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Huang WJ, Pannecouque C, De Clercq E, Wang S, Chen FE. Structure-based discovery of novel piperidine-biphenyl-DAPY derivatives as non-nucleoside reverse transcriptase inhibitors featuring improved potency, safety, and selectivity: From piperazine-biphenyl-DAPYs to piperidine-biphenyl-DAPYs. Eur J Med Chem 2024; 276:116668. [PMID: 38996652 DOI: 10.1016/j.ejmech.2024.116668] [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: 05/11/2024] [Revised: 07/08/2024] [Accepted: 07/08/2024] [Indexed: 07/14/2024]
Abstract
Starting from our previously reported nonnucleoside reverse transcriptase inhibitor (NNRTI, 3), continuous efforts were made to enhance its potency and safety through a structure-based drug design strategy. This led to the discovery of a series of novel piperidine-biphenyl-diarylpyrimidines (DAPYs). Compound 10p, the most active compound in this series, exhibited an EC50 value of 6 nM against wide-type HIV-1 strain, which was approximately 560-fold more potent than the initial compound 3 (EC50 = 3.36 μM). Furthermore, significant improvements were observed in cytotoxicity and selectivity (CC50 > 202.17 μM, SI > 33144) compared to compound 3 (CC50 = 14.84 μM, SI = 4). Additionally, compound 10p demonstrated increased inhibitory activity against clinically mutant virus strains (EC50 = 7-63 nM). Further toxicity evaluation revealed that compound 10p exhibited minimal CYP enzyme and hERG inhibition. Importantly, single-dose acute toxicity testing did not result in any fatalities or noticeable pathological damage in mice. Therefore, compound 10p can be regarded as a lead candidate for guiding further development of biphenyl-diarylpyrimidine NNRTIs with favorable druggability for HIV therapy.
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Affiliation(s)
- Wen-Juan Huang
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai, 200433, China; Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, 200433, China
| | | | - Erik De Clercq
- Rega Institute for Medical Research, KU Leuven, Herestraat 49, B-3000, Leuven, Belgium
| | - Shuai Wang
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai, 200433, China; Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, 200433, China.
| | - Fen-Er Chen
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai, 200433, China; Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai, 200433, China.
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2
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Karagiannis TC, Ververis K, Liang JJ, Pitsillou E, Kagarakis EA, Yi DTZ, Xu V, Hung A, El-Osta A. Investigation of the Anti-Inflammatory Properties of Bioactive Compounds from Olea europaea: In Silico Evaluation of Cyclooxygenase Enzyme Inhibition and Pharmacokinetic Profiling. Molecules 2024; 29:3502. [PMID: 39124908 PMCID: PMC11314539 DOI: 10.3390/molecules29153502] [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: 06/11/2024] [Revised: 07/22/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024] Open
Abstract
In a landmark study, oleocanthal (OLC), a major phenolic in extra virgin olive oil (EVOO), was found to possess anti-inflammatory activity similar to ibuprofen, involving inhibition of cyclooxygenase (COX) enzymes. EVOO is a rich source of bioactive compounds including fatty acids and phenolics; however, the biological activities of only a small subset of compounds associated with Olea europaea have been explored. Here, the OliveNetTM library (consisting of over 600 compounds) was utilized to investigate olive-derived compounds as potential modulators of the arachidonic acid pathway. Our first aim was to perform enzymatic assays to evaluate the inhibitory activity of a selection of phenolic compounds and fatty acids against COX isoforms (COX-1 and COX-2) and 15-lipoxygenase (15-LOX). Olive compounds were found to inhibit COX isoforms, with minimal activity against 15-LOX. Subsequent molecular docking indicated that the olive compounds possess strong binding affinities for the active site of COX isoforms, and molecular dynamics (MD) simulations confirmed the stability of binding. Moreover, olive compounds were predicted to have favorable pharmacokinetic properties, including a readiness to cross biological membranes as highlighted by steered MD simulations and umbrella sampling. Importantly, olive compounds including OLC were identified as non-inhibitors of the human ether-à-go-go-related gene (hERG) channel based on patch clamp assays. Overall, this study extends our understanding of the bioactivity of Olea-europaea-derived compounds, many of which are now known to be, at least in part, accountable for the beneficial health effects of the Mediterranean diet.
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Affiliation(s)
- Tom C. Karagiannis
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC 3004, Australia
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC 3053, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3010, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Katherine Ververis
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC 3053, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Julia J. Liang
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC 3004, Australia
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC 3053, Australia
- School of Science, STEM College, RMIT University, Melbourne, VIC 3001, Australia
| | - Eleni Pitsillou
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC 3053, Australia
- School of Science, STEM College, RMIT University, Melbourne, VIC 3001, Australia
| | - Evan A. Kagarakis
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC 3053, Australia
| | - Debbie T. Z. Yi
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC 3053, Australia
| | - Vivian Xu
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC 3053, Australia
| | - Andrew Hung
- School of Science, STEM College, RMIT University, Melbourne, VIC 3001, Australia
| | - Assam El-Osta
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC 3004, Australia
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
- Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, The Chinese University of Hong Kong, 3/F Lui Che Woo Clinical Sciences Building, 30–32 Ngan Shing Street, Sha Tin, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
- Biomedical Laboratory Science, Department of Technology, Faculty of Health, University College Copenhagen, 2200 Copenhagen, Denmark
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3
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Corbin A, Aromolaran KA, Aromolaran AS. STAT4 Mediates IL-6 Trans-Signaling Arrhythmias in High Fat Diet Guinea Pig Heart. Int J Mol Sci 2024; 25:7813. [PMID: 39063055 PMCID: PMC11277091 DOI: 10.3390/ijms25147813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 07/15/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
Obesity is a major risk factor for the development of life-threatening malignant ventricular tachyarrhythmias (VT) and sudden cardiac death (SCD). Risks may be highest for patients with high levels of the proinflammatory cytokine interleukin (IL)-6. We used our guinea pig model of high-fat diet (HFD)-induced arrhythmias that exhibit a heightened proinflammatory-like pathology, which is also observed in human obesity arrhythmias, as well as immunofluorescence and confocal microscopy approaches to evaluate the pathological IL-6 trans-signaling function and explore the underlying mechanisms. Using blind-stick and electrocardiogram (ECG) techniques, we tested the hypothesis that heightened IL-6 trans-signaling would exhibit increased ventricular arrhythmia/SCD incidence and underlying arrhythmia substrates. Remarkably, compared to low-fat diet (LFD)-fed controls, HFD promoted phosphorylation of the IL-6 signal transducer and activator of transcription 4 (STAT4), leading to its activation and enhanced nuclear translocation of pSTAT4/STAT4 compared to LFD controls and pSTAT3/STAT3 nuclear expression. Overactivation of IL-6 trans-signaling in guinea pigs prolonged the QT interval, which resulted in greater susceptibility to arrhythmias/SCD with isoproterenol challenge, as also observed with the downstream Janus kinase (JAK) 2 activator. These findings may have potentially profound implications for more effective arrhythmia therapy in the vulnerable obese patient population.
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Affiliation(s)
- Andrea Corbin
- Nora Eccles Harrison Cardiovascular Research and Training Institute (CVRTI), University of Utah School of Medicine, Salt Lake City, UT 84132, USA; (A.C.); (K.A.A.)
- Department of Biomedical Engineering, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Kelly A. Aromolaran
- Nora Eccles Harrison Cardiovascular Research and Training Institute (CVRTI), University of Utah School of Medicine, Salt Lake City, UT 84132, USA; (A.C.); (K.A.A.)
| | - Ademuyiwa S. Aromolaran
- Nora Eccles Harrison Cardiovascular Research and Training Institute (CVRTI), University of Utah School of Medicine, Salt Lake City, UT 84132, USA; (A.C.); (K.A.A.)
- Department of Biomedical Engineering, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
- Department of Surgery, Division of Cardiothoracic Surgery, Nutrition & Integrative Physiology, Biochemistry & Molecular Medicine Program, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
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4
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Oudah KH, Najm MAA, Barghash RF, Kutkat O, GabAllah M, Albohy A, Abouzid KAM. Drug repurposing of pyrazolotriazine derivatives as potential anti-SARS-CoV-2 agents: in vitro and in silico studies. BMC Chem 2024; 18:132. [PMID: 39014447 PMCID: PMC11253567 DOI: 10.1186/s13065-024-01233-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 06/25/2024] [Indexed: 07/18/2024] Open
Abstract
The search for new molecules targeting SARS-CoV-2 has been a priority since 2020. The continuous evolution of new mutants increases the need for more research in the area. One way to find new leads is to repurpose existing drugs and molecules against the required target. Here, we present the in vitro and in silico screening of ten previously synthesized and reported compounds as anti-COVID 19 agents. The compounds were screened in vitro against VERO-E6 cells to find their Cytotoxic Concentration (CC50) and their Inhibitory Concentration (IC50). Compounds 1, 2, and 5 revealed a promising anti-SARS-CoV-2 of (IC50 = 2.4, 11.2 and 2.8 µM), respectively while compounds 3 and 7 showed moderate activity of (IC50 = 17.8 and 26.1 µM) compared to Chloroquine which showed an IC50 of 24.9 µM. Among tested compounds, 1 showed the highest selectivity (CC50/IC50) of 192.8. Docking, molecular dynamics and ADME studies were done to investigate potential interactions between compounds and SARS-CoV-2 targets as well as to study the possibility of using them as lead compounds.
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Affiliation(s)
- Khulood H Oudah
- Department of Pharmacy, Mazaya University Collage, Nasiriyah, Thi-Qar, Iraq
| | - Mazin A A Najm
- Department of Pharmacy, Mazaya University Collage, Nasiriyah, Thi-Qar, Iraq
| | - Reham F Barghash
- Institute of Chemical Industries Research, National Research Centre, Dokki, Giza, 12622, Egypt
- Faculty of Biotechnology, October University for Modern Science and Arts (MSA University), Giza, Egypt
| | - Omnia Kutkat
- Center of Scientifc Excellence for Infuenza Viruses, National Research Centre, Dokki, Giza, 12622, Egypt
- Department of microbiology, Faculty of pharmacy, Ahram Canadian University, 6 th of October, Giza, 12566, Egypt
| | - Mohamed GabAllah
- Center of Scientifc Excellence for Infuenza Viruses, National Research Centre, Dokki, Giza, 12622, Egypt
| | - Amgad Albohy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The British University in Egypt, El-Sherouk City, 11837, Cairo, Egypt.
| | - Khaled A M Abouzid
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Abbassia, 11566, Cairo, Egypt.
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5
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Dziwornu GA, Seanego D, Fienberg S, Clements M, Ferreira J, Sypu VS, Samanta S, Bhana AD, Korkor CM, Garnie LF, Teixeira N, Wicht KJ, Taylor D, Olckers R, Njoroge M, Gibhard L, Salomane N, Wittlin S, Mahato R, Chakraborty A, Sevilleno N, Coyle R, Lee MCS, Godoy LC, Pasaje CF, Niles JC, Reader J, van der Watt M, Birkholtz LM, Bolscher JM, de Bruijni MHC, Coulson LB, Basarab GS, Ghorpade SR, Chibale K. 2,8-Disubstituted-1,5-naphthyridines as Dual Inhibitors of Plasmodium falciparum Phosphatidylinositol-4-kinase and Hemozoin Formation with In Vivo Efficacy. J Med Chem 2024; 67:11401-11420. [PMID: 38918002 PMCID: PMC11247499 DOI: 10.1021/acs.jmedchem.4c01154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
Structure-activity relationship studies of 2,8-disubstituted-1,5-naphthyridines, previously reported as potent inhibitors of Plasmodium falciparum (Pf) phosphatidylinositol-4-kinase β (PI4K), identified 1,5-naphthyridines with basic groups at 8-position, which retained Plasmodium PI4K inhibitory activity but switched primary mode of action to the host hemoglobin degradation pathway through inhibition of hemozoin formation. These compounds showed minimal off-target inhibitory activity against the human phosphoinositide kinases and MINK1 and MAP4K kinases, which were associated with the teratogenicity and testicular toxicity observed in rats for the PfPI4K inhibitor clinical candidate MMV390048. A representative compound from the series retained activity against field isolates and lab-raised drug-resistant strains of Pf. It was efficacious in the humanized NSG mouse malaria infection model at a single oral dose of 32 mg/kg. This compound was nonteratogenic in the zebrafish embryo model of teratogenicity and has a low predicted human dose, indicating that this series has the potential to deliver a preclinical candidate for malaria.
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Affiliation(s)
- Godwin Akpeko Dziwornu
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Donald Seanego
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Stephen Fienberg
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Monica Clements
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Jasmin Ferreira
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Venkata S Sypu
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Sauvik Samanta
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Ashlyn D Bhana
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Constance M Korkor
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Larnelle F Garnie
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Nicole Teixeira
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Kathryn J Wicht
- Drug Discovery and Development Centre (H3D), Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
| | - Dale Taylor
- Drug Discovery and Development Centre (H3D), Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Observatory 7925, South Africa
| | - Ronald Olckers
- Drug Discovery and Development Centre (H3D), Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Observatory 7925, South Africa
| | - Mathew Njoroge
- Drug Discovery and Development Centre (H3D), Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Observatory 7925, South Africa
| | - Liezl Gibhard
- Drug Discovery and Development Centre (H3D), Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Observatory 7925, South Africa
| | - Nicolaas Salomane
- Drug Discovery and Development Centre (H3D), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town 7925, South Africa
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123 Allschwil, Switzerland
- University of Basel, 4001 Basel, Switzerland
| | | | | | - Nicole Sevilleno
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, U.K
| | - Rachael Coyle
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, U.K
| | - Marcus C S Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, U.K
| | - Luiz C Godoy
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Charisse Flerida Pasaje
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jacquin C Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Janette Reader
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Hatfield, Pretoria 0028, South Africa
| | - Mariette van der Watt
- Institute for Sustainable Malaria Control, University of Pretoria, Hatfield, Pretoria 0028, South Africa
| | - Lyn-Marié Birkholtz
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Hatfield, Pretoria 0028, South Africa
| | - Judith M Bolscher
- TropIQ Health Sciences, Transistorweg 5, 6534 AT Nijmegen, The Netherlands
| | | | - Lauren B Coulson
- Drug Discovery and Development Centre (H3D), Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town 7925, South Africa
| | - Gregory S Basarab
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
- Drug Discovery and Development Centre (H3D), Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Observatory 7925, South Africa
| | - Sandeep R Ghorpade
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Kelly Chibale
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
- South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch 7701, South Africa
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6
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Krajewski S, Steczek L, Gotowicz K, Karczmarczyk U, Towpik J, Witkowska-Patena E, Łyczko K, Mazur M, Kozanecki P, Włostowska J, Knuuti J, Dziuk M, Garnuszek P, Kozanecki C. Preclinical evaluation of [ 18F]SYN1 and [ 18F]SYN2, novel radiotracers for PET myocardial perfusion imaging. EJNMMI Res 2024; 14:63. [PMID: 38976101 PMCID: PMC11231114 DOI: 10.1186/s13550-024-01122-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 06/20/2024] [Indexed: 07/09/2024] Open
Abstract
BACKGROUND Positron emission tomography (PET) is now an established diagnostic method for myocardial perfusion imaging (MPI) in coronary artery disease, which is the main cause of death globally. The available tracers show several limitations, therefore, the 18F-labelled tracer is in high demand nowadays. The preclinical studies on normal Wistar rats aimed to characterise two potential, novel radiotracers, [18F]SYN1 and [18F]SYN2, to evaluate which is a better candidate for PET MPI cardiotracer. RESULTS The dynamic microPET images showed rapid myocardial uptake for both tracers. However, the uptake was higher and also stable for [18F]SYN2, with an average standardized uptake value of 3.8. The biodistribution studies confirmed that [18F]SYN2 uptake in the cardiac muscle was high and stable (3.02%ID/g at 15 min and 2.79%ID/g at 6 h) compared to [18F]SYN1 (1.84%ID/g at 15 min and 0.32%ID/g at 6 h). The critical organs determined in dosimetry studies were the small intestine and the kidneys. The estimated effective dose for humans was 0.00714 mSv/MBq for [18F]SYN1 and 0.0109 mSv/MBq for [18F]SYN2. The tested dose level of 2 mg/kg was considered to be the No Observed Adverse Effect Level (NOAEL) for both candidates. The better results were achieved for [18F]SYN2, therefore, further preclinical studies were conducted only for this tracer. Radioligand binding assays showed significant responses in 3 from 68 assays: muscarinic acetylcholine M1 and M2 receptors and potassium channel hERG. The compound was mostly metabolised via an oxidative N-dealkylation, while the fluor substituent was not separated from the molecule. CONCLUSION [18F]SYN2 showed a favourable pharmacodynamic and pharmacokinetic profile, which enabled a clear visualization of the heart in microPET. The compound was well-tolerated in studies in normal rats with moderate radiation exposure. The results encourage further exploration of [18F]SYN2 in clinical studies.
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Affiliation(s)
| | - Lukasz Steczek
- Research & Development Centre, Synektik SA, Warsaw, Poland
| | - Karina Gotowicz
- Research & Development Centre, Synektik SA, Warsaw, Poland
- Department of Chemistry, University of Warsaw, Warsaw, Poland
| | - Urszula Karczmarczyk
- Radioisotope Centre POLATOM, National Centre for Nuclear Research, Otwock, Poland
| | - Joanna Towpik
- Research & Development Centre, Synektik SA, Warsaw, Poland
| | - Ewa Witkowska-Patena
- Nuclear Medicine Department, Military Institute of Medicine - National Research Institute, Warsaw, Poland
- Affidea Poland, Warsaw, Poland
| | | | - Maciej Mazur
- Department of Chemistry, University of Warsaw, Warsaw, Poland
| | | | | | - Juhani Knuuti
- Turku PET Centre, Turku University Hospital and University of Turku, Turku, Finland
- Department of Clinical Physiology, Nuclear Medicine, and PET, Turku University Hospital, Turku, Finland
| | - Mirosław Dziuk
- Nuclear Medicine Department, Military Institute of Medicine - National Research Institute, Warsaw, Poland
- Affidea Poland, Warsaw, Poland
| | - Piotr Garnuszek
- Radioisotope Centre POLATOM, National Centre for Nuclear Research, Otwock, Poland
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7
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Saha US, Vendruscolo M, Carpenter AE, Singh S, Bender A, Seal S. Step Forward Cross Validation for Bioactivity Prediction: Out of Distribution Validation in Drug Discovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.02.601740. [PMID: 39005404 PMCID: PMC11245006 DOI: 10.1101/2024.07.02.601740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Recent advances in machine learning methods for materials science have significantly enhanced accurate predictions of the properties of novel materials. Here, we explore whether these advances can be adapted to drug discovery by addressing the problem of prospective validation - the assessment of the performance of a method on out-of-distribution data. First, we tested whether k-fold n-step forward cross-validation could improve the accuracy of out-of-distribution small molecule bioactivity predictions. We found that it is more helpful than conventional random split cross-validation in describing the accuracy of a model in real-world drug discovery settings. We also analyzed discovery yield and novelty error, finding that these two metrics provide an understanding of the applicability domain of models and an assessment of their ability to predict molecules with desirable bioactivity compared to other small molecules. Based on these results, we recommend incorporating a k-fold n-step forward cross-validation and these metrics when building state-of-the-art models for bioactivity prediction in drug discovery.
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Affiliation(s)
| | | | | | | | - Andreas Bender
- Department of Chemistry, University of Cambridge, UK
- STAR-UBB Institute, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Srijit Seal
- Department of Chemistry, University of Cambridge, UK
- Broad Institute of MIT and Harvard, Cambridge, MA, US
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8
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El Sherbini A, Liblik K, Lee J, Baranchuk A, Zhang S, El-Diasty M. Opioids-induced inhibition of HERG ion channels and sudden cardiac death, a systematic review of current literature. Trends Cardiovasc Med 2024; 34:279-285. [PMID: 37015297 DOI: 10.1016/j.tcm.2023.03.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/28/2023] [Accepted: 03/28/2023] [Indexed: 04/06/2023]
Abstract
BACKGROUND It is estimated that over 60 million individuals regularly use opioids globally, with opioid use disorder increasing substantially in the past decade. Several reports have linked sudden cardiac death, QTc prolongation, and other adverse cardiovascular outcomes with opioid use through their inhibitory effect on the human ether-a-go-go-related gene (HERG) ion channel. Therefore, understanding this underlying mechanism may be critical for risk prevention and management in prescribing opioids and treating patients with opioid dependency. AIM The present systematic review summarizes the current literature on the impact of opioids-induced inhibition of HERG channel function and its relationship with sudden cardiac death, QTc prolongation, and other cardiovascular adverse effects. METHODS A systematic review was conducted of the databases PubMed, EMBASE, Cochrane, and ClinicalTrials.gov of primary studies that reported the effects of opioids on HERG channel function and associated cardiovascular outcomes. RESULTS The search identified 1,546 studies, of which 12 were finally included for data extraction. Based on the current literature, methadone, oliceridine, l-α-acetylmethadol (LAAM), and fentanyl were found to inhibit the HERG channel function and were associated with QTc prolongation. However, other opioids such as morphine, codeine, tramadol, and buprenorphine were not associated with inhibition of HERG channels or QTc prolongation. Additional cardiac outcomes associated with opioid related HERG channels dysfunction included sudden cardiac death and Torsade de Pointes. CONCLUSION Our findings suggest that certain opioid consumption may result in the inhibition of HERG channels, subsequently prolonging the QTc interval and increasing patient susceptibility to sudden cardiac death.
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Affiliation(s)
- Adham El Sherbini
- Faculty of Health Sciences, Queen's University, Kingston, ON, Canada
| | - Kiera Liblik
- School of Medicine, Queen's University, Kingston, ON, Canada
| | - Junsu Lee
- Faculty of Health Sciences, Queen's University, Kingston, ON, Canada
| | - Adrian Baranchuk
- Division of Cardiology, Department of Medicine, Queen's University, Kingston, ON, Canada
| | - Shetuan Zhang
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Mohammad El-Diasty
- Division of Cardiac Surgery, Department of Surgery, Queen's University, 76 Stuart St, Kingston, ON K7L2V7, Canada.
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9
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Angelia J, Duong L, Yun F, Mesic A, Yuan C, Carr D, Gunari S, Hudson PK, Morisseau C, Hammock BD, Kandasamy R, Pecic S. Quinolinyl-based multitarget-directed ligands with soluble epoxide hydrolase and fatty acid amide hydrolase inhibitory activities: Synthetic studies and pharmacological evaluations. Heliyon 2024; 10:e32262. [PMID: 38912512 PMCID: PMC11190605 DOI: 10.1016/j.heliyon.2024.e32262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/16/2024] [Accepted: 05/30/2024] [Indexed: 06/25/2024] Open
Abstract
Simultaneous inhibition of soluble epoxide hydrolase (sEH) and fatty acid amide hydrolase (FAAH) with a single small molecule represents a novel therapeutic approach in treating inflammatory pain, since both targets are involved in pain and inflammation processes. In this study using multi-target directed ligands methodology we designed and synthesized 7 quinolinyl-based dual sEH/FAAH inhibitors, using an optimized microwave-assisted Suzuki-Miyaura coupling reaction and tested their potency in human FAAH and human, rat, and mouse sEH inhibition assays. The structure-activity relationship study showed that quinolinyl moiety is well tolerated in the active sites of both enzymes, yielding several very potent dual sEH/FAAH inhibitors with the IC50 values in the low nanomolar range. The most potent dual inhibitor 4d was further evaluated in stability assay in human and rat plasma where it performed better than the standard Warfarin while in vivo study revealed that 1 mg/kg 4d can inhibit acute inflammatory pain in male rats to a similar degree as the traditional nonsteroidal anti-inflammatory drug ketoprofen (30 mg/kg) after intraperitoneal injection. ADMET prediction studies for this dual inhibitor show favorable pharmacokinetic properties which will guide the future in vivo evaluations.
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Affiliation(s)
- Jeannes Angelia
- Department of Chemistry & Biochemistry, California State University, Fullerton, 800 N. State College, Fullerton, CA, 92834, United States
| | - Leah Duong
- Department of Chemistry & Biochemistry, California State University, Fullerton, 800 N. State College, Fullerton, CA, 92834, United States
| | - Faye Yun
- Department of Chemistry & Biochemistry, California State University, Fullerton, 800 N. State College, Fullerton, CA, 92834, United States
| | - Anesa Mesic
- Department of Chemistry & Biochemistry, California State University, Fullerton, 800 N. State College, Fullerton, CA, 92834, United States
| | - Cassandra Yuan
- Department of Psychology, California State University, East Bay, 25800 Carlos Bee Blvd. Science S229, Hayward, CA, 94542, United States
| | - Daniel Carr
- Department of Psychology, California State University, East Bay, 25800 Carlos Bee Blvd. Science S229, Hayward, CA, 94542, United States
| | - Siena Gunari
- Department of Psychology, California State University, East Bay, 25800 Carlos Bee Blvd. Science S229, Hayward, CA, 94542, United States
| | - Paula K. Hudson
- Department of Chemistry & Biochemistry, California State University, Fullerton, 800 N. State College, Fullerton, CA, 92834, United States
| | - Christophe Morisseau
- Department of Entomology and Nematology, and UCD Comprehensive Cancer Center, University of California Davis, Davis, CA, 95616, United States
| | - Bruce D. Hammock
- Department of Entomology and Nematology, and UCD Comprehensive Cancer Center, University of California Davis, Davis, CA, 95616, United States
| | - Ram Kandasamy
- Department of Psychology, California State University, East Bay, 25800 Carlos Bee Blvd. Science S229, Hayward, CA, 94542, United States
| | - Stevan Pecic
- Department of Chemistry & Biochemistry, California State University, Fullerton, 800 N. State College, Fullerton, CA, 92834, United States
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10
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Corfu AI, Santarem N, Luelmo S, Mazza G, Greco A, Altomare A, Ferrario G, Nasta G, Keminer O, Aldini G, Tamborini L, Basilico N, Parapini S, Gul S, Cordeiro-da-Silva A, Conti P, Borsari C. Discovery of 1,3,4-Oxadiazole Derivatives as Broad-Spectrum Antiparasitic Agents. ACS Infect Dis 2024; 10:2222-2238. [PMID: 38717116 DOI: 10.1021/acsinfecdis.4c00181] [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] [Indexed: 06/15/2024]
Abstract
Vector-borne parasitic diseases (VBPDs) pose a significant threat to public health on a global scale. Collectively, Human African Trypanosomiasis (HAT), Leishmaniasis, and Malaria threaten millions of people, particularly in developing countries. Climate change might alter the transmission and spread of VBPDs, leading to a global burden of these diseases. Thus, novel agents are urgently needed to expand therapeutic options and limit the spread of drug-resistant parasites. Herein, we report the development of broad-spectrum antiparasitic agents by screening a known library of antileishmanial and antimalarial compounds toward Trypanosoma brucei (T. brucei) and identifying a 1,3,4-oxadiazole derivative (19) as anti-T. brucei hit with predicted blood-brain barrier permeability. Subsequently, extensive structure-activity-relationship studies around the lipophilic tail of 19 led to a potent antitrypanosomal and antimalarial compound (27), with moderate potency also toward Leishmania infantum (L. infantum) and Leishmania tropica. In addition, we discovered a pan-active antiparasitic molecule (24), showing low-micromolar IC50s toward T. brucei and Leishmania spp. promastigotes and amastigotes, and nanomolar IC50 against Plasmodium falciparum, together with high selectivity for the parasites over mammalian cells (THP-1). Early ADME-toxicity assays were used to assess the safety profile of the compounds. Overall, we characterized 24 and 27, bearing the 1,3,4-oxadiazole privileged scaffold, as broad-spectrum low-toxicity agents for the treatment of VBPDs. An alkyne-substituted chemical probe (30) was synthesized and will be utilized in proteomics experiments aimed at deconvoluting the mechanism of action in the T. brucei parasite.
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Affiliation(s)
- Alexandra Ioana Corfu
- Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli 25, 20133 Milan, Italy
| | - Nuno Santarem
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal
- Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Sara Luelmo
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal
- Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Gaia Mazza
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Via Pascal 36, 20133 Milan, Italy
| | - Alessandro Greco
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Alessandra Altomare
- Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli 25, 20133 Milan, Italy
| | - Giulio Ferrario
- Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli 25, 20133 Milan, Italy
| | - Giulia Nasta
- Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli 25, 20133 Milan, Italy
| | - Oliver Keminer
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Giancarlo Aldini
- Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli 25, 20133 Milan, Italy
| | - Lucia Tamborini
- Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli 25, 20133 Milan, Italy
| | - Nicoletta Basilico
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Via Pascal 36, 20133 Milan, Italy
| | - Silvia Parapini
- Department of Biomedical Sciences for Health, University of Milan, Via Pascal 36, 20133 Milan, Italy
| | - Sheraz Gul
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, 22525 Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), Schnackenburgallee 114, 22525 Hamburg, Germany
| | - Anabela Cordeiro-da-Silva
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal
- Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Paola Conti
- Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli 25, 20133 Milan, Italy
| | - Chiara Borsari
- Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli 25, 20133 Milan, Italy
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11
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Wang HY, Nguyen TP, Sternisha AC, Carroll CL, Cross B, Morlock L, Williams NS, McBrayer S, Nijhawan D, De Brabander JK. Discovery and Optimization of N-Arylated Tetracyclic Dicarboximides That Target Primary Glioma Stem-like Cells. J Med Chem 2024; 67:9277-9301. [PMID: 38804887 DOI: 10.1021/acs.jmedchem.4c00402] [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: 05/29/2024]
Abstract
We recently discovered a novel N-aryl tetracyclic dicarboximide MM0299 (1) with robust activity against glioma stem-like cells that potently and selectively inhibits lanosterol synthase leading to the accumulation of the toxic shunt metabolite 24(S),25-epoxycholesterol. Herein, we delineate a systematic and comprehensive SAR study that explores the structural space surrounding the N-aryl tetracyclic dicarboximide scaffold. A series of 100 analogs were synthesized and evaluated for activity against the murine glioma stem-like cell line Mut6 and for metabolic stability in mouse liver S9 fractions. This study led to several analogs with single-digit nanomolar activity in Mut6 glioblastoma cells that were metabolically stable in S9 fractions. In vivo pharmacokinetic analysis of selected analogs identified compound 52a (IC50 = 63 nM; S9 T1/2 > 240 min) which was orally available (39% plasma; 58% brain) and displayed excellent brain exposure. Chronic oral dosing of 52a during a 2-week tolerability study indicated no adverse effect on body weight nor signs of hematologic, liver, or kidney toxicity.
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Affiliation(s)
- Hua-Yu Wang
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Thu P Nguyen
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Alex C Sternisha
- Children's Medical Center Research Institute and Department of Pediatrics, UT Southwestern, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Christopher L Carroll
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Bethany Cross
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Lorraine Morlock
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Noelle S Williams
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Samuel McBrayer
- Children's Medical Center Research Institute and Department of Pediatrics, UT Southwestern, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Deepak Nijhawan
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
- Department of Internal Medicine, Division of Hematology/Oncology and Program in Molecular Medicine, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Jef K De Brabander
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
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12
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Murphy RE, Wang P, Ali S, Smith HR, Felsing DE, Chen H, Zhou J, Allen JA. Discovery of 3-((4-Benzylpyridin-2-yl)amino)benzamides as Potent GPR52 G Protein-Biased Agonists. J Med Chem 2024; 67:9709-9730. [PMID: 38788241 DOI: 10.1021/acs.jmedchem.4c00856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Orphan GPR52 is emerging as a promising neurotherapeutic target. Optimization of previously reported lead 4a employing an iterative drug design strategy led to the identification of a series of unique GPR52 agonists, such as 10a (PW0677), 15b (PW0729), and 24f (PW0866), with improved potency and efficacy. Intriguingly, compounds 10a and 24f showed greater bias for G protein/cAMP signaling and induced significantly less in vitro desensitization than parent compound 4a, indicating that reducing GPR52 β-arrestin activity with biased agonism results in sustained GPR52 activation. Further exploration of compounds 15b and 24f indicated improved potency and efficacy, and excellent target selectivity, but limited brain exposure warranting further optimization. These balanced and biased GPR52 agonists provide important pharmacological tools to study GPR52 activation, signaling bias, and therapeutic potential for neuropsychiatric and neurological diseases.
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Affiliation(s)
- Ryan E Murphy
- Center for Addiction Sciences and Therapeutics, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Pingyuan Wang
- Center for Addiction Sciences and Therapeutics, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Saghir Ali
- Center for Addiction Sciences and Therapeutics, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Hudson R Smith
- Center for Addiction Sciences and Therapeutics, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Daniel E Felsing
- Center for Addiction Sciences and Therapeutics, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Haiying Chen
- Center for Addiction Sciences and Therapeutics, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Jia Zhou
- Center for Addiction Sciences and Therapeutics, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - John A Allen
- Center for Addiction Sciences and Therapeutics, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
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13
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Liu C, Wang W, Zhao S, Chen S, Chen H, Wang S, Li Z, Qian H, Tian X. Discovery of first-in-class highly selective TRPV1 antagonists with dual analgesic and hypoglycemic effects. Bioorg Med Chem 2024; 107:117750. [PMID: 38776567 DOI: 10.1016/j.bmc.2024.117750] [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: 03/03/2024] [Revised: 05/04/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024]
Abstract
Analgesia and blood sugar control are considered as two main unmet clinical needs for diabetes related neuropathic pain patients. Transient receptor potential vanilloid type-1 (TRPV1) channel is a highly validated target for pain perception, while no TRPV1 antagonists have been approved due to hyperthermia side effects. Herein, two series of new TRPV1 antagonists with flavonoid skeleton were designed by the structure-based drug design (SBDD) strategy. After comprehensive evaluation, compound CX-3 was identified as a promising TRPV1 antagonist. CX-3 exhibited equivalent TRPV1 antagonistic activity with classical TRPV1 antagonist BCTC in vitro, and exerted better analgesic activity in vivo than that of BCTC in the formalin induced inflammatory pain model without hyperthermia risk. Moreover, CX-3 exhibited robust glucose-lowering effects and showed high selectivity over other ion channels. Overall, these findings identified a first-in-class highly selective TRPV1 antagonist CX-3, which is a promising candidate to target the pathogenesis of diabetes related neuropathic pain.
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Affiliation(s)
- Chunxia Liu
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, PR China; Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, PR China
| | - Wenxin Wang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Shiyu Zhao
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, PR China; Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, PR China
| | - Siliang Chen
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Haoyang Chen
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, PR China; Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, PR China
| | - Suhua Wang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, PR China; Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, PR China
| | - Zheng Li
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China.
| | - Hai Qian
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China.
| | - Xin Tian
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, PR China; Henan Key Laboratory of Precision Clinical Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, PR China.
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14
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Meyer EA, Croxford AL, Gnerre C, Kulig P, Murphy MJ, Jacob EM, Schäfer G, Richard-Bildstein S, Aissaoui H, Bouis P, Ertel EA, de Kanter R, Keller MP, Lüthi U, Caroff E. Discovery of the Clinical Candidate IDOR-1117-2520: A Potent and Selective Antagonist of CCR6 for Autoimmune Diseases. J Med Chem 2024; 67:8077-8098. [PMID: 38727100 DOI: 10.1021/acs.jmedchem.4c00186] [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: 05/24/2024]
Abstract
Migration of immune cells to sites of inflammation is a critical step in the body's response to infections but also during autoimmune flares. Chemokine receptors, members of the GPCR receptors, are instrumental in directing specific cell types to their target organs. Herein, we describe a highly potent small molecule antagonist of the chemokine receptor CCR6, which came out of fine-tuned structural elaborations from a proprietary HTS hit. Three main issues in the parent chemical series-cytotoxicity, phototoxicity, and hERG, were successfully solved. Biological characterization demonstrated that compound 45 (IDOR-1117-2520) is a selective and insurmountable antagonist of CCR6. In vivo proof-of-mechanism studies in a mouse lung inflammation model using a representative compound from the chemical class of 45 confirmed that the targeted CCR6+ cells were efficiently inhibited from migrating into the bronchoalveoli. Finally, ADMET and physicochemical properties were well balanced and the preclinical package warranted progress in the clinic.
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Affiliation(s)
- Emmanuel A Meyer
- Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Andrew L Croxford
- Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Carmela Gnerre
- Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Paulina Kulig
- Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Mark J Murphy
- Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Elise M Jacob
- Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Gabriel Schäfer
- Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | | | - Hamed Aissaoui
- Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Patrick Bouis
- Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Eric A Ertel
- Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Ruben de Kanter
- Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Marcel P Keller
- Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Urs Lüthi
- Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
| | - Eva Caroff
- Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
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15
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Herlina T, Akili AWR, Nishinarizki V, Hardianto A, Latip J. Bioinformatics Study of Flavonoids From Genus Erythrina As Ace2 inhibitor Candidates For Covid-19 Treatment. Adv Appl Bioinform Chem 2024; 17:61-70. [PMID: 38764460 PMCID: PMC11102127 DOI: 10.2147/aabc.s454961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 05/03/2024] [Indexed: 05/21/2024] Open
Abstract
Purpose This study aimed to screen potential drug candidates from the flavonoids of the genus Erythrina for the Corona Virus Disease 2019 (COVID-19) treatment. Patients and Methods A comprehensive screening was conducted on the structures of 473 flavonoids derived from the genus Erythrina, focusing on their potential toxicity and pharmacokinetic profiles. Subsequently, flavonoids that were non-toxic and possessed favorable pharmacokinetic properties underwent further analysis to explore their interactions with the angiotensin-converting enzyme 2 (ACE2) receptor, employing molecular docking and molecular dynamics simulations. Results Among 473 flavonoids, 104 were predicted to be safe from being mutagenic, hepatotoxic, and inhibitors of the human ether-a-go-go-related gene (hERG). Among these 104 flavonoids, 18 compounds were predicted not to be substrates of P-glycoprotein (P-gp). Among these 18 flavonoids, gangetinin (471) and erybraedin D (310) exhibit low binding affinities and root mean square deviation (RMSD) values, indicating stable binding to the ACE2 receptor. The physicochemical attributes of compounds 310 and 471 suggest that they possess drug-like properties. Conclusion Gangetinin (471) and erybraedin D (310) may serve as promising candidates for COVID-19 treatment due to their potential to inhibit the ACE2-RBD interaction. This warrants further investigation into their inhibitory effects on ACE2-RBD binding through in vitro experiments.
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Affiliation(s)
- Tati Herlina
- Department of Chemistry, Universitas Padjadjaran, Jatinangor, West Java, Indonesia
| | | | - Vicki Nishinarizki
- Department of Chemistry, Universitas Padjadjaran, Jatinangor, West Java, Indonesia
| | - Ari Hardianto
- Department of Chemistry, Universitas Padjadjaran, Jatinangor, West Java, Indonesia
| | - Jalifah Latip
- Department of Chemical Sciences, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
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16
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Camara MD, Zhou Y, Dara A, Tékété MM, Nóbrega de Sousa T, Sissoko S, Dembélé L, Ouologuem N, Hamidou Togo A, Alhousseini ML, Fofana B, Sagara I, Djimde AA, Gil PJ, Lauschke VM. Population-specific variations in KCNH2 predispose patients to delayed ventricular repolarization upon dihydroartemisinin-piperaquine therapy. Antimicrob Agents Chemother 2024; 68:e0139023. [PMID: 38546223 PMCID: PMC11064487 DOI: 10.1128/aac.01390-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 03/05/2024] [Indexed: 05/03/2024] Open
Abstract
Dihydroartemisinin-piperaquine is efficacious for the treatment of uncomplicated malaria and its use is increasing globally. Despite the positive results in fighting malaria, inhibition of the Kv11.1 channel (hERG; encoded by the KCNH2 gene) by piperaquine has raised concerns about cardiac safety. Whether genetic factors could modulate the risk of piperaquine-mediated QT prolongations remained unclear. Here, we first profiled the genetic landscape of KCNH2 variability using data from 141,614 individuals. Overall, we found 1,007 exonic variants distributed over the entire gene body, 555 of which were missense. By optimizing the gene-specific parametrization of 16 partly orthogonal computational algorithms, we developed a KCNH2-specific ensemble classifier that identified a total of 116 putatively deleterious missense variations. To evaluate the clinical relevance of KCNH2 variability, we then sequenced 293 Malian patients with uncomplicated malaria and identified 13 variations within the voltage sensing and pore domains of Kv11.1 that directly interact with channel blockers. Cross-referencing of genetic and electrocardiographic data before and after piperaquine exposure revealed that carriers of two common variants, rs1805121 and rs41314375, experienced significantly higher QT prolongations (ΔQTc of 41.8 ms and 61 ms, respectively, vs 14.4 ms in controls) with more than 50% of carriers having increases in QTc >30 ms. Furthermore, we identified three carriers of rare population-specific variations who experienced clinically relevant delayed ventricular repolarization. Combined, our results map population-scale genetic variability of KCNH2 and identify genetic biomarkers for piperaquine-induced QT prolongation that could help to flag at-risk patients and optimize efficacy and adherence to antimalarial therapy.
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Affiliation(s)
- Mahamadou D. Camara
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Department of Epidemiology of Parasitic Diseases, Malaria Research and Training Center, Faculty of Pharmacy, University of Science, Techniques and Technologies, Bamako, Mali
| | - Yitian Zhou
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Antoine Dara
- Department of Epidemiology of Parasitic Diseases, Malaria Research and Training Center, Faculty of Pharmacy, University of Science, Techniques and Technologies, Bamako, Mali
| | - Mamadou M. Tékété
- Department of Epidemiology of Parasitic Diseases, Malaria Research and Training Center, Faculty of Pharmacy, University of Science, Techniques and Technologies, Bamako, Mali
| | - Taís Nóbrega de Sousa
- Department of Microbiology and Tumour Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Molecular Biology and Malaria Immunology Research Group, Instituto René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil
| | - Sékou Sissoko
- Department of Epidemiology of Parasitic Diseases, Malaria Research and Training Center, Faculty of Pharmacy, University of Science, Techniques and Technologies, Bamako, Mali
| | - Laurent Dembélé
- Department of Epidemiology of Parasitic Diseases, Malaria Research and Training Center, Faculty of Pharmacy, University of Science, Techniques and Technologies, Bamako, Mali
| | - Nouhoun Ouologuem
- Department of Epidemiology of Parasitic Diseases, Malaria Research and Training Center, Faculty of Pharmacy, University of Science, Techniques and Technologies, Bamako, Mali
| | - Amadou Hamidou Togo
- Department of Epidemiology of Parasitic Diseases, Malaria Research and Training Center, Faculty of Pharmacy, University of Science, Techniques and Technologies, Bamako, Mali
| | - Mohamed L. Alhousseini
- Department of Epidemiology of Parasitic Diseases, Malaria Research and Training Center, Faculty of Pharmacy, University of Science, Techniques and Technologies, Bamako, Mali
| | - Bakary Fofana
- Department of Epidemiology of Parasitic Diseases, Malaria Research and Training Center, Faculty of Pharmacy, University of Science, Techniques and Technologies, Bamako, Mali
| | - Issaka Sagara
- Department of Epidemiology of Parasitic Diseases, Malaria Research and Training Center, Faculty of Pharmacy, University of Science, Techniques and Technologies, Bamako, Mali
| | - Abdoulaye A. Djimde
- Department of Epidemiology of Parasitic Diseases, Malaria Research and Training Center, Faculty of Pharmacy, University of Science, Techniques and Technologies, Bamako, Mali
| | - Pedro J. Gil
- Department of Microbiology and Tumour Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, Nova University of Lisbon, Lisbon, Portugal
| | - Volker M. Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
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17
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Wu J, Zhang Z, Zhang Q, Li J. Design, synthesis, and biological evaluation of aralkyl piperazine and piperidine derivatives targeting SSRI/5-HT 1A/5-HT 7. Bioorg Med Chem 2024; 104:117698. [PMID: 38552597 DOI: 10.1016/j.bmc.2024.117698] [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: 02/20/2024] [Revised: 03/17/2024] [Accepted: 03/25/2024] [Indexed: 04/20/2024]
Abstract
Serotonin reuptake inhibition combined with the action targeting 5-hydroxytryptamine receptor subtypes can serve as a potential target for the development of antidepressant drugs. Herein a series of new aralkyl piperazines and piperidines were designed and synthesized by the structural modifications of the previously discovered aralkyl piperidine compound 1, targeting SSRI/5-HT1A/5-HT7. The results exhibited that compound 5a showed strong binding to 5-HT1A and 5-HT7 (Ki of 0.46 nM, 2.7 nM, respectively) and a high level of serotonin reuptake inhibition (IC50 of 1.9 nM), all of which were significantly elevated compared to 1. In particular, compound 5a showed weaker inhibitory activity against hERG than 1, and demonstrated good stability in liver microsomes in vitro. The preliminary screening using FST indicated that orally administered 5a, at a high dose, could reduce immobility time in mice markedly, indicating potential antidepressant activity.
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Affiliation(s)
- Jianwei Wu
- Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai 201203, China; National Key Laboratory of Lead Druggability Research, Shanghai Institute of Pharmaceutical Industry Co. Ltd., Shanghai 201203, China
| | - Zixue Zhang
- Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai 201203, China; National Key Laboratory of Lead Druggability Research, Shanghai Institute of Pharmaceutical Industry Co. Ltd., Shanghai 201203, China
| | - Qingwei Zhang
- Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai 201203, China; National Key Laboratory of Lead Druggability Research, Shanghai Institute of Pharmaceutical Industry Co. Ltd., Shanghai 201203, China; School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Jianqi Li
- Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai 201203, China; National Key Laboratory of Lead Druggability Research, Shanghai Institute of Pharmaceutical Industry Co. Ltd., Shanghai 201203, China.
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18
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Mambwe D, Coertzen D, Leshabane M, Mulubwa M, Njoroge M, Gibhard L, Girling G, Wicht KJ, Lee MCS, Wittlin S, Moreira DRM, Birkholtz LM, Chibale K. hERG, Plasmodium Life Cycle, and Cross Resistance Profiling of New Azabenzimidazole Analogues of Astemizole. ACS Med Chem Lett 2024; 15:463-469. [PMID: 38628794 PMCID: PMC11017395 DOI: 10.1021/acsmedchemlett.3c00496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/01/2024] [Accepted: 03/06/2024] [Indexed: 04/19/2024] Open
Abstract
Toward addressing the cardiotoxicity liability associated with the antimalarial drug astemizole (AST, hERG IC50 = 0.0042 μM) and its derivatives, we designed and synthesized analogues based on compound 1 (Pf NF54 IC50 = 0.012 μM; hERG IC50 = 0.63 μM), our previously identified 3-trifluoromethyl-1,2,4-oxadiazole AST analogue. Compound 11 retained in vitro multistage antiplasmodium activity (ABS PfNF54 IC50 = 0.017 μM; gametocytes PfiGc/PfLGc IC50 = 1.24/1.39 μM, and liver-stage PbHepG2 IC50 = 2.30 μM), good microsomal metabolic stability (MLM CLint < 11 μL·min-1·mg-1, EH < 0.33), and solubility (150 μM). It shows a ∼6-fold and >6000-fold higher selectivity against human ether-á-go-go-related gene higher selectively potential over hERG relative to 1 and AST, respectively. Despite the excellent in vitro antiplasmodium activity profile, in vivo efficacy in the Plasmodium berghei mouse infection model was diminished, attributable to suboptimal oral bioavailability (F = 14.9%) at 10 mg·kg-1 resulting from poor permeability (log D7.4 = -0.82). No cross-resistance was observed against 44 common Pf mutant lines, suggesting activity via a novel mechanism of action.
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Affiliation(s)
- Dickson Mambwe
- Department
of Chemistry, University of Cape Town, Rondebosch, 7701 Cape Town, South Africa
| | - Dina Coertzen
- Department
of Biochemistry, Genetics & Microbiology, Institute for Sustainable
Malaria Control, University of Pretoria, Private Bag X20, Hatfield, 0028 Pretoria, South Africa
| | - Meta Leshabane
- Department
of Biochemistry, Genetics & Microbiology, Institute for Sustainable
Malaria Control, University of Pretoria, Private Bag X20, Hatfield, 0028 Pretoria, South Africa
| | - Mwila Mulubwa
- Drug
Discovery and Development Centre (H3D), DMPK & Pharmacology, University of Cape Town, Observatory, 7925 Cape Town, South Africa
| | - Mathew Njoroge
- Drug
Discovery and Development Centre (H3D), DMPK & Pharmacology, University of Cape Town, Observatory, 7925 Cape Town, South Africa
| | - Liezl Gibhard
- Drug
Discovery and Development Centre (H3D), DMPK & Pharmacology, University of Cape Town, Observatory, 7925 Cape Town, South Africa
| | - Gareth Girling
- Wellcome
Sanger Institute, Wellcome
Trust Genome Campus, Hinxton CB10 1SA, United Kingdom
| | - Kathryn J. Wicht
- Department
of Chemistry, University of Cape Town, Rondebosch, 7701 Cape Town, South Africa
| | - Marcus C. S. Lee
- Wellcome
Sanger Institute, Wellcome
Trust Genome Campus, Hinxton CB10 1SA, United Kingdom
- Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 4HN, Scotland, United Kingdom
| | - Sergio Wittlin
- Swiss
Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland
- University
of Basel, 4003 Basel, Switzerland
| | | | - Lyn-Marie Birkholtz
- Department
of Biochemistry, Genetics & Microbiology, Institute for Sustainable
Malaria Control, University of Pretoria, Private Bag X20, Hatfield, 0028 Pretoria, South Africa
| | - Kelly Chibale
- Department
of Chemistry, University of Cape Town, Rondebosch, 7701 Cape Town, South Africa
- Drug
Discovery and Development Centre (H3D), DMPK & Pharmacology, University of Cape Town, Observatory, 7925 Cape Town, South Africa
- South
African Medical Research Council Drug Discovery and Development Research
Unit, University of Cape Town, Rondebosch, 7701 Cape Town, South Africa
- Institute
of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, 7701 Cape Town, South Africa
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19
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Le Roch M, Renault J, Argouarch G, Lenci E, Trabocchi A, Roisnel T, Gouault N, Lalli C. Synthesis and Chemoinformatic Analysis of Fluorinated Piperidines as 3D Fragments for Fragment-Based Drug Discovery. J Org Chem 2024; 89:4932-4946. [PMID: 38451837 DOI: 10.1021/acs.joc.4c00143] [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: 03/09/2024]
Abstract
The concise synthesis of a small library of fluorinated piperidines from readily available dihydropyridinone derivatives has been described. The effect of the fluorination on different positions has then been evaluated by chemoinformatic tools. In particular, the compounds' pKa's have been calculated, revealing that the fluorine atoms notably lowered their basicity, which is correlated to the affinity for hERG channels resulting in cardiac toxicity. The "lead-likeness" and three-dimensionality have also been evaluated to assess their ability as useful fragments for drug design. A random screening on a panel of representative proteolytic enzymes was then carried out and revealed that one scaffold is recognized by the catalytic pocket of 3CLPro (main protease of SARS-CoV-2 coronavirus).
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Affiliation(s)
- Myriam Le Roch
- Univ Rennes, CNRS, ISCR-UMR 6226, Rennes F-35000, France
| | | | | | - Elena Lenci
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, Sesto Fiorentino, Florence 50019, Italy
| | - Andrea Trabocchi
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, Sesto Fiorentino, Florence 50019, Italy
| | - Thierry Roisnel
- Univ Rennes, Centre de Diffractométrie X (CDIFX), ISCR-UMR 6226, Rennes F-35000, France
| | | | - Claudia Lalli
- Univ Rennes, CNRS, ISCR-UMR 6226, Rennes F-35000, France
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20
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Ahmad I, Rabbi F, Nisar A, Ul-Haq Z, Khan A. In vitro-in silico pharmacology and chemistry of Stercularin, isolated from Sterculia diversifolia. Comput Biol Chem 2024; 109:108008. [PMID: 38198964 DOI: 10.1016/j.compbiolchem.2023.108008] [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: 10/08/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024]
Abstract
Stercularin is a coumarin, isolated from the ethyl acetate fraction of stem bark and leaves of S. diversifolia. Pharmacologically it is active against cancer, diabetes, and inflammation etc. The molecule is further screened for in vitro pharmacological activities. In addition, a detailed description on its drug likeness and pharmacokinetic profile has been established to further explore its fate as a drug candidate. Stercularin exhibited antiglycation, immunomodulatory, and leishmanicidal activity in three different in vitro models. The IC50 values obtained in these three assays were 80.22 ± 0.46 mg/ml, 12.8 ± 1.6 μg/ml, and 8.32 ± 0.42 μg/ml, respectively. In case of drug likeness evaluation, Stercularin has acceptable physicochemical properties and compliant with major drug likeness descriptors i.e., Lipinski rule, Pfizer rule, GSK rule, and "golden triangle". Accepting Lipinski rule implies the oral drug development of Stercularin. Pharmacokinetically, Stercularin is permeable to Caco-2 and MDCK cell lines. 'Boiled-egg' plot suggest intestinal route of absorption, blood brain barrier nonpermeating, and not affected by p-glycoprotein. Stercularin has high plasma protein binding with low free fraction circulating in the plasma. Stercularin proved to be the substrate and/or inhibitor of CYP 450 system with a moderate half-life and clearance rate to allow flexible dosing regimen. Finally, slight risk of toxicity exists for Stercularin, but not being limiting factors of drug knock out. A nature isolated Stercularin possess pharmacological activities and is predicted to have acceptable pharmacokinetic profile. Further drug development and in vivo studies are desirable for optimization.
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Affiliation(s)
- Imad Ahmad
- Department of Pharmacy, The Professional Institute of Health Sciences, Mardan, Khyber Pakhtunkhwa, Pakistan; Department of Pharmacy, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Fazle Rabbi
- Department of Pharmacy, Abasyn University Peshawar, Peshawar, Khyber Pakhtunkhwa 25000, Pakistan.
| | - Amna Nisar
- Department of Pharmacy, University of Peshawar, Peshawar, Khyber Pakhtunkhwa 25120, Pakistan
| | - Zaheer Ul-Haq
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan; Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Alamgir Khan
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
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21
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Vinh T, Nguyen L, Trinh QH, Nguyen-Vo TH, Nguyen BP. Predicting Cardiotoxicity of Molecules Using Attention-Based Graph Neural Networks. J Chem Inf Model 2024; 64:1816-1827. [PMID: 38438914 DOI: 10.1021/acs.jcim.3c01286] [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: 03/06/2024]
Abstract
In drug discovery, the search for new and effective medications is often hindered by concerns about toxicity. Numerous promising molecules fail to pass the later phases of drug development due to strict toxicity assessments. This challenge significantly increases the cost, time, and human effort needed to discover new therapeutic molecules. Additionally, a considerable number of drugs already on the market have been withdrawn or re-evaluated because of their unwanted side effects. Among the various types of toxicity, drug-induced heart damage is a severe adverse effect commonly associated with several medications, especially those used in cancer treatments. Although a number of computational approaches have been proposed to identify the cardiotoxicity of molecules, the performance and interpretability of the existing approaches are limited. In our study, we proposed a more effective computational framework to predict the cardiotoxicity of molecules using an attention-based graph neural network. Experimental results indicated that the proposed framework outperformed the other methods. The stability of the model was also confirmed by our experiments. To assist researchers in evaluating the cardiotoxicity of molecules, we have developed an easy-to-use online web server that incorporates our model.
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Affiliation(s)
- Tuan Vinh
- Department of Chemistry, Emory University, 201 Dowman Drive, Atlanta, Georgia 30322-1007, United States
| | - Loc Nguyen
- School of Mathematics and Statistics, Victoria University of Wellington, Kelburn Parade, Wellington 6012, New Zealand
| | - Quang H Trinh
- School of Information and Communication Technology, Hanoi University of Science and Technology, Hanoi 100000, Vietnam
| | - Thanh-Hoang Nguyen-Vo
- School of Mathematics and Statistics, Victoria University of Wellington, Kelburn Parade, Wellington 6012, New Zealand
- School of Innovation, Design and Technology, Wellington Institute of Technology, 21 Kensington Avenue, Lower Hutt 5012, New Zealand
| | - Binh P Nguyen
- School of Mathematics and Statistics, Victoria University of Wellington, Kelburn Parade, Wellington 6012, New Zealand
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22
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de Souza AS, Dias DS, Ribeiro RCB, Costa DCS, de Moraes MG, Pinho DR, Masset MEG, Marins LM, Valle SP, de Carvalho CJC, de Carvalho GSG, Mello ALN, Sola-Penna M, Palmeira-Mello MV, Conceição RA, Rodrigues CR, Souza AMT, Forezi LDSM, Zancan P, Ferreira VF, da Silva FDC. Novel naphthoquinone-1H-1,2,3-triazole hybrids: Design, synthesis and evaluation as inductors of ROS-mediated apoptosis in the MCF-7 cells. Bioorg Med Chem 2024; 102:117671. [PMID: 38452407 DOI: 10.1016/j.bmc.2024.117671] [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: 01/12/2024] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 03/09/2024]
Abstract
The search for novel anticancer drugs is essential to expand treatment options, overcome drug resistance, reduce toxicity, promote innovation, and tackle the economic impact. The importance of these studies lies in their contribution to advancing cancer research and enhancing patient outcomes in the battle against cancer. Here, we developed new asymmetric hybrids containing two different naphthoquinones linked by a 1,2,3-1H-triazole nucleus, which are potential new drugs for cancer treatment. The antitumor activity of the novel compounds was tested using the breast cancer cell lines MCF-7 and MDA-MB-231, using the non-cancer cell line MCF10A as control. Our results showed that two out of twenty-two substances tested presented potential antitumor activity against the breast cancer cell lines. These potential drugs, named here 12g and 12h were effective in reducing cell viability and promoting cell death of the tumor cell lines, exhibiting minimal effects on the control cell line. The mechanism of action of the novel drugs was assessed revealing that both drugs increased reactive oxygen species production with consequent activation of the AMPK pathway. Therefore, we concluded that 12g and 12h are novel AMPK activators presenting selective antitumor effects.
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Affiliation(s)
- Acácio S de Souza
- Universidade Federal Fluminense, Faculdade de Farmácia, Departamento de Tecnologia Farmacêutica, CEP 24241-000 Niterói, RJ, Brazil
| | - Deborah S Dias
- Laboratório de Enzimologia e Controle do Metabolismo (LabECoM), Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ CEP 21941-902, Brazil
| | - Ruan C B Ribeiro
- Universidade Federal Fluminense, Departamento de Química Orgânica, Instituto de Química, Campus do Valonguinho, CEP 24020-150 Niterói, RJ, Brazil
| | - Dora C S Costa
- Universidade Federal Fluminense, Departamento de Química Orgânica, Instituto de Química, Campus do Valonguinho, CEP 24020-150 Niterói, RJ, Brazil
| | - Matheus G de Moraes
- Universidade Federal Fluminense, Departamento de Química Orgânica, Instituto de Química, Campus do Valonguinho, CEP 24020-150 Niterói, RJ, Brazil
| | - David R Pinho
- Universidade Federal Fluminense, Departamento de Química Orgânica, Instituto de Química, Campus do Valonguinho, CEP 24020-150 Niterói, RJ, Brazil
| | - Maria E G Masset
- Universidade Federal Fluminense, Faculdade de Farmácia, Departamento de Tecnologia Farmacêutica, CEP 24241-000 Niterói, RJ, Brazil
| | - Laís M Marins
- Universidade Federal Fluminense, Departamento de Química Orgânica, Instituto de Química, Campus do Valonguinho, CEP 24020-150 Niterói, RJ, Brazil
| | - Sandy P Valle
- Universidade Federal Fluminense, Departamento de Química Orgânica, Instituto de Química, Campus do Valonguinho, CEP 24020-150 Niterói, RJ, Brazil
| | - Cláudio J C de Carvalho
- Universidade Federal Fluminense, Departamento de Química Orgânica, Instituto de Química, Campus do Valonguinho, CEP 24020-150 Niterói, RJ, Brazil
| | - Gustavo S G de Carvalho
- Universidade Federal Fluminense, Departamento de Química Orgânica, Instituto de Química, Campus do Valonguinho, CEP 24020-150 Niterói, RJ, Brazil
| | - Angélica Lauria N Mello
- Laboratório de Enzimologia e Controle do Metabolismo (LabECoM), Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ CEP 21941-902, Brazil
| | - Mauro Sola-Penna
- Universidade Federal do Rio de Janeiro, Laboratório de Oncobiologia Molecular (LabOMol), Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, CEP 21941-902 Rio de Janeiro, RJ, Brazil
| | - Marcos V Palmeira-Mello
- Laboratório de Modelagem Molecular & QSAR (ModMolQSAR), Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ CEP 21941-590, Brazil
| | - Raissa A Conceição
- Laboratório de Modelagem Molecular & QSAR (ModMolQSAR), Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ CEP 21941-590, Brazil
| | - Carlos R Rodrigues
- Laboratório de Modelagem Molecular & QSAR (ModMolQSAR), Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ CEP 21941-590, Brazil
| | - Alessandra M T Souza
- Laboratório de Modelagem Molecular & QSAR (ModMolQSAR), Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ CEP 21941-590, Brazil
| | - Luana da S M Forezi
- Universidade Federal Fluminense, Departamento de Química Orgânica, Instituto de Química, Campus do Valonguinho, CEP 24020-150 Niterói, RJ, Brazil
| | - Patricia Zancan
- Laboratório de Enzimologia e Controle do Metabolismo (LabECoM), Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ CEP 21941-902, Brazil.
| | - Vitor F Ferreira
- Universidade Federal Fluminense, Faculdade de Farmácia, Departamento de Tecnologia Farmacêutica, CEP 24241-000 Niterói, RJ, Brazil.
| | - Fernando de C da Silva
- Universidade Federal Fluminense, Departamento de Química Orgânica, Instituto de Química, Campus do Valonguinho, CEP 24020-150 Niterói, RJ, Brazil.
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23
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Czestkowski W, Krzemiński Ł, Piotrowicz MC, Mazur M, Pluta E, Andryianau G, Koralewski R, Matyszewski K, Olejniczak S, Kowalski M, Lisiecka K, Kozieł R, Piwowar K, Papiernik D, Nowotny M, Napiórkowska-Gromadzka A, Nowak E, Niedziałek D, Wieczorek G, Siwińska A, Rejczak T, Jędrzejczak K, Mulewski K, Olczak J, Zasłona Z, Gołębiowski A, Drzewicka K, Bartoszewicz A. Structure-Based Discovery of High-Affinity Small Molecule Ligands and Development of Tool Probes to Study the Role of Chitinase-3-Like Protein 1. J Med Chem 2024; 67:3959-3985. [PMID: 38427954 DOI: 10.1021/acs.jmedchem.3c02255] [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: 03/03/2024]
Abstract
Chitinase-3-like-1 (CHI3L1), also known as YKL-40, is a glycoprotein linked to inflammation, fibrosis, and cancer. This study explored CHI3L1's interactions with various oligosaccharides using microscale thermophoresis (MST) and AlphaScreen (AS). These investigations guided the development of high-throughput screening assays to assess interference of small molecules in binding between CHI3L1 and biotinylated small molecules or heparan sulfate-based probes. Small molecule binders of YKL-40 were identified in our chitotriosidase inhibitors library with MST and confirmed through X-ray crystallography. Based on cocrystal structures of potent hit compounds with CHI3L1, small molecule probes 19 and 20 were designed for an AS assay. Structure-based optimization led to compounds 30 and 31 with nanomolar activities and drug-like properties. Additionally, an orthogonal AS assay using biotinylated heparan sulfate as a probe was developed. The compounds' affinity showed a significant correlation in both assays. These screening tools and compounds offer novel avenues for investigating the role of CHI3L1.
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Affiliation(s)
| | | | | | - Marzena Mazur
- Molecure S.A., Żwirki I Wigury 101, Warsaw 02-089, Poland
| | - Elżbieta Pluta
- Molecure S.A., Żwirki I Wigury 101, Warsaw 02-089, Poland
| | | | | | | | | | | | | | - Rafał Kozieł
- Molecure S.A., Żwirki I Wigury 101, Warsaw 02-089, Poland
| | | | | | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology in Warsaw, Ks. Trojdena 4, Warsaw 02-109, Poland
| | - Agnieszka Napiórkowska-Gromadzka
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology in Warsaw, Ks. Trojdena 4, Warsaw 02-109, Poland
| | - Elżbieta Nowak
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology in Warsaw, Ks. Trojdena 4, Warsaw 02-109, Poland
| | | | | | - Anna Siwińska
- Molecure S.A., Żwirki I Wigury 101, Warsaw 02-089, Poland
| | - Tomasz Rejczak
- Molecure S.A., Żwirki I Wigury 101, Warsaw 02-089, Poland
| | | | | | - Jacek Olczak
- Molecure S.A., Żwirki I Wigury 101, Warsaw 02-089, Poland
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24
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Dorel R, Sun D, Carruthers N, Castanedo GM, Ung PMU, Factor DC, Li T, Baumann H, Janota D, Pang J, Salphati L, Meklemburg R, Korman AJ, Harper HE, Stubblefield S, Payandeh J, McHugh D, Lang BT, Tesar PJ, Dere E, Masureel M, Adams DJ, Volgraf M, Braun MG. Discovery and Optimization of Selective Brain-Penetrant EBP Inhibitors that Enhance Oligodendrocyte Formation. J Med Chem 2024. [PMID: 38470227 DOI: 10.1021/acs.jmedchem.3c02396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
The inhibition of emopamil binding protein (EBP), a sterol isomerase within the cholesterol biosynthesis pathway, promotes oligodendrocyte formation, which has been proposed as a potential therapeutic approach for treating multiple sclerosis. Herein, we describe the discovery and optimization of brain-penetrant, orally bioavailable inhibitors of EBP. A structure-based drug design approach from literature compound 1 led to the discovery of a hydantoin-based scaffold, which provided balanced physicochemical properties and potency and an improved in vitro safety profile. The long half-lives of early hydantoin-based EBP inhibitors in rodents prompted an unconventional optimization strategy, focused on increasing metabolic turnover while maintaining potency and a brain-penetrant profile. The resulting EBP inhibitor 11 demonstrated strong in vivo target engagement in the brain, as illustrated by the accumulation of EBP substrate zymostenol after repeated dosing. Furthermore, compound 11 enhanced the formation of oligodendrocytes in human cortical organoids, providing additional support for our therapeutic hypothesis.
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Affiliation(s)
- Ruth Dorel
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Dawei Sun
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Nicholas Carruthers
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | | | - Peter M-U Ung
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Daniel C Factor
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Tianbo Li
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Hannah Baumann
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Danielle Janota
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Jodie Pang
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Laurent Salphati
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Robert Meklemburg
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Allison J Korman
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Halie E Harper
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | | | - Jian Payandeh
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Daniel McHugh
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Bradley T Lang
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Paul J Tesar
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Edward Dere
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Matthieu Masureel
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Drew J Adams
- Convelo Therapeutics, 11000 Cedar Avenue, Cleveland, Ohio 44106, United States
| | - Matthew Volgraf
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
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25
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Jamrozik E, Śmieja M, Podlewska S. ADMET-PrInt: Evaluation of ADMET Properties: Prediction and Interpretation. J Chem Inf Model 2024; 64:1425-1432. [PMID: 38373602 DOI: 10.1021/acs.jcim.3c02038] [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: 02/21/2024]
Abstract
Great progress in the development of computational strategies for drug design applications has revolutionized the process of searching for new drugs. Although the focus of in silico strategies is still put on the provision of the desired activity of a compound to the considered target, characterization of a compound in terms of its physicochemical and ADMET properties becomes an indispensable element of computer-aided drug design protocols. In the study, an online application ADMET-PrInt for in silico assessment of selected compound features: cardiotoxicity, solubility, genotoxicity, membrane permeability, and plasma protein binding was prepared. In addition to the prediction of particular property, ADMET-PrInt enables also the identification of compound features influencing this property thanks to the application of two explainability approaches: local interpretabile model-agnostic explanations and counterfactual analysis. It is an important factor for medicinal chemists, as it greatly facilitates the process of optimization of the compound structure in terms of the evaluated properties. The intuitive webpage, available at admet.if-pan.krakow.pl, allows making use of all predictive and interpretability models also by nonexperts and nonprogrammers.
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Affiliation(s)
- Ewelina Jamrozik
- Faculty of Mathematics and Computer Science, Jagiellonian University, Łojasiewicza 6, 30-348 Kraków, Poland
| | - Marek Śmieja
- Faculty of Mathematics and Computer Science, Jagiellonian University, Łojasiewicza 6, 30-348 Kraków, Poland
| | - Sabina Podlewska
- Maj Institute of Pharmacology, Polish Academy of Sciences, Smętna 12, 31-343 Kraków, Poland
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26
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Arcangeli A, Iorio J, Duranti C. Targeting the hERG1 and β1 integrin complex for cancer treatment. Expert Opin Ther Targets 2024; 28:145-157. [PMID: 38372580 DOI: 10.1080/14728222.2024.2318449] [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: 10/02/2023] [Accepted: 02/09/2024] [Indexed: 02/20/2024]
Abstract
INTRODUCTION Despite great advances, novel therapeutic targets and strategies are still needed, in particular for some carcinomas in the metastatic stage (breast cancer, colorectal cancer, pancreatic ductal adenocarcinoma and the clear cell renal carcinoma). Ion channels may be considered good cancer biomarkers and targets for antineoplastic therapy. These concepts are particularly relevant considering the hERG1 potassium channel as a novel target for antineoplastic therapy. AREAS COVERED A great deal of evidence demonstrates that hERG1 is aberrantly expressed in human cancers, in particular in aggressive carcinomas. A relevant cornerstone was the discovery that, in cancer cells, the channel is present in a very peculiar conformation, strictly bound to the β1 subunit of integrin receptors. The hERG1/β1 integrin complex does not occur in the heart. Starting from this evidence, we developed a novel single chain bispecific antibody (scDb-hERG1-β1), which specifically targets the hERG1/β1 integrin complex and exerts antineoplastic effects in preclinical experiments. EXPERT OPINION Since hERG1 blockade cannot be pursued for antineoplastic therapy due to the severe cardiac toxic effects (ventricular arrhythmias) that many hERG1 blockers exert, different strategies must be identified to specifically target hERG1 in cancer. The targeting of the hERG1/β1 integrin complex through the bispecific antibody scDb-hERG1-β1 can overcome such hindrances.
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Affiliation(s)
- Annarosa Arcangeli
- Department of Experimental and Clinical Medicine, Section of Internal Medicine, University of Florence, Firenze, Italy
- CSDC (Center for the Study of complex dynamics), University of Florence, Sesto Fiorentino (FI), Italy
- MCK Therapeutics srl, Pistoia (PT), Italy
| | - Jessica Iorio
- Department of Experimental and Clinical Medicine, Section of Internal Medicine, University of Florence, Firenze, Italy
| | - Claudia Duranti
- Department of Experimental and Clinical Medicine, Section of Internal Medicine, University of Florence, Firenze, Italy
- MCK Therapeutics srl, Pistoia (PT), Italy
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27
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Seal S, Spjuth O, Hosseini-Gerami L, García-Ortegón M, Singh S, Bender A, Carpenter AE. Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank. J Chem Inf Model 2024; 64:1172-1186. [PMID: 38300851 PMCID: PMC10900289 DOI: 10.1021/acs.jcim.3c01834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 02/03/2024]
Abstract
Drug-induced cardiotoxicity (DICT) is a major concern in drug development, accounting for 10-14% of postmarket withdrawals. In this study, we explored the capabilities of chemical and biological data to predict cardiotoxicity, using the recently released DICTrank data set from the United States FDA. We found that such data, including protein targets, especially those related to ion channels (e.g., hERG), physicochemical properties (e.g., electrotopological state), and peak concentration in plasma offer strong predictive ability for DICT. Compounds annotated with mechanisms of action such as cyclooxygenase inhibition could distinguish between most-concern and no-concern DICT. Cell Painting features for ER stress discerned most-concern cardiotoxic from nontoxic compounds. Models based on physicochemical properties provided substantial predictive accuracy (AUCPR = 0.93). With the availability of omics data in the future, using biological data promises enhanced predictability and deeper mechanistic insights, paving the way for safer drug development. All models from this study are available at https://broad.io/DICTrank_Predictor.
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Affiliation(s)
- Srijit Seal
- Imaging
Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Ola Spjuth
- Department
of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Box
591, SE-75124 Uppsala, Sweden
| | - Layla Hosseini-Gerami
- Ignota
Labs, The Bradfield Centre, Cambridge Science Park, County Hall, Westminster Bridge Road, Cambridge CB4 0GA, U.K.
| | - Miguel García-Ortegón
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Shantanu Singh
- Imaging
Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Andreas Bender
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Anne E. Carpenter
- Imaging
Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
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28
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Manelfi C, Tazzari V, Lunghini F, Cerchia C, Fava A, Pedretti A, Stouten PFW, Vistoli G, Beccari AR. "DompeKeys": a set of novel substructure-based descriptors for efficient chemical space mapping, development and structural interpretation of machine learning models, and indexing of large databases. J Cheminform 2024; 16:21. [PMID: 38395961 PMCID: PMC10893756 DOI: 10.1186/s13321-024-00813-4] [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: 10/17/2023] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
The conversion of chemical structures into computer-readable descriptors, able to capture key structural aspects, is of pivotal importance in the field of cheminformatics and computer-aided drug design. Molecular fingerprints represent a widely employed class of descriptors; however, their generation process is time-consuming for large databases and is susceptible to bias. Therefore, descriptors able to accurately detect predefined structural fragments and devoid of lengthy generation procedures would be highly desirable. To meet additional needs, such descriptors should also be interpretable by medicinal chemists, and suitable for indexing databases with trillions of compounds. To this end, we developed-as integral part of EXSCALATE, Dompé's end-to-end drug discovery platform-the DompeKeys (DK), a new substructure-based descriptor set, which encodes the chemical features that characterize compounds of pharmaceutical interest. DK represent an exhaustive collection of curated SMARTS strings, defining chemical features at different levels of complexity, from specific functional groups and structural patterns to simpler pharmacophoric points, corresponding to a network of hierarchically interconnected substructures. Because of their extended and hierarchical structure, DK can be used, with good performance, in different kinds of applications. In particular, we demonstrate how they are very well suited for effective mapping of chemical space, as well as substructure search and virtual screening. Notably, the incorporation of DK yields highly performing machine learning models for the prediction of both compounds' activity and metabolic reaction occurrence. The protocol to generate the DK is freely available at https://dompekeys.exscalate.eu and is fully integrated with the Molecular Anatomy protocol for the generation and analysis of hierarchically interconnected molecular scaffolds and frameworks, thus providing a comprehensive and flexible tool for drug design applications.
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Affiliation(s)
- Candida Manelfi
- EXSCALATE, Dompé Farmaceutici SpA, Via Tommaso de Amicis 95, 80123, Napoli, Italy
| | - Valerio Tazzari
- EXSCALATE, Dompé Farmaceutici SpA, Via Tommaso de Amicis 95, 80123, Napoli, Italy
| | - Filippo Lunghini
- EXSCALATE, Dompé Farmaceutici SpA, Via Tommaso de Amicis 95, 80123, Napoli, Italy
| | - Carmen Cerchia
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131, Napoli, Italy
| | - Anna Fava
- EXSCALATE, Dompé Farmaceutici SpA, Via Tommaso de Amicis 95, 80123, Napoli, Italy
| | - Alessandro Pedretti
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli, 25, 20133, Milano, Italy
| | - Pieter F W Stouten
- EXSCALATE, Dompé Farmaceutici SpA, Via Tommaso de Amicis 95, 80123, Napoli, Italy
- Stouten Pharma Consultancy BV, Kempenarestraat 47, 2860, Sint-Katelijne-Waver, Belgium
| | - Giulio Vistoli
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli, 25, 20133, Milano, Italy
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29
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Betzemeier B, Braun C, Sieger P, Heckel A, Linz G, Linehan B, Veser T, Wiedenmayer D, Kley JT. Discovery and development of BI 1265162, an ENaC inhibitor for the treatment of cystic fibrosis. Eur J Med Chem 2024; 265:116038. [PMID: 38157597 DOI: 10.1016/j.ejmech.2023.116038] [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: 10/20/2023] [Revised: 12/01/2023] [Accepted: 12/08/2023] [Indexed: 01/03/2024]
Abstract
Lung selective inhibition of the endothelial sodium channel (ENaC) is a potential mutation agnostic treatment of Cystic Fibrosis (CF). We describe the discovery and development of BI 1265162, the first ENaC inhibitor devoid of the amiloride structural motif that entered clinical trials. The design of BI 1265162 focused on its suitability for inhalation via the Respimat® Soft Mist™ Inhaler and a long duration of action. A convergent and scalable route for the synthesis of BI 1265162 as dihydrogen phosphate salt is presented, that was applied to support clinical trials. A phase 2 study with BI 1265162 did not provide a clear sign of clinical benefit. Whether ENaC inhibition will be able to hold its promise for CF patients remains an open question.
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Affiliation(s)
- Bodo Betzemeier
- Boehringer Ingelheim Pharma GmbH & Co. KG, Chemical Development Germany, Birkendorfer Straße 65, 88397, Biberach an der Riß, Germany
| | - Clemens Braun
- Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences Germany, Birkendorfer Straße 65, 88397, Biberach an der Riß, Germany
| | - Peter Sieger
- Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences Germany, Birkendorfer Straße 65, 88397, Biberach an der Riß, Germany
| | - Armin Heckel
- Boehringer Ingelheim Pharma GmbH & Co. KG, Medicinal Chemistry Germany, Birkendorfer Straße 65, 88397, Biberach an der Riß, Germany
| | - Günter Linz
- Boehringer Ingelheim Pharma GmbH & Co. KG, Chemical Development Germany, Birkendorfer Straße 65, 88397, Biberach an der Riß, Germany
| | - Brian Linehan
- Material & Analytical Sciences, Boehringer-Ingelheim, Ridgefield, 06877, Connecticut, USA
| | - Thomas Veser
- Boehringer Ingelheim Pharma GmbH & Co. KG, Medicinal Chemistry Germany, Birkendorfer Straße 65, 88397, Biberach an der Riß, Germany
| | - Dieter Wiedenmayer
- Boehringer Ingelheim Pharma GmbH & Co. KG, Medicinal Chemistry Germany, Birkendorfer Straße 65, 88397, Biberach an der Riß, Germany
| | - Jörg T Kley
- Boehringer Ingelheim Pharma GmbH & Co. KG, Medicinal Chemistry Germany, Birkendorfer Straße 65, 88397, Biberach an der Riß, Germany.
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30
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Wiley AM, Yang J, Madhani R, Nath A, Totah RA. Investigating the association between CYP2J2 inhibitors and QT prolongation: a literature review. Drug Metab Rev 2024; 56:145-163. [PMID: 38478383 DOI: 10.1080/03602532.2024.2329928] [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: 12/22/2023] [Accepted: 03/06/2024] [Indexed: 03/21/2024]
Abstract
Drug withdrawal post-marketing due to cardiotoxicity is a major concern for drug developers, regulatory agencies, and patients. One common mechanism of cardiotoxicity is through inhibition of cardiac ion channels, leading to prolongation of the QT interval and sometimes fatal arrythmias. Recently, oxylipin signaling compounds have been shown to bind to and alter ion channel function, and disruption in their cardiac levels may contribute to QT prolongation. Cytochrome P450 2J2 (CYP2J2) is the predominant CYP isoform expressed in cardiomyocytes, where it oxidizes arachidonic acid to cardioprotective epoxyeicosatrienoic acids (EETs). In addition to roles in vasodilation and angiogenesis, EETs bind to and activate various ion channels. CYP2J2 inhibition can lower EET levels and decrease their ability to preserve cardiac rhythm. In this review, we investigated the ability of known CYP inhibitors to cause QT prolongation using Certara's Drug Interaction Database. We discovered that among the multiple CYP isozymes, CYP2J2 inhibitors were more likely to also be QT-prolonging drugs (by approximately 2-fold). We explored potential binding interactions between these inhibitors and CYP2J2 using molecular docking and identified four amino acid residues (Phe61, Ala223, Asn231, and Leu402) predicted to interact with QT-prolonging drugs. The four residues are located near the opening of egress channel 2, highlighting the potential importance of this channel in CYP2J2 binding and inhibition. These findings suggest that if a drug inhibits CYP2J2 and interacts with one of these four residues, then it may have a higher risk of QT prolongation and more preclinical studies are warranted to assess cardiovascular safety.
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Affiliation(s)
- Alexandra M Wiley
- Department of Medicinal Chemistry, University of WA School of Pharmacy, Seattle, WA, USA
| | - Jade Yang
- Department of Medicinal Chemistry, University of WA School of Pharmacy, Seattle, WA, USA
| | - Rivcka Madhani
- Department of Medicinal Chemistry, University of WA School of Pharmacy, Seattle, WA, USA
| | - Abhinav Nath
- Department of Medicinal Chemistry, University of WA School of Pharmacy, Seattle, WA, USA
| | - Rheem A Totah
- Department of Medicinal Chemistry, University of WA School of Pharmacy, Seattle, WA, USA
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31
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Jiang W, Hou Q, Xu H, Yang K, Wang X, Zhang K, Zeng Y, Li W, Wang B, Luo G, Zhao X, Shen H, Xu Y, Wu X. Discovery of Novel Phenoxyaryl Pyridones as Bromodomain and Extra-Terminal Domain (BET) Inhibitors with High Selectivity for the Second Bromodomain (BD2) to Potentially Treat Acute Myeloid Leukemia. J Med Chem 2024; 67:1513-1532. [PMID: 38175809 DOI: 10.1021/acs.jmedchem.3c02104] [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: 01/06/2024]
Abstract
Bromodomain-selective BET inhibition has emerged as a promising strategy to improve the safety profiles of pan-BET inhibitors. Herein, we report the discovery of potent phenoxyaryl pyridones as highly BD2-selective BET inhibitors. Compound 23 (IC50 = 2.9 nM) exhibited a comparable BRD4 BD2 inhibitory activity relative to 10 (IC50 = 1.0 nM) and remarkably improved selectivity over BRD4 BD1 (23: 2583-fold; 10: 344-fold). This lead compound significantly inhibited the proliferation of acute myeloid leukemia (AML) cell lines through induction of G0/G1 arrest and apoptosis in vitro. Excellent in vivo antitumor efficacy with 23 was achieved in an MV;411 mouse xenograft model. Pleasingly, compound 23 (hERG IC50 > 30 μM) mitigated the inhibition of the human ether-à-go-go-related gene (hERG) ion channel compared with 10 (hERG IC50 = 2.8 μM). This work provides a promising BD2-selective lead for the development of more effective and safe BET inhibitors as anticancer agents.
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Affiliation(s)
- Wenhua Jiang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Qiangqiang Hou
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Hongrui Xu
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Kexin Yang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Xiaohui Wang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Kuojun Zhang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Yi Zeng
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Wenqiang Li
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Bingrui Wang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Guangmei Luo
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
| | - Xiaofan Zhao
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Hui Shen
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Yong Xu
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, 510530, China
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Xiaoxing Wu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing 211198, China
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32
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Jiang G, Zhang B, Zhang X, Chen F, Qin W, Chen JL, Tian S, Shui W, Ye N. Identification of Spiro[chromene-2,4'-piperidine]s as Potent, Selective, and G q-Biased 5-HT 2C Receptor Partial Agonists. ACS Med Chem Lett 2024; 15:99-106. [PMID: 38229745 PMCID: PMC10788947 DOI: 10.1021/acsmedchemlett.3c00454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/10/2023] [Accepted: 12/13/2023] [Indexed: 01/18/2024] Open
Abstract
A series of spiropiperidines was designed and synthesized by structural modifications based on our previous lead compound 1 and evaluated with cellular signaling assays for the discovery of 5-HT2C receptor (5-HT2CR) selective agonists with a Gq bias. Structure-activity relationship (SAR) studies of spiropiperidines uncovered spiro[chromene-2,4'-piperidine]s as a novel chemotype of 5-HT2CR selective agonists. Among this new series, the 7-chloro analogue 8 was identified as the most potent and selective 5-HT2CR partial agonist (Emax = 71.09%) with an EC50 value of 121.5 nM and no observed activity toward 5-HT2AR or 5-HT2BR. Moreover, compound 8 exhibited no recruitment activity for β-arrestin and showed low inhibition of hERG at 10 μM. These findings may pave the way to develop more potent Gq-biased 5-HT2CR partial agonists as useful pharmacological tool compounds or potential drug candidates.
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Affiliation(s)
- Guangqian Jiang
- Jiangsu
Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical
Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Bingjie Zhang
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai, 201210, China
| | - Xiaoya Zhang
- Jiangsu
Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical
Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Fan Chen
- Jiangsu
Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical
Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Wangzhi Qin
- Jiangsu
Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical
Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Jing-Lei Chen
- Jiangsu
Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical
Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Sheng Tian
- Jiangsu
Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical
Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Wenqing Shui
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai, 201210, China
| | - Na Ye
- Jiangsu
Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical
Sciences, Soochow University, Suzhou, Jiangsu 215123, China
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33
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Kawsar SMA, Munia NS, Saha S, Ozeki Y. In Silico Pharmacokinetics, Molecular Docking and Molecular Dynamics Simulation Studies of Nucleoside Analogs for Drug Discovery- A Mini Review. Mini Rev Med Chem 2024; 24:1070-1088. [PMID: 37957918 DOI: 10.2174/0113895575258033231024073521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 08/26/2023] [Accepted: 09/22/2023] [Indexed: 11/15/2023]
Abstract
Nucleoside analogs have been widely used as antiviral, antitumor, and antiparasitic agents due to their ability to inhibit nucleic acid synthesis. Adenosine, cytidine, guanosine, thymidine and uridine analogs such as didanosine, vidarabine, remdesivir, gemcitabine, lamivudine, acyclovir, abacavir, zidovusine, stavudine, and idoxuridine showed remarkable anticancer and antiviral activities. In our previously published articles, our main intention was to develop newer generation nucleoside analogs with acylation-induced modification of the hydroxyl group and showcase their biological potencies. In the process of developing nucleoside analogs, in silico studies play an important role and provide a scientific background for biological data. Molecular interactions between drugs and receptors followed by assessment of their stability in physiological environments, help to optimize the drug development process and minimize the burden of unwanted synthesis. Computational approaches, such as DFT, FMO, MEP, ADMET prediction, PASS prediction, POM analysis, molecular docking, and molecular dynamics simulation, are the most popular tools to culminate all preclinical study data and deliver a molecule with maximum bioactivity and minimum toxicity. Although clinical drug trials are crucial for providing dosage recommendations, they can only indirectly provide mechanistic information through researchers for pathological, physiological, and pharmacological determinants. As a result, in silico approaches are increasingly used in drug discovery and development to provide mechanistic information of clinical value. This article portrays the current status of these methods and highlights some remarkable contributions to the development of nucleoside analogs with optimized bioactivity.
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Affiliation(s)
- Sarkar M A Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Nasrin S Munia
- Laboratory of Carbohydrate and Nucleoside Chemistry (LCNC), Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Supriyo Saha
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Premnagar, 248007, Dehradun, Uttarakhand, 248007, India
| | - Yasuhiro Ozeki
- School of Sciences, Yokohama City University, 22-2, Seto, Kanazawa-ku, Yokohama, 236-0027, Japan
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34
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Miller JL, Damodaran K, Floreancig PE. Nitrogen Heterocycle Synthesis through Hydride Abstraction of Acyclic Carbamates and Related Species: Scope, Mechanism, Stereoselectivity, and Product Conformation Studies. Chemistry 2023; 29:e202302977. [PMID: 37796745 DOI: 10.1002/chem.202302977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 10/07/2023]
Abstract
Acyliminium ions and related species are potent electrophiles that can be quite valuable in the synthesis of nitrogen-containing molecules. This manuscript describes a protocol to form these intermediates through hydride abstractions of easily accessible allylic carbamates, amides, and sulfonamides that avoids the reversibility that is possible in classical condensation-based routes. These intermediates are used in the preparation of a range of nitrogen-containing heterocycles, and in many cases high levels of stereocontrol are observed. Specifically areas of investigation include the impact of chemical structure on oxidation efficiency, the geometry of the intermediate iminium ions, the impact of a substrate stereocenter on stereocontrol, and an examination of transition state geometry.
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Affiliation(s)
- Jenna L Miller
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Krishnan Damodaran
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Paul E Floreancig
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
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35
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Sun L, Nie P, Luan L, Herdewijn P, Wang YT. Synthetic approaches and application of clinically approved small-molecule Anti-HIV drugs: An update. Eur J Med Chem 2023; 261:115847. [PMID: 37801826 DOI: 10.1016/j.ejmech.2023.115847] [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: 09/01/2023] [Revised: 09/18/2023] [Accepted: 09/29/2023] [Indexed: 10/08/2023]
Abstract
Application of chemotherapeutic agents to inhibit the HIV replication process has brought about a significant metamorphosis in the landscape of AIDS. Substantial declines in morbidity and mortality rates have been attained, accompanied by notable decreases in healthcare resource utilization. However, treatment modalities do not uniformly inhibit HIV replication in every patient, while the emergence of drug-resistant viral strains poses a substantial obstacle to subsequent therapeutic interventions. Furthermore, chronic administration of therapy may lead to the manifestation of toxicities. These challenges necessitate the exploration of novel pharmacological agents and innovative therapeutic approaches aimed at effectively managing the persistent viral replication characteristic of chronic infection. This review examines the role of clinically approved small-molecule drugs in the treatment of HIV/AIDS, which provides an in-depth analysis of the major classes of small-molecule drugs, including nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs), protease inhibitors (PIs), integrase inhibitors, entry inhibitors, and pharmacokinetic enhancers. The review mainly discusses the application, synthetic routes, and mechanisms of action of small-molecule drugs employed in the treatment of HIV, as well as their use in combination with antiretroviral therapy, presenting viewpoints on forthcoming avenues in the development of novel anti-HIV drugs.
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Affiliation(s)
- Lu Sun
- Zhongshan Hospital Affiliated to Dalian University, Dalian, 116001, China
| | - Peng Nie
- Medicinal Chemistry, Rega Institute of Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Li Luan
- Zhongshan Hospital Affiliated to Dalian University, Dalian, 116001, China.
| | - Piet Herdewijn
- Medicinal Chemistry, Rega Institute of Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
| | - Ya-Tao Wang
- First People's Hospital of Shangqiu, Henan Province, Shangqiu, 476100, China; Medicinal Chemistry, Rega Institute of Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
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Zhao LM, Pannecouque C, Clercq ED, Wang S, Chen FE. Structure-based design of novel heterocycle-substituted ATDP analogs as non-nucleoside reverse transcriptase inhibitors with improved selectivity and solubility. Acta Pharm Sin B 2023; 13:4906-4917. [PMID: 38045058 PMCID: PMC10692386 DOI: 10.1016/j.apsb.2023.07.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/10/2023] [Accepted: 07/11/2023] [Indexed: 12/05/2023] Open
Abstract
Following on our recently developed biphenyl-ATDP non-nucleoside reverse transcriptase inhibitor ZLM-66 (SI = 2019.80, S = 1.9 μg/mL), a series of novel heterocycle-substituted ATDP derivatives with significantly improved selectivity and solubility were identified by replacement of the biphenyl moiety of ZLM-66 with heterocyclic group with lower lipophilicity. Evidently, the representative analog 7w in this series exhibited dramatically enhanced selectivity and solubility (SI = 12,497.73, S = 4472 μg/mL) in comparison with ZLM-66 (SI = 2019.80, S = 1.9 μg/mL). This new NNRTI conferred low nanomolar inhibition of wild-type HIV-1 strain and tested mutant strains (K103N, L100I, Y181C, E138K, and K103N + Y181C). The analog also demonstrated favorable safety and pharmacokinetic profiles, as evidenced by its insensitivity to CYP and hERG, lack of mortality and pathological damage, and good oral bioavailability in rats (F = 27.1%). Further development of 7w for HIV therapy will be facilitated by this valuable information.
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Affiliation(s)
- Li-Min Zhao
- Key Laboratory of Natural Resources of Changbai Mountain & Functional Molecules, Ministry of Education, Yanbian University College of Pharmacy, Yanbian University, Yanji 133002, China
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China
- Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai 200433, China
| | | | - Erik De Clercq
- Rega Institute for Medical Research, KU Leuven, Leuven B-3000, Belgium
| | - Shuai Wang
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China
- Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai 200433, China
| | - Fen-Er Chen
- Key Laboratory of Natural Resources of Changbai Mountain & Functional Molecules, Ministry of Education, Yanbian University College of Pharmacy, Yanbian University, Yanji 133002, China
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai 200433, China
- Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai 200433, China
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Pitsillou E, Beh RC, Liang JJ, Tang TS, Zhou X, Siow YY, Ma Y, Hu Z, Wu Z, Hung A, Karagiannis TC. EpiMed Coronabank Chemical Collection: Compound selection, ADMET analysis, and utilisation in the context of potential SARS-CoV-2 antivirals. J Mol Graph Model 2023; 125:108602. [PMID: 37597309 DOI: 10.1016/j.jmgm.2023.108602] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/08/2023] [Accepted: 08/13/2023] [Indexed: 08/21/2023]
Abstract
Antiviral drugs are important for the coronavirus disease 2019 (COVID-19) response, as vaccines and antibodies may have reduced efficacy against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. Antiviral drugs that have been made available for use, albeit with questionable efficacy, include remdesivir (Veklury®), nirmatrelvir-ritonavir (Paxlovid™), and molnupiravir (Lagevrio®). To expand the options available for COVID-19 and prepare for future pandemics, there is a need to investigate new uses for existing drugs and design novel compounds. To support these efforts, we have created a comprehensive library of 750 molecules that have been sourced from in vitro, in vivo, and in silico studies. It is publicly available at our dedicated website (https://epimedlab.org/crl/). The EpiMed Coronabank Chemical Collection consists of compounds that have been divided into 10 main classes based on antiviral properties, as well as the potential to be used for the management, prevention, or treatment of COVID-19 related complications. A detailed description of each compound is provided, along with the molecular formula, canonical SMILES, and U.S. Food and Drug Administration approval status. The chemical structures have been obtained and are available for download. Moreover, the pharmacokinetic properties of the ligands have been characterised. To demonstrate an application of the EpiMed Coronabank Chemical Collection, molecular docking was used to evaluate the binding characteristics of ligands against SARS-CoV-2 nonstructural and accessory proteins. Overall, our database can be used to aid the drug repositioning process, and for gaining further insight into the molecular mechanisms of action of potential compounds of interest.
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Affiliation(s)
- Eleni Pitsillou
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia; School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Raymond C Beh
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia; School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Julia J Liang
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia; School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Thinh Sieu Tang
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Xun Zhou
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ya Yun Siow
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Yinghao Ma
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Zifang Hu
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Zifei Wu
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Andrew Hung
- School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Tom C Karagiannis
- Epigenomic Medicine Laboratory at prospED, Carlton, VIC, 3053, Australia; Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia.
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38
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Buchanan D, Pham AM, Singh SK, Panda SS. Molecular Hybridization of Alkaloids Using 1,2,3-Triazole-Based Click Chemistry. Molecules 2023; 28:7593. [PMID: 38005315 PMCID: PMC10674395 DOI: 10.3390/molecules28227593] [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: 09/30/2023] [Revised: 10/30/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Alkaloids found in multiple species, known as 'driver species', are more likely to be included in early-stage drug development due to their high biodiversity compared to rare alkaloids. Many synthetic approaches have been employed to hybridize the natural alkaloids in drug development. Click chemistry is a highly efficient and versatile reaction targeting specific areas, making it a valuable tool for creating complex natural products and diverse molecular structures. It has been used to create hybrid alkaloids that address their limitations and serve as potential drugs that mimic natural products. In this review, we highlight the recent advancements made in modifying alkaloids using click chemistry and their potential medicinal applications. We discuss the significance, current trends, and prospects of click chemistry in natural product-based medicine. Furthermore, we have employed computational methods to evaluate the ADMET properties and drug-like qualities of hybrid molecules.
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Affiliation(s)
- Devan Buchanan
- Department of Chemistry and Biochemistry, Augusta University, Augusta, GA 30912, USA; (D.B.); (A.M.P.)
| | - Ashley M. Pham
- Department of Chemistry and Biochemistry, Augusta University, Augusta, GA 30912, USA; (D.B.); (A.M.P.)
| | - Sandeep K. Singh
- Jindal Global Business School, OP Jindal Global University, Sonipat 131001, India;
| | - Siva S. Panda
- Department of Chemistry and Biochemistry, Augusta University, Augusta, GA 30912, USA; (D.B.); (A.M.P.)
- Department Biochemistry and Molecular Biology, Augusta University Augusta, GA 30912, USA
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Kattar SD, Gulati A, Margrey KA, Keylor MH, Ardolino M, Yan X, Johnson R, Palte RL, McMinn SE, Nogle L, Su J, Xiao D, Piesvaux J, Lee S, Hegde LG, Woodhouse JD, Faltus R, Moy LY, Xiong T, Ciaccio PJ, Pearson K, Patel M, Otte KM, Leyns CEG, Kennedy ME, Bennett DJ, DiMauro EF, Fell MJ, Fuller PH. Discovery of MK-1468: A Potent, Kinome-Selective, Brain-Penetrant Amidoisoquinoline LRRK2 Inhibitor for the Potential Treatment of Parkinson's Disease. J Med Chem 2023; 66:14912-14927. [PMID: 37861679 DOI: 10.1021/acs.jmedchem.3c01486] [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: 10/21/2023]
Abstract
Genetic mutation of the leucine-rich repeat kinase 2 (LRRK2) protein has been associated with Parkinson's disease (PD), a disabling and progressive neurodegenerative disorder that is devoid of efficacious disease-modifying therapies. Herein, we describe the invention of an amidoisoquinoline (IQ)-derived LRRK2 inhibitor lead chemical series. Knowledge-, structure-, and property-based drug design in concert with rigorous application of in silico calculations and presynthesis predictions enabled the prioritization of molecules with favorable CNS "drug-like" physicochemical properties. This resulted in the discovery of compound 8, which was profiled extensively before human ether-a-go-go (hERG) ion channel inhibition halted its progression. Strategic reduction of lipophilicity and basicity resulted in attenuation of hERG ion channel inhibition while maintaining a favorable CNS efflux transporter profile. Further structure- and property-based optimizations resulted in the discovery of preclinical candidate MK-1468. This exquisitely selective LRRK2 inhibitor has a projected human dose of 48 mg BID and a preclinical safety profile that supported advancement toward GLP toxicology studies.
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Affiliation(s)
- Solomon D Kattar
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Anmol Gulati
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Kaila A Margrey
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Mitchell H Keylor
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Michael Ardolino
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Xin Yan
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Rebecca Johnson
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Rachel L Palte
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Spencer E McMinn
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Lisa Nogle
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Jing Su
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Dong Xiao
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Jennifer Piesvaux
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Susi Lee
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, New Jersey 07065, United States
| | - Laxminarayan G Hegde
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Janice D Woodhouse
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Robert Faltus
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Lily Y Moy
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Tina Xiong
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Paul J Ciaccio
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Kara Pearson
- Merck & Co., Inc., 770 Sumneytown Pike., West Point, Pennsylvania 19486, United States
| | - Mayankbhai Patel
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Karin M Otte
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Cheryl E G Leyns
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Matthew E Kennedy
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | | | - Erin F DiMauro
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Matthew J Fell
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Peter H Fuller
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
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40
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Huang C, Zeng R, Qiao J, Quan B, Luo R, Huang Q, Guo N, Li Y, Long X, Ma R, Xia A, Fang Z, Wang Y, Li Y, Zheng Y, Li L, Lei J, Yang S. Discovery and structure-activity relationship studies of novel α-ketoamide derivatives targeting the SARS-CoV-2 main protease. Eur J Med Chem 2023; 259:115657. [PMID: 37517202 DOI: 10.1016/j.ejmech.2023.115657] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 08/01/2023]
Abstract
The SARS-CoV-2 main protease (Mpro, also named 3CLpro) is a promising antiviral target against COVID-19 due to its functional importance in viral replication and transcription. Herein, we report the discovery of a series of α-ketoamide derivatives as a new class of SARS-CoV-2 Mpro inhibitors. Structure-activity relationship (SAR) of these compounds was analyzed, which led to the identification of a potent Mpro inhibitor (27h) with an IC50 value of 10.9 nM. The crystal structure of Mpro in complex with 27h revealed that α-ketoamide warhead covalently bound to Cys145s of the protease. In an in vitro antiviral assay, 27h showed excellent activity with an EC50 value of 43.6 nM, comparable to the positive control, Nirmatrelvir. This compound displayed high target specificity for Mpro against human proteases and low toxicity. It also possesses favorable pharmacokinetic properties. Overall, compound 27h could be a promising lead compound for drug discovery targeting SARS-CoV-2 Mpro and deserves further in-depth studies.
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Affiliation(s)
- Chong Huang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Rui Zeng
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Jingxin Qiao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Baoxue Quan
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Ronghua Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Qiao Huang
- Key Laboratory of Drug Targeting and Drug Delivery Systems, Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Nihong Guo
- Key Laboratory of Drug Targeting and Drug Delivery Systems, Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yueyue Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Xinyan Long
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Ronggang Ma
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Anjie Xia
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Zhen Fang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yifei Wang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yueshan Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yongtang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.
| | - Linli Li
- Key Laboratory of Drug Targeting and Drug Delivery Systems, Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Jian Lei
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China; National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Shengyong Yang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
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Yang W, Wang W, Cai S, Li P, Zhang D, Ning J, Ke J, Hou A, Chen L, Ma Y, Jin W. Synthesis and In Vivo Antiarrhythmic Activity Evaluation of Novel Scutellarein Analogues as Voltage-Gated Nav1.5 and Cav1.2 Channels Blockers. Molecules 2023; 28:7417. [PMID: 37959836 PMCID: PMC10650756 DOI: 10.3390/molecules28217417] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/21/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023] Open
Abstract
Malignant cardiac arrhythmias with high morbidity and mortality have posed a significant threat to our human health. Scutellarein, a metabolite of Scutellarin which is isolated from Scutellaria altissima L., presents excellent therapeutic effects on cardiovascular diseases and could further be metabolized into methylated forms. A series of 22 new scutellarein derivatives with hydroxyl-substitution based on the scutellarin metabolite in vivo was designed, synthesized via the conjugation of the scutellarein scaffold with pharmacophores of FDA-approved antiarrhythmic medications and evaluated for their antiarrhythmic activity through the analyzation of the rat number of arrhythmia recovery, corresponding to the recovery time and maintenance time in the rat model of barium chloride-induced arrhythmia, as well as the cumulative dosage of aconitine required to induce VP, VT, VF and CA in the rat model of aconitine-induced arrhythmia. All designed compounds could shorten the time of the arrhythmia continuum induced by barium chloride, indicating that 4'-hydroxy substituents of scutellarein had rapid-onset antiarrhythmic effects. In addition, nearly all of the compounds could normalize the HR, RR, QRS, QT and QTc interval, as well as the P/T waves' amplitude. The most promising compound 10e showed the best antiarrhythmic activity with long-term efficacy and extremely low cytotoxicity, better than the positive control scutellarein. This result was also approved by the computational docking simulation. Most importantly, patch clamp measurements on Nav1.5 and Cav1.2 channels indicated that compound 10e was able to reduce the INa and ICa in a concentration-dependent manner and left-shifted the inactivation curve of Nav1.5. Taken together, all compounds were considered to be antiarrhythmic. Compound 10e even showed no proarrhythmic effect and could be classified as Ib Vaughan Williams antiarrhythmic agents. What is more, compound 10e did not block the hERG potassium channel which highly associated with cardiotoxicity.
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Affiliation(s)
- Wei Yang
- Key Laboratory of External Drug Delivery System and Preparation Technology in Universities of Yunnan, Yunnan University of Chinese Medicine, Kunming 650500, China (D.Z.)
- Faculty of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming 650500, China
| | - Wenping Wang
- Key Laboratory of External Drug Delivery System and Preparation Technology in Universities of Yunnan, Yunnan University of Chinese Medicine, Kunming 650500, China (D.Z.)
- Faculty of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming 650500, China
| | - Song Cai
- Department of Anatomy and Histology, Shenzhen University Medical School, Shenzhen 518060, China
| | - Peng Li
- School of Food and Drug, Shenzhen Polytechnic, Shenzhen 518000, China
| | - Die Zhang
- Key Laboratory of External Drug Delivery System and Preparation Technology in Universities of Yunnan, Yunnan University of Chinese Medicine, Kunming 650500, China (D.Z.)
- Faculty of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming 650500, China
| | - Jinhua Ning
- Key Laboratory of External Drug Delivery System and Preparation Technology in Universities of Yunnan, Yunnan University of Chinese Medicine, Kunming 650500, China (D.Z.)
- Faculty of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming 650500, China
| | - Jin Ke
- Key Laboratory of External Drug Delivery System and Preparation Technology in Universities of Yunnan, Yunnan University of Chinese Medicine, Kunming 650500, China (D.Z.)
- Faculty of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming 650500, China
| | - Anguo Hou
- Key Laboratory of External Drug Delivery System and Preparation Technology in Universities of Yunnan, Yunnan University of Chinese Medicine, Kunming 650500, China (D.Z.)
- Faculty of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming 650500, China
| | - Linyun Chen
- Key Laboratory of External Drug Delivery System and Preparation Technology in Universities of Yunnan, Yunnan University of Chinese Medicine, Kunming 650500, China (D.Z.)
- Faculty of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming 650500, China
| | - Yunshu Ma
- Key Laboratory of External Drug Delivery System and Preparation Technology in Universities of Yunnan, Yunnan University of Chinese Medicine, Kunming 650500, China (D.Z.)
- Faculty of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming 650500, China
| | - Wenbin Jin
- Key Laboratory of External Drug Delivery System and Preparation Technology in Universities of Yunnan, Yunnan University of Chinese Medicine, Kunming 650500, China (D.Z.)
- Faculty of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming 650500, China
- State Key Laboratory of Chemical Biology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
- Drug Discovery and Department of Applied Biology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
- Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
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42
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Zhou RL, Pannecouque C, De Clercq E, Wang S, Chen FE. Development of novel HEPT analogs featuring significantly improved anti-resistance potency against HIV-1 through chemical space exploration of the tolerant region I. Bioorg Chem 2023; 140:106783. [PMID: 37595396 DOI: 10.1016/j.bioorg.2023.106783] [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: 06/22/2023] [Revised: 07/26/2023] [Accepted: 08/08/2023] [Indexed: 08/20/2023]
Abstract
Our recent great interest in developing 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine (HEPT) analogs for HIV therapy identified a potent non-nucleoside reverse transcriptase inhibitor (NNRTI) 3 (EC50 = 0.01681 μM), but its therapeutic efficacy was limited by its poor anti-resistance potency. This prompted us to search for potential HEPT analogs with broad-spectrum activities, leading to the generation of a series of novel HEPT analogs through exploring the chemical space of the solvent - protein interface. Encouraging improvements in anti-resistance efficacy were observed in some of these analogs, with the most promising compound 7 g being 3 to 26 - fold more potent than 3 against five mutant strains (E138K, Y181C, L100I, K103N, and Y188L). This analog surpassed the activity and selectivity of compound 3 by approximately 2-fold (EC50 = 0.007468 μM, SI = 4260). Furthermore, it was found to demonstrate feeble inhibition of CYP and hERG in vitro, and no in vivo acute toxicity. This study will further enrich the structure-activity relationships (SARs) of the HEPT scaffold, providing new guidance for the development of NNRTIs.
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Affiliation(s)
- Ruo-Lan Zhou
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of C∼hemistry, Fudan University, Shanghai 200433, China; Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai 200433, China; Institute of Pharmaceutical Science and Technology, Zhejiang University of Technology, Hangzhou 310014, China
| | | | - Erik De Clercq
- Rega Institute for Medical Research, KU Leuven, Herestraat 49, B-3000, Leuven, Belgium
| | - Shuai Wang
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of C∼hemistry, Fudan University, Shanghai 200433, China; Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai 200433, China.
| | - Fen-Er Chen
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of C∼hemistry, Fudan University, Shanghai 200433, China; Shanghai Engineering Center of Industrial Asymmetric Catalysis for Chiral Drugs, Shanghai 200433, China; Institute of Pharmaceutical Science and Technology, Zhejiang University of Technology, Hangzhou 310014, China.
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43
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Seal S, Spjuth O, Hosseini-Gerami L, García-Ortegón M, Singh S, Bender A, Carpenter AE. Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA DICTrank. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.15.562398. [PMID: 37905146 PMCID: PMC10614794 DOI: 10.1101/2023.10.15.562398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Drug-induced cardiotoxicity (DICT) is a major concern in drug development, accounting for 10-14% of postmarket withdrawals. In this study, we explored the capabilities of various chemical and biological data to predict cardiotoxicity, using the recently released Drug-Induced Cardiotoxicity Rank (DICTrank) dataset from the United States FDA. We analyzed a diverse set of data sources, including physicochemical properties, annotated mechanisms of action (MOA), Cell Painting, Gene Expression, and more, to identify indications of cardiotoxicity. We found that such data, including protein targets, especially those related to ion channels (such as hERG), physicochemical properties (such as electrotopological state) as well as peak concentration in plasma offer strong predictive ability as well as valuable insights into DICT. We also found compounds annotated with particular mechanisms of action, such as cyclooxygenase inhibition, could distinguish between most-concern and no-concern DICT compounds. Cell Painting features related to ER stress discern the most-concern cardiotoxic compounds from non-toxic compounds. While models based on physicochemical properties currently provide substantial predictive accuracy (AUCPR = 0.93), this study also underscores the potential benefits of incorporating more comprehensive biological data in future DICT predictive models. With the availability of - omics data in the future, using biological data promises enhanced predictability and delivers deeper mechanistic insights, paving the way for safer therapeutic drug development. All models and data used in this study are publicly released at https://broad.io/DICTrank_Predictor.
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Affiliation(s)
- Srijit Seal
- Imaging Platform, Broad Institute of MIT and Harvard, US
| | - Ola Spjuth
- Department of Pharmaceutical Biosciences, Uppsala University, Sweden
| | | | | | - Shantanu Singh
- Imaging Platform, Broad Institute of MIT and Harvard, US
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44
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Lobato-Tapia CA, Moreno-Hernández Y, Olivo-Vidal ZE. In Silico Studies of Four Compounds of Cecropia obtusifolia against Malaria Parasite. Molecules 2023; 28:6912. [PMID: 37836757 PMCID: PMC10574735 DOI: 10.3390/molecules28196912] [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: 08/10/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 10/15/2023] Open
Abstract
Malaria is a disease that affects many people in the world. In Mexico, malaria remains an active disease in certain regions, particularly in the states of Chiapas and Chihuahua. While antimalarial effects have been attributed to some species of Cecropia in various countries, no such studies have been conducted in Mexico. Therefore, the objective of this study was to evaluate the in silico antimalarial activity of some active compounds identified according to the literature in the species of Cecropia obtusifolia, belonging to the Cecropiaceae family, such as ursolic acid, α-amyrin, chrysin, and isoorientin. These compounds were evaluated with specific molecular docking and molecular dynamics (MD) studies using three different malarial targets with the PDB codes 1CET, 2BL9, and 4ZL4 as well as the prediction of their pharmacokinetic (Pk) properties. Docking analysis revealed the following best binding energies (kcal/mol): isoorientin-1CET (-9.1), isoorientin-2BL9 (-8.8), and chrysin-4ZL4 (-9.6). MD simulation validated the stability of the complexes. Pharmacokinetics analysis suggested that the compounds would generally perform well if administered. Therefore, these results suggest that these compounds may be used as potential drugs for the treatment of malaria.
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Affiliation(s)
- Carlos Alberto Lobato-Tapia
- Departamento de Ingeniería en Biotecnología, Universidad Politécnica Metropolitana de Puebla, Popocatépetl s/n, Reserva Territorial Atlixcáyotl, Tres Cerritos, Puebla 72480, Mexico
| | - Yolotl Moreno-Hernández
- Departamento de Salud, El Colegio de la Frontera Sur Unidad Villahermosa, Carretrea Federal Villa-Hermosa-Reforma Km 15.5, Ra. Guineo Segunda Sección, C.P., Villahermosa 86280, Mexico;
| | - Zendy Evelyn Olivo-Vidal
- Departamento de Salud, El Colegio de la Frontera Sur Unidad Villahermosa, Carretrea Federal Villa-Hermosa-Reforma Km 15.5, Ra. Guineo Segunda Sección, C.P., Villahermosa 86280, Mexico;
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45
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Balaji S. Metabophore-mediated retro-metabolic ('MeMeReMe') approach in drug design. Drug Discov Today 2023; 28:103736. [PMID: 37586644 DOI: 10.1016/j.drudis.2023.103736] [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: 03/01/2023] [Revised: 06/13/2023] [Accepted: 08/09/2023] [Indexed: 08/18/2023]
Abstract
Preclinical toxicity assessments of new drugs require the use of in silico prediction techniques as ethics, cost, time, and complexity limit in vitro and in vivo methods. This review discusses the fundamental concepts of biophores especially toxicophores and their detection methodologies, tools and techniques, as well as ongoing challenges, and methods for overcoming them. This will guide the design community in manipulating lead compounds via a pre-determined pathway based on the MeMeReMe approach. The ideas discussed will be useful both for predicting toxicity and for de-risking leads through optimization.
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Affiliation(s)
- Seetharaman Balaji
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka 57614, India.
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46
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Li X, Wang P, Wang C, Jin T, Xu R, Tong L, Hu X, Shen L, Li J, Zhou Y, Liu T. Discovery of 2-Aminopyrimidine Derivatives as Potent Dual FLT3/CHK1 Inhibitors with Significantly Reduced hERG Inhibitory Activities. J Med Chem 2023; 66:11792-11814. [PMID: 37584545 DOI: 10.1021/acs.jmedchem.3c00245] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
FLT3 inhibitors as single agents have limited effects because of acquired and adaptive resistance and the cardiotoxicity related to human ether-a-go-go-related gene (hERG) channel blockade further impedes safe drugs to the market. Inhibitors having potential to overcome resistance and reduce hERG affinity are highly demanded. Here, we reported a dual FLT3/CHK1 inhibitor 18, which displayed potencies to overcome varying acquired resistance in BaF3 cells with FLT3-TKD and FLT3-ITD-TKD mutations. Moreover, 18 displayed high selectivity over c-KIT more than 1700-fold and greatly reduced hERG affinity, with an IC50 value of 58.4 μM. Further mechanistic studies demonstrated 18 can upregulate p53 and abolish the outgrowth of adaptive resistant cells. In the in vivo studies, 18 demonstrated favorable PK profiles and good safety, suppressed the tumor growth in the MV-4-11 cell inoculated mouse xenograft model, and prolonged the survival in the Molm-13 transplantation model, supporting its further development.
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Affiliation(s)
- Xuemei Li
- ZJU-ENS Joint Laboratory of Medicinal Chemistry, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P.R. China
| | - Peipei Wang
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, P.R. China
| | - Chang Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P.R. China
| | - Tingting Jin
- Department of Clinical Pharmacy, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou310006, P.R. China
| | - Ran Xu
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, P.R. China
| | - Lexian Tong
- ZJU-ENS Joint Laboratory of Medicinal Chemistry, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P.R. China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou 310018, P. R. China
| | - Xiaobei Hu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P.R. China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan Tsuihang New District,Guangdong 528400, P. R. China
| | - Liteng Shen
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou310058, P.R. China
| | - Jia Li
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, P.R. China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P.R. China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan Tsuihang New District,Guangdong 528400, P. R. China
| | - Yubo Zhou
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, P.R. China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P.R. China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan Tsuihang New District,Guangdong 528400, P. R. China
| | - Tao Liu
- ZJU-ENS Joint Laboratory of Medicinal Chemistry, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P.R. China
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou310058, P.R. China
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47
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El Harchi A, Hancox JC. hERG agonists pose challenges to web-based machine learning methods for prediction of drug-hERG channel interaction. J Pharmacol Toxicol Methods 2023; 123:107293. [PMID: 37468081 DOI: 10.1016/j.vascn.2023.107293] [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: 02/07/2023] [Revised: 05/23/2023] [Accepted: 07/12/2023] [Indexed: 07/21/2023]
Abstract
Pharmacological blockade of the IKr channel (hERG) by diverse drugs in clinical use is associated with the Long QT Syndrome that can lead to life threatening arrhythmia. Various computational tools including machine learning models (MLM) for the prediction of hERG inhibition have been developed to facilitate the throughput screening of drugs in development and optimise thus the prediction of hERG liabilities. The use of MLM relies on large libraries of training compounds for the quantitative structure-activity relationship (QSAR) modelling of hERG inhibition. The focus on inhibition omits potential effects of hERG channel agonist molecules and their associated QT shortening risk. It is instructive, therefore, to consider how known hERG agonists are handled by MLM. Here, two highly developed online computational tools for the prediction of hERG liability, Pred-hERG and HergSPred were probed for their ability to detect hERG activator drug molecules as hERG interactors. In total, 73 hERG blockers were tested with both computational tools giving overall good predictions for hERG blockers with reported IC50s below Pred-hERG and HergSPred cut-off threshold for hERG inhibition. However, for compounds with reported IC50s above this threshold such as disopyramide or sotalol discrepancies were observed. HergSPred identified all 20 hERG agonists selected as interacting with the hERG channel. Further studies are warranted to improve online MLM prediction of hERG related cardiotoxicity, by explicitly taking into account channel agonism as well as inhibition.
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Affiliation(s)
- Aziza El Harchi
- School of Physiology and Pharmacology and Neuroscience, Biomedical Sciences Building, The University of Bristol, University Walk, Bristol BS8 1TD, UK.
| | - Jules C Hancox
- School of Physiology and Pharmacology and Neuroscience, Biomedical Sciences Building, The University of Bristol, University Walk, Bristol BS8 1TD, UK
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48
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Dichiara M, Ambrosio FA, Lee SM, Ruiz-Cantero MC, Lombino J, Coricello A, Costa G, Shah D, Costanzo G, Pasquinucci L, Son KN, Cosentino G, González-Cano R, Marrazzo A, Aakalu VK, Cobos EJ, Alcaro S, Amata E. Discovery of AD258 as a Sigma Receptor Ligand with Potent Antiallodynic Activity. J Med Chem 2023; 66:11447-11463. [PMID: 37535861 PMCID: PMC10461227 DOI: 10.1021/acs.jmedchem.3c00959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Indexed: 08/05/2023]
Abstract
The design and synthesis of a series of 2,7-diazaspiro[4.4]nonane derivatives as potent sigma receptor (SR) ligands, associated with analgesic activity, are the focus of this work. In this study, affinities at S1R and S2R were measured, and molecular modeling studies were performed to investigate the binding pose characteristics. The most promising compounds were subjected to in vitro toxicity testing and subsequently screened for in vivo analgesic properties. Compound 9d (AD258) exhibited negligible in vitro cellular toxicity and a high binding affinity to both SRs (KiS1R = 3.5 nM, KiS2R = 2.6 nM), but not for other pain-related targets, and exerted high potency in a model of capsaicin-induced allodynia, reaching the maximum antiallodynic effect at very low doses (0.6-1.25 mg/kg). Functional activity experiments showed that S1R antagonism is needed for the effects of 9d and that it did not induce motor impairment. In addition, 9d exhibited a favorable pharmacokinetic profile.
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Affiliation(s)
- Maria Dichiara
- Dipartimento
di Scienze del Farmaco e della Salute, Università
degli Studi di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Francesca Alessandra Ambrosio
- Dipartimento
di Medicina Sperimentale e Clinica, Università
degli Studi “Magna Græcia” di Catanzaro, Campus
“S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Sang Min Lee
- Department
of Ophthalmology and Visual Sciences, University
of Illinois at Chicago, 1905 W Taylor St, Chicago, Illinois 60612, United States
| | - M. Carmen Ruiz-Cantero
- Departamento
de Farmacología e Instituto de Neurociencias, Facultad de Medicina, Universitad de Granada e Instituto de Investigación
Biosanitaria de Granada ibs.GRANADA, Avenida de la Investigación, 18016 Granada, Spain
| | - Jessica Lombino
- Dipartimento
di Scienze del Farmaco e della Salute, Università
degli Studi di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Adriana Coricello
- Dipartimento
di Scienze della Salute, Università
“Magna Græcia” di Catanzaro, Campus “S.
Venuta”, 88100 Catanzaro, Italy
| | - Giosuè Costa
- Dipartimento
di Scienze della Salute, Università
“Magna Græcia” di Catanzaro, Campus “S.
Venuta”, 88100 Catanzaro, Italy
- Net4Science
Academic Spin-Off, Università “Magna
Græcia” di Catanzaro, Campus “S. Venuta”, 88100 Catanzaro, Italy
| | - Dhara Shah
- Department
of Ophthalmology and Visual Sciences, University
of Illinois at Chicago, 1905 W Taylor St, Chicago, Illinois 60612, United States
| | - Giuliana Costanzo
- Dipartimento
di Scienze del Farmaco e della Salute, Università
degli Studi di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Lorella Pasquinucci
- Dipartimento
di Scienze del Farmaco e della Salute, Università
degli Studi di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Kyung No Son
- Department
of Ophthalmology and Visual Sciences, University
of Michigan, 1000 Wall
Street, Ann Arbor, Michigan 48105, United States
| | - Giuseppe Cosentino
- Dipartimento
di Scienze del Farmaco e della Salute, Università
degli Studi di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Rafael González-Cano
- Departamento
de Farmacología e Instituto de Neurociencias, Facultad de Medicina, Universitad de Granada e Instituto de Investigación
Biosanitaria de Granada ibs.GRANADA, Avenida de la Investigación, 18016 Granada, Spain
| | - Agostino Marrazzo
- Dipartimento
di Scienze del Farmaco e della Salute, Università
degli Studi di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Vinay Kumar Aakalu
- Department
of Ophthalmology and Visual Sciences, University
of Michigan, 1000 Wall
Street, Ann Arbor, Michigan 48105, United States
| | - Enrique J. Cobos
- Departamento
de Farmacología e Instituto de Neurociencias, Facultad de Medicina, Universitad de Granada e Instituto de Investigación
Biosanitaria de Granada ibs.GRANADA, Avenida de la Investigación, 18016 Granada, Spain
| | - Stefano Alcaro
- Dipartimento
di Scienze della Salute, Università
“Magna Græcia” di Catanzaro, Campus “S.
Venuta”, 88100 Catanzaro, Italy
- Net4Science
Academic Spin-Off, Università “Magna
Græcia” di Catanzaro, Campus “S. Venuta”, 88100 Catanzaro, Italy
| | - Emanuele Amata
- Dipartimento
di Scienze del Farmaco e della Salute, Università
degli Studi di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
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49
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Kato T, Fukao K, Ohara T, Naya N, Tokuyama R, Muto S, Fukasawa H, Itai A, Matsumura KI. Design, Synthesis, and Anti-Inflammatory Evaluation of a Novel PPARδ Agonist with a 4-(1-Pyrrolidinyl)piperidine Structure. J Med Chem 2023; 66:11428-11446. [PMID: 37552807 DOI: 10.1021/acs.jmedchem.3c00932] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Peroxisome proliferator-activated receptor δ (PPARδ) is considered to be a pharmaceutical target to treat metabolic diseases including atherosclerosis, but there is no PPARδ agonist available for clinical use. We have previously reported the discovery of piperidinyl/piperazinyl benzothiazole derivatives as a new series of PPARδ agonists using docking-based virtual screening methods. In the present study, we found that introduction of a pyrrolidine group into the 4-position of their central piperidine rings enhances hPPARδ activity and subtype selectivity. This led to the discovery of 21 having strong PPARδ agonist activity (EC50 = 3.6 nM) with excellent ADME properties. Furthermore, 21 significantly suppressed atherosclerosis progression by 50-60% with reduction of the serum level of MCP-1 in LDLr-KO mice.
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Affiliation(s)
- Terukazu Kato
- Shionogi Pharmaceutical Research Center, Shionogi & Co., Ltd., Toyonaka, Osaka 561-0825, Japan
| | - Keita Fukao
- Shionogi Pharmaceutical Research Center, Shionogi & Co., Ltd., Toyonaka, Osaka 561-0825, Japan
| | - Takafumi Ohara
- Shionogi Pharmaceutical Research Center, Shionogi & Co., Ltd., Toyonaka, Osaka 561-0825, Japan
| | - Noriyuki Naya
- Shionogi Pharmaceutical Research Center, Shionogi & Co., Ltd., Toyonaka, Osaka 561-0825, Japan
| | - Ryukou Tokuyama
- Institute of Medicinal Molecular Design, Inc., Tokyo 113-0033, Japan
| | - Susumu Muto
- Institute of Medicinal Molecular Design, Inc., Tokyo 113-0033, Japan
| | - Hiroshi Fukasawa
- Institute of Medicinal Molecular Design, Inc., Tokyo 113-0033, Japan
| | - Akiko Itai
- Institute of Medicinal Molecular Design, Inc., Tokyo 113-0033, Japan
| | - Ken-Ichi Matsumura
- Shionogi Pharmaceutical Research Center, Shionogi & Co., Ltd., Toyonaka, Osaka 561-0825, Japan
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50
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Azzouzi M, Ouafi ZE, Azougagh O, Daoudi W, Ghazal H, Barkany SE, Abderrazak R, Mazières S, Aatiaoui AE, Oussaid A. Design, synthesis, and computational studies of novel imidazo[1,2- a]pyrimidine derivatives as potential dual inhibitors of hACE2 and spike protein for blocking SARS-CoV-2 cell entry. J Mol Struct 2023; 1285:135525. [PMID: 37057139 PMCID: PMC10080474 DOI: 10.1016/j.molstruc.2023.135525] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 04/15/2023]
Abstract
In the present work, a new series of imidazo[1,2-a]pyrimidine Schiff base derivatives have been obtained using an easy and conventional synthetic route. The synthesized compounds were spectroscopically characterized using 1H, 13C NMR, LC-MS(ESI), and FT-IR techniques. Green metric calculations indicate adherence to several green chemistry principles. The energy of Frontier Molecular Orbitals (FMO), Molecular Electrostatic Potential (MEP), Quantum Theory of Atoms in Molecules (QTAIM), and Reduced Density Gradient (RDG) were determined by the Density Functional Theory (DFT) method at B3LYP/6-31 G (d, p) as the basis set. Moreover, molecular docking studies targeting the human ACE2 and the spike, key entrance proteins of the severe acute respiratory syndrome coronavirus-2 were carried out along with hACE2 natural ligand Angiotensin II, the MLN-4760 inhibitor as well as the Cannabidiolic Acid CBDA which has been demonstrated to bind to the spike protein and block cell entry. The molecular modeling results showed auspicious results in terms of binding affinity as the top-scoring compound exhibited a remarkable affinity (-9.1 and -7.3 kcal/mol) to the ACE2 and spike protein respectively compared to CBDA (-5.7 kcal/mol), the MLN-4760 inhibitor (-7.3 kcal/mol), and angiotensin II (-9.2 kcal/mol). These findings suggest that the synthesized compounds may potentially act as effective entrance inhibitors, preventing the SARS-CoV-2 infection of human cells. Furthermore, in silico, ADMET, and drug-likeness prediction expressed promising drug-like characteristics.
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Affiliation(s)
- Mohamed Azzouzi
- Laboratory of Molecular Chemistry, Materials and Environment (LCM2E), Department of Chemistry, Multidisciplinary Faculty of Nador, University Mohamed I, Nador 60700, Morocco
| | - Zainab El Ouafi
- Laboratory of Genomics and Bioinformatics, School of Pharmacy, Mohammed VI University of Health Sciences Casablanca, Casablanca, Morocco
| | - Omar Azougagh
- Laboratory of Molecular Chemistry, Materials and Environment (LCM2E), Department of Chemistry, Multidisciplinary Faculty of Nador, University Mohamed I, Nador 60700, Morocco
| | - Walid Daoudi
- Laboratory of Molecular Chemistry, Materials and Environment (LCM2E), Department of Chemistry, Multidisciplinary Faculty of Nador, University Mohamed I, Nador 60700, Morocco
| | - Hassan Ghazal
- Laboratory of Genomics and Bioinformatics, School of Pharmacy, Mohammed VI University of Health Sciences Casablanca, Casablanca, Morocco
- Electronic Systems, Sensors and Nanobiotechnologies (E2SN), École Nationale Supérieure des Arts et Métiers (ENSAM), Mohammed V University, Rabat, Morocco
| | - Soufian El Barkany
- Laboratory of Molecular Chemistry, Materials and Environment (LCM2E), Department of Chemistry, Multidisciplinary Faculty of Nador, University Mohamed I, Nador 60700, Morocco
| | - Rfaki Abderrazak
- National Center for Scientific and Technical Research (CNRST), Rabat, Morocco
| | - Stéphane Mazières
- Laboratory of IMRCP, University Paul Sabatier, CNRS UMR 5623, 118 route de Narbonne, Toulouse 31062, France
| | - Abdelmalik El Aatiaoui
- Laboratory of Molecular Chemistry, Materials and Environment (LCM2E), Department of Chemistry, Multidisciplinary Faculty of Nador, University Mohamed I, Nador 60700, Morocco
| | - Adyl Oussaid
- Laboratory of Molecular Chemistry, Materials and Environment (LCM2E), Department of Chemistry, Multidisciplinary Faculty of Nador, University Mohamed I, Nador 60700, Morocco
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