Chapter 24,  Attacking DNA (HSP for DNA , Drugs, and Biological Membranes Compared)

DNA is at the centre of our lives. An attack on our DNA is an attack on our life or on our quality of life. Such an attack is also required of the drugs used in chemotherapy. It is therefore rather important that we know if a chemical is likely to interact in some way with this complex molecule, for example being cytotoxic.

A few moments thought would suggest that HSP could have nothing to say on the subject. Cytotoxicity must be a hugely complex activity in a complex environment.

However, when a group of well-known cytotoxic chemicals used in chemotherapy all showed HSP values clustering around a certain value, it seemed a good idea to check whether this was chance or a deep insight. The gold standard of science is disconfirmation of a hypothesis so it seemed fairly easy to hunt for cytotoxic molecules with utterly different HSP, thereby refuting the hypothesis.

The fact that we’re writing this chapter means that finding such a refutation has proven harder than we’d supposed!

The core data came from work designed to find gloves that were safe for handling well-known cytotoxic drugs and is described in C.M. Hansen, Polymer science applied to biological problems: Prediction of cytotoxic drug interactions with DNA, European Polymer Journal 44, 2008, 2741–2748. The technique used for estimating breakthrough times was the based on the same type of correlation as described in the chapter on skin/glove diffusion and the following results emerged:

 

Group 1	δD	δP	δH	V	Ra (ave.)
Fluorouracil	18.0	11.7	11.6	118.3	1.68
Gemcitabine	19.0	12.6	15.5	260.6	4.12
Cyclophosphamide	17.5	11.9	12.6	279.1	2.28
Ifosfamide	17.5	11.9	9.8	261.1	3.37
Methotrexate	18.0	10.2	14.2	378.7	1.99
Etoposide	20.0	7.5	12.5	588.5	4.40
Paclitaxel (Taxol)	18.0	6.6	9.8	853.9	4.50
Average of Group 1	18.3	10.3	12.3	-	-
Group 2
Cytarabine	19.0	15.2	20.1	187.1
Carboplatin	27.3	9.0	10.4	185.1

Table 1‑1 HSP properties of many cytotoxic drugs. The Ra is the distance to the average

What is interesting is that the 4 base segments included in DNA have the following values:

Segment	δD	δP	δH	V
Guanine	20.0	12.7	12.5	126.1
Cytosine	19.5	12.1	9.9	107.8
Adenine	20.0	10.2	13.7	131.5
Thymine	19.5	14.2	12.6	121.7
Average	19.75	12.3	12.2	-

Table 1‑2 HSP of DNA bases

At the very least, the “coincidental” similarity of the HSP of the bases and of the cytotoxic drugs was worth investigating further.

For a drug to be cytotoxic it actually has to reach the DNA. It therefore has to pass through cell walls. The chapter on Skin has already indicated that passage through (skin) cells requires the following HSP:

	δD	δP	δH
Skin	17.6	12.5	11.0

Table 1‑3 HSP of Skin

Again, is this another coincidence?

So let’s look at another set of well-known harmful chemicals:

	δD	δP	δH	V	Ra (DNA bases)
Average for Group 1	18.3	10.3	12.3	-	2.00
Thalidomide	20.0	11.3	10.2	195.6	2.29
Pyrimidine	20.5	9.4	11.3	78.8	3.39
1,2-Benzoisothiazolin (BIT)	20.0	9.4	9.2	126.0	4.20
Doxorubricin	19.9	8.6	15.1	483.3	4.71
Dioxin	20.0	9.2	7.6	208.2	5.57

Table 1‑4 Some well-known harmful chemicals

We now introduce the HSP distance (Ra) from DNA bases as a predictor of cytotoxicity. By the time we reach dioxin we are at a bigger distance and at a far less potent molecule. Doxorubricin is a potent molecule but its distance is rather large. However, it is a complex molecule for which the group contribution calculation may not be too accurate and intuition suggests that the δH should be closer to 13 rather than 15.1, leading to a distance of 3.8. It will be interesting to obtain more accurate values via molecular dynamics or by experiment.

It’s worth attempting another challenge. So let’s look for other cytotoxic papers in the literature. Carr J Smith’s group at Reynolds Tobacco identified the cytotoxicity of various substituted quinolines. The 4 most potent have the estimated HSP (using HSPiP’s Stefanis-Panayiotou estimator) shown below. The fit with the hypothesis is quite acceptable.

Substituent	δD	δP	δH
8-OCOCH3	19.9	7.7	8.6
8-NH2	22	10.4	12
8-OH	20.8	9.8	14.4
8-Cl	21.2	8.6	6.6
8-OCH2Ac	21.9	7	4.7
Average	21.2	8.7	9.3

Table 1‑5 HSP of some substituted quinolines

 

So far, the hypothesis is looking reasonable. But there are plenty of other molecules with HSP in the area of interest. How toxic are they? By entering the DNA average into the Polymer table, selecting a Radius of 4 and clicking the Solvent button, the following plot appears if the whole Sphere Solvent Data are loaded:

Figure 1‑1 DNA (hidden in the cloud of blue) compared to the whole solvent range

Here we hit an immediate problem. Of those molecules with RED < 1 both Caffeine and Vanillin stand out as chemicals we don’t think of as cytotoxic. However, there is a large body of evidence showing strong association of caffeine with DNA. For Vanillin there no major effect, but there is still some doubt in the literature as to just what is going on (it may convert to its acid form, changing its HSP).

Is this sufficient to refute the hypothesis? Against the naïve claim that HSP match = Cytotoxicity then a refutation is easily found. But the claim is an “HSP and…” hypothesis. We are making the claim that the HSP match is a necessary condition for a molecule to be able to get through to, and associate with, DNA. Necessary and sufficient requires something more than getting through to the DNA. The obvious extra function would be reactivity - and some anti-cancer drugs are known to be reactive once they associate. Also, the way an associated molecule affects binding during the replication/transcription processes will be a factor in cytotoxicity as it may change the way that the processes are carried out.

We can use HSP to speculate a little further. Could it be, for example, that the well-known secondary effects of ethanol are due to its ability to “help” a “bad” molecule to cross biological membranes? Here are two simple examples.

The following figure shows the HSP sphere for the cytotoxic drugs.  The red cubes are for ethanol, dioctyl phthalate (DOP), and their mixture at 50/50. The 54/46 ethanol/DOP is in blue, being defined as being just inside the sphere. This shows the distinct possibility for synergism of given chemicals with alcohol to allow passage of biological membranes. Once inside a cell, such chemicals can physically get in the way of a process.

 

Figure 1‑2 A 54/46 Ethanol/DOP mix is shown just inside (RED=0.992) the cytotoxic sphere

The next figure uses the solvent optimizer with a choice of chemicals to give an essentially perfect HSP match to the center of the cytotoxic drug HSP sphere. Methyl paraben is already within the sphere from the start with a distance 3.26 compared to the radius 4.4. This emphasizes that mixtures of chemicals, and perhaps especially alcohol, can give synergistic effects in biological systems. This is clearly no proof of any effect, but deserves thought and perhaps also experiment.

Figure 1‑3 Methyl paraben combined with DOP and ethanol produces a perfect match

It is obvious that we are not experts on cytotoxicity. But what we feel is that the “HSP match is necessary” hypothesis is, at the very least, worthy of further consideration. Because the biology world have hardly heard of HSP it’s not surprising that they’ve not tried to take them seriously. We believe that HSP, because of their thermodynamic grounding, are a worthy alternative to endless QSAR correlations which provide nice numbers but lack the fundamental grounding (and success over a wide field of research endeavours) of HSP. Perhaps this chapter will persuade those in the biological world that it’s worth a try.

 

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