AUTOSTERE: Systematic Search for Scaffold Replacement Opportunities within Structural Databases.

Medicinal chemists often bias toward working with scaffolds with which previously they have had direct experience and successes. In this way, it is often the case that scaffolds which have proven tractable within a research group are "reused" across multiple and sometimes unrelated drug targets. With this concept in mind, we designed a new computer algorithm AUTOSTERE which could systematically assess the opportunities to replace any part of any molecule within an entire database of known ligand structures with a target scaffold and automatically evaluate the potential designs in the context of the original ligand's protein environment. As such, it performs scaffold replacement on an unprecedented scale and suggests new target opportunities for preferred chemistries rather than the conventional reverse situation. The results of this approach for one scaffold, a substituted triazolinone, applied to a set of 10 426 ligand conformations extracted from the PDB are described. This led to the identification of ∼600 novel ligands incorporating the triazolinone scaffolds in complex with their predicted drug targets. From these, design examples are provided for HSP-90, cathepsin K, and TIE-2 kinase. A further study involved the searching for possible drug targets for unusual pyridopyrimidine cores. This process resulted in the identification of potential novel HIV reverse transcriptase inhibitors which were synthesized and shown to exhibit similar in vitro potencies to marketed compounds. Overall, the methodology described provides a powerful new approach to identify new target opportunities for scaffolds of provenance.

Yeast synthetic biology platform generates novel chemical structures as scaffolds for drug discovery.

Synthetic biology has been heralded as a new bioengineering platform for the production of bulk and specialty chemicals, drugs, and fuels. Here, we report for the first time a series of 74 novel compounds produced using a combinatorial genetics approach in baker's yeast. Based on the concept of "coevolution" with target proteins in an intracellular primary survival assay, the identified, mostly scaffold-sized (200-350 MW) compounds, which displayed excellent biological activity, can be considered as prevalidated hits. Of the molecules found, >75% have not been described previously; 20% of the compounds exhibit novel scaffolds. Their structural and physicochemical properties comply with established rules of drug- and fragment-likeness and exhibit increased structural complexities compared to synthetically produced fragments. In summary, the synthetic biology approach described here represents a completely new, complementary strategy for hit and early lead identification that can be easily integrated into the existing drug discovery process.

Synthesis of novel PPARα/γ dual agonists as potential drugs for the treatment of the metabolic syndrome and diabetes type II designed using a new de novo design program PROTOBUILD.

Peroxisome proliferator activated receptors (PPARs) have been shown to have critical roles in fatty acid oxidation, triglyceride synthesis, and lipid metabolism - making them an important target in drug discovery. Here we describe the in silico design, synthesis and in vitro characterisation of a novel series of 2,5-disubstituted indoles as PPARα/γ dual agonists. PPAR activation assays are performed with known agonists diazabenzene (WY14.643), aminopyridine (BRL49653) and bisaryl (L165.041), as positive controls. All the indole compounds synthesized are found to be active PPARα and PPARγ agonists, with particular efficacy from those with 2-naphthylmethyl substitution. This is a useful demonstration of a new de novo design methodology implemented by the protobuild program and its ability to rapidly produce novel modulators for a well characterized drug target.

An inhibitor of FtsZ with potent and selective anti-staphylococcal activity.

FtsZ is an essential bacterial guanosine triphosphatase and homolog of mammalian beta-tubulin that polymerizes and assembles into a ring to initiate cell division. We have created a class of small synthetic antibacterials, exemplified by PC190723, which inhibits FtsZ and prevents cell division. PC190723 has potent and selective in vitro bactericidal activity against staphylococci, including methicillin- and multi-drug-resistant Staphylococcus aureus. The putative inhibitor-binding site of PC190723 was mapped to a region of FtsZ that is analogous to the Taxol-binding site of tubulin. PC190723 was efficacious in an in vivo model of infection, curing mice infected with a lethal dose of S. aureus. The data validate FtsZ as a target for antibacterial intervention and identify PC190723 as suitable for optimization into a new anti-staphylococcal therapy.

De-novo design of complementary (antisense) peptide mini-receptor inhibitor of interleukin 18 (IL-18).

Complementary (antisense) peptide mini-receptor inhibitors are complementary peptides designed to be receptor-surrogates that act by binding to selected surface features of biologically important proteins thereby inhibiting protein-cognate receptor interactions and subsequent biological effects. Previously, we described a complementary peptide mini-receptor inhibitor of interleukin-1beta (IL-1beta) that was designed to bind to an external surface loop (beta-bulge) of IL-1beta (Boraschi loop) clearly identified in the X-ray crystal structure of this cytokine. Here, we report the de-novo design and rational development of a complementary peptide mini-receptor inhibitor of cytokine interleukin-18 (IL-18), a protein for which there is no known X-ray crystal structure. Using sequence homology comparisons with IL-1beta, putative IL-18 surface loops are identified and used as a starting point for design, including a loop region 1 thought to be equivalent with the Boraschi loop of IL-1beta. Only loop region 1 complementary peptides are found to be promising leads as mini-receptor inhibitors of IL-18 but these are prevented from being properly successful owing to solubility problems. The application of "M-I pair mutagenesis" and inclusion of a C-terminal arginine residue are then sufficient to solve this problem and convert one lead peptide into a functional complementary peptide mini-receptor inhibitor of IL-18. This suggests that the biophysical and biological properties of complementary peptides can be improved in a rational and logical manner where appropriate, further strengthening the potential importance of complementary peptides as inhibitors of protein-protein interactions, even when X-ray crystal structural information is not readily available.

Specific interactions between sense and complementary peptides: the basis for the proteomic code.

The discovery of the genetic code was one of the milestone events in biology: a conserved, universal code defining the primary amino acid sequences of all proteins of all organisms. However, this code has been thought to be limited, unable to provide additional information appropriate to defining the three-dimensional structure and function of these proteins. This raises important questions. Can there be more to the genetic code? Is there a code embedded within the code? Does a two-dimensional genetic code exist? In our view, the answer to all three of these questions is a qualified "yes". This review describes how sense and complementary peptides coded for by mutually complementary nucleic acid sequences are capable of interacting specifically, thereby suggesting the existence of a second, two-dimensional genetic code (proteomic code). Theories attempting to explain such specific interactions between sense and complementary peptides are discussed including the Mekler-Idlis (M-I) pair theory that suggests that each codon-directed amino acid residue in a sense peptide may make a specific pair-wise interaction with the corresponding complementary codon-directed residue in the complementary peptide. In effect, through-space interactions between pairs of amino acid residues are suggested as being specified by the genetic code and its complement. The biological implications of sense/complementary peptide interactions are potentially vast but still to be fully understood and appreciated. That such peptide/peptide interactions could provide the basis for understanding and constructing the proteomic code remains to be properly established but research to date suggests that we should be able to make a start in that direction.

Inhibition of beta-amyloid aggregation and neurotoxicity by complementary (antisense) peptides.

Complementary peptides are coded for by the nucleotide sequence (read 5'-->3') of the complementary strand of DNA. By reading the sequence of complementary DNA in the 3'-->5' direction, alternative complementary peptides may be derived. We describe the derivation, testing and analysis of six complementary peptides designed against beta-amyloid peptide 1-40 (Abeta, 40). Data is presented to show that one peptide, designated 3' -->5' betaCP1-15, binds specifically to Abeta 1-40, and inhibits both fibrilisation and neurotoxicity in vitro. This suggests that complementary peptides could be useful leads for drug discovery, especially where diseases of protein misfolding are concerned.