Shingo Makino

AUTOMATED FLEXIBLE LIGAND DOCKING METHOD AND ITS APPLICATION FOR DATABASE SEARCH

We have developed a new docking program that explores ligand flexibility. This program can be applied to database searches. The program is similar in concept to earlier efforts, but it has been automated and improved. The algorithm begins by selecting an anchor fragment of a ligand. This fragment is protonated, as needed, and then placed in the receptor by the DOCK algorithm, followed by minimization using a simplex method. Finally, the conformations of the remaining parts of the putative ligands are searched by a limited backtrack method and minimized to get the most stable conformation. To test the efficiency of this method, the program was used to regenerate ten ligand–protein complex structures. In all cases, the docked ligands basically reproduced the crystallographic binding modes. The efficiency of this method was further tested by a database search. Ten percent of molecules from the Available Chemicals Directory (ACD) were docked to a dihydrofolate reductase structure. Most of the top‐ranking molecules (7 of the top 13 hits) are dihydrofolate or methotrexate derivatives, which are known to be DHFR inhibitors, demonstrating the suitability of this program for screening molecular databases. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 1812–1825, 1997

Efficient solid-phase synthesis of quinazoline-2-thioxo-4-ones with SynPhase™ lanterns

We wish to report the efficient solid-phase synthesis of diverse quinazoline-2-thioxo-4-ones using SynPhase™ lanterns as solid supports. Although target compounds were obtained only with low purity using Wang resin, lanterns derivatized with long chain hydroxymethyl phenoxy linkers successfully gave products with high purity. Furthermore, subsequent reactions of quinazoline-2-thioxo-4-ones with various types of halides gave S-alkylated or S-arylated products with high purity, showing the usefulness of this chemistry for synthesizing diverse quinazoline-2-thioxo-4-one libraries.

Efficient solid-phase synthesis of quinazoline-2,4-diones with various substituents on aromatic rings

We have developed a method for the solid-phase synthesis of quinazoline-2,4-diones with various substituents on the aromatic ring. Although there have been numerous reports of the solid-phase synthesis of quinazoline-2,4-diones, they were not applicable to the synthesis of the quinazoline-2,4-diones with electron-withdrawing substituents on the aromatic ring. Considering the poor nucleophilicity of the amino group of anthranilic acids, coupling of anthranilic acids to solid-supported amines was investigated without protecting the amino group. Various anthranilamides were prepared using anthranilic acids with electron-withdrawing substituents because a wide range of anthranilic acids are commercially available. These anthranilamides were successfully cyclized with carbonyldiimidazole to give quinazoline-2,4-diones with high purity.

Solid-phase synthesis of 2-substituted-3-(substituted sulfanyl)-1,2,4-benzothiadiazine 1,1-dioxide library

Abstract The first solid-phase synthesis of 2-substituted-3-(substituted sulfanyl)-1,2,4-benzothiadiazine 1,1-dioxides has been developed. Synthesis of the title compounds was achieved as follows: (1) sulfonylation of solid-supported primary amines with 2-nitrobenzenesulfonylchlorides, (2) reduction of the nitro group, (3) cyclization with thiocarbonyldiimidazole (formation of thiourea), (4) S-alkylation or S-arylation of the thiourea. In addition to the excellent purity of the product, a large-size library can be synthesized with the method as this synthesis includes three diversity points.

Solid-phase synthesis of 1,3-disubstituted 2-thioxoquinazoline-4-ones using SNAr reaction

Abstract We have developed a solid-phase synthesis of diverse 1,3-disubstituted 2-thioxoquinazoline-4-ones. In this synthesis, the fluorine atom on support-bound 2-fluoro-5-nitrobenzoyl amides was substituted with various primary amines, followed by cyclization with thiocarbonyldiimidazole. Since 1-substitutions can be achieved with primary amines, diverse 1,3-disubstituted 2-thioxoquinazoline-4-ones can be efficiently synthesized using this method. Although solid-phase synthesis of 2-thioxoquinazoline-4-ones using 2-methoxycarbonylphenylisothiocyanate has been reported previously, the introduction of 1-substitutions could not be achieved due to the reactivity of the 2-sulfur atom with alkyl or aryl halide.

ELECT++: Faster conformational search method for docking flexible molecules using molecular similarity

We have developed a program, ELECT++ (Effective LEssening of Conformations by Template molecules in C++), to speed up the conformational search for small flexible molecules using the similar property principle. We apply this principle to molecular shape and, importantly, to molecular flexibility. After molecules in a database are clustered according to flexibility and shape (FCLUST++), additional reagents are generated to screen the conformational space of molecules in each cluster (TEMPLATE++). We call these representative reagents of each cluster template reagents. Template reagents and clustered reagents produce, after reaction, template molecules and clustered molecules, respectively (tREACT++). The conformations of a template molecule are searched in the context of a macromolecular target. Acceptable conformational choices are then applied to all molecules in its cluster, thus effectively biasing conformational space to speed up conformational searches (tSEARCH++). In our incremental search method, it is necessary to calculate the root‐mean‐square deviations (RMSD) matrix of distances between different conformations of the same molecule to reduce the number of conformations. Instead of calculating the RMSD matrix for all molecules in a cluster, the RMSD matrix of a template molecule is chosen as a reference and applied to all the molecules in its cluster. We demonstrate that FCLUST++ clusters the primary amine reagents from the Available Chemicals Directory (ACD) successfully. The program tSEARCH++ was applied to dihydrofolate reductase with virtual molecules generated by tREACT++ using clustered primary amine reagents. The conformational search by the program tSEARCH++ was about 4.8 times faster than by SEARCH++, with an acceptable range of errors. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1834–1852, 1998

Discovery of a novel serine protease inhibitor utilizing a structure-based and experimental selection of fragments technique.

We report a set of strategies to develop novel ligands (Structure Based and Experimental Selection of Fragments: SbE-SF). First, a docking simulation utilizing DOCK3.5 is performed in order to screen the fragment database, which was generated with the in-house program FRAGMENT++ specifically for docking simulation purposes. Although the affinity of these small molecules (fragments) is expected to be low, the affinity of fragments selected by computation is assayed by experiment to determine which ones can be potent inhibitors. After determining such key fragments, additional fragments are attached to the key ones in order to increase the binding affinity,taking into account the binding modes predicted by computation. This method has been applied to a thrombin inhibitor study, resulting in the discovery of a novel inhibitor exhibiting pIC50 = 7.9.

Solid-phase synthesis of quinazoline-2,4-diones and their analogues from resin-bound compounds with primary amines.

Solid-phase organic synthesis of heterocyclic compounds on solid-support has been a focus of recent investigations because of the potential applicability of these compounds toward a variety of drug targets. Among the various heterocycles, we have been especially interested in quinazoline-2,4-diones because of the wide range of their bioactivities. Therefore, in this article we review methods for the solid-phase synthesis of quinazoline-2,4-diones and their analogues. Since all of these heterocycles can be speedily derivatized from resin-bound primary amines, incorporating the amines at the 3N-position of quinazoline-2,4-diones or corresponding positions of its analogues, it becomes possible to efficiently compare the bioactivities of these quinazoline-2,4-diones and their analogues. Various methods of solid-phase synthesis described herein should be practical and useful tools for the medicinal chemist in supporting drug discovery initiatives.