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Abstract
The Human Genome Project ultimately aimed to translate DNA sequence into drugs. With the draft in hand, the Molecular Libraries Program set out to prosecute all genome-encoded proteins for drug discovery with automated high-throughput screening (HTS). This ambitious vision remains unfulfilled, even while innovations in sequencing technology have fully democratized access to genome-scale sequencing. Why? While the central dogma of biology allows us to chart the entirety of cellular metabolism through sequencing, there is no direct coding for chemistry. The rules of base pairing that relate DNA gene to RNA transcript and amino acid sequence do not exist for relating small-molecule structure with macromolecular binding partners and subsequently cellular function. Obtaining such relationships genome-wide is unapproachable via state-of-the-art HTS, akin to attempting genome-wide association studies using turn-of-the-millennium Sanger DNA sequencing.Our laboratory has been engaged in a multipronged technology development campaign to revolutionize molecular screening through miniaturization in pursuit of genome-scale drug discovery capabilities. The compound library was ripe for miniaturization: it clearly needed to become a consumable. We employed DNA-encoded library (DEL) synthesis principles in the development of solid-phase DELs prepared on microscopic beads, each harboring 100 fmol of a single library member and a DNA tag whose sequence describes the structure of the library member. Loading these DEL beads into 100 pL microfluidic droplets followed by online photocleavage, incubation, fluorescence-activated droplet sorting, and DNA sequencing of the sorted DEL beads reveals the chemical structures of bioactive compounds. This scalable library synthesis and screening platform has proven useful in several proof-of-concept projects involving current clinical targets.Moving forward, we face the problem of druggability and proteome-scale assay development. Developing biochemical or cellular assays for all genome-encoded targets is not scalable and likely impossible as most proteins have ill-defined or unknown activity and may not function outside of their native contexts. These are the dark undruggable expanses, and charting them will require advanced synthesis and analytical technologies that can generalize probe discovery, irrespective of mature protein function, to fulfill the Genome Project's vision of proteome-wide control of cellular pharmacology.
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2
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Co (II) Complexes Based on the Bis-Pyrazol-S-Triazine Pincer Ligand: Synthesis, X-ray Structure Studies, and Cytotoxic Evaluation. CRYSTALS 2022. [DOI: 10.3390/cryst12050741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Four pincer-type Co (II) complexes of the 2,4-bis (3,5-dimethyl-1H-pyrazol-1-yl)-6-methoxy-1,3,5-triazine ligand (L) were evaluated for their cytotoxic activities against lung and breast cancer cell lines using cell viability assay. The X-ray single crystal structure of [Co(L)(H2O)2Br]Br (1) confirmed the pincer coordination behavior of the ligand L as an N-tridentate chelate. The hexa-coordination environment of Co (II) is completed by one bromide ion completing the equatorial plane of the octahedral structure and two trans water molecules at the axial positions. It crystallized in the monoclinic crystal system and P21/m space group with crystal parameters of a = 11.3170(10) Å, b = 7.4613(7) Å, c = 12.6917(12) Å and β = 95.927(3)°. Based on Hirshfeld analysis, the most dominant contacts are H…H (48.8%), Br…H (17.6%), H…C (11.2%) and O…H (10.1%), where the Br…H interactions are the most significant. The cytotoxic evaluation of the studied systems indicated that complex [Co(L)(NO3)2] (4) has the highest activity against lung (A-549) and breast (MCF-7) cell lines. In contrast, complex [Co(L)(H2O)3](ClO4)2.H2O(3) has the lowest cytotoxic activity against both cell lines.
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3
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Cochrane W, Fitzgerald PR, Paegel BM. Antibacterial Discovery via Phenotypic DNA-Encoded Library Screening. ACS Chem Biol 2021; 16:2752-2756. [PMID: 34806373 PMCID: PMC8688339 DOI: 10.1021/acschembio.1c00714] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The global rise of multidrug resistant infections poses an imminent, existential threat. Numerous pipelines have failed to convert biochemically active molecules into bona fide antibacterials, owing to a lack of chemical material with antibacterial-like physical properties in high-throughput screening compound libraries. Here, we demonstrate scalable design and synthesis of an antibacterial-like solid-phase DNA-encoded library (DEL, 7488 members) and facile hit deconvolution from whole-cell Escherichia coli and Bacillus subtilis cytotoxicity screens. The screen output identified two low-micromolar inhibitors of B. subtilis growth and recapitulated known structure-activity relationships of the fluoroquinolone antibacterial class. This phenotypic DEL screening strategy is also potentially applicable to adherent cells and will broadly enable the discovery and optimization of cell-active molecules.
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Affiliation(s)
- Wesley
G. Cochrane
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
| | - Patrick R. Fitzgerald
- Skaggs
Doctoral Program in the Chemical and Biological Sciences, Scripps Research, La Jolla, California 92037, United States
| | - Brian M. Paegel
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
- Departments
of Chemistry & Biomedical Engineering, University of California, Irvine, California 92697, United States
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4
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Abstract
Click chemistry, proposed nearly 20 years ago, promised access to novel chemical space by empowering combinatorial library synthesis with a "few good reactions". These click reactions fulfilled key criteria (broad scope, quantitative yield, abundant starting material, mild reaction conditions, and high chemoselectivity), keeping the focus on molecules that would be easy to make, yet structurally diverse. This philosophy bears a striking resemblance to DNA-encoded library (DEL) technology, the now-dominant combinatorial chemistry paradigm. This review highlights the similarities between click and DEL reaction design and deployment in combinatorial library settings, providing a framework for the design of new DEL synthesis technologies to enable next-generation drug discovery.
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Affiliation(s)
- Patrick R Fitzgerald
- Skaggs Doctoral Program in the Chemical and Biological Sciences, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Brian M Paegel
- Departments of Pharmaceutical Sciences, Chemistry, & Biomedical Engineering, University of California, Irvine, 101 Theory Suite 100, Irvine, California 92617, United States
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
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5
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Efficient Synthesis of Multiply Substituted Triazines Using GO@N-Ligand-Cu Nano-Composite as a Novel Catalyst. J Inorg Organomet Polym Mater 2021. [DOI: 10.1007/s10904-020-01830-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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6
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Singh S, Mandal MK, Masih A, Saha A, Ghosh SK, Bhat HR, Singh UP. 1,3,5-Triazine: A versatile pharmacophore with diverse biological activities. Arch Pharm (Weinheim) 2021; 354:e2000363. [PMID: 33760298 DOI: 10.1002/ardp.202000363] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 02/05/2021] [Accepted: 02/12/2021] [Indexed: 12/14/2022]
Abstract
1,3,5-Triazine and its derivatives have been the epicenter of chemotherapeutic molecules due to their effective biological activities, such as antibacterial, fungicidal, antimalarial, anticancer, antiviral, antimicrobial, anti-inflammatory, antiamoebic, and antitubercular activities. The present review represents a summarized report of the crucial biological activities possessed by substituted 1,3,5-triazine derivatives, with special attention to the most potent compounds.
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Affiliation(s)
- Saumya Singh
- Drug Design and Discovery Laboratory, Department of Pharmaceutical Sciences, Sam Higginbottom University of Agriculture, Technology, and Sciences, Allahabad, Uttar Pradesh, India
| | - Milan K Mandal
- Drug Design and Discovery Laboratory, Department of Pharmaceutical Sciences, Sam Higginbottom University of Agriculture, Technology, and Sciences, Allahabad, Uttar Pradesh, India
| | - Anup Masih
- Drug Design and Discovery Laboratory, Department of Pharmaceutical Sciences, Sam Higginbottom University of Agriculture, Technology, and Sciences, Allahabad, Uttar Pradesh, India
| | - Ashmita Saha
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh, Assam, India
| | - Surajit K Ghosh
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh, Assam, India
| | - Hans R Bhat
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh, Assam, India
| | - Udaya P Singh
- Drug Design and Discovery Laboratory, Department of Pharmaceutical Sciences, Sam Higginbottom University of Agriculture, Technology, and Sciences, Allahabad, Uttar Pradesh, India
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7
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Kodadek T, Paciaroni NG, Balzarini M, Dickson P. Beyond protein binding: recent advances in screening DNA-encoded libraries. Chem Commun (Camb) 2019; 55:13330-13341. [PMID: 31633708 PMCID: PMC6939232 DOI: 10.1039/c9cc06256d] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
DNA-encoded library (DEL) screening has emerged as an important method for early stage drug and probe molecule discovery. The vast majority of screens using DELs have been relatively simple binding assays. The library is incubated with a target molecule, which is almost always a protein, and the DNAs that remain associated with the target after thorough washing are amplified and deep sequenced to reveal the chemical structures of the ligands they encode. Recently however, a number of different screening formats have been introduced that demand more than simple binding. These include a format that demands hits exhibit high selectivity for target vs. off-targets, a protocol to screen for enzyme inhibitors and another to identify organocatalysts in a DEL. These and other novel assay formats are reviewed in this article. We also consider some of the most significant remaining challenges in DEL assay development.
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Affiliation(s)
- Thomas Kodadek
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Nicholas G Paciaroni
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Madeline Balzarini
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Paige Dickson
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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8
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Design, synthesis and molecular modeling studies of new series of s-triazine derivatives as antimicrobial agents against multi-drug resistant clinical isolates. Bioorg Chem 2019; 89:103013. [DOI: 10.1016/j.bioorg.2019.103013] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 05/08/2019] [Accepted: 05/24/2019] [Indexed: 01/13/2023]
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9
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Cochrane WG, Malone ML, Dang VQ, Cavett V, Satz AL, Paegel BM. Activity-Based DNA-Encoded Library Screening. ACS COMBINATORIAL SCIENCE 2019; 21:425-435. [PMID: 30884226 DOI: 10.1021/acscombsci.9b00037] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Robotic high-throughput compound screening (HTS) and, increasingly, DNA-encoded library (DEL) screening are driving bioactive chemical matter discovery in the postgenomic era. HTS enables activity-based investigation of highly complex targets using static compound libraries. Conversely, DEL grants efficient access to novel chemical diversity, although screening is limited to affinity-based selections. Here, we describe an integrated droplet-based microfluidic circuit that directly screens solid-phase DELs for activity. An example screen of a 67 100-member library for inhibitors of the phosphodiesterase autotaxin yielded 35 high-priority structures for nanomole-scale synthesis and validation (20 active), guiding candidate selection for synthesis at scale (5/5 compounds with IC50 values of 4-10 μM). We further compared activity-based hits with those of an analogous affinity-based DEL selection. This miniaturized screening platform paves the way toward applying DELs to more complex targets (signaling pathways, cellular response) and represents a distributable approach to small molecule discovery.
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Affiliation(s)
| | | | | | | | - Alexander L. Satz
- Roche Pharma Research and Early Development (pRED) Roche Innovation Center Basel F. Hoffman-La Roche Ltd Grenzacherstrasse 124 CH-4070 Basel Switzerland
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10
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Shajari N, Ghiasi R. Theoretical Study of Tautomerization in 1,5-Dimethyl-6-Thioxo-1,3,5-Triazinane-2,4-Dione. J STRUCT CHEM+ 2018. [DOI: 10.1134/s002247661803006x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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11
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Shanmugam M, Narayanan K, Prasad KH, Karthikeyan D, Chandrasekaran L, Atchudan R, Chidambaranathan V. Synthesis, characterization, and antiproliferative and apoptosis inducing effects of novel s-triazine derivatives. NEW J CHEM 2018. [DOI: 10.1039/c7nj03348f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In an attempt to design and synthesize a new class of antitumor agents, a mild and eco-friendly protocol for nucleophilic substitution using ans-triazine scaffold,viaamine and Schiff base derivatives, has been developed.
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Affiliation(s)
- Mani Shanmugam
- Department of Science and Humanities
- Institute of Aeronautical Engineering
- Dundigal
- India
- Chemistry Section
| | | | - Kamatam Hari Prasad
- Department of Science and Humanities
- Institute of Aeronautical Engineering
- Dundigal
- India
- Department of Physics
| | | | | | - Raji Atchudan
- School of Chemical Engineering
- Yeungnam University
- Gyeongsan-38541
- Republic of Korea
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12
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Shen F, Ou ZB, Liu YJ, Liu W, Wang BF, Mao ZW, Le XY. Two Cu(II) complexes containing 2,4-diamino-6-(2-pyridyl)-1,3,5-triazine and amino acids: Synthesis, crystal structures, DNA/HSA binding, molecular docking, and in vitro cytotoxicity studies. Inorganica Chim Acta 2017. [DOI: 10.1016/j.ica.2017.05.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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13
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Al-Zaydi KM, Khalil HH, El-Faham A, Khattab SN. Synthesis, characterization and evaluation of 1,3,5-triazine aminobenzoic acid derivatives for their antimicrobial activity. Chem Cent J 2017; 11:39. [PMID: 29086830 PMCID: PMC5423881 DOI: 10.1186/s13065-017-0267-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 05/02/2017] [Indexed: 02/03/2023] Open
Abstract
Background Replacement of chloride ions in cyanuric chloride give several variants of 1,3,5-triazine derivatives which were investigated as biologically active small molecules. These compounds exhibit antimalarial, antimicrobial, anti-cancer and anti-viral activities, among other beneficial properties. On the other hand, treatment of bacterial infections remains a challenging therapeutic problem because of the emerging infectious diseases and the increasing number of multidrug-resistant microbial pathogens. As multidrug-resistant bacterial strains proliferate, the necessity for effective therapy has stimulated research into the design and synthesis of novel antimicrobial molecules. Results 1,3,5-Triazine 4-aminobenzoic acid derivatives were prepared by conventional method or by using microwave irradiation. Using microwave irradiation gave the desired products in less time, good yield and higher purity. Esterification of the 4-aminobenzoic acid moiety afforded methyl ester analogues. The s-triazine derivatives and their methyl ester analogues were fully characterized by FT-IR, NMR (1H-NMR and 13C-NMR), mass spectra and elemental analysis. All the synthesized compounds were evaluated for their antimicrobial activity. Some tested compounds showed promising activity against Staphylococcus aureus and Escherichia coli. Conclusions Three series of mono-, di- and trisubstituted s-triazine derivatives and their methyl ester analogues were synthesized and fully characterized. All the synthesized compounds were evaluated for their antimicrobial activity. Compounds (10), (16), (25) and (30) have antimicrobial activity against S. aureus comparable to that of ampicillin, while the activity of compound (13) is about 50% of that of ampicillin. Compounds (13) and (14) have antimicrobial activity against E. coli comparable to that of ampicillin, while the activity of compounds (9–12) and (15) is about 50% of that of ampicillin. Furthermore, minimum inhibitory concentrations values for clinical isolates of compounds (10), (13), (14), (16), (25) and (30) were measured. Compounds (10) and (13) were more active against MRSA and E. coli than ampicillin. Invitro cytotoxicity results revealed that compounds (10) and (13) were nontoxic up to 250 µg/mL (with SI = 10) and 125 µg/mL (with SI = 5), respectively.Three series of mono-, di- and trisubstituted s-triazine derivatives and their methyl ester analogues were synthesized and evaluated for their antimicrobial activity. Several compounds have antimicrobial activity against S. aureus and E. coli comparable to that of ampicillin. ![]() Electronic supplementary material The online version of this article (doi:10.1186/s13065-017-0267-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Khadijah M Al-Zaydi
- Department of Chemistry, Faculty of Sciences-AL Faisaliah, King Abdulaziz University, Jeddah, P.O. Box 50918, Jeddah, 21533, Kingdom of Saudi Arabia.
| | - Hosam H Khalil
- Department of Chemistry, Faculty of Science, Alexandria University, P.O. Box 426, Ibrahimia, Alexandria, 21321, Egypt
| | - Ayman El-Faham
- Department of Chemistry, Faculty of Science, Alexandria University, P.O. Box 426, Ibrahimia, Alexandria, 21321, Egypt
| | - Sherine N Khattab
- Department of Chemistry, Faculty of Science, Alexandria University, P.O. Box 426, Ibrahimia, Alexandria, 21321, Egypt.
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14
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MacConnell AB, Price AK, Paegel BM. An Integrated Microfluidic Processor for DNA-Encoded Combinatorial Library Functional Screening. ACS COMBINATORIAL SCIENCE 2017; 19:181-192. [PMID: 28199790 PMCID: PMC5350604 DOI: 10.1021/acscombsci.6b00192] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
DNA-encoded synthesis
is rekindling interest in combinatorial compound
libraries for drug discovery and in technology for automated and quantitative
library screening. Here, we disclose a microfluidic circuit that enables
functional screens of DNA-encoded compound beads. The device carries
out library bead distribution into picoliter-scale assay reagent droplets,
photochemical cleavage of
compound from the bead, assay incubation, laser-induced fluorescence-based
assay detection, and fluorescence-activated droplet sorting to isolate
hits. DNA-encoded compound beads (10-μm diameter) displaying
a photocleavable positive control inhibitor pepstatin A were mixed
(1920 beads, 729 encoding sequences) with negative control beads (58 000
beads, 1728 encoding sequences) and screened for cathepsin D inhibition
using a biochemical enzyme activity assay. The circuit sorted 1518
hit droplets for collection following 18 min incubation over a 240
min analysis. Visual inspection of a subset of droplets (1188 droplets)
yielded a 24% false discovery rate (1166 pepstatin A beads; 366 negative
control beads). Using template barcoding strategies, it was possible
to count hit collection beads (1863) using next-generation sequencing
data. Bead-specific barcodes enabled replicate counting, and the false
discovery rate was reduced to 2.6% by only considering hit-encoding
sequences that were observed on >2 beads. This work represents
a complete
distributable small molecule discovery platform, from microfluidic
miniaturized automation to ultrahigh-throughput hit deconvolution
by sequencing.
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Affiliation(s)
- Andrew B. MacConnell
- Department
of Chemistry and ‡Doctoral Program in Chemical and Biological
Sciences, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Alexander K. Price
- Department
of Chemistry and ‡Doctoral Program in Chemical and Biological
Sciences, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Brian M. Paegel
- Department
of Chemistry and ‡Doctoral Program in Chemical and Biological
Sciences, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
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15
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Fisher KJ, Turkett JA, Corson AE, Bicker KL. Peptoid Library Agar Diffusion (PLAD) Assay for the High-Throughput Identification of Antimicrobial Peptoids. ACS COMBINATORIAL SCIENCE 2016; 18:287-91. [PMID: 27186808 DOI: 10.1021/acscombsci.6b00039] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Rapid emergence of antimicrobial resistant organisms necessitates equally rapid methods for the development of new antimicrobial compounds. Of recent interest have been mimics of antimicrobial peptides known as antimicrobial peptoids, which exhibit similar potency to the former but with improved proteolytic stability. Presented herein is a high-throughput method to screen libraries of antimicrobial peptoids immobilized on beads embedded into solid media. Termed the peptoid library agar diffusion (PLAD) assay, this assay allows for individual chemical manipulation of two identical peptoid strands. One strand can be released to diffuse out from a solid support bead and interact with the microorganism during screening. The other strand can be cleaved after screening from beads showing strong antimicrobial activity and analyzed by mass spectrometry to deconvolute the structure of the peptoid. This method was applied to a small library of peptoids to identify an antimicrobial peptoid with modest efficacy against the ESKAPE pathogens.
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Affiliation(s)
- Kevin J. Fisher
- Middle Tennessee State University, Department of
Chemistry, 1301 East Main
Street, Murfreesboro, Tennessee 37132, United States
| | - Jeremy A. Turkett
- Middle Tennessee State University, Department of
Chemistry, 1301 East Main
Street, Murfreesboro, Tennessee 37132, United States
| | - Ashley E. Corson
- Middle Tennessee State University, Department of
Chemistry, 1301 East Main
Street, Murfreesboro, Tennessee 37132, United States
| | - Kevin L. Bicker
- Middle Tennessee State University, Department of
Chemistry, 1301 East Main
Street, Murfreesboro, Tennessee 37132, United States
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16
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Synthesis and Preliminary Biological Evaluation of 1,3,5-Triazine Amino Acid Derivatives to Study Their MAO Inhibitors. Molecules 2015; 20:15976-88. [PMID: 26364629 PMCID: PMC6332092 DOI: 10.3390/molecules200915976] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 08/14/2015] [Accepted: 08/24/2015] [Indexed: 11/16/2022] Open
Abstract
Three series of 4,6-dimethoxy-, 4,6-dipiperidino- and 4,6-dimorpholino-1,3,5-triazin-2-yl) amino acid derivatives were synthesized and characterized. A preliminary study for their monoamine oxidase inhibitory activity showed that compounds 7, 18, and 25 had MAO-A inhibition activity comparable to that of the standard clorgyline, with apparently more selective inhibitory activity toward MAO-A than MAO-B and no significant acute toxicity.
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17
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Xiao SC, Liu CZ, Liu WK, Xie WZ, Lin WY, Jiang GF, Guo CC. Selective synthesis and biological activity of triazine-porphyrins as potential anti-cancer agents. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s1088424610001805] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Ten new triazine-porphyrin derivatives were synthesized using a simple one-pot procedure from the reaction of tetraphenylporphyrin bearing a hydroxyl group with 2,4,6-trichloro-1,3,5-triazine, and then with amines or alcohols. The structures of the products were characterized by 1H NMR, LC/MS, UV-vis and elemental analysis. The cytotoxic activity of the triazine-porphyrin derivatives was evaluated in vitro against MCF-7 cell. All new compounds showed similar activity against MCF-7 cells in the absence of light when compared to 5-fluorouracil and hematoporphyrin.
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Affiliation(s)
- Shen-Chu Xiao
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Chao-Zhou Liu
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Wu-Kun Liu
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Wen-Zhong Xie
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Wei-Ying Lin
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Guo-Fang Jiang
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Can-Cheng Guo
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
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18
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Stach M, Maillard N, Kadam RU, Kalbermatter D, Meury M, Page MGP, Fotiadis D, Darbre T, Reymond JL. Membrane disrupting antimicrobial peptide dendrimers with multiple amino termini. MEDCHEMCOMM 2012. [DOI: 10.1039/c1md00272d] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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19
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Xu B, Ding J, Chen KX, Miao ZH, Huang H, Liu H, Luo XM. Advances in Cancer Chemotherapeutic Drug Research in China. RECENT ADVANCES IN CANCER RESEARCH AND THERAPY 2012. [PMCID: PMC7158183 DOI: 10.1016/b978-0-12-397833-2.00012-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Bin Xu
- Corresponding author: Bin Xu, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zi Road, Shanghai 201203, People’s Republic of China. Tel: O21-54920515 (o), 13501793936 (mobile), Fax: 021-54920568, e-mail:
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20
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Sachdeva N, Dolzhenko AV, Chui WK. Synthesis and tautomerism study of 6-benzoylmethyl-1,3,5-triazin-2,4-diamine. CR CHIM 2011. [DOI: 10.1016/j.crci.2010.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Fluxà VS, Maillard N, Page MGP, Reymond JL. Bead diffusion assay for discovering antimicrobial cyclic peptides. Chem Commun (Camb) 2011; 47:1434-6. [DOI: 10.1039/c0cc04670a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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22
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Townsend JB, Shaheen F, Liu R, Lam KS. Jeffamine derivatized TentaGel beads and poly(dimethylsiloxane) microbead cassettes for ultrahigh-throughput in situ releasable solution-phase cell-based screening of one-bead-one-compound combinatorial small molecule libraries. ACTA ACUST UNITED AC 2010; 12:700-12. [PMID: 20593859 DOI: 10.1021/cc100083f] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A method to efficiently immobilize and partition large quantities of microbeads in an array format in microfabricated poly(dimethylsiloxane) (PDMS) cassette for ultrahigh-throughput in situ releasable solution-phase cell-based screening of one-bead-one-compound (OBOC) combinatorial libraries is described. Commercially available Jeffamine triamine T-403 (∼440 Da) was derivatized such that two of its amino groups were protected by Fmoc and the remaining amino group capped with succinic anhydride to generate a carboxyl group. This resulting trifunctional hydrophilic polymer was then sequentially coupled two times to the outer layer of topologically segregated bilayer TentaGel (TG) beads with solid phase peptide synthesis chemistry resulting in beads with increased loading capacity, hydrophilicity, and porosity at the outer layer. We have found that such bead configuration can facilitate ultrahigh-throughput in situ releasable solution-phase screening of OBOC libraries. An encoded releasable OBOC small molecule library was constructed on Jeffamine derivatized TG beads with library compounds tethered to the outer layer via a disulfide linker and coding tags in the interior of the beads. Compound-beads could be efficiently loaded (5-10 min) into a 5 cm diameter Petri dish containing a 10,000-well PDMS microbead cassette, such that over 90% of the microwells were each filled with only one compound-bead. Jurkat T-lymphoid cancer cells suspended in Matrigel were then layered over the microbead cassette to immobilize the compound-beads. After 24 h of incubation at 37 °C, dithiothreitol was added to trigger the release of library compounds. Forty-eight hours later, MTT reporter assay was used to identify regions of reduced cell viability surrounding each positive bead. From a total of about 20,000 beads screened, 3 positive beads were detected and physically isolated for decoding. A strong consensus motif was identified for these three positive compounds. These compounds were resynthesized and found to be cytotoxic (IC(50) 50-150 μM) against two T-lymphoma cell lines and less so against the MDA-MB 231 breast cancer cell line. This novel ultrahigh-throughput OBOC releasable method can potentially be adapted to many existing 96- or 384-well solution-phase cell-based or biochemical assays.
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Affiliation(s)
- Jared B Townsend
- Department of Biochemistry and Molecular Medicine, Division of Hematology & Oncology, University of California Davis Cancer Center, University of California Davis, 4501 X Street, Sacramento, California 95817, USA
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Baek HG, Liu R, Lam KS. Development of hydrogel TentaGel shell-core beads for ultrahigh throughput solution-phase screening of encoded OBOC combinatorial small molecule libraries. ACTA ACUST UNITED AC 2009; 11:91-102. [PMID: 19061339 DOI: 10.1021/cc800092y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The one-bead one-compound (OBOC) combinatorial library method enables the rapid generation and screening of millions of discrete chemical compounds on beads. Most of the OBOC screening methods require the library compounds to remain tethered to the bead during screening process. Methods have also been developed to release library compounds from immobilized beads for in situ solution phase or "lawn" assays. However, this latter approach, while extremely powerful, is severely limited by the lack of suitable solid supports for such assays. Here, we report on the development of a novel hydrogel TentaGel shell-core (HTSC) bead in which hydrogel is grafted onto the polystyrene-based TentaGel (TG) bead as an outer shell (5-80 mum thick) via free radical surface-initiated polymerization. This novel shell-core bilayer resin enables the preparation of encoded OBOC combinatorial small molecule libraries, such that the library compounds reside on the highly hydrophilic outer layer and the coding tags reside in the polystyrene-based TG core. Using fluorescein as a model small molecule compound, we have demonstrated that fluorescein molecules that have been linked covalently to the hydrogel shell via a disulfide bond could readily diffuse out of the hydrogel layer into the bead surrounding after reduction with dithiothreitol. In contrast, under identical condition, the released fluorescein molecules remained bound to unmodified TG bead. We have prepared an encoded OBOC small molecule library on the novel shell-core beads and demonstrated that the beads can be readily decoded.
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Affiliation(s)
- Hyoung Gee Baek
- Division of Hematology and Oncology, Department of Internal Medicine, University of California Davis Cancer Center, Sacramento, California 95817, USA
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Liu K, Xia B, Ma W, Zheng B, Zhang X, Fan B. Quantitative Structure-Activity Relationship Modeling of Triaminotriazine Drugs Based on Heuristic Method. ACTA ACUST UNITED AC 2008. [DOI: 10.1002/qsar.200730045] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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25
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Synthesis and biological evaluation of novel 1,3,5-triazine derivatives as antimicrobial agents. Bioorg Med Chem Lett 2008; 18:1308-11. [DOI: 10.1016/j.bmcl.2008.01.031] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Revised: 01/03/2008] [Accepted: 01/08/2008] [Indexed: 11/18/2022]
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26
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Aina OH, Liu R, Sutcliffe JL, Marik J, Pan CX, Lam KS. From Combinatorial Chemistry to Cancer-Targeting Peptides. Mol Pharm 2007; 4:631-51. [PMID: 17880166 DOI: 10.1021/mp700073y] [Citation(s) in RCA: 220] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Several monoclonal antibodies that target cell surface receptors have gained approval by the U.S. Food and Drug Administration and are widely used in the treatment of some cancers. These include but are not limited to the anti-CD20 antibody Rituximab, used in lymphoma treatment, as well as anti-HER-2 antibody for breast cancer therapy. The efficacy of this cancer immunotherapy modality is, however, limited by the large size of the antibody (160 kd) and its relatively nonspecific binding to the reticuloendothelial system. This latter property is particularly problematic if the antibody is used as a vehicle to deliver radionuclides, cytotoxic drugs, or toxins to the tumor site. Peptides, peptidomimetic, or small molecules are thus attractive as alternative cell surface targeting agents for cancer imaging and therapy. Cancer cell surface targeting peptides can be derived from known native peptide hormones such as somatostatin and bombesin, or they can be identified through screening combinatorial peptide libraries against unknown cell surface receptor targets. Phage-display peptide library and one-bead one-compound (OBOC) combinatorial library methods have been successfully used to discover peptides that target cancer cells or tumor blood vessel endothelial cells. The phage-display peptide library method, because of its biological nature, can only display l-amino acid peptides. In contrast, the OBOC combinatorial library method allows for bead-surface display of peptides that contain l-amino acids, d-amino acids, unnatural amino acids, or other organic moieties. We have successfully used the OBOC method to discover and optimize ligands against unique cell surface receptors of prostate cancer, T- and B-cell lymphoma, as well as ovarian and lung cancers, and we have used some of these peptides to image xenografts in nude mice with high specificity. Here, we (i) review the literature on the use of phage-display and OBOC combinatorial library methods to discover cancer and tumor blood vessel targeting ligands, and (ii) report on the use of an ovarian cancer targeting ligand, OA02, as an in vivo PET imaging probe in a xenograft model in nude mice.
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Affiliation(s)
- Olulanu H Aina
- U.C. Davis Cancer Center, Division of Hematology/Oncology, Department of Internal Medicine, University of California-Davis, 4501 X Street, Sacramento, CA 95817, USA
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Miyashita M, Otake Y, Oda M, Miyagawa H. Development of a high-throughput screening method using a cell-based, lawn format assay for the identification of novel plant defense activators from combinatorial peptide libraries. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2007; 55:806-11. [PMID: 17263478 DOI: 10.1021/jf062930t] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Plants respond to attack by pathogens through various defense mechanisms. These defense responses are triggered by a variety of molecules derived from pathogenic microorganisms as well as host plants. In this study, we developed a high-throughput screening method using a cell-based lawn format assay for the identification of novel peptides that can induce plant defense responses from combinatorial peptide libraries. Solid-phase peptide libraries were synthesized using a photocleavable linker and immobilized using agarose gel. The peptides were partially cleaved from beads, and the agarose gel was layered on the tobacco cells. The defense response was then observed by detecting the generated H2O2 using a sensitive H2O2 indicator dye, N-(carboxymethylaminocarbonyl)-4,4'-bis(dimethylamino)diphenylamine sodium salt (DA-64). Using this assay format, a 6859-member peptide library based on the sequence of flagellin-derived peptides was screened, and several structural features important for the activity were obtained.
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Affiliation(s)
- Masahiro Miyashita
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan.
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28
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Zheng M, Xu C, Ma J, Sun Y, Du F, Liu H, Lin L, Li C, Ding J, Chen K, Jiang H. Synthesis and antitumor evaluation of a novel series of triaminotriazine derivatives. Bioorg Med Chem 2007; 15:1815-27. [PMID: 17157510 DOI: 10.1016/j.bmc.2006.11.028] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2006] [Revised: 11/16/2006] [Accepted: 11/17/2006] [Indexed: 11/19/2022]
Abstract
A series of triaminotriazine derivatives (compounds 5a-f, 6a-x, and 7a-g) was designed, synthesized, and evaluated for their inhibition activities to colorectal cancer (CRC) cell lines (HCT-116 and HT-29). Most of the synthesized compounds demonstrated moderate anti-proliferatory effects on both HCT-116 and HT-29 cell lines at the concentration of 10 microM. The inhibitory activities against HCT-116 and HT-29 cell lines were discussed to develop the structure-activity relationships of this new series. Compounds 6l and 6o exhibited prominent inhibition activities toward HCT-116, with IC50s of 0.76 and 0.92 microM, respectively. The in vivo antitumor studies and pharmacokinetics of compound 6l showed that it might be a promising new hit for further development of antitumor agents.
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Affiliation(s)
- Mingfang Zheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201203, China
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29
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Kumar V, Gupta M, Mahajan MP. Effect of the nature of substituents on aromatic aldehydes in microwave induced N-cyclohexylamidinealdehyde condensation reactions. CAN J CHEM 2006. [DOI: 10.1139/v06-014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A simple, environmentally friendly protocol for the selective synthesis of the 4-aryl substituted acyclic 1,3-dienes and the medicinally potent triazines has been developed using a domestic microwave oven with excellent yields and reproducibility.Key words: microwave, dihydrotriazine, triazine, imine metathesis.
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30
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Affiliation(s)
- Patrick Gamez
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P. O. Box 9502, 2300 RA Leiden, The Netherlands, Fax: + 31‐71‐527‐4671
| | - Jan Reedijk
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P. O. Box 9502, 2300 RA Leiden, The Netherlands, Fax: + 31‐71‐527‐4671
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31
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Navre M. Application of combinatorial chemistry to antimicrobial drug discovery. Expert Opin Investig Drugs 2005; 7:1257-71. [PMID: 15992029 DOI: 10.1517/13543784.7.8.1257] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The emergence of pathogens resistant to currently available treatments is seen as a public health crisis. Since few new classes of antimicrobial drugs have been developed in the last two decades, it is becoming increasingly probable that healthcare providers will be faced with infections for which no chemotherapeutic agent is available. A renewed emphasis is being placed on employing the most advanced drug discovery technologies in the development of new antimicrobials. The recently introduced technologies of combinatorial chemistry offer new sources of chemical diversity, as well as methods with which to produce and rapidly test them. In the last few years, many groups have adopted a number of approaches in order to apply combinatorial chemistry to antimicrobial drug discovery. These combinatorial strategies, and the manner in which they are used to develop new screening formats or to identify new chemical leads are, reviewed.
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Affiliation(s)
- M Navre
- Affymax Research Institute, Santa Clara, CA 95051, USA
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32
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Nikitin S, Zaitseva N, Demina O, Solovieva V, Mazin E, Mikhalev S, Smolov M, Rubinov A, Vlasov P, Lepikhin D, Khachko D, Fokin V, Queen C, Zosimov V. A very large diversity space of synthetically accessible compounds for use with drug design programs. J Comput Aided Mol Des 2005; 19:47-63. [PMID: 16059666 DOI: 10.1007/s10822-005-0097-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2004] [Accepted: 01/03/2005] [Indexed: 10/25/2022]
Abstract
We have constructed a very large virtual diversity space containing more than 10(13) chemical compounds. The diversity space is built from about 400 combinatorial libraries, which have been expanded by choosing sizeable collections of suitable R-groups that can be attached to each link point of their scaffolds. These R-group collections have been created by selecting reagents that have drug-like properties from catalogs of available chemicals. As members of known combinatorial libraries, the compounds in the diversity space are in general synthetically accessible and useful as potential drug leads. Hence, the diversity space can be used as a vast source of compounds by a de novo drug design program. For example, we have used such a program to generate inhibitors of HIV integrase enzyme that exhibited activity in the micromolar range.
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Affiliation(s)
- Sergey Nikitin
- Algodign LLC, Bolshaya Sadovaya 8, Moscow 103001, Russia.
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Marron BE, Jayawickreme CK. Going to the well no more: lawn format assays for ultra-high-throughput screening. Curr Opin Chem Biol 2003; 7:395-401. [PMID: 12826128 DOI: 10.1016/s1367-5931(03)00064-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Screening in a 'well-less' or lawn format provides a means to screen large compound collections against many targets in a fast, versatile and cost effective manner. The development of generic lawn format assays to screen various gene families against large compound collections should facilitate the identification of hits and tools to use in drug discovery and chemogenomic endeavours. Lawn format holds particular promise for screening GPCRs and selected enzyme families with potential use in other gene families.
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Affiliation(s)
- Brian E Marron
- Icagen Inc., 4222 Emperor Blvd, Suite 390, Durham NC 27703, USA.
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35
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Abstract
To address the worsening problem of antibiotic-resistant bacteria there is an urgent need to develop new antibiotics. Comparative genomics and molecular genetics are being applied to produce lists of essential new targets for compound screening programmes. Combinatorial chemistry and structural biology are being applied to rapidly explore and optimize the interactions between lead compounds and their biological targets. Several compounds that have been identified from target-based screens are now in development, but technical and economic constraints might result in a trickle, rather than a flood, of new antibiotics onto the market in the near future.
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Affiliation(s)
- Diarmaid Hughes
- Department of Cell and Molecular Biology, Box 596, The Biomedical Center, Uppsala University, S-751 24 Uppsala, Sweden.
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36
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Lee RE, Protopopova M, Crooks E, Slayden RA, Terrot M, Barry CE. Combinatorial lead optimization of [1,2]-diamines based on ethambutol as potential antituberculosis preclinical candidates. JOURNAL OF COMBINATORIAL CHEMISTRY 2003; 5:172-87. [PMID: 12625709 DOI: 10.1021/cc020071p] [Citation(s) in RCA: 156] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Despite relatively modest potency, ethambutol (EMB, (S,S)-[N,N-di-2-amino-1-butanol]ethylenediamine) is a mainstay of contemporary chemotherapy for the treatment of tuberculosis. We have developed a solid-phase synthesis of 1,2-diamine analogues of EMB using a novel acylation-reduction sequence that is compatible with high-throughput 96-well format chemistry. Using this procedure, we have synthesized 63 238 diamine analogues in pools of 10 that are suitable for testing. MIC and a target-based reporter assay were used to direct deconvolution of 2796 individual compounds from these mixtures, and the 69 most potent molecules were resynthesized in milligram quantities for hit confirmation. Purification of these individual active diamine analogues allowed the identification of 26 compounds with activity equal to or greater than EMB. Amines which occurred most frequently in active compounds included many with large hydrophobic moieties, suggesting that optimization was perhaps selecting for the isoprenoid binding site of the arabinosyltransferase target of EMB. N-Geranyl-N'-(2-adamantyl)ethane-1,2-diamine (109), the most active of these diamines, displayed a 14-35-fold improvement in activity in vitro against Mycobacterium tuberculosis, as compared to EMB.
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Affiliation(s)
- Richard E Lee
- Tuberculosis Research Section, NIAID, National Institutes of Health, Rockville, Maryland 20850, USA
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37
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Bork JT, Lee JW, Khersonsky SM, Moon HS, Chang YT. Novel orthogonal strategy toward solid-phase synthesis of 1,3,5-substituted triazines. Org Lett 2003; 5:117-20. [PMID: 12529119 DOI: 10.1021/ol027195v] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[reaction: see text] To improve upon the previous orthogonal method for synthesis of a triazine library, an alternative strategy has been developed via oxidation-activation of the thioether to the sulfone. Through a comparison between these two methods, the sulfone strategy was demonstrated as an enhanced method in the generation of highly pure triazine library compounds.
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Affiliation(s)
- Jacqueline T Bork
- Department of Chemistry, New York University, New York, New York 10003, USA
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38
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Moon HS, Jacobson EM, Khersonsky SM, Luzung MR, Walsh DP, Xiong W, Lee JW, Parikh PB, Lam JC, Kang TW, Rosania GR, Schier AF, Chang YT. A novel microtubule destabilizing entity from orthogonal synthesis of triazine library and zebrafish embryo screening. J Am Chem Soc 2002; 124:11608-9. [PMID: 12296721 DOI: 10.1021/ja026720i] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The first orthogonal combinatorial synthesis of a high-purity triazine library was demonstrated. Novel triazine-based microtubule inhibitors were discovered by an efficient zebrafish embryo screening and in vitro microtubule polymerization assay.
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Affiliation(s)
- Ho-Sang Moon
- Department of Chemistry, New York University, New York, NY 10003, USA
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39
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Scott CP, Abel-Santos E, Jones AD, Benkovic SJ. Structural requirements for the biosynthesis of backbone cyclic peptide libraries. CHEMISTRY & BIOLOGY 2001; 8:801-15. [PMID: 11514229 DOI: 10.1016/s1074-5521(01)00052-7] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND Combinatorial methods for the production of molecular libraries are an important source of ligand diversity for chemical biology. Synthetic methods focus on the production of small molecules that must traverse the cell membrane to elicit a response. Genetic methods enable intracellular ligand production, but products must typically be large molecules in order to withstand cellular catabolism. Here we describe an intein-based approach to biosynthesis of backbone cyclic peptide libraries that combines the strengths of synthetic and genetic methods. RESULTS Through site-directed mutagenesis we show that the DnaE intein from Synechocystis sp. PCC6803 is very promiscuous with respect to peptide substrate composition, and can generate cyclic products ranging from four to nine amino acids. Libraries with five variable amino acids and either one or four fixed residues were prepared, yielding between 10(7) and 10(8) transformants. The majority of randomly selected clones from each library gave cyclic products. CONCLUSIONS We have developed a versatile method for producing intracellular libraries of small, stable cyclic peptides. Genetic encoding enables facile manipulation of vast numbers of compounds, while low molecular weight ensures ready pharmacophore identification. The demonstrated flexibility of the method towards both peptide length and composition makes it a valuable addition to existing methods for generating ligand diversity.
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Affiliation(s)
- C P Scott
- Department of Chemistry, The Pennsylvania State University, University Park 16802, USA
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40
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Burns DJ, Kofron JL, Warrior U, Beutel BA. Well-less, gel-permeation formats for ultra-HTS. Drug Discov Today 2001. [DOI: 10.1016/s1359-6446(01)00152-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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41
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Dolle RE, Guo J, O'Brien L, Jin Y, Piznik M, Bowman KJ, Li W, Egan WJ, Cavallaro CL, Roughton AL, Zhao Q, Reader JC, Orlowski M, Jacob-Samuel B, Carroll CD. A statistical-based approach to assessing the fidelity of combinatorial libraries encoded with electrophoric molecular tags. Development and application of tag decode-assisted single bead LC/MS analysis. JOURNAL OF COMBINATORIAL CHEMISTRY 2000; 2:716-31. [PMID: 11126300 DOI: 10.1021/cc000052k] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A statistical sampling protocol is described to assess the fidelity of libraries encoded with molecular tags. The methodology, termed library QA, is based on the combined application of tag decode analysis and single bead LC/MS. The physical existence of library compounds eluted from beads is established by comparing the molecular weight predicted by tag decode with empirical measurement. The goal of sampling is to provide information on overall library fidelity and an indication of the performance of individual library synthons. The minimal sampling size n for library QA is l0 x the largest synthon set. Data are reported as proportion (p) +/- lower and upper boundary (lb-ub) computed at the 95% confidence level (alpha = 0.05). As a practical demonstration, library QA was performed on a 25,200-member library of statine amides (size = 40 x 63 x 10). Sampling was conducted three times at n approximately 630 beads per run for a total of 1902 beads. The overall proportions found for the three runs were consistent with one another: p = 84.4%, lb-ub = 81.5-87.2%; p = 83.1%, lb-ub = 80.2-85.95; and p = 84.5%, lb-ub = 81.8-87.3%, suggesting the true value of p is close to 84% compound confirmation. The performance pi of individual synthons was also computed. Corroboration of QA data with biological screening results obtained from assaying the library against cathepsin D and plasmepsin II is discussed.
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Affiliation(s)
- R E Dolle
- Department of Chemistry, and the Center For Informatics and Drug Discovery, Pharmacopeia, Inc, Princeton, New Jersey 08543, USA.
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42
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Dolle RE. Comprehensive survey of combinatorial library synthesis: 1999. JOURNAL OF COMBINATORIAL CHEMISTRY 2000; 2:383-433. [PMID: 11029163 DOI: 10.1021/cc000055x] [Citation(s) in RCA: 136] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- R E Dolle
- Department of Chemistry, Pharmacopeia, Inc., P.O. Box 5350, Princeton, New Jersey 08543-5350, USA.
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Abstract
After a gap of some 30 years, the prospect of finding completely new agents with which to combat infectious disease is promising. New discovery approaches based on the application of genomics and associated technologies are leading to the identification of genes essential for bacterial viability and pathogenesis. This article reviews the current status of the search for new antimicrobial targets and points to future developments and issues.
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Jayawickreme CK, Sauls H, Bolio N, Ruan J, Moyer M, Burkhart W, Marron B, Rimele T, Shaffer J. Use of a cell-based, lawn format assay to rapidly screen a 442,368 bead-based peptide library. J Pharmacol Toxicol Methods 1999; 42:189-97. [PMID: 11033434 DOI: 10.1016/s1056-8719(00)00083-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A cell-based, lawn format assay utilizing an in situ photocleavage method has been developed that allows the rapid examination of large bead-based compound libraries as discrete molecules. The format uses frog melanophore cells in a contiguous, adherent, confluent layer in small petri dishes covered with a 0.5-1-mm layer of agarose containing 130 micron diameter TentaGel beads at a density of 2-20 beads/mm2. Employing this technique a 9-mer, 442,368-member peptide library (designed around the 13 amino acid alpha-MSH peptide sequence) made up of 12 separate pools of 36,864 peptides/pool was assayed. Initially, a fraction (approximately 10%) of each pool was scanned (approximately 3700 beads from each pool) in 60-mm petri dishes to identify the most active pools. Upon direct photocleavage of the beads with UV light (365 nm), each petri dish was photographed over a 60-min period with a CCD camera to record changes in light intensity as an index of melanosome dispersion. Active beads were those that were surrounded by a localized decrease in light transmittance indicating melanosome dispersed cells. Upon examination with a dissecting microscope, single beads centrally located to a circular array of dispersed cells were identified and removed from the agarose and sequenced by Edman degradation to determine the peptide sequence. Re-synthesized peptides were re-examined against alpha-MSH receptor to confirm and quantify the activity. Several 9-mer peptides were identified with potencies similar to the natural 13-mer peptide. This method allows for the rapid screening of large bead-based photo-cleavable peptide libraries with the advantage that each compound is screened as a discrete molecule in a well-less format.
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Affiliation(s)
- C K Jayawickreme
- Department of Receptor Biochemistry, Glaxo Wellcome Research and Development, Research Triangle Park, NC 27709, USA.
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45
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Dolle RE, Nelson KH. Comprehensive survey of combinatorial library synthesis: 1998. JOURNAL OF COMBINATORIAL CHEMISTRY 1999; 1:235-82. [PMID: 10748736 DOI: 10.1021/cc9900192] [Citation(s) in RCA: 243] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- R E Dolle
- Department of Chemistry, Pharmacopeia, Inc., Princeton, New Jersey 08543-5350, USA.
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Boutin JA, Lambert PH, Bertin S, Volland JP, Fauchère JL. Physico-chemical and biological analysis of true combinatorial libraries. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS 1999; 725:17-37. [PMID: 10226875 DOI: 10.1016/s0378-4347(98)00569-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Combinatorial libraries offer new sources of compounds for the research of pharmacological agents such as receptor ligands, enzyme inhibitors or substrates and antibody-binding epitopes. The present review stresses the main roles played by both physico-chemical analysis, particularly when complex mixture of compounds are synthesized as libraries, and biological analysis from which active compounds are identified. After a brief discussion of semantic problems related to the designation of the product mixtures, the physico-chemical analysis of mixtures is reviewed with special emphasis on mass spectrometric techniques. These methods are able both to give a representative view of a library composition and to identify single critical compounds in large libraries. Then the biological screening of such combinatorial libraries is critically discussed with respect to the power and limitations of the methods used for the identification of the active components. Special attention is given to the complex process of library deconvolution. It is pointed out that while combinatorial techniques have evolved towards sophisticated high-tech methods, simple and robust biochemical tests should be used to deconvolute. From a large panel of published examples, a set of trends are identified which should help investigators to choose the most appropriate assay for the discovery of new entities.
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Affiliation(s)
- J A Boutin
- Department of Molecular and Cellular Pharmacology, Institut de Recherches SERVIER, Croissy-sur-Seine, France
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