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Journal articles on the topic 'Peptidomimetic inhibitors'

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Published: 10 December 2022
Last updated: 28 January 2023

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1

Kikelj, Danijel. "Peptidomimetic Thrombin Inhibitors." Pathophysiology of Haemostasis and Thrombosis 33, no. 5-6 (2003): 487–91. http://dx.doi.org/10.1159/000083850.

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2

Dong, Guangping, Iredia D. Iyamu, Jonah Z. Vilseck, Dongxing Chen, and Rong Huang. "Improved Cell-Potent and Selective Peptidomimetic Inhibitors of Protein N-Terminal Methyltransferase 1." Molecules 27, no. 4 (February 18, 2022): 1381. http://dx.doi.org/10.3390/molecules27041381.

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Protein N-terminal methyltransferase 1 (NTMT1) recognizes a unique N-terminal X-P-K/R motif (X represents any amino acid other than D/E) and transfers 1–3 methyl groups to the N-terminal region of its substrates. Guided by the co-crystal structures of NTMT1 in complex with the previously reported peptidomimetic inhibitor DC113, we designed and synthesized a series of new peptidomimetic inhibitors. Through a focused optimization of DC113, we discovered a new cell-potent peptidomimetic inhibitor GD562 (IC50 = 0.93 ± 0.04 µM). GD562 exhibited improved inhibition of the cellular N-terminal methylation levels of both the regulator of chromosome condensation 1 and the oncoprotein SET with an IC50 value of ~50 µM in human colorectal cancer HCT116 cells. Notably, the inhibitory activity of GD562 for the SET protein increased over 6-fold compared with the previously reported cell-potent inhibitor DC541. Furthermore, GD562 also exhibited over 100-fold selectivity for NTMT1 against several other methyltransferases. Thus, this study provides a valuable probe to investigate the biological functions of NTMT1.
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3

Turkson, James, Joon S. Kim, Shumin Zhang, Jing Yuan, Mei Huang, Matthew Glenn, Eric Haura, Said Sebti, Andrew D. Hamilton, and Richard Jove. "Novel peptidomimetic inhibitors of signal transducer and activator of transcription 3 dimerization and biological activity." Molecular Cancer Therapeutics 3, no. 3 (March 1, 2004): 261–69. http://dx.doi.org/10.1158/1535-7163.261.3.3.

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Abstract The critical role of signal transducer and activator of transcription 3 (Stat3) in the growth and survival of human tumor cells identifies it as a promising target for cancer drug discovery. We previously identified a Stat3 SH2 domain-binding phosphopeptide, PY*LKTK, and its tripeptide derivatives, PY*L and AY*L (where Y* represents phosphotyrosine), which inhibit Stat3 biochemical activity and biological function. Here, we report novel peptidomimetic compounds based on PY*L (or AY*L) with substitution of the Y-1 residue by benzyl, pyridyl, or pyrazinyl derivatives that are selective and greater than 5-fold more potent in disrupting Stat3 activity in vitro than lead tripeptides. The biological activities of these derivatives mirror that originally observed for peptides. In this context, the representative peptidomimetic ISS 610 with 4-cyanobenzoate substitution inhibits constitutive Stat3 activity in Src-transformed mouse fibroblasts and human breast and lung carcinoma cells. This effect is not evident with the non-phosphorylated counterpart, ISS 610NP, consistent with interaction of peptidomimetics with the SH2 domain of Stat3. Moreover, ISS 610 induces cell growth inhibition and apoptosis of Src-transformed fibroblasts that contain persistently active Stat3. We present the first report of a peptidomimetic approach to design of small-molecule inhibitors of Stat3 that are also among the first examples of disruptors of transcription factor dimerization with the potential for novel cancer therapy.
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4

Randolph, John, and David DeGoey. "Peptidomimetic Inhibitors of HIV Protease." Current Topics in Medicinal Chemistry 4, no. 10 (June 1, 2004): 1079–95. http://dx.doi.org/10.2174/1568026043388330.

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5

Cameron Black, W. "Peptidomimetic Inhibitors of Cathepsin K." Current Topics in Medicinal Chemistry 10, no. 7 (May 1, 2010): 745–51. http://dx.doi.org/10.2174/156802610791113450.

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6

Marsters, James C., Robert S. McDowell, Mark E. Reynolds, David A. Oare, Todd C. Somers, Mark S. Stanley, Thomas E. Rawson, et al. "Benzodiazepine peptidomimetic inhibitors of farnesyltransferase." Bioorganic & Medicinal Chemistry 2, no. 9 (September 1994): 949–57. http://dx.doi.org/10.1016/s0968-0896(00)82044-1.

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7

Marsters, James C., Robert S. McDowelll, Mark E. Reynolds, Todd C. Somers, Joseph L. Goldstein, Michael S. Brown, and Guy L. James. "Peptidomimetic inhibitors of Ras farnesylation." Chemistry & Biology 1 (April 1994): viii—ix. http://dx.doi.org/10.1016/1074-5521(94)90021-3.

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8

Santos, André L. S., Filipe P. Matteoli, Leandro S. Sangenito, Marta H. Branquinha, Bruno A. Cotrim, and Gabriel O. Resende. "Asymmetric peptidomimetics containing L-tartaric acid core inhibit the aspartyl peptidase activity and growth of Leishmania amazonensis promastigotes." Acta Parasitologica 63, no. 1 (March 26, 2018): 114–24. http://dx.doi.org/10.1515/ap-2018-0013.

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AbstractAspartyl-type peptidases are promising chemotherapeutic targets in protozoan parasites. In the present work, we identified an aspartyl peptidase activity from the soluble extract ofLeishmania amazonensispromastigotes, which cleaved the fluorogenic peptide 7-methoxycoumarin-4-acetyl-Gly-Lys-Pro-Ile-Leu-Phe-Phe-Arg-Leu-Lys(DNP)-D-Arg-amide (cathepsin D substrate) under acidic pH conditions at 37°C, showing aKMof 0.58 μM andVmaxof 129.87 fluorescence arbitrary units/s mg protein. The leishmanial aspartyl peptidase activity was blocked by pepstatin A (IC50= 6.8 μM) and diazo-acetyl-norleucinemetilester (IC50= 10.2 μM), two classical aspartyl peptidase inhibitors. Subsequently, the effects of 6 asymmetric peptidomimetics, containingL-tartaric acid core, were tested on both aspartyl peptidase and growth ofL.amazonensispromastigotes. The peptidomimetics named 88, 154 and 158 promoted a reduction of 50% on the leishmanial aspartyl peptidase activity at concentrations ranging from 40 to 85 μM, whereas the peptidomimetic 157 was by far the most effective, presenting IC50of 0.04 μM. Furthermore, the peptidomimetics 157 and 154 reduced the parasite proliferation in a dose-dependent manner, displaying IC50values of 33.7 and 44.5 μM, respectively. Collectively, the peptidomimetic 157 was the most efficient compound able to arrest both aspartyl peptidase activity and leishmanial proliferation, which raises excellent perspectives regarding its use against this human pathogenic protozoan.
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9

Barbotte, Laetitia, Abdelhakim Ahmed-Belkacem, Stéphane Chevaliez, Alexandre Soulier, Christophe Hézode, Henri Wajcman, Doug J. Bartels, et al. "Characterization of V36C, a Novel Amino Acid Substitution Conferring Hepatitis C Virus (HCV) Resistance to Telaprevir, a Potent Peptidomimetic Inhibitor of HCV Protease." Antimicrobial Agents and Chemotherapy 54, no. 6 (April 5, 2010): 2681–83. http://dx.doi.org/10.1128/aac.01796-09.

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ABSTRACT We characterized a novel substitution conferring moderate resistance to telaprevir, a peptidomimetic inhibitor of hepatitis C virus protease. V36C conferred a 4.0-fold increase in the telaprevir 50% inhibitory concentration in an enzyme assay and a 9.5-fold increase in the replicon model. The replication capacity of a replicon harboring V36C was close to that of the wild-type protease. This case emphasizes the complexity of hepatitis C virus resistance to protease inhibitors.
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10

Kinena, Linda, Gundars Leitis, Iveta Kanepe-Lapsa, Raitis Bobrovs, Kristaps Jaudzems, Vita Ozola, Edgars Suna, and Aigars Jirgensons. "Azole-based non-peptidomimetic plasmepsin inhibitors." Archiv der Pharmazie 351, no. 9 (July 31, 2018): 1800151. http://dx.doi.org/10.1002/ardp.201800151.

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11

Kinena, Linda, and Vita Ozola. "Tetrahydroisoquinoline-Based Non-Peptidomimetic Plasmepsin Inhibitors." Chemistry of Heterocyclic Compounds 56, no. 1 (January 2020): 60–66. http://dx.doi.org/10.1007/s10593-020-02623-6.

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12

East, Stephen P., Andrew Ayscough, Ian Toogood-Johnson, Steven Taylor, and Wayne Thomas. "Peptidomimetic inhibitors of bacterial peptide deformylase." Bioorganic & Medicinal Chemistry Letters 21, no. 13 (July 2011): 4032–35. http://dx.doi.org/10.1016/j.bmcl.2011.04.132.

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13

Frecer, Vladimir, and Stanislav Miertus. "Antiviral agents against COVID-19: structure-based design of specific peptidomimetic inhibitors of SARS-CoV-2 main protease." RSC Advances 10, no. 66 (2020): 40244–63. http://dx.doi.org/10.1039/d0ra08304f.

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14

Martins, Lucas Sousa, Hendrik Gerhardus Kruger, Tricia Naicker, Cláudio Nahum Alves, Jerônimo Lameira, and José Rogério Araújo Silva. "Computational insights for predicting the binding and selectivity of peptidomimetic plasmepsin IV inhibitors against cathepsin D." RSC Advances 13, no. 1 (2023): 602–14. http://dx.doi.org/10.1039/d2ra06246a.

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15

Sawyer, Tomi, Regine Bohacek, David Dalgarno, Charles Eyermann, Noriyuki Kawahata, Chester Metcalf III, William Shakespeare, Raji Sundaramoorthi, Yihan Wang, and Michael Yang. "Src Homology-2 Inhibitors: Peptidomimetic and Nonpeptide." Mini-Reviews in Medicinal Chemistry 2, no. 5 (October 1, 2002): 475–88. http://dx.doi.org/10.2174/1389557023405765.

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16

Pang, X., Z. Liu, and G. Zhai. "Advances in Non-peptidomimetic HIV Protease Inhibitors." Current Medicinal Chemistry 21, no. 17 (April 2014): 1997–2011. http://dx.doi.org/10.2174/0929867321666140217115951.

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17

Zimmerman, Craig N. "Peptide and peptidomimetic inhibitors of VLA-4." Expert Opinion on Therapeutic Patents 9, no. 2 (February 1999): 129–33. http://dx.doi.org/10.1517/13543776.9.2.129.

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18

Ogilvie, William, Murray Bailey, Marc-André Poupart, Abraham, Amit Bhavsar, Pierre Bonneau, Josée Bordeleau, et al. "Peptidomimetic Inhibitors of the Human Cytomegalovirus Protease." Journal of Medicinal Chemistry 40, no. 25 (December 1997): 4113–35. http://dx.doi.org/10.1021/jm970104t.

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19

Yin, Hang, Kendra K. Frederick, Dahui Liu, A. Joshua Wand, and William F. DeGrado. "Arylamide Derivatives as Peptidomimetic Inhibitors of Calmodulin." Organic Letters 8, no. 2 (January 2006): 223–25. http://dx.doi.org/10.1021/ol052478j.

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20

Shen, Kui, Lixin Qi, and Lynn Stiff. "Peptidomimetic Competitive Inhibitors of Protein Tyrosine Phosphatases." Current Pharmaceutical Design 16, no. 28 (September 1, 2010): 3101–17. http://dx.doi.org/10.2174/138161210793292537.

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21

Micale, Nicola, Roberta Ettari, Antonio Lavecchia, Carmen Di Giovanni, Kety Scarbaci, Valeria Troiano, Silvana Grasso, Ettore Novellino, Tanja Schirmeister, and Maria Zappalà. "Development of peptidomimetic boronates as proteasome inhibitors." European Journal of Medicinal Chemistry 64 (June 2013): 23–34. http://dx.doi.org/10.1016/j.ejmech.2013.03.032.

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22

Butini, Stefania, Emanuele Gabellieri, Margherita Brindisi, Simone Giovani, Samuele Maramai, Giridhar Kshirsagar, Egeria Guarino, et al. "A stereoselective approach to peptidomimetic BACE1 inhibitors." European Journal of Medicinal Chemistry 70 (December 2013): 233–47. http://dx.doi.org/10.1016/j.ejmech.2013.09.056.

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23

Majer, Filip, Libuše Pavlíčková, Pavel Majer, Martin Hradilek, Elena Dolejší, Olga Hrušková-Heidingsfeldová, and Iva Pichová. "Structure-based specificity mapping of secreted aspartic proteases of Candida parapsilosis, Candida albicans, and Candida tropicalis using peptidomimetic inhibitors and homology modeling." Biological Chemistry 387, no. 9 (September 1, 2006): 1247–54. http://dx.doi.org/10.1515/bc.2006.154.

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AbstractSecreted aspartic proteases (Saps) of pathogenicCandidaspp. represent a specific target for antifungal drug development. We synthesized a series of peptidomimetic inhibitors with different isosteric groups and modifications at individual positions and tested them with purified Saps fromC. albicans(Sap2p),C. tropicalis(Sapt1p), andC. parapsilosis(Sapp1p). The kinetic parameters indicated that all three proteases prefer binding of inhibitors containing bulky hydrophobic residues between positions P3 and P3′. The most divergent specificity was found for Sapp1p. The sequence alignment of Sap2p, Sapt1p, and Sapp1p, and homology modeling of Sapp1p with the crystal structure of Sapt1p and the complex of Sap2p with a peptidomimetic inhibitor showed that the overall folds of Sap2p, Sapt1p, and Sapp1p are similar. However, the N- and C-terminal loops formed by disulfide bonds between residues 47–53 and 258–292 are significantly shorter in Sapp1p, and a unique insertion following Tyr 129 in Sapp1p results in the formation of a loop that can interact with inhibitor residues. These Sapp1p structural differences might lead to its altered susceptibility to inhibition.
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24

Doro, Fabio, Cinzia Colombo, Chiara Alberti, Daniela Arosio, Laura Belvisi, Cesare Casagrande, Roberto Fanelli, et al. "Computational design of novel peptidomimetic inhibitors of cadherin homophilic interactions." Organic & Biomolecular Chemistry 13, no. 9 (2015): 2570–73. http://dx.doi.org/10.1039/c4ob02538e.

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25

Sanders, Alyssa, Samuel Ricci, Sarah Uribe, Bridget Boyle, Brian Nepper, and Nathaniel Nucci. "A Survey of Inhibitors for the Main Protease of Coronaviruses with the Potential for Development of Broad-Spectrum Therapeutics." American Journal of Undergraduate Research 17, no. 4 (March 31, 2021): 71–84. http://dx.doi.org/10.33697/ajur.2020.037.

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The coronaviruses plaguing humanity in the 21st century share much in common: a spontaneous route of origin from wild animals, a propensity to take human life, and, importantly, a highly conserved set of biological machinery necessary for viral replication. Most recently, the SARS-CoV-2 is decimating economies around the world and has claimed over two million human lives, reminding the world of a need for an effective drug against present and future coronaviruses. To date, attempts to repurpose clinically approved antiviral medications show minimal promise, highlighting the need for development of new antiviral drugs. Nucleotide analog inhibitors are a promising therapeutic candidate, but early data from clinical studies suggests these compounds have limited efficacy. However, novel compounds targeting the main protease responsible for critical steps in viral assembly are gaining considerable interest because they offer the potential for broad-spectrum coronavirus therapy. Here, we review the literature regarding potential inhibitors for the main protease of coronaviruses, especially SARS-CoV-2, analyze receptor-drug interactions, and draw conclusions about candidate inhibitors for future outbreaks. Promising candidates for development of a broad-spectrum coronavirus protease inhibitor include the neuraminidase inhibitor 3K, the peptidomimetic inhibitor 11a and 11b, the α-ketoamide inhibitor 13b, the aldehyde prodrug, and the phosphate prodrug developed by Pfizer. In silico and in vitro analyses have shown that these inhibitors strongly interact with the active site of the main protease, and to varying degrees, prevent viral replication via interactions with the largely conserved active site pockets. KEYWORDS: Severe Acute Respiratory Syndrome Coronavirus; Middle East Respiratory Syndrome Coronavirus; Severe Acute Respiratory Syndrome Coronavirus 2; Replicase Polypeptide; Protease; Neuraminidase Inhibitor; Peptidomimetic Inhibitor; α-Ketoamide Inhibitor; Molecular Docking
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26

Brožková, Kateřina, Ivana Křížová, Libuše Pavlíčková, Martin Hradilek, Martin Fusek, Tomáš Ruml, Milan Souček, and Iva Pichová. "Peptidomimetic Inhibitors of Extracellular Aspartic Proteinases of Candida albicans and Candida tropicalis." Collection of Czechoslovak Chemical Communications 64, no. 1 (1999): 130–37. http://dx.doi.org/10.1135/cccc19990130.

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In an attempt to develop effective inhibitors of Candida secreted aspartic proteinases, we have prepared a series of N-protected peptides varying in the type of scissile bond replacement, in the P and P' side chains as well as in the N- and C-terminal modifications. The compounds were tested in vitro with the chromogenic peptide substrate using purified secreted proteinases of C. albicans and C. tropicalis. Our results have confirmed that the binding of inhibitors and their effectiveness is influenced by a number of enzyme-inhibitor interactions. Moreover, factors like solvation/desolvation contribute to the optimal binding energy of the inhibitors.
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27

Masłowska, Katarzyna, Ewa Witkowska, Dagmara Tymecka, Paweł Krzysztof Halik, Aleksandra Misicka, and Ewa Gniazdowska. "Synthesis, Physicochemical and Biological Study of Gallium-68- and Lutetium-177-Labeled VEGF-A165/NRP-1 Complex Inhibitors Based on Peptide A7R and Branched Peptidomimetic." Pharmaceutics 14, no. 1 (January 1, 2022): 100. http://dx.doi.org/10.3390/pharmaceutics14010100.

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Neuropilin-1 (NRP-1) is a surface receptor found on many types of cancer cells. The overexpression of NRP-1 and its interaction with vascular endothelial growth factor-165 (VEGF165) are associated with tumor growth and metastasis. Therefore, compounds that block the VEGF165/NRP-1 interaction represent a promising strategy to image and treat NRP-1-related pathologies. The aim of the presented work was to design and synthesize radioconjugates of two known peptide-type inhibitors of the VEGF165/NRP-1 complex: A7R peptide and its shorter analog, the branched peptidomimetic Lys(hArg)-Dab-Pro-Arg. Both peptide-type inhibitors were coupled to a radionuclide chelator (DOTA) via a linker (Ahx) and so radiolabeled with Ga-68 and Lu-177 radionuclides, for diagnostic and therapeutic uses, respectively. The synthesized radioconjugates were tested for their possible use as theranostic-like radiopharmaceuticals for the imaging and therapy of cancers that overexpress NRP-1. The obtained results indicate good efficiency of the radiolabeling reaction and satisfactory stability, at least 3t1/2 for the 68Ga- and 1t1/2 for the 177Lu-radiocompounds, in solutions mimicking human body fluids. However, enzymatic degradation of both the studied inhibitors caused insufficient stability of the radiocompounds in human serum, indicating that further modifications are needed to sufficiently stabilize the peptidomimetics with inhibitory properties against VEGF165/NRP-1 complex formation.
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28

Karlsson, Christoffer, Magnus Blom, Miranda Johansson (neé Varedian), Anna M. Jansson, Enzo Scifo, Anders Karlén, Thavendran Govender, and Adolf Gogoll. "Phototriggerable peptidomimetics for the inhibition of Mycobacterium tuberculosis ribonucleotide reductase by targeting protein–protein binding." Organic & Biomolecular Chemistry 13, no. 9 (2015): 2612–21. http://dx.doi.org/10.1039/c4ob01926a.

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29

Abdel-Rahman, Hamdy, Gamal Al-karamany, Nawal El-Koussi, Adel Youssef, and Yoshiaki Kiso. "HIV Protease Inhibitors: Peptidomimetic Drugs and Future Perspectives." Current Medicinal Chemistry 9, no. 21 (November 1, 2002): 1905–22. http://dx.doi.org/10.2174/0929867023368890.

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30

Qiu, X., and Z. P. Liu. "Recent Developments of Peptidomimetic HIV-1 Protease Inhibitors." Current Medicinal Chemistry 18, no. 29 (October 1, 2011): 4513–37. http://dx.doi.org/10.2174/092986711797287566.

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31

Ibrahim, Medhat, Noha A. Saleh, Wael M. Elshemey, and Anwar A. Elsayed. "QSAR Properties of Novel Peptidomimetic NS3 Protease Inhibitors." Journal of Computational and Theoretical Nanoscience 10, no. 4 (April 1, 2013): 785–88. http://dx.doi.org/10.1166/jctn.2013.2771.

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32

Chun, Jiong, Ye Ingrid Yin, Guangli Yang, Leonid Tarassishin, and Yue-Ming Li. "Stereoselective Synthesis of Photoreactive Peptidomimetic γ-Secretase Inhibitors." Journal of Organic Chemistry 69, no. 21 (October 2004): 7344–47. http://dx.doi.org/10.1021/jo0486948.

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33

Van der Veken, Pieter, Kristel Senten, István Kertèsz, Ingrid De Meester, Anne-Marie Lambeir, Marie-Berthe Maes, Simon Scharpé, Achiel Haemers, and Koen Augustyns. "Fluoro-Olefins as Peptidomimetic Inhibitors of Dipeptidyl Peptidases." Journal of Medicinal Chemistry 48, no. 6 (March 2005): 1768–80. http://dx.doi.org/10.1021/jm0495982.

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34

Shiraishi, Takuya, Shojiro Kadono, Masayuki Haramura, Hirofumi Kodama, Yoshiyuki Ono, Hitoshi Iikura, Tohru Esaki, et al. "Design and Synthesis of Peptidomimetic Factor VIIa Inhibitors." CHEMICAL & PHARMACEUTICAL BULLETIN 58, no. 1 (2010): 38–44. http://dx.doi.org/10.1248/cpb.58.38.

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35

Olaleye, Tayo O., James A. Brannigan, Shirley M. Roberts, Robin J. Leatherbarrow, Anthony J. Wilkinson, and Edward W. Tate. "Peptidomimetic inhibitors of N-myristoyltransferase from human malaria and leishmaniasis parasites." Org. Biomol. Chem. 12, no. 41 (2014): 8132–37. http://dx.doi.org/10.1039/c4ob01669f.

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Peptidomimetic inhibitors of N-myristoyltransferase from malaria and leishmaniasis parasites have been designed with nanomolar potency, and reveal the first direct structural evidence for a ternary NMT/CoA/myristoyl peptide product complex.
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36

Hammoudan, Imad, Soumaya Matchi, Mohamed Bakhouch, Salah Belaidi, and Samir Chtita. "QSAR Modelling of Peptidomimetic Derivatives towards HKU4-CoV 3CLpro Inhibitors against MERS-CoV." Chemistry 3, no. 1 (March 9, 2021): 391–401. http://dx.doi.org/10.3390/chemistry3010029.

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In this paper, we report the relationship between the anti-MERS-CoV activities of the HKU4 derived peptides for some peptidomimetic compounds and various descriptors using the quantitative structure activity relationships (QSAR) methods. The used descriptors were computed using ChemSketch, Marvin Sketch and ChemOffice software. The principal components analysis (PCA) and the multiple linear regression (MLR) methods were used to propose a model with reliable predictive capacity. The original data set of 41 peptidomimetic derivatives was randomly divided into training and test sets of 34 and 7 compounds, respectively. The predictive ability of the best MLR model was assessed by determination coefficient R2 = 0.691, cross-validation parameter Q2cv = 0.528 and the external validation parameter R2test = 0.794.
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37

Damalanka, Vishnu C., Scott A. Wildman, and James W. Janetka. "Piperidine carbamate peptidomimetic inhibitors of the serine proteases HGFA, matriptase and hepsin." MedChemComm 10, no. 9 (2019): 1646–55. http://dx.doi.org/10.1039/c9md00234k.

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A series of piperidine-based peptidomimetic inhibitors have been synthesized and evaluated their activity against the three serine proteases HGFA, matriptase, and hepsin. All analogs showed nanomolar activity against matriptase and hepsin.
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38

Bekono, Boris D., Akori E. Esmel, Brice Dali, Fidele Ntie-Kang, Melalie Keita, Luc C. O. Owono, and Eugene Megnassan. "Computer-Aided Design of Peptidomimetic Inhibitors of Falcipain-3: QSAR and Pharmacophore Models." Scientia Pharmaceutica 89, no. 4 (September 29, 2021): 44. http://dx.doi.org/10.3390/scipharm89040044.

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In this work, antiparasitic peptidomimetics inhibitors (PEP) of falcipain-3 (FP3) of Plasmodium falciparum (Pf) are proposed using structure-based and computer-aided molecular design. Beginning with the crystal structure of PfFP3-K11017 complex (PDB ID: 3BWK), three-dimensional (3D) models of FP3-PEPx complexes with known activities ( IC50exp) were prepared by in situ modification, based on molecular mechanics and implicit solvation to compute Gibbs free energies (GFE) of inhibitor-FP3 complex formation. This resulted in a quantitative structure–activity relationships (QSAR) model based on a linear correlation between computed GFE (ΔΔGcom) and the experimentally measured IC50exp. Apart from the structure-based relationship, a ligand-based quantitative pharmacophore model (PH4) of novel PEP analogues where substitutions were directed by comparative analysis of the active site interactions was derived using the proposed bound conformations of the PEPx. This provided structural information useful for the design of virtual combinatorial libraries (VL), which was virtually screened based on the 3D-QSAR PH4. The end results were predictive inhibitory activities falling within the low nanomolar concentration range.
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39

Klei, Herbert E., Kevin Kish, Pin-Fang M. Lin, Qi Guo, Jacques Friborg, Ronald E. Rose, Yaqun Zhang, et al. "X-Ray Crystal Structures of Human Immunodeficiency Virus Type 1 Protease Mutants Complexed with Atazanavir." Journal of Virology 81, no. 17 (May 30, 2007): 9525–35. http://dx.doi.org/10.1128/jvi.02503-05.

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ABSTRACT Atazanavir, which is marketed as REYATAZ, is the first human immunodeficiency virus type 1 (HIV-1) protease inhibitor approved for once-daily administration. As previously reported, atazanavir offers improved inhibitory profiles against several common variants of HIV-1 protease over those of the other peptidomimetic inhibitors currently on the market. This work describes the X-ray crystal structures of complexes of atazanavir with two HIV-1 protease variants, namely, (i) an enzyme optimized for resistance to autolysis and oxidation, referred to as the cleavage-resistant mutant (CRM); and (ii) the M46I/V82F/I84V/L90M mutant of the CRM enzyme, which is resistant to all approved HIV-1 protease inhibitors, referred to as the inhibitor-resistant mutant. In these two complexes, atazanavir adopts distinct bound conformations in response to the V82F substitution, which may explain why this substitution, at least in isolation, has yet to be selected in vitro or in the clinic. Because of its nearly symmetrical chemical structure, atazanavir is able to make several analogous contacts with each monomer of the biological dimer.
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Pandit, Rakesh K. R., Dinesh Gupta, and Tapan K. Mukherjee. "IDENTIFICATION OF POTENTIAL SALMONELLA TYPHI BETA-LACTAMASE TEM 1 INHIBITORS USING PEPTIDOMIMETICS, VIRTUAL SCREENING, AND MOLECULAR DYNAMICS SIMULATIONS." International Journal of Pharmacy and Pharmaceutical Sciences 10, no. 1 (January 1, 2018): 91. http://dx.doi.org/10.22159/ijpps.2018v10i1.21520.

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Objective: The purpose of this study was to identify a potential peptidomimetic S. typhi Beta-lactamase TEM 1 inhibitor to tackle the antibiotic resistance among S. typhi.Methods: The potential peptidomimetic inhibitor was identified by in silico docking of the small peptide WFRKQLKW with S. typhi Beta-lactamase TEM 1. The 3D coordinate geometry of the residues of small peptide interacting with the active site of the receptor was generated and mimics were identified using PEP: MMs: MIMIC server. All the identified mimics were docked at the active site of the receptor using Autodock 4.2 and the best-docked complex was selected on the basis of binding energy and number of H-bonds. The complex was then subjected to molecular dynamics simulations of 30 ns using AMBER 12 software package. The stereochemical stability of the Beta-lactamase TEM 1-WFRKQLKW complex was estimated with the help of Ramachandran plot using PROCHECK tool.Results: In the present study, a new potential peptidomimetic inhibitor (ZINC05839264) of Beta-lactamase TEM 1 has been identified based on antimicrobial peptide WFRKQLKW by virtual screening of the MMsINC database. The docking and molecular simulation studies revealed that the mimic binds more tightly to the active site of the receptor than the peptide. The Ramachandran plot also shows that the Beta-lactamase TEM 1-mimic complex is stereo chemically more stable than Beta-lactamase TEM 1-WFRKQLKW complex as more number of residues (93.6%) are falling under the core region of the plot in case of the former.Conclusion: The study shows that the peptidomimetic compound can act as a potential inhibitor of S. typhi Beta-lactamase TEM 1 and further it can be developed into more effective therapeutic to tackle the problem of antibiotic resistance.
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Yadav, Mange R., Anil K. Shinde, Bishram S. Chouhan, Rajani Giridhar, and Robert Menard. "Peptidomimetic 2-cyanopyrrolidines as potent selective cathepsin L inhibitors." Journal of Enzyme Inhibition and Medicinal Chemistry 23, no. 2 (January 1, 2008): 190–97. http://dx.doi.org/10.1080/14756360701504842.

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Micale, Nicola, Alan P. Kozikowski, Roberta Ettari, Silvana Grasso, Maria Zappalà, Jong-Jin Jeong, Ajay Kumar, Manjit Hanspal, and Athar H. Chishti. "Novel Peptidomimetic Cysteine Protease Inhibitors as Potential Antimalarial Agents." Journal of Medicinal Chemistry 49, no. 11 (June 2006): 3064–67. http://dx.doi.org/10.1021/jm060405f.

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Fear, Georgie, Slavko Komarnytsky, and Ilya Raskin. "Protease inhibitors and their peptidomimetic derivatives as potential drugs." Pharmacology & Therapeutics 113, no. 2 (February 2007): 354–68. http://dx.doi.org/10.1016/j.pharmthera.2006.09.001.

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Burg, Danny, Dmitri V. Filippov, Ralph Hermanns, Gijs A. van der Marel, Jacques H. van Boom, and Gerard J. Mulder. "Peptidomimetic Glutathione Analogues as Novel γGT Stable GST Inhibitors." Bioorganic & Medicinal Chemistry 10, no. 1 (January 2002): 195–205. http://dx.doi.org/10.1016/s0968-0896(01)00269-3.

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Ohkanda, Junko, Jeffrey W. Lockman, Kohei Yokoyama, Michael H. Gelb, Simon L. Croft, Howard Kendrick, Maria Isabel Harrell, et al. "Peptidomimetic inhibitors of protein farnesyltransferase show potent antimalarial activity." Bioorganic & Medicinal Chemistry Letters 11, no. 6 (March 2001): 761–64. http://dx.doi.org/10.1016/s0960-894x(01)00055-5.

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Sanders, M. Lee, and Isaac O. Donkor. "A novel series of urea-based peptidomimetic calpain inhibitors." Bioorganic & Medicinal Chemistry Letters 16, no. 7 (April 2006): 1965–68. http://dx.doi.org/10.1016/j.bmcl.2005.12.068.

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Chenna, Bala C., Linfeng Li, Drake M. Mellott, Xiang Zhai, Jair L. Siqueira-Neto, Claudia Calvet Alvarez, Jean A. Bernatchez, et al. "Peptidomimetic Vinyl Heterocyclic Inhibitors of Cruzain Effect Antitrypanosomal Activity." Journal of Medicinal Chemistry 63, no. 6 (March 3, 2020): 3298–316. http://dx.doi.org/10.1021/acs.jmedchem.9b02078.

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Gokhale, Kunal M., and Vikas N. Telvekar. "Novel peptidomimetic peptide deformylase (PDF) inhibitors of Mycobacterium tuberculosis." Chemical Biology & Drug Design 97, no. 1 (August 24, 2020): 148–56. http://dx.doi.org/10.1111/cbdd.13769.

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Hatahet, Feras, and Lloyd Ruddock. "Modulating Proteostasis: Peptidomimetic Inhibitors and Activators of Protein Folding." Current Pharmaceutical Design 15, no. 21 (July 1, 2009): 2488–507. http://dx.doi.org/10.2174/138161209788682343.

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Calugi, Chiara, Andrea Trabocchi, Claudia Lalli, and Antonio Guarna. "d-Proline-based peptidomimetic inhibitors of anthrax lethal factor." European Journal of Medicinal Chemistry 56 (October 2012): 96–107. http://dx.doi.org/10.1016/j.ejmech.2012.08.028.

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