Synthesis and biological activity of cyclic peptide inhibitors of ribonucleotide reductase

Interactions of disulfide-constrained cyclic tetrapeptides with Cu(2+)

The purpose of this work is to characterize the interactions of two disulfide-constrained cyclic tetrapeptides [c(Ac-Cys-Pro-Phe-Cys-NH(2)), SS1; c(Ac-Cys-Pro-Gly-Cys-NH(2)), SS2] with Cu(2+) ions in order to facilitate the design of cyclic peptides as sensors for metal ions. The Cu(2+)-peptide complex cations at m/z 569.1315 for Cu(2+)-SS1 and m/z 479.0815 for Cu(2+)-SS2 were detected by mass spectrometry. The gas-phase fragmentation of the Cu(2+)-peptide complexes was studied by collision-induced dissociation and suggests the atoms involved in the coordination. Cu(2+) ion binds to a single SS1 or SS2 with K (d(app)) of 0.57 ± 0.02 and 0.55 ± 0.01 μM, respectively. Isothermal titration calorimetry data indicate both enthalpic and entropic contributions for the binding of Cu(2+) ion to SS1 and SS2. The characteristic wavenumber of 947 cm(-1) and the changes at 1,664 and 1,530 cm(-1) in the infrared spectrum suggest that the sulfydryl of cysteine, the carbonyl group, and amide II are involved in the coordination of Cu(2+). The X-ray absorption near-edge structure signal from the Cu(2+)-peptide complex corresponds to the four-coordination structure. The extended X-ray absorption fine structure and electron paramagnetic resonance results demonstrate the Cu(2+) ion is in an S/N/2O coordination environment, and is a distinct type II copper center. Theoretical calculations further demonstrate that Cu(2+) ion binds to SS1 or SS2 in a slightly distorted tetragonal geometry with an S/N/2O environment and the minimum potential energy.

The structural basis for the allosteric regulation of ribonucleotide reductase

Ribonucleotide reductases (RRs) catalyze a crucial step of de novo DNA synthesis by converting ribonucleoside diphosphates to deoxyribonucleoside diphosphates. Tight control of the dNTP pool is essential for cellular homeostasis. The activity of the enzyme is tightly regulated at the S-phase by allosteric regulation. Recent structural studies by our group and others provided the molecular basis for understanding how RR recognizes substrates, how it interacts with chemotherapeutic agents, and how it is regulated by its allosteric regulators ATP and dATP. This review discusses the molecular basis of allosteric regulation and substrate recognition of RR, and particularly the discovery that subunit oligomerization is an important prerequisite step in enzyme inhibition.

Targeting the Large Subunit of Human Ribonucleotide Reductase for Cancer Chemotherapy

Ribonucleotide reductase (RR) is a crucial enzyme in de novo DNA synthesis, where it catalyses the rate determining step of dNTP synthesis. RRs consist of a large subunit called RR1 (α), that contains two allosteric sites and one catalytic site, and a small subunit called RR2 (β), which houses a tyrosyl free radical essential for initiating catalysis. The active form of mammalian RR is an α_nβ_m hetero oligomer. RR inhibitors are cytotoxic to proliferating cancer cells. In this brief review we will discuss the three classes of RR, the catalytic mechanism of RR, the regulation of the dNTP pool, the substrate selection, the allosteric activation, inactivation by ATP and dATP, and the nucleoside drugs that target RR. We will also discuss possible strategies for developing a new class of drugs that disrupts the RR assembly.

The structural basis for peptidomimetic inhibition of eukaryotic ribonucleotide reductase: a conformationally flexible pharmacophore

Eukaryotic ribonucleotide reductase (RR) catalyzes nucleoside diphosphate conversion to deoxynucleoside diphosphate. Crucial for rapidly dividing cells, RR is a target for cancer therapy. RR activity requires formation of a complex between subunits R1 and R2 in which the R2 C-terminal peptide binds to R1. Here we report crystal structures of heterocomplexes containing mammalian R2 C-terminal heptapeptide, P7 (Ac-1FTLDADF7) and its peptidomimetic P6 (1Fmoc(Me)PhgLDChaDF7) bound to Saccharomyces cerevisiae R1 (ScR1). P7 and P6, both of which inhibit ScRR, each bind at two contiguous sites containing residues that are highly conserved among eukaryotes. Such binding is quite distinct from that reported for prokaryotes. The Fmoc group in P6 peptide makes several hydrophobic interactions that contribute to its enhanced potency in binding to ScR1. Combining all of our results, we observe three distinct conformations for peptide binding to ScR1. These structures provide pharmacophores for designing highly potent nonpeptide class I RR inhibitors.

Design, synthesis, and evaluation of octahydropyranopyrrole-based inhibitors of mammalian ribonucleotide reductase

Inhibitors of mammalian ribonucleotide reductase possessing a novel octahydropyranopyrrole scaffold based on a cyclic heptapeptide inhibitor have been designed, synthesized, and evaluated. Structure-function studies reveal that the bicyclic scaffold is indeed necessary to maintain inhibitory activity.

Mechanisms of action of peptide inhibitors of mammalian ribonucleotide reductase targeting quaternary structure

Mammalian ribonucleotide reductase (mRR) is a chemotherapeutic target. The enzyme is composed of 2 subunits (mR1 and mR2) and is inhibited by Ac-FTLDADF (denoted P7), corresponding to the C-terminus of mR2, which competes with mR2 for binding to mR1. mRR has 2 physiologically important active forms, mR12mR22 and mR16(mR22)j (j = 1-3). Here we report on the mechanism of action of recently identified peptide derivatives having higher activities than P7 toward inhibition of one or both active forms. A significant feature of both P7 and these new inhibitors is that they are more potent vs. mR12mR22 than mR16(mR22)j. For some of these peptides, this is due in part to their preferential binding to the mR1 monomer. The possible application of these peptide derivatives in cancer chemotherapy is discussed.

Peptide inhibitors of mammalian ribonucleotide reductase

Mammalian ribonucleotide reductase (mRR) is a chemotherapeutic target. In common with other class Ia RRs, the enzyme is composed of two subunits (mR1 and mR2), with mR1 containing both the active site and allosteric effector sites and mR2 containing a stable tyrosyl radical that is essential for enzymatic activity. mRR is inhibited by Ac-FTLDADF (denoted P7), corresponding to the C-terminus of mR2, which competes with mR2 for binding to mR1. The enzyme has two physiologically important active forms, mR12mR22 and mR16(mR22)j (j=1-3), with high ATP concentrations favoring the latter. Here, we report on our progress in using structural and functional studies in conjunction with library screening to identify derivatives of tri-, tetra- and hexapeptides, and cyclic heptapeptides, having equal or significantly higher activities than P7 toward inhibition of one or both active forms. These identifications were made by screening candidate peptides both for their abilities to bind to mR1 competitively with P7 and to inhibit ribonucleotide reductase activity. A significant feature of both P7 and the newly identified derivatives is that they are stronger inhibitors of mR12mR22 than of mR16(mR22)j. For the tetrapeptides, this is due in part to their preferential binding to mR1 monomer. The possible application of these peptide derivatives in cancer chemotherapy, exploiting their preferential inhibition of mR12mR22, is considered.

Oligopeptide inhibition of class I ribonucleotide reductases

Class I ribonucleotide reductases (RRs), which are well-recognized targets for cancer chemotherapeutic and antiviral agents, are composed of two different subunits, R1 and R2, and are inhibited by oligopeptides corresponding to the C-terminus of R2, which compete with R2 for binding to R1. These peptides specifically inhibit the RRs from which they are derived, and closely homologous RRs, but do not inhibit less homologous RRs. Here we review results obtained for oligopeptide inhibition of RRs from several sources, including related x-ray, NMR, and modeling results. The most extensive studies have been performed on herpes simplex virus-RR (HSV-RR) and mammalian-RR (mRR). A common model fits the data obtained for both enzymes, in which the C-terminal residue of the oligopeptide (Leu for HSV-RR, Phe for mRR) binds with high specificity to a narrow and deep hydrophobic subsite, and two or more hydrophobic groups at the N-terminal portion of the peptide bind to a broad and shallow second hydrophobic subsite. The studies have led to the development of highly potent and specific inhibitors of HSV-RR and promising inhibitors of mRR, and indicate possible directions for the development of inhibitors of bacterial and fungal RRs.

Peptides with anticancer use or potential

This review is an attempt to illustrate the diversity of peptides reported for a potential or an established use in cancer therapy. With 612 references, this work aims at covering the patents and publications up to year 2000 with many inroads in years 2001-2002. The peptides are classed according to four categories of effective (or plausible) biological mechanisms of action: receptor-interacting compounds; inhibitors of protein-protein interaction; enzymes inhibitors; nucleic acid-interacting compounds. The fifth group is made of the peptides for which no mechanism of action has been found yet. Incidentally this work provides an overview of many of the modern targets of anticancer research.

Structure and function of the radical enzyme ribonucleotide reductase

Ribonucleotide reductases (RNRs) catalyze all new production in nature of deoxyribonucleotides for DNA synthesis by reducing the corresponding ribonucleotides. The reaction involves the action of a radical that is produced differently for different classes of the enzyme. Class I enzymes, which are present in eukaryotes and microorganisms, use an iron center to produce a stable tyrosyl radical that is stored in one of the subunits of the enzyme. The other classes are only present in microorganisms. Class II enzymes use cobalamin for radical generation and class III enzymes, which are found only in anaerobic organisms, use a glycyl radical. The reductase activity is in all three classes contained in enzyme subunits that have similar structures containing active site cysteines. The initiation of the reaction by removal of the 3'-hydrogen of the ribose by a transient cysteinyl radical is a common feature of the different classes of RNR. This cysteine is in all RNRs located on the tip of a finger loop inserted into the center of a special barrel structure. A wealth of structural and functional information on the class I and class III enzymes can now give detailed views on how these enzymes perform their task. The class I enzymes demonstrate a sophisticated pattern as to how the free radical is used in the reaction, in that it is only delivered to the active site at exactly the right moment. RNRs are also allosterically regulated, for which the structural molecular background is now starting to be revealed.

Sequencing cyclic peptide inhibitors of mammalian ribonucleotide reductase by electrospray ionization mass spectrometry

Mammalian ribonucleotide reductase (mRR) is a potential target for cancer intervention. A series of lactam-bridged cyclic peptide inhibitors (1-9) of mRR have been synthesized and tested in previous work. These inhibitors consist of cyclic and linear regions, causing their mass spectral characterization to be a challenge. We determined the fragmentation mechanism of cyclic peptides 1-9 using an ion-trap mass spectrometer equipped with an ESI source. Low-energy collision-induced dissociation of sodiated cyclic peptides containing linear branches follows a general pathway. Fragmentation of the linear peptide region produced mainly a and b ions. The ring peptide region was more stable and ring opening required higher collision energy, mainly occurring at the amide bond adjacent to the lactam bridge. The sodium ion, which bound to the carbonyl oxygen of the lactam bridge, acted as a fixed charge site and directed a charge-remote, sequence-specific fragmentation of the ring-opened peptide. Amino acid residues were cleaved sequentially from the C-terminus to the N-terminus. Our findings have established a new way to sequence cyclic peptides containing a lactam bridge based on charge-remote fragmentation. This methodology will permit unambiguous identification of high-affinity ligands within cyclic peptide libraries.

Toward a rational design of peptide inhibitors of ribonucleotide reductase: structure-function and modeling studies

Mammalian ribonucleotide reductase, a chemotherapeutic target, has two subunits, mR1 and mR2, and is inhibited by AcF(1)TLDADF(7), denoted P7. P7 corresponds to the C-terminus of mR2 and competes with mR2 for binding to mR1. We report results of a structure-function analysis of P7, obtained using a new assay measuring peptide ligand binding to mR1, that demonstrate stringent specificity for Phe at F(7), high specificity for Phe at F(1), and little specificity for the N-acyl group. They support a structural model in which the dominant interactions of P7 occur at two mR1 sites, the F(1) and F(7) subsites. The model is constructed from the structure of Escherichia coli R1 (eR1) complexed with the C-terminal peptide from eR2, aligned sequences of mR1 and eR1, and the trNOE-derived structure of mR1-bound P7. Comparison of this model with similar models constructed for mR1 complexed with other inhibitory ligands indicates that increased F(1) subsite interaction can offset lower F(7) subsite interaction and suggests strategies for the design of new, higher affinity inhibitors.

Structure-based optimization of peptide inhibitors of mammalian ribonucleotide reductase

Mammalian ribonucleotide reductase (mRR), a potential target for cancer intervention, is composed of two subunits, mR1 and mR2, whose association is critical for enzyme activity. In this article we describe the structural features of the mRR-inhibitor Ac-F-c[ELAK]-DF (Peptide 3) while bound to the mR1 subunit as determined by transferred NOEs. Peptide 3 is a cyclic analogue of the N-acetylated form of the heptapeptide C-terminus of the mR2 subunit (Ac-FTLDADF), which is the link between the two subunits and previously shown to be the minimal sequence inhibitor mRR by competing with mR2 for binding to mR1. Structural refinement employing an ensemble-based, full-relaxation matrix approach resulted in two structures varying in the conformations of F(1) and the cyclic lactam side chains of E(2) and K(5). The remainder of the molecule, both backbone and side chains, is extremely well-defined, with an RMSD of 0.54 A. The structural features of this conformationally constrained analogue provide unique insight into the requirements for binding to mR1, critical for further inhibitor development.