In vitro metabolism of a rifamycin derivative by animal and human liver microsomes, whole blood and expressed human CYP3A isoform

Functioning of drug-metabolizing microsomal cytochrome P450s: In silico probing of proteins suggests that the distal heme 'active site' pocket plays a relatively 'passive role' in some enzyme-substrate interactions

PURPOSE

The currently held mechanistic understanding of microsomal cytochrome P450s (CYPs) seeks that diverse drug molecules bind within the deep-seated distal heme pocket and subsequently react at the heme centre. To explain a bevy of experimental observations and meta-analyses, we indulge a hypothesis that involves a "diffusible radical mediated" mechanism. This new hypothesis posits that many substrates could also bind at alternate loci on/within the enzyme and be reacted without the pertinent moiety accessing a bonding proximity to the purported catalytic Fe-O enzyme intermediate.

METHODS

Through blind and heme-distal pocket centered dockings of various substrates and non-substrates (drug molecules of diverse sizes, classes, topographies etc.) of microsomal CYPs, we explored the possibility of access of substrates via the distal channels, its binding energies, docking orientations, distance of reactive moieties (or molecule per se) to/from the heme centre, etc. We investigated specific cases like- (a) large drug molecules as substrates, (b) classical marker drug substrates, (c) class of drugs as substrates (Sartans, Statins etc.), (d) substrate preferences between related and unrelated CYPs, (e) man-made site-directed mutants' and naturally occurring mutants' reactivity and metabolic disposition, (f) drug-drug interactions, (g) overall affinities of drug substrate versus oxidized product, (h) meta-analysis of in silico versus experimental binding constants and reaction/residence times etc.

RESULTS

It was found that heme-centered dockings of the substrate/modulator drug molecules with the available CYP crystal structures gave poor docking geometries and distances from Fe-heme centre. In conjunction with several other arguments, the findings discount the relevance of erstwhile hypothesis in many CYP systems. Consequently, the newly proposed hypothesis is deemed a viable alternate, as it satisfies Occam's razor.

CONCLUSIONS

The new proposal affords expanded scope for explaining the mechanism, kinetics and overall phenomenology of CYP mediated drug metabolism. It is now understood that the heme-iron and the hydrophobic distal pocket of CYPs serve primarily to stabilize the reactive intermediate (diffusible radical) and the surface or crypts of the apoprotein bind to the xenobiotic substrate (and in some cases, the heme distal pocket could also serve the latter function). Thus, CYPs enhance reaction rates and selectivity/specificity via a hitherto unrecognized modality.

Rifamycins--obstacles and opportunities

With nearly one-third of the global population infected by Mycobacterium tuberculosis, TB remains a major cause of death (1.7 million in 2006). TB is particularly severe in parts of Asia and Africa where it is often present in AIDS patients. Difficulties in treatment are exacerbated by the 6-9 month treatment times and numerous side effects. There is significant concern about the multi-drug-resistant (MDR) strains of TB (0.5 million MDR-TB cases worldwide in 2006). The rifamycins, long considered a mainstay of TB treatment, were a tremendous breakthrough when they were developed in the 1960's. While the rifamycins display many admirable qualities, they still have a number of shortfalls including: rapid selection of resistant mutants, hepatotoxicity, a flu-like syndrome (especially at higher doses), potent induction of cytochromes P450 (CYP) and inhibition of hepatic transporters. This review of the state-of-the-art regarding rifamycins suggests that it is quite possible to devise improved rifamycin analogs. Studies showing the potential of shortening the duration of treatment if higher doses could be tolerated, also suggest that more potent (or less toxic) rifamycin analogs might accomplish the same end. The improved activity against rifampin-resistant strains by some analogs promises that further work in this area, especially if the information from co-crystal structures with RNA polymerase is applied, should lead to even better analogs. The extensive drug-drug interactions seen with rifampin have already been somewhat ameliorated with rifabutin and rifalazil, and the use of a CYP-induction screening assay should serve to efficiently identify even better analogs. The toxicity due to the flu-like syndrome is an issue that needs effective resolution, particularly for analogs in the rifalazil class. It would be of interest to profile rifalazil and analogs in relation to rifampin, rifapentine, and rifabutin in a variety of screens, particularly those that might relate to hypersensitivity or immunomodulatory processes.

A Randomized, Double-Blind Study Comparing Single-Dose Rifalazil With Single-Dose Azithromycin for the Empirical Treatment of Nongonococcal Urethritis in Men

OBJECTIVES

To determine the safety and effectiveness of single-dose rifalazil, a new rifamycin, for the treatment of nongonococcal urethritis (NGU).

STUDY DESIGN

Randomized, double-blind trial comparing rifalazil, 2.5, 12.5 or 25 mg, with 1.0 g azithromycin for the treatment of NGU. One hundred and seventy men were evaluated for Chlamydia trachomatis, Ureaplasma urealyticum, and Mycoplasma genitalium infection before therapy and 2- and 5-weeks posttreatment.

RESULTS

C. trachomatis, M. genitalium, and U. urealyticum were present in 42%, 24%, and 28% of subjects, respectively. Microbiologic eradication of C. trachomatis with rifalazil 25 mg at 2- and 5- weeks was 85% and 83%, respectively. Rifalazil was ineffective in eradicating M. genitalium and U. urealyticum. Overall clinical cure rates at 2- and 5-weeks were 86% (95% CI 67-96) and 59% (39-78) in the rifalazil-treated 25 mg group, and 77% (56-91) and 63% (41-81) in the azithromycin-treated group.

CONCLUSIONS

Rifalazil was well tolerated and eradicates C. trachomatis but not M. genitalium and U. ureaplasma in men with NGU.

Summary of information on human CYP enzymes: human P450 metabolism data

This chapter is an update of the data on substrates, reactions, inducers, and inhibitors of human CYP enzymes published previously by Rendic and DiCarlo (1), now covering selection of the literature through 2001 in the reference section. The data are presented in a tabular form (Table 1) to provide a framework for predicting and interpreting the new P450 metabolic data. The data are formatted in an Excel format as most suitable for off-line searching and management of the Web-database. The data are presented as stated by the author(s) and in the case when several references are cited the data are presented according to the latest published information. The searchable database is available either as an Excel file (for information contact the author), or as a Web-searchable database (Human P450 Metabolism Database, www.gentest.com) enabling the readers easy and quick approach to the latest updates on human CYP metabolic reactions.

Isolation and identification of major metabolites of rifalazil in mouse and human

1. Three metabolites of rifalazil have been isolated from dog urine and identified as 25-deacetyl-rifalazil, 30-hydroxy-rifalazil and 25-deacetyl-30-hydroxy-rifalazil. In the current study major metabolites of rifalazil in mouse and human were isolated and identified, and their antimicrobial activities determined. 2. Urinary excretion of rifalazil and its metabolites in six mouse strains, CD-1 (ICR), BALB/c, C57BL/6, C3H/He, DBA/2 and CBA/J, was examined. Two major metabolites were detected in mouse urine obtained after several oral doses, and the proportion of rifalazil metabolites against total urinary excretion varied over a 2-fold range (4.8-8.7%) in the different mouse strains. 3. One of two major metabolites in mouse urine was 25-deacetyl-rifalazil and the other was unknown: it was isolated from mouse urine and identified by ms and 1H- and 13C-nmr as 32-hydroxy-rifalazil. 4. In human, two major metabolites of rifalazil were detected in urine obtained after administration of a single oral dose. These metabolites were also produced by incubation of rifalazil with pooled human liver microsomes, and identified by lc/ms and lc/ms/ms as 25-deacetyl-rifalazil and 32-hydroxy-rifalazil. 5. The antimicrobial activities of 32-hydroxy-rifalazil against gram-positive bacteria and mycobacteria were similar with those of the parent compound.

HIV protease inhibitors, saquinavir, indinavir and ritonavir: inhibition of CYP3A4-mediated metabolism of testosterone and benzoxazinorifamycin, KRM-1648, in human liver microsomes

The protease inhibitors, ritonavir, indinavir and saquinavir, the most potent anti-HIV drugs developed to date, interact with many drugs by competing for CYP3A4, an enzyme central to the metabolism of a wide variety of compounds. Human liver microsomes were used to compare inhibition by these three protease inhibitors. The inhibition was the greatest with ritonavir and indinavir and less potent with saquinavir.