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Ancajas CMF, Oyedele AS, Butt CM, Walker AS. Advances, opportunities, and challenges in methods for interrogating the structure activity relationships of natural products. Nat Prod Rep 2024. [PMID: 38912779 DOI: 10.1039/d4np00009a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Time span in literature: 1985-early 2024Natural products play a key role in drug discovery, both as a direct source of drugs and as a starting point for the development of synthetic compounds. Most natural products are not suitable to be used as drugs without further modification due to insufficient activity or poor pharmacokinetic properties. Choosing what modifications to make requires an understanding of the compound's structure-activity relationships. Use of structure-activity relationships is commonplace and essential in medicinal chemistry campaigns applied to human-designed synthetic compounds. Structure-activity relationships have also been used to improve the properties of natural products, but several challenges still limit these efforts. Here, we review methods for studying the structure-activity relationships of natural products and their limitations. Specifically, we will discuss how synthesis, including total synthesis, late-stage derivatization, chemoenzymatic synthetic pathways, and engineering and genome mining of biosynthetic pathways can be used to produce natural product analogs and discuss the challenges of each of these approaches. Finally, we will discuss computational methods including machine learning methods for analyzing the relationship between biosynthetic genes and product activity, computer aided drug design techniques, and interpretable artificial intelligence approaches towards elucidating structure-activity relationships from models trained to predict bioactivity from chemical structure. Our focus will be on these latter topics as their applications for natural products have not been extensively reviewed. We suggest that these methods are all complementary to each other, and that only collaborative efforts using a combination of these techniques will result in a full understanding of the structure-activity relationships of natural products.
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Affiliation(s)
| | | | - Caitlin M Butt
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
| | - Allison S Walker
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
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2
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Yñigez-Gutierrez AE, Wurm JE, Froese JT, Rosenthal NE, Bachmann BO. Characterization of Dichloroisoeverninic Acid Biosynthesis and Chemoenzymatic Synthesis of New Orthosomycins. ACS Chem Biol 2024; 19:526-535. [PMID: 38289021 DOI: 10.1021/acschembio.3c00693] [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: 02/17/2024]
Abstract
The orthosomycins are highly modified oligosaccharide natural products with a broad spectrum and potent antimicrobial activities. These include everninomicins and avilamycins, which inhibit protein translation by binding a unique site on the bacterial ribosome. Notably, ribosomal bound structures reveal a network of interactions between the 50S subunit and dichloroisoeverninic acid (DCIE), the aromatic A1-ring conserved across orthosomycins, but the relationship of these interactions to their antimicrobial activity remains undetermined. Genetic functional analysis of three genes putatively associated with DCIE biosynthesis in the everninomicin producer Micromonospora carbonacea delineates the native biosynthetic pathway and provides previously unreported advanced biosynthetic intermediates. Subsequent in vitro biochemical analyses demonstrate the complete DCIE biosynthetic pathway and provide access to novel everninomicin analogs. In addition to the orsellinate synthase EvdD3 and a flavin-dependent halogenase EvdD2, our results identified a key acyltransferase, EvdD1, responsible for transferring orsellinate from the acyl carrier protein domain of EvdD3 to a heptasaccharide orthosomycin biosynthetic intermediate. We have also shown that EvdD1 is able to transfer unnatural aryl groups via their N-acyl cysteamine thioesters to the everninomicin scaffold and used this as a biocatalyst to generate a panel of unnatural aryl analogs. The impact of diverse aryl functional group substitution on both ribosome inhibition and antibacterial activities demonstrates the importance of the DCIE moiety in the pharmacology of orthosomycins, notably revealing an uncoupling between ribosomal engagement and antibiotic activity. Control of A1-ring functionality in this class of molecules provides a potential handle to explore and address pharmacological roles of the DCIE ring in this potent and unique class of antibiotics.
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Affiliation(s)
| | - Jennifer E Wurm
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Chemical and Physical Biology Graduate Program, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jordan T Froese
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Nicholas E Rosenthal
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Brian O Bachmann
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
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3
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Turnaturi R, Piana S, Spoto S, Costanzo G, Reina L, Pasquinucci L, Parenti C. From Plant to Chemistry: Sources of Active Opioid Antinociceptive Principles for Medicinal Chemistry and Drug Design. Molecules 2023; 28:7089. [PMID: 37894567 PMCID: PMC10609244 DOI: 10.3390/molecules28207089] [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: 09/05/2023] [Revised: 09/28/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Pain continues to be an enormous global health challenge, with millions of new untreated or inadequately treated patients reported annually. With respect to current clinical applications, opioids remain the mainstay for the treatment of pain, although they are often associated with serious side effects. To optimize their tolerability profiles, medicinal chemistry continues to study novel ligands and innovative approaches. Among them, natural products are known to be a rich source of lead compounds for drug discovery, and they hold potential for pain management. Traditional medicine has had a long history in clinical practice due to the fact that nature provides a rich source of active principles. For instance, opium had been used for pain management until the 19th century when its individual components, such as morphine, were purified and identified. In this review article, we conducted a literature survey aimed at identifying natural products interacting either directly with opioid receptors or indirectly through other mechanisms controlling opioid receptor signaling, whose structures could be interesting from a drug design perspective.
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Affiliation(s)
- Rita Turnaturi
- Department of Drug and Health Sciences, Medicinal Chemistry Section, University of Catania, Viale A. Doria 6, 95125 Catania, Italy;
| | - Silvia Piana
- Department of Drug and Health Sciences, Medicinal Chemistry Section, University of Catania, Viale A. Doria 6, 95125 Catania, Italy;
| | - Salvatore Spoto
- Department of Drug and Health Sciences, Section of Pharmacology and Toxicology, University of Catania, 95125 Catania, Italy; (S.S.); (C.P.)
| | - Giuliana Costanzo
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via Santa Sofia 97, 95123 Catania, Italy;
| | - Lorena Reina
- Postgraduate School of Clinical Pharmacology, Toxicology University of Catania, Via Santa Sofia n. 97, 95100 Catania, Italy;
| | - Lorella Pasquinucci
- Department of Drug and Health Sciences, Medicinal Chemistry Section, University of Catania, Viale A. Doria 6, 95125 Catania, Italy;
| | - Carmela Parenti
- Department of Drug and Health Sciences, Section of Pharmacology and Toxicology, University of Catania, 95125 Catania, Italy; (S.S.); (C.P.)
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Stojković P, Kostić A, Lupšić E, Jovanović NT, Novaković M, Nedialkov P, Trendafilova A, Pešić M, Opsenica IM. Novel hybrids of sclareol and 1,2,4-triazolo[1,5-a]pyrimidine show collateral sensitivity in multidrug-resistant glioblastoma cells. Bioorg Chem 2023; 138:106605. [PMID: 37201322 DOI: 10.1016/j.bioorg.2023.106605] [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: 03/29/2023] [Revised: 04/27/2023] [Accepted: 05/08/2023] [Indexed: 05/20/2023]
Abstract
The synthesis of 24 hybrid molecules, consisting of naturally occurring sclareol (SCL) and synthetic 1,2,4-triazolo[1,5-a]pyrimidines (TPs), is described. New compounds were designed with the aim of improving the cytotoxic properties, activity, and selectivity of the parent compounds. Six analogs (12a-f) contained 4-benzylpiperazine linkage, while 4-benzyldiamine linkage was present in eighteen derivatives (12g-r and 13a-f). Hybrids 13a-f consist of two TP units. After purification, all hybrids (12a-r and 13a-f), as well as their precursors (9a-e and 11a-c), were tested on human glioblastoma U87 cells. More than half of the tested synthesized molecules, 16 out of 31, caused a significant reduction of U87 cell viability (more than 75% reduction) at 30 µM. The concentration-dependent cytotoxicity of these 16 compounds was also examined on U87 cells, corresponding multidrug-resistant (MDR) U87-TxR cells with increased P-glycoprotein (P-gp) expression and activity, and normal lung fibroblasts MRC-5. Importantly, 12l and 12r were active in the nanomolar range, while seven compounds (11b, 11c, 12i, 12l, 12n, 12q, and 12r) were more selective towards glioblastoma cells than SCL. All compounds except 12r evaded MDR, showing even better cytotoxicity in U87-TxR cells. In particular, 11c, 12a, 12g, 12j, 12k, 12m, 12n, and SCL showed collateral sensitivity. Hybrid compounds 12l, 12q, and 12r decreased P-gp activity to the same extent as a well-known P-gp inhibitor - tariquidar (TQ). Hybrid compound 12l and its precursor 11c affected different cellular processes including the cell cycle, cell death, and mitochondrial membrane potential, and changed the levels of reactive oxygen and nitrogen species (ROS/RNS) in glioblastoma cells. Collateral sensitivity towards MDR glioblastoma cells was caused by the modulation of oxidative stress accompanied by inhibition of mitochondria.
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Affiliation(s)
- Pavle Stojković
- University of Belgrade - Faculty of Chemistry, PO Box 51, Studentski Trg 16, 11158 Belgrade, Serbia
| | - Ana Kostić
- Institute for Biological Research "Siniša Stanković" - National Institute of the Republic of Serbia, University of Belgrade, Despota Stefana 142, 11060 Belgrade, Serbia
| | - Ema Lupšić
- Institute for Biological Research "Siniša Stanković" - National Institute of the Republic of Serbia, University of Belgrade, Despota Stefana 142, 11060 Belgrade, Serbia
| | - Nataša Terzić Jovanović
- University of Belgrade - Institute of Chemistry, Technology, and Metallurgy, National Institute of the Republic of Serbia, Njegoševa 12, 11000 Belgrade, Serbia
| | - Miroslav Novaković
- University of Belgrade - Institute of Chemistry, Technology, and Metallurgy, National Institute of the Republic of Serbia, Njegoševa 12, 11000 Belgrade, Serbia.
| | - Paraskev Nedialkov
- Department of Pharmacognosy, Faculty of Pharmacy, Medical University of Sofia, 2, Dunav St., 1000, Sofia, Bulgaria
| | - Antoaneta Trendafilova
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Acad. G. Bonchev St, Bl. 9, 1113, Sofia, Bulgaria
| | - Milica Pešić
- Institute for Biological Research "Siniša Stanković" - National Institute of the Republic of Serbia, University of Belgrade, Despota Stefana 142, 11060 Belgrade, Serbia
| | - Igor M Opsenica
- University of Belgrade - Faculty of Chemistry, PO Box 51, Studentski Trg 16, 11158 Belgrade, Serbia.
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Buyuklyan JA, Zakalyukina YV, Osterman IA, Biryukov MV. Modern Approaches to the Genome Editing of Antibiotic Biosynthetic Clusters in Actinomycetes. Acta Naturae 2023; 15:4-16. [PMID: 37908767 PMCID: PMC10615194 DOI: 10.32607/actanaturae.23426] [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: 07/13/2023] [Accepted: 08/19/2023] [Indexed: 11/02/2023] Open
Abstract
Representatives of the phylum Actinomycetota are one of the main sources of secondary metabolites, including antibiotics of various classes. Modern studies using high-throughput sequencing techniques enable the detection of dozens of potential antibiotic biosynthetic genome clusters in many actinomycetes; however, under laboratory conditions, production of secondary metabolites amounts to less than 5% of the total coding potential of producer strains. However, many of these antibiotics have already been described. There is a continuous "rediscovery" of known antibiotics, and new molecules become almost invisible against the general background. The established approaches aimed at increasing the production of novel antibiotics include: selection of optimal cultivation conditions by modifying the composition of nutrient media; co-cultivation methods; microfluidics, and the use of various transcription factors to activate silent genes. Unfortunately, these tools are non-universal for various actinomycete strains, stochastic in nature, and therefore do not always lead to success. The use of genetic engineering technologies is much more efficient, because they allow for a directed and controlled change in the production of target metabolites. One example of such technologies is mutagenesis-based genome editing of antibiotic biosynthetic clusters. This targeted approach allows one to alter gene expression, suppressing the production of previously characterized molecules, and thereby promoting the synthesis of other unknown antibiotic variants. In addition, mutagenesis techniques can be successfully applied both to new producer strains and to the genes of known isolates to identify new compounds.
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Affiliation(s)
- J A Buyuklyan
- Center for Translational Medicine, Sirius University of Science and Technology, Sochi, 354340 Russian Federation
| | - Yu V Zakalyukina
- Center for Translational Medicine, Sirius University of Science and Technology, Sochi, 354340 Russian Federation
- Lomonosov Moscow State University, Moscow, 119234 Russian Federation
| | - I A Osterman
- Center for Translational Medicine, Sirius University of Science and Technology, Sochi, 354340 Russian Federation
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region, 143025 Russian Federation
| | - M V Biryukov
- Center for Translational Medicine, Sirius University of Science and Technology, Sochi, 354340 Russian Federation
- Lomonosov Moscow State University, Moscow, 119234 Russian Federation
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6
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Li J, Sheng H, Wang Y, Lai Z, Wang Y, Cui S. Scaffold Hybrid of the Natural Product Tanshinone I with Piperidine for the Discovery of a Potent NLRP3 Inflammasome Inhibitor. J Med Chem 2023; 66:2946-2963. [PMID: 36786612 DOI: 10.1021/acs.jmedchem.2c01967] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Natural products provide inspiration and have proven to be the most valuable source for drug discovery. Herein, we report a scaffold hybrid strategy of Tanshinone I for the discovery of NLRP3 inflammasome inhibitors. 36 compounds were designed and synthesized, and the cheminformatic analyses showed that these compounds occupy a unique chemical space. The biological evaluation identified compounds 5j, 12a, and 12d as NLRP3 inflammasome inhibitors with significant potency, selectivity, and drug-likeness. Mechanistic studies revealed that these Tanshinone I derivatives could inhibit the degradation of the protein NLRP3 and block the oligomerization of NLRP3-induced apoptosis-associated speck-like proteins, thus inhibiting NLRP3 inflammasome activation. In addition, the water solubility, in vitro metabolic stability, and oral bioavailability of these compounds were also greatly improved compared to Tanshinone I. Therefore, this protocol provides a new structural evolution of Tanshinone I and a new class of potent NLRP3 inflammasome inhibitors.
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Affiliation(s)
- Jiaming Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hongda Sheng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yingchao Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhencheng Lai
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yi Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Sunliang Cui
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
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7
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Kim S, Lim SW, Choi J. Drug discovery inspired by bioactive small molecules from nature. Anim Cells Syst (Seoul) 2022; 26:254-265. [PMID: 36605590 PMCID: PMC9809404 DOI: 10.1080/19768354.2022.2157480] [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] [Indexed: 12/24/2022] Open
Abstract
Natural products (NPs) have greatly contributed to the development of novel treatments for human diseases such as cancer, metabolic disorders, and infections. Compared to synthetic chemical compounds, primary and secondary metabolites from medicinal plants, fungi, microorganisms, and our bodies are promising resources with immense chemical diversity and favorable properties for drug development. In addition to the well-validated significance of secondary metabolites, endogenous small molecules derived from central metabolism and signaling events have shown great potential as drug candidates due to their unique metabolite-protein interactions. In this short review, we highlight the values of NPs, discuss recent scientific and technological advances including metabolomics tools, chemoproteomics approaches, and artificial intelligence-based computation platforms, and explore potential strategies to overcome the current challenges in NP-driven drug discovery.
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Affiliation(s)
- Seyun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea, Seyun Kim
| | - Seol-Wa Lim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Jiyeon Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
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8
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Tharra PR, Mikhaylov AA, Švejkar J, Gysin M, Hobbie SN, Švenda J. Short Synthesis of (+)‐Actinobolin: Simple Entry to Complex Small‐Molecule Inhibitors of Protein Synthesis. Angew Chem Int Ed Engl 2022; 61:e202116520. [DOI: 10.1002/anie.202116520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Indexed: 01/19/2023]
Affiliation(s)
- Prabhakara R. Tharra
- Department of Chemistry Faculty of Science Masaryk University Kamenice 5 Brno 625 00 Czech Republic
- International Clinical Research Center St. Anne's University Hospital Pekařská 53 Brno 656 91 Czech Republic
| | - Andrey A. Mikhaylov
- Department of Chemistry Faculty of Science Masaryk University Kamenice 5 Brno 625 00 Czech Republic
- International Clinical Research Center St. Anne's University Hospital Pekařská 53 Brno 656 91 Czech Republic
| | - Jiří Švejkar
- Department of Chemistry Faculty of Science Masaryk University Kamenice 5 Brno 625 00 Czech Republic
| | - Marina Gysin
- Institute of Medical Microbiology University of Zürich Gloriastrasse 30 Zürich 8006 Switzerland
| | - Sven N. Hobbie
- Institute of Medical Microbiology University of Zürich Gloriastrasse 30 Zürich 8006 Switzerland
| | - Jakub Švenda
- Department of Chemistry Faculty of Science Masaryk University Kamenice 5 Brno 625 00 Czech Republic
- International Clinical Research Center St. Anne's University Hospital Pekařská 53 Brno 656 91 Czech Republic
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9
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Ren M, Zhang M, Zhang X, Wang C, Zheng Y, Hu Y. Hydroxysafflor Yellow A Inhibits Aβ 1-42-Induced Neuroinflammation by Modulating the Phenotypic Transformation of Microglia via TREM2/TLR4/NF-κB Pathway in BV-2 Cells. Neurochem Res 2022; 47:748-761. [PMID: 34783973 DOI: 10.1007/s11064-021-03484-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/31/2021] [Accepted: 11/08/2021] [Indexed: 12/30/2022]
Abstract
Hydroxysafflor yellow A (HSYA) is an extract from Carthamus tinctorius L. dry flowers (Compositae). HSYA has been shown to have neuroprotective effects on several Alzheimer's disease (AD) models. However, the exact mechanisms by which HSYA regulates neuroinflammation have still not been clarified. In this study, we investigated the mechanism by which HSYA regulates microglial activation and neuroinflammation via TREM2, and further clarified its underlying molecular mechanism. We silenced TREM2 in BV-2 cells and evaluated the expression of inflammatory markers (TNF-α, IL-1β, IL-4, IL-6, IL-10, and IL-13). The results showed that HSYA could up-regulate cell viability and improve the morphology of BV-2 cells injured by Aβ1-42. The results showed that Aβ1-42 could induce microglia to upregulate the expression of M1 markers (iNOS, IL-1β, IL-6) and downregulate M2 marker (Arg-1, IL-4, IL-10, IL-13) expression. HSYA reversed the effects of Aβ1-42 via TREM2, switching microglia from an M1 proinflammatory phenotype to an M2 anti-inflammatory phenotype. HSYA inhibited the Aβ1-42-induced activation of the TLR4/NF-κB transduction pathway by upregulating TREM2 and regulated the transcription of inflammatory cytokines via the downstream transcription factors NF-κB p65 and IκB-α. In conclusion, HSYA regulated the microglial inflammatory phenotype by regulating microglial (M1/M2) polarization in Aβ1-42-induced BV-2 cells which may be mediated by the TREM2/TLR4/NF-κB pathway.
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Affiliation(s)
- Mengqiao Ren
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, Department of Pharmacology, Shihezi University, Shihezi, 832000, Xinjiang, People's Republic of China
| | - Mengyu Zhang
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, Department of Pharmacology, Shihezi University, Shihezi, 832000, Xinjiang, People's Republic of China
| | - Xiaoyan Zhang
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, Department of Pharmacology, Shihezi University, Shihezi, 832000, Xinjiang, People's Republic of China
| | - Chunhui Wang
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, Department of Pharmacology, Shihezi University, Shihezi, 832000, Xinjiang, People's Republic of China
| | - Yanjie Zheng
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, Department of Pharmacology, Shihezi University, Shihezi, 832000, Xinjiang, People's Republic of China
| | - Yanli Hu
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization, Ministry of Education, Department of Pharmacology, Shihezi University, Shihezi, 832000, Xinjiang, People's Republic of China.
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10
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Tharra PR, Mikhaylov AA, Švejkar J, Gysin M, Hobbie SN, Švenda J. Short Synthesis of (+)‐Actinobolin: Simple Entry to Complex Small‐Molecule Inhibitors of Protein Synthesis. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202116520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Prabhakara R. Tharra
- Department of Chemistry Faculty of Science Masaryk University Kamenice 5 Brno 625 00 Czech Republic
- International Clinical Research Center St. Anne's University Hospital Pekařská 53 Brno 656 91 Czech Republic
| | - Andrey A. Mikhaylov
- Department of Chemistry Faculty of Science Masaryk University Kamenice 5 Brno 625 00 Czech Republic
- International Clinical Research Center St. Anne's University Hospital Pekařská 53 Brno 656 91 Czech Republic
| | - Jiří Švejkar
- Department of Chemistry Faculty of Science Masaryk University Kamenice 5 Brno 625 00 Czech Republic
| | - Marina Gysin
- Institute of Medical Microbiology University of Zürich Gloriastrasse 30 Zürich 8006 Switzerland
| | - Sven N. Hobbie
- Institute of Medical Microbiology University of Zürich Gloriastrasse 30 Zürich 8006 Switzerland
| | - Jakub Švenda
- Department of Chemistry Faculty of Science Masaryk University Kamenice 5 Brno 625 00 Czech Republic
- International Clinical Research Center St. Anne's University Hospital Pekařská 53 Brno 656 91 Czech Republic
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11
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Bailly C. The bacterial thiopeptide thiostrepton. An update of its mode of action, pharmacological properties and applications. Eur J Pharmacol 2022; 914:174661. [PMID: 34863996 DOI: 10.1016/j.ejphar.2021.174661] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 11/29/2021] [Indexed: 12/20/2022]
Abstract
The bacterial thiopeptide thiostrepton (TS) is used as a veterinary medicine to treat bacterial infections. TS is a protein translation inhibitor, essentially active against Gram-positive bacteria and some Gram-negative bacteria. In procaryotes, TS abrogates binding of GTPase elongation factors to the 70S ribosome, by altering the structure of rRNA-L11 protein complexes. TS exerts also antimalarial effects by disrupting protein synthesis in the apicoplast genome of Plasmodium falciparum. Interestingly, the drug targets both the infectious pathogen (bacteria or parasite) and host cell, by inducing endoplasmic reticulum stress-mediated autophagy which contributes to enhance the host cell defense. In addition, TS has been characterized as a potent chemical inhibitor of the oncogenic transcription factor FoxM1, frequently overexpressed in cancers or other diseases. The capacity of TS to crosslink FoxM1, and a few other proteins such as peroxiredoxin 3 (PRX3) and the 19S proteasome, contributes to the anticancer effects of the thiopeptide. The anticancer activities of TS evidenced using diverse tumor cell lines, in vivo models and drug combinations are reviewed here, together with the implicated targets and mechanisms. The difficulty to formulate TS is a drag on the pharmaceutical development of the natural product. However, the design of hemisynthetic analogues and the use of micellar drug delivery systems should facilitate a broader utilization of the compound in human and veterinary medicines. This review shed light on the many pharmacological properties of TS, with the objective to promote its use as a pharmacological tool and medicinal product.
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Affiliation(s)
- Christian Bailly
- OncoWitan, Scientific Consulting Office, Lille, Wasquehal, 59290, France.
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12
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Li G, Lou M, Qi X. A brief overview of classical natural product drug synthesis and bioactivity. Org Chem Front 2022. [DOI: 10.1039/d1qo01341f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This manuscript briefly overviewed the total synthesis and structure–activity relationship studies of eight classical natural products, which emphasizes the important role of total synthesis in natural product-based drug development.
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Affiliation(s)
- Gen Li
- National Institute of Biological Sciences (NIBS), 7 Science Park Road ZGC Life Science Park, Beijing 102206, China
| | - Mingliang Lou
- National Institute of Biological Sciences (NIBS), 7 Science Park Road ZGC Life Science Park, Beijing 102206, China
| | - Xiangbing Qi
- National Institute of Biological Sciences (NIBS), 7 Science Park Road ZGC Life Science Park, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
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13
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Zhang H, Li S, Si Y, Xu H. Andrographolide and its derivatives: Current achievements and future perspectives. Eur J Med Chem 2021; 224:113710. [PMID: 34315039 DOI: 10.1016/j.ejmech.2021.113710] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/16/2021] [Accepted: 07/16/2021] [Indexed: 12/22/2022]
Abstract
Natural product andrographolide isolated from the plant Andrographis paniculata shows a plethora of biological activities, including anti-tumor, anti-bacterial, anti-inflammation, anti-virus, anti-fibrosis, anti-obesity, immunomodulatory and hypoglycemic activities. Based on extensive chemical structural modifications, a series of andrographolide derivatives with improved bioavailability and druggability has been developed. Moreover, greater understanding of their mechanisms of action at the molecular and cellular level has been thoroughly investigated. In this review, we give an outlook for the therapeutical potential of andrographolide and its derivatives in diverse diseases and highlighted the drug design, pharmacokinetic and mechanistic studies for the past ten years, together with a brief overview of the pharmacological effects. Notably, we focused to provide a critical enlightenment of the area of andrographolide and its derivatives with the intent of indicating the future perspectives, challenges and limitations. We believe that this review paper will benefit drug discovery where andrographolide was used as a template, shed light on the identification of drug targets for andrographolide and its analogs, as well as increase our knowledge for using them for therapeutic application, including the treatment for various forms of cancers.
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Affiliation(s)
- Hang Zhang
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Co-innovation Center of Henan Province for New Drug R&D and Preclinical Safety, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Shufeng Li
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Co-innovation Center of Henan Province for New Drug R&D and Preclinical Safety, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Yongsheng Si
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Co-innovation Center of Henan Province for New Drug R&D and Preclinical Safety, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Haiwei Xu
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Co-innovation Center of Henan Province for New Drug R&D and Preclinical Safety, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, China.
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14
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Chemical Composition and Biological Activities of the Essential Oils of Chrysophyllum albidum G. Don (African Star Apple). Biochem Res Int 2021; 2021:9911713. [PMID: 34221505 PMCID: PMC8213500 DOI: 10.1155/2021/9911713] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 06/01/2021] [Indexed: 02/07/2023] Open
Abstract
The volatile compounds of the fruit and leaf essential oils of the African star fruit, Chrysophyllum albidum G. Don, were characterized by gas chromatography-mass spectrometry in this study. The antimicrobial, antibiofilm, and antioxidant activities of the essential oils were also investigated. Thirty-five and thirty-four compounds, representing 97.84% and 97.87%, were identified in the leaf and fruit essential oils, respectively. The antimicrobial activity of the oils was evaluated in vitro against eight pathogens using the broth microdilution method. The fruit essential oil exhibited broad-spectrum antimicrobial activity in the antimicrobial susceptibility test, with minimum inhibitory concentrations (MICs) ranging from 0.195 to 6.250 mg/mL, while the leaf essential oils showed antimicrobial activity with MICs in the range of 6.875–13.750 mg/mL. The antibiofilm activity was assessed via the crystal violet staining assay, with Pseudomonas aeruginosa as the model organism. The concentrations of the leaf and fruit essential oil required for half-maximal inhibition of biofilm formation (BIC50) were 6.97 ± 0.56 and 4.78 ± 0.21 mg/mL, respectively. In evaluating antioxidant activity, the total antioxidant capacity obtained from the phosphomolybdenum assay was 104.8 ± 2.4 and 101.6 ± 0.8 μg/g AAE for leaf and fruit essential oils, respectively. The IC50 values obtained from the hydrogen peroxide scavenging, 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging, and inhibition of lipid peroxidation assays were 301.8 ± 0.7 and 669.2 ± 2.1 μg/mL, 1048.0 ± 0.3 and 1454.0 ± 0.3 μg/mL, and 460.1 ± 2.7 and 457.4 ± 0.3 μg/mL for both leaf and fruit essential oils, respectively. The results obtained in this study suggest that the leaf and fruit essential oil of Chrysophyllum albidum G. Don could find potential use in the food, cosmetic, and pharmaceutical industries as preservative and pharmaceutical agents.
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15
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Al Subeh ZY, Raja HA, Obike JC, Pearce CJ, Croatt MP, Oberlies NH. Media and strain studies for the scaled production of cis-enone resorcylic acid lactones as feedstocks for semisynthesis. J Antibiot (Tokyo) 2021; 74:496-507. [PMID: 34155352 PMCID: PMC8313427 DOI: 10.1038/s41429-021-00432-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/01/2021] [Accepted: 06/07/2021] [Indexed: 12/18/2022]
Abstract
Resorcylic acid lactones (RALs) with a cis-enone moiety, represented by hypothemycin (1) and (5Z)-7-oxozeaenol (2), are fungal secondary metabolites with irreversible inhibitory activity against protein kinases, with particularly selective activity for inhibition of TAK1 (transforming growth factor beta-activated kinase 1). Gram-scale quantities of these compounds were needed as feedstock for semi-synthesizing RAL-analogues in a step-economical fashion. To do so, this study had three primary goals: identifying fungi that biosynthesized 1 and 2, enhancing their production by optimizing the fermentation conditions on the lab scale, and developing straight forward purification processes. After evaluating 536 fungal extracts via an in-house dereplication protocol, three strains were identified as producing cis-enone RALs (i.e., MSX78495, MSX63935, MSX45109). Screening these fungal strains on three grain-based media revealed enhanced production of 1 by strain MSX78495 on oatmeal medium, while rice medium increased the biosynthesis of 2 by strain MSX63935. Furthermore, the purification processes were improved, moving away from HPLC purification to utilizing two to four cycles of resuspension and centrifugation in small volumes of organic solvents, generating gram-scale quantities of these metabolites readily. In addition, studying the chemistry profiles of strains MSX78495 and MSX63935 resulted in the isolation of ten other RALs (3-12), two radicinin analogues (13-14), and six benzopyranones (15-20), with 19 and 20 being newly described chlorinated benzopyranones.
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Affiliation(s)
- Zeinab Y Al Subeh
- Department of Chemistry and Biochemistry, The University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Huzefa A Raja
- Department of Chemistry and Biochemistry, The University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Jennifer C Obike
- Department of Chemistry and Biochemistry, The University of North Carolina at Greensboro, Greensboro, NC, USA
| | | | - Mitchell P Croatt
- Department of Chemistry and Biochemistry, The University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Nicholas H Oberlies
- Department of Chemistry and Biochemistry, The University of North Carolina at Greensboro, Greensboro, NC, USA.
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16
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Wang Z, Hui C. Contemporary advancements in the semi-synthesis of bioactive terpenoids and steroids. Org Biomol Chem 2021; 19:3791-3812. [PMID: 33949606 DOI: 10.1039/d1ob00448d] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Many natural products have intriguing biological properties that arise from their fascinating chemical structures. However, the intrinsic complexity of the structural skeleton and the reactive functional groups on natural products pose tremendous challenges to chemical syntheses. Semi-synthesis uses chemical compounds isolated from natural sources as the starting materials to produce other novel compounds with distinct chemical and medicinal properties. In particular, advancements in various types of sp3 C-H bond functionalization reactions and skeletal rearrangement methods have contributed to the re-emergence of semi-synthesis as an efficient approach for the synthesis of structurally complex bioactive natural products. Here, we begin with a brief discussion of several bioactive natural products that were obtained via a semi-synthetic approach between 2008 and 2015 and we then discuss in-depth contemporary advancements in the semi-synthesis of bioactive terpenoids and steroids reported during 2016-2020.
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Affiliation(s)
- Zhuo Wang
- Southern University of Science and Technology, School of Medicine, Shenzhen, 518055, People's Republic of China.
| | - Chunngai Hui
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China
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17
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Atanasov AG, Zotchev SB, Dirsch VM, Supuran CT. Natural products in drug discovery: advances and opportunities. Nat Rev Drug Discov 2021; 20:200-216. [PMID: 33510482 PMCID: PMC7841765 DOI: 10.1038/s41573-020-00114-z] [Citation(s) in RCA: 1683] [Impact Index Per Article: 561.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/12/2020] [Indexed: 02/07/2023]
Abstract
Natural products and their structural analogues have historically made a major contribution to pharmacotherapy, especially for cancer and infectious diseases. Nevertheless, natural products also present challenges for drug discovery, such as technical barriers to screening, isolation, characterization and optimization, which contributed to a decline in their pursuit by the pharmaceutical industry from the 1990s onwards. In recent years, several technological and scientific developments - including improved analytical tools, genome mining and engineering strategies, and microbial culturing advances - are addressing such challenges and opening up new opportunities. Consequently, interest in natural products as drug leads is being revitalized, particularly for tackling antimicrobial resistance. Here, we summarize recent technological developments that are enabling natural product-based drug discovery, highlight selected applications and discuss key opportunities.
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Affiliation(s)
- Atanas G Atanasov
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Jastrzebiec, Poland.
- Department of Pharmacognosy, University of Vienna, Vienna, Austria.
- Institute of Neurobiology, Bulgarian Academy of Sciences, Sofia, Bulgaria.
- Ludwig Boltzmann Institute for Digital Health and Patient Safety, Medical University of Vienna, Vienna, Austria.
| | - Sergey B Zotchev
- Department of Pharmacognosy, University of Vienna, Vienna, Austria
| | - Verena M Dirsch
- Department of Pharmacognosy, University of Vienna, Vienna, Austria
| | - Claudiu T Supuran
- Università degli Studi di Firenze, NEUROFARBA Dept, Sezione di Scienze Farmaceutiche, Florence, Italy.
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18
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Parthasarathy A, Borrego EJ, Savka MA, Dobson RCJ, Hudson AO. Amino acid-derived defense metabolites from plants: A potential source to facilitate novel antimicrobial development. J Biol Chem 2021; 296:100438. [PMID: 33610552 PMCID: PMC8024917 DOI: 10.1016/j.jbc.2021.100438] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 12/23/2022] Open
Abstract
For millennia, humanity has relied on plants for its medicines, and modern pharmacology continues to reexamine and mine plant metabolites for novel compounds and to guide improvements in biological activity, bioavailability, and chemical stability. The critical problem of antibiotic resistance and increasing exposure to viral and parasitic diseases has spurred renewed interest into drug treatments for infectious diseases. In this context, an urgent revival of natural product discovery is globally underway with special attention directed toward the numerous and chemically diverse plant defensive compounds such as phytoalexins and phytoanticipins that combat herbivores, microbial pathogens, or competing plants. Moreover, advancements in “omics,” chemistry, and heterologous expression systems have facilitated the purification and characterization of plant metabolites and the identification of possible therapeutic targets. In this review, we describe several important amino acid–derived classes of plant defensive compounds, including antimicrobial peptides (e.g., defensins, thionins, and knottins), alkaloids, nonproteogenic amino acids, and phenylpropanoids as potential drug leads, examining their mechanisms of action, therapeutic targets, and structure–function relationships. Given their potent antibacterial, antifungal, antiparasitic, and antiviral properties, which can be superior to existing drugs, phytoalexins and phytoanticipins are an excellent resource to facilitate the rational design and development of antimicrobial drugs.
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Affiliation(s)
- Anutthaman Parthasarathy
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, New York, USA
| | - Eli J Borrego
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, New York, USA
| | - Michael A Savka
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, New York, USA
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, Australia
| | - André O Hudson
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, New York, USA.
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19
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Combinatorial biosynthesis for the generation of new-to-nature peptide antimicrobials. Biochem Soc Trans 2021; 49:203-215. [PMID: 33439248 DOI: 10.1042/bst20200425] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 12/12/2022]
Abstract
Natural peptide products are a valuable source of important therapeutic agents, including antibiotics, antivirals and crop protection agents. Aided by an increased understanding of structure-activity relationships of these complex molecules and the biosynthetic machineries that produce them, it has become possible to re-engineer complete machineries and biosynthetic pathways to create novel products with improved pharmacological properties or modified structures to combat antimicrobial resistance. In this review, we will address the progress that has been made using non-ribosomally produced peptides and ribosomally synthesized and post-translationally modified peptides as scaffolds for designed biosynthetic pathways or combinatorial synthesis for the creation of novel peptide antimicrobials.
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20
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Wu ZC, Boger DL. The quest for supernatural products: the impact of total synthesis in complex natural products medicinal chemistry. Nat Prod Rep 2020; 37:1511-1531. [PMID: 33169762 PMCID: PMC7678878 DOI: 10.1039/d0np00060d] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Covering: 2000 up to 2020This review presents select recent advances in the medicinal chemistry of complex natural products that are prepared by total synthesis. The underlying studies highlight enabling divergent synthetic strategies and methods that permit the systematic medicinal chemistry studies of key analogues bearing deep-seated structural changes not readily accessible by semisynthetic or biosynthetic means. Select and recent examples are detailed where the key structural changes are designed to improve defined properties or to overcome an intrinsic limitation of the natural product itself. In the examples presented, the synthetic efforts provided supernatural products, a term first introduced by our colleague Ryan Shenvi (Synlett, 2016, 27, 1145-1164), with properties superseding the parent natural product. The design principles and approaches for creating the supernatural products are highlighted with an emphasis on the properties addressed that include those that improve activity or potency, increase selectivity, enhance durability, broaden the spectrum of activity, improve chemical or metabolic stability, overcome limiting physical properties, add mechanisms of action, enhance PK properties, overcome drug resistance, and/or improve in vivo efficacy. Some such improvements may be regarded by some as iterative enhancements whereas others, we believe, truly live up to their characterization as supernatural products. Most such efforts are also accompanied by advances in synthetic organic chemistry, inspiring the development of new synthetic methodology and providing supernatural products with improved synthetic accessibility.
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Affiliation(s)
- Zhi-Chen Wu
- Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA.
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21
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Hwang N, Pei Y, Clement J, Robertson ES, Du Y. Identification of a 3-β-homoalanine conjugate of brusatol with reduced toxicity in mice. Bioorg Med Chem Lett 2020; 30:127553. [PMID: 32971261 DOI: 10.1016/j.bmcl.2020.127553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/08/2020] [Accepted: 09/10/2020] [Indexed: 12/18/2022]
Abstract
Brusatol, a quassinoid natural product, is effective against multiple diseases including hematologic malignancies, as we reported recently by targeting the PI3Kγ isoform, but toxicity limits its further development. Herein, we report the synthesis of a series of conjugates of brusatol with amino acids and short peptides at its enolic hydroxyl at C-3. A number of conjugates with smaller amino acids and peptides demonstrated activities comparable to brusatol. Through in vitro and in vivo evaluations, we identified UPB-26, a conjugate of brusatol with a L- β-homoalanine, which exhibits good chemical stability at physiological pH's (SGF and SIF), moderate rate of conversion to brusatol in both human and rat plasmas, improved mouse liver microsomal stability, and most encouragingly, enhanced safety compared to brusatol in mice upon IP administration.
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Affiliation(s)
- Nicky Hwang
- Baruch S. Blumberg Institute, Doylestown, PA, USA
| | - Yonggang Pei
- Departments of Otorhinolaryngology-Head and Neck Surgery, and Microbiology, and the Tumor Virology Program, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | | | - Erle S Robertson
- Departments of Otorhinolaryngology-Head and Neck Surgery, and Microbiology, and the Tumor Virology Program, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
| | - Yanming Du
- Baruch S. Blumberg Institute, Doylestown, PA, USA.
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22
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Iheagwam FN, Rotimi SO. Computer-Aided Analysis of Multiple SARS-CoV-2 Therapeutic Targets: Identification of Potent Molecules from African Medicinal Plants. SCIENTIFICA 2020; 2020:1878410. [PMID: 32963884 PMCID: PMC7492903 DOI: 10.1155/2020/1878410] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/03/2020] [Accepted: 08/13/2020] [Indexed: 05/05/2023]
Abstract
The COVID-19 pandemic, which started in Wuhan, China, has spread rapidly over the world with no known antiviral therapy or vaccine. Interestingly, traditional Chinese medicine helped in flattening the pandemic curve in China. In this study, molecules from African medicinal plants were analysed as potential candidates against multiple SARS-CoV-2 therapeutic targets. Sixty-five molecules from the ZINC database subset (AfroDb Natural Products) were virtually screened with some reported repurposed therapeutics against six SARS-CoV-2 and two human targets. Molecular docking, druglikeness, absorption, distribution, metabolism, excretion, and toxicity (ADMET) of the best hits were further simulated. Of the 65 compounds, only three, namely, 3-galloylcatechin, proanthocyanidin B1, and luteolin 7-galactoside found in almond (Terminalia catappa), grape (Vitis vinifera), and common verbena (Verbena officinalis), were able to bind to all eight targets better than the reported repurposed drugs. The findings suggest these molecules may play a role as therapeutic leads in tackling this pandemic due to their multitarget activity.
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Affiliation(s)
- Franklyn Nonso Iheagwam
- Department of Biochemistry, College of Science and Technology, Covenant University, Canaanland, P.M.B. 1023, Ota, Ogun, Nigeria
- Covenant University Public Health and Wellness Research Cluster (CUPHWERC), College of Science and Technology, Covenant University, Canaanland, P.M.B. 1023, Ota, Ogun, Nigeria
| | - Solomon Oladapo Rotimi
- Department of Biochemistry, College of Science and Technology, Covenant University, Canaanland, P.M.B. 1023, Ota, Ogun, Nigeria
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23
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Limbrick EM, Yñigez-Gutierrez AE, Dulin CC, Derewacz DK, Spraggins JM, McCulloch KM, Iverson TM, Bachmann BO. Methyltransferase Contingencies in the Pathway of Everninomicin D Antibiotics and Analogues. Chembiochem 2020; 21:3349-3358. [PMID: 32686210 DOI: 10.1002/cbic.202000305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/17/2020] [Indexed: 12/11/2022]
Abstract
Everninomicins are orthoester oligosaccharide antibiotics with potent activity against multidrug-resistant bacterial pathogens. Everninomicins act by disrupting ribosomal assembly in a distinct region in comparison to clinically prescribed drugs. We employed microporous intergeneric conjugation with Escherichia coli to manipulate Micromonospora for targeted gene-replacement studies of multiple putative methyltransferases across the octasaccharide scaffold of everninomicin effecting the A1 , C, F, and H rings. Analyses of gene-replacement and genetic complementation mutants established the mutability of the everninomicin scaffold through the generation of 12 previously unreported analogues and, together with previous results, permitted assignment of the ten methyltransferases required for everninomicin biosynthesis. The in vitro activity of A1 - and H-ring-modifying methyltransferases demonstrated the ability to catalyze late-stage modification of the scaffold on an A1 -ring phenol and H-ring C-4' hydroxy moiety. Together these results establish the potential of the everninomicin scaffold for modification through mutagenesis and in vitro modification of advanced biosynthetic intermediates.
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Affiliation(s)
- Emilianne M Limbrick
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Ctr, Nashville, TN 37235, USA.,Department of Chemistry, Mercer University, 1501 Mercer University Drive, Macon, GA 31207, USA
| | | | - Callie C Dulin
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Ctr, Nashville, TN 37235, USA
| | - Dagmara K Derewacz
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Ctr, Nashville, TN 37235, USA
| | - Jeffrey M Spraggins
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Ctr, Nashville, TN 37235, USA.,Department of Biochemistry, Vanderbilt University School of Medicine, 607 Light Hall, Nashville, TN 37205, USA.,Mass Spectrometry Research Center, Vanderbilt University School of Medicine, 465 21st Ave S, Nashville, TN 37240, USA
| | - Kathryn M McCulloch
- Department of Pharmacology, Vanderbilt University 7124 MRBIII, 465 21st Ave S, Nashville, TN 37232, USA.,Department of Chemistry & Biochemistry, California State Polytechnic University, Pomona, 3801 West Temple Ave, Pomona, CA 91768, USA
| | - T M Iverson
- Department of Biochemistry, Vanderbilt University School of Medicine, 607 Light Hall, Nashville, TN 37205, USA.,Department of Pharmacology, Vanderbilt University 7124 MRBIII, 465 21st Ave S, Nashville, TN 37232, USA.,Vanderbilt Institute of Chemical Biology.,Vanderbilt Center for Structural Biology
| | - Brian O Bachmann
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Ctr, Nashville, TN 37235, USA.,Department of Biochemistry, Vanderbilt University School of Medicine, 607 Light Hall, Nashville, TN 37205, USA.,Department of Pharmacology, Vanderbilt University 7124 MRBIII, 465 21st Ave S, Nashville, TN 37232, USA.,Vanderbilt Institute of Chemical Biology
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24
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Lautié E, Russo O, Ducrot P, Boutin JA. Unraveling Plant Natural Chemical Diversity for Drug Discovery Purposes. Front Pharmacol 2020; 11:397. [PMID: 32317969 PMCID: PMC7154113 DOI: 10.3389/fphar.2020.00397] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 03/16/2020] [Indexed: 12/11/2022] Open
Abstract
The screening and testing of extracts against a variety of pharmacological targets in order to benefit from the immense natural chemical diversity is a concern in many laboratories worldwide. And several successes have been recorded in finding new actives in natural products, some of which have become new drugs or new sources of inspiration for drugs. But in view of the vast amount of research on the subject, it is surprising that not more drug candidates were found. In our view, it is fundamental to reflect upon the approaches of such drug discovery programs and the technical processes that are used, along with their inherent difficulties and biases. Based on an extensive survey of recent publications, we discuss the origin and the variety of natural chemical diversity as well as the strategies to having the potential to embrace this diversity. It seemed to us that some of the difficulties of the area could be related with the technical approaches that are used, so the present review begins with synthetizing some of the more used discovery strategies, exemplifying some key points, in order to address some of their limitations. It appears that one of the challenges of natural product-based drug discovery programs should be an easier access to renewable sources of plant-derived products. Maximizing the use of the data together with the exploration of chemical diversity while working on reasonable supply of natural product-based entities could be a way to answer this challenge. We suggested alternative ways to access and explore part of this chemical diversity with in vitro cultures. We also reinforced how important it was organizing and making available this worldwide knowledge in an "inventory" of natural products and their sources. And finally, we focused on strategies based on synthetic biology and syntheses that allow reaching industrial scale supply. Approaches based on the opportunities lying in untapped natural plant chemical diversity are also considered.
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Affiliation(s)
- Emmanuelle Lautié
- Centro de Valorização de Compostos Bioativos da Amazônia (CVACBA)-Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Brazil
| | - Olivier Russo
- Institut de Recherches Internationales SERVIER, Suresnes, France
| | - Pierre Ducrot
- Molecular Modelling Department, 'PEX Biotechnologie, Chimie & Biologie, Institut de Recherches SERVIER, Croissy-sur-Seine, France
| | - Jean A Boutin
- Institut de Recherches Internationales SERVIER, Suresnes, France
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25
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Hilton M, Brackett CM, Mercado BQ, Blagg BSJ, Miller SJ. Catalysis-Enabled Access to Cryptic Geldanamycin Oxides. ACS CENTRAL SCIENCE 2020; 6:426-435. [PMID: 32232143 PMCID: PMC7099596 DOI: 10.1021/acscentsci.0c00024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Indexed: 05/30/2023]
Abstract
Catalytic, selective modifications of natural products can be a fertile platform for not only unveiling new natural product analogues with altered biological activity, but also for revealing new reactivity and selectivity hierarchies for embedded functional groups in complex environments. Motivated by these intersecting aims, we report site- and stereoselective oxidation reactions of geldanamycin facilitated by aspartyl-peptide catalysts. Through the isolation and characterization of four new geldanamycin oxides, we discovered a synergistic effect between lead peptide-based catalysts and geldanamycin, resulting in an unexpected reaction pathway. Curiously, our discoveries would likely not have been possible absent the attractive noncovalent interactions intrinsic to both the catalysts and the natural product. The result is a set of new "meta" catalytic reactions that deliver both unknown and previously incompletely characterized geldanamycin analogues. Enabled by the catalytic, site-selective epoxidation of geldanamycin, biological assays were carried out to document the bioactivities of the new compounds.
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Affiliation(s)
- Margaret
J. Hilton
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Christopher M. Brackett
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre
Dame, Indiana 46556, United States
| | - Brandon Q. Mercado
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Brian S. J. Blagg
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre
Dame, Indiana 46556, United States
| | - Scott J. Miller
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
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26
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Li F, Wang H, Wang Y, Feng S, Hu B, Zhang X, Wang J, Li W, Cheng M. Computational investigation reveals Picrasidine C as selective PPARα lead: binding pattern, selectivity mechanism and ADME/tox profile. J Biomol Struct Dyn 2019; 38:5401-5418. [PMID: 31787028 DOI: 10.1080/07391102.2019.1699861] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Natural products and their derivatives have been recognized as an important source of therapeutic agents for many years. Previously we isolated a dimeric β-carboline-type alkaloid Picrasidine C from the root of Picrasma quassioides as subtype-selective peroxisome proliferator-activated receptor α (PPARα) agonist. In order to modify this natural product for better affinity and druggability, we investigated a series of properties exhibited by Picrasidine C, such as its binding mode with PPARα, the selectivity mechanism over PPARγ, as well as ADME/Tox profile through computational methods including sequence alignment, molecular docking, pharmacophore modeling and molecular dynamics simulations. The detailed information of binding pattern and affinity for Picrasidine C elucidated here will be valuable for chemical modification. Besides, the steric hindrance of residue Phe363 in PPARγ pocket was speculated as the main isoform selectivity mechanism for Picrasidine C, which would be helpful for the design of selective derivatives. ADME/Tox prediction was conducted to avoid potential undesirable pharmacokinetic properties for reducing the risk of failure. Finally, novel skeletons were derived from lead compound by core hopping method, validated through molecular dynamic simulations and MM-GBSA calculation. In short, the information obtained from computational strategy would be valuable for us to find more potent, safe and selective PPARα agonists during structural optimization.
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Affiliation(s)
- Fangfei Li
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, P. R. China
| | - Hanxun Wang
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, P. R. China
| | - Ying Wang
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, P. R. China.,Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, P. R. China
| | - Shasha Feng
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, P. R. China
| | - Baichun Hu
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, P. R. China.,School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, P. R. China
| | - Xiangyu Zhang
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, P. R. China
| | - Jian Wang
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, P. R. China
| | - Wei Li
- Faculty of Pharmaceutical Sciences, Toho University, Funabashi, Japan
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, P. R. China
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Kornfuehrer T, Eustáquio AS. Diversification of polyketide structures via synthase engineering. MEDCHEMCOMM 2019; 10:1256-1272. [PMID: 32180918 PMCID: PMC7053703 DOI: 10.1039/c9md00141g] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 05/09/2019] [Indexed: 12/16/2022]
Abstract
Polyketide natural products possess diverse biological activities including antibiotic, anticancer, and immunosuppressive. Their equally varied and complex structures arise from head-to-tail condensation of simple carboxyacyl monomers. Since the seminal discovery that biosynthesis of polyketides such as the macrolide erythromycin is catalyzed by uncharacteristically large, multifunctional enzymes, termed modular type I polyketide synthases, chemists and biologists alike have been inspired to harness the apparent modularity of the synthases to further diversify polyketide structures. Yet, initial attempts to perform "combinatorial biosynthesis" failed due to challenges associated with maintaining the structural and catalytic integrity of large, chimeric synthases. Fast forward nearly 30 years, and advancements in our understanding of polyketide synthase structure and function have allowed the field to make significant progress toward effecting desired modifications to polyketide scaffolds in addition to engineering small, chiral fragments. This review highlights selected examples of polyketide diversification via control of monomer selection, oxidation state, stereochemistry, and cyclization. We conclude with a perspective on the present and future of polyketide structure diversification and hope that the examples presented here will encourage medicinal chemists to embrace polyketide synthetic biology as a means to revitalize polyketide drug discovery.
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Affiliation(s)
- Taylor Kornfuehrer
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences , College of Pharmacy , University of Illinois at Chicago , Chicago , Illinois 60607 , USA . ; Tel: +1 3124137082
| | - Alessandra S Eustáquio
- Department of Medicinal Chemistry and Pharmacognosy and Center for Biomolecular Sciences , College of Pharmacy , University of Illinois at Chicago , Chicago , Illinois 60607 , USA . ; Tel: +1 3124137082
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