1
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Tom G, Schmid SP, Baird SG, Cao Y, Darvish K, Hao H, Lo S, Pablo-García S, Rajaonson EM, Skreta M, Yoshikawa N, Corapi S, Akkoc GD, Strieth-Kalthoff F, Seifrid M, Aspuru-Guzik A. Self-Driving Laboratories for Chemistry and Materials Science. Chem Rev 2024; 124:9633-9732. [PMID: 39137296 PMCID: PMC11363023 DOI: 10.1021/acs.chemrev.4c00055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
Self-driving laboratories (SDLs) promise an accelerated application of the scientific method. Through the automation of experimental workflows, along with autonomous experimental planning, SDLs hold the potential to greatly accelerate research in chemistry and materials discovery. This review provides an in-depth analysis of the state-of-the-art in SDL technology, its applications across various scientific disciplines, and the potential implications for research and industry. This review additionally provides an overview of the enabling technologies for SDLs, including their hardware, software, and integration with laboratory infrastructure. Most importantly, this review explores the diverse range of scientific domains where SDLs have made significant contributions, from drug discovery and materials science to genomics and chemistry. We provide a comprehensive review of existing real-world examples of SDLs, their different levels of automation, and the challenges and limitations associated with each domain.
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Affiliation(s)
- Gary Tom
- Department
of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H6, Canada
- Department
of Computer Science, University of Toronto, 40 St. George St, Toronto, Ontario M5S 2E4, Canada
- Vector Institute
for Artificial Intelligence, 661 University Ave Suite 710, Toronto, Ontario M5G 1M1, Canada
| | - Stefan P. Schmid
- Department
of Chemistry and Applied Biosciences, ETH
Zurich, Vladimir-Prelog-Weg 1, CH-8093 Zurich, Switzerland
| | - Sterling G. Baird
- Acceleration
Consortium, 80 St. George
St, Toronto, Ontario M5S 3H6, Canada
| | - Yang Cao
- Department
of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H6, Canada
- Department
of Computer Science, University of Toronto, 40 St. George St, Toronto, Ontario M5S 2E4, Canada
- Acceleration
Consortium, 80 St. George
St, Toronto, Ontario M5S 3H6, Canada
| | - Kourosh Darvish
- Department
of Computer Science, University of Toronto, 40 St. George St, Toronto, Ontario M5S 2E4, Canada
- Vector Institute
for Artificial Intelligence, 661 University Ave Suite 710, Toronto, Ontario M5G 1M1, Canada
- Acceleration
Consortium, 80 St. George
St, Toronto, Ontario M5S 3H6, Canada
| | - Han Hao
- Department
of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H6, Canada
- Department
of Computer Science, University of Toronto, 40 St. George St, Toronto, Ontario M5S 2E4, Canada
- Acceleration
Consortium, 80 St. George
St, Toronto, Ontario M5S 3H6, Canada
| | - Stanley Lo
- Department
of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H6, Canada
| | - Sergio Pablo-García
- Department
of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H6, Canada
- Department
of Computer Science, University of Toronto, 40 St. George St, Toronto, Ontario M5S 2E4, Canada
| | - Ella M. Rajaonson
- Department
of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H6, Canada
- Vector Institute
for Artificial Intelligence, 661 University Ave Suite 710, Toronto, Ontario M5G 1M1, Canada
| | - Marta Skreta
- Department
of Computer Science, University of Toronto, 40 St. George St, Toronto, Ontario M5S 2E4, Canada
- Vector Institute
for Artificial Intelligence, 661 University Ave Suite 710, Toronto, Ontario M5G 1M1, Canada
| | - Naruki Yoshikawa
- Department
of Computer Science, University of Toronto, 40 St. George St, Toronto, Ontario M5S 2E4, Canada
- Vector Institute
for Artificial Intelligence, 661 University Ave Suite 710, Toronto, Ontario M5G 1M1, Canada
| | - Samantha Corapi
- Department
of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H6, Canada
| | - Gun Deniz Akkoc
- Forschungszentrum
Jülich GmbH, Helmholtz Institute
for Renewable Energy Erlangen-Nürnberg, Cauerstr. 1, 91058 Erlangen, Germany
- Department
of Chemical and Biological Engineering, Friedrich-Alexander Universität Erlangen-Nürnberg, Egerlandstr. 3, 91058 Erlangen, Germany
| | - Felix Strieth-Kalthoff
- Department
of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H6, Canada
- Department
of Computer Science, University of Toronto, 40 St. George St, Toronto, Ontario M5S 2E4, Canada
- School of
Mathematics and Natural Sciences, University
of Wuppertal, Gaußstraße
20, 42119 Wuppertal, Germany
| | - Martin Seifrid
- Department
of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H6, Canada
- Department
of Computer Science, University of Toronto, 40 St. George St, Toronto, Ontario M5S 2E4, Canada
- Department
of Materials Science and Engineering, North
Carolina State University, Raleigh, North Carolina 27695, United States of America
| | - Alán Aspuru-Guzik
- Department
of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario M5S 3H6, Canada
- Department
of Computer Science, University of Toronto, 40 St. George St, Toronto, Ontario M5S 2E4, Canada
- Vector Institute
for Artificial Intelligence, 661 University Ave Suite 710, Toronto, Ontario M5G 1M1, Canada
- Acceleration
Consortium, 80 St. George
St, Toronto, Ontario M5S 3H6, Canada
- Department
of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
- Department
of Materials Science & Engineering, University of Toronto, Toronto, Ontario M5S 3E4, Canada
- Lebovic
Fellow, Canadian Institute for Advanced
Research (CIFAR), 661
University Ave, Toronto, Ontario M5G 1M1, Canada
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2
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Mahoney MW, Helander J, Kooner AS, Norman M, Damalanka VC, De Bona P, Kasperkiewicz P, Rut W, Poreba M, Kashipathy MM, Battaile KP, Lovell S, O'Donoghue AJ, Craik CS, Drag M, Janetka JW. Use of protease substrate specificity screening in the rational design of selective protease inhibitors with unnatural amino acids: Application to HGFA, matriptase, and hepsin. Protein Sci 2024; 33:e5110. [PMID: 39073183 PMCID: PMC11284329 DOI: 10.1002/pro.5110] [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: 02/21/2024] [Revised: 05/22/2024] [Accepted: 06/26/2024] [Indexed: 07/30/2024]
Abstract
Inhibition of the proteolytic processing of hepatocyte growth factor (HGF) and macrophage stimulating protein (MSP) is an attractive approach for the drug discovery of novel anticancer therapeutics which prevent tumor progression and metastasis. Here, we utilized an improved and expanded version of positional scanning of substrate combinatorial libraries (PS-SCL) technique called HyCoSuL to optimize peptidomimetic inhibitors of the HGF/MSP activating serine proteases, HGFA, matriptase, and hepsin. These inhibitors have an electrophilic ketone serine trapping warhead and thus form a reversible covalent bond to the protease. We demonstrate that by varying the P2, P3, and P4 positions of the inhibitor with unnatural amino acids based on the protease substrate preferences learned from HyCoSuL, we can predictably modify the potency and selectivity of the inhibitor. We identified the tetrapeptide JH-1144 (8) as a single digit nM inhibitor of HGFA, matriptase and hepsin with excellent selectivity over Factor Xa and thrombin. These unnatural peptides have increased metabolic stability relative to natural peptides of similar structure. The tripeptide inhibitor PK-1-89 (2) has excellent pharmacokinetics in mice with good compound exposure out to 24 h. In addition, we obtained an X-ray structure of the inhibitor MM1132 (15) bound to matriptase revealing an interesting binding conformation useful for future inhibitor design.
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Affiliation(s)
- Matthew W. Mahoney
- Department of Biochemistry and Molecular BiophysicsWashington University School of MedicineSaint LouisMissouriUSA
| | - Jonathan Helander
- Department of Biochemistry and Molecular BiophysicsWashington University School of MedicineSaint LouisMissouriUSA
| | - Anoopjit S. Kooner
- Department of Biochemistry and Molecular BiophysicsWashington University School of MedicineSaint LouisMissouriUSA
| | - Mariah Norman
- Department of Biochemistry and Molecular BiophysicsWashington University School of MedicineSaint LouisMissouriUSA
| | - Vishnu C. Damalanka
- Department of Biochemistry and Molecular BiophysicsWashington University School of MedicineSaint LouisMissouriUSA
| | - Paolo De Bona
- Department of Biochemistry and Molecular BiophysicsWashington University School of MedicineSaint LouisMissouriUSA
| | - Paulina Kasperkiewicz
- Division of Chemical Biology and Bioimaging, Department of ChemistryWroclaw University of Science and TechnologyWroclawPoland
| | - Wioletta Rut
- Division of Chemical Biology and Bioimaging, Department of ChemistryWroclaw University of Science and TechnologyWroclawPoland
| | - Marcin Poreba
- Division of Chemical Biology and Bioimaging, Department of ChemistryWroclaw University of Science and TechnologyWroclawPoland
| | - Maithri M. Kashipathy
- Protein Structure Laboratory, Del Shankel Structural Biology Center, University of KansasLawrenceKansasUSA
| | | | - Scott Lovell
- Protein Structure Laboratory, Del Shankel Structural Biology Center, University of KansasLawrenceKansasUSA
| | - Anthony J. O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of CaliforniaSan DiegoCaliforniaUSA
| | - Charles S. Craik
- Department of Pharmaceutical ChemistryUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Marcin Drag
- Division of Chemical Biology and Bioimaging, Department of ChemistryWroclaw University of Science and TechnologyWroclawPoland
| | - James W. Janetka
- Department of Biochemistry and Molecular BiophysicsWashington University School of MedicineSaint LouisMissouriUSA
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3
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Mohamadighader N, Zivari-Moshfegh F, Nematollahi D. Electrochemical generation of phenothiazin-5-ium. A sustainable strategy for the synthesis of new bis(phenylsulfonyl)-10H-phenothiazine derivatives. Sci Rep 2024; 14:4276. [PMID: 38383682 PMCID: PMC10881970 DOI: 10.1038/s41598-024-53620-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/02/2024] [Indexed: 02/23/2024] Open
Abstract
In this work, the electrochemical generation of phenothiazin-5-ium (PTZox) from the direct oxidation of phenothiazine (PTZ) in a water/acetonitrile mixture using a commercial carbon anode and conventional stainless steel cathode is reported. PTZox is a reactive intermediate with high potential synthetic applications, which is used in this paper for the synthesis of new phenothiazine derivatives. In this work a novel and simple electrochemical methodology for the synthesis of some bis(phenylsulfonyl)-10H-phenothiazine derivatives was established. In this paper, a mechanism for PTZ oxidation in the presence of arylsulfinic acids has been proposed based on the results obtained from voltammetric and coulometric experiments as well as spectroscopic data of the products. These syntheses are performed in a simple cell by applying constant current under mild conditions and at room temperature with high atom economy.
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Affiliation(s)
- Niloofar Mohamadighader
- Faculty of Chemistry and Petroleum Sciences, Bu-Ali-Sina University, Hamedan, 65174-38683, Iran
| | - Faezeh Zivari-Moshfegh
- Faculty of Chemistry and Petroleum Sciences, Bu-Ali-Sina University, Hamedan, 65174-38683, Iran
| | - Davood Nematollahi
- Faculty of Chemistry and Petroleum Sciences, Bu-Ali-Sina University, Hamedan, 65174-38683, Iran.
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4
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Santa Maria JP, Wang Y, Camargo LM. Perspective on the challenges and opportunities of accelerating drug discovery with artificial intelligence. FRONTIERS IN BIOINFORMATICS 2023; 3:1121591. [PMID: 36909937 PMCID: PMC9997711 DOI: 10.3389/fbinf.2023.1121591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/06/2023] [Indexed: 02/25/2023] Open
Affiliation(s)
- John P Santa Maria
- Data and Translational Sciences, UCB Biosciences Inc., Cambridge, MA, United States
| | - Yuan Wang
- Data and Translational Sciences, UCB Biosciences Inc., Cambridge, MA, United States
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5
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Zhang K, Liu XF, Zhang WZ, Ren WM, Lu XB. Electrocarboxylation of N-Acylimines with Carbon Dioxide: Access to Substituted α-Amino Acids. Org Lett 2022; 24:3565-3569. [DOI: 10.1021/acs.orglett.2c01267] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ke Zhang
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, PR China
| | - Xiao-Fei Liu
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, PR China
| | - Wen-Zhen Zhang
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, PR China
| | - Wei-Min Ren
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, PR China
| | - Xiao-Bing Lu
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, PR China
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6
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Belitškin D, Pant SM, Munne P, Suleymanova I, Belitškina K, Hongisto HA, Englund J, Raatikainen T, Klezovitch O, Vasioukhin V, Li S, Wu Q, Monni O, Kuure S, Laakkonen P, Pouwels J, Tervonen TA, Klefström J. Hepsin regulates TGFβ signaling via fibronectin proteolysis. EMBO Rep 2021; 22:e52532. [PMID: 34515392 PMCID: PMC8567232 DOI: 10.15252/embr.202152532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 08/04/2021] [Accepted: 08/10/2021] [Indexed: 01/17/2023] Open
Abstract
Transforming growth factor‐beta (TGFβ) is a multifunctional cytokine with a well‐established role in mammary gland development and both oncogenic and tumor‐suppressive functions. The extracellular matrix (ECM) indirectly regulates TGFβ activity by acting as a storage compartment of latent‐TGFβ, but how TGFβ is released from the ECM via proteolytic mechanisms remains largely unknown. In this study, we demonstrate that hepsin, a type II transmembrane protease overexpressed in 70% of breast tumors, promotes canonical TGFβ signaling through the release of latent‐TGFβ from the ECM storage compartment. Mammary glands in hepsin CRISPR knockout mice showed reduced TGFβ signaling and increased epithelial branching, accompanied by increased levels of fibronectin and latent‐TGFβ1, while overexpression of hepsin in mammary tumors increased TGFβ signaling. Cell‐free and cell‐based experiments showed that hepsin is capable of direct proteolytic cleavage of fibronectin but not latent‐TGFβ and, importantly, that the ability of hepsin to activate TGFβ signaling is dependent on fibronectin. Altogether, this study demonstrates a role for hepsin as a regulator of the TGFβ pathway in the mammary gland via a novel mechanism involving proteolytic downmodulation of fibronectin.
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Affiliation(s)
- Denis Belitškin
- Research Programs Unit/Translational Cancer Medicine Research Program and Medicum, Faculty of Medicine, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
| | - Shishir M Pant
- Research Programs Unit/Translational Cancer Medicine Research Program and Medicum, Faculty of Medicine, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
| | - Pauliina Munne
- Research Programs Unit/Translational Cancer Medicine Research Program and Medicum, Faculty of Medicine, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
| | - Ilida Suleymanova
- Research Programs Unit/Translational Cancer Medicine Research Program and Medicum, Faculty of Medicine, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
| | - Kati Belitškina
- Pathology Department, North Estonia Medical Centre, Tallinn, Estonia
| | - Hanna-Ala Hongisto
- Research Programs Unit/Translational Cancer Medicine Research Program and Medicum, Faculty of Medicine, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
| | - Johanna Englund
- Research Programs Unit/Translational Cancer Medicine Research Program and Medicum, Faculty of Medicine, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
| | - Tiina Raatikainen
- Research Programs Unit/Translational Cancer Medicine Research Program and Medicum, Faculty of Medicine, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
| | - Olga Klezovitch
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Valeri Vasioukhin
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Shuo Li
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Qingyu Wu
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Outi Monni
- Research Programs Unit/Applied Tumor Genomics Research Program, Faculty of Medicine, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
| | - Satu Kuure
- GM-Unit, Laboratory Animal Centre, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Pirjo Laakkonen
- Laboratory Animal Center, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Jeroen Pouwels
- Research Programs Unit/Translational Cancer Medicine Research Program and Medicum, Faculty of Medicine, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
| | - Topi A Tervonen
- Research Programs Unit/Translational Cancer Medicine Research Program and Medicum, Faculty of Medicine, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
| | - Juha Klefström
- Research Programs Unit/Translational Cancer Medicine Research Program and Medicum, Faculty of Medicine, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland.,Finnish Cancer Institute & FICAN South, Helsinki University Hospital (HUS), Helsinki, Finland
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7
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Grisoni F, Huisman BJH, Button AL, Moret M, Atz K, Merk D, Schneider G. Combining generative artificial intelligence and on-chip synthesis for de novo drug design. SCIENCE ADVANCES 2021; 7:eabg3338. [PMID: 34117066 PMCID: PMC8195470 DOI: 10.1126/sciadv.abg3338] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 04/23/2021] [Indexed: 05/24/2023]
Abstract
Automating the molecular design-make-test-analyze cycle accelerates hit and lead finding for drug discovery. Using deep learning for molecular design and a microfluidics platform for on-chip chemical synthesis, liver X receptor (LXR) agonists were generated from scratch. The computational pipeline was tuned to explore the chemical space of known LXRα agonists and generate novel molecular candidates. To ensure compatibility with automated on-chip synthesis, the chemical space was confined to the virtual products obtainable from 17 one-step reactions. Twenty-five de novo designs were successfully synthesized in flow. In vitro screening of the crude reaction products revealed 17 (68%) hits, with up to 60-fold LXR activation. The batch resynthesis, purification, and retesting of 14 of these compounds confirmed that 12 of them were potent LXR agonists. These results support the suitability of the proposed design-make-test-analyze framework as a blueprint for automated drug design with artificial intelligence and miniaturized bench-top synthesis.
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Affiliation(s)
- Francesca Grisoni
- ETH Zurich, Department of Chemistry and Applied Biosciences, RETHINK, Zurich, Switzerland.
- Eindhoven University of Technology, Department of Biomedical Engineering, Eindhoven, Netherlands
| | - Berend J H Huisman
- ETH Zurich, Department of Chemistry and Applied Biosciences, RETHINK, Zurich, Switzerland
| | - Alexander L Button
- ETH Zurich, Department of Chemistry and Applied Biosciences, RETHINK, Zurich, Switzerland
- University of Lausanne, Department of Computational Biology, Lausanne, Switzerland
| | - Michael Moret
- ETH Zurich, Department of Chemistry and Applied Biosciences, RETHINK, Zurich, Switzerland
| | - Kenneth Atz
- ETH Zurich, Department of Chemistry and Applied Biosciences, RETHINK, Zurich, Switzerland
| | - Daniel Merk
- ETH Zurich, Department of Chemistry and Applied Biosciences, RETHINK, Zurich, Switzerland.
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, Frankfurt, Germany
| | - Gisbert Schneider
- ETH Zurich, Department of Chemistry and Applied Biosciences, RETHINK, Zurich, Switzerland.
- ETH Singapore SEC Ltd, Singapore, Singapore
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8
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Li S, Wang L, Sun S, Wu Q. Hepsin: a multifunctional transmembrane serine protease in pathobiology. FEBS J 2020; 288:5252-5264. [PMID: 33300264 DOI: 10.1111/febs.15663] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/30/2020] [Accepted: 12/07/2020] [Indexed: 12/14/2022]
Abstract
Cell membrane-bound serine proteases are important in the maintenance of physiological homeostasis. Hepsin is a type II transmembrane serine protease highly expressed in the liver. Recent studies indicate that hepsin activates prohepatocyte growth factor in the liver to enhance Met signaling, thereby regulating glucose, lipid, and protein metabolism. In addition, hepsin functions in nonhepatic tissues, including the adipose tissue, kidney, and inner ear, to regulate adipocyte differentiation, urinary protein processing, and auditory function, respectively. In mouse models, hepsin deficiency lowers blood glucose, lipid, and protein levels, impairs uromodulin assembly in renal epithelial cells, and causes hearing loss. Elevated hepsin expression has also been found in many cancers. As a type II transmembrane protease, cell surface expression and zymogen activation are essential for hepsin activity. In this review, we discuss the current knowledge regarding hepsin biosynthesis, activation, and functions in pathobiology.
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Affiliation(s)
- Shuo Li
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, OH, USA
| | - Lina Wang
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Prevention, Soochow University, Suzhou, China
| | - Shijin Sun
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Prevention, Soochow University, Suzhou, China
| | - Qingyu Wu
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, OH, USA.,Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Prevention, Soochow University, Suzhou, China
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9
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Kwon H, Ha H, Jeon H, Jang J, Son SH, Lee K, Park SK, Byun Y. Structure-activity relationship studies of dipeptide-based hepsin inhibitors with Arg bioisosteres. Bioorg Chem 2020; 107:104521. [PMID: 33334587 DOI: 10.1016/j.bioorg.2020.104521] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 02/09/2023]
Abstract
Hepsin is a type II transmembrane serine protease (TTSP) associated with cell proliferation and overexpressed in several types of cancer including prostate cancer (PCa). Because of its significant role in cancer progression and metastasis, hepsin is an attractive protein as a potential therapeutic and diagnostic biomarker for PCa. Based on the reported Leu-Arg dipeptide-based hepsin inhibitors, we performed structural modification and determined in vitro hepsin- and matriptase-inhibitory activities. Comprehensive structure-activity relationship studies identified that the p-guanidinophenylalanine-based dipeptide analog 22a exhibited a strong hepsin-inhibitory activity (Ki = 50.5 nM) and 22-fold hepsin selectivity over matriptase. Compound 22a could be a prototype molecule for structural optimization of dipeptide-based hepsin inhibitors.
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Affiliation(s)
- Hongmok Kwon
- College of Pharmacy, Korea University, 2511 Sejong-ro, Jochiwon-eup, Sejong 30019, Republic of Korea
| | - Hyunsoo Ha
- College of Pharmacy, Korea University, 2511 Sejong-ro, Jochiwon-eup, Sejong 30019, Republic of Korea
| | - Hayoung Jeon
- College of Pharmacy, Korea University, 2511 Sejong-ro, Jochiwon-eup, Sejong 30019, Republic of Korea
| | - Jaebong Jang
- College of Pharmacy, Korea University, 2511 Sejong-ro, Jochiwon-eup, Sejong 30019, Republic of Korea
| | - Sang-Hyun Son
- College of Pharmacy, Korea University, 2511 Sejong-ro, Jochiwon-eup, Sejong 30019, Republic of Korea
| | - Kiho Lee
- College of Pharmacy, Korea University, 2511 Sejong-ro, Jochiwon-eup, Sejong 30019, Republic of Korea
| | - Song-Kyu Park
- College of Pharmacy, Korea University, 2511 Sejong-ro, Jochiwon-eup, Sejong 30019, Republic of Korea
| | - Youngjoo Byun
- College of Pharmacy, Korea University, 2511 Sejong-ro, Jochiwon-eup, Sejong 30019, Republic of Korea; Biomedical Research Center, Korea University Guro Hospital, 148 Gurodong-ro, Guro-gu, Seoul 08308, Republic of Korea.
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10
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Yang P, Zhang L, Fu K, Sun Y, Wang X, Yue J, Ma Y, Tang B. Nickel-Catalyzed Asymmetric Transfer Hydrogenation and α-Selective Deuteration of N-Sulfonyl Imines with Alcohols: Access to α-Deuterated Chiral Amines. Org Lett 2020; 22:8278-8284. [PMID: 33044081 DOI: 10.1021/acs.orglett.0c02921] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A nickel-catalyzed enantioselective transfer hydrogenation and deuteration of N-sulfonyl imines was developed. Excellent α-selectivity and high deuterium content were achieved by using inexpensive 2-propanol-d8 as a deuterium source. As a highlight, no deuteration of β-C-H and the remote C-H of N-sulfonyl amines occurred, which is hard to achieve using other imines or by hydrogen isotope exchange with D2O. Mechanism studies indicated a stepwise pathway through the [Ni-D] intermediate.
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Affiliation(s)
- Peng Yang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China
| | - Li Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China
| | - Kaiyue Fu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China
| | - Yaxin Sun
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China
| | - Xiuhua Wang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China
| | - Jieyu Yue
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China
| | - Yu Ma
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, P. R. China
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11
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Cao Y, Zhu H, He R, Kong L, Shao J, Zhuang R, Xi J, Zhang J. Proteasome, a Promising Therapeutic Target for Multiple Diseases Beyond Cancer. DRUG DESIGN DEVELOPMENT AND THERAPY 2020; 14:4327-4342. [PMID: 33116419 PMCID: PMC7585272 DOI: 10.2147/dddt.s265793] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/22/2020] [Indexed: 12/14/2022]
Abstract
Proteasome is vital for intracellular protein homeostasis as it eliminates misfolded and damaged protein. Inhibition of proteasome has been validated as a powerful strategy for anti-cancer therapy, and several drugs have been approved for treatment of multiple myeloma. Recent studies indicate that proteasome has potent therapeutic effects on a variety of diseases besides cancer, including parasite infectious diseases, bacterial/fungal infections diseases, neurodegenerative diseases and autoimmune diseases. In this review, recent developments of proteasome inhibitors for various diseases and related structure activity relationships are going to be summarized.
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Affiliation(s)
- Yu Cao
- School of Medicine, Zhejiang University City College, Hangzhou, Zhejiang Province, 310015, People's Republic of China
| | - Huajian Zhu
- School of Medicine, Zhejiang University City College, Hangzhou, Zhejiang Province, 310015, People's Republic of China
| | - Ruoyu He
- Department of Pharmaceutical Preparation, Hangzhou Xixi Hospital, Hangzhou, Zhejiang Province, 310023 People's Republic of China
| | - Limin Kong
- Department of Pharmacy, The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang Province, 310003, People's Republic of China
| | - Jiaan Shao
- School of Medicine, Zhejiang University City College, Hangzhou, Zhejiang Province, 310015, People's Republic of China
| | - Rangxiao Zhuang
- Department of Pharmaceutical Preparation, Hangzhou Xixi Hospital, Hangzhou, Zhejiang Province, 310023 People's Republic of China
| | - Jianjun Xi
- Department of Pharmaceutical Preparation, Hangzhou Xixi Hospital, Hangzhou, Zhejiang Province, 310023 People's Republic of China
| | - Jiankang Zhang
- School of Medicine, Zhejiang University City College, Hangzhou, Zhejiang Province, 310015, People's Republic of China
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12
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Flow chemistry as a tool to access novel chemical space for drug discovery. Future Med Chem 2020; 12:1547-1563. [DOI: 10.4155/fmc-2020-0075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
This perspective scrutinizes flow chemistry as a useful tool for medicinal chemists to expand the current chemical capabilities in drug discovery. This technology has demonstrated his value not only for the traditional reactions used in Pharma for the last 20 years, but also for bringing back to the lab underused chemistries to access novel chemical space. The combination with other technologies, such as photochemistry and electrochemistry, is opening new avenues for reactivity that will smoothen the access to complex molecules. The introduction of all these technologies in automated platforms will improve the productivity of medicinal chemistry labs reducing the cycle times to get novel and differentiated bioactive molecules, accelerating discovery cycle times.
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13
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A comprehensive electrochemical study of 2-mercaptobenzoheterocyclic derivatives. Air-assisted electrochemical synthesis of new sulfonamide derivatives. Electrochim Acta 2020. [DOI: 10.1016/j.electacta.2020.136451] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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14
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Struble T, Alvarez JC, Brown SP, Chytil M, Cisar J, DesJarlais RL, Engkvist O, Frank SA, Greve DR, Griffin DJ, Hou X, Johannes JW, Kreatsoulas C, Lahue B, Mathea M, Mogk G, Nicolaou CA, Palmer AD, Price DJ, Robinson RI, Salentin S, Xing L, Jaakkola T, Green WH, Barzilay R, Coley CW, Jensen KF. Current and Future Roles of Artificial Intelligence in Medicinal Chemistry Synthesis. J Med Chem 2020; 63:8667-8682. [PMID: 32243158 PMCID: PMC7457232 DOI: 10.1021/acs.jmedchem.9b02120] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Indexed: 12/20/2022]
Abstract
Artificial intelligence and machine learning have demonstrated their potential role in predictive chemistry and synthetic planning of small molecules; there are at least a few reports of companies employing in silico synthetic planning into their overall approach to accessing target molecules. A data-driven synthesis planning program is one component being developed and evaluated by the Machine Learning for Pharmaceutical Discovery and Synthesis (MLPDS) consortium, comprising MIT and 13 chemical and pharmaceutical company members. Together, we wrote this perspective to share how we think predictive models can be integrated into medicinal chemistry synthesis workflows, how they are currently used within MLPDS member companies, and the outlook for this field.
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Affiliation(s)
- Thomas
J. Struble
- Department
of Chemical Engineering, MIT, Cambridge, Massachusetts 02139, United States
| | - Juan C. Alvarez
- Computational
and Structural Chemistry, Merck & Co.
Inc., Kenilworth, New Jersey 07033, United States
| | - Scott P. Brown
- Sunovion
Pharmaceuticals Inc., Marlborough, Massachusetts 01752, United States
| | - Milan Chytil
- Sunovion
Pharmaceuticals Inc., Marlborough, Massachusetts 01752, United States
| | - Justin Cisar
- Janssen
Research & Development LLC, Spring House, Pennsylvania 19477, United States
| | - Renee L. DesJarlais
- Janssen
Research & Development LLC, Spring House, Pennsylvania 19477, United States
| | - Ola Engkvist
- Hit
Discovery, Discovery Sciences, R&D, AstraZeneca, 431 83 Mölndal, Sweden
| | - Scott A. Frank
- Eli Lilly
and Company, Indianapolis, Indiana 46285, United States
| | - Daniel R. Greve
- LEO
Pharma A/S, Industriparken 55, DK-2750 Ballerup, Denmark
| | | | - Xinjun Hou
- Pfizer
Inc., Cambridge, Massachusetts 02139, United States
| | - Jeffrey W. Johannes
- Medicinal Chemistry, Early Oncology, Oncology
R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | | | - Brian Lahue
- Computational
and Structural Chemistry, Merck & Co.
Inc., Kenilworth, New Jersey 07033, United States
| | - Miriam Mathea
- BASF
SE, Carl-Bosch-Strasse
38, 67056 Ludwigshafen
am Rhein, Germany
| | | | | | - Andrew D. Palmer
- BASF
SE, Carl-Bosch-Strasse
38, 67056 Ludwigshafen
am Rhein, Germany
| | - Daniel J. Price
- GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Richard I. Robinson
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | | | - Li Xing
- WuXi
AppTec, Cambridge, Massachusetts 02142, United States
| | - Tommi Jaakkola
- Computer
Science and Artificial Intelligence Laboratory, MIT, Cambridge, Massachusetts 02139, United States
| | - William. H. Green
- Department
of Chemical Engineering, MIT, Cambridge, Massachusetts 02139, United States
| | - Regina Barzilay
- Computer
Science and Artificial Intelligence Laboratory, MIT, Cambridge, Massachusetts 02139, United States
| | - Connor W. Coley
- Department
of Chemical Engineering, MIT, Cambridge, Massachusetts 02139, United States
| | - Klavs F. Jensen
- Department
of Chemical Engineering, MIT, Cambridge, Massachusetts 02139, United States
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15
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Green DVS, Pickett S, Luscombe C, Senger S, Marcus D, Meslamani J, Brett D, Powell A, Masson J. BRADSHAW: a system for automated molecular design. J Comput Aided Mol Des 2020; 34:747-765. [PMID: 31637565 PMCID: PMC7292824 DOI: 10.1007/s10822-019-00234-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 10/05/2019] [Indexed: 12/18/2022]
Abstract
This paper introduces BRADSHAW (Biological Response Analysis and Design System using an Heterogenous, Automated Workflow), a system for automated molecular design which integrates methods for chemical structure generation, experimental design, active learning and cheminformatics tools. The simple user interface is designed to facilitate access to large scale automated design whilst minimising software development required to introduce new algorithms, a critical requirement in what is a very fast moving field. The system embodies a philosophy of automation, best practice, experimental design and the use of both traditional cheminformatics and modern machine learning algorithms.
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Affiliation(s)
- Darren V S Green
- Department of Molecular Design, Data and Computational Sciences, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK.
| | - Stephen Pickett
- Department of Molecular Design, Data and Computational Sciences, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Chris Luscombe
- Department of Molecular Design, Data and Computational Sciences, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Stefan Senger
- Department of Molecular Design, Data and Computational Sciences, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - David Marcus
- Department of Molecular Design, Data and Computational Sciences, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Jamel Meslamani
- Department of Molecular Design, Data and Computational Sciences, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA, 19426, USA
| | - David Brett
- Tessella Ltd, Walkern Road, Stevenage, Hertfordshire, SG1 3QP, UK
| | - Adam Powell
- Tessella Ltd, Walkern Road, Stevenage, Hertfordshire, SG1 3QP, UK
| | - Jonathan Masson
- Tessella Ltd, Walkern Road, Stevenage, Hertfordshire, SG1 3QP, UK
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16
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Gioiello A, Piccinno A, Lozza AM, Cerra B. The Medicinal Chemistry in the Era of Machines and Automation: Recent Advances in Continuous Flow Technology. J Med Chem 2020; 63:6624-6647. [PMID: 32049517 PMCID: PMC7997576 DOI: 10.1021/acs.jmedchem.9b01956] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Medicinal
chemistry plays a fundamental and underlying role in
chemical biology, pharmacology, and medicine to discover safe and
efficacious drugs. Small molecule medicinal chemistry relies on iterative
learning cycles composed of compound design, synthesis, testing, and
data analysis to provide new chemical probes and lead compounds for
novel and druggable targets. Using traditional approaches, the time
from hypothesis to obtaining the results can be protracted, thus limiting
the number of compounds that can be advanced into clinical studies.
This challenge can be tackled with the recourse of enabling technologies
that are showing great potential in improving the drug discovery process.
In this Perspective, we highlight recent developments toward innovative
medicinal chemistry strategies based on continuous flow systems coupled
with automation and bioassays. After a discussion of the aims and
concepts, we describe equipment and representative examples of automated
flow systems and end-to-end prototypes realized to expedite medicinal
chemistry discovery cycles.
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Affiliation(s)
- Antimo Gioiello
- Laboratory of Medicinal and Advanced Synthetic Chemistry (Lab MASC), Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Alessandro Piccinno
- Laboratory of Medicinal and Advanced Synthetic Chemistry (Lab MASC), Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Anna Maria Lozza
- Laboratory of Medicinal and Advanced Synthetic Chemistry (Lab MASC), Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Bruno Cerra
- Laboratory of Medicinal and Advanced Synthetic Chemistry (Lab MASC), Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
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17
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Schneider P, Walters WP, Plowright AT, Sieroka N, Listgarten J, Goodnow RA, Fisher J, Jansen JM, Duca JS, Rush TS, Zentgraf M, Hill JE, Krutoholow E, Kohler M, Blaney J, Funatsu K, Luebkemann C, Schneider G. Rethinking drug design in the artificial intelligence era. Nat Rev Drug Discov 2019. [DOI: 78495111110.1038/s41573-019-0050-3' target='_blank'>'"<>78495111110.1038/s41573-019-0050-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [78495111110.1038/s41573-019-0050-3','', '10.1021/acs.jmedchem.7b01698')">Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2022]
78495111110.1038/s41573-019-0050-3" />
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18
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Rethinking drug design in the artificial intelligence era. Nat Rev Drug Discov 2019; 19:353-364. [DOI: 10.1038/s41573-019-0050-3] [Citation(s) in RCA: 222] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2019] [Indexed: 12/17/2022]
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19
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Zhan W, Hsu HC, Morgan T, Ouellette T, Burns-Huang K, Hara R, Wright AG, Imaeda T, Okamoto R, Sato K, Michino M, Ramjee M, Aso K, Meinke PT, Foley M, Nathan CF, Li H, Lin G. Selective Phenylimidazole-Based Inhibitors of the Mycobacterium tuberculosis Proteasome. J Med Chem 2019; 62:9246-9253. [PMID: 31560200 DOI: 10.1021/acs.jmedchem.9b01187] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Proteasomes of pathogenic microbes have become attractive targets for anti-infectives. Coevolving with its human host, Mycobacterium tuberculosis (Mtb) has developed mechanisms to resist host-imposed nitrosative and oxidative stresses. Genetic deletion or pharmacological inhibition of the Mtb proteasome (Mtb20S) renders nonreplicating Mtb susceptible to reactive nitrogen species in vitro and unable to survive in the lungs of mice, validating the Mtb proteasome as a promising target for anti-Mtb agents. Using a structure-guided and flow chemistry-enabled study of structure-activity relationships, we developed phenylimidazole-based peptidomimetics that are highly potent for Mtb20S. X-ray structures of selected compounds with Mtb20S shed light on their selectivity for mycobacterial over human proteasomes.
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Affiliation(s)
- Wenhu Zhan
- Department of Microbiology & Immunology , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States
| | - Hao-Chi Hsu
- Structural Biology Program , Van Andel Institute , 333 Bostwick Avenue Northeast , Grand Rapids , Michigan 49503 , United States
| | - Trevor Morgan
- Cyclofluidic Limited , Biopark Broadwater Road , Welwyn Garden City AL7 3AX , U.K
| | - Tierra Ouellette
- Department of Microbiology & Immunology , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States
| | - Kristin Burns-Huang
- Department of Microbiology & Immunology , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States
| | - Ryoma Hara
- Tri-Institutional Therapeutics Discovery Institute , 413 East 69th Street , New York , New York 10065 , United States
| | - Adrian G Wright
- Cyclofluidic Limited , Biopark Broadwater Road , Welwyn Garden City AL7 3AX , U.K
| | - Toshihiro Imaeda
- Tri-Institutional Therapeutics Discovery Institute , 413 East 69th Street , New York , New York 10065 , United States
| | - Rei Okamoto
- Tri-Institutional Therapeutics Discovery Institute , 413 East 69th Street , New York , New York 10065 , United States
| | - Kenjiro Sato
- Tri-Institutional Therapeutics Discovery Institute , 413 East 69th Street , New York , New York 10065 , United States
| | - Mayako Michino
- Tri-Institutional Therapeutics Discovery Institute , 413 East 69th Street , New York , New York 10065 , United States
| | - Manoj Ramjee
- Cyclofluidic Limited , Biopark Broadwater Road , Welwyn Garden City AL7 3AX , U.K
| | - Kazuyoshi Aso
- Tri-Institutional Therapeutics Discovery Institute , 413 East 69th Street , New York , New York 10065 , United States
| | - Peter T Meinke
- Tri-Institutional Therapeutics Discovery Institute , 413 East 69th Street , New York , New York 10065 , United States
| | - Michael Foley
- Tri-Institutional Therapeutics Discovery Institute , 413 East 69th Street , New York , New York 10065 , United States
| | - Carl F Nathan
- Department of Microbiology & Immunology , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States
| | - Huilin Li
- Structural Biology Program , Van Andel Institute , 333 Bostwick Avenue Northeast , Grand Rapids , Michigan 49503 , United States
| | - Gang Lin
- Department of Microbiology & Immunology , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States
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20
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Damalanka VC, Wildman SA, Janetka JW. Piperidine carbamate peptidomimetic inhibitors of the serine proteases HGFA, matriptase and hepsin. MEDCHEMCOMM 2019; 10:1646-1655. [PMID: 31803403 DOI: 10.1039/c9md00234k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/17/2019] [Indexed: 12/21/2022]
Abstract
Matriptase and hepsin are type II transmembrane serine proteases (TTSPs). Along with related S1 trypsin like serine protease HGFA (hepatocyte growth factor activator), their unregulated proteolytic activity has been associated with cancer including tumor progression and metastasis. These three proteases have two substrates in common, hepatocyte growth factor (HGF) and macrophage stimulating protein (MSP), the ligands for MET and recepteur d'origine nantais (RON) receptor tyrosine kinases. Mechanism-based tetrapeptide and benzamidine inhibitors of these proteases have been shown to block HGF/MET and MSP/RON cancer cell signaling. Herein, we have rationally designed a new class of peptidomimetic hybrid small molecule piperidine carbamate dipeptide inhibitors comparable in potency to much larger tetrapeptides. We have identified multiple compounds which have potent activity against matriptase and hepsin and with excellent selectivity over the off-target serine proteases factor Xa and thrombin.
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Affiliation(s)
- Vishnu C Damalanka
- Department of Biochemistry and Molecular Biophysics , Washington University School of Medicine , St. Louis , Missouri , USA . ; Tel: +314 362 0509
| | - Scott A Wildman
- University of Wisconsin Carbone Cancer Center , Drug Development Core , University of Wisconsin-Madison , Madison , Wisconsin , USA
| | - James W Janetka
- Department of Biochemistry and Molecular Biophysics , Washington University School of Medicine , St. Louis , Missouri , USA . ; Tel: +314 362 0509
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21
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Parry DM. Closing the Loop: Developing an Integrated Design, Make, and Test Platform for Discovery. ACS Med Chem Lett 2019; 10:848-856. [PMID: 31223437 DOI: 10.1021/acsmedchemlett.9b00095] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 05/06/2019] [Indexed: 11/30/2022] Open
Abstract
The relatively slow cycle time within medicinal chemistry from synthesis to assay is constantly being challenged to help improve the efficiency of the discovery process. While both synthesis and assay have been automated to varying degrees, there has, until recently, been limited focus on the complete design, make, and test process. This Innovations article outlines the development of Cyclofluidic from inception through to the commercialization of a fully integrated closed loop design, synthesis, and screen platform.
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Affiliation(s)
- David M. Parry
- Cyclofluidic Ltd., BioPark, Broadwater Road, Welwyn Garden City AL7 3AX, U.K
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22
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Recent progress on inhibitors of the type II transmembrane serine proteases, hepsin, matriptase and matriptase-2. Future Med Chem 2019; 11:743-769. [DOI: 10.4155/fmc-2018-0446] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Members of the type II transmembrane serine proteases (TTSP) family play a vital role in cell growth and development but many are also implicated in disease. Two of the well-studied TTSPs, matriptase and hepsin proteolytically process multiple protein substrates such as the inactive single-chain zymogens pro-HGF and pro-macrophage stimulating protein into the active heterodimeric forms, HGF and macrophage stimulating protein. These two proteases also have many other substrates which are associated with cancer and tumor progression. Another related TTSP, matriptase-2 is expressed in the liver and functions by regulating iron homoeostasis through the cleavage of hemojuvelin and thus is implicated in iron overload diseases. In the present review, we will discuss inhibitor design strategy and Structure activity relationships of TTSP inhibitors, which have been reported in the literature.
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23
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Bogdan AR, Dombrowski AW. Emerging Trends in Flow Chemistry and Applications to the Pharmaceutical Industry. J Med Chem 2019; 62:6422-6468. [DOI: 10.1021/acs.jmedchem.8b01760] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Andrew R. Bogdan
- Discovery Chemistry and Technology, AbbVie, Inc. 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Amanda W. Dombrowski
- Discovery Chemistry and Technology, AbbVie, Inc. 1 North Waukegan Road, North Chicago, Illinois 60064, United States
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24
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Damalanka VC, Han Z, Karmakar P, O’Donoghue AJ, La Greca F, Kim T, Pant SM, Helander J, Klefström J, Craik CS, Janetka JW. Discovery of Selective Matriptase and Hepsin Serine Protease Inhibitors: Useful Chemical Tools for Cancer Cell Biology. J Med Chem 2018; 62:480-490. [DOI: 10.1021/acs.jmedchem.8b01536] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Vishnu C. Damalanka
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, 63110, United States
| | - Zhenfu Han
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, 63110, United States
| | - Partha Karmakar
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, 63110, United States
| | - Anthony J. O’Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, 92093, United States
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, 94158, United States
| | - Florencia La Greca
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, 94158, United States
| | - Tommy Kim
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, 63110, United States
| | - Shishir M. Pant
- Cancer Cell Circuitry Laboratory, Research Programs Unit/Translational Cancer Biology & Medicum, University of Helsinki, P.O. Box 63, Haartmaninkatu 8, 00014 Helsinki, Finland
| | - Jonathan Helander
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, 63110, United States
| | - Juha Klefström
- Cancer Cell Circuitry Laboratory, Research Programs Unit/Translational Cancer Biology & Medicum, University of Helsinki, P.O. Box 63, Haartmaninkatu 8, 00014 Helsinki, Finland
| | - Charles S. Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, 94158, United States
| | - James W. Janetka
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, 63110, United States
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25
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Zhao X, Xu H, Huang X, Zhou JS. Asymmetric Stepwise Reductive Amination of Sulfonamides, Sulfamates, and a Phosphinamide by Nickel Catalysis. Angew Chem Int Ed Engl 2018; 58:292-296. [DOI: 10.1002/anie.201809930] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 10/12/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Xiaohu Zhao
- Division of Chemistry and Biological Chemistry; School of Physical and Mathematical Sciences; Nanyang Technological University; 21 Nanyang Link, SPMS-CBC-06-06 Singapore 637371 Singapore
| | - Haiyan Xu
- Division of Chemistry and Biological Chemistry; School of Physical and Mathematical Sciences; Nanyang Technological University; 21 Nanyang Link, SPMS-CBC-06-06 Singapore 637371 Singapore
| | - Xiaolei Huang
- Division of Chemistry and Biological Chemistry; School of Physical and Mathematical Sciences; Nanyang Technological University; 21 Nanyang Link, SPMS-CBC-06-06 Singapore 637371 Singapore
| | - Jianrong Steve Zhou
- Division of Chemistry and Biological Chemistry; School of Physical and Mathematical Sciences; Nanyang Technological University; 21 Nanyang Link, SPMS-CBC-06-06 Singapore 637371 Singapore
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26
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Zhao X, Xu H, Huang X, Zhou JS. Asymmetric Stepwise Reductive Amination of Sulfonamides, Sulfamates, and a Phosphinamide by Nickel Catalysis. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201809930] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Xiaohu Zhao
- Division of Chemistry and Biological Chemistry; School of Physical and Mathematical Sciences; Nanyang Technological University; 21 Nanyang Link, SPMS-CBC-06-06 Singapore 637371 Singapore
| | - Haiyan Xu
- Division of Chemistry and Biological Chemistry; School of Physical and Mathematical Sciences; Nanyang Technological University; 21 Nanyang Link, SPMS-CBC-06-06 Singapore 637371 Singapore
| | - Xiaolei Huang
- Division of Chemistry and Biological Chemistry; School of Physical and Mathematical Sciences; Nanyang Technological University; 21 Nanyang Link, SPMS-CBC-06-06 Singapore 637371 Singapore
| | - Jianrong Steve Zhou
- Division of Chemistry and Biological Chemistry; School of Physical and Mathematical Sciences; Nanyang Technological University; 21 Nanyang Link, SPMS-CBC-06-06 Singapore 637371 Singapore
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27
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Boström J, Brown DG, Young RJ, Keserü GM. Expanding the medicinal chemistry synthetic toolbox. Nat Rev Drug Discov 2018; 17:709-727. [DOI: 10.1038/nrd.2018.116] [Citation(s) in RCA: 267] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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