Difference of binding modes among three ligands to a receptor mSin3B corresponding to their inhibitory activities

A preceding experiment suggested that a compound, which inhibits binding of the REST/NRSF segment to the cleft of a receptor protein mSin3B, can be a potential drug candidate to ameliorate many neuropathies. We have recently developed an enhanced conformational sampling method, genetic-algorithm-guided multi-dimensional virtual-system-coupled canonical molecular dynamics, and in the present study, applied it to three systems consisting of mSin3B and one of three compounds, sertraline, YN3, and acitretin. Other preceding experiments showed that only sertraline inhibits the binding of REST/NRSF to mSin3B. The current simulation study produced the spatial distribution of the compounds around mSin3B, and showed that sertraline and YN3 bound to the cleft of mSin3B with a high propensity, although acitretin did not. Further analyses of the simulation data indicated that only the sertraline–mSin3B complex produced a hydrophobic core similar to that observed in the molecular interface of the REST/NRSF-mSin3B complex: An aromatic ring of sertraline sunk deeply in the mSin3B’s cleft forming a hydrophobic core contacting to hydrophobic amino-acid residues located at the bottom of the cleft. The present study proposes a step to design a compound that inhibits competitively the binding of a ligand to its receptor.

: (a) Complex structure of PAH1 domain and NRSF/REST. In this paper, the PAH1 domain of mSin3B is denoted simply as "mSin3B". Four helices, composing mSin3B, are denoted as 1-4. The "C" and "N" are respectively the N-and C-termini for each chain. Shown structure is a snapshot from a sampling simulation 1   Chemical structure of YN3. The ring is named as "head", and the opposite side of the ring as "tail" in this study. (right) Three reaction coordinates, (') , ()) , and (*) , are introduced in the YN3-mSin3B system.
(c) (left) Chemical structure of acitretin. The ring is named as "head", and the opposite side of the ring as "tail" in this study. (right) Three reaction coordinates, (') , ()) , and (*) , are introduced in the acitretin-mSin3B system. In each panel, four helices of mSin3B are indicated by "H1", "H2", "H3", and "H4" from the N-to C-terminal. Label "N" shows the position of the N-terminal of mSin3B. (') is defined by the distance between the center of mass of red-colored segments of mSin3B and that of blue-colored segment of mSin3B. ()) is defined by the distance between the center of mass of green-colored segments of mSin3B and that of purple-colored part of compound. (*) is defined by the distance between the center of mass of cyan-colored segments of mSin3B and that of orange-colored part of compound.

Supplementary Section 1. Definition of a reaction coordinate (RC).
Consider two atom groups , and , . (ℎ = , , , …) in a molecular system. The reaction coordinate (RC) (,) is defined by the distance between centers of mass of , and , . (Supplementary Figure S3). Superscripts and indicate simply that two atom groups are pairing to define (,) , and then, one can exchange the superscripts as: , -→ , . and , . → , without changing the value of (,) .  , which are pairing to define (,) . groups in mSin3B.

Supplementary Table S2. Parameters a) for RC-space division
] @EF P.
c) Zone width for each reaction coordinate (,) .

Supplementary Section 2. Restraints applied to the C-terminal tail of mSin3B.
We introduced distance-restraint energy, RS= , between a part of PAH1 domain of mSin3B and its C-terminal tail to prevent the C-terminal tail from being inserted into the binding cleft of PAH1 domain. The function form is: where A,Z and A,Z \ are the C atomic distance between residues and in a simulation snapshot and the reference complex structure (the NMR structure of the NRSF/REST-mSin3B complex; PDB ID: 2CZY), respectively, and ]^_ and gh specify tolerances set to 2.0 Å. Thus, no restraint ( ) is applied to the atom-pair distance A,Z when A,Z \ − ]^_ < A,Z < A,Z \ + gh . This distance restraint was applied to three C atomic distance pairs between Gly 92 and Asp 104, between Phe 93 and Ile 105, and between Asn 94 and Arg 106.

Supplementary Section 3. Parameters used.
The atom groups adopted for the current study to define the three RCs are given in Table  S1 of SI. Three RCs are illustrated in Figure S2 of SI.GA-guided mD-VcMD consists of iterative simulations, through which the conformational ensemble converges on an equilibrated one, mEB^( ) ( = (') , ()) , (*) ), at a simulation temperature (300 K) in the 3D-RC space. A thermodynamic weight is assigned to each of stored snapshots using mEB^( ) 2,3 . This means that a thermally equilibrated conformational ensemble (canonical ensemble) is obtained in the allowed RC space. Table S2 lists actual values of parameters which control the simulations: <= (ℎ), ] @EF , and ∆ (,) . Table S3 Table S2. d) Parameters for (*) are not shown because they are exactly the same as those for (') .

Supplementary Section 4. Spatial density of ligand's quantity.
The GA-guided mD-VcMD assigns a thermodynamic weight (statistical weight at equilibrium) to each sampled snapshot 2 . Here we present a method to calculate spatial distribution of the center of mass of the ligands around the receptor mSin3B. First, we divide the 3D real space into cubes, whose volume ∆ is 2 Å × 2 Å × 2 Å. The cube position is specified by its center = [ , , ]. Next, we calculate the geometrical center (GC) of the ligand for each snapshot, and assign the snapshot to a cube that involves the GC. Then, we assign all of the snapshots to cubes. Last, we calculate the spatial density The superscript is set to sertraline-mSin3B. (') , ()) , (*) • ≥ 0.01 relatively well in the last iteration for each system (the 14-th, 13-th, and 27 the iterations for the sertraline-mSin3B, YN3-mSin3B, and acitretin-mSin3B systems, respectively). . [2] Cyan contours, i.e., the equidensity region of     In the present study, we calculate the minimum heavy-atomic distance oe  Supplementary References.