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Nair NU, Greninger P, Zhang X, Friedman AA, Amzallag A, Cortez E, Sahu AD, Lee JS, Dastur A, Egan RK, Murchie E, Ceribelli M, Crowther GS, Beck E, McClanaghan J, Klump-Thomas C, Boisvert JL, Damon LJ, Wilson KM, Ho J, Tam A, McKnight C, Michael S, Itkin Z, Garnett MJ, Engelman JA, Haber DA, Thomas CJ, Ruppin E, Benes CH. A landscape of response to drug combinations in non-small cell lung cancer. Nat Commun 2023; 14:3830. [PMID: 37380628 PMCID: PMC10307832 DOI: 10.1038/s41467-023-39528-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/14/2023] [Indexed: 06/30/2023] Open
Abstract
Combination of anti-cancer drugs is broadly seen as way to overcome the often-limited efficacy of single agents. The design and testing of combinations are however very challenging. Here we present a uniquely large dataset screening over 5000 targeted agent combinations across 81 non-small cell lung cancer cell lines. Our analysis reveals a profound heterogeneity of response across the tumor models. Notably, combinations very rarely result in a strong gain in efficacy over the range of response observable with single agents. Importantly, gain of activity over single agents is more often seen when co-targeting functionally proximal genes, offering a strategy for designing more efficient combinations. Because combinatorial effect is strongly context specific, tumor specificity should be achievable. The resource provided, together with an additional validation screen sheds light on major challenges and opportunities in building efficacious combinations against cancer and provides an opportunity for training computational models for synergy prediction.
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Affiliation(s)
- Nishanth Ulhas Nair
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Xiaohu Zhang
- Howard Hughes Medical Institute, Bethesda, MD, USA
| | - Adam A Friedman
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Arnaud Amzallag
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Eliane Cortez
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Avinash Das Sahu
- University of New Mexico, Comprehensive Cancer Center, Albuquerque, NM, USA
| | - Joo Sang Lee
- Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea
| | - Anahita Dastur
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Regina K Egan
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ellen Murchie
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Erin Beck
- Howard Hughes Medical Institute, Bethesda, MD, USA
| | | | | | | | - Leah J Damon
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Jeffrey Ho
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Angela Tam
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Sam Michael
- Howard Hughes Medical Institute, Bethesda, MD, USA
| | - Zina Itkin
- Howard Hughes Medical Institute, Bethesda, MD, USA
| | - Mathew J Garnett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
| | | | - Daniel A Haber
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Bethesda, MD, USA
| | - Craig J Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institute of Health, Rockville, MD, 20850, USA
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Cyril H Benes
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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Design, synthesis and biological evaluation of novel histone deacetylase1/2 (HDAC1/2) and cyclin-dependent Kinase2 (CDK2) dual inhibitors against malignant cancer. Eur J Med Chem 2020; 198:112322. [PMID: 32361064 DOI: 10.1016/j.ejmech.2020.112322] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 04/07/2020] [Accepted: 04/07/2020] [Indexed: 12/25/2022]
Abstract
In the current study, we have designed and synthesized a series of novel histone deacetylase1/2 (HDAC1/2) and cyclin-dependent kinase2 (CDK2) dual inhibitors by integrating purine-based pharmacophore into the recognition cap group of CS055. The representative compound 14d with excellent antiproliferative activities towards five solid cancer cells, showed potent inhibitory activities against HDAC1, HDAC2 and CDK2 with IC50 values of 70.7 nM, 23.1 nM and 0.80 μM, respectively. Besides, compound 14d could effectively block the cell cycle in the G2/M phase and induce apoptosis, which might be related to increasing intracellular ROS levels. Importantly, compound 14d exhibited desirable pharmacokinetic (PK) properties with the intraperitoneal bioavailability of 50.8% in ICR mice, and potent in vivo antitumor activity in the HCT116 xenograft model. Therefore, compound 14d could be considered as a promising lead compound for the development of multitargeting anticancer agents.
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Jorda R, Havlíček L, Šturc A, Tušková D, Daumová L, Alam M, Škerlová J, Nekardová M, Peřina M, Pospíšil T, Široká J, Urbánek L, Pachl P, Řezáčová P, Strnad M, Klener P, Kryštof V. 3,5,7-Substituted Pyrazolo[4,3-d]pyrimidine Inhibitors of Cyclin-Dependent Kinases and Their Evaluation in Lymphoma Models. J Med Chem 2019; 62:4606-4623. [DOI: 10.1021/acs.jmedchem.9b00189] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Radek Jorda
- Laboratory of Growth Regulators, Palacký University and Institute of Experimental Botany, The Czech Academy of Sciences, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Libor Havlíček
- Isotope Laboratory, Institute of Experimental Botany, The Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Antonín Šturc
- Isotope Laboratory, Institute of Experimental Botany, The Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Diana Tušková
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, 128 53 Prague, Czech Republic
| | - Lenka Daumová
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, 128 53 Prague, Czech Republic
| | - Mahmudul Alam
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, 128 53 Prague, Czech Republic
| | - Jana Škerlová
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
- Institute of Molecular Genetics, The Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Michaela Nekardová
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
- Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 3, 121 16 Prague 2, Czech Republic
| | - Miroslav Peřina
- Laboratory of Growth Regulators, Palacký University and Institute of Experimental Botany, The Czech Academy of Sciences, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Tomáš Pospíšil
- Laboratory of Growth Regulators, Palacký University and Institute of Experimental Botany, The Czech Academy of Sciences, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Jitka Široká
- Laboratory of Growth Regulators, Palacký University and Institute of Experimental Botany, The Czech Academy of Sciences, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Lubor Urbánek
- Laboratory of Growth Regulators, Palacký University and Institute of Experimental Botany, The Czech Academy of Sciences, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Petr Pachl
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
- Institute of Molecular Genetics, The Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Palacký University and Institute of Experimental Botany, The Czech Academy of Sciences, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Pavel Klener
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, 128 53 Prague, Czech Republic
| | - Vladimír Kryštof
- Laboratory of Growth Regulators, Palacký University and Institute of Experimental Botany, The Czech Academy of Sciences, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
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Gavrilov KN, Mikhel IS, Zheglov SV, Gavrilov VK, Chuchelkin IV, Firsin ID, Birin KP, Pytskii IS, Paseshnichenko KA, Tafeenko VA, Chernyshev VV, Shiryaev AA. Oxalamide-based bisdiamidophosphites: synthesis, coordination, and application in asymmetric metallocatalysis. Org Chem Front 2019. [DOI: 10.1039/c9qo00237e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A new group of P*-chiral bisdiamidophosphites has been developed for Pd- and Rh-catalyzed asymmetric reactions with good to excellent enantioselectivities.
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Pathak A, Rohilla A, Gupta T, Akhtar MJ, Haider MR, Sharma K, Haider K, Yar MS. DYRK1A kinase inhibition with emphasis on neurodegeneration: A comprehensive evolution story-cum-perspective. Eur J Med Chem 2018; 158:559-592. [PMID: 30243157 DOI: 10.1016/j.ejmech.2018.08.093] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/15/2018] [Accepted: 08/30/2018] [Indexed: 02/08/2023]
Abstract
Alzheimer, the fourth leading cause of death embodies a key responsible event including formation of β-amyloid protein clustering to amyloid plaque on blood vessels. The origin of above events is Amyloid precursor protein (APP) which is an integral membrane protein known for its function in synapses formation. Modern research had proposed that the over expression of DYRK1A (Dual specificity tyrosine phosphorylation regulated kinase1A, a family of protein kinases, positioned within the Down's syndrome critical region (DSCR) on human chromosome 21causes phosphorylation of APP protein resulting in its cleavage to Aβ 40, 42 and tau proteins (regulated by beta and gamma secretase) which plays critical role in early onset of Alzheimer's disease (AD) detected in Down's syndrome (DS), leading to permanent functional and structural deformities which results ultimately into neuro-degeneration and neuronal death. Therefore, DYRK1A emerges as a potential target for prevention of neuro-degeneration and hence Alzheimer. Presently, the treatment methods for Down's syndrome, as well as Alzheimer's disease are extremely biased and represent a major deficiency for therapeutic necessities. We hereby, focus our review on the current status of the research and contributions in the development of DYRK1A inhibitors.
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Affiliation(s)
- Ankita Pathak
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, Hamdard Nagar, New Delhi, 110062, India
| | - Ankit Rohilla
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, Hamdard Nagar, New Delhi, 110062, India
| | - Tanya Gupta
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, Hamdard Nagar, New Delhi, 110062, India
| | - Md Jawaid Akhtar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, Hamdard Nagar, New Delhi, 110062, India
| | - Md Rafi Haider
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, Hamdard Nagar, New Delhi, 110062, India
| | - Kalicharan Sharma
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, Hamdard Nagar, New Delhi, 110062, India
| | - Kashif Haider
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, Hamdard Nagar, New Delhi, 110062, India
| | - M Shahar Yar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education & Research, Jamia Hamdard, Hamdard Nagar, New Delhi, 110062, India.
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Design strategies, structure activity relationship and mechanistic insights for purines as kinase inhibitors. Eur J Med Chem 2016; 112:298-346. [PMID: 26907156 DOI: 10.1016/j.ejmech.2016.02.018] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Revised: 02/04/2016] [Accepted: 02/05/2016] [Indexed: 12/22/2022]
Abstract
Kinases control a diverse set of cellular processes comprising of reversible phosphorylation of proteins. Protein kinases play a pivotal role in human tumor cell proliferation, migration and survival of neoplasia. In the recent past, purine based molecules have emerged as significantly potent kinase inhibitors. In view of their promising potential for the inhibition of kinases, this review article focuses on purines which have progressed as kinase inhibitors during the last five years. A detailed account of the design strategies employed for the synthesis of purine analogs exerting inhibitory effects on diverse kinases has been presented. Apart from presenting the design strategies, the article also highlights the structure activity relationship along with mechanistic insights revealed during the biological evaluation of the purine analogs for kinase inhibition. The interactions with the amino acid residues responsible for kinase inhibitory potential of purine based molecules have also been discussed. In this assemblage, purine based protein kinase inhibitors patented in the past have also been summarized in the tabular form. This compilation will be of great interest for the researchers working in the area of protein kinase inhibitors.
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Gavrilov KN, Zheglov SV, Gavrilov VK, Maksimova MG, Zamilatskov IA. Palladium-catalyzed asymmetric synthesis of N,N-dibenzylcyclohex-2-en-1-amine. Russ Chem Bull 2015. [DOI: 10.1007/s11172-015-0966-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Wang J, Wang Q, Zhang L, Fang H. Design, Synthesis and Preliminary Biological Evaluation of Purine-2,6-diamine Derivatives as Cyclin-dependent Kinase (CDK) Inhibitors. CHINESE J CHEM 2013. [DOI: 10.1002/cjoc.201300420] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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