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Kannampuzha S, Murali R, Gopalakrishnan AV, Mukherjee AG, Wanjari UR, Namachivayam A, George A, Dey A, Vellingiri B. Novel biomolecules in targeted cancer therapy: a new approach towards precision medicine. Med Oncol 2023; 40:323. [PMID: 37804361 DOI: 10.1007/s12032-023-02168-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/18/2023] [Indexed: 10/09/2023]
Abstract
Cancer is a major threat to human life around the globe, and the discovery of novel biomolecules continue to be an urgent therapeutic need that is still unmet. Precision medicine relies on targeted therapeutic strategies. Researchers are better equipped to develop therapies that target proteins as they understand more about the genetic alterations and molecules that cause progression of cancer. There has been a recent diversification of the sorts of targets exploited in treatment. Therapeutic antibody and biotechnology advancements enabled curative treatments to reach previously inaccessible sites. New treatment strategies have been initiated for several undruggable targets. The application of tailored therapy has been proven to have efficient results in controlling cancer progression. Novel biomolecules like SMDCs, ADCs, mABs, and PROTACS has gained vast attention in the recent years. Several studies have shown that using these novel technology helps in reducing the drug dosage as well as to overcome drug resistance in different cancer types. Therefore, it is crucial to fully untangle the mechanism and collect evidence to understand the significance of these novel drug targets and strategies. This review article will be discussing the importance and role of these novel biomolecules in targeted cancer therapies.
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Affiliation(s)
- Sandra Kannampuzha
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - Reshma Murali
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - Abilash Valsala Gopalakrishnan
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India.
| | - Anirban Goutam Mukherjee
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - Uddesh Ramesh Wanjari
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - Arunraj Namachivayam
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - Alex George
- Jubilee Centre for Medical Research, Jubilee Mission Medical College and Research Institute, Thrissur, Kerala, India
| | - Abhijit Dey
- Department of Medical Services, MGM Cancer Institute, Chennai, Tamil Nadu, 600029, India
| | - Balachandar Vellingiri
- Human Molecular Cytogenetics and Stem Cell Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore, Tamil Nadu, 641046, India
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2
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Wang Z, Li H, Gou L, Li W, Wang Y. Antibody-drug conjugates: Recent advances in payloads. Acta Pharm Sin B 2023; 13:4025-4059. [PMID: 37799390 PMCID: PMC10547921 DOI: 10.1016/j.apsb.2023.06.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/30/2023] [Accepted: 06/23/2023] [Indexed: 10/05/2023] Open
Abstract
Antibody‒drug conjugates (ADCs), which combine the advantages of monoclonal antibodies with precise targeting and payloads with efficient killing, show great clinical therapeutic value. The ADCs' payloads play a key role in determining the efficacy of ADC drugs and thus have attracted great attention in the field. An ideal ADC payload should possess sufficient toxicity, low immunogenicity, high stability, and modifiable functional groups. Common ADC payloads include tubulin inhibitors and DNA damaging agents, with tubulin inhibitors accounting for more than half of the ADC drugs in clinical development. However, due to clinical limitations of traditional ADC payloads, such as inadequate efficacy and the development of acquired drug resistance, novel highly efficient payloads with diverse targets and reduced side effects are being developed. This perspective summarizes the recent research advances of traditional and novel ADC payloads with main focuses on the structure-activity relationship studies, co-crystal structures, and designing strategies, and further discusses the future research directions of ADC payloads. This review also aims to provide valuable references and future directions for the development of novel ADC payloads that will have high efficacy, low toxicity, adequate stability, and abilities to overcome drug resistance.
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Affiliation(s)
- Zhijia Wang
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu 610041, China
- Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu 610212, China
| | - Hanxuan Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Lantu Gou
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Wei Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Yuxi Wang
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy, Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu 610041, China
- Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu 610212, China
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3
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Is the AT-rich DNA of malaria parasites a drug target? Trends Pharmacol Sci 2022; 43:266-268. [DOI: 10.1016/j.tips.2022.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 11/20/2022]
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4
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Boot A, Ng AWT, Chong FT, Ho SC, Yu W, Tan DSW, Iyer NG, Rozen SG. Characterization of colibactin-associated mutational signature in an Asian oral squamous cell carcinoma and in other mucosal tumor types. Genome Res 2020; 30:803-813. [PMID: 32661091 PMCID: PMC7370881 DOI: 10.1101/gr.255620.119] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 06/04/2020] [Indexed: 12/24/2022]
Abstract
Mutational signatures can reveal the history of mutagenic processes that cells were exposed to before and during tumorigenesis. We expect that as-yet-undiscovered mutational processes will shed further light on mutagenesis leading to carcinogenesis. With this in mind, we analyzed the mutational spectra of 36 Asian oral squamous cell carcinomas. The mutational spectra of two samples from patients who presented with oral bacterial infections showed novel mutational signatures. One of these novel signatures, SBS_AnT, is characterized by a preponderance of thymine mutations, strong transcriptional strand bias, and enrichment for adenines in the 4 bp 5′ of mutation sites. The mutational signature described in this manuscript was shown to be caused by colibactin, a bacterial mutagen produced by E. coli carrying the pks-island. Examination of publicly available sequencing data revealed SBS_AnT in 25 tumors from several mucosal tissue types, expanding the list of tissues in which this mutational signature is observed.
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Affiliation(s)
- Arnoud Boot
- Cancer and Stem Cell Biology, Duke-NUS Medical School, 169857, Singapore.,Center for Computational Biology, Duke-NUS Medical School, 169857, Singapore
| | - Alvin W T Ng
- Center for Computational Biology, Duke-NUS Medical School, 169857, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, 117456, Singapore
| | - Fui Teen Chong
- Cancer Therapeutics Research Laboratory, Division of Medical Science, National Cancer Centre Singapore, 169610, Singapore
| | - Szu-Chi Ho
- Cancer and Stem Cell Biology, Duke-NUS Medical School, 169857, Singapore
| | - Willie Yu
- Cancer and Stem Cell Biology, Duke-NUS Medical School, 169857, Singapore.,Center for Computational Biology, Duke-NUS Medical School, 169857, Singapore
| | - Daniel S W Tan
- Cancer Therapeutics Research Laboratory, Division of Medical Science, National Cancer Centre Singapore, 169610, Singapore
| | - N Gopalakrishna Iyer
- Cancer and Stem Cell Biology, Duke-NUS Medical School, 169857, Singapore.,Cancer Therapeutics Research Laboratory, Division of Medical Science, National Cancer Centre Singapore, 169610, Singapore
| | - Steven G Rozen
- Cancer and Stem Cell Biology, Duke-NUS Medical School, 169857, Singapore.,Center for Computational Biology, Duke-NUS Medical School, 169857, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, 117456, Singapore
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Zhang J, Shukla V, Boger DL. Inverse Electron Demand Diels-Alder Reactions of Heterocyclic Azadienes, 1-Aza-1,3-Butadienes, Cyclopropenone Ketals, and Related Systems. A Retrospective. J Org Chem 2019; 84:9397-9445. [PMID: 31062977 DOI: 10.1021/acs.joc.9b00834] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A summary of the investigation and applications of the inverse electron demand Diels-Alder reaction is provided that have been conducted in our laboratory over a period that now spans more than 35 years. The work, which continues to provide solutions to complex synthetic challenges, is presented in the context of more than 70 natural product total syntheses in which the reactions served as a key strategic step in the approach. The studies include the development and use of the cycloaddition reactions of heterocyclic azadienes (1,2,4,5-tetrazines; 1,2,4-, 1,3,5-, and 1,2,3-triazines; 1,2-diazines; and 1,3,4-oxadiazoles), 1-aza-1,3-butadienes, α-pyrones, and cyclopropenone ketals. Their applications illustrate the power of the methodology, often provided concise and nonobvious total syntheses of the targeted natural products, typically were extended to the synthesis of analogues that contain deep-seated structural changes in more comprehensive studies to explore or optimize their biological properties, and highlight a wealth of opportunities not yet tapped.
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Affiliation(s)
- Jiajun Zhang
- Department of Chemistry and The Skaggs Institute for Chemical Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Vyom Shukla
- Department of Chemistry and The Skaggs Institute for Chemical Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - 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 , United States
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6
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Boger DL. The Difference a Single Atom Can Make: Synthesis and Design at the Chemistry-Biology Interface. J Org Chem 2017; 82:11961-11980. [PMID: 28945374 PMCID: PMC5712263 DOI: 10.1021/acs.joc.7b02088] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Indexed: 01/24/2023]
Abstract
A Perspective of work in our laboratory on the examination of biologically active compounds, especially natural products, is presented. In the context of individual programs and along with a summary of our work, selected cases are presented that illustrate the impact single atom changes can have on the biological properties of the compounds. The examples were chosen to highlight single heavy atom changes that improve activity, rather than those that involve informative alterations that reduce or abolish activity. The examples were also chosen to illustrate that the impact of such single-atom changes can originate from steric, electronic, conformational, or H-bonding effects, from changes in functional reactivity, from fundamental intermolecular interactions with a biological target, from introduction of a new or altered functionalization site, or from features as simple as improvements in stability or physical properties. Nearly all the examples highlighted represent not only unusual instances of productive deep-seated natural product modifications and were introduced through total synthesis but are also remarkable in that they are derived from only a single heavy atom change in the structure.
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Affiliation(s)
- Dale L. Boger
- Department of Chemistry and
The Skaggs Research Institute, The Scripps
Research Institute, 10550
North Torrey Pines Road, La Jolla, California 92037, United States
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7
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Wolfe AL, Duncan KK, Lajiness JP, Zhu K, Duerfeldt AS, Boger DL. A fundamental relationship between hydrophobic properties and biological activity for the duocarmycin class of DNA-alkylating antitumor drugs: hydrophobic-binding-driven bonding. J Med Chem 2013; 56:6845-57. [PMID: 23944748 DOI: 10.1021/jm400665c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Two systematic series of increasingly hydrophilic derivatives of duocarmycin SA that feature the incorporation of ethylene glycol units (n = 1-5) into the methoxy substituents of the trimethoxyindole subunit are described. These derivatives exhibit progressively increasing water solubility along with progressive decreases in cell growth inhibitory activity and DNA alkylation efficiency with the incremental ethylene glycol unit incorporations. Linear relationships of cLogP with -log IC50 for cell growth inhibition and -log AE (AE = cell-free DNA alkylation efficiency) were observed, with the cLogP values spanning the productive range of 2.5-0.49 and the -log IC50 values spanning the range of 11.2-6.4, representing IC50 values that vary by a factor of 10(5) (0.008 to 370 nM). The results quantify the fundamental role played by the hydrophobic character of the compound in the expression of the biological activity of members in this class (driving the intrinsically reversible DNA alkylation reaction) and define the stunning magnitude of its effect.
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Affiliation(s)
- Amanda L Wolfe
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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WU WENJUAN, CHEN JINCAN, QIAN LI, ZHENG KANGCHENG. QSAR AND MOLECULAR DESIGN OF BENZO[B]ACRONYCINE DERIVATIVES AS ANTITUMOR AGENTS. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633607003039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Quantitative structure-activity relationship (QSAR) studies of a series of benzo[b]acronycine derivatives as a novel class of antitumor agents have been carried out using the density functional theory (DFT), molecular mechanics (MM+) and statistical methods. Some calculated parameters of geometric structures, electronic structures and molecular properties of the compounds were adopted as generalized descriptors (variables). Via a stepwise regression analysis, some main independent factors affecting the activities of the compounds were selected out, and then the quantitative structure-activity relationship (QSAR) equation was established. The results suggest that the energy difference (Δ εL-H) between the lowest unoccupied molecular orbital and the highest occupied molecular orbital, the net charges of the nitrogen atom N 11 and the first atom of the substituent R2, and the hydrophobic parameter (log P1) of the substituent R1 are the main independent factors contributing to the antitumor activities of the compounds. The fitting correlation coefficient (r2) and the cross-validation coefficient (q2) for the model established by this study are 0.865 and 0.721, respectively, showing this model with a good predictability. The QSAR equation can be used to estimate unknown antitumor activity of this kind of compound, and thus design new compounds with high antitumor activities. Here, based on this QASR study, 4 new compounds with predicted high antitumor activities have been theoretically designed and they are expecting experimental verification.
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Affiliation(s)
- WEN JUAN WU
- Department of Physical Chemistry, Guangdong Pharmaceutical University, Guangzhou, 510006, P. R. China
| | - JIN CAN CHEN
- School of Chemistry and Chemical Engineering, Zhongshan (Sun Yat-Sen) University, Guangzhou, 510275, P. R. China
| | - LI QIAN
- School of Chemistry and Chemical Engineering, Zhongshan (Sun Yat-Sen) University, Guangzhou, 510275, P. R. China
| | - KANG CHENG ZHENG
- School of Chemistry and Chemical Engineering, Zhongshan (Sun Yat-Sen) University, Guangzhou, 510275, P. R. China
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Robertson WM, Kastrinsky DB, Hwang I, Boger DL. Synthesis and evaluation of a series of C5'-substituted duocarmycin SA analogs. Bioorg Med Chem Lett 2010; 20:2722-5. [PMID: 20381346 PMCID: PMC2867475 DOI: 10.1016/j.bmcl.2010.03.078] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2010] [Revised: 03/17/2010] [Accepted: 03/19/2010] [Indexed: 10/19/2022]
Abstract
The synthesis and evaluation of a key series of analogs of duocarmycin SA, bearing a single substituent at the C5' position of the DNA binding subunit, are described.
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Affiliation(s)
- William M. Robertson
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - David B. Kastrinsky
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Inkyu Hwang
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - 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, USA
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Tietze LF, Krewer B, Frauendorf H. Investigation of the transformations of a novel anti-cancer agent combining HPLC, HPLC-MS and direct ESI-HRMS analyses. Anal Bioanal Chem 2009; 395:437-48. [PMID: 19641906 PMCID: PMC2727581 DOI: 10.1007/s00216-009-2963-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2009] [Revised: 07/07/2009] [Accepted: 07/08/2009] [Indexed: 11/26/2022]
Abstract
One of the main problems of anti-cancer therapy is an insufficient differentiation between normal and malignant cells by the known anti-proliferant agents. The antibody-directed enzyme prodrug therapy is a promising approach for a selective treatment of cancer, in which a non-toxic prodrug is enzymatically converted into a highly cytotoxic drug at the surface of malignant cells by a targeted antibody-enzyme conjugate. The transformations and the stability of a very promising novel prodrug and its corresponding cytotoxic derivative were now investigated in detail by high-performance liquid chromatography (HPLC)-mass spectrometry (MS). In order to determine the time-dependent DNA alkylation efficiency and the sequence selectivity of the novel compounds, DNA binding studies using direct electrospray-Fourier transform ion cyclotron resonance-MS (ESI-FTICR-MS) have been performed. These measurements were accompanied by HPLC analyses followed by MS of the separated species to confirm the results of the direct ESI-FTICR-MS measurements. The sites of DNA alkylation could be identified unambiguously by the mass spectrometric fragmentation pattern of the alkylated oligodeoxynucleotides as well as by the results of HPLC followed by MS. A combination of all techniques applied led to a better understanding of the mode of action of the new therapeutics and might be used for an estimation of the cytotoxicity of different prodrugs and drugs since the alkylation efficiency correlates with the bioactivity of the compounds in cell culture investigations.
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Affiliation(s)
- Lutz F Tietze
- Department of Organic and Biomolecular Chemistry, Georg-August-University Göttingen, Tammannstrasse 2, 37077, Göttingen, Germany.
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11
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Di Micco S, Boger DL, Riccio R, Bifulco G. Structural Features of the (+)-Yatakemycin/d(GACTAATTGAC)-(GTCAATTAGTC) Complex – Quantum Mechanical Calculation of NMR Parameters as a Tool for the Characterization of Ligand/DNA Interactions. European J Org Chem 2008. [DOI: 10.1002/ejoc.200701212] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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12
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Tietze LF, Krewer B, Frauendorf H, Major F, Schuberth I. Investigation of reactivity and selectivity of DNA-alkylating duocarmycin analogues by high-resolution mass spectrometry. Angew Chem Int Ed Engl 2007; 45:6570-4. [PMID: 16960904 DOI: 10.1002/anie.200600935] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Lutz F Tietze
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstrasse 2, 37077 Göttingen, Germany.
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Tietze LF, Krewer B, Frauendorf H, Major F, Schuberth I. Untersuchung der Reaktivität und Selektivität DNA-alkylierender Duocarmycin-Analoga mittels hochauflösender Massenspektrometrie. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200600935] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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14
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Cimino P, Bifulco G, Riccio R, Gomez-Paloma L, Barone V. On the role of stereo-electronic effects in tuning the selectivity and rate of DNA alkylation by duocarmycins. Org Biomol Chem 2006; 4:1242-51. [PMID: 16557312 DOI: 10.1039/b514890a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The role of local geometric and stereo-electronic effects in tuning the alkylation of DNA by duocarmycins has been analyzed by an integrated computational tool rooted in the density functional theory and the polarizable continuum model. Our study points out that together with steric accessibility, different electronic delocalisations also contribute to determine the higher reactivity of adenine with respect to guanine. Also the effect of the methyl ester group on the alkylating agent has an electronic origin. Furthermore, deviations from the planarity in the drug structure (conformational catalysis) could be less important than currently accepted since, according to our computations, compounds with strongly different reactivity have nearly constant and very similar out of plane distortions before and after the reaction. Model computations suggest, instead, that specific non covalent interactions could discriminate between different drugs selectively reducing some activation energies with respect to the corresponding processes in solution.
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Affiliation(s)
- Paola Cimino
- Dipartimento di Chimica, Università Federico II, Complesso Universitario Monte S. Angelo, via Cintia, I-80126, Napoli, Italy
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15
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Freccero M, Gandolfi R. Modeling Acid and Cationic Catalysis on the Reactivity of Duocarmycins. J Org Chem 2005; 70:7098-106. [PMID: 16122228 DOI: 10.1021/jo050751p] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Several catalyzed alkylation reactions of 9-methyladenine by a model [CPI, cyclopropa[c]pyrrolo[3,2-e]indol-4(5H)-one (1)] of duocarmycin anticancer drugs have been compared to the uncatalyzed reaction in gas phase and in water solvent bulk, using density functional theory at the B3LYP level with the 6-31+G(d,p) basis set and C-PCM solvation model. The effect on the CPI reactivity induced by water, formic and phosphoric acids (general acid catalysis), H3O+ (specific acid catalysis), sodium, and ammonium cation complexation (cationic catalysis) has been investigated. The calculations indicate that the specific acid catalysis and the catalysis induced by sodium cation complexation are strong in the gas phase, but solvation reduces them dramatically by electrostatic effects. The specific acid catalysis is still operative, but strongly reduced in water solution, where the reaction barrier is reduced by 8.6 kcal mol(-1) in comparison to the uncatalyzed reaction. The general acid catalysis induced by phosphoric acid (-7.3 kcal mol(-1)) and the catalysis induced by Na+ and NH4+ complexation become competitive, with a catalytic effect of -3.6 and -4.1 kcal mol(-1) in water, respectively. With the specific acid catalysis, the high acidity (low pK(a) value) of the conjugated acid of CPI (CPIH+), computed in water solution using both C-PCM (pK(a) = +2.6) and PCM-B3LYP/6-31+G(d,p) (pK(a) = +2.4) solvation models, suggests that the catalytic effects induced by NH4+ complexation could become more important than the specific acid catalysis and the general catalysis by H3PO4 under physiological conditions, due to concentration effects of the catalysts.
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Affiliation(s)
- Mauro Freccero
- Dipartimento di Chimica Organica, Università di Pavia, V.le Taramelli 10, 27100 Pavia Italy.
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Freccero M, Gandolfi R. Modeling Substituent and Conformational Effects on the Reactivity of Antitumor Agents Containing a Cyclopropylcyclohexadienone Subunit. J Org Chem 2004; 69:6202-13. [PMID: 15357577 DOI: 10.1021/jo049193p] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The uncatalyzed alkylation reactions of ammonia by the parent spirocyclopropylcyclohexadienone (6), its 3-amino analogue (7), the cyclic derivative (8), its N-formyl derivative (9), and a closer model (10) of the CPI (1-4) drugs have been investigated in gas phase and in water solvent bulk, using density functional theory at the B3LYP level with several basis sets and the C-PCM solvation model. The effect of several structural key features such as the vinylogous amide conjugation, the acylation of the 2-amino substituent, the ring constraint of the heterocyclic nitrogen atom at C(2) carbon in a ring, and the presence of a condensed pyrrole ring on the reaction activation energy have been investigated. Substrate 7, which is a flexible conformational model of the cyclopropylpyrroloindole moiety (CPI) contained in the duocarmycins, has been used to model the shape-dependent reactivity of these drugs, in gas phase and water solutions. The calculations indicate that shape dependence of reactivity is strongly operative both in gas phase and in polar solvents, since conformational effects are capable of reducing the reaction activation energy by -8.4 and -4.3 kcal mol(-1) in gas phase and in water solution, respectively, that is required to promote "conformational catalysis".
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Affiliation(s)
- Mauro Freccero
- Dipartimento di Chimica Organica, Università di Pavia, V.le Taramelli 10, 27100 Pavia, Italy.
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17
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David-Cordonnier MH, Laine W, Kouach M, Briand G, Vezin H, Gaslonde T, Michel S, Doan Thi Mai H, Tillequin F, Koch M, Léonce S, Pierré A, Bailly C. A transesterification reaction is implicated in the covalent binding of benzo[b]acronycine anticancer agents with DNA and glutathion. Bioorg Med Chem 2004; 12:23-9. [PMID: 14697766 DOI: 10.1016/j.bmc.2003.10.056] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The benzo[b]acronycine derivative S23906-1 has been recently identified as a promising antitumor agent, showing remarkable in vivo activities against a panel of solid tumors. The anticancer activity is attributed to the capacity of the drug to alkylate DNA, selectively at the exocyclic 2-amino group of guanine residues. Hydrolysis of the C-1 and C-2 acetate groups of S23906-1 provides the diol compound S28907-1 which is inactive whereas the intermediate C-2 monoacetate derivative S28687-1 is both highly reactive toward DNA and cytotoxic. The reactivity of this later compound S28687-1 toward two bionucleophiles, DNA and the tripeptide glutathion, has been investigated by mass spectrometry to identify the nature of the (type II) covalent adducts characterized by the loss of the acetate group at position 2. On the basis of NMR and molecular modeling analyses, the reaction mechanism is explained by a transesterification process where the acetate leaving group is transferred from position C-2 to C-1. Altogether, the study validates the reaction scheme of benzo[b]acronycine derivative with its target.
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18
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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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19
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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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20
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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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21
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Honda T, Favaloro FG, Janosik T, Honda Y, Suh N, Sporn MB, Gribble GW. Efficient synthesis of (−)- and (+)-tricyclic compounds with enone functionalities in rings A and C. A novel class of orally active anti-inflammatory and cancer chemopreventive agents. Org Biomol Chem 2003; 1:4384-91. [PMID: 14685310 DOI: 10.1039/b307491a] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Novel tricyclic compounds with enone functionalities in rings A and C [tricyclic-bis-enone (TBE) compounds] were designed on the basis of the structure of a synthetic triterpenoid, 2-cyano-3,12-dioxooleana-1,9(11)-dien-28-oic acid (CDDO)(1), which is a promising drug candidate for prevention and/or treatment of cancer and inflammatory diseases whose pathogenesis may involve excessive production of nitric oxide (NO) and/or prostaglandins. A series of TBE compounds in racemic form shows high inhibitory activity against production of NO induced by interferon-[gamma](IFN-[gamma]) in mouse macrophages. One of these compounds, (+/-)-(4a[small beta],8a[small beta],10a[small alpha])-1,2,4a,6,8a,9,10,10a-octahydro-1,1,4a,8a-tetramethyl-2,6-dioxophenanthrene-3,7-dicarbonitrile ((+/-)-3), is orally active at 15 mg kg(-1)(single administration) in a preliminary study using mouse peritoneal inflammation induced by thioglycollate and IFN-[gamma]. Therefore, we desired to synthesize optically active TBE compounds for a comparison of the biological potency of both enantiomers. We now describe the synthesis of both enantiomers of (4a[small beta],8a[small beta],10a[small alpha])-1,2,4a,6,8a,9,10,10a-octahydro-1,1,4a,8a-tetramethyl-2,6-dioxophenanthrene-3-carbonitrile (2) and 3 from commercially available simple compounds. Interestingly, (+)-3 having the same configuration as the CDDO antipode shows about 10 times higher inhibitory activity than (-)-3 on NO production in mouse macrophages. In contrast, (-)-3 inhibits proliferation of MCF-7 breast cancer cells, whereas (+)-3 does not.
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Affiliation(s)
- Tadashi Honda
- Department of Chemistry, Dartmouth College, 6128 Burke Laboratory, Hanover, New Hampshire 03755, USA.
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22
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Favaloro FG, Honda T, Honda Y, Gribble GW, Suh N, Risingsong R, Sporn MB. Design and synthesis of tricyclic compounds with enone functionalities in rings A and C: a novel class of highly active inhibitors of nitric oxide production in mouse macrophages. J Med Chem 2002; 45:4801-5. [PMID: 12383005 DOI: 10.1021/jm025565f] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Novel tricyclic compounds with enone functionalities in rings A and C, which were designed on the basis of the structure of a synthetic triterpenoid, 2-cyano-3,12-dioxooleana-1,9(11)-dien-28-oic acid, have been synthesized. Among them, 10 shows high inhibitory activity (IC(50) = 1 nM level) against production of nitric oxide induced by interferon-gamma in mouse macrophages and is orally active at 15 mg/kg (once) in a preliminary in vivo study using mouse peritoneal inflammation induced by thioglycollate and interferon-gamma.
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Affiliation(s)
- Frank G Favaloro
- Department of Chemistry, 6128 Burke Laboratory, Dartmouth College, Hanover, New Hampshire 03755, USA
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23
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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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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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25
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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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26
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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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