- Design of Transmembrane Mimetic Structural Probes to Trap Different Stages of γ-Secretase-Substrate Interaction
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The transmembrane domain (TMD) of the amyloid precursor protein of Alzheimer's disease is cut processively by γ-secretase through endoproteolysis and tricarboxypeptidase "trimming". We recently developed a prototype substrate TMD mimetic for structural analysis - composed of a helical peptide inhibitor linked to a transition-state analogue - that simultaneously engages a substrate exosite and the active site and is pre-organized to trap the carboxypeptidase transition state. Here, we developed variants of this prototype designed to allow visualization of transition states for endoproteolysis, TMD helix unwinding, and lateral gating of the substrate, identifying potent inhibitors for each class. These TMD mimetics exhibited non-competitive inhibition and occupy both the exosite and the active site, as demonstrated by inhibitor cross-competition experiments and photoaffinity probe binding assays. The new probes should be important structural tools for trapping different stages of substrate recognition and processing via ongoing cryo-electron microscopy with γ-secretase, ultimately aiding rational drug design.
- Bhattarai, Sanjay,Devkota, Sujan,Wolfe, Michael S.
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p. 15367 - 15378
(2021/11/01)
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- Design of Substrate Transmembrane Mimetics as Structural Probes for ?3-Secretase
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?3-Secretase is a membrane-embedded aspartyl protease complex central in biology and medicine. How this enzyme recognizes transmembrane substrates and catalyzes hydrolysis in the lipid bilayer is unclear. Inhibitors that mimic the entire substrate transmembrane domain and engage the active site should provide important tools for structural biology, yielding insight into substrate gating and trapping the protease in the active state. Here, we report transmembrane peptidomimetic inhibitors of the ?3-secretase complex that contain an N-terminal helical peptide region that engages a substrate docking exosite and a C-terminal transition-state analog moiety targeted to the active site. Both regions are required for stoichiometric inhibition of ?3-secretase. Moreover, enzyme inhibition kinetics and photoaffinity probe displacement experiments demonstrate that both the docking exosite and the active site are engaged by the bipartite inhibitors. The solution conformations of these potent transmembrane-mimetic inhibitors are similar to those of bound natural substrates, suggesting these probes are preorganized for high-affinity binding and should allow visualization of the active ?3-secretase complex, poised for intramembrane proteolysis, by cryo-electron microscopy.
- Bhattarai, Sanjay,Devkota, Sujan,Douglas, Justin T.,Meneely, Kathleen M.,Wolfe, Michael S.,Xing, Minli
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supporting information
p. 3351 - 3355
(2020/03/06)
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- Structure-Guided Optimization of Dipeptidyl Inhibitors of Norovirus 3CL Protease
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Acute gastroenteritis caused by noroviruses has a major impact on public health worldwide in terms of morbidity, mortality, and economic burden. The disease impacts most severely immunocompromised patients, the elderly, and children. The current lack of approved vaccines and small-molecule therapeutics for the treatment and prophylaxis of norovirus infections underscores the need for the development of norovirus-specific drugs. The studies described herein entail the use of the gem-dimethyl moiety as a means of improving the pharmacological activity and physicochemical properties of a dipeptidyl series of transition state inhibitors of norovirus 3CL protease, an enzyme essential for viral replication. Several compounds were found to be potent inhibitors of the enzyme in biochemical and cell-based assays. The pharmacological activity and cellular permeability of the inhibitors were found to be sensitive to the location of the gem-dimethyl group.
- Rathnayake, Athri D.,Kim, Yunjeong,Dampalla, Chamandi S.,Nguyen, Harry Nhat,Jesri, Abdul-Rahman M.,Kashipathy, Maithri M.,Lushington, Gerald H.,Battaile, Kevin P.,Lovell, Scott,Chang, Kyeong-Ok,Groutas, William C.
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p. 11945 - 11963
(2020/11/26)
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- COMPOUNDS AND METHODS FOR TREATING CANCER, VIRAL INFECTIONS, AND ALLERGIC CONDITIONS
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The present invention generally relates to compounds that are useful for inhibiting one or more trypsin-like S1 serine proteases, HGFA, matriptase, hepsin, KLK5 and/or TMPRSS2 as well as cysteine proteases including trypsin-like cysteine proteases (e.g. C
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Paragraph 0276; 0278
(2021/01/23)
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- Piperidine carbamate peptidomimetic inhibitors of the serine proteases HGFA, matriptase and hepsin
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Matriptase and hepsin are type II transmembrane serine proteases (TTSPs). Along with related S1 trypsin like serine protease HGFA (hepatocyte growth factor activator), their unregulated proteolytic activity has been associated with cancer including tumor progression and metastasis. These three proteases have two substrates in common, hepatocyte growth factor (HGF) and macrophage stimulating protein (MSP), the ligands for MET and recepteur d'origine nantais (RON) receptor tyrosine kinases. Mechanism-based tetrapeptide and benzamidine inhibitors of these proteases have been shown to block HGF/MET and MSP/RON cancer cell signaling. Herein, we have rationally designed a new class of peptidomimetic hybrid small molecule piperidine carbamate dipeptide inhibitors comparable in potency to much larger tetrapeptides. We have identified multiple compounds which have potent activity against matriptase and hepsin and with excellent selectivity over the off-target serine proteases factor Xa and thrombin.
- Damalanka, Vishnu C.,Wildman, Scott A.,Janetka, James W.
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p. 1646 - 1655
(2019/09/30)
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- Structure-guided design of potent and permeable inhibitors of MERS coronavirus 3CL protease that utilize a piperidine moiety as a novel design element
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There are currently no approved vaccines or small molecule therapeutics available for the prophylaxis or treatment of Middle East Respiratory Syndrome coronavirus (MERS-CoV) infections. MERS-CoV 3CL protease is essential for viral replication; consequently, it is an attractive target that provides a potentially effective means of developing small molecule therapeutics for combatting MERS-CoV. We describe herein the structure-guided design and evaluation of a novel class of inhibitors of MERS-CoV 3CL protease that embody a piperidine moiety as a design element that is well-suited to exploiting favorable subsite binding interactions to attain optimal pharmacological activity and PK properties. The mechanism of action of the compounds and the structural determinants associated with binding were illuminated using X-ray crystallography.
- Galasiti Kankanamalage, Anushka C.,Kim, Yunjeong,Damalanka, Vishnu C.,Rathnayake, Athri D.,Fehr, Anthony R.,Mehzabeen, Nurjahan,Battaile, Kevin P.,Lovell, Scott,Lushington, Gerald H.,Perlman, Stanley,Chang, Kyeong-Ok,Groutas, William C.
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supporting information
p. 334 - 346
(2018/03/21)
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- SMALL MOLECULE THERAPEUTIC INHIBITORS AGAINST PICORNAVIRUSES, CALICIVIRUSES, AND CORONAVIRUSES
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Antiviral protease inhibitors are disclosed, along with related antiviral dipeptidyl compounds, macrocyclic derivatives thereof, and methods of using the same to treat or prevent viral infection and disease from coronaviruses, caliciviruses, and picornaviruses.
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- Design, synthesis, and evaluation of a novel series of macrocyclic inhibitors of norovirus 3CL protease
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Norovirus infections have a major impact on public health worldwide, yet there is a current dearth of norovirus-specific therapeutics and prophylactics. This report describes the discovery of a novel class of macrocyclic inhibitors of norovirus 3C-like pr
- Damalanka, Vishnu C.,Kim, Yunjeong,Galasiti Kankanamalage, Anushka C.,Lushington, Gerald H.,Mehzabeen, Nurjahan,Battaile, Kevin P.,Lovell, Scott,Chang, Kyeong-Ok,Groutas, William C.
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- Novel leucine ureido derivatives as aminopeptidase N inhibitors. Design, synthesis and activity evaluation
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Aminopeptidase N (APN/CD13) over-expressed on tumor cells and tumor microenvironment, plays critical roles in tumor invasion, metastasis and angiogenesis. Here we described the design, synthesis and preliminary activity studies of novel leucine ureido derivatives as aminopeptidase N (APN/CD13) inhibitors. The results showed that compound 7a had the most potent inhibitory activity against APN with the IC50 value of 20 nM, which could be used for further anticancer agent research.
- Ma, Chunhua,Cao, Jiangying,Liang, Xuewu,Huang, Yongxue,Wu, Ping,Li, Yingxia,Xu, Wenfang,Zhang, Yingjie
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- Synthesis of N-Acylamino-Acid Derivatives of Cytisine
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N-acylamino-acid derivatives of cytisine were prepared by reacting cytisine with methyl esters of aminoacid isocyanates.
- Yazlovitskii,Garazd,Kartsev
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p. 272 - 275
(2016/07/06)
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- Structure-guided design and optimization of dipeptidyl inhibitors of norovirus 3CL protease. Structure-activity relationships and biochemical, X-ray crystallographic, cell-based, and in vivo studies
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Norovirus infection constitutes the primary cause of acute viral gastroenteritis. There are currently no vaccines or norovirus-specific antiviral therapeutics available for the management of norovirus infection. Norovirus 3C-like protease is essential for viral replication, consequently, inhibition of this enzyme is a fruitful avenue of investigation that may lead to the emergence of antinorovirus therapeutics. We describe herein the optimization of dipeptidyl inhibitors of norovirus 3C-like protease using iterative SAR, X-ray crystallographic, and enzyme and cell-based studies. We also demonstrate herein in vivo efficacy of an inhibitor using the murine model of norovirus infection.
- Galasiti Kankanamalage, Anushka C.,Kim, Yunjeong,Weerawarna, Pathum M.,Uy, Roxanne Adeline Z.,Damalanka, Vishnu C.,Mandadapu, Sivakoteswara Rao,Alliston, Kevin R.,Mehzabeen, Nurjahan,Battaile, Kevin P.,Lovell, Scott,Chang, Kyeong-Ok,Groutas, William C.
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p. 3144 - 3155
(2015/04/27)
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- Novel leucine ureido derivatives as inhibitors of aminopeptidase N (APN)
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Aminopeptidase N (APN/CD13) over expressed on tumor cells, plays a critical role in tumor invasion, metastasis, and tumor angiogenesis. Here we described the design, synthesis and preliminary activity studies of novel leucine ureido derivatives as aminopeptidase N (APN/CD13) inhibitors. The results showed that compound 8c had the most potent inhibitory activity against APN with the IC 50 value to 0.06 ± 0.041 μM, which could be used for further anticancer agent research.
- Ma, Chunhua,Jin, Kang,Cao, Jiangying,Zhang, Lei,Li, Xiaoguang,Xu, Wenfang
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p. 1621 - 1627
(2013/04/24)
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- Inhibition of norovirus 3CL protease by bisulfite adducts of transition state inhibitors
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Noroviruses are the most common cause of acute viral gastroenteritis, accounting for >21 million cases annually in the US alone. Norovirus infections constitute an important health problem for which there are no specific antiviral therapeutics or vaccines. In this study, a series of bisulfite adducts derived from representative transition state inhibitors (dipeptidyl aldehydes and α-ketoamides) was synthesized and shown to exhibit anti-norovirus activity in a cell-based replicon system. The ED 50 of the most effective inhibitor was 60 nM. This study demonstrates for the first time the utilization of bisulfite adducts of transition state inhibitors in the inhibition of norovirus 3C-like protease in vitro and in a cell-based replicon system. The approach described herein can be extended to the synthesis of the bisulfite adducts of other classes of transition state inhibitors of serine and cysteine proteases, such as α-ketoheterocycles and α-ketoesters.
- Mandadapu, Sivakoteswara Rao,Gunnam, Mallikarjuna Reddy,Tiew, Kok-Chuan,Uy, Roxanne Adeline Z.,Prior, Allan M.,Alliston, Kevin R.,Hua, Duy H.,Kim, Yunjeong,Chang, Kyeong-Ok,Groutas, William C.
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- Design, synthesis and biological evaluation of novel amino acid ureido derivatives as aminopeptidase N/CD13 inhibitors
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A series of amino acid ureido derivatives as aminopeptidase N (APN/CD13) inhibitors were synthesized and evaluated for their APN inhibitory activities and anti-cancer effects. The results showed that most of these amino acid ureido derivatives exhibited good inhibition against APN, several of which were better than Bestatin. The most active compound 12j (IC50 = 1.1 μM, compared with Bestatin IC50 = 8.1 μM) not only possessed much better APN inhibitory activity and anti-proliferation effect on cancer cells, but also exhibited significant block effect of human cancer cell invasion compared with the positive control, Bestatin. These amino acid ureido derivatives could be possibly developed as new APN inhibitors for cancer chemotherapy in the future.
- Su, Li,Jia, Yuping,Zhang, Lei,Xu, Yingying,Fang, Hao,Xu, Wenfang
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p. 3807 - 3815
(2012/08/27)
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- Development of synthetic aminopeptidase N/CD13 inhibitors to overcome cancer metastasis and angiogenesis
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Cancer metastasis is a major barrier to its treatment and an important cause of patient death. Antimetastatic agents hold promise for patients with advanced metastatic tumors. Aminopeptidase N/CD13 (APN) is being pursued by many as an important target against cancer metastasis and angiogenesis, but there are few reports on the in vivo evaluation of synthetic APN inhibitors. Herein, a series of compounds targeting APN were synthesized and evaluated for their antimetastasis and antiangiogenesis potency both in vitro and in vivo. Excitingly, compounds 4m, 4t, and 4cc, with the most potent APN inhibitory activities, displayed significant antimetastasis and antiangiogenesis effects in vitro and in vivo, suggesting that those synthetic APN inhibitors have the potential to overcome cancer metastasis and angiogenesis.
- Su, Li,Cao, Jiangying,Jia, Yuping,Zhang, Xiaonan,Fang, Hao,Xu, Wenfang
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supporting information
p. 959 - 964
(2013/02/23)
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- Bioisosterism of urea-based GCPII inhibitors: Synthesis and structure-activity relationship studies
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We report a strategy based on bioisosterism to improve the physicochemical properties of existing hydrophilic, urea-based GCPII inhibitors. Comprehensive structure-activity relationship studies of the P1′ site of ZJ-43- and DCIBzL-based compounds identifi
- Wang, Haofan,Byun, Youngjoo,Barinka, Cyril,Pullambhatla, Mrudula,Bhang, Hyo-eun C.,Fox, James J.,Lubkowski, Jacek,Mease, Ronnie C.,Pomper, Martin G.
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supporting information; experimental part
p. 392 - 397
(2010/04/02)
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- Unnatural amino acid-substituted (hydroxyethyl)urea peptidomimetics inhibit γ-secretase and promote the neuronal differentiation of neuroblastoma cells
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γ-Secretase, exhibiting characteristics of aspartyl protease, mediates the intramembranous proteolysis of β-amyloid precursor protein (APP) and Notch, and it is considered to be a prime pharmacological target in the development of therapeutics for Alzheimer's disease (AD). To identify compounds that block γ-secretase-mediated proteolysis, we used a highly sensitive cell-based reporter gene assay for γ-secretase in which Gal4/VP16-tagged C99-APP was expressed as the immediate substrate of γ-secretase, and Gal4/VP16-tagged APP intracellular domain released by the γ-secretase cleavage then activated the expression of the Gal4-driven luciferase reporter gene. Using this reporter assay, we demonstrated that the newly synthesized (hydroxyethyl)urea peptidomimetics, which contain unnatural amino acid moieties at positions P1′ and/or P3′, can effectively inhibit γ-secretase activity and significantly reduce Aβ production. The γ-secretase-dependent S3 cleavage of Notch was also consistently blocked by these (hydroxyethyl) ureas as evidenced by the decreased generation of the Notch intracellular domain, a prerequisite for the activation of Notch signaling. The inhibition of Notch signaling by active Jia compounds efficiently promotes the neuronal differentiation of neuroblastoma cells, intervening in tumorigenesis and the malignancy of neuroblastomas. Our results suggest that (hydroxyethyl) urea peptidomimetics containing unnatural amino acid substitutions could represent a novel class of γ-secretase inhibitors with enhanced stability, providing the basis for the further development of effective therapeutics for AD and neuroblastomas. Copyright
- Liao, Yung-Feng,Wang, Bo-Jeng,Hsu, Wen-Ming,Lee, Hsinyu,Liao, Chia-Yin,Wu, Shin-Ying,Cheng, Hui-Ting,Hu, Ming-Kuan
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p. 588 - 601
(2008/02/03)
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- Synthesis and evaluation of potent, highly-selective, 3-aryl-piperazinone inhibitors of protein geranylgeranyltransferase-I
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A series of compounds based on the carboxyl-terminal CAAL sequence of PGGTase-I substrates was designed and synthesized. Using piperazin-2-one as a semi-rigid scaffold, we have introduced critical pharmacophores in a well-defined arrangement to mimic the CAAL sequence. High potency and exceptional selectivity were obtained for inhibition of PGGTase-I with structures such as 45 and 70. Potency of this series of GGTIs was dependent on the presence of an l-leucine residue with a free carboxyl terminus, as well as an S configuration of the 3-aryl group. The selectivity was significantly enhanced by 5-methyl substitution on the imidazole ring and fluorine substitution on the 3-aryl group. Modification of the 6-position of the piperazinone scaffold was found to be unfavorable. Compounds 44 and 69, the corresponding methyl esters of 45 and 70, were found to selectively block processing of Rap1A by PGGTase-I in whole cells with IC50 values of 0.4 M and 0.7 M respectively. The Royal Society of Chemistry 2006.
- Peng, Hairuo,Carrico, Dora,Thai, Van,Blaskovich, Michelle,Bucher, Cynthia,Pusateri, Erin E.,Sebti, Said M.,Hamilton, Andrew D.
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p. 1768 - 1784
(2008/02/05)
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- Synthesis and biological evaluation of new tetrahydro-β-carbolines as inhibitors of the mitotic kinesin Eg5
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The mitotic kinesin Eg5 (or KSP) is a crucial player in the development and function of the mitotic spindle. Inhibition of this protein leads to cell cycle arrest and apoptosis without interfering with other microtubule-dependent processes. Therefore, it
- Sunder-Plassmann, Nils,Sarli, Vasiliki,Gartner, Michael,Utz, Mathias,Seiler, Jeanette,Huemmer, Stefan,Mayer, Thomas U.,Surrey, Thomas,Giannis, Athanassios
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p. 6094 - 6111
(2007/10/03)
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- Stereochemical analysis of (hydroxyethyl)urea peptidomimetic inhibitors of γ-secretase
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(Hydroxyethyl)urea peptidomimetics systematically altered at positions P2-P3′ with hydrophobic D-amino acids were synthesized. An all D-amino acid containing analogue was identified that effectively blocked γ-secretase activity in a cell-free system (IC50 = 30 nM). Systematic alteration of the stereocenters of a potent compound revealed interdependence between the various positions. Although typically less potent than their L-peptidomimetic counterparts, selected all D-amino acid containing analogues were equipotent to their counterparts in a cell-based assay when incubated for extended times.
- Bakshi, Pancham,Wolfe, Michael S.
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p. 6485 - 6489
(2007/10/03)
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- Identification of potent and selective mechanism-based inhibitors of the cysteine protease cruzain using solid-phase parallel synthesis
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Targeted libraries of ketone-based cysteine protease inhibitors were synthesized and screened against cruzain, a cysteine protease implicated in Chagas' disease. A number of single digit nanomolar, low molecular weight inhibitors were identified and optimized for solubility and potency. Specifically, the best inhibitors identified have Ki values of 0.9-10 nM and molecular weights between 499 and 609 Da. The most effective inhibitor was also found to be greater than 1000-fold selective for cruzain relative to cathepsin B and 100-fold selective for cruzain relative to cathepsin L.
- Huang, Lily,Lee, Alice,Ellman, Jonathan A.
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p. 676 - 684
(2007/10/03)
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- Synthesis of a series of stromelysin-selective thiadiazole urea matrix metalloproteinase inhibitors
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The synthesis and enzyme inhibition data for a series of thiadiazole urea matrix metalloproteinase (MMP) inhibitors are described. A broad screening effort was utilized to identify several thiadiazoles which were weak inhibitors of stromelysin. Optimization of the thiadiazole leads to include an α-amino acid side chain with variable terminal amide substituents provided a series of ureas which were moderately effective stromelysin inhibitors, with K(i)'s between 0.3 and 1.0 μM. The most effective analogues utilized an L-phenylalanine as the amino acid component. In particular, unsubstituted 46 had a K(i) of 710 nM, while the p-fluoro analogue 52 displayed increased potency (100 nM). Stromelysin inhibition was further improved using a pentafluorophenylalanine substituent which resulted in 70, a 14 nM inhibitor. While gelatinase inhibition was generally poor, the use of 1-(2-pyridyl)piperazine as the amide component usually provided for enhanced activity, with 71 inhibiting gelatinase with a K(i) of 770 nM. The combination of this heterocycle with a p-fluorophenylalanine substituent provided the only analogue, 69, with collagenase activity (13 μM). The SAR for analogues described within this series can be rationalized through consideration of the X-ray structure recently attained for 70 complexed to stromelysin. Uniquely, this structure showed the inhibitor to be completely orientated on the left side of the enzyme cleft. These results suggest that thiadiazole urea heterocycles which incorporate a substituted phenylalanine can provide selective inhibitors of stromelysin. Careful selection of the amide substituent can also provide for analogues with modest gelatinase inhibition.
- Jacobsen, E. Jon,Mitchell, Mark A.,Hendges, Susan K.,Belonga, Kenneth L.,Skaletzky, Louis L.,Stelzer, Lindsay S.,Lindberg, Thomas J.,Fritzen, Edward L.,Schostarez, Heinrich J.,O'Sullivan, Theresa J.,Maggiora, Linda L.,Stuchly, Christopher W.,Laborde, Alice L.,Kubicek, Marc F.,Poorman, Roger A.,Beck, Joan M.,Miller, Henry R.,Petzold, Gary L.,Scott, Pam S.,Truesdell, Scott E.,Wallace, Tanya L.,Wilks, John W.,Fisher, Christopher,Goodman, Linda V.,Kaytes, Paul S.,Ledbetter, Stephen R.,Powers, Elaine A.,Vogeli, Gabriel,Mott, John E.,Trepod, Catherine M.,Staples, Douglas J.,Baldwin, Eric T.,Finzel, Barry C.
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p. 1525 - 1536
(2007/10/03)
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- Topographically constrained aromatic α-aza-amino acids. Part 2. New azaTic-containing peptides: Synthesis, conformation, and intramolecular NH···N interaction
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The new pseudodipeptide Boc-azaTic-Leu-OMe (1), incorporating the conformationally and topographically constrained 3,4-dihydro-2(1H)- phthalazinecarboxylic acid (azaTic) residue, has been synthesized together with the three related models Boc-azaTic-NHMe
- Torrini, Ines,Pagani Zecchini, Giampiero,Paglialunga Paradisi, Mario,Mastropietro, Gaia,Lucente, Gino,Gavuzzo, Enrico,Mazza, Fernando
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p. 2077 - 2090
(2007/10/03)
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- Isocyanates, Part 4.10 Convenient Phosgene-Free Method for the Synthesis and Derivatization of Enantiopure α-Isocyanato Carboxylic Acid Esters
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A novel phosgene-free procedure for the synthesis of α-isocyanato carboxylic acid esters starting from α-amino acid esters has been achieved. The isocyanates are obtained enantiomerically pure (> 99% ee) by a DMAP-catalyzed isocyanation with di-tert-butyl
- Kn?lker, Hans-Joachim,Braxmeier, Tobias
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p. 925 - 928
(2007/10/03)
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- Isocyanates From Primary Amines and Carbon Dioxide: 'Dehydration' of Carbamate Anions
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Carbamate anions, derived from primary amines CO2 and an added base (e.g.NEt3), undergo rapid reaction with electrophilic 'dehydrating agents' (e.g.POCl3, P4O10) to give the corresponding isocyanates in excellent yields.
- Waldman, Thomas E.,McGhee, William D.
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p. 957 - 958
(2007/10/02)
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