Some applications of pharmacogenomics and epigenetics in drug development and use in pursuit of personalized medicine.

Personalized medicine has become the most recent mantra of the pharmaceutical industry. While truly affordable bespoke drugs may never be totally achievable, pharmacogenomics and epigenetics will play significant roles in developing targeted therapy tailored to subpopulations of disease sufferers most likely to benefit. Personalized medicine is a very attractive concept, but an extremely difficult reality to achieve due to theoretical and practical considerations. Foremost among the theoretical reasons is our dearth of knowledge of individual physiology and metabolism, as well as the interactions of genetics and environment in the development of most diseases. Amongst the practical reasons, there is the cost of new drug development, considered to be about 800 million to one billion dollars (J Health Econ 22:151-185, DiMasi et al. 2003; Health Econ 19:130-141, Adams and Vu Brantner 2010) and the fact that many drugs now on the market do display reasonable efficacy in large segments of the population with acceptable side effects. Thus, the market for "personalized" drugs may not be large enough to support the costs of development. Another factor is the limitations put on healthcare by governments and insurance companies which promote the use of generics rather than the creation of new chemical entities. Finally, there are the social and ethical considerations of turning individual biology into noughts and ones with the possibility of such information becoming public and/or being used to constrain the way one lives or the care one receives (Nat Rev Drug Discov 1:300-308, Issa 2002). That said, to the degree that personalized medicine does become possible, pharmacogenomics and epigenetics will play significant roles in drug development and use.

Conversion of the Alzheimer's beta-amyloid precursor protein (APP) Kunitz domain into a potent human neutrophil elastase inhibitor.

Site-specific mutagenesis techniques have been used to construct active site variants of the Kunitz-type protease inhibitor domain present in the Alzheimer's beta-amyloid precursor protein (APP-KD). Striking alteration of its protease inhibitory properties were obtained when the putative P1 residue, arginine, was replaced with the small hydrophobic residue valine. The altered protein was no longer inhibitory toward bovine pancreatic trypsin, human Factor XIa, mouse epidermal growth factor-binding protein, or bovine chymotrypsin, all of which are strongly inhibited by the unaltered APP-KD (Sinha, S., Dovey, H. F., Seubert, P., Ward, P. J., Blacher, R. W., Blaber, M., Bradshaw, R. A., Arici, M., Mobley, W. C., and Lieberburg, I. (1990) J. Biol. Chem. 265, 8983-8985). Instead, the P1-Val-APP-KD was a potent inhibitor of human neutrophil elastase, with a Ki = 0.8 nM, as estimated by the inhibition of the activity of human neutrophil elastase measured using a chromogenic substrate. It also inhibited the degradation of insoluble elastin by the enzyme virtually stoichiometrically. Replacement of the P1' (Ala) and P2' (Met) residues of P1-Val-MKD with the corresponding residues (Ser, Ile) from alpha 1-proteinase inhibitor resulted in an inactive protein, underscoring the mechanistic differences between the serpins from the Kunitz-type protease inhibitor family. These results confirm the importance of the P1 arginine residue of APP-KD in determining inhibitory specificity, and are also the first time that a single amino acid replacement has been shown to generate a specific potent human neutrophil elastase inhibitor from a human KD sequence.

Effects of alpha-ketoisocaproate and of leucine on nitrogen metabolism in postoperative patients.

21 patients undergoing major abdominal surgery were randomly assigned to one of three groups. On the day of surgery and for the succeeding 4 days each group received a daily infusion of one of the following: 10 g glucose plus 70 mmol NaHCO3, 70 mmol leucine plus 70 mmol NaHCO3, or 70 mmol of sodium alpha-ketoisocaproate (KIC). No other calories were given. Leucine infusions had no significant effect on nitrogen (N) balance, 3-methylhistidine excretion, or plasma concentrations of pre-albumin or retinol-binding protein, but they increased blood acetoacetate concentration (p = 0.004). N balance was less negative (p = 0.002) and 3-methylhistidine excretion lower (p = 0.002) in the group receiving KIC than in those receiving glucose. Blood ketone bodies, plasma prealbumin, and plasma retinol-binding protein concentrations at the end of the study were significantly higher in the KIC group than in the others. These N-sparing effects of KIC may be related to the heightened ketosis that followed its administration, to suppression of protein degradation, or to an effect on liver protein turnover. KIC alone in small doses diminishes N wastage in postoperative but under the same conditions leucine does not.

Plasma proteins and wound healing.

In response to injury, the concentrations of several plasma proteins are characteristically altered. In part, these changes reflect an essential contribution of many of these proteins, acting in concert, to the processes involved in wound healing. There is evidence that plasma proteins support tissue repair by metabolic as well as functional activity. Specifically, plasma proteins may directly facilitate wound healing by: provision of carbohydrates, lipids and amino acids in a usable form as biosynthetic precursors and energetic substrates; the transport of trace metal cofactors involved in various wound repair processes; adhesion of regenerating tissue; modulation of the rate of structural protein synthesis; alignment of collagen subunits; organization of cellular elements wound repair; prevention of autoimmune reactions; hormone transport and local modulation of hormonal effects; neutralization of the potentially toxic products of the inflammatory response and the inhibition of microbial invasion and colonization.

Multiple systems organ failure: V. Alterations in the plasma protein profile in septic trauma - effects of intravenous amino acids.

The correlations between the acute phase and nutritional plasma proteins and intravenous amino acid dosage have been explored in a group of 25 trauma septic patients of whom 14 survived. The two groups of patients appeared to have equal cardiopulmonary function and exogenous nutritional support. The surviving group showed significant associated changes (p less than or equal to 0.05) between alpha1 acid glycoprotein, alpha2 HS glycoprotein, and ceruloplasmin (acute-phase proteins) and between prealbumin, retinol-binding protein, and transferrin (nutritional proteins). There were no correlations in concentration changes between these two groups of plasma proteins. The surviving group showed significant positive correlations between the nutritional plasma protein and intravenous amino acid dosage (prealbumin, p less than or equal to 0.001; transferrin, p less than or equal to 0.008; retinol-binding protein, p less than or equal to 0.001; and albumin, p less than or equal to 0.004) but no correlations with the acute-phase proteins. The nonsurviving patients showed significant intercorrelations between the acute-phase and nutritional proteins that were not seen in the surviving patients, and showed no relationship between intravenous amino acid dosage and the plasma levels of nutritional proteins. The data are consistent with increased obligatory catabolism of amino acids in the nonsurviving patient which based upon the amino acid behavior documented in the first paper in this series probably involves the branched-chain amino acids.

Multiple systems organ failure: IV. Imbalances in plasma amino acids associated with exogenous albumin in the trauma-septic patient.

In a survey study of septic trauma patients, the response of plasma amino acid concentration to albumin infusion was contrasted in survivors (14 patients) and nonsurvivors (11 patients). Plasma albumin levels were maintained at 3 gm/dl by albumin infusion (0-128 gm/day) because of central venous pressure/adequate circulation considerations. Survivors showed no significant increase in plasma essential amino acid concentration as a function of albumin infusion. In nonsurvivors threonine, valine, leucine, phenylalanine, lysine, and histidine all rose significantly (p less than or equal to 0.025) with albumin infusion. Isoleucine (8 residues/molecule albumin), in contrast to leucine (60 residues/molecule) did not increase. As a result, the ratio of isoleucine to leucine (Ile/Leu) decreased with albumin infusion from 0.47 (no albumin infused) to 0.27 (60 gm albumin/day). Survivors did not exhibit a similar response. The low Ile/Leu increased in most nonsurvivors with amino acid infusion from 0.27 (no amino acids) to 0.59 (150 gm amino acids/day). The data strongly suggest that nonsurvivors had an increased rate of albumin catabolism with subsequent amino acid release. Moreover, hypoalbuminemia treated with albumin infusion without amino acid infusion appears to produce a relative isoleucine deficiency which may detrimentally affect protein synthesis.

Multiple systems organ failure: III Contrasts in plasma amino acid profiles in septic trauma patients who subsequently survive and do not survive-effects of intravenous amino acids.

The response of the plasma substrate and hormone profile of survivor and nonsurvivor septic trauma patients to varying rates of amino acid infusion (IVAA) were contrasted. When IVAA=0 levels of most plasma amino acids (except aspartate, tryptophan, cysteine, and proline) were lower in nonsurvivors. At IVAA=1 to 100, however, 11 of 20 plasma amino acids were significantly (p less than or equal to 0.05) higher in nonsurvivors: only glutamate was significantly lower (p less than or equal to 0.001) and valine, isoleucine, and arginine on average lower. At IVAA less than or equal to 101 to 200, only alanine, methionine, tyrosine, and phenylalanine were significantly (p less than or equal to 0.005) higher in nonsurvivors; isoleucine was significantly (p less than or equal to 0.02) lower. The sharp increase in methionine and decrease in tryptophan in nonsurvivors with IVAA was particularly marked. Polynomial regression analysis showed that urea increased significantly with IVAA in both patient groups, while free fatty acids and cortisol decreased only in nonsurvivors. Insulin increased with IVAA only in survivors, glucagon only in nonsurvivors. Triglycerides, glycerol, acetoacetate, beta OH butyrate, and glucose appeared to show no significant response to IVAA in either patient group. The data are consistent with increased peripheral protein catabolism and branched-chain amino acid oxidation in association with decreased tissue uptake of conventional energetic fuels. These results may be interpreted to be consistent with an impairment of mitochondrial translocase systems.