Synthetic Bioactive Molecules Section
Section Chief: Daniel Appella, Ph.D.

Publications

A selection of recent and significant publications can be viewed below.

Select Publications

Preclinical evaluation of a mercaptobenzamide and its prodrug for NCp7-targeted inhibition of human immunodeficiency virus.
Hartman TL, Yang L, Helfrick AN, Hassink M, Shank NI, George Rosenker K, Scerba MT, Saha M, Hughes E, Wang AQ, Xu X, Gupta P, Buckheit RW Jr, Appella DH.
Antiviral Res (2016 Oct) 134:216-225. Abstract/Full Text
Reaction Kinetics Direct a Rational Synthesis of an HIV-1 Inactivator of Nucleocapsid Protein 7 and Provide Mechanistic Insight into Cellular Metabolism and Antiviral Activity.
Nikolayevskiy H, Scerba MT, Deschamps JR, Appella DH.
Chemistry (2018 Jul 5) 24:9485-9489. Abstract/Full Text
Programmable nanoscaffolds that control ligand display to a G-protein-coupled receptor in membranes to allow dissection of multivalent effects.
Dix AV, Moss SM, Phan K, Hoppe T, Paoletta S, Kozma E, Gao ZG, Durell SR, Jacobson KA, Appella DH.
J Am Chem Soc (2014 Sep 3) 136:12296-303. Abstract/Full Text
Probing Mercaptobenzamides as HIV Inactivators via Nucleocapsid Protein 7.
Saha M, Scerba MT, Shank NI, Hartman TL, Buchholz CA, Buckheit RW Jr, Durell SR, Appella DH.
ChemMedChem (2017 May 22) 12:714-721. Abstract/Full Text
Quantification of plasma HIV RNA using chemically engineered peptide nucleic acids.
Zhao C, Hoppe T, Setty MK, Murray D, Chun TW, Hewlett I, Appella DH.
Nat Commun (2014 Oct 6) 5:5079. Abstract/Full Text

Additional Publications

A trapped human PPM1A-phosphopeptide complex reveals structural features critical for regulation of PPM protein phosphatase activity.
Debnath S, Kosek D, Tagad HD, Durell SR, Appella DH, Acevedo R, Grishaev A, Dyda F, Appella E, Mazur SJ.
J Biol Chem (2018 May 25) 293:7993-8008. Abstract/Full Text
Chemical Features Important for Activity in a Class of Inhibitors Targeting the Wip1 Flap Subdomain.
Tagad HD, Debnath S, Clausse V, Saha M, Mazur SJ, Appella E, Appella DH.
ChemMedChem (2018 May 8) 13:894-901. Abstract/Full Text
6-Methoxyethylamino-numonafide inhibits hepatocellular carcinoma xenograft growth as a single agent and in combination with sorafenib.
Liu Y, Lou G, Norton JT, Wang C, Kandela I, Tang S, Shank NI, Gupta P, Huang M, Avram MJ, Green R, Mazar A, Appella D, Chen Z, Huang S.
FASEB J (2017 Dec) 31:5453-5465. Abstract/Full Text
A novel preventive strategy against HIV-1 infection: combinatorial use of inhibitors targeting the nucleocapsid and fusion proteins.
Yang Y, Zhu J, Hassink M, Jenkins LMM, Wan Y, Appella DH, Xu J, Appella E, Zhang X.
Emerg Microbes Infect (2017 Jun 7) 6:e40. Abstract/Full Text
Multivalent LKγ-PNA oligomers bind to a human telomere DNA G-rich sequence to form quadruplexes.
Gupta P, Rastede EE, Appella DH.
Bioorg Med Chem Lett (2015 Nov 1) 25:4757-4760. Abstract/Full Text
An Intravaginal Ring for the Simultaneous Delivery of an HIV-1 Maturation Inhibitor and Reverse-Transcriptase Inhibitor for Prophylaxis of HIV Transmission.
Ugaonkar SR, Clark JT, English LB, Johnson TJ, Buckheit KW, Bahde RJ, Appella DH, Buckheit RW Jr, Kiser PF.
J Pharm Sci (2015 Oct) 104:3426-39. Abstract/Full Text
G-quadruplex formation between G-rich PNA and homologous sequences in oligonucleotides and supercoiled plasmid DNA.
Gaynutdinov TI, Englund EA, Appella DH, Onyshchenko MI, Neumann RD, Panyutin IG.
Nucleic Acid Ther (2015 Apr) 25:78-84. Abstract/Full Text
PNA-Based Multivalent Scaffolds Activate the Dopamine D2 Receptor.
Dix AV, Conroy JL, George Rosenker KM, Sibley DR, Appella DH.
ACS Med Chem Lett (2015 Apr 9) 6:425-9. Abstract/Full Text
PPG peptide nucleic acids that promote DNA guanine quadruplexes.
Englund EA, Gupta P, Micklitsch CM, Onyshchenko MI, Remeeva E, Neumann RD, Panyutin IG, Appella DH.
Chembiochem (2014 Sep 5) 15:1887-90. Abstract/Full Text
Cyclopentane peptide nucleic acids.
Englund EA, Zhang N, Appella DH.
Methods Mol Biol (2014) 1050:13-8. Abstract/Full Text
Recognition of HIV-TAR RNA using neomycin-benzimidazole conjugates.
Ranjan N, Kumar S, Watkins D, Wang D, Appella DH, Arya DP.
Bioorg Med Chem Lett (2013 Oct 15) 23:5689-93. Abstract/Full Text
Novel inhibitors of a Grb2 SH3C domain interaction identified by a virtual screen.
Simister PC, Luccarelli J, Thompson S, Appella DH, Feller SM, Hamilton AD.
Bioorg Med Chem (2013 Jul 15) 21:4027-33. Abstract/Full Text
Cyclopentane-peptide nucleic acids for qualitative, quantitative, and repetitive detection of nucleic acids.
Micklitsch CM, Oquare BY, Zhao C, Appella DH.
Anal Chem (2013 Jan 2) 85:251-7. Abstract/Full Text
Click dimers to target HIV TAR RNA conformation.
Kumar S, Kellish P, Robinson WE Jr, Wang D, Appella DH, Arya DP.
Biochemistry (2012 Mar 20) 51:2331-47. Abstract/Full Text
Programmable multivalent display of receptor ligands using peptide nucleic acid nanoscaffolds.
Englund EA, Wang D, Fujigaki H, Sakai H, Micklitsch CM, Ghirlando R, Martin-Manso G, Pendrak ML, Roberts DD, Durell SR, Appella DH.
Nat Commun (2012 Jan 10) 3:614. Abstract/Full Text
Targeting DNA G-quadruplex structures with peptide nucleic acids.
Panyutin IG, Onyshchenko MI, Englund EA, Appella DH, Neumann RD.
Curr Pharm Des (2012) 18:1984-91. Abstract/Full Text
Combinatorial Synthesis, Screening, and Binding Studies of Highly Functionalized Polyamino-amido Oligomers for Binding to Folded RNA.
Pokorski JK, Appella DH.
J Nucleic Acids (2012) 2012:971581. Abstract/Full Text
Quadruplex formation is necessary for stable PNA invasion into duplex DNA of BCL2 promoter region.
Onyshchenko MI, Gaynutdinov TI, Englund EA, Appella DH, Neumann RD, Panyutin IG.
Nucleic Acids Res (2011 Sep 1) 39:7114-23. Abstract/Full Text
A one-pot preparation of N-2-mercaptobenzoyl-amino amides.
Bahde RJ, Appella DH, Trenkle WC.
Tetrahedron Lett (2011 Aug 10) 52:4103-4105. Abstract/Full Text
Optimization of a cyclic peptide inhibitor of Ser/Thr phosphatase PPM1D (Wip1).
Hayashi R, Tanoue K, Durell SR, Chatterjee DK, Jenkins LM, Appella DH, Appella E.
Biochemistry (2011 May 31) 50:4537-49. Abstract/Full Text
Methoxyethylamino-numonafide is an efficacious and minimally toxic amonafide derivative in murine models of human cancer.
Liu Y, Norton JT, Witschi MA, Xu Q, Lou G, Wang C, Appella DH, Chen Z, Huang S.
Neoplasia (2011 May) 13:453-60. Abstract/Full Text
Inhibition of multidrug resistance by SV40 pseudovirion delivery of an antigene peptide nucleic acid (PNA) in cultured cells.
Macadangdang B, Zhang N, Lund PE, Marple AH, Okabe M, Gottesman MM, Appella DH, Kimchi-Sarfaty C.
PLoS One (2011 Mar 22) 6:e17981. Abstract/Full Text
Small-molecule inactivation of HIV-1 NCp7 by repetitive intracellular acyl transfer.
Miller Jenkins LM, Ott DE, Hayashi R, Coren LV, Wang D, Xu Q, Schito ML, Inman JK, Appella DH, Appella E.
Nat Chem Biol (2010 Dec) 6:887-9. Abstract/Full Text
Solid-phase synthesis and screening of N-acylated polyamine (NAPA) combinatorial libraries for protein binding.
Iera JA, Jenkins LM, Kajiyama H, Kopp JB, Appella DH.
Bioorg Med Chem Lett (2010 Nov 15) 20:6500-3. Abstract/Full Text
Advantages of peptide nucleic acids as diagnostic platforms for detection of nucleic acids in resource-limited settings.
Zhang N, Appella DH.
J Infect Dis (2010 Apr 15) 201 Suppl 1:S42-5. Abstract/Full Text
Directed evolution: overcoming biology's limitations.
Appella DH.
Nat Chem Biol (2010 Feb) 6:87-8. Abstract/Full Text
Multivalent binding oligomers inhibit HIV Tat-TAR interaction critical for viral replication.
Wang D, Iera J, Baker H, Hogan P, Ptak R, Yang L, Hartman T, Buckheit RW Jr, Desjardins A, Yang A, Legault P, Yedavalli V, Jeang KT, Appella DH.
Bioorg Med Chem Lett (2009 Dec 15) 19:6893-7. Abstract/Full Text
Stabilization of G-quadruplex in the BCL2 promoter region in double-stranded DNA by invading short PNAs.
Onyshchenko MI, Gaynutdinov TI, Englund EA, Appella DH, Neumann RD, Panyutin IG.
Nucleic Acids Res (2009 Dec) 37:7570-80. Abstract/Full Text
Mimicking nature: from fundamentals to applications.
Waters ML, Appella DH.
Curr Opin Chem Biol (2009 Dec) 13:641-2. Abstract/Full Text
Non-natural nucleic acids for synthetic biology.
Appella DH.
Curr Opin Chem Biol (2009 Dec) 13:687-96. Abstract/Full Text
N-acylpolyamine inhibitors of HDM2 and HDMX binding to p53.
Hayashi R, Wang D, Hara T, Iera JA, Durell SR, Appella DH.
Bioorg Med Chem (2009 Dec 1) 17:7884-93. Abstract/Full Text
Induction of apoptosis promoted by Bang52; a small molecule that downregulates Bcl-x(L).
Rossi M, Bang JK, Mazur S, Iera JA, Phillips DC, Zambetti GP, Appella DH.
Bioorg Med Chem Lett (2009 May 1) 19:2429-34. Abstract/Full Text
Aziridination of aliphatic alkenes catalyzed by N-heterocyclic carbene copper complexes.
Xu Q, Appella DH.
Org Lett (2008 Apr 3) 10:1497-500. Abstract/Full Text
A small molecular scaffold for selective inhibition of Wip1 phosphatase.
Bang J, Yamaguchi H, Durell SR, Appella E, Appella DH.
ChemMedChem (2008 Feb) 3:230-2. Abstract/Full Text
Synthesis and anticancer activities of 6-amino amonafide derivatives.
Norton JT, Witschi MA, Luong L, Kawamura A, Ghosh S, Stack MS, Sim E, Avram MJ, Appella DH, Huang S.
Anticancer Drugs (2008 Jan) 19:23-36. Abstract/Full Text
Colorimetric detection of anthrax DNA with a Peptide nucleic acid sandwich-hybridization assay.
Zhang N, Appella DH.
J Am Chem Soc (2007 Jul 11) 129:8424-5. Abstract/Full Text
Introduction of a triazole amino acid into a peptoid oligomer induces turn formation in aqueous solution.
Pokorski JK, Jenkins LM, Feng H, Durell SR, Bai Y, Appella DH.
Org Lett (2007 Jun 7) 9:2381-3. Abstract/Full Text
Gamma-substituted peptide nucleic acids constructed from L-lysine are a versatile scaffold for multifunctional display.
Englund EA, Appella DH.
Angew Chem Int Ed Engl (2007) 46:1414-8. Abstract/Full Text
PNA-DNA duplexes, triplexes, and quadruplexes are stabilized with trans-cyclopentane units.
Englund EA, Xu Q, Witschi MA, Appella DH.
J Am Chem Soc (2006 Dec 27) 128:16456-7. Abstract/Full Text
Practical synthesis of trans-tert-butyl-2-aminocyclopentylcarbamate and resolution of enantiomers.
Xu Q, Appella DH.
J Org Chem (2006 Oct 27) 71:8655-7. Abstract/Full Text
Probing the structural requirements of peptoids that inhibit HDM2-p53 interactions.
Hara T, Durell SR, Myers MC, Appella DH.
J Am Chem Soc (2006 Feb 15) 128:1995-2004. Abstract/Full Text
Peptide nucleic acid microarrays made with (S,S)-trans-cyclopentane-constrained peptide nucleic acids.
Witschi MA, Pokorski JK, Appella DH.
Methods Enzymol (2006) 410:189-200. Abstract/Full Text
A new family of small molecules to probe the reactivation of mutant p53.
Myers MC, Wang J, Iera JA, Bang JK, Hara T, Saito S, Zambetti GP, Appella DH.
J Am Chem Soc (2005 May 4) 127:6152-3. Abstract/Full Text
Enhanced oligonucleotide binding to self-assembled nanofibers.
Guler MO, Pokorski JK, Appella DH, Stupp SI.
Bioconjug Chem (2005 May-Jun) 16:501-3. Abstract/Full Text
Cyclopentane-modified PNA improves the sensitivity of nanoparticle-based scanometric DNA detection.
Pokorski JK, Nam JM, Vega RA, Mirkin CA, Appella DH.
Chem Commun (Camb) (2005 Apr 28) 2101-3. Abstract/Full Text