CCL: W:Computational drug design blues

As other people have mentioned estimating synthetic accessibility is a
 difficult problem particularly when considering compounds designed by people or
 computers with little knowledge of synthetic chemistry.
 A number of groups working on de novo design programs have attempted to include
 synthetic accessibility in their systems to various levels. These include SPROUT
 (from Peter Johnson's group in Leeds) and SkelGen (from Denovo Pharmaceuticals).
 There have also been a number of methods applied to estimating synthetic
 accessibility including expert systems (CAESA, again from Leeds) and neural
 networks (Takaoka et al, JCICS, 2003, 42, 1269-1275). We recently wrote a review
 paper on the subject (Mini-Reviews in Medicinal Chemistry, Volume 4, No. 6,
 2004, 681-692) which covers a wide range of techniques and uses.
 This is certainly an important area and anything that that could reliably stop
 us suggesting synthetically infeasible compounds to medicinal chemists would be
 very welcome.
 Best of luck,
 > -----Original Message-----
 > From: CCL [mailto:owner-chemistry/a\]
 > Sent: Wednesday, 14 September, 2005 7:10 AM
 > To: Baber, Christian
 > Subject: CCL: W:Computational drug design blues
 > Sent to CCL by: "Sandeep  Kumar" [kumarsan\a/]
 > Dear CCLers:
 > I need some advice about the drug discovery/design. Using
 > structure based design, one could develope several potential
 > small molecular inhibitors/drugs for a given protein target.
 > Many of these compounds may appear very attractive as they
 > satisfy all lipinski's rules and your requirements for
 > selectivity/specificity and may even have desirable
 > solubility/ADME profiles. These days its possible to
 > incorporate all these features right at the computational
 > design stage. However, the organic synthesis of the compound
 > still remains a bottleneck as it turns out that many of the
 > designed compounds are 'hard' to synthesize or may require
 > many steps of synthesis. I was wondering if there are some
 > simple guidelines in the form of literature or 'hands on'
 > experience available which could tell the
 > computational/medicinal chemist whether a designed compound
 > would be easy or hard to synthesize before he/she talks to
 > the organic chemist.
 > All your responses are greatly appreciated.
 > Yours sincerely
 > Sandeep Kumar, Ph.D.
 > Johns Hopkins University,
 > Dept. of Biology,
 > 106 Mudd Hall,
 > 3400 N. Charles St.
 > Baltimore, MD 21218.
 > Phone: 410-516-8433
 > Email: kumarsan/a\
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