Novel pharmacological modulators of autophagy: an updated patent review (2012-2015)

Introduction: Autophagy is a lysosome-dependent degradation pathway that maintains cellular homeostasis in response to a variety of cellular stresses. Accumulating reports based on animal models have indicated the importance of this catabolic program in many human pathophysiological conditions, including diabetes, neurodegenerative diseases, aging, and cancers. Therefore, autophagy has been highlighted as a novel therapeutic target with a wide range of beneficial effects on human diseases. Here, we review the recent advances of our knowledge toward autophagy, as well as the efforts for developing autophagy modulators.

Areas covered: The relevant patents (published at 2012–2015) and the research literature claiming the pharmacological modulation of autophagy are reviewed. Also, their molecular mechanisms and potential therapeutic utilities are discussed.

Expert opinion: Considering the molecular machinery involved in autophagy induction, the targeting of autophagy-specific protein is very important to design the therapeutic interventions for specifically treating a variety of autophagy-associated disorders. Many patents and the research literature described in this review have shown promising applications of the relevant autophagy modulators for cancer or neurodegeneration treatments, a few of which are already being considered for clinical evaluation. However, most patents have claimed the modulators of autophagy with little information regarding their mechanisms of action. To design highly potent therapeutics, further work, such as developing compounds that specifically target the autophagy-specific machinery, are required.     

MIF,a controversial cytokine: a review of structural features,challenges, and opportunities for drug development

Introduction: Macrophage migration inhibitory factor (MIF) has emerged as a promising drug target in diseases including sepsis, rheumatoid arthritis, and cancer. MIF has multiple properties that favor development of specific, targeted therapies: it is expressed broadly among human cells, has noted roles in diverse inflammatory and oncological processes, and has intrinsic enzymatic activity amenable to high-throughput screening. Despite these advantages, anti-MIF therapy remains well behind other cytokine-targeted therapeutics, with no small molecules in the pipeline for clinical development and anti-MIF antibodies only recently beginning clinical trials.

Areas covered: In this review we summarize current literature regarding MIF structure and function–including challenges and controversies that have arisen in studies of anti-MIF therapeutics–and propose a strategy for development of clinically relevant anti-MIF drugs.

Expert opinion: We believe that the field of anti-MIF therapeutics would benefit from capitalizing on the protein’s multiple assets while acknowledging their flaws. The tautomerase enzymatic site of MIF may not be active biologically, but can nonetheless offer a high-throughput method to highlight molecules of interest that can affect its other, frequently intertwined bioactivities. Future work should also focus on developing more robust assays for MIF bioactivity that can be used for second-pass screening and specificity studies.     

Development of drugs for Epstein–Barr virus using high-throughput in silico virtual screening

Importance of the field: Epstein–Barr virus (EBV) is a ubiquitous human herpesvirus that is causally associated with endemic forms of Burkitt's lymphoma, nasopharyngeal carcinoma and lymphoproliferative disease in immunosuppressed individuals. On a global scale, EBV infects > 90% of the adult population and is responsible for ～ 1% of all human cancers. To date, there is no efficacious drug or therapy for the treatment of EBV infection and EBV-related diseases.

Areas covered in this review: In this review, we discuss the existing anti-EBV inhibitors and those under development. We discuss the value of different molecular targets, including EBV lytic DNA replication enzymes as well as proteins that are expressed exclusively during latent infection, such as EBV nuclear antigen 1 (EBNA-1) and latent membrane protein 1. As the atomic structure of the EBNA-1 DNA binding domain has been described, it is an attractive target for in silico methods of drug design and small molecule screening. We discuss the use of computational methods that can greatly facilitate the development of novel inhibitors and how in silico screening methods can be applied to target proteins with known structures, such as EBNA-1, to treat EBV infection and disease.

What the reader will gain: The reader is familiarized with the problems in targeting of EBV for inhibition by small molecules and how computational methods can greatly facilitate this process.

Take home message: Despite the impressive efficacy of nucleoside analogs for the treatment of herpesvirus lytic infection, there remain few effective treatments for latent infections. As EBV latent infection persists within and contributes to the formation of EBV-associated cancers, targeting EBV latent proteins is an unmet medical need. High-throughput in silico screening can accelerate the process of drug discovery for novel and selective agents that inhibit EBV latent infection and associated disease.     

Design of chemical libraries for screening

Importance of the field: The ultimate goal of discovery screening is to have a fast and cost-effective strategy to meet the demands of producing high-content lead series with improved prospects for clinical success. While high-throughput screening (HTS) dominates the drug discovery landscape, other processes and technologies have emerged, including high-content screening and fragment-based design to provide alternatives that may be more suitable for certain targets. There has been a growing interest in reducing the number of compounds to be screened to prevent the escalation in the costs, time and resources associated with HTS campaigns. Library design plays a central role in these efforts.

Areas covered in this review: This opinion provides a survey of some recent developments in the diversity based library design process, but within a historical context. In particular, the importance of chemotyping and substructure analysis and the challenges presented by novel lead discovery technologies that require the design of libraries for screening are discussed.

What the reader will gain: Readers will gain an appreciation of some developments in the field of library design and the factors that are driving the development of new library design technologies; specifically, challenges presented for chemoinformatics with the novel screening technologies in diversity based screening and compound filtering.

Take home message: Chemotyping and substrutural analysis are techniques that have been underutilized in the process of library design. However, they offer a direct way to evaluate libraries and have been successfully used to develop predictive methodologies. Tools are available to this end, but the full power of the approach has not been realized yet.     

Cell-impedance-based label-free technology for the identification of new drugs

Introduction: Drug discovery has progressed from relatively simple binding or activity screening assays to high-throughput screening of sophisticated compound libraries with emphasis on miniaturization and automation. The development of functional assays has enhanced the success rate in discovering novel drug molecules. Many technologies, originally based on radioactive labeling, have sequentially been replaced by methods based on fluorescence labeling. Recently, the focus has switched to label-free technologies in cell-based screening assays.

Areas covered: Label-free, cell-impedance-based methods comprise of different technologies including surface plasmon resonance, mass spectrometry and biosensors applied for screening of anticancer drugs, G protein-coupled receptors, receptor tyrosine kinase and virus inhibitors, drug and nanoparticle cytotoxicity. Many of the developed methods have been used for high-throughput screening in cell lines. Cell viability and morphological damage prediction have been monitored in three-dimensional spheroid human HT-29 carcinoma cells and whole Schistosomula larvae.

Expert opinion: Progress in label-free, cell-impedance-based technologies has facilitated drug screening and may enhance the discovery of potential novel drug molecules through, and improve target molecule identification in, alternative signal pathways. The variety of technologies to measure cellular responses through label-free cell-impedance based approaches all support future drug development and should provide excellent assets for finding better medicines.     

Functional genomic and high-content screening for target discovery and deconvolution

Introduction: Functional genomic screens apply knowledge gained from the sequencing of the human genome toward rapid methods of identifying genes involved in cellular function based on a specific phenotype. This approach has been made possible through advances in both molecular biology and automation. The utility of this approach has been further enhanced through the application of image-based high-content screening: an automated microscopy and quantitative image analysis platform. These approaches can significantly enhance the acquisition of novel targets for drug discovery.

Areas covered: Both the utility and potential issues associated with functional genomic screening approaches are discussed in this review, along with examples that illustrate both. The considerations for high-content screening applied to functional genomics are also presented.

Expert opinion: Functional genomic screening and high-content screening are extremely useful in the identification of new drug targets. However, the technical, experimental, and computational parameters have an enormous influence on the results. Thus, although new targets are identified, caution should be applied to the interpretation of screening data in isolation. Genomic screens should be viewed as an integral component of a target identification campaign that requires both the acquisition of orthogonal data, as well as a rigorous validation strategy.     

Optimization of siRNA delivery to target sites: issues and future directions

ABSTRACT

Introduction: The discovery of RNA interference (RNAi) earned the 2006 Nobel Prize in Physiology or Medicine for its biological significance and potential for developing novel therapeutics. The small interfering RNA (siRNA) is the most promising tool for translating RNAi to clinical use. Efforts are ongoing to improve siRNA delivery through developing novel biomaterials and delivery strategies. Given time, it appears that siRNA drugs will eventually become a reality.

Areas covered: The currently used approaches for siRNA delivery are discussed with a focus on siRNA therapeutics currently in clinical testing. A comparison of advantageous aspects of currently available platforms and the possibility of further optimization for increased efficiency and safety are presented. Future directions in siRNA delivery are also highlighted.

Expert opinion: The recent success in the field of siRNA delivery is based mainly on developing new biomaterials with extraordinarily high activities. Notably, the introduction of ionizable lipids and novel targeting ligands represent two huge steps for realizing siRNA therapy. The currently available systems are largely directed to the liver and the new challenge is to extend their applicability for treating diseases of other organs. Active targeting to different organs is the most promising approach for developing new siRNA-based therapeutics.     

Fluorescence polarization assays in small molecule screening

Importance of the field: Fluorescence polarization (FP) is a homogeneous method that allows rapid and quantitative analysis of diverse molecular interactions and enzyme activities. This technique has been widely utilized in clinical and biomedical settings, including the diagnosis of certain diseases and monitoring therapeutic drug levels in body fluids. Recent developments in the field have been symbolized by the facile adoption of FP in high-throughput screening and small molecule drug discovery of an increasing range of target classes.

Areas covered in this review: The article provides a brief overview of the theoretical foundation of FP, followed by updates on recent advancements in its application for various drug target classes, including GPCRs, enzymes and protein–protein interactions. The strengths and weaknesses of this method, practical considerations in assay design, novel applications and future directions are also discussed.

What the reader will gain: The reader is informed of the most recent advancements and future directions of FP application to small molecule screening.

Take home message: In addition to its continued utilization in high-throughput screening, FP has expanded into new disease and target areas and has been marked by increased use of labeled small molecule ligands for receptor-binding studies.     

In silico screening strategies for novel inhibitors of parasitic diseases

Introduction: Parasitic diseases are a major global problem causing long-term disability and death, with severe medical and psychological consequences around the world. Despite the prevalence of parasitic disease, the treatment options for many of these illnesses are still inadequate and there is a dire need for new antiparasitic drugs. In silico screening techniques, which are powerful strategies for hit generation, are widely being applied in the design of new ligands for parasitic diseases.

Areas covered: This article analyses the application of ligand- and structure-based virtual screening strategies against a variety of parasitic diseases and discusses the benefits of the integration between computational and experimental approaches toward the discovery of new antiparasitic agents. The analysis is illustrated by recent examples, with emphasis on the strategies reported within the past 2 years.

Expert opinion: Virtual screening techniques are powerful tools commonly used in drug discovery against parasitic diseases, which have provided new opportunities for the identification of several novel compound classes with antiparasitic activity.     

Systematic identification of small molecule adjuvants

Introduction: Adjuvants potentiate immune responses, reducing the amount and dosing frequency of antigen required for inducing protective immunity. Adjuvants are of special importance when considering subunit, epitope-based or more unusual vaccine formulations lacking significant innate immunogenicity. While numerous adjuvants are known, only a few are licensed for human use; principally alum, and squalene-based oil-in-water adjuvants. Alum, the most commonly used, is suboptimal. There are many varieties of adjuvant: proteins, oligonucleotides, drug-like small molecules and liposome-based delivery systems with intrinsic adjuvant activity being perhaps the most prominent.

Areas covered: This article focuses on small molecules acting as adjuvants, with the author reviewing their current status while highlighting their potential for systematic discovery and rational optimisation. Known small molecule adjuvants (SMAs) can be synthetically complex natural products, small oligonucleotides or drug-like synthetic molecules. The author provides examples of each class, discussing adjuvant mechanisms relevant to SMAs, and exploring the high-throughput discovery of SMAs.

Expert opinion: SMAs, particularly synthetic drug-like adjuvants, are amenable to the plethora of drug-discovery techniques able to optimise the properties of biologically active small molecules. These range from laborious synthetic modifications to modern, rational, effort-efficient computational approaches, such as QSAR and structure-based drug design. In principal, any property or characteristic can thus be designed in or out of compounds, allowing us to tailor SMAs to specific biological functions, such as targeting specific cells or pathways, in turn affording the power to tailor SMAs to better address different diseases.     

Re-education begins at home: an overview of the discovery of in vivo-active small molecule modulators of endogenous stem cells

Introduction: Degenerative diseases, such as Alzheimer’s disease, heart disease and arthritis cause great suffering and are major socioeconomic burdens. An attractive treatment approach is stem cell transplantation to regenerate damaged or destroyed tissues. However, this can be problematic. For example, donor cells may not functionally integrate into the host tissue. An alternative methodology is to deliver bioactive agents, such as small molecules, directly into the diseased tissue to enhance the regenerative potential of endogenous stem cells.

Areas covered: In this review, the authors discuss the necessity of developing these small molecules to treat degenerative diseases and survey progress in their application as therapeutics. They describe both the successes and caveats of developing small molecules that target endogenous stem cells to induce tissue regeneration. This article is based on literature searches which encompass databases for biomedical research and clinical trials. These small molecules are also categorized per their target disease and mechanism of action.

Expert opinion: The development of small molecules targeting endogenous stem cells is a high-profile research area. Some compounds have made the successful transition to the clinic. Novel approaches, such as modulating the stem cell niche or targeted delivery to disease sites, should increase the likelihood of future successes in this field.     

Platelet-derived growth factor receptor tyrosine kinase inhibitors: a review of the recent patent literature

Importance of the field: Platelet-derived growth factor receptor (PDGFR) is a compelling target for developing therapeutic agents to treat diseases associated with overactivated platelet-derived growth factor (PDGF) signaling and has proved to be particularly encouraging for cancer treatment. The efforts in this area have been greatly enhanced by the approval of tyrosine kinase inhibitors with PDGFR inhibitory activity such as imatinib, sunitinib and sorafenib.

Areas covered in this review: This review surveys the small molecule PDGFR inhibitors reported in patent literature over the past 5 years (2005 – 2009).

What the reader will gain: The reader will gain an overview of the chemical scaffolds and the activity/selectivity of the newly discovered PDGFR inhibitors.

Take home message: Targeting PDGFR kinase with small molecule inhibitors has remained a very active area. Many new and novel PDGFR inhibitors with different selectivity profiles are being discovered and evaluated. In cancer therapy, the identification of novel and potent PDGFR inhibitors with preferred kinase inhibitory profiles that deliver superior antitumor efficacy, yet have manageable side effects and toxicities, will continue to be the key for success. Additionally, interest in targeting PDGF signaling for intervention of various vascular diseases and fibrotic conditions is expected to continue to grow.     

Screening-based approaches to identify small molecules that inhibit protein–protein interactions

Introduction: Protein–protein interactions (PPIs) are very attractive targets for drug development as they play important roles in regulating many aspects of pathophysiologies. It has recently been revealed that the functionally important region of most PPIs is small enough to be modulated by small molecules. Thus, many studies in this field have achieved amazing progress, together with diverse and advanced screening technologies.

Areas covered: This article presents screening technologies to identify small molecule inhibitors of PPIs in addition to discussing the suitability of PPIs as molecular targets. The phases in the processes of selecting compounds are discussed and appropriate steps are proposed, including methodologies to test binding affinity, kinetics, structural analysis, and cellular function.

Expert opinion: Targeting PPIs is still a challenging approach in drug development and relatively few small molecules have reached clinical development. Potential candidates should be assessed and optimized by properly using the multiple assay systems to develop ideal small molecule drugs. Although there remain some barriers to be overcome, small molecule inhibitors of PPIs are fascinating and first-in-class as therapeutic agents to treat various diseases.     

How can monoclonal antibodies be harnessed against neglected tropical diseases and other infectious diseases?

ABSTRACT

Introduction: Monoclonal antibody-based therapies now represent the single-largest class of molecules undergoing clinical investigation. Although a handful of different monoclonal antibodies have been clinically approved for bacterial and viral indications, including rabies, therapies based on monoclonal antibodies are yet to fully enter the fields of neglected tropical diseases and other infectious diseases.

Areas covered: This review presents the current state-of-the-art in the development and use of monoclonal antibodies against neglected tropical diseases and other infectious diseases, including viral, bacterial, and parasitic infections, as well as envenomings by animal bites and stings. Additionally, a short section on mushroom poisonings is included. Key challenges for developing antibody-based therapeutics are discussed for each of these fields.

Expert opinion: Neglected tropical diseases and other infectious diseases represent a golden opportunity for academics and technology developers for advancing our scientific capabilities within the understanding and design of antibody cross-reactivity, use of oligoclonal antibody mixtures for multi-target neutralization, novel immunization methodologies, targeting of evasive pathogens, and development of fundamentally novel therapeutic mechanisms of action. Furthermore, a huge humanitarian and societal impact is to gain by exploiting antibody technologies for the development of biotherapies against diseases, for which current treatment options are suboptimal or non-existent.     

Targeting autophagy and mitophagy for mitochondrial diseases treatment

Introduction: Mitochondrial diseases are a group of rare genetic diseases with complex and heterogeneous origins which manifest a great variety of phenotypes. Disruption of the oxidative phosphorylation system is the main cause of pathogenicity in mitochondrial diseases since it causes accumulation of reactive oxygen species (ROS) and ATP depletion.

Areas covered: Current evidences support the main protective role of autophagy and mitophagy in mitochondrial diseases and other diseases associated with mitochondrial dysfunction.

Expert Opinion: The use of autophagy and/or mitophagy inducers may allow a novel strategy for improving mitochondrial function for both mitochondrial diseases and other diseases with altered mitochondrial metabolism. However, a deeper investigation of the molecular mechanisms behind mitophagy and mitochondrial biogenesis is needed in order to safely modulate these processes. In the coming years, we will also see an increase in awareness of mitochondrial dynamics modulation that will allow the therapeutic use of new drugs for improving mitochondrial function in a great variety of mitochondrial disorders.     

Recent advances in proteasome inhibitor discovery

Introduction: Proteasome inhibition is a quickly advancing subject of research and has a significant potential to become a potent therapeutic modality for many diseases and disorders. The aim of this review is to present the reader with the variety of approaches to the proteasome inhibitor discovery as well as highlight the diversity of scaffolds being considered for this task.

Areas covered: This review focuses on current developments in proteasome inhibitor discovery, including an account of research efforts covered in the literature from the years 2009 – 2012, although some of the earlier work is also mentioned. Specifically, presented are the type of experiments performed, the compounds and compound families investigated along with their activities and assessment for potential therapeutic value. In particular, authors highlight different paths to discovery of the proteasome inhibitors such as screening of large libraries, repurposing of existing therapeutics, development of compounds with known proteasome inhibitory activities as well as utilizing novel scaffolds.

Expert opinion: Discovery of therapeutically successful proteasome inhibitors depends on a number of factors and demands a multipronged approach. Screening protocols, choice of assays, desired mode of action, selection of a binding pocket, targeting and delivery strategy, all require careful consideration when attempting to target the proteasome.     

Virtual screening with AutoDock: theory and practice

Importance of the field: Virtual screening is a computer-based technique for identifying promising compounds to bind to a target molecule of known structure. Given the rapidly increasing number of protein and nucleic acid structures, virtual screening continues to grow as an effective method for the discovery of new inhibitors and drug molecules.

Areas covered in this review: We describe virtual screening methods that are available in the AutoDock suite of programs and several of our successes in using AutoDock virtual screening in pharmaceutical lead discovery.

What the reader will gain: A general overview of the challenges of virtual screening is presented, along with the tools available in the AutoDock suite of programs for addressing these challenges.

Take home message: Virtual screening is an effective tool for the discovery of compounds for use as leads in drug discovery, and the free, open source program AutoDock is an effective tool for virtual screening.