Small molecule protein-protein inhibitors for the p53-MDM2 interaction

This article describes recent progress in the development of small molecule protein-protein inhibitors of the p53-MDM2 (purine double minute 2, or HDM2 for the human congener) protein-protein interaction, with special attention to the diversity of chemotypes reported to disrupt this protein-protein interaction. In >50% of all human cancers, the tumor suppressor 53 KDa phospho-protein p53 is either mutated or deleted. The discovery that MDM2 (HDM2) negatively regulates p53 and therefore inhibits the tumor-suppressor activity of p53 has instigated numerous drug discovery campaigns aimed at disrupting this protein-protein interaction as a potential cancer therapy. Once regarded as intractable targets disrupted by only large macromolecules, protein-protein interactions (PPI) are now mainstream targets due in large part to the intensive effort applied to the study of p53 and the surprising diversity of small molecules (peptides, natural products, terphenyl and other alpha-helix mimetics, chalcones, piperidines, piperazines, fused indoles, isoindolinones, spiro-oxindoles, cis-imidazolines (nutlins), quinolinol and benzodiazepines) capable of disrupting the p53-HDM2 PPI. In addition, drug discovery researchers have employed a number of screening approaches and technologies to identify SMPPIs of the p53-HDM2 interaction, and these discovery paradigms will be discussed. This review will detail the biology of the p53-MDM2 interaction, the major classes of SMPPIs and key medicinal chemistry and in vitro/in vivo biological data reported through October 2006.     

Small molecule inhibitors of p53/MDM2 interaction

The discovery of the key negative regulator MDM2 (mouse double minute 2, also termed HDM2 for its human equivalent) provided a great opportunity to manipulate the levels of the tumor suppressor p53 in cancer cells. Activation of p53 in tumor cells by inhibiting the interaction of MDM2 with p53 has therefore been the focus of a large effort in drug discovery. The modulation of protein-protein interactions, however, has historically been very difficult to achieve owing to the large surface area of interaction. In this article, we review the recent accomplishments in this area and our quest for a clinically viable MDM2 inhibitor.     

Division of Medicinal Chemistry--small molecule inhibitors of protein-protein interactions

Protein-protein interactions lie at the heart of the majority of cell recognition and signal transduction processes. Increasingly, medicinal chemistry researchers are interested in small molecule inhibitors of such interactions. This contrasts with approaches based on the design of small molecule receptor ligands mimicking physiological ligands, eg, neurotransmitters and small hormones. However, there have been significant successes, and two symposia at the 220th ACS meeting were devoted to this theme. One half-day symposium focused on general issues of protein-protein interaction, and a whole-day symposium focused on the integrin family of proteins (reviewed by Giancotti and Ruoslahti, Science (1999) 285:1028).     

Small molecule inhibitors of histone deacetylase

This patent deals with novel histone deacetylase (HDAC) inhibitors and methods of their use for treating cell proliferative diseases or conditions, such as cancer, restenosis and psoriasis. Claimed herein are pharmaceutical compositions comprising small molecule HDAC inhibitors as the active ingredient, optionally combined with the use of an antisense oligonucleotide that inhibits HDAC expression. The claimed compounds were synthesised according to given reaction schemes and tested for their inhibition of HDAC enzymatic activity using nuclear extracts from cancer cells (pooled HDACs) and recombinant human HDAC1. An exemplified compound is stated to have caused a significant reduction in tumour weight and volume relative to saline-treated controls in BALB/c nude mice subcutaneously bearing A549 human lung carcinoma cells.     

Small molecule inhibitors of urokinase-type plasminogen activator

The urokinase-type plasminogen activator (uPA) protein is a multifunctional protein involved in a myriad of biological activities including extracellular matrix degradation and cell invasion. Active uPA is a 411 amino acid protein consisting of 3 domains, each of which confers a particular biological function to the overall protein. The amino terminal domain or growth factor domain (GFD), comprised of amino acid residues 1 – 48, is involved in uPA interaction with its cell surface receptor, urokinase-type plasminogen activator receptor (UPAR). The interaction of uPA with UPAR promotes, in part, cell adhesion, migration and invasion. A second domain is the kringle domain, comprising amino acid residues 49 – 135. Initially thought to bind heparin, the kringle domain has more recently been shown to possess antiangiogenic activity. A third domain comprising amino acid residues 159 – 411, the serine protease domain, is involved in the proteolytic activation of plasminogen to plasmin. The production of plasmin by uPA begins a cascade of events manifested by extracellular matrix degradation. The recent patent literature describes small molecule compounds, which inhibit the interaction of uPA with UPAR, inhibit the proteolytic activity of the uPA serine protease domain and inhibit the interaction of uPA with its natural inhibitor, plasminogen activator inhibitor-1 (PAI-1). Small peptides encompassing residues 19 – 31 of the GFD have been developed which exhibit potent inhibition of the uPA–UPAR interaction and show efficacy in tumour-bearing animal models. Small molecules have been disclosed by Corvas, which are reported to be inhibitors of PAI-1. Finally, two approaches toward the development of inhibitors of the uPA serine protease domain have been described in the recent patent literature. The first approach describes non-covalent peptidederived inhibitors discovered by phage display techniques, which bind in the substrate-binding groove of the uPA active site. An alternative approach describes non-covalent small molecule inhibitors, which bind in the enzyme active site in a slightly different binding mode than the peptide-derived inhibitors. These small molecule non-peptide analogues inhibit the uPA proteolytic activity quite effectively and are reported to possess excellent enzyme selectivity and highly improved oral activity. The clinical utility of small molecule uPA enzyme inhibitor analogues awaits the results of a preliminary clinical evaluation of compounds described by Wilex.     

Small molecule coagulation cascade inhibitors in the clinic

Venous thromboembolic disease, including deep vein thrombosis and pulmonary embolism, is a cause of significant mortality and morbidity. For several decades, anticoagulant options for the treatment and prevention of thrombosis have been limited mainly to agents such as unfractionated heparin and oral vitamin K antagonists such as warfarin. Although these therapies have proven benefits, they also have important limitations that result in their underuse in routine clinical practice. A variety of novel anticoagulants with improved pharmacologic and clinical profiles are in development, offering benefits over traditional therapies. Specifically, progress has been made in the development of small molecule Factor Xa inhibitors and thrombin inhibitors. The most advanced drugs reviewed include DPC-423, DPC-602, razaxaban, GSK's 813893, Portola's Xa inhibitors (formerly Millennium), otamixaban, DU-176b, KFA-1982, BAY-59-7939, DX-9065a, YM-150, LY-517717, Exanta, 3DP's thrombin inhibitors, SSR-182289, LB-30057, LB-30870, BIBR-1048 and Merck's thrombin inhibitors. With their potentially consistent and predictable pharmacological profile, oral formulation, and decreased need for coagulation monitoring, these new agents will likely increase the use and duration of anticoagulation treatment in thromboembolic disorders and reduce the burden associated with long-term management.     

Small molecule inhibitors in the treatment of cerebral ischemia

Introduction: Stroke is the world's second leading cause of death. Although recombinant tissue plasminogen activator is an effective treatment for cerebral ischemia, its limitations and ischemic stroke's complex pathophysiology dictate an increased need for the development of new therapeutic interventions. Small molecule inhibitors (SMIs) have the potential to be used as novel therapeutic modalities for stroke, since many preclinical and clinical trials have established their neuroprotective capabilities.

Areas covered: This paper provides a summary of the pathophysiology of stroke as well as clinical and preclinical evaluations of SMIs as therapeutic interventions for cerebral ischemia. Cerebral ischemia is broken down into four mechanisms in this article: thrombosis, ischemic insult, mitochondrial injury and immune response. Insight is provided into preclinical and current clinical assessments of SMIs targeting each mechanism as well as a summary of reported results.

Expert opinion: Many studies demonstrated that pre- or post-treatment with certain SMIs significantly ameliorated adverse effects from stroke. Although some of these promising SMIs moved on to clinical trials, they generally failed, possibly due to the poor translation of preclinical to clinical experiments. Yet, there are many steps being taken to improve the quality of experimental research and translation to clinical trials.     

Small molecule inhibitors of the p53-MDM2

Recent researches have discovered that MDM2 (murine double minute 2, or HDM2 for the human congener) protein is the main negative regulator of p53, which is an attractive therapeutic target in oncology because its tumor-suppressor activity which can be stimulated to eradicate tumor cells. Inhibiting the p53-MDM2 interaction is a promising approach for activating p53, because this association is well characterized at the structural and biological levels. A number of drug screening approaches and technologies have been used to identity novel inhibitors of the p53-MDM2 interaction. This review will detail the development history of MDM2 protein and the p53-MDM2 interaction, the major classes of novel small-molecular p53-MDM2 binding inhibitors, key medicinal action with the protein-protein interaction and in vitro or in vivo biological activities.     

Small molecule kinase inhibitors as anti-cancer therapeutics

Protein kinases have emerged as the most important class of targets in oncology drug discovery because of their major roles in regulating cellular growth and survival. At least, 11 kinase inhibitors have received FDA approval to be used as cancer treatments, and there are continuous efforts to bring more candidates from laboratory benches to the clinic. Although many protein kinase inhibitors directly interact with the ATP binding site, other can alter the kinase conformation to prevent productive ATP binding. Herein we discuss the different mechanisms of action of kinase inhibitors and provide classification of the inhibitors according to their binding sites. Some of these are allosteric inhibitors, ATP competitive inhibitors, protein substrate competitive inhibitors, and covalent bond forming inhibitors. This review provides a broad overview of the relation between mechanism of action and the issues of target selectivity and resistance. Special attention was given to the kinase inhibitors currently in clinical trials.     

Small molecule tyrosine kinase inhibitors in glioblastoma

Archives of Pharmacal Research - Glioblastoma (GBM) is the most common malignant primary brain tumor, with poor survival despite treatment with surgery, radiotherapy, and chemotherapy with...     

Small molecule FLT3 tyrosine kinase inhibitors

Activating mutations of FLT3 (FMS-Like Tyrosine kinase-3) are the most common molecular abnormality in acute myeloid leukemia (AML). Their presence is associated with a worse prognosis, and the recognition of this has led to the development of several new small molecule FLT3 tyrosine kinase inhibitors. In this review, we summarize these developments and compare and contrast these novel agents both with regards to the assays used to characterize them as well as to their clinical potential.     

A screen to identify small molecule inhibitors of protein-protein interactions in mycobacteria

Despite extensive efforts in tuberculosis (TB) drug research, very few novel inhibitors have been discovered. This issue emphasizes the need for innovative methods to discover new anti-TB drugs. In this study, we established a new high-throughput screen (HTS) platform technology that differs from traditional TB drug screens because it utilizes Mycobacterial-Protein Fragment Complementation (M-PFC) to identify small molecule inhibitors of protein-protein interactions in mycobacteria. Several examples of protein-protein interactions were tested with M-PFC to highlight the diversity of selectable drug targets that could be used for screening. These included interactions of essential regulators (IdeR dimerization), enzymatic complexes (LeuCD), secretory antigens (Cfp10-Esat6), and signaling pathways (DevR dimerization). The feasibility of M-PFC in a HTS platform setting was tested by performing a proof-of-concept quantitative HTS of 3,600 small molecule compounds on DevR-DevR interaction, which was chosen because of its strong implications in Mycobacterium tuberculosis persistence and the need for effective drugs against latent TB. The calculated Z'-factor was consistently ≥0.8, indicating a robust and reproducible assay. Completion of the proof-of-concept screen allowed for the identification of advantages and disadvantages in the current assay design, where improvements made will further pioneer M-PFC-based applications in a large-scale HTS format.     

Small molecule inhibition of the Bcl-X(L)-BH3 protein-protein interaction: proof-of-concept of an in vivo chemopotentiator ABT-737

The Bcl-2 family of anti-apoptotic proteins are key regulators of programmed cell death. Bcl-2 and its closely related Bcl-X(L) counterpart are one of several pro-survival proteins which can share up to four highly conserved domains known as the BH1, BH2, BH3 and BH4 domains. These domains form the basis of a well defined groove whereupon a heterodimeric protein-protein interaction can occur with pro-apoptotic BH3 proteins such as Bad, Bid and Bim. Extensive evidence clearly indicates a strong correlation between neoplastic progression and deregulation of apoptotic pathways. Overexpression of Bcl-X(L) is associated with tumor progression, poor prognosis and resistance to chemotherapy. Antagonism of Bcl-X(L) is therefore viewed as a means to mimic the endogenous apoptotic pathways initiated by Bad, Bid and other pro-apoptotic proteins. Several successful approaches to block the Bcl-X(L)-BH3 binding groove have been reported but only recently have proteomimetics been found which could prove to be clinically useful as new anticancer agents capable of overcoming apoptosis resistance. ABT-737 is an example of one of the first small-molecule inhibitors of Bcl-2/X(L) proteins shown to be efficacious in vivo, causing complete regression in small-cell lung carcinoma tumour xenografts in mice. This review will focus on the recent advances surrounding the non-peptidic Bcl-2/X(L) inhibitor ABT-737 developed by Abbot laboratories and highlight the key structural characteristics found within this unique BH3 alpha-helical mimetic.     

Small molecule inhibitors of serine/threonine protein phosphatases

Serine/threonine protein phosphatases have long been ignored as potential therapeutic targets for two reasons, one the biochemical significance of these proteins has not been appreciated and two, many natural protein phosphatase inhibitors are potent toxins and are considered unsuitable for clinical use. This review outlines the biochemical role of this protein family in cancer, cystic fibrosis, immunosuppression and, cardiac and neurological disorders. Particular emphasis is also given to the synthesis of selective small molecule inhibitors and their clinical exploitation.     

Small molecule inhibitors of integrin alpha2beta1

Interactions between the integrin, alpha2beta1, and extracellular matrix (ECM), particularly collagen, play a pivotal role in platelet adhesion and thrombus formation. Platelets interact with collagen in the subendothelial matrix that is exposed by vascular damage. To evaluate the potential of alpha2beta1 inhibitors for anticancer and antithrombotic applications, we have developed a series of small molecule inhibitors of this integrin based on a prolyl-2,3-diaminopropionic acid (DAP) scaffold using solid-phase parallel synthesis. A benzenesulfonamide substituent at the N-terminus of the dipepetide and a benzyl urea at the DAP side chain resulted in tight and highly selective inhibition of alpha2beta1-mediated adhesion of human platelets and other cells to collagen.     

Small molecule inhibitors of peptidoglycan synthesis targeting the lipid II precursor

Bacterial peptidoglycan glycosyltransferases (GTs) of family 51 catalyze the polymerization of the lipid II precursor into linear peptidoglycan strands. This activity is essential to bacteria and represents a validated target for the development of new antibacterials. Application of structure-based virtual screening to the National Cancer Institute library using eHits program and the structure of the glycosyltransferase domain of the Staphylococcus aureus penicillin-binding protein 2 resulted in the identification of two small molecules analogues 5, a 2-[1-[(2-chlorophenyl)methyl]-2-methyl-5-methylsulfanylindol-3-yl]ethanamine and 5b, a 2-[1-[(3,4-dichlorophenyl)methyl]-2-methyl-5-methylsulfanylindol-3-yl]ethanamine that exhibit antibacterial activity against several Gram-positive bacteria but were less active on Gram-negative bacteria. The two compounds inhibit the activity of five GTs in the micromolar range. Investigation of the mechanism of action shows that the compounds specifically target peptidoglycan synthesis. Unexpectedly, despite the fact that the compounds were predicted to bind to the GT active site, compound 5b was found to interact with the lipid II substrate via the pyrophosphate motif. In addition, this compound showed a negatively charged phospholipid-dependent membrane depolarization and disruption activity. These small molecules are promising leads for the development of more active and specific compounds to target the essential GT step in cell wall synthesis.