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Covalent inhibitors

James J Crawford, Adam R Johnson, Dinah L Misner, Lisa D Belmont, Georgette M Castanedo, Regina Choy, Melis Coraggio, Liming Dong, Charles Eigenbrot, Rebecca Erickson, Nico Ghilardi, Jonathan Hau, Arna Katewa, Pawan Bir Kohli, Wendy Lee, Joseph W Lubach, Brent S McKenzie, Daniel Fred Ortwine, Leah Schutt, Suzanne Tay, Binqing Wei, Karin Reif, Lichuan Liu, Harvey Wong, Wendy B Young
Btk is a non-receptor cytoplasmic tyrosine kinase involved in B-cell and myeloid cell activation, downstream of B-cell and Fcγ receptors, respectively. Pre-clinical studies have indicated that inhibition of Btk activity might offer a potential therapy in autoimmune diseases such as rheumatoid arthritis and systemic lupus erythematosus. Here we disclose the discovery and pre-clinical characterization of a potent, selective, and non-covalent Btk inhibitor currently in clinical development. GDC-0853 (29) suppresses B cell- and myeloid cell-mediated components of disease, and demonstrates dose-dependent activity in an in vivo rat model of inflammatory arthritis...
February 19, 2018: Journal of Medicinal Chemistry
Andrew M Kidger, James Sipthorp, Simon J Cook
The RAS-regulated RAF-MEK1/2-ERK1/2 signalling pathway is de-regulated in a variety of cancers due to mutations in receptor tyrosine kinases (RTKs), negative regulators of RAS (such as NF1) and core pathway components themselves (RAS, BRAF, CRAF, MEK1 or MEK2). This has driven the development of a variety of pharmaceutical agents to inhibit RAF-MEK1/2-ERK1/2 signalling in cancer and both RAF and MEK inhibitors are now approved and used in the clinic. There is now much interest in targeting at the level of ERK1/2 for a variety of reasons...
February 15, 2018: Pharmacology & Therapeutics
Mahboob Alam, Mohammad Jane Alam, Shaista Azaz, Mehtab Parveen, Soonheum Park, Shabbir Ahmad
The quantum chemical study, spectroscopic characterization and biological activity of the pharmaceutically active 7-benzoyloxycoumarin (2) molecule have been presented. Potential energy surface (PES) scanning has been performed to search for the most stable molecular geometry of the present compound. The stable geometry in the ground state, IR, UV-Vis absorption and NMR ( 13 C, 1 H) spectra of the title compound were theoretically obtained and compared with the experimental one. Various theoretical molecular parameters like molecular energy, atomic charges, dipole moment, thermodynamic parameters, donor-acceptor natural bond orbital (NBO) hyperconjugative interaction energies, frontier molecular orbitals energies, HOMO-LUMO gap, molecular electrostatic potential, chemical reactivity descriptors, molecular polarizability and non-linear optical (NLO) properties are presented...
February 8, 2018: Computational Biology and Chemistry
Jun Hosogi, Rui Ohashi, Hiroshi Maeda, Kazuhiro Fujita, Junko Ushiki, Takashi Kuwabara, Yorihiro Yamamoto, Toru Imamura
We previously reported that KW-2449, (E)-1-{4-[2-(1H-Indazol-3-yl)vinyl]benzoyl}piperazine, a novel multikinase inhibitor developed for the treatment of leukemia patients, was oxidized to an iminium ion intermediate by monoamine oxidase B (MAO-B) and then converted to its oxo-piperazine form (M1) by aldehyde oxidase (AO). However, we found that the significant decrease in the pharmacologically active metabolite M1 following repeated administration of KW-2449 in primates might hamper the effectiveness of the drug...
February 16, 2018: Biopharmaceutics & Drug Disposition
Alan C Gibbs, Ruth Steele, Gaohua Liu, Brett A Tounge, Gaetano Montelione
Dengue virus poses a significant global health threat as the source of increasingly deleterious dengue fever, dengue hemorrhagic fever, and dengue shock syndrome. As no specific antiviral treatment exists for dengue infection, considerable effort is being applied to discover therapies and drugs for maintenance and prevention of these afflictions. The virus is primarily transmitted by mosquitoes, and infection occurs following viral endocytosis by host cells. Upon entering the cell, viral RNA is translated into a large multi-subunit polyprotein which is post-translationally cleaved into mature, structural and non-structural (NS) proteins...
February 15, 2018: Biochemistry
Lorena Infante Lara, Sabine Fenner, Steven Ratcliffe, Albert Isidro-Llobet, Michael Hann, Ben Bax, Neil Osheroff
Etoposide and other topoisomerase II-targeted drugs are important anticancer therapeutics. Unfortunately, the safe usage of these agents is limited by their indiscriminate induction of topoisomerase II-mediated DNA cleavage throughout the genome and by a lack of specificity toward cancer cells. Therefore, as a first step toward constraining the distribution of etoposide-induced DNA cleavage sites and developing sequence-specific topoisomerase II-targeted anticancer agents, we covalently coupled the core of etoposide to oligonucleotides centered on a topoisomerase II cleavage site in the PML gene...
February 13, 2018: Nucleic Acids Research
Andrea Brigitta Alber, David Michael Suter
Proteins are in a dynamic state of synthesis and degradation and their half-lives can be adjusted under various circumstances. However, most commonly used approaches to determine protein half-life are either limited to population averages from lysed cells or require the use of protein synthesis inhibitors. This protocol describes a method to measure protein half-lives in single living adherent cells, using SNAP-tag fusion proteins in combination with fluorescence time-lapse microscopy. Any protein of interest fused to a SNAP-tag can be covalently bound by a fluorescent, cell permeable dye that is coupled to a benzylguanine derivative, and the decay of the labeled protein population can be monitored after washout of the residual dye...
February 4, 2018: Journal of Visualized Experiments: JoVE
Young Kim, William A Abplanalp, Andrew D Jung, Rebecca M Schuster, Alex B Lentsch, Erich Gulbins, Charles C Caldwell, Timothy A Pritts
Microparticles are submicron vesicles shed from aging erythrocytes as a characteristic feature of the red blood cell (RBC) storage lesion. Exposure of pulmonary endothelial cells to RBC-derived microparticles promotes an inflammatory response, but the mechanisms underlying microparticle-induced endothelial cell activation are poorly understood. In the present study, cultured murine lung endothelial cells (MLECs) were treated with microparticles isolated from aged murine packed RBCs or vehicle. Microparticle-treated cells demonstrated increased expression of the adhesion molecules ICAM and E-selectin, as well as the cytokine, IL-6...
March 2018: Shock
Paul G Richardson, William I Bensinger, Carol Ann Huff, Caitlin L Costello, Nikoletta Lendvai, Jesus G Berdeja, Larry D Anderson, David S Siegel, Daniel Lebovic, Sundar Jagannath, Jacob P Laubach, Keith E Stockerl-Goldstein, Long Kwei, Fong Clow, Laurence Elias, Zeena Salman, Thorsten Graef, Elizabeth Bilotti, Ravi Vij
Novel therapies with unique new targets are needed for patients who are relapsed/refractory to current treatments for multiple myeloma. Ibrutinib is a first-in-class, once-daily, oral covalent inhibitor of Bruton tyrosine kinase, which is overexpressed in the myeloma stem cell population. This study examined various doses of ibrutinib ± low-dose dexamethasone in patients who received ≥2 prior lines of therapy, including an immunomodulatory agent. Daily ibrutinib ± weekly dexamethasone 40 mg was assessed in 4 cohorts using a Simon 2-stage design...
February 13, 2018: British Journal of Haematology
Hongwu Liu, Jianwei Wu, Ying Ge, Aibo Li, Jia Li, Zhengshi Liu, Yungen Xu, Qingxiang Xu, Yuyan Li
A novel series of non-peptide proteasome inhibitors (PIs) that act on chymotrypsin-like (ChT-L) of the proteasome were developed. These PIs bearing 4-aromatic sulfonyl naphthalene-based scaffold and Leu-boronic moiety as covalent bonding group displayed far better activity than PI-8182 for inhibiting ChT-L in preliminary biological activity test. The results showed that 2a (IC50 = 6.942 μM, MCF-7) and 2c (IC50 = 6.905 μM, MCF-7) displayed higher anti-proliferative activities than Bortezomib (IC50 = 18...
February 6, 2018: Bioorganic & Medicinal Chemistry
Sonia Ciotti, Riccardo Sgarra, Andrea Sgorbissa, Carlotta Penzo, Andrea Tomasella, Federico Casarsa, Fabio Benedetti, Federico Berti, Guidalberto Manfioletti, Claudio Brancolini
Diaryldienone derivatives with accessible β-carbons show strong anti-neoplastic properties, related to their ability to make covalent adducts with free thiols by Michael addition, and low toxicity in vivo. Accumulation of poly-ubiquitylated proteins, activation of the unfolded protein response (UPR) and induction of cell death are universal hallmarks of their activities. These compounds have been characterized as inhibitors of isopeptidases, a family of cysteine-proteases, which de-conjugate ubiquitin and ubiquitin-like proteins from their targets...
February 7, 2018: Cell Death & Disease
Linhong He, Mingfeng Shao, Taijin Wang, Tingxuan Lan, Chufeng Zhang, Lijuan Chen
Here, we report the design and synthesis of pyrimidinyl heterocyclic compounds containing terminal electrophiles as irreversible covalent JAK3 inhibitors that exploit a unique cysteine (Cys909) residue in JAK3. Investigation of the structure-activity relationship utilizing kinase assays resulted in the identification of potent and selective JAK3 inhibitors such as T1, T8, T15, T22, and T29. Among them, T29 was verified as a promising JAK3 irreversible inhibitor that possessed the best bioactivity and selectivity against JAKs and kinases containing a cysteine in the residue analogous to Cys909 in JAK3, suggesting that covalent modification of this Cys residue allowed the identification of a highly selective JAK3 inhibitor...
February 6, 2018: Molecular Diversity
Philip Eliades, Brian J Abraham, Zhenyu Ji, David M Miller, Camilla L Christensen, Nicholas Kwiatkowski, Raj Kumar, Ching Ni Njauw, Michael Taylor, Benchun Miao, Tinghu Zhang, Kwok-Kin Wong, Nathanael S Gray, Richard A Young, Hensin Tsao
Cutaneous melanoma is an aggressive tumor which accounts for most of the skin cancer deaths. Among the physiological barriers against therapeutic success is a strong survival program driven by genes that specify melanocyte identity such as MITF - a phenomenon known in melanoma biology as "lineage dependency." MITF overexpression is occasionally explained by gene amplification, but here we demonstrate that "super-enhancers" are also important determinants of MITF overexpression in some melanoma cell lines and tumors...
February 2, 2018: Journal of Investigative Dermatology
David Limon, Maria Jose Fabrega, Ana C Calpena, Josefa Badía, Laura Baldoma, Lluïsa Pérez-García
The overexpression and increased activity of the serine protease Kallikrein 5 (KLK5) is characteristic of inflammatory skin diseases such as Rosacea. The use of inhibitors of this enzyme - such as 4-(2-aminoethyl)benzenesulfonyl fluoride hydrochloride (AEBSF·HCl) or the anti-human recombinant Kallikrein 5 (anti-KLK5) antibody - in the treatment of the disease has been limited due to their low bioavailability, for which their immobilization in drug delivery agents can contribute to making serine protease inhibitors clinically useful...
February 6, 2018: Bioconjugate Chemistry
Jennifer Lois McKimm-Breschkin, Susan Barrett, Patricia A Pilling, Stefan Hader, Andrew G Watts, Victor A Streltsov
Competitive inhibitors of the influenza neuraminidase (NA) were discovered almost 20 years ago, with zanamivir and oseltamivir licensed globally. These compounds are based on a transition state analogue of the sialic acid substrate. We recently showed that 5-(Acetylamino)-2,3,5-trideoxy-2,3-difluoro-D-erythro-β-L-manno-2-nonulopyranosonic acid (DFSA) and its derivatives are also potent inhibitors of the influenza NA. They are mechanism based inhibitors, forming a covalent bond between the C2 of the sugar ring and Y406 in the NA active site, thus inactivating the enzyme...
February 3, 2018: Journal of Medicinal Chemistry
Kousuke Sato, Yuma Kunitomo, Yukiko Kasai, Shohei Utsumi, Isao Suetake, Shoji Tajima, Satoshi Ichikawa, Akira Matsuda
In chromatin, 5-methylcytosine (mC), which represents the 5th nucleobase in genomic DNA, plays a role as an inducer of epigenetic changes. Tumor cells exhibit aberrant DNA methylation patterns, and inhibition of human DNA cytosine-5 methyltransferase (DNMT), which is responsible for generating mC in CpG sequences, is an effective strategy to treat various cancers. Here, we describe the design, synthesis, and evaluation of the properties of 2-amino-4-halopyridine-C-nucleosides (dXP) and oligodeoxyribonucleotides (ODNs) containing dXP as a novel mechanism-based inhibitor of DNMTs...
February 2, 2018: Chembiochem: a European Journal of Chemical Biology
Qilu Ye, Robert L Campbell, Peter L Davies
Limb-girdle muscular dystrophy type 2a arises from mutations in the Ca2+-activated intracellular cysteine protease calpain-3. This calpain isoform is abundant in skeletal muscle and differs from the main isoforms, calpain-1 and -2, in being a homodimer and having two short insertion sequences. The first of these, IS1, interrupts the protease core and must be cleaved for activation and substrate binding. Here, to learn how calpain-3 can be regulated and inhibited, we determined the structures of the calpain-3 protease core with IS1 present or proteolytically excised...
January 30, 2018: Journal of Biological Chemistry
Jaru Taechalertpaisarn, Bosheng Zhao, Xiaowen Liang, Kevin Burgess
The protein-protein interaction between proprotein convertase subtilisin/kexin type 9 (PCSK9) and low-density lipoprotein receptor (LDLR) is a relatively new, and extremely important, validated therapeutic target for treatment and prevention of heart disease. Experts in the area agree that the first small molecules to disrupt PCSK9•LDLR would represent a milestone in this field, yet no credible leads have been reported. This paper describes how side-chain orientations in preferred conformations of carefully designed chemotypes were compared with LDLR side-chains at the PCSK9•LDLR interface to find molecules that would mimic interface regions of LDLR...
January 29, 2018: Journal of the American Chemical Society
Xiaoyun Lu, Lei Yu, Zhang Zhang, Xiaomei Ren, Jeff B Smaill, Ke Ding
Both the first-generation reversible epidermal growth factor receptor (EGFR) inhibitors gefitinib and erlotinib and the second-generation covalent epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI) afatinib have significantly improved the survival of non-small-cell lung cancer (NSCLC) patients with activating EGFR mutations. However, a secondary EGFRT790M mutation leads to the clinically acquired resistance to the first- and second-generation EGFR-TKIs drugs. A number of the third-generation wild-type sparing EGFR inhibitors, for example, WZ4002, CO1686, AZD9291, HM61713, EGF816, ASP8173, and PF0674775, have been developed, among which AZD9291 has been approved by US FDA for the treatment of NSCLC patients with EGFRT790M ...
January 26, 2018: Medicinal Research Reviews
Matthew R Janes, Jingchuan Zhang, Lian-Sheng Li, Rasmus Hansen, Ulf Peters, Xin Guo, Yuching Chen, Anjali Babbar, Sarah J Firdaus, Levan Darjania, Jun Feng, Jeffrey H Chen, Shuangwei Li, Shisheng Li, Yun O Long, Carol Thach, Yuan Liu, Ata Zarieh, Tess Ely, Jeff M Kucharski, Linda V Kessler, Tao Wu, Ke Yu, Yi Wang, Yvonne Yao, Xiaohu Deng, Patrick P Zarrinkar, Dirk Brehmer, Dashyant Dhanak, Matthew V Lorenzi, Dana Hu-Lowe, Matthew P Patricelli, Pingda Ren, Yi Liu
KRASG12C was recently identified to be potentially druggable by allele-specific covalent targeting of Cys-12 in vicinity to an inducible allosteric switch II pocket (S-IIP). Success of this approach requires active cycling of KRASG12C between its active-GTP and inactive-GDP conformations as accessibility of the S-IIP is restricted only to the GDP-bound state. This strategy proved feasible for inhibiting mutant KRAS in vitro; however, it is uncertain whether this approach would translate to in vivo. Here, we describe structure-based design and identification of ARS-1620, a covalent compound with high potency and selectivity for KRASG12C...
January 25, 2018: Cell
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