1
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Ratnayake AS, Flanagan ME, Foley TL, Hultgren SL, Bellenger J, Montgomery JI, Lall MS, Liu B, Ryder T, Kölmel DK, Shavnya A, Feng X, Lefker B, Byrnes LJ, Sahasrabudhe PV, Farley KA, Chen S, Wan J. Toward the assembly and characterization of an encoded library hit confirmation platform: Bead-Assisted Ligand Isolation Mass Spectrometry (BALI-MS). Bioorg Med Chem 2021; 41:116205. [PMID: 34000509 DOI: 10.1016/j.bmc.2021.116205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 12/15/2022]
Abstract
The ability to predict chemical structure from DNA sequence has to date been a necessary cornerstone of DNA-encoded library technology. DNA-encoded libraries (DELs) are typically screened by immobilized affinity selection and enriched library members are identified by counting the number of times an individual compound's sequence is observed in the resultant dataset. Those with high signal reads (DEL hits) are subsequently followed up through off-DNA synthesis of the predicted small molecule structures. However, hits followed-up in this manner often fail to translate to confirmed ligands. To address this low conversion rate of DEL hits to off-DNA ligands, we have developed an approach that eliminates the reliance on chemical structure prediction from DNA sequence. Here we describe our method of combining non-combinatorial resynthesis on-DNA following library procedures as a rapid means to assess the probable molecules attached to the DNA barcode. Furthermore, we apply our Bead-Assisted Ligand Isolation Mass Spectrometry (BALI-MS) technique to identify the true binders found within the mixtures of on-DNA synthesis products. Finally, we describe a Normalized Enrichment (NE) metric that allows for the quantitative assessment of affinity selection in these studies. We exemplify how this combined approach enables the identification of putative hit matter against a clinically relevant therapeutic target bisphosphoglycerate mutase, BPGM.
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Affiliation(s)
- Anokha S Ratnayake
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Mark E Flanagan
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Timothy L Foley
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Scott L Hultgren
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Justin Bellenger
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Justin I Montgomery
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Manjinder S Lall
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Bo Liu
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Tim Ryder
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Dominik K Kölmel
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Andre Shavnya
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Xidong Feng
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Bruce Lefker
- Lefker Biopharma Consulting LLC, Arlington, MA 02474 United States.
| | - Laura J Byrnes
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Parag V Sahasrabudhe
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Kathleen A Farley
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Shi Chen
- HitGen Inc., Shuangliu District, Chengdu, China.
| | - Jinqiao Wan
- HitGen Inc., Shuangliu District, Chengdu, China.
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2
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Foley TL, Burchett W, Chen Q, Flanagan ME, Kapinos B, Li X, Montgomery JI, Ratnayake AS, Zhu H, Peakman MC. Selecting Approaches for Hit Identification and Increasing Options by Building the Efficient Discovery of Actionable Chemical Matter from DNA-Encoded Libraries. SLAS Discov 2021; 26:263-280. [PMID: 33412987 DOI: 10.1177/2472555220979589] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Over the past 20 years, the toolbox for discovering small-molecule therapeutic starting points has expanded considerably. Pharmaceutical researchers can now choose from technologies that, in addition to traditional high-throughput knowledge-based and diversity screening, now include the screening of fragment and fragment-like libraries, affinity selection mass spectrometry, and selection against DNA-encoded libraries (DELs). Each of these techniques has its own unique combination of advantages and limitations that makes them more, or less, suitable for different target classes or discovery objectives, such as desired mechanism of action. Layered on top of this are the constraints of the drug-hunters themselves, including budgets, timelines, and available platform capacity; each of these can play a part in dictating the hit identification strategy for a discovery program. In this article, we discuss some of the factors that we use to govern our building of a hit identification roadmap for a program and describe the increasing role that DELs are playing in our discovery strategy. Furthermore, we share our learning during our initial exploration of DEL and highlight the approaches we have evolved to maximize the value returned from DEL selections. Topics addressed include the optimization of library design and production, reagent validation, data analysis, and hit confirmation. We describe how our thinking in these areas has led us to build a DEL platform that has begun to deliver tractable matter to our global discovery portfolio.
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Affiliation(s)
| | | | - Qiuxia Chen
- Lead Generation Unit, HitGen Inc., Chengdu, Shuangliu District, China
| | | | | | - Xianyang Li
- Lead Generation Unit, HitGen Inc., Chengdu, Shuangliu District, China
| | | | | | - Hongyao Zhu
- Simulation and Modelling Sciences, Pfizer Inc., Groton, CT, USA
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3
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Kölmel DK, Ratnayake AS, Flanagan ME. Photoredox cross-electrophile coupling in DNA-encoded chemistry. Biochem Biophys Res Commun 2020; 533:201-208. [DOI: 10.1016/j.bbrc.2020.04.028] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 04/06/2020] [Indexed: 12/22/2022]
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4
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Fan Z, Zhao S, Liu T, Shen PX, Cui ZN, Zhuang Z, Shao Q, Chen JS, Ratnayake AS, Flanagan ME, Kölmel DK, Piotrowski DW, Richardson P, Yu JQ. Merging C(sp 3)-H activation with DNA-encoding. Chem Sci 2020; 11:12282-12288. [PMID: 34094436 PMCID: PMC8162953 DOI: 10.1039/d0sc03935g] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
DNA-encoded library (DEL) technology has the potential to dramatically expedite hit identification in drug discovery owing to its ability to perform protein affinity selection with millions or billions of molecules in a few experiments. To expand the molecular diversity of DEL, it is critical to develop different types of DNA-encoded transformations that produce billions of molecules with distinct molecular scaffolds. Sequential functionalization of multiple C–H bonds provides a unique avenue for creating diversity and complexity from simple starting materials. However, the use of water as solvent, the presence of DNA, and the extremely low concentration of DNA-encoded coupling partners (0.001 M) have hampered the development of DNA-encoded C(sp3)–H activation reactions. Herein, we report the realization of palladium-catalyzed C(sp3)–H arylation of aliphatic carboxylic acids, amides and ketones with DNA-encoded aryl iodides in water. Notably, the present method enables the use of alternative sets of monofunctional building blocks, providing a linchpin to facilitate further setup for DELs. Furthermore, the C–H arylation chemistry enabled the on-DNA synthesis of structurally-diverse scaffolds containing enriched C(sp3) character, chiral centers, cyclopropane, cyclobutane, and heterocycles. DNA-compatible C(sp3)–H activation reactions of aliphatic carboxylic acids, amides, and ketones were developed for efficient access to DEL synthesis.![]()
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Affiliation(s)
- Zhoulong Fan
- Department of Chemistry, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla CA 92037 USA
| | - Shuai Zhao
- Department of Chemistry, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla CA 92037 USA
| | - Tao Liu
- Department of Chemistry, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla CA 92037 USA
| | - Peng-Xiang Shen
- Department of Chemistry, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla CA 92037 USA
| | - Zi-Ning Cui
- Department of Chemistry, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla CA 92037 USA
| | - Zhe Zhuang
- Department of Chemistry, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla CA 92037 USA
| | - Qian Shao
- Department of Chemistry, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla CA 92037 USA
| | - Jason S Chen
- Automated Synthesis Facility, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla CA 92037 USA
| | - Anokha S Ratnayake
- Pfizer Medicinal Chemistry Eastern Point Road, Groton Connecticut 06340 USA
| | - Mark E Flanagan
- Pfizer Medicinal Chemistry Eastern Point Road, Groton Connecticut 06340 USA
| | - Dominik K Kölmel
- Pfizer Medicinal Chemistry Eastern Point Road, Groton Connecticut 06340 USA
| | - David W Piotrowski
- Pfizer Medicinal Chemistry Eastern Point Road, Groton Connecticut 06340 USA
| | - Paul Richardson
- Pfizer Medicinal Chemistry, 10578 Science Center Drive San Diego CA 09121 USA
| | - Jin-Quan Yu
- Department of Chemistry, The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla CA 92037 USA
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5
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DiRico K, Hua W, Liu C, Tucker JW, Ratnayake AS, Flanagan ME, Troutman MD, Noe MC, Zhang H. Ultra-High-Throughput Acoustic Droplet Ejection-Open Port Interface-Mass Spectrometry for Parallel Medicinal Chemistry. ACS Med Chem Lett 2020; 11:1101-1110. [PMID: 32550988 PMCID: PMC7294554 DOI: 10.1021/acsmedchemlett.0c00066] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/01/2020] [Indexed: 12/20/2022] Open
Abstract
High-throughput experimentation (HTE) has emerged as an important tool in drug discovery, providing a platform for preparing large compound libraries and enabling swift reaction screening over wide-ranging conditions. Recent advances in automated high-density, material-sparing HTE have necessitated the development of rapid analytics with sensitivity and resolution sufficient to identify products and/or assess reaction performance in a timely and data-rich manner. Combination of an ultrathroughput (UT) reader platform with Acoustic Droplet Ejection-Open Port Interface-Mass Spectrometry (ADE-OPI-MS) provides the requisite speed and sensitivity. Herein, we report the application of ADE-OPI-MS to HTE in the areas of parallel medicinal chemistry and reaction screening.
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Affiliation(s)
- Kenneth
J. DiRico
- Pfizer
Global Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Wenyi Hua
- Pfizer
Global Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Chang Liu
- SCIEX, 71 Four Valley Drive, Concord, Ontario L4K 4V8, Canada
| | - Joseph W. Tucker
- Pfizer
Global Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Anokha S. Ratnayake
- Pfizer
Global Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Mark E. Flanagan
- Pfizer
Global Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Matthew D. Troutman
- Pfizer
Global Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Mark C. Noe
- Pfizer
Global Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Hui Zhang
- Pfizer
Global Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
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6
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Abstract
The on-DNA synthesis of highly substituted cyclobutanes was achieved through a photocatalytic [2 + 2] cycloaddition reaction in aqueous solution. Readily available DNA-tagged styrene derivatives were reacted with structurally diverse cinnamates in the presence of an iridium-based photocatalyst, Ir(ppy)2(dtbbpy)PF6, to forge two new C(sp3)-C(sp3) bonds. This transformation was demonstrated to have excellent functional group tolerance and allowed for the facile installation of a variety of heteroaromatic substituents on a densely functionalized cyclobutane scaffold.
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Affiliation(s)
- Dominik K Kölmel
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Anokha S Ratnayake
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Mark E Flanagan
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Mei-Hsuan Tsai
- HitGen Inc, Building 6, No. 8, Huigu first East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu City, Sichuan Province P. R. China
| | - Cong Duan
- HitGen Inc, Building 6, No. 8, Huigu first East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu City, Sichuan Province P. R. China
| | - Chao Song
- HitGen Inc, Building 6, No. 8, Huigu first East Road, Tianfu International Bio-Town, Shuangliu District, Chengdu City, Sichuan Province P. R. China
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7
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Abstract
Incomplete removal of free (unconjugated) drug or drug-linker species used to prepare ADCs results in contaminated ADC samples which may pose a risk for toxicity. Due to the extreme potency of typical small molecule toxins employed in ADCs, even relatively low levels of free drug contaminants in ADC samples have been hypothesized to result in nonspecific (i.e., off-target) activity in biological systems. It is possible for trace levels of certain free drug species to persist in final ADC samples despite the inclusion of common purification steps during the preparation processes. Therefore, methods for the detection, quantification, and removal of residual free drug present in ADC samples are ultimately required for the preparation of safe and efficacious final ADC drug products. Herein we report general methods for the detection and removal of such contaminants.
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Affiliation(s)
| | | | - Sujiet Puthenveetil
- AbbVie Bioresearch Center, R&D, Worchester, MA, USA
- Pfizer, Inc., Groton, CT, USA
| | - L Nathan Tumey
- Department of Pharmacy and Pharmaceutical Sciences, Binghamton University, Binghamton, NY, USA
- Pfizer, Inc., Groton, CT, USA
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8
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Ratnayake AS, Flanagan ME, Foley TL, Smith JD, Johnson JG, Bellenger J, Montgomery JI, Paegel BM. A Solution Phase Platform to Characterize Chemical Reaction Compatibility with DNA-Encoded Chemical Library Synthesis. ACS Comb Sci 2019; 21:650-655. [PMID: 31425646 PMCID: PMC6938256 DOI: 10.1021/acscombsci.9b00113] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA-encoded chemical library (DECL) synthesis must occur in aqueous media under conditions that preserve the integrity of the DNA encoding tag. While the identification of "DNA-compatible" reaction conditions is critical for the development of DECL designs that explore previously inaccessible chemical space, reports measuring such compatibility have been largely restricted to methods that do not faithfully capture the impact of reaction conditions on DNA fidelity in solution phase. Here we report a comprehensive methodology that uses soluble DNA substrates that exactly recapitulate DNA's exposure to the chemically reactive species of DECL synthesis. This approach includes the assessment of chemical fidelity (reaction yield and purity), encoding fidelity (ligation efficiency), and readability (DNA compatibility), revealing the fate of the DNA tag during DECL chemistry from a single platform.
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Affiliation(s)
- Anokha S. Ratnayake
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Mark E. Flanagan
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Timothy L. Foley
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Justin D. Smith
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Jillian G. Johnson
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Justin Bellenger
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Justin I. Montgomery
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Brian M. Paegel
- Department of Chemistry, The Scripps Research Institute 130 Scripps Way Jupiter, Florida 33458, United States
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9
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Ratnayake AS, Chang LP, Tumey LN, Loganzo F, Chemler JA, Wagenaar M, Musto S, Li F, Janso JE, Ballard TE, Rago B, Steele GL, Ding W, Feng X, Hosselet C, Buklan V, Lucas J, Koehn FE, O'Donnell CJ, Graziani EI. Natural Product Bis-Intercalator Depsipeptides as a New Class of Payloads for Antibody-Drug Conjugates. Bioconjug Chem 2018; 30:200-209. [PMID: 30543418 DOI: 10.1021/acs.bioconjchem.8b00843] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A potent class of DNA-damaging agents, natural product bis-intercalator depsipeptides (NPBIDs), was evaluated as ultrapotent payloads for use in antibody-drug conjugates (ADCs). Detailed investigation of potency (both in cells and via biophysical characterization of DNA binding), chemical tractability, and in vitro and in vivo stability of the compounds in this class eliminated a number of potential candidates, greatly reducing the complexity and resources required for conjugate preparation and evaluation. This effort yielded a potent, stable, and efficacious ADC, PF-06888667, consisting of the bis-intercalator, SW-163D, conjugated via an N-acetyl-lysine-valine-citrulline- p-aminobenzyl alcohol- N, N-dimethylethylenediamine (AcLysValCit-PABC-DMAE) linker to an engineered variant of the anti-Her2 mAb, trastuzumab, catalyzed by transglutaminase.
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Affiliation(s)
- Anokha S Ratnayake
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Li-Ping Chang
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - L Nathan Tumey
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Frank Loganzo
- Oncology Research , Pfizer Worldwide Research and Development , 401 North Middletown Road , Pearl River , New York 10965 , United States
| | - Joseph A Chemler
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Melissa Wagenaar
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Sylvia Musto
- Oncology Research , Pfizer Worldwide Research and Development , 401 North Middletown Road , Pearl River , New York 10965 , United States
| | - Fengping Li
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Jeffrey E Janso
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - T Eric Ballard
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Brian Rago
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Greg L Steele
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - WeiDong Ding
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Xidong Feng
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Christine Hosselet
- Oncology Research , Pfizer Worldwide Research and Development , 401 North Middletown Road , Pearl River , New York 10965 , United States
| | - Vlad Buklan
- Oncology Research , Pfizer Worldwide Research and Development , 401 North Middletown Road , Pearl River , New York 10965 , United States
| | - Judy Lucas
- Oncology Research , Pfizer Worldwide Research and Development , 401 North Middletown Road , Pearl River , New York 10965 , United States
| | - Frank E Koehn
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Christopher J O'Donnell
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
| | - Edmund I Graziani
- Medicine Design , Pfizer Worldwide Research and Development , 445 Eastern Point Road , Groton , Connecticut 06340 , United States
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10
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He H, Ratnayake AS, Janso JE, He M, Yang HY, Loganzo F, Shor B, O'Donnell CJ, Koehn FE. Cytotoxic Spliceostatins from Burkholderia sp. and Their Semisynthetic Analogues. J Nat Prod 2014; 77:1864-1870. [PMID: 25098528 DOI: 10.1021/np500342m] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The spliceostatin class of natural products was reported to be potent cytotoxic agents via inhibition of the spliceosome, a key protein complex in the biosynthesis of mature mRNA. As part of an effort to discover novel leads for cancer chemotherapy, we re-examined this class of compounds from several angles, including fermentation of the producing strains, isolation and structure determination of new analogues, and semisynthetic modification. Accordingly, a group of spliceostatins were isolated from a culture broth of Burkholderia sp. FERM BP-3421, and their structures identified by analysis of spectroscopic data. Semisynthesis was performed on the major components 4 and 5 to generate ester and amide derivatives with improved in vitro potency. With their potent activity against tumor cells and unique mode of action, spliceostatins can be considered potential leads for development of cancer drugs.
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Affiliation(s)
- Haiyin He
- Natural Products Laboratory, Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development , 558 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Anokha S Ratnayake
- Natural Products Laboratory, Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development , 558 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Jeffrey E Janso
- Natural Products Laboratory, Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development , 558 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Min He
- Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health , 9609 Medical Center Drive, Bethesda, Maryland 20892, United States
| | - Hui Y Yang
- Novartis Institutes for BioMedical, Research, Inc. , 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Frank Loganzo
- Pfizer Oncology , 401 N. Middletown Road, Pearl River, New York 10965, United States
| | - Boris Shor
- Pfizer Oncology , 401 N. Middletown Road, Pearl River, New York 10965, United States
| | - Christopher J O'Donnell
- Natural Products Laboratory, Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development , 558 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Frank E Koehn
- Natural Products Laboratory, Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development , 558 Eastern Point Road, Groton, Connecticut 06340, United States
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11
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Ratnayake AS, Janso JE, Feng X, Schlingmann G, Goljer I, Carter GT. Evaluating indole-related derivatives as precursors in the directed biosynthesis of diazepinomicin analogues. J Nat Prod 2009; 72:496-499. [PMID: 19199816 DOI: 10.1021/np800664u] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The effectiveness of precursor-directed biosynthesis to generate diazepinomicin (1) analogues with varied ring-A substitutents was investigated by feeding commercially available, potential ring-A precursors such as fluorinated tryptophans, halogenated anthranilates, and various substituted indoles into growing actinomycete culture DPJ15 (genus Micromonospora). Two new monofluorinated diazepinomicin analogues (2 and 3) were identified and characterized by spectroscopic methods. Both derivatives showed modest antibacterial activity against the Gram-positive coccus Staphylococcus aureus with MIC values in the range 8-32 microg/mL.
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Affiliation(s)
- Anokha S Ratnayake
- Chemical and Screening Sciences, Wyeth Research, 401 North Middletown Road, Pearl River, New York 10965, USA.
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12
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Feng X, Ratnayake AS, Charan RD, Janso JE, Bernan VS, Schlingmann G, He H, Tischler M, Koehn FE, Carter GT. Probing natural product biosynthetic pathways using Fourier transform ion cyclotron resonance mass spectrometry. Bioorg Med Chem 2009; 17:2154-61. [DOI: 10.1016/j.bmc.2008.10.073] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Revised: 09/26/2008] [Accepted: 10/31/2008] [Indexed: 10/21/2022]
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13
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Whitson EL, Ratnayake AS, Bugni TS, Harper MK, Ireland CM. Isolation, structure elucidation, and synthesis of eudistomides A and B, lipopeptides from a Fijian ascidian Eudistoma sp. J Org Chem 2009; 74:1156-62. [PMID: 19053188 PMCID: PMC2670194 DOI: 10.1021/jo8022582] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Eudistomides A (1) and B (2), two new cyclic peptides, were isolated from a Fijian ascidian Eudistoma sp. These five-residue cystine-linked cyclic peptides are flanked by a C-terminal methyl ester and a 12-oxo- or 12-hydroxy-tetradecanoyl moiety. The complete structures of the eudistomides were determined using a combination of spectroscopic and chemical methods. Chiral HPLC analysis revealed that all five amino acid residues in 1 and 2 had the L-configuration. Total synthesis of eudistomides A (1) and B (2) confirmed the proposed structures. Enantioselective lipase-catalyzed hydrolysis of a mixture of C-35 acetoxy epimers indicated a 35R absolute configuration for 2.
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Affiliation(s)
- Emily L. Whitson
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112
| | - Anokha S. Ratnayake
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112
| | - Tim S. Bugni
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112
| | - Mary Kay Harper
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112
| | - Chris M. Ireland
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112
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Ratnayake AS, Haltli B, Feng X, Bernan VS, Singh MP, He H, Carter GT. Investigating the biosynthetic origin of the nitro group in pyrrolomycins. J Nat Prod 2008; 71:1923-1926. [PMID: 18986197 DOI: 10.1021/np800401h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Feasible modes of introducing the nitro group into pyrrolomycin antibiotics were investigated based on incorporation of (15)N-labeled arginine and proline into dioxapyrrolomycin, produced by the actinomycete culture LL-F42248. Biosynthesis of nitrated pyrrolomycins was unaffected by the presence of nitric oxide synthase (NOS) inhibitors. The culture was able to grow in nitrogen-free (minimal) media and produce nitrated secondary metabolites. These results indicate that LL-F42248 is capable of fixing nitrogen.
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Affiliation(s)
- Anokha S Ratnayake
- Chemical and Screening Sciences, Wyeth Research, 401 North Middletown Road, Pearl River, New York 10965, USA.
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15
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Ratnayake AS, Bugni TS, Veltri CA, Skalicky JJ, Ireland CM. Chemical transformation of prostaglandin-A2: a novel series of C-10 halogenated, C-12 hydroxylated prostaglandin-A2 analogues. Org Lett 2007; 8:2171-4. [PMID: 16671809 PMCID: PMC2533845 DOI: 10.1021/ol0606583] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[reaction: see text] Synthesis of a novel class of C-10 halogenated and C-12 oxygenated prostaglandin-A(2) derivatives (6a-6c) has been accomplished. (15S)-Prostaglandin-A(2) (1), from the gorgonian Plexaura homomalla, served as the starting material for the synthesis. The absolute configuration was determined using NMR.
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Ratnayake AS, Bugni TS, Feng X, Harper MK, Skalicky JJ, Mohammed KA, Andjelic CD, Barrows LR, Ireland CM. Theopapuamide, a cyclic depsipeptide from a Papua New Guinea lithistid sponge Theonella swinhoei. J Nat Prod 2006; 69:1582-6. [PMID: 17125225 PMCID: PMC2566935 DOI: 10.1021/np060229d] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Theopapuamide (1), a new cytotoxic peptide, has been isolated from the lithistid sponge Theonella swinhoei from Papua New Guinea. The structure was established by analysis of NMR, mass spectrometry, and chemical methods. The undecapeptide (1) contains several unusual amino acid residues, of which the occurrence of beta-methoxyasparagine and 4-amino-5-methyl-2,3,5-trihydroxyhexanoic acid (Amtha) is unprecedented in natural peptides. Compound 1 also contains an amide-linked fatty acid moiety, 3-hydroxy-2,4,6-trimethyloctanoic acid (Htoa). Theopapuamide (1) was cytotoxic against CEM-TART and HCT-116 cell lines, with EC50 values of 0.5 and 0.9 microM, respectively.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Chris M. Ireland
- To whom correspondence should be addressed. Tel: (801) 581-8305. Fax: (801) 585-6208. E-mail:
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Ratnayake AS, Davis RA, Harper MK, Veltri CA, Andjelic CD, Barrows LR, Ireland CM. Aurantosides G, H, and I: three new tetramic acid glycosides from a Papua New Guinea Theonella swinhoei. J Nat Prod 2005; 68:104-107. [PMID: 15679329 DOI: 10.1021/np049721s] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Aurantosides G-I (1-3) have been isolated from the lithistid sponge Theonella swinhoei from Papua New Guinea. Their structures were established by spectroscopic and chemical methods. Compounds 1-3 represent new monochloropentaenoyl tetramic acids with mono-, di-, and tri-N-saccharide substituents, respectively. Aurantosides G-I (1-3) failed to show any significant cytotoxicity against the human colon tumor cell line HCT-116.
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Affiliation(s)
- Anokha S Ratnayake
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
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Ratnayake AS, Hemscheidt T. Olefin Cross-Metathesis as a Tool in Natural Product Degradation. The Stereochemistry of (+)-Falcarindiol. Org Lett 2003. [DOI: 10.1021/ol034004v] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
[reaction: see text] There are conflicting reports in the literature concerning the absolute sterochemistry at C-3 of the common plant polyacetylene oxylipin (+)-falcarindiol. We have employed olefin cross-metathesis using Grubbs' second generation catalyst and ethylene gas to degrade falcarindiol to the symmetrical 1,9-decadiene-4,6-diyne-3,8-diol. The reaction is completely selective for net removal of the aliphatic side chain. Degradation of (+)-falcarindiol from Tetraplasandra hawaiiensis yields a meso product as shown by chiral HPLC. Hence, (+)-falcarindiol from this source has a (3R,8S)-configuration.
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Affiliation(s)
- Anokha S Ratnayake
- Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, Honolulu, Hawaii 96822, USA
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Abstract
A new alkaloid, nomofungin, has been isolated from the fermentation broth of an unidentified endophytic fungus obtained from the bark of Ficus microcarpa L. The structure of nomofungin was determined by application of spectroscopic methods. The absolute stereochemistry of nomofungin was assigned by using the exciton chirality method. Nomofungin disrupts microfilaments in cultured mammalian cells and is moderately cytotoxic with minimum inhibitory concentrations (MICs) of 2 and 4.5 microg/mL against LoVo and KB cells, respectively. The ring system of nomofungin is unprecedented.
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Affiliation(s)
- A S Ratnayake
- Department of Chemistry, University of Hawaii at Manoa, 2545 McCarthy Mall, Honolulu, HI 96822-2275, USA
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Ratnayake AS, Yoshida WY, Mooberry SL, Hemscheidt T. The structure of microcarpalide, a microfilament disrupting agent from an endophytic fungus. Org Lett 2001; 3:3479-81. [PMID: 11678687 DOI: 10.1021/ol016515s] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[structure: see text]. A new alkyl-substituted nonenolide, microcarpalide 1, has been isolated from fermentation broths of an unidentified endophytic fungus. Microcarpalide is weakly cytotoxic to mammalian cells and acts as a microfilament disrupting agent. The structure of 1 was elucidated by application of spectroscopic methods. The absolute configuration was determined by the exciton chirality method.
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Affiliation(s)
- A S Ratnayake
- Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, Honolulu, Hawaii 96822, USA
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