Identification of Highly Selective Inhibitors of Collagenase-1 from Combinatorial Libraries of Diketopiperazines

Abstract

Thiol-containing diketopiperazines have been recently identified as novel heterocyclic inhibitors of matrix metalloproteinase (MMPs). The compounds described had similar activities against the MMPs collagenase-1 and gelatinase-B. An inhibitor that showed greater than 10-fold selectivity for collagenase-1 over gelatinase-B was desired. Previously published work with peptidyl hydroxamates and thiols indicated that while preparing gelatinase selective inhibitors was straightforward, there was not an obvious route to selective inhibitors of collagenase-1. Combinatorial libraries were prepared and evaluated for their ability to inhibit collagenase-1 and gelatinase-B substrate hydrolysis. A method for estimating the IC50 values of compounds generated by high-throughput parallel synthesis aided in the identification of compounds with the desired properties. We have found that thiol diketopiperazines derived from nitrophenylalanine are both potent and selective inhibitors of collagenase-1. In addition, we have demonstrated that combinatorial chemistry can be utilized to identify molecules with a desired selectivity profile without access to the traditional tools of rational drug design.

Discovery of Novel Inhibitors of a Disintegrin and Metalloprotease 17 (ADAM17) Using Glycosylated and Non-glycosylated Substrates

“…3C) is two piperazine-2,3-dione moieties. Piperazine-and diketo-piperazine-based MMP and ADAM inhibitors have been described in the literature; however, they also have other zinc-binding groups present and as a consequence have broad inhibition profiles (71,72). The piperazine group was shown to interact with catalytic zinc of farnesyl protein transferase via the nitrogen atom (73).…”

The cyclization of peptides and depsipeptides

“…These aspects, and a great deal more about diketopiperazines have been the subject of a detailed 217-reference review [74], and a Tetrahedron report [75] covering synthesis. For combinatorial synthesis there has been a resurgence of interest in the Ugi reactions exemplified in Scheme 13 [76,77]. A new resinbound isonitrile has also been designed [78] for the Ugi 4CC reaction and has been shown to work according to Scheme 14. In the synthesis [79] of building blocks based on cyclo (Aax-Bbx) consisting of Glu or Asp (Aax) and Lys, Orn or Dab (Bbx), the authors have returned to conventional cyclization of linear dipeptide esters.…”

Using Fluorogenic Peptide Substrates to Assay Matrix Metalloproteinases

“…Mca fluorophore is compatible with commercial plate readers, and thus HTS for MMPs has been previously established using FRET substrates with Mca as fluorophore and Dnp as quencher (75)(76)(77). For example, Mca-Pro-Leu-Gly~Leu-Dpa-Ala-Arg-NH 2 was used for screening a 324 member library of dipeptides acylated with isobutyl succinate (75), a combinatorial library of Cys-diketopiperazines (76), and a combinatorial library of phosphinic peptides (77,78).…”

“…For example, Mca-Pro-Leu-Gly~Leu-Dpa-Ala-Arg-NH 2 was used for screening a 324 member library of dipeptides acylated with isobutyl succinate (75), a combinatorial library of Cys-diketopiperazines (76), and a combinatorial library of phosphinic peptides (77,78).…”