1
|
Huang KH, Morato NM, Feng Y, Cooks RG. High-Throughput Diversification of Complex Bioactive Molecules by Accelerated Synthesis in Microdroplets. Angew Chem Int Ed Engl 2023; 62:e202300956. [PMID: 36941213 PMCID: PMC10182919 DOI: 10.1002/anie.202300956] [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: 01/18/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 03/23/2023]
Abstract
Late-stage diversification of drug molecules is an important strategy in drug discovery that can be facilitated by reaction screening using high-throughput experimentation. Here we present a rapid method for functionalizing bioactive molecules based on accelerated reactions in microdroplets. Reaction mixtures are nebulized at throughputs better than 1 reaction/second and the accelerated reactions occurring in the microdroplets are followed by desorption electrospray ionization mass spectrometry (DESI-MS). Because the accelerated reactions occur on the millisecond timescale, they allow an overall screening throughput of 1 Hz working at the low nanogram scale. Using this approach, an opioid agonist (PZM21) and an antagonist (naloxone) were diversified using three reactions important in medicinal chemistry: sulfur fluoride exchange (SuFEx) click reactions, imine formation reactions, and ene-type click reactions. Some 269 functionalized analogs of naloxone and PZM21 were generated and characterized by tandem mass spectrometry (MS/MS) after screening over 500 reactions.
Collapse
Affiliation(s)
- Kai-Hung Huang
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Nicolás M Morato
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Yunfei Feng
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - R Graham Cooks
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| |
Collapse
|
2
|
Morato NM, Brown HM, Garcia D, Middlebrooks EH, Jentoft M, Chaichana K, Quiñones-Hinojosa A, Cooks RG. High-throughput analysis of tissue microarrays using automated desorption electrospray ionization mass spectrometry. Sci Rep 2022; 12:18851. [PMID: 36344609 PMCID: PMC9640715 DOI: 10.1038/s41598-022-22924-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/20/2022] [Indexed: 11/09/2022] Open
Abstract
Tissue microarrays (TMAs) are commonly used for the rapid analysis of large numbers of tissue samples, often in morphological assessments but increasingly in spectroscopic analysis, where specific molecular markers are targeted via immunostaining. Here we report the use of an automated high-throughput system based on desorption electrospray ionization (DESI) mass spectrometry (MS) for the rapid generation and online analysis of high-density (6144 samples/array) TMAs, at rates better than 1 sample/second. Direct open-air analysis of tissue samples (hundreds of nanograms) not subjected to prior preparation, plus the ability to provide molecular characterization by tandem mass spectrometry (MS/MS), make this experiment versatile and applicable to both targeted and untargeted analysis in a label-free manner. These capabilities are demonstrated in a proof-of-concept study of frozen brain tissue biopsies where we showcase (i) a targeted MS/MS application aimed at identification of isocitrate dehydrogenase mutation in glioma samples and (ii) an untargeted MS tissue type classification using lipid profiles and correlation with tumor cell percentage estimates from histopathology. The small sample sizes and large sample numbers accessible with this methodology make for a powerful analytical system that facilitates the identification of molecular markers for later use in intraoperative applications to guide precision surgeries and ultimately improve patient outcomes.
Collapse
Affiliation(s)
- Nicolás M. Morato
- grid.169077.e0000 0004 1937 2197Department of Chemistry, Purdue Center for Cancer Research, and Bindley Bioscience Center, Purdue University, 560 Oval Drive, West Lafayette, IN 47907 USA
| | - Hannah Marie Brown
- grid.169077.e0000 0004 1937 2197Department of Chemistry, Purdue Center for Cancer Research, and Bindley Bioscience Center, Purdue University, 560 Oval Drive, West Lafayette, IN 47907 USA ,grid.4367.60000 0001 2355 7002Present Address: Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO USA
| | - Diogo Garcia
- grid.417467.70000 0004 0443 9942Department of Neurosurgery, Mayo Clinic, Jacksonville, FL USA
| | - Erik H. Middlebrooks
- grid.417467.70000 0004 0443 9942Department of Neurosurgery, Mayo Clinic, Jacksonville, FL USA ,grid.417467.70000 0004 0443 9942Department of Radiology, Mayo Clinic, Jacksonville, FL USA
| | - Mark Jentoft
- grid.417467.70000 0004 0443 9942Department of Laboratory Medicine and Pathology, Mayo Clinic, Jacksonville, FL USA
| | - Kaisorn Chaichana
- grid.417467.70000 0004 0443 9942Department of Neurosurgery, Mayo Clinic, Jacksonville, FL USA
| | | | - R. Graham Cooks
- grid.169077.e0000 0004 1937 2197Department of Chemistry, Purdue Center for Cancer Research, and Bindley Bioscience Center, Purdue University, 560 Oval Drive, West Lafayette, IN 47907 USA
| |
Collapse
|
3
|
Biyani SA, Lytle C, Hyun SH, McGuire MA, Pendyala R, Thompson DH. Development of a Continuous Flow Synthesis of Lorazepam. Org Process Res Dev 2022. [DOI: 10.1021/acs.oprd.2c00184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shruti A. Biyani
- Department of Chemistry, Multi-disciplinary Cancer Research Facility, Purdue University, Bindley Bioscience Center, 1203 West State Street, West Lafayette, Indiana 47907, United States
| | - Corryn Lytle
- School of Chemical Engineering, Purdue University, 480 West Stadium Avenue, West Lafayette, Indiana 47907, United States
| | - Seok-Hee Hyun
- Continuity Pharma, LLC, West Lafayette, Indiana 47907, United States
| | | | - Ranya Pendyala
- The Weldon School of Biomedical Engineering, Purdue University, 206 South Martin Jischke Drive, West Lafayette, Indiana 47907, United States
| | - David H. Thompson
- Department of Chemistry, Multi-disciplinary Cancer Research Facility, Purdue University, Bindley Bioscience Center, 1203 West State Street, West Lafayette, Indiana 47907, United States
| |
Collapse
|
4
|
Murbach-Oliveira G, Banerjee K, Nociari MM, Thompson DH. Continuous Flow Synthesis of A2E Guided by Design of Experiments and High-Throughput Studies. ACS BIO & MED CHEM AU 2022; 2:297-306. [PMID: 37101569 PMCID: PMC10114832 DOI: 10.1021/acsbiomedchemau.1c00060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
N-Retinylidene-N-retinylethanolamine (A2E) is the most studied lipid bisretinoid. It forms lipofuscin deposits in the retinal pigment epithelium (RPE), causing vision impairment and blindness in eye conditions, such as Stargardt's disease, cone-rod dystrophy, Best's macular dystrophy, and potentially age-related macular degeneration. Synthetic A2E is often used for inducing the accumulation of lipofuscins within the lysosomes of RPE cells in culture as an in vitro surrogate of retinal lipofuscin buildup, providing insights into the mechanisms of these eye conditions. Many reports describing the use of synthetic A2E employ material that has been prepared using a one-pot reaction of all-trans-retinal (ATR) and ethanolamine at room temperature for 48 h. We have revisited this synthesis by performing a design of experiments (DoE) and high-throughput experimentation workflow that was tailored to identify the most productive combination of the variables (temperature, solvent, and reagent equivalences) for optimization of A2E yield. Our DoE findings revealed that the interaction of ethanolamine with acetic acid and ATR was pivotal for the formation of A2E in high yield, indicating that imine formation is the critical step in the reaction. Armed with these results, we were able to optimize the method using a microfluidic reactor system before upscaling those conditions for continuous flow synthesis of A2E. This revised method enabled a more efficient production of material, from a reaction time of 48 h to a residence time of 33 min, with an accompanying yield improvement from 49 to 78%. Furthermore, we implemented a simple method to evaluate the quality of the A2E produced using optical spectroscopy and LC-MS characteristics to assure that the biological properties observed with A2E samples are not confounded by the presence of oxidized impurities that are commonly present in conventional A2E samples.
Collapse
Affiliation(s)
- Giulia Murbach-Oliveira
- Department
of Chemistry, Multidisciplinary Cancer Research Facility, Purdue University, West Lafayette, Indiana 47907, United States
| | - Kalpita Banerjee
- Weil
Cornell Medical College, Ophthalmology Department, Dyson Research Institute, 1300 York Avenue, New York, New York 10065, United
States
| | - Marcelo M. Nociari
- Weil
Cornell Medical College, Ophthalmology Department, Dyson Research Institute, 1300 York Avenue, New York, New York 10065, United
States
| | - David H. Thompson
- Department
of Chemistry, Multidisciplinary Cancer Research Facility, Purdue University, West Lafayette, Indiana 47907, United States
| |
Collapse
|
5
|
Qiu L, Morato NM, Huang KH, Cooks RG. Spontaneous Water Radical Cation Oxidation at Double Bonds in Microdroplets. Front Chem 2022; 10:903774. [PMID: 35559217 PMCID: PMC9086510 DOI: 10.3389/fchem.2022.903774] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/11/2022] [Indexed: 12/20/2022] Open
Abstract
Spontaneous oxidation of compounds containing diverse X=Y moieties (e.g., sulfonamides, ketones, esters, sulfones) occurs readily in organic-solvent microdroplets. This surprising phenomenon is proposed to be driven by the generation of an intermediate species [M+H2O]+·: a covalent adduct of water radical cation (H2O+·) with the reactant molecule (M). The adduct is observed in the positive ion mass spectrum while its formation in the interfacial region of the microdroplet (i.e., at the air-droplet interface) is indicated by the strong dependence of the oxidation product formation on the spray distance (which reflects the droplet size and consequently the surface-to-volume ratio) and the solvent composition. Importantly, based on the screening of a ca. 21,000-compound library and the detailed consideration of six functional groups, the formation of a molecular adduct with the water radical cation is a significant route to ionization in positive ion mode electrospray, where it is favored in those compounds with X=Y moieties which lack basic groups. A set of model monofunctional systems was studied and in one case, benzyl benzoate, evidence was found for oxidation driven by hydroxyl radical adduct formation followed by protonation in addition to the dominant water radical cation addition process. Significant implications of molecular ionization by water radical cations for oxidation processes in atmospheric aerosols, analytical mass spectrometry and small-scale synthesis are noted.
Collapse
|
6
|
Palem RR, Shimoga G, Kim SY, Bathula C, Ghodake GS, Lee SH. Biogenic palladium nanoparticles: An effectual environmental benign catalyst for organic coupling reactions. J IND ENG CHEM 2022. [DOI: 10.1016/j.jiec.2021.11.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|
7
|
Abe Y, Emori K. Application of a Statistical Approach to Process Development of Futibatinib by Employing Quality-by-Design Principles. Part 1: Identification of Critical Process Parameters for Impurities. Org Process Res Dev 2022. [DOI: 10.1021/acs.oprd.1c00145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yasunori Abe
- Chemical Technology Laboratory, CMC Division, Taiho Pharmaceutical Co., Ltd., 200-22 Motohara, Kamikawa-machi, Kodama-gun, Saitama 367-0241, Japan
| | - Kosuke Emori
- Chemical Technology Laboratory, CMC Division, Taiho Pharmaceutical Co., Ltd., 200-22 Motohara, Kamikawa-machi, Kodama-gun, Saitama 367-0241, Japan
| |
Collapse
|
8
|
SOMOphilic Alkynylation of Unreactive Alkenes Enabled by Iron-Catalyzed Hydrogen Atom Transfer. Molecules 2021; 27:molecules27010033. [PMID: 35011265 PMCID: PMC8746543 DOI: 10.3390/molecules27010033] [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: 12/02/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022] Open
Abstract
We report an efficient and practical iron-catalyzed hydrogen atom transfer protocol for assembling acetylenic motifs into functional alkenes. Diversities of internal alkynes could be obtained from readily available alkenes and acetylenic sulfones with excellent Markovnikov selectivity. An iron hydride hydrogen atom transfer catalytic cycle was described to clarify the mechanism of this reaction.
Collapse
|
9
|
Overhoff B, Falls Z, Mangione W, Samudrala R. A Deep-Learning Proteomic-Scale Approach for Drug Design. Pharmaceuticals (Basel) 2021; 14:1277. [PMID: 34959678 PMCID: PMC8709297 DOI: 10.3390/ph14121277] [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: 09/24/2021] [Revised: 11/27/2021] [Accepted: 11/29/2021] [Indexed: 12/26/2022] Open
Abstract
Computational approaches have accelerated novel therapeutic discovery in recent decades. The Computational Analysis of Novel Drug Opportunities (CANDO) platform for shotgun multitarget therapeutic discovery, repurposing, and design aims to improve their efficacy and safety by employing a holistic approach that computes interaction signatures between every drug/compound and a large library of non-redundant protein structures corresponding to the human proteome fold space. These signatures are compared and analyzed to determine if a given drug/compound is efficacious and safe for a given indication/disease. In this study, we used a deep learning-based autoencoder to first reduce the dimensionality of CANDO-computed drug-proteome interaction signatures. We then employed a reduced conditional variational autoencoder to generate novel drug-like compounds when given a target encoded "objective" signature. Using this approach, we designed compounds to recreate the interaction signatures for twenty approved and experimental drugs and showed that 16/20 designed compounds were predicted to be significantly (p-value ≤ 0.05) more behaviorally similar relative to all corresponding controls, and 20/20 were predicted to be more behaviorally similar relative to a random control. We further observed that redesigns of objectives developed via rational drug design performed significantly better than those derived from natural sources (p-value ≤ 0.05), suggesting that the model learned an abstraction of rational drug design. We also show that the designed compounds are structurally diverse and synthetically feasible when compared to their respective objective drugs despite consistently high predicted behavioral similarity. Finally, we generated new designs that enhanced thirteen drugs/compounds associated with non-small cell lung cancer and anti-aging properties using their predicted proteomic interaction signatures. his study represents a significant step forward in automating holistic therapeutic design with machine learning, enabling the rapid generation of novel, effective, and safe drug leads for any indication.
Collapse
Affiliation(s)
| | | | | | - Ram Samudrala
- Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY 14203, USA; (B.O.); (Z.F.); (W.M.)
| |
Collapse
|
10
|
Inter-platform assessment of performance of high-throughput desorption electrospray ionization mass spectrometry. TALANTA OPEN 2021. [DOI: 10.1016/j.talo.2021.100046] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
|
11
|
Continuous Flow Synthesis of Anticancer Drugs. Molecules 2021; 26:molecules26226992. [PMID: 34834084 PMCID: PMC8625794 DOI: 10.3390/molecules26226992] [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: 11/03/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 12/27/2022] Open
Abstract
Continuous flow chemistry is by now an established and valued synthesis technology regularly exploited in academic and industrial laboratories to bring about the improved preparation of a variety of molecular structures. Benefits such as better heat and mass transfer, improved process control and safety, a small equipment footprint, as well as the ability to integrate in-line analysis and purification tools into telescoped sequences are often cited when comparing flow to analogous batch processes. In this short review, the latest developments regarding the exploitation of continuous flow protocols towards the synthesis of anticancer drugs are evaluated. Our efforts focus predominately on the period of 2016-2021 and highlight key case studies where either the final active pharmaceutical ingredient (API) or its building blocks were produced continuously. It is hoped that this manuscript will serve as a useful synopsis showcasing the impact of continuous flow chemistry towards the generation of important anticancer drugs.
Collapse
|
12
|
Morato NM, Le MT, Holden DT, Graham Cooks R. Automated High-Throughput System Combining Small-Scale Synthesis with Bioassays and Reaction Screening. SLAS Technol 2021; 26:555-571. [PMID: 34697962 DOI: 10.1177/24726303211047839] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The Purdue Make It system is a unique automated platform capable of small-scale in situ synthesis, screening small-molecule reactions, and performing direct label-free bioassays. The platform is based on desorption electrospray ionization (DESI), an ambient ionization method that allows for minimal sample workup and is capable of accelerating reactions in secondary droplets, thus conferring unique advantages compared with other high-throughput screening technologies. By combining DESI with liquid handling robotics, the system achieves throughputs of more than 1 sample/s, handling up to 6144 samples in a single run. As little as 100 fmol/spot of analyte is required to perform both initial analysis by mass spectrometry (MS) and further MSn structural characterization. The data obtained are processed using custom software so that results are easily visualized as interactive heatmaps of reaction plates based on the peak intensities of m/z values of interest. In this paper, we review the system's capabilities as described in previous publications and demonstrate its utilization in two new high-throughput campaigns: (1) the screening of 188 unique combinatorial reactions (24 reaction types, 188 unique reaction mixtures) to determine reactivity trends and (2) label-free studies of the nicotinamide N-methyltransferase enzyme directly from the bioassay buffer. The system's versatility holds promise for several future directions, including the collection of secondary droplets containing the products from successful reaction screening measurements, the development of machine learning algorithms using data collected from compound library screening, and the adaption of a variety of relevant bioassays to high-throughput MS.
Collapse
Affiliation(s)
- Nicolás M Morato
- Department of Chemistry and Center for Analytical Instrumentation Development, Purdue University, West Lafayette, IN, USA
| | - MyPhuong T Le
- Department of Chemistry and Center for Analytical Instrumentation Development, Purdue University, West Lafayette, IN, USA
| | - Dylan T Holden
- Department of Chemistry and Center for Analytical Instrumentation Development, Purdue University, West Lafayette, IN, USA
| | - R Graham Cooks
- Department of Chemistry and Center for Analytical Instrumentation Development, Purdue University, West Lafayette, IN, USA
| |
Collapse
|
13
|
Suseelan Sarala A, Bhowmick S, Carvalho RL, Al‐Thabaiti SA, Mokhtar M, Silva Júnior EN, Maiti D. Transition‐Metal‐Catalyzed Selective Alkynylation of C−H Bonds. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202100992] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Anjana Suseelan Sarala
- Department of Chemistry Indian Institute of Technology Bombay Powai 400076 Mumbai India
- Department of Chemistry Saarland University 66123 Saarbrucken Germany
| | - Suman Bhowmick
- Department of Chemistry Indian Institute of Technology Bombay Powai 400076 Mumbai India
| | - Renato L. Carvalho
- Department of Chemistry Federal University of Minas Gerais 31270-901 Belo Horizonte MG Brazil
| | | | - Mohamed Mokhtar
- Chemistry Department Faculty of Science King Abdulaziz University 21589 Jeddah Saudi Arabia
| | | | - Debabrata Maiti
- Department of Chemistry Indian Institute of Technology Bombay Powai 400076 Mumbai India
| |
Collapse
|