Cheminformatics: An Emerging Field

Cheminformatics is an emerging field that uses information technology to a range of problems in the field of chemistry as well as drug discovery. Cheminformatics is a fast growing field and there is a lack of qualified scientific professionals who can use computers and databases for chemical compounds or drug development. Basically it is the application of information technology to chemistry. The efficient search of such stored information includes topics that are dealt with in computer science as data mining, information retrieval, information extraction and machine learning. The applications are the Chemical data collection, analysis and management, chemical data representation, database design, chemical structure prediction, compound library, database mining, QSAR/ QSPR, Statistical models and descriptors. The various aspects are the Information Acquisition i.e. methods for collecting data from the source or from various theories, Information Management i.e. storage and retrieval and Information use i.e. analysis, correlation and application to problem. The methods that included are force fields, molecular dynamics, QSAR, molecular docking and pharmacophore. The software that used are Amber (use for protein and DNA), OPLS (Optimized Potentials for Liquid Simulations), Charmm (C-22 for protein and C-27 for DNA, RNA, and Protein). These in silico techniques are used in pharmaceutical companies in the process of drug discovery. These methods can realize its immense potential, the chemical and pharmaceutical industries are now going in for qualified and trained staff in cheminformatics. New career avenues have also opened up for IT as well as computer-proficient science graduates for acquiring, managing, or utilizing chemical information with the help of computer software. The aim of Cheminformatics is to provide comprehensive understanding of this fast growing field in science and technology starting from basic principles to the point of application in various fields of chemistry, biotechnology, drug development and drug designing.

Author: Bashah Javed

Faculty Bioinformatics,

BII.

Parkinson’s disease|Bioinformatics Institute in Noida

Parkinson’s disease is a neurological illness named after Dr. James Parkinson, a physician who was the first to describe in his essay “An essay on the Shaking palsy” 1817. Parkinson‘s disease is a disorder caused by the gradual loss of cells in a small part of the brain called the substantial nigra. The loss (death) of these cells produces a reduction in a vital chemical called “dopamine”, which causes symptoms that may include loss of facial expression, reduction in speech volume and clarity, change in size of handwriting, dry skin, constipation, urinary difficulties and depression. It is a progressive disorder; hence these symptoms worsen with time. Parkinson’s disease belongs to a group of conditions called movement disorders. It is characterized by muscle rigidity, tremor, a slowing of physical movement (Bradykinesia) and in extreme cases, a loss of physical movement (Akinesia). The primary symptoms are the results of decreased stimulation of the motor cortex by the basal ganglia, normally caused by the insufficient formation and action of dopamine, which is produced in the dopaminergic neurons of the brain. Secondary symptoms may include high level cognitive dysfunction and subtle language problem. Most people with Parkinson’s disease are described as having idiopathic Parkinson’s disease (having no specific cause). There are far less common causes of Parkinson’s disease including genetic, toxins, head trauma, cerebral anoxia, and drug- induced Parkinson’s disease. In recent year, a number of specific genetic mutations causing Parkinson’s disease have been discovered, including in certain population (Contursi, Italy). These account for a small minority of cases of Parkinson’s disease. Someone who has Parkinson’s disease is more likely to have relatives that also have Parkinson’s disease. However, this does not mean that the disorder has been passed on genetically. There is also recent evidence that a common gene defect contributes susceptibility to both Parkinson’ disease and Alzheimer’s disease.

Author Name Mr. Ranjan Kumar

HOD, Bioinformatics Institute of India

INDIAN PHARMACEUTICAL MARKET- REVIEW

Today I feel enthusiastic while writing this article as Pharmaceutical market is a big ocean; and I had tried my best to hold few drops on Indian economical face.

The Indian pharmaceutical market is highly competitive and remains dominated by low-priced, domestically-produced generics. Despite having the second largest population in the world and a growing middle class with high healthcare expectations, India accounts for less than 2% of the world pharmaceutical market in value terms. In one of the world's better performing economies, spending on pharmaceuticals accounts for less than 1% of GDP and average per capita spending remains one of the lowest levels in the region.

India’s biopharmaceutical sector is currently experiencing double digit growth and this is expected to continue, driven by the vaccines market. Growth drivers include education and increased awareness of disease prevention, increases in disposable income and government participation in immunization programmes. Continued growth is also expected in the diagnostic and therapeutic segments, including cancer and diabetes.

The Indian Pharma industry is responsible for around 10% of world pharmaceutical production. Over the last few years, a number of Indian pharmaceutical companies have been targeted for foreign acquisition. Concerns have been raised that this trend could adversely affect generic drug prices in India. The need to maintain low prices for essential medicines has been addressed in the government’s draft National Pharmaceutical Pricing Policy (NPPP), released in 2011. The proposed NPPP focuses on the National List of Essential Medicines (NLEM), which is periodically revised. The headline major change is a move from the principle of cost-based pricing to a market-based pricing model. The Department of Pharmaceuticals argues that market-based pricing would result in more transparent and fair pricing, as well as increasing competition in the marketplace. Price regulation will encompass all drugs listed in the NLEM, as well as formulations containing combinations of drugs listed in the NLEM; this will include combinations comprising listed drugs and unlisted drugs. If the NPPP is implemented, around 60% of the drugs currently available in India will come under price control.

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Biotechnology in Pharmacology|9810535368

Finding a chance to write on the blog of BII is a subject of honor for me. I am just trying to make reader familiar with the world of Biotechnology/life sciences and there relation with Pharmacology, Here I am trying to set some epic of DNA which is most fascinating thing in health care system as per my view. After the discovery of nuclein (nucleic acid) by Johannes Friedrich Miescher in 1869 which is one of most remarkable work in the world of Life Sciences. It initiate a new era in Life sciences especially in molecular biology. In the initial of 20^th century when protein is regarded as the most complex structure as well as genetic material, DNA comes as a medicine. Structure of DNA reveals how the characters are transferred from parents to offspring and transcript the information from genotype to phenotype via RNA and Protein. Writing anything is looks less as per broad view of DNA but 5’ to 3’ end always attract me so I will try my level best to sum-up maximum stuff about DNA and its relation with pharmaceutical industry in my this and upcoming next blogs.

Structure of DNA is very important because it is the key role for remedy of viral, bacterial and mutational problems. As its chemical structure elaborate with addition of pentose sugar purine, pyrimidine and tri phosphate molecule. Where sugar molecule deoxygenate at 2’ no of carbon while Nitrogenous bases are at 1’, when we talk about phosphate structure its added at 5’.That whole compound is regarded as nucleotide, and every new nucleotide join at 3’ end and constitute a new DNA.

Source: Mr. Gourav Kumar

Faculty:Bioinformatics Institute of India

Molecular Connections Ranked Number 24 Fastest Growing Technology Company on the Deloitte Technology Fast 50 India 2011 | Molecular Connections

Molecular Connections Ranked Number 24 Fastest Growing Technology Company on the Deloitte Technology Fast 50 India 2011 | Molecular Connections

BII Exam Notification

BII EXAM NOTIFICATION

BII's Exams would be held on 23rd & 24th April 2010 at the following cities Ahemdabad, Kottayam, Chennai, Hyderabad, Bangalore, Mumbai, Pune, Kolkata, Lucknow, Noida, Chandigarh, Bhopal & Bhubneshwar.

Changing Pharma Education in India: Join BII Pharma Programs for the New Paradigm of Pharmacy Profession in India

Due to the mushrooming of the pharmacy institutions, quality pharmacy education has faltered. As a result various institutions are finding it difficult to fill the approved quota of seats. Many institutions have a scant regard for maintaining education standards.

Pharmacy education in India had its beginning in mid of 19th century in Madras Medical College with introduction of pharmacy classes to impart pharmaceutical skills for the students qualifying for medical degrees or diploma or hospital assistance ship. Later it was helpful for the students who intended to qualify as chemist and druggists. Duration of study was increased to two years and entry qualification was made matriculation. The classes didn’t receive popularity and there were only a few students who used to opt for it. However, the course remained in operation and received Government sanction for its continuation. But the pharmacy education gained popularity only when Prof. M. L. Schroff with the consent of Madan Mohan Malviya introduced Pharmaceutical Chemistry and Pharmacognosy as one of the subjects for B.Sc. Degree in July 1937 in Banaras Hindu University. Then onwards there was no looking back. Pharmacy became a full pledged course with introduction of Diploma in Pharmacy and Bachelors of Pharmacy. Later Master of Pharmacy in various specializations was introduced. It is said that the first ever Pharmacy course was introduced along with the medical course in 1842 at the Old Portuguese school known as "Escola Medica de Goa" and later named as "Escola Medica Cirurgica de Goa". The Pharmacists (farmaceuticos) and Doctors (Medica Cirurgiao) were educated and trained in the same medical school and they had almost the same status in the Goan society.

Pharmacy education played a very crucial role in the economic development of the country. Now Pharmaceutical Sector is considered to be one of the very important sectors which significantly contribute to country’s economy. Although the pharmacy education has its enormous contribution for the development of pharma industry, its contribution for the development of pharmacy practice was modest with just a Masters programme in Pharmacy Practice. Hence, it was decided that there is a need to start a full-pledged course which would impart sufficient knowledge to student to practice the profession of pharmacy. And then the birth of Pharm D in India took place with the untiring efforts of a few visionaries. Doctor of pharmacy is patient-oriented whereas, bachelors of pharmacy is industry — oriented. The students are shaping to enter with pride and knowledge to take up the challenges of patient care.

In general, there should be a re-look at the pharmacy courses. Diploma in Pharmacy course, as a prerequisite to run a pharmacy (medical shop), is said to be outdated and only a few students opt for the course. Bachelor in Pharmacy needs an update to adapt to the advanced technology at which pharmaceutical industry is operating. Although been criticized, there should be a second thought to be given to introduce specialization at bachelor’s level. There should be an amalgamation of a few specializations at post graduate level as there are various offshoot specializations, which have come up in recent past for just commercial purposes. Instead there should be an initiation of courses in Pharmaceutical Management, Intellectual Property Right, Regulatory Affairs, Pharmacoeconomics, Pharmacovigilance, Clinical trial data management and Nanopharmaceuticals.

There should be self-regulation by pharmacy teachers. Being in very pious profession, they should update themselves with recent happenings and maintain high professional standards. They should enthuse students to take up challenges of the industry and profession of pharmacy.

Future strategies for pharmaceutical education

Curriculum design and reorganisation of the degree programme requires a ‘visionary’ approach. We should try to imagine, what is most likely to be happening in about 10 to 15 years in the future at any point of time. It is necessary to prepare the student for tackling problems and situations of the future rather than for the current state. Present will be outdated very quickly. The state-of-the-art is not a static state but is very much dynamic. The concept of the state-of-the-art itself implies a parallel and constant change in our endeavour to keep pace with the rapid changes taking place in technology, basic sciences and information. A student needs the past and present states-of-art only as basis for his future states. Attempts to do this sublime approach of jumping to the future from the past without going through the present have not yielded satisfactory outcomes. Students and the educators tended to see the ‘present’ more clearly than visualise the future possibilities. Skepticism has always been responsible in delaying progress. We exist in a social and educational system that has limited vision and consequently limited goals of achievement. Our attention and focus have been distorted by the numbers of students involved rather than the quality of education. Every student has to necessarily learn many new concepts and skills just to be able to remain in the profession of the future. We should prepare students with the right skills to learn new states-of-the-art with less effort! Nobody can visualise the entire future and design a strategy suited for that. But we could concentrate on incorporating the mental skills in the educational activities that are more permanent and provide the student a capability for learning new concepts.

Strategy in education should shift to ‘concept’ approach from the present ‘content’ approach. All content should be chosen to demonstrate and strengthen a ‘concept’ with an objective that is basic to the topic. The approach should reflect in curriculum design, its implementation and evaluation areas of education. All evaluation methods like written, oral, practical, assignments, seminars, projects, discussions etc. should be concept oriented. A student will benefit most with orientation of educational process to such mental skills like observation, analysis, correlation, application, evaluation or judgement etc. Such a system will go a long way to lessen the effort required by the students to acquire such skills all by themselves.

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Collagen manufactured from transgenic tobacco plants has great commercial promise for Hebrew University

A scientist at the Hebrew University of Jerusalem’s Robert H. Smith Faculty of Agriculture, Food and Environment has succeeded in producing a replica of human collagen from tobacco plants – an achievement with tremendous commercial implications for use in a variety of human medical procedures. Natural human type I collagen is the most abundant protein in the human body and is the main protein found in all connective tissue. Commercially produced collagen (pro-collagen) is used in surgical implants and many wound healing devices in regenerative medicine.

The current market for collagen-based medical devices in orthopedics and wound healing exceeds US $30 billion annually worldwide. Currently, commercial collagen is produced from farm animals such as cows and pigs as well as from human cadavers. These materials are prone to harbor human pathogens such as viruses or prions (mad-cow disease). Human cadaver is scarce, and for certain indications possesses serious ethical issues. Producing human recombinant type I pro-collagen requires the coordinated expression of five different genes. Prof. Oded Shoseyov of the Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture has established the only laboratory in the world that has reported successful co-expression all the five essential genes in transgenic tobacco plants for the production of processed pro-collagen. For this work, Shoseyov was one of the recipients of a Kaye Innovation Award during the Hebrew University Board of Governors meeting in June. Shoseyov’s invention on has been patented, and the scientific findings behind it were published recently in the journal Biomacromolecules.

A company, CollPlant Ltd., has been established based on patents and technology that were developed in Shoseyov’s laboratory. It has raised US$15 million to establish the first commercial molecular farming company in Israel and is already manufacturing collagen-based products that have attracted collaborative commercial interest from companies in the US, Japan Europe and Israel. Yissum, the technology transfer company of the Hebrew University, is one of the shareholders of CollPlant. CollPlant is a public company traded in “TASE”, and the potential revenue for the Hebrew University from this invention is estimated to reach into the multi-million dollar range. The Kaye Awards have been given annually since 1994. Isaac Kaye of England, a prominent industrialist in the pharmaceutical industry, established the awards to encourage faculty, staff, and students of the Hebrew University to develop innovative methods and inventions with good commercial potential which will benefit the university and society.

Genes? It's complicated
The advance heralded a decade ago in mapping human DNA is yet to lead to the answers we craved

Ten years ago the $10bn Human Genome Project announced it had completed the first draft of the blueprint for human life. It was hailed as a huge scientific advance, comparable to putting a man on the moon. President Bill Clinton declared: "We'll go from knowing almost nothing about how our genes work to enlisting genes in the struggle to prevent and cure illness. This will be the scientific breakthrough of the century, perhaps of all time."

The project at last laid bare the entire human genetic code – 22,000 or so genes (the precise number is still uncertain) – that make us into the people we are. Several decades of research into the cause of diseases before the project had firmly identified genes as a significant cause of many important diseases.

The first haul of genetic diseases was of those fairly rare but devastating inherited diseases, such as cystic fibrosis and haemophilia, that are caused by single genes. Most of the genes responsible for those had been fished out of the genome long before the sequencing project hauled in its net. But the project was expected to find genes for various far more common conditions, such as cancer, diabetes, heart disease, autism, depression and schizophrenia, because most of these conditions tend to run in families. Studies of families in which these diseases were common, particularly of twins, had established a level of heritability for each condition, and the levels were high. Autism comes out at a whopping 90%, indicating that most autism is caused by faulty genes (and certainly not by faulty vaccines). The heritability of schizophrenia was about 80% whereas conditions such as heart disease, diabetes and cancer came in anywhere between 30% and 70%.

And it wasn't just diseases that were caused by genes. Many behavioural studies indicated that intelligence, personality, sexual orientation and even voting preference seemed to be highly heritable. If genes were so powerful, it should be straightforward to identify the culprits in the genome.

But a decade later these expectations have not been fulfilled. The project that promised so much has, so far, delivered very little. Very few genes have been found that account for more than 1% of the risk of any of those common diseases. And even the most significant intelligence gene yet found is responsible for variation in individual intelligence equivalent to less than one IQ point. The scientists who went in search of whoppers netted only a host of minnows. Where are the missing genes?

Like most things in life, it turns out that genes are more complex than we thought. Those genes responsible for single-gene defects such as cystic fibrosis and haemophilia are the low-hanging fruit. Common diseases, and such attributes as intelligence, are not caused by single genes or even handfuls of genes, but probably by networks of hundreds or even thousands of genes.

To understand these networks, we need to look, not at the branches, but at the roots of the genetic tree. Genes form tangles of interactions with each other such that the effect of chopping one or another is unpredictable and depends on the connectivity of the whole network. Finding a gene responsible for a disease is mostly like finding a root responsible for maintaining a tree.

The task of unravelling the roots of biology is the new science of system biology, in which biologists work with mathematicians and computer scientists to build models of complex networks. This is where the causes of heart disease, diabetes and autism are now being sought. To paraphrase Winston Churchill, the genome project was not the end. It was not even the beginning of the end. But it was, perhaps, the end of the beginning in the search for our genes.

The Mystery of Type 1 Diabetes Unraveled

Type 1 diabetes is increasing three percent per annum globally, according to Eurodiab and WHO registry. Several factors are thought to play a part including increasing recognition of slow onset, non-classical Type 1 in children and LADA (late onset Type 1) in older adults. The possible environmental factors include infectious exposure, Vitamin D deficiency, less exercise and more obesity. Scientists at Scripps Research Institute in the US recently unraveled the forty year old mystery of how certain genetic mutations lead to Type 1 diabetes.

The researchers said their findings could lead to novel therapies for Type 1 diabetes and other autoimmune disease. Three genetic variations in particular (HLA-DQ2, HLA-DQ8, AND HLA-DR0405)- all located in the region of the genome called HLA for “human leukocyte antigen”- are known to increase risk of diabetes.

These three genes encode molecules that present peptides (protein fragments) to the body’s T cells than determine whether the peptide being presented is dangerous and need to be eliminated from the body as in the case of foreign invaders such as bacteria or viruses- or whether the peptides is “self,” part of the host and something the immune system needs to leave alone. However, in the context of Type 1 diabetes, T cells aggressively attack the body’s own cells.

Type 2 is responsible for most of the increase in diabetes with the complications for example, renal failure or severe hypoglycemia.

For many people, Type 2 diabetes can be managed or prevented by a healthy diet and regular exercise. Many people worldwide do not know they have diabetes, and many of those who do know are in poor control of their diabetes. Lifestyle change is still the first option for the treatment for Type 2 diabetes, experts say treating diabetes early and well not only improves quality of life, but is cost-effective, especially if it prevents hospitalization. There is now conclusive evidence that good control of blood glucose levels can substantially reduce the risk of developing complications and slow their progression in all Types of diabetes.

NanoString Technology Introduces Novel Solution for microRNA Research

Nanostring Technologies, Inc., announced a unique new product for miRNA analysis that includes a multiplexed assay for profiling the human miRNA transcriptome in a single tube. The company introduced the new assay kit, which expands the applications for its nCounter Analysis System, at the American Association for Cancer Research annual meeting.

MicroRNA (miRNAs) are small, single-stranded, non-coding RNA molecules that have generated intense interest in the scientific community for their recently discovered roles in tumor formation and important biological processes. The primary application areas of miRNA studies are in cancer, neurobiology, developmental biology, and stem cell research.

The nCounter miRNA Expression Assay Kits enabkle researchers to perform highly multiplexed, direct digital detection and counting of miRNA at single-base resolution, without the need for PCR amplification. NanoString’s Human miRNA Expression Assay kit enables researchers to profile more than 700 human and human viral miRNAs with specificity and sensitive comaparable to qPCR at a fraction of the cost.

Carlo Croce, a leading miRNA researcher, was part of an early access program for the Human miRNA Expression Assay Kit on the nCounter Analysis System at the Ohio State University Comprehensive Cancer Center Nucleic Acids Shared Resource directed by Hansjuerg Alder.

The nCounter Analysis System is a fully automated target profiling system that is extraordinarily easy to use. The reagents and consumables required to conduct miRNA and gene expression experiments. In addition to the new miRNA assays, the company is developing assays for copy number variation. NanoString also offers custom and off-the shelf assays for gene expression analysis. More information is available at www.nanostring.com.

Genocea Biosciences Agreement with U.S. Military to Develop Malaria vaccine

Cambridge: Genocea Biosciences, a leading vaccine discovery and development company, announced that it has entered into a Cooperative Research and Development Agreement (CRADA) with the Naval Medical Research Center (NMRC). NMRC will collaborate with Genocea to identify antigens that will be used in the development of a vaccine candidate against Plasmodium falciparum for the prevention of malaria. Genocea and NMRC will leverage their expertise to identify novel malaria vaccine candidate antigens and move promising antigens through preclinical development. Genocea will apply its technology to the rapid.

Identification of novel T-cell antigens from a proteomic screen of the P.falciparum organism, and NMRC will share material as well as their extensive experience developing subunit malaria vaccines. This work is funded by a $2.7 million award that was granted to Genocea from the U.S. Army Medical Research and Material Command (USAMRMC) for rapid T-cell screens of a P.falciparum proteomic library

New England Launches New Line of Proteomics Services

New England Peptide (NEP) introduced NEPTuneTM, a new Propriety line of custom proteomics reagents to help its customers to quickly and inexpensively maximize biomarker assay development and produce consistent result.

“Proteomics is an exciting research field that is poised to deliver the next generation of life- changing diagnosis tools and drug therapies diagnostics tools and drug therapies,” said Dave Robinson, NEP’s Executive Officer. “We have great interest in proteomic research and are pleased to be the only company providing this high quality, proprietary line of services to our customers. It marks a revolutionary step forward for NEP and the field of proteomics as a whole.” Proteomics is the large scale study of the set of proteins specified by genes within an organism with the aim to understand how biological systems operate on a fundamental level. Proteomics based (human) diagnostics and resultant therapies have the potential to allow physician treat disease states in a more specific and targeted approach, which will help deliver on the promise of personalized medicine and tailored therapies that have been discussed in the health care industry in recent years.

The NEPTuneTM line comprises a suite of four distinct solutions that align with the various needs of proteomics researcher and clinician, ranging from biomarker discovery through clinical assay production:

• NEPTuneTM Assay Discovery Peptides- NEP’s technology allows customers to quickly and less inexpensively increase the number of peptides they screen, enabling them to more efficiently reach their research goals.
• NEPTuneTM Assay Verification Peptides-Since proteomics verification is a critical stage in the development of a viable biomarker assay, NEP offers peptide and antibody reagents tailored to complement this phase of the proteomics project lifecycle.
• NEPTuneTM Assay Refinement Peptides- The culmination of rigorous discovery and verification studies has its own unique set of needs, which are met by NEP’s assay refinement solution.
• NEPTuneTM Clinical Assay Peptides – NEP already supports many ongoing clinical assays around the world with its reagents.

Robinson noted that NEP has been a leader in proteomics research for years has assembled a team – led by Chemical Development Vice President Robert Hammer, PhD and Proteomics Product Manager John Antogoni with consultation from NEP’s industry-leading scientific advisory board – that delivers the industry’s only single source of peptides optimized for quantitative proteomics.

NEPTuneTM is the latest in a line of proprietary product and process innovations developed by NEP’s in-house team. Last December, NEP launched PepScale TM, a proprietary peptide synthesis instrument, that better anables peptide scale-up and process development projects for its customers. In September, NEP rolled out PepCROTM, the first peptide –focused contract research service for drug, vaccine and diagnostic discovery projects. Last July, NEP unveiled FlashPureTM, the peptide industry’s first flash purification system.