Nanomedicine, Volume I: Basic Capabilities

© 1999 Robert A. Freitas Jr. All Rights Reserved.

Robert A. Freitas Jr., Nanomedicine, Volume I: Basic Capabilities, Landes Bioscience, Georgetown, TX, 1999


3.5.3 Ligand-Receptor Specificity

While affinity measures the strength of the binding of a ligand to a receptor, specificity defines the degree to which a receptor can distinguish between similar ligands. That is, the affinity of the target molecule for the receptor must be greater than the affinity of any other ligand in the environment that is competing for that same receptor, by some threshold multiple.

How much greater is enough? In natural dynamic cellular systems, the threshold multiple appears to be a factor of ~102-103. For example, the carrier which expels Ca++ from erythrocytes presents a variation in Kd of 10-6 to 10-3 in going from the interior to the exterior of the cell.404 The active transport of amino acids by hepatocytes normally involves Kd ~10-1, but under conditions of deprivation a high affinity carrier with Kd ~10-3 comes into play.405

However, the key to assessing specificity in the nanomedical context would be to tally all the competing molecules in the in vivo environment, determine which are the nearest competitors, and then design to avoid them by imposing appropriate energy barriers. By 1998, only a very few competitive ligand-receptor binding analyses had been performed.1078 Until a complete molecular inventory of the human body becomes available, the following crude estimate of nearest-neighbor differences must suffice.

The human body contains a minimum of Nprot ~105 distinguishable proteins (Section 3.1). The maximum number of distinguishable proteins in the biosphere was given by Kauffman766 who estimates a useful biological catalytic task space of Nprot ~108 distinct protein forms, a tiny subset of the ~20500 possible 500-residue protein sequences. If the average protein is constructed from Nresidue ~ 500 amino acids (MW ~50,000 daltons), then the average protein may differ from its most similar neighbor by nvar ~ log (Nprot)/log (Nresidue) = 1.9-3.0 residues. (The precise magnitudes of Nprot and Nresidue are not crucial to our conclusion.) Most proteins are confined to cells containing Nprot ~ 5000 different protein types each (Table 3.2); given that evolution has probably optimized local specificity to ensure that closely competing crucial ligands rarely appear in the same cell, it seems reasonable to assume that the average closestneighbor ligand may differ from the average target ligand by at least nvar ~ 1 residue.

How much is receptor affinity reduced when binding molecules differing by nvar ~1 residue from the target ligand on receptor-accessible surfaces -- the minimum threshold required to ensure specificity within a cell? In one experiment the relative affinity of an antibody constructed for succinylglycinamide-linked histamine (histamine-SGA), which was the target molecule, and the same molecule but with one methyl group or one carboxylic group removed and replaced with a hydrogen, was 1.45 x 104 or 2.5 x 105, respectively, due to steric hindrance.401 Similar investigations with antibodies for SGA-linked serotonin produced relative affinities of 500-1000,408 and with antibodies for single alanine substitutions in Human Growth Hormone (HGH), ~1000.418 The relative affinity of a particular RNA oligomer for theophylline and caffeine, two ligands which differ by only a single methyl group, was measured experimentally as 10,900.1078 Computational receptor experiments in which CH replaces N suggest a decline in relative affinity of ~5x104.10 Indeed, the change of a single hydrogen atom on a ligand is usually sufficient to destroy its specificity for, or activity within, a particular enzyme. The single-residue affinity reduction at a receptor-accessible surface appears to be of order ~103 - 105.

Each increase of ~10 zJ in bonding energy causes the reaction equilibrium constant to decline (hence receptor affinity to rise) by a factor of ~10 (Eqn. 3.25). If a difference in affinities of ~103-105 between the target molecule and its nearest competitor likely to be present in the environment provides sufficient receptor specificity for nanomedical purposes, this requirement corresponds to a binding energy differential affinity of ~30-50 zJ at 310 K between target and closest-neighbor ligands.


Last updated on 7 February 2003