HIV Interaction and Viral Evolution Center Research

Research Highlights

The central theme of the HIVE Center is to further our structural and functional knowledge of HIV assembly, maturation, reverse transcription, and integration with the human host with the goal of determining the atomic resolution structures and the dynamic mechanisms of the macromolecular complexes involved in these processes. The ultimate aim is to relate this knowledge to the evolution of drug resistance and to the improvement of drug design methodologies in the treatment of HIV infected individuals.

This page includes publications from the HIVE Center (as compiled by NIH Reporter). Links are provided to the journal publication, the abstract at Pubmed, and in many cases, a free version of the full publication at Pubmed Central. Note that for some of the most recent articles, the Pubmed Central version may be embargoed by the journal for up to a year.

2017 Research Highlights

Physiological Mg2+ conditions significantly alter the inhibition of HIV-1 and HIV-2 reverse transcriptases by nucleoside and non-nucleoside inhibitors in vitro

The efficacy of RT inhibitors is dramatically affected by the level of magnesium, unscoring the need to test inhibitors using physiological conditions.

Achuthan B, Singh K & DeStefano JJ. Biochem. 56, 33-46 (2017).

PubMed PMID: 27936595

2017Achuthan

An experimental check of backscattering interferometry

HIVE Center researchers validate BSI, a powerful method for rapid measuring of association constants.

Baksh MM & Finn MG. Sensors Actuators B 243, 9770981 (2017)

2017Baksh

RiboCAT: a new capillary electrophoresis data analysis tool for nucleic acid probing

A new software package streamlines the analysis of data that probes the structure of RNA.

Cantara WA, Hatterschide J, Wu W & Musier-Forsyth. RNA, 23, 240-249 (2017)

PubMed PMID: 27821510

PMCID: PMC5238798 [Available on 2018-02-01]

2016Cantara2

Analysis of RNA structure using small-angle X-ray scattering

A review of best practices for using SAXS to determine the tertiary structure of RNA under physiological conditions.

Cantara WA, Olson ED & Musier-Forsyth K. Methods , 113, 46-55 (2017)

PubMed PMID: 27777026

PMCID: PMC5253320 [Available on 2018-01-15]

2016Cantara

Multidimensional SuFEx click chemistry: sequential sulfur(VI) fluoride exchange connection of diverse modules launched from an SOF4 hub.

A new family of transformations allow click chemistry connections between diverse chemical modules, including linkages between small molecules and protein sidechains.

Li S, Wu P, Moses JE & Sharpless KB. Angewandte Chemie, epub ahead of press (2017).

PubMed PMID: 28165188

2017 Li

Cryo-EM structures and atomic model of the HIV-1 strand transfer complex intasome

Cryo-EM reveals tetrameric and higher-order assemblies of integrase within the HIV-1 intasome.

Passos DO, Li M, Yang R, Rebensburg SV, Jeon Y, Shkriabai N, Kvaratskhelia M, Craigie R & Lyumkis D. Science 355, aah5163 (2017)

PubMed PMID: 28059769

2017Passos

2016 Research Highlights

Cryo-EM reveals a novel octameric integrase structure for betaretroviral intasome function

An unexpected octameric structure for a retroviral intasome is revealed using single-particle cryo-electron microscopy.

Ballandras-Colas A, Brown M, Cook NJ, Dewdney T, Demeler B, Cherepanov P, Lyumkis D & Engelman AN. Nature 530, 358-361 (2016)

PubMed PMID: 26887496

PubMed Central PMCID: PMC4908968

2016 Ballandras

Rapid experimental SAD phasing and hot-spot identification with halogenated fragments

Small molecules with halogens are shown to be an effective new tool for solving the phase problem in x-ray crystallography.

Bauman JD, Harrison JJEK & Arnold E IUCrJ 3, 51-60 (2016)

PubMed PMID: 26870381

PubMedCentral PMCID: PMC4704079

2016 Bauman et al.

Fragment-based analysis of ligand dockings improves classification of actives

Results from virtual screening are analyzed to improve ranking of compounds for discovery of new inhibitors.

Belew RK, Forli S, Goodsell DS, O'Donnell TJ & Olson AJ J Chem. Inf. Model. 56, 1597-1607 (2016)
PubMed PMID: 27384036

PubMedCentral PMCID: 5023760 (embargoed until Aug 2017)

2016 Belew

Conformational states of HIV-1 reverse transcriptase for nucleotide incorporation vs pyrophosphorolysis--binding of foscarnet

A DNA aptamer is used to trap complexes of reverse transcriptase in a new structural state, providing insights for developing new inhibitors.

Das K, Balzarini J, Miller MT, Maguire AR, DeStefano JJ & Arnold E ACS Chem. Biol. 11, 2158-2164 (2016).

PubMed PMID: 27192549

PubMedCentral PMCID: PMC4992415 (embargoed until August 2017)

2016 Das

Allosteric HIV-1 integrase inhibitors promote aberrant protein multimerization by directly mediating inter-subunit interactions: structure and thermodynamic modeling studies

ALLINIs stabilize the interaction between integrase catalytic domains and C-terminal domains, causing aggregation that impares virus maturation.

Deng N, Hoyte A, Mansour YE, Mohamed MS, Fuchs JR, Engelman AN, Kvaratskhelia M & Levy R Prot. Sci. (Epub)

PubMed PMID: 27503276

PMCID: PMC5079246 [Available on 2017-11-01]

2016 Deng

The competitive interplay between allosteric HIV-1 integrase inhibitor BI/D and LEDGF/p75 during the early stage of HIV-1 replication adversely affects inhibitor potency

Binding of the cellular protein LEDGF/p17 blocks the multimerization of HIV-1 integrase by an ALLINI, reducing the inhibitor's antiviral activity.

Feng L, Dharmarajan V, Serrao E, Hoyte A, Larue RC, Slaughter A, Sharma A, Plumb MR, Kessl JJ, Fuchs JR, Bushman FD, Engelman AN, Griffin PR & Kvaratskhelia M. ACS Chem. Biol. 11, 1313-1321 (2016).

PubMed PMID: 26910179

PubMedCentral PMCID: PMC4874862

2016 Feng

Virological failure in patients with HIV-1 subtype C receiving antiretroviral therapy: an analysis of a prospective national cohort in Sweden

Analysis of clinical data reveals that patients with HIV-1C may have an increased risk of virological failure.

Haggblom A, Svedhem V, Singh K, Sonnerborg A & Neogi U. Lancet HIV 3, e166-174 (2016).

Pubmed PMID: 27036992

2016Haggblom

HIV-1 integrase binds the viral RNA genome and is essential during virion morphogenesis

A new role of integrase in formation of infectious HIV-1 particles is discovered.

Kessl JJ, Kutluay SB, Townsend D, Rebensburg S, Slaughter A, Larue RC, Shkriabai N, Bakouche N, Fuchs JR, Bienaisz PD & Kvaratshelia M Cell 166, 1257-1268 (2016)

PubMed PMID: 27565348

PubMedCenter PMCID: PMC5003418 (embargoed until August 2017)

2016 Kessl

Binding energy distribution analysis method: Hamiltonian replica exchange with torsional flattening for binding mode prediction and binding free energy estimation

A new method for broadening the reach of a computational search provides better estimates of an inhibitor's effectiveness.

Mentes A, Deng JN, Vijayan RSK, Xia J, Gallicchio E & Levy RM J. Chem. Theory Comput. 12, 2459-2470 (2016).

PubMed PMID: 27070865

PubMedCentral PMCID: PMC4862910 (embargoed until May 2017)

2016 Mentes

Structure of HIV-1 reverse transcriptase bound to a novel 38-mer hairpin template-primer DNA aptamer

A DNA aptamer is used to determine the structure of reverse transcriptase without the need for crosslinking or a Fab.

Miller MT, Tuske S, Das K, DeStefano JJ & Arnold E. Prot. Sci. 25, 46-55 (2016).

PubMed PMID: 26296781

PubMedCentral PMCID: 4815302 (embargoed until January 2017)

HIV-1 RT and aptamer

Factors influencing the efficacy of rilpivirine in HIV-1 subtype C in low- and middle-income countries

The development of resistance limits the use of rilpivirine as a first-line drug in HIV-1C-dominated epidemics.

Neogi U, Haggblom A, Singh K, Rogers LC, Rao SD, Amogne W, Schulter E, Zazzi M, Arnold E, Sarafionos SG & Sonnerborg A J. Antimicrob. Chemother. 71, 367-371 (2016).

PubMed PMID: 26518047

PubMedCentral PMCID: PMC4710214

2016 Neogi

A new class of allosteric HIV-1 integrase inhibitors identified by crystallographic fragment screening of the catalytic core domain

HIVE researchers have discovered a new lead for design of integrase inhibitors, which shows improved action against resitant mutants

Patel D, Antwi J, Koneru PC, Serrao E, Forli S, Kessl JJ, Fenk L, Deng N, Levy RM, Fuchs JR, Olson AJ, Engelman AN, Bauman JD, Kvaratskhelia M & Arnold E. J Biol Chem epub ahead of print (2016)

PubMed PMID: 27645997

PMCID: PMC5095411 [Available on 2017-11-04]

2016 Patel

Structural basis of HIV inhibition by translocation-defective RT inhibitor 4'-ethynyl-2-fluoro-2'-deoxyadenosine (EFdA)

HIVE researchers reveal the mechanism of action of the most potent nucleoside analog inhibitor of HIV reverse transcriptase.

Salie ZL, Kirby KA, Michailidis E, Marchand B, Singh K, Rohan LC, Kodama EN, Mitsuya H, Parniak MA & Sarafianos SG. Proc Natl Acad Sci USA 113, 9274-9279 (2016)

PubMed PMID: 27489345

PubMed Central PMCID: PMC4995989 [Available on 2017-02-16]

2016 Salie

Locally weighted histogram analysis and stochastic solution for large-scale multi-state free energy estimation

A fast and accurate new method for estimating binding free energies is reported.

Tan Z, Xia J, Zhang BW & Levy RM J. Chem. Phys. 144, 034107 (2016)

PubMed PMID: 26801020

PubMedCentral PMCID: PMC4729400 (embargoed until January 2017)

2016 Tan

Role of cysteines in stabilizing the randomized receptor binding domains within feline leukenia virus envelope proteins

Envelope protein is retargeted by addition of new cysteine amino acids.

Valdivieso-Torres L, Sarangi A, Whidby J, Marcotrigiano J & Roth MJ. J Virol 90, 2971-2980 (2016)

PubMed PMID: 26719270

PubMed Central PMCID: PMC4810629

2016 Valdevieso

Chemoselective synthesis of polysubstituted pyridines from hetroaryl fluorosulfates

A selective new method is reported for creating inhibitors with polysubstituted pyridines

Zhang E, Tang J, Li S, Wu P, Moses JE & Sharpless KB Chem. Eur. J. 22, 5692-5697 (2106)

PubMed PMID: 26990693

PubMedCentral PMCID: PMC4929982 (embargoed until April 2017)

2016 Zhang
HIV and Antibodies
Balzarini 2015

Distinguishing Binders from False Positives by Free Energy Calculations: Fragment Screening against the Flap Site of HIV Protease

The Binding Energy Distribution Analysis Method improves discrimination of binders and nonbinders in virtual screening results against HIV protease.

Deng, N., Forli, S., He, P., Perryman, A., Wickstrom, L., Vijayan, R. S., Tiefenbrunn, T., Stout, D., Gallicchio, E., Olson, A. J., and Levy, R. M., J Phys Chem B 119, 976-988 (2015).

Pubmed PMID: 25189630

PubMedCentral PMCID: PMC4306491

image

Deep Sequencing of Protease Inhibitor Resistant HIV Patient Isolates Reveals Patterns of Correlated Mutations in Gag and Protease

Deep sequencing of viruses from 93 patients has revealed mutations in Gag proteins contribute to recurrent treatment failure.

Flynn WF, Chang MW, Tan Z, Oliveira G, Yuan J, Okulicz JF, Torbett BE, Levy RM. PLoS Comput Biol. 11, e1004249 (2015).

PubMed PMID: 25894830

PubMed Central PMCID: PMC4404092

Flynn2105

Distribution and redistribution of HIV-1 nucleocapsid in immature, mature, and integrase-inhibited virions: a role for integrase in maturation

An important role of integrase in packaging of the HIV-1 genome is revealed.

Fontana J, Jurado KA, Cheng N, Ly NL, Fuchs JR, Gorelick RJ, Engelman AN & Steven AC. J. Virol. 89, 9765-9780 (2015).

PubMed PMID: 26178982

PubMed Central PMCID: PMC4577894

2015 Fontana

Asynchronous replica exchange software for grid and heterogenous computing

Methods for performing molecular dynamics simulations on large clusters of computers are presented.

Gallicchio E, Xia J, Flynn WF, Zhang B, Samlalsingh S, Mentes A & Levy RM. Comp. Phys. Commun. 196, 236-246 (2015)

PubMed PMID: 27103749

PubMed Central PMCID: PMC4834714

2015 Gallicchio

Differential isotopic enrichment to facilitate characterization of asymmetric multimeric proteins using hydrogen/deuterium exchange mass spectrometry

By labeling the two subunits of reverse transcriptase with different isotopes of nitrogen, the subunits may be distinguished in hydrogen/deuterium exchange experiments.

Goswami D, Tuske S, Pascal BD, Bauman JD, Patel D, Arnold E, Griffin PR. Anal Chem 87, 4015-22 (2015).

PubMed PMID: 25763479

PubMedCentral PMCID: PMC4445842

Goswami 2015

X-ray structures of native HIV-1 capsid protein reveal conformational variability

A crystallographic structure of full-length HIV-1 capsid shows new variability in capsid assembly.

Gres, AT, Kirby, KA, KewalRamani VN, Tanner JJ, Pornillos O & Sarafianos SG. Science 349, 99-103 (2015).

PubMed PMID: 26044298

PubMedCentral PMCID: PMC4584149

HIV capsid structure

Pronounced inhibition shift from HIV reverse transcriptase to herpetic DNA polymerases by increasing the flexibility of alpha-carboxy nucleotide phosphates.

A new class of polymerase inhibitors is tuned to target different viruses.

John J, Kim Y, Bennett N, Das K, Liekens S, Naesens L, Arnold E, Maguire AR, Gotte M, Dehaen W & Balzarini J. J Med Chem 58, 8110-8127 (2015)

PubMed PMID: 26450273

PubMed Central PMCID: PMC4893804

2015 John

CellPACK: A Virtual Mesoscope to Model and Visualize Structural Systems Biology

A new method for creating 3D models of cellular systems is applied to the analysis of envelope glycoprotein distribution in HIV.

Johnson, G. T., Autin, L., Al-Alusi, M., Goodsell, D. S., Sanner, M. F., and Olson, A. J., Nat Methods 12, 85-91 (2015).

Pubmed PMID: 25437435

PubMedCentral PMCID: PMC4281296

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HCV glycoprotein structures: what to expect from the unexpected

Recent structural insights into the envelope glycoproteins of hepatitis C virus are reviewed.

Khan AG, Miller MT, Marcotrigiano J Curr Opin Virol 12, 53-58 (2015).

PubMed PMID: 25790756

PubMedCentral PMCID: PMC4505365

Khan 250

Structural basis of clade-specific HIV-1 neutralization by humanized anti-V3 monoclonal antibody KD-247

Structure of an antibody that binds to HIV envelope glycoprotein reveals an unusual mode of interaction centered around the light chain of the antibody.

Kirby KA, Ong YT, Hachiya A, Laughlin TG, Chiang LA, Pan Y, Moran JL, Marchand B, Singh K, Gallazzi F, Quinn TP, Yoshimura K, Murakami T, Matsushita S, Sarafianos SG. FASEB J 29, 70-80 (2015).

PubMed PMID: 25351987

PubMed Central PMCID: PMC4285544

kirby 2105

Fast hepatitis C virus RNA elimination and NS5A redistribution by NS5A inhibitors studied by multiplex assay approach

A new method is presented to assess the effectiveness of novel inhibitors of hepatitis C virus.

Liu D, Ji J, Ndongwe TP, Michallidis E, Rice CM, Ralston R & Sarafianos SG. Antimicrobial Agents Chemotherapy 59, 3482-3492 (2015)

PubMed PMID: 25845863

PubMed Central PMCID: PMC4432190

2015 Liu

Synthesis and properties of 2'-deoxy-2',4'-difluoroarabinose-modified nucleic acids

A modified nucleoside is used to build RNA strands that are more resistant to degradation, for use in gene silencing applications.

Martínez-Montero S, Deleavey GF, Dierker-Viik A, Lindovska P, Ilina T, Portella G, Orozco M, Parniak MA, González C, Damha MJ. J Org Chem 80, 3083-91 (2015).

PubMed PMID: 25723361

PubMedCentral PMCID: PMC4484724

MartinezMontero 2015

New structure sheds light on selective HIV-1 genomic RNA packaging

HIVE members review current work probing the structure and function of the HIV genome.

Olson ED, Cantara WA & Musier-Forsyth K. Viruses 7, 4826-4835 (2015)

PubMed PMID: 26305251

PubMed Center PMCID: PMC4576207

2015 Olson

CoVaMa: Co-variation Mapper for disequilibrium analysis of mutant loci in viral populations using next-generation sequence data

A new method has been developed to analyze linked variations in large sequence datasets from viral populations.

Routh A, Chang MW, Okulicz JF, Johnson JE & Torbett BE. Methods 91, 40-47 (2015)

PubMed PMID: 26408523

PubMed Central PMCID: PMC4684750

2015 Routh

Structural integrity of the ribonuclease H domain in HIV-1 reverse transcriptase

The role of several mutations in the folding of reverse transcriptase is revealed.

Slack RL, Spiriti J, Ahn J, Parniak MA, Zuckerman DM & Ishima R. Proteins Struct Funct Bioinform 83, 1526-1538 (2015)

PubMed PMID: 26061827

PubMed Central PMCID: PMC4509971

2015 Slack

Design, synthesis, biochemical, and antiviral evaluations of C6 benzyl and C6 biarylmethyl substituted 2-hydroxylisoquinoline-1,3-diones: dual inhibition agains HIV reverse transcriptase-associated RNase H and polymerase with antiviral activities

Inhibitors that block the RNase H site of reverse transcriptase have been discovered.

Vernekar SKV, Liu Z, Nagy E, Miller L, Kirby KA, Wilson DJ, Kankanala J, Sarafianos SG, Parniak MA & Wang Z. J. Med. Chem. 58, 651-664 (2015).

PubMed PMID: 25522204

PubMedCentral PMCID: PMC4306517

2015Vernekar

Role of the mammalian target of rapamycin pathway in lentiviral vector transduction of hematopoietic stem cells

Rapamycin improves lentiviral delivery of genes to hematopoietic stem cells.

Wang CX & Torbett BE. Curr Opin Hematol 22, 302-308 (2015)

PubMed PMID: 26049750

PubMed Central PMCID: PMC4688901

2015 Wang

Large-scale asynchronous and distributed multidimensional replical exchange molecular simulations and efficiency analysis

New methods are developed for rapid molecular dyamics simulations on large clusters of computers.

Xia J, Flynn WF, Gallicchio E, Zhang BW, He P, Tan Z & Levy RM. J Comput Chem 36, 1772-1785 (2015)

Pubmed PMID: 26149645

PubMed Central PMCID: PMC4512903

2015 Xia

2014 Research Highlights

Mutations in HIV-1 reverse transcriptase affect the errors made in a single cycle of viral replication

Drug resistant forms of reverse transcriptase are shown to cause an unusual pattern of errors during viral replication.

Abram ME, Ferris AL, Das K, Quinoñes O, Shao W, Tuske S, Alvord WG, Arnold E, Hughes SH. J Virol 88, 7589-601 (2014).

PubMed PMID: 24760888

PubMed Central PMCID: PMC4054409
Abram 2015

Antiviral drugs specific for coronaviruses in preclinical development

This review describes new inhibitors for SARS and MERS coronaviruses.

Adedeji AO, Sarafianos SG. Curr Opin Virol 8, 45-53 (2014).

PubMed PMID: 24997250

PubMed Central PMCID: PMC4195804

Adedeji 104

Evaluation of SSYA10-001 as a replication inhibitor of severe acute respiratory syndrome, mouse hepatitis, and Middle East respiratory syndrome coronaviruses

An inhibitor has been discovered that inhibits replication of three coronaviruses.

Adedeji AO, Singh K, Kassim A, Coleman CM, Elliott R, Weiss SR, Frieman MB, Sarafianos SG. Antimicrob Agents Chemother 58, 4894-8 (2014).

PubMed PMID: 24841268

PubMed Central PMCID: PMC4136041

Adedeji 2014 2

Undesired versus design enzymatic cleavage of linkers for liver targeting

A novel chemical method for selective release of drug molecules is presented.

Chirapu SR, Bauman JN, Eng H, Goosen TC, Strelevitz TJ, Sinha SC, Dow RL & Finn MG. Bioorg. Med. Chem. Lett. 24, 1144-1147 (2014).

PubMed PMID: 24461291

PubMedCentral PMCID: PMC4319531

2014CHirapu

Structures of HIV-1 RT-RNA/DNA Ternary Complexes with dATP and Nevirapine Reveal Conformational Flexibility of RNA/DNA: Insights into Requirements for RNase H Cleavage

Changes in the conformation of DNA and RNA may be important in the cleavage of RNA strands by RT.

Das, K., Martinez, S. E., Bandwar, R. P., and Arnold, E., Nucleic Acids Res 42, 8125-8137 (2014).

Pubmed PMID: 24880687

Pubmed Central PMCID: PMC4081091

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Virtual Screening of Integrase Inhibitors by Large Scale Binding Free Energy Calculations: The SAMPL4 Challenge

The Binding Energy Distribution Analysis Method improves discrimination of binders and nonbinders in a docking challenge of inhibitors to integrase.

Gallicchio, E., Deng, N., He, P., Wickstrom, L., Perryman, A. L., Santiago, D. N., Forli, S., Olson, A. J., and Levy, R. M., J Comput Aided Mol Des 28, 475-490 (2014).

Pubmed PMID: 24504704

Pubmed Central PMCID: PMC4137862

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Advances in Targeting Nucleocapsid-Nucleic Acid Interactions in HIV-1 Therapy

The authors review approaches for fighting HIV with drugs that block the functions of nucleocapsid protein.

Garg, D. and Torbett, B. E., Virus Res. 193, 135-143 (2014).

Pubmed PMID: 25026536

Pubmed Central PMCID: PMC4252855

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Structure of a dihydroxycoumarin active-site inhibitor in complex with the RNase H domain of HIV-1 reverse transcriptase and structure-activity analysis of inhibitor analogs

A new chemical scaffold has been validated for the design of HIV RNase H inhibitors.

Himmel DM, Myshankina NS, Ilina T, Van Ry A, Ho WC, Parniak MA & Arnold E. J. Mol. Biol. 426, 2617-2631 (2014).

PubMed PMID: 24840303

PubMedCentral PMCID: PMC4116331

2014Himmel

SAMHD1 has differential impact on the efficacies of HIV nucleoside reverse transcriptase inhibitors

SAMHD1 is an enzyme that cleaves the nucleotides needed for HIV replication, but is shown to be less active against nucleotide reverse transcriptase inhibitors.

Huber AD, Michailidis E, Schultz ML, Ong YT, Bloch N, Puray-Chavez MN, Leslie  MD, Ji J, Lucas AD, Kirby KA, Landau NR, Sarafianos SG. Antimicrob Agents Chemother 58, 4915-9 (2014).

PubMed PMID: 24867973

PubMed Central PMCID: PMC4136039

Huber 2014

Structure of the core ectodomain of the hepatitis C virus envelope glycoprotein 2

The structure of the envelope glycoprotein of hepatitis C virus provides a new target for development of inhibitors and vaccines.

Khan AG, Whidby J, Miller MT, Scarborough H, Zatorski AV, Cygan A, Price AA, Yost SA, Bohannon CD, Jacob J, Grakoui A, Marcotrigiano J. Nature 509, 381-4 (2014).

PubMed PMID: 24553139

PubMed Central PMCID: PMC4126800

Khan 2014

Molecular Mechanisms of Retroviral Integration Site Selection

HIVE researchers review the process of site selection in retroviral integration.

Kvaratskhelia, M., Sharma, A., Larue, R. C., Serrao, E., and Engelman, A., Nucleic Acids Res 42, 10209-10225 (2014).

Pubmed PMID: 25147212

Pubmed Central PMCID: PMC4176367

image

HDX-MS guided drug discovery: small molecules and biopharmaceuticals

HIVE Center researchers review methods for integrating HDX-MS into drug discovery programs.

Marciano DP, Dharmarajan V & Griffin PR. Curr Op Struct Biol 28, 105-111 (2014)

PubMed PMID: 25179005

PubMed Central PMCID: PMC4253076

2014 Marciano

4'-Ethynyl-2-Fluoro-2'-Deoxyadenosine (Efda) Inhibits Hiv-1 Reverse Transcriptase with Multiple Mechanisms

EFdA blocks HIV RT by several mechanisms, making it an effective antiviral agent with a favorable resistance profile.

Michailidis, E., Huber, A. D., Ryan, E. M., Ong, Y. T., Leslie, M. D., Matzek, K. B., Singh, K., Marchand, B., Hagedorn, A. N., Kirby, K. A., Rohan, L. C., Kodama, E. N., Mitsuya, H., Parniak, M. A., and Sarafianos, S. G., J Biol Chem 289, 24533-24548 (2014).

Pubmed PMID: 24970894

Pubmed Central PMCID: PMC4148878

image
image

Probing the molecular mechanism of action of the HIV-1 reverse transcriptase inhibitor 4'-ethynyl-2-fluoro-2'-deoxyadenosine (EFdA) using pre-steady-state kinetics

The inhibitor EFdA is added to a growing DNA chain by reverse transcriptase, then slows further extension of the DNA chain.

Muftuoglu Y, Sohl CD, Mislak AC, Mitsuya H, Sarafianos SG, Anderson KS. Antiviral Res 106, 1-4 (2014).

PubMed PMID: 24632447

PubMed Central PMCID: PMC4020981

Muftuoglu 2014

Ruthenium-catalyzed cycloaddition of 1-haloalkynes with nitrile oxides and organic azides; Synthesis of 4-halo isoxazoles and 5-halo triazoles

A new method is presented for inhibitor synthesis using click chemistry.

Oakdale JS, Sit RK & Fokin VV. Chemistry 20, 11101-11110 (2014)

PubMed PMID: 25059647

PubMedCentral PMCID:PMC4442801

Oakdale 2014

Advantages of crystallographic fragment screening: functional and mechanistic insights from a powerful platform for efficient drug discovery

The authors review a powerful method for using crystallography to discover new inhibitors.

Patel D, Bauman JD, Arnold E. Prog Biophys Mol Biol 116, 92-100 (2014).

PubMed PMID: 25117499

PubMedCentral PMCID: PMC4501029

Patel 2014

Virtual Screening with AutoDock Vina and the Common Pharmacophore Engine of a Low Diversity Library of Fragments and Hits against the Three Allosteric Sites of HIV Integrase: Participation in the SAMPL4 Protein-Ligand Binding Challenge

HIVE members perform well in a docking challenge to predict the binding of inhibitors to integrase.

Perryman, A. L., Santiago, D. N., Forli, S., Santos-Martins, D., and Olson, A. J., J Comput Aided Mol Des 28, 429-441 (2014).

Pubmed PMID: 24493410

Pubmed Central PMCID: PMC4053500

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Phenyl substituted 4-hydroxypyridazine-3(2H)-ones and 5-hydroxypyridazin-4(3H)-ones: inhibitors of influenza A endonuclease

Inhibitors are tuned for action against influenza virus.

Sagong HY, Bauman JD, Patel D, Das K, Arnold E & Lavoie EJ. J. Med. Chem. 57, 8086-8098 (2014).

PubMed PMID: 25225968

PubMedCentral PMCID: PMC4191602

2014Sagong
image

A Critical Role of the C-Terminal Segment for Allosteric Inhibitor-Induced Aberrant Multimerization of HIV-1 Integrase

Mass spectrometry-based protein footprinting reveals that the C-terminal segment of integrase is important in multimerization by ALLINIs.

Shkriabai, N., Dharmarajan, V., Slaughter, A., Kessl, J. J., Larue, R. C., Feng, L., Fuchs, J. R., Griffin, P. R., and Kvaratskhelia, M., J Biol Chem 289, 26430-26440 (2014).

Pubmed PMID: 25118283

Pubmed Central PMCID: PMC4176244

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Drug Resistance in Non-B Subtype HIV-1: Impact of HIV-1 Reverse Transcriptase Inhibitors

HIVE members review how polymorphisms, transmission efficiency of drug-resistant strains, and differences in genetic barrier for drug resistance can differentially alter the response to reverse transcriptase-targeting therapies in various subtypes.

Singh, K., Flores, J. A., Kirby, K. A., Neogi, U., Sonnerborg, A., Hachiya, A., Das, K., Arnold, E., McArthur, C., Parniak, M., and Sarafianos, S. G., Viruses 6, 3535-3562 (2014).

Pubmed PMID: 25254383

Pubmed Central PMCID: PMC4189038

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The Mechanism of H171T Resistance Reveals the Importance of N Inverted Question Mark -Protonated His171 for the Binding of Allosteric Inhibitor Bi-D to HIV-1 Integrase

The atomic basis of ALLINI resistance is revealed by crystallography.

Slaughter, A., Jurado, K. A., Deng, N., Feng, L., Kessl, J. J., Shkriabai, N., Larue, R. C., Fadel, H. J., Patel, P. A., Jena, N., Fuchs, J. R., Poeschla, E., Levy, R. M., Engelman, A., and Kvaratskhelia, M., Retrovirology 11, 100 (2014).

Pubmed PMID: 25421939

Pubmed Central PMCID: PMC4251946

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Crystallographic Fragment-Based Drug Discovery: Use of a Brominated Fragment Library Targeting HIV Protease

Brominated compounds are used to determine the position of small molecules bound to the HIV protease exosites.

Tiefenbrunn, T., Forli, S., Happer, M., Gonzalez, A., Tsai, Y., Soltis, M., Elder, J. H., Olson, A. J., and Stout, C. D., Chem Biol Drug Des 83, 141-148 (2014).

Pubmed PMID: 23998903

Pubmed Central PMCID: PMC3898673

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Molecular dynamics study of HIV-1 RT-DNA-nevirapine complexes explains NNRTI inhibition and resistance by connection mutations

Computational analysis gives new insight into the dynamic coupling of subdomains in RT, and their implications for drug resistance.

Vijayan RSK, Arnold E & Das K. Proteins 82, 815-829 (2014).

PubMed PMID: 24174331

PubMedCentral PMCID: PMC4502926

2014Vijayan

Rapamycin relieves lentiviral vector transduction resistance in human and mouse hematopoietic stem cells

Potential treatments for HIV infection using genetically-modified hematopoietic stem cells may be enhanced with rapamycin.

Wang CX, Sather BD, Wang X, Adair J, Khan I, Singh S, Lang S, Adams A, Curinga G, Kiem HP, Miao CH, Rawlings DJ & Torbett BE. Blood 124, 913-923 (2014)

PubMed PMID: 24914132

PubMed Central PMCID: PMC4126331

2014 Wang

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

2013Bauman

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

2013Das

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

A new resistance mutation in HIV integrase reveals an unexpected mechanism for action for integrase inhibitors.

Feng L, Sharma A, Slaughter A, Jena N, Koh Y, Shkriabai N, Larue RC, Patel PA, Mitsuya H, Kessl JJ, Engelman A, Fuchs JR, Kvaratskhelia M.J Biol Chem. 288, 15813-20 (2013).

PubMed PMID: 23615903

PubMed Central PMCID: PMC3668738

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

The potent antiviral activity of EfdA is found to be synergistic with rilpivirine.

Hachiya, A., Reeve, A. B., Marchand, B., Michailidis, E., Ong, Y. T., Kirby, K. A., Leslie, M. D., Oka, S., Kodama, E. N., Rohan, L. C., Mitsuya, H., Parniak, M. A., and Sarafianos, S. G., Antimicrob Agents Chemother (2013).

Pubmed PMID: 23796932

Pubmed Central PMCID: PMC3754316

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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

2013 Jurado

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

Allosteric integrase inhibitors, originally developed to block viral integration, are also surprisingly found to be potent inhibitors of viral maturation.

Jurado, K. A., Wang, H., Slaughter, A., Feng, L. Kessl, J. J., Koh, Y., Wang, W., Ballandras-Colas, A., Patel, P. A., Fuchs, J. R., Kvaratskhelia, M. & Engelman, A. PNAS 110, 8690-8695 (2013)

PubMed PMID: 23610442

PubMed Central PMCID: PMC3666754.



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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

2013Kuroda
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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

2013Tsai

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

2013Yost

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

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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

Methods for creating 3D models of mature HIV are presented.

Johnson, G. T., Goodsell, D. S., Autin, L., Forli, S., Sanner, M. F., and Olson, A. J., Faraday Discuss 169, 23-44 (2014).

Pubmed PMID: 25253262

PubMedCentral PMCID: PMC4569901
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Snapshot of the equilibrium dynamics of a drug bound to HIV-1 reverse transcriptase.

Femtosecond experiments and theory expose the molecular level dynamics of rilpivirine bound to HIV-1 RT.

Kuroda DG, Bauman JD, Challa JR, Patel D, Troxler T, Das K, Arnold E, Hochstrasser RM.  Nat Chem. 5(3):174-81 (2013)

PubMed PMID: 23422558

PubMed Central PMCID: PMC3607437.

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

Crystallographic structures of two small indoles reveal a binding site that favors a closed conformation of the HIV protease flaps.

T. Tiefenbrunn, S. Forli, M. M. Baksh, M. W. Chang, M. Happer, Y.-C. Lin, A. L. Perryman, J.-K. Rhee, B. E. Torbett, A. J. Olson, J. H. Elder, M. G. Finn & C. D. Stout. ACS Chem Biol 8, 1223-1231 (2013)

PubMed PMID: 23540839

Pubmed Central PMCID: PMC3769432