Discovery and development of small molecule c-Met inhibitors
Encyclopedia
The c-Met
(mesenchymal-epithelial transition) tyrosine kinase
stimulates cell scattering, invasion, protection from apoptosis
and angiogenesis
.
c-Met is a receptor tyrosine kinase
, which can cause a wide variety of different cancers, such as renal
, gastric
and small cell lung carcinomas, central nervous system
tumours, as well as several sarcomas
when its activity is dysregulated. Targeting the ATP
binding site of Met by small molecules inhibitors is one strategy for inhibition of the tyrosine kinase.
product of a transforming oncogene
.
Initial attempts to identify ATP-competitive
c-Met inhibitors in 2002 led to the discovery of K252a
, a staurosporine
-like inhibitor which blocks c-Met.
K252a was the first structure to be solved in complex with the unphosphorylated MET kinase domain. It forms two hydrogen bonds between the hinge and pyrralocarbazole subunit.
Later, series of more selective c-Met inhibitors were designed, where an indolin-2-one core (encircled in figure 1) was present in several kinase inhibitors. SU-11274 was evolved by substitution at the 5-position of the indolinone and by adding a 3,5-dimethyl pyrrole
group, PHA-665752 was evolved – a second-generation inhibitor with better potency and activity.
Interest in this field has risen rapidly since 2007 and over 70 patent applications had been published in mid-2009.
Intensive efforts have been exerted in the pharmaceutical industry following the acceptance of c-Met as a suitable target for cancer therapy. 20 crystal structures with and without ligands have been published and in 2010 nearly a dozen small molecule c-Met inhibitors have been tested clinically.
signal transduction pathways.
Met tyrosine kinase is the receptor for hepatocyte growth factor
(HGF a.k.a. scatter factor, SF). HGF is mostly expressed on epithelial cells and mesenchymal cells (f.ex. smooth muscle cells and fibroblasts). HGF is normally active in wound healing, liver
regeneration, embryo
and normal mammalian development, organ morphogenesis
.
c-Met dysregulation can be due to overexpression, gene amplification, mutation
, a ligand-dependent auto- or paracrine loop or an untimely activation of RTK. All these factors affect the survival of cells, their proliferation
and motility. They also lead to cancers and resistance to therapies which aim to treat them. Patients with aberrant c-Met activity usually have a poor prognosis
, aggressive disease, increased metastasis
and shortened survival. This is why targeting the HGF/MET signalling pathway has grown in popularity as a treatment for cancer, and several different therapeutic approaches are being clinically tested. A variety of approaches have been used to target c-Met, each focusing on one of the serial steps that regulate c-Met activation by antibodies, peptide agonists, decoy receptors and other biologic inhibitors
or small molecules inhibitors.
HGF is the natural high-affinity ligand for Met. Its N-terminal region binds to Met and receptor dimerization as well as autophosphorylation
of two tyrosines occur in the activation loop (A-loop) in the kinase domain of Met.
Phosphorylation
occurs in tyrosines close to the C-terminus, creating a multi-functional docking site
which recruits adaptor proteins and leads to downstream signalling. The signaling is mediated by Ras/Mapk, PI3K/Akt, c-Src and STAT3/5 and include cell proliferation, reduced apoptosis, altered cytoskeletal
function and more.
The kinase domain usually consists of a bi-lobed structure, where the lobes are connected with a hinge region, adjacent to the very conserved ATP binding site.
thiourea
group led to compounds with c-Met activity, e.g. quinoline
. This was a key step in the progress of c-Met inhibitor development in that the acyl binding gives the terminal aryl group the ability to penetrate a deep hydrophobic
pocket and so it enhances the potency of the compounds. Alternatives to the acyl thiourea linkage have been found, which have a pyrimidone
group, as in AM7.
AM7 and SU11274 offered the first proof that relatively selective c-Met inhibitors could be identified and that the inhibition leads to an anti-tumour effect in vivo
. When the co-crystal structures of AM7 and SU11274 with c-Met were compared, they were found to be different: SU-11274 binds adjacent to the hinge region with a U-shaped conformation; but AM7 binds to c-Met in an extended conformation which spans the area from the hinge region to the C-helix. It then binds in a hydrophobic pocket. c-Met assumes an inactive, unphosphorylated conformation with AM7, which can bind to both phosphorylated and unphosphorylated conformations of the kinase.
Due to these two different types of binding, small molecule Met inhibitors have been divided into two classes; class I (SU-11274-like) and class II (AM7-like).
There is however another type of small-molecule inhibitors, which does not fit into either of the two classes; a non-competitive
ATP inhibitor that binds in a different way to the other two.
The small molecule inhibitors vary in selectivity, are either very specific or have a broad selectivity. They are either ATP competitive or non-competitive.
of ATP. BMS-777607 and PF-02341066 have a 2-amino-pyridine group, AMG-458 has a quinoline
group and MK-2461 has a tricyclic aromatic group.
group linked to the triazine
ring and an appropriate hydrogen bond acceptor (e.g. hydroxyl group) attached to the pendant benzyl
ring but it seems like the phenol
acts as a hinge binder (with Met1160) and the that the triazine
interacts with Tyr1230.
A number of similar analogues were found and assayed. Structurally similar series of c-Met inhibitors in which a phenolic hinge binding element was linked to an arylamino-triazolopyridazine or aryl-triazolothiapyridazine. One-atom linker was more efficient than a two-atom linker and that substitution at the benzylic position seemed to be tolerated. Compounds with heterocyclic
hinge binding elmements (quinoline, pyridine
, azaindole) linked to fused, nitrogen-dense heteroaromatics (triazolopyridazines, triazolopyrazines and triazolotriazines) have been described.
See figure 4 for details.
quinoline group, was undergoing clinical trials of Phase I for advanced and refractory solid tumours in 2010.
PF-04217903, an ATP-competitive and exceptionally selective compound, has an N-hydroxyethyl pyrazole group tethered to C-7 of the triazolopyrazine. It was undergoing phase I clinical trials in 2010.
The SAR of the unique kinase inhibitor scaffold with powerful c-Met inhibitory activity, MK-2461, has been explored.
The pyridine nitrogen is necessary for inhibition activity and central ring saturation reduced potency. Planarity of the molecule has proven to be essential for maximum potency. Cyclic ethers balance acceptable cell-based activities and pharmacokinetic
characteristics. The following elements are thought to be key in the optimization process:
1) Aryl
groups at the 7-position, as if to maximize hydrophobic packing and planarity,
2) The tight SAR upon the addition of a sulfonamide
group and
3) The relatively flat SAR of solvent-exposed groups.
Often, oncogenic mutations of c-Met cause a resistance to small molecule inhibitors. An MK-2461 analog was therefore tested against a variety of c-Met mutants but proved to be no less potent against them. This gives the molecule a big advantage as a treatment for tumours caused by c-Met dysregulation. MK-2461 was undergoing phase I dose escalation trials in 2010.
groups are also a common feature of class II inhibitors, either in cyclic or acyclic forms. Class II of inhibitors contains a number of different molecules, a common scaffold of which can be seen in figure 4.
linkage (e.g. malonamide, oxalamide, pyrazolones) and constraining of the acyclic acylthiourea structure fragment with various aromatic heterocycles. Further refinement included the blocking of the p-position of the pendant phenyl ring with a fluorine
atom.
Example of interactions between c-Met and a small molecules (marked in a red circle) of class II are as follows: The scaffold of c-Met lodges into the ATP pocket by three key hydrogen bonds, the terminal amine
interacts with the ribose
pocket (of ATP), the terminal 4-fluorophenyl group is oriented in a hydrophobic pocket and pyrrolotriazine plays the role of the hinge-binding group.
AMG 458 is a potent small molecule c-MET inhbitor which proved to have more than a 100-fold selectivity for c-MET across a panel of 55 kinases. Also, AMG 458 was 100% bioavailable across species and the intrinsic half-life
increased with higher mammals.
residues.
The structure of ARQ 197 in complex with the c-Met kinase domain shows that the inhibitor binds a conformation that is distinct from published kinase structures. ARQ 197 strongly inhibits c-Met autoactivation by selectively targeting the inactive form of the kinase between the N- and C- lobes and occupies the ATP binding site.
Increased understanding of the binding modes and structural design brings us closer to the use of other protein interactions and binding pockets, creating inhibitors with alternative structures and optimized profiles.
Thus far, over a dozen Met pathway inhibitors, with varying kinase selectivty profiles ranging from highly selective to multi-targeted, have been studied in the clinic and good progress has been achieved (See table 1). However, as the trials progress many questions and challenges will also arise and need to be addressed.
Also, most approved small molecule agents do not cure patients and most patients who show good response to treatments to begin with tend to develop resistance to them later on. The tumours which then develop are often more aggressive and harder to treat.
The the use of c-Met inhibitors with other therapeutic agents could be crucial for overcoming potential resistance as well as for improving overall clinical benefit. Met pathway inhibitors might be used in combination with other treatments, including chemo
-, radio- or immunotherapy
as well as different Met pathway inhibitor, f.ex. in with HGF and Met biological antagonists or antibodies against HGF and MET. Still, the risk of accumulated toxicity and interactions with other drugs remains.
Ultimately, as a key element in the development of any targeted therapy, the molecular and biochemical determination of the precise functions of the Met pathway in the context of other relevant pro-cancer pathways will undoubtedly play a significant role in this effort.
C-MET
c-Met is a proto-oncogene that encodes a protein known as hepatocyte growth factor receptor . The hepatocyte growth factor receptor protein possesses tyrosine-kinase activity...
(mesenchymal-epithelial transition) tyrosine kinase
Tyrosine kinase
A tyrosine kinase is an enzyme that can transfer a phosphate group from ATP to a protein in a cell. It functions as an "on" or "off" switch in many cellular functions....
stimulates cell scattering, invasion, protection from apoptosis
Apoptosis
Apoptosis is the process of programmed cell death that may occur in multicellular organisms. Biochemical events lead to characteristic cell changes and death. These changes include blebbing, cell shrinkage, nuclear fragmentation, chromatin condensation, and chromosomal DNA fragmentation...
and angiogenesis
Angiogenesis
Angiogenesis is the physiological process involving the growth of new blood vessels from pre-existing vessels. Though there has been some debate over terminology, vasculogenesis is the term used for spontaneous blood-vessel formation, and intussusception is the term for the formation of new blood...
.
c-Met is a receptor tyrosine kinase
Receptor tyrosine kinase
Receptor tyrosine kinases s are the high-affinity cell surface receptors for many polypeptide growth factors, cytokines, and hormones. Of the 90 unique tyrosine kinase genes identified in the human genome, 58 encode receptor tyrosine kinase proteins....
, which can cause a wide variety of different cancers, such as renal
Renal cell carcinoma
Renal cell carcinoma is a kidney cancer that originates in the lining of the proximal convoluted tubule, the very small tubes in the kidney that filter the blood and remove waste products. RCC is the most common type of kidney cancer in adults, responsible for approximately 80% of cases...
, gastric
Stomach cancer
Gastric cancer, commonly referred to as stomach cancer, can develop in any part of the stomach and may spread throughout the stomach and to other organs; particularly the esophagus, lungs, lymph nodes, and the liver...
and small cell lung carcinomas, central nervous system
Central nervous system
The central nervous system is the part of the nervous system that integrates the information that it receives from, and coordinates the activity of, all parts of the bodies of bilaterian animals—that is, all multicellular animals except sponges and radially symmetric animals such as jellyfish...
tumours, as well as several sarcomas
when its activity is dysregulated. Targeting the ATP
Adenosine triphosphate
Adenosine-5'-triphosphate is a multifunctional nucleoside triphosphate used in cells as a coenzyme. It is often called the "molecular unit of currency" of intracellular energy transfer. ATP transports chemical energy within cells for metabolism...
binding site of Met by small molecules inhibitors is one strategy for inhibition of the tyrosine kinase.
History
Early in the 1980‘s MET was described as the proteinProtein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
product of a transforming oncogene
Oncogene
An oncogene is a gene that has the potential to cause cancer. In tumor cells, they are often mutated or expressed at high levels.An oncogene is a gene found in the chromosomes of tumor cells whose activation is associated with the initial and continuing conversion of normal cells into cancer...
.
Initial attempts to identify ATP-competitive
Competitive inhibition
Competitive inhibition is a form of enzyme inhibition where binding of the inhibitor to the active site on the enzyme prevents binding of the substrate and vice versa.-Mechanism:...
c-Met inhibitors in 2002 led to the discovery of K252a
K252a
K252a is an alkaloid isolated from Nocardiopisis sp. soil fungi. This staurosporine analog is a highly potent cell permeable inhibitor of CaM kinase and phosphorylase kinase...
, a staurosporine
Staurosporine
Staurosporine is a natural product originally isolated in 1977 from the bacterium Streptomyces staurosporeus.It was the first of over 50 alkaloids to be isolated with this type of bis-indole chemical structure...
-like inhibitor which blocks c-Met.
K252a was the first structure to be solved in complex with the unphosphorylated MET kinase domain. It forms two hydrogen bonds between the hinge and pyrralocarbazole subunit.
Later, series of more selective c-Met inhibitors were designed, where an indolin-2-one core (encircled in figure 1) was present in several kinase inhibitors. SU-11274 was evolved by substitution at the 5-position of the indolinone and by adding a 3,5-dimethyl pyrrole
Pyrrole
Pyrrole is a heterocyclic aromatic organic compound, a five-membered ring with the formula C4H4NH. It is a colourless volatile liquid that darkens readily upon exposure to air. Substituted derivatives are also called pyrroles, e.g., N-methylpyrrole, C4H4NCH3...
group, PHA-665752 was evolved – a second-generation inhibitor with better potency and activity.
Interest in this field has risen rapidly since 2007 and over 70 patent applications had been published in mid-2009.
Intensive efforts have been exerted in the pharmaceutical industry following the acceptance of c-Met as a suitable target for cancer therapy. 20 crystal structures with and without ligands have been published and in 2010 nearly a dozen small molecule c-Met inhibitors have been tested clinically.
Introduction
Receptor tyrosine kinases (RTKs) are a vital element in regulating many intracellularIntracellular
Not to be confused with intercellular, meaning "between cells".In cell biology, molecular biology and related fields, the word intracellular means "inside the cell".It is used in contrast to extracellular...
signal transduction pathways.
Met tyrosine kinase is the receptor for hepatocyte growth factor
Hepatocyte growth factor
Hepatocyte growth factor/scatter factor is a paracrine cellular growth, motility and morphogenic factor. It is secreted by mesenchymal cells and targets and acts primarily upon epithelial cells and endothelial cells, but also acts on haemopoietic progenitor cells...
(HGF a.k.a. scatter factor, SF). HGF is mostly expressed on epithelial cells and mesenchymal cells (f.ex. smooth muscle cells and fibroblasts). HGF is normally active in wound healing, liver
Liver
The liver is a vital organ present in vertebrates and some other animals. It has a wide range of functions, including detoxification, protein synthesis, and production of biochemicals necessary for digestion...
regeneration, embryo
Embryo
An embryo is a multicellular diploid eukaryote in its earliest stage of development, from the time of first cell division until birth, hatching, or germination...
and normal mammalian development, organ morphogenesis
Morphogenesis
Morphogenesis , is the biological process that causes an organism to develop its shape...
.
c-Met dysregulation can be due to overexpression, gene amplification, mutation
Mutation
In molecular biology and genetics, mutations are changes in a genomic sequence: the DNA sequence of a cell's genome or the DNA or RNA sequence of a virus. They can be defined as sudden and spontaneous changes in the cell. Mutations are caused by radiation, viruses, transposons and mutagenic...
, a ligand-dependent auto- or paracrine loop or an untimely activation of RTK. All these factors affect the survival of cells, their proliferation
Cell growth
The term cell growth is used in the contexts of cell development and cell division . When used in the context of cell division, it refers to growth of cell populations, where one cell grows and divides to produce two "daughter cells"...
and motility. They also lead to cancers and resistance to therapies which aim to treat them. Patients with aberrant c-Met activity usually have a poor prognosis
Prognosis
Prognosis is a medical term to describe the likely outcome of an illness.When applied to large statistical populations, prognostic estimates can be very accurate: for example the statement "45% of patients with severe septic shock will die within 28 days" can be made with some confidence, because...
, aggressive disease, increased metastasis
Metastasis
Metastasis, or metastatic disease , is the spread of a disease from one organ or part to another non-adjacent organ or part. It was previously thought that only malignant tumor cells and infections have the capacity to metastasize; however, this is being reconsidered due to new research...
and shortened survival. This is why targeting the HGF/MET signalling pathway has grown in popularity as a treatment for cancer, and several different therapeutic approaches are being clinically tested. A variety of approaches have been used to target c-Met, each focusing on one of the serial steps that regulate c-Met activation by antibodies, peptide agonists, decoy receptors and other biologic inhibitors
or small molecules inhibitors.
Structure and function
The c-Met RTK subfamily is different in structure to many other RTK families: The mature form has an extracellular α-chain (50kDa) and a transmembrane β-chain (140kDa) that are linked together by a disulphide bond. The beta chain contains the intracellular tyrosine kinase domain and a tail on the C-terminal which is vital for the docking of substrates and downstream signalling.HGF is the natural high-affinity ligand for Met. Its N-terminal region binds to Met and receptor dimerization as well as autophosphorylation
Autophosphorylation
In biochemistry, autophosphorylation is the process in which a protein kinase attaches a phosphate group to itself. This usually lead to kinase activation or regulation, and phosphorylation of other kinase substrates....
of two tyrosines occur in the activation loop (A-loop) in the kinase domain of Met.
Phosphorylation
Phosphorylation
Phosphorylation is the addition of a phosphate group to a protein or other organic molecule. Phosphorylation activates or deactivates many protein enzymes....
occurs in tyrosines close to the C-terminus, creating a multi-functional docking site
which recruits adaptor proteins and leads to downstream signalling. The signaling is mediated by Ras/Mapk, PI3K/Akt, c-Src and STAT3/5 and include cell proliferation, reduced apoptosis, altered cytoskeletal
Cytoskeleton
The cytoskeleton is a cellular "scaffolding" or "skeleton" contained within a cell's cytoplasm and is made out of protein. The cytoskeleton is present in all cells; it was once thought to be unique to eukaryotes, but recent research has identified the prokaryotic cytoskeleton...
function and more.
The kinase domain usually consists of a bi-lobed structure, where the lobes are connected with a hinge region, adjacent to the very conserved ATP binding site.
Development
Using information from the co-crystal structure of PHA-66752 and c-Met, the selective inhibitor PF-2341066 was designed. It was undergoing Phase I/II clinical trials in 2010. Changing a series of 4-phenoxyquinoline compounds with an acylAcyl
An acyl group is a functional group derived by the removal of one or more hydroxyl groups from an oxoacid, including inorganic acids.In organic chemistry, the acyl group is usually derived from a carboxylic acid . Therefore, it has the formula RCO-, where R represents an alkyl group that is...
thiourea
Thiourea
Thiourea is an organosulfur compound of with the formula SC2 . It is structurally similar to urea, except that the oxygen atom is replaced by a sulfur atom, but the properties of urea and thiourea differ significantly. Thiourea is a reagent in organic synthesis. "Thioureas" refers to a broad...
group led to compounds with c-Met activity, e.g. quinoline
Quinoline
Quinoline is a heterocyclic aromatic organic compound. It has the formula C9H7N and is a colourless hygroscopic liquid with a strong odour. Aged samples, if exposed to light, become yellow and later brown...
. This was a key step in the progress of c-Met inhibitor development in that the acyl binding gives the terminal aryl group the ability to penetrate a deep hydrophobic
Hydrophobe
In chemistry, hydrophobicity is the physical property of a molecule that is repelled from a mass of water....
pocket and so it enhances the potency of the compounds. Alternatives to the acyl thiourea linkage have been found, which have a pyrimidone
Pyrimidone
Pyrimidone is the name given to either of two heterocyclic compounds with the formula C4H4N2O: 2-pyrimidone and 4-pyrimidone. The compounds can also be called 2-hydroxypyrimidine or 4-hydroxypyrimidine respectively, based on a substituted pyrimidine, or 1,3-diazine, ring.-Derivatives:Derivatives of...
group, as in AM7.
AM7 and SU11274 offered the first proof that relatively selective c-Met inhibitors could be identified and that the inhibition leads to an anti-tumour effect in vivo
In vivo
In vivo is experimentation using a whole, living organism as opposed to a partial or dead organism, or an in vitro controlled environment. Animal testing and clinical trials are two forms of in vivo research...
. When the co-crystal structures of AM7 and SU11274 with c-Met were compared, they were found to be different: SU-11274 binds adjacent to the hinge region with a U-shaped conformation; but AM7 binds to c-Met in an extended conformation which spans the area from the hinge region to the C-helix. It then binds in a hydrophobic pocket. c-Met assumes an inactive, unphosphorylated conformation with AM7, which can bind to both phosphorylated and unphosphorylated conformations of the kinase.
Due to these two different types of binding, small molecule Met inhibitors have been divided into two classes; class I (SU-11274-like) and class II (AM7-like).
There is however another type of small-molecule inhibitors, which does not fit into either of the two classes; a non-competitive
Non-competitive inhibition
Non-competitive inhibition is a type of enzyme inhibition where the inhibitor reduces the activity of the enzyme, by binding not to the active site on the enzyme, but to a different site...
ATP inhibitor that binds in a different way to the other two.
The small molecule inhibitors vary in selectivity, are either very specific or have a broad selectivity. They are either ATP competitive or non-competitive.
ATP-competitive small molecule c-Met inhibitors
Even though the two classes are structurally different, they do share some properties: They both bind at the kinase hinge region (although they occupy different parts of the c-Met active site) and they all aim to mimic the purinePurine
A purine is a heterocyclic aromatic organic compound, consisting of a pyrimidine ring fused to an imidazole ring. Purines, including substituted purines and their tautomers, are the most widely distributed kind of nitrogen-containing heterocycle in nature....
of ATP. BMS-777607 and PF-02341066 have a 2-amino-pyridine group, AMG-458 has a quinoline
Quinoline
Quinoline is a heterocyclic aromatic organic compound. It has the formula C9H7N and is a colourless hygroscopic liquid with a strong odour. Aged samples, if exposed to light, become yellow and later brown...
group and MK-2461 has a tricyclic aromatic group.
Class I
Class I inhibitors have many different structures, are relatively selective and have a U-shaped conformation and binds to the activation loop of c-Met.Structure-activity relationship of Class I inhibitors
A series of triazolotriazines was discovered, which showed great promise as a c-MET inhibitors. Structure activity relationship (SAR) implies the necessity of an arylAryl
In the context of organic molecules, aryl refers to any functional group or substituent derived from an aromatic ring, be it phenyl, naphthyl, thienyl, indolyl, etc....
group linked to the triazine
Triazine
A triazine is one of three organic chemicals, isomeric with each other, whose molecular formula is 333 and whose empirical formula is CHN.- Structure :...
ring and an appropriate hydrogen bond acceptor (e.g. hydroxyl group) attached to the pendant benzyl
Benzyl
In organic chemistry, benzyl is the term used to describe the substituent or molecular fragment possessing the structure C6H5CH2-. Benzyl features a benzene ring attached to a CH2 group.-Nomenclature:...
ring but it seems like the phenol
Phenol
Phenol, also known as carbolic acid, phenic acid, is an organic compound with the chemical formula C6H5OH. It is a white crystalline solid. The molecule consists of a phenyl , bonded to a hydroxyl group. It is produced on a large scale as a precursor to many materials and useful compounds...
acts as a hinge binder (with Met1160) and the that the triazine
Triazine
A triazine is one of three organic chemicals, isomeric with each other, whose molecular formula is 333 and whose empirical formula is CHN.- Structure :...
interacts with Tyr1230.
A number of similar analogues were found and assayed. Structurally similar series of c-Met inhibitors in which a phenolic hinge binding element was linked to an arylamino-triazolopyridazine or aryl-triazolothiapyridazine. One-atom linker was more efficient than a two-atom linker and that substitution at the benzylic position seemed to be tolerated. Compounds with heterocyclic
Heterocyclic compound
A heterocyclic compound is a cyclic compound which has atoms of at least two different elements as members of its ring. The counterparts of heterocyclic compounds are homocyclic compounds, the rings of which are made of a single element....
hinge binding elmements (quinoline, pyridine
Pyridine
Pyridine is a basic heterocyclic organic compound with the chemical formula C5H5N. It is structurally related to benzene, with one C-H group replaced by a nitrogen atom...
, azaindole) linked to fused, nitrogen-dense heteroaromatics (triazolopyridazines, triazolopyrazines and triazolotriazines) have been described.
See figure 4 for details.
Examples of Class I inhibitors
JNJ-38877605, which contains a difluoro methyl linker and a bioavailableBioavailability
In pharmacology, bioavailability is a subcategory of absorption and is used to describe the fraction of an administered dose of unchanged drug that reaches the systemic circulation, one of the principal pharmacokinetic properties of drugs. By definition, when a medication is administered...
quinoline group, was undergoing clinical trials of Phase I for advanced and refractory solid tumours in 2010.
PF-04217903, an ATP-competitive and exceptionally selective compound, has an N-hydroxyethyl pyrazole group tethered to C-7 of the triazolopyrazine. It was undergoing phase I clinical trials in 2010.
The SAR of the unique kinase inhibitor scaffold with powerful c-Met inhibitory activity, MK-2461, has been explored.
The pyridine nitrogen is necessary for inhibition activity and central ring saturation reduced potency. Planarity of the molecule has proven to be essential for maximum potency. Cyclic ethers balance acceptable cell-based activities and pharmacokinetic
Pharmacokinetics
Pharmacokinetics, sometimes abbreviated as PK, is a branch of pharmacology dedicated to the determination of the fate of substances administered externally to a living organism...
characteristics. The following elements are thought to be key in the optimization process:
1) Aryl
Aryl
In the context of organic molecules, aryl refers to any functional group or substituent derived from an aromatic ring, be it phenyl, naphthyl, thienyl, indolyl, etc....
groups at the 7-position, as if to maximize hydrophobic packing and planarity,
2) The tight SAR upon the addition of a sulfonamide
Sulfonamide (chemistry)
In chemistry, the sulfonamide functional group is -S2-NH2, a sulfonyl group connected to an amine group.A sulfonamide is a compound that contains this group. The general formula is RSO2NH2, where R is some organic group. For example, "methanesulfonamide" is CH3SO2NH2...
group and
3) The relatively flat SAR of solvent-exposed groups.
Often, oncogenic mutations of c-Met cause a resistance to small molecule inhibitors. An MK-2461 analog was therefore tested against a variety of c-Met mutants but proved to be no less potent against them. This gives the molecule a big advantage as a treatment for tumours caused by c-Met dysregulation. MK-2461 was undergoing phase I dose escalation trials in 2010.
Class II
Class II inhibitors are usually not as selective as those of class I. UreaUrea
Urea or carbamide is an organic compound with the chemical formula CO2. The molecule has two —NH2 groups joined by a carbonyl functional group....
groups are also a common feature of class II inhibitors, either in cyclic or acyclic forms. Class II of inhibitors contains a number of different molecules, a common scaffold of which can be seen in figure 4.
Structure-activity relationship of Class II inhibitors
Series of quinoline c-Met inhibitors with an acylthiourea linkage have been explored. Multiple series of analogs have been found with alternative hinge binding groups (e.g. replacement of the quinoline group), replacement of the thioureaThiourea
Thiourea is an organosulfur compound of with the formula SC2 . It is structurally similar to urea, except that the oxygen atom is replaced by a sulfur atom, but the properties of urea and thiourea differ significantly. Thiourea is a reagent in organic synthesis. "Thioureas" refers to a broad...
linkage (e.g. malonamide, oxalamide, pyrazolones) and constraining of the acyclic acylthiourea structure fragment with various aromatic heterocycles. Further refinement included the blocking of the p-position of the pendant phenyl ring with a fluorine
Fluorine
Fluorine is the chemical element with atomic number 9, represented by the symbol F. It is the lightest element of the halogen column of the periodic table and has a single stable isotope, fluorine-19. At standard pressure and temperature, fluorine is a pale yellow gas composed of diatomic...
atom.
Example of interactions between c-Met and a small molecules (marked in a red circle) of class II are as follows: The scaffold of c-Met lodges into the ATP pocket by three key hydrogen bonds, the terminal amine
Amine
Amines are organic compounds and functional groups that contain a basic nitrogen atom with a lone pair. Amines are derivatives of ammonia, wherein one or more hydrogen atoms have been replaced by a substituent such as an alkyl or aryl group. Important amines include amino acids, biogenic amines,...
interacts with the ribose
Ribose
Ribose is an organic compound with the formula C5H10O5; specifically, a monosaccharide with linear form H––4–H, which has all the hydroxyl groups on the same side in the Fischer projection....
pocket (of ATP), the terminal 4-fluorophenyl group is oriented in a hydrophobic pocket and pyrrolotriazine plays the role of the hinge-binding group.
Examples of Class II inhibitors
In phase II clinical trials, GSK 1363089 (XL880, foretinib) was well tolerated. It led to slight regressions or stable disease in patients with papillary renal carcinoma and poorly differentiated gastric cancer.AMG 458 is a potent small molecule c-MET inhbitor which proved to have more than a 100-fold selectivity for c-MET across a panel of 55 kinases. Also, AMG 458 was 100% bioavailable across species and the intrinsic half-life
Half-life
Half-life, abbreviated t½, is the period of time it takes for the amount of a substance undergoing decay to decrease by half. The name was originally used to describe a characteristic of unstable atoms , but it may apply to any quantity which follows a set-rate decay.The original term, dating to...
increased with higher mammals.
ATP non-competitive small molecule c-Met inhibitors
ARQ197 is a selective, orally bioavailable, clinically advanced low-molecular weight and well-tolerated c-MET inhibitor, which is currently in Phase 3 clinical trials in non-small cell lung cancer patients. ARQ197 is a non-ATP competitive c-MET autophosphorylation inhibitor with a high selectivity for the unphosphorylated conformation of the kinase. ARQ197 cuts off the interactions between the key catalyticCatalysis
Catalysis is the change in rate of a chemical reaction due to the participation of a substance called a catalyst. Unlike other reagents that participate in the chemical reaction, a catalyst is not consumed by the reaction itself. A catalyst may participate in multiple chemical transformations....
residues.
The structure of ARQ 197 in complex with the c-Met kinase domain shows that the inhibitor binds a conformation that is distinct from published kinase structures. ARQ 197 strongly inhibits c-Met autoactivation by selectively targeting the inactive form of the kinase between the N- and C- lobes and occupies the ATP binding site.
Current status
Since the discovery of Met and HGF, much research interest has focused on their roles in cancer. The Met pathway is one of the most frequently dysregulated pathways in human cancer.Increased understanding of the binding modes and structural design brings us closer to the use of other protein interactions and binding pockets, creating inhibitors with alternative structures and optimized profiles.
| SND: structure not disclosed; RON: Recepteur d'origine nantais ALK: Anaplastic lymphoma kinase Anaplastic lymphoma kinase Anaplastic lymphoma kinase also known as ALK tyrosine kinase receptor or CD246 is an enzyme that in humans is encoded by the ALK gene.-Function:... ; VEGFR2: Vascular-Endothelial Growth Factor Receptor 2; MiT: microphthalmia transcription factor tumors; PDAC: pancreatic ductal adenocarcinoma; NSCLC: non-small cell lung carcinoma; HCC: hepatocellular carinoma; MTC: medullary thyroid carcinoma; GBM: glioblastoma; RCC: renal cell carcinoma; HNSCC: head and neck squamous cell cainoma; IND: Investigational New Drug. |
Thus far, over a dozen Met pathway inhibitors, with varying kinase selectivty profiles ranging from highly selective to multi-targeted, have been studied in the clinic and good progress has been achieved (See table 1). However, as the trials progress many questions and challenges will also arise and need to be addressed.
Also, most approved small molecule agents do not cure patients and most patients who show good response to treatments to begin with tend to develop resistance to them later on. The tumours which then develop are often more aggressive and harder to treat.
The the use of c-Met inhibitors with other therapeutic agents could be crucial for overcoming potential resistance as well as for improving overall clinical benefit. Met pathway inhibitors might be used in combination with other treatments, including chemo
Chemotherapy
Chemotherapy is the treatment of cancer with an antineoplastic drug or with a combination of such drugs into a standardized treatment regimen....
-, radio- or immunotherapy
Immunotherapy
Immunotherapy is a medical term defined as the "treatment of disease by inducing, enhancing, or suppressing an immune response". Immunotherapies designed to elicit or amplify an immune response are classified as activation immunotherapies. While immunotherapies that reduce or suppress are...
as well as different Met pathway inhibitor, f.ex. in with HGF and Met biological antagonists or antibodies against HGF and MET. Still, the risk of accumulated toxicity and interactions with other drugs remains.
Ultimately, as a key element in the development of any targeted therapy, the molecular and biochemical determination of the precise functions of the Met pathway in the context of other relevant pro-cancer pathways will undoubtedly play a significant role in this effort.
See also
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- Discovery and development of CCR5 receptor antagonistsDiscovery and development of CCR5 receptor antagonistsCCR5 receptor antagonists are a class of small molecules that antagonize the CCR5 receptor. The C-C motif chemokine receptor CCR5 is involved in the HIV entry process...
- Discovery and development of TRPV1 antagonistsDiscovery and development of TRPV1 antagonistsChronic pain remains a recognized unmet medical need. Consequently, the search for new analgesic agents is being intensively studied by the pharmaceutical industry. The TRPV1 receptor is an ion channel that has been implicated in mediation of many types of pain and therefore studied most extensively...
- Discovery and development of HIV protease inhibitorsDiscovery and development of HIV protease inhibitorsMany major physiological processes depend on regulation of proteolytic enzyme activity and there can be dramatic consequences when equilibrium between an enzyme and its substrates is disturbed. In this prospective, the discovery of small-molecule ligands, like protease inhibitors, that can modulate...
- Discovery and development of non-nucleoside reverse transcriptase inhibitorsDiscovery and development of non-nucleoside reverse transcriptase inhibitorsNon-nucleoside reverse-transcriptase inhibitors are antiretroviral drugs used in the treatment of human immunodeficiency virus . NNRTIs inhibit reverse transcriptase , an enzyme that controls the replication of the genetic material of HIV...
- Cannabinoid receptor antagonistCannabinoid receptor antagonistThe discovery of the endogenous cannabinoid system led to the development of CB1 receptor antagonists. The first cannabinoid receptor "antagonist," rimonabant, was described in 1994. Rimonabant blocks the CB1 receptor selectively and it has been shown to decrease food intake and regulate...
- Development of dipeptidyl peptidase-4 inhibitorsDevelopment of dipeptidyl peptidase-4 inhibitorsDipeptidyl peptidase-4 inhibitors are enzyme inhibitors that inhibit the enzyme dipeptidyl peptidase-4 and are a potent treatment for type 2 diabetes...
- Mesenchymal-epithelial transitionMesenchymal-epithelial transitionA mesenchymal-epithelial transition is a reversible biological process that involves the transition from motile, multipolar or spindle-shaped mesenchymal cells to planar arrays of polarized cells called epithelia. MET is the reverse process of epithelial-mesenchymal transition...
- Hepatocyte growth factorHepatocyte growth factorHepatocyte growth factor/scatter factor is a paracrine cellular growth, motility and morphogenic factor. It is secreted by mesenchymal cells and targets and acts primarily upon epithelial cells and endothelial cells, but also acts on haemopoietic progenitor cells...
- Discovery and development of cyclooxygenase 2 inhibitors
- 5-HT3 antagonist5-HT3 antagonistThe 5-HT3 antagonists are a class of medications that act as receptor antagonists at the 5-HT3 receptor, a subtype of serotonin receptor found in terminals of the vagus nerve and in certain areas of the brain....
- Discovery and development of cyclooxygenase 2 inhibitors
- Melatonin receptor agonists
- K252aK252aK252a is an alkaloid isolated from Nocardiopisis sp. soil fungi. This staurosporine analog is a highly potent cell permeable inhibitor of CaM kinase and phosphorylase kinase...
- Epithelial-mesenchymal transitionEpithelial-mesenchymal transitionEpithelial-mesenchymal transition or transformation is a hypothesized program of development of biological cells characterized by loss of cell adhesion, repression of E-cadherin expression, and increased cell mobility...
- c-MetC-METc-Met is a proto-oncogene that encodes a protein known as hepatocyte growth factor receptor . The hepatocyte growth factor receptor protein possesses tyrosine-kinase activity...