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Organic Synthesis in Drug Discovery

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Medicinal Chemistry".

Deadline for manuscript submissions: closed (31 March 2022) | Viewed by 44658

Special Issue Editor

Department of Chemistry, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, UK
Interests: organic synthesis; aromatic chemistry; heteroaromatic chemistry; stereochemistry; history of dyes; supramolecular chemistry; prebiotic chemistry; drug-DNP complexing; optical limiting; organic minerals; ammonia free hair dyeing
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This is a Special Issue of Molecules on organic synthesis in drug discovery. This can be interpreted in a broad light and can cover those topics listed in the key words. It is recommended that each paper should have a short introduction which indicates which classes of biologically active compounds that the work is relevant to. Compounds reported in the papers do not need to have biological data but should have full synthetic characterisation data for all new compounds. Known compounds should have a reference. The issue is not targeted at industrial drug synthesis or late stage drug selection. The aim is to highlight the role that organic synthesis plays in developing methods that may be exploited for finding lead compounds and drugs by the pharmaceutical industry.

Dr. Michael John Plater
Guest Editor

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Keywords

  • Medicinal chemistry synthesis
  • Organic synthesis
  • Heterocyclic synthesis
  • Synthetic methodology
  • Asymmetric synthesis
  • Organometallic synthesis
  • Flow chemistry
  • Diversity in synthesis
  • Total synthesis
  • Synthesis of new ring systems
  • Stereoelectronic effects
  • Molecular rearrangements
  • Reactive intermediates in synthesis

Published Papers (12 papers)

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Research

Jump to: Review

14 pages, 1988 KiB  
Article
Synthesis of New Spiro-Cyclopropanes Prepared by Non-Stabilized Diazoalkane Exhibiting an Extremely High Insecticidal Activity
by Naoufel Ben Hamadi and Ahlem Guesmi
Molecules 2022, 27(8), 2470; https://doi.org/10.3390/molecules27082470 - 12 Apr 2022
Cited by 3 | Viewed by 1747
Abstract
The synthesis of new insecticidal gem-dimethyspiro-cyclopropanes derived from pyrrolidine-2,3-dione have been described, and their biological effect against different insect species has been evaluated. The presented results demonstrate the excellent insecticidal activity of cyclopropane 5c against Aedes aegypti and Musca domestica. Cyclopropane [...] Read more.
The synthesis of new insecticidal gem-dimethyspiro-cyclopropanes derived from pyrrolidine-2,3-dione have been described, and their biological effect against different insect species has been evaluated. The presented results demonstrate the excellent insecticidal activity of cyclopropane 5c against Aedes aegypti and Musca domestica. Cyclopropane 5c showed the quickest knockdown and the best killing against Aedes aegypti and Musca domestica compared to trans-chrysanthemic acid and pyrethrin. The biological results of the high insecticidal activity were confirmed by the results of docking. This is evident in the binding affinity obtained for cyclopropane 5c, indicating good binding with an important active amino acid residue of the 5FT3 protein. Full article
(This article belongs to the Special Issue Organic Synthesis in Drug Discovery)
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17 pages, 2725 KiB  
Article
Attenuation of Scopolamine-Induced Amnesia via Cholinergic Modulation in Mice by Synthetic Curcumin Analogs
by Haya Hussain, Shujaat Ahmad, Syed Wadood Ali Shah, Abid Ullah, Niaz Ali, Mazen Almehmadi, Manzoor Ahmad, Atif Ali Khan Khalil, Syed Babar Jamal, Hanif Ahmad and Mustafa Halawi
Molecules 2022, 27(8), 2468; https://doi.org/10.3390/molecules27082468 - 11 Apr 2022
Cited by 17 | Viewed by 2583
Abstract
Alzheimer’s disease is an emerging health disorder associated with cognitive decline and memory loss. In this study, six curcumin analogs (1a1f) were synthesized and screened for in vitro cholinesterase inhibitory potential. On the basis of promising results, they were [...] Read more.
Alzheimer’s disease is an emerging health disorder associated with cognitive decline and memory loss. In this study, six curcumin analogs (1a1f) were synthesized and screened for in vitro cholinesterase inhibitory potential. On the basis of promising results, they were further investigated for in vivo analysis using elevated plus maze (EPM), Y-maze, and novel object recognition (NOR) behavioral models. The binding mode of the synthesized compounds with the active sites of cholinesterases, and the involvement of the cholinergic system in brain hippocampus was determined. The synthesized curcumin analog 1d (p < 0.001, n = 6), and 1c (p < 0.01, n = 6) showed promising results by decreasing retention time in EPM, significantly increasing % SAP in Y-maze, while significantly (p < 0.001) enhancing the % discrimination index (DI) and the time exploring the novel objects in NORT mice behavioral models. A molecular docking study using MOE software was used for validation of the inhibition of cholinesterase(s). It has been indicated from the current research work that the synthesized curcumin analogs enhanced memory functions in mice models and could be used as valuable therapeutic molecules against neurodegenerative disorders. To determine their exact mechanism of action, further studies are suggested. Full article
(This article belongs to the Special Issue Organic Synthesis in Drug Discovery)
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16 pages, 3066 KiB  
Article
Synthesis of Novel C/D Ring Modified Bile Acids
by Roselis A. Landaeta Aponte, Andreas Luxenburger, Scott A. Cameron, Alex Weymouth-Wilson, Richard H. Furneaux, Lawrence D. Harris and Benjamin J. Compton
Molecules 2022, 27(7), 2364; https://doi.org/10.3390/molecules27072364 - 06 Apr 2022
Cited by 2 | Viewed by 2138
Abstract
Bile acid receptors have been identified as important targets for the development of new therapeutics to treat various metabolic and inflammatory diseases. The synthesis of new bile acid analogues can help elucidate structure–activity relationships and define compounds that activate these receptors selectively. Towards [...] Read more.
Bile acid receptors have been identified as important targets for the development of new therapeutics to treat various metabolic and inflammatory diseases. The synthesis of new bile acid analogues can help elucidate structure–activity relationships and define compounds that activate these receptors selectively. Towards this, access to large quantities of a chenodeoxycholic acid derivative bearing a C-12 methyl and a C-13 to C-14 double bond provided an interesting scaffold to investigate the chemical manipulation of the C/D ring junction in bile acids. The reactivity of this alkene substrate with various zinc carbenoid species showed that those generated using the Furukawa methodology achieved selective α-cyclopropanation, whereas those generated using the Shi methodology reacted in an unexpected manner giving rise to a rearranged skeleton whereby the C ring has undergone contraction to form a novel spiro–furan ring system. Further derivatization of the cyclopropanated steroid included O-7 oxidation and epimerization to afford new bile acid derivatives for biological evaluation. Full article
(This article belongs to the Special Issue Organic Synthesis in Drug Discovery)
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13 pages, 2078 KiB  
Article
Intermolecular Mechanism and Dynamic Investigation of Avian Influenza H7N9 Virus’ Susceptibility to E119V-Substituted Peramivir–Neuraminidase Complex
by Sphamandla E. Mtambo, Samuel C. Ugbaja, Aganze G. Mushebenge, Bahijjahtu H. Abubakar, Mthobisi L. Ntuli and Hezekiel M. Kumalo
Molecules 2022, 27(5), 1640; https://doi.org/10.3390/molecules27051640 - 02 Mar 2022
Cited by 1 | Viewed by 2386
Abstract
The H7N9 virus attaches itself to the human cell receptor protein containing the polysaccharide that terminates with sialic acid. The mutation of neuraminidase at residue E119 has been explored experimentally. However, there is no adequate information on the substitution with E119V in peramivir [...] Read more.
The H7N9 virus attaches itself to the human cell receptor protein containing the polysaccharide that terminates with sialic acid. The mutation of neuraminidase at residue E119 has been explored experimentally. However, there is no adequate information on the substitution with E119V in peramivir at the intermolecular level. Therefore, a good knowledge of the interatomic interactions is a prerequisite in understanding its transmission mode and subsequent effective inhibitions of the sialic acid receptor cleavage by neuraminidase. Herein, we investigated the mechanism and dynamism on the susceptibility of the E119V mutation on the peramivir–neuraminidase complex relative to the wildtype complex at the intermolecular level. This study aims to investigate the impact of the 119V substitution on the neuraminidase–peramivir complex and unveil the residues responsible for the complex conformations. We employed molecular dynamic (MD) simulations and extensive post-MD analyses in the study. These extensive computational investigations were carried out on the wildtype and the E119V mutant complex of the protein for holistic insights in unveiling the effects of this mutation on the binding affinity and the conformational terrain of peramivir–neuraminidase E119V mutation. The calculated total binding energy (ΔGbind) for the peramivir wildtype is −49.09 ± 0.13 kcal/mol, while the E119V mutant is −58.55 ± 0.15 kcal/mol. The increase in binding energy (9.46 kcal/mol) is consistent with other post-MD analyses results, confirming that E119V substitution confers a higher degree of stability on the protein complex. This study promises to proffer contributory insight and additional knowledge that would enhance future drug designs and help in the fight targeted at controlling the avian influenza H7N9 virus. Therefore, we suggest that experimentalists collaborate with computational chemists for all investigations of this topic, as we have done in our previous studies. Full article
(This article belongs to the Special Issue Organic Synthesis in Drug Discovery)
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11 pages, 1124 KiB  
Article
Synthesis and Evaluation of Trypanocidal Activity of Chromane-Type Compounds and Acetophenones
by Luis A. González, Sara Robledo, Yulieth Upegui, Gustavo Escobar and Wiston Quiñones
Molecules 2021, 26(23), 7067; https://doi.org/10.3390/molecules26237067 - 23 Nov 2021
Cited by 5 | Viewed by 1782
Abstract
American trypanosomiasis (Chagas disease) caused by the Trypanosoma cruzi parasite, is a severe health problem in different regions of Latin America and is currently reported to be spreading to Europe, North America, Japan, and Australia, due to the migration of populations from South [...] Read more.
American trypanosomiasis (Chagas disease) caused by the Trypanosoma cruzi parasite, is a severe health problem in different regions of Latin America and is currently reported to be spreading to Europe, North America, Japan, and Australia, due to the migration of populations from South and Central America. At present, there is no vaccine available and chemotherapeutic options are reduced to nifurtimox and benznidazole. Therefore, the discovery of new molecules is urgently needed to initiate the drug development process. Some acetophenones and chalcones, as well as chromane-type substances, such as chromones and flavones, are natural products that have been studied as trypanocides, but the relationships between structure and activity are not yet fully understood. In this work, 26 compounds were synthesized to determine the effect of hydroxyl and isoprenyl substituents on trypanocide activity. One of the compounds showed interesting activity against a resistant strain of T. cruzi, with a half effective concentration of 18.3 µM ± 1.1 and an index of selectivity > 10.9. Full article
(This article belongs to the Special Issue Organic Synthesis in Drug Discovery)
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13 pages, 1725 KiB  
Article
One-Pot Multicomponent Synthesis of Methoxybenzo[h]quinoline-3-carbonitrile Derivatives; Anti-Chagas, X-ray, and In Silico ADME/Tox Profiling Studies
by Hegira Ramírez, Katiuska Charris, Esteban Fernandez-Moreira, Benjamín Nogueda-Torres, Mario V. Capparelli, Jorge Ángel and Jaime Charris
Molecules 2021, 26(22), 6977; https://doi.org/10.3390/molecules26226977 - 19 Nov 2021
Cited by 1 | Viewed by 1770
Abstract
Several methoxybenzo[h]quinoline-3-carbonitrile analogs were designed and synthesized in a repositioning approach to developing compounds with anti-prostate cancer and anti-Chagas disease properties. The compounds were synthesized through a sequential multicomponent reaction of aromatic aldehydes, malononitrile, and 1-tetralone in the presence of ammonium [...] Read more.
Several methoxybenzo[h]quinoline-3-carbonitrile analogs were designed and synthesized in a repositioning approach to developing compounds with anti-prostate cancer and anti-Chagas disease properties. The compounds were synthesized through a sequential multicomponent reaction of aromatic aldehydes, malononitrile, and 1-tetralone in the presence of ammonium acetate and acetic acid (catalytic). The effect of the one-pot method on the generation of the target product has been studied. The compounds were in vitro screened against bloodstream trypomastigotes of T. cruzi (NINOA and INC-5 strains) and were most effective at showing a better activity profile than nifurtimox and benznidazole (reference drugs). A study in silico on absorption, distribution, metabolism, excretion, and toxicity (ADME/Tox) profiling to help describe the molecular properties related to the pharmacokinetic aspects in the human body of these compounds was reported. In addition, X-ray data for the compound 2-Amino-5,6-dihydro-4-(3-hydroxy-4-methoxy-phenyl)-8-methoxybenzo[h]quinoline-3-carbonitrile 6 was being reported. Spectral (IR, NMR, and elemental analyses) data on all final compounds were consistent with the proposed structures. Full article
(This article belongs to the Special Issue Organic Synthesis in Drug Discovery)
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14 pages, 1754 KiB  
Article
T3P-Promoted Synthesis of a Series of 2-Aryl-3-phenyl-2,3-dihydro-4H-pyrido[3,2-e][1,3]thiazin-4-ones and Their Activity against the Kinetoplastid Parasite Trypanosoma brucei
by Lee J. Silverberg, Tapas K. Mal, Carlos N. Pacheco, Megan L. Povelones, Madeline F. Malfara, Anthony F. Lagalante, Mark A. Olsen, Hemant P. Yennawar, Hany F. Sobhi, Kayla R. Baney, Robin L. Bozeman, Craig S. Eroh, Michael J. Fleming, Tracy L. Garcia, Casey L. Gregory, Julia E. Hahn, Alyssa M. Hatter, Lexi L. Johns, Tianna L. Klinger, Jennie J. Li, Andrew J. Menig, Grace C. Muench, Melissa E. Ramirez, Jordyn Reilly, Nicole Sacco, Alexandra M. Sheidy, Marla M. Stoner, Eric N. Thompson and Soroush F. Yazdaniadd Show full author list remove Hide full author list
Molecules 2021, 26(20), 6099; https://doi.org/10.3390/molecules26206099 - 09 Oct 2021
Cited by 3 | Viewed by 2335
Abstract
A series of fourteen 2-aryl-3-phenyl-2,3-dihydro-4H-pyrido[3,2-e][1,3]thiazin-4-ones was prepared at room temperature by T3P-mediated cyclization of N-phenyl-C-aryl imines with thionicotinic acid, two difficult substrates. The reactions were operationally simple, did not require specialized equipment or anhydrous solvents, could [...] Read more.
A series of fourteen 2-aryl-3-phenyl-2,3-dihydro-4H-pyrido[3,2-e][1,3]thiazin-4-ones was prepared at room temperature by T3P-mediated cyclization of N-phenyl-C-aryl imines with thionicotinic acid, two difficult substrates. The reactions were operationally simple, did not require specialized equipment or anhydrous solvents, could be performed as either two or three component reactions, and gave moderate–good yields as high as 63%. This provides ready access to N-phenyl compounds in this family, which have been generally difficult to prepare. As part of the study, the first crystal structure of neutral thionicotinic acid is also reported, and showed the molecule to be in the form of the thione tautomer. Additionally, the synthesized compounds were tested against T. brucei, the causative agent of Human African Sleeping Sickness. Screening at 50 µM concentration showed that five of the compounds strongly inhibited growth and killed parasites. Full article
(This article belongs to the Special Issue Organic Synthesis in Drug Discovery)
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11 pages, 3857 KiB  
Article
Crystalline Forms of Trazodone Dihydrates
by M. John Plater and William T. A. Harrison
Molecules 2021, 26(17), 5361; https://doi.org/10.3390/molecules26175361 - 03 Sep 2021
Viewed by 1890
Abstract
In this study, treatment of anhydrous trazodone powder with ammonium carbamate in warm water crystallised two new polymorphs or dihydrates of trazodone after 5 h, whose structures were determined by X-ray single crystal diffraction. Each dihydrate contains infinite zigzag hydrogen-bonded chains of water [...] Read more.
In this study, treatment of anhydrous trazodone powder with ammonium carbamate in warm water crystallised two new polymorphs or dihydrates of trazodone after 5 h, whose structures were determined by X-ray single crystal diffraction. Each dihydrate contains infinite zigzag hydrogen-bonded chains of water molecules, which are stabilised by the N4 acceptor atom of the piperazine ring and the pendant carbonyl O1 atom of the triazole ring, as well as other water molecules. The strong dipole moment expected for the O1 atom makes it a good hydrogen bond acceptor for stabilising the chains of water molecules. Each molecule of trazodone has a similar conformation in both hydrates, except for the propyl chains, which adopt different conformations: anti-gauche in the β hydrate (triazole N-C-C-C and C-C-C-piperazine N) and anti-anti in the γ hydrate. Both piperazine rings adopt chair conformations, and the exocyclic N-C bonds are in equatorial orientations. The Hirshfeld surfaces and two-dimensional fingerprint plots for the polymorphs were calculated using CrystalExplorer17, which indicated contacts significantly shorter than the sum of the van der Waals radii in the vicinity of the piperazine N4 and triazole O1 atoms corresponding to the strong hydrogen bonds accepted by these atoms. Full article
(This article belongs to the Special Issue Organic Synthesis in Drug Discovery)
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12 pages, 3138 KiB  
Communication
Δ8(14)-Ergostenol Glycoside Derivatives Inhibit the Expression of Inflammatory Mediators and Matrix Metalloproteinase
by Hyejin Moon, Myoungsil Ko, Yujin Park, Jeonguk Kim, Dowon Yoon, Eunjoohwang Lee, Taehoon Lee and Hakwon Kim
Molecules 2021, 26(15), 4547; https://doi.org/10.3390/molecules26154547 - 28 Jul 2021
Cited by 2 | Viewed by 1932
Abstract
Arthritis is a chronic inflammatory disease accompanied by pathological reactions such as swelling, redness, fever, and pain in various joint areas. The drugs currently available to treat arthritis are associated with diverse side-effects. Therefore, there is a need for safer and more effective [...] Read more.
Arthritis is a chronic inflammatory disease accompanied by pathological reactions such as swelling, redness, fever, and pain in various joint areas. The drugs currently available to treat arthritis are associated with diverse side-effects. Therefore, there is a need for safer and more effective treatments to alleviate the inflammation of arthritis with fewer side-effects. In this study, a new sterol, Δ8(14)-ergostenol, was discovered, and its glycosides were synthesized and found to be more efficient in terms of synthesis or anti-inflammatory activity than either spinasterol or 5,6-dihydroergosterol is. Among these synthetic glycosides, galactosyl ergostenol inhibited the expression of inflammatory mediators in TNF-α-stimulated FLS and TNF-α-induced MMPs and collagen type II A1 degradation in human chondrocytes. These results suggest the new galactosyl ergostenol as a treatment candidate for arthritis. Full article
(This article belongs to the Special Issue Organic Synthesis in Drug Discovery)
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20 pages, 2912 KiB  
Article
Synthesis of New Triazolopyrazine Antimalarial Compounds
by Daniel J. G. Johnson, Ian D. Jenkins, Cohan Huxley, Mark J. Coster, Kah Yean Lum, Jonathan M. White, Vicky M. Avery and Rohan A. Davis
Molecules 2021, 26(9), 2421; https://doi.org/10.3390/molecules26092421 - 21 Apr 2021
Cited by 3 | Viewed by 3675
Abstract
A radical approach to late-stage functionalization using photoredox and Diversinate chemistry on the Open Source Malaria (OSM) triazolopyrazine scaffold (Series 4) resulted in the synthesis of 12 new analogues, which were characterized by NMR, UV, and MS data analysis. The structures of [...] Read more.
A radical approach to late-stage functionalization using photoredox and Diversinate chemistry on the Open Source Malaria (OSM) triazolopyrazine scaffold (Series 4) resulted in the synthesis of 12 new analogues, which were characterized by NMR, UV, and MS data analysis. The structures of four triazolopyrazines were confirmed by X-ray crystal structure analysis. Several minor and unexpected side products were generated during these studies, including two resulting from a possible disproportionation reaction. All compounds were tested for their ability to inhibit the growth of the malaria parasite Plasmodium falciparum (3D7 and Dd2 strains) and for cytotoxicity against a human embryonic kidney (HEK293) cell line. Moderate antimalarial activity was observed for some of the compounds, with IC50 values ranging from 0.3 to >20 µM; none of the compounds displayed any toxicity against HEK293 at 80 µM. Full article
(This article belongs to the Special Issue Organic Synthesis in Drug Discovery)
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Review

Jump to: Research

17 pages, 6811 KiB  
Review
Synthetic Strategies of Pyrimidine-Based Scaffolds as Aurora Kinase and Polo-like Kinase Inhibitors
by Mrunal Jadhav, Kaksha Sankhe, Richie R. Bhandare, Zehra Edis, Samir Haj Bloukh and Tabassum Asif Khan
Molecules 2021, 26(17), 5170; https://doi.org/10.3390/molecules26175170 - 26 Aug 2021
Cited by 6 | Viewed by 3263
Abstract
The past few decades have witnessed significant progress in anticancer drug discovery. Small molecules containing heterocyclic moieties have attracted considerable interest for designing new antitumor agents. Of these, the pyrimidine ring system is found in multitude of drug structures, and being the building [...] Read more.
The past few decades have witnessed significant progress in anticancer drug discovery. Small molecules containing heterocyclic moieties have attracted considerable interest for designing new antitumor agents. Of these, the pyrimidine ring system is found in multitude of drug structures, and being the building unit of DNA and RNA makes it an attractive scaffold for the design and development of anticancer drugs. Currently, 22 pyrimidine-containing entities are approved for clinical use as anticancer drugs by the FDA. An exhaustive literature search indicates several publications and more than 59 patents from the year 2009 onwards on pyrimidine derivatives exhibiting potent antiproliferative activity. These pyrimidine derivatives exert their activity via diverse mechanisms, one of them being inhibition of protein kinases. Aurora kinase (AURK) and polo-like kinase (PLK) are protein kinases involved in the regulation of the cell cycle. Within the numerous pyrimidine-based small molecules developed as anticancer agents, this review focuses on the pyrimidine fused heterocyclic compounds modulating the AURK and PLK proteins in different phases of clinical trials as anticancer agents. This article aims to provide a comprehensive overview of synthetic strategies for the preparation of pyrimidine derivatives and their associated biological activity on AURK/PLK. It will also present an overview of the synthesis of the heterocyclic-2-aminopyrimidine, 4-aminopyrimidine and 2,4-diaminopyrimidine scaffolds, and one of the pharmacophores in AURK/PLK inhibitors is described systematically. Full article
(This article belongs to the Special Issue Organic Synthesis in Drug Discovery)
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22 pages, 11190 KiB  
Review
Recent Advances in the Synthesis of Ibuprofen and Naproxen
by Min-Woo Ha and Seung-Mann Paek
Molecules 2021, 26(16), 4792; https://doi.org/10.3390/molecules26164792 - 07 Aug 2021
Cited by 22 | Viewed by 16663
Abstract
Herein, we review the recent progress in the synthesis of representative nonsteroidal anti-inflammatory drugs (NSAIDs), ibuprofen and naproxen. Although these drugs were discovered over 50 years ago, novel practical and asymmetric approaches are still being developed for their synthesis. In addition, this endeavor [...] Read more.
Herein, we review the recent progress in the synthesis of representative nonsteroidal anti-inflammatory drugs (NSAIDs), ibuprofen and naproxen. Although these drugs were discovered over 50 years ago, novel practical and asymmetric approaches are still being developed for their synthesis. In addition, this endeavor has enabled access to more potent and selective derivatives from the key frameworks of ibuprofen and naproxen. The development of a synthetic route to ibuprofen and naproxen over the last 10 years is summarized, including developing methodologies, finding novel synthetic routes, and applying continuous-flow chemistry. Full article
(This article belongs to the Special Issue Organic Synthesis in Drug Discovery)
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