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Bro FS, Laraia L. Unifying principles for the design and evaluation of natural product-inspired compound collections. Chem Sci 2025; 16:2961-2979. [PMID: 39906386 PMCID: PMC11788825 DOI: 10.1039/d4sc08017c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2024] [Accepted: 01/24/2025] [Indexed: 02/06/2025] Open
Abstract
Natural products play a major role in the discovery of novel bioactive compounds. In this regard, the synthesis of natural product-inspired and -derived analogues is an active field that is further developing. Several strategies and principles for the design of such compounds have been developed to streamline their access and synthesis. This perspective describes how individual strategies or their elements can be combined depending on the project goal. Illustrative examples are shown that demonstrate the blurred lines between approaches and how they can work in concert to discover new biologically active molecules. Lastly, a general set of guidelines for choosing an appropriate strategy combination for the specific purpose is presented.
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Affiliation(s)
- Frederik Simonsen Bro
- Department of Chemistry, Technical University of Denmark 2800 Kongens Lyngby Denmark
| | - Luca Laraia
- Department of Chemistry, Technical University of Denmark 2800 Kongens Lyngby Denmark
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Gentry ZO, McAteer OD, Hamad JL, Moran JA, Kim JT, Marsden MD, Zack JA, Wender PA. Synthesis and preclinical evaluation of tigilanol tiglate analogs as latency-reversing agents for the eradication of HIV. SCIENCE ADVANCES 2025; 11:eads1911. [PMID: 39854456 PMCID: PMC11778240 DOI: 10.1126/sciadv.ads1911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Accepted: 12/20/2024] [Indexed: 01/26/2025]
Abstract
Tigilanol tiglate (EBC-46) is a selective modulator of protein kinase C (PKC) isoforms that is Food and Drug Administration (FDA) approved for the treatment of mast cell tumors in canines with up to an 88% cure rate. Recently, it has been FDA approved for the treatment of soft tissue sarcomas in humans. The role of EBC-46 and, especially, its analogs in efforts to eradicate HIV, treat neurological and cardiovascular disorders, or enhance antigen density in antigen-targeted chimeric antigen receptor-T cell and chimeric antigen receptor-natural killer cell immunotherapies has not been reported. Enabled by our previously reported scalable synthesis of EBC-46, we report herein the systematic design, synthesis, and evaluation of EBC-46 analogs, including those inaccessible from the natural source and their PKC affinities, ability to translocate PKC, nuclear factor κB activity, and efficacy in reversing HIV latency in Jurkat-Latency cells. Leading analogs show exceptional PKC affinities, isoform selectivities, and functional activities, serving as promising candidates for therapeutic applications.
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Affiliation(s)
- Zachary O. Gentry
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Owen D. McAteer
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Jennifer L. Hamad
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Jose A. Moran
- Department of Microbiology & Molecular Genetics, School of Medicine, University of California Irvine, Irvine, CA 92697, USA
| | - Jocelyn T. Kim
- Department of Medicine, Division of Infectious Diseases, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Matthew D. Marsden
- Department of Microbiology & Molecular Genetics, School of Medicine, University of California Irvine, Irvine, CA 92697, USA
- Department of Medicine (Division of Infectious Diseases), School of Medicine, University of California Irvine, Irvine, CA 92697, USA
| | - Jerome A. Zack
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Medicine, Division of Hematology and Oncology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Paul A. Wender
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
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Munawar S, Zahoor AF, Hussain SM, Ahmad S, Mansha A, Parveen B, Ali KG, Irfan A. Steglich esterification: A versatile synthetic approach toward the synthesis of natural products, their analogues/derivatives. Heliyon 2024; 10:e23416. [PMID: 38170008 PMCID: PMC10758822 DOI: 10.1016/j.heliyon.2023.e23416] [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: 07/11/2023] [Revised: 12/03/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024] Open
Abstract
The exploitation of natural products and their analogues in the field of pharmacology has been regarded as of great importance. It can be attributed to the fact that these scaffolds exhibit diverse chemical properties, distinct biological activities and zenith specificity in their biochemical processes, enabling them to act as favorable structures for lead compounds. The synthesis of natural products has been a crafty and hard-to-achieve task. Steglich esterification reaction has played a significant role in that area. It is a mild and efficient technique for constructing ester linkages. This technique involves the establishment of ester moiety via a carbodiimide-based condensation of a carboxylic acid with an alcohol, thiol or an amine catalyzed by dimethyl aminopyridine (DMAP). Specifically, labile reagents with multiple reactive sites are esterified efficiently with the classical and modified Steglich esterification conditions, which accounts for their synthetic utility. This review encloses the performance of the Steglich esterification reaction in forging the ester linkage for executing the total synthesis of natural products and their derivatives since 2018.
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Affiliation(s)
- Saba Munawar
- Department of Chemistry, Government College University Faisalabad, 38000, Faisalabad, Pakistan
| | - Ameer Fawad Zahoor
- Department of Chemistry, Government College University Faisalabad, 38000, Faisalabad, Pakistan
| | - Syed Makhdoom Hussain
- Department of Zoology, Government College University Faisalabad, 38000, Faisalabad, Pakistan
| | - Sajjad Ahmad
- Department of Chemistry, University of Engineering and Technology Lahore, Faisalabad Campus, 38000, Faisalabad, Pakistan
| | - Asim Mansha
- Department of Chemistry, Government College University Faisalabad, 38000, Faisalabad, Pakistan
| | - Bushra Parveen
- Department of Chemistry, Government College University Faisalabad, 38000, Faisalabad, Pakistan
| | - Kulsoom Ghulam Ali
- Department of Chemistry, Government College University Faisalabad, 38000, Faisalabad, Pakistan
| | - Ahmad Irfan
- Department of Chemistry, King Khalid University, Abha, 61413, P.O. Box 9004, Saudi Arabia
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Fisher JF, Mobashery S. β-Lactams from the Ocean. Mar Drugs 2023; 21:86. [PMID: 36827127 PMCID: PMC9963991 DOI: 10.3390/md21020086] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/21/2023] [Accepted: 01/24/2023] [Indexed: 01/27/2023] Open
Abstract
The title of this essay is as much a question as it is a statement. The discovery of the β-lactam antibiotics-including penicillins, cephalosporins, and carbapenems-as largely (if not exclusively) secondary metabolites of terrestrial fungi and bacteria, transformed modern medicine. The antibiotic β-lactams inactivate essential enzymes of bacterial cell-wall biosynthesis. Moreover, the ability of the β-lactams to function as enzyme inhibitors is of such great medical value, that inhibitors of the enzymes which degrade hydrolytically the β-lactams, the β-lactamases, have equal value. Given this privileged status for the β-lactam ring, it is therefore a disappointment that the exemplification of this ring in marine secondary metabolites is sparse. It may be that biologically active marine β-lactams are there, and simply have yet to be encountered. In this report, we posit a second explanation: that the value of the β-lactam to secure an ecological advantage in the marine environment might be compromised by its close structural similarity to the β-lactones of quorum sensing. The steric and reactivity similarities between the β-lactams and the β-lactones represent an outside-of-the-box opportunity for correlating new structures and new enzyme targets for the discovery of compelling biological activities.
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Affiliation(s)
- Jed F Fisher
- Department of Chemistry & Biochemistry, 354 McCourtney Hall, University of Note Dame, Notre Dame, IN 46656-5670, USA
| | - Shahriar Mobashery
- Department of Chemistry & Biochemistry, 354 McCourtney Hall, University of Note Dame, Notre Dame, IN 46656-5670, USA
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Li Y, Cheng S, Tian Y, Zhang Y, Zhao Y. Recent ring distortion reactions for diversifying complex natural products. Nat Prod Rep 2022; 39:1970-1992. [PMID: 35972343 DOI: 10.1039/d2np00027j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: 2013-2022.Chemical diversification of natural products is an efficient way to generate natural product-like compounds for modern drug discovery programs. Utilizing ring-distortion reactions for diversifying natural products would directly alter the core ring systems of small molecules and lead to the production of structurally complex and diverse compounds for high-throughput screening. We review the ring distortion reactions recently used in complexity-to-diversity (CtD) and pseudo natural products (pseudo-NPs) strategies for diversifying complex natural products. The core ring structures of natural products are altered via ring expansion, ring cleavage, ring edge-fusion, ring spiro-fusion, ring rearrangement, and ring contraction. These reactions can rapidly provide natural product-like collections with properties suitable for a wide variety of biological and medicinal applications. The challenges and limitations of current ring distortion reactions are critically assessed, and avenues for future improvements of this rapidly expanding field are discussed. We also provide a toolbox for chemists for the application of ring distortion reactions to access natural product-like molecules.
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Affiliation(s)
- Yu Li
- School of Pharmacy, Nantong University, Nantong 226001, China.
| | - Shihao Cheng
- School of Pharmacy, Nantong University, Nantong 226001, China.
| | - Yun Tian
- School of Pharmacy, Nantong University, Nantong 226001, China.
| | - Yanan Zhang
- School of Pharmacy, Nantong University, Nantong 226001, China.
| | - Yu Zhao
- School of Pharmacy, Nantong University, Nantong 226001, China.
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Abstract
Covering: 2020This review covers the literature published in 2020 for marine natural products (MNPs), with 757 citations (747 for the period January to December 2020) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1407 in 420 papers for 2020), together with the relevant biological activities, source organisms and country of origin. Pertinent reviews, biosynthetic studies, first syntheses, and syntheses that led to the revision of structures or stereochemistries, have been included. A meta analysis of bioactivity data relating to new MNPs reported over the last five years is also presented.
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Affiliation(s)
- Anthony R Carroll
- School of Environment and Science, Griffith University, Gold Coast, Australia. .,Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - Brent R Copp
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Rohan A Davis
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia.,School of Enivironment and Science, Griffith University, Brisbane, Australia
| | - Robert A Keyzers
- Centre for Biodiscovery, School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
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Katti S, Igumenova TI. Structural insights into C1-ligand interactions: Filling the gaps by in silico methods. Adv Biol Regul 2021; 79:100784. [PMID: 33526356 PMCID: PMC8867786 DOI: 10.1016/j.jbior.2020.100784] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/24/2020] [Accepted: 12/28/2020] [Indexed: 02/05/2023]
Abstract
Protein Kinase C isoenzymes (PKCs) are the key mediators of the phosphoinositide signaling pathway, which involves regulated hydrolysis of phosphatidylinositol (4,5)-bisphosphate to diacylglycerol (DAG) and inositol-1,4,5-trisphosphate. Dysregulation of PKCs is implicated in many human diseases making this class of enzymes an important therapeutic target. Specifically, the DAG-sensing cysteine-rich conserved homology-1 (C1) domains of PKCs have emerged as promising targets for pharmaceutical modulation. Despite significant progress, the rational design of the C1 modulators remains challenging due to difficulties associated with structure determination of the C1-ligand complexes. Given the dearth of experimental structural data, computationally derived models have been instrumental in providing atomistic insight into the interactions of the C1 domains with PKC agonists. In this review, we provide an overview of the in silico approaches for seven classes of C1 modulators and outline promising future directions.
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Affiliation(s)
- Sachin Katti
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, TX, 77843, United States
| | - Tatyana I Igumenova
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, TX, 77843, United States.
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