Structure-based de novo design, synthesis, and biological evaluation of the indole-based PPARγ ligands (I)

Design of Angiotensin-converting Enzyme 2 (ACE2) Inhibitors by Virtual Lead Optimization and Screening

A group of presumed drug-like molecules that possess high in silico affinity for angiotensin-converting enzyme 2 were computationally designed. This enzyme is a promising new target in both cardiorenal disease and some coronavirus infections. A set of substrate analogous molecules were optimized by means of the LeapFrog module of the SYBYL package. Later, Molinspiration and Molsoft were used for screening out the compounds with low oral bioavailability. Similarly, OSIRIS was used for screening out the compounds having serious side effects. At the end of several stages of screening, seven candidates to anti-viral drugs fulfiling all the evaluated criteria were obtained. They are amenable for future studies in vitro and in vivo. These designed ligands were finally evaluated by Quantitative Structure Activity Relationship studies. 21 molecules were used to carry out the qsar models. Fom these four molecules were taken as external sets yielding models with q 2 = 0.652 and r 2 = 0.962 values.

[Synthesis of biosynthetic precursors of red fluorescent proteins' chromophores]

A method for the synthesis of 5-arylidene-3,5-dihydro-4H-imidazol-4-ones, the corresponding chromophore of green fluorescent protein (GFP) with acylaminoalkyl substituents at position 2 of imidazole core have been developed. These structures represent biosynthetic precursors of the chromophores of red fluorescent proteins. The method is based on masking of the dehydrotyrosine fragment with beta-hydroxytyrosine moiety The key stages of the synthesis include peptide coupling of beta-hydroxytyrosine with the N-acetylamino acid of choice, unmasking of dehydrotyrosine by O-acylation with subsequent elimination, and cyclization of the obtained derivatives of 3-acylaminocinnamic acid in basic media.

Development of an indole-based boron-dipyrromethene fluorescent probe for benzenethiols

Discrimination between chemically related benzenethiols and aliphatic thiols represents a big problem. In this paper, a fluorescent probe, Bodipy-1, containing an indole-based Bodipy as a fluorophore and a 2,4-dinitrobenzenesulfonyl group as a recognition unit was constructed to achieve the selectivity between them. The Bodipy group in the prepared probe was selectively released through aromatic nucleophilic substitution by thiolate anions from benzenethiols, resulting in blue-red switching in the emission spectra in buffer solutions; that is, two new peaks of the phenol/phenolate state of Bodipy-2 at 565 and 629 nm appeared in emission spectra. By varying the pH value from 6.6 to 8.8, the intensity ratio of I(565)/I(629) varies from 2.0 to 0.3 after complete conversion to Bodipy-2, a ca. 7-fold emission ratio change. This ratiometric emission property by varying the pH value makes Bodipy-1 a promising probe to discriminate benzenethiols from aliphatic thiols by careful selection of the reaction pH.

Substituent diversity-directed synthesis of indole derivatives

This paper reports a versatile, good-yielding, solution-phase method that is a substituent diversity-directed synthesis of 1H-indoles (6-13, 17-20) and 1-hydroxyindoles (14, 15) starting from commercially available 1,5-difluoro-2,4-dinitrobenzene. The synthetic products possessed the maximum six diversity points.

De novo design: balancing novelty and confined chemical space

IMPORTANCE OF THE FIELD

De novo drug design serves as a tool for the discovery of new ligands for macromolecular targets as well as optimization of known ligands. Recently developed tools aim to address the multi-objective nature of drug design in an unprecedented manner.

AREAS COVERED IN THIS REVIEW

This article discusses recent advances in de novo drug design programs and accessory programs used to evaluate compounds post-generation.

WHAT THE READER WILL GAIN

The reader is introduced to the challenges inherent in de novo drug design and will become familiar with current trends in de novo design. Furthermore, the reader will be better prepared to assess the value of a tool, and be equipped to design more elegant tools in the future.

TAKE HOME MESSAGE

De novo drug design can assist in the efficient discovery of new compounds with a high affinity for a given target. The inclusion of existing chemoinformatic methods with current structure-based de novo design tools provides a means of enhancing the therapeutic value of these generated compounds.