A Maltose-Binding Protein Fusion Construct Yields a Robust Crystallography Platform for MCL1

<div><p>Crystallization of a maltose-binding protein MCL1 fusion has yielded a robust crystallography platform that generated the first apo MCL1 crystal structure, as well as five ligand-bound structures. The ability to obtain fragment-bound structures advances structure-based drug design efforts that, despite considerable effort, had previously been intractable by crystallography. In the ligand-independent crystal form we identify inhibitor binding modes not observed in earlier crystallographic systems. This MBP-MCL1 construct dramatically improves the structural understanding of well-validated MCL1 ligands, and will likely catalyze the structure-based optimization of high affinity MCL1 inhibitors.</p></div

The structure of Apo MBP-MCL1 determined at 1.90 Å.

<p>(A) The MBP domain (red) is connected by a short GS linker (orange) to MCL1 173–321 (blue). A portion of alpha helix four is not ordered in the structure (red dashed-line). Maltose ligand is shown in yellow. (B) The MCL1 domain is structurally very similar to the NMR structure of Apo-MCL1 (gray).</p

Comparison of PDB 4HW3 and MBP-MCL1 with fragment 4.

<p>The structure of MBP-MCL1 with fragment <b>4</b> (yellow) determined to 2.4 Å (blue) overlaid with the structure of MCL1 171–323 determined at 2.4 Å (PDB ID 4HW3, gray). The carboxylic acid of 4HW3 adopts multiple conformations depending on the chain; only chain A is shown for clarity.</p

Binding affinity (K_D) of ligands to MCL1 and MBP-MCL1.

<p>All experiments are n ≥ 3, and averaged values for K_D are reported.</p><p>Binding affinity (K_D) of ligands to MCL1 and MBP-MCL1.</p

MCL1 ligands used in co-crystallization experiments.

<p>MCL1 ligands used in co-crystallization experiments.</p

The structure of MBP-MCL1 bound to fragment 5 determined at 1.9 Å.

<p>Fragment <b>5</b> (yellow) binds similarly in comparison to the elaborated ligand from PDB ID 4OQ6 (gray).</p

The conformational flexibility of the binding pocket of MCL1.

<p>Surface representations are shown as side views and ligands are shown as yellow sticks. (A and B) Fragment 4 maps onto L78 of NoxaB from PDB ID 2NLA, with only minor structural perturbation of the BH3-binding groove of MCL1. In contrast, binding of fragment 6 creates a significant pocket (C) which is further expanded upon binding of ligand 1 (D).</p

Structure of MBP-MCL1 bound to fragment 6 determined at 2.0 Å.

<p>(A) The surface side-view shows that fragment <b>6</b> shifts and makes water mediated hydrogen bond contacts with the peptide backbone of R263. (B) The elaborated ligand of fragment <b>6</b> (PDB ID 4OQ5) shifts to allow the methyl-naphthalene to bind in the hydrophobic pocket, requiring the carboxylic acid to make a single hydrogen bond with the sidechain of R263. (C) Overlay of crystallized fragment <b>6</b> and the elaborated ligand in PDB ID 4OQ5 reveals a distinct binding pose for <b>6</b>.</p

Crystal packing of MCL1 173–321 is mediated by zinc and pyrophosphate.

<p>(A) The structure of MCL1 173–321 was determined to 1.70 Å. (B) In the ligand-bound MCL1 173–321 structure, the imidazole group of <b>1</b> coordinates with zinc along with H224 and pyrophosphate.</p

Comparison of PDB 4HW2 and MBP-MCL1 with ligand 2.

<p>The structure of MBP-MCL1 with ligand <b>2</b> (yellow) determined to 1.55 Å (blue) overlaid with the structure of MCL1 171–323 determined at 2.4 Å (PDB ID 4HW2, gray).</p