PDBsum entry 1if8

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Lyase PDB id
Protein chain
258 a.a. *
Waters ×67
* Residue conservation analysis

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Key reference
Title Combinatorial computational method gives new picomolar ligands for a known enzyme.
Authors B.A.Grzybowski, A.V.Ishchenko, C.Y.Kim, G.Topalov, R.Chapman, D.W.Christianson, G.M.Whitesides, E.I.Shakhnovich.
Ref. Proc Natl Acad Sci U S A, 2002, 99, 1270-1273. [DOI no: 10.1073/pnas.032673399]
PubMed id 11818565
Combinatorial small molecule growth algorithm was used to design inhibitors for human carbonic anhydrase II. Two enantiomeric candidate molecules were predicted to bind with high potency (with R isomer binding stronger than S), but in two distinct conformations. The experiments verified that computational predictions concerning the binding affinities and the binding modes were correct for both isomers. The designed R isomer is the best-known inhibitor (K(d) approximately 30 pM) of human carbonic anhydrase II.
Figure 1.
Fig. 1. (A) illustrates the principle of the CombiSMoG algorithm. The design begins with specifying a starting molecular fragment (dark green) within the binding region of the protein (light green); this fragment can be as small as a single hydrogen atom, or can consist of several heavy atoms. In the first step, a functional group (dark blue) from a diverse library of 100 common organic groups is joined by a single bond to the starting fragment. The new fragment is rotated around the newly formed bond in increments of 60°, and the conformation without steric clashes and with the lowest CombiSMoG score (which has the meaning of free energy) is chosen. The CombiSMoG score g per heavy atom of the newly formed molecule g[n] is compared with that of the starting fragment g[s]. If the difference in scores g = g[n] g[s] is less than zero, the newly formed molecule is always accepted, and if it is greater than zero, the probability of acceptance is proportional to exp( g/T). The above sequence is repeated for each new fragment added to the currently accepted structure. The ligands are grown until a stop condition (usually a maximum number of heavy atoms) is matched. The structures and CombiSMoG scores of the five top-scoring inhibitors of HCA are shown in B. The scores of the structures minimized in CHARMM are in parentheses. The R and S stereoisomers that were subsequently synthesized and tested are colored violet and blue, respectively.
Figure 2.
Fig. 2. A shows schematically the interactions of HCA II with the R (Left) and S (Right) stereoisomers grown by CombiSMoG. The surface of the protein is represented by a black curve, on which the approximate positions of the protein residues contacting the ligand are indicated. Three distinct binding pockets are separated by Pro-202 and Phe-131. The red arrows indicate the contacts between the ligand and the protein residues. The predicted and x-ray binding conformations of the R (Left) and S (Right) ligands are compared in B. The conformations predicted by CombiSMoG are colored red, and the x-ray difference electron density maps are shown in purple. These maps were calculated with Fourier coefficients |Fo| |Fc| and phases derived from the final model less the inhibitor and active-site solvent molecules; their contours are at 2 sigma. The fits to the electron density maps are shown in yellow. There are two different viewing angles: the top shows the contacts formed by methyl groups, and the bottom illustrates the interactions of the indole group with the protein. The protein residues making contacts with these groups are marked by letter codes.
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