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Ness M, Peramuna T, Wendt KL, Collins JE, King JB, Paes R, Santos NM, Okeke C, Miller CR, Chakrabarti D, Cichewicz RH, McCall LI. Rationally Minimizing Natural Product Libraries Using Mass Spectrometry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595232. [PMID: 38826280 PMCID: PMC11142144 DOI: 10.1101/2024.05.22.595232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Natural product libraries are crucial to drug development, but large libraries drastically increase the time and cost during initial high throughput screens. Here, we developed a method that leverages liquid chromatography-tandem mass spectrometry spectral similarity to dramatically reduce library size, with minimal bioactive loss. This method offers a broadly applicable strategy for accelerated drug discovery with cost reductions, which enable implementation in resource-limited settings.
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Affiliation(s)
- Monica Ness
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, California, 92182, United States
| | - Thilini Peramuna
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Karen L. Wendt
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Jennifer E. Collins
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, 32826, United States
| | - Jarrod B. King
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Raphaella Paes
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, 32826, United States
| | - Natalia Mojica Santos
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, 32826, United States
| | - Crystal Okeke
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Cameron R. Miller
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Debopam Chakrabarti
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, 32826, United States
| | - Robert H. Cichewicz
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Laura-Isobel McCall
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, California, 92182, United States
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2
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Lee JH, Ma R, Nguyen L, Khan S, Qader M, Mpofu E, Shetye G, Krull NK, Augustinović M, Omarsdottir S, Cho S, Franzblau SG, Murphy BT. Discovery of a New Antibiotic Demethoxytetronasin Using a Dual-Sided Agar Plate Assay (DAPA). ACS Infect Dis 2023; 9:1593-1601. [PMID: 37450563 PMCID: PMC10426401 DOI: 10.1021/acsinfecdis.3c00171] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Indexed: 07/18/2023]
Abstract
For over a century, researchers have cultured microorganisms together on solid support─typically agar─in order to observe growth inhibition via antibiotic production. These simple bioassays have been critical to both academic researchers that study antibiotic production in microorganisms and to the pharmaceutical industry's global effort to discover drugs. Despite the utility of agar assays to researchers around the globe, several limitations have prevented their widespread adoption in advanced high-throughput compound discovery and dereplication campaigns. To address a list of specific shortcomings, we developed the dual-sided agar plate assay (DAPA), which exists in a 96-well plate format, allows microorganisms to compete through opposing sides of a solid support in individual wells, is amenable to high-throughput screening and automation, is reusable, and is low-cost. Herein, we validate the use of DAPA as a tool for drug discovery and show its utility to discover new antibiotic natural products. From the screening of 217 bacterial isolates on multiple nutrient media against 3 pathogens, 55 hits were observed, 9 known antibiotics were dereplicated directly from agar plugs, and a new antibiotic, demethoxytetronasin (1), was isolated from a Streptomyces sp. These results demonstrate that DAPA is an effective, accessible, and low-cost tool to screen, dereplicate, and prioritize bacteria directly from solid support in the front end of antibiotic discovery pipelines.
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Affiliation(s)
- Jung-Ho Lee
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago,, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Rui Ma
- Institute
for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Linh Nguyen
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago,, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute
of Marine Biochemistry, Vietnam Academy
of Science and Technology, Nghiado, Caugiay, Hanoi 11307, Vietnam
| | - Shahebraj Khan
- Institute
for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Mallique Qader
- Institute
for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Enock Mpofu
- Institute
for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Gauri Shetye
- Institute
for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Nyssa K. Krull
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago,, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Mario Augustinović
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago,, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Sesselja Omarsdottir
- Faculty
of Pharmaceutical Sciences, University of
Iceland, Hagi, Hofsvallagata 53, Reykjavík IS-107, Iceland
| | - Sanghyun Cho
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago,, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute
for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Scott G. Franzblau
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago,, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute
for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Brian T. Murphy
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago,, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Institute
for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
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3
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Atta H, Alzahaby N, Hamdy NM, Emam SH, Sonousi A, Ziko L. New trends in synthetic drugs and natural products targeting 20S proteasomes in cancers. Bioorg Chem 2023; 133:106427. [PMID: 36841046 DOI: 10.1016/j.bioorg.2023.106427] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/15/2023] [Accepted: 02/12/2023] [Indexed: 02/19/2023]
Abstract
Cancer is a global health challenge that remains to be a field of extensive research aiming to find new anticancer therapeutics. The 20S proteasome complex is one of the targets of anticancerdrugs, as it is correlated with several cancer types. Herein, we aim to discuss the 20S proteasome subunits and investigatethe currently studied proteasome inhibitors targeting the catalytically active proteasome subunits. In this review, we summarize the proteindegradation mechanism of the 20S proteasome complex and compareit with the 26S proteasome complex. Afterwards, the localization of the 20S proteasome is summarized as well as its use as a diagnosticandprognostic marker. The FDA-approved proteasome inhibitors (PIs) under clinical trials are summarized and their current limited use in solid tumors is also reviewed in addition to the expression of theβ5 subunit in differentcell lines. The review discusses in-silico analysis of the active subunit of the 20S proteasome complex. For development of new proteasome inhibitor drugs, the natural products inhibiting the 20S proteasome are summarized, as well as novel methodologies and challenges for the natural product discovery and current information about the biosynthetic gene clusters encoding them. We herein briefly summarize some resistancemechanismsto the proteasomeinhibitors. Additionally, we focus on the three main classes of proteasome inhibitors: 1] boronic acid, 2] beta-lactone and 3] epoxide inhibitor classes, as well as other PI classes, and their IC50 values and their structure-activity relationship (SAR). Lastly,we summarize several future prospects of developing new proteasome inhibitors towards the treatment of tumors, especially solid tumors.
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Affiliation(s)
- Hind Atta
- School of Life and Medical Sciences, University of Hertfordshire Hosted By Global Academic Foundation, Egypt
| | - Nouran Alzahaby
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Abassia 11566, Cairo, Egypt
| | - Nadia M Hamdy
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Abassia 11566, Cairo, Egypt
| | - Soha H Emam
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Amr Sonousi
- School of Life and Medical Sciences, University of Hertfordshire Hosted By Global Academic Foundation, Egypt; Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Laila Ziko
- School of Life and Medical Sciences, University of Hertfordshire Hosted By Global Academic Foundation, Egypt; Biology Department, School of Sciences and Engineering, American University in Cairo, Egypt.
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Quantitative and Qualitative Changes in the Genetic Diversity of Bacterial Communities in Anaerobic Bioreactors with the Diatomaceous Earth/Peat Cell Carrier. Cells 2022; 11:cells11162571. [PMID: 36010646 PMCID: PMC9406963 DOI: 10.3390/cells11162571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/14/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
This paper analyses the impact of the diatomaceous earth/peat (DEP; 3:1) microbial carrier on changes in the bacterial microbiome and the development of biofilm in the anaerobic digestion (AD) of confectionery waste, combined with digested sewage sludge as inoculum. The physicochemical properties of the carrier material are presented, with particular focus on its morphological and dispersion characteristics, as well as adsorption and thermal properties. In this respect, the DEP system was found to be a suitable carrier for both mesophilic and thermophilic AD. The evaluation of quantitative and qualitative changes in the genetic diversity of bacterial communities, carried out using next-generation sequencing (NGS), showed that the material has a modifying effect on the bacterial microbiome. While Actinobacteria was the most abundant cluster in the WF-control sample (WF—waste wafers), Firmicutes was the dominant cluster in the digested samples without the carrier (WF-dig.; dig.—digested) and with the carrier (WF + DEP). The same was true for the count of Proteobacteria, which decreased twofold during biodegradation in favor of Synergistetes. The Syntrophomonas cluster was identified as the most abundant genus in the two samples, particularly in WF + DEP. This information was supplemented by observations of morphological features of microorganisms carried out using fluorescence microscopy. The biodegradation process itself had a significant impact on changes in the microbiome of samples taken from anaerobic bioreactors, reducing its biodiversity. As demonstrated by the results of this innovative method, namely the BioFlux microfluidic flow system, the decrease in the number of taxa in the digested samples and the addition of DEP contributed to the microbial adhesion in the microfluidic system and the formation of a stable biofilm.
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Classification of Environmental Strains from Order to Genus Levels Using Lipid and Protein MALDI-ToF Fingerprintings and Chemotaxonomic Network Analysis. Microorganisms 2022; 10:microorganisms10040831. [PMID: 35456880 PMCID: PMC9032901 DOI: 10.3390/microorganisms10040831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/30/2022] [Accepted: 04/13/2022] [Indexed: 11/16/2022] Open
Abstract
During the last two decades, MALDI-ToF mass spectrometry has become an efficient and widely-used tool for identifying clinical isolates. However, its use for classification and identification of environmental microorganisms remains limited by the lack of reference spectra in current databases. In addition, the interpretation of the classical dendrogram-based data representation is more difficult when the quantity of taxa or chemotaxa is larger, which implies problems of reproducibility between users. Here, we propose a workflow including a concurrent standardized protein and lipid extraction protocol as well as an analysis methodology using the reliable spectra comparison algorithm available in MetGem software. We first validated our method by comparing protein fingerprints of highly pathogenic bacteria from the Robert Koch Institute (RKI) open database and then implemented protein fingerprints of environmental isolates from French Guiana. We then applied our workflow for the classification of a set of protein and lipid fingerprints from environmental microorganisms and compared our results to classical genetic identifications using 16S and ITS region sequencing for bacteria and fungi, respectively. We demonstrated that our protocol allowed general classification at the order and genus level for bacteria whereas only the Botryosphaeriales order can be finely classified for fungi.
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Clark CM, Nguyen L, Pham VC, Sanchez LM, Murphy BT. Automated Microbial Library Generation Using the Bioinformatics Platform IDBac. Molecules 2022; 27:2038. [PMID: 35408437 PMCID: PMC9000433 DOI: 10.3390/molecules27072038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 11/21/2022] Open
Abstract
Libraries of microorganisms have served as a cornerstone of therapeutic drug discovery, though the continued re-isolation of known natural product chemical entities has remained a significant obstacle to discovery efforts. A major contributing factor to this redundancy is the duplication of bacterial taxa in a library, which can be mitigated through the use of a variety of DNA sequencing strategies and/or mass spectrometry-informed bioinformatics platforms so that the library is created with minimal phylogenetic, and thus minimal natural product overlap. IDBac is a MALDI-TOF mass spectrometry-based bioinformatics platform used to assess overlap within collections of environmental bacterial isolates. It allows environmental isolate redundancy to be reduced while considering both phylogeny and natural product production. However, manually selecting isolates for addition to a library during this process was time intensive and left to the researcher's discretion. Here, we developed an algorithm that automates the prioritization of hundreds to thousands of environmental microorganisms in IDBac. The algorithm performs iterative reduction of natural product mass feature overlap within groups of isolates that share high homology of protein mass features. Employing this automation serves to minimize human bias and greatly increase efficiency in the microbial strain prioritization process.
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Affiliation(s)
- Chase M. Clark
- Department of Pharmaceutical Sciences, Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA;
| | - Linh Nguyen
- Institute of Marine Biochemistry, Vietnam Academy of Science and Technology, Nghiado, Caugiay, Hanoi 10000, Vietnam; (L.N.); (V.C.P.)
| | - Van Cuong Pham
- Institute of Marine Biochemistry, Vietnam Academy of Science and Technology, Nghiado, Caugiay, Hanoi 10000, Vietnam; (L.N.); (V.C.P.)
| | - Laura M. Sanchez
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA;
| | - Brian T. Murphy
- Department of Pharmaceutical Sciences, Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, USA;
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7
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Clark CM, Hernandez A, Mullowney MW, Fitz-Henley J, Li E, Romanowski SB, Pronzato R, Manconi R, Sanchez LM, Murphy BT. Relationship between bacterial phylotype and specialized metabolite production in the culturable microbiome of two freshwater sponges. ISME COMMUNICATIONS 2022; 2:22. [PMID: 37938725 PMCID: PMC9723699 DOI: 10.1038/s43705-022-00105-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 11/09/2023]
Abstract
Microbial drug discovery programs rely heavily on accessing bacterial diversity from the environment to acquire new specialized metabolite (SM) lead compounds for the therapeutic pipeline. Therefore, knowledge of how commonly culturable bacterial taxa are distributed in nature, in addition to the degree of variation of SM production within those taxa, is critical to informing these front-end discovery efforts and making the overall sample collection and bacterial library creation process more efficient. In the current study, we employed MALDI-TOF mass spectrometry and the bioinformatics pipeline IDBac to analyze diversity within phylotype groupings and SM profiles of hundreds of bacterial isolates from two Eunapius fragilis freshwater sponges, collected 1.5 km apart. We demonstrated that within two sponge samples of the same species, the culturable bacterial populations contained significant overlap in approximate genus-level phylotypes but mostly nonoverlapping populations of isolates when grouped lower than the level of genus. Further, correlations between bacterial phylotype and SM production varied at the species level and below, suggesting SM distribution within bacterial taxa must be analyzed on a case-by-case basis. Our results suggest that two E. fragilis freshwater sponges collected in similar environments can exhibit large culturable diversity on a species-level scale, thus researchers should scrutinize the isolates with analyses that take both phylogeny and SM production into account to optimize the chemical space entering into a downstream bacterial library.
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Affiliation(s)
- Chase M Clark
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Antonio Hernandez
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Michael W Mullowney
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Jhewelle Fitz-Henley
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Emma Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Sean B Romanowski
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Roberto Pronzato
- Dipartimento di Scienze della Terra, dell'Ambiente e della Vita, Università di Genova, Genova, Italy
| | - Renata Manconi
- Dipartimento Medicina Veterinaria, Università di Sassari, Sassari, Italy
| | - Laura M Sanchez
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Brian T Murphy
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA.
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Abstract
BACKGROUND Marine ecosystems are hosts to a vast array of organisms, being among the most richly biodiverse locations on the planet. The study of these ecosystems is very important, as they are not only a significant source of food for the world but also have, in recent years, become a prolific source of compounds with therapeutic potential. Studies of aspects of marine life have involved diverse fields of marine science, and the use of metabolomics as an experimental approach has increased in recent years. As part of the "omics" technologies, metabolomics has been used to deepen the understanding of interactions between marine organisms and their environment at a metabolic level and to discover new metabolites produced by these organisms. AIM OF REVIEW This review provides an overview of the use of metabolomics in the study of marine organisms. It also explores the use of metabolomics tools common to other fields such as plants and human metabolomics that could potentially contribute to marine organism studies. It deals with the entire process of a metabolomic study, from sample collection considerations, metabolite extraction, analytical techniques, and data analysis. It also includes an overview of recent applications of metabolomics in fields such as marine ecology and drug discovery and future perspectives of its use in the study of marine organisms. KEY SCIENTIFIC CONCEPTS OF REVIEW The review covers all the steps involved in metabolomic studies of marine organisms including, collection, extraction methods, analytical tools, statistical analysis, and dereplication. It aims to provide insight into all aspects that a newcomer to the field should consider when undertaking marine metabolomics.
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Affiliation(s)
- Lina M Bayona
- Natural Products Laboratory, Institute of Biology, Leiden University, 2333 BE, Leiden, The Netherlands
| | - Nicole J de Voogd
- Naturalis Biodiversity Center, Marine Biodiversity, 2333 CR, Leiden, The Netherlands
- Institute of Environmental Sciences, Leiden University, 2333 CC, Leiden, The Netherlands
| | - Young Hae Choi
- Natural Products Laboratory, Institute of Biology, Leiden University, 2333 BE, Leiden, The Netherlands.
- College of Pharmacy, Kyung Hee University, 130-701, Seoul, Republic of Korea.
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Anderson VM, Wendt KL, Najar FZ, McCall LI, Cichewicz RH. Building Natural Product Libraries Using Quantitative Clade-Based and Chemical Clustering Strategies. mSystems 2021; 6:e0064421. [PMID: 34698546 PMCID: PMC8547436 DOI: 10.1128/msystems.00644-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 09/16/2021] [Indexed: 12/01/2022] Open
Abstract
The success of natural product-based drug discovery is predicated on having chemical collections that offer broad coverage of metabolite diversity. We propose a simple set of tools combining genetic barcoding and metabolomics to help investigators build natural product libraries aimed at achieving predetermined levels of chemical coverage. It was found that such tools aided in identifying overlooked pockets of chemical diversity within taxa, which could be useful for refocusing collection strategies. We have used fungal isolates identified as Alternaria from a citizen-science-based soil collection to demonstrate the application of these tools for assessing and carrying out predictive measurements of chemical diversity in a natural product collection. Within Alternaria, different subclades were found to contain nonequivalent levels of chemical diversity. It was also determined that a surprisingly modest number of isolates (195 isolates) was sufficient to afford nearly 99% of Alternaria chemical features in the data set. However, this result must be considered in the context that 17.9% of chemical features appeared in single isolates, suggesting that fungi like Alternaria might be engaged in an ongoing process of actively exploring nature's metabolic landscape. Our results demonstrate that combining modest investments in securing internal transcribed spacer (ITS)-based sequence information (i.e., establishing gene-based clades) with data from liquid chromatography-mass spectrometry (i.e., generating feature accumulation curves) offers a useful route to obtaining actionable insights into chemical diversity coverage trends in a natural product library. It is anticipated that these outcomes could be used to improve opportunities for accessing bioactive molecules that serve as the cornerstone of natural product-based drug discovery. IMPORTANCE Natural product drug discovery efforts rely on libraries of organisms to provide access to diverse pools of compounds. Actionable strategies to rationally maximize chemical diversity, rather than relying on serendipity, can add value to such efforts. Readily implementable biological (i.e., ITS sequence analysis) and chemical (i.e., mass spectrometry-based feature and scaffold measurements) diversity assessment tools can be employed to monitor and adjust library development tactics in real time. In summary, metabolomics-driven technologies and simple gene-based specimen barcoding approaches have broad applicability to building chemically diverse natural product libraries.
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Affiliation(s)
- Victoria M. Anderson
- Natural Products Discovery Group, University of Oklahoma, Norman, Oklahoma, USA
- Institute for Natural Products Applications and Research Technologies, University of Oklahoma, Norman, Oklahoma, USA
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Karen L. Wendt
- Natural Products Discovery Group, University of Oklahoma, Norman, Oklahoma, USA
- Institute for Natural Products Applications and Research Technologies, University of Oklahoma, Norman, Oklahoma, USA
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Fares Z. Najar
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
- Chemistry and Biochemistry Bioinformatics Core, University of Oklahoma, Norman, Oklahoma, USA
| | - Laura-Isobel McCall
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, Oklahoma, USA
| | - Robert H. Cichewicz
- Natural Products Discovery Group, University of Oklahoma, Norman, Oklahoma, USA
- Institute for Natural Products Applications and Research Technologies, University of Oklahoma, Norman, Oklahoma, USA
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
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10
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Silica/Lignin Carrier as a Factor Increasing the Process Performance and Genetic Diversity of Microbial Communities in Laboratory-Scale Anaerobic Digesters. ENERGIES 2021. [DOI: 10.3390/en14154429] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The article aims to present results of research on anaerobic digestion (AD) of waste wafers (WF-control) and co-substrate system–waste wafers and cheese (WFC-control), combined with digested sewage sludge, as inoculum. The purpose of this paper is to confirm the outcome of adding silica/lignin (S/L; 4:1) material, as a microbial carrier, on the process performance and genetic diversity of microbial communities. The experiment was conducted in a laboratory under mesophilic conditions, in a periodical operation mode of bioreactors. Selected physicochemical parameters of the tested carrier, along with the microstructure and thermal stability, were determined. Substrates, batches and fermenting slurries were subjected to standard parameter analysis. As part of the conducted analysis, samples of fermented food were also tested for total bacterial count, dehydrogenase activity. Additionally, DNA extraction and next-generation sequencing (NGS) were carried out. As a result of the conducted study, an increase in the volume of produced biogas was recorded for samples fermented with S/L carrier: in the case of WF + S/L by 18.18% to a cumulative biogas yield of 833.35 m3 Mg−1 VS, and in the case of WFC + S/L by 17.49% to a yield of 950.64 m3 Mg−1 VS. The largest total bacterial count, during the process of dehydrogenase activity, was maintained in the WFC + S/L system. The largest bacterial biodiversity was recorded in samples fermented with the addition of cheese, both in the case of the control variant and in the variant when the carrier was used. In contrast, three phyla of bacteria Firmicutes, Proteobacteria and Actinobacteria predominated in all experimental facilities.
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11
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Hernandez A, Nguyen LT, Dhakal R, Murphy BT. The need to innovate sample collection and library generation in microbial drug discovery: a focus on academia. Nat Prod Rep 2021; 38:292-300. [PMID: 32706349 PMCID: PMC7855266 DOI: 10.1039/d0np00029a] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The question of whether culturable microorganisms will continue to be a viable source of new drug leads is inherently married to the strategies used to collect samples from the environment, the methods used to cultivate microorganisms from these samples, and the processes used to create microbial libraries. An academic microbial natural products (NP) drug discovery program with the latest innovative chromatographic and spectroscopic technology, high-throughput capacity, and bioassays will remain at the mercy of the quality of its microorganism source library. This viewpoint will discuss limitations of sample collection and microbial strain library generation practices. Additionally, it will offer suggestions to innovate these areas, particularly through the targeted cultivation of several understudied bacterial phyla and the untargeted use of mass spectrometry and bioinformatics to generate diverse microbial libraries. Such innovations have potential to impact downstream therapeutic discovery, and make its front end more informed, efficient, and less reliant on serendipity. This viewpoint is not intended to be a comprehensive review of contributing literature and was written with a focus on bacteria. Strategies to discover NPs from microbial libraries, including a variety of genomics and "OSMAC" style approaches, are considered downstream of sample collection and library creation, and thus are out of the scope of this viewpoint.
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Affiliation(s)
- Antonio Hernandez
- Dept. of Pharmaceutical Sciences, Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA.
| | - Linh T Nguyen
- Dept. of Pharmaceutical Sciences, Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA. and Institute of Marine Biochemistry, Vietnam Academy of Science and Technology, Nghiado, Caugiay, Hanoi, Vietnam
| | - Radhika Dhakal
- Dept. of Pharmaceutical Sciences, Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA.
| | - Brian T Murphy
- Dept. of Pharmaceutical Sciences, Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA.
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Parthasarathy A, Mantravadi PK, Kalesh K. Detectives and helpers: Natural products as resources for chemical probes and compound libraries. Pharmacol Ther 2020; 216:107688. [PMID: 32980442 DOI: 10.1016/j.pharmthera.2020.107688] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 09/20/2020] [Accepted: 09/21/2020] [Indexed: 02/06/2023]
Abstract
About 70% of the drugs in use are derived from natural products, either used directly or in chemically modified form. Among all possible small molecules (not greater than 5 kDa), only a few of them are biologically active. Natural product libraries may have a higher rate of finding "hits" than synthetic libraries, even with the use of fewer compounds. This is due to the complementarity between the "chemical space" of small molecules and biological macromolecules such as proteins, DNA and RNA, in addition to the three-dimensional complexity of NPs. Chemical probes are molecules which aid in the elucidation of the biological mechanisms behind the action of drugs or drug-like molecules by binding with macromolecular/cellular interaction partners. Probe development and application have been spurred by advancements in photoaffinity label synthesis, affinity chromatography, activity based protein profiling (ABPP) and instrumental methods such as cellular thermal shift assay (CETSA) and advanced/hyphenated mass spectrometry (MS) techniques, as well as genome sequencing and bioengineering technologies. In this review, we restrict ourselves to a survey of natural products (including peptides/mini-proteins and excluding antibodies), which have been applied largely in the last 5 years for the target identification of drugs/drug-like molecules used in research on infectious diseases, and the description of their mechanisms of action.
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Affiliation(s)
- Anutthaman Parthasarathy
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, 85 Lomb Memorial Dr, Rochester, NY 14623, USA
| | | | - Karunakaran Kalesh
- Department of Chemistry, Durham University, Lower Mount Joy, South Road, Durham DH1 3LE, UK.
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Clark CM, Murphy BT, Sanchez LM. A Call to Action: the Need for Standardization in Developing Open-Source Mass Spectrometry-Based Methods for Microbial Subspecies Discrimination. mSystems 2020; 5:e00813-19. [PMID: 32071161 PMCID: PMC7029221 DOI: 10.1128/msystems.00813-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Chase M Clark
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Brian T Murphy
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Laura M Sanchez
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
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14
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Bajaj S, Ong ST, Chandy KG. Contributions of natural products to ion channel pharmacology. Nat Prod Rep 2020; 37:703-716. [PMID: 32065187 DOI: 10.1039/c9np00056a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Covering: Up to 2020Ion channels are a vast super-family of membrane proteins that play critical physiological roles in excitable and non-excitable cells. Their biomedical importance makes them valuable and attractive drug targets for neurological, cardiovascular, gastrointestinal and metabolic diseases, and for cancer therapy and immune modulation. Current therapeutics target only a minor subset of ion channels, leaving a large unexploited space within the ion channel field. Natural products harnessed from the almost unlimited and diverse universe of compounds within the bioenvironment have been used to modulate channels for decades. In this review we highlight the impact made by natural products on ion channel pharmacology, specifically on K+, NaV and CaV channels, and use case studies to describe the development of ion channel-modulating drugs from natural sources for the treatment of pain, heart disease and autoimmune diseases.
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Affiliation(s)
- Saumya Bajaj
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Experimental Medicine Building, 59 Nanyang Drive, 636921, Singapore.
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15
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Rahi P, Vaishampayan P. Editorial: MALDI-TOF MS Application in Microbial Ecology Studies. Front Microbiol 2020; 10:2954. [PMID: 31998259 PMCID: PMC6966959 DOI: 10.3389/fmicb.2019.02954] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 12/09/2019] [Indexed: 12/11/2022] Open
Affiliation(s)
- Praveen Rahi
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Parag Vaishampayan
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
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