Celia Schiffer to HIV Protease
This is a "connection" page, showing publications Celia Schiffer has written about HIV Protease.
Connection Strength
16.134
-
Leidner F, Kurt Yilmaz N, Schiffer CA. Deciphering Complex Mechanisms of Resistance and Loss of Potency through Coupled Molecular Dynamics and Machine Learning. J Chem Theory Comput. 2021 Apr 13; 17(4):2054-2064.
Score: 0.639
-
Whitfield TW, Ragland DA, Zeldovich KB, Schiffer CA. Characterizing Protein-Ligand Binding Using Atomistic Simulation and Machine Learning: Application to Drug Resistance in HIV-1 Protease. J Chem Theory Comput. 2020 Feb 11; 16(2):1284-1299.
Score: 0.588
-
Leidner F, Kurt Yilmaz N, Schiffer CA. Target-Specific Prediction of Ligand Affinity with Structure-Based Interaction Fingerprints. J Chem Inf Model. 2019 09 23; 59(9):3679-3691.
Score: 0.571
-
Henes M, Lockbaum GJ, Kosovrasti K, Leidner F, Nachum GS, Nalivaika EA, Lee SK, Spielvogel E, Zhou S, Swanstrom R, Bolon DNA, Kurt Yilmaz N, Schiffer CA. Picomolar to Micromolar: Elucidating the Role of Distal Mutations in HIV-1 Protease in Conferring Drug Resistance. ACS Chem Biol. 2019 11 15; 14(11):2441-2452.
Score: 0.571
-
Ishima R, Kurt Yilmaz N, Schiffer CA. NMR and MD studies combined to elucidate inhibitor and water interactions of HIV-1 protease and their modulations with resistance mutations. J Biomol NMR. 2019 Jul; 73(6-7):365-374.
Score: 0.566
-
Lockbaum GJ, Leidner F, Rusere LN, Henes M, Kosovrasti K, Nachum GS, Nalivaika EA, Ali A, Yilmaz NK, Schiffer CA. Structural Adaptation of Darunavir Analogues against Primary Mutations in HIV-1 Protease. ACS Infect Dis. 2019 02 08; 5(2):316-325.
Score: 0.547
-
Leidner F, Kurt Yilmaz N, Paulsen J, Muller YA, Schiffer CA. Hydration Structure and Dynamics of Inhibitor-Bound HIV-1 Protease. J Chem Theory Comput. 2018 May 08; 14(5):2784-2796.
Score: 0.521
-
Ragland DA, Whitfield TW, Lee SK, Swanstrom R, Zeldovich KB, Kurt-Yilmaz N, Schiffer CA. Elucidating the Interdependence of Drug Resistance from Combinations of Mutations. J Chem Theory Comput. 2017 Nov 14; 13(11):5671-5682.
Score: 0.502
-
Paulsen JL, Leidner F, Ragland DA, Kurt Yilmaz N, Schiffer CA. Interdependence of Inhibitor Recognition in HIV-1 Protease. J Chem Theory Comput. 2017 May 09; 13(5):2300-2309.
Score: 0.485
-
?zen A, Lin KH, Kurt Yilmaz N, Schiffer CA. Structural basis and distal effects of Gag substrate coevolution in drug resistance to HIV-1 protease. Proc Natl Acad Sci U S A. 2014 Nov 11; 111(45):15993-8.
Score: 0.410
-
Ragland DA, Nalivaika EA, Nalam MN, Prachanronarong KL, Cao H, Bandaranayake RM, Cai Y, Kurt-Yilmaz N, Schiffer CA. Drug resistance conferred by mutations outside the active site through alterations in the dynamic and structural ensemble of HIV-1 protease. J Am Chem Soc. 2014 Aug 27; 136(34):11956-63.
Score: 0.404
-
Kolli M, Ozen A, Kurt-Yilmaz N, Schiffer CA. HIV-1 protease-substrate coevolution in nelfinavir resistance. J Virol. 2014 Jul; 88(13):7145-54.
Score: 0.394
-
Nalam MN, Ali A, Reddy GS, Cao H, Anjum SG, Altman MD, Yilmaz NK, Tidor B, Rana TM, Schiffer CA. Substrate envelope-designed potent HIV-1 protease inhibitors to avoid drug resistance. Chem Biol. 2013 Sep 19; 20(9):1116-24.
Score: 0.378
-
Mittal S, Bandaranayake RM, King NM, Prabu-Jeyabalan M, Nalam MN, Nalivaika EA, Yilmaz NK, Schiffer CA. Structural and thermodynamic basis of amprenavir/darunavir and atazanavir resistance in HIV-1 protease with mutations at residue 50. J Virol. 2013 Apr; 87(8):4176-84.
Score: 0.363
-
Foulkes-Murzycki JE, Rosi C, Kurt Yilmaz N, Shafer RW, Schiffer CA. Cooperative effects of drug-resistance mutations in the flap region of HIV-1 protease. ACS Chem Biol. 2013 Mar 15; 8(3):513-8.
Score: 0.361
-
King NM, Prabu-Jeyabalan M, Bandaranayake RM, Nalam MN, Nalivaika EA, ?zen A, Haliloglu T, Yilmaz NK, Schiffer CA. Extreme entropy-enthalpy compensation in a drug-resistant variant of HIV-1 protease. ACS Chem Biol. 2012 Sep 21; 7(9):1536-46.
Score: 0.349
-
Alvizo O, Mittal S, Mayo SL, Schiffer CA. Structural, kinetic, and thermodynamic studies of specificity designed HIV-1 protease. Protein Sci. 2012 Jul; 21(7):1029-41.
Score: 0.347
-
Mittal S, Cai Y, Nalam MN, Bolon DN, Schiffer CA. Hydrophobic core flexibility modulates enzyme activity in HIV-1 protease. J Am Chem Soc. 2012 Mar 07; 134(9):4163-8.
Score: 0.340
-
Cai Y, Schiffer C. Decomposing the energetic impact of drug-resistant mutations: the example of HIV-1 protease-DRV binding. Methods Mol Biol. 2012; 819:551-60.
Score: 0.337
-
Ozen A, Haliloglu T, Schiffer CA. Dynamics of preferential substrate recognition in HIV-1 protease: redefining the substrate envelope. J Mol Biol. 2011 Jul 22; 410(4):726-44.
Score: 0.326
-
Bandaranayake RM, Kolli M, King NM, Nalivaika EA, Heroux A, Kakizawa J, Sugiura W, Schiffer CA. The effect of clade-specific sequence polymorphisms on HIV-1 protease activity and inhibitor resistance pathways. J Virol. 2010 Oct; 84(19):9995-10003.
Score: 0.305
-
Nalam MN, Ali A, Altman MD, Reddy GS, Chellappan S, Kairys V, Ozen A, Cao H, Gilson MK, Tidor B, Rana TM, Schiffer CA. Evaluating the substrate-envelope hypothesis: structural analysis of novel HIV-1 protease inhibitors designed to be robust against drug resistance. J Virol. 2010 May; 84(10):5368-78.
Score: 0.297
-
Kolli M, Stawiski E, Chappey C, Schiffer CA. Human immunodeficiency virus type 1 protease-correlated cleavage site mutations enhance inhibitor resistance. J Virol. 2009 Nov; 83(21):11027-42.
Score: 0.285
-
Lefebvre E, Schiffer CA. Resilience to resistance of HIV-1 protease inhibitors: profile of darunavir. AIDS Rev. 2008 Jul-Sep; 10(3):131-42.
Score: 0.264
-
Bandaranayake RM, Prabu-Jeyabalan M, Kakizawa J, Sugiura W, Schiffer CA. Structural analysis of human immunodeficiency virus type 1 CRF01_AE protease in complex with the substrate p1-p6. J Virol. 2008 Jul; 82(13):6762-6.
Score: 0.261
-
Nalam MN, Peeters A, Jonckers TH, Dierynck I, Schiffer CA. Crystal structure of lysine sulfonamide inhibitor reveals the displacement of the conserved flap water molecule in human immunodeficiency virus type 1 protease. J Virol. 2007 Sep; 81(17):9512-8.
Score: 0.246
-
Foulkes-Murzycki JE, Scott WR, Schiffer CA. Hydrophobic sliding: a possible mechanism for drug resistance in human immunodeficiency virus type 1 protease. Structure. 2007 Feb; 15(2):225-33.
Score: 0.239
-
Ozer N, Haliloglu T, Schiffer CA. Substrate specificity in HIV-1 protease by a biased sequence search method. Proteins. 2006 Aug 01; 64(2):444-56.
Score: 0.231
-
Foulkes JE, Prabu-Jeyabalan M, Cooper D, Henderson GJ, Harris J, Swanstrom R, Schiffer CA. Role of invariant Thr80 in human immunodeficiency virus type 1 protease structure, function, and viral infectivity. J Virol. 2006 Jul; 80(14):6906-16.
Score: 0.230
-
Prabu-Jeyabalan M, Nalivaika EA, Romano K, Schiffer CA. Mechanism of substrate recognition by drug-resistant human immunodeficiency virus type 1 protease variants revealed by a novel structural intermediate. J Virol. 2006 Apr; 80(7):3607-16.
Score: 0.226
-
Prabu-Jeyabalan M, King NM, Nalivaika EA, Heilek-Snyder G, Cammack N, Schiffer CA. Substrate envelope and drug resistance: crystal structure of RO1 in complex with wild-type human immunodeficiency virus type 1 protease. Antimicrob Agents Chemother. 2006 Apr; 50(4):1518-21.
Score: 0.226
-
Kolli M, Lastere S, Schiffer CA. Co-evolution of nelfinavir-resistant HIV-1 protease and the p1-p6 substrate. Virology. 2006 Apr 10; 347(2):405-9.
Score: 0.223
-
Prabu-Jeyabalan M, Nalivaika EA, King NM, Schiffer CA. Structural basis for coevolution of a human immunodeficiency virus type 1 nucleocapsid-p1 cleavage site with a V82A drug-resistant mutation in viral protease. J Virol. 2004 Nov; 78(22):12446-54.
Score: 0.205
-
King NM, Prabu-Jeyabalan M, Nalivaika EA, Schiffer CA. Combating susceptibility to drug resistance: lessons from HIV-1 protease. Chem Biol. 2004 Oct; 11(10):1333-8.
Score: 0.204
-
Kurt N, Haliloglu T, Schiffer CA. Structure-based prediction of potential binding and nonbinding peptides to HIV-1 protease. Biophys J. 2003 Aug; 85(2):853-63.
Score: 0.188
-
Prabu-Jeyabalan M, Nalivaika EA, King NM, Schiffer CA. Viability of a drug-resistant human immunodeficiency virus type 1 protease variant: structural insights for better antiviral therapy. J Virol. 2003 Jan; 77(2):1306-15.
Score: 0.180
-
Prabu-Jeyabalan M, Nalivaika E, Schiffer CA. Substrate shape determines specificity of recognition for HIV-1 protease: analysis of crystal structures of six substrate complexes. Structure. 2002 Mar; 10(3):369-81.
Score: 0.170
-
King NM, Melnick L, Prabu-Jeyabalan M, Nalivaika EA, Yang SS, Gao Y, Nie X, Zepp C, Heefner DL, Schiffer CA. Lack of synergy for inhibitors targeting a multi-drug-resistant HIV-1 protease. Protein Sci. 2002 Feb; 11(2):418-29.
Score: 0.169
-
Scott WR, Schiffer CA. Curling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance. Structure. 2000 Dec 15; 8(12):1259-65.
Score: 0.157
-
Prabu-Jeyabalan M, Nalivaika E, Schiffer CA. How does a symmetric dimer recognize an asymmetric substrate? A substrate complex of HIV-1 protease. J Mol Biol. 2000 Sep 01; 301(5):1207-20.
Score: 0.153
-
Rusere LN, Lockbaum GJ, Henes M, Lee SK, Spielvogel E, Rao DN, Kosovrasti K, Nalivaika EA, Swanstrom R, Kurt Yilmaz N, Schiffer CA, Ali A. Structural Analysis of Potent Hybrid HIV-1 Protease Inhibitors Containing Bis-tetrahydrofuran in a Pseudosymmetric Dipeptide Isostere. J Med Chem. 2020 08 13; 63(15):8296-8313.
Score: 0.153
-
Rusere LN, Lockbaum GJ, Lee SK, Henes M, Kosovrasti K, Spielvogel E, Nalivaika EA, Swanstrom R, Yilmaz NK, Schiffer CA, Ali A. HIV-1 Protease Inhibitors Incorporating Stereochemically Defined P2' Ligands To Optimize Hydrogen Bonding in the Substrate Envelope. J Med Chem. 2019 09 12; 62(17):8062-8079.
Score: 0.143
-
Henes M, Kosovrasti K, Lockbaum GJ, Leidner F, Nachum GS, Nalivaika EA, Bolon DNA, Kurt Yilmaz N, Schiffer CA, Whitfield TW. Molecular Determinants of Epistasis in HIV-1 Protease: Elucidating the Interdependence of L89V and L90M Mutations in Resistance. Biochemistry. 2019 09 03; 58(35):3711-3726.
Score: 0.143
-
Boucher JI, Whitfield TW, Dauphin A, Nachum G, Hollins C, Zeldovich KB, Swanstrom R, Schiffer CA, Luban J, Bolon DNA. Constrained Mutational Sampling of Amino Acids in HIV-1 Protease Evolution. Mol Biol Evol. 2019 04 01; 36(4):798-810.
Score: 0.139
-
Potempa M, Lee SK, Kurt Yilmaz N, Nalivaika EA, Rogers A, Spielvogel E, Carter CW, Schiffer CA, Swanstrom R. HIV-1 Protease Uses Bi-Specific S2/S2' Subsites to Optimize Cleavage of Two Classes of Target Sites. J Mol Biol. 2018 12 07; 430(24):5182-5195.
Score: 0.135
-
Khan SN, Persons JD, Paulsen JL, Guerrero M, Schiffer CA, Kurt-Yilmaz N, Ishima R. Probing Structural Changes among Analogous Inhibitor-Bound Forms of HIV-1 Protease and a Drug-Resistant Mutant in Solution by Nuclear Magnetic Resonance. Biochemistry. 2018 03 13; 57(10):1652-1662.
Score: 0.129
-
Kurt Yilmaz N, Swanstrom R, Schiffer CA. Improving Viral Protease Inhibitors to Counter Drug Resistance. Trends Microbiol. 2016 07; 24(7):547-557.
Score: 0.113
-
Zhou H, Li S, Badger J, Nalivaika E, Cai Y, Foulkes-Murzycki J, Schiffer C, Makowski L. Modulation of HIV protease flexibility by the T80N mutation. Proteins. 2015 Nov; 83(11):1929-39.
Score: 0.109
-
Potempa M, Nalivaika E, Ragland D, Lee SK, Schiffer CA, Swanstrom R. A Direct Interaction with RNA Dramatically Enhances the Catalytic Activity of the HIV-1 Protease In Vitro. J Mol Biol. 2015 Jul 17; 427(14):2360-78.
Score: 0.106
-
Cheng N, Lee SK, Donover PS, Reichman M, Schiffer CA, Hull-Ryde EA, Swanstrom R, Janzen WP. Development of a Novel Screening Strategy Designed to Discover a New Class of HIV Drugs. J Lab Autom. 2014 Jun; 19(3):297-303.
Score: 0.096
-
Lee SK, Cheng N, Hull-Ryde E, Potempa M, Schiffer CA, Janzen W, Swanstrom R. A sensitive assay using a native protein substrate for screening HIV-1 maturation inhibitors targeting the protease cleavage site between the matrix and capsid. Biochemistry. 2013 Jul 23; 52(29):4929-40.
Score: 0.094
-
Schiffer C. Interview with Celia Schiffer. Future Med Chem. 2013 Jul; 5(11):1193-7.
Score: 0.093
-
Babrzadeh F, Varghese V, Pacold M, Liu TF, Nyr?n P, Schiffer C, Fessel WJ, Shafer RW. Collinearity of protease mutations in HIV-1 samples with high-level protease inhibitor class resistance. J Antimicrob Chemother. 2013 Feb; 68(2):414-8.
Score: 0.089
-
Parai MK, Huggins DJ, Cao H, Nalam MN, Ali A, Schiffer CA, Tidor B, Rana TM. Design, synthesis, and biological and structural evaluations of novel HIV-1 protease inhibitors to combat drug resistance. J Med Chem. 2012 Jul 26; 55(14):6328-41.
Score: 0.087
-
Lee SK, Potempa M, Kolli M, ?zen A, Schiffer CA, Swanstrom R. Context surrounding processing sites is crucial in determining cleavage rate of a subset of processing sites in HIV-1 Gag and Gag-Pro-Pol polyprotein precursors by viral protease. J Biol Chem. 2012 Apr 13; 287(16):13279-90.
Score: 0.085
-
Dierynck I, Van Marck H, Van Ginderen M, Jonckers TH, Nalam MN, Schiffer CA, Raoof A, Kraus G, Picchio G. TMC310911, a novel human immunodeficiency virus type 1 protease inhibitor, shows in vitro an improved resistance profile and higher genetic barrier to resistance compared with current protease inhibitors. Antimicrob Agents Chemother. 2011 Dec; 55(12):5723-31.
Score: 0.082
-
Ozer N, Schiffer CA, Haliloglu T. Rationale for more diverse inhibitors in competition with substrates in HIV-1 protease. Biophys J. 2010 Sep 08; 99(5):1650-9.
Score: 0.077
-
Altman MD, Ali A, Reddy GS, Nalam MN, Anjum SG, Cao H, Chellappan S, Kairys V, Fernandes MX, Gilson MK, Schiffer CA, Rana TM, Tidor B. HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants. J Am Chem Soc. 2008 May 14; 130(19):6099-113.
Score: 0.065
-
Altman MD, Nalivaika EA, Prabu-Jeyabalan M, Schiffer CA, Tidor B. Computational design and experimental study of tighter binding peptides to an inactivated mutant of HIV-1 protease. Proteins. 2008 Feb 15; 70(3):678-94.
Score: 0.064
-
Reddy GS, Ali A, Nalam MN, Anjum SG, Cao H, Nathans RS, Schiffer CA, Rana TM. Design and synthesis of HIV-1 protease inhibitors incorporating oxazolidinones as P2/P2' ligands in pseudosymmetric dipeptide isosteres. J Med Chem. 2007 Sep 06; 50(18):4316-28.
Score: 0.062
-
Chellappan S, Kairys V, Fernandes MX, Schiffer C, Gilson MK. Evaluation of the substrate envelope hypothesis for inhibitors of HIV-1 protease. Proteins. 2007 Aug 01; 68(2):561-7.
Score: 0.062
-
Chellappan S, Kiran Kumar Reddy GS, Ali A, Nalam MN, Anjum SG, Cao H, Kairys V, Fernandes MX, Altman MD, Tidor B, Rana TM, Schiffer CA, Gilson MK. Design of mutation-resistant HIV protease inhibitors with the substrate envelope hypothesis. Chem Biol Drug Des. 2007 May; 69(5):298-313.
Score: 0.061
-
Ali A, Reddy GS, Cao H, Anjum SG, Nalam MN, Schiffer CA, Rana TM. Discovery of HIV-1 protease inhibitors with picomolar affinities incorporating N-aryl-oxazolidinone-5-carboxamides as novel P2 ligands. J Med Chem. 2006 Dec 14; 49(25):7342-56.
Score: 0.059
-
Mitsuya Y, Winters MA, Fessel WJ, Rhee SY, Hurley L, Horberg M, Schiffer CA, Zolopa AR, Shafer RW. N88D facilitates the co-occurrence of D30N and L90M and the development of multidrug resistance in HIV type 1 protease following nelfinavir treatment failure. AIDS Res Hum Retroviruses. 2006 Dec; 22(12):1300-5.
Score: 0.059
-
Surleraux DL, Tahri A, Verschueren WG, Pille GM, de Kock HA, Jonckers TH, Peeters A, De Meyer S, Azijn H, Pauwels R, de Bethune MP, King NM, Prabu-Jeyabalan M, Schiffer CA, Wigerinck PB. Discovery and selection of TMC114, a next generation HIV-1 protease inhibitor. J Med Chem. 2005 Mar 24; 48(6):1813-22.
Score: 0.053
-
Johnston E, Winters MA, Rhee SY, Merigan TC, Schiffer CA, Shafer RW. Association of a novel human immunodeficiency virus type 1 protease substrate cleft mutation, L23I, with protease inhibitor therapy and in vitro drug resistance. Antimicrob Agents Chemother. 2004 Dec; 48(12):4864-8.
Score: 0.052
-
Hoffman NG, Schiffer CA, Swanstrom R. Covariation of amino acid positions in HIV-1 protease. Virology. 2003 Sep 30; 314(2):536-48.
Score: 0.047
-
Lockbaum GJ, Rusere LN, Henes M, Kosovrasti K, Rao DN, Spielvogel E, Lee SK, Nalivaika EA, Swanstrom R, Yilmaz NK, Schiffer CA, Ali A. HIV-1 protease inhibitors with a P1 phosphonate modification maintain potency against drug-resistant variants by increased interactions with flap residues. Eur J Med Chem. 2023 Sep 05; 257:115501.
Score: 0.046
-
Kurt N, Scott WR, Schiffer CA, Haliloglu T. Cooperative fluctuations of unliganded and substrate-bound HIV-1 protease: a structure-based analysis on a variety of conformations from crystallography and molecular dynamics simulations. Proteins. 2003 May 15; 51(3):409-22.
Score: 0.046
-
Wu TD, Schiffer CA, Gonzales MJ, Taylor J, Kantor R, Chou S, Israelski D, Zolopa AR, Fessel WJ, Shafer RW. Mutation patterns and structural correlates in human immunodeficiency virus type 1 protease following different protease inhibitor treatments. J Virol. 2003 Apr; 77(8):4836-47.
Score: 0.046
-
Pettit SC, Henderson GJ, Schiffer CA, Swanstrom R. Replacement of the P1 amino acid of human immunodeficiency virus type 1 Gag processing sites can inhibit or enhance the rate of cleavage by the viral protease. J Virol. 2002 Oct; 76(20):10226-33.
Score: 0.044
-
Kairys V, Gilson MK, Lather V, Schiffer CA, Fernandes MX. Toward the design of mutation-resistant enzyme inhibitors: further evaluation of the substrate envelope hypothesis. Chem Biol Drug Des. 2009 Sep; 74(3):234-45.
Score: 0.018
-
Jorissen RN, Reddy GS, Ali A, Altman MD, Chellappan S, Anjum SG, Tidor B, Schiffer CA, Rana TM, Gilson MK. Additivity in the analysis and design of HIV protease inhibitors. J Med Chem. 2009 Feb 12; 52(3):737-54.
Score: 0.017