Crystal Structure of HIV‐1 Reverse Transcriptase Bound to a Non‐Nucleoside Inhibitor with a Novel Mechanism of Action

Freisz, Séverine; Bec, Guillaume; Radi, Marco; Wolff, Philippe; Crespan, Emmanuele; Angeli, Lucilla; Dumas, Philippe; Maga, Giovanni; Botta, Maurizio; Ennifar, Eric

doi:10.1002/ange.200905651

Cited by 10 publications

(16 citation statements)

References 16 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Our fragment screen and substructure analysis of one hit identified a total of seven active fragments that are chemically dissimilar to all other known HIV-1 RT inhibitors (Binding DB; www.bindingdb.org) (4,7,15), including those HIV-1 RT inhibitors identified in two previously published FBDD programs that used either SPR-based (16) or X-ray crystallography-based (6) screening. Three of the seven scaffolds that we identified have activities consistent with their ability to bind to sites distinct from the NNIBP on the HIV-1 RT, with one of these fragments inhibiting HIV-1 replication in cell culture at the reverse transcription step.…”

Section: Significancementioning

confidence: 99%

“…Supporting the Dixon plot analysis, we found that the IC 50 value of fragment 5 increased with increasing dNTP concentrations (Table S2). Competition with dNTPs suggests that oxime 5 binds at or near the polymerase active site, possibly to the allosteric binding pocket described for nucleotide-competing RT inhibitors (NcRTIs) (7) or another allosteric site. p-Hydroxyaniline 8 was shown to compete with the DNA T/P substrate using steady-state kinetic DDDP inhibition assays ( Fig.…”

Section: Chemical Similarity Search Of Hiv-1 Rt Inhibitor Database Rementioning

confidence: 99%

See 1 more Smart Citation

Identification of mechanistically distinct inhibitors of HIV-1 reverse transcriptase through fragment screening

Latham

Tinetti

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Fragment-based screening methods can be used to discover novel active site or allosteric inhibitors for therapeutic intervention. Using saturation transfer difference (STD) NMR and in vitro activity assays, we have identified fragment-sized inhibitors of HIV-1 reverse transcriptase (RT) with distinct chemical scaffolds and mechanisms compared to nonnucleoside RT inhibitors (NNRTIs) and nucleoside/ nucleotide RT inhibitors (NRTIs). Three compounds were found to inhibit RNA-and DNA-dependent DNA polymerase activity of HIV-1 RT in the micromolar range while retaining potency against RT variants carrying one of three major NNRTI resistance mutations: K103N, Y181C, or G190A. These compounds also inhibit Moloney murine leukemia virus RT but not the Klenow fragment of Escherichia coli DNA polymerase I. Steady-state kinetic analyses demonstrate that one of these fragments is a competitive inhibitor of HIV-1 RT with respect to deoxyribonucleoside triphosphate (dNTP) substrate, whereas a second compound is a competitive inhibitor of RT polymerase activity with respect to the DNA template/primer (T/P), and consequently also inhibits RNase H activity. The dNTP competing RT inhibitor retains activity against the NRTI-resistant mutants K65R and M184V, demonstrating a drug resistance profile distinct from the nucleotide competing RT inhibitors indolopyridone-1 (INDOPY-1) and 4-dimethylamino-6-vinylpyrimidine-1 (DAVP-1). In antiviral assays, the T/P competing compound inhibits HIV-1 replication at a step consistent with an RT inhibitor. Screening of additional structurally related compounds to the three fragments led to the discovery of molecules with improved potency against HIV-1 RT. These fragment inhibitors represent previously unidentified scaffolds for development of novel drugs for HIV-1 prevention or treatment.HIV | reverse transcriptase | fragment-based drug discovery | allosteric inhibitors | STD-NMR

show abstract

Section: Significancementioning

confidence: 99%

Section: Chemical Similarity Search Of Hiv-1 Rt Inhibitor Database Rementioning

confidence: 99%

Identification of mechanistically distinct inhibitors of HIV-1 reverse transcriptase through fragment screening

Latham

Tinetti

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…In contrast to Bauman et al [98], this group [100] then used biochemical assays to gather evidence about the mechanisms of action and possible binding sites on the enzyme for the top three fragment hits. Two of three fragments, 9 and 10, were shown to compete with the HIV-1 RT substrates, nucleotide and T/P, respectively, suggesting that these two compounds could be inhibiting the enzyme allosterically with fragment 9 likely acting at or near the polymerase active site, such as the NcRTI binding site [101] or another allosteric site. Fragment 10 was also shown to inhibit RNase H activity, although it is unclear whether inhibition of both polymerase and RNase H activities are the result of binding at one or more sites on RT.…”

Section: Fbdd Screening Against Hiv-1 Rt To Discover Novel Allostericmentioning

confidence: 99%

Fragment Based Strategies for Discovery of Novel HIV-1 Reverse Transcriptase and Integrase Inhibitors

Latham

Tinetti

et al. 2015

CTMC

View full text Add to dashboard Cite

Human immunodeficiency virus (HIV) remains a global health problem. While combined antiretroviral therapy has been successful in controlling the virus in patients, HIV can develop resistance to drugs used for treatment, rendering available drugs less effective and limiting treatment options. Initiatives to find novel drugs for HIV treatment are ongoing, although traditional drug design approaches often focus on known binding sites for inhibition of established drug targets like reverse transcriptase and integrase. These approaches tend towards generating more inhibitors in the same drug classes already used in the clinic. Lack of diversity in antiretroviral drug classes can result in limited treatment options, as cross-resistance can emerge to a whole drug class in patients treated with only one drug from that class. A fresh approach in the search for new HIV-1 drugs is fragment-based drug discovery (FBDD), a validated strategy for drug discovery based on using smaller libraries of low molecular weight molecules (<300 Da) screened using primarily biophysical assays. FBDD is aimed at not only finding novel drug scaffolds, but also probing the target protein to find new, often allosteric, inhibitory binding sites. Several fragment-based strategies have been successful in identifying novel inhibitory sites or scaffolds for two proven drug targets for HIV-1, reverse transcriptase and integrase. While any FBDD-generated HIV-1 drugs have yet to enter the clinic, recent FBDD initiatives against these two well-characterised HIV-1 targets have reinvigorated antiretroviral drug discovery and the search for novel classes of HIV-1 drugs.

show abstract

“…However, at variance with NNRTIs that were successfully co-crystallized with the free RT, attempts to co-crystallize INDOPY-1 with the unliganded RT failed [ 23 ], likely because it is highly specific for the binary RT/primer-template complex. Unlike INDOPY-1, DAVPs bind the unliganded RT in addition to the binary complex and DAVP-1 was successfully co-crystallized with the RT in absence of nucleic acids [ 47 ]. Obtained crystals revealed a novel crystal packing differing from previously-reported RT structures.…”

Section: Structural Biology Studies Of Ncrtismentioning

confidence: 99%

“…, in the presence of a stably bound dNTP), binding of DAVP-1 is unfavored [ 24 ]. The peculiar resistance profile observed for DAVP-1 suggests that it gains access to its novel binding site not through the same route of the incoming dNTPs, but using structural elements in common with the NNIBP [ 47 ]. In this respect, it has to be mentioned that the Y181 residue is located on the same structural element of the catalytic D185 and D186 and that its mutation (as in the case of the Y181I substitution) can induce resistance to NRTIs [ 69 ].…”

Section: Structural Biology Studies Of Ncrtismentioning

confidence: 99%

HIV-1 RT Inhibitors with a Novel Mechanism of Action: NNRTIs that Compete with the Nucleotide Substrate

Maga

Radi

Gérard

et al. 2010

Viruses

Self Cite

View full text Add to dashboard Cite

HIV-1 reverse transcriptase (RT) inhibitors currently used in antiretroviral therapy can be divided into two classes: (i) nucleoside analog RT inhibitors (NRTIs), which compete with natural nucleoside substrates and act as terminators of proviral DNA synthesis, and (ii) non-nucleoside RT inhibitors (NNRTIs), which bind to a hydrophobic pocket close to the RT active site. In spite of the efficiency of NRTIs and NNRTIs, the rapid emergence of multidrug-resistant mutations requires the development of new RT inhibitors with an alternative mechanism of action. Recently, several studies reported the discovery of novel non-nucleoside inhibitors with a distinct mechanism of action. Unlike classical NNRTIs, they compete with the nucleotide substrate, thus forming a new class of RT inhibitors: nucleotide-competing RT inhibitors (NcRTIs). In this review, we discuss current progress in the understanding of the peculiar behavior of these compounds.

show abstract

Crystal Structure of HIV‐1 Reverse Transcriptase Bound to a Non‐Nucleoside Inhibitor with a Novel Mechanism of Action

Cited by 10 publications

References 16 publications

Identification of mechanistically distinct inhibitors of HIV-1 reverse transcriptase through fragment screening

Identification of mechanistically distinct inhibitors of HIV-1 reverse transcriptase through fragment screening

Fragment Based Strategies for Discovery of Novel HIV-1 Reverse Transcriptase and Integrase Inhibitors

HIV-1 RT Inhibitors with a Novel Mechanism of Action: NNRTIs that Compete with the Nucleotide Substrate

Contact Info

Product

Resources

About