Drug Design and Enzymes

By Michael Edmonds 07/03/2013 3

I went to a fascinating talk last night by Professor Vern Schramm of the Albert Einstein College of Medicine on “Enzymatic Transition States and Drug Design”.

Professor Schramm’s group work on developing enzyme inhibitors to treat diseases such as t-cell leukemia, gout, cancers and antibiotic resistant bacteria by carefully examining the structure of the enzyme and designing molecules based on the 3-D structure of the enzyme and it’s transition state. Some of the compounds they have developed are effective at femtomolar concentrations!

For those who aren’t familiar with enzymes, these are protein molecules which speed up biochemical reactions in the living organisms. Some enzymes are used to help assemble molecules in organisms, while others help break large molecules down to smaller, useful molecules. It has been estimated that there are around 55,000 different enzymes in the human body, helping create all of the molecules our bodies need to function.

Enzymes’s typically work as a 3-D template, aligning  and activating molecules in such a way that they will react. For example, a protease enzyme (one that breaks up proteins) will align the protein in a configuration where the bond to be broken is exposed to chemical groups in the enzyme which activate the bond so it can be broken. Because water molecules are involved in this process it may also align water molecules in a position so that they can help the reaction take place. All of this occurs in an area of an enzyme called the active site. Some enzymes can complete >100,000 reactions a second.

About 1/3 of all FDA approved drugs are enzyme inhibitors. Enzyme inhibitors can work in several different ways, for example they can inhibit enzymes that are used by micro-organisms to grow. HIV protease inhibitors, for example, are very effective at slowing down the replication of HIV and are at the core of many successful treatments for HIV infection and AIDS.  Other enzymes are can be used to adjust the rates of reactions occurring in our own bodies, for example the drug  losec, used to treat excess stomach acid, works by inhibiting an enzyme associated with the production of stomach acid.

To inhibit an enzyme, scientists typically look for molecules that will fit into the active site of the enzyme. This stops the molecules the enzyme normally react with (substrates) from getting into the active site, thereby slowing down the reaction. However, most inhibitors do not permanently occupy the active site – they will move in, then move out of the active site, slowing down rather than stopping the enzyme from acting on the substrate.

Professor Schramm’s group designs enzyme inhibitors by carefully examining the “transition state” that occurs when enzymes are reacting the substrate molecule(s). During the reaction there is a transient point where bonds between the enzyme, substrate and related molecules are halfway between being formed and broken. The 3-D shape of this transition state provides an excellent fit with the active site – the better this fit, the longer a molecule will tend to stay in the active site.

Using these transition structures, Professor Schramm and his team have developed enzyme inhibitors ( and potential drug candidates) such as DADME-immucillin-H which can occupy an active site for days (half life of 11.5 days in mice, 21 days in humans). Such inhibition is the equivalent of the Holy Grail in drug design, as if translated into a drug it could mean drugs which could be taken once a week or even once a month.

Professor Schramm’s work has an exciting New Zealand connection – while his group works on designing these new inhibitors, researchers at GlycoSyn, part of Callaghan Innovation, are working on the actual preparation of these compounds (another fascinating and challenging field of research) so they can be tested. Several molecules developed as a result of this collaboration are already in phase II trials, with some spectacular results.

An interview with Professor Schramm can also be found on Youtube:


3 Responses to “Drug Design and Enzymes”

  • Those transition-state inhibitors are quite interesting.

    1. In what way are those inhibitors different from conventional irreversible inhibitors? In other words, do they offer a specific advantage?
    2. With such slow off-rates the biological response may become a function of protein turnover rates. These differ widely.
    3. Why is such slow kinetics of reversible inhibition the equivalent of “the Holy Grail in drug design”? Besides the fact that pharmaceutical companies favour selling more rather than fewer dosages I don’t think anybody in his (!) right mind would contemplate a very long-lasting Viagra analogue, for example.
    4. Femtomolar potency is impressive, particularly if this refers to a cell-based assay. We have a paper in press describing a compound that inhibits cell growth in culture with femtomolar potency after only 4 h exposure. However, this compound is a DNA cross-linker and thus an irreversible inhibitor. The reversible binding between biotin and avidin is of the order of 10^-15 M, which is the highest affinity I know of.

  • Frederik
    Most irreversible inhibitors tend to bond covalently to the enzyme. This typically necessistates a reactive group being present which will usually be relatively unselective and inclined to react with other biological entities in the body which is usually undersirable. These inhibitors “lock” into place based on complementary shape, therefore should be highly selective.
    While slow kinetics would indeed be undesirable in terms of drugs such as viagra, for the treatment of other conditions it would not, for example, HIV. If it was possible to develop HIV protease inhibitors which bind tightly then there would be no need for daily treatments, plus I would suspect tight binding would reduce the opportunity for resistant strains to develop.
    I can’t remember which inhibitor and target demonstrated femtomolar inhibition, I wish I had taken better notes.
    Here is a link to some of his work, which you may find interesting

  • Michael,

    A very hot area at the moment is activity-based protein-profiling (ABPP in short) that seems to bridge (a very short one) the transition-state and conventional irreversible inhibitors. ABPP probes (or ABPs) do contain an active group that only reacts in the active site or a group that becomes reactive upon enzymatic action. Either way, ABPs are irreversible probes and not used as (therapeutic) inhibitors because they have to have some level of promiscuity (nothing to do with my tongue-in-cheek comment about a long-lasting Viagra analogue). In fact, some ABPs turned out to be too selective! We are currently using ABPP for target identification in our anticancer drug development; it is a nice interface between chemistry and biology to work at.

    Your comment about countering or overcoming the development of resistance makes sense. This argument has been used to develop irreversible kinase inhibitors. In fact, my colleagues have one such irreversible kinase inhibitor (PR-610) currently in clinical trial for erlotinib-resistant (relapsed) non-small-cell lung cancer. However, there are other issues at play here as well in relation to resistance.

    The link (review) looks very interesting, thank you, but 25 pages of text and 34 pages in total is too much for a late Friday afternoon.

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