Preliminary Work

Fragment screening and HIV therapeutics

Fragment screening is reviewed, providing opportunities for discovery of novel anti-HIV drugs.

Bauman JD, Patel D & Arnold A. Top. Curr. Chem. 317 181-200 (2012)

PubMed PMID: 21972022

PubMedCentral PMCID: PMC3565459

Identification of HIV-1 Inhibitors Targeting the Nucleocapsid Protein

A high-throughput assay is used to discover drugs that block the action of HIV nucleocapsid

Breuer, S., Chang, M. W., Yuan, J. and Torbett, B. E. J. Med. Chem. 55, 4968-4977 (2012).

Pubmed PMID: 22587465

Pubmed Central PMCID: PMC3499629

HIV-1 Reverse Transcriptase Complex with DNA and Nevirapine Reveals Non-nucleoside Inhibition Mechanism

The crystal structures of reverse transcriptase with DNA and two types of inhibitors have been solved. The RT-DNA complex in the crystal could bind either the non-nucleoside inhibitor nevirapine or the nucleoside inhibitor AST-triphosphate, but not both. The structures reveal the complementary roles these different classes of inhibitor play in widely-used anti-AIDS therapies.

K. Das, S. E. Martinez & E. Arnold (2012) Nat. Struct. Mol. Biol. 19, 253-259.

Pubmed PMID: 22266819

Pubmed Central PMCID: PMC3359132

Retroviral Intasome Assembly and Inhibition of DNA Strand Transfer

The structure was solved of full-length retroviral integrase from prototype foamy virus in complex with its cognate DNA. The structure shows the organization of retroviral intasome , with an integrase tetramer tightly associated with a pair of viral DNA ends. The structure reveals the extensive protein-DNA and protein-protein interactions involved in retroviral integration, and provides a model for the HIV-1 intasome.

S. Hare, S. S. Gupta, E. Valkov, A. Engelman & P. Cherepanov (2010) Nature 464, 232-236.

Pubmed PMID: 20118915

Pubmed Central PMCID: PMC2837123

A comparison of the ability of rilpivirine (TMC278) and selected analogues to inhibit clinically relevant HIV-1 reverse transcriptase mutants.

A combination of structure activity relationships and X-ray crystallography was used to examine non-nucleoside reverse transcriptase inhibitors that are structurally related to rilpivirine to determine their ability to inhibit wildtype reverse transcriptase and several clinically relevant mutants.

Johnson BC, Pauly GT, Rai G, Patel D, Bauman JD, Baker HL, Das K, Schneider JP, Maloney DJ, Arnold E, Thomas CJ, Hughes SH. Retrovirology 9:99 (2012).

PubMed PMID: 23217210

PubMed Central PMCID: PMC3549755.

3D Molecular Models of Whole HIV-1 Virions Generated with CellPACK

Snapshot of the equilibrium dynamics of a drug bound to HIV-1 reverse transcriptase.

Fragment-Based Screen Against HIV Protease

Two new inhibitor binding sites were discovered on wild-type HIV protease using fragment-based screening techniques. Protease was cocrystallized or soaked with chemical fragments using five different crystal forms, and 378 data sets were collected. Fragment binding induces a new conformation and crystal form in protease with the active site inhibitor TL-3. This study is the first fragment-based crystallographic screen against HIV protease, revealing two new exosites that stabilize inhibitor binding at the active site.

A. L. Perryman, Q. Zhang, H. H. Soutter, R. Rosenfeld, D. E. McRee, A. J. Olson, J. E. Elder & C. D. Stout (2010) Chem Biol. Drug Des. 75, 257-268.

Pubmed PMID: 20659109

Pubmed Central PMCID: PMC2911974

Structural and Functional Insights into Alphavirus Polyprotein Processing and Pathogenesis

The alphavirus replication machinery consists of four nonstructural proteins produced as a single polyprotein. The structure has been solved of P23 in a precleavage form. The P2/3 cleavage site is located at the base of a narrow cleft and is not readily accessible, and the nsP2 protease active site is over 40 Angstroms away, supporting a regulated, trans cleavage mechanism.

G. Shin, S. A. Yost, M. T. Miller, E. J. Elrod, A. Grakoui & J. Marcotrigiano (2012) Proc. Natl. Acad. Sci. USA 109, 16534-16539.

Pubmed PMID: 23010928

Pubmed Central PMCID: PMC3478664

Theory of binless multi-state free energy estimation with applications to protein-ligand binding.

The paper describes a simplified technique for computing free energies and expectations from multiple ensembles.

Tan Z, Gallicchio E, Lapelosa M, Levy RM.  J Chem Phys. 136(14):144102 (2012).

PubMed PMID: 22502496

PubMed Central PMCID: PMC3339880.

Small Molecule Regulation of Protein Conformation by Binding in the Flap of HIV Protease