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Varghese S, Jisha MS, Rajeshkumar KC, Gajbhiye V, Haldar N, Shaikh A. Molecular authentication, metabolite profiling and in silico-in vitro cytotoxicity screening of endophytic Penicillium ramusculum from Withania somnifera for breast cancer therapeutics. 3 Biotech 2024; 14:64. [PMID: 38344285 PMCID: PMC10858009 DOI: 10.1007/s13205-023-03906-3] [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: 05/02/2023] [Accepted: 12/14/2023] [Indexed: 03/10/2024] Open
Abstract
In the present study, we isolated a potent endophytic fungus from the roots of Withania somnifera. The endophytic fungal strain was authenticated as Penicillium ramusculum SVWS3 based on morphological and molecular sequencing using four gene data and phylogenetic analyses. In vitro cytotoxicity studies unveiled the remarkable cytotoxic potential of the crude extract derived from P. ramusculum, exhibiting dose-dependent effects on MDA-MB-468 and MCF-7 cells. At a concentration of 100 µg/mL, the crude extract resulted in cell viability of 29.78% for MDA-MB-468 cells and 14.61% for MCF-7 cells. The IC50 values were calculated as 62.83 ± 0.93 µg/mL and 17.23 ± 1.43 µg/mL, respectively for MDA-MB-468 and MCF-7 cells. Caspase activation assay established the underlying mechanism of the crude extract depicting the activation of caspases 3 and 7, indicating the induction of apoptosis in MCF-7 cells. Chemotaxonomic profiling elucidated the ability of P. ramusculum to synthesize a diverse array of bioactive compounds, including Fasoracetam, Tryprostatin B, Odorinol, Thyronine, Brevianamide F, Proglumide, Perlolyrine, Tyrphostin B48, Baptifoline, etc. Molecular docking studies inferred that Baptifoline, Brevianamide F, Odorinol, Perlolyrine, Thyronine, Tryphostin B48, and Tryprostatin B were the lead compounds that could effectively interact with the five selected target receptors of breast cancer, further surpassing the positive controls analyzed. Pharmacokinetic profiling revealed that Baptifoline, Odorinol, and Thyronine depicted an excellent therapeutic profile of druggability. These findings collectively substantiate the anticancer activity of bioactive metabolites synthesized by P. ramusculum SVWS3. Hence, the endophytic P. ramusculum SVWS3 can be an authentic source for developing novel chemotherapeutic drug formulations. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03906-3.
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Affiliation(s)
- Sherin Varghese
- School of Biosciences, Mahatma Gandhi University, Kottayam, Kerala 686560 India
| | - M. S. Jisha
- School of Biosciences, Mahatma Gandhi University, Kottayam, Kerala 686560 India
- National Institute of Plant Science Technology (NIPST), Mahatma Gandhi University, Kottayam, Kerala 686560 India
- School of Food Science and Technology, Mahatma Gandhi University, Kottayam, Kerala 686560 India
| | - K. C. Rajeshkumar
- National Fungal Culture Collection of India (NFCCI), Biodiversity and Palaeobiology (Fungi) Gr., Agharkar Research Institute, G.G. Agharkar Road, Pune, 411 004 Maharashtra India
| | - Virendra Gajbhiye
- Nanobioscience Group, Agharkar Research Institute, G.G. Agharkar Road, Pune, Maharashtra 411004 India
| | - Niladri Haldar
- Nanobioscience Group, Agharkar Research Institute, G.G. Agharkar Road, Pune, Maharashtra 411004 India
| | - Aazam Shaikh
- Nanobioscience Group, Agharkar Research Institute, G.G. Agharkar Road, Pune, Maharashtra 411004 India
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Miller ET, Tsodikov OV, Garneau-Tsodikova S. Structural insights into the diverse prenylating capabilities of DMATS prenyltransferases. Nat Prod Rep 2024; 41:113-147. [PMID: 37929638 DOI: 10.1039/d3np00036b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Covering: 2009 up to August 2023Prenyltransferases (PTs) are involved in the primary and the secondary metabolism of plants, bacteria, and fungi, and they are key enzymes in the biosynthesis of many clinically relevant natural products (NPs). The continued biochemical and structural characterization of the soluble dimethylallyl tryptophan synthase (DMATS) PTs over the past two decades have revealed the significant promise that these enzymes hold as biocatalysts for the chemoenzymatic synthesis of novel drug leads. This is a comprehensive review of DMATSs describing the structure-function relationships that have shaped the mechanistic underpinnings of these enzymes, as well as the application of this knowledge to the engineering of DMATSs. We summarize the key findings and lessons learned from these studies over the past 14 years (2009-2023). In addition, we identify current gaps in our understanding of these fascinating enzymes.
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Affiliation(s)
- Evan T Miller
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA.
| | - Oleg V Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA.
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA.
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Gardner ED, Johnson BP, Dimas DA, McClurg HE, Severance ZC, Burgett AW, Singh S. Unlocking New Prenylation Modes: Azaindoles as a New Substrate Class for Indole Prenyltransferases. ChemCatChem 2023; 15:e202300650. [PMID: 37954549 PMCID: PMC10634513 DOI: 10.1002/cctc.202300650] [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: 05/16/2023] [Indexed: 11/14/2023]
Abstract
Aza-substitution, the replacement of aromatic CH groups with nitrogen atoms, is an established medicinal chemistry strategy for increasing solubility, but current methods of accessing functionalized azaindoles are limited. In this work, indole-alkylating aromatic prenyltransferases (PTs) were explored as a strategy to directly functionalize azaindole-substituted analogs of natural products. For this, a series of aza-l-tryptophans (Aza-Trp) featuring N-substitution of every aromatic CH position of the indole ring and their corresponding cyclic Aza-l-Trp-l-proline dipeptides (Aza-CyWP), were synthesized as substrate mimetics for the indole-alkylating PTs FgaPT2, CdpNPT, and FtmPT1. We then demonstrated most of these substrate analogs were accepted by a PT, and the regioselectivity of each prenylation was heavily influenced by the position of the N-substitution. Remarkably, FgaPT2 was found to produce cationic N-prenylpyridinium products, representing not only a new substrate class for indole PTs but also a previously unobserved prenylation mode. The discovery that nitrogenous indole bioisosteres can be accepted by PTs thus provides access to previously unavailable chemical space in the search for bioactive indolediketopiperazine analogs.
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Affiliation(s)
- Eric D. Gardner
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Bryce P. Johnson
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Dustin A. Dimas
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Heather E. McClurg
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Zachary C. Severance
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73117, United States
| | - Anthony W. Burgett
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73117, United States
| | - Shanteri Singh
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
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Alexander AK, Elshahawi SI. Promiscuous Enzymes for Residue-Specific Peptide and Protein Late-Stage Functionalization. Chembiochem 2023; 24:e202300372. [PMID: 37338668 PMCID: PMC10496146 DOI: 10.1002/cbic.202300372] [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: 05/18/2023] [Revised: 06/20/2023] [Accepted: 06/20/2023] [Indexed: 06/21/2023]
Abstract
The late-stage functionalization of peptides and proteins holds significant promise for drug discovery and facilitates bioorthogonal chemistry. This selective functionalization leads to innovative advances in in vitro and in vivo biological research. However, it is a challenging endeavor to selectively target a certain amino acid or position in the presence of other residues containing reactive groups. Biocatalysis has emerged as a powerful tool for selective, efficient, and economical modifications of molecules. Enzymes that have the ability to modify multiple complex substrates or selectively install nonnative handles have wide applications. Herein, we highlight enzymes with broad substrate tolerance that have been demonstrated to modify a specific amino acid residue in simple or complex peptides and/or proteins at late-stage. The different substrates accepted by these enzymes are mentioned together with the reported downstream bioorthogonal reactions that have benefited from the enzymatic selective modifications.
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Affiliation(s)
- Ashley K Alexander
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Rinker Health Science Campus, Irvine, CA 92618, USA
| | - Sherif I Elshahawi
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Rinker Health Science Campus, Irvine, CA 92618, USA
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Colombano A, Dalponte L, Dall'Angelo S, Clemente C, Idress M, Ghazal A, Houssen WE. Chemoenzymatic Late-Stage Modifications Enable Downstream Click-Mediated Fluorescent Tagging of Peptides. Angew Chem Int Ed Engl 2023; 62:e202215979. [PMID: 36815722 PMCID: PMC10946513 DOI: 10.1002/anie.202215979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 02/17/2023] [Accepted: 02/22/2023] [Indexed: 02/24/2023]
Abstract
Aromatic prenyltransferases from cyanobactin biosynthetic pathways catalyse the chemoselective and regioselective intramolecular transfer of prenyl/geranyl groups from isoprene donors to an electron-rich position in these macrocyclic and linear peptides. These enzymes often demonstrate relaxed substrate specificity and are considered useful biocatalysts for structural diversification of peptides. Herein, we assess the isoprene donor specificity of the N1-tryptophan prenyltransferase AcyF from the anacyclamide A8P pathway using a library of 22 synthetic alkyl pyrophosphate analogues, of which many display reactive groups that are amenable to additional functionalization. We further used AcyF to introduce a reactive moiety into a tryptophan-containing cyclic peptide and subsequently used click chemistry to fluorescently label the enzymatically modified peptide. This chemoenzymatic strategy allows late-stage modification of peptides and is useful for many applications.
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Affiliation(s)
- Alessandro Colombano
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
| | - Luca Dalponte
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
- Department of ChemistryUniversity of AberdeenAberdeenAB24 3UEUK
| | - Sergio Dall'Angelo
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
| | - Claudia Clemente
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
| | - Mohannad Idress
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
- Department of ChemistryUniversity of AberdeenAberdeenAB24 3UEUK
- Abzena, Babraham Research CampusCambridgeUK
| | - Ahmad Ghazal
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
- Department of ChemistryUniversity of AberdeenAberdeenAB24 3UEUK
| | - Wael E. Houssen
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
- Department of ChemistryUniversity of AberdeenAberdeenAB24 3UEUK
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Hamdy SA, Kodama T, Nakashima Y, Han X, Morita H. Catalytic potential of a fungal indole prenyltransferase toward β-carbolines, harmine and harman, and their prenylation effects on antibacterial activity. J Biosci Bioeng 2022; 134:311-317. [PMID: 35931602 DOI: 10.1016/j.jbiosc.2022.07.004] [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: 06/20/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 10/16/2022]
Abstract
The prenylation of compounds has attracted much attention, since it often adds bioactivity to non-prenylated compounds. We employed an enzyme assay with CdpNPT, an indole prenyltransferase from Aspergillus fumigatus with two naturally occurring β-carbolines, harmine (3) and harman (4) as prenyl acceptors, in the presence of dimethylallyl diphosphate (DMAPP) as the prenyl donor. The enzyme accepted these two prenyl acceptor substrates to produce 6-(3',3'-dimethylallyl)harmine (5) from 3 and 9-(3',3'-dimethylallyl)harman (6) and 6-(3',3'-dimethylallyl)harman (7) from 4. The X-ray crystal structure analysis of the CdpNPT (38-440) truncated mutant complexed with 4, and docking simulation studies of DMAPP to the crystal structure of the CdpNPT (38-440) mutant, suggested that CdpNPT could employ the two-step prenylation mechanism to produce 7, while the enzyme produced 6 with either one- or two-step prenylation mechanisms. Furthermore, the antibacterial assays revealed that the 3',3'-dimethylallylation of 3 and 4, as well as harmol (1), at C-6 enhanced the activities against Staphylococcus aureus and Bacillus subtilis.
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Affiliation(s)
- Sherif Ahmed Hamdy
- Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, Kasr El-Aini St., Cairo 11562, Egypt; Institute of Natural Medicine, University of Toyama, 2630-Sugitani, Toyama 930-0194, Japan
| | - Takeshi Kodama
- Institute of Natural Medicine, University of Toyama, 2630-Sugitani, Toyama 930-0194, Japan
| | - Yu Nakashima
- Institute of Natural Medicine, University of Toyama, 2630-Sugitani, Toyama 930-0194, Japan
| | - Xiaojie Han
- Institute of Natural Medicine, University of Toyama, 2630-Sugitani, Toyama 930-0194, Japan
| | - Hiroyuki Morita
- Institute of Natural Medicine, University of Toyama, 2630-Sugitani, Toyama 930-0194, Japan.
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7
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Enzymatic formation of a prenyl β-carboline by a fungal indole prenyltransferase. J Nat Med 2022; 76:873-879. [PMID: 35767141 DOI: 10.1007/s11418-022-01635-0] [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: 05/25/2022] [Accepted: 06/09/2022] [Indexed: 10/17/2022]
Abstract
CdpNPT from Aspergillus fumigatus is a fungal indole prenyltransferase (IPT) with remarkable substrate promiscuity to generate prenylated compounds. Our first investigation of the catalytic potential of CdpNPT against a β-carboline, harmol (1), revealed that the enzyme also accepts 1 as the prenyl acceptor with dimethylallyl diphosphate (DMAPP) as the prenyl donor and selectively prenylates the C-6 position of 1 by the "regular-type" dimethylallylation to produce 6-(3-dimethylallyl)harmol (2). Furthermore, our X-ray crystal structure analysis of the C-His6-tagged CdpNPT (38-440) truncated mutant complexed with 1 and docking studies of DMAPP to the crystal structure of the CdpNPT (38-440) mutant suggested that CdpNPT could employ the two-step prenylation system to produce 2.
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Johnson BP, Kumar V, Scull EM, Thomas LM, Bourne CR, Singh S. Molecular Basis for the Substrate Promiscuity of Isopentenyl Phosphate Kinase from Candidatus methanomethylophilus alvus. ACS Chem Biol 2022; 17:85-102. [PMID: 34905349 PMCID: PMC9745668 DOI: 10.1021/acschembio.1c00655] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Isopentenyl phosphate kinases (IPKs) catalyze the ATP-dependent phosphorylation of isopentenyl monophosphate (IP) to isopentenyl diphosphate (IPP) in the alternate mevalonate pathways of the archaea and plant cytoplasm. In recent years, IPKs have also been employed in artificial biosynthetic pathways called "(iso) prenol pathways" that utilize promiscuous kinases to sequentially phosphorylate (iso) prenol and generate the isoprenoid precursors IPP and dimethylallyl diphosphate (DMAPP). Furthermore, IPKs have garnered attention for their impressive substrate promiscuity toward non-natural alkyl-monophosphates (alkyl-Ps), which has prompted their utilization as biocatalysts for the generation of novel isoprenoids. However, none of the IPK crystal structures currently available contain non-natural substrates, leaving the roles of active-site residues in substrate promiscuity ambiguous. To address this, we present herein the high-resolution crystal structures of an IPK from Candidatus methanomethylophilus alvus (CMA) in the apo form and bound to natural and non-natural substrates. Additionally, we describe active-site engineering studies leading to enzyme variants with broadened substrate scope, as well as structure determination of two such variants (Ile74Ala and Ile146Ala) bound to non-natural alkyl-Ps. Collectively, our crystallographic studies compare six structures of CMA variants in different ligand-bound forms and highlight contrasting structural dynamics of the two substrate-binding sites. Furthermore, the structural and mutational studies confirm a novel role of the highly conserved DVTGG motif in catalysis, both in CMA and in IPKs at large. As such, the current study provides a molecular basis for the substrate-binding modes and catalytic performance of CMA toward the goal of developing IPKs into useful biocatalysts.
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Affiliation(s)
- Bryce P. Johnson
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Vikas Kumar
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Erin M. Scull
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Leonard M. Thomas
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Christina R. Bourne
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Shanteri Singh
- Department of Chemistry and Biochemistry, University of Oklahoma, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
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