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Bai YR, Seng DJ, Xu Y, Zhang YD, Zhou WJ, Jia YY, Song J, He ZX, Liu HM, Yuan S. A comprehensive review of small molecule drugs approved by the FDA in 2023: Advances and prospects. Eur J Med Chem 2024; 276:116706. [PMID: 39053188 DOI: 10.1016/j.ejmech.2024.116706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 07/21/2024] [Indexed: 07/27/2024]
Abstract
In 2023, the U.S. Food and Drug Administration has approved 55 novel medications, consisting of 17 biologics license applications and 38 new molecular entities. Although the biologics license applications including antibody and enzyme replacement therapy set a historical record, the new molecular entities comprising small molecule drugs, diagnostic agent, RNA interference therapy and biomacromolecular peptide still account for over 50 % of the newly approved medications. The novel and privileged scaffolds derived from drugs, active molecules and natural products are consistently associated with the discovery of new mechanisms, the expansion of clinical indications and the reduction of side effects. Moreover, the structural modifications based on the promising scaffolds can provide the clinical candidates with the improved biological activities, bypass the patent protection and greatly shorten the period of new drug discovery. Therefore, conducting an appraisal of drug approval experience and related information will expedite the identification of more potent drug molecules. In this review, we comprehensively summarized the pertinent information encompassing the clinical application, mechanism, elegant design and development processes of 28 small molecule drugs, and expected to provide the promising structural basis and design inspiration for pharmaceutical chemists.
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Affiliation(s)
- Yi-Ru Bai
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China; School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Zhengzhou, 450001, China
| | - Dong-Jie Seng
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Ying Xu
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Yao-Dong Zhang
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Wen-Juan Zhou
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Yang-Yang Jia
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Jian Song
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Zhang-Xu He
- Pharmacy College, Henan University of Chinese Medicine, Zhengzhou, 450046, China.
| | - Hong-Min Liu
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China; School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Zhengzhou, 450001, China.
| | - Shuo Yuan
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China; School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Zhengzhou, 450001, China.
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2
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Wu Z, Chen S, Wang Y, Li F, Xu H, Li M, Zeng Y, Wu Z, Gao Y. Current perspectives and trend of computer-aided drug design: a review and bibliometric analysis. Int J Surg 2024; 110:3848-3878. [PMID: 38502850 PMCID: PMC11175770 DOI: 10.1097/js9.0000000000001289] [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: 11/08/2023] [Accepted: 02/22/2024] [Indexed: 03/21/2024]
Abstract
AIM Computer-aided drug design (CADD) is a drug design technique for computing ligand-receptor interactions and is involved in various stages of drug development. To better grasp the frontiers and hotspots of CADD, we conducted a review analysis through bibliometrics. METHODS A systematic review of studies published between 2000 and 20 July 2023 was conducted following the PRISMA guidelines. Literature on CADD was selected from the Web of Science Core Collection. General information, publications, output trends, countries/regions, institutions, journals, keywords, and influential authors were visually analyzed using software such as Excel, VOSviewer, RStudio, and CiteSpace. RESULTS A total of 2031 publications were included. These publications primarily originated from 99 countries or regions led by the U.S. and China. Among the contributors, MacKerell AD had the highest number of articles and the greatest influence. The Journal of Medicinal Chemistry was the most cited journal, whereas the Journal of Chemical Information and Modeling had the highest number of publications. CONCLUSIONS Influential authors in the field were identified. Current research shows active collaboration between countries, institutions, and companies. CADD technologies such as homology modeling, pharmacophore modeling, quantitative conformational relationships, molecular docking, molecular dynamics simulation, binding free energy prediction, and high-throughput virtual screening can effectively improve the efficiency of new drug discovery. Artificial intelligence-assisted drug design and screening based on CADD represent key topics that will influence future development. Furthermore, this paper will be helpful in better understanding the frontiers and hotspots of CADD.
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Affiliation(s)
- Zhenhui Wu
- School of Pharmacy, Jiangxi University of Chinese Medicine
- School of Clinical Medicine, Jiangxi University of Chinese Medicine, Nanchang
- Beijing Institute of Radiation Medicine, Academy of Military Sciences, Beijing, People’s Republic of China
| | - Shupeng Chen
- School of Clinical Medicine, Jiangxi University of Chinese Medicine, Nanchang
| | - Yihao Wang
- Beijing Institute of Radiation Medicine, Academy of Military Sciences, Beijing, People’s Republic of China
| | - Fangyang Li
- Beijing Institute of Radiation Medicine, Academy of Military Sciences, Beijing, People’s Republic of China
| | - Huanhua Xu
- School of Pharmacy, Jiangxi University of Chinese Medicine
| | - Maoxing Li
- Beijing Institute of Radiation Medicine, Academy of Military Sciences, Beijing, People’s Republic of China
| | - Yingjian Zeng
- School of Clinical Medicine, Jiangxi University of Chinese Medicine, Nanchang
| | - Zhenfeng Wu
- School of Pharmacy, Jiangxi University of Chinese Medicine
| | - Yue Gao
- School of Pharmacy, Jiangxi University of Chinese Medicine
- Beijing Institute of Radiation Medicine, Academy of Military Sciences, Beijing, People’s Republic of China
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3
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Michaelides IN, Collie GW. E3 Ligases Meet Their Match: Fragment-Based Approaches to Discover New E3 Ligands and to Unravel E3 Biology. J Med Chem 2023; 66:3173-3194. [PMID: 36821822 PMCID: PMC10009759 DOI: 10.1021/acs.jmedchem.2c01882] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Indexed: 02/25/2023]
Abstract
Ubiquitination is a key post-translational modification of proteins, affecting the regulation of multiple cellular processes. Cells are equipped with over 600 ubiquitin orchestrators, called E3 ubiquitin ligases, responsible for directing the covalent attachment of ubiquitin to substrate proteins. Due to their regulatory role in cells, significant efforts have been made to discover ligands for E3 ligases. The recent emergence of the proteolysis targeting chimera (PROTAC) and molecular glue degrader (MGD) modalities has further increased interest in E3 ligases as drug targets. This perspective focuses on how fragment based lead discovery (FBLD) methods have been used to discover new ligands for this important target class. In some cases these efforts have led to clinical candidates; in others, they have provided tools for deepening our understanding of E3 ligase biology. Recently, FBLD-derived ligands have inspired the design of PROTACs that are able to artificially modulate protein levels in cells.
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Affiliation(s)
- Iacovos N. Michaelides
- Discovery Sciences, BioPharmaceuticals
R&D, AstraZeneca, Cambridge, CB4 0WG, United
Kingdom
| | - Gavin W. Collie
- Discovery Sciences, BioPharmaceuticals
R&D, AstraZeneca, Cambridge, CB4 0WG, United
Kingdom
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4
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Izmest'ev AN, Kravchenko AN, Gazieva GA. A new reversible transformation of oxindolylidene derivatives of imidazothiazolotriazine into 3-[(imidazotriazin-3-yl)thio]-2-oxoquinoline-4-carboxylates. Org Biomol Chem 2023; 21:1827-1834. [PMID: 36751947 DOI: 10.1039/d2ob02242g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A simple method for the synthesis of water-soluble potassium 3-[(imidazotriazin-3-yl)thio]-2-oxoquinoline-4-carboxylates was developed based on a new reversible transformation of oxindolylidene derivatives of imidazothiazolotriazine that results from their treatment with potassium hydroxide. The antiproliferative activity of the synthesized compounds was evaluated against 58 cell lines and compared with oxindolylidene derivatives of imidazothiazolotriazine. Quinoline derivatives 3 demonstrated high activity with average GI50 values of <10 μM which are comparable or higher than those of the oxindolylidene imidazothiazolotriazines. Compound 3a, with a pent-3-yl substituent at the nitrogen atom of the quinoline fragment, possessed the highest antiproliferative activity with an average GI50 value of 1.71 μM. The GI50 values of compound 3a against 52 of the 58 cell lines were <1 μM; against the remaining 6 of the 58 cell lines, they were in the range 1.21-39.2 μM.
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Affiliation(s)
- Alexei N Izmest'ev
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prosp., 47, Moscow 119991, Russian Federation.
| | - Angelina N Kravchenko
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prosp., 47, Moscow 119991, Russian Federation.
| | - Galina A Gazieva
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prosp., 47, Moscow 119991, Russian Federation.
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Humphreys PG, Anderson NA, Bamborough P, Baxter A, Chung CW, Cookson R, Craggs PD, Dalton T, Fournier JCL, Gordon LJ, Gray HF, Gray MW, Gregory R, Hirst DJ, Jamieson C, Jones KL, Kessedjian H, Lugo D, McGonagle G, Patel VK, Patten C, Poole DL, Prinjha RK, Ramirez-Molina C, Rioja I, Seal G, Stafford KAJ, Shah RR, Tape D, Theodoulou NH, Tomlinson L, Ukuser S, Wall ID, Wellaway N, White G. Identification and Optimization of a Ligand-Efficient Benzoazepinone Bromodomain and Extra Terminal (BET) Family Acetyl-Lysine Mimetic into the Oral Candidate Quality Molecule I-BET432. J Med Chem 2022; 65:15174-15207. [DOI: 10.1021/acs.jmedchem.2c01102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
| | - Niall A. Anderson
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Paul Bamborough
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Andrew Baxter
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Chun-wa Chung
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Rosa Cookson
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Peter D. Craggs
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Toryn Dalton
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | | | - Laurie J. Gordon
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Heather F. Gray
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Matthew W. Gray
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Richard Gregory
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - David J. Hirst
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Craig Jamieson
- WestCHEM, Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K
| | | | | | - David Lugo
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Grant McGonagle
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | | | | | - Darren L. Poole
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Rab K. Prinjha
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | | | - Inmaculada Rioja
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Gail Seal
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | | | - Rishi R. Shah
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Daniel Tape
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | | | - Laura Tomlinson
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Sabri Ukuser
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Ian D. Wall
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Natalie Wellaway
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Gemma White
- GSK, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, U.K
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6
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Aldrich CC, Calderón F, Conway SJ, He C, Hooker JM, Huryn DM, Lindsley CW, Liotta DC, Müller CE. Virtual Special Issue: Epigenetics 2022. ACS Chem Biol 2022; 17:2673-2678. [PMID: 36268572 DOI: 10.1021/acschembio.2c00661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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7
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Aldrich CC, Calderón F, Conway SJ, He C, Hooker JM, Huryn DM, Lindsley CW, Liotta DC, Müller CE. Virtual Special Issue: Epigenetics 2022. ACS Pharmacol Transl Sci 2022; 5:829-834. [PMID: 36268124 PMCID: PMC9578134 DOI: 10.1021/acsptsci.2c00169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Indexed: 11/28/2022]
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8
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Aldrich CC, Calderón F, Conway SJ, He C, Hooker JM, Huryn DM, Lindsley CW, Liotta DC, Müller CE. Virtual Special Issue: Epigenetics 2022. ACS Infect Dis 2022; 8:1975-1980. [PMID: 36073808 DOI: 10.1021/acsinfecdis.2c00434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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9
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Aldrich CC, Calderón F, Conway SJ, He C, Hooker JM, Huryn DM, Lindsley CW, Liotta DC, Müller CE. Virtual Special Issue: Epigenetics 2022. ACS Med Chem Lett 2022; 13:1524-1529. [PMID: 36262399 PMCID: PMC9575161 DOI: 10.1021/acsmedchemlett.2c00393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Indexed: 11/30/2022] Open
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10
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Lucas SCC, Börjesson U, Bostock MJ, Cuff J, Edfeldt F, Embrey KJ, Eriksson PO, Gohlke A, Gunnarson A, Lainchbury M, Milbradt AG, Moore R, Rawlins PB, Sinclair I, Stubbs C, Storer RI. Fragment screening at AstraZeneca: developing the next generation biophysics fragment set. RSC Med Chem 2022; 13:1052-1057. [PMID: 36324499 PMCID: PMC9491351 DOI: 10.1039/d2md00154c] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/29/2022] [Indexed: 05/18/2024] Open
Abstract
Fragment based drug discovery is a critical part of the lead generation toolbox and relies heavily on a readily available, high quality fragment library. Over years of use, the AstraZeneca fragment set had become partially depleted and instances of compound deterioration had been found. It was recognised that a redevelopment was required. This provided an opportunity to evolve our screening sets strategy, whilst ensuring that the quality of the fragment set met the robust requirements of fragment screening campaigns. In this communication we share the strategy employed, in particular highlighting two aspects of our approach that we believe others in the community would benefit from, namely that; (i) fragments were selected with input from Medicinal Chemists at an early stage, and (ii) the library was arranged in a layered format to ensure maximum flexibility on a per target basis.
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Affiliation(s)
- Simon C C Lucas
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca Cambridge UK
| | - Ulf Börjesson
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca Gothenburg Sweden
| | - Mark J Bostock
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca Cambridge UK
| | - John Cuff
- Compound Synthesis and Management, Discovery Sciences, R&D, AstraZeneca Alderley Park UK
| | - Fredrik Edfeldt
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca Gothenburg Sweden
| | - Kevin J Embrey
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca Cambridge UK
| | - Per-Olof Eriksson
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca Gothenburg Sweden
| | - Andrea Gohlke
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca Cambridge UK
| | - Anders Gunnarson
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca Gothenburg Sweden
| | | | - Alexander G Milbradt
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca Cambridge UK
| | - Rachel Moore
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca Alderley Park UK
| | - Philip B Rawlins
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca Cambridge UK
| | - Ian Sinclair
- Compound Synthesis and Management, Discovery Sciences, R&D, AstraZeneca Alderley Park UK
| | - Christopher Stubbs
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca Cambridge UK
| | - R Ian Storer
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca Cambridge UK
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11
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Aldrich CC, Calderón F, Conway SJ, He C, Hooker JM, Huryn DM, Lindsley CW, Liotta DC, Müller CE. Virtual Special Issue: Epigenetics 2022. J Med Chem 2022; 65:11894-11899. [PMID: 36073827 DOI: 10.1021/acs.jmedchem.2c01386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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12
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Aldrich CC, Calderón F, Conway SJ, He C, Hooker JM, Huryn DM, Lindsley CW, Liotta DC, Müller CE. Virtual Special Issue: Epigenetics 2022. ACS Chem Neurosci 2022. [PMID: 36067366 DOI: 10.1021/acschemneuro.2c00501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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13
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Song J, Jiang X, Wang Z, Pei J, Li H. 4-Chloro-5-(dimethylamino)-2-[(5-phenyl-1,3,4-oxadiazol-2-yl)methyl]pyridazin-3(2 H)-one. IUCRDATA 2022; 7:x220342. [DOI: 10.1107/s241431462200342x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 03/26/2022] [Indexed: 11/11/2022] Open
Abstract
In the structure of the title compound, C15H14ClN5O2, the terminal phenyl ring and the adjacent furan ring subtend a dihedral angle of 6.77 (17)°. The 4-chloro-5-(dimethylamino)-pyridazin-3(2H)-one group is linked to the oxadiazole ring by a methylene bridge, and the dihedral angle between the pyridazine and oxadiazole rings is 88.66 (14)°. In the crystal, C—H...O and C—H...N hydrogen bonds extend the structure into a three-dimensional network.
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Eliandro da Silva, Jr. P, Melo SMGD, Helder de Paula M, Vessecchi R, Opatz T, Day J, Ganesan A, da Silva Emery F. Growth vector elaboration of fragments: regioselective functionalization of 5-hydroxy-6-azaindazole and 3-hydroxy-2,6-naphtyridine. Org Biomol Chem 2022; 20:7483-7490. [DOI: 10.1039/d2ob00968d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This article discusses the reactivity of an 6-azaindazole (1) and a 2,6-naphthyridine (2), proposed to be “heteroaromatic rings of the future” which would be useful for fragment-based drug discovery (FBDD)...
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