A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery

Functional relationships between proteins that do not share global structure similarity can be established by detecting their ligand-binding-site similarity. For a large-scale comparison, it is critical to accurately and efficiently assess the statistical significance of this similarity. Here, we report an efficient statistical model that supports local sequence order independent ligand–binding-site similarity searching. Most existing statistical models only take into account the matching vertices between two sites that are defined by a fixed number of points. In reality, the boundary of the binding site is not known or is dependent on the bound ligand making these approaches limited. To address these shortcomings and to perform binding-site mapping on a genome-wide scale, we developed a sequence-order independent profile–profile alignment (SOIPPA) algorithm that is able to detect local similarity between unknown binding sites a priori. The SOIPPA scoring integrates geometric, evolutionary and physical information into a unified framework. However, this imposes a significant challenge in assessing the statistical significance of the similarity because the conventional probability model that is based on fixed-point matching cannot be applied. Here we find that scores for binding-site matching by SOIPPA follow an extreme value distribution (EVD). Benchmark studies show that the EVD model performs at least two-orders faster and is more accurate than the non-parametric statistical method in the previous SOIPPA version. Efficient statistical analysis makes it possible to apply SOIPPA to genome-based drug discovery. Consequently, we have applied the approach to the structural genome of Mycobacterium tuberculosis to construct a protein–ligand interaction network. The network reveals highly connected proteins, which represent suitable targets for promiscuous drugs

SYNTHESIS OF NAD ANALOGS AS SELECTIVE INHIBITORS OF INOSINE MONOPHOSPHATE DEHYDROGENASE

C-nucleosides are composed of an aromatic moiety linked to a carbohydrate derivative thanks to a stable carbon-carbon bond rather than a hydrolysable carbon-nitrogen bond present in regular nucleosides. C-nucleosides are generally synthesized by two main approaches. In the first approach heterocyclic bases are built, starting from a functional group introduced at the anomeric position of the carbohydrate. The second approach is based on the direct attachment of aromatic or heterocylic moieties to the protected ribose derivative. Two C-nucleosides, tiazofurin and benzamide riboside, show a potent inhibitory activity against Inosine Monophosphate Dehydrogenase (IMPDH) when converted to their corresponding tiazofurin- and benzamide adenine dinucleotide (TAD and BAD). We will discuss the synthesis of TAD analogues containing a substituent at the C2 of adenine ring that inhibit IMPDH with Ki in 1-10 nM range. We will also report modified BAD analogues with inhibitory activity against NAD kinase and M. tuberculosis enoyl ACP reductase

Nicotinamide adenine dinucleotide based therapeutics.

Nicotinamide adenine dinucleotide (NAD), generally considered a key component involved in redox reactions, has been found to participate in an increasingly diverse range of cellular processes, including signal transduction, DNA repair, and post-translational protein modifications. In recent years, medicinal chemists have become interested in the therapeutic potential of molecules affecting interactions of NAD with NAD-dependent enzymes. Also, enzymes involved in de novo biosynthesis, salvage pathways, and down-stream utilization of NAD have been extensively investigated and implicated in a wide variety of diseases. These studies have bolstered NAD-based therapeutics as a new avenue for the discovery and development of novel treatments for medical conditions ranging from cancer to aging. Industrial and academic groups have produced structurally diverse molecules which target NAD metabolic pathways, with some candidates advancing into clinical trials. However, further intensive structural, biological, and medical studies are needed to facilitate the design and evaluation of new generations of NAD-based therapeutics. At this time, the field of NAD-therapeutics is most likely at a stage similar to that of the early successful development of protein kinase inhibitors, where analogs of ATP (a more widely utilized metabolite than NAD) began to show selectivity against target enzymes. This review focuses on key representative opportunities for research in this area, which extends beyond the scope of this article

Synthesis and reactivity of novel γ-phosphate modified ATP analogues

We hereby present a simple yet novel chemical synthesis of a family of γ-modified ATPs bearing functional groups on the γ-phosphate that are amenable to further derivatization by highly selective chemical manipulations (e.g., click chemistry, Staudinger ligations). A preliminary screen of these compounds as phosphate donors with a typical wild type protein kinase (cdk2) and one of its known substrates p27kip1 is also presented. © 2009 Elsevier Ltd. All rights reserved

Synthesis and reactivity of novel gamma-phosphate modified ATP analogues.

We hereby present a simple yet novel chemical synthesis of a family of gamma-modified ATPs bearing functional groups on the gamma-phosphate that are amenable to further derivatization by highly selective chemical manipulations (e.g., click chemistry, Staudinger ligations). A preliminary screen of these compounds as phosphate donors with a typical wild type protein kinase (cdk2) and one of its known substrates p27(kip1) is also presented

DESIGN AND SYNTHESIS OF NOVEL INHIBITORS OF INOSINE MONOPHOSPHATE DEHYDROGENASE

Inosine Monophosphate Dehydrogenase (IMPDH) is a well known therapeutic target for new drug development against organ transplant rejection, viral infection and cancer due to its key role in de novo synthesis of purine nucleotides. Following our discovery of mycophenolic adenine dinucleotide (MAD) analogues such as C2-MAD, we designed and synthesized a series of C2-MAD analogues and evaluated their activities against IMPDH (type I and type II). We introduced different functional groups at the 2-position of adenine improving the potency and selectivity of new compounds against the type I and type II isoforms of the human enzyme. We also designed and synthesized compounds with new linkages between adenosine and mycophenolic moiety. Some of them showed more potent inhibition of IMPDH than the parent MAD analogues

Synthesis and O-phosphorylation of 3,3,4,4-tetrafluoroaryl-C-nucleoside analogues

Enantioenriched tetrafluorinated aryl-C-nucleosides were synthesised in four steps from 1-benzyloxy-4-bromo-3,3,4,4-tetrafluorobutan-2-ol. The presence of the tetrafluorinated ethylene group is compatible with O-phosphorylation of the primary alcohol, as demonstrated by the successful preparation of the tetrafluorinated naphthyl-C-nucleotide. © 2010 The Royal Society of Chemistry

Exploring the roles of protein kinases using chemical genetics

The protein kinase superfamily is one of the most important families of enzymes in molecular biology. Protein kinases typically catalyze the transfer of the -phosphate from ATP to a protein substrate (a highly ubiquitous cellular reaction), thereby controlling key areas of cell regulation. Deregulation of protein kinases is known to contribute to many human diseases, and selective inhibitors of protein kinases are a major area of interest in medicinal chemistry. However, a detailed understanding of many kinase pathways is currently lacking. Before we can effectively design medicinally relevant selective kinase inhibitors, it is necessary to understand the role played by a given kinase in specific signal-transduction cascades and to decipher its protein targets. Here, we describe recent advances towards dissecting protein kinase function through the use of chemical genetics. © 2009 Future Science Ltd