Phase I and Phase II biotransformation reactions

This chapter answers parts from Section B(iv) of the 2017 CICM Primary Syllabus, which expects the exam candidate to "describe the mechanisms of drug clearance and metabolism". Specifically, this chapter exists because in Question 20 from the first paper of 2016 the official college answer chided the candidates for not knowing enough about Phase I and Phase II reactions. In fact the official college textbook of pharmacokinetics (Birkett et al, 2009) has an entire chapter devoted to the topic of  How drugs are cleared by the liver (Ch.4, p.38) but  Phase I and Phase II reactions are not included in that textbook, and the time-poor exam candidate may take this as an indication to omit these from their preparation. 

Because there is nothing on this in the official resource, one needs to hunt around for additional literature. Instead of buying or gaining illegal access to the other recommended texts, one could go to this free chapter from Katzung (Correia, 2007). Or, one may instead make use of Parkinson and Ogilvie's "Biotransformation of xenobiotics", a chapter (probably) from Casarett and Doull's Toxicology. A vicious takedown of the Phase I / Phase II classification system is available from Josephy et al (2005).

The pointless attachment to Phase I and Phase II classification structure

In their answer to Question 20 from the first paper of 2016, the college alluded to the terms "Phase I and Phase II reactions" as something the trainees should have known more about. This refers to the classification of hepatic metabolism first introduced by Richard Tecwyn Williams (1909–1979), the grand guru of drug detoxification mechanisms. In the second edition of his 1959 book, Williams' concluding chapter offers the following definition:

“...It appears that the metabolism of most foreign compounds occurs in two phases. The first phase involves oxidations, reductions or hydrolyses or a combination of any of these three, and for convenience these may be termed “phase I reactions”; the second phase (“phase II reactions”) consists of synthesis, mainly conjugations such as glucuronide, ethereal sulphate, thiocyanate, and hippuric acid formation."

So, that's where the Phase I and Phase II thing comes from. Williams' argument for making this distinction was that Phase II conjugation reactions were always "deactivating" (i.e. resulting in a relatively inert and readily excreted metabolite) whereas Phase I reactions could either "activate" or "deactivate" a compound, potentially rendering it even more toxic.  However, this is completely untrue and that was even obvious to Williams in 1959 ("...there are exceptions to this trend and perhaps the most notable case is that of fluoroacetic acid which is converted by synthesis to fluorocitric acid, with consequent poisoning of the organism"). Many conjugation reaction in fact lead to increased toxicity, for instance the conjugation of the pesticide ethylene dibromide with glutathione leads to nightmarish intermediates which bind irreversibly to DNA. So outdated is this classification that Josephy et al (2005) have called for it to be phased out, citing concerns that they as teachers spend considerable time on disabusing their students of the fixed idea that conjugation reactions are uniformly detoxifying.

However, the convention is well-established, and  people who use this terminology keep getting published. The conspiracy extends to the highest echelons. Canonic textbooks are produced giving people the impression that this Phase I-Phase II distinction is some sort of natural phenomenon, a law of nature which was discovered by pharmacologists. Obviously that's not the case. Moreover people end up developing the impression that Phase I reactions must by necessity precede Phase II, but in fact many drugs can bypass all Phase I chemical manipulations and undergo conjugation directly. For other drugs (eg. paracetamol) Phase I and Phase II reactions are competitive processes. On top of that, biotransformation can occur when drugs undergo further metabolic steps following conjugation, including things like covalent binding to DNA and proteins. 

But, convention is convention. The college expects their trainees to know all about Phase I and Phase II reactions. 

Phase I reactions

Examples of Phase I reactions:

• Hydrolysis
• Reduction
• Oxidation.

Characteristics of Phase I reactions:

• these reactions expose or introduce a functional group (–OH, –NH2, – SH or –COOH)
• They usually result in a small increase in hydrophilicity.

Phase II reactions

Examples of Phase II reactions:

• Glucouronidation
• Sulfation
• Acetylation
• Methylation
• Conjugation with glutathione
• Conjugation with amino acids eg. taurine, glutamine, glycine

Characteristics of Phase II reactions:

• The products are supposed to be significantly more hydrophilic than the original substrate

Alternative classification structures

Instead of the dodgy non-mechanistic Williams classification, there's also a more official Enzyme Commission Numbering System which classifies enzymes according to the sorts of reactions they catalyse. The system is divided into six top-level domains and offers an excellent degree of granularity in the level of descriptive detail. For instance, Wikipedia uses the example of the code "EC 3.4.11.4" which is a classification describing hydrolases which cleave off the amino-terminal end from a tripeptide. There is no need for the classification tree to have such a number of generational branches, but one can make a strong argument for a classification system which bears at least some scientific relevance to the chemical manipulations it describes.