Pradip K. Bhatnagar, Ph.D.
Former President & Head, Daiichi Sankyo Life Science Research Centre, India
Strategies for Diseases/Target Selection for Drug Discovery and a Multi-Targeted Approach to Metabolic Disorder
Drug discovery and development is a high risk and expensive undertaking. Although, technologies, such as, bioinformatics, genomics, high throughput screening and computer-aided design have helped identify targets, biomarkers, lead candidates and reduced the time required for advancing an idea from bench to clinic, but it still takes 10-12 years and costs approximately one billion dollars to bring a drug to market globally. Therefore, it is imperative that the strategies to reduce the risk and increase efficiency are carefully selected. In this presentation I would discuss strategies for selecting potential diseases, targets and provide an example of multi-targeted approach to metabolic disorder.
Sanjeeva Srivastava, Ph.D.
Assistant Professor, Proteomics Lab, IIT-Bombay, India
Identification of Potential Early Diagnostic Biomarkers for Gliomas and Various Infectious Diseases using Proteomic Technologies
The spectacular advancements achieved in the field of proteomics research during the last decade have propelled the growth of proteomics for clinical research. Recently, comprehensive proteomic analyses of different biological samples such as serum or plasma, tissue, CSF, urine, saliva etc. have attracted considerable attention for the identification of protein biomarkers as early detection surrogates for diseases (Ray et al., 2011). Biomarkers are biomolecules that can be used for early disease detection, differentiation between closely related diseases with similar clinical manifestations as well as aid in scrutinizing disease progression. Our research group is performing in-depth analysis of alteration in human proteome in different types of brain tumors and various pathogenic infections to obtain mechanistic insight about the disease pathogenesis and host immune responses, and identification of surrogate protein markers for these fatal human diseases.
Applying 2D-DIGE in combination with MALDI-TOF/TOF MS we have analyzed the serum and tissue proteome profiles of glioblastoma multiforme; the most common and lethal adult malignant brain tumor (Gollapalli et al., 2012) (Figure 1). Results obtained were validated by employing different immunoassay-based approaches. In serum proteomic analysis we have identified some interesting proteins like haptoglobin, ceruloplasmin, vitamin-D binding protein etc. Moreover, proteomic analysis of different grades (grade-I to IV) of gliomas and normal brain tissue was performed and differential expressions of quite a few proteins such as SIRT2, GFAP, SOD, CDC42 have been identified, which have significant correlation with the tumor growth. While proteomic analysis of cerebrospinal fluid from low grade (grade I & II) vs. high grade (grade III & IV) gliomas revealed modulation of CSF levels of apolipoprotein E, dickkopf related protein 3, vitamin D binding protein and albumin in high grade gliomas. The prospective candidates identified in our studies provide a mechanistic insight of glioma pathogenesis and identification of potential biomarkers. We are also studying the role of JAK/STAT interactome and therapeutic potential of STAT3 inhibitors in gliomas using proteomics approach. Several candidates of the JAK/STAT interactome were identified with altered expression and a significant correlation was observed between STAT3 and PDK1 transcript expression level.
We have also investigated the changes in human serum proteome in different infectious diseases including falciparum and vivax malaria (Ray et al., 2012a; Ray et al., 2012b), dengue (Ray et al., 2012c) and leptospirosis (Srivastava et al., 2012). Although, quite a few serum proteins were found to be commonly altered in different infectious diseases and might be a consequence of inflammation mediated acute phase response signaling, uniquely modulated candidates were identified in each pathogenic infection indicating the some inimitable responses. Further, a panel of identified proteins consists of six candidates; serum amyloid A, hemopexin, apolipoprotein E, haptoglobin, retinol-binding protein and apolipoprotein A-I was used to build statistical sample class prediction models employing PLSDA and other classification methods to predict the clinical phenotypic classes and 91.37% overall prediction accuracy was achieved (Figure 2). ROC curve analysis was carried out to evaluate the individual performance of classifier proteins. The excellent discrimination among the different disease groups on the basis of differentially expressed proteins demonstrates the potential diagnostic implications of this analytical approach.
Keywords: Diagnostic biomarkers, Gliomas, Infectious Diseases, Proteomics, Serum proteome
Acknowledgments: This disease biomarker discovery research was supported by Department of Biotechnology, India grant (No. BT/PR14359/MED/30/916/2010), Board of Research in Nuclear Sciences (BRNS) DAE young scientist award (2009/20/37/4/BRNS) and a startup grant 09IRCC007 from the IIT Bombay. The active support from Advanced Center for Treatment Research and Education in Cancer (ACTREC), Tata Memorial Hospital (TMH), and Seth GS Medical College and KEM Hospital Mumbai, India in clinical sample collection process is gratefully acknowledged.
References :
- Ray S, Reddy PJ, Jain R, Gollapalli K. Moiyadi A, Srivastava S. Proteomic technologies for the identification of disease biomarkers in serum: advances and challenges ahead. Proteomics 11: 2139-61, 2011.
- Gollapalli K, Ray S, Srivastava R, Renu D, Singh P, Dhali S, Dikshit JB, Srikanth R, Moiyadi A, Srivastava S. Investigation of serum proteome alterations in human glioblastoma multiforme. Proteomics 12(14): 2378-90, 2012.
- Ray S, Renu D, Srivastava R, Gollapalli K, Taur S, Jhaveri T, Dhali S, Chennareddy S, Potla A, Dikshit JB, Srikanth R, Gogtay N, Thatte U, Patankar S, Srivastava S. Proteomic investigation of falciparum and vivax malaria for identification of surrogate protein markers. PLoS One 7(8): e41751, 2012a.
- Ray S, Kamath KS, Srivastava R, Raghu D, Gollapalli K, Jain R, Gupta SV, Ray S, Taur S, Dhali S, Gogtay N, Thatte U, Srikanth R, Patankar S, Srivastava S. Serum proteome analysis of vivax malaria: An insight into the disease pathogenesis and host immune response. J Proteomics 75(10): 3063-80, 2012b.
- Srivastava R, Ray S, Vaibhav V, Gollapalli K, Jhaveri T, Taur S, Dhali S, Gogtay N, Thatte U, Srikanth R, Srivastava S. Serum profiling of leptospirosis patients to investigate proteomic alterations. J Proteomics 76: 56-68, 2012.
- Ray S, Srivastava R, Tripathi K, Vaibhav V, Srivastava S. Serum proteome changes in dengue virus-infected patients from a dengue-endemic area of India: towards new molecular targets? OMICS 16(10): 527-36, 2012c.
* Correspondence: Dr. Sanjeeva Srivastava, Department of Biosciences and Bioengineering, IIT Bombay, Mumbai 400 076, India: E-mail: sanjeeva@iitb.ac.in; Phone: +91-22-2576-7779, Fax: +91-22-2572-3480
David Ibanez, Laura Dubreuil and Alejandro Rier
Neurofeedback (NF) is a type of biofeedback that uses real time display of electroencephalography to illustrate brain activity. EEG features are extracted and displayed allowing the user to, with practice, modulate their temporal evolution. Neurofeedback training has many therapeutic applications such as attention deficit hyperactivity disorder (ADHD), migraine, depression or conduct disorders. This document presents NeuroSurfer, a novel general-purpose tool for neurofeedback training with a use case of attention deficit hyperactivity disorder (ADHD) treatment.
Suryaprakash Sambhara, DVM, Ph.D
Chief, Immunology Section, Influenza Division, CDC, Atlanta, USA
Making sense of pathogen sensors of Innate Immunity: Utility of their ligands as antiviral agents and adjuvants for vaccines.
Currently used antiviral agents act by inhibiting viral entry, replication, or release of viral progeny. However, recent emergence of drug-resistant viruses has become a major public health concern as it is limiting our ability to prevent and treat viral diseases. Furthermore, very few antiviral agents with novel modes of action are currently in development. It is well established that the innate immune system is the first line of defense against invading pathogens. The recognition of diverse pathogen-associated molecular patterns (PAMPs) is accomplished by several classes of pattern recognition receptors (PRRs) and the ligand/receptor interactions trigger an effective innate antiviral response. In the past several years, remarkable progress has been made towards understanding both the structural and functional nature of PAMPs and PRRs. As a result of their indispensable role in virus infection, these ligands have become potential pharmacological agents against viral infections. Since their pathways of action are evolutionarily conserved, the likelihood of viruses developing resistance to PRR activation is diminished. I will discuss the recent developments investigating the potential utility of the ligands of innate immune receptors as antiviral agents and molecular adjuvants for vaccines.
Kal Ramnarayan, Ph.D.
Co-founder President & Chief Scientific Officer, Sapient Discovery, San Diego, CA, USA
A cost-effective approach to Protein Structure-guided Drug Discovery: Aided by Bioinformatics, Chemoinformatics and computational chemistry
With the mapping of the human genome completed almost a decade ago, efforts are still underway to understand the gene products (i.e., proteins) in the human biological and disease pathways. Deciphering such information is very important for the discovery and development of small molecule drugs as well as protein therapeutics for various human diseases for which no cure exists. As an example, with more than 500 members, the kinase family of protein targets continues to be an important and attractive class for drug discovery. While how many of the members in this family are actually druggable is still to be established, there are several ongoing efforts on this class of proteins across a broad spectrum of disease categories. Even though in general the protein structural topology might looks similar, there are issues with respect selectivity of identified small molecule inhibitors when, the lead molecule discovery is carried out at the ATP binding site. As an added complexity, allosteric modulators are needed for some of the members, but the actual site for such modulation on the protein target can not resolved with uncertainty. In this presentation we will describe a bioinformatics and computational based platform for small molecule discovery for protein targets that are involved in protein-protein interactions as well as targets like kinases and phosphatases. We will describe a computational approach in which we have used an informatics based platform with several hundred kinases to sort through in silico and identify inhibitors that are likely to be highly selective in the lead generation phase. We will discuss the implication of this approach on the drug discovery of the kinase and phosphatase classes in general and independent of the disease category.
Seeram Ramakrishna, Ph.D.
Director, Center for Nanofibers & Nanotechnology, National University of Singapore
Biomaterials: Future Perspectives
From the perspective of thousands of years of history, the role of biomaterials in healthcare and wellbeing of humans is at best accidental. However, since 1970s with the introduction of national regulatory frameworks for medical devices, the biomaterials field evolved and reinforced with strong science and engineering understandings. The biomaterials field also flourished on the backdrop of growing need for better medical devices and medical treatments, and sustained investments in research and development. It is estimated that the world market size for medical devices is ~300 billion dollars and for biomaterials it is ~30 billion dollars. Healthcare is now one of the fastest growing sectors worldwide. Legions of scientists, engineers, and clinicians worldwide are attempting to design and develop newer medical treatments involving tissue engineering, regenerative medicine, nanotech enabled drug delivery, and stem cells. They are also engineering ex-vivo tissues and disease models to evaluate therapeutic drugs, biomolecules, and medical treatments. Engineered nanoparticles and nanofiber scaffolds have emerged as important class of biomaterials as many see them as necessary in creating suitable biomimetic micro-environment for engineering and regeneration of various tissues, expansion & differentiation of stem cells, site specific controlled delivery of biomolecules & drugs, and faster & accurate diagnostics. This lecture will capture the progress made thus far in pre-clinical and clinical studies. Further this lecture will discuss the way forward for translation of bench side research into the bed side practice. This lecture also seeks to identify newer opportunities for biomaterials beyond the medical devices.
Aswath Balakrishnan, Kapaettu Satyamoorthy and Manjunath B Joshi
Introduction
Insulin resistance is a hall mark of metabolic disorders such as diabetes. Reduced insulin response in vasculature leads to disruption of IR/Akt/eNOS signaling pathway resulting in vasoconstriction and subsequently to cardiovascular diseases. Recent studies have demonstrated that inflammatory regulator interleukin-6 (IL-6), as one of the potential mediators that can link chronic inflammation with insulin resistance. Accumulating evidences suggest a significant role of epigenetic mechanisms such as DNA methylation in progression of metabolic disorders. Hence the present study aimed to understand the role of epigenetic mechanisms involved during IL-6 induced vascular insulin resistance and its consequences in cardiovascular diseases.
Materials and Methods
Human umbilical vein endothelial cells (HUVEC) and Human dermal microvascular endothelial cells (HDMEC) were used for this study. Endothelial cells were treated in presence or absence of IL-6 (20ng/ml) for 36 hours and followed by insulin (100nM) stimulation for 15 minutes. Using immunoblotting, cell lysates were stained for phosphor- and total Akt levels to measure insulin resistance. To investigate changes in DNA methylation, cells were treated with or without neutrophil conditioned medium (NCM) as a physiological source of inflammation or IL-6 (at various concentrations) for 36 hours. Genomic DNA was processed for HPLC analysis for methyl cytosine content and cell lysates were analyzed for DNMT1 (DNA (cytosine-5)-methyltransferase 1) and DNMT3A (DNA (cytosine-5)-methyltransferase 3A) levels using immunoblotting.
Results
Endothelial cells stimulated with insulin exhibited an increase in phosphorylation of Aktser 473 in serum free conditions but such insulin response was not observed in cells treated with IL-6, suggesting chronic exposure of endothelial cells to IL-6 leads to insulin resistance. HPLC analysis for global DNA methylation resulted in decreased levels of 5-methyl cytosine in cells treated with pro-inflammatory molecules (both by NCM and IL-6) as compared to untreated controls. Subsequently, analysis in cells treated with IL-6 showed a significant decrease in DNMT1 levels but not in DNMT3A. Other pro-inflammatory marker such as TNF-α did not exhibit such changes.
Conclusion
Our study suggests: a) Chronic treatment of endothelial cells with IL-6 results in insulin resistance b) Neutrophil conditioned medium and IL-6 decreases methyl cytosine levels c) DNMT1 but not DNMT3a levels are reduced in cells treated with IL-6.
The global healthcare scene of which the pharmaceutical industry and its products are integral components is today at the cross roads. The high and unaffordable costs of drug research with estimates of over 1 billion dollars for every new drug discovered and developed, the very low success rates, the high degree of obsolescence due to undesirable adverse drug reactions, the decline in the development pipeline of new drugs, patent expiries leading to generic competition and the public’s disillusionment with use of chemicals for human consumption as drugs have all significantly contributed to the problems of this lifeline industry. The strategy adopted by the large R&D based Corporations to get bigger and bigger through mergers and acquisitions to improve cost-effectiveness and productivity of R&D has so far not worked effectively. Consequently, one of the recent trends in healthcare, articulated by many experts is to look for alternate or even complementary approaches to reduce the impact of rising costs of drugs on healthcare. Various new strategies for drug discovery such as the use of Natural Products especially medicinal plants are being actively pursued by healthcare planners and providers. Side by side, traditional systems of medicine whether from the oriental countries or the western nations are also having a serious relook to understand their usefulness in healthcare. To achieve its legitimate position in the healthcare scenario, it is essential to scientifically validate their claimed utility through appropriate and systematic research efforts including pre-clinical and clinical studies. In addition to their own use as medicines, knowledge on the Indian Traditional Medicines can be used as a platform for new drug discovery. The huge potential for carrying out systematic R&D programs for new Drug Discovery based on natural products and possible strategies to realise them in the coming decades will be explained in this presentation.
Ramani A. Aiyer, Ph.D., MBA
Principal, Shasta BioVentures, San Jose, CA, USA
New Drug R&D in India: Challenges & Opportunities
New drug discovery and development has become a global endeavor, with Western big pharmaceutical companies farming out more and more chemistry and biology research to Asia, particularly India and China. During the last decade, several Indian pharmaceutical companies have embarked on ambitious R&D programs, with slow but steady progress in developing new chemical / molecular entities. The Indian government has also made a strong commitment to promote innovation and entrepreneurship in the biotechnology sector. The first part of the talk will focus on a case study showing the entire process of discovery and development of a new drug recently launched for Rheumatoid Arthritis. We will then address the challenges of conducting innovative R&D in India and actions necessary to overcome them. The second part of the talk will make the case for developing Ayurvedic drug formulations for the Western / Global markets, again using the example of Rheumatoid Arthritis (Aamavaata). Ayurveda takes a holistic approach to disease diagnosis and therapy based on interactions among body type (prakriti), tri-doshas (three body humors), sapta-dhatus (seven tissues) and malas (excretions). The drugs prescribed are usually herbo-mineral formulations comprising multiple medicinal plants and / or metals. The manufacturing processes date back to Ayurvedic texts several thousand years old, and are compiled in the Ayurvedic Pharmacopeia. Also, the treatment modalities and drug formulations are “personalized” to fit different patient types, based on the holistic diagnoses mentioned earlier. There is a tremendous need to establish a sound basis for Ayurvedic drug discovery R&D for the modern world. We must find a scientific and ethical way to leverage the vast body of anecdotal and possibly retrospective data on patients undergoing Ayurvedic treatment. Combined with in vitro and in vivo biological data on Ayurvedic herbo-mineral formulations, the adoption of stringent manufacturing practices, and designing sound clinical trials to establish the safety and efficacy, India has a golden opportunity to expand the reach of Ayurvedic drugs into Western / Global medical practice.