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Publications

HIV-1 Protease Inhibitors Incorporating Stereochemically Defined P2' Ligands To Optimize Hydrogen Bonding in the Substrate Envelope.
Rusere LN, Lockbaum GJ, Lee SK, Henes M, Kosovrasti K, Spielvogel E, Nalivaika EA, Swanstrom R, Yilmaz NK, Schiffer CA, Ali A.
J Med Chem. 2019 Sep 12;62(17):8062-8079. doi: 10.1021/acs.jmedchem.9b00838. Epub 2019 Aug 21.

Structural Adaptation of Darunavir Analogues against Primary Mutations in HIV-1 Protease.
Lockbaum GJ, Leidner F, Rusere LN, Henes M, Kosovrasti K, Nachum GS, Nalivaika EA, Ali A, Yilmaz NK, Schiffer CA.
ACS Infect Dis. 2019 Feb 8;5(2):316-325. doi: 10.1021/acsinfecdis.8b00336. Epub 2018 Dec 31. PMID: 30543749

Molecular Mechanism of Resistance in a Clinically Significant Double-Mutant Variant of HCV NS3/4A Protease.
Matthew AN, Leidner F, Newton A, Petropoulos CJ, Huang W, Ali A, KurtYilmaz N, Schiffer CA.
Structure. 2018 Oct 2;26(10):1360-1372.e5. PMID: 30146168.

Quinoxaline-Based Linear HCV NS3/4A Protease Inhibitors Exhibit Potent Activity against Drug Resistant Variants.
Rusere LN, Matthew AN, Lockbaum GJ, Jahangir M, Newton A, Petropoulos CJ, Huang W, Kurt Yilmaz N, Schiffer CA, Ali A.
ACS Med Chem Lett. 2018 Jul 12; 9(7):691-696. PMID: 30034602.

Hepatitis C Virus NS3/4A Protease Inhibitors Incorporating Flexible P2 Quinoxalines Target Drug Resistant Viral Variants.
Matthew AN, Zephyr J, Hill CJ, Jahangir M, Newton A, Petropoulos CJ, Huang W, Kurt Yilmaz N, Schiffer CA, Ali A.
J Med Chem. 2017 Jun 08. PMID: 28594175.

Dengue Virus NS2B/NS3 Protease Inhibitors Exploiting the Prime Side.
Lin KH, Ali A, Rusere L, Soumana DI, Yilmaz NK, Schiffer CA.
J Virol. 2017 Mar 15. PMID: 28298600.

Molecular and Dynamic Mechanism Underlying Drug Resistance in Genotype 3 Hepatitis C NS3/4A Protease.
Soumana DI, Kurt Yilmaz N, Ali A, Prachanronarong KL, Schiffer CA.
J Am Chem Soc. 2016 Sep 14; 138(36):11850-9. PMID: 27512818.

Structural and Thermodynamic Effects of Macrocyclization in HCV NS3/4A Inhibitor MK-5172.
Soumana DI, Kurt Yilmaz N, Prachanronarong KL, Aydin C, Ali A, Schiffer CA.
ACS Chem Biol. 2016 Apr 15; 11(4):900-9. PMID: 26682473.

P-TEFb regulation of transcription termination factor Xrn2 revealed by a chemical genetic screen for Cdk9 substrates.
Sansó M, Levin RS, Lipp JJ, Wang VY, Greifenberg AK, Quezada EM, Ali A, Ghosh A, Larochelle S, Rana TM, Geyer M, Tong L, Shokat KM, Fisher RP.
Genes Dev. 2016 Jan 01; 30(1):117-31. PMID: 26728557.

Simultaneously Targeting the NS3 Protease and Helicase Activities for More Effective Hepatitis C Virus Therapy.
Ndjomou J, Corby MJ, Sweeney NL, Hanson AM, Aydin C, Ali A, Schiffer CA, Li K, Frankowski KJ, Schoenen FJ, Frick DN.
ACS Chem Biol. 2015 Aug 21; 10(8):1887-96. PMID: 25961497.

Structural analysis of asunaprevir resistance in HCV NS3/4A protease.
Soumana DI, Ali A, Schiffer CA.
ACS Chem Biol. 2014 Nov 21; 9(11):2485-90. PMID: 25243902.

Evaluating the Role of Macrocycles in the Susceptibility of Hepatitis C Virus NS3/4A Protease Inhibitors to Drug Resistance.
Ali A, Aydin C, Gildemeister R, Romano KP, Cao H, Özen A, Soumana D, Newton A, Petropoulos CJ, Huang W, Schiffer CA. 
ACS Chem. Biol. 2013, 8, 1469–1478. PMID: 23594083.

Substrate Envelope Designed Potent HIV-1 Protease Inhibitors to Avoid Drug Resistance.
Nalam MNL, Ali A, Reddy GSKK, Cao H, Anjum SG, Altman MD, Yilmaz NK, Tidor B, Rana TM, Schiffer CA. 
Chem. Biol. 2013, 20, 1116–1124. PMID: 24012370

Testing the Substrate-Envelope Hypothesis with Designed Pairs of Compounds.
Shen Y, Altman MD, Ali A, Nalam MNL, Cao H, Rana TM, Schiffer CA, Tidor B.
ACS Chem. Biol. 2013, 8, 2433–2441.Equal contribution. PMID: 23952265.

Chemical Screening Identifies A Small Molecule Inhibitor of Candida Albicans Adhesion, Morphogenesis and Pathogenesis.
Fazly A, Jain C, Dehner AC, Issa L, Lilly EA, Ali A, Cao H, Fidel PL, Rao RP, Kaufman PD.
Proc. Natl. Acad. Sci. U.S.A. 2013, 110, 13594–13599. PMID: 23904484.

Efficient Computation of Small-Molecule Configurational Binding Entropy and Free Energy Changes by Ensemble Enumeration.
Silver NW, King B, Nalam MNL, Cao H, Ali A, Reddy GSKK, Rana TM, Schiffer CA, Tidor B.
J. Chem. Theory Comput. 2013, 9, 5098–5115. PMID: 24250277.

Synthesis and Structure-Activity Relationship Studies of HIV-1 Virion Infectivity Factor (Vif) Inhibitors that Block Viral Replication.
Ali A, Wang J, Nathans RS, Cao H, Sharova N, Stevenson M, Rana TM.
ChemMedChem 2012, 7, 1217–1229. PMID: 22555953.

The Molecular Basis of Drug Resistance against Hepatitis C Virus NS3/4A Protease Inhibitors.
Romano KP, Ali A, Aydin C, Soumana D, Özen A, Deveau LM, Silver C, Cao H, Newton A, Petropoulos CJ, Huang W, Schiffer CA.
PLoS Pathog. 2012, 8, e1002832. PMID: 22910833.

Design, Synthesis, and Biological and Structural Evaluations of Novel HIV-1 Protease Inhibitors to Combat Drug Resistance. 
Parai MK, Huggins DJ, Cao H, Nalam MNL, Ali A, Schiffer CA, Tidor B, Rana TM.
J. Med. Chem. 2012, 55, 6328–6341. PMID: 22708897.

First-in-Class Small Molecule Inhibitors of the Single-Strand DNA Cytosine Deaminase APOBEC3G.
Li M, Shandilya SMD, Carpenter MA, Rathore A, Brown WL, Perkins AL, Harki DA, Solberg J, Hook DJ, Pandey KK, Parniak MA, Johnson JR, Krogan NJ, Somasundaran M, Ali A, Schiffer CA, Harris RS.
ACS Chem. Biol. 2012, 7, 506–517. PMID: 22181350.

Structure-Based Design, Synthesis, and Structure-Activity Relationship Studies of HIV-1 Protease Inhibitors Incorporating Phenyloxazolidinones.
Ali A, Reddy GSKK, Nalam MNL, Anjum SG, Cao H, Schiffer CA, Rana TM.
J. Med. Chem. 2010, 53, 7699–7708. PMID: 20958050.

Drug Resistance against HCV NS3/4A Protease Inhibitors is Defined by the Balance of Substrate Recognition Versus Inhibitor Binding.
Romano KP, Ali A, Royer WE, Schiffer CA.
Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 20986–20991.Equal first authors. PMID: 21084633.

Evaluating the Substrate-Envelope Hypothesis: Structural Analysis of Novel HIV-1 Protease Inhibitors Designed to be Robust against Drug Resistance.
Nalam MNL, Ali A, Altman MD, Reddy GSKK, Chellappan S, Kairys V, Özen A, Gilson MK, Tidor B, Rana TM, Schiffer CA.
J. Virol. 2010, 84, 5368–5378. PMID: 20237088.

Molecular Basis for Drug Resistance in HIV-1 Protease.
Ali A, Bandaranayake R, Cai Y, Kolli M, Mittal M, Nalam M, Ozen A, Thayer K, Nalivaika E, King N, Prabu-Jeyabalan M, Murzycki J, Schiffer CA.
Viruses 2010, 2, 2509–2535. PMID: 21994628.

P-TEFb Kinase Complex Phosphorylates Histone H1 to Regulate Expression of Cellular and HIV-1 Genes.
O'Brien SK, Cao H, Nathans R, Ali A, Rana TM.
J. Biol. Chem. 2010, 285, 29713–29720. PMID: 20551309.

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