MedChemCommPub Date : 2024-05-31DOI: 10.1039/D4MD00245H
Zhou Xu, Zhongyuan Wang, Xiaona Shi, Rui Ding, Li Han, Xueping Yang, Hongmei Zhang and Adrian D. Hobson
{"title":"Impact of atropisomerism on a non-steroidal glucocorticoid receptor agonist†","authors":"Zhou Xu, Zhongyuan Wang, Xiaona Shi, Rui Ding, Li Han, Xueping Yang, Hongmei Zhang and Adrian D. Hobson","doi":"10.1039/D4MD00245H","DOIUrl":"10.1039/D4MD00245H","url":null,"abstract":"<p >To investigate atropisomers of non-steroidal glucocorticoid receptor modulator GSK866, a virtual library of substituted benzoic acid analogues was enumerated. Compounds from this library were subjected to a torsion angle scan using Spartan'20 to calculate the torsion rotation energy barrier which identified compounds predicted to be stable as atropisomers. After synthesis of the library, analysis showed that compounds <strong>13</strong> and <strong>14</strong> existed as stable atropisomers <strong>13a</strong>, <strong>13b</strong>, <strong>14a</strong> and <strong>14b</strong>, in agreement with the earlier calculations. Screening in a glucocorticoid receptor cellular assay showed that one compound from each atropisomer pair was significantly more potent than the other. Docking in a public structure of the glucocorticoid receptor (PBD code 3E7C) enabled the stereochemistry of the two most potent compounds <strong>13a</strong> and <strong>14b</strong> to be assigned as (<em>R</em><small><sub>a</sub></small>) and (<em>S</em><small><sub>a</sub></small>), respectively.</p>","PeriodicalId":88,"journal":{"name":"MedChemComm","volume":" 7","pages":" 2357-2371"},"PeriodicalIF":3.597,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141523128","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
MedChemCommPub Date : 2024-05-31DOI: 10.1039/D4MD00223G
Arti Kataria, Ankit Srivastava, Desh Deepak Singh, Shafiul Haque, Ihn Han and Dharmendra Kumar Yadav
{"title":"Systematic computational strategies for identifying protein targets and lead discovery","authors":"Arti Kataria, Ankit Srivastava, Desh Deepak Singh, Shafiul Haque, Ihn Han and Dharmendra Kumar Yadav","doi":"10.1039/D4MD00223G","DOIUrl":"10.1039/D4MD00223G","url":null,"abstract":"<p >Computational algorithms and tools have retrenched the drug discovery and development timeline. The applicability of computational approaches has gained immense relevance owing to the dramatic surge in the structural information of biomacromolecules and their heteromolecular complexes. Computational methods are now extensively used in identifying new protein targets, druggability assessment, pharmacophore mapping, molecular docking, the virtual screening of lead molecules, bioactivity prediction, molecular dynamics of protein–ligand complexes, affinity prediction, and for designing better ligands. Herein, we provide an overview of salient components of recently reported computational drug-discovery workflows that includes algorithms, tools, and databases for protein target identification and optimized ligand selection.</p>","PeriodicalId":88,"journal":{"name":"MedChemComm","volume":" 7","pages":" 2254-2269"},"PeriodicalIF":3.597,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141190500","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Novel flexible biphenyl PfDHFR inhibitors with improved antimalarial activity†","authors":"Sasithorn Decharuangsilp, Uthai Arwon, Nawarat Sooksai, Roonglawan Rattanajak, Thanaya Saeyang, Danoo Vitsupakorn, Jarunee Vanichtanankul, Yongyuth Yuthavong, Sumalee Kamchonwongpaisan and Marie Hoarau","doi":"10.1039/D4MD00197D","DOIUrl":"10.1039/D4MD00197D","url":null,"abstract":"<p >As pregnant women and young children remain the first victims of malaria worldwide, the search for new antimalarials has been focusing on compounds with a high safety profile and extended efficacy. In a previous study, a rigid biphenyl <em>Pf</em>DHFR inhibitor was developed by fragment-based screening, displaying sub nM enzyme inhibition but poor antiparasitic activity, presumably due to its low flexibility. Here, we report a new series of compounds that combines the biphenyl fragment with a flexible linker. Interestingly, their mode of binding differs from previously reported compounds, taking advantage of strong hydrophobic interaction. The new flexible biphenyl compounds show overall improved antiparasitic activity compared to rigid ones, with the best compound displaying a 2 nM antiplasmodial IC<small><sub>50</sub></small> and suitable drug-like properties. This confirms the importance of compound flexibility for antimalarial activity and opens the way to new opportunities for antimalarial drug design.</p>","PeriodicalId":88,"journal":{"name":"MedChemComm","volume":" 7","pages":" 2496-2507"},"PeriodicalIF":3.597,"publicationDate":"2024-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141523130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
MedChemCommPub Date : 2024-05-24DOI: 10.1039/D4MD00042K
Asmita Choithramani, Rudradip Das, Gourav Bothra, Priyanka Patel Vatsa, Venkatesh Muthukumar, Bombothu Kavya Sai Bhuvana, Saumya Kapoor, Deepshika Moola, Moumita Ghosh Chowdhury, Amit Mandoli and Amit Shard
{"title":"Targeted suppression of oral squamous cell carcinoma by pyrimidine-tethered quinoxaline derivatives†","authors":"Asmita Choithramani, Rudradip Das, Gourav Bothra, Priyanka Patel Vatsa, Venkatesh Muthukumar, Bombothu Kavya Sai Bhuvana, Saumya Kapoor, Deepshika Moola, Moumita Ghosh Chowdhury, Amit Mandoli and Amit Shard","doi":"10.1039/D4MD00042K","DOIUrl":"10.1039/D4MD00042K","url":null,"abstract":"<p >Oral cancer (OC) stands as a prominent cause of global mortality. Despite numerous efforts in recent decades, the efficacy of novel therapies to extend the lifespan of OC patients remains disappointingly low. Consequently, the demand for innovative therapeutic agents has become all the more pressing. In this context, we present our work on the design and synthesis of twenty-five novel quinoxaline-tethered imidazopyri(mi)dine derivatives. This was followed by comprehensive investigations into the impact of these molecules on the OC cell line. The <em>in vitro</em> cytotoxicity studies performed in CAL-27 and normal oral epithelial (NOE) cell lines revealed that some of the synthesized molecules like <strong>12d</strong> have potent antiproliferative activity specifically towards OC cells with an IC<small><sub>50</sub></small> of 0.79 μM and show negligible cytotoxicity over NOE cells. Further, <strong>12d</strong> arrested cell growth in the S phase of the cell cycle and induced cell death by early apoptosis. The <em>in silico</em> studies validated that <strong>12d</strong> binds to the activator binding site on pyruvate kinase M2 (PKM2) overexpressed in OC while the lactate dehydrogenase (LDH)-coupled enzyme assay established <strong>12d</strong> as a potent PKM2 activator with an AC<small><sub>50</sub></small> of 0.6 nM. Hence, this study provides fruitful evidence for the designed compounds as anticancer agents against OC.</p>","PeriodicalId":88,"journal":{"name":"MedChemComm","volume":" 8","pages":" 2729-2744"},"PeriodicalIF":3.597,"publicationDate":"2024-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141568321","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
MedChemCommPub Date : 2024-05-24DOI: 10.1039/D4MD00107A
Aishvarya Tandon, Anna Santura, Herbert Waldmann, Axel Pahl and Paul Czodrowski
{"title":"Identification of lysosomotropism using explainable machine learning and morphological profiling cell painting data†","authors":"Aishvarya Tandon, Anna Santura, Herbert Waldmann, Axel Pahl and Paul Czodrowski","doi":"10.1039/D4MD00107A","DOIUrl":"10.1039/D4MD00107A","url":null,"abstract":"<p >Lysosomotropism is a phenomenon of diverse pharmaceutical interests because it is a property of compounds with diverse chemical structures and primary targets. While it is primarily reported to be caused by compounds having suitable lipophilicity and basicity values, not all compounds that fulfill such criteria are in fact lysosomotropic. Here, we use morphological profiling by means of the cell painting assay (CPA) as a reliable surrogate to identify lysosomotropism. We noticed that only 35% of the compound subset with matching physicochemical properties show the lysosomotropic phenotype. Based on a matched molecular pair analysis (MMPA), no key substructures driving lysosomotropism could be identified. However, using explainable machine learning (XML), we were able to highlight that higher lipophilicity, basicity, molecular weight, and lower topological polar surface area are among the important properties that induce lysosomotropism in the compounds of this subset.</p>","PeriodicalId":88,"journal":{"name":"MedChemComm","volume":" 8","pages":" 2677-2691"},"PeriodicalIF":3.597,"publicationDate":"2024-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2024/md/d4md00107a?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141523132","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
MedChemCommPub Date : 2024-05-22DOI: 10.1039/D4MD00273C
Louise M. Sternicki and Sally-Ann Poulsen
{"title":"Fragment-based drug discovery campaigns guided by native mass spectrometry","authors":"Louise M. Sternicki and Sally-Ann Poulsen","doi":"10.1039/D4MD00273C","DOIUrl":"10.1039/D4MD00273C","url":null,"abstract":"<p >Native mass spectrometry (nMS) is well established as a biophysical technique for characterising biomolecules and their interactions with endogenous or investigational small molecule ligands. The high sensitivity mass measurements make nMS particularly well suited for applications in fragment-based drug discovery (FBDD) screening campaigns where the detection of weakly binding ligands to a target biomolecule is crucial. We first reviewed the contributions of nMS to guiding FBDD hit identification in 2013, providing a comprehensive perspective on the early adoption of nMS for fragment screening. Here we update this initial progress with a focus on contributions of nMS that have guided FBDD for the period 2014 until end of 2023. We highlight the development of nMS adoption in FBDD in the context of other biophysical fragment screening techniques. We also discuss the roadmap for increased adoption of nMS for fragment screening beyond soluble proteins, including for guiding the discovery of fragments supporting advances in PROTAC discovery, RNA-binding small molecules and covalent therapeutic drug discovery.</p>","PeriodicalId":88,"journal":{"name":"MedChemComm","volume":" 7","pages":" 2270-2285"},"PeriodicalIF":3.597,"publicationDate":"2024-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141190497","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
MedChemCommPub Date : 2024-05-21DOI: 10.1039/D4MD00211C
Soumaila Zebret, Mouna Hadiji, Jan Romano-deGea, Aurélien Bornet, Daniel Ortiz, Farzaneh Fadaei-Tirani, Christina Stathopoulos, Patrycja Nowak-Sliwinska, Francis L. Munier and Paul J. Dyson
{"title":"New melphalan derivatives for the treatment of retinoblastoma in combination with thermotherapy†","authors":"Soumaila Zebret, Mouna Hadiji, Jan Romano-deGea, Aurélien Bornet, Daniel Ortiz, Farzaneh Fadaei-Tirani, Christina Stathopoulos, Patrycja Nowak-Sliwinska, Francis L. Munier and Paul J. Dyson","doi":"10.1039/D4MD00211C","DOIUrl":"10.1039/D4MD00211C","url":null,"abstract":"<p >Of the different modalities used to treat retinoblastoma, a chemothermotherapeutic regimen combining carboplatin and thermotherapy (also termed focal therapy), and the application of melphalan as a monotherapy, are particularly successful. Some studies indicate that melphalan shows potential when applied in combination with focal therapy, and yet is not applied in this combination. Here we describe a series of synthetically modified melphalan derivatives that display enhanced cytotoxicity relative to melphalan itself, with some displaying further enhancements in cytotoxicity when applied in combination with heat (used as a model for thermotherapy). The synthetic approach, which involves modifying melphalan with perfluorous chains of varying lengths <em>via</em> an ester linker, could lead to a more effective treatment option for retinoblastoma with reduced side-effects, which is a key limitation of melphalan.</p>","PeriodicalId":88,"journal":{"name":"MedChemComm","volume":" 7","pages":" 2300-2304"},"PeriodicalIF":3.597,"publicationDate":"2024-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2024/md/d4md00211c?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141190336","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
MedChemCommPub Date : 2024-05-17DOI: 10.1039/D4MD00232F
Li-Er Deng, Yuzhi Qiu, Yana Zeng, Jiafeng Zou, Abhinav Kumar, Ying Pan, Alireza Nezamzadeh-Ejhieh, Jianqiang Liu and Xingyan Liu
{"title":"Current and promising applications of MOF composites in the healing of diabetes wounds","authors":"Li-Er Deng, Yuzhi Qiu, Yana Zeng, Jiafeng Zou, Abhinav Kumar, Ying Pan, Alireza Nezamzadeh-Ejhieh, Jianqiang Liu and Xingyan Liu","doi":"10.1039/D4MD00232F","DOIUrl":"10.1039/D4MD00232F","url":null,"abstract":"<p >Diabetes mellitus is an exponentially growing chronic metabolic disease identified by prolonged hyperglycemia that leads to a plethora of health problems. It is well established that the skin of diabetic patients is more prone to injury, and hence, wound healing is an utmost critical restorative process for injured skin and other tissues. Diabetes patients have problems with wound healing at all stages, which ultimately results in delays in the healing process. Therefore, it is vital to find new medications or techniques to hasten the healing of wounds. Metal–organic frameworks (MOFs), an assorted class of porous hybrid materials comprising metal ions coordinated to organic ligands, can display great potential in accelerating diabetic wound healing due to their good physicochemical properties. The release of metal ions during the degradation of MOFs can promote the differentiation of fibroblasts into myofibroblasts and subsequently angiogenesis. Secondly, similar to enzyme-like active substances, they can eliminate reactive oxygen species (ROS) overproduction (secondary to the bio-load of wound bacteria), which is conducive to accelerating diabetic wound healing. Subsequently, MOFs can support the slow release of drugs (molecular or gas therapeutics) in diabetic wounds and promote wound healing by regulating pathological signaling pathways in the wound microenvironment or inhibiting the expression of inflammatory factors. In addition, the combination of photodynamic and photothermal therapies using photo-stimulated porphyrin-based MOF nanosystems has brought up a new idea for treating complicated diabetic wound microenvironments. In this review, recent advances affecting diabetic wound healing, current means of rapid diabetic wound healing, and the limitations of traditional approaches are discussed. Further, the diabetic wound healing applications of MOFs have been discussed followed by the future challenges and directions of MOF materials in diabetic wound healing.</p>","PeriodicalId":88,"journal":{"name":"MedChemComm","volume":" 8","pages":" 2601-2621"},"PeriodicalIF":3.597,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141531764","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
MedChemCommPub Date : 2024-05-10DOI: 10.1039/D4MD00224E
Meijun Pang, Ruitian Xu, Rongjiao Xi, Hong Yao, Kechen Bao, Rui Peng, Hui Zhi, Kuo Zhang, Runnan He, Yanfang Su, Xiuyun Liu and Dong Ming
{"title":"Molecular understanding of the therapeutic potential of melanin inhibiting natural products","authors":"Meijun Pang, Ruitian Xu, Rongjiao Xi, Hong Yao, Kechen Bao, Rui Peng, Hui Zhi, Kuo Zhang, Runnan He, Yanfang Su, Xiuyun Liu and Dong Ming","doi":"10.1039/D4MD00224E","DOIUrl":"10.1039/D4MD00224E","url":null,"abstract":"<p >With the development of society and the improvement of people's living standards, there is an increasing demand for melanin-inhibiting products that prioritize health, safety, and efficacy. Therefore, the development of natural products that can safely and efficiently inhibit melanin synthesis is of great social significance and has significant market potential. In this paper, by reviewing the literature reported in recent years, we summarized the natural products with inhibition of melanin synthesis effects that have been put into or not yet put into the market, and classified them according to the chemical groups of their compounds or the extraction methods of the natural products. Through the summary analysis, we found that these compounds mainly include terpenoids, phenylpropanoids, flavonoids and so on, while the natural product extracts mainly include methanol extracts, ethanol extracts, and aqueous extracts. Their main inhibition of melanin synthesis mechanisms include: (1) direct inhibition of tyrosinase activity; (2) down-regulation of the α-MSH-MC1R, Wnt, NO, PI3K/Akt and MAPK pathways through the expression of MITF and its downstream genes TYR, TRP-1, and TRP-2; (3) antioxidant; (4) inhibition of melanocyte growth through cytotoxicity; (5) inhibition of melanosome production and transport. This paper provides an in-depth discussion on the research progress of whitening natural products and their market value. The aim is to offer guidance for future research and development of natural skin whitening products.</p>","PeriodicalId":88,"journal":{"name":"MedChemComm","volume":" 7","pages":" 2226-2253"},"PeriodicalIF":3.597,"publicationDate":"2024-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141147994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
MedChemCommPub Date : 2024-05-06DOI: 10.1039/D4MD00105B
V. V. Gandhi, M. K. Pal, B. G. Singh, R. P. Das, A. P. Wadawale, S. Dey and A. Kunwar
{"title":"Deuterium labeling improves the therapeutic index of 3,3′-diselenodipropionic acid as an anticancer agent: insights from redox reactions†","authors":"V. V. Gandhi, M. K. Pal, B. G. Singh, R. P. Das, A. P. Wadawale, S. Dey and A. Kunwar","doi":"10.1039/D4MD00105B","DOIUrl":"10.1039/D4MD00105B","url":null,"abstract":"<p >3,3′-Diselenodipropionic acid (DSePA), a selenocystine derivative, has been previously reported as an oral supplement for anticancer/radio-modulation activities. The present study is focused on devising a strategy to synthesize and characterize the deuterated derivative of DSePA and on understanding the effect of deuteration on its therapeutic index by comparing its cytotoxicity in cancerous <em>versus</em> non-cancerous cell types. In this context, the synthesis of 3,3′-diselenodipropionic acid-D<small><sub>8</sub></small> (D-DSePA) was accomplished in ∼42% yield. Further, the results clearly established that the deuteration of DSePA significantly reduced its cytotoxicity in non-cancerous cell types while retaining its cytotoxicity in cancerous cell lines. Together, D-DSePA displayed a ∼5-fold higher therapeutic index than the non-deuterated derivative for anticancer activity. The biochemical and NMR studies confirmed that the better biocompatibility of D-DSePA than its non-deuterated derivative in non-cancerous cells was due to its ability to undergo slower redox reactions and to cause lesser inhibition of intracellular redox enzymes.</p>","PeriodicalId":88,"journal":{"name":"MedChemComm","volume":" 6","pages":" 2165-2178"},"PeriodicalIF":3.597,"publicationDate":"2024-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141147898","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}