DownloadmRNA Transcript Diversity Creates New Opportunities for Pharmacological Intervention
by Ryan Smith
Published in Molecular Pharmacology 02/07/2012
Most protein coding genes generate multiple RNA transcripts through alternative splicing, variable 3' and 5'UTRs, and... more Most protein coding genes generate multiple RNA transcripts through alternative splicing, variable 3' and 5'UTRs, and RNA editing. While drug design typically targets the main transcript, alternative transcripts can have profound physiological effects, encoding proteins with distinct functions or regulatory properties. Formation of these alternative transcripts is tissue-selective and context-dependent, creating opportunities for more effective and targeted therapies with reduced adverse effects. Moreover, genetic variation can tilt the balance of alternative versus constitutive transcripts or generate aberrant transcripts that contribute to disease risk. Additionally, environmental factors and drugs modulate RNA splicing, affording new opportunities for the treatment of splicing disorders. For example, therapies targeting specific mRNA transcripts with splice-site directed oligonucleotides that correct aberrant splicing are already in clinical trials for genetic disorders such as Duchenne muscular dystrophy. High-throughput sequencing technologies facilitate discovery of novel RNA transcripts and protein isoforms, with applications ranging from neuromuscular disorders to cancer. Consideration of a gene’s transcript diversity should become an integral part of drug design, development, and therapy.
Game Models of the Defection Dilemma In Biopharmaceutical Discovery Research
Recent trends in biopharmaceutical discovery research toward the systems biology paradigm have created a need for... more Recent trends in biopharmaceutical discovery research toward the systems biology paradigm have created a need for interdisciplinary teams with a wide range of skills. Success, especially economic success, will depend on the ability of team members to learn from each other. The mechanisms used for knowledge transfer and the motives of team members during knowledge production are crucial to this sharing of knowledge. Moreover, the timing of appropriation may determine whether downstream developments can be pursued. In this article we use game models to represent and analyze interactions between partners in collaborative alliances. Our contention is that a researcher's "freedom to operate" downstream is determined by cooperate-versus-defect decisions upstream, as discovery knowledge is being produced and subsequently disseminated. These decisions therefore determine whether researchers can equitably pursue downstream opportunities for medical application development.
A Knowledge Perspective of Strategic Alliances and Management of Biopharmaceutical Innovation: Evolving Research Paradigms
Information from the Human Genome Project is being integrated into the drug discovery and development process to... more Information from the Human Genome Project is being integrated into the drug discovery and development process to permit novel drug targets to be identified, clinical trial testing to be made more efficient, and efficacious therapeutics to be approved and made widely available. Knowledge of the genome will allow for the description and quantification of disease and susceptibility to disease as informational errors or deficits. The creation and application of knowledge occur through cooperative or competitive interactions, often reflecting the perceived value of the knowledge. The public or private value of the knowledge, both for itself and for potential applications, can be determined through an understanding of the classification and characterization of this knowledge, as well as the position of the knowledge within the drug discovery and development pipeline. The transformation of knowledge from a purely public good to a quasi-private good has highlighted the need for balance between incentives for the market provision of scientific and technological knowledge by an innovator and incentives for the market provision of incremental knowledge by a follow-on developer. It has been suggested that a patent system developed for a discrete model of innovation may no longer be optimal for an information-based, cumulative model of innovation. Consequently, it is necessary to reanalyze models of intellectual property protection and strategies of knowledge sharing in biopharmaceutical discovery research. Under certain conditions, the biotech commons is an efficient institution that can preserve downstream opportunities for multiple researchers fairly and efficiently. A framework for classifying and characterizing discovery knowledge is developed in this research and the role of research consortia in preserving the biotech commons is analyzed. This study also addresses the value of pooling versus unilaterally holding knowledge, the benefits associated with appropriating from the commons, the role of knowledge characteristics in bargaining between licensor and licensee, and the overall management of the biotech commons.
HIV-1 RT inhibitors with a novel mechanism of action: NNRTIs that are competing with the nucleotide substrate
by Marco Radi
HIV-1 reverse transcriptase (RT) inhibitors currently used in antiretroviral therapy can be divided into two classes:... more HIV-1 reverse transcriptase (RT) inhibitors currently used in antiretroviral therapy can be divided into two classes: (i) nucleoside analog RT inhibitors (NRTIs), which compete with natural nucleoside substrates and act as terminators of proviral DNA synthesis, and (ii) non-nucleoside RT inhibitors (NNRTIs), which bind to a hydrophobic pocket close to the RT active site. In spite of the efficiency of NRTIs and NNRTIs, the rapid emergence of multidrug-resistant mutations requires the development of new RT inhibitors with an alternative mechanism of action. Recently, several studies reported the discovery of novel non-nucleoside inhibitors with a distinct mechanism of action. Unlike classical NNRTIs, they compete with the nucleotide substrate, thus forming a new class of RT inhibitors: nucleotide-competing RT inhibitors (NcRTIs). In this review, we discuss current progress in the understanding of the peculiar behavior of these compounds.
Design and Synthesis of Thiadiazoles and Thiazoles Targeting the Bcr-Abl T315I Mutant: from Docking False Positives to ATP-Noncompetitive Inhibitors
by Marco Radi
In an effort to optimize our previously identified dual Src/Abl hits, a new series of 1,3,4-thiadiazoles and... more In an effort to optimize our previously identified dual Src/Abl hits, a new series of 1,3,4-thiadiazoles and 1,3-thiazoles were designed and synthesized, paying particular attention to the reduction of their lipophilicity and to the improvement of the affinity towards the drug-resistant T315I mutant. Compound 5 was identified as a promising allosteric inhibitor of the T315I mutant.
Identification and characterization of novel c-Abl / c-Src dual kinase inhibitors which are active against a large panel of tumour progenitor cells that express stem cell marker
by Marco Radi
Background
The non-receptor tyrosine kinases c-Abl and c-Src are overexpressed in various solid human... more
Background
The non-receptor tyrosine kinases c-Abl and c-Src are overexpressed in various solid human tumours. Inhibition of their hyperactivity represents a molecular rationale in the combat of cancerous diseases. Here we examined the effects of a new family of pyrazolo [3,4-d] pyrimidines on a panel of 11 different murine lung tumour progenitor cell lines, that express stem cell markers, as well as on the human lung adenocarcinoma cell line A549, the human hepatoma cell line HepG2 and the human colon cancer cell line CaCo2 to obtain insight into the mode of action of these experimental drugs.
Methodology/Principal Findings
Treatment with the dual kinase inhibitors blocked c-Abl and c-Src kinase activity efficiently in the nanomolar range, induced apoptosis, reduced cell viability and caused cell cycle arrest predominantly at G0/G1 phase while western blot analysis confirmed repressed protein expression of c-Abl and c-Src as well as the interacting partners p38 mitogen activated protein kinase, heterogenous ribonucleoprotein K, cyclin dependent kinase 1 and further proteins that are crucial for tumour progression. Importantly, a significant repression of the epidermal growth factor receptor was observed while whole genome gene expression analysis evidenced regulation of many cell cycle regulated genes as well integrin and focal adhesion kinase (FAK) signalling to impact cytoskeleton dynamics, migration, invasion and metastasis.
Conclusions/Significance
Our experiments and recently published in vivo engraftment studies with various tumour cell lines revealed the dual kinase inhibitors to be efficient in their antitumour activity.
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New insight into small molecules inhibitors of Bcr-Abl
by Marco Radi
Chronic myelogenous leukemia (CML) is a myeloproliferative disease associated with a defined genetic abnormality, the... more Chronic myelogenous leukemia (CML) is a myeloproliferative disease associated with a defined genetic abnormality, the Bcr-Abl fusion gene on the Philadelphia chromosome that expresses the constitutively activated tyrosine kinase (TK) Bcr-Abl. This enzyme leads to the malignant transformation of primitive hematopoietic cells and to the consequent disease. The central role of Bcr-Abl in the pathogenesis of CML culminated in the discovery of imatinib (an ATP-competitive inhibitor), which is currently the frontline therapy for CML. Unfortunately, the initial enthusiasm generated by its high response rate has been dampened by the development of resistance, especially in the advanced phases of CML. To overcome imatinib resistance, several second-generation ATP-competitive inhibitors endowed with increased potency against imatinib-resistant mutants have been developed: the dual Src/Abl inhibitor dasatinib and the Abl inhibitor nilotinib have been recently approved by US-FDA for the treatment of imatinib-resistant CML, and many other compounds are currently in clinical trial. Although second-generation TK inhibitors have shown to be clinically effective against most of the imatinib-resistant mutants, to date poor results have been obtained in the treatment of the Bcr-Abl T315I mutant. In this review we will report the most interesting second-generation Abl and dual Src/Abl inhibitors recently entered in clinical trial, but also the new ATP-competitive and uncompetitive inhibitors published in the last few years, focusing on their chemical structure, mechanism of action, and structure-activity relationship.
Targeting the human DEAD-box polypeptide 3 (DDX3) RNA helicase as a novel strategy to inhibit viral replication
by Marco Radi
Compounds currently used for the treatment of HIV-1 Infections are targeted to viral proteins. However, the high... more Compounds currently used for the treatment of HIV-1 Infections are targeted to viral proteins. However, the high intrinsic mutation and replication rates of HIV-1 often lead to the emergence of drug resistant strains and consequent therapeutic failure. On this basis, cellular cofactors represent attractive new targets for HIV-1 chemotherapy, since targeting a cellular factor that is required for viral replication should help to overcome the problem of viral resistance. We and others have recently reported the identification of compounds suppressing HIV-1 replication by targeting the cellular DEAD-box helicase DDX3. These results provide a proof-of-principle for the feasibility of blocking HIV-1 infection by rendering the host cell environment less favorable for the virus. The rationale for such an approach and its implications in potentially overcoming the problem of drug resistance related to drugs targeting viral proteins will be discussed in the context of the known cellular functions of the DEAD-box helicase DDX3.
Src kinase inhibitors: an update on patented compounds
by Marco Radi
The cytoplasmatic tyrosine in kinase c-Src is involved in the regulation of several cell functions including adhesion,... more The cytoplasmatic tyrosine in kinase c-Src is involved in the regulation of several cell functions including adhesion, invasion, proliferation, survival and angiogenesis. Src activity is strictly regulated in healthy cells, whereas its overexpression or hyperactivation plays a critical role during tumor development. Recently it has been suggested that the oncogenic potential of Src is linked to its role in the activation of key signaling molecules involved in several cell pathways, rather than its direct activity. For all these reasons Src represents a promising therapeutic target for the treatment of tumors. In this article a number of examples of c-Src inhibitors appeared in selected patents from 2006 to early 2011 will be reported, focusing on their chemical features and, whenever possible, on structureactivity relationships and mechanism of action. Examples of type I or II ATP-competitive inhibitors or substrate competitive inhibitors will be presented. The research in this field is very active and will probably lead to the discovery of therapeutically useful compounds, both c-Src selective and multitargeted inhibitors, that acting on different cell pathways could be more effective in blocking cancer development. However, only the results of clinical trials will show in the near future the most promising compounds.