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John L, Nagamani S, Mahanta HJ, Vaikundamani S, Kumar N, Kumar A, Jamir E, Priyadarsinee L, Sastry GN. Molecular Property Diagnostic Suite Compound Library (MPDS-CL): a structure-based classification of the chemical space. Mol Divers 2023:10.1007/s11030-023-10752-1. [PMID: 37902900 DOI: 10.1007/s11030-023-10752-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 10/17/2023] [Indexed: 11/01/2023]
Abstract
Molecular Property Diagnostic Suite Compound Library (MPDS-CL) is an open-source Galaxy-based cheminformatics web portal which presents a structure-based classification of the molecules. A structure-based classification of nearly 150 million unique compounds, obtained from 42 publicly available databases and curated for redundancy removal through 97 hierarchically well-defined atom composition-based portions, has been done. These are further subjected to 56-bit fingerprint-based classification algorithm which led to the formation of 56 structurally well-defined classes. The classes thus obtained were further divided into clusters based on their molecular weight. Thus, the entire set of molecules was put into 56 different classes and 625 clusters. This led to the assignment of a unique ID, named as MPDS-AadharID, for each of these 149,169,443 molecules. MPDS-AadharID is akin to the unique number given to citizens in India (similar to SSN in the US and NINO in the UK). The unique features of MPDS-CL are (a) several search options, such as exact structure search, substructure search, property-based search, fingerprint-based search, using SMILES, InChIKey and key-in; (b) automatic generation of information for the processing for MPDS and other galaxy tools; (c) providing the class and cluster of a molecule which makes it easier and fast to search for similar molecules and (d) information related to the presence of the molecules in multiple databases. The MPDS-CL can be accessed at https://mpds.neist.res.in:8086/ .
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Affiliation(s)
- Lijo John
- Advanced Computation and Data Sciences Division, CSIR - North East Institute of Science and Technology, Jorhat, 785006, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Selvaraman Nagamani
- Advanced Computation and Data Sciences Division, CSIR - North East Institute of Science and Technology, Jorhat, 785006, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Hridoy Jyoti Mahanta
- Advanced Computation and Data Sciences Division, CSIR - North East Institute of Science and Technology, Jorhat, 785006, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - S Vaikundamani
- Advanced Computation and Data Sciences Division, CSIR - North East Institute of Science and Technology, Jorhat, 785006, India
| | - Nandan Kumar
- Advanced Computation and Data Sciences Division, CSIR - North East Institute of Science and Technology, Jorhat, 785006, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Asheesh Kumar
- Advanced Computation and Data Sciences Division, CSIR - North East Institute of Science and Technology, Jorhat, 785006, India
| | - Esther Jamir
- Advanced Computation and Data Sciences Division, CSIR - North East Institute of Science and Technology, Jorhat, 785006, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Lipsa Priyadarsinee
- Advanced Computation and Data Sciences Division, CSIR - North East Institute of Science and Technology, Jorhat, 785006, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - G Narahari Sastry
- Advanced Computation and Data Sciences Division, CSIR - North East Institute of Science and Technology, Jorhat, 785006, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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2
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Lyu J, Irwin JJ, Shoichet BK. Modeling the expansion of virtual screening libraries. Nat Chem Biol 2023; 19:712-718. [PMID: 36646956 PMCID: PMC10243288 DOI: 10.1038/s41589-022-01234-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/22/2022] [Indexed: 01/17/2023]
Abstract
Recently, 'tangible' virtual libraries have made billions of molecules readily available. Prioritizing these molecules for synthesis and testing demands computational approaches, such as docking. Their success may depend on library diversity, their similarity to bio-like molecules and how receptor fit and artifacts change with library size. We compared a library of 3 million 'in-stock' molecules with billion-plus tangible libraries. The bias toward bio-like molecules in the tangible library decreases 19,000-fold versus those 'in-stock'. Similarly, thousands of high-ranking molecules, including experimental actives, from five ultra-large-library docking campaigns are also dissimilar to bio-like molecules. Meanwhile, better-fitting molecules are found as the library grows, with the score improving log-linearly with library size. Finally, as library size increases, so too do rare molecules that rank artifactually well. Although the nature of these artifacts changes from target to target, the expectation of their occurrence does not, and simple strategies can minimize their impact.
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Affiliation(s)
- Jiankun Lyu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - John J Irwin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA.
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA.
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3
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Uygun Cebeci Y, Ceylan Ş, Altun M, Alpay Karaoğlu Ş. Synthesis and Characterization of Some Azole Derivatives as Potential Biological and Anticancer Agents. ChemistrySelect 2023. [DOI: 10.1002/slct.202300385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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4
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Young RJ, Flitsch SL, Grigalunas M, Leeson PD, Quinn RJ, Turner NJ, Waldmann H. The Time and Place for Nature in Drug Discovery. JACS AU 2022; 2:2400-2416. [PMID: 36465532 PMCID: PMC9709949 DOI: 10.1021/jacsau.2c00415] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/06/2022] [Accepted: 10/06/2022] [Indexed: 05/31/2023]
Abstract
The case for a renewed focus on Nature in drug discovery is reviewed; not in terms of natural product screening, but how and why biomimetic molecules, especially those produced by natural processes, should deliver in the age of artificial intelligence and screening of vast collections both in vitro and in silico. The declining natural product-likeness of licensed drugs and the consequent physicochemical implications of this trend in the context of current practices are noted. To arrest these trends, the logic of seeking new bioactive agents with enhanced natural mimicry is considered; notably that molecules constructed by proteins (enzymes) are more likely to interact with other proteins (e.g., targets and transporters), a notion validated by natural products. Nature's finite number of building blocks and their interactions necessarily reduce potential numbers of structures, yet these enable expansion of chemical space with their inherent diversity of physical characteristics, pertinent to property-based design. The feasible variations on natural motifs are considered and expanded to encompass pseudo-natural products, leading to the further logical step of harnessing bioprocessing routes to access them. Together, these offer opportunities for enhancing natural mimicry, thereby bringing innovation to drug synthesis exploiting the characteristics of natural recognition processes. The potential for computational guidance to help identifying binding commonalities in the route map is a logical opportunity to enable the design of tailored molecules, with a focus on "organic/biological" rather than purely "synthetic" structures. The design and synthesis of prototype structures should pay dividends in the disposition and efficacy of the molecules, while inherently enabling greener and more sustainable manufacturing techniques.
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Affiliation(s)
| | - Sabine L. Flitsch
- Department
of Chemistry, University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Michael Grigalunas
- Department
of Chemical Biology, Max-Planck-Institute
of Molecular Physiology, Otto-Hahn Strasse 11, 44227 Dortmund, Germany
| | - Paul D. Leeson
- Paul
Leeson Consulting Limited, The Malt House, Main Street, Congerstone, Nuneaton, Warwickshire CV13 6LZ, U.K.
| | - Ronald J. Quinn
- Griffith
Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Nicholas J. Turner
- Department
of Chemistry, University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Herbert Waldmann
- Department
of Chemical Biology, Max-Planck-Institute
of Molecular Physiology, Otto-Hahn Strasse 11, 44227 Dortmund, Germany
- Faculty of
Chemistry and Chemical Biology, Technical
University of Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
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5
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Samala R, Kumar Nukala S, Swamy Thirukovela N, Reddy Nagavelli V, Narsimha S. Cu(I)‐Catalyzed One‐Pot Synthesis of [1,2,3]Triazolo[5,1‐
a
] isoquinolin‐6(5H)‐one Derivatives as EGFR‐Targeting Anticancer Agents. ChemistrySelect 2022. [DOI: 10.1002/slct.202203388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Rajkumar Samala
- Department of Chemistry Chaitanya (Deemed to be University) Warangal Telangana India
| | - Satheesh Kumar Nukala
- Department of Chemistry Chaitanya (Deemed to be University) Warangal Telangana India
| | | | | | - Sirassu Narsimha
- Department of Chemistry Chaitanya (Deemed to be University) Warangal Telangana India
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N MK, Nukala SK, Thirukovela NS, Sreerama R, E RS, Kamarajugadda P, Narsimha S. Ramachary-Bressy-Wang [3+2]cycloaddition reaction: Synthesis of fully decorated 1,2,3-triazoles as potent anticancer and EGFR inhibitors. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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7
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Kumar N M, Nukala SK, Swamy T N, M R, Krishna TM, Narsimha S. Benzothiazole-[1,2,3]triazolo[5,1-a]isoindoles: Synthesis, anticancer activity, bioavailability and in silico studies against Gama-Tubulin protein. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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8
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Karthik B, Swamy TN, Kumar AK, Ravinder M, Nukala SK. One-Pot Regioselective Synthesis of 7-Bromo-2H-Benzo[b][1,4]Oxazin-3(4H)-One Linked Isoxazole Hybrids as Anti-Cancer Agents and Their Molecular Docking Studies. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021060091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Bile-Acid-Appended Triazolyl Aryl Ketones: Design, Synthesis, In Vitro Anticancer Activity and Pharmacokinetics in Rats. Molecules 2021; 26:molecules26195741. [PMID: 34641285 PMCID: PMC8510344 DOI: 10.3390/molecules26195741] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/17/2021] [Accepted: 09/17/2021] [Indexed: 11/27/2022] Open
Abstract
A library of bile-acid-appended triazolyl aryl ketones was synthesized and characterized by detailed spectroscopic techniques such as 1H and 13C NMR, HRMS and HPLC. All the synthesized conjugates were evaluated for their cytotoxicity at 10 µM against MCF-7 (human breast adenocarcinoma) and 4T1 (mouse mammary carcinoma) cells. In vitro cytotoxicity studies on the synthesized conjugates against MCF-7 and 4T1 cells indicated one of the conjugate 6cf to be most active against both cancer cell lines, with IC50 values of 5.71 µM and 8.71 µM, respectively, as compared to the reference drug docetaxel, possessing IC50 values of 9.46 µM and 13.85 µM, respectively. Interestingly, another compound 6af (IC50 = 2.61 µM) was found to possess pronounced anticancer activity as compared to the reference drug docetaxel (IC50 = 9.46 µM) against MCF-7. In addition, the potent compounds (6cf and 6af) were found to be non-toxic to normal human embryonic kidney cell line (HEK 293), as evident from their cell viability of greater than 86%. Compound 6cf induces higher apoptosis in comparison to 6af (46.09% vs. 33.89%) in MCF-7 cells, while similar apoptotic potential was observed for 6cf and 6af in 4T1 cells. The pharmacokinetics of 6cf in Wistar rats showed an MRT of 8.47 h with a half-life of 5.63 h. Clearly, these results suggest 6cf to be a potential candidate for the development of anticancer agents.
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Sagam RR, Nukala SK, Nagavath R, Sirassu N, Gundepaka P, Manchal R, Thirukovela NS. In‐vitro Anticancer and Molecular Docking Studies of 4‐Azaindole‐1,2,4‐Oxadiazole Hybrids. ChemistrySelect 2021. [DOI: 10.1002/slct.202101820] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Ravikumar Reddy Sagam
- Department of Chemistry Chaitanya (Deemed to be University) Warangal Telangana India
| | - Satheesh Kumar Nukala
- Department of Chemistry Chaitanya (Deemed to be University) Warangal Telangana India
| | - Rajkumar Nagavath
- Department of Chemistry Chaitanya (Deemed to be University) Warangal Telangana India
| | - Narsimha Sirassu
- Department of Chemistry Chaitanya (Deemed to be University) Warangal Telangana India
| | - Prasad Gundepaka
- Centre for Pharmaceutical Science Jawaharlal Nehru Technlogical University Hyderabad India
| | - Ravinder Manchal
- Department of Chemistry Chaitanya (Deemed to be University) Warangal Telangana India
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11
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Endoori S, Gulipalli KC, Bodige S, Ravula P, Seelam N. Design, synthesis, anticancer activity, and in silico studies of novel imidazo[1,2‐
a
]pyridine based
1
H
‐1,2,3‐triazole derivatives. J Heterocycl Chem 2021. [DOI: 10.1002/jhet.4259] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Srinivas Endoori
- Department of Chemistry Koneru Lakshmaiah Education Foundation Guntur India
| | | | - Srinu Bodige
- Department of Chemistry Koneru Lakshmaiah Education Foundation Guntur India
| | - Parameshwar Ravula
- Department of Pharmaceutical Chemistry, Guru Nanak Institutions Technical Campus, School of Pharmacy Jawaharlal Nehru Technological University Hyderabad India
| | - Nareshvarma Seelam
- Department of Chemistry Koneru Lakshmaiah Education Foundation Guntur India
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12
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Thirukovela NS, Nukala SK, Sirassu N, Manchal R, Gundepaka P, Paidakula S. Design and Synthesis of Some Novel Aromatic Amide Derivatives of Nilutamide as In Vitro Anticancer Agents. ChemistrySelect 2020. [DOI: 10.1002/slct.202002786] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | | | - Narsimha Sirassu
- Department of Chemistry Chaitanya Deemed to be University Warangal Telangana India
| | - Ravinder Manchal
- Department of Chemistry Chaitanya Deemed to be University Warangal Telangana India
| | | | - Suresh Paidakula
- Akshaj Molecular Research Private Ltd Uppal Hyderabad, Telanagna India
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13
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Battula KS, Narsimha S, Thatipamula RK, Reddy YN, Nagavelli VR. Synthesis and Biological Evaluation of (N-(3-methoxyphenyl)-4-((aryl-1H
-1,2,3-triazol-4-yl)methyl)thiomorpholine-2-carboxamide 1,1-Dioxide Hybrids as Antiproliferative Agents. ChemistrySelect 2017. [DOI: 10.1002/slct.201701902] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Sirassu Narsimha
- Department of Chemistry; Kakatiya University; Warangal-506009, Telangana India
| | | | - Yellu Narsimha Reddy
- Department of Pharmacology and Toxicology; Kakatiya University; Warangal-506009, Telangana India
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14
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Mali PR, Shirsat PK, Khomane N, Nayak L, Nanubolu JB, Meshram HM. 1,3-Dipolar Cycloaddition Reactions for the Synthesis of Novel Oxindole Derivatives and Their Cytotoxic Properties. ACS COMBINATORIAL SCIENCE 2017; 19:633-639. [PMID: 28816439 DOI: 10.1021/acscombsci.7b00044] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The multicomponent reaction between isatin, amino acid, but-2-ynedioates, and phenacyl bromide has been developed using microwave irradiation under catalyst and base-free conditions in aqueous medium. This synthetic protocol is useful for the synthesis of various functionalized spirooxindole derivatives. This MCR exhibits a broad substrate scope with excellent yields and shorter reaction time. Additionally the synthesized spirooxindole derivatives were evaluated for their anticancer activity against three human cancer cell lines: MCF-7 (breast), A549 (lung), and HeLa cervical. Most of the compounds showed moderate to potent cytotoxic activity against the tested cell lines.
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Affiliation(s)
- Prakash R. Mali
- Medicinal
Chemistry and Biotechnology Division, CSIR-Indian Institute of Chemical Technology Hyderabad 500 007, India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi 110020, India
| | - Prashishkumar K. Shirsat
- Medicinal
Chemistry and Biotechnology Division, CSIR-Indian Institute of Chemical Technology Hyderabad 500 007, India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi 110020, India
| | - Navnath Khomane
- Medicinal
Chemistry and Biotechnology Division, CSIR-Indian Institute of Chemical Technology Hyderabad 500 007, India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi 110020, India
| | - Lakshama Nayak
- Medicinal
Chemistry and Biotechnology Division, CSIR-Indian Institute of Chemical Technology Hyderabad 500 007, India
| | - Jagadeesh Babu Nanubolu
- Laboratory
of X-ray Crystallography, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500007, India
| | - H. M. Meshram
- Medicinal
Chemistry and Biotechnology Division, CSIR-Indian Institute of Chemical Technology Hyderabad 500 007, India
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15
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Battula KS, Narsimha S, Thatipamula RK, Reddy YN, Nagavelli VR. Synthesis and Biological Evaluation of Novel Thiomorpholine 1,1-Dioxide Derived 1,2,3-Triazole Hybrids as Potential Anticancer Agents. ChemistrySelect 2017. [DOI: 10.1002/slct.201700524] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Sirassu Narsimha
- Department of Chemistry; Kakatiya University; Warangal-506009, Telangana India
| | | | - Yellu Narsimha Reddy
- Department of Pharmacology and Toxicology; Kakatiya University; Warangal-506009, Telangana India
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16
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Garcia-Castro M, Zimmermann S, Sankar MG, Kumar K. Gerüstdiversitätsbasierte Synthese und ihre Anwendung bei der Sonden- und Wirkstoffsuche. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201508818] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Miguel Garcia-Castro
- Abteilung Chemische Biologie; Max-Planck-Institut für molekulare Physiologie; Otto-Hahn-Straße 11 44227 Dortmund Deutschland
| | - Stefan Zimmermann
- Abteilung Chemische Biologie; Max-Planck-Institut für molekulare Physiologie; Otto-Hahn-Straße 11 44227 Dortmund Deutschland
| | - Muthukumar G. Sankar
- Abteilung Chemische Biologie; Max-Planck-Institut für molekulare Physiologie; Otto-Hahn-Straße 11 44227 Dortmund Deutschland
| | - Kamal Kumar
- Abteilung Chemische Biologie; Max-Planck-Institut für molekulare Physiologie; Otto-Hahn-Straße 11 44227 Dortmund Deutschland
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17
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Garcia-Castro M, Zimmermann S, Sankar MG, Kumar K. Scaffold Diversity Synthesis and Its Application in Probe and Drug Discovery. Angew Chem Int Ed Engl 2016; 55:7586-605. [DOI: 10.1002/anie.201508818] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Revised: 01/19/2016] [Indexed: 01/19/2023]
Affiliation(s)
- Miguel Garcia-Castro
- Department of Chemical Biology; Max Planck Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Stefan Zimmermann
- Department of Chemical Biology; Max Planck Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Muthukumar G. Sankar
- Department of Chemical Biology; Max Planck Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Kamal Kumar
- Department of Chemical Biology; Max Planck Institute of Molecular Physiology; Otto-Hahn-Strasse 11 44227 Dortmund Germany
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18
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Narsimha S, Satheesh Kumar N, Kumara Swamy B, Vasudeva Reddy N, Althaf Hussain S, Srinivasa Rao M. Indole-2-carboxylic acid derived mono and bis 1,4-disubstituted 1,2,3-triazoles: Synthesis, characterization and evaluation of anticancer, antibacterial, and DNA-cleavage activities. Bioorg Med Chem Lett 2016; 26:1639-1644. [DOI: 10.1016/j.bmcl.2016.01.055] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 12/10/2015] [Accepted: 01/20/2016] [Indexed: 10/22/2022]
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19
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Indolylmethylene benzo[h]thiazolo[2,3-b]quinazolinones: synthesis, characterization and evaluation of anticancer and antimicrobial activities. Bioorg Med Chem Lett 2014; 24:4239-42. [PMID: 25096298 DOI: 10.1016/j.bmcl.2014.07.030] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 06/23/2014] [Accepted: 07/11/2014] [Indexed: 01/25/2023]
Abstract
A series of novel 10-((1H-indol-3-yl)methylene)-7-aryl-7,10-dihydro-5H-benzo[h]thiazolo[2,3-b]quinazolin-9(6H)-ones (8a-t) have been synthesized in good yields by the reaction of benzo[h]quinazoline-2(1H)-thiones (4a-f) with 2-chloro-N-phenylacetamide (5) followed by Knoevenagel condensation with various indole-3-carbaldehydes (7a-d) under conventional method. All the synthesized compounds were characterized by spectral studies and screened for their in vitro anticancer and antimicrobial activities. Compound 8c has exhibited excellent activity against MCF-7 (breast cancer cell line) than the standard drug Doxorubicin. Compound 8d against both the cancer cell lines, 8q against MCF-7 and 8c, 8h against HepG2 have also shown good activity. Remaining compounds have shown moderate activity against both the cell lines. Antimicrobial activity revealed that, the compound 8q and 8t against Staphylococcus aureus and 8i, 8k, 8l, 8q &8t against Klebsiella pneumoniae have shown equipotent activity on comparing with the standard drug Streptomycin. Remaining compounds have shown significant antibacterial and comparable antifungal activities against all the tested microorganisms.
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Cragg GM, Grothaus PG, Newman DJ. New horizons for old drugs and drug leads. JOURNAL OF NATURAL PRODUCTS 2014; 77:703-23. [PMID: 24499205 DOI: 10.1021/np5000796] [Citation(s) in RCA: 168] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
There is mounting urgency to find new drugs for the treatment of serious infectious diseases and cancer that are rapidly developing resistance to previously effective drugs. One approach to addressing this need is through drug repurposing, which refers to the discovery of new useful activities for "old" clinically used drugs through screening them against relevant disease targets. A large number of potential drug that, for various reasons, have failed to advance to clinical and commercial use can be added to the candidates available for such purposes. The application of new techniques and methodology developed through the impressive progress made in multidisciplinary, natural product-related research in recent years should aid substantially in expediting the discovery and development process. This review briefly outlines some of these developments as applied to a number of selected natural product examples, which may also include advances in chemical synthesis of derivatives with extended biological activities.
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Affiliation(s)
- Gordon M Cragg
- Natural Products Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, Frederick National Laboratory , P.O. Box B, Frederick, Maryland 21702, United States
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SPF32629A and SPF32629B: enantioselective synthesis, determination of absolute configuration, cytotoxicity and antibacterial evaluation. Eur J Med Chem 2011; 46:1803-12. [PMID: 21397370 DOI: 10.1016/j.ejmech.2011.02.039] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Revised: 02/14/2011] [Accepted: 02/15/2011] [Indexed: 11/23/2022]
Abstract
We report herein an efficient enantioselective synthesis of SPF32629A and SPF32629B through one-pot enantioselective reduction and protecting-group-free regioselective O-acylation strategy. The absolute configuration of the enantiomerically pure isomers was established by Mosher ester analysis. The inhibitory potencies of the synthesized compounds were assayed in vitro against a panel of microorganisms and against A549 human lung adenocarcinoma cell line. Compounds 2, 11 and 12 displayed moderate to potent antibacterial activity against all the tested strains and compounds 7, 8, 2, 11 and 12 exhibited significant cytotoxicity in a dose-dependent manner with an IC50 values ranging from 2.92 to 4.14 μg/ml and 8-11 μM.
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Drewry DH, Macarron R. Enhancements of screening collections to address areas of unmet medical need: an industry perspective. Curr Opin Chem Biol 2010; 14:289-98. [PMID: 20413343 DOI: 10.1016/j.cbpa.2010.03.024] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Revised: 02/19/2010] [Accepted: 03/24/2010] [Indexed: 01/31/2023]
Abstract
The past 20 years have witnessed an impressive expansion of the 'drug space'; defined as the intersection of the Medicinal Chemistry space and the Biologically Active space relevant in the quest for new treatments for disease. Despite the success of known lead discovery tactics, areas of unmet medical need are often linked to challenging or novel targets and are poorly served by current screening collections. A successful strategy to fill the gaps is to diversify the approaches taken in the enhancement of screening collections. Possible strategies include investments through proven methods, exploring areas of chemical space previously neglected (e.g. hydrophilic compounds, natural product mimics), and applying tactics to the lead discovery process that are complementary to HTS (e.g. fragment based screening or multidisciplinary team efforts to tackle new target classes).
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Affiliation(s)
- David H Drewry
- Molecular Discovery Research, GlaxoSmithKline, 5 Moore Drive, Research Triangle Park, NC 27709, USA.
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23
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Jenkins ID, Lacrampe F, Ripper J, Alcaraz L, Le PV, Nikolakopoulos G, de Almeida Leone P, White RH, Quinn RJ. Synthesis of four novel natural product inspired scaffolds for drug discovery. J Org Chem 2009; 74:1304-13. [PMID: 19105637 DOI: 10.1021/jo802456w] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Inspired by the novel spiro structures of a number of bioactive natural products such as the histrionicotoxins, a series of novel spiro scaffolds have been designed and robust syntheses developed. The scaffolds are ready-to-use building blocks and can be easily prepared on a 5-20 g scale. They contain two amino groups (one Boc-protected) and have been designed for ease of conversion to a lead generation library, using either amide formation or reductive amination procedures. The synthesis of the 1,9-diazaspiro[5.5]undecane and 3,7-diazaspiro[5.6]dodecane ring systems was achieved using RCM as the key step. A simple workup procedure is reported for the removal of highly colored ruthenium residues. The synthesis of the 1,8-diazaspiro[4.5]decane scaffold has been achieved using a bromine-mediated 5-endo cyclization of the corresponding 4-aminobutene intermediate under acidic conditions. This is the first example of this type of cyclization to be reported. A novel mechanism involving a bromine transfer reaction from an initially formed bromonium ion to a neighboring nitrogen atom is suggested as the reason for the failure of this type of reaction under "normal" bromination conditions. An unusual rearrangement of a 1-acyl-1,9-diazaspiro[5.5]undecane to the corresponding 9-acyl-1,9-diazaspiro[5.5]undecane is reported.
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Affiliation(s)
- Ian D Jenkins
- Eskitis Institute, Griffith University, Brisbane, QLD, 4111, Australia.
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24
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Lindell SD, Pattenden LC, Shannon J. Combinatorial chemistry in the agrosciences. Bioorg Med Chem 2009; 17:4035-46. [DOI: 10.1016/j.bmc.2009.03.027] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2008] [Revised: 03/05/2009] [Accepted: 03/13/2009] [Indexed: 01/07/2023]
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Hert J, Irwin JJ, Laggner C, Keiser MJ, Shoichet BK. Quantifying biogenic bias in screening libraries. Nat Chem Biol 2009; 5:479-83. [PMID: 19483698 PMCID: PMC2783405 DOI: 10.1038/nchembio.180] [Citation(s) in RCA: 162] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Accepted: 04/10/2009] [Indexed: 01/07/2023]
Abstract
In lead discovery, libraries of 106 molecules are screened for biological activity. Given the over 1060 drug-like molecules thought possible, such screens might never succeed. That they do, even occasionally, implies a biased selection of library molecules. Here a method is developed to quantify the bias in screening libraries towards biogenic molecules. With this approach, we consider what is missing from screening libraries and how they can be optimized.
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Affiliation(s)
- Jérôme Hert
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
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26
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Shaw JT. Naturally diverse: highlights in versatile synthetic methods enabling target- and diversity-oriented synthesis. Nat Prod Rep 2009; 26:11-26. [DOI: 10.1039/b814468k] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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27
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Zimmermann TJ, Niesen FH, Pilka ES, Knapp S, Oppermann U, Maier ME. Discovery of a potent and selective inhibitor for human carbonyl reductase 1 from propionate scanning applied to the macrolide zearalenone. Bioorg Med Chem 2009; 17:530-6. [DOI: 10.1016/j.bmc.2008.11.076] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2008] [Revised: 11/26/2008] [Accepted: 11/29/2008] [Indexed: 11/26/2022]
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28
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Rivera DG, Pando O, Bosch R, Wessjohann LA. A Biomimetic Approach for Polyfunctional Secocholanes: Tuning Flexibility and Functionality on Peptidic and Macrocyclic Scaffolds Derived from Bile Acids. J Org Chem 2008; 73:6229-38. [DOI: 10.1021/jo800708m] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daniel G. Rivera
- Center for Natural Products Study, Faculty of Chemistry, University of Havana, 10400 Havana, Cuba, and Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120 Halle/Saale, Germany
| | - Orlando Pando
- Center for Natural Products Study, Faculty of Chemistry, University of Havana, 10400 Havana, Cuba, and Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120 Halle/Saale, Germany
| | - Rayser Bosch
- Center for Natural Products Study, Faculty of Chemistry, University of Havana, 10400 Havana, Cuba, and Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120 Halle/Saale, Germany
| | - Ludger A. Wessjohann
- Center for Natural Products Study, Faculty of Chemistry, University of Havana, 10400 Havana, Cuba, and Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120 Halle/Saale, Germany
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29
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Fadeyi OO, Adamson ST, Myles EL, Okoro CO. Novel fluorinated acridone derivatives. Part 1: Synthesis and evaluation as potential anticancer agents. Bioorg Med Chem Lett 2008; 18:4172-6. [PMID: 18541426 DOI: 10.1016/j.bmcl.2008.05.078] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2008] [Revised: 05/19/2008] [Accepted: 05/19/2008] [Indexed: 11/16/2022]
Affiliation(s)
- Olugbeminiyi O Fadeyi
- Department of Chemistry, Tennessee State University, 3500 John A. Merritt Boulevard, Nashville, TN 37209-1561, USA
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30
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Newman DJ. Natural products as leads to potential drugs: an old process or the new hope for drug discovery? J Med Chem 2008; 51:2589-99. [PMID: 18393402 DOI: 10.1021/jm0704090] [Citation(s) in RCA: 438] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- David J Newman
- Natural Products Branch, Developmental Therapeutics Program, DCTD, National Cancer Institute-Frederick, P.O. Box B, Frederick, Maryland 21702, USA.
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31
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Magedov IV, Manpadi M, Ogasawara MA, Dhawan AS, Rogelj S, Van Slambrouck S, Steelant WFA, Evdokimov NM, Uglinskii PY, Elias EM, Knee EJ, Tongwa P, Antipin MY, Kornienko A. Structural simplification of bioactive natural products with multicomponent synthesis. 2. antiproliferative and antitubulin activities of pyrano[3,2-c]pyridones and pyrano[3,2-c]quinolones. J Med Chem 2008; 51:2561-70. [PMID: 18361483 DOI: 10.1021/jm701499n] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pyrano[3,2- c]pyridone and pyrano[3,2- c]quinolone structural motifs are commonly found in alkaloids manifesting diverse biological activities. As part of a program aimed at structural simplification of bioactive natural products utilizing multicomponent synthetic processes, we developed compound libraries based on these privileged heterocyclic scaffolds. The selected library members display low nanomolar antiproliferative activity and induce apoptosis in human cancer cell lines. Mechanistic studies reveal that these compounds induce cell cycle arrest in the G2/M phase and block in vitro tubulin polymerization. Because of the successful clinical use of microtubule-targeting agents, these heterocyclic libraries are expected to provide promising new leads in anticancer drug design.
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Affiliation(s)
- Igor V Magedov
- Department of Chemistry, New Mexico Institute of Mining and Technology, Socorro, New Mexico 87801, USA.
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Groenendaal B, Ruijter E, de Kanter FJJ, Lutz M, Spek AL, Orru RVA. Generation of molecular diversity using a complexity-generating MCR-platform towards triazinane diones. Org Biomol Chem 2008; 6:3158-65. [DOI: 10.1039/b807138a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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33
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Nielsen T, Schreiber S. Der optimale Molekülsatz für Screening-Anwendungen: eine Synthesestrategie. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200703073] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Abstract
The development of effective small-molecule probes and drugs entails at least three stages: 1) a discovery phase, often requiring the synthesis and screening of candidate compounds, 2) an optimization phase, requiring the synthesis and analysis of structural variants, 3) and a manufacturing phase, requiring the efficient, large-scale synthesis of the optimized probe or drug. Specialized project groups tend to undertake the individual activities without prior coordination; for example, contracted (outsourced) chemists may perform the first activity while in-house medicinal and process chemists perform the second and third development stages, respectively. The coordinated planning of these activities in advance of the first small-molecule screen tends not to be undertaken, and each project group can encounter a bottleneck that could, in principle, have been avoided with advance planning. Therefore, a challenge for synthetic chemistry is to develop a new kind of chemistry that yields a screening collection comprising small molecules that increase the probability of success in all three phases. Although this transformative chemistry remains elusive, progress is being made. Herein, we review a newly emerging strategy in diversity-oriented small-molecule synthesis that may have the potential to achieve these challenging goals.
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Affiliation(s)
- Thomas E Nielsen
- Department of Chemistry and Chemical Biology, Harvard University, Howard Hughes Medical Institute, Cambridge, MA 02142, USA
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35
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Magedov IV, Manpadi M, Slambrouck SV, Steelant WFA, Rozhkova E, Przheval'skii NM, Rogelj S, Kornienko A. Discovery and investigation of antiproliferative and apoptosis-inducing properties of new heterocyclic podophyllotoxin analogues accessible by a one-step multicomponent synthesis. J Med Chem 2007; 50:5183-92. [PMID: 17894480 DOI: 10.1021/jm070528f] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Podophyllotoxin has been extensively used as a lead agent in the development of new anticancer drugs. On the basis of the previously reported simplified 4-aza-2,3-didehydro podophyllotoxin analogues, we implemented a bioisosteric replacement of the methylenedioxybenzene subunit with a pyrazole moiety to afford tetracyclic dihydropyridopyrazoles. Libraries of these structurally simple analogues are prepared by a straightforward one-step multicomponent synthesis and demonstrated to display antiproliferative properties in a number of human cancer cell lines. These new heterocycles potently induce apoptosis in cancerous Jurkat cells even after a short 24 h exposure. In contrast, no apoptosis is detected in primary lymphocytes under the same treatment conditions. The ease of synthesis and encouraging biological activities make the presented library of dihydropyridopyrazoles promising new leads in anticancer drug design.
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Affiliation(s)
- Igor V Magedov
- Department of Organic Chemistry, Timiryazev Agriculture Academy, Moscow 127550, Russia.
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36
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