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Covalent inhibitors

Daniel R Gentile, Manoj K Rathinaswamy, Meredith L Jenkins, Steven M Moss, Braden D Siempelkamp, Adam R Renslo, John E Burke, Kevan M Shokat
Covalent inhibitors of K-Ras(G12C) have been reported that exclusively recognize the GDP state. Here, we utilize disulfide tethering of a non-natural cysteine (K-Ras(M72C)) to identify a new switch-II pocket (S-IIP) binding ligand (2C07) that engages the active GTP state. Co-crystal structures of 2C07 bound to H-Ras(M72C) reveal binding in a cryptic groove we term S-IIG. In the GppNHp state, 2C07 binding to a modified S-IIP pushes switch I away from the nucleotide, breaking the network of polar contacts essential for adopting the canonical GTP state...
September 19, 2017: Cell Chemical Biology
Kelly A Manthei, Joomi Ahn, Alisa Glukhova, Wenmin Yuan, Christopher Larkin, Taylor D Manett, Louise Chang, James A Shayman, Milton J Axley, Anna Schwendeman, John J G Tesmer
Lecithin:cholesterol acyltransferase (LCAT) plays a key role in reverse cholesterol transport by transferring an acyl group from phosphatidylcholine to cholesterol, promoting the maturation of high density lipoproteins (HDL) from discoidal to spherical particles. LCAT is activated through an unknown mechanism by apolipoprotein A-I (ApoA-I) and other mimetic peptides that form a belt around HDL. Here we report the crystal structure of LCAT with an extended lid that blocks access to the active site, consistent with an inactive conformation...
October 13, 2017: Journal of Biological Chemistry
Tianying Liu, Tyler M Marcinko, Patrick A Kiefer, Richard W Vachet
Amyloid aggregates are associated with several debilitating diseases, and there are numerous efforts to develop small molecule treatments against these diseases. One challenge associated with these efforts is determining protein binding site information for potential therapeutics because amyloid-forming proteins rapidly form oligomers and aggregates, making traditional protein structural analysis techniques challenging. Using β-2-microglobulin (β2m) as a model amyloid-forming protein along with two recently identified small molecule amyloid inhibitors (i...
October 13, 2017: Analytical Chemistry
Matthew R Jensen, Brandon R Goblirsch, James K Christenson, Morgan A Esler, Fatuma A Mohamed, Lawrence P Wackett, Carrie M Wilmot
In the interest of decreasing dependence on fossil fuels, microbial hydrocarbon biosynthesis pathways are being studied for renewable, tailored production of specialty chemicals and biofuels. One candidate is long-chain olefin biosynthesis, a widespread bacterial pathway that produces waxy hydrocarbons. Found in three- and four-gene clusters, oleABCD encode the enzymes necessary to produce cis -olefins that differ by alkyl chain length, degree of unsaturation, and alkyl chain branching. The first enzyme in the pathway, OleA, catalyzes the Claisen condensation of two fatty acyl-coenzyme A molecules to form a β-keto acid...
October 12, 2017: Biochemical Journal
Sampada Kalan, Ramon Amat, Miriam Merzel Schachter, Nicholas Kwiatkowski, Brian J Abraham, Yanke Liang, Tinghu Zhang, Calla M Olson, Stéphane Larochelle, Richard A Young, Nathanael S Gray, Robert P Fisher
Cdk7, the CDK-activating kinase and transcription factor IIH component, is a target of inhibitors that kill cancer cells by exploiting tumor-specific transcriptional dependencies. However, whereas selective inhibition of analog-sensitive (AS) Cdk7 in colon cancer-derived cells arrests division and disrupts transcription, it does not by itself trigger apoptosis efficiently. Here, we show that p53 activation by 5-fluorouracil or nutlin-3 synergizes with a reversible Cdk7(as) inhibitor to induce cell death. Synthetic lethality was recapitulated with covalent inhibitors of wild-type Cdk7, THZ1, or the more selective YKL-1-116...
October 10, 2017: Cell Reports
Tsveta Stoyanova, Iglika Lessigiarska, Momir Mikov, Ilza Pajeva, Stanislav Yanev
Xanthates (alkyl or aryl derivatives of dithiocarbonic acid) have been shown to be selective mechanism-based inactivators of cytochromes P450 2B1/2B6 and 2E1 due to covalent binding of a reactive intermediate to apoprotein after double hydrogen abstraction at α-carbon atom, suggesting interaction of the xanthate dithiocarbonic head with the enzyme heme. The structures of xanthates with a long alkyl chain are similar to the fatty acids. Saturated fatty acids (FA) such as lauric acid (LA), are metabolized by different cytochrome P450 isoforms to ω- and (ω-1)-hydroxy products, in humans done by CYP4A11 and CYP2E1, respectively...
2017: Frontiers in Pharmacology
Matthew G McDonald, Sutapa Ray, Clara J Amorosi, Katherine A Sitko, John P Kowalski, Lorela Paco, Abhinav Nath, Byron M Gallis, Rheem A Totah, Maitreya J Dunham, Douglas M Fowler, Allan E Rettie
CYP4Z1 is an 'orphan' P450 enzyme that has provoked interest because of its hypothesized role in breast cancer through formation of the signaling molecule 20-HETE. We expressed human CYP4Z1 in Saccharomyces cerevisiae and evaluated its catalytic capabilities towards arachidonic and lauric acids (AA and LA). Specific and sensitive mass spectrometry assays enabled discrimination of the regioselectivity of hydroxylation of these two fatty acids. CYP4Z1 generated 7-, 8-, 9-, 10- and 11-hydroxy LA, while the 12-hydroxy metabolite was not detected...
October 10, 2017: Drug Metabolism and Disposition: the Biological Fate of Chemicals
Yuriy K Bashmakov, Ivan M Petyaev
Dendrimers are unimolecular architectural nano- or microparticle entities that can accommodate various nutraceuticals and pharmaceuticals between their branches (dendrons) and provide targeted delivery of biomimetics into different tissues upon addition of functionalized groups to the dendrimer's surface. Covalent binding, hydrogen bonds, and electrostatic interactions between dendrimer-composing molecules are known to form and stabilize dendrimer structure. Carotenoids have recently been shown to form dendrimer-like structures and promote targeted delivery of "cargo" molecules into organs characterized by high-carotenoid uptake (adrenal glands, prostate, liver, and brain)...
October 10, 2017: Monoclonal Antibodies in Immunodiagnosis and Immunotherapy
Apirat Chaikuad, Pierre Koch, Stefan Laufer, Stefan Knapp
Drugs that function by covalent bond formation represent a considerable fraction of our repository of effective medicines but safety concerns and the complexity of developing covalent inhibitors has rendered covalent targeting a less attractive strategy for rational drug design. The recent approval of four covalent kinase inhibitors and the development of highly potent covalent kinase probes with exceptional selectivity has raised significant interest in industry and academic research and validated the concept of covalent kinase targeting for clinical applications...
October 10, 2017: Angewandte Chemie
Charu Dwivedi, Ishan Pandey, Himanshu Pandey, Sandip Patil, Shanti Bhushan Mishra, Avinash C Pandey, Paolo Zamboni, Pramod W Ramteke, Ajay Vikram Singh
Diabetic wounds are susceptible to microbial infection. The treatment of these wounds requires a higher payload of growth factors. With this in mind, the strategy for this study was to utilize a novel payload comprising of Eudragit RL/RS 100 nanofibers carrying the bacterial inhibitor gentamicin sulphate (GS) in concert with human epidermal growth factor (rhEGF); an accelerator of wound healing. GS containing Eudragit was electrospun to yield nanofiber scaffolds, which were further modified by covalent immobilization of rhEGF to their surface...
October 7, 2017: Journal of Biomedical Materials Research. Part A
Kirtikar Shukla, Himangshu Sonowal, Ashish Saxena, Kota V Ramana, Satish K Srivastava
Although we have shown earlier that aldose reductase (AR) inhibitors prevent colorectal cancer cell (CRC) growth in culture as well as in nude mice xenografts, the mechanism(s) is not well understood. In this study, we have investigated how AR inhibition prevents CRC growth by regulating the mitochondrial biogenesis via Nrf2/HO-1 pathway. Incubation of CRC cells such as SW-480, HT29, and HCT116 with AR inhibitor, fidarestat that non-covalently binds to the enzyme, increases the expression of Nrf2. Further, fidarestat augmented the EGF-induced expression of Nrf2 in CRC cells...
October 3, 2017: Cancer Letters
Luhong Wang, Jingyuan Zhao, Yao Yao, Changyuan Wang, Jianbin Zhang, Xiaohong Shu, Xiuli Sun, Yanxia Li, Kexin Liu, Hong Yuan, Xiaodong Ma
Cancer remains the most serious disease that threatens human health. Molecularly targeted cancer therapies, specifically small-molecule protein kinase inhibitors, form an important part of cancer therapy. Targeted covalent modification represents a proven approach to drug discovery with the recent FDA approvals of afatanib, ibrutinib, and osimertinib agents, which were designed to undergo an irreversible hetero-Michael addition reaction with a unique cysteine residue of a specific protein. Covalent inhibitors possess numerous advantages, including increased biochemical efficacy, longer duration of action, the high potential for improved therapeutic index due to lower effective dose, and the potential to inhibit certain drug resistance mechanisms...
September 20, 2017: European Journal of Medicinal Chemistry
Shu-Bin Gao, Kang-Li Li, Huan Qiu, Ling-Yu Zhu, Chang-Bao Pan, Yue Zhao, Shu-Hua Wei, Shu Shi, Guang-Hui Jin, Li-Xiang Xue
Histone modification and chromatin remodeling are important events in response to DNA damage, and Polycomb group (PcG) proteins, catalyzing H3K27 methylation, are involved. However, the biological function and mechanism of PcG in DNA damage are not fully understood. Additionally, downstream effectors in hepatocellular carcinoma (HCC) remain unclear. The present study investigated the biological and mechanistic roles of PcG in the DNA damage response induced by chemotherapeutic drugs in HCC. It was found that chemotherapy drugs, such as epirubicin (EPB) and mitomycin C (MMC), effectively blocked expression of PcG in p53-wild-type HepG2 cells but not in PLC/PRF5 and Hep3B cells with p53 mutation or deletion...
2017: American Journal of Cancer Research
Eleni Venetsanakos, Ken A Brameld, Vernon T Phan, Erik Verner, Timothy D Owens, Yan Xing, Danny Tam, Jacob LaStant, Kwan Leung, Dane E Karr, Ronald J Hill, Mary E Gerritsen, David M Goldstein, Jens Oliver Funk, J Michael Bradshaw
An increasing number of cancers are known to harbor mutations, translocations, or amplifications in the fibroblast growth factor receptor (FGFR) family of kinases. The FGFR inhibitors evaluated in clinical trials to date have shown promise at treating these cancers. Here we describe PRN1371, an irreversible covalent inhibitor of FGFR1-4 targeting a cysteine within the kinase active site. PRN1371 demonstrated strong FGFR potency and excellent kinome-wide selectivity in a number of biochemical and cellular assays, including in various cancer cell lines exhibiting FGFR alterations...
October 4, 2017: Molecular Cancer Therapeutics
Zhi-Qiang Wei, Yong-Hong Zhang, Chang-Zheng Ke, Hong-Xia Chen, Pan Ren, Yu-Lin He, Pei Hu, De-Qiang Ma, Jie Luo, Zhong-Ji Meng
AIM: To investigate the potential effect of curcumin on hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) and the underlying mechanism. METHODS: A HepG2.2.15 cell line stably transfected with HBV was treated with curcumin, and HBV surface antigen (HBsAg) and e antigen (HBeAg) expression levels were assessed by ELISA. Intracellular HBV DNA replication intermediates and cccDNA were detected by Southern blot and real-time PCR, respectively. The acetylation levels of histones H3 and H4 were measured by Western blot...
September 14, 2017: World Journal of Gastroenterology: WJG
Bobo Dang, Haifan Wu, Vikram Khipple Mulligan, Marco Mravic, Yibing Wu, Thomas Lemmin, Alexander Ford, Daniel-Adriano Silva, David Baker, William F DeGrado
The folding of natural proteins typically relies on hydrophobic packing, metal binding, or disulfide bond formation in the protein core. Alternatively, a 3D structure can be defined by incorporating a multivalent cross-linking agent, and this approach has been successfully developed for the selection of bicyclic peptides from large random-sequence libraries. By contrast, there is no general method for the de novo computational design of multicross-linked proteins with predictable and well-defined folds, including ones not found in nature...
September 25, 2017: Proceedings of the National Academy of Sciences of the United States of America
K Kondo, H Shaim, P A Thompson, J A Burger, M Keating, Z Estrov, D Harris, E Kim, A Ferrajoli, M Daher, R Basar, M Muftuoglu, N Imahashi, A Alsuliman, C Sobieski, E Gokdemir, W Wierda, N Jain, E Liu, E J Shpall, K Rezvani
Ibrutinib, a covalent inhibitor of Bruton Tyrosine Kinase (BTK), is approved for treatment of patients with relapsed/refractory or treatment-naïve CLL. Besides directly inhibiting BTK, ibrutinib possesses immunomodulatory properties through targeting multiple signaling pathways. Understanding how this ancillary property of ibrutinib modifies the CLL microenvironment is crucial for further exploration of immune responses in this disease and devising future combination therapies. Here, we investigated the mechanisms underlying the immunomodulatory properties of ibrutinib...
October 3, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
Paul W Heron, Jurgen Sygusch
Fructose-1,6-bisphosphate (FBP) aldolase, a glycolytic enzyme, catalyzes the reversible and stereospecific aldol addition of dihydroxyacetone-P (DHAP) and D-glyceraldehyde-3-P (D-G3P) by an unresolved mechanism. To afford insight into the molecular determinants of FBP aldolase stereospecificity during aldol addition, a key ternary complex formed by DHAP and D-G3P, comprising 2 % of the equilibrium population at physiological pH, was cryotrapped in the active site of Toxoplasma gondii aldolase (TgALD) crystals to high resolution...
September 27, 2017: Journal of Biological Chemistry
Mohammad Khalid Zia, Tooba Siddiqui, Syed Saqib Ali, Ahmed Abdur Rehman, Haseeb Ahsan, Fahim Halim Khan
In the last few decades, advances in the cancer chemotherapy have been a marked success. A large number of anticancer drugs currently in use include drugs based on platinum complexes such as cisplatin, base analogues such as 5-florouracil and some ruthenium drugs. This review provides a bird's eye view of interaction of a number of clinically important drugs currently in use that show covalent or non-covalent interaction with serum proteins. . Platinum drug-cisplatin interacts covalently and alters the function of the key plasma protease inhibitor molecule -alpha-2-macroglobulin and induces the conformational changes in the protein molecule and inactivates it...
October 2, 2017: Current Protein & Peptide Science
Yosuke Masuda, Noriyuki Yamaotsu, Shuichi Hirono
In order to predict the potencies of mechanism-based reversible covalent inhibitors, the relationships between calculated Gibbs free energy of hydrolytic water molecule in acyl-trypsin intermediates and experimentally measured catalytic rate constants (kcat) were investigated. After obtaining representative solution structures by molecular dynamics (MD) simulations, hydration thermodynamics analyses using WaterMap™ were conducted. Consequently, we found for the first time that when Gibbs free energy of the hydrolytic water molecule was lower, logarithms of kcat were also lower...
2017: Chemical & Pharmaceutical Bulletin
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