1
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Krieger IV, Yalamanchili S, Dickson P, Engelhart CA, Zimmerman MD, Wood J, Clary E, Nguyen J, Thornton N, Centrella PA, Chan B, Cuozzo JW, Gengenbacher M, Guié MA, Guilinger JP, Bienstock C, Hartl H, Hupp CD, Jetson R, Satoh T, Yeoman JTS, Zhang Y, Dartois V, Schnappinger D, Keefe AD, Sacchettini JC. Inhibitors of the Thioesterase Activity of Mycobacterium tuberculosis Pks13 Discovered Using DNA-Encoded Chemical Library Screening. ACS Infect Dis 2024; 10:1561-1575. [PMID: 38577994 PMCID: PMC11091879 DOI: 10.1021/acsinfecdis.3c00592] [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: 11/02/2023] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 04/06/2024]
Abstract
DNA-encoded chemical library (DEL) technology provides a time- and cost-efficient method to simultaneously screen billions of compounds for their affinity to a protein target of interest. Here we report its use to identify a novel chemical series of inhibitors of the thioesterase activity of polyketide synthase 13 (Pks13) from Mycobacterium tuberculosis (Mtb). We present three chemically distinct series of inhibitors along with their enzymatic and Mtb whole cell potency, the measure of on-target activity in cells, and the crystal structures of inhibitor-enzyme complexes illuminating their interactions with the active site of the enzyme. One of these inhibitors showed a favorable pharmacokinetic profile and demonstrated efficacy in an acute mouse model of tuberculosis (TB) infection. These findings and assay developments will aid in the advancement of TB drug discovery.
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Affiliation(s)
- Inna V. Krieger
- Department
of Biochemistry & Biophysics, Texas
A&M University, College
Station, Texas 77843, United States
| | | | - Paige Dickson
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Curtis A. Engelhart
- Department
of Microbiology and Immunology, Weill Cornell
Medicine, New York, New York 10021, United States
| | - Matthew D Zimmerman
- Center for
Discovery and Innovation, Hackensack Meridian
Health, Nutley, New Jersey 07110, United States
| | - Jeremy Wood
- Department
of Biochemistry & Biophysics, Texas
A&M University, College
Station, Texas 77843, United States
| | - Ethan Clary
- Department
of Biochemistry & Biophysics, Texas
A&M University, College
Station, Texas 77843, United States
| | - Jasmine Nguyen
- Department
of Biochemistry & Biophysics, Texas
A&M University, College
Station, Texas 77843, United States
| | - Natalie Thornton
- Department
of Microbiology and Immunology, Weill Cornell
Medicine, New York, New York 10021, United States
| | - Paolo A. Centrella
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Betty Chan
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Auron
Therapeutics, 55 Chapel
Street, Newton, Massachusetts 02458, United States
| | - John W Cuozzo
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Relay
Therapeutics, 399 Binney Street, Cambridge, Massachusetts 02141, United States
| | - Martin Gengenbacher
- Center for
Discovery and Innovation, Hackensack Meridian
Health, Nutley, New Jersey 07110, United States
| | - Marie-Aude Guié
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - John P Guilinger
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Corey Bienstock
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Hajnalka Hartl
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Orogen
Therapeutics, 12 Gill
Street, Woburn, Massachusetts 01801, United States
| | - Christopher D. Hupp
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Ipsen Bioscience
Inc., 1 Main Street, Cambridge, Massachusetts 02142, United States
| | - Rachael Jetson
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Valo
Health, 75 Hayden Avenue, Lexington, Massachusetts 02141, United States
| | - Takashi Satoh
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- EXO
Therapeutics, 150 Cambridgepark
Drive, suite 300, Cambridge, Massachusetts 02140, United States
| | - John T. S. Yeoman
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
- Recludix
Pharmaceuticals, 222
Third Street, Cambridge, Massachusetts 02142, United States
| | - Ying Zhang
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Veronique Dartois
- Center for
Discovery and Innovation, Hackensack Meridian
Health, Nutley, New Jersey 07110, United States
- Hackensack
Meridian School of Medicine, Hackensack
Meridian Health, Nutley, New Jersey 07110, United States
| | - Dirk Schnappinger
- Department
of Microbiology and Immunology, Weill Cornell
Medicine, New York, New York 10021, United States
| | - Anthony D. Keefe
- X-Chem Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - James C. Sacchettini
- Department
of Biochemistry & Biophysics, Texas
A&M University, College
Station, Texas 77843, United States
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2
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Collie GW, Clark MA, Keefe AD, Madin A, Read JA, Rivers EL, Zhang Y. Screening Ultra-Large Encoded Compound Libraries Leads to Novel Protein-Ligand Interactions and High Selectivity. J Med Chem 2024; 67:864-884. [PMID: 38197367 PMCID: PMC10823476 DOI: 10.1021/acs.jmedchem.3c01861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/17/2023] [Accepted: 12/04/2023] [Indexed: 01/11/2024]
Abstract
The DNA-encoded library (DEL) discovery platform has emerged as a powerful technology for hit identification in recent years. It has become one of the major parallel workstreams for small molecule drug discovery along with other strategies such as HTS and data mining. For many researchers working in the DEL field, it has become increasingly evident that many hits and leads discovered via DEL screening bind to target proteins with unique and unprecedented binding modes. This Perspective is our attempt to analyze reports of DEL screening with the purpose of providing a rigorous and useful account of the binding modes observed for DEL-derived ligands with a focus on binding mode novelty.
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Affiliation(s)
| | | | | | | | | | | | - Ying Zhang
- X-Chem,
Inc., Waltham, Massachusetts 02453, United States
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3
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Zhang Q, Han J, Zhu Y, Yu F, Hu X, Tong HHY, Liu H. Discovery of novel and potent InhA direct inhibitors by ensemble docking-based virtual screening and biological assays. J Comput Aided Mol Des 2023; 37:695-706. [PMID: 37642861 DOI: 10.1007/s10822-023-00530-4] [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: 05/09/2023] [Accepted: 08/15/2023] [Indexed: 08/31/2023]
Abstract
Multidrug-resistant tuberculosis (MDR-TB) continues to spread worldwide and remains one of the leading causes of death among infectious diseases. The enoyl-acyl carrier protein reductase (InhA) belongs to FAS-II family and is essential for the formation of the Mycobacterium tuberculosis cell wall. Recent years, InhA direct inhibitors have been extensively studied to overcome MDR-TB. However, there are still no inhibitors that have entered clinical research. Here, the ensemble docking-based virtual screening along with biological assay were used to identify potent InhA direct inhibitors from Chembridge, Chemdiv, and Specs. Ultimately, 34 compounds were purchased and first assayed for the binding affinity, of which four compounds can bind InhA well with KD values ranging from 48.4 to 56.2 µM. Among them, compound 9,222,034 has the best inhibitory activity against InhA enzyme with an IC50 value of 18.05 µM. In addition, the molecular dynamic simulation and binding free energy calculation indicate that the identified compounds bind to InhA with "extended" conformation. Residue energy decomposition shows that residues such as Tyr158, Met161, and Met191 have higher energy contributions in the binding of compounds. By analyzing the binding modes, we found that these compounds can bind to a hydrophobic sub-pocket formed by residues Tyr158, Phe149, Ile215, Leu218, etc., resulting in extensive van der Waals interactions. In summary, this study proposed an efficient strategy for discovering InhA direct inhibitors through ensemble docking-based virtual screening, and finally identified four active compounds with new skeletons, which can provide valuable information for the discovery and optimization of InhA direct inhibitors.
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Affiliation(s)
- Qianqian Zhang
- Faculty of Applied Sciences, Macao Polytechnic University, Macao, SAR, China
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, China
| | - Jianting Han
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, China
| | - Yongchang Zhu
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, China
| | - Fansen Yu
- School of Pharmacy, Lanzhou University, Lanzhou, 730000, China
| | - Xiaopeng Hu
- Faculty of Applied Sciences, Macao Polytechnic University, Macao, SAR, China
| | - Henry H Y Tong
- Faculty of Applied Sciences, Macao Polytechnic University, Macao, SAR, China
| | - Huanxiang Liu
- Faculty of Applied Sciences, Macao Polytechnic University, Macao, SAR, China.
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4
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Davoodi S, Daryaee F, Iuliano JN, Collado JT, He Y, Pollard AC, Gil AA, Aramini JM, Tonge PJ. Evaluating the Impact of the Tyr158 p Ka on the Mechanism and Inhibition of InhA, the Enoyl-ACP Reductase from Mycobacterium tuberculosis. Biochemistry 2023; 62:1943-1952. [PMID: 37270808 PMCID: PMC10329767 DOI: 10.1021/acs.biochem.2c00606] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
InhA, the Mycobacterium tuberculosis enoyl-ACP reductase, is a target for the tuberculosis (TB) drug isoniazid (INH). InhA inhibitors that do not require KatG activation avoid the most common mechanism of INH resistance, and there are continuing efforts to fully elucidate the enzyme mechanism to drive inhibitor discovery. InhA is a member of the short-chain dehydrogenase/reductase superfamily characterized by a conserved active site Tyr, Y158 in InhA. To explore the role of Y158 in the InhA mechanism, this residue has been replaced by fluoroTyr residues that increase the acidity of Y158 up to ∼3200-fold. Replacement of Y158 with 3-fluoroTyr (3-FY) and 3,5-difluoroTyr (3,5-F2Y) has no effect on kcatapp/KMapp nor on the binding of inhibitors to the open form of the enzyme (Kiapp), whereas both kcatapp/KMapp and Kiapp are altered by seven-fold for the 2,3,5-trifluoroTyr variant (2,3,5-F3Y158 InhA). 19F NMR spectroscopy suggests that 2,3,5-F3Y158 is ionized at neutral pH indicating that neither the acidity nor ionization state of residue 158 has a major impact on catalysis or on the binding of substrate-like inhibitors. In contrast, Ki*app is decreased 6- and 35-fold for the binding of the slow-onset inhibitor PT504 to 3,5-F2Y158 and 2,3,5-F3Y158 InhA, respectively, indicating that Y158 stabilizes the closed form of the enzyme adopted by EI*. The residence time of PT504 is reduced ∼four-fold for 2,3,5-F3Y158 InhA compared to wild-type, and thus, the hydrogen bonding interaction of the inhibitor with Y158 is an important factor in the design of InhA inhibitors with increased residence times on the enzyme.
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Affiliation(s)
- Shabnam Davoodi
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, United States
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, United States
| | - Fereidoon Daryaee
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, United States
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, United States
| | - James N. Iuliano
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, United States
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, United States
| | - Jinnette Tolentino Collado
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, United States
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, United States
| | - Yongle He
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, United States
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, United States
| | - Alyssa C. Pollard
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, United States
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, United States
| | - Agnieszka A. Gil
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, United States
| | - James M. Aramini
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, United States
| | - Peter J. Tonge
- Center for Advanced Study of Drug Action, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, United States
- Department of Chemistry, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, United States
- Department of Radiology, John S. Toll Drive, Stony Brook University, Stony Brook, NY 11794-3400, United States
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5
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Wen X, Wu X, Jin R, Lu X. Privileged heterocycles for DNA-encoded library design and hit-to-lead optimization. Eur J Med Chem 2023; 248:115079. [PMID: 36669370 DOI: 10.1016/j.ejmech.2022.115079] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 12/22/2022] [Accepted: 12/29/2022] [Indexed: 01/15/2023]
Abstract
It is well known that heterocyclic compounds play a key role in improving drug activity, target selectivity, physicochemical properties as well as reducing toxicity. In this review, we summarized the representative heterocyclic structures involved in hit compounds which were obtained from DNA-encoded library from 2013 to 2021. In some examples, the state of the art in heterocycle-based DEL synthesis and hit-to-lead optimization are highlighted. We hope that more and more novel heterocycle-based DEL toolboxes and in-depth pharmaceutical research on these lead compounds can be developed to accelerate the discovery of new drugs.
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Affiliation(s)
- Xin Wen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China.
| | - Xinyuan Wu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China.
| | - Rui Jin
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China.
| | - Xiaojie Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China.
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6
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Simple to Complex Amide Derivatives as Potent Anti‐Tuberculosis Agents: A Literature Survey of the Past Decade. ChemistrySelect 2022. [DOI: 10.1002/slct.202202584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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7
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Binding Thermodynamics and Dissociation Kinetics Analysis Uncover the Key Structural Motifs of Phenoxyphenol Derivatives as the Direct InhA Inhibitors and the Hotspot Residues of InhA. Int J Mol Sci 2022; 23:ijms231710102. [PMID: 36077494 PMCID: PMC9456180 DOI: 10.3390/ijms231710102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
Given the current epidemic of multidrug-resistant tuberculosis, there is an urgent need to develop new drugs to combat drug-resistant tuberculosis. Direct inhibitors of the InhA target do not require activation and thus can overcome drug resistance caused by mutations in drug-activating enzymes. In this work, the binding thermodynamic and kinetic information of InhA to its direct inhibitors, phenoxyphenol derivatives, were explored through multiple computer-aided drug design (CADD) strategies. The results show that the van der Waals interactions were the main driving force for protein–ligand binding, among which hydrophobic residues such as Tyr158, Phe149, Met199 and Ile202 have high energy contribution. The AHRR pharmacophore model generated by multiple ligands demonstrated that phenoxyphenol derivatives inhibitors can form pi–pi stacking and hydrophobic interactions with InhA target. In addition, the order of residence time predicted by random acceleration molecular dynamics was consistent with the experimental values. The intermediate states of these inhibitors could form hydrogen bonds and van der Waals interactions with surrounding residues during dissociation. Overall, the binding and dissociation mechanisms at the atomic level obtained in this work can provide important theoretical guidance for the development of InhA direct inhibitors with higher activity and proper residence time.
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8
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El Sawy MA, Elshatanofy MM, El Kilany Y, Kandeel K, Elwakil BH, Hagar M, Aouad MR, Albelwi FF, Rezki N, Jaremko M, El Ashry ESH. Novel Hybrid 1,2,4- and 1,2,3-Triazoles Targeting Mycobacterium Tuberculosis Enoyl Acyl Carrier Protein Reductase (InhA): Design, Synthesis, and Molecular Docking. Int J Mol Sci 2022; 23:4706. [PMID: 35563096 PMCID: PMC9103244 DOI: 10.3390/ijms23094706] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/11/2022] [Accepted: 04/15/2022] [Indexed: 12/28/2022] Open
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis is still a serious public health concern around the world. More treatment strategies or more specific molecular targets have been sought by researchers. One of the most important targets is M. tuberculosis' enoyl-acyl carrier protein reductase InhA which is considered a promising, well-studied target for anti-tuberculosis medication development. Our team has made it a goal to find new lead structures that could be useful in the creation of new antitubercular drugs. In this study, a new class of 1,2,3- and 1,2,4-triazole hybrid compounds was prepared. Click synthesis was used to afford 1,2,3-triazoles scaffold linked to 1,2,4-triazole by fixable mercaptomethylene linker. The new prepared compounds have been characterized by different spectroscopic tools. The designed compounds were tested in vitro against the InhA enzyme. At 10 nM, the inhibitors 5b, 5c, 7c, 7d, 7e, and 7f successfully and totally (100%) inhibited the InhA enzyme. The IC50 values were calculated using different concentrations. With IC50 values of 0.074 and 0.13 nM, 7c and 7e were the most promising InhA inhibitors. Furthermore, a molecular docking investigation was carried out to support antitubercular activity as well as to analyze the binding manner of the screened compounds with the target InhA enzyme's binding site.
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Affiliation(s)
- Maged A. El Sawy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Pharos University, Alexandria 21311, Egypt
| | - Maram M. Elshatanofy
- Department of Chemistry, Faculty of Science, Alexandria University, Alexandria 21321, Egypt; (M.M.E.); (Y.E.K.); (M.H.)
| | - Yeldez El Kilany
- Department of Chemistry, Faculty of Science, Alexandria University, Alexandria 21321, Egypt; (M.M.E.); (Y.E.K.); (M.H.)
| | - Kamal Kandeel
- Department of Biochemistry, Faculty of Science, Alexandria University, Moharam Beik, Alexandria 21547, Egypt;
| | - Bassma H. Elwakil
- Department of Medical Laboratory Technology, Faculty of Applied Health Sciences Technology, Pharos University in Alexandria, Alexandria 21311, Egypt;
| | - Mohamed Hagar
- Department of Chemistry, Faculty of Science, Alexandria University, Alexandria 21321, Egypt; (M.M.E.); (Y.E.K.); (M.H.)
| | - Mohamed Reda Aouad
- Department of Chemistry, Faculty of Science, Taibah University, Al-Madinah Al-Munawarah 30002, Saudi Arabia; (M.R.A.); (F.F.A.); (N.R.)
| | - Fawzia Faleh Albelwi
- Department of Chemistry, Faculty of Science, Taibah University, Al-Madinah Al-Munawarah 30002, Saudi Arabia; (M.R.A.); (F.F.A.); (N.R.)
| | - Nadjet Rezki
- Department of Chemistry, Faculty of Science, Taibah University, Al-Madinah Al-Munawarah 30002, Saudi Arabia; (M.R.A.); (F.F.A.); (N.R.)
| | - Mariusz Jaremko
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), P.O. Box 4700, Thuwal 23955-6900, Saudi Arabia;
| | - El Sayed H. El Ashry
- Department of Chemistry, Faculty of Science, Alexandria University, Alexandria 21321, Egypt; (M.M.E.); (Y.E.K.); (M.H.)
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9
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Sunkari YK, Siripuram VK, Nguyen TL, Flajolet M. High-power screening (HPS) empowered by DNA-encoded libraries. Trends Pharmacol Sci 2021; 43:4-15. [PMID: 34782164 DOI: 10.1016/j.tips.2021.10.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/29/2021] [Accepted: 10/14/2021] [Indexed: 01/19/2023]
Abstract
The world is totally dependent on medications. As science progresses, new, better, and cheaper drugs are needed more than ever. The pharmaceutical industry has been predominantly dependent on high-throughput screening (HTS) for the past three decades. Considering that the discovery rate has been relatively constant, can one hope for a much-needed sudden trend uptick? DNA-encoded libraries (DELs) and similar technologies, that have several orders of magnitude more screening power than HTS, and that we propose to group together under the umbrella term of high-power screening (HPS), are very well positioned to do exactly that. HPS also offers novel screening options such as parallel screening, ex vivo and in vivo screening, as well as a new path to druggable alternatives such as proteolysis targeting chimeras (PROTACs). Altogether, HPS unlocks novel powerful drug discovery avenues.
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Affiliation(s)
- Yashoda Krishna Sunkari
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY, USA
| | - Vijay Kumar Siripuram
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY, USA
| | - Thu-Lan Nguyen
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY, USA
| | - Marc Flajolet
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY, USA.
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10
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Castan IFSF, Graham JS, Salvini CLA, Stanway-Gordon HA, Waring MJ. On the design of lead-like DNA-encoded chemical libraries. Bioorg Med Chem 2021; 43:116273. [PMID: 34147943 DOI: 10.1016/j.bmc.2021.116273] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/25/2021] [Accepted: 06/04/2021] [Indexed: 01/11/2023]
Abstract
DNA-encoded libraries (DELs) are becoming an established technology for finding ligands for protein targets. We have abstracted and analysed libraries from the literature to assess the synthesis strategy, selections of reactions and monomers and their propensity to reveal hits. DELs have led to hit compounds across a range of diverse protein classes. The range of reactions and monomers utilised has been relatively limited and the hits are often higher in molecular weight than might be considered ideal. Considerations for future library designs with reference to chemical diversity and lead-like properties are discussed.
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Affiliation(s)
- Isaline F S F Castan
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Jessica S Graham
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Catherine L A Salvini
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Harriet A Stanway-Gordon
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Michael J Waring
- Cancer Research UK Newcastle Drug Discovery Unit, Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
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11
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Venugopala KN, Deb PK, Pillay M, Chopra D, Chandrashekharappa S, Morsy MA, Aldhubiab BE, Attimarad M, Nair AB, Sreeharsha N, Kandeel M, Venugopala R, Mohanlall V. 4-Aryl-1,4-Dihydropyridines as Potential Enoyl-Acyl Carrier Protein Reductase Inhibitors: Antitubercular Activity and Molecular Docking Study. Curr Top Med Chem 2021; 21:295-306. [PMID: 33138763 DOI: 10.2174/1568026620666201102121606] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/16/2020] [Accepted: 10/05/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Tuberculosis remains one of the most deadly infectious diseases worldwide due to the emergence of multi-drug resistance (MDR) and extensively drug resistance (XDR) strains of Mycobacterium tuberculosis (MTB). AIMS Currently, available drugs are getting resistant and toxic. Hence, there is an urgent need for the development of potent molecules to treat tuberculosis. MATERIALS AND METHODS Herein, the screening of a total of eight symmetrical 1,4-dihydropyridine (1,4- DHP) derivatives (4a-4h) was carried out for whole-cell anti-TB activity against the susceptible H37Rv and MDR strains of MTB. RESULTS AND DISCUSSION Most of the compounds exhibited moderate to excellent activity against the susceptible H37Rv. Moreover, the most promising compound 4f (against H37Rv) having paratrifluoromethyl phenyl group at 4-position and bis para-methoxy benzyl ester group at 3- and 5- positions of 1,4-dihydropyridine pharmacophore, exhibited no toxicity, but demonstrated weak activity against MTB strains resistant to isoniazid and rifampicin. In light of the inhibitory profile of the title compounds, enoyl-acyl carrier protein reductase (InhA) appeared to be the appropriate molecular target. A docking study of these derivatives against InhA receptor revealed favorable binding interactions. Further, in silico predicted ADME properties of these compounds 4a-4h were found to be in the acceptable ranges, including satisfactory Lipinski's rule of five, thereby indicating their potential as drug-like molecules. CONCLUSION In particular, the 1,4-DHP derivative 4f can be considered an attractive lead molecule for further exploration and development of more potent anti-TB agents as InhA inhibitors.
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Affiliation(s)
- Katharigatta N Venugopala
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Pran Kishore Deb
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Philadelphia University, Amman 19392, Jordan
| | - Melendhran Pillay
- Department of Microbiology, National Health Laboratory Services, KZN Academic Complex, Inkosi Albert Luthuli Central Hospital, Durban 4001, South Africa
| | - Deepak Chopra
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal By-pass Road, Bhauri, Bhopal 462 066, Madhya Pradesh, India
| | | | - Mohamed A Morsy
- Department of Pharmacology, Faculty of Medicine, Minia University, El-Minia 61511, Egypt
| | - Bandar E Aldhubiab
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Mahesh Attimarad
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Anroop B Nair
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Nagaraja Sreeharsha
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Mahmoud Kandeel
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Rashmi Venugopala
- Department of Public Health Medicine, University of KwaZulu-Natal, Howard College Campus, Durban 4001, South Africa
| | - Viresh Mohanlall
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban 4001, South Africa
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Venugopala KN, Chandrashekharappa S, Deb PK, Tratrat C, Pillay M, Chopra D, Al-Shar'i NA, Hourani W, Dahabiyeh LA, Borah P, Nagdeve RD, Nayak SK, Padmashali B, Morsy MA, Aldhubiab BE, Attimarad M, Nair AB, Sreeharsha N, Haroun M, Shashikanth S, Mohanlall V, Mailavaram R. Anti-tubercular activity and molecular docking studies of indolizine derivatives targeting mycobacterial InhA enzyme. J Enzyme Inhib Med Chem 2021; 36:1472-1487. [PMID: 34210233 PMCID: PMC8259857 DOI: 10.1080/14756366.2021.1919889] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
A series of 1,2,3-trisubstituted indolizines (2a-2f, 3a-3d, and 4a-4c) were screened for in vitro whole-cell anti-tubercular activity against the susceptible H37Rv and multidrug-resistant (MDR) Mycobacterium tuberculosis (MTB) strains. Compounds 2b-2d, 3a-3d, and 4a-4c were active against the H37Rv-MTB strain with minimum inhibitory concentration (MIC) ranging from 4 to 32 µg/mL, whereas the indolizines 4a-4c, with ethyl ester group at the 4-position of the benzoyl ring also exhibited anti-MDR-MTB activity (MIC = 16-64 µg/mL). In silico docking study revealed the enoyl-acyl carrier protein reductase (InhA) and anthranilate phosphoribosyltransferase as potential molecular targets for the indolizines. The X-ray diffraction analysis of the compound 4b was also carried out. Further, a safety study (in silico and in vitro) demonstrated no toxicity for these compounds. Thus, the indolizines warrant further development and may represent a novel promising class of InhA inhibitors and multi-targeting agents to combat drug-sensitive and drug-resistant MTB strains.
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Affiliation(s)
- Katharigatta N Venugopala
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia.,Department of Biotechnology and Food Technology, Durban University of Technology, Durban, South Africa
| | | | - Pran Kishore Deb
- Faculty of Pharmacy, Department of Pharmaceutical Sciences, Philadelphia University, Amman, Jordan
| | - Christophe Tratrat
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Melendhran Pillay
- Department of Microbiology, National Health Laboratory Services, KZN Academic Complex, Inkosi Albert Luthuli Central Hospital, Durban, South Africa
| | - Deepak Chopra
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Nizar A Al-Shar'i
- Faculty of Pharmacy, Department of Medicinal Chemistry and Pharmacognosy, Jordan University of Science and Technology, Irbid, Jordan
| | - Wafa Hourani
- Faculty of Pharmacy, Department of Pharmaceutical Sciences, Philadelphia University, Amman, Jordan
| | - Lina A Dahabiyeh
- Department of Pharmaceutical Sciences, School of Pharmacy, The University of Jordan, Amman, Jordan
| | - Pobitra Borah
- Pratiksha Institute of Pharmaceutical Sciences, Guwahati, India
| | - Rahul D Nagdeve
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, India
| | - Susanta K Nayak
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur, India
| | - Basavaraj Padmashali
- Department of Chemistry, School of Basic Science, Rani Channamma University, Belagavi, India
| | - Mohamed A Morsy
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia.,Faculty of Medicine, Department of Pharmacology, Minia University, El-Minia, Egypt
| | - Bandar E Aldhubiab
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Mahesh Attimarad
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Anroop B Nair
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Nagaraja Sreeharsha
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia.,Department of Pharmaceutics, Vidya Siri College of Pharmacy, Bangalore, India
| | - Michelyne Haroun
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Sheena Shashikanth
- Department of Studies in Organic Chemistry, University of Mysore, Mysore, India
| | - Viresh Mohanlall
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, South Africa
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13
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Oh S, Trifonov L, Yadav VD, Barry CE, Boshoff HI. Tuberculosis Drug Discovery: A Decade of Hit Assessment for Defined Targets. Front Cell Infect Microbiol 2021; 11:611304. [PMID: 33791235 PMCID: PMC8005628 DOI: 10.3389/fcimb.2021.611304] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/25/2021] [Indexed: 11/20/2022] Open
Abstract
More than two decades have elapsed since the publication of the first genome sequence of Mycobacterium tuberculosis (Mtb) which, shortly thereafter, enabled methods to determine gene essentiality in the pathogen. Despite this, target-based approaches have not yielded drugs that have progressed to clinical testing. Whole-cell screening followed by elucidation of mechanism of action has to date been the most fruitful approach to progressing inhibitors into the tuberculosis drug discovery pipeline although target-based approaches are gaining momentum. This review discusses scaffolds that have been identified over the last decade from screens of small molecule libraries against Mtb or defined targets where mechanism of action investigation has defined target-hit couples and structure-activity relationship studies have described the pharmacophore.
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Affiliation(s)
- Sangmi Oh
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Lena Trifonov
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Veena D Yadav
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Clifton E Barry
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Helena I Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
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14
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Gaikwad NB, Nirmale K, Sahoo SK, Ahmad MN, Kaul G, Shukla M, Nanduri S, Das Gupta A, Chopra S, Yaddanapudi MV. Design, synthesis, in silico, and in vitro evaluation of 3-phenylpyrazole acetamide derivatives as antimycobacterial agents. Arch Pharm (Weinheim) 2020; 354:e2000349. [PMID: 33351199 DOI: 10.1002/ardp.202000349] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/12/2020] [Accepted: 11/21/2020] [Indexed: 11/12/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is one of the most dangerous pathogens affecting immunocompetent and immunocompromised patients worldwide. Novel molecules, which are efficient and can reduce the duration of therapy against drug-resistant strains, are an urgent unmet need of the hour. In our current study, a series of new 2-(3-phenyl-1H-pyrazol-1-yl)acetamide and N'-benzylidene-2-(3-phenyl-1H-pyrazol-1-yl)acetohydrazide derivatives were designed, synthesized, and evaluated for their antimycobacterial potential. The biological evaluation revealed that 6b, 6m, 6l, 7a, and 7k exhibited selective and potent inhibitory activity against Mtb. Furthermore, compounds 6m and 7h were found to be nontoxic to Vero cells with CC50 of greater than 20 and 80 mg/ml, respectively, and exhibited promising selectivity indices (SI) of greater than 666 and 320, respectively. All derivatives exhibited excellent ADME (absorption, distribution, metabolism, and excretion) properties in silico. Also, all the derivatives were found compliant with Lipinski's rule of five, showing their druggability profile. Molecular docking insights of these derivatives have shown outstanding binding energies on the mycobacterial membrane protein large transporters. These results indicate that this scaffold may lead to a potential antimycobacterial drug candidate in the discovery of antitubercular agents.
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Affiliation(s)
- Nikhil B Gaikwad
- Department of Pharmaceutical Technology and Process Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, India
| | - Krishna Nirmale
- Department of Pharmaceutical Technology and Process Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, India
| | - Santosh K Sahoo
- Department of Pharmaceutical Technology and Process Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, India
| | - Mohammad N Ahmad
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Grace Kaul
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, India
| | - Manjulika Shukla
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, India
| | - Srinivas Nanduri
- Department of Pharmaceutical Technology and Process Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, India
| | - Arunava Das Gupta
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, India
| | - Sidharth Chopra
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, India
| | - Madhavi V Yaddanapudi
- Department of Pharmaceutical Technology and Process Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, India
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15
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Armstrong T, Lamont M, Lanne A, Alderwick LJ, Thomas NR. Inhibition of Mycobacterium tuberculosis InhA: Design, synthesis and evaluation of new di-triclosan derivatives. Bioorg Med Chem 2020; 28:115744. [PMID: 33007556 DOI: 10.1016/j.bmc.2020.115744] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/24/2020] [Accepted: 08/27/2020] [Indexed: 11/25/2022]
Abstract
Multi-drug resistant tuberculosis (MDR-TB) represents a growing problem for global healthcare systems. In addition to 1.3 million deaths in 2018, the World Health Organisation reported 484,000 new cases of MDR-TB. Isoniazid is a key anti-TB drug that inhibits InhA, a crucial enzyme in the cell wall biosynthesis pathway and identical in Mycobacterium tuberculosis and M. bovis. Isoniazid is a pro-drug which requires activation by the enzyme KatG, mutations in KatG prevent activation and confer INH-resistance. 'Direct inhibitors' of InhA are attractive as they would circumvent the main clinically observed resistance mechanisms. A library of new 1,5-triazoles, designed to mimic the structures of both triclosan molecules uniquely bound to InhA have been synthesised. The inhibitory activity of these compounds was evaluated using isolated enzyme assays with 2 (5-chloro-2-(4-(5-(((4-(4-chloro-2-hydroxyphenoxy)benzyl)oxy)methyl)-1H-1,2,3-triazol-1-yl)phenoxy)phenol) exhibiting an IC50 of 5.6 µM. Whole-cell evaluation was also performed, with 11 (5-chloro-2-(4-(5-(((4-(cyclopropylmethoxy)benzyl)oxy)methyl)-1H-1,2,3-triazol-1-yl)phenoxy)phenol) showing the greatest potency, with an MIC99 of 12.9 µM against M. bovis.
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Affiliation(s)
- Tom Armstrong
- Biodiscovery Institute, School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Malcolm Lamont
- Biodiscovery Institute, School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Alice Lanne
- Institute of Microbiology and Infection, School of Bioscience, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Luke J Alderwick
- Institute of Microbiology and Infection, School of Bioscience, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Neil R Thomas
- Biodiscovery Institute, School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom.
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16
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Anti-Tubercular Properties of 4-Amino-5-(4-Fluoro-3- Phenoxyphenyl)-4 H-1,2,4-Triazole-3-Thiol and Its Schiff Bases: Computational Input and Molecular Dynamics. Antibiotics (Basel) 2020; 9:antibiotics9090559. [PMID: 32878018 PMCID: PMC7560126 DOI: 10.3390/antibiotics9090559] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/26/2020] [Accepted: 08/29/2020] [Indexed: 12/26/2022] Open
Abstract
In the present investigation, the parent compound 4-amino-5-(4-fluoro-3-phenoxyphenyl)-4H-1,2,4-triazole-3-thiol (1) and its Schiff bases 2, 3, and 4 were subjected to whole-cell anti-TB against H37Rv and multi-drug-resistant (MDR) strains of Mycobacterium tuberculosis (MTB) by resazurin microtiter assay (REMA) plate method. Test compound 1 exhibited promising anti-TB activity against H37Rv and MDR strains of MTB at 5.5 µg/mL and 11 µg/mL, respectively. An attempt to identify the suitable molecular target for compound 1 was performed using a set of triazole thiol cellular targets, including β-ketoacyl carrier protein synthase III (FABH), β-ketoacyl ACP synthase I (KasA), CYP121, dihydrofolate reductase, enoyl-acyl carrier protein reductase, and N-acetylglucosamine-1-phosphate uridyltransferase. MTB β-ketoacyl ACP synthase I (KasA) was identified as the cellular target for the promising anti-TB parent compound 1 via docking and molecular dynamics simulation. MM(GB/PB)SA binding free energy calculation revealed stronger binding of compound 1 compared with KasA standard inhibitor thiolactomycin (TLM). The inhibitory mechanism of test compound 1 involves the formation of hydrogen bonding with the catalytic histidine residues, and it also impedes access of fatty-acid substrates to the active site through interference with α5–α6 helix movement. Test compound 1-specific structural changes at the ALA274–ALA281 loop might be the contributing factor underlying the stronger anti-TB effect of compound 1 when compared with TLM, as it tends to adopt a closed conformation for the access of malonyl substrate to its binding site.
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17
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Wen X, Duan Z, Liu J, Lu W, Lu X. On-DNA Cross-Dehydrogenative Coupling Reaction toward the Synthesis of Focused DNA-Encoded Tetrahydroisoquinoline Libraries. Org Lett 2020; 22:5721-5725. [DOI: 10.1021/acs.orglett.0c01565] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xin Wen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road,
Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, P. R. China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Zhiqiang Duan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road,
Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, P. R. China
| | - Jiaxiang Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road,
Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, P. R. China
| | - Weiwei Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road,
Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, P. R. China
| | - Xiaojie Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road,
Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, P. R. China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
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18
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Ramesh D, Joji A, Vijayakumar BG, Sethumadhavan A, Mani M, Kannan T. Indole chalcones: Design, synthesis, in vitro and in silico evaluation against Mycobacterium tuberculosis. Eur J Med Chem 2020; 198:112358. [DOI: 10.1016/j.ejmech.2020.112358] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/04/2020] [Accepted: 04/16/2020] [Indexed: 12/18/2022]
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19
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Li K, Liu X, Liu S, An Y, Shen Y, Sun Q, Shi X, Su W, Cui W, Duan Z, Kuai L, Yang H, Satz AL, Chen K, Jiang H, Zheng M, Peng X, Lu X. Solution-Phase DNA-Compatible Pictet-Spengler Reaction Aided by Machine Learning Building Block Filtering. iScience 2020; 23:101142. [PMID: 32446221 PMCID: PMC7243192 DOI: 10.1016/j.isci.2020.101142] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 04/14/2020] [Accepted: 05/04/2020] [Indexed: 02/05/2023] Open
Abstract
The application of machine learning toward DNA encoded library (DEL) technology is lacking despite obvious synergy between these two advancing technologies. Herein, a machine learning algorithm has been developed that predicts the conversion rate for the DNA-compatible reaction of a building block with a model DNA-conjugate. We exemplify the value of this technique with a challenging reaction, the Pictet-Spengler, where acidic conditions are normally required to achieve the desired cyclization between tryptophan and aldehydes to provide tryptolines. This is the first demonstration of using a machine learning algorithm to cull potential building blocks prior to their purchase and testing for DNA-encoded library synthesis. Importantly, this allows for a challenging reaction, with an otherwise very low building block pass rate in the test reaction, to still be used in DEL synthesis. Furthermore, because our protocol is solution phase it is directly applicable to standard plate-based DEL synthesis.
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Affiliation(s)
- Ke Li
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Xiaohong Liu
- Shanghai Institute for Advanced Immunochemical Studies, and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Sixiu Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, P. R. China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yulong An
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Yanfang Shen
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Qingxia Sun
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Xiaodong Shi
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Wenji Su
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Weiren Cui
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Zhiqiang Duan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, P. R. China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Letian Kuai
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Hongfang Yang
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Alexander L Satz
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Kaixian Chen
- Shanghai Institute for Advanced Immunochemical Studies, and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Hualiang Jiang
- Shanghai Institute for Advanced Immunochemical Studies, and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Mingyue Zheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China.
| | - Xuanjia Peng
- DNA Encoded Library Platform, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China.
| | - Xiaojie Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai 201203, P. R. China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China.
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20
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Padmini T, Bhikshapathi D, Suresh K, Kulkarni R, Kamal BR. Novel Aminopyrazole Tagged Hydrazones as Anti-Tubercular Agents: Synthesis and Molecular Docking Studies. Med Chem 2020; 17:344-351. [PMID: 32407282 DOI: 10.2174/1573406416666200514084747] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 04/09/2020] [Accepted: 04/20/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Pyrazole derivatives have been reported to possess numerous pharmacological activities viz., anti-inflammatory, antipsychotic, etc. Our group has disclosed that pyrazole benzamides display potent antibacterial and anti-tubercular activities. OBJECTIVE Synthesis of new pyrazole acetamides which possess hydrazone group to be evaluated for antitubercular activity. METHODS The key intermediate 5-aminopyrazole was synthesized with the known procedure, which is then converted into chloroacetamide. This compound than resulted in hydrazine derivative and finally converted into aromatic hydrazones. All the compounds were screened for antitubercular activity. RESULTS All the synthesized compounds have been characterized by their spectral data obtained and subjected to anti-tubercular activity. Among all the twenty tested compounds, three compounds, 5a5, 5b5 and 5b7 have demonstrated MIC value of 3.12 μg/mL against MTB H37Rv. Docking studies revealed important hydrogen bonding interactions with InhA. CONCLUSION Three compounds 5a5, 5b5 and 5b7 were found to be most potent among the series of compounds. Docking studies of compounds explained the presence of hydrogen bonding and π- π stacking interactions with InhA. Further synthesis of more such derivatives with optimized groups would produce compounds with more potent anti-tubercular activity.
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Affiliation(s)
| | - Darna Bhikshapathi
- Teegala Ram Reddy College of Pharmacy, Pragathi Colony, Meerpet, Hyderabad- 500097, Telangana, India
| | - Kandagatla Suresh
- Vijaya College of Pharmacy, Hayatnagar, Hyderabad-501511, Telangana, Hyderabad, India
| | - Ravindra Kulkarni
- Bharati Vidyapeeth's Poona College of Pharmacy, Erandwane, Pune-411038, Maharashtra, India
| | - Bigala R Kamal
- Research Supervisor, Mewar University, Chittorgarh, Rajasthan, India
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Madsen D, Azevedo C, Micco I, Petersen LK, Hansen NJV. An overview of DNA-encoded libraries: A versatile tool for drug discovery. PROGRESS IN MEDICINAL CHEMISTRY 2020; 59:181-249. [PMID: 32362328 DOI: 10.1016/bs.pmch.2020.03.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNA-encoded libraries (DELs) are collections of small molecules covalently attached to amplifiable DNA tags carrying unique information about the structure of each library member. A combinatorial approach is used to construct the libraries with iterative DNA encoding steps, facilitating tracking of the synthetic history of the attached compounds by DNA sequencing. Various screening protocols have been developed which allow protein target binders to be selected out of pools containing up to billions of different small molecules. The versatile methodology has allowed identification of numerous biologically active compounds and is now increasingly being adopted as a tool for lead discovery campaigns and identification of chemical probes. A great focus in recent years has been on developing DNA compatible chemistries that expand the structural diversity of the small molecule library members in DELs. This chapter provides an overview of the challenges and accomplishments in DEL technology, reviewing the technological aspects of producing and screening DELs with a perspective on opportunities, limitations, and future directions.
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22
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Sabbah M, Mendes V, Vistal RG, Dias DMG, Záhorszká M, Mikušová K, Korduláková J, Coyne AG, Blundell TL, Abell C. Fragment-Based Design of Mycobacterium tuberculosis InhA Inhibitors. J Med Chem 2020; 63:4749-4761. [PMID: 32240584 PMCID: PMC7232676 DOI: 10.1021/acs.jmedchem.0c00007] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Tuberculosis (TB) remains a leading cause of mortality among infectious diseases worldwide. InhA has been the focus of numerous drug discovery efforts as this is the target of the first line pro-drug isoniazid. However, with resistance to this drug becoming more common, the aim has been to find new clinical candidates that directly inhibit this enzyme and that do not require activation by the catalase peroxidase KatG, thus circumventing the majority of the resistance mechanisms. In this work, the screening and validation of a fragment library are described, and the development of the fragment hits using a fragment growing strategy was employed, which led to the development of InhA inhibitors with affinities of up to 250 nM.
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Affiliation(s)
- Mohamad Sabbah
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Vitor Mendes
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Robert G Vistal
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - David M G Dias
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Monika Záhorszká
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Katarína Mikušová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Jana Korduláková
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Anthony G Coyne
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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23
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Mycobacterial Cell Wall: A Source of Successful Targets for Old and New Drugs. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10072278] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Eighty years after the introduction of the first antituberculosis (TB) drug, the treatment of drug-susceptible TB remains very cumbersome, requiring the use of four drugs (isoniazid, rifampicin, ethambutol and pyrazinamide) for two months followed by four months on isoniazid and rifampicin. Two of the drugs used in this “short”-course, six-month chemotherapy, isoniazid and ethambutol, target the mycobacterial cell wall. Disruption of the cell wall structure can enhance the entry of other TB drugs, resulting in a more potent chemotherapy. More importantly, inhibition of cell wall components can lead to mycobacterial cell death. The complexity of the mycobacterial cell wall offers numerous opportunities to develop drugs to eradicate Mycobacterium tuberculosis, the causative agent of TB. In the past 20 years, researchers from industrial and academic laboratories have tested new molecules to find the best candidates that will change the face of TB treatment: drugs that will shorten TB treatment and be efficacious against active and latent, as well as drug-resistant TB. Two of these new TB drugs block components of the mycobacterial cell wall and have reached phase 3 clinical trial. This article reviews TB drugs targeting the mycobacterial cell wall in use clinically and those in clinical development.
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24
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Kamsri P, Hanwarinroj C, Phusi N, Pornprom T, Chayajarus K, Punkvang A, Suttipanta N, Srimanote P, Suttisintong K, Songsiriritthigul C, Saparpakorn P, Hannongbua S, Rattanabunyong S, Seetaha S, Choowongkomon K, Sureram S, Kittakoop P, Hongmanee P, Santanirand P, Chen Z, Zhu W, Blood RA, Takebayashi Y, Hinchliffe P, Mulholland AJ, Spencer J, Pungpo P. Discovery of New and Potent InhA Inhibitors as Antituberculosis Agents: Structure-Based Virtual Screening Validated by Biological Assays and X-ray Crystallography. J Chem Inf Model 2019; 60:226-234. [PMID: 31820972 DOI: 10.1021/acs.jcim.9b00918] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The enoyl-acyl carrier protein reductase InhA of Mycobacterium tuberculosis is an attractive, validated target for antituberculosis drug development. Moreover, direct inhibitors of InhA remain effective against InhA variants with mutations associated with isoniazid resistance, offering the potential for activity against MDR isolates. Here, structure-based virtual screening supported by biological assays was applied to identify novel InhA inhibitors as potential antituberculosis agents. High-speed Glide SP docking was initially performed against two conformations of InhA differing in the orientation of the active site Tyr158. The resulting hits were filtered for drug-likeness based on Lipinski's rule and avoidance of PAINS-like properties and finally subjected to Glide XP docking to improve accuracy. Sixteen compounds were identified and selected for in vitro biological assays, of which two (compounds 1 and 7) showed MIC of 12.5 and 25 μg/mL against M. tuberculosis H37Rv, respectively. Inhibition assays against purified recombinant InhA determined IC50 values for these compounds of 0.38 and 0.22 μM, respectively. A crystal structure of the most potent compound, compound 7, bound to InhA revealed the inhibitor to occupy a hydrophobic pocket implicated in binding the aliphatic portions of InhA substrates but distant from the NADH cofactor, i.e., in a site distinct from those occupied by the great majority of known InhA inhibitors. This compound provides an attractive starting template for ligand optimization aimed at discovery of new and effective compounds against M. tuberculosis that act by targeting InhA.
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Affiliation(s)
- Pharit Kamsri
- Division of Chemistry, Faculty of Science , Nakhon Phanom University , 48000 Nakhon Phanom , Thailand
| | | | | | | | | | - Auradee Punkvang
- Division of Chemistry, Faculty of Science , Nakhon Phanom University , 48000 Nakhon Phanom , Thailand
| | | | - Potjanee Srimanote
- Faculty of Allied Health Sciences , Thammasat University , Rangsit Campus , 12120 Pathumthani , Thailand
| | - Khomson Suttisintong
- National Nanotechnology Center , National Science and Technology Development Agency , Thailand Science Park , 12120 Pathumthani , Thailand
| | | | | | | | | | | | | | - Sanya Sureram
- Chulabhorn Research Institute , 10210 Bangkok , Thailand
| | - Prasat Kittakoop
- Chulabhorn Research Institute , 10210 Bangkok , Thailand.,Chulabhorn Graduate Institute, Chemical Biology Program , Chulabhorn Royal Academy , 10210 Bangkok , Thailand.,Center of Excellence on Environmental Health and Toxicology (EHT), CHE , Ministry of Education , 10300 Bangkok , Thailand
| | - Poonpilas Hongmanee
- Division of Microbiology, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital , Mahidol University , 10400 Bangkok , Thailand
| | - Pitak Santanirand
- Division of Microbiology, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital , Mahidol University , 10400 Bangkok , Thailand
| | - Zhaoqiang Chen
- State Key Laboratory of Drug Research, Drug Discovery and Design Center , Shanghai Institute of Materia Medica , 201203 Shanghai , China
| | - Weiliang Zhu
- State Key Laboratory of Drug Research, Drug Discovery and Design Center , Shanghai Institute of Materia Medica , 201203 Shanghai , China
| | - Rosemary A Blood
- School of Cellular and Molecular Medicine , University of Bristol , Biomedical Sciences Building, University Walk , BS8 1TD Bristol , United Kingdom
| | - Yuiko Takebayashi
- School of Cellular and Molecular Medicine , University of Bristol , Biomedical Sciences Building, University Walk , BS8 1TD Bristol , United Kingdom
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine , University of Bristol , Biomedical Sciences Building, University Walk , BS8 1TD Bristol , United Kingdom
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , BS8 1TS Bristol , United Kingdom
| | - James Spencer
- School of Cellular and Molecular Medicine , University of Bristol , Biomedical Sciences Building, University Walk , BS8 1TD Bristol , United Kingdom
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25
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New potential drug leads against MDR-MTB: A short review. Bioorg Chem 2019; 95:103534. [PMID: 31884135 DOI: 10.1016/j.bioorg.2019.103534] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 11/26/2019] [Accepted: 12/20/2019] [Indexed: 12/25/2022]
Abstract
Multidrug resistant Mycobacterium tuberculosis (MDR-MTB) infections have created a critical health problem globally. The appalling rise in drug resistance to all the current therapeutics has triggered the need for identifying new antimycobacterial agents effective against multidrug-resistant Mycobacterium tuberculosis. Structurally unique chemical entities with new mode of action will be required to combat this pressing issue. This review gives an overview of the structures and outlines on various aspects of in vitro pharmacological activities of new antimycobacterial agents, mechanism of action and brief structure activity relationships in the perspective of drug discovery and development. This review also summarizes on recent reports of new antimycobacterial agents.
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26
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Abstract
Introduction: Benzofuran is a fundamental unit in numerous bioactive heterocycles. They have attracted chemists and medical researchers due to their broad range of biological activity, where some of them possess unique anticancer, antitubercular, antidiabetic, anti-Alzheimer and anti-inflammatory properties. The benzofuran nucleus is present in a huge number of bioactive natural and synthetic compounds. Benzofuran derivatives have potent applications in pharmaceuticals, agriculture, and polymers. The recent developments considering the biological activities of benzofuran compounds are reported. They have a vital role as pronounced inhibitors against a number of diseases, viruses, fungus, microbes, and enzymes. Areas covered: This review covers the recent developments of biological activities of benzofurans during the period 2014-2019. The covered areas here comprised antimicrobial, anti-inflammatory, antitumor, antitubercular, antidiabetic, anti-Alzheimer, antioxidant, antiviral, vasorelaxant, anti-osteoporotic and enzyme inhibitory activities. Expert opinion: In addition to the already commercialized 34 benzofurans-based drugs in the market, this chapter outlines several potent benzofuran derivatives that may be useful as potential pro-drugs. It is also focused on providing details of SAR and the effect of certain functional groups on the activity of the benzofuran compounds. The presence of -OH, -OMe, sulfonamide, or halogen contributed greatly to increasing the therapeutic activities comparing with reference drugs.
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Affiliation(s)
- Kamal M Dawood
- Department of Chemistry, Faculty of Science, Cairo University , Giza , Egypt
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27
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Kouman KC, Keita M, Kre N’Guessan R, Owono Owono LC, Megnassan E, Frecer V, Miertus S. Structure-Based Design and in Silico Screening of Virtual Combinatorial Library of Benzamides Inhibiting 2-trans Enoyl-Acyl Carrier Protein Reductase of Mycobacterium tuberculosis with Favorable Predicted Pharmacokinetic Profiles. Int J Mol Sci 2019; 20:ijms20194730. [PMID: 31554227 PMCID: PMC6802012 DOI: 10.3390/ijms20194730] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 09/18/2019] [Accepted: 09/21/2019] [Indexed: 01/24/2023] Open
Abstract
Background: During the previous decade a new class of benzamide-based inhibitors of 2-trans enoyl-acyl carrier protein reductase (InhA) of Mycobacterium tuberculosis (Mt) with unusual binding mode have emerged. Here we report in silico design and evaluation of novel benzamide InhA-Mt inhibitors with favorable predicted pharmacokinetic profiles. Methods: By using in situ modifications of the crystal structure of N-benzyl-4-((heteroaryl)methyl) benzamide (BHMB)-InhA complex (PDB entry 4QXM), 3D models of InhA-BHMBx complexes were prepared for a training set of 19 BHMBs with experimentally determined inhibitory potencies (half-maximal inhibitory concentrations IC50exp). In the search for active conformation of the BHMB1-19, linear QSAR model was prepared, which correlated computed gas phase enthalpies of formation (∆∆HMM) of InhA-BHMBx complexes with the IC50exp. Further, taking into account the solvent effect and entropy changes upon ligand, binding resulted in a superior QSAR model correlating computed complexation Gibbs free energies (∆∆Gcom). The successive pharmacophore model (PH4) generated from the active conformations of BHMBs served as a virtual screening tool of novel analogs included in a virtual combinatorial library (VCL) of compounds containing benzamide scaffolds. The VCL filtered by Lipinski’s rule-of-five was screened by the PH4 model to identify new BHMB analogs. Results: Gas phase QSAR model: −log10(IC50exp) = pIC50exp = −0.2465 × ∆∆HMM + 7.95503, R2 = 0.94; superior aqueous phase QSAR model: pIC50exp = −0.2370 × ∆∆Gcom + 7.8783, R2 = 0.97 and PH4 pharmacophore model: pIC50exp = 1.0013 × pIC50exp − 0.0085, R2 = 0.95. The VCL of more than 114 thousand BHMBs was filtered down to 73,565 analogs Lipinski’s rule. The five-point PH4 screening retained 90 new and potent BHMBs with predicted inhibitory potencies IC50pre up to 65 times lower than that of BHMB1 (IC50exp = 20 nM). Predicted pharmacokinetic profile of the new analogs showed enhanced cell membrane permeability and high human oral absorption compared to current anti-tuberculotics. Conclusions: Combined use of QSAR models that considered binding of the BHMBs to InhA, pharmacophore model, and ADME properties helped to recognize bound active conformation of the benzamide inhibitors, permitted in silico screening of VCL of compounds sharing benzamide scaffold and identification of new analogs with predicted high inhibitory potencies and favorable pharmacokinetic profiles.
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Affiliation(s)
- Koffi Charles Kouman
- Laboratoire de Physique Fondamentale et Appliquée (LPFA), University of Abobo Adjamé (now Nangui Abrogoua), Abidjan 02, Côte d’Ivoire; (K.C.K.); (M.K.)
| | - Melalie Keita
- Laboratoire de Physique Fondamentale et Appliquée (LPFA), University of Abobo Adjamé (now Nangui Abrogoua), Abidjan 02, Côte d’Ivoire; (K.C.K.); (M.K.)
| | - Raymond Kre N’Guessan
- Laboratoire de Physique Fondamentale et Appliquée (LPFA), University of Abobo Adjamé (now Nangui Abrogoua), Abidjan 02, Côte d’Ivoire; (K.C.K.); (M.K.)
| | - Luc Calvin Owono Owono
- International Centre for Theoretical Physics, ICTP-UNESCO, Strada Costiera 11, I-34151 Trieste, Italy;
- Department of Physics, Ecole Normale Supérieure, University of Yaoundé I, P.O. Box 47, Yaoundé 1, Cameroon
- International Centre for Applied Research and Sustainable Technology, SK-84104 Bratislava, Slovakia; (V.F.); (S.M.)
| | - Eugene Megnassan
- Laboratoire de Physique Fondamentale et Appliquée (LPFA), University of Abobo Adjamé (now Nangui Abrogoua), Abidjan 02, Côte d’Ivoire; (K.C.K.); (M.K.)
- International Centre for Theoretical Physics, ICTP-UNESCO, Strada Costiera 11, I-34151 Trieste, Italy;
- International Centre for Applied Research and Sustainable Technology, SK-84104 Bratislava, Slovakia; (V.F.); (S.M.)
- Laboratoire de Cristallographie—Physique Moléculaire, University of Cocody (now Felix Houphouët-Boigny), Abidjan 22, Côte d’Ivoire
- Laboratoire de Chimie Organique Structurale et Théorique, University of Cocody (now Felix Houphouët-Boigny), Abidjan 22, Côte d’Ivoire
- Correspondence: ; Tel.: +225-02-36-30-08
| | - Vladimir Frecer
- International Centre for Applied Research and Sustainable Technology, SK-84104 Bratislava, Slovakia; (V.F.); (S.M.)
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University in Bratislava, SK-83232 Bratislava, Slovakia
| | - Stanislav Miertus
- International Centre for Applied Research and Sustainable Technology, SK-84104 Bratislava, Slovakia; (V.F.); (S.M.)
- Department of Biotechnologies, Faculty of Natural Sciences, University of SS. Cyril and Methodius, SK-91701 Trnava, Slovakia
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28
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Ibrahim HM, Behbehani H. Sustainable Synthetic Approach for (Pyrazol-4-ylidene)pyridines By Metal Catalyst-Free Aerobic C(sp 2)-C(sp 3) Coupling Reactions between 1-Amino-2-imino-pyridines and 1-Aryl-5-pyrazolones. ACS OMEGA 2019; 4:11701-11711. [PMID: 31460276 PMCID: PMC6682090 DOI: 10.1021/acsomega.9b01650] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 06/21/2019] [Indexed: 05/26/2023]
Abstract
A novel, metal catalyst-free, and efficient method has been developed for the synthesis of (pyrazol-4-ylidene)pyridine derivatives. The process involves dehydrogenative coupling of 1-amino-2-imino-pyridines with 1-aryl-5-pyrazolone derivatives utilizing O2 as the sole oxidant. The new method benefits from a high atom economy, efficiency, and substrate scope, as well as the simplicity of reaction and product purification procedures.
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Affiliation(s)
- Hamada Mohamed Ibrahim
- Chemistry
Department, Faculty of Science, Kuwait University, P.O. Box 5969, Safat 13060, Kuwait
- Chemistry
Department, Faculty of Science, Fayoum University, P.O. Box 63514, Fayoum, Egypt
| | - Haider Behbehani
- Chemistry
Department, Faculty of Science, Kuwait University, P.O. Box 5969, Safat 13060, Kuwait
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29
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Kunig V, Potowski M, Gohla A, Brunschweiger A. DNA-encoded libraries - an efficient small molecule discovery technology for the biomedical sciences. Biol Chem 2019; 399:691-710. [PMID: 29894294 DOI: 10.1515/hsz-2018-0119] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 04/12/2018] [Indexed: 12/12/2022]
Abstract
DNA-encoded compound libraries are a highly attractive technology for the discovery of small molecule protein ligands. These compound collections consist of small molecules covalently connected to individual DNA sequences carrying readable information about the compound structure. DNA-tagging allows for efficient synthesis, handling and interrogation of vast numbers of chemically synthesized, drug-like compounds. They are screened on proteins by an efficient, generic assay based on Darwinian principles of selection. To date, selection of DNA-encoded libraries allowed for the identification of numerous bioactive compounds. Some of these compounds uncovered hitherto unknown allosteric binding sites on target proteins; several compounds proved their value as chemical biology probes unraveling complex biology; and the first examples of clinical candidates that trace their ancestry to a DNA-encoded library were reported. Thus, DNA-encoded libraries proved their value for the biomedical sciences as a generic technology for the identification of bioactive drug-like molecules numerous times. However, large scale experiments showed that even the selection of billions of compounds failed to deliver bioactive compounds for the majority of proteins in an unbiased panel of target proteins. This raises the question of compound library design.
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Affiliation(s)
- Verena Kunig
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
| | - Marco Potowski
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
| | - Anne Gohla
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
| | - Andreas Brunschweiger
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
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30
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Faver JC, Riehle K, Lancia DR, Milbank JBJ, Kollmann CS, Simmons N, Yu Z, Matzuk MM. Quantitative Comparison of Enrichment from DNA-Encoded Chemical Library Selections. ACS COMBINATORIAL SCIENCE 2019; 21:75-82. [PMID: 30672692 PMCID: PMC6372980 DOI: 10.1021/acscombsci.8b00116] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
DNA-encoded
chemical libraries (DELs) provide a high-throughput
and cost-effective route for screening billions of unique molecules
for binding affinity for diverse protein targets. Identifying candidate
compounds from these libraries involves affinity selection, DNA sequencing,
and measuring enrichment in a sample pool of DNA barcodes. Successful
detection of potent binders is affected by many factors, including
selection parameters, chemical yields, library amplification, sequencing
depth, sequencing errors, library sizes, and the chosen enrichment
metric. To date, there has not been a clear consensus about how enrichment
from DEL selections should be measured or reported. We propose a normalized z-score enrichment metric using a binomial distribution
model that satisfies important criteria that are relevant for analysis
of DEL selection data. The introduced metric is robust with respect
to library diversity and sampling and allows for quantitative comparisons
of enrichment of n-synthons from parallel DEL selections.
These features enable a comparative enrichment analysis strategy that can
provide valuable information about hit compounds in early stage drug
discovery.
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Affiliation(s)
| | | | - David R. Lancia
- FORMA Therapeutics Inc., 500 Arsenal Street, Suite 100, Watertown, Massachusetts 02472, United States
| | - Jared B. J. Milbank
- FORMA Therapeutics Inc., 500 Arsenal Street, Suite 100, Watertown, Massachusetts 02472, United States
| | - Christopher S. Kollmann
- FORMA Therapeutics Inc., 500 Arsenal Street, Suite 100, Watertown, Massachusetts 02472, United States
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31
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Benzofuran-oxadiazole hybrids: Design, synthesis, antitubercular activity and molecular docking studies. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.cdc.2019.100178] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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32
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Benzofuran derivatives and their anti-tubercular, anti-bacterial activities. Eur J Med Chem 2018; 162:266-276. [PMID: 30448416 DOI: 10.1016/j.ejmech.2018.11.025] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/03/2018] [Accepted: 11/09/2018] [Indexed: 01/04/2023]
Abstract
Benzofuran is a fundamental structural unit in a variety of biologically active natural products, and its derivatives display various biological properties. Some benzofuran derivatives possess unique anti-tubercular and anti-bacterial action mechanism, and exhibit excellent in vitro and in vivo activities against both drug-sensitive and drug-resistant pathogens. Moreover, several benzofuran derivatives have already used in clinics for the treatment of various diseases. Thus, benzofuran is a useful pharmacophore to develop new anti-tubercular and anti-bacterial drugs. This review covers the recent advances of benzofuran derivatives as potential anti-tubercular and anti-bacterial agents, and the structure-activity relationship is also discussed to pave the way for the further rational development of this kind of derivatives.
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33
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Favalli N, Biendl S, Hartmann M, Piazzi J, Sladojevich F, Gräslund S, Brown PJ, Näreoja K, Schüler H, Scheuermann J, Franzini R, Neri D. A DNA-Encoded Library of Chemical Compounds Based on Common Scaffolding Structures Reveals the Impact of Ligand Geometry on Protein Recognition. ChemMedChem 2018; 13:1303-1307. [PMID: 29856130 PMCID: PMC6126618 DOI: 10.1002/cmdc.201800193] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Indexed: 11/06/2022]
Abstract
A DNA-encoded chemical library (DECL) with 1.2 million compounds was synthesized by combinatorial reaction of seven central scaffolds with two sets of 343×492 building blocks. Library screening by affinity capture revealed that for some target proteins, the chemical nature of building blocks dominated the selection results, whereas for other proteins, the central scaffold also crucially contributed to ligand affinity. Molecules based on a 3,5-bis(aminomethyl)benzoic acid core structure were found to bind human serum albumin with a Kd value of 6 nm, while compounds with the same substituents on an equidistant but flexible l-lysine scaffold showed 140-fold lower affinity. A 18 nm tankyrase-1 binder featured l-lysine as linking moiety, while molecules based on d-Lysine or (2S,4S)-amino-l-proline showed no detectable binding to the target. This work suggests that central scaffolds which predispose the orientation of chemical building blocks toward the protein target may enhance the screening productivity of encoded libraries.
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Affiliation(s)
- Nicholas Favalli
- Institute of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
| | - Stefan Biendl
- Institute of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
| | - Marco Hartmann
- Institute of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
| | | | - Filippo Sladojevich
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La, Roche Ltd., Grenzacherstrasse 124, 4070 Basel (Switzerland)
| | - Susanne Gräslund
- Structural Genomics Consortium (SGC), University of Toronto, Toronto, M5G 1L7 (Canada)
- Department Structural Biology, Dept. of Medical Biochemistry and Biophysics (MBB), Karolinska Institutet, Scheeles väg 2, S-17177 Stockholm
| | - Peter J. Brown
- Structural Genomics Consortium (SGC), University of Toronto, Toronto, M5G 1L7 (Canada)
| | - Katja Näreoja
- Department Structural Biology, Dept. of Medical Biochemistry and Biophysics (MBB), Karolinska Institutet, Scheeles väg 2, S-17177 Stockholm
| | - Herwig Schüler
- Department Structural Biology, Dept. of Medical Biochemistry and Biophysics (MBB), Karolinska Institutet, Scheeles väg 2, S-17177 Stockholm
| | - Jörg Scheuermann
- Institute of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
| | - Raphael Franzini
- Institute of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
- University of Utah, College of Pharmacy, 30 South 2000 East, Salt Lake City, UT 84112 (801) 581-6731
| | - Dario Neri
- Institute of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich (Switzerland)
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34
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Affiliation(s)
- Veronika Šlachtová
- Department of Organic Chemistry; Faculty of Science; 17. listopadu 12 Olomouc Czech Republic 77146
| | - Lucie Brulíková
- Department of Medicinal Chemistry; Institute of Molecular and Translational Medicine; Hněvotínská 5 Olomouc Czech Republic 77900
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35
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Prati F, Zuccotto F, Fletcher D, Convery MA, Fernandez‐Menendez R, Bates R, Encinas L, Zeng J, Chung C, De Dios Anton P, Mendoza‐Losana A, Mackenzie C, Green SR, Huggett M, Barros D, Wyatt PG, Ray PC. Screening of a Novel Fragment Library with Functional Complexity against Mycobacterium tuberculosis InhA. ChemMedChem 2018; 13:672-677. [PMID: 29399991 PMCID: PMC5915743 DOI: 10.1002/cmdc.201700774] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Indexed: 11/17/2022]
Abstract
Our findings reported herein provide support for the benefits of including functional group complexity (FGC) within fragments when screening against protein targets such as Mycobacterium tuberculosis InhA. We show that InhA fragment actives with FGC maintained their binding pose during elaboration. Furthermore, weak fragment hits with functional group handles also allowed for facile fragment elaboration to afford novel and potent InhA inhibitors with good ligand efficiency metrics for optimization.
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Affiliation(s)
- Federica Prati
- Drug Discovery Unit, College of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
- DPU TB Diseases of the Developing WorldTres Cantos Medicines Development CampusGlaxoSmithKline Severo Ochoa 2Tres Cantos28760MadridSpain
| | - Fabio Zuccotto
- Drug Discovery Unit, College of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
| | - Daniel Fletcher
- Drug Discovery Unit, College of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
| | - Maire A. Convery
- Platform Technology and SciencesMedicines Research Centre, GlaxoSmithKlineGunnels Wood RoadStevenage HertsSG1 2NYHertfordshireUK
| | - Raquel Fernandez‐Menendez
- DPU TB Diseases of the Developing WorldTres Cantos Medicines Development CampusGlaxoSmithKline Severo Ochoa 2Tres Cantos28760MadridSpain
| | - Robert Bates
- DPU TB Diseases of the Developing WorldTres Cantos Medicines Development CampusGlaxoSmithKline Severo Ochoa 2Tres Cantos28760MadridSpain
| | - Lourdes Encinas
- DPU TB Diseases of the Developing WorldTres Cantos Medicines Development CampusGlaxoSmithKline Severo Ochoa 2Tres Cantos28760MadridSpain
| | - Jingkun Zeng
- Platform Technology and SciencesMedicines Research Centre, GlaxoSmithKlineGunnels Wood RoadStevenage HertsSG1 2NYHertfordshireUK
| | - Chun‐wa Chung
- Platform Technology and SciencesMedicines Research Centre, GlaxoSmithKlineGunnels Wood RoadStevenage HertsSG1 2NYHertfordshireUK
| | - Paco De Dios Anton
- DPU TB Diseases of the Developing WorldTres Cantos Medicines Development CampusGlaxoSmithKline Severo Ochoa 2Tres Cantos28760MadridSpain
| | - Alfonso Mendoza‐Losana
- DPU TB Diseases of the Developing WorldTres Cantos Medicines Development CampusGlaxoSmithKline Severo Ochoa 2Tres Cantos28760MadridSpain
| | - Claire Mackenzie
- Drug Discovery Unit, College of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
| | - Simon R. Green
- Drug Discovery Unit, College of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
| | - Margaret Huggett
- Drug Discovery Unit, College of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
| | - David Barros
- DPU TB Diseases of the Developing WorldTres Cantos Medicines Development CampusGlaxoSmithKline Severo Ochoa 2Tres Cantos28760MadridSpain
| | - Paul G. Wyatt
- Drug Discovery Unit, College of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
| | - Peter C. Ray
- Drug Discovery Unit, College of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHScotlandUK
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36
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Campaniço A, Moreira R, Lopes F. Drug discovery in tuberculosis. New drug targets and antimycobacterial agents. Eur J Med Chem 2018; 150:525-545. [DOI: 10.1016/j.ejmech.2018.03.020] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/05/2018] [Accepted: 03/06/2018] [Indexed: 01/24/2023]
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37
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An overview on crystal structures of InhA protein: Apo-form, in complex with its natural ligands and inhibitors. Eur J Med Chem 2018; 146:318-343. [PMID: 29407960 DOI: 10.1016/j.ejmech.2018.01.047] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 01/02/2018] [Accepted: 01/15/2018] [Indexed: 11/23/2022]
Abstract
The enoyl-ACP reductase InhA from the mycobacterial fatty acid biosynthesis pathway has become a target of interest for the development of new anti-tubercular drugs. This protein has been identified as essential for the survival of Mycobacterium tuberculosis, the causative agent of tuberculosis, and as the main target of two pro-drugs: isoniazid, the frontline anti-tubercular drug, and ethionamide, a second-line medicine. Since most cases of resistance to isoniazid and ethionamide result from mutations in the mycobacterial activating enzyme (KatG for isoniazid and EthA for ethionamide), research of direct InhA inhibitors, avoiding the activation step, has emerged as a promising strategy for combating tuberculosis. Thereby, InhA is drawing much attention and its three-dimensional structure has been particularly studied. A better understanding of key sites of interactions responsible for InhA inhibition arises thus as an essential tool for the rational design of new potent inhibitors. In this paper, we propose an overview of the 80 available crystal structures of wild-type and mutant InhA, in its apo form, in complex with its cofactor, with an analogue of its natural ligands (C16 fatty acid and/or NADH) or with inhibitors. We will first discuss structural and mechanistic aspects in order to highlight key features of the protein before delivering thorough inventory of structures of InhA in the presence of synthetic ligands to underline the key interactions implicated in high affinity inhibition.
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38
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Karrouchi K, Radi S, Ramli Y, Taoufik J, Mabkhot YN, Al-Aizari FA, Ansar M. Synthesis and Pharmacological Activities of Pyrazole Derivatives: A Review. Molecules 2018; 23:molecules23010134. [PMID: 29329257 PMCID: PMC6017056 DOI: 10.3390/molecules23010134] [Citation(s) in RCA: 448] [Impact Index Per Article: 74.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 01/03/2018] [Accepted: 01/05/2018] [Indexed: 12/31/2022] Open
Abstract
Pyrazole and its derivatives are considered a pharmacologically important active scaffold that possesses almost all types of pharmacological activities. The presence of this nucleus in pharmacological agents of diverse therapeutic categories such as celecoxib, a potent anti-inflammatory, the antipsychotic CDPPB, the anti-obesity drug rimonabant, difenamizole, an analgesic, betazole, a H2-receptor agonist and the antidepressant agent fezolamide have proved the pharmacological potential of the pyrazole moiety. Owing to this diversity in the biological field, this nucleus has attracted the attention of many researchers to study its skeleton chemically and biologically. This review highlights the different synthesis methods and the pharmacological properties of pyrazole derivatives. Studies on the synthesis and biological activity of pyrazole derivatives developed by many scientists around the globe are reported.
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Affiliation(s)
- Khalid Karrouchi
- Medicinal Chemistry Laboratory, Faculty of Medicine and Pharmacy, Mohammed V University, 10100 Rabat, Morocco.
- LCAE, Department of Chemistry, Faculty of Sciences, University Mohamed I, 60000 Oujda, Morocco.
- Physicochemical service, Drugs Quality Control Laboratory, Division of Drugs and Pharmacy, Ministry of Health, 10100 Rabat, Morocco.
| | - Smaail Radi
- LCAE, Department of Chemistry, Faculty of Sciences, University Mohamed I, 60000 Oujda, Morocco.
| | - Youssef Ramli
- Medicinal Chemistry Laboratory, Faculty of Medicine and Pharmacy, Mohammed V University, 10100 Rabat, Morocco.
| | - Jamal Taoufik
- Medicinal Chemistry Laboratory, Faculty of Medicine and Pharmacy, Mohammed V University, 10100 Rabat, Morocco.
| | - Yahia N Mabkhot
- Department of Chemistry, Faculty of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia.
| | - Faiz A Al-Aizari
- Department of Chemistry, Faculty of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia.
| | - M'hammed Ansar
- Medicinal Chemistry Laboratory, Faculty of Medicine and Pharmacy, Mohammed V University, 10100 Rabat, Morocco.
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39
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Karrouchi K, Radi S, Ramli Y, Taoufik J, Mabkhot YN, Al-Aizari FA, Ansar M. Synthesis and Pharmacological Activities of Pyrazole Derivatives: A Review. Molecules 2018. [PMID: 29329257 DOI: 10.3390/molecules23010134k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Pyrazole and its derivatives are considered a pharmacologically important active scaffold that possesses almost all types of pharmacological activities. The presence of this nucleus in pharmacological agents of diverse therapeutic categories such as celecoxib, a potent anti-inflammatory, the antipsychotic CDPPB, the anti-obesity drug rimonabant, difenamizole, an analgesic, betazole, a H2-receptor agonist and the antidepressant agent fezolamide have proved the pharmacological potential of the pyrazole moiety. Owing to this diversity in the biological field, this nucleus has attracted the attention of many researchers to study its skeleton chemically and biologically. This review highlights the different synthesis methods and the pharmacological properties of pyrazole derivatives. Studies on the synthesis and biological activity of pyrazole derivatives developed by many scientists around the globe are reported.
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Affiliation(s)
- Khalid Karrouchi
- Medicinal Chemistry Laboratory, Faculty of Medicine and Pharmacy, Mohammed V University, 10100 Rabat, Morocco.
- LCAE, Department of Chemistry, Faculty of Sciences, University Mohamed I, 60000 Oujda, Morocco.
- Physicochemical service, Drugs Quality Control Laboratory, Division of Drugs and Pharmacy, Ministry of Health, 10100 Rabat, Morocco.
| | - Smaail Radi
- LCAE, Department of Chemistry, Faculty of Sciences, University Mohamed I, 60000 Oujda, Morocco.
| | - Youssef Ramli
- Medicinal Chemistry Laboratory, Faculty of Medicine and Pharmacy, Mohammed V University, 10100 Rabat, Morocco.
| | - Jamal Taoufik
- Medicinal Chemistry Laboratory, Faculty of Medicine and Pharmacy, Mohammed V University, 10100 Rabat, Morocco.
| | - Yahia N Mabkhot
- Department of Chemistry, Faculty of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia.
| | - Faiz A Al-Aizari
- Department of Chemistry, Faculty of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia.
| | - M'hammed Ansar
- Medicinal Chemistry Laboratory, Faculty of Medicine and Pharmacy, Mohammed V University, 10100 Rabat, Morocco.
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40
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Lone MY, Manhas A, Athar M, Jha PC. Identification of InhA inhibitors: A combination of virtual screening, molecular dynamics simulations and quantum chemical studies. J Biomol Struct Dyn 2017; 36:2951-2965. [DOI: 10.1080/07391102.2017.1372313] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Mohsin Y. Lone
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar 382030, Gujarat, India
| | - Anu Manhas
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar 382030, Gujarat, India
| | - Mohd. Athar
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar 382030, Gujarat, India
| | - Prakash C. Jha
- Centre for Applied Chemistry, Central University of Gujarat, Gandhinagar 382030, Gujarat, India
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41
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Xu Z, Gao C, Ren QC, Song XF, Feng LS, Lv ZS. Recent advances of pyrazole-containing derivatives as anti-tubercular agents. Eur J Med Chem 2017; 139:429-440. [PMID: 28818767 DOI: 10.1016/j.ejmech.2017.07.059] [Citation(s) in RCA: 157] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 07/23/2017] [Accepted: 07/24/2017] [Indexed: 01/18/2023]
Abstract
One-third of the world's population infected tuberculosis (TB), and more than 1 million deaths annually. The co-infection between the mainly pathogen Mycobacterium tuberculosis (MTB) and HIV, and the incidence of drug-resistant TB, multi-drug resistant TB, extensively drug-resistant TB as well as totally drug-resistant TB have further aggravated the mortality and spread of this disease. Thus, there is an urgent need to develop novel anti-TB agents against both drug-susceptible and drug-resistant TB. The wide spectrum of biological activities and successful utilization of pyrazole-containing drugs in clinic have inspired more and more attention towards this kind of heterocycles. Numerous of pyrazole-containing derivatives have been synthesized for searching new anti-TB agents, and some of them showed promising potency and may have novel mechanism of action. This review aims to outline the recent achievements in pyrazole-containing derivatives as anti-TB agents and their structure-activity relationship.
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Affiliation(s)
- Zhi Xu
- Key Laboratory of Hubei Province for Coal Conversion and New Carbon Materials, Wuhan University of Science and Technology, Hubei, PR China
| | - Chuan Gao
- WuXi AppTec (Wuhan), Hubei, PR China
| | | | - Xu-Feng Song
- Beijing University of Technology, Beijing, PR China
| | | | - Zao-Sheng Lv
- Key Laboratory of Hubei Province for Coal Conversion and New Carbon Materials, Wuhan University of Science and Technology, Hubei, PR China.
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42
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Prioritizing multiple therapeutic targets in parallel using automated DNA-encoded library screening. Nat Commun 2017; 8:16081. [PMID: 28714473 PMCID: PMC5520047 DOI: 10.1038/ncomms16081] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 05/24/2017] [Indexed: 12/18/2022] Open
Abstract
The identification and prioritization of chemically tractable therapeutic targets is a significant challenge in the discovery of new medicines. We have developed a novel method that rapidly screens multiple proteins in parallel using DNA-encoded library technology (ELT). Initial efforts were focused on the efficient discovery of antibacterial leads against 119 targets from Acinetobacter baumannii and Staphylococcus aureus. The success of this effort led to the hypothesis that the relative number of ELT binders alone could be used to assess the ligandability of large sets of proteins. This concept was further explored by screening 42 targets from Mycobacterium tuberculosis. Active chemical series for six targets from our initial effort as well as three chemotypes for DHFR from M. tuberculosis are reported. The findings demonstrate that parallel ELT selections can be used to assess ligandability and highlight opportunities for successful lead and tool discovery. Encoded Library Technology (ELT) has streamlined the identification of chemical ligands for protein targets in drug discovery. Here, the authors optimize the ELT approach to screen multiple proteins in parallel and identify promising targets and antibacterial compounds for S. aureus, A. baumannii and M. tuberculosis.
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43
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Kumar V, Patel S, Jain R. New structural classes of antituberculosis agents. Med Res Rev 2017; 38:684-740. [DOI: 10.1002/med.21454] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 04/03/2017] [Accepted: 05/02/2017] [Indexed: 01/02/2023]
Affiliation(s)
- Vajinder Kumar
- Department of Medicinal Chemistry; National Institute of Pharmaceutical Education and Research; S.A.S. Nagar Punjab India
- Present address: Department of Chemistry; Akal University; Talwandi Sabo Punjab 151 302 India
| | - Sanjay Patel
- Department of Medicinal Chemistry; National Institute of Pharmaceutical Education and Research; S.A.S. Nagar Punjab India
| | - Rahul Jain
- Department of Medicinal Chemistry; National Institute of Pharmaceutical Education and Research; S.A.S. Nagar Punjab India
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44
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45
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Satz AL, Hochstrasser R, Petersen AC. Analysis of Current DNA Encoded Library Screening Data Indicates Higher False Negative Rates for Numerically Larger Libraries. ACS COMBINATORIAL SCIENCE 2017; 19:234-238. [PMID: 28287689 DOI: 10.1021/acscombsci.7b00023] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
To optimize future DNA-encoded library design, we have attempted to quantify the library size at which the signal becomes undetectable. To accomplish this we (i) have calculated that percent yields of individual library members following a screen range from 0.002 to 1%, (ii) extrapolated that ∼1 million copies per library member are required at the outset of a screen, and (iii) from this extrapolation predict that false negative rates will begin to outweigh the benefit of increased diversity at library sizes >108. The above analysis is based upon a large internal data set comprising multiple screens, targets, and libraries; we also augmented our internal data with all currently available literature data. In theory, high false negative rates may be overcome by employing larger amounts of library; however, we argue that using more than currently reported amounts of library (≫10 nmoles) is impractical. The above conclusions may be generally applicable to other DNA encoded library platforms, particularly those platforms that do not allow for library amplification.
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Affiliation(s)
- Alexander L. Satz
- Roche Pharmaceutical Research
and Early Development (pRED) Roche Innovation Center Basel, F. Hoffmann-La Roche, Ltd., Grenzacherstrasse 124 CH-4070 Basel, Switzerland
| | - Remo Hochstrasser
- Roche Pharmaceutical Research
and Early Development (pRED) Roche Innovation Center Basel, F. Hoffmann-La Roche, Ltd., Grenzacherstrasse 124 CH-4070 Basel, Switzerland
| | - Ann C. Petersen
- Roche Pharmaceutical Research
and Early Development (pRED) Roche Innovation Center Basel, F. Hoffmann-La Roche, Ltd., Grenzacherstrasse 124 CH-4070 Basel, Switzerland
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46
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MacConnell AB, Price AK, Paegel BM. An Integrated Microfluidic Processor for DNA-Encoded Combinatorial Library Functional Screening. ACS COMBINATORIAL SCIENCE 2017; 19:181-192. [PMID: 28199790 PMCID: PMC5350604 DOI: 10.1021/acscombsci.6b00192] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
DNA-encoded synthesis
is rekindling interest in combinatorial compound
libraries for drug discovery and in technology for automated and quantitative
library screening. Here, we disclose a microfluidic circuit that enables
functional screens of DNA-encoded compound beads. The device carries
out library bead distribution into picoliter-scale assay reagent droplets,
photochemical cleavage of
compound from the bead, assay incubation, laser-induced fluorescence-based
assay detection, and fluorescence-activated droplet sorting to isolate
hits. DNA-encoded compound beads (10-μm diameter) displaying
a photocleavable positive control inhibitor pepstatin A were mixed
(1920 beads, 729 encoding sequences) with negative control beads (58 000
beads, 1728 encoding sequences) and screened for cathepsin D inhibition
using a biochemical enzyme activity assay. The circuit sorted 1518
hit droplets for collection following 18 min incubation over a 240
min analysis. Visual inspection of a subset of droplets (1188 droplets)
yielded a 24% false discovery rate (1166 pepstatin A beads; 366 negative
control beads). Using template barcoding strategies, it was possible
to count hit collection beads (1863) using next-generation sequencing
data. Bead-specific barcodes enabled replicate counting, and the false
discovery rate was reduced to 2.6% by only considering hit-encoding
sequences that were observed on >2 beads. This work represents
a complete
distributable small molecule discovery platform, from microfluidic
miniaturized automation to ultrahigh-throughput hit deconvolution
by sequencing.
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Affiliation(s)
- Andrew B. MacConnell
- Department
of Chemistry and ‡Doctoral Program in Chemical and Biological
Sciences, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Alexander K. Price
- Department
of Chemistry and ‡Doctoral Program in Chemical and Biological
Sciences, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Brian M. Paegel
- Department
of Chemistry and ‡Doctoral Program in Chemical and Biological
Sciences, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
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47
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Spagnuolo LA, Eltschkner S, Yu W, Daryaee F, Davoodi S, Knudson SE, Allen EKH, Merino J, Pschibul A, Moree B, Thivalapill N, Truglio JJ, Salafsky J, Slayden RA, Kisker C, Tonge PJ. Evaluating the Contribution of Transition-State Destabilization to Changes in the Residence Time of Triazole-Based InhA Inhibitors. J Am Chem Soc 2017; 139:3417-3429. [PMID: 28151657 DOI: 10.1021/jacs.6b11148] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A critical goal of lead compound selection and optimization is to maximize target engagement while minimizing off-target binding. Since target engagement is a function of both the thermodynamics and kinetics of drug-target interactions, it follows that the structures of both the ground states and transition states on the binding reaction coordinate are needed to rationally modulate the lifetime of the drug-target complex. Previously, we predicted the structure of the rate-limiting transition state that controlled the time-dependent inhibition of the enoyl-ACP reductase InhA. This led to the discovery of a triazole-containing diphenyl ether with an increased residence time on InhA due to transition-state destabilization rather than ground-state stabilization. In the present work, we evaluate the inhibition of InhA by 14 triazole-based diphenyl ethers and use a combination of enzyme kinetics and X-ray crystallography to generate a structure-kinetic relationship for time-dependent binding. We show that the triazole motif slows the rate of formation for the final drug-target complex by up to 3 orders of magnitude. In addition, we identify a novel inhibitor with a residence time on InhA of 220 min, which is 3.5-fold longer than that of the INH-NAD adduct formed by the tuberculosis drug, isoniazid. This study provides a clear example in which the lifetime of the drug-target complex is controlled by interactions in the transition state for inhibitor binding rather than the ground state of the enzyme-inhibitor complex, and demonstrates the important role that on-rates can play in drug-target residence time.
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Affiliation(s)
- Lauren A Spagnuolo
- Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794-3400, United States
| | - Sandra Eltschkner
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg , 97080 Würzburg, Germany
| | - Weixuan Yu
- Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794-3400, United States
| | - Fereidoon Daryaee
- Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794-3400, United States
| | - Shabnam Davoodi
- Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794-3400, United States
| | - Susan E Knudson
- Department of Microbiology, Immunology and Pathology, Colorado State University , Fort Collins, Colorado 80523-2025, United States
| | - Eleanor K H Allen
- Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794-3400, United States
| | - Jonathan Merino
- Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794-3400, United States
| | - Annica Pschibul
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg , 97080 Würzburg, Germany
| | - Ben Moree
- Biodesy, Inc. , 384 Oyster Point Boulevard, South San Francisco, California 94080, United States
| | - Neil Thivalapill
- Great Neck South High School , 341 Lakeville Road, Great Neck, New York 11020, United States
| | - James J Truglio
- Great Neck South High School , 341 Lakeville Road, Great Neck, New York 11020, United States
| | - Joshua Salafsky
- Biodesy, Inc. , 384 Oyster Point Boulevard, South San Francisco, California 94080, United States
| | - Richard A Slayden
- Department of Microbiology, Immunology and Pathology, Colorado State University , Fort Collins, Colorado 80523-2025, United States
| | - Caroline Kisker
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg , 97080 Würzburg, Germany
| | - Peter J Tonge
- Institute of Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794-3400, United States
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48
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Mendes KR, Malone ML, Ndungu JM, Suponitsky-Kroyter I, Cavett VJ, McEnaney PJ, MacConnell AB, Doran TM, Ronacher K, Stanley K, Utset O, Walzl G, Paegel BM, Kodadek T. High-throughput Identification of DNA-Encoded IgG Ligands that Distinguish Active and Latent Mycobacterium tuberculosis Infections. ACS Chem Biol 2017; 12:234-243. [PMID: 27957856 DOI: 10.1021/acschembio.6b00855] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The circulating antibody repertoire encodes a patient's health status and pathogen exposure history, but identifying antibodies with diagnostic potential usually requires knowledge of the antigen(s). We previously circumvented this problem by screening libraries of bead-displayed small molecules against case and control serum samples to discover "epitope surrogates" (ligands of IgGs enriched in the case sample). Here, we describe an improved version of this technology that employs DNA-encoded libraries and high-throughput FACS-based screening to discover epitope surrogates that differentiate noninfectious/latent (LTB) patients from infectious/active TB (ATB) patients, which is imperative for proper treatment selection and antibiotic stewardship. Normal control/LTB (10 patients each, NCL) and ATB (10 patients) serum pools were screened against a library (5 × 106 beads, 448 000 unique compounds) using fluorescent antihuman IgG to label hit compound beads for FACS. Deep sequencing decoded all hit structures and each hit's occurrence frequencies. ATB hits were pruned of NCL hits and prioritized for resynthesis based on occurrence and homology. Several structurally homologous families were identified and 16/21 resynthesized representative hits validated as selective ligands of ATB serum IgGs (p < 0.005). The native secreted TB protein Ag85B (though not the E. coli recombinant form) competed with one of the validated ligands for binding to antibodies, suggesting that it mimics a native Ag85B epitope. The use of DNA-encoded libraries and FACS-based screening in epitope surrogate discovery reveals thousands of potential hit structures. Distilling this list down to several consensus chemical structures yielded a diagnostic panel for ATB composed of thermally stable and economically produced small molecule ligands in place of protein antigens.
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Affiliation(s)
- Kimberly R. Mendes
- Opko Health, Inc., 5353 Parkside
Drive Jupiter, Florida 33458, United States
| | | | - John Maina Ndungu
- Opko Health, Inc., 5353 Parkside
Drive Jupiter, Florida 33458, United States
| | | | | | | | | | | | - Katharina Ronacher
- Department
of Science and Technology/National Research Foundation Centre of Excellence
for Biomedical TB Research/Medical Research Council Centre for Molecular
and Cellular Biology, Division of Molecular Biology and Human Genetics,
Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Kim Stanley
- Department
of Science and Technology/National Research Foundation Centre of Excellence
for Biomedical TB Research/Medical Research Council Centre for Molecular
and Cellular Biology, Division of Molecular Biology and Human Genetics,
Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Ofelia Utset
- Opko Health, Inc., 5353 Parkside
Drive Jupiter, Florida 33458, United States
| | - Gerhard Walzl
- Department
of Science and Technology/National Research Foundation Centre of Excellence
for Biomedical TB Research/Medical Research Council Centre for Molecular
and Cellular Biology, Division of Molecular Biology and Human Genetics,
Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
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49
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Abstract
Mycobacterium tuberculosis (Mtb), the etiological agent of tuberculosis (TB), is recognized as a global health emergency as promoted by the World Health Organization. Over 1 million deaths per year, along with the emergence of multi- and extensively-drug resistant strains of Mtb, have triggered intensive research into the pathogenicity and biochemistry of this microorganism, guiding the development of anti-TB chemotherapeutic agents. The essential mycobacterial cell wall, sharing some common features with all bacteria, represents an apparent ‘Achilles heel’ that has been targeted by TB chemotherapy since the advent of TB treatment. This complex structure composed of three distinct layers, peptidoglycan, arabinogalactan and mycolic acids, is vital in supporting cell growth, virulence and providing a barrier to antibiotics. The fundamental nature of cell wall synthesis and assembly has rendered the mycobacterial cell wall as the most widely exploited target of anti-TB drugs. This review provides an overview of the biosynthesis of the prominent cell wall components, highlighting the inhibitory mechanisms of existing clinical drugs and illustrating the potential of other unexploited enzymes as future drug targets.
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50
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Abstract
DNA-encoded chemical library technologies are increasingly being adopted in drug discovery for hit and lead generation. DNA-encoded chemistry enables the exploration of chemical spaces four to five orders of magnitude more deeply than is achievable by traditional high-throughput screening methods. Operation of this technology requires developing a range of capabilities including aqueous synthetic chemistry, building block acquisition, oligonucleotide conjugation, large-scale molecular biological transformations, selection methodologies, PCR, sequencing, sequence data analysis and the analysis of large chemistry spaces. This Review provides an overview of the development and applications of DNA-encoded chemistry, highlighting the challenges and future directions for the use of this technology.
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