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Lam YC, Hamchand R, Mucci NC, Kauffman SJ, Dudkina N, Reagle EV, Casanova-Torres ÁM, DeCuyper J, Chen H, Song D, Thomas MG, Palm NW, Goodrich-Blair H, Crawford JM. The Xenorhabdus nematophila LrhA transcriptional regulator modulates production of γ-keto- N-acyl amides with inhibitory activity against mutualistic host nematode egg hatching. Appl Environ Microbiol 2024; 90:e0052824. [PMID: 38916293 PMCID: PMC11267870 DOI: 10.1128/aem.00528-24] [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: 03/21/2024] [Accepted: 06/01/2024] [Indexed: 06/26/2024] Open
Abstract
Xenorhabdus nematophila is a symbiotic Gammaproteobacterium that produces diverse natural products that facilitate mutualistic and pathogenic interactions in their nematode and insect hosts, respectively. The interplay between X. nematophila secondary metabolism and symbiosis stage is tuned by various global regulators. An example of such a regulator is the LysR-type protein transcription factor LrhA, which regulates amino acid metabolism and is necessary for virulence in insects and normal nematode progeny production. Here, we utilized comparative metabolomics and molecular networking to identify small molecule factors regulated by LrhA and characterized a rare γ-ketoacid (GKA) and two new N-acyl amides, GKA-Arg (1) and GKA-Pro (2) which harbor a γ-keto acyl appendage. A lrhA null mutant produced elevated levels of compound 1 and reduced levels of compound 2 relative to wild type. N-acyl amides 1 and 2 were shown to be selective agonists for the human G-protein-coupled receptors (GPCRs) C3AR1 and CHRM2, respectively. The CHRM2 agonist 2 deleteriously affected the hatch rate and length of Steinernema nematodes. This work further highlights the utility of exploiting regulators of host-bacteria interactions for the identification of the bioactive small molecule signals that they control. IMPORTANCE Xenorhabdus bacteria are of interest due to their symbiotic relationship with Steinernema nematodes and their ability to produce a variety of natural bioactive compounds. Despite their importance, the regulatory hierarchy connecting specific natural products and their regulators is poorly understood. In this study, comparative metabolomic profiling was utilized to identify the secondary metabolites modulated by the X. nematophila global regulator LrhA. This analysis led to the discovery of three metabolites, including an N-acyl amide that inhibited the egg hatching rate and length of Steinernema carpocapsae nematodes. These findings support the notion that X. nematophila LrhA influences the symbiosis between X. nematophila and S. carpocapsae through N-acyl amide signaling. A deeper understanding of the regulatory hierarchy of these natural products could contribute to a better comprehension of the symbiotic relationship between X. nematophila and S. carpocapsae.
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Affiliation(s)
- Yick Chong Lam
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, Connecticut, USA
| | - Randy Hamchand
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, Connecticut, USA
| | - Nicholas C. Mucci
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Sarah J. Kauffman
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Natavan Dudkina
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, Connecticut, USA
| | - Emily V. Reagle
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, Connecticut, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | - Jessica DeCuyper
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Haiwei Chen
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Deguang Song
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Michael G. Thomas
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Noah W. Palm
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Heidi Goodrich-Blair
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jason M. Crawford
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
- Institute of Biomolecular Design & Discovery, Yale University, West Haven, Connecticut, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
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102
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Özçelik R, de Ruiter S, Criscuolo E, Grisoni F. Chemical language modeling with structured state space sequence models. Nat Commun 2024; 15:6176. [PMID: 39039051 PMCID: PMC11263548 DOI: 10.1038/s41467-024-50469-9] [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: 09/22/2023] [Accepted: 07/05/2024] [Indexed: 07/24/2024] Open
Abstract
Generative deep learning is reshaping drug design. Chemical language models (CLMs) - which generate molecules in the form of molecular strings - bear particular promise for this endeavor. Here, we introduce a recent deep learning architecture, termed Structured State Space Sequence (S4) model, into de novo drug design. In addition to its unprecedented performance in various fields, S4 has shown remarkable capabilities to learn the global properties of sequences. This aspect is intriguing in chemical language modeling, where complex molecular properties like bioactivity can 'emerge' from separated portions in the molecular string. This observation gives rise to the following question: Can S4 advance chemical language modeling for de novo design? To provide an answer, we systematically benchmark S4 with state-of-the-art CLMs on an array of drug discovery tasks, such as the identification of bioactive compounds, and the design of drug-like molecules and natural products. S4 shows a superior capacity to learn complex molecular properties, while at the same time exploring diverse scaffolds. Finally, when applied prospectively to kinase inhibition, S4 designs eight of out ten molecules that are predicted as highly active by molecular dynamics simulations. Taken together, these findings advocate for the introduction of S4 into chemical language modeling - uncovering its untapped potential in the molecular sciences.
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Affiliation(s)
- Rıza Özçelik
- Institute for Complex Molecular Systems and Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Utrecht, The Netherlands
| | - Sarah de Ruiter
- Institute for Complex Molecular Systems and Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Emanuele Criscuolo
- Institute for Complex Molecular Systems and Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Francesca Grisoni
- Institute for Complex Molecular Systems and Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Utrecht, The Netherlands.
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103
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Iazzetti A, Arcadi A, Chiarini M, Fabrizi G, Goggiamani A, Marrone F, Serraiocco A, Zoppoli R. Palladium-Catalyzed Tsuji-Trost-Type Reaction of 3-Indolylmethylacetates with O, and S Soft Nucleophiles. Molecules 2024; 29:3434. [PMID: 39065012 PMCID: PMC11280231 DOI: 10.3390/molecules29143434] [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: 07/04/2024] [Revised: 07/17/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
The chemical valorization of widespread molecules in renewable sources is a field of research widely investigated in the last decades. In this context, we envisaged that indole-3-carbinol, present in different Cruciferae plants, could be a readily available building block for the synthesis of various classes of indoles through a palladium-catalyzed Tsuji-Trost-type reaction with O and S soft nucleophiles. The regiochemical outcome of this high-yielding functionalization shows that the nucleophilic substitution occurs only at the benzylic position. Interestingly, with this protocol, the sulfonyl unit could be appended to the indole nucleus, providing convenient access to new classes of molecules with potential bioactivity.
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Affiliation(s)
- Antonia Iazzetti
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, L. go Francesco Vito 1, 00168 Rome, RM, Italy
- Policlinico Universitario ‘A. Gemelli’ Foundation-IRCCS, 00168 Rome, RM, Italy
| | - Antonio Arcadi
- Dipartimento di Scienze Fisiche e Chimiche, Università degli Studi di L’Aquila, Via Vetoio, 67100 Coppito, AQ, Italy;
| | - Marco Chiarini
- Dipartimento di Bioscienze e Tecnologie Agro-Alimentari e Ambientali, Università di Teramo, Via R. Balzarini, 64100 Teramo, TE, Italy;
| | - Giancarlo Fabrizi
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza, Università di Roma, P. le A. Moro 5, 00185 Rome, RM, Italy; (A.G.); (F.M.); (A.S.); (R.Z.)
| | - Antonella Goggiamani
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza, Università di Roma, P. le A. Moro 5, 00185 Rome, RM, Italy; (A.G.); (F.M.); (A.S.); (R.Z.)
| | - Federico Marrone
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza, Università di Roma, P. le A. Moro 5, 00185 Rome, RM, Italy; (A.G.); (F.M.); (A.S.); (R.Z.)
| | - Andrea Serraiocco
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza, Università di Roma, P. le A. Moro 5, 00185 Rome, RM, Italy; (A.G.); (F.M.); (A.S.); (R.Z.)
| | - Roberta Zoppoli
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza, Università di Roma, P. le A. Moro 5, 00185 Rome, RM, Italy; (A.G.); (F.M.); (A.S.); (R.Z.)
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104
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Guo X, Luo W, Wu L, Zhang L, Chen Y, Li T, Li H, Zhang W, Liu Y, Zheng J, Wang Y. Natural Products from Herbal Medicine Self-Assemble into Advanced Bioactive Materials. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2403388. [PMID: 39033533 DOI: 10.1002/advs.202403388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/09/2024] [Indexed: 07/23/2024]
Abstract
Novel biomaterials are becoming more crucial in treating human diseases. However, many materials require complex artificial modifications and synthesis, leading to potential difficulties in preparation, side effects, and clinical translation. Recently, significant progress has been achieved in terms of direct self-assembly of natural products from herbal medicine (NPHM), an important source for novel medications, resulting in a wide range of bioactive supramolecular materials including gels, and nanoparticles. The NPHM-based supramolecular bioactive materials are produced from renewable resources, are simple to prepare, and have demonstrated multi-functionality including slow-release, smart-responsive release, and especially possess powerful biological effects to treat various diseases. In this review, NPHM-based supramolecular bioactive materials have been revealed as an emerging, revolutionary, and promising strategy. The development, advantages, and limitations of NPHM, as well as the advantageous position of NPHM-based materials, are first reviewed. Subsequently, a systematic and comprehensive analysis of the self-assembly strategies specific to seven major classes of NPHM is highlighted. Insights into the influence of NPHM structural features on the formation of supramolecular materials are also provided. Finally, the drivers and preparations are summarized, emphasizing the biomedical applications, future scientific challenges, and opportunities, with the hope of igniting inspiration for future research and applications.
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Affiliation(s)
- Xiaohang Guo
- School of Medicine, Hunan University of Chinese Medicine, Changsha, 410208, China
| | - Weikang Luo
- Institute of Integrative Medicine, Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, 410008, China
- Center for Interdisciplinary Research in Traditional Chinese Medicine, Xiangya Hospital, Central South University, Changsha, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Lingyu Wu
- College of Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha, 410208, China
| | - Lianglin Zhang
- Institute of Integrative Medicine, Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, 410008, China
- Center for Interdisciplinary Research in Traditional Chinese Medicine, Xiangya Hospital, Central South University, Changsha, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Yuxuan Chen
- Beijing Normal University-Hong Kong Baptist University United International College, Zhuhai, 519087, China
| | - Teng Li
- Institute of Integrative Medicine, Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, 410008, China
- Center for Interdisciplinary Research in Traditional Chinese Medicine, Xiangya Hospital, Central South University, Changsha, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Haigang Li
- Hunan key laboratory of the research and development of novel pharmaceutical preparations, Changsha Medical University, Changsha, 410219, China
| | - Wei Zhang
- College of Integrated Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, 410208, China
| | - Yawei Liu
- School of Medicine, Hunan University of Chinese Medicine, Changsha, 410208, China
| | - Jun Zheng
- Institute of Integrative Medicine, Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, 410008, China
- Center for Interdisciplinary Research in Traditional Chinese Medicine, Xiangya Hospital, Central South University, Changsha, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Yang Wang
- Institute of Integrative Medicine, Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, 410008, China
- Center for Interdisciplinary Research in Traditional Chinese Medicine, Xiangya Hospital, Central South University, Changsha, 410008, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
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105
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Li J, Wang K, Luo S, Tian Y, Li Y, Hu S, Tan H, Zhang J, Li J. Co-expression of a pair of interdependent regulators coding genes ovmZ and ovmW awakens the production of angucyclinones antibiotics in Streptomyces neyagawaensis. Microb Cell Fact 2024; 23:202. [PMID: 39026365 PMCID: PMC11264864 DOI: 10.1186/s12934-024-02478-y] [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: 05/20/2024] [Accepted: 07/08/2024] [Indexed: 07/20/2024] Open
Abstract
BACKGROUND Microbial genome sequencing and analysis revealed the presence of abundant silent secondary metabolites biosynthetic gene clusters (BGCs) in streptomycetes. Activating these BGCs has great significance for discovering new compounds and novel biosynthetic pathways. RESULTS In this study, we found that ovmZ and ovmW homologs, a pair of interdependent transcriptional regulators coding genes, are widespread in actinobacteria and closely associated with the biosynthesis of secondary metabolites. Through co-overexpression of native ovmZ and ovmW in Streptomyces neyagawaensis NRRL B-3092, a silent type II polyketide synthase (PKS) gene cluster was activated to produce gephyromycin A, tetrangomycin and fridamycin E with the yields of 22.3 ± 8.0 mg/L, 4.8 ± 0.5 mg/L and 20.3 ± 4.1 mg/L respectively in the recombinant strain of S.ne/pZnWn. However, expression of either ovmZ or ovmW failed to activate this gene cluster. Interestingly, overexpression of the heterologous ovmZ and ovmW pair from oviedomycin BGC of S. ansochromogenes 7100 also led to awakening of this silent angucyclinone BGC in S. neyagawaensis. CONCLUSION A silent angucyclinone BGC was activated by overexpressing both ovmZ and ovmW in S. neyagawaensis. Due to the wide distribution of ovmZ and ovmW in the BGCs of actinobacteria, co-overexpression of ovmZ and ovmW could be a strategy for activating silent BGCs, thus stimulating the biosynthesis of secondary metabolites.
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Affiliation(s)
- Junyue Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kai Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Sainan Luo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuqing Tian
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yue Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huarong Tan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jihui Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jine Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
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106
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Khwathisi A, Madala NE, Traore AN, Samie A. Bioprospecting of soil-borne microorganisms and chemical dereplication of their anti-microbial constituents with the aid of UPLC-QTOF-MS and molecular networking approach. PeerJ 2024; 12:e17364. [PMID: 39035159 PMCID: PMC11260408 DOI: 10.7717/peerj.17364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/18/2024] [Indexed: 07/23/2024] Open
Abstract
Due to the emergence of drug-resistant microorganisms, the search for broad-spectrum antimicrobial compounds has become extremely crucial. Natural sources like plants and soils have been explored for diverse metabolites with antimicrobial properties. This study aimed to identify microorganisms from agricultural soils exhibiting antimicrobial effects against known human pathogens, and to highlight the chemical space of the responsible compounds through the computational metabolomics-based bioprospecting approach. Herein, bacteria were extracted from soil samples and their antimicrobial potential was measured via the agar well diffusion method. Methanolic extracts from the active bacteria were analyzed using the liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QTOF-MS) technique, and the subsequent data was further analyzed through molecular networking approach which aided in identification of potential anti-microbial compounds. Furthermore, 16S rRNA gene sequencing enabled identification of the active bacterial isolates, where isolate 1 and 2 were identified as strains of Bacillus pumilus, whilst isolate 3 was found to be Bacillus subtilis. Interestingly, isolate 3 (Bacillus subtilis) displayed wide-ranging antimicrobial activity against the tested human pathogens. Molecular networking revealed the presence of Diketopiperazine compounds such as cyclo (D-Pro-D-Leu), cyclo (L-Tyr-L-Pro), cyclo (L-Pro-D-Phe), and cyclo (L-Pro-L-Val), alongside Surfactin C, Surfactin B, Pumilacidin E, and Isarrin D in the Bacillus strains as the main anti-microbial compounds. The application of the molecular networking approach represents an innovation in the field of bio-guided bioprospection of microorganisms and has proved to be an effective and feasible towards unearthing potent antimicrobial compounds. Additionally, the (computational metabolomics-based) approach accelerates the discovery of bioactive compounds and isolation of strains which offer a promising avenue for discovering new clinical antimicrobials. Finally, soil microbial flora could serve an alternative source of anti-microbial compounds which can assist in the fight against emergence of multi-drug resistance bacterial pathogens.
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Affiliation(s)
- Adivhaho Khwathisi
- Biochemistry and Microbiology, University of Venda for Science and Technology, Thohoyandou, South Africa
| | - Ntakadzeni Edwin Madala
- Biochemistry and Microbiology, University of Venda for Science and Technology, Thohoyandou, South Africa
| | - Afsatou Ndama Traore
- Biochemistry and Microbiology, University of Venda for Science and Technology, Thohoyandou, South Africa
| | - Amidou Samie
- Biochemistry and Microbiology, University of Venda for Science and Technology, Thohoyandou, South Africa
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107
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Narayanankutty A, Famurewa AC, Oprea E. Natural Bioactive Compounds and Human Health. Molecules 2024; 29:3372. [PMID: 39064950 PMCID: PMC11279386 DOI: 10.3390/molecules29143372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
Natural bioactive compounds encompass a vast array of molecules derived from plants, fungi, marine organisms, and other natural sources [...].
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Affiliation(s)
- Arunaksharan Narayanankutty
- Division of Cell and Molecular Biology, PG and Research Department of Zoology, St. Joseph’s College (Autonomous), Devagiri, Kozhikode 673008, Kerala, India
| | - Ademola C. Famurewa
- Department of Medical Biochemistry, Faculty of Basic Medical Sciences, College of Medicine, Alex Ekwueme Federal University, Ndufu-Alike lkwo, P.M.B. 1010, Abakaliki 482131, Nigeria;
| | - Eliza Oprea
- Department of Botany and Microbiology, Faculty of Biology, University of Bucharest, 1-3 Portocalelor Street, 060101 Bucharest, Romania;
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108
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Li J, Zhao J, Tian C, Dong L, Kang Z, Wang J, Zhao S, Li M, Tong X. Mechanisms of regulation of glycolipid metabolism by natural compounds in plants: effects on short-chain fatty acids. Nutr Metab (Lond) 2024; 21:49. [PMID: 39026248 PMCID: PMC11256480 DOI: 10.1186/s12986-024-00829-5] [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: 05/15/2024] [Accepted: 07/10/2024] [Indexed: 07/20/2024] Open
Abstract
BACKGROUND Natural compounds can positively impact health, and various studies suggest that they regulate glucose‒lipid metabolism by influencing short-chain fatty acids (SCFAs). This metabolism is key to maintaining energy balance and normal physiological functions in the body. This review explores how SCFAs regulate glucose and lipid metabolism and the natural compounds that can modulate these processes through SCFAs. This provides a healthier approach to treating glucose and lipid metabolism disorders in the future. METHODS This article reviews relevant literature on SCFAs and glycolipid metabolism from PubMed and the Web of Science Core Collection (WoSCC). It also highlights a range of natural compounds, including polysaccharides, anthocyanins, quercetins, resveratrols, carotenoids, and betaines, that can regulate glycolipid metabolism through modulation of the SCFA pathway. RESULTS Natural compounds enrich SCFA-producing bacteria, inhibit harmful bacteria, and regulate operational taxonomic unit (OTU) abundance and the intestinal transport rate in the gut microbiota to affect SCFA content in the intestine. However, most studies have been conducted in animals, lack clinical trials, and involve fewer natural compounds that target SCFAs. More research is needed to support the conclusions and to develop healthier interventions. CONCLUSIONS SCFAs are crucial for human health and are produced mainly by the gut microbiota via dietary fiber fermentation. Eating foods rich in natural compounds, including fruits, vegetables, tea, and coarse fiber foods, can hinder harmful intestinal bacterial growth and promote beneficial bacterial proliferation, thus increasing SCFA levels and regulating glucose and lipid metabolism. By investigating how these compounds impact glycolipid metabolism via the SCFA pathway, novel insights and directions for treating glucolipid metabolism disorders can be provided.
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Affiliation(s)
- Jiarui Li
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Jinyue Zhao
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Chuanxi Tian
- Beijing University of Chinese Medicine, Beijing, China
| | - Lishuo Dong
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Zezheng Kang
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Jingshuo Wang
- The Affiliated Hospital, Changchun University of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Shuang Zhao
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Min Li
- Research Laboratory of Molecular Biology, Guang'anmen Hospital of China Academy of Chinese Medical Sciences, Beijing, China.
| | - Xiaolin Tong
- Guang'anmen Hospital, Academician of Chinese Academy of Sciences, China Academy of Traditional Chinese Medical Sciences, Beijing, China.
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109
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Carrero JC, Espinoza B, Huerta L, Silva-Miranda M, Guzmán-Gutierrez SL, Dorazco-González A, Reyes-Chilpa R, Espitia C, Sánchez S. Introducing the NUATEI Consortium: A Mexican Research Program for the Identification of Natural and Synthetic Antimicrobial Compounds for Prevalent Infectious Diseases. Pharmaceuticals (Basel) 2024; 17:957. [PMID: 39065807 PMCID: PMC11280322 DOI: 10.3390/ph17070957] [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: 06/07/2024] [Revised: 07/09/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
The need for new drugs to treat human infections is a global health concern. Diseases like tuberculosis, trypanosomiasis, amoebiasis, and AIDS remain significant problems, especially in developing countries like Mexico. Despite existing treatments, issues such as resistance and adverse effects drive the search for new alternatives. Herein, we introduce the NUATEI research consortium, made up of experts from the Institute of Biomedical Research at UNAM, who identify and obtain natural and synthetic compounds and test their effects against human pathogens using in vitro and in vivo models. The consortium has evaluated hundreds of natural extracts and compounds against the pathogens causing tuberculosis, trypanosomiasis, amoebiasis, and AIDS, rendering promising results, including a patent with potential for preclinical studies. This paper presents the rationale behind the formation of this consortium, as well as its objectives and strategies, emphasizing the importance of natural and synthetic products as sources of antimicrobial compounds and the relevance of the diseases studied. Finally, we briefly describe the methods of the evaluation of the compounds in each biological model and the main achievements. The potential of the consortium to screen numerous compounds and identify new therapeutic agents is highlighted, demonstrating its significant contribution to addressing these infectious diseases.
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Affiliation(s)
- Julio César Carrero
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (B.E.); (L.H.); (C.E.)
| | - Bertha Espinoza
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (B.E.); (L.H.); (C.E.)
| | - Leonor Huerta
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (B.E.); (L.H.); (C.E.)
| | - Mayra Silva-Miranda
- CONAHCyT-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (M.S.-M.); (S.-L.G.-G.)
| | - Silvia-Laura Guzmán-Gutierrez
- CONAHCyT-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (M.S.-M.); (S.-L.G.-G.)
| | - Alejandro Dorazco-González
- Departmento de Química Inorgánica, Instituto de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Ricardo Reyes-Chilpa
- Departamento de Productos Naturales, Instituto de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Clara Espitia
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (B.E.); (L.H.); (C.E.)
| | - Sergio Sánchez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
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110
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Amtaghri S, Slaoui M, Eddouks M. Phytomedical compounds as promising therapeutic agents for COVID-19 targeting angiotensin-converting enzyme 2: a review. J Pharm Pharmacol 2024:rgae101. [PMID: 39018169 DOI: 10.1093/jpp/rgae101] [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: 04/02/2024] [Accepted: 07/07/2024] [Indexed: 07/19/2024]
Abstract
AIMS The aim of the present review was to highlight natural product investigations in silico and in vitro to find plants and chemicals that inhibit or stimulate angiotensin-converting enzyme 2 (ACE-2). BACKGROUND The global reduction of incidents and fatalities attributable to infections with SARS-CoV-2 is one of the most public health problems. In the absence of specific therapy for coronavirus disease 2019 (COVID-19), phytocompounds generated from plant extracts may be a promising strategy worth further investigation, motivating researchers to evaluate the safety and anti-SARS-CoV-2 effectiveness of these ingredients. OBJECTIVE To review phytochemicals in silico for anti-SARS-CoV-2 activity and to assess their safety and effectiveness in vitro and in vivo. METHODS The present review was conducted using various scientific databases and studies on anti-SARS-CoV-2 phytochemicals were analyzed and summarized. The results obtained from the in silico screening were subjected to extraction, isolation, and purification. The in vitro studies on anti-SarcoV-2 were also included in this review. In addition, the results of this research were interpreted, analyzed, and documented on the basis of the bibliographic information obtained. RESULTS This review discusses recent research on using natural remedies to cure or prevent COVID-19 infection. The literature analysis shows that the various herbal preparations (extracts) and purified compounds can block the replication or entrance of the virus directly to carry out their anti-SARS-CoV-2 effects. It is interesting to note that certain items can prevent SARS-CoV-2 from infecting human cells by blocking the ACE-2 receptor or the serine protease TMPRRS2. Moreover, natural substances have been demonstrated to block proteins involved in the SARS-CoV-2 life cycle, such as papain- or chymotrypsin-like proteases. CONCLUSION The natural products may have the potential for use singly or in combination as alternative drugs to treat/prevent COVID-19 infection, including blocking or stimulating ACE-2. In addition, their structures may provide indications for the development of anti-SARS-CoV-2 drugs.
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Affiliation(s)
- Smail Amtaghri
- Team of Ethnopharmacology and Pharmacognosy, Faculty of Sciences and Techniques Errachidia, Moulay Ismail University of Meknes, BP 509, Boutalamine, Errachidia 52000, Morocco
- Energy, Materials and Sustainable Development (EMDD) Team-Higher School of Technology-SALE, Center for Water, Natural Resources Environment and Sustainable Development (CERNE2D), Mohammed V University in Rabat, Rabat, Morocco
| | - Miloudia Slaoui
- Energy, Materials and Sustainable Development (EMDD) Team-Higher School of Technology-SALE, Center for Water, Natural Resources Environment and Sustainable Development (CERNE2D), Mohammed V University in Rabat, Rabat, Morocco
| | - Mohamed Eddouks
- Team of Ethnopharmacology and Pharmacognosy, Faculty of Sciences and Techniques Errachidia, Moulay Ismail University of Meknes, BP 509, Boutalamine, Errachidia 52000, Morocco
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111
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Zhong W, Agarwal V. Polymer degrading marine Microbulbifer bacteria: an un(der)utilized source of chemical and biocatalytic novelty. Beilstein J Org Chem 2024; 20:1635-1651. [PMID: 39076296 PMCID: PMC11285056 DOI: 10.3762/bjoc.20.146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 07/02/2024] [Indexed: 07/31/2024] Open
Abstract
Microbulbifer is a genus of halophilic bacteria that are commonly detected in the commensal marine microbiomes. These bacteria have been recognized for their ability to degrade polysaccharides and other polymeric materials. Increasingly, Microbulbifer genomes indicate these bacteria to be an untapped reservoir for novel natural product discovery and biosynthetic novelty. In this review, we summarize the distribution of Microbulbifer bacteria, activities of the various polymer degrading enzymes that these bacteria produce, and an up-to-date summary of the natural products that have been isolated from Microbulbifer strains. We argue that these bacteria have been hiding in plain sight, and contemporary efforts into their genome and metabolome mining are going to lead to a proliferation of Microbulbifer-derived natural products in the future. We also describe, where possible, the ecological interactions of these bacteria in marine microbiomes.
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Affiliation(s)
- Weimao Zhong
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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112
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Cheng B, Wang Q, An Y, Chen F. Recent advances in the total synthesis of galantamine, a natural medicine for Alzheimer's disease. Nat Prod Rep 2024; 41:1060-1090. [PMID: 38450550 DOI: 10.1039/d4np00001c] [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: 03/08/2024]
Abstract
Covering: 2006 to 2023(-)-Galantamine is a natural product with distinctive structural features and potent inhibitory activity against acetylcholine esterase (AChE). It is clinically approved for the treatment of Alzheimer's disease. The clinical significance and scarcity of this natural product have prompted extensive and ongoing efforts towards the chemical synthesis of this challenging tetracyclic structure. The objective of this review is to summarize and discuss recent progress in the total synthesis of galantamine from 2006 to 2023. The contents are organized according to the synthetic strategies for the construction of the quaternary center. Key features of each synthesis have been highlighted, followed by a summary and outlook at the end.
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Affiliation(s)
- Bichu Cheng
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China.
- School of Science, Green Pharmaceutical Engineering Research Center, Harbin Institute of Technology, Shenzhen 518055, China
| | - Qi Wang
- School of Science, Green Pharmaceutical Engineering Research Center, Harbin Institute of Technology, Shenzhen 518055, China
| | - Yi An
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China.
| | - Fener Chen
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China.
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, Jiangxi 330022, China
- School of Science, Green Pharmaceutical Engineering Research Center, Harbin Institute of Technology, Shenzhen 518055, China
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113
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Kshatri A, Rivero-Pérez B, Giraldez T. Subunit-specific inhibition of BK channels by piperine. Biophys J 2024; 123:1942-1953. [PMID: 37700524 PMCID: PMC11309970 DOI: 10.1016/j.bpj.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 08/03/2023] [Accepted: 09/08/2023] [Indexed: 09/14/2023] Open
Abstract
Piperine is the principal alkaloid present in black pepper and is well-known for its diverse pharmacological effects, including inhibition of different ion channels. Large conductance Ca2+-activated K+ channels (BK) are widely expressed across several tissues and play a vital role in many physiological functions. In this study, we investigated the pharmacological effects of piperine on various BK channel subunit compositions (BKα, BKαβ1,4, BKαγ1,3) expressed in HEK293T cells. Piperine in zero Ca2+ reversibly inhibited currents from the pore-forming BKα channels in a dose-dependent manner with a half-maximal inhibitory concentration (IC50) of 4.8 μM. Elevating the internal Ca2+ concentration from 0 to 100 μM significantly attenuated the inhibitory effects of piperine on BKα channels. The mutation G311S in the pore domain failed to alter the modulatory effects of piperine, whereas deletion of the entire cytoplasmic domain from BKα channels ablated its inhibitory effects. Addition of either BKβ1 or β4 regulatory subunits did not alter the efficacy of piperine on BKα channels. Interestingly, co-expression of either BKγ1 or BKγ3 subunits greatly diminished the ability of piperine to inhibit BKα channels. Our findings demonstrate that piperine is a potent natural modulator of BKα/BKαβ1,4 subunits but not BKαγ1,3 subunits. The mechanism of piperine modulation appeared to be allosteric and differs from that of other BK pore blockers (paxilline, peptide toxins, and quaternary ammonium compounds). Together, our results unravel the potential of piperine to inhibit BK channels, providing a new tool to explore mechanisms underlying the effects of regulatory subunits.
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Affiliation(s)
- Aravind Kshatri
- Department of Basic Medical Sciences, Medical School, Universidad de La Laguna, Tenerife, Spain; Instituto de Tecnologias Biomedicas, Universidad de La Laguna, Tenerife, Spain
| | - Belinda Rivero-Pérez
- Department of Basic Medical Sciences, Medical School, Universidad de La Laguna, Tenerife, Spain; Instituto de Tecnologias Biomedicas, Universidad de La Laguna, Tenerife, Spain
| | - Teresa Giraldez
- Department of Basic Medical Sciences, Medical School, Universidad de La Laguna, Tenerife, Spain; Instituto de Tecnologias Biomedicas, Universidad de La Laguna, Tenerife, Spain.
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114
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Kathiresan N, Harini K, Veera Ravi A, Veerabharathi P, Pandi S, Ramesh M, Awere CO, Langeswaran K. Deciphering the Potential Therapeutic Effects of Hydnocarpus wightianus Seed Extracts using in vitro and in silico approaches. Microb Pathog 2024; 194:106798. [PMID: 39025383 DOI: 10.1016/j.micpath.2024.106798] [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: 03/04/2024] [Revised: 06/11/2024] [Accepted: 07/15/2024] [Indexed: 07/20/2024]
Abstract
Phytocompounds possess the potential to treat a broad spectrum of disorders due to their remarkable bioactivity. Naturally occurring compounds possess lower toxicity profiles, which making them attractive targets for drug development. Hydnocarpus wightianus seeds were extracted using ethanol, acetone, and hexane solvents. The extracts were evaluated for phytochemicals screening and other therapeutic characteristics, such as free radicals scavenging, anti α-amylase, anti α-glucosidase, and anti-bacterial activities. The ethanolic extract exhibited noteworthy antibacterial characteristics and demonstrated considerable antioxidant, and anti-diabetic effects. The IC50 value of the ethanolic extract for Dpph, α-amylase, and α-glucosidase were found to be 77.299 ± 3.381 μg/mL, 165.56 2.56 μg/mL, and 136.58 ± 5.82 μg/mL, respectively. The ethanolic extract was effective against Methicillin resistant Staphylococcus aureus (26 mm zone of inhibition at 100 μL concentration). Molecular docking investigations revealed the phytoconstituent's inhibitory mechanisms against diabetic, free radicals, and bacterial activity. Docking score for phytocompounds against targeted protein varies from -7.2 to -5.1 kcal/mol. The bioactive compounds present in the ethanolic extract were identified by Gas chromatography/Mass spectrometry analysis, followed by molecular docking and molecular dynamic simulation studies to further explore the phytoconstituent's inhibitory mechanism of α-glucosidase, ∝-amylase, radical scavenging, and bacterial activity. The electronic structure and possible pharmacological actions of the phytocompound were revealed through the use of Density Functional Theory (DFT) analysis. Computational and in vitro studies revealed that these identified compounds have anti-diabetic, anti-oxidant, and anti-bacterial activities against antibiotic-resistant strain of Staphylococcus aureus.
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Affiliation(s)
- Nachammai Kathiresan
- Department of Biotechnology, Alagappa University, Science Campus, Karaikudi, Tamil Nadu, India
| | - Kasilingam Harini
- Department of Biotechnology, Alagappa University, Science Campus, Karaikudi, Tamil Nadu, India
| | - Arumugam Veera Ravi
- Department of Biotechnology, Alagappa University, Science Campus, Karaikudi, Tamil Nadu, India
| | | | - Sangavi Pandi
- Department of Bioinformatics, Alagappa University, Science Campus, Karaikudi, Tamil Nadu, India
| | - Manikandan Ramesh
- Department of Biotechnology, Alagappa University, Science Campus, Karaikudi, Tamil Nadu, India
| | - Collince Omondi Awere
- Department of Biotechnology, Alagappa University, Science Campus, Karaikudi, Tamil Nadu, India
| | - Kulanthaivel Langeswaran
- Department of Biotechnology, Alagappa University, Science Campus, Karaikudi, Tamil Nadu, India; Department of Biomedical Science, Alagappa University, Science Campus, Karaikudi, Tamil Nadu, India.
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115
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Yadav M, Roy N, Mandal K, Nagpure M, Santra MK, Guchhait SK. Rutaecarpine-inspired scaffold-hopping strategy and Ullmann cross-coupling based synthetic approach: Identification of pyridopyrimidinone-indole based novel anticancer chemotypes. Bioorg Med Chem 2024; 109:117799. [PMID: 38897138 DOI: 10.1016/j.bmc.2024.117799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/10/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024]
Abstract
Natural products as starting templates have shown historically major contribution to development of drugs. Inspired by the structure-function of an anticancer natural alkaloid Rutaecarpine, the Scaffold-hopped Acyclic Analogues of Rutaecarpine (SAAR) with 'N'-atom switch (1°-hop) and ring-opening (2°-hop) were investigated. A new synthetic route was developed for an effective access to the analogues, i.e. 2-indolyl-pyrido[1,2-a]pyrimidinones, which involved preparation of N-Boc-N'-phthaloyltryptamine/mexamine-bromides and pyridopyrmidinon-2-yl triflate, a nickel/palladium-catalysed Ullmann cross-coupling of these bromides and triflate, deprotection of phthalimide followed by N-aroylation, and Boc-deprotection. Fourteen novel SAAR-compounds were prepared, and they showed characteristic antiproliferative activity against various cancer cells. Three most active compounds (11a, 11b, and 11c) exhibited good antiproliferative activity, IC50 7.7-15.8 µM against human breast adenocarcinoma cells (MCF-7), lung cancer cells (A549), and colon cancer cells (HCT-116). The antiproliferative property was also observed in the colony formation assay. The SAAR compound 11b was found to have superior potency than original natural product Rutaecarpine and an anticancer drug 5-FU in antiproliferative activities with relatively lower cytotoxicity towards normal breast epithelial cells (MCF10A) and significantly higher inhibitory effect on cancer cells' migration. The compound 11b was found to possess favourable in silico physicochemical characteristics (lipophilicity-MLOGP, TPSA, and water solubility-ESOL, and others), bioavailability score, and pharmacokinetic properties (GI absorption, BBB non-permeant, P-gp, and CYP2D6). Interestingly, the compound 11b did not show any medicinal chemistry structural alert of PAINS and Brenk filter. The study represents for the first time the successful discovery of new potent anticancer chemotypes using Rutaecarpine natural alkaloid as starting template and reaffirms the significance of natural product-inspired scaffold-hopping technique in drug discovery research.
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Affiliation(s)
- Mukul Yadav
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Mohali, Punjab 160062, India
| | - Nibedita Roy
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Mohali, Punjab 160062, India
| | - Kartik Mandal
- National Centre for Cell Science, NCCS Complex, Pune University Campus Ganeshkhind, Pune, Maharastra 411007, India
| | - Mithilesh Nagpure
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Mohali, Punjab 160062, India
| | - Manas K Santra
- National Centre for Cell Science, NCCS Complex, Pune University Campus Ganeshkhind, Pune, Maharastra 411007, India
| | - Sankar K Guchhait
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Mohali, Punjab 160062, India.
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116
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La Monica G, Bono A, Alamia F, Lauria A, Martorana A. Bioisosteric heterocyclic analogues of natural bioactive flavonoids by scaffold-hopping approaches: State-of-the-art and perspectives in medicinal chemistry. Bioorg Med Chem 2024; 109:117791. [PMID: 38870715 DOI: 10.1016/j.bmc.2024.117791] [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: 03/07/2024] [Revised: 05/13/2024] [Accepted: 06/05/2024] [Indexed: 06/15/2024]
Abstract
The flavonoid family is a set of well-known bioactive natural molecules, with a wide range of potential therapeutic applications. Despite the promising results obtained in preliminary in vitro/vivo studies, their pharmacokinetic and pharmacodynamic profiles are severely compromised by chemical instability. To address this issue, the scaffold-hopping approach is a promising strategy for the structural optimization of natural leads to discover more potent analogues. In this scenario, this Perspective provides a critical analysis on how the replacement of the chromon-4-one flavonoid core with other bioisosteric nitrogen/sulphur heterocycles might affect the chemical, pharmaceutical and biological properties of the resulting new chemical entities. The investigated derivatives were classified on the basis of their biological activity and potential therapeutic indications. For each session, the target(s), the specific mechanism of action, if available, and the key pharmacophoric moieties were highlighted, as revealed by X-ray crystal structures and in silico structure-based studies. Biological activity data, in vitro/vivo studies, were examined: a particular focus was given on the improvements observed with the new heterocyclic analogues compared to the natural flavonoids. This overview of the scaffold-hopping advantages in flavonoid compounds is of great interest to the medicinal chemistry community to better exploit the vast potential of these natural molecules and to identify new bioactive molecules.
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Affiliation(s)
- Gabriele La Monica
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, University of Palermo, Viale delle Scienze, Ed. 17, I-90128 Palermo, Italy
| | - Alessia Bono
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, University of Palermo, Viale delle Scienze, Ed. 17, I-90128 Palermo, Italy
| | - Federica Alamia
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, University of Palermo, Viale delle Scienze, Ed. 17, I-90128 Palermo, Italy
| | - Antonino Lauria
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, University of Palermo, Viale delle Scienze, Ed. 17, I-90128 Palermo, Italy
| | - Annamaria Martorana
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche, University of Palermo, Viale delle Scienze, Ed. 17, I-90128 Palermo, Italy.
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Luan J, Song C, Liu Y, He R, Guo R, Cui Q, Jiang C, Li X, Hao K, Stewart AF, Fu J, Zhang Y, Wang H. Seamless site-directed mutagenesis in complex cloned DNA sequences using the RedEx method. Nat Protoc 2024:10.1038/s41596-024-01016-9. [PMID: 39009664 DOI: 10.1038/s41596-024-01016-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 05/01/2024] [Indexed: 07/17/2024]
Abstract
Seamless site-directed mutagenesis is an important technique for studying protein functions, tuning enzyme catalytic activities and modifying genetic elements in multiple rounds because it can insert, delete or substitute nucleotides, DNA segments or even entire genes at the target site without introducing any unwanted change. To facilitate seamless site-directed mutagenesis in large plasmids and bacterial artificial chromosomes (BACs) with repetitive sequences, we recently developed the RedEx strategy. Compared with previous methods, our approach achieves the recovery of correct recombinants with high accuracy by circumventing unwanted recombination between repetitive sequences. RedEx readily yields more than 80% accuracy in seamless DNA insertion and deletion in large multimodular polyketide synthase gene clusters, which are among the most difficult targets due to the large number of repetitive DNA sequences in modules encoding almost identical enzymes. Here we present the RedEx method by describing in detail the seamless site-directed mutagenesis in a BAC vector. Overall, the process includes three parts: (1) insertion of the RedEx cassette containing the desired mutation together with selection-counterselection markers flanked by unique restriction sites and 20-bp overlapping sequences into the target site by recombineering, (2) removal of the selection-counterselection markers in the BAC by restriction digestion and (3) circularization of the linear BAC by exonuclease-mediated in vitro DNA annealing. This protocol can be performed within 3 weeks and will enable researchers with DNA cloning experience to master seamless site-directed mutagenesis to accelerate their research.
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Affiliation(s)
- Ji Luan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Chaoyi Song
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Yan Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Ruoting He
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Ruofei Guo
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Qingwen Cui
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Chanjuan Jiang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Xiaochen Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Kexin Hao
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - A Francis Stewart
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Jun Fu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China
| | - Hailong Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, Shandong, China.
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Janem A, Omar G, Hamed O, Jodeh S, Deghles A, Berisha A, Mansour W, Jabal SA, Fares O, Jaser A, Amireh A, Adwan G. Water soluble curcumin with alkyl sulfonate moiety: Synthesis, and anticancer efficacy. Heliyon 2024; 10:e33808. [PMID: 39040342 PMCID: PMC11261864 DOI: 10.1016/j.heliyon.2024.e33808] [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: 02/06/2024] [Revised: 06/20/2024] [Accepted: 06/27/2024] [Indexed: 07/24/2024] Open
Abstract
Curcumin is classified as a chemotherapeutic medication because of its potential against numerous cancer cell lines and ability to inhibit cancer cell proliferation. Despite these findings, curcumin has yet to be commercialized as a drug due to its low water solubility, low absorption, and restricted bioavailability. As a result, there is a demand for water-soluble curcumin with improved solubility, bioavailability, and thus bioactivity. In this study we report the synthesis and the anticancer activities of water-soluble curcumins derivatives with alkyl sulfonate moiety. The target water-soluble curcumin with alkyl sulfonate moieties was created utilizing a straightforward technique that involved reacting curcumin with various sultones. The cytotoxic (24 h) and cytostatic (72 h) anticancer effect on breast carcinoma (MCF-7), liver carcinoma (HepG2), skin melanoma (B16-F110), colon human cancer and HeLa cervical carcinoma cell lines viability % via MTT assay were determined for the prepared derivatives. Results showed that curcumin-derived compounds have a pronounced cytostatic anticancer effect rather than cytotoxic one in relation to the compound type, cancer cell line type, and examined concentration compared to curcumin. The curcumin sulfonates outperformed curcumin activity against the tested cancer cells and showed to be powerful anticancer candidate drugs as supported by the theoretical calculations. This is evident by their high capacity to form H-bonding during docking with the amino acid side chains and the Vina docking score.
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Affiliation(s)
- Alaa Janem
- Chemistry Department, Faculty of Science, An-Najah National University, P.O. Box 7, Nablus, Palestine
| | - Ghader Omar
- Biology Department, Faculty of Sciences An-Najah National University, P.O. Box 7, Nablus, Palestine
| | - Othman Hamed
- Chemistry Department, Faculty of Science, An-Najah National University, P.O. Box 7, Nablus, Palestine
| | - Shehdeh Jodeh
- Chemistry Department, Faculty of Science, An-Najah National University, P.O. Box 7, Nablus, Palestine
| | | | - Avni Berisha
- Department of Chemistry, Faculty of Natural and Mathematics Science, University of Prishtina, Prishtina, 10000, Republic of Kosovo
- Materials Science-Nanochemistry Research Group, Nano Alb-Unit of Albanian Nanoscience and Nanotechnology, Tirana, 1000 Albania
| | - Waseem Mansour
- Chemistry Department, Faculty of Science, An-Najah National University, P.O. Box 7, Nablus, Palestine
| | - Saber Abu Jabal
- Chemistry Department, Faculty of Science, An-Najah National University, P.O. Box 7, Nablus, Palestine
| | - Oswa Fares
- Chemistry Department, Faculty of Science, An-Najah National University, P.O. Box 7, Nablus, Palestine
| | - Ataa Jaser
- Chemistry Department, Faculty of Science, An-Najah National University, P.O. Box 7, Nablus, Palestine
| | - Ameed Amireh
- Chemistry Department, Faculty of Science, An-Najah National University, P.O. Box 7, Nablus, Palestine
| | - Ghaleb Adwan
- Biology Department, Faculty of Sciences An-Najah National University, P.O. Box 7, Nablus, Palestine
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Jung HS, Park YJ, Gu BH, Han G, Ji W, Hwang SM, Kim M. Coumarin derivatives ameliorate the intestinal inflammation and pathogenic gut microbiome changes in the model of infectious colitis through antibacterial activity. Front Cell Infect Microbiol 2024; 14:1362773. [PMID: 39081865 PMCID: PMC11287663 DOI: 10.3389/fcimb.2024.1362773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 06/24/2024] [Indexed: 08/02/2024] Open
Abstract
Coumarin, a phenolic compound, is a secondary metabolite produced by plants such as Tanga and Lime. Coumarin derivatives were prepared via Pechmann condensation. In this study, we performed in vitro and in vivo experiments to determine the antimicrobial and gut immune-regulatory functions of coumarin derivatives. For the in vitro antimicrobial activity assay, coumarin derivatives C1 and C2 were selected based on their pathogen-killing activity against various pathogenic microbes. We further demonstrated that the selected coumarin derivatives disrupted bacterial cell membranes. Next, we examined the regulatory function of the coumarin derivatives in gut inflammation using an infectious colitis model. In an in vivo infectious colitis model, administration of selected C1 coumarin derivatives reduced pathogen loads, the number of inflammatory immune cells (Th1 cells and Th17 cells), and inflammatory cytokine levels (IL-6 and IL-1b) in the intestinal tissue after pathogen infection. In addition, we found that the administration of C1 coumarin derivatives minimized abnormal gut microbiome shift-driven pathogen infection. Potential pathogenic gut microbes, such as Enterobacteriaceae and Staphylococcaceae, were increased by pathogen infection. However, this pathogenic microbial expansion was minimized and beneficial bacteria, such as Ligilactobacillus and Limosilactobacillus, increased with C1 coumarin derivative treatment. Functional gene enrichment assessment revealed that the relative abundance of genes associated with lipid and nucleotide metabolism was reduced by pathogen infection; however, this phenomenon was not observed in C1 coumarin derivative-treated animals. Collectively, our data suggest that C1 coumarin derivative is effective antibacterial agents that minimize pathogen-induced gut inflammation and abnormal gut microbiome modulation through their antibacterial activity.
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Affiliation(s)
- Hui-su Jung
- Laboratory of Animal Immunology, Department of Animal Science, College of Natural Resource & Life Science, Pusan National University, Miryang, Republic of Korea
| | - Yei Ju Park
- R & D Center, EyeGene, Goyang, Republic of Korea
| | - Bon-Hee Gu
- Life and Industry Convergence Research Institute, Pusan National University, Miryang, Republic of Korea
| | - Goeun Han
- Laboratory of Animal Immunology, Department of Animal Science, College of Natural Resource & Life Science, Pusan National University, Miryang, Republic of Korea
- Future Earth Research Institute, PNU JYS Science Academy, Pusan National University, Busan, Republic of Korea
| | - Woonhak Ji
- Laboratory of Animal Immunology, Department of Animal Science, College of Natural Resource & Life Science, Pusan National University, Miryang, Republic of Korea
| | - Su mi Hwang
- Department of Biomedical Laboratory Science, College of Health and Medical Science, Sangji University, Wonju, Republic of Korea
| | - Myunghoo Kim
- Laboratory of Animal Immunology, Department of Animal Science, College of Natural Resource & Life Science, Pusan National University, Miryang, Republic of Korea
- Future Earth Research Institute, PNU JYS Science Academy, Pusan National University, Busan, Republic of Korea
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120
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Shirani H, Hashemianzadeh SM. Quantum-level machine learning calculations of Levodopa. Comput Biol Chem 2024; 112:108146. [PMID: 39067350 DOI: 10.1016/j.compbiolchem.2024.108146] [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: 02/14/2024] [Revised: 06/20/2024] [Accepted: 07/08/2024] [Indexed: 07/30/2024]
Abstract
Many drug molecules contain functional groups, resulting in a torsional barrier corresponding to rotation around the bond linking the fragments. In medicinal chemistry and pharmaceutical sciences, inclusive of drug design studies, the exact calculation of the potential energy surface (PES) of these molecular torsions is extremely important and precious. Machine learning (ML), including deep learning (DL), is currently one of the most rapidly evolving tools in computer-aided drug discovery and molecular simulations. In this work, we used ANI-1x neural network potential as a quantum-level ML to predict the PESs of the L-3,4-dihydroxyphenylalanine (Levodopa) antiparkinsonian drug molecule. The electronic energies and structural parameters calculated by density functional theory (DFT) using the wB97X method and all possible Pople's basis sets indicated the 6-31G(d) basis set, when used with the wB97X functional, exhibits behavior similar to that of the ANI-1x model. The vibrational frequencies investigation showed a linear correlation between DFT and ML data. All ANI-1x calculations were completed quickly in a very short computing time. From this perspective, we expect the ANI-1x dataset applied in this work to be appreciably efficient and effective in computational structure-based drug design studies.
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Affiliation(s)
- Hossein Shirani
- Molecular Simulation Research Laboratory, Department of Chemistry, Iran University of Science and Technology, P.O. Box 16846-13114, Tehran, Iran.
| | - Seyed Majid Hashemianzadeh
- Molecular Simulation Research Laboratory, Department of Chemistry, Iran University of Science and Technology, P.O. Box 16846-13114, Tehran, Iran.
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121
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Xiao C, Li Y, Liu Y, Dong R, He X, Lin Q, Zang X, Wang K, Xia Y, Kong L. Overcoming Cancer Persister Cells by Stabilizing the ATF4 Promoter G-quadruplex. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401748. [PMID: 38994891 DOI: 10.1002/advs.202401748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 06/23/2024] [Indexed: 07/13/2024]
Abstract
Persister cells (PS) selected for anticancer therapy have been recognized as a significant contributor to the development of treatment-resistant malignancies. It is found that imposing glutamine restriction induces the generation of PS, which paradoxically bestows heightened resistance to glutamine restriction treatment by activating the integrated stress response and initiating the general control nonderepressible 2-activating transcription factor 4-alanine, serine, cysteine-preferring transporter 2 (GCN2-ATF4-ASCT2) axis. Central to this phenomenon is the stress-induced ATF4 translational reprogramming. Unfortunately, directly targeting ATF4 protein has proven to be a formidable challenge because of its flat surface. Nonetheless, a G-quadruplex structure located within the promoter region of ATF4 (ATF4-G4) is uncovered and resolved, which functions as a transcriptional regulator and can be targeted by small molecules. The investigation identifies the natural compound coptisine (COP) as a potent binder that interacts with and stabilizes ATF4-G4. For the first time, the high-resolution structure of the COP-ATF4-G4 complex is determined. The formation of this stable complex disrupts the interaction between transcription factor AP-2 alpha (TFAP2A) and ATF4-G4, resulting in a substantial reduction in intracellular ATF4 levels and the eventual death of cancer cells. These seminal findings underscore the potential of targeting the ATF4-G4 structure to yield significant therapeutic advantages within the realm of persister cancer cells induced by glutamine-restricted therapy.
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Affiliation(s)
- Chengmei Xiao
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Yipu Li
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Yushuang Liu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Ruifang Dong
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Xiaoyu He
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qing Lin
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Xin Zang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Kaibo Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Yuanzheng Xia
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
- Shenzhen Research Institute of China Pharmaceutical University, Shenzhen, 518057, China
| | - Lingyi Kong
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
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122
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Ayaz H, Aşır F, Korak T. Skimmianine Showed Neuroprotection against Cerebral Ischemia/Reperfusion Injury. Curr Issues Mol Biol 2024; 46:7373-7385. [PMID: 39057078 PMCID: PMC11276333 DOI: 10.3390/cimb46070437] [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: 06/11/2024] [Revised: 07/03/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
The aim of this study was to investigate the antioxidant and anti-inflammatory effects of skimmianine on cerebral ischemia-reperfusion (IR) injury. Twenty-four female Wistar albino rats were randomly divided into three groups: Sham, Ischemia-Reperfusion (IR), and IR + Skimmianine (40 mg/kg Skimmianine). Cerebral ischemia was induced using a monofilament nylon suture to occlude the middle cerebral artery for 60 min. Following 23 h of reperfusion, the animals were sacrificed 14 days later. The effects of skimmianine on brain tissue post-IR injury were examined through biochemical and immunochemical analyses. In silico analysis using the Enrichr platform explored skimmianine's potential biological processes involving IBA-1, IL-6, and NF-κB proteins. In the IR group, MDA levels increased, while SOD and CAT antioxidant enzyme activities decreased. In the IR + Skimmianine group, skimmianine treatment resulted in decreased MDA levels and increased SOD and CAT activities. Significant increases in IBA-1 expression were observed in the IR group, which skimmianine treatment significantly reduced, modulating microglial activation. High levels of IL-6 expression were noted in pyramidal neurons, vascular structures, and neuroglial cells in the IR group; skimmianine treatment reduced IL-6 expression, demonstrating anti-inflammatory effects. Increased NF-κB expression was observed in neurons and blood vessels in the gray and white matter in the IR group; skimmianine treatment reduced NF-κB expression. Gene Ontology results suggest skimmianine impacts immune and inflammatory responses via IBA-1 and IL-6, with potential effects on estrogen mechanisms mediated by NF-κB. Skimmianine may be a potential therapeutic strategy due to its antioxidant and anti-inflammatory effects on cerebral IR injury.
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Affiliation(s)
- Hayat Ayaz
- Department of Histology and Embryology, Medical Faculty, Dicle University, 21280 Diyarbakır, Turkey
| | - Fırat Aşır
- Department of Histology and Embryology, Medical Faculty, Dicle University, 21280 Diyarbakır, Turkey
| | - Tuğcan Korak
- Department of Medical Biology, Medical Faculty, Kocaeli University, 41001 Kocaeli, Turkey;
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Heinzke AL, Pahl A, Zdrazil B, Leach AR, Waldmann H, Young RJ, Leeson PD. Occurrence of "Natural Selection" in Successful Small Molecule Drug Discovery. J Med Chem 2024; 67:11226-11241. [PMID: 38949112 PMCID: PMC11247505 DOI: 10.1021/acs.jmedchem.4c00811] [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: 04/05/2024] [Revised: 06/08/2024] [Accepted: 06/13/2024] [Indexed: 07/02/2024]
Abstract
Published compounds from ChEMBL version 32 are used to seek evidence for the occurrence of "natural selection" in drug discovery. Three measures of natural product (NP) character were applied, to compare time- and target-matched compounds reaching the clinic (clinical compounds in phase 1-3 development and approved drugs) with background compounds (reference compounds). Pseudo-NPs (PNPs), containing NP fragments combined in ways inaccessible by nature, are increasing over time, reaching 67% of clinical compounds first disclosed since 2010. PNPs are 54% more likely to be found in post-2008 clinical versus reference compounds. The majority of target classes show increased clinical compound NP character versus their reference compounds. Only 176 NP fragments appear in >1000 clinical compounds published since 2008, yet these make up on average 63% of the clinical compound's core scaffolds. There is untapped potential awaiting exploitation, by applying nature's building blocks─"natural intelligence"─to drug design.
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Affiliation(s)
- A. Lina Heinzke
- European
Molecular Biology Laboratory, European Bioinformatics
Institute, Wellcome Genome Campus, Hinxton CB10 1SD, Cambridgeshire, U.K.
| | - Axel Pahl
- Compound
Management and Screening Center, Max-Planck-Institute
of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Barbara Zdrazil
- European
Molecular Biology Laboratory, European Bioinformatics
Institute, Wellcome Genome Campus, Hinxton CB10 1SD, Cambridgeshire, U.K.
| | - Andrew R. Leach
- European
Molecular Biology Laboratory, European Bioinformatics
Institute, Wellcome Genome Campus, Hinxton CB10 1SD, Cambridgeshire, U.K.
| | - Herbert Waldmann
- Department
of Chemical Biology, Max-Planck-Institute
of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
- Faculty
of Chemistry and Chemical Biology, Technical
University Dortmund, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | | | - Paul D. Leeson
- Paul Leeson
Consulting Ltd., Nuneaton CV13 6LZ, Warwickshire, U.K.
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124
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Qi K, Li J, Hu Y, Qiao Y, Mu Y. Research progress in mechanism of anticancer action of shikonin targeting reactive oxygen species. Front Pharmacol 2024; 15:1416781. [PMID: 39076592 PMCID: PMC11284502 DOI: 10.3389/fphar.2024.1416781] [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: 04/13/2024] [Accepted: 06/13/2024] [Indexed: 07/31/2024] Open
Abstract
Excessive buildup of highly reactive molecules can occur due to the generation and dysregulation of reactive oxygen species (ROS) and their associated signaling pathways. ROS have a dual function in cancer development, either leading to DNA mutations that promote the growth and dissemination of cancer cells, or triggering the death of cancer cells. Cancer cells strategically balance their fate by modulating ROS levels, activating pro-cancer signaling pathways, and suppressing antioxidant defenses. Consequently, targeting ROS has emerged as a promising strategy in cancer therapy. Shikonin and its derivatives, along with related drug carriers, can impact several signaling pathways by targeting components involved with oxidative stress to induce processes such as apoptosis, necroptosis, cell cycle arrest, autophagy, as well as modulation of ferroptosis. Moreover, they can increase the responsiveness of drug-resistant cells to chemotherapy drugs, based on the specific characteristics of ROS, as well as the kind and stage of cancer. This research explores the pro-cancer and anti-cancer impacts of ROS, summarize the mechanisms and research achievements of shikonin-targeted ROS in anti-cancer effects and provide suggestions for designing further anti-tumor experiments and undertaking further experimental and practical research.
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Affiliation(s)
- Ke Qi
- Department of Diagnostic Clinical Laboratory Science, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Jiayi Li
- Department of Clinical Test Center, Medical Laboratory, Peking University Cancer Hospital (Inner Mongolia Campus), Affiliated Cancer Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Yang Hu
- Department of Diagnostic Clinical Laboratory Science, Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Yiyun Qiao
- Department of Clinical Test Center, Peking University Cancer Hospital (Inner Mongolia Campus), Affiliated Cancer Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Yongping Mu
- Department of Clinical Test Center, Peking University Cancer Hospital (Inner Mongolia Campus), Affiliated Cancer Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
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125
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Rivi V, Batabyal A, Lukowiak K. The multifaceted effects of flavonoids on neuroplasticity. Restor Neurol Neurosci 2024:RNN230150. [PMID: 38995810 DOI: 10.3233/rnn-230150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2024]
Abstract
There has been a significant increase in the incidence of multiple neurodegenerative and terminal diseases in the human population with life expectancy increasing in the current times. This highlights the urgent need for a more comprehensive understanding of how different aspects of lifestyle, in particular diet, may affect neural functioning and consequently cognitive performance as well as in enhancing overall health. Flavonoids, found in a variety of fruits, vegetables, and derived beverages, provide a new avenue of research that shows a promising influence on different aspects of brain function. However, despite the promising evidence, most bioactive compounds lack strong clinical research efficacy. In the current scoping review, we highlight the effects of Flavonoids on cognition and neural plasticity across vertebrates and invertebrates with special emphasis on the studies conducted in the pond snail, Lymnaea stagnalis, which has emerged to be a functionally dynamic model for studies on learning and memory. In conclusion, we suggest future research directions and discuss the social, cultural, and ethnic dependencies of bioactive compounds that influence how these compounds are used and accepted globally. Bridging the gap between preclinical and clinical studies about the effects of bioactive natural compounds on brain health will surely lead to lifestyle choices such as dietary Flavonoids being used complementarily rather than as replacements to classical drugs bringing about a healthier future.
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Affiliation(s)
- Veronica Rivi
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Anuradha Batabyal
- Department of Physical and Natural Sciences, FLAME University, India
- Department of Physiology and Pharmacology, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Ken Lukowiak
- Department of Physiology and Pharmacology, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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126
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Zheng D, Jin S, Liu PS, Ye J, Xie X. Targeting ferroptosis by natural products in pathophysiological conditions. Arch Toxicol 2024:10.1007/s00204-024-03812-4. [PMID: 38987487 DOI: 10.1007/s00204-024-03812-4] [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: 05/09/2024] [Accepted: 06/26/2024] [Indexed: 07/12/2024]
Abstract
Ferroptosis is a form of cell death that is induced by iron-mediated accumulation of lipid peroxidation. The involvement of ferroptosis in different pathophysiological conditions has offered new perspectives on potential therapeutic interventions. Natural products, which are widely recognized for their significance in drug discovery and repurposing, have shown great promise in regulating ferroptosis by targeting various ferroptosis players. In this review, we discuss the regulatory mechanisms of ferroptosis and its implications in different pathological conditions. We dissect the interactions between natural products and ferroptosis in cancer, ischemia/reperfusion, neurodegenerative diseases, acute kidney injury, liver injury, and cardiomyopathy, with an emphasis on the relevance of ferroptosis players to disease targetability.
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Affiliation(s)
- Daheng Zheng
- School of Life and Environmental Sciences, Shaoxing University, Shaoxing, Zhejiang, China
| | - Shikai Jin
- School of Life and Environmental Sciences, Shaoxing University, Shaoxing, Zhejiang, China
| | - Pu-Ste Liu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Jianping Ye
- School of Life and Environmental Sciences, Shaoxing University, Shaoxing, Zhejiang, China.
| | - Xin Xie
- School of Life and Environmental Sciences, Shaoxing University, Shaoxing, Zhejiang, China.
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127
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Li J, Lardon R, Mangelinckx S, Geelen D. A practical guide to the discovery of biomolecules with biostimulant activity. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:3797-3817. [PMID: 38630561 DOI: 10.1093/jxb/erae156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 04/16/2024] [Indexed: 04/19/2024]
Abstract
The growing demand for sustainable solutions in agriculture, which are critical for crop productivity and food quality in the face of climate change and the need to reduce agrochemical usage, has brought biostimulants into the spotlight as valuable tools for regenerative agriculture. With their diverse biological activities, biostimulants can contribute to crop growth, nutrient use efficiency, and abiotic stress resilience, as well as to the restoration of soil health. Biomolecules include humic substances, protein lysates, phenolics, and carbohydrates have undergone thorough investigation because of their demonstrated biostimulant activities. Here, we review the process of the discovery and development of extract-based biostimulants, and propose a practical step-by-step pipeline that starts with initial identification of biomolecules, followed by extraction and isolation, determination of bioactivity, identification of active compound(s), elucidation of mechanisms, formulation, and assessment of effectiveness. The different steps generate a roadmap that aims to expedite the transfer of interdisciplinary knowledge from laboratory-scale studies to pilot-scale production in practical scenarios that are aligned with the prevailing regulatory frameworks.
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Affiliation(s)
- Jing Li
- HortiCell, Department Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Robin Lardon
- HortiCell, Department Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Sven Mangelinckx
- SynBioC, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Danny Geelen
- HortiCell, Department Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
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Valenza C, Trapani D, Loibl S, Chia SKL, Burstein HJ, Curigliano G. Optimizing Postneoadjuvant Treatment in Patients With Early Breast Cancer Achieving Pathologic Complete Response. J Clin Oncol 2024; 42:2372-2376. [PMID: 38569132 DOI: 10.1200/jco.23.01935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/03/2023] [Accepted: 01/22/2024] [Indexed: 04/05/2024] Open
Abstract
pCR should be integrated with other prognostic factors to optimize postneoadjuvant treatments in BC.
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Affiliation(s)
- Carmine Valenza
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Dario Trapani
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Sibylle Loibl
- Center for Hematology and Oncology Bethanien, Frankfurt, Germany
| | | | - Harold J Burstein
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA
- Harvard Medical School, Boston, MA
| | - Giuseppe Curigliano
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
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129
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Alawfi MS, Alzahrani DA, Albokhari EJ. Complete plastome genomes of three medicinal heliotropiaceae species: comparative analyses and phylogenetic relationships. BMC PLANT BIOLOGY 2024; 24:654. [PMID: 38987665 PMCID: PMC11234707 DOI: 10.1186/s12870-024-05388-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 07/05/2024] [Indexed: 07/12/2024]
Abstract
BACKGROUND Heliotropiaceae is a family of the order Boraginales and has over 450 species. The members of the family Heliotropiaceae have been widely reported to be used in traditional medicine Over time, the classification of Heliotropiaceae has remained uncertain and has moved from family to subfamily, or conversely. RESULTS In the present study, we sequenced, analyzed, and compared the complete plastomes of Euploca strigosa, Heliotropium arbainense, and Heliotropium longiflorum with the genomes of related taxa. The lengths of the plastomes of E. strigosa, H. arbainense, and H. longiflorum were 155,174 bp, 154,709 bp, and 154,496 bp, respectively. Each plastome consisted of 114 genes: 80 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. The long repeats analysis indicated that reverse, palindromic, complement and forward repeats were all found in the three plastomes. The simple repeats analysis showed that the plastomes of E. strigosa, H. arbainense, and H. longiflorum contained 158, 165, and 151 microsatellites, respectively. The phylogenetic analysis confirmed two major clades in the Boraginales: clade I comprised Boraginaceae, while clade II included Heliotropiaceae, Ehretiaceae, Lennoaceae, and Cordiaceae. Inside the family Heliotropiaceae, E. strigosa is nested within the Heliotropium genus. CONCLUSIONS This study expands our knowledge of the evolutionary relationships within Heliotropiaceae and offers useful genetic resources.
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Affiliation(s)
- Mohammad S Alawfi
- Department of Biology, College of Sciences, King Khalid University, Abha, Saudi Arabia.
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Dhafer A Alzahrani
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Enas J Albokhari
- Department of Biological Sciences, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
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130
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Hassan SM, Farid A, Panda SS, Bekheit MS, Dinkins H, Fayad W, Girgis AS. Indole Compounds in Oncology: Therapeutic Potential and Mechanistic Insights. Pharmaceuticals (Basel) 2024; 17:922. [PMID: 39065774 PMCID: PMC11280311 DOI: 10.3390/ph17070922] [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: 06/18/2024] [Revised: 06/28/2024] [Accepted: 07/04/2024] [Indexed: 07/28/2024] Open
Abstract
Cancer remains a formidable global health challenge, with current treatment modalities such as chemotherapy, radiotherapy, surgery, and targeted therapy often hindered by low efficacy and adverse side effects. The indole scaffold, a prominent heterocyclic structure, has emerged as a promising candidate in the fight against cancer. This review consolidates recent advancements in developing natural and synthetic indolyl analogs, highlighting their antiproliferative activities against various cancer types over the past five years. These analogs are categorized based on their efficacy against common cancer types, supported by biochemical assays demonstrating their antiproliferative properties. In this review, emphasis is placed on elucidating the mechanisms of action of these compounds. Given the limitations of conventional cancer therapies, developing targeted therapeutics with enhanced selectivity and reduced side effects remains a critical focus in oncological research.
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Affiliation(s)
- Sara M. Hassan
- Biotechnology Department, Faculty of Science, Cairo University, Giza 12613, Egypt
| | - Alyaa Farid
- Biotechnology Department, Faculty of Science, Cairo University, Giza 12613, Egypt
| | - Siva S. Panda
- Department of Chemistry and Biochemistry, Augusta University, Augusta, GA 30912, USA
- Department of Biochemistry and Molecular Biology, Augusta University, Augusta, GA 30912, USA
| | - Mohamed S. Bekheit
- Department of Pesticide Chemistry, National Research Centre, Dokki, Giza 12622, Egypt;
| | - Holden Dinkins
- Department of Chemistry and Biochemistry, Augusta University, Augusta, GA 30912, USA
| | - Walid Fayad
- Drug Bioassay-Cell Culture Laboratory, Pharmacognosy Department, National Research Centre, Dokki, Giza 12622, Egypt
| | - Adel S. Girgis
- Department of Pesticide Chemistry, National Research Centre, Dokki, Giza 12622, Egypt;
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131
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Dvir K, Giordano S, Leone JP. Immunotherapy in Breast Cancer. Int J Mol Sci 2024; 25:7517. [PMID: 39062758 PMCID: PMC11276856 DOI: 10.3390/ijms25147517] [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: 06/12/2024] [Revised: 06/29/2024] [Accepted: 07/04/2024] [Indexed: 07/28/2024] Open
Abstract
Breast cancer is a disease encompassing a spectrum of molecular subtypes and clinical presentations, each with distinct prognostic implications and treatment responses. Breast cancer has traditionally been considered an immunologically "cold" tumor, unresponsive to immunotherapy. However, clinical trials in recent years have found immunotherapy to be an efficacious therapeutic option for select patients. Breast cancer is categorized into different subtypes ranging from the most common positive hormone receptor (HR+), human epidermal growth factor receptor 2 (HER2)-negative type, to less frequent HER2- positive breast cancer and triple-negative breast cancer (TNBC), highlighting the necessity for tailored treatment strategies aimed at maximizing patient outcomes. Despite notable progress in early detection and new therapeutic modalities, breast cancer remains the second leading cause of cancer death in the USA. Moreover, in recent decades, breast cancer incidence rates have been increasing, especially in women younger than the age of 50. This has prompted the exploration of new therapeutic approaches to address this trend, offering new therapeutic prospects for breast cancer patients. Immunotherapy is a class of therapeutic agents that has revolutionized the treatment landscape of many cancers, namely melanoma, lung cancer, and gastroesophageal cancers, amongst others. Though belatedly, immunotherapy has entered the treatment armamentarium of breast cancer, with the approval of pembrolizumab in combination with chemotherapy in triple-negative breast cancer (TNBC) in the neoadjuvant and advanced settings, thereby paving the path for further research and integration of immune checkpoint inhibitors in other subtypes of breast cancer. Trials exploring various combination therapies to harness the power of immunotherapy in symbiosis with various chemotherapeutic agents are ongoing in hopes of improving response rates and prolonging survival for breast cancer patients. Biomarkers and precise patient selection for the utilization of immunotherapy remain cardinal and are currently under investigation, with some biomarkers showing promise, such as Program Death Lignat-1 (PDL-1) Combined Positive Score, Tumor Mutation Burden (TMB), and Tumor Infiltrating Lymphocytes (TILs). This review will present the current landscape of immunotherapy, particularly checkpoint inhibitors, in different types of breast cancer.
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Affiliation(s)
- Kathrin Dvir
- Dana Farber Cancer Institute, Boston, MA 02215, USA; (K.D.)
- St. Elizabeth’s Medical Center, Boston, MA 02111, USA
| | - Sara Giordano
- Dana Farber Cancer Institute, Boston, MA 02215, USA; (K.D.)
- St. Elizabeth’s Medical Center, Boston, MA 02111, USA
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Moraru L, Mitranovici MI, Moraru R, Voidazan S, Munteanu M, Georgescu R, Costachescu D, Turdean SG. Combining Molecular and Traditional Prognostic Factors: A Holistic Approach to Breast Cancer Prognostication. Diagnostics (Basel) 2024; 14:1449. [PMID: 39001339 PMCID: PMC11241232 DOI: 10.3390/diagnostics14131449] [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: 05/21/2024] [Revised: 06/20/2024] [Accepted: 07/05/2024] [Indexed: 07/16/2024] Open
Abstract
Breast cancer is a heterogeneous disease with various morphologies and molecular features, and it is the second leading cause of cancer death in women in developed countries. According to the literature, we currently lack both prognostic biomarkers and therapeutic targets. The most important prognostic factors are disease stage and Nottingham grade. We conducted a retrospective analysis involving 273 patients with BC who underwent neoadjuvant therapy before proceeding to curative surgical treatment between 1 January 2014 and 31 December 2023. Pathological procedures were conducted at the Department of Pathology, Emergency County Hospital of Targu Mureș, Romania. A statistical analysis was performed. Regarding the relationship between Nottingham grade and Ki67, grade I was associated with a Ki67 of less than 14. The relationship between tumor grade and luminal was similar (p = 0.0001): Grade I was associated with luminal A. Regarding TNM stage, it was statistically significantly correlated with TILs (p = 0.01) and RCB (p = 0.0001). Stages III and IV were associated with a high RCB and poor prognosis. Regarding the prognostic value, Nottingham grade 3 and TNM stages III and IV were correlated with low overall survival and disease-free survival, with poor prognosis, and, among the molecular variables, RCB played the most important prognostic role.
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Affiliation(s)
- Liviu Moraru
- Department of Anatomy, "George Emil Palade" University of Medicine, Pharmacy, Sciences and Technology, 540142 Targu Mures, Romania
| | - Melinda Ildiko Mitranovici
- Department of Obstetrics and Gynecology, Emergency County Hospital Hunedoara, 14 Victoriei Street, 331057 Hunedoara, Romania
| | - Raluca Moraru
- Faculty of Medicine, "George Emil Palade" University of Medicine, Pharmacy, Sciences and Technology, 540142 Targu Mures, Romania
| | - Septimiu Voidazan
- Department of Epidemiology, "George Emil Palade" University of Medicine, Pharmacy, Sciences and Technology, 540142 Targu Mures, Romania
| | - Mihai Munteanu
- Faculty of Electrical Engineering, Technical University, George Baritiu Street, 400394 Cluj Napoca, Romania
| | - Rares Georgescu
- Department of Surgery, "George Emil Palade" University of Medicine, Pharmacy, Sciences and Technology, 540142 Targu Mures, Romania
| | - Dan Costachescu
- Department of Orthopedisc-Traumatology, Urology, Radiology and Medical Imaging, University of Medicine and Pharmacy Victor Babes, Square Eftimie Murgu, 300041 Timisoara, Romania
| | - Sabin Gligore Turdean
- Department of Pathology, County Clinical Hospital of Targu Mures, 540072 Targu Mures, Romania
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133
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Podlesainski D, Adeniyi ET, Gröner Y, Schulz F, Krisilia V, Rehberg N, Richter T, Sehr D, Xie H, Simons VE, Kiffe-Delf AL, Kaschani F, Ioerger TR, Kaiser M, Kalscheuer R. The anti-tubercular callyaerins target the Mycobacterium tuberculosis-specific non-essential membrane protein Rv2113. Cell Chem Biol 2024:S2451-9456(24)00221-6. [PMID: 38981479 DOI: 10.1016/j.chembiol.2024.06.002] [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: 09/01/2023] [Revised: 04/19/2024] [Accepted: 06/11/2024] [Indexed: 07/11/2024]
Abstract
Spread of antimicrobial resistances urges a need for new drugs against Mycobacterium tuberculosis (Mtb) with mechanisms differing from current antibiotics. Previously, callyaerins were identified as promising anti-tubercular agents, representing a class of hydrophobic cyclopeptides with an unusual (Z)-2,3-di-aminoacrylamide unit. Here, we investigated the molecular mechanisms underlying their antimycobacterial properties. Structure-activity relationship studies enabled the identification of structural determinants relevant for antibacterial activity. Callyaerins are bacteriostatics selectively active against Mtb, including extensively drug-resistant strains, with minimal cytotoxicity against human cells and promising intracellular activity. By combining mutant screens and various chemical proteomics approaches, we showed that callyaerins target the non-essential, Mtb-specific membrane protein Rv2113, triggering a complex dysregulation of the proteome, characterized by global downregulation of lipid biosynthesis, cell division, DNA repair, and replication. Our study thus identifies Rv2113 as a previously undescribed Mtb-specific drug target and demonstrates that also non-essential proteins may represent efficacious targets for antimycobacterial drugs.
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Affiliation(s)
- David Podlesainski
- Center of Medical Biotechnology (ZMB), Faculty of Biology, Chemical Biology, University of Duisburg-Essen, 45141 Essen, Germany
| | - Emmanuel T Adeniyi
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical Biology and Biotechnology, 40225 Düsseldorf, Germany
| | - Yvonne Gröner
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical Biology and Biotechnology, 40225 Düsseldorf, Germany
| | - Florian Schulz
- Center of Medical Biotechnology (ZMB), Faculty of Biology, Chemical Biology, University of Duisburg-Essen, 45141 Essen, Germany
| | - Violetta Krisilia
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical Biology and Biotechnology, 40225 Düsseldorf, Germany
| | - Nidja Rehberg
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical Biology and Biotechnology, 40225 Düsseldorf, Germany
| | - Tim Richter
- Center of Medical Biotechnology (ZMB), Faculty of Biology, Chemical Biology, University of Duisburg-Essen, 45141 Essen, Germany
| | - Daria Sehr
- Center of Medical Biotechnology (ZMB), Faculty of Biology, Chemical Biology, University of Duisburg-Essen, 45141 Essen, Germany
| | - Huzhuyue Xie
- Center of Medical Biotechnology (ZMB), Faculty of Biology, Chemical Biology, University of Duisburg-Essen, 45141 Essen, Germany
| | - Viktor E Simons
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical Biology and Biotechnology, 40225 Düsseldorf, Germany
| | - Anna-Lene Kiffe-Delf
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical Biology and Biotechnology, 40225 Düsseldorf, Germany
| | - Farnusch Kaschani
- Center of Medical Biotechnology (ZMB), Faculty of Biology, Chemical Biology, University of Duisburg-Essen, 45141 Essen, Germany
| | - Thomas R Ioerger
- Department of Computer Science, Texas A&M University, College Station, TX 77843, USA
| | - Markus Kaiser
- Center of Medical Biotechnology (ZMB), Faculty of Biology, Chemical Biology, University of Duisburg-Essen, 45141 Essen, Germany.
| | - Rainer Kalscheuer
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical Biology and Biotechnology, 40225 Düsseldorf, Germany.
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Chiodi D, Ishihara Y. The role of the methoxy group in approved drugs. Eur J Med Chem 2024; 273:116364. [PMID: 38781921 DOI: 10.1016/j.ejmech.2024.116364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/12/2024] [Accepted: 03/23/2024] [Indexed: 05/25/2024]
Abstract
The methoxy substituent is prevalent in natural products and, consequently, is present in many natural product-derived drugs. It has also been installed in modern drug molecules with no remnant of natural product features because medicinal chemists have been taking advantage of the benefits that this small functional group can bestow on ligand-target binding, physicochemical properties, and ADME parameters. Herein, over 230 methoxy-containing small-molecule drugs, as well as several fluoromethoxy-containing drugs, are presented from the vantage point of the methoxy group. Biochemical mechanisms of action, medicinal chemistry SAR studies, and numerous X-ray cocrystal structures are analyzed to identify the precise role of the methoxy group for many of the drugs and drug classes. Although the methoxy substituent can be considered as the hybridization of a hydroxy and a methyl group, the combination of these functionalities often results in unique effects that can amount to more than the sum of the individual parts.
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Affiliation(s)
- Debora Chiodi
- Department of Chemistry, Takeda Pharmaceuticals, 9625 Towne Centre Drive, San Diego, CA, 92121, USA
| | - Yoshihiro Ishihara
- Department of Chemistry, Vividion Therapeutics, 5820 Nancy Ridge Drive, San Diego, CA, 92121, USA.
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135
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Mikan CP, Watson JO, Walton R, Waddell PG, Knowles JP. Stereoselective Access to Diverse Alkaloid-Like Scaffolds via an Oxidation/Double-Mannich Reaction Sequence. Org Lett 2024; 26:5549-5553. [PMID: 38905202 PMCID: PMC11232018 DOI: 10.1021/acs.orglett.4c01924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2024]
Abstract
Sequential oxidative cleavage and double-Mannich reactions enable the stereoselective conversion of simple norbornenes into complex alkaloid-like structures. The products undergo a wide range of derivatization reactions, including regioselective enol triflate formation/cross-coupling sequences and highly efficient conversion to an unusual tricyclic 8,5,5-fused lactam. Overall, the process represents a formal one-atom aza-ring expansion with concomitant bridging annulation, making it of interest for the broader derivatization of alkene feedstocks.
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Affiliation(s)
- Charles P Mikan
- Department of Applied Sciences, Northumbria University, Ellison Place, Newcastle upon Tyne NE1 8ST, United Kingdom
| | - Joseph O Watson
- Department of Applied Sciences, Northumbria University, Ellison Place, Newcastle upon Tyne NE1 8ST, United Kingdom
| | - Ryan Walton
- Department of Applied Sciences, Northumbria University, Ellison Place, Newcastle upon Tyne NE1 8ST, United Kingdom
| | - Paul G Waddell
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Jonathan P Knowles
- Department of Applied Sciences, Northumbria University, Ellison Place, Newcastle upon Tyne NE1 8ST, United Kingdom
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Tsutsumi E, Macy AM, LoBello J, Hastings KT, Kim S. Tumor immune microenvironment permissive to metastatic progression of ING4-deficient breast cancer. PLoS One 2024; 19:e0304194. [PMID: 38968186 PMCID: PMC11226078 DOI: 10.1371/journal.pone.0304194] [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: 05/06/2024] [Accepted: 06/20/2024] [Indexed: 07/07/2024] Open
Abstract
Deficiencies in the ING4 tumor suppressor are associated with advanced stage tumors and poor patient survival in cancer. ING4 was shown to inhibit NF-kB in several cancers. As NF-kB is a key mediator of immune response, the ING4/NF-kB axis is likely to manifest in tumor-immune modulation but has not been investigated. To characterize the tumor immune microenvironment associated with ING4-deficient tumors, three approaches were employed in this study: First, tissue microarrays composed of 246 primary breast tumors including 97 ING4-deficient tumors were evaluated for the presence of selective immune markers, CD68, CD4, CD8, and PD-1, using immunohistochemical staining. Second, an immune-competent mouse model of ING4-deficient breast cancer was devised utilizing CRISPR-mediated deletion of Ing4 in a Tp53 deletion-derived mammary tumor cell line; mammary tumors were evaluated for immune markers using flow cytometry. Lastly, the METABRIC gene expression dataset was evaluated for patient survival related to the immune markers associated with Ing4-deleted tumors. The results showed that CD68, CD4, CD8, or PD-1, was not significantly associated with ING4-deficient breast tumors, indicating no enrichment of macrophages, T cells, or exhausted T cell types. In mice, Ing4-deleted mammary tumors had a growth rate comparable to Ing4-intact tumors but showed increased tumor penetrance and metastasis. Immune marker analyses of Ing4-deleted tumors revealed a significant increase in tumor-associated macrophages (Gr-1loCD11b+F4/80+) and a decrease in granzyme B-positive (GzmB+) CD4+ T cells, indicating a suppressive and/or less tumoricidal immune microenvironment. The METABRIC data analyses showed that low expression of GZMB was significantly associated with poor patient survival, as was ING4-low expression, in the basal subtype of breast cancer. Patients with GZMB-low/ING4-low tumors had the worst survival outcomes (HR = 2.80, 95% CI 1.36-5.75, p = 0.0004), supportive of the idea that the GZMB-low immune environment contributes to ING4-deficient tumor progression. Collectively, the study results demonstrate that ING4-deficient tumors harbor a microenvironment that contributes to immune evasion and metastasis.
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Affiliation(s)
- Emily Tsutsumi
- Department of Basic Medical Sciences, University of Arizona College of Medicine-Phoenix, Phoenix, Arizona, United States of America
- Cancer and Cell Biology Division, Translational Genomic Research Institute, Phoenix, Arizona, United States of America
| | - Anne M. Macy
- Department of Dermatology, University of Arizona College of Medicine-Phoenix, Phoenix, Arizona, United States of America
- Phoenix Veterans Affairs Health Care System, Phoenix, Arizona, United States of America
| | - Janine LoBello
- Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Karen T. Hastings
- Department of Dermatology, University of Arizona College of Medicine-Phoenix, Phoenix, Arizona, United States of America
- Phoenix Veterans Affairs Health Care System, Phoenix, Arizona, United States of America
| | - Suwon Kim
- Department of Basic Medical Sciences, University of Arizona College of Medicine-Phoenix, Phoenix, Arizona, United States of America
- Cancer and Cell Biology Division, Translational Genomic Research Institute, Phoenix, Arizona, United States of America
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137
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Dong H, Yao L, Fan J, Gao P, Yang X, Yuan Z, Zhang T, Lu M, Chen X, Suo C. Characteristics of auto-quantified tumor-infiltrating lymphocytes and the prognostic value in adenocarcinoma of the esophagogastric junction, gastric adenocarcinoma, and esophageal squamous cell carcinoma. Aging (Albany NY) 2024; 16:11027-11061. [PMID: 38975889 PMCID: PMC11272125 DOI: 10.18632/aging.205999] [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: 10/04/2023] [Accepted: 06/10/2024] [Indexed: 07/09/2024]
Abstract
BACKGROUND Adenocarcinoma of the esophagogastric junction (AEGJ) with a specific pathological profile and poor prognosis has limited therapeutic options. Previous studies have found that TILs exhibit distinct characteristics in different tumors and are correlated with tumor prognosis. We established cellular training sets to obtain auto-quantified TILs in pathological images. And we compared the characteristics of TILs in AEGJ with those in esophageal squamous cell carcinoma (ESCC) and gastric adenocarcinoma (GAC) to gain insight into the unique immune environments of these three tumors and investigate the prognostic value of TILs in these three tumors. METHODS Utilizing a case-control study design, we analyzed 214 AEGJ, 256 GAC, and 752 ESCC cases. The TCGA dataset was used to validate prognostic value of auto-quantified TILs. The specific cellular training sets were established by experienced pathologists to determine TILs counts. Kruskal-Wallis test and multi-variable linear regression were conducted to explore TILs characteristics. Survival analyses were performed with Kaplan-Meier method and Cox proportional hazards model. RESULTS The three cellular training sets of these cancers achieved a classification accuracy of 87.55 at least. The median auto-quantified TILs of AEGJ, GAC, and ESCC cases were 4.82%, 1.92%, and 0.12%, respectively. The TILs demonstrated varied characteristics under distinctive clinicopathological traits. The higher TILs proportion was associated with better prognosis in esophagogastric cancers (all P < 0.05) and was an independent prognostic biomarker on AEGJ in both datasets (Taixing: HR = 0.965, 95% CI = 0.938-0.994; TCGA: HR = 0.811, 95% CI = 0.712-0.925). CONCLUSIONS We found variations in TILs across ESCC, GAC, and AEGJ, as assessed by image processing algorithms. Additionally, TILs in these three cancers are an independent prognostic factor. This enhances our understanding of the unique immune characteristics of the three tumors, improving patient outcomes.
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Affiliation(s)
- Hao Dong
- Department of Epidemiology and Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China
| | - Longqing Yao
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, China
| | - Jiahui Fan
- Department of Clinical Laboratory, Shanghai Fourth People’s Hospital Affiliated to Tongji University School of Medicine, Shanghai, China
| | - Peipei Gao
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, China
- Fudan University Taizhou Institute of Health Sciences, Taizhou, China
| | - Xiaorong Yang
- Fudan University Taizhou Institute of Health Sciences, Taizhou, China
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, China
| | - Ziyu Yuan
- Fudan University Taizhou Institute of Health Sciences, Taizhou, China
| | - Tiejun Zhang
- Department of Epidemiology and Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China
- Fudan University Taizhou Institute of Health Sciences, Taizhou, China
| | - Ming Lu
- Fudan University Taizhou Institute of Health Sciences, Taizhou, China
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, China
| | - Xingdong Chen
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, China
- Fudan University Taizhou Institute of Health Sciences, Taizhou, China
- Yiwu Research Institute of Fudan University, Yiwu, Zhejiang, China
| | - Chen Suo
- Department of Epidemiology and Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China
- Fudan University Taizhou Institute of Health Sciences, Taizhou, China
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
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138
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Hanessian S. My 50-Plus Years of Academic Research Collaborations with Industry. A Retrospective. J Org Chem 2024; 89:9147-9186. [PMID: 38865159 DOI: 10.1021/acs.joc.4c00652] [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: 06/13/2024]
Abstract
A retrospective is presented highlighting the synthesis of selected "first-in-kind" natural products, their synthetic analogues, structure elucidations, and rationally designed bioactive synthetic compounds that were accomplished because of collaborations with past and present pharmaceutical and agrochemical companies. Medicinal chemistry projects involving structure-based design exploiting cocrystal structures of small molecules with biologically relevant enzymes, receptors, and bacterial ribosomes with synthetic small molecules leading to marketed products, clinical candidates, and novel drug prototypes were realized in collaboration. Personal reflections, historical insights, behind the scenes stories from various long-term projects are shared in this retrospective article.
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Affiliation(s)
- Stephen Hanessian
- Department of Chemistry, Université de Montréal, P.O. Box 6128, Succ. Centre-ville, Montréal, Québec, Canada H3C 3J7
- Department of Pharmaceutical Sciences, University of California, Irvine, California 91266, United States
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139
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Drif AI, Yücer R, Damiescu R, Ali NT, Abu Hagar TH, Avula B, Khan IA, Efferth T. Anti-Inflammatory and Cancer-Preventive Potential of Chamomile ( Matricaria chamomilla L.): A Comprehensive In Silico and In Vitro Study. Biomedicines 2024; 12:1484. [PMID: 39062057 PMCID: PMC11275008 DOI: 10.3390/biomedicines12071484] [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: 03/01/2024] [Revised: 06/14/2024] [Accepted: 06/26/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND AND AIM Chamomile tea, renowned for its exquisite taste, has been appreciated for centuries not only for its flavor but also for its myriad health benefits. In this study, we investigated the preventive potential of chamomile (Matricaria chamomilla L.) towards cancer by focusing on its anti-inflammatory activity. METHODS AND RESULTS A virtual drug screening of 212 phytochemicals from chamomile revealed β-amyrin, β-eudesmol, β-sitosterol, apigenin, daucosterol, and myricetin as potent NF-κB inhibitors. The in silico results were verified through microscale thermophoresis, reporter cell line experiments, and flow cytometric determination of reactive oxygen species and mitochondrial membrane potential. An oncobiogram generated through comparison of 91 anticancer agents with known modes of action using the NCI tumor cell line panel revealed significant relationships of cytotoxic chamomile compounds, lupeol, and quercetin to microtubule inhibitors. This hypothesis was verified by confocal microscopy using α-tubulin-GFP-transfected U2OS cells and molecular docking of lupeol and quercetin to tubulins. Both compounds induced G2/M cell cycle arrest and necrosis rather than apoptosis. Interestingly, lupeol and quercetin were not involved in major mechanisms of resistance to established anticancer drugs (ABC transporters, TP53, or EGFR). Performing hierarchical cluster analyses of proteomic expression data of the NCI cell line panel identified two sets of 40 proteins determining sensitivity and resistance to lupeol and quercetin, further pointing to the multi-specific nature of chamomile compounds. Furthermore, lupeol, quercetin, and β-amyrin inhibited the mRNA expression of the proinflammatory cytokines IL-1β and IL6 in NF-κB reporter cells (HEK-Blue Null1). Moreover, Kaplan-Meier-based survival analyses with NF-κB as the target protein of these compounds were performed by mining the TCGA-based KM-Plotter repository with 7489 cancer patients. Renal clear cell carcinomas (grade 3, low mutational rate, low neoantigen load) were significantly associated with shorter survival of patients, indicating that these subgroups of tumors might benefit from NF-κB inhibition by chamomile compounds. CONCLUSION This study revealed the potential of chamomile, positioning it as a promising preventive agent against inflammation and cancer. Further research and clinical studies are recommended.
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Affiliation(s)
- Assia I. Drif
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany; (A.I.D.); (R.Y.); (R.D.); (N.T.A.)
| | - Rümeysa Yücer
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany; (A.I.D.); (R.Y.); (R.D.); (N.T.A.)
| | - Roxana Damiescu
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany; (A.I.D.); (R.Y.); (R.D.); (N.T.A.)
| | - Nadeen T. Ali
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany; (A.I.D.); (R.Y.); (R.D.); (N.T.A.)
| | - Tobias H. Abu Hagar
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany; (A.I.D.); (R.Y.); (R.D.); (N.T.A.)
| | - Bharati Avula
- National Center for Natural Products Research (NCNPR), School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA; (B.A.); (I.A.K.)
| | - Ikhlas A. Khan
- National Center for Natural Products Research (NCNPR), School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA; (B.A.); (I.A.K.)
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany; (A.I.D.); (R.Y.); (R.D.); (N.T.A.)
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140
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Laddha AP, Oza MJ, Kulkarni YA. Editorial: Molecular aspects of natural products in diabetic complications. Front Endocrinol (Lausanne) 2024; 15:1431775. [PMID: 39027468 PMCID: PMC11254786 DOI: 10.3389/fendo.2024.1431775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Accepted: 06/03/2024] [Indexed: 07/20/2024] Open
Affiliation(s)
- Ankit P. Laddha
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, United States
| | - Manisha J. Oza
- Lemole Center for Integrated Lymphatics and Vascular Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Yogesh A. Kulkarni
- Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, SVKM‘s NMIMS, Mumbai, India
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141
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Afzal MZ, Vahdat LT. Evolving Management of Breast Cancer in the Era of Predictive Biomarkers and Precision Medicine. J Pers Med 2024; 14:719. [PMID: 39063972 PMCID: PMC11278458 DOI: 10.3390/jpm14070719] [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: 05/22/2024] [Revised: 06/17/2024] [Accepted: 06/30/2024] [Indexed: 07/28/2024] Open
Abstract
Breast cancer is the most common cancer among women in the world as well as in the United States. Molecular and histological differentiation have helped clinicians optimize treatments with various therapeutics, including hormonal therapy, chemotherapy, immunotherapy, and radiation therapy. Recently, immunotherapy has become the standard of care in locally advanced triple-negative breast cancer and an option across molecular subtypes for tumors with a high tumor mutation burden. Despite the advancements in personalized medicine directing the management of localized and advanced breast cancers, the emergence of resistance to these therapies is the leading cause of death among breast cancer patients. Therefore, there is a critical need to identify and validate predictive biomarkers to direct treatment selection, identify potential responders, and detect emerging resistance to standard therapies. Areas of active scientific and clinical research include novel personalized and predictive biomarkers incorporating tumor microenvironment, tumor immune profiling, molecular characterization, and histopathological differentiation to predict response and the potential emergence of resistance.
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Affiliation(s)
- Muhammad Zubair Afzal
- Medical Oncology, Comprehensive Breast Program, Dartmouth Cancer Center, Lebanon, NH 03755, USA
| | - Linda T. Vahdat
- Medical Oncology and Hematology (Interim), Dartmouth Cancer Center, Lebanon, NH 03755, USA;
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Zhang K, Liu J, Jiang Y, Sun S, Wang R, Sun J, Ma C, Chen Y, Wang W, Hou X, Zhu T, Zhang G, Che Q, Keyzers RA, Liu M, Li D. Sorbremnoids A and B: NLRP3 Inflammasome Inhibitors Discovered from Spatially Restricted Crosstalk of Biosynthetic Pathways. J Am Chem Soc 2024; 146:18172-18183. [PMID: 38888159 DOI: 10.1021/jacs.4c06538] [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: 06/20/2024]
Abstract
Crosstalk-oriented chemical evolution of natural products (NPs) is an efficacious strategy for generating novel skeletons through coupling reactions between NP fragments. In this study, two NOD-like receptor protein 3 (NLRP3) inflammasome inhibitors, sorbremnoids A and B (1 and 2), with unprecedented chemical architectures were identified from a fungus Penicillium citrinum. Compounds 1 and 2 exemplify rare instances of hybrid NPs formed via a major facilitator superfamily (MFS)-like enzyme by coupling reactive intermediates from two separate biosynthetic gene clusters (BGCs), pcisor and pci56. Both sorbremnoids A and B are NLRP3 inflammasome inhibitors. Sorbremnoid A demonstrated strong inhibition of IL-1β by directly binding to the NLRP3 protein, inhibiting the assembly and activation of the NLRP3 inflammasome in vitro, with potential application in diabetic refractory wound healing through the suppression of excessive inflammatory responses. This research will inspire the development of anti-NLRP3 inflammasome agents as lead treatments and enhance knowledge pertaining to NPs derived from biosynthetic crosstalk.
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Affiliation(s)
- Kaijin Zhang
- Key Laboratory of Marine Drugs, Ministry of Education, Sanya Oceanographic Institute, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Junyu Liu
- Key Laboratory of Marine Drugs, Ministry of Education, Sanya Oceanographic Institute, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Yuqi Jiang
- Key Laboratory of Marine Drugs, Ministry of Education, Sanya Oceanographic Institute, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Simin Sun
- Key Laboratory of Marine Drugs, Ministry of Education, Sanya Oceanographic Institute, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Rongrong Wang
- Key Laboratory of Marine Drugs, Ministry of Education, Sanya Oceanographic Institute, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Jingxian Sun
- Key Laboratory of Marine Drugs, Ministry of Education, Sanya Oceanographic Institute, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Chuanteng Ma
- Key Laboratory of Marine Drugs, Ministry of Education, Sanya Oceanographic Institute, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Yinghan Chen
- Key Laboratory of Marine Drugs, Ministry of Education, Sanya Oceanographic Institute, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Wenxue Wang
- Key Laboratory of Marine Drugs, Ministry of Education, Sanya Oceanographic Institute, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Xuewen Hou
- Key Laboratory of Marine Drugs, Ministry of Education, Sanya Oceanographic Institute, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Tianjiao Zhu
- Key Laboratory of Marine Drugs, Ministry of Education, Sanya Oceanographic Institute, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Guojian Zhang
- Key Laboratory of Marine Drugs, Ministry of Education, Sanya Oceanographic Institute, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Qian Che
- Key Laboratory of Marine Drugs, Ministry of Education, Sanya Oceanographic Institute, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Robert A Keyzers
- School of Chemical and Physical Sciences and Centre for Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Ming Liu
- Key Laboratory of Marine Drugs, Ministry of Education, Sanya Oceanographic Institute, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Dehai Li
- Key Laboratory of Marine Drugs, Ministry of Education, Sanya Oceanographic Institute, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, Qingdao 266237, China
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143
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Shaikh S, Lee EJ, Ahmad K, Choi I. Therapeutic potential and action mechanisms of licochalcone B: a mini review. Front Mol Biosci 2024; 11:1440132. [PMID: 39021879 PMCID: PMC11251949 DOI: 10.3389/fmolb.2024.1440132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 06/19/2024] [Indexed: 07/20/2024] Open
Abstract
Licochalcone B (LicB), a chalcone derived from Glycyrrhiza uralensis and Glycyrrhiza glabra, has received considerable attention due to its diverse pharmacological properties. Accumulated data indicates that LicB has pharmacological effects that include anti-cancer, hepatoprotective, anti-inflammatory, and neuroprotective properties. The action mechanism of LicB has been linked to several molecular targets, such as phosphoinositide 3-kinase/Akt/mammalian target of rapamycin, p53, nuclear factor-κB, and p38, and the involvements of caspases, apoptosis, mitogen-activated protein kinase-associated inflammatory pathways, and anti-inflammatory nuclear factor erythroid 2-related factor 2 signaling pathways highlight the multifaceted therapeutic potential of LicB. This review systematically updates recent findings regarding the pharmacological effects of LicB, and the mechanistic pathways involved, and highlights the potential use of LicB as a promising lead compound for drug discovery.
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Affiliation(s)
- Sibhghatulla Shaikh
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, Republic of Korea
| | - Eun Ju Lee
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, Republic of Korea
| | - Khurshid Ahmad
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, Republic of Korea
| | - Inho Choi
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, Republic of Korea
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144
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Ma R, Feng XY, Tang JJ, Ha W, Shi YP. 5α-Epoxyalantolactone from Inula macrophylla attenuates cognitive deficits in scopolamine-induced Alzheimer's disease mice model. NATURAL PRODUCTS AND BIOPROSPECTING 2024; 14:39. [PMID: 38954263 PMCID: PMC11219692 DOI: 10.1007/s13659-024-00462-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 06/26/2024] [Indexed: 07/04/2024]
Abstract
Alzheimer's disease (AD) is a complex neurodegenerative condition. 5α-epoxyalantolactone (5α-EAL), a eudesmane-type sesquiterpene isolated from the herb of Inula macrophylla, has various pharmacological effects. This work supposed to investigate the improved impact of 5α-EAL on cognitive impairment. 5α-EAL inhibited the generation of nitric oxide (NO) in BV-2 cells stimulated with lipopolysaccharide (LPS) with an EC50 of 6.2 μM. 5α-EAL significantly reduced the production of prostaglandin E2 (PGE2) and tumor necrosis factor-α (TNF-α), while also inhibiting the production of cyclooxygenase-2 (COX-2) and inducible nitric oxide synthase (iNOS) proteins. The ability of 5α-EAL to penetrate the blood-brain barrier (BBB) was confirmed via a parallel artificial membrane permeation assay. Scopolamine (SCOP)-induced AD mice model was employed to assess the improved impacts of 5α-EAL on cognitive impairment in vivo. After the mice were pretreated with 5α-EAL (10 and 30 mg/kg per day, i.p.) for 21 days, the behavioral experiments indicated that the administration of the 5α-EAL could alleviate the cognitive and memory impairments. 5α-EAL significantly reduced the AChE activity in the brain of SCOP-induced AD mice. In summary, these findings highlight the beneficial effects of the natural product 5α-EAL as a potential bioactive compound for attenuating cognitive deficits in AD due to its pharmacological profile.
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Affiliation(s)
- Rui Ma
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources, Key Laboratory for Natural Medicines of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Lanzhou, 730000, People's Republic of China
| | - Xu-Yao Feng
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, No. 3 Taicheng Road, Yangling, 712100, Shaanxi, China
| | - Jiang-Jiang Tang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, No. 3 Taicheng Road, Yangling, 712100, Shaanxi, China
| | - Wei Ha
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources, Key Laboratory for Natural Medicines of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Lanzhou, 730000, People's Republic of China.
| | - Yan-Ping Shi
- CAS Key Laboratory of Chemistry of Northwestern Plant Resources, Key Laboratory for Natural Medicines of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Lanzhou, 730000, People's Republic of China.
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145
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Yi Y, Liang L, de Jong A, Kuipers OP. A systematic comparison of natural product potential, with an emphasis on RiPPs, by mining of bacteria of three large ecosystems. Genomics 2024; 116:110880. [PMID: 38857812 DOI: 10.1016/j.ygeno.2024.110880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/22/2024] [Accepted: 06/05/2024] [Indexed: 06/12/2024]
Abstract
The implementation of several global microbiome studies has yielded extensive insights into the biosynthetic potential of natural microbial communities. However, studies on the distribution of several classes of ribosomally synthesized and post-translationally modified peptides (RiPPs), non-ribosomal peptides (NRPs) and polyketides (PKs) in different large microbial ecosystems have been very limited. Here, we collected a large set of metagenome-assembled bacterial genomes from marine, freshwater and terrestrial ecosystems to investigate the biosynthetic potential of these bacteria. We demonstrate the utility of public dataset collections for revealing the different secondary metabolite biosynthetic potentials among these different living environments. We show that there is a higher occurrence of RiPPs in terrestrial systems, while in marine systems, we found relatively more terpene-, NRP-, and PK encoding gene clusters. Among the many new biosynthetic gene clusters (BGCs) identified, we analyzed various Nif-11-like and nitrile hydratase leader peptide (NHLP) containing gene clusters that would merit further study, including promising products, such as mersacidin-, LAP- and proteusin analogs. This research highlights the significance of public datasets in elucidating the biosynthetic potential of microbes in different living environments and underscores the wide bioengineering opportunities within the RiPP family.
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Affiliation(s)
- Yunhai Yi
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, the Netherlands
| | | | - Anne de Jong
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, the Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, the Netherlands.
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146
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Kissman EN, Sosa MB, Millar DC, Koleski EJ, Thevasundaram K, Chang MCY. Expanding chemistry through in vitro and in vivo biocatalysis. Nature 2024; 631:37-48. [PMID: 38961155 DOI: 10.1038/s41586-024-07506-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 05/01/2024] [Indexed: 07/05/2024]
Abstract
Living systems contain a vast network of metabolic reactions, providing a wealth of enzymes and cells as potential biocatalysts for chemical processes. The properties of protein and cell biocatalysts-high selectivity, the ability to control reaction sequence and operation in environmentally benign conditions-offer approaches to produce molecules at high efficiency while lowering the cost and environmental impact of industrial chemistry. Furthermore, biocatalysis offers the opportunity to generate chemical structures and functions that may be inaccessible to chemical synthesis. Here we consider developments in enzymes, biosynthetic pathways and cellular engineering that enable their use in catalysis for new chemistry and beyond.
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Affiliation(s)
- Elijah N Kissman
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Max B Sosa
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Douglas C Millar
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Edward J Koleski
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | | | - Michelle C Y Chang
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA.
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA.
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
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147
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Sánchez-Suárez J, Villamil L, Coy-Barrera E, Díaz L. Photoprotection-related properties of a raw extract from Gordonia hongkongensis EUFUS-Z928: A culturable rare actinomycete associated with the Caribbean octocoral Eunicea fusca. Sci Prog 2024; 107:368504241272454. [PMID: 39119690 PMCID: PMC11311175 DOI: 10.1177/00368504241272454] [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] [Indexed: 08/10/2024]
Abstract
UV filters in current sunscreen formulations can have negative effects on human health, such as endocrine disruption and allergic reactions, as well as on the environment, including bioaccumulation and coral health toxicity. As a result, there is a need to find alternative compounds that serve as safer and more ecofriendly active ingredients. This study successfully isolated actinomycetes from the octocoral Eunicea fusca and assessed their potential as producers of photoprotective compounds. The use of bio-based chemical agents, particularly natural products, has been a highly effective strategy for discovering bioactive compounds, especially in marine invertebrates and their associated microbiota. Eighteen bacterial isolates were obtained and subsequently employed to prepare raw methanolic extracts from seven-day submerged cultures in Zobell marine broth. The resulting extracts were screened for 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) radical scavenging capacity and characterized by total phenolic and flavonoid content measurements. After screening, the Gordonia hongkongensis EUFUS-Z928-derived raw extract exhibited the best antioxidant profile, i.e. DPPH and ABTS radical scavenging of 4.93 and 6.00 µmol Trolox per gram of extract, respectively, and selected for further photoprotection-related analysis. Thus, this extract demonstrated a UV-absorbing capacity of 46.33% of the in vitro sun protection factor calculated for 30 µg/mL oxybenzone but did not exhibit any cytotoxicity on human dermal fibroblasts (HDFa cell line) at concentrations up to 500 µg/mL. The liquid chromatography-mass spectrometry chemical characterization of this extract showed compounds with structural features associated with free radical scavenging and UV absorption (i.e. photoprotection-related activities). These findings highlighted the potential of the microbiota associated with E. fusca and confirmed the feasibility of exploiting its metabolites for photoprotection-related purposes.
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Affiliation(s)
- Jeysson Sánchez-Suárez
- Doctoral Program in Biosciences, School of Engineering, Universidad de La Sabana, Chía, Colombia
- Bioprospecting Research Group, School of Engineering, Universidad de La Sabana, Chía, Colombia
- Ecology and Biogeography Research Group, Department of Biology, School of Basic Sciences, Universidad de Pamplona, Pamplona, Colombia
| | - Luisa Villamil
- Doctoral Program in Biosciences, School of Engineering, Universidad de La Sabana, Chía, Colombia
| | - Ericsson Coy-Barrera
- Bioorganic Chemistry Laboratory, Universidad Militar Nueva Granada, Cajicá, Colombia
| | - Luis Díaz
- Doctoral Program in Biosciences, School of Engineering, Universidad de La Sabana, Chía, Colombia
- Bioprospecting Research Group, School of Engineering, Universidad de La Sabana, Chía, Colombia
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148
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Mohammed O, Gizaw ST, Degef M. Potential diagnostic, prognostic, and predictive biomarkers of gastric cancer. Health Sci Rep 2024; 7:e2261. [PMID: 39040881 PMCID: PMC11260885 DOI: 10.1002/hsr2.2261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 06/29/2024] [Accepted: 07/04/2024] [Indexed: 07/24/2024] Open
Abstract
Background Gastric cancer (GC), a malignant epithelial tumor, is the fourth leading cause of cancer-related death worldwide. Therapeutic strategies for GC, despite the biggest challenges, can significantly improve survival rates through early detection and effective screening methods. Aim To provide brief information on the necessity of multiple specific diagnostic, prognostic, and predictive markers for GC. Methods This review was conducted using a variety of search engines, including PubMed Central, Scopus, Web of Science, Google Scholar, and others. Results Some potential biomarkers that provide essential information include circulating tumor cells (CTCs), DNA methylation, claudin 18.2, fibroblast growth factor receptor 2 (FGFR2), long noncoding RNAs (lncRNAs), cell-free DNA (cfDNA), microRNAs, and serum pepsinogens. Conclusion Multiple tumor markers are essential for screening, tumor identification, staging, prognostic assessment, and monitoring recurrence after therapy due to the absence of a single tumor indicator for diagnosing, prognosticating, and predicting GC.
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Affiliation(s)
- Ousman Mohammed
- Department of Medical Laboratory SciencesCollege of Medicine and Health Sciences, Wollo UniversityDessieEthiopia
| | - Solomon Tebeje Gizaw
- Department of Medical BiochemistrySchool of Medicine, College of Health Sciences, AAUAddis AbabaEthiopia
| | - Maria Degef
- Department of Medical BiochemistrySchool of Medicine, College of Health Sciences, AAUAddis AbabaEthiopia
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Calado CRC. Bridging the gap between target-based and phenotypic-based drug discovery. Expert Opin Drug Discov 2024; 19:789-798. [PMID: 38747562 DOI: 10.1080/17460441.2024.2355330] [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: 09/05/2023] [Accepted: 05/10/2024] [Indexed: 06/26/2024]
Abstract
INTRODUCTION The unparalleled progress in science of the last decades has brought a better understanding of the molecular mechanisms of diseases. This promoted drug discovery processes based on a target approach. However, despite the high promises associated, a critical decrease in the number of first-in-class drugs has been observed. AREAS COVERED This review analyses the challenges, advances, and opportunities associated with the main strategies of the drug discovery process, i.e. based on a rational target approach and on an empirical phenotypic approach. This review also evaluates how the gap between these two crossroads can be bridged toward a more efficient drug discovery process. EXPERT OPINION The critical lack of knowledge of the complex biological networks is leading to targets not relevant for the clinical context or to drugs that present undesired adverse effects. The phenotypic systems designed by considering available molecular mechanisms can mitigate these knowledge gaps. Associated with the expansion of the chemical space and other technologies, these designs can lead to more efficient drug discoveries. Technological and scientific knowledge should also be applied to identify, as early as possible, both drug targets and mechanisms of action, leading to a more efficient drug discovery pipeline.
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Affiliation(s)
- Cecília R C Calado
- ISEL-Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, Lisboa, Portugal
- iBB - Institute for Bioengineering and Biosciences, i4HB - The Associate Laboratory Institute for Health and Bioeconomy, IST - Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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150
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Dong CH, Wang H, Ma YJ, Zhang Y, Si C, Zhao Y. Alkylide derivatives of diphyllin: synthesis and preliminary anticancer evaluation. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2024; 26:833-842. [PMID: 38584456 DOI: 10.1080/10286020.2024.2338265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 03/29/2024] [Indexed: 04/09/2024]
Abstract
Fourteen diphyllin 4-C-substituted alkylide derivatives were designed and synthesized using a Heck coupling and subsequent hydrogenation reaction. Olefins 3g and 3i exhibited the highest cytotoxicity on breast cancer cell lines MCF-7 with IC50 values of 0.08 and 0.07 µM, and they showed weaker V-ATPase inhibitory potency compared to diphyllin.
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Affiliation(s)
- Chen-Hu Dong
- School of Pharmacy, Nantong University, Nantong 226001, China
| | - Hui Wang
- R&D Department, Shanghai Rulink Biopharmaceutical Corporation, Shanghai 201203, China
| | - Yu-Jie Ma
- School of Pharmacy, Nantong University, Nantong 226001, China
| | - Ying Zhang
- School of Pharmacy, Nantong University, Nantong 226001, China
| | - Chao Si
- Pharmacy Department, Shandong Healthcare Group Xinwen Central Hospital, Xintai 271200, China
| | - Yu Zhao
- School of Pharmacy, Nantong University, Nantong 226001, China
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