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Spiegel K, Magistrato A. Modeling anticancer drug–DNA interactions via mixed QM/MM molecular dynamics simulations. Org Biomol Chem 2006; 4:2507-17. [PMID: 16791311 DOI: 10.1039/b604263p] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The development of anticancer drugs started over four decades ago, with the serendipitous discovery of the antitumor activity of cisplatin and its successful use in the treatment of various cancer types. Despite the efforts made in unraveling the mechanism of the action of cisplatin, as well as in the rational design of new anticancer compounds, in many cases detailed structural and mechanistic information is still lacking. Many of these drugs exert their anticancer activity by covalently binding to DNA inducing a distortion or simply impeding replication, thus triggering a cellular response, which eventually leads to cell death. A detailed understanding of the structural and electronic properties of drug-DNA complexes and their mechanism of binding is the key step in elucidating the principles of their anticancer activity. At the theoretical level, the description of covalent drug-DNA complexes requires the use of state-of-the-art computer simulation techniques such as hybrid quantum/classical molecular dynamics simulations. In this review we provide a general overview on: drugs which covalently bind to DNA duplexes, the basic concepts of quantum mechanics/molecular mechanics (QM/MM), molecular dynamics methods and a list of selected applications of these simulations to the study of drug-DNA adducts. Finally, the potential and the limitations of this approach to the study of such systems are critically evaluated.
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Affiliation(s)
- Katrin Spiegel
- University of Pennsylvania, Department of Chemistry, Philadelphia, PA, USA
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52
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Tse WC, Boger DL. Sequence-selective DNA recognition: natural products and nature's lessons. ACTA ACUST UNITED AC 2005; 11:1607-17. [PMID: 15610844 DOI: 10.1016/j.chembiol.2003.08.012] [Citation(s) in RCA: 185] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2003] [Revised: 08/21/2003] [Accepted: 08/25/2003] [Indexed: 11/24/2022]
Abstract
Biologically active, therapeutically useful, DNA binding natural products continue to reveal new paradigms for sequence-selective recognition, to enlist beautiful mechanisms of in situ activation for DNA modification, to define new therapeutic targets, to exploit new mechanisms to achieve cellular selectivity, and to provide a rich source of new drugs. These attributes arise in compact structures of complex integrated function.
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Affiliation(s)
- Winston C Tse
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
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53
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Parrish JP, Trzupek JD, Hughes TV, Hwang I, Boger DL. Synthesis and evaluation of N-aryl and N-alkenyl CBI derivatives. Bioorg Med Chem 2005; 12:5845-56. [PMID: 15498660 DOI: 10.1016/j.bmc.2004.08.032] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2004] [Revised: 08/23/2004] [Accepted: 08/23/2004] [Indexed: 11/29/2022]
Abstract
The preparation of a novel series of N-aryl CBI derivatives in which an aryl substituent could be used to predictably modulate the reactivity of the resulting CC-1065/duocarmycin alkylation subunit analogue is detailed and its extension to a unique series of N-alkenyl derivatives is reported. The N-aryl derivatives were found to be exceptionally stable and to exhibit well-defined relationships between structure (X-ray), reactivity, and cytotoxic potency. When combined with the results of past investigations, the studies define a fundamental parabolic relationship between reactivity and cytotoxic potency. The parabolic relationship establishes that compounds in the series should possess sufficient stability to reach their biological target (DNA), yet maintain sufficient reactivity to effectively alkylate DNA upon reaching the biological target. Just as importantly, it defined this optimal balance of stability and reactivity that may be used for future design of related analogues. Notably, the duocarmycin SA and yatakemycin alkylation subunit lies at this optimal stability/reactivity position, whereas the CC-1065 and duocarmycin A alkylation subunits lie progressively and significantly to the left of this optimal position (too reactive).
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Affiliation(s)
- Jay P Parrish
- Department of Chemistry and the Skaggs, Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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54
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Parrish JP, Hughes TV, Hwang I, Boger DL. Establishing the parabolic relationship between reactivity and activity for derivatives and analogues of the duocarmycin and CC-1065 alkylation subunits. J Am Chem Soc 2004; 126:80-1. [PMID: 14709069 DOI: 10.1021/ja038162t] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The preparation of a novel series of N-aryl CBI derivatives is detailed in which an aryl para substituent could be used to predictably modulate the reactivity of the resulting CC-1065/duocarmycin alkylation subunit analogue (rho = 0.17). The derivatives were found to be exceptionally stable and to exhibit a well-defined relationship between reactivity and cytotoxic potency. When combined with the results of an extensive series of N-acyl CBI analogues and derivatives assembled over the past 15 years, the studies define a fundamental parabolic relationship between reactivity and cytotoxic potency.
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Affiliation(s)
- Jay P Parrish
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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55
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Bassarello C, Cimino P, Bifulco G, Boger DL, Smith JA, Chazin WJ, Gomez-Paloma L. NMR Structure of the (+)-CPI-indole/d(GACTAATTGAC)-d(GTCAATTAGTC) Covalent Complex. Chembiochem 2003; 4:1188-93. [PMID: 14613110 DOI: 10.1002/cbic.200300642] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We report the NMR solution structure of (+)-CPI-indole (CPI, 1,2,8,8a-tetrahydrocyclopropa[c]pyrrolo[3,2-e]indol-4(5H)-one), an agent belonging to the CC-1065/duocarmycin family of antitumor compounds. This (+)-CPI-indole structure is covalently bound to d(G(1)ACTAATTGTC(11))-d(G(12)TCAATTAGTC(22)), a synthetic DNA duplex containing a high-affinity binding site. The three-dimensional structure has been determined by several cycles of restrained molecular dynamics calculations with a total of 563 NMR-derived constraints, both in vacuo and by using the generalized Born solvent continuum model. In-depth analysis of the structure of this ligand-DNA complex led to a detailed knowledge of the bound state conformation of the CPI-indole, the most simplified agent related to CC-1065 and duocarmycins, the parent members of a family of extremely potent antitumor compounds. Comparison of the CPI-indole bound conformation with those previously found for (+)-duocarmycin SA (DSA), its unnatural enantiomer (-)-DSA, and the demethoxylated analogue (+)-DSI in their DNA complexes provided additional evidence of the tight correlation between the catalytic effect exerted by DNA on the alkylation reaction and the extent of angular twist between the two planar heteroaromatic subunits of these agents. Additionally, comparison of the structural features of the DNA-bound state of a "naked" ligand, such as CPI-indole, with those of various other duocarmycin agents provided useful information for the interpretation of the observed effects on chemical reactivity of the different substitution patterns at the hemispheres of these types of complex.
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Affiliation(s)
- Carla Bassarello
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Salerno, 84084 Fisciano, Salerno, Italy
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56
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Parrish JP, Kastrinsky DB, Hwang I, Boger DL. Synthesis and Evaluation of Duocarmycin and CC-1065 Analogues Incorporating the 1,2,9,9a-Tetrahydrocyclopropa[c]benz[e]-3-azaindol-4-one (CBA) Alkylation Subunit. J Org Chem 2003; 68:8984-90. [PMID: 14604371 DOI: 10.1021/jo035119f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An efficient eight-step synthesis (53% overall) and the evaluation of 1,2,9,9a-tetrahydrocyclopropa[c]benz[e]-3-azaindol-4-one (CBA) and its derivatives containing an aza variant of the CC-1065/duocarmycin alkylation subunit are detailed. This unique deep-seated aza modification provided an unprecedented 2-aza-4,4-spirocyclopropacyclohexadienone that was characterized chemically and structurally (X-ray). CBA proved structurally identical with CBI, the carbon analogue, including the stereoelectronic alignment of the key cyclopropane, its bond lengths, and the bond length of the diagnostic C3a-N2 bond, reflecting the extent of vinylogous amide (amidine) conjugation. Despite these structural similarities, CBA and its derivatives were found to be much more reactive toward solvolysis and hydrolysis, much less effective DNA alkylating agents (1000-fold), and biologically much less potent (100- to 1000-fold) than the corresponding CBI derivatives.
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Affiliation(s)
- Jay P Parrish
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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57
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Parrish JP, Kastrinsky DB, Stauffer F, Hedrick MP, Hwang I, Boger DL. Establishment of substituent effects in the DNA binding subunit of CBI analogues of the duocarmycins and CC-1065. Bioorg Med Chem 2003; 11:3815-38. [PMID: 12901927 DOI: 10.1016/s0968-0896(03)00194-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
An extensive series of CBI analogues of the duocarmycins and CC-1065 exploring substituent effects within the first indole DNA binding subunit is detailed. In general, substitution at the indole C5 position led to cytotoxic potency enhancements that can be >/=1000-fold providing simplified analogues containing a single DNA binding subunit that are more potent (IC(50)=2-3 pM) than CBI-TMI, duocarmycin SA, or CC-1065.
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Affiliation(s)
- Jay P Parrish
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550North Torrey Pines Road, La Jolla, CA 92037, USA
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58
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Parrish JP, Kastrinsky DB, Boger DL. Synthesis and X-ray analysis of an unprecedented and stable 2-aza-4,4-spirocyclopropacyclohexadienone. Org Lett 2003; 5:2577-9. [PMID: 12841785 DOI: 10.1021/ol035000t] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[structure: see text] An efficient eight-step synthesis (54% overall) and the subsequent X-ray characterization of 1,2,9,9a-tetrahydrocyclopropa[c]benz[e]-3-azaindol-4-one (CBA) containing an aza variant of the CC-1065/duocarmycin alkylation subunit are detailed. Despite the unique deep-seated aza modification providing an unprecedented and stable 2-aza-4,4-spirocyclopropacyclohexadienone, CBA proved to be structurally identical with CBI, the carbon analogue, in terms of the stereoelectronic alignment of the key cyclopropane, its bond lengths, and the length of the diagnostic C3a-N2 bond reflecting the extent of vinylogous amide conjugation.
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Affiliation(s)
- Jay P Parrish
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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59
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Wolkenberg SE, Boger DL. Mechanisms of in situ activation for DNA-targeting antitumor agents. Chem Rev 2002; 102:2477-95. [PMID: 12105933 DOI: 10.1021/cr010046q] [Citation(s) in RCA: 288] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Scott E Wolkenberg
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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60
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Ambroise Y, Boger DL. The DNA phosphate backbone is not involved in catalysis of the duocarmycin and CC-1065 DNA alkylation reaction. Bioorg Med Chem Lett 2002; 12:303-6. [PMID: 11814783 DOI: 10.1016/s0960-894x(01)00740-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The rates of DNA alkylation were established for the reaction of (+)-duocarmycin SA (1) with the native duplex d(G(1)TCAATTAGTC(11))*d(G(12)ACTAATTGAC(22)), an 11 bp deoxyoligonucleotide that contains a single high-affinity alkylation site that has been structurally characterized at exquisite resolution, and modified duplexes in which the four backbone phosphates proximal to the C4 carbonyl of bound 1 were replaced with methylphosphonates. All were found to react at comparable rates establishing that these backbone phosphates do not participate in catalysis of the DNA alkylation reaction.
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Affiliation(s)
- Yves Ambroise
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550North Torrey Pines Road, La Jolla, CA 92037, USA
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61
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Molecular basis for recognition and binding of specific DNA sequences by calicheamicin and duocarmycin. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s1067-568x(02)80005-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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62
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Boger DL, Schmitt HW, Fink BE, Hedrick MP. Parallel synthesis and evaluation of 132 (+)-1,2,9,9a-tetrahydrocyclopropa[c]benz[e]indol-4-one (CBI) analogues of CC-1065 and the duocarmycins defining the contribution of the DNA-binding domain. J Org Chem 2001; 66:6654-61. [PMID: 11578217 DOI: 10.1021/jo010454u] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The solution-phase, parallel synthesis and evaluation of a library of 132 (+)-1,2,9,9a-tetrahydrocyclopropa[c]benz[e]indol-4-one (CBI) analogues of CC-1065 and the duocarmycins containing dimeric monocyclic, bicyclic, and tricyclic heteroaromatic replacements for the DNA-binding domain are described. This systematic study revealed clear trends in the structural requirements for observation of potent cytotoxic activity and DNA alkylation efficiency, the range of which spans a magnitude of > or =10 000-fold. Combined with related studies, these results highlight that the role of the DNA-binding domain goes beyond simply providing DNA-binding selectivity and affinity (10-100-fold enhancement in properties), consistent with the proposal that it contributes significantly to catalysis of the DNA alkylation reaction accounting for as much as an additional 1000-fold enhancement in properties.
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Affiliation(s)
- D L Boger
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
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63
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Boger DL, Stauffer F, Hedrick MP. Substituent effects within the DNA binding subunit of CBI analogues of the duocarmycins and CC-1065. Bioorg Med Chem Lett 2001; 11:2021-4. [PMID: 11454471 DOI: 10.1016/s0960-894x(01)00372-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A series of CBI analogues of the duocarmycins and CC-1065 exploring substituent effects within the first indole DNA binding subunit are detailed. Substitution at the indole C5 position led to cytotoxic potency enhancements that are > or =1000-fold, providing simplified analogues containing a single DNA binding subunit that are more potent (IC(50)=2-3 pM) than CBI-TMI, duocarmycin SA, or CC-1065.
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Affiliation(s)
- D L Boger
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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64
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Boger DL, Brunette SR, Garbaccio RM. Synthesis and evaluation of a series of C3-substituted CBI analogues of CC-1065 and the duocarmycins. J Org Chem 2001; 66:5163-73. [PMID: 11463270 DOI: 10.1021/jo010309g] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The synthesis and evaluation of a series of C3-substituted 1,2,9,9a-tetrahydrocyclopropa[c]benz[e]indol-4-one (CBI) analogues of the CC-1065 and duocarmycin alkylation subunits are detailed, including methyl and the full series of halogens. Introduction of the key substituent was accomplished through directed metalation of the seco-CBI core followed by reaction of the resultant aryllithium with an appropriate electrophile. C3-Bromo and iodo substituents were only effectively installed on the hindered aryllithium intermediate using a novel halogen source, 1-bromo- and 1-iodophenylacetylene, that should prove generally useful beyond the studies we describe. X-ray crystal structures of the series show substantial distortion in the vinylogous amide due to unfavorable steric interactions between the C3-substituent and the N(2)-carbamate. In the halogen series, the N2-C2a bond length and the torsional angle chi(1) smoothly increase with the increasing size of the C3 substituent indicative of decreasing vinylogous amide conjugation through the series (H > F > Cl > Br > I). Unlike N-Boc-CBI, this series of substituted CBI analogues proved remarkably reactive toward solvolysis even at pH 7, where the reaction is uncatalyzed and the reactivity order (I > Br > Cl > F > H) follows a trend consistent with the extent of vinylogous amide conjugation and stabilization. The implications of these observations on the source of catalysis for the DNA alkylation reaction of the natural products are discussed.
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Affiliation(s)
- D L Boger
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
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65
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Smith JA, Bifulco G, Case DA, Boger DL, Gomez-Paloma L, Chazin WJ. The structural basis for in situ activation of DNA alkylation by duocarmycin SA. J Mol Biol 2000; 300:1195-204. [PMID: 10903864 DOI: 10.1006/jmbi.2000.3887] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Duocarmycin SA is a member of a growing class of interesting lead compounds for chemotherapy, distinguished by the manner in which they bind to and react with DNA substrates. The first three-dimensional structure of a DNA adduct of an unnatural enantiomer from this family has been determined by (1)H NMR methods. Comparison to the previously determined structure of the natural enantiomer bound in the same DNA-binding site provides unique insights into the similarities and critical distinctions producing the respective alkylation products and site selectivities. The results also support the hypothesis that the duocarmycin SA alkylation reaction is catalyzed by the binding to DNA, and provide a deeper understanding of the structural basis for this unique mode of activation.
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Affiliation(s)
- J A Smith
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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66
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Boger DL, Wolkenberg SE, Boyce CW. A New Method of in Situ Activation for a Novel Class of DNA Alkylating Agents: Tunable Metal Cation Complexation and Activation. J Am Chem Soc 2000. [DOI: 10.1021/ja000653f] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dale L. Boger
- Department of Chemistry and Skaggs Institute for Chemical Biology The Scripps Research Institute, 10550 North Torrey Pines Road La Jolla, California 92037
| | - Scott E. Wolkenberg
- Department of Chemistry and Skaggs Institute for Chemical Biology The Scripps Research Institute, 10550 North Torrey Pines Road La Jolla, California 92037
| | - Christopher W. Boyce
- Department of Chemistry and Skaggs Institute for Chemical Biology The Scripps Research Institute, 10550 North Torrey Pines Road La Jolla, California 92037
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67
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Boger DL, Searcey M, Tse WC, Jin Q. Bifunctional alkylating agents derived from duocarmycin SA: potent antitumor activity with altered sequence selectivity. Bioorg Med Chem Lett 2000; 10:495-8. [PMID: 10743956 DOI: 10.1016/s0960-894x(00)00042-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The series of four dimers derived from head to tail coupling of the two enantiomers of the duocarmycin SA alkylation subunit are described.
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Affiliation(s)
- D L Boger
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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68
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Kirschner KN, Lee M, Stanley RC, Bowen JP. Density functional and Ab initio studies on N-acetylduocarmycin SA: insight into its DNA interaction properties. Bioorg Med Chem 2000; 8:329-35. [PMID: 10722155 DOI: 10.1016/s0968-0896(99)00278-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Density functional (DF) and Møller-Plesset second order perturbation (MP2) calculations were carried out on N-acetylduocarmycin SA (N-Ac-DSA), an analogue of a series of potent antitumor antibiotics that include the duocarmycins. These computational methods were used to investigate the degree of ground state destabilization of duocarmycins that would result upon binding to DNA. Ground state destabilization has been proposed as the origin of the ligand's enhanced rate of alkylation by more than a millionfold. The conformations of the 'Unbound' and 'DNA-Bound' N-Ac-DSA were generated using available geometric data for duocarmycin SA. Specifically, the dihedral angles chi1/chi2 were locked at 6.9 degrees/4.5 degrees for the Unbound and 22.0 degrees/11.0 degrees for the Bound form. The structures were optimized using DF theory, with subsequent MP2 calculations to improve the electronic energies. All of the calculations were performed on the unprotonated (1) as well as the C6-carbonyl protonated form (2). The results showed that the ground state destabilization energies of the Unbound and Bound forms, for the unprotonated and protonated series, were fairly small (< 0.8 kcal/mol). Similarly, the difference in the electronic nature of the Unbound and Bound forms, as indicated by changes in bond lengths and charge density, were also small. In summary, it appears that twisting of two key torsional angles, the concomitant ground state destabilization, and C6-carbonyl protonation may not fully account for the significant rate increase of adenine-N3 alkylation upon binding to DNA.
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Affiliation(s)
- K N Kirschner
- Computational Center for Molecular Structure and Design, Department of Chemistry, University of Georgia, Athens 30602-2556, USA
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69
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Boger DL, Garbaccio RM. Shape-Dependent Catalysis: Insights into the Source of Catalysis for the CC-1065 and Duocarmycin DNA Alkylation Reaction. Acc Chem Res 1999. [DOI: 10.1021/ar9800946] [Citation(s) in RCA: 126] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dale L. Boger
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Robert M. Garbaccio
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
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70
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Abstract
In this review, both cationic and neutral synthetic ligands that bind in the minor groove of DNA are discussed. Certain bis-distamycins and related lexitropsins show activities against human immunodeficiency virus (HIV)-1 and HIV-2 at low nanomolar concentrations. DAPI binds strongly to AT-containing polymers and is located in the minor groove of DNA. DAPI intercalates in DNA sequences that do not contain at least three consecutive AT bp. Berenil can also exhibit intercalative, as well as minor groove binding, properties depending on sequence. Furan-containing analogues of berenil play an important role in their activities against Pneumocystis carinii and Cryptosporidium parvuam infections in vivo. Pt(II)-berenil conjugates show a good activity profile against HL60 and U-937 human leukemic cells. Pt-pentamidine shows higher antiproliferative activity against small cell lung, non-small cell lung, and melanoma cancer cell lines compared with many other tumor cell lines. trans-Butenamidine shows good anti-P. carinii activity in rats. Pentamidine is used against P. carinii pneumonia in individuals infected with HIV who are at high risk from this infection. A comparison of the cytotoxic potencies of adozelesin, bizelesin, carzelesin, cisplatin, and doxorubicin indicates that adozelesin is a potent analog of CC-1065. Naturally occurring pyrrolo[2,1-c][l,4]benzodiazepines such as anthramycin have a 2- to 3-bp sequence specificity, but a synthetic PBD dimer spans 6 bp, actively recognizing a central 5'-GATC sequence. The crosslinking efficiency of PBD dimers is much greater than that of other major groove crosslinkers, such as cisplatin, melphalan, etc. Neothramycin is used clinically for the treatment of superficial carcinoma of the bladder.
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Affiliation(s)
- B S Reddy
- Department of Chemistry, University of Alberta, Edmonton, Canada
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71
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Boger DL, Garbaccio RM. Are the Duocarmycin and CC-1065 DNA Alkylation Reactions Acid-Catalyzed? Solvolysis pH-Rate Profiles Suggest They Are Not. J Org Chem 1999; 64:5666-5669. [PMID: 11674637 DOI: 10.1021/jo990762g] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A study of the solvolysis pH-rate profiles for two key reactive CC-1065/duocarmycin alkylation subunit analogues is detailed. Unlike the authentic alkylation subunits and N-BOC-CBI (4) which are too stable to establish complete solvolysis pH-rate profiles, the analogues N-BOC-CBQ (5) and N-BOC-CNA (6) are reactive throughout the pH range of 2-12. Moreover, they possess progressively diminished vinylogous amide conjugation resulting in a corresponding progressively increasing reactivity adopting and reflecting conformations analogous to that proposed for DNA-bound CC-1065. For both, the acid-catalyzed reaction was observed only at the lower pH of 2-5, and the uncatalyzed solvolysis reaction rate dominated at pH >/=6, indicating that the CC-1065 and duocarmycin DNA alkylation reaction observed at pH 7.4 need not be an acid-catalyzed reaction. The studies provide further strong evidence that catalysis for the DNA alkylation reaction (pH 7.4) is derived from a DNA binding-induced conformational change in the agents that disrupts the stabilizing alkylation subunit vinylogous amide conjugation activating the agents for nucleophilic attack independent of pH.
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Affiliation(s)
- Dale L. Boger
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
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Boger DL, Santillán A, Searcey M, Jin Q. Critical Role of the Linking Amide in CC-1065 and the Duocarmycins: Implications on the Source of DNA Alkylation Catalysis. J Am Chem Soc 1998. [DOI: 10.1021/ja9818093] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dale L. Boger
- Contribution from the Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Alejandro Santillán
- Contribution from the Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Mark Searcey
- Contribution from the Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Qing Jin
- Contribution from the Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
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Boger DL, Turnbull P. Synthesis and Evaluation of a Carbocyclic Analogue of the CC-1065 and Duocarmycin Alkylation Subunits: Role of the Vinylogous Amide and Implications on DNA Alkylation Catalysis. J Org Chem 1998. [DOI: 10.1021/jo981698q] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dale L. Boger
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Philip Turnbull
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
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Boger DL. Heterocyclic and acyclic azadiene diels-alder reactions: Total synthesis of nothapodytine B. J Heterocycl Chem 1998. [DOI: 10.1002/jhet.5570350502] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Synthesis of CC-1065 and duocarmycin analogs via intramolecular aryl radical cyclization of a tethered vinyl chloride. Tetrahedron Lett 1998. [DOI: 10.1016/s0040-4039(98)00232-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Boger DL, Garbaccio RM, Jin Q. Synthesis and Evaluation of CC-1065 and Duocarmycin Analogues Incorporating the Iso-CI and Iso-CBI Alkylation Subunits: Impact of Relocation of the C-4 Carbonyl. J Org Chem 1997. [DOI: 10.1021/jo971686p] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dale L. Boger
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Robert M. Garbaccio
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Qing Jin
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
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Eis PS, Smith JA, Rydzewski JM, Case DA, Boger DL, Chazin WJ. High resolution solution structure of a DNA duplex alkylated by the antitumor agent duocarmycin SA. J Mol Biol 1997; 272:237-52. [PMID: 9299351 DOI: 10.1006/jmbi.1997.1223] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The three-dimensional solution structure of duocarmycin SA in complex with d-(G1ACTAATTGAC11).d-(G12TCATTAGTC22) has been determined by restrained molecular dynamics and relaxation matrix calculations using experimental NOE distance and torsion angle constraints derived from 1H NMR spectroscopy. The final input data consisted of a total of 858 distance and 189 dihedral angle constraints, an average of 46 constraints per residue. In the ensemble of 20 final structures, there were no distance constraint violations >0.06 A or torsion angle violations >0.8 degrees. The average pairwise root mean square deviation (RMSD) over all 20 structures for the binding site region is 0.57 A (average RMSD from the mean: 0.39 A). Although the DNA is very B-like, the sugar-phosphate backbone torsion angles beta, epsilon, and zeta are distorted from standard values in the binding site region. The structure reveals site-specific bonding of duocarmycin SA at the N3 position of adenine 19 in the AT-rich minor groove of the duplex and binding stabilization via hydrophobic interactions. Comparisons have been made to the structure of a closely related complex of duocarmycin A bound to an AT-rich DNA duplex. These results provide insights into critical aspects of the alkylation site selectivity and source of catalysis of the DNA alkylating agents, and the unusual stability of the resulting adducts.
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Affiliation(s)
- P S Eis
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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Boger DL, Turnbull P. Synthesis and Evaluation of CC-1065 and Duocarmycin Analogs Incorporating the 1,2,3,4,11,11a-Hexahydrocyclopropa[c]naphtho[2,1-b]azepin-6-one (CNA) Alkylation Subunit: Structural Features that Govern Reactivity and Reaction Regioselectivity. J Org Chem 1997. [DOI: 10.1021/jo9707085] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dale L. Boger
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Philip Turnbull
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
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Boger DL, Hertzog DL, Bollinger B, Johnson DS, Cai H, Goldberg J, Turnbull P. Duocarmycin SA Shortened, Simplified, and Extended Agents: A Systematic Examination of the Role of the DNA Binding Subunit. J Am Chem Soc 1997. [DOI: 10.1021/ja9637208] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dale L. Boger
- Contribution from the Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Donald L. Hertzog
- Contribution from the Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Bernd Bollinger
- Contribution from the Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Douglas S. Johnson
- Contribution from the Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Hui Cai
- Contribution from the Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Joel Goldberg
- Contribution from the Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Philip Turnbull
- Contribution from the Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
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Boger DL, Bollinger B, Hertzog DL, Johnson DS, Cai H, Mésini P, Garbaccio RM, Jin Q, Kitos PA. Reversed and Sandwiched Analogs of Duocarmycin SA: Establishment of the Origin of the Sequence-Selective Alkylation of DNA and New Insights into the Source of Catalysis. J Am Chem Soc 1997. [DOI: 10.1021/ja9637210] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dale L. Boger
- Contribution from the Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Bernd Bollinger
- Contribution from the Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Donald L. Hertzog
- Contribution from the Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Douglas S. Johnson
- Contribution from the Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Hui Cai
- Contribution from the Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Philippe Mésini
- Contribution from the Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Robert M. Garbaccio
- Contribution from the Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Qing Jin
- Contribution from the Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Paul A. Kitos
- Contribution from the Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
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