Patent Evaluation: Nucleic Acid Hybridization as a Diagnostic Tool

Summary

Novelty: A novel gene detection method is reported which is safe, convenient, highly sensitive and quick.

Biology: A single stranded nucleic acid probe which has a base sequence complementary to the gene to be detected, is immobilized onto the surface of an electrode or the tip of an optical fibre. The nucleic probe is then reacted with the gene sample, which is denatured to a single stranded form, and then the nucleic acid probe which is hybridized with the gene, is detected. In this procedure, a substance capable of recognizing and binding specifically to the double stranded nucleic acid and being active electrochemically or optically, is added to the reaction system which consists of the nucleic acid probe and the gene sample. The detection of the nucleic acid probe is conducted by electrochemical or optical determination.     

Lipid and polymeric carrier-mediated nucleic acid delivery

Importance of the field: Nucleic acids such as plasmid DNA, antisense oligonucleotide, and RNA interference (RNAi) molecules, have a great potential to be used as therapeutics for the treatment of various genetic and acquired diseases. To design a successful nucleic acid delivery system, the pharmacological effect of nucleic acids, the physiological condition of the subjects or sites, and the physicochemical properties of nucleic acid and carriers have to be thoroughly examined.

Areas covered in this review: The commonly used lipids, polymers and corresponding delivery systems are reviewed in terms of their characteristics, applications, advantages and limitations.

What the reader will gain: This article aims to provide an overview of biological barriers and strategies to overcome these barriers by properly designing effective synthetic carriers for nucleic acid delivery.

Take home message: A thorough understanding of biological barriers and the structure–activity relationship of lipid and polymeric carriers is the key for effective nucleic acid therapy.     

Potential of polymeric nanoparticles in AIDS treatment and prevention

Importance of the field: Acquired immunodeficiency syndrome (AIDS) remains one of the greatest challenges in public health. The AIDS virus is now responsible for > 2.5 million new infections worldwide each year. Despite significant advances in understanding the mechanism of viral infection and identifying effective treatment approaches, the search for optimum treatment strategies for AIDS remains a major challenge. Recent advances in the field of drug delivery have provided evidence that engineered nanosystems may contribute to the enhancement of current antiretroviral therapy.

Areas covered in this review: This review describes the potential of polymeric nanoparticle-based drug delivery systems in the future treatment of AIDS. Polymeric nanoparticles have been developed to improve physicochemical drug characteristics (by increasing drug solubility and stability), to achieve sustained drug release profile, to provide targeting to the cellular and anatomic human immunodeficiency virus (HIV) latent reservoirs and to be applied as an adjuvant in anti-HIV vaccine formulations.

What the reader will gain: The insight that will be gained is knowledge about the progress in the development of polymeric nanoparticle-based drug delivery systems for antiretroviral drugs as alternative for AIDS treatment and prevention.

Take home message: The advances in the field of targeted drug delivery can result in more efficient strategies for AIDS treatment and prevention.     

Providing data science support for systems pharmacology and its implications to drug discovery

ABSTRACT

Introduction: The conventional one-drug-one-target-one-disease drug discovery process has been less successful in tracking multi-genic, multi-faceted complex diseases. Systems pharmacology has emerged as a new discipline to tackle the current challenges in drug discovery. The goal of systems pharmacology is to transform huge, heterogeneous, and dynamic biological and clinical data into interpretable and actionable mechanistic models for decision making in drug discovery and patient treatment. Thus, big data technology and data science will play an essential role in systems pharmacology.

Areas covered: This paper critically reviews the impact of three fundamental concepts of data science on systems pharmacology: similarity inference, overfitting avoidance, and disentangling causality from correlation. The authors then discuss recent advances and future directions in applying the three concepts of data science to drug discovery, with a focus on proteome-wide context-specific quantitative drug target deconvolution and personalized adverse drug reaction prediction.

Expert opinion: Data science will facilitate reducing the complexity of systems pharmacology modeling, detecting hidden correlations between complex data sets, and distinguishing causation from correlation. The power of data science can only be fully realized when integrated with mechanism-based multi-scale modeling that explicitly takes into account the hierarchical organization of biological systems from nucleic acid to proteins, to molecular interaction networks, to cells, to tissues, to patients, and to populations.     

Liposomal delivery of nucleic acid-based anticancer therapeutics: BP-100-1.01

Introduction: Antisense oligonucleotides, siRNA, anti-microRNA are designed to selectively bind to target mRNAs, and silence disease-causing or -associated proteins. The clinical development of nucleic acid drugs has been limited by their poor bioavailability.

Areas covered: This review article examines the strategies that have been utilized to improve the bioavailability of nucleic acids. The chemical modifications made to nucleic acids that have improved their resistance against nuclease degradation are briefly discussed. The design of cationic and neutral lipid nanoparticles that enable the systemic delivery of nucleic acids in vivo is reviewed, and the proof-of-concept evidence that intravenous administration of nucleic acids incorporated into lipid nanoparticles leads to decreased expression of target genes in humans. Preclinical results of the neutral BP-100-1.01 nanoparticle are highlighted.

Expert opinion: To further improve the clinical potential of nucleic acid cancer drugs, we predict research on the next generation of lipid nanoparticles will focus on: i) enhancing nucleic acid delivery to poorly vascularized tumors, as well as tumors behind the blood–brain barrier; and ii) improving the accessibility of nucleic acids to the cytoplasm by enhancing endosomal escape of nucleic acids and/or reducing exocytosis of nucleic acids to the external milieu.     

Patent Evaluation: A Transgenic Animal Model for Alzheimer's Disease

Summary

Novelty: A transgenic animal which harbours a mutant DNA sequence encoding amyloid precursor protein (APP), with a mutant amino acid residue at the position encoded by codon 717, or the copy of a human DNA sequence encoding mutant APP is claimed. A method for detecting an APP allele which cosegregates with a genetic predisposition to Alzheimer's disease, especially familial or early onset Alzheimer's, is also claimed.

Biology: Full recombinant details for the cloning of the relevant mutant DNA in E. coli, Bacillus, Pseudomonas etc. are given. Sequencing details, obtained by PCR, are also provided. The production of transgenic mice with a mutant APP allele is described, and the use of such animals for testing therapeutic agents is discussed. However, no biological data are provided.

Chemistry: Thirty-nine sequences are provided, six for DNA encoding variants of APP and thirty-three proteins. A core sequence claimed is Ile-Ala-Thr-Val-Ile-X-Ile-Thr-Leu, where X is any of the twenty conventional amino acids, bar valine.     

Patent Evaluation: A Diagnostic Kit for the Detection of Norwalk Virus

Summary

Novelty: A diagnostic kit for the detection of Norwalk virus is claimed. The kit comprises antibodies raised against a polypeptide expressed by one of six claimed polynucleotide sequences. A method for detecting Norwalk virus in human stools is also claimed.

Biology: No biological data are provided.

Chemistry: Full preparative details are presented for the preparation polypeptide antigens which are immunoreactive with infected sera. Cloning and expression of mono- and polyclonal antibodies in E. coli are also disclosed. Nineteen polynucleotide sequences are fully disclosed.     

Novel integrase inhibitors for HIV

Importance of the field: Integrase inhibitors are the newest class of antiretroviral agents developed to treat HIV-1 infection. Raltegravir (RAL), the only integrase inhibitor (INI) currently approved for the treatment of HIV-infected patients, has proven to be a potent and well-tolerated antiretroviral (ARV) agent. It is currently approved and used for the treatment of both ARV-experienced and ARV-naive patients. Nevertheless, the relatively low genetic barrier for resistance of RAL encourages the search for new INIs with different mechanisms of actions and resistance profiles.

Areas covered in this review: Here we review the data available about INI that are currently being tested in clinical trials or are in preclinical development: elvitegravir (EVG), S/GSK1349572, S/GSK1265744 and LEDGINs. We focus on their clinical efficacy, pharmacokinetic, safety and resistance profiles.

What the reader will gain: Up-to-date overview on the currently available, clinically relevant INIs and promising preclinical inhibitors at all phases of development.

Take home message: Integrase inhibitors represent the newest therapeutic class available to treat HIV-1 infection. There are a variety of compounds either available in the clinic (RAL), advancing to Phase III trials (EVG), or in earlier phases of development. Taken together, this class offers new treatment options for the HIV-infected individual.     

Patent Evaluation : WO9309141-: Josh Diabetes Center: Cloning of DNA encoding an islet protein (PM-1) associated with type I diabetes mellitus

Novelty: A neuroendocrine protein antigen is disclosed which is associated with Type I diabetes mellitus. The nucleic acid encoding the protein, methods and reagents for detecting antibody against the protein and for identifying individuals at risk of developing Type I diabetes mellitus are also reported.

Biology: A 69 kD protein, designated PM-1, is expressed in human pancreatic islet cells and a human insulinoma. Autoantibodies to the PM-1 protein have been found in sera of prediabetic patients. Natural, synthetic or recombinant forms of the PM-1 protein can be used in immunochemical assays to detect anti-PM-1 autoantibodies and to identify patients at risk of developing diabetes. Therapeutic compositions containing the PM-1 protein or an antigenic fragment can be administered to a diabetic or a prediabetic individual at risk of developing diabetes, to tolerize the individual or block the immune response to the PM-1 protein.

Chemistry: The amino acid protein sequence of the protein is listed.     

Evaluation of the cytotoxic potential of a new pentacyclic triterpene from Rhododendron arboreum stem bark

Context: Traditionally, Rhododendron arboreum Sm. (Ericaceae) is a very important medicinal plant having oxytocic, estrogenic, anti-inflammatory, analgesic and hepatoprotective activities; it also inhibits the prostaglandin synthetase.

Objectives: This study determines the cytotoxic potential of 15-oxoursolic acid isolated from R. arboreum against selected human cancer cell lines.

Materials and methods: Extraction from stem bark (5?kg) of R. arboreum was performed with methanol, which was successively partitioned into hexane, dichloromethane and ethyl acetate fractions, respectively. The new antitumor agent [15-oxoursolic acid (1)] was isolated from ethyl acetate fraction through column chromatography. Structure elucidation of new compound was performed through extensive spectroscopy i.e., IR, MS and 1D and 2D NMR. Cytotoxicity of isolated compound was determined at doses 5–100?μM for a period of 72?h on specified human cancer cell lines [renal cell carcinoma (A498), non-small cell lung (NCI-H226), squamous cell carcinoma (H157) and human ovarian carcinoma (MDR-2780AD)].

Results: Structure of isolated compound was characterized as 15-oxoursolic acid on the basis of various extensive spectroscopic techniques. 15-Oxoursolic acid revealed considerable anticancer activity with IC₅₀ values of 2.3?±?0.1?μM, 4.9?±?0.2?μM, 9.2?±?0.2?μM and 10.3?±?0.1?μM against MDR 2780AD, Hep G2, H157 and NCI-H226, respectively, while in the case of A498, the activity was good (IC₅₀ 32.8?±?1.2?μM).

Conclusions: This study highlighted the potential of 15-oxoursolic acid to be further explored as a new lead compound for cancer chemotherapy.     

Ellagic acid glycosides with hepatoprotective activity from traditional Tibetan medicine Potentilla anserina

Two new gallic acid glycosides, potentillanosides G (1) and H (2), were newly isolated from the methanol extract of the tuberous roots of Potentilla anserina (Rosaceae), together with a known compound, ellagic acid 3-O-α-l-rhamnopyranoside (3). Their structures were elucidated on the basis of chemical and physicochemical evidence. Among the constituents, potentillanoside H (2, IC₅₀ = 99.5 μM) was found to show hepatoprotective activity.

     

Modulation of GDP-fucose level for generating proteins with reduced rate of fucosylation (WO2010141855)

Background: The application (WO2010141855) is in the field of glycobiology, and involves the control of the rate of fucosylation of proteins by exogenous factors.

Objective: It aims at controlling the rate of protein fucosylation with inhibitors (drugs or nucleic acid antagonists) of enzymes involved in the synthesis of GDP-fucose.

Methods: Mammalian cell lines were cultured in the presence of inhibitors, for example, siRNA. The rates of GDP-fucose in cells and during protein fucosylation were characterized.

Results: The level of protein fucosylation decreases rapidly in response to a decrease in GDP-fucose level.

Conclusion: The relationship between the rate of fucosylation of proteins and the level of GDP-fucose in a cell is non-linear. Reduction in the rate of protein fucosylation can be achieved with a minimal reduction of the level of GDP-fucose in cells. The paradigm may be used to synthesize proteins and antibodies, with a reduced rate of fucosylation. The application claims that the use of drugs or nucleic acid antagonists that inhibit the enzymes involved in GDP-fucose biosynthesis optimizes the level of GDP-fucose present in cells, and reduces the rate of fucosylation of glycoproteins.     

Recent advances in the treatment of life-threatening,invasive fungal infections

Introduction: Invasive fungal infections (IFIs) pose significant morbidity and are often life-threatening to many high-risk patients. Timely diagnosis and treatment of these infections with optimal therapy is imperative.

Areas covered: Advances have been made in diagnostic biomarkers such as peptide nucleic acid fluorescent in situ hybridization, β-D-glucan and galactomannan, although more research is needed in this area to assist with both diagnosis and monitoring for improvement of IFI management. Novel antifungal agents (azole antifungals and echinocandins) are being investigated that have activity against Candida spp. and Aspergillus spp. Optimizing the pharmacodynamics (PD) of our current antifungal therapies through such strategies as continuous infusion of amphotericin B and dose escalation of echinocandins and liposomal formulations of amphotericin B have also been investigated with mixed results. Therapeutic drug monitoring (TDM) shows promise as evident from data with such agents as flucytosine, itraconazole, voriconazole and posaconazole.

Expert opinion: The goal for the future of biomarkers in IFIs will be to have excellent sensitivity and specificity to ideally identify a particular fungus causing the infection or eliminate its existence to prevent unnecessary costs, resistance and antifungal usage. In addition, further developments of new antifungals are needed and judicious use of the current regimens needs to be optimized through antifungal PD properties and TDM.     

Non-viral nucleic acid containing nanoparticles as cancer therapeutics

ABSTRACT

Introduction: The delivery of nucleic acids such as DNA and short interfering RNA (siRNA) is promising for the treatment of many diseases, including cancer, by enabling novel biological mechanisms of action. Non-viral nanoparticles are a promising class of nucleic acid carriers that can be designed to be safer and more versatile than traditional viral vectors.

Areas covered: In this review, recent advances in the intracellular delivery of DNA and siRNA are described with a focus on non-viral nanoparticle-based delivery methods. Material properties that have enabled successful delivery are discussed as well as applications that have directly been applied to cancer therapy. Strategies to co-deliver different nucleic acids are highlighted, as are novel targets for nucleic acid co-delivery.

Expert opinion: The treatment of complex genetically-based diseases such as cancer can be enabled by safe and effective intracellular delivery of multiple nucleic acids. Non-viral nanoparticles can be fabricated to deliver multiple nucleic acids to the same cell simultaneously to prevent tumor cells from easily compensating for the knockdown or overexpression of one genetic target. The continued innovation of new therapeutic modalities and non-viral nanotechnologies to provide target-specific and personalized forms of gene therapy hold promise for genetic medicine to treat diseases like cancer in the clinic.     

Contributions of HIV-1 Nef to immune dysregulation in HIV-infected patients: a therapeutic target?

Introduction: HIV accessory protein Nef is a factor responsible for many of the viral pathogenic effects. Progression to AIDS is dramatically delayed and in some well-documented cases completely abolished on infection with naturally occurring HIV strains lacking intact nef sequences in their genomes. The topic of this review is the contribution of Nef to the immune pathology as a possible target in HIV-infected patients.

Areas covered: An overview of known Nef functions accounting for its role in pathogenesis is presented, emphasizing interactions with dendritic cells and macrophages, and Nef-induced exosome secretion, all involved in immune dysregulation during the course of HIV infection. Current approaches to Nef inhibition by different classes of compounds are reviewed.

Expert opinion: Blocking Nef for therapeutic purposes is a challenging endeavor mainly due to intrinsic properties of this HIV accessory protein. Nef has multiple interfaces to interact with host proteins and lacks a catalytic domain. Potential benefits arising from the development of successful inhibitors could however prove beneficial for reducing gradual deterioration of immune system in chronically infected patients in absence of functional cure.     

Current treatment of nontuberculous mycobacteriosis: an update

Introduction: Nontuberculous mycobacteria (NTM) are becoming increasingly important. A growing number of patients with underlying conditions that make them prone to diseases caused by NTM. These diseases include the appearance of new syndromes, such as mesotherapy and other cosmetic-related infections, or diseases that affect patients who are being treated with tumor necrosis factor.

Areas covered: A literature search has been performed for each mycobacterium species. An introduction to the different aspects of the species and the diseases is provided, along with a review of the current therapeutic options; special emphasis is put on new research and discoveries.

Expert opinion: Recognition of the current role of NTM isolates remains the key step in the management of NTM infections. After recognition, treatment must be guided by attending to the isolated species, the specific syndromes, clinical experience and – for some species – the results of in-vitro susceptibility tests. Surgical therapy is also important for some species (Mycobacterium ulcerans, Mycobacterium scrofulaceum) and for localized infections. The treatment of uncommon species is not yet well defined and recent research on resistance mechanisms has described their importance. The role of biofilms is currently of special concern for various specific infections.     

New pharmacological treatments for methicillin-resistant Staphylococcus aureus infections

Introduction: Despite available treatment options for methicillin-resistant Staphylococcus aureus (MRSA), the morbidity and mortality attributed to the diverse infection manifestations of this pathogen remain high. More anti-MRSA agents are needed as options for treatment of these infections. Ideally, these new agents would be rapidly bactericidal for bloodstream clearance in septic patients, have few toxicities, be active against MRSA in biofilms, be easy to administer, and have oral bioavailability.

Areas covered: This review focuses on MRSA agents in Phase III trials or antibiotics currently in the market, which are being studied for new indications. For each agent, the antimicrobial potency against MRSA, pharmacokinetic and pharmacodynamic considerations and approved and potential new indications are presented. The role of novel combination therapies is also introduced.

Expert opinion: The new lipoglycopeptides oritavancin, telavancin and dalbavancin have the potential to make a large impact on the treatment of MRSA due to unique pharmacokinetic/pharmacodynamic properties and proposed dosing regimens. Other new agents (omadacycline and tedizolid) as well as revisited older agents (fosfomycin and fusidic acid) appear promising but require further study for their potential role. Combination therapy may improve outcomes in patients with high MRSA infection burden or when patient or pathogen factors predict a worse outcome with monotherapy.     

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.     

In pursuit of a moving target: nanotherapeutics for the treatment of non-Hodgkin B-cell lymphoma

Introduction: Non-Hodgkin lymphoma (NHL) is diagnosed in 70,000 Americans annually. Chemotherapy was the standard course of treatment until the addition of the monoclonal antibody (mAb) drug, rituximab, to therapy regimens in 1997. Although disease prognosis has improved dramatically since that time, nearly 20,000 patients succumb annually to the disease, with an average life expectancy beyond diagnosis of only 12 years. The advent of nanomedicine may fulfill the remaining need for novel therapy capable of eradicating solid tumor and disseminated B-cell lymphomas.

Areas covered: This review details the current landscape of B-cell NHL and nanoparticles now being developed for its treatment. Specifically, we discuss lipid, polymer and metal nanoparticles that deliver an array of drugs, including toxins, chemotherapeutic agents and nucleic acids.

Expert opinion: Because B-cell malignancies have responded quite well to new components in multi-drug regimens, nanomedicines that are mechanistically distinct from existing therapies hold significant promise. In our opinion, advancement of these technologies into the clinic will likely require significantly more effective targeting systems coupled with a better understanding of lymphoma biology. Furthermore, it is important for researchers to recognize the genetic and phenotypic heterogeneity of NHL and to develop therapeutic strategies for distinct subsets of NHL before attempting to generalize approaches.     

Novel CCR5 antagonists for the treatment of HIV infection: a review of compounds patented in 2006 – 2008

Importance of the field: The HIV/AIDS epidemic and the resultant therapeutic efforts have continued to evolve over the last several years. The continued challenges in vaccine development, the growing longevity of the patient population and the emergence of resistant strains to current highly active antiretroviral therapy necessitate the development of new, effective therapeutics which target novel mechanism of actions. CCR5, a member of the GPCR superfamily, plays a key role as a co-receptor during the HIV viral entry process. The utility of CCR5 antagonists in the clinical setting has been validated, culminating in the launch of maraviroc (Selzentry^®) by Pfizer (New York, NY, USA) in 2007.

Areas covered in this review: This review covers patent applications for small-molecule CCR5 selective antagonists published between 2006 and 2008 and related literature, with a focus on the treatment of HIV infection.

What the reader will gain: The reader will gain information on patent literature from 2006 to 2008 on CCR5 antagonists for the treatment of HIV infection.

Take home message: A variety of new chemotypes have emerged over this period. These efforts support the potential to develop the next generation of CCR5 antagonists for the treatment of HIV with improved potency, tolerability and convenience.