1
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Dash S, Rathi E, Kumar A, Chawla K, Joseph A, Kini SG. Structure-activity relationship mediated molecular insights of DprE1 inhibitors: A Comprehensive Review. J Biomol Struct Dyn 2024; 42:6472-6522. [PMID: 37395797 DOI: 10.1080/07391102.2023.2230312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/21/2023] [Indexed: 07/04/2023]
Abstract
Emerging threats of multi-drug resistant (MDR), extensively drug-resistant (XDR), and totally drug-resistant (TDR) tuberculosis led to the discovery of a novel target which was entitled Decaprenylphosphoryl-β-D-ribose 2'-epimerase (DprE1) enzyme. DprE1 is composed of two isoforms, decaprenylphosphoryl-β-D-ribose oxidase (DprE1) and decaprenylphosphoryl-D-2-keto erythro pentose reductase (DprE2). The enzymes, DprE1 and DprE2, regulate the two-step epimerization process to form DPA (Decaprenylphosphoryl arabinose) from DPX (Decaprenylphosphoryl-D-ribose), which is the sole precursor in the cell wall synthesis of arabinogalactan (AG) and lipoarabinomannan (LAM). Target-based and whole-cell-based screening played an imperative role in the identification of the druggable target, DprE1, whereas the druggability of the DprE2 enzyme is not proved yet. To date, diverse scaffolds of heterocyclic and aromatic ring systems have been reported as DprE1 inhibitors based on their interaction mode, i.e. covalent, and non-covalent inhibitors. This review describes the structure-activity relationship (SAR) of reported covalent and non-covalent inhibitors to enlighten about the crucial pharmacophoric features required for DprE1 inhibition, along with in-silico studies which characterize the amino acid residues responsible for covalent and non-covalent interactions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Swagatika Dash
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Ekta Rathi
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Avinash Kumar
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Kiran Chawla
- Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Alex Joseph
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Suvarna G Kini
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
- Manipal Mc Gill Centre for Infectious Diseases, Prasanna School of Public Health, Manipal Academy of Higher Education, Manipal, Karnataka, India
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2
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Yang J, Zhang L, Qiao W, Luo Y. Mycobacterium tuberculosis: Pathogenesis and therapeutic targets. MedComm (Beijing) 2023; 4:e353. [PMID: 37674971 PMCID: PMC10477518 DOI: 10.1002/mco2.353] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 09/08/2023] Open
Abstract
Tuberculosis (TB) remains a significant public health concern in the 21st century, especially due to drug resistance, coinfection with diseases like immunodeficiency syndrome (AIDS) and coronavirus disease 2019, and the lengthy and costly treatment protocols. In this review, we summarize the pathogenesis of TB infection, therapeutic targets, and corresponding modulators, including first-line medications, current clinical trial drugs and molecules in preclinical assessment. Understanding the mechanisms of Mycobacterium tuberculosis (Mtb) infection and important biological targets can lead to innovative treatments. While most antitubercular agents target pathogen-related processes, host-directed therapy (HDT) modalities addressing immune defense, survival mechanisms, and immunopathology also hold promise. Mtb's adaptation to the human host involves manipulating host cellular mechanisms, and HDT aims to disrupt this manipulation to enhance treatment effectiveness. Our review provides valuable insights for future anti-TB drug development efforts.
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Affiliation(s)
- Jiaxing Yang
- Center of Infectious Diseases and State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengduChina
| | - Laiying Zhang
- Center of Infectious Diseases and State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengduChina
| | - Wenliang Qiao
- Department of Thoracic Surgery, West China HospitalSichuan UniversityChengduSichuanChina
- Lung Cancer Center, West China HospitalSichuan UniversityChengduSichuanChina
| | - Youfu Luo
- Center of Infectious Diseases and State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengduChina
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3
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Chauhan M, Prajapati C, Mirza S, Barot R, Yadav R, Barmade M, Kakadiya D, Vijayvargia R, Haobam B, Baidya AT, Kumar R, Yadav MR, Murumkar P. Design, synthesis, biological evaluation and molecular dynamics of some novel 3-phenylpyrazolo[1,5- a]pyrimidine-2,7(1 H,4 H)-dione based compounds as anti-tubercular agents. J Biomol Struct Dyn 2023:1-19. [PMID: 37655680 DOI: 10.1080/07391102.2023.2249109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/12/2023] [Indexed: 09/02/2023]
Abstract
Decaprenylphosphoryl-β-d-ribose-2'-epimerase (DprE1) is a druggable target which is being exploited for the development of new anti-TB agents. In the present work, we report developing a pharmacophore model and performing virtual screening of Asinex database using the developed pharmacophore model to get eight hits as potential DprE1 inhibitors. The hits were used as leads to design new 3-phenylpyrazolo[1,5-a]pyrimidine-2,7(1H,4H)-dione based potential anti-TB agents. On the basis of the identified lead molecules, a total of 18 compounds were synthesized and evaluated for their anti-TB activity by using MABA. ADMET predictions for all the compounds revealed that these compounds have drug-like and lead-like properties. One of the final compounds was found to exhibit potent anti-TB activity against Mycobacterium bovis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Monica Chauhan
- Faculty of Pharmacy, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Chintu Prajapati
- Faculty of Pharmacy, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Sadaf Mirza
- Faculty of Pharmacy, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Rahul Barot
- Faculty of Pharmacy, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Rasana Yadav
- Faculty of Pharmacy, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Mahesh Barmade
- Faculty of Pharmacy, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Dhruvi Kakadiya
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Ravi Vijayvargia
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Bijaya Haobam
- Dr. Vikrama Sarabhai Institute of Cell & Molecular Biology, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Anurag Tk Baidya
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (B.H.U), Varanasi, U.P., India
| | - Rajnish Kumar
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (B.H.U), Varanasi, U.P., India
| | - M R Yadav
- Centre of Research for Development, Parul University, Vadodara, Gujarat, India
| | - Prashant Murumkar
- Faculty of Pharmacy, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
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4
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Yadav S, Soni A, Tanwar O, Bhadane R, Besra GS, Kawathekar N. DprE1 Inhibitors: Enduring Aspirations for Future Antituberculosis Drug Discovery. ChemMedChem 2023; 18:e202300099. [PMID: 37246503 DOI: 10.1002/cmdc.202300099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 05/30/2023]
Abstract
DprE1 is a crucial enzyme involved in the cell wall synthesis of Mycobacterium tuberculosis and a promising target for antituberculosis drug development. However, its unique structural characteristics for ligand binding and association with DprE2 make developing new clinical compounds challenging. This review provides an in-depth analysis of the structural requirements for both covalent and non-covalent inhibitors, their 2D and 3D binding patterns, as well as their biological activity data in vitro and in vivo, including pharmacokinetic information. We also introduce a protein quality score (PQS) and an active-site map of the DprE1 enzyme to help medicinal chemists better understand DprE1 inhibition and develop new and effective anti-TB drugs. Furthermore, we examine the resistance mechanisms associated with DprE1 inhibitors to understand future developments due to resistance emergence. This comprehensive review offers insight into the DprE1 active site, including protein-binding maps, PQS, and graphical representations of known inhibitors, making it a valuable resource for medicinal chemists working on future antitubercular compounds.
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Affiliation(s)
- Saloni Yadav
- Department of Pharmacy, Shri Govindram Seksaria Institute of Technology and Science, 23-Park Road, Indore, Madhya Pradesh, India
| | - Aastha Soni
- Department of Pharmacy, Shri Govindram Seksaria Institute of Technology and Science, 23-Park Road, Indore, Madhya Pradesh, India
| | - Omprakash Tanwar
- Department of Pharmacy, Shri Govindram Seksaria Institute of Technology and Science, 23-Park Road, Indore, Madhya Pradesh, India
| | - Rajendra Bhadane
- Turku Cellular Microbiology Laboratory (TCML), Åbo Akademi University, 20014, Turku, Finland
- Institute of Biomedicine, University of Turku, 20520, Turku, Finland
| | - Gurdyal S Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Neha Kawathekar
- Department of Pharmacy, Shri Govindram Seksaria Institute of Technology and Science, 23-Park Road, Indore, Madhya Pradesh, India
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5
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Finger V, Kucera T, Kafkova R, Muckova L, Dolezal R, Kubes J, Novak M, Prchal L, Lakatos L, Andrs M, Hympanova M, Marek J, Kufa M, Spiwok V, Soukup O, Mezeiova E, Janousek J, Nevosadova L, Benkova M, Kitson RRA, Kratky M, Bősze S, Mikusova K, Hartkoorn R, Roh J, Korabecny J. 2,6-Disubstituted 7-(naphthalen-2-ylmethyl)-7H-purines as a new class of potent antitubercular agents inhibiting DprE1. Eur J Med Chem 2023; 258:115611. [PMID: 37421887 DOI: 10.1016/j.ejmech.2023.115611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/27/2023] [Accepted: 06/27/2023] [Indexed: 07/10/2023]
Abstract
Phenotypic screening of an in-house library of small molecule purine derivatives against Mycobacterium tuberculosis (Mtb) led to the identification of 2-morpholino-7-(naphthalen-2-ylmethyl)-1,7-dihydro-6H-purin-6-one 10 as a potent antimycobacterial agent with MIC99 of 4 μM. Thorough structure-activity relationship studies revealed the importance of 7-(naphthalen-2-ylmethyl) substitution for antimycobacterial activity, yet opened the possibility of structural modifications at positions 2 and 6 of the purine core. As the result, optimized analogues with 6-amino or ethylamino substitution 56 and 64, respectively, were developed. These compounds showed strong in vitro antimycobacterial activity with MIC of 1 μM against Mtb H37Rv and against several clinically isolated drug-resistant strains, had limited toxicity to mammalian cell lines, medium clearance with respect to phase I metabolic deactivation (27 and 16.8 μL/min/mg), sufficient aqueous solubility (>90 μM) and high plasma stability. Interestingly, investigated purines, including compounds 56 and 64, lacked activity against a panel of Gram-negative and Gram-positive bacterial strains, indicating a specific mycobacterial molecular target. To investigate the mechanism of action, Mtb mutants resistant to hit compound 10 were isolated and their genomes were sequenced. Mutations were found in dprE1 (Rv3790), which encodes decaprenylphosphoryl-β-d-ribose oxidase DprE1, enzyme essential for the biosynthesis of arabinose, a vital component of the mycobacterial cell wall. Inhibition of DprE1 by 2,6-disubstituted 7-(naphthalen-2-ylmethyl)-7H-purines was proved using radiolabelling experiments in Mtb H37Rv in vitro. Finally, structure-binding relationships between selected purines and DprE1 using molecular modeling studies in tandem with molecular dynamic simulations revealed the key structural features for effective drug-target interaction.
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Affiliation(s)
- Vladimir Finger
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika, Heyrovskeho 1203, 50005, Hradec Králové, Czech Republic; Biomedical Research Center, University Hospital Hradec Králové, Sokolska 581, 500 05, Hradec Králové, Czech Republic
| | - Tomas Kucera
- Faculty of Military Health Sciences, University of Defence, Trebesska, 1575, 500 01, Hradec Králové, Czech Republic
| | - Radka Kafkova
- Faculty of Natural Sciences, Department of Biochemistry, Comenius University in Bratislava, Mlynská Dolina, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | - Lubica Muckova
- Biomedical Research Center, University Hospital Hradec Králové, Sokolska 581, 500 05, Hradec Králové, Czech Republic; Faculty of Military Health Sciences, University of Defence, Trebesska, 1575, 500 01, Hradec Králové, Czech Republic
| | - Rafael Dolezal
- Biomedical Research Center, University Hospital Hradec Králové, Sokolska 581, 500 05, Hradec Králové, Czech Republic
| | - Jan Kubes
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika, Heyrovskeho 1203, 50005, Hradec Králové, Czech Republic
| | - Martin Novak
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika, Heyrovskeho 1203, 50005, Hradec Králové, Czech Republic; Biomedical Research Center, University Hospital Hradec Králové, Sokolska 581, 500 05, Hradec Králové, Czech Republic
| | - Lukas Prchal
- Biomedical Research Center, University Hospital Hradec Králové, Sokolska 581, 500 05, Hradec Králové, Czech Republic
| | - Levente Lakatos
- ELKH-ELTE Research Group of Peptide Chemistry, Eötvös Loránd University, Pázmány Péter Sétány 1/A, H-1117, Budapest, Hungary; National Public Health Center, Albert Flórián út 2-6, Budapest, 1097, Hungary
| | - Martin Andrs
- Biomedical Research Center, University Hospital Hradec Králové, Sokolska 581, 500 05, Hradec Králové, Czech Republic
| | - Michaela Hympanova
- Biomedical Research Center, University Hospital Hradec Králové, Sokolska 581, 500 05, Hradec Králové, Czech Republic; Faculty of Military Health Sciences, University of Defence, Trebesska, 1575, 500 01, Hradec Králové, Czech Republic
| | - Jan Marek
- Biomedical Research Center, University Hospital Hradec Králové, Sokolska 581, 500 05, Hradec Králové, Czech Republic; Faculty of Military Health Sciences, University of Defence, Trebesska, 1575, 500 01, Hradec Králové, Czech Republic
| | - Martin Kufa
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika, Heyrovskeho 1203, 50005, Hradec Králové, Czech Republic; Biomedical Research Center, University Hospital Hradec Králové, Sokolska 581, 500 05, Hradec Králové, Czech Republic
| | - Vojtech Spiwok
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Technicka 5, 166 28, Prague, Czech Republic
| | - Ondrej Soukup
- Biomedical Research Center, University Hospital Hradec Králové, Sokolska 581, 500 05, Hradec Králové, Czech Republic
| | - Eva Mezeiova
- Biomedical Research Center, University Hospital Hradec Králové, Sokolska 581, 500 05, Hradec Králové, Czech Republic
| | - Jiri Janousek
- Biomedical Research Center, University Hospital Hradec Králové, Sokolska 581, 500 05, Hradec Králové, Czech Republic
| | - Lenka Nevosadova
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika, Heyrovskeho 1203, 50005, Hradec Králové, Czech Republic
| | - Marketa Benkova
- Biomedical Research Center, University Hospital Hradec Králové, Sokolska 581, 500 05, Hradec Králové, Czech Republic
| | - Russell R A Kitson
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika, Heyrovskeho 1203, 50005, Hradec Králové, Czech Republic
| | - Martin Kratky
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika, Heyrovskeho 1203, 50005, Hradec Králové, Czech Republic
| | - Szilvia Bősze
- ELKH-ELTE Research Group of Peptide Chemistry, Eötvös Loránd University, Pázmány Péter Sétány 1/A, H-1117, Budapest, Hungary; National Public Health Center, Albert Flórián út 2-6, Budapest, 1097, Hungary
| | - Katarina Mikusova
- Faculty of Natural Sciences, Department of Biochemistry, Comenius University in Bratislava, Mlynská Dolina, Ilkovičova 6, 842 15, Bratislava, Slovakia
| | - Ruben Hartkoorn
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Jaroslav Roh
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika, Heyrovskeho 1203, 50005, Hradec Králové, Czech Republic.
| | - Jan Korabecny
- Biomedical Research Center, University Hospital Hradec Králové, Sokolska 581, 500 05, Hradec Králové, Czech Republic.
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6
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Kumar G, Kapoor S. Targeting mycobacterial membranes and membrane proteins: Progress and limitations. Bioorg Med Chem 2023; 81:117212. [PMID: 36804747 DOI: 10.1016/j.bmc.2023.117212] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/13/2023]
Abstract
Among the various bacterial infections, tuberculosis continues to hold center stage. Its causative agent, Mycobacterium tuberculosis, possesses robust defense mechanisms against most front-line antibiotic drugs and host responses due to their complex cell membranes with unique lipid molecules. It is now well-established that bacteria change their membrane composition to optimize their environment to survive and elude drug action. Thus targeting membrane or membrane components is a promising avenue for exploiting the chemical space focussed on developing novel membrane-centric anti-bacterial small molecules. These approaches are more effective, non-toxic, and can attenuate resistance phenotype. We present the relevance of targeting the mycobacterial membrane as a practical therapeutic approach. The review highlights the direct and indirect targeting of membrane structure and function. Direct membrane targeting agents cause perturbation in the membrane potential and can cause leakage of the cytoplasmic contents. In contrast, indirect membrane targeting agents disrupt the function of membrane-associated proteins involved in cell wall biosynthesis or energy production. We discuss the chronological chemical improvements in various scaffolds targeting specific membrane-associated protein targets, their clinical evaluation, and up-to-date account of their ''mechanisms of action, potency, selectivity'' and limitations. The sources of anti-TB drugs/inhibitors discussed in this work have emerged from target-based identification, cell-based phenotypic screening, drug repurposing, and natural products. We believe this review will inspire the exploration of uncharted chemical space for informing the development of new scaffolds that can inhibit novel mycobacterial membrane targets.
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Affiliation(s)
- Gautam Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India; Departemnt of Natural Products, National Institute of Pharmaceutical Education and Research-Hyderabad, Hyderabad 500037, India.
| | - Shobhna Kapoor
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India; Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima 739-8528, Japan.
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7
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Villaescusa L, Hernández I, Azcune L, Rudi A, Mercero JM, Landa A, Oiarbide M, Palomo C. Rigidified Bis(sulfonyl)ethylenes as Effective Michael Acceptors for Asymmetric Catalysis: Application to the Enantioselective Synthesis of Quaternary Hydantoins. J Org Chem 2023; 88:972-987. [PMID: 36630318 PMCID: PMC10013931 DOI: 10.1021/acs.joc.2c02403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The catalytic, enantio- and diastereoselective addition of hydantoin surrogates II to "rigidified" vinylidene bis(sulfone) reagents is developed, thus overcoming the inability of commonly employed β-substituted vinylic sulfones to react. Adducts are transformed in enantioenriched 5,5-disubstituted hydantoins through hydrolysis and reductive desulfonylation processes providing new structures for eventual bioassays. Density functional theory studies that rationalize the observed reactivity and stereoselectivity trends are also provided.
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Affiliation(s)
- Leire Villaescusa
- Departamento de Química Orgánica I, Facultad de Química, Universidad del País Vasco UPV/EHU, Paseo Manuel Lardizabal 3, Donostia-San Sebastián 20018, Spain
| | - Iker Hernández
- Departamento de Química Orgánica I, Facultad de Química, Universidad del País Vasco UPV/EHU, Paseo Manuel Lardizabal 3, Donostia-San Sebastián 20018, Spain
| | - Laura Azcune
- Departamento de Química Orgánica I, Facultad de Química, Universidad del País Vasco UPV/EHU, Paseo Manuel Lardizabal 3, Donostia-San Sebastián 20018, Spain
| | - Ainhoa Rudi
- Departamento de Química Orgánica I, Facultad de Química, Universidad del País Vasco UPV/EHU, Paseo Manuel Lardizabal 3, Donostia-San Sebastián 20018, Spain
| | - José M Mercero
- Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU) & Donostia International Physics Center (DIPC), Donostia 20018, Spain
| | - Aitor Landa
- Departamento de Química Orgánica I, Facultad de Química, Universidad del País Vasco UPV/EHU, Paseo Manuel Lardizabal 3, Donostia-San Sebastián 20018, Spain
| | - Mikel Oiarbide
- Departamento de Química Orgánica I, Facultad de Química, Universidad del País Vasco UPV/EHU, Paseo Manuel Lardizabal 3, Donostia-San Sebastián 20018, Spain
| | - Claudio Palomo
- Departamento de Química Orgánica I, Facultad de Química, Universidad del País Vasco UPV/EHU, Paseo Manuel Lardizabal 3, Donostia-San Sebastián 20018, Spain
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8
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Han F, Zhang D, Salli S, Ye J, Li Y, Rosei F, Wen XD, Niemantsverdriet H, Richards E, Su R. Copper Cocatalyst Modulated Radical Generation for Selective Heterogeneous Photosynthesis of α-Haloketones. ACS Catal 2023; 13:248-255. [PMID: 36644650 PMCID: PMC9830627 DOI: 10.1021/acscatal.2c05189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/23/2022] [Indexed: 12/23/2022]
Abstract
The α-haloketones are important precursors for synthetic chemistry and pharmaceutical applications; however, their production relies heavily on traditional synthetic methods via halogenation of ketones that are toxic and environmentally risky. Here, we report a heterogeneous photosynthetic strategy of α-haloketone production from aromatic olefins using copper-modified graphitic carbon nitride (Cu-C3N4) under mild reaction conditions. By employing NiX2 (X = Cl, Br) as the halogen source, a series of α-haloketones can be synthesized using atmospheric air as the oxidant under visible-light irradiation. In comparison with pristine carbon nitride, the addition of Cu as a cocatalyst provides a moderate generation rate of halogen radicals and selective reduction of molecular oxygen into •OOH radicals, thus leading to a high selectivity to α-haloketones. The Cu-C3N4 also exhibits high stability and versatility, rendering it a promising candidate for solar-driven synthetic applications.
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Affiliation(s)
- Feiyu Han
- Soochow
Institute for Energy and Materials Innovations (SIEMIS), Soochow University, Suzhou, Jiangsu 215006, China,SynCat@Beijing, Synfuels China Technology Co. Ltd., Leyuan South Street II, No.1, Huairou, Beijing 101407, China
| | - Dongsheng Zhang
- Soochow
Institute for Energy and Materials Innovations (SIEMIS), Soochow University, Suzhou, Jiangsu 215006, China,SynCat@Beijing, Synfuels China Technology Co. Ltd., Leyuan South Street II, No.1, Huairou, Beijing 101407, China
| | - Sofia Salli
- School
of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, U.K.
| | - Jiani Ye
- Soochow
Institute for Energy and Materials Innovations (SIEMIS), Soochow University, Suzhou, Jiangsu 215006, China
| | - Yongwang Li
- SynCat@Beijing, Synfuels China Technology Co. Ltd., Leyuan South Street II, No.1, Huairou, Beijing 101407, China,State
Key Laboratory of Coal Conversion, Institute
of Coal Chemistry, CAS, Taiyuan 030001, China
| | - Federico Rosei
- Center
for Energy, Materials and Telecommunications, Institut National de la Recherche Scientifique, 1650 Boulevard Lionel-Boulet, Varennes, Québec J3X 1P7, Canada
| | - Xiao-Dong Wen
- SynCat@Beijing, Synfuels China Technology Co. Ltd., Leyuan South Street II, No.1, Huairou, Beijing 101407, China,State
Key Laboratory of Coal Conversion, Institute
of Coal Chemistry, CAS, Taiyuan 030001, China
| | - Hans Niemantsverdriet
- SynCat@Beijing, Synfuels China Technology Co. Ltd., Leyuan South Street II, No.1, Huairou, Beijing 101407, China,SynCat@DIFFER, Syngaschem BV, HH Eindhoven 6336, The
Netherlands
| | - Emma Richards
- School
of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, U.K.,
Emma Richards ()
| | - Ren Su
- Soochow
Institute for Energy and Materials Innovations (SIEMIS), Soochow University, Suzhou, Jiangsu 215006, China,SynCat@Beijing, Synfuels China Technology Co. Ltd., Leyuan South Street II, No.1, Huairou, Beijing 101407, China,Ren Su ()
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9
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Amado PM, Woodley C, Cristiano MLS, O’Neill PM. Recent Advances of DprE1 Inhibitors against Mycobacterium tuberculosis: Computational Analysis of Physicochemical and ADMET Properties. ACS OMEGA 2022; 7:40659-40681. [PMID: 36406587 PMCID: PMC9670723 DOI: 10.1021/acsomega.2c05307] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/21/2022] [Indexed: 05/14/2023]
Abstract
Decaprenylphosphoryl-β-d-ribose 2'-epimerase (DprE1) is a critical flavoenzyme in Mycobacterium tuberculosis, catalyzing a vital step in the production of lipoarabinomannan and arabinogalactan, both of which are essential for cell wall biosynthesis. Due to its periplasmic localization, DprE1 is a susceptible target, and several compounds with diverse scaffolds have been discovered that inhibit this enzyme, covalently or noncovalently. We evaluated a total of ∼1519 DprE1 inhibitors disclosed in the literature from 2009 to April 2022 by performing an in-depth analysis of physicochemical descriptors and absorption, distribution, metabolism, excretion, and toxicity (ADMET), to gain new insights into these properties in DprE1 inhibitors. Several molecular properties that should facilitate the design and optimization of future DprE1 inhibitors are described, allowing for the development of improved analogues targeting M. tuberculosis.
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Affiliation(s)
- Patrícia
S. M. Amado
- Center
of Marine Sciences - CCMAR, University of
Algarve, P-8005-039 Faro, Portugal
- Department
of Chemistry and Pharmacy, FCT, University
of Algarve, P-8005-039 Faro, Portugal
- Department
of Chemistry, University of Liverpool, Liverpool L69 7ZD, United Kingdom
| | - Christopher Woodley
- Department
of Chemistry, University of Liverpool, Liverpool L69 7ZD, United Kingdom
| | - Maria L. S. Cristiano
- Center
of Marine Sciences - CCMAR, University of
Algarve, P-8005-039 Faro, Portugal
- Department
of Chemistry and Pharmacy, FCT, University
of Algarve, P-8005-039 Faro, Portugal
- Email
for M.L.S.C.:
| | - Paul M. O’Neill
- Department
of Chemistry, University of Liverpool, Liverpool L69 7ZD, United Kingdom
- Email for P.M.O.:
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10
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Bonde C, Gawad J, Bonde S. Insights into development of Decaprenyl-phosphoryl-β-D-ribose 2'-epimerase (DprE1) inhibitors as antitubercular agents: A state of the art review. Indian J Tuberc 2022; 69:404-420. [PMID: 36460369 DOI: 10.1016/j.ijtb.2021.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/16/2021] [Accepted: 09/06/2021] [Indexed: 06/17/2023]
Abstract
Mycobacterium tuberculosis is a causative agent for the world threatening infectious disease known as tuberculosis. M. tuberculosis is also referred as Koch's bacillus as it was first defined by Robert Koch in 1821. In the entire history of M. tuberculosis infection, several different targets were identified and explored with a hope of effective therapeutic treatment against tuberculosis. Drug-resistant tuberculosis is the major obstacle for researchers and letting them fail continuously to discover new drug candidates. Among the numerous antitubercular targets, Decaprenyl-phosphoryl-β-D-ribose-2'-epimerase (DprE1) is novel target identified in the year 2009. The present article portrays insights of DprE1 enzyme in all the aspects i.e., identification, structural elucidation to designing strategies and synthesis of potential drug candidates to combat resistant strains. Along with the synthesis and biological activity of novel compounds, structure-activity relationship (SAR) data is given to help medicinal chemists and researchers working in this area for the development of new inhibitors to fight against M. tuberculosis. DprE1 is new ray of hope for antitubercular treatment. No single drug candidate (DprE1 inhibitor) has passed clinical trial yet and hence it nullifies the risk of development of resistance or mutations at specific residues. Researchers working in this area have to design and come up with new potent candidates with less dose, no toxicity to combat this deadly infection. This review emphasized on year wise systematic development and progress of DprE1 inhibitors.
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Affiliation(s)
- Chandrakant Bonde
- Department of Pharmaceutical Chemistry, SVKM's NMIMS School of Pharmacy and Technology Management, Shirpur Campus, MS, 425 405, India
| | - Jineetkumar Gawad
- Department of Pharmaceutical Chemistry, SVKM's NMIMS School of Pharmacy and Technology Management, Shirpur Campus, MS, 425 405, India.
| | - Smita Bonde
- Department of Pharmaceutical Chemistry, SVKM's NMIMS School of Pharmacy and Technology Management, Shirpur Campus, MS, 425 405, India
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11
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Volkov AA, Bugaenko DI, Bogdanov AV, Karchava AV. Visible-Light-Driven Thioesterification of Aryl Halides with Potassium Thiocarboxylates: Transition-Metal Catalyst-Free Incorporation of Sulfur Functionalities into an Aromatic Ring. J Org Chem 2022; 87:8170-8182. [PMID: 35653579 DOI: 10.1021/acs.joc.2c00913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reactions of acceptor-substituted aryl iodides and bromides with potassium thiocarboxylates under white light irradiation allow for the preparation of S-aryl thioesters including synthetically versatile S-aryl thioacetates. This transition-metal and external photocatalyst-free method features extremely mild reaction conditions compared with those used in transition-metal-catalyzed protocols. Reactions proceed via the initial formation of an electron donor-acceptor (EDA) complex in the ground state, which was supported by UV-vis spectra. Electron paramagnetic resonance (EPR) spin-trapping experiments using phenyl-N-tert-butylnitrone (PBN) have revealed the radical nature of the reaction.
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Affiliation(s)
- Alexey A Volkov
- Department of Chemistry, Moscow State University, Moscow 119234, Russia
| | - Dmitry I Bugaenko
- Department of Chemistry, Moscow State University, Moscow 119234, Russia
| | - Alexey V Bogdanov
- Department of Chemistry, Moscow State University, Moscow 119234, Russia
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12
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Fernandes GFS, Thompson AM, Castagnolo D, Denny WA, Dos Santos JL. Tuberculosis Drug Discovery: Challenges and New Horizons. J Med Chem 2022; 65:7489-7531. [PMID: 35612311 DOI: 10.1021/acs.jmedchem.2c00227] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Over the past 2000 years, tuberculosis (TB) has claimed more lives than any other infectious disease. In 2020 alone, TB was responsible for 1.5 million deaths worldwide, comparable to the 1.8 million deaths caused by COVID-19. The World Health Organization has stated that new TB drugs must be developed to end this pandemic. After decades of neglect in this field, a renaissance era of TB drug discovery has arrived, in which many novel candidates have entered clinical trials. However, while hundreds of molecules are reported annually as promising anti-TB agents, very few successfully progress to clinical development. In this Perspective, we critically review those anti-TB compounds published in the last 6 years that demonstrate good in vivo efficacy against Mycobacterium tuberculosis. Additionally, we highlight the main challenges and strategies for developing new TB drugs and the current global pipeline of drug candidates in clinical studies to foment fresh research perspectives.
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Affiliation(s)
- Guilherme F S Fernandes
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Andrew M Thompson
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Daniele Castagnolo
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - William A Denny
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Jean L Dos Santos
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara 14800903, Brazil
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13
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Kuang W, Zhang H, Wang X, Yang P. Overcoming Mycobacterium tuberculosis through small molecule inhibitors to break down cell wall synthesis. Acta Pharm Sin B 2022; 12:3201-3214. [PMID: 35967276 PMCID: PMC9366312 DOI: 10.1016/j.apsb.2022.04.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/08/2022] [Accepted: 04/19/2022] [Indexed: 12/16/2022] Open
Abstract
Mycobacterium tuberculosis (MTB) utilizes multiple mechanisms to obtain antibiotic resistance during the treatment of infections. In addition, the biofilms, secreted by MTB, can further protect the latter from the contact with drug molecules and immune cells. These self-defending mechanisms lay a formidable challenge to develop effective therapeutic agents against chronic and recurring antibiotic-tolerant MTB infections. Although several inexpensive and effective drugs (isoniazid, rifampicin, pyrazinamide and ethambutol) have been discovered for the treatment regimen, MTB continues to cause considerable morbidity and mortality worldwide. Antibiotic resistance and tolerance remain major global issues, and innovative therapeutic strategies are urgently needed to address the challenges associated with pathogenic bacteria. Gratifyingly, the cell wall synthesis of tubercle bacilli requires the participation of many enzymes which exclusively exist in prokaryotic organisms. These enzymes, absent in human hepatocytes, are recognized as promising targets to develop anti-tuberculosis drug. In this paper, we discussed the critical roles of potential drug targets in regulating cell wall synthesis of MTB. And also, we systematically reviewed the advanced development of novel bioactive compounds or drug leads for inhibition of cell wall synthesis, including their discovery, chemical modification, in vitro and in vivo evaluation.
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Affiliation(s)
- Wenbin Kuang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Haolin Zhang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Xiao Wang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Peng Yang
- State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
- Corresponding author.
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14
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Wang P, Batt SM, Wang B, Fu L, Qin R, Lu Y, Li G, Besra GS, Huang H. Discovery of Novel Thiophene-arylamide Derivatives as DprE1 Inhibitors with Potent Antimycobacterial Activities. J Med Chem 2021; 64:6241-6261. [PMID: 33852302 PMCID: PMC8154581 DOI: 10.1021/acs.jmedchem.1c00263] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In this study, we report the design and synthesis of a series of novel thiophene-arylamide compounds derived from the noncovalent decaprenylphosphoryl-β-d-ribose 2'-epimerase (DprE1) inhibitor TCA1 through a structure-based scaffold hopping strategy. Systematic optimization of the two side chains flanking the thiophene core led to new lead compounds bearing a thiophene-arylamide scaffold with potent antimycobacterial activity and low cytotoxicity. Compounds 23j, 24f, 25a, and 25b exhibited potent in vitro activity against both drug-susceptible (minimum inhibitory concentration (MIC) = 0.02-0.12 μg/mL) and drug-resistant (MIC = 0.031-0.24 μg/mL) tuberculosis strains while retaining potent DprE1 inhibition (half maximal inhibitory concentration (IC50) = 0.2-0.9 μg/mL) and good intracellular antimycobacterial activity. In addition, these compounds showed good hepatocyte stability and low inhibition of the human ether-à-go-go related gene (hERG) channel. The representative compound 25a with acceptable pharmacokinetic property demonstrated significant bactericidal activity in an acute mouse model of tuberculosis. Moreover, the molecular docking study of template compound 23j provides new insight into the discovery of novel antitubercular agents targeting DprE1.
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Affiliation(s)
- Pengxu Wang
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation & Chinese Academy of Medical Sciences Key Laboratory of Anti-DR TB Innovative Drug Research, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
| | - Sarah M Batt
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Bin Wang
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, 97 Ma Chang Street, Beijing 101149, P. R. China
| | - Lei Fu
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, 97 Ma Chang Street, Beijing 101149, P. R. China
| | - Rongfei Qin
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation & Chinese Academy of Medical Sciences Key Laboratory of Anti-DR TB Innovative Drug Research, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
| | - Yu Lu
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, 97 Ma Chang Street, Beijing 101149, P. R. China
| | - Gang Li
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation & Chinese Academy of Medical Sciences Key Laboratory of Anti-DR TB Innovative Drug Research, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
| | - Gurdyal S Besra
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Haihong Huang
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation & Chinese Academy of Medical Sciences Key Laboratory of Anti-DR TB Innovative Drug Research, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, P. R. China
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15
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Awale M, Hert J, Guasch L, Riniker S, Kramer C. The Playbooks of Medicinal Chemistry Design Moves. J Chem Inf Model 2021; 61:729-742. [PMID: 33522806 DOI: 10.1021/acs.jcim.0c01143] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Large databases of biologically relevant molecules, such as ChEMBL, SureChEMBL, or compound collections of pharmaceutical or agrochemical companies, are invaluable sources of medicinal chemistry information, albeit implicit. We developed a modified matched molecular pair approach to systematically and exhaustively extract the transformations in these databases and distill them into snippets of explicit design knowledge that are easily interpretable and directly applicable. The resulting "playbooks of medicinal chemistry design moves" capture the collective pharmaceutical and agrochemical research expertise across multiple chemists, companies, targets, and projects. They can be queried in an automated fashion for systematic prospective design and compound generation. The ChEMBL playbook and an application to exploit it are available at https://github.com/mahendra-awale/medchem_moves.
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Affiliation(s)
- Mahendra Awale
- Computer-Aided Drug Design/Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Jérôme Hert
- Computer-Aided Drug Design/Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Laura Guasch
- Computer-Aided Drug Design/Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Christian Kramer
- Computer-Aided Drug Design/Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
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