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Zhou L, Simonian AL. CRISPR/Cas Technology: The Unique Synthetic Biology Genome-Editing Tool Shifting the Paradigm in Viral Diagnostics, Defense, and Therapeutics. Annu Rev Biomed Eng 2024; 26:247-272. [PMID: 38346278 DOI: 10.1146/annurev-bioeng-081723-013033] [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] [Indexed: 07/05/2024]
Abstract
The emergence of the COVID-19 pandemic has starkly exposed our significantly limited ability to promptly identify and respond to emergent biological threats. Consequently, there is an urgent need to advance biotechnological methods for addressing both known and unforeseen biological hazards. Recently, the CRISPR/Cas system has revolutionized genetic engineering, enabling precise and efficient synthetic biology applications. Therefore, this review aims to provide a comprehensive introduction to the fundamental principles underlying the CRISPR/Cas system and assess the advantages and limitations of various CRISPR/Cas-based techniques applicable to the detection of, defense against, and treatment of viral infections. These techniques include viral diagnostics, the development of antiviral vaccines, B cell engineering for antibody production, viral activation/interference, and epigenetic modifications. Furthermore, this review delves into the challenges and bioethical considerations associated with use of the CRISPR/Cas system. With the continuous evolution of technology, the CRISPR/Cas system holds considerable promise for addressing both existing and unforeseen biological threats.
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Affiliation(s)
- Lang Zhou
- Department of Materials Engineering, Samuel Ginn College of Engineering, Auburn University, Auburn, Alabama, USA;
| | - Aleksandr L Simonian
- Department of Materials Engineering, Samuel Ginn College of Engineering, Auburn University, Auburn, Alabama, USA;
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2
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Bozhüyük KAJ, Präve L, Kegler C, Schenk L, Kaiser S, Schelhas C, Shi YN, Kuttenlochner W, Schreiber M, Kandler J, Alanjary M, Mohiuddin TM, Groll M, Hochberg GKA, Bode HB. Evolution-inspired engineering of nonribosomal peptide synthetases. Science 2024; 383:eadg4320. [PMID: 38513038 DOI: 10.1126/science.adg4320] [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: 12/23/2022] [Accepted: 02/09/2024] [Indexed: 03/23/2024]
Abstract
Many clinically used drugs are derived from or inspired by bacterial natural products that often are produced through nonribosomal peptide synthetases (NRPSs), megasynthetases that activate and join individual amino acids in an assembly line fashion. In this work, we describe a detailed phylogenetic analysis of several bacterial NRPSs that led to the identification of yet undescribed recombination sites within the thiolation (T) domain that can be used for NRPS engineering. We then developed an evolution-inspired "eXchange Unit between T domains" (XUT) approach, which allows the assembly of NRPS fragments over a broad range of GC contents, protein similarities, and extender unit specificities, as demonstrated for the specific production of a proteasome inhibitor designed and assembled from five different NRPS fragments.
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Affiliation(s)
- Kenan A J Bozhüyük
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
- Myria Biosciences AG, Tech Park Basel, Hochbergstrasse 60C, 4057 Basel, Switzerland
| | - Leonard Präve
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Carsten Kegler
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Leonie Schenk
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Sebastian Kaiser
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Christian Schelhas
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
| | - Yan-Ni Shi
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Wolfgang Kuttenlochner
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, 85748 Garching, Germany
| | - Max Schreiber
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Joshua Kandler
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Mohammad Alanjary
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - T M Mohiuddin
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Michael Groll
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, 85748 Garching, Germany
| | - Georg K A Hochberg
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Phillips University Marburg, 35043 Marburg, Germany
- Department of Chemistry, Phillips University Marburg, 35043 Marburg, Germany
| | - Helge B Bode
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Phillips University Marburg, 35043 Marburg, Germany
- Department of Chemistry, Phillips University Marburg, 35043 Marburg, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG) & Senckenberg Gesellschaft für Naturforschung, 60325 Frankfurt, Germany
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Roney M, Issahaku AR, Forid MS, Huq AKMM, Soliman MES, Mohd Aluwi MFF, Tajuddin SN. In silico evaluation of usnic acid derivatives to discover potential antibacterial drugs against DNA gyrase B and DNA topoisomerase IV. J Biomol Struct Dyn 2023; 41:14904-14913. [PMID: 36995164 DOI: 10.1080/07391102.2023.2193996] [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: 12/27/2022] [Accepted: 02/18/2023] [Indexed: 03/31/2023]
Abstract
Due to the rising increase in infectious diseases brought on by bacteria and anti-bacterial drug resistance, antibacterial therapy has become difficult. The majority of first-line antibiotics are no longer effective against numerous germs, posing a new hazard to global human health in the 21st century. Through the drug-likeness screening, 184 usnic acid derivatives were selected from an in-house database of 340 usnic acid compounds. The pharmacokinetics (ADMET) prediction produced fifteen hit compounds, of which the lead molecule was subsequently obtained through a molecular docking investigation. The lead compounds, labelled compound-277 and compound-276, respectively, with the substantial binding affinity towards the enzymes were obtained through further docking simulation on the DNA gyrase and DNA topoisomerase proteins. Additionally, molecular dynamic (MD) simulation was performed for 300 ns on the lead compounds in order to confirm the stability of the docked complexes and the binding pose discovered during docking tests. Due to their intriguing pharmacological characteristics, these substances may be promising therapeutic candidate for anti-bacterial medication.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Miah Roney
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Lebuhraya Tun Razak, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
- Bio Aromatic Research Centre, Universiti Malaysia Pahang Lebuhraya Tun Razak, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
| | - Abdul Rashid Issahaku
- West African Centre for Computational Analysis, Accra, Ghana
- Molecular Bio-computation and Drug Design Laboratory, Discipline of Pharmaceutical Sciences, University of KwaZulu-Natal, Westville Campus, Durban, South Africa
| | - Md Shaekh Forid
- Faculty of Chemical and Process Engineering Technology, Universiti Malaysia Pahang Lebuhraya Tun Razak, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
| | - A K M Moyeenul Huq
- Bio Aromatic Research Centre, Universiti Malaysia Pahang Lebuhraya Tun Razak, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
- Department of Pharmacy, School of Medicine, University of Asia Pacific, Dhaka, Bangladesh
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, Discipline of Pharmaceutical Sciences, University of KwaZulu-Natal, Westville Campus, Durban, South Africa
| | - Mohd Fadhlizil Fasihi Mohd Aluwi
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Lebuhraya Tun Razak, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
- Bio Aromatic Research Centre, Universiti Malaysia Pahang Lebuhraya Tun Razak, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
| | - Saiful Nizam Tajuddin
- Bio Aromatic Research Centre, Universiti Malaysia Pahang Lebuhraya Tun Razak, Gambang, Kuantan, Pahang Darul Makmur, Malaysia
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Scott L, Wigglesworth MJ, Siewers V, Davis AM, David F. Genetically Encoded Whole Cell Biosensor for Drug Discovery of HIF-1 Interaction Inhibitors. ACS Synth Biol 2022; 11:3182-3189. [PMID: 36223492 PMCID: PMC9594322 DOI: 10.1021/acssynbio.2c00274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The heterodimeric transcription factor, hypoxia inducible factor-1 (HIF-1), is an important anticancer target as it supports the adaptation and response of tumors to hypoxia. Here, we optimized the repressed transactivator yeast two-hybrid system to further develop it as part of a versatile yeast-based drug discovery platform and validated it using HIF-1. We demonstrate both fluorescence-based and auxotrophy-based selections that could detect HIF-1α/HIF-1β dimerization inhibition. The engineered genetic selection is tunable and able to differentiate between strong and weak interactions, shows a large dynamic range, and is stable over different growth phases. Furthermore, we engineered mechanisms to control for cellular activity and off-target drug effects. We thoroughly characterized all parts of the biosensor system and argue this tool will be generally applicable to a wide array of protein-protein interaction targets. We anticipate this biosensor will be useful as part of a drug discovery platform, particularly when screening DNA-encoded new modality drugs.
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Affiliation(s)
- Louis
H. Scott
- Discovery
Sciences, Biopharmaceuticals R&D, AstraZeneca, SE-41320 Gothenburg, Sweden,Department
of Biology and Biological Engineering, Division of Systems and Synthetic
Biology, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Mark J. Wigglesworth
- Discovery
Sciences, Biopharmaceuticals R&D, AstraZeneca, Alderley Park SK10 2NA, U.K.
| | - Verena Siewers
- Department
of Biology and Biological Engineering, Division of Systems and Synthetic
Biology, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Andrew M. Davis
- Discovery
Sciences, Biopharmaceutical R&D, AstraZeneca, Cambridge, CB2 0AA, U.K.
| | - Florian David
- Department
of Biology and Biological Engineering, Division of Systems and Synthetic
Biology, Chalmers University of Technology, SE-41296 Gothenburg, Sweden,
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Song H, Zhang Y, Souza JN, Li J. Guest Editorial AI-Driven Synthetic Biology for Human Wellbeing. IEEE J Biomed Health Inform 2022. [DOI: 10.1109/jbhi.2022.3204369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Houbing Song
- Embry-Riddle Aeronautical University, Daytona Beach, FL, USA
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Synthetic Protein Circuits and Devices Based on Reversible Protein-Protein Interactions: An Overview. Life (Basel) 2021; 11:life11111171. [PMID: 34833047 PMCID: PMC8623019 DOI: 10.3390/life11111171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 12/30/2022] Open
Abstract
Protein-protein interactions (PPIs) contribute to regulate many aspects of cell physiology and metabolism. Protein domains involved in PPIs are important building blocks for engineering genetic circuits through synthetic biology. These domains can be obtained from known proteins and rationally engineered to produce orthogonal scaffolds, or computationally designed de novo thanks to recent advances in structural biology and molecular dynamics prediction. Such circuits based on PPIs (or protein circuits) appear of particular interest, as they can directly affect transcriptional outputs, as well as induce behavioral/adaptational changes in cell metabolism, without the need for further protein synthesis. This last example was highlighted in recent works to enable the production of fast-responding circuits which can be exploited for biosensing and diagnostics. Notably, PPIs can also be engineered to develop new drugs able to bind specific intra- and extra-cellular targets. In this review, we summarize recent findings in the field of protein circuit design, with particular focus on the use of peptides as scaffolds to engineer these circuits.
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