PL37 (RAARISLGPRCIKAFTE) is an antisense homology box peptide composed of aa 37–53 of C5a-anaphylatoxin and is considered to be the region essential for C5a function. Using a computer program, we designed the complementary peptides ASGAPAPGPAGPLRPMF (Pep-A) and ASTAPARAGLPRLPKFF (Pep-B). Pep-A bound to PL37 and to C5a with very slow dissociation as determined by analysis using surface plasmon resonance, whereas Pep-B failed to bind at all. C5a was inactivated by concentrations of 7 nM or more of Pep-A, and this concentration of Pep-A inhibited induction of intracellular Ca2+ influx in neutrophils. Patch clamp electrophysiology experiments also showed the effectiveness of Pep-A in C5aR-expressing neuroblastoma cells. Furthermore, Pep-A administration prevented rats from C5a-mediated rapid lethal shock induced by an Ab to a membrane inhibitor of complement after LPS sensitization.

We designed an evolutionary software program, MIMETIC, which runs on any typical PC computer. MIMETIC generates a series of mimetic peptide sequences with potential to interact with a target peptide by comparing several physico-chemical parameters of each pair of the complementary peptides being analyzed. When the genetic algorithm has evolved through 5,000 iterations, the program ranks the generated peptide sequences by "goodness of fit" to the target. If generated peptides can interfere with the function of a target region in a protein, rational design using these sequences as templates could be a useful approach for drug design. Therefore, we attempted to generate mimetic peptides to recognize biologically active regions of HIV-1 reverse transcriptase (RT) expecting that some of these might interfere with RT function. RT is an intensively studied molecule, and both its sequence and 3 dimensional structure are known (8,10). RT is a heterodimer composed of p66 and p51 subunits, the latter being a truncated version of p66 and lacking the RNase H domain. The resemblance of the enzyme to a right hand has led to the division of each RT chain into structural subdomains known as the fingers, palm, thumb, connection and RNase H subdomains (8). The active catalytic site for DNA polymerization is in the palm domain, and the thumb, palm, and finger domains serve to grip the RNA/DNA template. The connection domain serves to connect these domains to the RNase H domain at the carboxy end of p66, and is also involved in the p66/p51 interaction. Based on this information, we selected the palm regions consisting of amino acids 96 115 and 178 191 which contain the polymerase catalytic site amino acids, D110, Y181, and Y188 (3, 11) as well as the YMDD motif which is highly conserved in many DNA polymerases (3). The second target sequence was the thumb domain consisting of amino acids 283 302 which contains two LT pairs believed to interact with the DNA/RNA template (1). The third target region was in the connection domain comprising amino acids 384 413 where mutation affected packaging (12) and genomic placement (6) of tRNA