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Leniak A, Pietruś W, Kurczab R. From NMR to AI: Designing a Novel Chemical Representation to Enhance Machine Learning Predictions of Physicochemical Properties. J Chem Inf Model 2024; 64:3302-3321. [PMID: 38529877 DOI: 10.1021/acs.jcim.3c02039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
A novel approach to the utilization of nuclear magnetic resonance (NMR) spectroscopy data in the prediction of logD through machine learning algorithms is shown. In the analysis, a data set of 754 chemical compounds, organized into 30 clusters, was evaluated using advanced machine learning models, such as Support Vector Regression (SVR), Gradient Boosting, and AdaBoost, and comprehensive validation and testing methods were employed, including 10-fold cross-validation, bootstrapping, and leave-one-out. The study revealed the superior performance of the Bucket Integration method for dimensionality reduction, consistently yielding the lowest root mean square error (RMSE) across all data sets and normalization schemes. The SVR prediction models demonstrated remarkable computational efficiency and low cost, with the best RMSE value reaching 0.66. Our best model outperformed existing tools like JChem Suite's logD Predictor (0.91) and CplogD (1.27), and a comparison with traditional molecular representations yielded a comparable RMSE (0.50), emphasizing the robustness of our NMR data integration. The widespread availability of NMR data in pharmaceutical and industrial research presents an untapped resource for predictive modeling, highlighting the need for accessible methodologies like ours that complement the analytical toolbox beyond conventional 2D approaches. Our approach, designed to leverage the rich spatial data from NMR spectroscopy, provides additional insights and enriches drug discovery and computational chemistry with a freely accessible tool.
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Affiliation(s)
- Arkadiusz Leniak
- Department of Medicinal Chemistry, Celon Pharma S.A., ul. Marymoncka 15, 05-152 Kazuń Nowy, Poland
| | - Wojciech Pietruś
- Department of Medicinal Chemistry, Celon Pharma S.A., ul. Marymoncka 15, 05-152 Kazuń Nowy, Poland
- Department of Medicinal Chemistry, Maj Institute of Pharmacology, Polish Academy of Sciences, Smetna 12, 31-343 Kraków, Poland
| | - Rafał Kurczab
- Department of Medicinal Chemistry, Maj Institute of Pharmacology, Polish Academy of Sciences, Smetna 12, 31-343 Kraków, Poland
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Bazydło-Guzenda K, Jarus-Dziedzic K, Gierczak-Pachulska A, Buda P, Rudzki PJ, Buś-Kwaśnik K, Juszczyk E, Tratkiewicz E, Rabczenko D, Segiet-Święcicka A, Wieczorek M. First-in-human study of CPL207280, a novel G-protein-coupled receptor 40/free fatty acid receptor 1 agonist, in healthy volunteers after single and multiple administration. Diabetes Obes Metab 2024; 26:1376-1385. [PMID: 38204407 DOI: 10.1111/dom.15439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/11/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024]
Abstract
AIM To assess the safety, tolerability and pharmacokinetic (PK) profile of single and multiple doses of CPL207280, a new G-protein-coupled receptor 40 agonist developed to treat type 2 diabetes (T2D). METHODS The phase 1 study in healthy volunteers (White, age 18-55 years, body mass index 18.5-29.9 kg/m2 ) was performed after single (24 subjects, 5-480 mg) and multiple (32 subjects, 60-480 mg) once-daily administration of CPL207280. The effect of food intake and interaction with metformin were evaluated in additional cohort (12 subjects, 120 mg). The primary objective was the safety and tolerability of CPL207280. Secondary objectives included PK and pharmacodynamic (PD) characteristics (glucose, insulin, C-peptide, proinsulin, glucagon levels) observed during the 14-day treatment period. RESULTS No deaths or serious adverse events (AEs) were reported. All reported AEs were classified as unrelated to the study product. No clinically significant differences in safety parameters were observed between cohorts and no food or metformin effect on safety parameters was identified. The ascending dose of CPL207280 caused an increase in the PK parameters maximum observed plasma concentration (Cmax ) or area under the plasma concentration-time curve up to 24 h. However, dose-normalized Cmax decreased with ascending dose. There was no relationship between the CPL207280 dose or prandial state and terminal elimination half-life and terminal elimination rate constant. No clear relationship between CPL207280 dose and PD area under the effect curve values was observed. CONCLUSIONS CPL207280 was found to be safe and well tolerated by healthy volunteers (with a low risk of hepatotoxicity) for up to 14 days of administration. The PK profile of CPL207280 supports single-daily administration and justifies further development of this therapy for patients with T2D.
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Affiliation(s)
| | | | | | - Paweł Buda
- R&D Center, Celon Pharma S.A., Kazuń Nowy, Poland
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Jin C, Chen H, Xie L, Zhou Y, Liu LL, Wu J. GPCRs involved in metabolic diseases: pharmacotherapeutic development updates. Acta Pharmacol Sin 2024:10.1038/s41401-023-01215-2. [PMID: 38326623 DOI: 10.1038/s41401-023-01215-2] [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: 09/21/2023] [Accepted: 12/11/2023] [Indexed: 02/09/2024] Open
Abstract
G protein-coupled receptors (GPCRs) are expressed in a variety of cell types and tissues, and activation of GPCRs is involved in enormous metabolic pathways, including nutrient synthesis, transportation, storage or insulin sensitivity, etc. This review intends to summarize the regulation of metabolic homeostasis and mechanisms by a series of GPCRs, such as GPR91, GPR55, GPR119, GPR109a, GPR142, GPR40, GPR41, GPR43 and GPR120. With deep understanding of GPCR's structure and signaling pathways, it is attempting to uncover the role of GPCRs in major metabolic diseases, including metabolic syndrome, diabetes, dyslipidemia and nonalcoholic steatohepatitis, for which the global prevalence has risen during last two decades. An extensive list of agonists and antagonists with their chemical structures in a nature of small molecular compounds for above-mentioned GPCRs is provided as pharmacologic candidates, and their preliminary data of preclinical studies are discussed. Moreover, their beneficial effects in correcting abnormalities of metabolic syndrome, diabetes and dyslipidemia are summarized when clinical trials have been undertaken. Thus, accumulating data suggest that these agonists or antagonists might become as new pharmacotherapeutic candidates for the treatment of metabolic diseases.
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Affiliation(s)
- Cheng Jin
- Department of Medical Microbiology & Parasitology, MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University Shanghai Medical College, Shanghai, 200032, China
- College of Clinical Medicine, Fudan University Shanghai Medical College, Shanghai, 200032, China
| | - Hui Chen
- Department of Medical Microbiology & Parasitology, MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University Shanghai Medical College, Shanghai, 200032, China
| | - Li Xie
- Department of Medical Microbiology & Parasitology, MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University Shanghai Medical College, Shanghai, 200032, China
| | - Yuan Zhou
- Department of Medical Microbiology & Parasitology, MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University Shanghai Medical College, Shanghai, 200032, China
| | - Li-Li Liu
- Department of Gastroenterology & Hepatology, Zhongshan Hospital of Fudan University, Shanghai, 200032, China.
- Shanghai Institute of Liver Diseases, Fudan University Shanghai Medical College, Shanghai, 200032, China.
| | - Jian Wu
- Department of Medical Microbiology & Parasitology, MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University Shanghai Medical College, Shanghai, 200032, China.
- Department of Gastroenterology & Hepatology, Zhongshan Hospital of Fudan University, Shanghai, 200032, China.
- Shanghai Institute of Liver Diseases, Fudan University Shanghai Medical College, Shanghai, 200032, China.
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Paul A, Nahar S, Nahata P, Sarkar A, Maji A, Samanta A, Karmakar S, Maity TK. Synthetic GPR40/FFAR1 agonists: An exhaustive survey on the most recent chemical classes and their structure-activity relationships. Eur J Med Chem 2024; 264:115990. [PMID: 38039791 DOI: 10.1016/j.ejmech.2023.115990] [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: 09/24/2023] [Revised: 11/18/2023] [Accepted: 11/20/2023] [Indexed: 12/03/2023]
Abstract
Free fatty acid receptor 1 (FFAR1 or GPR40) is a potential target for treating type 2 diabetes mellitus (T2DM) and related disorders that have been extensively researched for many years. GPR40/FFAR1 is a promising anti-diabetic target because it can activate insulin, promoting glucose metabolism. It controls T2DM by regulating glucose levels in the body through two separate mechanisms: glucose-stimulated insulin secretion and incretin production. In the last few years, various synthetic GPR40/FFAR1 agonists have been discovered that fall under several chemical classes, viz. phenylpropionic acid, phenoxyacetic acid, and dihydrobenzofuran acetic acid. However, only a few synthetic agonists have entered clinical trials due to various shortcomings like poor efficacy, low lipophilicity and toxicity issues. As a result, pharmaceutical firms and research institutions are interested in developing synthetic GPR40/FFAR1 agonists with superior effectiveness, lipophilicity, and safety profiles. This review encompasses the most recent research on synthetic GPR40/FFAR1 agonists, including their chemical classes, design strategies and structure-activity relationships. Additionally, we have emphasised the structural characteristics of the most potent GPR40/FFAR1 agonists from each chemical class of synthetic derivatives and analysed their chemico-biological interactions. This work will hopefully pave the way for developing more potent and selective synthetic GPR40/FFAR1 agonists for treating T2DM and related disorders.
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Affiliation(s)
- Abhik Paul
- Department of Pharmaceutical Technology, Jadavpur University, West Bengal, Kolkata, 700 032, India.
| | - Sourin Nahar
- Department of Pharmaceutical Technology, Jadavpur University, West Bengal, Kolkata, 700 032, India.
| | - Pankaj Nahata
- Department of Pharmaceutical Technology, Jadavpur University, West Bengal, Kolkata, 700 032, India.
| | - Arnab Sarkar
- Department of Pharmaceutical Technology, Jadavpur University, West Bengal, Kolkata, 700 032, India; Bioequivalence Study Centre, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India.
| | - Avik Maji
- Department of Pharmaceutical Technology, Jadavpur University, West Bengal, Kolkata, 700 032, India.
| | - Ajeya Samanta
- Department of Pharmaceutical Technology, Jadavpur University, West Bengal, Kolkata, 700 032, India.
| | - Sanmoy Karmakar
- Department of Pharmaceutical Technology, Jadavpur University, West Bengal, Kolkata, 700 032, India; Bioequivalence Study Centre, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India.
| | - Tapan Kumar Maity
- Department of Pharmaceutical Technology, Jadavpur University, West Bengal, Kolkata, 700 032, India.
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How Arrestins and GRKs Regulate the Function of Long Chain Fatty Acid Receptors. Int J Mol Sci 2022; 23:ijms232012237. [PMID: 36293091 PMCID: PMC9602559 DOI: 10.3390/ijms232012237] [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: 09/08/2022] [Revised: 10/03/2022] [Accepted: 10/08/2022] [Indexed: 11/16/2022] Open
Abstract
FFA1 and FFA4, two G protein-coupled receptors that are activated by long chain fatty acids, play crucial roles in mediating many biological functions in the body. As a result, these fatty acid receptors have gained considerable attention due to their potential to be targeted for the treatment of type-2 diabetes. However, the relative contribution of canonical G protein-mediated signalling versus the effects of agonist-induced phosphorylation and interactions with β-arrestins have yet to be fully defined. Recently, several reports have highlighted the ability of β-arrestins and GRKs to interact with and modulate different functions of both FFA1 and FFA4, suggesting that it is indeed important to consider these interactions when studying the roles of FFA1 and FFA4 in both normal physiology and in different disease settings. Here, we discuss what is currently known and show the importance of understanding fully how β-arrestins and GRKs regulate the function of long chain fatty acid receptors.
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Nath V, Paul RK, Kumar N, Kumar V. Identification of behenic acid as medicinal food for the diabetes mellitus: structure-based computational approach and molecular dynamics simulation studies. J Mol Model 2022; 28:73. [DOI: 10.1007/s00894-022-05060-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 02/15/2022] [Indexed: 11/27/2022]
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