Protein kinases: Structure modeling, inhibition, and protein-protein interactions

Human protein kinases belong to a large and diverse enzyme family that contains more than 500 members. Deregulation of protein kinases is associated with many disorders, and this is why protein kinases are attractive targets for drug discovery. Due to the high conservation of the ATP binding pocket among this family, designing specific and/or selective inhibitors against certain member(s) is challenging. Several studies have been conducted on protein kinases to validate them as suitable drug targets. Although there are numerous target-validated protein kinases, the efforts to develop small molecule inhibitors have so far led to only a limited number of therapeutic agents and drug candidates. In our studies, we tried to understand the basic structural features of protein kinases using available computational tools. There are wide structural variations between different states of the same protein kinase that affect the enzyme specificity and inhibition. Many protein kinases do not yet have an available X-ray crystal structure and have not yet been validated to be drug targets. For these reasons, we developed a new homology modeling approach to facilitate modeling non-crystallized protein kinases and protein kinase states. Our homology modeling approach was able to model proteins having long amino acid sequences and multiple protein domains with reliable model quality and a manageable amount of computational time. Then, we checked the applicability of different docking algorithms (the routinely used computational methodology in virtual screening) in protein kinase studies. After performing the basic study of kinase structure modeling, we focused our research on cyclin dependent kinase 2 (CDK2) and glycogen synthase kinase-3β (GSK-3β). We prepared a non-redundant database from 303 available CDK2 PDB structures. We removed all structural anomalies and proceeded to use the CDK2 database in studying CDK2 structure in its different states, upon ATP, ligand and cyclin binding. We clustered the database based on our findings, and the CDK2 clusters were used to generate protein ligand interaction fingerprints (PLIF). We generated a PLIF-based pharmacophore model which is highly selective for CDK2 ligands. A virtual screening workflow was developed making use of the PLIF-based pharmacophore model, ligand fitting into the CDK2 active site and selective CDK2 shape scoring. We studied the structural basis for selective inhibition of CDK2 and GSK-3β. We compared the amino acid sequence, the 3D features, the binding pockets, contact maps, structural geometry, and Sphoxel maps. From this study we found 1) the ligand structural features that are required for the selective inhibition of CDK2 and GSK-3β, and 2) the amino acid residues which are essential for ligand binding and selective inhibition. We used the findings of this study to design a virtual screening workflow to search for selective inhibitors for CDK2 and GSK-3β. Because protein–protein interactions are essential in the function of protein kinases, and in particular of CDK2, we used protein–protein docking knowledge and binding energy calculations to examine CDK2 and cyclin binding. We applied this study to the voltage dependent calcium channel 1 (VDAC1) binding to Bax. We were able to provide important data relevant to future experimental researchers such as on the possibility of Bax to cross biological membranes and the most relevant amino acid residues in VDAC1 that interact with Bax

Association between Low Adiponectin Level and Cardiovascular Complications in Diabetic and non Diabetic Patients with End Stage Renal Disease

Introduction: Adiponectin is a collagen-like protein synthesized by adipose tissue that has anti-inflammatory and anti-atherogenic properties. We aimed to evaluate adiponectin levels in end stage renal disease (ESRD) patients with and without diabetes mellitus and its relation to the presence of cardiovascular complications (CVC). Methods: The study included 20 healthy subjects who served as controls (group I), 20 non-diabetic ESRD patients without CVC (group IIA), 20 non-diabetic ESRD patients with CVC (group IIB), 20 diabetic ESRD patients without CVC (group IIIA) and 20 diabetic ESRD patients with CVC (group IIIB). Evaluation included mean arterial blood pressure (MABP), body mass index (BMI), fasting plasma glucose, fasting plasma insulin, homeostasis model assessment for insulin resistance (HOMA-IR), lipid profile, and serum adiponectin levels. Results: Adiponectin level in the control group was 6.4±1.2 mcg/ml, and was significantly lower than both group II and III (

Fluorescence Spectrometric Determination of Drugs Containing α-Methylene Sulfone/Sulfonamide Functional Groups Using N1-Methylnicotinamide Chloride as a Fluorogenic Agent

A simple spectrofluorometric method has been developed, adapted, and validated for the quantitative estimation of drugs containing α-methylene sulfone/sulfonamide functional groups using N1-methylnicotinamide chloride (NMNCl) as fluorogenic agent. The proposed method has been applied successfully to the determination of methyl sulfonyl methane (MSM) (1), tinidazole (2), rofecoxib (3), and nimesulide (4) in pure forms, laboratory-prepared mixtures, pharmaceutical dosage forms, spiked human plasma samples, and in volunteer's blood. The method showed linearity over concentration ranging from 1 to 150 μg/mL, 10 to 1000 ng/mL, 1 to 1800 ng/mL, and 30 to 2100 ng/mL for standard solutions of 1, 2, 3, and 4, respectively, and over concentration ranging from 5 to 150 μg/mL, 10 to 1000 ng/mL, 10 to 1700 ng/mL, and 30 to 2350 ng/mL in spiked human plasma samples of 1, 2, 3, and 4, respectively. The method showed good accuracy, specificity, and precision in both laboratory-prepared mixtures and in spiked human plasma samples. The proposed method is simple, does not need sophisticated instruments, and is suitable for quality control application, bioavailability, and bioequivalency studies. Besides, its detection limits are comparable to other sophisticated chromatographic methods

Selective Inhibition of Plasmodium falciparum ATPase 6 by Artemisinins and Identification of New Classes of Inhibitors after Expression in Yeast

Treatment failures with artemisinin combination therapies (ACTs) threaten global efforts to eradicate malaria. They highlight the importance of identifying drug targets and new inhibitors and of studying how existing antimalarial classes work. Here, we report the successful development of a heterologous expression-based compound-screening tool. The validated drug target Plasmodium falciparum ATPase 6 (PfATP6) and a mammalian orthologue (sarco/endoplasmic reticulum calcium ATPase 1a [SERCA1a]) were functionally expressed in Saccharomyces cerevisiae, providing a robust, sensitive, and specific screening tool. Whole-cell and in vitro assays consistently demonstrated inhibition and labeling of PfATP6 by artemisinins. Mutations in PfATP6 resulted in fitness costs that were ameliorated in the presence of artemisinin derivatives when studied in the yeast model. As previously hypothesized, PfATP6 is a target of artemisinins. Mammalian SERCA1a can be mutated to become more susceptible to artemisinins. The inexpensive, low-technology yeast screening platform has identified unrelated classes of druggable PfATP6 inhibitors. Resistance to artemisinins may depend on mechanisms that can concomitantly address multitargeting by artemisinins and fitness costs of mutations that reduce artemisinin susceptibility

Chronic pain in hemodialysis patients: Role of bone mineral metabolism

Background: Pain is one of the most common complaints in clinical practice because it is a symptom for a myriad of physical and mental problems. The high prevalence of pain in the chronic kidney disease (CKD) population is particularly concerning because pain has been shown to adversely affect quality of life. The aim of this study was to evaluate the prevalence and possible causes of chronic pain in patients with end stage renal disease on long-term hemodialysis (HD).Methods: We prospectively enrolled 100 patients who were undergoing maintenance HD for at least 6 months or more. Pain was evaluated using the Brief Pain Inventory (BPI). Data collected on each participant included age, gender, body mass index (BMI), time on dialysis and biochemical findings.Results: The average age was 42.06 years ranged from 22 to 58 years; the average duration on dialysis was 4.97 years. 52 patients were males and 48 were females. Although 52% of patients experienced chronic pain, only 25% described the pain as severe, 28% described pain as moderate while 52% of patients described as mild. Musculoskeletal pain was the most frequent form of chronic pain reported by patients who were on HD (54%). Malnutrition and high CRP were highly statistically associated with chronic pain (p< 0.001). High statistical significant correlation was found between lower calcium, lower 25(OH) D3 levels, higher parathyroid hormone (PTH) levels and experienced chronic pain (p< 0.001).Conclusion: Chronic pain is highly experienced in long-term hemodialysis patients. Malnutrition, high CRP and disturbed bone mineral metabolism are highly correlated with the incident of this pain

Discovery of novel class of histone deacetylase inhibitors as potential anticancer agents

Selective inhibition of histone deacetylases (HDACs) is an important strategy in the field of anticancer drug discovery. However, lack of inhibitors that possess high selectivity toward certain HDACs isozymes is associated with adverse side effects that limits their clinical applications. We have initiated a collaborative initiatives between multi-institutions aimed at the discovery of novel and selective HDACs inhibitors. To this end, a phenotypic screening of an in-house pilot library of about 70 small molecules against various HDAC isozymes led to the discovery of five compounds that displayed varying degrees of HDAC isozyme selectivity. The anticancer activities of these molecules were validated using various biological assays including transcriptomic studies. Compounds 15, 14, and 19 possessed selective inhibitory activity against HDAC5, while 28 displayed selective inhibition of HDAC1 and HDAC2. Compound 22 was found to be a selective inhibitor for HDAC3 and HDAC9. Importantly, we discovered a none-hydroxamate based HDAC inhibitor, compound 28, representing a distinct chemical probe of HDAC inhibitors. It contains a trifluoromethyloxadiazolyl moiety (TFMO) as a non-chelating metal-binding group. The new compounds showed potent anti-proliferative activity when tested against MCF7 breast cancer cell line, as well as increased acetylation of histones and induce cells apoptosis. The new compounds apoptotic effects were validated through the upregulation of proapoptotic proteins caspases3 and 7 and downregulation of the antiapoptotic biomarkers C-MYC, BCL2, BCL3 and NFĸB genes. Furthermore, the new compounds arrested cell cycle at different phases, which was confirmed through downregulation of the CDK1, 2, 4, 6, E2F1 and RB1 proteins. Taken together, our findings provide the foundation for the development of new chemical probes as potential lead drug candidates for the treatment of cancer

Selective Inhibition of Plasmodium falciparum ATPase 6 by Artemisinins and Identification of New Classes of Inhibitors after Expression in Yeast

Treatment failures with artemisinin combination therapies (ACTs) threaten global efforts to eradicate malaria. They highlight the importance of identifying drug targets and new inhibitors and of studying how existing antimalarial classes work. Here, we report the successful development of a heterologous expression-based compound-screening tool. The validated drug target Plasmodium falciparum ATPase 6 (PfATP6) and a mammalian orthologue (sarco/endoplasmic reticulum calcium ATPase 1a [SERCA1a]) were functionally expressed in Saccharomyces cerevisiae, providing a robust, sensitive, and specific screening tool. Whole-cell and in vitro assays consistently demonstrated inhibition and labeling of PfATP6 by artemisinins. Mutations in PfATP6 resulted in fitness costs that were ameliorated in the presence of artemisinin derivatives when studied in the yeast model. As previously hypothesized, PfATP6 is a target of artemisinins. Mammalian SERCA1a can be mutated to become more susceptible to artemisinins. The inexpensive, low-technology yeast screening platform has identified unrelated classes of druggable PfATP6 inhibitors. Resistance to artemisinins may depend on mechanisms that can concomitantly address multitargeting by artemisinins and fitness costs of mutations that reduce artemisinin susceptibility

Chemical-proteomics Identify Peroxiredoxin-1 as an Actionable Target in Triple-negative Breast Cancer

Triple-negative breast cancer (TNBC) is difficult to treat; therefore, the development of drugs directed against its oncogenic vulnerabilities is a desirable goal. Herein, we report the antitumor effects of CM728, a novel quinone-fused oxazepine, against this malignancy. CM728 potently inhibited TNBC cell viability and decreased the growth of MDA-MB-231-induced orthotopic tumors. Furthermore, CM728 exerted a strong synergistic antiproliferative effect with docetaxel in vitro and this combination was more effective than the individual treatments in vivo. Chemical proteomic approaches revealed that CM728 bound to peroxiredoxin-1 (Prdx1), thereby inducing its oxidation. Molecular docking corroborated these findings. CM728 induced oxidative stress and a multi-signal response, including JNK/p38 MAPK activation and STAT3 inhibition. Interestingly, Prdx1 downregulation mimicked these effects. Finally, CM728 led to DNA damage, cell cycle blockage at the S and G2/M phases, and the activation of caspase-dependent apoptosis. Taken together, our results identify a novel compound with antitumoral properties against TNBC. In addition, we describe the mechanism of action of this drug and provide a rationale for the use of Prdx1 inhibitors, such as CM728, alone or in combination with other drugs, for the treatment of TNBC.This project was supported by Centro Atlántico del Medicamento S.A. (CEAMED), CDTI [IDI-20111517], ACIISI [EATIC2017010006], Universidad de Las Palmas de Gran Canaria, Cabildo Insular de Gran Canaria, Fundación del Instituto Canario de Investigación del Cáncer (FICIC), and Miguel Ángel Rodríguez Cardenes. E. Spínola-Lasso is the recipient of a predoctoral fellowship from the Agencia Canaria de Investigación, Innovación y Sociedad de la Información de la Consejería de Economía, Conocimiento y Empleo y por el Fondo Social Europeo (FSE) Programa Operativo Integrado de Canarias 2014-2020, Eje 3 Tema Prioritario 74 (85%) [TESIS2020010081]. J.C. Montero was funded by the Instituto de Salud Carlos III through the Miguel Servet Program [CP12/03073 and CPII17/00015] and received research support from the same institution [PI15/00684 and PI18/00796]. A. Pandiella received funding from the Ministry of Economy and Competitiveness of Spain [BFU2015-71371-R and PID2020-115605RB-I00], Instituto de Salud Carlos III through CIBERONC, Junta de Castilla y León [CSI146P20], CRIS Cancer Foundation, ACMUMA, UCCTA, ALMOM, and the European Community through the Regional Development Funding Program (FEDER)

Chromogenic and Fluorogenic Probes for the Detection of Illicit Drugs

[EN] The consumption of illicit drugs has increased exponentially in recent years and has become a problem that worries both governments and international institutions. The rapid emergence of new compounds, their easy access, the low levels at which these substances are able to produce an effect, and their short time of permanence in the organism make it necessary to develop highly rapid, easy, sensitive, and selective methods for their detection. Currently, the most widely used methods for drug detection are based on techniques that require large measurement times, the use of sophisticated equipment, and qualified personnel. Chromo- and fluorogenic methods are an alternative to those classical procedures.We thank the Spanish Government [projects MAT2015-64139-C4-1-R and AGL2015-70235-C2-2-R (MINECO/FEDER)] and the Generalitat Valenciana (project PROMETEOII/2014/047) for support. S.E.S thanks the Ministerio de Economia y Competitividad for his Juan de la Cierva contract. 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