Vasu Nair

Inosine Monophosphate Dehydrogenase as a Probe in Antiviral Drug Discovery

Inosine monophosphate (IMP) dehydrogenase (IMPDH) is a significant enzyme in the purine nucleotide biosynthetic pathway. IMPDH is viewed as an important biological target in the quest for drugs in the antiviral therapeutic area. This review article is focused on the chemistry and biology of IMPDH inhibitors and the use of IMPDH inhibition data as a probe in antiviral drug discovery. Examples of both inosine 5′ monophosphate and NAD+site-directed inhibitors are presented. Correlation of antiviral activities with IMPDH inhibition is discussed.

A heterocyclic molecule with significant activity against dengue virus.

There are no specific approved drugs or vaccines for the treatment or prevention of infectious dengue virus and there are very few compounds known that inhibit the replication of this virus. This letter describes the concise synthesis of two uracil-based multifunctional compounds. One of these compounds (1) has strong activity against dengue virus. It also exhibits low activity against a few other RNA viruses, but is highly active against yellow fever virus, a related flavivirus. It is likely that the mechanism of action of the antiviral activity of this compound is through its inhibition of the enzyme, inosine monophosphate dehydrogenase (IMPDH). Molecular modeling studies reveal that the compound can have specific hydrogen bonding interactions with a number of amino acids in the active site of IMPDH, a stacking interaction with the bound natural substrate, IMP, and the ability to interfere with the binding of NAD(+) with IMPDH, prior to the hydration step.

Novel HIV integrase inhibitors with anti-HIV activity: insights into integrase inhibition from docking studies

The mechanism of integrase is generally accepted to be dependant on the presence of two divalent metal ions in the active site. However, the only available crystal structures of HIV-1 integrase contain either one or no metal ions, hampering structure-based design studies of integrase inhibitors. For this reason, a two-metal ion model of integrase was constructed. This model was used for computational docking studies with novel diketoacid integrase inhibitors containing pyrimidine nucleobase scaffolds. The docking protocol allowed for some steric contact between the ligand and protein during docking simulations, which implicitly accounted for potential conformational changes in the protein as a result of binding viral DNA or the ligand. The results suggest that the aromatic rings in these diketo acids bind to regions close to the viral DNA and may interfere with mobility of a vital catalytic loop. The docking data also suggest that the ligand can be prevented from adopting a favourable conformation by changes in the relative orientation of its diketo side-chain and aromatic rings. The docked pose of each of the active compounds coordinated both of the metal ions present in the active site of integrase through the diketo acid functionality of these compounds. This result is more consistent with theoretical data on inhibitor mechanism, and thus recommends this docking approach over rigid use of one-metal ion models derived from current crystal structures of integrase.

Enzymatic Synthesis of Thymidine Using Bacterial Whole Cells and Isolated Purine Nucleoside Phosphorylase

Whole cells of Escherichia coli and the thermostable bacteria, Bacillus stearothermophilus, were used for the efficient synthesis of the biologically and industrially important compound, thymidine, using 2′-deoxyinosine and thymine as substrates. In this conversion, the 2′-deoxyribose moiety of 2′-deoxyinosine was transferred to thymine by the transdeoxyglycosylation activity of these bacterial cells. For example, in the case of Bacillus stearothermophilus, the yield of pure thymidine was 56% (78% conversion). When xanthine oxidase was added to this whole cell process, the product yield increased to 68% (90% conversion). In this transformation, Bacillus stearothermophilus was used at a temperature of 55°C where the solubility of thymine is much higher than at 25°C. The bacterial cells have activity over a broad pH range (approximately 4.0 to 8.0) and the yield of product varied within this pH range with the optimum pH being at 5.2. Both bacterial cells showed a sharp decrease in activity at alkaline pHs. ...

Synthesis and biological activities of 2-functionalized purine nucleosides.

Abstract Novel purine nucleosides functionalized at the 2-position have been prepared using new applications of synthetic methodology. The target molecules were designed as potential inhibitors (as their monophosphates) of the enzyme, inosine monophosphate dehydrogenase (IMPDH), and representative inhibition data are presented. Antiviral data of the compounds are discussed.

Cyclopropyl and Related Analogs of the Anti-HIV Compound, Isodideoxyadenosine

Abstract Novel 3′-substituted isonucleoside analogs were designed on the basis of the similarities of their electrostatic potential with the active anti-HIV compound, (S,S)-isodideoxy-adenosine. The key synthetic step involved coupling between the dideoxygenated sugar derivatives, 10 and 14, and adenine under Mitsunobu conditions. Anti-HIV data are mentioned.

Anti-Human Immunodeficiency Virus Activities of Nucleosides and Nucleotides: Correlation with Molecular Electrostatic Potential Data

ABSTRACT Examination of the anti-human immunodeficiency virus (HIV) data of some normal and isomeric dideoxynucleosides (ddNs and isoddNs), their three-dimensional (3-D) electron density patterns, their electrostatic potential surfaces (EPS), and their conformational maps reveals some interesting correlations. For example, the EPS of (S,S)-isoddA shows regions of high and low electrostatic potential remarkably similar to those of β-d-3′-azido-3′-deoxythymidine (β-d-AZT), (−)-oxetanocin A, and (−)-carbovir. Such correlations involving EPS data and anti-HIV activity were also found with many other active nucleosides. Conversely, inactive compounds had EPS different from those of compounds in the same series that were active. For example, apio-ddNs, which are inactive against HIV, exhibit clear differences in electrostatic potential and 3-D electron density shape from isoddNs that are active against HIV. Additionally, the inactivity of (S,S)-isoddC and (S,S)-isoddT can be correlated convincingly with a combination of their EPS data and their conformational energy maps. The electrostatic potential distributions of active nucleoside triphosphates show remarkable correlations. For example, (S,S)-isoddATP, AZT triphosphate (AZTTP), and oxetanocin A TP have similar 3-D electron density surface patterns and similar high and low regions of electrostatic potential, which may suggest that these compounds proceed through related mechanisms in their interactions with, and inhibition of, HIV reverse transcriptase (RT). Docking of AZTTP, (S,S)-isoddATP, and other active triphosphates into the active site of HIV RT and calculation of the EPS of both the nucleotide and the active site show that there is excellent matching between inhibitor and enzyme binding site EPS data. The structure-activity profile discovered has contributed to the development of a first predictive quantitative structure-activity relationship analysis in the area.

Solid-state tautomeric structure and invariom refinement of a novel and potent HIV integrase inhibitor

The conformation and tautomeric structure of (Z)-4-[5-(2,6-difluorobenzyl)-1-(2-fluorobenzyl)-2-oxo-1,2-dihydropyridin-3-yl]-4-hydroxy-2-oxo-N-(2-oxopyrrolidin-1-yl)but-3-enamide, C27H22F3N3O5, in the solid state has been resolved by single-crystal X-ray crystallography. The electron distribution in the molecule was evaluated by refinements with invarioms, aspherical scattering factors by the method of Dittrich et al. [Acta Cryst. (2005), A61, 314-320] that are based on the Hansen-Coppens multipole model [Hansen & Coppens (1978). Acta Cryst. A34, 909-921]. The β-diketo portion of the molecule exists in the enol form. The enol -OH hydrogen forms a strong asymmetric hydrogen bond with the carbonyl O atom on the β-C atom of the chain. Weak intramolecular hydrogen bonds exist between the weakly acidic α-CH hydrogen of the keto-enol group and the pyridinone carbonyl O atom, and also between the hydrazine N-H group and the carbonyl group in the β-position from the hydrazine N-H group. The electrostatic properties of the molecule were derived from the molecular charge density. The molecule is in a lengthened conformation and the rings of the two benzyl groups are nearly orthogonal. Results from a high-field (1)H and (13)C NMR correlation spectroscopy study confirm that the same tautomer exists in solution as in the solid state.

Synthetic approaches to nuclease-resistant, nonnatural dinucleotides of anti-HIV integrase interest.

New, nonnatural dinucleotide 5′-monophosphates with a surrogate isonucleoside component of L-related stereochemistry, have been synthesized. Structures of the target compounds were confirmed by multinuclear NMR spectra (1H, 13C, 31P, COSY), UV hypochromicity, FAB HRMS data and X-ray crystallography. These compounds are totally resistant to cleavage by 3′- and 5′-exonucleases. Dinucleotides of this study with a terminal L-isonucleoside component showed remarkable selectivity for inhibition of the strand transfer step of HIV-1 integrase. To the best of our knowledge, these compounds represent only the second example of this type of selectivity of inhibition of the strand transfer step.

Integrase Inhibitor Prodrugs: Approaches to Enhancing the Anti-HIV Activity of β-Diketo Acids

HIV integrase, encoded at the 3′-end of the HIV pol gene, is essential for HIV replication. This enzyme catalyzes the incorporation of HIV DNA into human DNA, which represents the point of “no-return” in HIV infection. Integrase is a significant target in anti-HIV drug discovery. This review article focuses largely on the design of integrase inhibitors that are β-diketo acids constructed on pyridinone scaffolds. Methodologies for synthesis of these compounds are discussed. Integrase inhibition data for the strand transfer (ST) step are compared with in vitro anti-HIV data. The review also examines the issue of the lack of correlation between the ST enzymology data and anti-HIV assay results. Because this disconnect appeared to be a problem associated with permeability, prodrugs of these inhibitors were designed and synthesized. Prodrugs dramatically improved the anti-HIV activity data. For example, for compound, 96, the anti-HIV activity (EC50) improved from 500 nM for this diketo acid to 9 nM for its prodrug 116. In addition, there was excellent correlation between the IC50 and IC90 ST enzymology data for 96 (6 nM and 97 nM, respectively) and the EC50 and EC90 anti-HIV data for its prodrug 116 (9 nM and 94 nM, respectively). Finally, it was confirmed that the prodrug 116 was rapidly hydrolyzed in cells to the active compound 96.