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Jin N, Xia Y, Gao Q. Combined PARP inhibitors and small molecular inhibitors in solid tumor treatment (Review). Int J Oncol 2023; 62:28. [PMID: 36601757 PMCID: PMC9851129 DOI: 10.3892/ijo.2023.5476] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 09/23/2022] [Indexed: 01/05/2023] Open
Abstract
With the development of precision medicine, targeted therapy has attracted extensive attention. Poly(ADP‑ribose) polymerase inhibitors (PARPi) are critical clinical drugs designed to induce cell death and are major antitumor targeted agents. However, preclinical and clinical data have revealed the limitations of PARPi monotherapy. Therefore, their combination with other targeted drugs has become a research hotspot in tumor treatment. Recent studies have demonstrated the critical role of small molecular inhibitors in multiple haematological cancers and solid tumors via cellular signalling modulation, exhibiting potential as a combined pharmacotherapy. In the present review, studies focused on small molecular inhibitors targeting the homologous recombination pathway were summarized and clinical trials evaluating the safety and efficacy of combined treatment were discussed.
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Affiliation(s)
- Ning Jin
- Key Laboratory of The Ministry of Education, Cancer Biology Research Center, Tongji Hospital, Wuhan, Hubei 430000, P.R. China,Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430000, P.R. China
| | - Yu Xia
- Key Laboratory of The Ministry of Education, Cancer Biology Research Center, Tongji Hospital, Wuhan, Hubei 430000, P.R. China,Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430000, P.R. China,Correspondence to: Professor Qinglei Gao or Professor Yu Xia, Key Laboratory of The Ministry of Education, Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, Hubei 430000, P.R. China, E-mail: , E-mail:
| | - Qinglei Gao
- Key Laboratory of The Ministry of Education, Cancer Biology Research Center, Tongji Hospital, Wuhan, Hubei 430000, P.R. China,Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430000, P.R. China,Correspondence to: Professor Qinglei Gao or Professor Yu Xia, Key Laboratory of The Ministry of Education, Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, Hubei 430000, P.R. China, E-mail: , E-mail:
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2
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High-Throughput Development and Optimization of RNA-Based Fluorogenic Biosensors of Small Molecules Using Droplet-Based Microfluidics. Methods Mol Biol 2023; 2570:243-269. [PMID: 36156788 DOI: 10.1007/978-1-0716-2695-5_19] [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: 01/25/2023]
Abstract
Small-molecule sensing is a major issue as they can serve both in fundamental science and as makers of various diseases, contaminations, or even environment pollution. RNA aptamers are single-stranded nucleic acids that can adopt different conformations and specifically recognize a wide range of ligands, making them good candidates to develop biosensors of small molecules. Recently, light-up RNA aptamers have been introduced and used as starting building blocks of RNA-based fluorogenic biosensors. They are typically made of three domains: a reporter domain (a light-up aptamer), connected to a sensor domain (another aptamer) via a communication module. The latter is instrumental as being in charge of information transmission between the sensor and the reporting domains. Here we present an ultrahigh-throughput screening procedure to develop RNA-based fluorogenic biosensors by selecting optimized communication modules through an exhaustive functional exploration of every possible sequence permutation using droplet-based microfluidics and next-generation sequencing.
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Krumbholz J, Ishida K, Baunach M, Teikari JE, Rose MM, Sasso S, Hertweck C, Dittmann E. Deciphering Chemical Mediators Regulating Specialized Metabolism in a Symbiotic Cyanobacterium. Angew Chem Int Ed Engl 2022; 61:e202204545. [PMID: 35403785 PMCID: PMC9324945 DOI: 10.1002/anie.202204545] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Indexed: 11/11/2022]
Abstract
Genomes of cyanobacteria feature a variety of cryptic biosynthetic pathways for complex natural products, but the peculiarities limiting the discovery and exploitation of the metabolic dark matter are not well understood. Here we describe the discovery of two cell density‐dependent chemical mediators, nostoclide and nostovalerolactone, in the symbiotic model strain Nostoc punctiforme, and demonstrate their pronounced impact on the regulation of specialized metabolism. Through transcriptional, bioinformatic and labeling studies we assigned two adjacent biosynthetic gene clusters to the biosynthesis of the two polyketide mediators. Our findings provide insight into the orchestration of specialized metabolite production and give lessons for the genomic mining and high‐titer production of cyanobacterial bioactive compounds.
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Affiliation(s)
- Julia Krumbholz
- Institute of Biochemistry and BiologyUniversity of PotsdamKarl-Liebknecht-Str. 24/2514476Potsdam-GolmGermany
| | - Keishi Ishida
- Leibniz Institute for Natural Product Research and Infection BiologyHans Knöll InstituteBeutenbergstr. 11a07745JenaGermany
| | - Martin Baunach
- Institute of Biochemistry and BiologyUniversity of PotsdamKarl-Liebknecht-Str. 24/2514476Potsdam-GolmGermany
| | - Jonna E. Teikari
- Institute of Biochemistry and BiologyUniversity of PotsdamKarl-Liebknecht-Str. 24/2514476Potsdam-GolmGermany
| | - Magdalena M. Rose
- Institute for BiologyDepartment of Plant PhysiologyLeipzig UniversityJohannisallee 21–2304103LeipzigGermany
| | - Severin Sasso
- Institute for BiologyDepartment of Plant PhysiologyLeipzig UniversityJohannisallee 21–2304103LeipzigGermany
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection BiologyHans Knöll InstituteBeutenbergstr. 11a07745JenaGermany
- Institute of MicrobiologyFaculty of Biological SciencesFriedrich Schiller University Jena07743JenaGermany
| | - Elke Dittmann
- Institute of Biochemistry and BiologyUniversity of PotsdamKarl-Liebknecht-Str. 24/2514476Potsdam-GolmGermany
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Krumbholz J, Ishida K, Baunach M, Teikari JE, Rose MM, Sasso S, Hertweck C, Dittmann E. Entschlüsselung chemischer Mediatoren zur Regulierung des spezialisierten Stoffwechsels in einem symbiotischen Cyanobakterium. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Julia Krumbholz
- Institut für Biochemie und Biologie Universität Potsdam Karl-Liebknecht-Str. 24/25 14476 Potsdam-Golm Deutschland
| | - Keishi Ishida
- Leibniz Institut für Naturstoff-Forschung und Infektionsbiologie Hans Knöll Institute Beutenbergstr. 11a 07745 Jena Deutschland
| | - Martin Baunach
- Institut für Biochemie und Biologie Universität Potsdam Karl-Liebknecht-Str. 24/25 14476 Potsdam-Golm Deutschland
| | - Jonna E. Teikari
- Institut für Biochemie und Biologie Universität Potsdam Karl-Liebknecht-Str. 24/25 14476 Potsdam-Golm Deutschland
| | - Magdalena M. Rose
- Institut für Biologie AG Pflanzenphysiologie Universität Leipzig Johannisallee 21–23 04103 Leipzig Deutschland
| | - Severin Sasso
- Institut für Biologie AG Pflanzenphysiologie Universität Leipzig Johannisallee 21–23 04103 Leipzig Deutschland
| | - Christian Hertweck
- Leibniz Institut für Naturstoff-Forschung und Infektionsbiologie Hans Knöll Institute Beutenbergstr. 11a 07745 Jena Deutschland
- Institut für Mikrobiologie Fakultät für Biowissenschaften Friedrich-Schiller-Universität Jena 07743 Jena Deutschland
| | - Elke Dittmann
- Institut für Biochemie und Biologie Universität Potsdam Karl-Liebknecht-Str. 24/25 14476 Potsdam-Golm Deutschland
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5
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Ariza-Mateos A, Nuthanakanti A, Serganov A. Riboswitch Mechanisms: New Tricks for an Old Dog. BIOCHEMISTRY (MOSCOW) 2021; 86:962-975. [PMID: 34488573 DOI: 10.1134/s0006297921080071] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Discovered almost twenty years ago, riboswitches turned out to be one of the most common regulatory systems in bacteria, with representatives found in eukaryotes and archaea. Unlike many other regulatory elements, riboswitches are entirely composed of RNA and capable of modulating expression of genes by direct binding of small cellular molecules. While bacterial riboswitches had been initially thought to control production of enzymes and transporters associated with small organic molecules via feedback regulatory circuits, later findings identified riboswitches directing expression of a wide range of genes and responding to various classes of molecules, including ions, signaling molecules, and others. The 5'-untranslated mRNA regions host a vast majority of riboswitches, which modulate transcription or translation of downstream genes through conformational rearrangements in the ligand-sensing domains and adjacent expression-controlling platforms. Over years, the repertoire of regulatory mechanisms employed by riboswitches has greatly expanded; most recent studies have highlighted the importance of alternative mechanisms, such as RNA degradation, for the riboswitch-mediated genetic circuits. This review discusses the plethora of bacterial riboswitch mechanisms and illustrates how riboswitches utilize different features and approaches to elicit various regulatory responses.
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Affiliation(s)
- Ascensión Ariza-Mateos
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Ashok Nuthanakanti
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Alexander Serganov
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA.
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Chandrabhas S, Maiti S, Fortunati I, Ferrante C, Gabrielli L, Prins LJ. Nucleotide-Selective Templated Self-Assembly of Nanoreactors under Dissipative Conditions. Angew Chem Int Ed Engl 2020; 59:22223-22229. [PMID: 32833254 DOI: 10.1002/anie.202010199] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Indexed: 02/06/2023]
Abstract
Nature adopts complex chemical networks to finely tune biochemical processes. Indeed, small biomolecules play a key role in regulating the flux of metabolic pathways. Chemistry, which was traditionally focused on reactions in simple mixtures, is dedicating increasing attention to the network reactivity of highly complex synthetic systems, able to display new kinetic phenomena. Herein, we show that the addition of monophosphate nucleosides to a mixture of amphiphiles and reagents leads to the selective templated formation of self-assembled structures, which can accelerate a reaction between two hydrophobic reactants. The correct matching between nucleotide and the amphiphile head group is fundamental for the selective formation of the assemblies and for the consequent up-regulation of the chemical reaction. Transient stability of the nanoreactors is obtained under dissipative conditions, driven by enzymatic dephosphorylation of the templating nucleotides. These results show that small molecules can play a key role in modulating network reactivity, by selectively templating self-assembled structures that are able to up-regulate chemical reaction pathways.
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Affiliation(s)
- Sushmitha Chandrabhas
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Subhabrata Maiti
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Mohali Knowledge City, Manauli, 140306, India
| | - Ilaria Fortunati
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Camilla Ferrante
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Luca Gabrielli
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Leonard J Prins
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131, Padova, Italy
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Chandrabhas S, Maiti S, Fortunati I, Ferrante C, Gabrielli L, Prins LJ. Nucleotide‐Selective Templated Self‐Assembly of Nanoreactors under Dissipative Conditions. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202010199] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Sushmitha Chandrabhas
- Department of Chemical Sciences University of Padova Via Marzolo 1 35131 Padova Italy
| | - Subhabrata Maiti
- Department of Chemical Sciences Indian Institute of Science Education and Research (IISER) Mohali Knowledge City, Manauli 140306 India
| | - Ilaria Fortunati
- Department of Chemical Sciences University of Padova Via Marzolo 1 35131 Padova Italy
| | - Camilla Ferrante
- Department of Chemical Sciences University of Padova Via Marzolo 1 35131 Padova Italy
| | - Luca Gabrielli
- Department of Chemical Sciences University of Padova Via Marzolo 1 35131 Padova Italy
| | - Leonard J. Prins
- Department of Chemical Sciences University of Padova Via Marzolo 1 35131 Padova Italy
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Yadav M, Shukla P. Efficient engineered probiotics using synthetic biology approaches: A review. Biotechnol Appl Biochem 2019; 67:22-29. [PMID: 31538358 DOI: 10.1002/bab.1822] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 09/13/2019] [Indexed: 12/14/2022]
Abstract
The uses of probiotics-based food supplements are getting emphasis due to their power to ensure better health conditions. Probiotics have diverse and significant applications in the health sector, so probiotic strains require an understanding of the genome level organizations. Probiotics elucidate various functional parameters that control their metabolic functions. In this review, we have compiled aspects of synthetic biology, which are used for the optimization of metabolic processes in probiotics for their use as a supplement in allopathic medicines. Synthetic biology approaches provide information about diverse biosynthetic pathways and also facilitate the novel metabolic engineering approaches for probiotics strain improvement. We have discussed the synthetic biology approaches for producing engineered probiotics via genetic circuits, expression systems, and genome editing tools like CRISPR-Cas and PEVLAB. This review also enlightens future challenges in the development of engineered probiotics.
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Affiliation(s)
- Monika Yadav
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
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Miguez AM, McNerney MP, Styczynski MP. Metabolomics Analysis of the Toxic Effects of the Production of Lycopene and Its Precursors. Front Microbiol 2018; 9:760. [PMID: 29774011 PMCID: PMC5944366 DOI: 10.3389/fmicb.2018.00760] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 04/04/2018] [Indexed: 01/01/2023] Open
Abstract
Using cells as microbial factories enables highly specific production of chemicals with many advantages over chemical syntheses. A number of exciting new applications of this approach are in the area of precision metabolic engineering, which focuses on improving the specificity of target production. In recent work, we have used precision metabolic engineering to design lycopene-producing Escherichia coli for use as a low-cost diagnostic biosensor. To increase precursor availability and thus the rate of lycopene production, we heterologously expressed the mevalonate pathway. We found that simultaneous induction of these pathways increases lycopene production, but induction of the mevalonate pathway before induction of the lycopene pathway decreases both lycopene production and growth rate. Here, we aim to characterize the metabolic changes the cells may be undergoing during expression of either or both of these heterologous pathways. After establishing an improved method for quenching E. coli for metabolomics analysis, we used two-dimensional gas chromatography coupled to mass spectrometry (GCxGC-MS) to characterize the metabolomic profile of our lycopene-producing strains in growth conditions characteristic of our biosensor application. We found that the metabolic impacts of producing low, non-toxic levels of lycopene are of much smaller magnitude than the typical metabolic changes inherent to batch growth. We then used metabolomics to study differences in metabolism caused by the time of mevalonate pathway induction and the presence of the lycopene biosynthesis genes. We found that overnight induction of the mevalonate pathway was toxic to cells, but that the cells could recover if the lycopene pathway was not also heterologously expressed. The two pathways appeared to have an antagonistic metabolic effect that was clearly reflected in the cells’ metabolic profiles. The metabolites homocysteine and homoserine exhibited particularly interesting behaviors and may be linked to the growth inhibition seen when the mevalonate pathway is induced overnight, suggesting potential future work that may be useful in engineering increased lycopene biosynthesis.
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Affiliation(s)
- April M Miguez
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Monica P McNerney
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Mark P Styczynski
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, United States
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