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Yang J, Cai Y, Zhao K, Xie H, Chen X. Concepts and applications of chemical fingerprint for hit and lead screening. Drug Discov Today 2022; 27:103356. [PMID: 36113834 DOI: 10.1016/j.drudis.2022.103356] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 07/28/2022] [Accepted: 09/08/2022] [Indexed: 11/22/2022]
Abstract
Molecular fingerprints are used to represent chemical (structural, physicochemical, etc.) properties of large-scale chemical sets in a low computational cost way. They have a prominent role in transforming chemical data sets into consistent input formats (bit strings or numeric values) suitable for in silico approaches. In this review, we summarize and classify common and state-of-the-art fingerprints into eight different types (dictionary based, circular, topological, pharmacophore, protein-ligand interaction, shape based, reinforced, and multi). We also highlight applications of fingerprints in early drug research and development (R&D). Thus, this review provides a guide for the selection of appropriate fingerprints of compounds (or ligand-protein complexes) for use in drug R&D.
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Affiliation(s)
- Jingbo Yang
- Department of Pharmagenomics, College of Bioinformatics Science and Technology, Harbin Medical University, 150081 Harbin, Heilongjiang, China
| | - Yiyang Cai
- Department of Pharmagenomics, College of Bioinformatics Science and Technology, Harbin Medical University, 150081 Harbin, Heilongjiang, China
| | - Kairui Zhao
- Department of Pharmagenomics, College of Bioinformatics Science and Technology, Harbin Medical University, 150081 Harbin, Heilongjiang, China
| | - Hongbo Xie
- Department of Pharmagenomics, College of Bioinformatics Science and Technology, Harbin Medical University, 150081 Harbin, Heilongjiang, China.
| | - Xiujie Chen
- Department of Pharmagenomics, College of Bioinformatics Science and Technology, Harbin Medical University, 150081 Harbin, Heilongjiang, China.
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Aeluri M, Pramanik C, Chetia L, Mallurwar NK, Balasubramanian S, Chandrasekar G, Kitambi SS, Arya P. 14-Membered Macrocyclic Ring-Derived Toolbox: The Identification of Small Molecule Inhibitors of Angiogenesis and Early Embryo Development in Zebrafish Assay. Org Lett 2013; 15:436-9. [DOI: 10.1021/ol3032126] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Madhu Aeluri
- Dr. Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 607, India, School of Life Sciences, Södertörns Högskola, Sweden, and Department of Biosciences and Medical Nutrition and Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Sweden
| | - Chinmoy Pramanik
- Dr. Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 607, India, School of Life Sciences, Södertörns Högskola, Sweden, and Department of Biosciences and Medical Nutrition and Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Sweden
| | - Lakshindra Chetia
- Dr. Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 607, India, School of Life Sciences, Södertörns Högskola, Sweden, and Department of Biosciences and Medical Nutrition and Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Sweden
| | - Naveen Kumar Mallurwar
- Dr. Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 607, India, School of Life Sciences, Södertörns Högskola, Sweden, and Department of Biosciences and Medical Nutrition and Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Sweden
| | - Sridhar Balasubramanian
- Dr. Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 607, India, School of Life Sciences, Södertörns Högskola, Sweden, and Department of Biosciences and Medical Nutrition and Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Sweden
| | - Gayathri Chandrasekar
- Dr. Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 607, India, School of Life Sciences, Södertörns Högskola, Sweden, and Department of Biosciences and Medical Nutrition and Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Sweden
| | - Satish Srinivas Kitambi
- Dr. Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 607, India, School of Life Sciences, Södertörns Högskola, Sweden, and Department of Biosciences and Medical Nutrition and Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Sweden
| | - Prabhat Arya
- Dr. Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad 500046, India, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 607, India, School of Life Sciences, Södertörns Högskola, Sweden, and Department of Biosciences and Medical Nutrition and Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Sweden
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Kantevari S, Patpi SR, Addla D, Putapatri SR, Sridhar B, Yogeeswari P, Sriram D. Facile diversity-oriented synthesis and antitubercular evaluation of novel aryl and heteroaryl tethered pyridines and dihydro-6H-quinolin-5-ones derived via variants of the Bohlmann-Rahtz Reaction. ACS COMBINATORIAL SCIENCE 2011; 13:427-35. [PMID: 21699150 DOI: 10.1021/co2000604] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The diversity oriented synthesis of substituted pyridines and dihydro-6H-quinolin-5-ones tethered with aryls and heteroaryls was achieved in very good yields through CeCl(3)·7H(2)O-NaI catalyst via variants of the Bohlmann-Rahtz reaction. β-Enaminones derived from various aryl and heteroaryl methyl ketones were regioselectively reacted with ethyl acetoacetate or 5,5-dimethylcyclohexane-1,3-dione or 4,4-dimethylcyclohexane-1,3-dione and ammonium acetate refluxing in 2-propanol. Applicability of nontoxic cerium catalyst, high reactivity with wide range of aryl and heteroaryl β-enaminones leading to diverse analogues, operational simplicity, and shorter reaction time at comparatively low temperatures are prominent features of the developed protocol. These synthesized substituted pyridines and dihydro-6H-quinolin-5-one analogues have been evaluated for their in vitro antimycobacterial activity against Mycobacterium tuberculosis H37Rv (MTB) by agar dilution method. Among the 48 compounds screened, six compounds 2-(5-chlorothiophen-2-yl)-7,7-dimethyl-7,8-dihydro-6H-quinolin-5-one 4{13,2}, 2-(5-bromothiophen-2-yl)-7,7-dimethyl-7,8-dihydro-6H-quinolin-5-one 4{14,2}, 2-(5-chloro thiophen-2-yl)-6,6-dimethyl-7,8-dihydroquinolin-5(6H)-one 4{13,3}, and 2-(5-bromothiophen-2-yl)-6,6-dimethyl-7,8-dihydroquinolin-5(6H)-one 4{14,3}, 7,7-dimethyl-2-(naphthalen-2-yl)-7,8-dihydroquinoline-5(6H)-one 4{6,2}, 6,6-dimethyl-2-(naphthalen-2-yl)-7,8-di hydroquinolin-5(6H)-one 4{6,3} resulted as the most promising antitubercular agents.
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Affiliation(s)
| | | | | | | | | | - Perumal Yogeeswari
- Medicinal Chemistry and Antimycobacterial Research Laboratory, Pharmacy Group, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Jawahar Nagar, Hyderabad-500078, India
| | - Dharmarajan Sriram
- Medicinal Chemistry and Antimycobacterial Research Laboratory, Pharmacy Group, Birla Institute of Technology & Science-Pilani, Hyderabad Campus, Jawahar Nagar, Hyderabad-500078, India
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Isidro-Llobet A, Murillo T, Bello P, Cilibrizzi A, Hodgkinson JT, Galloway WRJD, Bender A, Welch M, Spring DR. Diversity-oriented synthesis of macrocyclic peptidomimetics. Proc Natl Acad Sci U S A 2011; 108:6793-8. [PMID: 21383137 PMCID: PMC3084124 DOI: 10.1073/pnas.1015267108] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Structurally diverse libraries of novel small molecules represent important sources of biologically active agents. In this paper we report the development of a diversity-oriented synthesis strategy for the generation of diverse small molecules based around a common macrocyclic peptidomimetic framework, containing structural motifs present in many naturally occurring bioactive compounds. Macrocyclic peptidomimetics are largely underrepresented in current small-molecule screening collections owing primarily to synthetic intractability; thus novel molecules based around these structures represent targets of significant interest, both from a biological and a synthetic perspective. In a proof-of-concept study, the synthesis of a library of 14 such compounds was achieved. Analysis of chemical space coverage confirmed that the compound structures indeed occupy underrepresented areas of chemistry in screening collections. Crucial to the success of this approach was the development of novel methodologies for the macrocyclic ring closure of chiral α-azido acids and for the synthesis of diketopiperazines using solid-supported N methylmorpholine. Owing to their robust and flexible natures, it is envisaged that both new methodologies will prove to be valuable in a wider synthetic context.
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Affiliation(s)
- Albert Isidro-Llobet
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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Nandy JP, Prakesch M, Khadem S, Reddy PT, Sharma U, Arya P. Advances in Solution- and Solid-Phase Synthesis toward the Generation of Natural Product-like Libraries. Chem Rev 2009; 109:1999-2060. [DOI: 10.1021/cr800188v] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Jyoti P. Nandy
- Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Toronto, Ontario M5G 1L7, Canada, Steacie Institute for Molecular Sciences, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada, and Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Michael Prakesch
- Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Toronto, Ontario M5G 1L7, Canada, Steacie Institute for Molecular Sciences, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada, and Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Shahriar Khadem
- Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Toronto, Ontario M5G 1L7, Canada, Steacie Institute for Molecular Sciences, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada, and Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - P. Thirupathi Reddy
- Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Toronto, Ontario M5G 1L7, Canada, Steacie Institute for Molecular Sciences, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada, and Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Utpal Sharma
- Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Toronto, Ontario M5G 1L7, Canada, Steacie Institute for Molecular Sciences, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada, and Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Prabhat Arya
- Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Toronto, Ontario M5G 1L7, Canada, Steacie Institute for Molecular Sciences, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada, and Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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Beghyn T, Deprez-Poulain R, Willand N, Folleas B, Deprez B. Natural compounds: leads or ideas? Bioinspired molecules for drug discovery. Chem Biol Drug Des 2008; 72:3-15. [PMID: 18554253 DOI: 10.1111/j.1747-0285.2008.00673.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this article, we compare drugs of natural origin to synthetic compounds and analyze the reasons why natural compounds occupy a place of choice in the current pharmacopoeia. The observations reported here support the design of synthetic compounds inspired from plant alkaloids and their biosynthetic pathway. Our reasoning leads to very efficient syntheses of compounds which complexity matches that of indolomonoterpenic alkaloids.
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Affiliation(s)
- Terence Beghyn
- INSERM U761, Biostructures and Drug Discovery, Lille, F-59006, France
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Ramana CV, Nageswara Reddy C, Gonnade RG. An expeditious one-step entry to the tetracyclic core of integrastatins. Chem Commun (Camb) 2008:3151-3. [DOI: 10.1039/b801755g] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Glen R, Adams S. Similarity Metrics and Descriptor Spaces – Which Combinations to Choose? ACTA ACUST UNITED AC 2006. [DOI: 10.1002/qsar.200610097] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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