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Posts tagged with "In Silico"

  • In Silico

    Virtual Covalent Screening

    Covalent drugs have been a big item in R&D over the last few years, and I wrote here about covalent fragments. The whole topic of reactive groups in small molecules and their interaction with living systems and biomolecules is a complicated one, with many interesting twists. Now the Shoichet group at UCSF has what could… Read More
  • Drug Assays

    Compound Properties: Starting a Renunciation

    I’ve been thinking a lot recently about compound properties, and what we use them for. My own opinions on this subject have been changing over the years, and I’m interested to see if I have any company on this. First off, why do we measure things like cLogP, polar surface area, aromatic ring count, and… Read More
  • Drug Development

    More on “Metabolite Likeness” as a Predictor

    A recent computational paper that suggested that similarity to known metabolites could help predict successful drug candidates brought in a lot of comments around here. Now the folks at Cambridge MedChem Consulting have another look at it here. The big concern (as was expressed by some commenters here as well) is the Tanimoto similarity cutoff… Read More
  • Drug Assays

    A New Way to Estimate a Compound’s Chances?

    Just a few days ago we were talking about whether anything could be predicted about a molecule’s toxicity by looking over its biophysical properties. Some have said yes, this is possible (that less polar compounds tend to be more toxic), but a recent paper has said no, that no such correlation exists. This is part… Read More
  • Drug Assays

    We Can’t Calculate Our Way Out of This One

    Clinical trial failure rates are killing us in this industry. I don’t think there’s much disagreement on that – between the drugs that just didn’t work (wrong target, wrong idea) and the ones that turn out to have unexpected safety problems, we incinerate a lot of money. An earlier, cheaper read on either of those… Read More
  • In Silico

    Chemical Space

    I’m listening to Jean-Louis Reymond of Bern talking about the GDB data set, the massive enumerated set of possible molecules. That’s the set of chemically feasible molecules at or below a certain heavy atom count – the first iteration was GDB11 (blogged about here), and it’s since been extended to GDB13, which has nearly one… Read More
  • Clinical Trials

    The Virtual Clinical Trial: Not Quite Around the Corner

    Here’s one of those “Drug Discovery of. . .the. . .Future-ure-ure-ure” articles in the popular press. (I need a reverb chamber to make that work property). At The Atlantic, they’re talking with “medical futurists” and coming up with this: The idea is to combine big data and computer simulations—the kind an engi… Read More
  • Drug Assays

    Hosed-Up X-Ray Structures: A Big Problem

    X-ray crystallography is great stuff, no doubt about it. But it’s not magic. It takes substantial human input to give a useful structure of a ligand bound to a protein – there are decisions to be made and differences to be split. It’s important to emphasize, for those of us who are not crystallographers, that… Read More
  • Drug Assays

    Predicting New Targets – Another Approach

    So you make a new chemical structure as part of a drug research program. What’s it going to hit when it goes into an animal? That question is a good indicator of the divide between the general public and actual chemists and pharmacologists. People without any med-chem background tend to think that we can predict… Read More
  • Drug Industry History

    Ancient Modeling

    I really got a kick out of this picture that Wavefunction put up on Twitter last night. It’s from a 1981 article in Fortune, and you’ll just have to see the quality of the computer graphics to really appreciate it. That sort of thing has hurt computer-aided drug design a vast amount over the years. Read More