1
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Bradley EK, Hoots BE, Bradley ES, Roehler DR. Unintentional ingestion of putative delta-8 tetrahydrocannabinol by two youth requiring critical care: a case report. J Cannabis Res 2023; 5:9. [PMID: 36941718 PMCID: PMC10029299 DOI: 10.1186/s42238-023-00176-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 02/13/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Delta-8 tetrahydrocannabinol (THC) is a psychoactive cannabinoid from the cannabis plant that can be synthetically converted from cannabidiol (CBD). Most states permit the full or restricted sale of hemp and hemp-derived CBD products, and therefore, delta-8 THC products are on the rise. Delta-8 THC consumption can cause intoxication. Products are often sold in edible form and occasionally in packaging that appears similar to candy. Clinical presentations for delta-8 THC ingestions are understudied and may differ from those described for delta-9 THC ingestions. CASE PRESENTATION This case report describes unintentional ingestions of putative delta-8 THC by two pediatric patients that results in admission to the pediatric intensive care unit. The ingestions were of putative delta-8 THC infused product that resembled popular candies. Both patients developed periods of bradypnea with continued intermittent periods of agitation. Medical intervention included observation, noninvasive positive pressure ventilation via high flow nasal cannula, and intubation-but was not needed for both patients. Although family noted ongoing irritability for the patients, both were discharged approximately 45 h after ingestion. Delta-8 THC ingestion is reliant on self-report. CONCLUSIONS As the availability of delta-8 THC increases, along with associated pediatric exposures, it is imperative for health care providers to quickly recognize and provide adequate treatment. While there is no specific antidote for THC intoxication beyond supportive care, providers can play an important role in prevention by educating parents and guardians on safe cannabis storage and by documenting cases for adverse event monitoring.
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Affiliation(s)
- Erin K Bradley
- Department of Pediatric Critical Care Medicine, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Brooke E Hoots
- Cannabis Strategy Unit, Division of Overdose Prevention, National Center for Injury Prevention and Control, Centers for Disease Control and Prevention, 4770 Buford Hwy, NE, Atlanta, GA, 30341, USA
| | - Evan S Bradley
- Department of Emergency Medicine, Division of Medical Toxicology, UMass Memorial Medical Center, University of Massachusetts Medical School, Worcester, MA, USA
| | - Douglas R Roehler
- Cannabis Strategy Unit, Division of Overdose Prevention, National Center for Injury Prevention and Control, Centers for Disease Control and Prevention, 4770 Buford Hwy, NE, Atlanta, GA, 30341, USA.
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2
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Johnson HWB, Anderl JL, Bradley EK, Bui J, Jones J, Arastu-Kapur S, Kelly LM, Lowe E, Moebius DC, Muchamuel T, Kirk C, Wang Z, McMinn D. Discovery of Highly Selective Inhibitors of the Immunoproteasome Low Molecular Mass Polypeptide 2 (LMP2) Subunit. ACS Med Chem Lett 2017; 8:413-417. [PMID: 28435528 DOI: 10.1021/acsmedchemlett.6b00496] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [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: 12/08/2016] [Accepted: 03/09/2017] [Indexed: 11/29/2022] Open
Abstract
Building upon the success of bortezomib (VELCADE) and carfilzomib (KYPROLIS), the design of a next generation of inhibitors targeting specific subunits within the immunoproteasome is of interest for the treatment of autoimmune disease. There are three catalytic subunits within the immunoproteasome (low molecular mass polypeptide-7, -2, and multicatalytic endopeptidase complex subunit-1; LMP7, LMP2, and MECL-1), and a campaign was undertaken to design a potent and selective LMP2 inhibitor with sufficient properties to allow for sustained inhibition in vivo. Screening a focused library of epoxyketones revealed a series of potent dipeptides that were optimized to provide the highly selective inhibitor KZR-504 (12).
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Affiliation(s)
- Henry W. B. Johnson
- Kezar Life Sciences, 300 Utah
Avenue, Suite 105, South San Francisco, California 94080, United States
| | - Janet L. Anderl
- Kezar Life Sciences, 300 Utah
Avenue, Suite 105, South San Francisco, California 94080, United States
| | - Erin K. Bradley
- Onyx Pharmaceuticals, An Amgen Subsidiary, 249 East Grand Avenue, South
San Francisco, California 94080, United States
| | - John Bui
- Onyx Pharmaceuticals, An Amgen Subsidiary, 249 East Grand Avenue, South
San Francisco, California 94080, United States
| | - Jeffrey Jones
- Onyx Pharmaceuticals, An Amgen Subsidiary, 249 East Grand Avenue, South
San Francisco, California 94080, United States
| | - Shirin Arastu-Kapur
- Onyx Pharmaceuticals, An Amgen Subsidiary, 249 East Grand Avenue, South
San Francisco, California 94080, United States
| | - Lisa M. Kelly
- Onyx Pharmaceuticals, An Amgen Subsidiary, 249 East Grand Avenue, South
San Francisco, California 94080, United States
| | - Eric Lowe
- Kezar Life Sciences, 300 Utah
Avenue, Suite 105, South San Francisco, California 94080, United States
| | - David C. Moebius
- Onyx Pharmaceuticals, An Amgen Subsidiary, 249 East Grand Avenue, South
San Francisco, California 94080, United States
| | - Tony Muchamuel
- Kezar Life Sciences, 300 Utah
Avenue, Suite 105, South San Francisco, California 94080, United States
| | - Christopher Kirk
- Kezar Life Sciences, 300 Utah
Avenue, Suite 105, South San Francisco, California 94080, United States
| | - Zhengping Wang
- Onyx Pharmaceuticals, An Amgen Subsidiary, 249 East Grand Avenue, South
San Francisco, California 94080, United States
| | - Dustin McMinn
- Kezar Life Sciences, 300 Utah
Avenue, Suite 105, South San Francisco, California 94080, United States
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3
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Ekins S, Godbole AA, Kéri G, Orfi L, Pato J, Bhat RS, Verma R, Bradley EK, Nagaraja V. Machine learning and docking models for Mycobacterium tuberculosis topoisomerase I. Tuberculosis (Edinb) 2017; 103:52-60. [PMID: 28237034 DOI: 10.1016/j.tube.2017.01.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [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: 06/29/2016] [Revised: 01/14/2017] [Accepted: 01/18/2017] [Indexed: 11/30/2022]
Abstract
There is a shortage of compounds that are directed towards new targets apart from those targeted by the FDA approved drugs used against Mycobacterium tuberculosis. Topoisomerase I (Mttopo I) is an essential mycobacterial enzyme and a promising target in this regard. However, it suffers from a shortage of known inhibitors. We have previously used computational approaches such as homology modeling and docking to propose 38 FDA approved drugs for testing and identified several active molecules. To follow on from this, we now describe the in vitro testing of a library of 639 compounds. These data were used to create machine learning models for Mttopo I which were further validated. The combined Mttopo I Bayesian model had a 5 fold cross validation receiver operator characteristic of 0.74 and sensitivity, specificity and concordance values above 0.76 and was used to select commercially available compounds for testing in vitro. The recently described crystal structure of Mttopo I was also compared with the previously described homology model and then used to dock the Mttopo I actives norclomipramine and imipramine. In summary, we describe our efforts to identify small molecule inhibitors of Mttopo I using a combination of machine learning modeling and docking studies in conjunction with screening of the selected molecules for enzyme inhibition. We demonstrate the experimental inhibition of Mttopo I by small molecule inhibitors and show that the enzyme can be readily targeted for lead molecule development.
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Affiliation(s)
- Sean Ekins
- Collaborative Drug Discovery, 1633 Bayshore Highway, Suite 342, Burlingame, CA 94403, USA; Collaborations in Chemistry, 5616 Hilltop Needmore Road, Fuquay-Varina, NC 27526, USA.
| | - Adwait Anand Godbole
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - György Kéri
- Vichem Chemie Research Ltd., Herman Ottó u. 15, H-1022, Budapest, Hungary; Semmelweis Univ, Dept Med Chem, MTA SE Pathobiochem Res Grp, H-1092, Budapest, Hungary
| | - Lászlo Orfi
- Vichem Chemie Research Ltd., Herman Ottó u. 15, H-1022, Budapest, Hungary; Semmelweis Univ, Dept Med Chem, MTA SE Pathobiochem Res Grp, H-1092, Budapest, Hungary
| | - János Pato
- Vichem Chemie Research Ltd., Herman Ottó u. 15, H-1022, Budapest, Hungary
| | - Rajeshwari Subray Bhat
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Rinkee Verma
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | | | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, 560064, India.
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4
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Godbole AA, Ahmed W, Bhat RS, Bradley EK, Ekins S, Nagaraja V. Inhibition of Mycobacterium tuberculosis topoisomerase I by m-AMSA, a eukaryotic type II topoisomerase poison. Biochem Biophys Res Commun 2014; 446:916-20. [PMID: 24642256 DOI: 10.1016/j.bbrc.2014.03.029] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [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: 02/26/2014] [Accepted: 03/09/2014] [Indexed: 11/26/2022]
Abstract
m-AMSA, an established inhibitor of eukaryotic type II topoisomerases, exerts its cidal effect by binding to the enzyme-DNA complex thus inhibiting the DNA religation step. The molecule and its analogues have been successfully used as chemotherapeutic agents against different forms of cancer. After virtual screening using a homology model of the Mycobacterium tuberculosis topoisomerase I, we identified m-AMSA as a high scoring hit. We demonstrate that m-AMSA can inhibit the DNA relaxation activity of topoisomerase I from M. tuberculosis and Mycobacterium smegmatis. In a whole cell assay, m-AMSA inhibited the growth of both the mycobacteria.
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Affiliation(s)
- Adwait Anand Godbole
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Wareed Ahmed
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Rajeshwari Subray Bhat
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | | | - Sean Ekins
- Collaborative Drug Discovery, 1633 Bayshore Highway, Suite 342, Burlingame, CA 94403, USA
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India.
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5
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Lamb ML, Bradley EK, Beaton G, Bondy SS, Castellino AJ, Gibbons PA, Suto MJ, Grootenhuis PDJ. Design of a gene family screening library targeting G-protein coupled receptors. J Mol Graph Model 2004; 23:15-21. [PMID: 15331050 DOI: 10.1016/j.jmgm.2004.03.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2003] [Revised: 12/15/2003] [Accepted: 03/03/2004] [Indexed: 11/19/2022]
Abstract
An iterative process for the design of a G-protein coupled receptor (GPCR) gene family screening library has been developed. A key element of this process is the computational generation of pharmacophore descriptors of known GPCR ligands. Subsequent iterative analysis allows prioritization of scaffolds and sub-libraries for inclusion in the library. The final library, which consisted of 13,769 compounds, displayed a 2.6% hit rate when screened against the micro-opioid receptor.
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Affiliation(s)
- Michelle L Lamb
- Deltagen Research Laboratories, 740 Bay Rd., Redwood City, CA 94063, USA.
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6
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Evensen E, Eksterowicz JE, Stanton RV, Oshiro C, Grootenhuis PDJ, Bradley EK. Comparing performance of computational tools for combinatorial library design. J Med Chem 2004; 46:5125-8. [PMID: 14613315 DOI: 10.1021/jm025618t] [Citation(s) in RCA: 12] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
In using computational tools for library design it is necessary to understand the performance and limitations of available methods. This letter reports systematic comparisons of applying ligand-based and structure-based tools across therapeutic project-derived data sets. Included are assessments of performance in real-world iterative design applications and the utility of target structural information. The results suggest that combining screening and target structure information is robust; further, a well-designed screening library can compensate for lacking structural information.
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Affiliation(s)
- Erik Evensen
- Deltagen Research Labs, Redwood City, CA 94063, USA.
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7
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Oshiro C, Bradley EK, Eksterowicz J, Evensen E, Lamb ML, Lanctot JK, Putta S, Stanton R, Grootenhuis PDJ. Performance of 3D-Database Molecular Docking Studies into Homology Models. J Med Chem 2004; 47:764-7. [PMID: 14736258 DOI: 10.1021/jm0300781] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.1] [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: 11/29/2022]
Abstract
The performance of docking studies into protein active sites constructed by homology model building was investigated using CDK2 and factor VIIa screening data sets. When the sequence identity between model and template near the binding site area is greater than approximately 50%, roughly 5 times more active compounds are identified than would be found randomly. This performance is comparable to docking to crystal structures.
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Affiliation(s)
- Connie Oshiro
- Deltagen Research Laboratories, 740 Bay Road, Redwood City, California 94063, USA.
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8
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Bradley EK, Miller JL, Saiah E, Grootenhuis PDJ. Informative Library Design as an Efficient Strategy to Identify and Optimize Leads: Application to Cyclin-Dependent Kinase 2 Antagonists. J Med Chem 2003; 46:4360-4. [PMID: 13678414 DOI: 10.1021/jm020472j] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [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
The application of an informative, iterative library design strategy is presented for lead identification and optimization. The computational algorithm underlying informative design systematically uses data from both active and inactive compounds and maximizes the information gained from subsequent design-synthesis-screening cycles. Retrospective analysis of a released dataset of 17 550 compounds and corresponding cyclin-dependent kinase-2 activities showed that informative library design yields significant enrichments of active compounds and efficiently discovers novel chemotypes in comparison with commonly used diversity-similarity protocols.
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Affiliation(s)
- Erin K Bradley
- Deltagen Research Laboratories, 740 Bay Road, Redwood City, California 94063, USA.
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9
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Robinson LA, Wilson DM, Delaet NGJ, Bradley EK, Dankwardt SM, Campbell JA, Martin RL, Van Wart HE, Walker KAM, Sullivan RW. Novel inhibitors of procollagen C-proteinase. Part 2: glutamic acid hydroxamates. Bioorg Med Chem Lett 2003; 13:2381-4. [PMID: 12824039 DOI: 10.1016/s0960-894x(03)00402-5] [Citation(s) in RCA: 18] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Glutamic acid derived hydroxamates were identified as potent and selective inhibitors of procollagen C-proteinase, an essential enzyme for the processing of procollagens to fibrillar collagens. Such compounds have potential therapeutic application in the treatment of fibrosis.
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Affiliation(s)
- L A Robinson
- CombiChem Inc., 4570 Executive Drive, 92121, San Diego, CA, USA
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10
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Delaet NGJ, Robinson LA, Wilson DM, Sullivan RW, Bradley EK, Dankwardt SM, Martin RL, Van Wart HE, Walker KAM. Novel inhibitors of procollagen C-terminal proteinase. Part 1: diamino Acid hydroxamates. Bioorg Med Chem Lett 2003; 13:2101-4. [PMID: 12798313 DOI: 10.1016/s0960-894x(03)00404-9] [Citation(s) in RCA: 18] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The parallel synthesis of novel inhibitors of procollagen C-terminal proteinase is described. The synthetic strategy allowed for the facile synthesis of a large number of side-chain diversified diamino acid hydroxamates, of which the D-diaminopropionic acid derivatives were shown to be single digit nanomolar PCP inhibitors.
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Affiliation(s)
- N G J Delaet
- CombiChem Inc., 4570 Executive Drive, 92121, San Diego, CA, USA.
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11
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Abstract
We present an algorithm for the design of either combinatorial or discrete informative libraries. This approach is based on information theoretic techniques used extensively in coding theory. We have extended the information theoretic formalism to include an arbitrary number of property distribution constraints, such as Lipinski "drug-like" distributions. The method is demonstrated by comparing and contrasting a variety of different libraries selected from a single combinatorial source pool of compounds.
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12
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Srinivasan J, Castellino A, Bradley EK, Eksterowicz JE, Grootenhuis PDJ, Putta S, Stanton RV. Evaluation of a novel shape-based computational filter for lead evolution: application to thrombin inhibitors. J Med Chem 2002; 45:2494-500. [PMID: 12036357 DOI: 10.1021/jm010494q] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [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: 11/29/2022]
Abstract
A novel shape-feature-based computational method is described and used to rapidly filter compound libraries. The computational model, built using three-dimensional conformations of active and inactive molecules, consists of a collection of whole molecule shapes and chemical feature positions that are ranked according to their correlation with activity. A small ensemble of these shapes and features is used to filter virtual compound libraries. The method is applied to two thrombin data sets and is shown to be efficient in identifying novel scaffolds with enhanced hit rates.
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Affiliation(s)
- Jayashree Srinivasan
- Deltagen Research Laboratories, 4570 Executive Drive, Suite 400, San Diego, CA 92121, USA.
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13
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Eksterowicz JE, Evensen E, Lemmen C, Brady GP, Lanctot JK, Bradley EK, Saiah E, Robinson LA, Grootenhuis PDJ, Blaney JM. Coupling structure-based design with combinatorial chemistry: application of active site derived pharmacophores with informative library design. J Mol Graph Model 2002; 20:469-77. [PMID: 12071281 DOI: 10.1016/s1093-3263(01)00148-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [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
Protein structural information is combined with combinatorial library design in the following protocol. Active site maps are generated from protein structures. All possible 2-, 3- and 4-point pharmacophores are enumerated from the active site map and encoded as bit strings. The pharmacophores define a design space that can be used to select compounds using an informative library design tool. The method was evaluated against a collection of compounds assayed previously against a cyclin-dependent kinase target, CDK-2, starting with 23 X-ray co-crystal structures. Performance was assessed based on the number of active scaffolds selected after four rounds of iterative informative library design. The method selects compounds from 12 out of the 15 active scaffolds from the CDK-2 library and outperforms a two-dimensional similarity search and docking calculations.
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Affiliation(s)
- John E Eksterowicz
- DuPont Pharmaceuticals Research Laboratories, San Francisco, CA 94111, USA.
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14
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Beroza P, Bradley EK, Eksterowicz JE, Feinstein R, Greene J, Grootenhuis PD, Henne RM, Mount J, Shirley WA, Smellie A, Stanton RV, Spellmeyer DC. Applications of random sampling to virtual screening of combinatorial libraries. J Mol Graph Model 2000; 18:335-42. [PMID: 11143553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
We describe statistical techniques for effective evaluation of large virtual combinatorial libraries (> 10(10) potential compounds). The methods described are used for computationally evaluating templates (prioritization of candidate libraries for synthesis and screening) and for the design of individual combinatorial libraries (e.g., for a given diversity site, reagents can be selected based on the estimated frequency with which they appear in products that pass a computational filter). These statistical methods are powerful because they provide a simple way to estimate the properties of the overall library without explicitly enumerating all of the possible products. In addition, they are fast and simple, and the amount of sampling required to achieve a desired precision is calculable. In this article, we discuss the computational methods that allow random product selection from a combinatorial library and the statistics involved in estimating errors from quantities obtained from such samples. We then describe three examples: (1) an estimate of average molecular weight for the several billion possible products in a four-component Ugi reaction, a quantity that can be calculated exactly for comparison; (2) the prioritization of four templates for combinatorial synthesis using a computational filter based on four-point pharmacophores; and (3) selection of reagents for the four-component Ugi reaction based on their frequency of occurrence in products that pass a pharmacophore filter.
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Affiliation(s)
- P Beroza
- DuPont Pharmaceuticals Research Laboratories, 150 California Street, San Francisco, CA 94111, USA
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15
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Bradley EK, Beroza P, Penzotti JE, Grootenhuis PD, Spellmeyer DC, Miller JL. A rapid computational method for lead evolution: description and application to alpha(1)-adrenergic antagonists. J Med Chem 2000; 43:2770-4. [PMID: 10893315 DOI: 10.1021/jm990578n] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.4] [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: 11/29/2022]
Abstract
The high failure rate of drugs in the development phase requires a strategy to reduce risks by generating lead candidates from different chemical classes. We describe a new three-dimensional computational approach for lead evolution, based on multiple pharmacophore hypotheses. Using full conformational models for both active and inactive compounds, a large number of pharmacophore hypotheses are analyzed to select the set or "ensemble" of hypotheses that, when combined, is most able to discriminate between active and inactive molecules. The ensemble hypothesis is then used to search virtual chemical libraries to identify compounds for synthesis. This method is very rapid, allowing very large virtual libraries on the order of a million compounds to be filtered efficiently. In applying this method to alpha(1)-adrenergic receptor ligands, we have demonstrated lead evolution from heterocyclic alpha(1)-adrenergic receptor ligands to highly dissimilar active N-substituted glycine compounds. Our results also show that the active N-substituted glycines are part of our smaller filtered library and thus could have been identified by synthesizing only a portion of the N-substituted glycine library.
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Affiliation(s)
- E K Bradley
- Molecular Design Group, CombiChem, Inc., 1804 Embarcadero Road, Suite 201, Palo Alto, California 94303, USA
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16
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Armand P, Kirshenbaum K, Goldsmith RA, Farr-Jones S, Barron AE, Truong KT, Dill KA, Mierke DF, Cohen FE, Zuckermann RN, Bradley EK. NMR determination of the major solution conformation of a peptoid pentamer with chiral side chains. Proc Natl Acad Sci U S A 1998; 95:4309-14. [PMID: 9539733 PMCID: PMC22485 DOI: 10.1073/pnas.95.8.4309] [Citation(s) in RCA: 268] [Impact Index Per Article: 10.3] [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: 02/07/2023] Open
Abstract
Polymers of N-substituted glycines ("peptoids") containing chiral centers at the alpha position of their side chains can form stable structures in solution. We studied a prototypical peptoid, consisting of five para-substituted (S)-N-(1-phenylethyl)glycine residues, by NMR spectroscopy. Multiple configurational isomers were observed, but because of extensive signal overlap, only the major isomer containing all cis-amide bonds was examined in detail. The NMR data for this molecule, in conjunction with previous CD spectroscopic results, indicate that the major species in methanol is a right-handed helix with cis-amide bonds. The periodicity of the helix is three residues per turn, with a pitch of approximately 6 A. This conformation is similar to that anticipated by computational studies of a chiral peptoid octamer. The helical repeat orients the amide bond chromophores in a manner consistent with the intensity of the CD signal exhibited by this molecule. Many other chiral polypeptoids have similar CD spectra, suggesting that a whole family of peptoids containing chiral side chains is capable of adopting this secondary structure motif. Taken together, our experimental and theoretical studies of the structural properties of chiral peptoids lay the groundwork for the rational design of more complex polypeptoid molecules, with a variety of applications, ranging from nanostructures to nonviral gene delivery systems.
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Affiliation(s)
- P Armand
- Chiron Technologies, Chiron Corporation, 4560 Horton Street, Emeryville, CA 94608, USA
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17
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Kirshenbaum K, Barron AE, Goldsmith RA, Armand P, Bradley EK, Truong KT, Dill KA, Cohen FE, Zuckermann RN. Sequence-specific polypeptoids: a diverse family of heteropolymers with stable secondary structure. Proc Natl Acad Sci U S A 1998; 95:4303-8. [PMID: 9539732 PMCID: PMC22484 DOI: 10.1073/pnas.95.8.4303] [Citation(s) in RCA: 377] [Impact Index Per Article: 14.5] [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: 02/07/2023] Open
Abstract
We have synthesized and characterized a family of structured oligo-N-substituted-glycines (peptoids) up to 36 residues in length by using an efficient solid-phase protocol to incorporate chemically diverse side chains in a sequence-specific fashion. We investigated polypeptoids containing side chains with a chiral center adjacent to the main chain nitrogen. Some of these sequences have stable secondary structure, despite the achirality of the polymer backbone and its lack of hydrogen bond donors. In both aqueous and organic solvents, peptoid oligomers as short as five residues give rise to CD spectra that strongly resemble those of peptide alpha-helices. Differential scanning calorimetry and CD measurements show that polypeptoid secondary structure is highly stable and that unfolding is reversible and cooperative. Thermodynamic parameters obtained for unfolding are similar to those obtained for the alpha-helix to coil transitions of peptides. This class of biomimetic polymers may enable the design of self-assembling macromolecules with novel structures and functions.
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Affiliation(s)
- K Kirshenbaum
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143
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Bradley EK, Kerr JM, Richter LS, Figliozzi GM, Goff DA, Zuckermann RN, Spellmeyer DC, Blaney JM. NMR structural characterization of oligo-N-substituted glycine lead compounds from a combinatorial library. Mol Divers 1998; 3:1-15. [PMID: 9527473 DOI: 10.1023/a:1009698309407] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [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: 02/06/2023]
Abstract
Synthesis and screening of combinatorial libraries for pharmaceutical lead discovery is a rapidly expanding field. Oligo-N-substituted glycines (NSGs) were one of the earliest sources of molecular diversity in combinatorial libraries. In one of the first demonstrations of the power of combinatorial chemistry, two NSG trimers, CHIR-2279 and CHIR-4531, were identified as nM ligands for two 7-transmembrane G-protein-coupled receptors. The NMR characterization of these two lead compounds was undertaken to verify covalent connectivity and to determine solution conformations, if any. The sequential chemical shift assignments were performed using a new strategy for assigning 1H and 13C resonances of NSGs. The conformational preferences were then determined in both an aqueous co-solvent system and an organic solvent to probe the effects of hydrophobic collapse. NSGs are expected to be more flexible than peptides due to the tertiary amide, with both cis and trans amide bond conformations being accessible. Solution NMR studies indicate that although CHIR-2279 and CHIR-4531 have identical backbones and termini, and very similar side chains, they do not display the same solution conformational characteristics.
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Affiliation(s)
- E K Bradley
- Small Molecule Drug Discovery, Chiron Corporation, Emeryville, CA 94608, USA
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Bradley EK, Ng SC, Simon RJ, Spellmeyer DC. Synthesis, molecular modelling, and NMR structure determination of four cyclic peptide antagonists of endothelin. Bioorg Med Chem 1994; 2:279-96. [PMID: 7922139 DOI: 10.1016/s0968-0896(00)82171-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [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: 01/27/2023]
Abstract
A combined distance geometry and molecular mechanics/dynamics (MM/MD) protocol was unable to predict the active conformation of the cyclic pentapeptide inhibitor of endothelin-1 receptor, BQ-123, and two analogues. However, the MM/MD method alone is sufficient to predict the solution conformation of a third analogue. In that one case, the combination of proline at residue 3 and an N alpha-methyl substitution at residue 5 provides enough internal constraints to eliminate conformational flexibility seen in the other three analogues. For this constrained analogue, the 50 lowest energy conformations (out of a set of 500 DGEOM-generated, MM/MD minimized conformations) differ by no more than 3.9 kcal/mol. Thirty three of these 50 conformations have backbone atom RMSDs of less than 0.33 A, relative to the lowest energy conformation. The accuracy of this MM/MD model is verified by determining the solution structure of each of the four analogues with 2D NMR techniques. Each of the cyclic pentapeptides has a well defined solution conformation where a proline residue is clearly in a gamma-turn, leaving the remaining residues in a loose beta-turn. All four experimental NMR conformations agree closely with the MM/MD model.
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Davis JH, Bradley EK, Miljanich GP, Nadasdi L, Ramachandran J, Basus VJ. Solution structure of omega-conotoxin GVIA using 2-D NMR spectroscopy and relaxation matrix analysis. Biochemistry 1993; 32:7396-405. [PMID: 8338837 DOI: 10.1021/bi00080a009] [Citation(s) in RCA: 86] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We report here the solution structure of omega-conotoxin GVIA, a peptide antagonist of the N-type neuronal voltage-sensitive calcium channel. The structure was determined using two-dimensional NMR in combination with distance geometry and restrained molecular dynamics. The full relaxation matrix analysis program MARDIGRAS was used to generate maximum and minimum distance restraints from the crosspeak intensities in NOESY spectra. The 187 restraints obtained were used in conjunction with 23 angle restraints from vicinal coupling constants as input for the structure calculations. The backbones of the best 21 structures match with an average pairwise RMSD of 0.58 A. The structures contain a short segment of triple-stranded beta-sheet involving residues 6-8, 18-21, and 24-27, making this the smallest published peptide structure to contain a triple-stranded beta-sheet. Conotoxins have been shown to be effective neuroprotective agents in animal models of brain ischemia. Our results should aid in the design of novel nonpeptide compounds with potential therapeutic utility.
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Affiliation(s)
- J H Davis
- Graduate Group in Biophysics, University of California, San Francisco 94143-0446
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Abstract
We have designed a set of 17-residue synthetic peptides to be monomeric helices in aqueous solution. Circular dichrosim experiments indicate the presence of helical structure in aqueous solution at low temperature and low pH. The two-dimensional nuclear magnetic resonance results for one of the peptides show a segment of ten residues which clearly meets all of the criteria for the existence of helical structure at both 5 degrees C and 15 degrees C. The first four residues of the peptide are in a largely extended conformation. Calculations suggest that residues 5 through 14 are significantly helical at 5 degrees C. When the temperature is increased, circular dichroism spectra indicate that the helical content decreases. At 15 degrees C, the 3JN alpha coupling constants increase in the helical region, indicating an increase in motion or conformational averaging in the helical segment. None of the peptides has pH titration behavior consistent with salt bridge stabilization of helical conformation. Our data lend themselves to interpretation with the helix dipole model and specific side-chain interactions. When the N and C termini charges are removed the helical content of the peptides increases. The amount of helicity increases as the pH is lowered, due to the ionization of His16. Much of the helical stabilization appears to be due to a specific side-chain interaction between His16 and Tyr12.
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Affiliation(s)
- E K Bradley
- Department of Pharmaceutical Chemistry, University of California, San Francisco 94143
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