2013 Research Highlights

Detecting allosteric sites of HIV-1 reverse transcriptase by X-ray crystallographic fragment screening

New sites for the design of inhibitors are discovered throughout the structure of HIV RT.

Bauman JD, Patel D, Dharia C, Fromer MW, Ahmed S, Frenkel Y, Vijayan RSK, Eck JT, Ho WC, Das K, Shatkin AJ & Arnold E. J. Med. Chem. 56, 2738-2746 (2013)

PubMed PMID: 23342998

PubMedCentral PMCID: PMC3906421

Rapid deep sequencing of patient-derived HIV with ion semiconductor technology

Ion Torrent devices are used for deep sequencing of drug resistant HIV samples, yielding high levels of sequencing coverage in HIV Gag and protease, and allowing the detection of mutations at low frequencies.

Chang MW, Oliveira G, Yuan J, Okulicz JF, Levy S, Torbett BE.  J Virol Methods. 189(1):232-4 (2013).

PubMed PMID: 23384677

PubMed Central PMCID: PMC3608812.

HIV-1 reverse transcriptase and antiviral drug resistance

A discussion of the current state of understanding of RT structure and function, and mechanisms of drug resistance.

Part 1: Das K & Arnold E. Curr. Op. Virol. 3, 119-128 (2013)

PubMed PMID: 23602471

PMCID: PMC4097814

Part 2: Das K & Arnold E. Curr. Op. Virol. 3, 119-128 (2013)

PubMed PMID: 23602470

PubMedCentral PMCID: PMC4097817

Allosteric Inhibition of HIV-1 Integrase Activity

A review of progress with the development of allosteric integrase inhibitors (ALLINIs) that compete with LEDGF/p75 for binding to integrase, disrupting viral maturation and inhibiting integrase function.

Engelman, A., Kessl, J. J. & Kvaratskhelia, M. Curr. Op. Chem. Biol. 17, 339-345 (2013)

PubMed PMID: 23647983

PubMed Central PMCID: PMC3679204

The A128T Resistance Mutation Reveals Aberrant Protein Multimerization as the Primary Mechanism of Action of Allosteric HIV-1 Integrase Inhibitors

­Evaluation of Combinations of 4′-Ethynyl-2-Fluoro-2′-Deoxyadenosine with Clinically Used Antiretroviral Drugs

Multimodal mechanism of action of allosteric HIV-1 integrase inhibitors

A review of the action of ALLINIs and their use in study of integrase function in the HIV life cycle.

Jurado KA & Engelman A. Expert Rev. Mol. Med. 15, e14 (2014).

PubMed PMID: 24274067

PMCID: PMC3919682

Allosteric Integrase Inhibitor Potency is Determined Through the Inhibition of HIV-1 Particle Maturation

Effects of Substitutions at the 4′ and 2 Positions on the Bioactivity of 4′-Ethynyl-2-Fluoro-2′-Deoxyadenosine

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

Spectroscopy, crystallography and computer simulation are used to probe the dynamics of HIV RT when interacting with rilpivirine.

Kuroda DG, Bauman JD, Challa JR, Patel D, Troxler T, Das K, Arnold J & Hochstrasser RM. Nature Chem. 5, 174-181 (2013).

PubMed PMID: 23422558

PubMedCentral PMCID: PMC3607437

Hypersusceptibility Mechanism of Tenofovir-Resistant HIV to EFdA

AutoDrug: fully automated macromolecular crystallography workflows for fragment-based drug screening

HIVE researchers have developed software that automates the entire process of crystallographic fragment screening for the discovery of inhibitors.

Tsai Y, McPhillips SE, Gonzalez A, McPhillips TM, Zinn D, Cohen AE, Feese MD, Bushnell D, Tiefenbrunn T, Stout CD, Ludaescher B, Hedman B, Hodgson KO & Soltis SM. Acta Cryst. D69, 796-803 (2013).

PubMed PMID: 23633588

PubMedCentral PMCID: PMC3640469

Viral precursor polypeptides: key of regulation from replication to maturation

Four recent structures of viral polyprotein precursors are reviewed.

Yost SA & Marcotrigiano J. Curr. Op. Virol. 3, 137-142 (2013).

PubMed PMID: 23602469

PubMedCentral PMCID: PMC3660988