Publications

• Strategy to overcome a nirmatrelvir resistance mechanism in the SARS-CoV-2 nsp5 protease.
  Sci Adv Volume: 11 Page(s): eadv8875
  06/06/2025 Authors: Neilsen G; Lan S; Slack RL; Lorson ZC; Emanuelli Castaner A; Lee R; Edwards KG; Zhang H; Lee J; Cantara WA
• Considerations for capsid-targeting antiretrovirals in pre-exposure prophylaxis.
  Trends Mol Med
  02/27/2025 Authors: McFadden WM; Faerch M; Kirby KA; Dick RA; Torbett BE; Sarafianos SG
• Adapting a Trapped Ion Mobility Spectrometry-Q-TOF for High m/z Native Mass Spectrometry and Surface-Induced Dissociation.
  Anal Chem Volume: 97 Page(s): 3827 - 3835
  02/25/2025 Authors: Lin Y-F; Jones BJ; Ridgeway ME; Panczyk EM; Somogyi A; Kaplan DA; Marathe I; Yun S; Kirby KA; Sarafianos SG
• Disruption of LEDGF/p75-directed integration derepresses antisense transcription of the HIV-1 genome.
  bioRxiv
  12/06/2024 Authors: Tedbury PR; Mahboubi D; Puray-Chavez M; Shah R; Ukah OB; Wahoski CC; Fadel HJ; Poeschla EM; Gao X; McFadden WM
• Quinazolinone-based Subchemotypes for Targeting HIV-1 Capsid Protein: Design and Synthesis.
  Med Chem Res Volume: 33 Page(s): 2431 - 2447
  12/01/2024 Authors: Akther T; McFadden WM; Zhang H; Kirby KA; Sarafianos SG; Wang Z
• Design and Synthesis of New GS-6207 Subtypes for Targeting HIV-1 Capsid Protein.
  Int J Mol Sci Volume: 25
  03/27/2024 Authors: Akther T; McFadden WM; Zhang H; Kirby KA; Sarafianos SG; Wang Z
• Identification of clickable HIV-1 capsid-targeting probes for viral replication inhibition.
  Cell Chem Biol Volume: 31 Page(s): 477 - 486.e7
  03/21/2024 Authors: McFadden WM; Casey-Moore MC; Bare GAL; Kirby KA; Wen X; Li G; Wang H; Slack RL; Snyder AA; Lorson ZC
• Use of TSAR, Thermal Shift Analysis in R, to identify Folic Acid as a Molecule that Interacts with HIV-1 Capsid.
  bioRxiv
  11/29/2023 Authors: Gao X; McFadden WM; Wen X; Emanuelli A; Lorson ZC; Zheng H; Kirby KA; Sarafianos SG
• Multidisciplinary studies with mutated HIV-1 capsid proteins reveal structural mechanisms of lattice stabilization.
  Nat Commun Volume: 14 Page(s): 5614
  09/12/2023 Authors: Gres AT; Kirby KA; McFadden WM; Du H; Liu D; Xu C; Bryer AJ; Perilla JR; Shi J; Aiken C
• Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid.
  J Comput Aided Mol Des Volume: 36 Page(s): 193 - 203
  03/01/2022 Authors: Sun Q; Biswas A; Vijayan RSK; Craveur P; Forli S; Olson AJ; Castaner AE; Kirby KA; Sarafianos SG; Deng N
• Specific mutations in the HIV-1 G-tract of the 3'-polypurine tract cause resistance to integrase strand transfer inhibitors.
  J Antimicrob Chemother Volume: 77 Page(s): 574 - 577
  02/23/2022 Authors: Hachiya A; Kubota M; Shigemi U; Ode H; Yokomaku Y; Kirby KA; Sarafianos SG; Iwatani Y
• TRIM5 Restriction of HIV-1-N74D Viruses in Lymphocytes Is Caused by a Loss of Cyclophilin A Protection.
  Viruses Volume: 14
  02/10/2022 Authors: Selyutina A; Simons LM; Kirby KA; Bulnes-Ramos A; Hu P; Sarafianos SG; Hultquist JF; Diaz-Griffero F
• Rotten to the core: antivirals targeting the HIV-1 capsid core.
  Retrovirology Volume: 18 Page(s): 41
  12/22/2021 Authors: McFadden WM; Snyder AA; Kirby KA; Tedbury PR; Raj M; Wang Z; Sarafianos SG
• Potency and metabolic stability: a molecular hybrid case in the design of novel PF74-like small molecules targeting HIV-1 capsid protein.
  RSC Med Chem Volume: 12 Page(s): 2031 - 2044
  12/15/2021 Authors: Sahani RL; Akther T; Cilento ME; Castaner AE; Zhang H; Kirby KA; Xie J; Sarafianos SG; Wang Z
• Molecular Dynamics Free Energy Simulations Reveal the Mechanism for the Antiviral Resistance of the M66I HIV-1 Capsid Mutation.
  Viruses Volume: 13
  05/15/2021 Authors: Sun Q; Levy RM; Kirby KA; Wang Z; Sarafianos SG; Deng N
• Discovery of New Small Molecule Hits as Hepatitis B Virus Capsid Assembly Modulators: Structure and Pharmacophore-Based Approaches.
  Viruses Volume: 13
  04/27/2021 Authors: Senaweera S; Du H; Zhang H; Kirby KA; Tedbury PR; Xie J; Sarafianos SG; Wang Z
• Baicalein and Baicalin Inhibit SARS-CoV-2 RNA-Dependent-RNA Polymerase.
  Microorganisms Volume: 9
  04/22/2021 Authors: Zandi K; Musall K; Oo A; Cao D; Liang B; Hassandarvish P; Lan S; Slack RL; Kirby KA; Bassit L
• Avoiding Drug Resistance in HIV Reverse Transcriptase.
  Chem Rev Volume: 121 Page(s): 3271 - 3296
  03/24/2021 Authors: Cilento ME; Kirby KA; Sarafianos SG
• Design, Synthesis and Characterization of HIV-1 CA-Targeting Small Molecules: Conformational Restriction of PF74.
  Viruses Volume: 13
  03/15/2021 Authors: Sahani RL; Diana-Rivero R; Vernekar SKV; Wang L; Du H; Zhang H; Castaner AE; Casey MC; Kirby KA; Tedbury PR
• Novel PF74-like small molecules targeting the HIV-1 capsid protein: Balance of potency and metabolic stability.
  Acta Pharm Sin B Volume: 11 Page(s): 810 - 822
  03/01/2021 Authors: Wang L; Casey MC; Vernekar SKV; Sahani RL; Kirby KA; Du H; Zhang H; Tedbury PR; Xie J; Sarafianos SG
• Novel HIV-1 capsid-targeting small molecules of the PF74 binding site.
  Eur J Med Chem Volume: 204 Page(s): 112626
  10/15/2020 Authors: Wang L; Casey MC; Vernekar SKV; Sahani RL; Kankanala J; Kirby KA; Du H; Hachiya A; Zhang H; Tedbury PR
• Chemical profiling of HIV-1 capsid-targeting antiviral PF74.
  Eur J Med Chem Volume: 200 Page(s): 112427
  08/15/2020 Authors: Wang L; Casey MC; Vernekar SKV; Do HT; Sahani RL; Kirby KA; Du H; Hachiya A; Zhang H; Tedbury PR
• Toward Structurally Novel and Metabolically Stable HIV-1 Capsid-Targeting Small Molecules.
  Viruses Volume: 12
  04/16/2020 Authors: Vernekar SKV; Sahani RL; Casey MC; Kankanala J; Wang L; Kirby KA; Du H; Zhang H; Tedbury PR; Xie J
• Novel Hepatitis B Virus Capsid-Targeting Antiviral That Aggregates Core Particles and Inhibits Nuclear Entry of Viral Cores.
  ACS Infect Dis Volume: 5 Page(s): 750 - 758
  05/10/2019 Authors: Huber AD; Pineda DL; Liu D; Boschert KN; Gres AT; Wolf JJ; Coonrod EM; Tang J; Laughlin TG; Yang Q
• Pharmacophore-based design of novel 3-hydroxypyrimidine-2,4-dione subtypes as inhibitors of HIV reverse transcriptase-associated RNase H: Tolerance of a nonflexible linker.
  Eur J Med Chem Volume: 166 Page(s): 390 - 399
  03/15/2019 Authors: Tang J; Do HT; Huber AD; Casey MC; Kirby KA; Wilson DJ; Kankanala J; Parniak MA; Sarafianos SG; Wang Z
• Novel Intersubunit Interaction Critical for HIV-1 Core Assembly Defines a Potentially Targetable Inhibitor Binding Pocket.
  mBio Volume: 10
  03/12/2019 Authors: Craveur P; Gres AT; Kirby KA; Liu D; Hammond JA; Deng Y; Forli S; Goodsell DS; Williamson JR; Sarafianos SG
• Small Molecule Inhibitor that Stabilizes the Autoinhibited Conformation of the Oncogenic Tyrosine Phosphatase SHP2.
  J Med Chem Volume: 62 Page(s): 1125 - 1137
  02/14/2019 Authors: Wu X; Xu G; Li X; Xu W; Li Q; Liu W; Kirby KA; Loh ML; Li J; Sarafianos SG
• 6-Biphenylmethyl-3-hydroxypyrimidine-2,4-diones potently and selectively inhibited HIV reverse transcriptase-associated RNase H.
  Eur J Med Chem Volume: 156 Page(s): 680 - 691
  08/05/2018 Authors: Wang L; Tang J; Huber AD; Casey MC; Kirby KA; Wilson DJ; Kankanala J; Parniak MA; Sarafianos SG; Wang Z
• 6-Arylthio-3-hydroxypyrimidine-2,4-diones potently inhibited HIV reverse transcriptase-associated RNase H with antiviral activity.
  Eur J Med Chem Volume: 156 Page(s): 652 - 665
  08/05/2018 Authors: Wang L; Tang J; Huber AD; Casey MC; Kirby KA; Wilson DJ; Kankanala J; Xie J; Parniak MA; Sarafianos SG
• The Heteroaryldihydropyrimidine Bay 38-7690 Induces Hepatitis B Virus Core Protein Aggregates Associated with Promyelocytic Leukemia Nuclear Bodies in Infected Cells.
  mSphere Volume: 3
  04/25/2018 Authors: Huber AD; Wolf JJ; Liu D; Gres AT; Tang J; Boschert KN; Puray-Chavez MN; Pineda DL; Laughlin TG; Coonrod EM
• Design, synthesis and biological evaluations of N-Hydroxy thienopyrimidine-2,4-diones as inhibitors of HIV reverse transcriptase-associated RNase H.
  Eur J Med Chem Volume: 141 Page(s): 149 - 161
  12/01/2017 Authors: Kankanala J; Kirby KA; Huber AD; Casey MC; Wilson DJ; Sarafianos SG; Wang Z
• A 2-Hydroxyisoquinoline-1,3-Dione Active-Site RNase H Inhibitor Binds in Multiple Modes to HIV-1 Reverse Transcriptase.
  Antimicrob Agents Chemother Volume: 61
  10/01/2017 Authors: Kirby KA; Myshakina NA; Christen MT; Chen Y-L; Schmidt HA; Huber AD; Xi Z; Kim S; Rao RK; Kramer ST
• Impact of HIV-1 Integrase L74F and V75I Mutations in a Clinical Isolate on Resistance to Second-Generation Integrase Strand Transfer Inhibitors.
  Antimicrob Agents Chemother Volume: 61
  08/01/2017 Authors: Hachiya A; Kirby KA; Ido Y; Shigemi U; Matsuda M; Okazaki R; Imamura J; Sarafianos SG; Yokomaku Y; Iwatani Y
• Double-Winged 3-Hydroxypyrimidine-2,4-diones: Potent and Selective Inhibition against HIV-1 RNase H with Significant Antiviral Activity.
  J Med Chem Volume: 60 Page(s): 5045 - 5056
  06/22/2017 Authors: Vernekar SKV; Tang J; Wu B; Huber AD; Casey MC; Myshakina N; Wilson DJ; Kankanala J; Kirby KA; Parniak MA
• 3-Hydroxypyrimidine-2,4-Diones as Novel Hepatitis B Virus Antivirals Targeting the Viral Ribonuclease H.
  Antimicrob Agents Chemother Volume: 61
  06/01/2017 Authors: Huber AD; Michailidis E; Tang J; Puray-Chavez MN; Boftsi M; Wolf JJ; Boschert KN; Sheridan MA; Leslie MD; Kirby KA
• 6-Cyclohexylmethyl-3-hydroxypyrimidine-2,4-dione as an inhibitor scaffold of HIV reverase transcriptase: Impacts of the 3-OH on inhibiting RNase H and polymerase.
  Eur J Med Chem Volume: 128 Page(s): 168 - 179
  03/10/2017 Authors: Tang J; Kirby KA; Huber AD; Casey MC; Ji J; Wilson DJ; Sarafianos SG; Wang Z
• Structural basis of HIV inhibition by translocation-defective RT inhibitor 4'-ethynyl-2-fluoro-2'-deoxyadenosine (EFdA).
  Proc Natl Acad Sci U S A Volume: 113 Page(s): 9274 - 9279
  08/16/2016 Authors: Salie ZL; Kirby KA; Michailidis E; Marchand B; Singh K; Rohan LC; Kodama EN; Mitsuya H; Parniak MA; Sarafianos SG
• Design, Synthesis, and Biological Evaluations of Hydroxypyridonecarboxylic Acids as Inhibitors of HIV Reverse Transcriptase Associated RNase H.
  J Med Chem Volume: 59 Page(s): 5051 - 5062
  05/26/2016 Authors: Kankanala J; Kirby KA; Liu F; Miller L; Nagy E; Wilson DJ; Parniak MA; Sarafianos SG; Wang Z
• 3-Hydroxypyrimidine-2,4-diones as Selective Active Site Inhibitors of HIV Reverse Transcriptase-Associated RNase H: Design, Synthesis, and Biochemical Evaluations.
  J Med Chem Volume: 59 Page(s): 2648 - 2659
  03/24/2016 Authors: Tang J; Liu F; Nagy E; Miller L; Kirby KA; Wilson DJ; Wu B; Sarafianos SG; Parniak MA; Wang Z
• STRUCTURAL VIROLOGY. X-ray crystal structures of native HIV-1 capsid protein reveal conformational variability.
  Science Volume: 349 Page(s): 99 - 103
  07/03/2015 Authors: Gres AT; Kirby KA; KewalRamani VN; Tanner JJ; Pornillos O; Sarafianos SG
• Design, synthesis, biochemical, and antiviral evaluations of C6 benzyl and C6 biarylmethyl substituted 2-hydroxylisoquinoline-1,3-diones: dual inhibition against HIV reverse transcriptase-associated RNase H and polymerase with antiviral activities.
  J Med Chem Volume: 58 Page(s): 651 - 664
  01/22/2015 Authors: Vernekar SKV; Liu Z; Nagy E; Miller L; Kirby KA; Wilson DJ; Kankanala J; Sarafianos SG; Parniak MA; Wang Z
• Structural basis of clade-specific HIV-1 neutralization by humanized anti-V3 monoclonal antibody KD-247.
  FASEB J Volume: 29 Page(s): 70 - 80
  01/01/2015 Authors: Kirby KA; Ong YT; Hachiya A; Laughlin TG; Chiang LA; Pan Y; Moran JL; Marchand B; Singh K; Gallazzi F
• Drug resistance in non-B subtype HIV-1: impact of HIV-1 reverse transcriptase inhibitors.
  Viruses Volume: 6 Page(s): 3535 - 3562
  09/24/2014 Authors: Singh K; Flores JA; Kirby KA; Neogi U; Sonnerborg A; Hachiya A; Das K; Arnold E; McArthur C; Parniak M
• 4'-Ethynyl-2-fluoro-2'-deoxyadenosine (EFdA) inhibits HIV-1 reverse transcriptase with multiple mechanisms.
  J Biol Chem Volume: 289 Page(s): 24533 - 24548
  08/29/2014 Authors: Michailidis E; Huber AD; Ryan EM; Ong YT; Leslie MD; Matzek KB; Singh K; Marchand B; Hagedorn AN; Kirby KA
• SAMHD1 has differential impact on the efficacies of HIV nucleoside reverse transcriptase inhibitors.
  Antimicrob Agents Chemother Volume: 58 Page(s): 4915 - 4919
  08/01/2014 Authors: Huber AD; Michailidis E; Schultz ML; Ong YT; Bloch N; Puray-Chavez MN; Leslie MD; Ji J; Lucas AD; Kirby KA
• Effects of substitutions at the 4' and 2 positions on the bioactivity of 4'-ethynyl-2-fluoro-2'-deoxyadenosine.
  Antimicrob Agents Chemother Volume: 57 Page(s): 6254 - 6264
  12/01/2013 Authors: Kirby KA; Michailidis E; Fetterly TL; Steinbach MA; Singh K; Marchand B; Leslie MD; Hagedorn AN; Kodama EN; Marquez VE
• Evaluation of Combinations of 4'-Ethynyl-2-Fluoro-2'-Deoxyadenosine with Clinically Used Antiretroviral Drugs.
  Antimicrob Agents Chemother Volume: 57 Page(s): 4554 - 4558
  09/01/2013 Authors: Hachiya A; Reeve AB; Marchand B; Michailidis E; Ong YT; Kirby KA; Leslie MD; Oka S; Kodama EN; Rohan LC
• Hypersusceptibility mechanism of Tenofovir-resistant HIV to EFdA.
  Retrovirology Volume: 10 Page(s): 65
  06/24/2013 Authors: Michailidis E; Ryan EM; Hachiya A; Kirby KA; Marchand B; Leslie MD; Huber AD; Ong YT; Jackson JC; Singh K
• Restriction fragment mass polymorphism (RFMP) analysis based on MALDI-TOF mass spectrometry for detecting antiretroviral resistance in HIV-1 infected patients.
  Clin Microbiol Infect Volume: 19 Page(s): E263 - E270
  06/01/2013 Authors: Lee J-H; Hachiya A; Shin S-K; Lee J; Gatanaga H; Oka S; Kirby KA; Ong YT; Sarafianos SG; Folk WR
• Effect of translocation defective reverse transcriptase inhibitors on the activity of N348I, a connection subdomain drug resistant HIV-1 reverse transcriptase mutant.
  Cell Mol Biol (Noisy-le-grand) Volume: 58 Page(s): 187 - 195
  12/22/2012 Authors: Michailidis E; Singh K; Ryan EM; Hachiya A; Ong YT; Kirby KA; Marchand B; Kodama EN; Mitsuya H; Parniak MA
• Preparation of biologically active single-chain variable antibody fragments that target the HIV-1 gp120 V3 loop.
  Cell Mol Biol (Noisy-le-grand) Volume: 58 Page(s): 71 - 79
  12/22/2012 Authors: Ong YT; Kirby KA; Hachiya A; Chiang LA; Marchand B; Yoshimura K; Murakami T; Singh K; Matsushita S; Sarafianos SG
• HIV-1 reverse transcriptase (RT) polymorphism 172K suppresses the effect of clinically relevant drug resistance mutations to both nucleoside and non-nucleoside RT inhibitors.
  J Biol Chem Volume: 287 Page(s): 29988 - 29999
  08/24/2012 Authors: Hachiya A; Marchand B; Kirby KA; Michailidis E; Tu X; Palczewski K; Ong YT; Li Z; Griffin DT; Schuckmann MM
• Antiviral therapies: focus on hepatitis B reverse transcriptase.
  Int J Biochem Cell Biol Volume: 44 Page(s): 1060 - 1071
  07/01/2012 Authors: Michailidis E; Kirby KA; Hachiya A; Yoo W; Hong SP; Kim S-O; Folk WR; Sarafianos SG
• Structural and inhibition studies of the RNase H function of xenotropic murine leukemia virus-related virus reverse transcriptase.
  Antimicrob Agents Chemother Volume: 56 Page(s): 2048 - 2061
  04/01/2012 Authors: Kirby KA; Marchand B; Ong YT; Ndongwe TP; Hachiya A; Michailidis E; Leslie MD; Sietsema DV; Fetterly TL; Dorst CA
• Biochemical, inhibition and inhibitor resistance studies of xenotropic murine leukemia virus-related virus reverse transcriptase.
  Nucleic Acids Res Volume: 40 Page(s): 345 - 359
  01/01/2012 Authors: Ndongwe TP; Adedeji AO; Michailidis E; Ong YT; Hachiya A; Marchand B; Ryan EM; Rai DK; Kirby KA; Whatley AS
• Hepatitis B Virus genotypic differences map structurally close to NRTI resistance hot spots.
  Int J Curr Chem Volume: 2 Page(s): 253 - 260
  10/01/2011 Authors: Michailidis E; Singh K; Kirby KA; Hachiya A; Yoo W; Hong SP; Kim S-O; Folk WR; Sarafianos SG
• The sugar ring conformation of 4'-ethynyl-2-fluoro-2'-deoxyadenosine and its recognition by the polymerase active site of HIV reverse transcriptase.
  Cell Mol Biol (Noisy-le-grand) Volume: 57 Page(s): 40 - 46
  02/12/2011 Authors: Kirby KA; Singh K; Michailidis E; Marchand B; Kodama EN; Ashida N; Mitsuya H; Parniak MA; Sarafianos SG
• K70Q adds high-level tenofovir resistance to "Q151M complex" HIV reverse transcriptase through the enhanced discrimination mechanism.
  PLoS One Volume: 6 Page(s): e16242
  01/13/2011 Authors: Hachiya A; Kodama EN; Schuckmann MM; Kirby KA; Michailidis E; Sakagami Y; Oka S; Singh K; Sarafianos SG
• The N348I mutation at the connection subdomain of HIV-1 reverse transcriptase decreases binding to nevirapine.
  J Biol Chem Volume: 285 Page(s): 38700 - 38709
  12/03/2010 Authors: Schuckmann MM; Marchand B; Hachiya A; Kodama EN; Kirby KA; Singh K; Sarafianos SG
• Structural Aspects of Drug Resistance and Inhibition of HIV-1 Reverse Transcriptase.
  Viruses Volume: 2 Page(s): 606 - 638
  02/11/2010 Authors: Singh K; Marchand B; Kirby KA; Michailidis E; Sarafianos SG
• Mechanism of inhibition of HIV-1 reverse transcriptase by 4'-Ethynyl-2-fluoro-2'-deoxyadenosine triphosphate, a translocation-defective reverse transcriptase inhibitor.
  J Biol Chem Volume: 284 Page(s): 35681 - 35691
  12/18/2009 Authors: Michailidis E; Marchand B; Kodama EN; Singh K; Matsuoka M; Kirby KA; Ryan EM; Sawani AM; Nagy E; Ashida N