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1、Probing Nature for Antibiotics,Struggle for living,www.photos-screensaver-,www.creswell-crags.org.uk,“History of humankind can be regarded from a medicinal point of view as a struggle against infectious diseases”,Yoneyama,H.,Katsumata,R.,Biosci.Biotechnol.Biochem.,2006,70,1060,Survival against infec
2、tious diseases,dodd.cmcvellore.ac.in,What are antibiotics?,Molecules that stop the microbial growth(both bacteria and fungi)or kill them outright,Walsh,C.,Antibiotics Actions origins and Resistance,2003,4,How do the antibiotics act against bacteria?,Walsh,C.,Antibiotics Actions origins and Resistanc
3、e,2003,Cell Wall Biosynthesis-lactams,Cyclosporins,Glycopeptides,How do the antibiotics act against bacteria?,Walsh,C.,Antibiotics Actions origins and Resistance,2003,19,Protein BiosynthesisAminoglycosides,Macrolides,Tetracyclines,Oxazolidinones,How do the antibiotics act against bacteria?,Walsh,C.,
4、Antibiotics Actions origins and Resistance,2003,19 publications.nigms.nih.gov,DNA BiosynthesisQuinolones,RNA BiosynthesisRifampicin,How do the antibiotics act against bacteria?,Walsh,C.,Antibiotics Actions origins and Resistance,2003,19,Metabolic pathways Folic Acid MetabolismTrimethoprim,Sulfonamid
5、esFatty Acid BiosynthesisTriclosan,Isoniazid,Ethionamide,Why do we need more antibiotics?,-Developing antimicrobial resistanceBacterial species Common types of Antimicrobial Types of Infections ResistanceStreptococcus pneumoniae-lactams,cephalosporins,macrolidesOtitis media,pneumonia,Tetracyclines s
6、inusitis,meningitis Staphylococcus aureusCommunity-associated Meticillin,cephalosporins,macrolides Skin,soft tissue,sepsis pneumoniaHealthcare-associated Meticillin,cephalosporins,quinolones,Endocarditis,pneumonia,aminoglycosides,macrolidessepsisEnterococcus spp.Ampicillin,vancomycin,aminoglycosides
7、 Sepsis,urinary tract,Furuya,E.Y.,Lowy,F.D.,Nature,2006,4,36,What should be targeted?,The compounds with,Novel structuresNew modes of action,Fernandes,P.,Nature Biotechnology,2006,24,1497,Where do the antibiotics come from?,NATURE,Where do the antibiotics come from?,NATURE,NP,SS,TS,Where do the anti
8、biotics come from?,NATURE,NP,SS,TS,Helps in designing the molecules,Natural products as antibiotics,Naturally occurring compounds that are end products of secondary metabolism.Mostly extracted from plants,marine organisms,or microorganisms.,Singh,S.B.,Barrett,J.F.,Biochemical Pharmacology,2006,71,10
9、06,Natural products as antibiotics,Naturally occurring compounds that are end products of secondary metabolism.Mostly extracted from plants,marine organisms,or microorganisms.Eg:,Singh,S.B.,Barrett,J.F.,Biochemical Pharmacology,2006,71,1006Pal,S.,Tetrahedron,2006,62,3171,Erythromycin,Isolation-Strep
10、tomyces erythreus in 1952Uses-Respiratory tract diseases,genital infectionsMOA-Inhibition of protein synthesis,Antibiotics which are semi-synthesized,Synthetically modified chemical compounds which are originated from natural products.,Walsh,C.,Antibiotics Actions origins and Resistance,2003,4,Eryth
11、romycin is,Acid unstable,Pal,S.,Tetrahedron,2006,62,3171,Antibiotics which are semi-synthesized,Clarithromycin,Azithromycin,HMR3647,TE802,Pal,S.,Tetrahedron,2006,62,3171,Antibiotics which are totally from synthesis,Totally synthesized molecules which are potent as antibiotics.Three main types.1.Sulf
12、a drugs 2.Quinolones 3.Oxazolidinones,Singh,S.B.,Barrett,J.F.,Biochemical Pharmacology,2006,71,1006,Antibiotics which are totally from synthesis,Sulfa drugs(Sulphonamides),Uses-Urinary tract infections,pneumonia etc.MOA-Inhibition of folate synthesis,Harold,P.L.,OGrady,F.W.,Antibiotic and Chemothera
13、py,1992,6,268-272,Sulfamethoxazole,Singh,S.B.,Barrett,J.F.,Biochemical Pharmacology,2006,71,1006,Antibiotics which are totally from synthesis,Sulfa drugs(Sulphonamides)Naturally occurring,Uses-Urinary tract infections,pneumonia etc.MOA-Inhibition of folic acid biosynthesis,Harold,P.L.,OGrady,F.W.,An
14、tibiotic and Chemotherapy,1992,6,268-272,Sulfamethoxazole,Singh,S.B.,Barrett,J.F.,Biochemical Pharmacology,2006,71,1006Walsh,C.,Antibiotics Actions origins and Resistance,2003,80-82,p-aminobenzoic acid,Antibiotics which are totally from synthesis,Quinolones,Ciprofloxacin,Uses-Urinary tract infection
15、s,Lower respiratory infections,Gastrointestinal infectionsMOA-Inhibition of DNA synthesis,Singh,S.B.,Barrett,J.F.,Biochemical Pharmacology,2006,71,1006,Antibiotics which are totally from synthesis,Quinolones Naturally occurring,Ciprofloxacin,Uses-Urinary tract infections,Lower respiratory infections
16、,Gastrointestinal infectionsMOA-Inhibition of DNA synthesis,Singh,S.B.,Barrett,J.F.,Biochemical Pharmacology,2006,71,1006Kunze,B.,Hofle,G.,Reichenbach,H.,J.Antibiotics,1987,40,258,Aurachin C,Aurachin D,Antibiotics which are totally from synthesis,Oxazolidinones,Ford,C.W.,Zurenko,G.E.,Barbachyn,M.R.,
17、Current Drug Targets-Infectious Disorders,2001,1,181,Linezolid,Uses-Soft tissue infections,skin infections,Tuberculosis etc.MOA-Inhibition of protein synthesis,Antibiotics which are totally from synthesis,Oxazolidinones Naturally occurring,Ford,C.W.,Zurenko,G.E.,Barbachyn,M.R.,Current Drug Targets-I
18、nfectious Disorders,2001,1,181Zappia,G.,et al.,Mini-Reviews in Medicinal Chemistry,2007,7,389,Linezolid,Uses-Soft tissue infections,skin infections,Tuberculosis etc.MOA-Inhibition of protein synthesis,(-)-Cytoxazone,(+)-Sreptazolin,Sources of antibacterial drugs from 1981 to 2002,Newman,D.J.,Cragg,G
19、.M.,Snader,K.M.,J.Nat.Prod.,2003,66,1022,Ways of probing nature for antibiotics,Ways of probing nature for antibiotics,New antibiotics New architectural scaffolds,Approach A,Conventional way of NP discovery,Singh,S.B.,Barrett,J.F.,Biochemical Pharmacology,2006,71,1006www.spc.int,www.oceanexplorer.no
20、aa.gov,Extraction to the solvents,Isolation and Structure Elucidation,Natural materials,Bioassay guided fractionation,Approach A,Conventional way of NP discoveryWhy isnt it successful?Problems associated with the growth or the availability of the sourceReplication of the hitsDo not distinguish novel
21、 from oldMostly miss the novel compounds due to the lack of sensitivityNo hints about MOACannot reveal potency at screening stage,Singh,S.B.,Barrett,J.F.,Biochemical Pharmacology,2006,71,1006Clardy,J.,Fischbach,M.A.,Walsh,C.,Nat.Rev.Biotechnol.,2006,24,1541,Approach A,What are the new strategies to
22、explore nature for NPs,Molecular Biology based Techniques,Novel culturing techniques,Heterologous expression of biosynthetic genes&Metagenomics,Genomics and Combinatorial biosynthesis,Precursor directed biosynthesis&Mutasynthesis,Differential sensitivity screening approach,Singh,S.B.,Barrett,J.F.,Bi
23、ochemical Pharmacology,2006,71,1006Clardy,J.,Fischbach,M.A.,Walsh,C.,Nat.Rev.Biotechnol.,2006,24,1541Donadio,S.,Chemistry&Biology,2006,13,560,Approach A,What are the new strategies to explore nature for NPs,Molecular Biology based Techniques,Novel culturing techniques,Heterologous expression of bios
24、ynthetic genes&Metagenomics,Genomics and Combinatorial biosynthesis,Precursor directed biosynthesis&Mutasynthesis,Differential sensitivity screening approach,Singh,S.B.,Barrett,J.F.,Biochemical Pharmacology,2006,71,1006Clardy,J.,Fischbach,M.A.,Walsh,C.,Nat.Rev.Biotechnol.,2006,24,1541Donadio,S.,Chem
25、istry&Biology,2006,13,560,Approach A,Extraction to the Solvents,Producing organismsfound in nature,Pathogen,Precursor Directed Biosynthesis&Mutasynthesis,Wild type,Mutant type,Approach A,Precursor Directed Biosynthesis&Mutasynthesis,Natural Biosynthetic pathway,Kennedy,J.,Nat.Prod.Rep.,2008,25,25Wei
26、st,S.,Sssmuth,R.D.,Appl.Microbiol.Biotechnol.,2005,68,141,Wild type,Approach A,Precursor Directed Biosynthesis and Mutasynthesis,Precursor-Directed Biosynthesis,Wild type,Kennedy,J.,Nat.Prod.Rep.,2008,25,25Weist,S.,Sssmuth,R.D.,Appl.Microbiol.Biotechnol.,2005,68,141,Approach A,Precursor Directed Bio
27、synthesis and Mutasynthesis,Mutasynthesis,Mutant,Mutasynthon,Kennedy,J.,Nat.Prod.Rep.,2008,25,25Weist,S.,Sssmuth,R.D.,Appl.Microbiol.Biotechnol.,2005,68,141,Approach A,Mutasynthesis,Pojer,F.,Li,S.M.,Heide,L.,Microbiology,2002,148,3901Galm,U.,et al,Chemistry&Biology,2004,11,173Weist,S.,Sssmuth,R.D.,A
28、ppl.Microbiol.Biotechnol.,2005,68,141,Ring A Ring B Ring CNovobiocin(Albamycin),Ring A Ring B Ring CClorobiocin,Approach A,Mutasynthesis,CloQ-mutants,Pojer,F.,Li,S.M.,Heide,L.,Microbiology,2002,148,3901Galm,U.,et al,Chemistry&Biology,2004,11,173Eustquio,A.S.,et al,Arch.Microbiol.,2003,180,25,Approac
29、h A,Mutasynthesis,Galm,U.,et al,Chemistry&Biology,2004,11,173 Pojer,F.,Li,S.M.,Heide,L.,Microbiology,2002,148,3901,CloQ-mutant,Clorobiocin,Approach A,Mutasynthesis,CloQ-mutant,Clorobiocin,Galm,U.,et al,Chemistry&Biology,2004,11,173 Pojer,F.,Li,S.M.,Heide,L.,Microbiology,2002,148,3901,Approach A,Muta
30、synthesis,CloQ-mutant,Analogs of Clorobiocin,Galm,U.,et al,Chemistry&Biology,2004,11,173 Galm,U.,et al,Antimicrob.Agents Chemother.,2004,48,1307 Pojer,F.,Li,S.M.,Heide,L.,Microbiology,2002,148,3901,Approach A,What are the new strategies to explore nature for NPs,Molecular Biology based Techniques,No
31、vel culturing techniques,Heterologous expression of biosynthetic genes&Metagenomics,Genomics and Combinatorial biosynthesis,Precursor directed biosynthesis&Mutasynthesis,Differential sensitivity screening approach,Singh,S.B.,Barrett,J.F.,Biochemical Pharmacology,2006,71,1006Clardy,J.,Fischbach,M.A.,
32、Walsh,C.,Nat.Rev.Biotechnol.,2006,24,1541Donadio,S.,Chemistry&Biology,2006,13,560,Approach A,Differential sensitivity screening approach,Extraction to the solvents,Couzin,J.,Nature,2006,314,34,ForsythR.A.,Molecular Biology,2002,43,1387 Wang,J.,et al,Antimicrob.Agents Chemother.,2006,50,519,Producing
33、organism from nature,Disabled type,Wild type,Increased sensitivity,Low,Normal,Pathogen,Expression of certain protein/s,Target the pathway,Approach A,Differential sensitivity screening approach,Fatty Acid Biosynthesis A good target,FAB Type I-In mammals,FAB Type II-In bacteria,Campbell,J.W.,Cronan,J.
34、E.Jr.,Annu.Rev.Microbiol.,2001,55,305,Biosynthesis of Saturated Fatty Acids,Campbell,J.W.,Cronan,J.E.Jr.,Annu.Rev.Microbiol.,2001,55,305,Biosynthesis of Saturated Fatty Acids,Campbell,J.W.,Cronan,J.E.Jr.,Annu.Rev.Microbiol.,2001,55,305,Biosynthesis of Saturated Fatty Acids,Campbell,J.W.,Cronan,J.E.J
35、r.,Annu.Rev.Microbiol.,2001,55,305,Singh,S.B.,et al,J.Am.Chem.Soc.,2006,128,11916Forsyth,R.A.,Molecular Biology,2002,43,1387 Wang,J.,et al,Antimicrob.Agents Chemother.,2006,50,519,Approach A,RNA-mediated gene silencing technique,Differential sensitivity screening approach,Reduced or No FabF expressi
36、on,5 AUGGCCUGGACUUCA33 UACCGGACCTGTTGU 5,ds RNA,Degradation of fabF mRNA or inhibition of translation,In Prokaryotes-,Higher sensitivity towards FabF inhibitors,Singh,S.B.,et al,J.Am.Chem.Soc.,2006,128,11916Forsyth,R.A.,Molecular Biology,2002,43,1387 Wang,J.,et al,Antimicrob.Agents Chemother.,2006,5
37、0,519,RNA-mediated gene silencing technique,Differential sensitivity screening approach,Approach A,Approach A,Differential sensitivity screening approach,Results-RNA-mediated gene silencing technique,Wild typefabF Anti-sense,Wang,J.,et al,Nature,2006,441,358,Inhibitor(g),Approach A,Differential sens
38、itivity screening approach,Results-RNA-mediated gene silencing technique,Wild typefabF Anti-sense,Wild typefabF Anti-sense,200 times more potent than Cerulenin,Wang,J.,et al,Nature,2006,441,358Price,A.C.,et al,The Journal of Biological Chemistry,2001,276,6551Heath,R.J.,White,S.W.,Rock,C.O.,Progress
39、in Lipid Research,2001,40,467,Inhibitor(g),Approach A,Differential sensitivity screening approach,Platensimycinfrom a strain of Streptomyces platensis,Singh,S.B.,et al,J.Am.Chem.Soc.,2006,128,11916,Discovery of Platensimycin,Approach A,Differential sensitivity screening approach,Potency of Platensim
40、ycin,Organism and genotype Platensimycin LinezolidAntibacterial activity(MIC,g/ml)S.aureus(MSSA)0.5 4 S.aureus(MRSA)0.5 2 S.aureus(MRSA,macrolideR)0.5 2 S.aureus(MRSA,linezolidR)1 32 Enterococcus faecium(VRE)0.1 2,MIC Concentration of inhibitor used to result no visible growth of the pathogens,Wang,
41、J.,et al,Nature,2006,441,358,Toxicity(g/ml)HeLa MTT(IC50)1,000 100,IC50 Concentration of the inhibitor used to kill 50%population of the living cells,Cell-free gel-elongation assay,Wang,J.,et al,Nature,2006,441,358,Malonyl-ACP,C4:1(2)-ACP,C4:0-ACP,6C-ACP,Approach A,Differential sensitivity screening
42、 approach,High FabF selectivity,Heath,R.J.,Nat.Prod.Rep.,2002,19,581,Ways of probing nature for antibiotics,New antibiotics New architectural scaffolds,Approach B,Singh,S.B.,Barrett,J.F.,Biochemical Pharmacology,2006,71,1006Clardy,J.,Fischbach,M.A.,Walsh,C.,Nat.Rev.Biotechnol.,2006,24,1541,Generatin
43、g Nature Mimics,Biosynthetic pathway,Designing theoretical chemical space that fits the active site or docking the database structures,Translate to a real structure by synthesis,Enzyme purification&3D structural determination,Approach B,Hutton,C.A.,Perugini,M.A.,Gerrard,J.A.,Mol.Biosyst.,2007,3,458H
44、utton,C.A.,Southwood,T.J.,Turner,J.J.,Mini-Reviews in Medicinal Chemistry,2003,3,115,Essential for the bacterial growth Does not exist in mammals,Generating Nature Mimics,Biosynthesis of lysine A good target,isoleucine,threonine,methionine,Hutton,C.A.,Perugini,M.A.,Gerrard,J.A.,Mol.Biosyst.,2007,3,4
45、58Hutton,C.A.,Southwood,T.J.,Turner,J.J.,Mini-Reviews in Medicinal Chemistry,2003,3,115,Biosynthesis of lysine,Hutton,C.A.,Perugini,M.A.,Gerrard,J.A.,Mol.Biosyst.,2007,3,458Hutton,C.A.,Southwood,T.J.,Turner,J.J.,Mini-Reviews in Medicinal Chemistry,2003,3,115,Biosynthesis of lysine,Approach B,Generat
46、ing Nature Mimics,Hutton,C.A.,Perugini,M.A.,Gerrard,J.A.,Mol.Biosyst.,2007,3,458Hutton,C.A.,Southwood,T.J.,Turner,J.J.,Mini-Reviews in Medicinal Chemistry,2003,3,115,Proposed mechanism,Approach B,Generating Nature Mimics,Supportive data,Faehnle,C.R.,Coq,J.L.,Liu,X.,Viola,R.E.,Journal of Biological C
47、hemistry,2006,281,31031 Cox,R.J.,Gibson,J.S.,Martn,M.B.M.,ChemBioChem,2002,3,874Hutton,C.A.,Southwood,T.J.,Turner,J.J.,Mini-Reviews in Medicinal Chemistry,2003,3,115,Approach B,Generating Nature Mimics,Cox,R.J.,Gibson,J.S.,Martn,M.B.M.,Chem.Commun.,2001,1710Cox,R.J.,Gibson,J.S.,Hadfield,A.T.,ChemBio
48、Chem,2005,6,2255Cox,R.J.,Gibson,J.S.,Martn,M.B.M.,ChemBioChem,2002,3,874,Inhibitors of lysine biosynthesis,Approach B,Generating Nature Mimics,Cox,R.J.,Gibson,J.S.,Martn,M.B.M.,Chem.Commun.,2001,1710Cox,R.J.,Gibson,J.S.,Hadfield,A.T.,ChemBioChem,2005,6,2255Cox,R.J.,Gibson,J.S.,Martn,M.B.M.,ChemBioCh
49、em,2002,3,874,Inhibitors of lysine biosynthesis,Approach B,Generating Nature Mimics,Cox,R.J.,Gibson,J.S.,Martn,M.B.M.,ChemBioChem,2002,3,874Cox,R.J.,Gibson,J.S.,Hadfield,A.T.,ChemBioChem,2005,6,2255,Reverse Biosynthesis,In vitro assays,Approach B,Cox,R.J.,Gibson,J.S.,Martn,M.B.M.,ChemBioChem,2002,3,
50、874Blanco,J.,Moore,R.A.,Viola,R.E.,PNAS,2003,100,12613Han,S.,Moore,R.A.,Viola,R.E.,Synlett,2003,6,845,Generating Nature Mimics,KI(ASA)KI(Phosphate),Direct assay,Competitive assays,Approach B,Generating Nature Mimics,Direct assay,Cox,R.J.,Gibson,J.S.,Martn,M.B.M.,ChemBioChem,2002,3,874Blanco,J.,Moore
