour of GFP-CCTδV390F and other mutants of CCTδ, previously used to assess functional interactions with p150Glued, in chemotaxis assays. We developed the assay system to incorporate a layer of the inert hydrogel GrowDex® to provide a 3D matrix for chemotaxis assessment and found subtle differences in the migration of B16F1 cells, depending on the presence of the hydrogel.

Systematic assessment of structure-promiscuity relationships between different types of kinase inhibitors.

Given the increasing quest for selective kinase inhibitors, we have systematically investigated structural and structure-promiscuity relationships between promiscuous kinase inhibitors and other types with increasing potential for selective kinase inhibition. Therefore, inhibitors with different modes of action were extracted from X-ray structures of kinase complexes. For more than 18,000 promiscuous kinase inhibitors and 1253 type I1/2, II, and allosteric inhibitors with structurally confirmed mechanisms, analogue space was systematically charted. These inhibitors were active against a total of 426 human kinases. While nearly 80% of the promiscuous inhibitors formed related analogues series, only ~30% of other types of inhibitors were involved in such structural relationships and many of these inhibitors also had multi-kinase activity. Thus, most of the investigated type I1/2, II, and allosteric inhibitors with reported single-kinase activity were distinguished from promiscuous inhibitors, thus indicating potential for kinase selectivity. Structural relationships between promiscuous inhibitors and the subset of other inhibitors were organized in a matrix format including kinase activity profiles, revealing structure-promiscuity relationships for follow-up investigations.

Assessment of PDK4 and TTN gene variants in 48 Doberman Pinschers with dilated cardiomyopathy.

OBJECTIVE: To evaluate the frequency of variants in the pyruvate kinase dehydrogenase 4 (PDK4) and titin (TTN) genes in a group of Doberman Pinschers with dilated cardiomyopathy (DCM) and to determine whether there were unique clinical attributes to each variant. ANIMALS: 48 Doberman Pinschers with DCM. PROCEDURES: Doberman Pinschers with recently diagnosed DCM were identified, and genomic DNA from each was genotyped with a PCR assay for detection of PDK4 and TTN genetic variants. Dogs were grouped on the basis of whether they had the TTN variant alone, PDK4 variant alone, both variants, or neither variant. Descriptive statistics were compiled for dog age, body weight, and left ventricular dimensions and fractional shortening and for the presence of ventricular and supraventricular arrhythmias and heart failure. Results were compared across groups. RESULTS: Of the 48 dogs, 28 had the TTN variant alone, 10 had both variants, 6 had neither variant, and 4 had the PDK4 variant alone. The mean age was younger for dogs with the PDK4 variant alone, compared with other dogs. However, the number of dogs with the PDK4 variant alone was very small, and there was an overlap in age across groups. No other meaningful differences were detected across groups, and independent genotype-phenotype relationships were not identified. CONCLUSIONS AND CLINICAL RELEVANCE: Although findings indicated that the TTN variant was most common, 6 dogs had neither variant, and this fact supported the concept of ≥ 1 other genetic contributor to DCM in Doberman Pinschers. Future studies are warranted to evaluate genotype-phenotype relationships in Doberman Pinschers with DCM.

Silicon Photomultipliers as a Low-Cost Fluorescence Detector for Capillary Electrophoresis.

Capillary electrophoresis (CE) is a highly efficient separation method capable of handling small sample volumes (∼pL) and low (∼yoctomole) detection limits and, as such, is ideal for applications that require high sensitivity, such as single-cell analysis (Chen et al. Anal. Chem. 1996, 68 (4), 690-696; Cohen et al. Annu. Rev. Anal. Chem. 2008, 1 (1), 165-190; Vickerman et al. ACS Chem. Biol. 2018, 13 (7), 1741-1751). Low-cost CE instrumentation is quickly expanding, but low-cost, open-source fluorescence detectors with ultrasensitive detection limits are lacking (Vickerman et al. ACS Chem. Biol. 2018, 13 (7), 1741-1751; Fang et al. Electrophoresis 2016, 37 (17-18), 2376-2383; Casto et al. Anal. Chem. 2019, 40 (1), 65-78). Silicon photomultipliers (SiPM) are inexpensive, low-footprint detectors with the potential to fill the role as a detector when cost, size, and customization are important. In this work, we demonstrate the use of a SiPM in CE with zeptomolar detection limits and a dynamic range spanning 5 orders of magnitude, comparable to photomultiplier detectors. The performance of these detectors was measured using a continuous wave excitation laser in an epifluorescence detection configuration. We characterize the performance of the SiPM as a highly sensitive detector by measuring enzyme activity in single cells. This simple, small footprint, and low-cost (<$130) light detection circuit will be beneficial for open-source, portable, and budget-friendly instrumentation requiring high sensitivity.

Comparative assessment of the effects of bumped kinase inhibitors on early zebrafish embryo development and pregnancy in mice.

Bumped kinase inhibitors (BKIs) are effective against a variety of apicomplexan parasites. Fifteen BKIs with promising in vitro efficacy against Neospora caninum tachyzoites, low cytotoxicity in mammalian cells, and no toxic effects in non-pregnant BALB/c mice were assessed in pregnant mice. Drugs were emulsified in corn oil and were applied by gavage for 5 days. Five BKIs did not affect pregnancy, five BKIs exhibited ~15-35% neonatal mortality and five compounds caused strong effects (infertility, abortion, stillbirth and pup mortality). Additionally, the impact of these compounds on zebrafish (Danio rerio) embryo development was assessed by exposing freshly fertilised eggs to 0.2-50 µM of BKIs and microscopic monitoring of embryo development in a blinded manner for 4 days. We propose an algorithm that includes quantification of malformations and embryo deaths, and established a scoring system that allows the calculation of an impact score (Si) indicating at which concentrations BKIs visibly affect zebrafish embryo development. Comparison of the two models showed that for nine compounds no clear correlation between Si and pregnancy outcome was observed. However, the three BKIs affecting zebrafish embryos only at high concentrations (≥40 µM) did not impair mouse pregnancy at all, and the three compounds that inhibited zebrafish embryo development already at 0.2 µM showed detrimental effects in the pregnancy model. Thus, the zebrafish embryo development test has limited predictive value to foresee pregnancy outcome in BKI-treated mice. We conclude that maternal health-related factors such as cardiovascular, pharmacokinetic and/or bioavailability properties also contribute to BKI-pregnancy effects.

Comprehensive assessment of PINK1 variants in Parkinson's disease.

Multiple genes have been associated with monogenic Parkinson's disease and Parkinsonism syndromes. Mutations in PINK1 (PARK6) have been shown to result in autosomal recessive early-onset Parkinson's disease. In the past decade, several studies have suggested that carrying a single heterozygous PINK1 mutation is associated with increased risk for Parkinson's disease. Here, we comprehensively assess the role of PINK1 variants in Parkinson's disease susceptibility using several large data sets totalling 376,558 individuals including 13,708 cases with Parkinson's disease and 362,850 control subjects. After combining these data, we did not find evidence to support a role for heterozygous PINK1 mutations as a robust risk factor for Parkinson's disease.

Unveiling Taenia solium kinome profile and its potential for new therapeutic targets.

Background: Helminth infections cause widespread morbidity and are a significant global disease burden. One among them is Neurocysticercosis, a central nervous system infection caused by the larvae Taenia solium, leading to epilepsy. Helminths are strong immune modulators and can survive for a long time in adverse host environments. Kinases are molecular switches and are essential to initiate/propagate signaling cascades and are detrimental to the regulation of homeostasis. They have been implicated in the progression of many diseases and are potentially lucrative drug targets.Objective: To identify kinases in T. solium proteome and prioritize them as drug targets.Methodology: A Hidden Markov Model (HMM) was used to curate and classify kinases into families based on sequence homology to model organisms followed by phylogenetic analysis of each family. To predict potential drug targets, kinases were identified based on a homologically lethal relationship to C. elegans but non-lethal to humans. Kinases thus selected were searched for matching ligands in SARFkinase and DrugBank databases.Result and conclusion: T. solium kinases make up 1.8% of its proteome, CMGC is the largest kinase family and RGC is the smallest and catalytically inactive family. We predict 23-potential kinases to be drug targets for T. solium.[Figure: see text].

Contribution to Carbapenem Resistance and Fitness Cost of DcuS/DcuR, RcsC/RcsB, and YehU/YehT Two-Component Systems in CTX-M-15-Producing Escherichia coli.

Alteration in two-component systems (TCSs), which are signal transduction pathways in prokaryotes, can result in antibiotic resistance. Recently, it has been shown that the overexpression, using a multicopy cloning vector, of the dcuR, rcsB, and yehT genes, which code for the response regulator (RR) part of TCSs, enhanced the minimal inhibitory concentrations (MICs) of carbapenems in Escherichia coli K-12 derivative KAM3. Herein, the contribution to carbapenem resistance of the DcuS/DcuR, RcsC/RcsB, and YehU/YehT TCSs was assessed in E. coli K-12 derivative BW25113 (A phylogroup) and 536 (B2 phylogroup) recipient strains in combination with extended-spectrum ß-lactamase that exhibit a weak carbapenemase activity. The genes encoding both the sensor kinase (SK) and the RR, on the one hand, and the genes encoding the SK only, on the other hand, of these regulating pathways were disrupted. Subsequently, the mutants and their parental strains were transformed by a recombinant plasmid encoding the CTX-M-15 gene, before testing their susceptibility to carbapenems and their fitness. Results showed a trade-off between enhanced MICs for ertapenem, which remained above the clinical resistance breakpoint, and decreased growth rate, specifically for the 536 strain SK mutants. In conclusion, mutations in dcuS/dcuR, rcsC/rcsB, and yehU/yehT genes may be a pivotal first-step event in the development of carbapenem resistance.

A Structurally-Validated Multiple Sequence Alignment of 497 Human Protein Kinase Domains.

Studies on the structures and functions of individual kinases have been used to understand the biological properties of other kinases that do not yet have experimental structures. The key factor in accurate inference by homology is an accurate sequence alignment. We present a parsimonious, structure-based multiple sequence alignment (MSA) of 497 human protein kinase domains excluding atypical kinases. The alignment is arranged in 17 blocks of conserved regions and unaligned blocks in between that contain insertions of varying lengths present in only a subset of kinases. The aligned blocks contain well-conserved elements of secondary structure and well-known functional motifs, such as the DFG and HRD motifs. From pairwise, all-against-all alignment of 272 human kinase structures, we estimate the accuracy of our MSA to be 97%. The remaining inaccuracy comes from a few structures with shifted elements of secondary structure, and from the boundaries of aligned and unaligned regions, where compromises need to be made to encompass the majority of kinases. A new phylogeny of the protein kinase domains in the human genome based on our alignment indicates that ten kinases previously labeled as "OTHER" can be confidently placed into the CAMK group. These kinases comprise the Aurora kinases, Polo kinases, and calcium/calmodulin-dependent kinase kinases.

The Michael J. Fox Foundation for Parkinson's Research Strategy to Advance Therapeutic Development of PINK1 and Parkin.

The role of mitochondria in Parkinson's disease (PD) has been investigated since the 1980s and is gaining attention with recent advances in PD genetics research. Mutations in PRKN and PTEN-Induced Putative Kinase 1 (PINK1) are well-established causes of autosomal recessive early-onset PD. Genetic and biochemical studies have revealed that PINK1 and Parkin proteins function together in the same biological pathway to govern mitochondrial quality control. These proteins have also been implicated in the regulation of innate and adaptive immunity and other mitochondrial functions. Additionally, structural studies on Parkin have delineated an activation mechanism and have identified druggable regions that are currently being explored by academic and industry groups. To de-risk therapeutic development for these genetic targets, The Michael J. Fox Foundation for Parkinson's Research (MJFF) has deployed a strategic funding and enabling framework that brings together the research community to discuss important breakthroughs and challenges in research on PINK1-Parkin biology, supports collaborative initiatives to further our understanding within this field and develops high-quality research tools and assays that are widely available to all researchers. The Foundation's efforts are leading to significant advances in understanding of the underlying biology of these genes, proteins and pathways and in the development of Parkinson's therapies.

KinaMetrix: a web resource to investigate kinase conformations and inhibitor space.

Protein kinases are among the most explored protein drug targets. Visualization of kinase conformations is critical for understanding structure-function relationship in this family and for developing chemically unique, conformation-specific small molecule drugs. We have developed Kinformation, a random forest classifier that annotates the conformation of over 3500 protein kinase structures in the Protein Data Bank. Kinformation was trained on structural descriptors derived from functionally important motifs to automatically categorize kinases into five major conformations with pharmacological relevance. Here we present KinaMetrix (http://KinaMetrix.com), a web resource enabling researchers to investigate the protein kinase conformational space as well as a subset of kinase inhibitors that exhibit conformational specificity. KinaMetrix allows users to classify uploaded kinase structures, as well as to derive structural descriptors of protein kinases. Uploaded structures can then be compared to atomic structures of other kinases, enabling users to identify kinases that occupy a similar conformational space to their uploaded structure. Finally, KinaMetrix also serves as a repository for both small molecule substructures that are significantly associated with each conformation type, and for homology models of kinases in inactive conformations. We expect KinaMetrix to serve as a resource for researchers studying kinase structural biology or developing conformation-specific kinase inhibitors.

Determination of a Focused Mini Kinase Panel for Early Identification of Selective Kinase Inhibitors.

We analyzed an extensive data set of 3000 Janssen kinase inhibitors (spanning some 40 therapeutic projects) profiled at 414 kinases in the DiscoverX KINOME scan to better understand the necessity of using such a full kinase panel versus simply profiling one's compound at a much smaller number of kinases, or mini kinase panel (MKP), to assess its selectivity. To this end, we generated a series of MKPs over a range of sizes and of varying kinase membership using Monte Carlo simulations. By defining the kinase hit index (KHI), we quantified a compound's selectivity based on the number of kinases it hits. We find that certain combinations (rather than a random selection) of kinases can result in a much lower average error. Indeed, we identified a focused MKP with a 45.1% improvement in the average error (compared to random) that yields an overall correlation of R2 = 0.786-0.826 for the KHI compared to the full kinase panel value. Unlike using a full kinase panel, which is both time and cost restrictive, a focused MKP is amenable to the triaging of all early stage compounds. In this way, promiscuous compounds are filtered out early on, leaving the most selective compounds for lead optimization.

Morin hydrate ameliorates cisplatin-induced ER stress, inflammation and autophagy in HEK-293 cells and mice kidney via PARP-1 regulation.

The present study assessed the possible therapeutic potential of a natural flavonoid morin hydrate (MH), against cisplatin (CP) induced toxicity in HEK-293 cells and mice kidney. Herein, we observed that exposure of HEK-293 cells to CP (20 µM, 24 h) reduced the cell viability, and increased the intracellular ROS generation, nuclear DNA damage, Ca++ release, and accumulation of acidic vacuoles. Concomitantly, acute exposure of CP (30 mg/kg, 72 h) to male ICR mice induced histopathological changes in kidney tissue, and alterations in serum creatinine and blood urea nitrogen (BUN) levels. Oxidative stress mediated ER-stress was evidenced by the reduced expression of antioxidant enzymes such as SOD-1, SOD-2, GR, and Trx, and increased expression levels of CytP450, IRE1-α, PERK, and CHOP. The expression levels of major inflammatory response markers such as NF-κB, TNF-α, IL-1ß, COX-2 and iNOS were significantly increased in the HEK-293 cells and mice kidney. Temporal up-regulation of p-AMPK and LC3I/II, and down regulation of mTOR was also noticed after CP treatment. CP-induced DNA damage led to activation of PARP-1, which plays a crucial role in inflammation, apoptosis and autophagy activation. Concurrently, co-treatment of CP-MH and CP-ANI (PARP-1 inhibitor) significantly attenuated the expression level of PARP-1, reduced cellular death, alleviated inflammatory responses, and inhibited autophagy stimulation in HEK-293 cells and mice kidney. On the basis of above findings, we suggest MH as a potential therapeutic agent against CP-induced nephrotoxicity.

Coevolutionary Landscape of Kinase Family Proteins: Sequence Probabilities and Functional Motifs.

The protein kinase catalytic domain is one of the most abundant domains across all branches of life. Although kinases share a common core function of phosphoryl-transfer, they also have wide functional diversity and play varied roles in cell signaling networks, and for this reason are implicated in a number of human diseases. This functional diversity is primarily achieved through sequence variation, and uncovering the sequence-function relationships for the kinase family is a major challenge. In this study we use a statistical inference technique inspired by statistical physics, which builds a coevolutionary "Potts" Hamiltonian model of sequence variation in a protein family. We show how this model has sufficient power to predict the probability of specific subsequences in the highly diverged kinase family, which we verify by comparing the model's predictions with experimental observations in the Uniprot database. We show that the pairwise (residue-residue) interaction terms of the statistical model are necessary and sufficient to capture higher-than-pairwise mutation patterns of natural kinase sequences. We observe that previously identified functional sets of residues have much stronger correlated interaction scores than are typical.