Bio Organic Chemistry of Natural Enediyne Anticancer Antibiotics PDF Download

 Page 1


NPTEL – Chemistry –  Bio-Organic Chemistry of Natural Enediyne Anticancer Antibiotics 
Joint initiative of IITs and IISc – Funded by MHRD                                               Page 1 of 89 
NPTEL Phase – II (Syllabus Template) 
 
Course Title: Bio-Organic Chemistry of Natural Enediyne 
Anticancer Antibiotics 
 
 
Module II:  
Synthesis/Biosynthesis of Enediynes Class of Natural Products: Classifications of Natural 
Enediynes-Calicheamicins/ Esperamicins class of enediynes (Class I), The Dynemicins class of 
enediynes (Class II), and The Chromoprotein  class of enediynes (Class III); Mechanism of DNA 
Cleavage by Each Class; Chemical Synthesis of a Few Members of Enediynes Natural Products; 
Biosynthesis of a Few Members of Natural Enediynes.  
                                                                                       
  
2.1. Classifications of Natural Enediynes 
 
2.1.1. Introduction  
Enediynes are a class of bacterial natural products characterized by either nine- and ten-
membered rings containing two triple bonds separated by a double bond. In the mid to late 
1980s, it became clear that an emerging series of naturally occurring antitumor antibiotics such 
as calicheamicin, esperamicin, dynemicin, kedarcidin chromophore and C-1027 chromophore 
possessing the enediyne core and showed biological activity through the generation of active 
biradical specis via Bergman cyclization. In addition to that neocarzinostatin (NCS) 
chromophore which does not contain the classical conjugated enediyne system also demonstrated 
very similar DNA cleavage mechanism via the generation biradical species through the Myers-
Saito cyclization. The enediynes are in their native form biologically inactive but undergo 
cycloaromatization reactions after being activated by a triggering reaction and produces the 
active biradical species. Therefore, the enediyne group in those compounds is often called a 
warhead. For example, the strain imposed by the double bond in calicheamicin or by the epoxide 
in dynemicin imparts stability to the system. Cycloaromatization of these natural products then 
give rise to cytotoxic diyl radicals which are capable of inducing DNA strand scission at low 
concentration by abstracting –H atom from the sugar phosphate backbone of DNA. Several of 
the naturally occurring enediynes have entered clinical trials against cancer and in Japan 
neocarzinostatin is used clinically. 
The biological profile of the calicheamicin and esperamicins are: 
 
(a) subpicogram potency against Gram positive bacteria, 
(b) activity in the biochemical induction assay at very low concentrations, 
(c) high potency against a number of animal tumor models and, 
(d) induction of double-stranded DNA cleavage with minimal concurrent single strand 
breakage. 
 
Page 2


NPTEL – Chemistry –  Bio-Organic Chemistry of Natural Enediyne Anticancer Antibiotics 
Joint initiative of IITs and IISc – Funded by MHRD                                               Page 1 of 89 
NPTEL Phase – II (Syllabus Template) 
 
Course Title: Bio-Organic Chemistry of Natural Enediyne 
Anticancer Antibiotics 
 
 
Module II:  
Synthesis/Biosynthesis of Enediynes Class of Natural Products: Classifications of Natural 
Enediynes-Calicheamicins/ Esperamicins class of enediynes (Class I), The Dynemicins class of 
enediynes (Class II), and The Chromoprotein  class of enediynes (Class III); Mechanism of DNA 
Cleavage by Each Class; Chemical Synthesis of a Few Members of Enediynes Natural Products; 
Biosynthesis of a Few Members of Natural Enediynes.  
                                                                                       
  
2.1. Classifications of Natural Enediynes 
 
2.1.1. Introduction  
Enediynes are a class of bacterial natural products characterized by either nine- and ten-
membered rings containing two triple bonds separated by a double bond. In the mid to late 
1980s, it became clear that an emerging series of naturally occurring antitumor antibiotics such 
as calicheamicin, esperamicin, dynemicin, kedarcidin chromophore and C-1027 chromophore 
possessing the enediyne core and showed biological activity through the generation of active 
biradical specis via Bergman cyclization. In addition to that neocarzinostatin (NCS) 
chromophore which does not contain the classical conjugated enediyne system also demonstrated 
very similar DNA cleavage mechanism via the generation biradical species through the Myers-
Saito cyclization. The enediynes are in their native form biologically inactive but undergo 
cycloaromatization reactions after being activated by a triggering reaction and produces the 
active biradical species. Therefore, the enediyne group in those compounds is often called a 
warhead. For example, the strain imposed by the double bond in calicheamicin or by the epoxide 
in dynemicin imparts stability to the system. Cycloaromatization of these natural products then 
give rise to cytotoxic diyl radicals which are capable of inducing DNA strand scission at low 
concentration by abstracting –H atom from the sugar phosphate backbone of DNA. Several of 
the naturally occurring enediynes have entered clinical trials against cancer and in Japan 
neocarzinostatin is used clinically. 
The biological profile of the calicheamicin and esperamicins are: 
 
(a) subpicogram potency against Gram positive bacteria, 
(b) activity in the biochemical induction assay at very low concentrations, 
(c) high potency against a number of animal tumor models and, 
(d) induction of double-stranded DNA cleavage with minimal concurrent single strand 
breakage. 
 
NPTEL – Chemistry –  Bio-Organic Chemistry of Natural Enediyne Anticancer Antibiotics 
Joint initiative of IITs and IISc – Funded by MHRD                                               Page 2 of 89 
2.1.2. Classifications of Natural Enediynes 
 
During the 1980s enediynes as a new class of natural products have been introduced with the 
structural elucidation of neocarzinostatin and calicheamicin. Since this time, thirteen enediynes 
have been structurally confirmed, which includes two probable enediynes isolated as inactive 
degradation products (Table 1; Figure 1).  
Table 1: Enediyne Natural Products 
Name Producer Year 
Nine-Membered Enediynes 
Auromomycin   Streptomyces macromomyceticus 1968 [3] 
Largomycin  Streptomyces pluricolorescens   1970 [4] 
Actinoxanthin  Actinomyces globisporus  1976 [5] 
Sporamycin  Streptosporangium pseudovulgare  1978 [6] 
Neocarzinostatin  Streptomyces carzinostaticus  1985 [1] 
C-1027  Streptomyces globisporus  1991 [7] 
Maduropeptin  Actinomadura madurea  1994 [8] 
Kedarcidin  Actinomycete L585-6  1997 [9] 
N1999A2  Streptomyces sp. AJ9493  1998 [10] 
Sporolides A and B  Salinispora tropica  2005 [11] 
Cyanosporasides A and B  Salinispora pacifica  2006 [12] 
Ten-Membered Enediynes 
Esperamicin  Actinomadura verrucosospora  1985 [13] 
Calicheamicin  Micromonospora echinospora ssp. calichensis  1987 [2] 
Dynemycin  Micromonospora chersina  1990 [14] 
Namenamicin  Polysyncraton lithostrotum  1996 [15] 
Shishijimicin  Didemnum proliferum  2003 [16] 
Uncialamycin  
 
Unknown 2005 [17] 
 
These natural antitumor antibiotics are classified under three classes: 
(a) The Calicheamicins and Esperamicins. 
(b) The Dynemicins 
(c) The Chromophore types; Kedarcidin chromophore, C-1027 and Neocarzinostatin. 
 
Even though these natural antitumor antibiotics possess phenomenal cytotoxicity against 
tumor cells they are too toxic and indiscriminant for use as drugs, hence efforts have been made 
to synthesize various derivatives of these compounds. A notable example is gemtuzumab 
ozogamicin (Mylotarg), which is a derivative of calicheamicin conjugated to a humanized anti-
CD33 antibody; the drug is indicated for the treatment of acute myeloid leukemia (AML). 
However this has been withdrawn because of its strong cytotoxicity. 
Page 3


NPTEL – Chemistry –  Bio-Organic Chemistry of Natural Enediyne Anticancer Antibiotics 
Joint initiative of IITs and IISc – Funded by MHRD                                               Page 1 of 89 
NPTEL Phase – II (Syllabus Template) 
 
Course Title: Bio-Organic Chemistry of Natural Enediyne 
Anticancer Antibiotics 
 
 
Module II:  
Synthesis/Biosynthesis of Enediynes Class of Natural Products: Classifications of Natural 
Enediynes-Calicheamicins/ Esperamicins class of enediynes (Class I), The Dynemicins class of 
enediynes (Class II), and The Chromoprotein  class of enediynes (Class III); Mechanism of DNA 
Cleavage by Each Class; Chemical Synthesis of a Few Members of Enediynes Natural Products; 
Biosynthesis of a Few Members of Natural Enediynes.  
                                                                                       
  
2.1. Classifications of Natural Enediynes 
 
2.1.1. Introduction  
Enediynes are a class of bacterial natural products characterized by either nine- and ten-
membered rings containing two triple bonds separated by a double bond. In the mid to late 
1980s, it became clear that an emerging series of naturally occurring antitumor antibiotics such 
as calicheamicin, esperamicin, dynemicin, kedarcidin chromophore and C-1027 chromophore 
possessing the enediyne core and showed biological activity through the generation of active 
biradical specis via Bergman cyclization. In addition to that neocarzinostatin (NCS) 
chromophore which does not contain the classical conjugated enediyne system also demonstrated 
very similar DNA cleavage mechanism via the generation biradical species through the Myers-
Saito cyclization. The enediynes are in their native form biologically inactive but undergo 
cycloaromatization reactions after being activated by a triggering reaction and produces the 
active biradical species. Therefore, the enediyne group in those compounds is often called a 
warhead. For example, the strain imposed by the double bond in calicheamicin or by the epoxide 
in dynemicin imparts stability to the system. Cycloaromatization of these natural products then 
give rise to cytotoxic diyl radicals which are capable of inducing DNA strand scission at low 
concentration by abstracting –H atom from the sugar phosphate backbone of DNA. Several of 
the naturally occurring enediynes have entered clinical trials against cancer and in Japan 
neocarzinostatin is used clinically. 
The biological profile of the calicheamicin and esperamicins are: 
 
(a) subpicogram potency against Gram positive bacteria, 
(b) activity in the biochemical induction assay at very low concentrations, 
(c) high potency against a number of animal tumor models and, 
(d) induction of double-stranded DNA cleavage with minimal concurrent single strand 
breakage. 
 
NPTEL – Chemistry –  Bio-Organic Chemistry of Natural Enediyne Anticancer Antibiotics 
Joint initiative of IITs and IISc – Funded by MHRD                                               Page 2 of 89 
2.1.2. Classifications of Natural Enediynes 
 
During the 1980s enediynes as a new class of natural products have been introduced with the 
structural elucidation of neocarzinostatin and calicheamicin. Since this time, thirteen enediynes 
have been structurally confirmed, which includes two probable enediynes isolated as inactive 
degradation products (Table 1; Figure 1).  
Table 1: Enediyne Natural Products 
Name Producer Year 
Nine-Membered Enediynes 
Auromomycin   Streptomyces macromomyceticus 1968 [3] 
Largomycin  Streptomyces pluricolorescens   1970 [4] 
Actinoxanthin  Actinomyces globisporus  1976 [5] 
Sporamycin  Streptosporangium pseudovulgare  1978 [6] 
Neocarzinostatin  Streptomyces carzinostaticus  1985 [1] 
C-1027  Streptomyces globisporus  1991 [7] 
Maduropeptin  Actinomadura madurea  1994 [8] 
Kedarcidin  Actinomycete L585-6  1997 [9] 
N1999A2  Streptomyces sp. AJ9493  1998 [10] 
Sporolides A and B  Salinispora tropica  2005 [11] 
Cyanosporasides A and B  Salinispora pacifica  2006 [12] 
Ten-Membered Enediynes 
Esperamicin  Actinomadura verrucosospora  1985 [13] 
Calicheamicin  Micromonospora echinospora ssp. calichensis  1987 [2] 
Dynemycin  Micromonospora chersina  1990 [14] 
Namenamicin  Polysyncraton lithostrotum  1996 [15] 
Shishijimicin  Didemnum proliferum  2003 [16] 
Uncialamycin  
 
Unknown 2005 [17] 
 
These natural antitumor antibiotics are classified under three classes: 
(a) The Calicheamicins and Esperamicins. 
(b) The Dynemicins 
(c) The Chromophore types; Kedarcidin chromophore, C-1027 and Neocarzinostatin. 
 
Even though these natural antitumor antibiotics possess phenomenal cytotoxicity against 
tumor cells they are too toxic and indiscriminant for use as drugs, hence efforts have been made 
to synthesize various derivatives of these compounds. A notable example is gemtuzumab 
ozogamicin (Mylotarg), which is a derivative of calicheamicin conjugated to a humanized anti-
CD33 antibody; the drug is indicated for the treatment of acute myeloid leukemia (AML). 
However this has been withdrawn because of its strong cytotoxicity. 
NPTEL – Chemistry –  Bio-Organic Chemistry of Natural Enediyne Anticancer Antibiotics 
Joint initiative of IITs and IISc – Funded by MHRD                                               Page 3 of 89 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Figure 1. Structures of Enediyne class of natural products. 
Page 4


NPTEL – Chemistry –  Bio-Organic Chemistry of Natural Enediyne Anticancer Antibiotics 
Joint initiative of IITs and IISc – Funded by MHRD                                               Page 1 of 89 
NPTEL Phase – II (Syllabus Template) 
 
Course Title: Bio-Organic Chemistry of Natural Enediyne 
Anticancer Antibiotics 
 
 
Module II:  
Synthesis/Biosynthesis of Enediynes Class of Natural Products: Classifications of Natural 
Enediynes-Calicheamicins/ Esperamicins class of enediynes (Class I), The Dynemicins class of 
enediynes (Class II), and The Chromoprotein  class of enediynes (Class III); Mechanism of DNA 
Cleavage by Each Class; Chemical Synthesis of a Few Members of Enediynes Natural Products; 
Biosynthesis of a Few Members of Natural Enediynes.  
                                                                                       
  
2.1. Classifications of Natural Enediynes 
 
2.1.1. Introduction  
Enediynes are a class of bacterial natural products characterized by either nine- and ten-
membered rings containing two triple bonds separated by a double bond. In the mid to late 
1980s, it became clear that an emerging series of naturally occurring antitumor antibiotics such 
as calicheamicin, esperamicin, dynemicin, kedarcidin chromophore and C-1027 chromophore 
possessing the enediyne core and showed biological activity through the generation of active 
biradical specis via Bergman cyclization. In addition to that neocarzinostatin (NCS) 
chromophore which does not contain the classical conjugated enediyne system also demonstrated 
very similar DNA cleavage mechanism via the generation biradical species through the Myers-
Saito cyclization. The enediynes are in their native form biologically inactive but undergo 
cycloaromatization reactions after being activated by a triggering reaction and produces the 
active biradical species. Therefore, the enediyne group in those compounds is often called a 
warhead. For example, the strain imposed by the double bond in calicheamicin or by the epoxide 
in dynemicin imparts stability to the system. Cycloaromatization of these natural products then 
give rise to cytotoxic diyl radicals which are capable of inducing DNA strand scission at low 
concentration by abstracting –H atom from the sugar phosphate backbone of DNA. Several of 
the naturally occurring enediynes have entered clinical trials against cancer and in Japan 
neocarzinostatin is used clinically. 
The biological profile of the calicheamicin and esperamicins are: 
 
(a) subpicogram potency against Gram positive bacteria, 
(b) activity in the biochemical induction assay at very low concentrations, 
(c) high potency against a number of animal tumor models and, 
(d) induction of double-stranded DNA cleavage with minimal concurrent single strand 
breakage. 
 
NPTEL – Chemistry –  Bio-Organic Chemistry of Natural Enediyne Anticancer Antibiotics 
Joint initiative of IITs and IISc – Funded by MHRD                                               Page 2 of 89 
2.1.2. Classifications of Natural Enediynes 
 
During the 1980s enediynes as a new class of natural products have been introduced with the 
structural elucidation of neocarzinostatin and calicheamicin. Since this time, thirteen enediynes 
have been structurally confirmed, which includes two probable enediynes isolated as inactive 
degradation products (Table 1; Figure 1).  
Table 1: Enediyne Natural Products 
Name Producer Year 
Nine-Membered Enediynes 
Auromomycin   Streptomyces macromomyceticus 1968 [3] 
Largomycin  Streptomyces pluricolorescens   1970 [4] 
Actinoxanthin  Actinomyces globisporus  1976 [5] 
Sporamycin  Streptosporangium pseudovulgare  1978 [6] 
Neocarzinostatin  Streptomyces carzinostaticus  1985 [1] 
C-1027  Streptomyces globisporus  1991 [7] 
Maduropeptin  Actinomadura madurea  1994 [8] 
Kedarcidin  Actinomycete L585-6  1997 [9] 
N1999A2  Streptomyces sp. AJ9493  1998 [10] 
Sporolides A and B  Salinispora tropica  2005 [11] 
Cyanosporasides A and B  Salinispora pacifica  2006 [12] 
Ten-Membered Enediynes 
Esperamicin  Actinomadura verrucosospora  1985 [13] 
Calicheamicin  Micromonospora echinospora ssp. calichensis  1987 [2] 
Dynemycin  Micromonospora chersina  1990 [14] 
Namenamicin  Polysyncraton lithostrotum  1996 [15] 
Shishijimicin  Didemnum proliferum  2003 [16] 
Uncialamycin  
 
Unknown 2005 [17] 
 
These natural antitumor antibiotics are classified under three classes: 
(a) The Calicheamicins and Esperamicins. 
(b) The Dynemicins 
(c) The Chromophore types; Kedarcidin chromophore, C-1027 and Neocarzinostatin. 
 
Even though these natural antitumor antibiotics possess phenomenal cytotoxicity against 
tumor cells they are too toxic and indiscriminant for use as drugs, hence efforts have been made 
to synthesize various derivatives of these compounds. A notable example is gemtuzumab 
ozogamicin (Mylotarg), which is a derivative of calicheamicin conjugated to a humanized anti-
CD33 antibody; the drug is indicated for the treatment of acute myeloid leukemia (AML). 
However this has been withdrawn because of its strong cytotoxicity. 
NPTEL – Chemistry –  Bio-Organic Chemistry of Natural Enediyne Anticancer Antibiotics 
Joint initiative of IITs and IISc – Funded by MHRD                                               Page 3 of 89 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Figure 1. Structures of Enediyne class of natural products. 
NPTEL – Chemistry –  Bio-Organic Chemistry of Natural Enediyne Anticancer Antibiotics 
Joint initiative of IITs and IISc – Funded by MHRD                                               Page 4 of 89 
2.2. Mechanism of DNA Cleavage 
 
2.2.1. Calicheamicins and Esperamicins 
 
The Calicheamicins (also known as the LL-E 33288 antibiotics) produced from 
Micromonospora echinospora spp. Calichensis, a bacterium was discovered by May. D. Lee et 
al., in 1987. It is the most important member of the enediyne class of natural products, and 
possesses potent cytotoxicity against murine tumor cells. 
 
Esperamicin A1 is also another member of the enediyne family of antibiotics exhibiting 
activity against marine tumor models in the 100ng/kg range. The families of Esperamicins were 
isolated from the bacterial Actinomadura verrucosospora and their structure elucidation was 
reported in 1987-89. The antitumor antibiotic drugs, calicheamicin, dynemicin, and esperamicin, 
all possessed bicyclo-[7,3,1]-enediyne substructure and become active p-benzyne biradical 
intermediates due to Bergman cyclizations. Precisely the reactive intermediate is proposed to be 
a 1, 4-dehydrobenzene derivative which is suggested to arise thermally from (Z)-enediyne in a 
cyclic version of the Bergman reaction. 
 
The mechanistic studies have revealed that at a minimum, three common features are 
essential to the show the potent DNA cleavage activity by these antibiotics: 
 
(a) non-destructive high-affinity binding to DNA,  
(b) a chemical trigging mechanism leading to a high–energy intermediate  
(c)  rapid formation of biradical specis at physiological temperatures which is mainly 
responsible for DNA strand scission. 
 
 
 
 
 
 
 
 
 
 
 
 
Figure 2. Structures of Calicheamicin ?1
I
 and Esperamicin A1. 
 
 
 
 
 
 
Natural enediyne Calicheamicins and Esperamicins family
O O
O
OH
Me
N
H
O O
OH
Me
S
OMe
OMe
Me
I
O
O
O
OH
Me
HO
MeO
O EtHN
MeO
SSSMe
O
HO
NHCO
2
Me
H
Calicheamicin ? 
1
I
O O
O
OH
Me
N
H
O O
OH
Me
SMe
SSSMe
O
NHCO
2
Me
H
O
OMe
NH
Me Me
O
Me
HO
O
O
MeO
MeO NH
OMe
O
Esperamicin A1
O
HO
Page 5


NPTEL – Chemistry –  Bio-Organic Chemistry of Natural Enediyne Anticancer Antibiotics 
Joint initiative of IITs and IISc – Funded by MHRD                                               Page 1 of 89 
NPTEL Phase – II (Syllabus Template) 
 
Course Title: Bio-Organic Chemistry of Natural Enediyne 
Anticancer Antibiotics 
 
 
Module II:  
Synthesis/Biosynthesis of Enediynes Class of Natural Products: Classifications of Natural 
Enediynes-Calicheamicins/ Esperamicins class of enediynes (Class I), The Dynemicins class of 
enediynes (Class II), and The Chromoprotein  class of enediynes (Class III); Mechanism of DNA 
Cleavage by Each Class; Chemical Synthesis of a Few Members of Enediynes Natural Products; 
Biosynthesis of a Few Members of Natural Enediynes.  
                                                                                       
  
2.1. Classifications of Natural Enediynes 
 
2.1.1. Introduction  
Enediynes are a class of bacterial natural products characterized by either nine- and ten-
membered rings containing two triple bonds separated by a double bond. In the mid to late 
1980s, it became clear that an emerging series of naturally occurring antitumor antibiotics such 
as calicheamicin, esperamicin, dynemicin, kedarcidin chromophore and C-1027 chromophore 
possessing the enediyne core and showed biological activity through the generation of active 
biradical specis via Bergman cyclization. In addition to that neocarzinostatin (NCS) 
chromophore which does not contain the classical conjugated enediyne system also demonstrated 
very similar DNA cleavage mechanism via the generation biradical species through the Myers-
Saito cyclization. The enediynes are in their native form biologically inactive but undergo 
cycloaromatization reactions after being activated by a triggering reaction and produces the 
active biradical species. Therefore, the enediyne group in those compounds is often called a 
warhead. For example, the strain imposed by the double bond in calicheamicin or by the epoxide 
in dynemicin imparts stability to the system. Cycloaromatization of these natural products then 
give rise to cytotoxic diyl radicals which are capable of inducing DNA strand scission at low 
concentration by abstracting –H atom from the sugar phosphate backbone of DNA. Several of 
the naturally occurring enediynes have entered clinical trials against cancer and in Japan 
neocarzinostatin is used clinically. 
The biological profile of the calicheamicin and esperamicins are: 
 
(a) subpicogram potency against Gram positive bacteria, 
(b) activity in the biochemical induction assay at very low concentrations, 
(c) high potency against a number of animal tumor models and, 
(d) induction of double-stranded DNA cleavage with minimal concurrent single strand 
breakage. 
 
NPTEL – Chemistry –  Bio-Organic Chemistry of Natural Enediyne Anticancer Antibiotics 
Joint initiative of IITs and IISc – Funded by MHRD                                               Page 2 of 89 
2.1.2. Classifications of Natural Enediynes 
 
During the 1980s enediynes as a new class of natural products have been introduced with the 
structural elucidation of neocarzinostatin and calicheamicin. Since this time, thirteen enediynes 
have been structurally confirmed, which includes two probable enediynes isolated as inactive 
degradation products (Table 1; Figure 1).  
Table 1: Enediyne Natural Products 
Name Producer Year 
Nine-Membered Enediynes 
Auromomycin   Streptomyces macromomyceticus 1968 [3] 
Largomycin  Streptomyces pluricolorescens   1970 [4] 
Actinoxanthin  Actinomyces globisporus  1976 [5] 
Sporamycin  Streptosporangium pseudovulgare  1978 [6] 
Neocarzinostatin  Streptomyces carzinostaticus  1985 [1] 
C-1027  Streptomyces globisporus  1991 [7] 
Maduropeptin  Actinomadura madurea  1994 [8] 
Kedarcidin  Actinomycete L585-6  1997 [9] 
N1999A2  Streptomyces sp. AJ9493  1998 [10] 
Sporolides A and B  Salinispora tropica  2005 [11] 
Cyanosporasides A and B  Salinispora pacifica  2006 [12] 
Ten-Membered Enediynes 
Esperamicin  Actinomadura verrucosospora  1985 [13] 
Calicheamicin  Micromonospora echinospora ssp. calichensis  1987 [2] 
Dynemycin  Micromonospora chersina  1990 [14] 
Namenamicin  Polysyncraton lithostrotum  1996 [15] 
Shishijimicin  Didemnum proliferum  2003 [16] 
Uncialamycin  
 
Unknown 2005 [17] 
 
These natural antitumor antibiotics are classified under three classes: 
(a) The Calicheamicins and Esperamicins. 
(b) The Dynemicins 
(c) The Chromophore types; Kedarcidin chromophore, C-1027 and Neocarzinostatin. 
 
Even though these natural antitumor antibiotics possess phenomenal cytotoxicity against 
tumor cells they are too toxic and indiscriminant for use as drugs, hence efforts have been made 
to synthesize various derivatives of these compounds. A notable example is gemtuzumab 
ozogamicin (Mylotarg), which is a derivative of calicheamicin conjugated to a humanized anti-
CD33 antibody; the drug is indicated for the treatment of acute myeloid leukemia (AML). 
However this has been withdrawn because of its strong cytotoxicity. 
NPTEL – Chemistry –  Bio-Organic Chemistry of Natural Enediyne Anticancer Antibiotics 
Joint initiative of IITs and IISc – Funded by MHRD                                               Page 3 of 89 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Figure 1. Structures of Enediyne class of natural products. 
NPTEL – Chemistry –  Bio-Organic Chemistry of Natural Enediyne Anticancer Antibiotics 
Joint initiative of IITs and IISc – Funded by MHRD                                               Page 4 of 89 
2.2. Mechanism of DNA Cleavage 
 
2.2.1. Calicheamicins and Esperamicins 
 
The Calicheamicins (also known as the LL-E 33288 antibiotics) produced from 
Micromonospora echinospora spp. Calichensis, a bacterium was discovered by May. D. Lee et 
al., in 1987. It is the most important member of the enediyne class of natural products, and 
possesses potent cytotoxicity against murine tumor cells. 
 
Esperamicin A1 is also another member of the enediyne family of antibiotics exhibiting 
activity against marine tumor models in the 100ng/kg range. The families of Esperamicins were 
isolated from the bacterial Actinomadura verrucosospora and their structure elucidation was 
reported in 1987-89. The antitumor antibiotic drugs, calicheamicin, dynemicin, and esperamicin, 
all possessed bicyclo-[7,3,1]-enediyne substructure and become active p-benzyne biradical 
intermediates due to Bergman cyclizations. Precisely the reactive intermediate is proposed to be 
a 1, 4-dehydrobenzene derivative which is suggested to arise thermally from (Z)-enediyne in a 
cyclic version of the Bergman reaction. 
 
The mechanistic studies have revealed that at a minimum, three common features are 
essential to the show the potent DNA cleavage activity by these antibiotics: 
 
(a) non-destructive high-affinity binding to DNA,  
(b) a chemical trigging mechanism leading to a high–energy intermediate  
(c)  rapid formation of biradical specis at physiological temperatures which is mainly 
responsible for DNA strand scission. 
 
 
 
 
 
 
 
 
 
 
 
 
Figure 2. Structures of Calicheamicin ?1
I
 and Esperamicin A1. 
 
 
 
 
 
 
Natural enediyne Calicheamicins and Esperamicins family
O O
O
OH
Me
N
H
O O
OH
Me
S
OMe
OMe
Me
I
O
O
O
OH
Me
HO
MeO
O EtHN
MeO
SSSMe
O
HO
NHCO
2
Me
H
Calicheamicin ? 
1
I
O O
O
OH
Me
N
H
O O
OH
Me
SMe
SSSMe
O
NHCO
2
Me
H
O
OMe
NH
Me Me
O
Me
HO
O
O
MeO
MeO NH
OMe
O
Esperamicin A1
O
HO
NPTEL – Chemistry –  Bio-Organic Chemistry of Natural Enediyne Anticancer Antibiotics 
Joint initiative of IITs and IISc – Funded by MHRD                                               Page 5 of 89 
The esperamicins and the calicheamicins both share similar structures and their structures 
possess three distinct domains: (a) an oligosaccharide chain, (b) a trisulphide moiety, and (c) an 
enediyne core. Each of these domains has a specific function in DNA cleavage. 
 
(a) The oligosaccharide chain recognises and targets selected base pair sequences in the 
minor groove of DNA. Thus, the molecule binds selectively to the minor groove through 
hydrophobic, electrostatic interactions and hydrogen bonding of the sugar side chain with 
DNA. The natural enediynes are actually stable until they are bonded to DNA and then 
become activated. 
(b) After binding to minor groove, the trisulphide then serves as a molecular trigger which 
upon reductive activation produces thiolate. The thiolate then performs an intramolecular 
Michael addition onto the proximally positioned enone moiety to unlock the enediyne 
warhead. This leads a change in the geometry of the molecule from a trigonal bridgehead 
to a tetragonal centre. Thus, “cd” distance between the two triple bonds is reduced. The 
decrease has been calculated to be from 3.35 to 3.16 Å distance which is close enough for 
spontaneous Bergman cyclization according to Nicolaou’s theory. 
(c) Bergman cycloaromatization of the enediyne structural motif generates a p-benzyne 
diradical which abstracts hydrogen from DNA backbone. The reaction of the DNA 
backbone radicals with molecular oxygen results in double strand cleavage which 
ultimately lead to permanent damage of the genetic material. 
The enediyne systems in both the calicheamicin and esperamicin could easily be triggered to 
aromatize via a free-radical intermediate by cleavage at the methyl trisulfide moiety. This 
aromatization process is responsible for the remarkable DNA damaging effects of the 
calcheamicin and the esperamicins. 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Scheme 1.? Mechanism of DNA cleavage by Calicheamicin. 
Trisulfide reduction
initiates the activation
Intercalates
into DNA
Responsible for 
DNA strand scission
Mechanism of DNA Cleavage by Calicheamicins
Calicheamicins