1
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Zelch D, Russo CM, Ruud KJ, O'Reilly MC. A General and Scalable Method toward Enantioenriched C2-Substituted Azetidines Using Chiral tert-Butanesulfinamides. J Org Chem 2024. [PMID: 39348268 DOI: 10.1021/acs.joc.4c01908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/02/2024]
Abstract
Diverse ranges of chiral nitrogen-containing heterocycles serve as a molecular toolbox for modulating a wide array of biological processes, but enantioenriched production of smaller chiral heterocycles is a bottleneck. There is a lack of general approaches for the stereoselective preparation of chiral 4-membered monocyclic C2-substituted azetidines, where many routes to different substitution types are possible, but no simple and common approach exists. To bridge this gap, inexpensive and widely available chiral tert-butanesulfinamides are harnessed for chiral induction with 1,3-bis-electrophilic 3-chloropropanal, providing a three-step approach to C2-substituted azetidines with aryl, vinyl, allyl, branched alkyl, and linear alkyl substituents. Eleven azetidine products are produced, and the approach is shown to be effective on a gram-scale with a single purification of the protected azetidine product in 44% yield over three steps in an 85:15 diastereomeric ratio. In most cases, the diastereomers are separable using normal phase chromatography, often resulting in previously elusive enantiopure azetidine products. Protected azetidines were shown to undergo rapid and efficient sulfinamide cleavage, producing an azetidine hydrochloride salt that was subjected to derivatization reactions, highlighting the method's applicability to medicinal chemistry approaches.
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Affiliation(s)
- Daniel Zelch
- Department of Chemistry, Villanova University, Villanova, Pennsylvania 19085, United States
| | - Christopher M Russo
- Department of Chemistry, Villanova University, Villanova, Pennsylvania 19085, United States
| | - Kirsten J Ruud
- Department of Chemistry and Biotechnology, University of Wisconsin-River Falls, River Falls, Wisconsin 54022, United States
| | - Matthew C O'Reilly
- Department of Chemistry, Villanova University, Villanova, Pennsylvania 19085, United States
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2
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Repac Antić D, Kovač B, Kolenc M, Brčić Karačonji I, Gobin I, Petković Didović M. Combinatory Effect of Nitroxoline and Gentamicin in the Control of Uropathogenic Enterococci Infections. Antibiotics (Basel) 2024; 13:829. [PMID: 39335003 PMCID: PMC11428728 DOI: 10.3390/antibiotics13090829] [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: 07/24/2024] [Revised: 08/24/2024] [Accepted: 08/28/2024] [Indexed: 09/30/2024] Open
Abstract
Enterococcus faecalis, responsible for a majority of human and nosocomial enterococcal infections, is intrinsically resistant to aminoglycoside antibiotics (such as gentamicin, GEN), which must be used in a combined therapy to be effective. Nitroxoline (NTX) is an old antibiotic, underused for decades, but rediscovered now in an era of growing antibiotic resistance. In this in vitro study, the types of interactions between NTX and GEN on 29 E. faecalis strains were analyzed with an aim to find synergistic antimicrobial and antiadhesion combinations. Transmission electron microscopy (TEM) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) were used to analyze changes in cell morphology and bacterial proteome after monotreatments and combined treatments. The results showed the synergistic effect for six combinations on eight strains, including the ATCC29212, and an additive effect for most strains. Combinations causing a complete inhibition of adhesion were established. Cell membrane integrity was affected by NTX, while combined NTX/GEN treatment caused dramatic changes in cell morphology. Upregulation of the expression of many proteins was established, with some emerging only after combined treatment. The results strongly imply that NTX has the potential for use in combined therapy with GEN against enterococci and it could further provide a substantial contribution to an ongoing fight against antimicrobial resistance and nosocomial infections.
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Affiliation(s)
- Davorka Repac Antić
- Department of Microbiology and Parasitology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
- Department of Clinical Microbiology, Clinical Hospital Center Rijeka, 51000 Rijeka, Croatia
| | - Bruno Kovač
- Chair of Buildings and Constructional Complexes, Faculty of Civil and Geodetic Engineering, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Marko Kolenc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Irena Brčić Karačonji
- Division of Toxicology, Institute for Medical Research and Occupational Health, 10000 Zagreb, Croatia
- Department of Basic Medical Sciences, Faculty of Health Studies, University of Rijeka, 51000 Rijeka, Croatia
| | - Ivana Gobin
- Department of Microbiology and Parasitology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
| | - Mirna Petković Didović
- Department of Medical Chemistry, Biochemistry and Clinical Chemistry, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
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3
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Jiang M, Zhang H, Song Y, Yin F, Hu Z, Li X, Wang Y, Wang Z, Li Y, Wang Z, Zhang Y, Wang S, Lu S, Xu G, Song T, Wang Z, Zhang Z. Discovery of Biphenyl Derivatives to Target Hsp70-Bim Protein-Protein Interaction in Chronic Myeloid Leukemia by Scaffold Hopping Strategy. J Med Chem 2024; 67:12068-12084. [PMID: 39012838 DOI: 10.1021/acs.jmedchem.4c00780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Hsp70-Bim protein-protein interaction (PPI) is the most recently identified specific target in chronic myeloid leukemia (CML) therapy. Herein, we developed a new class of Hsp70-Bim PPI inhibitors via scaffold hopping of S1g-10, the most potent Hsp70-Bim PPI inhibitor thus far. Through structure-activity relationship (SAR) study, we obtained a biphenyl scaffold compound JL-15 with a 5.6-fold improvement in Hsp70-Bim PPI suppression (Kd = 123 vs 688 nM) and a 4-fold improvement in water solubility (29.42 vs 7.19 μg/mL) compared to S1g-10. It maintains comparable apoptosis induction capability with S1g-10 against both TKI-sensitive and TKI-resistant CML cell lines in an Hsp70-Bim-dependent manner. Additionally, through SAR, 1H-15N TRSOY-NMR, and molecular docking, we revealed that Lys319 is a "hot spot" in the Hsp70-Bim PPI interface. Collectively, these results provide a novel chemical scaffold and structural insights for the rational design of Hsp70-Bim PPI inhibitors.
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MESH Headings
- Humans
- HSP70 Heat-Shock Proteins/metabolism
- HSP70 Heat-Shock Proteins/antagonists & inhibitors
- HSP70 Heat-Shock Proteins/chemistry
- Biphenyl Compounds/pharmacology
- Biphenyl Compounds/chemistry
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Structure-Activity Relationship
- Molecular Docking Simulation
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/chemistry
- Antineoplastic Agents/chemical synthesis
- Bcl-2-Like Protein 11/metabolism
- Cell Line, Tumor
- Apoptosis/drug effects
- Protein Binding
- Drug Discovery
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Affiliation(s)
- Maojun Jiang
- Cancer Hospital of Dalian University of Technology, School of Chemistry, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Hong Zhang
- Cancer Hospital of Dalian University of Technology, School of Chemistry, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Yang Song
- Department of Hematology, Central Hospital of Dalian University of Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Fangkui Yin
- Cancer Hospital of Dalian University of Technology, School of Chemistry, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Zhiyuan Hu
- School of Life Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Xin Li
- Cancer Hospital of Dalian University of Technology, School of Chemistry, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Yuying Wang
- School of Life Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Zheming Wang
- Cancer Hospital of Dalian University of Technology, School of Chemistry, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Yitong Li
- Cancer Hospital of Dalian University of Technology, School of Chemistry, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Zihan Wang
- Cancer Hospital of Dalian University of Technology, School of Chemistry, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Yanxin Zhang
- School of Life Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Siyao Wang
- Cancer Hospital of Dalian University of Technology, School of Chemistry, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Shaohua Lu
- Cancer Hospital of Dalian University of Technology, School of Chemistry, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Guanghong Xu
- Cancer Hospital of Dalian University of Technology, School of Chemistry, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Ting Song
- Cancer Hospital of Dalian University of Technology, School of Chemistry, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Ziqian Wang
- Cancer Hospital of Dalian University of Technology, School of Chemistry, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Zhichao Zhang
- Cancer Hospital of Dalian University of Technology, School of Chemistry, Dalian University of Technology, Dalian, Liaoning 116024, China
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4
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Stefan SM, Rafehi M. Medicinal polypharmacology-a scientific glossary of terminology and concepts. Front Pharmacol 2024; 15:1419110. [PMID: 39092220 PMCID: PMC11292611 DOI: 10.3389/fphar.2024.1419110] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 04/30/2024] [Indexed: 08/04/2024] Open
Abstract
Medicinal polypharmacology is one answer to the complex reality of multifactorial human diseases that are often unresponsive to single-targeted treatment. It is an admittance that intrinsic feedback mechanisms, crosstalk, and disease networks necessitate drugs with broad modes-of-action and multitarget affinities. Medicinal polypharmacology grew to be an independent research field within the last two decades and stretches from basic drug development to clinical research. It has developed its own terminology embedded in general terms of pharmaceutical drug discovery and development at the intersection of medicinal chemistry, chemical biology, and clinical pharmacology. A clear and precise language of critical terms and a thorough understanding of underlying concepts is imperative; however, no comprehensive work exists to this date that could support researchers in this and adjacent research fields. In order to explore novel options, establish interdisciplinary collaborations, and generate high-quality research outputs, the present work provides a first-in-field glossary to clarify the numerous terms that have originated from various individual disciplines.
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Affiliation(s)
- Sven Marcel Stefan
- Medicinal Chemistry and Systems Polypharmacology, Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology (LIED), University of Lübeck and University Medical Center Schleswig-Holstein (UKSH), Lübeck, Germany
- Department of Biopharmacy, Medical University of Lublin, Lublin, Poland
| | - Muhammad Rafehi
- Institute of Clinical Pharmacology, University Medical Center Göttingen, Göttingen, Germany
- Department of Medical Education, Augsburg University Medicine, Augsburg, Germany
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5
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Baliza LRSP, Freitas TR, Gonçalves EKS, Antunes GR, Souza AJF, Yoneda J, Duarte CL, Andrade SN, de Paula Sabino A, Varotti FP, Sangi DP. Synthesis and cytotoxic evaluation of heterocyclic compounds by vinylic substitution of ketene dithioacetals. Chem Biol Drug Des 2024; 104:e14581. [PMID: 38997237 DOI: 10.1111/cbdd.14581] [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: 03/20/2024] [Revised: 05/27/2024] [Accepted: 07/01/2024] [Indexed: 07/14/2024]
Abstract
N-heterocyclic compounds are important molecular scaffolds in the search for new drugs, since most drugs contain heterocyclic moieties in their molecular structure, and some of these classes of heterocycles are able to provide ligands for two or more biological targets. Ketene dithioacetals are important building blocks in organic synthesis and are widely used in the synthesis of N-heterocyclic compounds. In this work, we used double vinylic substitution reactions on ketene dithioacetals to synthesize a small library of heterocyclic derivatives and evaluated their cytotoxic activity in breast and ovarian cancer cells, identifying two benzoxazoles with good potency and selectivity. In silico predictions indicate that the two most active derivatives exhibit physicochemical properties within the range of drug-like compounds and showed potential to interact with HDAC8 and ERK1 cancer-related targets.
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Affiliation(s)
- Larissa R S P Baliza
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal Fluminense, Rio de Janeiro, Brazil
| | - Túlio R Freitas
- Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Edward K S Gonçalves
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal Fluminense, Rio de Janeiro, Brazil
| | - Gabriel R Antunes
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal Fluminense, Rio de Janeiro, Brazil
| | - Ana J F Souza
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal Fluminense, Rio de Janeiro, Brazil
| | - Julliane Yoneda
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal Fluminense, Rio de Janeiro, Brazil
| | - Caique Lopes Duarte
- Centro de Ciências da Saúde, Universidade Federal de São João Del-Rei, Divinópolis, Minas Gerais, Brazil
| | - Silmara N Andrade
- Centro de Ciências da Saúde, Universidade Federal de São João Del-Rei, Divinópolis, Minas Gerais, Brazil
| | - Adriano de Paula Sabino
- Departamento de Análises Clínicas e Toxicológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Fernando P Varotti
- Centro de Ciências da Saúde, Universidade Federal de São João Del-Rei, Divinópolis, Minas Gerais, Brazil
| | - Diego P Sangi
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal Fluminense, Rio de Janeiro, Brazil
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6
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Hong K, Liu M, Qian L, Bao M, Chen G, Jiang X, Huang J, Xu X. Catalytic [4+2]- and [4+4]-cycloaddition using furan-fused cyclobutanone as a privileged C4 synthon. Nat Commun 2024; 15:5407. [PMID: 38926359 PMCID: PMC11208666 DOI: 10.1038/s41467-024-49664-5] [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: 02/01/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Cycloaddition reactions play a pivotal role in synthetic chemistry for the direct assembly of cyclic architectures. However, hurdles remain for extending the C4 synthon to construct diverse heterocycles via programmable [4+n]-cycloaddition. Here we report an atom-economic and modular intermolecular cycloaddition using furan-fused cyclobutanones (FCBs) as a versatile C4 synthon. In contrast to the well-documented cycloaddition of benzocyclobutenones, this is a complementary version using FCB as a C4 reagent. It involves a C-C bond activation and cycloaddition sequence, including a Rh-catalyzed enantioselective [4 + 2]-cycloaddition with imines and an Au-catalyzed diastereoselective [4 + 4]-cycloaddition with anthranils. The obtained furan-fused lactams, which are pivotal motifs that present in many natural products, bioactive molecules, and materials, are inaccessible or difficult to prepare by other methods. Preliminary antitumor activity study indicates that 6e and 6 f exhibit high anticancer potency against colon cancer cells (HCT-116, IC50 = 0.50 ± 0.05 μM) and esophageal squamous cell carcinoma cells (KYSE-520, IC50 = 0.89 ± 0.13 μM), respectively.
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Affiliation(s)
- Kemiao Hong
- School of Chemistry and Chemical Engineering, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Mengting Liu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 510006, China
| | - Lixin Qian
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 510006, China
| | - Ming Bao
- School of Chemistry and Chemical Engineering, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Gang Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 510006, China
| | - Xinyu Jiang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 510006, China
| | - Jingjing Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 510006, China
| | - Xinfang Xu
- School of Chemistry and Chemical Engineering, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
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7
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Pedroso de Lima F, Costa M, Sousa A, Proença MF. The Chromenopyridine Scaffold: A Privileged Platform in Drug Design. Molecules 2024; 29:3004. [PMID: 38998955 PMCID: PMC11243271 DOI: 10.3390/molecules29133004] [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: 04/23/2024] [Revised: 06/07/2024] [Accepted: 06/19/2024] [Indexed: 07/14/2024] Open
Abstract
The chromenopyridine scaffold represents an important class of heterocyclic compounds exhibiting a broad spectrum of biological properties. This review describes novel and efficient procedures for the synthesis of this scaffold. Herein, several methods were detailed and grouped according to their starting material (e.g., salicylaldehydes, chromones, chromanones and coumarins) and respective biological activity, when reported. This review highlights the potential of the reported synthetic strategies for preparing chromenopyridine derivatives with promising biological activity, paving the way for further developments in drug discovery.
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Affiliation(s)
- Fábio Pedroso de Lima
- Chemistry Centre, School of Sciences, University of Minho, Gualtar Campus, 4715-303 Braga, Portugal
- Centre for Textile Science and Technology (2C2T), University of Minho, Azurém Campus, 4800-058 Guimarães, Portugal
| | - Marta Costa
- Life and Health Sciences Research Institute (ICVS), University of Minho, Gualtar Campus, 4710-057 Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Ana Sousa
- Chemistry Centre, School of Sciences, University of Minho, Gualtar Campus, 4715-303 Braga, Portugal
- Life and Health Sciences Research Institute (ICVS), University of Minho, Gualtar Campus, 4710-057 Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Maria Fernanda Proença
- Chemistry Centre, School of Sciences, University of Minho, Gualtar Campus, 4715-303 Braga, Portugal
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8
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Huang YT, Huang WW, Huang YT, Chen HR, Barve IJ, Sun CM. Substrate-Controlled Divergent Synthesis of Benzimidazole-Fused Quinolines and Spirocyclic Benzimidazole-Fused Isoindoles. J Org Chem 2024; 89:7513-7520. [PMID: 38722245 PMCID: PMC11165576 DOI: 10.1021/acs.joc.4c00164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/24/2024] [Accepted: 04/29/2024] [Indexed: 06/13/2024]
Abstract
A Rh(III)-catalyzed annulation of 2-arylbenzimidazoles with α-diazo carbonyl compounds via C-H activation/carbene insertion/intramolecular cyclization is explored. The switchable product selectivity is achieved by the use of distinct α-diazo carbonyl compounds. Benzimidazole-fused quinolines are obtained through [4 + 2] annulation exclusively when 2-diazocyclohexane-1,3-diones are used, where they act as a C2 synthon. Alternatively, diazonaphthalen-1(2H)-ones merely function as a one-carbon unit synthon to generate a quaternary center through [4 + 1] cyclization to afford spirocyclic benzimidazole-fused isoindole naphthalen-2-ones. A thorough mechanistic study reveals the course of the reaction.
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Affiliation(s)
- Ying-Ti Huang
- Department
of Applied Chemistry, National Yang Ming
Chiao Tung University, 1001 Ta-Hsueh Road, Hsinchu 300-10, Taiwan ROC
| | - Wan-Wen Huang
- Department
of Applied Chemistry, National Yang Ming
Chiao Tung University, 1001 Ta-Hsueh Road, Hsinchu 300-10, Taiwan ROC
| | - Yi-Ting Huang
- Department
of Applied Chemistry, National Yang Ming
Chiao Tung University, 1001 Ta-Hsueh Road, Hsinchu 300-10, Taiwan ROC
| | - Hong-Ren Chen
- Department
of Applied Chemistry, National Yang Ming
Chiao Tung University, 1001 Ta-Hsueh Road, Hsinchu 300-10, Taiwan ROC
| | - Indrajeet J. Barve
- Department
of Chemistry, MES Abasaheb Garware College, Pune 411004, Maharashtra India
| | - Chung-Ming Sun
- Department
of Applied Chemistry, National Yang Ming
Chiao Tung University, 1001 Ta-Hsueh Road, Hsinchu 300-10, Taiwan ROC
- Department
of Medicinal and Applied Chemistry, Kaohsiung
Medical University, 100,
Shih-Chuan first Road, Kaohsiung 807-08, Taiwan ROC
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9
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Huang Y, Li X, Mai BK, Tonogai EJ, Smith AJ, Hergenrother PJ, Liu P, Hoveyda AH. A catalytic process enables efficient and programmable access to precisely altered indole alkaloid scaffolds. Nat Chem 2024; 16:1003-1014. [PMID: 38374457 PMCID: PMC11328697 DOI: 10.1038/s41557-024-01455-7] [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: 02/05/2023] [Accepted: 01/18/2024] [Indexed: 02/21/2024]
Abstract
A compound's overall contour impacts its ability to elicit biological response, rendering access to distinctly shaped molecules desirable. A natural product's framework can be modified, but only if it is abundant and contains suitably modifiable functional groups. Here we introduce a programmable strategy for concise synthesis of precisely altered scaffolds of scarce bridged polycyclic alkaloids. Central to our approach is a scalable catalytic multi-component process that delivers diastereo- and enantiomerically enriched tertiary homoallylic alcohols bearing differentiable alkenyl moieties. We used one product to launch progressively divergent syntheses of a naturally occurring alkaloid and its precisely expanded, contracted and/or distorted framework analogues (average number of steps/scaffold of seven). In vitro testing showed that a skeleton expanded by one methylene in two regions is cytotoxic against four types of cancer cell line. Mechanistic and computational studies offer an account for several unanticipated selectivity trends.
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Affiliation(s)
- Youming Huang
- Supramolecular Science and Engineering Institute, University of Strasbourg, CNRS, Strasbourg, France
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA, USA
| | - Xinghan Li
- Supramolecular Science and Engineering Institute, University of Strasbourg, CNRS, Strasbourg, France
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA, USA
| | - Binh Khanh Mai
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Emily J Tonogai
- Department of Chemistry, Carl Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Amanda J Smith
- Department of Chemistry, Carl Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Paul J Hergenrother
- Department of Chemistry, Carl Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA.
- Cancer Center at Illinois, University of Illinois, Urbana, IL, USA.
| | - Peng Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Amir H Hoveyda
- Supramolecular Science and Engineering Institute, University of Strasbourg, CNRS, Strasbourg, France.
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, MA, USA.
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10
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Stefan K, Namasivayam V, Stefan SM. Computer-aided pattern scoring - A multitarget dataset-driven workflow to predict ligands of orphan targets. Sci Data 2024; 11:530. [PMID: 38783061 PMCID: PMC11116543 DOI: 10.1038/s41597-024-03343-8] [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: 02/28/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
The identification of lead molecules and the exploration of novel pharmacological drug targets are major challenges of medical life sciences today. Genome-wide association studies, multi-omics, and systems pharmacology steadily reveal new protein networks, extending the known and relevant disease-modifying proteome. Unfortunately, the vast majority of the disease-modifying proteome consists of 'orphan targets' of which intrinsic ligands/substrates, (patho)physiological roles, and/or modulators are unknown. Undruggability is a major challenge in drug development today, and medicinal chemistry efforts cannot keep up with hit identification and hit-to-lead optimization studies. New 'thinking-outside-the-box' approaches are necessary to identify structurally novel and functionally distinctive ligands for orphan targets. Here we present a unique dataset that includes critical information on the orphan target ABCA1, from which a novel cheminformatic workflow - computer-aided pattern scoring (C@PS) - for the identification of novel ligands was developed. Providing a hit rate of 95.5% and molecules with high potency and molecular-structural diversity, this dataset represents a suitable template for general deorphanization studies.
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Affiliation(s)
- Katja Stefan
- University of Oslo and Oslo University Hospital, Department of Pathology, Rikshospitalet, Sognsvannsveien 20, 0372, Oslo, Norway
- University of Lübeck and University Medical Center Schleswig-Holstein, Lübeck Institute of Experimental Dermatology, Medical Systems Biology Division, Medicinal Chemistry and Systems Polypharmacology, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - Vigneshwaran Namasivayam
- University of Lübeck and University Medical Center Schleswig-Holstein, Lübeck Institute of Experimental Dermatology, Medical Systems Biology Division, Medicinal Chemistry and Systems Polypharmacology, Ratzeburger Allee 160, 23538, Lübeck, Germany.
- University of Bonn, Pharmaceutical Institute, Department of Pharmaceutical and Cellbiological Chemistry, An der Immenburg 4, 53121, Bonn, Germany.
| | - Sven Marcel Stefan
- University of Oslo and Oslo University Hospital, Department of Pathology, Rikshospitalet, Sognsvannsveien 20, 0372, Oslo, Norway.
- University of Lübeck and University Medical Center Schleswig-Holstein, Lübeck Institute of Experimental Dermatology, Medical Systems Biology Division, Medicinal Chemistry and Systems Polypharmacology, Ratzeburger Allee 160, 23538, Lübeck, Germany.
- Medical University of Lublin, Department of Biopharmacy, Chodzki 4a, 20-093, Lublin, Poland.
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11
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Tang SA, Fults A, Boyd SR, Gattu N, Tran KA, Fan J, MacKenzie KR, Palzkill T, Young DW, Chamakuri S. Expanding Complex Morpholines Using Systematic Chemical Diversity. Org Lett 2024; 26:3493-3497. [PMID: 38506470 DOI: 10.1021/acs.orglett.4c00528] [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] [Indexed: 03/21/2024]
Abstract
The morpholine heterocycle is a structural unit found in many bioactive compounds and FDA-approved drugs, but the generation of more complex C-functionalized morpholine derivatives remains considerably underexplored. Using systematic chemical diversity (SCD), a concept that guides the expansion of saturated drug-like scaffolds through regiochemical and stereochemical variation, we describe the synthesis of a collection of methyl-substituted morpholine acetic acid esters starting from enantiomerically pure amino acids and amino alcohols. In total, 24 diverse substituted morpholines were produced that vary systematically in regiochemistry and stereochemistry (relative and absolute). These diverse C-substituted morpholines can be directly applied in fragment screening or incorporated as building blocks in medicinal chemistry and library synthesis.
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Affiliation(s)
- Sunny Ann Tang
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, United States
| | - Afton Fults
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Shelton R Boyd
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, United States
| | - Nikhil Gattu
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Kevin A Tran
- Center for Drug Discovery, Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, United States
| | - Jiayi Fan
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, United States
| | - Kevin R MacKenzie
- Center for Drug Discovery, Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, United States
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, United States
| | - Timothy Palzkill
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, United States
| | - Damian W Young
- Center for Drug Discovery, Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, United States
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, United States
| | - Srinivas Chamakuri
- Center for Drug Discovery, Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, United States
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12
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Sadeghi M. The untold story of starch as a catalyst for organic reactions. RSC Adv 2024; 14:12676-12702. [PMID: 38645516 PMCID: PMC11027044 DOI: 10.1039/d4ra00775a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/04/2024] [Indexed: 04/23/2024] Open
Abstract
Starch is one of the members of the polysaccharide family. This biopolymer has shown many potential applications in different fields such as catalytic reactions, water treatment, packaging, and food industries. In recent years, using starch as a catalyst has attracted much attention. From a catalytic point of view, starch can be used in organic chemistry reactions as a catalyst or catalyst support. Reports show that as a catalyst, simple starch can promote many heterocyclic compound reactions. On the other hand, functionalized starch is not only capable of advancing the synthesis of heterocycles but also is a good candidate catalyst for other reactions including oxidation and coupling reactions. This review tries to provide a fair survey of published organic reactions which include using starch as a catalyst or a part of the main catalyst. Therefore, the other types of starch applications are not the subject of this review.
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Affiliation(s)
- Masoud Sadeghi
- Department of Organic Chemistry, Faculty of Chemistry, University of Kashan P.O. Box: 87317-51167 Kashan Iran
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13
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Lee H, Kim J, Koh M. Medium-Sized Ring Expansion Strategies: Enhancing Small-Molecule Library Development. Molecules 2024; 29:1562. [PMID: 38611841 PMCID: PMC11013129 DOI: 10.3390/molecules29071562] [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: 03/11/2024] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024] Open
Abstract
The construction of a small molecule library that includes compounds with medium-sized rings is increasingly essential in drug discovery. These compounds are essential for identifying novel therapeutic agents capable of targeting "undruggable" targets through high-throughput and high-content screening, given their structural complexity and diversity. However, synthesizing medium-sized rings presents notable challenges, particularly with direct cyclization methods, due to issues such as transannular strain and reduced degrees of freedom. This review presents an overview of current strategies in synthesizing medium-sized rings, emphasizing innovative approaches like ring-expansion reactions. It highlights the challenges of synthesis and the potential of these compounds to diversify the chemical space for drug discovery, underscoring the importance of medium-sized rings in developing new bioactive compounds.
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Affiliation(s)
- Hwiyeong Lee
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Republic of Korea;
| | - Jonghoon Kim
- Department of Chemistry and Integrative Institute of Basic Science, Soongsil University, Seoul 06978, Republic of Korea;
| | - Minseob Koh
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Republic of Korea;
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14
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Cesarini S, Vicenti I, Poggialini F, Filippi S, Mancin E, Fiaschi L, De Marchi E, Giammarino F, Vagaggini C, Bizzarri BM, Saladino R, Dreassi E, Zazzi M, Botta L. Serendipitous Identification of Azine Anticancer Agents Using a Privileged Scaffold Morphing Strategy. Molecules 2024; 29:1452. [PMID: 38611732 PMCID: PMC11013010 DOI: 10.3390/molecules29071452] [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: 02/15/2024] [Revised: 03/11/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
The use of privileged scaffolds as a starting point for the construction of libraries of bioactive compounds is a widely used strategy in drug discovery and development. Scaffold decoration, morphing and hopping are additional techniques that enable the modification of the chosen privileged framework and better explore the chemical space around it. In this study, two series of highly functionalized pyrimidine and pyridine derivatives were synthesized using a scaffold morphing approach consisting of triazine compounds obtained previously as antiviral agents. Newly synthesized azines were evaluated against lymphoma, hepatocarcinoma, and colon epithelial carcinoma cells, showing in five cases acceptable to good anticancer activity associated with low cytotoxicity on healthy fibroblasts. Finally, ADME in vitro studies were conducted on the best derivatives of the two series showing good passive permeability and resistance to metabolic degradation.
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Affiliation(s)
- Silvia Cesarini
- Department of Biological and Ecological Sciences, University of Viterbo, Via S.C. De Lellis s.n.c., 01100 Viterbo, Italy; (S.C.); (S.F.); (E.M.); (E.D.M.); (B.M.B.); (R.S.)
| | - Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (I.V.); (L.F.); (F.G.); (M.Z.)
| | - Federica Poggialini
- Department of Biotechnology, Chemistry, and Pharmacy (DBCF), University of Siena, 53100 Siena, Italy; (F.P.); (C.V.); (E.D.)
| | - Silvia Filippi
- Department of Biological and Ecological Sciences, University of Viterbo, Via S.C. De Lellis s.n.c., 01100 Viterbo, Italy; (S.C.); (S.F.); (E.M.); (E.D.M.); (B.M.B.); (R.S.)
| | - Eleonora Mancin
- Department of Biological and Ecological Sciences, University of Viterbo, Via S.C. De Lellis s.n.c., 01100 Viterbo, Italy; (S.C.); (S.F.); (E.M.); (E.D.M.); (B.M.B.); (R.S.)
| | - Lia Fiaschi
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (I.V.); (L.F.); (F.G.); (M.Z.)
| | - Elisa De Marchi
- Department of Biological and Ecological Sciences, University of Viterbo, Via S.C. De Lellis s.n.c., 01100 Viterbo, Italy; (S.C.); (S.F.); (E.M.); (E.D.M.); (B.M.B.); (R.S.)
| | - Federica Giammarino
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (I.V.); (L.F.); (F.G.); (M.Z.)
| | - Chiara Vagaggini
- Department of Biotechnology, Chemistry, and Pharmacy (DBCF), University of Siena, 53100 Siena, Italy; (F.P.); (C.V.); (E.D.)
| | - Bruno Mattia Bizzarri
- Department of Biological and Ecological Sciences, University of Viterbo, Via S.C. De Lellis s.n.c., 01100 Viterbo, Italy; (S.C.); (S.F.); (E.M.); (E.D.M.); (B.M.B.); (R.S.)
| | - Raffaele Saladino
- Department of Biological and Ecological Sciences, University of Viterbo, Via S.C. De Lellis s.n.c., 01100 Viterbo, Italy; (S.C.); (S.F.); (E.M.); (E.D.M.); (B.M.B.); (R.S.)
| | - Elena Dreassi
- Department of Biotechnology, Chemistry, and Pharmacy (DBCF), University of Siena, 53100 Siena, Italy; (F.P.); (C.V.); (E.D.)
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (I.V.); (L.F.); (F.G.); (M.Z.)
| | - Lorenzo Botta
- Department of Biological and Ecological Sciences, University of Viterbo, Via S.C. De Lellis s.n.c., 01100 Viterbo, Italy; (S.C.); (S.F.); (E.M.); (E.D.M.); (B.M.B.); (R.S.)
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15
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Whitely C, Winburn H, Li Y. Synthesis and Identification of Heterobivalent Anticancer Compounds Containing Urea and 5-Arylidene-2-Thiohydantoin Motifs. ChemistrySelect 2024; 9:e202304688. [PMID: 38585446 PMCID: PMC10993625 DOI: 10.1002/slct.202304688] [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: 11/20/2023] [Accepted: 02/27/2024] [Indexed: 04/09/2024]
Abstract
Urea and thiohydantoin are among the important privileged structures for drug discovery. We have developed a synthetic approach to the high-throughput synthesis of the heterobivalent compounds containing both urea and 5-arylidene-2-thiohydantoin functional groups. This synthetic methodology was applied to the synthesis of a mixture-based library containing a total of 5280 compounds in a positional scanning format. The library was screened for its antiproliferative activity against cancer cells using a tetrazolium dye (MTT) based assay. Deconvolution of the library identified six hit compounds exhibiting moderate inhibitory potency against cancer cell proliferation.
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Affiliation(s)
- Chelsi Whitely
- Department of Drug Discovery & Biomedical Sciences, University of South Carolina, 517 Sumter St., CLS 617, Columbia, SC 29208
| | - Haley Winburn
- Department of Drug Discovery & Biomedical Sciences, University of South Carolina, 517 Sumter St., CLS 617, Columbia, SC 29208
| | - Yangmei Li
- Department of Drug Discovery & Biomedical Sciences, University of South Carolina, 517 Sumter St., CLS 617, Columbia, SC 29208
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16
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Yim J, Hwang YS, Lee JJ, Kim JH, Baek JY, Jeong J, Choi YI, Jin BK, Park SB. Inflachromene ameliorates Parkinson's disease by targeting Nrf2-binding Keap1. Chem Sci 2024; 15:3588-3595. [PMID: 38455026 PMCID: PMC10915859 DOI: 10.1039/d3sc06997d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 01/15/2024] [Indexed: 03/09/2024] Open
Abstract
Parkinson's disease (PD) is the most common neurodegenerative disease characterized by movement disorder. Despite current therapeutic efforts, PD progression and the loss of dopaminergic neurons in the substantia nigra remain challenging to prevent due to the complex and unclear molecular mechanism involved. We adopted a phenotype-based drug screening approach with neuronal cells to overcome these limitations. In this study, we successfully identified a small molecule with a promising therapeutic effect for PD treatment, called inflachromene (ICM), through our phenotypic screening strategy. Subsequent target identification using fluorescence difference in two-dimensional gel electrophoresis (FITGE) revealed that ICM ameliorates PD by targeting a specific form of Keap1. This interaction led to upregulating various antioxidants, including HO-1, NQO1, and glutathione, ultimately alleviating PD symptoms. Furthermore, ICM exhibited remarkable efficacy in inhibiting the loss of dopaminergic neurons and the activation of astrocytes and microglia, which are critical factors in PD pathology. Our findings suggest that the phenotypic approach employed in this study identified that ICM has potential for PD treatment, offering new hope for more effective therapeutic interventions in the future.
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Affiliation(s)
- Junhyeong Yim
- Department of Biophysics and Chemical Biology, Seoul National University Seoul 08826 Korea
| | - Yoon Soo Hwang
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University Seoul 08826 Korea
| | | | | | - Jeong Yeob Baek
- Department of Biochemistry & Molecular Biology, School of Medicine, Kyung Hee University Seoul 02447 Korea
| | - Jaeyeong Jeong
- Department of Biochemistry & Molecular Biology, School of Medicine, Kyung Hee University Seoul 02447 Korea
| | | | - Byung Kwan Jin
- Department of Biochemistry & Molecular Biology, School of Medicine, Kyung Hee University Seoul 02447 Korea
| | - Seung Bum Park
- Department of Biophysics and Chemical Biology, Seoul National University Seoul 08826 Korea
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University Seoul 08826 Korea
- SPARK Biopharma, Inc. Seoul 08791 Korea
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17
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Rafehi M, Möller M, Ismail Al-Khalil W, Stefan SM. Medicinal Polypharmacology in the Clinic - Translating the Polypharmacolome into Therapeutic Benefit. Pharm Res 2024; 41:411-417. [PMID: 38366233 DOI: 10.1007/s11095-024-03656-8] [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: 10/21/2023] [Accepted: 01/07/2024] [Indexed: 02/18/2024]
Abstract
Drugs with multiple targets, often annotated as 'unselective', 'promiscuous', 'multitarget', or 'polypharmacological', are widely considered in both academic and industrial research as a high risk due to the likelihood of adverse effects. However, retrospective analyses have shown that particularly approved drugs bear rich polypharmacological profiles. This raises the question whether our perception of the specificity paradigm ('one drug-one target concept') is correct - and if specifically multitarget drugs should be developed instead of being rejected. These questions provoke a paradigm shift - regarding the development of polypharmacological drugs not as a 'waste of investment', but acknowledging the existence of a 'lack of investment'. This perspective provides an insight into modern drug development highlighting latest drug candidates that have not been assessed in a broader polypharmacology-based context elsewhere embedded in a historic framework of classical and modern approved multitarget drugs. The article shall be an inspiration to the scientific community to re-consider current standards, and more, to evolve to a better understanding of polypharmacology from a challenge to an opportunity.
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Affiliation(s)
- Muhammad Rafehi
- Department of Medical Education Augsburg, Augsburg University Medicine, Stenglinstr. 2, 86156, Augsburg, Germany.
- Institute of Clinical Pharmacology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany.
| | - Marius Möller
- Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology (LIED), University of Lübeck and University Medical Center Schleswig-Holstein, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - Wouroud Ismail Al-Khalil
- Institute of Clinical Pharmacology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Sven Marcel Stefan
- Medicinal Chemistry and Systems Polypharmacology, Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology (LIED), University of Lübeck and University Medical Center Schleswig-Holstein, Ratzeburger Allee 160, 23538, Lübeck, Germany.
- Department of Pathology, University of Oslo and Oslo University Hospital, Sognsvannsveien 20, 0372, Oslo, Norway.
- Department of Biopharmacy, Medical University of Lublin, Chodzki 4a, Lublin, 20-093, Poland.
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18
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Pan J, Ho TO, Chen YC, Yang BM, Zhao Y. Enantioselective Construction of Eight-Membered N-Heterocycles from Simple 1,3-Dienes via Pd(0) Lewis Base Catalysis. Angew Chem Int Ed Engl 2024; 63:e202317703. [PMID: 38100515 DOI: 10.1002/anie.202317703] [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: 11/20/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 12/17/2023]
Abstract
We report herein an unprecedented enantioselective (4+4) cycloaddition of simple 1,3-dienes with azadienes for the construction of fused eight-membered N-heterocycles. In this transformation, the π-Lewis basic Pd(0) catalyst achieves activation of 1,3-dienes to induce nucleophilic addition to azadienes followed by ring cyclization via a selective terminal allylic substitution. Furthermore, highly efficient and diastereoselective derivatizations of the eight-membered rings provide a facile access to diverse enantiopure fused tetra- to hexacyclic compounds with potential application in medicinal chemistry.
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Affiliation(s)
- Jiaoting Pan
- Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University Binhai New City, Fuzhou, 350207, China
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Takumi Ogawa Ho
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Ying-Chun Chen
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Ministry of Education and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, P. R. China
| | - Bin-Miao Yang
- Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University Binhai New City, Fuzhou, 350207, China
| | - Yu Zhao
- Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University Binhai New City, Fuzhou, 350207, China
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
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19
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Stefan SM, Rafehi M. Medicinal polypharmacology: Exploration and exploitation of the polypharmacolome in modern drug development. Drug Dev Res 2024; 85:e22125. [PMID: 37920929 DOI: 10.1002/ddr.22125] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/23/2023] [Accepted: 10/12/2023] [Indexed: 11/04/2023]
Abstract
At the core of complex and multifactorial human diseases, such as cancer, metabolic syndrome, or neurodegeneration, are multiple players that cross-talk in robust biological networks which are intrinsically resilient to alterations. These multifactorial diseases are characterized by sophisticated feedback mechanisms which manifest cellular imbalance and resistance to drug therapy. By adhering to the specificity paradigm ("one target-one drug concept"), research focused for many years on drugs with very narrow mechanisms of action. This narrow focus promoted therapy ineffectiveness and resistance. However, modern drug discovery has evolved over the last years, increasingly emphasizing integral strategies for the development of clinically effective drugs. These integral strategies include the controlled engagement of multiple targets to overcome therapy resistance. Apart from the additive or even synergistic effects in therapy, multitarget drugs harbor molecular-structural attributes to explore orphan targets of which intrinsic substrates/physiological role(s) and/or modulators are unknown for future therapy purposes. We designated this multidisciplinary and translational research field between medicinal chemistry, chemical biology, and molecular pharmacology as 'medicinal polypharmacology'. Medicinal polypharmacology emerged as alternative approach to common single-targeted pharmacology stretching from basic drug and target identification processes to clinical evaluation of multitarget drugs, and the exploration and exploitation of the 'polypharmacolome' is at the forefront of modern drug development research.
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Affiliation(s)
- Sven Marcel Stefan
- Drug Development and Chemical Biology, Lübeck Institute of Experimental Dermatology (LIED), University of Lübeck and University Medical Center Schleswig-Holstein, Lübeck, Germany
- Translational Neurodegeneration Research and Neuropathology Lab, Department of Pathology, Section of Neuropathology and Oslo University Hospital, University of Oslo, Oslo, Norway
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, New South Wales, Australia
| | - Muhammad Rafehi
- Department of Medical Education, Augsburg University Medicine, Augsburg, Germany
- Institute of Clinical Pharmacology, University Medical Center Göttingen, Göttingen, Germany
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20
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Mokady D, Charish J, Barretto-Burns P, Grisé KN, Coles BLK, Raab S, Ortin-Martinez A, Müller A, Fasching B, Jain P, Drukker M, van der Kooy D, Steger M. Small-Molecule-Directed Endogenous Regeneration of Visual Function in a Mammalian Retinal Degeneration Model. Int J Mol Sci 2024; 25:1521. [PMID: 38338800 PMCID: PMC10855388 DOI: 10.3390/ijms25031521] [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: 10/18/2023] [Revised: 12/31/2023] [Accepted: 01/20/2024] [Indexed: 02/12/2024] Open
Abstract
Degenerative retinal diseases associated with photoreceptor loss are a leading cause of visual impairment worldwide, with limited treatment options. Phenotypic profiling coupled with medicinal chemistry were used to develop a small molecule with proliferative effects on retinal stem/progenitor cells, as assessed in vitro in a neurosphere assay and in vivo by measuring Msx1-positive ciliary body cell proliferation. The compound was identified as having kinase inhibitory activity and was subjected to cellular pathway analysis in non-retinal human primary cell systems. When tested in a disease-relevant murine model of adult retinal degeneration (MNU-induced retinal degeneration), we observed that four repeat intravitreal injections of the compound improved the thickness of the outer nuclear layer along with the regeneration of the visual function, as measured with ERG, visual acuity, and contrast sensitivity tests. This serves as a proof of concept for the use of a small molecule to promote endogenous regeneration in the eye.
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Affiliation(s)
- Daphna Mokady
- Endogena Therapeutics, Inc., 661 University Ave, Toronto, ON M5G 0B7, Canada (P.B.-B.)
| | - Jason Charish
- Endogena Therapeutics, Inc., 661 University Ave, Toronto, ON M5G 0B7, Canada (P.B.-B.)
| | | | - Kenneth N. Grisé
- Department of Molecular Genetics, University of Toronto, Donnelly Centre Rm 1110, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Brenda L. K. Coles
- Department of Molecular Genetics, University of Toronto, Donnelly Centre Rm 1110, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Susanne Raab
- Endogena Therapeutics, AG, Binzmuehlestrasse 170 d, CH-8050 Zuerich, Switzerland
| | - Arturo Ortin-Martinez
- Endogena Therapeutics, Inc., 661 University Ave, Toronto, ON M5G 0B7, Canada (P.B.-B.)
| | - Alex Müller
- Endogena Therapeutics, AG, Binzmuehlestrasse 170 d, CH-8050 Zuerich, Switzerland
| | - Bernhard Fasching
- Endogena Therapeutics, AG, Binzmuehlestrasse 170 d, CH-8050 Zuerich, Switzerland
| | - Payal Jain
- Endogena Therapeutics, Inc., 661 University Ave, Toronto, ON M5G 0B7, Canada (P.B.-B.)
| | - Micha Drukker
- Endogena Therapeutics, AG, Binzmuehlestrasse 170 d, CH-8050 Zuerich, Switzerland
| | - Derek van der Kooy
- Department of Molecular Genetics, University of Toronto, Donnelly Centre Rm 1110, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Matthias Steger
- Endogena Therapeutics, AG, Binzmuehlestrasse 170 d, CH-8050 Zuerich, Switzerland
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21
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Rode JE, Łyczko K, Kaczorek D, Kawęcki R, Dobrowolski JC. VCD spectra of chiral naphthalene-1-carboxamides in the solid-state. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 310:123939. [PMID: 38301569 DOI: 10.1016/j.saa.2024.123939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 01/14/2024] [Accepted: 01/20/2024] [Indexed: 02/03/2024]
Abstract
The VCD spectra of chiral 2,3-dihydro-1H-benzo[de]isoquinolin-1-one (8-substituted naphthalene-1-carboxamide, BIQ) were studied in KBr pellets. The X-ray diffractometry revealed that the Me, Ph, and pClPh BIQs crystalize in the monoclinic P21, while nBu, pMePh, and oMeOPh BIQs in the orthorhombic P212121 space group. Only the Me-BIQ crystal exhibits the presence of cyclic amide dimers, while the others contain chains of the amid group hydrogen bonds. For all BIQs, except pMePh, the most intense IR band in the 1750-1550 cm-1 region is located at ca. 1680 cm-1 and is accompanied by two weak ones at ca. 1618 and 1590 cm-1. For the pMePh derivative, four almost equally intense IR bands at 1662, 1639, 1614, and 1588 cm-1 are observed. This region of the IR spectra of BIQs, but pMePh, is well reproduced by calculations based on BIQ monomers. On the other hand, the complex IR pattern of pMePh is computationally reproduced when larger crystal fragments, like octamers, are considered. Registration of the VCD spectra enabled recognizing the complexity of IR contours at ca. 1680 cm-1 by the corresponding VCD motives. For (i) Me, Ph and pClPh (R)-enantiomers, two (+)(-) bands were distinguished and for (ii) nBu and pMePh ones, one VCD band with right-side asymmetry was found. For (iii) oMeOPh the VCD pattern cannot be unambiguously assigned. Thus, the VCD spectra in the ν(C=O) range diverse the studied compounds. Among the set of molecules, pMePh has exceptional crystal geometry. Therefore, its most intense ν(C=O) band position and shape can be connected with the geometry of the hydrogen bonds, interactions, and crystal packing. Interpretation of the VCD spectra is based on linear and packed BIQ octamers. This cluster model can reproduce the main features of the solid-state VCD of BIQs.
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Affiliation(s)
- Joanna E Rode
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street 03-195, Warsaw, Poland.
| | - Krzysztof Łyczko
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street 03-195, Warsaw, Poland
| | - Dorota Kaczorek
- University of Siedlce, Faculty of Science, 3 Maja Street No 54 08-110, Siedlce, Poland
| | - Robert Kawęcki
- University of Siedlce, Faculty of Science, 3 Maja Street No 54 08-110, Siedlce, Poland
| | - Jan Cz Dobrowolski
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street 03-195, Warsaw, Poland
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22
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Hamad M, Al-Marzooq F, Srinivasulu V, Sulaiman A, Menon V, Ramadan WS, El-Awady R, Al-Tel TH. Antimicrobial activity of nature-inspired molecules against multidrug-resistant bacteria. Front Microbiol 2024; 14:1336856. [PMID: 38318129 PMCID: PMC10838778 DOI: 10.3389/fmicb.2023.1336856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 12/27/2023] [Indexed: 02/07/2024] Open
Abstract
Multidrug-resistant bacterial infections present a serious challenge to global health. In addition to the spread of antibiotic resistance, some bacteria can form persister cells which are tolerant to most antibiotics and can lead to treatment failure or relapse. In the present work, we report the discovery of a new class of small molecules with potent antimicrobial activity against Gram-positive bacteria and moderate activity against Gram-negative drug-resistant bacterial pathogens. The lead compound SIMR 2404 had a minimal inhibitory concentration (MIC) of 2 μg/mL against methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-intermediate Staphylococcus aureus (VISA). The MIC values against Gram-negative bacteria such as Escherichia coli and Actinobacteria baumannii were between 8-32 μg/mL. Time-kill experiments show that compound SIMR 2404 can rapidly kill tested bacteria. Compound SIMR 2404 was also found to rapidly kill MRSA persisters which display high levels of tolerance to conventional antibiotics. In antibiotic evolution experiments, MRSA quickly developed resistance to ciprofloxacin but failed to develop resistance to compound SIMR 2404 even after 24 serial passages. Compound SIMR 2404 was not toxic to normal human fibroblast at a concentration of 4 μg/mL which is twice the MIC concentration against MRSA. However, at a concentration of 8 μg/mL or higher, it showed cytotoxic activity indicating that it is not ideal as a candidate against Gram-negative bacteria. The acceptable toxicity profile and rapid antibacterial activity against MRSA highlight the potential of these molecules for further studies as anti-MRSA agents.
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Affiliation(s)
- Mohamad Hamad
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
- College of Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Farah Al-Marzooq
- College of Medicine and Health Sciences, UAE University, Al Ain, United Arab Emirates
| | - Vunnam Srinivasulu
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Ashna Sulaiman
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Varsha Menon
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Wafaa S. Ramadan
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Raafat El-Awady
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
| | - Taleb H. Al-Tel
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
- College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
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23
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Wang B, Singh J, Deng Y. Photoredox-Catalyzed Divergent Radical Cascade Annulations of 1,6-Enynes via Pyridine N-Oxide-Promoted Vinyl Radical Generation. Org Lett 2023; 25:9219-9224. [PMID: 38112553 PMCID: PMC10842598 DOI: 10.1021/acs.orglett.3c03930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The divergent organophotoredox-catalyzed radical cascade annulation reactions of 1,6-enynes were developed. A series of cyclopropane-fused hetero- and carbo-bicyclic, tricyclic, and spiro-tetracyclic compounds were facilely synthesized from a broad scope of 1,6-enynes and 2,6-lutidine N-oxide under mild and metal-free conditions with blue light-emitting diode light irradiation. The cascade annulation reaction occurs with the intermediacy of a β-oxyvinyl radical, which is produced from photocatalytically generated pyridine N-oxy radical addition to the carbon-carbon triple bond.
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Affiliation(s)
- Ban Wang
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 North Blackford Street, Indianapolis, Indiana 46202, United States
| | - Jujhar Singh
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 North Blackford Street, Indianapolis, Indiana 46202, United States
| | - Yongming Deng
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 North Blackford Street, Indianapolis, Indiana 46202, United States
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24
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Kunnakkattu IR, Choudhary P, Pravda L, Nadzirin N, Smart OS, Yuan Q, Anyango S, Nair S, Varadi M, Velankar S. PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank. J Cheminform 2023; 15:117. [PMID: 38042830 PMCID: PMC10693035 DOI: 10.1186/s13321-023-00786-w] [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: 08/11/2023] [Accepted: 11/17/2023] [Indexed: 12/04/2023] Open
Abstract
While the Protein Data Bank (PDB) contains a wealth of structural information on ligands bound to macromolecules, their analysis can be challenging due to the large amount and diversity of data. Here, we present PDBe CCDUtils, a versatile toolkit for processing and analysing small molecules from the PDB in PDBx/mmCIF format. PDBe CCDUtils provides streamlined access to all the metadata for small molecules in the PDB and offers a set of convenient methods to compute various properties using RDKit, such as 2D depictions, 3D conformers, physicochemical properties, scaffolds, common fragments, and cross-references to small molecule databases using UniChem. The toolkit also provides methods for identifying all the covalently attached chemical components in a macromolecular structure and calculating similarity among small molecules. By providing a broad range of functionality, PDBe CCDUtils caters to the needs of researchers in cheminformatics, structural biology, bioinformatics and computational chemistry.
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Affiliation(s)
- Ibrahim Roshan Kunnakkattu
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Preeti Choudhary
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Lukas Pravda
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Nurul Nadzirin
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Oliver S Smart
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Qi Yuan
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stephen Anyango
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Sreenath Nair
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Mihaly Varadi
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Sameer Velankar
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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25
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Yao R, Jensen AA, Bryce-Rogers HP, Schultz-Knudsen K, Zhou L, Hovendal NP, Pedersen H, Kubus M, Ulven T, Laraia L. Identification of 5-HT2 Serotonin Receptor Modulators through the Synthesis of a Diverse, Tropane- and Quinuclidine-alkaloid-Inspired Compound Library. J Med Chem 2023; 66:11536-11554. [PMID: 37566000 DOI: 10.1021/acs.jmedchem.3c01059] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
The recombination of natural product (NP) fragments in unprecedented ways has emerged as an important strategy for bioactive compound discovery. In this context, we propose that privileged primary fragments predicted to be enriched in activity against a specific target class can be coupled to diverse secondary fragments to engineer selectivity among closely related targets. Here, we report the synthesis of an alkaloid-inspired compound library enriched in spirocyclic ring fusions, comprising 58 compounds from 12 tropane- or quinuclidine-containing scaffolds, all of which can be considered pseudo-NPs. The library displays excellent predicted drug-like properties including high Fsp3 content and Lipinski's rule-of-five compliance. Targeted screening against selected members of the serotonin and dopamine G protein-coupled receptor family led to the identification of several hits that displayed significant agonist or antagonist activity against 5-HT2A and/or 5-HT2C, and subsequent optimization of one of these delivered a lead dual 5-HT2B/C antagonist with a highly promising selectivity profile.
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Affiliation(s)
- Ruwei Yao
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kgs Lyngby, Denmark
| | - Anders A Jensen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Hogan P Bryce-Rogers
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kgs Lyngby, Denmark
| | - Katrine Schultz-Knudsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Libin Zhou
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Nicklas P Hovendal
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kgs Lyngby, Denmark
| | - Henrik Pedersen
- Medicinal Chemistry, H. Lundbeck A/S, Ottiliavej 9, 2500 Valby, Denmark
| | - Mariusz Kubus
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kgs Lyngby, Denmark
| | - Trond Ulven
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Luca Laraia
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, 2800 Kgs Lyngby, Denmark
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26
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Caramiello A, Bellucci MC, Cristina G, Castellano C, Meneghetti F, Mori M, Secundo F, Viani F, Sacchetti A, Volonterio A. Synthesis and Conformational Analysis of Hydantoin-Based Universal Peptidomimetics. J Org Chem 2023; 88:10381-10402. [PMID: 36226862 PMCID: PMC10407853 DOI: 10.1021/acs.joc.2c01903] [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: 08/10/2022] [Indexed: 11/30/2022]
Abstract
The synthesis of a collection of enantiomerically pure, systematically substituted hydantoins as structural privileged universal mimetic scaffolds is presented. It relies on a chemoselective condensation/cyclization domino process between isocyanates of quaternary or unsubstituted α-amino esters and N-alkyl aspartic acid diesters followed by standard hydrolysis/coupling reactions with amines, using liquid-liquid acid/base extraction protocols for the purification of the intermediates. Besides the nature of the α carbon on the isocyanate moiety, either a quaternary carbon or a more flexible methylene group, conformational studies in silico (molecular modeling), in solution (NMR, circular dichroism (CD), Fourier transform infrared (FTIR)), and in solid state (X-ray) showed that the presented hydantoin-based peptidomimetics are able to project their substituents in positions superimposable to the side chains of common protein secondary structures such as α-helix and β-turn, being the open α-helix conformation slightly favorable according to molecular modeling, while the closed β-turn conformation preferred in solution and in solid state.
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Affiliation(s)
- Alessio
M. Caramiello
- Department
of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, via Mancinelli 7, 20131Milano, Italy
| | - Maria Cristina Bellucci
- Department
of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, 20133Milano, Italy
| | - Gaetano Cristina
- Department
of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, via Mancinelli 7, 20131Milano, Italy
| | - Carlo Castellano
- Department
of Chemistry, Università degli Studi
di Milano, via Golgi
19, 20133Milano, Italy
| | - Fiorella Meneghetti
- Department
of Pharmaceutical Sciences, Università
degli Studi di Milano, via Mangiagalli 25, 20133Milano, Italy
| | - Matteo Mori
- Department
of Pharmaceutical Sciences, Università
degli Studi di Milano, via Mangiagalli 25, 20133Milano, Italy
| | - Francesco Secundo
- Consiglio
Nazionale delle Ricerche, Istituto di Scienze
e Tecnologie Chimiche “G. Natta” (SCITEC), via Mario Bianco 9, 20131Milan, Italy
| | - Fiorenza Viani
- Consiglio
Nazionale delle Ricerche, Istituto di Scienze
e Tecnologie Chimiche “G. Natta” (SCITEC), via Mario Bianco 9, 20131Milan, Italy
| | - Alessandro Sacchetti
- Department
of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, via Mancinelli 7, 20131Milano, Italy
| | - Alessandro Volonterio
- Department
of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, via Mancinelli 7, 20131Milano, Italy
- Consiglio
Nazionale delle Ricerche, Istituto di Scienze
e Tecnologie Chimiche “G. Natta” (SCITEC), via Mario Bianco 9, 20131Milan, Italy
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27
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Alniss HY, Chu C, Ramadan WS, Msallam YA, Srinivasulu V, El-Awady R, Macgregor RB, Al-Tel TH. Interaction of an anticancer benzopyrane derivative with DNA: Biophysical, biochemical, and molecular modeling studies. Biochim Biophys Acta Gen Subj 2023; 1867:130347. [PMID: 36958685 DOI: 10.1016/j.bbagen.2023.130347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 03/09/2023] [Accepted: 03/20/2023] [Indexed: 03/25/2023]
Abstract
BACKGROUND SIMR1281 is a potent anticancer lead candidate with multi- target activity against several proteins; however, its mechanism of action at the molecular level is not fully understood. Revealing the mechanism and the origin of multitarget activity is important for the rational identification and optimization of multitarget drugs. METHODS We have used a variety of biophysical (circular dichroism, isothermal titration calorimetry, viscosity, and UV DNA melting), biochemical (topoisomerase I & II assays) and computational (molecular docking and MD simulations) methods to study the interaction of SIMR1281 with duplex DNA structures. RESULTS The biophysical results revealed that SIMR1281 binds to dsDNA via an intercalation-binding mode with an average binding constant of 3.1 × 106 M-1. This binding mode was confirmed by the topoisomerases' inhibition assays and molecular modeling simulations, which showed the intercalation of the benzopyrane moiety between DNA base pairs, while the remaining moieties (thiazole and phenyl rings) sit in the minor groove and interact with the flanking base pairs adjacent to the intercalation site. CONCLUSIONS The DNA binding characteristics of SIMR1281, which can disrupt/inhibit DNA function as confirmed by the topoisomerases' inhibition assays, indicate that the observed multi-target activity might originate from ligand intervention at nucleic acids level rather than due to direct interactions with multiple biological targets at the protein level. GENERAL SIGNIFICANCE The findings of this study could be helpful to guide future optimization of benzopyrane-based ligands for therapeutic purposes.
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Affiliation(s)
- Hasan Y Alniss
- College of Pharmacy, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates; Sharjah Institute for Medical Research, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates.
| | - Chen Chu
- Graduate Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Wafaa S Ramadan
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
| | - Yousef A Msallam
- College of Pharmacy, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates; Sharjah Institute for Medical Research, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
| | - Vunnam Srinivasulu
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
| | - Raafat El-Awady
- College of Pharmacy, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates; Sharjah Institute for Medical Research, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
| | - Robert B Macgregor
- Graduate Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Taleb H Al-Tel
- College of Pharmacy, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates; Sharjah Institute for Medical Research, University of Sharjah, Sharjah, P.O. Box 27272, United Arab Emirates
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28
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Forrest I, Parker CG. Proteome-Wide Fragment-Based Ligand and Target Discovery. Isr J Chem 2023; 63:e202200098. [PMID: 38213795 PMCID: PMC10783656 DOI: 10.1002/ijch.202200098] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Indexed: 02/10/2023]
Abstract
Chemical probes are invaluable tools to investigate biological processes and can serve as lead molecules for the development of new therapies. However, despite their utility, only a fraction of human proteins have selective chemical probes, and more generally, our knowledge of the "chemically-tractable" proteome is limited, leaving many potential therapeutic targets unexploited. To help address these challenges, powerful chemical proteomic approaches have recently been developed to globally survey the ability of proteins to bind small molecules (i. e., ligandability) directly in native systems. In this review, we discuss the utility of such approaches, with a focus on the integration of chemoproteomic methods with fragment-based ligand discovery (FBLD), to facilitate the broad mapping of the ligandable proteome while also providing starting points for progression into lead chemical probes.
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Affiliation(s)
- Ines Forrest
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Christopher G Parker
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
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29
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George N, Akhtar MJ, Balushi KA, Safi SZ, Azmi SNH, Khan SA. The emerging role of proteolysis targeting chimeras (PROTACs) in the treatment of Alzheimer’s disease. Med Chem Res 2023. [DOI: 10.1007/s00044-023-03026-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/27/2023] [Indexed: 02/11/2023]
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30
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DFT analysis and in vitro studies of isoxazole derivatives as potent antioxidant and antibacterial agents synthesized via one-pot methodology. RESEARCH ON CHEMICAL INTERMEDIATES 2022. [DOI: 10.1007/s11164-022-04910-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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31
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Yim J, Lee J, Yi S, Koo JY, Oh S, Park H, Kim SS, Bae MA, Park J, Park SB. Phenotype-based screening rediscovered benzopyran-embedded microtubule inhibitors as anti-neuroinflammatory agents by modulating the tubulin-p65 interaction. Exp Mol Med 2022; 54:2200-2209. [PMID: 36509830 PMCID: PMC9743128 DOI: 10.1038/s12276-022-00903-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/28/2022] [Accepted: 10/13/2022] [Indexed: 12/14/2022] Open
Abstract
Neuroinflammation is one of the critical processes implicated in central nervous system (CNS) diseases. Therefore, alleviating neuroinflammation has been highlighted as a therapeutic strategy for treating CNS disorders. However, the complexity of neuroinflammatory processes and poor drug transport to the brain are considerable hurdles to the efficient control of neuroinflammation using small-molecule therapeutics. Thus, there is a significant demand for new chemical entities (NCEs) targeting neuroinflammation. Herein, we rediscovered benzopyran-embedded tubulin inhibitor 1 as an anti-neuroinflammatory agent via phenotype-based screening. A competitive photoaffinity labeling study revealed that compound 1 binds to tubulin at the colchicine-binding site. Structure-activity relationship analysis of 1's analogs identified SB26019 as a lead compound with enhanced anti-neuroinflammatory efficacy. Mechanistic studies revealed that upregulation of the tubulin monomer was critical for the anti-neuroinflammatory activity of SB26019. We serendipitously found that the tubulin monomer recruits p65, inhibiting its translocation from the cytosol to the nucleus and blocking NF-κB-mediated inflammatory pathways. Further in vivo validation using a neuroinflammation mouse model demonstrated that SB26019 suppressed microglial activation by downregulating lba-1 and proinflammatory cytokines. Intraperitoneal administration of SB26019 showed its therapeutic potential as an NCE for successful anti-neuroinflammatory regulation. Along with the recent growing demands on tubulin modulators for treating various inflammatory diseases, our results suggest that colchicine-binding site-specific modulation of tubulins can be a potential strategy for preventing neuroinflammation and treating CNS diseases.
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Affiliation(s)
- Junhyeong Yim
- grid.31501.360000 0004 0470 5905Department of Biophysics and Chemical Biology, Seoul National University, Seoul, 08826 Korea
| | - Jaeseok Lee
- grid.412010.60000 0001 0707 9039Department of Chemistry, Kangwon National University, Chuncheon, 24341 Korea
| | - Sihyeong Yi
- grid.31501.360000 0004 0470 5905CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, 08826 Korea
| | - Ja Young Koo
- grid.31501.360000 0004 0470 5905CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, 08826 Korea
| | - Sangmi Oh
- grid.31501.360000 0004 0470 5905CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, 08826 Korea
| | - Hankum Park
- grid.31501.360000 0004 0470 5905CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, 08826 Korea ,grid.31501.360000 0004 0470 5905Present Address: Department of Dental Sciences, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, 08826 Korea
| | - Seong Soon Kim
- grid.29869.3c0000 0001 2296 8192Bio Platform Technology Research Center, Korea Research Institute of Chemical Technology, Daejeon, 34114 Korea
| | - Myung Ae Bae
- grid.29869.3c0000 0001 2296 8192Bio Platform Technology Research Center, Korea Research Institute of Chemical Technology, Daejeon, 34114 Korea ,grid.412786.e0000 0004 1791 8264Department of Medicinal Chemistry and Pharmacology, University of Science & Technology, Daejeon, 34114 Korea
| | - Jongmin Park
- grid.412010.60000 0001 0707 9039Department of Chemistry, Kangwon National University, Chuncheon, 24341 Korea ,grid.412010.60000 0001 0707 9039Kangwon Institute of Inclusive Technology, Kangwon National University, Chuncheon, 24341 Korea
| | - Seung Bum Park
- grid.31501.360000 0004 0470 5905Department of Biophysics and Chemical Biology, Seoul National University, Seoul, 08826 Korea ,grid.31501.360000 0004 0470 5905CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, 08826 Korea
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32
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Li F, Hu Q, Zhang X, Sun R, Liu Z, Wu S, Tian S, Ma X, Dai Z, Yang X, Gao S, Bai F. DeepPROTACs is a deep learning-based targeted degradation predictor for PROTACs. Nat Commun 2022; 13:7133. [PMID: 36414666 PMCID: PMC9681730 DOI: 10.1038/s41467-022-34807-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/08/2022] [Indexed: 11/24/2022] Open
Abstract
The rational design of PROTACs is difficult due to their obscure structure-activity relationship. This study introduces a deep neural network model - DeepPROTACs to help design potent PROTACs molecules. It can predict the degradation capacity of a proposed PROTAC molecule based on structures of given target protein and E3 ligase. The experimental dataset is mainly collected from PROTAC-DB and appropriately labeled according to the DC50 and Dmax values. In the model of DeepPROTACs, the ligands as well as the ligand binding pockets are generated and represented with graphs and fed into Graph Convolutional Networks for feature extraction. While SMILES representations of linkers are fed into a Bidirectional Long Short-Term Memory layer to generate the features. Experiments show that DeepPROTACs model achieves 77.95% average prediction accuracy and 0.8470 area under receiver operating characteristic curve on the test set. DeepPROTACs is available online at a web server ( https://bailab.siais.shanghaitech.edu.cn/services/deepprotacs/ ) and at github ( https://github.com/fenglei104/DeepPROTACs ).
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Affiliation(s)
- Fenglei Li
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
- School of Information Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
| | - Qiaoyu Hu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
| | - Xianglei Zhang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
| | - Renhong Sun
- Gluetacs Therapeutics (Shanghai) Co., Ltd., 99 Haike Road, Zhangjiang Hi-Tech Park, Shanghai, 201210, China
| | - Zhuanghua Liu
- School of Information Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
| | - Sanan Wu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
| | - Siyuan Tian
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
| | - Xinyue Ma
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
- School of Information Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
| | - Zhizhuo Dai
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China
| | - Xiaobao Yang
- Gluetacs Therapeutics (Shanghai) Co., Ltd., 99 Haike Road, Zhangjiang Hi-Tech Park, Shanghai, 201210, China.
| | - Shenghua Gao
- School of Information Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China.
| | - Fang Bai
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China.
- School of Information Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China.
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai, 201210, China.
- Shanghai Clinical Research and Trial Center, Shanghai, 201210, China.
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33
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Toman D, Cankař P. Synthesis of Unsymmetrical 1,1’‐Bibenzimidazoles via an N‐Amination Reaction Forming the Key N‐N Bond. ChemistrySelect 2022. [DOI: 10.1002/slct.202203144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Daniel Toman
- Department of Organic Chemistry Faculty of Science Palacký University 17. Listopadu 1192/12 77900 Olomouc Czech Republic
| | - Petr Cankař
- Department of Organic Chemistry Faculty of Science Palacký University 17. Listopadu 1192/12 77900 Olomouc Czech Republic
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34
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Recent Advances in PROTACs for Drug Targeted Protein Research. Int J Mol Sci 2022; 23:ijms231810328. [PMID: 36142231 PMCID: PMC9499226 DOI: 10.3390/ijms231810328] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/04/2022] [Accepted: 09/05/2022] [Indexed: 01/30/2023] Open
Abstract
Proteolysis-targeting chimera (PROTAC) is a heterobifunctional molecule. Typically, PROTAC consists of two terminals which are the ligand of the protein of interest (POI) and the specific ligand of E3 ubiquitin ligase, respectively, via a suitable linker. PROTAC degradation of the target protein is performed through the ubiquitin–proteasome system (UPS). The general process is that PROTAC binds to the target protein and E3 ligase to form a ternary complex and label the target protein with ubiquitination. The ubiquitinated protein is recognized and degraded by the proteasome in the cell. At present, PROTAC, as a new type of drug, has been developed to degrade a variety of cancer target proteins and other disease target proteins, and has shown good curative effects on a variety of diseases. For example, PROTACs targeting AR, BR, BTK, Tau, IRAK4, and other proteins have shown unprecedented clinical efficacy in cancers, neurodegenerative diseases, inflammations, and other fields. Recently, PROTAC has entered a phase of rapid development, opening a new field for biomedical research and development. This paper reviews the various fields of targeted protein degradation by PROTAC in recent years and summarizes and prospects the hot targets and indications of PROTAC.
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35
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Zhang W, Vadlakonda S, Wu M, Chintareddy V, Vogeti LN, Juarez L, Muppa S, Parker C, Kellogg-Yelder D, Williams J, Polach K, Chen X, Raman K, Babu Y, Kotian P. Discovery and Optimization of Orally Bioavailable and Potent Plasma Kallikrein Inhibitors Bearing a Quaternary Carbon. Bioorg Med Chem 2022; 73:117035. [DOI: 10.1016/j.bmc.2022.117035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 11/02/2022]
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36
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Kim H, Park J, Kim JM. Targeted Protein Degradation to Overcome Resistance in Cancer Therapies: PROTAC and N-Degron Pathway. Biomedicines 2022; 10:2100. [PMID: 36140200 PMCID: PMC9495352 DOI: 10.3390/biomedicines10092100] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 11/17/2022] Open
Abstract
Extensive progress in understanding the molecular mechanisms of cancer growth and proliferation has led to the remarkable development of drugs that target cancer-driving molecules. Most target molecules are proteins such as kinases and kinase-associated receptors, which have enzymatic activities needed for the signaling cascades of cells. The small molecule inhibitors for these target molecules greatly improved therapeutic efficacy and lowered the systemic toxicity in cancer therapies. However, long-term and high-dosage treatment of small inhibitors for cancer has produced other obstacles, such as resistance to inhibitors. Among recent approaches to overcoming drug resistance to cancers, targeted protein degradation (TPD) such as proteolysis-targeting chimera (PROTAC) technology adopts a distinct mechanism of action by which a target protein is destroyed through the cellular proteolytic system, such as the ubiquitin-proteasome system or autophagy. Here, we review the currently developed PROTACs as the representative TPD molecules for cancer therapy and the N-degrons of the N-degron pathways as the potential TPD ligands.
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Affiliation(s)
- Hanbyeol Kim
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Jeongbae Park
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Jeong-Mok Kim
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
- Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul 04763, Korea
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37
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Guo JM, Mao ZY, Liu CH, Yang SY, Wei BG. Palladium-Catalyzed Sequential Heck Reactions of Olefin-Tethered Aryl Iodides with Alkenes. J Org Chem 2022; 87:11838-11845. [PMID: 35981349 DOI: 10.1021/acs.joc.2c01694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An efficient approach to functionalized (E)-3-cinnamyl-3-methyl-2,3-dihydrobenzofurans and (E)-(3-methyl-2,3-dihydrobenzofuran-3-yl)but-2-enones has been developed through a Pd-catalyzed one-pot cascade process involving two sequential Heck reactions, that is, an intramolecular Heck reaction of olefin-tethered aryl iodides and an intermolecular Heck reaction with substituted styrenes and α,β-unsaturated ketones. As a result, a series of desired products were obtained in moderate to good yields and with exclusive E-form selectivities.
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Affiliation(s)
- Jia-Ming Guo
- Department of Natural Medicine, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Zhuo-Ya Mao
- Department of Natural Medicine, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Chang-Hong Liu
- Department of Natural Medicine, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Shang-Ye Yang
- Department of Natural Medicine, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Bang-Guo Wei
- Department of Natural Medicine, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
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38
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Spasov AA, Brigadirova AA, Zhukovskaya ON, Morkovnik AS, Lifanova YV. Search for compounds with antioxidant and antiradical activity among N9-substituted 2-(biphenyl-4-yl)imidazo[1,2-a]benzimidazoles. RESEARCH RESULTS IN PHARMACOLOGY 2022. [DOI: 10.3897/rrpharmacology.8.85498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Introduction: Biphenyl and imidazobenzimidazole derivatives attract ongoing attention as a combination of these two privileged substructures with promising pharmacological activities. The aim of this study was to synthesize and investigate in vitro antioxidant activity of promising novel compounds: 2-(biphenyl-4-yl)imidazo[1,2-a]benzimidazoles.
Materials and methods: The newly synthesized compounds were characterized by IR, 1H NMR and CHBr(Cl)NO analyses. All newly synthesized compounds were screened for their in vitro antioxidant activity: inhibition of lipid peroxidation (LPO), 2,2’-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS•+) radical cation decolorization and inhibition of hemoglobin (Hb)-H2O2-induced luminol chemiluminescence.
Results and discussion: 2-Amino-3-[(2-biphenyl-4-yl)-2-oxo-ethyl)]-1-R-1Н-benzimidazolium bromides were synthesized, and their cyclization into functionalized imidazo[1,2-a]benzimidazole derivatives was studied. The resulting compounds showed LPO inhibitory activity comparable to that of dibunol. Compounds 1a and 1d (see graphical abstract), containing a methyl or dimethylaminoethyl substituent in the N9 position also proved to be equally highly active in the Hb-H2O2-induced luminol chemiluminescence model, while compound 1a was somewhat more active than 1d in the ABTS• radical scavenging assay.
Conclusion: The study showed that compounds 1a and 1d have the highest antioxidant activity. Thus, this new class of 2-(biphenyl-4-yl)imidazo[1,2-a]benzimidazole derivatives represents a valuable leading series with great potential for use as antioxidants and as promising candidates for further efficacy evaluation.
Graphical abstract:
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39
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Repac Antić D, Parčina M, Gobin I, Petković Didović M. Chelation in Antibacterial Drugs: From Nitroxoline to Cefiderocol and Beyond. Antibiotics (Basel) 2022; 11:1105. [PMID: 36009974 PMCID: PMC9405089 DOI: 10.3390/antibiotics11081105] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 11/16/2022] Open
Abstract
In the era of escalating antimicrobial resistance, the need for antibacterial drugs with novel or improved modes of action (MOAs) is a health concern of utmost importance. Adding or improving the chelating abilities of existing drugs or finding new, nature-inspired chelating agents seems to be one of the major ways to ensure progress. This review article provides insight into the modes of action of antibacterial agents, class by class, through the perspective of chelation. We covered a wide scope of antibacterials, from a century-old quintessential chelating agent nitroxoline, currently unearthed due to its newly discovered anticancer and antibiofilm activities, over the commonly used antibacterial classes, to new cephalosporin cefiderocol and a potential future class of tetramates. We show the impressive spectrum of roles that chelation plays in antibacterial MOAs. This, by itself, demonstrates the importance of understanding the fundamental chemistry behind such complex processes.
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Affiliation(s)
- Davorka Repac Antić
- Department of Microbiology and Parasitology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
- Department of Clinical Microbiology, Clinical Hospital Center Rijeka, 51000 Rijeka, Croatia
| | - Marijo Parčina
- Institute of Medical Microbiology, Immunology and Parasitology, Bonn University Hospital, 53127 Bonn, Germany
| | - Ivana Gobin
- Department of Microbiology and Parasitology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
| | - Mirna Petković Didović
- Department of Medical Chemistry, Biochemistry and Clinical Chemistry, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
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40
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Malone JA, Philkhana SC, Stepherson JR, Badmus FO, Fronczek FR, Kartika R. Copper(I)-Catalyzed Synthesis of Unsymmetrical All-Carbon Bis-Quaternary Centers at the Opposing α-Carbons of Cyclohexanones. Org Lett 2022; 24:4810-4815. [PMID: 35767696 PMCID: PMC9490817 DOI: 10.1021/acs.orglett.2c01890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
![]()
We describe a new
synthetic reaction that generates all-carbon
bis-quaternary centers at the opposing side of α-carbons in
cyclohexanone with four different substituents in a controlled manner.
Catalyzed by Cu(MeCN)4BF4 salt, this chemistry
is proposed to proceed via an intermediacy of unsymmetrical O-allyl oxyallyl cations, which undergo a sequence of regioselective
nucleophilic addition with substituted indoles and diastereoselective
Claisen rearrangement in a single synthetic operation. The stereochemical
outcome of the products features the cis diastereorelationship
between the two aryl groups at the α,α′-positions.
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Affiliation(s)
- Joshua A Malone
- Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803, United States
| | - Satish Chandra Philkhana
- Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803, United States
| | - Jacob R Stepherson
- Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803, United States
| | - Fatimat O Badmus
- Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803, United States
| | - Frank R Fronczek
- Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803, United States
| | - Rendy Kartika
- Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803, United States
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41
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Shearer J, Castro JL, Lawson ADG, MacCoss M, Taylor RD. Rings in Clinical Trials and Drugs: Present and Future. J Med Chem 2022; 65:8699-8712. [PMID: 35730680 PMCID: PMC9289879 DOI: 10.1021/acs.jmedchem.2c00473] [Citation(s) in RCA: 108] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a comprehensive analysis of all ring systems (both heterocyclic and nonheterocyclic) in clinical trial compounds and FDA-approved drugs. We show 67% of small molecules in clinical trials comprise only ring systems found in marketed drugs, which mirrors previously published findings for newly approved drugs. We also show there are approximately 450 000 unique ring systems derived from 2.24 billion molecules currently available in synthesized chemical space, and molecules in clinical trials utilize only 0.1% of this available pool. Moreover, there are fewer ring systems in drugs compared with those in clinical trials, but this is balanced by the drug ring systems being reused more often. Furthermore, systematic changes of up to two atoms on existing drug and clinical trial ring systems give a set of 3902 future clinical trial ring systems, which are predicted to cover approximately 50% of the novel ring systems entering clinical trials.
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Affiliation(s)
| | | | | | - Malcolm MacCoss
- Bohicket Pharma Consulting Limited Liability Company, 2556 Seabrook Island Road, Seabrook Island, South Carolina29455, United States
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42
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Spasov AA, Zhukovskaya ON, Gurova NA, Naumenko LV, Eliseeva NV, Kucheryavenko AF, Kosolapov VA, Yakovlev DS, Muravyeva VY, Babkova VA, Babkov DA, Lifanova JV, Morkovnik AS. Pharmacological Properties of 2-Aminobenzimidazole Halides and Imidazo[1,2-a]Benzimidazole Derivatives. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1068162022020236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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43
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Ping Y, Pan Q, Guo Y, Liu Y, Li X, Wang M, Kong W. Switchable 1,2-Rearrangement Enables Expedient Synthesis of Structurally Diverse Fluorine-Containing Scaffolds. J Am Chem Soc 2022; 144:11626-11637. [DOI: 10.1021/jacs.2c02487] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Yuanyuan Ping
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, P. R. China
| | - Qi Pan
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, P. R. China
| | - Ya Guo
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, P. R. China
| | - Yongli Liu
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, P. R. China
| | - Xiao Li
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, P. R. China
| | - Minyan Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Wangqing Kong
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, P. R. China
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44
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Choi Y, Lee S, Kim H, Park SB. Design and Synthesis of Conformationally Diverse Pyrimidine-Embedded Medium/Macro- and Bridged Cycles via Skeletal Transformation. Front Chem 2022; 10:841250. [PMID: 35444999 PMCID: PMC9014854 DOI: 10.3389/fchem.2022.841250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/02/2022] [Indexed: 11/13/2022] Open
Abstract
The rigidity and flexibility of small molecules are complementary in 3-dimensional ligand-protein interaction. Therefore, the chemical library with conformational diversity would be a valuable resource for investigating the influence of skeletal flexibility on the biological system. In this regard, we designed and synthesized ten conformationally diverse pyrimidine-embedded medium/macro- and bridged cyclic scaffolds covering 7- to 14-member rings via an efficient skeletal transformation strategy. Their high conformational and shape diversity was confirmed by chemoinformatic analysis.
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Affiliation(s)
- Yoona Choi
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Subin Lee
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Heejun Kim
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Seung Bum Park
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, South Korea
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45
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Recent Advances in Divergent Synthetic Strategies for Indole-Based Natural Product Libraries. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27072171. [PMID: 35408569 PMCID: PMC9000743 DOI: 10.3390/molecules27072171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 01/26/2023]
Abstract
Considering the potential bioactivities of natural product and natural product-like compounds with highly complex and diverse structures, the screening of collections and small-molecule libraries for high-throughput screening (HTS) and high-content screening (HCS) has emerged as a powerful tool in the development of novel therapeutic agents. Herein, we review the recent advances in divergent synthetic approaches such as complexity-to-diversity (Ctd) and biomimetic strategies for the generation of structurally complex and diverse indole-based natural product and natural product-like small-molecule libraries.
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46
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Shin Y, Jeong K, Lee J, Lee HJ, Yim J, Kim J, Kim S, Park SB. Inhibition of ACE2-Spike Interaction by an ACE2 Binder Suppresses SARS-CoV-2 Entry. Angew Chem Int Ed Engl 2022; 61:e202115695. [PMID: 35043545 PMCID: PMC9011661 DOI: 10.1002/anie.202115695] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Indexed: 12/20/2022]
Abstract
The emergence of SARS-CoV-2 variants is a significant concern in developing effective therapeutics and vaccines in the middle of the ongoing COVID-19 pandemic. Here, we have identified a novel small molecule that inhibited the interactions between SARS-CoV-2 spike RBDs and ACE2 by modulating ACE2 without impairing its enzymatic activity necessary for normal physiological functions. Furthermore, the identified compounds suppressed viral infection in cultured cells by inhibiting the entry of ancestral and variant SARS-CoV-2. Our study suggests that targeting ACE2 could be a novel therapeutic strategy to inhibit SARS-CoV-2 entry into host cells and prevent the development of COVID-19.
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Affiliation(s)
- Young‐Hee Shin
- CRI Center for Chemical ProteomicsDepartment of ChemistrySeoul National UniversitySeoul08826Korea
- Department of Chemical Engineering & BiotechnologyKorea Polytechnic UniversitySiheung15073Korea
| | - Kiyoung Jeong
- CRI Center for Chemical ProteomicsDepartment of ChemistrySeoul National UniversitySeoul08826Korea
| | - Jihye Lee
- Zoonotic Virus LaboratoryInstitut Pasteur KoreaSeongnam13488Korea
| | - Hyo Jung Lee
- Zoonotic Virus LaboratoryInstitut Pasteur KoreaSeongnam13488Korea
| | - Junhyeong Yim
- Department of Biophysics and Chemical BiologySeoul National UniversitySeoul08826Korea
| | - Jonghoon Kim
- Department of Chemistry and Integrative Institute of Basic ScienceSoongsil UniversitySeoul06978Korea
| | - Seungtaek Kim
- Zoonotic Virus LaboratoryInstitut Pasteur KoreaSeongnam13488Korea
| | - Seung Bum Park
- CRI Center for Chemical ProteomicsDepartment of ChemistrySeoul National UniversitySeoul08826Korea
- Department of Biophysics and Chemical BiologySeoul National UniversitySeoul08826Korea
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47
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Ge S, Zhu YM, Xu XP, Ji SJ. [4 + 1 + 1] Tandem Cyclization Reaction Involving Isocyanides: Access to 2-(Trifluoromethyl)quinazolin-4(3 H)-imines. J Org Chem 2022; 87:3422-3432. [PMID: 35133158 DOI: 10.1021/acs.joc.1c03008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A palladium-catalyzed three-component reaction of isocyanides, 2,2,2-trifluoro-N-(2-iodophenyl)acetimidoyl chlorides, and amines for the one-pot synthesis of 2-(trifluoromethyl)quinazolin-4(3H)-imines was described. The protocol features a wide substrate scope, high efficiency, and readily available raw materials.
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Affiliation(s)
- Shen Ge
- Key Laboratory of Organic Synthesis of Jiangsu Province, College of Chemistry, Chemical Engineering and Materials Science & Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou 215123, P. R. China
| | - Yi-Ming Zhu
- Key Laboratory of Organic Synthesis of Jiangsu Province, College of Chemistry, Chemical Engineering and Materials Science & Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou 215123, P. R. China
| | - Xiao-Ping Xu
- Key Laboratory of Organic Synthesis of Jiangsu Province, College of Chemistry, Chemical Engineering and Materials Science & Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou 215123, P. R. China.,Innovation Center for Chemical Science, Soochow University, Suzhou 215123, P. R. China
| | - Shun-Jun Ji
- Key Laboratory of Organic Synthesis of Jiangsu Province, College of Chemistry, Chemical Engineering and Materials Science & Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou 215123, P. R. China
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48
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Shin Y, Jeong K, Lee J, Lee HJ, Yim J, Kim J, Kim S, Park SB. Inhibition of ACE2‐Spike Interaction by an ACE2 Binder Suppresses SARS‐CoV‐2 Entry. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202115695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Young‐Hee Shin
- CRI Center for Chemical Proteomics Department of Chemistry Seoul National University Seoul 08826 Korea
- Department of Chemical Engineering & Biotechnology Korea Polytechnic University Siheung 15073 Korea
| | - Kiyoung Jeong
- CRI Center for Chemical Proteomics Department of Chemistry Seoul National University Seoul 08826 Korea
| | - Jihye Lee
- Zoonotic Virus Laboratory Institut Pasteur Korea Seongnam 13488 Korea
| | - Hyo Jung Lee
- Zoonotic Virus Laboratory Institut Pasteur Korea Seongnam 13488 Korea
| | - Junhyeong Yim
- Department of Biophysics and Chemical Biology Seoul National University Seoul 08826 Korea
| | - Jonghoon Kim
- Department of Chemistry and Integrative Institute of Basic Science Soongsil University Seoul 06978 Korea
| | - Seungtaek Kim
- Zoonotic Virus Laboratory Institut Pasteur Korea Seongnam 13488 Korea
| | - Seung Bum Park
- CRI Center for Chemical Proteomics Department of Chemistry Seoul National University Seoul 08826 Korea
- Department of Biophysics and Chemical Biology Seoul National University Seoul 08826 Korea
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49
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Srinivasulu V, Srikanth G, Khanfar MA, Abu-Yousef IA, Majdalawieh AF, Mazitschek R, Setty SC, Sebastian A, Al-Tel TH. Stereodivergent Complexity-to-Diversity Strategy en Route to the Synthesis of Nature-Inspired Skeleta. J Org Chem 2022; 87:1377-1397. [PMID: 35014258 DOI: 10.1021/acs.joc.1c02698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The complexity-to-diversity (CtD) strategy has become one of the most powerful tools used to transform complex natural products into diverse skeleta. However, the reactions utilized in this process are often limited by their compatibility with existing functional groups, which in turn restricts access to the desired skeletal diversity. In the course of employing a CtD strategy en route to the synthesis of natural product-inspired compounds, our group has developed several stereodivergent strategies employing indoloquinolizine natural product analogues as starting materials. These transformations led to the rapid and diastereoselective synthesis of diverse classes of natural product-like architectures, including camptothecin-inspired analogues, azecane medium-sized ring systems, arborescidine-inspired systems, etc. This manifestation required a drastic modification of the synthetic design that ultimately led to modular and diastereoselective access to a diverse collection of various classes of biologically significant natural product analogues. The reported strategies provide a unique platform that will be broadly applicable to other late-stage natural product transformation approaches.
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Affiliation(s)
- Vunnam Srinivasulu
- Sharjah Institute for Medical Research, University of Sharjah, P.O. Box 27272, Sharjah, UAE
| | - Gourishetty Srikanth
- Department of Biology, Chemistry and Environmental Sciences, American University of Sharjah, P.O. Box 26666, Sharjah, UAE
| | - Monther A Khanfar
- College of Science, Department of Chemistry, Pure and Applied Chemistry Group, University of Sharjah, P.O. Box 27272, Sharjah, UAE
| | - Imad A Abu-Yousef
- Department of Biology, Chemistry and Environmental Sciences, American University of Sharjah, P.O. Box 26666, Sharjah, UAE
| | - Amin F Majdalawieh
- Department of Biology, Chemistry and Environmental Sciences, American University of Sharjah, P.O. Box 26666, Sharjah, UAE
| | - Ralph Mazitschek
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Subbaiah Chennam Setty
- Department of Biology, Chemistry and Environmental Sciences, American University of Sharjah, P.O. Box 26666, Sharjah, UAE
| | - Anusha Sebastian
- Sharjah Institute for Medical Research, University of Sharjah, P.O. Box 27272, Sharjah, UAE
| | - Taleb H Al-Tel
- Sharjah Institute for Medical Research, University of Sharjah, P.O. Box 27272, Sharjah, UAE.,College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, UAE
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50
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Chatterjee R, Bhukta S, Dandela R. Ionic
liquid‐assisted
synthesis of
2‐amino‐3‐cyano‐4
H
‐chromenes: A sustainable overview. J Heterocycl Chem 2021. [DOI: 10.1002/jhet.4417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Rana Chatterjee
- Department of Industrial and Engineering Chemistry Institute of Chemical Technology‐Indian Oil Odisha Campus Bhubaneswar India
| | - Swadhapriya Bhukta
- Department of Industrial and Engineering Chemistry Institute of Chemical Technology‐Indian Oil Odisha Campus Bhubaneswar India
| | - Rambabu Dandela
- Department of Industrial and Engineering Chemistry Institute of Chemical Technology‐Indian Oil Odisha Campus Bhubaneswar India
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