Objective

To determine if some of the uncyclized Ugi products synthesized in our experiments dock with the malarial enoyl reductase active site located in chain B of the protein (1p45-q1.pdb).

Procedure

Using THINK (Sean)

The molecules docked in this experiment are the diketopiperazines with 1-(5-methylfurfuryl)- and 3-H substituents constant, with the 6- aromatic substituents on the ring varying as phenyl, piperonyl, 3,4-dimethoxyphenyl, and 3,4-dihydroxyphenyl with the chirality in this position as either R or S. The uncyclized forms will also be run to testing docking ability in both their Boc-protected as well as deprotected form, with the chirality specified at the variable aromatic group as with R or S, and inclusion of the leaving group (from the isocyanide used) as either benzyl or t-butyl. Some of the starting materials are also going to be attempted to be docked to see if they show any activity, including the aldehydes, amines, imines. SMILES obtained from this site, in which the structures of the molecules were drawn and submitted to the online translator. The SMILES codes were used as is.

The molecules were all opened in THINK, then saved as a .sdf.(DEXP005.sdf) They were run as a 3D site search with the settings of 4 centers, and a tolerance value of 1 and 0.5.

Using FlexX (Tan)

Tan - please include a brief summary of the procedure used with FlexX

Results

Using THINK

Raw .sdf's:
(Filename key in .sdf's: A=phenyl derivative, B=3,4-dihydroxyphenyl, C=3,4-dimethoxyphenyl, D=piperonyl, R or S for the chirality, tBu or Bz for isocyanide group, cycl=cyclized, uncycl=uncyclized, BOC indicates presence of Boc protecting group)

4 Centers, tolerance 0.5 (Docked 2 out of 40 molecules) see docking in Jmol compared to triclosan (Tan)
4 Centers, tolerance 1 (Docked 18 out of 40 molecules) see docking in Jmol (Tan)

The components of the Ugi sysnthesis are listed, the molecules' chirality at the generated stereocenter, and whether or not the product has been cyclized and/or Boc protected; along with it's docking free energy score:
(Notes: 5-MFA=5-methylfurfuryl amine and ICN=isocyanide, for page formatting purposes. Also, Isocyanide groups are not contained on the cyclized structure and are just listed as a component.)

Interaction data will also be included.

4 Centers, tolerance 0.5:
3,4-dihydroxybenzaldehyde, benzyl ICN, Boc-Gly-OH, 5-MFA; R, uncyclized, deprotected G= -17.676
3,4-dihydroxybenzaldehyde, t-butyl ICN, Boc-Gly-OH, 5-MFA; R, uncyclized, protected G= -22.606

4 Centers, tolerance 1:
3,4-dihydroxybenzaldehyde, benzyl ICN, Boc-Gly-OH, 5-MFA; R, cyclized, G= -29.186
3,4-dihydroxybenzaldehyde, benzyl ICN, Boc-Gly-OH, 5-MFA; R, uncyclized, deprotected G= -42.035
3,4-dihydroxybenzaldehyde, benzyl ICN, Boc-Gly-OH, 5-MFA; R, uncyclized, protected G= -25.449
3,4-dihydroxybenzaldehyde, t-butyl ICN, Boc-Gly-OH, 5-MFA; R, uncyclized, deprotected G= -32.813
3,4-dihydroxybenzaldehyde, t-butyl ICN, Boc-Gly-OH, 5-MFA; R, uncyclized, protected G= -37.443
3,4-dihydroxybenzaldehyde, benzyl ICN, Boc-Gly-OH, 5-MFA; S, uncyclized, deprotected G= -42.312
3,4-dihydroxybenzaldehyde, t-butyl ICN, Boc-Gly-OH, 5-MFA; S, uncyclized, deprotected G= -37.723
3,4-dihydroxybenzaldehyde, t-butyl ICN, Boc-Gly-OH, 5-MFA; S, uncyclized, protected G= -33.426
3,4-dimethoxybenzaldehyde, benzyl ICN, Boc-Gly-OH, 5-MFA; R, uncyclized, deprotected G= -13.935
3,4-dimethoxybenzaldehyde, t-butyl ICN, Boc-Gly-OH, 5-MFA; R, uncyclized, deprotected G= -8.067
3,4-dimethoxybenzaldehyde, t-butyl ICN, Boc-Gly-OH, 5-MFA; S, uncyclized, deprotected G= -22.367
piperonal, benzyl ICN, Boc-Gly-OH, 5-MFA; R, cyclized, G= -28.495
piperonal, benzyl ICN, Boc-Gly-OH, 5-MFA; R, uncyclized, deprotected G= -16.998
piperonal, t-butyl ICN, Boc-Gly-OH, 5-MFA; R, uncyclized, deprotected G= -6.645
piperonal, t-butyl ICN, Boc-Gly-OH, 5-MFA; R, uncyclized, protected G= -19.805
piperonal, benzyl ICN, Boc-Gly-OH, 5-MFA; S, uncyclized, deprotected G= -34.407
piperonal, t-butyl ICN, Boc-Gly-OH, 5-MFA; S, uncyclized, deprotected G= -38.001
piperonal, t-butyl ICN, Boc-Gly-OH, 5-MFA; S, uncyclized, protected G= -38.305

Using FlexX

  1. View Results on Jmol

Discussion

  1. Running 4 centers and a tolerance of 0.5, 2 molecules docked. Running 4 centers and a tolerance of 1, 18 of the molecules docked. The docking site that was used by THINK is near that for triclosan.
  2. With THINK, none of the phenyl control molecules docked, which supports the necessity of the oxygens on the aromatic ring for the 4 center docking at the triclosan site. However, some of the phenyl molecules did dock at a more shallow site.
  3. With THINK. at tolerance=1, at least Alicia's isolated Ugi product docked.
  4. Using FlexX, the deprotected Ugi products (R and S) that Alicia prepared in EXP062 are shown here to dock in a similar fairly shallow location, different from the triclosan site. (DRuncycltBu and DSuncycltBu) Others, like the catechol derivative BRuncycltBu bind deep into the pocket.

Conclusions

Some of the uncyclized Ugi products synthesized from the usefulchem library have been shown to dock into the triclosan binding site of malarial enoyl reductase using THINK. Pending: Using FlexX, 30 of the 40 molecules docked, although at different binding sites. For future reference, the use of a positive control (triclosan) and a negative control should be used for comparison if possible.





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