Novel Inhibitors of DNA Gyrase:  3D Structure Based Biased Needle Screening, Hit Validation by Biophysical Methods, and 3D Guided Optimization. A Promising Alternative to Random Screening

Abstract

Random screening provided no suitable lead structures in a search for novel inhibitors of the bacterial enzyme DNA gyrase. Therefore, an alternative approach had to be developed. Relying on the detailed 3D structural information of the targeted ATP binding site, our approach combines as key techniques (1) an in silico screening for potential low molecular weight inhibitors, (2) a biased high throughput DNA gyrase screen, (3) validation of the screening hits by biophysical methods, and (4) a 3D guided optimization process. When the in silico screening was performed, the initial data set containing 350 000 compounds could be reduced to 3000 molecules. Testing these 3000 selected compounds in the DNA gyrase assay provided 150 hits clustered in 14 classes. Seven classes could be validated as true, novel DNA gyrase inhibitors that act by binding to the ATP binding site located on subunit B: phenols, 2-amino-triazines, 4-amino-pyrimidines, 2-amino-pyrimidines, pyrrolopyrimidines, indazoles, and 2-hydroxymethyl-indoles. The 3D guided optimization provided highly potent DNA gyrase inhibitors, e. g., the 3,4-disubstituted indazole 23 being a 10 times more potent DNA gyrase inhibitor than novobiocin (3).

Small-Molecule Inhibitors of IL-2/IL-2R: Lessons Learned and Applied

“…The development and widespread availability of biophysical methods have clearly facilitated small-molecule PPI inhibitor discovery Boehm et al 2000;Carr et al 2005;Renaud and Delsuc 2009). The examples described above have made extensive use of the structure and mechanism-oriented approaches to build a sophisticated quantitative understanding of the smallmolecule inhibitor interaction.…”

“…In the past decade, numerous structural and biophysical approaches that measure the small molecule/protein interaction directly have come of age. In combination, methods such as SPR, NMR, and analytical centrifugation crossvalidate compounds for further investigation and generate a clear understanding of the mechanism of inhibition at work Boehm et al 2000;Giannetti et al 2008). These methods can also reveal general properties of the molecule, facilitating early removal of problematic aggregators or promiscuous inhibitors from compound sets.…”

Structure-based design of inhibitors of CXCR4.

“…Virtual screening presents the capability to prescreen vast databases, such as the Zinc compound library, a 13 million compound virtual database [208], by targeting a three dimensional structure to determine those compound which best fit, or dock, into a chosen allosteric or ligand binding site. This method has proven successful in the identification of a wide variety of targets [209][210][211][212][213][214][215][216][217][218][219][220][221][222][223][224][225].…”

“…[212], retinoic acid receptor [213], farnesyl transferase [214], kinesin [215], hypoxanthine-guanine-xanthine phosphoribosyl transferase [216], DNA gyrase [217], H IV -1 RNA transactivation response element [218], aldose reductase [219], rac GTPase [220], checkpoint kinase-1 [221], alpha amylase [222], BCR-ABL tyrosine kinase [223], protein kinase CK2 [224], and alpha-reductase [225]. In one documented case virtual screening targeting DNA gyrase identified lead compounds where experimental high throughput screening of libraries was unsuccessful [181,217].…”

Antichagásicos potenciais: síntese de bases de Mannich do hidroximetilnitrofural

“…Novas metodologias vêm sendo cada vez mais exploradas (KUBINYI, 1995;BOHM, 2000), observando-se desenvolvimento significativo em algumas delas, como: química combinatória (GORDON, KERWIN, Jr, 1998), engenharia genética (MEYER, 1996), cristalografia de proteínas (RONDEAU, SCHREUDER, 1996), técnicas multidimensionais em RMN (SHUKER, HAJDUK, MEADOWS, FESIK, 1996), relações quantitativas entre estrutura química e atividade biológica -QSAR (HANSCH, FUJITA, 1964;FUJITA, 1990; KUBINYI, 1995; KUBINYI, 1993) e a variante QSAR-3D, modelagem molecular, planejamento dirigido para estrutura e auxiliado por computador, CADD (KUBINYI, 1993;BOHM, 1993;KLEBE, 1993;KUBINYI, 1998a;KUBINYI, 1998b;KLEBE, 1999; SHUKER, HAJDUK, MEADOWS, et ai., 1996; BOHM, BOEHRINGER, BUR et ai., 2000), entre outras. Apesar do uso de novas e avançadas tecnologias, especialmente as computacionais, persiste o desafio de que para um ligante se tomar um fármaco deve-se considerar, em primeiro lugar, a biodisponibilidade, estreitamente ligada à sua lipofilicidade (AJAY et ai., 1998; KUBINYI, 1998c; PAGLIARA et ai., 1999 socorrem-se de processos mais clássicos e mais simples, com o objetivo de se transformar um ligante em fármaco.…”