1
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El-Gamil DS, Zaky MY, Maximous PM, Sharaky M, El-Dessouki AM, Riad NM, Shaaban S, Abdel-Halim M, Al-Karmalawy AA. Exploring chromone-2-carboxamide derivatives for triple-negative breast cancer targeting EGFR, FGFR3, and VEGF pathways: Design, synthesis, and preclinical insights. Drug Dev Res 2024; 85:e22228. [PMID: 38952003 DOI: 10.1002/ddr.22228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 03/27/2024] [Accepted: 06/17/2024] [Indexed: 07/03/2024]
Abstract
Chromone-based compounds have established cytotoxic, antiproliferative, antimetastatic, and antiangiogenic effects on various cancer cell types via modulating different molecular targets. Herein, 17 novel chromone-2-carboxamide derivatives were synthesized and evaluated for their in vitro anticancer activity against 15 human cancer cell lines. Among the tested cell lines, MDA-MB-231, the triple-negative breast cancer cell line, was found to be the most sensitive, where the N-(2-furylmethylene) (15) and the α-methylated N-benzyl (17) derivatives demonstrated the highest growth inhibition with GI50 values of 14.8 and 17.1 μM, respectively. In vitro mechanistic studies confirmed the significant roles of compounds 15 and 17 in the induction of apoptosis and suppression of EGFR, FGFR3, and VEGF protein levels in MDA-MB-231 cancer cells. Moreover, compound 15 exerted cell cycle arrest at both the G0-G1 and G2-M phases. The in vivo efficacy of compound 15 as an antitumor agent was further investigated in female mice bearing Solid Ehrlich Carcinoma. Notably, administration of compound 15 resulted in a marked decrease in both tumor weight and volume, accompanied by improvements in biochemical, hematological, histological, and immunohistochemical parameters that verified the repression of both angiogenesis and inflammation as additional Anticancer mechanisms. Moreover, the binding interactions of compounds 15 and 17 within the binding sites of all three target receptors (EGFR, FGFR3, and VEGF) were clearly illustrated using molecular docking.
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Affiliation(s)
- Dalia S El-Gamil
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ahram Canadian University, Giza, Egypt
| | - Mohamed Y Zaky
- Zoology Department, Molecular Physiology Division, Faculty of Science, Beni-Suef University, Beni Suef, Egypt
| | - Patrick M Maximous
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Marwa Sharaky
- Cancer Biology Department, Pharmacology Unit, National Cancer Institute (NCI), Cairo University, Cairo, Egypt
- Biochemistry Department, Faculty of Pharmacy, Ahram Canadian University, Giza, Egypt
| | - Ahmed M El-Dessouki
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Ahram Canadian University, Giza, Egypt
| | - Noura M Riad
- Department of Chemistry, School of Life and Medical Sciences, New Administrative Capital, University of Hertfordshire hosted by Global Academic Foundation, Cairo, Egypt
| | - Saad Shaaban
- Department of Chemistry, College of Science, King Faisal University, Al-Ahsa, Saudi Arabia
- Organic Chemistry Division, Department of Chemistry, College of Science, Mansoura University, Mansoura, Egypt
| | - Mohammad Abdel-Halim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egypt
| | - Ahmed A Al-Karmalawy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ahram Canadian University, Giza, Egypt
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Horus University-Egypt, New Damietta, Egypt
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2
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Fitzgerald P, Dixit A, Zhang C, Mobley DL, Paegel BM. Building Block-Centric Approach to DNA-Encoded Library Design. J Chem Inf Model 2024; 64:4661-4672. [PMID: 38860710 PMCID: PMC11200258 DOI: 10.1021/acs.jcim.4c00232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 06/02/2024] [Accepted: 06/03/2024] [Indexed: 06/12/2024]
Abstract
DNA-encoded library technology grants access to nearly infinite opportunities to explore the chemical structure space for drug discovery. Successful navigation depends on the design and synthesis of libraries with appropriate physicochemical properties (PCPs) and structural diversity while aligning with practical considerations. To this end, we analyze combinatorial library design constraints including the number of chemistry cycles, bond construction strategies, and building block (BB) class selection in pursuit of ideal library designs. We compare two-cycle library designs (amino acid + carboxylic acid, primary amine + carboxylic acid) in the context of PCPs and chemical space coverage, given different BB selection strategies and constraints. We find that broad availability of amines and acids is essential for enabling the widest exploration of chemical space. Surprisingly, cost is not a driving factor, and virtually, the same chemical space can be explored with "budget" BBs.
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Affiliation(s)
- Patrick
R. Fitzgerald
- Skaggs
Doctoral Program in the Chemical and Biological Sciences, Scripps Research, La Jolla, California 92037, United States
| | - Anjali Dixit
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
| | - Chris Zhang
- Department
of Chemistry, University of California, Irvine, California 92697, United States
| | - David L. Mobley
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
- Department
of Chemistry, University of California, Irvine, California 92697, United States
| | - Brian M. Paegel
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
- Department
of Chemistry, University of California, Irvine, California 92697, United States
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3
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Lin PC, Wong CD, Jarvo ER. Cross-selective Deoxygenative Coupling of Aliphatic Alcohols: Installation of Methyl Groups including Isotopic Labels by Nickel Catalysis. Angew Chem Int Ed Engl 2024; 63:e202403119. [PMID: 38604974 DOI: 10.1002/anie.202403119] [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: 02/13/2024] [Revised: 03/28/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024]
Abstract
Nickel-catalyzed cross-electrophile coupling reactions of two aliphatic alcohol derivatives remain a challenge. Herein, we report a nickel-catalyzed reductive methylation reaction of aliphatic mesylates with methyl tosylate. This reaction provides straightforward access to compounds bearing aliphatic methyl groups from alkyl alcohol derivatives. Isotopically labelled substrates and reagents can be employed in the reaction to provide perdeuterated and 13C-labelled products. This transformation can be achieved by employing stoichiometric Mn reductant or electrochemically. Additionally, mechanistic experiments show that alkyl iodides are key intermediates in the transformation which undergo a stereoablative reaction via radical intermediates.
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Affiliation(s)
- Patricia C Lin
- Department of Chemistry, University of California, Irvine, California, 92617, United States
| | - Chloe D Wong
- Department of Chemistry, University of California, Irvine, California, 92617, United States
| | - Elizabeth R Jarvo
- Department of Chemistry, University of California, Irvine, California, 92617, United States
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4
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Chahal S, Rani P, Shweta, Goel KK, Joshi G, Singh R, Kumar P, Singh D, Sindhu J. Pyrano[2,3-c]pyrazole fused spirooxindole-linked 1,2,3-triazoles as antioxidant agents: Exploring their utility in the development of antidiabetic drugs via inhibition of α-amylase and DPP4 activity. Bioorg Chem 2024; 147:107363. [PMID: 38657527 DOI: 10.1016/j.bioorg.2024.107363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/07/2024] [Accepted: 04/09/2024] [Indexed: 04/26/2024]
Abstract
Environment-benign, multicomponent synthetic methodologies are vital in modern pharmaceutical research and facilitates multi-targeted drug development via synergistic approach. Herein, we reported green and efficient synthesis of pyrano[2,3-c]pyrazole fused spirooxindole linked 1,2,3-triazoles using a tea waste supported copper catalyst (TWCu). The synthetic approach involves a one-pot, five-component reaction using N-propargylated isatin, hydrazine hydrate, ethyl acetoacetate, malononitrile/ethyl cyanoacetate and aryl azides as model substrates. Mechanistically, the reaction was found to proceed via in situ pyrazolone formation followed by Knoevenagel condensation, azide alkyne cycloaddition and Michael's addition reactions. The molecules were developed using structure-based drug design. The primary goal is to identifying anti-oxidant molecules with potential ability to modulate α-amylase and DPP4 (dipeptidyl-peptidase 4) activity. The anti-oxidant analysis, as determined via DPPH, suggested that the synthesized compounds, A6 and A10 possessed excellent anti-oxidant potential compared to butylated hydroxytoluene (BHT). In contrast, compounds A3, A5, A8, A9, A13, A15, and A18 were found to possess comparable anti-oxidant potential. Among these, A3 and A13 possessed potential α-amylase inhibitory activity compared to the acarbose, and A3 further emerged as dual inhibitors of both DPP4 and α-amylase with anti-oxidant potential. The relationship of functionalities on their anti-oxidant and enzymatic inhibition was explored in context to their SAR that was further corroborated using in silico techniques and enzyme kinetics.
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Affiliation(s)
- Sandhya Chahal
- Department of Chemistry, COBS&H, CCS Haryana Agricultural University, Hisar 125004, India
| | - Payal Rani
- Department of Chemistry, COBS&H, CCS Haryana Agricultural University, Hisar 125004, India
| | - Shweta
- Department of Chemistry, COBS&H, CCS Haryana Agricultural University, Hisar 125004, India
| | - Kapil Kumar Goel
- Department of Pharmaceutical Sciences, Gurukul Kangri (Deemed to be University), Haridwar 249404, India
| | - Gaurav Joshi
- Department of Pharmaceutical Science, Hemvati Nandan Bahuguna Garhwal (A Central) University, Srinagar-246174, Dist. Garhwal, Uttarakhand, India
| | - Rajvir Singh
- Department of Chemistry, COBS&H, CCS Haryana Agricultural University, Hisar 125004, India
| | - Parvin Kumar
- Department of Chemistry, Kurukshetra University, Kurukshetra, Haryana 136119, India.
| | - Devender Singh
- Department of Chemistry, Maharshi Dayanand University, Rohtak 124001, India
| | - Jayant Sindhu
- Department of Chemistry, COBS&H, CCS Haryana Agricultural University, Hisar 125004, India.
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5
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Ness M, Peramuna T, Wendt KL, Collins JE, King JB, Paes R, Santos NM, Okeke C, Miller CR, Chakrabarti D, Cichewicz RH, McCall LI. Rationally Minimizing Natural Product Libraries Using Mass Spectrometry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595232. [PMID: 38826280 PMCID: PMC11142144 DOI: 10.1101/2024.05.22.595232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Natural product libraries are crucial to drug development, but large libraries drastically increase the time and cost during initial high throughput screens. Here, we developed a method that leverages liquid chromatography-tandem mass spectrometry spectral similarity to dramatically reduce library size, with minimal bioactive loss. This method offers a broadly applicable strategy for accelerated drug discovery with cost reductions, which enable implementation in resource-limited settings.
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Affiliation(s)
- Monica Ness
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, California, 92182, United States
| | - Thilini Peramuna
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Karen L. Wendt
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Jennifer E. Collins
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, 32826, United States
| | - Jarrod B. King
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Raphaella Paes
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, 32826, United States
| | - Natalia Mojica Santos
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, 32826, United States
| | - Crystal Okeke
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Cameron R. Miller
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Debopam Chakrabarti
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, 32826, United States
| | - Robert H. Cichewicz
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Laura-Isobel McCall
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, California, 92182, United States
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6
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Gisbert Y, Fellert M, Stindt CN, Gerstner A, Feringa BL. Molecular Motors' Magic Methyl and Its Pivotal Influence on Rotation. J Am Chem Soc 2024; 146:12609-12619. [PMID: 38656891 PMCID: PMC11082891 DOI: 10.1021/jacs.4c01628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 04/26/2024]
Abstract
Molecular motors have found a wide range of applications, powering a transition from molecules to dynamic molecular systems for which their motion must be precisely tuned. To achieve this adjustment, strategies involving laborious changes in their design are often used. Herein, we show that control over a single methyl group allows a drastic change in rotational properties. In this regard, we present the straightforward asymmetric synthesis of β-methylated first-generation overcrowded-alkene-based molecular motors. Both enantiomers of the new motors were prepared in good yields and high enantiopurities, and these motors were thoroughly studied by variable-temperature nuclear magnetic resonance (VT-NMR), ultraviolet-visible (UV-vis), and circular dichroism (CD) spectroscopy, showing a crucial influence of the methylation pattern on the rotational behavior of the motors. Starting from a common chiral precursor, we demonstrate that subsequent methylation can drastically reduce the speed of the motor and reverse the direction of the rotation. We show for the first time that complete unidirectionality can be achieved even when the energy difference between the stable and metastable states is small, resulting in the coexistence of both states under ambient conditions without hampering the energy ratcheting process. This discovery opens the way for the design of more advanced first-generation motors.
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Affiliation(s)
| | | | - Charlotte N. Stindt
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The
Netherlands
| | - Alexander Gerstner
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The
Netherlands
| | - Ben L. Feringa
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The
Netherlands
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7
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Khuttan S, Gallicchio E. What to Make of Zero: Resolving the Statistical Noise from Conformational Reorganization in Alchemical Binding Free Energy Estimates with Metadynamics Sampling. J Chem Theory Comput 2024; 20:1489-1501. [PMID: 38252868 PMCID: PMC10867849 DOI: 10.1021/acs.jctc.3c01250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 01/03/2024] [Accepted: 01/03/2024] [Indexed: 01/24/2024]
Abstract
We introduce the self-relative binding free energy (self-RBFE) approach to evaluate the intrinsic statistical variance of dual-topology alchemical binding free energy estimators. The self-RBFE is the relative binding free energy between a ligand and a copy of the same ligand, and its true value is zero. Nevertheless, because the two copies of the ligand move independently, the self-RBFE value produced by a finite-length simulation fluctuates and can be used to measure the variance of the model. The results of this validation provide evidence that a significant fraction of the errors observed in benchmark studies reflect the statistical fluctuations of unconverged estimates rather than the models' accuracy. Furthermore, we find that ligand reorganization is a significant contributing factor to the statistical variance of binding free energy estimates and that metadynamics-accelerated conformational sampling of the torsional degrees of freedom of the ligand can drastically reduce the time to convergence.
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Affiliation(s)
- Sheenam Khuttan
- Department
of Chemistry and Biochemistry, Brooklyn
College of the City University of New York, New York, New York 11210, United States
- Ph.D.
Program in Biochemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
| | - Emilio Gallicchio
- Department
of Chemistry and Biochemistry, Brooklyn
College of the City University of New York, New York, New York 11210, United States
- Ph.D.
Program in Biochemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
- Ph.D.
Program in Chemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
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