Abhijit Roychowdhury

Selective Recognition of Synthetic Lysine and meso-Diaminopimelic Acid-type Peptidoglycan Fragments by Human Peptidoglycan Recognition Proteins Iα and S

The interactions of a range of synthetic peptidoglycan derivatives with PGRP-Iα and PGRP-S have been studied in real-time using surface plasmon resonance. A dissociation constant of KD = 62 μm was obtained for the interaction of peptidoglycan recognition protein (PGRP)-Iα with the lysine-containing muramyl pentapeptide (compound 6). The normalized data for the lysine-containing muramyl tetra- (compound 5) and pentapeptide (compound 6) showed that these compounds have similar affinities, whereas a much lower affinity for muramyl tripeptide (compound 3) was measured. Similar affinities were obtained when the lysine moiety of the muramyl peptides was replaced by meso-diaminopimelic acid (DAP). Furthermore, the compounds that contained only a stem peptide (pentapeptide, compound 1) and (DAP-PP, compound 2) as well as muramyldipeptide (compound 3) exhibited no binding indicating that the muramyltripeptide (compound 4) is the smallest peptidoglycan fragment that can be recognized by PGRP-Iα. Surprisingly, PGRP-S derived significantly higher affinities for the DAP-containing fragments to similar lysine-containing derivatives, and the following dissociation constants were measured: muramylpentapeptide-DAP, KD = 104 nm; muramyltetrapeptide-DAP, 92.4 nm; and muramyltripeptide-DAP, 326 nm. The binding profiles were rationalized by using a recently reported x-ray crystal structure of PGRP-Iα with the lysine-containing muramyltripeptide (4).

Crystal structure of human peptidoglycan recognition protein Iα bound to a muramyl pentapeptide from Gram-positive bacteria

Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors of the innate immune system that bind bacterial peptidoglycans (PGNs). We determined the crystal structure, to 2.1 Å resolution, of the C‐terminal PGN‐binding domain of human PGRP‐Iα in complex with a muramyl pentapeptide (MPP) from Gram‐positive bacteria containing a complete peptide stem (L‐Ala‐D‐isoGln‐L‐Lys‐D‐Ala‐D‐Ala). The structure reveals important features not observed previously in the complex between PGRP‐Iα and a muramyl tripeptide lacking D‐Ala at stem positions 4 and 5. Most notable are ligand‐induced structural rearrangements in the PGN‐binding site that are essential for entry of the C‐terminal portion of the peptide stem and for locking MPP in the binding groove. We propose that similar structural rearrangements to accommodate the PGN stem likely characterize many PGRPs, both mammalian and insect.

Modification of the structure of peptidoglycan is a strategy to avoid detection by nucleotide-binding oligomerization domain protein 1.

ABSTRACT Nucleotide-binding oligomerization domain (NOD) protein 1 (NOD1) and NOD2 are pathogen recognition receptors that sense breakdown products of peptidoglycan (PGN) (muropeptides). It is shown that a number of these muropeptides can induce tumor necrosis factor alpha (TNF-α) gene expression without significant TNF-α translation. This translation block is lifted when the muropeptides are coincubated with lipopolysaccharide (LPS), thereby accounting for an apparently synergistic effect of the muropeptides with LPS on TNF-α protein production. The compounds that induced synergistic effects were also able to activate NF-κB in a NOD1- or NOD2-dependent manner, implicating these proteins in synergistic TNF-α secretion. It was found that a diaminopimelic acid (DAP)-containing muramyl tetrapeptide could activate NF-κB in a NOD1-dependent manner, demonstrating that an exposed DAP is not essential for NOD1 sensing. The activity was lost when the α-carboxylic acid of iso-glutamic acid was modified as an amide. However, agonists of NOD2, such as muramyl dipeptide and lysine-containing muramyl tripeptides, were not affected by amidation of the α-carboxylic acid of iso-glutamic acid. Many pathogens modify the α-carboxylic acid of iso-glutamic acid of PGN, and thus it appears this is a strategy to avoid recognition by the host innate immune system. This type of immune evasion is in particular relevant for NOD1.

Modulation of cytochrome-P450 inhibition (CYP) in drug discovery: a medicinal chemistry perspective.

Cytochrome P450 (CYP450) has widely been implicated for drug-drug interactions (DDI) in the pharmaceutical industry. Inhibition or induction of this enzyme family has led to withdrawal of multiple drugs from the market leading to major time and financial losses for the pharmaceutical industry. CYP450 plays a prevailing role in the biotransformation of a large number of structurally diverse drugs. Few isoenzymes of the CYP enzyme family (CYP3A4, 2D6 and 2C9 family) are mainly involved in metabolism of most of the drugs. To avoid such interactions and potentially minimize DDI, major pharmaceutical organizations prefer to incorporate CYP enzyme screening at an early stage of their discovery program. While this has been a prevalent practice in the pharmaceutical industry lately, there is very limited literature available reviewing the relationship between chemotypes and CYP isoforms. This review will collate literature pertaining to CYP-inhibition modulation through physicochemical parameters and chemical modification and thus bring to focus commonly used trends by medicinal chemists world-wide.

Synthesis and Proinflammatory Properties of Muramyl Tripeptides Containing Lysine and Diaminopimelic Acid Moieties

The unusual amino acid diaminopimelic acid (DAP) was prepared by cross metathesis of appropriately protected vinyl glycine and allyl glycine derivatives. Catalytic hydrogenation of the cross‐coupling product resulted in reduction of the double bond and the removal of protecting groups. The resulting compounds were appropriately protected for the polymer‐supported and solution‐phase synthesis of muramyl tripeptides 2 and 3, which differ in the amidation of the α‐carboxylic acids of the isoglutamine and DAP moieties. Muramyl dipeptide (1, MDP), the DAP‐containing muramyl tripeptide 3, and the lysine‐containing muramyl tripeptides 4 and 5 induced TNF‐α gene expression without TNF‐α protein production in a human monocytic cell line. The observed block in translation could be removed by co‐incubation with LPS, resulting in an apparent synergistic effect. Compound 2 did not induce TNF‐α gene expression, neither did it exhibit a synergistic effect with LPS; this indicates that amidation of the α‐carboxylic acids of the isoglutamine and DAP moieties results in a loss of biological activity. It is proposed that amidation of α‐carboxylic acids is a strategy that may be used by pathogens to avoid detection by the innate immune system. Furthermore, the pattern recognition receptors Nod1 and Nod2 have been implicated in the possible induction of a synergistic effect of muropeptides with LPS.

Recent advances in the discovery of small molecule mTOR inhibitors

Mammalian target of rapamycin (mTOR) belongs to the atypical kinase family of phosphatidylinositol-3-kinase-related kinase and function as a master regulators of the switch between catabolic and anabolic metabolism. In the last decade mTOR has emerged as a therapeutic target for various diseases such as cancer, inflammation and metabolic disorders. mTOR plays a crucial role in the PI3K/AKT/PDK1 pathway. In this review we will provide an overview of both selective and nonselective mTOR inhibitors. Since rapamycin and rapalogs have been reviewed before, more emphasis has been placed on nonrapamycin-based small-molecule inhibitors and their modulation of mTOR selectivity. Recent efforts in obtaining mTOR-selective inhibitors have produced a range of compounds with more than 1000-fold selectivity over PI3K, but it is still a matter of debate whether an mTOR-selective inhibitor will be of more clinical significance over a PI3K/AKT/mTOR inhibitor.

Efficient Synthesis of Key Intermediate Toward Liphagal Synthesis

Liphagal (A) is a very potent and selective inhibitor of PI3Kα (p110α) and is under development for an oncolytic drug. We herein report the new and concise synthesis of key intermediates (7, 8), which have been used for liphagal synthesis and will be useful for generating liphagal-based chemical entities for drug discovery purposes.

Cyclopentyl-pyrimidine based analogues as novel and potent IGF-1R inhibitor

A series of novel 2-amino-4-pyrazolecyclopentylpyrimidines have been prepared and evaluated as IGF-1R tyrosin kinase inhibitors. The in vitro activity was found to depend strongly on the substitution pattern in the 2- amino ring, 4-pyrazolo moieties and size of fused saturated ring with the central pyrimidine core. A stepwise optimization by combination of active fragments led to discovery of compound 6f and 6k, two structures with IGF-1R IC50 of 20 nM and 10 nM, respectively. 6f was further profiled for its anti cancer activity across various cell lines and pharmacokinetic studies in Sprague Dawley rats.

Synthesis and therapeutic evaluation of pyridyl based novel mTOR inhibitors

A series of novel cyanopyridyl based molecules (1-14) were designed, synthesized and probed for inhibition of mammalian target of rapamycin (mTOR) activity. Compound 14 was found to be a potent inhibitor of mTOR activity as assessed by enzyme-linked immunoassays and Western blot analysis. Most importantly, systemic application (intraperitoneal; ip) of compound 14 significantly suppressed macroscopic and histological abnormalities associated with chemically-induced murine colitis.

First total synthesis of prasinic acid and its anticancer activity.

The first total synthesis of prasinic acid is being reported along with its biological evaluation. The ten step synthesis involved readily available and cheap starting materials and can easily be transposed to large scale manufacturing. The crucial steps of the synthesis included the formation of two different aromatic units (7 and 9) and their coupling reaction. The synthetic prasinic acid exhibited moderate antitumor activity (IC(50) 4.3-9.1 μM) in different lines of cancer cells.