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A COMPREHENSIVE AND AN UPDATE DATABASE ON ESSENTIAL FEATURES OF SEMISYNTHETIC ANTIBIOTICS WITH SPECIAL EMPHASIS ON BIOINFORMATICS

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Title: A COMPREHENSIVE AND AN UPDATE DATABASE ON ESSENTIAL FEATURES OF SEMISYNTHETIC ANTIBIOTICS WITH SPECIAL EMPHASIS ON BIOINFORMATICS


1
A COMPREHENSIVE AND AN UPDATE DATABASE ON
ESSENTIAL FEATURES OF SEMISYNTHETIC
ANTIBIOTICS WITH SPECIAL EMPHASIS ON
BIOINFORMATICS


September, 2009 Rajarajan .S , YogambalMuthu
, InduPurushothaman , PriyaRoosvelt and Madhan
Mohan Coordinator

Bioinformatics Infrastructure Facility
Center of DBT Govt. of India, New
Delhi Presidency College Chennai
2
Historical perspective
  • Extracts of plants and herbs used for centuries
    to treat illnesses before we understood that
    infectious illnesses are caused by
    microorganisms.
  • Some of these traditional treatments now known to
    contain therapeutic drugs eg quinine in bark
    from chinchona tree active against the malaria
    parasites.
  • 1908 Paul Ehrlich salvarsan arsenic
    compound effective treatment of syphilis First
    systematic approach to find compounds to treat
    infections
  • Concept of chemotherapy born - finding a specific
    chemical compound or drug that kills a
    microorganism without damaging the host (human)
    tissues.

3
  • Sulpha drugs Domagk 1930s sulphanilamide
    not used very much now.
  • Discovery of antibiotics 1928 Alexander
    Fleming growth of Staphylococcus aureuson an
    agar plate inhibited by growth of a common
    blue-green mould (fungus) Penicilliumnotatum
  • Florey (Australian) responsible for development
    of penicillin

4
ANTIBIOTICS
  • A comprehensive Antibiotic database with an
    emphasis on Bioinformatics has been developed
    and updated on March,2008 for free online access
  • Many pharmaceutical companies are developing semi
    synthetic form from natural antibiotic and
    purely synthetic chemicals with antibiotic
    activity.

5
NEED FOR SEMI-SYNTHETICS ANTIBIOTICS
  • The reactive beta lactam ring is common to all
    penicillins and cephalosporin C analogues.
  • This ring opens during acytelation of the
    bacterial wall-building enzymes, but previous
    opening of the ring by acid or beta lactamase
    destroys antibiotic activity.
  • Semi synthetic substitutions may protect the ring
    by steric hindrance

6
YellapragadaSubbarao
  • Yellapragada Subbarao (January 12 , 1895 -August
    9, 1948) remains in the views of many the most
    notable medical scientist to emerge from India.
  • He passed the Intermediate Examination from the
    Presidency College and entered the Madras Medical
    College
  • He discovered the role of Phosphocreatine and
    Adenosine Triphosphate(ATP) in muscular activity.
  • Under him Benjamin Duggar made his discovery of
    Aureomycin in 1945, the world's first
    tetracycline antibiotic

7
PENICILLIN
  • Penicillin
  • Penicillin G acid labile, narrow spectrum(mostly
    active against gram- positive organisms
    susceptible to the action of ß-lactam (enzyme
    which splits the ß-lactam ring)
  • Penicillin-V acid stable (a small change in
    structure gives on
  • important change in properties) can be used
    orally organism that
  • produce ß-lactamases are resistant to
    Penicillin and Penicillin G
  • Semi-synthetic Penicillin
  • Ampicillin,Oxacillin,Oxacillin,Cloxacillin,Fluclox
    acillin,Methicillin,Amoxycillin,Carbenicillin
    broad spectrum of activity active against
    Gram-negative organisms as well as Gram-positive
    organisms.

8
GENOMIC INFORMATION OF PENICILLIN
ANTIBIOTIC GENES DATA BASE-LINKS
PENICILLIN pcbAB, pcbC and penDE http//www.bifcpresidency.tn.gov.in/penicillin20main.html
Semi synthetic Penicillin Resistant Gene Gene-Links
AMPICILLIN (ampr) frame.html
CLOXACILLIN bl2d_lcr1,bl2d_moxa bl2d_oxa1,bl2d_oxa10 bl2d_oxa2,bl2d_oxa5 bl2d_oxa9,bl2d_r39 cloxacillinframe.html
METHICILLIN mecr1 methicillinframe.html
CARBENICILLIN bl2c_bro,bl2c_pse1 bl2c_pse3 carbenicillinframe.html
9
CEPHALOSPORIN
  • CEPHALOSPORIN-MICROBIAL ORIGIN
  • Bactericidal antibiotic. Isolated from culture
    Cephalosporiumacremonium. ß-lactam structure is
    very similar to penicillin.
  • Treat infections in different parts of the
    body-the ears, nose, throat, lungs, sinuses, and
    skin.
  • SEMI-SYNTHETIC CEPHALOSPORIN
  • Cephalothin,Cephaloridine,Cephaloglycin,Cephalexin
    ,Cephapirin,Cephalexin,Cepharoxadine,Cefaclor,Cefi
    xime active against Gram-negative organisms as
    well as Gram-positive organisms.


10
GENOMIC INFORMATION ON CEPHALOSPORIN
ANTIBIOTICS GENES DATA BASE-LINKS
CEPHALOSPORIN cefEF-cefG http//www.bifcpresidency.tn.gov.in/cephalosporin2020frame20.html
Semi-Synthetic Cephalosporin Resistant Gene Database-Links
Cephapirin bl2b_tem1, bl2b_tem2, cephapirinframe.html
Cefaclor bl2b_tem1, bl2be_ctxm cefaclorframe.html
cefixime bl2be_ctxm cefiximeframe.html
11
TETERACYCLIN
  • TETERACYCLIN-MICROBIAL ORIGIN
  • Is a broad-spectrum polyketide antibiotic used
    against many bacterial infections. Commonly used
    to treat acne.
  • It was released by the organism
    StreptomycesaureofaciensUsed to produce several
    semi-synthetic derivatives.
  • Known as the tetracycline antibiotic group.
  • The general chemical formula is C22H24N2O8. The
    molecular weight is 444.44 g.
  • SEMI-SYNTHETIC TETERACYCLIN
  • Methacycline, Doxycycline,Rolitetracyclin
  • The semi-synthetic, second-generation antibiotic
    doxycycline became available in 1967.
  • A number of other naturally occurring and
    semi-synthetic types of tetracycline are also
    available.
  • Each varies somewhat in the organisms it is
    effective against and in how long a dose remains
    effective.


12
GENOMIC INFORMATION ON TETRACYCLIN
ANTIBIOTICS Resistant Gene DATA BASE-LINKS
Tetracyclin mexa, mexb, oprm, Otra, otrb tetraresi.html
13
BIOLOGICAL DATABASE-WHY
  • A biological database is a large, organized body
    of persistent data, usually associated with
    computerized software
  • Designed to update, query, and retrieve
    components of the data stored within the system.
  • A simple database might be a single file
    containing many records, each of which includes
    the same set of information.
  • A record associated with a nucleotide sequence
    database typically contains information such as
    contact name
  • The input sequence with a description of the type
    of molecule
  • The scientific name of the source organism from
    which it was isolated

14
APPLICATION OF BIOINFORMATICS IN ANTIBIOTIC
RESISTANCE
  • Scientists examined the genome of
    Enterococcusfaecalis -a leading cause of
    bacterial infection among hospital patients.
  • They have discovered a virulence region made up
    of a number of antibiotic-resistant genes that
    contribute to the bacterium's transformation from
    a harmless gut bacteria to a menacing invader.
  • The discovery of the region, known as a
    pathogenicity , which provide useful markers for
    detecting pathogenic strains and help to
    establish controls to prevent the spread of
    infection inwards.

15
SUCCESS OF HUMAN GENOME PROJECT
  • The Human Genome Project provide researchers
    with powerful tools to understand the genetic
    factors in human diseases.
  • Paving the way for new strategies for their
    diagnosis, treatment and prevention.
  • The Human Genome project spurred a revolution in
    biotechnology innovation around the world.
  • It has already fueled the discovery of genes for
    more than 1,800 diseases
  • Pharmacogenomics holds the promise that drugs
    might one day be tailor-made for individuals
    and suited to each persons genome

16
  • Environment, diet, age, lifestyle, and state of
    health can influence a person's response to, but
    understanding an individual is thought to be the
    key to create personalized medicine with highest
    efficacy and safety.
  • Serious bacterial infections can lead to death in
    the absence of antibiotic therapy
  • Fungal infection is quite common among poor
    sections of society due to their occupational
    conduct in soil the geriatric population
    immunosuppressed patients namely, in organ
    recipients and in AIDS.
  • Hence the antibiotics remain a necessary weapon
    in the clinicians arsenal for ensuring diseases

17
REVIEW OF LITERATURE
  • Antibiotic Resistance Genes Database
  • Received August 14, 2008. Revised September 15,
  • 2008. Accepted September 16, 2008.
  • ARDB can help user to identify mutational
    resistance for 12
  • antibiotic target genes by BLAST
  • ARDB contains resistance information for 13293
    genes, 377 types, 257 antibiotics, 3369 species
    and 124 genera.
  • Sorted by
  • Resistance Type
  • Resistance Gene
  • Antibiotic
  • Resistance Gene(Non RD)
  • Resistance Gene(ALL)
  • Resistance Species
  • Resistance Genus

18
REVIEW OF LITERATURE
  • NOVEL ANTIBIOTIC DATABASE
  • This Data Base includes 5,430 novel substances
    published in the Journal of Antibiotics
    Vol.1-56, in 1947-2003.
  • The size of this data base is so large
    (ca.1,900KB) that it is divided into 5 parts.
  • Sorted by
  • Substance Name
  • Organism Name
  • Activity Index
  • Affiliation

19
MULTIFUNCTIONAL ANTIMICROBIAL PEPTIDE DATABASE
  • It contains detailedinformation for 525 peptides
    (498 antibacterial, 155 antifungal,28 antiviral
    and 18 antitumor)
  • It also provides statisticaldata for a select
    group of or all the peptides in the database.
  • Peptide information can be searched using
    keywords such as peptidename, ID, length, net
    charge, hydrophobic percentage, key
    residue,unique sequence motif, structure and
    activity.
  • APD (Antimicrobial Peptide Database ) is a
    usefultool for studying the structurefunction
    relationshipof antimicrobial peptides.

20
ANTIBIOTIC DATABASE LAUNCHED
  • Doctors may access the latest information on
    antibiotics and their proper use from a free,
    peer reviewed database provided on the internet
    by Johns Hopkins Medical Institutions
  • It offers diagnostic criteria and drug options
    and is continually updated to reflect the best
    available information. Emergency alerts, such as
    drug recalls, will be available immediately
  • Information on more than 160 drugs and more than
    140 diseases treated by both specialists and
    primary care physicians is featured.

21
ANTIBIOTIC RESISTANCE GENES ONLINE (ARGO)
  • A Database on vancomycin and ßlactam resistance
    genes
  • A database containing gene sequences conferring
    resistance to these two classes of antibiotics.
  • It is designed as a resource to enhance research
    on the prevalence and spread of antibiotic
    resistance genes.
  • ARGO is the first attempt to compile the
    resistance gene sequence data with state specific
    information.

22
  • None of the already available database have
    information on bioinformatics of antibiotics.
  • Namely the genomic component of antibiotic or the
    genomic component of target molecules also.
  • Hence there is a need for some database of a
    comprehensive, lucid data on antibiotic with
    specific information of on genome level.

23
Antibiotic Resistance Genes Online (ARGO)
  • Received  February 14, 2005 revised March 14,
    2005 accepted  March 15, 2005 published online
    March 17, 2005
  • Availability http//www.argodb.org/
  • A database containing gene sequences conferring
    resistance to these two classes of antibiotics.
  • It is designed as a resource to enhance research
    on the prevalence and spread of antibiotic
    resistance genes.
  • ARGO is the first attempt to compile the
    resistance gene sequence data with state specific
    information.

24
LANGUAGES USED
  • HTML(Hyper Text Markup Language)
  • Written by Tim Berners-Lee
  • Is the predominant markup language for Web pages
  • It provides a means to describe the structure of
    text-based information in a document by
    denoting certain text as links,
  • headings, paragraphs, lists.
  • HTML is written in the form of tags, surrounded
    by angle
  • brackets.

25
CSS(CASCADING STYLE SHEET)
  • Written by HåkonWium Lie and Bert Bos
  • Released by Microsoft's Internet Explorer 3
    ,1999
  • A new emerging technology.
  • Is a simple mechanism for adding style (e.g.
    fonts, colors, spacing) to Web documents

26
DATABASE CONSTRUCTION
  • This antibiotic database was built on the windows
  • Vista operating system
  • In addition to reference books, for specific
    informations.
  • Antibiotics of microbial origin were collected
    from the pub - med search using keywords such
    as,
  • Discoverer,
  • Antibiotic producing organisms,
  • Chemical structure., Dosage,
  • Susceptible organism,
  • Genomic information ,
  • Gene responsible ,
  • Patent and Industrial production.

27
DATABASE DESCRIPTION
  • Themain page of the database contains information
    about
  • Introduction,
  • Effectiveness,
  • Table information and links
  • providing detailed information of all the
    antibiotics of microbial origin.

28
APPLICATION
  • An user- friendly database on antibiotics of
    semisynthetic has been developed and made
    available on online in the website
  • semi-synthetic\semihome.html
  • This database is the first of its kind on
    antibiotics of semisynthetic origin on website, a
    comprehensive one with the main thrust on
    bioinformatics
  • This database has been made available for free
    access by all interested individuals on
    antibiotics

29
AVAILABILITY
  • This Database on microbial origin has been
    created, and will be uploaded into the website
    on 9th September 2009.
  • This is maintained and upgraded by the BIFC
    center, Presidency College
  • The database will be periodically updated

30
WHO BE WILL BENIFITED
  • Scientists
  • Research Scholars
  • Students

31
Thank you. We invite you to our website
www.bifcpresidency.tn.gov.in
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