PDBsum entry 3bgr

Transferase, hydrolase

PDB id: 3bgr

Contents

Protein chains

554 a.a.

412 a.a.

Ligands

T27

EDO

Waters ×475

References listed in PDB file

Key reference

Title

High-Resolution structures of HIV-1 reverse transcriptase/tmc278 complexes: strategic flexibility explains potency against resistance mutations.

Authors

K.Das, J.D.Bauman, A.D.Clark, Y.V.Frenkel, P.J.Lewi, A.J.Shatkin, S.H.Hughes, E.Arnold.

Ref.

Proc Natl Acad Sci U S A, 2008, 105, 1466-1471. [DOI no: 10.1073/pnas.0711209105]

PubMed id

18230722

Abstract

TMC278 is a diarylpyrimidine (DAPY) nonnucleoside reverse transcriptase inhibitor (NNRTI) that is highly effective in treating wild-type and drug-resistant HIV-1 infections in clinical trials at relatively low doses ( approximately 25-75 mg/day). We have determined the structure of wild-type HIV-1 RT complexed with TMC278 at 1.8 A resolution, using an RT crystal form engineered by systematic RT mutagenesis. This high-resolution structure reveals that the cyanovinyl group of TMC278 is positioned in a hydrophobic tunnel connecting the NNRTI-binding pocket to the nucleic acid-binding cleft. The crystal structures of TMC278 in complexes with the double mutant K103N/Y181C (2.1 A) and L100I/K103N HIV-1 RTs (2.9 A) demonstrated that TMC278 adapts to bind mutant RTs. In the K103N/Y181C RT/TMC278 structure, loss of the aromatic ring interaction caused by the Y181C mutation is counterbalanced by interactions between the cyanovinyl group of TMC278 and the aromatic side chain of Y183, which is facilitated by an approximately 1.5 A shift of the conserved Y(183)MDD motif. In the L100I/K103N RT/TMC278 structure, the binding mode of TMC278 is significantly altered so that the drug conforms to changes in the binding pocket primarily caused by the L100I mutation. The flexible binding pocket acts as a molecular "shrink wrap" that makes a shape complementary to the optimized TMC278 in wild-type and drug-resistant forms of HIV-1 RT. The crystal structures provide a better understanding of how the flexibility of an inhibitor can compensate for drug-resistance mutations.

Figure 2.
Binding mode of TMC278 to HIV-1 RT. (A) Interactions of TMC278 (gray) with NNRTI-binding pocket residues (in yellow). (B) The molecular surface (orange) defines the hydrophobic tunnel that accommodates the cyanovinyl group of TMC278.

Figure 4.
Comparison of L100I/K103N mutant RT (orange side chains)/TMC278 (cyan) structure with the wild-type RT (yellow side chains)/TMC278 (gray) structures reveals wiggling (A) and jiggling (B) of TMC278.

Secondary reference #1

Title

Crystal structures of clinically relevant lys103asn/tyr181cys double mutant HIV-1 reverse transcriptase in complexes with ATP and non-Nucleoside inhibitor hby 097.

Authors

K.Das, S.G.Sarafianos, A.D.Clark, P.L.Boyer, S.H.Hughes, E.Arnold.

Ref.

J Mol Biol, 2007, 365, 77-89. [DOI no: 10.1016/j.jmb.2006.08.097]

PubMed id

17056061

Figure 1.
Figure 1. Effects of the two mutations (Lys103Asn and Tyr181Cys) on the structure of unliganded HIV-1 RT. (a) A stereo view of the NNIBP region of the double mutant RT/ATP structure. The composite simulated annealing omit map (2|F[o]|–|F[c]|) electron density (cyan) contoured at 1.2σ defines the coordination of a Na ion at the NNIBP region; OW1 and OW2 are two water molecules. (b) The NNIBP region of the double mutant (Lys103Asn/Tyr181Cys) HIV-1 RT. The mutated amino acids have altered interactions with the surrounding amino acids. (c) The NNIBP region of the wild type unliganded HIV-1 RT structure.^13

Figure 2.
Figure 2. Binding mode of HBY 097 to the Lys103Asn/Tyr181Cys double mutant RT. (a) Stereo view of the (2|F[o]|–|F[c]|) electron density (contoured at 1.2σ) covering HBY 097 (cyan) and Cys181 (magenta). The dotted line represents the hydrogen bond between the thiol group of Cys181 and HBY 097. Electrostatic potential surface^62 showing the NNIBP region of (b) the double mutant RT/HBY 097 and (c) wild-type RT/HBY 097^13 structures.

The above figures are reproduced from the cited reference with permission from Elsevier

Secondary reference #2

Title

Roles of conformational and positional adaptability in structure-Based design of tmc125-R165335 (etravirine) and related non-Nucleoside reverse transcriptase inhibitors that are highly potent and effective against wild-Type and drug-Resistant HIV-1 variants.

Authors

K.Das, A.D.Clark, P.J.Lewi, J.Heeres, M.R.De jonge, L.M.Koymans, H.M.Vinkers, F.Daeyaert, D.W.Ludovici, M.J.Kukla, B.De corte, R.W.Kavash, C.Y.Ho, H.Ye, M.A.Lichtenstein, K.Andries, R.Pauwels, M.P.De béthune, P.L.Boyer, P.Clark, S.H.Hughes, P.A.Janssen, E.Arnold.

Ref.

J Med Chem, 2004, 47, 2550-2560. [DOI no: 10.1021/jm030558s]

PubMed id

15115397

Secondary reference #3

Title

Crystal structures of 8-Cl and 9-Cl tibo complexed with wild-Type HIV-1 rt and 8-Cl tibo complexed with the tyr181cys HIV-1 rt drug-Resistant mutant.

Authors

K.Das, J.Ding, Y.Hsiou, A.D.Clark, H.Moereels, L.Koymans, K.Andries, R.Pauwels, P.A.Janssen, P.L.Boyer, P.Clark, R.H.Smith, M.B.Kroeger smith, C.J.Michejda, S.H.Hughes, E.Arnold.

Ref.

J Mol Biol, 1996, 264, 1085-1100. [DOI no: 10.1006/jmbi.1996.0698]

PubMed id

9000632

Figure 1.
Figure 1. Chemical structures with the numbering scheme used and distances (E3.6 Å ) between atoms of the TIBO inhibitor and of the amino acid residues of the NNIBP for: (a) 8-Cl TIBO (R86183, tivirapine) complexed with wild- type HIV-1 RT; (b) 8-Cl TIBO complexed with Tyr181Cys mutant HIV-1 RT; and (c) 9-Cl TIBO (R82913) complexed with wild-type HIV-1 RT. An NNIBP residue is shown only if atoms of that residue are E3.6 Å from an inhibitor atom with the exception of Cys181 in (b). The wings I and II portions of the inhibitors in the butterfly-like anal- ogy for NNRTIs (Ding et al., 1995a) are indicated here and in sub- sequent Figures by Roman nu- merals I and II. The dotted line in (a) indicates the subdivision of atoms between wings I and II.

Figure 5.
Figure 5. A stereoview of the superposition (based on the C a atoms of the b6-b10-b9 sheet) of the HIV-1 RT/DNA/Fab complex structure (in gray) (Jacobo-Molina et al., 1993) on the HIV-1 RT/9-Cl TIBO complex structure (in cyan) in the regions near the NNIBP and the polymerase active site showing the disposition of the b12-b13-b14 sheet containing the primer grip. Bound 9-Cl TIBO in the HIV-1 RT/9-Cl TIBO complex is shown in gold and the two 3'-terminal nucleotides 17 and 18 of the primer strand in the HIV-1 RT/DNA/Fab complex are shown with a yellow ball-and-stick model. The broken line represents interactions between the primer grip and the primer terminal phosphate in the HIV-1 RT/DNA/Fab complex and the arrow indicates the movement of the primer grip that accompanies NNRTI binding.

The above figures are reproduced from the cited reference with permission from Elsevier

Secondary reference #4

Title

The lys103asn mutation of HIV-1 rt: a novel mechanism of drug resistance.

Authors

Y.Hsiou, J.Ding, K.Das, A.D.Clark, P.L.Boyer, P.Lewi, P.A.Janssen, J.P.Kleim, M.Rösner, S.H.Hughes, E.Arnold.

Ref.

J Mol Biol, 2001, 309, 437-445. [DOI no: 10.1006/jmbi.2001.4648]

PubMed id

11371163

Figure 3.
Figure 3. Stereoview of a SIGMAA weighted 2mFo - DFc difference Fourier map showing the electron density in the NNIBP region of p66 in the unliganded Lys103Asn mutant HIV-1 RT structure. The phases were computed from the final model at 2.7 Å resolution and the map was contoured at 2s. Selected hydrogen-bonding interactions are indicated with broken lines.

Figure 4.
Figure 4. Energy diagram for the binding of an NNRTI to wild-type and Lys103Asn mutant RT. The Lys103Asn mutant RT with the additional hydrogen bonding network in the NNIBP region is assumed to be more stable than wild-type HIV-1 RT. The relative stab- ility of wild-type and Lys103Asn mutant HIV-1 RT com- plexes with NNRTIs will depend on the inhibitor.

The above figures are reproduced from the cited reference with permission from Elsevier