Topic 02 -- Abstracts with Biological Entities (English) - 75 Topics / Sub-Topic Model 55 - 15 Topics

cite ad title authors publish year publish time dataset abstract mentions covid pmcid pubmed id doi cord uid topic weight Similarity scispacy Similarity specter
1 Zhang_2020 Alpha-ketoamides as broad-spectrum inhibitors of coronavirus and enterovirus replication Linlin Zhang; Daizong Lin; Yuri Kusov; Yong Nian; Qingjun Ma; Jiang Wang; Albrecht von Brunn; Pieter Leyssen; Kristina Lanko; Johan Neyts; Adriaan de Wilde; Eric J. Snijder; Hong Liu; Rolf Hilgenfeld 2020 2020-02-10 BioRxiv N 10.1101/2020.02.10.936898 7n8p9okf 0.992033 Yang_2010 van_der_Linden_2014, Zhang_2020, Kuo_C_2008
2 Zhang_2020 α-Ketoamides as Broad-Spectrum Inhibitors of Coronavirus and Enterovirus Replication: Structure-Based Design, Synthesis, and Activity Assessment Zhang, Linlin; Lin, Daizong; Kusov, Yuri; Nian, Yong; Ma, Qingjun; Wang, Jiang; von Brunn, Albrecht; Leyssen, Pieter; Lanko, Kristina; Neyts, Johan; de Wilde, Adriaan; Snijder, Eric J.; Liu, Hong; Hilgenfeld, Rolf 2020 2020-02-11 None N PMC7098070 32045235.0 10.1021/acs.jmedchem.9b01828 ou61mf3k 0.967189 Yang_2010 Zhang_2020, van_der_Linden_2014, Kuo_C_2008
3 Liu_W_2014 Synthesis, modification and docking studies of 5-sulfonyl isatin derivatives as SARS-CoV 3C-like protease inhibitors Liu, Wei; Zhu, He-Min; Niu, Guo-Jun; Shi, En-Zhi; Chen, Jie; Sun, Bo; Chen, Wei-Qiang; Zhou, Hong-Gang; Yang, Cheng 2014 2014-01-01 None N PMC7111328 24316352.0 10.1016/j.bmc.2013.11.028 r0h2zhj2 0.930197 Ramajayam_2010, Kuang_2005 Niu_C_2008, Zhu_L_2011, Kuo_C_2008
4 Mandadapu_2013 Macrocyclic inhibitors of 3C and 3C-like proteases of picornavirus, norovirus, and coronavirus Mandadapu, Sivakoteswara Rao; Weerawarna, Pathum M.; Prior, Allan M.; Uy, Roxanne Adeline Z.; Aravapalli, Sridhar; Alliston, Kevin R.; Lushington, Gerald H.; Kim, Yunjeong; Hua, Duy H.; Chang, Kyeong-Ok; Groutas, William C. 2013 2013-07-01 None N PMC3750990 23727045.0 10.1016/j.bmcl.2013.05.021 5d7rixs6 0.926679 van_der_Linden_2014
5 Martina_2005 Screening of electrophilic compounds yields an aziridinyl peptide as new active-site directed SARS-CoV main protease inhibitor Martina, Erika; Stiefl, Nikolaus; Degel, Björn; Schulz, Franziska; Breuning, Alexander; Schiller, Markus; Vicik, Radim; Baumann, Knut; Ziebuhr, John; Schirmeister, Tanja 2005 2005-12-15 PMC N PMC7127417 16216498.0 10.1016/j.bmcl.2005.09.012 lij14ztt 0.919753 Laporte_2017 Zhu_L_2011, Grazioso_2012, Niu_C_2008
6 Konno_2016 Design and synthesis of a series of serine derivatives as small molecule inhibitors of the SARS coronavirus 3CL protease Konno, Hiroyuki; Wakabayashi, Masaki; Takanuma, Daiki; Saito, Yota; Akaji, Kenichi 2016 2016-03-15 PMC N PMC7111485 26879854.0 10.1016/j.bmc.2016.01.052 9bw1z5ps 0.899494 Ramajayam_2010, Kuang_2005
7 Ramajayam_2010 Synthesis and evaluation of pyrazolone compounds as SARS-coronavirus 3C-like protease inhibitors Ramajayam, R.; Tan, Kian-Pin; Liu, Hun-Ge; Liang, Po-Huang 2010 2010-11-15 PMC N PMC7127448 20947359.0 10.1016/j.bmc.2010.09.050 2keibgne 0.896591 Saura_1999, Kuang_2005 Konno_2016
8 Park_2013 Dieckol, a SARS-CoV 3CLpro inhibitor, isolated from the edible brown algae Ecklonia cava Park, Ji-Young; Kim, Jang Hoon; Kwon, Jung Min; Kwon, Hyung-Jun; Jeong, Hyung Jae; Kim, Young Min; Kim, Doman; Lee, Woo Song; Ryu, Young Bae 2013 2013-07-01 PMC N PMC7126891 23647823.0 10.1016/j.bmc.2013.04.026 3uhjmocf 0.882880
9 Damalanka_2016 Oxadiazole-Based Cell Permeable Macrocyclic Transition State Inhibitors of Norovirus 3CL Protease Damalanka, Vishnu C.; Kim, Yunjeong; Alliston, Kevin R.; Weerawarna, Pathum M.; Galasiti Kankanamalage, Anushka C.; Lushington, Gerald H.; Mehzabeen, Nurjahan; Battaile, Kevin P.; Lovell, Scott; Chang, Kyeong-Ok; Groutas, William C. 2016 2016-02-08 PMC N PMC5156532 26823007.0 10.1021/acs.jmedchem.5b01464 aycioxsc 0.846142 Kuo_C_2008
10 Chng_2004 Synthetic studies towards anti-SARS agents: application of an indium-mediated allylation of α-aminoaldehydes as the key step towards an intermediate Chng, Shu-Sin; Hoang, Truong-Giang; Wayne Lee, Wei-Woon; Tham, Mun-Pun; Ling, Hui Yvonne; Loh, Teck-Peng 2004 2004-12-20 PMC N PMC7119068 10.1016/j.tetlet.2004.10.146 x8xntne7 0.830269 Ramajayam_2010 Grazioso_2012
11 Ghosh_2006 Progress in Anti-SARS Coronavirus Chemistry, Biology and Chemotherapy Ghosh, Arun K.; Xi, Kai; Johnson, Michael E.; Baker, Susan C.; Mesecar, Andrew D. 2006 2006-12-31 PMC N PMC2718771 19649165.0 10.1016/s0065-7743(06)41011-3 1wae0134 0.822315 van_der_Linden_2014, Zhu_L_2011
12 Kao_R_2004 Characterization of SARS-CoV main protease and identification of biologically active small molecule inhibitors using a continuous fluorescence-based assay Kao, Richard Y.; To, Amanda P.C.; Ng, Louisa W.Y.; Tsui, Wayne H.W.; Lee, Terri S.W.; Tsoi, Hoi-Wah; Yuen, Kwok-Yung 2004 2004-10-22 PMC N PMC7134596 15498556.0 10.1016/j.febslet.2004.09.026 uv3uoyr1 0.811890 Kuo_C_2004, Zhu_L_2011
13 Lee_C_2009 Structural Basis of Inhibition Specificities of 3C and 3C-like Proteases by Zinc-coordinating and Peptidomimetic Compounds Lee, Cheng-Chung; Kuo, Chih-Jung; Ko, Tzu-Ping; Hsu, Min-Feng; Tsui, Yao-Chen; Chang, Shih-Cheng; Yang, Syaulan; Chen, Shu-Jen; Chen, Hua-Chien; Hsu, Ming-Chu; Shih, Shin-Ru; Liang, Po-Huang; Wang, Andrew H.-J. 2009 2009-01-14 PMC N PMC2658058 19144641.0 10.1074/jbc.m807947200 2d1sio6w 0.806301 Kuo_C_2008, van_der_Linden_2014, Kanitz_2019, Grazioso_2012
14 Chuck_2013 Design, synthesis and crystallographic analysis of nitrile-based broad-spectrum peptidomimetic inhibitors for coronavirus 3C-like proteases Chuck, Chi-Pang; Chen, Chao; Ke, Zhihai; Chi-Cheong Wan, David; Chow, Hak-Fun; Wong, Kam-Bo 2013 2013-01-31 None N PMC7115530 23202846.0 10.1016/j.ejmech.2012.10.053 ee3v08wd 0.788625 van_der_Linden_2014, Kuo_C_2008, Becker_2016, Lee_C_2009
15 Chen_2005 Enzymatic activity characterization of SARS coronavirus 3C-like protease by fluorescence resonance energy transfer technique Chen, Shuai; Chen, Li-li; Luo, Hai-bin; Sun, Tao; Chen, Jing; Ye, Fei; Cai, Jian-hua; Shen, Jing-kang; Shen, Xu; Jiang, Hua-liang 2005 2005-01-23 PMC N PMC7091904 15659121.0 10.1111/j.1745-7254.2005.00010.x 35u01je6 0.784024 Yang_2010 Kuang_2005, Kuo_C_2009, Lin_C_2004
16 Grum-Tokars_2008 Evaluating the 3C-like protease activity of SARS-Coronavirus: Recommendations for standardized assays for drug discovery Grum-Tokars, Valerie; Ratia, Kiira; Begaye, Adrian; Baker, Susan C.; Mesecar, Andrew D. 2008 2008-04-30 None N PMC4036818 17397958.0 10.1016/j.virusres.2007.02.015 qk36ujik 0.773945 van_der_Linden_2014
17 Ghosh_2007 Structure-based design, synthesis, and biological evaluation of peptidomimetic SARS-CoV 3CLpro inhibitors Ghosh, Arun K.; Xi, Kai; Grum-Tokars, Valerie; Xu, Xiaoming; Ratia, Kiira; Fu, Wentao; Houser, Katherine V.; Baker, Susan C.; Johnson, Michael E.; Mesecar, Andrew D. 2007 2007-11-01 None N PMC2112940 17855091.0 10.1016/j.bmcl.2007.08.031 lfhy70b5 0.756339 Ramajayam_2010, Kuang_2005 Konno_2016
18 Takahashi_2013 Structural and Inhibitor Studies of Norovirus 3C-like Proteases Takahashi, Daisuke; Kim, Yunjeong; Lovell, Scott; Prakash, Om; Groutas, William C; Chang, Kyeong-Ok 2013 2013-12-01 PMC N PMC3840063 24055466.0 10.1016/j.virusres.2013.09.008 ed90alpi 0.748715 van_der_Linden_2014, Someya_2008
19 Ye_G_2020 Structural Basis for Inhibiting Porcine Epidemic Diarrhea Virus Replication with the 3C-Like Protease Inhibitor GC376 Ye, Gang; Wang, Xiaowei; Tong, Xiaohan; Shi, Yuejun; Fu, Zhen F.; Peng, Guiqing 2020 2020-02-21 COMM-USE N PMC7077318 32098094.0 10.3390/v12020240 7hty6li9 0.739138 van_der_Linden_2014
20 Ehmke_2011 Potent and Selective Inhibition of Cysteine Proteases from Plasmodium falciparum and Trypanosoma brucei Ehmke, Veronika; Heindl, Cornelia; Rottmann, Matthias; Freymond, Céline; Schweizer, W. Bernd; Brun, Reto; Stich, August; Schirmeister, Tanja; Diederich, François 2011 2011-02-07 None N PMC7162187 21275051.0 10.1002/cmdc.201000449 g14kt2dv 0.723016
21 Kuang_2005 Mutational and inhibitive analysis of SARS coronavirus 3C-like protease by fluorescence resonance energy transfer-based assays Kuang, Wan-Fen; Chow, Lu-Ping; Wu, Mei-Hua; Hwang, Lih-Hwa 2005 2005-06-17 PMC N PMC7092943 15883050.0 10.1016/j.bbrc.2005.04.072 ieucykbf 0.712530 Yang_2010, Cheng_2005 Lin_C_2004, van_der_Linden_2014, Zhu_L_2011, Wei_P_2006
22 Lin_C_2004 Characterization of trans- and cis-cleavage activity of the SARS coronavirus 3CLpro protease: basis for the in vitro screening of anti-SARS drugs Lin, Cheng-Wen; Tsai, Chang-Hai; Tsai, Fuu-Jen; Chen, Pei-Jer; Lai, Chien-Chen; Wan, Lei; Chiu, Hua-Hao; Lin, Kuan-Hsun 2004 2004-09-10 PMC Y PMC7127318 15358553.0 10.1016/j.febslet.2004.08.017 kczhig5k 0.688931 van_der_Linden_2014, Kuang_2005, Zhu_L_2011
23 Jacobs_2013 Discovery, synthesis, and structure-based optimization of a series of N-(tert-butyl)-2-(N-arylamido)-2-(pyridin-3-yl) acetamides (ML188) as potent non-covalent small molecule inhibitors of the severe acute respiratory syndrome coronavirus (SARS-CoV) 3CL protease Jacobs, Jon; Tokars, Valerie; Zhou, Ya; Turlington, Mark; Saldanha, S. Adrian; Chase, Peter; Eggler, Aimee; Dawson, Eric S.; Baez-Santos, Yahira M.; Tomar, Sakshi; Mielech, Anna M.; Baker, Susan C.; Lindsley, Craig W.; Hodder, Peter; Mesecar, Andrew; Stauffer, Shaun R. 2013 2013-01-03 PMC N PMC3569073 23231439.0 10.1021/jm301580n 53vslprn 0.671087 Turlington_2013
24 Shie_2005 Inhibition of the severe acute respiratory syndrome 3CL protease by peptidomimetic α,β-unsaturated esters Shie, Jiun-Jie; Fang, Jim-Min; Kuo, Tun-Hsun; Kuo, Chih-Jung; Liang, Po-Huang; Huang, Hung-Jyun; Wu, Yin-Ta; Jan, Jia-Tsrong; Cheng, Yih-Shyun E.; Wong, Chi-Huey 2005 2005-09-01 PMC N PMC7119063 15994085.0 10.1016/j.bmc.2005.05.065 9fiqf6lk 0.660402 Ramajayam_2010, Yang_2010, Vaughan_2012, Kuang_2005, Lu_Y_1997 Grazioso_2012, Kuo_C_2008, Akaji_2008, van_der_Linden_2014
25 Hanh_Nguyen_2011 Virtual screening identification of novel severe acute respiratory syndrome 3C-like protease inhibitors and in vitro confirmation Hanh Nguyen, Thi Thanh; Ryu, Hwa-Ja; Lee, Se-Hoon; Hwang, Soonwook; Breton, Vincent; Rhee, Joon Haeng; Kim, Doman 2011 2011-05-15 PMC N PMC7126700 21470860.0 10.1016/j.bmcl.2011.03.034 h37vfvjy 0.652271 Yang_2010, Kuang_2005, Lu_Y_1997 Liu_W_2014
26 Graziano_2006 Enzymatic activity of the SARS coronavirus main proteinase dimer Graziano, Vito; McGrath, William J.; DeGruccio, Ann Marie; Dunn, John J.; Mangel, Walter F. 2006 2006-05-15 PMC N PMC7094300 16647061.0 10.1016/j.febslet.2006.04.004 9dm493sn 0.649970 Yang_2010, Cheng_2005 Wei_P_2006, Cheng_2010, Kuo_C_2004
27 Ye_G_2016 Structural basis for the dimerization and substrate recognition specificity of porcine epidemic diarrhea virus 3C-like protease Ye, Gang; Deng, Feng; Shen, Zhou; Luo, Rui; Zhao, Ling; Xiao, Shaobo; Fu, Zhen F.; Peng, Guiqing 2016 2016-07-31 PMC N PMC7111274 27128350.0 10.1016/j.virol.2016.04.018 xfnbv6o9 0.646217 van_der_Linden_2014, Lin_C_2004
28 Zhang_2020 X-ray Structure of Main Protease of the Novel Coronavirus SARS-CoV-2 Enables Design of α-Ketoamide Inhibitors Linlin Zhang; Daizong Lin; Xinyuanyuan Sun; Katharina Rox; Rolf Hilgenfeld 2020 2020-02-20 BioRxiv Y 10.1101/2020.02.17.952879 xhachzby 0.645182 Verschueren_2008, Lee_T_2005, Grazioso_2012, Wei_P_2006
29 Bacha_2008 Development of Broad-Spectrum Halomethyl Ketone Inhibitors Against Coronavirus Main Protease 3CL(pro) Bacha, Usman; Barrila, Jennifer; Gabelli, Sandra B.; Kiso, Yoshiaki; Amzel, L. Mario; Freire, Ernesto 2008 2008-07-01 PMC N PMC2597651 18611220.0 10.1111/j.1747-0285.2008.00679.x h451at18 0.638045 Zhu_L_2011
30 Sun_H_2003 Molecular cloning, expression, purification, and mass spectrometric characterization of 3C-like protease of SARS coronavirus Sun, Haifang; Luo, Haibin; Yu, Changying; Sun, Tao; Chen, Jing; Peng, Shuying; Qin, Jun; Shen, Jianhua; Yang, Yiming; Xie, Youhua; Chen, Kaixian; Wang, Yuan; Shen, Xu; Jiang, Hualiang 2003 2003-12-31 PMC N PMC7129208 14965777.0 10.1016/j.pep.2003.08.016 7wfdwou8 0.617186 Lin_C_2004
31 Tomar_2015 Ligand-induced Dimerization of Middle East Respiratory Syndrome (MERS) Coronavirus nsp5 Protease (3CL(pro)): IMPLICATIONS FOR nsp5 REGULATION AND THE DEVELOPMENT OF ANTIVIRALS Tomar, Sakshi; Johnston, Melanie L.; St. John, Sarah E.; Osswald, Heather L.; Nyalapatla, Prasanth R.; Paul, Lake N.; Ghosh, Arun K.; Denison, Mark R.; Mesecar, Andrew D. 2015 2015-06-08 PMC N PMC4528106 26055715.0 10.1074/jbc.m115.651463 rgdynmla 0.613305
32 Kuo_C_2004 Characterization of SARS main protease and inhibitor assay using a fluorogenic substrate Kuo, Chih-Jung; Chi, Ya-Hui; Hsu, John T.-A; Liang, Po-Huang 2004 2004-06-11 PMC N PMC7134607 15147951.0 10.1016/j.bbrc.2004.04.098 n0fa076h 0.599295 Yang_2010, Vaughan_2012 van_der_Linden_2014, Zhu_L_2011, Wei_P_2006, Kao_R_2004
33 Aggarwal_2015 Kinetic characterization of trans-proteolytic activity of Chikungunya virus capsid protease and development of a FRET-based HTS assay Aggarwal, Megha; Sharma, Rajesh; Kumar, Pravindra; Parida, Manmohan; Tomar, Shailly 2015 2015-10-06 COMM-USE N PMC4593962 26439734.0 10.1038/srep14753 tt0fhp8c 0.578950 van_der_Linden_2014, Pastorino_2008, Saraswat_2020
34 Chou_2008 Thiopurine analogues inhibit papain-like protease of severe acute respiratory syndrome coronavirus Chou, Chi-Yuan; Chien, Chia-Hui; Han, Yu-San; Prebanda, Mojca Trstenjak; Hsieh, Hsing-Pang; Turk, Boris; Chang, Gu-Gang; Chen, Xin 2008 2008-04-15 PMC N PMC7092826 18313035.0 10.1016/j.bcp.2008.01.005 5szqfufh 0.574640 Zhu_L_2011
35 Zhang_2004 Old drugs as lead compounds for a new disease? Binding analysis of SARS coronavirus main proteinase with HIV, psychotic and parasite drugs Zhang, Xue Wu; Yap, Yee Leng 2004 2004-05-15 PMC N PMC7126105 15110833.0 10.1016/j.bmc.2004.03.035 d4loia11 0.570716 Kao_R_2004, Zhang_2004
36 John_2016 X-Ray Structure and Inhibition of 3C-like Protease from Porcine Epidemic Diarrhea Virus St. John, Sarah E.; Anson, Brandon J.; Mesecar, Andrew D. 2016 2016-05-13 COMM-USE N PMC4865815 27173881.0 10.1038/srep25961 u4mvk89w 0.560505 Kuo_C_2008
37 Jin_Z_2020 Structural basis for the inhibition of COVID-19 virus main protease by carmofur, an antineoplastic drug Zhenming Jin; Yao Zhao; Yuan Sun; Bing Zhang; Haofeng Wang; Yan Wu; Yan Zhu; Chen Zhu; Tianyu Hu; Xiaoyu Du; Yinkai Duan; Jing Yu; Xiaobao Yang; Xiuna Yang; Xiang Liu; Luke W. Guddat; Gengfu Xiao; Leike Zhang; Haitao Yang; Zihe Rao 2020 2020-04-09 BioRxiv Y 10.1101/2020.04.09.033233 tpp40j0g 0.559529 Kuo_C_2008, van_der_Linden_2014
38 Chen_2010 Discovery of anti‐SARS coronavirus drug based on molecular docking and database screening Chen, Hai‐Feng; Yao, Jian‐Hua; Sun, Jing; Li, Qiang; Li, Feng; Fan, Bo‐Tao; Yuan, Shen‐Gang 2010 2010-08-26 PMC N PMC7162226 10.1002/cjoc.20040220825 go2tsomq 0.556890
39 Chang_2012 Characterization and inhibition of norovirus proteases of genogroups I and II using a fluorescence resonance energy transfer assay Chang, Kyeong-Ok; Takahashi, Daisuke; Prakash, Om; Kim, Yunjeong 2012 2012-02-20 PMC N PMC3259199 22200497.0 10.1016/j.virol.2011.12.002 g1ie0ahz 0.551456 van_der_Linden_2014
40 Kim_B_2015 Benserazide, the first allosteric inhibitor of Coxsackievirus B3 3C protease Kim, Bo-Kyoung; Cho, Joong-Heui; Jeong, Pyeonghwa; Lee, Youngjin; Lim, Jia Jia; Park, Kyoung Ryoung; Eom, Soo Hyun; Kim, Yong-Chul 2015 2015-07-08 PMC N PMC7094222 26022398.0 10.1016/j.febslet.2015.05.027 4szi4vyd 0.551358 Grazioso_2012
41 Lee_H_2015 Inhibitor Recognition Specificity of MERS-CoV Papain-like Protease May Differ from That of SARS-CoV Lee, Hyun; Lei, Hao; Santarsiero, Bernard\nD.; Gatuz, Joseph\nL.; Cao, Shuyi; Rice, Amy J.; Patel, Kavankumar; Szypulinski, Michael Z.; Ojeda, Isabel; Ghosh, Arun K.; Johnson, Michael E. 2015 2015-03-06 None N PMC4845099 25746232.0 10.1021/cb500917m wd5bzsol 0.550680 Zhu_L_2011
42 Zhang_2004 Exploring the binding mechanism of the main proteinase in SARS-associated coronavirus and its implication to anti-SARS drug design Zhang, Xue Wu; Yap, Yee Leng 2004 2004-05-01 PMC N PMC7125554 15080921.0 10.1016/j.bmc.2004.02.015 occ03hp0 0.538818 Zhu_L_2011
43 Niu_C_2008 Molecular docking identifies the binding of 3-chloropyridine moieties specifically to the S1 pocket of SARS-CoV Mpro Niu, Chunying; Yin, Jiang; Zhang, Jianmin; Vederas, John C.; James, Michael N.G. 2008 2008-01-01 PMC N PMC7127602 17931870.0 10.1016/j.bmc.2007.09.034 32ju2h1g 0.518793 Zhu_L_2011, Liu_W_2014
44 Needle_2015 Structures of the Middle East respiratory syndrome coronavirus 3C-like protease reveal insights into substrate specificity Needle, Danielle; Lountos, George T.; Waugh, David S. 2015 2015-04-24 None N PMC4427198 25945576.0 10.1107/s1399004715003521 1stnmrkk 0.511948
45 Turlington_2013 Discovery of N-(benzo[1,2,3]triazol-1-yl)-N-(benzyl)acetamido)phenyl) carboxamides as severe acute respiratory syndrome coronavirus (SARS-CoV) 3CLpro inhibitors: Identification of ML300 and noncovalent nanomolar inhibitors with an induced-fit binding Turlington, Mark; Chun, Aspen; Tomar, Sakshi; Eggler, Aimee; Grum-Tokars, Valerie; Jacobs, Jon; Daniels, J. Scott; Dawson, Eric; Saldanha, Adrian; Chase, Peter; Baez-Santos, Yahira M.; Lindsley, Craig W.; Hodder, Peter; Mesecar, Andrew D.; Stauffer, Shaun R. 2013 2013-11-15 None N PMC3878165 24080461.0 10.1016/j.bmcl.2013.08.112 e0qq0d75 0.502195 Schlieker_2007, Ghosh_2007 Grazioso_2012
46 Kuo_C_2015 Characterization and Inhibition of the Main Protease of Severe Acute Respiratory Syndrome Coronavirus Kuo, Chih‐Jung; Liang, Po‐Huang 2015 2015-02-25 PMC N PMC7159133 10.1002/cben.201400031 lgrk3w7w 0.494254 Yang_2010
47 Saha_2018 Development of nsP2 protease based cell free high throughput screening assay for evaluation of inhibitors against emerging Chikungunya virus Saha, Amrita; Acharya, Badri Narayan; Priya, Raj; Tripathi, Nagesh K.; Shrivastava, Ambuj; Rao, M. Kameswara; Kesari, Pooja; Narwal, Manju; Tomar, Shailly; Bhagyawant, Sameer S.; Parida, Manmohan; Dash, Paban Kumar 2018 2018-07-17 COMM-USE N PMC6050329 30018455.0 10.1038/s41598-018-29024-2 m7zp4muo 0.482343 van_der_Linden_2014, Pastorino_2008
48 Kim_Y_2013 Potent inhibition of feline coronaviruses with peptidyl compounds targeting coronavirus 3C-like protease Kim, Yunjeong; Mandadapu, Sivakoteswara Rao; Groutas, William C.; Chang, Kyeong-Ok 2013 2013-02-28 None N PMC3563934 23219425.0 10.1016/j.antiviral.2012.11.005 5gt5r2uu 0.476031
49 van_der_Linden_2014 Application of a cell-based protease assay for testing inhibitors of picornavirus 3C proteases van der Linden, Lonneke; Ulferts, Rachel; Nabuurs, Sander B.; Kusov, Yuri; Liu, Hong; George, Shyla; Lacroix, Céline; Goris, Nesya; Lefebvre, David; Lanke, Kjerstin H.W.; De Clercq, Kris; Hilgenfeld, Rolf; Neyts, Johan; van Kuppeveld, Frank J.M. 2014 2014-03-31 PMC N PMC7113757 24393668.0 10.1016/j.antiviral.2013.12.012 ul0k95x2 0.468014 Sun_D_2019, Deng_2019
50 Lee_C_2007 Structural basis of mercury- and zinc-conjugated complexes as SARS-CoV 3C-like protease inhibitors Lee, Cheng-Chung; Kuo, Chih-Jung; Hsu, Min-Feng; Liang, Po-Huang; Fang, Jim-Min; Shie, Jiun-Jie; Wang, Andrew H.-J. 2007 2007-11-27 PMC N PMC7094272 17981158.0 10.1016/j.febslet.2007.10.048 9lw756zk 0.453540 Sato_2019, Schlieker_2007 Grazioso_2012, Lee_C_2009
51 Sydnes_2006 Synthesis of glutamic acid and glutamine peptides possessing a trifluoromethyl ketone group as SARS-CoV 3CL protease inhibitors Sydnes, Magne O.; Hayashi, Yoshio; Sharma, Vinay K.; Hamada, Takashi; Bacha, Usman; Barrila, Jennifer; Freire, Ernesto; Kiso, Yoshiaki 2006 2006-09-04 None N PMC7111793 10.1016/j.tet.2006.06.052 mf0k7h27 0.453324 Yang_2010 Grazioso_2012
52 Ohnishi_2019 Evaluation of a non-prime site substituent and warheads combined with a decahydroisoquinolin scaffold as a SARS 3CL protease inhibitor Ohnishi, Kouji; Hattori, Yasunao; Kobayashi, Kazuya; Akaji, Kenichi 2019 2019-01-15 PMC N PMC7126642 30558861.0 10.1016/j.bmc.2018.12.019 960th627 0.446735 Schlieker_2007, Yang_2010, Vaughan_2012 Yoshizawa_2020, Shimamoto_2015
53 Wei_P_2006 The N-terminal octapeptide acts as a dimerization inhibitor of SARS coronavirus 3C-like proteinase Wei, Ping; Fan, Keqiang; Chen, Hao; Ma, Liang; Huang, Changkang; Tan, Lei; Xi, Dong; Li, Chunmei; Liu, Ying; Cao, Aoneng; Lai, Luhua 2006 2006-01-20 PMC N PMC7092940 16329994.0 10.1016/j.bbrc.2005.11.102 67brxejx 0.446252 Yang_2010 Cheng_2010, van_der_Linden_2014, Someya_2008
54 Hilgenfeld_2014 From SARS to MERS: crystallographic studies on coronaviral proteases enable antiviral drug design Hilgenfeld, Rolf 2014 2014-08-11 PMC N PMC7163996 25039866.0 10.1111/febs.12936 ac6m1uwp 0.439248
55 Xia_B_2011 Activation and maturation of SARS-CoV main protease Xia, Bin; Kang, Xue 2011 2011-04-01 PMC N PMC4875205 21533772.0 10.1007/s13238-011-1034-1 0oh701o3 0.434076
56 Verschueren_2008 A Structural View of the Inactivation of the SARS Coronavirus Main Proteinase by Benzotriazole Esters Verschueren, Koen H.G.; Pumpor, Ksenia; Anemüller, Stefan; Chen, Shuai; Mesters, Jeroen R.; Hilgenfeld, Rolf 2008 2008-06-23 PMC N PMC7110992 18559270.0 10.1016/j.chembiol.2008.04.011 wevcmq30 0.434076 Schlieker_2007 Wei_P_2006, Zhu_L_2011, Lee_T_2005, Grazioso_2012
57 Chen_2020 Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CL (pro)) structure: virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates Chen, Yu Wai; Yiu, Chin-Pang Bennu; Wong, Kwok-Yin 2020 2020-02-21 COMM-USE Y PMC7062204 32194944.0 10.12688/f1000research.22457.1 f6muhf3d 0.427060 Lin_C_2004, Niu_C_2008, Lee_C_2009
58 Polster_2006 Solid Phase Synthesis of Dual Labeled Peptides: Development of Cell Permeable Calpain Specific Substrates Polster, Brian M.; Arze, Rafael; Lyttle, Matthew H.; Nicholls, David G.; Hudson, Derek 2006 2006-11-30 PMC N PMC7088158 10.1007/s10989-006-9049-9 322skrqg 0.421792 Joshi_2017
59 Akaji_2008 Evaluation of peptide-aldehyde inhibitors using R188I mutant of SARS 3CL protease as a proteolysis-resistant mutant Akaji, Kenichi; Konno, Hiroyuki; Onozuka, Mari; Makino, Ayumi; Saito, Hiroyuki; Nosaka, Kazuto 2008 2008-11-01 PMC N PMC7126698 18845442.0 10.1016/j.bmc.2008.09.057 0w04si16 0.420583 Yang_2010, Vaughan_2012, Lu_Y_1997 Someya_2008, van_der_Linden_2014, Wei_P_2006
60 Shan_2004 A novel auto-cleavage assay for studying mutational effects on the active site of severe acute respiratory syndrome coronavirus 3C-like protease Shan, Yu-Fei; Li, Shou-Feng; Xu, Gen-Jun 2004 2004-11-12 PMC N PMC7092848 15474466.0 10.1016/j.bbrc.2004.09.088 ukco9p7s 0.414390 Yang_2010 Someya_2008, van_der_Linden_2014, Wei_P_2006
61 Huitema_2008 Heteroaromatic ester inhibitors of hepatitis A virus 3C proteinase: Evaluation of mode of action Huitema, Carly; Zhang, Jianmin; Yin, Jiang; James, Michael N.G.; Vederas, John C.; Eltis, Lindsay D. 2008 2008-05-15 PMC N PMC7125897 18407505.0 10.1016/j.bmc.2008.03.059 r1mkkg54 0.413649 Yang_2010 Grazioso_2012, Kuo_C_2008, van_der_Linden_2014, Becker_2016
62 Kuo_C_2008 Design, synthesis, and evaluation of 3C protease inhibitors as anti-enterovirus 71 agents Kuo, Chih-Jung; Shie, Jiun-Jie; Fang, Jim-Min; Yen, Guei-Rung; Hsu, John T.-A.; Liu, Hun-Ge; Tseng, Sung-Nain; Chang, Shih-Cheng; Lee, Ching-Yin; Shih, Shin-Ru; Liang, Po-Huang 2008 2008-08-01 PMC N PMC7125518 18583140.0 10.1016/j.bmc.2008.06.015 r15wx6qf 0.411318 Yang_2010, Vaughan_2012 van_der_Linden_2014, Grazioso_2012
63 Xue_X_2007 Production of Authentic SARS-CoV Mpro with Enhanced Activity: Application as a Novel Tag-cleavage Endopeptidase for Protein Overproduction Xue, Xiaoyu; Yang, Haitao; Shen, Wei; Zhao, Qi; Li, Jun; Yang, Kailin; Chen, Cheng; Jin, Yinghua; Bartlam, Mark; Rao, Zihe 2007 2007-02-23 PMC N PMC7094453 17189639.0 10.1016/j.jmb.2006.11.073 fjfc3rto 0.405330 Yang_2010 Lin_C_2004, van_der_Linden_2014, Zhu_L_2011
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66 Ke_M_2012 Short peptides derived from the interaction domain of SARS coronavirus nonstructural protein nsp10 can suppress the 2′-O-methyltransferase activity of nsp10/nsp16 complex Ke, Min; Chen, Yu; Wu, Andong; Sun, Ying; Su, Ceyang; Wu, Hao; Jin, Xu; Tao, Jiali; Wang, Yi; Ma, Xiao; Pan, Ji-An; Guo, Deyin 2012 2012-08-31 PMC N PMC7114426 22659295.0 10.1016/j.virusres.2012.05.017 z5109axc 0.401193
67 Zhu_L_2011 Peptide aldehyde inhibitors challenge the substrate specificity of the SARS-coronavirus main protease Zhu, Lili; George, Shyla; Schmidt, Marco F.; Al-Gharabli, Samer I.; Rademann, Jörg; Hilgenfeld, Rolf 2011 2011-11-30 PMC N PMC7114241 21854807.0 10.1016/j.antiviral.2011.08.001 71wj0ajq 0.399614 Yang_2010, Vaughan_2012 Kuo_C_2004, Lee_T_2005, Cheng_2010, Wei_P_2006
68 Barrila_2006 Long Range Cooperative Interactions Modulate Dimerization in SARS 3CL(pro) Barrila, Jennifer; Bacha, Usman; Freire, Ernesto 2006 2006-12-01 PMC N PMC2570436 17154528.0 10.1021/bi0616302 fxz80tr1 0.397983 Vaughan_2012 Wei_P_2006, Cheng_2010, Barrila_2010
69 Lin_M_2014 Structural and functional characterization of MERS coronavirus papain-like protease Lin, Min-Han; Chuang, Shang-Ju; Chen, Chiao-Che; Cheng, Shu-Chun; Cheng, Kai-Wen; Lin, Chao-Hsiung; Sun, Chiao-Yin; Chou, Chi-Yuan 2014 2014-06-04 COMM-USE N PMC4051379 24898546.0 10.1186/1423-0127-21-54 fb04slz0 0.395080 Yu_L_2017
70 Fan_K_2005 The substrate specificity of SARS coronavirus 3C-like proteinase Fan, Keqiang; Ma, Liang; Han, Xiaofeng; Liang, Huanhuan; Wei, Ping; Liu, Ying; Lai, Luhua 2005 2005-04-15 PMC N PMC7092912 15752746.0 10.1016/j.bbrc.2005.02.061 02o93wlh 0.393054 Wei_P_2006, van_der_Linden_2014, Zhu_L_2011
71 Becker_2016 Irreversible inhibitors of the 3C protease of Coxsackie virus through templated assembly of protein-binding fragments Becker, Daniel; Kaczmarska, Zuzanna; Arkona, Christoph; Schulz, Robert; Tauber, Carolin; Wolber, Gerhard; Hilgenfeld, Rolf; Coll, Miquel; Rademann, Jörg 2016 2016-09-28 None N PMC5052702 27677239.0 10.1038/ncomms12761 0oq4kkn5 0.393054 van_der_Linden_2014, Grazioso_2012, Kuo_C_2008
72 Ehrnhoefer_2011 A Quantitative Method for the Specific Assessment of Caspase-6 Activity in Cell Culture Ehrnhoefer, Dagmar E.; Skotte, Niels H.; Savill, Jane; Nguyen, Yen T. N.; Ladha, Safia; Cao, Li-Ping; Dullaghan, Edie; Hayden, Michael R. 2011 2011-11-29 COMM-USE N PMC3226564 22140457.0 10.1371/journal.pone.0027680 73hw8922 0.387394 van_der_Linden_2014
73 Tian_2011 Characterization of Selective Ubiquitin and Ubiquitin-Like Protease Inhibitors Using a Fluorescence-Based Multiplex Assay Format Tian, Xufan; Isamiddinova, Nigora S.; Peroutka, Raymond J.; Goldenberg, Seth J.; Mattern, Michael R.; Nicholson, Benjamin; Leach, Craig 2011 2011-04-01 PMC N PMC3065724 21133675.0 10.1089/adt.2010.0317 gf9c8vf3 0.380834 Lindner_2007 Kramer_2012, van_der_Linden_2014
74 Xu_T_2005 Structure of the SARS coronavirus main proteinase as an active C(2) crystallographic dimer Xu, Ting; Ooi, Amy; Lee, Hooi Chen; Wilmouth, Rupert; Liu, Ding Xiang; Lescar, Julien 2005 2005-10-20 PMC N PMC1978130 16511208.0 10.1107/s1744309105033257 i3w7beuj 0.378284 Wei_P_2006, Graziano_2006, Xia_B_2011, Lee_T_2007
75 Lei_J_2014 Crystal structure of the papain-like protease of MERS coronavirus reveals unusual, potentially druggable active-site features Lei, Jian; Mesters, Jeroen R.; Drosten, Christian; Anemüller, Stefan; Ma, Qingjun; Hilgenfeld, Rolf 2014 2014-09-30 PMC N PMC7113875 24992731.0 10.1016/j.antiviral.2014.06.011 xtb68nk3 0.376067 Lee_T_2005
76 Pastorino_2008 Expression and biochemical characterization of nsP2 cysteine protease of Chikungunya virus Pastorino, Boris A.M.; Peyrefitte, Christophe N.; Almeras, Lionel; Grandadam, Marc; Rolland, Dominique; Tolou, Hugues J.; Bessaud, Maël 2008 2008-02-29 PMC N PMC7114110 17961784.0 10.1016/j.virusres.2007.09.009 nqz4co2b 0.373894 van_der_Linden_2014, Sun_D_2019, Karpe_2011
77 Chu_L_2006 Rapid peptide-based screening on the substrate specificity of severe acute respiratory syndrome (SARS) coronavirus 3C-like protease by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry Chu, Ling-Hon Matthew; Choy, Wai-Yan; Tsai, Sau-Na; Rao, Zihe; Ngai, Sai-Ming 2006 2006-03-07 PMC N PMC2242481 16600962.0 10.1110/ps.052007306 arivkkj0 0.366826 Yang_2010 Lin_C_2004, Kuang_2005, Shan_2004
78 Nicholson_2008 Characterization of ubiquitin and ubiquitin-like-protein isopeptidase activities Nicholson, Benjamin; Leach, Craig A.; Goldenberg, Seth J.; Francis, Dana M.; Kodrasov, Matthew P.; Tian, Xufan; Shanks, John; Sterner, David E.; Bernal, Alejandro; Mattern, Michael R.; Wilkinson, Keith D.; Butt, Tauseef R. 2008 2008-06-01 PMC N PMC2386736 18424514.0 10.1110/ps.083450408 vi1fgbug 0.365343 Yu_L_2017, Catic_2007, Mielech_2014
79 Shimamoto_2015 Fused-ring structure of decahydroisoquinolin as a novel scaffold for SARS 3CL protease inhibitors Shimamoto, Yasuhiro; Hattori, Yasunao; Kobayashi, Kazuya; Teruya, Kenta; Sanjoh, Akira; Nakagawa, Atsushi; Yamashita, Eiki; Akaji, Kenichi 2015 2015-02-15 None N PMC7111320 25614110.0 10.1016/j.bmc.2014.12.028 3sgbpn13 0.361973 Yang_2010, Schlieker_2007 Yoshizawa_2020, Niu_C_2008
80 Zhang_2010 (1)H, (13)C and (15)N resonance assignments of SARS-CoV main protease N-terminal domain Zhang, Shengnan; Zhong, Nan; Ren, Xiaobai; Jin, Changwen; Xia, Bin 2010 2010-12-23 PMC N PMC7091140 21181312.0 10.1007/s12104-010-9287-9 iy57tjx5 0.361729 Yang_2010 Zhong_2009, Lee_T_2007
81 Lin_C_2005 Anti-SARS coronavirus 3C-like protease effects of Isatis indigotica root and plant-derived phenolic compounds Lin, Cheng-Wen; Tsai, Fuu-Jen; Tsai, Chang-Hai; Lai, Chien-Chen; Wan, Lei; Ho, Tin-Yun; Hsieh, Chang-Chi; Chao, Pei-Dawn Lee 2005 2005-10-31 PMC N PMC7114321 16115693.0 10.1016/j.antiviral.2005.07.002 x0z68jos 0.358470 Ramajayam_2010 Lin_C_2004
82 Krichel_2020 Processing of the SARS-CoV pp1a/ab nsp7–10 region Krichel, Boris; Falke, Sven; Hilgenfeld, Rolf; Redecke, Lars; Uetrecht, Charlotte 2020 2020-03-13 None N PMC7078746 32083638.0 10.1042/bcj20200029 6jdvrggp 0.357021 Krichel_2019, Yu_L_2017
83 Barrila_2010 Mutation of Asn28 disrupts the dimerization and enzymatic activity of SARS 3CL(pro) Barrila, Jennifer; Gabelli, Sandra B.; Bacha, Usman; Amzel, L. Mario; Freire, Ernesto 2010 2010-05-25 PMC N PMC2877132 20420403.0 10.1021/bi1002585 iccni6od 0.354203 Wei_P_2006, Barrila_2006, Cheng_2010
84 Mielech_2014 MERS-CoV papain-like protease has deISGylating and deubiquitinating activities Mielech, Anna M.; Kilianski, Andy; Baez-Santos, Yahira M.; Mesecar, Andrew D.; Baker, Susan C. 2014 2014-02-28 PMC N PMC3957432 24503068.0 10.1016/j.virol.2013.11.040 n9jnu2ah 0.353061 Yu_L_2017, Mielech_2014
85 Shan_2005 Study on Substrate Specificity at Subsites for Severe Acute Respiratory Syndrome Coronavirus 3CL Protease Shan, Yu-Fei; Xu, Gen-Jun 2005 2005-12-23 PMC N PMC7109883 16331324.0 10.1111/j.1745-7270.2005.00114.x 32z5llgd 0.351308 van_der_Linden_2014, Someya_2008
86 Chuck_2011 Profiling of Substrate Specificities of 3C-Like Proteases from Group 1, 2a, 2b, and 3 Coronaviruses Chuck, Chi-Pang; Chow, Hak-Fun; Wan, David Chi-Cheong; Wong, Kam-Bo 2011 2011-11-02 COMM-USE N PMC3206940 22073294.0 10.1371/journal.pone.0027228 0vu7bobr 0.340771 Yang_2010 Lee_C_2009, Kuo_C_2009
87 Tan_Y_2014 Crystallization and preliminary crystallographic study of Porcine epidemic diarrhea virus main protease in complex with an inhibitor Tan, Yusheng; Wang, Fenghua; Chen, Xia; Wang, Jinshan; Zhao, Qi; Li, Shuang; Wang, Zefang; Fu, Sheng; Chen, Cheng; Yang, Haitao 2014 2014-11-14 PMC N PMC4259222 25484208.0 10.1107/s2053230x14021876 0cyi5262 0.338234 Wang_2014, Yang_2009, Ma_Y_2010
88 Wang_2014 Crystallization and preliminary crystallographic study of human coronavirus NL63 main protease in complex with an inhibitor Wang, Fenghua; Tan, Yusheng; Li, Huiyan; Chen, Xia; Wang, Jinshan; Li, Shuang; Fu, Sheng; Zhao, Qi; Chen, Cheng; Su, Dan; Yang, Haitao 2014 2014-07-23 PMC N PMC4118806 25084384.0 10.1107/s2053230x14012953 ulua84c8 0.322231 Wang_2014, Yu_K_2012, Yang_2009
89 Hu_T_2009 Two adjacent mutations on the dimer interface of SARS coronavirus 3C-like protease cause different conformational changes in crystal structure Hu, Tiancen; Zhang, Yu; Li, Lianwei; Wang, Kuifeng; Chen, Shuai; Chen, Jing; Ding, Jianping; Jiang, Hualiang; Shen, Xu 2009 2009-06-05 PMC N PMC7103376 19409595.0 10.1016/j.virol.2009.03.034 qk8g4c7e 0.309181 Someya_2008, Chen_2008, Wei_P_2006, Cheng_2010
90 Chen_2008 Residues on the Dimer Interface of SARS Coronavirus 3C-like Protease: Dimer Stability Characterization and Enzyme Catalytic Activity Analysis Chen, Shuai; Zhang, Jian; Hu, Tiancen; Chen, Kaixian; Jiang, Hualiang; Shen, Xu 2008 2008-01-07 PMC N PMC7109808 18182387.0 10.1093/jb/mvm246 m6iocvo7 0.308154 Wei_P_2006, Hu_T_2009, Someya_2008, Kanitz_2019
91 Schmidt_2008 Sensitized Detection of Inhibitory Fragments and Iterative Development of Non‐Peptidic Protease Inhibitors by Dynamic Ligation Screening Schmidt, Marco Florian; Isidro‐Llobet, Albert; Lisurek, Michael; El‐Dahshan, Adeeb; Tan, Jinzhi; Hilgenfeld, Rolf; Rademann, Jörg 2008 2008-03-17 PMC N PMC7159527 18348134.0 10.1002/anie.200704594 7dgbc4um 0.305486
92 Gao_Y_2020 Structure of RNA-dependent RNA polymerase from 2019-nCoV, a major antiviral drug target Yan Gao; Liming Yan; Yucen Huang; Fengjiang Liu; Yao Zhao; Lin Cao; Tao Wang; Qianqian Sun; Zhenhua Ming; Lianqi Zhang; Ji Ge; Litao Zheng; Ying Zhang; Haofeng Wang; Yan Zhu; Chen Zhu; Tianyu Hu; Tian Hua; Bing Zhang; Xiuna Yang; Jun Li; Haitao Yang; Zhijie Liu; Wenqing Xu; Luke W. Guddat; Quan Wang; Zhiyong Lou; Zihe Rao 2020 2020-03-17 BioRxiv Y 10.1101/2020.03.16.993386 glfxrla9 0.304785
93 Tao_H_2006 Template‐assisted rational design of peptide inhibitors of furin using the lysine fragment of the mung bean trypsin inhibitor Tao, Hu; Zhang, Zhen; Shi, Jiahao; Shao, Xiao‐xia; Cui, Dafu; Chi, Cheng‐wu 2006 2006-07-28 PMC N PMC7164071 16934032.0 10.1111/j.1742-4658.2006.05393.x k8nh8pd5 0.301808 Yang_2010