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Nedyalkova M, Robeva R, Romanova J, Yovcheva K, Lattuada M, Simeonov V. In silico screening of potential agonists of a glucagon-like peptide-1 receptor among female sex hormone derivatives. J Biomol Struct Dyn 2024:1-12. [PMID: 38587907 DOI: 10.1080/07391102.2024.2330714] [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: 08/16/2023] [Accepted: 03/09/2024] [Indexed: 04/10/2024]
Abstract
Glucagon-like peptide-1 (GLP-1) is an intestinal hormone that exerts its pleiotropic effects through a specific GLP-1 receptor (GLP-1R). The hormone-receptor complex might regulate glucose-dependent insulin secretion, and energy homeostasis; moreover, it could decrease inflammation and provide cardio- and neuroprotection. Additionally, the beneficial influence of GLP-1 on obesity in women might lead to improvement of their ovarian function. The links between metabolism and reproduction are tightly connected, and it is not surprising that different estrogen derivatives, estrogen-receptor modulator (SERM) and progestins used for gonadal and oncological disorders might influence carbohydrate and lipid metabolism. However, their possible influence on the GLP-1R has not been studied. The docking scores and top-ranked poses of raloxifene were much higher than those observed for other investigated SERMs and estradiol per se. Among different studied progestins, drospirenone showed slightly higher affinity to GLP-1R. Herein, the same data set of the drugs is evaluated by molecular dynamics (MD) simulations and compared with the obtained docking result. Notably, it is demonstrated that the used docking protocol and the applied MD calculations ranked the same ligand (raloxifene) as the best one. In the present study, raloxifene might exert an allosteric influence on GLP-1R signaling, which might contribute to potential beneficial effects on metabolism and weight regulation. However, further experimental and clinical studies are needed to reveal if the GLP-1R modulation has a real biological impact.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Miroslava Nedyalkova
- Department of Chemistry, Fribourg University, Fribourg, Switzerland
- Department of Inorganic Chemistry, Faculty of Chemistry and Pharmacy, University of Sofia 'St. Kl. Ohridski', Sofia, Bulgaria
- Swiss National Center for Competence in Research (NCCR) Bio-inspired Materials, University of Fribourg, Fribourg, Switzerland
| | - Ralitsa Robeva
- Department of Endocrinology, Faculty of Medicine, Medical University-Sofia, Sofia, Bulgaria
| | - Julia Romanova
- Department of Inorganic Chemistry, Faculty of Chemistry and Pharmacy, University of Sofia 'St. Kl. Ohridski', Sofia, Bulgaria
| | - Kirila Yovcheva
- Department of Inorganic Chemistry, Faculty of Chemistry and Pharmacy, University of Sofia 'St. Kl. Ohridski', Sofia, Bulgaria
| | - Marco Lattuada
- Department of Chemistry, Fribourg University, Fribourg, Switzerland
| | - Vasil Simeonov
- Department of Inorganic Chemistry, Faculty of Chemistry and Pharmacy, University of Sofia 'St. Kl. Ohridski', Sofia, Bulgaria
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Lehrer S, Rheinstein PH. Re: Suppressing c-FOS expression by G-quadruplex ligands inhibits osimertinib-resistant non-small cell lung cancers. J Natl Cancer Inst 2023; 115:1427-1428. [PMID: 37603719 PMCID: PMC10637030 DOI: 10.1093/jnci/djad167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 07/31/2023] [Indexed: 08/23/2023] Open
Affiliation(s)
- Steven Lehrer
- Department of Radiation Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Cortat Y, Nedyalkova M, Schindler K, Kadakia P, Demirci G, Nasiri Sovari S, Crochet A, Salentinig S, Lattuada M, Steiner OM, Zobi F. Computer-Aided Drug Design and Synthesis of Rhenium Clotrimazole Antimicrobial Agents. Antibiotics (Basel) 2023; 12:antibiotics12030619. [PMID: 36978486 PMCID: PMC10044843 DOI: 10.3390/antibiotics12030619] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
In the context of the global health issue caused by the growing occurrence of antimicrobial resistance (AMR), the need for novel antimicrobial agents is becoming alarming. Inorganic and organometallic complexes represent a relatively untapped source of antibiotics. Here, we report a computer-aided drug design (CADD) based on a 'scaffold-hopping' approach for the synthesis and antibacterial evaluation of fac-Re(I) tricarbonyl complexes bearing clotrimazole (ctz) as a monodentate ligand. The prepared molecules were selected following a pre-screening in silico analysis according to modification of the 2,2'-bipyridine (bpy) ligand in the coordination sphere of the complexes. CADD pointed to chiral 4,5-pinene and 5,6-pinene bipyridine derivatives as the most promising candidates. The corresponding complexes were synthesized, tested toward methicillin-sensitive and -resistant S. aureus strains, and the obtained results evaluated with regard to their binding affinity with a homology model of the S. aureus MurG enzyme. Overall, the title species revealed very similar minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values as those of the reference compound used as the scaffold in our approach. The obtained docking scores advocate the viability of 'scaffold-hopping' for de novo design, a potential strategy for more cost- and time-efficient discovery of new antibiotics.
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Affiliation(s)
- Youri Cortat
- Department of Chemistry, Fribourg University, Chemin Du Musée 9, 1700 Fribourg, Switzerland
| | - Miroslava Nedyalkova
- Department of Chemistry, Fribourg University, Chemin Du Musée 9, 1700 Fribourg, Switzerland
| | - Kevin Schindler
- Department of Chemistry, Fribourg University, Chemin Du Musée 9, 1700 Fribourg, Switzerland
| | - Parth Kadakia
- Department of Chemistry, Fribourg University, Chemin Du Musée 9, 1700 Fribourg, Switzerland
| | - Gozde Demirci
- Department of Chemistry, Fribourg University, Chemin Du Musée 9, 1700 Fribourg, Switzerland
| | - Sara Nasiri Sovari
- Department of Chemistry, Fribourg University, Chemin Du Musée 9, 1700 Fribourg, Switzerland
| | - Aurelien Crochet
- Department of Chemistry, Fribourg University, Chemin Du Musée 9, 1700 Fribourg, Switzerland
| | - Stefan Salentinig
- Department of Chemistry, Fribourg University, Chemin Du Musée 9, 1700 Fribourg, Switzerland
| | - Marco Lattuada
- Department of Chemistry, Fribourg University, Chemin Du Musée 9, 1700 Fribourg, Switzerland
| | - Olimpia Mamula Steiner
- Haute école d'Ingénierie et d'Architecture, University of Applied Sciences Western Switzerland HES-SO, Pérolles 80, 1700 Fribourg, Switzerland
| | - Fabio Zobi
- Department of Chemistry, Fribourg University, Chemin Du Musée 9, 1700 Fribourg, Switzerland
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Joshi PB. Navigating with chemometrics and machine learning in chemistry. Artif Intell Rev 2023; 56:1-26. [PMID: 36714038 PMCID: PMC9870782 DOI: 10.1007/s10462-023-10391-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2023] [Indexed: 01/25/2023]
Abstract
Chemometrics and machine learning are artificial intelligence-based methods stirring a transformative change in chemistry. Organic synthesis, drug discovery and analytical techniques are incorporating machine learning techniques at an accelerated pace. However, machine-assisted chemistry faces challenges while solving critical problems in chemistry due to complex relationships in data sets. Even with increasing publishing volumes on machine learning, its application in areas of chemistry is not a straightforward endeavour. A particular concern in applying machine learning in chemistry is data availability and reproducibility. The present review article discusses the various chemometric methods, expert systems, and machine learning techniques developed for solving problems of organic synthesis and drug discovery with selected examples. Further, a concise discussion on chemometrics and ML deployed in analytical techniques such as, spectroscopy, microscopy and chromatography are presented. Finally, the review reflects the challenges, opportunities and future perspectives on machine learning and automation in chemistry. The review concludes by pondering on some tough questions on applying machine learning and their possibility of navigation in the different terrains of chemistry.
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Affiliation(s)
- Payal B. Joshi
- Operations and Method Development, Shefali Research Laboratories, Ambernath (East), Thane, Maharashtra 421501 India
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Gider V, Budak C. Instruction of molecular structure similarity and scaffolds of drugs under investigation in ebola virus treatment by atom-pair and graph network: A combination of favipiravir and molnupiravir. Comput Biol Chem 2022; 101:107778. [DOI: 10.1016/j.compbiolchem.2022.107778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 11/26/2022]
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Jamal QMS. Antiviral Potential of Plants against COVID-19 during Outbreaks-An Update. Int J Mol Sci 2022; 23:13564. [PMID: 36362351 PMCID: PMC9655040 DOI: 10.3390/ijms232113564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/06/2022] [Accepted: 11/02/2022] [Indexed: 12/01/2023] Open
Abstract
Several human diseases are caused by viruses, including cancer, Type I diabetes, Alzheimer's disease, and hepatocellular carcinoma. In the past, people have suffered greatly from viral diseases such as polio, mumps, measles, dengue fever, SARS, MERS, AIDS, chikungunya fever, encephalitis, and influenza. Recently, COVID-19 has become a pandemic in most parts of the world. Although vaccines are available to fight the infection, their safety and clinical trial data are still questionable. Social distancing, isolation, the use of sanitizer, and personal productive strategies have been implemented to prevent the spread of the virus. Moreover, the search for a potential therapeutic molecule is ongoing. Based on experiences with outbreaks of SARS and MERS, many research studies reveal the potential of medicinal herbs/plants or chemical compounds extracted from them to counteract the effects of these viral diseases. COVID-19's current status includes a decrease in infection rates as a result of large-scale vaccination program implementation by several countries. But it is still very close and needs to boost people's natural immunity in a cost-effective way through phytomedicines because many underdeveloped countries do not have their own vaccination facilities. In this article, phytomedicines as plant parts or plant-derived metabolites that can affect the entry of a virus or its infectiousness inside hosts are described. Finally, it is concluded that the therapeutic potential of medicinal plants must be analyzed and evaluated entirely in the control of COVID-19 in cases of uncontrollable SARS infection.
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Affiliation(s)
- Qazi Mohammad Sajid Jamal
- Department of Health Informatics, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
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Antimicrobial Activity of Rhenium Di- and Tricarbonyl Diimine Complexes: Insights on Membrane-Bound S. aureus Protein Binding. Pharmaceuticals (Basel) 2022; 15:ph15091107. [PMID: 36145328 PMCID: PMC9501577 DOI: 10.3390/ph15091107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/31/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial resistance is one of the major human health threats, with significant impacts on the global economy. Antibiotics are becoming increasingly ineffective as drug-resistance spreads, imposing an urgent need for new and innovative antimicrobial agents. Metal complexes are an untapped source of antimicrobial potential. Rhenium complexes, amongst others, are particularly attractive due to their low in vivo toxicity and high antimicrobial activity, but little is known about their targets and mechanism of action. In this study, a series of rhenium di- and tricarbonyl diimine complexes were prepared and evaluated for their antimicrobial potential against eight different microorganisms comprising Gram-negative and -positive bacteria. Our data showed that none of the Re dicarbonyl or neutral tricarbonyl species have either bactericidal or bacteriostatic potential. In order to identify possible targets of the molecules, and thus possibly understand the observed differences in the antimicrobial efficacy of the molecules, we computationally evaluated the binding affinity of active and inactive complexes against structurally characterized membrane-bound S. aureus proteins. The computational analysis indicates two possible major targets for this class of compounds, namely lipoteichoic acids flippase (LtaA) and lipoprotein signal peptidase II (LspA). Our results, consistent with the published in vitro studies, will be useful for the future design of rhenium tricarbonyl diimine-based antibiotics.
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