About this Author
DBL%20Hendrix%20small.png College chemistry, 1983

Derek Lowe The 2002 Model

Dbl%20new%20portrait%20B%26W.png After 10 years of blogging. . .

Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases. To contact Derek email him directly: Twitter: Dereklowe

Chemistry and Drug Data: Drugbank
Chempedia Lab
Synthetic Pages
Organic Chemistry Portal
Not Voodoo

Chemistry and Pharma Blogs:
Org Prep Daily
The Haystack
A New Merck, Reviewed
Liberal Arts Chemistry
Electron Pusher
All Things Metathesis
C&E News Blogs
Chemiotics II
Chemical Space
Noel O'Blog
In Vivo Blog
Terra Sigilatta
BBSRC/Douglas Kell
Realizations in Biostatistics
ChemSpider Blog
Organic Chem - Education & Industry
Pharma Strategy Blog
No Name No Slogan
Practical Fragments
The Curious Wavefunction
Natural Product Man
Fragment Literature
Chemistry World Blog
Synthetic Nature
Chemistry Blog
Synthesizing Ideas
Eye on FDA
Chemical Forums
Symyx Blog
Sceptical Chymist
Lamentations on Chemistry
Computational Organic Chemistry
Mining Drugs
Henry Rzepa

Science Blogs and News:
Bad Science
The Loom
Uncertain Principles
Fierce Biotech
Blogs for Industry
Omics! Omics!
Young Female Scientist
Notional Slurry
Nobel Intent
SciTech Daily
Science Blog
Gene Expression (I)
Gene Expression (II)
Adventures in Ethics and Science
Transterrestrial Musings
Slashdot Science
Cosmic Variance
Biology News Net

Medical Blogs
DB's Medical Rants
Science-Based Medicine
Respectful Insolence
Diabetes Mine

Economics and Business
Marginal Revolution
The Volokh Conspiracy
Knowledge Problem

Politics / Current Events
Virginia Postrel
Belmont Club
Mickey Kaus

Belles Lettres
Uncouth Reflections
Arts and Letters Daily
In the Pipeline: Don't miss Derek Lowe's excellent commentary on drug discovery and the pharma industry in general at In the Pipeline

In the Pipeline

« Pfizer's Prospects | Main | Glaxo v. Pfizer: Sales Force Stand-Down? »

February 14, 2005

Bigger and Greasier

Email This Entry

Posted by Derek

When I was talking about chemical space the other day, I alluded to the attempts to cut it down to "druglike space" by use of rules of thumb. The most famous of these is Chris Lipinski's "Rule of Five", a summary of which can be found here. Lipinski and his Pfizer co-workers looked over a data set of drug candidates and noticed that there were some reasonably clear cutoffs for oral absorption and general cell permability. They suggested that you need:

1. Fewer than five hydrogen bond donors (which can be estimated by counting the total number of OH and NH groups in the molecule.)
2. A molecular weight of less than 500.
3. A logP of less than 5
4. And fewer than 10 hydrogen-bond acceptors (estimated by the total of N and O atoms in the molecule.)

The "rule of five" name came from the cutoffs all being multiples of five, in case you're wondering why there are only four rules.

(A quick explanation for non-chemistry types: "logP" is a measure of how greasy your compound is, and I mean that quite literally. Although it's often estimated computationally these days, experimentally it's determined by shaking a standard amount of a compound in a flask containing water and the oily 8-carbon alcohol, octanol. Those form two layers, as you'd imagine. The log of the ratio of how much of your compound goes into the octanol layer versus the water layer is your logP. A thousand-fold preference for octanol (a logP of 3) is considered to be just fine for a drug, so you can imagine how greasy a compound with a logP of 6 is.)

There's a recent paper by John Proudfoot at Boehringer Ingleheim (Bioorganic and Medicinal Chemistry Letter 15, 1087, for those of you playing along at home) which looks at a more comprehensive list of compounds than the original Lipinski batch. He finds that the cutoffs might be more like 470 for molecular weight and 3 for hydrogen-bond donors, but otherwise his analysis tracks Lipinski's pretty closely. (He notes that only a handful of drugs ever violate both those cutoffs simultaneously.)

His paper also includes a year-by-year analysis from 1937 to 1997. The only clear trend is that molecular weights have been increasing, from under 300 to the point where we're banging up right against that 500 line. Personally, the largest molecule I've ever submitted for testing weighed quite a bit more than that, but I had my reasons. It came in at exactly 747, and I couldn't resist.

Lipinski's done a lot of publishing and speaking on this topic in the eight years since he first published his rules, and they've seen a tremendous amount of use. Perhaps they've seen some abuse, too, because (as he himself would no doubt tell you), they're not written in stone. They're based on the 90th-percentile cutoffs for each property, so there are outliers. The "Rule of Five" is a tool meant to pare huge lists of compounds down to manageable size, not to blindly decide the fate of individual drug candidates.

I've seen people make Rule-of-Five objections to a compound after its in vivo behavior has already been demonstrated, to which the proper response is "Who cares?" You wouldn't want to stuff your drug discovery project with compounds that violate several of the rules, but if you have good activity after an oral dose, then what more are you looking for? Other things being equal, we try to make compounds that don't step over too many of these boundaries, but being dogmatic about them, especially single rule violations, is foolish.

Comments (2) + TrackBacks (0) | Category: Drug Development


1. Novice Chemist on February 15, 2005 9:46 AM writes...

So what happens when you break the rule of five's hydrogen bond guidelines? I can easily see the problems with the logP and the molecular weight, but the others... I can imagine that it might be solubility that would be at stake with some of these factors.

By the way, what's the opposite end of the rule of five? In other words, these are all maximums -- what are the minimums?

Permalink to Comment

2. Derek Lowe on February 15, 2005 11:07 AM writes...

You know, that's a good question about the limits on the other end. Looking at Proudfoot's graphs, I'd say you need at least 1 hydrogen bond donor, a molecular weight of more than 150, a logP of at least -1, and one or two hydrogen-bond acceptors. Needless to say, violations in these directions aren't as much of an issue - although I'd note that the volatile anaesthetics violate the rules at both ends. But those aren't dosed orally. . .

Permalink to Comment


Email this entry to:

Your email address:

Message (optional):

The Last Post
The GSK Layoffs Continue, By Proxy
The Move is Nigh
Another Alzheimer's IPO
Cutbacks at C&E News
Sanofi Pays to Get Back Into Oncology
An Irresponsible Statement About Curing Cancer
Oliver Sacks on Turning Back to Chemistry